Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 132 of 349
Found at i:42014077 original size:25 final size:26
Alignment explanation
Indices: 42014049--42014123 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 26
42014039 CTGGAGGCCT
42014049 AGCCTCTTTTAAT-AACTGGGGCAAA
1 AGCCTCTTTTAATAAACTGGGGCAAA
*
42014074 AGCC-CTTTTTGATAAACTGGGGCAAA
1 AGCCTC-TTTTAATAAACTGGGGCAAA
**
42014100 AGCCT-TTTTCGGTAAACTGGGGCA
1 AGCCTCTTTT-AATAAACTGGGGCA
42014124 TAGCCCTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 1 0.02
25 14 0.32
26 29 0.66
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (26 bp):
AGCCTCTTTTAATAAACTGGGGCAAA
Found at i:42014128 original size:25 final size:27
Alignment explanation
Indices: 42014062--42014135 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 27
42014052 CTCTTTTAAT
42014062 AACTGGGGCAAAAGCCCTTTTT-GATA
1 AACTGGGGCAAAAGCCCTTTTTCGATA
*
42014088 AACTGGGGCAAAAG-CCTTTTTCGGTA
1 AACTGGGGCAAAAGCCCTTTTTCGATA
*
42014114 AACTGGGGC-ATAGCCCTTTTTC
1 AACTGGGGCAAAAGCCCTTTTTC
42014136 ACTTCCTCCA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.23
26 34 0.77
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (27 bp):
AACTGGGGCAAAAGCCCTTTTTCGATA
Found at i:42014211 original size:11 final size:11
Alignment explanation
Indices: 42014180--42014227 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
42014170 AAATGAATAC
42014180 ATCATGTGCAT
1 ATCATGTGCAT
*
42014191 ATCA--TACAT
1 ATCATGTGCAT
42014200 ATCATGTGCAT
1 ATCATGTGCAT
*
42014211 ATCATGT-CAA
1 ATCATGTGCAT
42014221 ATCATGT
1 ATCATGT
42014228 ATATCAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:42014291 original size:25 final size:25
Alignment explanation
Indices: 42014263--42014310 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
42014253 ATAATTAAAC
* *
42014263 CCTAGGGGTAAAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
42014288 CCTAGGGGCAAAATAGTCATTTT
1 CCTAGGGGCAAAATAGTCATTTT
42014311 CATATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:42017368 original size:43 final size:43
Alignment explanation
Indices: 42017239--42017369 Score: 138
Period size: 43 Copynumber: 3.0 Consensus size: 43
42017229 ACATAGGATT
*
42017239 TCGATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCA
* * * * * *
42017282 TCAATTTTTTATTTACGTGTAAGACC-CTATCTGGGACAGTGGCA
1 TCGATATGTGA-TTACGTGTAAGACCAC-GTCTGGGACATTGGCA
* * * *
42017326 TCGACATGTGATTACATGTAACACCACGTCTAGGACATTGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCA
42017369 T
1 T
42017370 TGTACGAGTT
Statistics
Matches: 68, Mismatches: 17, Indels: 6
0.75 0.19 0.07
Matches are distributed among these distances:
43 34 0.50
44 34 0.50
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (43 bp):
TCGATATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCA
Found at i:42022797 original size:29 final size:29
Alignment explanation
Indices: 42022724--42022841 Score: 107
Period size: 29 Copynumber: 4.1 Consensus size: 29
42022714 ACATACATGT
*
42022724 ATATGGCCCACTAGGCCC-AATCTTATTC
1 ATATGGCCCACTAGGCCCAAATCATATTC
* * **
42022752 AAATGGCCTATCT-GGCCCAGTTCATATTC
1 ATATGGCCCA-CTAGGCCCAAATCATATTC
* * **
42022781 TTATGGCCCACTAGGCCCAATTCCCATTC
1 ATATGGCCCACTAGGCCCAAATCATATTC
* *
42022810 CTATGGCCCATTAGGCCCAAATCATATT-
1 ATATGGCCCACTAGGCCCAAATCATATTC
42022838 ATAT
1 ATAT
42022842 TCATGCTCAC
Statistics
Matches: 70, Mismatches: 17, Indels: 6
0.75 0.18 0.06
Matches are distributed among these distances:
28 18 0.26
29 52 0.74
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.30
Consensus pattern (29 bp):
ATATGGCCCACTAGGCCCAAATCATATTC
Found at i:42024315 original size:16 final size:16
Alignment explanation
Indices: 42024291--42024322 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42024281 AAGTTCAGGA
42024291 TTTCAGGATTTTTGGG
1 TTTCAGGATTTTTGGG
*
42024307 TTTCGGGATTTTTGGG
1 TTTCAGGATTTTTGGG
42024323 GCGTTACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.06, G:0.34, T:0.50
Consensus pattern (16 bp):
TTTCAGGATTTTTGGG
Found at i:42029701 original size:28 final size:28
Alignment explanation
Indices: 42029659--42029803 Score: 109
Period size: 28 Copynumber: 5.2 Consensus size: 28
42029649 TAATTATATG
* *
42029659 TGGCACTTAACGTGCGAAGTATCGGGGA
1 TGGCACTTAATGTGCGAAGTATCGAGGA
* *
42029687 TGGCACTTAATGTGC-AA-TACATCCAGAA
1 TGGCACTTAATGTGCGAAGT--ATCGAGGA
* *
42029715 TGGCACTTAGTGTGCGAAGTAACGAGGA
1 TGGCACTTAATGTGCGAAGTATCGAGGA
* ** * *
42029743 TGGCACTTAGTGTGCGAAACATCCAGAA
1 TGGCACTTAATGTGCGAAGTATCGAGGA
* *
42029771 TGACACTTAGTGTGC-AAGGTATCG-GGTA
1 TGGCACTTAATGTGCGAA-GTATCGAGG-A
42029799 TGGCA
1 TGGCA
42029804 TCTAGTGTGC
Statistics
Matches: 92, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
26 1 0.01
27 5 0.05
28 83 0.90
29 2 0.02
30 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (28 bp):
TGGCACTTAATGTGCGAAGTATCGAGGA
Found at i:42029730 original size:56 final size:56
Alignment explanation
Indices: 42029659--42029820 Score: 204
Period size: 56 Copynumber: 2.9 Consensus size: 56
42029649 TAATTATATG
** *
42029659 TGGCACTTAACGTGCGAAGTATCGGGGATGGCACTTAATGTGCAATACATCCAGAA
1 TGGCACTTAGTGTGCGAAGTATCGGGGATGGCACTTAGTGTGCAATACATCCAGAA
* *
42029715 TGGCACTTAGTGTGCGAAGTAACGAGGATGGCACTTAGTGTGCGAA-ACATCCAGAA
1 TGGCACTTAGTGTGCGAAGTATCGGGGATGGCACTTAGTGTGC-AATACATCCAGAA
* * *
42029771 TGACACTTAGTGTGC-AAGGTATCGGGTATGGCA-TCTAGTGTGCGATACAT
1 TGGCACTTAGTGTGCGAA-GTATCGGGGATGGCACT-TAGTGTGCAATACAT
42029821 TGAATATTCA
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
55 4 0.04
56 86 0.93
57 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (56 bp):
TGGCACTTAGTGTGCGAAGTATCGGGGATGGCACTTAGTGTGCAATACATCCAGAA
Found at i:42029929 original size:31 final size:32
Alignment explanation
Indices: 42029889--42029960 Score: 119
Period size: 31 Copynumber: 2.3 Consensus size: 32
42029879 ACCGGTATCT
*
42029889 ACGGAAATTGGTACAATATGGTACA-GTATGC
1 ACGGAAATTGGAACAATATGGTACAGGTATGC
*
42029920 ATGGAAATTGGAACAATATGGTACAGGTATGC
1 ACGGAAATTGGAACAATATGGTACAGGTATGC
42029952 ACGGAAATT
1 ACGGAAATT
42029961 CAATTGAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
31 23 0.62
32 14 0.38
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (32 bp):
ACGGAAATTGGAACAATATGGTACAGGTATGC
Found at i:42033079 original size:24 final size:24
Alignment explanation
Indices: 42033052--42033129 Score: 97
Period size: 24 Copynumber: 3.2 Consensus size: 24
42033042 TTGATTTATT
*
42033052 AGCTCGTAAGAGCTTACTATTCTC
1 AGCTCGTAAGAGCTTACTGTTCTC
*
42033076 AGCTCGTCAGAGCTTACTGTT-TCC
1 AGCTCGTAAGAGCTTACTGTTCT-C
42033100 AGCTCG-ATAGAGCTTACTGTTCATC
1 AGCTCGTA-AGAGCTTACTGTTC-TC
42033125 AGCTC
1 AGCTC
42033130 AAAAGGAGCT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
23 1 0.02
24 39 0.83
25 6 0.13
26 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (24 bp):
AGCTCGTAAGAGCTTACTGTTCTC
Found at i:42035044 original size:28 final size:27
Alignment explanation
Indices: 42034979--42035048 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
42034969 CTATATATGT
42034979 ATATGGCACTTAGTGTGCAAAATATTA
1 ATATGGCACTTAGTGTGCAAAATATTA
* * * *
42035006 ATAATGACACTTGGTGTGCGATATATTGA
1 AT-ATGGCACTTAGTGTGCAAAATATT-A
*
42035035 GTATGGCACTTAGT
1 ATATGGCACTTAGT
42035049 ATACGAGACA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (27 bp):
ATATGGCACTTAGTGTGCAAAATATTA
Found at i:42037825 original size:27 final size:27
Alignment explanation
Indices: 42037794--42037971 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42037784 TAAATTGTAC
42037794 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42037821 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42037847 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42037875 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42037903 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42037930 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42037957 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42037972 GACTTAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42037908 original size:82 final size:81
Alignment explanation
Indices: 42037795--42037950 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42037785 AAATTGTACA
* *
42037795 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42037859 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42037876 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42037941 TGCGAGTTGA
65 TGCGAATTGA
42037951 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42037962 original size:82 final size:81
Alignment explanation
Indices: 42037791--42037971 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42037781 GATTAAATTG
* *
42037791 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42037856 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42037872 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42037936 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42037954 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42037972 GACTTAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42038741 original size:11 final size:10
Alignment explanation
Indices: 42038717--42038741 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42038707 CATGAGATTG
42038717 AAAAATCACT
1 AAAAATCACT
42038727 AAAAATCACT
1 AAAAATCACT
42038737 AAAAA
1 AAAAA
42038742 CGTGTGGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATCACT
Found at i:42049855 original size:13 final size:13
Alignment explanation
Indices: 42049833--42049867 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
42049823 TCCACACGCC
*
42049833 CGTGTCCCAAAAT
1 CGTGTTCCAAAAT
42049846 CGTGTTCCAAAAT
1 CGTGTTCCAAAAT
42049859 CGTGTTCCA
1 CGTGTTCCA
42049868 TACATGGCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (13 bp):
CGTGTTCCAAAAT
Found at i:42051885 original size:28 final size:28
Alignment explanation
Indices: 42051853--42051922 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
42051843 AATGAGATTG
42051853 GCACTAAGTGTGCGAGTTT-AAT-TGTATA
1 GCACTAAGTGTGCGAGTTTGAATAT-TA-A
*
42051881 GCACTAAGTGTGCGAGTTTGACTATTAA
1 GCACTAAGTGTGCGAGTTTGAATATTAA
42051909 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42051923 GACTTACTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 34 0.87
29 4 0.10
30 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGAATATTAA
Found at i:42059289 original size:27 final size:27
Alignment explanation
Indices: 42059258--42059435 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42059248 TAAATTGTAC
42059258 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42059285 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42059311 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42059339 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42059367 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42059394 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42059421 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42059436 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42059372 original size:82 final size:81
Alignment explanation
Indices: 42059259--42059414 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42059249 AAATTGTACA
* *
42059259 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42059323 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42059340 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42059405 TGCGAGTTGA
65 TGCGAATTGA
42059415 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42059426 original size:82 final size:81
Alignment explanation
Indices: 42059255--42059435 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42059245 GATTAAATTG
* *
42059255 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42059320 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42059336 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42059400 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42059418 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42059436 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42063120 original size:41 final size:40
Alignment explanation
Indices: 42063075--42063287 Score: 236
Period size: 40 Copynumber: 5.3 Consensus size: 40
42063065 GGACTAAGAT
*
42063075 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCC
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAG-TC
*
42063116 CCGAAGGCCTTTGTGCGAGATA-CTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATATC-AAATCCGGGTTAAGTC
* * *
42063156 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGTC
* * * *
42063196 CCGTAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGTC
* * * * *
42063236 CCGAAGGCA-TTGTGTGAGTTA-CTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATATC-AAATCCGGGTTAAGTC
42063275 CCGAAGGCATTTG
1 CCGAAGGCATTTG
42063288 AACGAGGAGC
Statistics
Matches: 154, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.21
40 86 0.56
41 33 0.21
42 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGTC
Found at i:42063240 original size:80 final size:78
Alignment explanation
Indices: 42063075--42063285 Score: 260
Period size: 80 Copynumber: 2.6 Consensus size: 78
42063065 GGACTAAGAT
* * * * *
42063075 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCA-TTGTGCGAGTTATAAA-TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGATACT
42063140 AAATCCGGGTTAAGTC
63 AAATCCGGGTTAAGTC
* * *
42063156 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGTAGGCATTCGTGCGAGTTATTA
1 CCGAAGGCATT-GTGCGAGTTA-TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTA
42063221 AATCCGGGTTAAGTC
64 AATCCGGGTTAAGTC
* * * *
42063236 CCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 CCGAAGGCATTGTGCGAGTTA-TAAATCCGGGTTAAGTCCCGAAGGCATT
42063286 TGAACGAGGA
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
79 33 0.29
80 49 0.43
81 29 0.25
82 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (78 bp):
CCGAAGGCATTGTGCGAGTTATAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
TCCGGGTTAAGTC
Found at i:42063305 original size:79 final size:80
Alignment explanation
Indices: 42063023--42063320 Score: 223
Period size: 80 Copynumber: 3.7 Consensus size: 80
42063013 TGAATGCTGT
* ** * * * **
42063023 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
42063086 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
42063103 CCGGGTTAAGCCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 CCGGGCTAAG-TCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATT
* *
42063167 CGTGCGAGTTATTAAAT
64 CGTGCGAGTTACTAAAA
* * ** * *
42063184 CCGGGTTAAGTCCCGTAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
42063248 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
42063263 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
42063321 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
78 16 0.09
79 45 0.25
80 56 0.31
81 55 0.30
82 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:42063305 original size:119 final size:120
Alignment explanation
Indices: 42063079--42063316 Score: 268
Period size: 119 Copynumber: 2.0 Consensus size: 120
42063069 TAAGATCCGA
* * *
42063079 AGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCCCCCGAAGGCCTTTGTGCGAGATACTAAAT
1 AGGCATTCGTGCGAGATACAAATTCCGGGTTAAGCCCCCGAAGGCCATTGTGCGAGATACTAAAA
* ** * * *
42063144 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGT
66 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCC-GGTTAAATCCCGT
* * * * *
42063200 AGGCATTCGTGCGAGTTATTAAA-TCCGGGTTAAG-TCCCGAAGG-CATTGTGTGAGTTACTAAA
1 AGGCATTCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCCGAAGGCCATTGTGCGAGATACTAAA
* * *
42063262 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCCGGTTAAATCCCG
65 ACCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGTTAAATCCCG
42063317 AAGGTACGTG
Statistics
Matches: 98, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
118 12 0.12
119 48 0.49
120 8 0.08
121 27 0.28
122 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
AGGCATTCGTGCGAGATACAAATTCCGGGTTAAGCCCCCGAAGGCCATTGTGCGAGATACTAAAA
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGTTAAATCCCGT
Found at i:42087373 original size:27 final size:27
Alignment explanation
Indices: 42087342--42087519 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42087332 TAAATTGTAC
42087342 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42087369 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42087395 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42087423 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42087451 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42087478 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42087505 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42087520 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42087456 original size:82 final size:81
Alignment explanation
Indices: 42087343--42087498 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42087333 AAATTGTACA
* *
42087343 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42087407 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42087424 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42087489 TGCGAGTTGA
65 TGCGAATTGA
42087499 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42087510 original size:82 final size:81
Alignment explanation
Indices: 42087339--42087519 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42087329 GATTAAATTG
* *
42087339 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42087404 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42087420 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42087484 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42087502 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42087520 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42090235 original size:48 final size:48
Alignment explanation
Indices: 42090175--42090280 Score: 158
Period size: 48 Copynumber: 2.2 Consensus size: 48
42090165 CGACCACAAT
* *
42090175 ATATACACATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
* *
42090223 ATATACATATCTCATACGTATTTCACACTAGCCATTCGTCTTTACCAC
1 ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
* *
42090271 ACATATATAT
1 ATATACATAT
42090281 ATTTATCTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (48 bp):
ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
Found at i:42095683 original size:29 final size:29
Alignment explanation
Indices: 42095649--42095708 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
42095639 TTTATTCTTT
42095649 TAATGCTTTGATATTATATAAATTGTATC
1 TAATGCTTTGATATTATATAAATTGTATC
42095678 TAATGCTTTGATATTATATAAATTGTATC
1 TAATGCTTTGATATTATATAAATTGTATC
42095707 TA
1 TA
42095709 CATGACTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.48
Consensus pattern (29 bp):
TAATGCTTTGATATTATATAAATTGTATC
Found at i:42095721 original size:29 final size:28
Alignment explanation
Indices: 42095649--42095723 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
42095639 TTTATTCTTT
*
42095649 TAATGCTTTGATATTATATAAATTGTATC
1 TAATGCTAT-ATATTATATAAATTGTATC
*
42095678 TAATGCTTTGATATTATATAAATTGTATC
1 TAATGCTAT-ATATTATATAAATTGTATC
42095707 TACATGACTAT-TATTAT
1 TA-ATG-CTATATATTAT
42095724 GTTTAACGAC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
29 37 0.86
30 3 0.07
31 3 0.07
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (28 bp):
TAATGCTATATATTATATAAATTGTATC
Found at i:42096799 original size:224 final size:224
Alignment explanation
Indices: 42096409--42096852 Score: 879
Period size: 224 Copynumber: 2.0 Consensus size: 224
42096399 TTATGGGTTA
42096409 TAGTTTATATGCTCAGAATCTTTGATGAGTCTATTTTCTAAATAAACAAACAGGAACATTATTCA
1 TAGTTTATATGCTCAGAATCTTTGATGAGTCTATTTTCTAAATAAACAAACAGGAACATTATTCA
42096474 TATTCTTTATGAGGATGTAATTAATTTTTAGTGAAGAGGGGTCGGAACTGTCGGACAGCAAAAAA
66 TATTCTTTATGAGGATGTAATTAATTTTTAGTGAAGAGGGGTCGGAACTGTCGGACAGCAAAAAA
42096539 GGGGTAACTTTGAAGAATAAACTGTACTTATTAGATAAACTAAATTTTTTTTAAATTTTATGGTA
131 GGGGTAACTTTGAAGAATAAACTGTACTTATTAGATAAACTAAATTTTTTTTAAATTTTATGGTA
42096604 AGAAGATATGTGAGTCTAGTTTCAGAATC
196 AGAAGATATGTGAGTCTAGTTTCAGAATC
42096633 TAGTTTATATGCTCAGAATCTTTGATGAGTCTATTTTCTAAATAAACAAACAGGAACATTATTCA
1 TAGTTTATATGCTCAGAATCTTTGATGAGTCTATTTTCTAAATAAACAAACAGGAACATTATTCA
*
42096698 TATTCTTTATGAGGATGTAATTAATTTTTAGTGAAGAGGGGTTGGAACTGTCGGACAGCAAAAAA
66 TATTCTTTATGAGGATGTAATTAATTTTTAGTGAAGAGGGGTCGGAACTGTCGGACAGCAAAAAA
42096763 GGGGTAACTTTGAAGAATAAACTGTACTTATTAGATAAACTAAATTTTTTTTAAATTTTATGGTA
131 GGGGTAACTTTGAAGAATAAACTGTACTTATTAGATAAACTAAATTTTTTTTAAATTTTATGGTA
42096828 AGAAGATATGTGAGTCTAGTTTCAG
196 AGAAGATATGTGAGTCTAGTTTCAG
42096853 GTAAAATTAA
Statistics
Matches: 219, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
224 219 1.00
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (224 bp):
TAGTTTATATGCTCAGAATCTTTGATGAGTCTATTTTCTAAATAAACAAACAGGAACATTATTCA
TATTCTTTATGAGGATGTAATTAATTTTTAGTGAAGAGGGGTCGGAACTGTCGGACAGCAAAAAA
GGGGTAACTTTGAAGAATAAACTGTACTTATTAGATAAACTAAATTTTTTTTAAATTTTATGGTA
AGAAGATATGTGAGTCTAGTTTCAGAATC
Found at i:42116414 original size:18 final size:19
Alignment explanation
Indices: 42116377--42116433 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
42116367 TATGACAAGC
*
42116377 ATAA-ATTAAAAAAAATTAA
1 ATAATATTAAAAAATA-TAA
*
42116396 A-GATATTAAAAAATATAA
1 ATAATATTAAAAAATATAA
*
42116414 ATTAATTTTAAAAAATATAA
1 A-TAATATTAAAAAATATAA
42116434 TTTTTTGACT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 15 0.48
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
ATAATATTAAAAAATATAA
Found at i:42119977 original size:25 final size:25
Alignment explanation
Indices: 42119949--42120024 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
42119939 AGAAAATAAA
42119949 AACAAAGGTCAAGTCAGTGTTTATC
1 AACAAAGGTCAAGTCAGTGTTTATC
*** **
42119974 AACAAAGGTCAAG--A--AAATAAA
1 AACAAAGGTCAAGTCAGTGTTTATC
42119995 AACAAAGGTCAAGTCAGTGTTTATC
1 AACAAAGGTCAAGTCAGTGTTTATC
42120020 AACAA
1 AACAA
42120025 CATGTCAACC
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
21 15 0.41
23 2 0.05
25 20 0.54
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.21
Consensus pattern (25 bp):
AACAAAGGTCAAGTCAGTGTTTATC
Found at i:42121606 original size:65 final size:65
Alignment explanation
Indices: 42121525--42121653 Score: 249
Period size: 65 Copynumber: 2.0 Consensus size: 65
42121515 TTTTAACTAA
42121525 GAATCTAAGTTTATGTAATAAAATATTTCATACAATAAAAATTATCCATAAATTATAAGTATGTT
1 GAATCTAAGTTTATGTAATAAAATATTTCATACAATAAAAATTATCCATAAATTATAAGTATGTT
*
42121590 GAATCTAAGTTTATGTAATAAAATATTTCATACAATAAAAATTATCGATAAATTATAAGTATGT
1 GAATCTAAGTTTATGTAATAAAATATTTCATACAATAAAAATTATCCATAAATTATAAGTATGT
42121654 GAAAATATTA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.38
Consensus pattern (65 bp):
GAATCTAAGTTTATGTAATAAAATATTTCATACAATAAAAATTATCCATAAATTATAAGTATGTT
Found at i:42125705 original size:18 final size:17
Alignment explanation
Indices: 42125668--42125701 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42125658 AACTATTCTT
*
42125668 TATTTTTGAATTTTAAA
1 TATTTTTCAATTTTAAA
*
42125685 TATTTTTCATTTTTAAA
1 TATTTTTCAATTTTAAA
42125702 ATATAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
TATTTTTCAATTTTAAA
Found at i:42134725 original size:17 final size:18
Alignment explanation
Indices: 42134703--42134739 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42134693 ACGCTTAAAA
*
42134703 AATTATGA-AACGAATAT
1 AATTATGATAACAAATAT
42134720 AATTATGATAACAAATAT
1 AATTATGATAACAAATAT
42134738 AA
1 AA
42134740 AATATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (18 bp):
AATTATGATAACAAATAT
Found at i:42144013 original size:15 final size:14
Alignment explanation
Indices: 42143976--42144018 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
42143966 AAAATTTATC
42143976 AAAGAAAAGAAAGAA
1 AAAGAAAA-AAAGAA
*
42143991 AAAGAAAAAGAGAA
1 AAAGAAAAAAAGAA
*
42144005 AAAGAAAAATAGAA
1 AAAGAAAAAAAGAA
42144019 CACACGGCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAGAAAAAAAGAA
Found at i:42154007 original size:34 final size:34
Alignment explanation
Indices: 42153957--42154022 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
42153947 GTCTCAGTTA
*
42153957 GGGCCTTAGCCAATTTCAGTAACAGTAACAGTCT
1 GGGCCTGAGCCAATTTCAGTAACAGTAACAGTCT
* *
42153991 GGGCCTGAGCCTATTTCAGTAACAGTATCAGT
1 GGGCCTGAGCCAATTTCAGTAACAGTAACAGT
42154023 GGGGCCTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (34 bp):
GGGCCTGAGCCAATTTCAGTAACAGTAACAGTCT
Found at i:42158331 original size:29 final size:29
Alignment explanation
Indices: 42158273--42158429 Score: 221
Period size: 29 Copynumber: 5.5 Consensus size: 29
42158263 ATAGTAAGTC
*
42158273 CGCACACTTAGTG-TTATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
42158301 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
42158330 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
*
42158359 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
* * * * *
42158387 TGCACACTTAGTGCTATGCA-ATTTAAACC
1 CGCACACTTAGTGCT-TACATAATCAAACT
42158416 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42158430 CAATCTCATG
Statistics
Matches: 117, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
28 39 0.33
29 76 0.65
30 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCAAACT
Found at i:42158380 original size:57 final size:58
Alignment explanation
Indices: 42158273--42158429 Score: 221
Period size: 57 Copynumber: 2.7 Consensus size: 58
42158263 ATAGTAAGTC
*
42158273 CGCACACTTAGTG-TTATATAATCAAACTCGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACTCGCACACTTAGTGCTTACATAATCAAACT
*
42158330 CGCACACTTAGTGCTTACATAATCAAACTCGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACTCGCACACTTAGTGCTTACATAATCAAACT
* * * * *
42158387 TGCACACTTAGTGCTATGCA-ATTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCT-TACATAATCAAACTCGCACACTTAGTGC
42158430 CAATCTCATG
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
57 60 0.66
58 31 0.34
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (58 bp):
CGCACACTTAGTGCTTACATAATCAAACTCGCACACTTAGTGCTTACATAATCAAACT
Found at i:42160400 original size:48 final size:48
Alignment explanation
Indices: 42160338--42160555 Score: 391
Period size: 48 Copynumber: 4.5 Consensus size: 48
42160328 TACAAGATAA
* *
42160338 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
42160386 AAATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
42160434 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
42160482 ATATATATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
42160530 ATATGTATATGTGGTAAAGTCGAATG
1 ATATGTATATGTGGTAAAGCCGAATG
42160556 AGATATGTAT
Statistics
Matches: 163, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 163 1.00
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
Found at i:42160582 original size:124 final size:123
Alignment explanation
Indices: 42160429--42160678 Score: 446
Period size: 124 Copynumber: 2.0 Consensus size: 123
42160419 TGAAATATGT
* * *
42160429 ATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATATATATGT
1 ATGAGATATGTATATGAGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATATATATGT
*
42160494 GGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGTCGA
66 GGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGA-ATGTATATGTGGTAAAGCCGA
*
42160553 ATGAGATATGTATATGAGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGT
1 ATGAGATATGTATATGAGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATATATATGT
42160618 GGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAATGTATATGTGGTAAAGCCGA
66 GGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAATGTATATGTGGTAAAGCCGA
42160676 ATG
1 ATG
42160679 GCTAGTGTGA
Statistics
Matches: 121, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
123 23 0.19
124 98 0.81
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (123 bp):
ATGAGATATGTATATGAGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATATATATGT
GGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAATGTATATGTGGTAAAGCCGA
Found at i:42160591 original size:28 final size:28
Alignment explanation
Indices: 42160525--42160583 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
42160515 TGAAATATGT
* *
42160525 ATGAGATATGTATATGTGGTAAAGTCGA
1 ATGAGATATGTATATGAGGTAAAGCCGA
42160553 ATGAGATATGTATATGAGGTAAAGCCGA
1 ATGAGATATGTATATGAGGTAAAGCCGA
42160581 ATG
1 ATG
42160584 GCTAATGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.29
Consensus pattern (28 bp):
ATGAGATATGTATATGAGGTAAAGCCGA
Found at i:42160604 original size:76 final size:76
Alignment explanation
Indices: 42160477--42160631 Score: 265
Period size: 76 Copynumber: 2.0 Consensus size: 76
42160467 TGAAATATGT
* * *
42160477 ATGAGATATATATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGT
1 ATGAGATATATATATGAGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGT
*
42160542 GGTAAAGTCGA
66 GGTAAAGCCGA
*
42160553 ATGAGATATGTATATGAGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGT
1 ATGAGATATATATATGAGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGT
42160618 GGTAAAGCCGA
66 GGTAAAGCCGA
42160629 ATG
1 ATG
42160632 GCTAGTGTGA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.30
Consensus pattern (76 bp):
ATGAGATATATATATGAGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGT
GGTAAAGCCGA
Found at i:42160677 original size:47 final size:48
Alignment explanation
Indices: 42160553--42160796 Score: 431
Period size: 48 Copynumber: 5.1 Consensus size: 48
42160543 GTAAAGTCGA
* * *
42160553 ATGAGATATGTATATGAGGTAAAGCCGAATGGCTAATGTGAAATATAT
1 ATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGT
42160601 ATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGT
1 ATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGT
42160649 ATGAGA-ATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGT
1 ATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGT
42160696 ATGAGA-ATGTATATGT-GTAAAGCCGAATGGCTAGTGTGAAATATGT
1 ATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGT
42160742 ATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGT
1 ATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGT
*
42160790 AGGAGAT
1 ATGAGAT
42160797 GTGTGTATAT
Statistics
Matches: 190, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
46 36 0.19
47 67 0.35
48 87 0.46
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.30
Consensus pattern (48 bp):
ATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGT
Found at i:42160829 original size:141 final size:142
Alignment explanation
Indices: 42160553--42160831 Score: 402
Period size: 141 Copynumber: 2.0 Consensus size: 142
42160543 GTAAAGTCGA
42160553 ATGAGATATGTATATGAGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGT
1 ATGAGATATGTATATGAGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGT
* * * *
42160618 GGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAATGTATATGTGGTAAAGCCGAATGGCTA
66 GGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAATGTATATATGGT-AAGCCGAATGCCAA
*
42160683 GTGTGAAATATGT
130 ATGTGAAATATGT
* * *
42160696 ATGAGA-ATGTATATG-TGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGT
1 ATGAGATATGTATATGAGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGT
* * * *
42160759 GGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGATGTGTGTATATTGT-GGCCGAATGACCA
66 GGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGA-ATGTATATATGGTAAGCCGAATG-CCA
42160823 AATGTGAAA
129 AATGTGAAA
42160832 GGTGTGTATT
Statistics
Matches: 122, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
140 8 0.07
141 90 0.74
142 18 0.15
143 6 0.05
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.30
Consensus pattern (142 bp):
ATGAGATATGTATATGAGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGT
GGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAATGTATATATGGTAAGCCGAATGCCAAA
TGTGAAATATGT
Found at i:42160987 original size:37 final size:37
Alignment explanation
Indices: 42160937--42161073 Score: 244
Period size: 37 Copynumber: 3.8 Consensus size: 37
42160927 GGAAATATAT
42160937 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
42160974 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
42161011 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT-TG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
42161047 TCCGGGTAAGA-CCGATAACTACG-GTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
42161074 GGACTATTCG
Statistics
Matches: 99, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
34 4 0.04
35 11 0.11
36 13 0.13
37 71 0.72
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.23
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:42162567 original size:40 final size:40
Alignment explanation
Indices: 42162344--42162558 Score: 385
Period size: 40 Copynumber: 5.4 Consensus size: 40
42162334 ATTGAGAGTT
*
42162344 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTTCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
42162384 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* *
42162424 ATATATCTGGGCTAAGTCCCGAAGAGCATTTGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
42162464 ATATATCCGGGCTAAGTCCCGAAGAGCATTTGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
42162504 ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
42162544 ATATATCCGGGCTAA
1 ATATATCCGGGCTAA
42162559 ACCTCGAAGG
Statistics
Matches: 169, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 169 1.00
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
Found at i:42162630 original size:28 final size:28
Alignment explanation
Indices: 42162590--42162717 Score: 159
Period size: 28 Copynumber: 4.5 Consensus size: 28
42162580 GAGTTATGAG
* * *
42162590 GCACTGTGTGTGCAAGTTCTTCAACCGA
1 GCACTATGTGTGCGAGTTCTTCAATCGA
42162618 GCACTATGTGTGCGAGTTCTTCAATCGA
1 GCACTATGTGTGCGAGTTCTTCAATCGA
** *
42162646 GCACTATGTGTGCGAGATTGGT-AATTGA
1 GCACTATGTGTGCGAG-TTCTTCAATCGA
*
42162674 GGCACTATGTGTGCGAGTTCTTTAATCGA
1 -GCACTATGTGTGCGAGTTCTTCAATCGA
*
42162703 GCGCTATGTGTGCGA
1 GCACTATGTGTGCGA
42162718 AATCAGTCAG
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
28 63 0.72
29 24 0.28
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (28 bp):
GCACTATGTGTGCGAGTTCTTCAATCGA
Found at i:42162735 original size:85 final size:85
Alignment explanation
Indices: 42162586--42162745 Score: 196
Period size: 85 Copynumber: 1.9 Consensus size: 85
42162576 GCTGGAGTTA
* ** *
42162586 TGAGGCACTGTGTGTGCAAGTTCTTCAACCGAGCACTATGTGTGCGAGTTCTTCAATCGAGCACT
1 TGAGGCACTATGTGTGCAAGTTCTTCAACCGAGCACTATGTGTGCGAAATCGTCAATCGAGCACT
*
42162651 ATGTGTGCGAGATTGGTAAT
66 ATGTATGCGAGATTGGTAAT
* * * * * *
42162671 TGAGGCACTATGTGTGCGAGTTCTTTAATCGAGCGCTATGTGTGCGAAATCAGTCAGT-GGGCAC
1 TGAGGCACTATGTGTGCAAGTTCTTCAACCGAGCACTATGTGTGCGAAATC-GTCAATCGAGCAC
*
42162735 TGTGTATGCGA
65 TATGTATGCGA
42162746 AGTGTGTTTC
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
85 58 0.94
86 4 0.06
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (85 bp):
TGAGGCACTATGTGTGCAAGTTCTTCAACCGAGCACTATGTGTGCGAAATCGTCAATCGAGCACT
ATGTATGCGAGATTGGTAAT
Found at i:42166319 original size:48 final size:48
Alignment explanation
Indices: 42166252--42166750 Score: 737
Period size: 48 Copynumber: 10.1 Consensus size: 48
42166242 TACAAGATAA
* *
42166252 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* * *
42166300 ATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
42166348 ATATGTATATGTGGTAAAGCCGAATGGCCAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
42166396 ATATGTATATGTGGTTAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
42166444 ATATGTATATGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
42166492 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGATG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGA-G
42166541 AAATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ----A--TAT--G---T--ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
42166602 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* * *
42166650 ATATGTATATGTGGTAAAGTCGAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* * *
42166698 ATATGTATAAGTGGTAAAGCCGAATGGCTAGCGGGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
42166746 ATATG
1 ATATG
42166751 GCTAGTGTGA
Statistics
Matches: 416, Mismatches: 21, Indels: 28
0.89 0.05 0.06
Matches are distributed among these distances:
48 361 0.87
49 1 0.00
50 1 0.00
53 2 0.00
55 6 0.01
57 2 0.00
60 1 0.00
61 1 0.00
62 41 0.10
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
Found at i:42166544 original size:14 final size:14
Alignment explanation
Indices: 42166525--42166552 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42166515 ATGGCTAGTG
42166525 TGAAATATGTATGA
1 TGAAATATGTATGA
42166539 TGAAATATGTATGA
1 TGAAATATGTATGA
42166553 GATATGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (14 bp):
TGAAATATGTATGA
Found at i:42166550 original size:62 final size:62
Alignment explanation
Indices: 42166477--42166600 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
42166467 ATGGCTAGTG
*
42166477 TGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGA
1 TGAAATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGA
42166539 TGAAATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGA
1 TGAAATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGA
42166601 GATATGTATA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.31
Consensus pattern (62 bp):
TGAAATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGA
Found at i:42166554 original size:158 final size:158
Alignment explanation
Indices: 42166381--42166696 Score: 569
Period size: 158 Copynumber: 2.0 Consensus size: 158
42166371 ATGGCCAGTG
* *
42166381 TGAAATATGTATGAGATATGTATATGTGGTTAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
1 TGAAATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
*
42166446 ATGTATATGTGGTAAAGCCAAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAG
66 ATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG
* *
42166511 CCGAATGGCTAGTGTGAAATATGTATGA
131 CCGAATGGCTAATGTGAAATATATATGA
42166539 TGAAATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
1 TGAAATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
*
42166604 ATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG
66 ATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG
*
42166669 TCGAATGGCTAATGTGAAATATATATGA
131 CCGAATGGCTAATGTGAAATATATATGA
42166697 GATATGTATA
Statistics
Matches: 151, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
158 151 1.00
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.32
Consensus pattern (158 bp):
TGAAATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
ATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG
CCGAATGGCTAATGTGAAATATATATGA
Found at i:42166594 original size:31 final size:31
Alignment explanation
Indices: 42166498--42166596 Score: 80
Period size: 31 Copynumber: 3.2 Consensus size: 31
42166488 TGAGATATGT
42166498 ATATGTGGTAAAGCCGAATGGCTAGTGTGAA
1 ATATGTGGTAAAGCCGAATGGCTAGTGTGAA
* *** * *
42166529 ATATGTATGATGAAATATGTAT-G--AGATATG-A
1 ATATG--TGGT-AAAGCCGAATGGCTAG-TGTGAA
42166560 ATATGTGGTAAAGCCGAATGGCTAGTGTGAA
1 ATATGTGGTAAAGCCGAATGGCTAGTGTGAA
42166591 ATATGT
1 ATATGT
42166597 ATGAGATATG
Statistics
Matches: 48, Mismatches: 12, Indels: 16
0.63 0.16 0.21
Matches are distributed among these distances:
28 6 0.12
29 4 0.08
30 3 0.06
31 22 0.46
32 3 0.06
33 4 0.08
34 6 0.12
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.30
Consensus pattern (31 bp):
ATATGTGGTAAAGCCGAATGGCTAGTGTGAA
Found at i:42166687 original size:206 final size:213
Alignment explanation
Indices: 42166332--42166870 Score: 849
Period size: 206 Copynumber: 2.5 Consensus size: 213
42166322 AATGGCTAAT
* *
42166332 ATGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCCAGTGTGAAATATGTATGAGA
1 ATGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGA
*
42166397 TATGTATATGTGGTTAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAA
66 TATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAA
* * * * *
42166462 GCCAAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTG
131 GCCAAATGGCTAATGTGAAATATATATGAGATATGTATAAGTGGTAAAGCCGAATGGCTAGCGGG
42166527 -AA-A-TAT-G-TAT-G-
196 AAATAGTATAGATATGGC
*
42166538 ATGAAATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGA
1 ATGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGA
*
42166603 TATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAA
66 TATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAA
* *
42166668 GTCGAATGGCTAATGTGAAATATATATGAGATATGTATAAGTGGTAAAGCCGAATGGCTAGCGGG
131 GCCAAATGGCTAATGTGAAATATATATGAGATATGTATAAGTGGTAAAGCCGAATGGCTAGCGGG
42166733 AAATATGTATGAGATATGGC
196 AAATA-GTAT-AGATATGGC
*
42166753 TAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTAT
1 -A---TGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAT
*
42166818 GAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
62 GAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
42166871 GTGTGTATAT
Statistics
Matches: 304, Mismatches: 16, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
206 183 0.60
207 2 0.01
208 1 0.00
210 3 0.01
212 1 0.00
213 3 0.01
214 1 0.00
216 1 0.00
219 109 0.36
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (213 bp):
ATGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGA
TATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAA
GCCAAATGGCTAATGTGAAATATATATGAGATATGTATAAGTGGTAAAGCCGAATGGCTAGCGGG
AAATAGTATAGATATGGC
Found at i:42166738 original size:254 final size:254
Alignment explanation
Indices: 42166285--42166750 Score: 806
Period size: 254 Copynumber: 1.8 Consensus size: 254
42166275 ATGGCTAATG
*
42166285 TGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATATATGAGAT
1 TGAAATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCTAATATGAAATATATATGAGAT
* *
42166350 ATGTATATGTGGTAAAGCCGAATGGCCAGTGTGAAATATGTATGAGATATGTATATGTGGTTAAG
66 ATGTATATGTGGTAAAGCCGAATGGCCAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG
* * * * *
42166415 CCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCAAATGGCTAGTGTGA
131 CCGAATGGCTAATGTGAAATATATATGAGATATGTATAAGTGGTAAAGCCAAATGGCTAGCGGGA
42166480 AATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGA
196 AATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGA
* * *
42166539 TGAAATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
1 TGAAATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCTAATATGAAATATATATGAGAT
*
42166604 ATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG
66 ATGTATATGTGGTAAAGCCGAATGGCCAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG
* *
42166669 TCGAATGGCTAATGTGAAATATATATGAGATATGTATAAGTGGTAAAGCCGAATGGCTAGCGGGA
131 CCGAATGGCTAATGTGAAATATATATGAGATATGTATAAGTGGTAAAGCCAAATGGCTAGCGGGA
42166734 AATATGTATGAGATATG
196 AATATGTATGAGATATG
42166751 GCTAGTGTGA
Statistics
Matches: 198, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
254 198 1.00
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (254 bp):
TGAAATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCTAATATGAAATATATATGAGAT
ATGTATATGTGGTAAAGCCGAATGGCCAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG
CCGAATGGCTAATGTGAAATATATATGAGATATGTATAAGTGGTAAAGCCAAATGGCTAGCGGGA
AATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGA
Found at i:42166762 original size:27 final size:27
Alignment explanation
Indices: 42166721--42166825 Score: 98
Period size: 27 Copynumber: 4.1 Consensus size: 27
42166711 GTAAAGCCGA
* *
42166721 ATGGCTAGCGGGAAATATGTATGAGAT
1 ATGGCTAGTGTGAAATATGTATGAGAT
42166748 ATGGCTAGTGTGAAATATGTATGAGAT
1 ATGGCTAGTGTGAAATATGTATGAGAT
** * *
42166775 ATGTATA-TGTGGTAA-A-G-CT--GA-
1 ATGGCTAGTGT-GAAATATGTATGAGAT
42166796 ATGGCTAGTGTGAAATATGTATGAGAT
1 ATGGCTAGTGTGAAATATGTATGAGAT
42166823 ATG
1 ATG
42166826 TATATGTGGT
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
21 8 0.13
22 6 0.10
23 1 0.02
24 2 0.03
25 1 0.02
26 6 0.10
27 36 0.60
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.31
Consensus pattern (27 bp):
ATGGCTAGTGTGAAATATGTATGAGAT
Found at i:42166763 original size:75 final size:75
Alignment explanation
Indices: 42166673--42166825 Score: 252
Period size: 75 Copynumber: 2.0 Consensus size: 75
42166663 GTAAAGTCGA
42166673 ATGGCTAATGTGAAATATATATGAGATATGTATAAGTGGTAAAGCCGAATGGCTAGCGGGAAATA
1 ATGGCTAATGTGAAATATATATGAGATATGTATAAGTGGTAAAGCCGAATGGCTAGCGGGAAATA
42166738 TGTATGAGAT
66 TGTATGAGAT
* * * * * *
42166748 ATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCTGAATGGCTAGTGTGAAATA
1 ATGGCTAATGTGAAATATATATGAGATATGTATAAGTGGTAAAGCCGAATGGCTAGCGGGAAATA
42166813 TGTATGAGAT
66 TGTATGAGAT
42166823 ATG
1 ATG
42166826 TATATGTGGT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (75 bp):
ATGGCTAATGTGAAATATATATGAGATATGTATAAGTGGTAAAGCCGAATGGCTAGCGGGAAATA
TGTATGAGAT
Found at i:42166773 original size:123 final size:123
Alignment explanation
Indices: 42166625--42166870 Score: 413
Period size: 123 Copynumber: 2.0 Consensus size: 123
42166615 GTAAAGCCGA
42166625 ATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAG-TCGAATGGCTAATGTGAAAT
1 ATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCT-GAATGGCTAATGTGAAAT
*
42166689 ATATATGAGATATGTATAAGTGGTAAAGCCGAATGGCTAGCGGGAAATATGTATGAGAT
65 ATATATGAGATATGTATAAGTGGTAAAGCCGAATGGCTAGCGGGAAATATGTAGGAGAT
* *
42166748 ATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCTGAATGGCTAGTGTGAAATA
1 ATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCTGAATGGCTAATGTGAAATA
* * * *
42166813 TGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAGAT
66 TATATGAGATATGTATAAGTGGTAAAGCCGAATGGCTAGCGGGAAATATGTAGGAGAT
42166871 GTGTGTATAT
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
123 114 0.99
124 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (123 bp):
ATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCTGAATGGCTAATGTGAAATA
TATATGAGATATGTATAAGTGGTAAAGCCGAATGGCTAGCGGGAAATATGTAGGAGAT
Found at i:42166803 original size:48 final size:48
Alignment explanation
Indices: 42166748--42166870 Score: 228
Period size: 48 Copynumber: 2.6 Consensus size: 48
42166738 TGTATGAGAT
*
42166748 ATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCTGA
1 ATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
42166796 ATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
1 ATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
*
42166844 ATGGCTAGTGTGAAATATGTAGGAGAT
1 ATGGCTAGTGTGAAATATGTATGAGAT
42166871 GTGTGTATAT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 73 1.00
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (48 bp):
ATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
Found at i:42167064 original size:37 final size:37
Alignment explanation
Indices: 42167014--42167150 Score: 231
Period size: 37 Copynumber: 3.7 Consensus size: 37
42167004 AATATATTCT
42167014 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
42167051 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
42167088 GGGTAAGACCCGATGACTACGTGTGGAGAATT-TGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAG-ATTATGTCC
* * *
42167125 AGGTAAGACCCGATAACTACGCGTGG
1 GGGTAAGACCCGATGACTACGTGTGG
42167151 GGACTATTCA
Statistics
Matches: 96, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
37 93 0.97
38 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.23
Consensus pattern (37 bp):
GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
Found at i:42171463 original size:25 final size:25
Alignment explanation
Indices: 42171410--42171504 Score: 75
Period size: 25 Copynumber: 3.8 Consensus size: 25
42171400 CATTTGAGCA
* *
42171410 CATA-AACGGGAAGCTCTCTCTCAAGC
1 CATATAACAGGAAGCTC-ATCT-AAGC
* * *
42171436 CATATAACAGAAAGCTCATGTGAGC
1 CATATAACAGGAAGCTCATCTAAGC
* * *
42171461 CATGTAACGGGAAGCTTATCTAAGC
1 CATATAACAGGAAGCTCATCTAAGC
**
42171486 TGTATAACAGGAAGCTCAT
1 CATATAACAGGAAGCTCAT
42171505 AAGAGTCATA
Statistics
Matches: 52, Mismatches: 16, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
25 36 0.69
26 6 0.12
27 10 0.19
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (25 bp):
CATATAACAGGAAGCTCATCTAAGC
Found at i:42171470 original size:52 final size:50
Alignment explanation
Indices: 42171392--42171504 Score: 129
Period size: 52 Copynumber: 2.2 Consensus size: 50
42171382 TTCATATTTG
* * *
42171392 AGAATGCTCATTTGAGCACATAAACGGGAAGCTCTCTCTCAAGCCATATAAC
1 AGAAAGCTCATGTGAGCACATAAACGGGAAGCT-TATCT-AAGCCATATAAC
* **
42171444 AGAAAGCTCATGTGAGC-CATGTAACGGGAAGCTTATCTAAGCTGTATAAC
1 AGAAAGCTCATGTGAGCACAT-AAACGGGAAGCTTATCTAAGCCATATAAC
*
42171494 AGGAAGCTCAT
1 AGAAAGCTCAT
42171505 AAGAGTCATA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
50 20 0.38
51 7 0.13
52 26 0.49
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (50 bp):
AGAAAGCTCATGTGAGCACATAAACGGGAAGCTTATCTAAGCCATATAAC
Found at i:42173027 original size:69 final size:69
Alignment explanation
Indices: 42172833--42173015 Score: 228
Period size: 69 Copynumber: 2.7 Consensus size: 69
42172823 CTATGTGCTG
* * * * * *
42172833 CCATGTTTATTTTCTTGGTG-GACTTCAAATGTTGCCGTGGCCCTAGTTGTGGTCTTACATAATA
1 CCATGTTTATTATCTTGGTGAG-CTTCATATGTTGCCATAGCCCCAGTTGTGGTCTTACACAATA
42172897 AGATC
65 AGATC
*
42172902 CCATGTTTATTATCCTTGCG-GA-CTTTATATGTTGCCATAGCCCCAGTTGTGGTCTTACACAAT
1 CCATGTTTATTAT-CTTG-GTGAGCTTCATATGTTGCCATAGCCCCAGTTGTGGTCTTACACAAT
*
42172965 ATGATC
64 AAGATC
* *
42172971 CCATGTTTATTGTCTCGGTGAGCTTCATATGTTGCCATAGCCCCA
1 CCATGTTTATTATCTTGGTGAGCTTCATATGTTGCCATAGCCCCA
42173016 ACTATGGTCT
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
67 1 0.01
68 5 0.05
69 86 0.88
70 5 0.05
71 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (69 bp):
CCATGTTTATTATCTTGGTGAGCTTCATATGTTGCCATAGCCCCAGTTGTGGTCTTACACAATAA
GATC
Found at i:42180675 original size:40 final size:41
Alignment explanation
Indices: 42180631--42180798 Score: 207
Period size: 41 Copynumber: 4.1 Consensus size: 41
42180621 GCGTTTTACC
* * *
42180631 AAAAATGCCAC-AAAAACCAGAGCAATAGCGGCG-TTTTAGTA
1 AAAAATGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTT-G-G
* *
42180672 AAAAACGCCGCGAAAAA-CAGAGCATTAGCGGCGCTTTTGG
1 AAAAATGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
* * * *
42180712 CAAAATGCCGCTAAAAACGAGAGCATTAGTGGTGCTTTTGG
1 AAAAATGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
*
42180753 CAAAATGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
1 AAAAATGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
42180794 AAAAA
1 AAAAA
42180799 ACGCCACTAA
Statistics
Matches: 110, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
40 14 0.13
41 87 0.79
42 9 0.08
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (41 bp):
AAAAATGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGG
Found at i:42180982 original size:7 final size:7
Alignment explanation
Indices: 42180967--42181020 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
42180957 TTAATTATCA
*
42180967 TTATAGT
1 TTATGGT
42180974 TTATGGT
1 TTATGGT
42180981 TTATGGT
1 TTATGGT
* *
42180988 TTAAGAT
1 TTATGGT
*
42180995 ATATGGT
1 TTATGGT
*
42181002 TTAGGGT
1 TTATGGT
*
42181009 TTAAGGT
1 TTATGGT
42181016 TTATG
1 TTATG
42181021 AGTTAATTAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (7 bp):
TTATGGT
Found at i:42180999 original size:21 final size:21
Alignment explanation
Indices: 42180975--42181059 Score: 89
Period size: 21 Copynumber: 3.9 Consensus size: 21
42180965 CATTATAGTT
*
42180975 TATGGTTTATGGTTTAAGATA
1 TATGGTTTAGGGTTTAAGATA
* *
42180996 TATGGTTTAGGGTTTAAGGTT
1 TATGGTTTAGGGTTTAAGATA
*
42181017 TATGAGTTAATTATGGTTTAAGATA
1 TATG-G-T--TTAGGGTTTAAGATA
*
42181042 TATAGTTTAGGGTTTAAG
1 TATGGTTTAGGGTTTAAG
42181060 GTTTAGGAGT
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
21 33 0.63
22 1 0.02
23 2 0.04
24 1 0.02
25 15 0.29
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (21 bp):
TATGGTTTAGGGTTTAAGATA
Found at i:42181033 original size:46 final size:46
Alignment explanation
Indices: 42180981--42181072 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
42180971 AGTTTATGGT
* *
42180981 TTATGGTTTAAGATATATGGTTTAGGGTTTAAGGTTTATGAGTTAA
1 TTATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAGGAGTTAA
42181027 TTATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAGGAGTTAA
1 TTATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAGGAGTTAA
42181073 CTAGTATTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (46 bp):
TTATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAGGAGTTAA
Found at i:42181341 original size:22 final size:22
Alignment explanation
Indices: 42181313--42181376 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
42181303 AAAACAGGTT
42181313 TTAAGGGGATAGAGGTTAGGCG
1 TTAAGGGGATAGAGGTTAGGCG
42181335 TTAAGGGGATA-AGGGTTAGGCG
1 TTAAGGGGATAGA-GGTTAGGCG
* *
42181357 TTAAGGGGATTGGGGTTAGG
1 TTAAGGGGATAGAGGTTAGG
42181377 GGTTTATGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.03
22 37 0.97
ACGTcount: A:0.25, C:0.03, G:0.47, T:0.25
Consensus pattern (22 bp):
TTAAGGGGATAGAGGTTAGGCG
Found at i:42181917 original size:76 final size:75
Alignment explanation
Indices: 42181749--42181976 Score: 350
Period size: 76 Copynumber: 3.0 Consensus size: 75
42181739 TGGCTTCCAA
* *
42181749 ATTATAACAAATAAAAATAAAAATGAAAATTAAGAGATTAGTGGCG-TTTTTAAAAAAACGCCAA
1 ATTATAACAAATAAAAATAAATATGAAAATTAAGAGATTAGTGGCGTTTTTTAAAAAAACGCCAC
42181813 AAAAAACACT
66 AAAAAACACT
* * *
42181823 ATTATAAGAAATAAAAATAAATATGAAAATTAAAAGATTAGTGGCGTTTTTTAAAAAAAACGTCA
1 ATTATAACAAATAAAAATAAATATGAAAATTAAGAGATTAGTGGCGTTTTTT-AAAAAAACGCCA
42181888 CAAAAAACACT
65 CAAAAAACACT
* ** *
42181899 ATTATAACAAATAAAAATAAATATGTAAATTAAGAGATTAGTGGTATTTTTTTAAAAAACGCCAC
1 ATTATAACAAATAAAAATAAATATGAAAATTAAGAGATTAGTGGCGTTTTTTAAAAAAACGCCAC
42181964 AAAAAAACACT
66 -AAAAAACACT
42181975 AT
1 AT
42181977 GAAAATGACG
Statistics
Matches: 139, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
74 43 0.31
75 16 0.12
76 80 0.58
ACGTcount: A:0.55, C:0.09, G:0.10, T:0.26
Consensus pattern (75 bp):
ATTATAACAAATAAAAATAAATATGAAAATTAAGAGATTAGTGGCGTTTTTTAAAAAAACGCCAC
AAAAAACACT
Found at i:42182129 original size:18 final size:18
Alignment explanation
Indices: 42182106--42182149 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
42182096 CCCAAAATAG
* *
42182106 ATTTCCCC-AATTCTCTAC
1 ATTTCCCCTAA-TCCCTAA
42182124 ATTTCCCCTAATCCCTAA
1 ATTTCCCCTAATCCCTAA
42182142 ATTTCCCC
1 ATTTCCCC
42182150 CAAAATCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.23, C:0.41, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTTCCCCTAATCCCTAA
Found at i:42185622 original size:19 final size:19
Alignment explanation
Indices: 42185600--42185640 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
42185590 TTTATTGACA
42185600 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
42185618 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
42185637 TTTT
1 TTTT
42185641 GATTCTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:42185960 original size:43 final size:43
Alignment explanation
Indices: 42185889--42185992 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 43
42185879 TTTTGAATTT
* * * *
42185889 CATGACCTTTAGTGGTGTTTTTGAGAAAAGCGCCGCTAAAGGC
1 CATGGCCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGC
* *
42185932 CATGGCCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT
1 CATGGCCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGC
*
42185975 CATGGCTTTTAGCGGCGT
1 CATGGCCTTTAGCGGCGT
42185993 CGGAAATAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.21, C:0.20, G:0.32, T:0.27
Consensus pattern (43 bp):
CATGGCCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGC
Found at i:42190566 original size:17 final size:17
Alignment explanation
Indices: 42190526--42190586 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 17
42190516 TCTTTGATGA
*
42190526 ATTGTATCGCTTGAAGG
1 ATTGTATCGCTTGGAGG
* * *
42190543 ATAGTATCGCTTGGTGC
1 ATTGTATCGCTTGGAGG
* * *
42190560 ATTGTATCACCTGGCGG
1 ATTGTATCGCTTGGAGG
42190577 ATTGTATCGC
1 ATTGTATCGC
42190587 CTAGAGGACA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (17 bp):
ATTGTATCGCTTGGAGG
Found at i:42195326 original size:23 final size:23
Alignment explanation
Indices: 42195299--42195346 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
42195289 CTAAATCGCG
42195299 TAAAATGCAAAAGTAGCATCCTA
1 TAAAATGCAAAAGTAGCATCCTA
* *
42195322 TAAAATGCAAAAGTGGCATCTTA
1 TAAAATGCAAAAGTAGCATCCTA
42195345 TA
1 TA
42195347 TGTTAAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (23 bp):
TAAAATGCAAAAGTAGCATCCTA
Found at i:42196373 original size:28 final size:28
Alignment explanation
Indices: 42196333--42196560 Score: 238
Period size: 28 Copynumber: 8.3 Consensus size: 28
42196323 CTATATACGA
*
42196333 CACTTAGTGTGTGAAACATTGAATATGG
1 CACTTAGTGTGTGAGACATTGAATATGG
* *
42196361 CACTTAGTGTGTGAGACATTGAGTATAG
1 CACTTAGTGTGTGAGACATTGAATATGG
42196389 CACTTAGTGTGTGAGACATTGAGA-ATGG
1 CACTTAGTGTGTGAGACATTGA-ATATGG
*
42196417 CACTTAGTTTGTGAGACA-T--ATA--G
1 CACTTAGTGTGTGAGACATTGAATATGG
42196440 CACTTAGTGTGTGAGACATTGAGA-ATGG
1 CACTTAGTGTGTGAGACATTGA-ATATGG
* *
42196468 CACTTAGTTTGTGAGACATTGAGTATGG
1 CACTTAGTGTGTGAGACATTGAATATGG
* * *
42196496 CACTTAGTGTGCGAGACATCGAGCT-TGG
1 CACTTAGTGTGTGAGACATTGA-ATATGG
* ** * **
42196524 CACTTATTGTGCAAGAAATTGGGTATGG
1 CACTTAGTGTGTGAGACATTGAATATGG
42196552 CACTTAGTG
1 CACTTAGTG
42196561 CGCGAAATAT
Statistics
Matches: 169, Mismatches: 20, Indels: 22
0.80 0.09 0.10
Matches are distributed among these distances:
23 18 0.11
24 2 0.01
25 1 0.01
26 1 0.01
27 3 0.02
28 143 0.85
29 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.31
Consensus pattern (28 bp):
CACTTAGTGTGTGAGACATTGAATATGG
Found at i:42196419 original size:56 final size:56
Alignment explanation
Indices: 42196333--42196560 Score: 279
Period size: 56 Copynumber: 4.2 Consensus size: 56
42196323 CTATATACGA
*
42196333 CACTTAGTGTGTGAAACATTGA-ATATGGCACTTAGTGTGTGAGACATTGAGTATAG
1 CACTTAGTGTGTGAGACATTGAGA-ATGGCACTTAGTGTGTGAGACATTGAGTATAG
*
42196389 CACTTAGTGTGTGAGACATTGAGAATGGCACTTAGTTTGTGAGAC----A-TATAG
1 CACTTAGTGTGTGAGACATTGAGAATGGCACTTAGTGTGTGAGACATTGAGTATAG
* *
42196440 CACTTAGTGTGTGAGACATTGAGAATGGCACTTAGTTTGTGAGACATTGAGTATGG
1 CACTTAGTGTGTGAGACATTGAGAATGGCACTTAGTGTGTGAGACATTGAGTATAG
* * ** * ** * * *
42196496 CACTTAGTGTGCGAGACATCGAGCTTGGCACTTATTGTGCAAGAAATTGGGTATGG
1 CACTTAGTGTGTGAGACATTGAGAATGGCACTTAGTGTGTGAGACATTGAGTATAG
42196552 CACTTAGTG
1 CACTTAGTG
42196561 CGCGAAATAT
Statistics
Matches: 153, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
51 50 0.33
52 1 0.01
55 1 0.01
56 100 0.65
57 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.31
Consensus pattern (56 bp):
CACTTAGTGTGTGAGACATTGAGAATGGCACTTAGTGTGTGAGACATTGAGTATAG
Found at i:42196471 original size:79 final size:79
Alignment explanation
Indices: 42196355--42196514 Score: 257
Period size: 79 Copynumber: 2.0 Consensus size: 79
42196345 GAAACATTGA
* *
42196355 ATATGGCACTTAGTGTGTGAGACATTGAGTATAGCACTTAGTGTGTGAGACATTGAGAATGGCAC
1 ATATAGCACTTAGTGTGTGAGACATTGAGAATAGCACTTAGTGTGTGAGACATTGAGAATGGCAC
* *
42196420 TTAGTTTGTGAGAC
66 TTAGTGTGCGAGAC
* * *
42196434 ATATAGCACTTAGTGTGTGAGACATTGAGAATGGCACTTAGTTTGTGAGACATTGAGTATGGCAC
1 ATATAGCACTTAGTGTGTGAGACATTGAGAATAGCACTTAGTGTGTGAGACATTGAGAATGGCAC
42196499 TTAGTGTGCGAGAC
66 TTAGTGTGCGAGAC
42196513 AT
1 AT
42196515 CGAGCTTGGC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.31
Consensus pattern (79 bp):
ATATAGCACTTAGTGTGTGAGACATTGAGAATAGCACTTAGTGTGTGAGACATTGAGAATGGCAC
TTAGTGTGCGAGAC
Found at i:42196525 original size:107 final size:107
Alignment explanation
Indices: 42196333--42196529 Score: 315
Period size: 107 Copynumber: 1.8 Consensus size: 107
42196323 CTATATACGA
42196333 CACTTAGTGTGTGAAACATTGAATATGGCACTTAGTGTGTGAGACATTGAGTATAGCACTTAGTG
1 CACTTAGTGTGTGAAACATTGAATATGGCACTTAGTGTGTGAGACATTGAGTATAGCACTTAGTG
* *
42196398 TGTGAGACATTGAGAATGGCACTTAGTTTGTGAGACATATAG
66 TGCGAGACATCGAGAATGGCACTTAGTTTGTGAGACATATAG
* * *
42196440 CACTTAGTGTGTGAGACATTGAGA-ATGGCACTTAGTTTGTGAGACATTGAGTATGGCACTTAGT
1 CACTTAGTGTGTGAAACATTGA-ATATGGCACTTAGTGTGTGAGACATTGAGTATAGCACTTAGT
**
42196504 GTGCGAGACATCGAGCTTGGCACTTA
65 GTGCGAGACATCGAGAATGGCACTTA
42196530 TTGTGCAAGA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
107 81 0.99
108 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (107 bp):
CACTTAGTGTGTGAAACATTGAATATGGCACTTAGTGTGTGAGACATTGAGTATAGCACTTAGTG
TGCGAGACATCGAGAATGGCACTTAGTTTGTGAGACATATAG
Found at i:42196577 original size:28 final size:28
Alignment explanation
Indices: 42196488--42196577 Score: 78
Period size: 28 Copynumber: 3.2 Consensus size: 28
42196478 GTGAGACATT
* * *
42196488 GAGTATGGCACTTAGTGTGCGAGACATC
1 GAGTATGGCACTTAGTGCGCGAAATATC
**
42196516 GAGCT-TGGCACTTATTGTGCAAGAAAT-T-
1 GAG-TATGGCACTTA--GTGCGCGAAATATC
*
42196544 GGGTATGGCACTTAGTGCGCGAAATATC
1 GAGTATGGCACTTAGTGCGCGAAATATC
42196572 GAGTAT
1 GAGTAT
42196578 TCAAAGGCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
26 9 0.19
27 2 0.04
28 28 0.60
29 2 0.04
30 6 0.13
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.28
Consensus pattern (28 bp):
GAGTATGGCACTTAGTGCGCGAAATATC
Found at i:42203692 original size:41 final size:39
Alignment explanation
Indices: 42203647--42203765 Score: 134
Period size: 41 Copynumber: 2.9 Consensus size: 39
42203637 CAATTATAAT
*
42203647 CTTGCACACTAAGTGCCTTTCATAGCCGAAGCTATCTCAG
1 CTTGCACACTAAGTGCCTTT-ATAGCTGAAGCTATCTCAG
* *
42203687 CCTTGCACACTAAGTGCCATATATAGCTGAAGCTAT-TCCG
1 -CTTGCACACTAAGTGCC-TTTATAGCTGAAGCTATCTCAG
*
42203727 ATTCGCACACTAAGTG-CTTTATAAAGCTGAAGCTATCTC
1 CTT-GCACACTAAGTGCCTTTAT--AGCTGAAGCTATCTC
42203766 GATACACACA
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
38 4 0.06
39 3 0.04
40 27 0.40
41 32 0.47
42 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (39 bp):
CTTGCACACTAAGTGCCTTTATAGCTGAAGCTATCTCAG
Found at i:42203755 original size:40 final size:40
Alignment explanation
Indices: 42203691--42203783 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 40
42203681 TCTCAGCCTT
* *
42203691 GCACACTAAGTGCCATATATAGCTGAAGCTAT-TCCGATTC
1 GCACACTAAGTGCCATATAAAGCTGAAGCTATCT-CGATAC
**
42203731 GCACACTAAGTGCTTTATAAAGCTGAAGCTATCTCGATAC
1 GCACACTAAGTGCCATATAAAGCTGAAGCTATCTCGATAC
*
42203771 ACACACTAAGTGC
1 GCACACTAAGTGC
42203784 GAAACATAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 46 0.98
41 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (40 bp):
GCACACTAAGTGCCATATAAAGCTGAAGCTATCTCGATAC
Found at i:42207196 original size:40 final size:40
Alignment explanation
Indices: 42207149--42207416 Score: 464
Period size: 40 Copynumber: 6.7 Consensus size: 40
42207139 GCAAACACAT
* * *
42207149 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
42207189 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
42207229 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
42207269 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
42207309 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
42207349 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
42207389 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
42207417 TCCAATGCTC
Statistics
Matches: 217, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 217 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:42216939 original size:40 final size:40
Alignment explanation
Indices: 42216891--42217195 Score: 551
Period size: 40 Copynumber: 7.7 Consensus size: 40
42216881 ACAAACACAT
* *
42216891 TTGCCTTCGGGTCATAACCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
42216931 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
42216971 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
42217011 TTGCCTTCGGGTC--AGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
42217049 TTGCCTTCGGGTCTTAGCCCGGATACATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
42217089 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
42217129 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
42217169 TTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
42217196 ATCCAATGTT
Statistics
Matches: 256, Mismatches: 7, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
38 37 0.14
40 219 0.86
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:42217179 original size:158 final size:159
Alignment explanation
Indices: 42216891--42217195 Score: 567
Period size: 158 Copynumber: 1.9 Consensus size: 159
42216881 ACAAACACAT
*
42216891 TTGCCTTCGGGTCATAACCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCATAACCCGGATACATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
42216956 TATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAATTGCCTTCGG
66 TATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAATTGCCTTCGG
42217021 GTC-AGCCCGGATATATCAACTCGCATAA
131 GTCTAGCCCGGATATATCAACTCGCATAA
* *
42217049 TTGCCTTCGGGTCTTAGCCCGGATACATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCATAACCCGGATACATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
42217114 TATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAATTGCCTTCGG
66 TATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAATTGCCTTCGG
42217179 GTCTTAGCCCGGATATA
131 GTC-TAGCCCGGATATA
42217196 ATCCAATGTT
Statistics
Matches: 142, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
158 130 0.92
160 12 0.08
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (159 bp):
TTGCCTTCGGGTCATAACCCGGATACATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
TATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAATTGCCTTCGG
GTCTAGCCCGGATATATCAACTCGCATAA
Found at i:42220010 original size:40 final size:40
Alignment explanation
Indices: 42219963--42220230 Score: 464
Period size: 40 Copynumber: 6.7 Consensus size: 40
42219953 GCAAACACAT
* * *
42219963 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
42220003 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
42220043 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
42220083 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
42220123 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
42220163 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
42220203 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
42220231 TCCAATGCTC
Statistics
Matches: 217, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 217 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:42227072 original size:28 final size:29
Alignment explanation
Indices: 42227041--42227097 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
42227031 TAAAGTGATT
* *
42227041 TTTGACAAAAATGTTAATT-AGGGATTAA
1 TTTGACAAAAATATAAATTGAGGGATTAA
*
42227069 TTTGAGAAAAATATAAATTGAGGGATTAA
1 TTTGACAAAAATATAAATTGAGGGATTAA
42227098 ATTGTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.46, C:0.02, G:0.19, T:0.33
Consensus pattern (29 bp):
TTTGACAAAAATATAAATTGAGGGATTAA
Found at i:42227093 original size:29 final size:28
Alignment explanation
Indices: 42227041--42227106 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
42227031 TAAAGTGATT
* * *
42227041 TTTGACAAAAATGTTAATTAGGGATTAA
1 TTTGAGAAAAATATAAATTAGGGATTAA
42227069 TTTGAGAAAAATATAAATTGAGGGATTAA
1 TTTGAGAAAAATATAAATT-AGGGATTAA
* *
42227098 ATTGTGAAA
1 TTTGAGAAA
42227107 TAAATGAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 16 0.50
29 16 0.50
ACGTcount: A:0.45, C:0.02, G:0.20, T:0.33
Consensus pattern (28 bp):
TTTGAGAAAAATATAAATTAGGGATTAA
Found at i:42228784 original size:46 final size:46
Alignment explanation
Indices: 42228731--42228867 Score: 193
Period size: 46 Copynumber: 3.0 Consensus size: 46
42228721 TATATATACA
* * * *
42228731 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
42228777 CATCTCATACACGTTTCGTATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* *
42228823 TATCTCATACACATTTCGCATTAGCCATTCGGCCTTACCACATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
42228868 ATACATGTTC
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.35
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:42228906 original size:47 final size:47
Alignment explanation
Indices: 42228841--42229082 Score: 349
Period size: 47 Copynumber: 5.1 Consensus size: 47
42228831 ACACATTTCG
* * *
42228841 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
42228888 CATTGGCCATTCGACCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
42228935 CATTGGCCATTCGGCCTTATCACGCATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C--ATATATGCATGTTCACATTCATCA
* *
42228986 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
42229033 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
42229080 CAT
1 CAT
42229083 AAAATCCTAA
Statistics
Matches: 178, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
47 132 0.74
49 2 0.01
51 44 0.25
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.32
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
Found at i:42228981 original size:98 final size:97
Alignment explanation
Indices: 42228841--42229060 Score: 338
Period size: 98 Copynumber: 2.3 Consensus size: 97
42228831 ACACATTTCG
* * *
42228841 CATTAGCCATTCGGCC-T-T-ACCACATATATACATGTTCACATTCATCACATTGGCCATTCGAC
1 CATTGGCCATTCGGCCTTATCACCATATATATACAGGTTCACATTCATCACATTGGCCATTCGAC
* * *
42228903 CTTATCTCATATATGCATGTTCACATTCATCA
66 CTTATCACACATACGCATGTTCACATTCATCA
*
42228935 CATTGGCCATTCGGCCTTATCACGCATATATATACAGGTTCACATTCATCACATTGGCCATTCGG
1 CATTGGCCATTCGGCCTTATCAC-CATATATATACAGGTTCACATTCATCACATTGGCCATTCGA
42229000 CCTTATCACACATACGCATGTTCACATTCATCA
65 CCTTATCACACATACGCATGTTCACATTCATCA
42229033 CATTGGCCATTCGGCCTTATCACACATA
1 CATTGGCCATTCGGCCTTATCAC-CATA
42229061 CGCATGTTCA
Statistics
Matches: 114, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
94 15 0.13
95 1 0.01
96 1 0.01
97 2 0.02
98 95 0.83
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.32
Consensus pattern (97 bp):
CATTGGCCATTCGGCCTTATCACCATATATATACAGGTTCACATTCATCACATTGGCCATTCGAC
CTTATCACACATACGCATGTTCACATTCATCA
Found at i:42229083 original size:23 final size:23
Alignment explanation
Indices: 42229008--42229083 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 23
42228998 GGCCTTATCA
42229008 CACATACGCATGTTCACATTCAT
1 CACATACGCATGTTCACATTCAT
** * *
42229031 CACATTGGCCA--TTCGGCCTT-AT
1 CACATACG-CATGTTC-ACATTCAT
42229053 CACACATACGCATGTTCACATTCAT
1 --CACATACGCATGTTCACATTCAT
42229078 CACATA
1 CACATA
42229084 AAATCCTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
22 5 0.13
23 17 0.45
24 11 0.29
25 5 0.13
ACGTcount: A:0.29, C:0.32, G:0.11, T:0.29
Consensus pattern (23 bp):
CACATACGCATGTTCACATTCAT
Found at i:42241262 original size:79 final size:79
Alignment explanation
Indices: 42241128--42241278 Score: 248
Period size: 79 Copynumber: 1.9 Consensus size: 79
42241118 ACTCGAAAGG
* *
42241128 TACCCCAGGGGACACACGGTCGAGTAACTTAATCGTGTGTTGCACAAGGATGAGACACACGCCCG
1 TACCCCAGGGGACACACGGTCGAGTAACTTAATCATGTGTTGCACAAGGACGAGACACACGCCCG
42241193 TGCCTCTGCTTGTT
66 TGCCTCTGCTTGTT
* * *
42241207 TACCCCAGGGGACACACGGTCGTGTAACTTAATCATGTGTTGCACACGGACGAGACATACGCCCG
1 TACCCCAGGGGACACACGGTCGAGTAACTTAATCATGTGTTGCACAAGGACGAGACACACGCCCG
*
42241272 TGTCTCT
66 TGCCTCT
42241279 ACTCGTTTGG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 66 1.00
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (79 bp):
TACCCCAGGGGACACACGGTCGAGTAACTTAATCATGTGTTGCACAAGGACGAGACACACGCCCG
TGCCTCTGCTTGTT
Found at i:42242260 original size:40 final size:40
Alignment explanation
Indices: 42242163--42242293 Score: 151
Period size: 40 Copynumber: 3.3 Consensus size: 40
42242153 ATAATCTCGT
* *
42242163 ACACTAAGTGCCTTT-CATAGTCGAAGCTATCTCAATCTCGC
1 ACACTAAGTG-CTTTATATAGCCGAAGCTATCTCAAT-TCGC
* *
42242204 ACACTAAGTGC-CTATATAGCCCAAGCTAT-TCCAATTCGC
1 ACACTAAGTGCTTTATATAGCCGAAGCTATCT-CAATTCGC
* * *
42242243 ACACTAAGTGCTTTATATGGCCGAAGCTATCTCGATACGC
1 ACACTAAGTGCTTTATATAGCCGAAGCTATCTCAATTCGC
42242283 ACACTAAGTGC
1 ACACTAAGTGC
42242294 CAAACATAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
39 17 0.22
40 49 0.64
41 11 0.14
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (40 bp):
ACACTAAGTGCTTTATATAGCCGAAGCTATCTCAATTCGC
Found at i:42243987 original size:26 final size:27
Alignment explanation
Indices: 42243958--42244017 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
42243948 CCACATATAT
*
42243958 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
42243984 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
42244011 ATATCTG
1 ATATCTG
42244018 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:42247495 original size:28 final size:28
Alignment explanation
Indices: 42247450--42247642 Score: 242
Period size: 28 Copynumber: 6.9 Consensus size: 28
42247440 TATATACGGG
* * **
42247450 ACTTAGTGTGCGAAACATTGAATATGAA
1 ACTTAGTGTGCGAGACATTGAGTATGGC
**
42247478 ACTTAGTGTATGAGACATTGAGTATGGC
1 ACTTAGTGTGCGAGACATTGAGTATGGC
* *
42247506 ACTTAGTGTGTGAGAAATTGAGTATGGC
1 ACTTAGTGTGCGAGACATTGAGTATGGC
* *
42247534 ACTTAGTGTGCGAGACATTGAGCATGAC
1 ACTTAGTGTGCGAGACATTGAGTATGGC
* *
42247562 ATTTAGTGTGCGAAACATTGAGTATGGC
1 ACTTAGTGTGCGAGACATTGAGTATGGC
* *
42247590 ACTTAGTGTGCGAGACATTGGGTATAGC
1 ACTTAGTGTGCGAGACATTGAGTATGGC
* *
42247618 ACTTAGTGTGCGAAATATTGAGTAT
1 ACTTAGTGTGCGAGACATTGAGTAT
42247643 TCAAAGGCAT
Statistics
Matches: 142, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 142 1.00
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.31
Consensus pattern (28 bp):
ACTTAGTGTGCGAGACATTGAGTATGGC
Found at i:42255068 original size:40 final size:40
Alignment explanation
Indices: 42255011--42255234 Score: 252
Period size: 40 Copynumber: 5.5 Consensus size: 40
42255001 TATTCGGATG
* *
42255011 ATATCCGGGATAAGTCCCCAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
42255051 ACATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * * *
42255094 ATACCCGGGCTAAGTCTCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * *
42255134 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * *
42255174 ATATCCAGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
42255214 ATATTC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
42255235 ATACTTGGGT
Statistics
Matches: 157, Mismatches: 24, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
39 13 0.08
40 108 0.69
41 1 0.01
43 35 0.22
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:42255154 original size:83 final size:80
Alignment explanation
Indices: 42255015--42255234 Score: 248
Period size: 83 Copynumber: 2.7 Consensus size: 80
42255005 CGGATGATAT
* * * * **
42255015 CCGGGATAAGTCCCCAAGGCATTTGTGCAAGTTACTACATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
42255080 TGCGAGTAGTTG-CTATAC
66 TGC---TAG-TGACTATAC
* *
42255098 CCGGGCTAAGTCTCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
*
42255163 TGCTAGTGACTATAT
66 TGCTAGTGACTATAC
* * * * *
42255178 CCAGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATTC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCCCGAAG
42255235 ATACTTGGGT
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
79 16 0.13
80 42 0.35
81 2 0.02
83 60 0.50
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
TGCTAGTGACTATAC
Found at i:42258189 original size:41 final size:40
Alignment explanation
Indices: 42258144--42258277 Score: 132
Period size: 40 Copynumber: 3.3 Consensus size: 40
42258134 TTATAATCTC
* *
42258144 GCACACTAAATGCCTTTCATAGCCGAAGCTATCTCAG-TCTT
1 GCACACTAAGTGCCTTT-ATAGCTGAAGCTATCTCAGAT-TT
* *
42258185 GCACACTAAGTGCCATATATAGCTGAAGCTAT-TCCGATTT
1 GCACACTAAGTGCC-TTTATAGCTGAAGCTATCTCAGATTT
**
42258225 GCACACTAAGTG-CTTTATAAAGCTGAAGCTATCTC-GATAC
1 GCACACTAAGTGCCTTTAT--AGCTGAAGCTATCTCAGATTT
*
42258265 ACACACTAAGTGC
1 GCACACTAAGTGC
42258278 GAAACATAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
38 4 0.05
39 1 0.01
40 43 0.54
41 29 0.37
42 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (40 bp):
GCACACTAAGTGCCTTTATAGCTGAAGCTATCTCAGATTT
Found at i:42264804 original size:28 final size:29
Alignment explanation
Indices: 42264773--42264829 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
42264763 TAATGTGATT
*
42264773 TTTGACAAAAATGTTAATT-AGGGATTAA
1 TTTGACAAAAATGTAAATTGAGGGATTAA
*
42264801 TTTGAGAAAAATGTAAATTGAGGGATTAA
1 TTTGACAAAAATGTAAATTGAGGGATTAA
42264830 ATTGTGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (29 bp):
TTTGACAAAAATGTAAATTGAGGGATTAA
Found at i:42264825 original size:29 final size:28
Alignment explanation
Indices: 42264773--42264838 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
42264763 TAATGTGATT
* *
42264773 TTTGACAAAAATGTTAATTAGGGATTAA
1 TTTGAGAAAAATGTAAATTAGGGATTAA
42264801 TTTGAGAAAAATGTAAATTGAGGGATTAA
1 TTTGAGAAAAATGTAAATT-AGGGATTAA
* *
42264830 ATTGTGAAA
1 TTTGAGAAA
42264839 TAACTAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (28 bp):
TTTGAGAAAAATGTAAATTAGGGATTAA
Found at i:42264846 original size:29 final size:28
Alignment explanation
Indices: 42264774--42264846 Score: 67
Period size: 29 Copynumber: 2.6 Consensus size: 28
42264764 AATGTGATTT
* * * *
42264774 TTGACAAAAATGTTAATTAGGGATTAAT
1 TTGAGAAAAATCTAAATTAGGGATTAAA
*
42264802 TTGAGAAAAATGTAAATTGAGGGATTAAA
1 TTGAGAAAAATCTAAATT-AGGGATTAAA
*
42264831 TTGTGAAATAA-CTAAA
1 TTGAGAAA-AATCTAAA
42264847 AGTTTTGGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
28 16 0.42
29 20 0.53
30 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.19, T:0.32
Consensus pattern (28 bp):
TTGAGAAAAATCTAAATTAGGGATTAAA
Found at i:42266928 original size:40 final size:40
Alignment explanation
Indices: 42266874--42266999 Score: 198
Period size: 40 Copynumber: 3.1 Consensus size: 40
42266864 CCCGGATGTC
*
42266874 ATTCCAGCATGAAGCCTGCGGGTCTTTAAGCCAGGATACA
1 ATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCAGGATACA
* *
42266914 ATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCTGGATATA
1 ATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCAGGATACA
* * *
42266954 ATTCCAGCACGAAGCCTGTGGGTTTTTAAGCCCGGATACA
1 ATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCAGGATACA
42266994 ATTCCA
1 ATTCCA
42267000 CATCAAATAA
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (40 bp):
ATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCAGGATACA
Found at i:42266968 original size:80 final size:79
Alignment explanation
Indices: 42266847--42266999 Score: 216
Period size: 80 Copynumber: 1.9 Consensus size: 79
42266837 TATCTAGCAC
* * * *
42266847 AGCCTGCAGGTTTTTAACCCGGATGTCATTCCAGCATGAAGCCTGCGGGTCTTTAAGCCAGGATA
1 AGCCTGCAGGTCTTTAACCCGGATATAATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCAGGATA
42266912 CAATTCCAGCACGA
66 CAATTCCAGCACGA
* * * * *
42266926 AGCCTGCGGGTCTTTAAGCCTGGATATAATTCCAGCACGAAGCCTGTGGGTTTTTAAGCCCGGAT
1 AGCCTGCAGGTCTTTAA-CCCGGATATAATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCAGGAT
42266991 ACAATTCCA
65 ACAATTCCA
42267000 CATCAAATAA
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
79 15 0.23
80 49 0.77
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (79 bp):
AGCCTGCAGGTCTTTAACCCGGATATAATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCAGGATA
CAATTCCAGCACGA
Found at i:42271761 original size:79 final size:80
Alignment explanation
Indices: 42271625--42271848 Score: 280
Period size: 79 Copynumber: 2.8 Consensus size: 80
42271615 TCGAATGATG
* * * * *
42271625 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCAT
*
42271688 TTGTGC-AGATACTAAT
64 TTGTGCGAGATACTAAA
*
42271704 TCCGGGCTAAG-CCCGAAGGCATTTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTT-GTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATT
*
42271768 TGTGCGAGTTACTAAA
65 TGTGCGAGATACTAAA
* *
42271784 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CC-GGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
42271847 TG
65 TG
42271849 AACGAGTAGC
Statistics
Matches: 128, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
78 10 0.08
79 66 0.52
80 37 0.29
81 15 0.12
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:42271773 original size:40 final size:40
Alignment explanation
Indices: 42271625--42271848 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
42271615 TCGAATGATG
* * * *
42271625 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
42271665 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-AGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
42271704 TCCGGGCTAAG-CCCGAAGGCATTTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTT-GTGCGAGTTACTAAA
*
42271744 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42271784 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
42271825 -CC-GGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42271849 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 12, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
38 12 0.07
39 39 0.24
40 91 0.55
41 23 0.14
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42271855 original size:119 final size:119
Alignment explanation
Indices: 42271625--42271881 Score: 276
Period size: 119 Copynumber: 2.2 Consensus size: 119
42271615 TCGAATGATG
* *
42271625 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* **
42271690 GTGCAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGGTGCGAGTTA-CTAAA
66 GTGCAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGGAACGAG-TAGCTAAA
* * * **
42271744 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * *
42271807 TTGTGCGAGTTACT-ATAACC-GGCTATGTCCCGAAGGCATTT-GAACGAGTAGCTATA
64 TTGTGC-AGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGGAACGAGTAGCTAAA
* *
42271863 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
42271882 TACGTGATTT
Statistics
Matches: 117, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
118 17 0.15
119 72 0.62
120 28 0.24
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGGAACGAGTAGCTAAA
Found at i:42300335 original size:79 final size:79
Alignment explanation
Indices: 42300203--42300361 Score: 264
Period size: 79 Copynumber: 2.0 Consensus size: 79
42300193 ACTCGAAAGG
* * ** *
42300203 TACCCCAGGGGACGCACGGTCGAGTAACTTAATCGTGTGTTGCACACGGATGAGACACACGCCCG
1 TACCCCAGAGGACACACGGTCGAGTAACTTAATCACGTGTTGCACACGAATGAGACACACGCCCG
42300268 TGTCTCTGCTCGTT
66 TGTCTCTGCTCGTT
*
42300282 TACCCCAGAGGACACACGGTCGTGTAACTTAATCACGTGTTGCACACGAATGAGACACACGCCCG
1 TACCCCAGAGGACACACGGTCGAGTAACTTAATCACGTGTTGCACACGAATGAGACACACGCCCG
42300347 TGTCTCTGCTCGTT
66 TGTCTCTGCTCGTT
42300361 T
1 T
42300362 GGACAAAAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.22, C:0.30, G:0.25, T:0.23
Consensus pattern (79 bp):
TACCCCAGAGGACACACGGTCGAGTAACTTAATCACGTGTTGCACACGAATGAGACACACGCCCG
TGTCTCTGCTCGTT
Found at i:42301263 original size:41 final size:41
Alignment explanation
Indices: 42301211--42301368 Score: 130
Period size: 40 Copynumber: 3.9 Consensus size: 41
42301201 AGTGACAAAG
* * * *
42301211 CATAGCTGAAGCAAT-TATAATCTCGTACACTAAGTGCCTTT
1 CATAGCCGAAGCAATCT-CAATCTCGCACACTAAGTGCCTAT
*
42301252 CATAGCCGAAGCTATCTCAATCTCGCACACTAAGTGCCTAT
1 CATAGCCGAAGCAATCTCAATCTCGCACACTAAGTGCCTAT
* * * *
42301293 -ATAGCCCAAGCTAT-TCCAAT-TCACACACTAAGTGCTTTAT
1 CATAGCCGAAGCAATCT-CAATCTCGCACACTAAGTGC-CTAT
* * * *
42301333 -ATGGCCGAAGCTATCTCGAT-ACGCACACTAAGTGCC
1 CATAGCCGAAGCAATCTCAATCTCGCACACTAAGTGCC
42301369 AAACATAATC
Statistics
Matches: 99, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
39 15 0.15
40 48 0.48
41 35 0.35
42 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (41 bp):
CATAGCCGAAGCAATCTCAATCTCGCACACTAAGTGCCTAT
Found at i:42301334 original size:40 final size:42
Alignment explanation
Indices: 42301237--42301367 Score: 132
Period size: 40 Copynumber: 3.3 Consensus size: 42
42301227 ATAATCTCGT
* *
42301237 ACACTAAGTGCCTTT-CATAGCCGAAGCTA-TCTCAATCTCGC
1 ACACTAAGTG-CTTTATATAGCCGAAGCTATTCTCAATCTCAC
* *
42301278 ACACTAAGTGC-CTATATAGCCCAAGCTATTC-CAAT-TCAC
1 ACACTAAGTGCTTTATATAGCCGAAGCTATTCTCAATCTCAC
* * * *
42301317 ACACTAAGTGCTTTATATGGCCGAAGCTA-TCTCGAT-ACGC
1 ACACTAAGTGCTTTATATAGCCGAAGCTATTCTCAATCTCAC
42301357 ACACTAAGTGC
1 ACACTAAGTGC
42301368 CAAACATAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
39 17 0.22
40 47 0.62
41 12 0.16
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (42 bp):
ACACTAAGTGCTTTATATAGCCGAAGCTATTCTCAATCTCAC
Found at i:42303049 original size:26 final size:27
Alignment explanation
Indices: 42303020--42303079 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
42303010 CCACATATAT
*
42303020 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
42303046 ATATCTGTATCTGGTGACTTTGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
42303073 ATATCTG
1 ATATCTG
42303080 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:42306564 original size:28 final size:28
Alignment explanation
Indices: 42306519--42306708 Score: 218
Period size: 28 Copynumber: 6.8 Consensus size: 28
42306509 TATATACGGG
* * *
42306519 ACTTAGTGTGCGAAACATTGAATATGAC
1 ACTTAGTGTGCGAGACATTGAGTATGGC
**
42306547 ACTTAGTGTATGAGACATTGAGTATGGC
1 ACTTAGTGTGCGAGACATTGAGTATGGC
*
42306575 ACTTAGTGTGCGAGAAATTGAGTATGGC
1 ACTTAGTGTGCGAGACATTGAGTATGGC
* * * * *
42306603 ACTTAGTCTGCGAGGCATCGAGCATGAC
1 ACTTAGTGTGCGAGACATTGAGTATGGC
* * *
42306631 ATTTAATGTGCGAAACATTGAGTATGGC
1 ACTTAGTGTGCGAGACATTGAGTATGGC
* *
42306659 ACTTAGTGTGCGAGACATTGGGTATAGC
1 ACTTAGTGTGCGAGACATTGAGTATGGC
* *
42306687 ACTTAGTGTGCGAAATATTGAG
1 ACTTAGTGTGCGAGACATTGAG
42306709 CATTCAAAGG
Statistics
Matches: 132, Mismatches: 30, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 132 1.00
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (28 bp):
ACTTAGTGTGCGAGACATTGAGTATGGC
Found at i:42306710 original size:84 final size:84
Alignment explanation
Indices: 42306519--42306711 Score: 251
Period size: 84 Copynumber: 2.3 Consensus size: 84
42306509 TATATACGGG
** * * *
42306519 ACTTAGTGTGCGAAACATTGAATATGACACTTAGTGTATGAGACATTGAGTATGGCACTTAGTGT
1 ACTTAGTGTGCGAAACATTGAGCATGACACTTAATGTACGAAACATTGAGTATGGCACTTAGTGT
*
42306584 GCGAGAAATTGAGTATGGC
66 GCGAGAAATTGAGTATAGC
* ** * * *
42306603 ACTTAGTCTGCGAGGCATCGAGCATGACATTTAATGTGCGAAACATTGAGTATGGCACTTAGTGT
1 ACTTAGTGTGCGAAACATTGAGCATGACACTTAATGTACGAAACATTGAGTATGGCACTTAGTGT
* *
42306668 GCGAGACATTGGGTATAGC
66 GCGAGAAATTGAGTATAGC
*
42306687 ACTTAGTGTGCGAAATATTGAGCAT
1 ACTTAGTGTGCGAAACATTGAGCAT
42306712 TCAAAGGCAT
Statistics
Matches: 90, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (84 bp):
ACTTAGTGTGCGAAACATTGAGCATGACACTTAATGTACGAAACATTGAGTATGGCACTTAGTGT
GCGAGAAATTGAGTATAGC
Found at i:42309963 original size:27 final size:27
Alignment explanation
Indices: 42309933--42310110 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42309923 ATATTGAGTC
* * * *
42309933 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
42309960 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42309987 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
42310015 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
42310042 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
42310069 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42310096 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42310111 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:42310046 original size:82 final size:81
Alignment explanation
Indices: 42309954--42310109 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42309944 TGCTATATAA
* *
42309954 TCAACTCGCACACTTAGTGC-TACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGC
1 TCAACTCGCACACTTAGTGCAT-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGC
42310018 ACACTTAGTGCCGCATGG
64 ACACTTAGTGCCGCATGG
* * **
42310036 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
1 TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
42310101 ACTTAGTGC
66 ACTTAGTGC
42310110 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:42315843 original size:27 final size:27
Alignment explanation
Indices: 42315813--42315988 Score: 194
Period size: 27 Copynumber: 6.6 Consensus size: 27
42315803 ATATTGAGTC
* * *
42315813 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
*
42315840 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
* *
42315867 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
** ** *
42315894 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
**
42315921 CGCACACTTAGTGC-ATCAT-ATCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* *
42315947 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
42315974 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42315989 GTACAATTTA
Statistics
Matches: 128, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
26 22 0.17
27 106 0.83
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:42315895 original size:54 final size:53
Alignment explanation
Indices: 42315813--42315988 Score: 219
Period size: 54 Copynumber: 3.3 Consensus size: 53
42315803 ATATTGAGTC
* * * * *
42315813 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACAT-ATCAACTCGCACACTTAGTGCAACATAGTCAAAT
** * *
42315867 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATA-TCAACTCGCACACTTAGTGCAACATAGTCAAAT
**
42315921 CGCACACTTAGTGC-ATCATATCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATATCAACTCGCACACTTAGTGCAACATAGTCAAAT
42315974 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42315989 GTACAATTTA
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
53 43 0.41
54 62 0.59
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (53 bp):
CGCACACTTAGTGCTACATATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:42315977 original size:80 final size:81
Alignment explanation
Indices: 42315834--42315987 Score: 231
Period size: 80 Copynumber: 1.9 Consensus size: 81
42315824 TGCTATATAA
* * *
42315834 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAACTCGCAC
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
42315899 ACTTAGTGCCGCATGG
66 ACTTAGTGCCGCATGG
* **
42315915 TCAATTCGCACACTTAGTGC-ATCAT-ATCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42315978 CACTTAGTGC
65 CACTTAGTGC
42315988 TGTACAATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
80 45 0.68
81 21 0.32
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Done.