Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 376 of 433
Found at i:117680762 original size:40 final size:39
Alignment explanation
Indices: 117680647--117680766 Score: 120
Period size: 40 Copynumber: 3.1 Consensus size: 39
117680637 AAACATTGGA
* *
117680647 TGTCAATTTACTACTTCGGATTTATTCAATGAGGCATTGGG
1 TGTCAATTTACTACTTC-GATTTA-TCGATGAGGCACTGGG
* * * *
117680688 TGTCAA-TT--TACTTCGGTTTAATCGATTAGACACTGTG
1 TGTCAATTTACTACTTCGATTT-ATCGATGAGGCACTGGG
*
117680725 TGTCAATTTACTACTTCGAATTATCCGATGAGGCACTGGG
1 TGTCAATTTACTACTTCGATTTAT-CGATGAGGCACTGGG
117680765 TG
1 TG
117680767 CCAAACTAGT
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
37 21 0.33
38 9 0.14
39 2 0.03
40 25 0.40
41 6 0.10
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.38
Consensus pattern (39 bp):
TGTCAATTTACTACTTCGATTTATCGATGAGGCACTGGG
Found at i:117683944 original size:18 final size:19
Alignment explanation
Indices: 117683904--117683947 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
117683894 ATACATTATT
*
117683904 TTTTTAATAGTTTTACAAC
1 TTTTTAATAGTTTTACAAA
117683923 TTTTTAATA-TTTTA-ATAA
1 TTTTTAATAGTTTTACA-AA
117683941 TTTTTAA
1 TTTTTAA
117683948 ACTTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 13 0.57
19 9 0.39
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTTAATAGTTTTACAAA
Found at i:117683944 original size:27 final size:28
Alignment explanation
Indices: 117683905--117683973 Score: 90
Period size: 27 Copynumber: 2.5 Consensus size: 28
117683895 TACATTATTT
*
117683905 TTTTAAT-AGTTTTACAACTTTTT-AATA
1 TTTTAATAATTTTTA-AACTTTTTAAATA
117683932 TTTTAATAATTTTTAAACTTTTTAAATA
1 TTTTAATAATTTTTAAACTTTTTAAATA
*
117683960 TTTT-ACAATTTTTA
1 TTTTAATAATTTTTA
117683974 TAATTTTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (28 bp):
TTTTAATAATTTTTAAACTTTTTAAATA
Found at i:117683954 original size:19 final size:18
Alignment explanation
Indices: 117683931--117683980 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
117683921 ACTTTTTAAT
*
117683931 ATTTTAATAATTTTTA-A
1 ATTTTTATAATTTTTACA
117683948 ACTTTTTA-AATATTTTACA
1 A-TTTTTATAAT-TTTTACA
117683967 ATTTTTATAATTTT
1 ATTTTTATAATTTT
117683981 ATAAGTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 4 0.14
18 19 0.68
19 5 0.18
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTATAATTTTTACA
Found at i:117683978 original size:9 final size:9
Alignment explanation
Indices: 117683931--117683989 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
117683921 ACTTTTTAAT
*
117683931 ATTTTAATA
1 ATTTTTATA
117683940 ATTTTTA-A
1 ATTTTTATA
117683948 ACTTTTTA-A
1 A-TTTTTATA
*
117683957 ATATTTTACA
1 AT-TTTTATA
117683967 ATTTTTATA
1 ATTTTTATA
117683976 A-TTTTATA
1 ATTTTTATA
117683984 AGTTTT
1 A-TTTT
117683990 GTTTTACATT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
8 11 0.26
9 26 0.60
10 6 0.14
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (9 bp):
ATTTTTATA
Found at i:117684062 original size:15 final size:16
Alignment explanation
Indices: 117684036--117684065 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
117684026 TGTTTCTTTT
117684036 TATTTATTGTAATTTG
1 TATTTATTGTAATTTG
117684052 TATTT-TTGTAATTT
1 TATTTATTGTAATTT
117684066 TTATGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (16 bp):
TATTTATTGTAATTTG
Found at i:117685248 original size:20 final size:19
Alignment explanation
Indices: 117685225--117685265 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
117685215 AATACAACAC
117685225 TATTGCAATCAATTCTCTTT
1 TATT-CAATCAATTCTCTTT
**
117685245 TATTCTTTCAATTCTCTTT
1 TATTCAATCAATTCTCTTT
117685264 TA
1 TA
117685266 GTTTGTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.22, C:0.20, G:0.02, T:0.56
Consensus pattern (19 bp):
TATTCAATCAATTCTCTTT
Found at i:117688610 original size:42 final size:41
Alignment explanation
Indices: 117688488--117688637 Score: 183
Period size: 42 Copynumber: 3.6 Consensus size: 41
117688478 ATACCAATGC
* * *
117688488 CATATCCCAGATATGGTCTTACATGCAATCTCGTATCGATGC
1 CATATCCCAGATATGGTCTTACATG-AATCTCATATTGATGT
* * * *
117688530 CAATAGCCCAGCTATGGTCTTACACGAAATCTCTTATTGATGT
1 C-ATATCCCAGATATGGTCTTACATG-AATCTCATATTGATGT
* *
117688573 CATATCCTAAATATGGTCTTACATGAAGTCTCATATTGATGT
1 CATATCCCAGATATGGTCTTACATGAA-TCTCATATTGATGT
117688615 CATATCCCAGATATGGTCTTACA
1 CATATCCCAGATATGGTCTTACA
117688638 CATAGACTTA
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
41 2 0.02
42 54 0.59
43 35 0.38
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (41 bp):
CATATCCCAGATATGGTCTTACATGAATCTCATATTGATGT
Found at i:117690097 original size:12 final size:12
Alignment explanation
Indices: 117690082--117690125 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
117690072 GGGTAGATTC
117690082 TTGGGCAGTCTG
1 TTGGGCAGTCTG
**
117690094 TTGGGTCA-AATG
1 TTGGG-CAGTCTG
117690106 TTGGGCAGTCTG
1 TTGGGCAGTCTG
117690118 TTGGGCAG
1 TTGGGCAG
117690126 AATAATGGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.14, C:0.14, G:0.41, T:0.32
Consensus pattern (12 bp):
TTGGGCAGTCTG
Found at i:117690134 original size:24 final size:24
Alignment explanation
Indices: 117690083--117690135 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
117690073 GGTAGATTCT
**
117690083 TGGGCAGTCTGTTGGGTCAAATGT
1 TGGGCAGTCTGTTGGGTCAAATAA
117690107 TGGGCAGTCTGTTGGG-CAGAATAA
1 TGGGCAGTCTGTTGGGTCA-AATAA
117690131 TGGGC
1 TGGGC
117690136 CGCATAGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.19, C:0.13, G:0.40, T:0.28
Consensus pattern (24 bp):
TGGGCAGTCTGTTGGGTCAAATAA
Found at i:117691340 original size:39 final size:39
Alignment explanation
Indices: 117691297--117691412 Score: 205
Period size: 39 Copynumber: 3.0 Consensus size: 39
117691287 CCTGACATAT
* * *
117691297 TTCCAGCACGTAGCCTGCGGACCTTAAGTCTGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
117691336 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
117691375 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATA
117691413 CATCACTGAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
Found at i:117691342 original size:78 final size:78
Alignment explanation
Indices: 117691249--117691412 Score: 190
Period size: 78 Copynumber: 2.1 Consensus size: 78
117691239 GAATTTAAAC
* * * * * *
117691249 CCGG-TATAATACCAGCTCGA-AGCCTGCGGGA-CTTTAGCCCTGACATATTTCCAGCACGTAGC
1 CCGGATATAATACCAGCAC-ATAGCCTGC-GGACCCTAAGCCCGGACATAATTCCAGCACATAGC
*
117691311 CTGCGGACCTTAAGT
64 CTGCGGACCCTAAGT
* * * *
117691326 CTGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAATTCCAGCACATAGCCT
1 CCGGATATAATACCAGCACATAGCCTGCGGACCCTAAGCCCGGACATAATTCCAGCACATAGCCT
117691391 GCGGACCCTAAGT
66 GCGGACCCTAAGT
117691404 CCGGATATA
1 CCGGATATA
117691413 CATCACTGAA
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
77 7 0.10
78 65 0.90
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (78 bp):
CCGGATATAATACCAGCACATAGCCTGCGGACCCTAAGCCCGGACATAATTCCAGCACATAGCCT
GCGGACCCTAAGT
Found at i:117704563 original size:2 final size:2
Alignment explanation
Indices: 117704556--117704582 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
117704546 TGTTATCATT
117704556 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
117704583 CATAAACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:117707618 original size:49 final size:50
Alignment explanation
Indices: 117707540--117707734 Score: 187
Period size: 50 Copynumber: 3.9 Consensus size: 50
117707530 AGCCGAAGCT
* *
117707540 ATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAAC
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCACAAC
* * * * * *
117707588 AGTCTGGTACACGTAGTAGCCTGCATTTAGTACTACGCACGTGACCTCACC
1 A-TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCACAAC
** * * * * *
117707639 ATCTAATACACGTAGTAGCTTGCACTTAGTACTACACACGTGATCACAATT
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCACAA-C
* * * *
117707690 TTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC
117707735 TCACAATAGA
Statistics
Matches: 117, Mismatches: 26, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
48 1 0.01
49 36 0.31
50 41 0.35
51 39 0.33
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (50 bp):
ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCACAAC
Found at i:117707735 original size:101 final size:99
Alignment explanation
Indices: 117707552--117707738 Score: 239
Period size: 101 Copynumber: 1.9 Consensus size: 99
117707542 CTGGTACGCA
* * * *
117707552 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACGTAGTAGCCTGCATTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTGCACTTA
* *
117707617 GTACTACGCACGTGACCTCACCATCTAATACACG
66 GTACTACACACGCGACCTCACCATCTAATACACG
* * *** *
117707651 TAGTAGCTTGCACTTAGTACTACACACGTGATCACAATTTTCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-C-CAACAGTCGGGTACACATAGTAGCCTGCACT
*
117707716 TAGTACTACACATGCGACCTCAC
64 TAGTACTACACACGCGACCTCAC
117707739 AATAGATCAT
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
99 28 0.38
100 1 0.01
101 44 0.60
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTCACCATCTAATACACG
Found at i:117708379 original size:2 final size:2
Alignment explanation
Indices: 117708372--117708402 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
117708362 GAGACTAGTC
117708372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
117708403 CATGTCATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:117709358 original size:24 final size:24
Alignment explanation
Indices: 117709320--117709369 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
117709310 ATAACCTTAC
117709320 CACATCCTGGTCACTTAATTCATTCA
1 CACATCCTGGTCACTT-ATTCA-TCA
117709346 CACATCCT-G-CACTTATTCATCA
1 CACATCCTGGTCACTTATTCATCA
117709368 CA
1 CA
117709370 AAACTCACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.21
23 5 0.21
24 5 0.21
25 1 0.04
26 8 0.33
ACGTcount: A:0.28, C:0.34, G:0.06, T:0.32
Consensus pattern (24 bp):
CACATCCTGGTCACTTATTCATCA
Found at i:117719936 original size:12 final size:13
Alignment explanation
Indices: 117719919--117719952 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
117719909 GTCCATATTT
*
117719919 AAAAAAGGAAAA-
1 AAAAAAGAAAAAG
117719931 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
117719944 AAAAAAGAA
1 AAAAAAGAA
117719953 GAAGGCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:117720316 original size:24 final size:22
Alignment explanation
Indices: 117720275--117720334 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 22
117720265 TGTGTCTGTG
* * *
117720275 TTTTTAAATCTTTGTATTTTAAT
1 TTTTTACATATTT-TATTCTAAT
117720298 TGTTTTACATTATTTTATTCTAAT
1 T-TTTTACA-TATTTTATTCTAAT
*
117720322 TTTTTTCATATTT
1 TTTTTACATATTT
117720335 ATATGAAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 5 0.16
23 7 0.23
24 15 0.48
25 4 0.13
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (22 bp):
TTTTTACATATTTTATTCTAAT
Found at i:117720566 original size:9 final size:9
Alignment explanation
Indices: 117720525--117720560 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
117720515 AAAAAATTTT
*
117720525 ATTTACAAA
1 ATTTAAAAA
117720534 ATTTAAAAA
1 ATTTAAAAA
117720543 ATTTAAAAA
1 ATTTAAAAA
117720552 ATTTAAAAA
1 ATTTAAAAA
117720561 TATTAACTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (9 bp):
ATTTAAAAA
Found at i:117729753 original size:40 final size:40
Alignment explanation
Indices: 117729668--117729799 Score: 158
Period size: 40 Copynumber: 3.2 Consensus size: 40
117729658 TTTTGAGCCT
* *
117729668 TCGAGGCATTAGCGGCACTTTTTCAAGAAATGCCGCTATAGA
1 TCGA-GCATTAGCGGCGCTTTTTCAA-AAACGCCGCTATAGA
* * *
117729710 TCGAG-ATTTAGCGGTGCTTTTTTAAAAACGCCGCTATATA
1 TCGAGCA-TTAGCGGCGCTTTTTCAAAAACGCCGCTATAGA
* *
117729750 TCGAGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGG
1 TCGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTATAGA
*
117729790 TCTAGCATTA
1 TCGAGCATTA
117729800 TGGCATTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
40 57 0.73
41 17 0.22
42 4 0.05
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (40 bp):
TCGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTATAGA
Found at i:117729822 original size:39 final size:39
Alignment explanation
Indices: 117729668--117729815 Score: 140
Period size: 40 Copynumber: 3.7 Consensus size: 39
117729658 TTTTGAGCCT
* *
117729668 TCGAGGCATTAGCGGCACTTTTTCAAGAAATGCCGCTATAGA
1 TCGA-GCATTAGCGGCA-TTTTTTAA-AAACGCCGCTATAGA
*
117729710 TCGAG-ATTTAGCGGTGC-TTTTTTAAAAACGCCGCTATATA
1 TCGAGCA-TTAGC-G-GCATTTTTTAAAAACGCCGCTATAGA
* * *
117729750 TCGAGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGG
1 TCGAGCATTAGCGGC-ATTTTTTAAAAACGCCGCTATAGA
* *
117729790 TCTAGCATTA-TGGCATTTTTTAAAAA
1 TCGAGCATTAGCGGCATTTTTTAAAAA
117729816 ATGCCGCAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
38 12 0.13
39 4 0.04
40 53 0.59
41 14 0.16
42 5 0.06
43 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (39 bp):
TCGAGCATTAGCGGCATTTTTTAAAAACGCCGCTATAGA
Found at i:117731501 original size:93 final size:93
Alignment explanation
Indices: 117731388--117731558 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
117731378 GCCCTTAAGT
*
117731388 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
117731453 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * * *
117731481 GAACTCGGACTCAGCTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
117731546 CGAGTTCGGATGC
66 CGAGTTCGGATGC
117731559 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:117731555 original size:46 final size:46
Alignment explanation
Indices: 117731383--117731555 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
117731373 AACCCGCCCT
* * *
117731383 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
117731429 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* * *
117731477 TCA-CGAACTCGGACTCAGCTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
117731522 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
117731556 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 59 0.56
47 28 0.26
48 2 0.02
49 2 0.02
50 5 0.05
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:117732012 original size:30 final size:30
Alignment explanation
Indices: 117731978--117732037 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
117731968 ATTTAATACG
117731978 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
117732008 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
117732038 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:117733025 original size:22 final size:22
Alignment explanation
Indices: 117732995--117733042 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
117732985 GAGTTAATAT
* *
117732995 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGTTTAAGGATTAGGGG
* *
117733017 TTTAGGGTTTAAGGTTTAGGGG
1 TTTAAGGTTTAAGGATTAGGGG
117733039 TTTA
1 TTTA
117733043 TATTTTATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (22 bp):
TTTAAGGTTTAAGGATTAGGGG
Found at i:117733065 original size:66 final size:68
Alignment explanation
Indices: 117732949--117733081 Score: 218
Period size: 66 Copynumber: 2.0 Consensus size: 68
117732939 AGGTTTATGA
*
117732949 TTTAGGGTATATGGTTTAGGGTTTATAGTTTATGATGAGTTAATATTTTAAGGTTTATGGATTAT
1 TTTAGGGTATAAGGTTTAGGGTTTATAGTTTATGATGAGTTAATATTTTAAGGTTTATGGATTAT
117733014 GGG
66 GGG
*
117733017 TTTAGGGTTTAAGGTTTAGGGGTTTATA-TTT-T-ATGAGTTAATATTTTAAGGTTTATGGATTA
1 TTTAGGGTATAAGGTTTA-GGGTTTATAGTTTATGATGAGTTAATATTTTAAGGTTTATGGATTA
117733079 TGG
65 TGG
117733082 ATTATGGATT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
66 33 0.53
67 1 0.02
68 19 0.31
69 9 0.15
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (68 bp):
TTTAGGGTATAAGGTTTAGGGTTTATAGTTTATGATGAGTTAATATTTTAAGGTTTATGGATTAT
GGG
Found at i:117733093 original size:22 final size:22
Alignment explanation
Indices: 117733068--117733110 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
117733058 TATTTTAAGG
*
117733068 TTTATGGATTATGGATTATGGA
1 TTTAGGGATTATGGATTATGGA
*
117733090 TTTAGGGATTATGGTTTATGG
1 TTTAGGGATTATGGATTATGG
117733111 TTCAAGGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (22 bp):
TTTAGGGATTATGGATTATGGA
Found at i:117733111 original size:7 final size:7
Alignment explanation
Indices: 117732929--117733134 Score: 72
Period size: 7 Copynumber: 28.3 Consensus size: 7
117732919 TTAATTATCA
*
117732929 TTATAGT
1 TTATGGT
*
117732936 TTAAGGT
1 TTATGGT
*
117732943 TTATGAT
1 TTATGGT
*
117732950 TTAGGGT
1 TTATGGT
*
117732957 ATATGGT
1 TTATGGT
*
117732964 TTAGGGT
1 TTATGGT
*
117732971 TTATAGTT
1 TTAT-GGT
117732979 TATGATGAGT
1 T-T-ATG-GT
* **
117732989 TAATATT
1 TTATGGT
*
117732996 TTAAGGT
1 TTATGGT
*
117733003 TTATGGA
1 TTATGGT
117733010 TTATGGGT
1 TTAT-GGT
*
117733018 TTAGGGT
1 TTATGGT
*
117733025 TTAAGGT
1 TTATGGT
*
117733032 TTAGGGGT
1 TTA-TGGT
**
117733040 TTATATT
1 TTATGGT
117733047 TTATGAGT
1 TTATG-GT
* **
117733055 TAATATT
1 TTATGGT
*
117733062 TTAAGGT
1 TTATGGT
*
117733069 TTATGGA
1 TTATGGT
*
117733076 TTATGGA
1 TTATGGT
117733083 TTATGGAT
1 TTATGG-T
* *
117733091 TTAGGGA
1 TTATGGT
117733098 TTATGGT
1 TTATGGT
117733105 TTATGGT
1 TTATGGT
* *
117733112 TCAAGGGT
1 T-TATGGT
*
117733120 TGA-GGT
1 TTATGGT
117733126 TTATGGT
1 TTATGGT
117733133 TT
1 TT
117733135 TAGGATTTAT
Statistics
Matches: 140, Mismatches: 49, Indels: 20
0.67 0.23 0.10
Matches are distributed among these distances:
6 5 0.04
7 99 0.71
8 30 0.21
9 2 0.01
10 4 0.03
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (7 bp):
TTATGGT
Found at i:117733118 original size:22 final size:21
Alignment explanation
Indices: 117733073--117733133 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
117733063 TAAGGTTTAT
* *
117733073 GGATTATGGATTATGGATTTAG
1 GGATTATGGTTTATGG-TTAAG
117733095 GGATTATGGTTTATGGTTCAAG
1 GGATTATGGTTTATGGTT-AAG
117733117 GG-TTGA-GGTTTATGGTT
1 GGATT-ATGGTTTATGGTT
117733134 TTAGGATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 15 0.43
22 20 0.57
ACGTcount: A:0.21, C:0.02, G:0.34, T:0.43
Consensus pattern (21 bp):
GGATTATGGTTTATGGTTAAG
Found at i:117733175 original size:7 final size:7
Alignment explanation
Indices: 117733090--117733203 Score: 50
Period size: 7 Copynumber: 15.6 Consensus size: 7
117733080 GGATTATGGA
117733090 TTTAGGG
1 TTTAGGG
* *
117733097 ATTATGG
1 TTTAGGG
*
117733104 TTTATGG
1 TTTAGGG
*
117733111 TTCAAGGG
1 TT-TAGGG
*
117733119 TTGA-GG
1 TTTAGGG
*
117733125 TTTATGGT
1 TTTA-GGG
*
117733133 TTTAGGA
1 TTTAGGG
* *
117733140 TTTATGA
1 TTTAGGG
117733147 TTTAGGGG
1 TTTA-GGG
* *
117733155 TTAAGAG
1 TTTAGGG
*
117733162 TTAAGGG
1 TTTAGGG
117733169 TTTAGGGG
1 TTTA-GGG
117733177 TTTAGGG
1 TTTAGGG
*
117733184 GTTAGGGG
1 TTTA-GGG
117733192 TTTAGGGG
1 TTTA-GGG
117733200 TTTA
1 TTTA
117733204 AGGGGCATTG
Statistics
Matches: 83, Mismatches: 18, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
6 5 0.06
7 43 0.52
8 35 0.42
ACGTcount: A:0.20, C:0.01, G:0.38, T:0.41
Consensus pattern (7 bp):
TTTAGGG
Found at i:117733179 original size:8 final size:8
Alignment explanation
Indices: 117733166--117733294 Score: 81
Period size: 8 Copynumber: 16.1 Consensus size: 8
117733156 TAAGAGTTAA
117733166 GGGTTTAG
1 GGGTTTAG
117733174 GGGTTTAG
1 GGGTTTAG
117733182 GGG-TTAG
1 GGGTTTAG
117733189 GGGTTTAG
1 GGGTTTAG
117733197 GGGTTTAAG
1 GGGTTT-AG
117733206 GGGCATTGGTTAG
1 GGG---T--TTAG
*
117733219 GAGTTTAG
1 GGGTTTAG
*
117733227 GGG-TTAA
1 GGGTTTAG
*
117733234 GGGTTAAG
1 GGGTTTAG
* *
117733242 GGG--CAT
1 GGGTTTAG
117733248 GGG-TTAG
1 GGGTTTAG
117733255 GGG-TTAG
1 GGGTTTAG
117733262 GGGTTTAG
1 GGGTTTAG
*
117733270 GGGTTAAG
1 GGGTTTAG
** *
117733278 GCATTAAG
1 GGGTTTAG
117733286 GGGTTTAG
1 GGGTTTAG
117733294 G
1 G
117733295 ATAATTAGTG
Statistics
Matches: 96, Mismatches: 15, Indels: 20
0.73 0.11 0.15
Matches are distributed among these distances:
6 4 0.04
7 24 0.25
8 55 0.57
9 5 0.05
10 1 0.01
12 1 0.01
13 4 0.04
14 2 0.02
ACGTcount: A:0.19, C:0.02, G:0.48, T:0.31
Consensus pattern (8 bp):
GGGTTTAG
Found at i:117733183 original size:15 final size:15
Alignment explanation
Indices: 117733165--117733294 Score: 77
Period size: 15 Copynumber: 8.2 Consensus size: 15
117733155 TTAAGAGTTA
117733165 AGGGTTTAGGGGTTT
1 AGGGTTTAGGGGTTT
*
117733180 AGGGGTTAGGGGTTT
1 AGGGTTTAGGGGTTT
117733195 AGGGGTTTAAGGGGCATTGGTT
1 A-GGGTTT-AGGGG---T--TT
*
117733217 AGGAGTTTAGGGGTTA
1 AGG-GTTTAGGGGTTT
* **
117733233 AGGGTTAAGGGGCAT
1 AGGGTTTAGGGGTTT
117733248 -GGG-TTAGGGG-TT
1 AGGGTTTAGGGGTTT
*
117733260 AGGGGTTTAGGGGTTA
1 A-GGGTTTAGGGGTTT
* *
117733276 AGGCATTAAGGGGTTT
1 AGG-GTTTAGGGGTTT
117733292 AGG
1 AGG
117733295 ATAATTAGTG
Statistics
Matches: 89, Mismatches: 13, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
12 1 0.01
13 6 0.07
14 6 0.07
15 32 0.36
16 23 0.26
17 5 0.06
18 1 0.01
20 1 0.01
21 7 0.08
22 7 0.08
ACGTcount: A:0.19, C:0.02, G:0.48, T:0.31
Consensus pattern (15 bp):
AGGGTTTAGGGGTTT
Found at i:117733246 original size:36 final size:36
Alignment explanation
Indices: 117733178--117733278 Score: 150
Period size: 36 Copynumber: 2.8 Consensus size: 36
117733168 GTTTAGGGGT
*
117733178 TTAGGGGTTAGGGGTTTAGGGGTTTAAGGGGCATTGG
1 TTAGGGGTTAGGGGTTTAGGGG-TTAAGGGGCATGGG
* *
117733215 TTAGGAGTTTAGGGG-TTAAGGGTTAAGGGGCATGGG
1 TTAGG-GGTTAGGGGTTTAGGGGTTAAGGGGCATGGG
117733251 TTAGGGGTTAGGGGTTTAGGGGTTAAGG
1 TTAGGGGTTAGGGGTTTAGGGGTTAAGG
117733279 CATTAAGGGG
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
35 8 0.14
36 30 0.53
37 11 0.19
38 8 0.14
ACGTcount: A:0.19, C:0.02, G:0.49, T:0.31
Consensus pattern (36 bp):
TTAGGGGTTAGGGGTTTAGGGGTTAAGGGGCATGGG
Found at i:117733414 original size:17 final size:17
Alignment explanation
Indices: 117733394--117733438 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
117733384 AATTTATATA
117733394 TTAAATAATTTTAAATT
1 TTAAATAATTTTAAATT
* *
117733411 TTAAGT-ATTTCAAATT
1 TTAAATAATTTTAAATT
*
117733427 TTCAATAATTTT
1 TTAAATAATTTT
117733439 CAAGATTTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
TTAAATAATTTTAAATT
Found at i:117736486 original size:24 final size:24
Alignment explanation
Indices: 117736437--117736488 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
117736427 CTATGTCATA
*
117736437 ATATTTGTAACTAAAATTAATATT
1 ATATTTGTAACTAAAATTAACATT
* * *
117736461 ATATTTGTATCTAAAATTACCGTT
1 ATATTTGTAACTAAAATTAACATT
117736485 ATAT
1 ATAT
117736489 CATAAAACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (24 bp):
ATATTTGTAACTAAAATTAACATT
Found at i:117737547 original size:9 final size:9
Alignment explanation
Indices: 117737524--117737561 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
117737514 TTAAAGTTTA
117737524 AATTT-CAT
1 AATTTACAT
*
117737532 AACTTACAT
1 AATTTACAT
117737541 AATTTACAT
1 AATTTACAT
*
117737550 AACTTACAT
1 AATTTACAT
117737559 AAT
1 AAT
117737562 ACATAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
8 4 0.16
9 21 0.84
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (9 bp):
AATTTACAT
Found at i:117737552 original size:18 final size:17
Alignment explanation
Indices: 117737524--117737594 Score: 72
Period size: 18 Copynumber: 4.1 Consensus size: 17
117737514 TTAAAGTTTA
117737524 AATTTCATAACTTACAT
1 AATTTCATAACTTACAT
117737541 AATTTACATAACTTACAT
1 AATTT-CATAACTTACAT
* * *
117737559 AA-TACATAAATATATAT
1 AATTTCATAACT-TACAT
* *
117737576 CATATCATAACTTACAT
1 AATTTCATAACTTACAT
117737593 AA
1 AA
117737595 CTCACACTGT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
16 6 0.14
17 16 0.38
18 20 0.48
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (17 bp):
AATTTCATAACTTACAT
Found at i:117738643 original size:26 final size:26
Alignment explanation
Indices: 117738544--117738705 Score: 188
Period size: 26 Copynumber: 6.3 Consensus size: 26
117738534 CTAGAGGCCT
*
117738544 AGCCTCTTTT-AAT-AACTGGGGCAAA
1 AGCC-CTTTTCAATAAACTGGGGCATA
** * *
117738569 AGCCC-TTTCGGTAATCTGGGGCGTA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
117738594 AGCTCTTTTCAAT-AACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
* ** *
117738619 AGCCTTTTTCGGTAAACTAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
117738645 AGCCCTTTTTAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
117738671 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
117738697 AGCCCTTTT
1 AGCCCTTTT
117738706 GCACTTCCTC
Statistics
Matches: 112, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
23 3 0.03
24 2 0.02
25 36 0.32
26 71 0.63
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:117738687 original size:52 final size:51
Alignment explanation
Indices: 117738550--117738705 Score: 215
Period size: 52 Copynumber: 3.1 Consensus size: 51
117738540 GCCTAGCCTC
* * * *
117738550 TTTTAATAACTGGGGCAAAAGCCC-TTTCGGTAATCTGGGGCGTAAGCTCT
1 TTTTAATAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCT
* * *
117738600 TTTCAATAACTGGGGCATAAGCCTTTTTCGGTAAACTAGGGCATAAGCCCT
1 TTTTAATAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCT
**
117738651 TTTTAATAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCT
1 TTTTAAT-AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCT
117738703 TTT
1 TTT
117738706 GCACTTCCTC
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 21 0.23
51 28 0.30
52 43 0.47
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (51 bp):
TTTTAATAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCT
Found at i:117738780 original size:20 final size:20
Alignment explanation
Indices: 117738755--117738811 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
117738745 TTATGAATAC
117738755 ATCATGTGCATATCATA-CA
1 ATCATGTGCATATCATATCA
117738774 TATCATGTGCATATCATATCA
1 -ATCATGTGCATATCATATCA
117738795 ATCATGT--ATATCATATC
1 ATCATGTGCATATCATATC
117738812 CCACGTATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.28
20 24 0.67
21 2 0.06
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (20 bp):
ATCATGTGCATATCATATCA
Found at i:117738793 original size:5 final size:5
Alignment explanation
Indices: 117738763--117738811 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
117738753 ACATCATGTG
* *
117738763 CATAT CATA- CATAT CATGT GCATAT CATAT CA-AT CATGT -ATAT CATAT
1 CATAT CATAT CATAT CATAT -CATAT CATAT CATAT CATAT CATAT CATAT
117738811 C
1 C
117738812 CCACGTATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
4 11 0.31
5 21 0.58
6 4 0.11
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (5 bp):
CATAT
Found at i:117738807 original size:9 final size:10
Alignment explanation
Indices: 117738755--117738808 Score: 51
Period size: 9 Copynumber: 5.5 Consensus size: 10
117738745 TTATGAATAC
117738755 ATCATGTGCAT
1 ATCATGT-CAT
*
117738766 ATCAT-ACAT
1 ATCATGTCAT
117738775 ATCATGTGCAT
1 ATCATGT-CAT
*
117738786 ATCATATCA-
1 ATCATGTCAT
117738795 ATCATGT-AT
1 ATCATGTCAT
117738804 ATCAT
1 ATCAT
117738809 ATCCCACGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
8 1 0.03
9 19 0.53
10 2 0.06
11 14 0.39
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (10 bp):
ATCATGTCAT
Found at i:117740603 original size:8 final size:9
Alignment explanation
Indices: 117740583--117740684 Score: 91
Period size: 9 Copynumber: 11.1 Consensus size: 9
117740573 TTATACACAC
117740583 AACTTACAT
1 AACTTACAT
117740592 AACTTA-AT
1 AACTTACAT
*
117740600 AACTTATAT
1 AACTTACAT
117740609 ATA-TAATATCAT
1 A-ACT--TA-CAT
117740621 AACTTACAT
1 AACTTACAT
* *
117740630 AACTCATAT
1 AACTTACAT
* *
117740639 AGCTCACAT
1 AACTTACAT
*
117740648 AAGTTACAT
1 AACTTACAT
*
117740657 AACTCACAT
1 AACTTACAT
117740666 AACTTACAT
1 AACTTACAT
117740675 AACTTACAT
1 AACTTACAT
117740684 A
1 A
117740685 TATAATACAT
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
8 8 0.11
9 58 0.76
10 3 0.04
11 3 0.04
12 4 0.05
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.33
Consensus pattern (9 bp):
AACTTACAT
Found at i:117745802 original size:13 final size:14
Alignment explanation
Indices: 117745786--117745814 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
117745776 TTTTAAATAT
117745786 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
117745799 TTATAATGGTTTAA
1 TTATAATGGTTTAA
117745813 TT
1 TT
117745815 TTTCATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:117746492 original size:47 final size:47
Alignment explanation
Indices: 117746423--117746516 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
117746413 CGTTGAATTT
*
117746423 TTGAAGTATCATTTAGATTTGCTGTTATTGGTTGGATTTGATGTTGC
1 TTGAAGTATCATTTAGATTTGCTATTATTGGTTGGATTTGATGTTGC
*
117746470 TTGAAGTATCATTTAGATTTGCTATTATTGGTTGGATTTGATTTTGC
1 TTGAAGTATCATTTAGATTTGCTATTATTGGTTGGATTTGATGTTGC
117746517 AGGAAGGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.20, C:0.06, G:0.23, T:0.50
Consensus pattern (47 bp):
TTGAAGTATCATTTAGATTTGCTATTATTGGTTGGATTTGATGTTGC
Found at i:117751167 original size:16 final size:16
Alignment explanation
Indices: 117751146--117751176 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
117751136 GTGTGGTGTC
117751146 TGCAAGTGTATAGGTT
1 TGCAAGTGTATAGGTT
117751162 TGCAAGTGTATAGGT
1 TGCAAGTGTATAGGT
117751177 CAAATTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.32, T:0.35
Consensus pattern (16 bp):
TGCAAGTGTATAGGTT
Found at i:117757003 original size:43 final size:42
Alignment explanation
Indices: 117756955--117757113 Score: 158
Period size: 43 Copynumber: 3.7 Consensus size: 42
117756945 AGCTCGTACA
** * *
117756955 ATGCCAATGTCTTAGACGTGGTCTTACATGTAATCAAATATTG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCAAAT-TCG
* * * *
117756998 ATGCCACTGTCCCAGATAG-GGTCTTACCCGAAATCAAATTCG
1 ATGCCAATGTCCCAGA-CGTGGTCTTACACGTAATCAAATTCG
** * * *
117757040 ATGCCAACATCCTAGACATGGTCTTACACGTAAATCATAAGTCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGT-AATCA-AATTCG
117757084 ATGCCAATGTCCCAGACGTGGTCTTACACG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG
117757114 ATAACACATA
Statistics
Matches: 91, Mismatches: 21, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
42 24 0.26
43 35 0.38
44 32 0.35
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCAAATTCG
Found at i:117757063 original size:42 final size:44
Alignment explanation
Indices: 117757007--117757113 Score: 128
Period size: 44 Copynumber: 2.5 Consensus size: 44
117756997 GATGCCACTG
* * * *
117757007 TCCCAGATAGGGTCTTACCCG-AAATCA-AATTCGATGCCAACA
1 TCCCAGACATGGTCTTACACGTAAATCATAAGTCGATGCCAACA
* **
117757049 TCCTAGACATGGTCTTACACGTAAATCATAAGTCGATGCCAATG
1 TCCCAGACATGGTCTTACACGTAAATCATAAGTCGATGCCAACA
*
117757093 TCCCAGACGTGGTCTTACACG
1 TCCCAGACATGGTCTTACACG
117757114 ATAACACATA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 17 0.31
43 6 0.11
44 31 0.57
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (44 bp):
TCCCAGACATGGTCTTACACGTAAATCATAAGTCGATGCCAACA
Found at i:117764540 original size:40 final size:40
Alignment explanation
Indices: 117764503--117764690 Score: 299
Period size: 40 Copynumber: 4.7 Consensus size: 40
117764493 GCTACTTGCT
* *
117764503 CAAATGCCTTCGGGACTTCGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
117764543 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
117764583 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
117764623 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
117764662 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
117764691 CGTCCGAATA
Statistics
Matches: 137, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
38 1 0.01
39 34 0.25
40 101 0.74
41 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:117764681 original size:79 final size:80
Alignment explanation
Indices: 117764470--117764690 Score: 324
Period size: 80 Copynumber: 2.8 Consensus size: 80
117764460 AAACCAAGTA
* * * * *
117764470 CCTTCGGAATTTAG-CCGGATATAGCT-ACTTGCTCAAATGCCTTCGGGACTTCGCCCGGTTATA
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATA
*
117764533 GTAACTTGCACAAATG
65 GTAACTCGCACAAATG
*
117764549 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
117764614 TAACTCGCACAAATG
66 TAACTCGCACAAATG
*
117764629 CCTTCGGG-CTTAGCCCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
117764691 CGTCCGAATA
Statistics
Matches: 131, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
78 1 0.01
79 63 0.48
80 67 0.51
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
TAACTCGCACAAATG
Found at i:117766658 original size:12 final size:11
Alignment explanation
Indices: 117766619--117766662 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
117766609 TAAAGAAGAT
117766619 AAATAAAGATAA
1 AAATAAA-ATAA
*
117766631 AAGTGAAAATAA
1 AAAT-AAAATAA
117766643 AAATAAAATAA
1 AAATAAAATAA
117766654 TAAATAAAA
1 -AAATAAAA
117766663 AGTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.25
12 18 0.64
13 3 0.11
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:117766658 original size:18 final size:19
Alignment explanation
Indices: 117766617--117766663 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
117766607 CTTAAAGAAG
* *
117766617 ATAAATAAAGATAAAAGTG
1 ATAAATAAAAATAAAAGTA
117766636 A-AAATAAAAATAAAA-TA
1 ATAAATAAAAATAAAAGTA
117766653 ATAAATAAAAA
1 ATAAATAAAAA
117766664 GTTTTTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 2 0.08
18 22 0.88
19 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (19 bp):
ATAAATAAAAATAAAAGTA
Found at i:117778743 original size:28 final size:28
Alignment explanation
Indices: 117778712--117778867 Score: 213
Period size: 28 Copynumber: 5.5 Consensus size: 28
117778702 TCGATATTTT
*
117778712 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
117778740 GCACACTAAGTGCCATTCTCAATATCTA
1 GCACACTAAGTGCCATTCTCAATATCTC
117778768 GCACACTAAGTGCCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
117778796 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* * * * * * *
117778824 GTACACTAAGTACCATATTTGATTACCCC
1 GCACACTAAGTGCCAT-TCTCAATATCTC
117778853 GCACACTAAGTGCCA
1 GCACACTAAGTGCCA
117778868 CATTTTGTCG
Statistics
Matches: 113, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
28 94 0.83
29 19 0.17
ACGTcount: A:0.30, C:0.29, G:0.12, T:0.29
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:117783864 original size:25 final size:25
Alignment explanation
Indices: 117783836--117783911 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
117783826 GTCTTACACT
117783836 TTTCATATCATGTTGCCATGGTATC
1 TTTCATATCATGTTGCCATGGTATC
* * *
117783861 TTTCA-ACCATG--GTC-T--TACAC
1 TTTCATATCATGTTGCCATGGTA-TC
117783881 TTTTCATATCATGTTGCCATGGTATC
1 -TTTCATATCATGTTGCCATGGTATC
117783907 TTTCA
1 TTTCA
117783912 ACCATGGTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 6 0.16
22 7 0.19
24 7 0.19
25 11 0.30
26 1 0.03
27 2 0.05
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.43
Consensus pattern (25 bp):
TTTCATATCATGTTGCCATGGTATC
Found at i:117783932 original size:46 final size:46
Alignment explanation
Indices: 117783706--117783933 Score: 323
Period size: 46 Copynumber: 5.0 Consensus size: 46
117783696 TTATCTTCGA
* * * * * *
117783706 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
* ** *
117783752 CATGTTGCCATGGTATCTGTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
117783798 CATGTTGCCATGGTATCATTCAACCATGGTCTTACACTTTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
117783844 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACTTTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
117783890 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
117783934 TTCAGAAAGC
Statistics
Matches: 167, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 4 0.02
46 163 0.98
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:117784794 original size:51 final size:51
Alignment explanation
Indices: 117784721--117784832 Score: 172
Period size: 51 Copynumber: 2.2 Consensus size: 51
117784711 TACTTCATGC
* *
117784721 TTCATTCGGAATTATTATTTTGTTGCCCTAGCTTCAACAAGAGCTTCATAAT
1 TTCATCCGGAATTATTACTTTGTTGCCCTAGCTTCAACAAGAGCTTCAT-AT
* *
117784773 TT-ATCCGGAATTGTTACTTTGTTGCTCTAGCTTCAACAAGAGCTTCATAT
1 TTCATCCGGAATTATTACTTTGTTGCCCTAGCTTCAACAAGAGCTTCATAT
117784823 TTCATCCGGA
1 TTCATCCGGA
117784833 TAACTTAGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
50 4 0.07
51 49 0.89
52 2 0.04
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (51 bp):
TTCATCCGGAATTATTACTTTGTTGCCCTAGCTTCAACAAGAGCTTCATAT
Found at i:117786060 original size:11 final size:11
Alignment explanation
Indices: 117786044--117786071 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
117786034 ACTAAATAAT
117786044 TAATAATAAAA
1 TAATAATAAAA
117786055 TAATAATAAAA
1 TAATAATAAAA
117786066 TAATAA
1 TAATAA
117786072 AATATCTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:117793536 original size:14 final size:14
Alignment explanation
Indices: 117793517--117793545 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
117793507 ATCAACCTAG
117793517 AGTCAGTTGTTCTT
1 AGTCAGTTGTTCTT
117793531 AGTCAGTTGTTCTT
1 AGTCAGTTGTTCTT
117793545 A
1 A
117793546 CTCTCAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (14 bp):
AGTCAGTTGTTCTT
Found at i:117793898 original size:13 final size:13
Alignment explanation
Indices: 117793880--117793906 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
117793870 GCCTTTGTCA
117793880 TATTTATTGTTAG
1 TATTTATTGTTAG
117793893 TATTTATTGTTAG
1 TATTTATTGTTAG
117793906 T
1 T
117793907 TTAGTGACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (13 bp):
TATTTATTGTTAG
Found at i:117795394 original size:27 final size:27
Alignment explanation
Indices: 117795309--117795425 Score: 78
Period size: 27 Copynumber: 4.3 Consensus size: 27
117795299 GTCCTAATGG
* * * * *
117795309 ACTTTCCAATTACGACAGTCCTGGCAG
1 ACTTCCCAATTAAGACTGTCCTGACAA
* * **
117795336 ACTT-CTACATTAAGACTGTCTTGACGG
1 ACTTCCCA-ATTAAGACTGTCCTGACAA
* *
117795363 GCTTCCCAATTACGA-TCGTCCTGACAA
1 ACTTCCCAATTAAGACT-GTCCTGACAA
*
117795390 ACTT-CCACATTAAGACTGTCCTGACGA
1 ACTTCCCA-ATTAAGACTGTCCTGACAA
117795417 ACTTCCCAA
1 ACTTCCCAA
117795426 ATAGATAGTC
Statistics
Matches: 69, Mismatches: 15, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
26 6 0.09
27 57 0.83
28 6 0.09
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (27 bp):
ACTTCCCAATTAAGACTGTCCTGACAA
Found at i:117795400 original size:54 final size:54
Alignment explanation
Indices: 117795309--117795425 Score: 155
Period size: 54 Copynumber: 2.2 Consensus size: 54
117795299 GTCCTAATGG
* * * * * *
117795309 ACTTTCCAATTACGACAGTCCTGGCAGACTTCTACATTAAGACTGTCTTGACGG
1 ACTTCCCAATTACGACAGTCCTGACAAACTTCCACATTAAGACTGTCCTGACGA
*
117795363 GCTTCCCAATTACGATC-GTCCTGACAAACTTCCACATTAAGACTGTCCTGACGA
1 ACTTCCCAATTACGA-CAGTCCTGACAAACTTCCACATTAAGACTGTCCTGACGA
117795417 ACTTCCCAA
1 ACTTCCCAA
117795426 ATAGATAGTC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
54 53 0.98
55 1 0.02
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (54 bp):
ACTTCCCAATTACGACAGTCCTGACAAACTTCCACATTAAGACTGTCCTGACGA
Found at i:117795525 original size:22 final size:23
Alignment explanation
Indices: 117795500--117795554 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
117795490 CCCCACTAAA
* *
117795500 GGCTCTCATACGTCCCCT-AATG
1 GGCTCTCATACGTCCCATAAAAG
* *
117795522 GGCTCTCAAATGTCCCATAAAAG
1 GGCTCTCATACGTCCCATAAAAG
117795545 GGCTCTCATA
1 GGCTCTCATA
117795555 AATGAGTGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (23 bp):
GGCTCTCATACGTCCCATAAAAG
Found at i:117797546 original size:22 final size:22
Alignment explanation
Indices: 117797521--117797578 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
117797511 TAGCTCGTAT
*
117797521 GAGCTTATTGTTCAGCTCAATA
1 GAGCTTACTGTTCAGCTCAATA
* *
117797543 GAGCTTACTGTTTAGCTCGATA
1 GAGCTTACTGTTCAGCTCAATA
117797565 GAGCTTACTGTTCA
1 GAGCTTACTGTTCA
117797579 TCAGCTTAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (22 bp):
GAGCTTACTGTTCAGCTCAATA
Found at i:117797571 original size:44 final size:45
Alignment explanation
Indices: 117797465--117797578 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 45
117797455 CCGATATATC
* * * *
117797465 AGCTCGTAAGAGCTTACTATTTTCAGCTCATTGCAGCTTACCTTTTT
1 AGCTCGTATGAGCTTA-T-TGTTCAGCTCATAGCAGCTTACCTGTTT
117797512 AGCTCGTATGAGCTTATTGTTCAGCTCAATAG-AGCTTA-CTGTTT
1 AGCTCGTATGAGCTTATTGTTCAGCTC-ATAGCAGCTTACCTGTTT
*
117797556 AGCTCG-ATAGAGCTTACTGTTCA
1 AGCTCGTAT-GAGCTTATTGTTCA
117797579 TCAGCTTAGG
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
43 2 0.03
44 24 0.40
45 15 0.25
46 4 0.07
47 15 0.25
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (45 bp):
AGCTCGTATGAGCTTATTGTTCAGCTCATAGCAGCTTACCTGTTT
Found at i:117801105 original size:12 final size:12
Alignment explanation
Indices: 117801088--117801112 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
117801078 AGTGTCGAAT
117801088 CGGTAACAGTAA
1 CGGTAACAGTAA
117801100 CGGTAACAGTAA
1 CGGTAACAGTAA
117801112 C
1 C
117801113 AATTTATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:117801108 original size:45 final size:45
Alignment explanation
Indices: 117801000--117801110 Score: 143
Period size: 45 Copynumber: 2.5 Consensus size: 45
117800990 AACGGTAGCA
* * **
117801000 GTAACAGTAACAGTAACAATATTTAACACACAAAGTGCTAAATTT
1 GTAACAGTAACGGTAACAGTATTTAACACACAAAGTGCTAAATCG
* * *
117801045 GTAACAGTAATGGTAACAGTATTTGACACACAAAGTG-TCGAATCG
1 GTAACAGTAACGGTAACAGTATTTAACACACAAAGTGCT-AAATCG
117801090 GTAACAGTAACGGTAACAGTA
1 GTAACAGTAACGGTAACAGTA
117801111 ACAATTTATA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 1 0.02
45 56 0.98
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.24
Consensus pattern (45 bp):
GTAACAGTAACGGTAACAGTATTTAACACACAAAGTGCTAAATCG
Found at i:117806863 original size:2 final size:2
Alignment explanation
Indices: 117806856--117806886 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
117806846 TTGTTCTTAA
117806856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
117806887 ATACATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:117809885 original size:14 final size:13
Alignment explanation
Indices: 117809852--117809901 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
117809842 TTCTTCTTTA
* *
117809852 CTTTGTTTTGTTT
1 CTTTATTTTATTT
117809865 CTTTATTTTATTT
1 CTTTATTTTATTT
117809878 CATTTATTTTA-TT
1 C-TTTATTTTATTT
117809891 CTTT-TTTTATT
1 CTTTATTTTATT
117809902 AACTTAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 5 0.15
12 4 0.12
13 15 0.45
14 9 0.27
ACGTcount: A:0.12, C:0.08, G:0.04, T:0.76
Consensus pattern (13 bp):
CTTTATTTTATTT
Found at i:117810181 original size:3 final size:3
Alignment explanation
Indices: 117810173--117810282 Score: 57
Period size: 3 Copynumber: 36.3 Consensus size: 3
117810163 AATTTATTTT
* * * * *
117810173 TAA TAA TAA TAA TAA TCA TAA TCA TAA T-T TAA TAT TAA TAC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * * *
117810220 TAA T-A TAA -AA CCA TAA CAA TTAA TAA TTA TAA TAA TCAA TTA T-A
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA
117810264 TAA TATA TATA TATA TAA T
1 TAA TA-A TA-A TA-A TAA T
117810283 CTAAATAAAA
Statistics
Matches: 82, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
2 7 0.09
3 59 0.72
4 16 0.20
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:117810202 original size:35 final size:34
Alignment explanation
Indices: 117810162--117810227 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
117810152 GTCTTTATTT
* *
117810162 TAATTTATTTTTAATAATAATAATAATCATAATCA
1 TAATTTAATATTAATAATAATAATAAT-ATAATCA
*
117810197 TAATTTAATATTAATACTAATAATAATATAA
1 TAATTTAATATTAATAATAATAATAATATAA
117810228 AACCATAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 4 0.14
35 24 0.86
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (34 bp):
TAATTTAATATTAATAATAATAATAATATAATCA
Found at i:117810204 original size:29 final size:28
Alignment explanation
Indices: 117810171--117810227 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
117810161 TTAATTTATT
*
117810171 TTTAATAATAATAATAATCATAATCATAA
1 TTTAATAATAATAATAATAATAAT-ATAA
* *
117810200 TTTAATATTAATACTAATAATAATATAA
1 TTTAATAATAATAATAATAATAATATAA
117810228 AACCATAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.40
Consensus pattern (28 bp):
TTTAATAATAATAATAATAATAATATAA
Found at i:117815304 original size:25 final size:25
Alignment explanation
Indices: 117815256--117815304 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
117815246 TGATAATATG
* * * *
117815256 AAAAATGACTGTTTTGCCCTTAGGT
1 AAAAATGACTATTATACCCCTAGGT
117815281 AAAAATGACTATTATACCCCTAGG
1 AAAAATGACTATTATACCCCTAGG
117815305 GTTTAATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (25 bp):
AAAAATGACTATTATACCCCTAGGT
Found at i:117815367 original size:11 final size:11
Alignment explanation
Indices: 117815340--117815390 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
117815330 GATTTTGACA
*
117815340 TACATGATTTG
1 TACATGATATG
117815351 -ACATGATATG
1 TACATGATATG
117815361 TACATGATATG
1 TACATGATATG
*
117815372 T--ATGAAATG
1 TACATGATATG
*
117815381 CACATGATAT
1 TACATGATAT
117815391 AGTCATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 7 0.21
10 9 0.27
11 17 0.52
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (11 bp):
TACATGATATG
Found at i:117815471 original size:25 final size:25
Alignment explanation
Indices: 117815435--117815501 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
117815425 GAGGAAGTGA
*
117815435 AAAAGGGTTTTGCCCCAATTTACCG
1 AAAAGGGCTTTGCCCCAATTTACCG
**
117815460 AAAAGGGCTTTGCCCCTGTTTACCG
1 AAAAGGGCTTTGCCCCAATTTACCG
*
117815485 AAGAGGGCTTTGCCCCA
1 AAAAGGGCTTTGCCCCA
117815502 GTTATTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAATTTACCG
Found at i:117816915 original size:33 final size:33
Alignment explanation
Indices: 117816878--117816943 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
117816868 GATGTGGCAG
* * *
117816878 GTGTACTACTTTGAGTTCTCGGACAATCTTTAA
1 GTGTACTACTCTGAGTTCACAGACAATCTTTAA
117816911 GTGTACTACTCTGAGTTCACAGACAATCTTTAA
1 GTGTACTACTCTGAGTTCACAGACAATCTTTAA
117816944 CAAAGTGTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (33 bp):
GTGTACTACTCTGAGTTCACAGACAATCTTTAA
Found at i:117819073 original size:45 final size:45
Alignment explanation
Indices: 117819007--117819106 Score: 112
Period size: 45 Copynumber: 2.2 Consensus size: 45
117818997 AACGGTAGCA
* * ** *
117819007 GTAACTGTAACAATAATAGTATTCAACGTACAAAGTG-CTGAATCT
1 GTAACAGTAACAATAACAGTATTCAACACACAAAGTGTC-GAATCG
* * *
117819052 GTAATAGTAACGATAACAGTATTCGACACACAAAGTGTCGAATCG
1 GTAACAGTAACAATAACAGTATTCAACACACAAAGTGTCGAATCG
117819097 GTAACAGTAA
1 GTAACAGTAA
117819107 AGGTAACAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
45 44 0.98
46 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (45 bp):
GTAACAGTAACAATAACAGTATTCAACACACAAAGTGTCGAATCG
Found at i:117820281 original size:19 final size:19
Alignment explanation
Indices: 117820237--117820288 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
117820227 TATTAACTTA
117820237 ATAATAAT-AATAATTTATT
1 ATAATAATAAAT-ATTTATT
*
117820256 ATTATAATAAATATCTTATT
1 ATAATAATAAATAT-TTATT
*
117820276 -TAATAACAAATAT
1 ATAATAATAAATAT
117820289 ATAAATTACA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 20 0.71
20 8 0.29
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATAATAAATATTTATT
Found at i:117820506 original size:3 final size:3
Alignment explanation
Indices: 117820498--117820592 Score: 70
Period size: 3 Copynumber: 32.3 Consensus size: 3
117820488 AATTTATTTT
* * * * *
117820498 TAA TAA TAA TAA TAA TAA TAA TAA TAA TCA TCA TCA TAA T-T TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* ** * *
117820545 TAA TAC TAA TAA TAA T-A TAA -AA CCA TAA CAA TTAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
117820589 TAA T
1 TAA T
117820593 CACTTATATA
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
2 5 0.07
3 66 0.90
4 2 0.03
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:117826776 original size:39 final size:39
Alignment explanation
Indices: 117826709--117826931 Score: 322
Period size: 39 Copynumber: 5.7 Consensus size: 39
117826699 ACAAACCATG
* ** *
117826709 CGGGACTTTAAGCCCGGATATAATACCAGCAC-AAACCCTG
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
*
117826749 CGGGACTTTATCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
117826789 CGGGGCTTAGCCCGAATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
117826828 CGGGACTTAGCCCGGATATAACACCAGCATGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
117826867 CAGGACTTAGCCCGGATATAACACCAACACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
117826906 CGGGACTTAGCCCGGATATAACACCA
1 CGGGACTTAGCCCGGATATAACACCA
117826932 TTATAAAGTC
Statistics
Matches: 167, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 148 0.89
40 19 0.11
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:117827037 original size:28 final size:28
Alignment explanation
Indices: 117827004--117827085 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
117826994 ATTTAATCAT
* *
117827004 TCAATATTTTGCACACTAAGTGTCATTC
1 TCAATATTTCGCACACTAAGTGCCATTC
* *
117827032 TCAATATCTCGCACATTAAGTGCCATTC
1 TCAATATTTCGCACACTAAGTGCCATTC
* * *
117827060 TCAATATTTCGTACACTGAGTACCAT
1 TCAATATTTCGCACACTAAGTGCCAT
117827086 ATTTGATTGC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (28 bp):
TCAATATTTCGCACACTAAGTGCCATTC
Found at i:117829345 original size:139 final size:138
Alignment explanation
Indices: 117829096--117829368 Score: 501
Period size: 139 Copynumber: 2.0 Consensus size: 138
117829086 CATGCAAATG
*
117829096 TCATCTTTTCCCCCGAAATGAAAGCTTGAGAAAGCTATAAAACAAGTTTGAACATTTGGCTACTT
1 TCATCTTTTCCCCCGAAATGAAAGCTTGAGAAAGCTATAAAACAAGTTTGAACATTCGGCTACTT
117829161 TGAGGGCTAGATTAAGGTATGTTTTTAGATCGATTTTTAATGATATTTACGTTTTTGAGATCATT
66 TGAGGGCTAGATTAAGGTATGTTTTTAGATCGATTTTTAATGATATTTACGTTTTTGAGATCATT
117829226 GCTTATGT
131 GCTTATGT
117829234 TCATCTTTTCCCCCGAAATGAAAGCTTGAGAAAGCTATAAGAACAAGTTTGAACATTCGGCTACT
1 TCATCTTTTCCCCCGAAATGAAAGCTTGAGAAAGCTATAA-AACAAGTTTGAACATTCGGCTACT
* * *
117829299 TTGAGGGCTAGATTAAGGTATGTTTTTGGATCGGTTTTTAATGATATTTACGTTTTTGAGATCGT
65 TTGAGGGCTAGATTAAGGTATGTTTTTAGATCGATTTTTAATGATATTTACGTTTTTGAGATCAT
117829364 TGCTT
130 TGCTT
117829369 TGTACTCTAG
Statistics
Matches: 130, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
138 40 0.31
139 90 0.69
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (138 bp):
TCATCTTTTCCCCCGAAATGAAAGCTTGAGAAAGCTATAAAACAAGTTTGAACATTCGGCTACTT
TGAGGGCTAGATTAAGGTATGTTTTTAGATCGATTTTTAATGATATTTACGTTTTTGAGATCATT
GCTTATGT
Found at i:117830140 original size:22 final size:22
Alignment explanation
Indices: 117830080--117830192 Score: 75
Period size: 22 Copynumber: 5.0 Consensus size: 22
117830070 TACTATTTTT
* * *
117830080 AGCTCATTGGAGCTTATTGTTTC
1 AGCTCAATAGAGCTTACTG-TTC
* * *
117830103 AGCTC-GTATGATCTTATTGTTC
1 AGCTCAATA-GAGCTTACTGTTC
*
117830125 AGCTCAATAGAGCTTACTGTTT
1 AGCTCAATAGAGCTTACTGTTC
* * * *
117830147 AACTCGATCGAGCTTACCGTTTC
1 AGCTCAATAGAGCTTACTG-TTC
* *
117830170 AGCTTATTAGAGCTTACTGTTC
1 AGCTCAATAGAGCTTACTGTTC
117830192 A
1 A
117830193 TCAGCTCAGG
Statistics
Matches: 69, Mismatches: 18, Indels: 7
0.73 0.19 0.07
Matches are distributed among these distances:
22 38 0.55
23 31 0.45
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (22 bp):
AGCTCAATAGAGCTTACTGTTC
Found at i:117838605 original size:28 final size:28
Alignment explanation
Indices: 117838565--117838622 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
117838555 CCGGATGGTA
*
117838565 AGATTCTACGGGTCGAATCAAGAGAATT
1 AGATTCTACGGGTCAAATCAAGAGAATT
117838593 AGATTCTACGGGTCAAATCAAGAGAATT
1 AGATTCTACGGGTCAAATCAAGAGAATT
117838621 AG
1 AG
117838623 GTTCGCCGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (28 bp):
AGATTCTACGGGTCAAATCAAGAGAATT
Found at i:117848878 original size:71 final size:71
Alignment explanation
Indices: 117848794--117848957 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
117848784 CGATTTGTCT
117848794 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
117848859 CTTTCA
66 CTTTCA
* *
117848865 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
117848930 CTTTCA
66 CTTTCA
117848936 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
117848958 GATACATCTC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
CTTTCA
Found at i:117848995 original size:71 final size:70
Alignment explanation
Indices: 117848794--117848991 Score: 249
Period size: 71 Copynumber: 2.8 Consensus size: 70
117848784 CGATTTGTCT
* * * * *
117848794 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
117848859 CTTTCA
65 CTTTCA
* * * *
117848865 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
117848930 CTTTCA
65 CTTTCA
* *
117848936 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
117848992 TACAGGGTGT
Statistics
Matches: 118, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
68 22 0.19
69 1 0.01
70 1 0.01
71 94 0.80
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.33
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:117851344 original size:38 final size:38
Alignment explanation
Indices: 117851293--117851369 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
117851283 CTGAACCAAG
117851293 TATGTTTCGAGCCTTTAAAGATTGACATGTTGGCAAAA
1 TATGTTTCGAGCCTTTAAAGATTGACATGTTGGCAAAA
*
117851331 TATGTTTCGAGCCTTTAAAGATTGTCATGTTGGCAAAA
1 TATGTTTCGAGCCTTTAAAGATTGACATGTTGGCAAAA
117851369 T
1 T
117851370 TTCTAGTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (38 bp):
TATGTTTCGAGCCTTTAAAGATTGACATGTTGGCAAAA
Found at i:117855732 original size:20 final size:20
Alignment explanation
Indices: 117855707--117855767 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
117855697 AAGAATCAAC
117855707 AAAGAAAGAAAGAAAAGAAA
1 AAAGAAAGAAAGAAAAGAAA
* * **
117855727 AAAGAAACAATGTGAAGAAA
1 AAAGAAAGAAAGAAAAGAAA
* * *
117855747 AAAAAAAGGAAGAAAACAAA
1 AAAGAAAGAAAGAAAAGAAA
117855767 A
1 A
117855768 TGTGAGGAAA
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.75, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAGAAAGAAAAGAAA
Found at i:117855777 original size:16 final size:16
Alignment explanation
Indices: 117855735--117855777 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
117855725 AAAAAGAAAC
117855735 AATGTGAAGAAAAAAA
1 AATGTGAAGAAAAAAA
* *
117855751 AAAG-GAAGAAAACAA
1 AATGTGAAGAAAAAAA
*
117855766 AATGTGAGGAAA
1 AATGTGAAGAAA
117855778 GTGATGGAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.65, C:0.02, G:0.23, T:0.09
Consensus pattern (16 bp):
AATGTGAAGAAAAAAA
Found at i:117856610 original size:17 final size:19
Alignment explanation
Indices: 117856590--117856638 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
117856580 TTTTAAACTT
*
117856590 TTTTATTATTTTTTG-A-A
1 TTTTATAATTTTTTGAATA
117856607 TTTTA-AATTTTTTTGAATA
1 TTTTATAA-TTTTTTGAATA
117856626 TTTTATAATTTTT
1 TTTTATAATTTTT
117856639 AAATTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 1 0.04
17 12 0.44
18 1 0.04
19 11 0.41
20 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (19 bp):
TTTTATAATTTTTTGAATA
Found at i:117856610 original size:28 final size:28
Alignment explanation
Indices: 117856579--117856641 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
117856569 ATTTTCTTAT
* *
117856579 TTTTTAAACTTTTTT-ATTATTTTTTGAA
1 TTTTTAAACTTTTTTGAATATTTTAT-AA
*
117856607 -TTTTAAATTTTTTTGAATATTTTATAA
1 TTTTTAAACTTTTTTGAATATTTTATAA
117856634 TTTTTAAA
1 TTTTTAAA
117856642 TTATTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (28 bp):
TTTTTAAACTTTTTTGAATATTTTATAA
Found at i:117856642 original size:28 final size:28
Alignment explanation
Indices: 117856579--117856649 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
117856569 ATTTTCTTAT
* * *
117856579 TTTTTAAACTTTTTTATTATTTTTTGAA
1 TTTTTAAATTTTTTTAATATTTTATGAA
117856607 -TTTTAAATTTTTTTGAATATTTTAT-AA
1 TTTTTAAATTTTTTT-AATATTTTATGAA
117856634 TTTTTAAATTATTTTT
1 TTTTTAAATT-TTTTT
117856650 TAACATGACA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 15 0.41
28 17 0.46
29 5 0.14
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (28 bp):
TTTTTAAATTTTTTTAATATTTTATGAA
Found at i:117856764 original size:17 final size:18
Alignment explanation
Indices: 117856744--117856779 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
117856734 ATGACCAAAC
117856744 ATTG-AAAGAAAATTAAG
1 ATTGAAAAGAAAATTAAG
117856761 ATTGAAAAGAAAATTAAG
1 ATTGAAAAGAAAATTAAG
117856779 A
1 A
117856780 GTGTGTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (18 bp):
ATTGAAAAGAAAATTAAG
Found at i:117857041 original size:27 final size:28
Alignment explanation
Indices: 117857004--117857058 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
117856994 TTTGTAAGAT
* *
117857004 TTTATAAATAT-TTTTAATAAAATAAAA
1 TTTAAAAATATATTATAATAAAATAAAA
*
117857031 TTTAAAAATATATTATAATTAAATAAAA
1 TTTAAAAATATATTATAATAAAATAAAA
117857059 ATTATTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TTTAAAAATATATTATAATAAAATAAAA
Found at i:117861559 original size:30 final size:30
Alignment explanation
Indices: 117861525--117861581 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
117861515 TTGAATTATT
*
117861525 AGGACTAAATTGAAAAATATAAT-AAATTGA
1 AGGACTAAAATGAAAAATA-AATGAAATTGA
*
117861555 AGGACTAAAATGCAAAATAAATGAAAT
1 AGGACTAAAATGAAAAATAAATGAAAT
117861582 ATATGGATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.58, C:0.05, G:0.14, T:0.23
Consensus pattern (30 bp):
AGGACTAAAATGAAAAATAAATGAAATTGA
Found at i:117862535 original size:35 final size:35
Alignment explanation
Indices: 117862359--117862537 Score: 173
Period size: 35 Copynumber: 5.1 Consensus size: 35
117862349 TAGGTATGTA
*
117862359 CATATGTGATGATATATTGAACTTGTATATTTGGC
1 CATATGTGATGATATATTGAACTTGTATATTCGGC
* * * * * *
117862394 CACATGTGATGTTATATTAAACTTGAATATTTGAC
1 CATATGTGATGATATATTGAACTTGTATATTCGGC
* * * * * *
117862429 TACATGTGATGTTTTATTGAGCTTGTATATTCGGT
1 CATATGTGATGATATATTGAACTTGTATATTCGGC
* * *
117862464 CATATATGATGATTTATTGTACTTGTATAGTT-GGC
1 CATATGTGATGATATATTGAACTTGTATA-TTCGGC
*
117862499 CATATGTGATGATATAATGAACTTG-AGTATTCGGC
1 CATATGTGATGATATATTGAACTTGTA-TATTCGGC
117862534 CATA
1 CATA
117862538 CAAGTAAGTA
Statistics
Matches: 117, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
34 3 0.03
35 112 0.96
36 2 0.02
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (35 bp):
CATATGTGATGATATATTGAACTTGTATATTCGGC
Found at i:117863492 original size:2 final size:2
Alignment explanation
Indices: 117863485--117863517 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
117863475 ATGTTGATTG
117863485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
117863518 GCATACGTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:117869615 original size:26 final size:26
Alignment explanation
Indices: 117869575--117869684 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
117869565 CATGAAATTC
*
117869575 TTATCATGAAGCATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
117869601 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
117869627 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
117869653 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
117869679 TTATCA
1 TTATCA
117869685 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:117874826 original size:86 final size:86
Alignment explanation
Indices: 117874681--117874863 Score: 357
Period size: 86 Copynumber: 2.1 Consensus size: 86
117874671 AAACAAATTG
*
117874681 TACTCTTTTCCTTTAACTAAGGTTTTGTCCCACTTGGTTTTCCTAATAAAAGTTTTTAACGAGTC
1 TACTCTTTTTCTTTAACTAAGGTTTTGTCCCACTTGGTTTTCCTAATAAAAGTTTTTAACGAGTC
117874746 AGCTTGCAATAGAAGATTGTA
66 AGCTTGCAATAGAAGATTGTA
117874767 TACTCTTTTTCTTTAACTAAGGTTTTGTCCCACTTGGTTTTCCTAATAAAAGTTTTTAACGAGTC
1 TACTCTTTTTCTTTAACTAAGGTTTTGTCCCACTTGGTTTTCCTAATAAAAGTTTTTAACGAGTC
117874832 AGCTTGCAATAGAAGATTGTA
66 AGCTTGCAATAGAAGATTGTA
117874853 TACTCTTTTTC
1 TACTCTTTTTC
117874864 CTTTCATTAG
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 96 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (86 bp):
TACTCTTTTTCTTTAACTAAGGTTTTGTCCCACTTGGTTTTCCTAATAAAAGTTTTTAACGAGTC
AGCTTGCAATAGAAGATTGTA
Found at i:117880944 original size:2 final size:2
Alignment explanation
Indices: 117880927--117880969 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
117880917 TTTGCCCACA
* *
117880927 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
117880969 A
1 A
117880970 CCATAGTAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:117881955 original size:20 final size:21
Alignment explanation
Indices: 117881930--117881971 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
117881920 ACTAAACTAA
*
117881930 TCAAAAC-ATAAAATTTTAGG
1 TCAAAACTATAAAATTTGAGG
*
117881950 TCAAAACTGTAAAATTTGAGG
1 TCAAAACTATAAAATTTGAGG
117881971 T
1 T
117881972 ACAAGGAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (21 bp):
TCAAAACTATAAAATTTGAGG
Found at i:117892491 original size:40 final size:40
Alignment explanation
Indices: 117892349--117892484 Score: 254
Period size: 40 Copynumber: 3.4 Consensus size: 40
117892339 ATAGCAACTC
* *
117892349 GCACGAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
117892389 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
117892429 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
117892469 GCACAAATGCCTTCGG
1 GCACAAATGCCTTCGG
117892485 ATCTTAGTCC
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 94 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
Found at i:117900359 original size:80 final size:80
Alignment explanation
Indices: 117900221--117900415 Score: 306
Period size: 80 Copynumber: 2.5 Consensus size: 80
117900211 ACCTTCGAAT
* * *
117900221 TTAG-CCGGATATAG-CAACTCGCACGAATGCCTTCGGGACTTAGCCCGGACATAGTCACTAGCA
1 TTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGACATAATCACTAGCA
*
117900284 CAAATGCCTTCGGGAC
65 CAAATGCCTTCAGGAC
*
117900300 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTAGCAC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGACATAATCACTAGCAC
117900365 AAATGCCTTCAGGAC
66 AAATGCCTTCAGGAC
*
117900380 TTAGCCCGGA-ATAATCACTAGCACAAATGCCTTCGG
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGG
117900416 ATCTTAGTCC
Statistics
Matches: 108, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
79 29 0.27
80 78 0.72
81 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (80 bp):
TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGACATAATCACTAGCAC
AAATGCCTTCAGGAC
Found at i:117900422 original size:39 final size:40
Alignment explanation
Indices: 117900241--117900415 Score: 298
Period size: 40 Copynumber: 4.4 Consensus size: 40
117900231 ATAGCAACTC
* * *
117900241 GCACGAATGCCTTCGGGACTTAGCCCGGACATAGTCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
*
117900281 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
117900321 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
*
117900361 GCACAAATGCCTTCAGGACTTAGCCCGGA-ATAATCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
117900400 GCACAAATGCCTTCGG
1 GCACAAATGCCTTCGG
117900416 ATCTTAGTCC
Statistics
Matches: 130, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
39 25 0.19
40 105 0.81
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGATATAATCACTA
Found at i:117902591 original size:108 final size:108
Alignment explanation
Indices: 117902402--117902605 Score: 300
Period size: 108 Copynumber: 1.9 Consensus size: 108
117902392 CACTTTATTG
* * *
117902402 ATTTACAATTATGAACACTTCACTAAGAGTTCACTGATTTATGATCACAACTTCATTTAAATAGC
1 ATTTACAATTATGAACACTTCACTAAGAATTCACTGATTTACGATCACAACTTCATTTAAACAGC
*
117902467 TCATTGATTTATGATCATAACTTTCATTTTTTAAAACTCACTA
66 TCATTGATTTATGATCACAACTTTCATTTTTTAAAACTCACTA
* * ** ** * *
117902510 ATTTACGATTATGAACACTTCATTAAGAATTCGTTGATTTACGATTGCAGCTTCATTTAAACAGT
1 ATTTACAATTATGAACACTTCACTAAGAATTCACTGATTTACGATCACAACTTCATTTAAACAGC
117902575 TCATTGATTTATGATCACAACTTTCATTTTT
66 TCATTGATTTATGATCACAACTTTCATTTTT
117902606 CAAAGTTCGT
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
108 84 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (108 bp):
ATTTACAATTATGAACACTTCACTAAGAATTCACTGATTTACGATCACAACTTCATTTAAACAGC
TCATTGATTTATGATCACAACTTTCATTTTTTAAAACTCACTA
Found at i:117902622 original size:108 final size:108
Alignment explanation
Indices: 117902398--117902626 Score: 296
Period size: 108 Copynumber: 2.1 Consensus size: 108
117902388 GCTTCACTTT
* * *
117902398 ATTGATTTACAATTATGAACACTTCACTAAGAGTTCACTGATTTATGATCACAACTTCATTTAAA
1 ATTGATTTACGATTATGAACACTTCACTAAGAATTCACTGATTTACGATCACAACTTCATTTAAA
* * *
117902463 TAGCTCATTGATTTATGATCATAACTTTCATTTTTTAAAACTC
66 CAGCTCATTGATTTATGATCACAACTTTCATTTTTCAAAACTC
* * * ** ** *
117902506 ACTAATTTACGATTATGAACACTTCATTAAGAATTCGTTGATTTACGATTGCAGCTTCATTTAAA
1 ATTGATTTACGATTATGAACACTTCACTAAGAATTCACTGATTTACGATCACAACTTCATTTAAA
* **
117902571 CAGTTCATTGATTTATGATCACAACTTTCATTTTTCAAAGTTC
66 CAGCTCATTGATTTATGATCACAACTTTCATTTTTCAAAACTC
*
117902614 GTTGATTTACGAT
1 ATTGATTTACGAT
117902627 CACAGCTACA
Statistics
Matches: 101, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
108 101 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.41
Consensus pattern (108 bp):
ATTGATTTACGATTATGAACACTTCACTAAGAATTCACTGATTTACGATCACAACTTCATTTAAA
CAGCTCATTGATTTATGATCACAACTTTCATTTTTCAAAACTC
Found at i:117902806 original size:136 final size:136
Alignment explanation
Indices: 117902545--117902812 Score: 311
Period size: 136 Copynumber: 2.0 Consensus size: 136
117902535 AGAATTCGTT
* * ** * ** * *
117902545 GATTTACGATTGCAGCTTCATTTAAACAGTTCATTGATTTATGATCACAACTTTCATTTTTCAAA
1 GATTTACGATCGCAACACCATTTAAACAGTTCACTGATTTACAATCACAACTGTAATTTTTCAAA
* * * * * * *
117902610 GTTCGTTGATTTACGATCACAGCTACAGTTCATTGATTTACAATCATGACCATTTTATTAAGAGT
66 GCTCGTTGATTTACGATCACAACTACAGTTCATTCATTTACAATCATAAACAATTCATTAAGAGT
117902675 TTCACC
131 TTCACC
* *
117902681 GATTTACGATCGCAACACCATTTAAATAGTTCACTGATTTACAATCACAACTGTAATTTTTTAAA
1 GATTTACGATCGCAACACCATTTAAACAGTTCACTGATTTACAATCACAACTGTAATTTTTCAAA
* ** * * * *
117902746 GCTCGTTGATTTATGATCACAACTTTAGTTTATTCATTTATAATTATAAATAATTCATTAAGAGT
66 GCTCGTTGATTTACGATCACAACTACAGTTCATTCATTTACAATCATAAACAATTCATTAAGAGT
117902811 TT
131 TT
117902813 GTTTATTTAC
Statistics
Matches: 107, Mismatches: 25, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
136 107 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.40
Consensus pattern (136 bp):
GATTTACGATCGCAACACCATTTAAACAGTTCACTGATTTACAATCACAACTGTAATTTTTCAAA
GCTCGTTGATTTACGATCACAACTACAGTTCATTCATTTACAATCATAAACAATTCATTAAGAGT
TTCACC
Found at i:117902821 original size:36 final size:36
Alignment explanation
Indices: 117902772--117902858 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
117902762 TCACAACTTT
* * * *
117902772 AGTTTATTCATTTATAATTATAAATAATTCATTAAG
1 AGTTTGTTCATTTACAATCATAAACAATTCATTAAG
* *
117902808 AGTTTGTTTATTTACAATCATGAACAATTCATTAAG
1 AGTTTGTTCATTTACAATCATAAACAATTCATTAAG
* *
117902844 AGTTCGTTGATTTAC
1 AGTTTGTTCATTTAC
117902859 GATCGTAACT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (36 bp):
AGTTTGTTCATTTACAATCATAAACAATTCATTAAG
Found at i:117904408 original size:5 final size:5
Alignment explanation
Indices: 117904398--117904454 Score: 64
Period size: 5 Copynumber: 11.0 Consensus size: 5
117904388 TAGGAAGATA
117904398 TTATT TTATTT TTATT TT-TAT TTATT TT-TAT TTATTT TTATT TTATT
1 TTATT TTA-TT TTATT TTAT-T TTATT TTAT-T TTA-TT TTATT TTATT
117904445 TTATT TTATT
1 TTATT TTATT
117904455 AAATTAGTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
4 2 0.04
5 33 0.72
6 10 0.22
7 1 0.02
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:117904412 original size:6 final size:6
Alignment explanation
Indices: 117904401--117904451 Score: 61
Period size: 6 Copynumber: 8.5 Consensus size: 6
117904391 GAAGATATTA
*
117904401 TTTTAT TTTTAT TTTTAT TTATTTT TATTTAT TTTTA- TTTTA- TTTTAT
1 TTTTAT TTTTAT TTTTAT TT-TTAT T-TTTAT TTTTAT TTTTAT TTTTAT
117904449 TTT
1 TTT
117904452 ATTAAATTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 10 0.25
6 21 0.52
7 8 0.20
8 1 0.03
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:117904423 original size:10 final size:10
Alignment explanation
Indices: 117904398--117904450 Score: 72
Period size: 10 Copynumber: 5.2 Consensus size: 10
117904388 TAGGAAGATA
*
117904398 TTATTTTATTT
1 TTATTTT-TAT
117904409 TTATTTTTAT
1 TTATTTTTAT
117904419 TTATTTTTAT
1 TTATTTTTAT
117904429 TTATTTTTAT
1 TTATTTTTAT
117904439 TT-TATTTTAT
1 TTAT-TTTTAT
117904449 TT
1 TT
117904451 TATTAAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
9 1 0.03
10 32 0.80
11 7 0.17
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TTATTTTTAT
Found at i:117904423 original size:16 final size:16
Alignment explanation
Indices: 117904401--117904451 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
117904391 GAAGATATTA
117904401 TTTTATTTTTATTT-T
1 TTTTATTTTTATTTAT
117904416 TATTTATTTTTATTTAT
1 T-TTTATTTTTATTTAT
117904433 TTTTA-TTTTATTTTAT
1 TTTTATTTTTA-TTTAT
117904449 TTT
1 TTT
117904452 ATTAAATTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.18
16 25 0.76
17 2 0.06
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTATTTTTATTTAT
Found at i:117904561 original size:43 final size:43
Alignment explanation
Indices: 117904500--117904585 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
117904490 TATAAATAGG
*
117904500 GGTATTTTGTTCTTTGAAAATCATCCATTTATTTTGTCTTCCT
1 GGTATTTTGTTCTTTGAAAATCATCCATTCATTTTGTCTTCCT
117904543 GGTATTTTGTTCTTTGAAAATCATCCATTCATTTTGTCTTCCT
1 GGTATTTTGTTCTTTGAAAATCATCCATTCATTTTGTCTTCCT
117904586 ACTCTAATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (43 bp):
GGTATTTTGTTCTTTGAAAATCATCCATTCATTTTGTCTTCCT
Found at i:117911561 original size:166 final size:167
Alignment explanation
Indices: 117911287--117911622 Score: 620
Period size: 166 Copynumber: 2.0 Consensus size: 167
117911277 TTTCATGAAT
117911287 TTGTGATTTGATGAAATAAGGACTAAATTGTAAAAGTTGTGAAATTCTATGGGCAAATGTGTAAA
1 TTGTGATTTGATGAAATAAGGACTAAATTGTAAAAGTTGTGAAATTCTATGGGCAAATGTGTAAA
*
117911352 AATTCCTTCAAGTGAATTTTTGGATTAAATTGAATAGAGAGATAATTGAATAAGCTGAATTTGAT
66 AATGCCTTCAAGTGAATTTTTGGATTAAATTGAATAGAGAGATAATTGAATAAGCTGAATTTGAT
* *
117911417 ATTATATAGATAAAGAAAAGTGAAATACGGAC-TAAA
131 ATTATATAGATAAAGAAAAGCGAAATACAGACTTAAA
*
117911453 TTGTGATTTGATGAAATAAGGACTAAATTGTAAAAGTTGTGAAATTTTATGGGCAAATGTGTAAA
1 TTGTGATTTGATGAAATAAGGACTAAATTGTAAAAGTTGTGAAATTCTATGGGCAAATGTGTAAA
117911518 AATGCCTTCAAGTGAATTTTTGGATTAAATTGAATAGAGAGATAATTGAATAAGCTGAATTTGAT
66 AATGCCTTCAAGTGAATTTTTGGATTAAATTGAATAGAGAGATAATTGAATAAGCTGAATTTGAT
*
117911583 ATTATATAGATCAAGAAAAGCGAAATACAGACTTAAA
131 ATTATATAGATAAAGAAAAGCGAAATACAGACTTAAA
117911620 TTG
1 TTG
117911623 GGGAAAGAAC
Statistics
Matches: 164, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
166 157 0.96
167 7 0.04
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.33
Consensus pattern (167 bp):
TTGTGATTTGATGAAATAAGGACTAAATTGTAAAAGTTGTGAAATTCTATGGGCAAATGTGTAAA
AATGCCTTCAAGTGAATTTTTGGATTAAATTGAATAGAGAGATAATTGAATAAGCTGAATTTGAT
ATTATATAGATAAAGAAAAGCGAAATACAGACTTAAA
Found at i:117913510 original size:83 final size:83
Alignment explanation
Indices: 117913369--117913534 Score: 215
Period size: 83 Copynumber: 2.0 Consensus size: 83
117913359 ACTGTATGTG
* * ** ** * * *
117913369 AAATGTATGTTTGAATGTGTTATAAGTCTGGTAATGCTCCGTAACCCCATTTCGGCATTGAATAT
1 AAATGTATGTTTAAATGTGTTATAAGTATAATAACACTCCGTAACCCCATTCCAGCATTGAATAC
117913434 GGGTAAAGGGTGTTACAT
66 GGGTAAAGGGTGTTACAT
* *
117913452 AAATGTATGTTTAAATGTGTTATAAGTATAATAACACTTCGTAACCCTATTCCAGCATTGAATAC
1 AAATGTATGTTTAAATGTGTTATAAGTATAATAACACTCCGTAACCCCATTCCAGCATTGAATAC
* *
117913517 GGGTGAGGGGTGTTACAT
66 GGGTAAAGGGTGTTACAT
117913535 TCTTACTCAG
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
83 70 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.34
Consensus pattern (83 bp):
AAATGTATGTTTAAATGTGTTATAAGTATAATAACACTCCGTAACCCCATTCCAGCATTGAATAC
GGGTAAAGGGTGTTACAT
Found at i:117916098 original size:47 final size:46
Alignment explanation
Indices: 117916029--117916438 Score: 291
Period size: 47 Copynumber: 8.8 Consensus size: 46
117916019 TGATTTGTGC
*
117916029 GCCAGTGTAAGACATGTCTGGGACATGGAATCGGCACAAAGATGAGT
1 GCCAGTGTAAGACATGTCTGGGACAT-GCATCGGCACAAAGATGAGT
* * *
117916076 GCCAGAGTAAGACATGTCTGGGACATGCATCGGCCTCGACAGA-GA-T
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGG-CAC-AAAGATGAGT
* * * ** *
117916122 AGCCAGTGTAAGACGTGTCTGGGACACGTATCGG--GTAAGA-GTTGT
1 -GCCAGTGTAAGACATGTCTGGGACATGCATCGGCACAAAGATG-AGT
* * * * *
117916167 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCACGCATATATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCA--CAAAGATGAGT
* * *
117916215 GCCAGTGTAAGACCATGTCTAGGACATGGCATCAGCACAGAGATGAGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCACAAAGATGAGT
* * * * * *
117916263 GCCAGAGTGAGACATGTCTGGGACATACATTGGCTTCGACAGA-GA-T
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGC-AC-AAAGATGAGT
* * * *
117916309 AGCCAGTGTAAGACGTGTCTGGGACACGCATC-G-ACTAAGA-GTTGT
1 -GCCAGTGTAAGACATGTCTGGGACATGCATCGGCACAAAGATG-AGT
* * * *
117916354 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCACACATATATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCACA-A-AGATGAGT
* *
117916402 GCCAGTGTAAGGCCATGTTTGGGACATGGCATCGGCA
1 GCCAGTGTAA-GACATGTCTGGGACAT-GCATCGGCA
117916439 ATTTATCCCA
Statistics
Matches: 282, Mismatches: 57, Indels: 45
0.73 0.15 0.12
Matches are distributed among these distances:
43 8 0.03
44 57 0.20
45 3 0.01
46 16 0.06
47 100 0.35
48 52 0.18
49 29 0.10
50 17 0.06
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.21
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCACAAAGATGAGT
Found at i:117916196 original size:91 final size:91
Alignment explanation
Indices: 117916082--117916384 Score: 358
Period size: 91 Copynumber: 3.3 Consensus size: 91
117916072 GAGTGCCAGA
117916082 GTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGATAGCCAGTGTAAGACGTGTCTGGGAC
1 GTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGATAGCCAGTGTAAGACGTGTCTGGGAC
* *
117916147 ACGTATCGGGTAAGAGTTGTGCTAGT
66 ACGCATCGAGTAAGAGTTGTGCTAGT
* * * * * * *
117916173 GTAAGACATGTCTGGGACATGCATCAG-CACGCATATATGAGAGCCAGTGTAAGACCATGTCTAG
1 GTAAGACATGTCTGGGACATGCATCGGCCTCG-ACAGA-GATAGCCAGTGTAAGA-CGTGTCTGG
* * * * *
117916237 GACATGGCATC-AGCACAGAGATGAGTGCCAGA
63 GACA-CGCATCGAGTA-AGAG-T-TGTGCTAGT
* * * *
117916269 GTGAGACATGTCTGGGACATACATTGGCTTCGACAGAGATAGCCAGTGTAAGACGTGTCTGGGAC
1 GTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGATAGCCAGTGTAAGACGTGTCTGGGAC
*
117916334 ACGCATCGACTAAGAGTTGTGCTAGT
66 ACGCATCGAGTAAGAGTTGTGCTAGT
117916360 GTAAGACATGTCTGGGACATGCATC
1 GTAAGACATGTCTGGGACATGCATC
117916385 AGCACACATA
Statistics
Matches: 169, Mismatches: 34, Indels: 18
0.76 0.15 0.08
Matches are distributed among these distances:
90 3 0.02
91 57 0.34
92 16 0.09
93 22 0.13
94 21 0.12
95 16 0.09
96 32 0.19
97 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.22
Consensus pattern (91 bp):
GTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGATAGCCAGTGTAAGACGTGTCTGGGAC
ACGCATCGAGTAAGAGTTGTGCTAGT
Found at i:117916281 original size:140 final size:136
Alignment explanation
Indices: 117916032--117916287 Score: 311
Period size: 140 Copynumber: 1.8 Consensus size: 136
117916022 TTTGTGCGCC
* * *
117916032 AGTGTAAGACATGTCTGGGACATGGAATCGGCACAAAGATGAGTGCCAGAGTAAGACATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGGAATCAGCACAAAGATGAGAGCCAGAGTAAGACATGTCTAG
* * *
117916097 GACATGCATCGGCCTCGACAGAGATAGCCAGTGTAAGACGTGTCTGGGACACGTATCGGGTAAGA
66 GACATGCATCAG-C-CGACAGAGATAGCCAGAGTAAGACATGTCTGGGACACGTATCGGGTAAGA
117916162 GTTGTGCT
129 GTTGTGCT
* * * *
117916170 AGTGTAAGACATGTCTGGGACAT-GCATCAGCACGCATATATGAGAGCCAGTGTAAGACCATGTC
1 AGTGTAAGACATGTCTGGGACATGGAATCAGCA--CAAAGATGAGAGCCAGAGTAAGA-CATGTC
*
117916234 TAGGACATGGCATCAG-C-ACAGAGATGAGTGCCAGAGTGAGACATGTCTGGGACA
63 TAGGACAT-GCATCAGCCGACAGAGAT-A--GCCAGAGTAAGACATGTCTGGGACA
117916288 TACATTGGCT
Statistics
Matches: 100, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
137 15 0.15
138 25 0.25
139 19 0.19
140 35 0.35
141 6 0.06
ACGTcount: A:0.30, C:0.19, G:0.31, T:0.20
Consensus pattern (136 bp):
AGTGTAAGACATGTCTGGGACATGGAATCAGCACAAAGATGAGAGCCAGAGTAAGACATGTCTAG
GACATGCATCAGCCGACAGAGATAGCCAGAGTAAGACATGTCTGGGACACGTATCGGGTAAGAGT
TGTGCT
Found at i:117916356 original size:187 final size:187
Alignment explanation
Indices: 117916029--117916434 Score: 679
Period size: 187 Copynumber: 2.2 Consensus size: 187
117916019 TGATTTGTGC
* *
117916029 GCCAGTGTAAGA-CATGTCTGGGACATGGAATCGGCACAAAGATGAGTGCCAGAGTAAGACATGT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACAAAGATGAGTGCCAGAGTAAGACATGT
* * **
117916093 CTGGGACATGCATCGGCCTCGACAGAGATAGCCAGTGTAAGACGTGTCTGGGACACGTATCGGGT
66 CTGGGACATACATCGGCCTCGACAGAGATAGCCAGTGTAAGACGTGTCTGGGACACGCATCGACT
*
117916158 AAGAGTTGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCACGCATATATGAGA
131 AAGAGTTGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCACACATATATGAGA
* * *
117916215 GCCAGTGTAAGACCATGTCTAGGACATGGCATCAGCACAGAGATGAGTGCCAGAGTGAGACATGT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACAAAGATGAGTGCCAGAGTAAGACATGT
* *
117916280 CTGGGACATACATTGGCTTCGACAGAGATAGCCAGTGTAAGACGTGTCTGGGACACGCATCGACT
66 CTGGGACATACATCGGCCTCGACAGAGATAGCCAGTGTAAGACGTGTCTGGGACACGCATCGACT
117916345 AAGAGTTGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCACACATATATGAGA
131 AAGAGTTGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCACACATATATGAGA
* *
117916402 GCCAGTGTAAGGCCATGTTTGGGACATGGCATC
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATC
117916435 GGCAATTTAT
Statistics
Matches: 204, Mismatches: 15, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
186 12 0.06
187 192 0.94
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.21
Consensus pattern (187 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACAAAGATGAGTGCCAGAGTAAGACATGT
CTGGGACATACATCGGCCTCGACAGAGATAGCCAGTGTAAGACGTGTCTGGGACACGCATCGACT
AAGAGTTGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCACACATATATGAGA
Found at i:117920188 original size:9 final size:9
Alignment explanation
Indices: 117920174--117920207 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
117920164 TAATGTTAGT
*
117920174 AAAAGAAGA
1 AAAAGAAAA
117920183 AAAAGAAAA
1 AAAAGAAAA
*
117920192 AAAAAAAAA
1 AAAAGAAAA
117920201 AAAAGAA
1 AAAAGAA
117920208 TGCTCATCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Done.