Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 188 of 216
Found at i:58628101 original size:21 final size:21
Alignment explanation
Indices: 58628077--58628125 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
58628067 CCAATCAAGT
*
58628077 TACCATTTCTGACTCACTCCA
1 TACCATTTCTGACTCAATCCA
58628098 TACCATTTCTGACTCAATCCA
1 TACCATTTCTGACTCAATCCA
58628119 TACCATT
1 TACCATT
58628126 CCATATACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.35, G:0.04, T:0.35
Consensus pattern (21 bp):
TACCATTTCTGACTCAATCCA
Found at i:58634371 original size:17 final size:18
Alignment explanation
Indices: 58634331--58634375 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
58634321 TAAAATTTTA
* *
58634331 GGCCCATATTCTCATGTG
1 GGCCCACATGCTCATGTG
58634349 GGCCCACATGCTCATGT-
1 GGCCCACATGCTCATGTG
58634366 GGCCCACATG
1 GGCCCACATG
58634376 GCCTGGCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.18, C:0.33, G:0.24, T:0.24
Consensus pattern (18 bp):
GGCCCACATGCTCATGTG
Found at i:58636637 original size:5 final size:6
Alignment explanation
Indices: 58636614--58636671 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
58636604 AAATATTGTG
* * **
58636614 ATAATT ATAATT ATAATT -TAATTT AAAATT ATTATT -TAAAA ATAATT
1 ATAATT ATAATT ATAATT ATAA-TT ATAATT ATAATT ATAATT ATAATT
58636661 ATAATT -TAATT
1 ATAATT ATAATT
58636672 TTGAAATTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
5 10 0.24
6 29 0.71
7 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:58636703 original size:35 final size:34
Alignment explanation
Indices: 58636620--58636704 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 34
58636610 TGTGATAATT
*
58636620 ATAATTATAATTTAATTTAAAATTATTATTTAAAA
1 ATAATTATAATTTAATTTAAAATTACTA-TTAAAA
*
58636655 ATAATTATAATTTAATTTTGAAATTACTA-TAAAA
1 ATAATTATAATTTAA-TTTAAAATTACTATTAAAA
* *
58636689 ATTATTTATTATTTAA
1 A-TAATTATAATTTAA
58636705 AAAATGGGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
34 6 0.14
35 27 0.61
36 11 0.25
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (34 bp):
ATAATTATAATTTAATTTAAAATTACTATTAAAA
Found at i:58638968 original size:28 final size:28
Alignment explanation
Indices: 58638936--58638992 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
58638926 TACTCTTTAA
58638936 GTACAAATGTATGATCTCTATACTTGAG
1 GTACAAATGTATGATCTCTATACTTGAG
58638964 GTACAAATGTATGATCTCTATACTTGAG
1 GTACAAATGTATGATCTCTATACTTGAG
58638992 G
1 G
58638993 AGTGATAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (28 bp):
GTACAAATGTATGATCTCTATACTTGAG
Found at i:58647003 original size:25 final size:27
Alignment explanation
Indices: 58646944--58647003 Score: 78
Period size: 25 Copynumber: 2.4 Consensus size: 27
58646934 CAGGTAAGGC
58646944 TCCTTCTC-T-TTCTTCCGTTCTTCAT
1 TCCTTCTCTTCTTCTTCCGTTCTTCAT
58646969 TCCTT-T-TTCTTCTTCCGTTCTTCA-
1 TCCTTCTCTTCTTCTTCCGTTCTTCAT
58646993 T-CTTCTCTTCT
1 TCCTTCTCTTCT
58647004 CAGCATATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
23 3 0.10
24 4 0.13
25 24 0.77
ACGTcount: A:0.03, C:0.35, G:0.03, T:0.58
Consensus pattern (27 bp):
TCCTTCTCTTCTTCTTCCGTTCTTCAT
Found at i:58649906 original size:21 final size:21
Alignment explanation
Indices: 58649882--58649934 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
58649872 CGCTGTTTCT
* *
58649882 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
58649903 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
58649924 AATCTCACCGC
1 AATCTCACCGC
58649935 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:58650930 original size:18 final size:17
Alignment explanation
Indices: 58650907--58650984 Score: 75
Period size: 18 Copynumber: 4.2 Consensus size: 17
58650897 TTAAAATTAA
58650907 ATAAAAATATTAAAAATT
1 ATAAAAA-ATTAAAAATT
*
58650925 ATAAAACAATTAGAAATTT
1 ATAAAA-AATTA-AAAATT
58650944 ATAAAAAATTAAAAATT
1 ATAAAAAATTAAAAATT
* *
58650961 CTAAATATATTATAAAAATT
1 ATAAA-A-AAT-TAAAAATT
58650981 ATAA
1 ATAA
58650985 TCAAGTATGT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
17 9 0.18
18 16 0.32
19 14 0.28
20 11 0.22
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (17 bp):
ATAAAAAATTAAAAATT
Found at i:58650982 original size:9 final size:9
Alignment explanation
Indices: 58650907--58650984 Score: 54
Period size: 9 Copynumber: 8.4 Consensus size: 9
58650897 TTAAAATTAA
58650907 ATAAAAA-T
1 ATAAAAATT
58650915 ATTAAAAATT
1 A-TAAAAATT
58650925 ATAAAACAATT
1 AT-AAA-AATT
* *
58650936 A-GAAATTT
1 ATAAAAATT
*
58650944 ATAAAAAAT
1 ATAAAAATT
58650953 -TAAAAATT
1 ATAAAAATT
*
58650961 CTAAATATATT
1 ATAAA-A-ATT
58650972 ATAAAAATT
1 ATAAAAATT
58650981 ATAA
1 ATAA
58650985 TCAAGTATGT
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
8 12 0.22
9 24 0.44
10 7 0.13
11 12 0.22
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:58653044 original size:33 final size:31
Alignment explanation
Indices: 58653006--58653068 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
58652996 TAATTATTTA
*
58653006 TATTTAAGAATATAATTTGTTATTTTAATAAAT
1 TATTTAAGAATACAA-TT-TTATTTTAATAAAT
* *
58653039 TATTTAATATTACAATTTTATTTTAATAAA
1 TATTTAAGAATACAATTTTATTTTAATAAA
58653069 AAATTAACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 13 0.48
32 2 0.07
33 12 0.44
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (31 bp):
TATTTAAGAATACAATTTTATTTTAATAAAT
Found at i:58653110 original size:11 final size:12
Alignment explanation
Indices: 58653077--58653143 Score: 50
Period size: 12 Copynumber: 5.6 Consensus size: 12
58653067 AAAAATTAAC
*
58653077 AATAATAATTTTA
1 AATAAT-ATTATA
58653090 AATAATATTATA
1 AATAATATTATA
58653102 AAT-ATATTATTA
1 AATAATATTA-TA
*
58653114 AAAAATATT-TA
1 AATAATATTATA
* *
58653125 TATTAATATT-TT
1 -AATAATATTATA
58653137 AATAATA
1 AATAATA
58653144 AATATATATT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
11 14 0.31
12 20 0.44
13 11 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AATAATATTATA
Found at i:58653119 original size:27 final size:28
Alignment explanation
Indices: 58653089--58653154 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
58653079 TAATAATTTT
*
58653089 AAATAATATTATA-AATATATTATTAAA
1 AAATAATATTATATAATATATTAATAAA
* *
58653116 AAAT-AT-TTATATTAATATTTTAATAAT
1 AAATAATATTATA-TAATATATTAATAAA
58653143 AAATATATATTA
1 AAATA-ATATTA
58653155 CAATTTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 5 0.16
26 2 0.06
27 19 0.61
29 2 0.06
30 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AAATAATATTATATAATATATTAATAAA
Found at i:58653138 original size:24 final size:22
Alignment explanation
Indices: 58653078--58653138 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 22
58653068 AAAATTAACA
*
58653078 ATAATAATTTTAAATAATATTAT
1 ATAAT-ATTTTAAAAAATATTAT
*
58653101 AAATATATTATTAAAAAATATTTAT
1 ATA-ATATT-TTAAAAAATA-TTAT
58653126 ATTAATATTTTAA
1 A-TAATATTTTAA
58653139 TAATAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 5 0.16
24 15 0.48
25 10 0.32
26 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAATATTTTAAAAAATATTAT
Found at i:58656357 original size:50 final size:49
Alignment explanation
Indices: 58656283--58656557 Score: 167
Period size: 50 Copynumber: 5.5 Consensus size: 49
58656273 CAGGGAAACC
* * **
58656283 AGATCCGCCGTCGTAGCTTTAATCTATTCCACCACACCATCAGGGAAGTA
1 AGATCCGCCGTTGTAGCTTCAATCTATTCCACTGCA-CATCAGGGAAGTA
* * * ** * * ***
58656333 AGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTATTCCACTGC-ACATCAGGGAAGTA
*
58656383 AGATCCGCCGTTGTAGCTTCAATCTATTCCACTGCAC-TGCTAAGGAAGTA
1 AGATCCGCCGTTGTAGCTTCAATCTATTCCACTGCACAT-C-AGGGAAGTA
* * * ** * * * ***
58656433 AGATCCACCGTTGTGGCTTCAATCTTTTTAATTACAATATCAGGGAAACC
1 AGATCCGCCGTTGTAGCTTCAATCTATTCCACTGC-ACATCAGGGAAGTA
* ** * * *
58656483 AGATCTGCCGTCATAGCTTCAATCTGTTCCGCTGCAC-TGCTAAGGAAGTA
1 AGATCCGCCGTTGTAGCTTCAATCTATTCCACTGCACAT-C-AGGGAAGTA
* *
58656533 AGATCCGCCGTTGTGGCTTTAATCT
1 AGATCCGCCGTTGTAGCTTCAATCT
58656558 TTTTACTTTT
Statistics
Matches: 160, Mismatches: 58, Indels: 14
0.69 0.25 0.06
Matches are distributed among these distances:
48 2 0.01
49 4 0.03
50 150 0.94
51 3 0.02
52 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (49 bp):
AGATCCGCCGTTGTAGCTTCAATCTATTCCACTGCACATCAGGGAAGTA
Found at i:58656399 original size:100 final size:100
Alignment explanation
Indices: 58656265--58656562 Score: 438
Period size: 100 Copynumber: 3.0 Consensus size: 100
58656255 TTTGTTCAAC
* * ** *
58656265 TACAATGTCAGGGAAACCAGATCCGCCGTCGTAGCTTTAATCTATTCCAC--CACACCATCAGGG
1 TACAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGC-T-AAGG
*
58656328 AAGTAAGATCTGCCGTTGTGGCTTCAATCTTTTTAAT
64 AAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* *
58656365 TGCAATATCAGGGAAACCAGATCCGCCGTTGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAA
1 TACAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAA
*
58656430 GTAAGATCCACCGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* * * *
58656465 TACAATATCAGGGAAACCAGATCTGCCGTCATAGCTTCAATCTGTTCCGCTGCACTGCTAAGGAA
1 TACAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAA
*
58656530 GTAAGATCCGCCGTTGTGGCTTTAATCTTTTTA
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTA
58656563 CTTTTCAACC
Statistics
Matches: 179, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
100 174 0.97
101 1 0.01
102 4 0.02
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (100 bp):
TACAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAA
GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
Found at i:58664323 original size:20 final size:20
Alignment explanation
Indices: 58664298--58664337 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
58664288 ATAAAGGTCT
58664298 TTAATGCATATGATGCGATG
1 TTAATGCATATGATGCGATG
58664318 TTAATGCATATGATGCGATG
1 TTAATGCATATGATGCGATG
58664338 CATGGGGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (20 bp):
TTAATGCATATGATGCGATG
Found at i:58676077 original size:12 final size:13
Alignment explanation
Indices: 58676059--58676100 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
58676049 AGGAAAGATT
58676059 TAATAATAATATA
1 TAATAATAATATA
58676072 -AATAATAACATATA
1 TAATAAT-A-ATATA
58676086 TACATAATAATATA
1 TA-ATAATAATATA
58676100 T
1 T
58676101 TAAAGTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 6 0.24
13 1 0.04
14 11 0.44
15 2 0.08
16 5 0.20
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATAATAATATA
Found at i:58676092 original size:16 final size:16
Alignment explanation
Indices: 58676067--58676104 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
58676057 TTTAATAATA
58676067 ATATAAATAATAACAT
1 ATATAAATAATAACAT
* *
58676083 ATATACATAATAATAT
1 ATATAAATAATAACAT
58676099 AT-TAAA
1 ATATAAA
58676105 GTTGAAGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATAAATAATAACAT
Found at i:58676338 original size:16 final size:16
Alignment explanation
Indices: 58676293--58676339 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
58676283 TTAAAATAAT
58676293 ATTATATAATAAAATA
1 ATTATATAATAAAATA
*
58676309 ATGCATATACATAAAA-A
1 AT-TATATA-ATAAAATA
58676326 ATTATATAGATAAA
1 ATTATATA-ATAAA
58676340 TATATGAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 8 0.31
18 6 0.23
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (16 bp):
ATTATATAATAAAATA
Found at i:58676368 original size:18 final size:18
Alignment explanation
Indices: 58676347--58676381 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
58676337 AAATATATGA
58676347 ACTAAT-ATAAATAATAAC
1 ACTAATAAT-AATAATAAC
58676365 ACTAATAATAATAATAA
1 ACTAATAATAATAATAA
58676382 TGATAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (18 bp):
ACTAATAATAATAATAAC
Found at i:58677126 original size:22 final size:23
Alignment explanation
Indices: 58677084--58677127 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
58677074 TGTAAATCAC
58677084 CTTTCAAATTTTTGGTCTTTTTT
1 CTTTCAAATTTTTGGTCTTTTTT
*
58677107 CTTTGAAATTTTT-GT-TTTTTT
1 CTTTCAAATTTTTGGTCTTTTTT
58677128 ATTCAATAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 2 0.10
23 12 0.60
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.68
Consensus pattern (23 bp):
CTTTCAAATTTTTGGTCTTTTTT
Found at i:58686986 original size:15 final size:15
Alignment explanation
Indices: 58686966--58687072 Score: 76
Period size: 15 Copynumber: 7.3 Consensus size: 15
58686956 AGGTTGCACA
58686966 TAGGGGTTCACACCT
1 TAGGGGTTCACACCT
* * *
58686981 TAGGGGTTTATA-CA
1 TAGGGGTTCACACCT
* *
58686995 TATGGGTTCACACTT
1 TAGGGGTTCACACCT
* *
58687010 TAGAGGTTCGCACCT
1 TAGGGGTTCACACCT
* * * *
58687025 TAGAGTTTCTCACAT
1 TAGGGGTTCACACCT
*
58687040 TA-GGGTTCGCACC-
1 TAGGGGTTCACACCT
*
58687053 TAGGGGTTCACACGT
1 TAGGGGTTCACACCT
58687068 TAGGG
1 TAGGG
58687073 TTTGCACCTG
Statistics
Matches: 68, Mismatches: 21, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
13 2 0.03
14 26 0.38
15 40 0.59
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (15 bp):
TAGGGGTTCACACCT
Found at i:58687061 original size:14 final size:14
Alignment explanation
Indices: 58687042--58687113 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 14
58687032 TCTCACATTA
58687042 GGGTTCGCACCTAG
1 GGGTTCGCACCTAG
* *
58687056 GGGTTCACACGTTA-
1 GGGTTCGCAC-CTAG
*
58687070 GGGTTTGCACCT-G
1 GGGTTCGCACCTAG
* *
58687083 GGGTTCGTACATTA-
1 GGGTTCGCAC-CTAG
*
58687097 GGGTTCGCATCTAG
1 GGGTTCGCACCTAG
58687111 GGG
1 GGG
58687114 GTCACACCTT
Statistics
Matches: 42, Mismatches: 11, Indels: 10
0.67 0.17 0.16
Matches are distributed among these distances:
13 11 0.26
14 29 0.69
15 2 0.05
ACGTcount: A:0.15, C:0.21, G:0.36, T:0.28
Consensus pattern (14 bp):
GGGTTCGCACCTAG
Found at i:58687129 original size:28 final size:28
Alignment explanation
Indices: 58686946--58687129 Score: 138
Period size: 28 Copynumber: 6.5 Consensus size: 28
58686936 ATACAGGGGC
* *
58686946 CACACATATAAGGTT-GCACATAGGGGTT
1 CACACAT-TAGGGTTCGCACCTAGGGGTT
* *** * *
58686974 CACACCTTAGGGGTTTATACATATGGGTT
1 CACACATTA-GGGTTCGCACCTAGGGGTT
* * *
58687003 CACACTTTAGAGGTTCGCACCTTAGAGTTT
1 CACACATTAG-GGTTCGCACC-TAGGGGTT
*
58687033 CTCACATTAGGGTTCGCACCTAGGGGTT
1 CACACATTAGGGTTCGCACCTAGGGGTT
* *
58687061 CACACGTTAGGGTTTGCACCT-GGGGTT
1 CACACATTAGGGTTCGCACCTAGGGGTT
** * *
58687088 CGTACATTAGGGTTCGCATCTAGGGGGT
1 CACACATTAGGGTTCGCACCTAGGGGTT
* *
58687116 CACACCTTACGGTT
1 CACACATTAGGGTT
58687130 TACAAACCTA
Statistics
Matches: 121, Mismatches: 30, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
27 24 0.20
28 50 0.41
29 34 0.28
30 13 0.11
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.30
Consensus pattern (28 bp):
CACACATTAGGGTTCGCACCTAGGGGTT
Found at i:58689499 original size:19 final size:19
Alignment explanation
Indices: 58689475--58689512 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
58689465 TATTGTCTGA
58689475 GGTTCGCA-TACTGTAGGGG
1 GGTTCGCACTACT-TAGGGG
58689494 GGTTCGCACTACTTAGGGG
1 GGTTCGCACTACTTAGGGG
58689513 TTGCAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.16, C:0.18, G:0.39, T:0.26
Consensus pattern (19 bp):
GGTTCGCACTACTTAGGGG
Found at i:58692666 original size:28 final size:29
Alignment explanation
Indices: 58692600--58692666 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
58692590 ATAAAAAATA
** *
58692600 ACCAAAATATTATAACTTTTTATTTTTTT
1 ACCAAAATATTATAAAATTTTATTTATTT
58692629 ACCAAAATATTATAAAATTTT-TTTATTT
1 ACCAAAATATTATAAAATTTTATTTATTT
*
58692657 ACTAAAATAT
1 ACCAAAATAT
58692667 ACAAAAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 15 0.44
29 19 0.56
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (29 bp):
ACCAAAATATTATAAAATTTTATTTATTT
Found at i:58692814 original size:4 final size:4
Alignment explanation
Indices: 58692807--58692950 Score: 63
Period size: 4 Copynumber: 36.0 Consensus size: 4
58692797 GAAGGAGAGG
* * * *
58692807 GAAA GAAA GAAA GAAA GAAA GGAAG GAAG GAAG GAGAG GAAA GAAA G-AA
1 GAAA GAAA GAAA GAAA GAAA -GAAA GAAA GAAA GA-AA GAAA GAAA GAAA
* * *
58692856 -AAA GAAG GAAA GAAAA GGAAA G-GA GAAAA GAAA -AAA AAAA GAAA G-AA
1 GAAA GAAA GAAA G-AAA -GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA
* *
58692903 G-AA GAAGA GGAAA TGAGAG GAAA -AAA GAAA G-AA -AAA GAAG GAAA
1 GAAA GAA-A -GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
58692947 GAAA
1 GAAA
58692951 AGGAAAGGAG
Statistics
Matches: 112, Mismatches: 12, Indels: 32
0.72 0.08 0.21
Matches are distributed among these distances:
3 22 0.20
4 64 0.57
5 21 0.19
6 5 0.04
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:58692861 original size:10 final size:10
Alignment explanation
Indices: 58692850--58692981 Score: 54
Period size: 10 Copynumber: 12.6 Consensus size: 10
58692840 GAGAGGAAAG
58692850 AAAGAAA-AA
1 AAAGAAAGAA
*
58692859 GAAGGAAAGAA
1 -AAAGAAAGAA
*
58692870 AAGGAAAGGAGA
1 AAAGAAA-GA-A
*
58692882 AAAGAAAAAAA
1 AAAG-AAAGAA
58692893 AAAGAAAGAA
1 AAAGAAAGAA
* *
58692903 GAAGAAGAGGA
1 AAAGAA-AGAA
* *
58692914 AATGAGAGGAAA
1 AAAGA-AAG-AA
58692926 AAAGAAAGAA
1 AAAGAAAGAA
*
58692936 AAAGAAGGAA
1 AAAGAAAGAA
* *
58692946 AGA-AAAGGA
1 AAAGAAAGAA
*
58692955 AAGGAGAAGAGA
1 AAAGA-AAGA-A
58692967 AAA-AAAGAA
1 AAAGAAAGAA
*
58692976 GAAGAA
1 AAAGAA
58692982 GAAGCGGGAA
Statistics
Matches: 90, Mismatches: 21, Indels: 22
0.68 0.16 0.17
Matches are distributed among these distances:
9 8 0.09
10 43 0.48
11 22 0.24
12 14 0.16
13 3 0.03
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:58692867 original size:44 final size:43
Alignment explanation
Indices: 58692812--58692982 Score: 122
Period size: 44 Copynumber: 4.2 Consensus size: 43
58692802 AGAGGGAAAG
*
58692812 AAAGAAAGAAAGAAAGGAAGGAAGGAAGGAGAGGAAAGAAAGAA
1 AAAGAAGGAAAGAAAGGAAGG-AGGAAGGAGAGGAAAGAAAGAA
58692856 AAAGAAGGAAAG-AA--AAGGA--AAGGAGA--AAAGAAA-AA
1 AAAGAAGGAAAGAAAGGAAGGAGGAAGGAGAGGAAAGAAAGAA
* *
58692891 AAA-AA-GAAAGAAGAAGAA-GAGGAAATGAGAGGAAAAAAGAAAGAA
1 AAAGAAGGAAAGAA-AGGAAGGAGG-AAGGAGAGG---AAAGAAAGAA
58692936 AAAGAAGGAAAGAAAAGGAAAGGA-GAA-GAGA--AAA-AAAGAA
1 AAAGAAGGAAAG-AAAGG-AAGGAGGAAGGAGAGGAAAGAAAGAA
*
58692976 GAAGAAG
1 AAAGAAG
58692983 AAGCGGGAAG
Statistics
Matches: 105, Mismatches: 4, Indels: 40
0.70 0.03 0.27
Matches are distributed among these distances:
33 5 0.05
34 3 0.03
35 6 0.06
36 9 0.09
37 2 0.02
38 7 0.07
39 6 0.06
40 13 0.12
41 7 0.07
43 2 0.02
44 18 0.17
45 5 0.05
46 6 0.06
47 9 0.09
48 5 0.05
49 2 0.02
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.01
Consensus pattern (43 bp):
AAAGAAGGAAAGAAAGGAAGGAGGAAGGAGAGGAAAGAAAGAA
Found at i:58692941 original size:80 final size:75
Alignment explanation
Indices: 58692846--58693012 Score: 246
Period size: 80 Copynumber: 2.2 Consensus size: 75
58692836 GAAGGAGAGG
58692846 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAAAGAAAAAAAAAAGAAAGAAGAAGAAGA
1 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAG--AAG-AAAAAAAAAG-AAGAAGAAGAAGA
*
58692911 GGAAATGAGAGGAAA
62 GGAAAGGA-AGGAAA
* * *
58692926 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAGAAGAAGAAGCGGGA
1 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAAAAGAAGAAGAAGAAGAGGAA
58692991 AGGAAGGAAA
66 AGGAAGGAAA
58693001 AAA-AAAGAAAAA
1 AAAGAAAGAAAAA
58693013 AAATATAATT
Statistics
Matches: 83, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
74 9 0.11
75 9 0.11
76 18 0.22
77 9 0.11
78 3 0.04
80 35 0.42
ACGTcount: A:0.69, C:0.01, G:0.29, T:0.01
Consensus pattern (75 bp):
AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAAAAAAAAGAAGAAGAAGAAGAGGAA
AGGAAGGAAA
Found at i:58692981 original size:19 final size:19
Alignment explanation
Indices: 58692925--58692983 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 19
58692915 ATGAGAGGAA
*
58692925 AAAAGAAAGAAAAAGAAG-G
1 AAAA-AAAGAAGAAGAAGAG
*
58692944 AAAGAAAAGGAAAGGAGAAGAG
1 AAA-AAAA-G-AAGAAGAAGAG
58692966 AAAAAAAGAAGAAGAAGA
1 AAAAAAAGAAGAAGAAGA
58692984 AGCGGGAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
19 15 0.45
20 3 0.09
21 11 0.33
22 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAGAAGAAGAG
Found at i:58698809 original size:18 final size:18
Alignment explanation
Indices: 58698788--58698832 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
58698778 ATCCCAATGA
*
58698788 TCGCTACCATCTTCTTCT
1 TCGCTACCACCTTCTTCT
* *
58698806 TCGCCAGCACCTTCTTCT
1 TCGCTACCACCTTCTTCT
*
58698824 TCACTACCA
1 TCGCTACCA
58698833 ACCATATCAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.16, C:0.42, G:0.07, T:0.36
Consensus pattern (18 bp):
TCGCTACCACCTTCTTCT
Found at i:58699694 original size:3 final size:3
Alignment explanation
Indices: 58699686--58699714 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
58699676 TCTTAATACT
58699686 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
58699715 TAATAATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:58700003 original size:27 final size:27
Alignment explanation
Indices: 58699931--58700004 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
58699921 AACACGAGTA
*
58699931 GTGCCGCCAATCA-GTATGGCACCATTG
1 GTGCCGCCAATCACCT-TGGCACCATTG
* ** * **
58699958 GTGCCGCTAATGGCTTTGGCACTTTTG
1 GTGCCGCCAATCACCTTGGCACCATTG
58699985 GTGCCGCCAATCACCTTGGC
1 GTGCCGCCAATCACCTTGGC
58700005 CTGACCAGGG
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
27 35 0.97
28 1 0.03
ACGTcount: A:0.16, C:0.30, G:0.27, T:0.27
Consensus pattern (27 bp):
GTGCCGCCAATCACCTTGGCACCATTG
Found at i:58700106 original size:27 final size:28
Alignment explanation
Indices: 58700076--58700140 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
58700066 GTTTTTTGGT
* *
58700076 ATATTTTGGTAAAT-AAAAAAATTTATA
1 ATATTTTAGTAAATAAAAAAAACTTATA
58700103 ATATTTTAGTAAATAAAAAAAACTTATA
1 ATATTTTAGTAAATAAAAAAAACTTATA
58700131 ATATTTTAGT
1 ATATTTTAGT
58700141 TATTTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 13 0.37
28 22 0.63
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.42
Consensus pattern (28 bp):
ATATTTTAGTAAATAAAAAAAACTTATA
Found at i:58700447 original size:31 final size:31
Alignment explanation
Indices: 58700394--58700452 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
58700384 CCGAATATAA
*
58700394 TAAATATATATTTTTTAATTTTAAAATACAT
1 TAAAAATATATTTTTTAATTTTAAAATACAT
* *
58700425 TAAAAATATTTTTTTTATTTTTAAAATA
1 TAAAAATATATTTTTTAATTTTAAAATA
58700453 TTTTTTTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (31 bp):
TAAAAATATATTTTTTAATTTTAAAATACAT
Found at i:58701107 original size:9 final size:9
Alignment explanation
Indices: 58701076--58701126 Score: 57
Period size: 10 Copynumber: 5.3 Consensus size: 9
58701066 TAAAAAATCT
*
58701076 TTAAAATAA
1 TTAAAATTA
*
58701085 TTATAAAGTA
1 TTA-AAATTA
58701095 TTAAAATTA
1 TTAAAATTA
58701104 TTAAAAATATA
1 TT-AAAAT-TA
58701115 TTAAAATTA
1 TTAAAATTA
58701124 TTA
1 TTA
58701127 TTTTAGCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 15 0.42
10 17 0.47
11 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (9 bp):
TTAAAATTA
Found at i:58701187 original size:23 final size:23
Alignment explanation
Indices: 58701142--58701192 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
58701132 GCATAAATTT
*
58701142 TAATAATTTTAATATAATCTTAA
1 TAATAATTTTAACATAATCTTAA
* * *
58701165 TAATTATTTTAACATGATTTTAA
1 TAATAATTTTAACATAATCTTAA
58701188 -AATAA
1 TAATAA
58701193 AATCGGAGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (23 bp):
TAATAATTTTAACATAATCTTAA
Found at i:58702031 original size:7 final size:7
Alignment explanation
Indices: 58702019--58702079 Score: 52
Period size: 7 Copynumber: 8.3 Consensus size: 7
58702009 GGTTCAAAAC
58702019 AAAATAA
1 AAAATAA
58702026 AAAATAAA
1 AAAAT-AA
58702034 AAAATTAA
1 AAAA-TAA
*
58702042 AAAATTA
1 AAAATAA
*
58702049 AAATTAA
1 AAAATAA
*
58702056 AAATTAA
1 AAAATAA
58702063 AATAA-AA
1 AA-AATAA
58702070 AAAATTAA
1 AAAA-TAA
58702078 AA
1 AA
58702080 TCTTAAATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
6 2 0.04
7 25 0.56
8 17 0.38
9 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (7 bp):
AAAATAA
Found at i:58702057 original size:28 final size:30
Alignment explanation
Indices: 58702025--58702082 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
58702015 AAACAAAATA
58702025 AAAAATAAAAAAATTAAAAAATTAAAAT-T
1 AAAAATAAAAAAATTAAAAAATTAAAATCT
*
58702054 AAAAATTAAAATAA--AAAAAATTAAAATCT
1 AAAAA-TAAAAAAATTAAAAAATTAAAATCT
58702083 TAAATCCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 13 0.50
29 6 0.23
30 7 0.27
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (30 bp):
AAAAATAAAAAAATTAAAAAATTAAAATCT
Found at i:58702071 original size:13 final size:13
Alignment explanation
Indices: 58702019--58702071 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 13
58702009 GGTTCAAAAC
*
58702019 AAAATAAAAAATAAA
1 AAAATAAAAAAT--T
58702034 AAAATTAAAAAATT
1 AAAA-TAAAAAATT
*
58702048 AAAATTAAAAATT
1 AAAATAAAAAATT
58702061 AAAATAAAAAA
1 AAAATAAAAAA
58702072 AATTAAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 18 0.53
14 4 0.12
15 4 0.12
16 8 0.24
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATAAAAAATT
Found at i:58702087 original size:22 final size:23
Alignment explanation
Indices: 58702048--58702098 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
58702038 TTAAAAAATT
58702048 AAAATTAAAAATTAAAAT-AAAA
1 AAAATTAAAAATTAAAATCAAAA
* *
58702070 AAAATT-AAAATCTTAAATCCAAA
1 AAAATTAAAAAT-TAAAATCAAAA
58702093 AAAATT
1 AAAATT
58702099 GAATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.20
22 11 0.44
23 9 0.36
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (23 bp):
AAAATTAAAAATTAAAATCAAAA
Found at i:58707357 original size:23 final size:23
Alignment explanation
Indices: 58707305--58707358 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
58707295 GTAATTATAA
*
58707305 ATACATGTGTAATAAATATATGT
1 ATACATTTGTAATAAATATATGT
*
58707328 ATACATTTGTAATTAATATATGT
1 ATACATTTGTAATAAATATATGT
58707351 ATACATTT
1 ATACATTT
58707359 ATATATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (23 bp):
ATACATTTGTAATAAATATATGT
Found at i:58707369 original size:23 final size:23
Alignment explanation
Indices: 58707305--58707366 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
58707295 GTAATTATAA
* * *
58707305 ATACATGTGTAATAAATATATGT
1 ATACATTTATAATTAATATATGT
*
58707328 ATACATTTGTAATTAATATATGT
1 ATACATTTATAATTAATATATGT
58707351 ATACATTTATATATTA
1 ATACATTTATA-ATTA
58707367 TATTATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 31 0.89
24 4 0.11
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (23 bp):
ATACATTTATAATTAATATATGT
Found at i:58707418 original size:18 final size:18
Alignment explanation
Indices: 58707385--58707423 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
58707375 TTAATTAAAC
58707385 AAAAGAAAGAAATGAAAAT
1 AAAAGAAAGAAATG-AAAT
*
58707404 AAAAGAAA-CAATGAAAT
1 AAAAGAAAGAAATGAAAT
58707421 AAA
1 AAA
58707424 GATTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (18 bp):
AAAAGAAAGAAATGAAAT
Found at i:58711597 original size:20 final size:20
Alignment explanation
Indices: 58711583--58711620 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
58711573 CTTCTATCAT
*
58711583 TATAAGTCCACTTCTGCCGA
1 TATAAGTCCACTTCTACCGA
58711603 TATAAGTCCACTTCTACC
1 TATAAGTCCACTTCTACC
58711621 CATACATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.32
Consensus pattern (20 bp):
TATAAGTCCACTTCTACCGA
Found at i:58718926 original size:37 final size:36
Alignment explanation
Indices: 58718866--58719012 Score: 141
Period size: 37 Copynumber: 3.9 Consensus size: 36
58718856 AGTACGCTTT
* *
58718866 ATCGAGCCAAATCTTACCGTTATACTGAATAAAGCTCA
1 ATCGAG-CAAAT-TTACCATTATACTGAATGAAGCTCA
58718904 ATCGAGCAAATTATACCATTATACTGAATGAAGCTCA
1 ATCGAGCAAATT-TACCATTATACTGAATGAAGCTCA
* * * * *
58718941 ATTGAGCAAACCTTACTATTATACTGAATGATGTTCA
1 ATCGAGCAAA-TTTACCATTATACTGAATGAAGCTCA
* ** * *
58718978 ATAGAGCAAATTCTACTGTAATACTGAGTGAAGCT
1 ATCGAGCAAATT-TACCATTATACTGAATGAAGCT
58719013 TAAACGAGTA
Statistics
Matches: 92, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
36 2 0.02
37 83 0.90
38 7 0.08
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (36 bp):
ATCGAGCAAATTTACCATTATACTGAATGAAGCTCA
Found at i:58723906 original size:13 final size:14
Alignment explanation
Indices: 58723890--58723923 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
58723880 AAACCCTAAT
*
58723890 CACAAAAGCAGAG-
1 CACAAAACCAGAGA
58723903 CACAAAACCAGAGA
1 CACAAAACCAGAGA
58723917 CACAAAA
1 CACAAAA
58723924 ATCCAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.59, C:0.26, G:0.15, T:0.00
Consensus pattern (14 bp):
CACAAAACCAGAGA
Found at i:58726734 original size:37 final size:38
Alignment explanation
Indices: 58726647--58726738 Score: 107
Period size: 37 Copynumber: 2.4 Consensus size: 38
58726637 GCCACCCCGA
* * *
58726647 CCACCCTGCACACCACTTATGGGCCATATTAAGCTCAT
1 CCACCCTGCACACCACATATGGACCATATTAAGCCCAT
* *
58726685 CCACCGTGCACACCACATA-GGACCATGA-TAGGCCCAT
1 CCACCCTGCACACCACATATGGACCAT-ATTAAGCCCAT
*
58726722 CCACCCTACACACCACA
1 CCACCCTGCACACCACA
58726739 AATATGGAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
37 28 0.61
38 18 0.39
ACGTcount: A:0.29, C:0.41, G:0.13, T:0.16
Consensus pattern (38 bp):
CCACCCTGCACACCACATATGGACCATATTAAGCCCAT
Found at i:58727290 original size:21 final size:21
Alignment explanation
Indices: 58727264--58727305 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
58727254 GTGCGATAGA
* *
58727264 GGCACACGCCCATGTGAAAAG
1 GGCACACACCCATGCGAAAAG
*
58727285 GGCACACACCCGTGCGAAAAG
1 GGCACACACCCATGCGAAAAG
58727306 ACGCACATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.07
Consensus pattern (21 bp):
GGCACACACCCATGCGAAAAG
Found at i:58734609 original size:3 final size:3
Alignment explanation
Indices: 58734601--58734648 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
58734591 TTTTGCTAAA
*
58734601 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
58734649 TACTTCTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.31, C:0.33, G:0.02, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:58750272 original size:18 final size:18
Alignment explanation
Indices: 58750251--58750299 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
58750241 AAAAAATCAA
58750251 AAAAATATATAAAAATTG
1 AAAAATATATAAAAATTG
* *
58750269 -AAAATGTTATAAAAATTT
1 AAAAAT-ATATAAAAATTG
*
58750287 AAAAATATTTAAA
1 AAAAATATATAAA
58750300 TTTCAAGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (18 bp):
AAAAATATATAAAAATTG
Found at i:58750418 original size:9 final size:9
Alignment explanation
Indices: 58750406--58750438 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
58750396 TTTTTTTTAT
58750406 TTTTTAGAA
1 TTTTTAGAA
*
58750415 TTTTTATAA
1 TTTTTAGAA
58750424 TTTTTAGAA
1 TTTTTAGAA
58750433 TTTTTA
1 TTTTTA
58750439 TAATATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (9 bp):
TTTTTAGAA
Found at i:58750418 original size:18 final size:17
Alignment explanation
Indices: 58750380--58750437 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 17
58750370 AATTTAATAA
58750380 TTTTTTATTTTTA-AACTT
1 TTTTTTATTTTTAGAA--T
58750398 TTTTTTATTTTTTAGAAT
1 TTTTTTA-TTTTTAGAAT
*
58750416 TTTTATAATTTTTAGAAT
1 TTTT-TTATTTTTAGAAT
58750434 TTTT
1 TTTT
58750438 ATAATATTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 26 0.72
19 8 0.22
20 2 0.06
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTTATTTTTAGAAT
Found at i:58750438 original size:18 final size:18
Alignment explanation
Indices: 58750406--58750442 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
58750396 TTTTTTTTAT
58750406 TTTTTAGAATTTTTATAA
1 TTTTTAGAATTTTTATAA
58750424 TTTTTAGAATTTTTATAA
1 TTTTTAGAATTTTTATAA
58750442 T
1 T
58750443 ATTATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTTTAGAATTTTTATAA
Found at i:58751190 original size:26 final size:26
Alignment explanation
Indices: 58751160--58751214 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
58751150 TGTCACAAGT
58751160 AATACACAAGTTATTCTTCCATTATC
1 AATACACAAGTTATTCTTCCATTATC
58751186 AATACACAAGTTATTCTTCCATTATC
1 AATACACAAGTTATTCTTCCATTATC
58751212 AAT
1 AAT
58751215 TCTACACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (26 bp):
AATACACAAGTTATTCTTCCATTATC
Found at i:58759839 original size:20 final size:20
Alignment explanation
Indices: 58759816--58759862 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
58759806 TCTTAAATTT
58759816 ATTTTTATT-TTTATTTTTTC
1 ATTTTT-TTCTTTATTTTTTC
* *
58759836 ATTTTTTTCTTTGTTTTTTT
1 ATTTTTTTCTTTATTTTTTC
58759856 ATTTTTT
1 ATTTTTT
58759863 ATATATCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (20 bp):
ATTTTTTTCTTTATTTTTTC
Found at i:58767970 original size:49 final size:49
Alignment explanation
Indices: 58767912--58768052 Score: 189
Period size: 49 Copynumber: 2.9 Consensus size: 49
58767902 AAGGAAAAGG
*
58767912 GACCAAGGCGAAAACCCGCAAAGGGTGCTTTGAGTCCTAAAAAAAGAAA
1 GACCAAGGCGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAGAAA
* *
58767961 GACCAAGGCGAAAACCCGTAAAGAGCGCTTTGAGTCCT--AAAAA-AAA
1 GACCAAGGCGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAGAAA
*** * *
58768007 GACCAAATAGAAAACTCGCAAATGGCGCTTTGAGTCCTAAAAAAAG
1 GACCAAGGCGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAG
58768053 GAGAGGCCAA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
46 34 0.43
47 5 0.06
48 5 0.06
49 35 0.44
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.14
Consensus pattern (49 bp):
GACCAAGGCGAAAACCCGCAAAGGGCGCTTTGAGTCCTAAAAAAAGAAA
Found at i:58768035 original size:46 final size:45
Alignment explanation
Indices: 58767912--58768051 Score: 154
Period size: 46 Copynumber: 3.0 Consensus size: 45
58767902 AAGGAAAAGG
* * *
58767912 GACCAAGGCGAAAACCCGCAAAGGGTGCTTTGAGTCCTAAAAAAAGAAA
1 GACCAAAGAGAAAACCCGCAAA-GGCGCTTTGAGTCCT--AAAAA-AAA
* * *
58767961 GACCAAGGCGAAAACCCGTAAAGAGCGCTTTGAGTCCTAAAAAAAA
1 GACCAAAGAGAAAACCCGCAAAG-GCGCTTTGAGTCCTAAAAAAAA
* *
58768007 GACCAAATAGAAAACTCGCAAATGGCGCTTTGAGTCCTAAAAAAA
1 GACCAAAGAGAAAACCCGCAAA-GGCGCTTTGAGTCCTAAAAAAA
58768052 GGAGAGGCCA
Statistics
Matches: 82, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
46 41 0.50
47 6 0.07
48 1 0.01
49 34 0.41
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (45 bp):
GACCAAAGAGAAAACCCGCAAAGGCGCTTTGAGTCCTAAAAAAAA
Found at i:58769388 original size:44 final size:44
Alignment explanation
Indices: 58769311--58769481 Score: 180
Period size: 44 Copynumber: 3.9 Consensus size: 44
58769301 TTTATGGCGG
* * *
58769311 ATCTTATCCCCCTGAAGTTGCAGTGGGGTAGATTAAAGTTACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACAA
* * * * * *
58769355 ATTTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTGAGGATAACTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAG-TTACAA
* * *
58769400 ATCCTATCTTCCTGAGGTTGCAGTGGAGTAGATTGAAGTTACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACAA
* * * * *
58769444 GTCTTATCCCCCTGACGTTGCAGTGGATTAGACTGAAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAG
58769482 ATAGCATATC
Statistics
Matches: 101, Mismatches: 25, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
44 66 0.65
45 35 0.35
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTTACAA
Found at i:58777459 original size:8 final size:8
Alignment explanation
Indices: 58777446--58777490 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
58777436 CTTTGCCTAC
*
58777446 TTATTTTT
1 TTATTTTA
*
58777454 TTA-TTTG
1 TTATTTTA
*
58777461 TTATTTTG
1 TTATTTTA
58777469 TTATTTTA
1 TTATTTTA
58777477 TTATTTTA
1 TTATTTTA
58777485 TTATTT
1 TTATTT
58777491 CTGGCATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
7 6 0.18
8 28 0.82
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (8 bp):
TTATTTTA
Found at i:58779950 original size:30 final size:30
Alignment explanation
Indices: 58779916--58779977 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
58779906 TTAACTTTTT
58779916 TTAATGTTTGAATCTCAGAGAA-TCTGATTC
1 TTAATGTTTGAATCTCAGAGAATTC-GATTC
58779946 TTAATGTTTGAATCTCAGAGAATTCGATTC
1 TTAATGTTTGAATCTCAGAGAATTCGATTC
58779976 TT
1 TT
58779978 GGAGAATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (30 bp):
TTAATGTTTGAATCTCAGAGAATTCGATTC
Found at i:58785937 original size:3 final size:3
Alignment explanation
Indices: 58785929--58785954 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
58785919 AAATTGAATG
58785929 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
58785955 GTATGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:58790709 original size:16 final size:16
Alignment explanation
Indices: 58790688--58790741 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
58790678 ACAATAGTAG
58790688 TAATTACACTTTCATT
1 TAATTACACTTTCATT
*
58790704 TAATTACTACTTT-A-G
1 TAATTAC-ACTTTCATT
* *
58790719 TAGTTACATTTTCATT
1 TAATTACACTTTCATT
58790735 TAATTAC
1 TAATTAC
58790742 TCTATGTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 4 0.13
15 7 0.23
16 14 0.47
17 5 0.17
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (16 bp):
TAATTACACTTTCATT
Found at i:58795522 original size:18 final size:17
Alignment explanation
Indices: 58795495--58795530 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
58795485 ATAAAATACT
*
58795495 ATTAAGATTAAGTATTAA
1 ATTAAAATTAA-TATTAA
58795513 ATTAAAATTAATATTAA
1 ATTAAAATTAATATTAA
58795530 A
1 A
58795531 CTATTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
ATTAAAATTAATATTAA
Found at i:58795546 original size:24 final size:23
Alignment explanation
Indices: 58795488--58795546 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
58795478 TAAATTAATA
* *
58795488 AAATACTATTAAGATTAAGTATT
1 AAATAATATTAAGATTAACTATT
* *
58795511 AAATTAAAATTAATATTAAACTATT
1 AAA-TAATATTAAGATT-AACTATT
58795536 AAATAATATTA
1 AAATAATATTA
58795547 TTTTTGGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 3 0.10
24 17 0.59
25 9 0.31
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (23 bp):
AAATAATATTAAGATTAACTATT
Found at i:58799934 original size:44 final size:44
Alignment explanation
Indices: 58799877--58800762 Score: 573
Period size: 44 Copynumber: 19.5 Consensus size: 44
58799867 GAAATGTAAT
* * * *
58799877 TTCAACCTACTCCACTGCAACTTTAGGGACATAAGATTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* **
58799921 TTTAATCTGCTCCACTATAACTTCAGGGAGATAAGATTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * ** * * *
58799965 TTCAATCAGGTTTACTGCAGCTTCAGAGAGATAAGATTTGCTATC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
* * *
58800010 TTCAATTTGCTCCACTGTAACTTCAGGGAAATAAGATTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * * *
58800054 TTCAATCTGCTCCACTACAACTTTAGGAAGATGAGATTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * * *
58800098 TTCAATCTGCTCCACGGCAACTTCAGGGAGATGAGATTCGCTATC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
** * *
58800143 TTCAATCTATTCCACCGCAACTTCAGGAAGATAAGATTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* *
58800187 -TCTAACCTGCTCCACTGCAACTTCAGGGAGATGAGATTTGTAACTTGTAGC
1 TTC-AATCTGCTCCACTGCAACTTCAGGGAGAT-A-A---G--ATTTGTAGC
* * * * ** * * * *
58800238 TTTAATCTGTTCCACTACAAGTTTGGGGAAATAATATTTTCTATC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTTGTAGC
* * * * **
58800283 TTCAATCTGCTCCACTGCAAATTCAGGGAAATAAGATTCGCATA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * * *
58800327 TTCAATCTGCTCCATTGTAACTTCAGAGAGATAAGGTTTGTAACTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAA-----G--ATTTGTAGC
* ** * * * *
58800378 TTTAATCTATTCCGCTGC-ACTTCAAGGAAATAAGACTCATTACGATAGA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-T--TT--G-TAGC
* * * * *
58800427 TTTAATCTGAC-CCACTGCAACTTCAGAGG-TATATGATTTATCGC
1 TTCAATCTG-CTCCACTGCAACTTCAG-GGAGATAAGATTTGTAGC
* * * * *
58800471 TTCAATCTACTCTACTGTAACTTTAGGGAGATAAGATTTGCTATC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
* * * *
58800516 TTCAATCTGTTCCACTACAACTTCAGGAAGATAAGATTTGTGGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* *
58800560 TTTAATCTGCTCCACTACAACTTCAGGTG-GATAAGATTCACTACAGT-GAC
1 TTCAATCTGCTCCACTGCAACTTCAGG-GAGATAAGATT---T---GTAG-C
* * * *
58800610 TTCAATTTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTTATC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
* * * * * *
58800655 TTCAATCTACTCTACTACAACTTTAGAGAGATAAGATTTGTAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * ** **
58800699 TTCAATTTGTTGTACTGCAACTTCA--GAGATAAGATTTGTTATT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
58800742 TTCAATCTGCTCCACTGCAAC
1 TTCAATCTGCTCCACTGCAAC
58800763 CTAAAGGAGA
Statistics
Matches: 648, Mismatches: 151, Indels: 87
0.73 0.17 0.10
Matches are distributed among these distances:
42 13 0.02
43 25 0.04
44 292 0.45
45 180 0.28
46 3 0.00
47 4 0.01
48 1 0.00
49 23 0.04
50 58 0.09
51 48 0.07
52 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (44 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
Found at i:58800038 original size:89 final size:87
Alignment explanation
Indices: 58799889--58800762 Score: 458
Period size: 89 Copynumber: 9.6 Consensus size: 87
58799879 CAACCTACTC
* * * * **
58799889 CACTGCAACTTTAGGGACATAAGATTTGTAGCTTTAATCTGCTCCACTATAACTTCAGGGAGATA
1 CACTGCAACTTCAGGAAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
58799954 AGATTTGTAGCTTCAATCAGGTT
66 AGATTTGTAGCTTCAATCA-GTT
* * * * * *
58799977 TACTGCAGCTTCA-GAGAGATAAGATTTGCTATCTTCAATTTGCTCCACTGTAACTTCAGGGAAA
1 CACTGCAACTTCAGGA-AGATAAGATTTG-TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGA
* *
58800041 TAAGATTTGTAGCTTCAATCTGCTC
64 TAAGATTTGTAGCTTCAATCAG-TT
* * * * *
58800066 CACTACAACTTTAGGAAGATGAGATTTGTAGCTTCAATCTGCTCCACGGCAACTTCAGGGAGATG
1 CACTGCAACTTCAGGAAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
* *
58800131 AGATTCGCTATCTTCAATCTA-TT
66 AGATTTG-TAGCTTCAATC-AGTT
* *
58800154 CCACCGCAACTTCAGGAAGATAAGATTTGTAGC-TCTAACCTGCTCCACTGCAACTTCAGGGAGA
1 -CACTGCAACTTCAGGAAGATAAGATTTGTAGCTTC-AATCTGCTCCACTGCAACTTCAGGGAGA
* * *
58800218 TGAGATTTGTAACTTGTAGCTTTAATCTGTT
64 T-A-A---G--ATTTGTAGCTTCAATCAGTT
* * ** * * * * *
58800249 CCACTACAAGTTTGGGGAA-ATAATATTTTCTATCTTCAATCTGCTCCACTGCAAATTCAGGGAA
1 -CACTGCAA-CTTCAGGAAGATAAGA-TTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAG
* * ** * *
58800313 ATAAGATTCGCATATTCAATCTGCTC
63 ATAAGATTTGTAGCTTCAATCAG-TT
* * * * ** *
58800339 CATTGTAACTTCA-GAGAGATAAGGTTTGTAACTTGTAGCTTTAATCTATTCCGCTGC-ACTTCA
1 CACTGCAACTTCAGGA-AGATAA-----G--ATTTGTAGCTTCAATCTGCTCCACTGCAACTTCA
* * * * * **
58800402 AGGAAATAAGACTCATTACGATAGATTTAATCTGACC
58 GGGAGATAAGA-T--TT--G-TAGCTTCAATCAG-TT
* * * * * * * *
58800439 CACTGCAACTTCA-GAGGTATATGATTTATCGCTTCAATCTACTCTACTGTAACTTTAGGGAGAT
1 CACTGCAACTTCAGGAAG-ATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGAT
* *
58800503 AAGATTTGCTATCTTCAATCTGTT
65 AAGATTTG-TAGCTTCAATCAGTT
* * * *
58800527 CCACTACAACTTCAGGAAGATAAGATTTGTGGCTTTAATCTGCTCCACTACAACTTCAGGTG-GA
1 -CACTGCAACTTCAGGAAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGG-GAGA
** *
58800591 TAAGATTCACTACAGT-GACTTCAATTTGCT
64 TAAGATT---T---GTAG-CTTCAATCAGTT
* * * * * *
58800621 CTACTGCAACTTCA-GAGAGATAAGATTTGTTATCTTCAATCTACTCTACTACAACTTTAGAGAG
1 C-ACTGCAACTTCAGGA-AGATAAGATTTG-TAGCTTCAATCTGCTCCACTGCAACTTCAGGGAG
* **
58800685 ATAAGATTTGTAACTTCAATTTGTT
63 ATAAGATTTGTAGCTTCAATCAGTT
* **
58800710 GTACTGCAACTTCA-G-AGATAAGATTTGTTATTTTCAATCTGCTCCACTGCAAC
1 -CACTGCAACTTCAGGAAGATAAGATTTG-TAGCTTCAATCTGCTCCACTGCAAC
58800763 CTAAAGGAGA
Statistics
Matches: 604, Mismatches: 129, Indels: 107
0.72 0.15 0.13
Matches are distributed among these distances:
87 37 0.06
88 65 0.11
89 247 0.41
90 7 0.01
91 4 0.01
92 2 0.00
93 23 0.04
94 66 0.11
95 79 0.13
96 42 0.07
97 3 0.00
99 2 0.00
100 27 0.04
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (87 bp):
CACTGCAACTTCAGGAAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
AGATTTGTAGCTTCAATCAGTT
Found at i:58800122 original size:133 final size:133
Alignment explanation
Indices: 58799877--58800228 Score: 456
Period size: 133 Copynumber: 2.6 Consensus size: 133
58799867 GAAATGTAAT
* * * * *
58799877 TTCAACCTACTCCACTGCAACTTTAGGGACATAAGATTTGTAGCTTTAATCTGCTCCACTATAAC
1 TTCAATCTACTCCACTGCAACTTCAGGGAAATAAGATTTGTAGCTTCAATCTGCTCCACTACAAC
* * ** * * *
58799942 TTCAGGGAGATAAGATTTGTAGCTTCAATCAGGTTTACTGCAGCTTCAGAGAGATAAGATTTGCT
66 TTCAGGGAGATGAGATTTGTAGCTTCAATCAGCTCCACGGCAACTTCAGAGAGATAAGATTCGCT
58800007 ATC
131 ATC
* * *
58800010 TTCAATTTGCTCCACTGTAACTTCAGGGAAATAAGATTTGTAGCTTCAATCTGCTCCACTACAAC
1 TTCAATCTACTCCACTGCAACTTCAGGGAAATAAGATTTGTAGCTTCAATCTGCTCCACTACAAC
* * * * *
58800075 TTTAGGAAGATGAGATTTGTAGCTTCAATCTGCTCCACGGCAACTTCAGGGAGATGAGATTCGCT
66 TTCAGGGAGATGAGATTTGTAGCTTCAATCAGCTCCACGGCAACTTCAGAGAGATAAGATTCGCT
58800140 ATC
131 ATC
* * * *
58800143 TTCAATCTATTCCACCGCAACTTCA-GGAAGATAAGATTTGTAGC-TCTAACCTGCTCCACTGCA
1 TTCAATCTACTCCACTGCAACTTCAGGGAA-ATAAGATTTGTAGCTTC-AATCTGCTCCACTACA
58800206 ACTTCAGGGAGATGAGATTTGTA
64 ACTTCAGGGAGATGAGATTTGTA
58800229 ACTTGTAGCT
Statistics
Matches: 188, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
132 6 0.03
133 182 0.97
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (133 bp):
TTCAATCTACTCCACTGCAACTTCAGGGAAATAAGATTTGTAGCTTCAATCTGCTCCACTACAAC
TTCAGGGAGATGAGATTTGTAGCTTCAATCAGCTCCACGGCAACTTCAGAGAGATAAGATTCGCT
ATC
Found at i:58800317 original size:140 final size:140
Alignment explanation
Indices: 58799877--58800586 Score: 451
Period size: 133 Copynumber: 5.2 Consensus size: 140
58799867 GAAATGTAAT
* * * * * **
58799877 TTCAACCTACTCCACTGCAACTTTAGGGACATAAGATTTGTAGCTTTAATCTGCTCCACTATAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGTAGCTCTAATCTGCTCCACTGCAAC
* * * * * * *
58799942 TTCAGGGAGAT-A-A---G--ATTTGTAGCTTCAATCAGGTT-TACTG-CAGCTTCAGAGAGATA
66 TTCAGGGAGATGAGATTTGTAACTTGTAGCTTTAATC-TGTTCCAC-GACAACTTCAGGGAAATA
58799998 AGATTTGCTATC
129 AGATTTGCTATC
* * *
58800010 TTCAATTTGCTCCACTGTAACTTCAGGGAAATAAGATTTGTAGCT-TCAATCTGCTCCACTACAA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGTAGCTCT-AATCTGCTCCACTGCAA
* * * * * * *
58800074 CTTTAGGAAGATGAGA----T---TTGTAGCTTCAATCTGCTCCACGGCAACTTCAGGGAGATGA
65 CTTCAGGGAGATGAGATTTGTAACTTGTAGCTTTAATCTGTTCCACGACAACTTCAGGGAAATAA
*
58800132 GATTCGCTATC
130 GATTTGCTATC
** * *
58800143 TTCAATCTATTCCACCGCAACTTCA-GGAAGATAAGATTTGTAGCTCTAACCTGCTCCACTGCAA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAA-ATAAGATTTGTAGCTCTAATCTGCTCCACTGCAA
* * **
58800207 CTTCAGGGAGATGAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTACAAGTTTGGGGAAATAA
65 CTTCAGGGAGATGAGATTTGTAACTTGTAGCTTTAATCTGTTCCACGACAACTTCAGGGAAATAA
* *
58800272 TATTTTCTATC
130 GATTTGCTATC
* * * * *
58800283 TTCAATCTGCTCCACTGCAAATTCAGGGAAATAAGATTCGCATA-TTC-AATCTGCTCCATTGTA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTG--TAGCTCTAATCTGCTCCACTGCA
* * * * * *
58800346 ACTTCAGAGAGATAAGGTTTGTAACTTGTAGCTTTAATCTATTCCGCTG-C-ACTTCAAGGAAAT
64 ACTTCAGGGAGATGAGATTTGTAACTTGTAGCTTTAATCTGTTCCAC-GACAACTTCAGGGAAAT
* **
58800409 AAGACTCATTACGATAGA
128 AAGA-T--TT--GCTATC
* * * * * * * *
58800427 TTTAATCTGAC-CCACTGCAACTTCAGAGG-TATATGATTTATCGCT-TCAATCTACTCTACTGT
1 TTCAATCTG-CTCCACTGCAACTTCAG-GGAAATAAGATTTGTAGCTCT-AATCTGCTCCACTGC
* * * * *
58800489 AACTTTAGGGAGATAAGATTTG---C---TATCTTCAATCTGTTCCACTACAACTTCA-GGAAGA
63 AACTTCAGGGAGATGAGATTTGTAACTTGTAGCTTTAATCTGTTCCACGACAACTTCAGGGAA-A
**
58800547 TAAGATTTG-TGGC
127 TAAGATTTGCTATC
* *
58800560 TTTAATCTGCTCCACTACAACTTCAGG
1 TTCAATCTGCTCCACTGCAACTTCAGG
58800587 TGGATAAGAT
Statistics
Matches: 461, Mismatches: 83, Indels: 67
0.75 0.14 0.11
Matches are distributed among these distances:
132 10 0.02
133 194 0.42
134 3 0.01
135 1 0.00
136 2 0.00
137 1 0.00
138 21 0.05
139 24 0.05
140 127 0.28
141 7 0.02
142 5 0.01
143 1 0.00
144 62 0.13
145 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (140 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGTAGCTCTAATCTGCTCCACTGCAAC
TTCAGGGAGATGAGATTTGTAACTTGTAGCTTTAATCTGTTCCACGACAACTTCAGGGAAATAAG
ATTTGCTATC
Found at i:58809629 original size:17 final size:17
Alignment explanation
Indices: 58809607--58809639 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
58809597 ATGAAGAAAT
*
58809607 ATTATAATAATAACATA
1 ATTATAACAATAACATA
58809624 ATTATAACAATAACAT
1 ATTATAACAATAACAT
58809640 TGACATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (17 bp):
ATTATAACAATAACATA
Found at i:58810071 original size:14 final size:15
Alignment explanation
Indices: 58810052--58810080 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
58810042 AAAACAATTT
58810052 AATAAA-GATTAAAA
1 AATAAATGATTAAAA
58810066 AATAAATGATTAAAA
1 AATAAATGATTAAAA
58810081 TGAAATGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (15 bp):
AATAAATGATTAAAA
Found at i:58819886 original size:14 final size:12
Alignment explanation
Indices: 58819857--58819887 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
58819847 TCGTATTAGG
58819857 TTTTTTATATTA
1 TTTTTTATATTA
*
58819869 TTTTTTATATAA
1 TTTTTTATATTA
58819881 TTTTTTA
1 TTTTTTA
58819888 AAAAAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTATATTA
Found at i:58820212 original size:27 final size:28
Alignment explanation
Indices: 58820157--58820221 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 28
58820147 ATAAAAAATA
*
58820157 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAACATTTTTTTATTT
58820185 ACCAAAATATTATAA-ATTTTTTTATTT
1 ACCAAAATATTATAACATTTTTTTATTT
58820212 ACCAAAATAT
1 ACCAAAATAT
58820222 ACCAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 21 0.58
28 15 0.42
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.48
Consensus pattern (28 bp):
ACCAAAATATTATAACATTTTTTTATTT
Found at i:58820658 original size:19 final size:19
Alignment explanation
Indices: 58820634--58820699 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
58820624 ATTAAAATAG
58820634 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
** *
58820653 TTTAATGCAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
58820671 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
58820690 TTTAATTTAA
1 TTTAATTTAA
58820700 AAAAATTAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
18 13 0.36
19 23 0.64
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:58820865 original size:82 final size:82
Alignment explanation
Indices: 58820779--58820943 Score: 303
Period size: 82 Copynumber: 2.0 Consensus size: 82
58820769 CAAAAGGAAA
*
58820779 AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCTTAATAGACTTATAA
1 AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCGTAATAGACTTATAA
*
58820844 CATAAGCATGTTAGACT
66 CATAAACATGTTAGACT
*
58820861 AAATAATGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCGTAATAGACTTATAA
1 AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCGTAATAGACTTATAA
58820926 CATAAACATGTTAGACT
66 CATAAACATGTTAGACT
58820943 A
1 A
58820944 TTTTAATTAA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (82 bp):
AAATAACGGAAACATAAACTATTTTATCTATTTATAAATTTAATATATTCGTAATAGACTTATAA
CATAAACATGTTAGACT
Found at i:58821497 original size:27 final size:28
Alignment explanation
Indices: 58821463--58821527 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
58821453 TTTTTTTGGT
*
58821463 ATATTTTGGTAAAT-AAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
58821490 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
58821518 ATATTTTGGT
1 ATATTTTGGT
58821528 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 14 0.39
28 22 0.61
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.42
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:58825863 original size:27 final size:28
Alignment explanation
Indices: 58825787--58825867 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
58825777 GGAATTTAGT
* *
58825787 TGAATCAAGTATAACACACATAAAGTAC
1 TGAATCAAATATAACACACATAAAGCAC
*
58825815 TGAATCAAATATAACACACATAAAGCAT
1 TGAATCAAATATAACACACATAAAGCAC
* * *
58825843 TGGATC-CATATAACACGCATAAAGC
1 TGAATCAAATATAACACACATAAAGC
58825868 GTTAGATCTC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 17 0.36
28 30 0.64
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.21
Consensus pattern (28 bp):
TGAATCAAATATAACACACATAAAGCAC
Found at i:58825875 original size:27 final size:27
Alignment explanation
Indices: 58825796--58825875 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
58825786 TTGAATCAAG
* * *
58825796 TATAACACACATAAAGTACT-GAATCAAA
1 TATAACACACATAAAGCATTAG-ATC-CA
*
58825824 TATAACACACATAAAGCATTGGATCCA
1 TATAACACACATAAAGCATTAGATCCA
* *
58825851 TATAACACGCATAAAGCGTTAGATC
1 TATAACACACATAAAGCATTAGATC
58825876 TCCCGCCTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 23 0.51
28 21 0.47
29 1 0.02
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (27 bp):
TATAACACACATAAAGCATTAGATCCA
Found at i:58827459 original size:21 final size:22
Alignment explanation
Indices: 58827433--58827478 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
58827423 AATCTATATA
58827433 TATACATGT-ATATTTATTTTT
1 TATACATGTAATATTTATTTTT
58827454 TATACATGTACATATTTATTTTT
1 TATACATGTA-ATATTTATTTTT
58827477 TA
1 TA
58827479 ACTAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.39
23 14 0.61
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (22 bp):
TATACATGTAATATTTATTTTT
Found at i:58827958 original size:19 final size:20
Alignment explanation
Indices: 58827917--58827958 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
58827907 ATTTCTATGC
* *
58827917 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
58827937 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
58827956 CAT
1 CAT
58827959 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:58828869 original size:2 final size:2
Alignment explanation
Indices: 58828862--58828888 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
58828852 AAGGTATCAC
58828862 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
58828889 ATTCTCTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58831095 original size:19 final size:17
Alignment explanation
Indices: 58831071--58831114 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
58831061 CAATGCATCT
*
58831071 AATAATTATACAGATTACC
1 AATAATAATACA-ATT-CC
*
58831090 AATAATAATTCAATTCC
1 AATAATAATACAATTCC
58831107 AATAATAA
1 AATAATAA
58831115 AACACATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
18 3 0.13
19 10 0.43
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (17 bp):
AATAATAATACAATTCC
Found at i:58838145 original size:5 final size:5
Alignment explanation
Indices: 58838135--58838165 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
58838125 AAACACATTT
58838135 GTTGG GTTGG GTTGG GTTGG GTTGG GTTGG G
1 GTTGG GTTGG GTTGG GTTGG GTTGG GTTGG G
58838166 GGTATAGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.61, T:0.39
Consensus pattern (5 bp):
GTTGG
Found at i:58847203 original size:30 final size:30
Alignment explanation
Indices: 58847167--58847236 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
58847157 GGTGAATTAA
* *
58847167 GTTGCTCACACAAGCTAACATTATATCAGG
1 GTTGCTCACACAAACTAACATTATATCAAG
*
58847197 GTTGCTCAAACAAACTAACATTATATCAAG
1 GTTGCTCACACAAACTAACATTATATCAAG
*
58847227 GTTGTTCACA
1 GTTGCTCACA
58847237 TAAGTTGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (30 bp):
GTTGCTCACACAAACTAACATTATATCAAG
Found at i:58847817 original size:21 final size:19
Alignment explanation
Indices: 58847780--58847821 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
58847770 TTTTCACCTC
*
58847780 AATATTAAATCATGCAATT
1 AATATTAAATCAGGCAATT
58847799 AATATATAAATGCAGGCAATT
1 AATAT-TAAAT-CAGGCAATT
58847820 AA
1 AA
58847822 ATCTATCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 10 0.50
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (19 bp):
AATATTAAATCAGGCAATT
Found at i:58849417 original size:32 final size:31
Alignment explanation
Indices: 58849372--58849467 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
58849362 CTTAGATAAT
58849372 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
58849403 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
58849435 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
58849466 TT
1 TT
58849468 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:58850693 original size:82 final size:82
Alignment explanation
Indices: 58850563--58850784 Score: 275
Period size: 82 Copynumber: 2.7 Consensus size: 82
58850553 GGTTCAAATA
* * * * * * ** *
58850563 TTGAGGACTACATTGTTGGGAGGGGCAGCCATAATTCCTAAACATAGATCGTAAAATGGACACAG
1 TTGAGGACGATATTGTTGGAAGGAGCAACCATAAATCCCGAACATAGATCGTAAAATGGACACAA
58850628 AGACGTAAATTCAAACC
66 AGACGTAAATTCAAACC
* * *
58850645 TTGAGGATGATATTGTTGGAA-GAGGCAACCATGAATCCCGAACATAGATCGTAAAATAGACACA
1 TTGAGGACGATATTGTTGGAAGGA-GCAACCATAAATCCCGAACATAGATCGTAAAATGGACACA
*
58850709 AAGACGTAAGTTCAAACC
65 AAGACGTAAATTCAAACC
* * * *
58850727 TTGAGGACGATATTGTTGGAAGGAGCAGCCATAAATCTCGAACATAAAGCGTAAAATG
1 TTGAGGACGATATTGTTGGAAGGAGCAACCATAAATCCCGAACATAGATCGTAAAATG
58850785 AATATGAAGA
Statistics
Matches: 118, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
81 1 0.01
82 115 0.97
83 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (82 bp):
TTGAGGACGATATTGTTGGAAGGAGCAACCATAAATCCCGAACATAGATCGTAAAATGGACACAA
AGACGTAAATTCAAACC
Found at i:58861372 original size:5 final size:5
Alignment explanation
Indices: 58861362--58861440 Score: 76
Period size: 5 Copynumber: 16.0 Consensus size: 5
58861352 TTTGGAAAGC
* *
58861362 TTTAA TTTAA TTTAA TTTAA TTTAA TTT-G TTT-T TTATAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT-TAA TTTAA TTTAA
*
58861411 TTATAA --TAT TTTAA TTTAA TTATAA TTTAA
1 TT-TAA TTTAA TTTAA TTTAA TT-TAA TTTAA
58861441 AAATGTCACA
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
3 2 0.03
4 5 0.08
5 46 0.73
6 10 0.16
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (5 bp):
TTTAA
Found at i:58861401 original size:24 final size:23
Alignment explanation
Indices: 58861372--58861440 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 23
58861362 TTTAATTTAA
** *
58861372 TTTAATTTAATTTAATTTGTTTT
1 TTTAATTTAATTTAATTTAATAT
58861395 TTATAATTTAATTTAATTATAATAT
1 TT-TAATTTAATTTAATT-TAATAT
58861420 TTTAATTTAATTATAATTTAA
1 TTTAATTTAATT-TAATTTAA
58861441 AAATGTCACA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
23 2 0.05
24 28 0.70
25 10 0.25
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (23 bp):
TTTAATTTAATTTAATTTAATAT
Found at i:58869359 original size:31 final size:31
Alignment explanation
Indices: 58869299--58869359 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
58869289 ATTATGCACG
*
58869299 TAAAACTTTAATTGTGATTCAAACCTATACT
1 TAAAACTTTAATTGTGATTCAAACATATACT
* * * *
58869330 TAAAATTTTAATTTTGATTTAATCATATAC
1 TAAAACTTTAATTGTGATTCAAACATATAC
58869360 ATTTAAAGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.44
Consensus pattern (31 bp):
TAAAACTTTAATTGTGATTCAAACATATACT
Found at i:58869507 original size:30 final size:30
Alignment explanation
Indices: 58869483--58869541 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
58869473 GAATTTGATC
58869483 AAATCAAAATTTATTATATAGAATTACACA
1 AAATCAAAATTTATTATATAGAATTACACA
*
58869513 AAATCAAAATTTA-TATATACAATTACACA
1 AAATCAAAATTTATTATATAGAATTACACA
58869542 TTAAATCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTATTATATAGAATTACACA
Found at i:58869560 original size:31 final size:29
Alignment explanation
Indices: 58869483--58869562 Score: 106
Period size: 31 Copynumber: 2.7 Consensus size: 29
58869473 GAATTTGATC
*
58869483 AAATCAAAATTTATTATATAGAATTACACA
1 AAATCAAAATTTA-TATATACAATTACACA
58869513 AAATCAAAATTTATATATACAATTACACA
1 AAATCAAAATTTATATATACAATTACACA
* *
58869542 TTAAATCATAATTGATATATA
1 --AAATCAAAATTTATATATA
58869563 ATTTTGATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 15 0.33
30 13 0.29
31 17 0.38
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.35
Consensus pattern (29 bp):
AAATCAAAATTTATATATACAATTACACA
Found at i:58879404 original size:25 final size:25
Alignment explanation
Indices: 58879350--58879405 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
58879340 ATGTAAACGA
* *
58879350 GAAGCTCTTTCGAGCCATATAATAG
1 GAAGCTCTTGCGAGCCAAATAATAG
*
58879375 AAAGCTCTTGCGAGCCAAAT-ATCAG
1 GAAGCTCTTGCGAGCCAAATAAT-AG
58879400 GAAGCT
1 GAAGCT
58879406 TAAGAGAGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (25 bp):
GAAGCTCTTGCGAGCCAAATAATAG
Found at i:58879414 original size:25 final size:25
Alignment explanation
Indices: 58879386--58879472 Score: 86
Period size: 25 Copynumber: 3.5 Consensus size: 25
58879376 AAGCTCTTGC
* *
58879386 GAGCCAAATATCAGGAAGCTTAAGA
1 GAGCCAATTATCAGGAAGCTTATGA
* * * *
58879411 GAGCC-ATTAACCAAGAAGCTCATGG
1 GAGCCAATT-ATCAGGAAGCTTATGA
*
58879436 GAGCCAATTATCAGGAAGCTTGTGA
1 GAGCCAATTATCAGGAAGCTTATGA
*
58879461 GAGCCAAGTATC
1 GAGCCAATTATC
58879473 GAGAAGATCA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
24 2 0.04
25 43 0.90
26 3 0.06
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (25 bp):
GAGCCAATTATCAGGAAGCTTATGA
Found at i:58891422 original size:13 final size:14
Alignment explanation
Indices: 58891404--58891432 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
58891394 CCAATAATTA
58891404 AAAATAAAAT-ACC
1 AAAATAAAATAACC
58891417 AAAATAAAATAACC
1 AAAATAAAATAACC
58891431 AA
1 AA
58891433 GAAATCCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAATAAAATAACC
Found at i:58892964 original size:15 final size:14
Alignment explanation
Indices: 58892944--58892982 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 14
58892934 TTTTATTTAA
58892944 TTATGTTAAATATT
1 TTATGTTAAATATT
58892958 TTCATGTTATAAATATT
1 TT-ATG-T-TAAATATT
58892975 TTATGTTA
1 TTATGTTA
58892983 TAAATAGGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.18
15 4 0.18
16 4 0.18
17 10 0.45
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (14 bp):
TTATGTTAAATATT
Found at i:58892982 original size:16 final size:17
Alignment explanation
Indices: 58892950--58892988 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
58892940 TTAATTATGT
58892950 TAAATATTTTCATGTTA
1 TAAATATTTTCATGTTA
58892967 TAAATATTTT-ATGTTA
1 TAAATATTTTCATGTTA
58892983 TAAATA
1 TAAATA
58892989 GGCGAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (17 bp):
TAAATATTTTCATGTTA
Found at i:58899774 original size:21 final size:20
Alignment explanation
Indices: 58899746--58899798 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
58899736 ACAGCGGTGG
58899746 CAGTGAGATTAATTACTGTAA
1 CAGTGAGATTAA-TACTGTAA
* * *
58899767 CGGTGAGATTGGATACTGTAG
1 CAGTGAGATT-AATACTGTAA
58899788 CAGTGAGATTA
1 CAGTGAGATTA
58899799 GAAACAATGG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.32, C:0.09, G:0.28, T:0.30
Consensus pattern (20 bp):
CAGTGAGATTAATACTGTAA
Found at i:58900765 original size:16 final size:16
Alignment explanation
Indices: 58900744--58900775 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
58900734 TTGAAAATGG
58900744 TTGAAAAGTCCACAAA
1 TTGAAAAGTCCACAAA
58900760 TTGAAAAGTCCACAAA
1 TTGAAAAGTCCACAAA
58900776 AGTCCACTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (16 bp):
TTGAAAAGTCCACAAA
Found at i:58902682 original size:18 final size:18
Alignment explanation
Indices: 58902658--58902700 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
58902648 TTCGTTTCCA
58902658 AAACATTATTC-ATTTAC
1 AAACATTATTCAATTTAC
*
58902675 AAATCATTATTCAATTTCC
1 AAA-CATTATTCAATTTAC
58902694 AAACATT
1 AAACATT
58902701 TTTTTATTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
19 8 0.35
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.40
Consensus pattern (18 bp):
AAACATTATTCAATTTAC
Found at i:58903672 original size:17 final size:18
Alignment explanation
Indices: 58903641--58903674 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
58903631 CATGATGTTT
58903641 GCCCGTGTAGGCCCACAC
1 GCCCGTGTAGGCCCACAC
58903659 GCCCGTGT-GGCCCACA
1 GCCCGTGTAGGCCCACA
58903675 TGGCTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.15, C:0.44, G:0.29, T:0.12
Consensus pattern (18 bp):
GCCCGTGTAGGCCCACAC
Found at i:58909662 original size:17 final size:17
Alignment explanation
Indices: 58909640--58909681 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
58909630 CGCCTGTGTA
58909640 GGCCCACACGCCCATGT
1 GGCCCACACGCCCATGT
*
58909657 GGCCCACACGCCCGTGT
1 GGCCCACACGCCCATGT
58909674 GGCCCACA
1 GGCCCACA
58909682 TGGCTGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.17, C:0.48, G:0.26, T:0.10
Consensus pattern (17 bp):
GGCCCACACGCCCATGT
Found at i:58918994 original size:51 final size:51
Alignment explanation
Indices: 58918914--58919102 Score: 222
Period size: 51 Copynumber: 3.7 Consensus size: 51
58918904 CATGAGAACT
* * * * **
58918914 CATGTGTAGTACTATGTGTAGGCTCCTATGAGTATAAGATAGTTATGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTATGGTCA
58918965 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCTT-TGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG-TTATGGTCA
* * * *
58919016 -AGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-GGTATTGGTCA
1 CA-TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTA-TGGTCA
* *
58919067 CGTGTGTAGTACTAAGTGTAGGCTACTATGTGTACC
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACC
58919103 GAATAGCATT
Statistics
Matches: 119, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
49 1 0.01
50 2 0.02
51 114 0.96
52 2 0.02
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (51 bp):
CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTATGGTCA
Found at i:58919130 original size:51 final size:50
Alignment explanation
Indices: 58918970--58919136 Score: 160
Period size: 51 Copynumber: 3.3 Consensus size: 50
58918960 GGTCACATGT
*
58918970 GTAGTACTAAGTGCAGGCTACTATGTGTACC-AGATAGCTTTGGTC-AAGTG
1 GTAGTACTAAGTGCAGGCTACTATGTGTACCGA-ATAGCATTGGTCAAAG-G
* * * * * *
58919020 TGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGGTATTGGTC-ACGTG
1 -GTAGTACTAAGTGCAGGCTACTATGTGTACCGAATAGCATTGGTCAAAG-G
* *
58919071 TGTAGTACTAAGTGTAGGCTACTATGTGTACCGAATAGCATTGATCATAAGG
1 -GTAGTACTAAGTGCAGGCTACTATGTGTACCGAATAGCATTGGTCA-AAGG
* *
58919123 GTGGTACTATGTGC
1 GTAGTACTAAGTGC
58919137 GGAACCACCG
Statistics
Matches: 95, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
51 92 0.97
52 1 0.01
53 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.31
Consensus pattern (50 bp):
GTAGTACTAAGTGCAGGCTACTATGTGTACCGAATAGCATTGGTCAAAGG
Found at i:58921492 original size:39 final size:39
Alignment explanation
Indices: 58921448--58921590 Score: 223
Period size: 39 Copynumber: 3.7 Consensus size: 39
58921438 CATATTCACT
*
58921448 TTTAAGCATATATCACATTACACATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* * *
58921487 TTTAAGCAAATATCACAATACTCATATAATCACATAAAA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
*
58921526 TTTAAGCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* *
58921565 TTCAAGTATATATCACAATACACATA
1 TTTAAGCATATATCACAATACACATA
58921591 ACATGTTTAT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 95 1.00
ACGTcount: A:0.48, C:0.20, G:0.03, T:0.30
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACACATATAATCACATAACA
Found at i:58938336 original size:28 final size:30
Alignment explanation
Indices: 58938297--58938353 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
58938287 ATATGAATGG
58938297 AAAGTGGAACTTTAATGCAA-T-ACAGTGA
1 AAAGTGGAACTTTAATGCAACTGACAGTGA
* *
58938325 AAAGTGGCACTTTGATGCAACTGACAGTG
1 AAAGTGGAACTTTAATGCAACTGACAGTG
58938354 GCACTATGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.72
29 1 0.04
30 6 0.24
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.25
Consensus pattern (30 bp):
AAAGTGGAACTTTAATGCAACTGACAGTGA
Found at i:58941436 original size:3 final size:3
Alignment explanation
Indices: 58941423--58941463 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
58941413 CATTTAATTG
*
58941423 TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
58941464 AAAACTAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:58945098 original size:22 final size:22
Alignment explanation
Indices: 58945073--58945115 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
58945063 ATAAGCTTCT
*
58945073 TTACATTCAATTAATAAATGTA
1 TTACATTCAATCAATAAATGTA
58945095 TTACATTCAATCAATAAATGT
1 TTACATTCAATCAATAAATGT
58945116 GAATTAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (22 bp):
TTACATTCAATCAATAAATGTA
Found at i:58949266 original size:274 final size:274
Alignment explanation
Indices: 58948762--58949318 Score: 898
Period size: 274 Copynumber: 2.0 Consensus size: 274
58948752 TACTCAAAAA
*
58948762 TTGAGGGATGTTGTGTCCCTATTCCGGGACGAAGCTTATCAGTGGTGGTTGACAGTTGAGCAAGG
1 TTGAGGGATGTTGTGTCCCTATTCCGGGACGAAGCTTATCAGTGGTGGTTGACAGTTGAGCAAAG
* *
58948827 TGTTCAACTTGAACAGGTGAACTGAGACTATTTCAAGAACACCTTCCAAGGTAAGTATGTGAGGG
66 TGTTCAACCTGAACAGGTGAACTGAGACTATTTCAAGAACACATTCCAAGGTAAGTATGTGAGGG
*
58948892 CAAATTATGTTGAAGCTCATCGATACGAGTTCATGAGCCTAGTTTAGGGCGACCGATCGGTGGCC
131 CAAATTATGTTGAAGCTCACCGATACGAGTTCATGAGCCTAGTTTAGGGCGACCGATCGGTGGCC
* * * * * * *
58948957 AAATATGAAGTCGAGTTTTTACGACTGAGTAGGTATGTATGGACTCTAGTAGCGTCTAATTATGA
196 AAATATAAAGCCAAGTTTTTACGACTAAATAGGTATGCATGGACTCTAGTAGCGTCTAATTACGA
58949022 AAAGTGTGTAAAGT
261 AAAGTGTGTAAAGT
* * * *
58949036 TTGAGGGGTGTTGTTTCCTTATTTCGGGACGAAGCTTATCAGTGGTGGTTGACAGTTGAGCAAAG
1 TTGAGGGATGTTGTGTCCCTATTCCGGGACGAAGCTTATCAGTGGTGGTTGACAGTTGAGCAAAG
* * * *
58949101 TGTTCATCCTGAACAGGTGAACTGGGACTATTTCAAGAACATATTCCAAGGTTAGTATGTGAGGG
66 TGTTCAACCTGAACAGGTGAACTGAGACTATTTCAAGAACACATTCCAAGGTAAGTATGTGAGGG
58949166 CAAATTATGTTGAAGCTCACCGATACGAGTTCATGAGCCTAGTTTAGGGCGACCGATCGGTGGCC
131 CAAATTATGTTGAAGCTCACCGATACGAGTTCATGAGCCTAGTTTAGGGCGACCGATCGGTGGCC
* *
58949231 AAATATAAAGCCAAGTTTTTGCGACTAAATAGGTATGCATGGACTCTAGTAGCTTCTAATTACGA
196 AAATATAAAGCCAAGTTTTTACGACTAAATAGGTATGCATGGACTCTAGTAGCGTCTAATTACGA
* * *
58949296 TAAGTGTGTGAGGT
261 AAAGTGTGTAAAGT
58949310 TTGAGGGAT
1 TTGAGGGAT
58949319 TGAGATATGA
Statistics
Matches: 258, Mismatches: 25, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
274 258 1.00
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (274 bp):
TTGAGGGATGTTGTGTCCCTATTCCGGGACGAAGCTTATCAGTGGTGGTTGACAGTTGAGCAAAG
TGTTCAACCTGAACAGGTGAACTGAGACTATTTCAAGAACACATTCCAAGGTAAGTATGTGAGGG
CAAATTATGTTGAAGCTCACCGATACGAGTTCATGAGCCTAGTTTAGGGCGACCGATCGGTGGCC
AAATATAAAGCCAAGTTTTTACGACTAAATAGGTATGCATGGACTCTAGTAGCGTCTAATTACGA
AAAGTGTGTAAAGT
Found at i:58957059 original size:30 final size:30
Alignment explanation
Indices: 58957025--58957089 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
58957015 GGAAGTAAAC
58957025 CTTAAAATTCAGAATTTTGGA-GGAAGAGGA
1 CTTAAAATTCAGAATTTTGGAGGGAA-AGGA
58957055 CTTAAAATTCAGAATTTTGGAGGGAAAGGA
1 CTTAAAATTCAGAATTTTGGAGGGAAAGGA
58957085 -TTAAA
1 CTTAAA
58957090 TAGTAAAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
29 5 0.15
30 25 0.74
31 4 0.12
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (30 bp):
CTTAAAATTCAGAATTTTGGAGGGAAAGGA
Found at i:58962735 original size:22 final size:22
Alignment explanation
Indices: 58962710--58962752 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
58962700 ATAAGCTCCT
*
58962710 TTACATTAAATTAATAAATGTA
1 TTACATTAAATCAATAAATGTA
*
58962732 TTACATTCAATCAATAAATGT
1 TTACATTAAATCAATAAATGT
58962753 GAATTAAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (22 bp):
TTACATTAAATCAATAAATGTA
Found at i:58967862 original size:18 final size:18
Alignment explanation
Indices: 58967835--58967870 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
58967825 GCAAGATATC
*
58967835 CCAAATTAAAATCCAAAT
1 CCAAAATAAAATCCAAAT
58967853 CCAAAATAAAATCCAAAT
1 CCAAAATAAAATCCAAAT
58967871 GTCTAGAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.22, G:0.00, T:0.19
Consensus pattern (18 bp):
CCAAAATAAAATCCAAAT
Found at i:58969555 original size:51 final size:51
Alignment explanation
Indices: 58969490--58969713 Score: 190
Period size: 51 Copynumber: 4.4 Consensus size: 51
58969480 GCATGGACTG
* * * *
58969490 TGTGTAGGCCACTATGTGAAAGTGAAAGTGAT-GGTCACGTGTGTAGTACTA
1 TGTGCAGGCTACTATGTGAACG-GAAAGTGATAGGTCACATGTGTAGTACTA
* * * * *
58969541 TGTGTAGGCTACTATGCGTAC-CAGAA-TGATAGGTCGCATGTGTAGTACTA
1 TGTGCAGGCTACTATGTGAACGGA-AAGTGATAGGTCACATGTGTAGTACTA
* * * * *
58969591 TGTGCAGGCTACTATGCGTACCGGATAGCT--TCGATCACATGTGTAGTACTA
1 TGTGCAGGCTACTATGTG-AACGGAAAG-TGATAGGTCACATGTGTAGTACTA
* * * * *
58969642 TGTGCAGGCCATTACGTGTATCGGATAGTGAT-GGTCACATGTGTAGTACTA
1 TGTGCAGGCTACTATGTG-AACGGAAAGTGATAGGTCACATGTGTAGTACTA
58969693 TGTGCAGGCTACTATGTGAAC
1 TGTGCAGGCTACTATGTGAAC
58969714 CGGTATCATT
Statistics
Matches: 140, Mismatches: 25, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
49 5 0.04
50 39 0.28
51 93 0.66
52 2 0.01
53 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (51 bp):
TGTGCAGGCTACTATGTGAACGGAAAGTGATAGGTCACATGTGTAGTACTA
Found at i:58969700 original size:102 final size:101
Alignment explanation
Indices: 58969524--58969708 Score: 264
Period size: 102 Copynumber: 1.8 Consensus size: 101
58969514 AAAGTGATGG
* * * * *
58969524 TCACGTGTGTAGTACTATGTGTAGGCTACTATGCGTACCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACATGTGTAGTACTATGTGCAGGCCACTACGCGTACCAGAATGATAGGTCACATGTGTAGTAC
58969589 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* * * *
58969625 TCACATGTGTAGTACTATGTGCAGGCCATTACGTGTATCGGATAGTGAT-GGTCACATGTGTAGT
1 TCACATGTGTAGTACTATGTGCAGGCCACTACGCGTACCAGA-A-TGATAGGTCACATGTGTAGT
58969689 ACTATGTGCAGGCTACTATG
64 ACTATGTGCAGGCTACTATG
58969709 TGAACCGGTA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
101 34 0.47
102 35 0.48
103 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (101 bp):
TCACATGTGTAGTACTATGTGCAGGCCACTACGCGTACCAGAATGATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:58969803 original size:46 final size:43
Alignment explanation
Indices: 58969712--58969796 Score: 116
Period size: 46 Copynumber: 1.9 Consensus size: 43
58969702 TACTATGTGA
*
58969712 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTGATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGATCCC
* *
58969755 ACCGGATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGA
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGA
58969797 ATCCACCATG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 5 0.14
44 11 0.31
45 2 0.06
46 18 0.50
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGATCCC
Found at i:58969955 original size:16 final size:16
Alignment explanation
Indices: 58969934--58969965 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
58969924 TGATTGAAAG
*
58969934 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
58969950 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
58969966 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:58984097 original size:27 final size:28
Alignment explanation
Indices: 58984069--58984122 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
58984059 AAATAGGATA
*
58984069 AAAT-AAATAATAA-GTTAATAATAATT
1 AAATAAAATAATAATGGTAATAATAATT
*
58984095 AAATAAAATAATAATGGTATTAATAATT
1 AAATAAAATAATAATGGTAATAATAATT
58984123 GAGGAAATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 9 0.38
28 11 0.46
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (28 bp):
AAATAAAATAATAATGGTAATAATAATT
Found at i:58985355 original size:28 final size:27
Alignment explanation
Indices: 58985287--58985355 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
58985277 TATATATATA
* * *
58985287 ATATATACGTATAGGGGTTTTGTTATTT
1 ATATATA-ATATATGGGTTTTGGTATTT
*
58985315 ATATATAATATATGGGTTTTGGTGTTAT
1 ATATATAATATATGGGTTTTGGTATT-T
*
58985343 ATGTATAATATAT
1 ATATATAATATAT
58985356 TTACATGGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 15 0.43
28 20 0.57
ACGTcount: A:0.30, C:0.01, G:0.19, T:0.49
Consensus pattern (27 bp):
ATATATAATATATGGGTTTTGGTATTT
Found at i:58985441 original size:29 final size:28
Alignment explanation
Indices: 58985384--58985451 Score: 100
Period size: 29 Copynumber: 2.4 Consensus size: 28
58985374 CACATAGTAC
*
58985384 ATATATATGCGTGGTTTTGCTATACATA
1 ATATATATGCGTGGTTTTACTATACATA
* *
58985412 ATATATATGTGTGGGTTTTACTATATATA
1 ATATATATGCGT-GGTTTTACTATACATA
58985441 ATATATATGCG
1 ATATATATGCG
58985452 ACTATAGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
28 11 0.31
29 24 0.69
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (28 bp):
ATATATATGCGTGGTTTTACTATACATA
Done.