Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold370
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1088289
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 123460 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:26955 original size:26 final size:26
Alignment explanation
Indices: 26919--27010 Score: 175
Period size: 26 Copynumber: 3.5 Consensus size: 26
26909 CAATTTTCCC
26919 ATTTAATCTCAATAATTAAATCTACG
1 ATTTAATCTCAATAATTAAATCTACG
26945 ATTTAATCTCAATAATTAAATCTACG
1 ATTTAATCTCAATAATTAAATCTACG
26971 ATTTAATCTCAATAATTAAATCTACG
1 ATTTAATCTCAATAATTAAATCTACG
*
26997 ACTTAATCTCAATA
1 ATTTAATCTCAATA
27011 GTCAATATTA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 65 1.00
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.38
Consensus pattern (26 bp):
ATTTAATCTCAATAATTAAATCTACG
Found at i:29991 original size:80 final size:80
Alignment explanation
Indices: 29857--30017 Score: 243
Period size: 80 Copynumber: 2.0 Consensus size: 80
29847 AATTAGCAAC
*
29857 TGGCCACATTTATATAAACGTTTTTAAATCGACTAAAAGCTATGCTTTTCAGAAAGGCATTTCTA
1 TGGCCACATTGATATAAACGTTTTTAAATCGACTAAAAGCTATGCTTTTCAGAAAGGCATTTCTA
29922 CAAGTGTATATATCT
66 CAAGTGTATATATCT
* * * *
29937 TGGCCACATTGCTGTAAACGTTTTTAAATCGACTAAAAGCT-TCTCTTTTTAGAAAGGCATTTCT
1 TGGCCACATTGATATAAACGTTTTTAAATCGACTAAAAGCTAT-GCTTTTCAGAAAGGCATTTCT
**
30001 TTAAGTGTATATATCT
65 ACAAGTGTATATATCT
30017 T
1 T
30018 ATAGGCTTTA
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
79 1 0.01
80 72 0.99
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (80 bp):
TGGCCACATTGATATAAACGTTTTTAAATCGACTAAAAGCTATGCTTTTCAGAAAGGCATTTCTA
CAAGTGTATATATCT
Found at i:30244 original size:2 final size:2
Alignment explanation
Indices: 30237--30264 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30227 CGTACAGGAA
30237 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30265 NGTTGTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42921 original size:16 final size:16
Alignment explanation
Indices: 42876--42921 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
42866 TAGACAAAAC
42876 CTATTCATTGATTTACA
1 CTATTCA-TGATTTACA
* *
42893 TTATTCATCATTTACA
1 CTATTCATGATTTACA
*
42909 CTATTTATGATTT
1 CTATTCATGATTT
42922 TGTAAAATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.52
Consensus pattern (16 bp):
CTATTCATGATTTACA
Found at i:55332 original size:11 final size:12
Alignment explanation
Indices: 55308--55338 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
55298 ATTTGAAAGG
55308 AAAACAAAACAA
1 AAAACAAAACAA
55320 AAAACAAAA-AA
1 AAAACAAAACAA
55331 AAAACAAA
1 AAAACAAA
55339 CATCTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAACAAAACAA
Found at i:56963 original size:64 final size:64
Alignment explanation
Indices: 56867--57195 Score: 378
Period size: 64 Copynumber: 5.1 Consensus size: 64
56857 ATACCATACG
* * * * *
56867 ACTCAATCTGTAAGTTATTACATTCCTGTACTCAGTACGATCACAGTGTAATTCTTACATCACA
1 ACTCAATCTGTAAGTTACTACAATCCTATACTCAGTACGATCACAGTGTAATTCCTACATTACA
* * *
56931 ATTCAATCCGTAAGTTACTACAAAT-CTATACTCAGTACGATCACAGAGTAATTCCTACATTACA
1 ACTCAATCTGTAAGTTACTAC-AATCCTATACTCAGTACGATCACAGTGTAATTCCTACATTACA
* * * * * *
56995 ATTTAATCTGTAAGTTACTACATTCCTATACTCAGTACCATCACAGCGTAACTCCTACATTACA
1 ACTCAATCTGTAAGTTACTACAATCCTATACTCAGTACGATCACAGTGTAATTCCTACATTACA
* * * * *
57059 ACTCAATCTGTTAGTTACTAC-ATAGCTATAATACA-TTCGATCACATGCAGTGTAATTCCTATA
1 ACTCAATCTGTAAGTTACTACAAT-CCTATACT-CAGTACGAT--CA--CAGTGTAATTCCTACA
57122 TTACA
60 TTACA
* *
57127 ACTCAATCTGTAAGTTAC-ACATTCCTATACTCAGTACGATCACAGTGTAATTCCAACATTACA
1 ACTCAATCTGTAAGTTACTACAATCCTATACTCAGTACGATCACAGTGTAATTCCTACATTACA
57190 ACTCAA
1 ACTCAA
57196 AATGTTCACA
Statistics
Matches: 223, Mismatches: 32, Indels: 21
0.81 0.12 0.08
Matches are distributed among these distances:
63 28 0.13
64 136 0.61
65 6 0.03
66 4 0.02
67 13 0.06
68 36 0.16
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.32
Consensus pattern (64 bp):
ACTCAATCTGTAAGTTACTACAATCCTATACTCAGTACGATCACAGTGTAATTCCTACATTACA
Found at i:57017 original size:128 final size:131
Alignment explanation
Indices: 56867--57195 Score: 434
Period size: 128 Copynumber: 2.5 Consensus size: 131
56857 ATACCATACG
* * *
56867 ACTCAATCTGTAAGTTATTACATTCCTGTACTCAGTACGATCACAGTGTAATTCTTACATCACAA
1 ACTCAATCTGTAAGTTACTACATTCCTATACTCAGTACGATCACAGTGTAATTCCTACATCACAA
* * *
56932 TTCAATCCGTAAGTTACTACAAATCTATACT-CAGTACGATCACA-G-A-GTAATTCCTACATTA
66 CTCAATCCGTAAGTTACTACAAAGCTATAATACA-TACGATCACATGCAGGTAATTCCTACATTA
56993 CA
130 CA
* * * * * *
56995 ATTTAATCTGTAAGTTACTACATTCCTATACTCAGTACCATCACAGCGTAACTCCTACATTACAA
1 ACTCAATCTGTAAGTTACTACATTCCTATACTCAGTACGATCACAGTGTAATTCCTACATCACAA
* * * * *
57060 CTCAATCTGTTAGTTACTACATAGCTATAATACATTCGATCACATGCAGTGTAATTCCTATATTA
66 CTCAATCCGTAAGTTACTACAAAGCTATAATACATACGATCACATGCAG-GTAATTCCTACATTA
57125 CA
130 CA
* *
57127 ACTCAATCTGTAAGTTAC-ACATTCCTATACTCAGTACGATCACAGTGTAATTCCAACATTACAA
1 ACTCAATCTGTAAGTTACTACATTCCTATACTCAGTACGATCACAGTGTAATTCCTACATCACAA
57191 CTCAA
66 CTCAA
57196 AATGTTCACA
Statistics
Matches: 173, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
128 90 0.52
129 3 0.02
130 1 0.01
131 47 0.27
132 32 0.18
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.32
Consensus pattern (131 bp):
ACTCAATCTGTAAGTTACTACATTCCTATACTCAGTACGATCACAGTGTAATTCCTACATCACAA
CTCAATCCGTAAGTTACTACAAAGCTATAATACATACGATCACATGCAGGTAATTCCTACATTAC
A
Found at i:65823 original size:17 final size:19
Alignment explanation
Indices: 65786--65823 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
65776 GGACATGGAG
*
65786 CTAAAATATTAACATGGAT
1 CTAAAATATTAACATGCAT
65805 CTAAAATA-T-ACATGCAT
1 CTAAAATATTAACATGCAT
65822 CT
1 CT
65824 TAGTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 1 0.06
19 8 0.44
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (19 bp):
CTAAAATATTAACATGCAT
Found at i:68958 original size:12 final size:12
Alignment explanation
Indices: 68941--68971 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
68931 TTAATATACA
*
68941 AGAGAGAGAGAC
1 AGAGAGACAGAC
68953 AGAGAGACAGAC
1 AGAGAGACAGAC
68965 AGAGAGA
1 AGAGAGA
68972 AAGAGAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.10, G:0.39, T:0.00
Consensus pattern (12 bp):
AGAGAGACAGAC
Found at i:74744 original size:22 final size:21
Alignment explanation
Indices: 74716--74776 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
74706 GGCCACTTCG
74716 AGTGCGAAGTTGCGAAGGCGAA
1 AGTGCGAAG-TGCGAAGGCGAA
*
74738 AGTGCGAGAGTGCGACGGCGAA
1 AGTGCGA-AGTGCGAAGGCGAA
* *
74760 GGAGCGAAAGTGCGAAG
1 AGTGCG-AAGTGCGAAG
74777 ATGCGACGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 30 0.91
23 3 0.09
ACGTcount: A:0.31, C:0.15, G:0.44, T:0.10
Consensus pattern (21 bp):
AGTGCGAAGTGCGAAGGCGAA
Found at i:74749 original size:30 final size:30
Alignment explanation
Indices: 74715--74790 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 30
74705 GGGCCACTTC
74715 GAGTGCGAAGTTGCGAA-G-GCGAAAGTGCGA
1 GAGTGCGAAG--GCGAAGGAGCGAAAGTGCGA
*
74745 GAGTGCGACGGCGAAGGAGCGAAAGTGCGA
1 GAGTGCGAAGGCGAAGGAGCGAAAGTGCGA
*
74775 -AGATGCGACGGCGAAG
1 GAG-TGCGAAGGCGAAG
74791 CGCGAAGATG
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
28 5 0.12
29 3 0.07
30 34 0.81
ACGTcount: A:0.30, C:0.16, G:0.45, T:0.09
Consensus pattern (30 bp):
GAGTGCGAAGGCGAAGGAGCGAAAGTGCGA
Found at i:74781 original size:8 final size:7
Alignment explanation
Indices: 74716--74831 Score: 64
Period size: 8 Copynumber: 16.3 Consensus size: 7
74706 GGCCACTTCG
74716 AGTGCGA
1 AGTGCGA
74723 AGTTGCGA
1 AG-TGCGA
74731 AG-GCGAA
1 AGTGCG-A
74738 AGTGCGA
1 AGTGCGA
74745 GAGTGCGA
1 -AGTGCGA
*
74753 CG-GCGA
1 AGTGCGA
*
74759 AGGAGCGAA
1 A-GTGCG-A
74768 AGTGCGA
1 AGTGCGA
74775 AGATGCGA
1 AG-TGCGA
*
74783 CG-GCGA
1 AGTGCGA
*
74789 AGCGCGA
1 AGTGCGA
74796 AGATGCGA
1 AG-TGCGA
* *
74804 TG-GCAAA
1 AGTGC-GA
74811 AGTGCGA
1 AGTGCGA
74818 AG-GCGA
1 AGTGCGA
74824 AG-GCGA
1 AGTGCGA
74830 AG
1 AG
74832 GAGCGATACT
Statistics
Matches: 87, Mismatches: 10, Indels: 25
0.71 0.08 0.20
Matches are distributed among these distances:
6 26 0.30
7 22 0.25
8 37 0.43
9 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (7 bp):
AGTGCGA
Found at i:74862 original size:6 final size:6
Alignment explanation
Indices: 74851--74902 Score: 50
Period size: 6 Copynumber: 7.7 Consensus size: 6
74841 TACTATCGCT
74851 CCTTCG CCTTCG CACTCTCG CCTTCG CAACTTCG CACTTTCG CCTTCG
1 CCTTCG CCTTCG C-CT-TCG CCTTCG C--CTTCG C-C-TTCG CCTTCG
74899 CCTT
1 CCTT
74903 TTTTTATAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
6 19 0.46
7 7 0.17
8 15 0.37
ACGTcount: A:0.08, C:0.46, G:0.13, T:0.33
Consensus pattern (6 bp):
CCTTCG
Found at i:74885 original size:14 final size:13
Alignment explanation
Indices: 74852--74902 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 13
74842 ACTATCGCTC
74852 CTTCGCCTTCGCA
1 CTTCGCCTTCGCA
74865 CTCTCGCCTTCGCAA
1 CT-TCGCCTTCGC-A
74880 CTTCGCACTTTCGC-
1 CTTCGC-C-TTCGCA
74894 CTTCGCCTT
1 CTTCGCCTT
74903 TTTTTATAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.06
13 3 0.09
14 20 0.59
15 4 0.12
16 5 0.15
ACGTcount: A:0.08, C:0.45, G:0.14, T:0.33
Consensus pattern (13 bp):
CTTCGCCTTCGCA
Found at i:75369 original size:22 final size:21
Alignment explanation
Indices: 75341--75401 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
75331 GGCCACTTCG
75341 AGTGCGAAGTTGCGAAGGCGAA
1 AGTGCGAAG-TGCGAAGGCGAA
*
75363 AGTGCGAGAGTGCGACGGCGAA
1 AGTGCGA-AGTGCGAAGGCGAA
* *
75385 GGAGCGAAAGTGCGAAG
1 AGTGCG-AAGTGCGAAG
75402 ATGCGACGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 30 0.91
23 3 0.09
ACGTcount: A:0.31, C:0.15, G:0.44, T:0.10
Consensus pattern (21 bp):
AGTGCGAAGTGCGAAGGCGAA
Found at i:75374 original size:30 final size:30
Alignment explanation
Indices: 75340--75415 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 30
75330 GGGCCACTTC
75340 GAGTGCGAAGTTGCGAA-G-GCGAAAGTGCGA
1 GAGTGCGAAG--GCGAAGGAGCGAAAGTGCGA
*
75370 GAGTGCGACGGCGAAGGAGCGAAAGTGCGA
1 GAGTGCGAAGGCGAAGGAGCGAAAGTGCGA
*
75400 -AGATGCGACGGCGAAG
1 GAG-TGCGAAGGCGAAG
75416 CGCGAAGATG
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
28 5 0.12
29 3 0.07
30 34 0.81
ACGTcount: A:0.30, C:0.16, G:0.45, T:0.09
Consensus pattern (30 bp):
GAGTGCGAAGGCGAAGGAGCGAAAGTGCGA
Found at i:75421 original size:21 final size:21
Alignment explanation
Indices: 75396--75456 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
75386 GAGCGAAAGT
*
75396 GCGAAGATGCGACGGCGAAGC
1 GCGAAGATGCGAAGGCGAAGC
* *
75417 GCGAAGATGCGATGGCGAAAGT
1 GCGAAGATGCGAAGGCG-AAGC
75439 GCGAAG--GCGAAGGCGAAG
1 GCGAAGATGCGAAGGCGAAG
75457 GAGCGATACT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 3 0.08
20 8 0.22
21 16 0.44
22 9 0.25
ACGTcount: A:0.31, C:0.18, G:0.44, T:0.07
Consensus pattern (21 bp):
GCGAAGATGCGAAGGCGAAGC
Found at i:75457 original size:6 final size:7
Alignment explanation
Indices: 75341--75456 Score: 73
Period size: 8 Copynumber: 16.3 Consensus size: 7
75331 GGCCACTTCG
75341 AGTGCGA
1 AGTGCGA
75348 AGTTGCGA
1 AG-TGCGA
75356 AG-GCGAA
1 AGTGCG-A
75363 AGTGCGA
1 AGTGCGA
75370 GAGTGCGA
1 -AGTGCGA
*
75378 CG-GCGA
1 AGTGCGA
*
75384 AGGAGCGAA
1 A-GTGCG-A
75393 AGTGCGA
1 AGTGCGA
75400 AGATGCGA
1 AG-TGCGA
*
75408 CG-GCGA
1 AGTGCGA
*
75414 AGCGCGA
1 AGTGCGA
75421 AGATGCGA
1 AG-TGCGA
*
75429 TG-GCGAA
1 AGTGCG-A
75436 AGTGCGA
1 AGTGCGA
75443 AG-GCGA
1 AGTGCGA
75449 AG-GCGA
1 AGTGCGA
75455 AG
1 AG
75457 GAGCGATACT
Statistics
Matches: 89, Mismatches: 8, Indels: 25
0.73 0.07 0.20
Matches are distributed among these distances:
6 27 0.30
7 22 0.25
8 38 0.43
9 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.44, T:0.09
Consensus pattern (7 bp):
AGTGCGA
Found at i:75462 original size:14 final size:14
Alignment explanation
Indices: 75344--75462 Score: 70
Period size: 14 Copynumber: 8.3 Consensus size: 14
75334 CACTTCGAGT
75344 GCGAAGTTGCGAAG-
1 GCGAAG-TGCGAAGA
*
75358 GCGAAAGTGCGAGAGT
1 GCG-AAGTGCGA-AGA
*
75374 GCGACG-GCGAAGGA
1 GCGAAGTGCGAA-GA
75388 GCGAAAGTGCGAAGA
1 GCG-AAGTGCGAAGA
* *
75403 TGCGACG-GCGAAGC
1 -GCGAAGTGCGAAGA
*
75417 GCGAAGATGCGATG-
1 GCGAAG-TGCGAAGA
75431 GCGAAAGTGCGAAG-
1 GCG-AAGTGCGAAGA
75445 GCGAAG-GCGAAGGA
1 GCGAAGTGCGAA-GA
75459 GCGA
1 GCGA
75463 TACTACTATC
Statistics
Matches: 85, Mismatches: 8, Indels: 24
0.73 0.07 0.21
Matches are distributed among these distances:
12 5 0.06
13 10 0.12
14 38 0.45
15 21 0.25
16 11 0.13
ACGTcount: A:0.31, C:0.17, G:0.45, T:0.08
Consensus pattern (14 bp):
GCGAAGTGCGAAGA
Found at i:75462 original size:20 final size:20
Alignment explanation
Indices: 75352--75462 Score: 62
Period size: 22 Copynumber: 5.2 Consensus size: 20
75342 GTGCGAAGTT
* *
75352 GCGAAGGCGAAAGTGCGAGAGT
1 GCGAAGGCG-AAG-GCGAAAGA
* *
75374 GCGACGGCGAAGGAGCGAAAGT
1 GCGAAGGCGAA-G-GCGAAAGA
* *
75396 GCGAAGATGCGACGGCG-AAGC
1 GCGAAG--GCGAAGGCGAAAGA
* *
75417 GCGAAGATGCGATGGCGAAAGT
1 GCGAAG--GCGAAGGCGAAAGA
*
75439 GCGAAGGCGAAGGCGAAGGA
1 GCGAAGGCGAAGGCGAAAGA
75459 GCGA
1 GCGA
75463 TACTACTATC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
20 15 0.20
21 21 0.28
22 33 0.45
23 1 0.01
24 4 0.05
ACGTcount: A:0.32, C:0.17, G:0.45, T:0.06
Consensus pattern (20 bp):
GCGAAGGCGAAGGCGAAAGA
Found at i:76041 original size:14 final size:14
Alignment explanation
Indices: 76022--76055 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
76012 TTATAAAAAG
76022 GCGAAGGCGA-AGAT
1 GCGAAGGCGAGAG-T
76036 GCGAAGGCGAGAGT
1 GCGAAGGCGAGAGT
76050 GCGAAG
1 GCGAAG
76056 TTGCGAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.32, C:0.15, G:0.47, T:0.06
Consensus pattern (14 bp):
GCGAAGGCGAGAGT
Found at i:76113 original size:22 final size:22
Alignment explanation
Indices: 76085--76198 Score: 90
Period size: 22 Copynumber: 5.2 Consensus size: 22
76075 GTATCGCTTC
*
76085 TTCGCCTTCGCAACTTCTCACT
1 TTCGCCTTCGCAACTTCGCACT
* * *
76107 TTCGCCTTCGCATCTTTGCGC-
1 TTCGCCTTCGCAACTTCGCACT
* * * *
76128 TTCGCCGTCGCATCTTCACACC
1 TTCGCCTTCGCAACTTCGCACT
*
76150 TTCGCCCCTTCGC--CGTCGCACT
1 TTCG--CCTTCGCAACTTCGCACT
*
76172 TTCGCCGTCGCAACTTCGCACT
1 TTCGCCTTCGCAACTTCGCACT
*
76194 CTCGC
1 TTCGC
76199 ACCTCGACCT
Statistics
Matches: 72, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
20 6 0.08
21 17 0.24
22 43 0.60
24 6 0.08
ACGTcount: A:0.10, C:0.44, G:0.16, T:0.31
Consensus pattern (22 bp):
TTCGCCTTCGCAACTTCGCACT
Found at i:76189 original size:14 final size:13
Alignment explanation
Indices: 76157--76190 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
76147 ACCTTCGCCC
76157 CTTCGCCGTCGCA
1 CTTCGCCGTCGCA
76170 CTTTCGCCGTCGCAA
1 C-TTCGCCGTCGC-A
76185 CTTCGC
1 CTTCGC
76191 ACTCTCGCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 16 0.84
15 2 0.11
ACGTcount: A:0.09, C:0.44, G:0.21, T:0.26
Consensus pattern (13 bp):
CTTCGCCGTCGCA
Found at i:84228 original size:41 final size:40
Alignment explanation
Indices: 84151--84254 Score: 118
Period size: 40 Copynumber: 2.5 Consensus size: 40
84141 TGTTTTCGTG
* * * *
84151 TATGGATTATTCGTTGTGGCGTTTTAGTCACCTGACTTAGTC
1 TATGGATTATT-GTTGTGGCGTTCTAGGCACATGAC-TAGTA
* *
84193 TATGGATTATTGTGGTGGCGTTCTAGGCACATGACTATTA
1 TATGGATTATTGTTGTGGCGTTCTAGGCACATGACTAGTA
* *
84233 TATGGATTTTTGTTGTGACGTT
1 TATGGATTATTGTTGTGGCGTT
84255 TTAGTCATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 22 0.42
41 20 0.38
42 11 0.21
ACGTcount: A:0.18, C:0.12, G:0.26, T:0.43
Consensus pattern (40 bp):
TATGGATTATTGTTGTGGCGTTCTAGGCACATGACTAGTA
Found at i:98476 original size:41 final size:40
Alignment explanation
Indices: 98413--98523 Score: 159
Period size: 40 Copynumber: 2.7 Consensus size: 40
98403 TGTTTTCGTG
* *
98413 TATGGATTATTCGTTGTGGCGTTTTAGTCACCTGACTTAGTC
1 TATGGATTATT-GTTGTGGCGTTTTAGTCACATGAC-TAGTA
* *
98455 TATGGATTATTGTTGTGGCGTTCTAGTCACATGACTATTA
1 TATGGATTATTGTTGTGGCGTTTTAGTCACATGACTAGTA
*
98495 TATGGATTTTTGTTGTGGCGTTTTAGTCA
1 TATGGATTATTGTTGTGGCGTTTTAGTCA
98524 TTTGACTATG
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 30 0.48
41 22 0.35
42 11 0.17
ACGTcount: A:0.18, C:0.13, G:0.24, T:0.45
Consensus pattern (40 bp):
TATGGATTATTGTTGTGGCGTTTTAGTCACATGACTAGTA
Found at i:98510 original size:40 final size:40
Alignment explanation
Indices: 98413--98559 Score: 151
Period size: 40 Copynumber: 3.8 Consensus size: 40
98403 TGTTTTCGTG
* * * *
98413 TATGGATTATTCGTTGTGGCGTTTTAGTCACCTGACTTAGTC
1 TATGGATT-TTTGTTGTGGCGTTTTAGTCACATGAC-TATTA
* *
98455 TATGGATTATTGTTGTGGCGTTCTAGTCACATGACTATTA
1 TATGGATTTTTGTTGTGGCGTTTTAGTCACATGACTATTA
**
98495 TATGGATTTTTGTTGTGGCGTTTTAGTCATTTGACTA-T-
1 TATGGATTTTTGTTGTGGCGTTTTAGTCACATGACTATTA
* *
98533 GA--G-TTTTTGTGGTGGCGTTTTAGTCAC
1 TATGGATTTTTGTTGTGGCGTTTTAGTCAC
98560 CAATAAATTG
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
35 22 0.24
36 1 0.01
38 1 0.01
39 1 0.01
40 36 0.39
41 23 0.25
42 8 0.09
ACGTcount: A:0.17, C:0.12, G:0.25, T:0.46
Consensus pattern (40 bp):
TATGGATTTTTGTTGTGGCGTTTTAGTCACATGACTATTA
Found at i:114415 original size:82 final size:82
Alignment explanation
Indices: 114321--114488 Score: 257
Period size: 82 Copynumber: 2.0 Consensus size: 82
114311 CTTCAATAAT
114321 GCAAAATTTGCAAAGGAAATAACTAAATTTTCATAGTTCAACTAAAATTTA-AAAAAAAAGTTAT
1 GCAAAATTTGCAAAGGAAATAACTAAATTTTCATAGTTCAACTAAAATTTACAAAAAAAAGTTAT
*
114385 TCCCCTTTTTCACAAAAA
66 TCCCCCTTTTCA-AAAAA
* * ***
114403 GCAAAATTTGCAAAGGGAATAACTAAATTTTCATATTTCAACTAAAATTTATCAAAATCGAGTTA
1 GCAAAATTTGCAAAGGAAATAACTAAATTTTCATAGTTCAACTAAAATTTA-CAAAAAAAAGTTA
114468 TTCCCCCTTTTCAAAAAA
65 TTCCCCCTTTTCAAAAAA
114486 GCA
1 GCA
114489 TTTCCATAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
82 49 0.63
83 8 0.10
84 21 0.27
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (82 bp):
GCAAAATTTGCAAAGGAAATAACTAAATTTTCATAGTTCAACTAAAATTTACAAAAAAAAGTTAT
TCCCCCTTTTCAAAAAA
Found at i:124799 original size:15 final size:15
Alignment explanation
Indices: 124779--124808 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
124769 TTTTCTTTTG
*
124779 TTGAAATATTTTCTT
1 TTGAAACATTTTCTT
124794 TTGAAACATTTTCTT
1 TTGAAACATTTTCTT
124809 CCATTTTATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.57
Consensus pattern (15 bp):
TTGAAACATTTTCTT
Found at i:125240 original size:21 final size:21
Alignment explanation
Indices: 125216--125263 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
125206 CTGCATACTT
*
125216 TCTTCCTTTACTGCTGTGGTC
1 TCTTCCTTAACTGCTGTGGTC
* *
125237 TCTTCCTTAACTGTTGTGGTT
1 TCTTCCTTAACTGCTGTGGTC
125258 TCTTCC
1 TCTTCC
125264 AAACTCACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.06, C:0.27, G:0.17, T:0.50
Consensus pattern (21 bp):
TCTTCCTTAACTGCTGTGGTC
Found at i:125305 original size:21 final size:21
Alignment explanation
Indices: 125280--125348 Score: 111
Period size: 21 Copynumber: 3.2 Consensus size: 21
125270 ACTGAACATT
**
125280 CTTCTTTGACCTCTGCTTTCA
1 CTTCTTTGACCTCCACTTTCA
125301 CTTCTTTGACCTCCACTTTCA
1 CTTCTTTGACCTCCACTTTCA
125322 CTTCTTTGACCTCCACTTTCA
1 CTTCTTTGACCTCCACTTTCA
125343 CATTCT
1 C-TTCT
125349 GATCTTTGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
21 41 0.91
22 4 0.09
ACGTcount: A:0.13, C:0.36, G:0.06, T:0.45
Consensus pattern (21 bp):
CTTCTTTGACCTCCACTTTCA
Found at i:130884 original size:90 final size:90
Alignment explanation
Indices: 130716--130891 Score: 205
Period size: 90 Copynumber: 2.0 Consensus size: 90
130706 ACCATTTGGC
* ***
130716 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCCGATAGTGTAGATTCAAGTTTGTTCCAATCAT
1 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCCGATAGTGTAGATTAAAGTTTGTGAAAATCAT
**
130781 GACCTCCTTGGGTAAGGTGGGACCA
66 GACCTCCAGGGGTAAGGTGGGACCA
* * * *
130806 CAGGAAAGCTGGAACTTGTTTGGAAGCATCCTCATG-TTGTGTAGATTTAAAG-TTGTGAAAATC
1 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTC-CGATAGTGTAGA-TTAAAGTTTGTGAAAATC
*
130869 ATGACC-CCAAGGGGTAGGGTGGG
64 ATGACCTCC-AGGGGTAAGGTGGG
130892 GCGAAAATGG
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
89 2 0.03
90 64 0.89
91 6 0.08
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (90 bp):
CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCCGATAGTGTAGATTAAAGTTTGTGAAAATCAT
GACCTCCAGGGGTAAGGTGGGACCA
Found at i:147610 original size:161 final size:161
Alignment explanation
Indices: 147416--147899 Score: 641
Period size: 161 Copynumber: 3.0 Consensus size: 161
147406 ATCTTCTTCA
** *
147416 CAGAGGATGATTATATTTG-AATGAAATTTGGTATACAAGTTTATCATGATAATATCTAGGTCAA
1 CAGAGGATGAACATA-TTGAAATGAAATTTGGTATACAGGTTTATCATGATAATATCTAGGTCAA
* *
147480 GTTCGATATTGGGTACCATCGAGCAATTTTCGACAGAGTTATGGCCCTTGGACTTAGTAAAATTC
65 GTTCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGGCCCTTGGACTTAGAAAAATTC
**
147545 CAGTTATTTGCAGTTTCCGCTCATTTTCTTTG
130 CAGTTATTTGCAGTTTATGCTCATTTTCTTTG
* * *
147577 CAGAGGATGAACATATTGAAATGACATTTGGTATACAGGTTTATCATGATAATATCTAGATCAAC
1 CAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCATGATAATATCTAGGTCAAG
* *
147642 TTCGATATTGGGTACAATCGAGCAATTTTCAACAGAGTTATGGCCCTTGGACATAGAAAAATTCC
66 TTCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGGCCCTTGGACTTAGAAAAATTCC
* *
147707 AGTTATTTGCAGTTTTTGCTCATTTTCTTCG
131 AGTTATTTGCAGTTTATGCTCATTTTCTTTG
* * * * * * *
147738 CATATGG-TGCACATATTGATATGATATTTAGTATACAGGTTTATC-TAAGTTATATCTAGGTCA
1 CAGA-GGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCATGA-TAATATCTAGGTCA
* * * ** * ***
147801 GGTTTGATTTTGGGTATGATAGAGCAATTTTCGACAGAGTTATATTCCTTGGACTTAAGAAAAAT
64 AGTTCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGGCCCTTGGACTT-AGAAAAAT
147866 TCCAGTTATTTGCAGTTTATGCTCATTTTCTTTG
128 TCCAGTTATTTGCAGTTTATGCTCATTTTCTTTG
147900 TGGATGTTTC
Statistics
Matches: 284, Mismatches: 35, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
160 5 0.02
161 237 0.83
162 42 0.15
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (161 bp):
CAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTATCATGATAATATCTAGGTCAAG
TTCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGGCCCTTGGACTTAGAAAAATTCC
AGTTATTTGCAGTTTATGCTCATTTTCTTTG
Found at i:148714 original size:2 final size:2
Alignment explanation
Indices: 148707--148753 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
148697 TGCGAACAAA
148707 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
148749 AG AG A
1 AG AG A
148754 ATTTTGAGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:150190 original size:15 final size:15
Alignment explanation
Indices: 150172--150266 Score: 138
Period size: 15 Copynumber: 6.4 Consensus size: 15
150162 ACTATTCCTG
*
150172 TGATATTGAATCATA
1 TGATATTGTATCATA
150187 TGATATT-TATCATA
1 TGATATTGTATCATA
*
150201 TGATATTGTAGCATA
1 TGATATTGTATCATA
150216 TGATATTGTATCATA
1 TGATATTGTATCATA
* *
150231 TGAGATTGTGTCATA
1 TGATATTGTATCATA
*
150246 TGATATTGTATCCTA
1 TGATATTGTATCATA
150261 TGATAT
1 TGATAT
150267 ATGACATTGT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
14 13 0.18
15 58 0.82
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (15 bp):
TGATATTGTATCATA
Found at i:150313 original size:15 final size:15
Alignment explanation
Indices: 150295--150351 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
150285 ATCTGATATG
*
150295 ATATAATCTTGTATT
1 ATATAATATTGTATT
* *
150310 ATATGATATTGCTCTTTT
1 ATATAATATTG---TATT
150328 ATATAATATTGTATT
1 ATATAATATTGTATT
*
150343 ATATTATAT
1 ATATAATAT
150352 AAATAGTGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
15 20 0.61
18 13 0.39
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.54
Consensus pattern (15 bp):
ATATAATATTGTATT
Found at i:159962 original size:32 final size:32
Alignment explanation
Indices: 159918--159979 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
159908 CTTCGAAGTC
159918 GCAGAACAAGTTTCTTAATTACTTTGTATGAA
1 GCAGAACAAGTTTCTTAATTACTTTGTATGAA
*
159950 GCAGAACTAGTTTCTTAATTACTTTGTATG
1 GCAGAACAAGTTTCTTAATTACTTTGTATG
159980 CAAATTCATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (32 bp):
GCAGAACAAGTTTCTTAATTACTTTGTATGAA
Found at i:161459 original size:2 final size:2
Alignment explanation
Indices: 161454--161498 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
161444 CCTCTCCTAG
*
161454 TC TC TC TC TC TC TC TC -C TC TC TC TC TC TC -C TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
161494 TC TC T
1 TC TC T
161499 TCTTCTTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:161475 original size:13 final size:13
Alignment explanation
Indices: 161437--161495 Score: 70
Period size: 13 Copynumber: 4.7 Consensus size: 13
161427 ATTTTTGCAA
161437 CTCTCTC-CCTCT
1 CTCTCTCTCCTCT
*
161449 C-CTAGTCT-CTCT
1 CTCT-CTCTCCTCT
161461 CTCTCTCTCCTCT
1 CTCTCTCTCCTCT
*
161474 CTCTCTCTCCTTT
1 CTCTCTCTCCTCT
161487 CTCTCTCTC
1 CTCTCTCTC
161496 TCTTCTTCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
11 2 0.05
12 11 0.28
13 27 0.68
ACGTcount: A:0.02, C:0.51, G:0.02, T:0.46
Consensus pattern (13 bp):
CTCTCTCTCCTCT
Found at i:161475 original size:15 final size:15
Alignment explanation
Indices: 161454--161497 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
161444 CCTCTCCTAG
161454 TCTCTCTCTCTCT-C
1 TCTCTCTCTCTCTCC
161468 TCCTCTCTCTCTCTCC
1 T-CTCTCTCTCTCTCC
*
161484 TTTCTCTCTCTCTC
1 TCTCTCTCTCTCTC
161498 TTCTTCTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 1 0.04
15 24 0.89
16 2 0.07
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (15 bp):
TCTCTCTCTCTCTCC
Found at i:166600 original size:21 final size:21
Alignment explanation
Indices: 166576--166850 Score: 285
Period size: 21 Copynumber: 13.2 Consensus size: 21
166566 GATAATATGA
*
166576 TGATACTTTAACATTATATGC
1 TGATACTTTAACATTACATGC
* * *
166597 TGAT-CATTCAACATTATATGA
1 TGATAC-TTTAACATTACATGC
166618 TGATACTTTAACATTACATGC
1 TGATACTTTAACATTACATGC
* *
166639 TGATACTTCAACATTACATGA
1 TGATACTTTAACATTACATGC
* *
166660 TGGTACTTTAACATTACGTGC
1 TGATACTTTAACATTACATGC
* *
166681 TGATACTTCAACATTACATGA
1 TGATACTTTAACATTACATGC
*
166702 TGGTACTTTAACATTACATGC
1 TGATACTTTAACATTACATGC
* *
166723 TGATACTTTAATATTACATGA
1 TGATACTTTAACATTACATGC
** *
166744 TGGCACTCCTT--CATT--AT-A
1 TGATACT--TTAACATTACATGC
*
166762 TGATACTTTATCATTACATGC
1 TGATACTTTAACATTACATGC
*
166783 T-ATTACTTCAACATTACATGC
1 TGA-TACTTTAACATTACATGC
*
166804 TGATACTTCAACATTACATGC
1 TGATACTTTAACATTACATGC
*
166825 TGATACTTTAACACTACATGC
1 TGATACTTTAACATTACATGC
166846 TGATA
1 TGATA
166851 TTTCATACAA
Statistics
Matches: 212, Mismatches: 31, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
16 2 0.01
18 10 0.05
19 2 0.01
20 4 0.02
21 190 0.90
22 2 0.01
23 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (21 bp):
TGATACTTTAACATTACATGC
Found at i:166629 original size:42 final size:42
Alignment explanation
Indices: 166572--166855 Score: 330
Period size: 42 Copynumber: 6.8 Consensus size: 42
166562 TGGTGATAAT
* *
166572 ATGATGATACTTTAACATTATATGCTGAT-CATTCAACATTAT
1 ATGATGATACTTTAACATTACATGCTGATAC-TTCAACATTAC
166614 ATGATGATACTTTAACATTACATGCTGATACTTCAACATTAC
1 ATGATGATACTTTAACATTACATGCTGATACTTCAACATTAC
* *
166656 ATGATGGTACTTTAACATTACGTGCTGATACTTCAACATTAC
1 ATGATGATACTTTAACATTACATGCTGATACTTCAACATTAC
* * *
166698 ATGATGGTACTTTAACATTACATGCTGATACTTTAATATTAC
1 ATGATGATACTTTAACATTACATGCTGATACTTCAACATTAC
** * * *
166740 ATGATGGCACTCCTT--CATT--AT-ATGATACTTTATCATTAC
1 ATGATGATACT--TTAACATTACATGCTGATACTTCAACATTAC
* *
166779 ATGCT-ATTACTTCAACATTACATGCTGATACTTCAACATTAC
1 ATGATGA-TACTTTAACATTACATGCTGATACTTCAACATTAC
* * *
166821 ATGCTGATACTTTAACACTACATGCTGATATTTCA
1 ATGATGATACTTTAACATTACATGCTGATACTTCA
166856 TACAATGATG
Statistics
Matches: 211, Mismatches: 21, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
37 1 0.00
39 26 0.12
40 2 0.01
41 2 0.01
42 176 0.83
43 2 0.01
44 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (42 bp):
ATGATGATACTTTAACATTACATGCTGATACTTCAACATTAC
Found at i:167374 original size:21 final size:21
Alignment explanation
Indices: 167345--167543 Score: 211
Period size: 21 Copynumber: 9.5 Consensus size: 21
167335 CACTCTTTCN
*
167345 TGTTGAAGTATCAGCACGTAA
1 TGTTAAAGTATCAGCACGTAA
* * **
167366 TGTTAAAGTACCATCAATTAA
1 TGTTAAAGTATCAGCACGTAA
* *
167387 TGTTGAAGTATCAGCATGTAA
1 TGTTAAAGTATCAGCACGTAA
* * * *
167408 TGTTAAAGTACCATCATGCAA
1 TGTTAAAGTATCAGCACGTAA
*
167429 TGTTGAAGTATCAGCACGTAA
1 TGTTAAAGTATCAGCACGTAA
* * *
167450 TGTTAAAGTACCATCAAGTAA
1 TGTTAAAGTATCAGCACGTAA
*
167471 TGTTGAAGTATCAGCACGTAA
1 TGTTAAAGTATCAGCACGTAA
* *
167492 TGTTAAAGTACCATCA-GTCAA
1 TGTTAAAGTATCAGCACGT-AA
*
167513 TGTTGAAGTATCAGCACGTAA
1 TGTTAAAGTATCAGCACGTAA
167534 TGTTAAAGTA
1 TGTTAAAGTA
167544 CCATCANNNN
Statistics
Matches: 142, Mismatches: 34, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
20 2 0.01
21 138 0.97
22 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (21 bp):
TGTTAAAGTATCAGCACGTAA
Found at i:167408 original size:42 final size:42
Alignment explanation
Indices: 167345--167549 Score: 351
Period size: 42 Copynumber: 4.9 Consensus size: 42
167335 CACTCTTTCN
*
167345 TGTTGAAGTATCAGCACGTAATGTTAAAGTACCATCAATTAA
1 TGTTGAAGTATCAGCACGTAATGTTAAAGTACCATCAATCAA
*
167387 TGTTGAAGTATCAGCATGTAATGTTAAAGTACCATC-ATGCAA
1 TGTTGAAGTATCAGCACGTAATGTTAAAGTACCATCAAT-CAA
167429 TGTTGAAGTATCAGCACGTAATGTTAAAGTACCATCAAGT-AA
1 TGTTGAAGTATCAGCACGTAATGTTAAAGTACCATCAA-TCAA
*
167471 TGTTGAAGTATCAGCACGTAATGTTAAAGTACCATCAGTCAA
1 TGTTGAAGTATCAGCACGTAATGTTAAAGTACCATCAATCAA
167513 TGTTGAAGTATCAGCACGTAATGTTAAAGTACCATCA
1 TGTTGAAGTATCAGCACGTAATGTTAAAGTACCATCA
167550 NNNNNNNNNN
Statistics
Matches: 155, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
41 3 0.02
42 150 0.97
43 1 0.01
44 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (42 bp):
TGTTGAAGTATCAGCACGTAATGTTAAAGTACCATCAATCAA
Found at i:169473 original size:15 final size:15
Alignment explanation
Indices: 169453--169482 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
169443 GTTAATTCTA
169453 TCTTGACCATCACCC
1 TCTTGACCATCACCC
*
169468 TCTTGACCTTCACCC
1 TCTTGACCATCACCC
169483 ACTTCTAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.47, G:0.07, T:0.30
Consensus pattern (15 bp):
TCTTGACCATCACCC
Found at i:175041 original size:12 final size:12
Alignment explanation
Indices: 175024--175048 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
175014 CTCTTATATG
175024 AACATTCTATTT
1 AACATTCTATTT
175036 AACATTCTATTT
1 AACATTCTATTT
175048 A
1 A
175049 TCAAAAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (12 bp):
AACATTCTATTT
Found at i:175847 original size:2 final size:2
Alignment explanation
Indices: 175840--175879 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
175830 TTAAAAGCAT
175840 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
175880 TTTTCAGTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:178411 original size:4 final size:4
Alignment explanation
Indices: 178409--178464 Score: 58
Period size: 4 Copynumber: 14.0 Consensus size: 4
178399 GTTACGGACG
* ** * * *
178409 GACA GACA GACG GACA GACA GATT GACA GACA GACG GACG GACG GACA
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA
178457 GACA GACA
1 GACA GACA
178465 CACAAGGGTA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.41, C:0.23, G:0.32, T:0.04
Consensus pattern (4 bp):
GACA
Found at i:178422 original size:12 final size:12
Alignment explanation
Indices: 178405--178464 Score: 75
Period size: 12 Copynumber: 5.0 Consensus size: 12
178395 TTTTGTTACG
178405 GACGGACAGACA
1 GACGGACAGACA
178417 GACGGACAGACA
1 GACGGACAGACA
**
178429 GATTGACAGACA
1 GACGGACAGACA
* *
178441 GACGGACGGACG
1 GACGGACAGACA
*
178453 GACAGACAGACA
1 GACGGACAGACA
178465 CACAAGGGTA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.40, C:0.23, G:0.33, T:0.03
Consensus pattern (12 bp):
GACGGACAGACA
Found at i:182929 original size:69 final size:68
Alignment explanation
Indices: 182775--182973 Score: 199
Period size: 70 Copynumber: 2.9 Consensus size: 68
182765 AAAGTTAAAG
*
182775 ACCTGCAGCTAGCCAATATAAACCAAAAGAAAATTATCTTTAGTTTCTTCAGCCAAAACTTTAAA
1 ACCTGCAGCTAGCCAATATAAGCCAAAA-AAAA-TATCTTTAGTTTCTTCAGCCAAAACTTTAAA
182840 ATAAT
64 ATAAT
* * * *
182845 ACCTGCAGCTGGCCAATATAAGCCGAAAAAACA-AT-TTTAGTTTCCTT-GGCTAAAA-TGTTCA
1 ACCTGCAGCTAGCCAATATAAGCC-AAAAAAAATATCTTTAGTTT-CTTCAGCCAAAACT-TT-A
*
182906 AATTATAT
62 AAATA-AT
*** * * *
182914 ACCTGCAGCTAGCCAATATAAGCCAAAAATTTTTTTTTTAGTTTTTTCAGCCAAAACTTT
1 ACCTGCAGCTAGCCAATATAAGCCAAAAAAAATATCTTTAGTTTCTTCAGCCAAAACTTT
182974 CAAACTATAA
Statistics
Matches: 106, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
66 1 0.01
67 16 0.15
68 15 0.14
69 28 0.26
70 41 0.39
71 5 0.05
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (68 bp):
ACCTGCAGCTAGCCAATATAAGCCAAAAAAAATATCTTTAGTTTCTTCAGCCAAAACTTTAAAAT
AAT
Found at i:184049 original size:21 final size:21
Alignment explanation
Indices: 184025--184116 Score: 130
Period size: 21 Copynumber: 4.4 Consensus size: 21
184015 ATCTGCCACC
184025 ACTTGTCAGATAATTATGTCG
1 ACTTGTCAGATAATTATGTCG
* ** *
184046 ACTTGTCAGGTCCTGATGTCG
1 ACTTGTCAGATAATTATGTCG
*
184067 ACTTGCCAGATAATTATGTCG
1 ACTTGTCAGATAATTATGTCG
*
184088 ACTTGTCAGATAATTATGTAG
1 ACTTGTCAGATAATTATGTCG
184109 ACTTGTCA
1 ACTTGTCA
184117 CTTATCCACG
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (21 bp):
ACTTGTCAGATAATTATGTCG
Found at i:184220 original size:21 final size:21
Alignment explanation
Indices: 184194--184353 Score: 169
Period size: 21 Copynumber: 7.7 Consensus size: 21
184184 AATAATATTT
**
184194 TCTGACAAGTCGACATAAGGA
1 TCTGACAAGTCGACATAATTA
* **
184215 TCTGACAAGTCGACATTAGCA
1 TCTGACAAGTCGACATAATTA
***
184236 TCTTTTAAGTCGACATAATTA
1 TCTGACAAGTCGACATAATTA
*
184257 TTTGACAAGTCGACATAATTA
1 TCTGACAAGTCGACATAATTA
*
184278 TTTGACAAGTCGACATAATTA
1 TCTGACAAGTCGACATAATTA
* * *
184299 TTTGACAAGACGACATAA-CA
1 TCTGACAAGTCGACATAATTA
* *
184319 TCTGACAAGTCAACATCATTA
1 TCTGACAAGTCGACATAATTA
*
184340 TTTGACAAGTCGAC
1 TCTGACAAGTCGAC
184354 TTATAATATG
Statistics
Matches: 117, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
20 15 0.13
21 102 0.87
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (21 bp):
TCTGACAAGTCGACATAATTA
Found at i:184545 original size:21 final size:21
Alignment explanation
Indices: 184519--184612 Score: 127
Period size: 21 Copynumber: 4.5 Consensus size: 21
184509 ATGGTTATTT
* *
184519 TCTGACAAGTCAACATAAAGA
1 TCTGACAAGTCGACATAAATA
*
184540 TCTGACAAGTTGACATAAATA
1 TCTGACAAGTCGACATAAATA
*
184561 TCTGACAAGTCGATAT-AATCA
1 TCTGACAAGTCGACATAAAT-A
*
184582 TCTGACAAGTCGACATAACTA
1 TCTGACAAGTCGACATAAATA
184603 TCTGACAAGT
1 TCTGACAAGT
184613 GGTGGCAGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
20 3 0.05
21 59 0.92
22 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (21 bp):
TCTGACAAGTCGACATAAATA
Found at i:185310 original size:20 final size:20
Alignment explanation
Indices: 185287--185337 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
185277 AACATTATTA
**
185287 TATATAATACAATATTGTAT
1 TATATAATACAATATCATAT
*
185307 TATATGATACAATATCATAT
1 TATATAATACAATATCATAT
*
185327 TACATAATACA
1 TATATAATACA
185338 TCATAACATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (20 bp):
TATATAATACAATATCATAT
Found at i:185444 original size:15 final size:15
Alignment explanation
Indices: 185421--185462 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
185411 TATTTGATAC
185421 ATAATATGATATTGT
1 ATAATATGATATTGT
* *
185436 ATCATATGATACTGT
1 ATAATATGATATTGT
*
185451 ATAATTTGATAT
1 ATAATATGATAT
185463 AACATTGTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (15 bp):
ATAATATGATATTGT
Found at i:186824 original size:177 final size:177
Alignment explanation
Indices: 186521--187263 Score: 950
Period size: 177 Copynumber: 4.2 Consensus size: 177
186511 CTAAACCATA
* * * *
186521 TCCAGCATCTGAAACCTATGGCTCAGACTCAGCATTCAGGCCTGTCAGGTGCATCAGTATCATAA
1 TCCAGCATCTGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAA
* * * *
186586 GACACACCATCCATGGAAGTCTGGTGAAGTTA-GGACAAGCAATAACTAAGATATAAT-C-ATCA
66 AACACACCATCCATGCAAGTCTGGTGAAG-TACGGACCAGCAGTAACTAAGATAT--TGCTATCA
* * ***
186648 GAGGGCACCAGTTTCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
128 AAGGGCACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
* * *
186698 TCCAGCATCCGAAACCTATGGCTCGGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAA
1 TCCAGCATCTGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAA
* * * *
186763 GACGCACCTTCCATAG-AAGTCTGGTGAAGTTA-GGACCAGTAGTAACTAAGATA-T-CATCATC
66 AACACACCATCCAT-GCAAGTCTGGTGAAG-TACGGACCAGCAGTAACTAAGATATTGC-T-ATC
*
186824 AGAGGGCACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
127 AAAGGGCACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
* * * *
186875 TTCAGCATCTGTAACCTATAGCTCAGATTCAGCA-CCAAAGCCTGCCTGGTGCATCAGTATCATA
1 TCCAGCATCTGAAACCTATAGCTCAGATTCAGCATTC-AAGCCTGTCTGGTGCATCAGTATCATA
* * *
186939 AAACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAACTTAGATATTGCTATCAAA
65 AAACACACCATCCATGCAAGTCTGGTGAAGTACGGACCAGCAGTAACTAAGATATTGCTATCAAA
* *
187004 GGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCC
130 GGGCACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
* *
187052 TCCAGCATCTGAAACCTATAGCTCAGATTCAGCACTCAAACCTGTCTGGTGCATCAGTATCATAA
1 TCCAGCATCTGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAA
* * * * *
187117 AACACACCATCCATGCAAGTTTGGTGAAGTATGGAACTGCAGTAACTTAGATATTGCTATCAAAG
66 AACACACCATCCATGCAAGTCTGGTGAAGTACGGACCAGCAGTAACTAAGATATTGCTATCAAAG
* *
187182 GGCACCTGCAACAAAAACTTTAACCTGGTC-AAACAACCTTAACCTCC
131 GGCACCTGCAACAAAAACTTTAACCAGCTCTAAA-AACCTTAACCTCC
*
187229 TCCAGCATCTGAAA--TTTAGGACTCAGATTCAGCAT
1 TCCAGCATCTGAAACCTATA-G-CTCAGATTCAGCAT
187264 CCTAGTCTTT
Statistics
Matches: 512, Mismatches: 41, Indels: 26
0.88 0.07 0.04
Matches are distributed among these distances:
174 2 0.00
175 3 0.01
176 8 0.02
177 494 0.96
178 4 0.01
179 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (177 bp):
TCCAGCATCTGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAA
AACACACCATCCATGCAAGTCTGGTGAAGTACGGACCAGCAGTAACTAAGATATTGCTATCAAAG
GGCACCTGCAACAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCC
Found at i:187032 original size:19 final size:19
Alignment explanation
Indices: 187008--187049 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
186998 ATCAAAGGGC
*
187008 ACCTGCAACAAAAACTTTA
1 ACCTGCAACAAAAACCTTA
**
187027 ACCTGCTCCAAAAACCTTA
1 ACCTGCAACAAAAACCTTA
187046 ACCT
1 ACCT
187050 CCTCCAGCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.33, G:0.05, T:0.21
Consensus pattern (19 bp):
ACCTGCAACAAAAACCTTA
Found at i:187054 original size:19 final size:19
Alignment explanation
Indices: 187016--187055 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
187006 GCACCTGCAA
* *
187016 CAAAAACTTTAACCTGCTC
1 CAAAAACCTTAACCTCCTC
187035 CAAAAACCTTAACCTCCTC
1 CAAAAACCTTAACCTCCTC
187054 CA
1 CA
187056 GCATCTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.38, G:0.03, T:0.23
Consensus pattern (19 bp):
CAAAAACCTTAACCTCCTC
Found at i:187345 original size:354 final size:351
Alignment explanation
Indices: 186521--187346 Score: 882
Period size: 354 Copynumber: 2.3 Consensus size: 351
186511 CTAAACCATA
* * * * * * * * * *
186521 TCCAGCATCTGAAACCTATGGCTCAGACTCAGCATTC-AGGCCTGTCAGGTGCATCAGTATCATA
1 TCCAGCATCTGTAACATATAGCTCAGATTCAGCA-CCAAAGCCTGCCAAGTCCATAAGTATCA-A
* * * * *
186585 AGACACACCATCCATGGAAGTCTGGTGAAGTTAGGACAAGCAATAACTAAGATATAATCATCAGA
64 AAACACACCATCCATGCAAGTTTGGTGAAG-TAGGACAAGCAATAACTTAGATAT-ATCATCAAA
*** *
186650 GGGCACCAGTTTCAAAAACTTTAACCAGCTCTAAAAACCTTAACCTCCTCCAGCATCCGAAACCT
127 GGGCACCAGCAACAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCT
* * * * * * *
186715 ATGGCTCGGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAAGACGCACCTTCCATAGA
192 ATAGCTCAGATTCAGCACTCAAACCTGTCTGGTGCATCAGTATCATAAAACACACCATCCATAGA
* * *
186780 AGTCTGGTGAAGTTAGGACCAGTAGTAACTAAGATATCATCATCAGAGGGCACCTGCAACAAAAA
257 AGTCTGGTGAAGTTAGGAACAGCAGTAACTAAGATATCATCATCAAAGGGCACCTGCAACAAAAA
186845 CTTTAACCAGCTCTAAAAACCTTAACCTCC
322 CTTTAACCAGCTCTAAAAACCTTAACCTCC
* * ** * *
186875 TTCAGCATCTGTAACCTATAGCTCAGATTCAGCACCAAAGCCTGCCTGGTGCATCAGTATCATAA
1 TCCAGCATCTGTAACATATAGCTCAGATTCAGCACCAAAGCCTGCCAAGTCCATAAGTATCA-AA
** *
186940 AACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAACTTAGATAT-TGCTATCAAA
65 AACACACCATCCATGCAAGTTTGGTGAAGTA-GGACAAGCAATAACTTAGATATAT-C-ATCAAA
* * *
187004 GGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTCCTCCAGCATCTGAAACCT
127 GGGCACCAGCAACAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCT
187069 ATAGCTCAGATTCAGCACTCAAACCTGTCTGGTGCATCAGTATCATAAAACACACCATCCAT-GC
192 ATAGCTCAGATTCAGCACTCAAACCTGTCTGGTGCATCAGTATCATAAAACACACCATCCATAG-
* * *
187133 AAGTTTGGTGAAG-TATGGAACTGCAGTAACTTAGATAT--TGCTATCAAAGGGCACCTGCAACA
256 AAGTCTGGTGAAGTTA-GGAACAGCAGTAACTAAGATATCAT-C-ATCAAAGGGCACCTGCAACA
* *
187195 AAAACTTTAACCTGGTC-AAACAACCTTAACCTCC
318 AAAACTTTAACCAGCTCTAAA-AACCTTAACCTCC
* * * **
187229 TCCAGCATCTG-AA-ATTTAGGACTCAGATTCAGCATCC-TAGTCTTTCAAGTCCATAAGTAGGT
1 TCCAGCATCTGTAACATATA-G-CTCAGATTCAGCA-CCAAAGCCTGCCAAGTCCATAAGTA--T
* * ** * * *
187291 C-CAGATGCATCATCCATGCAAGTTTGGTGAAGATAGGACAAGTAATAGCTTAGATA
61 CAAAAACACACCATCCATGCAAGTTTGGTGAAG-TAGGACAAGCAATAACTTAGATA
187347 CAGGACATGC
Statistics
Matches: 398, Mismatches: 59, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
352 5 0.01
353 14 0.04
354 373 0.94
355 4 0.01
356 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (351 bp):
TCCAGCATCTGTAACATATAGCTCAGATTCAGCACCAAAGCCTGCCAAGTCCATAAGTATCAAAA
ACACACCATCCATGCAAGTTTGGTGAAGTAGGACAAGCAATAACTTAGATATATCATCAAAGGGC
ACCAGCAACAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAG
CTCAGATTCAGCACTCAAACCTGTCTGGTGCATCAGTATCATAAAACACACCATCCATAGAAGTC
TGGTGAAGTTAGGAACAGCAGTAACTAAGATATCATCATCAAAGGGCACCTGCAACAAAAACTTT
AACCAGCTCTAAAAACCTTAACCTCC
Found at i:214099 original size:16 final size:16
Alignment explanation
Indices: 214054--214099 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
214044 TGTATACAGG
*
214054 GTTATTTTCGCCCCGT
1 GTTATTTTCGCCCTGT
214070 GTTATTTTCGCCCTGT
1 GTTATTTTCGCCCTGT
214086 GTTATTTTCGCCCT
1 GTTATTTTCGCCCT
214100 TCAATTCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.07, C:0.28, G:0.17, T:0.48
Consensus pattern (16 bp):
GTTATTTTCGCCCTGT
Found at i:220103 original size:30 final size:30
Alignment explanation
Indices: 219943--220331 Score: 231
Period size: 30 Copynumber: 13.4 Consensus size: 30
219933 TGATCCCCTT
** * * *
219943 GTGCTCCTTGCGAGATACTGAGTCCTGATG
1 GTGCTCCTTGCGAGATGTTGAGCCCCGGTG
*
219973 GTGCTCCTTGCGAGATATTGAGCCCCGGCT-
1 GTGCTCCTTGCGAGATGTTGAGCCCCGG-TG
* *
220003 GTGTTTCTTGCGAGATGTTGAGCCCCGGTG
1 GTGCTCCTTGCGAGATGTTGAGCCCCGGTG
* * *
220033 GTGCTCCTTGC-ACGTTGTTGAGTCTCGGTG
1 GTGCTCCTTGCGA-GATGTTGAGCCCCGGTG
* *
220063 GTGTTTCTTGCGAGATGTTGAGCCCCGGTG
1 GTGCTCCTTGCGAGATGTTGAGCCCCGGTG
* ****
220093 GTGCTCCTTGC---ATGTTG-TCATTTTGTG
1 GTGCTCCTTGCGAGATGTTGAGC-CCCGGTG
*
220120 GTGCTCCTTGAGAGATGTTGAGCCCCGGTG
1 GTGCTCCTTGCGAGATGTTGAGCCCCGGTG
* ****
220150 GTGCTCCTTGC---ATGTTG-TCATTTTGTG
1 GTGCTCCTTGCGAGATGTTGAGC-CCCGGTG
*
220177 GTGCTCCTTGAGAGATGTTGAGCCCCGGTG
1 GTGCTCCTTGCGAGATGTTGAGCCCCGGTG
** * ****
220207 GTATTCCTTGC---ATGTTG-TCATTTTGTG
1 GTGCTCCTTGCGAGATGTTGAGC-CCCGGTG
*
220234 GTGCTCCTTGAGAGATGTTGAGCCCCGGTG
1 GTGCTCCTTGCGAGATGTTGAGCCCCGGTG
****
220264 GTGCTCCTTGC---ATGTTGTCATTTTC--TG
1 GTGCTCCTTGCGAGATGTTG--AGCCCCGGTG
220291 GTGCTCCTTGCGAGATGTTGAGCCCCGGTG
1 GTGCTCCTTGCGAGATGTTGAGCCCCGGTG
**
220321 GTATTCCTTGC
1 GTGCTCCTTGC
220332 ATGTTGTCAT
Statistics
Matches: 264, Mismatches: 69, Indels: 52
0.69 0.18 0.14
Matches are distributed among these distances:
26 3 0.01
27 74 0.28
28 2 0.01
29 4 0.02
30 176 0.67
31 5 0.02
ACGTcount: A:0.11, C:0.22, G:0.31, T:0.35
Consensus pattern (30 bp):
GTGCTCCTTGCGAGATGTTGAGCCCCGGTG
Found at i:220358 original size:57 final size:57
Alignment explanation
Indices: 220009--220359 Score: 531
Period size: 57 Copynumber: 6.1 Consensus size: 57
219999 GGCTGTGTTT
* * ** * *
220009 CTTGCGAGATGTTGAGCCCCGGTGGTGCTCCTTGCACGTTGTTGAGTCTCGGTGGTGTTT
1 CTTGCGAGATGTTGAGCCCCGGTGGTGCTCCTTGCATGTTG-TCA-T-TTTGTGGTGCTC
220069 CTTGCGAGATGTTGAGCCCCGGTGGTGCTCCTTGCATGTTGTCATTTTGTGGTGCTC
1 CTTGCGAGATGTTGAGCCCCGGTGGTGCTCCTTGCATGTTGTCATTTTGTGGTGCTC
*
220126 CTTGAGAGATGTTGAGCCCCGGTGGTGCTCCTTGCATGTTGTCATTTTGTGGTGCTC
1 CTTGCGAGATGTTGAGCCCCGGTGGTGCTCCTTGCATGTTGTCATTTTGTGGTGCTC
* **
220183 CTTGAGAGATGTTGAGCCCCGGTGGTATTCCTTGCATGTTGTCATTTTGTGGTGCTC
1 CTTGCGAGATGTTGAGCCCCGGTGGTGCTCCTTGCATGTTGTCATTTTGTGGTGCTC
* *
220240 CTTGAGAGATGTTGAGCCCCGGTGGTGCTCCTTGCATGTTGTCATTTTCTGGTGCTC
1 CTTGCGAGATGTTGAGCCCCGGTGGTGCTCCTTGCATGTTGTCATTTTGTGGTGCTC
** * *
220297 CTTGCGAGATGTTGAGCCCCGGTGGTATTCCTTGCATGTTGTCATTTTGTGGTGTTT
1 CTTGCGAGATGTTGAGCCCCGGTGGTGCTCCTTGCATGTTGTCATTTTGTGGTGCTC
220354 CTTGCG
1 CTTGCG
220360 TATTGTTTTC
Statistics
Matches: 273, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
57 230 0.84
58 1 0.00
59 2 0.01
60 40 0.15
ACGTcount: A:0.10, C:0.21, G:0.31, T:0.38
Consensus pattern (57 bp):
CTTGCGAGATGTTGAGCCCCGGTGGTGCTCCTTGCATGTTGTCATTTTGTGGTGCTC
Found at i:227974 original size:2 final size:2
Alignment explanation
Indices: 227967--228046 Score: 144
Period size: 2 Copynumber: 40.5 Consensus size: 2
227957 TAGTAGGCTC
227967 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
228009 AG AG AG AG AG -G AA AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
228047 CGTACATTTC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:234407 original size:26 final size:26
Alignment explanation
Indices: 234377--234576 Score: 161
Period size: 26 Copynumber: 7.5 Consensus size: 26
234367 AGTGGAAATC
*
234377 CGTAACATGTAAAATCCAGCCTACAA
1 CGTAACATGTAAAATCCAACCTACAA
* *
234403 TGTAACATGTAAAATCCAGCCTACAA
1 CGTAACATGTAAAATCCAACCTACAA
* **
234429 CGTAACATGTAAAGTTTAACCTACAA
1 CGTAACATGTAAAATCCAACCTACAA
* * * *
234455 AGTAGCATGAAAAATCTAACCTACAA
1 CGTAACATGTAAAATCCAACCTACAA
* ** **
234481 CGTAACATGTGATGTTTAACCTACAA
1 CGTAACATGTAAAATCCAACCTACAA
* * *
234507 AGTAACATG-CAAATGCTAACCTACAA
1 CGTAACATGTAAAAT-CCAACCTACAA
234533 CGTAACATGTAACTAAAAATCCAACCT-CAAA
1 CGTAACATG----T-AAAATCCAACCTAC-AA
234564 CGTAACATGTAAA
1 CGTAACATGTAAA
234577 CTAAAATCTA
Statistics
Matches: 140, Mismatches: 26, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
25 2 0.01
26 115 0.82
27 1 0.01
30 1 0.01
31 17 0.12
32 4 0.03
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.23
Consensus pattern (26 bp):
CGTAACATGTAAAATCCAACCTACAA
Found at i:234469 original size:52 final size:51
Alignment explanation
Indices: 234377--234544 Score: 210
Period size: 52 Copynumber: 3.2 Consensus size: 51
234367 AGTGGAAATC
* ** * * * *
234377 CGTAACATGTAAAATCCAGCCTACAATGTAACATGTAAAATCCAGCCTACAA
1 CGTAACATGTAAAGTTTAACCTACAAAGTAACATG-AAAATCTAACCTACAA
*
234429 CGTAACATGTAAAGTTTAACCTACAAAGTAGCATGAAAAATCTAACCTACAA
1 CGTAACATGTAAAGTTTAACCTACAAAGTAACATG-AAAATCTAACCTACAA
* * *
234481 CGTAACATGTGATGTTTAACCTACAAAGTAACATGCAAATGCTAACCTACAA
1 CGTAACATGTAAAGTTTAACCTACAAAGTAACATGAAAAT-CTAACCTACAA
234533 CGTAACATGTAA
1 CGTAACATGTAA
234545 CTAAAAATCC
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
51 4 0.04
52 97 0.96
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.23
Consensus pattern (51 bp):
CGTAACATGTAAAGTTTAACCTACAAAGTAACATGAAAATCTAACCTACAA
Found at i:234559 original size:31 final size:30
Alignment explanation
Indices: 234524--234608 Score: 118
Period size: 31 Copynumber: 2.8 Consensus size: 30
234514 TGCAAATGCT
234524 AACCTACAACGTAACATGTAACTAAAAATCC
1 AACCTACAACGTAACATGTAACT-AAAATCC
*
234555 AACCT-CAAACGTAACATGTAAACTAAAATCT
1 AACCTAC-AACGTAACATGT-AACTAAAATCC
*
234586 AACCTAAAACGTAACATGTAACT
1 AACCTACAACGTAACATGTAACT
234609 TTTTAAGTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
30 5 0.10
31 40 0.82
32 4 0.08
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.21
Consensus pattern (30 bp):
AACCTACAACGTAACATGTAACTAAAATCC
Found at i:236152 original size:4 final size:4
Alignment explanation
Indices: 236143--236170 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
236133 TTCTTTTGAA
236143 CATT CATT CATT CATT CATT CATT CATT
1 CATT CATT CATT CATT CATT CATT CATT
236171 TTATTAGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
CATT
Found at i:239072 original size:4 final size:4
Alignment explanation
Indices: 239063--239097 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
239053 TTAACTGAAT
239063 AATA AATA AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AATA AAT
239098 GAACTATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:241308 original size:24 final size:24
Alignment explanation
Indices: 241281--241332 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
241271 TTCACACTGC
*
241281 CCATCACTTGAATTTTCCC-CTTTT
1 CCATCACTCGAA-TTTCCCTCTTTT
*
241305 CCATCACTCGAATTTCCCTGTTTT
1 CCATCACTCGAATTTCCCTCTTTT
241329 CCAT
1 CCAT
241333 GAATTATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.17, C:0.35, G:0.06, T:0.42
Consensus pattern (24 bp):
CCATCACTCGAATTTCCCTCTTTT
Found at i:246403 original size:30 final size:30
Alignment explanation
Indices: 246368--246458 Score: 164
Period size: 30 Copynumber: 3.0 Consensus size: 30
246358 ATTTTGAACT
*
246368 GCCGGTCAATAGACTGCGATCTATTAGACC
1 GCCGGTCAATAGACTGCGATCTATTGGACC
*
246398 GCCGGTCAATAGACTTCGATCTATTGGACC
1 GCCGGTCAATAGACTGCGATCTATTGGACC
246428 GCCGGTCAATAGACTGCGATCTATTGGACC
1 GCCGGTCAATAGACTGCGATCTATTGGACC
246458 G
1 G
246459 GCAACGTATT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.24
Consensus pattern (30 bp):
GCCGGTCAATAGACTGCGATCTATTGGACC
Found at i:278124 original size:11 final size:11
Alignment explanation
Indices: 278108--278132 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
278098 GCTATTCTAT
278108 AGGTTCATATA
1 AGGTTCATATA
278119 AGGTTCATATA
1 AGGTTCATATA
278130 AGG
1 AGG
278133 AAACCTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (11 bp):
AGGTTCATATA
Found at i:281044 original size:16 final size:17
Alignment explanation
Indices: 281011--281049 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
281001 TGGTTAGTAG
*
281011 TATCT-TGATCTTTATT
1 TATCTATGATCATTATT
281027 TATCTATGATCATT-TT
1 TATCTATGATCATTATT
281043 TATCTAT
1 TATCTAT
281050 TTATCTTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.23, C:0.13, G:0.05, T:0.59
Consensus pattern (17 bp):
TATCTATGATCATTATT
Found at i:289182 original size:1 final size:1
Alignment explanation
Indices: 289176--289208 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
289166 AAGCAAAATC
289176 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
289209 ATAGGTGGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:306738 original size:9 final size:9
Alignment explanation
Indices: 306724--306792 Score: 57
Period size: 9 Copynumber: 6.9 Consensus size: 9
306714 TAACACTTAT
306724 ACACATACA
1 ACACATACA
306733 ACACATACTTA
1 ACACATAC--A
*
306744 ACACATATA
1 ACACATACA
306753 ACACATACTTA
1 ACACATAC--A
306764 ACACATATACA
1 ACAC--ATACA
*
306775 TGCACATACA
1 -ACACATACA
306785 ACACATAC
1 ACACATAC
306793 TTAACATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
9 23 0.47
10 5 0.10
11 14 0.29
12 3 0.06
13 4 0.08
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.20
Consensus pattern (9 bp):
ACACATACA
Found at i:306771 original size:20 final size:20
Alignment explanation
Indices: 306718--306772 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
306708 CAACATTAAC
*
306718 ACTTATACACATACAACACAT
1 ACTTA-ACACATATAACACAT
306739 ACTTAACACATATAACACAT
1 ACTTAACACATATAACACAT
306759 ACTTAACACATATA
1 ACTTAACACATATA
306773 CATGCACATA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 28 0.85
21 5 0.15
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (20 bp):
ACTTAACACATATAACACAT
Found at i:354321 original size:13 final size:13
Alignment explanation
Indices: 354285--354323 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
354275 ACCAAAATTT
354285 TCAAATCCCTCAAC
1 TCAAAT-CCTCAAC
*
354299 TC-ATTCCTCAAC
1 TCAAATCCTCAAC
354311 TCAAATCCTCAAC
1 TCAAATCCTCAAC
354324 AAAAACATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 9 0.41
13 11 0.50
14 2 0.09
ACGTcount: A:0.33, C:0.41, G:0.00, T:0.26
Consensus pattern (13 bp):
TCAAATCCTCAAC
Found at i:357830 original size:10 final size:10
Alignment explanation
Indices: 357815--357884 Score: 122
Period size: 10 Copynumber: 6.8 Consensus size: 10
357805 CACGTCTTTT
357815 AACCCCAAGG
1 AACCCCAAGG
357825 AACCCCAAGG
1 AACCCCAAGG
357835 AACCCCAAGG
1 AACCCCAAGG
357845 AAACCCCAAGG
1 -AACCCCAAGG
357856 AACCCCAAGG
1 AACCCCAAGG
357866 AACCCCAAGG
1 AACCCCAAGG
357876 ATACCCCAA
1 A-ACCCCAA
357885 TAACAGAAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
10 41 0.71
11 17 0.29
ACGTcount: A:0.41, C:0.40, G:0.17, T:0.01
Consensus pattern (10 bp):
AACCCCAAGG
Found at i:357851 original size:21 final size:20
Alignment explanation
Indices: 357815--357884 Score: 122
Period size: 21 Copynumber: 3.4 Consensus size: 20
357805 CACGTCTTTT
357815 AACCCCAAGGAACCCCAAGG
1 AACCCCAAGGAACCCCAAGG
357835 AACCCCAAGGAAACCCCAAGG
1 AACCCCAAGG-AACCCCAAGG
357856 AACCCCAAGGAACCCCAAGG
1 AACCCCAAGGAACCCCAAGG
357876 ATACCCCAA
1 A-ACCCCAA
357885 TAACAGAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
20 21 0.44
21 27 0.56
ACGTcount: A:0.41, C:0.40, G:0.17, T:0.01
Consensus pattern (20 bp):
AACCCCAAGGAACCCCAAGG
Found at i:357853 original size:31 final size:31
Alignment explanation
Indices: 357815--357884 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
357805 CACGTCTTTT
357815 AACCCCAAGGAACCCCAAGGAACCCCAAGGA
1 AACCCCAAGGAACCCCAAGGAACCCCAAGGA
357846 AACCCCAAGGAACCCCAAGGAACCCCAAGGA
1 AACCCCAAGGAACCCCAAGGAACCCCAAGGA
*
357877 TACCCCAA
1 AACCCCAA
357885 TAACAGAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.41, C:0.40, G:0.17, T:0.01
Consensus pattern (31 bp):
AACCCCAAGGAACCCCAAGGAACCCCAAGGA
Found at i:358449 original size:331 final size:336
Alignment explanation
Indices: 358085--358724 Score: 972
Period size: 331 Copynumber: 1.9 Consensus size: 336
358075 CTCGTGGTAC
*
358085 CCCTGGGGACTCACTGGTATTCCAGACACACCTCTAAGAA-CCACAGGGAACCCCTGGGATATCC
1 CCCTGGGGACTCACTGGTATTCCAGACACACCTCTAAGAATCC-CAGGGAACCCCAGGGATATCC
*
358149 CAAGGAACTCCAAGAATACCCTAATAATACAGAATCATAACTCTTGATACTCCATAGAACCCCAA
65 CAAGGAACTCCAAGAATACCCTAATAATACAGAATCATAAATCTTGATACTCCATAGAACCCCAA
*
358214 GGATACCCT-A-A-T-AATACAAATTTAAAACTCTT-ATTAACCCTGAGGACTCATTGGTATTCC
130 GGATACCCTAATACTCAATACAAATCTAAAACT-TTGA-TAACCCTGAGGACTCATTGGTATTCC
* * *
358274 AGATACACCTCTAGGAATCCCAGGGAACCCCATGGATATCCCAAGGAA-C-TACCCTAATAATAC
193 AGATACACCTCTAAGAATCCCAGGGAACCCCAGGGATATCCCAAGGAACCATACCCTAAAAATAC
* *
358337 AGAATCATAACTCTTAATACTCCATAGAACCCCAAGGATACCCTAATACATTGTAATACAAATGT
258 AGAATCATAACTCTTAATACACCACAGAACCCCAAGGATACCCTAATACATTGTAATACAAATGT
358402 AAAACTTTTGATAA
323 AAAACTTTTGATAA
* * *
358416 CCCTGGGGACTCATTGGTATTCCAGATACACCTCTAGGAATCCCAGGGAACCCCAGGGATATCCC
1 CCCTGGGGACTCACTGGTATTCCAGACACACCTCTAAGAATCCCAGGGAACCCCAGGGATATCCC
358481 AAGGAACTCCAAGAATACCCTAATAATACAGAATCATAAATCTTGATACTCCATAGAACCCCAAG
66 AAGGAACTCCAAGAATACCCTAATAATACAGAATCATAAATCTTGATACTCCATAGAACCCCAAG
* *
358546 GATACCGTAATACGCTGCAATACAAATCTAAAACTTTGGATAACCCTGGGGACTCATTGGTATTC
131 GATACCCTAATA--CT-CAATACAAATCTAAAACTTT-GATAACCCTGAGGACTCATTGGTATTC
358611 CAGATACACCTCTAAGAATCCCAGGGAACCCCAGGGATATCCCAAGGAACTCCAAGAATACCCTA
192 CAGATACACCTCTAAGAATCCCAGGGAACCCCAGGGATATCCCAAGGAA--CC----ATACCCTA
* *
358676 AAAATACAGATTCATAACTCTTGATACACCACAGAACCCCAAGGATACC
251 AAAATACAGAATCATAACTCTTAATACACCACAGAACCCCAAGGATACC
358725 TCAAGGAACT
Statistics
Matches: 276, Mismatches: 15, Indels: 21
0.88 0.05 0.07
Matches are distributed among these distances:
331 129 0.47
332 3 0.01
333 1 0.00
336 1 0.00
337 2 0.01
338 87 0.32
339 1 0.00
341 1 0.00
346 51 0.18
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.22
Consensus pattern (336 bp):
CCCTGGGGACTCACTGGTATTCCAGACACACCTCTAAGAATCCCAGGGAACCCCAGGGATATCCC
AAGGAACTCCAAGAATACCCTAATAATACAGAATCATAAATCTTGATACTCCATAGAACCCCAAG
GATACCCTAATACTCAATACAAATCTAAAACTTTGATAACCCTGAGGACTCATTGGTATTCCAGA
TACACCTCTAAGAATCCCAGGGAACCCCAGGGATATCCCAAGGAACCATACCCTAAAAATACAGA
ATCATAACTCTTAATACACCACAGAACCCCAAGGATACCCTAATACATTGTAATACAAATGTAAA
ACTTTTGATAA
Found at i:358457 original size:165 final size:166
Alignment explanation
Indices: 358085--358724 Score: 832
Period size: 173 Copynumber: 3.8 Consensus size: 166
358075 CTCGTGGTAC
* * * *
358085 CCCTGGGGACTCACTGGTATTCCAGACACACCTCTAAGAA-CCACAGGGAACCCCTGGGATATCC
1 CCCTGGGGACTCATTGGTATTCCAGATACACCTCTAGGAATCC-CAGGGAACCCCAGGGATATCC
358149 CAAGGAACTCCAAGAATACCCTAATAATACAGAATCATAACTCTTGATACTCCATAGAACCCCAA
65 CAAGGAA--CC----ATACCCTAATAATACAGAATCATAACTCTTGATACTCCATAGAACCCCAA
* *
358214 GGATACCC---TA-A--TAATACAAATTTAAAACTCTT-ATTAA
124 GGATACCCTAATACATGTAATACAAATCTAAAACTTTTGA-TAA
* *
358251 CCCTGAGGACTCATTGGTATTCCAGATACACCTCTAGGAATCCCAGGGAACCCCATGGATATCCC
1 CCCTGGGGACTCATTGGTATTCCAGATACACCTCTAGGAATCCCAGGGAACCCCAGGGATATCCC
*
358316 AAGGAA-C-TACCCTAATAATACAGAATCATAACTCTTAATACTCCATAGAACCCCAAGGATACC
66 AAGGAACCATACCCTAATAATACAGAATCATAACTCTTGATACTCCATAGAACCCCAAGGATACC
*
358379 CTAATACATTGTAATACAAATGTAAAACTTTTGATAA
131 CTAATACA-TGTAATACAAATCTAAAACTTTTGATAA
358416 CCCTGGGGACTCATTGGTATTCCAGATACACCTCTAGGAATCCCAGGGAACCCCAGGGATATCCC
1 CCCTGGGGACTCATTGGTATTCCAGATACACCTCTAGGAATCCCAGGGAACCCCAGGGATATCCC
*
358481 AAGGAACTCCAAGAATACCCTAATAATACAGAATCATAAATCTTGATACTCCATAGAACCCCAAG
66 AAGGAA--CC----ATACCCTAATAATACAGAATCATAACTCTTGATACTCCATAGAACCCCAAG
* * * *
358546 GATACCGTAATACGCTGCAATACAAATCTAAAACTTTGGATAA
125 GATACCCTAATAC-ATGTAATACAAATCTAAAACTTTTGATAA
*
358589 CCCTGGGGACTCATTGGTATTCCAGATACACCTCTAAGAATCCCAGGGAACCCCAGGGATATCCC
1 CCCTGGGGACTCATTGGTATTCCAGATACACCTCTAGGAATCCCAGGGAACCCCAGGGATATCCC
* * * *
358654 AAGGAACTCCAAGAATACCCTAAAAATACAGATTCATAACTCTTGATACACCACAGAACCCCAAG
66 AAGGAA--CC----ATACCCTAATAATACAGAATCATAACTCTTGATACTCCATAGAACCCCAAG
358719 GATACC
125 GATACC
358725 TCAAGGAACT
Statistics
Matches: 432, Mismatches: 24, Indels: 29
0.89 0.05 0.06
Matches are distributed among these distances:
158 56 0.13
161 2 0.00
162 1 0.00
163 1 0.00
165 91 0.21
166 63 0.15
167 2 0.00
168 1 0.00
173 215 0.50
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.22
Consensus pattern (166 bp):
CCCTGGGGACTCATTGGTATTCCAGATACACCTCTAGGAATCCCAGGGAACCCCAGGGATATCCC
AAGGAACCATACCCTAATAATACAGAATCATAACTCTTGATACTCCATAGAACCCCAAGGATACC
CTAATACATGTAATACAAATCTAAAACTTTTGATAA
Found at i:358755 original size:73 final size:72
Alignment explanation
Indices: 358636--358774 Score: 163
Period size: 73 Copynumber: 1.9 Consensus size: 72
358626 GAATCCCAGG
* * * *
358636 GAACCCCAGGGATATCCCAAGGAACTCCAAGAATACCCTAAAAATACAGATTCATAACTCTTGAT
1 GAACCCCAAGGATATCCCAAGGAACTCAAAGAATAACCTAAAAATACAAATTCA-AACTCTTGAT
358701 ACACCACA
65 ACACCACA
* * * * * *
358709 GAACCCCAAGGATA-CCTCAAGGAACTTAAAGGATAACTTAATAATACAAATTTAAATTCTTGAT
1 GAACCCCAAGGATATCC-CAAGGAACTCAAAGAATAACCTAAAAATACAAATTCAAACTCTTGAT
358773 AC
65 AC
358775 CCGTAGGGAC
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
72 13 0.24
73 42 0.76
ACGTcount: A:0.42, C:0.24, G:0.12, T:0.22
Consensus pattern (72 bp):
GAACCCCAAGGATATCCCAAGGAACTCAAAGAATAACCTAAAAATACAAATTCAAACTCTTGATA
CACCACA
Found at i:361812 original size:184 final size:184
Alignment explanation
Indices: 361503--361856 Score: 433
Period size: 184 Copynumber: 1.9 Consensus size: 184
361493 ATAGGGGTAT
* * * * *
361503 AATGAGACTCCTGGGGTATCACTAGTTACTAATTTCTATTATTGGGGTTACTTGGGGTTCTAACG
1 AATGAGACCCCTGGGGTATCACTAGTTAATAACTTCTATCATTGGGGTTACATGGGGTTCTAACG
**** * * *
361568 AGTATACTTGGGGTTCCTTGGGGTATCCTTGGTGACCCTTGGATTCAAATGAGACCCCTTGGGTA
66 AGTATACTTGGGGTTCCTTGGGGTATAAGAGGTGACCCTTGAAGTCAAATAAGACCCCTTGGGTA
361633 -TAAATAGTTATCAATTTCTATCACTGGGGTACCTTGGGGTGAGCCTTTGATTTG
131 TTAAA-AGTTATCAATTTCTATCACTGGGGTACCTTGGGGTGAGCCTTTGATTTG
* * * * *
361687 AATGAGACCCCTTGGGTATCACTGGTTAATAACTT-TATCATTTGGGTTCCATGGGGTTCTTACG
1 AATGAGACCCCTGGGGTATCACTAGTTAATAACTTCTATCATTGGGGTTACATGGGGTTCTAACG
* * * *
361751 GGTTTCCTTGGGGTTCCTTGGGGTACTAAGAGGTGACCCTTGAAGTCCAATAAGACCCCTTGGGT
66 AGTATACTTGGGGTTCCTTGGGGTA-TAAGAGGTGACCCTTGAAGTCAAATAAGACCCCTTGGGT
* * * * * *
361816 ATTAAAATTTATTAATTTTTGTCATTGGGGTTCCTTGGGGT
130 ATTAAAAGTTATCAATTTCTATCACTGGGGTACCTTGGGGT
361857 ATCCTTGAGG
Statistics
Matches: 141, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
183 46 0.33
184 91 0.65
185 4 0.03
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (184 bp):
AATGAGACCCCTGGGGTATCACTAGTTAATAACTTCTATCATTGGGGTTACATGGGGTTCTAACG
AGTATACTTGGGGTTCCTTGGGGTATAAGAGGTGACCCTTGAAGTCAAATAAGACCCCTTGGGTA
TTAAAAGTTATCAATTTCTATCACTGGGGTACCTTGGGGTGAGCCTTTGATTTG
Found at i:361855 original size:10 final size:10
Alignment explanation
Indices: 361840--361919 Score: 133
Period size: 10 Copynumber: 7.8 Consensus size: 10
361830 ATTTTTGTCA
361840 TTGGGGTTCC
1 TTGGGGTTCC
361850 TTGGGGTATCC
1 TTGGGGT-TCC
*
361861 TTGAGGTTCC
1 TTGGGGTTCC
361871 TTGGGGTTCC
1 TTGGGGTTCC
361881 TTGGGGTTCC
1 TTGGGGTTCC
361891 TTGGGGTTTCC
1 TTGGGG-TTCC
361902 TTGGGGTTCC
1 TTGGGGTTCC
361912 TTGGGGTT
1 TTGGGGTT
361920 AAAAGACGCA
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
10 47 0.71
11 19 0.29
ACGTcount: A:0.03, C:0.17, G:0.39, T:0.41
Consensus pattern (10 bp):
TTGGGGTTCC
Found at i:361870 original size:21 final size:20
Alignment explanation
Indices: 361840--361919 Score: 133
Period size: 21 Copynumber: 3.9 Consensus size: 20
361830 ATTTTTGTCA
361840 TTGGGGTTCCTTGGGGTATCC
1 TTGGGGTTCCTTGGGGT-TCC
*
361861 TTGAGGTTCCTTGGGGTTCC
1 TTGGGGTTCCTTGGGGTTCC
361881 TTGGGGTTCCTTGGGGTTTCC
1 TTGGGGTTCCTTGGGG-TTCC
361902 TTGGGGTTCCTTGGGGTT
1 TTGGGGTTCCTTGGGGTT
361920 AAAAGACGCA
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
20 20 0.36
21 36 0.64
ACGTcount: A:0.03, C:0.17, G:0.39, T:0.41
Consensus pattern (20 bp):
TTGGGGTTCCTTGGGGTTCC
Found at i:361878 original size:31 final size:31
Alignment explanation
Indices: 361840--361919 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
361830 ATTTTTGTCA
361840 TTGGGGTTCCTTGGGGTATCCTTGAGG-TTCC
1 TTGGGGTTCCTTGGGGT-TCCTTGAGGTTTCC
*
361871 TTGGGGTTCCTTGGGGTTCCTTGGGGTTTCC
1 TTGGGGTTCCTTGGGGTTCCTTGAGGTTTCC
361902 TTGGGGTTCCTTGGGGTT
1 TTGGGGTTCCTTGGGGTT
361920 AAAAGACGCA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 8 0.17
31 39 0.83
ACGTcount: A:0.03, C:0.17, G:0.39, T:0.41
Consensus pattern (31 bp):
TTGGGGTTCCTTGGGGTTCCTTGAGGTTTCC
Found at i:369958 original size:3 final size:3
Alignment explanation
Indices: 369938--369991 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
369928 TTTTCATATC
* * * * * *
369938 CAT CAT CCT CCT CTT CAT CAT CGT CAT TAT CAT TAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
369986 CAT CAT
1 CAT CAT
369992 GGCCCCTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.26, C:0.33, G:0.02, T:0.39
Consensus pattern (3 bp):
CAT
Found at i:390916 original size:2 final size:2
Alignment explanation
Indices: 390909--390941 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
390899 TTTTACTTAA
390909 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
390942 CATTAATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:401604 original size:2 final size:2
Alignment explanation
Indices: 401597--401626 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
401587 NNNNNNNNNN
401597 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
401627 AATCGGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:404426 original size:21 final size:21
Alignment explanation
Indices: 404402--404457 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
404392 CTGTACTTAC
*
404402 GATAGTAAGTCGTAATAACGA
1 GATAATAAGTCGTAATAACGA
* * *
404423 GATACTAAGTCTTTATAACGA
1 GATAATAAGTCGTAATAACGA
*
404444 GATAATATGTCGTA
1 GATAATAAGTCGTA
404458 CAAAAAAATA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (21 bp):
GATAATAAGTCGTAATAACGA
Found at i:407081 original size:2 final size:2
Alignment explanation
Indices: 407074--407113 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
407064 TAAAGTCAGA
407074 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
407114 ATATATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:410540 original size:2 final size:2
Alignment explanation
Indices: 410535--410560 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
410525 TCTAATTAAT
410535 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
410561 TCATGTTTGA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:413026 original size:80 final size:80
Alignment explanation
Indices: 412802--413067 Score: 383
Period size: 80 Copynumber: 3.3 Consensus size: 80
412792 TGGATATACA
* * * * *
412802 CGTTTAGATTTTCCTTGCACCCTGTATGTCTACAGTAACATCATTAAGTACTTGAGCTATTATGT
1 CGTTTTGATTTACCTTGCCCCCTCTAGGTCTACAGTAACATCATTAAGTACTTGAGCTATTATGT
** * *
412867 ATATACTGAGGCTGCC
66 ATGCACTGGGGAT-CC
412883 CGTTTTGATTTACCTTGCCCCCTCT--GTCTACAGTAACATCATTAAGTACTTGAGCTATTATGT
1 CGTTTTGATTTACCTTGCCCCCTCTAGGTCTACAGTAACATCATTAAGTACTTGAGCTATTATGT
412946 ATGCACTGGGGATCC
66 ATGCACTGGGGATCC
* * *
412961 CGTTTTGATTTACCTTGCCCCCTCTAGGTCAACAGTACCATCATTGAGTACTTGAGCTATTATGT
1 CGTTTTGATTTACCTTGCCCCCTCTAGGTCTACAGTAACATCATTAAGTACTTGAGCTATTATGT
*
413026 ATGCACTGGGTATCC
66 ATGCACTGGGGATCC
*
413041 CGATTTGATTTACCTTGCCCCCTCTAG
1 CGTTTTGATTTACCTTGCCCCCTCTAG
413068 ATCGCCGGAC
Statistics
Matches: 170, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
78 27 0.16
79 47 0.28
80 75 0.44
81 21 0.12
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (80 bp):
CGTTTTGATTTACCTTGCCCCCTCTAGGTCTACAGTAACATCATTAAGTACTTGAGCTATTATGT
ATGCACTGGGGATCC
Found at i:426714 original size:2 final size:2
Alignment explanation
Indices: 426707--426747 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
426697 AATCATGCAA
426707 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
426748 ATGTGTATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:437553 original size:167 final size:166
Alignment explanation
Indices: 437219--437826 Score: 758
Period size: 166 Copynumber: 3.6 Consensus size: 166
437209 GGTATTTTTC
* * * * *** *
437219 AAAAATCTTCTTCTCAAAAACTGTTCA-GCCTGAAAAGCTTACACTT-GTGTGGAGGCATCCTCA
1 AAAAATCTTCTTCTCAAAAACTATT-AGGCCAGAAAAGCTCA-AATTAAAATGGAAGCATCCTCA
*
437282 GGTAGTGTAGATTCAAGTTTGTTCACATCATGGTCCCCGGGGGTAGGGTGGGGCCACAA-GAGGG
64 GGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATG-GGG
* **
437346 GGATCAAGTTTTACATAGGAATATATAGAGAAATTCTTT
128 GAATCAAGTTTTACATAGGAATATATAGAGAAAAACTTT
* * *
437385 AAAAATCTTCTTCTCAAAGACTATTAGGCCAGAAAAGCTCATATTAAAGTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
* * * * *
437450 TAGTGTAGATTCAAATTTTGTTCAAATCATAGTCCCTGGTGGTATGGTGGGGCCACAATGGGGGA
66 TAGTGTAGATTC-AAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGGA
** * *
437515 ATGGATTTTTACATAGGAATATATAGAGAAAATCTTT
130 ATCAAGTTTTACATAGGAATATATAGAGAAAAACTTT
* * * * * *
437552 AAAAATCTTCCTCTCAAAAACAATTTGGCCAGAAAAGCTCAAATTAAAATAGAAGTATTCC-GAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCA-TCCTCAG
* * *
437616 GTAGTGTACATTCAAGTTTGTCCAAATCATGGTCCCCAGGGGTAGGGTGGGGCCACAATAGGGGG
65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAAT-GGGGG
* *
437681 -ATCATGTTTTACATAGGAATATATTGAGAAAAACTTT
129 AATCAAGTTTTACATAGGAATATATAGAGAAAAACTTT
* * *
437718 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAACCTCAAATTAAAATAGAATGCATACTCAG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAA-GCATCCTCAG
*
437783 GTAGTGTAGATTCAAGTTTGTCCAAATCATGGTCCCCCGGGGGT
65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGT-CCCCGGGGGT
437827 TTTACATAAG
Statistics
Matches: 381, Mismatches: 52, Indels: 16
0.85 0.12 0.04
Matches are distributed among these distances:
165 3 0.01
166 185 0.49
167 180 0.47
168 13 0.03
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (166 bp):
AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATGGGGGAA
TCAAGTTTTACATAGGAATATATAGAGAAAAACTTT
Found at i:437712 original size:166 final size:165
Alignment explanation
Indices: 437280--438276 Score: 873
Period size: 166 Copynumber: 6.1 Consensus size: 165
437270 GAGGCATCCT
* * * *
437280 CAGGTAGTGTAGATTCAAGTTTGTTCACATCATGGTCCCCGGGGGTAGGGTGGGGCCACAAGAGG
1 CAGGTAGTGTAGATTCAAGTTTGTCCAAATCATGGTCCCCAGGGGTAGGGTGGGGCCACAATAGG
* * *
437345 GGGATCAAGTTTTACATAGGAATATATAGAGAAATTCTTTAAAAATCTTCTTCTCAAAGACTATT
66 GGGATCATGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATT
* * * *
437410 AGGCCAGAAAAGCTCATATTAAAGTGGAAGCATCC
131 AGGCCAGAAAAGCTCAAATTAAAATAGAAGCATTC
* * * * *
437445 TCAGGTAGTGTAGATTCAAATTTTGTTCAAATCATAGT-CCCTGGTGGTATGGTGGGGCCACAAT
1 -CAGGTAGTGTAGATTC-AAGTTTGTCCAAATCATGGTCCCCAGG-GGTAGGGTGGGGCCACAAT
* *
437509 -GGGGGAATGGAT-TTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCCTCTCAAAAA
63 AGGGGG-AT-CATGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAA
* * *
437572 CAATTTGGCCAGAAAAGCTCAAATTAAAATAGAAGTATTC
126 CTATTAGGCCAGAAAAGCTCAAATTAAAATAGAAGCATTC
*
437612 CGAGGTAGTGTACATTCAAGTTTGTCCAAATCATGGTCCCCAGGGGTAGGGTGGGGCCACAATAG
1 C-AGGTAGTGTAGATTCAAGTTTGTCCAAATCATGGTCCCCAGGGGTAGGGTGGGGCCACAATAG
* *
437677 GGGGATCATGTTTTACATAGGAATATATTGAGAAAAACTTTAAAAATCTTCTTCTCAAAAACTAT
65 GGGGATCATGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTAT
* *
437742 TAGGCCAGAAAACCTCAAATTAAAATAGAATGCATAC
130 TAGGCCAGAAAAGCTCAAATTAAAATAGAA-GCATTC
* ***
437779 TCAGGTAGTGTAGATTCAAGTTTGTCCAAATCATGGTCCCC--CGG--GGGT---TTTAC-ATA-
1 -CAGGTAGTGTAGATTCAAGTTTGTCCAAATCATGGTCCCCAGGGGTAGGGTGGGGCCACAATAG
* * * * * * * * *
437835 --AGAT--T-ATATAGAGA-AAATCTTTA-A-AAATCTTCTTCTCAAAAA----C----------
65 GGGGATCATGTTTTACATAGGAATATATAGAGAAA--ATCTT-T-AAAAATCTTCTTCTCAAAAA
* ** * * *
437878 -TATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCC
126 CTATTAGGCCAGAAAAGCTCAAATTAAAATAGAAGCATTC
* * * * * *
437917 TCAGATAGCGTAGATTCAAGTTTGTTCAAATCATGTTCCCCGGGGGTAGGGTGGGGCCACAATGG
1 -CAGGTAGTGTAGATTCAAGTTTGTCCAAATCATGGTCCCCAGGGGTAGGGTGGGGCCACAATAG
* *
437982 GGGGATCAAGTTTTACATAGGAATATATAGAGAAAAACTTTAAAAATCTTCTTCTCAAAAACTAT
65 GGGGATCATGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTAT
* * * *
438047 CAGGCCAGAAAAGCTCAAATTAAAATGGGAGCATCC
130 TAGGCCAGAAAAGCTCAAATTAAAATAGAAGCATTC
* * * * *
438083 TCAGATAGCGTAGATTCAAGTTTGTTCAAACCATGGTTCCCGGGAGTAGGAGTAGGGTGGGGCCA
1 -CAGGTAGTGTAGATTCAAGTTTGTCCAAATCATGG-TCCC--CAG--GG-GTAGGGTGGGGCCA
* ** * ** *
438148 CAATTGGAAGATCAAGTTTTACATAGGAATATATAGAGAAAAAATTTAAAAA---TCTTCTAAAA
59 CAATAGGGGGATCATGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAA
* * * *
438210 AACTATCAGGCCAGAAAAGCTCAAATTAAAATGGGAGCATCC
124 AACTATTAGGCCAGAAAAGCTCAAATTAAAATAGAAGCATTC
*
438252 TCAGATAGTGTAGATTCAAGTTTGT
1 -CAGGTAGTGTAGATTCAAGTTTGT
438277 TCAANNNNNN
Statistics
Matches: 687, Mismatches: 92, Indels: 101
0.78 0.10 0.11
Matches are distributed among these distances:
138 42 0.06
139 27 0.04
140 2 0.00
142 4 0.01
145 2 0.00
146 2 0.00
149 3 0.00
150 4 0.01
151 6 0.01
152 14 0.02
153 15 0.02
154 7 0.01
155 4 0.01
156 3 0.00
159 3 0.00
160 2 0.00
163 4 0.01
165 4 0.01
166 210 0.31
167 187 0.27
168 2 0.00
169 76 0.11
171 2 0.00
172 62 0.09
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (165 bp):
CAGGTAGTGTAGATTCAAGTTTGTCCAAATCATGGTCCCCAGGGGTAGGGTGGGGCCACAATAGG
GGGATCATGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATT
AGGCCAGAAAAGCTCAAATTAAAATAGAAGCATTC
Found at i:438072 original size:305 final size:304
Alignment explanation
Indices: 437521--438119 Score: 903
Period size: 305 Copynumber: 2.0 Consensus size: 304
437511 GGGAATGGAT
* *
437521 TTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCCTCTCAAAAACAATTTGGCCAGAA
1 TTTTACATAAGAATATATAGAGAAAATCTTTAAAAATCTTCCTCTCAAAAACAATTAGGCCAGAA
* * * *
437586 AAGCTCAAATTAAAATAGAAGTATTCCGAGGTAGTGTACATTCAAGTTTGTCCAAATCATGGTCC
66 AAGCTCAAATTAAAATAGAAGCATTCCCAGATAGCGTACATTCAAGTTTGTCCAAATCATGGTCC
* *
437651 CCAGGGGTAGGGTGGGGCCACAATAGGGGGATCATGTTTTACATAGGAATATATTGAGAAAAACT
131 CCAGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAAACT
*
437716 TTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAACCTCAAATTAAAATAGAATGCATACTC
196 TTAAAAATCTTCTTCTCAAAAACTATCAGGCCAGAAAACCTCAAATTAAAATAGAA-GCATACTC
* * *
437781 AGGTAGTGTAGATTCAAGTTTGTCCAAATCATGGTCCCCCGGGGG
260 AGATAGCGTAGATTCAAGTTTGTCCAAACCATGGTCCCCCGGGGG
* * * *
437826 TTTTACATAAGATTATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGGA
1 TTTTACATAAGAATATATAGAGAAAATCTTTAAAAATCTTCCTCTCAAAAACAATTAGGCCAGAA
** * * * * *
437891 AAGCTCAAATTTGAGTGGAAGCA-TCCTCAGATAGCGTAGATTCAAGTTTGTTCAAATCATGTTC
66 AAGCTCAAATTAAAATAGAAGCATTCC-CAGATAGCGTACATTCAAGTTTGTCCAAATCATGGTC
* *
437955 CCCGGGGGTAGGGTGGGGCCACAATGGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAAAC
130 CCCAGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAAAC
* * * *
438020 TTTAAAAATCTTCTTCTCAAAAACTATCAGGCCAGAAAAGCTCAAATTAAAATGGGAGCATCCTC
195 TTTAAAAATCTTCTTCTCAAAAACTATCAGGCCAGAAAACCTCAAATTAAAATAGAAGCATACTC
*
438085 AGATAGCGTAGATTCAAGTTTGTTCAAACCATGGT
260 AGATAGCGTAGATTCAAGTTTGTCCAAACCATGGT
438120 TCCCGGGAGT
Statistics
Matches: 263, Mismatches: 30, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
304 41 0.16
305 222 0.84
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (304 bp):
TTTTACATAAGAATATATAGAGAAAATCTTTAAAAATCTTCCTCTCAAAAACAATTAGGCCAGAA
AAGCTCAAATTAAAATAGAAGCATTCCCAGATAGCGTACATTCAAGTTTGTCCAAATCATGGTCC
CCAGGGGTAGGGTGGGGCCACAATAGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAAACT
TTAAAAATCTTCTTCTCAAAAACTATCAGGCCAGAAAACCTCAAATTAAAATAGAAGCATACTCA
GATAGCGTAGATTCAAGTTTGTCCAAACCATGGTCCCCCGGGGG
Found at i:447888 original size:167 final size:166
Alignment explanation
Indices: 447613--448955 Score: 1872
Period size: 166 Copynumber: 8.0 Consensus size: 166
447603 GGCAGTAGTN
* *
447613 ACATAGGAATATATAGAGAAAATCTTTTTAAAAA-ATTCTT-TTAAAAACTATTAGGCCAGAAAA
1 ACATAGGAATATATAGAGAAAATC--TTTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAA
*
447676 GCTCAAATTAAAATGGAAGCATCCTCATGTAA-TGTAGATTCAAGTTTGTTCAAATCATGGTCCC
64 GCTCAAATTAAAATGGAAGCATCCTCA-GGAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCC
*
447740 CGGGGGTAGGTTGGGGCCACAATTGGGGGATCAAGTTTT
128 CGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTT
* * *
447779 ACATAGGAATATATAGATAAAAATCTTTAAAAATTTTCTTCTCAAAAACTATTTGGCCAGAAAAA
1 ACATAGGAATATATAGA-GAAAATCTTTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAG
* ** * *
447844 CTCAACTTTGAGTGGAGGCATCCTCAGGAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCG
65 CTCAAATTAAAATGGAAGCATCCTCAGGAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCG
*
447909 GGGGTAGGGTGGGGCCACAATTGGGGAATCAAGTTTT
130 GGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTT
447946 ACATAGGAATATATAGAGAAAATCTTTAAAAATATAGAGAAATCTTTAAAAATTTTCTTCTCAAA
1 ACATAGGAATATATAGAGAAAATC--T-----T-TA-A-AAA----T------TTTCTTCTCAAA
*
448011 AACTATTAAGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGGAAGTGTAGATTCAAGTTT
46 AACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGGAAGTGTAGATTCAAGTTT
448076 GTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTT
111 GTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTT
** *
448132 ACATAGGAATATATAGAGAAAATCTTTAAAAAAAATTCTT-TTAAAAACTATTAGGCCAGAAAAG
1 ACATAGGAATATATAGAGAAAATCTTT-AAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAG
* * *
448196 CTAAAATTAAAATGGAAGCATCCTCAGGAAGTGTTGATTCAAATTTGTTCAAATCATGGTCCCCG
65 CTCAAATTAAAATGGAAGCATCCTCAGGAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCG
*
448261 GGGGTAGGGTGGGGCCTCAATTGGGGGATCAAGTTTT
130 GGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTT
* *
448298 ACATAGAAATATATAGAGAAAATCTTTAAAAAATTTTCTTCTCAAAAACTATTAGGCCAGGAAAG
1 ACATAGGAATATATAGAGAAAATCTTT-AAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAG
* ** * * * * * *
448363 CTCAACTTTGAGTGGAGGCATCATCACGTAA-TGTAGATTCAAGTTTTTTCAAATCAAGGTCCCC
65 CTCAAATTAAAATGGAAGCATCCTCA-GGAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCC
*
448427 GGGGTTAGGGTGGGGCCACAATTGGGGGATCAAGTTTT
129 GGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTT
* * *
448465 ACATAGGAATATACAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTTGGCCAGAAAAGC
1 ACATAGGAATATATAGAGAAAATCTTTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAGC
** * * *
448530 TCAAATTTGAGTGGAAGCATCCTCATGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGG
66 TCAAATTAAAATGGAAGCATCCTCAGGAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGG
448595 GGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTT
131 GGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTT
* * * * *
448631 ACATAGGAATATATAGGGAACATCTTTAAAAATCTTCTTCTCAAAAACTGTTTGGCCAGAAAAGC
1 ACATAGGAATATATAGAGAAAATCTTTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAGC
*
448696 TCAAATTAAAATGGAAGCATCCTCAGGAAGTGTAG-----A-----TTCAAATCATGGTCCCCAG
66 TCAAATTAAAATGGAAGCATCCTCAGGAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGG
448751 GGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTT
131 GGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTT
*
448787 ACATAGGAATATATAGAGAAAATCTTTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAAC
1 ACATAGGAATATATAGAGAAAATCTTTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAGC
* *
448852 TCAAATTAAAATGGAAGCATCCTCAGGAAGTGTTGATTCAAGTTTGTTTAAATCATGGTTCCCC-
66 TCAAATTAAAATGGAAGCATCCTCAGGAAGTGTAGATTCAAGTTTGTTCAAATCATGG-TCCCCG
448916 GGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTT
130 GGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTT
448953 ACA
1 ACA
448956 ATCCTTAAAA
Statistics
Matches: 1056, Mismatches: 82, Indels: 78
0.87 0.07 0.06
Matches are distributed among these distances:
156 147 0.14
161 2 0.00
165 9 0.01
166 455 0.43
167 275 0.26
168 4 0.00
173 1 0.00
174 2 0.00
175 1 0.00
176 3 0.00
177 3 0.00
178 2 0.00
179 2 0.00
180 1 0.00
184 1 0.00
186 148 0.14
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (166 bp):
ACATAGGAATATATAGAGAAAATCTTTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAGC
TCAAATTAAAATGGAAGCATCCTCAGGAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGG
GGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTT
Found at i:447990 original size:20 final size:21
Alignment explanation
Indices: 447956--447998 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
447946 ACATAGGAAT
447956 ATATAGAGAAAATCTTTAAAA
1 ATATAGAGAAAATCTTTAAAA
447977 ATATAGAG-AAATCTTTAAAA
1 ATATAGAGAAAATCTTTAAAA
447997 AT
1 AT
447999 TTTCTTCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (21 bp):
ATATAGAGAAAATCTTTAAAA
Found at i:448599 original size:333 final size:333
Alignment explanation
Indices: 447613--448955 Score: 1892
Period size: 333 Copynumber: 4.0 Consensus size: 333
447603 GGCAGTAGTN
*
447613 ACATAGGAATATATAGAGAAAATCTTTTTAAAAAA--TTCTT-TTAAAAACTATTAGGCCAGAAA
1 ACATAGGAATATATAGAGAAAATC-TTTTAAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAA
*
447675 AGCTCAAATTAAAATGGAAGCATCCTCATGTAATGTAGATTCAAGTTTGTTCAAATCATGGTCCC
65 AGCTCAAATTAAAATGGAAGCATCCTCA-GGAATGTAGATTCAAGTTTGTTCAAATCATGGTCCC
* *
447740 CGGGGGTAGGTTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGATAAAAATCT
129 CGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGA-GAAAATCT
* * ** * *
447805 TTAAAAATTTTCTTCTCAAAAACTATTTGGCCAGAAAAACTCAACTTTGAGTGGAGGCATCCTCA
193 TTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAACTCAAATTAAAATGGAAGCATCCTCA
447870 GGAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGG
258 GGAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGG
*
447935 AATCAAGTTTT
323 GATCAAGTTTT
447946 ACATAGGAATATATAGAGAAAATCTTTAAAAATATAGAGAAATCTTTAAAAATTTTCTTCTCAAA
1 ACATAGGAATATATAGAGAAAATC-TT-----T-T------A-----AAAAATTTTCTTCTCAAA
*
448011 AACTATTAAGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGGAAGTGTAGATTCAAGTTT
48 AACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGGAA-TGTAGATTCAAGTTT
448076 GTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAA
112 GTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAA
** * * *
448141 TATATAGAGAAAATCTTTAAAAAAAATTCTT-TTAAAAACTATTAGGCCAGAAAAGCTAAAATTA
177 TATATAGAGAAAATCTTT-AAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAACTCAAATTA
* *
448205 AAATGGAAGCATCCTCAGGAAGTGTTGATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTAGGG
241 AAATGGAAGCATCCTCAGGAAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGG
*
448270 TGGGGCCTCAATTGGGGGATCAAGTTTT
306 TGGGGCCACAATTGGGGGATCAAGTTTT
* *
448298 ACATAGAAATATATAGAGAAAATC-TTTAAAAAATTTTCTTCTCAAAAACTATTAGGCCAGGAAA
1 ACATAGGAATATATAGAGAAAATCTTTTAAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAA
* ** * * * * * *
448362 GCTCAACTTTGAGTGGAGGCATCATCACGTAATGTAGATTCAAGTTTTTTCAAATCAAGGTCCCC
66 GCTCAAATTAAAATGGAAGCATCCTCA-GGAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCC
* *
448427 GGGGTTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATACAGAGAAAATCTTT
130 GGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * * ** * *
448492 AAAAATCTTCTTCTCAAAAACTATTTGGCCAGAAAAGCTCAAATTTGAGTGGAAGCATCCTCATG
195 AAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAACTCAAATTAAAATGGAAGCATCCTCAGG
*
448557 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGA
260 AAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGA
448622 TCAAGTTTT
325 TCAAGTTTT
* * * * *
448631 ACATAGGAATATATAGGGAACATC-TTT-AAAAATCTTCTTCTCAAAAACTGTTTGGCCAGAAAA
1 ACATAGGAATATATAGAGAAAATCTTTTAAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAA
* *
448694 GCTCAAATTAAAATGGAAGCATCCTCAGGAA-GT-G--T--AG---ATTCAAATCATGGTCCCCA
66 GCTCAAATTAAAATGGAAGCATCCTCAGGAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCCG
448750 GGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTA
131 GGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTA
448815 AAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAACTCAAATTAAAATGGAAGCATCCTCAGGA
196 AAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAACTCAAATTAAAATGGAAGCATCCTCAGGA
* *
448880 AGTGTTGATTCAAGTTTGTTTAAATCATGGTTCCCC-GGGGTAGGGTGGGGCCACAATTGGGGGA
261 AGTGTAGATTCAAGTTTGTTCAAATCATGG-TCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGA
448944 TCAAGTTTT
325 TCAAGTTTT
448953 ACA
1 ACA
448956 ATCCTTAAAA
Statistics
Matches: 909, Mismatches: 76, Indels: 61
0.87 0.07 0.06
Matches are distributed among these distances:
322 204 0.22
323 5 0.01
325 2 0.00
327 1 0.00
329 1 0.00
330 2 0.00
331 3 0.00
332 63 0.07
333 315 0.35
334 3 0.00
338 2 0.00
339 1 0.00
344 1 0.00
345 2 0.00
350 6 0.01
352 153 0.17
353 145 0.16
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (333 bp):
ACATAGGAATATATAGAGAAAATCTTTTAAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAA
GCTCAAATTAAAATGGAAGCATCCTCAGGAATGTAGATTCAAGTTTGTTCAAATCATGGTCCCCG
GGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTA
AAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAACTCAAATTAAAATGGAAGCATCCTCAGGA
AGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGAT
CAAGTTTT
Found at i:448789 original size:156 final size:155
Alignment explanation
Indices: 448576--448955 Score: 580
Period size: 156 Copynumber: 2.4 Consensus size: 155
448566 TTCAAGTTTG
448576 TTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAAT
1 TTCAAATCATGGTCCCC-GGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAAT
* * * * *
448641 ATATAGGGAACATCTTTAAAAATCTTCTTCTCAAAAACTGTTTGGCCAGAAAAGCTCAAATTAAA
65 ATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAACTCAAATTAAA
448706 ATGGAAGCATCCTCAGGAAGTGTAGA
130 ATGGAAGCATCCTCAGGAAGTGTAGA
448732 TTCAAATCATGGTCCCCAGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAAT
1 TTCAAATCATGGTCCCC-GGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAAT
*
448797 ATATAGAGAAAATCTTTAAAAATTTTCTTCTCAAAAACTATTAGGCCAGAAAAACTCAAATTAAA
65 ATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAACTCAAATTAAA
*
448862 ATGGAAGCATCCTCAGGAAGTGTTGA
130 ATGGAAGCATCCTCAGGAAGTGTAGA
448888 TTCAAGTTTGTTTAAATCATGGTTCCCCGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTT
1 TTC----------AAATCATGG-TCCCCGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTT
448953 ACA
55 ACA
448956 ATCCTTAAAA
Statistics
Matches: 205, Mismatches: 8, Indels: 12
0.91 0.04 0.05
Matches are distributed among these distances:
156 151 0.74
166 49 0.24
167 5 0.02
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (155 bp):
TTCAAATCATGGTCCCCGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATA
TATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAACTCAAATTAAAA
TGGAAGCATCCTCAGGAAGTGTAGA
Found at i:460599 original size:20 final size:21
Alignment explanation
Indices: 460558--460606 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
460548 CCCGGGATTT
*
460558 ACCGAAATACCCGGTGAAAAC
1 ACCGAAATACCCGGTCAAAAC
*
460579 ACCGAAATACCC-TTCAAAAC
1 ACCGAAATACCCGGTCAAAAC
*
460599 ACCAAAAT
1 ACCGAAAT
460607 GCCCATTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.47, C:0.31, G:0.10, T:0.12
Consensus pattern (21 bp):
ACCGAAATACCCGGTCAAAAC
Found at i:463923 original size:31 final size:31
Alignment explanation
Indices: 463888--463951 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
463878 ACTTTCGAAT
*
463888 AAAAGATTAAAATCCTAAATAGTATATAAAG
1 AAAAGATTAAAATCCTAAATAGAATATAAAG
463919 AAAAGATTAAAATCCTAAATAGAATATAAAG
1 AAAAGATTAAAATCCTAAATAGAATATAAAG
463950 AA
1 AA
463952 CAAATGATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.61, C:0.06, G:0.09, T:0.23
Consensus pattern (31 bp):
AAAAGATTAAAATCCTAAATAGAATATAAAG
Found at i:466403 original size:101 final size:102
Alignment explanation
Indices: 466266--466464 Score: 330
Period size: 101 Copynumber: 2.0 Consensus size: 102
466256 TTATTGCTTT
466266 ATGACCAAAAACCTCAATGCATAAGACTATCTATTTACATGCACAAAAAACATTATTATGACTGA
1 ATGACCAAAAACCTCAATGCATAAGACTATCTATTTACATGCACAAAAAACATTATTATGACTGA
466331 AAA-TTTGAACCAGTTAGGA-ATTCATCAATCGGTAA
66 AAATTTTGAACCAGTTAGGATATTCATCAATCGGTAA
* *
466366 ATGACCAAAAAACCTCAATGCATACGACTGTCTATTTACATGCACAAAAAACATTATTATGACTG
1 ATGACC-AAAAACCTCAATGCATAAGACTATCTATTTACATGCACAAAAAACATTATTATGACTG
* *
466431 AAAATTTTGAATCAGTTTGGATTATTCATCAATC
65 AAAATTTTGAACCAGTTAGGA-TATTCATCAATC
466465 AGTAGATTTA
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
100 6 0.07
101 60 0.66
102 14 0.15
104 11 0.12
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (102 bp):
ATGACCAAAAACCTCAATGCATAAGACTATCTATTTACATGCACAAAAAACATTATTATGACTGA
AAATTTTGAACCAGTTAGGATATTCATCAATCGGTAA
Found at i:468695 original size:2 final size:2
Alignment explanation
Indices: 468690--468748 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
468680 ACACACATAC
468690 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
468732 AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A
468749 NNNNNNNNNN
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:474361 original size:143 final size:143
Alignment explanation
Indices: 474129--474456 Score: 394
Period size: 143 Copynumber: 2.3 Consensus size: 143
474119 GTGAATAGTG
** * *
474129 TTCACCGATTAAGCATATGTTGGT-CCTCGAAGCCTTCCAATGTGCTTGCACATTCGGAAGGCCT
1 TTCACCGATTAAGCATACCTTGGTCCCT-GAAGCCTTCCGATGAGCTTGCACATTCGGAAGGCCT
* * * * * *
474193 CGGAAACTTGGGAAGATAAGTGATCTATCCCAGTGAGCAGTGTTCACCGATT-GGTTTGTCTGTT
65 AGGAAACTTAGGAAGACAAGGGATCTAGCCCAGTGAGCAGTGTTCACCGATTAGG-TTGTCT-CT
* *
474257 A-CTTAGTGAGAAGTA
128 AGCCTAGAGAGAAGTA
*
474272 TTCACCGATTAAGCTTACCTTGGTCCCTGAAGCCTTCCGATGAGCTTGCACATTCGGAAGGCCTT
1 TTCACCGATTAAGCATACCTTGGTCCCTGAAGCCTTCCGATGAGCTTGCACATTCGGAAGGCC-T
* * * *
474337 AGG-AACTTAGGTAGACAAGGGATCTAGGCCAGTGAGTAGTGTTCACCGGTTAGGTTGTCTCTAG
65 AGGAAACTTAGGAAGACAAGGGATCTAGCCCAGTGAGCAGTGTTCACCGATTAGGTTGTCTCTAG
*
474401 CCTAGAGAGAAGTG
130 CCTAGAGAGAAGTA
* * * *
474415 TTCACCGATCAAGCCTACCCTGGTCCCCGAAGCCTTCCGATG
1 TTCACCGATTAAGCATACCTTGGTCCCTGAAGCCTTCCGATG
474457 TTTTTATGCA
Statistics
Matches: 159, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
142 2 0.01
143 149 0.94
144 8 0.05
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.27
Consensus pattern (143 bp):
TTCACCGATTAAGCATACCTTGGTCCCTGAAGCCTTCCGATGAGCTTGCACATTCGGAAGGCCTA
GGAAACTTAGGAAGACAAGGGATCTAGCCCAGTGAGCAGTGTTCACCGATTAGGTTGTCTCTAGC
CTAGAGAGAAGTA
Found at i:480830 original size:16 final size:15
Alignment explanation
Indices: 480809--480841 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
480799 TGACATAACC
480809 AAAAAATAAAATATAA
1 AAAAAATAAAATA-AA
480825 AAAAAATAAAATAAA
1 AAAAAATAAAATAAA
480840 AA
1 AA
480842 GTATTGAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAAATAAAATAAA
Found at i:488023 original size:2 final size:2
Alignment explanation
Indices: 487985--488015 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
487975 GAAGATAAAC
487985 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
488016 TGGAGAGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:492838 original size:4 final size:4
Alignment explanation
Indices: 492818--492861 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
492808 CTTTCCTCTG
* * * *
492818 CGTC CGTC AGTC TGTC CGTC CGTC TGTC CGTC TGTC CGTC CGTC
1 CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC
492862 TGTTTGTCCC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.02, C:0.41, G:0.25, T:0.32
Consensus pattern (4 bp):
CGTC
Found at i:492870 original size:12 final size:12
Alignment explanation
Indices: 492819--492870 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
492809 TTTCCTCTGC
*
492819 GTCCGTCAGTCT
1 GTCCGTCTGTCT
*
492831 GTCCGTCCGTCT
1 GTCCGTCTGTCT
*
492843 GTCCGTCTGTCC
1 GTCCGTCTGTCT
*
492855 GTCCGTCTGTTT
1 GTCCGTCTGTCT
492867 GTCC
1 GTCC
492871 CACTTCAGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.02, C:0.37, G:0.25, T:0.37
Consensus pattern (12 bp):
GTCCGTCTGTCT
Found at i:498252 original size:2 final size:2
Alignment explanation
Indices: 498245--498319 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
498235 TAATTTTGGC
498245 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
498287 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
498320 TGTAAAAAGA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:498816 original size:2 final size:2
Alignment explanation
Indices: 498809--498871 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
498799 CAGTCAGTCC
498809 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
498851 CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT C
498872 GTACGATGTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:501839 original size:3 final size:3
Alignment explanation
Indices: 501831--501877 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
501821 TTTGTCGTTT
501831 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
501878 TACGGAAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:503097 original size:2 final size:2
Alignment explanation
Indices: 503090--503130 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
503080 GTAGTAATAT
503090 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
503131 TTATGTTCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:505453 original size:21 final size:21
Alignment explanation
Indices: 505446--505546 Score: 114
Period size: 21 Copynumber: 4.9 Consensus size: 21
505436 AATTATGTTA
*
505446 ACTTGTCAAATCTTTATGTCG
1 ACTTGTCAAATCATTATGTCG
*
505467 ACTTGTCAAATCTTTATGTCG
1 ACTTGTCAAATCATTATGTCG
* **
505488 ACTTGTCAAATAATTATGTTA
1 ACTTGTCAAATCATTATGTCG
* * *
505509 AATTGTCAGATCTTTATGTCG
1 ACTTGTCAAATCATTATGTCG
*
505530 ACTTGTCAGAT-ATTATG
1 ACTTGTCAAATCATTATG
505547 ATGACAGGAA
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
20 5 0.07
21 63 0.93
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (21 bp):
ACTTGTCAAATCATTATGTCG
Found at i:505492 original size:42 final size:42
Alignment explanation
Indices: 505446--505546 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
505436 AATTATGTTA
** * *
505446 ACTTGTCAAATCTTTATGTCGACTTGTCAAATCTTTATGTCG
1 ACTTGTCAAATAATTATGTCAAATTGTCAAATCTTTATGTCG
* *
505488 ACTTGTCAAATAATTATGTTAAATTGTCAGATCTTTATGTCG
1 ACTTGTCAAATAATTATGTCAAATTGTCAAATCTTTATGTCG
*
505530 ACTTGTCAGAT-ATTATG
1 ACTTGTCAAATAATTATG
505547 ATGACAGGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
41 6 0.12
42 46 0.88
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (42 bp):
ACTTGTCAAATAATTATGTCAAATTGTCAAATCTTTATGTCG
Found at i:505651 original size:21 final size:21
Alignment explanation
Indices: 505625--505718 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
505615 ATGGTTATTT
* *
505625 TCTGACAAGTAAACATAAAGA
1 TCTGACAAGTTAACATAAATA
*
505646 TCTGACAAGTTGACATAAATA
1 TCTGACAAGTTAACATAAATA
**
505667 TCTGACAAGTCGACAT-AATCA
1 TCTGACAAGTTAACATAAAT-A
* * *
505688 TCTGACAACTTAACAGAATTA
1 TCTGACAAGTTAACATAAATA
505709 TCTGACAAGT
1 TCTGACAAGT
505719 GGTGGCAGAT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
20 3 0.05
21 56 0.92
22 2 0.03
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.26
Consensus pattern (21 bp):
TCTGACAAGTTAACATAAATA
Found at i:505684 original size:42 final size:42
Alignment explanation
Indices: 505625--505718 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
505615 ATGGTTATTT
* * * *
505625 TCTGACAAGTAAACATAAAGATCTGACAAGTTGACATAAATA
1 TCTGACAAGTAAACATAAACATCTGACAACTTAACAGAAATA
** * *
505667 TCTGACAAGTCGACATAATCATCTGACAACTTAACAGAATTA
1 TCTGACAAGTAAACATAAACATCTGACAACTTAACAGAAATA
505709 TCTGACAAGT
1 TCTGACAAGT
505719 GGTGGCAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.26
Consensus pattern (42 bp):
TCTGACAAGTAAACATAAACATCTGACAACTTAACAGAAATA
Found at i:505923 original size:16 final size:16
Alignment explanation
Indices: 505875--505923 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
505865 GACTTAATCG
505875 TTAATAACTCTCATTA
1 TTAATAACTCTCATTA
* *
505891 TTAATGAC-C-C--GA
1 TTAATAACTCTCATTA
505903 TTAATAACTCTCATTA
1 TTAATAACTCTCATTA
505919 TTAAT
1 TTAAT
505924 GACCTTAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
12 8 0.32
13 1 0.04
14 2 0.08
15 1 0.04
16 13 0.52
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.41
Consensus pattern (16 bp):
TTAATAACTCTCATTA
Found at i:505954 original size:2 final size:2
Alignment explanation
Indices: 505947--506042 Score: 176
Period size: 2 Copynumber: 48.5 Consensus size: 2
505937 TCATGTACAC
505947 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
505989 CT CT CT CT C- CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
506030 CT CT CT CT CT CT C
1 CT CT CT CT CT CT C
506043 ATGGGGATGC
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
1 1 0.01
2 91 0.99
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:509609 original size:16 final size:16
Alignment explanation
Indices: 509584--509623 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
509574 ATAAGGTTTA
*
509584 GTCGCAAAAATTAGTC
1 GTCGCGAAAATTAGTC
509600 GTCGCGAAAATTAGTC
1 GTCGCGAAAATTAGTC
509616 GTCGCGAA
1 GTCGCGAA
509624 CCCGGTAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.23
Consensus pattern (16 bp):
GTCGCGAAAATTAGTC
Done.