Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, whole genome shotgun sequence
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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 19 of 121
Found at i:3417003 original size:264 final size:262
Alignment explanation
Indices: 3416463--3417460 Score: 1026
Period size: 264 Copynumber: 3.7 Consensus size: 262
3416453 TTATACTTCT
* * * * * * *
3416463 CCACCACCACCATCTCACCCGCACAAGCCACCCCCGTACTATTACAAGTCACCACCTCCACCATC
1 CCACCACCTCCAACTCACCCGTACAAGCCACCACCGTACTACTATAAATCACCACCTCCACCATC
*
3416528 ACCTACCTACGTATACAAATCACCACCACCTCCAACTCACCCATACAAGCCACCACCATACTACT
66 ACCAACCTACGTATACAAATCACCACCACCTCCAACTCACCC-TACAAGCCACCACCATACTACT
3416593 ACAAGTCACCACCCCCACCAGCTCCCACTTACATCTACAAATCACCTCCACCTCCAACTCATCAA
130 ACAAGTCACCACCCCCACCAGCTCCCACTTACATCTACAAATCACCTCCACCTCCAACTCATC-A
* * **
3416658 CCGTACAAGCCACCACCATACTACTACAAGTCACCACCCCCACCAGCTCCCACTTACATCTACAA
194 CCGTACAAGCCACCACCATACTACTACAAGTCACCACCCCCACCACCTCCAAAATACATCTACAA
3416723 ATCA
259 ATCA
* * *
3416727 CCTCCACCTCCAACTCAACCGTACAAGCCACCACCGTACTACTATAATTCACCACCTCCACCATC
1 CCACCACCTCCAACTCACCCGTACAAGCCACCACCGTACTACTATAAATCACCACCTCCACCATC
* *
3416792 ACCAACCTACGTATACAAATCACCACCACCTCCAACTCACCCTTATAAGCCACCACCGTACTACT
66 ACCAACCTACGTATACAAATCACCACCACCTCCAACTCACCC-TACAAGCCACCACCATACTACT
3416857 ACAAGTCACCACCCCCACCAGCTCCCACTTACATCTACAAATCACCTCCACCTCCAACTCA-C-C
130 ACAAGTCACCACCCCCACCAGCTCCCACTTACATCTACAAATCACCTCCACCTCCAACTCATCAC
* * * *
3416920 CTTATAAGCCACCACCGTACTACTACAAGTCACCACCCCCACCTCCTCCAAAATAC-TACTACAA
195 CGTACAAGCCACCACCATACTACTACAAGTCACCACCCCCACCACCTCCAAAATACAT-CTACAA
*
3416984 GTCCCCA
259 AT---CA
* * * * *
3416991 CCACCCCCTCCAACTCTCCCTTACAAGCCACCACCGTACTACTATAAATCACCACCCCCACCAAC
1 CCACCACCTCCAACTCACCCGTACAAGCCACCACCGTACTACTATAAATCACCACCTCCACCATC
* * * ** ** *
3417056 TCCCACTTACGCCTACAAATCACCACCACCTCCGGCTCATCCCTACAAGCCACCACCATACTATT
66 ACCAACCTACGTATACAAATCACCACCACCTCCAACTCA-CCCTACAAGCCACCACCATACTACT
* * * * * * *
3417121 ATAAGTCACCACCTCCACCATCACCTACTTACATTTACAAGTCACCTCCACCTCC-AC-CAT-AC
130 ACAAGTCACCACCCCCACCAGCTCCCACTTACATCTACAAATCACCTCCACCTCCAACTCATCAC
** * ** ** * * * * *
3417183 TATTATAAATCACCACCCCCACCACCTCCAAAATACTACTACAAGTCCCCACCTCCTCCAAAATA
195 -CGTACAAGCCACCA-CCATACTA-CTAC-AAGT-C-AC--C-A-CCCCCACCACCTCCAAAATA
*
3417248 C-TACTACAAGTCCCCA
250 CAT-CTACAAAT---CA
* * * * *
3417264 CCACCCCCTCCAACTCTCCCTTACAAGCCACCACCGTACTACTATAAATCACCACCCCCACCACC
1 CCACCACCTCCAACTCACCCGTACAAGCCACCACCGTACTACTATAAATCACCACCTCCACCATC
* ** * * * *
3417329 TCCAAAATAC-TACTACAAGTCCCCACCACCTCCTCCAACTCTCCCTTACAAGCCACCACCGTAC
66 ACCAACCTACGTA-TACAAAT---CACCACCACCTCCAACTCACCC-TACAAGCCACCACCATAC
* * * ** *
3417393 TACTATAAATCACCACCCCCACCAACTCCCACTTACGCCTACAAATCACCACCACCTCC-AC-CA
126 TACTACAAGTCACCACCCCCACCAGCTCCCACTTACATCTACAAATCACCTCCACCTCCAACTCA
3417456 TCACC
191 TCACC
3417461 TACTTACATT
Statistics
Matches: 631, Mismatches: 80, Indels: 34
0.85 0.11 0.05
Matches are distributed among these distances:
260 1 0.00
261 56 0.09
262 2 0.00
263 4 0.01
264 347 0.55
265 8 0.01
266 3 0.00
267 3 0.00
268 1 0.00
269 2 0.00
271 1 0.00
272 1 0.00
273 112 0.18
275 3 0.00
276 85 0.13
277 2 0.00
ACGTcount: A:0.31, C:0.47, G:0.04, T:0.18
Consensus pattern (262 bp):
CCACCACCTCCAACTCACCCGTACAAGCCACCACCGTACTACTATAAATCACCACCTCCACCATC
ACCAACCTACGTATACAAATCACCACCACCTCCAACTCACCCTACAAGCCACCACCATACTACTA
CAAGTCACCACCCCCACCAGCTCCCACTTACATCTACAAATCACCTCCACCTCCAACTCATCACC
GTACAAGCCACCACCATACTACTACAAGTCACCACCCCCACCACCTCCAAAATACATCTACAAAT
CA
Found at i:3417226 original size:66 final size:66
Alignment explanation
Indices: 3417156--3417361 Score: 179
Period size: 66 Copynumber: 3.3 Consensus size: 66
3417146 TACTTACATT
* * *
3417156 TACAAGTCACCTCCACCTCCACCATACTATTATAAATCACCACCCCCACCACCTCCAAAATACTA
1 TACAAGTCCCCACCACCTCCACCATACTACTATAAATCACCACCCCCACCACCTCCAAAATACTA
3417221 C
66 C
* ** * * * * *
3417222 TACAAGTCCCCACCTCCTCCAAAATACTACTACAAGT--CC-CCACCACCCCCTCC-AACT-CTC
1 TACAAGTCCCCACCACCTCCACCATACTACTATAAATCACCACCCCCACCACCTCCAAAATACT-
*
3417282 CC
65 AC
*
3417284 TTACAAG------CCA---CCACCGTACTACTATAAATCACCACCCCCACCACCTCCAAAATACT
1 -TACAAGTCCCCACCACCTCCACCATACTACTATAAATCACCACCCCCACCACCTCCAAAATACT
3417340 AC
65 AC
3417342 TACAAGTCCCCACCACCTCC
1 TACAAGTCCCCACCACCTCC
3417362 TCCAACTCTC
Statistics
Matches: 102, Mismatches: 22, Indels: 32
0.65 0.14 0.21
Matches are distributed among these distances:
54 14 0.14
56 2 0.02
57 20 0.20
58 4 0.04
59 2 0.02
61 2 0.02
62 4 0.04
63 21 0.21
64 2 0.02
66 31 0.30
ACGTcount: A:0.32, C:0.47, G:0.03, T:0.18
Consensus pattern (66 bp):
TACAAGTCCCCACCACCTCCACCATACTACTATAAATCACCACCCCCACCACCTCCAAAATACTA
C
Found at i:3417235 original size:36 final size:35
Alignment explanation
Indices: 3417168--3417261 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 35
3417158 CAAGTCACCT
** * * *
3417168 CCACCTCCACCATACTATTATAAATCACCACCCCCA
1 CCACCTCCAAAATACTACTACAAGTC-CCACCCCCA
3417204 CCACCTCCAAAATACTACTACAAGT-----CCCCA
1 CCACCTCCAAAATACTACTACAAGTCCCACCCCCA
*
3417234 CCTCCTCCAAAATACTACTACAAGTCCC
1 CCACCTCCAAAATACTACTACAAGTCCC
3417262 CACCACCCCC
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
30 29 0.59
36 20 0.41
ACGTcount: A:0.34, C:0.45, G:0.02, T:0.19
Consensus pattern (35 bp):
CCACCTCCAAAATACTACTACAAGTCCCACCCCCA
Found at i:3417276 original size:33 final size:30
Alignment explanation
Indices: 3417199--3417268 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
3417189 AAATCACCAC
3417199 CCCCACCACCTCCAAAATACTACTACAAGT
1 CCCCACCACCTCCAAAATACTACTACAAGT
*
3417229 CCCCACCTCCTCCAAAATACTACTACAAGT
1 CCCCACCACCTCCAAAATACTACTACAAGT
3417259 CCCCACCACC
1 CCCCACCACC
3417269 CCCTCCAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.33, C:0.49, G:0.03, T:0.16
Consensus pattern (30 bp):
CCCCACCACCTCCAAAATACTACTACAAGT
Found at i:3417323 original size:90 final size:86
Alignment explanation
Indices: 3417262--3417452 Score: 247
Period size: 90 Copynumber: 2.2 Consensus size: 86
3417252 TACAAGTCCC
* *
3417262 CACCACCCCCTCCAACTCTCCCTTACAAGCCACCACCGTACTACTATAAATCACCACCCCCACCA
1 CACCACCACCTCCAACTCTCCCTTACAAGCCACCACCGTACTACTATAAGTCACCACCCCCACCA
** *
3417327 CCTCCAAAATACTACTACAAGT
66 CCTCCAACTTAC-ACTACAAAT
* *
3417349 CCCCACCACCTCCTCCAACTCTCCCTTACAAGCCACCACCGTACTACTATAAATCACCACCCCCA
1 ---CACCACCACCTCCAACTCTCCCTTACAAGCCACCACCGTACTACTATAAGTCACCACCCCCA
* * *
3417414 CCAACTCCCACTTACGCCTACAAAT
63 CCACCTCCAACTTAC-ACTACAAAT
3417439 CACCACCACCTCCA
1 CACCACCACCTCCA
3417453 CCATCACCTA
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
87 13 0.14
90 79 0.86
ACGTcount: A:0.30, C:0.50, G:0.03, T:0.17
Consensus pattern (86 bp):
CACCACCACCTCCAACTCTCCCTTACAAGCCACCACCGTACTACTATAAGTCACCACCCCCACCA
CCTCCAACTTACACTACAAAT
Found at i:3417454 original size:39 final size:39
Alignment explanation
Indices: 3417403--3417494 Score: 103
Period size: 39 Copynumber: 2.4 Consensus size: 39
3417393 TACTATAAAT
* * *
3417403 CACCACCCCCACCAACTCCCACTTACGCCTACAAATCAC
1 CACCACCTCCACCAACACCCACTTACACCTACAAATCAC
* * ** *
3417442 CACCACCTCCACCATCACCTACTTACATTTACAAGTCAC
1 CACCACCTCCACCAACACCCACTTACACCTACAAATCAC
*
3417481 CTCCACCTCCACCA
1 CACCACCTCCACCA
3417495 TACTATTATA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.29, C:0.51, G:0.02, T:0.17
Consensus pattern (39 bp):
CACCACCTCCACCAACACCCACTTACACCTACAAATCAC
Found at i:3417544 original size:66 final size:66
Alignment explanation
Indices: 3417431--3417655 Score: 263
Period size: 66 Copynumber: 3.4 Consensus size: 66
3417421 CCACTTACGC
* *
3417431 CTACAAATCACCACCACCTCCACCATCACCTACTTACATTTACAAGTCACCTCCACCTCCACCAT
1 CTACAAATCACCACCACCACCACC-TC-CC-ACTTACATTTACAAGTCACCACCACCTCCACCAT
3417496 ACTA
63 ACTA
* * * * * **
3417500 TTATAAATCACCACCCCCACCACCTCCCACTTACATCTACAAGTCACCACCTCCTCCAAAATACT
1 CTACAAATCACCACCACCACCACCTCCCACTTACATTTACAAGTCACCACCACCTCCACCATACT
3417565 A
66 A
* * ** * *
3417566 CTACAAGTCCCCACCACCACCAACC-CCCACTTATGTTTACAAGTCTCCACCGCCTCCACCATAC
1 CTACAAATCACCACCACCACC-ACCTCCCACTTACATTTACAAGTCACCACCACCTCCACCATAC
3417630 TA
65 TA
*
3417632 CTACAAATCTCCACCACCACCACC
1 CTACAAATCACCACCACCACCACC
3417656 GGTCCATTCT
Statistics
Matches: 132, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
65 3 0.02
66 102 0.77
67 5 0.04
68 2 0.02
69 20 0.15
ACGTcount: A:0.31, C:0.46, G:0.03, T:0.20
Consensus pattern (66 bp):
CTACAAATCACCACCACCACCACCTCCCACTTACATTTACAAGTCACCACCACCTCCACCATACT
A
Found at i:3417867 original size:96 final size:96
Alignment explanation
Indices: 3417767--3418088 Score: 303
Period size: 96 Copynumber: 3.4 Consensus size: 96
3417757 ACGAAGAGAA
*
3417767 ACCCCCATACTACTACAAATCTCCACCACCACCATCGCCATCTCCTCCTCCACCCTATTACTACA
1 ACCCCCATACTACTACAAATCTCCACCACCACCATCGCCATCTCCTCCTCCACCCTACTACTACA
* * *
3417832 AATCACCTCCACCTCCTTCTCCCTCTCCTCC
66 AATCACCACCACCTCCATCTCCCTCTCCACC
* * * * * * *
3417863 ACCCCCATATTATTACAAGTCTCCTCCACCACCA--GTCCATTCCCCTCCACCACCATACTACTA
1 ACCCCCATACTACTACAAATCTCCACCACCACCATCG-CCA-TCTCCTCCTCCACCCTACTACTA
* ***** *
3417926 CAATTCACCACCACCTCCAGT-AAAAGCTCCAGC
64 CAAATCACCACCACCTCCA-TCTCCCTCTCCACC
* * * * * * * * *
3417959 ACCAACC-TACCACTACAACTCCCCTCCTCCACCATCACCATCTCCTCCTCCTCCCTACTATTAC
1 ACC-CCCATACTACTACAAATCTCCACCACCACCATCGCCATCTCCTCCTCCACCCTACTACTAC
3418023 AAATTC-CCACCACCTCCATCTCCCTCTCCACC
65 AAA-TCACCACCACCTCCATCTCCCTCTCCACC
* *
3418055 TCCGCCATACTACTACAAATCTCCACCACCACCA
1 ACCCCCATACTACTACAAATCTCCACCACCACCA
3418089 AAACACGAAG
Statistics
Matches: 172, Mismatches: 45, Indels: 18
0.73 0.19 0.08
Matches are distributed among these distances:
94 1 0.01
95 6 0.03
96 157 0.91
97 8 0.05
ACGTcount: A:0.26, C:0.50, G:0.02, T:0.22
Consensus pattern (96 bp):
ACCCCCATACTACTACAAATCTCCACCACCACCATCGCCATCTCCTCCTCCACCCTACTACTACA
AATCACCACCACCTCCATCTCCCTCTCCACC
Found at i:3418159 original size:48 final size:45
Alignment explanation
Indices: 3418104--3418225 Score: 138
Period size: 45 Copynumber: 2.6 Consensus size: 45
3418094 CGAAGAGAAG
* * * *
3418104 CCCCCATACTATTACAAGTCCCCTCCTCCCCCA-TCGCCATCTCCTCCT
1 CCCCCATACTATTACAAGTCCCCGCCACCACCAGT--CCA-CT-CTCCA
*
3418152 CCGCCATACTATTACAAGTCCCCGCCACCACCAGTCCACTCTCCA
1 CCCCCATACTATTACAAGTCCCCGCCACCACCAGTCCACTCTCCA
* *
3418197 CCCCCATACTATTACAAGTCTCCACCACC
1 CCCCCATACTATTACAAGTCCCCGCCACC
3418226 GCCATACTAC
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
45 30 0.46
46 2 0.03
47 3 0.05
48 29 0.45
49 1 0.02
ACGTcount: A:0.22, C:0.51, G:0.06, T:0.21
Consensus pattern (45 bp):
CCCCCATACTATTACAAGTCCCCGCCACCACCAGTCCACTCTCCA
Found at i:3418225 original size:45 final size:47
Alignment explanation
Indices: 3417624--3418230 Score: 201
Period size: 48 Copynumber: 12.7 Consensus size: 47
3417614 ACCGCCTCCA
* * * * *
3417624 CCATACTACTACAAATCTCCACCACCACCACCGGTCCATTCTCCACC-CCC
1 CCATACTATTACAAGTCCCCACCACCACCATC---CCA-TCTCCTCCACCC
* * * * *
3417674 ACCATACTATTACAAGTCACCACCACCACCTTCTCCTTCACCACC-CCC
1 -CCATACTATTACAAGTCCCCACCACCACCATC-CCATCTCCTCCACCC
* *** ******
3417722 ACCATACTACTACAAGTCCCCACCACCACCAGAACA-CGAAGAGAAACCC
1 -CCATACTATTACAAGTCCCCACCACCACCATCCCATC--TCCTCCACCC
* * * *
3417771 CCATACTACTACAAATCTCCACCACCACCATCGCCATCTCCTCCTCCAC
1 CCATACTATTACAAGTCCCCACCACCACCATC-CCATCTCCTCCACC-C
* * * * * * * *
3417820 CC-TATTACTACAAATCACCTCCACCTCCTTCTCCCTCTCCTCCACCC
1 CCATACTATTACAAGTCCCCACCACCACCATC-CCATCTCCTCCACCC
* * * * *
3417867 CCATATTATTACAAGTCTCCTCCACCACCAGT-CCATTCCCCTCCACCA
1 CCATACTATTACAAGTCCCCACCACCACCA-TCCCA-TCTCCTCCACCC
* * * * *** * ** *
3417915 CCATACTACTACAATTCACCACCACCTCCAGTAAAAGCTCCAGCACCAA
1 CCATACTATTACAAGTCCCCACCACCACCA-TCCCATCTCCTCCACC-C
* * * * * *
3417964 CC-TACCACTACAACTCCCCTCCTCCACCATCACCATCTCCTCCTCCTC
1 CCATACTATTACAAGTCCCCACCACCACCATC-CCATCTCCTCCACC-C
* * * * * * *
3418012 CC-TACTATTACAAATTCCCACCACCTCCATCTCCCTCTCCACCTCCG
1 CCATACTATTACAAGTCCCCACCACCACCATC-CCATCTCCTCCACCC
* * * *** ******
3418059 CCATACTACTACAAATCTCCACCACCACCAAAACA-CGAAGAGAAGCCC
1 CCATACTATTACAAGTCCCCACCACCACCATCCCATC-TCCTCCA-CCC
* * * * *
3418107 CCATACTATTACAAGTCCCCTCCTCCCCCATCGCCATCTCCTCCTCCG
1 CCATACTATTACAAGTCCCCACCACCACCATC-CCATCTCCTCCACCC
*
3418155 CCATACTATTACAAGTCCCCGCCACCACCAGT-CCA-CT-CTCCACCC
1 CCATACTATTACAAGTCCCCACCACCACCA-TCCCATCTCCTCCACCC
* *
3418200 CCATACTATTACAAGTCTCCACCACCGCCAT
1 CCATACTATTACAAGTCCCCACCACCACCAT
3418231 ACTACTACAA
Statistics
Matches: 413, Mismatches: 125, Indels: 43
0.71 0.22 0.07
Matches are distributed among these distances:
44 1 0.00
45 33 0.08
46 4 0.01
47 14 0.03
48 313 0.76
49 19 0.05
50 2 0.00
51 27 0.07
ACGTcount: A:0.27, C:0.48, G:0.04, T:0.20
Consensus pattern (47 bp):
CCATACTATTACAAGTCCCCACCACCACCATCCCATCTCCTCCACCC
Found at i:3418252 original size:72 final size:73
Alignment explanation
Indices: 3418142--3418300 Score: 185
Period size: 72 Copynumber: 2.2 Consensus size: 73
3418132 CCCCATCGCC
* * * * * *
3418142 ATCTCCTCCTCCGCCATACTATTACAAGTCCCCGCCACCACCAGTCCA-CTCTCCACCCCCATAC
1 ATCTCCACCACCGCCATACTACTACAACTCCCCACCACCACCAGTCCATCCCTCCACCCCCATAC
*
3418206 TATTACAA
66 TACTACAA
* * * *
3418214 GTCTCCACCACCGCCATACTACTACAACTCTCCACCACCACCTGTCCATTCCCCTCCACCTCCAT
1 ATCTCCACCACCGCCATACTACTACAACTCCCCACCACCACCAGTCCA-T-CCCTCCACCCCCAT
3418279 ACTACTACAA
64 ACTACTACAA
*
3418289 ATCACCACCACC
1 ATCTCCACCACC
3418301 TCCTTCACCA
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
72 40 0.56
75 31 0.44
ACGTcount: A:0.26, C:0.49, G:0.04, T:0.21
Consensus pattern (73 bp):
ATCTCCACCACCGCCATACTACTACAACTCCCCACCACCACCAGTCCATCCCTCCACCCCCATAC
TACTACAA
Found at i:3418255 original size:30 final size:27
Alignment explanation
Indices: 3418194--3418252 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
3418184 AGTCCACTCT
* *
3418194 CCACCCCCATACTATTACAAGTCTCCA
1 CCACCCCCATACTACTACAACTCTCCA
*
3418221 CCACCGCCATACTACTACAACTCTCCA
1 CCACCCCCATACTACTACAACTCTCCA
3418248 CCACC
1 CCACC
3418253 ACCTGTCCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.49, G:0.03, T:0.19
Consensus pattern (27 bp):
CCACCCCCATACTACTACAACTCTCCA
Found at i:3418297 original size:48 final size:47
Alignment explanation
Indices: 3418215--3418348 Score: 146
Period size: 48 Copynumber: 2.8 Consensus size: 47
3418205 CTATTACAAG
* * * *
3418215 TCTCCACCACCGCCATACTACTACAACTCTCCACCACCACCTGT-CCA
1 TCTCCCCCACCACCATACTACTACAAATCACCACCACCACCT-TACCA
* *
3418262 T-TCCCCTCCACCTCCATACTACTACAAATCACCACCACCTCCTTCACCA
1 TCT-CCC-CCACCACCATACTACTACAAATCACCACCACCACCTT-ACCA
* *
3418311 TCTCCCCCACCACCATACTATTACGAATCACCACCACC
1 TCTCCCCCACCACCATACTACTACAAATCACCACCACC
3418349 TCCAGTAAAG
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
46 1 0.01
47 4 0.05
48 61 0.82
49 7 0.09
50 1 0.01
ACGTcount: A:0.27, C:0.51, G:0.02, T:0.20
Consensus pattern (47 bp):
TCTCCCCCACCACCATACTACTACAAATCACCACCACCACCTTACCA
Found at i:3418300 original size:27 final size:27
Alignment explanation
Indices: 3418194--3418352 Score: 81
Period size: 27 Copynumber: 6.3 Consensus size: 27
3418184 AGTCCACTCT
* * *
3418194 CCACCCCCATACTATTACAAGTCTCCA
1 CCACCTCCATACTACTACAAATCTCCA
* *
3418221 CCACCGCCATACTACTACAACTCTCCA
1 CCACCTCCATACTACTACAAATCTCCA
* * * * *
3418248 CCACCACC-T-GT-C--C-ATTCCCCT
1 CCACCTCCATACTACTACAAATCTCCA
*
3418269 CCACCTCCATACTACTACAAATCACCA
1 CCACCTCCATACTACTACAAATCTCCA
* *
3418296 CCACCTCC-T--T-C-AC-CATCTCCC
1 CCACCTCCATACTACTACAAATCTCCA
* * * *
3418317 CCACCACCATACTATTACGAATCACCA
1 CCACCTCCATACTACTACAAATCTCCA
3418344 CCACCTCCA
1 CCACCTCCA
3418353 GTAAAGGCTC
Statistics
Matches: 98, Mismatches: 22, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
21 24 0.24
22 5 0.05
23 2 0.02
24 4 0.04
25 1 0.01
26 5 0.05
27 57 0.58
ACGTcount: A:0.28, C:0.50, G:0.03, T:0.20
Consensus pattern (27 bp):
CCACCTCCATACTACTACAAATCTCCA
Found at i:3418570 original size:48 final size:48
Alignment explanation
Indices: 3418461--3418571 Score: 114
Period size: 48 Copynumber: 2.3 Consensus size: 48
3418451 CGAAGAGAAG
* * * *
3418461 CCCCCGTACTATTACAAGTCCCCACCCCCACCTTCCCCATCACCACCA
1 CCCCCATACTACTACAAATCCCCACCCCCACCATCCCCATCACCACCA
* * * * * * *
3418509 CCTCCTTACTACTACAAATCCCCACCTCCTCCATCCCCCTCACCCCCT
1 CCCCCATACTACTACAAATCCCCACCCCCACCATCCCCATCACCACCA
*
3418557 CCCCCATATTACTAC
1 CCCCCATACTACTAC
3418572 TACTCACCTC
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.22, C:0.56, G:0.02, T:0.21
Consensus pattern (48 bp):
CCCCCATACTACTACAAATCCCCACCCCCACCATCCCCATCACCACCA
Found at i:3422000 original size:11 final size:12
Alignment explanation
Indices: 3421976--3422006 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
3421966 TCATTATCAT
3421976 CATCACCGTCAC
1 CATCACCGTCAC
3421988 CATCACC-TCAC
1 CATCACCGTCAC
3421999 CATCACCG
1 CATCACCG
3422007 ACAAGTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.26, C:0.52, G:0.06, T:0.16
Consensus pattern (12 bp):
CATCACCGTCAC
Found at i:3422577 original size:29 final size:29
Alignment explanation
Indices: 3422545--3422600 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
3422535 TATAGTAAAT
* *
3422545 TATTTAATATAATGTTTAAATTTTAAAAA
1 TATTTAATATAATATTTAAATTATAAAAA
*
3422574 TATTTAATATATTATTTAAATTATAAA
1 TATTTAATATAATATTTAAATTATAAA
3422601 TTTATTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
TATTTAATATAATATTTAAATTATAAAAA
Found at i:3422606 original size:29 final size:28
Alignment explanation
Indices: 3422540--3422602 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
3422530 CAAACTATAG
* *
3422540 TAAATTATTTAATATAATGTTTAAATTT
1 TAAATTATTTAATATAATATTTAAATTA
* *
3422568 TAAAAATATTTAATATATTATTTAAATTA
1 T-AAATTATTTAATATAATATTTAAATTA
3422597 TAAATT
1 TAAATT
3422603 TATTAATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
TAAATTATTTAATATAATATTTAAATTA
Found at i:3423078 original size:27 final size:27
Alignment explanation
Indices: 3423043--3423117 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 27
3423033 TTATACATCA
3423043 AATATAATTTTTAAATATTATATTA-ATT
1 AATA-AATTTTTAAAT-TTATATTATATT
*
3423071 AATAAATTTAT-AATTTAAATATTATATT
1 AATAAATTTTTAAATTT--ATATTATATT
3423099 -A-AAATTTTTAAATTTATAT
1 AATAAATTTTTAAATTTATAT
3423118 AATGAATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
25 6 0.15
26 10 0.24
27 18 0.44
28 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
AATAAATTTTTAAATTTATATTATATT
Found at i:3423126 original size:27 final size:27
Alignment explanation
Indices: 3423048--3423126 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
3423038 CATCAAATAT
3423048 AATTTTTAAATATTATATTAATTAA-T-A
1 AATTTTTAAAT-TTATA-TAATTAATTAA
* *
3423075 AATTTAT-AATTTAAAT-ATTATATTAA
1 AATTTTTAAATTTATATAATTA-ATTAA
*
3423101 AATTTTTAAATTTATATAATGAATTA
1 AATTTTTAAATTTATATAATTAATTA
3423127 TTCGTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
23 4 0.10
24 2 0.05
25 5 0.12
26 10 0.24
27 18 0.43
28 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
AATTTTTAAATTTATATAATTAATTAA
Found at i:3431133 original size:2 final size:2
Alignment explanation
Indices: 3431120--3431169 Score: 68
Period size: 2 Copynumber: 25.0 Consensus size: 2
3431110 GAAATCAAAT
3431120 TA TA TA TCA TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA T-A TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3431163 TA -A TA TA
1 TA TA TA TA
3431170 CATAATTATC
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.05
2 38 0.86
3 4 0.09
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3431143 original size:18 final size:18
Alignment explanation
Indices: 3431120--3431184 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
3431110 GAAATCAAAT
3431120 TATATATCATATATCATA
1 TATATATCATATATCATA
3431138 TATATAT-ATATAT-ATA
1 TATATATCATATATCATA
*
3431154 TATATATTATAATATACATA
1 TATATATCAT-ATAT-CATA
3431174 -AT-TATCATATA
1 TATATATCATATA
3431185 GCATTTGTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
16 10 0.24
17 11 0.26
18 16 0.38
19 2 0.05
20 3 0.07
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
TATATATCATATATCATA
Found at i:3433212 original size:26 final size:26
Alignment explanation
Indices: 3433183--3433275 Score: 91
Period size: 26 Copynumber: 3.5 Consensus size: 26
3433173 TACACGCGAA
3433183 TAAATAAATAAAATCATTATTTCTCT
1 TAAATAAATAAAATCATTATTTCTCT
* * *
3433209 TAAATGAATAATATCGTATCTA-TTAT-T
1 TAAATAAATAAAATC--AT-TATTTCTCT
** *
3433236 TAAATATTTAAAATAATTATTTCTCT
1 TAAATAAATAAAATCATTATTTCTCT
3433262 TAAATAAATAAAAT
1 TAAATAAATAAAAT
3433276 TAATCTTAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
24 2 0.04
25 5 0.10
26 26 0.51
27 11 0.22
28 5 0.10
29 2 0.04
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (26 bp):
TAAATAAATAAAATCATTATTTCTCT
Found at i:3435457 original size:11 final size:11
Alignment explanation
Indices: 3435441--3435484 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
3435431 AAATTTTAAA
3435441 TTATATTATTT
1 TTATATTATTT
*
3435452 TTATATTTTTTAT
1 TTATA-TTATT-T
3435465 TTATATTATTT
1 TTATATTATTT
3435476 TTATATTAT
1 TTATATTAT
3435485 GTCACTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 15 0.52
12 8 0.28
13 6 0.21
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATATTATTT
Found at i:3435461 original size:24 final size:24
Alignment explanation
Indices: 3435424--3435482 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
3435414 TTATTTATGG
* *
3435424 ATTTTTAAAATTTTAAATTATATT
1 ATTTTTATATTTTTAAATTATATT
* *
3435448 ATTTTTATATTTTTTATTTATATT
1 ATTTTTATATTTTTAAATTATATT
3435472 ATTTTTATATT
1 ATTTTTATATT
3435483 ATGTCACTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
ATTTTTATATTTTTAAATTATATT
Found at i:3444130 original size:33 final size:33
Alignment explanation
Indices: 3444093--3444322 Score: 147
Period size: 33 Copynumber: 7.2 Consensus size: 33
3444083 AATATGTACA
*
3444093 GCCAACCCACACAGCCAAGTGCTAATCCATATG
1 GCCAACCCGCACAGCCAAGTGCTAATCCATATG
* * * *
3444126 GCCAACCTGCACGGCCAAGTGCTAACCCGTATG
1 GCCAACCCGCACAGCCAAGTGCTAATCCATATG
* * * * *
3444159 GCCAGCCTGGACAGCCAACTGCTAACCCATATG
1 GCCAACCCGCACAGCCAAGTGCTAATCCATATG
* * * * *
3444192 GCCAACCTGGACAGCCGAGTGTTAATCCTTAT-
1 GCCAACCCGCACAGCCAAGTGCTAATCCATATG
*
3444224 ----A---GC-CAACCAAGTGCTAATTCC-TATG
1 GCCAACCCGCACAGCCAAGTGCTAA-TCCATATG
* * * * *
3444249 ACCAATCCACACAGCCAAATGCCAATCCATATG
1 GCCAACCCGCACAGCCAAGTGCTAATCCATATG
* * * *
3444282 GCCAAACTGCACAGCTAAATGCTAATCCATATG
1 GCCAACCCGCACAGCCAAGTGCTAATCCATATG
*
3444315 CCCAACCC
1 GCCAACCC
3444323 ACTCAACCAA
Statistics
Matches: 153, Mismatches: 33, Indels: 22
0.74 0.16 0.11
Matches are distributed among these distances:
24 14 0.09
25 4 0.03
28 1 0.01
29 1 0.01
32 4 0.03
33 129 0.84
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.18
Consensus pattern (33 bp):
GCCAACCCGCACAGCCAAGTGCTAATCCATATG
Found at i:3445079 original size:6 final size:6
Alignment explanation
Indices: 3445068--3445119 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
3445058 AATCCTATGG
* * * * *
3445068 TGGGTA TGGGTA TGGGTA TGGGAA TGGGCA TGGGGA TGGGGA TGGGAA
1 TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA
3445116 TGGG
1 TGGG
3445120 AATAGGTGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.19, C:0.02, G:0.56, T:0.23
Consensus pattern (6 bp):
TGGGTA
Found at i:3445085 original size:12 final size:12
Alignment explanation
Indices: 3445068--3445119 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
3445058 AATCCTATGG
*
3445068 TGGGTATGGGTA
1 TGGGTATGGGAA
3445080 TGGGTATGGGAA
1 TGGGTATGGGAA
* *
3445092 TGGGCATGGGGA
1 TGGGTATGGGAA
*
3445104 TGGGGATGGGAA
1 TGGGTATGGGAA
3445116 TGGG
1 TGGG
3445120 AATAGGTGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.19, C:0.02, G:0.56, T:0.23
Consensus pattern (12 bp):
TGGGTATGGGAA
Found at i:3445252 original size:18 final size:18
Alignment explanation
Indices: 3445211--3445252 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3445201 GATGAACAAC
* *
3445211 ATGGGCATGAATGCGGGC
1 ATGGGGATGAATGCGGGA
*
3445229 ATGGGGATGAATGTGGGA
1 ATGGGGATGAATGCGGGA
3445247 ATGGGG
1 ATGGGG
3445253 CAAAGACCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.07, G:0.50, T:0.19
Consensus pattern (18 bp):
ATGGGGATGAATGCGGGA
Found at i:3448076 original size:18 final size:18
Alignment explanation
Indices: 3448053--3448087 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3448043 ACTTACCTGT
*
3448053 ATGCAAACATATTGGCAA
1 ATGCAAACAAATTGGCAA
*
3448071 ATGCAAATAAATTGGCA
1 ATGCAAACAAATTGGCA
3448088 TCAAACAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (18 bp):
ATGCAAACAAATTGGCAA
Found at i:3457045 original size:24 final size:25
Alignment explanation
Indices: 3457018--3457064 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
3457008 TAAATATTTC
3457018 TCTTATATT-A-TTAAAAACAATACG
1 TCTTATATTAATTTAAAAA-AATACG
*
3457042 TCTTATTTTAATTTAAAAAAATA
1 TCTTATATTAATTTAAAAAAATA
3457065 AATAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 5 0.25
26 7 0.35
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (25 bp):
TCTTATATTAATTTAAAAAAATACG
Found at i:3463808 original size:17 final size:17
Alignment explanation
Indices: 3463786--3463820 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3463776 AATTCTCTTT
*
3463786 AAAAAATTAAAAAATTA
1 AAAAAAATAAAAAATTA
*
3463803 AAAAAAATAAAATATTA
1 AAAAAAATAAAAAATTA
3463820 A
1 A
3463821 TATTTTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAAAATAAAAAATTA
Found at i:3464616 original size:30 final size:30
Alignment explanation
Indices: 3464582--3464639 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
3464572 GTCTAGTCTA
*
3464582 AACCTAATCCATTAACAAATAAATCTTTAC
1 AACCTAATCCACTAACAAATAAATCTTTAC
3464612 AACCTAATCCACTAACAAATAAATCTTT
1 AACCTAATCCACTAACAAATAAATCTTT
3464640 GTAACTGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (30 bp):
AACCTAATCCACTAACAAATAAATCTTTAC
Found at i:3466439 original size:20 final size:20
Alignment explanation
Indices: 3466401--3466440 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3466391 GCATTCACAC
*
3466401 AAAAATAAGAAGCTCAAATA
1 AAAAATAAGAAGCTAAAATA
3466421 AAAAATAAGAA-CGTAAAATA
1 AAAAATAAGAAGC-TAAAATA
3466441 TATTTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.68, C:0.07, G:0.10, T:0.15
Consensus pattern (20 bp):
AAAAATAAGAAGCTAAAATA
Found at i:3467650 original size:20 final size:20
Alignment explanation
Indices: 3467625--3467705 Score: 108
Period size: 20 Copynumber: 4.0 Consensus size: 20
3467615 TGAAAATTCA
*
3467625 TAACTTACCAAAAATAAATT
1 TAACTTACCAAAAATGAATT
*
3467645 TAACTTACCAAAAATGGATT
1 TAACTTACCAAAAATGAATT
* *
3467665 TAACTTTCCAAAAATGAGTT
1 TAACTTACCAAAAATGAATT
**
3467685 TAACTTTTCAAAAATGAATT
1 TAACTTACCAAAAATGAATT
3467705 T
1 T
3467706 TCAAAGAGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.35
Consensus pattern (20 bp):
TAACTTACCAAAAATGAATT
Found at i:3476872 original size:184 final size:185
Alignment explanation
Indices: 3476549--3476914 Score: 536
Period size: 184 Copynumber: 2.0 Consensus size: 185
3476539 TGGATGCTCA
* * *
3476549 GATCTCGAAGCCGCGCGAGTTCGGAGCTTGAGTCTCAACCCGTGACAAGTGGTATCAAAGCCAGC
1 GATCCCGAAGCCGCGCGAGTTCAGAGCTTAAGTCTCAACCCGTGACAAGTGGTATCAAAGCCAGC
* * * *
3476614 CCTATACCATTCGATTCACTCGAAGTACCTCGAGGGAGGTAGGCAGGGTGGCCAGCCTCAGTGAC
66 CCTATACCATTCGATCCACGCCAAGTACCTCGAGGGAGGTAGGCAGGATGGCCAGCCTCAGTGAC
* ** * * *
3476679 GAGGGCGTCACGAAGTTGGGTGAGGGAGAATGTCACGGACCTAAGGAAGAATTCG
131 GAAGGCGTCACGAAGTTAAGTAAGGGAAAATATCACGGACCTAAGGAAGAATTCG
* * * *
3476734 GATCCCGAAGTCGCGCGAGTTCAGAGCTTAAGTCTCTACCCGTGACAAGTGGTATCAGAGCCAGT
1 GATCCCGAAGCCGCGCGAGTTCAGAGCTTAAGTCTCAACCCGTGACAAGTGGTATCAAAGCCAGC
* *
3476799 CCTATACCGTTCGATCCACGCCAAG-ACCTCGAGGGAGGTAGGCAGGATGGCCAGCCTCCGTGAC
66 CCTATACCATTCGATCCACGCCAAGTACCTCGAGGGAGGTAGGCAGGATGGCCAGCCTCAGTGAC
* *
3476863 GAAGGCGTCACGAGGTTAAGTAAGGGAAAATATCATGGACCTAAGGAAGAAT
131 GAAGGCGTCACGAAGTTAAGTAAGGGAAAATATCACGGACCTAAGGAAGAAT
3476915 CCTGACGAGG
Statistics
Matches: 160, Mismatches: 21, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
184 81 0.51
185 79 0.49
ACGTcount: A:0.27, C:0.24, G:0.31, T:0.18
Consensus pattern (185 bp):
GATCCCGAAGCCGCGCGAGTTCAGAGCTTAAGTCTCAACCCGTGACAAGTGGTATCAAAGCCAGC
CCTATACCATTCGATCCACGCCAAGTACCTCGAGGGAGGTAGGCAGGATGGCCAGCCTCAGTGAC
GAAGGCGTCACGAAGTTAAGTAAGGGAAAATATCACGGACCTAAGGAAGAATTCG
Found at i:3480462 original size:30 final size:30
Alignment explanation
Indices: 3480428--3480484 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3480418 AAAGGGTCTA
3480428 TTTTTTTTTCTTT-AAGAAAGAAAGGAAAAG
1 TTTTTTTTTCTTTGAA-AAAGAAAGGAAAAG
* *
3480458 TTTTTTTTTTTTTGAAATAGAAAGGAA
1 TTTTTTTTTCTTTGAAAAAGAAAGGAA
3480485 GGAAAGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.46
Consensus pattern (30 bp):
TTTTTTTTTCTTTGAAAAAGAAAGGAAAAG
Found at i:3487293 original size:2 final size:2
Alignment explanation
Indices: 3487286--3487316 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3487276 TAAAGAAGTT
3487286 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3487317 TAATTTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3488012 original size:21 final size:20
Alignment explanation
Indices: 3487976--3488040 Score: 96
Period size: 20 Copynumber: 3.2 Consensus size: 20
3487966 TCAAAAATAA
3487976 ATTTAA-TTTACCAAAAATGG
1 ATTTAACTTT-CCAAAAATGG
*
3487996 ATTTAACTTTCTAAAAATGG
1 ATTTAACTTTCCAAAAATGG
3488016 ATTTAACTTTCCAAAAAATGG
1 ATTTAACTTTCC-AAAAATGG
3488037 ATTT
1 ATTT
3488041 CTACATAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (20 bp):
ATTTAACTTTCCAAAAATGG
Found at i:3500555 original size:2 final size:2
Alignment explanation
Indices: 3500548--3500584 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3500538 ATTAGCGCAC
3500548 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3500585 TATCAAAGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3502238 original size:69 final size:69
Alignment explanation
Indices: 3502127--3502260 Score: 223
Period size: 69 Copynumber: 1.9 Consensus size: 69
3502117 AATTAAGCTC
* *
3502127 AAAGTCTGCAATTTCTCGAAAGTGTCCTGCATATCCTTTACATTTTCAGTAAGAATATAAGTTTA
1 AAAGTCTGCAATTTCTCAAAACTGTCCTGCATATCCTTTACATTTTCAGTAAGAATATAAGTTTA
3502192 CTCA
66 CTCA
** *
3502196 AAAGTCTGCAATTTCTCAAAACTGTCCTGTTTATCTTTTACATTTTCAGTAAGAATATAAGTTTA
1 AAAGTCTGCAATTTCTCAAAACTGTCCTGCATATCCTTTACATTTTCAGTAAGAATATAAGTTTA
3502261 GTCTAAAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (69 bp):
AAAGTCTGCAATTTCTCAAAACTGTCCTGCATATCCTTTACATTTTCAGTAAGAATATAAGTTTA
CTCA
Found at i:3504448 original size:21 final size:21
Alignment explanation
Indices: 3504422--3504467 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3504412 TTTAGGCAAA
* *
3504422 TTTTTTAATC-ATGTTTTAGT
1 TTTTTTTATCAATGTTTTAAT
*
3504442 TTTTTTTATCAATTTTTTAAT
1 TTTTTTTATCAATGTTTTAAT
3504463 TTTTT
1 TTTTT
3504468 AAATAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (21 bp):
TTTTTTTATCAATGTTTTAAT
Found at i:3511620 original size:25 final size:24
Alignment explanation
Indices: 3511579--3511625 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
3511569 ACGTGGTAGT
3511579 AATCTTATATTATGAAGAGTGATCA
1 AATCTTATATTATGAAGA-TGATCA
*
3511604 AATCATTATGTTA-GAAGATGAT
1 AATC-TTATATTATGAAGATGAT
3511626 TTAATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 4 0.20
25 9 0.45
26 7 0.35
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.36
Consensus pattern (24 bp):
AATCTTATATTATGAAGATGATCA
Found at i:3513051 original size:18 final size:19
Alignment explanation
Indices: 3513014--3513058 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
3513004 TCCTATCATA
*
3513014 ATATCATATAAAATATTAT
1 ATATTATATAAAATATTAT
*
3513033 ATTTTATATAAAA-ATTAT
1 ATATTATATAAAATATTAT
3513051 ATATTATA
1 ATATTATA
3513059 ATTTATATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATTATATAAAATATTAT
Found at i:3514312 original size:18 final size:20
Alignment explanation
Indices: 3514289--3514326 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3514279 TGGGTTGTGT
3514289 GAAGCT-TCG-CTTTTTGAA
1 GAAGCTATCGACTTTTTGAA
*
3514307 GAAGCTATGGACTTTTTGAA
1 GAAGCTATCGACTTTTTGAA
3514327 TAGAATGCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (20 bp):
GAAGCTATCGACTTTTTGAA
Found at i:3518368 original size:10 final size:10
Alignment explanation
Indices: 3518353--3518385 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
3518343 TTTATAAATT
3518353 TAAAAATATA
1 TAAAAATATA
*
3518363 TAAAAATAAA
1 TAAAAATATA
3518373 TAAAAATATA
1 TAAAAATATA
3518383 TAA
1 TAA
3518386 CATTTTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
TAAAAATATA
Found at i:3521979 original size:2 final size:2
Alignment explanation
Indices: 3521972--3522020 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3521962 CTCGTCCTTA
3521972 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3522014 TC TC TC T
1 TC TC TC T
3522021 ATATATATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3522025 original size:2 final size:2
Alignment explanation
Indices: 3522020--3522055 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3522010 TCTCTCTCTC
3522020 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3522056 GCAATTTCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3526029 original size:21 final size:20
Alignment explanation
Indices: 3526005--3526073 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 20
3525995 TGTTTGATAC
3526005 ATAAGGTTGTGATAGGATAGG
1 ATAAGGTT-TGATAGGATAGG
*
3526026 ATAAGATGATATTG-TA-AATAGG
1 ATAAG--G-T-TTGATAGGATAGG
*
3526048 ATAAGGTTATGACAGGATAGG
1 ATAAGGTT-TGATAGGATAGG
3526069 ATAAG
1 ATAAG
3526074 ATGATATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 14
0.69 0.05 0.25
Matches are distributed among these distances:
18 1 0.03
19 3 0.08
20 2 0.05
21 15 0.39
22 10 0.26
23 3 0.08
24 3 0.08
25 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.30, T:0.28
Consensus pattern (20 bp):
ATAAGGTTTGATAGGATAGG
Found at i:3526066 original size:43 final size:43
Alignment explanation
Indices: 3526005--3526099 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 43
3525995 TGTTTGATAC
* * * *
3526005 ATAAGGTTGTGATAGGATAGGATAAGATGATATTGTAAATAGG
1 ATAAGGTTATGACAGGATAGGATAAGATGATATTATAAATAAG
3526048 ATAAGGTTATGACAGGATAGGATAAGATGATATTATAAATAAG
1 ATAAGGTTATGACAGGATAGGATAAGATGATATTATAAATAAG
*
3526091 ATTAGGTTA
1 ATAAGGTTA
3526100 AATAATATCA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.42, C:0.01, G:0.26, T:0.31
Consensus pattern (43 bp):
ATAAGGTTATGACAGGATAGGATAAGATGATATTATAAATAAG
Found at i:3528820 original size:20 final size:20
Alignment explanation
Indices: 3528795--3528835 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3528785 GTCAATTTTC
3528795 TTTGTTTTGATTAATATATA
1 TTTGTTTTGATTAATATATA
*
3528815 TTTGTTTTGGTTAATATATA
1 TTTGTTTTGATTAATATATA
3528835 T
1 T
3528836 ATATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (20 bp):
TTTGTTTTGATTAATATATA
Found at i:3534599 original size:2 final size:2
Alignment explanation
Indices: 3534592--3534628 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3534582 ATCATTCCTT
*
3534592 TC TC TC TC TC TC TC TC TC TC TC TC TC TA TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3534629 GTTTTTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.46, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3535205 original size:22 final size:22
Alignment explanation
Indices: 3535163--3535206 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3535153 TATTTTTTTA
**
3535163 TTTTATTAAATTTATTTATAAT
1 TTTTATTAAATTTATAAATAAT
3535185 TTTTATTACAATTT-TAAATAAT
1 TTTTATTA-AATTTATAAATAAT
3535207 ATCATCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTATTAAATTTATAAATAAT
Found at i:3535918 original size:2 final size:2
Alignment explanation
Indices: 3535911--3535939 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3535901 CTTTAATTTC
3535911 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3535940 TTAATGGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3544857 original size:2 final size:2
Alignment explanation
Indices: 3544852--3544888 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3544842 CAAAGTTTCA
3544852 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3544889 ATATCTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3544899 original size:2 final size:2
Alignment explanation
Indices: 3544888--3544928 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3544878 TCTCTCTCTC
*
3544888 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3544929 GCACAAAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3554719 original size:14 final size:14
Alignment explanation
Indices: 3554682--3554712 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3554672 TATGATTAAT
*
3554682 TAATTAAAATTTTA
1 TAATAAAAATTTTA
3554696 TAATAAAAATTTTA
1 TAATAAAAATTTTA
3554710 TAA
1 TAA
3554713 GTGAAATGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATAAAAATTTTA
Found at i:3555461 original size:14 final size:15
Alignment explanation
Indices: 3555424--3555463 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
3555414 TATTAAAATC
3555424 ATTTTAAA-TATATT
1 ATTTTAAATTATATT
3555438 A-TTTATAATTAT-TT
1 ATTTTA-AATTATATT
3555452 ATTTTAAATTAT
1 ATTTTAAATTAT
3555464 CAGAATCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 4 0.17
14 12 0.52
15 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTAAATTATATT
Found at i:3556155 original size:70 final size:71
Alignment explanation
Indices: 3556029--3556166 Score: 171
Period size: 70 Copynumber: 2.0 Consensus size: 71
3556019 TAAATTTAAT
* *
3556029 AAAATAAAAAATTATATTTTATATTTTTATATTAATATAAATTATAATACATAAATTTTA-TATA
1 AAAATAAAAAATTATATTTTATATTTTTATATTAATATAAATTAAAATACATAAATTTAATTATA
3556093 AAATAC
66 AAATAC
3556099 AAAATAAATAAA-TA-ATTTTA-ATATTTTATA-TAATATAAATATACAAATA-ATCAAATTTAA
1 AAAATAAA-AAATTATATTTTATAT-TTTTATATTAATATAAAT-TA-AAATACAT-AAATTTAA
3556159 TTATAAAA
61 TTATAAAA
3556167 AACATCAATG
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
68 12 0.20
69 17 0.28
70 21 0.35
71 10 0.17
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (71 bp):
AAAATAAAAAATTATATTTTATATTTTTATATTAATATAAATTAAAATACATAAATTTAATTATA
AAATAC
Found at i:3556812 original size:31 final size:31
Alignment explanation
Indices: 3556777--3556871 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 31
3556767 TATTTTATAT
3556777 TTTTATATTAATATAAAT-TATAATACATAAA
1 TTTTATATTAATATAAATATA-AATACATAAA
* *
3556808 TTTTATA-TAAAATATAATATAAATACGTAAA
1 TTTTATATTAATATA-AATATAAATACATAAA
* *
3556839 TTTTAATATT-TTATAAACATAAATACATAAA
1 TTTT-ATATTAATATAAATATAAATACATAAA
3556870 TT
1 TT
3556872 ATTAAATCTT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
30 6 0.11
31 39 0.72
32 8 0.15
33 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (31 bp):
TTTTATATTAATATAAATATAAATACATAAA
Found at i:3561767 original size:15 final size:15
Alignment explanation
Indices: 3561733--3561765 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
3561723 GCTCCATTTG
3561733 TTTTAAGAAAAATAA
1 TTTTAAGAAAAATAA
3561748 TTTTAA-AAAAATAA
1 TTTTAAGAAAAATAA
3561762 TTTT
1 TTTT
3561766 TACATTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TTTTAAGAAAAATAA
Found at i:3561953 original size:18 final size:17
Alignment explanation
Indices: 3561930--3561990 Score: 67
Period size: 18 Copynumber: 3.7 Consensus size: 17
3561920 AATTTTACTT
3561930 ATAAATAATATCATATTA
1 ATAAATAATAT-ATATTA
3561948 ATAAATAATATACTATTA
1 ATAAATAATATA-TATTA
*
3561966 AT--GT-A-ATATATTA
1 ATAAATAATATATATTA
3561979 ATAAATAATATA
1 ATAAATAATATA
3561991 AAAATAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
13 7 0.19
14 3 0.08
15 2 0.06
16 2 0.06
17 4 0.11
18 18 0.50
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (17 bp):
ATAAATAATATATATTA
Found at i:3562047 original size:19 final size:19
Alignment explanation
Indices: 3562015--3562088 Score: 55
Period size: 19 Copynumber: 3.9 Consensus size: 19
3562005 TTTTATTTTA
**
3562015 AATATTTTTTTATTAATAT
1 AATATTTTAATATTAATAT
3562034 AATATTTTAATATTAA-AT
1 AATATTTTAATATTAATAT
** *
3562052 ACCATTATTAAAATATAAT-T
1 AATATT-TTAATAT-TAATAT
*
3562072 AAT-TTTGAATATTAATA
1 AATATTTTAATATTAATA
3562089 ATTTTACTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
17 4 0.10
18 11 0.26
19 22 0.52
20 5 0.12
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (19 bp):
AATATTTTAATATTAATAT
Found at i:3564633 original size:33 final size:33
Alignment explanation
Indices: 3564591--3564659 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
3564581 TCGTGGGTCC
3564591 AAGAGATCGTGAAGCAGTGTTTGAAGATGTCTG
1 AAGAGATCGTGAAGCAGTGTTTGAAGATGTCTG
3564624 AAGAGATCGTGAAGCAGTGTTTGAAGATGTCTG
1 AAGAGATCGTGAAGCAGTGTTTGAAGATGTCTG
3564657 AAG
1 AAG
3564660 GTGGTATCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.32, C:0.09, G:0.33, T:0.26
Consensus pattern (33 bp):
AAGAGATCGTGAAGCAGTGTTTGAAGATGTCTG
Found at i:3564778 original size:79 final size:79
Alignment explanation
Indices: 3564694--3564851 Score: 316
Period size: 79 Copynumber: 2.0 Consensus size: 79
3564684 TTTGTGGGTC
3564694 CAAGAGATCGTGAAGCAGTGTTTGAAGATGTCTGAAGAAGGTATGTCTGGTATGTCTATGCCTAA
1 CAAGAGATCGTGAAGCAGTGTTTGAAGATGTCTGAAGAAGGTATGTCTGGTATGTCTATGCCTAA
3564759 GTTTGAGATTCCGT
66 GTTTGAGATTCCGT
3564773 CAAGAGATCGTGAAGCAGTGTTTGAAGATGTCTGAAGAAGGTATGTCTGGTATGTCTATGCCTAA
1 CAAGAGATCGTGAAGCAGTGTTTGAAGATGTCTGAAGAAGGTATGTCTGGTATGTCTATGCCTAA
3564838 GTTTGAGATTCCGT
66 GTTTGAGATTCCGT
3564852 TATTTGATGG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (79 bp):
CAAGAGATCGTGAAGCAGTGTTTGAAGATGTCTGAAGAAGGTATGTCTGGTATGTCTATGCCTAA
GTTTGAGATTCCGT
Found at i:3566904 original size:116 final size:116
Alignment explanation
Indices: 3566700--3566932 Score: 466
Period size: 116 Copynumber: 2.0 Consensus size: 116
3566690 CCGGTATCCC
3566700 ACATCGGGAGTTTAGTAAAGGTATAAAGGGTTTCACCCCTATAAATAAGATGTTTTGGTTTTAGT
1 ACATCGGGAGTTTAGTAAAGGTATAAAGGGTTTCACCCCTATAAATAAGATGTTTTGGTTTTAGT
3566765 TTAGTAACCCCAAAGAGTTAGACACCAAGAGAATAGCTAAGTGAGTAGGCT
66 TTAGTAACCCCAAAGAGTTAGACACCAAGAGAATAGCTAAGTGAGTAGGCT
3566816 ACATCGGGAGTTTAGTAAAGGTATAAAGGGTTTCACCCCTATAAATAAGATGTTTTGGTTTTAGT
1 ACATCGGGAGTTTAGTAAAGGTATAAAGGGTTTCACCCCTATAAATAAGATGTTTTGGTTTTAGT
3566881 TTAGTAACCCCAAAGAGTTAGACACCAAGAGAATAGCTAAGTGAGTAGGCT
66 TTAGTAACCCCAAAGAGTTAGACACCAAGAGAATAGCTAAGTGAGTAGGCT
3566932 A
1 A
3566933 TTAAAGGGTG
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 117 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (116 bp):
ACATCGGGAGTTTAGTAAAGGTATAAAGGGTTTCACCCCTATAAATAAGATGTTTTGGTTTTAGT
TTAGTAACCCCAAAGAGTTAGACACCAAGAGAATAGCTAAGTGAGTAGGCT
Found at i:3567485 original size:39 final size:39
Alignment explanation
Indices: 3567431--3567557 Score: 193
Period size: 39 Copynumber: 3.3 Consensus size: 39
3567421 TTCGACCTAT
*
3567431 GGAACATGATAAAATACAAAGAC-AGAGGTCAGAAGGCTC
1 GGAACATGATAAAATACAAGGACGA-AGGTCAGAAGGCTC
*
3567470 GGAACATGATAAAATACAAGGACGAAGGGCAGAAGGCTC
1 GGAACATGATAAAATACAAGGACGAAGGTCAGAAGGCTC
* * *
3567509 GGAACATAATAAAATACGAGGACGAAGATCAGAAGGCTC
1 GGAACATGATAAAATACAAGGACGAAGGTCAGAAGGCTC
3567548 GGAACATGAT
1 GGAACATGAT
3567558 GTAACAGAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
39 79 0.99
40 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.28, T:0.13
Consensus pattern (39 bp):
GGAACATGATAAAATACAAGGACGAAGGTCAGAAGGCTC
Found at i:3569116 original size:18 final size:18
Alignment explanation
Indices: 3569093--3569204 Score: 67
Period size: 18 Copynumber: 6.4 Consensus size: 18
3569083 AATTTTACAT
3569093 ATAAATAATATTATATTA
1 ATAAATAATATTATATTA
3569111 ATAAATAATA-TACTATTA
1 ATAAATAATATTA-TATTA
*
3569129 AT--GT-A-A-TATATTA
1 ATAAATAATATTATATTA
* **
3569142 ATAAATATTATTA-ACAA
1 ATAAATAATATTATATTA
*
3569159 ATAAATATTTATAATATATTA
1 ATAAATA---ATATTATATTA
* * *
3569180 ATAAATAATATAAAAATA
1 ATAAATAATATTATATTA
3569198 ATAAATA
1 ATAAATA
3569205 GTTTTATTTT
Statistics
Matches: 71, Mismatches: 13, Indels: 20
0.68 0.12 0.19
Matches are distributed among these distances:
13 7 0.10
14 3 0.04
15 2 0.03
16 1 0.01
17 12 0.17
18 33 0.46
20 4 0.06
21 9 0.13
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (18 bp):
ATAAATAATATTATATTA
Found at i:3569153 original size:13 final size:12
Alignment explanation
Indices: 3569114--3569186 Score: 58
Period size: 13 Copynumber: 5.7 Consensus size: 12
3569104 TATATTAATA
3569114 AATAATATACTATT
1 AATAA-ATA-TATT
*
3569128 AATGTAATATATT
1 AAT-AAATATATT
3569141 AATAAATATTATT
1 AATAAATA-TATT
*
3569154 AACAAATAAATATT
1 AATAAAT--ATATT
*
3569168 TAT-AATATATT
1 AATAAATATATT
3569179 AATAAATA
1 AATAAATA
3569187 ATATAAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
11 7 0.15
12 8 0.17
13 20 0.42
14 11 0.23
15 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (12 bp):
AATAAATATATT
Found at i:3569306 original size:16 final size:16
Alignment explanation
Indices: 3569223--3569314 Score: 64
Period size: 16 Copynumber: 5.5 Consensus size: 16
3569213 TTAAATACTT
*
3569223 TTTTATTAATATAAT-A
1 TTTTAATAATA-AATAA
*
3569239 TTTTAATATTAAATATCA
1 TTTTAATAATAAATA--A
3569257 TTATTAA-AATATAATTAA
1 TT-TTAATAATA-AA-TAA
*
3569275 TTTTTAAT-ATTAATAA
1 -TTTTAATAATAAATAA
3569291 TTTTAATAATAAATAA
1 TTTTAATAATAAATAA
*
3569307 TTTCAATA
1 TTTTAATA
3569315 TACTTTAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
15 10 0.16
16 26 0.43
17 2 0.03
18 13 0.21
19 8 0.13
20 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTAATAATAAATAA
Found at i:3569307 original size:25 final size:24
Alignment explanation
Indices: 3569279--3569349 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 24
3569269 AATTAATTTT
3569279 TAATATTAATAATTTTAATAATAAA
1 TAAT-TTAATAATTTTAATAATAAA
*
3569304 TAATTTCAATATACTTTAATAATAAA
1 TAATTT-AATA-ATTTTAATAATAAA
3569330 TAATTTTTAAT-ATTTTAATA
1 TAA--TTTAATAATTTTAATA
3569350 GTTATATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 16 0.40
27 3 0.08
28 3 0.08
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATTTAATAATTTTAATAATAAA
Found at i:3570000 original size:26 final size:25
Alignment explanation
Indices: 3569941--3570000 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 25
3569931 GTTTGAAAAA
3569941 AAAAAAGT-TTTTATTTTTATTTTTT
1 AAAAAA-TATTTTATTTTTATTTTTT
*
3569966 AGAATAATATTTTATTTTTTATTTTTT
1 A-AAAAATATTTTA-TTTTTATTTTTT
3569993 AAAAAATA
1 AAAAAATA
3570001 GTTGATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 2 0.07
26 15 0.50
27 13 0.43
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (25 bp):
AAAAAATATTTTATTTTTATTTTTT
Found at i:3570581 original size:21 final size:22
Alignment explanation
Indices: 3570542--3570582 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3570532 GTTTCATTCA
* *
3570542 TAATTATTATATTATAATTAAT
1 TAATTATTAAATTAAAATTAAT
3570564 TAATT-TTAAATTAAAATTA
1 TAATTATTAAATTAAAATTA
3570583 TGTTGGATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATTATTAAATTAAAATTAAT
Found at i:3570915 original size:27 final size:26
Alignment explanation
Indices: 3570862--3570916 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
3570852 ATTATTTTAT
* *
3570862 TTTATATATATTAATTCAAATTCAAA
1 TTTATATATAATAATTCAAATTAAAA
* *
3570888 TTTATATATAAATAATTGAATTTAAAA
1 TTTATATAT-AATAATTCAAATTAAAA
3570915 TT
1 TT
3570917 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (26 bp):
TTTATATATAATAATTCAAATTAAAA
Found at i:3571781 original size:29 final size:27
Alignment explanation
Indices: 3571739--3571799 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 27
3571729 TTTCGAGAGG
*
3571739 AATTAAACACAAATTAGATAAAATTAAAA
1 AATTAAAAACAAATTA-A-AAAATTAAAA
* * *
3571768 AATTAAAAATAAATTAAAAATTTTAAA
1 AATTAAAAACAAATTAAAAAATTAAAA
3571795 AATTA
1 AATTA
3571800 TATTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 13 0.46
28 1 0.04
29 14 0.50
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (27 bp):
AATTAAAAACAAATTAAAAAATTAAAA
Found at i:3571783 original size:19 final size:20
Alignment explanation
Indices: 3571759--3571797 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3571749 AAATTAGATA
3571759 AAATTAAAAA-ATTAAAAAT
1 AAATTAAAAATATTAAAAAT
*
3571778 AAATTAAAAATTTTAAAAAT
1 AAATTAAAAATATTAAAAAT
3571798 TATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATTAAAAATATTAAAAAT
Found at i:3572784 original size:14 final size:15
Alignment explanation
Indices: 3572758--3572786 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3572748 TAAAAAAAAA
3572758 AAAATTATAAATATT
1 AAAATTATAAATATT
3572773 AAAATT-TAAATATT
1 AAAATTATAAATATT
3572787 TATAGAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:3577907 original size:30 final size:30
Alignment explanation
Indices: 3577873--3577931 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
3577863 TACATGTCAA
*
3577873 GGATTTCTAAAGTTACTTTTATATGAGCTT
1 GGATTTCTAAAGTTACTTTCATATGAGCTT
3577903 GGATTTCTAAAGTTACTTTCATATGAGCT
1 GGATTTCTAAAGTTACTTTCATATGAGCT
3577932 AACACCTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (30 bp):
GGATTTCTAAAGTTACTTTCATATGAGCTT
Found at i:3580327 original size:2 final size:2
Alignment explanation
Indices: 3580322--3580352 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3580312 CATAGTACAC
3580322 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3580353 ACCTGCCAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3581489 original size:19 final size:17
Alignment explanation
Indices: 3581443--3581482 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3581433 TCAAATCAAA
3581443 TTAAATTTATATATATT
1 TTAAATTTATATATATT
*
3581460 TTTAATTTATATATATT
1 TTAAATTTATATATATT
3581477 TTAAAT
1 TTAAAT
3581483 ATTTATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTAAATTTATATATATT
Found at i:3581610 original size:23 final size:22
Alignment explanation
Indices: 3581596--3581642 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 22
3581586 TAAATCAAAT
3581596 TAAATTAAATTGATAAAATTCAG
1 TAAATTAAATTGAT-AAATTCAG
3581619 TAAATTAAATTGATAAAATTCAG
1 TAAATTAAATTGAT-AAATTCAG
3581642 T
1 T
3581643 TCGATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (22 bp):
TAAATTAAATTGATAAATTCAG
Found at i:3583491 original size:13 final size:14
Alignment explanation
Indices: 3583473--3583501 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3583463 TTGGGTACAT
3583473 TGCATAT-TCCTTC
1 TGCATATATCCTTC
3583486 TGCATATATCCTTC
1 TGCATATATCCTTC
3583500 TG
1 TG
3583502 TACCAAGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.17, C:0.28, G:0.10, T:0.45
Consensus pattern (14 bp):
TGCATATATCCTTC
Found at i:3583769 original size:33 final size:33
Alignment explanation
Indices: 3583732--3583797 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
3583722 CAGAAGTTCA
* *
3583732 AATTCCTGTAATCCTTTTTATTATTTTCAGGCT
1 AATTCCTATAATCCTTTTCATTATTTTCAGGCT
3583765 AATTCCTATAATCCTTTTCATTATTTTCAGGCT
1 AATTCCTATAATCCTTTTCATTATTTTCAGGCT
3583798 GACTTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.20, G:0.08, T:0.50
Consensus pattern (33 bp):
AATTCCTATAATCCTTTTCATTATTTTCAGGCT
Found at i:3590988 original size:33 final size:33
Alignment explanation
Indices: 3590946--3591017 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
3590936 CAGCAATGTT
3590946 AATTATGTTGCTATGATTTAATCTGTCTGATTA
1 AATTATGTTGCTATGATTTAATCTGTCTGATTA
3590979 AATTATGTTGCTATGATTTAATCTGTCTGATTA
1 AATTATGTTGCTATGATTTAATCTGTCTGATTA
3591012 AATTAT
1 AATTAT
3591018 ATTGTATTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (33 bp):
AATTATGTTGCTATGATTTAATCTGTCTGATTA
Found at i:3596018 original size:126 final size:126
Alignment explanation
Indices: 3595786--3596035 Score: 428
Period size: 126 Copynumber: 2.0 Consensus size: 126
3595776 GTCAAGGAAA
* * *
3595786 GTTTCTCATCTGCTGATGATGACTCTATGTGGTTGTCTTCAGGTTGTGTATCACCTTTATCATTT
1 GTTTCTCATCTGCTGATGATGACTCTATGTGGTTATCTTCAGGCTGTGTATCACCTTCATCATTT
* * *
3595851 TTTGAAGAGCATGAATTGTCGAGTCCTTTTGATCATGTGGCTGATGAATGGTTAGTTTCAT
66 TTTAAAGAGCATGAATTGTCGAGTCCCTTTGATCATATGGCTGATGAATGGTTAGTTTCAT
*
3595912 GTTTCTCATCTGCTGTTGATGACTCTATGTGGTTATCTTCAGGCTGTGTATCACCTTCATCATTT
1 GTTTCTCATCTGCTGATGATGACTCTATGTGGTTATCTTCAGGCTGTGTATCACCTTCATCATTT
*
3595977 TTTAAAGAGCATGAATTGTCGAGTCCCTTTGATCTTATGGCTGATGAATGGTTAGTTTC
66 TTTAAAGAGCATGAATTGTCGAGTCCCTTTGATCATATGGCTGATGAATGGTTAGTTTC
3596036 GTGGCTGTCA
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 116 1.00
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.42
Consensus pattern (126 bp):
GTTTCTCATCTGCTGATGATGACTCTATGTGGTTATCTTCAGGCTGTGTATCACCTTCATCATTT
TTTAAAGAGCATGAATTGTCGAGTCCCTTTGATCATATGGCTGATGAATGGTTAGTTTCAT
Found at i:3598209 original size:14 final size:15
Alignment explanation
Indices: 3598179--3598216 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
3598169 ATATGGTGAC
3598179 ATAAGATAAAAATTAT
1 ATAA-ATAAAAATTAT
3598195 ATAAATAAAAA-TAT
1 ATAAATAAAAATTAT
*
3598209 AAAAATAA
1 ATAAATAA
3598217 TATAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.48
15 7 0.33
16 4 0.19
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
ATAAATAAAAATTAT
Found at i:3598210 original size:12 final size:12
Alignment explanation
Indices: 3598193--3598239 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
3598183 GATAAAAATT
3598193 ATATAAATAAAA
1 ATATAAATAAAA
*
3598205 ATATAAA-AATA
1 ATATAAATAAAA
*
3598216 ATATAATTAAAA
1 ATATAAATAAAA
* *
3598228 ATTTTAATAAAA
1 ATATAAATAAAA
3598240 TTTAAAAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATATAAATAAAA
Found at i:3598210 original size:23 final size:23
Alignment explanation
Indices: 3598184--3598229 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3598174 GTGACATAAG
*
3598184 ATAAAAATTATATAAATAAAAAT
1 ATAAAAATAATATAAATAAAAAT
*
3598207 ATAAAAATAATATAATTAAAAAT
1 ATAAAAATAATATAAATAAAAAT
3598230 TTTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
ATAAAAATAATATAAATAAAAAT
Found at i:3598218 original size:11 final size:11
Alignment explanation
Indices: 3598179--3598221 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
3598169 ATATGGTGAC
*
3598179 ATAAGATAAAA
1 ATAATATAAAA
*
3598190 ATTATATAAATA
1 ATAATATAAA-A
*
3598202 AAAATATAAAA
1 ATAATATAAAA
3598213 ATAATATAA
1 ATAATATAA
3598222 TTAAAAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:3599487 original size:18 final size:19
Alignment explanation
Indices: 3599466--3599507 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
3599456 TTAAAATTTA
3599466 AAATTTAATTAAATT-CAT
1 AAATTTAATTAAATTACAT
* *
3599484 AAA-TTACTTAAATTACTT
1 AAATTTAATTAAATTACAT
3599502 AAATTT
1 AAATTT
3599508 GATGCATTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.50
18 8 0.40
19 2 0.10
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATTTAATTAAATTACAT
Found at i:3599497 original size:9 final size:9
Alignment explanation
Indices: 3599474--3599506 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
3599464 TAAAATTTAA
3599474 TTAAATT-C
1 TTAAATTAC
*
3599482 ATAAATTAC
1 TTAAATTAC
3599491 TTAAATTAC
1 TTAAATTAC
3599500 TTAAATT
1 TTAAATT
3599507 TGATGCATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 6 0.27
9 16 0.73
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (9 bp):
TTAAATTAC
Found at i:3599979 original size:1 final size:1
Alignment explanation
Indices: 3599973--3600009 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
3599963 TCATATATTC
3599973 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3600010 GAATTTGTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3602629 original size:18 final size:18
Alignment explanation
Indices: 3602586--3602629 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3602576 TTTTATTTTT
*
3602586 TTATAAATATTTTTTCTA
1 TTATAAATATTATTTCTA
*
3602604 TTAAAAATATTATTTC-A
1 TTATAAATATTATTTCTA
3602621 TTGATAAAT
1 TT-ATAAAT
3602630 CATATCATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATAAATATTATTTCTA
Found at i:3606206 original size:2 final size:2
Alignment explanation
Indices: 3606199--3606231 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3606189 TGCTGCACTC
3606199 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3606232 ATGATACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3608213 original size:11 final size:11
Alignment explanation
Indices: 3608199--3608239 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
3608189 ATAAAATTCA
3608199 ATTAAAAATTT
1 ATTAAAAATTT
*
3608210 ATTAAAAAATT
1 ATTAAAAATTT
3608221 A--AATAAATTT
1 ATTAA-AAATTT
3608231 ATTAAAAAT
1 ATTAAAAAT
3608240 ATATAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 2 0.08
10 6 0.24
11 15 0.60
12 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATTAAAAATTT
Found at i:3612941 original size:18 final size:18
Alignment explanation
Indices: 3612918--3612954 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3612908 TGCATTTTAT
3612918 GACTGGACCTTAAGAATA
1 GACTGGACCTTAAGAATA
*
3612936 GACTGGACCTTAAGGATA
1 GACTGGACCTTAAGAATA
3612954 G
1 G
3612955 GGGAATGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (18 bp):
GACTGGACCTTAAGAATA
Found at i:3619472 original size:9 final size:9
Alignment explanation
Indices: 3619455--3619753 Score: 102
Period size: 9 Copynumber: 31.0 Consensus size: 9
3619445 AAGAAATTTT
3619455 TTTTAAAAA
1 TTTTAAAAA
*
3619464 TTCTAAAAA
1 TTTTAAAAA
**
3619473 TTTTTTAAA
1 TTTTAAAAA
*
3619482 TTATAAAAAA
1 TT-TTAAAAA
*
3619492 TTTTCAAAA
1 TTTTAAAAA
3619501 --TTAAAAA
1 TTTTAAAAA
**
3619508 AATTAAGAAA
1 TTTTAA-AAA
*
3619518 TTCTAAAAA
1 TTTTAAAAA
3619527 TTTTTAAAAA
1 -TTTTAAAAA
3619537 TTTTAAAATAAA
1 TTTT--AA-AAA
3619549 TTTTCAAAAAA
1 TTTT--AAAAA
**
3619560 GTCTAAAAAAA
1 -T-TTTAAAAA
**
3619571 TTACGAAAAAA
1 TT--TTAAAAA
3619582 TTTTAAAAA
1 TTTTAAAAA
*
3619591 TTCTAACAAA
1 TTTTAA-AAA
3619601 TTTTGAAAAA
1 TTTT-AAAAA
*
3619611 TTTTGAAAA
1 TTTTAAAAA
*
3619620 TTATAAAATAA
1 TT-TTAAA-AA
*
3619631 TTTCAAAAA
1 TTTTAAAAA
3619640 TTTTTAGAAAA
1 -TTTTA-AAAA
* *
3619651 -CTAAAAAA
1 TTTTAAAAA
**
3619659 AATTAAAAA
1 TTTTAAAAA
*
3619668 TTCTAAAAA
1 TTTTAAAAA
*
3619677 CTTTAAAAA
1 TTTTAAAAA
3619686 GTTTTTAAAAA
1 --TTTTAAAAA
*
3619697 ATTT-AAAA
1 TTTTAAAAA
**
3619705 TATAAAAAAA
1 T-TTTAAAAA
3619715 TTTTGAAAAA
1 TTTT-AAAAA
*
3619725 GTTTAAAAAA
1 -TTTTAAAAA
**
3619735 TTCTGGAAAA
1 TT-TTAAAAA
3619745 TTTTAAAAA
1 TTTTAAAAA
3619754 ATTCAAAAAA
Statistics
Matches: 216, Mismatches: 48, Indels: 52
0.68 0.15 0.16
Matches are distributed among these distances:
7 6 0.03
8 8 0.04
9 84 0.39
10 67 0.31
11 39 0.18
12 11 0.05
13 1 0.00
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:3619482 original size:18 final size:18
Alignment explanation
Indices: 3619454--3619535 Score: 69
Period size: 19 Copynumber: 4.5 Consensus size: 18
3619444 AAAGAAATTT
3619454 TTTTTAAAAATTCTAAAAA
1 TTTTT-AAAATTCTAAAAA
* *
3619473 TTTTTTAAATTATAAAAAA
1 TTTTTAAAATTCT-AAAAA
*
3619492 TTTTCAAAA-T-TAAAAA
1 TTTTTAAAATTCTAAAAA
** *
3619508 AATTAAGAAATTCTAAAAA
1 TTTTTA-AAATTCTAAAAA
3619527 TTTTTAAAA
1 TTTTTAAAA
3619536 ATTTTAAAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
16 8 0.16
17 4 0.08
18 11 0.22
19 26 0.53
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (18 bp):
TTTTTAAAATTCTAAAAA
Found at i:3619537 original size:19 final size:19
Alignment explanation
Indices: 3619454--3619685 Score: 94
Period size: 20 Copynumber: 12.5 Consensus size: 19
3619444 AAAGAAATTT
3619454 TTTTTAAAAATTCTAAAAA
1 TTTTTAAAAATTCTAAAAA
* *
3619473 TTTTT-TAAATTATAAAAA
1 TTTTTAAAAATTCTAAAAA
* *
3619491 ATTTTCAAAA-T-TAAAAA
1 TTTTTAAAAATTCTAAAAA
**
3619508 -AATTAAGAAATTCTAAAAA
1 TTTTTAA-AAATTCTAAAAA
*
3619527 TTTTTAAAAATT-TTAAAA
1 TTTTTAAAAATTCTAAAAA
** *
3619545 ----TAAATTTTCAAAAAA
1 TTTTTAAAAATTCTAAAAA
* ** *
3619560 GTCTAAAAAAATTACGAAAAA
1 -TTTTTAAAAATT-CTAAAAA
*
3619581 ATTTTAAAAATTCTAACAAA
1 TTTTTAAAAATTCTAA-AAA
* * *
3619601 TTTTGAAAAATTTTGAAAA
1 TTTTTAAAAATTCTAAAAA
* *
3619620 TTATAAAATAATT-TCAAAAA
1 TTTTTAAA-AATTCT-AAAAA
3619640 TTTTTAGAAAA--CTAAAAA
1 TTTTTA-AAAATTCTAAAAA
***
3619658 AAATTAAAAATTCTAAAAA
1 TTTTTAAAAATTCTAAAAA
*
3619677 -CTTTAAAAA
1 TTTTTAAAAA
3619686 GTTTTTAAAA
Statistics
Matches: 157, Mismatches: 37, Indels: 39
0.67 0.16 0.17
Matches are distributed among these distances:
14 6 0.04
15 4 0.03
16 3 0.02
17 13 0.08
18 37 0.24
19 40 0.25
20 46 0.29
21 8 0.05
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (19 bp):
TTTTTAAAAATTCTAAAAA
Found at i:3619590 original size:11 final size:11
Alignment explanation
Indices: 3619522--3619590 Score: 59
Period size: 11 Copynumber: 6.3 Consensus size: 11
3619512 AAGAAATTCT
*
3619522 AAAAATTTT-T
1 AAAAATTTTAA
3619532 AAAAATTTTAA
1 AAAAATTTTAA
*
3619543 AATAAATTTTCA
1 AA-AAATTTTAA
* *
3619555 AAAAAGTCTAA
1 AAAAATTTTAA
***
3619566 AAAAATTACGA
1 AAAAATTTTAA
3619577 AAAAATTTTAA
1 AAAAATTTTAA
3619588 AAA
1 AAA
3619591 TTCTAACAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
10 9 0.20
11 26 0.58
12 10 0.22
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (11 bp):
AAAAATTTTAA
Found at i:3619619 original size:29 final size:29
Alignment explanation
Indices: 3619577--3619733 Score: 87
Period size: 29 Copynumber: 5.5 Consensus size: 29
3619567 AAAATTACGA
* * *
3619577 AAAAATTTTAAAAATTCTAACAA-ATTTTG
1 AAAAATTTTAAAAATTATAA-AATAATTTC
*
3619606 AAAAATTTTGAAAATTATAAAATAATTTC
1 AAAAATTTTAAAAATTATAAAATAATTTC
* *
3619635 AAAAATTTTTAGAAAACTA-AAAA-AAATT-
1 AAAAA-TTTTA-AAAATTATAAAATAATTTC
* * *
3619663 AAAAATTCTAAAAACTT-TAAAA-AGTTTTT
1 AAAAATTTTAAAAA-TTATAAAATA-ATTTC
* * *
3619692 AAAAAATTT-AAAA-TATAAAAAAATTTTG
1 AAAAATTTTAAAAATTATAAAATAA-TTTC
*
3619720 AAAAAGTTTAAAAA
1 AAAAATTTTAAAAA
3619734 ATTCTGGAAA
Statistics
Matches: 101, Mismatches: 16, Indels: 22
0.73 0.12 0.16
Matches are distributed among these distances:
26 5 0.05
27 15 0.15
28 25 0.25
29 42 0.42
30 8 0.08
31 6 0.06
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAATTTTAAAAATTATAAAATAATTTC
Found at i:3619696 original size:37 final size:37
Alignment explanation
Indices: 3619655--3619736 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
3619645 AGAAAACTAA
**
3619655 AAAAAATTAAAAAT-TCTAAAAACTTT-AAAAAGTTTTT
1 AAAAAATTAAAAATATAAAAAAACTTTGAAAAAG--TTT
* *
3619692 AAAAAATTTAAAATATAAAAAAATTTTGAAAAAGTTT
1 AAAAAATTAAAAATATAAAAAAACTTTGAAAAAGTTT
3619729 AAAAAATT
1 AAAAAATT
3619737 CTGGAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 24 0.62
38 9 0.23
39 6 0.15
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (37 bp):
AAAAAATTAAAAATATAAAAAAACTTTGAAAAAGTTT
Found at i:3619732 original size:20 final size:20
Alignment explanation
Indices: 3619709--3619757 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
3619699 TTAAAATATA
*
3619709 AAAAAATTTTGAAAAAGTTT
1 AAAAAATTCTGAAAAAGTTT
* *
3619729 AAAAAATTCTGGAAAATTTT
1 AAAAAATTCTGAAAAAGTTT
3619749 AAAAAATTC
1 AAAAAATTC
3619758 AAAAAAGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAAAATTCTGAAAAAGTTT
Found at i:3622159 original size:20 final size:20
Alignment explanation
Indices: 3622075--3622159 Score: 66
Period size: 19 Copynumber: 4.2 Consensus size: 20
3622065 TTTTAAAATT
3622075 TTTTTAGAAAAT-TTTAAAAGG
1 TTTTTA-AAAATATTTAAAA-G
* * *
3622096 TTTTTAAAAAAACTTTAGAAT
1 TTTTTAAAAATA-TTTAAAAG
* ** *
3622117 TTTTTTAAAATA-TTGGAAT
1 TTTTTAAAAATATTTAAAAG
3622136 TTTTTAAAAATATTTAAAAG
1 TTTTTAAAAATATTTAAAAG
3622156 TTTT
1 TTTT
3622160 AGAATTTTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
19 17 0.33
20 12 0.24
21 16 0.31
22 6 0.12
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.48
Consensus pattern (20 bp):
TTTTTAAAAATATTTAAAAG
Found at i:3622159 original size:21 final size:20
Alignment explanation
Indices: 3622066--3622159 Score: 75
Period size: 21 Copynumber: 4.6 Consensus size: 20
3622056 TTTTGAGGTT
3622066 TTTAAAATTTTTTTAGAAAAT-
1 TTTAAAA-TTTTTTA-AAAATA
* *
3622087 TTTAAAAGGTTTTTAAAAAAA
1 TTTAAAA-TTTTTTAAAAATA
* *
3622108 CTTTAGAATTTTTTTAAAATA
1 -TTTAAAATTTTTTAAAAATA
**
3622129 -TTGGAATTTTTTAAAAATA
1 TTTAAAATTTTTTAAAAATA
*
3622148 TTTAAAAGTTTT
1 TTTAAAATTTTT
3622160 AGAATTTTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
19 17 0.29
20 12 0.21
21 23 0.40
22 6 0.10
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (20 bp):
TTTAAAATTTTTTAAAAATA
Found at i:3622164 original size:29 final size:30
Alignment explanation
Indices: 3622132--3622209 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 30
3622122 TAAAATATTG
*
3622132 GAATTTTTTAAAAATATTTAAA-AGTTTTA
1 GAATTTTTTAAAAATTTTTAAATAGTTTTA
* * *
3622161 GAATTTTTTTATAATTTTTAAAATATTTTTA
1 GAATTTTTTAAAAATTTTT-AAATAGTTTTA
3622192 G-A-TTTTTAAAAATTTTTA
1 GAATTTTTTAAAAATTTTTA
3622210 GAAAATTGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
28 1 0.02
29 29 0.71
30 4 0.10
31 7 0.17
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (30 bp):
GAATTTTTTAAAAATTTTTAAATAGTTTTA
Found at i:3622171 original size:20 final size:20
Alignment explanation
Indices: 3622137--3622209 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
3622127 TATTGGAATT
*
3622137 TTTTAAAA-ATATTTAAAAG
1 TTTTAAAATATTTTTAAAAG
* * * *
3622156 TTTTAGAATTTTTTTATAAT
1 TTTTAAAATATTTTTAAAAG
* *
3622176 TTTTAAAATATTTTT-AGAT
1 TTTTAAAATATTTTTAAAAG
3622195 TTTTAAAA-ATTTTTA
1 TTTTAAAATATTTTTA
3622210 GAAAATTGTT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
18 6 0.14
19 17 0.40
20 20 0.47
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
TTTTAAAATATTTTTAAAAG
Found at i:3622189 original size:19 final size:19
Alignment explanation
Indices: 3622118--3622207 Score: 62
Period size: 19 Copynumber: 4.8 Consensus size: 19
3622108 CTTTAGAATT
** *
3622118 TTTTTAAAATATTGGA-AT
1 TTTTTAAAATATTTTATAA
*
3622136 TTTTTAAAA-ATATTTAAAA
1 TTTTTAAAATAT-TTTATAA
* * *
3622155 GTTTTAGAATTTTTTTATAA
1 TTTTTA-AAATATTTTATAA
3622175 TTTTTAAAATATTTT-TAGA
1 TTTTTAAAATATTTTATA-A
3622194 TTTTTAAAA-ATTTT
1 TTTTTAAAATATTTT
3622208 TAGAAAATTG
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
17 2 0.04
18 18 0.32
19 23 0.40
20 13 0.23
21 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTTTAAAATATTTTATAA
Found at i:3622206 original size:18 final size:19
Alignment explanation
Indices: 3622174--3622211 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3622164 TTTTTTTATA
3622174 ATTTTTAAAATATTTTTAG
1 ATTTTTAAAATATTTTTAG
3622193 ATTTTTAAAA-ATTTTTAG
1 ATTTTTAAAATATTTTTAG
3622211 A
1 A
3622212 AAATTGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTTTTAAAATATTTTTAG
Found at i:3623107 original size:29 final size:29
Alignment explanation
Indices: 3623047--3623124 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
3623037 TAAATGTAGT
*
3623047 ATTTTATTAAATTAATGTAT-TAAATAATA
1 ATTTTATTAAA-TAATATATATAAATAATA
3623076 ATTTTATTAATATAATATATATAAAT--TA
1 ATTTTATTAA-ATAATATATATAAATAATA
* * *
3623104 AATTAAATAAATAATATATAT
1 ATTTTATTAAATAATATATAT
3623125 TCTTATTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
27 11 0.26
28 9 0.21
29 17 0.40
30 6 0.14
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (29 bp):
ATTTTATTAAATAATATATATAAATAATA
Found at i:3624507 original size:19 final size:19
Alignment explanation
Indices: 3624485--3624523 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3624475 ATTTATCTAC
*
3624485 ATTTAACATGATTATTTAA
1 ATTTAACATAATTATTTAA
* *
3624504 ATTTATCATAATTTTTTAA
1 ATTTAACATAATTATTTAA
3624523 A
1 A
3624524 AATATTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (19 bp):
ATTTAACATAATTATTTAA
Found at i:3625402 original size:17 final size:17
Alignment explanation
Indices: 3625372--3625420 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
3625362 GTTTATTAAG
3625372 ATTTAAATGA-AAAATCA
1 ATTTAAATGATAAAAT-A
3625389 ATTTAAAT-ATAAAATA
1 ATTTAAATGATAAAATA
3625405 A-TTAAATAGATAAAAT
1 ATTTAAAT-GATAAAAT
3625421 TATTATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.21
16 3 0.10
17 20 0.69
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
ATTTAAATGATAAAATA
Found at i:3627211 original size:12 final size:13
Alignment explanation
Indices: 3627179--3627211 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3627169 ATTAATTTTT
3627179 AATTATTTATAAA
1 AATTATTTATAAA
3627192 AATATATTT-TAAA
1 AAT-TATTTATAAA
3627205 AATTATT
1 AATTATT
3627212 AAATTATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 10 0.53
14 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTATTTATAAA
Found at i:3627364 original size:30 final size:28
Alignment explanation
Indices: 3627316--3627374 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 28
3627306 ATTTTAAAGT
3627316 AATTTATCTATATTTAAAATGA-TATTTA
1 AATTTATCTATATTTAAAAT-ATTATTTA
*
3627344 AATTTATCATAATTTTTAAAATATTATTTA
1 AATTTATC-T-ATATTTAAAATATTATTTA
3627374 A
1 A
3627375 CATCTTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 8 0.30
29 2 0.07
30 17 0.63
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (28 bp):
AATTTATCTATATTTAAAATATTATTTA
Found at i:3627789 original size:16 final size:17
Alignment explanation
Indices: 3627768--3627810 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 17
3627758 TAAGTATTAT
3627768 TTCACTT-AACATACTA
1 TTCACTTAAACATACTA
3627784 TTCACTTACTAAACATACTA
1 TTCAC-T--TAAACATACTA
3627804 TTCACTT
1 TTCACTT
3627811 CATCAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 5 0.22
17 2 0.09
19 2 0.09
20 14 0.61
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.40
Consensus pattern (17 bp):
TTCACTTAAACATACTA
Found at i:3631836 original size:19 final size:18
Alignment explanation
Indices: 3631787--3631841 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
3631777 ATTTTTTATT
*
3631787 TTTTATGTTTTTAGAAAT
1 TTTTATGTTTTTAGAAAA
*
3631805 TGTTTATAATTTTT-GTAAAA
1 T-TTTAT-GTTTTTAG-AAAA
3631825 TTTTATGTTTTTA-AAAA
1 TTTTATGTTTTTAGAAAA
3631842 GACTTTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
17 4 0.13
18 6 0.20
19 11 0.37
20 9 0.30
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (18 bp):
TTTTATGTTTTTAGAAAA
Found at i:3631863 original size:38 final size:38
Alignment explanation
Indices: 3631787--3631865 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
3631777 ATTTTTTATT
* *** *
3631787 TTTTATGTTTTTAGAAATTGTTTATAATTTTTGTAAAA
1 TTTTATGTTTTTAAAAAGACTTTATAATTTTTGAAAAA
3631825 TTTTATGTTTTTAAAAAGACTTTATAAATTTTT-AAAAA
1 TTTTATGTTTTTAAAAAGACTTTAT-AATTTTTGAAAAA
3631863 TTT
1 TTT
3631866 CTACATGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 28 0.80
39 7 0.20
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.56
Consensus pattern (38 bp):
TTTTATGTTTTTAAAAAGACTTTATAATTTTTGAAAAA
Found at i:3632167 original size:22 final size:20
Alignment explanation
Indices: 3632111--3632170 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
3632101 AAATTTTCAA
*
3632111 AAAATTAAAAACTAAAAGTT
1 AAAATTAAAAAATAAAAGTT
**
3632131 AAATATTAACTAATAAAATGTT
1 AAA-ATTAAAAAATAAAA-GTT
3632153 AAAATTGAAAAAATAAAA
1 AAAATT-AAAAAATAAAA
3632171 AGAACTATCA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 3 0.09
21 14 0.44
22 15 0.47
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (20 bp):
AAAATTAAAAAATAAAAGTT
Found at i:3632408 original size:23 final size:24
Alignment explanation
Indices: 3632349--3632425 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 24
3632339 AAAAAATTTA
* **
3632349 AAAATATTGAATATCTCTAAAAATTT
1 AAAATATTG-ATAT-TTTAAAAAAGT
* *
3632375 TAAATATTGATTTTTTAAAGAAA-T
1 AAAATATTGATATTTTAAA-AAAGT
3632399 AAAATA-TGATATTTTAAAAAAGT
1 AAAATATTGATATTTTAAAAAAGT
3632422 AAAA
1 AAAA
3632426 AATATTATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
22 3 0.07
23 16 0.37
24 11 0.26
25 5 0.12
26 8 0.19
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (24 bp):
AAAATATTGATATTTTAAAAAAGT
Found at i:3632434 original size:23 final size:23
Alignment explanation
Indices: 3632382--3632436 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
3632372 TTTTAAATAT
* *
3632382 TGATTTTTTAAAGAAATAAAATA
1 TGATATTTTAAAGAAATAAAAAA
3632405 TGATATTTTAAA-AAAGTAAAAAA
1 TGATATTTTAAAGAAA-TAAAAAA
3632428 T-ATTATTTT
1 TGA-TATTTT
3632437 TATTTGTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (23 bp):
TGATATTTTAAAGAAATAAAAAA
Done.