Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 88 of 141
Found at i:28607919 original size:23 final size:23
Alignment explanation
Indices: 28607887--28607948 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
28607877 TACTCATGTA
*
28607887 TTTTTACTTTTCATTTATTTTAT
1 TTTTTTCTTTTCATTTATTTTAT
* *
28607910 TTTTTTCTTTTC-TTCTCTTTTCT
1 TTTTTTCTTTTCATT-TATTTTAT
28607933 TTCTTTT-TTTTCATTT
1 TT-TTTTCTTTTCATTT
28607949 TGAATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 2 0.06
23 25 0.76
24 6 0.18
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTTCTTTTCATTTATTTTAT
Found at i:28610570 original size:13 final size:13
Alignment explanation
Indices: 28610552--28610578 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28610542 AAAACAATGG
28610552 AAAAAATAGAGAA
1 AAAAAATAGAGAA
28610565 AAAAAATAGAGAA
1 AAAAAATAGAGAA
28610578 A
1 A
28610579 TGAGAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (13 bp):
AAAAAATAGAGAA
Found at i:28613686 original size:14 final size:14
Alignment explanation
Indices: 28613667--28613698 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
28613657 TCAAGCAAAG
28613667 TAGTGTATTTTCCA
1 TAGTGTATTTTCCA
28613681 TAGTGTATTTTCCA
1 TAGTGTATTTTCCA
28613695 TAGT
1 TAGT
28613699 TTTTGGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (14 bp):
TAGTGTATTTTCCA
Found at i:28614940 original size:20 final size:20
Alignment explanation
Indices: 28614900--28614939 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
28614890 TTCTTTAAAA
28614900 TAAAAATGAATGTCAAATTT
1 TAAAAATGAATGTCAAATTT
28614920 TAAAAAT-ATATGTC-AATTT
1 TAAAAATGA-ATGTCAAATTT
28614939 T
1 T
28614940 TGGGGGGGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (20 bp):
TAAAAATGAATGTCAAATTT
Found at i:28617562 original size:21 final size:22
Alignment explanation
Indices: 28617523--28617580 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
28617513 CTCAAAAGTA
* * * *
28617523 AATAATTTTAATATCTAGATAT
1 AATATTTTTTATATCTAGAAAG
*
28617545 TATATTTTTTATAT-TAGAAAG
1 AATATTTTTTATATCTAGAAAG
28617566 AATATTGTTTTATAT
1 AATATT-TTTTATAT
28617581 AATTATAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.52
Consensus pattern (22 bp):
AATATTTTTTATATCTAGAAAG
Found at i:28621231 original size:1 final size:1
Alignment explanation
Indices: 28621225--28621253 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
28621215 TACAAATTAC
28621225 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28621254 TGGGTCGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28622890 original size:15 final size:17
Alignment explanation
Indices: 28622867--28622909 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
28622857 TAACCATAAT
28622867 TAATATATTAAT-AAATA
1 TAAT-TATTAATAAAATA
28622884 -AATTATTAAATAAAATA
1 TAATTATT-AATAAAATA
28622901 TAATTATTA
1 TAATTATTA
28622910 TAATTGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.17
16 6 0.26
17 6 0.26
18 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATTATTAATAAAATA
Found at i:28627443 original size:16 final size:15
Alignment explanation
Indices: 28627418--28627447 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28627408 TCGTACTTTC
28627418 ATAGATATTAATTAT
1 ATAGATATTAATTAT
28627433 ATAGCATATTAATTA
1 ATAG-ATATTAATTA
28627448 GTTAGAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (15 bp):
ATAGATATTAATTAT
Found at i:28627457 original size:16 final size:16
Alignment explanation
Indices: 28627418--28627458 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
28627408 TCGTACTTTC
28627418 ATAG-ATATTAATTAT
1 ATAGAATATTAATTAT
*
28627433 ATAGCATATTAATTAGT
1 ATAGAATATTAATTA-T
28627450 -TAGAATATT
1 ATAGAATATT
28627459 TATAGATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 18 0.78
17 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (16 bp):
ATAGAATATTAATTAT
Found at i:28627811 original size:22 final size:22
Alignment explanation
Indices: 28627786--28627830 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
28627776 CTCTAATTTA
*
28627786 TTAGCACATCGGTGCTCTCTGT
1 TTAGCACATCGGAGCTCTCTGT
*
28627808 TTAGCACATTGGAGCTCTCTGT
1 TTAGCACATCGGAGCTCTCTGT
28627830 T
1 T
28627831 CTATTAGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (22 bp):
TTAGCACATCGGAGCTCTCTGT
Found at i:28628431 original size:18 final size:18
Alignment explanation
Indices: 28628358--28628525 Score: 134
Period size: 17 Copynumber: 9.5 Consensus size: 18
28628348 TTAATGATGT
* * *
28628358 AAACACGAGATTTTTTTA
1 AAACACGAAAATTTTTGA
*
28628376 AAACACGAGAA-TTTTGA
1 AAACACGAAAATTTTTGA
*
28628393 AATACGA-TAATAATTTTTGA
1 AA-AC-ACGAA-AATTTTTGA
*
28628413 AAACACGAAAATTTGTG-
1 AAACACGAAAATTTTTGA
** *
28628430 AAACACGGGAATTGTTGA
1 AAACACGAAAATTTTTGA
*
28628448 AAACACGAAAATTTTAG-
1 AAACACGAAAATTTTTGA
28628465 AAACAACG-AAATTTTTGA
1 AAAC-ACGAAAATTTTTGA
* *
28628483 AAACACTAAGATTTTTG-
1 AAACACGAAAATTTTTGA
*
28628500 AAACACGAAGATTTTTG-
1 AAACACGAAAATTTTTGA
28628517 AAACACGAA
1 AAACACGAA
28628526 TTTTATTTTT
Statistics
Matches: 123, Mismatches: 18, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
17 59 0.48
18 49 0.40
19 7 0.06
20 8 0.07
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (18 bp):
AAACACGAAAATTTTTGA
Found at i:28628455 original size:35 final size:34
Alignment explanation
Indices: 28628369--28628525 Score: 149
Period size: 35 Copynumber: 4.5 Consensus size: 34
28628359 AACACGAGAT
* * * *
28628369 TTTTTTAAAACACGAGAATTTTGAAATACGATAATAA
1 TTTTTGAAAACACGAAAATTTTGAAACACG--GA-AA
*
28628406 TTTTTGAAAACACGAAAATTTGTGAAACACGGGAA
1 TTTTTGAAAACACGAAAATTT-TGAAACACGGAAA
*
28628441 TTGTTGAAAACACGAAAATTTTAGAAACAAC-GAAA
1 TTTTTGAAAACACGAAAATTTT-GAAAC-ACGGAAA
* *
28628476 TTTTTGAAAACACTAAGATTTTTGAAACAC-GAAGA
1 TTTTTGAAAACACGAA-AATTTTGAAACACGGAA-A
28628511 TTTTTG-AAACACGAA
1 TTTTTGAAAACACGAA
28628526 TTTTATTTTT
Statistics
Matches: 104, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
34 14 0.13
35 56 0.54
36 7 0.07
37 19 0.18
38 8 0.08
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (34 bp):
TTTTTGAAAACACGAAAATTTTGAAACACGGAAA
Found at i:28628572 original size:29 final size:29
Alignment explanation
Indices: 28628539--28628594 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
28628529 TATTTTTTTT
28628539 AAGAAACACAAAAATTTGTGAAAACACGG
1 AAGAAACACAAAAATTTGTGAAAACACGG
* *
28628568 AAGAAACACGAAGATTTGTGAAAACAC
1 AAGAAACACAAAAATTTGTGAAAACAC
28628595 AATTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.54, C:0.14, G:0.18, T:0.14
Consensus pattern (29 bp):
AAGAAACACAAAAATTTGTGAAAACACGG
Found at i:28628794 original size:28 final size:28
Alignment explanation
Indices: 28628741--28628794 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
28628731 TGATTCTATT
* *
28628741 AAAACACGAGAAATTTTTATTTTTTTTA
1 AAAACACGAGAAATTTTTAATATTTTTA
*
28628769 AAAACACGAGAATTTTTTAATATTTT
1 AAAACACGAGAAATTTTTAATATTTT
28628795 CGATTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (28 bp):
AAAACACGAGAAATTTTTAATATTTTTA
Found at i:28629059 original size:8 final size:8
Alignment explanation
Indices: 28629048--28629109 Score: 56
Period size: 8 Copynumber: 8.0 Consensus size: 8
28629038 GCCCTTTTCC
28629048 CTTTTTTT
1 CTTTTTTT
28629056 CTTTTTTT
1 CTTTTTTT
* *
28629064 CTCTTCTT
1 CTTTTTTT
**
28629072 -TTTTCCT
1 CTTTTTTT
28629079 CTTTTTTT
1 CTTTTTTT
28629087 C-TTTTTT
1 CTTTTTTT
* *
28629094 CATTTTTC
1 CTTTTTTT
28629102 CTTTTTTT
1 CTTTTTTT
28629110 TCTGCTTGCT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
7 12 0.28
8 31 0.72
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (8 bp):
CTTTTTTT
Found at i:28629062 original size:10 final size:10
Alignment explanation
Indices: 28629049--28629093 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
28629039 CCCTTTTCCC
28629049 TTTTTTTCTT
1 TTTTTTTCTT
*
28629059 TTTTTCTCTT
1 TTTTTTTCTT
* *
28629069 CTTTTTTCCTC
1 -TTTTTTTCTT
28629080 TTTTTTTCTT
1 TTTTTTTCTT
28629090 TTTT
1 TTTT
28629094 CATTTTTCCT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
10 21 0.75
11 7 0.25
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:28629072 original size:13 final size:13
Alignment explanation
Indices: 28629054--28629086 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
28629044 TTCCCTTTTT
*
28629054 TTCTTTTTTTCTC
1 TTCTTTTTTCCTC
28629067 TTCTTTTTTCCTC
1 TTCTTTTTTCCTC
28629080 TT-TTTTT
1 TTCTTTTT
28629087 CTTTTTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTTTTTTCCTC
Found at i:28629099 original size:25 final size:24
Alignment explanation
Indices: 28629055--28629112 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 24
28629045 TCCCTTTTTT
*
28629055 TCTTTTTTTC-TCTTCTTTTTTCC
1 TCTTTTTTTCTTCTTCATTTTTCC
*
28629078 TCTTTTTTTCTTTTTTCATTTTTCC
1 TCTTTTTTTC-TTCTTCATTTTTCC
28629103 T-TTTTTTTCT
1 TCTTTTTTTCT
28629113 GCTTGCTGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 11 0.35
24 8 0.26
25 12 0.39
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.78
Consensus pattern (24 bp):
TCTTTTTTTCTTCTTCATTTTTCC
Found at i:28629403 original size:11 final size:11
Alignment explanation
Indices: 28629389--28629429 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 11
28629379 TTTTTTCATT
28629389 TTTTTCTTTCC
1 TTTTTCTTTCC
28629400 TTTTT-TTTCTC
1 TTTTTCTTTC-C
28629411 TTTTTTCTTT-C
1 -TTTTTCTTTCC
28629422 TTTTTCTT
1 TTTTTCTT
28629430 CTTCTTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 12 0.44
11 7 0.26
12 5 0.19
13 3 0.11
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTCTTTCC
Found at i:28629403 original size:13 final size:12
Alignment explanation
Indices: 28629378--28629432 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
28629368 CTGTTTTAGG
28629378 TTTT-TTTCATTT
1 TTTTCTTTC-TTT
*
28629390 TTTTCTTTC-CT
1 TTTTCTTTCTTT
28629401 TTTT-TTTCTCTT
1 TTTTCTTTCT-TT
28629413 TTTTCTTTCTTT
1 TTTTCTTTCTTT
28629425 TTCTTCTT
1 TT-TTCTT
28629433 CTTCTTCAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 4 0.11
11 5 0.14
12 13 0.36
13 14 0.39
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTCTTTCTTT
Found at i:28629407 original size:23 final size:22
Alignment explanation
Indices: 28629378--28629431 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
28629368 CTGTTTTAGG
28629378 TTTTTTTCAT-TTTTTTCTTTCCT
1 TTTTTTTC-TCTTTTTTCTTT-CT
28629401 TTTTTTTCTCTTTTTTCTTTCT
1 TTTTTTTCTCTTTTTTCTTTCT
*
28629423 TTTTCTTCT
1 TTTTTTTCT
28629432 TCTTCTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTTTCTCTTTTTTCTTTCT
Found at i:28629435 original size:23 final size:23
Alignment explanation
Indices: 28629388--28629431 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
28629378 TTTTTTTCAT
*
28629388 TTTTTTCTTTCCTTTTTTTTCTC
1 TTTTTTCTTTCCTTTTTCTTCTC
28629411 TTTTTTCTTT-CTTTTTCTTCT
1 TTTTTTCTTTCCTTTTTCTTCT
28629432 TCTTCTTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTCTTTCCTTTTTCTTCTC
Found at i:28629786 original size:12 final size:12
Alignment explanation
Indices: 28629758--28629787 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28629748 TTTGCTATTG
*
28629758 TTTTGTTTGGTT
1 TTTTTTTTGGTT
28629770 TTTTTTTTGGTT
1 TTTTTTTTGGTT
28629782 TTTTTT
1 TTTTTT
28629788 GATTGATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (12 bp):
TTTTTTTTGGTT
Found at i:28630289 original size:59 final size:57
Alignment explanation
Indices: 28630177--28630291 Score: 133
Period size: 59 Copynumber: 2.0 Consensus size: 57
28630167 TAATTTTAGA
* * **
28630177 AAAATATAGGGCCAAAATGTAATTTTTGGAAAGTTTAGGGGACCGAATATAATTTAC
1 AAAATATAGGGCCAAAATGTAAATTTTGAAAAGTTTAGGGGACAAAATATAATTTAC
* * *
28630234 AAAATATTAAGGGTCAAGATGTAAATTTTGAAAAGTTTAGGGG-CTAAAATGTAATTTA
1 AAAATA-T-AGGGCCAAAATGTAAATTTTGAAAAGTTTAGGGGAC-AAAATATAATTTA
28630292 TATTTTTTTG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
57 6 0.12
58 2 0.04
59 40 0.83
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (57 bp):
AAAATATAGGGCCAAAATGTAAATTTTGAAAAGTTTAGGGGACAAAATATAATTTAC
Found at i:28630314 original size:16 final size:17
Alignment explanation
Indices: 28630283--28630317 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
28630273 GGGGCTAAAA
28630283 TGTAATTTATATTTTTT
1 TGTAATTTATATTTTTT
*
28630300 TGTATTTTATATTTTTT
1 TGTAATTTATATTTTTT
28630317 T
1 T
28630318 TCAAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (17 bp):
TGTAATTTATATTTTTT
Found at i:28630835 original size:81 final size:78
Alignment explanation
Indices: 28630635--28631030 Score: 486
Period size: 81 Copynumber: 5.1 Consensus size: 78
28630625 TGGGTTGACC
* * * * * *
28630635 TTTGAAAAATAGAAATTGAAAAATACCTTGGCATGTAACCCGAGGCTCAACTTATCTCTCACAAT
1 TTTGAAAAATAGAAATTAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAAT
28630700 ATGAGTTGA--TT
66 ATGAGTTGATTTT
* * *
28630711 TTTGAAAAGTAGAAATTTAAAAAAAGTACCTCGGCATGTGACCCGAGGCTCAACTCACCTCCCGT
1 TTTGAAAAATAGAAA-TT-AAAAAA-TACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGC
*
28630776 AATATAAGTTGATTTT
63 AATATGAGTTGATTTT
*
28630792 TTTGAAAAATAGAAATTAAAAAGTAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTTGC
1 TTTGAAAAATAGAAATT-AAAA--AATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGC
28630857 AATATGAGTTGATTTT
63 AATATGAGTTGATTTT
* * * **
28630873 TTT-ATAAACAAAAATTAAAAAATACCTCGATATGTGACCCGAGGCTCAACTCACCTCTCGCAAT
1 TTTGAAAAATAGAAATTAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAAT
28630937 ATGAGTTGA--TT
66 ATGAGTTGATTTT
** * * *
28630948 TTTG-AAAA-A-AAA-TAAAAAATACCTCAACGTGCGAACCGAGGCTCAACTCACCTCTCGCAAT
1 TTTGAAAAATAGAAATTAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAAT
28631009 ATGAGTTGATTTT
66 ATGAGTTGATTTT
28631022 TTTGAAAAA
1 TTTGAAAAA
28631031 AATTGAAATT
Statistics
Matches: 282, Mismatches: 27, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
72 53 0.19
73 3 0.01
74 7 0.02
75 12 0.04
76 14 0.05
77 52 0.18
78 5 0.02
79 47 0.17
80 17 0.06
81 70 0.25
82 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (78 bp):
TTTGAAAAATAGAAATTAAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAAT
ATGAGTTGATTTT
Found at i:28641451 original size:11 final size:11
Alignment explanation
Indices: 28641401--28641453 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
28641391 ATAAAAGTTC
28641401 TAAAATA-AAT
1 TAAAATAGAAT
28641411 TAAATATATGAAT
1 TAAA-ATA-GAAT
*
28641424 TCAAAATAGACT
1 T-AAAATAGAAT
*
28641436 CAAAATAGAAT
1 TAAAATAGAAT
28641447 TAAAATA
1 TAAAATA
28641454 ACCATTGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 4 0.11
11 18 0.51
12 3 0.09
13 7 0.20
14 3 0.09
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (11 bp):
TAAAATAGAAT
Found at i:28643229 original size:30 final size:30
Alignment explanation
Indices: 28643195--28643260 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
28643185 TTTTGGGCTC
28643195 ATTGGGCTAAAGTTCGGGTTTAGGTATTGT
1 ATTGGGCTAAAGTTCGGGTTTAGGTATTGT
* *
28643225 ATTGGGCTAGAGTTTGGGTTTAGGTATTGT
1 ATTGGGCTAAAGTTCGGGTTTAGGTATTGT
28643255 ATTGGG
1 ATTGGG
28643261 TATTAGATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.18, C:0.05, G:0.36, T:0.41
Consensus pattern (30 bp):
ATTGGGCTAAAGTTCGGGTTTAGGTATTGT
Found at i:28643261 original size:18 final size:18
Alignment explanation
Indices: 28643210--28643266 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
28643200 GCTAAAGTTC
28643210 GGGTTTAGGTATTGTATT
1 GGGTTTAGGTATTGTATT
*
28643228 GGG-CTA-G-A--GT-TT
1 GGGTTTAGGTATTGTATT
28643240 GGGTTTAGGTATTGTATT
1 GGGTTTAGGTATTGTATT
28643258 GGGTATTAG
1 GGGT-TTAG
28643267 ATTAAAACGA
Statistics
Matches: 30, Mismatches: 2, Indels: 13
0.67 0.04 0.29
Matches are distributed among these distances:
12 5 0.17
13 4 0.13
14 1 0.03
15 2 0.07
16 1 0.03
17 4 0.13
18 9 0.30
19 4 0.13
ACGTcount: A:0.18, C:0.02, G:0.37, T:0.44
Consensus pattern (18 bp):
GGGTTTAGGTATTGTATT
Found at i:28644659 original size:19 final size:16
Alignment explanation
Indices: 28644623--28644749 Score: 101
Period size: 17 Copynumber: 7.2 Consensus size: 16
28644613 CACGAGATTT
* *
28644623 TTTTAAAACACGAGAA
1 TTTTGAAACACGAAAA
28644639 TTTTGAAACACGATAATAA
1 TTTTGAAACACG--AA-AA
28644658 TTTTTGAAAACACGAAAA
1 -TTTTG-AAACACGAAAA
**
28644676 TTTGTGAAACACGGGAA
1 TTT-TGAAACACGAAAA
28644693 TTGTTGAAAACACGAAAA
1 TT-TTG-AAACACGAAAA
*
28644711 TTTTAGAAACACCAAAA
1 TTTT-GAAACACGAAAA
*
28644728 TTTTTGAAAACACGAAGA
1 -TTTTG-AAACACGAAAA
28644746 TTTT
1 TTTT
28644750 TAAAACACAA
Statistics
Matches: 91, Mismatches: 9, Indels: 21
0.75 0.07 0.17
Matches are distributed among these distances:
16 11 0.12
17 33 0.36
18 31 0.34
19 4 0.04
20 5 0.05
21 7 0.08
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (16 bp):
TTTTGAAACACGAAAA
Found at i:28644683 original size:18 final size:18
Alignment explanation
Indices: 28644627--28644815 Score: 115
Period size: 18 Copynumber: 10.6 Consensus size: 18
28644617 AGATTTTTTT
*
28644627 AAAACACGAGAATTT-TG
1 AAAACACGAAAATTTGTG
*
28644644 -AAACACGATAATAATTTTTG
1 AAAACACG--AA-AATTTGTG
28644664 AAAACACGAAAATTTGTG
1 AAAACACGAAAATTTGTG
**
28644682 -AAACACGGGAA-TTGTTG
1 AAAACACGAAAATTTG-TG
28644699 AAAACACGAAAATTT-T-
1 AAAACACGAAAATTTGTG
* *
28644715 AGAAACACCAAAATTTTTG
1 A-AAACACGAAAATTTGTG
* *
28644734 AAAACACGAAGATTT-TT
1 AAAACACGAAAATTTGTG
** * *
28644751 AAAACAC-AATTTTTTTTA
1 AAAACACGAA-AATTTGTG
* *
28644769 AGAAACACAAAAATTTGTA
1 A-AAACACGAAAATTTGTG
*
28644788 AAAACACGAAGATTTGTG
1 AAAACACGAAAATTTGTG
*
28644806 AACACACGAA
1 AAAACACGAA
28644816 TTTTTCAATT
Statistics
Matches: 137, Mismatches: 20, Indels: 29
0.74 0.11 0.16
Matches are distributed among these distances:
16 13 0.09
17 36 0.26
18 55 0.40
19 22 0.16
20 4 0.03
21 7 0.05
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (18 bp):
AAAACACGAAAATTTGTG
Found at i:28644707 original size:35 final size:34
Alignment explanation
Indices: 28644607--28644749 Score: 142
Period size: 35 Copynumber: 4.1 Consensus size: 34
28644597 AGTGATCCGA
* * * * *
28644607 TTGAAACACGAGATTTTTTTAAAACACGAGAATT
1 TTGAAACACCAAAATTTTTGAAAACACGAAAATT
*
28644641 TTGAAACACGATAATAATTTTTGAAAACACGAAAATT
1 TTGAAACAC--CAA-AATTTTTGAAAACACGAAAATT
*** *
28644678 TGTGAAACACGGGAATTGTTGAAAACACGAAAATT
1 T-TGAAACACCAAAATTTTTGAAAACACGAAAATT
*
28644713 TTAGAAACACCAAAATTTTTGAAAACACGAAGATT
1 TT-GAAACACCAAAATTTTTGAAAACACGAAAATT
28644748 TT
1 TT
28644750 TAAAACACAA
Statistics
Matches: 90, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
34 10 0.11
35 51 0.57
36 1 0.01
37 20 0.22
38 8 0.09
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.29
Consensus pattern (34 bp):
TTGAAACACCAAAATTTTTGAAAACACGAAAATT
Found at i:28644792 original size:54 final size:55
Alignment explanation
Indices: 28644665--28644820 Score: 153
Period size: 54 Copynumber: 2.9 Consensus size: 55
28644655 TAATTTTTGA
* * * * **
28644665 AAACACGAAAATTTGT-GAAACACG-GGAATTGTTGAAAACACGAA--AATTTTAG
1 AAACACAAAAATTTGTAAAAACACGAAGATTTG-TGAAAACACGAATTTTTTTTAG
* * * *
28644717 AAACACCAAAATTTTTGAAAACACGAAGATTT-TTAAAACAC-AATTTTTTTTAAG
1 AAACACAAAAATTTGTAAAAACACGAAGATTTGTGAAAACACGAATTTTTTTT-AG
*
28644771 AAACACAAAAATTTGTAAAAACACGAAGATTTGTGAACACACGAATTTTT
1 AAACACAAAAATTTGTAAAAACACGAAGATTTGTGAAAACACGAATTTTT
28644821 CAATTTTTTT
Statistics
Matches: 84, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
51 2 0.02
52 22 0.26
53 11 0.13
54 35 0.42
55 7 0.08
56 7 0.08
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.28
Consensus pattern (55 bp):
AAACACAAAAATTTGTAAAAACACGAAGATTTGTGAAAACACGAATTTTTTTTAG
Found at i:28645850 original size:11 final size:11
Alignment explanation
Indices: 28645836--28645875 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
28645826 TTTTCTCTCA
28645836 TTTCCTTTCTT
1 TTTCCTTTCTT
28645847 TTTCCTTTCTT
1 TTTCCTTTCTT
*
28645858 TTTCTTTTCTT
1 TTTCCTTTCTT
28645869 TTTCCTT
1 TTTCCTT
28645876 CGAAAGCTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTCCTTTCTT
Found at i:28645864 original size:21 final size:21
Alignment explanation
Indices: 28645808--28645875 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
28645798 TTCTCTCCTC
* *
28645808 CCTTTCACTTTCTCTCTTTTT
1 CCTTTCATTTTCTTTCTTTTT
* * *
28645829 TCTCTCATTTCCTTTCTTTTT
1 CCTTTCATTTTCTTTCTTTTT
*
28645850 CCTTTCTTTTTCTTTTCTTTTT
1 CCTTTCATTTTC-TTTCTTTTT
28645872 CCTT
1 CCTT
28645876 CGAAAGCTCG
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (21 bp):
CCTTTCATTTTCTTTCTTTTT
Found at i:28646556 original size:16 final size:17
Alignment explanation
Indices: 28646525--28646559 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
28646515 AGGGCTAAAA
28646525 TGTAATTTATATTTTTT
1 TGTAATTTATATTTTTT
*
28646542 TGTATTTTATATTTTTT
1 TGTAATTTATATTTTTT
28646559 T
1 T
28646560 TCAAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (17 bp):
TGTAATTTATATTTTTT
Found at i:28647522 original size:194 final size:194
Alignment explanation
Indices: 28647193--28647585 Score: 610
Period size: 194 Copynumber: 2.0 Consensus size: 194
28647183 AAAATATGAG
28647193 AAAAACTAAAAACAGATGTCACATGGCTGTGTGGCCAGATCGTGTGACAGAGGTCAGCCCGTGTG
1 AAAAACTAAAAACAGATGTCACATGGCTGTGTGGCCAGATCGTGTGACAGAGGTCAGCCCGTGTG
*
28647258 GCCCCAAGCATGGTCGTGTGGCTACTTCACATGCCCGTGTGCTTAGACTGTGTACAAATCGAAAA
66 GCCCCAAGCATGGTCGTGTGACTACTTCACATGCCCGTGTGCTTAGACTGTGTACAAATCGAAAA
* * * * *
28647323 TAGGGTCACACGGTCGTGTCCTCAAGCCGTGTAACTAATTGTGC-CTGTGTGAAAAATCCTGCAC
131 TAGGGTCACACGGTCATGTCCCCAAGCCGTGTAACTAACTATGCTC-GTATGAAAAATCCTGCAC
* * * * * *
28647387 AAAAACTGAAAATAGATGTCTCATGGCTGTTTGGTCAG-GCTGTGTGACAGAGGTCAGCCCGTGT
1 AAAAACTAAAAACAGATGTCACATGGCTGTGTGGCCAGATC-GTGTGACAGAGGTCAGCCCGTGT
*
28647451 GGCCCCAAGCATGGTCGTGTGACTACTTCACATGCCTGTGTGCTTAGACTGTGTACAAATCGAAA
65 GGCCCCAAGCATGGTCGTGTGACTACTTCACATGCCCGTGTGCTTAGACTGTGTACAAATCGAAA
* **
28647516 ATAGGGTCACATGGTCATGTCCCCCGGCCGTGTAACTAACTATGCTCGTATGAAAAATCCTGCAC
130 ATAGGGTCACACGGTCATGTCCCCAAGCCGTGTAACTAACTATGCTCGTATGAAAAATCCTGCAC
28647581 AAAAA
1 AAAAA
28647586 ATCAAGCAAC
Statistics
Matches: 181, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
193 1 0.01
194 179 0.99
195 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.24
Consensus pattern (194 bp):
AAAAACTAAAAACAGATGTCACATGGCTGTGTGGCCAGATCGTGTGACAGAGGTCAGCCCGTGTG
GCCCCAAGCATGGTCGTGTGACTACTTCACATGCCCGTGTGCTTAGACTGTGTACAAATCGAAAA
TAGGGTCACACGGTCATGTCCCCAAGCCGTGTAACTAACTATGCTCGTATGAAAAATCCTGCAC
Found at i:28651679 original size:13 final size:13
Alignment explanation
Indices: 28651663--28651706 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
28651653 TTTGTATAAC
28651663 CATTTCATTTAAA
1 CATTTCATTTAAA
* *
28651676 CATTTCATTTTAC
1 CATTTCATTTAAA
* *
28651689 CACTTCATTTACA
1 CATTTCATTTAAA
28651702 CATTT
1 CATTT
28651707 AACACATTAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.48
Consensus pattern (13 bp):
CATTTCATTTAAA
Found at i:28651682 original size:39 final size:39
Alignment explanation
Indices: 28651598--28651683 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 39
28651588 TCATACATCT
*
28651598 ATTTCCATATAACCAATTTATATAACCATCTCATGTAATC
1 ATTT-CATATAACCAATTTATATAACCATCTCATGTAAAC
* * * * * *
28651638 GTTTCATATAACTATTTTGTATAACCATTTCATTTAAAC
1 ATTTCATATAACCAATTTATATAACCATCTCATGTAAAC
28651677 ATTTCAT
1 ATTTCAT
28651684 TTTACCACTT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
39 35 0.92
40 3 0.08
ACGTcount: A:0.35, C:0.19, G:0.03, T:0.43
Consensus pattern (39 bp):
ATTTCATATAACCAATTTATATAACCATCTCATGTAAAC
Found at i:28653390 original size:139 final size:139
Alignment explanation
Indices: 28653140--28653408 Score: 502
Period size: 139 Copynumber: 1.9 Consensus size: 139
28653130 GACGGCAGCA
*
28653140 GTAGTCTAACTTTGAAAAATCACCAAAAATTGTAAAGATCTAATTGGAGGATGAATAAAATATTA
1 GTAGTCTAACTTTGAAAAATCACCAAAAATTGTAAAGATCTAATTAGAGGATGAATAAAATATTA
*
28653205 AATTAAAGCTTATTGAGTCTAGTTTCTTATAAAAGAAACAGTGTAAGCAATGGAATTGTAAATCA
66 AATTAAAGCTTATTGAGTCTAGTTTCTTATAAAAGAAACAATGTAAGCAATGGAATTGTAAATCA
28653270 CCACAAATT
131 CCACAAATT
* *
28653279 GTAGTCTAATTTTGAAAAATCACCAAAAATTGTAGAGATCTAATTAGAGGATGAATAAAATATTA
1 GTAGTCTAACTTTGAAAAATCACCAAAAATTGTAAAGATCTAATTAGAGGATGAATAAAATATTA
28653344 AATTAAAGCTTATTGAGTCTAGTTTCTTATAAAAGAAACAATGTAAGCAATGGAATTGTAAATCA
66 AATTAAAGCTTATTGAGTCTAGTTTCTTATAAAAGAAACAATGTAAGCAATGGAATTGTAAATCA
28653409 TGAGATATAA
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 126 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (139 bp):
GTAGTCTAACTTTGAAAAATCACCAAAAATTGTAAAGATCTAATTAGAGGATGAATAAAATATTA
AATTAAAGCTTATTGAGTCTAGTTTCTTATAAAAGAAACAATGTAAGCAATGGAATTGTAAATCA
CCACAAATT
Found at i:28655976 original size:3 final size:3
Alignment explanation
Indices: 28655968--28656004 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
28655958 TTTAATTCAT
28655968 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
28656005 CATTAACCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:28656568 original size:25 final size:25
Alignment explanation
Indices: 28656534--28656581 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
28656524 CATCTCATAC
28656534 AGTGATACCTAACG-CTAAAAGTAAA
1 AGTGATACCTAACGTC-AAAAGTAAA
28656559 AGTGATACCTAACGTCAAAAGTA
1 AGTGATACCTAACGTCAAAAGTA
28656582 TAGCAATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.21
Consensus pattern (25 bp):
AGTGATACCTAACGTCAAAAGTAAA
Found at i:28657584 original size:60 final size:59
Alignment explanation
Indices: 28657462--28657577 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 59
28657452 TTAATATAAT
* * * * *
28657462 ATTTGGTACTTGAATTTAACTTTTTTCTAATTTGGTATCTAAACTTTATTTTGGGCAAA
1 ATTTGGTACATGAATTGAACTTTTTCCTAATTTGGCACCTAAACTTTATTTTGGGCAAA
28657521 ATTTGGTACATGAACTTGACACTTTTTCCTAATTTGGCACCTAAACTTT-TTTTGGGC
1 ATTTGGTACATGAA-TTGA-ACTTTTTCCTAATTTGGCACCTAAACTTTATTTTGGGC
28657578 CCAATTTACA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 13 0.26
60 11 0.22
61 26 0.52
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.46
Consensus pattern (59 bp):
ATTTGGTACATGAATTGAACTTTTTCCTAATTTGGCACCTAAACTTTATTTTGGGCAAA
Found at i:28657837 original size:4 final size:4
Alignment explanation
Indices: 28657828--28657853 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
28657818 CATTATTTTC
28657828 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
28657854 AACTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:28658312 original size:4 final size:4
Alignment explanation
Indices: 28658303--28658328 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
28658293 CATTATTTTC
28658303 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
28658329 AACTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:28658606 original size:31 final size:31
Alignment explanation
Indices: 28658571--28658629 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
28658561 ATCAACTTAC
* * *
28658571 GAAAAAGTATCAAGTTTAGGTACTAAATTAA
1 GAAAAAGTAACAAGTTCAAGTACTAAATTAA
28658602 GAAAAAGTAACAAGTTCAAGTACTAAAT
1 GAAAAAGTAACAAGTTCAAGTACTAAAT
28658630 GTTATATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.25
Consensus pattern (31 bp):
GAAAAAGTAACAAGTTCAAGTACTAAATTAA
Found at i:28673446 original size:20 final size:19
Alignment explanation
Indices: 28673401--28673438 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28673391 CATCCAAACA
28673401 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
28673420 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
28673439 TTCAGAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:28673467 original size:14 final size:14
Alignment explanation
Indices: 28673430--28673460 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28673420 CCAGAAAAGT
*
28673430 AAATCATTTTTCAG
1 AAATCATTTTCCAG
28673444 AAATCATTTTCCAG
1 AAATCATTTTCCAG
28673458 AAA
1 AAA
28673461 ATATTTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:28673665 original size:14 final size:14
Alignment explanation
Indices: 28673646--28673677 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
28673636 GAATCTTCTA
*
28673646 GTTCTTTAATGAAT
1 GTTCTTTAACGAAT
28673660 GTTCTTTAACGAAT
1 GTTCTTTAACGAAT
28673674 GTTC
1 GTTC
28673678 ATATAAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (14 bp):
GTTCTTTAACGAAT
Found at i:28680877 original size:25 final size:26
Alignment explanation
Indices: 28680849--28680899 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
28680839 AATGCCAATA
*
28680849 AATAATTTAAAAATTATA-AAAAATT
1 AATAATTTAAAAAGTATATAAAAATT
*
28680874 AATAATTTGAAAAGTATATAAAAATT
1 AATAATTTAAAAAGTATATAAAAATT
28680900 CAAAAACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (26 bp):
AATAATTTAAAAAGTATATAAAAATT
Found at i:28691295 original size:4 final size:4
Alignment explanation
Indices: 28691286--28691310 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
28691276 TCCACAATTC
28691286 TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
28691311 TCTCTCTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:28711317 original size:5 final size:5
Alignment explanation
Indices: 28711307--28711332 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28711297 TAAGCATTCG
28711307 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
28711333 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:28712013 original size:9 final size:9
Alignment explanation
Indices: 28711999--28712035 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28711989 TATAGTTTGA
28711999 TATTCGAAT
1 TATTCGAAT
28712008 TATTCGAAT
1 TATTCGAAT
*
28712017 TATTCGAGT
1 TATTCGAAT
28712026 TATTCGAAT
1 TATTCGAAT
28712035 T
1 T
28712036 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:28714454 original size:33 final size:33
Alignment explanation
Indices: 28714412--28714478 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
28714402 ACTATATGCT
28714412 TAAGTTTAGATAACAATAGCAATCATGGGCAAA
1 TAAGTTTAGATAACAATAGCAATCATGGGCAAA
28714445 TAAGTTTAGATAACAATAGCAATCATGGGCAAA
1 TAAGTTTAGATAACAATAGCAATCATGGGCAAA
28714478 T
1 T
28714479 TTACAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (33 bp):
TAAGTTTAGATAACAATAGCAATCATGGGCAAA
Found at i:28717151 original size:15 final size:15
Alignment explanation
Indices: 28717133--28717187 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
28717123 AACCCTAATC
*
28717133 CTATTAGACACATCA
1 CTATCAGACACATCA
* *
28717148 CTATCAAATACATCA
1 CTATCAGACACATCA
* *
28717163 CTAACATACACATCA
1 CTATCAGACACATCA
28717178 CTATCAGACA
1 CTATCAGACA
28717188 TTTCTTCTTC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.44, C:0.29, G:0.04, T:0.24
Consensus pattern (15 bp):
CTATCAGACACATCA
Found at i:28719278 original size:37 final size:38
Alignment explanation
Indices: 28719236--28719324 Score: 162
Period size: 37 Copynumber: 2.4 Consensus size: 38
28719226 TTTTGATTTT
28719236 TGCTGTTAATGGTGTTCTAATTTTGA-TTTGCTGTTAA
1 TGCTGTTAATGGTGTTCTAATTTTGATTTTGCTGTTAA
*
28719273 TGCTGTTAATGGTGTTCTGATTTTGATTTTGCTGTTAA
1 TGCTGTTAATGGTGTTCTAATTTTGATTTTGCTGTTAA
28719311 TGCTGTTAATGGTG
1 TGCTGTTAATGGTG
28719325 GTGTTTTTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 25 0.50
38 25 0.50
ACGTcount: A:0.17, C:0.08, G:0.25, T:0.51
Consensus pattern (38 bp):
TGCTGTTAATGGTGTTCTAATTTTGATTTTGCTGTTAA
Found at i:28719360 original size:42 final size:42
Alignment explanation
Indices: 28719313--28719405 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
28719303 GCTGTTAATG
*
28719313 CTGTTAATGGTGGTGTTTTTTATTTTTGTTGTTAATGGTGTT
1 CTGTTAATGGTGGTGTTTTTTATTTTTGCTGTTAATGGTGTT
*
28719355 CTGTTAATGGTTGTGTTTTTTATTTTTGCTGTTAATGGTGTT
1 CTGTTAATGGTGGTGTTTTTTATTTTTGCTGTTAATGGTGTT
28719397 CTGTTAATG
1 CTGTTAATG
28719406 TTGCCATATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.13, C:0.04, G:0.25, T:0.58
Consensus pattern (42 bp):
CTGTTAATGGTGGTGTTTTTTATTTTTGCTGTTAATGGTGTT
Found at i:28719371 original size:12 final size:14
Alignment explanation
Indices: 28719342--28719405 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
28719332 TTATTTTTGT
28719342 TGTTAATGGTGTTC
1 TGTTAATGGTGTTC
28719356 TGTTAATGGTTGTGT-
1 TGTTAATGG-TGT-TC
* * *
28719371 TTTTTAT--TTTTGC
1 TGTTAATGGTGTT-C
28719384 TGTTAATGGTGTTC
1 TGTTAATGGTGTTC
28719398 TGTTAATG
1 TGTTAATG
28719406 TTGCCATATT
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
11 1 0.03
12 2 0.05
13 5 0.13
14 18 0.47
15 11 0.29
16 1 0.03
ACGTcount: A:0.14, C:0.05, G:0.25, T:0.56
Consensus pattern (14 bp):
TGTTAATGGTGTTC
Found at i:28722924 original size:18 final size:18
Alignment explanation
Indices: 28722901--28722935 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28722891 TTGCAAAAAG
* *
28722901 GACGATGAGGACGATGAC
1 GACGATAAGAACGATGAC
28722919 GACGATAAGAACGATGA
1 GACGATAAGAACGATGA
28722936 TGATGATGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.14, G:0.34, T:0.11
Consensus pattern (18 bp):
GACGATAAGAACGATGAC
Found at i:28723049 original size:39 final size:39
Alignment explanation
Indices: 28723006--28723108 Score: 206
Period size: 39 Copynumber: 2.6 Consensus size: 39
28722996 AATTTAGCTT
28723006 ACAATTTATATTTTGTTATGAAATTAAATATGTTGATGG
1 ACAATTTATATTTTGTTATGAAATTAAATATGTTGATGG
28723045 ACAATTTATATTTTGTTATGAAATTAAATATGTTGATGG
1 ACAATTTATATTTTGTTATGAAATTAAATATGTTGATGG
28723084 ACAATTTATATTTTGTTATGAAATT
1 ACAATTTATATTTTGTTATGAAATT
28723109 GTTGAACTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 64 1.00
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.48
Consensus pattern (39 bp):
ACAATTTATATTTTGTTATGAAATTAAATATGTTGATGG
Found at i:28723050 original size:20 final size:20
Alignment explanation
Indices: 28723027--28723089 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
28723017 TTTGTTATGA
28723027 AATTAAATATGTTGATGGAC
1 AATTAAATATGTTGATGGAC
* *
28723047 AATT-TATATTTTGTTAT-GA-
1 AATTAAATATGTTG--ATGGAC
28723066 AATTAAATATGTTGATGGAC
1 AATTAAATATGTTGATGGAC
28723086 AATT
1 AATT
28723090 TATATTTTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
18 2 0.06
19 13 0.38
20 17 0.50
21 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (20 bp):
AATTAAATATGTTGATGGAC
Found at i:28723069 original size:19 final size:19
Alignment explanation
Indices: 28723008--28723108 Score: 84
Period size: 17 Copynumber: 5.2 Consensus size: 19
28722998 TTTAGCTTAC
28723008 AATTTATATTTTGTTATGA
1 AATTTATATTTTGTTATGA
* *
28723027 AA-TTA-AATATGTTGATGGA
1 AATTTATATTTTGTT-AT-GA
28723046 CAATTTATATTTTGTTATGA
1 -AATTTATATTTTGTTATGA
* *
28723066 AA-TTA-AATATGTTGATGGA
1 AATTTATATTTTGTT-AT-GA
28723085 CAATTTATATTTTGTTATGA
1 -AATTTATATTTTGTTATGA
28723105 AATT
1 AATT
28723109 GTTGAACTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
17 12 0.19
18 10 0.16
19 12 0.19
20 8 0.12
21 10 0.16
22 12 0.19
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.49
Consensus pattern (19 bp):
AATTTATATTTTGTTATGA
Found at i:28723644 original size:8 final size:8
Alignment explanation
Indices: 28723631--28723663 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
28723621 TAAAATATTT
28723631 AAGTTAAA
1 AAGTTAAA
28723639 AAGTTAAA
1 AAGTTAAA
28723647 AAGTTAAA
1 AAGTTAAA
28723655 AAGTTAAA
1 AAGTTAAA
28723663 A
1 A
28723664 GTAATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (8 bp):
AAGTTAAA
Found at i:28723768 original size:25 final size:25
Alignment explanation
Indices: 28723734--28723781 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
28723724 TTAAGATTTG
28723734 ATTGTTTGTAATTAAATTCAAATTA
1 ATTGTTTGTAATTAAATTCAAATTA
28723759 ATTGTTTGTAATTAAATTCAAAT
1 ATTGTTTGTAATTAAATTCAAAT
28723782 AAGTAATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (25 bp):
ATTGTTTGTAATTAAATTCAAATTA
Found at i:28742154 original size:14 final size:15
Alignment explanation
Indices: 28742125--28742154 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28742115 TCATGCCAGT
28742125 TTTTAACAATAAAAA
1 TTTTAACAATAAAAA
28742140 TTTTAACAA-AAAAA
1 TTTTAACAATAAAAA
28742154 T
1 T
28742155 CAATTTACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (15 bp):
TTTTAACAATAAAAA
Found at i:28762539 original size:19 final size:21
Alignment explanation
Indices: 28762505--28762545 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
28762495 TTTGGGTGAA
28762505 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
28762526 TCAGCT-TT-CGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
28762545 T
1 T
28762546 GACATATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.60
20 2 0.10
21 6 0.30
ACGTcount: A:0.12, C:0.27, G:0.20, T:0.41
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTCTGT
Found at i:28762745 original size:21 final size:20
Alignment explanation
Indices: 28762721--28762768 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
28762711 ATAGAAGTTG
28762721 TGAATGACAGGAAATTGACAA
1 TGAATGACAGGAAATTGAC-A
*
28762742 TGAATGACAGGGAATTGACA
1 TGAATGACAGGAAATTGACA
28762762 TGAATGA
1 TGAATGA
28762769 TTTTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.44, C:0.08, G:0.27, T:0.21
Consensus pattern (20 bp):
TGAATGACAGGAAATTGACA
Found at i:28769237 original size:27 final size:26
Alignment explanation
Indices: 28769207--28769272 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
28769197 ATATTTAAAA
28769207 AAAATAAAGAAAAAAGAAAAAAGAAGG
1 AAAATAAAGAAAAAAGAAAAAAGAA-G
* *
28769234 AAAATAAAGGAAAAAGAAAGAAGAAG
1 AAAATAAAGAAAAAAGAAAAAAGAAG
*
28769260 AAGA-AAAGAAAAA
1 AAAATAAAGAAAAA
28769273 TAAAAAGGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 8 0.23
26 4 0.11
27 23 0.66
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (26 bp):
AAAATAAAGAAAAAAGAAAAAAGAAG
Found at i:28770600 original size:44 final size:45
Alignment explanation
Indices: 28770526--28770654 Score: 154
Period size: 44 Copynumber: 2.9 Consensus size: 45
28770516 GTAAAGATAG
* * *
28770526 CAGATCTTGCCTTCCTGTACTGGCAATGAAGCAGATCGAAGACAC
1 CAGACCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGACAC
* * *
28770571 CAG-CCTTGCATTCCTGTACTGACAGTGAAGCAGA-CTGAAGATAG
1 CAGACCTTGCCTTCCTGTACTGACAGTGAAGCAGATC-GAAGACAC
* * *
28770615 TAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAA
1 CAGACCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAA
28770655 ACCATTAGTC
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
43 1 0.01
44 35 0.49
45 34 0.48
46 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (45 bp):
CAGACCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGACAC
Found at i:28770635 original size:45 final size:45
Alignment explanation
Indices: 28770519--28770654 Score: 177
Period size: 45 Copynumber: 3.0 Consensus size: 45
28770509 CAAATATGTA
* *
28770519 AAGATAGCAGATCTTGCCTTCCTGTACTGGCAATGAAGCAGATCG
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCG
* * * *
28770564 AAGACACCAG-CCTTGCATTCCTGTACTGACAGTGAAGCAGA-CTG
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATC-G
* *
28770608 AAGATAGTAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCG
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCG
28770653 AA
1 AA
28770655 ACCATTAGTC
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
43 1 0.01
44 35 0.46
45 39 0.51
46 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.23
Consensus pattern (45 bp):
AAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCG
Found at i:28770810 original size:44 final size:44
Alignment explanation
Indices: 28770753--28771875 Score: 349
Period size: 44 Copynumber: 25.5 Consensus size: 44
28770743 GCCATTAGTC
*
28770753 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTAAAGATTGTAGATT
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
* * * * ** ** *
28770797 CTGTCTCCTTAAGCAGTAGTGGAGCAGATCAAAGA-TGGCGAAT
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
* * *
28770840 CTTATCTTCCC-AAG-A-TAGTGGAGAAGCAGATTTAAGCCA-T-TAG-TC
1 C-TATC-TCCCTAAGCAGTAGTGGAGTAG--G-TTGAAG--ATTGTAGATT
*
28770885 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATT
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
* * * * * * *
28770929 CTGTCTCCCTAAGCAGTAGTAGAGCAGATCGAAGATGGT-GAAT
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
* * *
28770972 CTTATCTTCCC-AAG-A-TAGTGGAGAAGCAGATTTAAGCCA-T-TAG-TC
1 C-TATC-TCCCTAAGCAGTAGTGGAGTAG--G-TTGAAG--ATTGTAGATT
*
28771017 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATT
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
* * * ** *
28771061 CTGTCTCCCTAAGCAGTAGTGGAGTAGATCGAAGA-TGGCGAAT
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
* * * ** * *
28771104 CTTATCTCCCCAAG-A-TCGTGGAAAAGCATATTTAAGCCA-T-TAG-TC
1 C-TATCTCCCTAAGCAGTAGTGG---AGTAGGTTGAAG--ATTGTAGATT
* * *
28771149 CTATATCCCTAAGCAGTAGTGGAGTAGGTTAAAGATTGCAGATT
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
* * * * * * * *
28771193 CTGTCTCCCTAAGCAGTAGTAGAGCAGATCGAAAATGGT-GAAT
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
* * * * * * *
28771236 CTTATCT-TCTCAAG-ATGGTAGAGAAGCAGATTTAAGCCA-T-TAG-TC
1 C-TATCTCCCT-AAGCA--GTAGTGGAGTAGGTTGAAG--ATTGTAGATT
*
28771281 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATT
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
* * * * * * *
28771325 CTGTCCCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTA-AAT
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
* *
28771368 CTTATCTTCCC-AAG-A-TAGTGGAGAAGCAGGTTTAAGCCA-T-TAG-TT
1 C-TATC-TCCCTAAGCAGTAGT-G-G-AGTAGGTTGAAG--ATTGTAGATT
* * * *
28771413 CTATCTCCCTAAGCAATACTGGAGTAGGTTGAAAATTGCAGATT
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
* * * * * * *
28771457 CTATCCCCCTAAACAATAGTGGAGTAGATCGAAGATGGT-GAAT
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
* * * * * *
28771500 CT-TACTTTCC-AAG-A-TCGTGGAGAAGCAGATTTAAGACAT-TAG-TC
1 CTAT-C-TCCCTAAGCAGTAGTGGAGTAG--G-TTGAAGA-TTGTAGATT
* **
28771544 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGGGT
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
* * * * * * *
28771588 CTGTCCCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGT-GAAT
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
* * *
28771631 CTTATCTTCCC-AAG-A-TAGTGGAGAAGCAGATTTAAGCCA-T-TAG-TC
1 C-TATC-TCCCTAAGCAGTAGTGGAGTAG--G-TTGAAG--ATTGTAGATT
* * **
28771676 CTATCTCCCTAAGCAGTAGTGGAGTAAGTTGAAGATTGCAGGGT
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
* * * * * * * *
28771720 CTGTCCCCCTAAGCAGTAGTGGAGCAGATCGAACATGGT-GAAT
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
* *
28771763 CTTATCTTCCC-AAG-A-TAGTGGAGAAGTAGATTTAAGCCA-T-TAG--T
1 C-TATC-TCCCTAAGCAGTAGT-G-G-AGTAGGTTGAAG--ATTGTAGATT
* * *
28771807 CATATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAGATC
1 C-TATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
*
28771852 CTGTCTCCCTAAGCAGTAGTGGAG
1 CTATCTCCCTAAGCAGTAGTGGAG
28771876 CAGATCGAAG
Statistics
Matches: 776, Mismatches: 197, Indels: 212
0.65 0.17 0.18
Matches are distributed among these distances:
41 16 0.02
42 52 0.07
43 148 0.19
44 401 0.52
45 94 0.12
46 56 0.07
47 9 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (44 bp):
CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATT
Found at i:28771926 original size:132 final size:132
Alignment explanation
Indices: 28770668--28771903 Score: 1999
Period size: 132 Copynumber: 9.4 Consensus size: 132
28770658 ATTAGTCCTA
* *
28770668 TCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTCCCAAGATAGTGGAGAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
* * *
28770733 GCAAATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTAAAGATTGTAGATTC
66 GCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
28770798 TG
131 TG
* * *
28770800 TCTCCTTAAGCAGTAGTGGAGCAGATCAAAGATGGCGAATCTTATCTTCCCAAGATAGTGGAGAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
28770865 GCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
66 GCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
28770930 TG
131 TG
*
28770932 TCTCCCTAAGCAGTAGTAGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
28770997 GCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
66 GCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
28771062 TG
131 TG
* * * * *
28771064 TCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGCGAATCTTATCTCCCCAAGATCGTGGAAAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
* * *
28771129 GCATATTTAAGCCATTAGTCCTATATCCCTAAGCAGTAGTGGAGTAGGTTAAAGATTGCAGATTC
66 GCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
28771194 TG
131 TG
* * * * *
28771196 TCTCCCTAAGCAGTAGTAGAGCAGATCGAAAATGGTGAATCTTATCTTCTCAAGATGGTAGAGAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
28771261 GCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
66 GCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
28771326 TG
131 TG
* *
28771328 TCCCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTAAATCTTATCTTCCCAAGATAGTGGAGAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
* * * * *
28771393 GCAGGTTTAAGCCATTAGTTCTATCTCCCTAAGCAATACTGGAGTAGGTTGAAAATTGCAGATTC
66 GCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
*
28771458 TA
131 TG
* * * * * *
28771460 TCCCCCTAAACAATAGTGGAGTAGATCGAAGATGGTGAATCTTA-CTTTCCAAGATCGTGGAGAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
* **
28771524 GCAGATTTAAGACATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGGGTC
66 GCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
28771589 TG
131 TG
*
28771591 TCCCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
* **
28771656 GCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAAGTTGAAGATTGCAGGGTC
66 GCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
28771721 TG
131 TG
* *
28771723 TCCCCCTAAGCAGTAGTGGAGCAGATCGAACATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
* * * *
28771788 GTAGATTTAAGCCATTAGTCATATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAGATCC
66 GCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
28771853 TG
131 TG
* *
28771855 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTAT-TTCC
1 TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCC
28771904 TAGGCGGTGC
Statistics
Matches: 1025, Mismatches: 78, Indels: 3
0.93 0.07 0.00
Matches are distributed among these distances:
131 121 0.12
132 904 0.88
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (132 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGATAGTGGAGAA
GCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
TG
Found at i:28776987 original size:40 final size:41
Alignment explanation
Indices: 28776929--28777058 Score: 133
Period size: 40 Copynumber: 3.2 Consensus size: 41
28776919 ACGTTTGGAT
* * *
28776929 AAAAAAGCCGTTAAAGATCGAGCATTAGCGGCGCTTTC-T-
1 AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTCTTG
* * **
28776968 AACAAACGCCTCTATAGATCGAGCATTAGAGATGC-TTCTTG
1 AA-AAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTCTTG
**
28777009 AAAAATTCCGCTATAGATCGAGCATTAGCGGCGCTTT-TTG
1 AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTCTTG
*
28777049 AAAAATGCCG
1 AAAAACGCCG
28777059 TAAAAAATTT
Statistics
Matches: 73, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
39 5 0.07
40 64 0.88
41 4 0.05
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (41 bp):
AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTCTTG
Found at i:28777233 original size:15 final size:15
Alignment explanation
Indices: 28777213--28777271 Score: 75
Period size: 15 Copynumber: 4.0 Consensus size: 15
28777203 ACTATTTTAA
28777213 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
28777228 GGTTTAGGGATTAT-
1 GGTTTATGGATTATG
*
28777242 GGTTTATGGTTTATG
1 GGTTTATGGATTATG
* *
28777257 GGTTAATGGTTTATG
1 GGTTTATGGATTATG
28777272 TTTTATGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 12 0.31
15 27 0.69
ACGTcount: A:0.19, C:0.00, G:0.34, T:0.47
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:28777233 original size:22 final size:21
Alignment explanation
Indices: 28777153--28777254 Score: 64
Period size: 22 Copynumber: 4.8 Consensus size: 21
28777143 GAGCATTAGC
* *
28777153 TATGGATTATAGG-TTAGGGTA
1 TATGGATTAT-GGTTTAAGGTT
* * *
28777174 TATGGTTTAGGGTTTAAAGTT
1 TATGGATTATGGTTTAAGGTT
**
28777195 TA-GGAGTTACTATTTTAAGGTT
1 TATGGA-TTA-TGGTTTAAGGTT
* *
28777217 TATGGATTATGGGTTTAGGGAT
1 TATGGATTAT-GGTTTAAGGTT
*
28777239 TATGGTTTATGGTTTA
1 TATGGATTATGGTTTA
28777255 TGGGTTAATG
Statistics
Matches: 61, Mismatches: 15, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
20 4 0.07
21 25 0.41
22 29 0.48
23 3 0.05
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.45
Consensus pattern (21 bp):
TATGGATTATGGTTTAAGGTT
Found at i:28777245 original size:29 final size:29
Alignment explanation
Indices: 28777213--28777319 Score: 94
Period size: 29 Copynumber: 3.8 Consensus size: 29
28777203 ACTATTTTAA
28777213 GGTTTATGGATTATGGGTTTAGGGATTAT
1 GGTTTATGGATTATGGGTTTAGGGATTAT
* * * *
28777242 GGTTTATGGTTTATGGGTTAATGGTTTAT
1 GGTTTATGGATTATGGGTTTAGGGATTAT
* * *
28777271 GTTTTAT-GATT-TAGGGTTTAGGGGTTAG
1 GGTTTATGGATTAT-GGGTTTAGGGATTAT
* * *
28777299 GGTTAAGGGTTTA-GGGTTTAG
1 GGTTTATGGATTATGGGTTTAG
28777320 ATTAATTAGT
Statistics
Matches: 61, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
27 1 0.02
28 26 0.43
29 34 0.56
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.46
Consensus pattern (29 bp):
GGTTTATGGATTATGGGTTTAGGGATTAT
Found at i:28777290 original size:14 final size:14
Alignment explanation
Indices: 28777166--28777318 Score: 103
Period size: 14 Copynumber: 10.7 Consensus size: 14
28777156 GGATTATAGG
*
28777166 TTAGGGTATATGGT
1 TTAGGGTTTATGGT
**
28777180 TTAGGGTTTAAAGT
1 TTAGGGTTTATGGT
28777194 TTAGGAGTTACTAT--T
1 TTAGG-GTT--TATGGT
* *
28777209 TTAAGGTTTATGGA
1 TTAGGGTTTATGGT
* *
28777223 TTATGGGTTTAGGGA
1 TTA-GGGTTTATGGT
*
28777238 TTATGGTTTATGGT
1 TTAGGGTTTATGGT
*
28777252 TTATGGGTTAATGGT
1 TTA-GGGTTTATGGT
* * *
28777267 TTATGTTTTATGAT
1 TTAGGGTTTATGGT
* *
28777281 TTAGGGTTTAGGGG
1 TTAGGGTTTATGGT
* *
28777295 TTAGGGTTAAGGGT
1 TTAGGGTTTATGGT
28777309 TTAGGGTTTA
1 TTAGGGTTTA
28777319 GATTAATTAG
Statistics
Matches: 107, Mismatches: 25, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
12 3 0.03
14 70 0.65
15 32 0.30
17 2 0.02
ACGTcount: A:0.22, C:0.01, G:0.32, T:0.46
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:28777319 original size:7 final size:7
Alignment explanation
Indices: 28777208--28777319 Score: 80
Period size: 7 Copynumber: 15.7 Consensus size: 7
28777198 GAGTTACTAT
*
28777208 TTTAAGG
1 TTTAGGG
*
28777215 TTTATGG
1 TTTAGGG
*
28777222 ATTATGGG
1 TTTA-GGG
28777230 TTTAGGG
1 TTTAGGG
* *
28777237 ATTATGG
1 TTTAGGG
*
28777244 TTTATGG
1 TTTAGGG
28777251 TTTATGGG
1 TTTA-GGG
* *
28777259 TTAATGG
1 TTTAGGG
* *
28777266 TTTATGT
1 TTTAGGG
* *
28777273 TTTATGA
1 TTTAGGG
28777280 TTTAGGG
1 TTTAGGG
28777287 TTTAGGG
1 TTTAGGG
*
28777294 GTTAGGG
1 TTTAGGG
*
28777301 TTAAGGG
1 TTTAGGG
28777308 TTTAGGG
1 TTTAGGG
28777315 TTTAG
1 TTTAG
28777320 ATTAATTAGT
Statistics
Matches: 84, Mismatches: 19, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
7 74 0.88
8 10 0.12
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:28779391 original size:23 final size:22
Alignment explanation
Indices: 28779348--28779391 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
28779338 TTCTAAGTCG
28779348 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
28779371 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
28779392 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:28779508 original size:45 final size:45
Alignment explanation
Indices: 28779444--28779529 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
28779434 CTCTGTAGAT
*
28779444 TCAGCACATAACAACCACCTTATTAATCAATGATGTCCGGTGGAA
1 TCAGCACATAACAACCACCTTACTAATCAATGATGTCCGGTGGAA
* *
28779489 TCAGCACATAGCAACCACCTTACTAATCAATGATGTTCGGT
1 TCAGCACATAACAACCACCTTACTAATCAATGATGTCCGGT
28779530 TCACATAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (45 bp):
TCAGCACATAACAACCACCTTACTAATCAATGATGTCCGGTGGAA
Found at i:28779593 original size:51 final size:50
Alignment explanation
Indices: 28779535--28779720 Score: 205
Period size: 51 Copynumber: 3.7 Consensus size: 50
28779525 TCGGTTCACA
* *
28779535 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATAGACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATCCGGTAGACG
* * * *
28779586 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGTACG-CA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATCCGGTA-GACG
* * * * * *
28779637 TAGTATCCTGCACATAGTACTTCACAAGCGA-CATATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TCCGGTAGACG
*
28779687 TAGTAGCCTGCACATAGTACTATACACGTGACCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA
28779721 NNNNNNNNNN
Statistics
Matches: 109, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
49 3 0.03
50 34 0.31
51 69 0.63
52 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATCCGGTAGACG
Found at i:28779714 original size:101 final size:102
Alignment explanation
Indices: 28779533--28779717 Score: 275
Period size: 101 Copynumber: 1.8 Consensus size: 102
28779523 GTTCGGTTCA
* * *
28779533 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATAGACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACAAGCGACCATTACCATCCGATACACGTAGTAGCCTGCA
28779598 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * * *
28779635 CATAGTATCCTGCACATAGTACTTCACAAGCGA-CA-TATCATTCCGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACAAGCGACCATTACCA-TCCGATACACGTAGTAGCCTGC
*
28779698 ACATAGTACTATACACGTGA
65 ACATAGTACTACACACGTGA
28779718 CCANNNNNNN
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
100 4 0.05
101 41 0.55
102 29 0.39
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACAAGCGACCATTACCATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:28787687 original size:47 final size:45
Alignment explanation
Indices: 28787633--28787761 Score: 132
Period size: 47 Copynumber: 2.7 Consensus size: 45
28787623 CATTATCTCC
* * *
28787633 ATCTCTTTGATTATCTTGAGACATGTTAAGGTTTTTAATATTTTACT
1 ATCTCTTT-ATTATCTTGAAACAT-TTAAGGTTTTAAATAATTTACT
* * * *
28787680 CTCTCTTTCTTTGTCTTGAAACATTCTAAGATTTTAAATAATTTACT
1 ATCTCTTT-ATTATCTTGAAACATT-TAAGGTTTTAAATAATTTACT
*
28787727 ATCTCTTTATCAGTCTTGAAACATTTTAAGGTTTT
1 ATCTCTTTATTA-TCTTGAAACA-TTTAAGGTTTT
28787762 CTTGAAATAT
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
46 2 0.03
47 62 0.94
48 2 0.03
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.50
Consensus pattern (45 bp):
ATCTCTTTATTATCTTGAAACATTTAAGGTTTTAAATAATTTACT
Found at i:28787764 original size:21 final size:21
Alignment explanation
Indices: 28787740--28787782 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
28787730 TCTTTATCAG
28787740 TCTTGAAACATTTTAAGGTTT
1 TCTTGAAACATTTTAAGGTTT
* *
28787761 TCTTGAAATATTTTGAGGTTT
1 TCTTGAAACATTTTAAGGTTT
28787782 T
1 T
28787783 TTTTTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (21 bp):
TCTTGAAACATTTTAAGGTTT
Found at i:28787885 original size:77 final size:77
Alignment explanation
Indices: 28787792--28787940 Score: 210
Period size: 77 Copynumber: 1.9 Consensus size: 77
28787782 TTTTTTTATA
* * *
28787792 ATTTACTATGTCTTTGTCTCTCTTAAAACATTTTGAGGTTTTTAATAATTTACTATTTCTTTGGT
1 ATTTACTATCTCTTTGTCTCTCTTAAAACATTTTGAGGTTTTAAATAATTTACTATATCTTT-GT
28787857 -TGTCTTGGAATG
65 CTGTCTTGGAATG
* * * * *
28787869 ATTTACTATCTCTTTGTTTGTTTTGAAATATTTTGAGGTTTTAAATAATTTACTATATCTTTGTC
1 ATTTACTATCTCTTTGTCTCTCTTAAAACATTTTGAGGTTTTAAATAATTTACTATATCTTTGTC
28787934 TGTCTTG
66 TGTCTTG
28787941 AAACATTTTG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
76 2 0.03
77 61 0.97
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.54
Consensus pattern (77 bp):
ATTTACTATCTCTTTGTCTCTCTTAAAACATTTTGAGGTTTTAAATAATTTACTATATCTTTGTC
TGTCTTGGAATG
Found at i:28787942 original size:47 final size:47
Alignment explanation
Indices: 28787869--28787958 Score: 144
Period size: 47 Copynumber: 1.9 Consensus size: 47
28787859 TCTTGGAATG
* * * *
28787869 ATTTACTATCTCTTTGTTTGTTTTGAAATATTTTGAGGTTTTAAATA
1 ATTTACTATATCTTTGTCTGTCTTGAAACATTTTGAGGTTTTAAATA
28787916 ATTTACTATATCTTTGTCTGTCTTGAAACATTTTGAGGTTTTA
1 ATTTACTATATCTTTGTCTGTCTTGAAACATTTTGAGGTTTTA
28787959 TTGAAATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.24, C:0.09, G:0.13, T:0.53
Consensus pattern (47 bp):
ATTTACTATATCTTTGTCTGTCTTGAAACATTTTGAGGTTTTAAATA
Found at i:28787962 original size:21 final size:21
Alignment explanation
Indices: 28787938--28787979 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
28787928 TTTGTCTGTC
*
28787938 TTGAAACATTTTGAGGTTTTA
1 TTGAAACATTTTGAGGCTTTA
*
28787959 TTGAAATATTTTGAGGCTTTA
1 TTGAAACATTTTGAGGCTTTA
28787980 AATAATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.48
Consensus pattern (21 bp):
TTGAAACATTTTGAGGCTTTA
Found at i:28788004 original size:68 final size:68
Alignment explanation
Indices: 28787891--28788027 Score: 238
Period size: 68 Copynumber: 2.0 Consensus size: 68
28787881 TTTGTTTGTT
* *
28787891 TTGAAATATTTTGAGGTTTTAAATAATTTACTATATCTTTGTCTGTCTTGAAACATTTTGAGGTT
1 TTGAAATATTTTGAGGCTTTAAATAATTTACTATATCTTTATCTGTCTTGAAACATTTTGAGGTT
28787956 TTA
66 TTA
* *
28787959 TTGAAATATTTTGAGGCTTTAAATAATTTATTATCTCTTTATCTGTCTTGAAACATTTTGAGGTT
1 TTGAAATATTTTGAGGCTTTAAATAATTTACTATATCTTTATCTGTCTTGAAACATTTTGAGGTT
28788024 TTA
66 TTA
28788027 T
1 T
28788028 GGTCTTCGAT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.50
Consensus pattern (68 bp):
TTGAAATATTTTGAGGCTTTAAATAATTTACTATATCTTTATCTGTCTTGAAACATTTTGAGGTT
TTA
Found at i:28789280 original size:42 final size:43
Alignment explanation
Indices: 28789199--28789327 Score: 161
Period size: 43 Copynumber: 3.0 Consensus size: 43
28789189 GAACGGTACT
* * *
28789199 TTTAGCGGCGTTTGTCGGTACAGTGCCGCTAAAGGTCATGTTC
1 TTTAACGGCGTTTGTCGGTAAAGCGCCGCTAAAGGTCATGTTC
* * **
28789242 TTTAATGGCGTTTGT-GATAAAGCGCCGCTAAAACTCATGTTC
1 TTTAACGGCGTTTGTCGGTAAAGCGCCGCTAAAGGTCATGTTC
* * *
28789284 TTTAGCGGCGTTTGTGGGTAAAGCGCCACTAAAGGTCATGTTC
1 TTTAACGGCGTTTGTCGGTAAAGCGCCGCTAAAGGTCATGTTC
28789327 T
1 T
28789328 ATAGCAGTAT
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 35 0.49
43 37 0.51
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (43 bp):
TTTAACGGCGTTTGTCGGTAAAGCGCCGCTAAAGGTCATGTTC
Found at i:28789602 original size:19 final size:19
Alignment explanation
Indices: 28789578--28789618 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
28789568 TCCAATTCAA
*
28789578 TCTCAACTCTCTCTCACAT
1 TCTCAACTCTCTCTCAAAT
*
28789597 TCTCAATTCTCTCTCAAAT
1 TCTCAACTCTCTCTCAAAT
28789616 TCT
1 TCT
28789619 TCTCAATACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.22, C:0.37, G:0.00, T:0.41
Consensus pattern (19 bp):
TCTCAACTCTCTCTCAAAT
Found at i:28795603 original size:31 final size:32
Alignment explanation
Indices: 28795546--28795606 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
28795536 ACTATATATG
*
28795546 AATTTTGATTTGATATGTAGTTTCATAAATGA
1 AATTTTGATTTGATATGTAATTTCATAAATGA
28795578 AATTTTGATTTGAT-T-TAATTCTCATAAAT
1 AATTTTGATTTGATATGTAATT-TCATAAAT
28795607 TATTAATACG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 4 0.15
31 9 0.33
32 14 0.52
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.49
Consensus pattern (32 bp):
AATTTTGATTTGATATGTAATTTCATAAATGA
Found at i:28797784 original size:7 final size:7
Alignment explanation
Indices: 28797772--28797802 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
28797762 AGGTGTAATC
28797772 GCTTAAA
1 GCTTAAA
28797779 GCTTAAA
1 GCTTAAA
28797786 GCTTAAA
1 GCTTAAA
28797793 GCTTAAA
1 GCTTAAA
28797800 GCT
1 GCT
28797803 GACAGAGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (7 bp):
GCTTAAA
Found at i:28798499 original size:14 final size:14
Alignment explanation
Indices: 28798477--28798506 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28798467 AAAGTTATTA
*
28798477 ATCATTATATATGT
1 ATCAATATATATGT
28798491 ATCAATATATATGT
1 ATCAATATATATGT
28798505 AT
1 AT
28798507 AGAATTAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (14 bp):
ATCAATATATATGT
Found at i:28799040 original size:3 final size:3
Alignment explanation
Indices: 28799032--28799077 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
28799022 TTTAGGCCCT
*
28799032 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
28799078 GATATACCGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:28799565 original size:16 final size:16
Alignment explanation
Indices: 28799544--28799613 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
28799534 TTTGGTTCGC
* *
28799544 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
28799560 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
28799576 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
28799592 TGTAATGGAATAGATG
1 TGTAATGGAATAGAGG
28799608 TGTAAT
1 TGTAAT
28799614 AGCAAATCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:28799643 original size:45 final size:44
Alignment explanation
Indices: 28799592--28799682 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
28799582 GGAATAGAGG
* *
28799592 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAAGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
28799637 TGTAATGGAATAGAAGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAAGCGTAATAGAAATCAACTGTTTGGTTGAA
28799681 TG
1 TG
28799683 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 18 0.45
45 22 0.55
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAAGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:28799868 original size:18 final size:17
Alignment explanation
Indices: 28799847--28799881 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28799837 TTATTATTAA
*
28799847 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28799865 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28799882 TCTNNNNNNN
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28805498 original size:3 final size:3
Alignment explanation
Indices: 28805490--28805535 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
28805480 TTTAGGCCCT
*
28805490 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
28805536 GATATACCGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:28806023 original size:16 final size:16
Alignment explanation
Indices: 28806002--28806071 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
28805992 TTTGGTTCGC
* *
28806002 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
28806018 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
28806034 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
28806050 TGTAATGGAATAGATG
1 TGTAATGGAATAGAGG
28806066 TGTAAT
1 TGTAAT
28806072 AGCAAATCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:28806101 original size:45 final size:44
Alignment explanation
Indices: 28806050--28806140 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
28806040 GGAATAGAGG
* *
28806050 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAAGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
28806095 TGTAATGGAATAGAAGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAAGCGTAATAGAAATCAACTGTTTGGTTGAA
28806139 TG
1 TG
28806141 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 18 0.45
45 22 0.55
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAAGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:28806322 original size:16 final size:16
Alignment explanation
Indices: 28806303--28806348 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
28806293 AATTATTATT
28806303 AAATATAT-TTTAATTA
1 AAATATATATTTAA-TA
28806319 AAATATATAATTTAATA
1 AAATATAT-ATTTAATA
*
28806336 AAAT-TCTATTTAA
1 AAATATATATTTAA
28806349 ATTTTAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 6 0.22
16 10 0.37
17 6 0.22
18 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATATATATTTAATA
Found at i:28806326 original size:18 final size:17
Alignment explanation
Indices: 28806305--28806339 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28806295 TTATTATTAA
*
28806305 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28806323 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28806340 TCTATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28806332 original size:55 final size:55
Alignment explanation
Indices: 28806265--28806444 Score: 206
Period size: 55 Copynumber: 3.3 Consensus size: 55
28806255 TATTATCAAT
28806265 AATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAA
1 AATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAA
* * * *** * *
28806320 AATATATAATTTAATAAAATTCTATTTA-AATT-TTAATAAGAT-TATTATT-ATCAA
1 AATAAATAATTTAATCATATT-TAAACATAATTATTATTAA-ATATATT-TTAATTAA
*
28806374 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAA
1 -AATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAA
*
28806430 AATATATAATTTAAT
1 AATAAATAATTTAAT
28806445 AAATTTCTTA
Statistics
Matches: 99, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
54 17 0.17
55 65 0.66
56 17 0.17
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.46
Consensus pattern (55 bp):
AATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAA
Found at i:28806364 original size:110 final size:110
Alignment explanation
Indices: 28806232--28806452 Score: 424
Period size: 110 Copynumber: 2.0 Consensus size: 110
28806222 TTGTTATTGT
28806232 TATTTAAATTTTAATAAGATTATTATTATCAATAATAAATAATTTAATCATATTTAAACATAATT
1 TATTTAAATTTTAATAAGATTATTATTATCAATAATAAATAATTTAATCATATTTAAACATAATT
*
28806297 ATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC
66 ATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTC
28806342 TATTTAAATTTTAATAAGATTATTATTATCAATAATAAATAATTTAATCATATTTAAACATAATT
1 TATTTAAATTTTAATAAGATTATTATTATCAATAATAAATAATTTAATCATATTTAAACATAATT
*
28806407 ATTATTAAATATATTATAATTAAAATATATAATTTAATAAATTTC
66 ATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTC
28806452 T
1 T
28806453 TAATAATTAA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 109 1.00
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.47
Consensus pattern (110 bp):
TATTTAAATTTTAATAAGATTATTATTATCAATAATAAATAATTTAATCATATTTAAACATAATT
ATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTC
Found at i:28806432 original size:16 final size:16
Alignment explanation
Indices: 28806395--28806436 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28806385 TTAATCATAT
*
28806395 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28806411 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28806426 TTAAAATATAT
1 TTAAAATATAT
28806437 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28806443 original size:14 final size:15
Alignment explanation
Indices: 28806404--28806445 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28806394 TTTAAACATA
*
28806404 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28806419 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28806433 A-TATAATTTAATA
1 ATTATAATTAAATA
28806446 AATTTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28809755 original size:35 final size:34
Alignment explanation
Indices: 28809716--28809783 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
28809706 TTGAGGTTCA
*
28809716 AGTTTATGGTTCAAGGATTT-GAGGTTTATGGGTTG
1 AGTTTAAGGTTCAAGGATTTCG-GG-TTATGGGTTG
* *
28809751 AGTTTAAGGTTTAAGGGTTTCGGGTTATGGGTT
1 AGTTTAAGGTTCAAGGATTTCGGGTTATGGGTT
28809784 ATGAGCTCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 9 0.31
35 19 0.66
36 1 0.03
ACGTcount: A:0.19, C:0.03, G:0.35, T:0.43
Consensus pattern (34 bp):
AGTTTAAGGTTCAAGGATTTCGGGTTATGGGTTG
Found at i:28810309 original size:14 final size:13
Alignment explanation
Indices: 28810286--28810333 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
28810276 AACCCTAATC
28810286 AAATTATAAACACT
1 AAATT-TAAACACT
*
28810300 AAATTCTAAACCCT
1 AAATT-TAAACACT
*
28810314 AAATATGAAACACT
1 AAAT-TTAAACACT
28810328 AAATTT
1 AAATTT
28810334 TACTCAACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 1 0.04
14 26 0.93
15 1 0.04
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (13 bp):
AAATTTAAACACT
Found at i:28816138 original size:15 final size:15
Alignment explanation
Indices: 28816120--28816151 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28816110 AAATGTCGCG
28816120 ATAACAAATACAACA
1 ATAACAAATACAACA
*
28816135 ATAATAAATACAACA
1 ATAACAAATACAACA
28816150 AT
1 AT
28816152 GGCATAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAACAAATACAACA
Found at i:28816177 original size:13 final size:14
Alignment explanation
Indices: 28816158--28816194 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
28816148 CAATGGCATA
28816158 GAAATAATATAAAC
1 GAAATAATATAAAC
28816172 -AAATAA-ATAAAC
1 GAAATAATATAAAC
28816184 GAAACTAATAT
1 GAAA-TAATAT
28816195 TCATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 6 0.30
13 9 0.45
14 3 0.15
15 2 0.10
ACGTcount: A:0.65, C:0.08, G:0.05, T:0.22
Consensus pattern (14 bp):
GAAATAATATAAAC
Found at i:28818250 original size:18 final size:18
Alignment explanation
Indices: 28818199--28818250 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
28818189 TATGTTGTTA
*
28818199 TTATTTTATTGTTAATGT
1 TTATTTTATTGTTAATAT
**
28818217 TTA-CATATTGTATAATAT
1 TTATTTTATTGT-TAATAT
28818235 TTATTTTATTGTTAAT
1 TTATTTTATTGTTAAT
28818251 TTTGTTATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 6 0.22
18 15 0.56
19 6 0.22
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.62
Consensus pattern (18 bp):
TTATTTTATTGTTAATAT
Found at i:28840693 original size:44 final size:44
Alignment explanation
Indices: 28840660--28840875 Score: 299
Period size: 44 Copynumber: 4.9 Consensus size: 44
28840650 GACAGGATCC
**
28840660 ACAATCTTCAACCTATTCCACTGCTATTCAGGGAGATAGGA-TAT
1 ACAATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACT-T
* *
28840704 ACAATCTTCCACCTATTCCACTGCTGGTCAGGGAGTTAGGACTT
1 ACAATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTT
* * * *
28840748 GCAATCTTCAACCTATTCCACTGCTAGTCAGGGAGTTAGGACTG
1 ACAATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTT
* * **
28840792 GCAATCTTCTACCTATTCGTCTGCTGGTCAGGGAGATAGGACTT
1 ACAATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTT
*
28840836 ACAATCTTCAACCTATTCCACTGCTGGTCAGGGAGCTAGG
1 ACAATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGG
28840876 TTTTGTGATT
Statistics
Matches: 152, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
44 151 0.99
45 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (44 bp):
ACAATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTT
Found at i:28842089 original size:5 final size:5
Alignment explanation
Indices: 28842079--28842108 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
28842069 GCCTCTCTAT
28842079 TTTTA TTTTA TTTTA TTTTA TTTTA GTTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTT
28842109 TTGAAAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:28847753 original size:2 final size:2
Alignment explanation
Indices: 28847746--28847770 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28847736 TGTTAAGTTT
28847746 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28847771 TCGGATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28848187 original size:37 final size:37
Alignment explanation
Indices: 28848145--28848259 Score: 176
Period size: 37 Copynumber: 3.1 Consensus size: 37
28848135 ATAGATAAAA
* *
28848145 ATATATGTATGTATTCGGCATAGGTGAATATAAGGGT
1 ATATATGTATGCATTCGGCATAGGTGAATATAAGTGT
*
28848182 ATATATGTATGCATTCGGCATAGGTGAAAATAAGTGT
1 ATATATGTATGCATTCGGCATAGGTGAATATAAGTGT
* **
28848219 ATATATGTATGCATTCGGCATAAGTGGGTATAAGTGT
1 ATATATGTATGCATTCGGCATAGGTGAATATAAGTGT
28848256 ATAT
1 ATAT
28848260 GTGCATTCGG
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.35
Consensus pattern (37 bp):
ATATATGTATGCATTCGGCATAGGTGAATATAAGTGT
Found at i:28848270 original size:33 final size:35
Alignment explanation
Indices: 28848145--28848272 Score: 125
Period size: 37 Copynumber: 3.6 Consensus size: 35
28848135 ATAGATAAAA
* * * *
28848145 ATATATGTATGTATTCGGCATAGGTGAATATAAGGG
1 ATATATG-ATGCATTCGGCATAAGTGAAAATAAGTG
*
28848181 TATATATGTATGCATTCGGCATAGGTGAAAATAAGTG
1 -ATATATG-ATGCATTCGGCATAAGTGAAAATAAGTG
***
28848218 TATATATGTATGCATTCGGCATAAGTGGGTATAAGTG
1 -ATATATG-ATGCATTCGGCATAAGTGAAAATAAGTG
28848255 -TATATG-TGCATTCGGCAT
1 ATATATGATGCATTCGGCAT
28848273 TTATGGTTGA
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
33 12 0.14
35 6 0.07
37 66 0.79
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (35 bp):
ATATATGATGCATTCGGCATAAGTGAAAATAAGTG
Found at i:28857585 original size:27 final size:26
Alignment explanation
Indices: 28857555--28857606 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
28857545 TTTTTTGGAC
28857555 ATTTAATTT-TTAATTTGGTTTTATTTT
1 ATTT-ATTTGTTAATTTGG-TTTATTTT
*
28857582 ATTTATTTGTTTATTTGGTTTATTT
1 ATTTATTTGTTAATTTGGTTTATTT
28857607 CACTAACGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (26 bp):
ATTTATTTGTTAATTTGGTTTATTTT
Found at i:28857711 original size:5 final size:6
Alignment explanation
Indices: 28857684--28857722 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
28857674 GAATGATGCC
* *
28857684 AAAAGA AAGAAGC AAAAGA AAAAGA AAAATA AAAAGA AA
1 AAAAGA AA-AAGA AAAAGA AAAAGA AAAAGA AAAAGA AA
28857723 CGGTGAGGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:28861453 original size:64 final size:64
Alignment explanation
Indices: 28861344--28861468 Score: 178
Period size: 64 Copynumber: 2.0 Consensus size: 64
28861334 CATCCCGATT
* ** ***
28861344 GGTATTGATCTTGCATGTGTTGTGGACATACCGCAGCTTTTTGTGAGCGTCCTATTATATGATC
1 GGTAGTGATCTTGCATGTGTTGCAGACATACCGCAGCTCACTGTGAGCGTCCTATTATATGATC
* *
28861408 GGTAGTGATCTTGCATGTGTTGCAGATATACCGCAGCTCACTGTGAGCGTCCTGTTATATG
1 GGTAGTGATCTTGCATGTGTTGCAGACATACCGCAGCTCACTGTGAGCGTCCTATTATATG
28861469 GTTCTCCGGA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.36
Consensus pattern (64 bp):
GGTAGTGATCTTGCATGTGTTGCAGACATACCGCAGCTCACTGTGAGCGTCCTATTATATGATC
Found at i:28861553 original size:24 final size:24
Alignment explanation
Indices: 28861511--28861556 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
28861501 AACTTCCAGA
*
28861511 ATTTATGGCTATCCGGAGCTTCTG
1 ATTTATGGCTATCCAGAGCTTCTG
* *
28861535 ATTTATGGCTCTTCAGAGCTTC
1 ATTTATGGCTATCCAGAGCTTC
28861557 CCGTTAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (24 bp):
ATTTATGGCTATCCAGAGCTTCTG
Done.