Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold46
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: 2524624
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 119418 characters in sequence are not A, C, G, or T
File 7 of 15
Found at i:1024569 original size:21 final size:23
Alignment explanation
Indices: 1024535--1024578 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
1024525 TATCGATCGT
*
1024535 AAATATGAACAAAAGAGA-ATTG
1 AAATATGAAAAAAAGAGAGATTG
*
1024557 AAAT-TGAAAAAAATAGAGATTG
1 AAATATGAAAAAAAGAGAGATTG
1024579 TAATGCTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.59, C:0.02, G:0.18, T:0.20
Consensus pattern (23 bp):
AAATATGAAAAAAAGAGAGATTG
Found at i:1025815 original size:28 final size:28
Alignment explanation
Indices: 1025761--1025815 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
1025751 TTGCTATATA
*
1025761 AAAATCATATTCAAAGATCAAATCAAAAC
1 AAAATCATATTC-AAGATCAAAACAAAAC
1025790 AAAATCATATCTC-AGATCAAAACAAA
1 AAAATCATAT-TCAAGATCAAAACAAA
1025816 GAAATCTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 12 0.50
29 10 0.42
30 2 0.08
ACGTcount: A:0.58, C:0.18, G:0.04, T:0.20
Consensus pattern (28 bp):
AAAATCATATTCAAGATCAAAACAAAAC
Found at i:1027409 original size:14 final size:14
Alignment explanation
Indices: 1027377--1027416 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1027367 ATGAACAGTG
1027377 ATGAATAGTGATAC
1 ATGAATAGTGATAC
* *
1027391 ATGAACAGTGATAT
1 ATGAATAGTGATAC
*
1027405 GTGAATAGTGAT
1 ATGAATAGTGAT
1027417 GAACAGTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (14 bp):
ATGAATAGTGATAC
Found at i:1031260 original size:21 final size:21
Alignment explanation
Indices: 1031221--1031260 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1031211 AGCCATTTCT
* *
1031221 TCATTTTCATCAACCTCTTGA
1 TCATCTTCATCAACATCTTGA
*
1031242 TCATCTTCATCATCATCTT
1 TCATCTTCATCAACATCTT
1031261 CTTGAATGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.30, G:0.03, T:0.45
Consensus pattern (21 bp):
TCATCTTCATCAACATCTTGA
Found at i:1032880 original size:20 final size:20
Alignment explanation
Indices: 1032855--1032908 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
1032845 ATTTGGGACA
1032855 ATGTATCGATACAAT-T-CTTC
1 ATGTATCGATACAATGTGC--C
1032875 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTGCC
1032895 ATGTATCGATACAA
1 ATGTATCGATACAA
1032909 ATAGTGGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTGCC
Found at i:1039989 original size:15 final size:15
Alignment explanation
Indices: 1039971--1040005 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1039961 CGAGTCAACT
1039971 TCATCATTATCATCA
1 TCATCATTATCATCA
*
1039986 TCATCATTATCTTCA
1 TCATCATTATCATCA
1040001 TCATC
1 TCATC
1040006 TTTGATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:1041372 original size:98 final size:96
Alignment explanation
Indices: 1041086--1041423 Score: 446
Period size: 98 Copynumber: 3.5 Consensus size: 96
1041076 ATTGAAAAAT
* * *
1041086 GGGGTTAGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCAATGATGACAATTTAATCGAA
1 GGGGTTAGAGTATCCCCTCGGAGGAATAGGGTTGGAGTGTCCCCGATGATGATAATTTAAT-GAA
* * * *
1041151 AATAAGATTTAAATTTTAATAAGTTTAAAAAC
65 AATAAGATTTAAACTTTGATATGTTTAAAAGC
* * *
1041183 GGGGTTGGAGGATCCCATCGGAGGAAT-GGGATTGGAGTGTCCCCGATG-TGATAATTTAAATGA
1 GGGGTTAGAGTATCCCCTCGGAGGAATAGGG-TTGGAGTGTCCCCGATGATGATAATTT-AATGA
*
1041246 GAATAAGATTTAAACTTTGATATGTTTAAAAGC
64 AAATAAGATTTAAACTTTGATATGTTTAAAAGC
* * * *
1041279 GGGGTTGGAGTATCCCCTTGGAGGAATAGGGTTAGAGTGTCACCCGATGATGATAATTTAAGTAA
1 GGGGTTAGAGTATCCCCTCGGAGGAATAGGGTTGGAGTGTC-CCCGATGATGATAATTTAA-TGA
* *
1041344 AAATAAGACTTAAACTTTGATGTGTTTAAAAGC
64 AAATAAGATTTAAACTTTGATATGTTTAAAAGC
* *
1041377 GGGGTTAGAGTATCCCCTCGGAGGAATAGAGTTGGAGTATCCCCGAT
1 GGGGTTAGAGTATCCCCTCGGAGGAATAGGGTTGGAGTGTCCCCGAT
1041424 TAATAAATTT
Statistics
Matches: 212, Mismatches: 23, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
96 74 0.35
97 61 0.29
98 77 0.36
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (96 bp):
GGGGTTAGAGTATCCCCTCGGAGGAATAGGGTTGGAGTGTCCCCGATGATGATAATTTAATGAAA
ATAAGATTTAAACTTTGATATGTTTAAAAGC
Found at i:1045905 original size:13 final size:13
Alignment explanation
Indices: 1045887--1045911 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1045877 CTATTTATGA
1045887 TGTATCGATACAC
1 TGTATCGATACAC
1045900 TGTATCGATACA
1 TGTATCGATACA
1045912 TGAATAGTGA
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1045986 original size:23 final size:23
Alignment explanation
Indices: 1045946--1045991 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1045936 TAACGATACA
* *
1045946 TGAATAGTGATATGTGAATAGTG
1 TGAATAGTGACATATGAATAGTG
*
1045969 TGAATAGTGACCTATGAATAGTG
1 TGAATAGTGACATATGAATAGTG
1045992 ATGTATCGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (23 bp):
TGAATAGTGACATATGAATAGTG
Found at i:1046014 original size:21 final size:21
Alignment explanation
Indices: 1045989--1046029 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1045979 CCTATGAATA
1045989 GTGATGTATCGATACATGAAG
1 GTGATGTATCGATACATGAAG
1046010 GTGATGTATCGATACATGAA
1 GTGATGTATCGATACATGAA
1046030 CAGTGATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
GTGATGTATCGATACATGAAG
Found at i:1046143 original size:53 final size:53
Alignment explanation
Indices: 1046079--1046215 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
1046069 CTACTACCAA
1046079 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATAACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATAACC
* **
1046132 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATAACC
1046185 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
1046216 TATGCAATCT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 66 0.84
54 13 0.16
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATAACC
Found at i:1046248 original size:20 final size:20
Alignment explanation
Indices: 1046185--1046255 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1046175 GCCAATGTCC
**
1046185 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
1046205 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
1046225 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
1046245 TGTATCGATAC
1 TGTATCGATAC
1046256 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:1046321 original size:21 final size:21
Alignment explanation
Indices: 1046295--1046335 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1046285 GTCAACCTTG
1046295 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
1046316 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
1046336 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:1046812 original size:20 final size:20
Alignment explanation
Indices: 1046787--1046841 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1046777 GTTTAGGACA
* *
1046787 ATGTATCGATATAATTCTTT
1 ATGTATCGATACAATTCTTC
1046807 ATGTATCGATACAATTCTTC
1 ATGTATCGATACAATTCTTC
*
1046827 ATGTATAGATACAAT
1 ATGTATCGATACAAT
1046842 GTGCCATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACAATTCTTC
Found at i:1051860 original size:21 final size:21
Alignment explanation
Indices: 1051821--1051860 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1051811 AGCCATTTCT
* *
1051821 TCATTTTCATCAACCTCTTGA
1 TCATCTTCATCAACATCTTGA
*
1051842 TCATCTTCATCATCATCTT
1 TCATCTTCATCAACATCTT
1051861 CTCGAATGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.30, G:0.03, T:0.45
Consensus pattern (21 bp):
TCATCTTCATCAACATCTTGA
Found at i:1053517 original size:13 final size:13
Alignment explanation
Indices: 1053499--1053524 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1053489 TACTATTCAC
1053499 ATGTATCAAAACA
1 ATGTATCAAAACA
1053512 ATGTATCAAAACA
1 ATGTATCAAAACA
1053525 TGAATAGTAA
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:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
ATGTATCAAAACA
Found at i:1053573 original size:14 final size:14
Alignment explanation
Indices: 1053534--1053560 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1053524 ATGAATAGTA
1053534 ATGAATAGTGATAC
1 ATGAATAGTGATAC
1053548 ATGAATAGTGATA
1 ATGAATAGTGATA
1053561 TGTGAACAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.30
Consensus pattern (14 bp):
ATGAATAGTGATAC
Found at i:1053683 original size:32 final size:33
Alignment explanation
Indices: 1053642--1053706 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
1053632 ACAATTCATC
*
1053642 ATGTATCGATACTAAG-AACATGTATTGATACA
1 ATGTATCGATACTAAGCAACATGTATCGATACA
*
1053674 ATGTATCGATACTAAGCAATATGTATCGATACA
1 ATGTATCGATACTAAGCAACATGTATCGATACA
1053707 TCTAGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (33 bp):
ATGTATCGATACTAAGCAACATGTATCGATACA
Found at i:1055355 original size:37 final size:36
Alignment explanation
Indices: 1055314--1055422 Score: 107
Period size: 37 Copynumber: 2.9 Consensus size: 36
1055304 AATAAATATT
1055314 TTATTATTTAATATAAATATAATTTAATCATTT-TAAA
1 TTATTATTTAATATAAATATAATTTAAT-ATTTAT-AA
* * *
1055351 TTATTATTCAATATAAAAATAATTT--TATTTATAT
1 TTATTATTTAATATAAATATAATTTAATATTTATAA
*
1055385 TTCATTATTTAATATAAATACATATTTAAATTATTTAT
1 TT-ATTATTTAATATAAATATA-ATTT-AA-TATTTAT
1055423 TATATACACA
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
34 7 0.12
35 18 0.31
36 4 0.07
37 23 0.39
40 7 0.12
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (36 bp):
TTATTATTTAATATAAATATAATTTAATATTTATAA
Found at i:1055436 original size:28 final size:26
Alignment explanation
Indices: 1055388--1055439 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
1055378 TTTATATTTC
*
1055388 ATTATTTAATATAAATACATATTTAA
1 ATTATTTAATATAAACACATATTTAA
*
1055414 ATTATTTATTATATACACACATATTT
1 ATTATTTA--ATATAAACACATATTT
1055440 TAGTTTGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
28 14 0.64
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTATTTAATATAAACACATATTTAA
Found at i:1055818 original size:24 final size:20
Alignment explanation
Indices: 1055782--1055836 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
1055772 ATACATGTTC
*
1055782 ATTGTATCGATACATAATCA
1 ATTGTATCGATACATACTCA
1055802 ATTGTATCGATACATACTCA
1 ATTGTATCGATACATACTCA
1055822 ATTGTATCGATACAT
1 ATTGTATCGATACAT
1055837 GAAACTGGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATACTCA
Found at i:1055904 original size:33 final size:32
Alignment explanation
Indices: 1055867--1055929 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
1055857 TATCACATTT
*
1055867 TGTATTGATACATG-GCACATTGTATCGATATAG
1 TGTATCGATACATGAG-A-ATTGTATCGATATAG
1055900 TGTATCGATACATGAAGAATTGTATCGATA
1 TGTATCGATACATG-AGAATTGTATCGATA
1055930 CATTATGCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 25 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATGAGAATTGTATCGATATAG
Found at i:1064371 original size:13 final size:13
Alignment explanation
Indices: 1064353--1064392 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
1064343 ACATTATGCT
1064353 TTGTATCGATACA
1 TTGTATCGATACA
1064366 TTGTATCGATACA
1 TTGTATCGATACA
*
1064379 TTGTATCAATACA
1 TTGTATCGATACA
1064392 T
1 T
1064393 ACTTAATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1067207 original size:13 final size:13
Alignment explanation
Indices: 1067189--1067213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1067179 CATAAAGTGT
1067189 TGTATCGATACAA
1 TGTATCGATACAA
1067202 TGTATCGATACA
1 TGTATCGATACA
1067214 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1067211 original size:33 final size:33
Alignment explanation
Indices: 1067169--1067235 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1067159 TTCAATGATT
1067169 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1067202 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1067235 T
1 T
1067236 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1067294 original size:13 final size:13
Alignment explanation
Indices: 1067276--1067300 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1067266 ATTACTCAAA
1067276 TGTATCGATACAT
1 TGTATCGATACAT
1067289 TGTATCGATACA
1 TGTATCGATACA
1067301 CTGATCTTTG
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:1067365 original size:52 final size:52
Alignment explanation
Indices: 1067309--1067437 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
1067299 CACTGATCTT
*
1067309 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
1067361 TGTATCGATACATGCAGGCAAATTTGCCCAGATTTATCGATACACTATTACA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1067413 TGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1067438 TCATATTTTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1069579 original size:27 final size:27
Alignment explanation
Indices: 1069549--1069617 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
1069539 TTTATTCATC
1069549 GGGGACACTCCAACCCCATTCTTCCGA
1 GGGGACACTCCAACCCCATTCTTCCGA
1069576 GGGGACACTCCAACCCCATTCTTCCGA
1 GGGGACACTCCAACCCCATTCTTCCGA
*
1069603 GGGGATACTCCAACC
1 GGGGACACTCCAACC
1069618 TCGTTTTCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.23, C:0.39, G:0.20, T:0.17
Consensus pattern (27 bp):
GGGGACACTCCAACCCCATTCTTCCGA
Found at i:1076202 original size:20 final size:20
Alignment explanation
Indices: 1076156--1076230 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
1076146 TTTTAACTAG
* *
1076156 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTCAAAA
* * * *
1076176 ATATATCAATACATTCATAC
1 ATGTATCGATACATTCAAAA
* *
1076196 ATGTATCGATATATTGAAAA
1 ATGTATCGATACATTCAAAA
1076216 ATGTATCGATACATT
1 ATGTATCGATACATT
1076231 TGGGTAAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTCAAAA
Found at i:1076899 original size:28 final size:29
Alignment explanation
Indices: 1076782--1077231 Score: 475
Period size: 28 Copynumber: 15.3 Consensus size: 29
1076772 TTTTTTTTTA
* *
1076782 AAAAAGGTGCCACTAACTTATGTGGGCCTTT-
1 AAAAGGGTGCCACTGAC-T-TGTGGG-CTTTG
* *
1076813 AAAAGAGTTGCCACCGACTCGTGTGGGCTTTG
1 AAAAG-GGTGCCACTGACT--TGTGGGCTTTG
* * * *
1076845 AAAAGAGTTACCATTGGCTTGTGGGCTTT-
1 AAAAG-GGTGCCACTGACTTGTGGGCTTTG
*
1076874 AAAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* * * *
1076903 -GAAGGTTGCCACTGATTTGTGTGTACTTTG
1 AAAAGGGTGCCACTGACTTGTG-G-GCTTTG
* * *
1076933 AAAAGAGTTGCCACCGACTCGTGTAGGCTTTG
1 AAAAG-GGTGCCACTGACT--TGTGGGCTTTG
* *
1076965 AAAAGAGTTCCACTGACTTGTGGGCTTT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1076993 AAAAAGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1077022 AAAAGAGTTGCCACCGACTCGTGTGGGCTTTG
1 AAAAG-GGTGCCACTGACT--TGTGGGCTTTG
*
1077054 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1077083 AAAA-GGTACCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
1077111 -AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1077139 AAAGGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
1077168 AAAGGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
1077197 -AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
1077225 -AAAGGGT
1 AAAAGGGT
1077232 TTGAACGTTC
Statistics
Matches: 358, Mismatches: 45, Indels: 35
0.82 0.10 0.08
Matches are distributed among these distances:
27 3 0.01
28 138 0.39
29 90 0.25
30 25 0.07
31 31 0.09
32 67 0.19
33 1 0.00
34 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.29
Consensus pattern (29 bp):
AAAAGGGTGCCACTGACTTGTGGGCTTTG
Found at i:1077052 original size:89 final size:87
Alignment explanation
Indices: 1076783--1077227 Score: 490
Period size: 89 Copynumber: 5.0 Consensus size: 87
1076773 TTTTTTTTAA
* * *
1076783 AAAAG-GTGCCACTAACTTATGTGGGCCTTTAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAA
1 AAAAGAGTGCCACTGAC-T-TGTGGG-CTTTAAAA-AGGTGCCACTGACT--TGTGGGCTTTGAA
* * *
1076847 AAGAGTTACCATTGGCTTGTGGGCTTT-
60 AAGAGTTGCCACTGACTTGTGGGCTTTG
* * ** * *
1076874 AAAAGGGTGCCACTAACTTGTGGGCTTT-GGAAGGTTGCCACTGATTTGTGTGTACTTTGAAAAG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTAAAAAGG-TGCCACTGACTTGTG-G-GCTTTGAAAAG
* *
1076938 AGTTGCCACCGACTCGTGTAGGCTTTG
63 AGTTGCCACTGACT--TGTGGGCTTTG
* *
1076965 AAAAGAGTTCCACTGACTTGTGGGCTTTAAAAAGGTGCCACTAACTTGTGGGCTTTGAAAAGAGT
1 AAAAGAGTGCCACTGACTTGTGGGCTTTAAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGT
*
1077030 TGCCACCGACTCGTGTGGGCTTTG
66 TGCCACTGACT--TGTGGGCTTTG
* * *
1077054 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTACCACTGACTTGTGGGCTTTG-AAAG-GG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTAAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGT
1077117 TGCCACTGACTTGTGGGCTTTG
66 TGCCACTGACTTGTGGGCTTTG
* * **
1077139 AAAGGGGTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTG-AAAG-G
1 AAAAGAGTGCCACTGACTTGTGGGCTTT-AAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAG
*
1077202 GTGCCACTGACTTGTGGGCTTTG
65 TTGCCACTGACTTGTGGGCTTTG
1077225 AAA
1 AAA
1077228 GGGTTTGAAC
Statistics
Matches: 313, Mismatches: 32, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
85 37 0.12
86 60 0.19
87 14 0.04
88 34 0.11
89 93 0.30
90 16 0.05
91 44 0.14
92 15 0.05
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.29
Consensus pattern (87 bp):
AAAAGAGTGCCACTGACTTGTGGGCTTTAAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGT
TGCCACTGACTTGTGGGCTTTG
Found at i:1078492 original size:27 final size:26
Alignment explanation
Indices: 1078462--1078517 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
1078452 TTTTTTGCTA
*
1078462 TTTTTTCTTGTTTTTTTTTTGTTTTGT
1 TTTTTTCTTGTTTTTTTTCTGTTTT-T
*
1078489 TTTTTTTTTGTTTTTTTTCTGTTTTT
1 TTTTTTCTTGTTTTTTTTCTGTTTTT
1078515 TTT
1 TTT
1078518 AGGTGTAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.88
Consensus pattern (26 bp):
TTTTTTCTTGTTTTTTTTCTGTTTTT
Found at i:1078513 original size:16 final size:16
Alignment explanation
Indices: 1078469--1078506 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1078459 CTATTTTTTC
1078469 TTGTTTTTTTTTTGTT
1 TTGTTTTTTTTTTGTT
1078485 TTGTTTTTTTTTTGTT
1 TTGTTTTTTTTTTGTT
1078501 TT-TTTT
1 TTGTTTT
1078507 CTGTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (16 bp):
TTGTTTTTTTTTTGTT
Found at i:1078515 original size:11 final size:11
Alignment explanation
Indices: 1078472--1078517 Score: 67
Period size: 11 Copynumber: 4.3 Consensus size: 11
1078462 TTTTTTCTTG
1078472 TTTTT-TTTTT
1 TTTTTGTTTTT
*
1078482 GTTTTGTTTTT
1 TTTTTGTTTTT
1078493 TTTTTGTTTTT
1 TTTTTGTTTTT
*
1078504 TTTCTGTTTTT
1 TTTTTGTTTTT
1078515 TTT
1 TTT
1078518 AGGTGTAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
10 4 0.12
11 28 0.88
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (11 bp):
TTTTTGTTTTT
Found at i:1088253 original size:19 final size:20
Alignment explanation
Indices: 1088229--1088272 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1088219 AAATAATAGG
* *
1088229 AATGAATAGCAA-GAAAAAA
1 AATGAACAGCAATCAAAAAA
*
1088248 AATGAACATCAATCAAAAAA
1 AATGAACAGCAATCAAAAAA
1088268 AATGA
1 AATGA
1088273 CCCTTTCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.66, C:0.09, G:0.11, T:0.14
Consensus pattern (20 bp):
AATGAACAGCAATCAAAAAA
Found at i:1092567 original size:20 final size:20
Alignment explanation
Indices: 1092493--1092564 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
1092483 AAAAAGACAT
*
1092493 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTGAAA
* * * *
1092513 AATATATTGATACATTCATA
1 AATGTATCGATACATTGAAA
* *
1092533 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGAAA
1092553 AATGTATCGATA
1 AATGTATCGATA
1092565 TATCTGGGTA
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:1092889 original size:50 final size:50
Alignment explanation
Indices: 1092814--1092998 Score: 257
Period size: 50 Copynumber: 3.7 Consensus size: 50
1092804 TTTCACGGTT
*
1092814 TGTATCGATACATTCTTCATTGTATCGATACTTTCT-GTGTTTTACCTAGA
1 TGTATCGATACATTCTTCATTGTATCGATACATTCTAG-GTTTTACCTAGA
* * * *
1092864 TGTATCGATATATTATTCATTGTATCGATACATTCTAGGTATTACCCAGA
1 TGTATCGATACATTCTTCATTGTATCGATACATTCTAGGTTTTACCTAGA
* *
1092914 TGTATCGATACATTCTTCATTGTATCGATACACTCTAGATTTTACCTAGA
1 TGTATCGATACATTCTTCATTGTATCGATACATTCTAGGTTTTACCTAGA
* *
1092964 TGTATCGATACATT-TCTCAATGTATCTATACATTC
1 TGTATCGATACATTCT-TCATTGTATCGATACATTC
1092999 AGGCATTTTT
Statistics
Matches: 119, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
49 1 0.01
50 117 0.98
51 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (50 bp):
TGTATCGATACATTCTTCATTGTATCGATACATTCTAGGTTTTACCTAGA
Found at i:1092988 original size:100 final size:100
Alignment explanation
Indices: 1092814--1092998 Score: 284
Period size: 100 Copynumber: 1.9 Consensus size: 100
1092804 TTTCACGGTT
** * *
1092814 TGTATCGATACATTCTTCATTGTATCGATACTTTCTGTGTTTTACCTAGATGTATCGATATATTA
1 TGTATCGATACATTCTTCATTGTATCGATACACTCTGTATTTTACCTAGATGTATCGATACATTA
*
1092879 TTCATTGTATCGATACATTCTAGGTATTACCCAGA
66 TTCAATGTATCGATACATTCTAGGTATTACCCAGA
1092914 TGTATCGATACATTCTTCATTGTATCGATACACTCTAG-ATTTTACCTAGATGTATCGATACATT
1 TGTATCGATACATTCTTCATTGTATCGATACACTCT-GTATTTTACCTAGATGTATCGATACATT
*
1092978 -TCTCAATGTATCTATACATTC
65 AT-TCAATGTATCGATACATTC
1092999 AGGCATTTTT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
99 1 0.01
100 75 0.97
101 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (100 bp):
TGTATCGATACATTCTTCATTGTATCGATACACTCTGTATTTTACCTAGATGTATCGATACATTA
TTCAATGTATCGATACATTCTAGGTATTACCCAGA
Found at i:1095806 original size:31 final size:31
Alignment explanation
Indices: 1095737--1095808 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
1095727 CCCTAATCAC
1095737 GTCAATTTTCATCTTTATAATCTTCGCTCAT
1 GTCAATTTTCATCTTTATAATCTTCGCTCAT
* *
1095768 GTTAATTTTCATCTTTGTAATCTTCGCTCAAT
1 GTCAATTTTCATCTTTATAATCTTCGCTC-AT
1095800 -TCAATTTTC
1 GTCAATTTTC
1095809 TTCATAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 35 0.95
32 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.07, T:0.50
Consensus pattern (31 bp):
GTCAATTTTCATCTTTATAATCTTCGCTCAT
Found at i:1096115 original size:78 final size:78
Alignment explanation
Indices: 1096021--1096234 Score: 279
Period size: 78 Copynumber: 2.7 Consensus size: 78
1096011 ATTTTTCATC
* * *
1096021 ATTGGGGATACTCCAACCCCATTATTTCTGAGGGATACTTCAACCCCGATTTTATTTCTAAGACA
1 ATTGGGGATATTCCAACCCCGTTATTTCTGAGGGATACTTCAACCCCGATTTTATTTCTAAAACA
1096086 TCGATTTTCCACA
66 TCGATTTTCCACA
* * *
1096099 ATTGGAGATATTCCAACTCCGTTATTTCTGAGGGGATACTCCAA-CCCGATTTTATTTCTAAAAC
1 ATTGGGGATATTCCAACCCCGTTATTTCTGA-GGGATACTTCAACCCCGATTTTATTTCTAAAAC
**
1096163 ATCGATTTTTTACA
65 ATCGATTTTCCACA
* * * *
1096177 ATCGGGGATATTTCAATCCCGTTATTTTTGAAGGGATAC-TCTAACCCCGATTTTATTT
1 ATTGGGGATATTCCAACCCCGTTATTTCTG-AGGGATACTTC-AACCCCGATTTTATTT
1096235 TCAAATACCG
Statistics
Matches: 117, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
77 1 0.01
78 91 0.78
79 25 0.21
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (78 bp):
ATTGGGGATATTCCAACCCCGTTATTTCTGAGGGATACTTCAACCCCGATTTTATTTCTAAAACA
TCGATTTTCCACA
Found at i:1096247 original size:78 final size:77
Alignment explanation
Indices: 1096024--1096264 Score: 247
Period size: 78 Copynumber: 3.1 Consensus size: 77
1096014 TTTCATCATT
* *
1096024 GGGGATACTCCAACCCCATTATTTCTG-AGGGATACT-TCAACCCCGATTTTA-TTTCTAAGACA
1 GGGGATATTCCAA-CCCGTTATTTCTGAAGGGATACTCT-AACCCCGATTTTATTTTC-AA-ACA
*
1096086 TCGATTTTCCACAATT
62 TCGATTTTCCACAATC
* * * *
1096102 GGAGATATTCCAACTCCGTTATTTCTGAGGGGATACTCCAA-CCCGATTTTATTTCTAAAACATC
1 GGGGATATTCCAAC-CCGTTATTTCTGAAGGGATACTCTAACCCCGATTTTATTT-TCAAACATC
**
1096166 GATTTTTTACAATC
64 GATTTTCCACAATC
* * * *
1096180 GGGGATATTTCAATCCCGTTATTTTTGAAGGGATACTCTAACCCCGATTTTATTTTCAAATACCG
1 GGGGATATTCCAA-CCCGTTATTTCTGAAGGGATACTCTAACCCCGATTTTATTTTCAAACATCG
* *
1096245 ATTGTCCACCATC
65 ATTTTCCACAATC
*
1096258 AGGGATA
1 GGGGATA
1096265 CTCTATCCTT
Statistics
Matches: 134, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
77 1 0.01
78 104 0.78
79 28 0.21
80 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.34
Consensus pattern (77 bp):
GGGGATATTCCAACCCGTTATTTCTGAAGGGATACTCTAACCCCGATTTTATTTTCAAACATCGA
TTTTCCACAATC
Found at i:1102384 original size:28 final size:30
Alignment explanation
Indices: 1102326--1102385 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
1102316 GCAACCTTTC
* * *
1102326 TTCAAAGTCCATGACTTAGTGGCATCTCTT
1 TTCAAAGTCCACGACTTAGTGGCACCCCTT
1102356 TTCAAAGTCCACGAC-T-GTGGCACCCCTT
1 TTCAAAGTCCACGACTTAGTGGCACCCCTT
1102384 TT
1 TT
1102386 AGCCTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 12 0.44
29 1 0.04
30 14 0.52
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (30 bp):
TTCAAAGTCCACGACTTAGTGGCACCCCTT
Found at i:1102523 original size:62 final size:62
Alignment explanation
Indices: 1102414--1103020 Score: 765
Period size: 62 Copynumber: 9.8 Consensus size: 62
1102404 AAGCTGGACA
**
1102414 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGTGCCCTGTT-GTCCTCAAAGAGTAGGATG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCT-TTAGTCCTCAAAGAGTAGGATG
* * **
1102476 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAAAATAGGACA
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGATG
* * * * *
1102538 TCTTTTTCTTTTTCAGAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG
1 CCTTTTTC-TTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGATG
* * * * * *
1102601 TCTTTTTCTTTTCAAAACCCACATGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGACG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGATG
* * ** * *
1102663 CCTTTTTTTTTTC-AAGCCCACATGAGTTGGTGGCTTCCTTTAGTCCTCAAAGAGCAAGATG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGATG
* *
1102724 CCTTTTTCTTTTCAAAGCCCACACAAGTT--TGGC-GCCTTTAGTCCTCAAAGAGTAGGATG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGATG
* * * * * *
1102783 CTTTTTTCTTTTCAAAGCTCATACGAGTTGGTGGTACCCTTTAGTCCTTAAAGAGCAGGATG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGATG
* * * * *
1102845 ACTTTTCCTTTTCAAAGCCCATACGAATTGGTGGCACCCTTTACTCCTCAAAGAGTAGGATG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGATG
* * * *
1102907 CCTTTTCCTTTTCAAAGTCTACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGGGTAGGATG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGATG
* * * *
1102969 CCTTTTTCTTTTCAAAGCCTATACGAGTTGGTGGTACACTTTAGTCCTCAAA
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAA
1103021 AAGCAGGACA
Statistics
Matches: 480, Mismatches: 59, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
59 48 0.10
60 4 0.01
61 61 0.13
62 311 0.65
63 56 0.12
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (62 bp):
CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGGATG
Found at i:1103142 original size:43 final size:42
Alignment explanation
Indices: 1103007--1103328 Score: 337
Period size: 43 Copynumber: 7.6 Consensus size: 42
1102997 TGGTGGTACA
* * *
1103007 CTTTAGTCCTCAAAAAGCAGGACACATTTCATTTCCTTTTTTTTC
1 CTTT-GTCCTCAAAGAGCAGGACGCACTTCATTT-C-TTTTTTTC
*
1103052 CTTTGTCCTCAAAGAGCAGGATGCAC-T-ATTT-TTTTTCTT-
1 CTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCTTTTT-TTC
* * *
1103091 CTTTGTCCTCAAAAAGTAGGACGCACTTCATTTCTTTCTTTTT
1 CTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCTTT-TTTTC
* * * * *
1103134 TTTTGTCCTCAAAGGGCAAGACACATTTCATTTCTTTCTTTTCC
1 CTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCTTT-TTTT-C
* *
1103178 CTTTGTCCTTAAAGAGCAGGACGCACTTTATTTCTTTTTTTC
1 CTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCTTTTTTTC
* * * *
1103220 CTTTGTCCTTAAAGAGTAGGATGCACTTCATTTCCTTCTTTTC
1 CTTTGTCCTCAAAGAGCAGGACGCACTTCATTT-CTTTTTTTC
* * *
1103263 CTTTGTCCTCAAAGAGCAAGACACACTTCATTTCCTTTTTTC
1 CTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCTTTTTTTC
* *
1103305 CTTTGTCCTCGAAGAACAGGACGC
1 CTTTGTCCTCAAAGAGCAGGACGC
1103329 GTTCTTTTTC
Statistics
Matches: 232, Mismatches: 37, Indels: 19
0.81 0.13 0.07
Matches are distributed among these distances:
39 28 0.12
40 3 0.01
41 4 0.02
42 67 0.29
43 78 0.34
44 48 0.21
45 4 0.02
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.41
Consensus pattern (42 bp):
CTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCTTTTTTTC
Found at i:1103268 original size:129 final size:124
Alignment explanation
Indices: 1103007--1103328 Score: 421
Period size: 129 Copynumber: 2.5 Consensus size: 124
1102997 TGGTGGTACA
* *
1103007 CTTTAGTCCTCAAAAAGCAGGACACATTTCATTTCCTTTTTTTTCCTTTGTCCTCAAAGAGCAGG
1 CTTT-GTCCTCAAAGAGCAAGACACATTTCATTT-C-TTTTTTTCCTTTGTCCTCAAAGAGCAGG
* * *
1103072 ATGCACTATTTTTTTTCTTCTTTGTCCTCAAAAAGTAGGACGCACTTCATTTCTTTCTTTTT
63 ACGCACTATTTTTTTTCTTCTTTGTCCTCAAAAAGTAGGACGCACTTCATTTCCTTCTTTTC
* * *
1103134 TTTTGTCCTCAAAGGGCAAGACACATTTCATTTCTTTCTTTTCCCTTTGTCCTTAAAGAGCAGGA
1 CTTTGTCCTCAAAGAGCAAGACACATTTCATTTCTTT-TTTT-CCTTTGTCCTCAAAGAGCAGGA
* * *
1103199 CGCACTTTATTTCTTTTT-TTCCTTTGTCCTTAAAGAGTAGGATGCACTTCATTTCCTTCTTTTC
64 CGCAC--TATTT-TTTTTCTT-CTTTGTCCTCAAAAAGTAGGACGCACTTCATTTCCTTCTTTTC
* * * *
1103263 CTTTGTCCTCAAAGAGCAAGACACACTTCATTTCCTTTTTTCCTTTGTCCTCGAAGAACAGGACG
1 CTTTGTCCTCAAAGAGCAAGACACATTTCATTTCTTTTTTTCCTTTGTCCTCAAAGAGCAGGACG
1103328 C
66 C
1103329 GTTCTTTTTC
Statistics
Matches: 171, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
124 3 0.02
125 5 0.03
126 51 0.30
127 25 0.15
128 11 0.06
129 76 0.44
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.41
Consensus pattern (124 bp):
CTTTGTCCTCAAAGAGCAAGACACATTTCATTTCTTTTTTTCCTTTGTCCTCAAAGAGCAGGACG
CACTATTTTTTTTCTTCTTTGTCCTCAAAAAGTAGGACGCACTTCATTTCCTTCTTTTC
Found at i:1103360 original size:35 final size:36
Alignment explanation
Indices: 1103294--1103383 Score: 94
Period size: 35 Copynumber: 2.5 Consensus size: 36
1103284 CACACTTCAT
* * * *
1103294 TTCCTTTTTTCC-TTTGTCCTCGAAGAACAGGACGCG
1 TTCC-TTTTTCCTTTTATCCCCAAAGAACAGGACACG
* *
1103330 TT-CTTTTTCCTTTTATCCCCAAAGACCAGGACACT
1 TTCCTTTTTCCTTTTATCCCCAAAGAACAGGACACG
*
1103365 TTCCTTTTTCTTTTTATCC
1 TTCCTTTTTCCTTTTATCC
1103384 TTTGTACCCA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
34 7 0.16
35 21 0.47
36 17 0.38
ACGTcount: A:0.17, C:0.29, G:0.11, T:0.43
Consensus pattern (36 bp):
TTCCTTTTTCCTTTTATCCCCAAAGAACAGGACACG
Found at i:1106649 original size:13 final size:13
Alignment explanation
Indices: 1106631--1106655 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1106621 CAATTCATCA
1106631 TGTATCGATACAT
1 TGTATCGATACAT
1106644 TGTATCGATACA
1 TGTATCGATACA
1106656 ATGTGCCACG
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:1106737 original size:20 final size:19
Alignment explanation
Indices: 1106709--1106755 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1106699 TAGTTTCATA
* *
1106709 TATCAATACAATTGTACATG
1 TATCAATAC-AGTGAACATG
*
1106729 TATCGATACAGTGAACATG
1 TATCAATACAGTGAACATG
1106748 TATCAATA
1 TATCAATA
1106756 TAATGTATCG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (19 bp):
TATCAATACAGTGAACATG
Found at i:1110351 original size:21 final size:18
Alignment explanation
Indices: 1110305--1110355 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 18
1110295 TAGCGATACA
1110305 TTGTATCGATACAACACT
1 TTGTATCGATACAACACT
*
1110323 TATGTATCGATACATTTACTCT
1 T-TGTATCGATACA---ACACT
1110345 TTGTATCGATA
1 TTGTATCGATA
1110356 AAAATTGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 1 0.04
19 12 0.43
21 10 0.36
22 5 0.18
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (18 bp):
TTGTATCGATACAACACT
Found at i:1110421 original size:21 final size:20
Alignment explanation
Indices: 1110395--1110433 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
1110385 GTTGGGACCT
1110395 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
1110416 TGTATCGATACATTTAGA
1 TGTATCGATACATTTAGA
1110434 TAAAAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:1114364 original size:13 final size:13
Alignment explanation
Indices: 1114346--1114371 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1114336 TACACAAAGT
1114346 ATGTATCGATACA
1 ATGTATCGATACA
1114359 ATGTATCGATACA
1 ATGTATCGATACA
1114372 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:1120374 original size:20 final size:20
Alignment explanation
Indices: 1120348--1120427 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
1120338 AATGTCCAAA
1120348 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
* * *
1120368 GTGTATCGATACATATGGAAATTCA
1 ATGTATCGATAC--AT-G--TTTCT
*
1120393 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATGTTTCT
*
1120413 TTGTATCGATACATG
1 ATGTATCGATACATG
1120428 GTATCGATAC
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
20 27 0.59
22 2 0.04
23 3 0.07
25 14 0.30
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:1120433 original size:13 final size:13
Alignment explanation
Indices: 1120414--1120451 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
1120404 CATTTTTCTT
1120414 TGTATCGATACA-
1 TGTATCGATACAC
1120426 TGGTATCGATACAC
1 T-GTATCGATACAC
1120440 TGTATCGATACA
1 TGTATCGATACA
1120452 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 1 0.04
13 22 0.92
14 1 0.04
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1120615 original size:20 final size:20
Alignment explanation
Indices: 1120572--1120617 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1120562 AAATCTTTTG
1120572 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1120593 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1120613 CAAAA
1 CAAAA
1120618 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1122259 original size:11 final size:11
Alignment explanation
Indices: 1122243--1122267 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1122233 GTATGTGCAA
1122243 ATAAATTTTTG
1 ATAAATTTTTG
1122254 ATAAATTTTTG
1 ATAAATTTTTG
1122265 ATA
1 ATA
1122268 TGTGTGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (11 bp):
ATAAATTTTTG
Found at i:1123040 original size:13 final size:13
Alignment explanation
Indices: 1123022--1123047 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1123012 TACACAAAGT
1123022 ATGTATCGATACA
1 ATGTATCGATACA
1123035 ATGTATCGATACA
1 ATGTATCGATACA
1123048 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:1128711 original size:33 final size:33
Alignment explanation
Indices: 1128669--1128733 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1128659 TTAGAAGCAA
*
1128669 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCGATACAATAT-ACCATGTATCGATACAT
1128702 TGTATCGATACAATATACCATGTATCGATACA
1 TGTATCGATACAATATACCATGTATCGATACA
1128734 AACAGTGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAATATACCATGTATCGATACAT
Found at i:1128732 original size:13 final size:13
Alignment explanation
Indices: 1128689--1128713 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1128679 CAATTCATCA
1128689 TGTATCGATACAT
1 TGTATCGATACAT
1128702 TGTATCGATACA
1 TGTATCGATACA
1128714 ATATACCATG
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:1128805 original size:19 final size:20
Alignment explanation
Indices: 1128762--1128811 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
1128752 CTGGCAGTTT
* *
1128762 CATGTATCGATACAATTGTA
1 CATGTATCGATACAAGTGAA
1128782 CATGTATCGATAC-AGTGAA
1 CATGTATCGATACAAGTGAA
1128801 CATGTATCGAT
1 CATGTATCGAT
1128812 GCAAAGCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAAGTGAA
Found at i:1132998 original size:32 final size:34
Alignment explanation
Indices: 1132935--1133008 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 34
1132925 GAGTTCCCTT
*
1132935 GAAAAATGACAAAAAAAAAGTCAAAAGCAAAAGCAC
1 GAAAAATGA-AAAAAAAAAG-CAAAAACAAAAGCAC
*
1132971 GAAAAATG-AAAAAAAAAG-AAAAACAAAAGGAC
1 GAAAAATGAAAAAAAAAAGCAAAAACAAAAGCAC
*
1133003 AAAAAA
1 GAAAAA
1133009 AAGTGCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 17 0.49
34 10 0.29
36 8 0.23
ACGTcount: A:0.73, C:0.09, G:0.14, T:0.04
Consensus pattern (34 bp):
GAAAAATGAAAAAAAAAAGCAAAAACAAAAGCAC
Found at i:1134516 original size:33 final size:33
Alignment explanation
Indices: 1134460--1134889 Score: 247
Period size: 33 Copynumber: 13.6 Consensus size: 33
1134450 TTCATGACTC
*
1134460 CGTGGCA-CTTTTT-TTTTCAAAGTCCACAACTT
1 CGTGGCACCTTTTTCTTTT-TAAGTCCACAACTT
*
1134492 CATGGCACCTTTTTCTTTTTAAGTCCACAA-TT
1 CGTGGCACCTTTTTCTTTTTAAGTCCACAACTT
*
1134524 CCATGGCACCTTTTTTCTTTTTAAGTCCACAACTT
1 -CGTGGCACC-TTTTTCTTTTTAAGTCCACAACTT
** *
1134559 CGTGGCACC-----CTTTCAAAGTCCACATC-T
1 CGTGGCACCTTTTTCTTTTTAAGTCCACAACTT
* ** *
1134586 CTATGGCACCTTTTTC-TTCAAAGTCCACAACTC
1 C-GTGGCACCTTTTTCTTTTTAAGTCCACAACTT
** ** *
1134619 CGTGGCACGGTTTTCTTTCAAAGTCCATAAC-T
1 CGTGGCACCTTTTTCTTTTTAAGTCCACAACTT
*
1134651 CTGTGGCACC-----CTTTTTAAGTTCACAAC-T
1 C-GTGGCACCTTTTTCTTTTTAAGTCCACAACTT
* * * *
1134679 CTGTGGTACATTTTTCTTTTAAAGTCCACAACTC
1 C-GTGGCACCTTTTTCTTTTTAAGTCCACAACTT
1134713 CGTGGCA-C-----CTTTTTAAGTCCACAAC-T
1 CGTGGCACCTTTTTCTTTTTAAGTCCACAACTT
* * * * *
1134739 CTGTGGTACCTTTTTCTTTTAAAGTTCACGATTT
1 C-GTGGCACCTTTTTCTTTTTAAGTCCACAACTT
*
1134773 CGTGGCACC-----CTTTTCAAGTCCACAAC-T
1 CGTGGCACCTTTTTCTTTTTAAGTCCACAACTT
* *
1134800 CTGTGGCACCCTTTTTCTTTTTAAGCCCATAACTT
1 C-GTGGCA-CCTTTTTCTTTTTAAGTCCACAACTT
* * *
1134835 GGTGGCACCTTTTTTCTTTTTAGGCCCACAAC-T
1 CGTGGCACC-TTTTTCTTTTTAAGTCCACAACTT
* *
1134868 CTATGGTACCTTTTTCTTTTTA
1 C-GTGGCACCTTTTTCTTTTTA
1134890 TGCCTATAAC
Statistics
Matches: 313, Mismatches: 47, Indels: 75
0.72 0.11 0.17
Matches are distributed among these distances:
26 1 0.00
27 25 0.08
28 63 0.20
29 2 0.01
32 34 0.11
33 103 0.33
34 82 0.26
35 3 0.01
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.39
Consensus pattern (33 bp):
CGTGGCACCTTTTTCTTTTTAAGTCCACAACTT
Found at i:1134544 original size:34 final size:34
Alignment explanation
Indices: 1134462--1134567 Score: 148
Period size: 34 Copynumber: 3.2 Consensus size: 34
1134452 CATGACTCCG
**
1134462 TGGCA-CTTTTTT-TTTCAAAGTCCACAACTTCA
1 TGGCACCTTTTTTCTTTTTAAGTCCACAACTTCA
1134494 TGGCACC-TTTTTCTTTTTAAGTCCACAA-TTCCA
1 TGGCACCTTTTTTCTTTTTAAGTCCACAACTT-CA
*
1134527 TGGCACCTTTTTTCTTTTTAAGTCCACAACTTCG
1 TGGCACCTTTTTTCTTTTTAAGTCCACAACTTCA
1134561 TGGCACC
1 TGGCACC
1134568 CTTTCAAAGT
Statistics
Matches: 66, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
32 12 0.18
33 23 0.35
34 29 0.44
35 2 0.03
ACGTcount: A:0.21, C:0.27, G:0.11, T:0.41
Consensus pattern (34 bp):
TGGCACCTTTTTTCTTTTTAAGTCCACAACTTCA
Found at i:1134693 original size:93 final size:94
Alignment explanation
Indices: 1134474--1134720 Score: 284
Period size: 93 Copynumber: 2.6 Consensus size: 94
1134464 GCACTTTTTT
* ** * * **
1134474 TTTCAAAGTCCACAACT-TCATGGCACCTTTTTCTTTTTAAGTCCACAATTCCATGGCACCTTTT
1 TTTCAAAGTCCACAACTCT-ATGGCACATTTTTCTTTCAAAGTCCACAACTCCGTGGCA-CGGTT
**
1134538 TTCTTTTTAAGTCCACAACTTCGTGGCACCC
64 TTCTTTCAAAGTCCACAACTTCGTGGCACCC
* *
1134569 TTTCAAAGTCCACATCTCTATGGCACCTTTTTC-TTCAAAGTCCACAACTCCGTGGCACGGTTTT
1 TTTCAAAGTCCACAACTCTATGGCACATTTTTCTTTCAAAGTCCACAACTCCGTGGCACGGTTTT
*
1134633 CTTTCAAAGTCCATAAC-TCTGTGGCACCC
66 CTTTCAAAGTCCACAACTTC-GTGGCACCC
** * * * *
1134662 TTTTTAAGTTCACAACTCTGTGGTACATTTTTCTTTTAAAGTCCACAACTCCGTGGCAC
1 TTTCAAAGTCCACAACTCTATGGCACATTTTTCTTTCAAAGTCCACAACTCCGTGGCAC
1134721 CTTTTTAAGT
Statistics
Matches: 131, Mismatches: 18, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
92 2 0.02
93 54 0.41
94 44 0.34
95 30 0.23
96 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.13, T:0.36
Consensus pattern (94 bp):
TTTCAAAGTCCACAACTCTATGGCACATTTTTCTTTCAAAGTCCACAACTCCGTGGCACGGTTTT
CTTTCAAAGTCCACAACTTCGTGGCACCC
Found at i:1134703 original size:61 final size:61
Alignment explanation
Indices: 1134606--1134924 Score: 306
Period size: 61 Copynumber: 5.1 Consensus size: 61
1134596 TTTTTCTTCA
* * ** *
1134606 AAGTCCACAACTCCGTGGCACGGTTTTCTTTCAAAGTCCATAACTCTGTGGCACCCTTTTT
1 AAGTCCACAACTCTGTGGTACCTTTTTCTTTTAAAGTCCATAACTCTGTGGCACCCTTTTT
* * * *
1134667 AAGTTCACAACTCTGTGGTACATTTTTCTTTTAAAGTCCACAACTCCGTGGCA-CCTTTTT
1 AAGTCCACAACTCTGTGGTACCTTTTTCTTTTAAAGTCCATAACTCTGTGGCACCCTTTTT
* ** * *
1134727 AAGTCCACAACTCTGTGGTACCTTTTTCTTTTAAAGTTCACGA-TTTCGTGGCACCCTTTTC
1 AAGTCCACAACTCTGTGGTACCTTTTTCTTTTAAAGTCCATAACTCT-GTGGCACCCTTTTT
* * *
1134788 AAGTCCACAACTCTGTGGCACCCTTTTTCTTTTTAAGCCCATAACT-TGGTGGCACCTTTTTTCT
1 AAGTCCACAACTCTGTGGTA-CCTTTTTCTTTTAAAGTCCATAACTCT-GTGGCACC------CT
1134852 TTTT
58 TTTT
* * * * * *
1134856 AGGCCCACAACTCTATGGTACCTTTTTCTTTTTATG-CCTATAACTCTGTGGC-CCCTTGTT
1 AAGTCCACAACTCTGTGGTACCTTTTTCTTTTAAAGTCC-ATAACTCTGTGGCACCCTTTTT
1134916 AAGTCCACA
1 AAGTCCACA
1134925 TAACCCGATC
Statistics
Matches: 215, Mismatches: 31, Indels: 25
0.79 0.11 0.09
Matches are distributed among these distances:
59 1 0.00
60 64 0.30
61 70 0.33
62 27 0.13
63 1 0.00
66 4 0.02
67 26 0.12
68 22 0.10
ACGTcount: A:0.20, C:0.27, G:0.14, T:0.38
Consensus pattern (61 bp):
AAGTCCACAACTCTGTGGTACCTTTTTCTTTTAAAGTCCATAACTCTGTGGCACCCTTTTT
Found at i:1134754 original size:121 final size:122
Alignment explanation
Indices: 1134606--1134848 Score: 301
Period size: 121 Copynumber: 2.0 Consensus size: 122
1134596 TTTTTCTTCA
* * *
1134606 AAGTCCACAACTCCGTGGCACGGTTTTCTTTCAAAGTCCATAA-CTCTGTGGCACCCTTTTTAAG
1 AAGTCCACAACTCCGTGGCACCGTTTTCTTTCAAAGTCCACAATCTC-GTGGCACCCTTTTCAAG
* * *
1134670 TTCACAACTCTGTGGTA-CATTTTTCTTTTAAAGTCCACAACTCCGTGGCACCTTTTT
65 TCCACAACTCTGTGGCACCATTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
* * * * * * *
1134727 AAGTCCACAACTCTGTGGTACCTTTTTCTTTTAAAGTTCACGATTTCGTGGCACCCTTTTCAAGT
1 AAGTCCACAACTCCGTGGCACCGTTTTCTTTCAAAGTCCACAATCTCGTGGCACCCTTTTCAAGT
* * * **
1134792 CCACAACTCTGTGGCACCCTTTTTCTTTTTAAGCCCATAACTTGGTGGCACCTTTTT
66 CCACAACTCTGTGGCACCATTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
1134849 TCTTTTTAGG
Statistics
Matches: 102, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
121 66 0.65
122 36 0.35
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (122 bp):
AAGTCCACAACTCCGTGGCACCGTTTTCTTTCAAAGTCCACAATCTCGTGGCACCCTTTTCAAGT
CCACAACTCTGTGGCACCATTTTTCTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
Found at i:1134840 original size:34 final size:34
Alignment explanation
Indices: 1134782--1134912 Score: 142
Period size: 34 Copynumber: 3.9 Consensus size: 34
1134772 TCGTGGCACC
* * *
1134782 CTTTTCAAGTCCACAACTCTGTGGCACCCTTTTT
1 CTTTTTAAGCCCATAACTCTGTGGCACCCTTTTT
*
1134816 CTTTTTAAGCCCATAACT-TGGTGGCACCTTTTTT
1 CTTTTTAAGCCCATAACTCT-GTGGCACCCTTTTT
* * * *
1134850 CTTTTTAGGCCCACAACTCTATGGTA-CCTTTTT
1 CTTTTTAAGCCCATAACTCTGTGGCACCCTTTTT
* *
1134883 CTTTTTATGCCTATAACTCTGTGGC-CCCTT
1 CTTTTTAAGCCCATAACTCTGTGGCACCCTT
1134913 GTTAAGTCCA
Statistics
Matches: 80, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
33 31 0.39
34 48 0.60
35 1 0.01
ACGTcount: A:0.17, C:0.28, G:0.13, T:0.42
Consensus pattern (34 bp):
CTTTTTAAGCCCATAACTCTGTGGCACCCTTTTT
Found at i:1134956 original size:32 final size:31
Alignment explanation
Indices: 1134920--1134990 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 31
1134910 CTTGTTAAGT
* *
1134920 CCACATAACCCGATCGTAACCCTTTCTAAAGC
1 CCACACAACCCGATCGCAACCCTTT-TAAAGC
** * *
1134952 CCACACAAGTCGGTGGCAACCCTTTTAAAGC
1 CCACACAACCCGATCGCAACCCTTTTAAAGC
1134983 CCACACAA
1 CCACACAA
1134991 GTCGGTGGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 14 0.42
32 19 0.58
ACGTcount: A:0.32, C:0.37, G:0.13, T:0.18
Consensus pattern (31 bp):
CCACACAACCCGATCGCAACCCTTTTAAAGC
Found at i:1135021 original size:64 final size:64
Alignment explanation
Indices: 1134942--1135062 Score: 199
Period size: 64 Copynumber: 1.9 Consensus size: 64
1134932 ATCGTAACCC
*
1134942 TTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTT-TAAAGCCCACACAAGTCGGTGGTAACTCT
1 TTTCTAAAGCCCACACAAGTCGATGGCAA-CCTTTCTAAAGCCCACACAAGTCGGTGGTAACTCT
* *
1135006 TTTCTAAAGGCCACACAAGTCGATGGCAATCTTTCTAAAGCCCACACAAGTCGGTGG
1 TTTCTAAAGCCCACACAAGTCGATGGCAACCTTTCTAAAGCCCACACAAGTCGGTGG
1135063 CAACCCCTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
63 4 0.08
64 49 0.92
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (64 bp):
TTTCTAAAGCCCACACAAGTCGATGGCAACCTTTCTAAAGCCCACACAAGTCGGTGGTAACTCT
Found at i:1135078 original size:31 final size:32
Alignment explanation
Indices: 1134937--1135075 Score: 201
Period size: 31 Copynumber: 4.4 Consensus size: 32
1134927 ACCCGATCGT
1134937 AACCCTTTCTAAAGCCCACACAAGTCGGTGGC
1 AACCCTTTCTAAAGCCCACACAAGTCGGTGGC
*
1134969 AACCCTTT-TAAAGCCCACACAAGTCGGTGGT
1 AACCCTTTCTAAAGCCCACACAAGTCGGTGGC
* * *
1135000 AACTCTTTTCTAAAGGCCACACAAGTCGATGGC
1 AAC-CCTTTCTAAAGCCCACACAAGTCGGTGGC
*
1135033 AA-TCTTTCTAAAGCCCACACAAGTCGGTGGC
1 AACCCTTTCTAAAGCCCACACAAGTCGGTGGC
*
1135064 AACCCCTTCTAA
1 AACCCTTTCTAA
1135076 GCCTAATGTC
Statistics
Matches: 93, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
31 52 0.56
32 19 0.20
33 22 0.24
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.22
Consensus pattern (32 bp):
AACCCTTTCTAAAGCCCACACAAGTCGGTGGC
Found at i:1135375 original size:52 final size:52
Alignment explanation
Indices: 1135231--1136037 Score: 350
Period size: 52 Copynumber: 15.6 Consensus size: 52
1135221 AATCCTTGTT
* * * * * *
1135231 ATCTGTAAGTCCATTGTCGCTGGTCTTGAATCAGCATATTGGCATTCTTCTC
1 ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATTCTTATC
* ** * * *
1135283 AAAT-TTTAAGTCTAATATCACTGGCCTTGAATTAGTACATTGGCATTCTTATC
1 --ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATTCTTATC
* * * * * *
1135336 ATTTTTAAGTCCAATGTCGTTGGCCTTAAATCAGCACATTGGCATTTTTCTC
1 ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATTCTTATC
* * * * *
1135388 ATCTTTAAGTCCGATATCGTTGGCCGTGAGTCAACATATTGGCACAT-TTATC
1 ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCA-TTCTTATC
* * * * * * *
1135440 ATCTTTAAGTCCGATATCATTGGCCGTGAGTCAACATATTAGCACAT-TTATC
1 ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCA-TTCTTATC
* * ** * * *
1135492 ATTTTTAAGTCCGATATCACTAGCCTTGAATCAGCGTATTGGTA-TCTTTAT-
1 ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATTC-TTATC
* * ** * * * * * ** *
1135543 TTTTTTAAACCCAATGTCGTTGCCCTTTAATCAGCACATTAGCACAC-TCT-
1 ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATTCTTATC
* * * * * * *
1135593 GTCTTTAAGTCTAATATTGTTGGCCTTGAATAAGCATATTAGCACTTTTTATT
1 ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCA-TTCTTATC
* * * * * * *
1135646 ATCTTTAAG-CCCATTTCATTGGCCTTGGATCAGCACATTGGCATTTTTCTC
1 ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATTCTTATC
* * *** * * * *
1135697 ATCTTTAAGTCCGATATCATTGGTAGTGAGTCAACATATTGGGA-CCTTTATC
1 ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATTC-TTATC
* * * * * *
1135749 ATTTTTAAGTTCGATATCGCTGGCCTTGAATTAGCATATTGGCA-CCTT-TAC
1 ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATTCTTAT-C
* ** * * * **
1135800 TTTCTTTAAACCCAATGTCGTTAGCCTTGAATCAGCACATTGGCACAC-T-TC
1 -ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATTCTTATC
* * * * * * *
1135851 ATCTTTGAGTCCAATATCGCTAGCCTTTAATCAGTATATTGGCATTTTTTATT
1 ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCA-TTCTTATC
* ** * * * * *
1135904 ATCTTTGAG-CCTAACGTCGCTGGCCTT-AGGTCAGCACATTGGCATTTTTCTC
1 ATCTTTAAGTCC-AATATCGTTGGCCTTGA-ATCAGCATATTGGCATTCTTATC
* *** * * * * *
1135956 ATCTCTAAGTTTGATATCATTGGCCATGAGTCAACATATTGGC-TCCTTTATC
1 ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATTC-TTATC
* * * * *
1136008 ATTTTTAGGTCTAATGTTGTTGGCCTTGAA
1 ATCTTTAAGTCCAATATCGTTGGCCTTGAA
1136038 ACATCACATT
Statistics
Matches: 567, Mismatches: 165, Indels: 44
0.73 0.21 0.06
Matches are distributed among these distances:
50 72 0.13
51 52 0.09
52 357 0.63
53 84 0.15
54 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (52 bp):
ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATTCTTATC
Found at i:1135877 original size:50 final size:52
Alignment explanation
Indices: 1135762--1135894 Score: 137
Period size: 50 Copynumber: 2.6 Consensus size: 52
1135752 TTTAAGTTCG
* * *
1135762 ATATCGCTGGCCTTGAATTAGCATATTGGCACCTTTACTTTCTTTAAACCCA
1 ATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTACTATCTTTAAACCCA
* * * * **
1135814 ATGTCGTTAGCCTTGAATCAGCACATTGGCACAC-TT-C-ATCTTTGAGTCCA
1 ATATCGCTAGCCTTGAATCAGCATATTGGCAC-CTTTACTATCTTTAAACCCA
* *
1135864 ATATCGCTAGCCTTTAATCAGTATATTGGCA
1 ATATCGCTAGCCTTGAATCAGCATATTGGCA
1135895 TTTTTTATTA
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
50 35 0.53
51 1 0.02
52 29 0.44
53 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.35
Consensus pattern (52 bp):
ATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTACTATCTTTAAACCCA
Found at i:1135988 original size:259 final size:257
Alignment explanation
Indices: 1135438--1136014 Score: 748
Period size: 258 Copynumber: 2.2 Consensus size: 257
1135428 GGCACATTTA
* * *
1135438 TCATCTTTAAGTCCGATATCATTGGCCGTGAGTCAACATATTAGCACATTTATCATTTTTAAGTC
1 TCATCTTTAAGTCCGATATCATTGGCCATGAGTCAACATATTGGCACCTTTATCATTTTTAAGTC
* * * *
1135503 CGATATCACTAGCCTTGAATCAGCGTATTGGTATCTTTATTTTTTTAAACCCAATGTCGTTGCCC
66 CGATATCACTAGCCTTGAATCAGCATATTGGCACCTTTATTTCTTTAAACCCAATGTCGTTGCCC
* * * * * *
1135568 TTTAATCAGCACATTAGCACACTCTGTCTTTAAGTCTAATATTGTTGGCCTTGAATAAGCATATT
131 TTGAATCAGCACATTAGCACACTCTATCTTTAAGTCCAATATCGCTAGCCTTGAATAAGCATATT
* ** *
1135633 AGCACTTTTTATTATCTTTAAGCCCATTTCATTGGCCTTGGATCAGCACATTGGCATTTTTC
196 AGCACTTTTTATTATCTTTAAGCCAACGTCACTGGCCTTGGATCAGCACATTGGCATTTTTC
* *
1135695 TCATCTTTAAGTCCGATATCATTGG-TAGTGAGTCAACATATTGGGACCTTTATCATTTTTAAGT
1 TCATCTTTAAGTCCGATATCATTGGCCA-TGAGTCAACATATTGGCACCTTTATCATTTTTAAGT
* * * *
1135759 TCGATATCGCTGGCCTTGAATTAGCATATTGGCACCTTTACTTTCTTTAAACCCAATGTCGTTAG
65 CCGATATCACTAGCCTTGAATCAGCATATTGGCACCTTTA-TTTCTTTAAACCCAATGTCGTT-G
* * * * *
1135824 -CCTTGAATCAGCACATTGGCACACT-TCATCTTTGAGTCCAATATCGCTAGCCTTTAATCAGTA
128 CCCTTGAATCAGCACATTAGCACACTCT-ATCTTTAAGTCCAATATCGCTAGCCTTGAATAAGCA
* * * *
1135887 TATTGGCATTTTTTATTATCTTTGAGCCTAACGTCGCTGGCCTTAGG-TCAGCACATTGGCATTT
192 TATTAGCACTTTTTATTATCTTTAAGCC-AACGTCACTGGCCTT-GGATCAGCACATTGGCATTT
1135951 TTC
255 TTC
* ** *
1135954 TCATCTCTAAGTTTGATATCATTGGCCATGAGTCAACATATTGGCTCCTTTATCATTTTTA
1 TCATCTTTAAGTCCGATATCATTGGCCATGAGTCAACATATTGGCACCTTTATCATTTTTA
1136015 GGTCTAATGT
Statistics
Matches: 275, Mismatches: 38, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
257 92 0.33
258 96 0.35
259 84 0.31
260 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.39
Consensus pattern (257 bp):
TCATCTTTAAGTCCGATATCATTGGCCATGAGTCAACATATTGGCACCTTTATCATTTTTAAGTC
CGATATCACTAGCCTTGAATCAGCATATTGGCACCTTTATTTCTTTAAACCCAATGTCGTTGCCC
TTGAATCAGCACATTAGCACACTCTATCTTTAAGTCCAATATCGCTAGCCTTGAATAAGCATATT
AGCACTTTTTATTATCTTTAAGCCAACGTCACTGGCCTTGGATCAGCACATTGGCATTTTTC
Found at i:1136034 original size:259 final size:257
Alignment explanation
Indices: 1135438--1136037 Score: 733
Period size: 259 Copynumber: 2.3 Consensus size: 257
1135428 GGCACATTTA
* * *
1135438 TCATCTTTAAGTCCGATATCATTGGCCGTGAGTCAACATATTAGCACATTTATCATTTTTAAGTC
1 TCATCTTTAAGTCCGATATCATTGGCCATGAGTCAACATATTGGCACCTTTATCATTTTTAAGTC
* * * * * * *
1135503 CGATATCACTAGCCTTGAATCAGCGTATTGGTATCTTTATTTTTTTAAACCCAATGTCGTTGCCC
66 TGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATTTCTTTAAACCCAATGTCGTTGCCC
* * * * * *
1135568 TTTAATCAGCACATTAGCACACTCTGTCTTTAAGTCTAATATTGTTGGCCTTGAATAAGCATATT
131 TTGAATCAGCACATTAGCACACTCTATCTTTAAGTCCAATATCGCTAGCCTTGAATAAGCATATT
* ** *
1135633 AGCACTTTTTATTATCTTTAAGCCCATTTCATTGGCCTTGGATCAGCACATTGGCATTTTTC
196 AGCACTTTTTATTATCTTTAAGCCAACGTCACTGGCCTTGGATCAGCACATTGGCATTTTTC
* *
1135695 TCATCTTTAAGTCCGATATCATTGG-TAGTGAGTCAACATATTGGGACCTTTATCATTTTTAAGT
1 TCATCTTTAAGTCCGATATCATTGGCCA-TGAGTCAACATATTGGCACCTTTATCATTTTTAAGT
*
1135759 -TCGATATCGCTGGCCTTGAATTAGCATATTGGCACCTTTACTTTCTTTAAACCCAATGTCGTTA
65 CT-GATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA-TTTCTTTAAACCCAATGTCGTT-
* * * * *
1135823 G-CCTTGAATCAGCACATTGGCACACT-TCATCTTTGAGTCCAATATCGCTAGCCTTTAATCAGT
127 GCCCTTGAATCAGCACATTAGCACACTCT-ATCTTTAAGTCCAATATCGCTAGCCTTGAATAAGC
* * * *
1135886 ATATTGGCATTTTTTATTATCTTTGAGCCTAACGTCGCTGGCCTTAGG-TCAGCACATTGGCATT
191 ATATTAGCACTTTTTATTATCTTTAAGCC-AACGTCACTGGCCTT-GGATCAGCACATTGGCATT
1135950 TTTC
254 TTTC
* ** * *
1135954 TCATCTCTAAGTTTGATATCATTGGCCATGAGTCAACATATTGGCTCCTTTATCATTTTTAGGTC
1 TCATCTTTAAGTCCGATATCATTGGCCATGAGTCAACATATTGGCACCTTTATCATTTTTAAGTC
* * * *
1136019 TAATGTTGTTGGCCTTGAA
66 TGATATCGCTGGCCTTGAA
1136038 ACATCACATT
Statistics
Matches: 291, Mismatches: 43, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
257 91 0.31
258 96 0.33
259 100 0.34
260 4 0.01
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (257 bp):
TCATCTTTAAGTCCGATATCATTGGCCATGAGTCAACATATTGGCACCTTTATCATTTTTAAGTC
TGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATTTCTTTAAACCCAATGTCGTTGCCC
TTGAATCAGCACATTAGCACACTCTATCTTTAAGTCCAATATCGCTAGCCTTGAATAAGCATATT
AGCACTTTTTATTATCTTTAAGCCAACGTCACTGGCCTTGGATCAGCACATTGGCATTTTTC
Found at i:1136731 original size:20 final size:21
Alignment explanation
Indices: 1136699--1136769 Score: 83
Period size: 20 Copynumber: 3.4 Consensus size: 21
1136689 ACAATTTGTT
*
1136699 TCGATACAATAAGGCAATGTA
1 TCGATACAATAAGGAAATGTA
1136720 TCGATA-AATAAGGAAATGTA
1 TCGATACAATAAGGAAATGTA
***
1136740 TCGATAC-ATGCCTGAAATGTA
1 TCGATACAAT-AAGGAAATGTA
1136761 TCGATACAA
1 TCGATACAA
1136770 GCCATGTGGC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
20 21 0.49
21 21 0.49
22 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (21 bp):
TCGATACAATAAGGAAATGTA
Found at i:1136827 original size:20 final size:21
Alignment explanation
Indices: 1136802--1136848 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
1136792 TATTATATAA
1136802 ATACATTAA-AAAATGTATCG
1 ATACATTAAGAAAATGTATCG
*
1136822 ATACA-TAAGAAATTGTATCG
1 ATACATTAAGAAAATGTATCG
1136842 ATACATT
1 ATACATT
1136849 TCTCATTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 3 0.12
20 20 0.83
21 1 0.04
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (21 bp):
ATACATTAAGAAAATGTATCG
Found at i:1144523 original size:20 final size:21
Alignment explanation
Indices: 1144498--1144551 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1144488 TTTTGCCTAG
* *
1144498 ATGTATCAATACAT-CCTTGA
1 ATGTATCGATACATGCCTTAA
1144518 ATGTATCGATACATGCCTTAA
1 ATGTATCGATACATGCCTTAA
*
1144539 ATATATCGATACA
1 ATGTATCGATACA
1144552 AGGTCCTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATGCCTTAA
Found at i:1144635 original size:20 final size:20
Alignment explanation
Indices: 1144589--1144641 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
1144579 TTTAATAATT
*
1144589 TGTATCAATATAATAAGGCAA
1 TGTATCAATA-CATAAGGCAA
*
1144610 TATATCAATACATAAGTG-AA
1 TGTATCAATACATAAG-GCAA
*
1144630 TGTATCGATACA
1 TGTATCAATACA
1144642 GGACCATGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.30
Consensus pattern (20 bp):
TGTATCAATACATAAGGCAA
Found at i:1145164 original size:14 final size:14
Alignment explanation
Indices: 1145132--1145164 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1145122 CCATCCATAT
1145132 CTCAAC-CAAAACA
1 CTCAACACAAAACA
1145145 -TCAACACAAAACA
1 CTCAACACAAAACA
1145158 CTCAACA
1 CTCAACA
1145165 AAGATCCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.28
13 7 0.39
14 6 0.33
ACGTcount: A:0.55, C:0.36, G:0.00, T:0.09
Consensus pattern (14 bp):
CTCAACACAAAACA
Found at i:1151514 original size:14 final size:14
Alignment explanation
Indices: 1151495--1151522 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1151485 AGACATAAAA
1151495 CTCTTATTTTATGT
1 CTCTTATTTTATGT
1151509 CTCTTATTTTATGT
1 CTCTTATTTTATGT
1151523 TTAATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (14 bp):
CTCTTATTTTATGT
Found at i:1152906 original size:20 final size:20
Alignment explanation
Indices: 1152883--1152957 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
1152873 AAGTACCTAG
1152883 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1152903 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1152923 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1152943 ATGTATCGATACATT
1 ATGTATCGATACATT
1152958 CTATCTTTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1153895 original size:22 final size:22
Alignment explanation
Indices: 1153864--1153918 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1153854 AGCCTTTGAC
*
1153864 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTACTATGTTT
*
1153886 CATGCTTTTTTTTACTATGTTT
1 CATGCATTTTTTTACTATGTTT
1153908 CATGCATTTTT
1 CATGCATTTTT
1153919 AATATGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.16, C:0.13, G:0.09, T:0.62
Consensus pattern (22 bp):
CATGCATTTTTTTACTATGTTT
Found at i:1153896 original size:20 final size:21
Alignment explanation
Indices: 1153864--1153925 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
1153854 AGCCTTTGAC
*
1153864 CATGCATTTTTTTATTATGTTT
1 CATGC-TTTTTTTAATATGTTT
*
1153886 CATGCTTTTTTTTACTATGTTT
1 CATGC-TTTTTTTAATATGTTT
*
1153908 CATGC-ATTTTTAATATGT
1 CATGCTTTTTTTAATATGT
1153926 CCAGCATCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.31
22 25 0.69
ACGTcount: A:0.19, C:0.11, G:0.10, T:0.60
Consensus pattern (21 bp):
CATGCTTTTTTTAATATGTTT
Found at i:1156746 original size:3 final size:3
Alignment explanation
Indices: 1156738--1156778 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
1156728 CACTTGCTTT
* * *
1156738 TTC TTC TTC TTT TTC TTC ATC TTC TTC TTC TCC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1156779 GATGAAACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:1157366 original size:7 final size:8
Alignment explanation
Indices: 1157346--1157370 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1157336 ATATATTAAA
1157346 ATTTTTAT
1 ATTTTTAT
1157354 ATTTTTAT
1 ATTTTTAT
1157362 ATTTTTAT
1 ATTTTTAT
1157370 A
1 A
1157371 ATTAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
ATTTTTAT
Found at i:1157905 original size:11 final size:11
Alignment explanation
Indices: 1157889--1157914 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1157879 TTATATTGCC
1157889 AAAAAAAAGAA
1 AAAAAAAAGAA
1157900 AAAAAAAAGAA
1 AAAAAAAAGAA
1157911 AAAA
1 AAAA
1157915 CCATGAACCA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:1161533 original size:52 final size:52
Alignment explanation
Indices: 1161385--1161513 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1161375 CGAAATATGA
*
1161385 AAATTTGCGTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1161437 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1161489 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1161514 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:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1161540 original size:13 final size:13
Alignment explanation
Indices: 1161522--1161546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1161512 CAAAGATCAG
1161522 TGTATCGATACAA
1 TGTATCGATACAA
1161535 TGTATCGATACA
1 TGTATCGATACA
1161547 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1161613 original size:19 final size:18
Alignment explanation
Indices: 1161589--1161686 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
1161579 TAGCTTATAT
1161589 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1161608 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1161621 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1161640 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1161653 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
1161673 TGTATCGATACAAA
1 TGTATCGATACAAA
1161687 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1161626 original size:13 final size:13
Alignment explanation
Indices: 1161608--1161664 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1161598 ACAAAACTTA
1161608 TGTATCGATACAT
1 TGTATCGATACAT
1161621 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1161639 ATGTATCGATACAT
1 -TGTATCGATACAT
1161653 TGTATCGATACA
1 TGTATCGATACA
1161665 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1161628 original size:32 final size:32
Alignment explanation
Indices: 1161587--1161684 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
1161577 AGTAGCTTAT
*
1161587 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
1161619 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
1161651 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
1161684 A
1 A
1161685 AATCGTTGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 49 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:1162208 original size:20 final size:20
Alignment explanation
Indices: 1162180--1162333 Score: 161
Period size: 20 Copynumber: 7.7 Consensus size: 20
1162170 TACCCAGATA
* *
1162180 TATCAATACATTCTTGAATG
1 TATCGATACATTCTTAAATG
*
1162200 TATCGATACATGT-ATAAATG
1 TATCGATACAT-TCTTAAATG
* *
1162220 TATTGATACATTCTTGAATG
1 TATCGATACATTCTTAAATG
*
1162240 TATCGATACATGT-ATAAATG
1 TATCGATACAT-TCTTAAATG
* *
1162260 TATTGATACATTCTTGAATG
1 TATCGATACATTCTTAAATG
*
1162280 TATCGATACATGT-ATAAATG
1 TATCGATACAT-TCTTAAATG
* *
1162300 TATTGATACATTCTTCAATG
1 TATCGATACATTCTTAAATG
1162320 TATCGATACATTCT
1 TATCGATACATTCT
1162334 GTCTTTTTAC
Statistics
Matches: 109, Mismatches: 19, Indels: 12
0.78 0.14 0.09
Matches are distributed among these distances:
19 3 0.03
20 103 0.94
21 3 0.03
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (20 bp):
TATCGATACATTCTTAAATG
Found at i:1162240 original size:40 final size:40
Alignment explanation
Indices: 1162185--1162330 Score: 283
Period size: 40 Copynumber: 3.6 Consensus size: 40
1162175 AGATATATCA
1162185 ATACATTCTTGAATGTATCGATACATGTATAAATGTATTG
1 ATACATTCTTGAATGTATCGATACATGTATAAATGTATTG
1162225 ATACATTCTTGAATGTATCGATACATGTATAAATGTATTG
1 ATACATTCTTGAATGTATCGATACATGTATAAATGTATTG
1162265 ATACATTCTTGAATGTATCGATACATGTATAAATGTATTG
1 ATACATTCTTGAATGTATCGATACATGTATAAATGTATTG
*
1162305 ATACATTCTTCAATGTATCGATACAT
1 ATACATTCTTGAATGTATCGATACAT
1162331 TCTGTCTTTT
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 105 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.40
Consensus pattern (40 bp):
ATACATTCTTGAATGTATCGATACATGTATAAATGTATTG
Found at i:1162373 original size:20 final size:20
Alignment explanation
Indices: 1162348--1162398 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1162338 TTTTACCTAG
*
1162348 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
1162368 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
*
1162388 ATGTATTGATA
1 ATGTATCGATA
1162399 TATCTAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1175462 original size:59 final size:59
Alignment explanation
Indices: 1175312--1176578 Score: 1993
Period size: 59 Copynumber: 21.5 Consensus size: 59
1175302 CCTTCTGCTT
* **
1175312 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTATTAAAGCCCACACAAGTTGGTGGCATT
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1175371 TTCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TT-CAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1175431 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1175490 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* *
1175549 TTCAGTCTTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCGCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1175608 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1175667 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1175726 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
1175785 TCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
1175844 TTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1175903 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1175962 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
1176021 TTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACC
* * * ** *
1176081 TTTCCGTCCCCAAAAAGTAGGAC-CC----ATTTTAAAGCCCACACAAGTTGGTGGCA-C
1 -TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * **
1176135 TTCCCAGTCCTCAAAGAGCAGAACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGAATT
1 TT--CAGTCCTCAAAGAGCGGGACGCCTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1176197 TTCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TT-CAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
1176257 TTCAGTCCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1176316 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
1176375 TTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACC
* * * *
1176435 TTTTC-GTCCCCAAAAAGCAGGAC-CC----ATTTTAAAGCCCACACAAGTTGGTGGCA-C
1 --TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * **
1176489 TTCCCAGTCCTCAAAGAGCAGAACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGAATT
1 TT--CAGTCCTCAAAGAGCGGGACGCCTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1176551 TTCCAGTCCTCAAAGAGCGGGACGCCTT
1 TT-CAGTCCTCAAAGAGCGGGACGCCTT
1176579 AGAAAATCTC
Statistics
Matches: 1130, Mismatches: 53, Indels: 48
0.92 0.04 0.04
Matches are distributed among these distances:
52 2 0.00
53 2 0.00
54 3 0.00
55 76 0.07
56 12 0.01
59 758 0.67
60 138 0.12
61 132 0.12
62 7 0.01
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (59 bp):
TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:1179204 original size:51 final size:51
Alignment explanation
Indices: 1179136--1179459 Score: 254
Period size: 52 Copynumber: 6.4 Consensus size: 51
1179126 ATTCTCCAGC
*
1179136 AATCGGGGATA-TCCCAACTCCGATTTCATTTTCAAAACACTAA-TTTTCTAT
1 AATCGGGGATACT-CCAACTCCGATTTTATTTTCAAAACACTAATTTTTC-AT
* * *
1179187 AATCAGGGATACTCCAACTCTGATTTTA-TCTCTAAAACA-TCAATTTTTCAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACACT-AATTTTTCAT
* * * * *
1179238 --T-GGGAATACTCCAAC-CTCGACTTTATTTTCAAAATATTGATTTTTCAT
1 AATCGGGGATACTCCAACTC-CGATTTTATTTTCAAAACACTAATTTTTCAT
* * * * *
1179286 AATCGAGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTTTCAC
1 AATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACACTAA-TTTTTCAT
* * * * *
1179338 AATCGGGGATACTTCAAC-CCCAGTTTTATTTTCAAAACACCAATTTTCCTTT
1 AATCGGGGATACTCCAACTCCGA-TTTTATTTTCAAAACACTAATTTTTC-AT
* * * * * *
1179390 AATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAATACCATTTTTTCAC
1 AATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACACTAATTTTTCAT
*
1179442 AATCGAGGATACTCCAAC
1 AATCGGGGATACTCCAAC
1179460 CTCGTTATTT
Statistics
Matches: 216, Mismatches: 39, Indels: 35
0.74 0.13 0.12
Matches are distributed among these distances:
47 1 0.00
48 32 0.15
49 5 0.02
50 8 0.04
51 65 0.30
52 87 0.40
53 18 0.08
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.35
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTTCAT
Found at i:1179436 original size:104 final size:103
Alignment explanation
Indices: 1179135--1179460 Score: 330
Period size: 99 Copynumber: 3.2 Consensus size: 103
1179125 GATTCTCCAG
* *
1179135 CAATCGGGGATA-TCCCAACTCCGA-TTTCATTTTCAAAACACTAATTTTCTATAATCAGGGATA
1 CAATCGGGGATACT-CCAACCCCGACTTT-ATTTTCAAAACACTAATTTTCTATAATCGGGGATA
* *
1179198 CTCCAACTCTGATTTTATCTCTAAAACAT-CAATTTTT--
64 CTCCAACTCTGATTTTATTTCTAAAACATACATTTTTTCA
* * * * * * *
1179235 C-ATTGGGAATACTCCAACCTCGACTTTATTTTCAAAATATTGATTTT-TCATAATCGAGGATAC
1 CAATCGGGGATACTCCAACCCCGACTTTATTTTCAAAACACTAATTTTCT-ATAATCGGGGATAC
* * * *
1179298 TCCAACCCCGGTTTTATTGCTAAAACACTA-ATTTTTTCA
65 TCCAACTCTGATTTTATTTCTAAAACA-TACATTTTTTCA
* * * *
1179337 CAATCGGGGATACTTCAACCCC-AGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATA
1 CAATCGGGGATACTCCAACCCCGA-CTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGATA
*
1179401 CTCCAACTCTGATTTTATTTCCAAAA-ATACCATTTTTTCA
64 CTCCAACTCTGATTTTATTTCTAAAACATA-CATTTTTTCA
*
1179441 CAATCGAGGATACTCCAACC
1 CAATCGGGGATACTCCAACC
1179461 TCGTTATTTC
Statistics
Matches: 180, Mismatches: 33, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
98 1 0.01
99 67 0.37
100 12 0.07
102 4 0.02
103 36 0.20
104 59 0.33
105 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (103 bp):
CAATCGGGGATACTCCAACCCCGACTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACT
CCAACTCTGATTTTATTTCTAAAACATACATTTTTTCA
Found at i:1179494 original size:28 final size:27
Alignment explanation
Indices: 1179448--1179524 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 27
1179438 TCACAATCGA
1179448 GGATACTCCAA-CCTCGTTATTTC-ATTGG
1 GGATACTCCAACCCT-GTTATTTCGA--GG
1179476 GGATACTCCAACCCTGTTACTTTCGAGG
1 GGATACTCCAACCCTGTTA-TTTCGAGG
* * *
1179504 GAACACTCCAACCCCGTTATT
1 GGATACTCCAACCCTGTTATT
1179525 ATCTCCAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 2 0.05
28 33 0.77
29 7 0.16
30 1 0.02
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (27 bp):
GGATACTCCAACCCTGTTATTTCGAGG
Found at i:1191913 original size:1 final size:1
Alignment explanation
Indices: 1191907--1191966 Score: 57
Period size: 1 Copynumber: 60.0 Consensus size: 1
1191897 CATTCTCTTC
* * * * * * *
1191907 AAAAAAAGAAAAAAACAAAAACAAAAAAACAAAAAAACAAAACAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1191967 TCTGCTTAAG
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.88, C:0.08, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:1191920 original size:8 final size:8
Alignment explanation
Indices: 1191906--1191966 Score: 72
Period size: 8 Copynumber: 7.8 Consensus size: 8
1191896 ACATTCTCTT
1191906 CAAAAAAA
1 CAAAAAAA
*
1191914 GAAAAAAA
1 CAAAAAAA
1191922 C--AAAAA
1 CAAAAAAA
1191928 CAAAAAAA
1 CAAAAAAA
1191936 CAAAAAAA
1 CAAAAAAA
1191944 CAAAACAAA
1 CAAAA-AAA
*
1191953 AAAAAAAA
1 CAAAAAAA
*
1191961 GAAAAA
1 CAAAAA
1191967 TCTGCTTAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
6 6 0.13
8 33 0.72
9 7 0.15
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:1191932 original size:13 final size:12
Alignment explanation
Indices: 1191910--1191966 Score: 69
Period size: 13 Copynumber: 4.4 Consensus size: 12
1191900 TCTCTTCAAA
1191910 AAAAGAAAAAAAC
1 AAAA-AAAAAAAC
1191923 AAAAACAAAAAAAC
1 -AAAA-AAAAAAAC
1191937 AAAAAAACAAAAC
1 AAAAAAA-AAAAC
*
1191950 AAAAAAAAAAAG
1 AAAAAAAAAAAC
1191962 AAAAA
1 AAAAA
1191967 TCTGCTTAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
12 12 0.30
13 16 0.40
14 12 0.30
ACGTcount: A:0.88, C:0.09, G:0.04, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:1191932 original size:14 final size:13
Alignment explanation
Indices: 1191909--1191960 Score: 77
Period size: 14 Copynumber: 3.8 Consensus size: 13
1191899 TTCTCTTCAA
1191909 AAAAAGAAAAAAAC
1 AAAAA-AAAAAAAC
1191923 AAAAACAAAAAAAC
1 AAAAA-AAAAAAAC
*
1191937 AAAAAAACAAAAC
1 AAAAAAAAAAAAC
1191950 AAAAAAAAAAA
1 AAAAAAAAAAA
1191961 GAAAAATCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
13 17 0.49
14 18 0.51
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:1191965 original size:22 final size:22
Alignment explanation
Indices: 1191906--1191965 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
1191896 ACATTCTCTT
*
1191906 CAAAAAAAGAAAAAAACAAAAA
1 CAAAAAAAAAAAAAAACAAAAA
*
1191928 CAAAAAAACAAAAAAAC-AAAA
1 CAAAAAAAAAAAAAAACAAAAA
1191949 CAAAAAAAAAAAGAAAA
1 CAAAAAAAAAAA-AAAA
1191966 ATCTGCTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.43
22 20 0.57
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (22 bp):
CAAAAAAAAAAAAAAACAAAAA
Found at i:1193143 original size:59 final size:59
Alignment explanation
Indices: 1192929--1194114 Score: 1689
Period size: 59 Copynumber: 20.3 Consensus size: 59
1192919 CCTTCCGCTT
**
1192929 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATT
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
**
1192988 TTCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATT
1 TT-CAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
1193048 TTCCAGTCCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TT-CAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
1193108 TTCAGTCCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1193167 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
1193226 TTCAGTCCTCAAAGAGCGGGACGCCTTTTTTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1193285 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
1193344 TTCAGTCTTCAAAAAGCGGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1193403 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
1193462 TTCAGTCCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCACATAAGTTAGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
1193521 TTCAGTCCTTAAAGAGCGAGACGCCTTTTCTTTTAAAGCCCACAGAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
1193580 TTCAGTCCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
1193639 TTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACC
** * * *
1193699 TTTTTGTCCCCAAAGAGCAGGAC-CC----ATTTTAAAGCCCACACAAGTTGGTGGCA-C
1 -TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * **
1193753 TTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATT
1 TT--CAGTCCTCAAAGAGCGGGACGCCTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
1193815 TTCCAATCCTCAAAGAGCGGGATGCCTTTTCTTTTAAATCCCACACAAGTTGGTGGCACC
1 TT-CAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
1193875 TTCAGTCCTCAAAGAGAGGGACGCC-TTT-TTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * * **
1193932 TTTCAGTCCCCAAAGAGCAGGACACC-TTTC----AAAGCCCACATAAGTTGGTGACATT
1 -TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
1193987 TTCAAGTCCTCTAAGAGCAGGACACC---TC--TTAAAGCCCACACAAGTTGGTGGCACC
1 TTC-AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* *
1194042 TTTCAGTCCTCAAAGAGCAGGACGCC-TTTC----AAAGCCCACACAAGTTGGTGGCACTT
1 -TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-C
*
1194098 TTTAGTCCTCAAAGAGC
1 TTCAGTCCTCAAAGAGC
1194115 AGAATACACT
Statistics
Matches: 1040, Mismatches: 66, Indels: 46
0.90 0.06 0.04
Matches are distributed among these distances:
53 4 0.00
54 4 0.00
55 162 0.16
56 9 0.01
57 30 0.03
58 27 0.03
59 562 0.54
60 172 0.17
61 68 0.07
62 2 0.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (59 bp):
TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:1194987 original size:20 final size:20
Alignment explanation
Indices: 1194962--1195016 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1194952 GCCAAGGAAA
*
1194962 TGTATCGATACATTTTTCTG
1 TGTATCGATACATTTATCTG
** *
1194982 TGTATCGATACATGGATCTT
1 TGTATCGATACATTTATCTG
1195002 TGTATCGATACATTT
1 TGTATCGATACATTT
1195017 GGAAATTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTTATCTG
Found at i:1196684 original size:13 final size:13
Alignment explanation
Indices: 1196666--1196691 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1196656 TACACCAAGT
1196666 ATGTATCGATACA
1 ATGTATCGATACA
1196679 ATGTATCGATACA
1 ATGTATCGATACA
1196692 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:1196689 original size:32 final size:33
Alignment explanation
Indices: 1196648--1196711 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1196638 TAGCCAAACT
* **
1196648 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1196680 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1196712 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:1202879 original size:13 final size:13
Alignment explanation
Indices: 1202861--1202886 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1202851 ACATTTTTCT
1202861 TTGTATCGATACA
1 TTGTATCGATACA
1202874 TTGTATCGATACA
1 TTGTATCGATACA
1202887 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:1203050 original size:20 final size:20
Alignment explanation
Indices: 1203007--1203052 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1202997 AAATCTTTAG
1203007 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1203028 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1203048 CAAAA
1 CAAAA
1203053 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1205452 original size:13 final size:13
Alignment explanation
Indices: 1205434--1205459 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1205424 TACACCAAGT
1205434 ATGTATCGATACA
1 ATGTATCGATACA
1205447 ATGTATCGATACA
1 ATGTATCGATACA
1205460 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:1205457 original size:32 final size:33
Alignment explanation
Indices: 1205416--1205479 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1205406 TAGCCAAACT
* **
1205416 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1205448 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1205480 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:1207319 original size:51 final size:51
Alignment explanation
Indices: 1207258--1207547 Score: 265
Period size: 52 Copynumber: 5.7 Consensus size: 51
1207248 GATTCTCCGC
* *
1207258 AATCGGGGATA-TCCCAACTCCGATTTCATTTTCAAAACACTAATTTTCTAT
1 AATCGGGGATACT-CCAACCCCGATTTTATTTTCAAAACACTAATTTTCTAT
* *
1207309 AATCGAGGATACTCCAACTCCGATTTTA-TTTCTAAAACA-TCAATTTTC---
1 AATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACT-AATTTTCTAT
* * * * *
1207357 -ATCGGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTT-TCAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCT-AT
* * * *
1207407 AATCGGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACTAA-TTTTCTAT
* * *
1207459 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTT-CTAT
* * * * *
1207511 AATCGAGGATACTCCAACTCTGATTTTACTTCCAAAA
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAA
1207548 ATACCATTTT
Statistics
Matches: 197, Mismatches: 27, Indels: 29
0.78 0.11 0.11
Matches are distributed among these distances:
47 34 0.17
48 4 0.02
50 8 0.04
51 73 0.37
52 75 0.38
53 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (51 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTAT
Found at i:1207434 original size:98 final size:100
Alignment explanation
Indices: 1207257--1207581 Score: 320
Period size: 98 Copynumber: 3.2 Consensus size: 100
1207247 CGATTCTCCG
*
1207257 CAATCGGGGATA-TCCCAACTCCGATTTCATTTTCAAAACACTAATTTTCTATAATCGAGGATAC
1 CAATCGGGGATACT-CCAACCCCGATTT-ATTTTCAAAACACTAATTTTCTATAATCGAGGATAC
* *
1207321 TCCAACTCCGATTTTATTTCTAAAACA-TCAA-TTTT-
64 TCCAACCCCGATTTTATTGCTAAAACACT-AATTTTTC
* * * * *
1207356 C-ATCGGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTT-TCATAATCGGGGATAC
1 CAATCGGGGATACTCCAACCCCGA-TTTATTTTCAAAACACTAATTTTCT-ATAATCGAGGATAC
*
1207419 TCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCC
64 TCCAACCCCGATTTTATTGCTAAAACACTAATTTTT-C
* * *
1207457 ACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGAGGATA
1 -CAATCGGGGATACTCCAACCCC-GATTTATTTTCAAAACACTAATTTT-CTATAATCGAGGATA
* * * * * * *
1207522 CTCCAACTCTGATTTTACTTCCAAAAATACCATTTTTTC
63 CTCCAACCCCGATTTTA-TTGCTAAAACACTAATTTTTC
* *
1207561 ACAATCGAGGATACTCTAACC
1 -CAATCGGGGATACTCCAACC
1207582 TCGTTATTTC
Statistics
Matches: 186, Mismatches: 27, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
97 1 0.01
98 74 0.40
99 10 0.05
102 1 0.01
103 38 0.20
104 46 0.25
105 16 0.09
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (100 bp):
CAATCGGGGATACTCCAACCCCGATTTATTTTCAAAACACTAATTTTCTATAATCGAGGATACTC
CAACCCCGATTTTATTGCTAAAACACTAATTTTTC
Found at i:1207479 original size:52 final size:50
Alignment explanation
Indices: 1207257--1207581 Score: 239
Period size: 52 Copynumber: 6.4 Consensus size: 50
1207247 CGATTCTCCG
* * * *
1207257 CAATCGGGGATA-TCCCAACTCCGATTTCATTTTCAAAACACTAATTTTCTA
1 CAATCGGGGATACT-CCAACCCCGATTTTATTCT-AAAACACTAATTTTCCA
* * *
1207308 TAATCGAGGATACTCCAACTCCGATTTTATTTCTAAAACA-TCAATTTT---
1 CAATCGGGGATACTCCAACCCCGATTTTA-TTCTAAAACACT-AATTTTCCA
* * * * * *
1207356 C-ATCGGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCA
1 CAATCGGGGATACTCCAACCCCGATTTTA-TTCTAAAACACTAATTTTCCA
* *
1207406 TAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCA
1 CAATCGGGGATACTCCAACCCCGATTTTATT-CTAAAACACTAA-TTTTCCA
* * * *
1207458 CAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTT
1 CAATCGGGGATACTCCAACCCCGATTTTATTCT-AAAACACTAATTTTCC-A
* * * * * * * * *
1207510 TAATCGAGGATACTCCAACTCTGATTTTACTTCCAAAAATACCATTTTTTCA
1 CAATCGGGGATACTCCAACCCCGATTTTA-TT-CTAAAACACTAATTTTCCA
* *
1207562 CAATCGAGGATACTCTAACC
1 CAATCGGGGATACTCCAACC
1207582 TCGTTATTTC
Statistics
Matches: 223, Mismatches: 37, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
47 38 0.17
48 1 0.00
50 3 0.01
51 76 0.34
52 90 0.40
53 15 0.07
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (50 bp):
CAATCGGGGATACTCCAACCCCGATTTTATTCTAAAACACTAATTTTCCA
Found at i:1208947 original size:20 final size:20
Alignment explanation
Indices: 1208922--1208995 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
1208912 TTTTACCTAG
1208922 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1208942 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1208962 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1208982 ATGTATCGATACAT
1 ATGTATCGATACAT
1208996 CTAGTTAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1211312 original size:97 final size:97
Alignment explanation
Indices: 1211152--1211398 Score: 386
Period size: 97 Copynumber: 2.5 Consensus size: 97
1211142 AATTTTATTT
* *
1211152 ATCGGGGACACTCCAACCCTATTCCTTCGAGGGGATACTCCAACCCCACTTTTAAACATATCAAA
1 ATCGGGGACACTCCAACCCCATTCCTTCGAGGGGATACTCCAACCCCACTTTTAAACACATCAAA
1211217 GTTTAAATCTTATTCTCACTTAAATTGTCATC
66 GTTTAAATCTTATTCTCACTTAAATTGTCATC
* * * * **
1211249 ATCGGGGACACTTCAACCCCATTCCTTCGAGAGGATACTCTAACCCCGCTTTTAAATGCATCAAA
1 ATCGGGGACACTCCAACCCCATTCCTTCGAGGGGATACTCCAACCCCACTTTTAAACACATCAAA
*
1211314 GTTTAAATTTTATTCTCACTTAAATTGTCATC
66 GTTTAAATCTTATTCTCACTTAAATTGTCATC
* * *
1211346 ATTGGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCATTTTT
1 ATCGGGGACACTCCAACCCCATTCCTTCGAGGGGATACTCCAACCCCACTTTT
1211399 CAACTAAAAA
Statistics
Matches: 134, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
97 134 1.00
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (97 bp):
ATCGGGGACACTCCAACCCCATTCCTTCGAGGGGATACTCCAACCCCACTTTTAAACACATCAAA
GTTTAAATCTTATTCTCACTTAAATTGTCATC
Found at i:1212603 original size:19 final size:19
Alignment explanation
Indices: 1212579--1212617 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1212569 AAGTTATATA
*
1212579 TTATATAAATAATTAAAAT
1 TTATATAAACAATTAAAAT
* *
1212598 TTATATTAACATTTAAAAT
1 TTATATAAACAATTAAAAT
1212617 T
1 T
1212618 AGATTAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
TTATATAAACAATTAAAAT
Found at i:1213573 original size:158 final size:158
Alignment explanation
Indices: 1213281--1213659 Score: 543
Period size: 158 Copynumber: 2.4 Consensus size: 158
1213271 TTGAAAGTAT
1213281 TAAT-TCAATTTAATTTTATTTATTTTTAAAAATACCATTTCATACCCTT-ATAGAAG-CTCGAA
1 TAATATCAATTTAATTTTATTTATTTTTAAAAATACCATTTCATA-CCTTAATAGAAGCCT-GAA
* * * *
1213343 AGGATATGAAAAGTTTTTTAAAATCTTTTATACCCTTACGAATGCTCATAAGAATATAAAAGATT
64 AGAATATCAAAAGGTTTTTAAAATCTTTTATACCCTTACGAATGCCCATAAGAATATAAAAGATT
*
1213408 AGAAAAAATAACTATTAGAATTTATCCCAA
129 AGAAAAAATAAATATTAGAATTTATCCCAA
* ** *
1213438 TAATATCAATTTAATTTAATTTTATTTTTTTAAATACC-TTTCCATATCTTAATAGAAGCCTGAA
1 TAATATCAATTTAATTTTA-TTTATTTTTAAAAATACCATTT-CATACCTTAATAGAAGCCTGAA
* * *
1213502 AGAATA-CAAAAGGTTTTTGAAATCTTTTATACCCTTACGGATGCCCATAGGAATATAAAAGATT
64 AGAATATCAAAAGGTTTTTAAAATCTTTTATACCCTTACGAATGCCCATAAGAATATAAAAGATT
1213566 AGAAAAAATAAATATTAGAATTTATCCCAA
129 AGAAAAAATAAATATTAGAATTTATCCCAA
* * * *
1213596 TACTACCAATTTAATTTTATTTATTTTTAAAAATACCATTTTATACCTTAATGGAAGCCTGAAA
1 TAATATCAATTTAATTTTATTTATTTTTAAAAATACCATTTCATACCTTAATAGAAGCCTGAAA
1213660 CTGTTTTTTT
Statistics
Matches: 196, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
157 40 0.20
158 119 0.61
159 35 0.18
160 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (158 bp):
TAATATCAATTTAATTTTATTTATTTTTAAAAATACCATTTCATACCTTAATAGAAGCCTGAAAG
AATATCAAAAGGTTTTTAAAATCTTTTATACCCTTACGAATGCCCATAAGAATATAAAAGATTAG
AAAAAATAAATATTAGAATTTATCCCAA
Found at i:1214480 original size:21 final size:21
Alignment explanation
Indices: 1214454--1214495 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1214444 TTATTTTAGA
1214454 AATCTATATTTCTACATTATT
1 AATCTATATTTCTACATTATT
*
1214475 AATCTATATTTCTATATTATT
1 AATCTATATTTCTACATTATT
1214496 TATATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (21 bp):
AATCTATATTTCTACATTATT
Found at i:1214521 original size:20 final size:20
Alignment explanation
Indices: 1214458--1214548 Score: 71
Period size: 21 Copynumber: 4.3 Consensus size: 20
1214448 TTTAGAAATC
*
1214458 TATATTTC-TACATTATTAAT
1 TATATTTCTTATATTATT-AT
1214478 CTATATTTC-TATATTATTTATAT
1 -TATATTTCTTATATTA--T-TAT
1214501 TATTTATTTTCTTATATTATTAT
1 TA--TA-TTTCTTATATTATTAT
*
1214524 TATATTTCTTATATT-TTCT
1 TATATTTCTTATATTATTAT
1214543 TATATT
1 TATATT
1214549 ATTAATATAT
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
19 9 0.15
20 11 0.18
21 16 0.26
22 2 0.03
23 8 0.13
24 4 0.07
25 4 0.07
26 7 0.11
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.64
Consensus pattern (20 bp):
TATATTTCTTATATTATTAT
Found at i:1214543 original size:10 final size:10
Alignment explanation
Indices: 1214505--1214548 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
1214495 TTATATTATT
1214505 TATTTTCTTA
1 TATTTTCTTA
*
1214515 TATTATTATTA
1 TATT-TTCTTA
1214526 TA-TTTCTTA
1 TATTTTCTTA
1214535 TATTTTCTTA
1 TATTTTCTTA
1214545 TATT
1 TATT
1214549 ATTAATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 7 0.23
10 16 0.53
11 7 0.23
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (10 bp):
TATTTTCTTA
Done.