Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 131 of 325
Found at i:40892523 original size:43 final size:43
Alignment explanation
Indices: 40892475--40892813 Score: 342
Period size: 43 Copynumber: 7.9 Consensus size: 43
40892465 ATCGAGATGT
40892475 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
* * * * *
40892518 GATTACATGTAAGACCATGTCTAGGACATTGGAAATGTGTGGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
**
40892561 GATTATGTGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
* * *
40892604 GATTACATGTAAGACCATGTCTGGGACATTGGCAATGTGTGGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
** * * *
40892647 GATTATGTGTAAGACCATGTCTGGGACATTGGCAATGTGTGGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
** * * * *
40892690 GATTATGTGTAAGACCATGTCTGGGACATTAGCATCGTTAAT-C
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTG-TATTGA
* * * * * ** *
40892733 GATTTCGTATAAGACCCTGTCTGGGACAGTGGCA-TCAATATGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT-TGA
* * * *
40892776 GATAACATGTAAGACCATATTTGGGATA-TGGCATTGTA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTA
40892814 CGAGCTTTGT
Statistics
Matches: 245, Mismatches: 47, Indels: 8
0.82 0.16 0.03
Matches are distributed among these distances:
41 1 0.00
42 6 0.02
43 237 0.97
44 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
Found at i:40892620 original size:86 final size:86
Alignment explanation
Indices: 40892482--40892719 Score: 413
Period size: 86 Copynumber: 2.8 Consensus size: 86
40892472 TGTGATTACA
*
40892482 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTAGGACAT
1 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTGGGACAT
40892547 TGGAAATGTGTGGAGATTATG
66 TGGAAATGTGTGGAGATTATG
40892568 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTGGGACAT
1 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTGGGACAT
*
40892633 TGGCAATGTGTGGAGATTATG
66 TGGAAATGTGTGGAGATTATG
* * * **
40892654 TGTAAGACCATGTCTGGGACATTGGCAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACAT
1 TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTGGGACAT
40892719 T
66 T
40892720 AGCATCGTTA
Statistics
Matches: 145, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 145 1.00
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (86 bp):
TGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCTGGGACAT
TGGAAATGTGTGGAGATTATG
Found at i:40892705 original size:129 final size:129
Alignment explanation
Indices: 40892475--40892724 Score: 428
Period size: 129 Copynumber: 1.9 Consensus size: 129
40892465 ATCGAGATGT
* *
40892475 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCAATGTATGGAGATTACATGTAAGACCATGTCT
*
40892540 AGGACATTGGAAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
66 AGGACATTGGAAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACATTAGCATTGTATTGA
* **
40892604 GATTACATGTAAGACCATGTCTGGGACATTGGCAATGTGTGGAGATTATGTGTAAGACCATGTCT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCAATGTATGGAGATTACATGTAAGACCATGTCT
* *
40892669 GGGACATTGGCAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACATTAGCAT
66 AGGACATTGGAAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACATTAGCAT
40892725 CGTTAATCGA
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 113 1.00
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (129 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCAATGTATGGAGATTACATGTAAGACCATGTCT
AGGACATTGGAAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACATTAGCATTGTATTGA
Found at i:40892746 original size:129 final size:129
Alignment explanation
Indices: 40892475--40892766 Score: 415
Period size: 129 Copynumber: 2.3 Consensus size: 129
40892465 ATCGAGATGT
* * *
40892475 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACATGTAAGACCATGTCT
1 GATTACATATAAGACCATGTCTGGGACATTGGCAATGTATGGAGATTACATGTAAGACCATGTCT
* * *
40892540 AGGACATTGGAAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
66 AGGACATTGGAAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACATTAGCATCGTAATGA
* * **
40892604 GATTACATGTAAGACCATGTCTGGGACATTGGCAATGTGTGGAGATTATGTGTAAGACCATGTCT
1 GATTACATATAAGACCATGTCTGGGACATTGGCAATGTATGGAGATTACATGTAAGACCATGTCT
* * *
40892669 GGGACATTGGCAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACATTAGCATCGTTAAT-C
66 AGGACATTGGAAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACATTAGCATCG-TAATGA
* * * *
40892733 GATTTCGTATAAGACCCTGTCTGGGACAGTGGCA
1 GATTACATATAAGACCATGTCTGGGACATTGGCA
40892767 TCAATATGTG
Statistics
Matches: 146, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
129 143 0.98
130 3 0.02
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.30
Consensus pattern (129 bp):
GATTACATATAAGACCATGTCTGGGACATTGGCAATGTATGGAGATTACATGTAAGACCATGTCT
AGGACATTGGAAATGTGTGGAGATTATGTGTAAGACCATGTCTGGGACATTAGCATCGTAATGA
Found at i:40898766 original size:50 final size:50
Alignment explanation
Indices: 40898691--40898787 Score: 185
Period size: 50 Copynumber: 1.9 Consensus size: 50
40898681 AATTGATCCT
40898691 ATACCATTATTCAGAAGAATTATTGTACAACAGTCTCCAACATAAACCAA
1 ATACCATTATTCAGAAGAATTATTGTACAACAGTCTCCAACATAAACCAA
*
40898741 ATACCATTATTCAGAAGAATTATTGTACAACAGTCTCCAATATAAAC
1 ATACCATTATTCAGAAGAATTATTGTACAACAGTCTCCAACATAAAC
40898788 TCATTTGGTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (50 bp):
ATACCATTATTCAGAAGAATTATTGTACAACAGTCTCCAACATAAACCAA
Found at i:40899010 original size:51 final size:51
Alignment explanation
Indices: 40898951--40899052 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
40898941 ACCTGTTTTT
40898951 CACATACAAGGGCTCCAAACAACTTTAGCAAGAAATCTTAGAATTATTAGC
1 CACATACAAGGGCTCCAAACAACTTTAGCAAGAAATCTTAGAATTATTAGC
40899002 CACATACAAGGGCTCCAAACAACTTTAGCAAGAAATCTTAGAATTATTAGC
1 CACATACAAGGGCTCCAAACAACTTTAGCAAGAAATCTTAGAATTATTAGC
40899053 AGGAGGATTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24
Consensus pattern (51 bp):
CACATACAAGGGCTCCAAACAACTTTAGCAAGAAATCTTAGAATTATTAGC
Found at i:40906199 original size:27 final size:27
Alignment explanation
Indices: 40906150--40906222 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
40906140 TTGGCTATGG
* * * *
40906150 AAACATAAGG-AGTCCATCAGGACAGT
1 AAACATAGGGTAGCCCACCAGGACAAT
40906176 AAACAT-GGGATAGCCCACCAGGACAAT
1 AAACATAGGG-TAGCCCACCAGGACAAT
*
40906203 AAACATAGGGTAGTCCACCA
1 AAACATAGGGTAGCCCACCA
40906223 AGACGGTAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 2 0.05
26 6 0.15
27 28 0.72
28 3 0.08
ACGTcount: A:0.41, C:0.23, G:0.22, T:0.14
Consensus pattern (27 bp):
AAACATAGGGTAGCCCACCAGGACAAT
Found at i:40919341 original size:39 final size:39
Alignment explanation
Indices: 40919286--40919424 Score: 224
Period size: 39 Copynumber: 3.6 Consensus size: 39
40919276 GAATTTAAGC
* * *
40919286 CCGGATATAATTCCAGCTCATAGCCTGCTGATCTGAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
*
40919325 CCGGATATAATCCCAGCACATAGCCTGCGGACCTGAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
*
40919364 CTGGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
*
40919403 CTGGATATAATTCCAGCACATA
1 CCGGATATAATTCCAGCACATA
40919425 CAATTATGAT
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 94 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCTGAAGT
Found at i:40927576 original size:39 final size:39
Alignment explanation
Indices: 40927518--40927653 Score: 209
Period size: 39 Copynumber: 3.5 Consensus size: 39
40927508 TTTAAGCCCG
* * **
40927518 GATATAATTCCAGCTCATAGCCTGCGGATCTGAAGTCTT
1 GATATAATTCCAGCACATAGCCTGCGGACCTGAAGTCCA
*
40927557 GATATAATTCCAGCACATAGCCTGCAGACCTGAAGTCCA
1 GATATAATTCCAGCACATAGCCTGCGGACCTGAAGTCCA
*
40927596 GATATAATTCCAGCACATAGCCTGCGGACCTGAAGTCCG
1 GATATAATTCCAGCACATAGCCTGCGGACCTGAAGTCCA
*
40927635 GATATAATTCCAACACATA
1 GATATAATTCCAGCACATA
40927654 CAATTATGAT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (39 bp):
GATATAATTCCAGCACATAGCCTGCGGACCTGAAGTCCA
Found at i:40931097 original size:30 final size:30
Alignment explanation
Indices: 40931061--40931123 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
40931051 ACTTATATTA
40931061 TTGTTAATTCTGTTATTATTTTAAAGGCAT
1 TTGTTAATTCTGTTATTATTTTAAAGGCAT
* * **
40931091 TTGTTAATTTTTTTATTATTTTAGCGGCAT
1 TTGTTAATTCTGTTATTATTTTAAAGGCAT
40931121 TTG
1 TTG
40931124 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.06, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTCTGTTATTATTTTAAAGGCAT
Found at i:40957486 original size:27 final size:27
Alignment explanation
Indices: 40957456--40957725 Score: 258
Period size: 27 Copynumber: 10.1 Consensus size: 27
40957446 CACCAAGAAT
* * *
40957456 GCATTCCTTTCACAGTAAGCCATAAAG
1 GCATTCCTTTCAGAGTATGCCACAAAG
** * *
40957483 GCATTTATTTTAGAGTACGCCAC-AA-
1 GCATTCCTTTCAGAGTATGCCACAAAG
* *
40957508 GCATTTCTTTTAGAGTATGCCACAAAG
1 GCATTCCTTTCAGAGTATGCCACAAAG
* * *
40957535 GCATTACTTTTAGAGTACGCCACAAAG
1 GCATTCCTTTCAGAGTATGCCACAAAG
*
40957562 GCATTCCTTTCAGTGTATGCCACAAAG
1 GCATTCCTTTCAGAGTATGCCACAAAG
* * * * **
40957589 GCATTCTTTTCAGAATATGCAATAATT
1 GCATTCCTTTCAGAGTATGCCACAAAG
*
40957616 GCATTCCTTTCAGAGTATGCTACAAAG
1 GCATTCCTTTCAGAGTATGCCACAAAG
* * * *
40957643 GAATTCCTTTCACAGTATGCTAAAAAG
1 GCATTCCTTTCAGAGTATGCCACAAAG
* *
40957670 GCACTT-CTTTTAGAGTACGCCACAAAG
1 GCA-TTCCTTTCAGAGTATGCCACAAAG
* *
40957697 GCATTTCTTTCATAGTATGCCACAAAG
1 GCATTCCTTTCAGAGTATGCCACAAAG
40957724 GC
1 GC
40957726 TAACACGATG
Statistics
Matches: 200, Mismatches: 39, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
25 21 0.10
26 6 0.03
27 171 0.86
28 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (27 bp):
GCATTCCTTTCAGAGTATGCCACAAAG
Found at i:40957631 original size:81 final size:81
Alignment explanation
Indices: 40957456--40957725 Score: 285
Period size: 81 Copynumber: 3.4 Consensus size: 81
40957446 CACCAAGAAT
* * * ** * * *
40957456 GCATTCCTTTCACAGTAAGCCATAAAGGCATTTATTTTAGAGTACGCCAC-AA-GCATTTCTTTT
1 GCATTCCTTTCAGAGTATGCCACAAAGGCATTCCTTTCAGAGTATGCCACAAAGGCACTTCTTTT
40957519 AGAGTATGCCACAAAG
66 AGAGTATGCCACAAAG
* * * *
40957535 GCATTACTTTTAGAGTACGCCACAAAGGCATTCCTTTCAGTGTATGCCACAAAGGCA-TTCTTTT
1 GCATTCCTTTCAGAGTATGCCACAAAGGCATTCCTTTCAGAGTATGCCACAAAGGCACTTCTTTT
* * * **
40957599 CAGAATATGCAATAATT
66 -AGAGTATGCCACAAAG
* * * * *
40957616 GCATTCCTTTCAGAGTATGCTACAAAGGAATTCCTTTCACAGTATGCTAAAAAGGCACTTCTTTT
1 GCATTCCTTTCAGAGTATGCCACAAAGGCATTCCTTTCAGAGTATGCCACAAAGGCACTTCTTTT
*
40957681 AGAGTACGCCACAAAG
66 AGAGTATGCCACAAAG
* *
40957697 GCATTTCTTTCATAGTATGCCACAAAGGC
1 GCATTCCTTTCAGAGTATGCCACAAAGGC
40957726 TAACACGATG
Statistics
Matches: 153, Mismatches: 34, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
79 40 0.26
80 9 0.06
81 97 0.63
82 7 0.05
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (81 bp):
GCATTCCTTTCAGAGTATGCCACAAAGGCATTCCTTTCAGAGTATGCCACAAAGGCACTTCTTTT
AGAGTATGCCACAAAG
Found at i:40964918 original size:21 final size:21
Alignment explanation
Indices: 40964888--40964938 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
40964878 TGTAAAAAGG
40964888 AATGCATAAGTATTATGACAT
1 AATGCATAAGTATTATGACAT
*
40964909 AATGCGTAAGTATTATGACAT
1 AATGCATAAGTATTATGACAT
*
40964930 GATGCATAA
1 AATGCATAA
40964939 TTAGTTTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (21 bp):
AATGCATAAGTATTATGACAT
Found at i:40972099 original size:25 final size:25
Alignment explanation
Indices: 40972071--40972122 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
40972061 TAAGTTATAT
40972071 GTTTTTATATTATAAGAATGAACAG
1 GTTTTTATATTATAAGAATGAACAG
40972096 GTTTTTATATTATAAGAATGAACAG
1 GTTTTTATATTATAAGAATGAACAG
40972121 GT
1 GT
40972123 ATTAGTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.40
Consensus pattern (25 bp):
GTTTTTATATTATAAGAATGAACAG
Found at i:40972131 original size:25 final size:25
Alignment explanation
Indices: 40972075--40972131 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
40972065 TTATATGTTT
*
40972075 TTATATTATAAGAATGAACAGGTTT
1 TTATATTATAAGAATGAACAGGTTA
40972100 TTATATTATAAGAATGAACAGG-TA
1 TTATATTATAAGAATGAACAGGTTA
40972124 TTAGTATT
1 TTA-TATT
40972132 TGGGATAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (25 bp):
TTATATTATAAGAATGAACAGGTTA
Found at i:40972354 original size:16 final size:16
Alignment explanation
Indices: 40972333--40972371 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
40972323 ATATATTTTT
*
40972333 TTATAAATGCTATATA
1 TTATAAATGATATATA
*
40972349 TTATAAATTATATATA
1 TTATAAATGATATATA
40972365 TTATAAA
1 TTATAAA
40972372 ATTATTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (16 bp):
TTATAAATGATATATA
Found at i:40978296 original size:35 final size:35
Alignment explanation
Indices: 40978250--40978328 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
40978240 GTTTCAGAAT
*
40978250 ACATAC-AAGATCGACACCGGAGACTCGGTGTACC
1 ACATACTAAGATCGACACCGAAGACTCGGTGTACC
* *
40978284 ACATACTAAGATCGGCGCCGAAGACTCGGTGTACC
1 ACATACTAAGATCGACACCGAAGACTCGGTGTACC
40978319 ACATACTAAG
1 ACATACTAAG
40978329 TTAAATCATT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 6 0.15
35 35 0.85
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (35 bp):
ACATACTAAGATCGACACCGAAGACTCGGTGTACC
Found at i:40979075 original size:35 final size:35
Alignment explanation
Indices: 40979009--40979075 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
40978999 GTAGCAGTTT
* * * *
40979009 GGGCCTTAGCCTAGTTCAGTATCAGTTATGCACTA
1 GGGCCTTAGCCCAGTTCAATAACAGTCATGCACTA
40979044 GGGCCTTAGCCCA-TTACAATAACAGTCATGCA
1 GGGCCTTAGCCCAGTT-CAATAACAGTCATGCA
40979076 TACAGTAACC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 2 0.07
35 25 0.93
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (35 bp):
GGGCCTTAGCCCAGTTCAATAACAGTCATGCACTA
Found at i:40980953 original size:19 final size:19
Alignment explanation
Indices: 40980921--40980967 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
40980911 GTCCTATCAT
*
40980921 ATTTTATTTTTTT-AGATTA
1 ATTTT-TTTTTTTAAAATTA
40980940 ATTTTTTTTATTTAAAATTA
1 ATTTTTTTT-TTTAAAATTA
40980960 ATTTTTTT
1 ATTTTTTT
40980968 AAAAATATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 4 0.16
19 8 0.32
20 13 0.52
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
ATTTTTTTTTTTAAAATTA
Found at i:40993841 original size:35 final size:35
Alignment explanation
Indices: 40993795--40993865 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
40993785 GAAGTGCAAA
40993795 TGTTAGTATTTGATTACTAGTGTATATATGTGTAT
1 TGTTAGTATTTGATTACTAGTGTATATATGTGTAT
*
40993830 TGTTAGTATTTGATTTCTAGTGTATATATGTGTAT
1 TGTTAGTATTTGATTACTAGTGTATATATGTGTAT
40993865 T
1 T
40993866 AGCCGAGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.24, C:0.03, G:0.20, T:0.54
Consensus pattern (35 bp):
TGTTAGTATTTGATTACTAGTGTATATATGTGTAT
Found at i:40994718 original size:40 final size:40
Alignment explanation
Indices: 40994596--40994778 Score: 215
Period size: 40 Copynumber: 4.6 Consensus size: 40
40994586 TATTCGAATG
* * *
40994596 ATATACGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
* * * * * *
40994636 ATATCCGGACTAAAATCCAAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGACT
* *
40994676 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
* * *
40994716 ATATCCAGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
*
40994756 ATATCCGGGCTAAGACTCGAAGG
1 ATATCCGGGCTAAGACCCGAAGG
40994779 TCTTGTGCGA
Statistics
Matches: 118, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 115 0.97
41 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
Found at i:41001500 original size:47 final size:47
Alignment explanation
Indices: 41001430--41001524 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 47
41001420 GTTGGAGAAA
* *
41001430 AACCATATTTCCACTAATTGTCCGTGTACTTGGAGAAACAAAATAAC
1 AACCATATTTCCACTAATAGTCCGTGTACCTGGAGAAACAAAATAAC
** *
41001477 AACCATATTTCTGCTAATAGTCCGTGTACCTGGAGGAACAAAATAAC
1 AACCATATTTCCACTAATAGTCCGTGTACCTGGAGAAACAAAATAAC
41001524 A
1 A
41001525 CGAAGTAAGG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (47 bp):
AACCATATTTCCACTAATAGTCCGTGTACCTGGAGAAACAAAATAAC
Found at i:41002986 original size:22 final size:22
Alignment explanation
Indices: 41002947--41002989 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41002937 TGTGGCGAGG
* * *
41002947 GCGATGACTGTGGCAGATGACA
1 GCGATGACGGTAGAAGATGACA
41002969 GCGATGACGGTAGAAGATGAC
1 GCGATGACGGTAGAAGATGAC
41002990 GGTGGAAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.37, T:0.16
Consensus pattern (22 bp):
GCGATGACGGTAGAAGATGACA
Found at i:41003006 original size:13 final size:13
Alignment explanation
Indices: 41002971--41003006 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
41002961 AGATGACAGC
*
41002971 GATGACGGTAGAA
1 GATGACGGTGGAA
41002984 GATGACGGTGGAA
1 GATGACGGTGGAA
*
41002997 GATGAAGGTG
1 GATGACGGTG
41003007 TGGTTTGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.33, C:0.06, G:0.44, T:0.17
Consensus pattern (13 bp):
GATGACGGTGGAA
Found at i:41016369 original size:22 final size:21
Alignment explanation
Indices: 41016346--41016387 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41016336 AAGCTTTCAT
*
41016346 TTTAGTTATATTTTTAAAAAA
1 TTTACTTATATTTTTAAAAAA
*
41016367 TTTACTTTTATTTTTAAAAAA
1 TTTACTTATATTTTTAAAAAA
41016388 ATTGAATTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTACTTATATTTTTAAAAAA
Found at i:41018817 original size:25 final size:27
Alignment explanation
Indices: 41018780--41018832 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
41018770 TCGAACATGC
41018780 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
41018806 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
41018832 A
1 A
41018833 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:41020348 original size:26 final size:26
Alignment explanation
Indices: 41020317--41020424 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
41020307 TGAAATTCCC
41020317 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
41020343 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
41020369 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
41020395 ATCATGGAACATTTACCT-AACTCATT
1 ATCATGGAACATTTACCTAAAC-CATT
41020421 ATCA
1 ATCA
41020425 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 2 0.03
26 74 0.97
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:41021415 original size:22 final size:22
Alignment explanation
Indices: 41021373--41021416 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
41021363 TTTAGTAATA
*
41021373 AAGAAATCAAAAATAGTAAAAG
1 AAGAAATCAAAAATAGAAAAAG
* *
41021395 AAGAAATTTAAAAATAAAAAAA
1 AAGAAA-TCAAAAATAGAAAAA
41021417 TCATAAATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (22 bp):
AAGAAATCAAAAATAGAAAAAG
Found at i:41028690 original size:40 final size:39
Alignment explanation
Indices: 41028623--41028757 Score: 173
Period size: 40 Copynumber: 3.4 Consensus size: 39
41028613 ATGATATTCG
* *
41028623 GGCTAAGTCCCGAAAGCCTTTGTGCTAGTGACTATATCC
1 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCC
*
41028662 GAGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTATATCC
1 G-GCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCC
* * *
41028702 GGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCT
1 -GGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTATATCC
*
41028742 GGCTAATTCCCGAAGG
1 GGCTAAGTCCCGAAGG
41028758 TACTTGGGTT
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
39 15 0.18
40 66 0.79
41 3 0.04
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.26
Consensus pattern (39 bp):
GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCC
Found at i:41035482 original size:103 final size:103
Alignment explanation
Indices: 41035303--41035513 Score: 415
Period size: 103 Copynumber: 2.1 Consensus size: 103
41035293 CTAACATAAT
41035303 CATTATCTGCATATACAGATTTTTAGAGTACTTGTTATCCATACTTCATCGGATCCATTTATATA
1 CATTATCTGCATATACAGATTTTTAGAGTACTTGTTATCCATACTTCATCGGATCCATTTATATA
41035368 TTTGTTCAATTACGTATACCAAAAGCATAATTTTTATA
66 TTTGTTCAATTACGTATACCAAAAGCATAATTTTTATA
41035406 CATTATCTGCATATACAGATTTTTAGAGTACTTGTTATCCATACTTCATCGGATCCATTTATATA
1 CATTATCTGCATATACAGATTTTTAGAGTACTTGTTATCCATACTTCATCGGATCCATTTATATA
41035471 TTTGTTCAATTACGTATACCAAAAGCATAATTTTTATA
66 TTTGTTCAATTACGTATACCAAAAGCATAATTTTTATA
41035509 C-TTAT
1 CATTAT
41035514 AAACTATAAA
Statistics
Matches: 108, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
102 4 0.04
103 104 0.96
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (103 bp):
CATTATCTGCATATACAGATTTTTAGAGTACTTGTTATCCATACTTCATCGGATCCATTTATATA
TTTGTTCAATTACGTATACCAAAAGCATAATTTTTATA
Found at i:41035810 original size:41 final size:41
Alignment explanation
Indices: 41035760--41036263 Score: 783
Period size: 41 Copynumber: 12.3 Consensus size: 41
41035750 AATTCATCAT
* *
41035760 ATTCGGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
41035801 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
41035842 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
41035883 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
41035924 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
41035965 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
41036006 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
41036047 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
41036088 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
41036129 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
41036170 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
41036211 ATTCAGATCACCGGCGCTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
41036252 ATTCATATCACC
1 ATTCAGATCACC
41036264 AATTCCAAAC
Statistics
Matches: 418, Mismatches: 45, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 418 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
Found at i:41035903 original size:82 final size:82
Alignment explanation
Indices: 41035766--41036263 Score: 996
Period size: 82 Copynumber: 6.1 Consensus size: 82
41035756 TCATATTCGG
41035766 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
41035831 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
41035848 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
41035913 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
41035930 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
41035995 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
41036012 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
41036077 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
41036094 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
41036159 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
41036176 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
41036241 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
41036258 ATCACC
1 ATCACC
41036264 AATTCCAAAC
Statistics
Matches: 416, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 416 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.29
Consensus pattern (82 bp):
ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCGCTTAGCCTGCTAGG
TTTATAACCTGATTCAT
Found at i:41036499 original size:19 final size:19
Alignment explanation
Indices: 41036475--41036511 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41036465 TTGTTCGATC
*
41036475 CACACATATATATATATTA
1 CACACATATACATATATTA
41036494 CACACATATACATATATT
1 CACACATATACATATATT
41036512 CGCACATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (19 bp):
CACACATATACATATATTA
Found at i:41039830 original size:40 final size:40
Alignment explanation
Indices: 41039775--41039956 Score: 278
Period size: 40 Copynumber: 4.6 Consensus size: 40
41039765 TATTCGGATG
*
41039775 ATATCCGGGCTAAGTCCCGAAGGCCTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
41039815 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
41039855 ATATCCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
** *
41039895 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
41039935 ATATCC-GGCTAATTCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
41039957 TACTTGGGTT
Statistics
Matches: 131, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 14 0.11
40 115 0.88
41 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:41047286 original size:23 final size:23
Alignment explanation
Indices: 41047256--41047301 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
41047246 CCTATTCTGG
41047256 CAACGGATACGGGTTAGGGGTGT
1 CAACGGATACGGGTTAGGGGTGT
41047279 CAACGGATACGGGTTAGGGGTGT
1 CAACGGATACGGGTTAGGGGTGT
41047302 TACACACCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.43, T:0.22
Consensus pattern (23 bp):
CAACGGATACGGGTTAGGGGTGT
Found at i:41050341 original size:29 final size:29
Alignment explanation
Indices: 41050299--41050358 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
41050289 GAGGTTTCAA
*
41050299 AGCCTCTTCATATTCTTCCTCATCATCAT
1 AGCCTCTTCATATTCTTCATCATCATCAT
41050328 AGCCTCTTCATATTCTTCATCATCATCAT
1 AGCCTCTTCATATTCTTCATCATCATCAT
41050357 AG
1 AG
41050359 TCATAAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.23, C:0.32, G:0.05, T:0.40
Consensus pattern (29 bp):
AGCCTCTTCATATTCTTCATCATCATCAT
Found at i:41052786 original size:14 final size:14
Alignment explanation
Indices: 41052769--41052796 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41052759 TACAAAGAAA
41052769 CAAACTCCAAGAGT
1 CAAACTCCAAGAGT
41052783 CAAACTCCAAGAGT
1 CAAACTCCAAGAGT
41052797 TGAAAACTTT
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:0.29, G:0.14, T:0.14
Consensus pattern (14 bp):
CAAACTCCAAGAGT
Found at i:41055266 original size:5 final size:5
Alignment explanation
Indices: 41055256--41055285 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
41055246 GGTTATCAAA
*
41055256 ATTTT ATTTT ATTTT ATTTT ATTTT GTTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
41055286 CCCAAATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:41064251 original size:41 final size:41
Alignment explanation
Indices: 41064194--41064513 Score: 597
Period size: 41 Copynumber: 7.8 Consensus size: 41
41064184 GAATGTAATA
* *
41064194 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
41064235 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
*
41064276 CAGACTATATGTCTAGCAGGCTTAATGTCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
41064317 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
41064358 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
41064399 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
41064440 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
41064481 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG
1 CAGACTATATGTCTAGCAGGCTTAA-TGCCGGTG
41064514 TACTGAATCA
Statistics
Matches: 274, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
40 3 0.01
41 271 0.99
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (41 bp):
CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:41066491 original size:19 final size:21
Alignment explanation
Indices: 41066457--41066498 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
41066447 ATGGAGGTAG
*
41066457 GATTTTGTACATTTGA-ATCT
1 GATTCTGTACATTTGATATCT
41066477 GATTCTGTA-ATTTGATATCT
1 GATTCTGTACATTTGATATCT
41066497 GA
1 GA
41066499 ATCTTGATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.48
Consensus pattern (21 bp):
GATTCTGTACATTTGATATCT
Found at i:41069147 original size:29 final size:30
Alignment explanation
Indices: 41069092--41069149 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
41069082 TATTTTAGGT
41069092 CCACACGGCCAGACACACAGGCGTGTGGCC
1 CCACACGGCCAGACACACAGGCGTGTGGCC
* * *
41069122 CCACACGGCTAG-CACACGGGCTTGTGGC
1 CCACACGGCCAGACACACAGGCGTGTGGC
41069150 TTAGTTGTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.21, C:0.38, G:0.31, T:0.10
Consensus pattern (30 bp):
CCACACGGCCAGACACACAGGCGTGTGGCC
Found at i:41073459 original size:15 final size:14
Alignment explanation
Indices: 41073441--41073477 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
41073431 TATAAAGGTT
41073441 ATAATAATAAAAGCA
1 ATAATAATAAAAG-A
41073456 ATAATAATAAAAGA
1 ATAATAATAAAAGA
41073470 ATGAATAA
1 AT-AATAA
41073478 AGAAATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.22
Consensus pattern (14 bp):
ATAATAATAAAAGA
Found at i:41075328 original size:30 final size:30
Alignment explanation
Indices: 41075292--41075349 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
41075282 CTTGTATACT
41075292 ACCATAATAAGTAAGAAATGTAAATTAATA
1 ACCATAATAAGTAAGAAATGTAAATTAATA
*
41075322 ACCATAATAGGTAAGAAATGTAAATTAA
1 ACCATAATAAGTAAGAAATGTAAATTAA
41075350 CTATTAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.26
Consensus pattern (30 bp):
ACCATAATAAGTAAGAAATGTAAATTAATA
Found at i:41078067 original size:33 final size:33
Alignment explanation
Indices: 41078005--41078071 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
41077995 TCCGTGTATT
* * * *
41078005 TATGGCGTAAAAATCTGTCTGCTTTAGTGGTTA
1 TATGGCATAAAAATCCGTCTACTTCAGTGGTTA
*
41078038 TATGGCATAAACATCCGTCTACTTCAGTGGTTA
1 TATGGCATAAAAATCCGTCTACTTCAGTGGTTA
41078071 T
1 T
41078072 GTGTTCTATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.37
Consensus pattern (33 bp):
TATGGCATAAAAATCCGTCTACTTCAGTGGTTA
Found at i:41084358 original size:19 final size:18
Alignment explanation
Indices: 41084328--41084385 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
41084318 ATTATTAGTT
41084328 TTTTAAATAATTATAAAATA
1 TTTTAAA-AATTATAAAA-A
*
41084348 TTTTAAAAATTTTAAAAA
1 TTTTAAAAATTATAAAAA
41084366 TTTTAAAAATTATTAAAAA
1 TTTTAAAAATTA-TAAAAA
41084385 T
1 T
41084386 AATATTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
18 12 0.34
19 16 0.46
20 7 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTTAAAAATTATAAAAA
Found at i:41084361 original size:9 final size:9
Alignment explanation
Indices: 41084328--41084385 Score: 80
Period size: 9 Copynumber: 6.1 Consensus size: 9
41084318 ATTATTAGTT
41084328 TTTTAAATAA
1 TTTTAAA-AA
*
41084338 TTATAAAATA
1 TTTTAAAA-A
41084348 TTTTAAAAA
1 TTTTAAAAA
41084357 TTTTAAAAA
1 TTTTAAAAA
41084366 TTTTAAAAA
1 TTTTAAAAA
41084375 TTATTAAAAA
1 TT-TTAAAAA
41084385 T
1 T
41084386 AATATTAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
9 22 0.50
10 22 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:41084799 original size:10 final size:10
Alignment explanation
Indices: 41084757--41084835 Score: 63
Period size: 10 Copynumber: 8.1 Consensus size: 10
41084747 TAATTTTTAA
*
41084757 TTTTAATATT
1 TTTTAATAAT
**
41084767 TTTTTGTAAT
1 TTTTAATAAT
*
41084777 TTTAAATAA-
1 TTTTAATAAT
41084786 TTTTAAT-AT
1 TTTTAATAAT
*
41084795 TTTTTATAAT
1 TTTTAATAAT
* *
41084805 TCTTATTAAT
1 TTTTAATAAT
*
41084815 TTTTAATCAT
1 TTTTAATAAT
*
41084825 TTTTCATAAT
1 TTTTAATAAT
41084835 T
1 T
41084836 ACTTGAAAAA
Statistics
Matches: 51, Mismatches: 16, Indels: 4
0.72 0.23 0.06
Matches are distributed among these distances:
8 1 0.02
9 12 0.24
10 38 0.75
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:41084803 original size:18 final size:19
Alignment explanation
Indices: 41084782--41084819 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
41084772 GTAATTTTAA
*
41084782 ATAATT-TTAATATTTTTT
1 ATAATTCTTAATAATTTTT
*
41084800 ATAATTCTTATTAATTTTT
1 ATAATTCTTAATAATTTTT
41084819 A
1 A
41084820 ATCATTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
ATAATTCTTAATAATTTTT
Found at i:41084818 original size:29 final size:28
Alignment explanation
Indices: 41084753--41084835 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 28
41084743 TAATTAATTT
*
41084753 TTAATTTTAATATTTTTTTGTAATTTTAA
1 TTAATTTTAATA-TTTTTTATAATTTTAA
*
41084782 ATAATTTTAATATTTTTTATAATTCTT-A
1 TTAATTTTAATATTTTTTATAATT-TTAA
*
41084810 TTAATTTTTAATCATTTTTCATAATT
1 TTAA-TTTTAAT-ATTTTTTATAATT
41084836 ACTTGAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 15 0.32
29 20 0.43
30 12 0.26
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.63
Consensus pattern (28 bp):
TTAATTTTAATATTTTTTATAATTTTAA
Found at i:41084925 original size:19 final size:17
Alignment explanation
Indices: 41084897--41084939 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
41084887 TTCAAATAAT
41084897 TATTAAAAAAATTTGTTTA
1 TATT-AAAAAATTT-TTTA
*
41084916 TATTATAAAATTTTTTA
1 TATTAAAAAATTTTTTA
*
41084933 TTTTAAA
1 TATTAAA
41084940 GTTATTTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 9 0.43
18 8 0.38
19 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TATTAAAAAATTTTTTA
Found at i:41096893 original size:17 final size:19
Alignment explanation
Indices: 41096851--41096894 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
41096841 ACGAAATTTT
*
41096851 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
41096870 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
41096888 AA-TATTA
1 AATTATTA
41096895 CTGCATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:41099375 original size:27 final size:27
Alignment explanation
Indices: 41099336--41099461 Score: 80
Period size: 27 Copynumber: 4.4 Consensus size: 27
41099326 ACTTGTAATA
*
41099336 GGGCTACGGCCCAGATTGATACTGATAT
1 GGGCTA-GGCCCAGATTAATACTGATAT
*
41099364 GGGCTAGGCCCA-ATATACTCTGATACT-ATAAG
1 GGGCTAGGCCCAGAT-TA-----ATACTGAT-AT
*
41099396 GGGCTATGGCCCAGATTAATATTGATAT
1 GGGCTA-GGCCCAGATTAATACTGATAT
*
41099424 GGGCTAAGGCCCA-ATTAACACTGA-AT
1 GGGCT-AGGCCCAGATTAATACTGATAT
41099450 AGGGCTTAGGCC
1 -GGGC-TAGGCC
41099462 TAGTAAAGCT
Statistics
Matches: 79, Mismatches: 6, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
26 4 0.05
27 25 0.32
28 23 0.29
29 3 0.04
31 2 0.03
32 12 0.15
33 8 0.10
34 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.25
Consensus pattern (27 bp):
GGGCTAGGCCCAGATTAATACTGATAT
Found at i:41099376 original size:60 final size:59
Alignment explanation
Indices: 41099300--41099438 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 59
41099290 AACTATGTTA
* * * *
41099300 ATATGGCCAAGGCCCAATATA-TCTCGACT-TGTAATAGGGCTACGGCCCAGATTGATACTG
1 ATATGGGCTAGGCCCAATATACTCT-GA-TATATAA-AGGGCTACGGCCCAGATTAATACTG
* * *
41099360 ATATGGGCTAGGCCCAATATACTCTGATACTATAAGGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCTAGGCCCAATATACTCTGATA-TATAAAGGGCTACGGCCCAGATTAATACTG
41099420 ATATGGGCTAAGGCCCAAT
1 ATATGGGCT-AGGCCCAAT
41099439 TAACACTGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
59 1 0.01
60 51 0.75
61 16 0.24
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (59 bp):
ATATGGGCTAGGCCCAATATACTCTGATATATAAAGGGCTACGGCCCAGATTAATACTG
Found at i:41100423 original size:49 final size:49
Alignment explanation
Indices: 41100351--41100451 Score: 175
Period size: 49 Copynumber: 2.1 Consensus size: 49
41100341 TCTGTTGATT
41100351 GTGAATGCTAGGCATGTATAGGATAGCATAGGTAATTCGTTATCCGTAG
1 GTGAATGCTAGGCATGTATAGGATAGCATAGGTAATTCGTTATCCGTAG
* * *
41100400 GTGAATGCTAGGCATGTATAGGATGGGATAGGTAATTGGTTATCCGTAG
1 GTGAATGCTAGGCATGTATAGGATAGCATAGGTAATTCGTTATCCGTAG
41100449 GTG
1 GTG
41100452 TGGCTGTATG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.27, C:0.10, G:0.33, T:0.31
Consensus pattern (49 bp):
GTGAATGCTAGGCATGTATAGGATAGCATAGGTAATTCGTTATCCGTAG
Found at i:41102600 original size:5 final size:6
Alignment explanation
Indices: 41102587--41102634 Score: 60
Period size: 6 Copynumber: 7.5 Consensus size: 6
41102577 ATAATTTAAT
*
41102587 AAATAA AAATAA AAATCTAA AACTAA AAATAA AAATAA AAATTAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAA-TAA AAA
41102635 ATATATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
6 26 0.70
7 6 0.16
8 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:41102637 original size:20 final size:20
Alignment explanation
Indices: 41102590--41102634 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
41102580 ATTTAATAAA
*
41102590 TAAAAATAAAAATCTAAAAC
1 TAAAAATAAAAATCAAAAAC
*
41102610 TAAAAATAAAAAT-AAAAAT
1 TAAAAATAAAAATCAAAAAC
41102629 TAAAAA
1 TAAAAA
41102635 ATATATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (20 bp):
TAAAAATAAAAATCAAAAAC
Found at i:41102644 original size:15 final size:14
Alignment explanation
Indices: 41102591--41102637 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
41102581 TTTAATAAAT
41102591 AAAAATAAAAATCT-
1 AAAAATAAAAAT-TA
*
41102605 AAAACTAAAAA-T-
1 AAAAATAAAAATTA
41102617 AAAAATAAAAATTA
1 AAAAATAAAAATTA
41102631 AAAAATA
1 AAAAATA
41102638 TATAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 11 0.38
13 1 0.03
14 17 0.59
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAAATAAAAATTA
Found at i:41102668 original size:9 final size:9
Alignment explanation
Indices: 41102654--41102720 Score: 91
Period size: 9 Copynumber: 7.6 Consensus size: 9
41102644 TTTATACAAA
41102654 TAATTCGGT
1 TAATTCGGT
41102663 TAATTCGGT
1 TAATTCGGT
**
41102672 TAATTTAG-
1 TAATTCGGT
41102680 TAATTCGGT
1 TAATTCGGT
*
41102689 TAATTCGAT
1 TAATTCGGT
*
41102698 TAATTTGGT
1 TAATTCGGT
41102707 TAATTCGGT
1 TAATTCGGT
41102716 TAATT
1 TAATT
41102721 TTATACTTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
8 6 0.12
9 43 0.88
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (9 bp):
TAATTCGGT
Found at i:41102684 original size:26 final size:27
Alignment explanation
Indices: 41102654--41102720 Score: 109
Period size: 26 Copynumber: 2.5 Consensus size: 27
41102644 TTTATACAAA
*
41102654 TAATTCGGTTAATTCGGTTAATTTAG-
1 TAATTCGGTTAATTCGATTAATTTAGT
*
41102680 TAATTCGGTTAATTCGATTAATTTGGT
1 TAATTCGGTTAATTCGATTAATTTAGT
41102707 TAATTCGGTTAATT
1 TAATTCGGTTAATT
41102721 TTATACTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 24 0.63
27 14 0.37
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (27 bp):
TAATTCGGTTAATTCGATTAATTTAGT
Found at i:41104977 original size:18 final size:18
Alignment explanation
Indices: 41104919--41104978 Score: 52
Period size: 20 Copynumber: 3.3 Consensus size: 18
41104909 AAATATAAAT
41104919 TATTCTATTTATATTT-TA
1 TATT-TATTTATATTTATA
* **
41104937 T-TTTATATATATAAATAA
1 TATTTATTTATATTTAT-A
41104955 TTATTTATTTATATTTATA
1 -TATTTATTTATATTTATA
41104974 TATTT
1 TATTT
41104979 TCTTCGCTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 8 0.25
17 3 0.09
18 7 0.22
19 2 0.06
20 12 0.38
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTATTTATATTTATA
Found at i:41106192 original size:59 final size:59
Alignment explanation
Indices: 41106093--41106253 Score: 184
Period size: 59 Copynumber: 2.7 Consensus size: 59
41106083 TGAAAAAGAG
* * * * *
41106093 TTGGACCAATAAAAGTTCAAATCTCGATGTGGAAACAATTACCAAACTTA-GAAATTAAT
1 TTGGACAAAAAAAAGTTCAAATCTCAATGTGAAAACAATTACCAAACTTATG-AATTAAC
* ** *
41106152 TTGGACAAAAAAAAGTTCAAATCTCAATGTGAAAATAATTATTAAATTTATGAATTAAC
1 TTGGACAAAAAAAAGTTCAAATCTCAATGTGAAAACAATTACCAAACTTATGAATTAAC
* *
41106211 TTAGACAAAAAAAAATTCAAA-CATCAATGT-AAAACAATTACCA
1 TTGGACAAAAAAAAGTTCAAATC-TCAATGTGAAAACAATTACCA
41106254 TTAAGATTTC
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
58 11 0.13
59 74 0.86
60 1 0.01
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (59 bp):
TTGGACAAAAAAAAGTTCAAATCTCAATGTGAAAACAATTACCAAACTTATGAATTAAC
Found at i:41110859 original size:15 final size:16
Alignment explanation
Indices: 41110840--41110883 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
41110830 TAATATCTAT
*
41110840 TACATTAATAATAAAA
1 TACATTATTAATAAAA
*
41110856 -ACATTATTAGTAAAA
1 TACATTATTAATAAAA
41110871 TA-ATTATTAATAA
1 TACATTATTAATAA
41110884 TTTGTTATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 23 0.96
16 1 0.04
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (16 bp):
TACATTATTAATAAAA
Found at i:41111088 original size:19 final size:18
Alignment explanation
Indices: 41111046--41111082 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
41111036 ATTATTATTC
41111046 TATTTA-AAATAAAATAT
1 TATTTATAAATAAAATAT
41111063 TATTTATAAATAAAA-AT
1 TATTTATAAATAAAATAT
41111080 TAT
1 TAT
41111083 ATTTATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATTTATAAATAAAATAT
Found at i:41111102 original size:13 final size:13
Alignment explanation
Indices: 41111086--41111111 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41111076 AAATTATATT
41111086 TATTTAATTAAAA
1 TATTTAATTAAAA
41111099 TATTTAATTAAAA
1 TATTTAATTAAAA
41111112 AACTTGGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATTTAATTAAAA
Found at i:41111844 original size:12 final size:12
Alignment explanation
Indices: 41111823--41111856 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41111813 TATATATTTT
*
41111823 AAAATTATATAA
1 AAAATAATATAA
41111835 AAAATAATATAA
1 AAAATAATATAA
*
41111847 AAATTAATAT
1 AAAATAATAT
41111857 GGAAGGGGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:41112474 original size:12 final size:13
Alignment explanation
Indices: 41112456--41112494 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
41112446 TAAAACACAT
41112456 AAAAA-TTATAAA
1 AAAAAGTTATAAA
* *
41112468 CAAAATTTATAAA
1 AAAAAGTTATAAA
41112481 AAAAAGTTATAAA
1 AAAAAGTTATAAA
41112494 A
1 A
41112495 TTTTTATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (13 bp):
AAAAAGTTATAAA
Found at i:41112624 original size:18 final size:17
Alignment explanation
Indices: 41112602--41112635 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41112592 TTTTTAATAA
41112602 AAAAAATTTATAACTTT
1 AAAAAATTTATAACTTT
41112619 AAAAAATTTATAACTTT
1 AAAAAATTTATAACTTT
41112636 TATTTATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAAAATTTATAACTTT
Found at i:41117522 original size:63 final size:61
Alignment explanation
Indices: 41117334--41117525 Score: 206
Period size: 63 Copynumber: 3.1 Consensus size: 61
41117324 ACACAGCTGA
* ** *
41117334 GTAACTCACTATTTT-GAAGTTAGAGTCACATGAGCCAGAGACACGGATGTGTGTCTAGGCTGT
1 GTAACTCACT-TTTTGGAA-TTAGAGTCACATGA-CCAAAGACACGGGCGTGTGTCTAGGCCGT
* * * * * *
41117397 ATAACTCACTATTTGGAATTAGAGTCACACGGGCCAAGGACACGGGCGTGTGTTTAGGCCGT
1 GTAACTCACTTTTTGGAATTAGAGTCACA-TGACCAAAGACACGGGCGTGTGTCTAGGCCGT
* * *
41117459 GTAACTCACTGTTTTGGAATTAGAGACACATAGACCAAAGACACGGGCATGTGTCCAGGCCGT
1 GTAACTCACT-TTTTGGAATTAGAGTCACAT-GACCAAAGACACGGGCGTGTGTCTAGGCCGT
41117522 GTAA
1 GTAA
41117526 GATATATTTT
Statistics
Matches: 106, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
62 46 0.43
63 60 0.57
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (61 bp):
GTAACTCACTTTTTGGAATTAGAGTCACATGACCAAAGACACGGGCGTGTGTCTAGGCCGT
Found at i:41117743 original size:108 final size:108
Alignment explanation
Indices: 41117568--41117764 Score: 313
Period size: 108 Copynumber: 1.8 Consensus size: 108
41117558 GTGTTGAACT
* *
41117568 GTGTGCTAAACCGTGTAACTCAATATTTTGAGCCACATGGGCGTGTGTTAGGACATGTGACAGGT
1 GTGTGCTAAACCGTGTAACTCAATATTTTGAGCCACATGGGCGTGTGTTAGGACATATGACAAGT
*
41117633 CATGTGCGACACTGAGGTAGGCCACACTGGTATGTGCTGGGTC
66 CATGTACGACACTGAGGTAGGCCACACTGGTATGTGCTGGGTC
* * * * *
41117676 GTGTGCTATACCGTGTAACTCACTGTTTTGAGCCACATGGGCGTGTGTTAGGCCATATGATAAGT
1 GTGTGCTAAACCGTGTAACTCAATATTTTGAGCCACATGGGCGTGTGTTAGGACATATGACAAGT
*
41117741 CATGTACGACATTGAGGTAGGCCA
66 CATGTACGACACTGAGGTAGGCCA
41117765 TAGGGTGTGT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 80 1.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (108 bp):
GTGTGCTAAACCGTGTAACTCAATATTTTGAGCCACATGGGCGTGTGTTAGGACATATGACAAGT
CATGTACGACACTGAGGTAGGCCACACTGGTATGTGCTGGGTC
Found at i:41135080 original size:7 final size:7
Alignment explanation
Indices: 41135064--41135178 Score: 162
Period size: 7 Copynumber: 16.4 Consensus size: 7
41135054 TCCCTTCCTA
*
41135064 TTCCAAT
1 TTCCAGT
41135071 TTCCAGT
1 TTCCAGT
41135078 TTCCAG-
1 TTCCAGT
41135084 TTCCTAGT
1 TTCC-AGT
*
41135092 TTCTAGT
1 TTCCAGT
41135099 TTCCAG-
1 TTCCAGT
41135105 TTCCTAGT
1 TTCC-AGT
*
41135113 TTCTAGT
1 TTCCAGT
41135120 TTCCAGT
1 TTCCAGT
41135127 TTCCAGT
1 TTCCAGT
41135134 TTCCAGT
1 TTCCAGT
41135141 TTCCAGT
1 TTCCAGT
41135148 TTCCAGT
1 TTCCAGT
41135155 TTCCAGT
1 TTCCAGT
41135162 TTCCAGT
1 TTCCAGT
*
41135169 TTCCATT
1 TTCCAGT
41135176 TTC
1 TTC
41135179 TTTTCTTTTT
Statistics
Matches: 98, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
6 8 0.08
7 84 0.86
8 6 0.06
ACGTcount: A:0.15, C:0.27, G:0.12, T:0.46
Consensus pattern (7 bp):
TTCCAGT
Found at i:41137704 original size:23 final size:23
Alignment explanation
Indices: 41137685--41137730 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
41137675 GAGAAAAAGT
41137685 TTTGGGGGAAAAA-GTAAAAATA
1 TTTGGGGGAAAAATGTAAAAATA
*
41137707 TTTGGGGTAAAAATGT-AAAATA
1 TTTGGGGGAAAAATGTAAAAATA
41137729 TT
1 TT
41137731 ATAGTTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (23 bp):
TTTGGGGGAAAAATGTAAAAATA
Found at i:41139023 original size:41 final size:41
Alignment explanation
Indices: 41138966--41139047 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
41138956 TTGGTGGAAC
*
41138966 ACTGGTATAATCATAAGGCATCAAGGGTTTCCTAGGACAAT
1 ACTGGTATAATCATAAGGCATCAAGGGTATCCTAGGACAAT
41139007 ACTGGTATAATCATAAGGCATCAAGGGTATCCTAGGACAAT
1 ACTGGTATAATCATAAGGCATCAAGGGTATCCTAGGACAAT
41139048 CATTTGTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (41 bp):
ACTGGTATAATCATAAGGCATCAAGGGTATCCTAGGACAAT
Found at i:41139916 original size:14 final size:15
Alignment explanation
Indices: 41139892--41139920 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41139882 ATTAAATCTT
41139892 TAATATAAAATATTA
1 TAATATAAAATATTA
41139907 TAATAT-AAATATTA
1 TAATATAAAATATTA
41139921 AAAAAATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATATAAAATATTA
Found at i:41141282 original size:24 final size:24
Alignment explanation
Indices: 41141239--41141439 Score: 107
Period size: 26 Copynumber: 7.6 Consensus size: 24
41141229 AAAGAAAATG
* *
41141239 AAATAAATAATATATAAAACAATTTG
1 AAATAAAT-A-ATATAAAACAAATTA
* *
41141265 AAGTAGATAATATAAAACAAATTA
1 AAATAAATAATATAAAACAAATTA
* *
41141289 AAATAAATAATATACGAAGCAATTTA
1 AAATAAATAATATA--AAACAAATTA
41141315 AAATAAATAATATGTAAAA-AGAAGTTTA
1 AAATAAATAATA--TAAAACA-AA--TTA
**
41141343 AAATAAATAATATACAAAACAGTTTAA
1 AAATAAATAATAT--AAAACAAATT-A
*
41141370 AAATAAATGATATATAAAAAAATAATTCA
1 AAATAAAT-A-ATAT-AAAACA-AATT-A
* **
41141399 AAATAAATAATATATATGACAGTTTAA
1 AAATAAATAATATA-A-AACAAATT-A
41141426 AAATAAATAATATA
1 AAATAAATAATATA
41141440 TGAAAAATTT
Statistics
Matches: 137, Mismatches: 22, Indels: 31
0.72 0.12 0.16
Matches are distributed among these distances:
24 25 0.18
25 2 0.01
26 33 0.24
27 31 0.23
28 30 0.22
29 16 0.12
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (24 bp):
AAATAAATAATATAAAACAAATTA
Found at i:41141319 original size:26 final size:25
Alignment explanation
Indices: 41141239--41141454 Score: 168
Period size: 27 Copynumber: 8.2 Consensus size: 25
41141229 AAAGAAAATG
*
41141239 AAATAAATAATATATAAAACAATTTG
1 AAATAAATAATATA-AAAACAATTTA
* * *
41141265 AAGTAGATAATAT-AAAACAAATTA
1 AAATAAATAATATAAAAACAATTTA
* *
41141289 AAATAAATAATATACGAAGCAATTTA
1 AAATAAATAATATA-AAAACAATTTA
*
41141315 AAATAAATAATATGTAAAAAGAAGTTTA
1 AAATAAATAATA--TAAAAACAA-TTTA
*
41141343 AAATAAATAATATACAAAACAGTTTAA
1 AAATAAATAATATA-AAAACAATTT-A
41141370 AAATAAATGATATATAAAAA-AATAATTCA
1 AAATAAAT-A-ATATAAAAACAAT--TT-A
** *
41141399 AAATAAATAATATATATGACAGTTTAA
1 AAATAAATAATATA-AAAACAATTT-A
*
41141426 AAATAAATAATATATGAAA-AATTTA
1 AAATAAATAATATA-AAAACAATTTA
41141451 AAAT
1 AAAT
41141455 GGATAATAGT
Statistics
Matches: 153, Mismatches: 24, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
24 20 0.13
25 5 0.03
26 40 0.26
27 44 0.29
28 26 0.17
29 18 0.12
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.29
Consensus pattern (25 bp):
AAATAAATAATATAAAAACAATTTA
Found at i:41141411 original size:56 final size:53
Alignment explanation
Indices: 41141239--41141446 Score: 197
Period size: 56 Copynumber: 3.9 Consensus size: 53
41141229 AAAGAAAATG
* * * * *
41141239 AAATAAATAATATATAAAACAATTTGAAGTAGAT-A-ATAT-AAAACAAATTA
1 AAATAAATAATATACAAAACAATTTAAAATAAATAATATATAAAAAAAAATTA
* * * **
41141289 AAATAAATAATATACGAAGCAATTTAAAATAAATAATATGTAAAAAGAAGTTTA
1 AAATAAATAATATACAAAACAATTTAAAATAAATAATATATAAAAA-AAAATTA
* *
41141343 AAATAAATAATATACAAAACAGTTTAAAAATAAATGATATATAAAAAAATAATTCA
1 AAATAAATAATATACAAAACAATTT-AAAATAAATAATATATAAAAAAA-AATT-A
* ** * *
41141399 AAATAAATAATATATATGACAGTTTAAAAATAAATAATATATGAAAAA
1 AAATAAATAATATACAAAACAATTT-AAAATAAATAATATATAAAAAA
41141447 TTTAAAATGG
Statistics
Matches: 129, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
50 28 0.22
51 1 0.01
52 3 0.02
53 4 0.03
54 28 0.22
55 21 0.16
56 44 0.34
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (53 bp):
AAATAAATAATATACAAAACAATTTAAAATAAATAATATATAAAAAAAAATTA
Found at i:41141554 original size:29 final size:26
Alignment explanation
Indices: 41141493--41141587 Score: 86
Period size: 29 Copynumber: 3.4 Consensus size: 26
41141483 TGTAGAAAAC
41141493 TTAAAATAAATAATAATAAAACAATT
1 TTAAAATAAATAATAATAAAACAATT
*
41141519 TAAAAATAAATAATATATGAGAAA-AAGTT
1 TTAAAATAAATAATA-AT-A-AAACAA-TT
*
41141548 TTAAAATAAATAAATAA-ATAACAAATT
1 TTAAAATAAAT-AATAATAAAAC-AATT
41141575 TGTGAAAATAAAT
1 T-T-AAAATAAAT
41141588 TGAAATCAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
26 16 0.28
27 6 0.11
28 6 0.11
29 25 0.44
30 4 0.07
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (26 bp):
TTAAAATAAATAATAATAAAACAATT
Found at i:41154109 original size:46 final size:46
Alignment explanation
Indices: 41154057--41154376 Score: 426
Period size: 46 Copynumber: 7.0 Consensus size: 46
41154047 GCTTTCTGAA
*
41154057 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
41154103 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
41154149 ATAAAATGTGCAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
41154195 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* ** * *
41154241 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATGTAAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*** * *
41154287 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACCTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * * *
41154333 A-GAAAATGAGTAAGACCATAGTTGAAAGACACAATGGCATCATG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
41154377 TCAAAGATAA
Statistics
Matches: 247, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 1 0.00
46 246 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:41154678 original size:16 final size:17
Alignment explanation
Indices: 41154657--41154689 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41154647 ATGATGGAGC
41154657 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
41154673 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
41154690 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:41162201 original size:37 final size:37
Alignment explanation
Indices: 41162133--41162204 Score: 101
Period size: 39 Copynumber: 1.9 Consensus size: 37
41162123 TTCTTTTTTC
41162133 TTTTTTATGAAAAAGAAATTACAAGACACAACCTATTT
1 TTTTTTATGAAAAAGAAATTACAAGA-ACAACCTATTT
* *
41162171 TTTTATTATTAAAAAGAAATTATAAG-ACAACCTA
1 TTTT-TTATGAAAAAGAAATTACAAGAACAACCTA
41162205 CATAGGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 8 0.26
38 4 0.13
39 19 0.61
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (37 bp):
TTTTTTATGAAAAAGAAATTACAAGAACAACCTATTT
Found at i:41175294 original size:10 final size:11
Alignment explanation
Indices: 41175264--41175296 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
41175254 CGGCCCGCCC
41175264 ATATTAATTTT
1 ATATTAATTTT
41175275 ATATTAATTTT
1 ATATTAATTTT
41175286 ATA-TAATTTT
1 ATATTAATTTT
41175296 A
1 A
41175297 AAAAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATATTAATTTT
Found at i:41175320 original size:18 final size:18
Alignment explanation
Indices: 41175297--41175341 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
41175287 TATAATTTTA
*
41175297 AAAAATATATAAACCATC
1 AAAAATATATAAAACATC
41175315 AAAAATACTA-AAAACATC
1 AAAAATA-TATAAAACATC
41175333 AAAAA-ATAT
1 AAAAATATAT
41175342 TTCTCAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 2 0.08
17 1 0.04
18 19 0.79
19 2 0.08
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATATATAAAACATC
Found at i:41175453 original size:30 final size:29
Alignment explanation
Indices: 41175419--41175475 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
41175409 TTTAACAAGC
*
41175419 AAATGCCTCTAAAATAGTAACAAAATTAGA
1 AAATGCCTCTAAAATAATAA-AAAATTAGA
* *
41175449 AAATGTCTTTAAAATAATAAAAAATTA
1 AAATGCCTCTAAAATAATAAAAAATTA
41175476 ACAATAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (29 bp):
AAATGCCTCTAAAATAATAAAAAATTAGA
Found at i:41181437 original size:18 final size:19
Alignment explanation
Indices: 41181414--41181452 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
41181404 CTTGGCCTAT
* *
41181414 TACAGTATCA-ATATTCAG
1 TACAGTAACAGATATACAG
41181432 TACAGTAACAGATATACAG
1 TACAGTAACAGATATACAG
41181451 TA
1 TA
41181453 TCAAATCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (19 bp):
TACAGTAACAGATATACAG
Found at i:41187693 original size:21 final size:21
Alignment explanation
Indices: 41187664--41187717 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
41187654 TTATATGTTT
41187664 AGTATGATCTGTGATA-AGATA
1 AGTATGATCTGTGATATA-ATA
* *
41187685 AGTACGATCAGTGATATAATA
1 AGTATGATCTGTGATATAATA
41187706 AGTATGATCTGT
1 AGTATGATCTGT
41187718 ATTTGTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.33
Consensus pattern (21 bp):
AGTATGATCTGTGATATAATA
Found at i:41187744 original size:20 final size:20
Alignment explanation
Indices: 41187704--41187745 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
41187694 AGTGATATAA
* * *
41187704 TAAGTATGATCTGTATTTGT
1 TAAGCATGATCTGAATCTGT
41187724 TAAGCATGATCTGAATCTGT
1 TAAGCATGATCTGAATCTGT
41187744 TA
1 TA
41187746 TAAAAGCATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.43
Consensus pattern (20 bp):
TAAGCATGATCTGAATCTGT
Found at i:41192878 original size:23 final size:21
Alignment explanation
Indices: 41192851--41192892 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
41192841 ATGAATTAGA
41192851 ATGTTGAAATGTTATGTTTAAAT
1 ATGTTGAAATG--ATGTTTAAAT
*
41192874 ATGTTTAAATGATGTTTAA
1 ATGTTGAAATGATGTTTAA
41192893 GTCTCTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.48
Consensus pattern (21 bp):
ATGTTGAAATGATGTTTAAAT
Found at i:41192890 original size:11 final size:10
Alignment explanation
Indices: 41192863--41192892 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
41192853 GTTGAAATGT
41192863 TATGTTTAAA
1 TATGTTTAAA
41192873 TATGTTTAAA
1 TATGTTTAAA
41192883 TGATGTTTAA
1 T-ATGTTTAA
41192893 GTCTCTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (10 bp):
TATGTTTAAA
Found at i:41193787 original size:12 final size:12
Alignment explanation
Indices: 41193770--41193795 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41193760 ATATATTTTA
41193770 ATATTTTAAGGT
1 ATATTTTAAGGT
41193782 ATATTTTAAGGT
1 ATATTTTAAGGT
41193794 AT
1 AT
41193796 TTGGAATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (12 bp):
ATATTTTAAGGT
Found at i:41194332 original size:20 final size:20
Alignment explanation
Indices: 41194277--41194333 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
41194267 TGCTCCTAAC
*
41194277 AGTACCTTC-GTACTCCTGTT
1 AGTA-CTTCTGTACTCCTGAT
* *
41194297 AGTA-TTATTGTGCTCCTGAT
1 AGTACTT-CTGTACTCCTGAT
41194317 AGTACTTCTGTACTCCT
1 AGTACTTCTGTACTCCT
41194334 ATTAGCACTG
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.42
Consensus pattern (20 bp):
AGTACTTCTGTACTCCTGAT
Found at i:41200206 original size:15 final size:14
Alignment explanation
Indices: 41200178--41200214 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
41200168 ATTTTTTTTC
41200178 AAAATT-ATAT-AA
1 AAAATTAATATAAA
*
41200190 AAATTTAATATAAA
1 AAAATTAATATAAA
41200204 AAAATTAATAT
1 AAAATTAATAT
41200215 GGGTCGGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 5 0.24
13 4 0.19
14 12 0.57
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAATTAATATAAA
Found at i:41200440 original size:17 final size:17
Alignment explanation
Indices: 41200418--41200452 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
41200408 TTATAAAATT
* *
41200418 ATCTTTTAAAATTTAAA
1 ATCTTTAAAAATATAAA
41200435 ATCTTTAAAAATATAAA
1 ATCTTTAAAAATATAAA
41200452 A
1 A
41200453 ATGTAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
ATCTTTAAAAATATAAA
Found at i:41200861 original size:35 final size:35
Alignment explanation
Indices: 41200822--41200921 Score: 132
Period size: 35 Copynumber: 2.9 Consensus size: 35
41200812 GTCAAAGTCG
* *
41200822 ACCTTAAAGAGGTTGGGATAGACCCGTCTAA-GACA
1 ACCTTAAAAAGGTTGGGATAGACACGTCTAAGGA-A
* * *
41200857 ACCTTAAAAAGGTTGGGACAAACTCGTCTAAGGAA
1 ACCTTAAAAAGGTTGGGATAGACACGTCTAAGGAA
41200892 ACCTTAAAAAGGTTGGGATAGA-ACGTCTAA
1 ACCTTAAAAAGGTTGGGATAGACACGTCTAA
41200922 TAGGGTAGAC
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
34 7 0.12
35 48 0.84
36 2 0.04
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (35 bp):
ACCTTAAAAAGGTTGGGATAGACACGTCTAAGGAA
Found at i:41202995 original size:16 final size:15
Alignment explanation
Indices: 41202963--41203002 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
41202953 TTCTTTTTCA
*
41202963 TTTTAATCCTTGATT
1 TTTTTATCCTTGATT
41202978 TTTTTATCCTTGATT
1 TTTTTATCCTTGATT
41202993 TTTTTATCCT
1 TTTTTATCCT
41203003 AATCAATACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.65
Consensus pattern (15 bp):
TTTTTATCCTTGATT
Found at i:41204345 original size:20 final size:20
Alignment explanation
Indices: 41204320--41204398 Score: 99
Period size: 20 Copynumber: 4.0 Consensus size: 20
41204310 ATTATAAAAT
41204320 AATTCAAAATAATTTTTAAA
1 AATTCAAAATAATTTTTAAA
41204340 AATTCAAAATAATTTTT-AA
1 AATTCAAAATAATTTTTAAA
* *
41204359 AATTGAAAAT-ATTTATAAA
1 AATTCAAAATAATTTTTAAA
* *
41204378 AATTAAAAAATATTTTTTAAA
1 AATT-CAAAATAATTTTTAAA
41204399 TTAAAAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.10
19 17 0.33
20 22 0.43
21 7 0.14
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (20 bp):
AATTCAAAATAATTTTTAAA
Found at i:41204368 original size:39 final size:39
Alignment explanation
Indices: 41204320--41204398 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
41204310 ATTATAAAAT
* *
41204320 AATTCAAAATAATTTTTAAAAATT-CAAAATAATTTTTAA
1 AATTCAAAAT-ATTTATAAAAATTAAAAAATAATTTTTAA
* *
41204359 AATTGAAAATATTTATAAAAATTAAAAAATATTTTTTAA
1 AATTCAAAATATTTATAAAAATTAAAAAATAATTTTTAA
41204398 A
1 A
41204399 TTAAAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 12 0.34
39 23 0.66
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (39 bp):
AATTCAAAATATTTATAAAAATTAAAAAATAATTTTTAA
Found at i:41204399 original size:19 final size:19
Alignment explanation
Indices: 41204325--41204407 Score: 80
Period size: 19 Copynumber: 4.3 Consensus size: 19
41204315 AAAATAATTC
*
41204325 AAAATAATTTTTAAAAATT-C
1 AAAAT-ATTTTT-AAAATTAA
*
41204345 AAAATAATTTTTAAAATT-G
1 AAAAT-ATTTTTAAAATTAA
*
41204364 AAAATATTTATAAAAATTAA
1 AAAATATTT-TTAAAATTAA
*
41204384 AAAATATTTTTTAAATTAA
1 AAAATATTTTTAAAATTAA
41204403 AAAAT
1 AAAAT
41204408 TGGAATAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.07
19 31 0.55
20 21 0.38
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (19 bp):
AAAATATTTTTAAAATTAA
Found at i:41204400 original size:38 final size:39
Alignment explanation
Indices: 41204320--41204405 Score: 104
Period size: 38 Copynumber: 2.2 Consensus size: 39
41204310 ATTATAAAAT
* * *
41204320 AATTCAAAATAATTTTTAAAAATTCAAAATAATTTTTAA
1 AATTAAAAATAATTTATAAAAATTAAAAATAATTTTTAA
* *
41204359 AATTGAAAAT-ATTTATAAAAATTAAAAA-ATATTTTTTA
1 AATTAAAAATAATTTATAAAAATTAAAAATA-ATTTTTAA
41204397 AATTAAAAA
1 AATTAAAAA
41204406 ATTGGAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 1 0.02
38 31 0.76
39 9 0.22
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (39 bp):
AATTAAAAATAATTTATAAAAATTAAAAATAATTTTTAA
Found at i:41213187 original size:3 final size:3
Alignment explanation
Indices: 41213179--41213210 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41213169 ATTTATTTGT
41213179 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41213211 CTTTTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:41216788 original size:44 final size:44
Alignment explanation
Indices: 41216725--41216812 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
41216715 ATTACATGTA
* * * * * *
41216725 TCGCATCCATTATGAACTCAGACCAATTTAACGAGTTCGGATGC
1 TCGCATCCATAATGAACTCAAACCAACTCAACGAGCTCAGATGC
41216769 TCGCATCCATAATGAACTCAAACCAACTCAACGAGCTCAGATGC
1 TCGCATCCATAATGAACTCAAACCAACTCAACGAGCTCAGATGC
41216813 CTCATATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (44 bp):
TCGCATCCATAATGAACTCAAACCAACTCAACGAGCTCAGATGC
Found at i:41218810 original size:31 final size:31
Alignment explanation
Indices: 41218775--41218836 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
41218765 AATATAAGAC
41218775 TAAATCAACCACAACATGACAATTAAATACA
1 TAAATCAACCACAACATGACAATTAAATACA
41218806 TAAATCAACCACAACATGACAATTAAATACA
1 TAAATCAACCACAACATGACAATTAAATACA
41218837 AATCTCATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.55, C:0.23, G:0.03, T:0.19
Consensus pattern (31 bp):
TAAATCAACCACAACATGACAATTAAATACA
Found at i:41219637 original size:49 final size:48
Alignment explanation
Indices: 41219476--41219750 Score: 222
Period size: 49 Copynumber: 5.7 Consensus size: 48
41219466 AGGGTATGAT
* * * * *
41219476 GTCGATGCCATGTTCCAAACATGGTCTTACACTGACTCTCAC-ATCTAA
1 GTCGATGCCATGTCCCAGACA-GGTCTTACACTGGCTCTCACTATATAG
** * *
41219524 GTTAATGCCATG-CACCAGACAGGTCTTACACTGACT-TCCAC-ACATAAG
1 GTCGATGCCATGTC-CCAGACAGGTCTTACACTGGCTCT-CACTATAT-AG
* * **
41219572 GCCGATGCCATGTCCCAAACAGGTCTTACACTGGCTCTCACTTATATTT
1 GTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCAC-TATATAG
* *
41219621 GTCGATGCCATGTCCCAGACAGGTCTTACACTAGCT-TGCA-TATCTTGAG
1 GTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCT-CACTAT-AT-AG
* * * * *
41219670 GCCGATGCCGTGTCCCAGATAGGTCTTACACTGGCTCTCA-TCTATCG
1 GTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCACTATATAG
*
41219717 GTGCTGATGCCATGTCCCAGATAGGTCTTACACT
1 GT-C-GATGCCATGTCCCAGACAGGTCTTACACT
41219751 AGCACACACA
Statistics
Matches: 184, Mismatches: 30, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
46 1 0.01
47 25 0.14
48 53 0.29
49 101 0.55
50 4 0.02
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (48 bp):
GTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCACTATATAG
Found at i:41219697 original size:98 final size:97
Alignment explanation
Indices: 41219478--41219753 Score: 294
Period size: 98 Copynumber: 2.8 Consensus size: 97
41219468 GGTATGATGT
* * * * ** *
41219478 CGATGCCATGTTCCAAACATGGTCTTACACTGACTCTCACATCTAAGT--TAATGCCATG-CACC
1 CGATGCCATGTCCCAAACA-GGTCTTACACTGGCTCTCATATATCGGTGCTGATGCCATGTC-CC
41219540 AGACAGGTCTTACACT-GACTTCCACACATAAGGC
64 AGACAGGTCTTACACTAG-CTTCCACACATAAGGC
**
41219574 CGATGCCATGTCCCAAACAGGTCTTACACTGGCTCTCACTTATATTTGT-C-GATGCCATGTCCC
1 CGATGCCATGTCCCAAACAGGTCTTACACTGGCTCTCA--TATATCGGTGCTGATGCCATGTCCC
* * * *
41219637 AGACAGGTCTTACACTAGCTTGCATATCTTGAGGC
64 AGACAGGTCTTACACTAGCTTCCACA-CATAAGGC
* * * *
41219672 CGATGCCGTGTCCCAGATAGGTCTTACACTGGCTCTCATCTATCGGTGCTGATGCCATGTCCCAG
1 CGATGCCATGTCCCAAACAGGTCTTACACTGGCTCTCATATATCGGTGCTGATGCCATGTCCCAG
*
41219737 ATAGGTCTTACACTAGC
66 ACAGGTCTTACACTAGC
41219754 ACACACATCA
Statistics
Matches: 154, Mismatches: 18, Indels: 14
0.83 0.10 0.08
Matches are distributed among these distances:
95 18 0.12
96 24 0.16
97 38 0.25
98 74 0.48
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (97 bp):
CGATGCCATGTCCCAAACAGGTCTTACACTGGCTCTCATATATCGGTGCTGATGCCATGTCCCAG
ACAGGTCTTACACTAGCTTCCACACATAAGGC
Found at i:41221795 original size:19 final size:21
Alignment explanation
Indices: 41221771--41221811 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
41221761 AATATGCTGT
41221771 AAAATGAAAG-TT-TTGATAG
1 AAAATGAAAGATTATTGATAG
41221790 AAAATGAAAGATTATTGATAG
1 AAAATGAAAGATTATTGATAG
41221811 A
1 A
41221812 TAAACCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 2 0.10
21 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (21 bp):
AAAATGAAAGATTATTGATAG
Found at i:41222605 original size:33 final size:33
Alignment explanation
Indices: 41222522--41222607 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 33
41222512 GTACATTTTT
**
41222522 TGTGTA-CACTTGAAAAGGTTAGGTATACTTTG
1 TGTGTACCACTTGAAAAGGAAAGGTATACTTTG
* *
41222554 TATATACCA-TATGAAAAGGAAAGGTATACTTTG
1 TGTGTACCACT-TGAAAAGGAAAGGTATACTTTG
*
41222587 TGTGTACCACTTGGAAAGGAA
1 TGTGTACCACTTGAAAAGGAA
41222608 TGCACACCTC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
32 5 0.11
33 38 0.86
34 1 0.02
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.31
Consensus pattern (33 bp):
TGTGTACCACTTGAAAAGGAAAGGTATACTTTG
Found at i:41225850 original size:39 final size:40
Alignment explanation
Indices: 41225805--41226029 Score: 215
Period size: 40 Copynumber: 5.7 Consensus size: 40
41225795 GCTCCTCGTT
* * * * *
41225805 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
*
41225845 C-AATGCCTTCGGGACTTAACCCGGATTTAATGACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* *
41225884 CGAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * * * *
41225924 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAATAACTCGCA
** * * * *
41225964 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCA
*
41226005 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
41226030 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
39 37 0.24
40 104 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Found at i:41226038 original size:41 final size:41
Alignment explanation
Indices: 41225961--41226038 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41225951 CTTGTATCTC
* * *
41225961 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41226002 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41226039 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41227016 original size:11 final size:12
Alignment explanation
Indices: 41226991--41227023 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
41226981 ATTTTTGGCC
41226991 AAGGATGAACCA
1 AAGGATGAACCA
*
41227003 AAGGATGAA-GA
1 AAGGATGAACCA
41227014 AAGGATGAAC
1 AAGGATGAAC
41227024 AAAAATTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.52, C:0.09, G:0.30, T:0.09
Consensus pattern (12 bp):
AAGGATGAACCA
Found at i:41233416 original size:40 final size:38
Alignment explanation
Indices: 41233322--41233544 Score: 182
Period size: 40 Copynumber: 5.6 Consensus size: 38
41233312 TCCTCGTTCA
* ** * * *
41233322 AATGCCTTCGGGACATAGTCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAAT-ACTCGCAC
41233361 AATGCCTTCGGGACTTAACCCGGATTTAATGACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAAT-ACTCGCAC
41233400 GAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATA-CTCGCAC
* *
41233440 AAAGGCCTTCGGGGCTTAACCCGGAACTTGT-AT-CTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-A-TT-TAATACTCGCAC
** * * *
41233480 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAAT-AC-TCGCAC
* *
41233521 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41233545 CAGCATTCAA
Statistics
Matches: 154, Mismatches: 19, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
37 1 0.01
38 2 0.01
39 36 0.23
40 101 0.66
41 9 0.06
42 4 0.03
43 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (38 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATACTCGCAC
Found at i:41233553 original size:41 final size:41
Alignment explanation
Indices: 41233476--41233553 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41233466 CTTGTATCTC
* * *
41233476 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41233517 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41233554 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41240659 original size:49 final size:47
Alignment explanation
Indices: 41240409--41240731 Score: 171
Period size: 49 Copynumber: 6.8 Consensus size: 47
41240399 GTACGATGCC
* * * * * *
41240409 GATGCCATGTTCCAAACATGGTCTTACACTGGCTC-TCAAATCTAAGTTA
1 GATGCCATGTCCCAAACA-GGTCTTACACTAGCTCAT-ATATCGACG-CA
* * * * ** * *
41240458 -ATGCCATGTCCTAGACAGGTTTTACACTAACTTCCATACGTCGAGGCT
1 GATGCCATGTCCCAAACAGGTCTTACACTAGC-T-CATATATCGACGCA
* * * * *
41240506 GATGCCATGTCTCAGACAGGTCTTACACTGGCTC-TCACTTATCTATGTC-
1 GATGCCATGTCCCAAACAGGTCTTACACTAGCTCAT-A--TATCGACG-CA
* * * *
41240555 GATGCCATGTCCCAGACAGGTCTTACACTGGCACACCT-TA-AG-C-CA
1 GATGCCATGTCCCAAACAGGTCTTACACTAGCTCA--TATATCGACGCA
* * *
41240600 -ATGCCATGTCCCAAACATGTCTTACACTAGCTTGCATATCTTGACGCA
1 GATGCCATGTCCCAAACAGGTCTTACACTAGC-T-CATATATCGACGCA
* * * *
41240648 GATGCCGTGTCCCAAACAGGTCTTACACT-GACTCATCTATCGATGCC
1 GATGCCATGTCCCAAACAGGTCTTACACTAG-CTCATATATCGACGCA
*
41240695 GATGCCATGTCCCAAACAGGTCTTACACTAGCACATA
1 GATGCCATGTCCCAAACAGGTCTTACACTAGCTCATA
41240732 CATCACCCAA
Statistics
Matches: 211, Mismatches: 42, Indels: 44
0.71 0.14 0.15
Matches are distributed among these distances:
44 30 0.14
45 1 0.00
46 4 0.02
47 55 0.26
48 23 0.11
49 95 0.45
50 2 0.01
52 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (47 bp):
GATGCCATGTCCCAAACAGGTCTTACACTAGCTCATATATCGACGCA
Found at i:41241773 original size:180 final size:178
Alignment explanation
Indices: 41241458--41241816 Score: 664
Period size: 180 Copynumber: 2.0 Consensus size: 178
41241448 ACCACCAAAA
* *
41241458 TCACTTACTTGCAAGGGTGAAGAGTTGCTAAAATTTCAAGCTTTCAAAACCCTTATTTTGGTAAA
1 TCACTTACTTGCAAGGGTGAAGAGTTGCTAAAATTTCAAGCTTCCAAAACCCTTATTTTGCTAAA
*
41241523 AATTGGTGGAGAGGAGGAAAATGAAAGGTGATATCCTTTTCTCTTTATTTTATTTTATTTCAAGT
66 AATTGGTGGAGAGAAGGAAAATGAAAGGTGATATCCTTTTCTCTTTATTTTATTTTATTTCAAGT
41241588 CAAATTAGTCACCAAATTTCAGCTAACCTTTGACCATTTCATTTTCTT
131 CAAATTAGTCACCAAATTTCAGCTAACCTTTGACCATTTCATTTTCTT
*
41241636 TCACTTACTTGCAAGGGTGAAGAGTTGCTGAAATTTCAAGCTTCCAAAACCCTTATTTTGCTAAA
1 TCACTTACTTGCAAGGGTGAAGAGTTGCTAAAATTTCAAGCTTCCAAAACCCTTATTTTGCTAAA
41241701 AATTTCGGTGGAGAGAAGGAAAATGAAAGGTGATATCCTTTTCTCTTTATTTTATTTTATTTCAA
66 AA-TT-GGTGGAGAGAAGGAAAATGAAAGGTGATATCCTTTTCTCTTTATTTTATTTTATTTCAA
41241766 GTCAAATTAGTCACCAAATTTCAGCTAACCTTTGACCATTTCATTTTCTT
129 GTCAAATTAGTCACCAAATTTCAGCTAACCTTTGACCATTTCATTTTCTT
41241816 T
1 T
41241817 ATCTCTATGG
Statistics
Matches: 175, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
178 64 0.37
179 2 0.01
180 109 0.62
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (178 bp):
TCACTTACTTGCAAGGGTGAAGAGTTGCTAAAATTTCAAGCTTCCAAAACCCTTATTTTGCTAAA
AATTGGTGGAGAGAAGGAAAATGAAAGGTGATATCCTTTTCTCTTTATTTTATTTTATTTCAAGT
CAAATTAGTCACCAAATTTCAGCTAACCTTTGACCATTTCATTTTCTT
Found at i:41244240 original size:24 final size:25
Alignment explanation
Indices: 41244207--41244272 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 25
41244197 ACGAGTTGAC
*
41244207 ATATGGCACTATGTGTGCG-GTTTA
1 ATATGGCACTATGTGTGCGAGTATA
* *
41244231 CTATGGCACTATGTATGCGAGTATA
1 ATATGGCACTATGTGTGCGAGTATA
*
41244256 AT-TAGCACTATGTGTGC
1 ATATGGCACTATGTGTGC
41244273 AAATTTGGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 30 0.86
25 5 0.14
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (25 bp):
ATATGGCACTATGTGTGCGAGTATA
Found at i:41246773 original size:10 final size:9
Alignment explanation
Indices: 41246737--41246859 Score: 76
Period size: 10 Copynumber: 13.4 Consensus size: 9
41246727 ATTTTATTTG
41246737 AAAATTA-A
1 AAAATTATA
41246745 AATAATTATA
1 AA-AATTATA
*
41246755 TAAATTTATA
1 -AAAATTATA
41246765 AAAACTTATA
1 AAAA-TTATA
*
41246775 AAAATTCTAAA
1 AAAA-T-TATA
*
41246786 AAAATTCTA
1 AAAATTATA
41246795 ATAAATTATAA
1 A-AAATTAT-A
*
41246806 AAAAATATA
1 AAAATTATA
*
41246815 AATATTA-A
1 AAAATTATA
41246823 AAAATTAT-
1 AAAATTATA
*
41246831 -AAATTATT
1 AAAATTATA
*
41246839 AATA-TATA
1 AAAATTATA
*
41246847 TAAATTATA
1 AAAATTATA
41246856 AAAA
1 AAAA
41246860 AATCATTTAT
Statistics
Matches: 88, Mismatches: 16, Indels: 21
0.70 0.13 0.17
Matches are distributed among these distances:
7 7 0.08
8 14 0.16
9 26 0.30
10 30 0.34
11 11 0.12
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATTATA
Found at i:41246788 original size:11 final size:11
Alignment explanation
Indices: 41246774--41246811 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
41246764 AAAAACTTAT
41246774 AAAAATTCTAA
1 AAAAATTCTAA
41246785 AAAAATTCT-A
1 AAAAATTCTAA
* *
41246795 ATAAATTATAA
1 AAAAATTCTAA
41246806 AAAAAT
1 AAAAAT
41246812 ATAAATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAAATTCTAA
Found at i:41246817 original size:17 final size:17
Alignment explanation
Indices: 41246795--41246862 Score: 84
Period size: 17 Copynumber: 4.0 Consensus size: 17
41246785 AAAAATTCTA
41246795 ATAAATTATAAAAAAAT
1 ATAAATTATAAAAAAAT
*
41246812 ATAAA-TATTAAAAAATT
1 ATAAATTA-TAAAAAAAT
* * *
41246829 ATAAATTATTAATATAT
1 ATAAATTATAAAAAAAT
41246846 ATAAATTATAAAAAAAT
1 ATAAATTATAAAAAAAT
41246863 CATTTATTGA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 2 0.05
17 37 0.90
18 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAAATTATAAAAAAAT
Found at i:41246837 original size:34 final size:35
Alignment explanation
Indices: 41246753--41246862 Score: 96
Period size: 34 Copynumber: 3.0 Consensus size: 35
41246743 AAAATAATTA
* * *
41246753 TATAAATTTATAAAAACTTATAAAAATTCTAAAAAAATT
1 TATAAA-TTATAAAAA--AATATAAATTATAAAAAAA-T
*
41246792 CTAATAAATTATAAAAAAATATAAA-TATTAAAAAAT
1 -T-ATAAATTATAAAAAAATATAAATTATAAAAAAAT
* * *
41246828 TATAAATTATTAATATATATAAATTATAAAAAAAT
1 TATAAATTATAAAAAAATATAAATTATAAAAAAAT
41246863 CATTTATTGA
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
34 19 0.32
35 11 0.18
36 1 0.02
37 8 0.13
38 6 0.10
40 10 0.17
41 5 0.08
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (35 bp):
TATAAATTATAAAAAAATATAAATTATAAAAAAAT
Found at i:41247323 original size:11 final size:10
Alignment explanation
Indices: 41247298--41247339 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
41247288 AATTTATTAG
*
41247298 AATTTCTATA
1 AATTTTTATA
41247308 AATTTTTATGA
1 AATTTTTAT-A
41247319 AATTTTTA-A
1 AATTTTTATA
41247328 TAATTTTTATA
1 -AATTTTTATA
41247339 A
1 A
41247340 GTTCATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
9 1 0.04
10 17 0.61
11 10 0.36
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (10 bp):
AATTTTTATA
Found at i:41247323 original size:21 final size:21
Alignment explanation
Indices: 41247286--41247337 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
41247276 GATAAATTTG
41247286 ATAATTTATTA-G-AATTTCT-
1 ATAATTT-TTATGAAATTTCTA
*
41247305 ATAAATTTTTATGAAATTTTTA
1 AT-AATTTTTATGAAATTTCTA
41247327 ATAATTTTTAT
1 ATAATTTTTAT
41247338 AAGTTCATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.18
20 6 0.21
21 15 0.54
22 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (21 bp):
ATAATTTTTATGAAATTTCTA
Found at i:41253617 original size:22 final size:22
Alignment explanation
Indices: 41253570--41253617 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
41253560 GAAGCAAAGG
*
41253570 GACAAAGGCGTGCCAACAAGCC
1 GACAAAGGCGTGCCAACAAGCA
*
41253592 GACAAAGGCGTGCCAACAGGCA
1 GACAAAGGCGTGCCAACAAGCA
41253614 GACA
1 GACA
41253618 GGAATAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.29, G:0.29, T:0.04
Consensus pattern (22 bp):
GACAAAGGCGTGCCAACAAGCA
Done.