Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 96 of 279
Found at i:31006461 original size:16 final size:16
Alignment explanation
Indices: 31006440--31006471 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31006430 CATTCTGCAT
31006440 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
31006456 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
31006472 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:31011432 original size:37 final size:37
Alignment explanation
Indices: 31011381--31011451 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
31011371 CATTCTTGTA
31011381 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
31011418 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
31011452 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:31011451 original size:6 final size:6
Alignment explanation
Indices: 31011391--31011440 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
31011381 AAGAGAAAAC
*
31011391 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
31011440 A
1 A
31011441 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:31011533 original size:11 final size:12
Alignment explanation
Indices: 31011501--31011531 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
31011491 TTGAGAGAAC
31011501 TTGAAAAAGCCT
1 TTGAAAAAGCCT
31011513 TTGAAAAAGCCT
1 TTGAAAAAGCCT
31011525 TTGAAAA
1 TTGAAAA
31011532 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:31013746 original size:30 final size:30
Alignment explanation
Indices: 31013712--31013808 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
31013702 AGCTCACTCC
31013712 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
31013742 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
*
31013772 CAGCTCAACTTTAGCTCACGAGCTGAAA-CT
1 TAGCTCAACTTTAGCTCACGAGCT-AAACCT
31013802 TAGCTCA
1 TAGCTCA
31013809 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
29 1 0.02
30 49 0.96
31 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:31019585 original size:40 final size:39
Alignment explanation
Indices: 31019526--31019604 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 39
31019516 CGGTGACTCA
* *
31019526 AGTGCGCGAGGTAGTTGATCATCTGCAAACTCTAGCGGT
1 AGTGCGCGAAGTAGCTGATCATCTGCAAACTCTAGCGGT
31019565 NAGTGCGCGAAGTAGCTGATCATCTGCAAACTCTAGCGGT
1 -AGTGCGCGAAGTAGCTGATCATCTGCAAACTCTAGCGGT
31019605 TCAGGCTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (39 bp):
AGTGCGCGAAGTAGCTGATCATCTGCAAACTCTAGCGGT
Found at i:31028352 original size:46 final size:44
Alignment explanation
Indices: 31028285--31028614 Score: 204
Period size: 46 Copynumber: 7.6 Consensus size: 44
31028275 ATAATACAGG
*
31028285 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* *
31028331 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-T-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAG--A
* * * * * *
31028375 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG-----GA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * * * *
31028414 TCGTATCTCTCTGA-AGTTACAGTAGAGA-AGATC--ACA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGATTCAGA
*
31028455 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* * ** ****
31028501 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * * * *
31028545 TCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCA-GA
*
31028588 TCCTATCTCCCTGA-AGTTACAGTGGAA
1 TCTTATCTCCCTGAGA-TTACAGTGGAA
31028615 TGGATTAAAA
Statistics
Matches: 222, Mismatches: 45, Indels: 37
0.73 0.15 0.12
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
39 23 0.10
40 1 0.00
41 27 0.12
42 5 0.02
43 24 0.11
44 69 0.31
45 1 0.00
46 70 0.32
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
Found at i:31030242 original size:3 final size:3
Alignment explanation
Indices: 31030231--31030265 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
31030221 ATTATTTTGT
31030231 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA CTTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT
31030266 TGTTTATGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:31030827 original size:16 final size:16
Alignment explanation
Indices: 31030808--31030838 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31030798 TACACCCATA
*
31030808 TATATGTACATATTTT
1 TATATATACATATTTT
31030824 TATATATACATATTT
1 TATATATACATATTT
31030839 ATCGTTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATATACATATTTT
Found at i:31043184 original size:46 final size:44
Alignment explanation
Indices: 31043117--31043747 Score: 271
Period size: 44 Copynumber: 14.6 Consensus size: 44
31043107 ATAATACAGG
*
31043117 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* *
31043163 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-T-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAG--A
* * * * * *
31043207 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG-----GA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * * * *
31043246 TCGTATCTCTCTGA-AGTTACAGTAGAGA-AGATC--ACA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGATTCAGA
*
31043287 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* * ** ****
31043333 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * * * *
31043377 TCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCA-GA
* * ** * **
31043420 TCCTAACTCCCTGA-AGTTACAGTGGAATGGATTAAA-ATAAAAGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAACAGATCAAAGAT-TCAGA
* * * *
31043464 TCTCAACTCCCTGAGATTACAGCGGAGCAGATCAAAGA-T-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAG--A
* * * * * * * *
31043508 GCCTATCTCCTTGAGATTACAATGGAGCGGAT-TAAG----GGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * * * *
31043547 TCGTATCTCTCTGA-AGTTACAGTAGAGA-AGATC--ACA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGATTCAGA
*
31043588 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* * ** ****
31043634 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * * * *
31043678 TCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCA-GA
*
31043721 TCCTATCTCCCTGA-AGTTACAGTGGAA
1 TCTTATCTCCCTGAGA-TTACAGTGGAA
31043748 TGGATTAAAA
Statistics
Matches: 439, Mismatches: 107, Indels: 81
0.70 0.17 0.13
Matches are distributed among these distances:
37 1 0.00
38 3 0.01
39 45 0.10
40 2 0.00
41 54 0.12
42 11 0.03
43 54 0.12
44 159 0.36
45 4 0.01
46 106 0.24
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
Found at i:31043439 original size:87 final size:87
Alignment explanation
Indices: 31043339--31043501 Score: 227
Period size: 87 Copynumber: 1.9 Consensus size: 87
31043329 CAGATCTTAT
* * * * * * *
31043339 CTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTCATCTCCCTGAGATTACAGCGGAG
1 CTCCCTGAAGTTACAGTGGAACAGATTAAAACAAAAGATCTCAACTCCCTGAGATTACAGCGGAG
*
31043404 CAGATCGAAGACACTATCCTAA
66 CAGATCAAAGACACTATCCTAA
** *
31043426 CTCCCTGAAGTTACAGTGGAATGGATTAAAATAAAAGATCTCAACTCCCTGAGATTACAGCGGAG
1 CTCCCTGAAGTTACAGTGGAACAGATTAAAACAAAAGATCTCAACTCCCTGAGATTACAGCGGAG
31043491 CAGATCAAAGA
66 CAGATCAAAGA
31043502 TAGTAAGCCT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
87 65 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.21
Consensus pattern (87 bp):
CTCCCTGAAGTTACAGTGGAACAGATTAAAACAAAAGATCTCAACTCCCTGAGATTACAGCGGAG
CAGATCAAAGACACTATCCTAA
Found at i:31043787 original size:301 final size:301
Alignment explanation
Indices: 31043164--31043787 Score: 1167
Period size: 301 Copynumber: 2.1 Consensus size: 301
31043154 AATTTCAGAT
*
31043164 CTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATTACAA
1 CTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAAGCCTATCTCCTTGAGATTACAA
31043229 TGGAGCGGATTAAAGGATCGTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATC
66 TGGAGCGGATTAAAGGATCGTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATC
31043294 TCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGA
131 TCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGA
31043359 GCAGATTGAAGCCAGAGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCT
196 GCAGATTGAAGCCAGAGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCT
*
31043424 AACTCCCTGAAGTTACAGTGGAATGGATTAAAATAAAAGAT
261 AACTCCCTGAAGTTACAGTGGAATGGATTAAAATAAAAGAG
* *
31043465 CTCAACTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAAGCCTATCTCCTTGAGATTACAA
1 CTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAAGCCTATCTCCTTGAGATTACAA
*
31043530 TGGAGCGGATTAAGGGATCGTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATC
66 TGGAGCGGATTAAAGGATCGTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATC
31043595 TCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGA
131 TCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGA
31043660 GCAGATTGAAGCCAGAGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCT
196 GCAGATTGAAGCCAGAGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCT
* *
31043725 ATCTCCCTGAAGTTACAGTGGAATGGATTAAAATAAAGGAG
261 AACTCCCTGAAGTTACAGTGGAATGGATTAAAATAAAAGAG
* *
31043766 CTTATCTCTCTGAGGTTACAGC
1 CTTATCTCCCTGAGATTACAGC
31043788 AGAGTAGGTC
Statistics
Matches: 312, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
301 312 1.00
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (301 bp):
CTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAAGCCTATCTCCTTGAGATTACAA
TGGAGCGGATTAAAGGATCGTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATC
TCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGA
GCAGATTGAAGCCAGAGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCT
AACTCCCTGAAGTTACAGTGGAATGGATTAAAATAAAAGAG
Found at i:31045376 original size:3 final size:3
Alignment explanation
Indices: 31045365--31045399 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
31045355 ATTATTTTGT
31045365 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA CTTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT
31045400 TGTTTATGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:31045961 original size:16 final size:16
Alignment explanation
Indices: 31045942--31045972 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31045932 TACACCCATA
*
31045942 TATATGTACATATTTT
1 TATATATACATATTTT
31045958 TATATATACATATTT
1 TATATATACATATTT
31045973 ATCGTTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATATACATATTTT
Found at i:31047366 original size:23 final size:23
Alignment explanation
Indices: 31047347--31047393 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
31047337 TTAATTAATG
31047347 TTACA-TTTATATATAAATTAAAA
1 TTACACTTTAT-TATAAATTAAAA
*
31047370 TTGCACTTTATTATAAATTAAAA
1 TTACACTTTATTATAAATTAAAA
31047393 T
1 T
31047394 CTGATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (23 bp):
TTACACTTTATTATAAATTAAAA
Found at i:31047987 original size:17 final size:18
Alignment explanation
Indices: 31047958--31047991 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
31047948 ATTTCTTTTG
31047958 TATTTTCATATTTTAATT
1 TATTTTCATATTTTAATT
31047976 TATTTT-ATATTTTAAT
1 TATTTTCATATTTTAAT
31047992 AAAATTCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTTTCATATTTTAATT
Found at i:31049079 original size:17 final size:18
Alignment explanation
Indices: 31049054--31049087 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
31049044 AATGAAATTA
31049054 TTAAATGTAATA-ATAAT
1 TTAAATGTAATATATAAT
*
31049071 TTAATTGTAATATATAA
1 TTAAATGTAATATATAA
31049088 GAAATTACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
TTAAATGTAATATATAAT
Found at i:31058169 original size:7 final size:7
Alignment explanation
Indices: 31058154--31058185 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
31058144 AGTCGTTTCA
31058154 TATTTAG
1 TATTTAG
*
31058161 TACTTAG
1 TATTTAG
31058168 TATTTAG
1 TATTTAG
31058175 TATTTAG
1 TATTTAG
31058182 TATT
1 TATT
31058186 ATGTATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.56
Consensus pattern (7 bp):
TATTTAG
Found at i:31058698 original size:30 final size:30
Alignment explanation
Indices: 31058662--31058720 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
31058652 GATGATGGGA
*
31058662 CGGGCCCATCAACAACACCTACACAATCAT
1 CGGGCCCATCAACAACACCCACACAATCAT
**
31058692 CGGGCCCATCAACAGTACCCACACAATCA
1 CGGGCCCATCAACAACACCCACACAATCA
31058721 CTAGGCTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.41, G:0.12, T:0.12
Consensus pattern (30 bp):
CGGGCCCATCAACAACACCCACACAATCAT
Found at i:31058991 original size:13 final size:13
Alignment explanation
Indices: 31058973--31058998 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31058963 TTGTGGAATT
31058973 CAAACACCTCCAC
1 CAAACACCTCCAC
31058986 CAAACACCTCCAC
1 CAAACACCTCCAC
31058999 ATTCTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.54, G:0.00, T:0.08
Consensus pattern (13 bp):
CAAACACCTCCAC
Found at i:31070761 original size:21 final size:21
Alignment explanation
Indices: 31070732--31070786 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
31070722 ATACAGGGCA
*
31070732 CACACGCCCGTGTGGTCAAGG
1 CACATGCCCGTGTGGTCAAGG
31070753 CACATGCCCGTGTGGTCAAGG
1 CACATGCCCGTGTGGTCAAGG
31070774 CACATGCCCGTGT
1 CACATGCCCGTGT
31070787 CACAGGCTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.18, C:0.33, G:0.31, T:0.18
Consensus pattern (21 bp):
CACATGCCCGTGTGGTCAAGG
Found at i:31077490 original size:18 final size:18
Alignment explanation
Indices: 31077467--31077501 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31077457 TAAAATGATT
31077467 TTTATT-TCCTATTAATTA
1 TTTATTATCC-ATTAATTA
31077485 TTTATTATCCATTAATT
1 TTTATTATCCATTAATT
31077502 TTTCTCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTATTATCCATTAATTA
Found at i:31081667 original size:14 final size:15
Alignment explanation
Indices: 31081629--31081670 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
31081619 GAAAAGAAAA
*
31081629 GAAAAGAAAAGAAGG
1 GAAAAGGAAAGAAGG
* *
31081644 GAAAATGAAAGAA-T
1 GAAAAGGAAAGAAGG
31081658 GAAAAGGAAAGAA
1 GAAAAGGAAAGAA
31081671 ATAACGTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.05
Consensus pattern (15 bp):
GAAAAGGAAAGAAGG
Found at i:31087094 original size:13 final size:13
Alignment explanation
Indices: 31087076--31087102 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31087066 GCTCGACAGG
31087076 GACACGCCCATGT
1 GACACGCCCATGT
31087089 GACACGCCCATGT
1 GACACGCCCATGT
31087102 G
1 G
31087103 CGATAGCTTC
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:0.22, C:0.37, G:0.26, T:0.15
Consensus pattern (13 bp):
GACACGCCCATGT
Found at i:31088386 original size:27 final size:26
Alignment explanation
Indices: 31088326--31088387 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
31088316 ATAAGACTCC
31088326 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * * *
31088352 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
31088380 ATTTTATT
1 ATTTTATT
31088388 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 14 0.48
28 13 0.45
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:31089862 original size:17 final size:17
Alignment explanation
Indices: 31089840--31089880 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
31089830 ATTTAGGCTC
31089840 GTGGGCCACATGGGCAT
1 GTGGGCCACATGGGCAT
31089857 GTGGGCCACATGGGCAT
1 GTGGGCCACATGGGCAT
31089874 GTGGGCC
1 GTGGGCC
31089881 CATTTTTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.17
Consensus pattern (17 bp):
GTGGGCCACATGGGCAT
Found at i:31099070 original size:13 final size:14
Alignment explanation
Indices: 31099043--31099080 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
31099033 ATTAAAGAGG
31099043 GAAAAAGAAAAAAA
1 GAAAAAGAAAAAAA
*
31099057 GAAAAA-AAATAAA
1 GAAAAAGAAAAAAA
31099070 GAAGAAAGAAA
1 GAA-AAAGAAA
31099081 GGGAGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 9 0.43
14 9 0.43
15 3 0.14
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (14 bp):
GAAAAAGAAAAAAA
Found at i:31099112 original size:25 final size:25
Alignment explanation
Indices: 31099043--31099117 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 25
31099033 ATTAAAGAGG
31099043 GAAA-AAGAAA-AAAAGAAAAAAAA
1 GAAAGAAGAAAGAAAAGAAAAAAAA
*
31099066 TAAAGAAGAAAGAAAGGGAGAAAAAAAGA
1 GAAAGAAGAAAGAAA---AGAAAAAAA-A
*
31099095 GAAGGAA-AAAGAAAAGAAAAAAA
1 GAAAGAAGAAAGAAAAGAAAAAAA
31099118 TGGAAAAGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
23 3 0.07
24 6 0.14
25 12 0.28
28 16 0.37
29 6 0.14
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.01
Consensus pattern (25 bp):
GAAAGAAGAAAGAAAAGAAAAAAAA
Found at i:31099117 original size:28 final size:27
Alignment explanation
Indices: 31099036--31099117 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
31099026 TACGACAATT
*
31099036 AAAGAGGGAAAAAGAAAA-AAAGAAAAA
1 AAAGAAGGAAAAAGAAAAGAAA-AAAAA
* * * *
31099063 AAATAAAGAAGAAAGAAAGGGAGAAAAAA
1 AAAGAAGGAA-AAAGAAA-AGAAAAAAAA
*
31099092 AGAGAAGGAAAAAGAAAAGAAAAAAA
1 AAAGAAGGAAAAAGAAAAGAAAAAAA
31099118 TGGAAAAGAA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
27 14 0.33
28 14 0.33
29 12 0.29
30 2 0.05
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (27 bp):
AAAGAAGGAAAAAGAAAAGAAAAAAAA
Found at i:31111723 original size:16 final size:18
Alignment explanation
Indices: 31111702--31111739 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31111692 TTCTTTGTTC
31111702 TTTTGTT-C-TTCATCTA
1 TTTTGTTACTTTCATCTA
*
31111718 TTTTGTTACTTTCTTCTA
1 TTTTGTTACTTTCATCTA
31111736 TTTT
1 TTTT
31111740 TAGATCTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.11, C:0.16, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTGTTACTTTCATCTA
Found at i:31120523 original size:26 final size:27
Alignment explanation
Indices: 31120475--31120528 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
31120465 TACATTAATT
31120475 TATAAAATTAAATTTTAAATTTTAAAA
1 TATAAAATTAAATTTTAAATTTTAAAA
* *
31120502 TATAAAATT-ATTTTTATATTTTAAAA
1 TATAAAATTAAATTTTAAATTTTAAAA
31120528 T
1 T
31120529 TTTTTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TATAAAATTAAATTTTAAATTTTAAAA
Found at i:31120526 original size:19 final size:19
Alignment explanation
Indices: 31120504--31120556 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
31120494 TTTTAAAATA
31120504 TAAAATTATTTTTATATTT
1 TAAAATTATTTTTATATTT
31120523 TAAAATT-TTTTTA-ATTT
1 TAAAATTATTTTTATATTT
*
31120540 TAAAATTTAATTTTATA
1 TAAAA-TTATTTTTATA
31120557 AATTAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 9 0.30
18 8 0.27
19 12 0.40
20 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TAAAATTATTTTTATATTT
Found at i:31120539 original size:17 final size:18
Alignment explanation
Indices: 31120504--31120547 Score: 72
Period size: 17 Copynumber: 2.4 Consensus size: 18
31120494 TTTTAAAATA
31120504 TAAAATTATTTTTATATTT
1 TAAAATT-TTTTTATATTT
31120523 TAAAATTTTTTTA-ATTT
1 TAAAATTTTTTTATATTT
31120540 TAAAATTT
1 TAAAATTT
31120548 AATTTTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 12 0.48
18 6 0.24
19 7 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TAAAATTTTTTTATATTT
Found at i:31120550 original size:13 final size:14
Alignment explanation
Indices: 31120532--31120565 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
31120522 TTAAAATTTT
31120532 TTTAATTTTA-AAA
1 TTTAATTTTATAAA
31120545 TTTAATTTTATAAA
1 TTTAATTTTATAAA
31120559 -TTAATTT
1 TTTAATTT
31120566 AATATATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 17 0.85
14 3 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAATTTTATAAA
Found at i:31120665 original size:19 final size:20
Alignment explanation
Indices: 31120641--31120681 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
31120631 TCTATTTAAA
31120641 ATTTAATT-TTT-TAAATATT
1 ATTTAATTGTTTCTAAAT-TT
31120660 ATTTAATTGTTTCTAAATTT
1 ATTTAATTGTTTCTAAATTT
31120680 AT
1 AT
31120682 AAATATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 7 0.35
21 5 0.25
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTAATTGTTTCTAAATTT
Found at i:31122864 original size:10 final size:10
Alignment explanation
Indices: 31122849--31122883 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
31122839 TTAATTAATC
31122849 TTTTAAAATT
1 TTTTAAAATT
*
31122859 TTTTAAATTT
1 TTTTAAAATT
*
31122869 TTTTTAAATT
1 TTTTAAAATT
31122879 TTTTA
1 TTTTA
31122884 TAATCCATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTAAAATT
Found at i:31122873 original size:11 final size:11
Alignment explanation
Indices: 31122857--31122882 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
31122847 TCTTTTAAAA
31122857 TTTTTTAAATT
1 TTTTTTAAATT
31122868 TTTTTTAAATT
1 TTTTTTAAATT
31122879 TTTT
1 TTTT
31122883 ATAATCCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTAAATT
Found at i:31127211 original size:106 final size:106
Alignment explanation
Indices: 31127075--31127275 Score: 375
Period size: 106 Copynumber: 1.9 Consensus size: 106
31127065 AAAATTTTTC
31127075 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
*
31127140 TTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTT
66 TTCTCGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTT
*
31127181 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
*
31127246 TTCTCGTTCGACTAAACAGCCAAATATCCT
66 TTCTCGTTCGACCAAACAGCCAAATATCCT
31127276 CTTAAAGCTT
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 92 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (106 bp):
TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
TTCTCGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTT
Found at i:31128725 original size:30 final size:30
Alignment explanation
Indices: 31128691--31128810 Score: 131
Period size: 30 Copynumber: 4.1 Consensus size: 30
31128681 TTAAAAATAA
*
31128691 AAATTGCATTTTGACCCCTAAACTTTTCCT
1 AAATTTCATTTTGACCCCTAAACTTTTCCT
* *
31128721 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTC-CT
* * **
31128751 AAATTTCACTTAGACCCCTAAACTTTTATT
1 AAATTTCATTTTGACCCCTAAACTTTTCCT
*
31128781 AAATTTCATTTT-AACCCTAAA-TTTT-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCCT
31128808 AAA
1 AAA
31128811 AATTACATTT
Statistics
Matches: 77, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
27 4 0.05
28 4 0.05
29 12 0.16
30 54 0.70
31 3 0.04
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTTCCT
Found at i:31129920 original size:17 final size:17
Alignment explanation
Indices: 31129862--31129922 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
31129852 TCCGAATTTA
31129862 ATATATATATTTT-T--
1 ATATATATATTTTGTAC
*
31129876 ATA-ACTATATTATGTAC
1 ATATA-TATATTTTGTAC
31129893 ATATATATATTTTGTAC
1 ATATATATATTTTGTAC
31129910 ATATCAT-TATTTT
1 ATAT-ATATATTTT
31129923 ATATTATTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 1 0.03
14 10 0.26
15 1 0.03
17 24 0.62
18 3 0.08
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (17 bp):
ATATATATATTTTGTAC
Found at i:31141705 original size:78 final size:77
Alignment explanation
Indices: 31141558--31141869 Score: 284
Period size: 78 Copynumber: 3.8 Consensus size: 77
31141548 TTCTATTTTC
* * * *
31141558 AAAATTCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTCAA-TTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTA
31141622 CTGTTTGTCAAAA
66 -TGTTTGTCAAAA
** *
31141635 AAAAAGTTGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
*
31141700 ATGTTTTTCAATTTATA
65 ATGTTTGTCAA---A-A
* * *
31141717 TTTTGCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTATTTTT
1 ------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
* ****
31141782 AATTTCTGTTCTTAGTGACTGTTT
60 AATTTATG-T-TT-GT--C-AAAA
** *
31141806 TTAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGACACGCTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
31141870 CTATTTTTTT
Statistics
Matches: 191, Mismatches: 26, Indels: 30
0.77 0.11 0.12
Matches are distributed among these distances:
77 4 0.02
78 59 0.31
79 3 0.02
81 1 0.01
82 1 0.01
83 58 0.30
87 55 0.29
88 6 0.03
89 2 0.01
90 1 0.01
92 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (77 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTA
TGTTTGTCAAAA
Found at i:31141710 original size:14 final size:14
Alignment explanation
Indices: 31141691--31141720 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31141681 GCTGAGGTAA
*
31141691 TTTCAATTTATGTT
1 TTTCAATTTATATT
31141705 TTTCAATTTATATT
1 TTTCAATTTATATT
31141719 TT
1 TT
31141721 GCAAAAATCA
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:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (14 bp):
TTTCAATTTATATT
Found at i:31141765 original size:87 final size:86
Alignment explanation
Indices: 31141644--31142134 Score: 532
Period size: 87 Copynumber: 5.6 Consensus size: 86
31141634 AAAAAAGTTG
*
31141644 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTATGTTTTTC
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTATGTTTTTC
31141709 AATTTATATTTTGCAAAAATCA
66 AATTTATATTTT-CAAAAATCA
* * * * *
31141731 ATTCATATTGCGAGAGGTGAGTTGAGCCTTAGGACACGCTGAGGTATTTTTAATTTCTGTTCTT-
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTATGTTTTTC
* * * *
31141795 -AGTGACTGTTTT--TAAATCA
66 AATTTA-TATTTTCAAAAATCA
* *
31141814 ACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTATTTTTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA-TT-TATGTTTT
**
31141879 TCCAACCTATATTTTTCAAAAATCA
64 T-CAATTTATA-TTTTCAAAAATCA
* *
31141904 ACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTTTCAATTTATGTTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAATTTATG--T
* *
31141968 TTTTCAATCTATGCTTTTCAAAAATCA
61 TTTTCAATTTAT-ATTTTCAAAAATCA
* * * *
31141995 ACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG-CACGCTGAGGTATTTTCAATTTCTGCTTTA
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTATTTTCAATTTATGTTTTT
*
31142059 CTAATTCTA-CTTTTC--AAATCA
65 C-AATT-TATATTTTCAAAAATCA
* * *
31142080 ACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACACGCTGAGGTCTTTTCAA
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAA
31142135 ATTCTATTTT
Statistics
Matches: 343, Mismatches: 39, Indels: 44
0.81 0.09 0.10
Matches are distributed among these distances:
83 55 0.16
84 5 0.01
85 42 0.12
86 5 0.01
87 87 0.25
88 9 0.03
89 27 0.08
90 37 0.11
91 50 0.15
92 24 0.07
93 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (86 bp):
ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTATGTTTTTC
AATTTATATTTTCAAAAATCA
Found at i:31141973 original size:16 final size:17
Alignment explanation
Indices: 31141952--31141985 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
31141942 TGCTGAGGTA
*
31141952 TTTTCAATTTATG-TTT
1 TTTTCAATCTATGCTTT
31141968 TTTTCAATCTATGCTTT
1 TTTTCAATCTATGCTTT
31141985 T
1 T
31141986 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTCAATCTATGCTTT
Found at i:31142037 original size:181 final size:183
Alignment explanation
Indices: 31141808--31142302 Score: 557
Period size: 192 Copynumber: 2.7 Consensus size: 183
31141798 GACTGTTTTT
31141808 AAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTC-AGGACACGCTGAGGTATTTTCAATTTCT
1 AAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGG-CACGCTGAGGTATTTTCAATTTCT
* * *
31141872 ATTTTTTTCCAACCTATATTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GG
65 A-TCTTTTCCAA-TTCTATTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG
*
31141936 CTCACATGCTGAGGTATTTTC-AATT-TATGTTTT-TTTC-AATCTATGCT-TTTC-AA
128 C-CACACGCTGAGGTATTTTCAAATTCTAT-TTTTATTTCTAATCTATG-TGTTTCAAA
* *
31141989 AAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCT-
1 AAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTA
* * * * *
31142053 GCTTTACTAATTCTACTTTTC--AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCA
66 TCTTTTCCAATTCTATTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCA
* * *
31142116 CACGCTGAGGTCTTTTCAAATTCTATTTTTAATTTCTGTTTTTTTAATTTCTGTGTTTCAAAAAA
131 CACGCTGAGGTATTTTCAAATTCTATTTTT-ATTTC--------TAATCTATGTGTTTC---AAA
* * *
31142181 AAATCAACTCATATTGCAAGAGGTGAGTTAAGCCTCAGGGCACACTGAGGTATTTTCAATTTCTA
1 AAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTA
* *
31142246 -CTTTT-CAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
66 TCTTTTCCAA-TTCTATTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT
31142303 TTTGCAAATT
Statistics
Matches: 265, Mismatches: 25, Indels: 35
0.82 0.08 0.11
Matches are distributed among these distances:
176 52 0.20
177 11 0.04
178 11 0.04
179 10 0.04
181 58 0.22
182 3 0.01
187 1 0.00
188 10 0.04
191 2 0.01
192 74 0.28
194 33 0.12
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (183 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTA
TCTTTTCCAATTCTATTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCA
CACGCTGAGGTATTTTCAAATTCTATTTTTATTTCTAATCTATGTGTTTCAAA
Found at i:31142161 original size:15 final size:15
Alignment explanation
Indices: 31142141--31142169 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31142131 TCAAATTCTA
31142141 TTTTTAATTTCTGTT
1 TTTTTAATTTCTGTT
31142156 TTTTTAATTTCTGT
1 TTTTTAATTTCTGT
31142170 GTTTCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TTTTTAATTTCTGTT
Found at i:31142320 original size:55 final size:55
Alignment explanation
Indices: 31142246--31142358 Score: 192
Period size: 55 Copynumber: 2.1 Consensus size: 55
31142236 TCAATTTCTA
* *
31142246 CTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAAATTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
31142301 CTTTTGCAAATTCTG-TTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-CAAATTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
31142356 CTT
1 CTT
31142359 GGCTCACGTG
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
55 47 0.85
56 8 0.15
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (55 bp):
CTTTTCAAATTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
Found at i:31142692 original size:30 final size:30
Alignment explanation
Indices: 31142629--31142730 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
31142619 TAAAAAATAA
* *
31142629 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGACCCCTAAACTTTCT-TT
*
31142659 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
* ** *
31142689 AAATTTCACTTAAACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCTTT
31142719 AAATTTCATTTT
1 AAATTTCATTTT
31142731 AATCCTAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
30 60 0.98
31 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCTTT
Found at i:31144019 original size:19 final size:19
Alignment explanation
Indices: 31143951--31144019 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
31143941 ATTATTATTA
31143951 TTATTATTAT-TACATATAT
1 TTATT-TTATGTACATATAT
* *
31143970 TTATTATATGCATATATATAT
1 TTATTTTATG--TACATATAT
* *
31143991 GTATTTTTATGTACATATTT
1 TTA-TTTTATGTACATATAT
31144011 TTATTTTAT
1 TTATTTTAT
31144020 ATTATTATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 11 0.28
20 9 0.23
21 10 0.26
22 6 0.15
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.59
Consensus pattern (19 bp):
TTATTTTATGTACATATAT
Found at i:31154744 original size:12 final size:12
Alignment explanation
Indices: 31154725--31154756 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
31154715 TTAAGGAAAA
31154725 AAAAGGAAAGGG
1 AAAAGGAAAGGG
*
31154737 AAAGGGAAAGGG
1 AAAAGGAAAGGG
31154749 AAAAGGAA
1 AAAAGGAA
31154757 TTAATGTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (12 bp):
AAAAGGAAAGGG
Found at i:31161482 original size:51 final size:51
Alignment explanation
Indices: 31161361--31161548 Score: 229
Period size: 51 Copynumber: 3.7 Consensus size: 51
31161351 ATCTGGTATG
*
31161361 CATAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTAT-TTGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCTAATTATCTTGGTACA
* * * * *
31161410 CGTAATAGCCTGCACTTAGTACTACACACGTGACCTAACTATCTTGATACA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCTAATTATCTTGGTACA
* * * * * *
31161461 CATAGTAGTCTGCACTTAGTACTACACACGTGATCGAAGTTATC-GGGTACG
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCTAA-TTATCTTGGTACA
*
31161512 CATAGTAGCCTGCACTTAGTACTACACATGCGACCTA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCTA
31161549 GCTACATATA
Statistics
Matches: 116, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
49 31 0.27
50 5 0.04
51 76 0.66
52 4 0.03
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (51 bp):
CATAGTAGCCTGCACTTAGTACTACACACGCGACCTAATTATCTTGGTACA
Found at i:31161538 original size:102 final size:100
Alignment explanation
Indices: 31161361--31161548 Score: 259
Period size: 102 Copynumber: 1.9 Consensus size: 100
31161351 ATCTGGTATG
* ** *
31161361 CATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATTTGGTACACGTAATAGCCTGCACT
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCGGGTACACATAATAGCCTGCACT
*
31161426 TAGTACTACACACGTGACCTAACTATCTTGATACA
66 TAGTACTACACACGCGACCTAACTATCTTGATACA
* * * * *
31161461 CATAGTAGTCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCCTGCA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCGGGTACACATAATAGCCTGCA
*
31161526 CTTAGTACTACACATGCGACCTA
64 CTTAGTACTACACACGCGACCTA
31161549 GCTACATATA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
100 30 0.40
101 3 0.04
102 42 0.56
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (100 bp):
CATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCGGGTACACATAATAGCCTGCACT
TAGTACTACACACGCGACCTAACTATCTTGATACA
Found at i:31164939 original size:11 final size:10
Alignment explanation
Indices: 31164907--31164961 Score: 60
Period size: 11 Copynumber: 5.5 Consensus size: 10
31164897 CATGAGATTT
31164907 TGATATG-CA
1 TGATATGACA
*
31164916 TGATTTGACA
1 TGATATGACA
31164926 TGATATGCACA
1 TGATATG-ACA
*
31164937 TGATATG-TA
1 TGATATGACA
31164946 TGATATGCACA
1 TGATATG-ACA
31164957 TGATA
1 TGATA
31164962 AATTCATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 14 0.37
10 8 0.21
11 16 0.42
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (10 bp):
TGATATGACA
Found at i:31165065 original size:25 final size:25
Alignment explanation
Indices: 31165009--31165116 Score: 112
Period size: 24 Copynumber: 4.4 Consensus size: 25
31164999 GAGGAAGTGC
* * * *
31165009 AAAAGGGCTATGCCCCA-ATTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
**
31165033 AAAAGGGCTTTGCCCCAGTTTATTG
1 AAAAGGGCTTTGCCCCAGTTTATCA
31165058 AAAAGGGCTTTTGCCCCAGTTTATCA
1 AAAAGGGC-TTTGCCCCAGTTTATCA
* *
31165084 AAAAGGGATTTGCCCCAG-TTATTA
1 AAAAGGGCTTTGCCCCAGTTTATCA
*
31165108 AAAAAGGCT
1 AAAAGGGCT
31165117 AGGCCTCCAG
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
24 28 0.39
25 22 0.31
26 22 0.31
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:31165077 original size:26 final size:26
Alignment explanation
Indices: 31165033--31165116 Score: 111
Period size: 26 Copynumber: 3.3 Consensus size: 26
31165023 CCAATTACCG
*
31165033 AAAAGGGC-TTTGCCCCAGTTTATTG
1 AAAAGGGCTTTTGCCCCAGTTTATTA
*
31165058 AAAAGGGCTTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTTGCCCCAGTTTATTA
*
31165084 AAAAGGG-ATTTGCCCCAG-TTATTA
1 AAAAGGGCTTTTGCCCCAGTTTATTA
*
31165108 AAAAAGGCT
1 AAAAGGGCT
31165117 AGGCCTCCAG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
24 11 0.22
25 18 0.35
26 22 0.43
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (26 bp):
AAAAGGGCTTTTGCCCCAGTTTATTA
Found at i:31165308 original size:31 final size:31
Alignment explanation
Indices: 31165270--31165374 Score: 192
Period size: 31 Copynumber: 3.4 Consensus size: 31
31165260 TATTGCTACA
31165270 GAAAAGGCTTCGGCCCAGTGATATGAATAAT
1 GAAAAGGCTTCGGCCCAGTGATATGAATAAT
31165301 GAAAAGGCTTCGGCCCAGTGATATGAATAAT
1 GAAAAGGCTTCGGCCCAGTGATATGAATAAT
*
31165332 GAAAAGGCTTCGGCCCAGTGATATGAAAAAT
1 GAAAAGGCTTCGGCCCAGTGATATGAATAAT
*
31165363 GTAAAGGCTTCG
1 GAAAAGGCTTCG
31165375 ACCTAGTATG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (31 bp):
GAAAAGGCTTCGGCCCAGTGATATGAATAAT
Found at i:31166896 original size:96 final size:97
Alignment explanation
Indices: 31166723--31166905 Score: 262
Period size: 96 Copynumber: 1.9 Consensus size: 97
31166713 ATTTATTTAC
* * *
31166723 TTATTGTTGCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGATAGCCAAGCACCCTAC
1 TTATTGTTGCTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCTAC
*
31166788 CTCGATTACTCAGCCCAACATACTCCTAATTT
66 CCCGATTACTCAGCCCAACATACTCCTAATTT
* *
31166820 TTATT-TTTCTTAAGAACATATCGAACCTTTTGACGGGAAGAGAGATGACAGCCAAGCA-CCTCA
1 TTATTGTTGCTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCT-A
* * *
31166883 CCCCGGTTACTCAGGCCGACATA
65 CCCCGATTACTCAGCCCAACATA
31166906 TTCTTAAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
95 3 0.04
96 68 0.89
97 5 0.07
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (97 bp):
TTATTGTTGCTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCTAC
CCCGATTACTCAGCCCAACATACTCCTAATTT
Found at i:31168006 original size:19 final size:19
Alignment explanation
Indices: 31167984--31168038 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
31167974 ATATCTAAAA
31167984 AATAAAATAATAAAATAAT
1 AATAAAATAATAAAATAAT
31168003 AATAAAA-AGA-AAGAATAAT
1 AATAAAATA-ATAA-AATAAT
31168022 AATAAAAATAAATAAAA
1 AAT-AAAAT-AATAAAA
31168039 ATTGGGTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
18 3 0.10
19 17 0.57
20 4 0.13
21 3 0.10
22 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (19 bp):
AATAAAATAATAAAATAAT
Found at i:31168036 original size:16 final size:15
Alignment explanation
Indices: 31167981--31168032 Score: 63
Period size: 16 Copynumber: 3.5 Consensus size: 15
31167971 TTAATATCTA
31167981 AAAAATAA-AATAAT
1 AAAAATAATAATAAT
*
31167995 -AAAATAATAATAAA
1 AAAAATAATAATAAT
*
31168009 AAGAAAGAATAATAAT
1 AA-AAATAATAATAAT
31168025 AAAAATAA
1 AAAAATAA
31168033 ATAAAAATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 7 0.23
14 5 0.16
15 6 0.19
16 13 0.42
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (15 bp):
AAAAATAATAATAAT
Found at i:31171761 original size:10 final size:10
Alignment explanation
Indices: 31171742--31171791 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
31171732 TTAAATTCTA
31171742 AAAGATAAAT
1 AAAGATAAAT
31171752 ATAA-ATAAAT
1 A-AAGATAAAT
*
31171762 AAAGATAATT
1 AAAGATAAAT
31171772 AAAGATAAAT
1 AAAGATAAAT
31171782 GAAA-ATAAAT
1 -AAAGATAAAT
31171792 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:31172957 original size:38 final size:38
Alignment explanation
Indices: 31172906--31172982 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
31172896 TATATATGAG
31172906 TTAGCTTCTTTGCTTACTTAGTCACTTCAATTATCTTC
1 TTAGCTTCTTTGCTTACTTAGTCACTTCAATTATCTTC
31172944 TTAGCTTCTTTGCTTACTTAGTCACTTCAATTATCTTC
1 TTAGCTTCTTTGCTTACTTAGTCACTTCAATTATCTTC
31172982 T
1 T
31172983 AATTATGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.18, C:0.23, G:0.08, T:0.51
Consensus pattern (38 bp):
TTAGCTTCTTTGCTTACTTAGTCACTTCAATTATCTTC
Found at i:31173349 original size:12 final size:13
Alignment explanation
Indices: 31173332--31173378 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
31173322 GTTTGGGGTA
*
31173332 GATGGG-GGGTTG
1 GATGGGAGGGTGG
31173344 GATGGGAGGGTGG
1 GATGGGAGGGTGG
31173357 GATGGGATGGGATGG
1 GATGGGA-GGG-TGG
31173372 GATGGGA
1 GATGGGA
31173379 AGGGAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
12 6 0.19
13 12 0.39
14 3 0.10
15 10 0.32
ACGTcount: A:0.17, C:0.00, G:0.64, T:0.19
Consensus pattern (13 bp):
GATGGGAGGGTGG
Found at i:31173364 original size:5 final size:5
Alignment explanation
Indices: 31173343--31173383 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
31173333 ATGGGGGGTT
*
31173343 GGATG GGA-G GG-TG GGATG GGATG GGATG GGATG GGAAG GGA
1 GGATG GGATG GGATG GGATG GGATG GGATG GGATG GGATG GGA
31173384 GTAAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
4 6 0.18
5 27 0.82
ACGTcount: A:0.22, C:0.00, G:0.63, T:0.15
Consensus pattern (5 bp):
GGATG
Found at i:31173413 original size:30 final size:31
Alignment explanation
Indices: 31173374--31173433 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
31173364 TGGGATGGGA
31173374 TGGGAAGGGAGTAAAAATTTTA-GGGGAAAAG
1 TGGGAAGGGAGTAAAAA-TTTAGGGGGAAAAG
31173405 TGGG-AGGGAGTAAAAATTTAGGGGGAAAA
1 TGGGAAGGGAGTAAAAATTTAGGGGGAAAA
31173434 TGAAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 4 0.14
30 20 0.71
31 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.40, T:0.18
Consensus pattern (31 bp):
TGGGAAGGGAGTAAAAATTTAGGGGGAAAAG
Found at i:31181961 original size:42 final size:41
Alignment explanation
Indices: 31181914--31182071 Score: 126
Period size: 42 Copynumber: 3.8 Consensus size: 41
31181904 GCATATAAGT
*
31181914 GCTAAATGAAAACCCGTAAGGGTTAAATGGAAGCTAATAGGA
1 GCTAAATGAAAACCCATAAGGGTTAAATGGAAGCTAA-AGGA
* ** *
31181956 GCTAAA-CAGAAACCCATAAGGGTT-AATCTAAAGCTCAAACGA
1 GCTAAATGA-AAACCCATAAGGGTTAAAT-GGAAGCT-AAAGGA
* * **
31181998 GCTAAATTG-AAACCCAGAAGGGTTAAATTGAAGCTCGAGAGA
1 GCTAAA-TGAAAACCCATAAGGGTTAAATGGAAGCTAAAG-GA
* *
31182040 GCTGAACT-AAAACCCATTAGGGTTAAATGGAA
1 GCT-AAATGAAAACCCATAAGGGTTAAATGGAA
31182072 ACTTATATGG
Statistics
Matches: 92, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
41 5 0.05
42 80 0.87
43 7 0.08
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (41 bp):
GCTAAATGAAAACCCATAAGGGTTAAATGGAAGCTAAAGGA
Found at i:31187017 original size:18 final size:18
Alignment explanation
Indices: 31186994--31187029 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31186984 AATTGGTTTT
*
31186994 TATTTTATTTTATTTTGA
1 TATTTTATTCTATTTTGA
*
31187012 TATTTTCTTCTATTTTGA
1 TATTTTATTCTATTTTGA
31187030 CGTTTCTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (18 bp):
TATTTTATTCTATTTTGA
Found at i:31188723 original size:27 final size:27
Alignment explanation
Indices: 31188693--31188877 Score: 228
Period size: 27 Copynumber: 6.9 Consensus size: 27
31188683 ATTATGAAAG
31188693 TACCCCCGATTTACAGAATTACCGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
*
31188720 TACCCCCGATTTACATAATTACCGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
* *
31188747 TACCCCTGATTTACATAATTACCGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
* *
31188774 T-CCCCTCGACTTATAGAATTACCGTTT
1 TACCCC-CGATTTACAGAATTACCGTTT
* * *
31188801 TACCCTCGATTTACAAAATTACCATTT
1 TACCCCCGATTTACAGAATTACCGTTT
** * *
31188828 TACCCTTGATTTATAGAATTACTGTTT
1 TACCCCCGATTTACAGAATTACCGTTT
* *
31188855 TACCCTCGATTTACAAAATTACC
1 TACCCCCGATTTACAGAATTACC
31188878 AAAATACCCN
Statistics
Matches: 136, Mismatches: 20, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
26 4 0.03
27 129 0.95
28 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (27 bp):
TACCCCCGATTTACAGAATTACCGTTT
Found at i:31188886 original size:81 final size:81
Alignment explanation
Indices: 31188693--31188877 Score: 262
Period size: 81 Copynumber: 2.3 Consensus size: 81
31188683 ATTATGAAAG
* * *
31188693 TACCCCCGATTTACAGAATTACCGTTTTACCCCCGATTTACATAATTACCGTTTTACCCCTGATT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCCCGATTTACAAAATTACCATTTTACCCCTGATT
*
31188758 TACATAATTACCGTTT
66 TACAGAATTACCGTTT
* * * * *
31188774 TCCCCTCGACTTATAGAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTTGATT
1 TACCCTCGATTTACAGAATTACCGTTTTACCCCCGATTTACAAAATTACCATTTTACCCCTGATT
* *
31188839 TATAGAATTACTGTTT
66 TACAGAATTACCGTTT
*
31188855 TACCCTCGATTTACAAAATTACC
1 TACCCTCGATTTACAGAATTACC
31188878 AAAATACCCN
Statistics
Matches: 89, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 89 1.00
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (81 bp):
TACCCTCGATTTACAGAATTACCGTTTTACCCCCGATTTACAAAATTACCATTTTACCCCTGATT
TACAGAATTACCGTTT
Found at i:31189750 original size:20 final size:20
Alignment explanation
Indices: 31189725--31189773 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
31189715 ATTTTGATAA
31189725 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
31189745 ACATGACATGTATGATATGT
1 ACATGATATGTATGATATGC
31189765 ACATGATAT
1 ACATGATAT
31189774 TCATTAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:31190760 original size:13 final size:13
Alignment explanation
Indices: 31190742--31190768 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31190732 TTTCATATCA
31190742 GTTATTTGAATCT
1 GTTATTTGAATCT
31190755 GTTATTTGAATCT
1 GTTATTTGAATCT
31190768 G
1 G
31190769 AATCTATATC
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:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (13 bp):
GTTATTTGAATCT
Found at i:31195264 original size:42 final size:40
Alignment explanation
Indices: 31195205--31195288 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 40
31195195 GTGCAGGTTT
*
31195205 CACACGGCCAAGACACACGCCTGTGT-TCTAAGCCGTGTGTGA
1 CACACGGCCAAGACACACGCCTATGTCTCT--GCC-TGTGTGA
*
31195247 CACACGGCTAAGACACACGCCTATGTCTCTGCCTGTGTGA
1 CACACGGCCAAGACACACGCCTATGTCTCTGCCTGTGTGA
31195287 CA
1 CA
31195289 AATTTTGAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 9 0.23
41 3 0.08
42 24 0.62
43 3 0.08
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (40 bp):
CACACGGCCAAGACACACGCCTATGTCTCTGCCTGTGTGA
Found at i:31196387 original size:24 final size:24
Alignment explanation
Indices: 31196270--31196389 Score: 93
Period size: 24 Copynumber: 5.0 Consensus size: 24
31196260 AGCCATGTAA
*
31196270 CGGGAAGCCCATAAAGAGCC-TAT
1 CGGGAAGCTCATAAAGAGCCATAT
* ** *
31196293 CGGGAAGCTTATTTAG-GCTATAT
1 CGGGAAGCTCATAAAGAGCCATAT
* *
31196316 AACAGAAAGCTCAT-AAGAGCCATAAT
1 --CGGGAAGCTCATAAAGAGCCAT-AT
* * * *
31196342 CGGGAAGTTCACAAATAACCATAT
1 CGGGAAGCTCATAAAGAGCCATAT
31196366 CGGGAAGCTCATAAAGAGCCATAT
1 CGGGAAGCTCATAAAGAGCCATAT
31196390 AACAGAAGCT
Statistics
Matches: 71, Mismatches: 20, Indels: 11
0.70 0.20 0.11
Matches are distributed among these distances:
22 2 0.03
23 15 0.21
24 32 0.45
25 20 0.28
26 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (24 bp):
CGGGAAGCTCATAAAGAGCCATAT
Found at i:31201743 original size:42 final size:42
Alignment explanation
Indices: 31201677--31201821 Score: 130
Period size: 42 Copynumber: 3.5 Consensus size: 42
31201667 TGCTAAACGG
* * *
31201677 AAACCCATAAGGGATAAACAGAAGCTCATA-GGAGTTGAACAA
1 AAACCCATAAGGGTTAAACTGAAGCTCA-ACAGAGTTGAACAA
** **
31201719 AAACCCATAAGGGTTAATTTGAAGCTCAACAGAGTTGAACTG
1 AAACCCATAAGGGTTAAACTGAAGCTCAACAGAGTTGAACAA
* * * * * *
31201761 AAACCTAGAAGGGTTAAACTGAAGCTCGAGAGAGCTGAACTA
1 AAACCCATAAGGGTTAAACTGAAGCTCAACAGAGTTGAACAA
* * *
31201803 AAACCTATTAGCGTTAAAC
1 AAACCCATAAGGGTTAAAC
31201822 GAAAACTCAT
Statistics
Matches: 84, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
41 1 0.01
42 83 0.99
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.19
Consensus pattern (42 bp):
AAACCCATAAGGGTTAAACTGAAGCTCAACAGAGTTGAACAA
Found at i:31205262 original size:29 final size:29
Alignment explanation
Indices: 31205220--31205288 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
31205210 ACGTGTGTCT
31205220 CAGCCGTGTGTGATACACGGTTAAGTACA
1 CAGCCGTGTGTGATACACGGTTAAGTACA
31205249 CAGCCGTGTGTGATACACGGTTAAGTACA
1 CAGCCGTGTGTGATACACGGTTAAGTACA
31205278 CAGCCGTGTGT
1 CAGCCGTGTGT
31205289 CCCCTGGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (29 bp):
CAGCCGTGTGTGATACACGGTTAAGTACA
Found at i:31207027 original size:4 final size:4
Alignment explanation
Indices: 31207018--31207043 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
31207008 TAATATATAG
31207018 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
31207044 TGTCTATGAT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:31207821 original size:21 final size:21
Alignment explanation
Indices: 31207797--31207876 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
31207787 GTTCCTGGTC
*
31207797 CACACGGCTGTGTGCCTCAGT
1 CACACGGCTATGTGCCTCAGT
* *
31207818 CACACGGCCATGTGCCCCTC-TT
1 CACACGGCTATGTG--CCTCAGT
*
31207840 CACACGGGC-ATGTGCCTCAGC
1 CACAC-GGCTATGTGCCTCAGT
31207861 CACACGGCTATGTGCC
1 CACACGGCTATGTGCC
31207877 CTTCCTCATA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
20 7 0.14
21 24 0.49
22 11 0.22
23 7 0.14
ACGTcount: A:0.16, C:0.39, G:0.25, T:0.20
Consensus pattern (21 bp):
CACACGGCTATGTGCCTCAGT
Found at i:31210416 original size:6 final size:6
Alignment explanation
Indices: 31210405--31210439 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
31210395 TGATCCCAAC
31210405 TCTGTA TCTGTA TCTGTA TCTGTA TCTGTA TCTGT
1 TCTGTA TCTGTA TCTGTA TCTGTA TCTGTA TCTGT
31210440 TTCTAACTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.14, C:0.17, G:0.17, T:0.51
Consensus pattern (6 bp):
TCTGTA
Found at i:31225159 original size:64 final size:64
Alignment explanation
Indices: 31225091--31225248 Score: 158
Period size: 64 Copynumber: 2.5 Consensus size: 64
31225081 CACACGAGCC
* * *
31225091 AAGGACACGGGTGTGTGTCCTGGCCATGTAACTCACTAATTACAATATAATGAGCACACGGGTT
1 AAGGACACGGGTGTGTGTCCTGGCCATGTAACTCACTAATTACAAAATAATGAGCACAAGGGTG
* ** * *** * * *
31225155 AAGGACACAGGCATCTGTCCCAACCGTGTAACTCACTGATTACAAAATAATGATCACAAGGGTG
1 AAGGACACGGGTGTGTGTCCTGGCCATGTAACTCACTAATTACAAAATAATGAGCACAAGGGTG
**
31225219 AAGGACACGACTGTGTGT--TAGGCCATGTAA
1 AAGGACACGGGTGTGTGTCCT-GGCCATGTAA
31225249 GACACATGGG
Statistics
Matches: 70, Mismatches: 23, Indels: 3
0.73 0.24 0.03
Matches are distributed among these distances:
63 7 0.10
64 63 0.90
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (64 bp):
AAGGACACGGGTGTGTGTCCTGGCCATGTAACTCACTAATTACAAAATAATGAGCACAAGGGTG
Found at i:31228022 original size:27 final size:27
Alignment explanation
Indices: 31227984--31228040 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
31227974 TCCCTTTTAC
31227984 TTTCTATTTTTC-CTTT-CTTCTTCTTT
1 TTTCTATTTTTCGCTTTACTT-TTCTTT
*
31228010 TTTCGTATTTTTCGCTTTAGTTTTCTTT
1 TTTC-TATTTTTCGCTTTACTTTTCTTT
31228038 TTT
1 TTT
31228041 TTTTCTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 4 0.15
27 8 0.30
28 13 0.48
29 2 0.07
ACGTcount: A:0.05, C:0.18, G:0.05, T:0.72
Consensus pattern (27 bp):
TTTCTATTTTTCGCTTTACTTTTCTTT
Found at i:31229897 original size:30 final size:30
Alignment explanation
Indices: 31229863--31229925 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
31229853 ACTTATTTTA
*
31229863 TTGTTAATTTTCTTATTATTTTAAAGGTAT
1 TTGTTAATTTTCTTATTATTTTAAAGGCAT
* *
31229893 TTGTTAATTTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTCTTATTATTTTAAAGGCAT
31229923 TTG
1 TTG
31229926 CTTGTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.03, G:0.13, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAAAGGCAT
Found at i:31230401 original size:21 final size:21
Alignment explanation
Indices: 31230366--31230422 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
31230356 AAGGTTATAC
31230366 ATTTTTATGTTAAATAAATAATT
1 ATTTTTA--TTAAATAAATAATT
* * *
31230389 ATTTTTATTAAATTAGTATTT
1 ATTTTTATTAAATAAATAATT
*
31230410 GTTTTTATTAAAT
1 ATTTTTATTAAAT
31230423 GATATGTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 23 0.77
23 7 0.23
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (21 bp):
ATTTTTATTAAATAAATAATT
Found at i:31232016 original size:15 final size:15
Alignment explanation
Indices: 31231996--31232040 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
31231986 ATATATTATA
31231996 TAATAATTATAAATT
1 TAATAATTATAAATT
31232011 TAATAATTATGAAAATT
1 TAATAATTAT--AAATT
* *
31232028 TTATTATTATAAA
1 TAATAATTATAAA
31232041 AATGACATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 13 0.50
17 13 0.50
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
TAATAATTATAAATT
Found at i:31232028 original size:17 final size:16
Alignment explanation
Indices: 31231996--31232041 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
31231986 ATATATTATA
31231996 TAATAATTAT-AAATT
1 TAATAATTATAAAATT
31232011 TAATAATTATGAAAATT
1 TAATAATTAT-AAAATT
* *
31232028 TTATTATTATAAAA
1 TAATAATTATAAAA
31232042 ATGACATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 10 0.37
16 4 0.15
17 13 0.48
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
TAATAATTATAAAATT
Found at i:31232116 original size:18 final size:19
Alignment explanation
Indices: 31232080--31232117 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
31232070 GATCTAATAA
* *
31232080 ATATATGTAAACTTTTTTT
1 ATATATGTAAACGTATTTT
31232099 ATATAT-TAAACGTATTTT
1 ATATATGTAAACGTATTTT
31232117 A
1 A
31232118 ATTATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (19 bp):
ATATATGTAAACGTATTTT
Found at i:31235538 original size:14 final size:15
Alignment explanation
Indices: 31235519--31235547 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31235509 TCATGCTAGG
31235519 TCATATCAAA-CATA
1 TCATATCAAATCATA
31235533 TCATATCAAATCATA
1 TCATATCAAATCATA
31235548 ACATGCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (15 bp):
TCATATCAAATCATA
Found at i:31238007 original size:68 final size:68
Alignment explanation
Indices: 31237914--31238062 Score: 201
Period size: 68 Copynumber: 2.2 Consensus size: 68
31237904 ACATGGGCCA
* * * * * **
31237914 CTCATACGGTTTGAACATTTCCACAC-GGCTGTGTGCCTCACACGGTCTAGCCACACGGGTTGTT
1 CTCACACGGTCTGAACATTTCCACACAGTC-GTGTGCCTCACACAGTCTAGCCACACGGGCTACT
31237978 TATT
65 TATT
*
31237982 CTCACACGGTCTGAACATTTTCACACAGTCGTGTGCCTCACACAGTCTAGCCACACGGGCTACTT
1 CTCACACGGTCTGAACATTTCCACACAGTCGTGTGCCTCACACAGTCTAGCCACACGGGCTACTT
31238047 ATT
66 ATT
*
31238050 CTCACACAGTCTG
1 CTCACACGGTCTG
31238063 CAAAACCTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
68 69 0.97
69 2 0.03
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.28
Consensus pattern (68 bp):
CTCACACGGTCTGAACATTTCCACACAGTCGTGTGCCTCACACAGTCTAGCCACACGGGCTACTT
ATT
Found at i:31238091 original size:68 final size:68
Alignment explanation
Indices: 31237935--31238083 Score: 183
Period size: 68 Copynumber: 2.2 Consensus size: 68
31237925 TGAACATTTC
* * * ** * * *
31237935 CACACGGCTGTGTGCCTCACACGGTCTAGCCACACGGGTTGTTTATTCTCACACGGTCTGAACAT
1 CACACGGTTGTGTGCCTCACACAGTCTAGCCACACGGGCTACTTATTCTCACACAGTCTGAAAAC
*
31238000 TTT
66 CTT
* *
31238003 CACACAGTCGTGTGCCTCACACAGTCTAGCCACACGGGCTACTTATTCTCACACAGTCTGCAAAA
1 CACACGGTTGTGTGCCTCACACAGTCTAGCCACACGGGCTACTTATTCTCACACAGTCTG-AAAA
31238068 CCTT
65 CCTT
31238072 -ACACGGTTGTGT
1 CACACGGTTGTGT
31238084 ATCTCACAAG
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
68 62 0.93
69 5 0.07
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (68 bp):
CACACGGTTGTGTGCCTCACACAGTCTAGCCACACGGGCTACTTATTCTCACACAGTCTGAAAAC
CTT
Found at i:31241869 original size:30 final size:31
Alignment explanation
Indices: 31241809--31241870 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
31241799 TTATTTAATT
*
31241809 AATTATCATCTTTTATTTTTTTTCACTTTCC
1 AATTATCATCTTTTATTTATTTTCACTTTCC
* *
31241840 AATT-TCATCATTTTCTTTATTTT-ATTTTCC
1 AATTATCATC-TTTTATTTATTTTCACTTTCC
31241870 A
1 A
31241871 TGGATGAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (31 bp):
AATTATCATCTTTTATTTATTTTCACTTTCC
Found at i:31242749 original size:3 final size:3
Alignment explanation
Indices: 31242741--31242798 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
31242731 GATAGTATGT
31242741 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31242789 TTA TTA TTA T
1 TTA TTA TTA T
31242799 ATGCATGTCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:31243260 original size:53 final size:52
Alignment explanation
Indices: 31243160--31243259 Score: 148
Period size: 53 Copynumber: 1.9 Consensus size: 52
31243150 TTTTTTACTA
*
31243160 TTTTTGGTGCCACCTCCTTTAATGAAGGCACCTAATTGGATTAAAAAATTAT
1 TTTTTGGTGCCACCTCCTTTAATGAAGGCACCTAATTGGATAAAAAAATTAT
* * *
31243212 TTTTTGGTGCCAGCCTCCTTTAATGGAGGCACCTATTTTG-TAAAAAAA
1 TTTTTGGTGCCA-CCTCCTTTAATGAAGGCACCTAATTGGATAAAAAAA
31243260 AAAATCTCCC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 19 0.44
53 24 0.56
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
TTTTTGGTGCCACCTCCTTTAATGAAGGCACCTAATTGGATAAAAAAATTAT
Found at i:31244230 original size:20 final size:20
Alignment explanation
Indices: 31244205--31244250 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
31244195 GAAGAAACAG
31244205 GACAAGGCTCCAAGGCGTGT
1 GACAAGGCTCCAAGGCGTGT
31244225 GACAAGGCTCCAAGGCGTGT
1 GACAAGGCTCCAAGGCGTGT
*
31244245 AACAAG
1 GACAAG
31244251 CCACTATCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.24, G:0.33, T:0.13
Consensus pattern (20 bp):
GACAAGGCTCCAAGGCGTGT
Found at i:31244847 original size:39 final size:39
Alignment explanation
Indices: 31244772--31244858 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 39
31244762 GAAACACTAT
*
31244772 AAATATTTGAAAATGTTCCAACAACCTCCCCTCATTTTC
1 AAATATTTGAAAATGTTCCAACAACCTCACCTCATTTTC
* *
31244811 AAATATTTGAAAATGTTCCAACAATCTTCACC-CATTTTG
1 AAATATTTGAAAATGTTCCAACAA-CCTCACCTCATTTTC
31244850 AAATTATTT
1 AAA-TATTT
31244859 TAGATTTTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 33 0.77
40 10 0.23
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.37
Consensus pattern (39 bp):
AAATATTTGAAAATGTTCCAACAACCTCACCTCATTTTC
Found at i:31245847 original size:27 final size:28
Alignment explanation
Indices: 31245817--31245872 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
31245807 TATGTTCCCA
31245817 TTGATGAATAAATGAT-AAT-TTTGATGT
1 TTGATG-ATAAATGATGAATATTTGATGT
* *
31245844 TTGATGATAGATTATGAATATTTGATGT
1 TTGATGATAAATGATGAATATTTGATGT
31245872 T
1 T
31245873 AGATAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.28
27 9 0.36
28 9 0.36
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (28 bp):
TTGATGATAAATGATGAATATTTGATGT
Found at i:31246403 original size:40 final size:39
Alignment explanation
Indices: 31246359--31246508 Score: 192
Period size: 39 Copynumber: 3.7 Consensus size: 39
31246349 TTGACGACAA
31246359 TTCGGCTATGTATGGCACTTAGTGTGCGATTTGAGATAGC
1 TTCGGCTATGTATGGCACTTAGTGTGCGA-TTGAGATAGC
* *
31246399 TTCGGTTATGTATGGCACTTAGTGTGTGATTGAGATAGC
1 TTCGGCTATGTATGGCACTTAGTGTGCGATTGAGATAGC
* * * * *
31246438 TTTGGCTATGTATGGCATTTAGTGTACAGGATTAAAATAGC
1 TTCGGCTATGTATGGCACTTAGTGTGC--GATTGAGATAGC
*
31246479 TTCGACTATGTATTGGCACTTAGTGTGCGA
1 TTCGGCTATGTA-TGGCACTTAGTGTGCGA
31246509 AAATTTGAGT
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 32 0.34
40 29 0.31
41 20 0.21
42 13 0.14
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.37
Consensus pattern (39 bp):
TTCGGCTATGTATGGCACTTAGTGTGCGATTGAGATAGC
Found at i:31247979 original size:13 final size:13
Alignment explanation
Indices: 31247961--31247986 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31247951 TTTATCCTCA
31247961 CTTTTGTTATTAT
1 CTTTTGTTATTAT
31247974 CTTTTGTTATTAT
1 CTTTTGTTATTAT
31247987 TTATTTAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
CTTTTGTTATTAT
Found at i:31248209 original size:21 final size:21
Alignment explanation
Indices: 31248159--31248213 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
31248149 TTAGTTTTTT
*
31248159 CTTATTATTTTTATTTATTGG
1 CTTATTATTTTTATTTATTGC
* *
31248180 CTTGTTTATTTTTA-TTCTTGCC
1 CTT-ATTATTTTTATTTATTG-C
31248202 CTTATTATTTTT
1 CTTATTATTTTT
31248214 TCTTATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.15, C:0.11, G:0.07, T:0.67
Consensus pattern (21 bp):
CTTATTATTTTTATTTATTGC
Found at i:31248321 original size:19 final size:17
Alignment explanation
Indices: 31248280--31248327 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
31248270 ATTGCTATTT
31248280 ATATTATCATTTTCATC
1 ATATTATCATTTTCATC
*
31248297 ATTATTATTATTGTTCATGC
1 A-TATTATCATT-TTCAT-C
*
31248317 ATATTAACATT
1 ATATTATCATT
31248328 ATGATTTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 9 0.36
19 13 0.52
20 2 0.08
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.52
Consensus pattern (17 bp):
ATATTATCATTTTCATC
Found at i:31251111 original size:8 final size:8
Alignment explanation
Indices: 31251096--31251133 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
31251086 GAAATACTGA
31251096 CTTTTCGG
1 CTTTTCGG
*
31251104 CATTTCGG
1 CTTTTCGG
31251112 CTTTTCGG
1 CTTTTCGG
31251120 CTTTTCGG
1 CTTTTCGG
31251128 CTTTTC
1 CTTTTC
31251134 ATCTTTTGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.03, C:0.26, G:0.21, T:0.50
Consensus pattern (8 bp):
CTTTTCGG
Found at i:31251139 original size:16 final size:16
Alignment explanation
Indices: 31251096--31251140 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
31251086 GAAATACTGA
* *
31251096 CTTTTCGGCATTTCGG
1 CTTTTCAGCTTTTCGG
*
31251112 CTTTTCGGCTTTTCGG
1 CTTTTCAGCTTTTCGG
*
31251128 CTTTTCATCTTTT
1 CTTTTCAGCTTTT
31251141 GCCAATCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.04, C:0.24, G:0.18, T:0.53
Consensus pattern (16 bp):
CTTTTCAGCTTTTCGG
Found at i:31260970 original size:1 final size:1
Alignment explanation
Indices: 31260964--31261026 Score: 54
Period size: 1 Copynumber: 63.0 Consensus size: 1
31260954 ATTTCACCTT
* * * * * * * *
31260964 AAAAAAATAAAAAAAAAGAAAAAAAGAAAAAAAGAAAAGAAAAACAAAAAGAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31261027 GAAATAAAAG
Statistics
Matches: 46, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.87, C:0.02, G:0.08, T:0.03
Consensus pattern (1 bp):
A
Found at i:31260987 original size:12 final size:12
Alignment explanation
Indices: 31260964--31261074 Score: 105
Period size: 13 Copynumber: 8.4 Consensus size: 12
31260954 ATTTCACCTT
*
31260964 AAAAAAATAAAAA
1 AAAAAAA-AAAAG
31260977 AAAAGAAAAAAAG
1 AAAA-AAAAAAAG
31260990 AAAAAAAGAAAAG
1 AAAAAAA-AAAAG
*
31261003 AAAAACAAAAAG
1 AAAAAAAAAAAG
31261015 AAAATAAAAAAAG
1 AAAA-AAAAAAAG
31261028 AAATAAAAGGAAAAG
1 AAA-AAAA--AAAAG
31261043 AAAAAGCAAAAAAG
1 AAAAA--AAAAAAG
*
31261057 AAAAACAAAAGAG
1 AAAAA-AAAAAAG
31261070 AAAAA
1 AAAAA
31261075 GGAGAAACCA
Statistics
Matches: 86, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
12 12 0.14
13 48 0.56
14 16 0.19
15 8 0.09
16 2 0.02
ACGTcount: A:0.83, C:0.03, G:0.12, T:0.03
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:31261056 original size:8 final size:7
Alignment explanation
Indices: 31260975--31261074 Score: 61
Period size: 6 Copynumber: 14.7 Consensus size: 7
31260965 AAAAAATAAA
31260975 AAAAAAG
1 AAAAAAG
31260982 AAAAAAAG
1 -AAAAAAG
31260990 AAAAAA-
1 AAAAAAG
*
31260996 AGAAAAG
1 AAAAAAG
31261003 -AAAAA-
1 AAAAAAG
*
31261008 CAAAAAG
1 AAAAAAG
*
31261015 AAAATA-
1 AAAAAAG
31261021 AAAAAAG
1 AAAAAAG
31261028 AAATAAA-
1 AAA-AAAG
*
31261035 AGGAAAAG
1 A-AAAAAG
31261043 -AAAAAG
1 AAAAAAG
31261049 CAAAAAAG
1 -AAAAAAG
*
31261057 -AAAAAC
1 AAAAAAG
*
31261063 AAAAGAG
1 AAAAAAG
31261070 AAAAA
1 AAAAA
31261075 GGAGAAACCA
Statistics
Matches: 71, Mismatches: 11, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
6 29 0.41
7 25 0.35
8 17 0.24
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:31261082 original size:20 final size:19
Alignment explanation
Indices: 31260984--31261082 Score: 58
Period size: 19 Copynumber: 5.0 Consensus size: 19
31260974 AAAAAAAGAA
* * *
31260984 AAAAAGAAAAAAAGAAAAG
1 AAAAAGCAAAAAGGAAAAC
* *
31261003 AAAAA-CAAAAAGAAAATAA
1 AAAAAGCAAAAAGGAAA-AC
* *
31261022 AAAAAGAAATAAAAGGAAAAG
1 AAAAAG-CA-AAAAGGAAAAC
*
31261043 AAAAAGCAAAAAAGAAAAAC
1 AAAAAGC-AAAAAGGAAAAC
31261063 AAAAGAG-AAAAAGGAGAAAC
1 AAAA-AGCAAAAAGGA-AAAC
31261083 CAAGGCAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
18 8 0.13
19 18 0.29
20 17 0.27
21 11 0.18
22 8 0.13
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (19 bp):
AAAAAGCAAAAAGGAAAAC
Found at i:31261934 original size:30 final size:30
Alignment explanation
Indices: 31261898--31261959 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
31261888 AAGATAAGAT
31261898 ATTGTGTCAATGATAGAATCTTGATGAACA
1 ATTGTGTCAATGATAGAATCTTGATGAACA
31261928 ATTGTGTCAATGATAGAATCTTGATGAACA
1 ATTGTGTCAATGATAGAATCTTGATGAACA
31261958 AT
1 AT
31261960 GAGCAATGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (30 bp):
ATTGTGTCAATGATAGAATCTTGATGAACA
Found at i:31262224 original size:20 final size:20
Alignment explanation
Indices: 31262199--31262247 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
31262189 GTGGAGCAAA
31262199 TTGAAGTTGTAGATATCTCC
1 TTGAAGTTGTAGATATCTCC
31262219 TTGAAGTTGTAGATATCTCC
1 TTGAAGTTGTAGATATCTCC
*
31262239 TTGAGGTTG
1 TTGAAGTTG
31262248 CAATGGAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.41
Consensus pattern (20 bp):
TTGAAGTTGTAGATATCTCC
Found at i:31262445 original size:143 final size:143
Alignment explanation
Indices: 31262266--31262944 Score: 921
Period size: 143 Copynumber: 4.7 Consensus size: 143
31262256 TAGATCAAAG
* *
31262266 ATGGCAGATCTTATATTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAACCTTATCTCCCTG
1 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTG
* *
31262331 AACTTGCAGCGGAGCAGACTGAAGACAACGAATCTCATTTCCTTAACGTTGCAGTGGAATAGATT
66 AAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCTTAACGTTGCAGTGGAATAGATT
*
31262396 AAAGTTACAAATT
131 AAAGCTACAAATT
* * * *
31262409 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGCCACCCGCCTTATCTGCCTA
1 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTG
* * * * * * * *
31262474 AAGTTGCAACAGAGCAAACTGAAGACAACGAATCTTATTTCCTTGACATTGTAGTGGAACATATT
66 AAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCTTAACGTTGCAGTGGAATAGATT
31262539 AAAGCTACAAATT
131 AAAGCTACAAATT
* * * *
31262552 ATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAACAGATTGAAGCCACCACCCTTATCTCCTTG
1 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTG
* * * ** * * *
31262617 AAGTTGTAGTGGAGCAGACTAAAGACAGTGAATCTTATTTCCCTAATGTTGCAGTGGAATAGGTT
66 AAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCTTAACGTTGCAGTGGAATAGATT
*
31262682 AAAGTTACAAATT
131 AAAGCTACAAATT
* *
31262695 ATGGCGGATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCT-CCTA
1 ATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCT-
* * * *
31262759 GAATTTGCAGCGGAGCAGACTGAAGATAGCGAATCTTATTTCCTTGACGTTGCAGTGGAATAGAT
65 GAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCTTAACGTTGCAGTGGAATAGAT
31262824 TAAAGCTACAAATT
130 TAAAGCTACAAATT
* * *
31262838 ATGG-TGACTTTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACCAGCCTTATCTCCCT
1 ATGGCAGA-TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCT
* * * * **
31262902 AAAGTTGTAGCAGAGCAGACTGAAGATAGTGAATCTTATTTCC
65 GAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCC
31262945 CTAAAGTTCT
Statistics
Matches: 467, Mismatches: 66, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
142 4 0.01
143 460 0.99
144 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (143 bp):
ATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTG
AAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCTTAACGTTGCAGTGGAATAGATT
AAAGCTACAAATT
Found at i:31263400 original size:25 final size:25
Alignment explanation
Indices: 31263370--31263425 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
31263360 CCAAAACCCA
31263370 GCCCAAAAAATACAAAGCCCAAATG
1 GCCCAAAAAATACAAAGCCCAAATG
*
31263395 GCCCAAAAAATACAAGGCCCAAATG
1 GCCCAAAAAATACAAAGCCCAAATG
31263420 GCCCAA
1 GCCCAA
31263426 CAACTAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.48, C:0.30, G:0.14, T:0.07
Consensus pattern (25 bp):
GCCCAAAAAATACAAAGCCCAAATG
Found at i:31268205 original size:21 final size:17
Alignment explanation
Indices: 31268159--31268193 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
31268149 CGTGTGGACT
31268159 GCCTGTGTGCGACACAC
1 GCCTGTGTGCGACACAC
31268176 GCCTGTGTGCGACACAC
1 GCCTGTGTGCGACACAC
31268193 G
1 G
31268194 GCTACCTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.17
Consensus pattern (17 bp):
GCCTGTGTGCGACACAC
Found at i:31280580 original size:17 final size:17
Alignment explanation
Indices: 31280537--31280582 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
31280527 GGGCTTATAC
31280537 AAAAACCAAAA-AACAA
1 AAAAACCAAAATAACAA
* *
31280553 AATAAATCAAAATAATAA
1 AA-AAACCAAAATAACAA
31280571 AAAAACCAAAAT
1 AAAAACCAAAAT
31280583 TAAAGTCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 2 0.08
17 17 0.68
18 6 0.24
ACGTcount: A:0.76, C:0.13, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAAACCAAAATAACAA
Found at i:31281757 original size:24 final size:25
Alignment explanation
Indices: 31281733--31281816 Score: 75
Period size: 26 Copynumber: 3.3 Consensus size: 25
31281723 TTTCATTATT
31281733 TTTTTTAAAGATCCATTTCACATTTA
1 TTTTTTAAAGATCCATTTCACA-TTA
* * **
31281759 TTTTTT--A-ATTCTTGTTTTCATTA
1 TTTTTTAAAGATCCAT-TTCACATTA
31281782 TTTTTTCAAAGATCCATTTCACATTCA
1 TTTTTT-AAAGATCCATTTCACATT-A
31281809 TTTTTTAA
1 TTTTTTAA
31281817 TTCTTATTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
23 13 0.30
24 5 0.11
26 15 0.34
27 11 0.25
ACGTcount: A:0.26, C:0.14, G:0.04, T:0.56
Consensus pattern (25 bp):
TTTTTTAAAGATCCATTTCACATTA
Found at i:31281785 original size:51 final size:51
Alignment explanation
Indices: 31281722--31281835 Score: 178
Period size: 50 Copynumber: 2.3 Consensus size: 51
31281712 ATTGAGTTTT
* * *
31281722 TTTTCATTATTTTTTTTAAAGATCCATTTCACATTTATTTTTTAATTCTTG
1 TTTTCATTATTTTTTTCAAAGATCCATTTCACATTCATTTTTTAATTCTTA
31281773 TTTTCATTA-TTTTTTCAAAGATCCATTTCACATTCATTTTTTAATTCTTA
1 TTTTCATTATTTTTTTCAAAGATCCATTTCACATTCATTTTTTAATTCTTA
*
31281823 TTTAC-TTATTTTT
1 TTTTCATTATTTTT
31281836 ATATTTTGAG
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
49 3 0.05
50 46 0.79
51 9 0.16
ACGTcount: A:0.24, C:0.13, G:0.03, T:0.61
Consensus pattern (51 bp):
TTTTCATTATTTTTTTCAAAGATCCATTTCACATTCATTTTTTAATTCTTA
Found at i:31290228 original size:23 final size:23
Alignment explanation
Indices: 31290195--31290310 Score: 83
Period size: 23 Copynumber: 5.0 Consensus size: 23
31290185 CCAAAATACA
31290195 GCTCTTCGTGAGCTTCCCGATAG
1 GCTCTTCGTGAGCTTCCCGATAG
* * *
31290218 GCTCTTTGTGAGCCTCCCTATAG
1 GCTCTTCGTGAGCTTCCCGATAG
* * * *
31290241 TGCTC-GCTTGAACTTCTCGATATATG
1 -GCTCTTCGTGAGCTTCCCG--ATA-G
* * *
31290267 GCTATCCG-GAGCTTCCCAATAG
1 GCTCTTCGTGAGCTTCCCGATAG
*
31290289 GCTCTTCGTGAGCTTCACGATA
1 GCTCTTCGTGAGCTTCCCGATA
31290311 TGGTTCTTTG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
22 7 0.10
23 41 0.61
24 4 0.06
25 13 0.19
26 2 0.03
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.32
Consensus pattern (23 bp):
GCTCTTCGTGAGCTTCCCGATAG
Found at i:31290754 original size:46 final size:46
Alignment explanation
Indices: 31290697--31290832 Score: 175
Period size: 46 Copynumber: 3.0 Consensus size: 46
31290687 AGTGTGCTCT
31290697 CTGAAATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGAAATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
31290743 CTGATATGAAATGTGTAAGACCATGGCTGAAAGATACCATGGCAAC
1 CTGAAATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *** * *
31290789 ATGACA-GAAAACAAGTAAGACCATAGTTGAAAGATACTATGGCA
1 CTGAAATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
31290833 TCATGTCAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
45 1 0.01
46 78 0.99
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
CTGAAATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:31290962 original size:13 final size:13
Alignment explanation
Indices: 31290920--31290963 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
31290910 ACCAGATGAC
31290920 AAATGGTTATATG
1 AAATGGTTATATG
* **
31290933 AATTGGTTATACA
1 AAATGGTTATATG
*
31290946 AAATGGTTATGTG
1 AAATGGTTATATG
31290959 AAATG
1 AAATG
31290964 TTTACAGGAA
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:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (13 bp):
AAATGGTTATATG
Found at i:31299865 original size:28 final size:28
Alignment explanation
Indices: 31299811--31299873 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
31299801 AAAGGCATCC
31299811 AAAAAGAAAAACAAAAGTACAAAAATAGA
1 AAAAAGAAAAACAAAAG-ACAAAAATAGA
**
31299840 AAAAAGAAAAGGAAAAG-CAAACAATAGA
1 AAAAAGAAAAACAAAAGACAAA-AATAGA
*
31299868 ACAAAG
1 AAAAAG
31299874 GTCATAGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 4 0.13
28 11 0.37
29 15 0.50
ACGTcount: A:0.73, C:0.08, G:0.14, T:0.05
Consensus pattern (28 bp):
AAAAAGAAAAACAAAAGACAAAAATAGA
Found at i:31301643 original size:67 final size:64
Alignment explanation
Indices: 31301478--31301653 Score: 210
Period size: 64 Copynumber: 2.7 Consensus size: 64
31301468 ATAAATCTCG
* * *
31301478 CATCTAGTTAGGAGCATTTGATTCATTTTGATTATAGTATCCTAATTATTTGACATAAGCATTA
1 CATCTAGTTAAGAGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCATTA
* * * **
31301542 CCTCTAGTTAAGAGCATTTGATTCATTTCGATCATAGCGTCCTAATTATTTGACATCACTCATAT
1 CATCTAGTTAAGAGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACAT-AAGCAT-T
31301607 A
64 A
* * *
31301608 TCATTTAGTTAAGAGCATTTGATT-ATTTTTTATCATGGCATCCTAA
1 -CATCTAGTTAAGAGCATTTGATTCA-TTTTGATCATAGCATCCTAA
31301654 CTAGTTGGCA
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
64 50 0.53
65 4 0.04
66 3 0.03
67 37 0.39
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (64 bp):
CATCTAGTTAAGAGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCATTA
Found at i:31302019 original size:133 final size:133
Alignment explanation
Indices: 31301869--31302125 Score: 390
Period size: 133 Copynumber: 1.9 Consensus size: 133
31301859 TTAAAAGTTG
*
31301869 AGTCTTATCTTCCTGAGGTAGGAAGGAAGCAGACT-GAAGATTGAAGATCTTACCTCCCTAAGCA
1 AGTCTTATCTTCCTGAGGTAGGAAGAAAGCAGACTGGAA-ATTGAAGATCTTACCTCCCTAAGCA
* *
31301933 GTAGTGGAGCAGATCGAAGATAGTGAATCTTATCTCCATGTATCGACAATGGAGTAGATTGGCGA
65 GTAGTGGAGCAGATCGAAGATAGCGAATCTTATCTCCATGTATCGACAATGGAGCAGATTGGCGA
31301998 TTGT
130 TTGT
* * * *
31302002 AGTCTTATCTTCCTGAGGTAGGAAGAAAGCAGACTGGAATTTGTAGATCTTATCTCCCTAGGCAG
1 AGTCTTATCTTCCTGAGGTAGGAAGAAAGCAGACTGGAAATTGAAGATCTTACCTCCCTAAGCAG
* * * * *
31302067 TAGTGGGGCAGATTGATGATGGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATT
66 TAGTGGAGCAGATCGAAGATAGCGAATCTTATCTCCATGTATCGACAATGGAGCAGATT
31302126 TTAGCCACTG
Statistics
Matches: 111, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
133 108 0.97
134 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (133 bp):
AGTCTTATCTTCCTGAGGTAGGAAGAAAGCAGACTGGAAATTGAAGATCTTACCTCCCTAAGCAG
TAGTGGAGCAGATCGAAGATAGCGAATCTTATCTCCATGTATCGACAATGGAGCAGATTGGCGAT
TGT
Found at i:31302143 original size:133 final size:132
Alignment explanation
Indices: 31301872--31302185 Score: 359
Period size: 133 Copynumber: 2.4 Consensus size: 132
31301862 AAAGTTGAGT
*
31301872 CTTATCTTCCTGAGGTAGGAAGGAAGCAGACTGAAGATTGAAGATCTTACCTCCCTAAGCAGTAG
1 CTTATCTTCCTGAGGTAGGAAGAAAGCAGACTGAAGATTGAAGATCTTACCTCCCTAAGCAGTAG
* * * * *
31301937 TGGAGCAGATCGAAGATAGTGAATCTTATCTCCATGTATCGACAATGGAGTAGATTGGCGATTGT
66 TGGAGCAGATCGAAGATAGCGAATCTTATCTCCATGTATCGACAATGGAGCAGATTAGCCACTGT
31302002 AG
131 AG
* * * *
31302004 TCTTATCTTCCTGAGGTAGGAAGAAAGCAGACTGGAA-TTTGTAGATCTTATCTCCCTAGGCAGT
1 -CTTATCTTCCTGAGGTAGGAAGAAAGCAGACT-GAAGATTGAAGATCTTACCTCCCTAAGCAGT
* * * * *
31302068 AGTGGGGCAGATTGATGATGGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTTAGCCA
64 AGTGGAGCAGATCGAAGATAGCGAATCTTATCTCCATGTATCGACAATGGAGCAGA--TTAGCCA
31302133 CTG-A-
127 CTGTAG
* * * **
31302137 CATTATC-TCTCTAAGGTAGCAAGAGAGCAGGTTGAAGATTGAAG-TCTTA
1 C-TTATCTTC-CTGAGGTAGGAAGAAAGCAGACTGAAGATTGAAGATCTTA
31302186 TCTTCTTGAG
Statistics
Matches: 153, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
132 11 0.07
133 131 0.86
134 4 0.03
135 7 0.05
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (132 bp):
CTTATCTTCCTGAGGTAGGAAGAAAGCAGACTGAAGATTGAAGATCTTACCTCCCTAAGCAGTAG
TGGAGCAGATCGAAGATAGCGAATCTTATCTCCATGTATCGACAATGGAGCAGATTAGCCACTGT
AG
Found at i:31302553 original size:177 final size:176
Alignment explanation
Indices: 31302238--31303157 Score: 850
Period size: 176 Copynumber: 5.2 Consensus size: 176
31302228 GGAAGAGGCA
* * *
31302238 AATCTTATCTCCATGTATCGGCAATGGAGTAGATTTAAGCCCCAAACCTTATCTCTCTGAGGTAG
1 AATCTTATCTCCATGTATCGGCAATGGAGCAGATTTAAGCCACTAACCTTATCTCTCTGAGGTAG
* * * * * * * *
31302303 TAAGAGAGCATGTTGAAG-ATTGATGTCTTATCTTCTTGAGGTTGTAGTGGAA-CAGACTGAAAA
66 CAAGAGAGCAAGTTGAAGAAATGA-GTCTTATCTTCCTGAGGTAGCA--AGAAGCAGACTGAAGA
* * *
31302366 TCACAGATCTTATCTCCCTAAGCAGTAGCAGAACAGATTGAAAATGGTG
128 TTAAAGATCTTATCTCCCTAAGCAGTAGCAGAACAGATCGAAAATGGTG
* * * * *
31302415 AATCTTATCTCCATGTATTGGCAATGGAGCAGATTTTAGCCACTGACCTTATCTCTTTGAGGTAA
1 AATCTTATCTCCATGTATCGGCAATGGAGCAGATTTAAGCCACTAACCTTATCTCTCTGAGGTAG
* * * *
31302480 CAAGAGAGTAGGTTGAAGATAAT-AGTCTTATCTTCCTGAGGTAGCAATGAAGTAGACTAAAGAT
66 CAAGAGAGCAAGTTGAAGA-AATGAGTCTTATCTTCCTGAGGTAGCAA-GAAGCAGACTGAAGAT
* * * * ** *
31302544 TAAAGATCTTATCTCCTTAAGCAGTAGCGGAGCAGATCCAGGATGGCG
129 TAAAGATCTTATCTCCCTAAGCAGTAGCAGAACAGATCGAAAATGGTG
* * * *
31302592 AATCTTATCTCCATGTATTGGCAATGGAGCAGATTGAAGCC-CCAAGCCTTATCTCTCTGGGGTA
1 AATCTTATCTCCATGTATCGGCAATGGAGCAGATTTAAGCCACTAA-CCTTATCTCTCTGAGGTA
* * * *
31302656 GCAATAGAGAAAGTTAAAG-AATGAGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGACTGAAGAT
65 GCAAGAGAGCAAGTTGAAGAAATGAGTCTTATCTTCCTGAGGTAGCAAG-AAGCAGACTGAAGAT
* * * ** *
31302720 TAAAGATCTTATCTCCCT--CCACTTGCAGAGGAGTGGATCGAATATGGTG
129 TAAAGATCTTATCTCCCTAAGCAGTAGCAGA--A-CAGATCGAAAATGGTG
* * * * * *
31302769 AATTTTATCTCCATGTATCGGCAATGGAGAAGATTTTA-CCACCT-GCCTTACCTCTTTGAGGTA
1 AATCTTATCTCCATGTATCGGCAATGGAGCAGATTTAAGCCA-CTAACCTTATCTCTCTGAGGTA
* *
31302832 GCAAGAGAGCAAGTTGAAG-AATGAGTCTTATCTTTCTGAGGTAGTAAGAAAGCAGACTGAAGAT
65 GCAAGAGAGCAAGTTGAAGAAATGAGTCTTATCTTCCTGAGGTAGCAAG-AAGCAGACTGAAGAT
* * * * ** * **
31302896 TGAAGATCTTATCTCCTTGAAGCTGCAGTGGAGCAGATAAAAAATGGTG
129 TAAAGATCTTATCTCCCT-AAGCAGTAGCAGAACAGATCGAAAATGGTG
* * *
31302945 AATCTTATCTCCATGTATCGGCAATGGAGCAGACTTT-A-TCACCAGCCTTATCTCTCTGAGGTA
1 AATCTTATCTCCATGTATCGGCAATGGAGCAGA-TTTAAGCCACTAACCTTATCTCTCTGAGGTA
* * * * * *
31303008 GCAAGAGAACAAATTGAAG-AATAAGTCTTATCTTCCTGAGGTAACAAGGGAGCAGACTGAATAT
65 GCAAGAGAGCAAGTTGAAGAAATGAGTCTTATCTTCCTGAGGTAGCAA-GAAGCAGACTGAAGAT
* * * * * * * **
31303072 TGAAGATCTTATTTCCCTGAG--GTTGCAG--TAGATCGAAGAGGGCA
129 TAAAGATCTTATCTCCCTAAGCAGTAGCAGAACAGATCGAAAATGGTG
*
31303116 AATCTTATCTCCATGTA-CATGCAATGGAGCAGATTTAAGCCA
1 AATCTTATCTCCATGTATC-GGCAATGGAGCAGATTTAAGCCA
31303158 GTCTTATCTC
Statistics
Matches: 608, Mismatches: 114, Indels: 47
0.79 0.15 0.06
Matches are distributed among these distances:
170 4 0.01
171 40 0.07
172 2 0.00
173 3 0.00
174 7 0.01
175 7 0.01
176 283 0.47
177 254 0.42
178 2 0.00
179 6 0.01
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (176 bp):
AATCTTATCTCCATGTATCGGCAATGGAGCAGATTTAAGCCACTAACCTTATCTCTCTGAGGTAG
CAAGAGAGCAAGTTGAAGAAATGAGTCTTATCTTCCTGAGGTAGCAAGAAGCAGACTGAAGATTA
AAGATCTTATCTCCCTAAGCAGTAGCAGAACAGATCGAAAATGGTG
Found at i:31303317 original size:13 final size:13
Alignment explanation
Indices: 31303299--31303341 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
31303289 GGCCCACAAC
31303299 CAAAAAAATAAAA
1 CAAAAAAATAAAA
31303312 CAAAAAAAT-AAA
1 CAAAAAAATAAAA
*
31303324 -AATAAAATAAAA
1 CAAAAAAATAAAA
31303336 CCAAAA
1 -CAAAA
31303342 TAATTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 7 0.28
12 6 0.24
13 9 0.36
14 3 0.12
ACGTcount: A:0.81, C:0.09, G:0.00, T:0.09
Consensus pattern (13 bp):
CAAAAAAATAAAA
Done.