Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 130 of 193
Found at i:41022065 original size:30 final size:31
Alignment explanation
Indices: 41022031--41022249 Score: 131
Period size: 29 Copynumber: 7.5 Consensus size: 31
41022021 AAACTTTCCT
*
41022031 AAAATTA-CATTTTTAACCCCGATTTCACCG
1 AAAATTACCATTTTTAACCCCGATTTCATCG
* ** * **
41022061 AAAATTACCA-TTTT-ACCCCTAAATCTTTT
1 AAAATTACCATTTTTAACCCCGATTTCATCG
* *
41022090 AAAATT-CCATTTTTAACCCCGATTTTA-CC
1 AAAATTACCATTTTTAACCCCGATTTCATCG
* * * ** * *
41022119 AAAAATATCA-TTTTACCCCCGA-AGCTTCT
1 AAAATTACCATTTTTAACCCCGATTTCATCG
*
41022148 AAAATT-CTATTTTTAACCCCGATTTCATCG
1 AAAATTACCATTTTTAACCCCGATTTCATCG
* * **
41022178 AAAATTACCA-TTTT-ACCCCTGA-ATCTTTT
1 AAAATTACCATTTTTAACCCC-GATTTCATCG
* *
41022207 AAAATT-CCATTTTTAACCCCGATTACA-CT
1 AAAATTACCATTTTTAACCCCGATTTCATCG
41022236 AAAATTACCATTTT
1 AAAATTACCATTTT
41022250 GCCCCCGAGT
Statistics
Matches: 137, Mismatches: 39, Indels: 26
0.68 0.19 0.13
Matches are distributed among these distances:
28 7 0.05
29 78 0.57
30 48 0.35
31 4 0.03
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.37
Consensus pattern (31 bp):
AAAATTACCATTTTTAACCCCGATTTCATCG
Found at i:41022065 original size:90 final size:89
Alignment explanation
Indices: 41021881--41022109 Score: 243
Period size: 90 Copynumber: 2.6 Consensus size: 89
41021871 AAATTGTCCA
* * * * * * *
41021881 AAAATTATATTTTGACCCCAGAACTTTTCTAAAATTATATTTTGACCCCAGAACTTTTCTAAAAT
1 AAAATTACATTTTGACCCTAAAACTTTTCTAAAATTACATTTTAACCCCAAAACTTTCCTAAAAT
* *
41021946 TATATTTTGACCCCAAAACTTTACC
66 TACATTTTAACCCC-AAACTTTACC
*
41021971 AAAATTACATTTTGACCTTAAAACTTTTCTAAAATTACATTTTAACCCCAAAACTTTCCTAAAAT
1 AAAATTACATTTTGACCCTAAAACTTTTCTAAAATTACATTTTAACCCCAAAACTTTCCTAAAAT
*
41022036 TACATTTTTAACCCC-GA-TTTCACC
66 TACA-TTTTAACCCCAAACTTT-ACC
* *
41022060 GAAAATTACCATTTT-ACCCCTAAATC-TTT-TAAAATTCCATTTTTAACCCC
1 -AAAATTA-CATTTTGA-CCCTAAAACTTTTCTAAAATTACA-TTTTAACCCC
41022110 GATTTTACCA
Statistics
Matches: 119, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
88 3 0.03
89 13 0.11
90 81 0.68
91 22 0.18
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (89 bp):
AAAATTACATTTTGACCCTAAAACTTTTCTAAAATTACATTTTAACCCCAAAACTTTCCTAAAAT
TACATTTTAACCCCAAACTTTACC
Found at i:41022103 original size:59 final size:59
Alignment explanation
Indices: 41022001--41022254 Score: 318
Period size: 59 Copynumber: 4.3 Consensus size: 59
41021991 AAACTTTTCT
* *
41022001 AAAATTA-CATTTTAACCCC-AAAACTTTCCTAAAATTACATTTTTAACCCCGATTTCACCG
1 AAAATTACCATTTT-ACCCCTAAATCTTT--TAAAATTCCATTTTTAACCCCGATTTCACCG
*
41022061 AAAATTACCATTTTACCCCTAAATCTTTTAAAATTCCATTTTTAACCCCGATTTTACC-
1 AAAATTACCATTTTACCCCTAAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
* * ** * * * *
41022119 AAAAATATCATTTTACCCCCGAAGCTTCTAAAATTCTATTTTTAACCCCGATTTCATCG
1 AAAATTACCATTTTACCCCTAAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
* * *
41022178 AAAATTACCATTTTACCCCTGAATCTTTTAAAATTCCATTTTTAACCCCGATTACA-CT
1 AAAATTACCATTTTACCCCTAAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
*
41022236 AAAATTACCATTTTGCCCC
1 AAAATTACCATTTTACCCC
41022255 CGAGTATCCA
Statistics
Matches: 170, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
58 68 0.40
59 77 0.45
60 12 0.07
61 13 0.08
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTAAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACCG
Found at i:41022171 original size:117 final size:117
Alignment explanation
Indices: 41022029--41022257 Score: 370
Period size: 117 Copynumber: 2.0 Consensus size: 117
41022019 CAAAACTTTC
41022029 CTAAAATTACATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTAAATCTTTTAAAA
1 CTAAAATTACATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTAAATCTTTTAAAA
** *
41022094 TTCCATTTTTAACCCCGATTTTACCAAAAATATCATTTTACCCCCGAAGCTT
66 TTCCATTTTTAACCCCGATTACACCAAAAATACCATTTTACCCCCGAAGCTT
* *
41022146 CTAAAATT-CTATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCTGAATCTTTTAAA
1 CTAAAATTAC-ATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTAAATCTTTTAAA
* * *
41022210 ATTCCATTTTTAACCCCGATTACACTAAAATTACCATTTTGCCCCCGA
65 ATTCCATTTTTAACCCCGATTACACCAAAAATACCATTTTACCCCCGA
41022258 GTATCCATAA
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
116 1 0.01
117 102 0.99
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (117 bp):
CTAAAATTACATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTAAATCTTTTAAAA
TTCCATTTTTAACCCCGATTACACCAAAAATACCATTTTACCCCCGAAGCTT
Found at i:41022275 original size:58 final size:59
Alignment explanation
Indices: 41022038--41022293 Score: 225
Period size: 58 Copynumber: 4.4 Consensus size: 59
41022028 CCTAAAATTA
* * ** ** *
41022038 CATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTAAATCTTTTAAAATTC
1 CATTTTTAACCCCGATTACATCGAAAATTACCATTTTACCCCCGAATCTCATAAAATCC
** * * * * *
41022097 CATTTTTAACCCCGATTTTA-CCAAAAATATCATTTTACCCCCGAAGCTTC-TAAAATTC
1 CATTTTTAACCCCGATTACATCGAAAATTACCATTTTACCCCCGAATC-TCATAAAATCC
* * * ** *
41022155 TATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCTGAATCTTTTAAAATTC
1 CATTTTTAACCCCGATTACATCGAAAATTACCATTTTACCCCCGAATCTCATAAAATCC
* * *
41022214 CATTTTTAACCCCGATTACA-CTAAAATTACCATTTTGCCCCCGAGTATC-CAT-AAGTCC
1 CATTTTTAACCCCGATTACATCGAAAATTACCATTTTACCCCCGA--ATCTCATAAAATCC
* *
41022272 CATTTTTCACCCCGATTTCATC
1 CATTTTTAACCCCGATTACATC
41022294 ATATTCAATA
Statistics
Matches: 164, Mismatches: 27, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
58 91 0.55
59 70 0.43
60 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.36
Consensus pattern (59 bp):
CATTTTTAACCCCGATTACATCGAAAATTACCATTTTACCCCCGAATCTCATAAAATCC
Found at i:41022277 original size:117 final size:117
Alignment explanation
Indices: 41022038--41022293 Score: 363
Period size: 117 Copynumber: 2.2 Consensus size: 117
41022028 CCTAAAATTA
*
41022038 CATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTAAATCTTTTAAAATTCCATTTT
1 CATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCTAAATCTTTTAAAATTCCATTTT
** * * *
41022103 TAACCCCGATTTTACCAAAAATATCATTTTACCCCCGAAGCTTCTAAAATTC
66 TAACCCCGATTACACCAAAAATACCATTTTACCCCCGAAGCTTCCAAAATCC
* *
41022155 TATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCTGAATCTTTTAAAATTCCATTTT
1 CATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCTAAATCTTTTAAAATTCCATTTT
* * * *
41022220 TAACCCCGATTACACTAAAATTACCATTTTGCCCCCG-AG-TATCCATAAGTCC
66 TAACCCCGATTACACCAAAAATACCATTTTACCCCCGAAGCT-TCCA-AAATCC
*
41022272 CATTTTTCACCCCGATTTCATC
1 CATTTTTAACCCCGATTTCATC
41022294 ATATTCAATA
Statistics
Matches: 123, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
115 1 0.01
116 5 0.04
117 117 0.95
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.36
Consensus pattern (117 bp):
CATTTTTAACCCCGATTTCATCGAAAATTACCATTTTACCCCTAAATCTTTTAAAATTCCATTTT
TAACCCCGATTACACCAAAAATACCATTTTACCCCCGAAGCTTCCAAAATCC
Found at i:41023942 original size:30 final size:29
Alignment explanation
Indices: 41023899--41023985 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 29
41023889 TCTAATCCCA
* *
41023899 AAACTTTCTAAAATTCTATTTTTGACCCCG
1 AAAC-TTCCAAAATTCCATTTTTGACCCCG
**
41023929 AAACTTCCAAAAATTACCA-TTTT-ACCCTT
1 AAACTTCC-AAAATT-CCATTTTTGACCCCG
41023958 AAACTTTCCAAAATTCCATTTTTGACCC
1 AAAC-TTCCAAAATTCCATTTTTGACCC
41023986 TAATTTCACC
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
28 3 0.06
29 21 0.44
30 22 0.46
31 2 0.04
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
AAACTTCCAAAATTCCATTTTTGACCCCG
Found at i:41023979 original size:59 final size:59
Alignment explanation
Indices: 41023899--41024098 Score: 255
Period size: 60 Copynumber: 3.4 Consensus size: 59
41023889 TCTAATCCCA
* * *
41023899 AAACTTTCTAAAATTCTATTTTTGACCCCGAAACTT-CCAAAAATTACCATTTTACCCTT
1 AAACTTTCCAAAATTCCATTTTTGACCCCG-AATTTCCCAAAAATTACCATTTTACCCTT
* *
41023958 AAACTTTCCAAAATTCCATTTTTGA-CCCTAATTTCACCCAAAAATTATCATTTTACCCTT
1 AAACTTTCCAAAATTCCATTTTTGACCCCGAATTT--CCCAAAAATTACCATTTTACCCTT
* * *
41024018 AAACTTTCCAAAATTCCA-TTTTAACCCCG-ATTTCACCCAAAATTACCATTTTACCCTC
1 AAACTTTCCAAAATTCCATTTTTGACCCCGAATTTC-CCAAAAATTACCATTTTACCCTT
*
41024076 AAACTTTCCAAAATTCTATTTTT
1 AAACTTTCCAAAATTCCATTTTT
41024099 AAACTCAAAT
Statistics
Matches: 124, Mismatches: 11, Indels: 12
0.84 0.07 0.08
Matches are distributed among these distances:
57 5 0.04
58 40 0.32
59 36 0.29
60 43 0.35
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.38
Consensus pattern (59 bp):
AAACTTTCCAAAATTCCATTTTTGACCCCGAATTTCCCAAAAATTACCATTTTACCCTT
Found at i:41024021 original size:60 final size:60
Alignment explanation
Indices: 41023935--41024100 Score: 264
Period size: 60 Copynumber: 2.8 Consensus size: 60
41023925 CCCGAAACTT
* *
41023935 CCAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTCCATTTTTGACCCTAATTTCAC
1 CCAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCAC
* *
41023995 CCAAAAATTATCATTTTACCCTTAAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCAC
1 CCAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCAC
* *
41024054 CC-AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCTATTTTTAA
1 CCAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTCCATTTTTAA
41024101 ACTCAAATTT
Statistics
Matches: 98, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
58 35 0.36
59 23 0.23
60 40 0.41
ACGTcount: A:0.34, C:0.28, G:0.01, T:0.37
Consensus pattern (60 bp):
CCAAAAATTACCATTTTACCCTTAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCAC
Found at i:41024098 original size:29 final size:29
Alignment explanation
Indices: 41023899--41024128 Score: 131
Period size: 29 Copynumber: 7.8 Consensus size: 29
41023889 TCTAATCCCA
* *
41023899 AAACTTTCTAAAATTCTATTTTTGACCC-C
1 AAACTTTCCAAAATTCCATTTTT-ACCCTC
*
41023928 GAAAC-TTCCAAAAATTACCA-TTTTACCCTT
1 -AAACTTTCC-AAAATT-CCATTTTTACCCTC
41023958 AAACTTTCCAAAATTCCATTTTTGACCCT-
1 AAACTTTCCAAAATTCCATTTTT-ACCCTC
* *
41023987 -AA-TTTCACCCAAAAATTATCA-TTTTACCCTT
1 AAACTTT---CC-AAAATT-CCATTTTTACCCTC
*
41024018 AAACTTTCCAAAATTCCATTTTAACCC-C
1 AAACTTTCCAAAATTCCATTTTTACCCTC
*
41024046 -GA-TTTCACCCAAAATTACCA-TTTTACCCTC
1 AAACTTT---CCAAAATT-CCATTTTTACCCTC
* **
41024076 AAACTTTCCAAAATTCTATTTTTAAACTC
1 AAACTTTCCAAAATTCCATTTTTACCCTC
* * *
41024105 AAATTTTCCCGAAATTACATTTTT
1 AAACTTT-CCAAAATTCCATTTTT
41024129 GCCCCCGAGA
Statistics
Matches: 159, Mismatches: 17, Indels: 48
0.71 0.08 0.21
Matches are distributed among these distances:
26 3 0.02
27 4 0.03
28 9 0.06
29 71 0.45
30 49 0.31
31 13 0.08
32 7 0.04
33 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (29 bp):
AAACTTTCCAAAATTCCATTTTTACCCTC
Found at i:41024100 original size:59 final size:59
Alignment explanation
Indices: 41023899--41024100 Score: 257
Period size: 59 Copynumber: 3.4 Consensus size: 59
41023889 TCTAATCCCA
* * * * *
41023899 AAACTTTCTAAAATTCTATTTTTGACCCCGAAACTT--CCAAAAATTACCATTTTACCCTT
1 AAACTTTCCAAAATTCCATTTTTAACCCCG--ATTTCACCCAAAATTACCATTTTACCCTT
* ** *
41023958 AAACTTTCCAAAATTCCATTTTTGACCCTAATTTCACCCAAAAATTATCATTTTACCCTT
1 AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCC-AAAATTACCATTTTACCCTT
*
41024018 AAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCACCCAAAATTACCATTTTACCCTC
1 AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAATTACCATTTTACCCTT
*
41024076 AAACTTTCCAAAATTCTATTTTTAA
1 AAACTTTCCAAAATTCCATTTTTAA
41024101 ACTCAAATTT
Statistics
Matches: 126, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
57 3 0.02
58 35 0.28
59 51 0.40
60 37 0.29
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.37
Consensus pattern (59 bp):
AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAATTACCATTTTACCCTT
Found at i:41026619 original size:11 final size:11
Alignment explanation
Indices: 41026595--41026640 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
41026585 AAACTAAAAA
41026595 TATTTTTAATT
1 TATTTTTAATT
41026606 TATTATTTAA-T
1 TATT-TTTAATT
*
41026617 TA-TTTT-ATA
1 TATTTTTAATT
41026626 TATTTTTAATT
1 TATTTTTAATT
41026637 TATT
1 TATT
41026641 AAAATTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
8 1 0.03
9 5 0.17
10 5 0.17
11 13 0.45
12 5 0.17
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTTTTAATT
Found at i:41028671 original size:15 final size:14
Alignment explanation
Indices: 41028646--41028706 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 14
41028636 CTTCTCAATT
41028646 TAAATTTAATAACA
1 TAAATTTAATAACA
41028660 TAAATATTAATATAAGATCA
1 TAAAT-TT-A-AT-A-A-CA
41028680 CTAAATTTAATAACA
1 -TAAATTTAATAACA
41028695 TAAATATTAATA
1 TAAAT-TTAATA
41028707 TAAGATCACT
Statistics
Matches: 39, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
14 10 0.26
15 10 0.26
16 2 0.05
17 3 0.08
18 3 0.08
19 2 0.05
20 4 0.10
21 5 0.13
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (14 bp):
TAAATTTAATAACA
Found at i:41028691 original size:20 final size:21
Alignment explanation
Indices: 41028660--41028718 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
41028650 TTTAATAACA
41028660 TAAATATTAATATAAGATCAC
1 TAAATATTAATATAAGATCAC
41028681 TAAAT-TT-A-AT-A-A-CA-
1 TAAATATTAATATAAGATCAC
41028695 TAAATATTAATATAAGATCAC
1 TAAATATTAATATAAGATCAC
41028716 TAA
1 TAA
41028719 GGGATATGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 14
0.69 0.00 0.31
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 2 0.06
17 3 0.10
18 3 0.10
19 2 0.06
20 4 0.13
21 8 0.26
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (21 bp):
TAAATATTAATATAAGATCAC
Found at i:41028692 original size:35 final size:35
Alignment explanation
Indices: 41028646--41028718 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
41028636 CTTCTCAATT
41028646 TAAATTTAATAACATAAATATTAATATAAGATCAC
1 TAAATTTAATAACATAAATATTAATATAAGATCAC
41028681 TAAATTTAATAACATAAATATTAATATAAGATCAC
1 TAAATTTAATAACATAAATATTAATATAAGATCAC
41028716 TAA
1 TAA
41028719 GGGATATGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (35 bp):
TAAATTTAATAACATAAATATTAATATAAGATCAC
Found at i:41032358 original size:7 final size:7
Alignment explanation
Indices: 41032342--41032379 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
41032332 TACCCCCAAA
41032342 TTTTTA-
1 TTTTTAT
41032348 TTTTTAT
1 TTTTTAT
41032355 TTTTTAT
1 TTTTTAT
41032362 TTTTTAT
1 TTTTTAT
41032369 TTTTTAT
1 TTTTTAT
41032376 TTTT
1 TTTT
41032380 GGGTCCTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTAT
Found at i:41034951 original size:47 final size:47
Alignment explanation
Indices: 41034882--41034972 Score: 164
Period size: 47 Copynumber: 1.9 Consensus size: 47
41034872 TTAGATTTAA
* *
41034882 TATAAAAATAATTGTTAAATTCAATAACAACTTGAATAAAAAAAAAG
1 TATAAAAACAATTGTCAAATTCAATAACAACTTGAATAAAAAAAAAG
41034929 TATAAAAACAATTGTCAAATTCAATAACAACTTGAATAAAAAAA
1 TATAAAAACAATTGTCAAATTCAATAACAACTTGAATAAAAAAA
41034973 GTTTCAAACC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.26
Consensus pattern (47 bp):
TATAAAAACAATTGTCAAATTCAATAACAACTTGAATAAAAAAAAAG
Found at i:41035757 original size:56 final size:54
Alignment explanation
Indices: 41035671--41035802 Score: 176
Period size: 56 Copynumber: 2.4 Consensus size: 54
41035661 CGAGAATTTG
**
41035671 AAAAAAAATTTGGTGTTGGCCATTGCATGGCCGACA-CATTCTTTTTTATCTGAC
1 AAAAAAAATTTGGTGTTGGCCATTGCATGGCCGACACCCCT-TTTTTTATCTGAC
* * *
41035725 AAAAAAAAAATTTGGTGTTGGCCATTGTATGGCTGACACCCCTTTTTTTATTTGAC
1 --AAAAAAAATTTGGTGTTGGCCATTGCATGGCCGACACCCCTTTTTTTATCTGAC
*
41035781 ATAAAAAATTTGGTGTTGGCCA
1 AAAAAAAATTTGGTGTTGGCCA
41035803 ACACCCAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
54 21 0.30
56 46 0.67
57 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36
Consensus pattern (54 bp):
AAAAAAAATTTGGTGTTGGCCATTGCATGGCCGACACCCCTTTTTTTATCTGAC
Found at i:41050336 original size:17 final size:17
Alignment explanation
Indices: 41050314--41050370 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
41050304 TAAAAATAAT
41050314 ACAGATACAGTCATGTC
1 ACAGATACAGTCATGTC
41050331 ACAGATACAG---T-T-
1 ACAGATACAGTCATGTC
*
41050343 ACAGATACAATCATGTC
1 ACAGATACAGTCATGTC
*
41050360 ACAAATACAGT
1 ACAGATACAGT
41050371 TACAGATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
12 9 0.28
13 1 0.03
14 1 0.03
15 1 0.03
16 1 0.03
17 19 0.59
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (17 bp):
ACAGATACAGTCATGTC
Found at i:41050346 original size:29 final size:29
Alignment explanation
Indices: 41050313--41050406 Score: 152
Period size: 29 Copynumber: 3.2 Consensus size: 29
41050303 ATAAAAATAA
* *
41050313 TACAGATACAGTCATGTCACAGATACAGT
1 TACAGATACAATCATGTCACAAATACAGT
41050342 TACAGATACAATCATGTCACAAATACAGT
1 TACAGATACAATCATGTCACAAATACAGT
* *
41050371 TACAGATACAATCATATCACATATACAGT
1 TACAGATACAATCATGTCACAAATACAGT
41050400 TACAGAT
1 TACAGAT
41050407 GCAGACATGA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 61 1.00
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.26
Consensus pattern (29 bp):
TACAGATACAATCATGTCACAAATACAGT
Found at i:41050559 original size:40 final size:39
Alignment explanation
Indices: 41050504--41050612 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 39
41050494 AACACATCGT
* * *
41050504 AGTGTTTACAGTGTCACTGTCGATTCAGTTGAAATCTTGC
1 AGTGTTAATAGTGTCACTGTC-ATTCAGTTGAAATCTTAC
41050544 AGTGTTAATAGTGTCACTGTCAGTTCAGTTGAAATCTTAC
1 AGTGTTAATAGTGTCACTGTCA-TTCAGTTGAAATCTTAC
* *
41050584 TGTGTTAATAGTGTCACTGCCAATTCAGT
1 AGTGTTAATAGTGTCACTGTC-ATTCAGT
41050613 AAATATCCTC
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
39 1 0.02
40 60 0.97
41 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.38
Consensus pattern (39 bp):
AGTGTTAATAGTGTCACTGTCATTCAGTTGAAATCTTAC
Found at i:41051103 original size:53 final size:53
Alignment explanation
Indices: 41051031--41051169 Score: 154
Period size: 53 Copynumber: 2.6 Consensus size: 53
41051021 ATGTGTCTCA
* * *
41051031 AAACAGTATACACATACCTTGACACACGCCCATGTATCAGCCCATGTGCCCC-
1 AAACAGTATACACACACCTTGACACACGCCCATGTACCAGCACATGTGCCCCT
* ** * * *
41051083 AGAACAGTATACACACACCTTAACACGTGCTCGTGTACCAGCACGTGTGCCCCT
1 A-AACAGTATACACACACCTTGACACACGCCCATGTACCAGCACATGTGCCCCT
*
41051137 AAACAGTATATGCACACACCTTGGCACACGCCC
1 AAACAGTATA--CACACACCTTGACACACGCCC
41051170 GTATGCCTCC
Statistics
Matches: 69, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
52 1 0.01
53 51 0.74
54 1 0.01
55 16 0.23
ACGTcount: A:0.30, C:0.35, G:0.16, T:0.19
Consensus pattern (53 bp):
AAACAGTATACACACACCTTGACACACGCCCATGTACCAGCACATGTGCCCCT
Found at i:41051305 original size:43 final size:44
Alignment explanation
Indices: 41051222--41051306 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 44
41051212 TGTGCCAGTC
** * *
41051222 TGTGTGCCTCCAAGTAGTATACACACACACCCCCTGACACACGCT
1 TGTGTGCCTCCAAACAATATACACACACA-CCCCTAACACACGCT
*
41051267 TGTGTGCCTCCAAACAATATACACACATA-CCCTAACACAC
1 TGTGTGCCTCCAAACAATATACACACACACCCCTAACACAC
41051307 TCTCGTGCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 10 0.29
45 25 0.71
ACGTcount: A:0.32, C:0.36, G:0.12, T:0.20
Consensus pattern (44 bp):
TGTGTGCCTCCAAACAATATACACACACACCCCTAACACACGCT
Found at i:41069790 original size:18 final size:19
Alignment explanation
Indices: 41069767--41069804 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
41069757 TTTTTATATA
41069767 TTTTTTAAAATT-TTAAAT
1 TTTTTTAAAATTATTAAAT
*
41069785 TTTTTTATAATTATTAAAT
1 TTTTTTAAAATTATTAAAT
41069804 T
1 T
41069805 ATTTATTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTTAAAATTATTAAAT
Found at i:41087434 original size:17 final size:17
Alignment explanation
Indices: 41087414--41087446 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41087404 TTTAAATACT
41087414 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
41087431 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
41087447 TAAATGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:41087723 original size:50 final size:50
Alignment explanation
Indices: 41087656--41087778 Score: 133
Period size: 50 Copynumber: 2.4 Consensus size: 50
41087646 TCTCATAATC
* * *
41087656 AGTTAAGTTTGCATCATAAATAATGA-CATGCATTA-AGTAACTTACATGTT
1 AGTTAAATTTGCATCATAAAT-ATGATCATCCATTATA-TAACTCACATGTT
* * * *
41087706 AGTTAAATATGCATCATAAATCTTATCATCCATTATATAACTCCCATGTT
1 AGTTAAATTTGCATCATAAATATGATCATCCATTATATAACTCACATGTT
41087756 AGTTAAAGTTTGCATCATTAAAT
1 AGTTAAA-TTTGCATCA-TAAAT
41087779 CAAGTTATGC
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
49 2 0.03
50 45 0.74
51 9 0.15
52 5 0.08
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (50 bp):
AGTTAAATTTGCATCATAAATATGATCATCCATTATATAACTCACATGTT
Found at i:41097654 original size:21 final size:21
Alignment explanation
Indices: 41097630--41097683 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
41097620 GGAGTTTTTG
**
41097630 GTATCGGTAGTTAT-ATGACTT
1 GTATCGGTAGAAATCAT-ACTT
*
41097651 GTATTGGTAGAAATCATACTT
1 GTATCGGTAGAAATCATACTT
41097672 GTATCGGTAGAA
1 GTATCGGTAGAA
41097684 CTAGCATAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.37
Consensus pattern (21 bp):
GTATCGGTAGAAATCATACTT
Found at i:41100726 original size:21 final size:21
Alignment explanation
Indices: 41100702--41100741 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41100692 TTCATCATTA
*
41100702 AACTTTAATTAACCCATTTTT
1 AACTTTAATCAACCCATTTTT
*
41100723 AACTTTAATCAACCTATTT
1 AACTTTAATCAACCCATTT
41100742 ATACTTAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (21 bp):
AACTTTAATCAACCCATTTTT
Found at i:41107208 original size:26 final size:27
Alignment explanation
Indices: 41107173--41107244 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 27
41107163 AACTTGACAC
*
41107173 ATTTTTTTAATTTGATATTTAATTT-T
1 ATTTTTTTAATTTGATATTAAATTTAT
41107199 -TTTTTGTTAATTT-AGTATTAAATTTAT
1 ATTTTT-TTAATTTGA-TATTAAATTTAT
41107226 ACTTTTTTTTAATTTGATA
1 A--TTTTTTTAATTTGATA
41107245 ACTAAACTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
25 6 0.16
26 16 0.42
27 1 0.03
29 9 0.24
30 6 0.16
ACGTcount: A:0.28, C:0.01, G:0.06, T:0.65
Consensus pattern (27 bp):
ATTTTTTTAATTTGATATTAAATTTAT
Found at i:41107665 original size:24 final size:22
Alignment explanation
Indices: 41107618--41107666 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
41107608 TGTATAAAAG
*
41107618 ATTTGACAAATTTAAATACCAA
1 ATTTGACAAATTTAAATACAAA
*
41107640 ATTTGACTAAATATTAAATATAAA
1 ATTTGAC-AAAT-TTAAATACAAA
41107664 ATT
1 ATT
41107667 AGAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 7 0.30
23 4 0.17
24 12 0.52
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (22 bp):
ATTTGACAAATTTAAATACAAA
Found at i:41110178 original size:15 final size:15
Alignment explanation
Indices: 41110158--41110188 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41110148 CGTTAACCAG
41110158 TACCGAATATTACAT
1 TACCGAATATTACAT
41110173 TACCGAATATTACAT
1 TACCGAATATTACAT
41110188 T
1 T
41110189 TGATTTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (15 bp):
TACCGAATATTACAT
Found at i:41120875 original size:50 final size:51
Alignment explanation
Indices: 41120779--41120876 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
41120769 AAGAGATTTT
* * *
41120779 AAAAAAAAAATTGGTGTTGGCCAATGCATGGCCGACACCACCTTTTTTGTC
1 AAAAAAAAAATTGGTGTTGGCCAATGCATGACCGACACAACATTTTTTGTC
* *
41120830 AAAAAAAAATTTGGTGTTGGCC-ATGCATTGACCGACA-AATATTTTTT
1 AAAAAAAAAATTGGTGTTGGCCAATGCA-TGACCGACACAACATTTTTT
41120877 ATAAAATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 12 0.29
51 29 0.71
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (51 bp):
AAAAAAAAAATTGGTGTTGGCCAATGCATGACCGACACAACATTTTTTGTC
Found at i:41120947 original size:61 final size:58
Alignment explanation
Indices: 41120882--41121645 Score: 524
Period size: 59 Copynumber: 13.0 Consensus size: 58
41120872 TTTTTATAAA
* * *
41120882 ATTTTTTTTTGTATTGGCCATGCATTGGCCTACATCATCTTTTTTATCTGATAAAAAA-
1 ATTTTTTTTTGTGTTGGCCATGCATTGGCCGACATCA-CTTTTTTATCAGATAAAAAAT
* ** * *
41120940 ATGATTTTTTTGATGTTGATCATGCATTGGTCGACACCACTTTTTTATCAGATAAAAAAT
1 AT-TTTTTTTTG-TGTTGGCCATGCATTGGCCGACATCACTTTTTTATCAGATAAAAAAT
* * * * **
41121000 ATTTTTTTTGGTGTTGGCCAT-TACTTGGCCGACACCACCTTTATTATTTGATAAAAAATT
1 ATTTTTTTTTGTGTTGGCCATGCA-TTGGCCGACATCA-CTTTTTTATCAGATAAAAAA-T
** * *
41121060 CAAATTTTTTTGTGTTGGCCATGCATTGACCGACACTAACATTTTTTATCAGATAAAAAAT
1 -ATTTTTTTTTGTGTTGGCCATGCATTGGCCGACA-TCAC-TTTTTTATCAGATAAAAAAT
* * * ** * * *
41121121 ATTTATTTTCGTGTTGGCCTTGC-TTAACCGACACCACCTTTTTATCTGATAAAAAATT
1 ATTTTTTTTTGTGTTGGCCATGCATTGGCCGACATCACTTTTTTATCAGATAAAAAA-T
* * * * * * *
41121179 CAAATTTTTTTGGTGTTGACCATGCATTAGTCAACATCACCTTTTTATCAGATAAAAAAT
1 --ATTTTTTTTTGTGTTGGCCATGCATTGGCCGACATCACTTTTTTATCAGATAAAAAAT
* * * ** ** *
41121239 ATATTTTTTGGTGTTGGTCATTGC-TTAACCGACA-CTACCTTTTTTATTTGATAAAAATT
1 ATTTTTTTTTGTGTTGGCCA-TGCATTGGCCGACATC-A-CTTTTTTATCAGATAAAAAAT
* * ** *
41121298 CA-ATTTTTTT-T-AT---CATGCATTGATCGGCATCACTTTTTTATCAGAT--AAAAT
1 -ATTTTTTTTTGTGTTGGCCATGCATTGGCCGACATCACTTTTTTATCAGATAAAAAAT
* * * *
41121349 ATTTTTTTTTGTGTTAGCCATTGC-TTGGTCGACATCATTTTTTTTATCTGATAAAAAAT
1 ATTTTTTTTTGTGTTGGCCA-TGCATTGGCCGACATCA-CTTTTTTATCAGATAAAAAAT
* * *
41121408 -TTAAATTTTCTTGGTGTTGGCCATGCATTGGCCGACACCACCTTTTTATCAGATAAAAAAT
1 ATT---TTTT-TTTGTGTTGGCCATGCATTGGCCGACATCACTTTTTTATCAGATAAAAAAT
* * * * *
41121469 A--TTTTTTTGTGTTAGCAATTG-TTTGGCCGACATCACATTTTTTATCTGATAAAAACT
1 ATTTTTTTTTGTGTTGGCCA-TGCATTGGCCGACATCAC-TTTTTTATCAGATAAAAAAT
* *
41121526 AATTTTTTTTTGTTTTGACCATGCATTGGCCGACATCAACATTTTTTATCAGATAAAAAAT
1 -ATTTTTTTTTGTGTTGGCCATGCATTGGCCGACATC-AC-TTTTTTATCAGATAAAAAAT
* * * * *
41121587 A-TTTTTTTGGTGTTAGACAATAC-TTGGCCGACACCACCTTTTTTAATCAGATATAAAAA
1 ATTTTTTTTTGTGTT-GGCCATGCATTGGCCGACATCA-CTTTTTT-ATCAGATA-AAAAA
41121646 CAAATTTTTT
Statistics
Matches: 560, Mismatches: 99, Indels: 92
0.75 0.13 0.12
Matches are distributed among these distances:
50 1 0.00
51 11 0.02
52 1 0.00
53 16 0.03
54 10 0.02
55 1 0.00
56 36 0.06
57 58 0.10
58 60 0.11
59 125 0.22
60 98 0.17
61 103 0.18
62 40 0.07
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (58 bp):
ATTTTTTTTTGTGTTGGCCATGCATTGGCCGACATCACTTTTTTATCAGATAAAAAAT
Found at i:41120948 original size:58 final size:56
Alignment explanation
Indices: 41120886--41121655 Score: 434
Period size: 61 Copynumber: 13.1 Consensus size: 56
41120876 TATAAAATTT
* * *
41120886 TTTTTTGTATTGGCCATGCATTGGCCTACATCATCTTTTTTATCTGATAAAAAAATGA
1 TTTTTTGTGTTGGCCATGCATTGGCCGACATCA-CTTTTTTATCAGATAAAAAAAT-A
** * * *
41120944 TTTTTTTGATGTTGATCATGCATTGGTCGACACCACTTTTTTATCAGATAAAAAATATT
1 -TTTTTTG-TGTTGGCCATGCATTGGCCGACATCACTTTTTTATCAGATAAAAAA-ATA
* * * ** *
41121003 TTTTTTGGTGTTGGCCAT-TACTTGGCCGACACCACCTTTATTATTTGATAAAAAATTCAAA
1 TTTTTT-GTGTTGGCCATGCA-TTGGCCGACATCA-CTTTTTTATCAGATAAAAAA---ATA
* *
41121064 TTTTTTTGTGTTGGCCATGCATTGACCGACACTAACATTTTTTATCAGAT-AAAAAATA
1 -TTTTTTGTGTTGGCCATGCATTGGCCGACA-TCAC-TTTTTTATCAGATAAAAAAATA
* ** * * * *
41121122 TTTATTTTCGTGTTGGCCTTGC-TTAACCGACACCACCTTTTTATCTGATAAAAAATTCAAA
1 -TT-TTTT-GTGTTGGCCATGCATTGGCCGACATCACTTTTTTATCAGATAAAAAA---ATA
* * * * *
41121183 TTTTTTTGGTGTTGACCATGCATTAGTCAACATCACCTTTTTATCAGATAAAAAATATA
1 -TTTTTT-GTGTTGGCCATGCATTGGCCGACATCACTTTTTTATCAGATAAAAAA-ATA
* ** ** *
41121242 TTTTTTGGTGTTGGTCATTGC-TTAACCGACA-CTACCTTTTTTATTTGAT-AAAAATTCA
1 TTTTTT-GTGTTGGCCA-TGCATTGGCCGACATC-A-CTTTTTTATCAGATAAAAAAAT-A
* ** ** * * * *
41121300 ATTTTT-T-TT-ATCATGCATTGATCGGCATCACTTTTTTATCAGATAAAATATTT
1 TTTTTTGTGTTGGCCATGCATTGGCCGACATCACTTTTTTATCAGATAAAAAAATA
* * * * *
41121353 TTTTTTGTGTTAGCCATTGC-TTGGTCGACATCATTTTTTTTATCTGATAAAAAATTTAAA
1 TTTTTTGTGTTGGCCA-TGCATTGGCCGACATCA-CTTTTTTATCAGATAAAAAA---ATA
* *
41121413 TTTTCTTGGTGTTGGCCATGCATTGGCCGACACCACCTTTTTATCAGAT-AAAAAATA
1 TTTT-TT-GTGTTGGCCATGCATTGGCCGACATCACTTTTTTATCAGATAAAAAAATA
* * * * *
41121470 TTTTTTTGTGTTAGCAATTG-TTTGGCCGACATCACATTTTTTATCTGATAAAAACTAATTT
1 -TTTTTTGTGTTGGCCA-TGCATTGGCCGACATCAC-TTTTTTATCAGATAAAAA--AA-TA
* *
41121531 TTTTTTGTTTTGACCATGCATTGGCCGACATCAACATTTTTTATCAGAT-AAAAAATA
1 TTTTTTGTGTTGGCCATGCATTGGCCGACATC-AC-TTTTTTATCAGATAAAAAAATA
* * * * *
41121588 TTTTTTTGGTGTTAGACAATAC-TTGGCCGACACCACCTTTTTTAATCAGATATAAAAACAAA
1 -TTTTTT-GTGTT-GGCCATGCATTGGCCGACATCA-CTTTTTT-ATCAGATA-AAAAA-ATA
41121650 TTTTTT
1 TTTTTT
41121656 TGGTGTGTCC
Statistics
Matches: 560, Mismatches: 98, Indels: 104
0.73 0.13 0.14
Matches are distributed among these distances:
53 20 0.04
54 18 0.03
55 5 0.01
56 35 0.06
57 52 0.09
58 95 0.17
59 98 0.17
60 94 0.17
61 103 0.18
62 40 0.07
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (56 bp):
TTTTTTGTGTTGGCCATGCATTGGCCGACATCACTTTTTTATCAGATAAAAAAATA
Found at i:41121095 original size:119 final size:119
Alignment explanation
Indices: 41120879--41121657 Score: 760
Period size: 118 Copynumber: 6.6 Consensus size: 119
41120869 TATTTTTTAT
* * * * *
41120879 AAAAT-TTTTTTTT-GTATTGGCCA-TGCATTGGCCTACATCATCTTTTTTATCTGATAAAAAAA
1 AAAATATTTTTTTTGGTGTTGGCCATTGC-TTGGCCGACACCACCTTTTTTATCTGATAAAAAAT
* * **
41120941 T--GATTTTTTTGATGTTGATCATGCATTGGTCGACACCACTTTTTTATCAGATAA
65 TCAAATTTTTTTG-TGTTGACCATGCATTGACCGACACCACTTTTTTATCAGATAA
* * *
41120995 AAAATATTTTTTTTGGTGTTGGCCATTACTTGGCCGACACCACCTTTATTATTTGATAAAAAATT
1 AAAATATTTTTTTTGGTGTTGGCCATTGCTTGGCCGACACCACCTTTTTTATCTGATAAAAAATT
* *
41121060 CAAATTTTTTTGTGTTGGCCATGCATTGACCGACACTAACATTTTTTATCAGATAA
66 CAAATTTTTTTGTGTTGACCATGCATTGACCGACAC-CAC-TTTTTTATCAGATAA
* * **
41121116 AAAATATTTATTTTCGTGTTGGCC-TTGCTTAACCGACACCACC-TTTTTATCTGATAAAAAATT
1 AAAATATTTTTTTTGGTGTTGGCCATTGCTTGGCCGACACCACCTTTTTTATCTGATAAAAAATT
* * * *
41121179 CAAATTTTTTTGGTGTTGACCATGCATT-AGTCAACATCACCTTTTTATCAGATAA
66 CAAATTTTTTT-GTGTTGACCATGCATTGA-CCGACACCACTTTTTTATCAGATAA
* * ** * *
41121234 AAAATATATTTTTTGGTGTTGGTCATTGCTTAACCGACACTACCTTTTTTATTTGAT-AAAAATT
1 AAAATATTTTTTTTGGTGTTGGCCATTGCTTGGCCGACACCACCTTTTTTATCTGATAAAAAATT
* * * *
41121298 C-AA--TTTTT-T-TT-ATCATGCATTGATCGGCATCACTTTTTTATCAGAT--
66 CAAATTTTTTTGTGTTGACCATGCATTGACCGACACCACTTTTTTATCAGATAA
* * * * **
41121344 AAAATATTTTTTTTTGTGTTAGCCATTGCTTGGTCGACATCATTTTTTTTATCTGATAAAAAATT
1 AAAATATTTTTTTTGGTGTTGGCCATTGCTTGGCCGACACCACCTTTTTTATCTGATAAAAAATT
* * * * *
41121409 TAAATTTTCTTGGTGTTGGCCATGCATTGGCCGACACCACCTTTTTATCAGATAA
66 CAAATTTT-TTTGTGTTGACCATGCATTGACCGACACCACTTTTTTATCAGATAA
* * * * * *
41121464 AAAATA-TTTTTTT-GTGTTAGCAATTGTTTGGCCGACATCACATTTTTTATCTGAT-AAAAACT
1 AAAATATTTTTTTTGGTGTTGGCCATTGCTTGGCCGACACCACCTTTTTTATCTGATAAAAAATT
* * * *
41121526 -AATTTTTTTTTGTTTTGACCATGCATTGGCCGACATCAACATTTTTTATCAGATAA
66 CAA-ATTTTTTTGTGTTGACCATGCATTGACCGACA-CCAC-TTTTTTATCAGATAA
* * * * *
41121582 AAAATA-TTTTTTTGGTGTTAGACAATACTTGGCCGACACCACCTTTTTTAATCAGATATAAAAA
1 AAAATATTTTTTTTGGTGTTGGCCATTGCTTGGCCGACACCACCTTTTTT-ATCTGATA-AAAAA
41121646 --CAAATTTTTTTG
64 TTCAAATTTTTTTG
41121658 GTGTGTCCAT
Statistics
Matches: 554, Mismatches: 79, Indels: 56
0.80 0.11 0.08
Matches are distributed among these distances:
110 45 0.08
111 7 0.01
112 31 0.06
113 3 0.01
114 3 0.01
115 2 0.00
116 37 0.07
117 23 0.04
118 167 0.30
119 115 0.21
120 77 0.14
121 39 0.07
122 5 0.01
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (119 bp):
AAAATATTTTTTTTGGTGTTGGCCATTGCTTGGCCGACACCACCTTTTTTATCTGATAAAAAATT
CAAATTTTTTTGTGTTGACCATGCATTGACCGACACCACTTTTTTATCAGATAA
Found at i:41125504 original size:17 final size:16
Alignment explanation
Indices: 41125482--41125516 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
41125472 ATTTGTGTAA
*
41125482 AAATTAATTTGAAAATT
1 AAATTAAGTTG-AAATT
41125499 AAATTAAGTTGAAATT
1 AAATTAAGTTGAAATT
41125515 AA
1 AA
41125517 TTATACAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (16 bp):
AAATTAAGTTGAAATT
Found at i:41125600 original size:10 final size:11
Alignment explanation
Indices: 41125549--41125601 Score: 54
Period size: 12 Copynumber: 4.7 Consensus size: 11
41125539 TTCTACTTTA
*
41125549 AATTTAAAGTT
1 AATTTAAAATT
*
41125560 GAAATTAAAATT
1 -AATTTAAAATT
41125572 ACATTTAAAATT
1 A-ATTTAAAATT
*
41125584 AATTTAACATT
1 AATTTAAAATT
41125595 -ATTTAAA
1 AATTTAAA
41125602 TAAAAAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 6 0.17
11 10 0.29
12 19 0.54
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:41125685 original size:95 final size:94
Alignment explanation
Indices: 41125584--41125860 Score: 432
Period size: 92 Copynumber: 2.9 Consensus size: 94
41125574 ATTTAAAATT
* *
41125584 AATTTAACATTATTTAAATAAAAAATATTATTATAATATTTCAATTTATATCAAATAATGTGTTG
1 AATTTAAAATTATTTAAATAAAAAA-ATTATTATAATATTTCAATTTTTATCAAATAATGTGTTG
*
41125649 ATTTGATAATATATTATTTACCAAATTCAA
65 ATTTGACAATATATTATTTACCAAATTCAA
* * *
41125679 AATTTAAAATTATTTAAAT--AAAAAGTATTATAATATTTTAATTTTTATCAAATAATGTATTGA
1 AATTTAAAATTATTTAAATAAAAAAATTATTATAATATTTCAATTTTTATCAAATAATGTGTTGA
*
41125742 TTTGACAATATATTATTTACTAAATTCAA
66 TTTGACAATATATTATTTACCAAATTCAA
* *
41125771 ATTTTAAAATTATTTAAATAAAAAAGATTATTATATTATTTCAATTTTTATCAAATAATGTGTTG
1 AATTTAAAATTATTTAAATAAAAAA-ATTATTATAATATTTCAATTTTTATCAAATAATGTGTTG
*
41125836 ATTTGACAATACATTATTTACCAAA
65 ATTTGACAATATATTATTTACCAAA
41125861 ATACCCTTAA
Statistics
Matches: 165, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
92 81 0.49
93 4 0.02
94 4 0.02
95 76 0.46
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.45
Consensus pattern (94 bp):
AATTTAAAATTATTTAAATAAAAAAATTATTATAATATTTCAATTTTTATCAAATAATGTGTTGA
TTTGACAATATATTATTTACCAAATTCAA
Found at i:41126191 original size:23 final size:21
Alignment explanation
Indices: 41126139--41126206 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 21
41126129 ATTAAAAAAA
*
41126139 TACATTTTGGAAATATTTTTT
1 TACATTTTCGAAATATTTTTT
41126160 TACAAATTTT-GAATATTATATTTTT
1 TAC--ATTTTCGAA-A-TAT-TTTTT
41126185 TACATTTTCGAAATATTTTTT
1 TACATTTTCGAAATATTTTTT
41126206 T
1 T
41126207 TAGCCATGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
21 9 0.22
22 6 0.15
23 12 0.29
24 6 0.15
25 8 0.20
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (21 bp):
TACATTTTCGAAATATTTTTT
Found at i:41127256 original size:29 final size:29
Alignment explanation
Indices: 41127224--41127313 Score: 144
Period size: 29 Copynumber: 3.1 Consensus size: 29
41127214 ATTTTTTTAA
41127224 AATTTAATTTGTAATTTCGTTTATATTTT
1 AATTTAATTTGTAATTTCGTTTATATTTT
*
41127253 AATTTAATTTGTAATTTTGTTTATATTTT
1 AATTTAATTTGTAATTTCGTTTATATTTT
* *
41127282 AAATTTAATTTCTAATTTCATTTATATTTT
1 -AATTTAATTTGTAATTTCGTTTATATTTT
41127312 AA
1 AA
41127314 ATTTCTTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
29 30 0.54
30 26 0.46
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.61
Consensus pattern (29 bp):
AATTTAATTTGTAATTTCGTTTATATTTT
Found at i:41127269 original size:18 final size:18
Alignment explanation
Indices: 41127243--41127292 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
41127233 TGTAATTTCG
41127243 TTTATATTTTAATTTA-AT
1 TTTA-ATTTTAATTTATAT
*
41127261 TTGTAATTTT-GTTTATAT
1 TT-TAATTTTAATTTATAT
*
41127279 TTTAAATTTAATTT
1 TTTAATTTTAATTT
41127293 CTAATTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 10 0.38
18 14 0.54
19 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (18 bp):
TTTAATTTTAATTTATAT
Found at i:41127289 original size:30 final size:30
Alignment explanation
Indices: 41127218--41127317 Score: 157
Period size: 30 Copynumber: 3.3 Consensus size: 30
41127208 TTTTTCATTT
41127218 TTTTAAAATTTAATTTGTAATTTCGTTTATA
1 TTTT-AAATTTAATTTGTAATTTCGTTTATA
*
41127249 TTTT-AATTTAATTTGTAATTTTGTTTATA
1 TTTTAAATTTAATTTGTAATTTCGTTTATA
* *
41127278 TTTTAAATTTAATTTCTAATTTCATTTATA
1 TTTTAAATTTAATTTGTAATTTCGTTTATA
41127308 TTTTAAATTT
1 TTTTAAATTT
41127318 CTTTTCTAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
29 28 0.44
30 32 0.50
31 4 0.06
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (30 bp):
TTTTAAATTTAATTTGTAATTTCGTTTATA
Found at i:41127324 original size:30 final size:30
Alignment explanation
Indices: 41127210--41127328 Score: 145
Period size: 30 Copynumber: 4.1 Consensus size: 30
41127200 ATTTTGATTT
* *
41127210 TTTCATTT-T-TTTAAAATTTAATTTGTAA
1 TTTCATTTATATTTTAAATTTAATTTCTAA
* *
41127238 TTTCGTTTATATTTT-AATTTAATTTGTAA
1 TTTCATTTATATTTTAAATTTAATTTCTAA
**
41127267 TTTTGTTTATATTTTAAATTTAATTTCTAA
1 TTTCATTTATATTTTAAATTTAATTTCTAA
**
41127297 TTTCATTTATATTTTAAATTTCTTTTCTAA
1 TTTCATTTATATTTTAAATTTAATTTCTAA
41127327 TT
1 TT
41127329 ATTATTTTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
28 7 0.09
29 29 0.36
30 44 0.55
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (30 bp):
TTTCATTTATATTTTAAATTTAATTTCTAA
Found at i:41128290 original size:58 final size:58
Alignment explanation
Indices: 41128171--41128715 Score: 312
Period size: 54 Copynumber: 9.6 Consensus size: 58
41128161 GAGAAAAAAT
* * * * *
41128171 TGGTGTCAGTCAATGCATGACGAACACCAAAAAAATTTATTTTTTTATCAGATAAATAAG-
1 TGGTGTCGGCCAATGCATGGCCAACACCAAAAAAA--TA-TTTTTTATCAGATAAAAAAGC
* **
41128231 TGGTGTTGGTTAA-GCAATGGCCAACACCAAAAAAGATATTTTTTATCTA-ATAAAAAAG-
1 TGGTGTCGGCCAATGC-ATGGCCAACACCAAAAAA-ATATTTTTTATC-AGATAAAAAAGC
* *
41128289 TGGTGTCGGCCAA-GTAATTGCCAACACCAAAAAATATATTTTTTATCAGATAAAAAATGC
1 TGGTGTCGGCCAATG-CATGGCCAACACCAAAAAA-ATATTTTTTATCAGATAAAAAA-GC
* * * *
41128349 TAGTGTCGACTAATGCATGGCCAGCACCAAAAAAATATTTTTTATCAGATAAAAAATGC
1 TGGTGTCGGCCAATGCATGGCCAACACCAAAAAAATATTTTTTATCAGATAAAAAA-GC
* * * *
41128408 TGGTGTCGGTCAATGCATAGCCAACACAAAAAAAATTAATTTTTTTATCAGATAAAAAAGG
1 TGGTGTCGGCCAATGCATGGCCAACACCAAAAAAA-T-A-TTTTTTATCAGATAAAAAAGC
* * * * * *
41128469 TGATGTCGACCAATGCATGACCAATACC----AAATTTTTTTTATCTA-AT-AAAAAGG
1 TGGTGTCGGCCAATGCATGGCCAACACCAAAAAAATATTTTTTATC-AGATAAAAAAGC
* * * * * ** **
41128522 TTGAGTCAGCCAA-GCATTGCCAACACC----AAATTTTTTTTATTTGATAAAAAATAA
1 TGGTGTCGGCCAATGCATGGCCAACACCAAAAAAATATTTTTTATCAGATAAAAAA-GC
* * * * ** * *
41128576 TTGTGTCGGCCAATGCTTGACCAACACC----AAATTTTTTTTATTTGACAAAAAAGG
1 TGGTGTCGGCCAATGCATGGCCAACACCAAAAAAATATTTTTTATCAGATAAAAAAGC
* * * * * * * *
41128630 TGATGTCGACCAATGCATGTCCAATACC----AAATTTTTTTTATCTGACAAAAAAGG
1 TGGTGTCGGCCAATGCATGGCCAACACCAAAAAAATATTTTTTATCAGATAAAAAAGC
**
41128684 TGGTGTTAGCC-ATGCATTGGCCAACACCAAAA
1 TGGTGTCGGCCAATGCA-TGGCCAACACCAAAA
41128716 TATTTTTTTT
Statistics
Matches: 397, Mismatches: 67, Indels: 44
0.78 0.13 0.09
Matches are distributed among these distances:
52 26 0.07
53 25 0.06
54 85 0.21
55 35 0.09
56 1 0.00
57 4 0.01
58 65 0.16
59 59 0.15
60 53 0.13
61 25 0.06
62 19 0.05
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (58 bp):
TGGTGTCGGCCAATGCATGGCCAACACCAAAAAAATATTTTTTATCAGATAAAAAAGC
Found at i:41128322 original size:59 final size:58
Alignment explanation
Indices: 41128164--41128499 Score: 288
Period size: 58 Copynumber: 5.7 Consensus size: 58
41128154 GAGAAATGAG
* * * * *
41128164 AAAAAAT-TGGTGTCAGTCAATGCATGACGAACACCAAAAAAATTTATTTTTTTATCAGAT
1 AAAAAATGTGGTGTCGGCCAATGAATGGCCAACACCAAAAAAA--TA-TTTTTTATCAGAT
* * **
41128224 AAATAA-GTGGTGTTGGTTAA-GCAATGGCCAACACCAAAAAAGATATTTTTTATCTA-AT
1 AAAAAATGTGGTGTCGGCCAATG-AATGGCCAACACCAAAAAA-ATATTTTTTATC-AGAT
*
41128282 AAAAAA-GTGGTGTCGGCCAA-GTAATTGCCAACACCAAAAAATATATTTTTTATCAGAT
1 AAAAAATGTGGTGTCGGCCAATG-AATGGCCAACACCAAAAAA-ATATTTTTTATCAGAT
* * * * *
41128340 AAAAAATGCTAGTGTCGACTAATGCATGGCCAGCACCAAAAAAATATTTTTTATCAGAT
1 AAAAAATG-TGGTGTCGGCCAATGAATGGCCAACACCAAAAAAATATTTTTTATCAGAT
* * * *
41128399 AAAAAATGCTGGTGTCGGTCAATGCATAGCCAACACAAAAAAAATTAATTTTTTTATCAGAT
1 AAAAAATG-TGGTGTCGGCCAATGAATGGCCAACACCAAAAAAA-T-A-TTTTTTATCAGAT
* * * * * *
41128461 AAAAAAGGTGATGTCGACCAATGCATGACCAATACCAAA
1 AAAAAATGTGGTGTCGGCCAATGAATGGCCAACACCAAA
41128500 TTTTTTTTAT
Statistics
Matches: 230, Mismatches: 35, Indels: 21
0.80 0.12 0.07
Matches are distributed among these distances:
57 1 0.00
58 66 0.29
59 58 0.25
60 58 0.25
61 27 0.12
62 20 0.09
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (58 bp):
AAAAAATGTGGTGTCGGCCAATGAATGGCCAACACCAAAAAAATATTTTTTATCAGAT
Found at i:41155192 original size:28 final size:28
Alignment explanation
Indices: 41155139--41155202 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 28
41155129 TAATATAATT
41155139 TTTTAAAAGATTAAATTAAATTTTTATTA
1 TTTTAAAAGATTAAA-TAAATTTTTATTA
41155168 TTTTAAAAGA-TAAA-AAATGATTTTATTA
1 TTTTAAAAGATTAAATAAAT--TTTTATTA
41155196 TTATTAA
1 TT-TTAA
41155203 TTTAAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 4 0.12
28 14 0.44
29 14 0.44
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (28 bp):
TTTTAAAAGATTAAATAAATTTTTATTA
Found at i:41159935 original size:30 final size:31
Alignment explanation
Indices: 41159885--41159943 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
41159875 ACTTAATATC
*
41159885 TCATTGACTTAAATAAAAACTTTCGAATAGT
1 TCATTAACTTAAATAAAAACTTTCGAATAGT
*
41159916 TCATTAACTTAAA-AAAAACTTTTGAATA
1 TCATTAACTTAAATAAAAACTTTCGAATA
41159944 ATTTAATGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.36
Consensus pattern (31 bp):
TCATTAACTTAAATAAAAACTTTCGAATAGT
Found at i:41163543 original size:31 final size:31
Alignment explanation
Indices: 41163502--41163586 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
41163492 GAAAATTTCA
41163502 AAATTCGAAAAGTACAAGGACTAAAATTAACC
1 AAATT-GAAAAGTACAAGGACTAAAATTAACC
** *
41163534 AAATTGAAAAGTACAAACACTAAAATTAATC
1 AAATTGAAAAGTACAAGGACTAAAATTAACC
* *
41163565 AAATT--AAAGTACATGGATTAAA
1 AAATTGAAAAGTACAAGGACTAAA
41163587 TCCTAATTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
29 13 0.28
31 28 0.61
32 5 0.11
ACGTcount: A:0.55, C:0.12, G:0.11, T:0.22
Consensus pattern (31 bp):
AAATTGAAAAGTACAAGGACTAAAATTAACC
Found at i:41166919 original size:70 final size:72
Alignment explanation
Indices: 41166745--41166890 Score: 201
Period size: 70 Copynumber: 2.1 Consensus size: 72
41166735 TAGACTATGT
* * * * *
41166745 GTGG-CACACGGGCAAGCCAAACGGGCGTGTGTTAGA-C-TGTGTGGCTACTGTTTTCTGATTTA
1 GTGGTCACACGAGTAAGCCACACGGGCATGTGCTAGACCGTGTGTGGCTACTGTTTTCTGATTTA
41166807 AGGTGCA
66 AGGTGCA
* *
41166814 GTGGTCACACGGGTAAGCCACACGGGCATGTGCTAGACCGTGTGTGGCTACTGTTTT-TTATTTA
1 GTGGTCACACGAGTAAGCCACACGGGCATGTGCTAGACCGTGTGTGGCTACTGTTTTCTGATTTA
41166878 AGGTGCA
66 AGGTGCA
41166885 GTGGTC
1 GTGGTC
41166891 CCACTAGCAC
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
69 4 0.06
70 28 0.41
71 20 0.29
72 17 0.25
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (72 bp):
GTGGTCACACGAGTAAGCCACACGGGCATGTGCTAGACCGTGTGTGGCTACTGTTTTCTGATTTA
AGGTGCA
Found at i:41168412 original size:16 final size:18
Alignment explanation
Indices: 41168373--41168406 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41168363 TAAATTTATA
41168373 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
41168390 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
41168407 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:41169701 original size:16 final size:17
Alignment explanation
Indices: 41169669--41169701 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
41169659 GGTTGAATAA
41169669 CCTAAACATAAATAATG
1 CCTAAACATAAATAATG
*
41169686 CCTAAA-ATAGATAATG
1 CCTAAACATAAATAATG
41169702 TTACTGGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (17 bp):
CCTAAACATAAATAATG
Found at i:41169826 original size:59 final size:59
Alignment explanation
Indices: 41169754--41169899 Score: 177
Period size: 59 Copynumber: 2.5 Consensus size: 59
41169744 ATATTTGGTA
* ** * * *
41169754 TTTTTT-TAAATTTGATATTTAAATTTTTTTGACTCAATTTGGTATCTGAACTTGATAT
1 TTTTTTCTTAATTTGATACCTAAATTTTTTTGACCCAATTTGATACCTGAACTTGATAT
* * *
41169812 TTTTTTCTTAATTTGGTACCTAAATTTTTTTGACCCAATTTGATACCTGAATTTGGTAT
1 TTTTTTCTTAATTTGATACCTAAATTTTTTTGACCCAATTTGATACCTGAACTTGATAT
* *
41169871 TTTTTTCCTAATTTGATGCCTAAGATTTT
1 TTTTTTCTTAATTTGATACCTAA-ATTTT
41169900 ATTTTGATTT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
58 6 0.08
59 63 0.85
60 5 0.07
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.53
Consensus pattern (59 bp):
TTTTTTCTTAATTTGATACCTAAATTTTTTTGACCCAATTTGATACCTGAACTTGATAT
Found at i:41170158 original size:30 final size:31
Alignment explanation
Indices: 41170122--41170200 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
41170112 GGATCCTAAA
* * *
41170122 AAGTTTAAGTACTAACTT-AAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAATGTC
41170152 AAGTTTAAGTACCAAATTAAAAAAAAATGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAATGTC
41170183 AAGTTTGAA-TACCAAATT
1 AAGTTT-AAGTACCAAATT
41170201 GGATCAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 16 0.36
31 26 0.59
32 2 0.05
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.29
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAAATGTC
Found at i:41170983 original size:21 final size:22
Alignment explanation
Indices: 41170945--41170993 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
41170935 GAAACGACAT
*
41170945 AAAAATAGTGACAAAACAGCAGC
1 AAAAATAGTGA-AAAACAACAGC
*
41170968 AAAAATAGTG-AAAACAATAGC
1 AAAAATAGTGAAAAACAACAGC
41170989 AAAAA
1 AAAAA
41170994 GTAATAGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 14 0.58
23 10 0.42
ACGTcount: A:0.63, C:0.12, G:0.14, T:0.10
Consensus pattern (22 bp):
AAAAATAGTGAAAAACAACAGC
Found at i:41183939 original size:23 final size:23
Alignment explanation
Indices: 41183909--41183954 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
41183899 AGTAAAAGGG
41183909 TGACTGATGGGGAAGTGAAGAGA
1 TGACTGATGGGGAAGTGAAGAGA
41183932 TGACTGATGGGGAAGTGAAGAGA
1 TGACTGATGGGGAAGTGAAGAGA
41183955 GCCCTCTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.43, T:0.17
Consensus pattern (23 bp):
TGACTGATGGGGAAGTGAAGAGA
Found at i:41189607 original size:30 final size:29
Alignment explanation
Indices: 41189539--41189746 Score: 156
Period size: 30 Copynumber: 6.9 Consensus size: 29
41189529 AAGATTTTGG
* * * *
41189539 AAAGTTTTAGGGGCTAAAATGTAATTTTCTAG
1 AAAG-TTTGGGGGTTAAAATG-AAATTT-TAA
*
41189571 AAAGTTTGGGGGTTAAAATGCAATTTTCAA
1 AAAGTTTGGGGGTTAAAATGAAATTTT-AA
* *
41189601 AAAGTTTGAGGGTCAAAATGAAATTGTTAA
1 AAAGTTTGGGGGTTAAAATGAAATT-TTAA
*
41189631 AAAGATTGGGGGTTAAAAGTGAAATTTTAGA
1 AAAGTTTGGGGGTTAAAA-TGAAATTTTA-A
* *
41189662 AAA-TTTAGGTGTTAAAAAT-AAATTTTTAA
1 AAAGTTTGGGGGTT-AAAATGAAA-TTTTAA
* *
41189691 AAAGTTT-GGGGTCAAAAATGAATTTTTAGA
1 AAAGTTTGGGGGT-TAAAATGAAATTTTA-A
*
41189721 AAAGTTT-AGGGTTAAAAT-ATAATTTT
1 AAAGTTTGGGGGTTAAAATGA-AATTTT
41189747 TAAACAAAAC
Statistics
Matches: 145, Mismatches: 20, Indels: 25
0.76 0.11 0.13
Matches are distributed among these distances:
28 1 0.01
29 32 0.22
30 77 0.53
31 31 0.21
32 4 0.03
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (29 bp):
AAAGTTTGGGGGTTAAAATGAAATTTTAA
Found at i:41189647 original size:60 final size:57
Alignment explanation
Indices: 41189539--41189750 Score: 189
Period size: 60 Copynumber: 3.5 Consensus size: 57
41189529 AAGATTTTGG
* * *
41189539 AAAGTTTTAGGGGCTAAAATGTAATTTTCTAGAAAGTTTGGGGGTTAAAATGCAATTTTCA-A
1 AAAG-TTTAGGGTC-AAAATGAAATTTT-TAAAAAG-TTGGGGGTTAAAATG-AATTTT-AGA
*
41189601 AAAGTTTGAGGGTCAAAATGAAATTGTTAAAAAGATTGGGGGTTAAAAGTGAAATTTTAGA
1 AAAGTTT-AGGGTCAAAATGAAATTTTTAAAAAG-TTGGGGGTTAAAA-TG-AATTTTAGA
* * *
41189662 AAA-TTTAGGTGTTAAAAAT-AAATTTTTAAAAAGTTTGGGGTCAAAAATGAATTTTTAGA
1 AAAGTTTAGG-G-TCAAAATGAAATTTTTAAAAAGTTGGGGGT-TAAAATGAA-TTTTAGA
*
41189721 AAAGTTTAGGGTTAAAAT-ATAATTTTTAAA
1 AAAGTTTAGGGTCAAAATGA-AATTTTTAAA
41189751 CAAAACATAG
Statistics
Matches: 130, Mismatches: 11, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
58 9 0.07
59 33 0.25
60 47 0.36
61 32 0.25
62 9 0.07
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.35
Consensus pattern (57 bp):
AAAGTTTAGGGTCAAAATGAAATTTTTAAAAAGTTGGGGGTTAAAATGAATTTTAGA
Found at i:41189678 original size:90 final size:89
Alignment explanation
Indices: 41189568--41189737 Score: 211
Period size: 90 Copynumber: 1.9 Consensus size: 89
41189558 TGTAATTTTC
* * *
41189568 TAGAAAGTTTGGGGGTT-AAAATGCAATTTTCAAAAAGTTTGAGGGTC-AAAATGAAATTGTTA-
1 TAGAAAATTTAGGGGTTAAAAAT-AAATTTTCAAAAAGTTTG-GGGTCAAAAATG-AATTGTTAG
*
41189630 AAAAGATTGGGGGTTAAAAGTGAAATTT
63 AAAAG-TTGAGGGTTAAAAGTGAAATTT
* * *
41189658 TAGAAAATTTAGGTGTTAAAAATAAATTTTTAAAAAGTTTGGGGTCAAAAATGAATTTTTAGAAA
1 TAGAAAATTTAGGGGTTAAAAATAAATTTTCAAAAAGTTTGGGGTCAAAAATGAATTGTTAGAAA
*
41189723 AGTTTAGGGTTAAAA
66 AGTTGAGGGTTAAAA
41189738 TATAATTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
89 23 0.33
90 41 0.59
91 5 0.07
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.33
Consensus pattern (89 bp):
TAGAAAATTTAGGGGTTAAAAATAAATTTTCAAAAAGTTTGGGGTCAAAAATGAATTGTTAGAAA
AGTTGAGGGTTAAAAGTGAAATTT
Found at i:41189735 original size:59 final size:57
Alignment explanation
Indices: 41189561--41189750 Score: 195
Period size: 59 Copynumber: 3.2 Consensus size: 57
41189551 GCTAAAATGT
* * * *
41189561 AATTTTCTAGAAAGTTTGGGGGTTAAAATGCAATTTTCA-AAAAGTTTGAGGGTCAAAATGA
1 AATTTT-TAAAAAGTTT-GGGGTAAAAATG-AATTTTTAGAAAAGTTT-AGGGTTAAAAT-A
* * * *
41189622 AATTGTTAAAAAGATTGGGGGTTAAAAGTGAAATTTTAGAAAA-TTTAGGTGTTAAAAATA
1 AATTTTTAAAAAG-TTTGGGG-TAAAAATGAATTTTTAGAAAAGTTTAGG-GTT-AAAATA
41189682 AATTTTTAAAAAGTTTGGGGTCAAAAATGAATTTTTAGAAAAGTTTAGGGTTAAAATA
1 AATTTTTAAAAAGTTTGGGGT-AAAAATGAATTTTTAGAAAAGTTTAGGGTTAAAATA
41189740 TAATTTTTAAA
1 -AATTTTTAAA
41189751 CAAAACATAG
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
58 7 0.06
59 40 0.37
60 40 0.37
61 22 0.20
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (57 bp):
AATTTTTAAAAAGTTTGGGGTAAAAATGAATTTTTAGAAAAGTTTAGGGTTAAAATA
Found at i:41191010 original size:22 final size:23
Alignment explanation
Indices: 41190979--41191022 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
41190969 GAGTCACGTG
41190979 GCTGACGTGGC-GCTAACATGGT
1 GCTGACGTGGCTGCTAACATGGT
* *
41191001 GCTGATGTGGCTGCTGACATGG
1 GCTGACGTGGCTGCTAACATGG
41191023 CCACGAGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.16, C:0.20, G:0.39, T:0.25
Consensus pattern (23 bp):
GCTGACGTGGCTGCTAACATGGT
Found at i:41191854 original size:33 final size:33
Alignment explanation
Indices: 41191817--41191881 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
41191807 AATTACATAT
* *
41191817 ATTTAAAGGTTATATTTAAATATTTA-AAATAAA
1 ATTTAAAGATTATAATTAAA-ATTTATAAATAAA
* *
41191850 ATTTATATATTATAATTAAAATTTATAAATAA
1 ATTTAAAGATTATAATTAAAATTTATAAATAA
41191882 TTAATATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 5 0.19
33 22 0.81
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (33 bp):
ATTTAAAGATTATAATTAAAATTTATAAATAAA
Found at i:41191859 original size:20 final size:20
Alignment explanation
Indices: 41191830--41191876 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
41191820 TAAAGGTTAT
*
41191830 ATTTAAATATT-TAAAATAAA
1 ATTTATATATTAT-AAATAAA
*
41191850 ATTTATATATTATAATTAAA
1 ATTTATATATTATAAATAAA
41191870 ATTTATA
1 ATTTATA
41191877 AATAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTATATATTATAAATAAA
Found at i:41197603 original size:13 final size:13
Alignment explanation
Indices: 41197585--41197635 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
41197575 CTTAGACTAA
41197585 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
41197598 ACTTTTTCATAA-C
1 AC-TTTTCAAAAGC
*
41197611 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
*
41197624 ATTTTTCAAAAG
1 ACTTTTCAAAAG
41197636 TAATGTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 7 0.23
13 16 0.52
14 8 0.26
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:41212444 original size:21 final size:21
Alignment explanation
Indices: 41212418--41212469 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
41212408 TTTGAGAGCC
41212418 TTTTAAATCATTAAATTTTAT
1 TTTTAAATCATTAAATTTTAT
* *
41212439 TTTTAAATTA-TAATTTTTAT
1 TTTTAAATCATTAAATTTTAT
41212459 TTTTAAA-CATT
1 TTTTAAATCATT
41212470 TTAATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 17 0.63
21 9 0.33
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTAAATCATTAAATTTTAT
Found at i:41230116 original size:16 final size:16
Alignment explanation
Indices: 41230097--41230127 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41230087 TACATGTGAA
41230097 AAATAATAAAATAAAT
1 AAATAATAAAATAAAT
*
41230113 AAATAATAAATTAAA
1 AAATAATAAAATAAA
41230128 ATTTAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAATAAAATAAAT
Found at i:41235981 original size:15 final size:15
Alignment explanation
Indices: 41235961--41235990 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41235951 TTCTTAAACT
41235961 TTTCAAAATTTGAAA
1 TTTCAAAATTTGAAA
*
41235976 TTTCAAATTTTGAAA
1 TTTCAAAATTTGAAA
41235991 CAAACGACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (15 bp):
TTTCAAAATTTGAAA
Found at i:41239314 original size:13 final size:14
Alignment explanation
Indices: 41239285--41239322 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
41239275 TATTTCACTG
*
41239285 AAAATAATTTTTAA
1 AAAATAATTTCTAA
41239299 AAAATAATTTCTAA
1 AAAATAATTTCTAA
*
41239313 AAAATGATTT
1 AAAATAATTT
41239323 ATTTTTGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (14 bp):
AAAATAATTTCTAA
Found at i:41240222 original size:15 final size:15
Alignment explanation
Indices: 41240168--41240224 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
41240158 TTTATACTAC
*
41240168 AAAACATTTATTATT
1 AAAATATTTATTATT
* *
41240183 AATATATTTATAATTGT
1 AAAATATTTATTA-T-T
41240200 AAAAAATATTTATTATT
1 --AAAATATTTATTATT
41240217 AAAATATT
1 AAAATATT
41240225 AATATTGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 18 0.55
16 1 0.03
17 2 0.06
18 1 0.03
19 11 0.33
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:41249795 original size:21 final size:21
Alignment explanation
Indices: 41249771--41249822 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
41249761 CCGTTTTGGA
41249771 AATGGAGGTTGAATTTTAGGT
1 AATGGAGGTTGAATTTTAGGT
41249792 AATGGAGGTTGAATTTTAGGT
1 AATGGAGGTTGAATTTTAGGT
41249813 AATGGAGGTT
1 AATGGAGGTT
41249823 TCGACCGGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.37
Consensus pattern (21 bp):
AATGGAGGTTGAATTTTAGGT
Found at i:41257594 original size:68 final size:67
Alignment explanation
Indices: 41257484--41257618 Score: 164
Period size: 68 Copynumber: 2.0 Consensus size: 67
41257474 TGAGGGAGAA
* * * * * * *
41257484 TATTTAGCTTATGGGGTTTGCATTATGTGCATCTTGCATGTTATTAGTTTGTAATAGCTCTTATG
1 TATTTAGCCTATGGGCTTTACATCATGTGCATCTTGCATGTTATCAG-TTGGAATAACTCTTATG
41257549 AGC
65 AGC
**
41257552 TATTTAGCCTATGGGCTTTACATCATGTGCAT-TTGGTGTGTTATCAGTTGGAATAACTCTTATG
1 TATTTAGCCTATGGGCTTTACATCATGTGCATCTT-GCATGTTATCAGTTGGAATAACTCTTATG
41257616 AGC
65 AGC
41257619 AATCTAGCGT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
67 20 0.35
68 37 0.65
ACGTcount: A:0.21, C:0.13, G:0.22, T:0.43
Consensus pattern (67 bp):
TATTTAGCCTATGGGCTTTACATCATGTGCATCTTGCATGTTATCAGTTGGAATAACTCTTATGA
GC
Found at i:41259373 original size:31 final size:31
Alignment explanation
Indices: 41259322--41259387 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
41259312 AAAAATCTAA
* *
41259322 TGACTTAAATAAAAACTTTTGAATAGTTCAG
1 TGACTTAAATAAAAACTTTTGAATAATTCAC
***
41259353 TGACTTAAATAAATTTTTTTGAATAATTCAC
1 TGACTTAAATAAAAACTTTTGAATAATTCAC
41259384 TGAC
1 TGAC
41259388 CATTTTGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAATAATTCAC
Found at i:41262207 original size:40 final size:40
Alignment explanation
Indices: 41262157--41262251 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 40
41262147 GACAGAAAAA
**
41262157 GTCGCAAAAGGTAAAGTAATAGCGGC-GTTTTTCTATAAAC
1 GTCGCAAAAGGTAAAGTAATAGCGGCACATTTTC-ATAAAC
41262197 GTCGCAAAAGGTAAAGTAATAGCGGCACATTTTCATAAAC
1 GTCGCAAAAGGTAAAGTAATAGCGGCACATTTTCATAAAC
* *
41262237 GCCACAAAAGGTAAA
1 GTCGCAAAAGGTAAA
41262252 ACAATAATGG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 45 0.90
41 5 0.10
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (40 bp):
GTCGCAAAAGGTAAAGTAATAGCGGCACATTTTCATAAAC
Found at i:41262409 original size:41 final size:40
Alignment explanation
Indices: 41262364--41262500 Score: 132
Period size: 41 Copynumber: 3.4 Consensus size: 40
41262354 AGGAAGCACA
* *
41262364 GCTAAAGGTCAGACCATTAGCGACGCCTCCACATAAACGCC
1 GCTAAAGGTCAGAGCATTAGCGA-GCCTTCACATAAACGCC
* * * ***
41262405 GCTAAAGGTCGGAGCATTAGC-AGCGTTTATGGGAAAGCGCC
1 GCTAAAGGTCAGAGCATTAGCGAGCCTTCA-CATAAA-CGCC
* * *
41262446 GTTAAAGGTCAGAGCATTAGCGGTGCTTTCACATAAACGCC
1 GCTAAAGGTCAGAGCATTAGC-GAGCCTTCACATAAACGCC
41262487 GCTAAAGGTCAGAG
1 GCTAAAGGTCAGAG
41262501 TAATAGCGGC
Statistics
Matches: 75, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
39 4 0.05
40 4 0.05
41 59 0.79
42 3 0.04
43 5 0.07
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (40 bp):
GCTAAAGGTCAGAGCATTAGCGAGCCTTCACATAAACGCC
Found at i:41262432 original size:82 final size:82
Alignment explanation
Indices: 41262339--41262523 Score: 228
Period size: 82 Copynumber: 2.3 Consensus size: 82
41262329 GCTCTTACCT
*
41262339 TTAGCGGCGTTTTTGAGG-AAGCACAGCTAAAGGTCAGACCATTAGCGACGCCTCCACATAAACG
1 TTAGCGGCGTTTATG-GGAAAGCACAGCTAAAGGTCAGACCATTAGCGACGCCTCCACATAAACG
*
41262403 CCGCTAAAGGTCGGAGCA
65 CCGCTAAAGGTCAGAGCA
* * * * * ** * *
41262421 TTAGCAGCGTTTATGGGAAAGCGCCGTTAAAGGTCAGAGCATTAGCGGTGCTTTCACATAAACGC
1 TTAGCGGCGTTTATGGGAAAGCACAGCTAAAGGTCAGACCATTAGCGACGCCTCCACATAAACGC
*
41262486 CGCTAAAGGTCAGAGTA
66 CGCTAAAGGTCAGAGCA
* *
41262503 ATAGCGGCGTTTATGGAAAAG
1 TTAGCGGCGTTTATGGGAAAG
41262524 GCAAACATAG
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 2 0.02
82 85 0.98
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (82 bp):
TTAGCGGCGTTTATGGGAAAGCACAGCTAAAGGTCAGACCATTAGCGACGCCTCCACATAAACGC
CGCTAAAGGTCAGAGCA
Found at i:41268909 original size:25 final size:25
Alignment explanation
Indices: 41268859--41268909 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
41268849 TATTAATAAG
* * *
41268859 TAAAAATTTCTCTATATATTATATT
1 TAAAAATTTCTCTATACATCAAATT
41268884 TAAAAATTTCTCTATACATCAAATT
1 TAAAAATTTCTCTATACATCAAATT
41268909 T
1 T
41268910 GAACAGAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (25 bp):
TAAAAATTTCTCTATACATCAAATT
Found at i:41271393 original size:2 final size:2
Alignment explanation
Indices: 41271381--41271421 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
41271371 ATAAAAATGA
41271381 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41271422 GTAATTAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41273838 original size:43 final size:43
Alignment explanation
Indices: 41273790--41273950 Score: 180
Period size: 43 Copynumber: 3.7 Consensus size: 43
41273780 GGACATGATA
* * * **
41273790 TTTAGCGGC-TCTTTTACAACAACCGCCGCTAAATAAGGTGGTC
1 TTTAGCGGCGT-TTTTACCACAAACGCCGCTAAAGAACATGGTC
** * * *
41273833 TTTAGCGGCACTTTTCCCACAAACACCGCTAAAGAACATGGTT
1 TTTAGCGGCGTTTTTACCACAAACGCCGCTAAAGAACATGGTC
* * *
41273876 TTTAGCGCCGTTTTTACCACAAACGTCGCTAAAGAACATTGTC
1 TTTAGCGGCGTTTTTACCACAAACGCCGCTAAAGAACATGGTC
*
41273919 TTTAGCGGCGTTTTTCCCACAAACGCCGCTAA
1 TTTAGCGGCGTTTTTACCACAAACGCCGCTAA
41273951 CATTAATAGA
Statistics
Matches: 97, Mismatches: 20, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
43 97 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTTTACCACAAACGCCGCTAAAGAACATGGTC
Found at i:41280352 original size:71 final size:71
Alignment explanation
Indices: 41280194--41280339 Score: 202
Period size: 71 Copynumber: 2.1 Consensus size: 71
41280184 GGTTCTATCG
* **
41280194 ATACAACCAAGACTTTTATCAGTAGAACAAACTCCAGAGAGCAAAAAAGTTATGGCCTAGGACTT
1 ATACAACCAAGACTTCTATTGGTAGAACAAACTCCAGAGAGCAAAAAAGTTATGGCCTAGGACTT
*
41280259 TTACCA
66 CTACCA
* * * * *
41280265 ATACAACCAAGACTTCTATTGGTAGAACAAACTCTAGAGAGCAAAGAAGTTGTGGCTTGGGACTT
1 ATACAACCAAGACTTCTATTGGTAGAACAAACTCCAGAGAGCAAAAAAGTTATGGCCTAGGACTT
*
41280330 CTACCG
66 CTACCA
41280336 ATAC
1 ATAC
41280340 CTAGAAGGCT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (71 bp):
ATACAACCAAGACTTCTATTGGTAGAACAAACTCCAGAGAGCAAAAAAGTTATGGCCTAGGACTT
CTACCA
Found at i:41282400 original size:13 final size:13
Alignment explanation
Indices: 41282382--41282406 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41282372 AAATTGTATA
41282382 TTTTATACATATC
1 TTTTATACATATC
41282395 TTTTATACATAT
1 TTTTATACATAT
41282407 ATACTATTTT
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:0.12, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTATACATATC
Found at i:41284742 original size:71 final size:71
Alignment explanation
Indices: 41284575--41284728 Score: 272
Period size: 71 Copynumber: 2.2 Consensus size: 71
41284565 CATCTCTTGG
* *
41284575 TTCTACCAATACAACCAAGATTTCTATCGGTAGAACAAACTCCAGAGAGCAAAGAAGTTGTGGCC
1 TTCTACCGATACAACCAAGACTTCTATCGGTAGAACAAACTCCAGAGAGCAAAGAAGTTGTGGCC
41284640 TGAGAC
66 TGAGAC
*
41284646 TTCTACCGATACAACCAAGACTTCTATCGGTAGAACAAACTCTAGAGAGCAAAGAAGTTGTGGCC
1 TTCTACCGATACAACCAAGACTTCTATCGGTAGAACAAACTCCAGAGAGCAAAGAAGTTGTGGCC
*
41284711 TGGGAC
66 TGAGAC
41284717 TTCTACCGATAC
1 TTCTACCGATAC
41284729 TTGGAAGGCT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 79 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.22
Consensus pattern (71 bp):
TTCTACCGATACAACCAAGACTTCTATCGGTAGAACAAACTCCAGAGAGCAAAGAAGTTGTGGCC
TGAGAC
Found at i:41286903 original size:42 final size:41
Alignment explanation
Indices: 41286833--41286945 Score: 140
Period size: 41 Copynumber: 2.8 Consensus size: 41
41286823 TTTATGGGAA
* * * *
41286833 AACGCCGCTATTGCT-TAACCTTTAGCGGC-ATTTTTCCCATC
1 AACGCCGCTAATGCTCTTACCTTTTGCGGCGATTTGT--CATC
*
41286874 AACGCCGCTAATGCTCTTACCTTTTGCGGCGCTTTGTCATC
1 AACGCCGCTAATGCTCTTACCTTTTGCGGCGATTTGTCATC
*
41286915 AACACCGCTAATGCTCTTACCTTTTGCGGCG
1 AACGCCGCTAATGCTCTTACCTTTTGCGGCG
41286946 TTTATGAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
41 48 0.75
42 12 0.19
43 4 0.06
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.33
Consensus pattern (41 bp):
AACGCCGCTAATGCTCTTACCTTTTGCGGCGATTTGTCATC
Found at i:41290048 original size:29 final size:29
Alignment explanation
Indices: 41290006--41290066 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
41289996 ATATACTTTC
41290006 TAATTCATGGAACTGCAAATTATTAGAGA
1 TAATTCATGGAACTGCAAATTATTAGAGA
41290035 TAATTCATGGAACTGCAAATTATTAGAGA
1 TAATTCATGGAACTGCAAATTATTAGAGA
41290064 TAA
1 TAA
41290067 AAGAAAATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (29 bp):
TAATTCATGGAACTGCAAATTATTAGAGA
Found at i:41291307 original size:96 final size:96
Alignment explanation
Indices: 41291128--41291362 Score: 280
Period size: 96 Copynumber: 2.4 Consensus size: 96
41291118 GATGTTGTCG
* * * * * *
41291128 AAGAAGGAAAAGAAGATCACTTGATCAGCAAGTAAAAGAAACATAAGATGGAAGAAGAAAGTTGC
1 AAGAAGGAAAACAAGATTACTTGATCGGCAAGAAAAAGAAACAGAAGATGGAAGAACAAAGTTGC
**
41291193 CATGAAATTTGAAACCTAAGTT-TCATTGATA
66 CATGAAAAATGAAACCTAAGTTCT-ATTGATA
* *
41291224 AAGAAGGAAAACAAGATTACTTGACCGGCAAGAAAAAAGAAAC-GAAGATGGAAGACCAAAGTTG
1 AAGAAGGAAAACAAGATTACTTGATCGGCAAG-AAAAAGAAACAGAAGATGGAAGAACAAAGTTG
*
41291288 CCAT-AAAAATGAAACCCTAAGTTCTATTGGTA
65 CCATGAAAAATGAAA-CCTAAGTTCTATTGATA
* * *
41291320 AA-AGAGAAAAACAAGATTACTTGGTCGGCAAGCAAAAGAAACA
1 AAGA-AGGAAAACAAGATTACTTGATCGGCAAGAAAAAGAAACA
41291363 AAAAGACAAG
Statistics
Matches: 119, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
95 18 0.15
96 91 0.76
97 10 0.08
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.17
Consensus pattern (96 bp):
AAGAAGGAAAACAAGATTACTTGATCGGCAAGAAAAAGAAACAGAAGATGGAAGAACAAAGTTGC
CATGAAAAATGAAACCTAAGTTCTATTGATA
Found at i:41291819 original size:323 final size:324
Alignment explanation
Indices: 41291224--41292332 Score: 1517
Period size: 324 Copynumber: 3.4 Consensus size: 324
41291214 TTCATTGATA
* * * *
41291224 AAGAAGGAAAACAAGATTACTTGACCGGCAAGAAAAAAGAAA-CGAAGATGGAAGACCAAAGTTG
1 AAGAAGGAAAACAAGATTACTTGATCGGCAAG-TAAAAGAAATAGAAGATGGAAGACGAAAGTTG
* * * * * * * * *
41291288 CCATAAAAATGAAACCCTAAG-TTCTATTGGTAAAAGAGAAAAACAAGATTACTTGGTCGGCAAG
65 CCATGAAATTGGAACCCTAAGTTTC-GTTAGTGAAGGAGGAAAACAAGATTACTTGGTCAGCAAG
*
41291352 CAAAAGAAACAAAAAGACAAGCGACGATAGAAAGAAGAAGTAGAAGACAAACAACATTAATAATC
129 CAAAAGAAACAAAAAGACGAGCGACGATAGAAAGAAGAAGTAGAAGACAAACAACATTAATAATC
* * *
41291417 AGAGAAATAGATAAGATGTGCCATAACTCAGATGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCA
194 AGAGAAAGAGAAAAGATGTGCCATAACTTAGATGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCA
* *
41291482 TGGAGAAGGAGAACAAAATGATGATTGAGAAATAGGGTCTAAAATCCTATCATGAAGTTGTTGTG
259 TGGAGAAGGAGAACAAAATGATGATTGAGAAAAAGGGTCTAAAATCCTATCATGAAGTTGTTGTC
41291547 G
324 G
* * * * *
41291548 AAGAAGGAAAAGAAGATTACTTGATCGGCAAGCATAAGAAATAGAAGATGGAAGTCGAAAGTTTC
1 AAGAAGGAAAACAAGATTACTTGATCGGCAAGTAAAAGAAATAGAAGATGGAAGACGAAAGTTGC
* *
41291613 CATGAAATTGGAACCCTAAGTTTCGTTAGTGAAGGAGGAAATCAAGATTACTTGGTCAACAAGCA
66 CATGAAATTGGAACCCTAAGTTTCGTTAGTGAAGGAGGAAAACAAGATTACTTGGTCAGCAAGCA
* * * *
41291678 AAAGAAAC-AAAAGATGAGCGACAATAGAAAAAAGAAGTAGAAGACAAAAAACATTAATAATCAG
131 AAAGAAACAAAAAGACGAGCGACGATAGAAAGAAGAAGTAGAAGACAAACAACATTAATAATCAG
** * * * *
41291742 AGAAAGAGAAAAGATGTGGTATAACTTAGATGGAATTGGCCAAGTTTGTAACTCGCCTAGTCATG
196 AGAAAGAGAAAAGATGTGCCATAACTTAGATGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCATG
* * * * * *
41291807 GAGAAGGAGAACAAAATGATGATTAAGAAAAAGGGTCTTAAATCCTGTAATGAAGTTGTTATCA
261 GAGAAGGAGAACAAAATGATGATTGAGAAAAAGGGTCTAAAATCCTATCATGAAGTTGTTGTCG
* * *
41291871 AAGAAAGAAAACAAGATTACTTGATTGGCAAGTAAAAGAAATAGAAGATGAAAGACGAAAGTTGC
1 AAGAAGGAAAACAAGATTACTTGATCGGCAAGTAAAAGAAATAGAAGATGGAAGACGAAAGTTGC
* * * *
41291936 CATGAAATTGGAACACTAAGTTTCGTTAGTGAAGGAGGAAAACAAGATTACTTTGTTAGCAAGCG
66 CATGAAATTGGAACCCTAAGTTTCGTTAGTGAAGGAGGAAAACAAGATTACTTGGTCAGCAAGCA
* * * *
41292001 AAAGAAACAAAAAGACGAGCGACGGTAGAAAGAAGAAGCAAAAGACAAACAACATTAATAATTAG
131 AAAGAAACAAAAAGACGAGCGACGATAGAAAGAAGAAGTAGAAGACAAACAACATTAATAATCAG
* * * *
41292066 AGAAAGAGACAATATGTGCCATAACTTAAATGGTATTGCCCAAGTTTGTAGCTCGTTTAGTCATG
196 AGAAAGAGAAAAGATGTGCCATAACTTAGATGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCATG
* * *
41292131 GAGAAGGAGAACAAAATGATGATTGAGAAAGAA-GGTCTCAAATCCTATCATGAAGCTGTCGTCG
261 GAGAAGGAGAACAAAATGATGATTGAGAAA-AAGGGTCTAAAATCCTATCATGAAGTTGTTGTCG
* * ** *
41292195 AAGAAGGAAAAGAAGATTACTTTATCTACAAGTAAAAGAAACAGAAGATGGAAGATC-AAAGTTG
1 AAGAAGGAAAACAAGATTACTTGATCGGCAAGTAAAAGAAATAGAAGATGGAAGA-CGAAAGTTG
* * * * *
41292259 CCATGAAATTGGAAACCTAAGTTTCGTTGGTGAAGAAGGAAAACAAGATTACTTGATCGGCAAGC
65 CCATGAAATTGGAACCCTAAGTTTCGTTAGTGAAGGAGGAAAACAAGATTACTTGGTCAGCAAGC
41292324 AAAAGAAAC
130 AAAAGAAAC
41292333 GGAAGATGGA
Statistics
Matches: 682, Mismatches: 98, Indels: 10
0.86 0.12 0.01
Matches are distributed among these distances:
323 294 0.43
324 382 0.56
325 6 0.01
ACGTcount: A:0.45, C:0.12, G:0.23, T:0.20
Consensus pattern (324 bp):
AAGAAGGAAAACAAGATTACTTGATCGGCAAGTAAAAGAAATAGAAGATGGAAGACGAAAGTTGC
CATGAAATTGGAACCCTAAGTTTCGTTAGTGAAGGAGGAAAACAAGATTACTTGGTCAGCAAGCA
AAAGAAACAAAAAGACGAGCGACGATAGAAAGAAGAAGTAGAAGACAAACAACATTAATAATCAG
AGAAAGAGAAAAGATGTGCCATAACTTAGATGGTATTGCCCAAGTTTGTAGCTCGTCTAGTCATG
GAGAAGGAGAACAAAATGATGATTGAGAAAAAGGGTCTAAAATCCTATCATGAAGTTGTTGTCG
Found at i:41292358 original size:96 final size:96
Alignment explanation
Indices: 41292194--41292429 Score: 339
Period size: 96 Copynumber: 2.5 Consensus size: 96
41292184 AGCTGTCGTC
* * ** *
41292194 GAAGAAGGAAAAGAAGATTACTTTATCTACAAGTAAAAGAAACAGAAGATGGAAGATCAAAGTTG
1 GAAGAAGGAAAACAAGATTACTTGATCGGCAAGAAAAAGAAACAGAAGATGGAAGATCAAAGTTG
* * *
41292259 CCATGAAATTGGAAACCTAAGTTTCGTTGGT
66 CCATAAAATTGGAAACCTAAGTTCCGTTGAT
* * *
41292290 GAAGAAGGAAAACAAGATTACTTGATCGGCAAGCAAAAGAAACGGAAGATGGAAGATGAAAGTTG
1 GAAGAAGGAAAACAAGATTACTTGATCGGCAAGAAAAAGAAACAGAAGATGGAAGATCAAAGTTG
*
41292355 CCATAAAATTGGAACCCTAAGTTCCGTTGAT
66 CCATAAAATTGGAAACCTAAGTTCCGTTGAT
*
41292386 GAA-AGAGGAAAACAAGATTACTTGGTCGGCAAGAAAAAGAAACA
1 GAAGA-AGGAAAACAAGATTACTTGATCGGCAAGAAAAAGAAACA
41292430 AAAAGACAAG
Statistics
Matches: 125, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
95 1 0.01
96 124 0.99
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.19
Consensus pattern (96 bp):
GAAGAAGGAAAACAAGATTACTTGATCGGCAAGAAAAAGAAACAGAAGATGGAAGATCAAAGTTG
CCATAAAATTGGAAACCTAAGTTCCGTTGAT
Found at i:41296197 original size:15 final size:15
Alignment explanation
Indices: 41296177--41296210 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
41296167 CATCTCTACA
*
41296177 TTAGTGATTTTTTTT
1 TTAGTGATTTTTTTG
41296192 TTAGTGATTTTTTTG
1 TTAGTGATTTTTTTG
41296207 TTAG
1 TTAG
41296211 ATTATTATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.18, T:0.68
Consensus pattern (15 bp):
TTAGTGATTTTTTTG
Found at i:41305167 original size:29 final size:30
Alignment explanation
Indices: 41305135--41305196 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
41305125 TTAAGTTTGT
*
41305135 AATTTAATTTGATCCTT-AAAAATGATAAA
1 AATTTAATTTAATCCTTAAAAAATGATAAA
* ** *
41305164 AATTTGATTTAATTTTTAAAAAATTATAAA
1 AATTTAATTTAATCCTTAAAAAATGATAAA
41305194 AAT
1 AAT
41305197 ATAAATTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (30 bp):
AATTTAATTTAATCCTTAAAAAATGATAAA
Found at i:41305446 original size:2 final size:2
Alignment explanation
Indices: 41305439--41305475 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
41305429 GTCAATTTTC
41305439 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41305476 GGGGGTATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41307052 original size:69 final size:69
Alignment explanation
Indices: 41306967--41307112 Score: 220
Period size: 69 Copynumber: 2.1 Consensus size: 69
41306957 TCGAAATTTT
* * ** * * *
41306967 TAACTCGATTTAATTCAAAAAAAAATTCAAATTCAATTTAATTGTTAAAATAAGATTCGTCAACT
1 TAACTCGATTCAATTCAAAAAAAAATTCAAATTCAATTCAATTACTAAAATAAAATTCATCAACC
41307032 CAAC
66 CAAC
*
41307036 TAACTCGATTCAATTCAAAAAAAAATTCAAATTTAATTCAATTACTAAAATAAAATTCATCAACC
1 TAACTCGATTCAATTCAAAAAAAAATTCAAATTCAATTCAATTACTAAAATAAAATTCATCAACC
41307101 CAAC
66 CAAC
41307105 TAACTCGA
1 TAACTCGA
41307113 ATTTTTTTAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.31
Consensus pattern (69 bp):
TAACTCGATTCAATTCAAAAAAAAATTCAAATTCAATTCAATTACTAAAATAAAATTCATCAACC
CAAC
Found at i:41311281 original size:3 final size:3
Alignment explanation
Indices: 41311273--41311310 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
41311263 ATTAATTCAA
41311273 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
41311311 AGAATGATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:41317563 original size:24 final size:22
Alignment explanation
Indices: 41317511--41317584 Score: 78
Period size: 24 Copynumber: 3.2 Consensus size: 22
41317501 AAAACAGAGG
41317511 CAAAAATAATAGAAAAATAGCAAC
1 CAAAAATAATA-AAAAATAGC-AC
* *
41317535 AAAAAATAATAATAATAACAGCAC
1 CAAAAATAATAA-AA-AATAGCAC
*
41317559 C-AAAATAGTAAAAAATAGCAC
1 CAAAAATAATAAAAAATAGCAC
41317580 CAAAA
1 CAAAA
41317585 CAACAACCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
21 8 0.19
22 5 0.12
23 10 0.24
24 14 0.33
25 5 0.12
ACGTcount: A:0.66, C:0.14, G:0.07, T:0.14
Consensus pattern (22 bp):
CAAAAATAATAAAAAATAGCAC
Found at i:41317580 original size:21 final size:21
Alignment explanation
Indices: 41317513--41317647 Score: 85
Period size: 21 Copynumber: 6.2 Consensus size: 21
41317503 AACAGAGGCA
*
41317513 AAAATAATAGAAAAATAGCAACAA
1 AAAATAATA-AAAAATAGC-AC-C
*
41317537 AAAATAATAATAATAACAGCACC
1 AAAATAATAA-AA-AATAGCACC
*
41317560 AAAATAGTAAAAAATAGCACC
1 AAAATAATAAAAAATAGCACC
* * **
41317581 AAAACAACAACCAA-AGCACC
1 AAAATAATAAAAAATAGCACC
* * *
41317601 AAAATAGTAAAAACACAACACC
1 AAAATAATAAAAA-ATAGCACC
* *
41317623 AAAACAA-CAAAAATAGCAACC
1 AAAATAATAAAAAATAGC-ACC
41317644 AAAA
1 AAAA
41317648 CAGGAAAAAA
Statistics
Matches: 86, Mismatches: 20, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
20 17 0.20
21 29 0.34
22 12 0.14
23 10 0.12
24 13 0.15
25 5 0.06
ACGTcount: A:0.65, C:0.19, G:0.06, T:0.10
Consensus pattern (21 bp):
AAAATAATAAAAAATAGCACC
Found at i:41317599 original size:41 final size:42
Alignment explanation
Indices: 41317554--41317632 Score: 133
Period size: 41 Copynumber: 1.9 Consensus size: 42
41317544 TAATAATAAC
* *
41317554 AGCACCAAAATAGTAAAAA-ATAGCACCAAAACAACAACCAA
1 AGCACCAAAATAGTAAAAACACAACACCAAAACAACAACCAA
41317595 AGCACCAAAATAGTAAAAACACAACACCAAAACAACAA
1 AGCACCAAAATAGTAAAAACACAACACCAAAACAACAA
41317633 AAATAGCAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 19 0.54
42 16 0.46
ACGTcount: A:0.62, C:0.25, G:0.06, T:0.06
Consensus pattern (42 bp):
AGCACCAAAATAGTAAAAACACAACACCAAAACAACAACCAA
Found at i:41325302 original size:38 final size:38
Alignment explanation
Indices: 41325251--41325464 Score: 239
Period size: 38 Copynumber: 5.5 Consensus size: 38
41325241 AATTCCCCGG
*
41325251 TGTTTATCGGGCTTAGTGCCTACCAGGCTTCGTGCCAA
1 TGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCAA
* * * *
41325289 TGTTTATCGGGCTTAATGCCTAGTAGGCTTCTTGCCAG
1 TGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCAA
* *
41325327 TGTATTTATCGGGCTTAATGCCTAGCAGGCTTAGTGCCAA
1 TG--TTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCAA
* * * *
41325367 TGTTTATCGGGCTTAGTACCTAGCAGACTTAGTGTCAA
1 TGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCAA
* * * **
41325405 TGTATTTATCGGGCTTACTGCCTAGCAAGCTTCATGCCGG
1 TG--TTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCAA
*
41325445 TGTTTATCGAGCTTAGTGCC
1 TGTTTATCGGGCTTAGTGCC
41325465 GGTGTATTTA
Statistics
Matches: 148, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
38 85 0.57
40 63 0.43
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (38 bp):
TGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCAA
Found at i:41325389 original size:78 final size:78
Alignment explanation
Indices: 41325253--41325461 Score: 258
Period size: 78 Copynumber: 2.7 Consensus size: 78
41325243 TTCCCCGGTG
* * * * * * *
41325253 TTTATCGGGCTTAGTGCCTACCAGGCTTCGTGCCAATGTTTATCGGGCTTAATGCCTAGTAGGCT
1 TTTATCGGGCTTAATGCCTAGCAGGCTTAGTGCCAATGTTTATCGGGCTTAGTACCTAGCAGACT
** *
41325318 TCTTGCCAGTGTA
66 TAGTGCCAATGTA
41325331 TTTATCGGGCTTAATGCCTAGCAGGCTTAGTGCCAATGTTTATCGGGCTTAGTACCTAGCAGACT
1 TTTATCGGGCTTAATGCCTAGCAGGCTTAGTGCCAATGTTTATCGGGCTTAGTACCTAGCAGACT
*
41325396 TAGTGTCAATGTA
66 TAGTGCCAATGTA
* * ** *
41325409 TTTATCGGGCTTACTGCCTAGCAAGCTTCA-TGCCGGTGTTTATCGAGCTTAGT
1 TTTATCGGGCTTAATGCCTAGCAGGCTT-AGTGCCAATGTTTATCGGGCTTAGT
41325462 GCCGGTGTAT
Statistics
Matches: 114, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
78 113 0.99
79 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (78 bp):
TTTATCGGGCTTAATGCCTAGCAGGCTTAGTGCCAATGTTTATCGGGCTTAGTACCTAGCAGACT
TAGTGCCAATGTA
Found at i:41325464 original size:22 final size:22
Alignment explanation
Indices: 41325439--41325487 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
41325429 GCAAGCTTCA
41325439 TGCCGGTG-TTTATCGAGCTTAG
1 TGCCGGTGATTTATCGAG-TTAG
*
41325461 TGCCGGTGTATTTATCGAGTTTG
1 TGCCGGTG-ATTTATCGAGTTAG
41325484 TGCC
1 TGCC
41325488 TAGTAGGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 8 0.33
23 7 0.29
24 9 0.38
ACGTcount: A:0.12, C:0.18, G:0.31, T:0.39
Consensus pattern (22 bp):
TGCCGGTGATTTATCGAGTTAG
Found at i:41325541 original size:41 final size:41
Alignment explanation
Indices: 41325480--41325560 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
41325470 ATTTATCGAG
* * *
41325480 TTTGTGCCTAGTAGGCTTCGTGCCGATGTATACTATCAGGC
1 TTTGAGCCTAGCAGGCTTCGTGCCAATGTATACTATCAGGC
* **
41325521 TTTGAGCCTAGCAGGTTTCGTGCCAATGTATTGTATCAGG
1 TTTGAGCCTAGCAGGCTTCGTGCCAATGTATACTATCAGG
41325561 TAACTTGTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.35
Consensus pattern (41 bp):
TTTGAGCCTAGCAGGCTTCGTGCCAATGTATACTATCAGGC
Found at i:41325754 original size:45 final size:45
Alignment explanation
Indices: 41325704--41325793 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
41325694 CAAAATTTAA
41325704 ATGGATGATAATTTATCATATGATGGACGAAATATGCATGGAATC
1 ATGGATGATAATTTATCATATGATGGACGAAATATGCATGGAATC
*
41325749 ATGGATGATAATTTATCATGTGATGGACGAAATATGCATGGAATC
1 ATGGATGATAATTTATCATATGATGGACGAAATATGCATGGAATC
41325794 CATTTCTTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.31
Consensus pattern (45 bp):
ATGGATGATAATTTATCATATGATGGACGAAATATGCATGGAATC
Found at i:41327787 original size:24 final size:24
Alignment explanation
Indices: 41327726--41327788 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
41327716 TAGACTAATA
* *
41327726 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
41327750 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
41327774 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
41327789 TATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:41329755 original size:24 final size:24
Alignment explanation
Indices: 41329727--41329777 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
41329717 AATTTGACTC
41329727 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAATAGAGTTTAATTG
41329751 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAATAGAGTTTAATTG
41329775 AAA
1 AAA
41329778 GATTATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.57, C:0.04, G:0.12, T:0.27
Consensus pattern (24 bp):
AAACAAATAAATAGAGTTTAATTG
Found at i:41331792 original size:27 final size:27
Alignment explanation
Indices: 41331731--41331784 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
41331721 TACATAATTG
41331731 AATAAAGGAATAATATTTGGTACATTAA
1 AATAAA-GAATAATATTTGGTACATTAA
* *
41331759 AAAAAAGAATAATATTTGGTATATTA
1 AATAAAGAATAATATTTGGTACATTA
41331785 TAGTAAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.52, C:0.02, G:0.13, T:0.33
Consensus pattern (27 bp):
AATAAAGAATAATATTTGGTACATTAA
Found at i:41335117 original size:27 final size:27
Alignment explanation
Indices: 41335068--41335119 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
41335058 AAAATGATCA
* * **
41335068 TTAATTAATTATTTGAATTTTTTTAAG
1 TTAATTAACTATTCGAAAGTTTTTAAG
41335095 TTAATTAACTATTCGAAAGTTTTTA
1 TTAATTAACTATTCGAAAGTTTTTA
41335120 TTTAACTCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (27 bp):
TTAATTAACTATTCGAAAGTTTTTAAG
Found at i:41345271 original size:16 final size:17
Alignment explanation
Indices: 41345246--41345284 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
41345236 TAATTTTATC
*
41345246 TTTAATAATTT-AAAAT
1 TTTAAAAATTTAAAAAT
41345262 TTTAAAAATTTAAAAAT
1 TTTAAAAATTTAAAAAT
41345279 TTTAAA
1 TTTAAA
41345285 GGAACTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAAAATTTAAAAAT
Found at i:41358771 original size:5 final size:5
Alignment explanation
Indices: 41358755--41358786 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
41358745 ACCCATTGTT
41358755 TTTTA -TTT- TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
41358787 TCGTCATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 6 0.24
5 19 0.76
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTA
Found at i:41359731 original size:15 final size:16
Alignment explanation
Indices: 41359711--41359743 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
41359701 AAGGAGTTCG
41359711 AATAAAGAAGAAA-AA
1 AATAAAGAAGAAAGAA
41359726 AATAAAGAAGAAAGAA
1 AATAAAGAAGAAAGAA
41359742 AA
1 AA
41359744 GAACAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (16 bp):
AATAAAGAAGAAAGAA
Found at i:41371968 original size:17 final size:16
Alignment explanation
Indices: 41371928--41371972 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
41371918 GCCCAACAGA
*
41371928 GTTTAAATTTGTTTTG
1 GTTTAAATTTATTTTG
**
41371944 AATTAAATTTATTTTAG
1 GTTTAAATTTATTTT-G
41371961 GTTTAAATTTAT
1 GTTTAAATTTAT
41371973 CTAAAATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (16 bp):
GTTTAAATTTATTTTG
Found at i:41371982 original size:17 final size:17
Alignment explanation
Indices: 41371946--41372020 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 17
41371936 TTGTTTTGAA
* **
41371946 TTAAATTTATTTTAGGT
1 TTAAATTTATTATAAAT
41371963 TTAAATTTATCTA-AAAT
1 TTAAATTTAT-TATAAAT
*
41371980 TTAAACTTATTATAAAT
1 TTAAATTTATTATAAAT
**
41371997 TTAAATTTAAAATAAAT
1 TTAAATTTATTATAAAT
*
41372014 ATAAATT
1 TTAAATT
41372021 AAATATTCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
16 2 0.04
17 45 0.94
18 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (17 bp):
TTAAATTTATTATAAAT
Found at i:41372012 original size:11 final size:12
Alignment explanation
Indices: 41371998--41372043 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
41371988 ATTATAAATT
41371998 TAAAT-TTAAAA
1 TAAATATTAAAA
*
41372009 TAAATA-TAAAT
1 TAAATATTAAAA
*
41372020 TAAATATTCAAA
1 TAAATATTAAAA
*
41372032 TACATATTAAAA
1 TAAATATTAAAA
41372044 GTCCATTTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 15 0.54
12 13 0.46
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (12 bp):
TAAATATTAAAA
Found at i:41373942 original size:30 final size:30
Alignment explanation
Indices: 41373906--41374002 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
41373896 AAACTGTCCA
* *** *
41373906 AAAATTATATCTTGACCCTTTAACTTCTCC
1 AAAATTATATCTTAACCCCAAAAATTCTCC
* *
41373936 AAAATTACATTTTAACCCCAAAAATTCTCC
1 AAAATTATATCTTAACCCCAAAAATTCTCC
* * * *
41373966 AAAATTATATTTTTAACCTCAAAACTTCT-A
1 AAAATTATA-TCTTAACCCCAAAAATTCTCC
41373996 AAAATTA
1 AAAATTA
41374003 CATTTTGACC
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 38 0.69
31 17 0.31
ACGTcount: A:0.41, C:0.22, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAATTATATCTTAACCCCAAAAATTCTCC
Found at i:41374008 original size:30 final size:30
Alignment explanation
Indices: 41373927--41374239 Score: 315
Period size: 29 Copynumber: 10.7 Consensus size: 30
41373917 TTGACCCTTT
* *
41373927 AACTTCTCCAAAATTACA-TTTTAACCCCAA
1 AACTTC-CAAAAATTACATTTTTAACCTCAA
* * *
41373957 AAATTCTCCAAAATTATATTTTTAACCTCAA
1 AACTTC-CAAAAATTACATTTTTAACCTCAA
* *
41373988 AACTTCTAAAAATTACA-TTTTGACCTCAA
1 AACTTCCAAAAATTACATTTTTAACCTCAA
* *
41374017 AACTTCCAAAAATTACATTTTTGACCTTAA
1 AACTTCCAAAAATTACATTTTTAACCTCAA
*
41374047 AACTTCTAAAAATTACA-TTTTAACC-CTAA
1 AACTTCCAAAAATTACATTTTTAACCTC-AA
* *
41374076 AACTTCCAAAAATTCCA-TTTTAACCCCAA
1 AACTTCCAAAAATTACATTTTTAACCTCAA
**
41374105 AACTTCCAAAAATTACATTTTT--CC-CCT
1 AACTTCCAAAAATTACATTTTTAACCTCAA
* *
41374132 AACTTCCAAAAGTT-CATTTTTGACC-CAA
1 AACTTCCAAAAATTACATTTTTAACCTCAA
* * * *
41374160 AACTTCCCAAAATTATATTTTT-ACCCCTA
1 AACTTCCAAAAATTACATTTTTAACCTCAA
* *
41374189 AACTTCCAAAAATTTCATTTTTAACCTCGA
1 AACTTCCAAAAATTACATTTTTAACCTCAA
*
41374219 AACTTCCAAAAATTATATTTT
1 AACTTCCAAAAATTACATTTT
41374240 CCCCCAAACT
Statistics
Matches: 241, Mismatches: 32, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
26 7 0.03
27 14 0.06
28 20 0.08
29 104 0.43
30 80 0.33
31 16 0.07
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (30 bp):
AACTTCCAAAAATTACATTTTTAACCTCAA
Found at i:41374049 original size:59 final size:58
Alignment explanation
Indices: 41373927--41374294 Score: 363
Period size: 59 Copynumber: 6.4 Consensus size: 58
41373917 TTGACCCTTT
* * * *
41373927 AACTTCTCCAAAATTACATTTTAACCCCAAAAATTCTCCAAAATTATATTTTTAACCTCAA
1 AACTTC-CAAAAATTACATTTT-ACCCCAAAACTTC-CAAAAATTACATTTTTAACCTCAA
* * * *
41373988 AACTTCTAAAAATTACATTTTGACCTCAAAACTTCCAAAAATTACATTTTTGACCTTAA
1 AACTTCCAAAAATTACATTTT-ACCCCAAAACTTCCAAAAATTACATTTTTAACCTCAA
* * * *
41374047 AACTTCTAAAAATTACATTTTAACCCTAAAACTTCCAAAAATTCCA-TTTTAACCCCAA
1 AACTTCCAAAAATTACATTTT-ACCCCAAAACTTCCAAAAATTACATTTTTAACCTCAA
* * * *
41374105 AACTTCCAAAAATTACATTTTTCCCC-TAACTTCCAAAAGTT-CATTTTTGACC-CAA
1 AACTTCCAAAAATTACATTTTACCCCAAAACTTCCAAAAATTACATTTTTAACCTCAA
* * * * *
41374160 AACTTCCCAAAATTATATTTTTACCCCTAAACTTCCAAAAATTTCATTTTTAACCTCGA
1 AACTTCCAAAAATTACA-TTTTACCCCAAAACTTCCAAAAATTACATTTTTAACCTCAA
* * * *** **
41374219 AACTTCCAAAAATTATATTTT-CCCCCAAACTTCC-AAATTTTTTTTTTTAACC-CCG
1 AACTTCCAAAAATTACATTTTACCCCAAAACTTCCAAAAATTACATTTTTAACCTCAA
*
41374274 AACTTCCAAAAATTCCATTTT
1 AACTTCCAAAAATTACATTTT
41374295 TCACCTCGGG
Statistics
Matches: 264, Mismatches: 38, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
55 40 0.15
56 43 0.16
57 28 0.11
58 43 0.16
59 80 0.30
60 24 0.09
61 6 0.02
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.36
Consensus pattern (58 bp):
AACTTCCAAAAATTACATTTTACCCCAAAACTTCCAAAAATTACATTTTTAACCTCAA
Found at i:41374286 original size:85 final size:86
Alignment explanation
Indices: 41373927--41374302 Score: 302
Period size: 85 Copynumber: 4.3 Consensus size: 86
41373917 TTGACCCTTT
* * * * * * *
41373927 AACTTCTCCAAAATTACATTTTAACCCCAAAAATTCTCCAAAATTATATTTTTAACCTCAAAACT
1 AACTTC-CAAAAATTACATTTTTACCTCGAAACTTC-CAAAAATTATA-TTTT-ACCCCAAAACT
* * * * *
41373992 TCTAAAA-ATTACATTTTGACCTCAA
62 TCCAAAATTTTA-TTTTTAACCCCAA
** * * *
41374017 AACTTCCAAAAATTACATTTTTGACCTTAAAACTTCTAAAAATTACATTTTAACCCTAAAACTTC
1 AACTTCCAAAAATTACATTTTT-ACCTCGAAACTTCCAAAAATTATATTTT-ACCCCAAAACTTC
**
41374082 CAAAAATTCCA-TTTTAACCCCAA
64 C-AAAATTTTATTTTTAACCCCAA
** *
41374105 AACTTCCAAAAATTACATTTTT-CC-CCTAACTTCCAAAAGTTCAT-TTTTGA-CCCAAAACTTC
1 AACTTCCAAAAATTACATTTTTACCTCGAAACTTCCAAAAATT-ATATTTT-ACCCCAAAACTT-
* *
41374166 CCAAAATTATATTTTT-ACCCCTA
63 CCAAAATTTTATTTTTAACCCCAA
* *
41374189 AACTTCCAAAAATTTCATTTTTAACCTCGAAACTTCCAAAAATTATATTTT-CCCCCAAACTTCC
1 AACTTCCAAAAATTACATTTTT-ACCTCGAAACTTCCAAAAATTATATTTTACCCCAAAACTTCC
* * *
41374253 AAATTTTTTTTTTTAACCCC-G
65 AAAATTTTATTTTTAACCCCAA
*
41374274 AACTTCCAAAAATTCCATTTTTCACCTCG
1 AACTTCCAAAAATTACATTTTT-ACCTCG
41374303 GGAATCCCAA
Statistics
Matches: 236, Mismatches: 38, Indels: 29
0.78 0.13 0.10
Matches are distributed among these distances:
84 43 0.18
85 63 0.27
86 21 0.09
87 18 0.08
88 48 0.20
89 26 0.11
90 17 0.07
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (86 bp):
AACTTCCAAAAATTACATTTTTACCTCGAAACTTCCAAAAATTATATTTTACCCCAAAACTTCCA
AAATTTTATTTTTAACCCCAA
Found at i:41374294 original size:114 final size:114
Alignment explanation
Indices: 41373927--41374295 Score: 366
Period size: 114 Copynumber: 3.2 Consensus size: 114
41373917 TTGACCCTTT
* * * * ** *
41373927 AACTTCTCCAAAATTACA-TTTTAACCCCAAAAATTCTCCAAAATTATATTTTTAACCTCAAAAC
1 AACTTC-CAAAAATTACATTTTTAACCCTAAAACTTC-CAAAAATTCCA-TTTTAACCCCAAAAC
* * * * * *
41373991 TTCTAAAAATTACATTTTGACCTCAAAACTTCCAAAAATTACATTTTTGACCTTAA
63 TTCCAAAAATTACATTTT--CCCCCAAACTTCCAAAAGTT-CATTTTTAACC-CAA
*
41374047 AACTTCTAAAAATTACA-TTTTAACCCTAAAACTTCCAAAAATTCCATTTTAACCCCAAAACTTC
1 AACTTCCAAAAATTACATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTAACCCCAAAACTTC
* * *
41374111 CAAAAATTACATTTTTCCCCTAACTTCCAAAAGTTCATTTTTGACCCAA
66 CAAAAATTACATTTTCCCCCAAACTTCCAAAAGTTCATTTTTAACCCAA
* * * * * *
41374160 AACTTCCCAAAATTATATTTTTACCCCT-AAACTTCCAAAAATTTCATTTTTAACCTCGAAACTT
1 AACTTCCAAAAATTACATTTTTAACCCTAAAACTTCCAAAAATTCCA-TTTTAACCCCAAAACTT
* ** ** **
41374224 CCAAAAATTATATTTTCCCCCAAACTTCCAAATTTTTTTTTTTAACCCCG
65 CCAAAAATTACATTTTCCCCCAAACTTCCAAAAGTTCATTTTTAACCCAA
*
41374274 AACTTCCAAAAATTCCATTTTT
1 AACTTCCAAAAATTACATTTTT
41374296 CACCTCGGGA
Statistics
Matches: 212, Mismatches: 35, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
113 33 0.16
114 94 0.44
115 15 0.07
117 31 0.15
118 8 0.04
119 25 0.12
120 6 0.03
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.36
Consensus pattern (114 bp):
AACTTCCAAAAATTACATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTAACCCCAAAACTTC
CAAAAATTACATTTTCCCCCAAACTTCCAAAAGTTCATTTTTAACCCAA
Found at i:41374295 original size:29 final size:29
Alignment explanation
Indices: 41373927--41374295 Score: 301
Period size: 29 Copynumber: 12.8 Consensus size: 29
41373917 TTGACCCTTT
*
41373927 AACTTCTCCAAAATTACA-TTTTAACCCCAA
1 AACTTC-CAAAAATTACATTTTTAACCCC-A
* * * *
41373957 AAATTCTCCAAAATTATATTTTTAACCTCAA
1 AACTTC-CAAAAATTACATTTTTAACC-CCA
* * *
41373988 AACTTCTAAAAATTACA-TTTTGACCTCAA
1 AACTTCCAAAAATTACATTTTTAACC-CCA
* **
41374017 AACTTCCAAAAATTACATTTTTGACCTTAA
1 AACTTCCAAAAATTACATTTTTAACC-CCA
* *
41374047 AACTTCTAAAAATTACA-TTTTAACCCTAA
1 AACTTCCAAAAATTACATTTTTAACCC-CA
*
41374076 AACTTCCAAAAATTCCA-TTTTAACCCCAA
1 AACTTCCAAAAATTACATTTTTAACCCC-A
*
41374105 AACTTCCAAAAATTACATTTTT--CCCCT
1 AACTTCCAAAAATTACATTTTTAACCCCA
* * *
41374132 AACTTCCAAAAGTT-CATTTTTGACCCAA
1 AACTTCCAAAAATTACATTTTTAACCCCA
* *
41374160 AACTTCCCAAAATTATATTTTT-ACCCCTA
1 AACTTCCAAAAATTACATTTTTAACCCC-A
* *
41374189 AACTTCCAAAAATTTCATTTTTAACCTCGA
1 AACTTCCAAAAATTACATTTTTAACC-CCA
* *
41374219 AACTTCCAAAAATTATA-TTTT-CCCCCA
1 AACTTCCAAAAATTACATTTTTAACCCCA
* *** *
41374246 AACTTCC-AAATTTTTTTTTTTAACCCCG
1 AACTTCCAAAAATTACATTTTTAACCCCA
*
41374274 AACTTCCAAAAATTCCATTTTT
1 AACTTCCAAAAATTACATTTTT
41374296 CACCTCGGGA
Statistics
Matches: 282, Mismatches: 42, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
26 13 0.05
27 26 0.09
28 36 0.13
29 117 0.41
30 74 0.26
31 15 0.05
32 1 0.00
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.36
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTAACCCCA
Found at i:41374353 original size:29 final size:29
Alignment explanation
Indices: 41374279--41374354 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 29
41374269 CCCCGAACTT
* *
41374279 CCAAAAATTCCATTTTTCACCTCGGGAATC
1 CCAAAAATACCATTTTT-ACCTCCGGAATC
* *
41374309 CCAAAATTACCA-TTTTACC-CCTGAATGC
1 CCAAAAATACCATTTTTACCTCCGGAAT-C
*
41374337 CCAAAAATCCCATTTTTA
1 CCAAAAATACCATTTTTA
41374355 TCCCGATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 5 0.13
28 14 0.37
29 9 0.24
30 10 0.26
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (29 bp):
CCAAAAATACCATTTTTACCTCCGGAATC
Found at i:41387547 original size:92 final size:92
Alignment explanation
Indices: 41386348--41387503 Score: 1906
Period size: 92 Copynumber: 12.6 Consensus size: 92
41386338 TTATTTCAAA
*
41386348 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATCTCT
1 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATCTCT
41386413 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
41386440 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATCTCT
1 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATCTCT
*
41386505 ATCCTCTTGAAATTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
* * *
41386532 ATAGTAAGTCTTTATCTCTCTAAAGTTGTATTAAGAGCAAGATAAAGCTTCAAATATCAATCTCT
1 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATCTCT
41386597 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
* * *
41386624 ATAGTAAGTCTTTATCTTTTTGAAGTTGTAGTAAAAGCAAGATAAAGCTTCAAACATCAATCTCT
1 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATCTCT
41386689 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
41386716 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATCTCT
1 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATCTCT
41386781 ATCCTCTTGAAGATTGTAGTAAAGTTGG
66 ATCCTCTTGAAG-TTGTAGTAAAGTTGG
* * **
41386809 ATAGTAAGTCTTTATCTCTTTGAAGTTGTAGTAAGAGCAAGATAAAGTTTTGAACATCAATCTCT
1 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATCTCT
41386874 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
* * * *
41386901 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAACATAAAGTTTCGAACATCAATCTTT
1 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATCTCT
41386966 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
* *
41386993 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGTTTCAAATATCAATCTCT
1 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATCTCT
*
41387058 ATCCTCTTGAAGTTGCAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
* *
41387085 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAATAGCAAGATGAAGCTTCAAACATCAATC-CT
1 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATCTC-
41387149 TATCCTCTTGAAGTTGTAGTAAAGTTGG
65 TATCCTCTTGAAGTTGTAGTAAAGTTGG
* * *
41387177 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAAT-TCC
1 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATCT-C
41387241 TATCCTCTTGAAGTTGTAGTAAAGTTGG
65 TATCCTCTTGAAGTTGTAGTAAAGTTGG
* * * *
41387269 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGTAAGATGAAGTTTCAAACATCAAT-TCC
1 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATCT-C
*
41387333 TATCCTCTTGAAATTGTAGTAAAGTTGG
65 TATCCTCTTGAAGTTGTAGTAAAGTTGG
** * * *
41387361 ATAACAAGTCTTTATCTCTCTGAAGTTGTAGTAAGACCAAGATAAAGTTTCAAGCATCAAT-TCC
1 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATCT-C
41387425 TATCCTCTTGAAGTTGTAGTAAAGTTGG
65 TATCCTCTTGAAGTTGTAGTAAAGTTGG
* * *
41387453 ATTGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAACTTC
1 ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTC
41387504 GGCACCAAAT
Statistics
Matches: 1011, Mismatches: 49, Indels: 8
0.95 0.05 0.01
Matches are distributed among these distances:
91 1 0.00
92 921 0.91
93 89 0.09
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (92 bp):
ATAGTAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATAAAGCTTCAAACATCAATCTCT
ATCCTCTTGAAGTTGTAGTAAAGTTGG
Found at i:41388066 original size:17 final size:16
Alignment explanation
Indices: 41388026--41388070 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
41388016 GCCCAACAGA
*
41388026 GTTTAAATTTGTTTTG
1 GTTTAAATTTATTTTG
**
41388042 AATTAAATTTATTTTAG
1 GTTTAAATTTATTTT-G
41388059 GTTTAAATTTAT
1 GTTTAAATTTAT
41388071 CTAAAATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (16 bp):
GTTTAAATTTATTTTG
Found at i:41388080 original size:17 final size:17
Alignment explanation
Indices: 41388044--41388118 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 17
41388034 TTGTTTTGAA
* **
41388044 TTAAATTTATTTTAGGT
1 TTAAATTTATTATAAAT
41388061 TTAAATTTATCTA-AAAT
1 TTAAATTTAT-TATAAAT
*
41388078 TTAAACTTATTATAAAT
1 TTAAATTTATTATAAAT
**
41388095 TTAAATTTAAAATAAAT
1 TTAAATTTATTATAAAT
*
41388112 ATAAATT
1 TTAAATT
41388119 AAATGTCCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
16 2 0.04
17 45 0.94
18 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (17 bp):
TTAAATTTATTATAAAT
Found at i:41388136 original size:19 final size:19
Alignment explanation
Indices: 41388108--41388146 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41388098 AATTTAAAAT
*
41388108 AAATATAAATT-AAATGTCC
1 AAATACAAATTCAAA-GTCC
41388127 AAATACAAATTCAAAGTCC
1 AAATACAAATTCAAAGTCC
41388146 A
1 A
41388147 TTTACATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.26
Consensus pattern (19 bp):
AAATACAAATTCAAAGTCC
Found at i:41388339 original size:19 final size:19
Alignment explanation
Indices: 41388315--41388352 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
41388305 GTCAGCATTG
41388315 ACCAGCAGCAAGTTGCACC
1 ACCAGCAGCAAGTTGCACC
41388334 ACCAGCAGCAAGTTGCACC
1 ACCAGCAGCAAGTTGCACC
41388353 GCCACTGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.37, G:0.21, T:0.11
Consensus pattern (19 bp):
ACCAGCAGCAAGTTGCACC
Done.