Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 3 of 199
Found at i:963920 original size:2 final size:2
Alignment explanation
Indices: 963913--963944 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
963903 AATGGTTACA
963913 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
963945 GAATCACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:977560 original size:141 final size:141
Alignment explanation
Indices: 977358--978062 Score: 1049
Period size: 142 Copynumber: 5.0 Consensus size: 141
977348 CAAAAGTCTC
*
977358 GAAGAACGTGAA-TTTGAATTCAAATCTAGAATTACAAAAGCATTCGCATTGGAATCGGACTCAT
1 GAAGAACGT-AATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCAT
* *
977422 GAATTCAAATTTCAACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACA
65 GAATTCAAATTTCCACGTAATTTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACA
977487 CACAGATCAAAA
130 CACAGATCAAAA
* *
977499 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAATCGGACTCATG
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
* *
977564 AATTCAAATTTCCGCGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAACTCAATTACA
66 AATTCAAATTTCCACGTAATTTTGAAGAACTTTG-ATGAAAAATGAGGTAAAGAACTCAATTACA
977629 CACAGATCAAAA
130 CACAGATCAAAA
* * * * *
977641 GAAGAACGCAATTTCGAATTCAAATCTAAAATTACAAAAGCGTTCCCATTGGAACCGGACTCATG
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
* * * *
977706 AATTCAAATTTCCACGTAAATTTGAAGAATTTTGATGAAAACTGAGGTAAAGCACTCAATTACAC
66 AATTCAAATTTCCACGTAATTTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACAC
977771 ACAGATC--AA
131 ACAGATCAAAA
* * * * *
977780 -AAGAACGTAATTTTGAATTCAAATCTAAACTTACAAAAGCATTCGCATTGAAACCAGACTCGTG
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
* * *
977844 AATTCAAATTTCGACGTAATTTTGAAGAACTTGGAATGAAAAATGAGCTAAAGAACTCAAATTAC
66 AATTCAAATTTCCACGTAATTTTGAAGAACTTTG-ATGAAAAATGAGGTAAAGAACTC-AATTAC
977909 ACACAGATCAAAA
129 ACACAGATCAAAA
* * * * * * *
977922 CAAGAACGTGACTTTAAATTCAAATCTAAAGTTACAAATGCATTCGCATTGGAATCCGACTCATG
1 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
* *
977987 AATTCAAATTTCCACGTAATTTTGAAGAACTATAATGAAAAATGAGGTAAAGAACTCAATTACAC
66 AATTCAAATTTCCACGTAATTTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACAC
978052 ACAGATCAAAA
131 ACAGATCAAAA
978063 AGGAGAAAAC
Statistics
Matches: 509, Mismatches: 48, Indels: 14
0.89 0.08 0.02
Matches are distributed among these distances:
138 86 0.17
139 22 0.04
140 17 0.03
141 144 0.28
142 155 0.30
143 85 0.17
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (141 bp):
GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATG
AATTCAAATTTCCACGTAATTTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACAC
ACAGATCAAAA
Found at i:978046 original size:281 final size:279
Alignment explanation
Indices: 977359--978062 Score: 1108
Period size: 281 Copynumber: 2.5 Consensus size: 279
977349 AAAAGTCTCG
*
977359 AAGAACGTGAATTTGAATTCAAATCTAGAATTACAAAAGCATTCGCATTGGAATCGGACTCATGA
1 AAGAACGTGAATTTGAATTCAAATCTA-AATTACAAAAGCATTCGCATTGGAATCCGACTCATGA
*
977424 ATTCAAATTTCAACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACACA
65 ATTCAAATTTCCACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACACA
*
977489 CAGATCAAAAGAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAAT
130 CAGATC--AA-AAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAAC
* *
977554 CGGACTCATGAATTCAAATTTCCGCGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAA
192 CAGACTCATGAATTCAAATTTCCGCGTAATTTTGAAGAACTTGGAATGAAAAATGAGCTAAAGAA
*
977619 CTCAATTACACACAGATCAAAAG
257 CTCAATTACACACAGATCAAAAC
* * *
977642 AAGAACG-CAATTTCGAATTCAAATCTAAAATTACAAAAGCGTTCCCATTGGAA-CCGGACTCAT
1 AAGAACGTGAATTT-GAATTCAAATCT-AAATTACAAAAGCATTCGCATTGGAATCC-GACTCAT
* * *
977705 GAATTCAAATTTCCACGTAAATTTGAAGAATTTTGATGAAAACTGAGGTAAAGCACTCAATTACA
63 GAATTCAAATTTCCACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACA
* *
977770 CACAGATCAAAAGAACGTAATTTTGAATTCAAATCTAAACTTACAAAAGCATTCGCATTGAAACC
128 CACAGATCAAAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAACC
*
977835 AGACTCGTGAATTCAAATTT-CGACGTAATTTTGAAGAACTTGGAATGAAAAATGAGCTAAAGAA
193 AGACTCATGAATTCAAATTTCCG-CGTAATTTTGAAGAACTTGGAATGAAAAATGAGCTAAAGAA
977899 CTCAAATTACACACAGATCAAAAC
257 CTC-AATTACACACAGATCAAAAC
* * *
977923 AAGAACGTGACTTTAAATTCAAATCTAAAGTTACAAATGCATTCGCATTGGAATCCGACTCATGA
1 AAGAACGTGAATTTGAATTCAAATCTAAA-TTACAAAAGCATTCGCATTGGAATCCGACTCATGA
* * *
977988 ATTCAAATTTCCACGTAATTTTGAAGAACTATAATGAAAAATGAGGTAAAGAACTCAATTACACA
65 ATTCAAATTTCCACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACACA
978053 CAGATCAAAA
130 CAGATCAAAA
978063 AGGAGAAAAC
Statistics
Matches: 386, Mismatches: 27, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
279 2 0.01
280 116 0.30
281 137 0.35
282 12 0.03
283 118 0.31
284 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (279 bp):
AAGAACGTGAATTTGAATTCAAATCTAAATTACAAAAGCATTCGCATTGGAATCCGACTCATGAA
TTCAAATTTCCACGTAAATTTGAAGAACTTTGATGAAAAATGAGGTAAAGAACTCAATTACACAC
AGATCAAAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAACCAGA
CTCATGAATTCAAATTTCCGCGTAATTTTGAAGAACTTGGAATGAAAAATGAGCTAAAGAACTCA
ATTACACACAGATCAAAAC
Found at i:978132 original size:10 final size:10
Alignment explanation
Indices: 978117--978143 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
978107 AAAAAATGAG
978117 CAGATCCGAA
1 CAGATCCGAA
978127 CAGATCCGAA
1 CAGATCCGAA
978137 CAGATCC
1 CAGATCC
978144 AATTCATAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.33, G:0.19, T:0.11
Consensus pattern (10 bp):
CAGATCCGAA
Found at i:979053 original size:29 final size:28
Alignment explanation
Indices: 979020--979085 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
979010 ATAATTGGAT
979020 TTAAATT-TTAAAATTTAAAAA-ATAAAAAA
1 TTAAATTCTTAAAA--TAAAAATAT-AAAAA
*
979049 TTAAATTCGTTAAAATAAAAATATATAAA
1 TTAAATTC-TTAAAATAAAAATATAAAAA
979078 TTAAATTC
1 TTAAATTC
979086 AAAAATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 25 0.76
30 2 0.06
31 6 0.18
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (28 bp):
TTAAATTCTTAAAATAAAAATATAAAAA
Found at i:1009784 original size:8 final size:7
Alignment explanation
Indices: 1009737--1009775 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
1009727 ATTAATCTTT
1009737 AAATTTA
1 AAATTTA
1009744 AAATTTA
1 AAATTTA
1009751 AAATTTA
1 AAATTTA
1009758 AAATTTA
1 AAATTTA
1009765 AAATTTTA
1 AAA-TTTA
1009773 AAA
1 AAA
1009776 ATTTTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 24 0.77
8 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATTTA
Found at i:1011246 original size:25 final size:25
Alignment explanation
Indices: 1011188--1011249 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
1011178 ACATTTCAAT
** *
1011188 AAATAAAAAAT-GTATAAAATTATT
1 AAATAAAAAATAAAATAAAATTATA
*
1011212 AAATATAAAATAAAATAAAATTA-A
1 AAATAAAAAATAAAATAAAATTATA
1011236 AAATTAAAAAATAA
1 AAA-TAAAAAATAA
1011250 TATGAGCGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 13 0.42
25 18 0.58
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (25 bp):
AAATAAAAAATAAAATAAAATTATA
Found at i:1012165 original size:27 final size:27
Alignment explanation
Indices: 1012127--1012178 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1012117 TTGAAAAACA
1012127 AATTTCCTTGTAGAAGGTGTAAAGACT
1 AATTTCCTTGTAGAAGGTGTAAAGACT
*
1012154 AATTTTCTTGTAGAAGGTGTAAAGA
1 AATTTCCTTGTAGAAGGTGTAAAGA
1012179 TAAACTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (27 bp):
AATTTCCTTGTAGAAGGTGTAAAGACT
Found at i:1012385 original size:36 final size:36
Alignment explanation
Indices: 1012337--1012409 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
1012327 AGTTTCACAA
1012337 AGATACTATTAATGATCTTGAAATATTATATCAATG
1 AGATACTATTAATGATCTTGAAATATTATATCAATG
* *
1012373 AGATACTCTTAATGATCTTGAAATATTGTATCAATG
1 AGATACTATTAATGATCTTGAAATATTATATCAATG
1012409 A
1 A
1012410 CTATGACATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (36 bp):
AGATACTATTAATGATCTTGAAATATTATATCAATG
Found at i:1018473 original size:14 final size:14
Alignment explanation
Indices: 1018444--1018495 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
1018434 ATATGAGATT
* *
1018444 AGTAGAAACCAGAA
1 AGTAGAAAGCAAAA
*
1018458 AGCAGAAAGCAAAA
1 AGTAGAAAGCAAAA
* *
1018472 AGTAAAAAGTAAAA
1 AGTAGAAAGCAAAA
1018486 AGTAGAAAGC
1 AGTAGAAAGC
1018496 GGGATCAAAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.62, C:0.10, G:0.21, T:0.08
Consensus pattern (14 bp):
AGTAGAAAGCAAAA
Found at i:1022144 original size:26 final size:26
Alignment explanation
Indices: 1022127--1022176 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
1022117 ATATATGTAT
1022127 AAGTTTGGAATAAATAATATATAAAA
1 AAGTTTGGAATAAATAATATATAAAA
1022153 AAGTTTGGAATAAATAATATATAA
1 AAGTTTGGAATAAATAATATATAA
1022177 TAAATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (26 bp):
AAGTTTGGAATAAATAATATATAAAA
Found at i:1022180 original size:14 final size:14
Alignment explanation
Indices: 1022135--1022190 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
1022125 ATAAGTTTGG
1022135 AATAAATAATATAT
1 AATAAATAATATAT
* * **
1022149 AA-AAA-AGTTTGG
1 AATAAATAATATAT
1022161 AATAAATAATATAT
1 AATAAATAATATAT
1022175 AATAAATAATATAT
1 AATAAATAATATAT
1022189 AA
1 AA
1022191 ATGAGTTTAA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
12 5 0.16
13 6 0.19
14 21 0.66
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (14 bp):
AATAAATAATATAT
Found at i:1027326 original size:35 final size:35
Alignment explanation
Indices: 1027264--1027349 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
1027254 TTTTATTTGT
*
1027264 TTTA-ATTATATAATTAATGATATTTAAA-TATAA
1 TTTATATTATATAATTAATGATAATTAAATTATAA
*
1027297 TTTATATTATATGAATTTATGATAATTAAATTATAA
1 TTTATATTATAT-AATTAATGATAATTAAATTATAA
* *
1027333 -TGATATTATATTATTAA
1 TTTATATTATATAATTAA
1027350 ATAAATCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.09
34 11 0.24
35 25 0.56
36 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (35 bp):
TTTATATTATATAATTAATGATAATTAAATTATAA
Found at i:1027335 original size:25 final size:23
Alignment explanation
Indices: 1027291--1027351 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
1027281 TGATATTTAA
*
1027291 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
1027315 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
1027340 ATATTATTAAAT
1 ATATAATTAAAT
1027352 AAATCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:1052566 original size:20 final size:20
Alignment explanation
Indices: 1052529--1052566 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1052519 AATTTAATTT
*
1052529 TTTAAATTTTTTAAAATATA
1 TTTAAATTTTATAAAATATA
*
1052549 TTTAAATTTTATATAATA
1 TTTAAATTTTATAAAATA
1052567 AATATATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTAAATTTTATAAAATATA
Found at i:1056887 original size:15 final size:16
Alignment explanation
Indices: 1056841--1056887 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
1056831 TAAACCATTT
1056841 AAGGAATAGGATCTAA
1 AAGGAATAGGATCTAA
** *
1056857 AAGGAA-ATTATATAA
1 AAGGAATAGGATCTAA
1056872 AA-GAATAGGATCTAA
1 AAGGAATAGGATCTAA
1056887 A
1 A
1056888 TGTAAATTAC
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
14 3 0.12
15 15 0.62
16 6 0.25
ACGTcount: A:0.55, C:0.04, G:0.19, T:0.21
Consensus pattern (16 bp):
AAGGAATAGGATCTAA
Found at i:1059074 original size:51 final size:50
Alignment explanation
Indices: 1058957--1059102 Score: 136
Period size: 51 Copynumber: 2.8 Consensus size: 50
1058947 ATATTCTATG
* * * * * *
1058957 TAAATGTTGACAAAATGTGTAAATTTTGTGGGCTAATTTTGTTAAATCAGGA
1 TAAAT-TTGACAGAATATGTAAA-TTTGTGAGCTAAATTTATTAAATCAAGA
**
1059009 TCAAA-TTGGTAGAATATGTAAATATTGTGAGCTAAATTTATTAAATCAAGA
1 T-AAATTTGACAGAATATGTAAAT-TTGTGAGCTAAATTTATTAAATCAAGA
1059060 TAAATTTGACAGAATGA-GTAAACTTTGATGA-CTAAATTTATTA
1 TAAATTTGACAGAAT-ATGTAAA-TTTG-TGAGCTAAATTTATTA
1059103 TTATACTAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
50 4 0.05
51 65 0.83
52 6 0.08
53 3 0.04
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (50 bp):
TAAATTTGACAGAATATGTAAATTTGTGAGCTAAATTTATTAAATCAAGA
Found at i:1060075 original size:23 final size:24
Alignment explanation
Indices: 1060028--1060073 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1060018 GAAAAATATT
1060028 AAATATATATATTTTTTATTTTTA
1 AAATATATATATTTTTTATTTTTA
1060052 AAATATA-ATAGTTTTTTATTTT
1 AAATATATATA-TTTTTTATTTT
1060074 AAGTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATATATATTTTTTATTTTTA
Found at i:1060184 original size:9 final size:9
Alignment explanation
Indices: 1060170--1060197 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1060160 TTTTGTTACA
1060170 ACAATTAAT
1 ACAATTAAT
1060179 ACAATTAAT
1 ACAATTAAT
1060188 ACAATTAAT
1 ACAATTAAT
1060197 A
1 A
1060198 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:1060219 original size:68 final size:68
Alignment explanation
Indices: 1060140--1060349 Score: 388
Period size: 68 Copynumber: 3.1 Consensus size: 68
1060130 TCAAGTTTGT
*
1060140 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1060205 AAA
66 AAA
1060208 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1060273 AAA
66 AAA
1060276 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
1060339 AAT
66 AAA
1060342 TTTACTAA
1 TTTACTAA
1060350 CAATTAATTT
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 27 0.19
67 1 0.01
68 112 0.80
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:1060250 original size:9 final size:9
Alignment explanation
Indices: 1060238--1060265 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1060228 TTTTATTACA
1060238 ACAATTAAT
1 ACAATTAAT
1060247 ACAATTAAT
1 ACAATTAAT
1060256 ACAATTAAT
1 ACAATTAAT
1060265 A
1 A
1060266 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:1060359 original size:16 final size:16
Alignment explanation
Indices: 1060338--1060379 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1060328 AATAATTTGA
*
1060338 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
1060354 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
1060370 TAGTTTTAAT
1 TAATTTTAAT
1060380 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:1060363 original size:22 final size:23
Alignment explanation
Indices: 1060353--1060414 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1060343 TTACTAACAA
* * *
1060353 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
1060375 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
*
1060398 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
1060415 CGGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:1070293 original size:2 final size:2
Alignment explanation
Indices: 1070286--1070325 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1070276 NNNNNNNNNN
1070286 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1070326 ATAACTATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1080572 original size:2 final size:2
Alignment explanation
Indices: 1080565--1080599 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1080555 TATGTATGTC
1080565 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1080600 GTATTCGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1083220 original size:6 final size:6
Alignment explanation
Indices: 1083209--1083235 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1083199 GAACGACAAA
1083209 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1083236 CAAATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:1083762 original size:25 final size:26
Alignment explanation
Indices: 1083717--1083774 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
1083707 GGTCCTTCTG
1083717 TTAAAAATTTCATCCATTTTCTACTA
1 TTAAAAATTTCATCCATTTTCTACTA
* * * *
1083743 TTAAAATTTTCATTCA-TTTCTATTG
1 TTAAAAATTTCATCCATTTTCTACTA
1083768 TTAAAAA
1 TTAAAAA
1083775 CTGGTCTCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (26 bp):
TTAAAAATTTCATCCATTTTCTACTA
Found at i:1090292 original size:98 final size:98
Alignment explanation
Indices: 1090028--1090319 Score: 361
Period size: 98 Copynumber: 3.0 Consensus size: 98
1090018 ATACTTTAAC
** * *
1090028 TTTTTGACAAAAAAATGGTACCTCGACTTTTACAATATCATTAATTAACTCAAATACTTTATTTT
1 TTTTTGAC-AAAATTTGGTACCTCGACTTTTACAATATCATTGATTAGCTCAAATACTTTATTTT
* *
1090093 GATTAAGACGTTGATGTAACTTTTAAGAGTTATAT
65 GATTAAAACGTTGATATAACTTTTAAGAG-TATAT
* ** ** ** * *
1090128 TTTTTTACATGATTTGGTAATTTAACTTTTACAGTGTCATTGATTAGCTCAAATACTTTATTTTG
1 TTTTTGACAAAATTTGGTACCTCGACTTTTACAATATCATTGATTAGCTCAAATACTTTATTTTG
1090193 ATTAAAACGTTGATATAACTTTTAAGAGTAGTA-
66 ATTAAAACGTTGATATAACTTTTAAGAGTA-TAT
* *
1090226 TTTTTGACAAAATTTGGTACCACGACTTTTACAATATCATTGATTAGCCCAAATACTTTATTTTG
1 TTTTTGACAAAATTTGGTACCTCGACTTTTACAATATCATTGATTAGCTCAAATACTTTATTTTG
** * *
1090291 ATTAAAATATTGATTTAACTTTTACGAGT
66 ATTAAAACGTTGATATAACTTTTAAGAGT
1090320 TGTAAACACT
Statistics
Matches: 161, Mismatches: 30, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
98 81 0.50
99 73 0.45
100 7 0.04
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.43
Consensus pattern (98 bp):
TTTTTGACAAAATTTGGTACCTCGACTTTTACAATATCATTGATTAGCTCAAATACTTTATTTTG
ATTAAAACGTTGATATAACTTTTAAGAGTATAT
Found at i:1090545 original size:22 final size:23
Alignment explanation
Indices: 1090520--1090565 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
1090510 AAAATAAAAG
*
1090520 TACGAAAATTAAATTTTAA-ATA
1 TACGAAAAGTAAATTTTAATATA
* *
1090542 TACGAAGAGTATATTTTAATATA
1 TACGAAAAGTAAATTTTAATATA
1090565 T
1 T
1090566 TTTATAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (23 bp):
TACGAAAAGTAAATTTTAATATA
Found at i:1099334 original size:17 final size:19
Alignment explanation
Indices: 1099300--1099336 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
1099290 ACTACTCTTC
1099300 ATTTTCTAATCGAAAATAA
1 ATTTTCTAATCGAAAATAA
1099319 ATTTTCT-ATC-AAAATAA
1 ATTTTCTAATCGAAAATAA
1099336 A
1 A
1099337 CACAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 3 0.17
19 7 0.39
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.38
Consensus pattern (19 bp):
ATTTTCTAATCGAAAATAA
Found at i:1107633 original size:25 final size:25
Alignment explanation
Indices: 1107599--1107658 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
1107589 TAATATCATT
* *
1107599 TTATTATTATGTTGT-TACTATTTTG
1 TTATTATTAT-TTATATACTATCTTG
1107624 TTATTATTATTTATATACTATCTTG
1 TTATTATTATTTATATACTATCTTG
1107649 TT-TTATTATT
1 TTATTATTATT
1107659 ACTTTTGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 11 0.34
25 21 0.66
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (25 bp):
TTATTATTATTTATATACTATCTTG
Found at i:1108159 original size:23 final size:25
Alignment explanation
Indices: 1108113--1108162 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
1108103 AATATAAAAC
1108113 AAAATTTTTAAAATTAATACTATATT
1 AAAATTTTT-AAATTAATACTATATT
*
1108139 AAAATTTTT-AA-TAATATTATATT
1 AAAATTTTTAAATTAATACTATATT
1108162 A
1 A
1108163 TTTTAGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 12 0.52
24 2 0.09
26 9 0.39
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
AAAATTTTTAAATTAATACTATATT
Found at i:1110997 original size:43 final size:44
Alignment explanation
Indices: 1110919--1111008 Score: 164
Period size: 43 Copynumber: 2.1 Consensus size: 44
1110909 AACCACCTCC
*
1110919 GGATATGCGACAAGTATTCAAGGATTGCATTCAAGACTTTGGTG
1 GGATATGCCACAAGTATTCAAGGATTGCATTCAAGACTTTGGTG
1110963 GGATATGCCACAAGTATT-AAGGATTGCATTCAAGACTTTGGTG
1 GGATATGCCACAAGTATTCAAGGATTGCATTCAAGACTTTGGTG
1111006 GGA
1 GGA
1111009 GTGAAATAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 28 0.62
44 17 0.38
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (44 bp):
GGATATGCCACAAGTATTCAAGGATTGCATTCAAGACTTTGGTG
Found at i:1112323 original size:2 final size:2
Alignment explanation
Indices: 1112316--1112340 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1112306 AGAACTTCGA
1112316 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 A
1112341 GTACGTATNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1115540 original size:2 final size:2
Alignment explanation
Indices: 1115533--1115558 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1115523 NNNNNNNNNN
1115533 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1115559 GGTACTAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1117947 original size:22 final size:22
Alignment explanation
Indices: 1117916--1117958 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1117906 TTGTTGTTCA
*
1117916 TTGCTGCTATTTTGCTGTTATG
1 TTGCTACTATTTTGCTGTTATG
*
1117938 TTGCTACTATTTTGTTGTTAT
1 TTGCTACTATTTTGCTGTTAT
1117959 TGTTTGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.58
Consensus pattern (22 bp):
TTGCTACTATTTTGCTGTTATG
Found at i:1125360 original size:17 final size:17
Alignment explanation
Indices: 1125327--1125360 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1125317 AGAAGTAAAT
**
1125327 AGAAAAAAAAATTAGAA
1 AGAAAAAAAAAGAAGAA
1125344 AGAAAAAAAAAGAAGAA
1 AGAAAAAAAAAGAAGAA
1125361 GCAGATCTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (17 bp):
AGAAAAAAAAAGAAGAA
Found at i:1127772 original size:18 final size:18
Alignment explanation
Indices: 1127736--1127774 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1127726 CTCTGGACAT
*
1127736 TTTGGTTTAATTTTTGAA
1 TTTGGTTTAATTTTGGAA
1127754 TTTGGATTTAA-TTTGGAA
1 TTTGG-TTTAATTTTGGAA
1127772 TTT
1 TTT
1127775 TTGGCACGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.23, C:0.00, G:0.18, T:0.59
Consensus pattern (18 bp):
TTTGGTTTAATTTTGGAA
Found at i:1128731 original size:7 final size:7
Alignment explanation
Indices: 1128719--1128759 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
1128709 TGAGTTATTT
1128719 TTTTTAA
1 TTTTTAA
1128726 TTTTTAA
1 TTTTTAA
1128733 TTTTTAA
1 TTTTTAA
1128740 TTTTTAA
1 TTTTTAA
1128747 TTTTTAA
1 TTTTTAA
1128754 TTTTTA
1 TTTTTA
1128760 TTCTTTTTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTAA
Found at i:1142171 original size:23 final size:23
Alignment explanation
Indices: 1142141--1142184 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1142131 TACGAACTCT
*
1142141 AAATATAGACTGTAAAATAGACC
1 AAATATAGACCGTAAAATAGACC
1142164 AAATATAGACCGTAAAATAGA
1 AAATATAGACCGTAAAATAGA
1142185 TATGGAAGAT
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:0.55, C:0.11, G:0.14, T:0.20
Consensus pattern (23 bp):
AAATATAGACCGTAAAATAGACC
Found at i:1144254 original size:29 final size:30
Alignment explanation
Indices: 1144200--1144279 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 30
1144190 ATATCAAAAT
* *
1144200 TATACATGAATTATGGTTTAATGTGTAATTG
1 TATACATGAATTTTGATTT-ATGTGTAATTG
*
1144231 TATACATGAATTTTGATTT-TGTGTAATTT
1 TATACATGAATTTTGATTTATGTGTAATTG
*
1144260 TATACATAAAATTTTGATTT
1 TATACAT-GAATTTTGATTT
1144280 GATCCAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 16 0.36
30 11 0.25
31 17 0.39
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.50
Consensus pattern (30 bp):
TATACATGAATTTTGATTTATGTGTAATTG
Found at i:1144280 original size:29 final size:29
Alignment explanation
Indices: 1144221--1144279 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
1144211 TATGGTTTAA
*
1144221 TGTGTAATTGTATACATGAATTTTGATTT
1 TGTGTAATTGTATACATAAATTTTGATTT
*
1144250 TGTGTAATTTTATACATAAAATTTTGATTT
1 TGTGTAATTGTATACAT-AAATTTTGATTT
1144280 GATCCAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (29 bp):
TGTGTAATTGTATACATAAATTTTGATTT
Found at i:1149896 original size:19 final size:19
Alignment explanation
Indices: 1149872--1150249 Score: 134
Period size: 19 Copynumber: 18.3 Consensus size: 19
1149862 GTGCCAATGG
*
1149872 GTAATTTTGTATGTATATT
1 GTAATTTTGTATGAATATT
1149891 GTAATTTTTTGTATGAATATT
1 GTAA--TTTTGTATGAATATT
*
1149912 ATAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
1149931 GTAATTATTTTAT-AATTAATTTT
1 GTAATT-TTGTATGAA-T-A--TT
* * *
1149954 GT-ATTTATAGTTTTGGAT-TA
1 GTAATTT-T-G-TATGAATATT
*
1149974 GT-ATTTTGTACGAATATT
1 GTAATTTTGTATGAATATT
1149992 GTAATTTTGTAATTTTGCATGAATATT
1 GTAATTTTG------T--ATGAATATT
1150019 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
1150038 GTAATTTTGTAATTTTATATGAATATT
1 GTAATTTTG--------TATGAATATT
*
1150065 ATAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
1150084 GTAATTATTTTAT-AATTAATT
1 GTAATT-TTGTATGAA-T-ATT
* * *
1150105 TTATATTTATAGTTTTTG-AT-TA
1 GTA-ATTT-T-G--TATGAATATT
1150127 GT-ATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
1150145 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
1150164 GTAATTATT-T-T--ATAAT
1 GTAATT-TTGTATGAATATT
* *
1150180 -TAATTTTGTATTTATAGTTTTT
1 GTAATTTTGTA-TGA-A--TATT
*
1150202 GATTAGTATTTTGTATGAATGTT
1 G--TA--ATTTTGTATGAATATT
1150225 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
1150244 GTAATT
1 GTAATT
1150250 ATTTTATAAT
Statistics
Matches: 275, Mismatches: 29, Indels: 110
0.66 0.07 0.27
Matches are distributed among these distances:
14 2 0.01
15 6 0.02
16 7 0.03
17 7 0.03
18 9 0.03
19 113 0.41
20 26 0.09
21 28 0.10
22 12 0.04
23 8 0.03
24 4 0.01
25 8 0.03
26 2 0.01
27 43 0.16
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.56
Consensus pattern (19 bp):
GTAATTTTGTATGAATATT
Found at i:1150003 original size:8 final size:8
Alignment explanation
Indices: 1149990--1150053 Score: 56
Period size: 8 Copynumber: 7.2 Consensus size: 8
1149980 TGTACGAATA
1149990 TTGTAATT
1 TTGTAATT
1149998 TTGTAATT
1 TTGTAATT
*
1150006 TTGCATGAATA
1 TTG--T-AATT
1150017 TTGTAATT
1 TTGTAATT
*
1150025 TTGTATGAATA
1 TTG--T-AATT
1150036 TTGTAATT
1 TTGTAATT
1150044 TTGTAATT
1 TTGTAATT
1150052 TT
1 TT
1150054 ATATGAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
8 30 0.65
9 2 0.04
10 2 0.04
11 12 0.26
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (8 bp):
TTGTAATT
Found at i:1150006 original size:27 final size:27
Alignment explanation
Indices: 1149976--1150075 Score: 99
Period size: 27 Copynumber: 4.0 Consensus size: 27
1149966 TTGGATTAGT
1149976 ATTTTGTACGAATATTGTAATTTTGTA
1 ATTTTGTACGAATATTGTAATTTTGTA
*
1150003 ATTTTG--C----A-TG-AATATTGTA
1 ATTTTGTACGAATATTGTAATTTTGTA
*
1150022 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTACGAATATTGTAATTTTGTA
* * *
1150049 ATTTTATATGAATATTATAATTTTGTA
1 ATTTTGTACGAATATTGTAATTTTGTA
1150076 TGAATATTGT
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
19 14 0.23
20 2 0.03
21 1 0.02
25 2 0.03
26 2 0.03
27 39 0.65
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (27 bp):
ATTTTGTACGAATATTGTAATTTTGTA
Found at i:1150026 original size:46 final size:46
Alignment explanation
Indices: 1149976--1150089 Score: 192
Period size: 46 Copynumber: 2.5 Consensus size: 46
1149966 TTGGATTAGT
* * *
1149976 ATTTTGTACGAATATTGTAATTTTGTAATTTTGCATGAATATTGTA
1 ATTTTGTATGAATATTGTAATTTTGTAATTTTACATGAATATTATA
*
1150022 ATTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATATTATA
1 ATTTTGTATGAATATTGTAATTTTGTAATTTTACATGAATATTATA
1150068 ATTTTGTATGAATATTGTAATT
1 ATTTTGTATGAATATTGTAATT
1150090 ATTTTATAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (46 bp):
ATTTTGTATGAATATTGTAATTTTGTAATTTTACATGAATATTATA
Found at i:1150139 original size:80 final size:80
Alignment explanation
Indices: 1150049--1150398 Score: 556
Period size: 80 Copynumber: 4.3 Consensus size: 80
1150039 TAATTTTGTA
* * *
1150049 ATTTTATATGAATATTATAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTA
1 ATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTA
1150114 TAGTTTTTGATTAGT
66 TAGTTTTTGATTAGT
1150129 ATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTA
1 ATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTA
1150194 TAGTTTTTGATTAGT
66 TAGTTTTTGATTAGT
* *
1150209 ATTTTGTATGAATGTTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTTTATTTA
1 ATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTA
*
1150274 TATTTTTTGATTAGT
66 TAGTTTTTGATTAGT
*
1150289 ATTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATAGTGTAATTATTTTATAATTAATTT
1 ATTTTGTATG-A-A---T-A--TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTT
1150354 TGTATTTATAGTTTTTGATTAGT
58 TGTATTTATAGTTTTTGATTAGT
*
1150377 ATTTTGTATAAATATTGTAATT
1 ATTTTGTATGAATATTGTAATT
1150399 ATTTTATAAT
Statistics
Matches: 251, Mismatches: 11, Indels: 16
0.90 0.04 0.06
Matches are distributed among these distances:
80 172 0.69
81 1 0.00
82 2 0.01
83 1 0.00
85 1 0.00
86 1 0.00
87 1 0.00
88 72 0.29
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (80 bp):
ATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTA
TAGTTTTTGATTAGT
Found at i:1150321 original size:88 final size:87
Alignment explanation
Indices: 1150223--1150513 Score: 290
Period size: 88 Copynumber: 3.3 Consensus size: 87
1150213 TGTATGAATG
*
1150223 TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTTTATTTATATTTTTTGATTAG
1 TTGT-ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATATTTTTTGATTAG
*
1150288 TATTTTGTATGAATATTGTAATT
65 TATTTTGTATGAATATTGTAATA
* *
1150311 TTGTAATTTTGTATGAATAGTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAG
1 TTGT-ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATATTTTTTGATTAG
*
1150376 TATTTTGTATAAATATTGT-A-A
65 TATTTTGTATGAATATTGTAATA
* * * * * * * *
1150397 -T-TATTTTATAATTAATTTTGTATTTATAGTTT-TGGATTAGTATTTTGTA-TGA-ATTTTGTA
1 TTGTATTTTGT-ATGAATATTGTAATTAT--TTTAT-AATTA--ATTTTGTATTTATATTTTTTG
* *
1150457 ATTTTGTAATTTTGTATGAATATTGTAATT
60 A-TTAGT-ATTTTGTATGAATATTGTAATA
*
1150487 TTATAATTTTGTATGAATATTGTAATT
1 TTGT-ATTTTGTATGAATATTGTAATT
1150514 TTGTAATTTT
Statistics
Matches: 168, Mismatches: 22, Indels: 22
0.79 0.10 0.10
Matches are distributed among these distances:
83 6 0.04
84 14 0.08
85 2 0.01
86 13 0.08
87 7 0.04
88 105 0.62
89 1 0.01
91 1 0.01
92 13 0.08
93 6 0.04
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (87 bp):
TTGTATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATATTTTTTGATTAGT
ATTTTGTATGAATATTGTAATA
Found at i:1150353 original size:34 final size:32
Alignment explanation
Indices: 1150314--1150419 Score: 96
Period size: 34 Copynumber: 3.3 Consensus size: 32
1150304 TGTAATTTTG
1150314 TAATTTTGTATGAATAGTGTAATTATTTTATAAT
1 TAATTTTGTAT-AATA-TGTAATTATTTTATAAT
* * * * *
1150348 TAATTTTGTAT--T-TATAGTT-TTTGATTAG
1 TAATTTTGTATAATATGTAATTATTTTATAAT
1150376 T-ATTTTGTATAAATATTGTAATTATTTTATAAT
1 TAATTTTGTAT-AATA-TGTAATTATTTTATAAT
1150409 TAATTTTGTAT
1 TAATTTTGTAT
1150420 TTATAGTTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
27 9 0.16
28 7 0.13
29 5 0.09
30 1 0.02
31 1 0.02
32 5 0.09
33 7 0.13
34 20 0.36
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (32 bp):
TAATTTTGTATAATATGTAATTATTTTATAAT
Found at i:1150380 original size:27 final size:27
Alignment explanation
Indices: 1150350--1150446 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 27
1150340 TTTATAATTA
1150350 ATTTTGTATTTATAGTTTTTGATTAGT
1 ATTTTGTATTTATAGTTTTTGATTAGT
* * * * *
1150377 ATTTTGTATAAATATTGTAATTATTTTATAATT
1 ATTTTG--T--AT-TTATAGTT-TTTGATTAGT
*
1150410 AATTTTGTATTTATAGTTTTGGATTAGT
1 -ATTTTGTATTTATAGTTTTTGATTAGT
1150438 ATTTTGTAT
1 ATTTTGTAT
1150447 GAATTTTGTA
Statistics
Matches: 52, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
27 15 0.29
28 6 0.12
29 7 0.13
30 2 0.04
31 2 0.04
32 7 0.13
33 7 0.13
34 6 0.12
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (27 bp):
ATTTTGTATTTATAGTTTTTGATTAGT
Found at i:1150461 original size:8 final size:8
Alignment explanation
Indices: 1150448--1150649 Score: 113
Period size: 8 Copynumber: 23.1 Consensus size: 8
1150438 ATTTTGTATG
1150448 AATTTTGT
1 AATTTTGT
1150456 AATTTTGT
1 AATTTTGT
1150464 AATTTTGTAT
1 AATTTTG--T
*
1150474 GAATATTGT
1 -AATTTTGT
*
1150483 AATTTTAT
1 AATTTTGT
1150491 AATTTTGTAT
1 AATTTTG--T
*
1150501 GAATATTGT
1 -AATTTTGT
1150510 AATTTTGT
1 AATTTTGT
*
1150518 AATTTTATAT
1 AA-TTT-TGT
*
1150528 GAATATTGT
1 -AATTTTGT
1150537 AATTTTGT
1 AATTTTGT
1150545 AATTTTGTAT
1 AATTTTG--T
*
1150555 GAATATTGT
1 -AATTTTGT
*
1150564 AATATTGT
1 AATTTTGT
1150572 --TTGTATG-
1 AATT-T-TGT
*
1150579 AATATTGT
1 AATTTTGT
1150587 AATTTTGT
1 AATTTTGT
*
1150595 AATTTTATAT
1 AA-TTT-TGT
1150605 GAATTTTGT
1 -AATTTTGT
1150614 AATTTTGT
1 AATTTTGT
1150622 AATTTTGTAT
1 AATTTTG--T
*
1150632 GAATATTGT
1 -AATTTTGT
1150641 AATTTTGT
1 AATTTTGT
1150649 A
1 A
1150650 TGAATATTGT
Statistics
Matches: 153, Mismatches: 18, Indels: 46
0.71 0.08 0.21
Matches are distributed among these distances:
6 1 0.01
7 3 0.02
8 93 0.61
9 15 0.10
10 13 0.08
11 28 0.18
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (8 bp):
AATTTTGT
Found at i:1150462 original size:19 final size:19
Alignment explanation
Indices: 1150438--1150686 Score: 134
Period size: 19 Copynumber: 13.2 Consensus size: 19
1150428 TTGGATTAGT
1150438 ATTTTGTATGAATTTTGTA
1 ATTTTGTATGAATTTTGTA
1150457 ATTTTG--T-AATTTTGTATGA
1 ATTTTGTATGAATTTTG--T-A
* *
1150476 ATATTG--T-AATTTTATA
1 ATTTTGTATGAATTTTGTA
*
1150492 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATTTTGTA
* *
1150511 ATTTTGTA--ATTTTATATGA
1 ATTTTGTATGAATTT-TGT-A
*
1150530 ATATTG--T-AATTTTGTA
1 ATTTTGTATGAATTTTGTA
*
1150546 ATTTTGTATGAATATTGTAA
1 ATTTTGTATGAATTTTGT-A
*
1150566 TATTGTTTGTATGAATATTGTA
1 -A-T-TTTGTATGAATTTTGTA
* *
1150588 ATTTTGTA--ATTTTATATGA
1 ATTTTGTATGAATTT-TGT-A
1150607 ATTTTG--T-AATTTTGTA
1 ATTTTGTATGAATTTTGTA
*
1150623 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATTTTGTA
*
1150642 ATTTTGTATGAATATTGTAA
1 ATTTTGTATGAATTTTGT-A
*
1150662 TATTGTTTGTATGAATATTGTA
1 -A-T-TTTGTATGAATTTTGTA
1150684 ATT
1 ATT
1150687 ATTTTATAAT
Statistics
Matches: 185, Mismatches: 19, Indels: 52
0.72 0.07 0.20
Matches are distributed among these distances:
16 26 0.14
17 12 0.06
18 16 0.09
19 87 0.47
20 4 0.02
21 4 0.02
22 4 0.02
23 32 0.17
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (19 bp):
ATTTTGTATGAATTTTGTA
Found at i:1150468 original size:27 final size:27
Alignment explanation
Indices: 1150438--1150649 Score: 342
Period size: 27 Copynumber: 8.0 Consensus size: 27
1150428 TTGGATTAGT
*
1150438 ATTTTGTATGAATTTTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
1150465 ATTTTGTATGAATATTGTAATTTTATA
1 ATTTTGTATGAATATTGTAATTTTGTA
1150492 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
1150519 ATTTTATATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
1150546 ATTTTGTATGAATATTGTAATATTG--
1 ATTTTGTATGAATATTGTAATTTTGTA
1150571 --TTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
* *
1150596 ATTTTATATGAATTTTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
1150623 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
1150650 TGAATATTGT
Statistics
Matches: 170, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
23 22 0.13
27 148 0.87
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (27 bp):
ATTTTGTATGAATATTGTAATTTTGTA
Found at i:1150946 original size:15 final size:16
Alignment explanation
Indices: 1150910--1150946 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1150900 CTCATTTAAT
1150910 TTTTATATAATGTAAC
1 TTTTATATAATGTAAC
1150926 TTTTATAGT-ATGTAA-
1 TTTTATA-TAATGTAAC
1150941 TTTTAT
1 TTTTAT
1150947 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 13 0.65
17 1 0.05
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (16 bp):
TTTTATATAATGTAAC
Found at i:1151273 original size:13 final size:13
Alignment explanation
Indices: 1151255--1151279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1151245 AATGAAAAAA
1151255 GTAAATACTTTTG
1 GTAAATACTTTTG
1151268 GTAAATACTTTT
1 GTAAATACTTTT
1151280 TCTGACACCC
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:0.08, G:0.12, T:0.48
Consensus pattern (13 bp):
GTAAATACTTTTG
Found at i:1158004 original size:19 final size:19
Alignment explanation
Indices: 1157966--1158005 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1157956 GATTTTTATT
*
1157966 TTATTTAATATTATTATAA
1 TTATTAAATATTATTATAA
1157985 TTATTAAAT-TTATTATTAA
1 TTATTAAATATTATTA-TAA
1158004 TT
1 TT
1158006 TTTTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATTAAATATTATTATAA
Found at i:1158517 original size:34 final size:34
Alignment explanation
Indices: 1158474--1158541 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1158464 ATGTAACAAT
1158474 CCTTTGTTTTATAGTAACATTTTATTTTCTATAA
1 CCTTTGTTTTATAGTAACATTTTATTTTCTATAA
1158508 CCTTTGTTTTATAGTAACATTTTATTTTCTATAA
1 CCTTTGTTTTATAGTAACATTTTATTTTCTATAA
1158542 GTGGACATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (34 bp):
CCTTTGTTTTATAGTAACATTTTATTTTCTATAA
Found at i:1158525 original size:17 final size:17
Alignment explanation
Indices: 1158474--1158525 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
1158464 ATGTAACAAT
1158474 CCTTTGTTTTATAGTAA
1 CCTTTGTTTTATAGTAA
* * *
1158491 CATTTTATTTTCTA-TAA
1 C-CTTTGTTTTATAGTAA
1158508 CCTTTGTTTTATAGTAA
1 CCTTTGTTTTATAGTAA
1158525 C
1 C
1158526 ATTTTATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 9 0.33
17 9 0.33
18 9 0.33
ACGTcount: A:0.25, C:0.13, G:0.08, T:0.54
Consensus pattern (17 bp):
CCTTTGTTTTATAGTAA
Found at i:1158873 original size:6 final size:6
Alignment explanation
Indices: 1158862--1158887 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1158852 TAAGGGGGTG
1158862 TTTTGT TTTTGT TTTTGT TTTTGT TT
1 TTTTGT TTTTGT TTTTGT TTTTGT TT
1158888 ATATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTGT
Found at i:1158894 original size:2 final size:2
Alignment explanation
Indices: 1158887--1158918 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1158877 TGTTTTTGTT
*
1158887 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1158919 AATAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1159083 original size:31 final size:31
Alignment explanation
Indices: 1159024--1159083 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
1159014 ATTTGGTCAC
*
1159024 TGAACTATTTCAATATTTTCATTCAAGTCGT
1 TGAACTATTTCAAAATTTTCATTCAAGTCGT
* *
1159055 TGAACTA-TTCAAAAGTTTTTATTTAAGTC
1 TGAACTATTTCAAAA-TTTTCATTCAAGTC
1159084 ACTAGTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (31 bp):
TGAACTATTTCAAAATTTTCATTCAAGTCGT
Found at i:1160310 original size:60 final size:60
Alignment explanation
Indices: 1160211--1160325 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
1160201 TAACAGCCCA
* * * *
1160211 TTTTTGGGTCAAACCGGAATAGTGATTTCGGGACCACAAATCCGAAGTTAAAATAATATT
1 TTTTTGGGTCAAACCAGAATACTGATTTCGAGACCACAAATCCAAAGTTAAAATAATATT
* * * *
1160271 TTTTTGGGTCAAATCAGAATACTGGTTTCGAGACTACAAATCTAAAGTTAAAATA
1 TTTTTGGGTCAAACCAGAATACTGATTTCGAGACCACAAATCCAAAGTTAAAATA
1160326 TTAATTTTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (60 bp):
TTTTTGGGTCAAACCAGAATACTGATTTCGAGACCACAAATCCAAAGTTAAAATAATATT
Found at i:1160939 original size:61 final size:61
Alignment explanation
Indices: 1160862--1161250 Score: 539
Period size: 61 Copynumber: 6.4 Consensus size: 61
1160852 GTATATGTTT
* *
1160862 TATACATTGCCGAATTGGTTTGTATAAAGATATACATTGCCGAATTTGATTTGCT-TATAGA
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTG-TATATAGA
* * *
1160923 TATACATTGCCAAATTGATTTGTATATAGATATACATTGCCGAATTTGAATTGTTTATAGA
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * * * *
1160984 TGTACATTGCCGAATTGATTTGTTTATAGATATACATTGTCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * *
1161045 TATACATTACCGAATTTGATTTGTATATGGATATACATTGCTGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAA-TTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * * * *
1161106 TATACATTGCTGAATTTGATTTGTATATGGTTATACATTGCCGAAGTTGATTTGTATATGGA
1 TATACATTGCCGAA-TTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * *
1161168 TATACATTGCCGAATTGATTTGTATATAGATATTCATTGCCGAATTTGATTCGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
*
1161229 TATATATTGCCGAATTGATTTG
1 TATACATTGCCGAATTGATTTG
1161251 AGCATTGGAT
Statistics
Matches: 293, Mismatches: 32, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
60 1 0.00
61 238 0.81
62 54 0.18
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (61 bp):
TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
Found at i:1161260 original size:31 final size:31
Alignment explanation
Indices: 1160862--1161250 Score: 504
Period size: 31 Copynumber: 12.7 Consensus size: 31
1160852 GTATATGTTT
* **
1160862 TATACATTGCCGAA-TTGGTTTGTATAAAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
*
1160892 TATACATTGCCGAATTTGATTTGCT-TATAGA
1 TATACATTGCCGAATTTGATTTG-TATATGGA
* *
1160923 TATACATTGCC-AAATTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* * *
1160953 TATACATTGCCGAATTTGAATTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* * *
1160984 TGTACATTGCCGAA-TTGATTTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* *
1161014 TATACATTGTCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATGGA
*
1161045 TATACATTACCGAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* *
1161076 TATACATTGCTGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* *
1161106 TATACATTGCTGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATGGA
*
1161137 TATACATTGCCGAAGTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
*
1161168 TATACATTGCCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
* *
1161198 TATTCATTGCCGAATTTGATTCGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATGGA
*
1161229 TATATATTGCCGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
1161251 AGCATTGGAT
Statistics
Matches: 321, Mismatches: 31, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
29 1 0.00
30 132 0.41
31 187 0.58
32 1 0.00
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTTGTATATGGA
Found at i:1161260 original size:92 final size:92
Alignment explanation
Indices: 1160862--1161250 Score: 552
Period size: 92 Copynumber: 4.2 Consensus size: 92
1160852 GTATATGTTT
* **
1160862 TATACATTGCCGAA-TTGGTTTGTATAAAGATATACATTGCCGAATTTGATTTGCT-TATAGATA
1 TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAA-TTGATTTG-TATATAGATA
* *
1160925 TACATTGCC-AAATTGATTTGTATATAGA
64 TACATTGCCGAATTTGATTTGTATATGGA
* * * * *
1160953 TATACATTGCCGAATTTGAATTGTTTATAGATGTACATTGCCGAATTGATTTGTTTATAGATATA
1 TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGATATA
* *
1161018 CATTGTCGAATTTGATTTGTATATGGT
66 CATTGCCGAATTTGATTTGTATATGGA
* *
1161045 TATACATTACCGAATTTGATTTGTATATGGATATACATTGCTGAATTGATTTGTATATAGATATA
1 TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGATATA
* *
1161110 CATTGCTGAATTTGATTTGTATATGGT
66 CATTGCCGAATTTGATTTGTATATGGA
* *
1161137 TATACATTGCCGAAGTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGATATT
1 TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGATATA
*
1161202 CATTGCCGAATTTGATTCGTATATGGA
66 CATTGCCGAATTTGATTTGTATATGGA
*
1161229 TATATATTGCCGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
1161251 AGCATTGGAT
Statistics
Matches: 269, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
90 1 0.00
91 46 0.17
92 222 0.83
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (92 bp):
TATACATTGCCGAATTTGATTTGTATATGGATATACATTGCCGAATTGATTTGTATATAGATATA
CATTGCCGAATTTGATTTGTATATGGA
Found at i:1162618 original size:19 final size:19
Alignment explanation
Indices: 1162594--1162630 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1162584 TTAAAATATT
1162594 ATTTTA-ATAAAACATTTAA
1 ATTTTATATAAAA-ATTTAA
1162613 ATTTTATATAAAAATTTA
1 ATTTTATATAAAAATTTA
1162631 TTAATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTTATATAAAAATTTAA
Found at i:1162669 original size:20 final size:19
Alignment explanation
Indices: 1162641--1162682 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1162631 TTAATTATAT
*
1162641 TTTATTGAATGAATATAATA
1 TTTAATGAATGAA-ATAATA
*
1162661 TTTAATGAATGAAATTATA
1 TTTAATGAATGAAATAATA
1162680 TTT
1 TTT
1162683 GTAAATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (19 bp):
TTTAATGAATGAAATAATA
Found at i:1174478 original size:19 final size:18
Alignment explanation
Indices: 1174454--1174512 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 18
1174444 TTTTTGTTGC
1174454 TAATTTTTATGATTTTTTA
1 TAATTTTTAT-ATTTTTTA
1174473 TAATTTATT-TA-TTTTTA
1 TAATTT-TTATATTTTTTA
*
1174490 -AATATTTTATAATTTTTA
1 TAAT-TTTTATATTTTTTA
*
1174508 AAATT
1 TAATT
1174513 ATTTGTTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
16 5 0.14
17 10 0.29
18 8 0.23
19 10 0.29
20 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TAATTTTTATATTTTTTA
Found at i:1174506 original size:9 final size:9
Alignment explanation
Indices: 1174454--1174512 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
1174444 TTTTTGTTGC
1174454 TAATTTTTA
1 TAATTTTTA
*
1174463 TGATTTTTTA
1 T-AATTTTTA
1174473 TAATTTATT-
1 TAATTT-TTA
1174482 T-ATTTTTA
1 TAATTTTTA
1174490 -AATATTTTA
1 TAAT-TTTTA
1174499 TAATTTTTA
1 TAATTTTTA
*
1174508 AAATT
1 TAATT
1174513 ATTTGTTAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
7 2 0.05
8 6 0.15
9 20 0.49
10 13 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
TAATTTTTA
Found at i:1177723 original size:31 final size:31
Alignment explanation
Indices: 1177675--1177741 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1177665 GAAAATCCTA
* *
1177675 AAGTTTAGGCTCTAATGTGGGAACAACTGCC
1 AAGTTCAGGCTCTAATGTAGGAACAACTGCC
* *
1177706 AAGTTCAGGACTC-AATGTAGGAGCAATTGCC
1 AAGTTCAGG-CTCTAATGTAGGAACAACTGCC
1177737 AAGTT
1 AAGTT
1177742 TAGGGACTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (31 bp):
AAGTTCAGGCTCTAATGTAGGAACAACTGCC
Found at i:1177890 original size:88 final size:88
Alignment explanation
Indices: 1177725--1177890 Score: 187
Period size: 88 Copynumber: 1.9 Consensus size: 88
1177715 ACTCAATGTA
* * * * *
1177725 GGAGCAATTGCCAAGTTTAGGGACTAACTTGGACAAAAGAAATGTTCAACCCCAAGGTGAGAACA
1 GGAGCAATTGCCAAGTTCAGAGACTAACTTGGACAAAAGAAAGGTTCAACCACAAGGTGAGAAAA
*
1177790 GTTGCCTAGTCCAGACCCATATG
66 GTTGCCAAGTCCAGACCCATATG
* * *
1177813 GGAGCAATTGCCTAGTTCA-AGACCTAACTTGGAC-AAA-AAAGGTTCAAGCTACAATGTG-GAA
1 GGAGCAATTGCCAAGTTCAGAGA-CTAACTTGGACAAAAGAAAGGTTCAA-CCACAAGGTGAGAA
1177874 AATGTTGCCAAGGTCCA
64 AA-GTTGCCAA-GTCCA
1177891 AATAGTGATT
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
86 13 0.20
87 19 0.29
88 33 0.51
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.21
Consensus pattern (88 bp):
GGAGCAATTGCCAAGTTCAGAGACTAACTTGGACAAAAGAAAGGTTCAACCACAAGGTGAGAAAA
GTTGCCAAGTCCAGACCCATATG
Found at i:1180165 original size:2 final size:2
Alignment explanation
Indices: 1180158--1180204 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1180148 TTCAAGTTTC
*
1180158 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1180200 TA TA T
1 TA TA T
1180205 GCATCTGAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1197534 original size:9 final size:9
Alignment explanation
Indices: 1197522--1197569 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
1197512 AATATATTTA
1197522 TTTTTTAAT
1 TTTTTTAAT
1197531 TTTTTTAA-
1 TTTTTTAAT
**
1197539 TTTTAAAAT
1 TTTTTTAAT
*
1197548 ATTTTTTAAA
1 -TTTTTTAAT
1197558 TTTTTTAAT
1 TTTTTTAAT
1197567 TTT
1 TTT
1197570 AAAATACTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
8 6 0.19
9 19 0.61
10 6 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:1197550 original size:27 final size:27
Alignment explanation
Indices: 1197520--1197584 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
1197510 TAAATATATT
*
1197520 TATTTTTTAATTTTTTTAATTTTAAAA
1 TATTTTTTAAATTTTTTAATTTTAAAA
1197547 TATTTTTTAAATTTTTTAATTTTAAAA
1 TATTTTTTAAATTTTTTAATTTTAAAA
*
1197574 TACTTTTTAAA
1 TATTTTTTAAA
1197585 ATACTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
TATTTTTTAAATTTTTTAATTTTAAAA
Found at i:1204183 original size:31 final size:31
Alignment explanation
Indices: 1204148--1204235 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 31
1204138 TTGGTACGGA
1204148 AGTTTGGTTTTAATGTTCAATTTGATACTTG
1 AGTTTGGTTTTAATGTTCAATTTGATACTTG
** * * *
1204179 AGTTT--TTTTTTTGTCCCAATTTGGTACTTT
1 AGTTTGGTTTTAATGT-TCAATTTGATACTTG
* * *
1204209 AGTTTGGGTTCAATGTTTAATTTGATA
1 AGTTTGGTTTTAATGTTCAATTTGATA
1204236 TCCAGACCAT
Statistics
Matches: 42, Mismatches: 12, Indels: 6
0.70 0.20 0.10
Matches are distributed among these distances:
29 7 0.17
30 17 0.40
31 13 0.31
32 5 0.12
ACGTcount: A:0.20, C:0.08, G:0.18, T:0.53
Consensus pattern (31 bp):
AGTTTGGTTTTAATGTTCAATTTGATACTTG
Found at i:1204469 original size:55 final size:57
Alignment explanation
Indices: 1204333--1204482 Score: 148
Period size: 58 Copynumber: 2.6 Consensus size: 57
1204323 ATATCAAATT
* * * *
1204333 GAAAAAATTCAGGTACCAAAGTAAATATTGAAGTCAAACTCAGGTATCAGATTGGACG
1 GAAAAAACTCAGGTACCAAATTAAACATTGAAG-CCAACTCAGGTATCAGATTGGACG
* * * *
1204391 AAAAAAACTTAGGT-CTCAAATTAAACATTGAAGCCAACTCATGTA-CTA-ATTTGG-GG
1 GAAAAAACTCAGGTAC-CAAATTAAACATTGAAGCCAACTCAGGTATC-AGA-TTGGACG
*
1204447 GAAAAAA-TCAGGTACCAAATTAAACATTGAAACCAA
1 GAAAAAACTCAGGTACCAAATTAAACATTGAAGCCAA
1204483 AATTAGATAC
Statistics
Matches: 77, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
55 25 0.32
56 10 0.13
57 16 0.21
58 26 0.34
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (57 bp):
GAAAAAACTCAGGTACCAAATTAAACATTGAAGCCAACTCAGGTATCAGATTGGACG
Found at i:1208309 original size:14 final size:14
Alignment explanation
Indices: 1208290--1208319 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1208280 AAATTAATCC
1208290 TAACATTTAATTCA
1 TAACATTTAATTCA
1208304 TAACATTTAATTCA
1 TAACATTTAATTCA
1208318 TA
1 TA
1208320 CCTAAATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (14 bp):
TAACATTTAATTCA
Found at i:1212129 original size:26 final size:25
Alignment explanation
Indices: 1212081--1212130 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
1212071 TAGGCTAATC
**
1212081 AGAGTTTAAATGGAGAACTAAAAAT
1 AGAGTTTAAATGGAGAAAAAAAAAT
*
1212106 AGAGTTTAATTAGGAGAAAAAAAAA
1 AGAGTTTAAAT-GGAGAAAAAAAAA
1212131 CCAAAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.56, C:0.02, G:0.20, T:0.22
Consensus pattern (25 bp):
AGAGTTTAAATGGAGAAAAAAAAAT
Found at i:1217122 original size:17 final size:17
Alignment explanation
Indices: 1217100--1217134 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1217090 AAATAGTTAC
1217100 AATTAA-AATAATAATAA
1 AATTAACAATAA-AATAA
1217117 AATTAACAATAAAATAA
1 AATTAACAATAAAATAA
1217134 A
1 A
1217135 TGTTCTACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AATTAACAATAAAATAA
Found at i:1219985 original size:2 final size:2
Alignment explanation
Indices: 1219975--1220039 Score: 93
Period size: 2 Copynumber: 34.5 Consensus size: 2
1219965 ATATATAAAT
*
1219975 AG AG GG AG AG AG AG AG AG AG AG AG -G AG -G AG -G AG -G AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1220013 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1220040 TGGGACACTT
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
1 4 0.07
2 53 0.93
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1223260 original size:6 final size:6
Alignment explanation
Indices: 1223261--1223324 Score: 128
Period size: 6 Copynumber: 10.7 Consensus size: 6
1223251 TTCTTTTTCT
1223261 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1223309 TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTT
1223325 ATTACATGAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:1223263 original size:5 final size:6
Alignment explanation
Indices: 1223249--1223324 Score: 53
Period size: 6 Copynumber: 12.5 Consensus size: 6
1223239 CAGAAACGGA
* * * * * *
1223249 TTTTCT TTTTCTT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTCT TTTTC-T TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
* * * *
1223298 TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTT
1223325 ATTACATGAA
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
6 63 0.93
7 5 0.07
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:1223736 original size:31 final size:31
Alignment explanation
Indices: 1223691--1223764 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
1223681 TGTACGTTAG
*
1223691 TTAGTT-GATGACCAAAAAGACAAAATT-TAA
1 TTAGTTGGGTGACCAAAAA-ACAAAATTATAA
* *
1223721 TTAGTTGGGTGACCAAAAAATAAATTTATAA
1 TTAGTTGGGTGACCAAAAAACAAAATTATAA
*
1223752 ATAGTTGGGTGAC
1 TTAGTTGGGTGAC
1223765 TACTAATGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 12 0.32
31 26 0.68
ACGTcount: A:0.43, C:0.08, G:0.19, T:0.30
Consensus pattern (31 bp):
TTAGTTGGGTGACCAAAAAACAAAATTATAA
Found at i:1227013 original size:7 final size:7
Alignment explanation
Indices: 1227001--1227036 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
1226991 TTTTAACAAT
1227001 AAATAAG
1 AAATAAG
1227008 AAATAAG
1 AAATAAG
*
1227015 TAAATAAT
1 -AAATAAG
1227023 AAATAAG
1 AAATAAG
1227030 AAATAAG
1 AAATAAG
1227037 GGGTTCTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.19
Consensus pattern (7 bp):
AAATAAG
Found at i:1227034 original size:11 final size:11
Alignment explanation
Indices: 1226998--1227035 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1226988 TCCTTTTAAC
1226998 AATAAATAAGA
1 AATAAATAAGA
*
1227009 AATAAGTAA-A
1 AATAAATAAGA
1227019 TAATAAATAAGA
1 -AATAAATAAGA
1227031 AATAA
1 AATAA
1227036 GGGGTTCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 1 0.04
11 21 0.91
12 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (11 bp):
AATAAATAAGA
Found at i:1229493 original size:11 final size:11
Alignment explanation
Indices: 1229477--1229502 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1229467 AATCGGGAGG
1229477 CGAAGGTAGAA
1 CGAAGGTAGAA
1229488 CGAAGGTAGAA
1 CGAAGGTAGAA
1229499 CGAA
1 CGAA
1229503 AGAAGAGGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.12, G:0.35, T:0.08
Consensus pattern (11 bp):
CGAAGGTAGAA
Found at i:1229680 original size:24 final size:24
Alignment explanation
Indices: 1229653--1229701 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1229643 TTAGAAACAC
1229653 ATTGAACCAAACGACGGAATAAAG
1 ATTGAACCAAACGACGGAATAAAG
1229677 ATTGAACCAAACGACGGAATAAAG
1 ATTGAACCAAACGACGGAATAAAG
1229701 A
1 A
1229702 GGTATTAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.16, G:0.20, T:0.12
Consensus pattern (24 bp):
ATTGAACCAAACGACGGAATAAAG
Found at i:1234386 original size:25 final size:26
Alignment explanation
Indices: 1234358--1234417 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 26
1234348 TACGTGTTTT
1234358 TTTAATAATTATATA-TTTTA-AAAAA
1 TTTAATAATTATA-ACTTTTACAAAAA
*
1234383 TTTAA-AATTTTAACTTTTACAAAAA
1 TTTAATAATTATAACTTTTACAAAAA
1234408 -TTAATTAATT
1 TTTAA-TAATT
1234418 GTTGACATGG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 1 0.03
24 15 0.50
25 10 0.33
26 4 0.13
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
TTTAATAATTATAACTTTTACAAAAA
Found at i:1241298 original size:2 final size:2
Alignment explanation
Indices: 1241291--1241339 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
1241281 AGTCCAAGAA
* *
1241291 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1241333 AT AT AT A
1 AT AT AT A
1241340 CACTTTATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1243341 original size:5 final size:6
Alignment explanation
Indices: 1243324--1243360 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
1243314 ATTTAAAATT
1243324 TAAAAA TAAAAAA TAAAAA TAAAAA TAAAAA CTAAAA
1 TAAAAA T-AAAAA TAAAAA TAAAAA TAAAAA -TAAAA
1243361 TTTAAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 18 0.62
7 11 0.38
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (6 bp):
TAAAAA
Found at i:1243348 original size:19 final size:19
Alignment explanation
Indices: 1243324--1243360 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1243314 ATTTAAAATT
1243324 TAAAAATAAAAAATAAAAA
1 TAAAAATAAAAAATAAAAA
*
1243343 TAAAAATAAAAACTAAAA
1 TAAAAATAAAAAATAAAA
1243361 TTTAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (19 bp):
TAAAAATAAAAAATAAAAA
Found at i:1243361 original size:12 final size:12
Alignment explanation
Indices: 1243324--1243360 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
1243314 ATTTAAAATT
1243324 TAAAAATAAAAAA
1 TAAAAAT-AAAAA
1243337 TAAAAATAAAAA
1 TAAAAATAAAAA
1243349 TAAAAACTAAAA
1 TAAAAA-TAAAA
1243361 TTTAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (12 bp):
TAAAAATAAAAA
Found at i:1245606 original size:28 final size:27
Alignment explanation
Indices: 1245575--1245628 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
1245565 ATTTAGTGAG
1245575 AAAAACAAAATGAGAAAGAAAT-CTGAAT
1 AAAAACAAAATGA-AAA-AAATCCTGAAT
**
1245603 AAAAGGAAAATGAAAAAAATCCTGAA
1 AAAAACAAAATGAAAAAAATCCTGAA
1245629 CAGAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 4 0.17
27 8 0.35
28 11 0.48
ACGTcount: A:0.65, C:0.07, G:0.15, T:0.13
Consensus pattern (27 bp):
AAAAACAAAATGAAAAAAATCCTGAAT
Found at i:1252374 original size:14 final size:15
Alignment explanation
Indices: 1252345--1252379 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1252335 AAAAATTAAT
*
1252345 ATTTTTAATAATTTA
1 ATTTTTAATAACTTA
1252360 ATTTTTAAT-ACTTA
1 ATTTTTAATAACTTA
1252374 ATTTTT
1 ATTTTT
1252380 CAACACTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTTAATAACTTA
Found at i:1254333 original size:29 final size:28
Alignment explanation
Indices: 1254298--1254358 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
1254288 TATTATTTTG
*
1254298 AAAAATATATAAAAGCCTATAATATATAT
1 AAAAATATATAAAAACCTATAAT-TATAT
* *
1254327 AAAAATATATAAAAACGTATAATTTTAT
1 AAAAATATATAAAAACCTATAATTATAT
1254355 AAAA
1 AAAA
1254359 GTATGTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (28 bp):
AAAAATATATAAAAACCTATAATTATAT
Found at i:1254403 original size:23 final size:24
Alignment explanation
Indices: 1254366--1254421 Score: 80
Period size: 23 Copynumber: 2.3 Consensus size: 24
1254356 AAAGTATGTA
1254366 TTATAAAAAATTATAGTA-TATAAAT
1 TTAT-AAAAATTATA-TATTATAAAT
1254391 TTATAAAAA-TATATATTATAAAT
1 TTATAAAAATTATATATTATAAAT
1254414 TTATAAAA
1 TTATAAAA
1254422 TGTGTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 2 0.07
23 19 0.63
24 5 0.17
25 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
TTATAAAAATTATATATTATAAAT
Found at i:1259990 original size:47 final size:47
Alignment explanation
Indices: 1259936--1260029 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
1259926 TCATGCATGT
1259936 AAATTTTTAAAATCGGTTCAATATCTCTATCATATTGATCTAAAAAG
1 AAATTTTTAAAATCGGTTCAATATCTCTATCATATTGATCTAAAAAG
*
1259983 AAATTTTTAAAATCGGTTCAATATTTCTATCATATTGATCTAAAAAG
1 AAATTTTTAAAATCGGTTCAATATCTCTATCATATTGATCTAAAAAG
1260030 GTGTATGTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (47 bp):
AAATTTTTAAAATCGGTTCAATATCTCTATCATATTGATCTAAAAAG
Found at i:1261175 original size:16 final size:16
Alignment explanation
Indices: 1261154--1261187 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1261144 CAAAATCCTC
1261154 AACTCTTTCATCGAAT
1 AACTCTTTCATCGAAT
1261170 AACTCTTTCATCGAAT
1 AACTCTTTCATCGAAT
1261186 AA
1 AA
1261188 TATTTTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (16 bp):
AACTCTTTCATCGAAT
Found at i:1261197 original size:17 final size:16
Alignment explanation
Indices: 1261157--1261197 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1261147 AATCCTCAAC
*
1261157 TCTTTCATCGAATAAC
1 TCTTTCATCGAATAAA
1261173 TCTTTCATCGAATAATA
1 TCTTTCATCGAATAA-A
*
1261190 TTTTTCAT
1 TCTTTCAT
1261198 GTGAATAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (16 bp):
TCTTTCATCGAATAAA
Found at i:1265753 original size:9 final size:9
Alignment explanation
Indices: 1265710--1265762 Score: 61
Period size: 9 Copynumber: 5.8 Consensus size: 9
1265700 AATTTTAAAA
1265710 TGAGAGAGT
1 TGAGAGAGT
*
1265719 TGAAAGAGT
1 TGAGAGAGT
*
1265728 TGAGAGGGTT
1 TGAGAGAG-T
1265738 TGAGAGAGT
1 TGAGAGAGT
*
1265747 CGAGAGAGT
1 TGAGAGAGT
*
1265756 TAAGAGA
1 TGAGAGA
1265763 TGGATGTAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
9 28 0.78
10 8 0.22
ACGTcount: A:0.36, C:0.02, G:0.42, T:0.21
Consensus pattern (9 bp):
TGAGAGAGT
Found at i:1265965 original size:29 final size:28
Alignment explanation
Indices: 1265923--1265994 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
1265913 GCGCTTTCTA
* **
1265923 TTTAAATCGGCCTATTTCCCTAATTAAT
1 TTTAAAACGGCCTAAATCCCTAATTAAT
*
1265951 TTTAAAACGGGCCTAAATGCCTAATTAAT
1 TTTAAAAC-GGCCTAAATCCCTAATTAAT
**
1265980 TAAAAAAACGGCCTA
1 T-TTAAAACGGCCTA
1265995 TAGGCCTTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 7 0.19
29 24 0.67
30 5 0.14
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (28 bp):
TTTAAAACGGCCTAAATCCCTAATTAAT
Found at i:1266001 original size:29 final size:29
Alignment explanation
Indices: 1265941--1266001 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
1265931 GGCCTATTTC
** *
1265941 CCTAATTAATTTTAAAACGGGCCTAAATG
1 CCTAATTAATTAAAAAACGGGCCTAAAGG
*
1265970 CCTAATTAATTAAAAAAAC-GGCCTATAGG
1 CCTAATTAATT-AAAAAACGGGCCTAAAGG
1265999 CCT
1 CCT
1266002 TACTTTGCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (29 bp):
CCTAATTAATTAAAAAACGGGCCTAAAGG
Found at i:1266461 original size:20 final size:22
Alignment explanation
Indices: 1266422--1266461 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1266412 CAAAATTAAT
*
1266422 AAACTTTTATTATGAATTAGAC
1 AAACTTTAATTATGAATTAGAC
1266444 AAACTTTAATT-T-AATTAG
1 AAACTTTAATTATGAATTAG
1266462 TAGTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.42
Consensus pattern (22 bp):
AAACTTTAATTATGAATTAGAC
Found at i:1270961 original size:30 final size:31
Alignment explanation
Indices: 1270898--1270964 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
1270888 ATATGTTGAT
** *
1270898 AGTCCTTATACTTTGATAAAATTTGAGATTA
1 AGTCCTTATACTTTGATAAAATTAAAAATTA
1270929 AGTCCTTATA-TTT-ATAAAAGTTAAAAATTA
1 AGTCCTTATACTTTGATAAAA-TTAAAAATTA
1270959 AGTCCT
1 AGTCCT
1270965 CCTAGTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 6 0.19
30 16 0.50
31 10 0.31
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.40
Consensus pattern (31 bp):
AGTCCTTATACTTTGATAAAATTAAAAATTA
Found at i:1273434 original size:9 final size:9
Alignment explanation
Indices: 1273417--1273453 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1273407 TGAGTTTTCG
1273417 AATTCGAAT
1 AATTCGAAT
*
1273426 AACTCGAAT
1 AATTCGAAT
1273435 AATTCGAAT
1 AATTCGAAT
1273444 AATTCGAAT
1 AATTCGAAT
1273453 A
1 A
1273454 TCAAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1273530 original size:21 final size:21
Alignment explanation
Indices: 1273489--1273531 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1273479 ACCCCAAACT
* *
1273489 CCCAAACCTTTTTACTTTTCC
1 CCCAAAACTTTTTACTCTTCC
1273510 CCCAAAAC-TTTTACTCCTTCC
1 CCCAAAACTTTTTACT-CTTCC
1273531 C
1 C
1273532 ACTTCCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (21 bp):
CCCAAAACTTTTTACTCTTCC
Found at i:1273568 original size:29 final size:29
Alignment explanation
Indices: 1273508--1273568 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
1273498 TTTTACTTTT
* **
1273508 CCCCCAAAACTTTTACTCCTTCCCACTTC
1 CCCCCAAAACTTTTACTCCCTCCCACAAC
1273537 CCCCCAAAACTTTTACTCCCCTCCC-CAAC
1 CCCCCAAAACTTTTACT-CCCTCCCACAAC
1273566 CCC
1 CCC
1273569 ACAATCTACC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.21, C:0.54, G:0.00, T:0.25
Consensus pattern (29 bp):
CCCCCAAAACTTTTACTCCCTCCCACAAC
Found at i:1275287 original size:12 final size:12
Alignment explanation
Indices: 1275263--1275298 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1275253 TGACCTGCCC
1275263 ATATTACTTTTTT
1 ATATTA-TTTTTT
1275276 ATATTATTTTTT
1 ATATTATTTTTT
*
1275288 ATATAATTTTT
1 ATATTATTTTT
1275299 AAATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:1282987 original size:50 final size:47
Alignment explanation
Indices: 1282912--1283102 Score: 254
Period size: 44 Copynumber: 4.1 Consensus size: 47
1282902 TCATTTATCA
1282912 CTTGTCCTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGCC
1 CTTGTCC-TGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTG-C
1282961 GCTTGTCACTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTGC
1 -CTTGTC-CTGATCAGATAAGTGTAGCTAA-GCTACCACTTATCACTTGC
1283011 C--G--CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG-
1 CTTGTCCTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTGC
*
1283054 --T-CCCTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGTC
1 CTTGTCCTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTG-C
1283099 CTTG
1 CTTG
1283103 ATCAGAAGTA
Statistics
Matches: 130, Mismatches: 0, Indels: 24
0.84 0.00 0.16
Matches are distributed among these distances:
43 20 0.15
44 58 0.45
45 2 0.02
47 2 0.02
49 1 0.01
50 28 0.22
51 19 0.15
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (47 bp):
CTTGTCCTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGC
Found at i:1288402 original size:31 final size:30
Alignment explanation
Indices: 1288305--1288406 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 30
1288295 AAAAACCATA
* *
1288305 AAGTTTAGGCCTTAATGTGGGAACAATTATC
1 AAGTTCAGGCCTCAATGT-GGAACAATTATC
* * * * *
1288336 AAGCTCAAGCCCCAATGTGGAAACAATCATT
1 AAGTTCAGGCCTCAATGTGG-AACAATTATC
*
1288367 AAGTTCAGGCCTCAATGTGAGAACAATTGTC
1 AAGTTCAGGCCTCAATGTG-GAACAATTATC
1288398 AAGTTCAGG
1 AAGTTCAGG
1288407 GATTAACTTG
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
30 2 0.04
31 53 0.95
32 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (30 bp):
AAGTTCAGGCCTCAATGTGGAACAATTATC
Found at i:1292305 original size:13 final size:13
Alignment explanation
Indices: 1292269--1292306 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1292259 AGTTCTTCAT
1292269 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
1292282 TG-TTGTGGAAAAG
1 TGCTT-TTGAAAAG
1292295 TGCTTTTGAAAA
1 TGCTTTTGAAAA
1292307 CTTTGGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 2 0.10
13 17 0.81
14 2 0.10
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:1293983 original size:29 final size:30
Alignment explanation
Indices: 1293927--1293983 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1293917 GCGTAAAAAT
* *
1293927 TCTTTATTTGAGCACTTTTGTAAAGTTAGG
1 TCTTTATATGACCACTTTTGTAAAGTTAGG
1293957 TCTTTATATGACCA-TTTTG-AAATGTTA
1 TCTTTATATGACCACTTTTGTAAA-GTTA
1293984 ACATTTAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 9 0.38
30 12 0.50
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (30 bp):
TCTTTATATGACCACTTTTGTAAAGTTAGG
Found at i:1302662 original size:2 final size:2
Alignment explanation
Indices: 1302655--1302690 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1302645 AACAAGATTA
1302655 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1302691 TTTCACACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1303719 original size:25 final size:21
Alignment explanation
Indices: 1303674--1303715 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1303664 TCTCTATAAT
1303674 CACTTCATCCTAAAAAAAGAA
1 CACTTCATCCTAAAAAAAGAA
1303695 CACTTCATCCTAAAAAAAGAA
1 CACTTCATCCTAAAAAAAGAA
1303716 AGAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.05, T:0.19
Consensus pattern (21 bp):
CACTTCATCCTAAAAAAAGAA
Found at i:1304994 original size:24 final size:24
Alignment explanation
Indices: 1304961--1305040 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 24
1304951 TAAACATTAA
* **
1304961 AAAATGTTAAAAATTACTATATAT
1 AAAATTTTAAAAATTAAAATATAT
*
1304985 AAAATTTTAATAAATAAAAAATATAT
1 AAAATTTTAA-AAAT-TAAAATATAT
* *
1305011 AACATTATTAAAAATTAAAAAAATAT
1 AAAATT-TTAAAAATT-AAAATATAT
1305037 AAAA
1 AAAA
1305041 ATATTTATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
24 9 0.20
25 4 0.09
26 27 0.61
27 4 0.09
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.33
Consensus pattern (24 bp):
AAAATTTTAAAAATTAAAATATAT
Found at i:1305008 original size:26 final size:27
Alignment explanation
Indices: 1304979--1305045 Score: 86
Period size: 26 Copynumber: 2.6 Consensus size: 27
1304969 AAAAATTACT
1304979 ATATATAAAATT-TTAATAAA-TAAAAA
1 ATATATAAAATTATTAA-AAATTAAAAA
*
1305005 ATATATAACATTATTAAAAATTAAAAA
1 ATATATAAAATTATTAAAAATTAAAAA
*
1305032 A-ATATAAAAATATT
1 ATATATAAAATTATT
1305046 TATATTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 25 0.69
27 11 0.31
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (27 bp):
ATATATAAAATTATTAAAAATTAAAAA
Found at i:1308879 original size:18 final size:18
Alignment explanation
Indices: 1308837--1308894 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
1308827 TTTTAATTTT
*
1308837 TATAATATAT-CATATTA
1 TATAATTTATACATATTA
* * *
1308854 AATTATTTTTACATATTA
1 TATAATTTATACATATTA
1308872 TATAATTTATA-ATA-TA
1 TATAATTTATACATATTA
1308888 TATAATT
1 TATAATT
1308895 AATAGACTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
16 9 0.27
17 9 0.27
18 15 0.45
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (18 bp):
TATAATTTATACATATTA
Found at i:1311920 original size:12 final size:12
Alignment explanation
Indices: 1311903--1311928 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1311893 TTGTTCATTG
1311903 TTATTTTTTTAT
1 TTATTTTTTTAT
1311915 TTATTTTTTTAT
1 TTATTTTTTTAT
1311927 TT
1 TT
1311929 TGATTTGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTATTTTTTTAT
Found at i:1312592 original size:3 final size:3
Alignment explanation
Indices: 1312579--1312608 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1312569 TTATCATCTT
1312579 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
1312609 TTAATTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1312723 original size:4 final size:4
Alignment explanation
Indices: 1312712--1312758 Score: 78
Period size: 4 Copynumber: 11.8 Consensus size: 4
1312702 TTCTTTCATT
1312712 TTTA -TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTT
1312759 TTCTTTCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 3 0.07
4 34 0.83
5 4 0.10
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Done.