Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 19 of 210
Found at i:6555911 original size:21 final size:22
Alignment explanation
Indices: 6555868--6555911 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
6555858 ATGTATATTT
*
6555868 TGTTACATTAATGTTTTTAAAA
1 TGTTACATTAATGTTTATAAAA
*
6555890 TGTTATATTAAT-TTTATAAAA
1 TGTTACATTAATGTTTATAAAA
6555911 T
1 T
6555912 ATAAATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (22 bp):
TGTTACATTAATGTTTATAAAA
Found at i:6556938 original size:21 final size:20
Alignment explanation
Indices: 6556900--6556939 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6556890 AAATAATATA
*
6556900 TAATATATTTTTTATATTAG
1 TAATATATTTTTAATATTAG
*
6556920 TAATGTATTTTTAACTATTA
1 TAATATATTTTTAA-TATTA
6556940 TTTTTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (20 bp):
TAATATATTTTTAATATTAG
Found at i:6563849 original size:20 final size:20
Alignment explanation
Indices: 6563824--6563864 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
6563814 ACATACTATA
6563824 AGAAGTTATAACAAAATTTG
1 AGAAGTTATAACAAAATTTG
6563844 AGAAGTTATAACAAAATTTG
1 AGAAGTTATAACAAAATTTG
6563864 A
1 A
6563865 TCTTTTCGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (20 bp):
AGAAGTTATAACAAAATTTG
Found at i:6571998 original size:35 final size:35
Alignment explanation
Indices: 6571952--6572028 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
6571942 CCTAACTTCC
*
6571952 CATCTAAGTACAAAACATGTGTATGCTTTGCCATT
1 CATCTTAGTACAAAACATGTGTATGCTTTGCCATT
6571987 CATCTTAGTACAAAACATGTGTATGCTTTGCCATT
1 CATCTTAGTACAAAACATGTGTATGCTTTGCCATT
6572022 CATCTTA
1 CATCTTA
6572029 TCTTCTATTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (35 bp):
CATCTTAGTACAAAACATGTGTATGCTTTGCCATT
Found at i:6573770 original size:13 final size:14
Alignment explanation
Indices: 6573752--6573792 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
6573742 TTTTCAAAGA
6573752 TATGGTTTAGGA-T
1 TATGGTTTAGGACT
*
6573765 TATGGTTTATGACT
1 TATGGTTTAGGACT
*
6573779 TACGGTTTA-GACT
1 TATGGTTTAGGACT
6573792 T
1 T
6573793 TAGGGGTGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.46
Consensus pattern (14 bp):
TATGGTTTAGGACT
Found at i:6575235 original size:16 final size:16
Alignment explanation
Indices: 6575214--6575245 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6575204 ACTTAGTAAT
6575214 TAAAAGATACAGTTAA
1 TAAAAGATACAGTTAA
6575230 TAAAAGATACAGTTAA
1 TAAAAGATACAGTTAA
6575246 GAAATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.25
Consensus pattern (16 bp):
TAAAAGATACAGTTAA
Found at i:6576647 original size:47 final size:47
Alignment explanation
Indices: 6576578--6576671 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
6576568 TGCTTCGATT
*
6576578 CCCCTTCCAAAAGATAATTTAGGGCTTGATTAATGCATATGGAGGTG
1 CCCCTTCCAAAAGATAATTTAGGACTTGATTAATGCATATGGAGGTG
* * * *
6576625 CCCCTTCTAAAATATAATTTAGGATTTGATTAATGCATGTGGAGGTG
1 CCCCTTCCAAAAGATAATTTAGGACTTGATTAATGCATATGGAGGTG
6576672 GTCTAGCGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (47 bp):
CCCCTTCCAAAAGATAATTTAGGACTTGATTAATGCATATGGAGGTG
Found at i:6577177 original size:9 final size:9
Alignment explanation
Indices: 6577163--6577558 Score: 91
Period size: 9 Copynumber: 43.6 Consensus size: 9
6577153 ATTAATATTA
6577163 TACATAAAT
1 TACATAAAT
*
6577172 TACATAACT
1 TACATAAAT
*
6577181 TA-ATTAAT
1 TACATAAAT
*
6577189 TA-AT-ATT
1 TACATAAAT
*
6577196 ATACATAACT
1 -TACATAAAT
* *
6577206 TATATAACT
1 TACATAAAT
*
6577215 TAC--AACT
1 TACATAAAT
*
6577222 TACATAACT
1 TACATAAAT
6577231 TACATTAATATT
1 TACA-TAA-A-T
*
6577243 ATATATAAAT
1 -TACATAAAT
*
6577253 TACATAACT
1 TACATAAAT
6577262 TACATTAATATT
1 TACA-TAA-A-T
6577274 ATACATAAAT
1 -TACATAAAT
*
6577284 TACATAACT
1 TACATAAAT
*
6577293 TA-ATTAAT
1 TACATAAAT
*
6577301 TA-AT-ATT
1 TACATAAAT
* *
6577308 ATACCTAACT
1 -TACATAAAT
* *
6577318 TACCTAACT
1 TACATAAAT
*
6577327 TA-ATTAAT
1 TACATAAAT
*
6577335 TA-AT-ATT
1 TACATAAAT
*
6577342 ATACATAACT
1 -TACATAAAT
*
6577352 TAC--AACT
1 TACATAAAT
*
6577359 TACATAACT
1 TACATAAAT
6577368 TACATTAATAT
1 TACA-TAA-AT
6577379 TACACATAAAT
1 T--ACATAAAT
*
6577390 TACATAACT
1 TACATAAAT
*
6577399 TACATTAA-
1 TACATAAAT
6577407 TACAT--A-
1 TACATAAAT
*
6577413 -ACTTAAAT
1 TACATAAAT
*
6577421 TACATAACT
1 TACATAAAT
*
6577430 TA-ATTAAT
1 TACATAAAT
*
6577438 TA-AT-ACT
1 TACATAAAT
6577445 TACATTAATATT
1 TACA-TAA-A-T
6577457 ATACATAAAT
1 -TACATAAAT
*
6577467 TACATAACT
1 TACATAAAT
6577476 TACATTAATATT
1 TACA-TAA-A-T
6577488 ATACATAAAT
1 -TACATAAAT
*
6577498 TACATAACT
1 TACATAAAT
*
6577507 TAC--AACT
1 TACATAAAT
*
6577514 TACATAACT
1 TACATAAAT
6577523 TACATTAATATT
1 TACA-TAA-A-T
6577535 ATACATAAAT
1 -TACATAAAT
*
6577545 TACATAACT
1 TACATAAAT
6577554 TACAT
1 TACAT
6577559 TAATACGACA
Statistics
Matches: 303, Mismatches: 39, Indels: 90
0.70 0.09 0.21
Matches are distributed among these distances:
5 3 0.01
6 1 0.00
7 32 0.11
8 43 0.14
9 142 0.47
10 27 0.09
11 10 0.03
12 23 0.08
13 22 0.07
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (9 bp):
TACATAAAT
Found at i:6577221 original size:16 final size:16
Alignment explanation
Indices: 6577202--6577234 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6577192 TATTATACAT
*
6577202 AACTTATATAACTTAC
1 AACTTACATAACTTAC
6577218 AACTTACATAACTTAC
1 AACTTACATAACTTAC
6577234 A
1 A
6577235 TTAATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:6577256 original size:31 final size:31
Alignment explanation
Indices: 6577221--6577510 Score: 216
Period size: 31 Copynumber: 9.5 Consensus size: 31
6577211 AACTTACAAC
6577221 TTACATAACTTACATTAATATTATATATAAA
1 TTACATAACTTACATTAATATTATATATAAA
*
6577252 TTACATAACTTACATTAATATTATACATAAA
1 TTACATAACTTACATTAATATTATATATAAA
* *
6577283 TTACATAACTTA-ATTAATTAATATTATACCTAAC
1 TTACATAACTTACATTAA-TATTA-TATA--TAAA
* * * *
6577317 TTACCTAACTTAATTAATTAATATTATACATAAC
1 TTACATAACTT-A--CATTAATATTATATATAAA
* *
6577351 TTAC--AACTTACA-TAA-CTTACAT-TAATA
1 TTACATAACTTACATTAATATTATATATAA-A
* * *
6577378 TTACACATAAATTACA-TAA-CTTACAT-T-AA
1 TT--ACATAACTTACATTAATATTATATATAAA
*
6577407 -TACATAACTTAAATTACATAACTTA-AT-T-AA
1 TTACATAACTTACATTA-AT-A-TTATATATAAA
*
6577437 TTA-AT-ACTTACATTAATATTATACATAAA
1 TTACATAACTTACATTAATATTATATATAAA
*
6577466 TTACATAACTTACATTAATATTATACATAAA
1 TTACATAACTTACATTAATATTATATATAAA
6577497 TTACATAACTTACA
1 TTACATAACTTACA
6577511 ACTTACATAA
Statistics
Matches: 217, Mismatches: 18, Indels: 48
0.77 0.06 0.17
Matches are distributed among these distances:
26 16 0.07
27 10 0.05
28 8 0.04
29 18 0.08
30 15 0.07
31 108 0.50
32 8 0.04
34 21 0.10
35 1 0.00
36 3 0.01
37 4 0.02
38 5 0.02
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (31 bp):
TTACATAACTTACATTAATATTATATATAAA
Found at i:6577422 original size:137 final size:149
Alignment explanation
Indices: 6577151--6577564 Score: 539
Period size: 137 Copynumber: 2.8 Consensus size: 149
6577141 CGTAGAAGCC
* * *
6577151 ACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTATATAACTT
1 ACATTAATATTATACATAAATTACATAACTT-A--CATTAATATTATACATAAATTACATAACTT
* *
6577216 ACAACTTACATAACTTACATTAATATTATATATAAATTACATAACTTACATTAATA-TTATACAT
63 ACAACTTACATAACTTACATTAATATTATACATAAATTACATAACTTACATTAATACATATACAT
6577280 AAATTACATAAC-TT-A-A-TT
128 AAATTACATAACATTAATACTT
* * * * *
6577298 A-ATTAATATTATACCTAACTTACCTAACTTA-ATT-A-ATTA-ATAT-TA-TACATAACTTACA
1 ACATTAATATTATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTACA
* *
6577356 ACTTACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATACATA-ACTTAAA
66 ACTTACATAACTTACATTAATATTATACATAAATTACATAACTTACATTAATACATATACATAAA
6577420 TTACATAACTTAATTAATTAATACTT
131 TTACATAAC-------ATTAATACTT
6577446 ACATTAATATTATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTACA
1 ACATTAATATTATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTACA
6577511 ACTTACATAACTTACATTAATATTATACATAAATTACATAACTTACATTAATAC
66 ACTTACATAACTTACATTAATATTATACATAAATTACATAACTTACATTAATAC
6577565 GACATAACTT
Statistics
Matches: 231, Mismatches: 17, Indels: 30
0.83 0.06 0.11
Matches are distributed among these distances:
137 78 0.34
138 2 0.01
139 3 0.01
140 4 0.02
141 1 0.00
142 3 0.01
145 3 0.01
146 27 0.12
147 2 0.01
148 3 0.01
149 27 0.12
150 3 0.01
151 1 0.00
152 4 0.02
153 3 0.01
154 1 0.00
155 66 0.29
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (149 bp):
ACATTAATATTATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTACA
ACTTACATAACTTACATTAATATTATACATAAATTACATAACTTACATTAATACATATACATAAA
TTACATAACATTAATACTT
Found at i:6577425 original size:146 final size:145
Alignment explanation
Indices: 6577151--6577564 Score: 506
Period size: 155 Copynumber: 2.8 Consensus size: 145
6577141 CGTAGAAGCC
6577151 ACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTATATAACTT
1 ACATTAATATTATACATAAATTACATAACTTAATTAATTAATA-TAT--AT-AC----ATAACTT
*
6577216 ACAACTTACATAACTTACATTAATATTATATATAAATTACATAACTTACA-T--TA-ATATTATA
58 ACAACTTACATAACTTACATTAATATTATACATAAATTACATAACTTACATTAATACATATTATA
6577277 CATAAATTACA-TAACTT-A-A-TT
123 CATAAATTA-ATTAA-TTAATACTT
* * *
6577298 A-ATTAATATTATACCTAACTTACCTAACTTAATTAATTAATAT-TATACATAACTTACAACTTA
1 ACATTAATATTATACATAAATTACATAACTTAATTAATTAATATATATACATAACTTACAACTTA
*
6577361 CATAACTTACATTAATATTACACATAAATTACATAACTTACATTAATACATAACTTAAATTACAT
66 CATAACTTACATTAATATTATACATAAATTACATAACTTACATTAATACAT-A-TT--A-TACAT
*
6577426 AACTTAATTAATTAATACTT
126 AAATTAATTAATTAATACTT
* *
6577446 ACATTAATATTATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTACA
1 ACATTAATATTATACATAAATTACATAACTTA-ATT-A-ATTA-ATATATA-TACATAACTTACA
6577511 ACTTACATAACTTACATTAATATTATACATAAATTACATAACTTACATTAATAC
61 ACTTACATAACTTACATTAATATTATACATAAATTACATAACTTACATTAATAC
6577565 GACATAACTT
Statistics
Matches: 235, Mismatches: 12, Indels: 32
0.84 0.04 0.11
Matches are distributed among these distances:
137 55 0.23
138 1 0.00
140 2 0.01
141 4 0.02
142 3 0.01
143 2 0.01
144 1 0.00
145 5 0.02
146 52 0.22
147 2 0.01
148 3 0.01
149 27 0.11
150 3 0.01
151 1 0.00
152 4 0.02
153 3 0.01
154 1 0.00
155 66 0.28
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (145 bp):
ACATTAATATTATACATAAATTACATAACTTAATTAATTAATATATATACATAACTTACAACTTA
CATAACTTACATTAATATTATACATAAATTACATAACTTACATTAATACATATTATACATAAATT
AATTAATTAATACTT
Found at i:6577452 original size:77 final size:79
Alignment explanation
Indices: 6577343--6577564 Score: 346
Period size: 77 Copynumber: 2.8 Consensus size: 79
6577333 ATTAATATTA
* *
6577343 TACATAACTTACAACTTACATAACTTACATTAATATTACACATAAATTACATAACTTACATTAAT
1 TACATAACTTACAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTACATTAAT
*
6577408 ACATA-ACTTAAAT
66 ACATATACATAAAT
6577421 TACATAACTTA-ATTAATTA-AT-ACTTACATTAATATTATACATAAATTACATAACTTACATTA
1 TACATAACTTACA--AATTACATAACTTACATTAATATTATACATAAATTACATAACTTACATTA
*
6577483 ATA-TTATACATAAAT
64 ATACATATACATAAAT
*
6577498 TACATAACTTACAACTTACATAACTTACATTAATATTATACATAAATTACATAACTTACATTAAT
1 TACATAACTTACAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTACATTAAT
6577563 AC
66 AC
6577565 GACATAACTT
Statistics
Matches: 132, Mismatches: 5, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
76 6 0.05
77 64 0.48
78 58 0.44
79 4 0.03
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (79 bp):
TACATAACTTACAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTACATTAAT
ACATATACATAAAT
Found at i:6577519 original size:47 final size:46
Alignment explanation
Indices: 6577399--6577557 Score: 193
Period size: 47 Copynumber: 3.5 Consensus size: 46
6577389 TTACATAACT
* *
6577399 TACATTAA-TACATAACTTA-AATTACATAACTTA-ATTAAT-TAA
1 TACATAAATTACATAACTTACAATTACATAACTTACATTAATATTA
* * * *
6577441 TACTTACATTAATATTATACATA-AATTACATAACTTACATTAATATTA
1 TACATAAATT-ACA-TA-ACTTACAATTACATAACTTACATTAATATTA
6577489 TACATAAATTACATAACTTACAACTTACATAACTTACATTAATATTA
1 TACATAAATTACATAACTTACAA-TTACATAACTTACATTAATATTA
6577536 TACATAAATTACATAACTTACA
1 TACATAAATTACATAACTTACA
6577558 TTAATACGAC
Statistics
Matches: 99, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
42 5 0.05
43 1 0.01
44 2 0.02
45 6 0.06
46 22 0.22
47 53 0.54
48 10 0.10
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (46 bp):
TACATAAATTACATAACTTACAATTACATAACTTACATTAATATTA
Found at i:6577548 original size:31 final size:31
Alignment explanation
Indices: 6577358--6577564 Score: 150
Period size: 31 Copynumber: 6.7 Consensus size: 31
6577348 AACTTACAAC
* *
6577358 TTACATAACTTACATTAATATTACACATAAA
1 TTACATAACTTACATTAATACTATACATAAA
*
6577389 TTACATAACTTACATTAATAC-ATAACTTAAA
1 TTACATAACTTACATTAATACTAT-ACATAAA
*
6577420 TTACATAACTTA-ATTAATTAATACTTACATTAATA
1 TTACATAACTTACATTAA-TACTA--TACA-TAA-A
*
6577455 TTATACATAAATTACA-T-A-ACT-TACATTAATA
1 -T-TACATAACTTACATTAATACTATACA-TAA-A
* *
6577486 TTATACATAAATTACA-T-A-ACT-TAC--AAC
1 -T-TACATAACTTACATTAATACTATACATAAA
*
6577513 TTACATAACTTACATTAATATTATACATAAA
1 TTACATAACTTACATTAATACTATACATAAA
6577544 TTACATAACTTACATTAATAC
1 TTACATAACTTACATTAATAC
6577565 GACATAACTT
Statistics
Matches: 148, Mismatches: 12, Indels: 32
0.77 0.06 0.17
Matches are distributed among these distances:
25 12 0.08
26 2 0.01
27 1 0.01
28 4 0.03
29 3 0.02
30 6 0.04
31 96 0.65
32 1 0.01
33 2 0.01
34 6 0.04
35 1 0.01
36 2 0.01
37 11 0.07
38 1 0.01
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (31 bp):
TTACATAACTTACATTAATACTATACATAAA
Found at i:6583438 original size:21 final size:21
Alignment explanation
Indices: 6583412--6583462 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
6583402 ATACAACTTA
* *
6583412 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
6583433 AAGCAGAGGCAGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
*
6583454 AAGCTGAGG
1 AAGCAGAGG
6583463 TTCAACGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.43, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:6583452 original size:87 final size:87
Alignment explanation
Indices: 6583346--6583529 Score: 255
Period size: 87 Copynumber: 2.1 Consensus size: 87
6583336 ACACAACTTA
* *
6583346 AAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAG-ATACAAC
1 AAGCAGAGGCAACAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAGCA-ACAAC
*
6583409 TTAAAGCAGATGCGGCAGCGAGAG
64 TTAAAGCAGATGCGACAGCGAGAG
* * * *
6583433 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGCAGCTT
1 AAGCAGAGGCAACAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAACAACTT
* *
6583498 AAAGTAGATGTGACAGCGAGAG
66 AAAGCAGATGCGACAGCGAGAG
6583520 AAGCAGAGGC
1 AAGCAGAGGC
6583530 TAAAACGAGG
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
87 81 0.94
88 5 0.06
ACGTcount: A:0.40, C:0.17, G:0.31, T:0.12
Consensus pattern (87 bp):
AAGCAGAGGCAACAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAACAACTT
AAAGCAGATGCGACAGCGAGAG
Found at i:6583543 original size:21 final size:21
Alignment explanation
Indices: 6583514--6583568 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
6583504 GATGTGACAG
*
6583514 CGAGAGAAGCAGAGGCTAAAA
1 CGAGGGAAGCAGAGGCTAAAA
* * *
6583535 CGAGGGAAGTAGAGGCTACAG
1 CGAGGGAAGCAGAGGCTAAAA
*
6583556 TGAGGGAAGCAGA
1 CGAGGGAAGCAGA
6583569 ACAGCTTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.40, T:0.07
Consensus pattern (21 bp):
CGAGGGAAGCAGAGGCTAAAA
Found at i:6584027 original size:42 final size:42
Alignment explanation
Indices: 6583874--6584175 Score: 387
Period size: 42 Copynumber: 7.1 Consensus size: 42
6583864 CAAAATTAGC
* *
6583874 GGCGTTTTTTGCATAAGCGCCACTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTG-GTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
6583917 GGCGTTTTTCGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTG-GTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
6583960 GGCGTTTTTTGGTTAAGCGCCGCTAAATACCATCGTCTATAGT
1 GGCGTTTTTTGG-TAAGCGCCGCTAAAGACCATGGTCTATAGT
* * * *
6584003 GGCGTTTTTTGGTAAGCACTGCTAAAGA-CACGGTCTGTAGT
1 GGCGTTTTTTGGTAAGCGCCGCTAAAGACCATGGTCTATAGT
*
6584044 GGCGTTTTGTT-TTAAGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTT-TTGGTAAGCGCCGCTAAAGACCATGGTCTATAGT
*
6584086 GGCGTTTTGTT-TTAAGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTT-TTGGTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * *
6584128 GGCGTTTTTAT-TTAAGCGCCACTACAGACCATGGTCTATAGT
1 GGCGTTTTT-TGGTAAGCGCCGCTAAAGACCATGGTCTATAGT
6584170 GGCGTT
1 GGCGTT
6584176 GTAAAAAAAA
Statistics
Matches: 235, Mismatches: 20, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
41 33 0.14
42 112 0.48
43 90 0.38
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (42 bp):
GGCGTTTTTTGGTAAGCGCCGCTAAAGACCATGGTCTATAGT
Found at i:6584216 original size:84 final size:84
Alignment explanation
Indices: 6583870--6584233 Score: 229
Period size: 84 Copynumber: 4.3 Consensus size: 84
6583860 CTGCCAAAAT
* * ***** *
6583870 TAGCGGCGTTTTT-TGCATAAGCGCCACTAAAGACCATGGTCTATAGTGGCGTTTTTCGCCTAAG
1 TAGCGGCGTTTTTAT--TTAAGCGCCACTAAAGACCATGGTCTATAGTGGCG-TTGTAAAAAAAA
* *
6583934 CGCCGCTAAAGACCATGGTCTA
63 AGCCGCTAAAGACCATGATCTA
* * * * ******
6583956 TAGTGGCGTTTTT-TGGTTAAGCGCCGCTAAATACCATCGTCTATAGTGGCGTT-T-TTTGGTAA
1 TAGCGGCGTTTTTAT--TTAAGCGCCACTAAAGACCATGGTCTATAGTGGCGTTGTAAAAAAAAA
* * *
6584018 GCACTGCTAAAGA-CACGGTCTG
64 GC-C-GCTAAAGACCATGATCTA
* * * ***** **
6584040 TAGTGGCGTTTTGT-TTTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCGTTTTGTTTTAAGCG
1 TAGCGGCGTTTT-TATTTAAGCGCCACTAAAGACCATGGTCTATAGTGGCGTTGTAAAAAAAAAG
*
6584104 CCGCTAAAGACCATGGTCTA
65 CCGCTAAAGACCATGATCTA
* *
6584124 TAGTGGCGTTTTTATTTAAGCGCCACTACAGACCATGGTCTATAGTGGCGTTGTAAAAAAAAAGC
1 TAGCGGCGTTTTTATTTAAGCGCCACTAAAGACCATGGTCTATAGTGGCGTTGTAAAAAAAAAGC
* *
6584189 CGCTAAAGTTCC-TGATCTT
66 CGCTAAAG-ACCATGATCTA
*
6584208 TAGCGGCGTTTATTATATAAAGCGCC
1 TAGCGGCGTTT-TTAT-TTAAGCGCC
6584234 GCGAAAGTTA
Statistics
Matches: 228, Mismatches: 40, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
83 46 0.20
84 106 0.46
85 23 0.10
86 53 0.23
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
TAGCGGCGTTTTTATTTAAGCGCCACTAAAGACCATGGTCTATAGTGGCGTTGTAAAAAAAAAGC
CGCTAAAGACCATGATCTA
Found at i:6594800 original size:16 final size:16
Alignment explanation
Indices: 6594779--6594812 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
6594769 AATATACTAG
6594779 TTTAAGTTTTTTATGT
1 TTTAAGTTTTTTATGT
6594795 TTTAAGTTTTTTATGT
1 TTTAAGTTTTTTATGT
6594811 TT
1 TT
6594813 AAAATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.71
Consensus pattern (16 bp):
TTTAAGTTTTTTATGT
Found at i:6594821 original size:2 final size:2
Alignment explanation
Indices: 6594816--6594841 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6594806 TATGTTTAAA
6594816 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6594842 TTTATGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6595060 original size:16 final size:16
Alignment explanation
Indices: 6595039--6595080 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
6595029 AATAATTTGA
*
6595039 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
6595055 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
6595071 TAGTTTTAAT
1 TAATTTTAAT
6595081 TTTATCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:6609460 original size:25 final size:26
Alignment explanation
Indices: 6609431--6609487 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
6609421 AAAATTTCCA
6609431 ATATCA-TACCAAAATATT-TAACGTT
1 ATATCAGTACCAAAAT-TTATAACGTT
* *
6609456 ATATCAGTACTAAAATTTATAATGTT
1 ATATCAGTACCAAAATTTATAACGTT
6609482 ATATCA
1 ATATCA
6609488 AAATTTCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (26 bp):
ATATCAGTACCAAAATTTATAACGTT
Found at i:6612045 original size:25 final size:25
Alignment explanation
Indices: 6611988--6612058 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
6611978 AAAGATGCAT
*
6611988 ATATATATATTATAAAAAAACCATGC
1 ATATATATATTATATAAAAA-CATGC
* *
6612014 -GA-GTATATTATATAAAAACATGC
1 ATATATATATTATATAAAAACATGC
6612037 ATATATATATTATATAAAAACA
1 ATATATATATTATATAAAAACA
6612059 ATGCGTGTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
23 5 0.13
24 15 0.39
25 18 0.47
ACGTcount: A:0.54, C:0.08, G:0.06, T:0.32
Consensus pattern (25 bp):
ATATATATATTATATAAAAACATGC
Found at i:6612075 original size:25 final size:23
Alignment explanation
Indices: 6611993--6612075 Score: 67
Period size: 25 Copynumber: 3.4 Consensus size: 23
6611983 TGCATATATA
* * *
6611993 TATATTATAAAAAAACCATGCGAG
1 TATAATATATAAAAA-CATGCGTG
* * *
6612017 TATATTATATAAAAACATGCATA
1 TATAATATATAAAAACATGCGTG
6612040 TATATATTATATAAAAACAATGCGTG
1 TATA-A-TATATAAAAAC-ATGCGTG
6612066 TATGAATATA
1 TAT-AATATA
6612076 GAAATAATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
23 9 0.19
24 14 0.29
25 15 0.31
26 9 0.19
27 1 0.02
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (23 bp):
TATAATATATAAAAACATGCGTG
Found at i:6613601 original size:44 final size:43
Alignment explanation
Indices: 6613553--6614183 Score: 483
Period size: 45 Copynumber: 14.2 Consensus size: 43
6613543 TCAGGGGGAT
* **
6613553 AAGATTTG-TATCTTCGATCTACTTCGCCACCAGTATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCGCCA-CA-TACAGGAAGAC
* * * *
6613597 AAGATCTGCTATCTTTGAGCCACTTCACTGCCA-GTACAGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTT--C-GCCACATACAGGAAGAC
* * * **
6613642 AAGATCTGTTATCTTCGATCCACTTCACCACTAGTATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCGCCAC-A-TACAGGAAGAC
* * * *
6613687 AATATCTGCTATTTTTGATCTACTTCACTGCCA-GTACAGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTT--C-GCCACATACAGGAAGAC
* *
6613732 AAGGTCTGTTATCTTCGATCTACTTCACTGCCA-ATACAGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTT--C-GCCACATACAGGAAGAC
* *
6613777 AAGATCTGCTATCTTTGATCTACTTCATGCCA-ATACATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTC--GCCACATACAGGAAGAC
* * * *
6613821 AAGATCTGCTTTCTTCGATCTATTTTGCCA-ATACATGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCGCCACATACAGGAAGAC
**
6613863 AAGATCTG-TCATCTTCGATCTACTTCATGCCA-ATACATAAAGAC
1 AAGATCTGCT-ATCTTCGATCTACTTC--GCCACATACAGGAAGAC
* * * **
6613907 AAGATCTGCTTTTTTCGATCTACTTTGCCACTAGTATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCGCCAC-A-TACAGGAAGAC
* **
6613952 AAGATCTGCTATCTTCAATCTACTTCATGCCA-ATACATAAAGAC
1 AAGATCTGCTATCTTCGATCTACTTC--GCCACATACAGGAAGAC
* * **
6613996 AAGATCTGCCATCTTCGATTTACTTCATGCCA-ATACATAAAGAC
1 AAGATCTGCTATCTTCGATCTACTTC--GCCACATACAGGAAGAC
* *
6614040 AAGATCTGCTATCTTCGATCTACTTCATGCCA-ATACATGAAGAT
1 AAGATCTGCTATCTTCGATCTACTTC--GCCACATACAGGAAGAC
* **
6614084 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCGCCA-CA-TACAGGAAGAC
* * * *
6614129 AAGATCTGTTATCTTCGATCCACTTCGCTACCAATATAGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCGCCA-C-ATACAGGAAGAC
*
6614174 AGGATCTGCT
1 AAGATCTGCT
6614184 GCTTTTCAAC
Statistics
Matches: 488, Mismatches: 75, Indels: 47
0.80 0.12 0.08
Matches are distributed among these distances:
41 1 0.00
42 48 0.10
43 2 0.00
44 196 0.40
45 227 0.47
46 1 0.00
47 6 0.01
48 7 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (43 bp):
AAGATCTGCTATCTTCGATCTACTTCGCCACATACAGGAAGAC
Found at i:6613986 original size:89 final size:89
Alignment explanation
Indices: 6613563--6614183 Score: 681
Period size: 90 Copynumber: 7.0 Consensus size: 89
6613553 AAGATTTGTA
* * * * *
6613563 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGAGCCACTTCACTGC
1 TCTTCGATCTACTTTGCCACTAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCA-TGC
* *
6613628 CAGTACAGGAAGACAAGATCTG-TT
65 CAATACATGAAGACAAGATCTGCTT
* ** * * *
6613652 ATCTTCGATCCACTTCACCACTAGTATGGGAAGACAATATCTGCTATTTTTGATCTACTTCACTG
1 -TCTTCGATCTACTTTGCCACTAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCA-TG
* * *
6613717 CCAGTACAGGAAGACAAGGTCTG-TT
64 CCAATACATGAAGACAAGATCTGCTT
** *
6613742 ATCTTCGATCTACTTCACTGCCA--A-TACAGGAAGACAAGATCTGCTATCTTTGATCTACTTCA
1 -TCTTCGATCTACTT---TGCCACTAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCA
6613804 TGCCAATACATGAAGACAAGATCTGCTT
62 TGCCAATACATGAAGACAAGATCTGCTT
* * *
6613832 TCTTCGATCTATTTTGCCAATA-CAT--GAAGACAAGATCTG-TCATCTTCGATCTACTTCATGC
1 TCTTCGATCTACTTTGCCACTAGTATGGGAAGACAAGATCTGCT-ATCTTCGATCTACTTCATGC
*
6613893 CAATACATAAAGACAAGATCTGCTT
65 CAATACATGAAGACAAGATCTGCTT
* *
6613918 TTTTCGATCTACTTTGCCACTAGTATGGGAAGACAAGATCTGCTATCTTCAATCTACTTCATGCC
1 TCTTCGATCTACTTTGCCACTAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCATGCC
* **
6613983 AATACATAAAGACAAGATCTGCCA
66 AATACATGAAGACAAGATCTGCTT
* * * *
6614007 TCTTCGATTTACTTCATGCCAATA-CAT--AAAGACAAGATCTGCTATCTTCGATCTACTTCATG
1 TCTTCGATCTACTT--TGCCACTAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCATG
*
6614069 CCAATACATGAAGATAAGATCTGCTT
64 CCAATACATGAAGACAAGATCTGCTT
* * * * * *
6614095 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTCGATCCACTTCGCTAC
1 TCTTCGATCTACTTTGCCACTAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ATGC
* * *
6614160 CAATATAGGAAGACAGGATCTGCT
65 CAATACATGAAGACAAGATCTGCT
6614184 GCTTTTCAAC
Statistics
Matches: 460, Mismatches: 54, Indels: 34
0.84 0.10 0.06
Matches are distributed among these distances:
85 1 0.00
86 86 0.19
87 4 0.01
88 70 0.15
89 132 0.29
90 156 0.34
91 8 0.02
93 3 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (89 bp):
TCTTCGATCTACTTTGCCACTAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCATGCC
AATACATGAAGACAAGATCTGCTT
Found at i:6615484 original size:6 final size:6
Alignment explanation
Indices: 6615475--6615513 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
6615465 TGGCCTCTCA
*
6615475 TTTCTT TTTCTT TTTCTT TTTCTT TTTCCT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
6615514 TCATCATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:6616153 original size:18 final size:18
Alignment explanation
Indices: 6616127--6616169 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
6616117 TGGTTTGGCA
*
6616127 GAAAAAATCCAAAAGAAT
1 GAAAGAATCCAAAAGAAT
**
6616145 GAAAGAATCGTAAAGAAT
1 GAAAGAATCCAAAAGAAT
6616163 GAAAGAA
1 GAAAGAA
6616170 CATTTGCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.63, C:0.07, G:0.19, T:0.12
Consensus pattern (18 bp):
GAAAGAATCCAAAAGAAT
Found at i:6618000 original size:19 final size:20
Alignment explanation
Indices: 6617976--6618021 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
6617966 TAACGGTGTT
* *
6617976 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATGAAATG
6617995 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
6618015 -AATGCAA
1 TAATGCAA
6618022 GAAAGAGACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:6618068 original size:14 final size:14
Alignment explanation
Indices: 6618049--6618075 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6618039 TGGTTCAATT
6618049 CTTTACTAGAAAAA
1 CTTTACTAGAAAAA
6618063 CTTTACTAGAAAA
1 CTTTACTAGAAAA
6618076 CAAATCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (14 bp):
CTTTACTAGAAAAA
Found at i:6618489 original size:16 final size:16
Alignment explanation
Indices: 6618468--6618501 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
6618458 TTCTATAATG
6618468 AAATGCCATGCAGTCA
1 AAATGCCATGCAGTCA
6618484 AAATGCCATGCAGTCA
1 AAATGCCATGCAGTCA
6618500 AA
1 AA
6618502 GTGAAACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (16 bp):
AAATGCCATGCAGTCA
Found at i:6620015 original size:49 final size:48
Alignment explanation
Indices: 6619953--6620045 Score: 150
Period size: 49 Copynumber: 1.9 Consensus size: 48
6619943 CATATACTAC
*
6619953 ATAAAAGATGCATATATATATTATAAAAAAACCATGCGAGTATGTTAT
1 ATAAAAGATGCATATATATATTATAAAAAAACAATGCGAGTATGTTAT
* *
6620001 ATAAAAGCATGCATATATATATTATATAAAAACAATGCGTGTATG
1 ATAAAAG-ATGCATATATATATTATAAAAAAACAATGCGAGTATG
6620046 AATATAGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 7 0.17
49 34 0.83
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (48 bp):
ATAAAAGATGCATATATATATTATAAAAAAACAATGCGAGTATGTTAT
Found at i:6629327 original size:22 final size:23
Alignment explanation
Indices: 6629301--6629359 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
6629291 GGATGGTGAT
* *
6629301 GTTAAATTCATTAAGCATGATTA
1 GTTAAATTAATTAAGCATAATTA
* *
6629324 -TTAAGTTAATTAAGTATAATTA
1 GTTAAATTAATTAAGCATAATTA
6629346 GTTAAATTAATTAA
1 GTTAAATTAATTAA
6629360 ATCTTAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 18 0.60
23 12 0.40
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.42
Consensus pattern (23 bp):
GTTAAATTAATTAAGCATAATTA
Found at i:6636265 original size:16 final size:16
Alignment explanation
Indices: 6636240--6636285 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
6636230 ATTCAGCTTG
*
6636240 TAGCTTGCACTTTTCA
1 TAGCTCGCACTTTTCA
6636256 TAGCTCGCACATTTATCA
1 TAGCTCGCAC-TTT-TCA
6636274 -A-CTCGCACTTTT
1 TAGCTCGCACTTTT
6636286 GTTGAGTTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 1 0.04
15 3 0.11
16 16 0.59
17 4 0.15
18 3 0.11
ACGTcount: A:0.22, C:0.28, G:0.11, T:0.39
Consensus pattern (16 bp):
TAGCTCGCACTTTTCA
Found at i:6638318 original size:18 final size:17
Alignment explanation
Indices: 6638251--6638370 Score: 73
Period size: 17 Copynumber: 7.0 Consensus size: 17
6638241 GCAGCTTTAA
* *
6638251 TGAGCTCACACTATTGG
1 TGAGCTCACAATTTTGG
* * * *
6638268 AGAGCTCATAGTCTTGG
1 TGAGCTCACAATTTTGG
*
6638285 TGAGCTCAGAATTTTGGG
1 TGAGCTCACAATTTT-GG
6638303 TGAGCTCACACA-TTTGG
1 TGAGCTCACA-ATTTTGG
** * *
6638320 TGAGCTCGTAGTCTTGG
1 TGAGCTCACAATTTTGG
* *
6638337 TAAGCTCACAGA-TATGG
1 TGAGCTCACA-ATTTTGG
*
6638354 TGAGCTCACAAATTTGG
1 TGAGCTCACAATTTTGG
6638371 GTTAGCTTGC
Statistics
Matches: 77, Mismatches: 21, Indels: 10
0.71 0.19 0.09
Matches are distributed among these distances:
16 1 0.01
17 61 0.79
18 14 0.18
19 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (17 bp):
TGAGCTCACAATTTTGG
Found at i:6641009 original size:21 final size:20
Alignment explanation
Indices: 6640980--6641019 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
6640970 TAGGGTTGTT
* *
6640980 ATTTTATTTTTATTTTTTTTC
1 ATTTGATTTTT-TTTATTTTC
6641001 ATTTGATTTTTTTTATTTT
1 ATTTGATTTTTTTTATTTT
6641020 AGGTTGGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.80
Consensus pattern (20 bp):
ATTTGATTTTTTTTATTTTC
Found at i:6643216 original size:15 final size:16
Alignment explanation
Indices: 6643193--6643248 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
6643183 TTTTTATGTT
*
6643193 TTATATATATTATTTTA
1 TTATATATA-TATTATA
*
6643210 TTATATAATATAATATA
1 TTATAT-ATATATTATA
*
6643227 TTATAT-TGTATTATA
1 TTATATATATATTATA
6643242 TTATATA
1 TTATATA
6643249 AATTAAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
15 13 0.39
17 17 0.52
18 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TTATATATATATTATA
Found at i:6643232 original size:5 final size:5
Alignment explanation
Indices: 6643193--6643247 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
6643183 TTTTTATGTT
* *
6643193 TTATA -TATA TTAT- TT-TA TTATA TAATATA ATATA TTATA TTGTA TTATA
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
6643242 TTATA T
1 TTATA T
6643248 AAATTAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.20
5 28 0.68
7 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:6643233 original size:27 final size:29
Alignment explanation
Indices: 6643194--6643249 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
6643184 TTTTATGTTT
*
6643194 TATATATATTATTTTATTATATAATATAA
1 TATATATATTATTGTATTATATAATATAA
*
6643223 TATAT-TA-TATTGTATTATATTATATAA
1 TATATATATTATTGTATTATATAATATAA
6643250 ATTAAATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.72
28 2 0.08
29 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
TATATATATTATTGTATTATATAATATAA
Found at i:6649046 original size:22 final size:23
Alignment explanation
Indices: 6649020--6649074 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
6649010 TTTTATGTTT
*
6649020 TATATATATTATTTTATTATATAA
1 TATATATA-TATTGTATTATATAA
* *
6649044 TATA-ATATATTGTATTGTATTA
1 TATATATATATTGTATTATATAA
6649066 TAT-TATATA
1 TATATATATA
6649075 AATTAAATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 20 0.74
23 3 0.11
24 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
TATATATATATTGTATTATATAA
Found at i:6649059 original size:27 final size:27
Alignment explanation
Indices: 6649021--6649075 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
6649011 TTTATGTTTT
*
6649021 ATATATATTATTTTATTATATAATATA
1 ATATATATTATTGTATTATATAATATA
*
6649048 ATATAT-TGTATTGTATTATATTATATA
1 ATATATAT-TATTGTATTATATAATATA
6649075 A
1 A
6649076 ATTAAATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (27 bp):
ATATATATTATTGTATTATATAATATA
Found at i:6649265 original size:19 final size:19
Alignment explanation
Indices: 6649229--6649264 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6649219 TAAAAGAAAT
6649229 AAAGTAAAGTAAATAAAAG
1 AAAGTAAAGTAAATAAAAG
6649248 AAAGTAAAG-AAATAAAA
1 AAAGTAAAGTAAATAAAA
6649265 ACAAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (19 bp):
AAAGTAAAGTAAATAAAAG
Found at i:6650001 original size:12 final size:12
Alignment explanation
Indices: 6649984--6650026 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
6649974 ATGTGAAGTA
6649984 AGTATTAATATT
1 AGTATTAATATT
*
6649996 AGTATTAATATA
1 AGTATTAATATT
* *
6650008 ATTATTAGTATT
1 AGTATTAATATT
*
6650020 ATTATTA
1 AGTATTA
6650027 TTATGAGTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (12 bp):
AGTATTAATATT
Found at i:6650015 original size:18 final size:18
Alignment explanation
Indices: 6649992--6650030 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
6649982 TAAGTATTAA
6649992 TATTAGTATTAATATAAT
1 TATTAGTATTAATATAAT
* *
6650010 TATTAGTATTATTATTAT
1 TATTAGTATTAATATAAT
6650028 TAT
1 TAT
6650031 GAGTGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TATTAGTATTAATATAAT
Found at i:6662840 original size:14 final size:15
Alignment explanation
Indices: 6662810--6662841 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
6662800 AACAAGCTGC
6662810 TTTTGACTGAAATTT
1 TTTTGACTGAAATTT
6662825 TTTTGACTGAAATTT
1 TTTTGACTGAAATTT
6662840 TT
1 TT
6662842 AACTTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.56
Consensus pattern (15 bp):
TTTTGACTGAAATTT
Found at i:6663293 original size:33 final size:35
Alignment explanation
Indices: 6663256--6663352 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
6663246 ATGGTTATAT
6663256 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTGCTTAA
* *
6663289 TTAAAT-TTTATAA-ATAATTAATATTTATTGCTTAA
1 TTAAATATTTAAAATATAATT--TATATATTGCTTAA
*
6663324 --AAATATTTAAAATTTATATTTCATATATT
1 TTAAATATTTAAAATATA-ATTT-ATATATT
6663353 AAAATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 6 0.12
32 6 0.12
33 17 0.33
34 8 0.16
35 11 0.22
36 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTGCTTAA
Found at i:6663536 original size:13 final size:13
Alignment explanation
Indices: 6663520--6663553 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
6663510 TTTAAACCAA
6663520 ATTTTTTAAAAAT
1 ATTTTTTAAAAAT
* *
6663533 ATTTCTCAAAAAT
1 ATTTTTTAAAAAT
6663546 ATTTTTTA
1 ATTTTTTA
6663554 CACCACTTTT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTTTTTAAAAAT
Found at i:6665213 original size:3 final size:3
Alignment explanation
Indices: 6665205--6665231 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6665195 ATATTTTTGC
6665205 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
6665232 TTTTCTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:6668158 original size:26 final size:26
Alignment explanation
Indices: 6668128--6668177 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
6668118 TAAATATTTA
*
6668128 TTTTTAATTTTTTA-TTTTAAAATAC
1 TTTTTTATTTTTTATTTTTAAAATAC
6668153 TTTTTTATTTTTTATTTTTAAAATA
1 TTTTTTATTTTTTATTTTTAAAATA
6668178 AATTTTTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTTTATTTTTTATTTTTAAAATAC
Found at i:6668183 original size:25 final size:26
Alignment explanation
Indices: 6668129--6668183 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
6668119 AAATATTTAT
*
6668129 TTTTAATTTTTTATTTTAAAATAC-T
1 TTTTAATTTTTTATTTTAAAATACAA
*
6668154 TTTTTATTTTTTATTTTTAAAATA-AA
1 TTTTAATTTTTTA-TTTTAAAATACAA
6668180 TTTT
1 TTTT
6668184 TGGTGTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTTAATTTTTTATTTTAAAATACAA
Found at i:6668183 original size:26 final size:26
Alignment explanation
Indices: 6668127--6668184 Score: 82
Period size: 25 Copynumber: 2.2 Consensus size: 26
6668117 ATAAATATTT
6668127 ATTTTTAATTTTTTATTTTAAAAT-A
1 ATTTTTAATTTTTTATTTTAAAATAA
* *
6668152 CTTTTTTATTTTTTATTTTTAAAATAA
1 ATTTTTAATTTTTTA-TTTTAAAATAA
6668179 ATTTTT
1 ATTTTT
6668185 GGTGTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 13 0.46
26 9 0.32
27 6 0.21
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (26 bp):
ATTTTTAATTTTTTATTTTAAAATAA
Found at i:6670244 original size:2 final size:2
Alignment explanation
Indices: 6670237--6670261 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6670227 ATTTTGTAAG
6670237 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6670262 GTTGTTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6672451 original size:17 final size:17
Alignment explanation
Indices: 6672416--6672453 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
6672406 AGGAATAATT
*
6672416 ATATATAAAATTTAAAA
1 ATATATAAAATTAAAAA
6672433 ATATATAAAA-TAAATAA
1 ATATATAAAATTAAA-AA
6672450 ATAT
1 ATAT
6672454 TTTCAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATATAAAATTAAAAA
Found at i:6672484 original size:29 final size:27
Alignment explanation
Indices: 6672421--6672486 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
6672411 TAATTATATA
*
6672421 TAAAATTTAAAAATATATAAAATAAAT
1 TAAATTTTAAAAATATATAAAATAAAT
*
6672448 AAATATTTTCAAAAA-ATATAATAATAAATT
1 TAA-ATTTT-AAAAATATATAA-AATAAA-T
6672478 TAAATTTTA
1 TAAATTTTA
6672487 TATTAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
27 2 0.06
28 11 0.34
29 16 0.50
30 3 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
TAAATTTTAAAAATATATAAAATAAAT
Found at i:6672495 original size:6 final size:6
Alignment explanation
Indices: 6672486--6672535 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
6672476 TTTAAATTTT
* *
6672486 ATATTA ATATTA ATATTA ATATTA A-ATAA ATATAATT ATATTA ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATAT--TA ATATTA ATATTA
6672535 A
1 A
6672536 ATAAAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 4 0.11
6 29 0.78
8 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATATTA
Found at i:6672527 original size:25 final size:24
Alignment explanation
Indices: 6672498--6672544 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
6672488 ATTAATATTA
6672498 ATATTAATATTAAATAAATATAATT
1 ATATTAATATTAAATAAA-ATAATT
6672523 ATATTAATATTAAATAAAATAA
1 ATATTAATATTAAATAAAATAA
6672545 AAAACCCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATATTAATATTAAATAAAATAATT
Found at i:6674083 original size:24 final size:24
Alignment explanation
Indices: 6674032--6674093 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
6674022 TAGCTCGAAA
* * *
6674032 GAGCGTCCCATTATTAGCTCTCAT
1 GAGCATCCCGTTATTAGCCCTCAT
6674056 GAGCATCCCGTTATTAGCCCTC-T
1 GAGCATCCCGTTATTAGCCCTCAT
*
6674079 CGAGCTTCCCGTTAT
1 -GAGCATCCCGTTAT
6674094 ATAGTTCTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (24 bp):
GAGCATCCCGTTATTAGCCCTCAT
Found at i:6674339 original size:73 final size:75
Alignment explanation
Indices: 6674195--6674350 Score: 185
Period size: 73 Copynumber: 2.1 Consensus size: 75
6674185 AGCGTCTCGT
* * * * * *
6674195 TATATGGCTCTTCGTGAGCTTCCTGATTAAAGGCTCTTTGTGAGCTTCCCGATATGGCTTGCCTA
1 TATATGGCTATCCGTGAGCTTCCTGATTAAAGGCTCTTCGTGAGCTACCCGATATGGCTCGCATA
6674260 AACTTCCCGA
66 AACTTCCCGA
* *
6674270 TATATGGCTATCCG-GAGCTTCCTG-TTAATGGCTCTTCG-GAGCTACCCGTTATAGGCTCGCAT
1 TATATGGCTATCCGTGAGCTTCCTGATTAAAGGCTCTTCGTGAGCTACCCGATAT-GGCTCGCAT
* *
6674332 GAGCTTCCCGA
65 AAACTTCCCGA
6674343 T-TATGGCT
1 TATATGGCT
6674351 CTTATGAACT
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
72 19 0.27
73 29 0.41
74 10 0.14
75 12 0.17
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (75 bp):
TATATGGCTATCCGTGAGCTTCCTGATTAAAGGCTCTTCGTGAGCTACCCGATATGGCTCGCATA
AACTTCCCGA
Found at i:6674357 original size:24 final size:24
Alignment explanation
Indices: 6674176--6674362 Score: 78
Period size: 24 Copynumber: 7.6 Consensus size: 24
6674166 ACACACCGCA
* * *
6674176 GCTCTTATGAGCGTCTCGTTATATG
1 GCTCTTATGAGCTTCCCGAT-TATG
* * *
6674201 GCTCTTCGTGAGCTTCCTGATTAAAG
1 GCTCTT-ATGAGCTTCCCGATT-ATG
*
6674227 GCTCTTTGTGAGCTTCCCGA-TATG
1 GCTC-TTATGAGCTTCCCGATTATG
* *
6674251 GCTTGCCTA--AACTTCCCGATATATG
1 GC-T-CTTATGAGCTTCCCGAT-TATG
* *** *
6674276 GCTATCCGGAGCTTCCTG-TTAATG
1 GCTCTTATGAGCTTCCCGATT-ATG
** *
6674300 GCTCTTCGGAGCTACCCG-TTATAG
1 GCTCTTATGAGCTTCCCGATTAT-G
**
6674324 GCTCGCATGAGCTTCCCGATTATG
1 GCTCTTATGAGCTTCCCGATTATG
*
6674348 GCTCTTATGAACTTC
1 GCTCTTATGAGCTTC
6674363 TCGTATTACA
Statistics
Matches: 121, Mismatches: 29, Indels: 25
0.69 0.17 0.14
Matches are distributed among these distances:
23 12 0.10
24 52 0.43
25 27 0.22
26 28 0.23
27 2 0.02
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (24 bp):
GCTCTTATGAGCTTCCCGATTATG
Found at i:6681001 original size:42 final size:42
Alignment explanation
Indices: 6680909--6681087 Score: 153
Period size: 42 Copynumber: 4.3 Consensus size: 42
6680899 CCGAAGGCTG
** * * * *
6680909 AACAGAAGCTCATGAGAGCTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCAAAAGAGCTGAACAAAAACCCATAAGAGTTA
* * ** *
6680951 ATCGGAAGCTCGCAAGAGCTGAACAAAAACCCATAAGGGTTA
1 AACAGAAGCTCAAAAGAGCTGAACAAAAACCCATAAGAGTTA
* * * * *
6680993 AACAGAAGCTCAATAGAGCTGAA-AGGAAACTCATATGAGTTG
1 AACAGAAGCTCAAAAGAGCTGAACA-AAAACCCATAAGAGTTA
* * * *
6681035 AACAGAAGCTCAAAAGTGCTGAACGAAAACTCATATGAGTTA
1 AACAGAAGCTCAAAAGAGCTGAACAAAAACCCATAAGAGTTA
*
6681077 AACTGAAGCTC
1 AACAGAAGCTC
6681088 GTGAGAGCTA
Statistics
Matches: 111, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
41 1 0.01
42 110 0.99
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCAAAAGAGCTGAACAAAAACCCATAAGAGTTA
Found at i:6681046 original size:21 final size:21
Alignment explanation
Indices: 6680993--6681087 Score: 61
Period size: 21 Copynumber: 4.5 Consensus size: 21
6680983 ATAAGGGTTA
6680993 AACAGAAGCTCA-ATAGAGCTG
1 AACAGAAGCTCATAT-GAGCTG
* *
6681014 AA-AGGAAACTCATATGAGTTG
1 AACA-GAAGCTCATATGAGCTG
* * *
6681035 AACAGAAGCTCAAAAGTGCTG
1 AACAGAAGCTCATATGAGCTG
* * *
6681056 AAC-GAAAACTCATATGAGTTA
1 AACAG-AAGCTCATATGAGCTG
*
6681077 AACTGAAGCTC
1 AACAGAAGCTC
6681088 GTGAGAGCTA
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
20 2 0.04
21 49 0.89
22 4 0.07
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (21 bp):
AACAGAAGCTCATATGAGCTG
Found at i:6681056 original size:84 final size:84
Alignment explanation
Indices: 6680909--6681105 Score: 218
Period size: 84 Copynumber: 2.3 Consensus size: 84
6680899 CCGAAGGCTG
* * * **
6680909 AACAGAAGCTCATGAGAGCTAAACAGAAACCCATAAGGGTTGATCGGAAGCTCGCAAGAGCTGAA
1 AACAGAAGCTCATGAGAGCTAAACAGAAACCCATAAGAGTTGAACAGAAGCTCAAAAGAGCTGAA
*
6680974 CAAAAACCCATAAGGGTTA
66 CAAAAACCCATAAGAGTTA
* * * *
6680993 AACAGAAGCTCAAT-AGAGCTGAAA-GGAAACTCATATGAGTTGAACAGAAGCTCAAAAGTGCTG
1 AACAGAAGCTC-ATGAGAGCT-AAACAGAAACCCATAAGAGTTGAACAGAAGCTCAAAAGAGCTG
* * *
6681056 AACGAAAACTCATATGAGTTA
64 AACAAAAACCCATAAGAGTTA
* * *
6681077 AACTGAAGCTCGTGAGAGCTAAACGGAAA
1 AACAGAAGCTCATGAGAGCTAAACAGAAA
6681106 GTAAACATGA
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
83 4 0.04
84 85 0.90
85 5 0.05
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (84 bp):
AACAGAAGCTCATGAGAGCTAAACAGAAACCCATAAGAGTTGAACAGAAGCTCAAAAGAGCTGAA
CAAAAACCCATAAGAGTTA
Found at i:6681728 original size:16 final size:16
Alignment explanation
Indices: 6681707--6681737 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6681697 ATTTGGTCCT
6681707 AAAATTAATATCTAAC
1 AAAATTAATATCTAAC
*
6681723 AAAATTATTATCTAA
1 AAAATTAATATCTAA
6681738 AATCATCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTAATATCTAAC
Found at i:6684650 original size:20 final size:21
Alignment explanation
Indices: 6684600--6684667 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
6684590 TAAAAATATA
*
6684600 AATTCTGAAATTTTTATAAA-T
1 AATT-TGAAATTTTTAAAAACT
** *
6684621 -ATTTTTAA-TTTTAAAAATT
1 AATTTGAAATTTTTAAAAACT
*
6684640 AATTTGAAATTTTTGAAAACT
1 AATTTGAAATTTTTAAAAACT
6684661 AATTTGA
1 AATTTGA
6684668 TTTTTCTTCT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
18 8 0.22
19 4 0.11
20 9 0.24
21 16 0.43
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (21 bp):
AATTTGAAATTTTTAAAAACT
Found at i:6690389 original size:2 final size:2
Alignment explanation
Indices: 6690382--6690420 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6690372 ACAAATCTTT
6690382 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
6690421 TTTGTCTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:6699543 original size:3 final size:3
Alignment explanation
Indices: 6699535--6699566 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
6699525 ACAAATTATT
*
6699535 TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
6699567 CATAGAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:6700001 original size:21 final size:21
Alignment explanation
Indices: 6699958--6700005 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
6699948 TAATAAAATA
*
6699958 TTAAAAAATAAATATTTTCTT
1 TTAAAAAATAAATATTATCTT
* *
6699979 TTAAAAAATACATATTAATTTT
1 TTAAAAAATAAATATT-ATCTT
6700001 TTAAA
1 TTAAA
6700006 GTTGTTTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAAAAAATAAATATTATCTT
Found at i:6701743 original size:13 final size:13
Alignment explanation
Indices: 6701727--6701751 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6701717 TTTAGTTATA
6701727 TTTTTTCTTTCTT
1 TTTTTTCTTTCTT
6701740 TTTTTTCTTTCT
1 TTTTTTCTTTCT
6701752 CCTCTCTATC
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTCTTTCTT
Found at i:6705715 original size:30 final size:29
Alignment explanation
Indices: 6705681--6705737 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
6705671 TTATCAAATA
*
6705681 AATAAA-ATCTTTTAATATAATAATTTAATT
1 AATAAATATATTTTAAT-TAA-AATTTAATT
*
6705711 AATAAATATATTTTACTTAAAATTTAA
1 AATAAATATATTTTAATTAAAATTTAA
6705738 GAAAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 9 0.38
31 8 0.33
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (29 bp):
AATAAATATATTTTAATTAAAATTTAATT
Found at i:6705861 original size:17 final size:16
Alignment explanation
Indices: 6705830--6705873 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
6705820 GATTTATTTA
6705830 ATAATATAATATCATT
1 ATAATATAATATCATT
*
6705846 ATAATTTAATTATCATT
1 ATAATATAA-TATCATT
*
6705863 AATTATATAAT
1 -ATAATATAAT
6705874 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATAATATCATT
Found at i:6710725 original size:13 final size:13
Alignment explanation
Indices: 6710709--6710746 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
6710699 AGTTCTTCAT
6710709 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
6710722 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
6710735 TACTTTTGAGAA
1 TGCTTTTGAGAA
6710747 ATTTGAGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:6715100 original size:17 final size:16
Alignment explanation
Indices: 6715069--6715112 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
6715059 GATTTATTTA
6715069 ATAATATAATATCATT
1 ATAATATAATATCATT
*
6715085 ATAATTTAATTATCATT
1 ATAATATAA-TATCATT
*
6715102 AATTATATAAT
1 -ATAATATAAT
6715113 TAAACTAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATAATATCATT
Found at i:6725329 original size:21 final size:20
Alignment explanation
Indices: 6725305--6725395 Score: 76
Period size: 21 Copynumber: 4.3 Consensus size: 20
6725295 CACAAAAGCA
6725305 CATAAGTGCTGAACAGAAACC
1 CATAAG-GCTGAACAGAAACC
* *
6725326 CATAAAGGTTGAACGGAAACC
1 CAT-AAGGCTGAACAGAAACC
* * *
6725347 CATAAGGGTTAA-ACTAAACC
1 CATAAGGCTGAACA-GAAACC
*
6725367 TCAAAAGAGCTGAACAGAAACC
1 -CATAAG-GCTGAACAGAAACC
6725389 CATAAGG
1 CATAAGG
6725396 GTTAAACTGA
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
20 13 0.24
21 28 0.52
22 12 0.22
23 1 0.02
ACGTcount: A:0.45, C:0.21, G:0.20, T:0.14
Consensus pattern (20 bp):
CATAAGGCTGAACAGAAACC
Found at i:6725381 original size:42 final size:42
Alignment explanation
Indices: 6725335--6725450 Score: 187
Period size: 42 Copynumber: 2.7 Consensus size: 42
6725325 CCATAAAGGT
6725335 TGAACGGAAACCCATAAGGGTTAAACTAAACCTCAAAAGAGC
1 TGAACGGAAACCCATAAGGGTTAAACTAAACCTCAAAAGAGC
* * *
6725377 TGAACAGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGC
1 TGAACGGAAACCCATAAGGGTTAAACTAAACCTCAAAAGAGC
*
6725419 TGAACGAAAACCCATAAGGGTTAAACTGAAAC
1 TGAACGGAAACCCATAAGGGTTAAACT-AAAC
6725451 TCATATGAGT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
42 64 0.97
43 2 0.03
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.15
Consensus pattern (42 bp):
TGAACGGAAACCCATAAGGGTTAAACTAAACCTCAAAAGAGC
Found at i:6725455 original size:21 final size:21
Alignment explanation
Indices: 6725320--6725455 Score: 105
Period size: 21 Copynumber: 6.5 Consensus size: 21
6725310 GTGCTGAACA
* * *
6725320 GAAACCCATAAAGGTTGAACG
1 GAAACCCATAAGGGTTAAACT
6725341 GAAACCCATAAGGGTTAAACT
1 GAAACCCATAAGGGTTAAACT
* * * * *
6725362 -AAACCTCAAAAGAGCTGAACA
1 GAAACC-CATAAGGGTTAAACT
6725383 GAAACCCATAAGGGTTAAACT
1 GAAACCCATAAGGGTTAAACT
* * * * * *
6725404 GAAGCTCAAAAGAGCTGAAC-
1 GAAACCCATAAGGGTTAAACT
6725424 GAAAACCCATAAGGGTTAAACT
1 G-AAACCCATAAGGGTTAAACT
*
6725446 GAAACTCATA
1 GAAACCCATA
6725456 TGAGTTAATA
Statistics
Matches: 85, Mismatches: 26, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
20 6 0.07
21 73 0.86
22 6 0.07
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.15
Consensus pattern (21 bp):
GAAACCCATAAGGGTTAAACT
Found at i:6733935 original size:51 final size:50
Alignment explanation
Indices: 6733867--6734061 Score: 205
Period size: 51 Copynumber: 3.9 Consensus size: 50
6733857 TAAATGATAC
* * * *
6733867 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TATCAT
* * * *
6733918 CCGATACACGTAGTAGCCTGCACATAGTACTACACACGTAATCGA-AGCTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATATC-AT
* * * * ***
6733969 TCGGTACGCATAGTAGCCTGCACATAGTACTATACATACGACC-TATCATT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATATCA-T
6734019 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC
6734062 TAGCAACTTC
Statistics
Matches: 114, Mismatches: 26, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
49 1 0.01
50 41 0.36
51 70 0.61
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (50 bp):
CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATATCAT
Found at i:6734051 original size:101 final size:101
Alignment explanation
Indices: 6733875--6734057 Score: 296
Period size: 101 Copynumber: 1.8 Consensus size: 101
6733865 ACCCGGTTCA
** *
6733875 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATACGACCA-TATCATCCGATACACGTAGTAGCCTGCA
6733940 CATAGTACTACACACGTAATCGAAGCTATTCGGTACG
65 CATAGTACTACACACGTAATCGAAGCTATTCGGTACG
* *
6733977 CATAGTAGCCTGCACATAGTACTATACATACGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATACGACCATATCA-TCCGATACACGTAGTAGCCTGCA
6734041 CATAGTACTACACACGT
65 CATAGTACTACACACGT
6734058 GACCTAGCAA
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.52
102 32 0.43
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATACGACCATATCATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTAATCGAAGCTATTCGGTACG
Found at i:6738745 original size:14 final size:14
Alignment explanation
Indices: 6738728--6738762 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
6738718 ATAAAATATA
*
6738728 AATTTATATTTAAT
1 AATTCATATTTAAT
*
6738742 AATTCATTTTTAAT
1 AATTCATATTTAAT
6738756 AATTCAT
1 AATTCAT
6738763 TAATAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (14 bp):
AATTCATATTTAAT
Found at i:6738763 original size:14 final size:14
Alignment explanation
Indices: 6738736--6738763 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6738726 TAAATTTATA
6738736 TTTAATAATTCATT
1 TTTAATAATTCATT
6738750 TTTAATAATTCATT
1 TTTAATAATTCATT
6738764 AATAAATTGG
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:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATTCATT
Found at i:6739207 original size:19 final size:19
Alignment explanation
Indices: 6739185--6739222 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
6739175 TCCCTCATCC
6739185 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
6739204 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
6739223 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:6741507 original size:43 final size:41
Alignment explanation
Indices: 6741398--6741523 Score: 107
Period size: 43 Copynumber: 3.0 Consensus size: 41
6741388 CGTACAATGC
* *
6741398 CAACGTCCCAGACGTGCTCTTACATGTAATCACATATCGATG
1 CAACGT-CCAGACGTGGTCTTACATGTAAACACATATCGATG
*
6741440 CCACTGTCCTAGACAG-GG-CTTTACATGTAAACACA-AGTCGATG
1 CAAC-GTCC-AGAC-GTGGTC-TTACATGTAAACACATA-TCGATG
*
6741483 TCAACGTCTCAGACGTGGTCTTACAAG-ATAACACATATCGA
1 -CAACGTC-CAGACGTGGTCTTACATGTA-AACACATATCGA
6741524 AAATCCTATG
Statistics
Matches: 68, Mismatches: 5, Indels: 21
0.72 0.05 0.22
Matches are distributed among these distances:
42 9 0.13
43 52 0.76
44 7 0.10
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (41 bp):
CAACGTCCAGACGTGGTCTTACATGTAAACACATATCGATG
Found at i:6746230 original size:17 final size:17
Alignment explanation
Indices: 6746208--6746249 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
6746198 GTTACAAAGG
6746208 ACACACGGTCGTGTGTC
1 ACACACGGTCGTGTGTC
6746225 ACACACGGTCGTGTGTC
1 ACACACGGTCGTGTGTC
6746242 ACACACGG
1 ACACACGG
6746250 CTGAGACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.21, C:0.31, G:0.29, T:0.19
Consensus pattern (17 bp):
ACACACGGTCGTGTGTC
Found at i:6748894 original size:3 final size:3
Alignment explanation
Indices: 6748886--6748974 Score: 151
Period size: 3 Copynumber: 29.7 Consensus size: 3
6748876 ATCATTTTTA
6748886 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* **
6748934 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT CGT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
6748975 CCATTACTAT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:6748980 original size:21 final size:21
Alignment explanation
Indices: 6748945--6748984 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6748935 ATTATTATTA
**
6748945 TTATTATTATTATTACTATCG
1 TTATTATTACCATTACTATCG
6748966 TTATTATTACCATTACTAT
1 TTATTATTACCATTACTAT
6748985 TACTTCTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (21 bp):
TTATTATTACCATTACTATCG
Found at i:6749386 original size:20 final size:18
Alignment explanation
Indices: 6749345--6749388 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
6749335 GCTTTATTAT
* *
6749345 TATTGTCATTCATTGTTG
1 TATTGTCATTCATTATTC
6749363 TATTGTCATTCTCATTATTC
1 TATTGTCA-T-TCATTATTC
6749383 TATTGT
1 TATTGT
6749389 ATATATTAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 1 0.05
20 13 0.59
ACGTcount: A:0.18, C:0.14, G:0.11, T:0.57
Consensus pattern (18 bp):
TATTGTCATTCATTATTC
Found at i:6753306 original size:3 final size:3
Alignment explanation
Indices: 6753298--6753325 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6753288 AATTAAAAAC
6753298 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
6753326 GGTAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:6754294 original size:17 final size:18
Alignment explanation
Indices: 6754272--6754306 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6754262 TTGCCGCTTA
*
6754272 TTTCTCT-TTTTGTTTGT
1 TTTCTCTGTTGTGTTTGT
6754289 TTTCTCTGTTGTGTTTGT
1 TTTCTCTGTTGTGTTTGT
6754307 GGGTGTCTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.00, C:0.11, G:0.17, T:0.71
Consensus pattern (18 bp):
TTTCTCTGTTGTGTTTGT
Found at i:6764271 original size:12 final size:12
Alignment explanation
Indices: 6764254--6764294 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
6764244 TCAAATCCAA
6764254 TCAAAAAATATT
1 TCAAAAAATATT
6764266 TCAAAAAA-A--
1 TCAAAAAATATT
6764275 TCAAAAAATATT
1 TCAAAAAATATT
6764287 TCAAAAAA
1 TCAAAAAA
6764295 AATGAAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 8 0.31
10 1 0.04
11 1 0.04
12 16 0.62
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (12 bp):
TCAAAAAATATT
Found at i:6764302 original size:21 final size:21
Alignment explanation
Indices: 6764252--6764295 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
6764242 GTTCAAATCC
6764252 AATCAAAAAATATTTCAAAAA
1 AATCAAAAAATATTTCAAAAA
6764273 AATCAAAAAATATTTCAAAAA
1 AATCAAAAAATATTTCAAAAA
6764294 AA
1 AA
6764296 ATGAAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (21 bp):
AATCAAAAAATATTTCAAAAA
Found at i:6764324 original size:6 final size:6
Alignment explanation
Indices: 6764315--6764360 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
6764305 AAAATAATGA
* * *
6764315 AAAAAG -AAAAG AAAAAG AGAAGG AAAAAG -AAAAG GAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
6764361 GAGAGGCCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
5 10 0.30
6 23 0.70
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:6764329 original size:11 final size:11
Alignment explanation
Indices: 6764315--6764358 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
6764305 AAAATAATGA
6764315 AAAAAGAAAAG
1 AAAAAGAAAAG
*
6764326 AAAAAGAGAAGG
1 AAAAAGA-AAAG
6764338 AAAAAGAAAAG
1 AAAAAGAAAAG
*
6764349 GAAAAGAAAA
1 AAAAAGAAAA
6764359 AGGAGAGGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:6764344 original size:18 final size:17
Alignment explanation
Indices: 6764316--6764360 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
6764306 AAATAATGAA
6764316 AAAAG-AAAAGAAAAAG
1 AAAAGAAAAAGAAAAAG
* *
6764332 AGAAGGAAAAAGAAAAGG
1 A-AAAGAAAAAGAAAAAG
6764350 AAAAGAAAAAG
1 AAAAGAAAAAG
6764361 GAGAGGCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 12 0.50
18 11 0.46
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAGAAAAAG
Found at i:6765726 original size:6 final size:6
Alignment explanation
Indices: 6765695--6765743 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
6765685 CCAAACACAC
* *
6765695 CAGTAAA CAGTAA TCAGTAA CGGTAA CAGTAA CAGTAA AAGTAA CAGTA
1 CAGT-AA CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
6765744 TTCAACACAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 27 0.73
7 10 0.27
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.18
Consensus pattern (6 bp):
CAGTAA
Found at i:6765774 original size:45 final size:46
Alignment explanation
Indices: 6765723--6765829 Score: 146
Period size: 46 Copynumber: 2.3 Consensus size: 46
6765713 AACGGTAACA
* *
6765723 GTAACAGTAAAAGTAACAGTA-TTCAACACACAAAGTGCTGAATCT-
1 GTAACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAAT-TG
* * *
6765768 GTAACAGTACCGGTAACAGTATTTCGACACACAAAGTGCCGAATTG
1 GTAACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATTG
6765814 GTAACAGTAACAGTAA
1 GTAACAGTAACAGTAA
6765830 TCGGCACATA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 19 0.36
46 34 0.64
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (46 bp):
GTAACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATTG
Found at i:6767946 original size:7 final size:7
Alignment explanation
Indices: 6767929--6767961 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
6767919 TTGAGTCCTA
6767929 AAAAAAGG
1 AAAAAA-G
6767937 AAAAAAG
1 AAAAAAG
6767944 AAAAAAG
1 AAAAAAG
6767951 -AAAAAG
1 AAAAAAG
6767957 AAAAA
1 AAAAA
6767962 GGAGAGGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.25
7 12 0.50
8 6 0.25
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:6768863 original size:24 final size:24
Alignment explanation
Indices: 6768831--6768883 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
6768821 CTAAAAGTAT
6768831 AGTGGATTGAACCTTGAAGATTAA
1 AGTGGATTGAACCTTGAAGATTAA
*
6768855 AGTGGATTGAACCTTGAAGATTAT
1 AGTGGATTGAACCTTGAAGATTAA
6768879 AGTGG
1 AGTGG
6768884 GGGAAATCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (24 bp):
AGTGGATTGAACCTTGAAGATTAA
Found at i:6769273 original size:44 final size:43
Alignment explanation
Indices: 6769211--6770101 Score: 307
Period size: 44 Copynumber: 19.9 Consensus size: 43
6769201 GAATATGGCG
6769211 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA
* * * **
6769254 TAATCCTATCTCCCTGAAGTTGCAATGGAGCGGATTAAAGTTACA
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-A
* * * * * * **
6769299 AGTTTTATCTCCCTGAAGTTACGGTGGAGCAGACTGAAGAAAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA
* * *
6769342 CAAGTCTTATC-CCTCTGAAGTTGCAGTGGGGCAGACTGAAGATGGC-A
1 -AA-TCTTATCTCC-CTGAAGTTGCAGTGGAGCAGA-TTAA-A-GCCAA
*
6769389 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA
* * * * **
6769432 CAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTGAAGTTACA
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-A
* * * ** *
6769477 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA--A
* * * *
6769522 AATCTTATCTCCCTAAAGTTGCAATGGAACAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-A
** * * * * *
6769566 AATCACAGATTTTATCTCTTTGAAGTTACAGTAGAGCAGA-TCATGGC-A
1 AAT--C-----TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA
* * * * * * * *
6769614 GATCTTATCTCTCTGAAGGTGTAATGGAGCAGATTAAAACGATG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-A
* * * * *
6769658 AATCCTATACAT--CTGATGTTGCAGTAGG-TCGGATTAAATCTACCATTA
1 AATCTTAT-C-TCCCTGAAGTTGCAGT-GGAGCAGATTAAA---GCCA--A
* * * * * * **
6769706 CAAGTCTTATCTTCTTGAAGTTGTAGTGGAGTAGACTGAAGATATCA
1 -AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA--A
* * * **
6769753 AACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-A
* * * * *
6769797 AATCTTATCCCCCTAAAGTTGCAGTGGGGCAAATTAAAACTGC-A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC--CAA
* * * * * * **
6769841 AGTCTTGTCTCCTTGAAGTTGCAGTGGAGTAGACTGAAGATATCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA--A
* * * *
6769886 AATCTCAT-TCCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACA
1 AATCTTATCT-CCCTGAAGTTGCAGTGGAGCAGATTAAAGC-------CA-A
* * * * * *
6769937 AATCTTATCTCTCTAAAGTTGCAGTAGAGTAGATCATAG-C-A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA
* * * * * *
6769978 AACCCTACCTCCCTAAAGTTGCAGTGGAGCAAATTCAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-A
* * * **
6770022 AACCTTATC-CTCCTGAAG-TGCAGTGGAGCAGGTTGAAG-TTA
1 AATCTTATCTC-CCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA
* * * *
6770063 AGTCTTATCTCTCTGAAGTTGCAGTGGAGTATATTAAAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
6770102 ATAGCGAGTC
Statistics
Matches: 620, Mismatches: 173, Indels: 110
0.69 0.19 0.12
Matches are distributed among these distances:
41 67 0.11
42 22 0.04
43 21 0.03
44 248 0.40
45 155 0.25
46 10 0.02
47 8 0.01
48 6 0.01
49 5 0.01
50 23 0.04
51 52 0.08
52 3 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA
Found at i:6769360 original size:45 final size:45
Alignment explanation
Indices: 6769213--6769924 Score: 341
Period size: 44 Copynumber: 15.8 Consensus size: 45
6769203 ATATGGCGAA
* * ** *
6769213 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAG
* * * * * *
6769257 TCCTATCTCCCTGAAGTTGCAATGGAGCGGATTAAAG-TTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAG
* * * *
6769301 TTTTATCTCCCTGAAGTTACGGTGGAGCAGACTGAAGAAAACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAG
* ** *
6769346 TCTTATC-CCTCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAA
1 TCTTATCTCC-CTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAG
* * * **
6769391 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAACAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAG
* * * * *
6769435 TCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTGAAG-TTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAG
*
6769479 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAAC-AAG
* * * * *
6769524 TCTTATCTCCCTAAAGTTGCAATGGAACAGATTAAAGCTATAAATCACAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG--AT-AA-CA-AG
* ** * * * **
6769574 ATTTTATCTCTTTGAAGTTACAGTAGAGCAGA-T---CATGGC-AG
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAG
* * * * * * *
6769615 ATCTTATCTCTCTGAAGGTGTAATGGAGCAGATTAAAACGAT--GAA-
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAA-GATAACAAG
* * ** * ** *
6769660 TCCTATACAT--CTGATGTTGCAGTAGGTCGGATTAAATCT-ACCATTACAAG
1 TCTTAT-C-TCCCTGAAGTTGC---A-GT-GGAGCAGA-CTGAAGATAACAAG
* * * * * *
6769710 TCTTATCTTCTTGAAGTTGTAGTGGAGTAGACTGAAGATATCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAG
* ** *
6769755 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGAT-ACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAG
* * * * * * *
6769799 TCTTATCCCCCTAAAGTTGCAGTGGGGCA-AATTAAAACT-GCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA-TAACAAG
* * * * *
6769843 TCTTGTCTCCTTGAAGTTGCAGTGGAGTAGACTGAAGATATCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAG
* * *
6769888 TCTCAT-TCCCCTGAAGTTGCAGTGGAACAGATTGAAG
1 TCTTATCT-CCCTGAAGTTGCAGTGGAGCAGACTGAAG
6769925 CTATAAATTA
Statistics
Matches: 500, Mismatches: 129, Indels: 77
0.71 0.18 0.11
Matches are distributed among these distances:
41 27 0.05
42 1 0.00
43 12 0.02
44 202 0.40
45 190 0.38
46 8 0.02
47 8 0.02
48 5 0.01
49 10 0.02
50 14 0.03
51 23 0.05
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAACAAG
Found at i:6769530 original size:178 final size:178
Alignment explanation
Indices: 6769205--6769544 Score: 540
Period size: 178 Copynumber: 1.9 Consensus size: 178
6769195 ATTGAAGAAT
* * *
6769205 ATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTG
1 ATGGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAACAATCCTATCTCCCTG
* *
6769270 AAGTTGCAATGGAGCGGATTAAAGTTACAAGTTTTATCTCCCTGAAGTTACGGTGGAGCAGACTG
66 AAGTTGCAATGGAGCGGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTG
*
6769335 AAGAAAACAAGTCTTATC-CCTCTGAAGTTGCAGTGGGGCAGACTGAAG
131 AAGAAAACAAGTCTTATCTCC-CTAAAGTTGCAGTGGGGCAGACTGAAG
6769383 ATGGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAACAATCCTATCTCCCTG
1 ATGGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAACAATCCTATCTCCCTG
* * * *
6769448 AGGTTGCAGTGGAGCGGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG
66 AAGTTGCAATGGAGCGGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTG
* *
6769513 AAGATAGCGAA-TCTTATCTCCCTAAAGTTGCA
131 AAGAAAAC-AAGTCTTATCTCCCTAAAGTTGCA
6769545 ATGGAACAGA
Statistics
Matches: 148, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
178 144 0.97
179 4 0.03
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (178 bp):
ATGGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAACAATCCTATCTCCCTG
AAGTTGCAATGGAGCGGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTG
AAGAAAACAAGTCTTATCTCCCTAAAGTTGCAGTGGGGCAGACTGAAG
Found at i:6769535 original size:133 final size:135
Alignment explanation
Indices: 6769213--6769561 Score: 431
Period size: 133 Copynumber: 2.6 Consensus size: 135
6769203 ATATGGCGAA
* * ** * *
6769213 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA--ATAATCCTATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCA-AATCTTATCTCCCTAAAGTTG
* ** ** *
6769276 CAATGGAGCGGATTAAAG-TTACAAGTTTTATCTCCCTGAAGTTACGGTGGAGCAGACTGAAGAA
65 CAATGGAGCAGATTAAAGCCAACAAGTCCTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGAA
6769340 AACAAG
130 AACAAG
* *
6769346 TCTTATC-CCTCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAATCTTATCTCCCTAAAGTTG
1 TCTTATCTCC-CTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCCCTAAAGTTG
* * * * * *
6769410 CAGTGGAGCAGATTAAAGCCAACAA-TCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTGAAG-T
65 CAATGGAGCAGATTAAAGCCAACAAGTCCTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGAA
*
6769473 TACAAG
130 AACAAG
*
6769479 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATCTCCCTAAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCCCTAAAGTTGC
*
6769544 AATGGAACAGATTAAAGC
66 AATGGAGCAGATTAAAGC
6769562 TATAAATCAC
Statistics
Matches: 185, Mismatches: 26, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
132 2 0.01
133 111 0.60
134 67 0.36
135 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26
Consensus pattern (135 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATCTCCCTAAAGTTGC
AATGGAGCAGATTAAAGCCAACAAGTCCTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGAAA
ACAAG
Found at i:6771485 original size:26 final size:26
Alignment explanation
Indices: 6771454--6771581 Score: 127
Period size: 26 Copynumber: 4.9 Consensus size: 26
6771444 TATCATCCCC
6771454 TATTTTAAATTTTTATATATATTATT
1 TATTTTAAATTTTTATATATATTATT
* *
6771480 TATTTTAAGTTGTTT-TACATATTATT
1 TATTTTAAATT-TTTATATATATTATT
*
6771506 TA-TTTAAATTTCTTTTATATATTATT
1 TATTTTAAATTT-TTATATATATTATT
* * * *
6771532 TATTGTAAACTATTATATATA-TATA
1 TATTTTAAATTTTTATATATATTATT
*
6771557 TATCTTTCAAATTTATATATATATT
1 TAT-TTT-AAATTTTTATATATATT
6771582 TAAAACTATT
Statistics
Matches: 82, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
24 1 0.01
25 15 0.18
26 44 0.54
27 21 0.26
28 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.59
Consensus pattern (26 bp):
TATTTTAAATTTTTATATATATTATT
Found at i:6771649 original size:11 final size:11
Alignment explanation
Indices: 6771588--6771671 Score: 50
Period size: 10 Copynumber: 7.5 Consensus size: 11
6771578 TATTTAAAAC
*
6771588 TATTTTATATGT
1 TATTTTAT-TAT
6771600 TATTTT-TATAT
1 TATTTTAT-TAT
6771611 TATTTATATTATT
1 TATTT-TATTA-T
*
6771624 TATTTTA-AAT
1 TATTTTATTAT
*
6771634 TATTTTATTGT
1 TATTTTATTAT
*
6771645 TA-TTTATTTT
1 TATTTTATTAT
*
6771655 TAGTTTTTTTA-
1 TA-TTTTATTAT
6771666 TATTTT
1 TATTTT
6771672 GTTTACTTGA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
10 21 0.36
11 15 0.25
12 16 0.27
13 7 0.12
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:6771666 original size:25 final size:25
Alignment explanation
Indices: 6771578--6771654 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 25
6771568 TTTATATATA
* *
6771578 TATTTAAAACTATTTTATATGTTA--
1 TATTTTAAATTATTTTAT-TGTTATT
* *
6771602 T-TTTTATATTA-TTTA-TATTATT
1 TATTTTAAATTATTTTATTGTTATT
6771624 TATTTTAAATTATTTTATTGTTATT
1 TATTTTAAATTATTTTATTGTTATT
6771649 TATTTT
1 TATTTT
6771655 TAGTTTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
20 4 0.10
22 5 0.12
23 16 0.38
24 5 0.12
25 12 0.29
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (25 bp):
TATTTTAAATTATTTTATTGTTATT
Found at i:6774068 original size:22 final size:22
Alignment explanation
Indices: 6774033--6774086 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
6774023 GACCCTTTAC
** *
6774033 AAGCACGTGCTCCACTCCTCAA
1 AAGCACGTTTTCCACTCCTAAA
*
6774055 AAGCACGTTTTCCATTCCTAAA
1 AAGCACGTTTTCCACTCCTAAA
*
6774077 AAACACGTTT
1 AAGCACGTTT
6774087 ACATGACTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.31, G:0.11, T:0.26
Consensus pattern (22 bp):
AAGCACGTTTTCCACTCCTAAA
Found at i:6777443 original size:18 final size:18
Alignment explanation
Indices: 6777420--6777454 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6777410 TTTTAAAGGC
*
6777420 TTGAAAGTTTGAAAATAT
1 TTGAAAATTTGAAAATAT
*
6777438 TTGAAAATTTTAAAATA
1 TTGAAAATTTGAAAATA
6777455 AATGTTAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (18 bp):
TTGAAAATTTGAAAATAT
Found at i:6778918 original size:26 final size:26
Alignment explanation
Indices: 6778882--6778956 Score: 150
Period size: 26 Copynumber: 2.9 Consensus size: 26
6778872 ATCCTAGCCT
6778882 GTAAGGAGTGGCTCTTGTCTCGCCAC
1 GTAAGGAGTGGCTCTTGTCTCGCCAC
6778908 GTAAGGAGTGGCTCTTGTCTCGCCAC
1 GTAAGGAGTGGCTCTTGTCTCGCCAC
6778934 GTAAGGAGTGGCTCTTGTCTCGC
1 GTAAGGAGTGGCTCTTGTCTCGC
6778957 TGAGTGCTAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.15, C:0.25, G:0.32, T:0.28
Consensus pattern (26 bp):
GTAAGGAGTGGCTCTTGTCTCGCCAC
Found at i:6779433 original size:29 final size:30
Alignment explanation
Indices: 6779390--6779453 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
6779380 AAATTGGGAC
*
6779390 TTTAGTCCTTATACTTTT-A-TTTTTAGAAA
1 TTTAGTCCTTATACTTTTCAGATTTTA-AAA
6779419 TTTAGTTCCTT-TACTTTTCAGATTTTAAAA
1 TTTAG-TCCTTATACTTTTCAGATTTTAAAA
6779449 TTTAG
1 TTTAG
6779454 ATCCAACTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
29 12 0.39
30 14 0.45
31 5 0.16
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.55
Consensus pattern (30 bp):
TTTAGTCCTTATACTTTTCAGATTTTAAAA
Found at i:6780573 original size:21 final size:21
Alignment explanation
Indices: 6780539--6780581 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
6780529 TGTTACATAA
6780539 ATTTAATTTAAAAAT-TAAAT
1 ATTTAATTTAAAAATATAAAT
*
6780559 ATTTACATTTGAAAATATAAAT
1 ATTTA-ATTTAAAAATATAAAT
6780581 A
1 A
6780582 AAATTATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 9 0.45
22 6 0.30
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
ATTTAATTTAAAAATATAAAT
Found at i:6785385 original size:20 final size:20
Alignment explanation
Indices: 6785349--6785386 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6785339 AAATTATAAG
*
6785349 TAATTTTATTTAAGTTTAAA
1 TAATTTTATTAAAGTTTAAA
6785369 TAATTTT-TTAAATGTTTA
1 TAATTTTATTAAA-GTTTA
6785387 TTAGAAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
TAATTTTATTAAAGTTTAAA
Found at i:6789719 original size:12 final size:12
Alignment explanation
Indices: 6789702--6789783 Score: 62
Period size: 12 Copynumber: 7.0 Consensus size: 12
6789692 TAACCATTTA
6789702 ATTATTTTTATT
1 ATTATTTTTATT
**
6789714 ATTATTGCTATT
1 ATTATTTTTATT
*
6789726 ATTATTTTTATC
1 ATTATTTTTATT
*
6789738 ACTA--TTTATT
1 ATTATTTTTATT
* *
6789748 ATTGTTCTTATT
1 ATTATTTTTATT
*
6789760 ATTATATTTGATT
1 ATTAT-TTTTATT
*
6789773 A-TATTTCTATT
1 ATTATTTTTATT
6789784 TACCTATATG
Statistics
Matches: 52, Mismatches: 15, Indels: 7
0.70 0.20 0.09
Matches are distributed among these distances:
10 7 0.13
11 5 0.10
12 34 0.65
13 6 0.12
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.65
Consensus pattern (12 bp):
ATTATTTTTATT
Found at i:6789778 original size:34 final size:34
Alignment explanation
Indices: 6789697--6789778 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
6789687 TTTTTTAACC
*
6789697 ATTTAATTATTTTTATTATTATTGCTATTATTAT
1 ATTTAATTATATTTATTATTATTGCTATTATTAT
* * *
6789731 -TTTTATCACTATTTATTATTGTT-CTTATTATTAT
1 ATTTAATTA-TATTTATTATTATTGC-TATTATTAT
*
6789765 ATTTGATTATATTT
1 ATTTAATTATATTT
6789779 CTATTTACCT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
33 7 0.18
34 26 0.67
35 6 0.15
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.65
Consensus pattern (34 bp):
ATTTAATTATATTTATTATTATTGCTATTATTAT
Found at i:6796730 original size:25 final size:24
Alignment explanation
Indices: 6796685--6796768 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 24
6796675 TCCGACCCAC
*
6796685 AGAGCATACCGATTTATAGCTCGTG
1 AGAGCATACCGA-TTACAGCTCGTG
* *
6796710 AGAGCATACTGATCTACAGCTCGAG
1 AGAGCATACCGAT-TACAGCTCGTG
*
6796735 TGAGCATACCGATTCACAGCTCGT-
1 AGAGCATACCGATT-ACAGCTCGTG
6796759 ATGAGCATAC
1 A-GAGCATAC
6796769 ATGTACATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
24 2 0.04
25 47 0.96
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.24
Consensus pattern (24 bp):
AGAGCATACCGATTACAGCTCGTG
Found at i:6805573 original size:78 final size:78
Alignment explanation
Indices: 6805444--6805589 Score: 256
Period size: 78 Copynumber: 1.9 Consensus size: 78
6805434 TCCTCCTAAG
*
6805444 CTTCCCAAGAGCCTTGTTATCCATATTGATGTTCTTTCCATACTTTTTCTTAATTAATTTAATGA
1 CTTCCCAAGAGCCTTGTTATCCATATTGATGTCCTTTCCATACTTTTTCTTAATTAATTTAATGA
6805509 AGTGCTCTAAAAC
66 AGTGCTCTAAAAC
* **
6805522 CTTCCCAAGAGTCTTGTTATCCATATTGATGTCCTTTCCATGTTTTTTCTTAATTAATTTAATGA
1 CTTCCCAAGAGCCTTGTTATCCATATTGATGTCCTTTCCATACTTTTTCTTAATTAATTTAATGA
6805587 AGT
66 AGT
6805590 CAAACTCTCT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 64 1.00
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.45
Consensus pattern (78 bp):
CTTCCCAAGAGCCTTGTTATCCATATTGATGTCCTTTCCATACTTTTTCTTAATTAATTTAATGA
AGTGCTCTAAAAC
Found at i:6807210 original size:30 final size:31
Alignment explanation
Indices: 6807176--6807235 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
6807166 AAATCTTTTA
*
6807176 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
6807206 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
6807236 TCTCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:6808000 original size:5 final size:5
Alignment explanation
Indices: 6807990--6808015 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
6807980 CTCGAAAATT
6807990 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
6808016 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:6813606 original size:14 final size:14
Alignment explanation
Indices: 6813587--6813617 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
6813577 ATTGAGGAAT
6813587 TGTGTATTGAAGAG
1 TGTGTATTGAAGAG
6813601 TGTGTATTGAAGAG
1 TGTGTATTGAAGAG
6813615 TGT
1 TGT
6813618 TATCTCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.39
Consensus pattern (14 bp):
TGTGTATTGAAGAG
Found at i:6815814 original size:20 final size:19
Alignment explanation
Indices: 6815791--6815833 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
6815781 TTAGGATTTT
*
6815791 TTTTGCAGTTTTTAATGAAA
1 TTTTACAGTTTTTAA-GAAA
* *
6815811 TTTTATATTTTTTAAGAAA
1 TTTTACAGTTTTTAAGAAA
6815830 TTTT
1 TTTT
6815834 TACATTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.58
Consensus pattern (19 bp):
TTTTACAGTTTTTAAGAAA
Found at i:6815864 original size:16 final size:17
Alignment explanation
Indices: 6815838--6815872 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
6815828 AATTTTTACA
*
6815838 TTAATTTTTTTACTAAT
1 TTAATTTTTTTAATAAT
6815855 TTAA-TTTTTTAATAAT
1 TTAATTTTTTTAATAAT
6815871 TT
1 TT
6815873 CATAATAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TTAATTTTTTTAATAAT
Done.