Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold51
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: 3712191
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.32
Warning! 131352 characters in sequence are not A, C, G, or T
File 19 of 23
Found at i:3081463 original size:21 final size:21
Alignment explanation
Indices: 3081437--3081480 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3081427 TGGCTTACTA
*
3081437 AACCTCTATTGTGAGCCTCCC
1 AACCTCTATCGTGAGCCTCCC
*
3081458 AACCTCTATCGTGAGCCTTCC
1 AACCTCTATCGTGAGCCTCCC
3081479 AA
1 AA
3081481 ATGATTGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.36, G:0.14, T:0.27
Consensus pattern (21 bp):
AACCTCTATCGTGAGCCTCCC
Found at i:3083297 original size:141 final size:141
Alignment explanation
Indices: 3083043--3083327 Score: 543
Period size: 141 Copynumber: 2.0 Consensus size: 141
3083033 AATAGTGGAT
*
3083043 CTATTGTTTACCTCGAGCAACAAAATAAAACCCATAGTTTGTGCTTCTGATTTTGTCACCTTGAA
1 CTATTGTTTACCTCGAGCAACAAAATAAAACCCATAGTTTGGGCTTCTGATTTTGTCACCTTGAA
*
3083108 TGACTCCTTATCAATCAAAGTCACCTATAGCTTAGGTTCCTTCTGGCTTTGGTTGTACTCTTAGG
66 TGACTCCTTATCAATCAAAGTCACCTATAGCTTAGGTTCCTTCTGGCTTTGGTTGTACTCCTAGG
3083173 TGGCAACAGTG
131 TGGCAACAGTG
*
3083184 CTATTGTTTACCTCGAGCAACAAAATAAAAGCCATAGTTTGGGCTTCTGATTTTGTCACCTTGAA
1 CTATTGTTTACCTCGAGCAACAAAATAAAACCCATAGTTTGGGCTTCTGATTTTGTCACCTTGAA
3083249 TGACTCCTTATCAATCAAAGTCACCTATAGCTTAGGTTCCTTCTGGCTTTGGTTGTACTCCTAGG
66 TGACTCCTTATCAATCAAAGTCACCTATAGCTTAGGTTCCTTCTGGCTTTGGTTGTACTCCTAGG
3083314 TGGCAACAGTG
131 TGGCAACAGTG
3083325 CTA
1 CTA
3083328 GCTTGATCTT
Statistics
Matches: 141, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
141 141 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (141 bp):
CTATTGTTTACCTCGAGCAACAAAATAAAACCCATAGTTTGGGCTTCTGATTTTGTCACCTTGAA
TGACTCCTTATCAATCAAAGTCACCTATAGCTTAGGTTCCTTCTGGCTTTGGTTGTACTCCTAGG
TGGCAACAGTG
Found at i:3084933 original size:29 final size:28
Alignment explanation
Indices: 3084856--3084958 Score: 75
Period size: 29 Copynumber: 3.6 Consensus size: 28
3084846 GGAATGAAAT
* *
3084856 TTTTG-AAAGTTGAGAGGTTGATATGTAA
1 TTTTGAAAAGTTAAGA-GTTGATAAGTAA
* * * *
3084884 TTTTGAAAGGTCCAGGGGTTGATAAGTAA
1 TTTTGAAAAGT-TAAGAGTTGATAAGTAA
*
3084913 TTTTGAAAAGTTAAAGAGTTGTATTA-TAA
1 TTTTGAAAAGTT-AAGAGTTG-ATAAGTAA
* *
3084942 TTTTGGAAAGTTTAGAG
1 TTTTGAAAAGTTAAGAG
3084959 GGTTAGAGTG
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
28 9 0.16
29 45 0.78
30 4 0.07
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (28 bp):
TTTTGAAAAGTTAAGAGTTGATAAGTAA
Found at i:3085298 original size:156 final size:155
Alignment explanation
Indices: 3084997--3085355 Score: 423
Period size: 156 Copynumber: 2.3 Consensus size: 155
3084987 TGGCTGGGTA
* * * * * ** *
3084997 ATGACATGGTAATGAGGACACATGGCGGGTGATGGTTGGATGACGTGGCGATGACTGGATAACTA
1 ATGACATGGCAGTGAGGACACATGGCGGATGATGGTTGGATGACGTGGCAATGAATAAACAACTA
* * * * * *
3085062 GGCTAACTAGGTAATGAGTGGTAGTGAGCACATATGGCAGCTTATGGTTGGTTGATATGGTGTTG
66 GGCTAACTAGGTAATGAATGGTAGTGAGCACACATGGCAACTTATGGTTGGCTGACATGGTGATG
* *
3085127 ATTGGACAATTGGGCTAACTAAAG-G
131 ACTAGACAATTGGGCTAACT-AAGTG
* * * *
3085152 ATGATATGGCAGTGAGGACACATGGCGGTTGATGATTGGCTGACGTGGCAATGAATAAACAACTA
1 ATGACATGGCAGTGAGGACACATGGCGGATGATGGTTGGATGACGTGGCAATGAATAAACAACTA
* * * * * *
3085217 GGCTGACTGGGTGATGACATGGTAGTGAGGACACGTGGTAACTTATGGTTGGCTGACATGGTGAT
66 GGCTAACTAGGTAATGA-ATGGTAGTGAGCACACATGGCAACTTATGGTTGGCTGACATGGTGAT
* *
3085282 GACTAGACAATTGGGCTGACTAGGTG
130 GACTAGACAATTGGGCTAACTAAGTG
* *
3085308 ATGACATGGTAGTGAGGACACATGGCGGATGATGGTTGGATGGCGTGG
1 ATGACATGGCAGTGAGGACACATGGCGGATGATGGTTGGATGACGTGG
3085356 TGCTGATTGG
Statistics
Matches: 169, Mismatches: 33, Indels: 3
0.82 0.16 0.01
Matches are distributed among these distances:
155 70 0.41
156 99 0.59
ACGTcount: A:0.26, C:0.12, G:0.36, T:0.26
Consensus pattern (155 bp):
ATGACATGGCAGTGAGGACACATGGCGGATGATGGTTGGATGACGTGGCAATGAATAAACAACTA
GGCTAACTAGGTAATGAATGGTAGTGAGCACACATGGCAACTTATGGTTGGCTGACATGGTGATG
ACTAGACAATTGGGCTAACTAAGTG
Found at i:3085357 original size:78 final size:78
Alignment explanation
Indices: 3084997--3085357 Score: 305
Period size: 78 Copynumber: 4.6 Consensus size: 78
3084987 TGGCTGGGTA
* * * * *
3084997 ATGACATGGTAATGAGGACACATGGCGGGTGATGGTTGGATGACGTGGCGATGACTGGATAACTA
1 ATGACATGGTAGTGAGGACACATGGCGGATGATGGTTGGATGACGTGGTGATGACTAGACAACTA
*
3085062 GGCTAACTAGGTA
66 GGCTAACTAGGTG
* * * * * * * ** * * * * *
3085075 ATGA-GTGGTAGTGAGCACATATGGCAGCTTATGGTTGGTTGATATGGTGTTGATTGGACAATTG
1 ATGACATGGTAGTGAGGACACATGGCGGATGATGGTTGGATGACGTGGTGATGACTAGACAACTA
*
3085139 GGCTAACTAAAG-G
66 GGCTAACT-AGGTG
* * * * * ** * *
3085152 ATGATATGGCAGTGAGGACACATGGCGGTTGATGATTGGCTGACGTGGCAATGAATAAACAACTA
1 ATGACATGGTAGTGAGGACACATGGCGGATGATGGTTGGATGACGTGGTGATGACTAGACAACTA
* *
3085217 GGCTGACTGGGTG
66 GGCTAACTAGGTG
* ** * * * *
3085230 ATGACATGGTAGTGAGGACACGTGG-TAACTTATGGTTGGCTGACATGGTGATGACTAGACAATT
1 ATGACATGGTAGTGAGGACACATGGCGGA-TGATGGTTGGATGACGTGGTGATGACTAGACAACT
* *
3085294 GGGCTGACTAGGTG
65 AGGCTAACTAGGTG
*
3085308 ATGACATGGTAGTGAGGACACATGGCGGATGATGGTTGGATGGCGTGGTG
1 ATGACATGGTAGTGAGGACACATGGCGGATGATGGTTGGATGACGTGGTG
3085358 CTGATTGGAT
Statistics
Matches: 215, Mismatches: 63, Indels: 10
0.75 0.22 0.03
Matches are distributed among these distances:
77 57 0.27
78 157 0.73
79 1 0.00
ACGTcount: A:0.26, C:0.12, G:0.36, T:0.26
Consensus pattern (78 bp):
ATGACATGGTAGTGAGGACACATGGCGGATGATGGTTGGATGACGTGGTGATGACTAGACAACTA
GGCTAACTAGGTG
Found at i:3090676 original size:79 final size:78
Alignment explanation
Indices: 3090592--3090877 Score: 358
Period size: 79 Copynumber: 3.6 Consensus size: 78
3090582 TTTCATTGAT
*
3090592 GTTTTATTTCTAAAACA-TCGATTTTCCACCATCAGGGATACTCCAACCCCGTTATTTTTAAGGG
1 GTTTTATTTCTAAAACACT-GATTTTCCACCATC-GGGATACTCCAACCCCGTTATTTTTGAGGG
* *
3090656 GATATTTTAACCCCG
64 GATACTCTAACCCCG
* * ** * *
3090671 GTTTTATTTCTAAAACACTGATTTTTCACCATCGGGAATACTCCAATCATGTTATTTTCGAGAGG
1 GTTTTATTTCTAAAACACTGATTTTCCACCATCGGG-ATACTCCAACCCCGTTATTTTTGAGGGG
* *
3090736 ATACTCCAATCCCG
65 ATACTCTAACCCCG
* * *
3090750 GTTTTATTTCTAAAACACTGATTTTCCACCATCGTGGATACTCCAACCTCGTTATTTCTGAGGGA
1 GTTTTATTTCTAAAACACTGATTTTCCACCATCG-GGATACTCCAACCCCGTTATTTTTGAGGGG
*
3090815 ATACTCTAACCCTG
65 ATACTCTAACCCCG
* * *
3090829 ATTCTATTTCTAAAACACTAATTTTCCACCATCAGGGATACTCCAACCC
1 GTTTTATTTCTAAAACACTGATTTTCCACCATC-GGGATACTCCAACCC
3090878 TGGTTTTATT
Statistics
Matches: 177, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
78 3 0.02
79 170 0.96
80 4 0.02
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.35
Consensus pattern (78 bp):
GTTTTATTTCTAAAACACTGATTTTCCACCATCGGGATACTCCAACCCCGTTATTTTTGAGGGGA
TACTCTAACCCCG
Found at i:3090888 original size:51 final size:50
Alignment explanation
Indices: 3090810--3090927 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 50
3090800 GTTATTTCTG
*
3090810 AGGGAATACTCTAACCCTGATTCTATTTCTAAAACA-CTAATTTTCCACCATC
1 AGGG-ATACTCCAACCCTGATTCTATTTCTAAAACATC-AATTTT-CACCATC
* * *
3090862 AGGGATACTCCAACCCTGGTTTTATTTCTAAAACATCGATTTTCACCATC
1 AGGGATACTCCAACCCTGATTCTATTTCTAAAACATCAATTTTCACCATC
3090912 -GAGGATACTCCAACCC
1 AG-GGATACTCCAACCC
3090928 CGTTATTTTG
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
49 1 0.02
50 21 0.35
51 33 0.55
52 5 0.08
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (50 bp):
AGGGATACTCCAACCCTGATTCTATTTCTAAAACATCAATTTTCACCATC
Found at i:3090962 original size:78 final size:79
Alignment explanation
Indices: 3090868--3091161 Score: 324
Period size: 79 Copynumber: 3.7 Consensus size: 79
3090858 CATCAGGGAT
* * *
3090868 ACTCCAACCCTGGTTTTATTTCTAAAACATCGA-TTTTCACCATCGAGGATACTCCAACCCCGTT
1 ACTCCAACCCCGGTTTTATTTCTAAAATATCGATTTTTCACCATCGAAGATACTCCAACCCCGTT
*
3090932 ATTT-TGGAGAGGAC
66 ATTTCT-GAGAGGAA
* * ** ** *
3090946 ACTCCAACCCCAGTTTTATTTCTAAAATATCTATTTTTCACCATCGGGGATACTTAAACCCTGTT
1 ACTCCAACCCCGGTTTTATTTCTAAAATATCGATTTTTCACCATCGAAGATACTCCAACCCCGTT
**
3091011 ATTTCTGAGAAAAA
66 ATTTCTGAGAGGAA
* * * * * * *
3091025 ACTCCAACCCTGGTTTAATTTCTAAAATATCAATTTTTCACCATCGAAGATATTCTAGCCCCATT
1 ACTCCAACCCCGGTTTTATTTCTAAAATATCGATTTTTCACCATCGAAGATACTCCAACCCCGTT
* *
3091090 ATTTCTGAGGGGAT
66 ATTTCTGAGAGGAA
* * *
3091104 ACTCCAACCCCGATTTTATTT-TCAAAATATCGATTGTTCACCATCAAAGATACTCCAA
1 ACTCCAACCCCGGTTTTATTTCT-AAAATATCGATTTTTCACCATCGAAGATACTCCAA
3091162 TCCCATTTTT
Statistics
Matches: 177, Mismatches: 36, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
78 30 0.17
79 146 0.82
80 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (79 bp):
ACTCCAACCCCGGTTTTATTTCTAAAATATCGATTTTTCACCATCGAAGATACTCCAACCCCGTT
ATTTCTGAGAGGAA
Found at i:3090966 original size:129 final size:130
Alignment explanation
Indices: 3090734--3091008 Score: 348
Period size: 129 Copynumber: 2.1 Consensus size: 130
3090724 ATTTTCGAGA
*
3090734 GGATACTCCAATCCC-GGTTTTATTTCTAAAACACTGATTTTCCACCATCGTGGATACTCCAACC
1 GGATACTCCAA-CCCTGGTTTTATTTCTAAAACACTGATTTTCCACCATCGAGGATACTCCAACC
* * * *
3090798 TCGTTATTTCTGAGGGAATACTCTAACCCTGATTCTATTTCTAAAACA-CTAATTTTCCACCATC
65 CCGTTATTTCTGAGGGAACACTCCAACCCAGATTCTATTTCTAAAACATCT-ATTTTCCACCATC
3090862 AG
129 AG
3090864 GGATACTCCAACCCTGGTTTTATTTCTAAAACA-TCGATTTT-CACCATCGAGGATACTCCAACC
1 GGATACTCCAACCCTGGTTTTATTTCTAAAACACT-GATTTTCCACCATCGAGGATACTCCAACC
* * *
3090927 CCGTTATTT-TGGAGAGG-ACACTCCAACCCCAG-TTTTATTTCTAAAATATCTATTTTTCACCA
65 CCGTTATTTCT-GAG-GGAACACTCCAA-CCCAGATTCTATTTCTAAAACATCTATTTTCCACCA
*
3090989 TCGG
127 TCAG
**
3090993 GGATACTTAAACCCTG
1 GGATACTCCAACCCTG
3091009 TTATTTCTGA
Statistics
Matches: 128, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
128 1 0.01
129 84 0.66
130 43 0.34
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.33
Consensus pattern (130 bp):
GGATACTCCAACCCTGGTTTTATTTCTAAAACACTGATTTTCCACCATCGAGGATACTCCAACCC
CGTTATTTCTGAGGGAACACTCCAACCCAGATTCTATTTCTAAAACATCTATTTTCCACCATCAG
Found at i:3091051 original size:208 final size:209
Alignment explanation
Indices: 3090664--3091069 Score: 529
Period size: 208 Copynumber: 1.9 Consensus size: 209
3090654 GGGATATTTT
* *
3090664 AACCCCGGTTTTATTTCTAAAACACTGATTTTTCACCATCGGGAATACTCCAATCATGTTATTTT
1 AACCCCGGTTTTATTTCTAAAACACTGATTTTTCACCATCGGGAATACTCCAACCACGTTATTTT
* * * * *
3090729 CGAGAGGATACTCCAATCCCGGTTTTATTTCTAAAACACTGATTTTCCACCATCGTGGATACTCC
66 CGAGAGGACACTCCAACCCCAGTTTTATTTCTAAAACACTGATTTTCCACCATCGGGGATACTCA
** * *
3090794 AACCTCGTTATTTCTGAGGGAATACTCTAACCCTGATTCTATTTCTAAAACA-CTAATTTTCCAC
131 AACCTCGTTATTTCTGAGAAAAAACTCCAACCCTGATTCTATTTCTAAAACATC-AATTTTCCAC
3090858 CATCAGGGATACTCC
195 CATCAGGGATACTCC
* *
3090873 AACCCTGGTTTTATTTCTAAAACA-TCGA-TTTTCACCATCGAGG-ATACTCCAACCCCGTTATT
1 AACCCCGGTTTTATTTCTAAAACACT-GATTTTTCACCATCG-GGAATACTCCAACCACGTTATT
* * *
3090935 TTGGAGAGGACACTCCAACCCCAGTTTTATTTCTAAAATATCT-ATTTTTCACCATCGGGGATAC
64 TTCGAGAGGACACTCCAACCCCAGTTTTATTTCTAAAACA-CTGATTTTCCACCATCGGGGATAC
* * *
3090999 TTAAACC-CTGTTATTTCTGAGAAAAAACTCCAACCCTGGTT-TAATTTCTAAAATATCAATTTT
128 TCAAACCTC-GTTATTTCTGAGAAAAAACTCCAACCCTGATTCT-ATTTCTAAAACATCAATTTT
*
3091062 TCACCATC
191 CCACCATC
3091070 GAAGATATTC
Statistics
Matches: 171, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
207 2 0.01
208 139 0.81
209 30 0.18
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (209 bp):
AACCCCGGTTTTATTTCTAAAACACTGATTTTTCACCATCGGGAATACTCCAACCACGTTATTTT
CGAGAGGACACTCCAACCCCAGTTTTATTTCTAAAACACTGATTTTCCACCATCGGGGATACTCA
AACCTCGTTATTTCTGAGAAAAAACTCCAACCCTGATTCTATTTCTAAAACATCAATTTTCCACC
ATCAGGGATACTCC
Found at i:3091148 original size:287 final size:288
Alignment explanation
Indices: 3090590--3091215 Score: 700
Period size: 287 Copynumber: 2.2 Consensus size: 288
3090580 AATTTCATTG
*
3090590 ATGTTTTATTTCTAAAACATCGATTTTCCACCATC-AGGGATACTCCAACCCCGTTATTTTTAAG
1 ATGTTTTATTTCTAAAACATCGATTTT-CACCATCGA-GGATACTCCAACCCCGTTATTTTGAAG
* * * ** * * *
3090654 GGGATATTTTAACCCCGGTTTTATTTCTAAAACACTGATTTTTCACCATCGGGAATACTCCAATC
64 AGGACACTCCAACCCCAGTTTTATTTCTAAAACACTGATTTTTCACCATCGGGAATACTCAAACC
** * * *
3090719 ATGTTATTTTCGAGAGGATACTCCAATCCCGGTTTTATTTCTAAAACACTGATTTTCCACCATCG
129 ATGTTATTTTCGAGAAAAAACTCCAATCCCGGTTTAATTTCTAAAACACTAATTTTCCACCATCG
** * * * *
3090784 TGGATACTCCAACCTCGTTATTTCTGAGGGAATACTCTAACCCTGATTCTATTTCTAAAACACTA
194 AAGATACTCCAACCCCATTATTTCTGAGGGAATACTCCAACCCCGATTCTATTTCTAAAACACTA
**
3090849 ATTTTCCACCATCAGGGATACTCCAA-CCC
259 ATTTTCCACCATCAAAGATACTCCAATCCC
*
3090878 -TGGTTTTATTTCTAAAACATCGATTTTCACCATCGAGGATACTCCAACCCCGTTATTTTGGAGA
1 AT-GTTTTATTTCTAAAACATCGATTTTCACCATCGAGGATACTCCAACCCCGTTATTTTGAAGA
* * *
3090942 GGACACTCCAACCCCAGTTTTATTTCTAAAATATCT-ATTTTTCACCATCGGGGATACTTAAACC
65 GGACACTCCAACCCCAGTTTTATTTCTAAAACA-CTGATTTTTCACCATCGGGAATACTCAAACC
* * *
3091006 CTGTTA-TTTCTGAGAAAAAACTCCAA-CCCTGGTTTAATTTCTAAAATA-TCAATTTTTCACCA
129 ATGTTATTTTC-GAGAAAAAACTCCAATCCC-GGTTTAATTTCTAAAACACT-AATTTTCCACCA
* * * * * *
3091068 TCGAAGATATTCTAGCCCCATTATTTCTGAGGGGATACTCCAACCCCGATTTTATTT-TCAAAAT
191 TCGAAGATACTCCAACCCCATTATTTCTGAGGGAATACTCCAACCCCGATTCTATTTCT-AAAAC
*
3091132 A-TCGATTGTT-CACCATCAAAGATACTCCAATCCC
255 ACT-AATT-TTCCACCATCAAAGATACTCCAATCCC
* * * *
3091166 AT-TTTTATTTCCAAAATATCGATTTTTCACCATTG-GAGATACTCTAACCC
1 ATGTTTTATTTCTAAAACATCGA-TTTTCACCATCGAG-GATACTCCAACCC
3091216 TATTTTTATC
Statistics
Matches: 285, Mismatches: 40, Indels: 26
0.81 0.11 0.07
Matches are distributed among these distances:
286 10 0.04
287 218 0.76
288 56 0.20
289 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (288 bp):
ATGTTTTATTTCTAAAACATCGATTTTCACCATCGAGGATACTCCAACCCCGTTATTTTGAAGAG
GACACTCCAACCCCAGTTTTATTTCTAAAACACTGATTTTTCACCATCGGGAATACTCAAACCAT
GTTATTTTCGAGAAAAAACTCCAATCCCGGTTTAATTTCTAAAACACTAATTTTCCACCATCGAA
GATACTCCAACCCCATTATTTCTGAGGGAATACTCCAACCCCGATTCTATTTCTAAAACACTAAT
TTTCCACCATCAAAGATACTCCAATCCC
Found at i:3091156 original size:158 final size:157
Alignment explanation
Indices: 3090868--3091157 Score: 388
Period size: 158 Copynumber: 1.8 Consensus size: 157
3090858 CATCAGGGAT
* * * *
3090868 ACTCCAACCCTGGTTTTATTTCTAAAACATCGATTTTCACCATCGAGGATACTCCAACCCCGTTA
1 ACTCCAACCCTGGTTTAATTTCTAAAACATCAATTTTCACCATCGAAGATACTCCAACCCCATTA
* * ***
3090933 TTTTGGAGAGGACACTCCAACCCCAGTTTTATTTCTAAAATATCTATTTTTCACCATCGGGGATA
66 TTTTGGAGAGGACACTCCAACCCCAGTTTTATTTCTAAAATATCGATTGTTCACCATCAAAGATA
3090998 CTTAAACCCTGTTATTTCTGAGAAAAA
131 CTTAAACCCTGTTATTTCTGAGAAAAA
* * * *
3091025 ACTCCAACCCTGGTTTAATTTCTAAAATATCAATTTTTCACCATCGAAGATATTCTAGCCCCATT
1 ACTCCAACCCTGGTTTAATTTCTAAAACATCAA-TTTTCACCATCGAAGATACTCCAACCCCATT
* *
3091090 ATTTCT-GAGGGGATACTCCAACCCC-GATTTTATTT-TCAAAATATCGATTGTTCACCATCAAA
65 ATTT-TGGAGAGGACACTCCAACCCCAG-TTTTATTTCT-AAAATATCGATTGTTCACCATCAAA
3091152 GATACT
127 GATACT
3091158 CCAATCCCAT
Statistics
Matches: 114, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
157 32 0.28
158 81 0.71
159 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (157 bp):
ACTCCAACCCTGGTTTAATTTCTAAAACATCAATTTTCACCATCGAAGATACTCCAACCCCATTA
TTTTGGAGAGGACACTCCAACCCCAGTTTTATTTCTAAAATATCGATTGTTCACCATCAAAGATA
CTTAAACCCTGTTATTTCTGAGAAAAA
Found at i:3091181 original size:51 final size:51
Alignment explanation
Indices: 3091101--3091235 Score: 166
Period size: 51 Copynumber: 2.6 Consensus size: 51
3091091 TTTCTGAGGG
*
3091101 GATACTCCAACCCCGA-TTTTATTTTCAAAATATCGATTGTTCACCATCAAA
1 GATACTCCAA-CCCGATTTTTATTTCCAAAATATCGATTGTTCACCATCAAA
* ***
3091152 GATACTCCAATCCC-ATTTTTATTTCCAAAATATCGATTTTTCACCATTGGA
1 GATACTCCAA-CCCGATTTTTATTTCCAAAATATCGATTGTTCACCATCAAA
* * *
3091203 GATACTCTAACCCTATTTTTATCTCCAAAATAT
1 GATACTCCAACCCGATTTTTATTTCCAAAATAT
3091236 TAAATTTTTC
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
50 4 0.05
51 70 0.95
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.37
Consensus pattern (51 bp):
GATACTCCAACCCGATTTTTATTTCCAAAATATCGATTGTTCACCATCAAA
Found at i:3097492 original size:61 final size:61
Alignment explanation
Indices: 3097416--3099546 Score: 1830
Period size: 60 Copynumber: 35.3 Consensus size: 61
3097406 ATTTTAGCCC
* * ** * * * *
3097416 TTTAGTCCTTAAAGAGCAAGATGTATTTTTCTTTTAAAGCCCACATGAGTTGGCGACACCC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * ** *
3097477 TTTAGTCCTCGAAGAGCAAGATAACTTTTTCTTTTAAAGCCCATAC--GTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCT
** * * * * * * *
3097536 TTTAGTCCTTGAATAGCAGGACGTCTTTTTCTTTAAAAGCCTACACGAATTGGTGACACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * *
3097597 TTTAGTCCTCAAAGAGTAGGATGCCTTTTTCTTTTTAAAGCCCAGATGAGTTGGTGGCATCC-
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTC-TTTTAAAGCCCACACGAGTTGGTGGCA-CCT
* * * * **
3097659 TTTACTTCTCGAAGAGCAGGATGCCTCTTTTCTTTTTAAAGCCCACATGAGTTGGTGGCATTT
1 TTTAGTCCTCAAAGAGCAGGATGCCT-TTTTC-TTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * *
3097722 TTTAGTCCTCGAAGAGCAAGACGCCTTTTTCTTTT-AA-CCTACACGAGTTTGG-GGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAG-TTGGTGGCACCT
* * * * * * * *
3097781 TTTAGTCCTGGAAA-AGCAGGACGTCTTTTTCTTTTAAAGCCTATATGAATTGGTGGCAACT
1 TTTAGTCCT-CAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * ** *
3097842 TTTAGTCCTCAAGGAGCAAGAAACCTTTTTCTTTTTAAAGTCCACACGAGTTGGTGGCA-CT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTC-TTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * *
3097903 ATTTAGTCCTCAAAGAGTAGGATGCCTTTTTCTTTTTAAAGCCCACACAAATTGATGGAACCC
1 -TTTAGTCCTCAAAGAGCAGGATGCCTTTTTC-TTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * * *
3097966 TTTAGTCCTCAAAGAGTAAGATACCTTTTTCTTTTTAAAGCCCACGCAAGTTAGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTC-TTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * * *
3098028 TTTAGTCCTCAAAGAGTAGGACGCCTTTTT-TTTTAAAGTCCAAATGAATTGGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCT
** * * * * * **
3098088 TTTAAACATCAAAGAGTAAGATGCC-TTTTC--TAAAAACCCACATAAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
3098146 TTTAGTCCTCAAAGAGCAAGG-CGCCTTTTTCTTTTTAAAGCCCATACAAGTTGTTGGCATCT
1 TTTAGTCCTCAAAGAGC-AGGATGCCTTTTTC-TTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * *
3098208 TTTAGTCTTTAAAGAGCAGTATG-C-TTTCCTTTTTAAAGCCCACACAAGTTAGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTC-TTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * *
3098268 TTTAGTCCTCAAAGAGCATGACGTCTTTTTCTTTTAAAGCCCACATGAGTTTGTGGCACTT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * *
3098329 TTTAGTCCTCAAAGAGCAGGA--CACATTTTCTTTTTAAAGCCCACATGAGTTGGTGGTACCT
1 TTTAGTCCTCAAAGAGCAGGATGC-CTTTTTC-TTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
3098390 TTTAGTCCTTAAAGAGCAGGACG-C-TTTCCTTTTTAAAGCCCATACGAGTTGGTGGCACAT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTC-TTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * *
3098450 TTTTGTCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCTACACGAGTTGGTGGTACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTT-AAAGCCCACACGAGTTGGTGGCACCT
* * *
3098512 TTTAGTCCTCAAAGAGCAGGACGCC-TTTTCTTTTTAATGCCCACATGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTC-TTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
3098573 TTTAGTCCTCAAAGAGCAGGATG-C-TTTCCTTTTTAAAGCCTACATGAGCTGATGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTC-TTTTAAAGCCCACACGAGTTGGTGGCACCT
* * ** *
3098633 TTTAGTCCTTAAA-AG--GTA-G-CTTTTTCTTTTTAAAGTTCACACTAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTC-TTTTAAAGCCCACACGAGTTGGTGGCACCT
* * *
3098690 TTTAGTCCTCAAAGAGCAGGA--CGTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTC-TTTTAAAGCCCACACGAGTTGGTGGCACCT
* ** *
3098750 TTTAGTCCTCAAAGAGCTGGACACCTTTTTC-TTTAAAGCCCACACGAGTTTGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * * *
3098810 TTTAATCCTCAAAAAGTAGGATG--TTTTCCTTTTCAAAGCTCGCACGAGTTGGTGGTACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTT-AAAGCCCACACGAGTTGGTGGCACCT
* * * *
3098870 TTTAGTCCTTAAAGAGCAAGATGCCTTTTTCTTTTCAAAGGCCACACAAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTT-AAAGCCCACACGAGTTGGTGGCACCT
* * * * * *
3098932 TTTAGTCCTCAAAGAGCAAGACG-CATTTT-TTTTAATGCCCACACGAGTTGGAGGCACTT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * ** *
3098991 TTTAGTCCTTAAAGAGCAGGACG-C-TTTCCTTTTTAAAGCCCACATAAGTTGATGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTC-TTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * * *
3099051 TTTAGTCCTTAAAAAGTAGGATGCCTTTTTCTTATTGAAGCTCACACAAGTTGGTGGTACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTT-TTAAAGCCCACACGAGTTGGTGGCACCT
* * * ** *
3099113 TTTAGTCCTCAAAGAGTAGGA--CACTTTCGT-TTTTAAAGTCCACATAAGCTGGTGGCA-CT
1 TTTAGTCCTCAAAGAGCAGGATGC-CTTT-TTCTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * *
3099172 TTTAGTCCTCAAAGAGGAGGACGCC-TTTTCATTTATAGCTCACACGAGTTGGTGGTACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * ** *
3099232 TTTAGTCCTCAAAGAGTAGGA--CACTTTCGT-TTTTAAAGTCCACATAAGCTGGTGGCA-CT
1 TTTAGTCCTCAAAGAGCAGGATGC-CTTT-TTCTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
3099291 TTTAGTCCTCAAAGAGGAGGACGCC-TTTTCATTTATAGCTCACACGAGTTGGTGGCA-CT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * *
3099350 TTTAGTCTTCAAAGAGGAAGACG-CTTTCTT-TTTTAAAGCCCACAC-ACGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTT-TTCTTTTAAAGCCCACACGA-GTTGGTGGCACCT
* ** **
3099410 TTTAGTCCTCAAAGAGGAAAATGCC-TTTT-TTTTAAAGCTTACACGAGTTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *** *
3099469 TTTAGCCCTCAAAGAGCCGGACG-CTTTTTTTTTTAAAGCCCATGTGAATTGGTGGCACCT
1 TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCT
* *
3099529 TTCAGACCTCAAAGAGCA
1 TTTAGTCCTCAAAGAGCA
3099547 TGACGCATTT
Statistics
Matches: 1697, Mismatches: 305, Indels: 137
0.79 0.14 0.06
Matches are distributed among these distances:
56 2 0.00
57 42 0.02
58 53 0.03
59 331 0.20
60 526 0.31
61 286 0.17
62 400 0.24
63 57 0.03
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (61 bp):
TTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTAAAGCCCACACGAGTTGGTGGCACCT
Found at i:3098267 original size:122 final size:122
Alignment explanation
Indices: 3097416--3099546 Score: 1870
Period size: 122 Copynumber: 17.7 Consensus size: 122
3097406 ATTTTAGCCC
* * * ** ** * * *
3097416 TTTAGTCCTTAAAGAGCAAGATGTATTTTTC-TTTTAAAGCCCACATGAGTTGGCGACACCCTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* * * *
3097480 AGTCCTCGAAGAGCAAGATAACTTTT-TCTTTTAAAGCCCATAC--GTTGGTGGCACCT
66 AGTCCTCAAAGAGCAGGAT-GCTTTTCT-TTTTAAAGCCCACACGAGTTGGTGGCACCT
** * * * * *
3097536 TTTAGTCCTTGAATAGCAGGACGTCTTTTTC-TTTAAAAGCCTACACGAA-TTGGTGACACCTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACAC-AAGTTGGTGGCACCTTT
* * *
3097599 TAGTCCTCAAAGAGTAGGATGCCTTTTTCTTTTTAAAGCCCAGATGAGTTGGTGGCATCC-
65 TAGTCCTCAAAGAGCAGGATG-C-TTTTCTTTTTAAAGCCCACACGAGTTGGTGGCA-CCT
* * * * ** **
3097659 TTTACTTCTCGAAGAGCAGGATGCCTCTTTTCTTTTTAAAGCCCACATGAGTTGGTGGCATTTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCT-TTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* * * *
3097724 TAGTCCTCGAAGAGCAAGACGCCTTTT-TCTTTT-AA-CCTACACGAGTTTGG-GGCACCT
65 TAGTCCTCAAAGAGCAGGATG-CTTTTCT-TTTTAAAGCCCACACGAG-TTGGTGGCACCT
* * * * * *
3097781 TTTAGTCCTGGAAA-AGCAGGACGTCTTTTTC-TTTTAAAGCCTATATGAA-TTGGTGGCAACTT
1 TTTAGTCCT-CAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACA-CAAGTTGGTGGCACCTT
* * ** *
3097843 TTAGTCCTCAAGGAGCAAGAAACCTTTTTCTTTTTAAAGTCCACACGAGTTGGTGGCA-CT
64 TTAGTCCTCAAAGAGC-AGGATGC-TTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * * *
3097903 ATTTAGTCCTCAAAGAGTAGGATGCCTTTTTCTTTTTAAAGCCCACACAAATTGATGGAACCCTT
1 -TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* * * * * * *
3097968 TAGTCCTCAAAGAGTAAGATACCTTTTTCTTTTTAAAGCCCACGCAAGTTAGTGGCACCC
65 TAGTCCTCAAAGAGCAGGAT-GC-TTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
3098028 TTTAGTCCTCAAAGAGTAGGACGCC-TTTT-TTTTTAAAGTCCAAATGAA-TTGGTGGCACCCTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACA-CAAGTTGGTGGCACCTTT
** * * * * * **
3098090 TAAACATCAAAGAGTAAGATGCCTTTTC---TAAAAACCCACATAAGTTGGTGGCACCT
65 TAGTCCTCAAAGAGCAGGATG-CTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * *
3098146 TTTAGTCCTCAAAGAGCAAGG-CGCCTTTTTCTTTTTAAAGCCCATACAAGTTGTTGGCATCTTT
1 TTTAGTCCTCAAAGAGC-AGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* * * * * *
3098210 TAGTCTTTAAAGAGCAGTATGCTTTCCTTTTTAAAGCCCACACAAGTTAGTGGCACCT
65 TAGTCCTCAAAGAGCAGGATGCTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * ** * *
3098268 TTTAGTCCTCAAAGAGCATGACGTCTTTTTC-TTTTAAAGCCCACATGAGTTTGTGGCACTTTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
** * *
3098332 AGTCCTCAAAGAGCAGGACACATTTTCTTTTTAAAGCCCACATGAGTTGGTGGTACCT
66 AGTCCTCAAAGAGCAGGATGC-TTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
3098390 TTTAGTCCTTAAAGAGCAGGACG-C-TTTCCTTTTTAAAGCCCATACGAGTTGGTGGCACATTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* * * * *
3098453 TGTCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCTACACGAGTTGGTGGTACCT
66 AGTCCTCAAAGAGCAGGATG-C-TTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* **
3098512 TTTAGTCCTCAAAGAGCAGGACGCC-TTTTCTTTTTAATGCCCACATGAGTTGGTGGCACCTTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* * * * *
3098576 AGTCCTCAAAGAGCAGGATGCTTTCCTTTTTAAAGCCTACATGAGCTGATGGCACCT
66 AGTCCTCAAAGAGCAGGATGCTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * ** *
3098633 TTTAGTCCTTAAA-AG--GTA-G-CTTTTTCTTTTTAAAGTTCACACTAGTTGGTGGCACCTTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* *
3098693 AGTCCTCAAAGAGCAGGACG-TTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACCT
66 AGTCCTCAAAGAGCAGGATGCTTTT-CTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * *
3098750 TTTAGTCCTCAAAGAGCTGGACACCTTTTTC--TTTAAAGCCCACACGAGTTTGTGGCACCTTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* * * * * * *
3098813 AATCCTCAAAAAGTAGGATG-TTTTCCTTTTCAAAGCTCGCACGAGTTGGTGGTACCT
66 AGTCCTCAAAGAGCAGGATGCTTTT-CTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
3098870 TTTAGTCCTTAAAGAGCAAGATGCCTTTTTCTTTTCAAAGGCCACACAAGTTGGTGGCACCTTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* * * * * *
3098935 AGTCCTCAAAGAGCAAGACGCATTT-TTTTTAATGCCCACACGAGTTGGAGGCACTT
66 AGTCCTCAAAGAGCAGGATGCTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * *
3098991 TTTAGTCCTTAAAGAGCAGGACG-C-TTTCCTTTTTAAAGCCCACATAAGTTGATGGCACCTTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* * * * * * * *
3099054 AGTCCTTAAAAAGTAGGATGCCTTTTTCTTATTGAAGCTCACACAAGTTGGTGGTACCT
66 AGTCCTCAAAGAGCAGGATG-C-TTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
3099113 TTTAGTCCTCAAAGAGTAGGAC-AC--TTTCGTTTTTAAAGTCCACATAAGCTGGTGGCA-CTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTC-TTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* * * * * *
3099174 TAGTCCTCAAAGAGGAGGACGCCTTTTC-ATTTATAGCTCACACGAGTTGGTGGTACCT
65 TAGTCCTCAAAGAGCAGGATG-CTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
3099232 TTTAGTCCTCAAAGAGTAGGAC-AC--TTTCGTTTTTAAAGTCCACATAAGCTGGTGGCA-CTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTC-TTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* * * * *
3099293 TAGTCCTCAAAGAGGAGGACGCCTTTTC-ATTTATAGCTCACACGAGTTGGTGGCA-CT
65 TAGTCCTCAAAGAGCAGGATG-CTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * * * *
3099350 TTTAGTCTTCAAAGAGGAAGACG-CTTTCT-TTTTTAAAGCCCACACACGTTGGTGGCACCTTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
* ** * **
3099413 AGTCCTCAAAGAGGAAAATGCCTTT-TTTTTAAAGCTTACACGAGTTGGTGGCACCT
66 AGTCCTCAAAGAGCAGGATGCTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
* * ***
3099469 TTTAGCCCTCAAAGAGCCGGACG-CTTTTT-TTTTTAAAGCCCATGTGAA-TTGGTGGCACCTTT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCA-CACAAGTTGGTGGCACCTTT
* *
3099531 CAGACCTCAAAGAGCA
65 TAGTCCTCAAAGAGCA
3099547 TGACGCATTT
Statistics
Matches: 1670, Mismatches: 278, Indels: 127
0.80 0.13 0.06
Matches are distributed among these distances:
116 4 0.00
117 93 0.06
118 120 0.07
119 290 0.17
120 264 0.16
121 247 0.15
122 362 0.22
123 140 0.08
124 107 0.06
125 43 0.03
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (122 bp):
TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
AGTCCTCAAAGAGCAGGATGCTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCT
Found at i:3100525 original size:13 final size:13
Alignment explanation
Indices: 3100507--3100531 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3100497 ACAAACAATA
3100507 AATGTATTGATAT
1 AATGTATTGATAT
3100520 AATGTATTGATA
1 AATGTATTGATA
3100532 CATGCCTAAA
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:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
AATGTATTGATAT
Found at i:3100532 original size:34 final size:34
Alignment explanation
Indices: 3100488--3100561 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
3100478 TTCTACCATT
*
3100488 TGTATCGATACAAACA-ATAAATGTATTGATATAA
1 TGTATCGATACAAACATA-AAATGTATTGATAAAA
* ** *
3100522 TGTATTGATACATGCCTAAAATGTATTGATAAAA
1 TGTATCGATACAAACATAAAATGTATTGATAAAA
3100556 TGTATC
1 TGTATC
3100562 AATAGATGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
34 32 0.97
35 1 0.03
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (34 bp):
TGTATCGATACAAACATAAAATGTATTGATAAAA
Found at i:3100575 original size:34 final size:34
Alignment explanation
Indices: 3100506--3100586 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
3100496 TACAAACAAT
* **
3100506 AAATGTATTGATATAATGTATTGATACATGCCTA
1 AAATGTATTGATAAAATGTATCAATACATGCCTA
* *
3100540 AAATGTATTGATAAAATGTATCAATAGATGTCTA
1 AAATGTATTGATAAAATGTATCAATACATGCCTA
* *
3100574 AAATTTATCGATA
1 AAATGTATTGATA
3100587 CAAAAGTACT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (34 bp):
AAATGTATTGATAAAATGTATCAATACATGCCTA
Found at i:3100674 original size:20 final size:21
Alignment explanation
Indices: 3100636--3100690 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 21
3100626 CATAAGTAAA
3100636 TGTATCGATATATACTTATAAT
1 TGTATCGATATATA-TTATAAT
* *
3100658 TGTATCGGTATAT-TTATCAT
1 TGTATCGATATATATTATAAT
3100678 TGTATCGATATAT
1 TGTATCGATATAT
3100691 CTAGGTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 18 0.60
22 12 0.40
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (21 bp):
TGTATCGATATATATTATAAT
Found at i:3103259 original size:79 final size:79
Alignment explanation
Indices: 3103098--3103778 Score: 488
Period size: 79 Copynumber: 8.6 Consensus size: 79
3103088 TTTATTGGTG
* *
3103098 TTTTATTTCTAAAATATCGATTTTCTACCATCGGG-ATACTCCAACCCCGTTATTTTCGAGGGGA
1 TTTTATTTCTAAAACATCAATTTTCTACCATCGGGAATACTCCAACCCCGTTATTTTCGAGGGGA
* * ** *
3103162 TATTTCAACTTCGG
66 TACTCCAACCCCGA
**
3103176 TTTTATTTCTAAAACATCAATTTTCTACCATCGGGAATACTCCAACCTTGTTATTTTCGAGGGGA
1 TTTTATTTCTAAAACATCAATTTTCTACCATCGGGAATACTCCAACCCCGTTATTTTCGAGGGGA
3103241 TACTCCAACCCCGA
66 TACTCCAACCCCGA
* * *
3103255 TTTTATTTCTAAAACACCAATTTT-TCACCATC-GAAGATACTCCAACCCCATTATTTTCGAGGG
1 TTTTATTTCTAAAACATCAATTTTCT-ACCATCGGGA-ATACTCCAACCCCGTTATTTTCGAGGG
* * * * *
3103318 AAGACTCTAATCTCGA
64 GATACTCCAACCCCGA
* * * * * * *
3103334 TTTTATTTCTAAAACACCGATTTTAC-ACCATC-GAAGATACTGCAACCTCGTTATTTTTGAGGA
1 TTTTATTTCTAAAACATCAATTTT-CTACCATCGGGA-ATACTCCAACCCCGTTATTTTCGAGGG
* * *
3103397 GACACTCCAACCGCAA
64 GATACTCCAACCCCGA
* * * * * * *
3103413 TTTTATTTCTAAAA-AACTGATTTTCCACCATCGGGGATACTCCAACCCTGTTA-TTTCTGAAGA
1 TTTTATTTCTAAAACATC-AATTTTCTACCATCGGGAATACTCCAACCCCGTTATTTTC-GAGGG
* *
3103476 GACACTCCAACCTC-A
64 GATACTCCAACCCCGA
* ** * * *
3103491 GTTTTATTTCTAAAATATTGATTTT-TCACCATCGAGAATACTCCAACACCATTA-TTTCTGAGG
1 -TTTTATTTCTAAAACATCAATTTTCT-ACCATCGGGAATACTCCAACCCCGTTATTTTC-GAGG
* * *
3103554 GGATGCTCTAACCCTGA
63 GGATACTCCAACCCCGA
* * * * ** * * *
3103571 TTTTATTTTTAAAACATCAATTTTTTACTATCGGGGATACTCCAACCTTGTTGTTTCCGAGGAGA
1 TTTTATTTCTAAAACATCAATTTTCTACCATCGGGAATACTCCAACCCCGTTATTTTCGAGGGGA
* ** *
3103636 AACTCCAACCATGG
66 TACTCCAACCCCGA
* * * * * ** * * ** *
3103650 TTTAATTTCTAAAATACCAATTTTTTACTAT-TAGAGATATTCCAACCCTGTTATTACCGAAGGG
1 TTTTATTTCTAAAACATCAATTTTCTACCATCGGGA-ATACTCCAACCCCGTTATTTTCGAGGGG
3103714 ATACTCCAACCCCGA
65 ATACTCCAACCCCGA
* * * * *
3103729 TTTTATTT-TCAAAATATCGACTGTTC-ACCATTGGGGATACTCCAACCCCG
1 TTTTATTTCT-AAAACATC-AATTTTCTACCATCGGGAATACTCCAACCCCG
3103779 ATTTTATTTT
Statistics
Matches: 482, Mismatches: 102, Indels: 37
0.78 0.16 0.06
Matches are distributed among these distances:
78 45 0.09
79 425 0.88
80 12 0.02
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (79 bp):
TTTTATTTCTAAAACATCAATTTTCTACCATCGGGAATACTCCAACCCCGTTATTTTCGAGGGGA
TACTCCAACCCCGA
Found at i:3103745 original size:237 final size:237
Alignment explanation
Indices: 3103098--3103774 Score: 607
Period size: 237 Copynumber: 2.9 Consensus size: 237
3103088 TTTATTGGTG
* * * * * * *
3103098 TTTTATTTCTAAAATATCGATTTT-CTACCATCG-GGATACTCCAACCCCGTTATTTTCGAGGGG
1 TTTTATTTCTAAAACACCAATTTTAC-ACCATCGAAGATACTCCAACCTCGTTATTTCCGAGGAG
* * * ** ** * * * * * *
3103161 ATATTTCAACTTCGGTTTTATTTCTAAAACATCAATTTTCTACCATC-GGGAATACTCCAACCTT
65 AAACTCCAACCACAATTTAATTTCTAAAAAACCAATTTTCCACCATCAGAG-ATACTCCAACCCT
* * * * *
3103225 GTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACCATCGA-
129 GTTATTTCCGAAGGGATACTCCAACCCCGATTTTATTTCTAAAATATCGATTTTTCACCATCGAG
* *
3103289 AGATACTCCAACCCCATTATTTTCGAGGGAAGACTCTAATCTCGA
194 A-ATACTCCAACACCATTATTTTCGAGGGAAGACTCTAACCTCGA
* * **
3103334 TTTTATTTCTAAAACACCGATTTTACACCATCGAAGATACTGCAACCTCGTTATTTTTGAGGAGA
1 TTTTATTTCTAAAACACCAATTTTACACCATCGAAGATACTCCAACCTCGTTATTTCCGAGGAGA
* * * ** * *
3103399 CACTCCAACCGCAATTTTATTTCTAAAAAACTGATTTTCCACCATCGGGGATACTCCAACCCTGT
66 AACTCCAACCACAATTTAATTTCTAAAAAACCAATTTTCCACCATCAGAGATACTCCAACCCTGT
* * * * *
3103464 TATTTCTGAAGAGACACTCCAACCTC-AGTTTTATTTCTAAAATATTGATTTTTCACCATCGAGA
131 TATTTCCGAAGGGATACTCCAACCCCGA-TTTTATTTCTAAAATATCGATTTTTCACCATCGAGA
*
3103528 ATACTCCAACACCATTA-TTTCTGAGGGGATG-CTCTAACC-CTGA
195 ATACTCCAACACCATTATTTTC-GA-GGGAAGACTCTAACCTC-GA
* * ** * ** * *
3103571 TTTTATTTTTAAAACATCAATTTTTTACTATCGGGGATACTCCAACCTTGTTGTTTCCGAGGAGA
1 TTTTATTTCTAAAACACCAATTTTACACCATCGAAGATACTCCAACCTCGTTATTTCCGAGGAGA
*** * ** * * *
3103636 AACTCCAACCATGGTTTAATTTCTAAAATACCAATTTTTTACTATTAGAGATATTCCAACCCTGT
66 AACTCCAACCACAATTTAATTTCTAAAAAACCAATTTTCCACCATCAGAGATACTCCAACCCTGT
* * * * * *
3103701 TATTACCGAAGGGATACTCCAACCCCGATTTTATTT-TCAAAATATCGACTGTTCACCATTGGGG
131 TATTTCCGAAGGGATACTCCAACCCCGATTTTATTTCT-AAAATATCGATTTTTCACCATCGAGA
3103765 ATACTCCAAC
195 ATACTCCAAC
3103775 CCCGATTTTA
Statistics
Matches: 358, Mismatches: 73, Indels: 19
0.80 0.16 0.04
Matches are distributed among these distances:
236 36 0.10
237 312 0.87
238 10 0.03
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (237 bp):
TTTTATTTCTAAAACACCAATTTTACACCATCGAAGATACTCCAACCTCGTTATTTCCGAGGAGA
AACTCCAACCACAATTTAATTTCTAAAAAACCAATTTTCCACCATCAGAGATACTCCAACCCTGT
TATTTCCGAAGGGATACTCCAACCCCGATTTTATTTCTAAAATATCGATTTTTCACCATCGAGAA
TACTCCAACACCATTATTTTCGAGGGAAGACTCTAACCTCGA
Found at i:3103774 original size:51 final size:51
Alignment explanation
Indices: 3103711--3103847 Score: 249
Period size: 51 Copynumber: 2.7 Consensus size: 51
3103701 TATTACCGAA
3103711 GGGATACTCCAACCCCGATTTTATTTTCAAAATATCGACTGTTCACCATTG
1 GGGATACTCCAACCCCGATTTTATTTTCAAAATATCGACTGTTCACCATTG
3103762 GGGATACTCCAACCCCGATTTTATTTTCAAAATATCGACTGTTCACCATTG
1 GGGATACTCCAACCCCGATTTTATTTTCAAAATATCGACTGTTCACCATTG
*
3103813 GGGATACTCCAACCCC-ATTTTTATTTCCAAAATAT
1 GGGATACTCCAACCCCGA-TTTTATTTTCAAAATAT
3103848 TGATTTCTCG
Statistics
Matches: 84, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
50 1 0.01
51 83 0.99
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (51 bp):
GGGATACTCCAACCCCGATTTTATTTTCAAAATATCGACTGTTCACCATTG
Found at i:3105698 original size:30 final size:31
Alignment explanation
Indices: 3105662--3105788 Score: 112
Period size: 31 Copynumber: 4.0 Consensus size: 31
3105652 TCTTACGATA
*
3105662 CTATCTTTTGA-AGGCTAAGATAGAACCTCG
1 CTATCTTTTCACAGGCTAAGATAGAACCTCG
* * **
3105692 CTATCTTTTCATAGGCTAAGATATAACCTTT
1 CTATCTTTTCACAGGCTAAGATAGAACCTCG
* * *
3105723 CGATCTTTTCACAAGCTAAGATAGAACCTTTCTCC
1 CTATCTTTTCACAGGCTAAGATAGAA-C---CTCG
* *
3105758 CTATCTTTTTCAAAAGCTAAGATAGAACCTC
1 CTATC-TTTTCACAGGCTAAGATAGAACCTC
3105789 TCAATCACTT
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
30 10 0.13
31 38 0.48
32 4 0.05
35 7 0.09
36 20 0.25
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.34
Consensus pattern (31 bp):
CTATCTTTTCACAGGCTAAGATAGAACCTCG
Found at i:3110669 original size:21 final size:21
Alignment explanation
Indices: 3110643--3110718 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3110633 CTGCCAAGAA
*
3110643 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
3110664 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
3110684 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
3110705 ATGTATCGATACAT
1 ATGTATCGATACAT
3110719 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:3110689 original size:20 final size:20
Alignment explanation
Indices: 3110664--3110736 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3110654 CATCTTTTTT
3110664 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
3110684 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
3110705 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
3110725 ATGTATCGATAC
1 ATGTATCGATAC
3110737 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:3110700 original size:41 final size:41
Alignment explanation
Indices: 3110643--3110736 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
3110633 CTGCCAAGAA
*
3110643 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
3110684 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
3110725 ATGTATCGATAC
1 ATGTATCGATAC
3110737 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:3113198 original size:13 final size:13
Alignment explanation
Indices: 3113180--3113218 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3113170 ATAAACACCC
*
3113180 TGTATCGATACAG
1 TGTATCGATACAA
3113193 TGTATCGATACAA
1 TGTATCGATACAA
3113206 TGTATCGATACAA
1 TGTATCGATACAA
3113219 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3113229 original size:20 final size:20
Alignment explanation
Indices: 3113204--3113242 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3113194 GTATCGATAC
3113204 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
3113224 AATGTATCGATACATAGAA
1 AATGTATCGATACAAAGAA
3113243 TTTCTAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.23
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:3115316 original size:15 final size:15
Alignment explanation
Indices: 3115296--3115326 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3115286 ATTTCGTTTG
*
3115296 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3115311 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3115326 G
1 G
3115327 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3117159 original size:21 final size:21
Alignment explanation
Indices: 3117130--3117174 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3117120 AAGTTTTCAT
*
3117130 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3117150 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3117172 TTT
1 TTT
3117175 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:3119404 original size:13 final size:13
Alignment explanation
Indices: 3119386--3119411 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3119376 CAATTTTTTG
3119386 TGTATCGATACAT
1 TGTATCGATACAT
3119399 TGTATCGATACAT
1 TGTATCGATACAT
3119412 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3119476 original size:21 final size:21
Alignment explanation
Indices: 3119450--3119525 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3119440 CTGCCAAGAA
*
3119450 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
3119471 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
3119491 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
3119512 ATGTATCGATACAT
1 ATGTATCGATACAT
3119526 TACAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:3119496 original size:20 final size:20
Alignment explanation
Indices: 3119471--3119543 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
3119461 CATCTTTTTT
*
3119471 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTACAAC
****
3119491 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TACAAC
3119512 ATGTATCGATACATTACAAC
1 ATGTATCGATACATTACAAC
3119532 ATGTATCGATAC
1 ATGTATCGATAC
3119544 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTACAAC
Found at i:3119507 original size:41 final size:41
Alignment explanation
Indices: 3119450--3119543 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
3119440 CTGCCAAGAA
* *
3119450 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTACAAC
3119491 ATGTATCGATACATCTTTTTCATGTATCGATACATTACAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTACAAC
3119532 ATGTATCGATAC
1 ATGTATCGATAC
3119544 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTACAAC
Found at i:3120116 original size:21 final size:21
Alignment explanation
Indices: 3120087--3120138 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3120077 AACACATCAG
* *
3120087 TTTCATTTTCTAACTCACTTAT
1 TTTC-TTTTCCAACTCACTTAC
* *
3120109 TTTGTTTTCCAACTCATTTAC
1 TTTCTTTTCCAACTCACTTAC
3120130 TTTCTTTTC
1 TTTCTTTTC
3120139 AAGAATATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.17, C:0.23, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTCTTTTCCAACTCACTTAC
Found at i:3121884 original size:36 final size:33
Alignment explanation
Indices: 3121737--3121896 Score: 172
Period size: 31 Copynumber: 4.9 Consensus size: 33
3121727 CCTTACAACA
*
3121737 CTATCTTTT-GAAGGCTAAGATAGAACC--TCC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTTTCC
*
3121767 CTATCATTT-AACAGGCTAAGATAGAACC--TCC
1 CTATCTTTTCAA-AGGCTAAGATAGAACCTTTCC
*
3121798 CTATCTTTTCACAA-GCTAAGATAAAACCTCTTCC
1 CTATCTTTTCA-AAGGCTAAGATAGAACCT-TTCC
*
3121832 CTATCTTTTCATAGGCTAAGATAGAACCTTTCTC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTTTC-C
*
3121866 CTTAGCTTTTTCAAAGGCTAAGATAGAACCT
1 C-TATC-TTTTCAAAGGCTAAGATAGAACCT
3121897 CGCAATCACT
Statistics
Matches: 112, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
30 9 0.08
31 40 0.36
32 2 0.02
33 5 0.04
34 30 0.27
35 3 0.03
36 23 0.21
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.32
Consensus pattern (33 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTTTCC
Found at i:3125461 original size:21 final size:20
Alignment explanation
Indices: 3125414--3125467 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3125404 CGTTTAAGAC
* *
3125414 ATGTATCGATACATTTACTT
1 ATGTATCGATACATTCACTA
3125434 ATGTATCGATACATTCACTA
1 ATGTATCGATACATTCACTA
*
3125454 ATTGTATCAATACA
1 A-TGTATCGATACA
3125468 AATTGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:3128739 original size:23 final size:23
Alignment explanation
Indices: 3128708--3128751 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3128698 TAGTCAAGTG
3128708 TAAGCATACTTATTTTAGATTCC
1 TAAGCATACTTATTTTAGATTCC
*
3128731 TAAGTATACTTATTTTAGATT
1 TAAGCATACTTATTTTAGATT
3128752 TTTTAACTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (23 bp):
TAAGCATACTTATTTTAGATTCC
Found at i:3131416 original size:14 final size:14
Alignment explanation
Indices: 3131399--3131434 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
3131389 CGATTTTAGG
3131399 TTTTTTTTTTTGTT
1 TTTTTTTTTTTGTT
3131413 TTTTTTTTTTTGTT
1 TTTTTTTTTTTGTT
3131427 TTTGTTTT
1 TTT-TTTT
3131435 CTTTCGGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (14 bp):
TTTTTTTTTTTGTT
Found at i:3132646 original size:265 final size:261
Alignment explanation
Indices: 3132128--3132655 Score: 846
Period size: 265 Copynumber: 2.0 Consensus size: 261
3132118 GCAGCAAGTC
* *
3132128 TTTTGCCCTTTTCTTGTCTGGAATTATTTTTTGGTTCCTTTGACTAGAATTTTTTACTGTTGCTT
1 TTTTGCCCTTTCCTTGTCTGGAATTATTTTGTGGTTCCTTTGACTAGAATTTTTTACTGTTGCTT
* *
3132193 GCATATACACTGGCAAACAAACACTTGAAGAGCCAACATAGTGTTGTATTTACAGAATGTAGCTA
66 GCATATACACTGACAAACAAACACCTGAAGAGCCAACATAGTGTTGTATTTACAGAATGTAGCTA
* *
3132258 GGGTGATTTCAAGGAATATTCTGATTTTGAATGTTCATAACTTCATATGCAGCTTGTTCTTCTTG
131 GGATGATTTCAAGGAATATTCTGATTTTGAATGTTCATAACTTCATATGCAGCTTGTTCATCTTG
* * *
3132323 TGGGTGCAAAGCTGCAGCATATCATGGCAACCTTGGCGCTGAAGAGTTCTGGGATAACTGGCTAT
196 CGGGTACAAAGCTGCAGCATATCATGGCAACCTTGGCGCTGAAGAATTCTGGGATAACTGGCTAT
3132388 T
261 T
*
3132389 TTTTGGCCCTTTCCTTGTCTGGTATTATTTTGTGGTTCCTTTGGA-TAGAATTTTTTTAACTAG-
1 TTTT-GCCCTTTCCTTGTCTGGAATTATTTTGTGGTTCCTTT-GACTAGAA-TTTTTT-ACT-GT
3132452 TGCTTGCATATACACTGACAAACAAACACCTGAAGAGCCAACATAGTGTTGTATTTACAGAAAAT
61 TGCTTGCATATACACTGACAAACAAACACCTGAAGAGCCAACATAGTGTTGTATTTACAG--AAT
* *
3132517 TTAGCTAGGATGATTTCAAGGAATATTCTGATTTTGTATGTTCATAACTTCA-ATGCAGCTTGTT
124 GTAGCTAGGATGATTTCAAGGAATATTCTGATTTTGAATGTTCATAACTTCATATGCAGCTTGTT
* *
3132581 CATCTTGCGGGTACAAAGCTGCAGCATGTCATGGCAACCTTGGCGCTGGAGAATTCTGGGATAAC
189 CATCTTGCGGGTACAAAGCTGCAGCATATCATGGCAACCTTGGCGCTGAAGAATTCTGGGATAAC
3132646 TGGCTATT
254 TGGCTATT
3132654 TT
1 TT
3132656 ACCGGAGCAA
Statistics
Matches: 246, Mismatches: 14, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
261 4 0.02
262 39 0.16
263 8 0.03
264 61 0.25
265 82 0.33
266 52 0.21
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (261 bp):
TTTTGCCCTTTCCTTGTCTGGAATTATTTTGTGGTTCCTTTGACTAGAATTTTTTACTGTTGCTT
GCATATACACTGACAAACAAACACCTGAAGAGCCAACATAGTGTTGTATTTACAGAATGTAGCTA
GGATGATTTCAAGGAATATTCTGATTTTGAATGTTCATAACTTCATATGCAGCTTGTTCATCTTG
CGGGTACAAAGCTGCAGCATATCATGGCAACCTTGGCGCTGAAGAATTCTGGGATAACTGGCTAT
T
Found at i:3134309 original size:22 final size:22
Alignment explanation
Indices: 3134281--3134324 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3134271 AAGGGCAGTT
3134281 TTAAGTGTTACTATATTCATTC
1 TTAAGTGTTACTATATTCATTC
3134303 TTAAGTGTTACTATATTCATTC
1 TTAAGTGTTACTATATTCATTC
3134325 AACGAATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.50
Consensus pattern (22 bp):
TTAAGTGTTACTATATTCATTC
Found at i:3135204 original size:2 final size:2
Alignment explanation
Indices: 3135197--3135230 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3135187 GAACTGACCC
3135197 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
3135231 TATCAACAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3143816 original size:23 final size:23
Alignment explanation
Indices: 3143768--3143831 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
3143758 TAATAAAATA
* * * *
3143768 TAAATTTAAACT-TAAACTCATT
1 TAAATCTAAACTAAAAACCCATC
3143790 TAAATCTAAACTAAAAACCCATC
1 TAAATCTAAACTAAAAACCCATC
*
3143813 TAAA-CTTAAAATAAAAACC
1 TAAATC-TAAACTAAAAACC
3143832 TAATTTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 12 0.34
23 23 0.66
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAATCTAAACTAAAAACCCATC
Found at i:3144702 original size:18 final size:19
Alignment explanation
Indices: 3144666--3144703 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3144656 TATGTCTACC
3144666 AAACTTTGAGATGCGTAAA
1 AAACTTTGAGATGCGTAAA
*
3144685 AAACTTTGAG-TTCGTAAA
1 AAACTTTGAGATGCGTAAA
3144703 A
1 A
3144704 TTTGGGTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (19 bp):
AAACTTTGAGATGCGTAAA
Found at i:3146449 original size:19 final size:19
Alignment explanation
Indices: 3146411--3146464 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
3146401 TAATGTTAAG
* *
3146411 AATTTATCTTTTTTATTTTT
1 AATTTAT-TTTTTAAATTTT
3146431 AATTTATTTTTTAAATTTT
1 AATTTATTTTTTAAATTTT
* *
3146450 AATATATTTTATAAA
1 AATTTATTTTTTAAA
3146465 AATATATATC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 23 0.77
20 7 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
AATTTATTTTTTAAATTTT
Found at i:3148255 original size:14 final size:15
Alignment explanation
Indices: 3148229--3148257 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3148219 TCCGTTTTCC
3148229 TATTTTAAAATATAA
1 TATTTTAAAATATAA
3148244 TATTTT-AAATATAA
1 TATTTTAAAATATAA
3148258 AAAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTTTAAAATATAA
Found at i:3149155 original size:16 final size:16
Alignment explanation
Indices: 3149131--3149168 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3149121 AATAATATAC
*
3149131 ATATA-ATATAAATAT
1 ATATATATATAAAAAT
*
3149146 ATGTATATATAAAAAT
1 ATATATATATAAAAAT
3149162 ATATATA
1 ATATATA
3149169 AAATAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
ATATATATATAAAAAT
Found at i:3149180 original size:19 final size:19
Alignment explanation
Indices: 3149118--3149197 Score: 65
Period size: 19 Copynumber: 4.2 Consensus size: 19
3149108 AATATTACTT
* *
3149118 AAAAATAATATACATATAA
1 AAAAATTATATAAATATAA
* ** *
3149137 TATAAA-TATATGTATATAT
1 -AAAAATTATATAAATATAA
3149156 AAAAATATATATAAA-ATAA
1 AAAAAT-TATATAAATATAA
*
3149175 AAAAATTATTTAAATATAA
1 AAAAATTATATAAATATAA
3149194 AAAA
1 AAAA
3149198 TAAAAAAATA
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
18 11 0.23
19 26 0.55
20 10 0.21
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (19 bp):
AAAAATTATATAAATATAA
Found at i:3149197 original size:18 final size:19
Alignment explanation
Indices: 3149064--3149199 Score: 75
Period size: 18 Copynumber: 6.8 Consensus size: 19
3149054 TATTTTATTT
*
3149064 TAAACATAAAAAATATAAATA
1 TAAATATAAAAAATAT--ATA
*
3149085 TAATATTTATAAAAAATATTTA
1 TAA-A--TATAAAAAATATATA
3149107 -AAATATTACTTAAAAATA-ATA
1 TAAATA-TA---AAAAATATATA
* *
3149128 TACATATAATATAAATATATG
1 TAAATATAA-A-AAATATATA
*
3149149 TATATAT-AAAAATATATA
1 TAAATATAAAAAATATATA
*
3149167 TAAA-ATAAAAAA-ATTATT
1 TAAATATAAAAAATA-TATA
3149185 TAAATATAAAAAATA
1 TAAATATAAAAAATA
3149200 AAAAAATATA
Statistics
Matches: 91, Mismatches: 9, Indels: 31
0.69 0.07 0.24
Matches are distributed among these distances:
17 3 0.03
18 26 0.29
19 12 0.13
20 8 0.09
21 17 0.19
22 14 0.15
24 11 0.12
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (19 bp):
TAAATATAAAAAATATATA
Found at i:3149278 original size:24 final size:25
Alignment explanation
Indices: 3149261--3149310 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
3149251 TTTTATCTTT
3149261 TTCTTTCTTT-TTTTTTTTTCTCCT
1 TTCTTTCTTTCTTTTTTTTTCTCCT
*
3149285 TTCTTTCTTTCTTTCTTTTTTTTCCT
1 TTCTTTCTTTCTTT-TTTTTTCTCCT
3149311 GCCCGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.43
25 3 0.13
26 10 0.43
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (25 bp):
TTCTTTCTTTCTTTTTTTTTCTCCT
Found at i:3152919 original size:13 final size:12
Alignment explanation
Indices: 3152891--3152936 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
3152881 AATTAAGTTC
3152891 AAATTTAATTTA
1 AAATTTAATTTA
*
3152903 AAATTTAGATTTT
1 AAATTTA-ATTTA
3152916 AAATTTAATTTA
1 AAATTTAATTTA
*
3152928 AAAGTTAAT
1 AAATTTAAT
3152937 CAAGAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 19 0.63
13 11 0.37
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (12 bp):
AAATTTAATTTA
Found at i:3153326 original size:6 final size:6
Alignment explanation
Indices: 3153315--3153348 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
3153305 GACGGCGGCT
3153315 GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGA
1 GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGA
3153349 AGTTGAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.50, T:0.18
Consensus pattern (6 bp):
GTGAGA
Found at i:3153495 original size:17 final size:17
Alignment explanation
Indices: 3153469--3153513 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
3153459 ATTAATAATT
*
3153469 ATTATGTAAATAAAAAA
1 ATTATTTAAATAAAAAA
** *
3153486 ATTATTTAAATTTATAA
1 ATTATTTAAATAAAAAA
3153503 ATTATTTAAAT
1 ATTATTTAAAT
3153514 TAAATATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
ATTATTTAAATAAAAAA
Found at i:3153768 original size:13 final size:13
Alignment explanation
Indices: 3153750--3153795 Score: 65
Period size: 13 Copynumber: 3.4 Consensus size: 13
3153740 TTTTTATTTT
3153750 AAATAAATTATTA
1 AAATAAATTATTA
3153763 AAATAAATTAATTTA
1 AAATAAATT-A-TTA
*
3153778 AAATAAATAATTA
1 AAATAAATTATTA
3153791 AAATA
1 AAATA
3153796 TTATTGTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 17 0.57
14 2 0.07
15 11 0.37
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATAAATTATTA
Found at i:3153972 original size:23 final size:23
Alignment explanation
Indices: 3153938--3153999 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
3153928 ATTATTATGT
*
3153938 TGATATTTTTAAATTAATAAAAA
1 TGATATTATTAAATTAATAAAAA
3153961 TGATATTATT-AA-TAA-AAAAA
1 TGATATTATTAAATTAATAAAAA
*
3153981 T-AGATTA-TAAATATAATAA
1 TGATATTATTAAAT-TAATAA
3154000 CAATTTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 1 0.03
19 7 0.21
20 6 0.18
21 6 0.18
22 4 0.12
23 9 0.27
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (23 bp):
TGATATTATTAAATTAATAAAAA
Found at i:3154099 original size:14 final size:14
Alignment explanation
Indices: 3154075--3154125 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
3154065 ATGTAATAAT
*
3154075 TTTAAAATATTTAA
1 TTTAAATTATTTAA
*
3154089 TTTAATTTATTTAA
1 TTTAAATTATTTAA
*
3154103 TTTAAAAT-TTTAA
1 TTTAAATTATTTAA
3154116 TTTAAATTAT
1 TTTAAATTAT
3154126 AATCGTCTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 12 0.39
14 19 0.61
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAAATTATTTAA
Found at i:3154168 original size:34 final size:31
Alignment explanation
Indices: 3154110--3154171 Score: 79
Period size: 34 Copynumber: 1.9 Consensus size: 31
3154100 TAATTTAAAA
3154110 TTTTAATTTAAATTATAATCGTCTAATTATT
1 TTTTAATTTAAATTATAATCGTCTAATTATT
* *
3154141 TTTTAAATTTAAGAGTTATAGTTGTCTAATT
1 TTTT-AATTTAA-A-TTATAATCGTCTAATT
3154172 TAAATTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 4 0.15
32 7 0.27
33 1 0.04
34 14 0.54
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (31 bp):
TTTTAATTTAAATTATAATCGTCTAATTATT
Found at i:3154188 original size:20 final size:22
Alignment explanation
Indices: 3154146--3154191 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
3154136 TTATTTTTTA
* *
3154146 AATTTAAGAGTTATAGTTGTCT
1 AATTTAAGAGTTATAATTATCT
3154168 AATTTAA-A-TTATAATTATCT
1 AATTTAAGAGTTATAATTATCT
3154188 AATT
1 AATT
3154192 ATTTTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 1 0.05
22 7 0.32
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (22 bp):
AATTTAAGAGTTATAATTATCT
Found at i:3154410 original size:14 final size:15
Alignment explanation
Indices: 3154386--3154414 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3154376 AAATGATTAC
3154386 AATTCAAATTAAATA
1 AATTCAAATTAAATA
3154401 AATT-AAATTAAATA
1 AATTCAAATTAAATA
3154415 TTTTAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
AATTCAAATTAAATA
Found at i:3155752 original size:17 final size:16
Alignment explanation
Indices: 3155730--3155830 Score: 71
Period size: 17 Copynumber: 6.0 Consensus size: 16
3155720 TGTTAATCCT
3155730 TATTATATTTATAATAA
1 TATTAT-TTTATAATAA
3155747 TATTATTTTTTATTAATAA
1 TATTA--TTTTA-TAATAA
* * *
3155766 TATAATTTTTTATTAA
1 TATTATTTTATAATAA
3155782 TAATTATTTTA-AA-AA
1 T-ATTATTTTATAATAA
* * *
3155797 TACTAATATAATAATAA
1 TA-TTATTTTATAATAA
3155814 TATTATTATTATAATAA
1 TATTATT-TTATAATAA
3155831 CAATAGGCAA
Statistics
Matches: 64, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
14 1 0.02
15 8 0.12
16 12 0.19
17 28 0.44
18 4 0.06
19 11 0.17
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTATTTTATAATAA
Found at i:3155765 original size:22 final size:19
Alignment explanation
Indices: 3155737--3155785 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
3155727 CCTTATTATA
*
3155737 TTTA-TAATAATATTATTT
1 TTTATTAATAATATAATTT
3155755 TTTATTAATAATATAATTT
1 TTTATTAATAATATAATTT
3155774 TTTATTAATAAT
1 TTTATTAATAAT
3155786 TATTTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 4 0.14
19 25 0.86
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATTAATAATATAATTT
Found at i:3155791 original size:16 final size:17
Alignment explanation
Indices: 3155744--3155791 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 17
3155734 ATATTTATAA
3155744 TAAT-ATTATTTTTTAT
1 TAATAATTATTTTTTAT
3155760 TAATAATATAATTTTTTAT
1 TAATAAT-T-ATTTTTTAT
3155779 TAATAATTATTTT
1 TAATAATTATTTT
3155792 AAAAATACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 2 0.07
19 16 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATAATTATTTTTTAT
Found at i:3156761 original size:19 final size:19
Alignment explanation
Indices: 3156734--3156951 Score: 97
Period size: 19 Copynumber: 11.7 Consensus size: 19
3156724 TTTAAAAAAA
* *
3156734 TCATTTTTAGGTGAAAATC
1 TCATATTTAGGTGAGAATC
* * * *
3156753 TCGTATTTAGATAAAAAT-
1 TCATATTTAGGTGAGAATC
* *
3156771 TCTATATTTAAGTGGGAATC
1 TC-ATATTTAGGTGAGAATC
** * * *
3156791 TCATGCTTAGATGAAAATT
1 TCATATTTAGGTGAGAATC
*
3156810 TCATATTTAAGTGAGAATC
1 TCATATTTAGGTGAGAATC
* * *
3156829 TCATGTTTGGGTGAGAGTC
1 TCATATTTAGGTGAGAATC
* *
3156848 TCGTATTTTA-TTGAGAATC
1 TCATA-TTTAGGTGAGAATC
*
3156867 -CATATTTAGGTGAGAATG
1 TCATATTTAGGTGAGAATC
* *
3156885 T-AT-TTGA-GTGAGAATT
1 TCATATTTAGGTGAGAATC
* ** *
3156901 TCGTATTTAGACGAAAATC
1 TCATATTTAGGTGAGAATC
* * *
3156920 TCATATTTAAGTAAAAATC
1 TCATATTTAGGTGAGAATC
* *
3156939 TCTTTTTTAGGTG
1 TCATATTTAGGTG
3156952 TAAACCCCGT
Statistics
Matches: 139, Mismatches: 52, Indels: 16
0.67 0.25 0.08
Matches are distributed among these distances:
16 9 0.06
17 8 0.06
18 17 0.12
19 100 0.72
20 5 0.04
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (19 bp):
TCATATTTAGGTGAGAATC
Found at i:3156791 original size:38 final size:38
Alignment explanation
Indices: 3156734--3156832 Score: 110
Period size: 38 Copynumber: 2.6 Consensus size: 38
3156724 TTTAAAAAAA
* * * * *
3156734 TCATTTTTAGGTGAAAATCTCGTATTTAGATAAAAA-T
1 TCATATTTAAGTGAGAATCTCATACTTAGATAAAAATT
* * *
3156771 TCTATATTTAAGTGGGAATCTCATGCTTAGATGAAAATT
1 TC-ATATTTAAGTGAGAATCTCATACTTAGATAAAAATT
3156810 TCATATTTAAGTGAGAATCTCAT
1 TCATATTTAAGTGAGAATCTCAT
3156833 GTTTGGGTGA
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
37 2 0.04
38 46 0.90
39 3 0.06
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.39
Consensus pattern (38 bp):
TCATATTTAAGTGAGAATCTCATACTTAGATAAAAATT
Found at i:3156833 original size:38 final size:38
Alignment explanation
Indices: 3156759--3156833 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
3156749 AATCTCGTAT
*
3156759 TTAGATAAAAATTCTATATTTAAGTGGGAATCTCATGC
1 TTAGATAAAAATTCTATATTTAAGTGAGAATCTCATGC
*
3156797 TTAGATGAAAATT-TCATATTTAAGTGAGAATCTCATG
1 TTAGATAAAAATTCT-ATATTTAAGTGAGAATCTCATG
3156834 TTTGGGTGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 1 0.03
38 33 0.97
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (38 bp):
TTAGATAAAAATTCTATATTTAAGTGAGAATCTCATGC
Found at i:3156855 original size:38 final size:38
Alignment explanation
Indices: 3156774--3156951 Score: 121
Period size: 38 Copynumber: 4.8 Consensus size: 38
3156764 TAAAAATTCT
* * * * *
3156774 ATATTTAAGTGGGAATCTCATGCTTAGATGAAAATTTC
1 ATATTTAAGTGAGAATCTCATGTTTAGGTGAGAATCTC
* *
3156812 ATATTTAAGTGAGAATCTCATGTTTGGGTGAGAGTCTC
1 ATATTTAAGTGAGAATCTCATGTTTAGGTGAGAATCTC
* * * *
3156850 GTATTTTATTGAGAATC-CATATTTAGGTGAGAA--T-
1 ATATTTAAGTGAGAATCTCATGTTTAGGTGAGAATCTC
* * * * * ** *
3156884 GTATTTGAGTGAGAATTTCGTATTTAGACGAAAATCTC
1 ATATTTAAGTGAGAATCTCATGTTTAGGTGAGAATCTC
* * * *
3156922 ATATTTAAGTAAAAATCTCTTTTTTAGGTG
1 ATATTTAAGTGAGAATCTCATGTTTAGGTG
3156952 TAAACCCCGT
Statistics
Matches: 107, Mismatches: 29, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
34 14 0.13
35 13 0.12
37 14 0.13
38 66 0.62
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (38 bp):
ATATTTAAGTGAGAATCTCATGTTTAGGTGAGAATCTC
Found at i:3157106 original size:20 final size:20
Alignment explanation
Indices: 3157055--3157108 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
3157045 GAAACTTCGC
* **
3157055 AGTTTTGTTGAGAGTCTTTT
1 AGTTTTGTTGAGAATCTCAT
**
3157075 A-TTTTGACGAGAATCTCAT
1 AGTTTTGTTGAGAATCTCAT
3157094 AGTTTTGTTGAGAAT
1 AGTTTTGTTGAGAAT
3157109 TTTTTGTTTC
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.46
Consensus pattern (20 bp):
AGTTTTGTTGAGAATCTCAT
Found at i:3157207 original size:22 final size:22
Alignment explanation
Indices: 3157182--3157229 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3157172 ATTCAATATT
3157182 TTTAAAGAGTT-TATTTTATTCA
1 TTTAAAGA-TTATATTTTATTCA
* *
3157204 TTTATATATTATATTTTATTCA
1 TTTAAAGATTATATTTTATTCA
3157226 TTTA
1 TTTA
3157230 TGCATTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (22 bp):
TTTAAAGATTATATTTTATTCA
Found at i:3157236 original size:22 final size:22
Alignment explanation
Indices: 3157193--3157236 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3157183 TTAAAGAGTT
*
3157193 TATTTTATTCATTTATATATTA
1 TATTTTATTCATTTATACATTA
*
3157215 TATTTTATTCATTTATGCATTA
1 TATTTTATTCATTTATACATTA
3157237 ATACTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (22 bp):
TATTTTATTCATTTATACATTA
Found at i:3157593 original size:2 final size:2
Alignment explanation
Indices: 3157586--3157612 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3157576 ACATTGACTC
3157586 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 A
3157613 GGATTTGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3158228 original size:25 final size:23
Alignment explanation
Indices: 3158178--3158236 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 23
3158168 TTATAAATAA
* *
3158178 ATAATTATAAAAAATTTAATTTTT
1 ATAATTA-ATAAAATATAATTTTT
3158202 ATAATTAATAAAATATAATTATATT
1 ATAATTAATAAAATATAATT-T-TT
*
3158227 ATTATTAATA
1 ATAATTAATA
3158237 TTATTCAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.37
24 8 0.27
25 11 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAATTAATAAAATATAATTTTT
Found at i:3160147 original size:17 final size:18
Alignment explanation
Indices: 3160125--3160181 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 18
3160115 TTTAGAAATG
3160125 TAATTATATT-TTTATTT
1 TAATTATATTATTTATTT
3160142 TAATTATATTATTTA-TT
1 TAATTATATTATTTATTT
* *
3160159 TATTTAT-TTATTAATATT
1 TAATTATATTATTTAT-TT
3160177 TAATT
1 TAATT
3160182 CAAAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 6 0.18
17 18 0.53
18 10 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TAATTATATTATTTATTT
Found at i:3165301 original size:17 final size:18
Alignment explanation
Indices: 3165279--3165312 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3165269 TTAGAGATGC
3165279 AATTATATT-TTTATTTT
1 AATTATATTATTTATTTT
3165296 AATTATATTATTTATTT
1 AATTATATTATTTATTT
3165313 ACTTACTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:3168478 original size:24 final size:24
Alignment explanation
Indices: 3168451--3168503 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3168441 AAAAATTATT
* *
3168451 ATATATATAATAA-TATTTTATTTA
1 ATATAT-TAATAATTACTGTATTTA
3168475 ATATATTAATAATTACTGTATTTA
1 ATATATTAATAATTACTGTATTTA
3168499 ATATA
1 ATATA
3168504 ATATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
ATATATTAATAATTACTGTATTTA
Found at i:3169183 original size:22 final size:22
Alignment explanation
Indices: 3169150--3169191 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3169140 TAATATTCGA
*
3169150 ATAATAAATAAATTTAAATATT
1 ATAATAAATAAATTCAAATATT
3169172 ATAA-AAATTAAATTCAAATA
1 ATAATAAA-TAAATTCAAATA
3169192 AAAATACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAATAAATAAATTCAAATATT
Found at i:3171275 original size:21 final size:21
Alignment explanation
Indices: 3171230--3171273 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
3171220 AAATAAAATT
3171230 AAATAAAAAAATATATATTAA
1 AAATAAAAAAATATATATTAA
3171251 AAATATAAAAAAT-TA-ATTAA
1 AAATA-AAAAAATATATATTAA
3171271 AAA
1 AAA
3171274 ATTTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 7 0.32
22 7 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATAAAAAAATATATATTAA
Found at i:3172481 original size:18 final size:18
Alignment explanation
Indices: 3172442--3172481 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
3172432 AATTATTATT
3172442 TTAAATTTTTTATATTAA
1 TTAAATTTTTTATATTAA
3172460 -TAAATTTTTT-TATATAA
1 TTAAATTTTTTATAT-TAA
3172477 TTAAA
1 TTAAA
3172482 CAAATAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 3 0.15
17 13 0.65
18 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAATTTTTTATATTAA
Found at i:3173018 original size:15 final size:13
Alignment explanation
Indices: 3172996--3173053 Score: 71
Period size: 15 Copynumber: 4.2 Consensus size: 13
3172986 TTTAATTAAA
3172996 TATTAAATTTTGTT
1 TATTAAATTTT-TT
*
3173010 TATTTAAATTTTGT
1 TA-TTAAATTTTTT
3173024 TATTAAATTATTTAT
1 TATTAAATT-TTT-T
3173039 TATTAAATTTTTT
1 TATTAAATTTTTT
3173052 TA
1 TA
3173054 ATTTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
13 10 0.26
14 10 0.26
15 19 0.49
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (13 bp):
TATTAAATTTTTT
Found at i:3173030 original size:28 final size:28
Alignment explanation
Indices: 3172996--3173049 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
3172986 TTTAATTAAA
3172996 TATTAAATT-TTGT-TTATTTAAATTTTGT
1 TATTAAATTATT-TATTA-TTAAATTTTGT
3173024 TATTAAATTATTTATTATTAAATTTT
1 TATTAAATTATTTATTATTAAATTTT
3173050 TTTAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (28 bp):
TATTAAATTATTTATTATTAAATTTTGT
Found at i:3173133 original size:17 final size:16
Alignment explanation
Indices: 3173113--3173158 Score: 67
Period size: 17 Copynumber: 2.9 Consensus size: 16
3173103 ATATTTTATT
3173113 TTAATAAATAAAAATAA
1 TTAATAAATAAAAAT-A
*
3173130 TTAATTAATAAAAATA
1 TTAATAAATAAAAATA
3173146 TTAA-AAATAAAAA
1 TTAATAAATAAAAA
3173159 ATAAGATAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 8 0.30
16 5 0.19
17 14 0.52
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAATAAATAAAAATA
Found at i:3173372 original size:20 final size:19
Alignment explanation
Indices: 3173349--3173388 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3173339 ATTGAGTGAT
3173349 AAAATTTA-AATTAAAAATTA
1 AAAATTTATAA-T-AAAATTA
3173369 AAAATTTATAATAAAATTA
1 AAAATTTATAATAAAATTA
3173388 A
1 A
3173389 TTATATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 9 0.47
21 2 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATTTATAATAAAATTA
Found at i:3173468 original size:2 final size:2
Alignment explanation
Indices: 3173461--3173489 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3173451 TTAATGTAAC
3173461 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3173490 GTAGAGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3185663 original size:37 final size:37
Alignment explanation
Indices: 3185622--3185712 Score: 92
Period size: 38 Copynumber: 2.4 Consensus size: 37
3185612 TTTACATTGG
* * *
3185622 TGGCATGGTTCGAAATAAAACTACTATTTTAAGCCAA
1 TGGCATGGTTCGAAATAAAACTACAATTCTAAACCAA
* * * * *
3185659 TGGCAAGGTTCAAAACAAAAATTACAATTCTAAATCAA
1 TGGCATGGTTCGAAA-TAAAACTACAATTCTAAACCAA
*
3185697 TGGCATGGGTCGAAAT
1 TGGCATGGTTCGAAAT
3185713 TGGCTTCTAA
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
37 13 0.32
38 28 0.68
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (37 bp):
TGGCATGGTTCGAAATAAAACTACAATTCTAAACCAA
Found at i:3187620 original size:16 final size:17
Alignment explanation
Indices: 3187593--3187624 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3187583 CTTATTTACT
3187593 TTTTACTTTTAAAAAAG
1 TTTTACTTTTAAAAAAG
3187610 TTTTA-TTTTAAAAAA
1 TTTTACTTTTAAAAAA
3187625 TAAAAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTTACTTTTAAAAAAG
Found at i:3187783 original size:22 final size:22
Alignment explanation
Indices: 3187746--3187788 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
3187736 CATTTTTAGA
3187746 CTTTTGCTTCTATTTTTCTTTTT
1 CTTTTGCTTCTATTTTT-TTTTT
3187769 CTTTT-CTTCT-TTTTTTTTTT
1 CTTTTGCTTCTATTTTTTTTTT
3187789 ATATTTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 5 0.25
22 5 0.25
23 5 0.25
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (22 bp):
CTTTTGCTTCTATTTTTTTTTT
Found at i:3189641 original size:20 final size:21
Alignment explanation
Indices: 3189610--3189648 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
3189600 GATTTGGGGG
3189610 TTTGATTATGTTTTAAGATGC
1 TTTGATTATGTTTTAAGATGC
3189631 TTTGA-TATGTTTTAAGAT
1 TTTGATTATGTTTTAAGAT
3189649 AGTGATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.26, C:0.03, G:0.18, T:0.54
Consensus pattern (21 bp):
TTTGATTATGTTTTAAGATGC
Found at i:3195825 original size:52 final size:52
Alignment explanation
Indices: 3195677--3195805 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
3195667 CGAAATATGA
3195677 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
3195729 AAATTTGCCTACATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
3195781 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
3195806 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:3195905 original size:19 final size:19
Alignment explanation
Indices: 3195881--3195965 Score: 101
Period size: 19 Copynumber: 4.7 Consensus size: 19
3195871 TAGCTTACAT
3195881 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
3195900 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
3195919 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
3195932 TGTATCGATACAACACTTTA
1 TGTATCGATACAAAAC-TTA
3195952 TGTATCGATACAAA
1 TGTATCGATACAAA
3195966 TCGTTGAAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
13 11 0.19
14 1 0.02
16 2 0.04
19 30 0.53
20 13 0.23
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:3195937 original size:13 final size:13
Alignment explanation
Indices: 3195919--3195943 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3195909 ACAACACTTA
3195919 TGTATCGATACAT
1 TGTATCGATACAT
3195932 TGTATCGATACA
1 TGTATCGATACA
3195944 ACACTTTATG
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):
TGTATCGATACAT
Found at i:3195941 original size:32 final size:33
Alignment explanation
Indices: 3195900--3195963 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 33
3195890 ACAAAACTTA
3195900 TGTATCGATACAACAC-TTATGTATCGATACAT
1 TGTATCGATACAACACTTTATGTATCGATACAT
3195932 TGTATCGATACAACACTTTATGTATCGATACA
1 TGTATCGATACAACACTTTATGTATCGATACA
3195964 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAACACTTTATGTATCGATACAT
Found at i:3196707 original size:43 final size:44
Alignment explanation
Indices: 3196647--3196973 Score: 329
Period size: 43 Copynumber: 7.2 Consensus size: 44
3196637 TAAAGATGAT
* *
3196647 AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* * * *
3196690 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A
*
3196736 AGATGAGGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-
1 A-A--A-GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
** * * *
3196783 GGAGTTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-A
* *
3196828 AGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA-TTT
1 A-A--A-GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* *
3196875 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A
*
3196921 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-
1 -A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
3196967 AAAGGTG
1 AAAGGTG
3196974 AAAAAAAGGA
Statistics
Matches: 238, Mismatches: 27, Indels: 38
0.79 0.09 0.13
Matches are distributed among these distances:
43 115 0.48
44 4 0.02
45 1 0.00
46 2 0.01
47 3 0.01
48 3 0.01
49 73 0.31
50 37 0.16
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (44 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
Found at i:3196860 original size:49 final size:49
Alignment explanation
Indices: 3196535--3197263 Score: 767
Period size: 49 Copynumber: 15.1 Consensus size: 49
3196525 CTTAGGAATG
* * * *
3196535 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAT
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
** *
3196584 TTAAAGATGACAAAGACGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* *
3196636 TTAAAGATGATAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * * *
3196688 TT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* *
3196731 TTAAAAGATGAGGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TT-AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * *
3196781 TT---G--G-AGTTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* *
3196824 TTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA-
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * *
3196872 TT-----TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
*
3196916 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * * * *
3196965 TTAAAGGTGAAAAAAAGGATGTCAATCTGCTGATTCAAGGCCAGCTACATTGAAC
1 TTAAAGATG-----AAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
*
3197020 TTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCAAGCTATATTGGAC
1 TTAAAGAT-G--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* *
3197072 TT-AA-AT----GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
*
3197115 TTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
* * *
3197164 TT--AGA--ACGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
** *
3197209 TTAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATAGTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
3197258 TTAAAG
1 TTAAAG
3197264 GAAGATGCCA
Statistics
Matches: 582, Mismatches: 59, Indels: 78
0.81 0.08 0.11
Matches are distributed among these distances:
43 146 0.25
44 5 0.01
45 40 0.07
46 2 0.00
47 6 0.01
48 5 0.01
49 167 0.29
50 40 0.07
51 2 0.00
52 120 0.21
53 6 0.01
54 4 0.01
55 38 0.07
56 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
Found at i:3196884 original size:92 final size:92
Alignment explanation
Indices: 3196601--3197264 Score: 923
Period size: 92 Copynumber: 7.0 Consensus size: 92
3196591 TGACAAAGAC
* * * *
3196601 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATAAAGGCGCCAATATGCTGA
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG---AAGGTGCCAATATGCTGA
3196666 TTCAAGGCCAGCGATATTGGACTTAAAGGT
63 TTCAAGGCCAGCGATATTGGACTTAAAGGT
* * *
3196696 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGAGGGTGCCAATATGCTGATT
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT-AAAGATGAAGGTGCCAATATGCTGATT
** *
3196761 CAAGGCCAGCGATATTGGACTTGGAGTT
65 CAAGGCCAGCGATATTGGACTTAAAGGT
*
3196789 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTC
*
3196854 AAGGCCAGCGATATTGGATTTAAAGGT
66 AAGGCCAGCGATATTGGACTTAAAGGT
3196881 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTC
3196946 AAGGCCAGCGATATTGGACTTAAAGGTGAAAAAAAGGAT
66 AAGGCCAGCGATATTGGAC-T-----T-----AAAGG-T
* * *
3196985 GTCAATCTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGA
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATATGCTGA
* * *
3197050 TTCAAGGCAAGCTATATTGGACTTAAATGT
63 TTCAAGGCCAGCGATATTGGACTTAAAGGT
*
3197080 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTC
*
3197145 AAGGCCAGCTATATTGGACTTAGAACGGT
66 AAGGCCAGCGATATTGGACTTA-AA-GGT
**
3197174 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGACAAAGGTGCCAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTC
* *
3197239 AAGGCCAGCTATAGTGGACTTAAAGG
66 AAGGCCAGCGATATTGGACTTAAAGG
3197265 AAGATGCCAC
Statistics
Matches: 519, Mismatches: 32, Indels: 39
0.88 0.05 0.07
Matches are distributed among these distances:
92 176 0.34
93 83 0.16
94 87 0.17
95 74 0.14
96 11 0.02
98 1 0.00
101 1 0.00
103 5 0.01
104 41 0.08
105 1 0.00
106 1 0.00
107 38 0.07
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTC
AAGGCCAGCGATATTGGACTTAAAGGT
Found at i:3197133 original size:199 final size:187
Alignment explanation
Indices: 3196535--3197264 Score: 964
Period size: 199 Copynumber: 3.8 Consensus size: 187
3196525 CTTAGGAATG
* * * * *
3196535 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGATTTAAAGATGACAAAGA
1 TTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-G--AAAGG
* * * * *
3196600 CGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATAAAGGCGCCAATATGCTG
59 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG--AAAGGTGCCAATATGCTG
* * *
3196665 ATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGG
122 ATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
3196730 C
187 C
* * * *
3196731 TTAAAAGATGAGGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-G-GAGTTGCCAA
1 TT-AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAAGGTGCCAA
*
3196794 TGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-ATGGTGCCAATATGCTGATTCAAGG
65 TGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCCAATATGCTGATTCAAGG
* *
3196858 CCAGCGATATTGGATTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
130 CCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
*
3196916 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAAAAAA
1 TTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A---G----AAA
* * *
3196981 GGATGTCAATCTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATG
57 GG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-AAAGGTGCCAATATG
* *
3197046 CTGATTCAAGGCAAGCTATATTGGACTTAAATGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
119 CTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
3197111 GGAC
184 GGAC
* *
3197115 TTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAGAACGGTGCCAAT
1 TTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAAGGTGCCAAT
*
3197180 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-CAAAGGTGCCAATATGCTGATTCAAGGC
66 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCCAATATGCTGATTCAAGGC
*
3197244 CAGCTATAGTGGACTTAAAGG
131 CAGCTATATTGGACTTAAAGG
3197265 AAGATGCCAC
Statistics
Matches: 482, Mismatches: 36, Indels: 42
0.86 0.06 0.08
Matches are distributed among these distances:
184 48 0.10
185 80 0.17
186 45 0.09
188 43 0.09
189 40 0.08
190 5 0.01
191 1 0.00
194 1 0.00
195 2 0.00
196 43 0.09
197 47 0.10
199 127 0.26
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (187 bp):
TTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAAGGTGCCAAT
GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAGGTGCCAATATGCTGATTCAAGGC
CAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
Found at i:3197213 original size:94 final size:92
Alignment explanation
Indices: 3196978--3197264 Score: 441
Period size: 94 Copynumber: 3.1 Consensus size: 92
3196968 AAGGTGAAAA
* * *
3196978 AAAGGATGTCAATCTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA--G-AAAGGTGCCAAT
*
3197043 ATGCTGATTCAAGGCAAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCTATATTGGACTT
*
3197074 AAATGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAGA-AAGGTGCCAATATG
3197138 CTGATTCAAGGCCAGCTATATTGGACTT
65 CTGATTCAAGGCCAGCTATATTGGACTT
*
3197166 AGAACGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGACAAAGGTGCCAATAT
1 A-AA-GGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAGAAAGGTGCCAATAT
*
3197231 GCTGATTCAAGGCCAGCTATAGTGGACTT
64 GCTGATTCAAGGCCAGCTATATTGGACTT
3197260 AAAGG
1 AAAGG
3197265 AAGATGCCAC
Statistics
Matches: 180, Mismatches: 7, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
91 1 0.01
92 44 0.24
93 4 0.02
94 86 0.48
95 41 0.23
96 4 0.02
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAGAAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:3197346 original size:32 final size:31
Alignment explanation
Indices: 3197269--3197647 Score: 474
Period size: 32 Copynumber: 11.9 Consensus size: 31
3197259 TAAAGGAAGA
* *
3197269 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAG--GGT
*
3197302 TGCCACCGACTTGTGTGGGCTTTAGAGGGGAT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGG-T
* *
3197334 TGCCACCAACTTGTGTGGGCTTTAGAGGGGAT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGG-T
* ***
3197366 TGCCACCAACTTGTGTGGGCTTTAGAA-AAA
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
*
3197396 TGCCACCAACTTGTGTGGGCTTTGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTT-AGAAGGGT
* * **
3197428 TGCCTCCGACTTGTGTGGGCTTTGGAAATAGT
1 TGCCACCGACTTGTGTGGGCTTTAG-AAGGGT
* *
3197460 TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGT
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGT
*
3197493 TGCCACCAACTTGTGTGGGCTTTGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTT-AGAAGGGT
3197525 TGCCACCGACTTGTGTGGGCTTTGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTT-AGAAGGGT
3197557 TGCCACCGACTTGTGTGGGCTTTGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTT-AGAAGGGT
*
3197589 TGCCACCGACTTGTGTGGGCTTTGGAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAG-AAGGGT
3197621 TGCCACCGACTTGTGTGGGCTTT-GAAG
1 TGCCACCGACTTGTGTGGGCTTTAGAAG
3197648 AATGGTGAAA
Statistics
Matches: 313, Mismatches: 26, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
30 26 0.08
31 9 0.03
32 227 0.73
33 51 0.16
ACGTcount: A:0.18, C:0.19, G:0.34, T:0.29
Consensus pattern (31 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
Found at i:3197537 original size:97 final size:96
Alignment explanation
Indices: 3197269--3197644 Score: 514
Period size: 97 Copynumber: 3.9 Consensus size: 96
3197259 TAAAGGAAGA
* * *
3197269 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTT-AGAGGGGA
1 TGCCACCAACTTGTGTGGGC-TTTGAAAAAGGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGG-
* * *
3197333 TTGCCACCAACTTGTGTGGGCTTTAG-AGGGGAT
64 TTGCCACCGACTTGTGTGGGCTTTGGAAAGGG-T
3197366 TGCCACCAACTTGTGTGGGCTTTAGAAAAA---TGCCACCAACTTGTGTGGGCTTTGAGAAGGGT
1 TGCCACCAACTTGTGTGGGCTTT-GAAAAAGGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGT
* **
3197428 TGCCTCCGACTTGTGTGGGCTTTGGAAATAGT
65 TGCCACCGACTTGTGTGGGCTTTGGAAAGGGT
*
3197460 TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGT
1 TGCCACCAACTTGTGTGGGCTTT-GAAAAAGGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGT
3197525 TGCCACCGACTTGTGTGGGCTTT-GAGAAGGGT
65 TGCCACCGACTTGTGTGGGCTTTGGA-AAGGGT
* * * *
3197557 TGCCACCGACTTGTGTGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTG-GAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAAAAGGTTGCCACCAACTTGTGTGGGCTTTGAG-AAGGGT
3197621 TGCCACCGACTTGTGTGGGCTTTG
65 TGCCACCGACTTGTGTGGGCTTTG
3197645 AAGAATGGTG
Statistics
Matches: 253, Mismatches: 17, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
94 74 0.29
95 9 0.04
96 64 0.25
97 106 0.42
ACGTcount: A:0.18, C:0.19, G:0.34, T:0.29
Consensus pattern (96 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAAAGGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTT
GCCACCGACTTGTGTGGGCTTTGGAAAGGGT
Found at i:3197853 original size:28 final size:28
Alignment explanation
Indices: 3197822--3197915 Score: 91
Period size: 28 Copynumber: 3.1 Consensus size: 28
3197812 TTAAAAGGGG
*
3197822 AAAAGAGTGCCATGGAGTTGTGGGCTTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTTT
* *
3197850 AAAA-AGGTGCCACGGAGTTGTGGACTTAGAAGGA
1 AAAAGA-GTGCCACGGAGTTGTGGGCTT------T
3197884 AAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTTT
3197912 AAAA
1 AAAA
3197916 AGAAAAAAGT
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
27 1 0.02
28 27 0.51
34 24 0.45
35 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.34, T:0.22
Consensus pattern (28 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTT
Found at i:3197899 original size:34 final size:34
Alignment explanation
Indices: 3197655--3198148 Score: 426
Period size: 34 Copynumber: 14.9 Consensus size: 34
3197645 AAGAATGGTG
* *
3197655 AAAGA-TGACACGAAGTTGTGGACTTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
3197688 CAAG-GTGCCACGAAGTTGTGGACTTTAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGAC-TTAAAA-GGAA
* **
3197723 AAAGAGTGCCACGGAGTTGTGGGCTTTGAA--AA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
3197755 GAAG-GTGCCACGGAGTCGTGGACTTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
3197788 CAAG-GTGCCAC-GAGGTTATGGACTTTAAAAGGGGA
1 AAAGAGTGCCACGGA-GTTGTGGAC-TTAAAA-GGAA
* * *
3197823 AAAGAGTGCCATGGAGTTGTGGGCTT-----TAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
3197852 AAAG-GTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
3197885 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
** *
3197920 AAA-AGTGCCATAGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
3197953 AAAGAGTGCCACGGAGTTGTGGGCTTAAAA-G--
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
3197984 ---GA-TGCCACGAAGTTATGGACTTAAAA-GAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
3198013 AAAG-GTGTCATGGAGTTGTGGACTTTAAAA-GAA
1 AAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
* *
3198046 AAAAAGATGCCACAGAGTTGTGGACTTAAAAGGAA
1 AAAGAG-TGCCACGGAGTTGTGGACTTAAAAGGAA
* *
3198081 CTAAG-GTGCCACGGAGTTGTGGACTTTAAAGGAAA
1 -AAAGAGTGCCACGGAGTTGTGGACTTAAAAGG-AA
* *
3198116 AAAGGGTGCCACAGGAGTTATGGACTTAAAAGG
1 AAAGAGTGCCAC-GGAGTTGTGGACTTAAAAGG
3198149 GTGCCACAGA
Statistics
Matches: 373, Mismatches: 55, Indels: 63
0.76 0.11 0.13
Matches are distributed among these distances:
27 22 0.06
28 21 0.06
29 5 0.01
31 21 0.06
32 22 0.06
33 69 0.18
34 103 0.28
35 58 0.16
36 50 0.13
37 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.32, T:0.20
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:3197903 original size:162 final size:156
Alignment explanation
Indices: 3197689--3198219 Score: 524
Period size: 162 Copynumber: 3.3 Consensus size: 156
3197679 TAAAAGGAAC
* *
3197689 AAGGTGCCACGAAGTTGTGGACTTTA-AAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGTGCCACGGAGTTGTGGACTTTAGAAA--GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
* *
3197753 AAGAAGGTGCCACGGAGTCGTGGACTTAAAAGGAACAAGGTGCCACGAG-GTTATGGACTTTAAA
64 AAGAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACGAGAGTTATGGAC-TTAAA
*
3197817 AGGGGAAAAGAGTGCCATGGAGTTGTGGGCTTTAAA
128 A---G----GAGTGCCACGGAGTTGTGGGCTTTAAA
*
3197853 AAGGTGCCACGGAGTTGTGGAC-TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAA
1 AAGGTGCCACGGAGTTGTGGACTTTAGAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAA
* ** * * *
3197917 GAAAAAAGTGCCATAGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACG-GAGTTGTGGGCTTAA
66 G---AAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAG-GTGCCACGAGAGTTATGGACTTAA
* * * *
3197981 AAGGA-TGCCACGAAGTTATGGACTTAAAAGAAA
127 AAGGAGTGCCACGGAGTTGTGGGCTT----TAAA
* * * * * *
3198014 AAGGTGTCATGGAGTTGTGGACTTTA-AAAGAAAAAAAGATGCCACAGAGTTGTGGACTTAAAAG
1 AAGGTGCCACGGAGTTGTGGACTTTAGAAAGAAAAAGAG-TGCCACGGAGTTGTGGGCTTTAAA-
* *
3198078 GAACTAAGGTGCCACGGAGTTGTGGACTTTAAAGGAAAAAAGGGTGCCAC-AGGAGTTATGGACT
64 -AA-GAAGGTGCCACGGAGTTGTGGACTTAAAAGG-AAAAA-GGTGCCACGA-GAGTTATGGACT
*
3198142 TAAAAGG-GTGCCACAGAGTTGTGGGCTTTAAA
124 TAAAAGGAGTGCCACGGAGTTGTGGGCTTTAAA
3198174 AAGAGTGCCACGGAGTTGTGGACTTT-GAAAAGAAAAAG-GTGCCACG
1 AAG-GTGCCACGGAGTTGTGGACTTTAG-AAAGAAAAAGAGTGCCACG
3198220 AAGTCATGGA
Statistics
Matches: 304, Mismatches: 40, Indels: 50
0.77 0.10 0.13
Matches are distributed among these distances:
157 16 0.05
158 2 0.01
160 12 0.04
161 54 0.18
162 94 0.31
163 15 0.05
164 59 0.19
165 37 0.12
166 15 0.05
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.21
Consensus pattern (156 bp):
AAGGTGCCACGGAGTTGTGGACTTTAGAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAA
GAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACGAGAGTTATGGACTTAAAAGG
AGTGCCACGGAGTTGTGGGCTTTAAA
Found at i:3197936 original size:68 final size:65
Alignment explanation
Indices: 3197668--3198219 Score: 407
Period size: 68 Copynumber: 8.5 Consensus size: 65
3197658 GATGACACGA
* * *
3197668 AGTTGTGGACTTAAAAGGAACAAGGTGCCACGAAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCC
1 AGTTGTGGACTT-AAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA--GAAAAA-AGTGCC
*
3197733 ACGG
62 ACAG
* * * * * * *
3197737 AGTTGTGGGCTTTGAA--AAGAAGGTGCCACGGAGTCGTGGAC-TTAAAAGGAACAAGGTGCCAC
1 AGTTGTGGAC-TTAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA-GAAAAAAGTGCCAC
3197799 -G
64 AG
* * * *
3197800 AGGTTATGGACTTTAAAAGGGGAAAAGAGTGCCATGGAGTTGTGGGCTTT-----AAAAAGGTGC
1 A-GTTGTGGAC-TT-AAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGC
*
3197860 CACGG
61 CACAG
3197865 AGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCCA
1 AGTTGTGGACTTA-AAGGAAAAAG-GTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAAGTGCCA
*
3197930 TAG
63 CAG
*
3197933 AGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAAAAG----GA-TGCCAC
1 AGTTGTGGACTTA-AAGGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCAC
3197992 -G
64 AG
* * * * *
3197993 AAGTTATGGACTTAAAAGAAAAAGGTGTCATGGAGTTGTGGACTTTAAAAGAAAAAAAGATGCCA
1 -AGTTGTGGACTTAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAG-AAAAAAG-TGCCA
3198058 CAG
63 CAG
* * *
3198061 AGTTGTGGACTTAAAAGGAACTAAGGTGCCACGGAGTTGTGGACTTTAAAGGAAAAAAGGGTGCC
1 AGTTGTGGACTT-AAAGGAA-AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAA--GTGCC
3198126 ACAGG
62 ACA-G
* * * * *
3198131 AGTTATGGACTT-----AAAAGGGTGCCACAGAGTTGTGGGCTTT---A-AAAAGAGTGCCACGG
1 AGTTGTGGACTTAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACAG
*
3198187 AGTTGTGGACTTTGAAAAGAAAAAGGTGCCACG
1 AGTTGTGGAC-TT-AAAGGAAAAAGGTGCCACG
3198220 AAGTCATGGA
Statistics
Matches: 398, Mismatches: 47, Indels: 82
0.76 0.09 0.16
Matches are distributed among these distances:
56 10 0.03
57 9 0.02
59 21 0.05
60 17 0.04
61 17 0.04
62 31 0.08
63 40 0.10
64 39 0.10
65 11 0.03
66 11 0.03
67 41 0.10
68 73 0.18
69 61 0.15
70 17 0.04
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.21
Consensus pattern (65 bp):
AGTTGTGGACTTAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACAG
Found at i:3197990 original size:27 final size:27
Alignment explanation
Indices: 3197959--3198010 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
3197949 GGAAAAAGAG
* * *
3197959 TGCCACGGAGTTGTGGGCTTAAAAGGA
1 TGCCACGAAGTTATGGACTTAAAAGGA
3197986 TGCCACGAAGTTATGGACTTAAAAG
1 TGCCACGAAGTTATGGACTTAAAAG
3198011 AAAAAGGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (27 bp):
TGCCACGAAGTTATGGACTTAAAAGGA
Found at i:3198063 original size:128 final size:128
Alignment explanation
Indices: 3197756--3198113 Score: 431
Period size: 128 Copynumber: 2.8 Consensus size: 128
3197746 CTTTGAAAAG
* * * * *
3197756 AAGGTGCCACGGAGTCGTGGAC-TTAAAAGGAACAAGGTGCCAC-GAGGTTATGGACTTTAAAAG
1 AAGGTGCCACGGAGTTGTGGACTTTAAAAGAAAAAAAGTGCCACAGA-GTTGTGGAC-TTAAAA-
* * * * *
3197819 GGGAAAAGAGTGCCATGGAGTTGTGGGCTTTAAAAAGG-TGCCACGGAGTTGTGGACTTAGAAGG
63 GGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAGGATGCCACGAAGTTATGGACTTAGAAAG
3197883 AAA
126 AAA
* * *
3197886 AAGAGTGCCACGGAGTTGTGGGCTTTAAAA-AGAAAAAAGTGCCATAGAGTTGTGGACTTAGAAG
1 AAG-GTGCCACGGAGTTGTGGACTTTAAAAGA-AAAAAAGTGCCACAGAGTTGTGGACTTAAAAG
3197950 GAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGATGCCACGAAGTTATGGACTTA-AAAGAAA
64 GAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGATGCCACGAAGTTATGGACTTAGAAAGAAA
* *
3198014 AAGGTGTCATGGAGTTGTGGACTTTAAAAGAAAAAAAGATGCCACAGAGTTGTGGACTTAAAAGG
1 AAGGTGCCACGGAGTTGTGGACTTTAAAAGAAAAAAAG-TGCCACAGAGTTGTGGACTTAAAAGG
* * *
3198079 AACTAAG-GTGCCACGGAGTTGTGGACTTTAAAGGA
65 AA-AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGA
3198114 AAAAAGGGTG
Statistics
Matches: 199, Mismatches: 21, Indels: 18
0.84 0.09 0.08
Matches are distributed among these distances:
127 30 0.15
128 68 0.34
129 24 0.12
130 29 0.15
131 22 0.11
132 24 0.12
133 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.21
Consensus pattern (128 bp):
AAGGTGCCACGGAGTTGTGGACTTTAAAAGAAAAAAAGTGCCACAGAGTTGTGGACTTAAAAGGA
AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGATGCCACGAAGTTATGGACTTAGAAAGAAA
Found at i:3198064 original size:35 final size:34
Alignment explanation
Indices: 3197979--3198147 Score: 164
Period size: 35 Copynumber: 4.9 Consensus size: 34
3197969 TTGTGGGCTT
*
3197979 AAAAGGATGCCAC-GAAGTTATGGACTTAAAAG--A
1 AAAAGG-TGCCACAG-AGTTGTGGACTTAAAAGAAA
* **
3198012 AAAAGGTGTCATGGAGTTGTGGACTTTAAAAGAAA
1 AAAAGGTGCCACAGAGTTGTGGAC-TTAAAAGAAA
* *
3198047 AAAAGATGCCACAGAGTTGTGGACTTAAAAGGAA
1 AAAAGGTGCCACAGAGTTGTGGACTTAAAAGAAA
** * *
3198081 CTAAGGTGCCACGGAGTTGTGGACTTTAAAGGAAA
1 AAAAGGTGCCACAGAGTTGTGGAC-TTAAAAGAAA
* *
3198116 AAAGGGTGCCACAGGAGTTATGGACTTAAAAG
1 AAAAGGTGCCACA-GAGTTGTGGACTTAAAAG
3198148 GGTGCCACAG
Statistics
Matches: 110, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
32 13 0.12
33 14 0.13
34 29 0.26
35 44 0.40
36 10 0.09
ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21
Consensus pattern (34 bp):
AAAAGGTGCCACAGAGTTGTGGACTTAAAAGAAA
Found at i:3198155 original size:28 final size:29
Alignment explanation
Indices: 3198114--3198198 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 29
3198104 CTTTAAAGGA
*
3198114 AAAAAGGGTGCCACAGGAGTTATGGACTT
1 AAAAAGGGTGCCACAGGAGTTGTGGACTT
*
3198143 -AAAAGGGTGCCACA-GAGTTGTGGGCTTT
1 AAAAAGGGTGCCACAGGAGTTGTGGAC-TT
*
3198171 AAAAAGAGTGCCAC-GGAGTTGTGGACTT
1 AAAAAGGGTGCCACAGGAGTTGTGGACTT
3198199 TGAAAAGAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
27 9 0.18
28 18 0.37
29 22 0.45
ACGTcount: A:0.31, C:0.14, G:0.33, T:0.22
Consensus pattern (29 bp):
AAAAAGGGTGCCACAGGAGTTGTGGACTT
Found at i:3198217 original size:34 final size:36
Alignment explanation
Indices: 3198171--3198240 Score: 99
Period size: 34 Copynumber: 2.0 Consensus size: 36
3198161 TGTGGGCTTT
* **
3198171 AAAAAGAGTGCCACGGAGTTGTGGACTTTGA-AAAG
1 AAAAAGAGTGCCACGAAGTCATGGACTTTGAGAAAG
3198206 AAAAAG-GTGCCACGAAGTCATGGACTTTGAGAAAG
1 AAAAAGAGTGCCACGAAGTCATGGACTTTGAGAAAG
3198241 GATTTGAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 21 0.68
35 10 0.32
ACGTcount: A:0.39, C:0.13, G:0.30, T:0.19
Consensus pattern (36 bp):
AAAAAGAGTGCCACGAAGTCATGGACTTTGAGAAAG
Found at i:3199030 original size:13 final size:13
Alignment explanation
Indices: 3199012--3199037 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3199002 TACACCAAGT
3199012 ATGTATCGATACA
1 ATGTATCGATACA
3199025 ATGTATCGATACA
1 ATGTATCGATACA
3199038 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3199035 original size:32 final size:33
Alignment explanation
Indices: 3198994--3199057 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
3198984 TAGCCAAACT
* **
3198994 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
3199026 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
3199058 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:3201285 original size:21 final size:21
Alignment explanation
Indices: 3201252--3201296 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3201242 TTGCAAGTTG
*
3201252 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3201274 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3201294 AAA
1 AAA
3201297 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3203119 original size:15 final size:15
Alignment explanation
Indices: 3203099--3203129 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3203089 TAAAAATGTC
*
3203099 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3203114 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3203129 C
1 C
3203130 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3205225 original size:13 final size:13
Alignment explanation
Indices: 3205207--3205232 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3205197 ACATTTTTCT
3205207 TTGTATCGATACA
1 TTGTATCGATACA
3205220 TTGTATCGATACA
1 TTGTATCGATACA
3205233 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3207786 original size:19 final size:19
Alignment explanation
Indices: 3207764--3207826 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
3207754 TAGCCAAACT
3207764 TGTATCGATACACCAAGTA
1 TGTATCGATACACCAAGTA
3207783 TGTATCGAT--A-C-A--A
1 TGTATCGATACACCAAGTA
3207796 TGTATCGATACACCAAGTA
1 TGTATCGATACACCAAGTA
3207815 TGTATCGATACA
1 TGTATCGATACA
3207827 ATGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
16 2 0.05
17 2 0.05
19 22 0.58
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (19 bp):
TGTATCGATACACCAAGTA
Found at i:3207800 original size:13 final size:13
Alignment explanation
Indices: 3207782--3207839 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
3207772 TACACCAAGT
3207782 ATGTATCGATACA
1 ATGTATCGATACA
3207795 ATGTATCGATACACCAA
1 ATGTATCGAT--A-C-A
3207812 GTATGTATCGATACA
1 --ATGTATCGATACA
3207827 ATGTATCGATACA
1 ATGTATCGATACA
3207840 CAAAAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.59
15 2 0.05
16 2 0.05
17 2 0.05
19 10 0.26
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3207805 original size:32 final size:32
Alignment explanation
Indices: 3207764--3207859 Score: 156
Period size: 32 Copynumber: 3.0 Consensus size: 32
3207754 TAGCCAAACT
3207764 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAGTATGTATCGATACAA
3207796 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAGTATGTATCGATACAA
* **
3207828 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACCAAGTA-TGTATCGATACA
3207860 TTGGCTTGTA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 48 0.80
33 12 0.20
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAGTATGTATCGATACAA
Found at i:3209201 original size:26 final size:26
Alignment explanation
Indices: 3209154--3209216 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
3209144 GGTTTTTCCT
*
3209154 TTCTTCTTTTTTTGTTTGTTTGTTTC
1 TTCTTCTTTTTTTCTTTGTTTGTTTC
*
3209180 TTCTTTTTTTTTTCCTTT-TTTGTTT-
1 TTCTTCTTTTTTT-CTTTGTTTGTTTC
3209205 TGT-TTCTTTTTT
1 T-TCTTCTTTTTT
3209217 GGAAAAGAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 9 0.28
26 20 0.62
27 3 0.09
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (26 bp):
TTCTTCTTTTTTTCTTTGTTTGTTTC
Found at i:3209213 original size:16 final size:16
Alignment explanation
Indices: 3209168--3209217 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
3209158 TCTTTTTTTG
3209168 TTTG-TTTGTTTCTTCT
1 TTTGTTTTGTTTCTT-T
*
3209184 TTT-TTTT-TTCCTTT
1 TTTGTTTTGTTTCTTT
3209198 TTTGTTTTGTTTCTTT
1 TTTGTTTTGTTTCTTT
3209214 TTTG
1 TTTG
3209218 GAAAAGAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 16 0.55
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (16 bp):
TTTGTTTTGTTTCTTT
Found at i:3209499 original size:16 final size:16
Alignment explanation
Indices: 3209480--3209512 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3209470 TTTTGTTTTG
3209480 TTTTTT-TTTTGACTT
1 TTTTTTCTTTTGACTT
*
3209495 TTTTTTCTTTTGTCTT
1 TTTTTTCTTTTGACTT
3209511 TT
1 TT
3209513 GTTTGTGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.03, C:0.09, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTTTCTTTTGACTT
Found at i:3214706 original size:21 final size:21
Alignment explanation
Indices: 3214682--3214777 Score: 67
Period size: 21 Copynumber: 5.2 Consensus size: 21
3214672 TGAAAATCAA
3214682 GGAATATAAAAATGAAGGCAT
1 GGAATATAAAAATGAAGGCAT
*
3214703 GG-A-AT---GATG--GGCAT
1 GGAATATAAAAATGAAGGCAT
*
3214717 GGAATAAAAAAATGAAGGCAT
1 GGAATATAAAAATGAAGGCAT
*
3214738 GG-A-AT---GATG--GGCAT
1 GGAATATAAAAATGAAGGCAT
3214752 GGAATATAAAAATGAAGGCAT
1 GGAATATAAAAATGAAGGCAT
3214773 GGAAT
1 GGAAT
3214778 GATGGGCATG
Statistics
Matches: 55, Mismatches: 6, Indels: 28
0.62 0.07 0.31
Matches are distributed among these distances:
14 14 0.25
15 2 0.04
16 9 0.16
19 9 0.16
20 2 0.04
21 19 0.35
ACGTcount: A:0.46, C:0.05, G:0.30, T:0.19
Consensus pattern (21 bp):
GGAATATAAAAATGAAGGCAT
Found at i:3214728 original size:35 final size:35
Alignment explanation
Indices: 3214682--3214851 Score: 306
Period size: 35 Copynumber: 4.9 Consensus size: 35
3214672 TGAAAATCAA
*
3214682 GGAATATAAAAATGAAGGCATGGAATGATGGGCAT
1 GGAATAAAAAAATGAAGGCATGGAATGATGGGCAT
3214717 GGAATAAAAAAATGAAGGCATGGAATGATGGGCAT
1 GGAATAAAAAAATGAAGGCATGGAATGATGGGCAT
*
3214752 GGAATATAAAAATGAAGGCATGGAATGATGGGCAT
1 GGAATAAAAAAATGAAGGCATGGAATGATGGGCAT
*
3214787 GGAATAAAAAAATGAAGGCATAGAATGATGGGCAT
1 GGAATAAAAAAATGAAGGCATGGAATGATGGGCAT
3214822 GGAAT-AAAAAATGAAGGCATGGAATGATGG
1 GGAATAAAAAAATGAAGGCATGGAATGATGG
3214852 ATAAAAATGA
Statistics
Matches: 130, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
34 24 0.18
35 106 0.82
ACGTcount: A:0.45, C:0.05, G:0.31, T:0.18
Consensus pattern (35 bp):
GGAATAAAAAAATGAAGGCATGGAATGATGGGCAT
Found at i:3216160 original size:79 final size:79
Alignment explanation
Indices: 3216065--3216569 Score: 733
Period size: 79 Copynumber: 6.4 Consensus size: 79
3216055 GTTAAGTTTC
* * * *
3216065 TCAATTTTTTACAATCGGGGATACTCCAATCCCGTTATTTCCAAGGGGATACTCCAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
* **
3216130 TTATCTCTAAATTA
66 TTATTTCTAAAACA
* * * *
3216144 TCAATTTTTCATAATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGACACTCCAACCCTGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
*
3216209 TTATTTCTAAAATA
66 TTATTTCTAAAACA
* * * * *
3216223 TTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCTCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
*
3216288 TTATCTCTAAAACA
66 TTATTTCTAAAACA
* * *
3216302 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAATCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
*
3216367 TTATTTCTAAAATA
66 TTATTTCTAAAACA
* * * * *
3216381 TTAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCTGATGGGATACTCTAACCCCGGTT
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
3216446 TTATTTCTAAAACA
66 TTATTTCTAAAACA
*
3216460 -CTAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGC
1 TC-AATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGT
3216524 TTTATTTCTAAAACA
65 TTTATTTCTAAAACA
*
3216539 TCAATTTTTCATAATCGGGGATACTCTAACC
1 TCAATTTTTCATAATCGGGGATACTCCAACC
3216570 TCGATTTTAT
Statistics
Matches: 383, Mismatches: 41, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
79 382 1.00
80 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.34
Consensus pattern (79 bp):
TCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT
TTATTTCTAAAACA
Done.