Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold141
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: 2772588
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 118404 characters in sequence are not A, C, G, or T
File 10 of 18
Found at i:1645097 original size:43 final size:43
Alignment explanation
Indices: 1645050--1645393 Score: 270
Period size: 43 Copynumber: 7.8 Consensus size: 43
1645040 GCACCTCCTA
* *
1645050 GTCCTCAAAGAGCAGAACACACTTTATTTT-CTGTTTCCCCCTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCT-TTTCCCCCTT
* **
1645093 GTCCTCAAAGAGCAGGACGCACTTTATTTCCTTCTTTTCCCTGTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTT--TCCTTTTCCCCCTT
* *
1645138 GTCCTCAAAGAGCAAGACGCACTTTATTTTCCTTTT-CTCCTCT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTCCCCCT-T
* * * *
1645181 ATCCTCAAAGAGCAGGATGCACTTTATTTTCCTTTTCTCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTCCCCCTT
* **
1645224 GTCCTCAAAGAGCAGGA--CACGTTCCATTCCCTT-CTTTTCTCCTTTT
1 GTCCTCAAAGAGCAGGACGCAC-TT-TATT---TTCCTTTTC-CCCCTT
* * * * *
1645270 GTCCTCAAAGAGCAAGACGCACTTCATTTCCTTCTTTTCCCTTCTA
1 GTCCTCAAAGAGCAGGACGCACTTTATTT--TCCTTTTCCC-CCTT
* * * *
1645316 GTTCTTAAAGAGCAGGACGCACTTTATTTTCCTTTT-TCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTCCCCCTT
* * * *
1645358 ATCCTCAAAAAGCAGGCCGCA-TTTCATTTTCATTTT
1 GTCCTCAAAGAGCAGGACGCACTTT-ATTTTCCTTTT
1645394 TTTCTTTTGT
Statistics
Matches: 246, Mismatches: 37, Indels: 37
0.77 0.12 0.12
Matches are distributed among these distances:
41 6 0.02
42 31 0.13
43 89 0.36
44 8 0.03
45 46 0.19
46 61 0.25
47 2 0.01
48 3 0.01
ACGTcount: A:0.21, C:0.28, G:0.12, T:0.38
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTCCCCCTT
Found at i:1645203 original size:88 final size:86
Alignment explanation
Indices: 1645050--1645386 Score: 321
Period size: 88 Copynumber: 3.8 Consensus size: 86
1645040 GCACCTCCTA
* * *
1645050 GTCCTCAAAGAGC-AGAACACACTTTATTTTCTGTTTC-CCCCTTGTCCTCAAAGAGCAGGACGC
1 GTCCTCAAAGAGCAAG-ACGCACTTTATTTTCT-TTTCTCCTC-TATCCTCAAAGAGCAGGACGC
1645113 ACTTTATTTCCTTCTTTTCCCTGTT
63 ACTTTATTTCCTTCTTTTCCCT-TT
*
1645138 GTCCTCAAAGAGCAAGACGCACTTTATTTTCCTTTTCTCCTCTATCCTCAAAGAGCAGGATGCAC
1 GTCCTCAAAGAGCAAGACGCACTTTATTTT-CTTTTCTCCTCTATCCTCAAAGAGCAGGACGCAC
*
1645203 TTTATTT--TCCTTTTCTCCTTT
65 TTTATTTCCTTCTTTTC-CCTTT
* * * * *
1645224 GTCCTCAAAGAGCAGGA--CACGTTCCATTCCCTTCTTTTCTCCTTTTGTCCTCAAAGAGCAAGA
1 GTCCTCAAAGAGCAAGACGCAC-TT-TATT---TTCTTTTCTCC-TCTATCCTCAAAGAGCAGGA
*
1645287 CGCACTTCATTTCCTTCTTTTCCCTTCT
60 CGCACTTTATTTCCTTCTTTTCCCTT-T
* * * * * *
1645315 AGTTCTTAAAGAGCAGGACGCACTTTATTTTCCTTTT-TCCTTTATCCTCAAAAAGCAGGCCGCA
1 -GTCCTCAAAGAGCAAGACGCACTTTATTTT-CTTTTCTCCTCTATCCTCAAAGAGCAGGACGCA
1645379 -TTTCATTT
64 CTTT-ATTT
1645387 TCATTTTTTT
Statistics
Matches: 210, Mismatches: 21, Indels: 36
0.79 0.08 0.13
Matches are distributed among these distances:
84 3 0.01
85 2 0.01
86 28 0.13
87 5 0.02
88 91 0.43
89 41 0.20
90 9 0.04
91 8 0.04
92 18 0.09
93 2 0.01
94 3 0.01
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (86 bp):
GTCCTCAAAGAGCAAGACGCACTTTATTTTCTTTTCTCCTCTATCCTCAAAGAGCAGGACGCACT
TTATTTCCTTCTTTTCCCTTT
Found at i:1645466 original size:35 final size:35
Alignment explanation
Indices: 1645399--1645466 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
1645389 ATTTTTTTCT
* * * *
1645399 TTTGTCCTCGAGAAGTAGGACGTACTCTTTTTCAC
1 TTTGTCCTCAAGAAGCAGGACATACTCCTTTTCAC
**
1645434 TTTGTCCTCAAGAAGCAGGACATTTTCCTTTTC
1 TTTGTCCTCAAGAAGCAGGACATACTCCTTTTC
1645467 TTTCTTCCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.38
Consensus pattern (35 bp):
TTTGTCCTCAAGAAGCAGGACATACTCCTTTTCAC
Found at i:1646006 original size:20 final size:20
Alignment explanation
Indices: 1645981--1646133 Score: 90
Period size: 20 Copynumber: 7.5 Consensus size: 20
1645971 ATTTCACAAT
1645981 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
1646001 TTGTATCGATACATTCTGGGTTTACCTA
1 TTGTATCGATACA-T-T--G-TT--C-A
**
1646029 GACGTATCGATACATT-TTGCA
1 -TTGTATCGATACATTGTT-CA
*
1646050 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
*
1646070 TTGTATTGAT--A-----CA
1 TTGTATCGATACATTGTTCA
*
1646083 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
1646103 TTGTATCGATACATT-TTACA
1 TTGTATCGATACATTGTT-CA
*
1646123 ATGTATCGATA
1 TTGTATCGATA
1646134 TATTCAGGCA
Statistics
Matches: 105, Mismatches: 10, Indels: 36
0.70 0.07 0.24
Matches are distributed among these distances:
13 11 0.10
15 1 0.01
18 1 0.01
19 1 0.01
20 66 0.63
21 3 0.03
22 2 0.02
23 2 0.02
24 1 0.01
25 2 0.02
27 2 0.02
28 2 0.02
29 11 0.10
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:1646090 original size:33 final size:33
Alignment explanation
Indices: 1646048--1646117 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
1646038 ATACATTTTG
*
1646048 CATTGTATCGATACATTGCTCATTGTATTGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
1646081 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
1646114 CATT
1 CATT
1646118 TTACAATGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (33 bp):
CATTGTATCGATACATTGCTCATTGTATCGATA
Found at i:1646117 original size:13 final size:13
Alignment explanation
Indices: 1646068--1646098 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1646058 ATACATTGCT
*
1646068 CATTGTATTGATA
1 CATTGTATCGATA
1646081 CATTGTATCGATA
1 CATTGTATCGATA
1646094 CATTG
1 CATTG
1646099 CTCATTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1646128 original size:53 final size:53
Alignment explanation
Indices: 1646032--1646133 Score: 136
Period size: 53 Copynumber: 1.9 Consensus size: 53
1646022 TTACCTAGAC
* * *
1646032 GTATCGATACATTTTGCATTGTATCGATACATTGCTCATTGTATTGATACATT
1 GTATCGATACATTCTGCATTGTATCGATACATTGCTCAATGTATCGATACATT
*
1646085 GTATCGATACATTGCT-CATTGTATCGATACATT-TTACAATGTATCGATA
1 GTATCGATACATT-CTGCATTGTATCGATACATTGCT-CAATGTATCGATA
1646134 TATTCAGGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
52 1 0.02
53 41 0.95
54 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (53 bp):
GTATCGATACATTCTGCATTGTATCGATACATTGCTCAATGTATCGATACATT
Found at i:1646936 original size:49 final size:49
Alignment explanation
Indices: 1646880--1647509 Score: 635
Period size: 49 Copynumber: 13.0 Consensus size: 49
1646870 TCACTTTTCT
*
1646880 CACCTTCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGG
1 CACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
* *
1646929 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
1 CACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
* * *
1646978 CA----C--CTTTAAGTCTAATATCGTTGGCCTTGAATCAGCATATTGG
1 CACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
* * *
1647021 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATAGG
1 CACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
*
1647070 CA----C--CTTTAAGTCCAATATCA-CTAGCCTTGAATCAGCATATTGG
1 CACCTTCATCTTTAAGTCCAATAT-AGCTGGCCTTGAATCAGCATATTGG
* *
1647113 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
1 CACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
*
1647162 CA----C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
1 CACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
* * * *
1647205 CACTTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGA
1 CACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
1647254 CATCCTTTTTCTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
1 CA-CC----T-TCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
* * **
1647309 CACCTTCTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCGCATT-G
1 CACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
* *
1647357 ---C--CACCTTTAAGTCCAATATAGCTGGCCTTGAATTAGCATATTGG
1 CACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
* ** * * *
1647401 CACCTTTTCCATCTTTAAGTTCAATGCAGCTGGCCTTAAATCAGCACATTGA
1 CACC--TT-CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
* * * * *
1647453 CATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGG
1 CA-CC----T-TCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
1647508 CA
1 CA
1647510 TCTTTATCAC
Statistics
Matches: 481, Mismatches: 61, Indels: 72
0.78 0.10 0.12
Matches are distributed among these distances:
43 147 0.31
44 2 0.00
45 4 0.01
47 4 0.01
48 2 0.00
49 197 0.41
50 2 0.00
52 37 0.08
53 2 0.00
54 3 0.01
55 80 0.17
56 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.33
Consensus pattern (49 bp):
CACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
Found at i:1646979 original size:116 final size:119
Alignment explanation
Indices: 1646764--1646985 Score: 263
Period size: 116 Copynumber: 1.9 Consensus size: 119
1646754 GCATATTTTC
* *
1646764 CATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAT
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCC---TTCTCATCTTTAAT
* * * * *
1646829 CCCAATATCGTTGGTCATGAATCAACATATTGGCATCTTTATCACTTTTCTCACCTT
63 CCCAATATAGCTGGCCATGAATCAACACATTGGCACCTTTATCACTTTTCTCACCTT
* * *
1646886 CATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCA-CC-T-TCATCTTTAAGT-C
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTCTCATCTTTAA-TCC
* * *
1646947 CAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTA
65 CAATATAGCTGGCCATGAATCAACACATTGGCACCTTTA
1646986 AGTCTAATAT
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
116 42 0.49
117 2 0.02
121 2 0.02
122 40 0.47
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (119 bp):
CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTCTCATCTTTAATCCC
AATATAGCTGGCCATGAATCAACACATTGGCACCTTTATCACTTTTCTCACCTT
Found at i:1646983 original size:21 final size:21
Alignment explanation
Indices: 1646959--1647026 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
1646949 ATGTAGCTGG
1646959 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* ** *
1646980 CCTTTAAGTCTAATATCGTTGG--
1 CCTTGAA-TC-AGCA-CATTGGCA
*
1647002 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCACATTGGCA
1647023 CCTT
1 CCTT
1647027 CATCTTTAAG
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 12 0.36
22 8 0.24
23 2 0.06
24 5 0.15
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:1647046 original size:92 final size:92
Alignment explanation
Indices: 1646889--1647460 Score: 838
Period size: 92 Copynumber: 6.0 Consensus size: 92
1646879 TCACCTTCAT
*
1646889 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1646954 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
1646981 CTTTAAGTCTAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
*
1647046 GCTGGCCTTGAATCAGCACATAGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
1647073 CTTTAAGTCCAATATCACTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1647138 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
*
1647165 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
*
1647230 GCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTC
66 GCTGGCCTTGAATCAGCACATTGGCA----------C
* *
1647267 ATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATG
1 --CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* *
1647332 TAGCTGGCCTTGAATCAGCGCATTGCCAC
64 TAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
1647361 CTTTAAGTCCAATATAGCTGGCCTTGAATTAGCATATTGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAAT
* * *
1647426 GCAGCTGGCCTTAAATCAGCACATTGACATC
63 GTAGCTGGCCTTGAATCAGCACATTGGCA-C
1647457 CTTT
1 CTTT
1647461 TTCTCATCTT
Statistics
Matches: 439, Mismatches: 25, Indels: 28
0.89 0.05 0.06
Matches are distributed among these distances:
92 305 0.69
94 3 0.01
95 39 0.09
96 5 0.01
102 1 0.00
104 86 0.20
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (92 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1647345 original size:104 final size:104
Alignment explanation
Indices: 1647165--1647509 Score: 453
Period size: 104 Copynumber: 3.4 Consensus size: 104
1647155 ACATTGGCAC
* *
1647165 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1647230 GCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
66 GCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
*
1647269 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
* *
1647334 GCTGGCCTTGAATCAG--C---G-CA-----TTGC-CAC
66 GCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* *
1647361 CTTTAAGTCCAATATAGCTGGCCTTGAATTAGCATATTGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAAT
* *
1647426 GCAGCTGGCCTTAAATCAGCACATTGACATCCTTTTTCTCAT
63 GTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* * * * *
1647468 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
1647510 TCTTTATCAC
Statistics
Matches: 208, Mismatches: 18, Indels: 27
0.82 0.07 0.11
Matches are distributed among these distances:
92 45 0.22
93 3 0.01
94 2 0.01
95 31 0.15
97 1 0.00
98 2 0.01
99 1 0.00
100 1 0.00
101 2 0.01
102 1 0.00
104 78 0.38
106 3 0.01
107 38 0.18
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (104 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
Found at i:1647678 original size:49 final size:49
Alignment explanation
Indices: 1647529--1647678 Score: 174
Period size: 53 Copynumber: 3.0 Consensus size: 49
1647519 CTTTTCTCAT
* * *
1647529 CTTCAACTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTCATCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCAC
**
1647578 CTTCATCATCTTTAAAACCCAATGTTGCTGGCCTTGAATCAGCACATTGGCAC
1 C-T--TCATCTTT-AAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCAC
* * * * *
1647631 CTTCATCTTTAAGTCCAGTGTGGCAGGCCTTGAATCTGCACAGTGGCA
1 CTTCATCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCA
1647679 AATTGCAAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
49 32 0.38
50 9 0.11
52 8 0.09
53 36 0.42
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (49 bp):
CTTCATCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1648295 original size:13 final size:13
Alignment explanation
Indices: 1648277--1648333 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1648267 TATAAAGTGT
1648277 TGTATCGATACAA
1 TGTATCGATACAA
1648290 TGTATCGATACATAA
1 TGTATCGATAC--AA
1648305 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1648322 TGTATCGATACA
1 TGTATCGATACA
1648334 TAAGCTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1648312 original size:32 final size:32
Alignment explanation
Indices: 1648257--1648357 Score: 168
Period size: 32 Copynumber: 3.1 Consensus size: 32
1648247 TTCAACGATT
*
1648257 TGTATCGATATATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1648290 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1648322 TGTATCGATACATAAGCT-TTGTATCGATACAA
1 TGTATCGATACATAAG-TGTTGTATCGATACAA
1648354 TGTA
1 TGTA
1648358 AGCTACTGCC
Statistics
Matches: 66, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
32 53 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1648314 original size:19 final size:18
Alignment explanation
Indices: 1648255--1648352 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
1648245 ATTTCAACGA
*
1648255 TTTGTATCGATATATAAAG
1 TTTGTATCGATACAT-AAG
1648274 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1648290 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1648306 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1648322 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1648338 CTTTGTATCGATACA
1 -TTTGTATCGATACA
1648353 ATGTAAGCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 26
0.71 0.01 0.28
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 24 0.37
20 11 0.17
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1648413 original size:13 final size:13
Alignment explanation
Indices: 1648395--1648419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1648385 ATTACTCAAA
1648395 TGTATCGATACAT
1 TGTATCGATACAT
1648408 TGTATCGATACA
1 TGTATCGATACA
1648420 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1648470 original size:52 final size:52
Alignment explanation
Indices: 1648428--1648556 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
1648418 CACTGATCTT
*
1648428 TGTATCGATATATGCAGGCAAATTTGCCCAGATGTATTGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACACTATAAAA
1648480 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACACTATAAAA
1648532 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1648557 TCATATTTCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACACTATAAAA
Found at i:1649440 original size:20 final size:20
Alignment explanation
Indices: 1649402--1649440 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1649392 TAAACCTTGA
*
1649402 TCATGCATTTTTACTATGTT
1 TCATGCATTTTAACTATGTT
1649422 TCATGCATTTATAAC-ATGT
1 TCATGCATTT-TAACTATGT
1649441 CCAGCACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TCATGCATTTTAACTATGTT
Found at i:1650704 original size:27 final size:27
Alignment explanation
Indices: 1650674--1650744 Score: 142
Period size: 27 Copynumber: 2.6 Consensus size: 27
1650664 TTTATTCACC
1650674 GGGGACACTCCAACCCCATTCCTCCGA
1 GGGGACACTCCAACCCCATTCCTCCGA
1650701 GGGGACACTCCAACCCCATTCCTCCGA
1 GGGGACACTCCAACCCCATTCCTCCGA
1650728 GGGGACACTCCAACCCC
1 GGGGACACTCCAACCCC
1650745 GTTTTCAACC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.23, C:0.45, G:0.20, T:0.13
Consensus pattern (27 bp):
GGGGACACTCCAACCCCATTCCTCCGA
Found at i:1653488 original size:51 final size:52
Alignment explanation
Indices: 1653433--1653549 Score: 134
Period size: 51 Copynumber: 2.3 Consensus size: 52
1653423 ATTTTTCTGA
*
1653433 GGGGATACTTCAACCT-CGGTTTTA-TTTCTAAAACACAAATTCTCCACAATC
1 GGGGATACTTCAACCTCCGATTTTATTTTC-AAAACACAAATTCTCCACAATC
* * *
1653484 GGGGATAC-TCTAA-CTCCGATTTTATTTTCAAAACACCAATTTTTCACAATC
1 GGGGATACTTC-AACCTCCGATTTTATTTTCAAAACACAAATTCTCCACAATC
* *
1653535 GAGGATACTCCAACC
1 GGGGATACTTCAACC
1653550 CCGTTATTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
50 4 0.07
51 45 0.82
52 6 0.11
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.31
Consensus pattern (52 bp):
GGGGATACTTCAACCTCCGATTTTATTTTCAAAACACAAATTCTCCACAATC
Found at i:1653570 original size:28 final size:28
Alignment explanation
Indices: 1653537--1653605 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
1653527 TCACAATCGA
*
1653537 GGATACTCCAACCCCGTTAT-TTC-ATCG
1 GGATACTCCAACCCCGTTATATTCGA-AG
1653564 GGAATACTCCAACCCCGTTATATTCGAAG
1 GG-ATACTCCAACCCCGTTATATTCGAAG
1653593 GGATACTCCAACC
1 GGATACTCCAACC
1653606 TCGGCTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
27 2 0.05
28 29 0.76
29 6 0.16
30 1 0.03
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTATATTCGAAG
Found at i:1653681 original size:28 final size:28
Alignment explanation
Indices: 1653642--1653717 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
1653632 TTTTTTCATA
*
1653642 ATCGGGGGTACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
* **
1653670 ATCGGGGATACTCCAATCCTATTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
1653698 A-GGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1653718 ATTTTATTTC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 15 0.38
28 25 0.62
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:1653711 original size:27 final size:28
Alignment explanation
Indices: 1653645--1653716 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
1653635 TTTCATAATC
*
1653645 GGGGG-TACTCCAACCCCGTTATTTCAT
1 GGGGGATACTCCAACCCCATTATTTCAT
* * *
1653672 CGGGGATACTCCAATCCTATTATTTCA-
1 GGGGGATACTCCAACCCCATTATTTCAT
1653699 GGGGGATACTCCAACCCC
1 GGGGGATACTCCAACCCC
1653717 GATTTTATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
27 19 0.51
28 18 0.49
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (28 bp):
GGGGGATACTCCAACCCCATTATTTCAT
Found at i:1653764 original size:51 final size:51
Alignment explanation
Indices: 1653701--1653835 Score: 227
Period size: 50 Copynumber: 2.7 Consensus size: 51
1653691 TTATTTCAGG
*
1653701 GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATCA
1 GGGATACTCCAACCCCAATTTTATTTCTAAAATACCAATTTTCCACAATCA
*
1653752 GGGATACTCCAA-CCCAATTTTATTTCTAAAATACCAATTTTTCACAATCA
1 GGGATACTCCAACCCCAATTTTATTTCTAAAATACCAATTTTCCACAATCA
* *
1653802 GGGATACTCCAACTCCAATTTTATTTCCAAAATA
1 GGGATACTCCAACCCCAATTTTATTTCTAAAATA
1653836 TTGATTTCTC
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
50 48 0.61
51 31 0.39
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (51 bp):
GGGATACTCCAACCCCAATTTTATTTCTAAAATACCAATTTTCCACAATCA
Found at i:1653857 original size:51 final size:49
Alignment explanation
Indices: 1653701--1653867 Score: 217
Period size: 51 Copynumber: 3.3 Consensus size: 49
1653691 TTATTTCAGG
*
1653701 GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATCA
1 GGGATACTCCAA-CCCAATTTTATTTCTAAAATACCAATTTT-CACAATCA
1653752 GGGATACTCCAACCCAATTTTATTTCTAAAATACCAATTTTTCACAATCA
1 GGGATACTCCAACCCAATTTTATTTCTAAAATACCAA-TTTTCACAATCA
* *** * *
1653802 GGGATACTCCAACTCCAATTTTATTTCCAAAATATTGATTTCTCATAATCG
1 GGGATACTCCAAC-CCAATTTTATTTCTAAAATACCAATTT-TCACAATCA
*
1653853 GGGATACTTCAACCC
1 GGGATACTCCAACCC
1653868 CGGCCTTATT
Statistics
Matches: 105, Mismatches: 8, Indels: 7
0.88 0.07 0.06
Matches are distributed among these distances:
50 50 0.48
51 55 0.52
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (49 bp):
GGGATACTCCAACCCAATTTTATTTCTAAAATACCAATTTTCACAATCA
Found at i:1653857 original size:101 final size:102
Alignment explanation
Indices: 1653701--1653917 Score: 242
Period size: 101 Copynumber: 2.1 Consensus size: 102
1653691 TTATTTCAGG
* *
1653701 GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAATCAGGGATACTCCAA-C
1 GGGATACTCCAACCCCAATTTTATTTCCAAAATACCAATTTTCCACAATCAGGGATACTCCAACC
**
1653765 CCAATTTTATTTCTAAAAT-ACCAATTTTTCACAATCA
66 CCAACCTTATTTCT-AAATCACCAATTTTTCACAATCA
* *** * * *
1653802 GGGATACTCCAACTCCAATTTTATTTCCAAAATATTGA-TTTCTCATAATCGGGGATACTTCAAC
1 GGGATACTCCAACCCCAATTTTATTTCCAAAATACCAATTTTC-CACAATCAGGGATACTCCAAC
** * * *
1653866 CCCGGCCTTATTTCTAAATCATCGATTTTTCACAATCG
65 CCCAACCTTATTTCTAAATCACCAATTTTTCACAATCA
*
1653904 GGGATACTCTAACC
1 GGGATACTCCAACC
1653918 TCATTATTTT
Statistics
Matches: 95, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
100 4 0.04
101 53 0.56
102 38 0.40
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.33
Consensus pattern (102 bp):
GGGATACTCCAACCCCAATTTTATTTCCAAAATACCAATTTTCCACAATCAGGGATACTCCAACC
CCAACCTTATTTCTAAATCACCAATTTTTCACAATCA
Found at i:1653987 original size:79 final size:79
Alignment explanation
Indices: 1653890--1654072 Score: 199
Period size: 79 Copynumber: 2.3 Consensus size: 79
1653880 TAAATCATCG
* * * * ** *
1653890 ATTTTTCACAATCGGGGATACTCTAA-CCTCATTATTTTTGAGGGGATACTCCAACCCCGATTTT
1 ATTTCTCATAATCAGGGATACTCCAACCCT-ATTATTTCCGAGGGGATACTCCAACCCCAATTTT
*
1653954 ATTTTCAAAATACTAA
65 ATTTTCAAAACAC-AA
* * * *
1653970 ATTTCT-ATCATCAGGGATACTCCATCCCTGTTATTTCCGAGGGGATACTCCAGCCCCAATTTTA
1 ATTTCTCATAATCAGGGATACTCCAACCCTATTATTTCCGAGGGGATACTCCAACCCCAATTTTA
*
1654034 TTTTCAGAACACAA
66 TTTTCAAAACACAA
* *
1654048 ATTTTTCATAATCGGGGATACTCCA
1 ATTTCTCATAATCAGGGATACTCCA
1654073 GCCCCGTTGT
Statistics
Matches: 85, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
78 7 0.08
79 70 0.82
80 8 0.09
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (79 bp):
ATTTCTCATAATCAGGGATACTCCAACCCTATTATTTCCGAGGGGATACTCCAACCCCAATTTTA
TTTTCAAAACACAA
Found at i:1655140 original size:13 final size:13
Alignment explanation
Indices: 1655122--1655148 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1655112 ACATTTCTTC
1655122 ATGTATCGATACA
1 ATGTATCGATACA
1655135 ATGTATCGATACA
1 ATGTATCGATACA
1655148 A
1 A
1655149 ATAGTGATAG
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1655222 original size:19 final size:19
Alignment explanation
Indices: 1655177--1655233 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1655167 CTGCCAGTTT
**
1655177 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
1655198 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1655217 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1655234 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 19 0.56
21 15 0.44
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1655236 original size:13 final size:13
Alignment explanation
Indices: 1655218--1655244 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1655208 TACAATGAAC
1655218 ATGTATCGATACA
1 ATGTATCGATACA
1655231 ATGTATCGATACA
1 ATGTATCGATACA
1655244 A
1 A
1655245 AGCAGCATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1655259 original size:33 final size:32
Alignment explanation
Indices: 1655199--1655263 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1655189 CAATTTGTCC
*
1655199 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
1655231 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
1655264 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:1655844 original size:22 final size:18
Alignment explanation
Indices: 1655796--1655848 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 18
1655786 CTTTAAAAAA
1655796 TTCTCCCCCTTAAACGAT
1 TTCTCCCCCTTAAACGAT
1655814 TATCTCCCCCTTAAACAGTTAT
1 T-TCTCCCCCTTAAAC-G--AT
1655836 CTTCTCCCCCTTA
1 -TTCTCCCCCTTA
1655849 TGTAAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.03
19 14 0.47
20 1 0.03
22 13 0.43
23 1 0.03
ACGTcount: A:0.21, C:0.40, G:0.04, T:0.36
Consensus pattern (18 bp):
TTCTCCCCCTTAAACGAT
Found at i:1659256 original size:13 final size:13
Alignment explanation
Indices: 1659238--1659358 Score: 80
Period size: 13 Copynumber: 7.9 Consensus size: 13
1659228 CATAAAGTGT
1659238 TGTATCGATACAA
1 TGTATCGATACAA
1659251 TGTATCGATACATAA
1 TGTATCGATAC--AA
1659266 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1659283 TGTATCGATACATAA
1 TGTATCGATAC--AA
1659298 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
1659315 TGTATCGATACATAA
1 TGTATCGATAC--AA
1659330 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1659347 TGTATCGATACA
1 TGTATCGATACA
1659359 TAAGTTTTGT
Statistics
Matches: 90, Mismatches: 0, Indels: 36
0.71 0.00 0.29
Matches are distributed among these distances:
13 45 0.50
15 6 0.07
17 6 0.07
19 33 0.37
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1659273 original size:32 final size:32
Alignment explanation
Indices: 1659218--1659379 Score: 297
Period size: 32 Copynumber: 5.0 Consensus size: 32
1659208 TTCAACGATT
1659218 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1659251 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1659283 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1659315 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1659347 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1659379 T
1 T
1659380 TTAAGCTACT
Statistics
Matches: 126, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
32 113 0.90
33 13 0.10
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1659760 original size:17 final size:17
Alignment explanation
Indices: 1659712--1659753 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1659702 TGTTCTTTTC
*
1659712 CAAAAAAG-AAACAAAA
1 CAAAAAAGAAAAAAAAA
1659728 CAAAAAAGAAAAAAAAA
1 CAAAAAAGAAAAAAAAA
*
1659745 GAAAAAAGA
1 CAAAAAAGA
1659754 GGAAAAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (17 bp):
CAAAAAAGAAAAAAAAA
Found at i:1660797 original size:27 final size:28
Alignment explanation
Indices: 1660723--1660954 Score: 108
Period size: 35 Copynumber: 7.4 Consensus size: 28
1660713 GAAGTCCATG
* * *
1660723 ACTCAGTGGCATTTTGTCTTTAAGTCCACA
1 ACTCCGTGGCATTCT-T-TTTAAGCCCACA
* * *
1660753 ACTCTGTGGCA-CCATTTTAAGCCCACA
1 ACTCCGTGGCATTCTTTTTAAGCCCACA
1660780 ACTCCGTGGCATCTTTTTTCTTTTTAAAGCCCACA
1 ACTCCGTGGCA------TTCTTTTT-AAGCCCACA
* *
1660815 ACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACA
1 ACTCCGTGGCA------TT-CTTTTTAAGCCCACA
* *
1660850 ACTCCGTGGCA-CCCTTTTAAGCCCACA
1 ACTCCGTGGCATTCTTTTTAAGCCCACA
*
1660877 ACTCCGTGGCACCTTTCTCCTTCTAAGCCCACA
1 ACTCCGTGGCA---TTCT--TTTTAAGCCCACA
1660910 ACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACA
1 ACTCCGTGGCA-----TTCTTTTT-AAGCCCACA
1660944 ACTCCGTGGCA
1 ACTCCGTGGCA
1660955 CCTTTTTCTC
Statistics
Matches: 163, Mismatches: 21, Indels: 32
0.75 0.10 0.15
Matches are distributed among these distances:
27 46 0.28
28 1 0.01
30 10 0.06
31 1 0.01
33 26 0.16
34 25 0.15
35 49 0.30
36 5 0.03
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.32
Consensus pattern (28 bp):
ACTCCGTGGCATTCTTTTTAAGCCCACA
Found at i:1660841 original size:36 final size:34
Alignment explanation
Indices: 1660767--1661167 Score: 389
Period size: 35 Copynumber: 11.9 Consensus size: 34
1660757 TGTGGCACCA
* * *
1660767 TTTTAAGCCCACAACTCCGTGGCATCTTTTTTCT
1 TTTTAAGCCCACAACTCCGTGGCACCTTTTTCCC
1660801 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTT-AAGCCCACAACTCCGTGGCAC-CTTTTTCCC
*
1660837 TTTTAAGTCCACAACTCCGTGGCA-------CCC
1 TTTTAAGCCCACAACTCCGTGGCACCTTTTTCCC
*
1660864 TTTTAAGCCCACAACTCCGTGGCACCTTTCT-CC
1 TTTTAAGCCCACAACTCCGTGGCACCTTTTTCCC
* *
1660897 TTCTAAGCCCACAACTCCGTGGCACCTTTTT-CT
1 TTTTAAGCCCACAACTCCGTGGCACCTTTTTCCC
*
1660930 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTC
1 TTTT-AAGCCCACAACTCCGTGGCACCTTTTTCCC
* * *
1660965 TTCTAAGTCCATAACTCCGTGGCA-CTCTTTTCCC
1 TTTTAAGCCCACAACTCCGTGGCACCT-TTTTCCC
* * *
1660999 TTTTTAAAGTCCACAACCCCGTGGCACCTTGTT-CC
1 -TTTT-AAGCCCACAACTCCGTGGCACCTTTTTCCC
* * * *
1661034 TTTTAAGTCCACGACTTCGTGGCACCTTCTT---
1 TTTTAAGCCCACAACTCCGTGGCACCTTTTTCCC
**
1661065 TTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTTAAGCCCACAACTCCGTGGCAC-CTTTTTCCC
* *
1661100 TTTCAAAGCCCACAACTCTGTGGCACTCTTTTTCCC
1 TTT-TAAGCCCACAACTCCGTGGCAC-CTTTTTCCC
* * *
1661136 TTTTAAGTCCATAATTCCGTGGCACCCTTTTT
1 TTTTAAGCCCACAACTCCGTGGCA-CCTTTTT
1661168 AGTCTACAAC
Statistics
Matches: 310, Mismatches: 36, Indels: 41
0.80 0.09 0.11
Matches are distributed among these distances:
27 26 0.08
31 20 0.06
32 5 0.02
33 60 0.19
34 59 0.19
35 71 0.23
36 67 0.22
37 2 0.01
ACGTcount: A:0.19, C:0.34, G:0.12, T:0.34
Consensus pattern (34 bp):
TTTTAAGCCCACAACTCCGTGGCACCTTTTTCCC
Found at i:1661171 original size:27 final size:27
Alignment explanation
Indices: 1661133--1661186 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1661123 CACTCTTTTT
* *
1661133 CCCTTTTAAGTCCATAATTCCGTGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
* *
1661160 CCCTTTTTAGTCTACAACTCCGTGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
1661187 TCTTTCTCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.20, C:0.31, G:0.15, T:0.33
Consensus pattern (27 bp):
CCCTTTTAAGTCCACAACTCCGTGGCA
Found at i:1661245 original size:32 final size:32
Alignment explanation
Indices: 1661202--1661499 Score: 458
Period size: 32 Copynumber: 9.2 Consensus size: 32
1661192 CTCCTTTTCA
1661202 AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
* *
1661234 AAAGCCAACACAAGTCGGTGGCAACCCTTTTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
*
1661266 TAAAGCCCACACAAGTCGGTGGCAACCTTTCTC
1 -AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
* *
1661299 AAAGCCCACACAAGTTGGTGGCAACCCTTTTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
1661331 TAAAGCCCACACAAGTCGGTGGCAACCCTTCTC
1 -AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
*
1661364 AAAGCCCACACAAGTCGGTAGCAA-CCTTCTTCC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTC-T-C
1661397 AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
* *
1661429 AAAGCCCACACAAGTCGGTGGCAGCCATTCTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
1661461 TAAAGCCCACACAAGTCGGTGGCAACCCTTCT-
1 -AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
1661493 -AAGCCCA
1 AAAGCCCA
1661500 ATATAGCTGG
Statistics
Matches: 244, Mismatches: 16, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
30 7 0.03
31 5 0.02
32 114 0.47
33 113 0.46
34 5 0.02
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.18
Consensus pattern (32 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTCTC
Found at i:1661263 original size:65 final size:65
Alignment explanation
Indices: 1661194--1661499 Score: 501
Period size: 65 Copynumber: 4.7 Consensus size: 65
1661184 GCATCTTTCT
* *
1661194 CCTTTTCAAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCAACACAAGTCGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAAC
* *
1661259 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCTTTCTCAAAGCCCACACAAGTTGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAAC
*
1661324 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTAGCAA-
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAAC
* *
1661388 CCTTCTTCCAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAG
1 CCTT-TTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAA
1661453 C
65 C
* *
1661454 CATTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT--AAGCCCA
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCA
1661500 ATATAGCTGG
Statistics
Matches: 226, Mismatches: 13, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
63 7 0.03
64 4 0.02
65 212 0.94
66 3 0.01
ACGTcount: A:0.28, C:0.35, G:0.18, T:0.19
Consensus pattern (65 bp):
CCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAAC
Found at i:1661278 original size:33 final size:33
Alignment explanation
Indices: 1661194--1661490 Score: 435
Period size: 33 Copynumber: 9.1 Consensus size: 33
1661184 GCATCTTTCT
*
1661194 CCTTTTCAAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
* *
1661227 CCTTCTC-AAAGCCAACACAAGTCGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
1661259 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAA-
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
*
1661291 CC-TTTCTCAAAGCCCACACAAGTTGGTGGCAAC
1 CCTTTTCT-AAAGCCCACACAAGTCGGTGGCAAC
1661324 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
* *
1661357 CCTTCTC-AAAGCCCACACAAGTCGGTAGCAA-
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
*
1661388 CCTTCTTCCAAAGCCCACACAAGTCGGTGGCAAC
1 CCTT-TTCTAAAGCCCACACAAGTCGGTGGCAAC
* *
1661422 CCTTCTC-AAAGCCCACACAAGTCGGTGGCAGC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
* *
1661454 CATTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
1661487 CCTT
1 CCTT
1661491 CTAAGCCCAA
Statistics
Matches: 241, Mismatches: 15, Indels: 16
0.89 0.06 0.06
Matches are distributed among these distances:
31 9 0.04
32 110 0.46
33 113 0.47
34 9 0.04
ACGTcount: A:0.28, C:0.35, G:0.18, T:0.19
Consensus pattern (33 bp):
CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
Found at i:1661558 original size:49 final size:49
Alignment explanation
Indices: 1661492--1661827 Score: 423
Period size: 49 Copynumber: 6.9 Consensus size: 49
1661482 GCAACCCTTC
*
1661492 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
1661541 TAAGTCCAATATCGCTGGCCCTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * * * * *
1661590 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCATCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1661639 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * * *
1661688 TAAGTCCAATGTAGCTGGTCTTGACTCAGCACATTGGCA-C-----CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1661731 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTT
** * * *
1661783 TAAGTTTAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTT
1661828 TTCTCATCTT
Statistics
Matches: 245, Mismatches: 32, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
43 38 0.16
44 1 0.00
48 1 0.00
49 163 0.67
52 40 0.16
53 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
Found at i:1661746 original size:43 final size:43
Alignment explanation
Indices: 1661685--1661774 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
1661675 GCACCTTTAT
* * *
1661685 CTTTAAGTCCAATGTAGCTGGTCTTGACTCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
1661728 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
1661771 CTTT
1 CTTT
1661775 TCCATCTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1661806 original size:52 final size:55
Alignment explanation
Indices: 1661728--1661879 Score: 166
Period size: 52 Copynumber: 2.8 Consensus size: 55
1661718 ACATTGGCAC
* *
1661728 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
** *
1661780 CTTTAAGTTTAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
** * * * * *
1661835 CTTTAAACCCAATATCGTTGGCCGTGAATCAACATATTGGACATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT-GACATC
1661880 TTTATCACTT
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
52 37 0.46
53 2 0.02
54 5 0.06
55 31 0.38
56 6 0.07
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
Found at i:1662761 original size:13 final size:13
Alignment explanation
Indices: 1662743--1662767 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1662733 CATAAAGTGT
1662743 TGTATCGATACAA
1 TGTATCGATACAA
1662756 TGTATCGATACA
1 TGTATCGATACA
1662768 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1662765 original size:33 final size:33
Alignment explanation
Indices: 1662723--1662789 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1662713 TTCAACGATT
1662723 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1662756 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1662789 T
1 T
1662790 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1662907 original size:52 final size:52
Alignment explanation
Indices: 1662863--1662980 Score: 218
Period size: 52 Copynumber: 2.3 Consensus size: 52
1662853 CATTGATCTT
1662863 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
* *
1662915 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1662967 TGTATCGATACATG
1 TGTATCGATACATG
1662981 GAAGCAACTT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:1674166 original size:21 final size:20
Alignment explanation
Indices: 1674140--1674195 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
1674130 CTGCCAGTTT
**
1674140 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA-TTGAA
*
1674161 CATGTATCGATATAA-TGAA
1 CATGTATCGATACAATTGAA
1674180 CATGTATCGATACAAT
1 CATGTATCGATACAAT
1674196 GTATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 16 0.53
21 14 0.47
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1674199 original size:13 final size:13
Alignment explanation
Indices: 1674181--1674207 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1674171 TATAATGAAC
1674181 ATGTATCGATACA
1 ATGTATCGATACA
1674194 ATGTATCGATACA
1 ATGTATCGATACA
1674207 A
1 A
1674208 AGCAGCATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1674222 original size:33 final size:32
Alignment explanation
Indices: 1674162--1674226 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
1674152 CAATTTGTCC
* *
1674162 ATGTATCGATATAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
1674194 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
1674227 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:1676511 original size:28 final size:28
Alignment explanation
Indices: 1676479--1676534 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1676469 TAGTTGAATG
1676479 ATGTTGGATCCATTCTAAGGCCTCTGAC
1 ATGTTGGATCCATTCTAAGGCCTCTGAC
1676507 ATGTTGGATCCATTCTAAGGCCTCTGAC
1 ATGTTGGATCCATTCTAAGGCCTCTGAC
1676535 CCATTCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.32
Consensus pattern (28 bp):
ATGTTGGATCCATTCTAAGGCCTCTGAC
Found at i:1679136 original size:19 final size:16
Alignment explanation
Indices: 1679089--1679137 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1679079 TCAATTAAGT
1679089 TTTAAAATATATTTTA
1 TTTAAAATATATTTTA
* *
1679105 TTCAAAATTTATTTTA
1 TTTAAAATATATTTTA
1679121 TTAATTAAAATATATTT
1 -T--TTAAAATATATTT
1679138 AAATATTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 14 0.54
17 1 0.04
19 11 0.42
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAAAATATATTTTA
Found at i:1679472 original size:32 final size:33
Alignment explanation
Indices: 1679436--1679497 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
1679426 AAAAATAATA
*
1679436 AATTAATAATTAAATATTTT-ATAATTAAATTT
1 AATTAAAAATTAAATATTTTAATAATTAAATTT
* * *
1679468 AATTAAAAATTTATTATTTTAATTATTAAA
1 AATTAAAAATTAAATATTTTAATAATTAAA
1679498 AATATATCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 17 0.68
33 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (33 bp):
AATTAAAAATTAAATATTTTAATAATTAAATTT
Found at i:1679518 original size:23 final size:24
Alignment explanation
Indices: 1679442--1679520 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 24
1679432 AATAAATTAA
*
1679442 TAATTAAATATT-TTATAATTAAATT
1 TAATTAAAAATTATTAT--TTAAATT
*
1679467 TAATTAAAAATTTATTATTTTAA-T
1 TAATTAAAAA-TTATTATTTAAATT
1679491 T-ATTAAAAA-TA-TATCTTAAATT
1 TAATTAAAAATTATTAT-TTAAATT
1679513 TAATTAAA
1 TAATTAAA
1679521 TTTAATTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
20 3 0.07
21 6 0.13
22 2 0.04
23 14 0.30
24 2 0.04
25 13 0.28
26 2 0.04
27 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATTAAAAATTATTATTTAAATT
Found at i:1681735 original size:14 final size:14
Alignment explanation
Indices: 1681716--1681742 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1681706 AAGCTGTGAT
1681716 AATATGAATTTAAA
1 AATATGAATTTAAA
1681730 AATATGAATTTAA
1 AATATGAATTTAA
1681743 TTGCATTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (14 bp):
AATATGAATTTAAA
Found at i:1682028 original size:22 final size:22
Alignment explanation
Indices: 1682003--1682047 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1681993 ACACCAATGG
* *
1682003 ATTGGCCTTGATATAAATTACT
1 ATTGACCTTAATATAAATTACT
1682025 ATTGACCTTAATATAAATTACT
1 ATTGACCTTAATATAAATTACT
1682047 A
1 A
1682048 ATCCATAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (22 bp):
ATTGACCTTAATATAAATTACT
Found at i:1683055 original size:7 final size:7
Alignment explanation
Indices: 1683043--1683078 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
1683033 CTCAAAGTCA
1683043 TTTAAAT
1 TTTAAAT
1683050 TTTAAAT
1 TTTAAAT
1683057 TTTAAAT
1 TTTAAAT
1683064 TTTAAAT
1 TTTAAAT
1683071 TTTAAAT
1 TTTAAAT
1683078 T
1 T
1683079 CCAAAGATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTAAAT
Found at i:1689571 original size:22 final size:23
Alignment explanation
Indices: 1689541--1689599 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
1689531 ATAGCTAATA
1689541 TTTTCTTTAAAATTCATATGGAG
1 TTTTCTTTAAAATTCATATGGAG
*
1689564 TTTT-TTTAAAATTTATATGGAG
1 TTTTCTTTAAAATTCATATGGAG
1689586 TTTTCTTTAAAATT
1 TTTTCTTTAAAATT
1689600 AGCTTAACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 21 0.62
23 13 0.38
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (23 bp):
TTTTCTTTAAAATTCATATGGAG
Found at i:1693526 original size:147 final size:147
Alignment explanation
Indices: 1693353--1693633 Score: 467
Period size: 147 Copynumber: 1.9 Consensus size: 147
1693343 TAAAAATCAG
*
1693353 TTAAACTTGTTTAAAAAATATTTTAAGTATAAATATTCATTTGAAACATTATTTTTTG-GAATAT
1 TTAAACTTGTTTAAAAAATATTTTAAGTATAAATATTCATTTGAAACATTA-TTTTTGAGAAAAT
*
1693417 TAGAGGTAAAAAAATTAATTTAATATTTTTCAAAATATTTTCAATTTAATTCAAAGAAAAATACT
65 AAGAGGTAAAAAAATTAATTTAATATTTTTCAAAATATTTTCAATTTAATTCAAAGAAAAATACT
1693482 AAGTTTAGAAATAAACAC
130 AAGTTTAGAAATAAACAC
*
1693500 TTAAACTTGTCTT-AAAAATATTTTAAGTATAAATATTCATTTGAAACTTTATTTTTGAGAAAAT
1 TTAAACTTGT-TTAAAAAATATTTTAAGTATAAATATTCATTTGAAACATTATTTTTGAGAAAAT
* * * *
1693564 AAGAGGTAAGAAAATTAATTTAATATTTTTTAAAATATTTTCAATTTAATTCAAGGAAAATTACT
65 AAGAGGTAAAAAAATTAATTTAATATTTTTCAAAATATTTTCAATTTAATTCAAAGAAAAATACT
1693629 AAGTT
130 AAGTT
1693634 GGAAATGTAT
Statistics
Matches: 125, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
146 6 0.05
147 117 0.94
148 2 0.02
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (147 bp):
TTAAACTTGTTTAAAAAATATTTTAAGTATAAATATTCATTTGAAACATTATTTTTGAGAAAATA
AGAGGTAAAAAAATTAATTTAATATTTTTCAAAATATTTTCAATTTAATTCAAAGAAAAATACTA
AGTTTAGAAATAAACAC
Found at i:1697657 original size:2 final size:2
Alignment explanation
Indices: 1697634--1697692 Score: 57
Period size: 2 Copynumber: 30.0 Consensus size: 2
1697624 TATAAACACT
* * * * *
1697634 TA TA CA TA TA TA CA TA TG TA TA TA TA TA TA -A CA TA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1697675 TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1697693 CACACACGCG
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (2 bp):
TA
Found at i:1697667 original size:27 final size:27
Alignment explanation
Indices: 1697637--1697690 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1697627 AAACACTTAT
1697637 ACATATATACATATGTATATATATATA
1 ACATATATACATATGTATATATATATA
1697664 ACATATATACATATGTATATATATATA
1 ACATATATACATATGTATATATATATA
1697691 TACACACACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (27 bp):
ACATATATACATATGTATATATATATA
Found at i:1697859 original size:12 final size:12
Alignment explanation
Indices: 1697844--1697875 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1697834 ATATATATAT
*
1697844 AGAGAGAGAGAC
1 AGAGAGAGAGAA
1697856 AGAGAGAGAGAA
1 AGAGAGAGAGAA
1697868 AGAGAGAG
1 AGAGAGAG
1697876 GTGATGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.44, T:0.00
Consensus pattern (12 bp):
AGAGAGAGAGAA
Found at i:1699875 original size:9 final size:9
Alignment explanation
Indices: 1699858--1699891 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
1699848 GTCAACCATC
1699858 AATGATGAT
1 AATGATGAT
*
1699867 AAAGATGAT
1 AATGATGAT
1699876 AATGATGAT
1 AATGATGAT
1699885 AATGATG
1 AATGATG
1699892 GTGATTCGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (9 bp):
AATGATGAT
Found at i:1704396 original size:13 final size:13
Alignment explanation
Indices: 1704378--1704404 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1704368 ACAATATTCC
1704378 TTGTATCGATACA
1 TTGTATCGATACA
1704391 TTGTATCGATACA
1 TTGTATCGATACA
1704404 T
1 T
1704405 GGGTTACTAT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1708606 original size:52 final size:52
Alignment explanation
Indices: 1708543--1708671 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
1708533 CGAAATATGA
1708543 AAATTTACCTGCATGTATCGATACATTTCAAAGTGTATCGATACATCTAGGC
1 AAATTTACCTGCATGTATCGATACATTTCAAAGTGTATCGATACATCTAGGC
* * * *
1708595 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTCAAAGTGTATCGATACATCTAGGC
*
1708647 AAATTTTCCTGCATGTATCGATACA
1 AAATTTACCTGCATGTATCGATACA
1708672 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (52 bp):
AAATTTACCTGCATGTATCGATACATTTCAAAGTGTATCGATACATCTAGGC
Found at i:1708682 original size:52 final size:51
Alignment explanation
Indices: 1708543--1708691 Score: 185
Period size: 52 Copynumber: 2.9 Consensus size: 51
1708533 CGAAATATGA
*
1708543 AAATTTACCTGCATGTATCGATAC-ATTTCAAAGTGTATCGATACATCTAGGC
1 AAATTTACCTGCATGTATCGATACAATATC--AGTGTATCGATACATCTAGGC
* * *
1708595 AAATTTGCCTGCATGTATCGATACATTTTAT-AGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACA--ATATCAGTGTATCGATACATCTAGGC
* *
1708647 AAATTTTCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTACCTGCATGTATCGATAC-AATATCAGTGTATCGATACA
1708692 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
51 2 0.02
52 80 0.94
53 1 0.01
55 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTACCTGCATGTATCGATACAATATCAGTGTATCGATACATCTAGGC
Found at i:1708698 original size:13 final size:13
Alignment explanation
Indices: 1708680--1708704 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1708670 CAAAGATCAG
1708680 TGTATCGATACAA
1 TGTATCGATACAA
1708693 TGTATCGATACA
1 TGTATCGATACA
1708705 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1708772 original size:19 final size:19
Alignment explanation
Indices: 1708748--1708831 Score: 101
Period size: 19 Copynumber: 4.7 Consensus size: 19
1708738 TAGCTTATAT
1708748 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
1708767 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
1708786 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
1708799 TGTATCGATAC-AAACTTTA
1 TGTATCGATACAAAAC-TTA
1708818 TGTATCGATACAAA
1 TGTATCGATACAAA
1708832 TCGTTGAAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
13 11 0.19
14 1 0.02
15 1 0.02
16 1 0.02
18 1 0.02
19 40 0.70
20 2 0.04
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1708804 original size:13 final size:13
Alignment explanation
Indices: 1708786--1708810 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1708776 ACAACACTTA
1708786 TGTATCGATACAT
1 TGTATCGATACAT
1708799 TGTATCGATACA
1 TGTATCGATACA
1708811 AACTTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1708808 original size:32 final size:32
Alignment explanation
Indices: 1708767--1708829 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1708757 ACAAAACTTA
1708767 TGTATCGATACAACAC-TTATGTATCGATACAT
1 TGTATCGATACAA-ACTTTATGTATCGATACAT
1708799 TGTATCGATACAAACTTTATGTATCGATACA
1 TGTATCGATACAAACTTTATGTATCGATACA
1708830 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 2 0.07
32 28 0.93
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAACTTTATGTATCGATACAT
Found at i:1711580 original size:22 final size:22
Alignment explanation
Indices: 1711532--1711589 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
1711522 TATATAACTT
*
1711532 ATTTAAATT-TAAATATTTTAA
1 ATTTAAATTATTAATATTTTAA
1711553 ATTTAAATTATTAATATTTTATA
1 ATTTAAATTATTAATATTTTA-A
1711576 A-TTAAATTAATTAA
1 ATTTAAATT-ATTAA
1711590 ATCAAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 9 0.27
22 17 0.52
23 7 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTAAATTATTAATATTTTAA
Found at i:1712024 original size:46 final size:46
Alignment explanation
Indices: 1711972--1712064 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
1711962 CTAAAAGGAA
*
1711972 AACCCTGTACAAAGTTTCTATATTTTGACTATATACGTAGAAATAC
1 AACCCTGTACAAAGCTTCTATATTTTGACTATATACGTAGAAATAC
*
1712018 AACCCTGTACAAAGCTTCTATATTTTGACTATATACGTATAAATAC
1 AACCCTGTACAAAGCTTCTATATTTTGACTATATACGTAGAAATAC
1712064 A
1 A
1712065 CAATATTAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (46 bp):
AACCCTGTACAAAGCTTCTATATTTTGACTATATACGTAGAAATAC
Found at i:1715512 original size:3 final size:3
Alignment explanation
Indices: 1715504--1715549 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1715494 CTATTTTATC
1715504 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1715550 AAGGGTGGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1715981 original size:110 final size:108
Alignment explanation
Indices: 1715823--1716368 Score: 386
Period size: 109 Copynumber: 5.0 Consensus size: 108
1715813 TTACAAAAAA
* * * * * *
1715823 AAAAAAATGAATTGTCCTATATAAAAGGTATTCGTATGTCACTTTATAACTCTAAATGATAACCT
1 AAAAAAATAAATTAT-CTATATAAAAGGCATTCGTATGCCACTTTATAACTCTAAACGATGACCT
*
1715888 ATTTCAAGGCCAATCCTTTAGTGCCAGAATCTATGTAATTAATGT
65 ATTTCAAGGCCAATCCTTTAGTGCC-GAATTTATGTAATTAATGT
* * *
1715933 AAAAAAATAAATTATCATATATAAAGGGCATTCGTATGCCACATTATAACTCTAGACGATGACCT
1 AAAAAAATAAATTATC-TATATAAAAGGCATTCGTATGCCACTTTATAACTCTAAACGATGACCT
* * * * * * *
1715998 ATTT-TAGAGCTAATCTTTTGGTGCTCGATTTTACGTAATTAATAT
65 ATTTCAAG-GCCAATCCTTTAGTGC-CGAATTTATGTAATTAATGT
* * * **
1716043 -AAAAAATATATTATGCTATATAAAAGGCGTTCGTATGCCACTTTATAACTCTAAGCGATGATTT
1 AAAAAAATAAATTAT-CTATATAAAAGGCATTCGTATGCCACTTTATAACTCTAAACGATGACCT
* *
1716107 ATTTCAGGGCCAATCCCTTAGTGCCTGAATATTATGTAATTAATG-
65 ATTTCAAGGCCAATCCTTTAGTGCC-GAAT-TTATGTAATTAATGT
* * * * * * * * * **
1716152 CAAAAAA-GAATTGTCCTATATAAAAAGCGTTCGTACGCCGCTTTATGACTCTAGACGATGATTT
1 AAAAAAATAAATTAT-CTATATAAAAGGCATTCGTATGCCACTTTATAACTCTAAACGATGACCT
* * * * **
1716216 ATTTCAGGGTCAATCCCTTGGTGCCCGAATATTACATAATTAATG-
65 ATTTCAAGGCCAATCCTTTAGTG-CCGAAT-TTATGTAATTAATGT
* * * * * * * * * ** * * **
1716261 -CAAAAATGAATTATCCGATGTAAAGGGCATTTGTACGTCATTTTACGACTCTAGACAATGATTT
1 AAAAAAATAAATTAT-CTATATAAAAGGCATTCGTATGCCACTTTATAACTCTAAACGATGACCT
* * *
1716325 ATTTC-GGGACCAATCCCTTAGTAGCCGAATCTATGTAATTAATG
65 ATTTCAAGG-CCAATCCTTTAGT-GCCGAATTTATGTAATTAATG
1716369 CAATTGAATT
Statistics
Matches: 358, Mismatches: 66, Indels: 26
0.80 0.15 0.06
Matches are distributed among these distances:
108 20 0.06
109 228 0.64
110 109 0.30
111 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (108 bp):
AAAAAAATAAATTATCTATATAAAAGGCATTCGTATGCCACTTTATAACTCTAAACGATGACCTA
TTTCAAGGCCAATCCTTTAGTGCCGAATTTATGTAATTAATGT
Found at i:1716837 original size:13 final size:13
Alignment explanation
Indices: 1716819--1716875 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
1716809 TTCAACGATT
1716819 TGTATCGATACAG
1 TGTATCGATACAG
1716832 TGTATCGATACATAAGTG
1 TGTATCGATAC---A--G
*
1716850 TTGTATCGATACAA
1 -TGTATCGATACAG
1716864 TGTATCGATACA
1 TGTATCGATACA
1716876 TAGGTTTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 23 0.62
16 2 0.05
18 1 0.03
19 11 0.30
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1716856 original size:19 final size:17
Alignment explanation
Indices: 1716817--1716898 Score: 63
Period size: 19 Copynumber: 5.1 Consensus size: 17
1716807 ATTTCAACGA
1716817 TTTGTATCGATAC--AG
1 TTTGTATCGATACAAAG
1716832 --TGTATCGATACATAAG
1 TTTGTATCGATACA-AAG
1716848 TGTTGTATCGATAC-AA-
1 T-TTGTATCGATACAAAG
*
1716864 --TGTATCGATACATAGG
1 TTTGTATCGATACA-AAG
1716880 TTTTGTATCGATACAAAG
1 -TTTGTATCGATACAAAG
1716898 T
1 T
1716899 AAGCTACTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 22
0.69 0.03 0.29
Matches are distributed among these distances:
13 22 0.42
15 1 0.02
16 2 0.04
17 3 0.06
18 2 0.04
19 23 0.43
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (17 bp):
TTTGTATCGATACAAAG
Found at i:1716859 original size:32 final size:32
Alignment explanation
Indices: 1716818--1716895 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
1716808 TTTCAACGAT
*
1716818 TTGTATCGATACAGTGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
* *
1716850 TTGTATCGATACAATGTATCGATACATAGGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
1716882 TTGTATCGATACAA
1 TTGTATCGATACAA
1716896 AGTAAGCTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:1717015 original size:52 final size:51
Alignment explanation
Indices: 1716953--1717098 Score: 213
Period size: 52 Copynumber: 2.8 Consensus size: 51
1716943 GATACATTGC
*
1716953 ATCGATACACTGAT-CTTTGTATCGATACATGCAGGCAAATTTGCCCAGATGT
1 ATCGATACACT-ATAC-ATGTATCGATACATGCAGGCAAATTTGCCCAGATGT
* *
1717005 ATCGATACACTATAACATGTATCGATACATGTAGGCAAATTTGCCTAGATGT
1 ATCGATACACTAT-ACATGTATCGATACATGCAGGCAAATTTGCCCAGATGT
*
1717057 ATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTT
1 ATCGATACACTAT-ACATGTATCGATACATGCAGGCAAATTT
1717099 TCATATTTCG
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.97
53 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (51 bp):
ATCGATACACTATACATGTATCGATACATGCAGGCAAATTTGCCCAGATGT
Found at i:1720632 original size:14 final size:14
Alignment explanation
Indices: 1720604--1720647 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1720594 TTACTCCATT
1720604 TTTTTTCTTTCCTTC
1 TTTTTTCTTT-CTTC
1720619 TTTTTTCTTTCTTC
1 TTTTTTCTTTCTTC
* *
1720633 TTTCTTCCTTCTTC
1 TTTTTTCTTTCTTC
1720647 T
1 T
1720648 CCTTTTCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 17 0.63
15 10 0.37
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTTTCTTTCTTC
Found at i:1720636 original size:7 final size:7
Alignment explanation
Indices: 1720608--1720647 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
1720598 TCCATTTTTT
1720608 TTCTTTCC
1 TTCTTT-C
*
1720616 TTCTTTT
1 TTCTTTC
1720623 TTCTTTC
1 TTCTTTC
1720630 TTCTTTC
1 TTCTTTC
*
1720637 TTCCTTC
1 TTCTTTC
1720644 TTCT
1 TTCT
1720648 CCTTTTCTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (7 bp):
TTCTTTC
Found at i:1721506 original size:42 final size:42
Alignment explanation
Indices: 1721447--1721529 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
1721437 AGTACTTGAA
* *
1721447 CAATTAAAATTTTATTAGGGAAAACATGATATTTTGGTGGTT
1 CAATTAAAATCTTATTAGGGAAAACATGATATTTCGGTGGTT
1721489 CAATTAAAATCTTATTAGGGAAAACATGATATTTCGGTGGT
1 CAATTAAAATCTTATTAGGGAAAACATGATATTTCGGTGGT
1721530 GATTTTGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.37
Consensus pattern (42 bp):
CAATTAAAATCTTATTAGGGAAAACATGATATTTCGGTGGTT
Found at i:1721662 original size:28 final size:28
Alignment explanation
Indices: 1721619--1721966 Score: 119
Period size: 28 Copynumber: 12.6 Consensus size: 28
1721609 TTGACTTAGA
* *
1721619 TGCCAACTAATGTGGGCTTTGAATTATG
1 TGCCAACGAATATGGGCTTTGAATTATG
* * *
1721647 TAG-CAGCGAATATGGGCTTAGACTTATG
1 T-GCCAACGAATATGGGCTTTGAATTATG
*
1721675 TGCCAATGAATATGGGCTTT-AACTTA--
1 TGCCAACGAATATGGGCTTTGAA-TTATG
** * * *
1721701 TGCCAATAAATGTGGGCTCT-AACT-TG
1 TGCCAACGAATATGGGCTTTGAATTATG
* * ** *
1721727 TGCGAGC-AAGTATGGGCTTT-AACCAGGG
1 TGCCAACGAA-TATGGGCTTTGAATTA-TG
* * * * * * *
1721755 TGCTAGCTAGTGTGGGCTTAGACTTATG
1 TGCCAACGAATATGGGCTTTGAATTATG
* * * * *
1721783 TGCTAATGAATGTGGGCTTAGACTTATG
1 TGCCAACGAATATGGGCTTTGAATTATG
* * *
1721811 TGCCAACGAATGTGGGCTTAGACTTATG
1 TGCCAACGAATATGGGCTTTGAATTATG
**
1721839 TGCCAACGAATATGGGCTTTG-A-CGTG
1 TGCCAACGAATATGGGCTTTGAATTATG
**
1721865 TG-CAATC-AAGTATGGGCTTT-AACCAGTG
1 TGCCAA-CGAA-TATGGGCTTTGAATTA-TG
*** * *
1721893 TGCCAGTTAATATGGGCTTAGACTTATG
1 TGCCAACGAATATGGGCTTTGAATTATG
* * * * *
1721921 TGCCAGCGAATGTGGGCTTAGACTTTTG
1 TGCCAACGAATATGGGCTTTGAATTATG
* *
1721949 TGCCAATGAATGTGGGCT
1 TGCCAACGAATATGGGCT
1721967 GAGACTCATG
Statistics
Matches: 250, Mismatches: 52, Indels: 36
0.74 0.15 0.11
Matches are distributed among these distances:
25 8 0.03
26 50 0.20
27 3 0.01
28 179 0.72
29 10 0.04
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (28 bp):
TGCCAACGAATATGGGCTTTGAATTATG
Found at i:1721716 original size:26 final size:26
Alignment explanation
Indices: 1721655--1721725 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
1721645 TGTAGCAGCG
*
1721655 AATATGGGCT-TAGACTTATGTGCCAATG
1 AATATGGGCTCTA-ACTTA--TGCCAATA
*
1721683 AATATGGGCTTTAACTTATGCCAATA
1 AATATGGGCTCTAACTTATGCCAATA
*
1721709 AATGTGGGCTCTAACTT
1 AATATGGGCTCTAACTT
1721726 GTGCGAGCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 22 0.56
28 15 0.38
29 2 0.05
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (26 bp):
AATATGGGCTCTAACTTATGCCAATA
Found at i:1721895 original size:110 final size:109
Alignment explanation
Indices: 1721781--1722147 Score: 371
Period size: 110 Copynumber: 3.3 Consensus size: 109
1721771 CTTAGACTTA
* *
1721781 TGTGCTAATGAATGTGGGCTTAGACTTATGTGCCAACGAATGTGGGCTTAGACTTATGTGCCAAC
1 TGTGCCAAT-AATGTGGGCTTAGACTTATGTGCCAGCGAATGTGGGCTTAGACTTATGTGCCAAC
* * * *
1721846 GAATATGGGCTTTGACGT-GTGCAATCAAGTATGGGCTTTAACCAG
65 GAATGTGGGCTTTGAC-TCATGCAAGCAAGCATGGGCTTTAACCAG
* * * *
1721891 TGTGCCAGTTAATATGGGCTTAGACTTATGTGCCAGCGAATGTGGGCTTAGACTTTTGTGCCAAT
1 TGTGCCA-ATAATGTGGGCTTAGACTTATGTGCCAGCGAATGTGGGCTTAGACTTATGTGCCAAC
** * *
1721956 GAATGTGGGCTGAGACTCATGCCAGCAAGCATGGGCTTTAACTAG
65 GAATGTGGGCTTTGACTCATGCAAGCAAGCATGGGCTTTAACCAG
* * * * * * * *
1722001 TGTGCCAGCTAGTGTGGGCTTAGACTTTTGTGCTAGTGAATGTGGGCATAGATTTATATGCCAAC
1 TGTGCCA-ATAATGTGGGCTTAGACTTATGTGCCAGCGAATGTGGGCTTAGACTTATGTGCCAAC
* * * * * * *
1722066 GAATGTGGGCTTTAACTCGTGCCAGTAAGCGTAGGCTTTGACTC-G
65 GAATGTGGGCTTTGACTCATGCAAGCAAGCATGGGCTTTAAC-CAG
* *
1722111 -GATGCCAACTAATGTAGGCTTTGACTTATGTGCCAGC
1 TG-TGCCAA-TAATGTGGGCTTAGACTTATGTGCCAGC
1722148 TAGTGTAGGC
Statistics
Matches: 211, Mismatches: 41, Indels: 10
0.81 0.16 0.04
Matches are distributed among these distances:
109 2 0.01
110 208 0.99
111 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (109 bp):
TGTGCCAATAATGTGGGCTTAGACTTATGTGCCAGCGAATGTGGGCTTAGACTTATGTGCCAACG
AATGTGGGCTTTGACTCATGCAAGCAAGCATGGGCTTTAACCAG
Found at i:1721971 original size:28 final size:28
Alignment explanation
Indices: 1721765--1722077 Score: 220
Period size: 28 Copynumber: 11.3 Consensus size: 28
1721755 TGCTAGCTAG
*
1721765 TGTGGGCTTAGACTTATGTGCTAATGAA
1 TGTGGGCTTAGACTTATGTGCCAATGAA
*
1721793 TGTGGGCTTAGACTTATGTGCCAACGAA
1 TGTGGGCTTAGACTTATGTGCCAATGAA
*
1721821 TGTGGGCTTAGACTTATGTGCCAACGAA
1 TGTGGGCTTAGACTTATGTGCCAATGAA
* * * *
1721849 TATGGGCTTTGAC--GTGTG-CAATCAA
1 TGTGGGCTTAGACTTATGTGCCAATGAA
* * * *
1721874 GTATGGGCTTTA-AC-CAGTGTGCCAGTTAA
1 -TGTGGGC-TTAGACTTA-TGTGCCAATGAA
* **
1721903 TATGGGCTTAGACTTATGTGCCAGCGAA
1 TGTGGGCTTAGACTTATGTGCCAATGAA
*
1721931 TGTGGGCTTAGACTTTTGTGCCAATGAA
1 TGTGGGCTTAGACTTATGTGCCAATGAA
* *
1721959 TGTGGGCTGAGACTCA--TGCC-A-GCAA
1 TGTGGGCTTAGACTTATGTGCCAATG-AA
* *
1721984 -GCATGGGCTTTA-AC-TAGTGTGCCAGCT-AG
1 TG--TGGGC-TTAGACTTA-TGTGCCA-ATGAA
* * *
1722013 TGTGGGCTTAGACTTTTGTGCTAGTGAA
1 TGTGGGCTTAGACTTATGTGCCAATGAA
* * * *
1722041 TGTGGGCATAGATTTATATGCCAACGAA
1 TGTGGGCTTAGACTTATGTGCCAATGAA
1722069 TGTGGGCTT
1 TGTGGGCTT
1722078 TAACTCGTGC
Statistics
Matches: 227, Mismatches: 37, Indels: 42
0.74 0.12 0.14
Matches are distributed among these distances:
24 2 0.01
25 9 0.04
26 24 0.11
27 11 0.05
28 172 0.76
29 8 0.04
30 1 0.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.31
Consensus pattern (28 bp):
TGTGGGCTTAGACTTATGTGCCAATGAA
Found at i:1721979 original size:82 final size:82
Alignment explanation
Indices: 1721650--1722052 Score: 278
Period size: 82 Copynumber: 4.9 Consensus size: 82
1721640 AATTATGTAG
** * * *
1721650 CAGCGAATATGGGCTTAGACTTATGTGCCAATGAATATGGGCTTTA-AC--TTATGCCAATAAAT
1 CAGC-AATATGGGCTTAGACTTATGTGCCAGCGAATGTGGGC-TTAGACTTTTGTGCCAATGAAT
*
1721712 GTGGGCTCTA-ACT-TGTGC
64 GTGGGCT-TAGACTCAGTGC
* * * * * * * *
1721730 GAGCAAGTATGGGCTTTA-AC-CAGGGTGCTAGCTAGTGTGGGCTTAGACTTATGTGCTAATGAA
1 CAGCAA-TATGGGC-TTAGACTTA-TGTGCCAGCGAATGTGGGCTTAGACTTTTGTGCCAATGAA
*
1721793 TGTGGGCTTAGACTTATGTGC
63 TGTGGGCTTAGACTCA-GTGC
* * * * * * *
1721814 CAACGAATGTGGGCTTAGACTTATGTGCCAACGAATATGGGCTTTGAC--GTGTG-CAATCAAGT
1 CAGC-AATATGGGCTTAGACTTATGTGCCAGCGAATGTGGGCTTAGACTTTTGTGCCAATGAA-T
*
1721876 ATGGGCTTTA-AC-CAGTGTGC
64 GTGGGC-TTAGACTCA--GTGC
*
1721896 CAGTTAATATGGGCTTAGACTTATGTGCCAGCGAATGTGGGCTTAGACTTTTGTGCCAATGAATG
1 CAG-CAATATGGGCTTAGACTTATGTGCCAGCGAATGTGGGCTTAGACTTTTGTGCCAATGAATG
*
1721961 TGGGCTGAGACTCA-TGC
65 TGGGCTTAGACTCAGTGC
* * * * *
1721978 CAGCAAGCATGGGCTTTA-AC-TAGTGTGCCAGCTAGTGTGGGCTTAGACTTTTGTGCTAGTGAA
1 CAGCAA-TATGGGC-TTAGACTTA-TGTGCCAGCGAATGTGGGCTTAGACTTTTGTGCCAATGAA
*
1722041 TGTGGGCATAGA
63 TGTGGGCTTAGA
1722053 TTTATATGCC
Statistics
Matches: 251, Mismatches: 48, Indels: 46
0.73 0.14 0.13
Matches are distributed among these distances:
79 6 0.02
80 26 0.10
81 15 0.06
82 138 0.55
83 11 0.04
84 44 0.18
85 11 0.04
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (82 bp):
CAGCAATATGGGCTTAGACTTATGTGCCAGCGAATGTGGGCTTAGACTTTTGTGCCAATGAATGT
GGGCTTAGACTCAGTGC
Found at i:1722033 original size:138 final size:136
Alignment explanation
Indices: 1721619--1722077 Score: 462
Period size: 138 Copynumber: 3.3 Consensus size: 136
1721609 TTGACTTAGA
* * * * *
1721619 TGCCAACTAATGTGGGCTTTGAATTATGTAG-CAGCGAATATGGGCTTAGACTTATGTGCCAATG
1 TGCCAGCTAATGTGGGCTTAGACTTATGT-GCCAACGAATGTGGGCTTAGACTTATGTGCCAATG
* * * * *
1721683 AATATGGGCTTTA-ACTTATGCCAATAAATGTGGGCTCTAACT-TGTGCGAGCAAGTATGGGCTT
65 AATGTGGGC-TTAGACTTATGCCAA-CAATATGGGCTTTAACTGTGTGCCAGCAAGTATGGGCTT
*
1721746 TAACCAGGG
128 TAACCAGTG
* * * * *
1721755 TGCTAGCTAGTGTGGGCTTAGACTTATGTGCTAATGAATGTGGGCTTAGACTTATGTGCCAACGA
1 TGCCAGCTAATGTGGGCTTAGACTTATGTGCCAACGAATGTGGGCTTAGACTTATGTGCCAATGA
* * *
1721820 ATGTGGGCTTAGACTTATGTGCCAACGAATATGGGCTTTGAC-GTGTGCAATCAAGTATGGGCTT
66 ATGTGGGCTTAGACTTA--TGCCAAC-AATATGGGCTTTAACTGTGTGCCAGCAAGTATGGGCTT
1721884 TAACCAGTG
128 TAACCAGTG
* * * *
1721893 TGCCAGTTAATATGGGCTTAGACTTATGTGCCAGCGAATGTGGGCTTAGACTTTTGTGCCAATGA
1 TGCCAGCTAATGTGGGCTTAGACTTATGTGCCAACGAATGTGGGCTTAGACTTATGTGCCAATGA
* * * * * *
1721958 ATGTGGGCTGAGACTCATGCCAGCAAGCATGGGCTTTAACTAGTGTGCCAGCTAGTGTGGGC-TT
66 ATGTGGGCTTAGACTTATGCCAACAA-TATGGGCTTTAACT-GTGTGCCAGCAAGTATGGGCTTT
***
1722022 AGACTTTTG
129 A-ACCAGTG
* * * *
1722031 TGCTAG-TGAATGTGGGCATAGATTTATATGCCAACGAATGTGGGCTT
1 TGCCAGCT-AATGTGGGCTTAGACTTATGTGCCAACGAATGTGGGCTT
1722078 TAACTCGTGC
Statistics
Matches: 267, Mismatches: 45, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
135 6 0.02
136 82 0.31
137 4 0.01
138 175 0.66
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (136 bp):
TGCCAGCTAATGTGGGCTTAGACTTATGTGCCAACGAATGTGGGCTTAGACTTATGTGCCAATGA
ATGTGGGCTTAGACTTATGCCAACAATATGGGCTTTAACTGTGTGCCAGCAAGTATGGGCTTTAA
CCAGTG
Found at i:1722088 original size:82 final size:80
Alignment explanation
Indices: 1721920--1722090 Score: 186
Period size: 82 Copynumber: 2.1 Consensus size: 80
1721910 TTAGACTTAT
*
1721920 GTGCCAGCGAATGTGGGCTTAGACTTTTGTGCCAATGAATGTGGGCTGAGACTCATGCCAGCAAG
1 GTGCCAGCGAATGTGGGCTTAGACTTTTGTGCCAATGAATGTGGGCTGAGACTCATGCCAACAAG
*
1721985 CATGGGCTTTAACTAGT
66 -ATGGGCTTTAACTA-C
* * * * * *
1722002 GTGCCAGCTAGTGTGGGCTTAGACTTTTGTGCTAGTGAATGTGGGCAT-AGATTTATATGCCAAC
1 GTGCCAGCGAATGTGGGCTTAGACTTTTGTGCCAATGAATGTGGGC-TGAGA-CT-CATGCCAAC
1722066 GAATG-TGGGCTTTAACT-C
63 -AA-GATGGGCTTTAACTAC
1722084 GTGCCAG
1 GTGCCAG
1722091 TAAGCGTAGG
Statistics
Matches: 76, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
82 52 0.68
83 2 0.03
84 19 0.25
85 2 0.03
86 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.29
Consensus pattern (80 bp):
GTGCCAGCGAATGTGGGCTTAGACTTTTGTGCCAATGAATGTGGGCTGAGACTCATGCCAACAAG
ATGGGCTTTAACTAC
Found at i:1722127 original size:28 final size:26
Alignment explanation
Indices: 1722059--1722162 Score: 84
Period size: 28 Copynumber: 3.8 Consensus size: 26
1722049 TAGATTTATA
* * *
1722059 TGCCAACGAATGTGGGCTTTAACTCG
1 TGCCAACTAATGTAGGCTTTGACTCG
* *
1722085 TGCC-AGTAAGCGTAGGCTTTGACTCGG
1 TGCCAACTAA-TGTAGGCTTTGACTC-G
*
1722112 ATGCCAACTAATGTAGGCTTTGACTTATG
1 -TGCCAACTAATGTAGGCTTTGAC-T-CG
* *
1722141 TGCCAGCTAGTGTAGGCTTTGA
1 TGCCAACTAATGTAGGCTTTGA
1722163 TTCATATGCC
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
25 3 0.05
26 16 0.26
27 1 0.02
28 36 0.58
29 6 0.10
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (26 bp):
TGCCAACTAATGTAGGCTTTGACTCG
Found at i:1722172 original size:28 final size:28
Alignment explanation
Indices: 1722096--1722187 Score: 87
Period size: 28 Copynumber: 3.3 Consensus size: 28
1722086 GCCAGTAAGC
* **
1722096 GTAGGCTTTGACTCGGATGCCAACTAAT
1 GTAGGCTTTGATTCATATGCCAACTAAT
* * *
1722124 GTAGGCTTTGACTT-ATGTGCCAGCTAGT
1 GTAGGCTTTGA-TTCATATGCCAACTAAT
* *
1722152 GTAGGCTTTGATTCATATGCCGACTAAC
1 GTAGGCTTTGATTCATATGCCAACTAAT
*
1722180 ATAGGCTT
1 GTAGGCTT
1722188 CCTTTTAATA
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
27 2 0.04
28 47 0.94
29 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (28 bp):
GTAGGCTTTGATTCATATGCCAACTAAT
Found at i:1722172 original size:56 final size:54
Alignment explanation
Indices: 1722051--1722187 Score: 132
Period size: 56 Copynumber: 2.5 Consensus size: 54
1722041 TGTGGGCATA
* * *
1722051 GATTTATATGCCAACGAATGTGGGCTTTAACTCGTGCCAGTAAGCGTAGGCTTT
1 GATTCATATGCCAACTAATGTAGGCTTTAACTCGTGCCAGTAAGCGTAGGCTTT
* ** * * *
1722105 GACTCGGATGCCAACTAATGTAGGCTTTGACTTATGTGCCAGCT-AGTGTAGGCTTT
1 GATTCATATGCCAACTAATGTAGGCTTTAAC-T-CGTGCCAG-TAAGCGTAGGCTTT
* **
1722161 GATTCATATGCCGACTAACATAGGCTT
1 GATTCATATGCCAACTAATGTAGGCTT
1722188 CCTTTTAATA
Statistics
Matches: 65, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
54 24 0.37
55 1 0.02
56 39 0.60
57 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (54 bp):
GATTCATATGCCAACTAATGTAGGCTTTAACTCGTGCCAGTAAGCGTAGGCTTT
Found at i:1738962 original size:22 final size:22
Alignment explanation
Indices: 1738909--1738967 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 22
1738899 TTGCTTTTGA
* **
1738909 TTGCTGTTGCTTCTTTCTTTGC
1 TTGCTGTTTCTTCTTTCTTCAC
* * *
1738931 TTGTTATTTCTTTTTTCTTCAC
1 TTGCTGTTTCTTCTTTCTTCAC
*
1738953 TTGCTGTTTCGTCTT
1 TTGCTGTTTCTTCTT
1738968 GCTGTTTATT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.03, C:0.20, G:0.14, T:0.63
Consensus pattern (22 bp):
TTGCTGTTTCTTCTTTCTTCAC
Found at i:1739332 original size:20 final size:20
Alignment explanation
Indices: 1739304--1739359 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
1739294 TAAGTTACTG
*
1739304 CTATTTCATTTTTCTTGCTA
1 CTATCTCATTTTTCTTGCTA
*
1739324 CTATCTCATTTCTT-TTGCTG
1 CTATCTCATTT-TTCTTGCTA
*
1739344 CTA-CTC-TTCTTCTTGC
1 CTATCTCATTTTTCTTGC
1739360 CGTGAGTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 2 0.06
18 6 0.19
19 3 0.10
20 18 0.58
21 2 0.06
ACGTcount: A:0.11, C:0.27, G:0.07, T:0.55
Consensus pattern (20 bp):
CTATCTCATTTTTCTTGCTA
Found at i:1739767 original size:28 final size:28
Alignment explanation
Indices: 1739694--1739755 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
1739684 TCGGCTACTC
* **
1739694 GTTTCTTCTTTTAATTTTCTATTTGCTA
1 GTTTTTTCTTTTTCTTTTCTATTTGCTA
*
1739722 GTTTTTTCTTTTTCTTTTCTGTTTGCTA
1 GTTTTTTCTTTTTCTTTTCTATTTGCTA
1739750 GTTTTT
1 GTTTTT
1739756 ATTTTTTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.08, C:0.13, G:0.10, T:0.69
Consensus pattern (28 bp):
GTTTTTTCTTTTTCTTTTCTATTTGCTA
Found at i:1740398 original size:17 final size:17
Alignment explanation
Indices: 1740376--1740418 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
1740366 CCAAATAATC
*
1740376 AATGCATGAAGGTATGA
1 AATGCATGAAGGCATGA
1740393 AATGCATGAAGGCATGA
1 AATGCATGAAGGCATGA
*
1740410 AATGTATGA
1 AATGCATGA
1740419 TTTTTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.42, C:0.07, G:0.28, T:0.23
Consensus pattern (17 bp):
AATGCATGAAGGCATGA
Found at i:1740628 original size:3 final size:3
Alignment explanation
Indices: 1740622--1740671 Score: 91
Period size: 3 Copynumber: 16.3 Consensus size: 3
1740612 TTTTTTTTCA
1740622 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
1740668 ATT A
1 ATT A
1740672 AATAAACCGA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1741284 original size:42 final size:42
Alignment explanation
Indices: 1741219--1743004 Score: 1498
Period size: 42 Copynumber: 42.9 Consensus size: 42
1741209 AAGTCTCTCG
* * *
1741219 GGTCAAAACCGACAAGTAGACTAAAGGTAAGGAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * ** *
1741261 GGTCAAAGCCAATAGGCAAACTAAAGGTAAAAAAGTCTCTAAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTC-CAA
* *
1741304 GG-CAAAGCCGATAGGCAGACTAAAGGTAAAGAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
** * * * *
1741345 GGTCAAAGCTAACAAGTAGACTAGAGGT---G--CT-TCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * *
1741381 GCTCAAAGCCGACAGGCAAACTAGAGGTAAGGAAGTCTTCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
*
1741423 GGTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * *
1741465 GATCAAAGCCGAAAGGTAGACTAAAGGTTAA-GAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGG-TAAGGAAGTCTCCAA
** * * *
1741507 ACTCAAAGCCGACAGGCAGACTAAAGGTAAAGAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * * *
1741549 GGTCAAAGCCGATAGGCAAACTAAAGGTTAGGAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * *
1741591 GGTCAAAGTCGATAGGCAGACTAAACGTTAA-GAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAA-GGTAAGGAAGTCTCCAA
* **
1741633 GGTCAAAGTCG--A--CAGACTAAAGGTTTGGAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * * * * *
1741671 GATCAAAGCCGATAGGCAGACTAAGGGCAAAGAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* **
1741713 GGTCAAAGCCGACAGGCAAACTAAAGGTTTGGAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * ** *
1741755 GGTCAAAGCCGATAGGCAGACT-AAGCGCAAAAAAGTCT-CTA
1 GGTCAAAGCCGACAGGCAGACTAAAG-GTAAGGAAGTCTCCAA
* * * * * *
1741796 GAGTCAAACCCGATAGGCAAACTAAAGGTAAGAAAGTTTCTAA
1 G-GTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * * *
1741839 GGTCAAAGTCGATAGGTAGACTAAAGGTTAGGAAGTCTCTAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * *
1741881 GGTCAAAGCCAACAGGCAAACTAAAAGTTAGGAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * * * * * *
1741923 AGTCAAAGTCAACAGGCAGACTAAAAGTAAGAAAATCTTCAG
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * *
1741965 GGTCAAAGCTGAAAGGCAAACTAAAGGTTAA-GAAGCCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGG-TAAGGAAGTCTCCAA
* * * * *
1742007 GGTCAAAGCCGACATGCATAGTAAATGCT-AGGAAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTAAA-GGTAAGGAAGTCTCCAA
* ** * * *
1742049 GGTCAAAGCCGATATACAAACTAAAGGTTAA-GAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTAAAGG-TAAGGAAGTCTCCAA
* * * * *
1742091 GGTCAAAGCTGACATGCAGACTAGAGGTCAGGAAGTTTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * * *
1742133 GGTCAAAGCCGATAGGCAAACTAAAGGTAAAGAAGTCTCTAT
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
*** * *
1742175 GGTCAAAGCCGACATGG-AGACTAAAGGTGTTGAAGTCTCTAG
1 GGTCAAAGCCGACA-GGCAGACTAAAGGTAAGGAAGTCTCCAA
* *
1742217 GGTCAAAGCCGACAAGCAGACTAAAGGTAAGGAAGTCTCCAT
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * ** *
1742259 GGTCAAAGCCAACAGGTAGACTAAAGGTAAAAAAGTTTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * * * **
1742301 AGTCAAAGCCGACAAGTAAACTAAGGGTAAAAAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
*
1742343 GGTCAAAGCCGACAGGCAGACTAAAGGTTAGGAAGTCT-CAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * *
1742384 GGTCAAAACCGATAGGCAGACCAACGGTAAGGAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * *
1742426 GGTCAAAGCAGACAAGCAGACTAAAAGTTAGGAAGTCT-CAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * * ** * *
1742467 GGTCAAAACCGACAAGTAGACTAAAAGTTTGGAAGTTTTCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * * * * *
1742509 GTTTAAAGCCAATAGGCAAACTAAAGGTTAA-GAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTAAAGG-TAAGGAAGTCTCCAA
* *
1742551 GGTCAAAGCCGACAAGCAGACTAAAGGTAAGGAAGTCTCCAT
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * ** *
1742593 GGTCAAAGCCAACAGGTAGACTAAAGGTAAAAAAGTTTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * * * **
1742635 AGTCAAAGCCGACAAGTAAACTAAGGGTAAAAAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* *
1742677 GGTCAAAGCCGACAGGCAGACTAAAGGTTAGGAAGTCT-CAG
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * *
1742718 GGTCAAAACCGATAGGCAGACCAACGGTAAGGAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * * *
1742760 GGTCAAAGCAGGCAAGCAGACTAAAAGTTAGGAAGTCT-CAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * * ** * *
1742801 GGTCAAAACCGATAGGTAGACTAAAAGTTTGGAAGTTTTCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * * * * *
1742843 GTTTAAAGCCAATAGGCAAACTAAAGGTTAA-GAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTAAAGG-TAAGGAAGTCTCCAA
* * * * *
1742885 GGTCAAAGCCGACAAGCAGACTAAAGGTTAGGAAGTTTCTAG
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * * * *
1742927 GGTTAAAGTCGACAAGCAGACTAAAGATAAAGAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
* * *
1742969 GGTCAAAGCTGACAGGCAGACTAAATGTAAAGAAGT
1 GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGT
1743005 TAAAAGCATT
Statistics
Matches: 1396, Mismatches: 312, Indels: 72
0.78 0.18 0.04
Matches are distributed among these distances:
36 27 0.02
37 3 0.00
38 29 0.02
39 2 0.00
40 2 0.00
41 164 0.12
42 1145 0.82
43 24 0.02
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (42 bp):
GGTCAAAGCCGACAGGCAGACTAAAGGTAAGGAAGTCTCCAA
Found at i:1743238 original size:101 final size:101
Alignment explanation
Indices: 1743075--1743262 Score: 288
Period size: 101 Copynumber: 1.9 Consensus size: 101
1743065 AAAACCAATG
* * * *
1743075 AAGTCCATCAGTTAAAAGGTTAGTCAAAAGATTATAAGGGTTTGACCTGGGTGGTAACCATACGT
1 AAGTCAATCAGCTAAAAGGTTAGTCAAAAGATTACAAAGGTTTGACCTGGGTGGTAACCATACGT
*
1743140 CAAATCAAAATGAAAATAATCTGAGCAAAACTGATA
66 CAAATCAAAATGAAAAAAATCTGAGCAAAACTGATA
* *
1743176 AAGTCAATCAGCTAAAAGGTTAGTCAAAGGGTTACAAAGGTTTGA-CTAGGGTGGTAACCATACG
1 AAGTCAATCAGCTAAAAGGTTAGTCAAAAGATTACAAAGGTTTGACCT-GGGTGGTAACCATACG
*
1743240 TCAAATCAGAATGAAAAAAATCT
65 TCAAATCAAAATGAAAAAAATCT
1743263 AACTAGGGTG
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
100 2 0.03
101 76 0.97
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (101 bp):
AAGTCAATCAGCTAAAAGGTTAGTCAAAAGATTACAAAGGTTTGACCTGGGTGGTAACCATACGT
CAAATCAAAATGAAAAAAATCTGAGCAAAACTGATA
Found at i:1743269 original size:44 final size:44
Alignment explanation
Indices: 1743216--1744159 Score: 475
Period size: 44 Copynumber: 22.1 Consensus size: 44
1743206 GTTACAAAGG
1743216 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAAAA
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAAAA
* * * * *** *
1743260 TCTAACTAGGGTGGTAACCATATGTCAAA-CAGGAAAG-GGTAGA
1 TTTGACTAGGGTGGTAACCATACGTCAAATCA-GAATGAAAAAAA
* * * * * *
1743303 TTTGACTAAGGTTGTAAGCATACATCAAATCAAAATGAAAAGAA
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAAAA
* * * * * ** *
1743347 TCTAACTAGGGTGATAACCATACATCAAA-CTAAAATGGGAAAAG
1 TTTGACTAGGGTGGTAACCATACGTCAAATC-AGAATGAAAAAAA
* * * *
1743391 TTTGACTAGGGTGGTAACCATACGTC-AATCAAAATAGAGATAGA
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAAT-GAAAAAAA
* * * *
1743435 TTTGACCAAGGTGGTAACCATACATCAAATCAAAAT-AAAAAGAA
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAA-AA
* * * * * * * * *
1743479 TCTGACCAAGGTGGTAACCAAACATCAGATCAAAATGAGAAAAG
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAAAA
* * * * *
1743523 TTTGACCAAGGTGGTAACCATATGTCAAATC-GAAATGAGAAAAG
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAG-AATGAAAAAAA
* * * * * *
1743567 TTTGACCAAGGTGATAACTATATGTC-AA-C-----CAAAAAAA
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAAAA
* * * * * *
1743604 TCTGACGAAGGTGGTAACCATACGTCAAATCAAAATGAGAAAAG
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAAAA
* * *
1743648 TTTGACCAGGGTGGTAACAATACATCAAA-C---A--AAAAAAA
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAAAA
* * * * * *
1743686 TCTGA-TGAGGGTCGTAACCATACGTTAGATC-GAAATGAGAAAAG
1 TTTGACT-AGGGTGGTAACCATACGTCAAATCAG-AATGAAAAAAA
* * * * *
1743730 TTTGACTAGGGTAGTAACTATACGTCAAA-CAGAA-CAAAGGCAGA
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAA--AAAA
* * *
1743774 TTTGACTAGGGTGGTAACCATAAGTCAAATCTGAATGAAAAGAA
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAAAA
* * * * * *
1743818 TCTGACCAAGGTGGCAACCATACGTTAGAT-AG---GAAAGAAAA
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAA-AAAA
*
1743859 GTTTGACTAGGGTGGTAACCATACGTCAAA-CAGAAT-AAAAACGGA
1 -TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAA--AA
* * * *
1743904 TTTGACCAAGGTGGTAACCATACGTCAAATCAAAATGAAAAGAA
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAAAA
* * * * ** *
1743948 TCTGGCTAGGGTGGTAACCATACATCAGAT-AGAAATGGGAAAAG
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAG-AATGAAAAAAA
*
1743992 TTTGA-TCAGGGTGGTAACCATACGT---A--A-AA-CAAAAAAA
1 TTTGACT-AGGGTGGTAACCATACGTCAAATCAGAATGAAAAAAA
* * * * * * *
1744029 TTTAACTAGGGTGGTAACCATATGTTAGATTAAAATGAAAAAAG
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAAAA
*
1744073 TTTGACCAGGGTGGTAACCATACGTCAAA-C---A--AAAAAAA
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAAAA
* * * * * *
1744111 TCTGACGAGAGTGGTAACCATACGTCAGAT-AGAAATGAGAAAAG
1 TTTGACTAGGGTGGTAACCATACGTCAAATCAG-AATGAAAAAAA
1744155 TTTGA
1 TTTGA
1744160 TCAGGTCCTA
Statistics
Matches: 682, Mismatches: 161, Indels: 114
0.71 0.17 0.12
Matches are distributed among these distances:
37 51 0.07
38 62 0.09
39 2 0.00
40 8 0.01
41 4 0.01
42 31 0.05
43 53 0.08
44 440 0.65
45 24 0.04
46 7 0.01
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (44 bp):
TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAAAA
Found at i:1743375 original size:87 final size:87
Alignment explanation
Indices: 1743216--1743425 Score: 255
Period size: 87 Copynumber: 2.4 Consensus size: 87
1743206 GTTACAAAGG
* * * *
1743216 TTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAAAATCTAACTAGGGTGGTAACCAT
1 TTTGACTAAGGTGGTAACCATACATCAAATCAAAATGAAAAAAATCTAACTAGGGTGATAACCAT
**
1743281 ATGTCAAACAGGAAAGGGTAGA
66 ACATCAAACAGGAAAGGGTAGA
* * *
1743303 TTTGACTAAGGTTGTAAGCATACATCAAATCAAAATGAAAAGAATCTAACTAGGGTGATAACCAT
1 TTTGACTAAGGTGGTAACCATACATCAAATCAAAATGAAAAAAATCTAACTAGGGTGATAACCAT
* *
1743368 ACATCAAACTA--AAATGGGAAAA
66 ACATCAAAC-AGGAAA-GGGTAGA
* *
1743390 GTTTGACTAGGGTGGTAACCATACGTC-AATCAAAAT
1 -TTTGACTAAGGTGGTAACCATACATCAAATCAAAAT
1743426 AGAGATAGAT
Statistics
Matches: 105, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
86 3 0.03
87 79 0.75
88 23 0.22
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.23
Consensus pattern (87 bp):
TTTGACTAAGGTGGTAACCATACATCAAATCAAAATGAAAAAAATCTAACTAGGGTGATAACCAT
ACATCAAACAGGAAAGGGTAGA
Found at i:1743681 original size:81 final size:82
Alignment explanation
Indices: 1743215--1744164 Score: 625
Period size: 88 Copynumber: 11.1 Consensus size: 82
1743205 GGTTACAAAG
* *
1743215 GTTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAAAATCTAACTAGGGTGGTAACCA
1 GTTTGACCAGGGTGGTAACCATACGTCAAA-C---A--AAAAAAATCTGACTAGGGTGGTAACCA
* * * *
1743280 TATGTCAAA-CAGGAAA-GGGTAGA
60 TACGTCAAATCA--AAATGAGAAAA
* * * * * * *
1743303 -TTTGACTAAGGTTGTAAGCATACATCAAATCAAAATGAAAAGAATCTAACTAGGGTGATAACCA
1 GTTTGACCAGGGTGGTAACCATACGTCAAA-C--AA--AAAA-AATCTGACTAGGGTGGTAACCA
* *
1743367 TACATCAAA-CTAAAATGGGAAAA
60 TACGTCAAATC-AAAATGAGAAAA
* * * * *
1743390 GTTTGACTAGGGTGGTAACCATACGTCAATCAAAATAGAGATAGATTTGACCAAGGTGGTAACCA
1 GTTTGACCAGGGTGGTAACCATACGTCAAAC-AAA-A-A-A-A-ATCTGACTAGGGTGGTAACCA
*
1743455 TACATCAAATCAAAAT-A-AAAA
60 TACGTCAAATCAAAATGAGAAAA
* * * * * * * *
1743476 GAATCTGACCAAGGTGGTAACCAAACATCAGATCAAAATGAGAAAAGTTTGACCAAGGTGGTAAC
1 G--TTTGACCAGGGTGGTAACCATACGTCA-AAC-AAA--A-AAAA-TCTGACTAGGGTGGTAAC
* *
1743541 CATATGTCAAATCGAAATGAGAAAA
58 CATACGTCAAATCAAAATGAGAAAA
* * * * * * *
1743566 GTTTGACCAAGGTGATAACTATATGTC-AACCAAAAAAATCTGACGAAGGTGGTAACCATACGTC
1 GTTTGACCAGGGTGGTAACCATACGTCAAACAAAAAAAATCTGACTAGGGTGGTAACCATACGTC
1743630 AAATCAAAATGAGAAAA
66 AAATCAAAATGAGAAAA
* * *
1743647 GTTTGACCAGGGTGGTAACAATACATCAAACAAAAAAAATCTGA-TGAGGGTCGTAACCATACGT
1 GTTTGACCAGGGTGGTAACCATACGTCAAACAAAAAAAATCTGACT-AGGGTGGTAACCATACGT
* * *
1743711 TAGATCGAAATGAGAAAA
65 CAAATCAAAATGAGAAAA
* * * *
1743729 GTTTGACTAGGGTAGTAACTATACGTCAAACAGAACAAAGGCAGATTTGACTAGGGTGGTAACCA
1 GTTTGACCAGGGTGGTAACCATACGTCAAACA-AA-AAA---A-ATCTGACTAGGGTGGTAACCA
* **
1743794 TAAGTCAAATCTGAATGA-AAAGA
60 TACGTCAAATCAAAATGAGAAA-A
* * * * * * * *
1743817 ATCTGACCAAGGTGGCAACCATACGTTAGATAGGAAAGAAAAGTTTGACTAGGGTGGTAACCATA
1 GTTTGACCAGGGTGGTAACCATACGTCA-A-A-CAAA-AAAAATCTGACTAGGGTGGTAACCATA
*
1743882 CGTCAAA-CAGAAT-A-AAAA
62 CGTCAAATCAAAATGAGAAAA
* *
1743900 CGGATTTGACCAAGGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGGCTAGGGTGGTAA
1 --G-TTTGACCAGGGTGGTAACCATACGTCAAA-C--AA--AAAA-AATCTGACTAGGGTGGTAA
* * *
1743965 CCATACATCAGAT-AGAAATGGGAAAA
57 CCATACGTCAAATCA-AAATGAGAAAA
* * * * * *
1743991 GTTTGATCAGGGTGGTAACCATACGTAAAAC-AAAAAAATTTAACTAGGGTGGTAACCATATGTT
1 GTTTGACCAGGGTGGTAACCATACGTCAAACAAAAAAAATCTGACTAGGGTGGTAACCATACGTC
* * *
1744055 AGATTAAAATGAAAAAA
66 AAATCAAAATGAGAAAA
* *
1744072 GTTTGACCAGGGTGGTAACCATACGTCAAACAAAAAAAATCTGACGAGAGTGGTAACCATACGTC
1 GTTTGACCAGGGTGGTAACCATACGTCAAACAAAAAAAATCTGACTAGGGTGGTAACCATACGTC
*
1744137 AGAT-AGAAATGAGAAAA
66 AAATCA-AAATGAGAAAA
*
1744154 GTTTGATCAGG
1 GTTTGACCAGG
1744165 TCCTAATACC
Statistics
Matches: 703, Mismatches: 113, Indels: 98
0.77 0.12 0.11
Matches are distributed among these distances:
81 126 0.18
82 134 0.19
83 4 0.01
84 11 0.02
85 9 0.01
86 74 0.11
87 74 0.11
88 236 0.34
89 16 0.02
90 14 0.02
91 5 0.01
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (82 bp):
GTTTGACCAGGGTGGTAACCATACGTCAAACAAAAAAAATCTGACTAGGGTGGTAACCATACGTC
AAATCAAAATGAGAAAA
Found at i:1743884 original size:130 final size:130
Alignment explanation
Indices: 1743701--1744097 Score: 400
Period size: 130 Copynumber: 3.1 Consensus size: 130
1743691 TGAGGGTCGT
* * * *
1743701 AACCATACGTTAGATCGAAATGAGAAAAGTTTGACTAGGGTAGTAACTATACGTCAAACAGAACA
1 AACCATACGTTAGATAGGAA--AGAAAAGTTTGACTAGGGTGGTAACCATACGTCAAACAGAACA
** * * **
1743766 AAGGCAGATTTGACTAGGGTGGTAACCATAAGTCAAATCTGAATGAAAAGAATCTGACCAAGGTG
64 AAAACAGATTTGACCAAGGTGGTAACCATAAGTCAAATCAAAATGAAAAGAATCTGACCAAGGTG
1743831 GC
129 GC
*
1743833 AACCATACGTTAGATAGGAAAGAAAAGTTTGACTAGGGTGGTAACCATACGTCAAACAGAATAAA
1 AACCATACGTTAGATAGGAAAGAAAAGTTTGACTAGGGTGGTAACCATACGTCAAACAGAACAAA
* * * * * *
1743898 AACGGATTTGACCAAGGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGGCTAGGGTGGT
66 AACAGATTTGACCAAGGTGGTAACCATAAGTCAAATCAAAATGAAAAGAATCTGACCAAGGTGGC
* *
1743963 AACCATACATCAGATA-GAAATGGGAAAAGTTTGA-TCAGGGTGGTAACCATACGT---A-A-AA
1 AACCATACGTTAGATAGGAAA---GAAAAGTTTGACT-AGGGTGGTAACCATACGTCAAACAGAA
* * * * * * * * *
1744021 CAAAAA-A-ATTTAACTAGGGTGGTAACCATATGTTAGATTAAAATGAAAA-AAGTTTGACCAGG
62 CAAAAACAGATTTGACCAAGGTGGTAACCATAAGTCAAATCAAAATGAAAAGAA-TCTGACCAAG
*
1744083 GTGGT
126 GTGGC
1744088 AACCATACGT
1 AACCATACGT
1744098 CAAACAAAAA
Statistics
Matches: 228, Mismatches: 32, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
124 2 0.01
125 56 0.25
127 7 0.03
128 1 0.00
129 5 0.02
130 109 0.48
131 1 0.00
132 47 0.21
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (130 bp):
AACCATACGTTAGATAGGAAAGAAAAGTTTGACTAGGGTGGTAACCATACGTCAAACAGAACAAA
AACAGATTTGACCAAGGTGGTAACCATAAGTCAAATCAAAATGAAAAGAATCTGACCAAGGTGGC
Found at i:1744227 original size:48 final size:47
Alignment explanation
Indices: 1744145--1744403 Score: 263
Period size: 48 Copynumber: 5.4 Consensus size: 47
1744135 TCAGATAGAA
*
1744145 ATGAGAAA-AGTTTGA-TCAGGTCCTAATACCAATATAGTCAAATAAGGG
1 ATGA-AAAGAGTTTGACT-AGG-CCTAACACCAATATAGTCAAATAAGGG
* * *
1744193 ATGAAAAGAGTTTGACTAGGCTCTAACACTAATATAGTCAAACAAGAG
1 ATGAAAAGAGTTTGACTAGGC-CTAACACCAATATAGTCAAATAAGGG
* *
1744241 ATGAAAAGAGTTTGACCAGGCCCTAACACCAATACT-GTCAAATGAGGG
1 ATGAAAAGAGTTTGACTAGG-CCTAACACCAATA-TAGTCAAATAAGGG
* * * * *
1744289 ATCAAAAGAGTTTGACTAGGCGCTAACACCAATACAATCAAATGAGGA
1 ATGAAAAGAGTTTGACTAGGC-CTAACACCAATATAGTCAAATAAGGG
* * * * *
1744337 ATGAAAAGAGTTTGACCAGGACCTAACACCAATACAGTTAAACAAAGG
1 ATGAAAAGAGTTTGACTAGG-CCTAACACCAATATAGTCAAATAAGGG
* *
1744385 ATGAAAAAAGTTTAACTAG
1 ATGAAAAGAGTTTGACTAG
1744404 ATATAGTCAA
Statistics
Matches: 178, Mismatches: 25, Indels: 16
0.81 0.11 0.07
Matches are distributed among these distances:
47 5 0.03
48 169 0.95
49 4 0.02
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (47 bp):
ATGAAAAGAGTTTGACTAGGCCTAACACCAATATAGTCAAATAAGGG
Found at i:1744317 original size:96 final size:97
Alignment explanation
Indices: 1744144--1744403 Score: 305
Period size: 96 Copynumber: 2.7 Consensus size: 97
1744134 GTCAGATAGA
* * * *
1744144 AATGAGAAA-AGTTTGATCAGGTCCTAATACCAATA-TAGTCAAATAAGGGATGAAAAGAGTTTG
1 AATGA-AAAGAGTTTGACCAGGACCTAACACCAATACTAGTCAAATAAGGGATCAAAAGAGTTTG
* * * *
1744207 ACTAGGCTCTAACACTAATATAGTCAAACAA-G
65 ACTAGGCGCTAACACCAATACAATCAAACAAGG
* *
1744239 AGATGAAAAGAGTTTGACCAGGCCCTAACACCAATACT-GTCAAATGAGGGATCAAAAGAGTTTG
1 A-ATGAAAAGAGTTTGACCAGGACCTAACACCAATACTAGTCAAATAAGGGATCAAAAGAGTTTG
**
1744303 ACTAGGCGCTAACACCAATACAATCAAATGAGG
65 ACTAGGCGCTAACACCAATACAATCAAACAAGG
* * * * * *
1744336 AATGAAAAGAGTTTGACCAGGACCTAACACCAATAC-AGTTAAACAAAGGATGAAAAAAGTTTAA
1 AATGAAAAGAGTTTGACCAGGACCTAACACCAATACTAGTCAAATAAGGGATCAAAAGAGTTTGA
1744400 CTAG
66 CTAG
1744404 ATATAGTCAA
Statistics
Matches: 141, Mismatches: 19, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
95 4 0.03
96 134 0.95
97 3 0.02
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (97 bp):
AATGAAAAGAGTTTGACCAGGACCTAACACCAATACTAGTCAAATAAGGGATCAAAAGAGTTTGA
CTAGGCGCTAACACCAATACAATCAAACAAGG
Found at i:1744471 original size:84 final size:84
Alignment explanation
Indices: 1744326--1744481 Score: 224
Period size: 84 Copynumber: 1.9 Consensus size: 84
1744316 ACCAATACAA
* * *
1744326 TCAAATGAGGAATGAAAAGAGTTTGACCAGGACCTAACACCAATACAGTTAAACAAAGGATGAAA
1 TCAAACGAGGAATGAAAAAAGTTTGACCAGGACCTAACACCAATACAGTGAAACAAAGGATGAAA
1744391 AAAGTTTAACTAGATATAG
66 AAAGTTTAACTAGATATAG
* * * *
1744410 TCAAACGATGGAA-GAAAAAAGTTTGACTAGGCCCTAACACCAATACAGTGAAACGAGGGATGAA
1 TCAAACGA-GGAATGAAAAAAGTTTGACCAGGACCTAACACCAATACAGTGAAACAAAGGATGAA
*
1744474 AAGAGTTT
65 AAAAGTTT
1744482 GCTAGAAGTC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
84 59 0.94
85 4 0.06
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (84 bp):
TCAAACGAGGAATGAAAAAAGTTTGACCAGGACCTAACACCAATACAGTGAAACAAAGGATGAAA
AAAGTTTAACTAGATATAG
Found at i:1745115 original size:19 final size:21
Alignment explanation
Indices: 1745068--1745142 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
1745058 TGTTACAATT
*
1745068 TGTATCAATACAAATAGTAAA
1 TGTATCGATACAAATAGTAAA
* *
1745089 TATATCGATACAGA-AGT-AA
1 TGTATCGATACAAATAGTAAA
*
1745108 TGTATCGATAC--ATGGCTAAAA
1 TGTATCGATACAAATAG-T-AAA
1745129 TGTATCGATACAAA
1 TGTATCGATACAAA
1745143 ACCACCCTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
17 1 0.02
18 1 0.02
19 13 0.30
20 3 0.07
21 24 0.56
23 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (21 bp):
TGTATCGATACAAATAGTAAA
Found at i:1745487 original size:13 final size:13
Alignment explanation
Indices: 1745469--1745495 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1745459 ACATTATGCT
1745469 TTGTATCGATACA
1 TTGTATCGATACA
1745482 TTGTATCGATACA
1 TTGTATCGATACA
1745495 T
1 T
1745496 GTTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1745582 original size:13 final size:13
Alignment explanation
Indices: 1745564--1745588 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1745554 CATGGAACAT
1745564 TGTATCGATACAA
1 TGTATCGATACAA
1745577 TGTATCGATACA
1 TGTATCGATACA
1745589 TGATAAATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1745586 original size:33 final size:33
Alignment explanation
Indices: 1745544--1745608 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1745534 CTACCACTAT
*
1745544 TGTATCGATACATGGA-ACATTGTATCGATACAA
1 TGTATCGATACAT-GATAAATTGTATCGATACAA
1745577 TGTATCGATACATGATAAATTGTATCGATACA
1 TGTATCGATACATGATAAATTGTATCGATACA
1745609 TTGCTTCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATGATAAATTGTATCGATACAA
Found at i:1751882 original size:21 final size:22
Alignment explanation
Indices: 1751858--1751907 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1751848 ATCAAATCTT
* *
1751858 CTTCAAAGTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1751879 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1751901 --TCAAAAT
1 CTTCAAAAT
1751908 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.02, T:0.46
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:1752663 original size:15 final size:15
Alignment explanation
Indices: 1752643--1752672 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1752633 CATGGGTTAA
1752643 GACTTGATCCTTACT
1 GACTTGATCCTTACT
1752658 GACTTGATCCTTACT
1 GACTTGATCCTTACT
1752673 CCCTCCATTT
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:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (15 bp):
GACTTGATCCTTACT
Found at i:1753668 original size:20 final size:21
Alignment explanation
Indices: 1753626--1753678 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
1753616 TGAAAATAAA
*
1753626 TTTTTATCAAGGGGGAGAATTT
1 TTTTTATCAA-AGGGAGAATTT
*
1753648 TTTTTATCAAAGGGA-ATTTT
1 TTTTTATCAAAGGGAGAATTT
*
1753668 TTTTTAACAAA
1 TTTTTATCAAA
1753679 AGCCTTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 14 0.50
21 4 0.14
22 10 0.36
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (21 bp):
TTTTTATCAAAGGGAGAATTT
Found at i:1754189 original size:28 final size:28
Alignment explanation
Indices: 1754147--1754200 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1754137 AAAGTATCGA
*
1754147 TACATAGGTATTTGTATCGATACATTAT
1 TACATAGGTACTTGTATCGATACATTAT
1754175 TACATAGGTACTTGTATCGATACATT
1 TACATAGGTACTTGTATCGATACATT
1754201 GTGGTTGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (28 bp):
TACATAGGTACTTGTATCGATACATTAT
Found at i:1754366 original size:20 final size:20
Alignment explanation
Indices: 1754341--1754392 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1754331 ACCACTGTTC
* *
1754341 GTATCGATACATGGTACATT
1 GTATCGATACATGATAAATT
1754361 GTATCGATACATGATAAATT
1 GTATCGATACATGATAAATT
1754381 GTATCGATACAT
1 GTATCGATACAT
1754393 TGCTTCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (20 bp):
GTATCGATACATGATAAATT
Found at i:1759690 original size:13 final size:13
Alignment explanation
Indices: 1759672--1759697 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1759662 TACAGCAAGT
1759672 ATGTATCGATACA
1 ATGTATCGATACA
1759685 ATGTATCGATACA
1 ATGTATCGATACA
1759698 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1761939 original size:21 final size:21
Alignment explanation
Indices: 1761906--1761950 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
1761896 TTGCAAGTTG
*
1761906 AAATAAAGAAGTTGGCTAAAGA
1 AAATAAAGAAGTTAGCT-AAGA
*
1761928 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1761948 AAA
1 AAA
1761951 ATGAAAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 7 0.33
22 7 0.33
ACGTcount: A:0.56, C:0.04, G:0.20, T:0.20
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1763773 original size:15 final size:15
Alignment explanation
Indices: 1763753--1763783 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1763743 TAAAAATGTC
*
1763753 CAAAATGACGAAGCT
1 CAAAATGAAGAAGCT
1763768 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1763783 C
1 C
1763784 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1765880 original size:13 final size:13
Alignment explanation
Indices: 1765862--1765887 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1765852 ACATTTTTCT
1765862 TTGTATCGATACA
1 TTGTATCGATACA
1765875 TTGTATCGATACA
1 TTGTATCGATACA
1765888 GGGTGATTAT
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1768451 original size:13 final size:13
Alignment explanation
Indices: 1768433--1768458 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1768423 TACAGCAAGT
1768433 ATGTATCGATACA
1 ATGTATCGATACA
1768446 ATGTATCGATACA
1 ATGTATCGATACA
1768459 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Done.