Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 38 of 91
Found at i:13172357 original size:18 final size:18
Alignment explanation
Indices: 13172334--13172370 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
13172324 CAAAACTAAG
13172334 CTTTTTCTTCCTTCCTCT
1 CTTTTTCTTCCTTCCTCT
* *
13172352 CTTTTTCTTTCTTCTTCT
1 CTTTTTCTTCCTTCCTCT
13172370 C
1 C
13172371 CTAGGGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (18 bp):
CTTTTTCTTCCTTCCTCT
Found at i:13175198 original size:81 final size:81
Alignment explanation
Indices: 13174957--13175209 Score: 337
Period size: 81 Copynumber: 3.1 Consensus size: 81
13174947 ATCAGATGAT
* * * * *
13174957 GCTGAAGGAGTCCATGTTCCTCAAG-TTGATTCGGTTATTGATGCATCTGCTGGAGGGAAGGGGG
1 GCTGAAGGAGTCCATGTTCCTGAGGCTT-ATTCGGTTATCGATGCATCTGCGGGAGGGGAGGGGG
*
13175021 ACCTTCACTCACTCGTG
65 ACCTTCACTCACTTGTG
* * * * * *
13175038 GCTGAAGGAGTCCATGTTCTTGAGGCTGATTCGGTTATCGATGCATTTTCGAGAAGGGAGGGGGA
1 GCTGAAGGAGTCCATGTTCCTGAGGCTTATTCGGTTATCGATGCATCTGCGGGAGGGGAGGGGGA
13175103 CCTTCACTCACTTGTG
66 CCTTCACTCACTTGTG
* *
13175119 GCTGAAGAAGTCCATGTTCCTGAGGCTTATTCGGTTATCAATGCATCTGCGGGAGGGGAGGGGGA
1 GCTGAAGGAGTCCATGTTCCTGAGGCTTATTCGGTTATCGATGCATCTGCGGGAGGGGAGGGGGA
* *
13175184 CCTTCAGTCGCTTGTG
66 CCTTCACTCACTTGTG
*
13175200 GTTGAAGGAG
1 GCTGAAGGAG
13175210 AACATCTTTT
Statistics
Matches: 147, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
81 146 0.99
82 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (81 bp):
GCTGAAGGAGTCCATGTTCCTGAGGCTTATTCGGTTATCGATGCATCTGCGGGAGGGGAGGGGGA
CCTTCACTCACTTGTG
Found at i:13176773 original size:86 final size:86
Alignment explanation
Indices: 13176628--13177312 Score: 940
Period size: 86 Copynumber: 7.9 Consensus size: 86
13176618 TGGGGCATGG
* * * *
13176628 CGTGTCACCCCACAAGACTACAACAAGTTAGCATGTCACGCCAGAAGTTTGCATGCACTCAGCGT
1 CGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCAGAAGTCTGCATGCACTCAGCGT
* *
13176693 GTCAGCATAATTGGCCCGTGC
66 GTCACCACAATTGGCCCGTGC
* *
13176714 CGTGTCACCCCACAAGATTGCAACAAGTCAGCGTGTCACGTCAGAAGTCTGCATGCACTCAGCGT
1 CGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCAGAAGTCTGCATGCACTCAGCGT
* * *
13176779 GTTACCACAATTGGCCCCTGT
66 GTCACCACAATTGGCCCGTGC
* * *
13176800 CGTGTCACCCCACAAGACTGCAACAAGTTAGCGTATCACGCCAGAAGTATGCATGCAAGCACTCA
1 CGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCAGAAG--T-C-TGCATGCACTCA
*
13176865 GCGTGTCACCATAATTGGCCCGTGC
62 GCGTGTCACCACAATTGGCCCGTGC
* * * *
13176890 TGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCATGCCAGATGTTTGCATGCACTCAGCGT
1 CGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCAGAAGTCTGCATGCACTCAGCGT
*
13176955 GTCACCACAATTGGCCTC-TGT
66 GTCACCACAATTGGCC-CGTGC
** * * *
13176976 CGTGTCACCCCACAAGACTGCAACAAGTCAGAATGTCACGTCAAAAGTCTGCATGCACTCAACGT
1 CGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCAGAAGTCTGCATGCACTCAGCGT
*
13177041 GTCACCACAATTGGCCCCTGC
66 GTCACCACAATTGGCCCGTGC
* *
13177062 CGTGTCACCCCATAAGACTGCAACAAGTCAGCGTGTCACGCCAGAAGTCTGCATGCAAGCACTTA
1 CGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCAGAAGTCTGCAT----GCACTCA
*
13177127 GCGTGTCACCATAATTGGCCCGTGC
62 GCGTGTCACCACAATTGGCCCGTGC
* * * *
13177152 TGTGTCACCCCACAAGACTGCAACAAGTCAACGTGTCACGCCAGAAGTCTGCATGCGCTCAACGT
1 CGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCAGAAGTCTGCATGCACTCAGCGT
*
13177217 GTCACCACAATTGGCCAGTGC
66 GTCACCACAATTGGCCCGTGC
* * * *
13177238 TGTGTCACCCCACAAGACTACAACAAGTCAGCATGTCATGCCAGAAGTCTGCATGCACTCAGCGT
1 CGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCAGAAGTCTGCATGCACTCAGCGT
13177303 GTCACCACAA
66 GTCACCACAA
13177313 GCATTTGTTC
Statistics
Matches: 527, Mismatches: 62, Indels: 20
0.87 0.10 0.03
Matches are distributed among these distances:
85 1 0.00
86 369 0.70
87 1 0.00
88 2 0.00
89 1 0.00
90 153 0.29
ACGTcount: A:0.27, C:0.32, G:0.21, T:0.20
Consensus pattern (86 bp):
CGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCAGAAGTCTGCATGCACTCAGCGT
GTCACCACAATTGGCCCGTGC
Found at i:13176918 original size:176 final size:173
Alignment explanation
Indices: 13176628--13177312 Score: 955
Period size: 176 Copynumber: 3.9 Consensus size: 173
13176618 TGGGGCATGG
* * *
13176628 CGTGTCACCCCACAAGACTACAACAAGTTAGCATGTCACGCCAGAAGTT-TGCATGCACTCAGCG
1 CGTGTCACCCCACAAGACTGCAACAAGTCAGCATGTCACGCCAGAAGTTCTGCATGCACTCAACG
* * * *
13176692 TGTCAGCATAATTGGCCCGTGCCGTGTCACCCCACAAGATTGCAACAAGTCAGCGTGTCACGTCA
66 TGTCACCACAATTGGCCCGTGCCGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCA
*
13176757 GAAGTCTGCATGCACTCAGCGTGTTACCACAATTGGCCCCTGT
131 GAAGTCTGCATGCACTCAGCGTGTCACCACAATTGGCCCCTGT
* * * *
13176800 CGTGTCACCCCACAAGACTGCAACAAGTTAGCGTATCACGCCAGAAGTATGCATGCAAGCACTCA
1 CGTGTCACCCCACAAGACTGCAACAAGTCAGCATGTCACGCCAGAAGT-T-C-TGCATGCACTCA
* * * *
13176865 GCGTGTCACCATAATTGGCCCGTGCTGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCATG
63 ACGTGTCACCACAATTGGCCCGTGCCGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACG
* * *
13176930 CCAGATGTTTGCATGCACTCAGCGTGTCACCACAATTGGCCTCTGT
128 CCAGAAGTCTGCATGCACTCAGCGTGTCACCACAATTGGCCCCTGT
* * *
13176976 CGTGTCACCCCACAAGACTGCAACAAGTCAGAATGTCACGTCAAAAG-TCTGCATGCACTCAACG
1 CGTGTCACCCCACAAGACTGCAACAAGTCAGCATGTCACGCCAGAAGTTCTGCATGCACTCAACG
* *
13177040 TGTCACCACAATTGGCCCCTGCCGTGTCACCCCATAAGACTGCAACAAGTCAGCGTGTCACGCCA
66 TGTCACCACAATTGGCCCGTGCCGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCA
* * *
13177105 GAAGTCTGCATGCAAGCACTTAGCGTGTCACCATAATTGGCCCGTG-
131 GAAGTCTGCAT----GCACTCAGCGTGTCACCACAATTGGCCCCTGT
* * *
13177151 CTGTGTCACCCCACAAGACTGCAACAAGTCAACGTGTCACGCCAGAAG-TCTGCATGCGCTCAAC
1 C-GTGTCACCCCACAAGACTGCAACAAGTCAGCATGTCACGCCAGAAGTTCTGCATGCACTCAAC
* * * * *
13177215 GTGTCACCACAATTGGCCAGTGCTGTGTCACCCCACAAGACTACAACAAGTCAGCATGTCATGCC
65 GTGTCACCACAATTGGCCCGTGCCGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCC
13177280 AGAAGTCTGCATGCACTCAGCGTGTCACCACAA
130 AGAAGTCTGCATGCACTCAGCGTGTCACCACAA
13177313 GCATTTGTTC
Statistics
Matches: 457, Mismatches: 47, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
172 146 0.32
173 2 0.00
174 1 0.00
175 1 0.00
176 307 0.67
ACGTcount: A:0.27, C:0.32, G:0.21, T:0.20
Consensus pattern (173 bp):
CGTGTCACCCCACAAGACTGCAACAAGTCAGCATGTCACGCCAGAAGTTCTGCATGCACTCAACG
TGTCACCACAATTGGCCCGTGCCGTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCA
GAAGTCTGCATGCACTCAGCGTGTCACCACAATTGGCCCCTGT
Found at i:13177103 original size:262 final size:260
Alignment explanation
Indices: 13176629--13177312 Score: 1071
Period size: 262 Copynumber: 2.6 Consensus size: 260
13176619 GGGGCATGGC
* * *
13176629 GTGTCACCCCACAAGACTACAACAAGTTAGCATGTCACGCCAGAAGTTTGCATGCACTCAGCGTG
1 GTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCAGAAGTTTGCATGCACTCAGCGTG
* * * *
13176694 TCAGCATAATTGGCCCGTGCCGTGTCACCCCACAAGATTGCAACAAGTCAGCGTGTCACGTCAGA
66 TCACCACAATTGGCCC-TG-CGTGTCACCCCACAAGACTGCAACAAGTCAGCATGTCACGTCAGA
* *
13176759 AGTCTGCATGCACTCAGCGTGTTACCACAATTGGCCCCTGTCGTGTCACCCCACAAGACTGCAAC
129 AGTCTGCATGCACTCAGCGTGTCACCACAATTGGCCCCTGCCGTGTCACCCCACAAGACTGCAAC
*
13176824 AAGTTAGCGTATCACGCCAGAAGTATGCATGCAAGCACTCAGCGTGTCACCATAATTGGCCCGTG
194 AAGTCAGCGTATCACGCCAGAAGTATGCATGCAAGCACTCAGCGTGTCACCATAATTGGCCCGTG
13176889 CT
259 CT
* *
13176891 GTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCATGCCAGATGTTTGCATGCACTCAGCGTG
1 GTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCAGAAGTTTGCATGCACTCAGCGTG
* *
13176956 TCACCACAATTGGCCTCTGTCGTGTCACCCCACAAGACTGCAACAAGTCAGAATGTCACGTCAAA
66 TCACCACAATTGGCC-CTG-CGTGTCACCCCACAAGACTGCAACAAGTCAGCATGTCACGTCAGA
* *
13177021 AGTCTGCATGCACTCAACGTGTCACCACAATTGGCCCCTGCCGTGTCACCCCATAAGACTGCAAC
129 AGTCTGCATGCACTCAGCGTGTCACCACAATTGGCCCCTGCCGTGTCACCCCACAAGACTGCAAC
* * *
13177086 AAGTCAGCGTGTCACGCCAGAAGTCTGCATGCAAGCACTTAGCGTGTCACCATAATTGGCCCGTG
194 AAGTCAGCGTATCACGCCAGAAGTATGCATGCAAGCACTCAGCGTGTCACCATAATTGGCCCGTG
13177151 CT
259 CT
* * * *
13177153 GTGTCACCCCACAAGACTGCAACAAGTCAACGTGTCACGCCAGAAGTCTGCATGCGCTCAACGTG
1 GTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCAGAAGTTTGCATGCACTCAGCGTG
* * * *
13177218 TCACCACAATTGGCCAGTGCTGTGTCACCCCACAAGACTACAACAAGTCAGCATGTCATGCCAGA
66 TCACCACAATTGGCC-CTGC-GTGTCACCCCACAAGACTGCAACAAGTCAGCATGTCACGTCAGA
13177283 AGTCTGCATGCACTCAGCGTGTCACCACAA
129 AGTCTGCATGCACTCAGCGTGTCACCACAA
13177313 GCATTTGTTC
Statistics
Matches: 386, Mismatches: 34, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
261 1 0.00
262 384 0.99
263 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.20
Consensus pattern (260 bp):
GTGTCACCCCACAAGACTGCAACAAGTCAGCGTGTCACGCCAGAAGTTTGCATGCACTCAGCGTG
TCACCACAATTGGCCCTGCGTGTCACCCCACAAGACTGCAACAAGTCAGCATGTCACGTCAGAAG
TCTGCATGCACTCAGCGTGTCACCACAATTGGCCCCTGCCGTGTCACCCCACAAGACTGCAACAA
GTCAGCGTATCACGCCAGAAGTATGCATGCAAGCACTCAGCGTGTCACCATAATTGGCCCGTGCT
Found at i:13180133 original size:21 final size:21
Alignment explanation
Indices: 13180109--13180149 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13180099 ATGCAGTATT
*
13180109 ACCCTCCAGCATCATAGTGTC
1 ACCCTCCAACATCATAGTGTC
*
13180130 ACCCTCCAACCTCATAGTGT
1 ACCCTCCAACATCATAGTGT
13180150 TGTCCTCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.12, T:0.24
Consensus pattern (21 bp):
ACCCTCCAACATCATAGTGTC
Found at i:13180867 original size:31 final size:31
Alignment explanation
Indices: 13180827--13181145 Score: 458
Period size: 31 Copynumber: 10.3 Consensus size: 31
13180817 GTTAGTCATA
*
13180827 TTGTTACACGCCATGCATATAACGTAAAATG
1 TTGTAACACGCCATGCATATAACGTAAAATG
*
13180858 TTGTAACACGCTATGCATATAACGTAAAATG
1 TTGTAACACGCCATGCATATAACGTAAAATG
* * * *
13180889 TAGTAACATGGCATGCATATAACTTAAAATG
1 TTGTAACACGCCATGCATATAACGTAAAATG
* *
13180920 TTGTAACACACCATGCATATAATGTAAAATG
1 TTGTAACACGCCATGCATATAACGTAAAATG
* *
13180951 TGGTAACACGCCATGCATATAACTTAAAATG
1 TTGTAACACGCCATGCATATAACGTAAAATG
*
13180982 TGGTAACACGCCATGCATATAACGTAAAATG
1 TTGTAACACGCCATGCATATAACGTAAAATG
* *
13181013 TTGTAACACACCATGCATATGACGTAAAATG
1 TTGTAACACGCCATGCATATAACGTAAAATG
* *
13181044 TTGTAACACGCCATGCATATGATGTAAAATG
1 TTGTAACACGCCATGCATATAACGTAAAATG
* *
13181075 TGGTAACACGTCATGCATATAACGTAAAATG
1 TTGTAACACGCCATGCATATAACGTAAAATG
* * *
13181106 TTGTAACATGCCATGCATATAACATAAAATA
1 TTGTAACACGCCATGCATATAACGTAAAATG
13181137 TTGTAACAC
1 TTGTAACAC
13181146 ACCAACGTTG
Statistics
Matches: 255, Mismatches: 33, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 255 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (31 bp):
TTGTAACACGCCATGCATATAACGTAAAATG
Found at i:13181494 original size:63 final size:62
Alignment explanation
Indices: 13181401--13181521 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 62
13181391 ACAGCCCGAT
* *
13181401 GACGATGGTGCTCAACAAAAGTTGACAGAGTTCATACAGTTCAGAGA-TCTGAGAGAGATGAC
1 GACGATGGTACTCAACAAAAGTTGACAGAGTTCAGACAGTTCAGAGAGT-TGAGAGAGATGAC
* ** *
13181463 GACGATGGTACTCAACAGAGAGTTGGTAGAGTTGAGACAGTTCAGAGAGTTGAGAGAGA
1 GACGATGGTACTCAACA-AAAGTTGACAGAGTTCAGACAGTTCAGAGAGTTGAGAGAGA
13181522 AAGATGGCCG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
62 16 0.31
63 34 0.67
64 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.21
Consensus pattern (62 bp):
GACGATGGTACTCAACAAAAGTTGACAGAGTTCAGACAGTTCAGAGAGTTGAGAGAGATGAC
Found at i:13181518 original size:9 final size:9
Alignment explanation
Indices: 13181479--13181520 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
13181469 GGTACTCAAC
13181479 AGAGAGTTG
1 AGAGAGTTG
13181488 -GTAGAGTTG
1 AG-AGAGTTG
* *
13181497 AGACAGTTC
1 AGAGAGTTG
13181506 AGAGAGTTG
1 AGAGAGTTG
13181515 AGAGAG
1 AGAGAG
13181521 AAAGATGGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 1 0.04
9 25 0.93
10 1 0.04
ACGTcount: A:0.33, C:0.05, G:0.40, T:0.21
Consensus pattern (9 bp):
AGAGAGTTG
Found at i:13182456 original size:15 final size:15
Alignment explanation
Indices: 13182436--13182504 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
13182426 AGGATATAAA
13182436 TTTAAATTTAATTTG
1 TTTAAATTTAATTTG
* *
13182451 TTTAAATTTAAATTA
1 TTTAAATTTAATTTG
* **
13182466 TCT--A-TCCATTATG
1 TTTAAATTTAATT-TG
13182479 TTTAAATTTAATTTG
1 TTTAAATTTAATTTG
13182494 TTTAAATTTAA
1 TTTAAATTTAA
13182505 ATATAATATC
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
12 3 0.08
13 4 0.10
15 29 0.73
16 4 0.10
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (15 bp):
TTTAAATTTAATTTG
Found at i:13183677 original size:47 final size:48
Alignment explanation
Indices: 13183573--13183698 Score: 227
Period size: 47 Copynumber: 2.6 Consensus size: 48
13183563 GTATATTTTA
13183573 TAATTATTTTACTTATTTGTTAGGTAAAATTTATAAAAATGCATGATG
1 TAATTATTTTACTTATTTGTTAGGTAAAATTTATAAAAATGCATGATG
13183621 TAATTATTTTACTTATTTGTTAGGTAAAATTTAT-AAAATGCATGATG
1 TAATTATTTTACTTATTTGTTAGGTAAAATTTATAAAAATGCATGATG
* *
13183668 TAATTATTTTACTTAATTGTTAAGTAAAATT
1 TAATTATTTTACTTATTTGTTAGGTAAAATT
13183699 GTATGCAAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
47 42 0.55
48 34 0.45
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (48 bp):
TAATTATTTTACTTATTTGTTAGGTAAAATTTATAAAAATGCATGATG
Found at i:13188467 original size:32 final size:33
Alignment explanation
Indices: 13188383--13188531 Score: 140
Period size: 35 Copynumber: 4.5 Consensus size: 33
13188373 AAGTTAGTTG
* * *
13188383 TTGGGTTTTGGTTGATCCCGTGAAAAACCATTA
1 TTGGGTTTTGGTTGAGCCCTTGAAAAACCACTA
* *
13188416 TTGTAGGTTGTGGTTGAGCCTTTGAAAAACCACT-
1 TTG--GGTTTTGGTTGAGCCCTTGAAAAACCACTA
* * *
13188450 TTGGGTTTTGGTTGAGCCCATGAAAAACCATTG
1 TTGGGTTTTGGTTGAGCCCTTGAAAAACCACTA
* * *
13188483 TTGAAGGTTGTGGTTGAGCCTTTGAAAAATCACT-
1 TTG--GGTTTTGGTTGAGCCCTTGAAAAACCACTA
*
13188517 TTGGGTTTTAGTTGA
1 TTGGGTTTTGGTTGA
13188532 TCTCGATAAA
Statistics
Matches: 95, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
32 35 0.37
33 6 0.06
34 6 0.06
35 48 0.51
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.37
Consensus pattern (33 bp):
TTGGGTTTTGGTTGAGCCCTTGAAAAACCACTA
Found at i:13188491 original size:67 final size:67
Alignment explanation
Indices: 13188383--13188531 Score: 244
Period size: 67 Copynumber: 2.2 Consensus size: 67
13188373 AAGTTAGTTG
* * *
13188383 TTGGGTTTTGGTTGATCCCGTGAAAAACCATTATTGTAGGTTGTGGTTGAGCCTTTGAAAAACCA
1 TTGGGTTTTGGTTGAGCCCATGAAAAACCATTATTGAAGGTTGTGGTTGAGCCTTTGAAAAACCA
13188448 CT
66 CT
* *
13188450 TTGGGTTTTGGTTGAGCCCATGAAAAACCATTGTTGAAGGTTGTGGTTGAGCCTTTGAAAAATCA
1 TTGGGTTTTGGTTGAGCCCATGAAAAACCATTATTGAAGGTTGTGGTTGAGCCTTTGAAAAACCA
13188515 CT
66 CT
*
13188517 TTGGGTTTTAGTTGA
1 TTGGGTTTTGGTTGA
13188532 TCTCGATAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 76 1.00
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.37
Consensus pattern (67 bp):
TTGGGTTTTGGTTGAGCCCATGAAAAACCATTATTGAAGGTTGTGGTTGAGCCTTTGAAAAACCA
CT
Found at i:13188543 original size:67 final size:67
Alignment explanation
Indices: 13188383--13188558 Score: 241
Period size: 67 Copynumber: 2.6 Consensus size: 67
13188373 AAGTTAGTTG
* *
13188383 TTGGGTTTTGGTTGATCCCG-TGAAAAACCATTATTGTAGGTTGTGGTTGAGCCTTTGAAAAACC
1 TTGGGTTTTGGTTGAT-CCGATGAAAAACCATTGTTGAAGGTTGTGGTTGAGCCTTTGAAAAACC
13188447 ACT
65 ACT
* * *
13188450 TTGGGTTTTGGTTGAGCCCATGAAAAACCATTGTTGAAGGTTGTGGTTGAGCCTTTGAAAAATCA
1 TTGGGTTTTGGTTGATCCGATGAAAAACCATTGTTGAAGGTTGTGGTTGAGCCTTTGAAAAACCA
13188515 CT
66 CT
* *
13188517 TTGGGTTTTAGTTGATCTCGAT-AAAAACTATTG-TGAAAGGTT
1 TTGGGTTTTGGTTGATC-CGATGAAAAACCATTGTTG-AAGGTT
13188559 TTGGCTAAGC
Statistics
Matches: 97, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
66 4 0.04
67 90 0.93
68 3 0.03
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (67 bp):
TTGGGTTTTGGTTGATCCGATGAAAAACCATTGTTGAAGGTTGTGGTTGAGCCTTTGAAAAACCA
CT
Found at i:13191639 original size:2 final size:2
Alignment explanation
Indices: 13191627--13191670 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
13191617 GTTGTTCGTG
*
13191627 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13191670 T
1 T
13191671 GTAAAGTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13192092 original size:28 final size:25
Alignment explanation
Indices: 13192047--13192136 Score: 90
Period size: 25 Copynumber: 3.5 Consensus size: 25
13192037 ACCGACGGGC
* *
13192047 TGTTAGACGTGGCTAGGCCACGGTCT
1 TGTTATACGTGGCAAGGCCACGG-CT
* *
13192073 GTGATTATACGTGGCAAGGCCATGGGT
1 -TG-TTATACGTGGCAAGGCCACGGCT
* *
13192100 TGTTATACGTGGCAAGGCCATGGGT
1 TGTTATACGTGGCAAGGCCACGGCT
*
13192125 TGATATACGTGG
1 TGTTATACGTGG
13192137 TTGTGAAAAC
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
25 34 0.60
26 2 0.04
27 3 0.05
28 18 0.32
ACGTcount: A:0.20, C:0.17, G:0.36, T:0.28
Consensus pattern (25 bp):
TGTTATACGTGGCAAGGCCACGGCT
Found at i:13192111 original size:25 final size:25
Alignment explanation
Indices: 13192077--13192136 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
13192067 CGGTCTGTGA
13192077 TTATACGTGGCAAGGCCATGGGTTG
1 TTATACGTGGCAAGGCCATGGGTTG
13192102 TTATACGTGGCAAGGCCATGGGTTG
1 TTATACGTGGCAAGGCCATGGGTTG
*
13192127 ATATACGTGG
1 TTATACGTGG
13192137 TTGTGAAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.22, C:0.15, G:0.35, T:0.28
Consensus pattern (25 bp):
TTATACGTGGCAAGGCCATGGGTTG
Found at i:13195672 original size:15 final size:16
Alignment explanation
Indices: 13195652--13195687 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
13195642 ATATATATAT
13195652 TTTTTTTTTCTTT-TC
1 TTTTTTTTTCTTTCTC
13195667 TTTTTTTTTCTTTCTC
1 TTTTTTTTTCTTTCTC
13195683 TTTTT
1 TTTTT
13195688 CTCTTCCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTTTTTCTTTCTC
Found at i:13195896 original size:33 final size:34
Alignment explanation
Indices: 13195859--13195940 Score: 114
Period size: 33 Copynumber: 2.4 Consensus size: 34
13195849 CATATACACA
*
13195859 TCAAAATCAGTAGTTAAGCTGCTCTA-TTTCTCC-
1 TCAAAATCAGTAGCTAAGCTGCTCTATTTTC-CCT
*
13195892 TCAAAATCAGTAGCTAAGCTGTTCTATTTTCCCT
1 TCAAAATCAGTAGCTAAGCTGCTCTATTTTCCCT
13195926 TCAAAATCCAGTAGC
1 TCAAAAT-CAGTAGC
13195941 CAAAGCTACA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
33 26 0.59
34 11 0.25
35 7 0.16
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (34 bp):
TCAAAATCAGTAGCTAAGCTGCTCTATTTTCCCT
Found at i:13195999 original size:35 final size:35
Alignment explanation
Indices: 13195951--13196031 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 35
13195941 CAAAGCTACA
* *
13195951 AAAATTAGCAACCAAAA-TGGCACCTTTCAGCCTTC
1 AAAATCAGCAACCAAAACT-GCACCTTTCAGCCCTC
*
13195986 AAAATCAGTAACCAAAACTGCACCTTTCAGCCCTC
1 AAAATCAGCAACCAAAACTGCACCTTTCAGCCCTC
13196021 AAAATCAGCAA
1 AAAATCAGCAA
13196032 TTAAAGCCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 40 0.98
36 1 0.02
ACGTcount: A:0.41, C:0.30, G:0.10, T:0.20
Consensus pattern (35 bp):
AAAATCAGCAACCAAAACTGCACCTTTCAGCCCTC
Found at i:13212855 original size:5 final size:5
Alignment explanation
Indices: 13212845--13212886 Score: 66
Period size: 5 Copynumber: 8.2 Consensus size: 5
13212835 TATATATATA
*
13212845 TCTTT TCTTT TCTCT TCTTT TCTTT TCTTT TCTTT CTCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT -TCTTT T
13212887 TCTCTTCCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
TCTTT
Found at i:13212862 original size:10 final size:10
Alignment explanation
Indices: 13212849--13212893 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
13212839 TATATATCTT
13212849 TTCTTTTCTC
1 TTCTTTTCTC
*
13212859 TTCTTTTCTT
1 TTCTTTTCTC
*
13212869 TTCTTTTCTT
1 TTCTTTTCTC
13212879 TCTCTTTTTCTC
1 T-TC-TTTTCTC
13212891 TTC
1 TTC
13212894 CTCCTCTCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
10 20 0.65
11 4 0.13
12 7 0.23
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTCTTTTCTC
Found at i:13212865 original size:15 final size:15
Alignment explanation
Indices: 13212845--13212893 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
13212835 TATATATATA
13212845 TCTTTTCTTTTCTCT
1 TCTTTTCTTTTCTCT
*
13212860 TCTTTTCTTTTCTTT
1 TCTTTTCTTTTCTCT
13212875 TCTTTCTCTTTTTCTCT
1 TCTTT-TC-TTTTCTCT
13212892 TC
1 TC
13212894 CTCCTCTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 19 0.63
16 2 0.07
17 9 0.30
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
TCTTTTCTTTTCTCT
Found at i:13213190 original size:35 final size:35
Alignment explanation
Indices: 13213151--13213230 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
13213141 CAAAGCTACA
*
13213151 AAAATTAGCAACCAAAA-TCGCACCTTTCAGCCTTC
1 AAAATCAGCAACCAAAACT-GCACCTTTCAGCCTTC
* * *
13213186 AAAATCAACAACCAAAACTTCACTTTTCAGCCTTC
1 AAAATCAGCAACCAAAACTGCACCTTTCAGCCTTC
13213221 AAAATCAGCA
1 AAAATCAGCA
13213231 GTTAAAGCCT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 38 0.97
36 1 0.03
ACGTcount: A:0.41, C:0.30, G:0.06, T:0.23
Consensus pattern (35 bp):
AAAATCAGCAACCAAAACTGCACCTTTCAGCCTTC
Found at i:13217988 original size:172 final size:170
Alignment explanation
Indices: 13217682--13218541 Score: 935
Period size: 172 Copynumber: 5.0 Consensus size: 170
13217672 CAATAAGCAT
* * ** *
13217682 TTTTTG-TTAAAACATATCATAATTGGATGTTTGCATTGGGAAA-GATGAAGTGAAAGCCATCAA
1 TTTTTGTTTAAAATAGATCATAATTGGATGTTTGCA-TCAGAAATG-TGAAGTGAAAGCCATCCA
* * * **
13217745 TTGACAAGAAAGGTCCATTTATAGTCACTCATACCTTTAAAAGCCTTATTACTCGCCATAAATGG
64 TTGACAAGAAAAGTCCATTTATAGTCACTCATACCTTCAAAAGCCTTGTTACTCGCTTTAAATGG
* * *
13217810 TTTTTTAATCTTATAAATGATTTTAAATCAAAGTCTTTTTCG
129 TTTTTTAATCTTATAAATGATTTTAAATCAAAATATTTTTCA
* * * * * *
13217852 TTTGTGTTTAAAATAGATCATAATTGGATGTTTGCATCGAGTAATGTGAAAGCGGAAGTCATCTA
1 TTTTTGTTTAAAATAGATCATAATTGGATGTTTGCATC-AGAAATGTG-AAGTGAAAGCCATCCA
* * * ** * **
13217917 TTAACAAGAAAAGTCCATTTATGGTCATTTTTACCTTCAAAAGCCTTGTTACTCACTTTAAATCA
64 TTGACAAGAAAAGTCCATTTATAGTCACTCATACCTTCAAAAGCCTTGTTACTCGCTTTAAATGG
13217982 TTTTTTAATCTTATAAATGATTTTAAAT-AGAAATATTTTTCA
129 TTTTTTAATCTTATAAATGATTTTAAATCA-AAATATTTTTCA
* * * * * * * *
13218024 -TTTTGATCAAAACAGATCATAATTGTATGTTAGCATCAGGAAACGTGAAGCGAAAGCTATCCAT
1 TTTTTGTTTAAAATAGATCATAATTGGATGTTTGCATCA-GAAATGTGAAGTGAAAGCCATCCAT
** * * * * *
13218088 TGATTAGAAAAATCCATTTATAGTCACTCATACCTTCAATAGCTTTGTTACTTGCTTTAAATGAT
65 TGACAAGAAAAGTCCATTTATAGTCACTCATACCTTCAAAAGCCTTGTTACTCGCTTTAAATGGT
* *
13218153 TTTTTAATCTTATGAATAATTTTAAATCAAAATATTTTTCA
130 TTTTTAATCTTATAAATGATTTTAAATCAAAATATTTTTCA
* * * * *
13218194 TTTTTGGTTAAAATAGATCCTAATTGGATGTTTACATTAGAAAATGTGAAGTGAAAACCATCCAT
1 TTTTTGTTTAAAATAGATCATAATTGGATGTTTGCATCAG-AAATGTGAAGTGAAAGCCATCCAT
* * * * *
13218259 TAACAAGAAAAG-CTCGTTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGG
65 TGACAAGAAAAGTC-CATTTATAGTCACTCATACCTTCAAAAGCCTTGTTACTCGCTTTAAATGG
* * *
13218323 TTTTATAATCTTATAAATGATTTTAAATCGAAATATTTTTTTA
129 TTTTTTAATCTTATAAATGATTTTAAATCAAAATA-TTTTTCA
* * * *
13218366 TTTTT-TATTAAAATAAATTATAATTGGATGTTAGCATCAGGAAACT-TGAAGTGAAAGCCATTC
1 TTTTTGT-TTAAAATAGATCATAATTGGATGTTTGCATCA-GAAA-TGTGAAGTGAAAGCCATCC
* * * * *
13218429 ATTGACAAGAAAAGTCCATTTATAGCCACTCATGCCTTTAATAA-TCTTGTTACTTGCTTTAAAT
63 ATTGACAAGAAAAGTCCATTTATAGTCACTCATACCTTCAA-AAGCCTTGTTACTCGCTTTAAAT
* *
13218493 GGTTTTTTAATCTTATAAATGATTTTAAATCAAACTACTTTTCA
127 GGTTTTTTAATCTTATAAATGATTTTAAATCAAAATATTTTTCA
13218537 TTTTT
1 TTTTT
13218542 TATTAAAGCA
Statistics
Matches: 570, Mismatches: 104, Indels: 31
0.81 0.15 0.04
Matches are distributed among these distances:
170 111 0.19
171 212 0.37
172 242 0.42
173 5 0.01
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (170 bp):
TTTTTGTTTAAAATAGATCATAATTGGATGTTTGCATCAGAAATGTGAAGTGAAAGCCATCCATT
GACAAGAAAAGTCCATTTATAGTCACTCATACCTTCAAAAGCCTTGTTACTCGCTTTAAATGGTT
TTTTAATCTTATAAATGATTTTAAATCAAAATATTTTTCA
Found at i:13218688 original size:140 final size:140
Alignment explanation
Indices: 13218428--13218680 Score: 370
Period size: 140 Copynumber: 1.8 Consensus size: 140
13218418 GAAAGCCATT
* * * *
13218428 CATTGACAAGAAAAGTCCATTTATAGCCACTCATGCCTTTAATAATCTTGTTACTTGCTTTAAAT
1 CATTGACAAGAAAAGTCCATTTATAGCCACTCATACCTTCAATAAGCTTGTTACTCGCTTTAAAT
*
13218493 GGTTTTTTAATCTTATAAATGATTTTAAATCAAACTACTTTTCATTTTTTATTAAAGCATGAAGC
66 GATTTTTTAATCTTATAAATGATTTTAAATCAAACTACTTTTCATTTTTTATTAAAGCATGAAGC
13218558 GGAAGCTATC
131 GGAAGCTATC
* * *
13218568 CATTGACAAGAAAAGTCCATTTATAGTCA-TGCATATCTTCGA-AAGCGTTGTTACTCGCTTTAA
1 CATTGACAAGAAAAGTCCATTTATAGCCACT-CATACCTTCAATAAGC-TTGTTACTCGCTTTAA
*
13218631 ATGATTTTTTAATCTTATAAATGATTTTAAATTGAAA-TA-TTTTCATTTTT
64 ATGATTTTTTAATCTTATAAATGATTTTAAA-TCAAACTACTTTTCATTTTT
13218681 GGTTTAAACA
Statistics
Matches: 101, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
139 15 0.15
140 82 0.81
141 4 0.04
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (140 bp):
CATTGACAAGAAAAGTCCATTTATAGCCACTCATACCTTCAATAAGCTTGTTACTCGCTTTAAAT
GATTTTTTAATCTTATAAATGATTTTAAATCAAACTACTTTTCATTTTTTATTAAAGCATGAAGC
GGAAGCTATC
Found at i:13218851 original size:151 final size:150
Alignment explanation
Indices: 13218648--13218959 Score: 435
Period size: 151 Copynumber: 2.1 Consensus size: 150
13218638 TTTAATCTTA
** * *
13218648 TAAATGATTTTAAATTGAAATATTTTCATTTTTGGTTTAAACAGATCATAATTGGATGTTTGCAT
1 TAAATGATTTTAAATCAAAATATTTTCATTGTTGGTTAAAACAGATCATAATTGGATGTTTGCAT
* *
13218713 TGGGAAACATGAAGCAAAAGCCATCCATTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTC
66 TAGGAAACATGAAGCAAAAGCCATCCATTGACAAGAAAAATCCATTTATAGTCACTCATGCCTTC
* *
13218778 AAAAGCCTTGTTATTTGCTT
131 AAAAGCCTTGTTACTCGCTT
* * * **
13218798 TAAATGATTTTCAATCAAAATTTTTTTCATTGTTGGTTAAAACATATCATAATTGGATGTTTGTG
1 TAAATGATTTTAAATCAAAA-TATTTTCATTGTTGGTTAAAACAGATCATAATTGGATGTTTGCA
* * **
13218863 TTAGGAAACATGAAGCAGAAGCCATCTATTGACAAGAAAAATCCATTTATAGTCACTTGTGCCTT
65 TTAGGAAACATGAAGCAAAAGCCATCCATTGACAAGAAAAATCCATTTATAGTCACTCATGCCTT
* *
13218928 TAAAAGTCTTGTTACTCGCTT
130 CAAAAGCCTTGTTACTCGCTT
*
13218949 TAAATGGTTTT
1 TAAATGATTTT
13218960 TTAATCTTAT
Statistics
Matches: 141, Mismatches: 20, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
150 17 0.12
151 124 0.88
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (150 bp):
TAAATGATTTTAAATCAAAATATTTTCATTGTTGGTTAAAACAGATCATAATTGGATGTTTGCAT
TAGGAAACATGAAGCAAAAGCCATCCATTGACAAGAAAAATCCATTTATAGTCACTCATGCCTTC
AAAAGCCTTGTTACTCGCTT
Found at i:13219542 original size:36 final size:37
Alignment explanation
Indices: 13219500--13219573 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
13219490 GCATAAACTT
* *
13219500 TACAATGCCTTTCAAGGATCAAGCACAA-CTTCTCAA
1 TACAATGCCTTTCAAGGATCAAACACAACCTTCACAA
* * *
13219536 TACAATGGCTTTTATGGATCAAACACAACCTTCACAA
1 TACAATGCCTTTCAAGGATCAAACACAACCTTCACAA
13219573 T
1 T
13219574 GCCTTTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
36 24 0.75
37 8 0.25
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.27
Consensus pattern (37 bp):
TACAATGCCTTTCAAGGATCAAACACAACCTTCACAA
Found at i:13219580 original size:32 final size:34
Alignment explanation
Indices: 13219501--13219582 Score: 87
Period size: 36 Copynumber: 2.4 Consensus size: 34
13219491 CATAAACTTT
* * *
13219501 ACAATGCCTTTCAAGGATCAAGCACAACTTCTCAA
1 ACAATGCCTTTTAAGGATCAAACACAACCTCTC-A
* *
13219536 TACAATGGCTTTTATGGATCAAACACAACCT-TC-
1 -ACAATGCCTTTTAAGGATCAAACACAACCTCTCA
13219569 ACAATGCCTTTTAA
1 ACAATGCCTTTTAA
13219583 AGGCTAAGGC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
32 12 0.31
35 2 0.05
36 25 0.64
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.28
Consensus pattern (34 bp):
ACAATGCCTTTTAAGGATCAAACACAACCTCTCA
Found at i:13220040 original size:20 final size:20
Alignment explanation
Indices: 13219998--13220053 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
13219988 GTTCTGGACC
* *
13219998 AAATGTATCGATA-TTTTGG
1 AAATGTATCCATACATTTGG
13220017 -AATGTATCCATACATTTGG
1 AAATGTATCCATACATTTGG
13220036 AAATGTATCCATACATTT
1 AAATGTATCCATACATTT
13220054 TGGGCATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 11 0.33
19 5 0.15
20 17 0.52
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39
Consensus pattern (20 bp):
AAATGTATCCATACATTTGG
Found at i:13220246 original size:22 final size:22
Alignment explanation
Indices: 13220221--13220263 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
13220211 AAACAAGTTA
13220221 AAAAATCATTAAAGCAATTTTC
1 AAAAATCATTAAAGCAATTTTC
* * *
13220243 AAAACTCATTCAAGTAATTTT
1 AAAAATCATTAAAGCAATTTT
13220264 GAAACTTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.35
Consensus pattern (22 bp):
AAAAATCATTAAAGCAATTTTC
Found at i:13220327 original size:21 final size:21
Alignment explanation
Indices: 13220294--13220380 Score: 97
Period size: 21 Copynumber: 4.0 Consensus size: 21
13220284 AATTAGGCAC
*
13220294 TTAAAAACTTATTTAAA-AATGT
1 TTAAAAAC-TATTCAAACAA-GT
13220316 TTAAAAACTATTCAAACAAGT
1 TTAAAAACTATTCAAACAAGT
*
13220337 TCAAAAACTCATTCAAAC-AGCT
1 TTAAAAACT-ATTCAAACAAG-T
*
13220359 TTAAAAATTATTCAAACAAGT
1 TTAAAAACTATTCAAACAAGT
13220380 T
1 T
13220381 CAAAGATCAT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
21 29 0.51
22 28 0.49
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (21 bp):
TTAAAAACTATTCAAACAAGT
Found at i:13220531 original size:21 final size:21
Alignment explanation
Indices: 13220507--13220567 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
13220497 AACTTCAAAA
*
13220507 ATCATTCGAACAAGTTTAAGG
1 ATCATTCGAACAAGTTTAAAG
* * * *
13220528 ATCACTCAAAGAAGTTCAAAG
1 ATCATTCGAACAAGTTTAAAG
*
13220549 ATCATT-GAATCAATTTTAA
1 ATCATTCGAA-CAAGTTTAA
13220568 TCACTTTTGT
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.30
Consensus pattern (21 bp):
ATCATTCGAACAAGTTTAAAG
Found at i:13220785 original size:97 final size:96
Alignment explanation
Indices: 13220658--13220853 Score: 288
Period size: 97 Copynumber: 2.0 Consensus size: 96
13220648 TTGAGCAAAA
*
13220658 TTTGCGTGTAAAGAAACACTCCACCTAAGTTTAACCATGAAGTACTTTGCTTTGAAATGCTAAGC
1 TTTGCGTGTAAAGAAACACTCCACCTAAGTTTAACCATGAAGTACTTTGATTTGAAATGCTAAGC
*
13220723 TTTTATAAAACTTTGAGAAGGGTTAAAATGC
66 TTTTATAAAACTTTGAGAAGGGTTAAAATAC
* * * * *
13220754 TTTGCTTGT-AAGAAAACTACTCC-CACTAAGTTTAATCATGAATTACTTTGATTTGATATGTTA
1 TTTGCGTGTAAAG-AAAC-ACTCCAC-CTAAGTTTAACCATGAAGTACTTTGATTTGAAATGCTA
13220817 AGCTTTTATAAAACTTTGAGAAGGGTTAAAATAC
63 AGCTTTTATAAAACTTTGAGAAGGGTTAAAATAC
13220851 TTT
1 TTT
13220854 AAAAGATTCA
Statistics
Matches: 90, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
95 3 0.03
96 13 0.14
97 74 0.82
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (96 bp):
TTTGCGTGTAAAGAAACACTCCACCTAAGTTTAACCATGAAGTACTTTGATTTGAAATGCTAAGC
TTTTATAAAACTTTGAGAAGGGTTAAAATAC
Found at i:13223205 original size:24 final size:24
Alignment explanation
Indices: 13223173--13223228 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
13223163 ATGGGTTTTT
13223173 CCCACTTCTTT-TTAATTGGGCCATG
1 CCCA-TTCTTTCTT-ATTGGGCCATG
13223198 CCCATTCTTTCCTTATTGGGCCATG
1 CCCATTCTTT-CTTATTGGGCCATG
*
13223223 TCCATT
1 CCCATT
13223229 TATATGCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 6 0.21
25 20 0.71
26 2 0.07
ACGTcount: A:0.14, C:0.30, G:0.14, T:0.41
Consensus pattern (24 bp):
CCCATTCTTTCTTATTGGGCCATG
Found at i:13223264 original size:10 final size:10
Alignment explanation
Indices: 13223251--13223275 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
13223241 TATATATATA
13223251 TTTTTTCTTT
1 TTTTTTCTTT
13223261 TTTTTTCTTT
1 TTTTTTCTTT
13223271 TTTTT
1 TTTTT
13223276 CTCCCTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:13226701 original size:35 final size:35
Alignment explanation
Indices: 13226662--13226733 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
13226652 TACAAAGATT
*
13226662 AGCAACCAAAACTTCACCTTTCAGCCTTTAAAATC
1 AGCAACCAAAACTTCACCTTTCAGCCTTCAAAATC
13226697 AGCAACCAAAACTTCACCTTTCAGCCTTCAAAATC
1 AGCAACCAAAACTTCACCTTTCAGCCTTCAAAATC
13226732 AG
1 AG
13226734 TAGCTAAAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.32, G:0.07, T:0.24
Consensus pattern (35 bp):
AGCAACCAAAACTTCACCTTTCAGCCTTCAAAATC
Found at i:13229556 original size:20 final size:19
Alignment explanation
Indices: 13229527--13229564 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
13229517 TTTTGGCTCC
13229527 ATTGACTTATTGGAGTATA
1 ATTGACTTATTGGAGTATA
13229546 ATTGTACTTATTGGAGTAT
1 ATTG-ACTTATTGGAGTAT
13229565 GATTTGANNN
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (19 bp):
ATTGACTTATTGGAGTATA
Found at i:13231832 original size:7 final size:7
Alignment explanation
Indices: 13231820--13231854 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
13231810 ATAGATACTC
13231820 TTCATAA
1 TTCATAA
13231827 TTCATAA
1 TTCATAA
13231834 TTCATAA
1 TTCATAA
13231841 TCTTCATAA
1 --TTCATAA
13231850 TTCAT
1 TTCAT
13231855 GAATGATACC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 19 0.73
9 7 0.27
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (7 bp):
TTCATAA
Found at i:13233954 original size:64 final size:63
Alignment explanation
Indices: 13233861--13234061 Score: 276
Period size: 64 Copynumber: 3.2 Consensus size: 63
13233851 TCCCCACTTT
* **
13233861 GCACATGCACGGTAGTAATTATCACAACCTTTATCATTAAACCGGCGTTTATACTTCCCACTCC
1 GCACATGCACGGTCGTAATTATCACAACCTTTATCATTAAACCGGC-TTTGCACTTCCCACTCC
*
13233925 GCACATGCACGATCGTAATTATCACAACCTTTATCATTAAACCGGCATTTGCACTTCCCACTCC
1 GCACATGCACGGTCGTAATTATCACAACCTTTATCATTAAACCGGC-TTTGCACTTCCCACTCC
* * * * * * *
13233989 ACAAATGCACGGTCGTAATTATCACATCCTTTGTCATTCAACTGGCATTGCACTTCCCACTCC
1 GCACATGCACGGTCGTAATTATCACAACCTTTATCATTAAACCGGCTTTGCACTTCCCACTCC
*
13234052 GTACATGCAC
1 GCACATGCAC
13234062 AGTTGCATCA
Statistics
Matches: 121, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
63 23 0.19
64 98 0.81
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.29
Consensus pattern (63 bp):
GCACATGCACGGTCGTAATTATCACAACCTTTATCATTAAACCGGCTTTGCACTTCCCACTCC
Found at i:13238106 original size:35 final size:35
Alignment explanation
Indices: 13238068--13238186 Score: 175
Period size: 35 Copynumber: 3.4 Consensus size: 35
13238058 TGATGTGGGC
* *
13238068 GGGAGTGCACATGATGATATTGAAATGAGCGTGTC
1 GGGAGTGCACATGATGATATTGAAATGTGCGTGTA
13238103 GGGAGTGCACATGATGATATTGAAATGTGCGTGTA
1 GGGAGTGCACATGATGATATTGAAATGTGCGTGTA
* ***
13238138 GGGAGTGCACATAATGATATTGCCTTGTGCGTGTA
1 GGGAGTGCACATGATGATATTGAAATGTGCGTGTA
*
13238173 AGGAGTGCACATGA
1 GGGAGTGCACATGA
13238187 GCTGAGTAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 76 1.00
ACGTcount: A:0.28, C:0.12, G:0.34, T:0.27
Consensus pattern (35 bp):
GGGAGTGCACATGATGATATTGAAATGTGCGTGTA
Found at i:13240336 original size:43 final size:43
Alignment explanation
Indices: 13240275--13240444 Score: 198
Period size: 43 Copynumber: 4.0 Consensus size: 43
13240265 TTTTGTGTGA
* *
13240275 TAATGATGACCCAGCTATGTACGGTGTGGGAATGCACATGAGC
1 TAATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGC
*
13240318 TAATGATGACCCAGCTATGTGCGGTGTGGGAGTGAACATGAGC
1 TAATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGC
* * * * *
13240361 TGATGATGACTCGGCTATGTGCAGAGTGGGAGTGCACATGAGC
1 TAATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGC
* * * * * *
13240404 TGACGATTACCCGGCTATGTGTGAGT-AGGGAGTGCACATGA
1 TAATGATGACCCAGCTATGTGCG-GTGTGGGAGTGCACATGA
13240445 TGATGATATT
Statistics
Matches: 110, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
43 109 0.99
44 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.24
Consensus pattern (43 bp):
TAATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGC
Found at i:13240435 original size:86 final size:83
Alignment explanation
Indices: 13240272--13240487 Score: 208
Period size: 86 Copynumber: 2.6 Consensus size: 83
13240262 CCTTTTTGTG
* * * * * *
13240272 TGATAATGATGACCCAGCTATGTACGGTGTGGGAATGCACATGAGCTAATGATGACCCAGCTATG
1 TGATGATGATGACTCAGCTATGTGC-GTGTGGGAGTGCACATGAGCTGACGATGACCCAGCTATG
*
13240337 TGCGGTGTGGGAGTGAACA
65 TGCGGTGAGGGAGTGAACA
* * * *
13240356 TGAGCTGATGATGACTCGGCTATGTGCAGAGTGGGAGTGCACATGAGCTGACGATTACCCGGCTA
1 TGA--TGATGATGACTCAGCTATGTGC-GTGTGGGAGTGCACATGAGCTGACGATGACCCAGCTA
* *
13240421 TGTGTGAGT-AGGGAGTGCACA
63 TGTGCG-GTGAGGGAGTGAACA
*
13240442 TGATGATGAT-A-T-TGC-ATTGTGCGTGTAGGGAGTGCACATGAGCTGA
1 TGATGATGATGACTCAGCTA-TGTGCGTGT-GGGAGTGCACATGAGCTGA
13240488 GTGTGGCGGG
Statistics
Matches: 111, Mismatches: 16, Indels: 13
0.79 0.11 0.09
Matches are distributed among these distances:
80 4 0.04
81 26 0.23
82 1 0.01
83 1 0.01
84 10 0.09
86 67 0.60
87 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.34, T:0.25
Consensus pattern (83 bp):
TGATGATGATGACTCAGCTATGTGCGTGTGGGAGTGCACATGAGCTGACGATGACCCAGCTATGT
GCGGTGAGGGAGTGAACA
Found at i:13240799 original size:21 final size:22
Alignment explanation
Indices: 13240755--13240800 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
13240745 TCTAACTTTT
* * *
13240755 GCTGCAGCGAGAATGGATTCTC
1 GCTGCAGCAAAAATGGAATCTC
13240777 GCTGCAGCAAAAAT-GAATCTC
1 GCTGCAGCAAAAATGGAATCTC
13240798 GCT
1 GCT
13240801 ATAGCGAGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (22 bp):
GCTGCAGCAAAAATGGAATCTC
Found at i:13247680 original size:43 final size:42
Alignment explanation
Indices: 13247621--13247750 Score: 181
Period size: 43 Copynumber: 3.0 Consensus size: 42
13247611 TTGTGTGATA
*
13247621 ATGATGACCCAGCTATGTGCGATGTGGGAGTGTACATGAGCTG
1 ATGATGA-CCAGCTATGTGCGATGTGGGAGTGCACATGAGCTG
* *
13247664 ATGATGATCCAGCTATGTACGGTGTGGGAGTGCACATGAGCTG
1 ATGATGA-CCAGCTATGTGCGATGTGGGAGTGCACATGAGCTG
*
13247707 ATGATGACCTAGCTATCTGCGA-GTAGGGAGTGCACATGAGCTG
1 ATGATGACC-AGCTATGTGCGATGT-GGGAGTGCACATGAGCTG
13247750 A
1 A
13247751 GTGTGGCGGG
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
42 4 0.05
43 74 0.95
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.25
Consensus pattern (42 bp):
ATGATGACCAGCTATGTGCGATGTGGGAGTGCACATGAGCTG
Found at i:13258938 original size:37 final size:40
Alignment explanation
Indices: 13258850--13258951 Score: 138
Period size: 37 Copynumber: 2.6 Consensus size: 40
13258840 ACCCAGCTCA
13258850 TGTACATCCCCCCACATCGTGCACATAGCCGACACCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCCGACACCATCG
* * * **
13258890 TGTGCACCCCCCCACATCGTGCACA-A-TC-AGTCCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCCGACACCATCG
13258927 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
13258952 CGGGCACTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
37 30 0.55
38 1 0.02
39 1 0.02
40 23 0.42
ACGTcount: A:0.24, C:0.43, G:0.15, T:0.19
Consensus pattern (40 bp):
TGTACATCCCCCCACATCGTGCACATAGCCGACACCATCG
Found at i:13259614 original size:2 final size:2
Alignment explanation
Indices: 13259607--13259641 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
13259597 ATAGGGTAAT
13259607 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
13259642 AGAATGCCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:13260911 original size:35 final size:35
Alignment explanation
Indices: 13260862--13260979 Score: 155
Period size: 35 Copynumber: 3.4 Consensus size: 35
13260852 GATGTGGGTG
* * *
13260862 GGAGTGCACCTGATGATATTGAAATGTACGTGTAG
1 GGAGTGCACATGATGATATTGAAATGTGCGTGTAA
* *
13260897 GGAGTGTACATGATGATATTCAAATGTGCGTGTAA
1 GGAGTGCACATGATGATATTGAAATGTGCGTGTAA
* ***
13260932 GGAGAGCACATGATGATATTGCCTTGTGCGTGTAA
1 GGAGTGCACATGATGATATTGAAATGTGCGTGTAA
13260967 GGAGTGCACATGA
1 GGAGTGCACATGA
13260980 GCTGAGTACG
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 71 1.00
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.28
Consensus pattern (35 bp):
GGAGTGCACATGATGATATTGAAATGTGCGTGTAA
Found at i:13264806 original size:171 final size:169
Alignment explanation
Indices: 13264203--13264937 Score: 613
Period size: 171 Copynumber: 4.3 Consensus size: 169
13264193 ATAAGCTTCC
* * * * *
13264203 AATCAAACTCTTTTTCGTTTGTGGTTAAAATAGATCATAATTAGATGTTTGGATCAAGAAACGTG
1 AATCAAACTTTTTTTCATTTGTGGTTAAAACAGATCATAATTAGATGTTTGCATCAA-AAACATG
** * * * *
13264268 AAGCGGAAGCCATGCATTGATAAGAAAAGTCCATATATAGTCACCCATGTCTTTGAAAA-CTTTG
65 AAGCAAAAGCCAT-CATTGATAAGAAAAGTCTATTTATAGTCACTCATGTCTTT-AAAAGCCTTG
* ** * * * *
13264332 TTACTTGCTGCAAATGGTTTTATACTCTTAGAAATTATTTTA
128 TTACTCGCTTTAAATGGTTTTTTAATCTTATAAATGATTTTA
* * * * * *
13264374 AATCAAAATATTTTTAATTTTTGGTTAAAACAGAAT-ATAATT-GAATGTTTGCATTAGGAAACA
1 AATCAAACTTTTTTTCATTTGTGGTTAAAACAG-ATCATAATTAG-ATGTTTGCATCA-AAAACA
* * * * * *
13264437 T-AATGCGAAAGCCATCAATTGATAAAAAAAGTCTACTTATAGTCACTCATGCCTTCAAATGCCT
63 TGAA-GCAAAAGCCATC-ATTGATAAGAAAAGTCTATTTATAGTCACTCATGTCTTTAAAAGCCT
* * * * **
13264501 TGTTATTCGCTTTAAATGATTTTCTAATCTTGTAAATGCCTTTA
126 TGTTACTCGCTTTAAATGGTTTTTTAATCTTATAAATGATTTTA
* * * * *
13264545 AACCGAAA-TGTTTTTTCATTTTTGGTTAAAACATATCATAATTGGATGTTTGCA-CAAAAAAAT
1 AATC-AAACT-TTTTTTCATTTGTGGTTAAAACAGATCATAATTAGATGTTTGCATC--AAAAAC
* * * * **
13264608 ATGAAGCAGAAGCCATTCATTGATAAGAAAAGTTTATTTATAGTTACTTATAACTTTAAAAGCCT
62 ATGAAGCAAAAGCCA-TCATTGATAAGAAAAGTCTATTTATAGTCACTCATGTCTTTAAAAGCCT
*
13264673 TGTTACTCGCTTTAAAAGGTTTTTTAATCTTATAAATGATTTTA
126 TGTTACTCGCTTTAAATGGTTTTTTAATCTTATAAATGATTTTA
** * * * * *
13264717 AATCAAACTTTTTTTTGTTTGTAGTTAAAATAGATCATAATTAGATATTTGTATCGAAAAACGTG
1 AATCAAACTTTTTTTCATTTGTGGTTAAAACAGATCATAATTAGATGTTTGCATC-AAAAACATG
* * * * ** *
13264782 AAGCAAAAACCATCAATTGATAAGAAAAGCCTATTTATTGTCACTCATGTCTTAAAAAATCTTGG
65 AAGCAAAAGCCATC-ATTGATAAGAAAAGTCTATTTATAGTCACTCATGTCTTTAAAAGCCTTGT
* * * * *
13264847 TGCTCACTTTCAATGGTTTTTTAATCTTGTAAATAATTTTA
129 TACTCGCTTTAAATGGTTTTTTAATCTTATAAATGATTTTA
* * * * *
13264888 AATCGAAA-TATTTTTAATTTTTGATTAAAACAAATCATAATT-GAATGTTT
1 AATC-AAACTTTTTTTCATTTGTGGTTAAAACAGATCATAATTAG-ATGTTT
13264938 TTATTATTCA
Statistics
Matches: 447, Mismatches: 98, Indels: 38
0.77 0.17 0.07
Matches are distributed among these distances:
170 10 0.02
171 294 0.66
172 137 0.31
173 6 0.01
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.38
Consensus pattern (169 bp):
AATCAAACTTTTTTTCATTTGTGGTTAAAACAGATCATAATTAGATGTTTGCATCAAAAACATGA
AGCAAAAGCCATCATTGATAAGAAAAGTCTATTTATAGTCACTCATGTCTTTAAAAGCCTTGTTA
CTCGCTTTAAATGGTTTTTTAATCTTATAAATGATTTTA
Found at i:13265907 original size:2 final size:2
Alignment explanation
Indices: 13265900--13265931 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13265890 CATGCTTGTT
13265900 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
13265932 CCTGACTCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13265984 original size:2 final size:2
Alignment explanation
Indices: 13265977--13266004 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13265967 NNNNNNNNNN
13265977 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
13266005 CCTGATCCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13268917 original size:2 final size:2
Alignment explanation
Indices: 13268910--13268966 Score: 82
Period size: 2 Copynumber: 28.5 Consensus size: 2
13268900 TCTATAACAA
13268910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13268951 A- AT AT CAT AT CAT AT A
1 AT AT AT -AT AT -AT AT A
13268967 ATANTGTCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.04
2 45 0.88
3 4 0.08
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:13269191 original size:111 final size:111
Alignment explanation
Indices: 13268997--13269220 Score: 412
Period size: 111 Copynumber: 2.0 Consensus size: 111
13268987 AATAATATTC
13268997 AAGCAAATTAGGATCATTTTGTCATAATCAAAACTATAAACATTTTAAAGCTAGCATCTGTGTCA
1 AAGCAAATTAGGATCATTTTGTCATAATCAAAACTATAAACATTTTAAAGCTAGCATCTGTGTCA
*
13269062 ATATTCTAATTGCTTTATGTTGTGTTTTAAGTATTGGAGCTTTCAT
66 ATATTCTAATTACTTTATGTTGTGTTTTAAGTATTGGAGCTTTCAT
* *
13269108 AAGCAAATTATGATCATTTTGTCATAATCAAAACTATAAACATTTTAAAGCTAGCATCTGTGTTA
1 AAGCAAATTAGGATCATTTTGTCATAATCAAAACTATAAACATTTTAAAGCTAGCATCTGTGTCA
*
13269173 ATATTTTAATTACTTTATGTTGTGTTTTAAGTATTGGAGCTTTCAT
66 ATATTCTAATTACTTTATGTTGTGTTTTAAGTATTGGAGCTTTCAT
13269219 AA
1 AA
13269221 ATTAACTCTA
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (111 bp):
AAGCAAATTAGGATCATTTTGTCATAATCAAAACTATAAACATTTTAAAGCTAGCATCTGTGTCA
ATATTCTAATTACTTTATGTTGTGTTTTAAGTATTGGAGCTTTCAT
Found at i:13283234 original size:28 final size:28
Alignment explanation
Indices: 13283203--13283290 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 28
13283193 ACCGGCTCAT
13283203 TAGCTCATGTGCACTCCCACACCGCACA
1 TAGCTCATGTGCACTCCCACACCGCACA
* * * **
13283231 TAGCTGGA-AT-CA-TCATC-CACCGGTCA
1 TAGCT-CATGTGCACTC-CCACACCGCACA
13283257 TCAGCTCATGTGCACTCCCACACCGCACA
1 T-AGCTCATGTGCACTCCCACACCGCACA
13283286 TAGCT
1 TAGCT
13283291 GGAATCACCC
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
26 11 0.26
27 8 0.19
28 13 0.30
29 11 0.26
ACGTcount: A:0.25, C:0.39, G:0.16, T:0.20
Consensus pattern (28 bp):
TAGCTCATGTGCACTCCCACACCGCACA
Found at i:13283276 original size:55 final size:56
Alignment explanation
Indices: 13283191--13283297 Score: 198
Period size: 55 Copynumber: 1.9 Consensus size: 56
13283181 ATGTATACAA
*
13283191 CCACCGGCTCATTAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCAT
1 CCACCGGCTCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCAT
13283247 CCACCGG-TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCA
1 CCACCGGCTCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCA
13283298 CCCGTCATCA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
55 43 0.86
56 7 0.14
ACGTcount: A:0.25, C:0.38, G:0.17, T:0.20
Consensus pattern (56 bp):
CCACCGGCTCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCAT
Found at i:13283324 original size:49 final size:54
Alignment explanation
Indices: 13283204--13283334 Score: 173
Period size: 55 Copynumber: 2.5 Consensus size: 54
13283194 CCGGCTCATT
* *
13283204 AGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCACCGGTCATC
1 AGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCA-CCACCGATCACC
**
13283259 AGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCA-C-CCGTC-ATCACC
1 AGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCACCACCGATCACC
*
13283310 AG-T-ATGTGCACTCCCACACCACACA
1 AGCTCATGTGCACTCCCACACCGCACA
13283335 CGCGGGGTTA
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
49 21 0.30
50 1 0.01
51 6 0.08
52 3 0.04
54 1 0.01
55 39 0.55
ACGTcount: A:0.27, C:0.40, G:0.15, T:0.18
Consensus pattern (54 bp):
AGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCACCACCGATCACC
Found at i:13286963 original size:4 final size:4
Alignment explanation
Indices: 13286956--13287015 Score: 50
Period size: 4 Copynumber: 14.8 Consensus size: 4
13286946 TTTACAGCAA
* * * * *
13286956 AAAT AAAT AAAT AAAT AAAT AATT AATT AATGT AGAG AAAT AAAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT -AAAT AAAT
13287006 -AAT AAAT AAA
1 AAAT AAAT AAA
13287016 ATTAACTGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
3 3 0.07
4 37 0.80
5 6 0.13
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:13287016 original size:16 final size:15
Alignment explanation
Indices: 13286993--13287042 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
13286983 TAATGTAGAG
13286993 AAATAAAATAAATAA
1 AAATAAAATAAATAA
* *
13287008 TAAATAAAATTAACTGA
1 -AAATAAAA-TAAATAA
*
13287025 AAAGAAAATAAATAA
1 AAATAAAATAAATAA
13287040 AAA
1 AAA
13287043 AGAGTTTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 8 0.29
16 15 0.54
17 5 0.18
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (15 bp):
AAATAAAATAAATAA
Found at i:13287034 original size:37 final size:37
Alignment explanation
Indices: 13286955--13287040 Score: 106
Period size: 37 Copynumber: 2.3 Consensus size: 37
13286945 TTTTACAGCA
* *
13286955 AAAATAAATAAATAAATAAATAATTAATTAATGTAGAG
1 AAAATAAATAAATAAATAAATAA-TAATTAATGAAAAG
13286993 -AAATAAAATAAAT-AATAAATAA-AATTAACTGAAAAG
1 AAAAT-AAATAAATAAATAAATAATAATTAA-TGAAAAG
13287029 AAAATAAATAAA
1 AAAATAAATAAA
13287041 AAAGAGTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
35 6 0.14
36 12 0.28
37 17 0.40
38 8 0.19
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.24
Consensus pattern (37 bp):
AAAATAAATAAATAAATAAATAATAATTAATGAAAAG
Found at i:13289027 original size:28 final size:27
Alignment explanation
Indices: 13288976--13289028 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
13288966 TATCCTAGTG
**
13288976 GTGGAAAATTACAATTTTGGCCCTAGA
1 GTGGAAAATTACAATTTTACCCCTAGA
*
13289003 GTGGCAAAATTACCATTTTACCCCTA
1 GTGG-AAAATTACAATTTTACCCCTA
13289029 TACTCTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (27 bp):
GTGGAAAATTACAATTTTACCCCTAGA
Found at i:13289097 original size:20 final size:20
Alignment explanation
Indices: 13289072--13289117 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
13289062 CTTTTAAACC
13289072 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
13289092 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
13289112 TCAAAT
1 TCAAAT
13289118 GGGGACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:13289784 original size:19 final size:19
Alignment explanation
Indices: 13289760--13289796 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13289750 TACCACTTTT
13289760 TTTTTTGGAATTTTTTTAG
1 TTTTTTGGAATTTTTTTAG
**
13289779 TTTTTTTTAATTTTTTTA
1 TTTTTTGGAATTTTTTTA
13289797 AAATTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (19 bp):
TTTTTTGGAATTTTTTTAG
Found at i:13291266 original size:21 final size:21
Alignment explanation
Indices: 13291240--13291302 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
13291230 TTGAATGGAG
* *
13291240 GCATCAGTCCTTATCATAAAT
1 GCATCAGTCTTTGTCATAAAT
* *
13291261 GCATCAGTCTTTGTTATGAAT
1 GCATCAGTCTTTGTCATAAAT
13291282 GCATCAGTCTTTGTCATAAAT
1 GCATCAGTCTTTGTCATAAAT
13291303 TACATGAACA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (21 bp):
GCATCAGTCTTTGTCATAAAT
Found at i:13292863 original size:55 final size:55
Alignment explanation
Indices: 13292786--13292939 Score: 254
Period size: 55 Copynumber: 2.8 Consensus size: 55
13292776 AACCACCGGC
13292786 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCACCAG
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCACCAG
* * * *
13292841 TCATCAGCTCATGTGCACTCCCACACCGCACATGGCTAGAATCATCATCCATCGG
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCACCAG
* *
13292896 TCATCAGCTCATGTGCACTCCCACACCTCACATAGTTGGAATCA
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCA
13292940 CCCGTCATCA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 91 1.00
ACGTcount: A:0.27, C:0.36, G:0.15, T:0.22
Consensus pattern (55 bp):
TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCACCAG
Found at i:13296489 original size:26 final size:26
Alignment explanation
Indices: 13296451--13296537 Score: 111
Period size: 26 Copynumber: 3.3 Consensus size: 26
13296441 TTTTCCTATC
**
13296451 TCTTTCTAATTAGGCCATGCCCATTT
1 TCTTTCTTGTTAGGCCATGCCCATTT
*
13296477 TCTTTCTTGTTAGGCCATACCCATTTT
1 TCTTTCTTGTTAGGCCATGCCCA-TTT
* *
13296504 TCTTTCTTGTTAGGTCATGCCTATTT
1 TCTTTCTTGTTAGGCCATGCCCATTT
*
13296530 TTTTTCTT
1 TCTTTCTT
13296538 TNNNNNNNNN
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
26 30 0.57
27 23 0.43
ACGTcount: A:0.14, C:0.23, G:0.11, T:0.52
Consensus pattern (26 bp):
TCTTTCTTGTTAGGCCATGCCCATTT
Found at i:13296512 original size:27 final size:27
Alignment explanation
Indices: 13296451--13296537 Score: 115
Period size: 27 Copynumber: 3.3 Consensus size: 27
13296441 TTTTCCTATC
**
13296451 TCTTTCTAATTAGGCCATGCCCA-TTT
1 TCTTTCTTGTTAGGCCATGCCCATTTT
*
13296477 TCTTTCTTGTTAGGCCATACCCATTTT
1 TCTTTCTTGTTAGGCCATGCCCATTTT
* *
13296504 TCTTTCTTGTTAGGTCATGCCTATTTT
1 TCTTTCTTGTTAGGCCATGCCCATTTT
13296531 T-TTTCTT
1 TCTTTCTT
13296538 TNNNNNNNNN
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
26 26 0.48
27 28 0.52
ACGTcount: A:0.14, C:0.23, G:0.11, T:0.52
Consensus pattern (27 bp):
TCTTTCTTGTTAGGCCATGCCCATTTT
Found at i:13297816 original size:19 final size:19
Alignment explanation
Indices: 13297771--13297817 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
13297761 CGACATCCGA
13297771 CTAAATAATAATATTTTATT
1 CTAAA-AATAATATTTTATT
* *
13297791 -AATAAAATATTATTTTATT
1 CTA-AAAATAATATTTTATT
13297810 CTAAAAAT
1 CTAAAAAT
13297818 TTTTATCTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (19 bp):
CTAAAAATAATATTTTATT
Found at i:13301287 original size:21 final size:22
Alignment explanation
Indices: 13301263--13301305 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
13301253 TTTAAAACAA
13301263 CTTTAAAACCAAAA-CTCTGAT
1 CTTTAAAACCAAAAGCTCTGAT
*
13301284 CTTTAAAATCAAAAGCTCTGAT
1 CTTTAAAACCAAAAGCTCTGAT
13301306 ACCACTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (22 bp):
CTTTAAAACCAAAAGCTCTGAT
Found at i:13303591 original size:13 final size:13
Alignment explanation
Indices: 13303573--13303597 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13303563 GGAGAAATTG
13303573 TGATTTTATAAAA
1 TGATTTTATAAAA
13303586 TGATTTTATAAA
1 TGATTTTATAAA
13303598 TTTTTTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:13305341 original size:15 final size:15
Alignment explanation
Indices: 13305318--13305349 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
13305308 AGACAATTTA
13305318 TAAAATCATTTTGTT
1 TAAAATCATTTTGTT
*
13305333 TAAACTCATTTTGTT
1 TAAAATCATTTTGTT
13305348 TA
1 TA
13305350 TACACATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (15 bp):
TAAAATCATTTTGTT
Found at i:13318538 original size:20 final size:18
Alignment explanation
Indices: 13318515--13318567 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
13318505 TAATTATAAA
13318515 TAACATAAAACT-AACATCAT
1 TAACATAAAA-TAAACAT--T
*
13318535 TAACTTAAAATAAACATT
1 TAACATAAAATAAACATT
*
13318553 TAACATAAATTAAAC
1 TAACATAAAATAAAC
13318568 TAAACTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 14 0.48
19 1 0.03
20 14 0.48
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (18 bp):
TAACATAAAATAAACATT
Found at i:13326083 original size:22 final size:22
Alignment explanation
Indices: 13326055--13326098 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
13326045 TTTAAAACAA
13326055 CTTTAAACCCAAAAGCACTGAT
1 CTTTAAACCCAAAAGCACTGAT
*
13326077 CTTTAAACCCAAAAGCTCTGAT
1 CTTTAAACCCAAAAGCACTGAT
13326099 ACCAATGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25
Consensus pattern (22 bp):
CTTTAAACCCAAAAGCACTGAT
Found at i:13328388 original size:20 final size:20
Alignment explanation
Indices: 13328362--13328407 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
13328352 AATCTTACCT
* *
13328362 TTTTTCACTTGTTTCCTTGAA
1 TTTTACACTT-TTCCCTTGAA
13328383 TTTTCACACTTTTCCCTTGAA
1 TTTT-ACACTTTTCCCTTGAA
13328404 TTTT
1 TTTT
13328408 TTCCACCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTACACTTTTCCCTTGAA
Found at i:13328408 original size:22 final size:22
Alignment explanation
Indices: 13328367--13328407 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
13328357 TACCTTTTTT
*
13328367 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
13328389 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
13328408 TTCCACCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:13329717 original size:19 final size:19
Alignment explanation
Indices: 13329693--13329734 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
13329683 GATAAGAGAC
* *
13329693 AATTTTAAAGCTTGATGCT
1 AATTTTAAAGCTAGATACT
13329712 AATTTTAAAGCTAGATACT
1 AATTTTAAAGCTAGATACT
13329731 AATT
1 AATT
13329735 GAGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (19 bp):
AATTTTAAAGCTAGATACT
Found at i:13339958 original size:59 final size:58
Alignment explanation
Indices: 13339832--13339987 Score: 197
Period size: 59 Copynumber: 2.7 Consensus size: 58
13339822 TAGCAGCATT
* * * * *
13339832 AACATGTTTGTCTTAATTTAGACAAG-AAAACATGTTTGGTCTTAATTTTGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTGATCTTAATCTAGACAAGAA
* *
13339889 AATATGTTTGTCTTAATTTAAGACAAGAAAAATATTTTTTATCTTAATCTAGACAAGAA
1 AACATGTTTGTCTTAATTT-AGACAAGAAAAATATTTTTGATCTTAATCTAGACAAGAA
* * *
13339948 TACATATTTGTCTCAATTTAGACAAGATAAAATATTTTTG
1 AACATGTTTGTCTTAATTTAGACAAGA-AAAATATTTTTG
13339988 TTTTAATTAC
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
57 18 0.21
58 15 0.18
59 51 0.61
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (58 bp):
AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTGATCTTAATCTAGACAAGAA
Found at i:13339974 original size:28 final size:28
Alignment explanation
Indices: 13339832--13339974 Score: 169
Period size: 28 Copynumber: 5.0 Consensus size: 28
13339822 TAGCAGCATT
13339832 AACATGTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
*
13339860 AACATGTTTGGTCTTAATTTTGACAAGAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
*
13339889 AATATGTTTGTCTTAATTTAAGACAAGAAA
1 AACATGTTTGTCTTAATTT-AGACAAG-AA
* * * *
13339919 AATATTTTTTATCTTAATCTAGACAAGAA
1 AACA-TGTTTGTCTTAATTTAGACAAGAA
* * *
13339948 TACATATTTGTCTCAATTTAGACAAGA
1 AACATGTTTGTCTTAATTTAGACAAGA
13339975 TAAAATATTT
Statistics
Matches: 99, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
28 38 0.38
29 36 0.36
30 13 0.13
31 12 0.12
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:13341296 original size:36 final size:35
Alignment explanation
Indices: 13341219--13341298 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 35
13341209 TTTTTAAAAG
13341219 AAAAAAAGTTTTTCTTATATTAAAATTCTGTTATT
1 AAAAAAAGTTTTTCTTATATTAAAATTCTGTTATT
* * * *
13341254 ATAAAAATA-TTTTTTTTCTATTAAAATATTTTTTATT
1 A-AAAAA-AGTTTTTCTTATATTAAAAT-TCTGTTATT
13341291 AAAAAAAG
1 AAAAAAAG
13341299 AGAGGGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
35 2 0.05
36 26 0.70
37 9 0.24
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (35 bp):
AAAAAAAGTTTTTCTTATATTAAAATTCTGTTATT
Found at i:13344807 original size:2 final size:2
Alignment explanation
Indices: 13344800--13344836 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
13344790 ATGTGCTTAT
* *
13344800 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13344837 GAATGATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (2 bp):
TA
Found at i:13345283 original size:12 final size:12
Alignment explanation
Indices: 13345266--13345294 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
13345256 ATTACAGAAA
13345266 TATAATATAATT
1 TATAATATAATT
13345278 TATAATATAATT
1 TATAATATAATT
13345290 TATAA
1 TATAA
13345295 AACAAGTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TATAATATAATT
Found at i:13346892 original size:19 final size:19
Alignment explanation
Indices: 13346858--13346895 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
13346848 CTATTTGACT
**
13346858 TATTGGAGTATGATTTGAG
1 TATTGGAGTACAATTTGAG
13346877 TATTGGAGTACAATTTGAG
1 TATTGGAGTACAATTTGAG
13346896 GTTAAGAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.29, T:0.39
Consensus pattern (19 bp):
TATTGGAGTACAATTTGAG
Found at i:13349585 original size:11 final size:11
Alignment explanation
Indices: 13349569--13349609 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
13349559 AGAACTTTTG
13349569 GGTTTAAAGTT
1 GGTTTAAAGTT
13349580 GGTTTAAAGTT
1 GGTTTAAAGTT
*
13349591 GTTTTAAAGTT
1 GGTTTAAAGTT
*
13349602 GTTTTAAA
1 GGTTTAAA
13349610 TTTTACAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (11 bp):
GGTTTAAAGTT
Found at i:13353845 original size:28 final size:27
Alignment explanation
Indices: 13353814--13353867 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
13353804 TTTCGGAGCA
* *
13353814 TAGGGGTAAAATGGTAATTTTGCCACCC
1 TAGGGGCAAAATAGTAATTTT-CCACCC
13353842 TAGGGGCAAAATAGTAATTTTCCACC
1 TAGGGGCAAAATAGTAATTTTCCACC
13353868 ACCAGAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (27 bp):
TAGGGGCAAAATAGTAATTTTCCACCC
Found at i:13356553 original size:20 final size:20
Alignment explanation
Indices: 13356528--13356569 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
13356518 GTCCCCATTA
*
13356528 GACTTATTGGAGTATAATTT
1 GACTTATTAGAGTATAATTT
*
13356548 GACTTATTAGAGTATGATTT
1 GACTTATTAGAGTATAATTT
13356568 GA
1 GA
13356570 GGTTTAGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (20 bp):
GACTTATTAGAGTATAATTT
Found at i:13356645 original size:27 final size:27
Alignment explanation
Indices: 13356615--13356672 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
13356605 TTGGAGTAAA
*
13356615 AGGGTAAAATGGTAATTTTGCCACC-TC
1 AGGGAAAAATGGTAATTTT-CCACCATC
*
13356642 AGGGGAAAAATTGTAATTTTCCACCATC
1 A-GGGAAAAATGGTAATTTTCCACCATC
13356670 AGG
1 AGG
13356673 ACATTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (27 bp):
AGGGAAAAATGGTAATTTTCCACCATC
Found at i:13361557 original size:14 final size:14
Alignment explanation
Indices: 13361534--13361568 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
13361524 ATGAAAGATG
*
13361534 AAAGATAGAAAAGA
1 AAAGAAAGAAAAGA
*
13361548 TAAGAAAGAAAAGA
1 AAAGAAAGAAAAGA
13361562 AAAGAAA
1 AAAGAAA
13361569 AGTCAAAGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (14 bp):
AAAGAAAGAAAAGA
Found at i:13367222 original size:28 final size:29
Alignment explanation
Indices: 13367182--13367324 Score: 166
Period size: 28 Copynumber: 4.8 Consensus size: 29
13367172 CAGCATTAAC
*
13367182 ATGTTTGTCTTAATTTTGACAAG-AAAAT
1 ATGTTTGTCTTAATTTAGACAAGAAAAAT
13367210 ATGTTTGTCTTAATTTAAGACAAGAAAAAT
1 ATGTTTGTCTTAATTT-AGACAAGAAAAAT
*
13367240 ATTTTTTTGTCTTAATTTAGACAAGAAAACAT
1 A--TGTTTGTCTTAATTTAGACAAGAAAA-AT
*
13367272 A--TTTGTCTTAATTTAGATAAGATAAAAT
1 ATGTTTGTCTTAATTTAGACAAGA-AAAAT
* *
13367300 ATTTTTGTCTTAATTACAGACAAGA
1 ATGTTTGTCTTAATT-TAGACAAGA
13367325 GTTGTCTTAA
Statistics
Matches: 101, Mismatches: 5, Indels: 15
0.83 0.04 0.12
Matches are distributed among these distances:
28 39 0.39
29 9 0.09
30 18 0.18
31 18 0.18
32 17 0.17
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (29 bp):
ATGTTTGTCTTAATTTAGACAAGAAAAAT
Found at i:13367278 original size:60 final size:58
Alignment explanation
Indices: 13367185--13367324 Score: 192
Period size: 60 Copynumber: 2.4 Consensus size: 58
13367175 CATTAACATG
* * *
13367185 TTTGTCTTAATTTTGACAAGAAAATATGTTTGTCTTAATTTAAGACAAGA-AAAATATTTT
1 TTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTT-AGACAAGATAAAATA--TT
*
13367245 TTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTTAGATAAGATAAAATATT
1 TTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTTAGACAAGATAAAATATT
*
13367303 TTTGTCTTAATTACAGACAAGA
1 TTTGTCTTAATT-TAGACAAGA
13367325 GTTGTCTTAA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
58 14 0.19
59 15 0.21
60 44 0.60
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.41
Consensus pattern (58 bp):
TTTGTCTTAATTTAGACAAGAAAACATATTTGTCTTAATTTAGACAAGATAAAATATT
Found at i:13374348 original size:43 final size:42
Alignment explanation
Indices: 13374199--13374404 Score: 228
Period size: 40 Copynumber: 5.0 Consensus size: 42
13374189 TGTGATAATT
*
13374199 ATGACCCA-CCATGTGCGGTGCAGGAGTGCACATGAGCTGATG
1 ATGACCCAGCCATGTGCGGTG-GGGAGTGCACATGAGCTGATG
* *
13374241 ATGACCTAGCCATGT---GTGGAGGAGTACACATGAGCTGATG
1 ATGACCCAGCCATGTGCGGTGG-GGAGTGCACATGAGCTGATG
*
13374281 ATGACCCAGCCATGT---GTGGAGGAGTACACATGAGCTGATG
1 ATGACCCAGCCATGTGCGGTGG-GGAGTGCACATGAGCTGATG
* *
13374321 ATGACCCAGCTATGTGCGAGTGGGGAGTGCACATGAACTGATG
1 ATGACCCAGCCATGTGCG-GTGGGGAGTGCACATGAGCTGATG
* * * *
13374364 ATGACCTAGCTATGTGCGGTGTAGGAGTGCACATAAGCTGA
1 ATGACCCAGCCATGTGCGGTG-GGGAGTGCACATGAGCTGA
13374405 GAGAGAGTTG
Statistics
Matches: 146, Mismatches: 11, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
40 75 0.51
42 10 0.07
43 57 0.39
44 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.21
Consensus pattern (42 bp):
ATGACCCAGCCATGTGCGGTGGGGAGTGCACATGAGCTGATG
Found at i:13376616 original size:5 final size:5
Alignment explanation
Indices: 13376597--13376648 Score: 68
Period size: 5 Copynumber: 10.0 Consensus size: 5
13376587 TATATATATA
* *
13376597 TTTCT TTTGT TTTCT CTTCT TTTCT TTTCT TTTCT TTTCT TTCTCT CTTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TT-TCT -TTTCT
13376649 CTTCCTCTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
5 33 0.80
6 6 0.15
7 2 0.05
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTCT
Found at i:13376857 original size:33 final size:34
Alignment explanation
Indices: 13376820--13376898 Score: 106
Period size: 33 Copynumber: 2.3 Consensus size: 34
13376810 ATATCCACAC
*
13376820 CAAAATCAGCAGTTAAGCTGCTCTATTTCTCC-T
1 CAAAATCAGCAGCTAAGCTGCTCTATTTCTCCTT
* * *
13376853 CAAAATTAGCAGCTAAGCTGCTTTATTTTTCCTT
1 CAAAATCAGCAGCTAAGCTGCTCTATTTCTCCTT
13376887 CAAAAATCAGCA
1 C-AAAATCAGCA
13376899 ACCAAAGCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 28 0.72
34 2 0.05
35 9 0.23
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (34 bp):
CAAAATCAGCAGCTAAGCTGCTCTATTTCTCCTT
Found at i:13377225 original size:2 final size:2
Alignment explanation
Indices: 13377218--13377247 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
13377208 CTTATTCAAT
13377218 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13377248 TTTTTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:13379430 original size:16 final size:16
Alignment explanation
Indices: 13379409--13379446 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
13379399 CATGGAAGCT
13379409 TGATTTGGAGCTTGCA
1 TGATTTGGAGCTTGCA
13379425 TGATTTGGAGCTTGCA
1 TGATTTGGAGCTTGCA
13379441 TGATTT
1 TGATTT
13379447 TTTCTCTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.42
Consensus pattern (16 bp):
TGATTTGGAGCTTGCA
Found at i:13380220 original size:43 final size:43
Alignment explanation
Indices: 13380157--13380268 Score: 163
Period size: 43 Copynumber: 2.6 Consensus size: 43
13380147 CATTGACTCG
* **
13380157 GCTATGTACGAGTAGGGAGTGCGCATAAGTCGAG-GATGACCCA
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGATGACCCA
*
13380200 GTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCA
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCA
*
13380243 GCCATGTGCGAGTAGGGAGTGCGCAT
1 GCTATGTGCGAGTAGGGAGTGCGCAT
13380269 GAGCTGGTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.02
43 61 0.98
ACGTcount: A:0.24, C:0.20, G:0.37, T:0.20
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCA
Found at i:13380278 original size:43 final size:43
Alignment explanation
Indices: 13380160--13380281 Score: 158
Period size: 43 Copynumber: 2.8 Consensus size: 43
13380150 TGACTCGGCT
* **
13380160 ATGTACGAGTAGGGAGTGCGCATAAG-TCGAG-GATGACCCAGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCT-G-GTGATGACCCAGCC
* *
13380203 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGACCCAGCC
*
13380246 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGA
13380282 TGATGATGGG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.25, C:0.18, G:0.38, T:0.20
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCTGGTGATGACCCAGCC
Found at i:13381938 original size:55 final size:55
Alignment explanation
Indices: 13381852--13382003 Score: 234
Period size: 55 Copynumber: 2.8 Consensus size: 55
13381842 AACCACTGGC
* *
13381852 TCATCAGCTCATGTGCACTCCCACA-ACGCACATAGCTAGAATTATCACCCACCGG
1 TCATCAGCTCATGTGCACTCCCACACA-GCACATAGCTGGAATTATCACCCAACGG
* *
13381907 TCATCAGCTCATGTGCACTCTCACACAGCACATAGCTGGAATTATCACTCAACGG
1 TCATCAGCTCATGTGCACTCCCACACAGCACATAGCTGGAATTATCACCCAACGG
* *
13381962 TCATTAGCTCATGTGCACTCCCACACCGCACATAGCTGGAAT
1 TCATCAGCTCATGTGCACTCCCACACAGCACATAGCTGGAAT
13382004 CACTCGTCAT
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
55 88 0.99
56 1 0.01
ACGTcount: A:0.28, C:0.34, G:0.16, T:0.22
Consensus pattern (55 bp):
TCATCAGCTCATGTGCACTCCCACACAGCACATAGCTGGAATTATCACCCAACGG
Found at i:13382840 original size:16 final size:17
Alignment explanation
Indices: 13382808--13382843 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
13382798 TTTGGTGCCC
*
13382808 AAGAAGTTAAGAGAAGA
1 AAGAAGTTAAGAAAAGA
13382825 AAGAAG-TAAGAAAAGA
1 AAGAAGTTAAGAAAAGA
13382841 AAG
1 AAG
13382844 GAAAGGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (17 bp):
AAGAAGTTAAGAAAAGA
Found at i:13394237 original size:11 final size:11
Alignment explanation
Indices: 13394204--13394238 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
13394194 CCTAGGGTTC
13394204 TTGTTCTTCCT
1 TTGTTCTTCCT
13394215 TT-TTCTTCCT
1 TTGTTCTTCCT
*
13394225 TTGTTCTTGCT
1 TTGTTCTTCCT
13394236 TTG
1 TTG
13394239 GTCGGCCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.00, C:0.23, G:0.11, T:0.66
Consensus pattern (11 bp):
TTGTTCTTCCT
Found at i:13401153 original size:11 final size:11
Alignment explanation
Indices: 13401120--13401154 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
13401110 CCTAGGGTTC
13401120 TTGTTCTTCCT
1 TTGTTCTTCCT
13401131 TT-TTCTTCCT
1 TTGTTCTTCCT
*
13401141 TTGTTCTTGCT
1 TTGTTCTTCCT
13401152 TTG
1 TTG
13401155 GACGGCCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.00, C:0.23, G:0.11, T:0.66
Consensus pattern (11 bp):
TTGTTCTTCCT
Found at i:13405897 original size:18 final size:19
Alignment explanation
Indices: 13405874--13405913 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
13405864 CAAGTGAAAA
13405874 ATTTTAC-AATAAAATAAT
1 ATTTTACTAATAAAATAAT
*
13405892 ATTTTACTGATAAAATAAT
1 ATTTTACTAATAAAATAAT
13405911 ATT
1 ATT
13405914 AAAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (19 bp):
ATTTTACTAATAAAATAAT
Found at i:13406353 original size:14 final size:15
Alignment explanation
Indices: 13406324--13406357 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
13406314 AAAAAATCAA
13406324 TTTTCTTTCATTTTC
1 TTTTCTTTCATTTTC
*
13406339 TTTTCTTT-GTTTTC
1 TTTTCTTTCATTTTC
13406353 TTTTC
1 TTTTC
13406358 CATTCCTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTCTTTCATTTTC
Found at i:13410916 original size:2 final size:2
Alignment explanation
Indices: 13410909--13410933 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13410899 NNNNNNNNNN
13410909 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
13410934 CGTTCTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13411625 original size:55 final size:56
Alignment explanation
Indices: 13411540--13411646 Score: 171
Period size: 55 Copynumber: 1.9 Consensus size: 56
13411530 ATGTATACAA
* *
13411540 CCACCGGCTCATCAGCTCATGTGCACTCCCACAACGCACATAGCTGGAATCATCAC
1 CCACCGGCTCATCAGCACATGTGCACTCCCACAACGCACATAGCTAGAATCATCAC
**
13411596 CCACCGG-TCATCAGCACATGTGCACTCCCACATTGCACATAGCTAGAATCA
1 CCACCGGCTCATCAGCACATGTGCACTCCCACAACGCACATAGCTAGAATCA
13411647 GCCGTCATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
55 40 0.85
56 7 0.15
ACGTcount: A:0.28, C:0.37, G:0.16, T:0.19
Consensus pattern (56 bp):
CCACCGGCTCATCAGCACATGTGCACTCCCACAACGCACATAGCTAGAATCATCAC
Found at i:13412478 original size:5 final size:5
Alignment explanation
Indices: 13412468--13412518 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
13412458 AGAAAGAAGT
* * *
13412468 AAGAA AAGAA AGGAA AGGAA AAGAA AA-CA AAGAA AAGAA AATG-A AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AA-GAA AAGAA
13412517 AA
1 AA
13412519 TTGATTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 4 0.10
5 34 0.87
6 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:13412493 original size:20 final size:19
Alignment explanation
Indices: 13412468--13412517 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
13412458 AGAAAGAAGT
*
13412468 AAGAAAAGAAAGGAAAGGAA
1 AAGAAAAGAAA-GAAAAGAA
*
13412488 AAGAAAACAAAGAAAAGAA
1 AAGAAAAGAAAGAAAAGAA
13412507 AATG-AAAGAAA
1 AA-GAAAAGAAA
13412518 ATTGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.74, C:0.02, G:0.22, T:0.02
Consensus pattern (19 bp):
AAGAAAAGAAAGAAAAGAA
Found at i:13417625 original size:33 final size:33
Alignment explanation
Indices: 13417582--13417649 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
13417572 TTGTACTTGA
*
13417582 GTGTGATTATACCATAACTTTTAAAATA-TAGTT
1 GTGTGATTATACCATAACTATTAAAA-AGTAGTT
* *
13417615 GTGTGGTTATACCTTAACTATTAAAAAGTAGTT
1 GTGTGATTATACCATAACTATTAAAAAGTAGTT
13417648 GT
1 GT
13417650 CATAAGAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 1 0.03
33 30 0.97
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (33 bp):
GTGTGATTATACCATAACTATTAAAAAGTAGTT
Found at i:13421584 original size:19 final size:19
Alignment explanation
Indices: 13421557--13421595 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
13421547 TTCAAACAAC
*
13421557 AGTAATCAATCAACCAAAA
1 AGTAATCAAACAACCAAAA
* *
13421576 AGTATTCAAACAATCAAAA
1 AGTAATCAAACAACCAAAA
13421595 A
1 A
13421596 ATCATCTTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.18, G:0.05, T:0.18
Consensus pattern (19 bp):
AGTAATCAAACAACCAAAA
Found at i:13431407 original size:21 final size:21
Alignment explanation
Indices: 13431363--13431407 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
13431353 CAAGAGATGT
*
13431363 AATAATGGTGGCAAGTGAGGA
1 AATAATGGTGGCAAGTGAGAA
*
13431384 AATAATGGTGG-TAGTAGAGAA
1 AATAATGGTGGCAAGT-GAGAA
13431405 AAT
1 AAT
13431408 GTGGGGGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.42, C:0.02, G:0.33, T:0.22
Consensus pattern (21 bp):
AATAATGGTGGCAAGTGAGAA
Found at i:13435168 original size:29 final size:29
Alignment explanation
Indices: 13435094--13435186 Score: 105
Period size: 29 Copynumber: 3.0 Consensus size: 29
13435084 CTTACTCAGC
*
13435094 TCATGTGCACTCCCTACACGCACAAAGCAATATCA
1 TCATGTGCACTCCCTACACG--C--A-C-ATTTCA
13435129 TCATGTGCACTCCCTACACGCACATTTCA
1 TCATGTGCACTCCCTACACGCACATTTCA
* *
13435158 TCATGTGCACTCCTTGCACGCACATTTCA
1 TCATGTGCACTCCCTACACGCACATTTCA
13435187 ATATTATCAC
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
29 32 0.58
30 1 0.02
31 1 0.02
33 1 0.02
35 20 0.36
ACGTcount: A:0.27, C:0.35, G:0.12, T:0.26
Consensus pattern (29 bp):
TCATGTGCACTCCCTACACGCACATTTCA
Found at i:13440092 original size:36 final size:36
Alignment explanation
Indices: 13440045--13440118 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
13440035 ATGCCGATAG
*
13440045 CACAAACCCAAGAACAAAAACAATACAAAATACCAT
1 CACAAACCCAAGAACAAAAACAATACAAAACACCAT
13440081 CACAAACCCAAGAACAAAAACAATACAAAACACCAT
1 CACAAACCCAAGAACAAAAACAATACAAAACACCAT
13440117 CA
1 CA
13440119 ATCTGCAAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.61, C:0.30, G:0.03, T:0.07
Consensus pattern (36 bp):
CACAAACCCAAGAACAAAAACAATACAAAACACCAT
Found at i:13440398 original size:23 final size:23
Alignment explanation
Indices: 13440372--13440417 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
13440362 TAGAATAACA
*
13440372 ATTCCTAATTCTATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
13440395 ATTCCTAATTATATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
13440418 GTTATTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (23 bp):
ATTCCTAATTATATTAGGATAAG
Found at i:13444689 original size:208 final size:207
Alignment explanation
Indices: 13444329--13444743 Score: 755
Period size: 208 Copynumber: 2.0 Consensus size: 207
13444319 TAGAAGATCT
13444329 CAAACGGGGTATGTGTTCACTTCTCTCAGATCTGCAAATCAGTTGGGAAAACAGTTCTTCAATCA
1 CAAACGGGGTATGTGTTCACTTCTCTCAGATCTGCAAATCAGTTGGGAAAACAGTTCTTCAATCA
13444394 ACCGTTGCTTTGTCTACAACTGAAGCTGAATATATGGTTGTGACCGAGGCAGTGAAAGAGGCTTT
66 ACCGTTGCTTTGTCTACAACTGAAGCTGAATATATGGTTGTGACCGAGGCAGTGAAAGAGGCTTT
*
13444459 GTGGCTTAAAGGCTTGGTTAGTGATCTTGGTTTTGAACAGACACAAACAGTTGTGTTTTTTGTGA
131 GTGGCTTAAAGGCTTGGTTAGTGATCTTGGTTTTGAACAAACACAAACAGTTGTG--TTTTGTGA
13444524 TAGTCAAAGTGCTA
194 TAGTCAAAGTGCTA
13444538 NCAAACGGGGTATGTGTTCAC-TCTCTCAGGATCTGC-AATCAGTT-GGAAAACAGTTCTTCAAT
1 -CAAACGGGGTATGTGTTCACTTCTCTCA-GATCTGCAAATCAGTTGGGAAAACAGTTCTTCAAT
*
13444600 CAACCGTTGCTTTGTTTACAACTGAAGCTGAATATATGGTTGTGACCGAGGCAGTGAAAGAGGCT
64 CAACCGTTGCTTTGTCTACAACTGAAGCTGAATATATGGTTGTGACCGAGGCAGTGAAAGAGGCT
13444665 TTGTGGCTTAAAGGCTTGGTTAGTGATCTTGGTTTTGAACAAACACAAACAGTTGTGTTTTGTGA
129 TTGTGGCTTAAAGGCTTGGTTAGTGATCTTGGTTTTGAACAAACACAAACAGTTGTGTTTTGTGA
13444730 TAGTCAAAGTGCTA
194 TAGTCAAAGTGCTA
13444744 TACATTTGAC
Statistics
Matches: 202, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
206 22 0.11
208 138 0.68
209 15 0.07
210 27 0.13
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (207 bp):
CAAACGGGGTATGTGTTCACTTCTCTCAGATCTGCAAATCAGTTGGGAAAACAGTTCTTCAATCA
ACCGTTGCTTTGTCTACAACTGAAGCTGAATATATGGTTGTGACCGAGGCAGTGAAAGAGGCTTT
GTGGCTTAAAGGCTTGGTTAGTGATCTTGGTTTTGAACAAACACAAACAGTTGTGTTTTGTGATA
GTCAAAGTGCTA
Found at i:13445161 original size:23 final size:23
Alignment explanation
Indices: 13445135--13445180 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
13445125 TAGAATAATA
*
13445135 ATTCCTAATTCTATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
13445158 ATTCCTAATTATATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
13445181 GTTATTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (23 bp):
ATTCCTAATTATATTAGGATAAG
Found at i:13446263 original size:17 final size:18
Alignment explanation
Indices: 13446241--13446274 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13446231 TCACACTAAC
*
13446241 ACACATTACAC-CACACT
1 ACACATAACACACACACT
13446258 ACACATAACACACACAC
1 ACACATAACACACACAC
13446275 AAAGGTCCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.41, G:0.00, T:0.12
Consensus pattern (18 bp):
ACACATAACACACACACT
Found at i:13447407 original size:9 final size:9
Alignment explanation
Indices: 13447393--13447423 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
13447383 ATTTTAAAAT
13447393 AACTTAAAC
1 AACTTAAAC
13447402 AACTTAAAC
1 AACTTAAAC
*
13447411 AACTTAAAT
1 AACTTAAAC
13447420 AACT
1 AACT
13447424 AAAAACTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (9 bp):
AACTTAAAC
Found at i:13454490 original size:21 final size:21
Alignment explanation
Indices: 13454465--13454521 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
13454455 TTCTGTCTCC
*
13454465 AATGTATCGATACATGTTTAT
1 AATGTATCGATACATGTTCAT
13454486 AATGTA-CTGATACATGTTCAT
1 AATGTATC-GATACATGTTCAT
*
13454507 AATGTATTGATACAT
1 AATGTATCGATACAT
13454522 TTAGCCTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (21 bp):
AATGTATCGATACATGTTCAT
Found at i:13456139 original size:29 final size:29
Alignment explanation
Indices: 13456098--13456271 Score: 151
Period size: 29 Copynumber: 6.1 Consensus size: 29
13456088 TGAGGTTCAG
*
13456098 GGATTGA-ATAATGATTACTTGAGTTATAT
1 GGATTGATA-AATGATTACTTGGGTTATAT
* *
13456127 GGACTGATAAATGATTACTTGGGTTTTAT
1 GGATTGATAAATGATTACTTGGGTTATAT
* * * *
13456156 GGATTG-GACATGGATCAC-TGTGTTATAT
1 GGATTGATAAAT-GATTACTTGGGTTATAT
* * * *
13456184 GGACTAATAAATGATTACTTCGGTTTTAT
1 GGATTGATAAATGATTACTTGGGTTATAT
* * * *
13456213 GGATTGGA-CATTGATCA-TTGTGTTATAT
1 GGATT-GATAAATGATTACTTGGGTTATAT
13456241 GGATTGATAAATGATTACTTGGGTTATAT
1 GGATTGATAAATGATTACTTGGGTTATAT
13456270 GG
1 GG
13456272 CTTGGGTGTT
Statistics
Matches: 109, Mismatches: 29, Indels: 14
0.72 0.19 0.09
Matches are distributed among these distances:
27 2 0.02
28 39 0.36
29 66 0.61
30 2 0.02
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (29 bp):
GGATTGATAAATGATTACTTGGGTTATAT
Found at i:13456186 original size:28 final size:27
Alignment explanation
Indices: 13456153--13456246 Score: 73
Period size: 28 Copynumber: 3.3 Consensus size: 27
13456143 ACTTGGGTTT
13456153 TATGGATTGGACATGGATCACTGTGTTA
1 TATGGATTGGACAT-GATCACTGTGTTA
*** * * *
13456181 TATGGACTAATAAATGATTACT-TCGGTTT
1 TATGGA-TTGGACATGATCACTGT--GTTA
*
13456210 TATGGATTGGACATTGATCATTGTGTTA
1 TATGGATTGGACA-TGATCACTGTGTTA
13456238 TATGGATTG
1 TATGGATTG
13456247 ATAAATGATT
Statistics
Matches: 48, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
27 1 0.02
28 27 0.56
29 19 0.40
30 1 0.02
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (27 bp):
TATGGATTGGACATGATCACTGTGTTA
Found at i:13456284 original size:57 final size:57
Alignment explanation
Indices: 13456120--13456276 Score: 251
Period size: 57 Copynumber: 2.8 Consensus size: 57
13456110 GATTACTTGA
*
13456120 GTTATATGGACTGATAAATGATTACTTGGGTTTTATGGATTGGACATGGATCACTGT
1 GTTATATGGACTGATAAATGATTACTTGGGTTTTATGGATTGGACATTGATCACTGT
* * *
13456177 GTTATATGGACTAATAAATGATTACTTCGGTTTTATGGATTGGACATTGATCATTGT
1 GTTATATGGACTGATAAATGATTACTTGGGTTTTATGGATTGGACATTGATCACTGT
* * *
13456234 GTTATATGGATTGATAAATGATTACTTGGGTTATATGGCTTGG
1 GTTATATGGACTGATAAATGATTACTTGGGTTTTATGGATTGG
13456277 GTGTTGATTA
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 91 1.00
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.41
Consensus pattern (57 bp):
GTTATATGGACTGATAAATGATTACTTGGGTTTTATGGATTGGACATTGATCACTGT
Found at i:13457716 original size:4 final size:4
Alignment explanation
Indices: 13457707--13457753 Score: 69
Period size: 4 Copynumber: 12.0 Consensus size: 4
13457697 TAATAATTCC
* *
13457707 CATA CATA CATA CATA CATA CATA CGTA CGTA CATA CATA CA-A CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
13457754 TATAGGCATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 3 0.08
4 37 0.93
ACGTcount: A:0.47, C:0.26, G:0.04, T:0.23
Consensus pattern (4 bp):
CATA
Done.