Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 8 of 292
Found at i:2146140 original size:17 final size:18
Alignment explanation
Indices: 2146100--2146140 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2146090 TTGTAATTTA
2146100 TTTGTATAATATTTCATC
1 TTTGTATAATATTTCATC
* *
2146118 TATGTATAA-ATTTCATG
1 TTTGTATAATATTTCATC
2146135 TTTGTA
1 TTTGTA
2146141 ACTTTGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (18 bp):
TTTGTATAATATTTCATC
Found at i:2148899 original size:23 final size:23
Alignment explanation
Indices: 2148864--2148945 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 23
2148854 TGGCTATCCA
*
2148864 GAGCTTC-CTGATAGGCTCTTTGC
1 GAGCTTCTC-GATAGGCTCTTTGT
* *
2148887 GAGCTTTTCGATAGGCTTTTTGT
1 GAGCTTCTCGATAGGCTCTTTGT
* * *
2148910 AAGCTTCCCGATAGGCTCTTCGT
1 GAGCTTCTCGATAGGCTCTTTGT
2148933 GAGCTTCTCGATA
1 GAGCTTCTCGATA
2148946 TGATTCCTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
23 47 0.98
24 1 0.02
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (23 bp):
GAGCTTCTCGATAGGCTCTTTGT
Found at i:2153662 original size:16 final size:19
Alignment explanation
Indices: 2153630--2153667 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
2153620 GCAATTATAA
2153630 TTAAGTTGAGAAAATT-AT
1 TTAAGTTGAGAAAATTAAT
2153648 TTAA-TTGAG-AAATTAAT
1 TTAAGTTGAGAAAATTAAT
2153665 TTA
1 TTA
2153668 GTTAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 10 0.53
18 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (19 bp):
TTAAGTTGAGAAAATTAAT
Found at i:2153674 original size:9 final size:9
Alignment explanation
Indices: 2153658--2153698 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
2153648 TTAATTGAGA
2153658 AATTAATTT
1 AATTAATTT
*
2153667 AGTTAATTT
1 AATTAATTT
2153676 AATTAATTT
1 AATTAATTT
2153685 AATTAATTT
1 AATTAATTT
2153694 -ATTAA
1 AATTAA
2153699 ATGATATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 5 0.17
9 25 0.83
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
AATTAATTT
Found at i:2157805 original size:12 final size:12
Alignment explanation
Indices: 2157788--2157813 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2157778 AACTCTCTCT
2157788 CTCGCTCGTTCG
1 CTCGCTCGTTCG
2157800 CTCGCTCGTTCG
1 CTCGCTCGTTCG
2157812 CT
1 CT
2157814 TGTTCCTCCG
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:0.00, C:0.42, G:0.23, T:0.35
Consensus pattern (12 bp):
CTCGCTCGTTCG
Found at i:2183181 original size:25 final size:26
Alignment explanation
Indices: 2183152--2183234 Score: 89
Period size: 26 Copynumber: 3.3 Consensus size: 26
2183142 GCTTACCGTT
*
2183152 TCAGCTCAATA-GAACTTACTGTCCA
1 TCAGCTCAAGAGGAACTTACTGTCCA
* *
2183177 TCAGCTCAGGAGGAGCTTACTGTCCA
1 TCAGCTCAAGAGGAACTTACTGTCCA
** * *
2183203 TCAGCTCGGGAGGAGCTTACTGTTCA
1 TCAGCTCAAGAGGAACTTACTGTCCA
2183229 T-AGCTC
1 TCAGCTC
2183235 GAAAGAGCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
25 14 0.27
26 38 0.73
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27
Consensus pattern (26 bp):
TCAGCTCAAGAGGAACTTACTGTCCA
Found at i:2183199 original size:26 final size:26
Alignment explanation
Indices: 2183166--2183234 Score: 113
Period size: 26 Copynumber: 2.7 Consensus size: 26
2183156 CTCAATAGAA
2183166 CTTACTGTCCATCAGCTCAGGAGGAG
1 CTTACTGTCCATCAGCTCAGGAGGAG
*
2183192 CTTACTGTCCATCAGCTCGGGAGGAG
1 CTTACTGTCCATCAGCTCAGGAGGAG
*
2183218 CTTACTGTTCAT-AGCTC
1 CTTACTGTCCATCAGCTC
2183235 GAAAGAGCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
25 5 0.12
26 36 0.88
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.28
Consensus pattern (26 bp):
CTTACTGTCCATCAGCTCAGGAGGAG
Found at i:2185962 original size:43 final size:43
Alignment explanation
Indices: 2185914--2186083 Score: 175
Period size: 43 Copynumber: 4.0 Consensus size: 43
2185904 GTTACTGAGA
2185914 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* * * *
2185957 TGTGATTACATTTAAGACCATGTCTGGGGCATTGGCATCGTTAA
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTG-TAT
* * * * * *
2186001 T-CGATTACGTATAAGACCTTGTCTGGGACAGTGGCACTG-AT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* * * *
2186042 ATGTGATAAAATGTAAGACCATATCTGGGATA-TGGCATTGTA
1 -TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTA
2186084 CGAGCTATAT
Statistics
Matches: 101, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
41 1 0.01
42 8 0.08
43 89 0.88
44 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:2187632 original size:53 final size:53
Alignment explanation
Indices: 2187562--2187666 Score: 156
Period size: 53 Copynumber: 2.0 Consensus size: 53
2187552 GTATTATTTG
* * **
2187562 GTAATGCCTTGTAACCCTATTCTGGCGACAGATACGGGTTAAGGGTGTTACAA
1 GTAATACCTCGTAACCCTATTCCAGCGACAGATACGGGTTAAGGGTGTTACAA
* *
2187615 GTAATACCTCGTAACCCTATTCCAGCGACGGATACGGGTTAGGGGTGTTACA
1 GTAATACCTCGTAACCCTATTCCAGCGACAGATACGGGTTAAGGGTGTTACA
2187667 TTTCCACATA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (53 bp):
GTAATACCTCGTAACCCTATTCCAGCGACAGATACGGGTTAAGGGTGTTACAA
Found at i:2189861 original size:26 final size:26
Alignment explanation
Indices: 2189824--2189959 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
2189814 TGATACAAAT
* *
2189824 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
2189850 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
2189876 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
2189902 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
2189928 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
2189954 TGATAA
1 TGATAA
2189960 GAATATCATG
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:2194021 original size:35 final size:35
Alignment explanation
Indices: 2193975--2194046 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
2193965 GAAAAGGTGC
2193975 ATTGCTTCAATGAGAACATCACTAATGCAAATTCT
1 ATTGCTTCAATGAGAACATCACTAATGCAAATTCT
2194010 ATTGCTTCAATGAGAACATCACTAATGCAAATTCT
1 ATTGCTTCAATGAGAACATCACTAATGCAAATTCT
2194045 AT
1 AT
2194047 GTGATTGGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (35 bp):
ATTGCTTCAATGAGAACATCACTAATGCAAATTCT
Found at i:2219648 original size:21 final size:22
Alignment explanation
Indices: 2219624--2219668 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
2219614 TATTTAACCC
*
2219624 AAAATAAATTGGATTA-AAATT
1 AAAATAAATTAGATTATAAATT
* *
2219645 AAAATTAATTATATTATAAATT
1 AAAATAAATTAGATTATAAATT
2219667 AA
1 AA
2219669 TATTCATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
AAAATAAATTAGATTATAAATT
Found at i:2221057 original size:23 final size:24
Alignment explanation
Indices: 2221020--2221064 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
2221010 GATATTTTTT
*
2221020 TAATGTAACAAATATTTTAATATG
1 TAATATAACAAATATTTTAATATG
2221044 TAATATAA-AAATATTTTAATA
1 TAATATAACAAATATTTTAATA
2221065 AATAACTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (24 bp):
TAATATAACAAATATTTTAATATG
Found at i:2223041 original size:87 final size:91
Alignment explanation
Indices: 2222887--2223072 Score: 254
Period size: 87 Copynumber: 2.1 Consensus size: 91
2222877 CAAACTTAAA
* *
2222887 AAAAAAAAAAGCAATTAAGCCCTCCTTTTTTTTTTGCACTCAATTTAGAACTTGAACTTTCAAAA
1 AAAAAAAAAAGCAATTAAACCCTCC--TTTTTTTTGCACTCAATTGAGAACTTGAACTTTCAAAA
* * *
2222952 TACATCAAAAAGGCCCTCAAACTTCTTC
64 TACATAAAAAAGACCCTCAAAATTCTTC
* *
2222980 AAAAAAAAAA-CAATTAAACCC-CC-TTTTTTT-CACTCAATTGGGTACTTGAACTTTCAAAATA
1 AAAAAAAAAAGCAATTAAACCCTCCTTTTTTTTGCACTCAATTGAGAACTTGAACTTTCAAAATA
*
2223041 CATAAAAAAGACCCTCAAAATTTTTC
66 CATAAAAAAGACCCTCAAAATTCTTC
2223067 AAAAAA
1 AAAAAA
2223073 GCAATTAAGC
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
87 56 0.66
88 7 0.08
91 2 0.02
92 10 0.12
93 10 0.12
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (91 bp):
AAAAAAAAAAGCAATTAAACCCTCCTTTTTTTTGCACTCAATTGAGAACTTGAACTTTCAAAATA
CATAAAAAAGACCCTCAAAATTCTTC
Found at i:2223188 original size:39 final size:39
Alignment explanation
Indices: 2223114--2223193 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
2223104 GAAAAAAATT
* *
2223114 ATAAAAAATAATAAATTTTAGAAACATTATTAAATTTTA
1 ATAAAAAATAAAAAATTTTAGAAACATTATTAAATTATA
2223153 ATAAAAATATAAAAAATTTT-GAAA-A-TATTAAAAATTATA
1 ATAAAAA-ATAAAAAATTTTAGAAACATTATT--AAATTATA
2223192 AT
1 AT
2223194 TTTTATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
37 4 0.11
38 1 0.03
39 20 0.56
40 11 0.31
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (39 bp):
ATAAAAAATAAAAAATTTTAGAAACATTATTAAATTATA
Found at i:2223561 original size:22 final size:20
Alignment explanation
Indices: 2223488--2223577 Score: 73
Period size: 19 Copynumber: 4.6 Consensus size: 20
2223478 TTTCTATTTA
*
2223488 TTTTATA-ATTTTTTACGAT
1 TTTTATATATTTTTTACAAT
****
2223507 TTTTATA-AAAAATTACAAT
1 TTTTATATATTTTTTACAAT
2223526 TTTT-TATATTTTTTACAAT
1 TTTTATATATTTTTTACAAT
2223545 TTTTATATATATATTTT-CTAAT
1 TTTTATATAT-T-TTTTAC-AAT
2223567 TTTTAT-TATTT
1 TTTTATATATTT
2223578 GAATTTTTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
18 2 0.04
19 31 0.54
20 6 0.11
21 5 0.09
22 13 0.23
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (20 bp):
TTTTATATATTTTTTACAAT
Found at i:2223648 original size:47 final size:47
Alignment explanation
Indices: 2223523--2223648 Score: 118
Period size: 47 Copynumber: 2.7 Consensus size: 47
2223513 AAAAAATTAC
* *
2223523 AATTTTTTAT-ATTTTTTAC-AATTTTTATATATATATTTTCTAATTTT
1 AATTTTTTGTAATTTTTTTCTAATTTTTA-ATA-ATATTTTCTAATTTT
* * ** *
2223570 TATTATTTG-AATTTTTTAT-TAAAATTTAATAATATTTAT-TGATTTT
1 AATTTTTTGTAATTTTTT-TCTAATTTTTAATAATATTT-TCTAATTTT
2223616 AATTTTTTGTAATTTTTTTCTAATTTTTAATAA
1 AATTTTTTGTAATTTTTTTCTAATTTTTAATAA
2223649 GAGTAGGGGC
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
46 20 0.32
47 36 0.58
48 6 0.10
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (47 bp):
AATTTTTTGTAATTTTTTTCTAATTTTTAATAATATTTTCTAATTTT
Found at i:2223763 original size:92 final size:91
Alignment explanation
Indices: 2223655--2223826 Score: 240
Period size: 92 Copynumber: 1.9 Consensus size: 91
2223645 ATAAGAGTAG
* ** * *
2223655 GGGCTTAATTGCTTTTTTTGAAAAA-GTT-TGAGATTTTTTTAATACATTTTGAAAGTTTAAGTA
1 GGGCTTAATTG--TTTTTTAAAAAAGGTTCAAAGACTTTTTTAATACATTTTAAAAGTTTAAGTA
*
2223718 CCCAAATAAGTGTAAAAAAAGAAAAATAA
64 CCCAAATAA-TATAAAAAAAGAAAAATAA
*
2223747 GGGCTTAATTGTTTTTTAAAAAAGGTTCAAAGGCTTTTTTAATACATTTTAAAAGTTTAAGTACC
1 GGGCTTAATTGTTTTTTAAAAAAGGTTCAAAGACTTTTTTAATACATTTTAAAAGTTTAAGTACC
2223812 CAAATAATATAAAAA
66 CAAATAATATAAAAA
2223827 TAATAATTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
90 11 0.15
91 10 0.14
92 50 0.70
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (91 bp):
GGGCTTAATTGTTTTTTAAAAAAGGTTCAAAGACTTTTTTAATACATTTTAAAAGTTTAAGTACC
CAAATAATATAAAAAAAGAAAAATAA
Found at i:2224459 original size:13 final size:13
Alignment explanation
Indices: 2224443--2224476 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2224433 AATACTAAAT
2224443 TATCTTTAAATAA
1 TATCTTTAAATAA
**
2224456 TATCAATAAATAA
1 TATCTTTAAATAA
2224469 TATCTTTA
1 TATCTTTA
2224477 TAATTTTTCT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (13 bp):
TATCTTTAAATAA
Found at i:2231206 original size:13 final size:13
Alignment explanation
Indices: 2231188--2231212 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2231178 GTCTTGGTGA
2231188 TCTAGTAAAACAC
1 TCTAGTAAAACAC
2231201 TCTAGTAAAACA
1 TCTAGTAAAACA
2231213 AAAGTTACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (13 bp):
TCTAGTAAAACAC
Found at i:2231977 original size:31 final size:31
Alignment explanation
Indices: 2231907--2231990 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 31
2231897 ATTGGGGTTT
* ** **
2231907 AATTAAAATTTTTAAATTTTTTTTTGAGATT
1 AATTAAAATTTTTAAAATTTTTAATGAGAAA
*
2231938 AATGAAAATTTTCTAAAATTTTTAATGA-AAA
1 AATTAAAATTTT-TAAAATTTTTAATGAGAAA
*
2231969 AATTAAAATTGCTTAAAATTTT
1 AATTAAAATT-TTTAAAATTTT
2231991 GGGAGGGGTG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
31 30 0.70
32 13 0.30
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (31 bp):
AATTAAAATTTTTAAAATTTTTAATGAGAAA
Found at i:2233672 original size:18 final size:20
Alignment explanation
Indices: 2233649--2233686 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
2233639 ATCTCCACCT
2233649 TTAGATTT-TT-TTGCCTAA
1 TTAGATTTATTCTTGCCTAA
2233667 TTAGATTTATTCTTGCCTAA
1 TTAGATTTATTCTTGCCTAA
2233687 CCTTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 2 0.11
20 8 0.44
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.53
Consensus pattern (20 bp):
TTAGATTTATTCTTGCCTAA
Found at i:2234038 original size:112 final size:112
Alignment explanation
Indices: 2233841--2234055 Score: 376
Period size: 112 Copynumber: 1.9 Consensus size: 112
2233831 GCCTAACCTT
*
2233841 CTTTTTTTTGGCCTAATAACAAATTCAACCTTCCAATATTTCTAATTTTATTAATTTGATCCTAA
1 CTTTTTTTTGGCCTAATAACAAATTCAACCTTCAAATATTTCTAATTTTATTAATTTGATCCTAA
* *
2233906 ATCTAAAGAAATCAACGAATTTAGCCCTTAATGTTTTATATAGTTCA
66 ATCTAAAGAAACCAAAGAATTTAGCCCTTAATGTTTTATATAGTTCA
* *
2233953 CTTTTTTTTGGCCTAATAACAAATTTAACCTTCAAATATTTCTAATTTTATTAATTTGATCCTAC
1 CTTTTTTTTGGCCTAATAACAAATTCAACCTTCAAATATTTCTAATTTTATTAATTTGATCCTAA
*
2234018 ATCTAAAGCAACCAAAGAATTTAGCCCTTAATGTTTTA
66 ATCTAAAGAAACCAAAGAATTTAGCCCTTAATGTTTTA
2234056 ATTCTAATTC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 97 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (112 bp):
CTTTTTTTTGGCCTAATAACAAATTCAACCTTCAAATATTTCTAATTTTATTAATTTGATCCTAA
ATCTAAAGAAACCAAAGAATTTAGCCCTTAATGTTTTATATAGTTCA
Found at i:2234256 original size:15 final size:15
Alignment explanation
Indices: 2234217--2234261 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2234207 ACATTAAAGA
2234217 ATATTTTTAAAAAATGT
1 ATATTTTT--AAAATGT
*
2234234 ATTTTTTTAAAATGT
1 ATATTTTTAAAATGT
*
2234249 ATATTTTTGAAAT
1 ATATTTTTAAAAT
2234262 ATCTATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 18 0.72
17 7 0.28
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
ATATTTTTAAAATGT
Found at i:2234928 original size:13 final size:13
Alignment explanation
Indices: 2234910--2234935 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2234900 CTAAAAAAAA
2234910 CATCATCTAATTT
1 CATCATCTAATTT
2234923 CATCATCTAATTT
1 CATCATCTAATTT
2234936 AAATATAGTC
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:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
CATCATCTAATTT
Found at i:2241088 original size:12 final size:13
Alignment explanation
Indices: 2241073--2241101 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2241063 ATATATTTTT
2241073 ATATAAAAAA-TA
1 ATATAAAAAATTA
2241085 ATATAAAAAATTA
1 ATATAAAAAATTA
2241098 ATAT
1 ATAT
2241102 GGACGGACCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATAAAAAATTA
Found at i:2242212 original size:45 final size:45
Alignment explanation
Indices: 2242161--2242306 Score: 121
Period size: 45 Copynumber: 3.0 Consensus size: 45
2242151 TGGAAGTGGG
*
2242161 AGGAAATCGGATGATGAAGATGAAGGGTATAAGAAATCTAGTTAT
1 AGGAAATCGGATGATGAAGATGAAGGGTATAAGAAATCGAGTTAT
* * * * * ***
2242206 AGGAAATCGAGTTATGATAGATCAGATGAAAGAGAAGAAGGATATGGAGGTGGG
1 AGGAAATCG-G--ATGAT-GA--AGATG-AAGGGTATAA-GAAATCGA-GTTAT
*
2242260 AGGAAATCGGATGATGAAGATGAAGGGTATAAGAAGTCGAGTTAT
1 AGGAAATCGGATGATGAAGATGAAGGGTATAAGAAATCGAGTTAT
2242305 AG
1 AG
2242307 AAGAAATGAT
Statistics
Matches: 74, Mismatches: 18, Indels: 18
0.67 0.16 0.16
Matches are distributed among these distances:
45 13 0.18
46 6 0.08
47 7 0.09
48 10 0.14
49 2 0.03
50 2 0.03
51 10 0.14
52 7 0.09
53 6 0.08
54 11 0.15
ACGTcount: A:0.41, C:0.04, G:0.34, T:0.21
Consensus pattern (45 bp):
AGGAAATCGGATGATGAAGATGAAGGGTATAAGAAATCGAGTTAT
Found at i:2242330 original size:99 final size:99
Alignment explanation
Indices: 2242150--2242333 Score: 266
Period size: 99 Copynumber: 1.9 Consensus size: 99
2242140 AAGCAAAGCC
*
2242150 ATGGAAGTGGGAGGAAATCGGATGATGAAGATGAAGGGTATAAGAAATCTAGTTATAGGAAATCG
1 ATGGAAGTGGGAGGAAATCGGATGATGAAGATGAAGGGTATAAGAAATCGAGTTATAGGAAATCG
* **
2242215 AGTTATGATAGATCAGATGAAAGAGAAGAAGGAT
66 AGTGACAATAGATCAGATGAAAGAGAAGAAGGAT
* *
2242249 ATGGAGGTGGGAGGAAATCGGATGATGAAGATGAAGGGTATAAGAAGTCGAGTTATAGAAGAAAT
1 ATGGAAGTGGGAGGAAATCGGATGATGAAGATGAAGGGTATAAGAAATCGAGTTATAG--GAAAT
2242314 -GA-TGACAAT-GATTCAGATGA
64 CGAGTGACAATAGA-TCAGATGA
2242334 TGAAAGGAGG
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
98 2 0.03
99 67 0.88
100 2 0.03
101 5 0.07
ACGTcount: A:0.41, C:0.04, G:0.33, T:0.21
Consensus pattern (99 bp):
ATGGAAGTGGGAGGAAATCGGATGATGAAGATGAAGGGTATAAGAAATCGAGTTATAGGAAATCG
AGTGACAATAGATCAGATGAAAGAGAAGAAGGAT
Found at i:2245712 original size:2 final size:2
Alignment explanation
Indices: 2245705--2245737 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2245695 TCTTTTACAA
2245705 AT 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 AT A
2245738 AAAGCGTCAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2249958 original size:16 final size:16
Alignment explanation
Indices: 2249939--2249972 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2249929 AAATATTTGA
2249939 AAATGAAACTATATCT
1 AAATGAAACTATATCT
2249955 AAATGAAACTATATCT
1 AAATGAAACTATATCT
2249971 AA
1 AA
2249973 GTTTTTATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (16 bp):
AAATGAAACTATATCT
Found at i:2253002 original size:17 final size:16
Alignment explanation
Indices: 2252982--2253019 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
2252972 AATTTTTAAG
*
2252982 TTTTAAAATTATATAT
1 TTTTAAAATGATATAT
2252998 ATTTTAAAATGATATAT
1 -TTTTAAAATGATATAT
2253015 TTTTA
1 TTTTA
2253020 TTTTTTATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTTAAAATGATATAT
Found at i:2260704 original size:69 final size:69
Alignment explanation
Indices: 2260593--2260814 Score: 302
Period size: 69 Copynumber: 3.2 Consensus size: 69
2260583 GCTGGGGGCA
* *
2260593 TAGGTCCGCTAGCTGTTTTGGAGGTTGCGATCTTAAATCGTCAAACCTTTATGACATCAGTTGGG
1 TAGGTCCGCTAGCTGATTTGGAGGTTGCGATATTAAATCGTCAAACCTTTATGACATCAGTTGGG
*
2260658 AATG
66 AGTG
* * * *
2260662 TAGGTCCGTTAGCTGATTTGGAGGTTGTGATATTAAATCGTCAAACGTTTATGACATCAGTTAGG
1 TAGGTCCGCTAGCTGATTTGGAGGTTGCGATATTAAATCGTCAAACCTTTATGACATCAGTTGGG
*
2260727 AGCG
66 AGTG
** * * *
2260731 TAGGTTTGCTACCT-ATTTTGGAGGTTGCGATATTAAATCGTCAAACCTTTATGACATAAATTGG
1 TAGGTCCGCTAGCTGA-TTTGGAGGTTGCGATATTAAATCGTCAAACCTTTATGACATCAGTTGG
2260795 GAGTG
65 GAGTG
*
2260800 TAGGTTCGCTAGCTG
1 TAGGTCCGCTAGCTG
2260815 TATCAGAGTT
Statistics
Matches: 131, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
68 1 0.01
69 130 0.99
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (69 bp):
TAGGTCCGCTAGCTGATTTGGAGGTTGCGATATTAAATCGTCAAACCTTTATGACATCAGTTGGG
AGTG
Found at i:2266998 original size:47 final size:49
Alignment explanation
Indices: 2266940--2267047 Score: 123
Period size: 47 Copynumber: 2.3 Consensus size: 49
2266930 ACATAACAAT
* *
2266940 ATTTTATATTTTATAT-TTTAAATATTATGATTTAAATAAGATTTTTAG
1 ATTTTAGATTTTATATCTTTAAATATTAGGATTTAAATAAGATTTTTAG
* * * * * *
2266988 ATTTTA-ATTTT-TGTCTTTATATATTAGGTTTTGAATTAGCTTTTTAG
1 ATTTTAGATTTTATATCTTTAAATATTAGGATTTAAATAAGATTTTTAG
2267035 ATTTTAGATTTTA
1 ATTTTAGATTTTA
2267048 AATATTAAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
46 2 0.04
47 37 0.74
48 11 0.22
ACGTcount: A:0.31, C:0.02, G:0.09, T:0.58
Consensus pattern (49 bp):
ATTTTAGATTTTATATCTTTAAATATTAGGATTTAAATAAGATTTTTAG
Found at i:2268580 original size:44 final size:44
Alignment explanation
Indices: 2268519--2268605 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
2268509 GCTGACGATC
*
2268519 CCCGAGCTCGTAACTTGATTCCAAAATTTATAAAACAAAGACAT
1 CCCGAGCTCGTAACTTGATCCCAAAATTTATAAAACAAAGACAT
2268563 CCCGAGCTCGTAACTTGATCCCAAAATTTATAAAACAAAGACA
1 CCCGAGCTCGTAACTTGATCCCAAAATTTATAAAACAAAGACA
2268606 AACATATACA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.23
Consensus pattern (44 bp):
CCCGAGCTCGTAACTTGATCCCAAAATTTATAAAACAAAGACAT
Found at i:2269234 original size:41 final size:44
Alignment explanation
Indices: 2269174--2269306 Score: 139
Period size: 45 Copynumber: 3.0 Consensus size: 44
2269164 ATGCTATCTC
* * *
2269174 ATATCAATGCCACTGTCCCAGACAGGGTCTTACACGAATCA-A-
1 ATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAACCACAT
* * *
2269216 ATAT-GATGTCGATGTCCCAGACACGGTCTTACACGTAACCACAT
1 ATATCGATGCCAATGTCCCAGACAGGGTCTTACACG-AACCACAT
* *
2269260 ATATCGATGCCAACGTCCCAGAC-GTGGTCTTACACGAAAACACAT
1 ATATCGATGCCAATGTCCCAGACAG-GGTCTTACACG-AACCACAT
2269305 AT
1 AT
2269307 CGAAAAATCC
Statistics
Matches: 74, Mismatches: 12, Indels: 7
0.80 0.13 0.08
Matches are distributed among these distances:
41 26 0.35
42 8 0.11
43 1 0.01
44 4 0.05
45 35 0.47
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (44 bp):
ATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAACCACAT
Found at i:2270483 original size:47 final size:47
Alignment explanation
Indices: 2270431--2270573 Score: 157
Period size: 47 Copynumber: 3.3 Consensus size: 47
2270421 AATTATGTTA
2270431 TATTATAACATATATTAACCTATTATTTAATTTACATATTTAACCTT
1 TATTATAACATATATTAACCTATTATTTAATTTACATATTTAACCTT
* * *
2270478 TATTATAA-A-ATATGAAACC-ATTATGTAA-TT--AT-GTT-A----
1 TATTATAACATATAT-TAACCTATTATTTAATTTACATATTTAACCTT
2270514 TATTATAACATATATTAACCTATTATTTAATTTACATATTTAACCTT
1 TATTATAACATATATTAACCTATTATTTAATTTACATATTTAACCTT
*
2270561 TATTATAAAATAT
1 TATTATAACATAT
2270574 GAAACCATTA
Statistics
Matches: 76, Mismatches: 7, Indels: 26
0.70 0.06 0.24
Matches are distributed among these distances:
36 8 0.11
37 5 0.07
38 12 0.16
39 2 0.03
40 1 0.01
41 4 0.05
42 4 0.05
43 1 0.01
44 2 0.03
45 12 0.16
46 5 0.07
47 20 0.26
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (47 bp):
TATTATAACATATATTAACCTATTATTTAATTTACATATTTAACCTT
Found at i:2270521 original size:83 final size:83
Alignment explanation
Indices: 2270420--2270584 Score: 330
Period size: 83 Copynumber: 2.0 Consensus size: 83
2270410 CAATGGCTTT
2270420 TAATTATGTTATATTATAACATATATTAACCTATTATTTAATTTACATATTTAACCTTTATTATA
1 TAATTATGTTATATTATAACATATATTAACCTATTATTTAATTTACATATTTAACCTTTATTATA
2270485 AAATATGAAACCATTATG
66 AAATATGAAACCATTATG
2270503 TAATTATGTTATATTATAACATATATTAACCTATTATTTAATTTACATATTTAACCTTTATTATA
1 TAATTATGTTATATTATAACATATATTAACCTATTATTTAATTTACATATTTAACCTTTATTATA
2270568 AAATATGAAACCATTAT
66 AAATATGAAACCATTAT
2270585 AACATAAGGT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (83 bp):
TAATTATGTTATATTATAACATATATTAACCTATTATTTAATTTACATATTTAACCTTTATTATA
AAATATGAAACCATTATG
Found at i:2274454 original size:41 final size:42
Alignment explanation
Indices: 2274408--2274602 Score: 162
Period size: 49 Copynumber: 4.3 Consensus size: 42
2274398 CATAGTTCAA
2274408 CTATGGTCTTACACATCTTCATATAATGATGCCATAG-CCAG
1 CTATGGTCTTACACATCTTCATATAATGATGCCATAGCCCAG
* * * *
2274449 CTATGGTCTTACACATATTCATATATTGATGCCATAGTCCAA
1 CTATGGTCTTACACATCTTCATATAATGATGCCATAGCCCAG
*
2274491 CTATGGTCTTACACGTAATC-ACATATCACATATCGATGCCATAGCCCAG
1 CTATGGTCTTACAC---ATCTTCATAT---A-AT-GATGCCATAGCCCAG
* *
2274540 CTATGGTCTTACACGTAATC-ACATATCACATATCGATGCCATAACCCAG
1 CTATGGTCTTACAC---ATCTTCATAT---A-AT-GATGCCATAGCCCAG
2274589 CTATGGTCTTACAC
1 CTATGGTCTTACAC
2274603 GTAATCACAT
Statistics
Matches: 136, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
41 35 0.26
42 17 0.12
44 5 0.04
45 2 0.01
47 1 0.01
48 1 0.01
49 75 0.55
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.30
Consensus pattern (42 bp):
CTATGGTCTTACACATCTTCATATAATGATGCCATAGCCCAG
Found at i:2274533 original size:49 final size:49
Alignment explanation
Indices: 2274460--2274694 Score: 332
Period size: 49 Copynumber: 4.8 Consensus size: 49
2274450 TATGGTCTTA
* * ** *
2274460 CACATATTCATATATTGATGCCATAGTCCAACTATGGTCTTACACGTAAT
1 CACATA-TCACATATCGATGCCATAACCCAGCTATGGTCTTACACGTAAT
*
2274510 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
1 CACATATCACATATCGATGCCATAACCCAGCTATGGTCTTACACGTAAT
2274559 CACATATCACATATCGATGCCATAACCCAGCTATGGTCTTACACGTAAT
1 CACATATCACATATCGATGCCATAACCCAGCTATGGTCTTACACGTAAT
*
2274608 CACATATCACATATCGATGCCATAACCCATCTATGGTCTTACACG-AAT
1 CACATATCACATATCGATGCCATAACCCAGCTATGGTCTTACACGTAAT
* * * * *
2274656 CACATATCTCA-CT-GATGTCATATCCCAGATATGGTCTTA
1 CACATATCACATATCGATGCCATAACCCAGCTATGGTCTTA
2274695 TACAGTAGCA
Statistics
Matches: 173, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
46 22 0.13
47 1 0.01
48 13 0.08
49 131 0.76
50 6 0.03
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.29
Consensus pattern (49 bp):
CACATATCACATATCGATGCCATAACCCAGCTATGGTCTTACACGTAAT
Found at i:2274753 original size:95 final size:96
Alignment explanation
Indices: 2274435--2274741 Score: 287
Period size: 98 Copynumber: 3.3 Consensus size: 96
2274425 TTCATATAAT
* * * **
2274435 GATGCCAT-AGCCAGCTATGGTCTTACAC--AT---AT-TCATATATTGATGCCATAGTCCA-AC
1 GATGCCATAACCCAGCTATGGTCTTACACGAATCACATATCACATATCGATGCCATAACCCAGA-
* *
2274492 TATGGTCTTACACGTAATCACATATCACATATC
65 TATGGTCTTACACGTAAGCACATATCACA-ACC
* *
2274525 GATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATATCGATGCCATAACCCAGC
1 GATGCCATAACCCAGCTATGGTCTTACACG-AATCACATATCACATATCGATGCCATAACCCAGA
* *
2274590 TATGGTCTTACACGTAATCACATATCACATATC
65 TATGGTCTTACACGTAAGCACATATCACA-ACC
* * * * *
2274623 GATGCCATAACCCATCTATGGTCTTACACGAATCACATATCTCA-CT-GATGTCATATCCCAGAT
1 GATGCCATAACCCAGCTATGGTCTTACACGAATCACATATCACATATCGATGCCATAACCCAGAT
* **
2274686 ATGGTCTTATACAGT-AGCATTTATCAC-ACC
66 ATGGTCTTACAC-GTAAGCACATATCACAACC
** *
2274716 GATGCCATTTCCCAGATATGGTCTTA
1 GATGCCATAACCCAGCTATGGTCTTA
2274742 TACAGAAATC
Statistics
Matches: 184, Mismatches: 23, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
90 8 0.04
91 18 0.10
93 24 0.13
94 2 0.01
95 34 0.18
96 3 0.02
97 15 0.08
98 80 0.43
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (96 bp):
GATGCCATAACCCAGCTATGGTCTTACACGAATCACATATCACATATCGATGCCATAACCCAGAT
ATGGTCTTACACGTAAGCACATATCACAACC
Found at i:2274806 original size:31 final size:31
Alignment explanation
Indices: 2274763--2274880 Score: 173
Period size: 31 Copynumber: 3.8 Consensus size: 31
2274753 CTTGTCACTT
* * *
2274763 GTAGCCGAAGCTACTACTATTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
*
2274794 GTAGTCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
*
2274825 GTAGCCGGAGTTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
* *
2274856 GTAGCAGAAGCTACCACTTTTCACT
1 GTAGCCGGAGCTACCACTTTTCACT
2274881 TGTCATTTGT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.28
Consensus pattern (31 bp):
GTAGCCGGAGCTACCACTTTTCACTGATCAG
Found at i:2274950 original size:50 final size:51
Alignment explanation
Indices: 2274856--2274984 Score: 215
Period size: 50 Copynumber: 2.5 Consensus size: 51
2274846 CACTGATCAG
* * *
2274856 GTAGCAGAAGCTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCCTTGATCAGATAAGT
*
2274907 GTAGTCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCCTTGATCAGATAAGT
2274957 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
2274985 TGCCATGGTC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 49 0.68
51 23 0.32
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCCTTGATCAGATAAGT
Found at i:2277948 original size:43 final size:43
Alignment explanation
Indices: 2277888--2278007 Score: 168
Period size: 43 Copynumber: 2.8 Consensus size: 43
2277878 CATTTTCAAG
* * *
2277888 TCGAACCAAATATACTAGCACACGAGGTGCATCATCGGACAAA
1 TCGAAGCAATTATACTAGCACACGAGGTGCATCATCAGACAAA
* *
2277931 TCGAAGCAATTATACTAGCACAGGAGGTGCATTATCAGACAAA
1 TCGAAGCAATTATACTAGCACACGAGGTGCATCATCAGACAAA
* * *
2277974 CCGAGGCAATTATACTAGCACACAAGGTGCATCA
1 TCGAAGCAATTATACTAGCACACGAGGTGCATCA
2278008 CTGGAAAAGC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.18
Consensus pattern (43 bp):
TCGAAGCAATTATACTAGCACACGAGGTGCATCATCAGACAAA
Found at i:2281324 original size:25 final size:23
Alignment explanation
Indices: 2281272--2281329 Score: 84
Period size: 21 Copynumber: 2.5 Consensus size: 23
2281262 AACAATCATT
2281272 TTGTTAAAAATTTCATTCATTTC
1 TTGTTAAAAATTTCATTCATTTC
2281295 -T-TTAAAAATTTCATTCATTTC
1 TTGTTAAAAATTTCATTCATTTC
2281316 TATTGTTAAAAATT
1 --TTGTTAAAAATT
2281330 AATCCATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 20 0.65
22 1 0.03
24 1 0.03
25 9 0.29
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.52
Consensus pattern (23 bp):
TTGTTAAAAATTTCATTCATTTC
Found at i:2282426 original size:19 final size:21
Alignment explanation
Indices: 2282402--2282443 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
2282392 TTTCAACTCA
2282402 TAAAAAT-A-AAAATAATAAT
1 TAAAAATAAGAAAATAATAAT
2282421 TAAAAATAATGAAAATAATAAT
1 TAAAAATAA-GAAAATAATAAT
2282443 T
1 T
2282444 TCATTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
22 12 0.60
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
TAAAAATAAGAAAATAATAAT
Found at i:2283860 original size:19 final size:20
Alignment explanation
Indices: 2283822--2283860 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2283812 TTATCATTAA
*
2283822 ATATTTATAAATTGAAATAT
1 ATATTTATAAATTAAAATAT
*
2283842 ATATTTAT-TATTAAAATAT
1 ATATTTATAAATTAAAATAT
2283861 TGATATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
ATATTTATAAATTAAAATAT
Found at i:2290746 original size:37 final size:37
Alignment explanation
Indices: 2290697--2290771 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
2290687 TGACCATATG
2290697 TATGTAACTCATGTGCTTTGATATAAGTCGAGGCTTA
1 TATGTAACTCATGTGCTTTGATATAAGTCGAGGCTTA
2290734 TATGTAACTCATGTGCTTTGATATAAGTCGAGGCTTA
1 TATGTAACTCATGTGCTTTGATATAAGTCGAGGCTTA
2290771 T
1 T
2290772 GCTTTAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (37 bp):
TATGTAACTCATGTGCTTTGATATAAGTCGAGGCTTA
Found at i:2291989 original size:68 final size:69
Alignment explanation
Indices: 2291917--2292044 Score: 222
Period size: 69 Copynumber: 1.9 Consensus size: 69
2291907 ATTTTTTTAA
*
2291917 TAAATTTAATTTAATATTTATATTG-ATAGTATTTTATTAATTTAATATTAAAATAATTATCTTA
1 TAAATTTAATTTAATATTTATATTGAAAAGTATTTTATTAATTTAATATTAAAATAATTATCTTA
2291981 ATAT
66 ATAT
* *
2291985 TAAATTTAATTTAATATTTATCTTGAAAAGTATTTTATTAATTTAATATTAAAGTAATTA
1 TAAATTTAATTTAATATTTATATTGAAAAGTATTTTATTAATTTAATATTAAAATAATTA
2292045 AGTTTAATTA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
68 24 0.43
69 32 0.57
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (69 bp):
TAAATTTAATTTAATATTTATATTGAAAAGTATTTTATTAATTTAATATTAAAATAATTATCTTA
ATAT
Found at i:2301324 original size:46 final size:44
Alignment explanation
Indices: 2301235--2301325 Score: 103
Period size: 45 Copynumber: 2.0 Consensus size: 44
2301225 AATTTTCATT
* * *
2301235 TCCATTTTGAGGAAACCACATCATTTTCCAAATGATTCTATTTC
1 TCCATTTTGAGAAAACCAAATCATTTTCCAAATGATTCCATTTC
* *
2301279 TCCATTTCTGAGAAAACCATAATCA-TTTCTAAATGTTTTCCATTTC
1 TCCATTT-TGAGAAAACCA-AATCATTTTCCAAATG-ATTCCATTTC
2301325 T
1 T
2301326 TTATTTCTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
44 7 0.18
45 19 0.49
46 13 0.33
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (44 bp):
TCCATTTTGAGAAAACCAAATCATTTTCCAAATGATTCCATTTC
Found at i:2305672 original size:14 final size:14
Alignment explanation
Indices: 2305649--2305678 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2305639 TTGAAATTAT
2305649 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
2305663 GTTGATTTGGATTG
1 GTTGAATTGGATTG
2305677 GT
1 GT
2305679 CTCGATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:2306660 original size:14 final size:14
Alignment explanation
Indices: 2306641--2306668 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2306631 TCACATCCCA
2306641 AAAATCAGGTTAGT
1 AAAATCAGGTTAGT
2306655 AAAATCAGGTTAGT
1 AAAATCAGGTTAGT
2306669 GAACCGGATG
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:0.07, G:0.21, T:0.29
Consensus pattern (14 bp):
AAAATCAGGTTAGT
Found at i:2308524 original size:40 final size:43
Alignment explanation
Indices: 2308481--2308563 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
2308471 TTTATCTTAG
* * * *
2308481 AAAAA-AAATTTAAAA-ATGAGAAGATAATCTTGGGTTGTTGA
1 AAAAAGAAATTAAAAAGAGGAGAAGATAAACATGGGTTGTTGA
2308522 AAAAAGAAATTAAAAAGAGGAGAAGATAAACATGGGTTGTTG
1 AAAAAGAAATTAAAAAGAGGAGAAGATAAACATGGGTTGTTG
2308564 GATTTACCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 5 0.14
42 9 0.25
43 22 0.61
ACGTcount: A:0.51, C:0.02, G:0.23, T:0.24
Consensus pattern (43 bp):
AAAAAGAAATTAAAAAGAGGAGAAGATAAACATGGGTTGTTGA
Found at i:2314524 original size:46 final size:44
Alignment explanation
Indices: 2314420--2314527 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
2314410 TGTCTTTGAC
** * * *
2314420 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
2314464 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
2314510 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
2314528 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:2321909 original size:46 final size:44
Alignment explanation
Indices: 2321805--2321912 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
2321795 TGTCTTTGAC
** * * *
2321805 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
2321849 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
2321895 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
2321913 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:2325461 original size:57 final size:58
Alignment explanation
Indices: 2325390--2325529 Score: 142
Period size: 57 Copynumber: 2.4 Consensus size: 58
2325380 GTTATGGATT
* * * *
2325390 GGATTTAACTTAGACGGGTAATCCAGA-TCAAGCTCT-TTAGAGCAT-ATGTCATAAAAA
1 GGATTTAGCCTAGACTGGTAATCCAGACT-AAGCTCTATT-GAGCATAATATCATAAAAA
* * * * * *
2325447 GGATTTAGCCTAGACTGATAATCCTGACTAAGCTCTATTGAGTATAAATATTATAGATA
1 GGATTTAGCCTAGACTGGTAATCCAGACTAAGCTCTATTGAGCAT-AATATCATAAAAA
2325506 GGATTTAGCCTAGACTGGTAATCC
1 GGATTTAGCCTAGACTGGTAATCC
2325530 TATTGCATAC
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
57 34 0.50
58 3 0.04
59 31 0.46
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (58 bp):
GGATTTAGCCTAGACTGGTAATCCAGACTAAGCTCTATTGAGCATAATATCATAAAAA
Found at i:2327402 original size:48 final size:48
Alignment explanation
Indices: 2327347--2327442 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
2327337 CCACTTATCA
2327347 AAATCCACTATAAGAGATTGGGAGTATATATATGGTGAAAGGGTTTTT
1 AAATCCACTATAAGAGATTGGGAGTATATATATGGTGAAAGGGTTTTT
*
2327395 AAATCCACTATAAGAGATTGGGAGTATATATATGGTGAAGGGGTTTTT
1 AAATCCACTATAAGAGATTGGGAGTATATATATGGTGAAAGGGTTTTT
2327443 CTCTTCCGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.33
Consensus pattern (48 bp):
AAATCCACTATAAGAGATTGGGAGTATATATATGGTGAAAGGGTTTTT
Found at i:2328359 original size:25 final size:25
Alignment explanation
Indices: 2328295--2328361 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
2328285 AAATGGATTA
* * * *
2328295 TCTGTAAAGTCTTTATGGCAATCTC
1 TCTGGAAAGCCTTTGTGACAATCTC
*
2328320 TCTAGAAAGCCTTTGTGACAATCTC
1 TCTGGAAAGCCTTTGTGACAATCTC
2328345 TCTGGAAAGCCTTTGTG
1 TCTGGAAAGCCTTTGTG
2328362 GTATATTATC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (25 bp):
TCTGGAAAGCCTTTGTGACAATCTC
Found at i:2335371 original size:25 final size:25
Alignment explanation
Indices: 2335332--2335422 Score: 103
Period size: 25 Copynumber: 3.6 Consensus size: 25
2335322 CTATAAAACC
* *
2335332 TTATGGTGATCTCTCTGAAAAGCTT
1 TTATGGCGATATCTCTGAAAAGCTT
*
2335357 TTACGGCGATATCTCTGAAAAGCTT
1 TTATGGCGATATCTCTGAAAAGCTT
* * *
2335382 TTATGGTGATCTCTCTGGAAAGCCTT
1 TTATGGCGATATCTCTGAAAAG-CTT
*
2335408 TT-TGGCGATTTCTCT
1 TTATGGCGATATCTCT
2335423 ATAAAGCCAT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
25 51 0.91
26 5 0.09
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (25 bp):
TTATGGCGATATCTCTGAAAAGCTT
Found at i:2335428 original size:25 final size:25
Alignment explanation
Indices: 2335275--2335430 Score: 90
Period size: 25 Copynumber: 6.3 Consensus size: 25
2335265 AGACTATTTG
* *
2335275 TAAAGCCTTTGTGGCAATCTCTCTA
1 TAAAGCCTTTTTGGCGATCTCTCTA
* * * *
2335300 GAAAGCCTTTGTGGCAAAT-TCCCTA
1 TAAAGCCTTTTTGGC-GATCTCTCTA
* * *
2335325 TAAAACC-TTATGGTGATCTCTCTGA
1 TAAAGCCTTTTTGGCGATCTCTCT-A
* *
2335350 -AAAG-CTTTTACGGCGATATCTCTGA
1 TAAAGCCTTTT-TGGCGATCTCTCT-A
* *
2335375 -AAAG-CTTTTATGGTGATCTCTCTG
1 TAAAGCCTTTT-TGGCGATCTCTCTA
* *
2335399 GAAAGCCTTTTTGGCGATTTCTCTA
1 TAAAGCCTTTTTGGCGATCTCTCTA
2335424 TAAAGCC
1 TAAAGCC
2335431 ATTGTGGGAT
Statistics
Matches: 103, Mismatches: 21, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
23 3 0.03
24 14 0.14
25 78 0.76
26 8 0.08
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (25 bp):
TAAAGCCTTTTTGGCGATCTCTCTA
Found at i:2335429 original size:50 final size:49
Alignment explanation
Indices: 2335291--2335430 Score: 149
Period size: 50 Copynumber: 2.8 Consensus size: 49
2335281 CTTTGTGGCA
* * * * * *
2335291 ATCTCTCTAGAAAGCCTTTGTGGCAAATTCCCTATAAAACCTTATGGTG
1 ATCTCTCTGGAAAGCCTTTTTGGCGATTTCTCTATAAAGCCTTATGGTG
* * * *
2335340 ATCTCTCTGAAAAG-CTTTTACGGCGATATCTCTGA-AAAGCTTTTATGGTG
1 ATCTCTCTGGAAAGCCTTTT-TGGCGATTTCTCT-ATAAAGC-CTTATGGTG
2335390 ATCTCTCTGGAAAGCCTTTTTGGCGATTTCTCTATAAAGCC
1 ATCTCTCTGGAAAGCCTTTTTGGCGATTTCTCTATAAAGCC
2335431 ATTGTGGGAT
Statistics
Matches: 72, Mismatches: 14, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
48 4 0.06
49 25 0.35
50 38 0.53
51 5 0.07
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (49 bp):
ATCTCTCTGGAAAGCCTTTTTGGCGATTTCTCTATAAAGCCTTATGGTG
Found at i:2346595 original size:37 final size:38
Alignment explanation
Indices: 2346553--2346627 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 38
2346543 CCTGATCCCA
* * *
2346553 CACATATGGGGAGGCTTACGAGAGGTCCTGC-TCCTAC
1 CACATAAGGAGAGGCTTACGAGAGGTCCTACTTCCTAC
* *
2346590 CACATAAGGAGAGGCTTATGGGAGGTCCTACTTCCTAC
1 CACATAAGGAGAGGCTTACGAGAGGTCCTACTTCCTAC
2346628 TAGTTGACTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
37 26 0.81
38 6 0.19
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (38 bp):
CACATAAGGAGAGGCTTACGAGAGGTCCTACTTCCTAC
Found at i:2354558 original size:21 final size:21
Alignment explanation
Indices: 2354529--2354571 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2354519 TTCAGGTGGA
2354529 TCAGCTCTTATGAGATTT-TGT
1 TCAGCTCTTATGAG-TTTCTGT
*
2354550 TCAGTTCTTATGAGTTTCTGT
1 TCAGCTCTTATGAGTTTCTGT
2354571 T
1 T
2354572 GGCGTGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (21 bp):
TCAGCTCTTATGAGTTTCTGT
Found at i:2354637 original size:40 final size:40
Alignment explanation
Indices: 2354550--2354649 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 40
2354540 GAGATTTTGT
* * * *
2354550 TCAGTTCTTATGAGTTTCTG-TTGGCGTGTTTCGGGTGGA
1 TCAGCTCTTATGAGTTTCTGTTTGGCGTATTTCAGCTGGA
* * *
2354589 CCAACTCTTATGAGCTTCTGTTTGGCGTATTTCAGCTGGA
1 TCAGCTCTTATGAGTTTCTGTTTGGCGTATTTCAGCTGGA
2354629 TCAGCTCTTATGAGTTTCTGT
1 TCAGCTCTTATGAGTTTCTGT
2354650 CTAGTGTGTT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
39 16 0.32
40 34 0.68
ACGTcount: A:0.14, C:0.18, G:0.26, T:0.42
Consensus pattern (40 bp):
TCAGCTCTTATGAGTTTCTGTTTGGCGTATTTCAGCTGGA
Found at i:2358393 original size:21 final size:21
Alignment explanation
Indices: 2358363--2358411 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
2358353 TAAATTAGTT
*
2358363 AAAAAAATAAATTG-TATTAA
1 AAAAAAATAAACTGTTATTAA
*
2358383 AAAAAACATAAACTGTTTTTAA
1 AAAAAA-ATAAACTGTTATTAA
2358405 AAAAAAA
1 AAAAAAA
2358412 AAAGAGAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 8 0.32
22 11 0.44
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (21 bp):
AAAAAAATAAACTGTTATTAA
Found at i:2361035 original size:8 final size:8
Alignment explanation
Indices: 2360991--2361047 Score: 57
Period size: 8 Copynumber: 7.1 Consensus size: 8
2360981 TTTTTTATTC
*
2360991 TTTTATAA
1 TTTTAAAA
2360999 TTTATAATAA
1 TTT-TAA-AA
2361009 TTTTAAAA
1 TTTTAAAA
2361017 ---TAAATA
1 TTTTAAA-A
2361023 TTTTAAAA
1 TTTTAAAA
2361031 TTTTAAAA
1 TTTTAAAA
2361039 TTTTAAAA
1 TTTTAAAA
2361047 T
1 T
2361048 AATTAATTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
5 4 0.10
6 1 0.02
8 23 0.55
9 9 0.21
10 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
TTTTAAAA
Found at i:2361043 original size:30 final size:32
Alignment explanation
Indices: 2360991--2361049 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 32
2360981 TTTTTTATTC
*
2360991 TTTTATAATTTATAATAATTTTAAAATAAATA
1 TTTTAAAATTTATAATAATTTTAAAATAAATA
2361023 TTTTAAAATTT-TAA-AATTTTAAAATAA
1 TTTTAAAATTTATAATAATTTTAAAATAA
2361050 TTAATTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 13 0.50
31 3 0.12
32 10 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
TTTTAAAATTTATAATAATTTTAAAATAAATA
Found at i:2362930 original size:26 final size:26
Alignment explanation
Indices: 2362897--2363006 Score: 166
Period size: 26 Copynumber: 4.2 Consensus size: 26
2362887 TGATACAAAT
*
2362897 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
* *
2362923 TGACAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
* *
2362949 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
2362975 TGATAATGGATTAGGTAAATGTTTCA
1 TGATAATGGATTAGGTAAATGTTCCA
2363001 TGATAA
1 TGATAA
2363007 GAATTACATG
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:2362959 original size:52 final size:52
Alignment explanation
Indices: 2362897--2363006 Score: 184
Period size: 52 Copynumber: 2.1 Consensus size: 52
2362887 TGATACAAAT
2362897 TGATAATGGGTTAGGTAAATGTTCCATGACAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGACAATGGATTAGGTAAATATTCCA
* * * *
2362949 TGATAATGGGTTAGGTAAATGTTTCATGATAATGGATTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCATGACAATGGATTAGGTAAATATTCCA
2363001 TGATAA
1 TGATAA
2363007 GAATTACATG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (52 bp):
TGATAATGGGTTAGGTAAATGTTCCATGACAATGGATTAGGTAAATATTCCA
Found at i:2364517 original size:26 final size:26
Alignment explanation
Indices: 2364488--2364540 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2364478 TTTACAGTTT
2364488 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
2364514 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
2364540 T
1 T
2364541 GCATGTTTGA
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:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:2366161 original size:12 final size:12
Alignment explanation
Indices: 2366144--2366182 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
2366134 GGGGAAGAGA
2366144 CCGTGGTCGAGG
1 CCGTGGTCGAGG
*
2366156 CCGTGGTCGAGC
1 CCGTGGTCGAGG
2366168 CCGTGGTCGAGG
1 CCGTGGTCGAGG
2366180 CCG
1 CCG
2366183 AGGTAGTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.08, C:0.31, G:0.46, T:0.15
Consensus pattern (12 bp):
CCGTGGTCGAGG
Found at i:2371010 original size:26 final size:26
Alignment explanation
Indices: 2370977--2371086 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
2370967 TGATACAAAT
2370977 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
2371003 TGACAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
2371029 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
2371055 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
2371081 TGATAA
1 TGATAA
2371087 GAATTACATG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:2374371 original size:41 final size:41
Alignment explanation
Indices: 2374317--2374586 Score: 212
Period size: 41 Copynumber: 6.6 Consensus size: 41
2374307 AAAAAAGAGA
*
2374317 AATAGCGGCGTTTTTTGCCCAAACGCCACTAAAAACTGATC
1 AATAGCGGCGTTTTTTGCCCAAACGCCACTAAAAACTGAGC
* ** * *
2374358 AATAGCGGTGTTTTTAT-CTAAAACGCCACTAAAAATTGATC
1 AATAGCGGCGTTTTT-TGCCCAAACGCCACTAAAAACTGAGC
* * * *
2374399 AATAACGGCG-TTTTTGTCTAAGACGCCACTAAAAACTGGAGG
1 AATAGCGGCGTTTTTTGCCCAA-ACGCCACTAAAAACT-GAGC
* * *
2374441 AATAACGGCATTTTTAT--CCAAACGCCACTAAAAACTAGAGA
1 AATAGCGGCGTTTTT-TGCCCAAACGCCACTAAAAACT-GAGC
* * * * *
2374482 AATAACGACG-TTTTTGTCCAAACGCCACTAAAAACCGGAGA
1 AATAGCGGCGTTTTTTGCCCAAACGCCACTAAAAA-CTGAGC
* * * * *
2374523 AATAGCGGC-ATTTTTGTCCAAACACCACT-AAAATTGATC
1 AATAGCGGCGTTTTTTGCCCAAACGCCACTAAAAACTGAGC
**
2374562 AATAGCGGCGTTTTAGGCCCAAACG
1 AATAGCGGCGTTTTTTGCCCAAACG
2374587 ACGCAAAAAA
Statistics
Matches: 187, Mismatches: 31, Indels: 23
0.78 0.13 0.10
Matches are distributed among these distances:
39 13 0.07
40 24 0.13
41 129 0.69
42 16 0.09
43 4 0.02
44 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.24
Consensus pattern (41 bp):
AATAGCGGCGTTTTTTGCCCAAACGCCACTAAAAACTGAGC
Found at i:2374413 original size:82 final size:80
Alignment explanation
Indices: 2374317--2374586 Score: 290
Period size: 82 Copynumber: 3.3 Consensus size: 80
2374307 AAAAAAGAGA
* ** ** *
2374317 AATAGCGGCGTTTTTTGCCCAAACGCCACTAAAAACTGATCAATAGCGGTGTTTTTATCTAAAAC
1 AATAACGGCG-TTTTTGCCCAAACGCCACTAAAAACTGAGAAATAGCGGCATTTTTATC-CAAAC
2374382 GCCACTAAAAATTGATC
64 GCCACTAAAAATTGATC
* * * *
2374399 AATAACGGCGTTTTTGTCTAAGACGCCACTAAAAACTGGAGGAATAACGGCATTTTTATCCAAAC
1 AATAACGGCGTTTTTGCCCAA-ACGCCACTAAAAACT-GAGAAATAGCGGCATTTTTATCCAAAC
* **
2374464 GCCACTAAAAACTAGAGA
64 GCCACTAAAAA-TTGATC
* * * * *
2374482 AATAACGACGTTTTTGTCCAAACGCCACTAAAAACCGGAGAAATAGCGGCATTTTTGTCCAAACA
1 AATAACGGCGTTTTTGCCCAAACGCCACTAAAAA-CTGAGAAATAGCGGCATTTTTATCCAAACG
2374547 CCACT-AAAATTGATC
65 CCACTAAAAATTGATC
* *
2374562 AATAGCGGCGTTTTAGGCCCAAACG
1 AATAACGGCGTTTT-TGCCCAAACG
2374587 ACGCAAAAAA
Statistics
Matches: 157, Mismatches: 26, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
80 15 0.10
81 21 0.13
82 81 0.52
83 40 0.25
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.24
Consensus pattern (80 bp):
AATAACGGCGTTTTTGCCCAAACGCCACTAAAAACTGAGAAATAGCGGCATTTTTATCCAAACGC
CACTAAAAATTGATC
Found at i:2374712 original size:11 final size:11
Alignment explanation
Indices: 2374696--2374726 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
2374686 ATTTGATTTA
2374696 ATTTTCATATT
1 ATTTTCATATT
2374707 ATTTTCATATT
1 ATTTTCATATT
2374718 ATTTTCATA
1 ATTTTCATA
2374727 AATTTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTTTCATATT
Found at i:2376291 original size:40 final size:39
Alignment explanation
Indices: 2376247--2376357 Score: 141
Period size: 40 Copynumber: 2.7 Consensus size: 39
2376237 GTCTCCAAGG
* **
2376247 GAATTAGCGGCGCTTTTTAAAAAACGTCGTTAAAGATCGA
1 GAATTAGCGGCGCTTTTT-AAAAACGCCGCAAAAGATCGA
2376287 GAATTAGCGGCGCTTTTGTAAAAACGCCGCAAAAGATCGA
1 GAATTAGCGGCGCTTTT-TAAAAACGCCGCAAAAGATCGA
**
2376327 GTTTTAGCGGCGCTTTTTTCAAAAACGCCGC
1 GAATTAGCGGCGC-TTTTT-AAAAACGCCGC
2376358 TAATTCTCCA
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
40 47 0.75
41 16 0.25
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (39 bp):
GAATTAGCGGCGCTTTTTAAAAACGCCGCAAAAGATCGA
Found at i:2386659 original size:31 final size:29
Alignment explanation
Indices: 2386624--2386726 Score: 116
Period size: 31 Copynumber: 3.4 Consensus size: 29
2386614 TAATTACATT
2386624 AATATTAAATTAATAAAATATTATCAAGATA
1 AATATTAAATTAATAAAATA-TATC-AGATA
** * * *
2386655 AATATTAAATTAAATTTAATATCTCATATC
1 AATATTAAATT-AATAAAATATATCAGATA
2386685 AATATTAAATTAATAAAATACTATCTAGATA
1 AATATTAAATTAATAAAATA-TATC-AGATA
2386716 AATATTAAATT
1 AATATTAAATT
2386727 TATTAAAACA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
29 7 0.12
30 17 0.29
31 28 0.47
32 7 0.12
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (29 bp):
AATATTAAATTAATAAAATATATCAGATA
Found at i:2388888 original size:46 final size:45
Alignment explanation
Indices: 2388828--2389093 Score: 339
Period size: 46 Copynumber: 6.0 Consensus size: 45
2388818 TTTGACATGA
* * * * * *
2388828 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
** **
2388874 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
2388920 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
*
2388966 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
2389012 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
2389050 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAG
2389094 AGAGCACACT
Statistics
Matches: 197, Mismatches: 13, Indels: 20
0.86 0.06 0.09
Matches are distributed among these distances:
38 34 0.17
40 3 0.02
43 1 0.01
44 3 0.02
45 4 0.02
46 149 0.76
47 3 0.02
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.39
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
Found at i:2389057 original size:38 final size:38
Alignment explanation
Indices: 2389006--2389081 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
2388996 ACATTTTATA
2389006 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
2389044 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
2389082 ATTTCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:2391243 original size:11 final size:11
Alignment explanation
Indices: 2391227--2391278 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
2391217 TATACTAAAT
2391227 AAATAATAATA
1 AAATAATAATA
*
2391238 AAATAAT-ATT
1 AAATAATAATA
* *
2391248 AAATATCTCATA
1 AAATA-ATAATA
*
2391260 AAATATTAATA
1 AAATAATAATA
2391271 AAATAATA
1 AAATAATA
2391279 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:2392071 original size:64 final size:64
Alignment explanation
Indices: 2391970--2392098 Score: 206
Period size: 64 Copynumber: 2.0 Consensus size: 64
2391960 GTCATTCATG
* * *
2391970 TTACATCTAGTTATGGGCATTTGATTCATTTCGATCATAGCATCTTAATTATTTGGCATAAGCA
1 TTACATCTAGTTATGGGCATTTGATTCATTGCAATCATAGCATCCTAATTATTTGGCATAAGCA
*
2392034 TTACATCTAGTTA-GGAGCATTTTATTCATTGCAATCATAGCATCCTAATTATTTGGCATAAGCA
1 TTACATCTAGTTATGG-GCATTTGATTCATTGCAATCATAGCATCCTAATTATTTGGCATAAGCA
2392098 T
1 T
2392099 AGATACAGGA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
63 2 0.03
64 58 0.97
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (64 bp):
TTACATCTAGTTATGGGCATTTGATTCATTGCAATCATAGCATCCTAATTATTTGGCATAAGCA
Found at i:2392548 original size:177 final size:177
Alignment explanation
Indices: 2392252--2392657 Score: 616
Period size: 177 Copynumber: 2.3 Consensus size: 177
2392242 AAAGACAGCA
*
2392252 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGACTACAAATTACAGATCTTATCACCATGTATCGG
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTACAAATTACAGATCTTATCACCATGTATCGG
* ** * *
2392317 CTATAGAGCAGATCGAAAATGGTGAGTCTTATCTACATGTATCGGCTATGGAGTAGATTTTAGCC
66 CTATAGAACAGATAAAAAATGGAGAGTCTTATCTACATGTATCAGCTATGGAGTAGATTTTAGCC
*
2392382 ACCGGCCTTATCTCTCTTAGGTAGCAAGAGAGCAGGTT-AAAGATACG
131 ACCGGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAA-ATACG
* * * *
2392429 AGCCTTAACCCCCTAAGTAGTAGGGTTACAGGCTGCAAATTACAGATCTTATCTCCATGTATCGG
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTACAAATTACAGATCTTATCACCATGTATCGG
* * *
2392494 CTATGGAACAGATAAAAAATGGAGAGTCTTATCTCCATGTCTCAGCTATGGAGTAGATTTTAGCC
66 CTATAGAACAGATAAAAAATGGAGAGTCTTATCTACATGTATCAGCTATGGAGTAGATTTTAGCC
*
2392559 ACCGGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGTTTGAAAATACG
131 ACCGGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAAATACG
* * * * *
2392606 AGCCTTAACCCCTTAAGCAGTAGGGTGACAGGCTAAAAATTGCAAATCTTAT
1 AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTACAAATTACAGATCTTAT
2392658 ATTCCAGAAG
Statistics
Matches: 206, Mismatches: 22, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
177 203 0.99
178 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (177 bp):
AGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTACAAATTACAGATCTTATCACCATGTATCGG
CTATAGAACAGATAAAAAATGGAGAGTCTTATCTACATGTATCAGCTATGGAGTAGATTTTAGCC
ACCGGCCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAAATACG
Found at i:2394173 original size:2 final size:2
Alignment explanation
Indices: 2394166--2394197 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2394156 ACTTTCATTC
2394166 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
2394198 TTAAAATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2394216 original size:16 final size:16
Alignment explanation
Indices: 2394197--2394236 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2394187 TATATATATA
2394197 TTTAAAATTGT-TTTAT
1 TTTAAAATT-TATTTAT
*
2394213 TTTACAATTTATTTAT
1 TTTAAAATTTATTTAT
2394229 TTTAAAAT
1 TTTAAAAT
2394237 CCTCTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTAAAATTTATTTAT
Found at i:2394546 original size:2 final size:2
Alignment explanation
Indices: 2394539--2394569 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2394529 TTTCATTTTC
2394539 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
2394570 ATTAGTTAAA
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:2395241 original size:126 final size:126
Alignment explanation
Indices: 2394999--2395309 Score: 424
Period size: 126 Copynumber: 2.5 Consensus size: 126
2394989 CACATAAGGA
* *
2394999 AATATTTCGTGTTTGGAAGTTTGAGAGATCGTGCCCAATCGTGTTGGGTTTCGACTGTTTTTCAT
1 AATATTTCGTGTTTGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTC-AAT-TTTTTCAT
** ** *
2395064 TCAACTAAAATATGGAATATCCTTGTGAAATTTGGTCCATGTTTTCTTAAATTAAAATGAGGC
64 TCAACTAAAATACAGAATATCCTTGTGAAATTTCATCCACGTTTTCTTAAATTAAAATGAGGC
* *
2395127 AATATTTTGTGTTTGGGAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCAATTTTTTCATTC
1 AATATTTCGTGTTTGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCAATTTTTTCATTC
* *
2395192 GACTAAAATACAGAATATCCTTTTGAAATTTCATCCACGTTTTCTTAAATTAAAATGAGGC
66 AACTAAAATACAGAATATCCTTGTGAAATTTCATCCACGTTTTCTTAAATTAAAATGAGGC
* * * * * * * * *
2395253 AGTATTTCATATTTGGAAATTCGAAAAATCGTGCCCAATCGTGCAGGGTTTCGATTT
1 AATATTTCGTGTTTGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCAATTT
2395310 ATCGTTTGGC
Statistics
Matches: 161, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
126 110 0.68
127 2 0.01
128 49 0.30
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.38
Consensus pattern (126 bp):
AATATTTCGTGTTTGGAAGTTTGAGAGATCGTGCCCAATCGTGCTGGGTTTCAATTTTTTCATTC
AACTAAAATACAGAATATCCTTGTGAAATTTCATCCACGTTTTCTTAAATTAAAATGAGGC
Found at i:2397818 original size:4 final size:4
Alignment explanation
Indices: 2397811--2397848 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
2397801 ATATATATAT
2397811 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
2397849 TTTATACGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:2404164 original size:13 final size:13
Alignment explanation
Indices: 2404146--2404171 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2404136 TTATATTCGC
2404146 TTTGAAGATTTGG
1 TTTGAAGATTTGG
2404159 TTTGAAGATTTGG
1 TTTGAAGATTTGG
2404172 AGACATTATT
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:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (13 bp):
TTTGAAGATTTGG
Found at i:2416062 original size:49 final size:49
Alignment explanation
Indices: 2415988--2416176 Score: 243
Period size: 49 Copynumber: 3.8 Consensus size: 49
2415978 GTAGCCGAAG
* *
2415988 TTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAATCAA
1 TTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGATCAA
* * * *
2416037 TAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACA
1 TTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGATCA-A
* * * *
2416087 GTTTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 -TTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGATCAA
* * *
2416137 TTATCCGATACACGTAGTAGCCTGCACTTAGTACTACACA
1 TTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
2416177 CGTGACCTCA
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 77 0.65
50 2 0.02
51 40 0.34
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (49 bp):
TTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGATCAA
Found at i:2416108 original size:100 final size:100
Alignment explanation
Indices: 2415994--2416181 Score: 331
Period size: 100 Copynumber: 1.9 Consensus size: 100
2415984 GAAGTTATCT
* * *
2415994 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAATCAATAATCTGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAATAATCCGATACACGTAGTAGCC
2416059 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
66 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
* *
2416094 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGATACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAATAATCCGATACACGTAGTAGCC
2416159 TGCACTTAGTACTACACACGTGA
66 TGCACTTAGTACTACACACGTGA
2416182 CCTCACAATA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 83 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAATAATCCGATACACGTAGTAGCC
TGCACTTAGTACTACACACGTGATCACAGTTTTCG
Found at i:2424169 original size:58 final size:58
Alignment explanation
Indices: 2424079--2424197 Score: 238
Period size: 58 Copynumber: 2.1 Consensus size: 58
2424069 AAGATTTTAT
2424079 TACTTAAAAATAACCTGCACTTAGGTTGTAGACTTAGAAAGTCACTATCACTAAAGGA
1 TACTTAAAAATAACCTGCACTTAGGTTGTAGACTTAGAAAGTCACTATCACTAAAGGA
2424137 TACTTAAAAATAACCTGCACTTAGGTTGTAGACTTAGAAAGTCACTATCACTAAAGGA
1 TACTTAAAAATAACCTGCACTTAGGTTGTAGACTTAGAAAGTCACTATCACTAAAGGA
2424195 TAC
1 TAC
2424198 AATCCATCCA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (58 bp):
TACTTAAAAATAACCTGCACTTAGGTTGTAGACTTAGAAAGTCACTATCACTAAAGGA
Found at i:2431268 original size:288 final size:287
Alignment explanation
Indices: 2430752--2431304 Score: 1000
Period size: 288 Copynumber: 1.9 Consensus size: 287
2430742 TGTGTCCATA
*
2430752 TTTTTTTTTTGGTCAAATAAGATATTTACTCATAGCAATTTCTCAAGAAAGTGGAAAGTAAAGAG
1 TTTTTTTTTTGGTCAAATAAGATATTTACTCA-AGCAATTTCTCAAGAAAGTGGAAAGCAAAGAG
*
2430817 CAAAACTATCAGTAACAACATTGAAAACAAAACAGTTATATAAATCTTTAGCGCTCCATAGCTCA
65 CAAAACTATCAGTAACAACATTGAAAACAAAACAGTTATATAAATCTTTAGCACTCCATAGCTCA
* *
2430882 GCTTTACAACTAGACAAATTCAAAGATAAATTACTAACTGTATCTCAACTTTGACCCACAAGTTT
130 GCTTTAAAACTAGACAAATTCAAAGATAAATTACTAACTGTATCTCAACTTTGACCCACAAGTTC
2430947 ATCTTCTTACATAACAAATTAAAATCCCACTTCAAATCACCCATCCAAAATTAATATAACAGACA
195 ATCTTCTTACATAACAAATTAAAATCCCACTTCAAATCACCCATCCAAAATTAATATAACAGACA
2431012 ATAAATCTTTAGCAATTTCTCTCTTTTT
260 ATAAATCTTTAGCAATTTCTCTCTTTTT
*
2431040 TTTTTTTTTTGGGGTCAAATAAGATATTTACTC-AGCAATTTCTCAAGAAAGTGGAAAGCAAATA
1 TTTTTTTTTT--GGTCAAATAAGATATTTACTCAAGCAATTTCTCAAGAAAGTGGAAAGCAAAGA
*
2431104 GCAAAACTATCAGTAACAACATTGATAACAAAACAGTTATATAAATCTTTAGCACTCCATAGCTC
64 GCAAAACTATCAGTAACAACATTGAAAACAAAACAGTTATATAAATCTTTAGCACTCCATAGCTC
*
2431169 AGCTTTAAAACTAGGCAAATTCAAAGATAAATTACTAACTGTATCTCAACTTTGACCCACAAGTT
129 AGCTTTAAAACTAGACAAATTCAAAGATAAATTACTAACTGTATCTCAACTTTGACCCACAAGTT
*
2431234 CATCTTCTTCCATAACAAATTAAAATCCCACTTCAAATCACCCATCCAAAATTAATATAACAGAC
194 CATCTTCTTACATAACAAATTAAAATCCCACTTCAAATCACCCATCCAAAATTAATATAACAGAC
2431299 AATAAA
259 AATAAA
2431305 GGAAAACCCA
Statistics
Matches: 255, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
288 234 0.92
290 21 0.08
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.31
Consensus pattern (287 bp):
TTTTTTTTTTGGTCAAATAAGATATTTACTCAAGCAATTTCTCAAGAAAGTGGAAAGCAAAGAGC
AAAACTATCAGTAACAACATTGAAAACAAAACAGTTATATAAATCTTTAGCACTCCATAGCTCAG
CTTTAAAACTAGACAAATTCAAAGATAAATTACTAACTGTATCTCAACTTTGACCCACAAGTTCA
TCTTCTTACATAACAAATTAAAATCCCACTTCAAATCACCCATCCAAAATTAATATAACAGACAA
TAAATCTTTAGCAATTTCTCTCTTTTT
Found at i:2432047 original size:19 final size:19
Alignment explanation
Indices: 2432014--2432058 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2432004 ATTATAAAAA
2432014 AATAAAATTAATAAAATTT
1 AATAAAATTAATAAAATTT
* *
2432033 -ATAAATATTATTAAATTTT
1 AATAAA-ATTAATAAAATTT
2432052 AATAAAA
1 AATAAAA
2432059 GAATTCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 5 0.23
19 12 0.55
20 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATAAAATTAATAAAATTT
Found at i:2432104 original size:10 final size:10
Alignment explanation
Indices: 2432065--2432221 Score: 68
Period size: 10 Copynumber: 16.2 Consensus size: 10
2432055 AAAAGAATTC
2432065 AAATAT-TAA
1 AAATATATAA
*
2432074 AAATTTACTAA
1 AAATATA-TAA
2432085 AAAT-TA-AA
1 AAATATATAA
2432093 AAATATATAA
1 AAATATATAA
*
2432103 AAATCGTA-AA
1 AAAT-ATATAA
2432113 AAA-ATATAA
1 AAATATATAA
*
2432122 AAACT-TGT-A
1 AAA-TATATAA
* *
2432131 AAATTTTTATA
1 AAATATATA-A
2432142 AAATAGTA-AA
1 AAATA-TATAA
2432152 AAAT-TATAA
1 AAATATATAA
* *
2432161 AAAAATATAG
1 AAATATATAA
2432171 AAATATA-AA
1 AAATATATAA
2432180 AAAT-TATAA
1 AAATATATAA
* * *
2432189 AATTTTCT-A
1 AAATATATAA
2432198 AAATCATAATAA
1 AAAT-AT-ATAA
*
2432210 AATTATATAA
1 AAATATATAA
2432220 AA
1 AA
2432222 TGTAAATATT
Statistics
Matches: 112, Mismatches: 17, Indels: 37
0.67 0.10 0.22
Matches are distributed among these distances:
8 13 0.12
9 37 0.33
10 39 0.35
11 18 0.16
12 5 0.04
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (10 bp):
AAATATATAA
Found at i:2432113 original size:19 final size:19
Alignment explanation
Indices: 2432065--2432183 Score: 68
Period size: 19 Copynumber: 6.2 Consensus size: 19
2432055 AAAAGAATTC
* *
2432065 AAATATTAAAAATTTACTAA
1 AAATAGTAAAAATATA-TAA
2432085 AAAT--TAAAAAATATATAA
1 AAATAGT-AAAAATATATAA
* *
2432103 AAATCGTAAAAAAATATAA
1 AAATAGTAAAAATATATAA
* * *
2432122 AAACTTGT-AAAATTTTTATA
1 AAA-TAGTAAAAATATATA-A
*
2432142 AAATAGTAAAAAATTATAAAA
1 AAATAGT-AAAAA-TATATAA
*
2432163 AAATA-TAGAAATATA-AA
1 AAATAGTAAAAATATATAA
2432180 AAAT
1 AAAT
2432184 TATAAAATTT
Statistics
Matches: 80, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
17 6 0.08
18 12 0.15
19 36 0.45
20 13 0.16
21 10 0.12
22 3 0.04
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (19 bp):
AAATAGTAAAAATATATAA
Found at i:2432144 original size:28 final size:28
Alignment explanation
Indices: 2432113--2432216 Score: 104
Period size: 28 Copynumber: 3.6 Consensus size: 28
2432103 AAATCGTAAA
* *
2432113 AAAATATAAAAACTTGTAAAATTTTTAT
1 AAAATATAAAAAATTATAAAATTTTTAT
***
2432141 AAAATAGTAAAAAATTATAAAA-AAATAT
1 AAAATA-TAAAAAATTATAAAATTTTTAT
*
2432169 AGAAATATAAAAAATTATAAAA-TTTTCT
1 A-AAATATAAAAAATTATAAAATTTTTAT
2432197 AAAATCATAATAAAATTATA
1 AAAAT-ATAA-AAAATTATA
2432217 TAAAATGTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
27 4 0.06
28 32 0.51
29 27 0.43
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAATATAAAAAATTATAAAATTTTTAT
Found at i:2432176 original size:57 final size:57
Alignment explanation
Indices: 2432114--2432221 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 57
2432104 AATCGTAAAA
* *
2432114 AAATATAAAAACTTGTAAAATTTTTATAAAAT-AGTAA-AAAATTATAAAAAAATATAG
1 AAATATAAAAAATTATAAAA-TTTTATAAAATCA-TAATAAAATTATAAAAAAATATAG
* *
2432171 AAATATAAAAAATTATAAAATTTTCTAAAATCATAATAAAATTATATAAAA
1 AAATATAAAAAATTATAAAATTTTATAAAATCATAATAAAATTATAAAAAA
2432222 TGTAAATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
56 13 0.29
57 32 0.71
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (57 bp):
AAATATAAAAAATTATAAAATTTTATAAAATCATAATAAAATTATAAAAAAATATAG
Found at i:2432222 original size:67 final size:67
Alignment explanation
Indices: 2432083--2432212 Score: 154
Period size: 67 Copynumber: 1.9 Consensus size: 67
2432073 AAAATTTACT
* * * ** *
2432083 AAAAATTAAAAAATATATAAAAATCGTAAAAAAATATAAAAACTTGTAAAATTTTTATAAAATAG
1 AAAAATTAAAAAAAATATAAAAATCATAAAAAAATATAAAAACTTCTAAAATCATAATAAAATAG
2432148 TA
66 TA
* * **
2432150 AAAAATTATAAAAAAATATAGAAAT-ATAAAAAATTATAAAATTTTCTAAAATCATAATAAAAT
1 AAAAATTA-AAAAAAATATAAAAATCATAAAAAAATATAAAAACTTCTAAAATCATAATAAAAT
2432213 TATATAAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
67 38 0.73
68 14 0.27
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (67 bp):
AAAAATTAAAAAAAATATAAAAATCATAAAAAAATATAAAAACTTCTAAAATCATAATAAAATAG
TA
Found at i:2432484 original size:18 final size:19
Alignment explanation
Indices: 2432452--2432487 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2432442 AAATTTTTAT
2432452 TAAAATTTAATTATTTTTC
1 TAAAATTTAATTATTTTTC
2432471 TAAAATTT-ATTATTTTT
1 TAAAATTTAATTATTTTT
2432488 ATAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TAAAATTTAATTATTTTTC
Found at i:2432711 original size:89 final size:88
Alignment explanation
Indices: 2432520--2432741 Score: 250
Period size: 88 Copynumber: 2.5 Consensus size: 88
2432510 AGAGCAAGCA
* * * * *
2432520 CTTAATTGC-TTTTTTGAAAAAATTTGAGGGTCTTTGTGATGCATTTTGAAAATTCAAATACTCA
1 CTTAATTACTTTTTTTGAAAAAGTTTGAAGGTCTTT-TTATCCATTTTGAAAATTCAAATACTCA
* *
2432584 ATTGAGTGGGAAAAAAATCAGGGG
65 ATTAAGTGGAAAAAAAATCAGGGG
* * * *
2432608 CTTAATTACTTTTTTTGAAGAAGTTTGAAGGTCTTTTTATCCATTTTGAAAGTTCAAGTGCTCAA
1 CTTAATTACTTTTTTTGAAAAAGTTTGAAGGTCTTTTTATCCATTTTGAAAATTCAAATACTCAA
* *
2432673 TTAAGTGTAAAAAAAATGAGGGG
66 TTAAGTGGAAAAAAAATCAGGGG
* * * *
2432696 CTTGATTACTTTTTTTTTAAAAAGTTT-AAAGACTTTTTATACCATT
1 CTTAATTAC-TTTTTTTGAAAAAGTTTGAAGGTCTTTTTAT-CCATT
2432742 AATCCATCTT
Statistics
Matches: 113, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
88 70 0.62
89 43 0.38
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (88 bp):
CTTAATTACTTTTTTTGAAAAAGTTTGAAGGTCTTTTTATCCATTTTGAAAATTCAAATACTCAA
TTAAGTGGAAAAAAAATCAGGGG
Found at i:2435037 original size:31 final size:31
Alignment explanation
Indices: 2435002--2435071 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
2434992 AATATGGTGA
* *
2435002 GTGGTTATTTGTAGGACTTAGA-AGGATGTGG
1 GTGGTTAATTATAGGACTTA-ATAGGATGTGG
* *
2435033 GTGGTTAATTATGGGACTTAATGGGATGTGG
1 GTGGTTAATTATAGGACTTAATAGGATGTGG
2435064 GTGGTTAA
1 GTGGTTAA
2435072 GAAATTATCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 1 0.03
31 33 0.97
ACGTcount: A:0.23, C:0.03, G:0.39, T:0.36
Consensus pattern (31 bp):
GTGGTTAATTATAGGACTTAATAGGATGTGG
Found at i:2435147 original size:22 final size:22
Alignment explanation
Indices: 2435119--2435160 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2435109 TTTTCTTCCC
2435119 CTTTTCTCTAT-TTTTCTTTTTT
1 CTTTTCT-TATATTTTCTTTTTT
*
2435141 CTTTTCTTTTATTTTCTTTT
1 CTTTTCTTATATTTTCTTTT
2435161 CTCCATTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (22 bp):
CTTTTCTTATATTTTCTTTTTT
Found at i:2445832 original size:27 final size:27
Alignment explanation
Indices: 2445731--2445837 Score: 119
Period size: 27 Copynumber: 3.9 Consensus size: 27
2445721 AGGAAGCGTC
* * *
2445731 CTGGTGTCTATGCCACAAATATCTG-AT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
2445758 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACAT-TATCTGTAT
2445785 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
** *
2445813 CTGGTGATTCTGTCACATTATCTGT
1 CTGGTGGCTCTGCCACATTATCTGT
2445838 TCTAGCAGCC
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
26 1 0.01
27 53 0.76
28 16 0.23
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATTATCTGTAT
Found at i:2445835 original size:54 final size:54
Alignment explanation
Indices: 2445731--2445840 Score: 141
Period size: 54 Copynumber: 2.0 Consensus size: 54
2445721 AGGAAGCGTC
* *
2445731 CTGGTGTCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * * * *
2445785 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGATTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
2445839 CT
1 CT
2445841 AGCAGCCATG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 31 0.65
55 17 0.35
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:2461459 original size:42 final size:42
Alignment explanation
Indices: 2461400--2461479 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
2461390 ACTTTACGTC
2461400 TAATAAACCTAAATTAAATTATAATTAA-ATTTAAATGTCAAT
1 TAATAAACCTAAATTAAATTATAA-TAATATTTAAATGTCAAT
* *
2461442 TAATAAATCTAAATTAAATTATAATAATATTTAGATGT
1 TAATAAACCTAAATTAAATTATAATAATATTTAAATGT
2461480 GAATACAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 3 0.09
42 32 0.91
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (42 bp):
TAATAAACCTAAATTAAATTATAATAATATTTAAATGTCAAT
Found at i:2461966 original size:2 final size:2
Alignment explanation
Indices: 2461959--2462012 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
2461949 CACTAGTGTA
*
2461959 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2462000 AA AT AT AA AT AT A
1 AT AT AT AT AT AT A
2462013 GGGTTTAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2462886 original size:19 final size:19
Alignment explanation
Indices: 2462817--2462886 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 19
2462807 ATTTTAAACA
*
2462817 TAAAAA-ATATAAT-TTTT
1 TAAAAATATAAAATATTTT
* * *
2462834 TAAAAAAATAAAAAAACTCTT
1 TAAAAATAT-AAAATA-TTTT
* *
2462855 CAAAAATAAAAAATATTTT
1 TAAAAATATAAAATATTTT
2462874 TAAAAATATAAAA
1 TAAAAATATAAAA
2462887 GATCCCAATA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
17 6 0.15
18 2 0.05
19 17 0.44
20 5 0.13
21 9 0.23
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAAATATAAAATATTTT
Found at i:2466022 original size:30 final size:30
Alignment explanation
Indices: 2465974--2466031 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 30
2465964 CTTCATAAAT
* *
2465974 ATATATACGTACTAAAAGTATACATAATAATA
1 ATATATACATAC-AAAAGTACAC-TAATAATA
2466006 ATATATACATAC-AAAGTACACTAATA
1 ATATATACATACAAAAGTACACTAATA
2466032 TTTAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 8 0.33
32 11 0.46
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.29
Consensus pattern (30 bp):
ATATATACATACAAAAGTACACTAATAATA
Found at i:2466078 original size:16 final size:16
Alignment explanation
Indices: 2466054--2466084 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2466044 AATAGTAAAC
*
2466054 ATAATATTAATATTAA
1 ATAAAATTAATATTAA
2466070 ATAAAATTAATATTA
1 ATAAAATTAATATTA
2466085 CAAATTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTAATATTAA
Found at i:2468443 original size:2 final size:2
Alignment explanation
Indices: 2468436--2468460 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2468426 AAAGTTATTA
2468436 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 A
2468461 AACTCAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2473002 original size:22 final size:22
Alignment explanation
Indices: 2472972--2473013 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2472962 TTCGGCAGCA
2472972 AATAACAATCGGTTCTTGAATG
1 AATAACAATCGGTTCTTGAATG
*
2472994 AATAGCAATCGGTTCTTGAA
1 AATAACAATCGGTTCTTGAA
2473014 GGAGATCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (22 bp):
AATAACAATCGGTTCTTGAATG
Found at i:2474904 original size:15 final size:15
Alignment explanation
Indices: 2474884--2474913 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2474874 CATTTGATTA
2474884 AAGTTAATGTATAGT
1 AAGTTAATGTATAGT
2474899 AAGTTAATGTATAGT
1 AAGTTAATGTATAGT
2474914 TTTGAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (15 bp):
AAGTTAATGTATAGT
Found at i:2476842 original size:29 final size:28
Alignment explanation
Indices: 2476810--2476890 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 28
2476800 AAATTAAGAA
** *
2476810 TAAATTTTAAGTATAATCAGTATTTAAAT
1 TAAATTTT-AGTATAAAAAATATTTAAAT
*
2476839 TAAATTTCT-GTACAAAAAATATTTAAAT
1 TAAATTT-TAGTATAAAAAATATTTAAAT
2476867 TAAATTTTAGTATTTAAAAAATAT
1 TAAATTTTAGTA--TAAAAAATAT
2476891 AAAAAGGTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
27 1 0.02
28 25 0.58
29 7 0.16
30 10 0.23
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (28 bp):
TAAATTTTAGTATAAAAAATATTTAAAT
Found at i:2478733 original size:48 final size:48
Alignment explanation
Indices: 2478654--2478750 Score: 124
Period size: 48 Copynumber: 2.0 Consensus size: 48
2478644 TTATGCTATG
* *
2478654 CATTTCTAAACTTGGTCTTCCACTGTATACACTCTTACCACTATTTAT
1 CATTGCTAAACTTGGTCTTCCACTGTATACACTCTTACCACTAATTAT
* * * *
2478702 CATTGCTAAACTCT-GTGTTCCATTGTCTACACTCTTATCACTAATTAT
1 CATTGCTAAACT-TGGTCTTCCACTGTATACACTCTTACCACTAATTAT
2478750 C
1 C
2478751 CCTTCTTGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
48 41 0.98
49 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.07, T:0.41
Consensus pattern (48 bp):
CATTGCTAAACTTGGTCTTCCACTGTATACACTCTTACCACTAATTAT
Found at i:2481338 original size:3 final size:3
Alignment explanation
Indices: 2481330--2481386 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
2481320 GTTTCCTTTC
2481330 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2481378 TAT TAT TAT
1 TAT TAT TAT
2481387 ATAACATAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2494149 original size:18 final size:18
Alignment explanation
Indices: 2494126--2494162 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2494116 TCGACACTTG
2494126 TTAGCTTAAAAAGTCTAC
1 TTAGCTTAAAAAGTCTAC
2494144 TTAGCTTAAAAAGTCTAC
1 TTAGCTTAAAAAGTCTAC
2494162 T
1 T
2494163 AATTCGAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (18 bp):
TTAGCTTAAAAAGTCTAC
Found at i:2498274 original size:20 final size:20
Alignment explanation
Indices: 2498251--2498325 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 20
2498241 GTATGTTTCC
2498251 ATTAACTTATGTTAATTAAG
1 ATTAACTTATGTTAATTAAG
2498271 ATTATGAC-TA-GTTAATTAAG
1 ATTA--ACTTATGTTAATTAAG
* * *
2498291 ATTTAGTT-TAATTAATTAAG
1 ATTAACTTAT-GTTAATTAAG
2498311 ATTAA-TTAATGTTAA
1 ATTAACTT-ATGTTAA
2498326 ACAAAGTATA
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
18 1 0.02
19 3 0.07
20 34 0.79
21 3 0.07
22 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.45
Consensus pattern (20 bp):
ATTAACTTATGTTAATTAAG
Found at i:2502926 original size:50 final size:50
Alignment explanation
Indices: 2502799--2502926 Score: 193
Period size: 50 Copynumber: 2.5 Consensus size: 50
2502789 ATGAACAAAT
* *
2502799 GAGTTACTTAATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGG
1 GAGTTACATAATGCATGACTTAA-TTAATGATGCAAACTTAACTAACATGA
* * *
2502850 GAGTTACATAATGCATGTCATAATTAATGATGCAAACTTAACTTACATGA
1 GAGTTACATAATGCATGACTTAATTAATGATGCAAACTTAACTAACATGA
*
2502900 GAGTTACATAATGCATGACTTTATTAA
1 GAGTTACATAATGCATGACTTAATTAA
2502927 ATGCAGAACA
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
50 49 0.71
51 20 0.29
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (50 bp):
GAGTTACATAATGCATGACTTAATTAATGATGCAAACTTAACTAACATGA
Found at i:2504290 original size:6 final size:6
Alignment explanation
Indices: 2504252--2504302 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
2504242 TCGTTCGTTC
* * *
2504252 TCTTTT CCTTTT TGCTTTCT T-TTAT TCTTTT TCTATT TCTTTT TCTTTT
1 TCTTTT TCTTTT T-CTTT-T TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
2504301 TC
1 TC
2504303 ACATGCTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
5 2 0.06
6 28 0.78
7 4 0.11
8 2 0.06
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.75
Consensus pattern (6 bp):
TCTTTT
Found at i:2507112 original size:226 final size:226
Alignment explanation
Indices: 2506718--2507161 Score: 836
Period size: 226 Copynumber: 2.0 Consensus size: 226
2506708 ACACTATAAA
*
2506718 CACTCATACACAAATTTATTAATGAACATGCAGCTTAAATTACCTTATTTAAAATGAAAATAAAC
1 CACTCATACACAAATTTATTAATGAACATGCAGCTTAAATCACCTTATTTAAAATGAAAATAAAC
2506783 ACACTTTAATTTATGTAGTAAAAAGTAATAGCCAAATTAAATAACATACTTATATAAACAAACTC
66 ACACTTTAATTTATGTAGTAAAAAGTAATAGCCAAATTAAATAACATACTTATATAAACAAACTC
2506848 AAACACATTTAACAACTAAGATGCTTAAATGCATGGTTAAATGTAAACTAAATGAACAAACGAGT
131 AAACACATTTAACAACTAAGATGCTTAAATGCATGGTTAAATGTAAACTAAATGAACAAACGAGT
*
2506913 TACTT-AGTGCATGACTTAATTTATTAATGAG
196 TA-TTGAATGCATGACTTAATTTATTAATGAG
*
2506944 CACTCATACATAAATTTATTAATGAACATGCAGCTTAAATCACCTTATTTAAAATGAAAATAAAC
1 CACTCATACACAAATTTATTAATGAACATGCAGCTTAAATCACCTTATTTAAAATGAAAATAAAC
2507009 ACACTTTAATTTATGTAGTAAAAAGTAATAGCCAAATTAAATAACATACTTATATAAACAAACTC
66 ACACTTTAATTTATGTAGTAAAAAGTAATAGCCAAATTAAATAACATACTTATATAAACAAACTC
*
2507074 AAACATATTTAACAACTAAGATGCTTAAATGCATGGTTAAATGTAAACTAAATGAACAAACGAGT
131 AAACACATTTAACAACTAAGATGCTTAAATGCATGGTTAAATGTAAACTAAATGAACAAACGAGT
2507139 TATTGAATGCATGACTTAATTTA
196 TATTGAATGCATGACTTAATTTA
2507162 ATGAAGCAAA
Statistics
Matches: 213, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
225 2 0.01
226 211 0.99
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (226 bp):
CACTCATACACAAATTTATTAATGAACATGCAGCTTAAATCACCTTATTTAAAATGAAAATAAAC
ACACTTTAATTTATGTAGTAAAAAGTAATAGCCAAATTAAATAACATACTTATATAAACAAACTC
AAACACATTTAACAACTAAGATGCTTAAATGCATGGTTAAATGTAAACTAAATGAACAAACGAGT
TATTGAATGCATGACTTAATTTATTAATGAG
Found at i:2507191 original size:51 final size:51
Alignment explanation
Indices: 2507144--2507265 Score: 165
Period size: 50 Copynumber: 2.4 Consensus size: 51
2507134 CGAGTTATTG
*
2507144 AATGCATGACTTAATTTAATGAAGCAAACTTAACTAACATGGGAGTTACAT
1 AATGCATGACTTAATTTAATGAAGCAAACTTAACTAACATGAGAGTTACAT
* * * * *
2507195 AACGCATGTCATAATTT-ATGATGCAAACTTAACTTACATGAGAGTTACAT
1 AATGCATGACTTAATTTAATGAAGCAAACTTAACTAACATGAGAGTTACAT
* *
2507245 AATGCATGACTTTATTAAATG
1 AATGCATGACTTAATTTAATG
2507266 CAAAACACAT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 42 0.71
51 17 0.29
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (51 bp):
AATGCATGACTTAATTTAATGAAGCAAACTTAACTAACATGAGAGTTACAT
Done.