Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 179 of 410
Found at i:54743725 original size:9 final size:10
Alignment explanation
Indices: 54743718--54743774 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
54743708 AAGAGAAAAT
54743718 AAAGAAAAGA
1 AAAGAAAAGA
54743728 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
54743740 AAAGAAGA-A
1 AAAGAAAAGA
54743749 AAAGAAAATGA
1 AAAGAAAA-GA
54743760 AATA-AAAAGA
1 AA-AGAAAAGA
54743770 AAAGA
1 AAAGA
54743775 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:54743742 original size:6 final size:5
Alignment explanation
Indices: 54743718--54743774 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
54743708 AAGAGAAAAT
*
54743718 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
54743765 AAAGA AAAGA
1 AAAGA AAAGA
54743775 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:54743749 original size:15 final size:14
Alignment explanation
Indices: 54743718--54743774 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
54743708 AAGAGAAAAT
54743718 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
54743734 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
54743749 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
54743765 AAAGAAAAGA
1 AAAGAAAAGA
54743775 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:54743877 original size:30 final size:31
Alignment explanation
Indices: 54743843--54743924 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
54743833 TTTGAAAAGC
* *
54743843 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* *
54743873 AAAAAGAGAATG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
54743903 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
54743925 TGAAACAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.18
30 27 0.61
31 9 0.20
ACGTcount: A:0.66, C:0.00, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:54743897 original size:24 final size:24
Alignment explanation
Indices: 54743848--54743917 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
54743838 AAAGCAAAAA
*
54743848 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAATGAAATT
* *
54743872 GAAAAAGAGAATGAAAA-GAAATTT
1 GAAAAAGAAAAAGAAAATGAAA-TT
* ** *
54743896 GAGAGTGAAAAAGAAGATGAAA
1 GAAAAAGAAAAAGAAAATGAAA
54743918 AAGAAATTGA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
23 3 0.09
24 28 0.80
25 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.13
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAATGAAATT
Found at i:54753366 original size:40 final size:40
Alignment explanation
Indices: 54753281--54753431 Score: 132
Period size: 40 Copynumber: 3.8 Consensus size: 40
54753271 AATTGAATGA
* * * **
54753281 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTT
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACATAC
* * *
54753321 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
54753362 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
54753401 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
54753432 ACATGGTTAT
Statistics
Matches: 91, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 77 0.85
41 5 0.05
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:54753445 original size:40 final size:40
Alignment explanation
Indices: 54753321--54753447 Score: 132
Period size: 40 Copynumber: 3.2 Consensus size: 40
54753311 CTGGAAATTT
* * * * *
54753321 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGGTTA
* * ** *
54753361 CATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CATTC
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGGTTA
54753401 TATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGGTTA
54753441 TATCCGG
1 TATCCGG
54753448 TTATGTTCCG
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 67 0.97
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGGTTA
Found at i:54754917 original size:48 final size:47
Alignment explanation
Indices: 54754822--54754949 Score: 163
Period size: 47 Copynumber: 2.7 Consensus size: 47
54754812 ATCTCATAGT
*
54754822 CGATGCATGTCCCAGACATGTCTTACACTGGCT-TACATCTCGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTCTACATATCGAGGC
*
54754868 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTACAT-ATCGAGGC
* * *
54754916 CGATGCATGTCCTAGACATGTCTTATACTAGCTC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTC
54754950 ATGATAACCC
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
46 18 0.25
47 27 0.37
48 26 0.36
49 2 0.03
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (47 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTCTACATATCGAGGC
Found at i:54756792 original size:2 final size:2
Alignment explanation
Indices: 54756785--54756815 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54756775 TGATACATGG
54756785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54756816 AGGCTTCGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54757032 original size:56 final size:56
Alignment explanation
Indices: 54756826--54757000 Score: 296
Period size: 56 Copynumber: 3.1 Consensus size: 56
54756816 AGGCTTCGAT
* *
54756826 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTCTGCAA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGCGA
* *
54756882 GTAAGACCACGTTTAATACGTTGTCATCTATATGTGATTCTGATATATGTGTGCGA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGCGA
* *
54756938 GTAAGACCACATTCAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGCGA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGCGA
54756994 GTAAGAC
1 GTAAGAC
54757001 ATTGTTTGGG
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 111 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (56 bp):
GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGCGA
Found at i:54759381 original size:11 final size:11
Alignment explanation
Indices: 54759367--54759409 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
54759357 TCAAGTAAGT
54759367 TTCAAAAAAAA
1 TTCAAAAAAAA
54759378 TTCAAAAAAAA
1 TTCAAAAAAAA
*
54759389 ATCAAAAAAAA
1 TTCAAAAAAAA
*
54759400 GTTTAAAAAA
1 -TTCAAAAAA
54759410 TAGAAAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 21 0.75
12 7 0.25
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.19
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:54759387 original size:12 final size:12
Alignment explanation
Indices: 54759370--54759409 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
54759360 AGTAAGTTTC
54759370 AAAAAAAATTCA
1 AAAAAAAATTCA
54759382 AAAAAAAA-TCA
1 AAAAAAAATTCA
* *
54759393 AAAAAAAGTTTA
1 AAAAAAAATTCA
54759405 AAAAA
1 AAAAA
54759410 TAGAAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.15
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:54765848 original size:29 final size:29
Alignment explanation
Indices: 54765816--54765950 Score: 155
Period size: 29 Copynumber: 4.7 Consensus size: 29
54765806 ATACCCTCCG
** * *
54765816 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
* * * *
54765845 AGCTTGCACACATAGTGTCATATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
54765874 AGCAT-GCACACTTAGTGCCTTATATTTCC
1 AGC-TCGCACACTTAGTGCCATATATTTCC
*
54765903 AGCACGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
54765932 AGCACGCACACTTAGTGCC
1 AGCTCGCACACTTAGTGCC
54765951 GATCTCGTCA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 92 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.30
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCATATATTTCC
Found at i:54765883 original size:58 final size:58
Alignment explanation
Indices: 54765762--54765951 Score: 179
Period size: 58 Copynumber: 3.3 Consensus size: 58
54765752 TACTCGATTT
* * * *** *
54765762 CGCACACTTAGTGCCACGTA-ATTT-AAGCCCGCACACACAGTGCCATA-CCCTCCGAGCT
1 CGCACACTTAGTG-C-CGTATATTTCCAGCACGCACACATAGTGCCATATATTTCC-AGCA
** * ** * *
54765820 CGCACACCCAGTGCCGTATTTTTCCAGCTTGCACACATAGTGTCATATTTTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
* * *
54765878 TGCACACTTAGTGCCTTATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
54765936 CGCACACTTAGTGCCG
1 CGCACACTTAGTGCCG
54765952 ATCTCGTCAC
Statistics
Matches: 105, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
56 4 0.04
57 4 0.04
58 94 0.90
59 3 0.03
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.26
Consensus pattern (58 bp):
CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
Found at i:54773988 original size:29 final size:29
Alignment explanation
Indices: 54773956--54774056 Score: 157
Period size: 29 Copynumber: 3.5 Consensus size: 29
54773946 TTTTCCACTT
* * * *
54773956 GCACACATAGTGTCATATTTTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAC
*
54773985 GCACACTTAGTGCCTTATATTTCCAGCAC
1 GCACACTTAGTGCCATATATTTCCAGCAC
54774014 GCACACTTAGTGCCATATATTTCCAGCAC
1 GCACACTTAGTGCCATATATTTCCAGCAC
54774043 GCACACTTAGTGCC
1 GCACACTTAGTGCC
54774057 GATCTCGTCA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.30
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAC
Found at i:54774013 original size:25 final size:28
Alignment explanation
Indices: 54773927--54774056 Score: 134
Period size: 29 Copynumber: 4.5 Consensus size: 28
54773917 CCTCCGAGCT
** * * *
54773927 CGCACACCCAGTGCCGTATTTTTCCACT
1 CGCACACTTAGTGCCATATATTTCCACA
* * * *
54773955 TGCACACATAGTGTCATATTTTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCA-CA
* *
54773984 TGCACACTTAGTGCCTTATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCA-CA
54774013 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCA-CA
54774042 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
54774057 GATCTCGTCA
Statistics
Matches: 89, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
28 21 0.24
29 68 0.76
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTTCCACA
Found at i:54774461 original size:12 final size:12
Alignment explanation
Indices: 54774446--54774470 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54774436 CATTTGTCCA
54774446 TGCATTAGTTTT
1 TGCATTAGTTTT
54774458 TGCATTAGTTTT
1 TGCATTAGTTTT
54774470 T
1 T
54774471 AACACATTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TGCATTAGTTTT
Found at i:54777727 original size:29 final size:29
Alignment explanation
Indices: 54777687--54777784 Score: 108
Period size: 29 Copynumber: 3.4 Consensus size: 29
54777677 GGCCCGATCT
* *
54777687 CATTTATATGGCCTATCAGGCCCAATTCA
1 CATTCATATGGCCAATCAGGCCCAATTCA
* *
54777716 CATTCATATGGCCCATCAGGCCTAATTCA
1 CATTCATATGGCCAATCAGGCCCAATTCA
* * *
54777745 TATTCATAT-GCCAATTAGGCCCAAATCA
1 CATTCATATGGCCAATCAGGCCCAATTCA
* *
54777773 CCTTTATATGGC
1 CATTCATATGGC
54777785 TCGTTAGGTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 21 0.37
29 36 0.63
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.31
Consensus pattern (29 bp):
CATTCATATGGCCAATCAGGCCCAATTCA
Found at i:54782873 original size:18 final size:19
Alignment explanation
Indices: 54782837--54782885 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
54782827 CCTGCCCAGG
54782837 ACCCCTTGGTGGCATCTGACC
1 ACCCCTTGGTGG-A-CTGACC
*
54782858 ACCCCTTGGTGG-CTGAGC
1 ACCCCTTGGTGGACTGACC
54782876 ACCACCTTGG
1 ACC-CCTTGG
54782886 CCCACTACTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.31
19 6 0.23
21 12 0.46
ACGTcount: A:0.14, C:0.37, G:0.27, T:0.22
Consensus pattern (19 bp):
ACCCCTTGGTGGACTGACC
Found at i:54785514 original size:29 final size:27
Alignment explanation
Indices: 54785442--54785547 Score: 106
Period size: 29 Copynumber: 3.7 Consensus size: 27
54785432 ACATACATGC
*
54785442 ATATGACCCACTT-GGCCCAATCTCATTT
1 ATATGGCCCA-TTAGGCCCAAT-TCATTT
*
54785470 ATATGGCCCATCAGGCCCAATTCATATT
1 ATATGGCCCATTAGGCCCAATTCAT-TT
* *
54785498 CATATGGCTCATTAGGCCCAAATCACCTTT
1 -ATATGGCCCATTAGGCCCAATTCA--TTT
*
54785528 ATATGGCCCGTTAGGCCCAA
1 ATATGGCCCATTAGGCCCAA
54785548 ATCAACTAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
27 5 0.08
28 19 0.29
29 39 0.59
30 2 0.03
31 1 0.02
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.28
Consensus pattern (27 bp):
ATATGGCCCATTAGGCCCAATTCATTT
Found at i:54789321 original size:47 final size:46
Alignment explanation
Indices: 54789203--54789376 Score: 189
Period size: 45 Copynumber: 3.8 Consensus size: 46
54789193 GGGATATTTG
*
54789203 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCGA
* * *
54789250 TG--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATG---CGA
*
54789295 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCG-A
* *
54789343 CGC--CCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
54789377 TATGGGCGGG
Statistics
Matches: 108, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 4 0.04
44 2 0.02
45 32 0.30
46 30 0.28
47 31 0.29
48 5 0.05
50 4 0.04
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (46 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCGA
Found at i:54789372 original size:46 final size:46
Alignment explanation
Indices: 54789208--54789381 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
54789198 ATTTGGGCAT
* *
54789208 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-ATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * *
54789253 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
54789298 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
54789346 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54789382 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 9, Indels: 19
0.80 0.07 0.14
Matches are distributed among these distances:
42 5 0.05
44 2 0.02
45 29 0.26
46 35 0.32
47 28 0.25
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:54792361 original size:30 final size:30
Alignment explanation
Indices: 54792327--54792395 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
54792317 TATCGTATCT
54792327 TGGGTTTCTTTATCCTGGATCTCTTTATTC
1 TGGGTTTCTTTATCCTGGATCTCTTTATTC
* * * *
54792357 TGGGTTTCTCTATCTTGGATTTTTTTATTC
1 TGGGTTTCTTTATCCTGGATCTCTTTATTC
*
54792387 -GGTTTTCTT
1 TGGGTTTCTT
54792396 GTTATCTTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 7 0.21
30 26 0.79
ACGTcount: A:0.09, C:0.16, G:0.17, T:0.58
Consensus pattern (30 bp):
TGGGTTTCTTTATCCTGGATCTCTTTATTC
Found at i:54794736 original size:46 final size:46
Alignment explanation
Indices: 54794686--54794861 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
54794676 TATTTGGGCA
54794686 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54794732 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
54794777 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54794825 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54794862 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54794841 original size:93 final size:93
Alignment explanation
Indices: 54794682--54794853 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
54794672 TGGATATTTG
* *
54794682 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
54794747 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
54794775 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
54794840 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
54794854 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:54798277 original size:39 final size:40
Alignment explanation
Indices: 54798222--54798392 Score: 233
Period size: 39 Copynumber: 4.3 Consensus size: 40
54798212 GGACTAAGAT
* *
54798222 CCGAAGGCGTTCGTGCGAGTTAATAAATCCGGGTTAAG-C
1 CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAGTC
54798261 CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAG-C
1 CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAGTC
* *
54798300 CCGAAGGCATTTGTGCGAGTTACTAAACCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAGTC
* * *
54798340 CCGAAGGCATTCGTGCGAGTTACTATAA-CCGGGGTT-TGTC
1 CCGAAGGCATTTGTGCGAGTTAATA-AATCC-GGGTTAAGTC
54798380 CCGAAGGCATTTG
1 CCGAAGGCATTTG
54798393 ATCTAGTCGT
Statistics
Matches: 122, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
39 73 0.60
40 42 0.34
41 7 0.06
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAGTC
Found at i:54803558 original size:56 final size:56
Alignment explanation
Indices: 54803295--54803528 Score: 378
Period size: 56 Copynumber: 4.2 Consensus size: 56
54803285 TTGTGATCAT
* *
54803295 GAGTAAGACCACATTTAATACGTTGGCATTGATATGTGATTCTGATATATGTGTGC
1 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGC
* * *
54803351 GAGTAAGACCACGTTTAATACGTTGGCATTGATATGTGATTCTGATATATATGTGT
1 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGC
* * *
54803407 GAGTAAGACAACGCTTAAAACGTTGGCATCGATATGTGATTCTGATATATGTGTGC
1 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGC
* *
54803463 GAGTAAGACCACGTTTAATACATTGGCATCGATATGTGATTCTGATATATGTGTGT
1 GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGC
54803519 GAGTAAGACC
1 GAGTAAGACC
54803529 CTGTTTGGGA
Statistics
Matches: 164, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 164 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (56 bp):
GAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGC
Found at i:54817289 original size:13 final size:13
Alignment explanation
Indices: 54817273--54817310 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
54817263 GGACACATTA
*
54817273 CCGTGTCACATGG
1 CCGTGTCGCATGG
54817286 CCGTGTCGCAT-G
1 CCGTGTCGCATGG
*
54817298 CCATGTCGCATGG
1 CCGTGTCGCATGG
54817311 TCATGTGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.13, C:0.32, G:0.32, T:0.24
Consensus pattern (13 bp):
CCGTGTCGCATGG
Found at i:54825320 original size:40 final size:40
Alignment explanation
Indices: 54825212--54825398 Score: 261
Period size: 40 Copynumber: 4.7 Consensus size: 40
54825202 TCCAAACACA
* *
54825212 AATGCCTTCGGGACTTAGCCTGGATATAAC-ACCAGTACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACAACCAGCACG
* * *
54825251 AGTGCCTTCGGAACTT-GGCCGGATATAACAACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACAACCAGCACG
* * *
54825290 AATGCCTTCAGGACTTAGCCCGGATATAACAACCAGTACA
1 AATGCCTTCGGGACTTAGCCCGGATATAACAACCAGCACG
* *
54825330 AATGCCTTCGGGACTTAACCCGGATATAACAACCAACACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACAACCAGCACG
*
54825370 AATGCCTTCGGGACTTAACCCGGATATAA
1 AATGCCTTCGGGACTTAGCCCGGATATAA
54825399 TCCTCAATTA
Statistics
Matches: 130, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
38 11 0.08
39 35 0.27
40 84 0.65
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATATAACAACCAGCACG
Found at i:54826159 original size:2 final size:2
Alignment explanation
Indices: 54826152--54826176 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54826142 ATTAACATAC
54826152 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
54826177 CCTATGTGTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54829636 original size:2 final size:2
Alignment explanation
Indices: 54829629--54829685 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
54829619 TAAACATCAA
*
54829629 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
54829670 AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
54829686 CAAGTAGTCG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:54832710 original size:27 final size:27
Alignment explanation
Indices: 54832680--54833077 Score: 535
Period size: 27 Copynumber: 14.7 Consensus size: 27
54832670 TACTGAAATG
* * * *
54832680 CCCTCAATTTGTAAAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
54832707 CCCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
54832734 CCATCGATTTATAAAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
54832761 CCCTCGATTTATAAAATTACAATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
54832788 CCCTCGATTTACAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
54832815 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
54832842 CCCTTGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
54832869 CCCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
54832896 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
54832923 CTCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
54832950 CCCTTGATTTACAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
54832977 CCCTCGATTTATAGAATTACCGTGTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* * * **
54833004 CTCTCAATTTATAAAATTACTGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* * * *
54833031 CCCTTGATTTACAGAACTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
54833058 CCCTCGATTTACAAAATTAC
1 CCCTCGATTTATAGAATTAC
54833078 TAAAATACCC
Statistics
Matches: 330, Mismatches: 41, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 330 1.00
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCATTTTA
Found at i:54833086 original size:27 final size:27
Alignment explanation
Indices: 54833056--54833275 Score: 173
Period size: 27 Copynumber: 8.2 Consensus size: 27
54833046 ACTACCGTTT
* *
54833056 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* * *
54833083 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
*
54833110 TACCCTCGA-TCAGTAAAATTACCAAAA
1 TACCCTCGATTTA-TAAAATTACCAAAA
* * *
54833137 TACCC-CTGGTTTGTAAAATTACTAAAA
1 TACCCTC-GATTTATAAAATTACCAAAA
* *
54833164 TACCC-CTAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTATAAAATTACCAAAA
** *
54833191 TACCC-CTGGCTTGTAAAATTACCAAAA
1 TACCCTC-GATTTATAAAATTACCAAAA
* * *
54833218 TACCC-CTGATTTATGAAATTATCGAAA
1 TACCCTC-GATTTATAAAATTACCAAAA
* * *
54833245 TACTCTCGATTTGTAAAA-TATCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
54833271 TACCC
1 TACCC
54833276 CTGTACGATA
Statistics
Matches: 159, Mismatches: 28, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
26 14 0.09
27 143 0.90
28 2 0.01
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (27 bp):
TACCCTCGATTTATAAAATTACCAAAA
Found at i:54833114 original size:54 final size:53
Alignment explanation
Indices: 54833056--54833276 Score: 223
Period size: 54 Copynumber: 4.1 Consensus size: 53
54833046 ACTACCGTTT
* * * **
54833056 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAA
1 TACCC-CGATTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
* *
54833110 TACCCTCGA-TCAGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAA
1 TACCC-CGATTTA-TAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
* * *
54833164 TACCCCTAGTTTGTAAAATTACCAAAATACCCCTGGCTTGTAAAATTACCAAAA
1 TACCCCGA-TTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
* * * * * *
54833218 TACCCCTGATTTATGAAATTATCGAAATA-CTCTCGATTTGTAAAA-TATCAAAA
1 TACCCC-GATTTATAAAATTACCAAAATACCCCT-GGTTTGTAAAATTACCAAAA
54833271 TACCCC
1 TACCCC
54833277 TGTACGATAG
Statistics
Matches: 141, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
53 20 0.14
54 119 0.84
55 2 0.01
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (53 bp):
TACCCCGATTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
Found at i:54833237 original size:81 final size:82
Alignment explanation
Indices: 54833058--54833305 Score: 249
Period size: 81 Copynumber: 3.1 Consensus size: 82
54833048 TACCGTTTTA
* * * ** *
54833058 CCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATA-CCCTCGATCA
1 CCCT-GATTTATAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGGATCA
54833122 GTAAAATTACCAAAATAC
65 GTAAAATTACCAAAATAC
* * * *
54833140 CCCTGGTTTGTAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGGCT-TG
1 CCCTGATTTATAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGGATCAG
54833204 TAAAATTACCAAAATAC
66 TAAAATTACCAAAATAC
* * * * * *
54833221 CCCTGATTTATGAAATTA-TCGAAATA-CTCTCGATTTGTAAAA-TATCAAAATACCCCTGTA-C
1 CCCTGATTTATAAAATTACT-AAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCCTGGATC
* *
54833282 -GATAGAATTACCGAAATAC
64 AG-TAAAATTACCAAAATAC
54833301 CCCTG
1 CCCTG
54833306 TAAGGTCGAA
Statistics
Matches: 140, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
79 1 0.01
80 40 0.29
81 89 0.64
82 10 0.07
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.29
Consensus pattern (82 bp):
CCCTGATTTATAAAATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGGATCAG
TAAAATTACCAAAATAC
Found at i:54833306 original size:27 final size:27
Alignment explanation
Indices: 54833268--54833508 Score: 331
Period size: 27 Copynumber: 9.0 Consensus size: 27
54833258 TAAAATATCA
* *
54833268 AAATACCCCTGTACGATAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
54833295 AAATACCCCTGTAAGGTCGAATTACC-
1 AAATACCCCTGTAGGGTAGAATTACCG
**
54833321 AAATACCCCTGTAGGGTAGAATTACTA
1 AAATACCCCTGTAGGGTAGAATTACCG
*
54833348 AAATAACCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
*
54833375 AAATACCCCTGTAGGGTAGAATTACTG
1 AAATACCCCTGTAGGGTAGAATTACCG
54833402 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* * * *
54833429 AAATACCCTTGTAGGGTAAAAATACCA
1 AAATACCCCTGTAGGGTAGAATTACCG
54833456 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* * * *
54833483 AGATACCCTTGTGGGGTAAAATTACC
1 AAATACCCCTGTAGGGTAGAATTACC
54833509 ATTTTGCCCT
Statistics
Matches: 189, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
26 23 0.12
27 166 0.88
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.24
Consensus pattern (27 bp):
AAATACCCCTGTAGGGTAGAATTACCG
Found at i:54833782 original size:24 final size:25
Alignment explanation
Indices: 54833711--54833780 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
54833701 AGGAAGTGCT
* * *
54833711 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
54833736 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
*
54833761 AAAAGAGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
54833781 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:54833987 original size:42 final size:42
Alignment explanation
Indices: 54833928--54834019 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
54833918 TAGTCTCCCC
*
54833928 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
54833970 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
54834012 AAATGGGC
1 AAATGGGC
54834020 CTAAGGGCCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:54835700 original size:17 final size:17
Alignment explanation
Indices: 54835641--54835700 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
54835631 GAGACAGCCA
* * *
54835641 CCATACATGCACTTAAG
1 CCATTCATGCATTTAAT
54835658 CCATTCATGCATTCT-AT
1 CCATTCATGCATT-TAAT
*
54835675 -CATCCCATGCATTTAAT
1 CCAT-TCATGCATTTAAT
54835692 CCATTCATG
1 CCATTCATG
54835701 GACTAGACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 4 0.12
17 26 0.76
18 4 0.12
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.33
Consensus pattern (17 bp):
CCATTCATGCATTTAAT
Found at i:54837237 original size:29 final size:29
Alignment explanation
Indices: 54837205--54837309 Score: 142
Period size: 29 Copynumber: 3.7 Consensus size: 29
54837195 ATACCCTCCG
** * *
54837205 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
54837234 AGCTTGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
54837263 AGCACGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
54837292 AG--CGCACACTTAGTGCCA
1 AGCTCGCACACTTAGTGCCA
54837310 ATCTCGTCAC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 16 0.23
29 53 0.77
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.28
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCATATATTTCC
Found at i:54845184 original size:29 final size:29
Alignment explanation
Indices: 54845156--54845258 Score: 152
Period size: 29 Copynumber: 3.6 Consensus size: 29
54845146 CCTCCGAGCT
** * * *
54845156 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
54845185 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
54845214 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
54845243 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
54845259 ATCTCGTCAC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:54847835 original size:28 final size:28
Alignment explanation
Indices: 54847785--54847884 Score: 130
Period size: 28 Copynumber: 3.6 Consensus size: 28
54847775 CATGACTGTA
*
54847785 AATGTGATTTGGGCCTAGT-GGCCATATG
1 AATGTGA-TTGGGCCTAATGGGCCATATG
*
54847813 AATGTGATTGGGCCTAATGGGCCATATA
1 AATGTGATTGGGCCTAATGGGCCATATG
* *
54847841 AATGTGAATGGGCCTAATGGGCCATTTG
1 AATGTGATTGGGCCTAATGGGCCATATG
* *
54847869 AAAGAGATTGGGCCTA
1 AATGTGATTGGGCCTA
54847885 GTGGACCACA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 10 0.16
28 53 0.84
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.28
Consensus pattern (28 bp):
AATGTGATTGGGCCTAATGGGCCATATG
Found at i:54856625 original size:43 final size:43
Alignment explanation
Indices: 54856504--54856625 Score: 158
Period size: 43 Copynumber: 2.8 Consensus size: 43
54856494 TTATGTTTTA
* * *
54856504 ATTATGTGTAAGACCATGTCTGGGACATGGGCATCATTATATG
1 ATTACGTGTAAGACCATGTCTGGGACATCGGCATCGTTATATG
*
54856547 ATTACGTGTAAGACCATGTCTGGGACATCGACATCGTTA-ATCG
1 ATTACGTGTAAGACCATGTCTGGGACATCGGCATCGTTATAT-G
* *
54856590 ATTTCGTGTAAGACCCTGTCTGGGACAGT-GGCATCG
1 ATTACGTGTAAGACCATGTCTGGGACA-TCGGCATCG
54856626 ATATGTGTTA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
42 2 0.03
43 67 0.96
44 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
ATTACGTGTAAGACCATGTCTGGGACATCGGCATCGTTATATG
Found at i:54859834 original size:19 final size:18
Alignment explanation
Indices: 54859812--54859854 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
54859802 AAAATACAAA
*
54859812 AAAAATTAAAATAATTTTT
1 AAAAATTAAAAT-ATTTAT
*
54859831 AAAATTTAAAATATTTAT
1 AAAAATTAAAATATTTAT
54859849 AAAAAT
1 AAAAAT
54859855 CCCAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAAATTAAAATATTTAT
Found at i:54859893 original size:19 final size:18
Alignment explanation
Indices: 54859858--54859934 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
54859848 TAAAAATCCC
* *
54859858 AAAATTTATATTTTTAAA
1 AAAATTTAAAATTTTAAA
54859876 AAAATTATAAAATTTTAAA
1 AAAATT-TAAAATTTTAAA
*
54859895 AAAATTTCTAAAATTATAAA
1 AAAA-TT-TAAAATTTTAAA
* * *
54859915 GAAAGTGAAAATTTTAAA
1 AAAATTTAAAATTTTAAA
54859933 AA
1 AA
54859935 TTTTCTAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
18 17 0.35
19 15 0.31
20 16 0.33
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.36
Consensus pattern (18 bp):
AAAATTTAAAATTTTAAA
Found at i:54859896 original size:20 final size:20
Alignment explanation
Indices: 54859867--54859914 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
54859857 CAAAATTTAT
*
54859867 ATTTTTAAAAAAATTATAAA
1 ATTTTAAAAAAAATTATAAA
* *
54859887 ATTTTAAAAAAATTTCTAAA
1 ATTTTAAAAAAAATTATAAA
*
54859907 ATTATAAA
1 ATTTTAAA
54859915 GAAAGTGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTTAAAAAAAATTATAAA
Found at i:54860143 original size:24 final size:25
Alignment explanation
Indices: 54860111--54860159 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
54860101 TTAATTTTTT
* *
54860111 AATTTAACTTGAA-TAATTTTACTC
1 AATTCAACTTAAATTAATTTTACTC
*
54860135 AATTCAACTTAAATTTATTTTACTC
1 AATTCAACTTAAATTAATTTTACTC
54860160 TAACTTAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.37, C:0.14, G:0.02, T:0.47
Consensus pattern (25 bp):
AATTCAACTTAAATTAATTTTACTC
Found at i:54865978 original size:29 final size:29
Alignment explanation
Indices: 54865945--54866022 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
54865935 GTCATATTCT
* **
54865945 ATACAAGTCTTTAATATGTCTT-AGCTTAA
1 ATACATGT-TTTAATATGTCTTAAAATTAA
54865974 ATACATGTTATTAATATGTCTTAAAATTAA
1 ATACATGTT-TTAATATGTCTTAAAATTAA
54866004 A-ACATGTTTTTAATATGTC
1 ATACATG-TTTTAATATGTC
54866023 CTAGTGCAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
28 1 0.02
29 34 0.79
30 8 0.19
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (29 bp):
ATACATGTTTTAATATGTCTTAAAATTAA
Found at i:54868412 original size:46 final size:46
Alignment explanation
Indices: 54868362--54868533 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
54868352 TGGTTGAGCA
*
54868362 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
54868408 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
54868455 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
54868501 -CTCGAGCTCG-TGAGTTGAGTCCGAGTTCACTTA
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
54868534 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 11, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
43 6 0.06
45 27 0.25
46 37 0.35
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:54871262 original size:43 final size:43
Alignment explanation
Indices: 54871215--54871331 Score: 150
Period size: 43 Copynumber: 2.7 Consensus size: 43
54871205 TAACACATAT
*
54871215 CGATGCCACTGTCCCAGACAGGGTCTTACACGAAATCGAT-TAA
1 CGATGCCACTGTCCCAGACATGGTCTTACACGAAATC-ATATAA
* *
54871258 CGATGTCGA-TGTCCCAGACATGGTCTTACACGTAATCATATAA
1 CGATG-CCACTGTCCCAGACATGGTCTTACACGAAATCATATAA
*
54871301 TGATGCC-CATGTCCCAGACATGGTCTTACAC
1 CGATGCCAC-TGTCCCAGACATGGTCTTACAC
54871332 ATAATTAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
42 3 0.05
43 60 0.92
44 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (43 bp):
CGATGCCACTGTCCCAGACATGGTCTTACACGAAATCATATAA
Found at i:54880008 original size:28 final size:28
Alignment explanation
Indices: 54879958--54880059 Score: 127
Period size: 28 Copynumber: 3.6 Consensus size: 28
54879948 TGTGGTCCAC
* *
54879958 TAGGCCCAATCTC-TTTCAAATGGCCCAT
1 TAGGCCCAATCACATTT-ATATGGCCCAT
*
54879986 TAGGCCCATTCACATTTATATGGCCCAT
1 TAGGCCCAATCACATTTATATGGCCCAT
* *
54880014 TAGGCCCAATCACATTCATATGG-CCAC
1 TAGGCCCAATCACATTTATATGGCCCAT
54880041 TAGGCCCAAATCACATTTA
1 TAGGCCC-AATCACATTTA
54880060 CAGTCATGCT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
27 10 0.15
28 52 0.80
29 3 0.05
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.27
Consensus pattern (28 bp):
TAGGCCCAATCACATTTATATGGCCCAT
Found at i:54883410 original size:37 final size:37
Alignment explanation
Indices: 54883360--54883435 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
54883350 TTCAAGACTA
*
54883360 ACTTAAAAATTTATCCATTTTTGCATAGCTTAAATAT
1 ACTTAAAAATTTATCCATTTTCGCATAGCTTAAATAT
54883397 ACTTAAAAATTTATCCATTTTCGCATAGCTTAAATAT
1 ACTTAAAAATTTATCCATTTTCGCATAGCTTAAATAT
54883434 AC
1 AC
54883436 ATTCATTTCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (37 bp):
ACTTAAAAATTTATCCATTTTCGCATAGCTTAAATAT
Found at i:54886546 original size:30 final size:30
Alignment explanation
Indices: 54886489--54886547 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
54886479 CAAAAAGCAT
*
54886489 ACTTTTACAAATTTACATTTTTACCCCTAA
1 ACTTTTACAAATTTACATATTTACCCCTAA
* *
54886519 ACTTTTACATATTTGCA-ATTTAGCCCCTA
1 ACTTTTACAAATTTACATATTTA-CCCCTA
54886548 GGCTCGTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.42
Consensus pattern (30 bp):
ACTTTTACAAATTTACATATTTACCCCTAA
Found at i:54892546 original size:93 final size:93
Alignment explanation
Indices: 54892433--54892603 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
54892423 GCCCCTAAGT
* * *
54892433 GAACTCGGACTGAACTCAACGAGCTCTGG-CGTTCGCATCCATAAGTGAACTTGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54892497 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGGATGCCTAGTTACATCTCAC
* *
54892526 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54892591 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54892604 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54892598 original size:46 final size:45
Alignment explanation
Indices: 54892430--54892600 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 45
54892420 CCCGCCCCTA
* * *
54892430 AGTGAACTCGGACTGAACTCAACGAGCTCTGG-CGTTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCAT
* *
54892475 AAGTGAACTTGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-T
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCAT
*
54892523 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT
54892568 AGGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 A-GTGAACTCGGACTCAACTCAACGAGTTCGGA
54892601 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 10, Indels: 22
0.76 0.07 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 3 0.03
45 3 0.03
46 55 0.53
47 28 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT
Found at i:54893059 original size:30 final size:30
Alignment explanation
Indices: 54893025--54893084 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
54893015 ATTTAATACG
54893025 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
54893055 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
54893085 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:54895353 original size:177 final size:176
Alignment explanation
Indices: 54894974--54895365 Score: 467
Period size: 176 Copynumber: 2.2 Consensus size: 176
54894964 GGACTGATGA
* ** *
54894974 CTTAAATCTACTCCATTGCCAATACATGGAGATAAGATTCGCCATCTTCAATCTGCTCTGCAACT
1 CTTAAATCTGCTCCATTGCTGATACATGGAGATAAGATTCACCATCTTCAATCTGCTCTGCAACT
*
54895039 GCTTTAGGGAAACAGATCTTCAATCTCCAGTCTGCTTCCTTGCTACCTCAAGAAGATAAGACTAA
66 -CTTCAGGGAAACAGATCTTCAATCTCCAGTCTGCTTCCTTGCTACCTCAAGAAGATAAGACTAA
* *
54895104 AATCGCCAACCTGCTCACTTGCTACCTCAGAGAGATAAGGCTAGTGG
130 AATCGCCAACCTACTCACTTGCTACCTCAGAGAGATAAGGCTAGAGG
* * *
54895151 --TAGAATCTGTTCCATT-TTCGATACATGGAGATAAGATTCACCATCTTCGATCTGCCCTGCTG
1 CTTA-AATCTGCTCCATTGCT-GATACATGGAGATAAGATTCACCATCTTCAATCTG--CT-CTG
* ** *
54895213 CAA-T-TTCAGGGAGATA-AGATCTTCAATTTTTAGTCTGCTTTCTTGCTACCTC-AGAAAGATA
61 CAACTCTTCAGGGA-A-ACAGATCTTCAATCTCCAGTCTGCTTCCTTGCTACCTCAAG-AAGATA
* ** * *
54895274 AGACT-CAATCTTCAACCTACTCTCTTGCTACCTCAGAGAGATAAGGCTTGAGG
123 AGACTAAAATCGCCAACCTACTCACTTGCTACCTCAGAGAGATAAGGCTAGAGG
*
54895327 CTTAAATCTGCTCCATTGCTGATACATAGAGATAAGATT
1 CTTAAATCTGCTCCATTGCTGATACATGGAGATAAGATT
54895366 TGCCTCTTCC
Statistics
Matches: 182, Mismatches: 22, Indels: 22
0.81 0.10 0.10
Matches are distributed among these distances:
175 2 0.01
176 93 0.51
177 74 0.41
178 7 0.04
179 6 0.03
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (176 bp):
CTTAAATCTGCTCCATTGCTGATACATGGAGATAAGATTCACCATCTTCAATCTGCTCTGCAACT
CTTCAGGGAAACAGATCTTCAATCTCCAGTCTGCTTCCTTGCTACCTCAAGAAGATAAGACTAAA
ATCGCCAACCTACTCACTTGCTACCTCAGAGAGATAAGGCTAGAGG
Found at i:54895520 original size:146 final size:146
Alignment explanation
Indices: 54895231--54895520 Score: 379
Period size: 146 Copynumber: 2.0 Consensus size: 146
54895221 GGGAGATAAG
* * *
54895231 ATCTTCAATTTTTAGTCTGCTTTCTTGCTACCTCAGAAAGATAAGACTCAATCTTCAACCTACTC
1 ATCTTCAATCTTCAGTCTGCTTTCTTGCTACCCCAGAAAGATAAGACTCAATCTTCAACCTACTC
* * * *
54895296 TCTTGCTACCTCAGAGAGATAAGGCTTGAGGCTTAAATCTGCTCCATTGCTGATACATAGAGATA
66 TCTTGCAACCTCAGAGAGATAAGGCTGGAGGCTAAAATCTGCTCCATTGCCGATACATAGAGATA
**
54895361 AGATTTGCCTCTTCCA
131 AGATTCACCTCTTCCA
* * * * * *
54895377 ATCTTCAATCTTCAGTCTGCTTTCTTGTTACCCCAGAAAGATAAGACTCATTTTTTAACTTGCTC
1 ATCTTCAATCTTCAGTCTGCTTTCTTGCTACCCCAGAAAGATAAGACTCAATCTTCAACCTACTC
* *
54895442 TTTTGCAACCTTAGAGAGATAAGGCTGGTA-G-TAAAATCTGCTCCATTGCCGATACAT-GAAGA
66 TCTTGCAACCTCAGAGAGATAAGGCTGG-AGGCTAAAATCTGCTCCATTGCCGATACATAG-AGA
54895504 TAAGATTCACCATCTTC
129 TAAGATTCACC-TCTTC
54895521 AATTTGTTTC
Statistics
Matches: 124, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
144 1 0.01
145 36 0.29
146 86 0.69
147 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (146 bp):
ATCTTCAATCTTCAGTCTGCTTTCTTGCTACCCCAGAAAGATAAGACTCAATCTTCAACCTACTC
TCTTGCAACCTCAGAGAGATAAGGCTGGAGGCTAAAATCTGCTCCATTGCCGATACATAGAGATA
AGATTCACCTCTTCCA
Found at i:54895724 original size:88 final size:88
Alignment explanation
Indices: 54895632--54895904 Score: 222
Period size: 88 Copynumber: 3.1 Consensus size: 88
54895622 CTACCTCAGA
* *
54895632 GAGATAAGGTCAATAGCTAAAATCTACTCCATTACCGATACATGGAGATAAGATTCGCCGTCCTC
1 GAGATAAGGTCAATAGCTAAAATCTGCTCCATTACCGATACATGGAGATAAGATTCGCCATCCTC
54895697 GATCTGCTCCGCTACTGCTTAGG
66 GATCTGCTCCGCTACTGCTTAGG
* ** * * * * *
54895720 GAGATAAGATCTTCAAT--CTTCAGTCCGCTTCC-TTGCC-ACCT-CA-GGAAGATAAGACT-AC
1 GAGATAAG---GTCAATAGCTAAAATCTGC-TCCATTACCGA--TACATGG-AGATAAGATTCGC
* * * * * * *
54895778 AATCGCT-AACCTGCTCTC-TTACTACCTCAGA
59 CATC-CTCGATCTGCTC-CGCTACT-GCTTAGG
*
54895809 GAGATAAGGTCAATAGCTAAAATCTGCTCCATTACCGATACATGGAGATAAGATTCGTCATCCTC
1 GAGATAAGGTCAATAGCTAAAATCTGCTCCATTACCGATACATGGAGATAAGATTCGCCATCCTC
*
54895874 GATCTGCTCCGCTATTGCTTAGG
66 GATCTGCTCCGCTACTGCTTAGG
54895897 GAGATAAG
1 GAGATAAG
54895905 ATCTTCAATC
Statistics
Matches: 132, Mismatches: 34, Indels: 38
0.65 0.17 0.19
Matches are distributed among these distances:
86 5 0.04
87 4 0.03
88 62 0.47
89 52 0.39
90 4 0.03
91 5 0.04
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (88 bp):
GAGATAAGGTCAATAGCTAAAATCTGCTCCATTACCGATACATGGAGATAAGATTCGCCATCCTC
GATCTGCTCCGCTACTGCTTAGG
Found at i:54895851 original size:177 final size:176
Alignment explanation
Indices: 54895376--54896302 Score: 951
Period size: 177 Copynumber: 5.3 Consensus size: 176
54895366 TGCCTCTTCC
* * * * * *** *
54895376 AATCTTCAATCTTCAGTCTGCTTTCTTGTTACCCCAGAAAGATAAGACTCATTTTTTAACTTGCT
1 AATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCAATCGCTAACCTGCT
* * * ** *
54895441 CTTTTGCAACCTTAGAGAGATAAGG-CTGGTAG-TAAAATCTGCTCCATTGCCGATACATGAAGA
66 CTCTTGCTACCTCAGAGAGATAAGGTC-AATAGCTAAAATCTGCTCCATTGCCGATACATGGAGA
* * * * * * * * *
54895504 TAAGATTCACCATCTTCAATTTGTTTC-ATAGCTTCTCAAGGAGATAA
130 TAAGATTCACCATCCTCGATCTGCTCCGCTA-CTGCTTAGGGAGATAA
* * * *
54895551 AATCTTCAATCTTCAGTCTGCTTCCTTGCCACCTTAGGAAGATAAGACTCAATCGCCAACTTGCT
1 AATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCAATCGCTAACCTGCT
* *
54895616 CTCTTGCTACCTCAGAGAGATAAGGTCAATAGCTAAAATCTACTCCATTACCGATACATGGAGAT
66 CTCTTGCTACCTCAGAGAGATAAGGTCAATAGCTAAAATCTGCTCCATTGCCGATACATGGAGAT
* *
54895681 AAGATTCGCCGTCCTCGATCTGCTCCGCTACTGCTTAGGGAGATAA
131 AAGATTCACCATCCTCGATCTGCTCCGCTACTGCTTAGGGAGATAA
* * *
54895727 GATCTTCAATCTTCAGTCCGCTTCCTTGCCACCTCAGGAAGATAAGACTACAATCGCTAACCTGC
1 AATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACT-CAATCGCTAACCTGC
* *
54895792 TCTCTTACTACCTCAGAGAGATAAGGTCAATAGCTAAAATCTGCTCCATTACCGATACATGGAGA
65 TCTCTTGCTACCTCAGAGAGATAAGGTCAATAGCTAAAATCTGCTCCATTGCCGATACATGGAGA
** *
54895857 TAAGATTCGTCATCCTCGATCTGCTCCGCTATTGCTTAGGGAGATAA
130 TAAGATTCACCATCCTCGATCTGCTCCGCTACTGCTTAGGGAGATAA
* * * *
54895904 GATCTTCAATCTTCAGTCTACTTCCTTGCTACCTC---AAG--AAG-----ATGGCCAACCTGCT
1 AATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCAATCGCTAACCTGCT
* * *
54895959 CTCTTGCTACCTCAGAGAGATAAGGCTTAA-AGCTTAAATCTGCTCCATTGCCAATACATGGAGA
66 CTCTTGCTACCTCAGAGAGATAAGG-TCAATAGCTAAAATCTGCTCCATTGCCGATACATGGAGA
* * **
54896023 TAAGATTCATCAT-CTACGAATATCTGCTCCGCTGCAACTTCAGGGAGATAA
130 TAAGATTCACCATCCT-CG---ATCTGCTCCGCTACTGCTT-AGGGAGATAA
* *
54896074 AATCTTCAATTCTT-AGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATTC-TTCAACCTG
1 AATCTTCAA-TCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCAATCGCT-AACCTG
* * *** * *
54896137 CTCTCTTACTACGTCAGAGAGATAAGGCTTGGT-GGTAAAATCTGTTCCATTGCCGATACATGGA
64 CTCTCTTGCTACCTCAGAGAGATAAGG-TCAATAGCTAAAATCTGCTCCATTGCCGATACATGGA
** * * *
54896201 GATAAGATTCACCATATGTGAAGATCTGC-CCTGCTGCAAT-CTCAGGGAGATAA
128 GATAAGATTCACCAT-CCT--CGATCTGCTCC-GCT--ACTGCTTAGGGAGATAA
54896254 AATCTTCAAT-TCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACT
1 AATCTTCAATCT-TCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACT
54896303 ATTATCACAA
Statistics
Matches: 645, Mismatches: 76, Indels: 57
0.83 0.10 0.07
Matches are distributed among these distances:
165 2 0.00
166 81 0.13
167 3 0.00
169 15 0.02
170 38 0.06
171 4 0.01
172 3 0.00
173 3 0.00
174 3 0.00
175 82 0.13
176 108 0.17
177 154 0.24
178 1 0.00
179 4 0.01
180 139 0.22
181 2 0.00
182 1 0.00
183 2 0.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (176 bp):
AATCTTCAATCTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCAATCGCTAACCTGCT
CTCTTGCTACCTCAGAGAGATAAGGTCAATAGCTAAAATCTGCTCCATTGCCGATACATGGAGAT
AAGATTCACCATCCTCGATCTGCTCCGCTACTGCTTAGGGAGATAA
Found at i:54896252 original size:180 final size:180
Alignment explanation
Indices: 54895950--54896302 Score: 539
Period size: 180 Copynumber: 2.0 Consensus size: 180
54895940 AGAAGATGGC
* *
54895950 CAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTTAAAGCTTAAATCTGCTCCATTGCCAATA
1 CAACCTGCTCTCTTACTACCTCAGAGAGATAAGGCTTAAAGCTAAAATCTGCTCCATTGCCAATA
* * *
54896015 CATGGAGATAAGATTCATCATCTACGAATATCTGCTCCGCTGCAACTTCAGGGAGATAAAATCTT
66 CATGGAGATAAGATTCACCATATACGAAGATCTGCTCCGCTGCAACTTCAGGGAGATAAAATCTT
*
54896080 CAATTCTTAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATTCTT
131 CAATTCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATTCTT
* *** * * *
54896130 CAACCTGCTCTCTTACTACGTCAGAGAGATAAGGCTTGGTGGTAAAATCTGTTCCATTGCCGATA
1 CAACCTGCTCTCTTACTACCTCAGAGAGATAAGGCTTAAAGCTAAAATCTGCTCCATTGCCAATA
**
54896195 CATGGAGATAAGATTCACCATATGTGAAGATCTGC-CCTGCTGCAA-TCTCAGGGAGATAAAATC
66 CATGGAGATAAGATTCACCATATACGAAGATCTGCTCC-GCTGCAACT-TCAGGGAGATAAAATC
54896258 TTCAATTCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACT
129 TTCAATTCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACT
54896303 ATTATCACAA
Statistics
Matches: 156, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
179 3 0.02
180 153 0.98
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (180 bp):
CAACCTGCTCTCTTACTACCTCAGAGAGATAAGGCTTAAAGCTAAAATCTGCTCCATTGCCAATA
CATGGAGATAAGATTCACCATATACGAAGATCTGCTCCGCTGCAACTTCAGGGAGATAAAATCTT
CAATTCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTCATTCTT
Found at i:54896323 original size:137 final size:132
Alignment explanation
Indices: 54896174--54896437 Score: 336
Period size: 133 Copynumber: 2.0 Consensus size: 132
54896164 CTTGGTGGTA
* *
54896174 AAATCTGTTCCATTGCCGATACATGGAGATAAGATTCACCATATGTGAAGATCTG-CC-CTGCTG
1 AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCAT-T-T-AAGATCTGCCCACTACTG
* *
54896237 CAATCTCAGGGAGATAAAATCT-TCAATTCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGA
63 C--T-T-AGAGAGATAAAATCTGTAAATTC-CAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGA
54896301 CTATTATCAC
123 CTATTATCAC
* ***
54896311 AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCATCATTTTTTATCTGCTCCACTACTGCT
1 AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATTTAAGATCTGC-CCACTACTGCT
* *
54896376 TAGAGAGATAAAATCTGTAAATTCCAGTCTGCTTCCTTGCTATCTTAGGAAGATAAGACTAT
65 TAGAGAGATAAAATCTGTAAATTCCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTAT
54896438 CATCTTCAAC
Statistics
Matches: 113, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
133 50 0.44
134 12 0.11
135 2 0.02
136 3 0.03
137 46 0.41
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (132 bp):
AAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATTTAAGATCTGCCCACTACTGCTT
AGAGAGATAAAATCTGTAAATTCCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTATTATC
AC
Found at i:54896932 original size:64 final size:64
Alignment explanation
Indices: 54896800--54896975 Score: 193
Period size: 64 Copynumber: 2.8 Consensus size: 64
54896790 ATGTTTATGC
* * *
54896800 CAAATACTTAGGATGCTATGATCAAAATGAATCAAATGCTCCT-A-T-GA---AATGCTCATGT
1 CAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAGATGTGATACTCATGT
** * * * *
54896858 CAAACCATTAGGATGTTATGGTCGAAATGAATCAAATGCTCCTAACTAGATGTGATACTGATGT
1 CAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAGATGTGATACTCATGT
* * * *
54896922 CAAATAATTAGGATGCTATTATCAAAATGAATCAATTGCACCTAACTAAATGTG
1 CAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAGATGTG
54896976 TTATGAATGA
Statistics
Matches: 94, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
58 37 0.39
59 1 0.01
60 1 0.01
61 2 0.02
64 53 0.56
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (64 bp):
CAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCCTAACTAGATGTGATACTCATGT
Found at i:54897037 original size:14 final size:15
Alignment explanation
Indices: 54897009--54897037 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54896999 GTAAAAATGA
54897009 AAATGATCTTTTTTT
1 AAATGATCTTTTTTT
54897024 AAATGATCTTTTTT
1 AAATGATCTTTTTT
54897038 CTTTTTCTTG
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:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (15 bp):
AAATGATCTTTTTTT
Found at i:54898807 original size:15 final size:15
Alignment explanation
Indices: 54898787--54898815 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54898777 TTGTCAGCAA
54898787 TTTTTTTT-GAATTT
1 TTTTTTTTGGAATTT
54898801 TTTTTTTTGGAATTT
1 TTTTTTTTGGAATTT
54898816 GATGACTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (15 bp):
TTTTTTTTGGAATTT
Found at i:54915329 original size:27 final size:27
Alignment explanation
Indices: 54915290--54915430 Score: 228
Period size: 27 Copynumber: 5.2 Consensus size: 27
54915280 CAATTTGACG
*
54915290 AAATGACTGTTTTTCCCTTATGAGGTA
1 AAATGACTGTTTTGCCCTTATGAGGTA
*
54915317 AAATGACTATTTTGCCCTTATGAGGTA
1 AAATGACTGTTTTGCCCTTATGAGGTA
54915344 AAATGACTGTTTTGCCCTTATGAGGTA
1 AAATGACTGTTTTGCCCTTATGAGGTA
*
54915371 AAATGACTGTTTTGCCCTTATGTGGTA
1 AAATGACTGTTTTGCCCTTATGAGGTA
* * *
54915398 AAATGGCTGTTTTACCCTTATGTGGTA
1 AAATGACTGTTTTGCCCTTATGAGGTA
54915425 AAATGA
1 AAATGA
54915431 ATGAAATGCC
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 107 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (27 bp):
AAATGACTGTTTTGCCCTTATGAGGTA
Found at i:54915441 original size:81 final size:81
Alignment explanation
Indices: 54915290--54915478 Score: 218
Period size: 81 Copynumber: 2.3 Consensus size: 81
54915280 CAATTTGACG
* * * * **
54915290 AAATGACTGTTTTTCCCTTATGAGGTAAAATGACTATTTTGCCCTTATGAGGTAAAATGACTGTT
1 AAATGACTGTTTTGCCCTTATGTGGTAAAATGACTATTTTACCCTTATGAGGTAAAATGAATGAA
* * *
54915355 TTGCCCTTATGA-GGTA
66 ATGCCCCTA-CATGGTA
* * *
54915371 AAATGACTGTTTTGCCCTTATGTGGTAAAATGGCTGTTTTACCCTTATGTGGTAAAATGAATGAA
1 AAATGACTGTTTTGCCCTTATGTGGTAAAATGACTATTTTACCCTTATGAGGTAAAATGAATGAA
54915436 ATGCCCCTACATGGTA
66 ATGCCCCTACATGGTA
* * * *
54915452 AATTGACTATTCTGCCCCTATGTGGTA
1 AAATGACTGTTTTGCCCTTATGTGGTA
54915479 TATGTTTAGA
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
80 1 0.01
81 90 0.99
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (81 bp):
AAATGACTGTTTTGCCCTTATGTGGTAAAATGACTATTTTACCCTTATGAGGTAAAATGAATGAA
ATGCCCCTACATGGTA
Found at i:54915451 original size:54 final size:54
Alignment explanation
Indices: 54915290--54915459 Score: 155
Period size: 54 Copynumber: 3.1 Consensus size: 54
54915280 CAATTTGACG
* * ** * *
54915290 AAATGACTGTTTTTCCCTTATGAGGTAAAATGACT-ATTTTGCCCTTATGA-GGTA
1 AAATGACTGTTTTACCCTTATGAGGTAAAATGAATGA-AATGCCCCTA-CATGGTA
* * *** * **
54915344 AAATGACTGTTTTGCCCTTATGAGGTAAAATGACTGTTTTGCCCTTATGTGGTA
1 AAATGACTGTTTTACCCTTATGAGGTAAAATGAATGAAATGCCCCTACATGGTA
* *
54915398 AAATGGCTGTTTTACCCTTATGTGGTAAAATGAATGAAATGCCCCTACATGGTA
1 AAATGACTGTTTTACCCTTATGAGGTAAAATGAATGAAATGCCCCTACATGGTA
*
54915452 AATTGACT
1 AAATGACT
54915460 ATTCTGCCCC
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
54 98 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.36
Consensus pattern (54 bp):
AAATGACTGTTTTACCCTTATGAGGTAAAATGAATGAAATGCCCCTACATGGTA
Found at i:54920492 original size:18 final size:17
Alignment explanation
Indices: 54920430--54920492 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
54920420 AAGAGAATGA
54920430 GAAAAAGAAAAACAAAATT
1 GAAAAAG-AAAA-AAAATT
*
54920449 GAAAATGAAAAAGAAATT
1 GAAAAAGAAAAA-AAATT
**
54920467 GATCAAGAAAAGAAAATT
1 GAAAAAGAAAA-AAAATT
54920485 GAAAAAGA
1 GAAAAAGA
54920493 GAGTGAGTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
17 1 0.03
18 28 0.78
19 7 0.19
ACGTcount: A:0.68, C:0.03, G:0.16, T:0.13
Consensus pattern (17 bp):
GAAAAAGAAAAAAAATT
Found at i:54923651 original size:23 final size:21
Alignment explanation
Indices: 54923617--54923668 Score: 86
Period size: 23 Copynumber: 2.4 Consensus size: 21
54923607 AAAAAAAAAG
54923617 AAAAAAAAATATACGAAATTA
1 AAAAAAAAATATACGAAATTA
54923638 AAAAAAATATATATACGAAATTA
1 AAAAAAA-A-ATATACGAAATTA
54923661 AAAAAAAA
1 AAAAAAAA
54923669 TTGTGTGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.24
22 2 0.07
23 20 0.69
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (21 bp):
AAAAAAAAATATACGAAATTA
Found at i:54926027 original size:12 final size:14
Alignment explanation
Indices: 54925999--54926034 Score: 58
Period size: 12 Copynumber: 2.7 Consensus size: 14
54925989 ATACAAGTTT
54925999 GAAAAAAAAATTCC
1 GAAAAAAAAATTCC
54926013 GAAAAAAAAA-T-C
1 GAAAAAAAAATTCC
54926025 GAAAAAAAAA
1 GAAAAAAAAA
54926035 GTGATTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.50
13 1 0.05
14 10 0.45
ACGTcount: A:0.75, C:0.08, G:0.08, T:0.08
Consensus pattern (14 bp):
GAAAAAAAAATTCC
Found at i:54933042 original size:6 final size:5
Alignment explanation
Indices: 54933018--54933072 Score: 51
Period size: 5 Copynumber: 10.6 Consensus size: 5
54933008 ACGAGAAAAC
*
54933018 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
54933065 AAAGA AAA
1 AAAGA AAA
54933073 TAGAGGCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
4 4 0.10
5 23 0.55
6 14 0.33
7 1 0.02
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:54933049 original size:15 final size:14
Alignment explanation
Indices: 54933018--54933072 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 14
54933008 ACGAGAAAAC
54933018 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
54933034 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
54933049 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
54933065 AAAGAAAA
1 AAAGAAAA
54933073 TAGAGGCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
14 4 0.11
15 10 0.29
16 16 0.46
17 5 0.14
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:54933151 original size:12 final size:12
Alignment explanation
Indices: 54933136--54933177 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
54933126 AAAAGCCTTT
54933136 GAAAAACAAAAA
1 GAAAAACAAAAA
54933148 GAAAAACAAAAAA
1 GAAAAAC-AAAAA
**
54933161 GAAAATGAAAAA
1 GAAAAACAAAAA
54933173 GAAAA
1 GAAAA
54933178 TGAGATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (12 bp):
GAAAAACAAAAA
Found at i:54933153 original size:13 final size:13
Alignment explanation
Indices: 54933136--54933165 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
54933126 AAAAGCCTTT
54933136 GAAAAAC-AAAAA
1 GAAAAACAAAAAA
54933148 GAAAAACAAAAAA
1 GAAAAACAAAAAA
54933161 GAAAA
1 GAAAA
54933166 TGAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (13 bp):
GAAAAACAAAAAA
Found at i:54933178 original size:12 final size:12
Alignment explanation
Indices: 54933156--54933180 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54933146 AAGAAAAACA
54933156 AAAAAGAAAATG
1 AAAAAGAAAATG
54933168 AAAAAGAAAATG
1 AAAAAGAAAATG
54933180 A
1 A
54933181 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:54933212 original size:30 final size:28
Alignment explanation
Indices: 54933155--54933225 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 28
54933145 AAAGAAAAAC
*
54933155 AAAAAAGAAAATGAAAAAGAAAATGAGATTG
1 AAAAAA-AGAATGAAAAAGAAAATGAGA--G
***
54933186 AAAAAAAGAATGAAAAAGAGTTTGAGAG
1 AAAAAAAGAATGAAAAAGAAAATGAGAG
*
54933214 AGAAAAAGAATG
1 AAAAAAAGAATG
54933226 TGAACAAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 12 0.34
30 17 0.49
31 6 0.17
ACGTcount: A:0.65, C:0.00, G:0.23, T:0.13
Consensus pattern (28 bp):
AAAAAAAGAATGAAAAAGAAAATGAGAG
Found at i:54936046 original size:20 final size:21
Alignment explanation
Indices: 54936017--54936063 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
54936007 AGTTCCCATC
* *
54936017 AGCTCACTTGAGCTCG-TTTT
1 AGCTCGCTTGAGCTCGAATTT
54936037 AGCTCGCTTGAGCTCGAATTT
1 AGCTCGCTTGAGCTCGAATTT
54936058 AGCTCG
1 AGCTCG
54936064 TTTCAGATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.34
Consensus pattern (21 bp):
AGCTCGCTTGAGCTCGAATTT
Found at i:54936316 original size:13 final size:13
Alignment explanation
Indices: 54936298--54936326 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54936288 AATAGTTGTG
54936298 TGTTATTTAATTA
1 TGTTATTTAATTA
54936311 TGTTATTTAATTA
1 TGTTATTTAATTA
54936324 TGT
1 TGT
54936327 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:54937934 original size:612 final size:606
Alignment explanation
Indices: 54936850--54937953 Score: 1604
Period size: 612 Copynumber: 1.8 Consensus size: 606
54936840 AAGAAGCTAG
* *
54936850 TATAAATAGTTTGTTGATTTCATTTGTAAAGGACTTTTGCCAAATTTGTTAATGAACATTTGTTC
1 TATAAATAGTTTGTTCATTTCATTTGTAAAGGACTTTTGCCAAATTTGTTAATGAACATTTATTC
*
54936915 TTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCTAGTG
66 TTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTAGCTTGTGCTAGTG
* * *
54936980 GCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTATCCA
131 GCGTCAACCGTCTTATTTGAACTTATCACAAATCTTGGTGTGGCGTTCACCTATCCATCTATCCA
*
54937045 TACTTCACCTTAATAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCCTGACGTTG
196 TACTTCACCTTAACAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCCTGACGTTG
* *
54937110 AGTTCGTTTTTCCATCCCCCATCCCCCATCTTTCAACTTTCCTTCTTGTAACCAAACCGACCCAT
261 AGTTCGTTTTTCCAT----C-T-CCCCAACTTTCAACTTTCCTTCTTGTAACCAAACCGAACCAT
*
54937175 TTATCCATCACCCATCTTTGCTACACATAACCGAACCTATTACTAAACTTACCCTTCTTGAAACC
320 CTATCCATCACCCATCTTTGCTACACATAACCGAACCTATTACTAAACTTACCCTTCTTGAAACC
* ** * *
54937240 TTCCGCTTATTCTAATCCATTATTTTACTTTTATTACTAAAATCCGAGGCACGAACGACTCTCTC
385 TTCCACTTAACCTAATCCATTATTTTACTTTAATTACTAAAATCCGAAGCACGAACGACTCTCTC
54937305 GAACTACGATCGGGCAACT-ACGTGAATTCGACTCATCTATCCGGGCCGGATCACATCACCTTTA
450 GAACTACGATCGGGCAACTAAC-TGAATTCGACTCATCTATCCGGGCCGGATCACATCACCTTTA
54937369 ATGATTTATTCTAGAATATTCTAGTGCATTCTTAGCTGAATTTACTTAGTCTTTAAGCTACTAGT
514 ATGATTTATTCTAGAATATTCTAGTGCATTCTTAGCTGAATTTACTTAGTCTTTAAGCTACTAGT
54937434 TTGTCCATTTGGTTACTACATGATAGGT
579 TTGTCCATTTGGTTACTACATGATAGGT
54937462 TATAAATAGTTTGTTCATTTCA-TTGTAAGAGGGACTTTTTGCCAAATTTGTTAATGAACA-TTA
1 TATAAATAGTTTGTTCATTTCATTTGTAA-A-GGAC-TTTTGCCAAATTTGTTAATGAACATTTA
*
54937525 TTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCG-AAGACTTATCTAGTTTGTGCTA
63 TTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTAGCTTGTGCTA
*
54937589 GTGGCGTCTACCGTTCTTATTTAGAACTTATCACAAATCTTGGTGTGGCGTTCACCTATCCATCT
128 GTGGCGTCAACCG-TCTTATTT-GAACTTATCACAAATCTTGGTGTGGCGTTCACCTATCCATCT
* *
54937654 ATCCATAATTTTTTTCACCTTAACAATATAGGAATCGGGGTGACACTTCTTAGTGTTGAATCATT
191 ATCCAT-A----CTTCACCTTAACAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATT
* *
54937719 CCTGACGTTGAGTTCGTTTTT-CAT-T-CCCAACTTTTAACTTTCTTTCTTGTTAACCCAAACCG
251 CCTGACGTTGAGTTCGTTTTTCCATCTCCCCAACTTTCAACTTTCCTTCTTG-TAA-CCAAACCG
* * * * * **
54937781 AACCATCTATCCTTCATCCATCTTTGCTACCCTTAACTGAACCTATTGTTAAACTTACCCTTCTT
314 AACCATCTATCCATCACCCATCTTTGCTACACATAACCGAACCTATTACTAAACTTACCCTTCTT
* *
54937846 GAAACCTTCCAC-TAACCT-ATCCCTT-TTCATTCACTTCTAATT-TTAAAA-CTCGAAGCACGA
379 GAAACCTTCCACTTAACCTAATCCATTATT--TT-ACTT-TAATTACTAAAATC-CGAAGCACGA
* *
54937906 ATGACTCTCTCGAA-TGACGATTGGGCAACTAACTGAATTCGACTCATC
439 ACGACTCTCTCGAACT-ACGATCGGGCAACTAACTGAATTCGACTCATC
54937954 AACCCGAGCC
Statistics
Matches: 441, Mismatches: 32, Indels: 38
0.86 0.06 0.07
Matches are distributed among these distances:
609 2 0.00
610 27 0.06
611 17 0.04
612 188 0.43
613 61 0.14
614 71 0.16
615 1 0.00
618 3 0.01
619 71 0.16
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (606 bp):
TATAAATAGTTTGTTCATTTCATTTGTAAAGGACTTTTGCCAAATTTGTTAATGAACATTTATTC
TTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTAGCTTGTGCTAGTG
GCGTCAACCGTCTTATTTGAACTTATCACAAATCTTGGTGTGGCGTTCACCTATCCATCTATCCA
TACTTCACCTTAACAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCCTGACGTTG
AGTTCGTTTTTCCATCTCCCCAACTTTCAACTTTCCTTCTTGTAACCAAACCGAACCATCTATCC
ATCACCCATCTTTGCTACACATAACCGAACCTATTACTAAACTTACCCTTCTTGAAACCTTCCAC
TTAACCTAATCCATTATTTTACTTTAATTACTAAAATCCGAAGCACGAACGACTCTCTCGAACTA
CGATCGGGCAACTAACTGAATTCGACTCATCTATCCGGGCCGGATCACATCACCTTTAATGATTT
ATTCTAGAATATTCTAGTGCATTCTTAGCTGAATTTACTTAGTCTTTAAGCTACTAGTTTGTCCA
TTTGGTTACTACATGATAGGT
Found at i:54939846 original size:21 final size:20
Alignment explanation
Indices: 54939812--54939854 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
54939802 GGATGAGCTG
54939812 AAACGAGCTAAATTCGAACTC
1 AAACGAGCTAAATT-GAACTC
* * *
54939833 AAACGAGTTGAATTGAGCTC
1 AAACGAGCTAAATTGAACTC
54939853 AA
1 AA
54939855 GTGAGCTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (20 bp):
AAACGAGCTAAATTGAACTC
Found at i:54943444 original size:21 final size:20
Alignment explanation
Indices: 54943410--54943452 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
54943400 GGATGAGCTG
* *
54943410 AAACGAGATAAATTCGAACTC
1 AAACGAGCTGAATT-GAACTC
*
54943431 AAACGAGCTGAATTGAGCTC
1 AAACGAGCTGAATTGAACTC
54943451 AA
1 AA
54943453 GTGAGCTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (20 bp):
AAACGAGCTGAATTGAACTC
Found at i:54946402 original size:30 final size:30
Alignment explanation
Indices: 54946354--54946435 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
54946344 TACGGAATAG
* * *
54946354 AGATGACATGAAAACCAAGATAAAGTAGTCCA
1 AGAT-ACA-GAAATCCAAGATAAAGAAATCCA
*
54946386 GGATGA-AGAAATCCAAGATAAAGAAATCCA
1 AGAT-ACAGAAATCCAAGATAAAGAAATCCA
54946416 AGATACAGAAATCCAAGATA
1 AGATACAGAAATCCAAGATA
54946436 CAATATCATA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
29 1 0.02
30 37 0.84
31 1 0.02
32 5 0.11
ACGTcount: A:0.52, C:0.15, G:0.18, T:0.15
Consensus pattern (30 bp):
AGATACAGAAATCCAAGATAAAGAAATCCA
Found at i:54946409 original size:15 final size:15
Alignment explanation
Indices: 54946363--54946435 Score: 92
Period size: 15 Copynumber: 4.9 Consensus size: 15
54946353 GAGATGACAT
*
54946363 GAAAACCAAGATAAA
1 GAAATCCAAGATAAA
* * * *
54946378 GTAGTCCAGGATGAA
1 GAAATCCAAGATAAA
54946393 GAAATCCAAGATAAA
1 GAAATCCAAGATAAA
*
54946408 GAAATCCAAGATACA
1 GAAATCCAAGATAAA
54946423 GAAATCCAAGATA
1 GAAATCCAAGATA
54946436 CAATATCATA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 48 1.00
ACGTcount: A:0.53, C:0.15, G:0.18, T:0.14
Consensus pattern (15 bp):
GAAATCCAAGATAAA
Found at i:54950570 original size:34 final size:34
Alignment explanation
Indices: 54950497--54950583 Score: 95
Period size: 34 Copynumber: 2.6 Consensus size: 34
54950487 AGTACTGAAT
*
54950497 TGGGCTAAGGCCCACACTGATACTATTACCGTAA
1 TGGGCTAAGGCCCACACTGATACTACTACCGTAA
* * * *
54950531 TGGGCTAAGGTCCACACTGATATTGCTACTGTTAA
1 TGGGCTAAGGCCCACACTGATACTACTACCG-TAA
* *
54950566 -GGGCTTAGGCCCAGACTG
1 TGGGCTAAGGCCCACACTG
54950584 TTTGCACTGC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 41 0.93
35 3 0.07
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (34 bp):
TGGGCTAAGGCCCACACTGATACTACTACCGTAA
Found at i:54953078 original size:40 final size:40
Alignment explanation
Indices: 54953019--54953206 Score: 261
Period size: 40 Copynumber: 4.7 Consensus size: 40
54953009 ATAACCACAA
* * *
54953019 GCACAATTGCCTTCAGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
54953059 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
*
54953099 GCACAAATGCCTTCGGGTCTTAACCCAGATATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
54953139 GCACAAATGCCTTCGGGTCTTAACCCGGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT-AGCAACTC
* * *
54953179 GCATAAATGCCTTCGGGGCTTAGCCCGG
1 GCACAAATGCCTTCGGGTCTTAACCCGG
54953207 GTATCATTCA
Statistics
Matches: 133, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
40 131 0.98
41 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
Found at i:54953104 original size:80 final size:79
Alignment explanation
Indices: 54952999--54953210 Score: 300
Period size: 80 Copynumber: 2.7 Consensus size: 79
54952989 TCTTCGGAAT
* * *
54952999 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCAGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
54953063 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* * *
54953078 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAACCCAGATATAGCAACTCGCAC
1 TTAGCCCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
54953143 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* * * *
54953158 TTAACCCGGATATAATCACTAGCATAAATGCCTTCGGGGCTTAGCCCGGGTAT
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTAT
54953211 CATTCAATTG
Statistics
Matches: 117, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
79 5 0.04
80 111 0.95
81 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (79 bp):
TTAGCCCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACA
AATGCCTTCGGGTC
Found at i:54955454 original size:40 final size:40
Alignment explanation
Indices: 54955387--54955625 Score: 304
Period size: 40 Copynumber: 6.0 Consensus size: 40
54955377 GGATTTAACT
* * *
54955387 GGATATAGCT-ACTCGCTCGAATGCCTTCGGGACATAGCCC
1 GGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCC
* * *
54955427 GGATGTAGTAACTTGCACAAATGCCTTC-GGACTTAGCTC
1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
* * * *
54955466 GGATATAGTAACTCGCACAAATGCCTCCAGGACTTAACCT
1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
* *
54955506 GGATATAGTAACTCGCACAAATGCCTTTGGGACTTAACCC
1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
54955546 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
* * *
54955586 GGA-ACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGCCC
1 GGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
54955626 AGTTATCATC
Statistics
Matches: 175, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
39 36 0.21
40 139 0.79
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
Found at i:54963594 original size:40 final size:40
Alignment explanation
Indices: 54963490--54963705 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 40
54963480 AAGCCAGGTA
* * * *
54963490 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
54963529 CCTTC-GGACATAGCCCGGATGTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
54963568 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
54963608 CCTTCGGGACTTA-CCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
54963647 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
54963687 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
54963706 TTATCATCCG
Statistics
Matches: 161, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
38 6 0.04
39 70 0.43
40 85 0.53
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:54963625 original size:79 final size:79
Alignment explanation
Indices: 54963490--54963705 Score: 296
Period size: 79 Copynumber: 2.7 Consensus size: 79
54963480 AAGCCAGGTA
* * * * * *
54963490 CCTTCGGGATTTA-ACCGGATATAGCTACTCGCTCGAATGCCTTC-GGACATAGCCCGGATGTAG
1 CCTTCGGGACTTAGCCCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
54963553 TAACTCGCACAAATG
65 TAACTCGCACAAATG
54963568 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTA-CCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
54963632 TAACTCGCACAAATG
65 TAACTCGCACAAATG
* *
54963647 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGGATA-TAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
54963706 TTATCATCCG
Statistics
Matches: 124, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
78 14 0.11
79 99 0.80
80 11 0.09
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.23
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
AACTCGCACAAATG
Found at i:54971650 original size:40 final size:40
Alignment explanation
Indices: 54971571--54971824 Score: 320
Period size: 40 Copynumber: 6.4 Consensus size: 40
54971561 AAGCCAGGTA
* * * * *
54971571 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCACACAAATG
* *
54971610 CCTTCGGGACATAGCCCGGATGTAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
54971650 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
* *
54971690 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
* *
54971730 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
* *
54971770 CCTTCGGGACTTAGCCC-GA-ACTAGTCACT-AGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCA-CACAAATG
*
54971809 CCTTCAGGACTTAGCC
1 CCTTCGGGACTTAGCC
54971825 TGGTTATCAT
Statistics
Matches: 195, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
38 1 0.01
39 43 0.22
40 151 0.77
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
Found at i:54977677 original size:16 final size:16
Alignment explanation
Indices: 54977656--54977688 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54977646 CAGGTCTAAT
54977656 GGGGTTGAGATCTTTA
1 GGGGTTGAGATCTTTA
54977672 GGGGTTGAGATCTTTA
1 GGGGTTGAGATCTTTA
54977688 G
1 G
54977689 TGGTATCGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.39, T:0.36
Consensus pattern (16 bp):
GGGGTTGAGATCTTTA
Found at i:54988930 original size:13 final size:13
Alignment explanation
Indices: 54988912--54988936 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54988902 ACAAATAATA
54988912 AAATTTTCACACG
1 AAATTTTCACACG
54988925 AAATTTTCACAC
1 AAATTTTCACAC
54988937 ATATCAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:54991144 original size:81 final size:81
Alignment explanation
Indices: 54991018--54991217 Score: 244
Period size: 81 Copynumber: 2.5 Consensus size: 81
54991008 ACGATTCTTA
* * *
54991018 ACACTGGCTC-AAAGCCCTTCGAGACCAAGCTCGGATTAGGCCACTGGCTCGAAGGCCCTTCGGA
1 ACACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGGATTAGGCCACTGGCTCAAAAGCCCTTCGGA
*
54991082 ACTAAGTCCAGTTATG
66 ACTAAGTCCAATTATG
* *
54991098 ACACTGGCTCAAAAGCCCTTCGAAACTAAGTTCGGTTATTA-G-CACTGGCTCAAAAGCCCTTCG
1 ACACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGG--ATTAGGCCACTGGCTCAAAAGCCCTTCG
* ** * *
54991161 TATTTAAGTTCAATTATT
64 GAACTAAGTCCAATTATG
*
54991179 AGCACTGGCTCAAAAGCCCTTCGAACCCAAGCTCGGATT
1 A-CACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGGATT
54991218 TACACCCCGA
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
80 13 0.13
81 53 0.52
82 32 0.31
83 4 0.04
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (81 bp):
ACACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGGATTAGGCCACTGGCTCAAAAGCCCTTCGGA
ACTAAGTCCAATTATG
Found at i:54991156 original size:41 final size:41
Alignment explanation
Indices: 54991019--54991203 Score: 198
Period size: 41 Copynumber: 4.6 Consensus size: 41
54991009 CGATTCTTAA
* * * *
54991019 CACTGGCTC-AAAGCCCTTCGAGACCAAGCTC-G-GATTAGG
1 CACTGGCTCAAAAGCCCTTCGAAACTAAGTTCAGTTATTA-G
* * * * *
54991058 CCACTGGCTCGAAGGCCCTTCGGAACTAAGTCCAGTTATGA-
1 -CACTGGCTCAAAAGCCCTTCGAAACTAAGTTCAGTTATTAG
*
54991099 CACTGGCTCAAAAGCCCTTCGAAACTAAGTTCGGTTATTAG
1 CACTGGCTCAAAAGCCCTTCGAAACTAAGTTCAGTTATTAG
* ** *
54991140 CACTGGCTCAAAAGCCCTTCGTATTTAAGTTCAATTATTAG
1 CACTGGCTCAAAAGCCCTTCGAAACTAAGTTCAGTTATTAG
54991181 CACTGGCTCAAAAGCCCTTCGAA
1 CACTGGCTCAAAAGCCCTTCGAA
54991204 CCCAAGCTCG
Statistics
Matches: 121, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
40 43 0.36
41 74 0.61
42 1 0.01
43 3 0.02
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
CACTGGCTCAAAAGCCCTTCGAAACTAAGTTCAGTTATTAG
Found at i:54994637 original size:16 final size:17
Alignment explanation
Indices: 54994616--54994655 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
54994606 AGTTAGCTCC
54994616 CATTAGCTC-ACCAGCT
1 CATTAGCTCGACCAGCT
54994632 CATTAGCTCGGGACCAGCT
1 CATTAGCTC--GACCAGCT
54994651 CATTA
1 CATTA
54994656 TCAGCTCACG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
19 12 0.57
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (17 bp):
CATTAGCTCGACCAGCT
Found at i:54996320 original size:11 final size:12
Alignment explanation
Indices: 54996304--54996333 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
54996294 TACAAGTTTA
54996304 AAAAAAAT-TCG
1 AAAAAAATATCG
54996315 AAAAAAATATCG
1 AAAAAAATATCG
54996327 AAAAAAA
1 AAAAAAA
54996334 AGTGATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.13
Consensus pattern (12 bp):
AAAAAAATATCG
Found at i:54996320 original size:12 final size:13
Alignment explanation
Indices: 54996303--54996334 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
54996293 ATACAAGTTT
54996303 AAAAAAAAT-TCG
1 AAAAAAAATATCG
54996315 -AAAAAAATATCG
1 AAAAAAAATATCG
54996327 AAAAAAAA
1 AAAAAAAA
54996335 GTGATTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.44
12 3 0.17
13 7 0.39
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (13 bp):
AAAAAAAATATCG
Found at i:55001570 original size:19 final size:18
Alignment explanation
Indices: 55001546--55001584 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
55001536 AGCTCCCATG
55001546 TAGCTCCACACCAGCTCAT
1 TAGCT-CACACCAGCTCAT
**
55001565 TAGCTCGGACCAGCTCAT
1 TAGCTCACACCAGCTCAT
55001583 TA
1 TA
55001585 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.26, C:0.36, G:0.15, T:0.23
Consensus pattern (18 bp):
TAGCTCACACCAGCTCAT
Found at i:55002839 original size:14 final size:14
Alignment explanation
Indices: 55002817--55002864 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
55002807 ACCTAAACCG
* *
55002817 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
55002831 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
55002845 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
55002859 ACCATT
1 ACCATT
55002865 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:55006253 original size:5 final size:5
Alignment explanation
Indices: 55006243--55006303 Score: 63
Period size: 5 Copynumber: 12.0 Consensus size: 5
55006233 AAGAGAAAAC
* *
55006243 AAAGA AAAGA AAAGAA AAAGA AAAGC AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAGA AAAGA AAAGA AAA-GA AA-AGA
55006294 AAAGA AAAGA
1 AAAGA AAAGA
55006304 GAGGCAAGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
4 4 0.09
5 33 0.70
6 9 0.19
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:55006260 original size:19 final size:18
Alignment explanation
Indices: 55006236--55006290 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 18
55006226 TCTTGTAAAG
55006236 AGAAAACAAAGAAAAGAAA
1 AGAAAA-AAAGAAAAGAAA
*
55006255 AG--AAAAAGAAAAGCAA
1 AGAAAAAAAGAAAAGAAA
55006271 AGAAGAAAAAGAAAATGAAA
1 AGAA-AAAAAGAAAA-GAAA
55006291 TAAAAAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 13 0.43
17 2 0.07
19 12 0.40
20 3 0.10
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (18 bp):
AGAAAAAAAGAAAAGAAA
Found at i:55006262 original size:16 final size:16
Alignment explanation
Indices: 55006243--55006303 Score: 70
Period size: 16 Copynumber: 3.6 Consensus size: 16
55006233 AAGAGAAAAC
55006243 AAAGAAAAGAAAAGAA
1 AAAGAAAAGAAAAGAA
55006259 AAAGAAAAGCAAAGAAGAA
1 AAAGAAAAG--AA-AAGAA
*
55006278 AAAGAAAATG-AAATAA
1 AAAGAAAA-GAAAAGAA
55006294 AAAGAAAAGA
1 AAAGAAAAGA
55006304 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
15 1 0.03
16 21 0.54
17 1 0.03
18 2 0.05
19 13 0.33
20 1 0.03
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAGAAAAGAAAAGAA
Found at i:55006283 original size:30 final size:30
Alignment explanation
Indices: 55006247--55006303 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
55006237 GAAAACAAAG
*
55006247 AAAAGAAAA-GAAAAAGAAAAGCAAAGAAGA
1 AAAAGAAAATGAAAAA-AAAAGAAAAGAAGA
*
55006277 AAAAGAAAATGAAATAAAAAGAAAAGA
1 AAAAGAAAATGAAAAAAAAAGAAAAGA
55006304 GAGGCAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (30 bp):
AAAAGAAAATGAAAAAAAAAGAAAAGAAGA
Found at i:55006411 original size:30 final size:31
Alignment explanation
Indices: 55006377--55006447 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
55006367 AAAGCAAAAA
*
55006377 GAAAAAGAAA-ATGAGATTGAAAAAG-AGAAC
1 GAAAAAGAAATATGAGAGTGAAAAAGAAG-AC
* *
55006407 G-AAAAGAAATTTGAGAGTGAAAAAGAAGAT
1 GAAAAAGAAATATGAGAGTGAAAAAGAAGAC
55006437 GAAAAAGAAAT
1 GAAAAAGAAAT
55006448 TGAAACAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 8 0.23
30 16 0.46
31 11 0.31
ACGTcount: A:0.62, C:0.01, G:0.24, T:0.13
Consensus pattern (31 bp):
GAAAAAGAAATATGAGAGTGAAAAAGAAGAC
Found at i:55008652 original size:30 final size:30
Alignment explanation
Indices: 55008577--55008653 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 30
55008567 TCAACTCAAG
* **
55008577 AGCTAAACCTTAGCTCAACTTCAGCTTAGG
1 AGCTAAACCTTAGCTCAACTTCAGCTCACA
* * * * *
55008607 AGTTTAATCTCAGCTCAACTTTAGCTCACA
1 AGCTAAACCTTAGCTCAACTTCAGCTCACA
*
55008637 AGCTAAAGCTTAGCTCA
1 AGCTAAACCTTAGCTCA
55008654 TTTTAGTTTA
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (30 bp):
AGCTAAACCTTAGCTCAACTTCAGCTCACA
Found at i:55009108 original size:30 final size:31
Alignment explanation
Indices: 55009074--55009170 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
55009064 AGCTCACTCC
*
55009074 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
55009104 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
55009134 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
55009164 TAGCTCA
1 TAGCTCA
55009171 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:55009378 original size:517 final size:519
Alignment explanation
Indices: 55008396--55009425 Score: 1929
Period size: 517 Copynumber: 2.0 Consensus size: 519
55008386 GGAATTATAT
* *
55008396 GAGCACGCCCCGCGAACTTTATATAGCAAGTCTGTCAAGTCGAGCAATGACATGTTGGCAAGCTG
1 GAGCACGCCCCGCGAACTTTATAGAGCAAGTCTGTCAAGCCGAGCAATGACATGTTGGCAAGCTG
* *
55008461 ATCCCAGCTCATTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCTAGCTTATTCGAGCTCAATC
66 ATCCAAGCTCATTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCGAGCTCAATC
*
55008526 CATCTTGTCTGAGCTCAACCGAGCTCACTCCTAGCTCACTTTCAACTCAAGAGCTAAACCTTAGC
131 CATCTTGTCTGAGCTAAACCGAGCTCACTCCTAGCTCACTTTCAACTCAAGAGCTAAACCTTAGC
*
55008591 TCAACTTCAGCTTAGGAGTTTAATCTCAGCTCAACTTTAGCTCACAAGCTAAAGCTTAGCTCATT
196 TCAACTTCAGCTTAGGAGTTTAACCTCAGCTCAACTTTAGCTCACAAGCTAAAGCTTAGCTCATT
55008656 TTAGTTTAAACTCGGTTTTGTCTTTAATGCATTAAATAAAAATTTGCACATATTTATTTAAGCAT
261 TTAGTTTAAACTCGGTTTTGTCTTTAATGCATTAAATAAAAATTTGCACATATTTATTTAAGCAT
*
55008721 TAAACTTGTCTTATATTAATATTTGTTATTAATATGTCATAGTCATTACATAAATTGATTATGTT
326 TAAACTTGTCTTATATTAATATTTGTTATTAATATGCCATAGTCATTACATAAATTGATTATGTT
*
55008786 CACATAGCTGAATTAATGCATGACATTAATGTGTTCACATCATGCCGAATTTATGAGTGTTCATG
391 CACATAGCTGAATTAATGCATGACATTAATGTGTTCACATCATGCCGAATTTATGAGTGTCCATG
55008851 AGATATCTTAATGACTTGTTTATTTCATGTAGGTACATCCCTTTGGACGGTACAATGTTGATAC
456 AGATATCTTAATGACTTGTTTATTTCATGTAGGTACATCCCTTTGGACGGTACAATGTTGATAC
*
55008915 GAGCACG-CCCGCGAACTTTATCGAGCAAGTCTGTCAAGCCGAGCAATGACATGTTGGCAAGCTG
1 GAGCACGCCCCGCGAACTTTATAGAGCAAGTCTGTCAAGCCGAGCAATGACATGTTGGCAAGCTG
*
55008979 ATCCAAGCTCGTTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCGAGCTCAATC
66 ATCCAAGCTCATTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCGAGCTCAATC
*
55009044 CATCTTG-CTGAGCTAAACCGAGCTCACTCCTAGCTCACTTTCAACTCACGAGCTAAACCTTAGC
131 CATCTTGTCTGAGCTAAACCGAGCTCACTCCTAGCTCACTTTCAACTCAAGAGCTAAACCTTAGC
* *
55009108 TCAACTTCAGCTTAGGAGTTTAGCCTCAGCTCAACTTTAGCTCACGAGCTAAAGCTTAGCTCATT
196 TCAACTTCAGCTTAGGAGTTTAACCTCAGCTCAACTTTAGCTCACAAGCTAAAGCTTAGCTCATT
55009173 TTAGTTTAAACTCGGTTTTGTCTTTAATGCATTAAATAAAAATTTGCACATATTTATTTAAGCAT
261 TTAGTTTAAACTCGGTTTTGTCTTTAATGCATTAAATAAAAATTTGCACATATTTATTTAAGCAT
55009238 TAAACTTGTCTTATATTAATATTTGTTATTAATATGCCATAGTCATTACATAAATTGATTATGTT
326 TAAACTTGTCTTATATTAATATTTGTTATTAATATGCCATAGTCATTACATAAATTGATTATGTT
55009303 CACATAGCTGAATTAATGCATGACATTAATGTGTTCACATCATGCCGAATTTATGAGTGTCCATG
391 CACATAGCTGAATTAATGCATGACATTAATGTGTTCACATCATGCCGAATTTATGAGTGTCCATG
55009368 AGATATCTTAATGACTTGTTTATTTCATGTAGGTACATCCCTTTGGACGGTACAATGT
456 AGATATCTTAATGACTTGTTTATTTCATGTAGGTACATCCCTTTGGACGGTACAATGT
55009426 ATGGATGAAG
Statistics
Matches: 498, Mismatches: 13, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
517 368 0.74
518 123 0.25
519 7 0.01
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (519 bp):
GAGCACGCCCCGCGAACTTTATAGAGCAAGTCTGTCAAGCCGAGCAATGACATGTTGGCAAGCTG
ATCCAAGCTCATTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCGAGCTCAATC
CATCTTGTCTGAGCTAAACCGAGCTCACTCCTAGCTCACTTTCAACTCAAGAGCTAAACCTTAGC
TCAACTTCAGCTTAGGAGTTTAACCTCAGCTCAACTTTAGCTCACAAGCTAAAGCTTAGCTCATT
TTAGTTTAAACTCGGTTTTGTCTTTAATGCATTAAATAAAAATTTGCACATATTTATTTAAGCAT
TAAACTTGTCTTATATTAATATTTGTTATTAATATGCCATAGTCATTACATAAATTGATTATGTT
CACATAGCTGAATTAATGCATGACATTAATGTGTTCACATCATGCCGAATTTATGAGTGTCCATG
AGATATCTTAATGACTTGTTTATTTCATGTAGGTACATCCCTTTGGACGGTACAATGTTGATAC
Found at i:55010883 original size:11 final size:11
Alignment explanation
Indices: 55010867--55010908 Score: 77
Period size: 11 Copynumber: 3.9 Consensus size: 11
55010857 GTTATACAAG
55010867 TCAAAAAAAAT
1 TCAAAAAAAAT
55010878 TCAAAAAAAAT
1 TCAAAAAAAAT
55010889 TC-AAAAAAAT
1 TCAAAAAAAAT
55010899 TCAAAAAAAA
1 TCAAAAAAAA
55010909 ATCTGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 10 0.33
11 20 0.67
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.17
Consensus pattern (11 bp):
TCAAAAAAAAT
Found at i:55010885 original size:10 final size:10
Alignment explanation
Indices: 55010870--55010907 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
55010860 ATACAAGTCA
55010870 AAAAAAATTC
1 AAAAAAATTC
55010880 AAAAAAAATTC
1 -AAAAAAATTC
55010891 AAAAAAATTC
1 AAAAAAATTC
55010901 AAAAAAA
1 AAAAAAA
55010908 AATCTGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:55010917 original size:21 final size:21
Alignment explanation
Indices: 55010870--55010920 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 21
55010860 ATACAAGTCA
*
55010870 AAAAAAATTCAAAAAAAATTC
1 AAAAAAATTCAAAAAAAAATC
55010891 AAAAAAATTCAAAAAAAAATC
1 AAAAAAATTCAAAAAAAAATC
55010912 TGAAAAAAA
1 --AAAAAAA
55010921 GTGTTTAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 20 0.74
23 7 0.26
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.16
Consensus pattern (21 bp):
AAAAAAATTCAAAAAAAAATC
Found at i:55011842 original size:5 final size:5
Alignment explanation
Indices: 55011823--55011889 Score: 59
Period size: 5 Copynumber: 13.0 Consensus size: 5
55011813 ACATTCTTGT
*
55011823 AAAGA GAAA-A AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA
1 AAAGA -AAAGA AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA
55011869 AAATGA AATA-A AAAGA AAAGA
1 AAA-GA AA-AGA AAAGA AAAGA
55011890 GAGGCAAGAG
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
4 7 0.13
5 27 0.52
6 17 0.33
7 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:55011850 original size:15 final size:14
Alignment explanation
Indices: 55011823--55011889 Score: 71
Period size: 16 Copynumber: 4.4 Consensus size: 14
55011813 ACATTCTTGT
55011823 AAAGAGAAAAAAAGA
1 AAAGA-AAAAAAAGA
55011838 AAAGAAAAGAAAAAGCA
1 AAAG-AAA-AAAAAG-A
*
55011855 AAAGAAGAAAAAGA
1 AAAGAAAAAAAAGA
55011869 AAATGAAATAAAAAGA
1 AAA-GAAA-AAAAAGA
55011885 AAAGA
1 AAAGA
55011890 GAGGCAAGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
14 4 0.09
15 17 0.38
16 19 0.42
17 5 0.11
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (14 bp):
AAAGAAAAAAAAGA
Found at i:55011869 original size:31 final size:29
Alignment explanation
Indices: 55011827--55011889 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
55011817 TCTTGTAAAG
55011827 AGAAAAAAAGAAAA-GAAAAGAAAAAGCAAA
1 AGAAAAAAAGAAAATG-AAAGAAAAAG-AAA
*
55011857 AGAAGAAAAAGAAAATGAAATAAAAAGAAA
1 AGAA-AAAAAGAAAATGAAAGAAAAAGAAA
55011887 AGA
1 AGA
55011890 GAGGCAAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 10 0.33
31 19 0.63
32 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (29 bp):
AGAAAAAAAGAAAATGAAAGAAAAAGAAA
Found at i:55011954 original size:12 final size:12
Alignment explanation
Indices: 55011937--55011966 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
55011927 TTGAGAGAAC
55011937 TTGAAAAAGCCT
1 TTGAAAAAGCCT
55011949 TTG-AAAAGCCT
1 TTGAAAAAGCCT
55011960 TTGAAAA
1 TTGAAAA
55011967 GCAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:55011957 original size:11 final size:11
Alignment explanation
Indices: 55011941--55011968 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
55011931 GAGAACTTGA
55011941 AAAAGCCTTTG
1 AAAAGCCTTTG
55011952 AAAAGCCTTTG
1 AAAAGCCTTTG
55011963 AAAAGC
1 AAAAGC
55011969 AAAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (11 bp):
AAAAGCCTTTG
Found at i:55011984 original size:12 final size:12
Alignment explanation
Indices: 55011969--55011993 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55011959 TTTGAAAAGC
55011969 AAAAAGAAAATG
1 AAAAAGAAAATG
55011981 AAAAAGAAAATG
1 AAAAAGAAAATG
55011993 A
1 A
55011994 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:55011990 original size:18 final size:18
Alignment explanation
Indices: 55011963--55012018 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
55011953 AAAGCCTTTG
55011963 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
55011982 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
55012000 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
55012017 AA
1 AA
55012019 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:55012003 original size:30 final size:31
Alignment explanation
Indices: 55011969--55012050 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
55011959 TTTGAAAAGC
*
55011969 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
55011999 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
55012029 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
55012051 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:55014195 original size:30 final size:31
Alignment explanation
Indices: 55014161--55014257 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
55014151 AGCTCACTCC
*
55014161 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
55014191 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
55014221 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
55014251 TAGCTCA
1 TAGCTCA
55014258 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Done.