Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold319
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: 718924
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 5
Found at i:291451 original size:32 final size:33
Alignment explanation
Indices: 291391--291454 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
291381 TACAAGCCAA
** *
291391 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
291424 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
291455 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:293543 original size:20 final size:21
Alignment explanation
Indices: 293504--293546 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
293494 GACTAGTGTG
*
293504 GGGACTGCCTGGTTGCGACCT
1 GGGACTGCCTGGTCGCGACCT
*
293525 GGGAGTGCC-GGTCGCGACCT
1 GGGACTGCCTGGTCGCGACCT
293545 GG
1 GG
293547 TGGTGCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (21 bp):
GGGACTGCCTGGTCGCGACCT
Found at i:296092 original size:15 final size:15
Alignment explanation
Indices: 296072--296102 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
296062 ATTTCGTTTG
*
296072 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
296087 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
296102 G
1 G
296103 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:297934 original size:21 final size:21
Alignment explanation
Indices: 297905--297949 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
297895 AAGTTTTCAT
*
297905 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
297925 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
297947 TTT
1 TTT
297950 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:300191 original size:13 final size:13
Alignment explanation
Indices: 300173--300198 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
300163 CAATTTTTTG
300173 TGTATCGATACAT
1 TGTATCGATACAT
300186 TGTATCGATACAT
1 TGTATCGATACAT
300199 ACTTGGTGTA
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):
TGTATCGATACAT
Found at i:300213 original size:32 final size:33
Alignment explanation
Indices: 300153--300216 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
300143 TACAAGCCAA
** *
300153 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
300186 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
300217 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:301826 original size:57 final size:57
Alignment explanation
Indices: 301733--301851 Score: 220
Period size: 57 Copynumber: 2.1 Consensus size: 57
301723 GATCTTTGTC
*
301733 CTTCTTGCTCGATTCTCCTTTTACCATGGCTTTTCTTTGAAGCCTTCTCAATTTCAT
1 CTTCATGCTCGATTCTCCTTTTACCATGGCTTTTCTTTGAAGCCTTCTCAATTTCAT
*
301790 CTTCATGCTCGATTCTCCTTTTACCATGGCTTTTCTTTGAAGCCTTCTCGATTTCAT
1 CTTCATGCTCGATTCTCCTTTTACCATGGCTTTTCTTTGAAGCCTTCTCAATTTCAT
301847 CTTCA
1 CTTCA
301852 AGAACTTGTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.14, C:0.29, G:0.11, T:0.46
Consensus pattern (57 bp):
CTTCATGCTCGATTCTCCTTTTACCATGGCTTTTCTTTGAAGCCTTCTCAATTTCAT
Found at i:304281 original size:13 final size:13
Alignment explanation
Indices: 304263--304288 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
304253 CAATTTTTTG
304263 TGTATCGATACAT
1 TGTATCGATACAT
304276 TGTATCGATACAT
1 TGTATCGATACAT
304289 ACTTGGTGTA
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):
TGTATCGATACAT
Found at i:304303 original size:32 final size:33
Alignment explanation
Indices: 304243--304306 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
304233 TACAAGCCAA
** *
304243 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
304276 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
304307 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:308033 original size:19 final size:19
Alignment explanation
Indices: 308006--308101 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
307996 AGCTATACAT
308006 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
308025 TGCATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
308038 TGTATTGATACAACACTTA
1 TGTATCGATACAACACTTA
**
308057 TGCGTCGAT---ACA--T-
1 TGTATCGATACAACACTTA
308070 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
308089 TGTATCGATACAA
1 TGTATCGATACAA
308102 TTTCTGTTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 24
0.64 0.09 0.27
Matches are distributed among these distances:
13 14 0.25
14 2 0.04
16 12 0.21
18 2 0.04
19 27 0.47
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:308041 original size:32 final size:32
Alignment explanation
Indices: 308000--308100 Score: 175
Period size: 32 Copynumber: 3.2 Consensus size: 32
307990 CTTCGTAGCT
308000 ATACATTGTATCGATACAACACTTATGCATCG
1 ATACATTGTATCGATACAACACTTATGCATCG
* *
308032 ATACATTGTATTGATACAACACTTATGCGTCG
1 ATACATTGTATCGATACAACACTTATGCATCG
*
308064 ATACATTGTATCGATACAACACTTATGTATCG
1 ATACATTGTATCGATACAACACTTATGCATCG
308096 ATACA
1 ATACA
308101 ATTTCTGTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (32 bp):
ATACATTGTATCGATACAACACTTATGCATCG
Found at i:308907 original size:52 final size:51
Alignment explanation
Indices: 308771--309951 Score: 753
Period size: 52 Copynumber: 24.8 Consensus size: 51
308761 GTGATAAAGG
* * * *
308771 TGCCAATATGCTGATTC-AGGACCAGTGATATTGGGCTTAAAGATGAGAAAAAGGA
1 TGCCAATGTGCTGATTCAAGG-CCAGCGACATTGGACTTAAAGATGAG---AA-GA
* * * * * *
308826 TGTCAATGTACTGATTCACGGTCAGCGACATTAGACTTGAAGATGAGAAGAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAG-A
* **
308878 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGGTTTTAAAGATGACGAAGA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGATGA-GAAGA
* * * * *
308931 CGTCAATATGCTGATTCAAGGCCAGCGATATTGGATTTAAAGAT--GAAGA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
* * *
308980 TGCTAATGTGCTGATTC-AGGACCAGTGACATTGGACTTAAAGATGATGAAGG
1 TGCCAATGTGCTGATTCAAGG-CCAGCGACATTGGACTTAAAGATGA-GAAGA
* * *
309032 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--GAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
* * *
309081 TGCCAACGTGCTGATTC-AGGACCAGTGACATTGGACTTAAAGATGACGAAGG
1 TGCCAATGTGCTGATTCAAGG-CCAGCGACATTGGACTTAAAGATGA-GAAGA
* *
309133 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--GAAGA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
* *
309182 TGCCAATGTGCTGATTCAAGACCAGCGACATTGGGC-T-----T------A
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
* * * *
309221 TGCCAATGTGTTGATTTAAGGCCAACGACATTGGTCTTAAAGAT--GAAG-
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
* * **
309269 TGCCAATATGCTGATTCAAGGCCAGCGATACCGGACTTAAAGATGAG--GA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
*
309318 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGC-T-----T------A
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
* * * * * *
309357 TGCCAATATGTTGATTCAAGGCCAACGACATTGGTCTT-AA-A-GACAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
* * *
309405 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T------A
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
*
309444 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT---GA--AG--G-
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
* *
309487 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACAA-A
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
* * * *
309537 GGCACCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT--A-A--AG--G-
1 TG--CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
* * *
309582 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AA-A-GACAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
* *
309630 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-A--AG--G-
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
* * * * *
309673 TGCCAATGTGCTGATTCAAGGCTAGGGACATTGGTCTTAAAGATGACAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-GAAGA
* * * *
309725 CGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTT--A-A--AG--G-
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
* * *
309768 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AA-A-GACAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
* * * *
309816 TGCCAATATGCTGATTCAAGGCCAACTATATTGGACTT--A-A--AG--G-
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
* * * *
309859 TGCCAATGTGCTGATTGAAGGCCAGCGACATTGGTCTTAAAGATGACAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-GAAGA
* * * *
309911 CGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAA
309952 AGAAGATGCC
Statistics
Matches: 907, Mismatches: 136, Indels: 169
0.75 0.11 0.14
Matches are distributed among these distances:
39 99 0.11
40 3 0.00
43 169 0.19
44 7 0.01
45 6 0.01
46 6 0.01
47 9 0.01
48 148 0.16
49 148 0.16
50 4 0.00
51 3 0.00
52 221 0.24
53 44 0.05
54 4 0.00
55 34 0.04
56 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (51 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGA
Found at i:309046 original size:101 final size:101
Alignment explanation
Indices: 308771--309671 Score: 586
Period size: 101 Copynumber: 9.4 Consensus size: 101
308761 GTGATAAAGG
* * * * *
308771 TGCCAATATGCTGATTCAGGACCAGTGATATTGGGCTTAAAGATGA-GAAAAAGGATGTCAATGT
1 TGCCAATGTGCTGATTCAGGACCAGTGACATTGGACTTAAAGATGACG---AAGG-TGCCAATAT
* * * * * *
308835 ACTGATTCACGGTCAGCGACATTAGACTTGAAGATGAGAAGAA
62 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--GAAG-A
** ** ** *
308878 TGCCAATGTGCTGATTCAAGG-CCAACGACATTGGGTTTTAAAGATGACGAAGACGTCAATATGC
1 TGCCAATGTGCTGATTC-AGGACCAGTGACATT-GGACTTAAAGATGACGAAGGTGCCAATATGC
*
308942 TGATTCAAGGCCAGCGATATTGGATTTAAAGATGAAGA
64 TGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGA
* *
308980 TGCTAATGTGCTGATTCAGGACCAGTGACATTGGACTTAAAGATGATGAAGGTGCCAATATGCTG
1 TGCCAATGTGCTGATTCAGGACCAGTGACATTGGACTTAAAGATGACGAAGGTGCCAATATGCTG
*
309045 ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
66 ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGA
*
309081 TGCCAACGTGCTGATTCAGGACCAGTGACATTGGACTTAAAGATGACGAAGGTGCCAATATGCTG
1 TGCCAATGTGCTGATTCAGGACCAGTGACATTGGACTTAAAGATGACGAAGGTGCCAATATGCTG
309146 ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGA
66 ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGA
* * * * *
309182 TGCCAATGTGCTGATTCAAGACCAGCGACATTGGGC-T-----T-----A--TGCCAATGTGTTG
1 TGCCAATGTGCTGATTCAGGACCAGTGACATTGGACTTAAAGATGACGAAGGTGCCAATATGCTG
* * * *
309234 ATTTAAGGCCAACGACATTGGTCTTAAAGATGAAG-
66 ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGA
* * * ** * *
309269 TGCCAATATGCTGATTCAAGG-CCAGCGATACCGGACTTAAAGATGA-G--GATGCCAATGTGCT
1 TGCCAATGTGCTGATTC-AGGACCAGTGACATTGGACTTAAAGATGACGAAGGTGCCAATATGCT
* *
309330 GATTCAAGGCCAGCGACATTGGGC-T-----T----A
65 GATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGA
* * ** *
309357 TGCCAATATGTTGATTCAAGG-CCAACGACATTGGTCTT-AA-A-GAC-AAGGTGCCAATATGCT
1 TGCCAATGTGCTGATTC-AGGACCAGTGACATTGGACTTAAAGATGACGAAGGTGCCAATATGCT
*
309417 GATTCAAGGCCAGCGATATTGGGC-T-----T----A
65 GATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGA
* * *
309444 TGCCAATGTGCTGATTCAAGG-CCAGCGATATTGGAC-T-----T---GAAGGTGCCAATGTGCT
1 TGCCAATGTGCTGATTC-AGGACCAGTGACATTGGACTTAAAGATGACGAAGGTGCCAATATGCT
* * *
309499 GATTCAAGGCCAGCGACATTGGTCTTAAAGATGACAAA
65 GATTCAAGGCCAGCGATATTGGACTTAAAGATGA-AGA
* * * * * *
309537 GGCACCAATATGCTGATTCAAGG-CCAGCGATATTGGGC-T-----T-A--AAGGTGCCAATGTG
1 TG--CCAATGTGCTGATTC-AGGACCAGTGACATTGGACTTAAAGATGACGAAGGTGCCAATATG
* * * *
309592 CTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGG
63 CTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGA
* * *
309630 TGCCAATATGCTGATTCAAGG-CCAGCGATATTGGACTTAAAG
1 TGCCAATGTGCTGATTC-AGGACCAGTGACATTGGACTTAAAG
309672 GTGCCAATGT
Statistics
Matches: 677, Mismatches: 76, Indels: 93
0.80 0.09 0.11
Matches are distributed among these distances:
82 37 0.05
83 1 0.00
85 2 0.00
86 2 0.00
87 98 0.14
88 78 0.12
90 1 0.00
91 34 0.05
92 1 0.00
93 5 0.01
94 1 0.00
95 82 0.12
96 1 0.00
97 32 0.05
100 1 0.00
101 193 0.29
102 26 0.04
103 4 0.01
105 35 0.05
106 3 0.00
107 24 0.04
108 15 0.02
109 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (101 bp):
TGCCAATGTGCTGATTCAGGACCAGTGACATTGGACTTAAAGATGACGAAGGTGCCAATATGCTG
ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGA
Found at i:309236 original size:39 final size:39
Alignment explanation
Indices: 309181--309259 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
309171 AAAGATGAAG
*
309181 ATGCCAATGTGCTGATTCAAGACCAGCGACATTGGGCTT
1 ATGCCAATGTGCTGATTCAAGACCAACGACATTGGGCTT
* * * *
309220 ATGCCAATGTGTTGATTTAAGGCCAACGACATTGGTCTT
1 ATGCCAATGTGCTGATTCAAGACCAACGACATTGGGCTT
309259 A
1 A
309260 AAGATGAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (39 bp):
ATGCCAATGTGCTGATTCAAGACCAACGACATTGGGCTT
Found at i:309372 original size:39 final size:39
Alignment explanation
Indices: 309317--309525 Score: 220
Period size: 39 Copynumber: 5.0 Consensus size: 39
309307 AAAGATGAGG
309317 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTT
* * * *
309356 ATGCCAATATGTTGATTCAAGGCCAACGACATTGGTCTT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTT
* *
309395 AAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
1 -------A--TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTT
* *
309443 ATGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTT
*
309482 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
1 --A--TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTT
309525 A
1 A
309526 AAGATGACAA
Statistics
Matches: 145, Mismatches: 12, Indels: 24
0.80 0.07 0.13
Matches are distributed among these distances:
39 71 0.49
41 3 0.02
43 36 0.25
46 1 0.01
48 34 0.23
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (39 bp):
ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTT
Found at i:309438 original size:87 final size:86
Alignment explanation
Indices: 309269--309525 Score: 360
Period size: 87 Copynumber: 3.0 Consensus size: 86
309259 AAAGATGAAG
** *
309269 TGCCAATATGCTGATTCAAGGCCAGCGATACCGGACTTAAAGATGAGGATGCCAATGTGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA-AAGG-TGCCAATGTGCTGATT
309334 CAAGGCCAGCGACATTGGGCTTA
64 CAAGGCCAGCGACATTGGGCTTA
* * * * *
309357 TGCCAATATGTTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA-AAGGTGCCAATGTGCTGATTC
*
309422 AAGGCCAGCGATATTGGGCTTA
65 AAGGCCAGCGACATTGGGCTTA
*
309444 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT---G-AAGGTGCCAATGTGCTGATTCA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAAGGTGCCAATGTGCTGATTCA
*
309505 AGGCCAGCGACATTGGTCTTA
66 AGGCCAGCGACATTGGGCTTA
309526 AAGATGACAA
Statistics
Matches: 151, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
82 40 0.26
84 1 0.01
87 70 0.46
88 40 0.26
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (86 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAAGGTGCCAATGTGCTGATTCA
AGGCCAGCGACATTGGGCTTA
Found at i:309505 original size:43 final size:43
Alignment explanation
Indices: 309128--309892 Score: 555
Period size: 43 Copynumber: 16.9 Consensus size: 43
309118 TAAAGATGAC
* *
309128 GAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT
1 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC-T-----T
* * *
309177 GAAGATGCCAATGTGCTGATTCAAGACCAGCGACATTGGGCTT
1 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* * * *
309220 --A--TGCCAATGTGTTGATTTAAGGCCAACGACATTGGTCTT
1 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* * * **
309259 AAAGATGAAGTGCCAATATGCTGATTCAAGGCCAGCGATACCGGACTT
1 ---GA--AGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
*
309307 AAAGATGAGGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTT
1 ---GA--AGG-TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* * * *
309356 --A--TGCCAATATGTTGATTCAAGGCCAACGACATTGGTCTT
1 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* * *
309395 AAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
1 ---G--AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
*
309443 --A--TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT
1 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
*
309482 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT
1 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC-T-----T
** * * *
309531 GACAAAGGCACCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
1 G---AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* *
309577 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
1 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* *
309620 AAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ---G--AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* * * *
309668 AAAGGTGCCAATGTGCTGATTCAAGGCTAGGGACATTGGTCTTAAAGAT
1 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC-T-----T
* * * *
309717 GACAAAGGCGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTT
1 G---AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* *
309763 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
1 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* * * *
309806 AAAGACAAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGACTT
1 ---G--AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
* *
309854 AAAGGTGCCAATGTGCTGATTGAAGGCCAGCGACATTGG
1 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
309893 TCTTAAAGAT
Statistics
Matches: 582, Mismatches: 83, Indels: 108
0.75 0.11 0.14
Matches are distributed among these distances:
39 103 0.18
41 3 0.01
42 1 0.00
43 177 0.30
44 2 0.00
46 4 0.01
48 150 0.26
49 72 0.12
51 2 0.00
52 68 0.12
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (43 bp):
GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
Found at i:309609 original size:95 final size:95
Alignment explanation
Indices: 309445--309951 Score: 841
Period size: 95 Copynumber: 5.4 Consensus size: 95
309435 TTGGGCTTAT
* *
309445 GCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTGAAGGTGCCAATGTGCTGATTCAAGGCC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCC
309510 AGCGACATTGGTCTTAAAGATGACAAAGGC
66 AGCGACATTGGTCTTAAAGATGACAAAGGC
* *
309540 ACCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGGTGCCAATGTGCTGATTCAAGGCC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCC
*
309605 AGCGACATTGGTCTT-AA-A-GAC-AAGGT
66 AGCGACATTGGTCTTAAAGATGACAAAGGC
*
309631 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCC
*
309696 AGGGACATTGGTCTTAAAGATGACAAAGGC
66 AGCGACATTGGTCTTAAAGATGACAAAGGC
*
309726 GCCAATATGCTAATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCC
*
309791 AGCGACATTGGTCTT-AA-A-GAC-AAGGT
66 AGCGACATTGGTCTTAAAGATGACAAAGGC
* * *
309817 GCCAATATGCTGATTCAAGGCCAACTATATTGGACTTAAAGGTGCCAATGTGCTGATTGAAGGCC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCC
309882 AGCGACATTGGTCTTAAAGATGACAAAGGC
66 AGCGACATTGGTCTTAAAGATGACAAAGGC
*
309912 GCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAA
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
309952 AGAAGATGCC
Statistics
Matches: 382, Mismatches: 22, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
91 160 0.42
92 10 0.03
93 4 0.01
94 10 0.03
95 198 0.52
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.24
Consensus pattern (95 bp):
GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCC
AGCGACATTGGTCTTAAAGATGACAAAGGC
Found at i:309675 original size:186 final size:185
Alignment explanation
Indices: 309444--309951 Score: 899
Period size: 186 Copynumber: 2.7 Consensus size: 185
309434 ATTGGGCTTA
* *
309444 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTGAAGGTGCCAATGTGCTGATTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGC
*
309509 CAGCGACATTGGTCTTAAAGATGACAAAGGCACCAATATGCTGATTCAAGGCCAGCGATATTGGG
66 CAGCGACATTGGTCTTAAAGATGACAAAGGC-CCAATATGCTGATTCAAGGCCAGCGATATTGGA
309574 CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGG
130 CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGG
309630 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGC
* * *
309695 TAGGGACATTGGTCTTAAAGATGACAAAGGCGCCAATATGCTAATTCAAGGCCAGCGATATTGGA
66 CAGCGACATTGGTCTTAAAGATGACAAAGGC-CCAATATGCTGATTCAAGGCCAGCGATATTGGA
309760 CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGG
130 CTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGG
* * *
309816 TGCCAATATGCTGATTCAAGGCCAACTATATTGGACTTAAAGGTGCCAATGTGCTGATTGAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGC
*
309881 CAGCGACATTGGTCTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCTAGCGATATTGGA
66 CAGCGACATTGGTCTTAAAGATGACAAAGGC-CCAATATGCTGATTCAAGGCCAGCGATATTGGA
309946 CTTAAA
130 CTTAAA
309952 AGAAGATGCC
Statistics
Matches: 308, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
186 308 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.24
Consensus pattern (185 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGC
CAGCGACATTGGTCTTAAAGATGACAAAGGCCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGG
Found at i:310060 original size:27 final size:27
Alignment explanation
Indices: 310024--310077 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
310014 AGGAGAAAGA
*
310024 TGCCATGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
310051 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
310078 AAAAAGAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.13, G:0.37, T:0.24
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:310090 original size:35 final size:34
Alignment explanation
Indices: 310044--310264 Score: 221
Period size: 35 Copynumber: 6.7 Consensus size: 34
310034 TTGTGGACTT
*
310044 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAA-GGA
*
310079 AAAAGAGTGCCACGGAGTTGTGGACTTTAAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGA
* * * * *
310114 AAAATAATGCCACGGAGGTGTGGGCTTTAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* *
310148 AAAAGA-TGCCATGGAGTTATGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
*
310181 AAAAG-GTGCCACAGAGTTGTGGACTTTAAAA-G-
1 AAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGA
*
310213 ----GA-TGCCACGGAGTTGTGGGCTTTGAAAA-GA
1 AAAAGAGTGCCACGGAGTTGTGGAC-TT-AAAAGGA
310243 AAAAG-GTGCCACGGAGTTGTGG
1 AAAAGAGTGCCACGGAGTTGTGG
310265 GCTTTGAAGA
Statistics
Matches: 156, Mismatches: 19, Indels: 23
0.79 0.10 0.12
Matches are distributed among these distances:
28 20 0.13
29 5 0.03
33 43 0.28
34 35 0.22
35 47 0.30
36 6 0.04
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (34 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:310179 original size:33 final size:33
Alignment explanation
Indices: 310051--310299 Score: 219
Period size: 33 Copynumber: 7.6 Consensus size: 33
310041 CTTAAAAGGG
310051 TGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAA-GGAAAAAGA
* *
310085 GTGCCACGGAGTTGTGGACTTTAAAAAGAAAAATAA
1 -TGCCACGGAGTTGTGGAC-TTAAAAGGAAAAA-GA
* * *
310121 TGCCACGGAGGTGTGGGCTTTAAAGGAAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
* * *
310154 TGCCATGGAGTTATGGACTTAAAAGGAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
*
310187 TGCCACAGAGTTGTGGACTTTAAAA-G-----GA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAGA
* *
310215 TGCCACGGAGTTGTGGGCTTTGAAAA-GAAAAAGG
1 TGCCACGGAGTTGTGGAC-TT-AAAAGGAAAAAGA
* **
310249 TGCCACGGAGTTGTGGGCTTTGAA-GAAAAA-A
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
** *
310280 TGCCACTAAGTCGTGGACTT
1 TGCCACGGAGTTGTGGACTT
310300 TGAAAAAAGA
Statistics
Matches: 178, Mismatches: 27, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
28 20 0.11
29 5 0.03
31 16 0.09
32 8 0.04
33 46 0.26
34 36 0.20
35 40 0.22
36 7 0.04
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.22
Consensus pattern (33 bp):
TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
Found at i:310220 original size:28 final size:28
Alignment explanation
Indices: 310181--310241 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
310171 CTTAAAAGGA
310181 AAAAGGTGCCACAGAGTTGTGGACTTT-
1 AAAAGGTGCCACAGAGTTGTGGACTTTG
* *
310208 AAAAGGATGCCACGGAGTTGTGGGCTTTG
1 AAAAGG-TGCCACAGAGTTGTGGACTTTG
310237 AAAAG
1 AAAAG
310242 AAAAAGGTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 6 0.20
28 19 0.63
29 5 0.17
ACGTcount: A:0.31, C:0.13, G:0.33, T:0.23
Consensus pattern (28 bp):
AAAAGGTGCCACAGAGTTGTGGACTTTG
Found at i:310254 original size:34 final size:34
Alignment explanation
Indices: 310208--310305 Score: 121
Period size: 34 Copynumber: 2.9 Consensus size: 34
310198 TGTGGACTTT
310208 AAAAGGATGCCACGGAGTTGTGGGCTTTGAAAAGA
1 AAAAGG-TGCCACGGAGTTGTGGGCTTTGAAAAGA
310243 AAAAGGTGCCACGGAGTTGTGGGCTTTG--AAGA
1 AAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGA
* ** * *
310275 AAAA-ATGCCACTAAGTCGTGGACTTTGAAAA
1 AAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
310306 AAGATTGCCA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
31 18 0.32
32 8 0.14
33 2 0.04
34 22 0.39
35 6 0.11
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.21
Consensus pattern (34 bp):
AAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGA
Found at i:310301 original size:31 final size:32
Alignment explanation
Indices: 310261--310336 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 32
310251 CCACGGAGTT
*
310261 GTGGGCTTTGAAGAAAA-AATGCCACTAAGTC
1 GTGGACTTTGAAGAAAAGAATGCCACTAAGTC
* *
310292 GTGGACTTTGAA-AAAAGATTGCCACTGAGTC
1 GTGGACTTTGAAGAAAAGAATGCCACTAAGTC
310323 GTGGACTTT-AAGAA
1 GTGGACTTTGAAGAA
310337 GGTATTTGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
30 6 0.15
31 34 0.85
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.25
Consensus pattern (32 bp):
GTGGACTTTGAAGAAAAGAATGCCACTAAGTC
Found at i:311648 original size:13 final size:13
Alignment explanation
Indices: 311623--311655 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
311613 GCCTTTGCAC
311623 TTTTTTG-TGTGT
1 TTTTTTGTTGTGT
*
311635 TTTTTTGTTTTGT
1 TTTTTTGTTGTGT
311648 TTTTTTGT
1 TTTTTTGT
311656 GTTTACTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (13 bp):
TTTTTTGTTGTGT
Found at i:318688 original size:13 final size:13
Alignment explanation
Indices: 318670--318696 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
318660 GCAAAGATCA
318670 AATGTATCGATAC
1 AATGTATCGATAC
318683 AATGTATCGATAC
1 AATGTATCGATAC
318696 A
1 A
318697 TTGAGTAATG
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):
AATGTATCGATAC
Found at i:318772 original size:19 final size:19
Alignment explanation
Indices: 318748--318842 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
318738 AGCGATACAT
318748 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
318767 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
318780 TGTAT-GATACAACACTTA
1 TGTATCGATACAACACTTA
* *
318798 TGCAACGAT---ACA--T-
1 TGTATCGATACAACACTTA
318811 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
318830 TGTATCGATACAA
1 TGTATCGATACAA
318843 TTTCTGTTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 26
0.66 0.04 0.29
Matches are distributed among these distances:
12 3 0.05
13 12 0.20
14 2 0.03
15 3 0.05
16 9 0.15
17 1 0.02
18 4 0.07
19 25 0.42
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:318781 original size:32 final size:32
Alignment explanation
Indices: 318740--318841 Score: 179
Period size: 32 Copynumber: 3.2 Consensus size: 32
318730 AGCTTCGTAG
318740 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
* *
318772 CGATACATTGTAT-GATACAACACTTATGCAA
1 CGATACATTGTATCGATACAACACTTATGTAT
318803 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
318835 CGATACA
1 CGATACA
318842 ATTTCTGTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
31 29 0.45
32 36 0.55
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:320004 original size:67 final size:69
Alignment explanation
Indices: 319933--320080 Score: 176
Period size: 67 Copynumber: 2.2 Consensus size: 69
319923 TACGTTCATT
** * *
319933 ATTTTTAGAGTCTTTTAAAGACGTCAATAACTTTCATGTCAAAGGCATA-TTTAG-GGGTATGCT
1 ATTTTTAGAGTCTTTTAAAGACACCAAGAACTTTCATGTCAAAGACATACTTTAGAGGGTATG-T
319996 T-ATC
65 TGATC
* * * *
320000 ATTTTTAAAGTCTTTTAAAGTCACCGAGAACTTTTATGTCAAAGACATACTTTAGAGGGTATGTT
1 ATTTTTAGAGTCTTTTAAAGACACCAAGAACTTTCATGTCAAAGACATACTTTAGAGGGTATGTT
*
320065 GGTC
66 GATC
*
320069 ATCTTTAGAGTC
1 ATTTTTAGAGTC
320081 CGTTAAGGTC
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
67 41 0.61
68 7 0.10
69 19 0.28
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (69 bp):
ATTTTTAGAGTCTTTTAAAGACACCAAGAACTTTCATGTCAAAGACATACTTTAGAGGGTATGTT
GATC
Found at i:320100 original size:69 final size:67
Alignment explanation
Indices: 319961--320104 Score: 164
Period size: 69 Copynumber: 2.1 Consensus size: 67
319951 AGACGTCAAT
* * ** *
319961 AACTTTCATGTCAAAGGCATATTTAGGGGTATGCTTATCATTTTTAAAGTCTTTTAAAGTCACCG
1 AACTTTCATGTCAAAGACATATTTAGGGGTATGCTTATCATCTTTAAAGTCCGTTAAAGTCAACG
320026 AG
66 AG
* * * *
320028 AACTTTTATGTCAAAGACATACTTTAGAGGGTATG-TTGGTCATCTTTAGAGTCCGTTAAGGTCA
1 AACTTTCATGTCAAAGACATA-TTTAG-GGGTATGCTT-ATCATCTTTAAAGTCCGTTAAAGTCA
*
320092 AGGAG
63 ACGAG
320097 AACTTTCA
1 AACTTTCA
320105 CATAGAACAT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
67 19 0.30
68 7 0.11
69 37 0.59
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (67 bp):
AACTTTCATGTCAAAGACATATTTAGGGGTATGCTTATCATCTTTAAAGTCCGTTAAAGTCAACG
AG
Found at i:322773 original size:12 final size:12
Alignment explanation
Indices: 322756--322781 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
322746 GTATCGATAC
322756 ATAGGTATTTGT
1 ATAGGTATTTGT
322768 ATAGGTATTTGT
1 ATAGGTATTTGT
322780 AT
1 AT
322782 CGATACATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (12 bp):
ATAGGTATTTGT
Found at i:323020 original size:20 final size:20
Alignment explanation
Indices: 322991--323028 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
322981 GTATGTATCG
*
322991 ATAAATTGTATCGATACACC
1 ATAAAATGTATCGATACACC
323011 ATAAAATGTATCGATACA
1 ATAAAATGTATCGATACA
323029 TTGGCTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.29
Consensus pattern (20 bp):
ATAAAATGTATCGATACACC
Found at i:329397 original size:22 final size:21
Alignment explanation
Indices: 329354--329394 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
329344 CAAATTTCTT
329354 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAATACATC
329376 GTTTTTCA-TCAAAAT-CATC
1 GTTTTTCACTCAAAATACATC
329395 ATCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (21 bp):
GTTTTTCACTCAAAATACATC
Found at i:331096 original size:22 final size:21
Alignment explanation
Indices: 331075--331114 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
331065 AGTGTTAAAT
*
331075 TATTTTACTAAGGGGGAGAAA
1 TATTTGACTAAGGGGGAGAAA
* *
331096 TGTTTGATTAAGGGGGAGA
1 TATTTGACTAAGGGGGAGA
331115 GAAAAGAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.35, T:0.30
Consensus pattern (21 bp):
TATTTGACTAAGGGGGAGAAA
Found at i:331705 original size:20 final size:20
Alignment explanation
Indices: 331680--331733 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
331670 GTATCGATAC
**
331680 AATGTATCGATACATGACTA
1 AATGTATCGATACATGAAAA
*
331700 AATGTATCGATACTTGAAAA
1 AATGTATCGATACATGAAAA
331720 AATGTATCGATACA
1 AATGTATCGATACA
331734 AGTCATTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATGAAAA
Found at i:334632 original size:51 final size:51
Alignment explanation
Indices: 334469--334618 Score: 255
Period size: 51 Copynumber: 2.9 Consensus size: 51
334459 TTTAAAAATT
* *
334469 AAAATATCTTTCGTACCTATCTAGAAGACCAGAAGAACACGAAAGCTTATC
1 AAAATATCTTTCGTACCTATCTGGAAGACCAAAAGAACACGAAAGCTTATC
* * *
334520 AAAATATCTTTCATGCCTATCTGGAAGACTAAAAGAACACGAAAGCTTATC
1 AAAATATCTTTCGTACCTATCTGGAAGACCAAAAGAACACGAAAGCTTATC
334571 AAAATATCTTTCGTACCTATCTGGAAGACCAAAAGAACACGAAAGCTT
1 AAAATATCTTTCGTACCTATCTGGAAGACCAAAAGAACACGAAAGCTT
334619 CTTTATCATT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 91 1.00
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (51 bp):
AAAATATCTTTCGTACCTATCTGGAAGACCAAAAGAACACGAAAGCTTATC
Found at i:338386 original size:13 final size:13
Alignment explanation
Indices: 338368--338392 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
338358 CAAAGATCAG
338368 TGTATCGATACAA
1 TGTATCGATACAA
338381 TGTATCGATACA
1 TGTATCGATACA
338393 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:338471 original size:32 final size:32
Alignment explanation
Indices: 338430--338495 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
338420 GGCAGTAGCT
338430 TATATTGTATCGATACAAAACTTATGTATCGA
1 TATATTGTATCGATACAAAACTTATGTATCGA
* *
338462 TATATTGTATCGATGCAACACTTATGTATCGA
1 TATATTGTATCGATACAAAACTTATGTATCGA
338494 TA
1 TA
338496 CAACACTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (32 bp):
TATATTGTATCGATACAAAACTTATGTATCGA
Found at i:338508 original size:20 final size:19
Alignment explanation
Indices: 338435--338518 Score: 81
Period size: 19 Copynumber: 4.7 Consensus size: 19
338425 TAGCTTATAT
*
338435 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
*
338454 TGTATCGAT---ATA--T-
1 TGTATCGATACAACACTTA
*
338467 TGTATCGATGCAACACTTA
1 TGTATCGATACAACACTTA
338486 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
*
338506 TGTATCGCTACAA
1 TGTATCGATACAA
338519 ATCGTTGAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
13 9 0.17
14 1 0.02
16 4 0.07
18 1 0.02
19 24 0.44
20 15 0.28
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:339722 original size:19 final size:20
Alignment explanation
Indices: 339698--339748 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
339688 TTATGCTTTG
**
339698 TATCGATACATGTTC-ATTA
1 TATCGATACATGGACAATTA
*
339717 TATCGATACATGGACAATTG
1 TATCGATACATGGACAATTA
339737 TATCGATACATG
1 TATCGATACATG
339749 AAATTTGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TATCGATACATGGACAATTA
Found at i:339742 original size:20 final size:19
Alignment explanation
Indices: 339695--339748 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
339685 ACATTATGCT
**
339695 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGGACA
*
339714 TTATATCGATACATGGACAA
1 TTGTATCGATACATGGAC-A
339734 TTGTATCGATACATG
1 TTGTATCGATACATG
339749 AAATTTGCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATGGACA
Found at i:340133 original size:20 final size:20
Alignment explanation
Indices: 340108--340176 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
340098 CTGTCAAGGA
340108 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
340128 AATGTATCGATAC---A-T-
1 AATGTATCGATACATTATTC
340143 --TGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
340161 AATGTATCGATACATT
1 AATGTATCGATACATT
340177 GTATCGATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.26
16 2 0.05
17 2 0.05
20 27 0.64
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTATTC
Found at i:340148 original size:13 final size:13
Alignment explanation
Indices: 340130--340190 Score: 71
Period size: 13 Copynumber: 5.2 Consensus size: 13
340120 CATTATTCAA
340130 TGTATCGATACAT
1 TGTATCGATACAT
340143 TGTATCGATACA-
1 TGTATCGATACAT
*
340155 T-TAT---T-CAA
1 TGTATCGATACAT
340163 TGTATCGATACAT
1 TGTATCGATACAT
340176 TGTATCGATACAT
1 TGTATCGATACAT
340189 TG
1 TG
340191 ATCTTTGTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
7 2 0.05
8 2 0.05
9 3 0.07
11 3 0.07
12 2 0.05
13 29 0.71
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:340152 original size:33 final size:33
Alignment explanation
Indices: 340110--340208 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
340100 GTCAAGGAAA
340110 TGTATCGATACATTATTCAATGTATCGATACAT
1 TGTATCGATACATTATTCAATGTATCGATACAT
340143 TGTATCGATACATTATTCAATGTATCGATACAT
1 TGTATCGATACATTATTCAATGTATCGATACAT
**
340176 TGTATCGATACATTGA-TCTTTGTATCGATACAT
1 TGTATCGATACATT-ATTCAATGTATCGATACAT
340209 CAAGGAATTT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
33 62 0.98
34 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATTATTCAATGTATCGATACAT
Found at i:341887 original size:25 final size:25
Alignment explanation
Indices: 341856--341906 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
341846 ATCATATGCT
341856 TTTATCGCCTTATCAGTATGCTTCC
1 TTTATCGCCTTATCAGTATGCTTCC
341881 TTTATCGCCTTATCAGTATGCTTCC
1 TTTATCGCCTTATCAGTATGCTTCC
341906 T
1 T
341907 CCTTATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.27, G:0.12, T:0.45
Consensus pattern (25 bp):
TTTATCGCCTTATCAGTATGCTTCC
Found at i:354385 original size:37 final size:37
Alignment explanation
Indices: 354344--354428 Score: 170
Period size: 37 Copynumber: 2.3 Consensus size: 37
354334 TGCCACAATC
354344 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
354381 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
354418 ATGCATTTGTG
1 ATGCATTTGTG
354429 CTTCATCTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (37 bp):
ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
Found at i:354850 original size:28 final size:28
Alignment explanation
Indices: 354793--355081 Score: 313
Period size: 28 Copynumber: 10.4 Consensus size: 28
354783 CTCACTTTCC
* * *
354793 AAAGCCCACAAGTAAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
354822 AAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
*
354850 AAAGCCCACAAATC-GATGGCAACCTTCA
1 AAAGCCCACAAGTCAG-TGGCAACCTTCA
* *
354878 AAAGCCCATAAGTTAGTGGC-ACCTTTTC-
1 AAAGCCCACAAGTCAGTGGCAACC--TTCA
*
354906 AAAGTCCACAAGTCAGTGGCAACCTTC-
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * *
354933 AAAGTCCACAAATCGGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* *
354961 AAAGTCCACAAGTTAGTGGCAACCTTC-
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* *
354988 AAAGTCCACAAGTTAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
*
355016 AAA-CCCACAAGGCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * *
355043 AAAGCACACAATTCGGT-GCAACCCTTTCA
1 AAAGCCCACAAGTCAGTGGCAA-CC-TTCA
355072 AAAGCCCACA
1 AAAGCCCACA
355082 CAAGTTAGTG
Statistics
Matches: 227, Mismatches: 23, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
27 87 0.38
28 99 0.44
29 41 0.18
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCAACCTTCA
Found at i:354973 original size:55 final size:56
Alignment explanation
Indices: 354793--355081 Score: 313
Period size: 55 Copynumber: 5.2 Consensus size: 56
354783 CTCACTTTCC
* * *
354793 AAAGCCCACAAGTAAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCAAAAGCCCACAAGTCAGTGGCAACCTTCA
* * *
354850 AAAGCCCACAAATC-GATGGCAACCTTCAAAAGCCCATAAGTTAGTGGC-ACCTTTTC-
1 AAAGCCCACAAGTCAG-TGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACC--TTCA
* * * *
354906 AAAGTCCACAAGTCAGTGGCAACCTTC-AAAGTCCACAAATCGGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
354961 AAAGTCCACAAGTTAGTGGCAACCTTC-AAAGTCCACAAGTTAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
355016 AAA-CCCACAAGGCAGTGGCAACCTTCAAAAGCACACAATTCGGT-GCAACCCTTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAA-CC-TTCA
355072 AAAGCCCACA
1 AAAGCCCACA
355082 CAAGTTAGTG
Statistics
Matches: 197, Mismatches: 25, Indels: 20
0.81 0.10 0.08
Matches are distributed among these distances:
54 27 0.14
55 86 0.44
56 56 0.28
57 28 0.14
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (56 bp):
AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACCTTCA
Found at i:355392 original size:144 final size:144
Alignment explanation
Indices: 355103--355969 Score: 867
Period size: 144 Copynumber: 6.0 Consensus size: 144
355093 CATCTTTTTC
* * * *
355103 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA----C--CTTTAAGTCCAATGTTGCT
1 TAAGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCT
* * * * *
355162 GGCCTTAAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATCCCTGGCCTTGAATCAGCAT
66 GGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCAC
355227 ATTGGCACCTTTGTCATTTT
131 ATTGGCACC--T-TC---TT
* * * * *
355247 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTAGCACCTTCACCTTTAAGTCCAATGTTGCT
1 TAAGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCT
*
355312 GGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCTAATATCGCTGGCCTTGAATCAG
66 GGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
*
355377 CATATTGGCA-C-T-TT
128 CACATTGGCACCTTCTT
* * * * * *
355391 TAAGTCTAATGTTGCTGGCCTTAAATCAGCACATTGGCACCTTCACCTTTAAGTCCAACATCGTT
1 TAAGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCT
* * *
355456 GGCCTTGAATCAACATATTGGCACCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAT
66 GGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
*
355521 CACATTAGCACCTTCACCTT
128 CACATTGGCACCTT---CTT
* * * *
355541 TAAATCCAATGTTGTTGGCCTTGAATCAGCATATTGGCACTTTTGTCATCTTTAAGTCCAATAGC
1 TAAGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCAC--CT-TCATCTTTAAGTCCAATATC
* * * *
355606 GCTGGCCTTGAATTAGCATATTGGCA----C--CTTTAAGTCCAATATTGCTGGCCTTAAATCAA
63 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
*
355665 CACATTAGCACCTTCACCTT
128 CACATTGGCACCTT---CTT
* **
355685 TAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATATC
1 TAAGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAATATC
* * *
355750 GCTGGCCTTGAATCAGCATATTGGCA----C--CTTTAAGTCCAATGTTGCTGGCCTTAAATCAG
63 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
*
355809 CACCTTGGCACCTTCACCTT
128 CACATTGGCACCTT---CTT
* * * * * *
355829 TAAGTCCAATGTTGCTAGCCTTAAATCAGCACATTGGTACTTTCATCTTTAAGTCCAATATCGTT
1 TAAGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCT
* *
355894 GGCCTTAAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
66 GGCCTTGAATCAGCATATTGGCACCTT---CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
355959 CACATTGGCAC
128 CACATTGGCAC
355970 GTTCATCTTT
Statistics
Matches: 629, Mismatches: 65, Indels: 52
0.84 0.09 0.07
Matches are distributed among these distances:
141 43 0.07
142 1 0.00
144 375 0.60
145 1 0.00
146 2 0.00
148 3 0.00
150 118 0.19
152 3 0.00
153 83 0.13
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (144 bp):
TAAGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCT
GGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCAC
ATTGGCACCTTCTT
Found at i:355540 original size:245 final size:245
Alignment explanation
Indices: 355103--355985 Score: 1268
Period size: 245 Copynumber: 3.6 Consensus size: 245
355093 CATCTTTTTC
*
355103 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTTGCTGGCCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATATTGCTGGCCTT
*
355168 AAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATCCCTGGCCTTGAATCAGCATATTGGC
66 AAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
*
355233 ACCTTTGTCATTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTAGCACCTTCACCTTTA
131 ACCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTAGCACCTTCACCTTTA
355298 AGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
196 AGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
* * * *
355348 TAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTTAAGTCTAATGTTGCTGGCCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATATTGCTGGCCTT
* * *
355413 AAATCAGCACATTGGCACCTTCACCTTTAAGTCCAACATCGTTGGCCTTGAATCAACATATTGGC
66 AAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
* *
355478 ACCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCATCACATTAGCACCTTCACCTTTA
131 ACCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTAGCACCTTCACCTTTA
* * *
355543 AATCCAATGTTGTTGGCCTTGAATCAGCATATTGGCACTTTTGTCATCTT
196 AGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
* *
355593 TAAGTCCAATAGCGCTGGCCTTGAATTAGCATATTGGCACCTTTAAGTCCAATATTGCTGGCCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATATTGCTGGCCTT
* * *
355658 AAATCAACACATTAGCACCTTCACCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGC
66 AAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
* *
355723 ACCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT-G-----GCACCTTTA
131 ACCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTAGCACCTTCACCTTTA
* ** *
355782 AGTCCAATGTTGCTGGCCTTAAATCAGCACCTTGGCACC--T-TCACCTT
196 AGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
* * * * * * * *
355829 TAAGTCCAATGTTGCTAGCCTTAAATCAGCACATTGGTACTTTCATCTTTAAGTCCAATATCGTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG------CACCTTTAAGTCCAATATTGCT
*
355894 GGCCTTAAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
60 GGCCTTAAATCAGCACATTGGCACCTT---CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
* *
355959 CACATTGGCA-C-GT-TCATCTTTAAGTCC
122 CATATTGGCACCTTTGTCATCTTTAAGTCC
355986 GATATCACTG
Statistics
Matches: 577, Mismatches: 52, Indels: 21
0.89 0.08 0.03
Matches are distributed among these distances:
236 36 0.06
237 1 0.00
239 41 0.07
242 58 0.10
243 1 0.00
244 2 0.00
245 438 0.76
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (245 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATATTGCTGGCCTT
AAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
ACCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTAGCACCTTCACCTTTA
AGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
Found at i:355991 original size:101 final size:98
Alignment explanation
Indices: 355103--355996 Score: 900
Period size: 101 Copynumber: 9.2 Consensus size: 98
355093 CATCTTTTTC
* * *
355103 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA----C--CTTTAAGTCCAATGTTGCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCT
* * *
355162 GGCCTTAAATCAGCACATTGGCACCTTCACCTT
66 GGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * *
355195 TAAGTCCAATATCCCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATTTTTAAGTCCAATGTC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAATATC
* *
355260 GCTGGCCTTGAATCAGCATATTAGCACCTTCACCTT
63 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * *
355296 TAAGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCTAATATC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAATATC
355361 GCTGGCCTTGAATCAGCATATTGGCA----C-T-TT
63 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * * * *
355391 TAAGTCTAATGTTGCTGGCCTTAAATCAGCACATTGGCACCTTCACCTTTAAGTCCAACATCGTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCT
*
355456 GGCCTTGAATCAACATATTGGCACCTTTGTCATCTT
66 GGCCTTGAATCAGCATATTGGCACC--T-TCATCTT
* * * * * * * *
355492 TAAGTCCAATGTCGCTGGCCTTGAATCATCACATTAGCACCTTCACCTTTAAATCCAATGTTGTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCT
*
355557 GGCCTTGAATCAGCATATTGGCACTTTTGTCATCTT
66 GGCCTTGAATCAGCATATTGGCAC--CT-TCATCTT
* * * *
355593 TAAGTCCAATAGCGCTGGCCTTGAATTAGCATATTGGCA----C--CTTTAAGTCCAATATTGCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCT
* * * * *
355652 GGCCTTAAATCAACACATTAGCACCTTCACCTT
66 GGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
355685 TAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATATC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAATATC
355750 GCTGGCCTTGAATCAGCATATTGGCA----C--CTT
63 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * * * *
355780 TAAGTCCAATGTTGCTGGCCTTAAATCAGCACCTTGGCACCTTCACCTTTAAGTCCAATGTTGCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCT
* * * * *
355845 AGCCTTAAATCAGCACATTGGTACTTTCATCTT
66 GGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
355878 TAAGTCCAATATCGTTGGCCTTAAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATATC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT---CATCTTTAAGTCCAATATC
* *
355943 GCTGGCCTTGAATCAGCACATTGGCACGTTCATCTT
63 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
355979 TAAGTCCGATATCACTGG
1 TAAGTCCAATATCGCTGG
355997 TATATTTTCT
Statistics
Matches: 681, Mismatches: 83, Indels: 67
0.82 0.10 0.08
Matches are distributed among these distances:
92 160 0.23
93 3 0.00
95 114 0.17
96 1 0.00
97 3 0.00
98 42 0.06
99 3 0.00
100 1 0.00
101 354 0.52
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (98 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCT
GGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:356964 original size:28 final size:28
Alignment explanation
Indices: 356920--356982 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
356910 AGAACCCCTA
* *
356920 GGTTCAGTTGAATGCATTCTGTTTGGGC
1 GGTTCAGCTGAACGCATTCTGTTTGGGC
*
356948 GGTTCAGCTGAACGCATTCTTTTTGGGC
1 GGTTCAGCTGAACGCATTCTGTTTGGGC
*
356976 CGTTCAG
1 GGTTCAG
356983 GCCCAGCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.14, C:0.19, G:0.30, T:0.37
Consensus pattern (28 bp):
GGTTCAGCTGAACGCATTCTGTTTGGGC
Found at i:358577 original size:20 final size:20
Alignment explanation
Indices: 358552--358604 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
358542 TACCACTGTT
*
358552 TGTATCGATACATGGTAAAA
1 TGTATCGATACATGATAAAA
* *
358572 TGTATCGATACATGATGAAT
1 TGTATCGATACATGATAAAA
*
358592 TGTATTGATACAT
1 TGTATCGATACAT
358605 TGCCTGTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGATAAAA
Found at i:360853 original size:21 final size:20
Alignment explanation
Indices: 360819--360861 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
360809 TATTAAAAAG
*
360819 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAACAA-GAA
360840 TTAGCTAA-GAAAAACAAGAA
1 TTAGCTAATG-AAAACAAGAA
360860 TT
1 TT
360862 TGCATGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (20 bp):
TTAGCTAATGAAAACAAGAA
Found at i:360860 original size:20 final size:21
Alignment explanation
Indices: 360819--360861 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
360809 TATTAAAAAG
*
360819 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAATAAAGAA
360840 TTAGCTAA-GAAAA-ACAAGAA
1 TTAGCTAATGAAAATA-AAGAA
360860 TT
1 TT
360862 TGCATGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.55
21 8 0.40
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (21 bp):
TTAGCTAATGAAAATAAAGAA
Found at i:365464 original size:13 final size:13
Alignment explanation
Indices: 365446--365473 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
365436 ATACAAAGAT
365446 CAATGTATCGATA
1 CAATGTATCGATA
365459 CAATGTATCGATA
1 CAATGTATCGATA
365472 CA
1 CA
365474 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:365551 original size:33 final size:33
Alignment explanation
Indices: 365514--365580 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
365504 AGTAGCTTAA
365514 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
365547 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
365580 A
1 A
365581 AATCGTTGAA
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:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:365554 original size:13 final size:13
Alignment explanation
Indices: 365536--365560 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
365526 CAAAAAAATA
365536 TGTATCGATACAT
1 TGTATCGATACAT
365549 TGTATCGATACA
1 TGTATCGATACA
365561 ACACTTTATG
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:367628 original size:20 final size:20
Alignment explanation
Indices: 367605--367678 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
367595 ACAATTCAAA
367605 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
367625 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
367646 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
367666 GTATCGATACATG
1 GTATCGATACATG
367679 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:367649 original size:21 final size:21
Alignment explanation
Indices: 367623--367698 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
367613 ACATGTTGCA
367623 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
367644 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
367664 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
367685 ATGTATCGATACAT
1 ATGTATCGATACAT
367699 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:367656 original size:41 final size:41
Alignment explanation
Indices: 367605--367698 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
367595 ACAATTCAAA
367605 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
367646 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
367687 GTATCGATACAT
1 GTATCGATACAT
367699 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:367755 original size:13 final size:13
Alignment explanation
Indices: 367737--367762 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
367727 TACAGCAAGT
367737 ATGTATCGATACA
1 ATGTATCGATACA
367750 ATGTATCGATACA
1 ATGTATCGATACA
367763 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:368284 original size:34 final size:35
Alignment explanation
Indices: 368221--368287 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
368211 CTAAGTGATT
368221 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
368257 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
368288 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:369961 original size:84 final size:84
Alignment explanation
Indices: 369801--369961 Score: 186
Period size: 84 Copynumber: 1.9 Consensus size: 84
369791 ACTCAAAGAA
* * * *
369801 GAAAATAAATCAATAAGTGTAGAGAATCATATTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAG
1 GAAAATAAATCAATAAGTGTAGAAAATCATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAG
* *
369866 TATGAAAGAGTTACAAAAT
66 AAAGAAAGAGTTACAAAAT
* *
369885 GAAAATAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAAAAAGAAAATAAATGAATT--AGAAG
1 GAAAATAAATCAATAAGTGTAGAAAATCATATTC--TTAAAAAGAAAATAAATGAATTAGAGAAG
369946 AGAAAAGAAATGAGTT
64 AG-AAAGAAA-GAGTT
369962 GCAAGTCGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
82 11 0.17
83 6 0.09
84 48 0.74
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATCATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAG
AAAGAAAGAGTTACAAAAT
Found at i:371431 original size:13 final size:13
Alignment explanation
Indices: 371413--371437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
371403 TTTTCCAGAT
371413 TGTATCGATACAA
1 TGTATCGATACAA
371426 TGTATCGATACA
1 TGTATCGATACA
371438 TTGCTTCAGT
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:373119 original size:20 final size:20
Alignment explanation
Indices: 373096--373169 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
373086 ACAATTCAAA
373096 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
373116 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
373137 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
373157 GTATCGATACATG
1 GTATCGATACATG
373170 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:373140 original size:21 final size:21
Alignment explanation
Indices: 373114--373189 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
373104 ACATGTTGCA
373114 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
373135 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
373155 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
373176 ATGTATCGATACAT
1 ATGTATCGATACAT
373190 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:373147 original size:41 final size:41
Alignment explanation
Indices: 373096--373189 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
373086 ACAATTCAAA
373096 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
373137 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
373178 GTATCGATACAT
1 GTATCGATACAT
373190 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:373246 original size:13 final size:13
Alignment explanation
Indices: 373228--373253 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
373218 TACAGCAAGT
373228 ATGTATCGATACA
1 ATGTATCGATACA
373241 ATGTATCGATACA
1 ATGTATCGATACA
373254 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:373775 original size:34 final size:35
Alignment explanation
Indices: 373712--373778 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
373702 CTAAGTGATT
373712 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
373748 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
373779 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:374914 original size:21 final size:22
Alignment explanation
Indices: 374890--374933 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
374880 TGTGATGAAA
* *
374890 TGATTTTTGATG-ATTTTGTCT
1 TGATTTTGGATGAATTTGGTCT
374911 TGATTTTGGATGAATTTGGTCT
1 TGATTTTGGATGAATTTGGTCT
374933 T
1 T
374934 TAAATTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.16, C:0.05, G:0.23, T:0.57
Consensus pattern (22 bp):
TGATTTTGGATGAATTTGGTCT
Found at i:375121 original size:13 final size:13
Alignment explanation
Indices: 375103--375127 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
375093 ACAATATTCC
375103 TTGTATCGATACA
1 TTGTATCGATACA
375116 TTGTATCGATAC
1 TTGTATCGATAC
375128 CCTATCCCTA
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:376953 original size:22 final size:22
Alignment explanation
Indices: 376928--376969 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
376918 TTTTTAAAGA
376928 TTTGACAAAGGGGGAGAAATGC
1 TTTGACAAAGGGGGAGAAATGC
*
376950 TTTGATAAAGGGGGAGAAAT
1 TTTGACAAAGGGGGAGAAAT
376970 ATGTTTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.36, T:0.21
Consensus pattern (22 bp):
TTTGACAAAGGGGGAGAAATGC
Found at i:377566 original size:20 final size:20
Alignment explanation
Indices: 377543--377607 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
377533 CTCACCCAGA
377543 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
377563 TGTATCGATACA--A-----
1 TGTATCGATACATTATGCTT
377576 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
377596 TGTATCGATACA
1 TGTATCGATACA
377608 ATGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 12 0.32
15 1 0.03
18 1 0.03
20 24 0.63
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTATGCTT
Found at i:377581 original size:13 final size:13
Alignment explanation
Indices: 377563--377620 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
377553 CATTATGCTT
377563 TGTATCGATACAA
1 TGTATCGATACAA
377576 TGTATCGATAC-A
1 TGTATCGATACAA
**
377588 T-TAT-G---CTT
1 TGTATCGATACAA
377596 TGTATCGATACAA
1 TGTATCGATACAA
377609 TGTATCGATACA
1 TGTATCGATACA
377621 TATTCATTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.08
10 2 0.06
11 3 0.08
12 2 0.06
13 24 0.67
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:377584 original size:33 final size:33
Alignment explanation
Indices: 377542--377639 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
377532 ACTCACCCAG
377542 ATGTATCGATACATTATGCTTTGTATCGATACA
1 ATGTATCGATACATTATGCTTTGTATCGATACA
377575 ATGTATCGATACATTATGCTTTGTATCGATACA
1 ATGTATCGATACATTATGCTTTGTATCGATACA
* * *
377608 ATGTATCGATACA-TATTCATTGTATCAATACA
1 ATGTATCGATACATTATGCTTTGTATCGATACA
377640 TGGATAATTG
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 16 0.26
33 46 0.74
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (33 bp):
ATGTATCGATACATTATGCTTTGTATCGATACA
Found at i:377633 original size:19 final size:19
Alignment explanation
Indices: 377609--377667 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
377599 ATCGATACAA
*
377609 TGTATCGATACAT-ATTCAT
1 TGTATCGATACATGA-TAAT
*
377628 TGTATCAATACATGGATAAT
1 TGTATCGATACAT-GATAAT
377648 TGTATCGATACATGA-AAT
1 TGTATCGATACATGATAAT
377666 TG
1 TG
377668 GCAGTAGCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 5 0.14
19 14 0.40
20 15 0.43
21 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATGATAAT
Found at i:377727 original size:13 final size:13
Alignment explanation
Indices: 377706--377736 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
377696 CGATACATGG
*
377706 TACAATGTATCGA
1 TACATTGTATCGA
377719 TACATTGTATCGA
1 TACATTGTATCGA
377732 TACAT
1 TACAT
377737 GATGAATTGT
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:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:377732 original size:33 final size:33
Alignment explanation
Indices: 377690--377757 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
377680 CTACCACTGT
*
377690 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
*
377723 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
377756 TT
1 TT
377758 ACCTGTAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:380553 original size:22 final size:19
Alignment explanation
Indices: 380525--380566 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
380515 CTGATTTAAT
380525 ATGAATTTAATAAAAATATTTA
1 ATGAATTT--TAAAAAT-TTTA
380547 ATGAATTTTAAAAATTTTA
1 ATGAATTTTAAAAATTTTA
380566 A
1 A
380567 ACTAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
22 8 0.40
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
ATGAATTTTAAAAATTTTA
Found at i:382275 original size:14 final size:14
Alignment explanation
Indices: 382256--382283 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
382246 TATCTTACAT
382256 ATATTAAAATATAA
1 ATATTAAAATATAA
382270 ATATTAAAATATAA
1 ATATTAAAATATAA
382284 TTTTTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATTAAAATATAA
Found at i:382296 original size:15 final size:16
Alignment explanation
Indices: 382259--382315 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 16
382249 CTTACATATA
*
382259 TTAAAATATAAA--TA
1 TTAAAATATAAATTTT
382273 TTAAAATAT-AATTTT
1 TTAAAATATAAATTTT
*
382288 TTAATATATAAATTTT
1 TTAAAATATAAATTTT
*
382304 TTAAAAAATAAA
1 TTAAAATATAAA
382316 ATATAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
13 2 0.06
14 9 0.25
15 9 0.25
16 16 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATAAATTTT
Found at i:382317 original size:38 final size:36
Alignment explanation
Indices: 382274--382370 Score: 131
Period size: 36 Copynumber: 2.6 Consensus size: 36
382264 ATATAAATAT
382274 TAAAATATAATTTTTTAATATATAAATTTTTTAAAAAA
1 TAAAATATAATTTTTTAA-ATAT-AATTTTTTAAAAAA
* * *
382312 TAAAATATAATTTTTTAAAAATATTTTTTTTAAAAA
1 TAAAATATAATTTTTTAAATATAATTTTTTAAAAAA
*
382348 TAAAATATATTTTTATTAAATAT
1 TAAAATATAATTTT-TTAAATAT
382371 CTATTTATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
36 25 0.47
37 10 0.19
38 18 0.34
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
TAAAATATAATTTTTTAAATATAATTTTTTAAAAAA
Found at i:382332 original size:16 final size:15
Alignment explanation
Indices: 382313--382349 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
382303 TTTAAAAAAT
382313 AAAATATAATTTTTTA
1 AAAATAT-ATTTTTTA
*
382329 AAAATATTTTTTTTA
1 AAAATATATTTTTTA
382344 AAAATA
1 AAAATA
382350 AAATATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAAATATATTTTTTA
Found at i:382360 original size:22 final size:21
Alignment explanation
Indices: 382327--382367 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
382317 TATAATTTTT
*
382327 TAAAAATATTTTTTTTAAAAA
1 TAAAAATATTTTTATTAAAAA
382348 TAAAATATATTTTTATTAAA
1 TAAAA-ATATTTTTATTAAA
382368 TATCTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAAAATATTTTTATTAAAAA
Found at i:383138 original size:12 final size:12
Alignment explanation
Indices: 383121--383167 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
383111 ATTAGATATC
383121 AATATATATTTA
1 AATATATATTTA
*
383133 AATATAAATTTA
1 AATATATATTTA
383145 ATATATAATATTTTA
1 A-ATAT-ATA-TTTA
383160 AATATATA
1 AATATATA
383168 AAATATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 12 0.40
13 7 0.23
14 6 0.20
15 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AATATATATTTA
Found at i:383173 original size:23 final size:25
Alignment explanation
Indices: 383147--383199 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
383137 TAAATTTAAT
*
383147 ATATAATATTTTAAATA-TATA-AA
1 ATATAATATTTTAAAAATTATACAA
*
383170 ATATAATTTTTTAAAAATTATACAA
1 ATATAATATTTTAAAAATTATACAA
383195 ATATA
1 ATATA
383200 TATCGAGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 15 0.58
24 4 0.15
25 7 0.27
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
ATATAATATTTTAAAAATTATACAA
Found at i:383805 original size:10 final size:10
Alignment explanation
Indices: 383754--383807 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
383744 ATTATTACAG
383754 TTATAATTTT
1 TTATAATTTT
383764 TTAATAA-TTT
1 TT-ATAATTTT
* **
383774 TTAAAATAAT
1 TTATAATTTT
*
383784 TTATAATATT
1 TTATAATTTT
383794 TTATAATTTT
1 TTATAATTTT
383804 TTAT
1 TTAT
383808 TTATAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 3 0.08
10 29 0.81
11 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTATAATTTT
Found at i:383806 original size:20 final size:19
Alignment explanation
Indices: 383754--383807 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
383744 ATTATTACAG
383754 TTATAATTTTTTAATAATTT
1 TTATAATTTTTT-ATAATTT
* **
383774 TTAAAATAATTTATAATATT
1 TTATAATTTTTTATAAT-TT
383794 TTATAATTTTTTAT
1 TTATAATTTTTTAT
383808 TTATAAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATAATTTTTTATAATTT
Found at i:384008 original size:17 final size:17
Alignment explanation
Indices: 383976--384009 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
383966 AATAAATAGT
*
383976 AAAATTAATTACTATAA
1 AAAATTAAATACTATAA
*
383993 AAAATTAAATATTATAA
1 AAAATTAAATACTATAA
384010 TAATAATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATTAAATACTATAA
Found at i:391731 original size:67 final size:69
Alignment explanation
Indices: 391652--391792 Score: 200
Period size: 71 Copynumber: 2.0 Consensus size: 69
391642 TAACATATGC
391652 AATACAAGTGTTAAA-T-ATA-AATATTTTAATAAAAGTGA-AAGCGTAACATAGCTTAAGAAGC
1 AATACAAGTGTTAAATTAATAGAATATTTTAATAAAAGTGAGAA--GTAACATAGCTTAAGAAGC
391713 AAGAGG
64 AAGAGG
* *
391719 AATACAAGTGTTAAATTAAATATGAATATTTTAATGAAATTGAGAAGTAACATAGCTTAAGAAGC
1 AATACAAGTGTTAAATT-AATA-GAATATTTTAATAAAAGTGAGAAGTAACATAGCTTAAGAAGC
391784 AAGAGG
64 AAGAGG
391790 AAT
1 AAT
391793 TGTCCTGAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
67 15 0.23
68 1 0.02
70 3 0.05
71 28 0.42
72 17 0.26
73 2 0.03
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (69 bp):
AATACAAGTGTTAAATTAATAGAATATTTTAATAAAAGTGAGAAGTAACATAGCTTAAGAAGCAA
GAGG
Found at i:391862 original size:3 final size:3
Alignment explanation
Indices: 391854--391898 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
391844 AAATCACGGT
391854 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
391899 TTTTTAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:392456 original size:146 final size:146
Alignment explanation
Indices: 392229--392627 Score: 470
Period size: 146 Copynumber: 2.7 Consensus size: 146
392219 AGCGTTACGT
* * * * *
392229 GTATTATTTATCTTTGTTTGTAAAAGTTTAATTATAGTTTTTT-GATATGATTATATGA-TTTAA
1 GTATAATTTATTTTTATTTGTAAAAGTTTAAATAT-GTTTTTTGGGTATGATTATATGAGTTTAA
* * *
392292 ATTTTTAGGGTATTATTTATTTTTATTTACAGAAGTTTAAATTTA-TTTTTGGGTATAATTATAC
65 A-TTTTAGGGTATTATTTATTTTTATTTATAAAAGTTTAAATTTAGTTTTTGGATATAATTATAC
*
392356 GAGTTAAAATTTTT-A-G
129 AAGTTAAAATTTTTCATG
* * * *
392372 GATATAATTTATTTTTATTTATAAAAGTCTAAATATGTTTTTTAGGGTATGCTTATATAAGTTTA
1 G-TATAATTTATTTTTATTTGTAAAAGTTTAAATATGTTTTTT-GGGTATGATTATATGAGTTTA
* * *
392437 AATTTTGATGGTATAATTTATTTTTATTTATAAAAGTTTAAA-TGAGTTTTTTGGATATAATTAT
64 AATTTT-AGGGTATTATTTATTTTTATTTATAAAAGTTTAAATTTAG-TTTTTGGATATAATTAT
* *
392501 ACAAGTTTATATTTTTCATG
127 ACAAGTTAAAATTTTTCATG
* * *
392521 GTATAATTTATTTTTATTTGTAAAAATTTAAATTTGTTTTTTGGGT-TGATTACATGAGTTTAAA
1 GTATAATTTATTTTTATTTGTAAAAGTTTAAATATGTTTTTTGGGTATGATTATATGAGTTTAAA
* * *
392585 TATTTAGGGTATTAGTTATCTTTATTTGTAAAAGTTTAAATTT
66 T-TTTAGGGTATTATTTATTTTTATTTATAAAAGTTTAAATTT
392628 TTGTTTAAAT
Statistics
Matches: 214, Mismatches: 31, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
143 8 0.04
144 28 0.13
145 18 0.08
146 83 0.39
147 37 0.17
148 38 0.18
149 2 0.01
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (146 bp):
GTATAATTTATTTTTATTTGTAAAAGTTTAAATATGTTTTTTGGGTATGATTATATGAGTTTAAA
TTTTAGGGTATTATTTATTTTTATTTATAAAAGTTTAAATTTAGTTTTTGGATATAATTATACAA
GTTAAAATTTTTCATG
Found at i:392624 original size:72 final size:73
Alignment explanation
Indices: 392229--392627 Score: 412
Period size: 74 Copynumber: 5.5 Consensus size: 73
392219 AGCGTTACGT
* * * * *
392229 GTATTATTTATCTTTGTTTGTAAAAGTTT-AATTATAGTTTTTT-GATATGATTATATGA-TTTA
1 GTATAATTTATTTTTATTTATAAAAGTTTAAATT-T-GTTTTTTGGGTATGATTATATGAGTTTA
392291 AATTTTTAGG
64 AATTTTTAGG
* * * * * * *
392301 GTATTATTTATTTTTATTTACAGAAGTTTAAATTT-ATTTTTGGGTATAATTATACGAGTTAAAA
1 GTATAATTTATTTTTATTTATAAAAGTTTAAATTTGTTTTTTGGGTATGATTATATGAGTTTAAA
392365 TTTTTAGG
66 TTTTTAGG
* * * * *
392373 ATATAATTTATTTTTATTTATAAAAGTCTAAATATGTTTTTTAGGGTATGCTTATATAAGTTTAA
1 GTATAATTTATTTTTATTTATAAAAGTTTAAATTTGTTTTTT-GGGTATGATTATATGAGTTTAA
* *
392438 ATTTTGATG
65 ATTTTTAGG
** * * ** *
392447 GTATAATTTATTTTTATTTATAAAAGTTTAAATGAGTTTTTTGGATATAATTATACAAGTTTATA
1 GTATAATTTATTTTTATTTATAAAAGTTTAAATTTGTTTTTTGGGTATGATTATATGAGTTTAAA
*
392512 TTTTTCATG
66 TTTTT-AGG
* * *
392521 GTATAATTTATTTTTATTTGTAAAAATTTAAATTTGTTTTTTGGGT-TGATTACATGAGTTTAAA
1 GTATAATTTATTTTTATTTATAAAAGTTTAAATTTGTTTTTTGGGTATGATTATATGAGTTTAAA
*
392585 TATTTAGG
66 TTTTTAGG
* * * *
392593 GTATTAGTTATCTTTATTTGTAAAAGTTTAAATTT
1 GTATAATTTATTTTTATTTATAAAAGTTTAAATTT
392628 TTGTTTAAAT
Statistics
Matches: 271, Mismatches: 50, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
70 5 0.02
71 12 0.04
72 100 0.37
73 48 0.18
74 106 0.39
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (73 bp):
GTATAATTTATTTTTATTTATAAAAGTTTAAATTTGTTTTTTGGGTATGATTATATGAGTTTAAA
TTTTTAGG
Found at i:393450 original size:13 final size:13
Alignment explanation
Indices: 393432--393457 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
393422 TACAGCAAGT
393432 ATGTATCGATACA
1 ATGTATCGATACA
393445 ATGTATCGATACA
1 ATGTATCGATACA
393458 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:395712 original size:21 final size:21
Alignment explanation
Indices: 395674--395718 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
395664 TTGCAAGTTG
*
395674 AAATAAAGAAGTTGGCTAAAGA
1 AAATAAAGAAGTTAGCT-AAGA
*
395696 AAATAATGAA-TTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
395716 AAA
1 AAA
395719 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 5 0.24
22 9 0.43
ACGTcount: A:0.58, C:0.04, G:0.18, T:0.20
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:396856 original size:15 final size:15
Alignment explanation
Indices: 396836--396866 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
396826 TAAAAATGTC
*
396836 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
396851 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
396866 C
1 C
396867 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:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:398708 original size:20 final size:20
Alignment explanation
Indices: 398629--398708 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
398619 AATGTCCAAA
*
398629 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
398649 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
398674 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
398694 TTGTATCGATACATT
1 ATGTATCGATACATT
398709 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:398712 original size:13 final size:13
Alignment explanation
Indices: 398694--398732 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
398684 ACATTTTTCT
398694 TTGTATCGATACA
1 TTGTATCGATACA
398707 TTGTATCGATACA
1 TTGTATCGATACA
* *
398720 CTATATCGATACA
1 TTGTATCGATACA
398733 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:401271 original size:13 final size:13
Alignment explanation
Indices: 401253--401278 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
401243 TACAGCAAGT
401253 ATGTATCGATACA
1 ATGTATCGATACA
401266 ATGTATCGATACA
1 ATGTATCGATACA
401279 CAAAAAAATT
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:402658 original size:20 final size:21
Alignment explanation
Indices: 402579--402657 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
402569 AATGTCCAAA
*
402579 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
402599 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
402624 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
402644 TTGTATCGATACAT
1 ATGTATCGATACAT
402658 TGTATCGTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:402662 original size:13 final size:13
Alignment explanation
Indices: 402644--402682 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
402634 ACATTTTTCT
402644 TTGTATCGATACA
1 TTGTATCGATACA
*
402657 TTGTATCGTTACA
1 TTGTATCGATACA
*
402670 CTGTATCGATACA
1 TTGTATCGATACA
402683 GGGTGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:405241 original size:13 final size:13
Alignment explanation
Indices: 405223--405248 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
405213 TACAGCAAGT
405223 ATGTATCGATACA
1 ATGTATCGATACA
405236 ATGTATCGATACA
1 ATGTATCGATACA
405249 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:409003 original size:20 final size:20
Alignment explanation
Indices: 408974--409048 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
408964 AAAAAAATAG
408974 AATGTATCGATACATTGAAC
1 AATGTATCGATACATTGAAC
* * *
408994 AATATATCGATATATTCATAC
1 AATGTATCGATACATTGA-AC
* * *
409015 -ATGTATCAATATATTGAAA
1 AATGTATCGATACATTGAAC
409034 AATGTATCGATACAT
1 AATGTATCGATACAT
409049 CCAGGTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.93
21 2 0.05
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAAC
Found at i:409093 original size:21 final size:21
Alignment explanation
Indices: 409067--409119 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
409057 AAAATAGAAT
409067 GTATCGATACATGAACTGTTC
1 GTATCGATACATGAACTGTTC
409088 GTATCGATACATGAACTGTTC
1 GTATCGATACATGAACTGTTC
*
409109 ATATCGATACA
1 GTATCGATACA
409120 AATCATGGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (21 bp):
GTATCGATACATGAACTGTTC
Found at i:410113 original size:21 final size:19
Alignment explanation
Indices: 410087--410141 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
410077 TTTTACAATT
410087 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAA-AGT-AA
* **
410108 TGTATCGATACATAAGTTT
1 TGTATCGATACAAAAGTAA
410127 TGTATCGATACAAAA
1 TGTATCGATACAAAA
410142 CTCATTTGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:410132 original size:19 final size:21
Alignment explanation
Indices: 410084--410140 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
410074 AATTTTTACA
410084 ATTTGTATCGATACAAACAGT
1 ATTTGTATCGATACAAACAGT
** *
410105 AAATGTATCGATACATA-AGT
1 ATTTGTATCGATACAAACAGT
410125 -TTTGTATCGATACAAA
1 ATTTGTATCGATACAAA
410141 ACTCATTTGC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (21 bp):
ATTTGTATCGATACAAACAGT
Found at i:410242 original size:20 final size:20
Alignment explanation
Indices: 410172--410242 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
410162 GAAATATATT
* *
410172 GATACATTAATAAATGCATC
1 GATACATTTATAAATGTATC
410192 GATACATGCTT-TAAATTGTATC
1 GATACAT--TTATAAA-TGTATC
*
410214 GATACATTTATCAATGTATC
1 GATACATTTATAAATGTATC
410234 GATACATTT
1 GATACATTT
410243 GGGTTTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
20 24 0.55
21 7 0.16
22 13 0.30
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (20 bp):
GATACATTTATAAATGTATC
Found at i:414779 original size:21 final size:21
Alignment explanation
Indices: 414753--414793 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
414743 TATCATAAAA
*
414753 TTTTTACGGAATTTTATGTAG
1 TTTTTACGGAATTTCATGTAG
*
414774 TTTTTAGGGAATTTCATGTA
1 TTTTTACGGAATTTCATGTA
414794 ATTTCCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.05, G:0.20, T:0.51
Consensus pattern (21 bp):
TTTTTACGGAATTTCATGTAG
Found at i:414984 original size:18 final size:18
Alignment explanation
Indices: 414924--414989 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
414914 CTTCTACAGA
*
414924 TAAAAATAAATAATACCTT
1 TAAAAATAAATCATACC-T
* * **
414943 TAATCAAATTAATCTTACAA
1 TAA--AAATAAATCATACCT
414963 TAAAAATAAATCATACCT
1 TAAAAATAAATCATACCT
414981 T-AAAATAAA
1 TAAAAATAAA
414990 AGAAATTTAA
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
17 8 0.22
18 12 0.33
19 3 0.08
20 3 0.08
21 10 0.28
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAATAAATCATACCT
Found at i:415676 original size:27 final size:26
Alignment explanation
Indices: 415632--415682 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
415622 GTTAGTAAAA
415632 AAAAAAACATTTTGAAAAATATTTATC
1 AAAAAAACATTTTGAAAAAT-TTTATC
*
415659 AAAAAACCTATTTT-AAAAATTTTA
1 AAAAAAAC-ATTTTGAAAAATTTTA
415683 AAAAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 4 0.18
27 13 0.59
28 5 0.23
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (26 bp):
AAAAAAACATTTTGAAAAATTTTATC
Found at i:417313 original size:13 final size:13
Alignment explanation
Indices: 417297--417323 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
417287 CATGTATCGA
417297 TATCGATACAATG
1 TATCGATACAATG
417310 TATCGATACAATG
1 TATCGATACAATG
417323 T
1 T
417324 CTATGTATCG
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:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:417393 original size:20 final size:19
Alignment explanation
Indices: 417368--417416 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
417358 CTACCAGTTT
**
417368 CATGTATCGAAACAATTGTC
1 CATGTATCGAAACAA-TGAA
*
417388 CATGTATCGATACAATGAA
1 CATGTATCGAAACAATGAA
417407 CATGTATCGA
1 CATGTATCGA
417417 TACATCTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (19 bp):
CATGTATCGAAACAATGAA
Found at i:417412 original size:19 final size:20
Alignment explanation
Indices: 417368--417420 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
417358 CTACCAGTTT
* **
417368 CATGTATCGAAACAATTGTC
1 CATGTATCGATACAATTGAA
417388 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
417407 CATGTATCGATACA
1 CATGTATCGATACA
417421 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:418151 original size:99 final size:97
Alignment explanation
Indices: 417964--418164 Score: 357
Period size: 99 Copynumber: 2.1 Consensus size: 97
417954 AGTTTTTGTT
*
417964 TTTCTCCCCCTTTAGAAAATAATTAATGCTTATATTTAAAAAAAAATTCTTCCCCTTTAATCGGT
1 TTTCTCCCCCTTTAGAAAATAATTAATGCTTATATTTAAAAAAAAATTCTCCCCCTTTAATCGGT
418029 TAAAGAGATTTTCTCCCCCTAGATAAACAATA
66 TAAAGAGATTTTCTCCCCCTAGATAAACAATA
418061 TTTCTCCCCCTTTAGAAAATAATTAATGCTTATATTTTAAAAAAAAAATTCTCCCCCTTTAATCG
1 TTTCTCCCCCTTTAGAAAATAATTAATGCTTATA-TTT-AAAAAAAAATTCTCCCCCTTTAATCG
* *
418126 GTTAGAGAGATTTTCTCCCCCTAGATAAACTATA
64 GTTAAAGAGATTTTCTCCCCCTAGATAAACAATA
418160 TTTCT
1 TTTCT
418165 TCAAAACAAT
Statistics
Matches: 99, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
97 34 0.34
98 3 0.03
99 62 0.63
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.37
Consensus pattern (97 bp):
TTTCTCCCCCTTTAGAAAATAATTAATGCTTATATTTAAAAAAAAATTCTCCCCCTTTAATCGGT
TAAAGAGATTTTCTCCCCCTAGATAAACAATA
Found at i:419637 original size:20 final size:22
Alignment explanation
Indices: 419598--419642 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
419588 GTAGTGGGTG
*
419598 TGGGAGTTGCCCGGTTGCGACC
1 TGGGAGTTGCCCGATTGCGACC
419620 TGGGAG-TG-CCGATTGCGACC
1 TGGGAGTTGCCCGATTGCGACC
419640 TGG
1 TGG
419643 AGGTGGCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 2 0.09
22 6 0.27
ACGTcount: A:0.11, C:0.24, G:0.42, T:0.22
Consensus pattern (22 bp):
TGGGAGTTGCCCGATTGCGACC
Found at i:422981 original size:734 final size:733
Alignment explanation
Indices: 419728--423385 Score: 7208
Period size: 733 Copynumber: 5.0 Consensus size: 733
419718 TTGAAAAATG
*
419728 AAAGTGTTTTTATAAAAACCAAGATCACAAACCTAAACTAGGAGTGTTTATGAGTGGAAAGGAAC
1 AAAGTGTTTTTATAAAAACCAAGACCACAAACCTAAACTAGGAGTGTTTATGAGTGGAAAGGAAC
419793 AAAGATTTGGCTTAAAAACACTTTGAATGAAGAGTTTTGAGGGGATTAAAGAGGTGATAGAAAAT
66 AAAGATTTGGCTTAAAAACACTTTGAATGAAGAGTTTTGAGGGGATTAAAGAGGTGATAGAAAAT
419858 GGTTTTTGAAGATTTTGAAAGACTGATTTGATGGATTTAAAAACCGTTTTTGTTGGTGATTTTGA
131 GGTTTTTGAAGATTTTGAAAGACTGATTTGATGGATTTAAAAACCGTTTTTGTTGGTGATTTTGA
419923 TGGAAAATGAAGTGTTTTGAAGTAAAAATGAGGAAATTTGTAAAAAATTTGATGAATTTTGAAGA
196 TGGAAAATGAAGTGTTTTGAAGTAAAAATGAGGAAATTTGTAAAAAATTTGATGAATTTTGAAGA
419988 AAAGATGTGAGGGTTTGAGAGTATTTTGGGTAATTTGGGGTATAGGTATCGATACGAAATGAATG
261 AAAGATGTGAGGGTTTGAGAGTATTTTGGGTAATTTGGGGTATAGGTATCGATACGAAATGAATG
420053 AGGAAGGTTCGACTATTCAAATAGTAACCCATATATCGATACAATGTATCGATACATGGAATGTT
326 AGGAAGGTTCGACTATTCAAATAGTAACCCATATATCGATACAATGTATCGATACATGGAATGTT
420118 GTATCGATACATCTGGGTTTTCTAGATGTATCGATACATTCTTCAATGTATCGATACATTCTGGA
391 GTATCGATACATCTGGGTTTTCTAGATGTATCGATACATTCTTCAATGTATCGATACATTCTGGA
420183 AAATCTCCAGAAAAATGTTGAAAATTAGTATCGAATCTTACCCTATAGACCCTAAAACACATTAA
456 AAATCTCCAGAAAAATGTTGAAAATTAGTATCGAATCTTACCCTATAGACCCTAAAACACATTAA
420248 TCAACAAAAATTCAATAACATAACAAAATTAAGCAACAAATTCCTTCAATGACAAAGCAAAAACA
521 TCAACAAAAATTCAATAACATAACAAAATTAAGCAACAAATTCCTTCAATGACAAAGCAAAAACA
* *
420313 TCAAAAATCACTAGATCACATATTTTAACGAAATAAAACATCAAAAGTGCAACATTTTGTTTCAA
586 TCAAAAATCACTAGACCACATATTTTAACCAAATAAAACATCAAAAGTGCAACATTTTGTTTCAA
420378 GTGACCAAAAATGTCATTTTTGTACAAGCAAGGTCATTAAACAAGATTTTTCATAAAAAAATGAT
651 GTGACCAAAAATGTCATTTTTGTACAAGCAAGGTCATTAAACAAGATTTTTCATAAAAAAATGAT
420443 ATAGACAATGATATAAAA
716 ATAGACAATGATATAAAA
420461 AAAGTGTTTTTATAAAAACCAAGACCACAAACCTAAACTAGGAGTGTTTATGAGTGGAAAGGAAC
1 AAAGTGTTTTTATAAAAACCAAGACCACAAACCTAAACTAGGAGTGTTTATGAGTGGAAAGGAAC
420526 AAAGATTTGGCTTAAAAACACTTTGAATGAAGAGTTTTGAGGGGATTAAAGAGGTGATAGAAAAT
66 AAAGATTTGGCTTAAAAACACTTTGAATGAAGAGTTTTGAGGGGATTAAAGAGGTGATAGAAAAT
*
420591 GGTTTTTGAAGATTTTGAAAGACTGATTTGATGGATTTAAAAACTGTTTTTGTTGGTGATTTTGA
131 GGTTTTTGAAGATTTTGAAAGACTGATTTGATGGATTTAAAAACCGTTTTTGTTGGTGATTTTGA
420656 TGGAAAATGAAGTGTTTTGAAGTAAAAATGAGGAAATTTGTAAAAAATTTGATGAATTTTGAAGA
196 TGGAAAATGAAGTGTTTTGAAGTAAAAATGAGGAAATTTGTAAAAAATTTGATGAATTTTGAAGA
420721 AAAGATGTGAGGGTTTGAGAGTATTTTGGGTAATTTGGGGTATAGGTATCGATACGAAATGAATG
261 AAAGATGTGAGGGTTTGAGAGTATTTTGGGTAATTTGGGGTATAGGTATCGATACGAAATGAATG
*
420786 AGGAAGGTTCGACTATTCAAAAAGTAACCCATATATCGATACAATGTATCGATACATGGAATGTT
326 AGGAAGGTTCGACTATTCAAATAGTAACCCATATATCGATACAATGTATCGATACATGGAATGTT
420851 GTATCGATACATCTGGGTTTTCTAGATGTATCGATACATTCTTCAATGTATCGATACATTCTGGA
391 GTATCGATACATCTGGGTTTTCTAGATGTATCGATACATTCTTCAATGTATCGATACATTCTGGA
420916 AAATCTCCAGAAAAATGTTGAAAATTAGTATCGAATCTTACCCTATAGACCCTAAAACACATTAA
456 AAATCTCCAGAAAAATGTTGAAAATTAGTATCGAATCTTACCCTATAGACCCTAAAACACATTAA
420981 TCAACAAAAATTCAATAACATAACAAAATTAAGCAACAAATTCCTTCAATGACAAAGCAAAAACA
521 TCAACAAAAATTCAATAACATAACAAAATTAAGCAACAAATTCCTTCAATGACAAAGCAAAAACA
421046 TCAAAAATCACTAGACCACATATTTTAACCAAATAAAACATCAAAAGTGCAACATTTTGTTTCAA
586 TCAAAAATCACTAGACCACATATTTTAACCAAATAAAACATCAAAAGTGCAACATTTTGTTTCAA
421111 GTGACCAAAAATGTCATTTTTGTACAAGCAAGGTCATTAAACAAGATTTTTCATAAAAAAATGAT
651 GTGACCAAAAATGTCATTTTTGTACAAGCAAGGTCATTAAACAAGATTTTTCATAAAAAAATGAT
421176 ATAGACAATGATATAAAA
716 ATAGACAATGATATAAAA
421194 AAAGTGTTTTTATAAAAACCAAGACCACAAACCTAAACTAGGAGTGTTTATGAGTGGAAAGGAAC
1 AAAGTGTTTTTATAAAAACCAAGACCACAAACCTAAACTAGGAGTGTTTATGAGTGGAAAGGAAC
421259 AAAGATTTGGCTTAAAAACACTTTGAATGAAGAGTTTTGAGGGGATTAAAGAGGTGATAGAAAAT
66 AAAGATTTGGCTTAAAAACACTTTGAATGAAGAGTTTTGAGGGGATTAAAGAGGTGATAGAAAAT
421324 GGTTTTTGAAGATTTTGAAAGACTGATTTGATGGATTTAAAAACCGTTTTTGTTGGTGATTTTGA
131 GGTTTTTGAAGATTTTGAAAGACTGATTTGATGGATTTAAAAACCGTTTTTGTTGGTGATTTTGA
*
421389 TGGAAAATGAAGTGTTTTGAAGTAAAAATGAGGAAATTTGTAAAAACTTTGATGAATTTTGAAGA
196 TGGAAAATGAAGTGTTTTGAAGTAAAAATGAGGAAATTTGTAAAAAATTTGATGAATTTTGAAGA
421454 AAAGATGTGAGGGTTTGAGAGTATTTTGGGTAATTTGGGGTATAGGTATCGATACGAAATGAATG
261 AAAGATGTGAGGGTTTGAGAGTATTTTGGGTAATTTGGGGTATAGGTATCGATACGAAATGAATG
421519 AGGAAGGTTCGACTATTCAAATAGTAACCCATATATCGATACAATGTATCGATACATGGAATGTT
326 AGGAAGGTTCGACTATTCAAATAGTAACCCATATATCGATACAATGTATCGATACATGGAATGTT
421584 GTATCGATACATCTGGGTTTTCTAGATGTATCGATACATTCTTCAATGTATCGATACATTCTGGA
391 GTATCGATACATCTGGGTTTTCTAGATGTATCGATACATTCTTCAATGTATCGATACATTCTGGA
421649 AAATCTCCAGAAAAATGTTGAAAATTAGTATCGAATCTTACCCTATAGACCCTAAAACACATTAA
456 AAATCTCCAGAAAAATGTTGAAAATTAGTATCGAATCTTACCCTATAGACCCTAAAACACATTAA
*
421714 TCAACAAAAATTCAATAACATAACAAAATTAAGCAACAAATTCCTTCAATGACAAAGGAAAAACA
521 TCAACAAAAATTCAATAACATAACAAAATTAAGCAACAAATTCCTTCAATGACAAAGCAAAAACA
421779 TCAAAAATCACTAGACCACATATTTTAACCAAATAAAACATCAAAAGTGCAACATTTTGTTTCAA
586 TCAAAAATCACTAGACCACATATTTTAACCAAATAAAACATCAAAAGTGCAACATTTTGTTTCAA
421844 GTGACCAAAAATGTCATTTTTGTACAAGCAAGGTCATTAAACAAGATTTTTCATAAAAAAATGAT
651 GTGACCAAAAATGTCATTTTTGTACAAGCAAGGTCATTAAACAAGATTTTTCATAAAAAAATGAT
421909 ATAGACAATGATATAAAA
716 ATAGACAATGATATAAAA
421927 AAAGTGTTTTTATAAAAACCAAGACCACAAACCTAAACTAGGAGTGTTTATGAGTGGAAAGGAAC
1 AAAGTGTTTTTATAAAAACCAAGACCACAAACCTAAACTAGGAGTGTTTATGAGTGGAAAGGAAC
421992 AAAGATTTGGCTTAAAAACACTTTGAATGAAGAGTTTTGAGGGGATTAAAGAGGTGATAGAAAAT
66 AAAGATTTGGCTTAAAAACACTTTGAATGAAGAGTTTTGAGGGGATTAAAGAGGTGATAGAAAAT
422057 GGTTTTTGAAGATTTTGAAAGACTGATTTGATGGATTTAAAAACCGTTTTTGTTGGTGATTTTGA
131 GGTTTTTGAAGATTTTGAAAGACTGATTTGATGGATTTAAAAACCGTTTTTGTTGGTGATTTTGA
422122 TGGAAAATGAAGTGTTTTGAAGTAAAAATGAGGAAATTTGTAAAAAATTTGATGAATTTTGAAGA
196 TGGAAAATGAAGTGTTTTGAAGTAAAAATGAGGAAATTTGTAAAAAATTTGATGAATTTTGAAGA
422187 AAAGATGTGAGGGTTTGAGAGTATTTTGGGTAATTTGGGGTATAGGTATCGATACGAAATGAATG
261 AAAGATGTGAGGGTTTGAGAGTATTTTGGGTAATTTGGGGTATAGGTATCGATACGAAATGAATG
422252 AGGAAGGTTCGACTATTCAAATAGTAACCCATATATCGATACAATGTATCGATACATGGAATGTT
326 AGGAAGGTTCGACTATTCAAATAGTAACCCATATATCGATACAATGTATCGATACATGGAATGTT
422317 GTATCGATACATCTGGGTTTTCTAGATGTATCGATACATTCTTCAATGTATCGATACATTCTGGA
391 GTATCGATACATCTGGGTTTTCTAGATGTATCGATACATTCTTCAATGTATCGATACATTCTGGA
422382 AAATCTCCAGAAAAATGTTGAAAATTAGTATCGAATCTTACCCTATAGACCCTAAAACACATTAA
456 AAATCTCCAGAAAAATGTTGAAAATTAGTATCGAATCTTACCCTATAGACCCTAAAACACATTAA
422447 TCAACAAAAATTCAATAACATAACAAAATTAAGCAACAAATTCCTTCAATGACAAAGCAAAAACA
521 TCAACAAAAATTCAATAACATAACAAAATTAAGCAACAAATTCCTTCAATGACAAAGCAAAAACA
422512 TCAAAAATCACTAGACCACATATTTTAACCAAATAAAACATCAAAAGTGCAACATTTTGTTTCGA
586 TCAAAAATCACTAGACCACATATTTTAACCAAATAAAACATCAAAAGTGCAACATTTTGTTTC-A
422577 AGTGACCAAAAATGTCATTTTTGTACAAGCAAGGTCATTAAACAAGATTTTTCATAAAAAAATGA
650 AGTGACCAAAAATGTCATTTTTGTACAAGCAAGGTCATTAAACAAGATTTTTCATAAAAAAATGA
422642 TATAGACAATGATATAAAA
715 TATAGACAATGATATAAAA
422661 AAAGTGTTTTTATAAAAACCAAGACCACAAACCTAAACTAGGAGTGTTTATGAGTGGAAAGGAAC
1 AAAGTGTTTTTATAAAAACCAAGACCACAAACCTAAACTAGGAGTGTTTATGAGTGGAAAGGAAC
422726 AAAGATTTGGCTTAAAAACACTTTGAATGAAGAGTTTTGAGGGGATTAAAGAGGTGATAGAAAAT
66 AAAGATTTGGCTTAAAAACACTTTGAATGAAGAGTTTTGAGGGGATTAAAGAGGTGATAGAAAAT
*
422791 GGTTTTTCAAGATTTTGAAAGACTGATTTGATGGATTTAAAAACCGTTTTTGTTGGTGATTTTGA
131 GGTTTTTGAAGATTTTGAAAGACTGATTTGATGGATTTAAAAACCGTTTTTGTTGGTGATTTTGA
422856 TGGAAAATGAAGTGTTTTGAAGTAAAAATGAGGAAATTTGTAAAAAATTTGATGAATTTTGAAGA
196 TGGAAAATGAAGTGTTTTGAAGTAAAAATGAGGAAATTTGTAAAAAATTTGATGAATTTTGAAGA
422921 AAAGATGTGAGGGTTTGAGAGTATTTTGGGTAATTTGGGGTATAGGTATCGATACGAAATGAATG
261 AAAGATGTGAGGGTTTGAGAGTATTTTGGGTAATTTGGGGTATAGGTATCGATACGAAATGAATG
422986 AGGAAGGTTCGACTATTCAAATAGTAACCCATATATCGATACAATGTATCGATACATGGAATGTT
326 AGGAAGGTTCGACTATTCAAATAGTAACCCATATATCGATACAATGTATCGATACATGGAATGTT
*
423051 GTATCGATACATCTGGGTTTTCTAGATGTATCGATACATTCTTCAATGTATCGATACATTCTAGA
391 GTATCGATACATCTGGGTTTTCTAGATGTATCGATACATTCTTCAATGTATCGATACATTCTGGA
423116 AAATCTCCAGAAAAAATGTTGAAAATTAGTATCGAATCTTACCCTATAGACCCTAAAACACATTA
456 AAATCTCCAG-AAAAATGTTGAAAATTAGTATCGAATCTTACCCTATAGACCCTAAAACACATTA
423181 ATCAACAAAAATTCAATAACATAACAAAATTAAGCAACAAATTCCTTCAATGACAAAGCAAAAAC
520 ATCAACAAAAATTCAATAACATAACAAAATTAAGCAACAAATTCCTTCAATGACAAAGCAAAAAC
*
423246 ATCAAAAATCACTAGATCACATATTTTAACCAAATAAAACATCAAAAGTGCAACATTTTGTTTCA
585 ATCAAAAATCACTAGACCACATATTTTAACCAAATAAAACATCAAAAGTGCAACATTTTGTTTCA
423311 AGTGACCAAAAATGTCATTTTTGTACAAGCAAGGTCATTAAACAAGATTTTTCATAAAAAAATGA
650 AGTGACCAAAAATGTCATTTTTGTACAAGCAAGGTCATTAAACAAGATTTTTCATAAAAAAATGA
423376 TATAGACAAT
715 TATAGACAAT
423386 AAAAAAATAC
Statistics
Matches: 2909, Mismatches: 14, Indels: 3
0.99 0.00 0.00
Matches are distributed among these distances:
733 2103 0.72
734 624 0.21
735 182 0.06
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (733 bp):
AAAGTGTTTTTATAAAAACCAAGACCACAAACCTAAACTAGGAGTGTTTATGAGTGGAAAGGAAC
AAAGATTTGGCTTAAAAACACTTTGAATGAAGAGTTTTGAGGGGATTAAAGAGGTGATAGAAAAT
GGTTTTTGAAGATTTTGAAAGACTGATTTGATGGATTTAAAAACCGTTTTTGTTGGTGATTTTGA
TGGAAAATGAAGTGTTTTGAAGTAAAAATGAGGAAATTTGTAAAAAATTTGATGAATTTTGAAGA
AAAGATGTGAGGGTTTGAGAGTATTTTGGGTAATTTGGGGTATAGGTATCGATACGAAATGAATG
AGGAAGGTTCGACTATTCAAATAGTAACCCATATATCGATACAATGTATCGATACATGGAATGTT
GTATCGATACATCTGGGTTTTCTAGATGTATCGATACATTCTTCAATGTATCGATACATTCTGGA
AAATCTCCAGAAAAATGTTGAAAATTAGTATCGAATCTTACCCTATAGACCCTAAAACACATTAA
TCAACAAAAATTCAATAACATAACAAAATTAAGCAACAAATTCCTTCAATGACAAAGCAAAAACA
TCAAAAATCACTAGACCACATATTTTAACCAAATAAAACATCAAAAGTGCAACATTTTGTTTCAA
GTGACCAAAAATGTCATTTTTGTACAAGCAAGGTCATTAAACAAGATTTTTCATAAAAAAATGAT
ATAGACAATGATATAAAA
Found at i:424866 original size:13 final size:13
Alignment explanation
Indices: 424848--424873 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
424838 TACACAAAGT
424848 ATGTATCGATACA
1 ATGTATCGATACA
424861 ATGTATCGATACA
1 ATGTATCGATACA
424874 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:424871 original size:32 final size:33
Alignment explanation
Indices: 424830--424893 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
424820 TAGCCAAACT
**
424830 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
424862 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
424894 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Done.