Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 36 of 290
Found at i:12296743 original size:82 final size:81
Alignment explanation
Indices: 12296567--12296744 Score: 187
Period size: 82 Copynumber: 2.2 Consensus size: 81
12296557 CGTTTTTGTC
* ** * *
12296567 AAAACGCCGCTAAAAACTGAGCAATAGCGGCATTTTTTGTTAAAACGCCGCTAAAAATAGAGCAT
1 AAAACGCCGCTAAAAACAGAGCAATAGCGGCAGCTTTTGGTAAAACGCCGCTAAAAACAGAGCAT
*
12296632 TAGCGGCGCTTTTGGT
66 TAGCGACGCTTTTGGT
* *** * * * * *
12296648 GAAACGGTACTAAAGACCAGAGCATTAGCGGC-GCTTTTGGTGAAATGCCGCTAAATACCAGAGC
1 AAAACGCCGCTAAA-AACAGAGCAATAGCGGCAGCTTTTGGTAAAACGCCGCTAAA-AACAGAGC
*
12296712 ATTAGTGACGCTTTTGGT
64 ATTAGCGACGCTTTTGGT
12296730 AAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
12296745 TCCTAAACCC
Statistics
Matches: 75, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
81 29 0.39
82 46 0.61
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (81 bp):
AAAACGCCGCTAAAAACAGAGCAATAGCGGCAGCTTTTGGTAAAACGCCGCTAAAAACAGAGCAT
TAGCGACGCTTTTGGT
Found at i:12302552 original size:43 final size:43
Alignment explanation
Indices: 12302499--12302605 Score: 160
Period size: 43 Copynumber: 2.5 Consensus size: 43
12302489 TTAAATTTCA
* *
12302499 TGATTTTTAGCGGCGTTTTTGGGAAAAGTGCCGCTAAAGGCCG
1 TGATCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGCCG
* * *
12302542 TGATCTTTAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGGTCG
1 TGATCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGCCG
12302585 TGATCTTTAGCGGCGATTTTT
1 TGATCTTTAGCGGCG-TTTTT
12302606 TAAAATAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 53 0.93
44 4 0.07
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.33
Consensus pattern (43 bp):
TGATCTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGCCG
Found at i:12303715 original size:15 final size:15
Alignment explanation
Indices: 12303697--12303745 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
12303687 CTCAAAAAAA
12303697 AAAAAATCTGAA-CT
1 AAAAAATCTGAACCT
*
12303711 CAAAAAATCTTAACCT
1 -AAAAAATCTGAACCT
**
12303727 AAAAAATCAAAACCT
1 AAAAAATCTGAACCT
12303742 AAAA
1 AAAA
12303746 TTGACTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 28 0.93
16 2 0.07
ACGTcount: A:0.61, C:0.18, G:0.02, T:0.18
Consensus pattern (15 bp):
AAAAAATCTGAACCT
Found at i:12304864 original size:31 final size:32
Alignment explanation
Indices: 12304828--12304909 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
12304818 TTCCTACATT
12304828 AAAATCCAACCAAAAACAGA-AAATATAGCAT-
1 AAAATCCAACCAAAAACA-ACAAATATAGCATA
* * *
12304859 GAAATCCAATCAAAAACAACAAATGTAGCATAA
1 AAAATCCAACCAAAAACAACAAATATAGCAT-A
*
12304892 AAAATACAACCAAAAACA
1 AAAATCCAACCAAAAACA
12304910 TTAAATCTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
30 1 0.02
31 26 0.62
33 15 0.36
ACGTcount: A:0.62, C:0.20, G:0.06, T:0.12
Consensus pattern (32 bp):
AAAATCCAACCAAAAACAACAAATATAGCATA
Found at i:12305611 original size:13 final size:14
Alignment explanation
Indices: 12305585--12305613 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12305575 ACTAATGACG
12305585 AATTAAACCATTAT
1 AATTAAACCATTAT
12305599 AATTAAA-CATTAT
1 AATTAAACCATTAT
12305612 AA
1 AA
12305614 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:12312412 original size:40 final size:40
Alignment explanation
Indices: 12312342--12312519 Score: 243
Period size: 40 Copynumber: 4.5 Consensus size: 40
12312332 AAACCAAGTA
* * ** *
12312342 CCTTCAGGATTTAG-CCGGATATAGCT-ACTCGTTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
12312381 CCTTCGGGACTTAGCCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
12312421 CCTTTGGGACTTAGCCCGGATGTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
12312461 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
12312501 CCTTCGAGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
12312520 TTGTCATCCG
Statistics
Matches: 124, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 13 0.10
40 111 0.90
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:12314076 original size:24 final size:24
Alignment explanation
Indices: 12314049--12314094 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
12314039 TCACCCCCAA
12314049 TTTTCATTATT-TTATTACTAACCC
1 TTTTCATT-TTATTATTACTAACCC
* *
12314073 TTTTTATTTTATTATTTCTAAC
1 TTTTCATTTTATTATTACTAAC
12314095 ATAAAGCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTTCATTTTATTATTACTAACCC
Found at i:12317033 original size:39 final size:39
Alignment explanation
Indices: 12316989--12317147 Score: 264
Period size: 39 Copynumber: 4.1 Consensus size: 39
12316979 ATTATATTAT
* * *
12316989 CAGCACAAAGCTTGCGGGACTTTAACCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
* *
12317028 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
*
12317067 CAGCACGAAGCCTGCGGAACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
12317106 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
12317145 CAG
1 CAG
12317148 TGTCTTGCAT
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 111 1.00
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.21
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
Found at i:12319016 original size:6 final size:6
Alignment explanation
Indices: 12319005--12319038 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
12318995 ACATTGTGTT
* *
12319005 AGTAAC AGTAAC TGTAAC AGTAAT AGTAAC AGTA
1 AGTAAC AGTAAC AGTAAC AGTAAC AGTAAC AGTA
12319039 GCGGTACACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.24
Consensus pattern (6 bp):
AGTAAC
Found at i:12319994 original size:19 final size:19
Alignment explanation
Indices: 12319970--12320006 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12319960 TCGATTTTTC
*
12319970 CTTTTTCTTTCTTTCCTTT
1 CTTTTTCCTTCTTTCCTTT
12319989 CTTTTTCCTTCTTTCCTT
1 CTTTTTCCTTCTTTCCTT
12320007 CCCTTGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTTTCCTTCTTTCCTTT
Found at i:12321121 original size:9 final size:9
Alignment explanation
Indices: 12321107--12321301 Score: 118
Period size: 9 Copynumber: 22.1 Consensus size: 9
12321097 TATGTATTAC
*
12321107 GTAAGTTAA
1 GTAAGTTAT
*
12321116 GTAAGTTTT
1 GTAAGTTAT
12321125 GTAAGTTAT
1 GTAAGTTAT
12321134 GTAAGTTAT
1 GTAAGTTAT
* *
12321143 GATATGATAT
1 G-TAAGTTAT
* *
12321153 -AAATTTAT
1 GTAAGTTAT
*
12321161 GTAAGGTAT
1 GTAAGTTAT
12321170 GTAAGTTAT
1 GTAAGTTAT
*
12321179 GTAAATTAT
1 GTAAGTTAT
* * *
12321188 GTTA-TGAA
1 GTAAGTTAT
* *
12321196 ATATATTTAT
1 GTA-AGTTAT
*
12321206 GT-A-TTAC
1 GTAAGTTAT
12321213 GTAAGTTAT
1 GTAAGTTAT
12321222 GTAAGTTAT
1 GTAAGTTAT
*
12321231 GTAAGTTAC
1 GTAAGTTAT
12321240 GTAAGTTAT
1 GTAAGTTAT
*
12321249 -TATA-TGAT
1 GTA-AGTTAT
* *
12321257 ATATATTTAT
1 GTA-AGTTAT
*
12321267 AT-A-TTAT
1 GTAAGTTAT
12321274 GTAAGTTAT
1 GTAAGTTAT
*
12321283 ATAAGTTAT
1 GTAAGTTAT
12321292 GTAAGTTAT
1 GTAAGTTAT
12321301 G
1 G
12321302 ATATCATGTA
Statistics
Matches: 144, Mismatches: 31, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
7 10 0.07
8 16 0.11
9 104 0.72
10 14 0.10
ACGTcount: A:0.36, C:0.01, G:0.17, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:12321173 original size:45 final size:43
Alignment explanation
Indices: 12321124--12321231 Score: 144
Period size: 45 Copynumber: 2.5 Consensus size: 43
12321114 AAGTAAGTTT
*
12321124 TGTAAGTTATGTAAGTTATGATATGATATAAATTTATGTAAGGTA
1 TGTAAGTTATGTAAGTTATGATATGAAATAAATTTATGT-A-GTA
* * * *
12321169 TGTAAGTTATGTAAATTATGTTATGAAATATATTTATGTATTA
1 TGTAAGTTATGTAAGTTATGATATGAAATAAATTTATGTAGTA
*
12321212 CGTAAGTTATGTAAGTTATG
1 TGTAAGTTATGTAAGTTATG
12321232 TAAGTTACGT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
43 20 0.36
44 1 0.02
45 35 0.62
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.44
Consensus pattern (43 bp):
TGTAAGTTATGTAAGTTATGATATGAAATAAATTTATGTAGTA
Found at i:12321222 original size:61 final size:61
Alignment explanation
Indices: 12321157--12321301 Score: 211
Period size: 61 Copynumber: 2.4 Consensus size: 61
12321147 TGATATAAAT
* *
12321157 TTATGTAAGGTATGTAAGTTATGTAAATTATGT-TATGAAATATATTTATGTATTACGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAATTAT-TATATGAAATATATTTATATATTACGTAAG
* * * *
12321218 TTATGTAAGTTATGTAAGTTACGTAAGTTATTATATGATATATATTTATATATTATGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAATTATTATATGAAATATATTTATATATTACGTAAG
*
12321279 TTATATAAGTTATGTAAGTTATG
1 TTATGTAAGTTATGTAAGTTATG
12321302 ATATCATGTA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
60 1 0.01
61 74 0.99
ACGTcount: A:0.36, C:0.01, G:0.17, T:0.46
Consensus pattern (61 bp):
TTATGTAAGTTATGTAAGTTATGTAAATTATTATATGAAATATATTTATATATTACGTAAG
Found at i:12321504 original size:15 final size:15
Alignment explanation
Indices: 12321486--12321540 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
12321476 AAAAATTTAT
12321486 TTTAATTAAATAATA
1 TTTAATTAAATAATA
12321501 TTT-A-TAAA-AATTA
1 TTTAATTAAATAA-TA
12321514 TTTTAATTAAATAATA
1 -TTTAATTAAATAATA
*
12321530 TTTAAATAAAT
1 TTTAATTAAAT
12321541 TAATCCAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.18
14 4 0.12
15 14 0.41
16 6 0.18
17 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAATTAAATAATA
Found at i:12321514 original size:29 final size:28
Alignment explanation
Indices: 12321476--12321542 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 28
12321466 AATCACCAAC
*
12321476 AAAAATTTATTTTAATTAAATAATATTT
1 AAAAAATTATTTTAATTAAATAATATTT
12321504 ATAAAAATTATTTTAATTAAATAATATTT
1 A-AAAAATTATTTTAATTAAATAATATTT
12321533 AAATAAATTA
1 AAA-AAATTA
12321543 ATCCAAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 3 0.08
29 33 0.92
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
AAAAAATTATTTTAATTAAATAATATTT
Found at i:12321531 original size:16 final size:16
Alignment explanation
Indices: 12321483--12321532 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
12321473 AACAAAAATT
12321483 TATTTTAATTAAATAA
1 TATTTTAATTAAATAA
12321499 TA-TTT-A-TAAA-AA
1 TATTTTAATTAAATAA
12321511 TTATTTTAATTAAATAA
1 -TATTTTAATTAAATAA
12321528 TATTT
1 TATTT
12321533 AAATAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 2 0.07
13 6 0.21
14 4 0.14
15 4 0.14
16 11 0.38
17 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTTTAATTAAATAA
Found at i:12321559 original size:39 final size:39
Alignment explanation
Indices: 12321508--12321598 Score: 157
Period size: 39 Copynumber: 2.4 Consensus size: 39
12321498 ATATTTATAA
*
12321508 AAATTATTTTAATTAAATAATATTTAAATAAATTAATCC
1 AAATTATATTAATTAAATAATATTTAAATAAATTAATCC
*
12321547 AAATTATATTAATTAATTAATATTTAAATAAATTAATCC
1 AAATTATATTAATTAAATAATATTTAAATAAATTAATCC
12321586 AAATTATA-TAATT
1 AAATTATATTAATT
12321599 TAAAAAATTA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 5 0.10
39 45 0.90
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (39 bp):
AAATTATATTAATTAAATAATATTTAAATAAATTAATCC
Found at i:12321562 original size:19 final size:19
Alignment explanation
Indices: 12321538--12321598 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
12321528 TATTTAAATA
12321538 AATTAATCCAAATTATATT
1 AATTAATCCAAATTATATT
* * *
12321557 AATTAAT-TAATATTTAAATA
1 AATTAATCCAA-A-TTATATT
12321577 AATTAATCCAAATTATA-T
1 AATTAATCCAAATTATATT
12321595 AATT
1 AATT
12321599 TAAAAAATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 6 0.18
19 12 0.36
20 13 0.39
21 2 0.06
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTAATCCAAATTATATT
Found at i:12321583 original size:20 final size:20
Alignment explanation
Indices: 12321518--12321583 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
12321508 AAATTATTTT
*
12321518 AATTAAATAATATTTAAATA
1 AATTAATTAATATTTAAATA
* * *
12321538 AATTAATCCAA-A-TTATATT
1 AATTAAT-TAATATTTAAATA
12321557 AATTAATTAATATTTAAATA
1 AATTAATTAATATTTAAATA
12321577 AATTAAT
1 AATTAAT
12321584 CCAAATTATA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 2 0.06
19 13 0.36
20 19 0.53
21 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTAATTAATATTTAAATA
Found at i:12321601 original size:19 final size:19
Alignment explanation
Indices: 12321535--12321601 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
12321525 TAATATTTAA
12321535 ATAAATTAATCCAAATTAT
1 ATAAATTAATCCAAATTAT
* * *
12321554 ATTAATTAAT-TAATATTTAA
1 ATAAATTAATCCAA-A-TTAT
12321574 ATAAATTAATCCAAATTAT
1 ATAAATTAATCCAAATTAT
*
12321593 ATAATTTAA
1 ATAAATTAA
12321602 AAAATTACGT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
18 2 0.05
19 21 0.55
20 13 0.34
21 2 0.05
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAAATTAATCCAAATTAT
Found at i:12322015 original size:8 final size:9
Alignment explanation
Indices: 12321994--12322027 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
12321984 TGAGTAAGAA
12321994 AATAAAATT
1 AATAAAATT
12322003 AATAAAA-T
1 AATAAAATT
12322011 AATAAAATT
1 AATAAAATT
12322020 AATAAAAT
1 AATAAAAT
12322028 ATGACATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AATAAAATT
Found at i:12322016 original size:17 final size:17
Alignment explanation
Indices: 12321994--12322028 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12321984 TGAGTAAGAA
12321994 AATAAAATTAATAAAAT
1 AATAAAATTAATAAAAT
12322011 AATAAAATTAATAAAAT
1 AATAAAATTAATAAAAT
12322028 A
1 A
12322029 TGACATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAAAATTAATAAAAT
Found at i:12322843 original size:19 final size:19
Alignment explanation
Indices: 12322821--12322858 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12322811 TCAATTCAAT
12322821 CCGAATTAATTATAATTGC
1 CCGAATTAATTATAATTGC
12322840 CCGAATTAATTATAATTGC
1 CCGAATTAATTATAATTGC
12322859 TCTCTACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
CCGAATTAATTATAATTGC
Found at i:12324240 original size:115 final size:114
Alignment explanation
Indices: 12324065--12324457 Score: 289
Period size: 115 Copynumber: 3.4 Consensus size: 114
12324055 AAAAACGTGG
* ** * * ** * * * *
12324065 ACGTTTTGCACTCTTAATACAACTTAGCGGCATTTTT-CCGAAAACGCCTGTAATGCACAACCTT
1 ACGTTTTGCACTCTTAATGCAGTTTTGCGGCGTTTTTATTGAAAACACCAGTAAAGAACAACCTT
* * * * * *
12324129 TTGCGGCTTTTTTTGGGGAAATGCCACTAAAAACAAGGAT-AACAACCGACA
66 TTGCGGC-GTTTATGAGGAAACGACACTAAAAACAAGCATGAA-AA-CGACA
* * ** * *
12324180 ACGTTTTGTACTCTTAATGCA-TTTTGTGGCGTTTTTATTGTGAACACCGGTAAAGAACAACATT
1 ACGTTTTGCACTCTTAATGCAGTTTTGCGGCGTTTTTATTGAAAACACCAGTAAAGAACAACCTT
* *
12324244 TTGCGGCGTTTATGAGGAAACGACACTATAAACAAGCATGGAAAACGACG
66 TTGCGGCGTTTATGAGGAAACGACACTAAAAACAAGCAT-GAAAACGACA
* *
12324294 ACGTTTTGCACTCTTAATGCAGTTTTGCGGCGTTTTTGTTGAAAACGCCAGTAAAGAACAA-CTT
1 ACGTTTTGCACTCTTAATGCAGTTTTGCGGCGTTTTTATTGAAAACACCAGTAAAGAACAACCTT
* * * * * * *
12324358 ATTGCGACGTGCT-TGAGGAAACGCCGCTAAAGAA-AAGGATAAAAACGA-T
66 -TTGCGGCGT-TTATGAGGAAACGACACTAAA-AACAAGCATGAAAACGACA
* * * * *
12324407 GCTGTTTTGCACTCTTATTACATTTTTGCGCCGTATTTTGA-TGAAAACACC
1 AC-GTTTTGCACTCTTAATGCAGTTTTGCGGCGT-TTTT-ATTGAAAACACC
12324458 GGAAATGCAT
Statistics
Matches: 222, Mismatches: 46, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
113 1 0.00
114 96 0.43
115 120 0.54
116 5 0.02
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (114 bp):
ACGTTTTGCACTCTTAATGCAGTTTTGCGGCGTTTTTATTGAAAACACCAGTAAAGAACAACCTT
TTGCGGCGTTTATGAGGAAACGACACTAAAAACAAGCATGAAAACGACA
Found at i:12324523 original size:7 final size:7
Alignment explanation
Indices: 12324511--12324561 Score: 59
Period size: 7 Copynumber: 7.3 Consensus size: 7
12324501 CACTGGTAAT
12324511 CCTAAAC
1 CCTAAAC
12324518 CCTAAAC
1 CCTAAAC
*
12324525 ACT-AAC
1 CCTAAAC
*
12324531 CCTTAAC
1 CCTAAAC
*
12324538 CCTTAAC
1 CCTAAAC
12324545 CCTTAAAC
1 CC-TAAAC
12324553 CCTAAAC
1 CCTAAAC
12324560 CC
1 CC
12324562 AAAATCCCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
6 5 0.13
7 28 0.72
8 6 0.15
ACGTcount: A:0.37, C:0.43, G:0.00, T:0.20
Consensus pattern (7 bp):
CCTAAAC
Found at i:12324544 original size:14 final size:15
Alignment explanation
Indices: 12324515--12324561 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
12324505 GGTAATCCTA
*
12324515 AACCC-TAAACAC-T
1 AACCCTTAAACCCTT
12324528 AACCCTT-AACCCTT
1 AACCCTTAAACCCTT
*
12324542 AACCCTTAAACCCTA
1 AACCCTTAAACCCTT
12324557 AACCC
1 AACCC
12324562 AAAATCCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 9 0.31
14 9 0.31
15 11 0.38
ACGTcount: A:0.38, C:0.43, G:0.00, T:0.19
Consensus pattern (15 bp):
AACCCTTAAACCCTT
Found at i:12324762 original size:7 final size:7
Alignment explanation
Indices: 12324723--12324921 Score: 66
Period size: 7 Copynumber: 27.9 Consensus size: 7
12324713 ACTAATTACT
12324723 CTAAACC
1 CTAAACC
*
12324730 CTAACCC
1 CTAAACC
12324737 CT-AACC
1 CTAAACC
*
12324743 CTATATACT
1 CTA-A-ACC
12324752 CTAAACC
1 CTAAACC
*
12324759 CTAAA-T
1 CTAAACC
* *
12324765 CAAAATC
1 CTAAACC
*
12324772 ATAAACC
1 CTAAACC
*
12324779 ATAAACCTC
1 CTAAA-C-C
12324788 CT-AACC
1 CTAAACC
12324794 CTAAACC
1 CTAAACC
12324801 CTAAACC
1 CTAAACC
12324808 CATAAA--
1 C-TAAACC
*
12324814 TTAAACC
1 CTAAACC
12324821 CTAAACC
1 CTAAACC
* *
12324828 ATAATCATCA
1 CTAA--A-CC
12324838 CTAAACC
1 CTAAACC
*
12324845 CATAATCC
1 C-TAAACC
** *
12324853 AAAAACT
1 CTAAACC
12324860 CTAAACC
1 CTAAACC
* *
12324867 ATATACC
1 CTAAACC
* *
12324874 CTAAGCA
1 CTAAACC
*
12324881 TTAAACC
1 CTAAACC
* *
12324888 TTAAATC
1 CTAAACC
* *
12324895 ATATACC
1 CTAAACC
12324902 CTAAACC
1 CTAAACC
*
12324909 ATAAACC
1 CTAAACC
12324916 CTAAAC
1 CTAAAC
12324922 TATAATGATA
Statistics
Matches: 136, Mismatches: 42, Indels: 28
0.66 0.20 0.14
Matches are distributed among these distances:
5 4 0.03
6 12 0.09
7 93 0.68
8 15 0.11
9 8 0.06
10 4 0.03
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:12324826 original size:49 final size:50
Alignment explanation
Indices: 12324723--12324831 Score: 127
Period size: 49 Copynumber: 2.2 Consensus size: 50
12324713 ACTAATTACT
* * *
12324723 CTAAACCCT-AACCCCTAACCCTATATACTCTAAACCCTAAATCAAAATC
1 CTAAACCATAAACCCCTAACCCTATATACCCTAAACCCTAAATCAAAACC
* *
12324772 ATAAACCATAAACCTCCTAACCCTA-A-ACCCTAAACCCATAAAT-TAAACC
1 CTAAACCATAAACC-CCTAACCCTATATACCCTAAACCC-TAAATCAAAACC
12324821 CTAAACCATAA
1 CTAAACCATAA
12324832 TCATCACTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
49 31 0.61
50 10 0.20
51 10 0.20
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.20
Consensus pattern (50 bp):
CTAAACCATAAACCCCTAACCCTATATACCCTAAACCCTAAATCAAAACC
Found at i:12324911 original size:14 final size:14
Alignment explanation
Indices: 12324753--12324926 Score: 88
Period size: 14 Copynumber: 12.2 Consensus size: 14
12324743 CTATATACTC
*
12324753 TAAACCCTAAATCA
1 TAAACCCTAAACCA
* *
12324767 -AAATCATAAACCA
1 TAAACCCTAAACCA
*
12324780 TAAACCTCCT-AACCC
1 TAAA-C-CCTAAACCA
12324795 TAAACCCTAAACCCA
1 TAAACCCTAAA-CCA
* *
12324810 TAAA--TTAAACCC
1 TAAACCCTAAACCA
* *
12324822 TAAACCATAATCATCA
1 TAAACCCTAA--ACCA
*
12324838 CTAAACCCATAATCCA
1 -TAAACCC-TAAACCA
* *
12324854 AAAACTCTAAACCA
1 TAAACCCTAAACCA
* *
12324868 TATACCCT-AAGCA
1 TAAACCCTAAACCA
* *
12324881 TTAAACCTTAAATCA
1 -TAAACCCTAAACCA
*
12324896 TATACCCTAAACCA
1 TAAACCCTAAACCA
*
12324910 TAAACCCTAAACTA
1 TAAACCCTAAACCA
12324924 TAA
1 TAA
12324927 TGATAATTAA
Statistics
Matches: 117, Mismatches: 30, Indels: 26
0.68 0.17 0.15
Matches are distributed among these distances:
12 6 0.05
13 21 0.18
14 52 0.44
15 23 0.20
16 6 0.05
17 6 0.05
18 3 0.03
ACGTcount: A:0.48, C:0.30, G:0.01, T:0.21
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:12325403 original size:41 final size:41
Alignment explanation
Indices: 12325312--12325403 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 41
12325302 TAATTTTTTT
* * * *
12325312 GCGGCATTTTTTGAAAAAGCGCTGCTAATGGTCGACCTATA
1 GCGGCATTTTTTGAAAAAGCGCAGCTAATGCTCAACCAATA
* *
12325353 GCGGCATTTTTT-AAAAAGTGCAGCTAATGCTCAATCAATA
1 GCGGCATTTTTTGAAAAAGCGCAGCTAATGCTCAACCAATA
12325393 GCGGCGATTTT
1 GCGGC-ATTTT
12325404 ATAGAAGCGC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
40 27 0.61
41 17 0.39
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (41 bp):
GCGGCATTTTTTGAAAAAGCGCAGCTAATGCTCAACCAATA
Found at i:12325483 original size:40 final size:39
Alignment explanation
Indices: 12325376--12325485 Score: 121
Period size: 40 Copynumber: 2.8 Consensus size: 39
12325366 AAAAGTGCAG
* * * *
12325376 CTAATGCTCAATCAATAGCGGCGATTTTATAGAAGCGCCA
1 CTAATTCTCAATCTATAGCGGCG-TTTTTTAGAAGCACCA
* * *
12325416 CTAATTGTCAATCTATAGTGGCGTTTTTTAGGAAGCACCG
1 CTAATTCTCAATCTATAGCGGCGTTTTTTA-GAAGCACCA
* *
12325456 CTAATTCTCGATCTTTAGCGGCGTTTTTTA
1 CTAATTCTCAATCTATAGCGGCGTTTTTTA
12325486 TTCAAACGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 6 0.10
40 52 0.90
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (39 bp):
CTAATTCTCAATCTATAGCGGCGTTTTTTAGAAGCACCA
Found at i:12334973 original size:20 final size:19
Alignment explanation
Indices: 12334948--12335041 Score: 82
Period size: 20 Copynumber: 4.8 Consensus size: 19
12334938 TATGTAACAA
12334948 AGGCACCGAAGTGCAGATAG
1 AGGCACCGAAGTGCA-ATAG
* *
12334968 AGGCA-CGATTGTGCAATCAA
1 AGGCACCGA-AGTGCAAT-AG
* *
12334988 AGGCACCAAAGTGCAAACAG
1 AGGCACCGAAGTGC-AATAG
* *
12335008 AGACACCGAAGTGTAATAG
1 AGGCACCGAAGTGCAATAG
*
12335027 AGGCATCGAAGTGCA
1 AGGCACCGAAGTGCA
12335042 GACCCATACA
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
19 21 0.37
20 32 0.56
21 4 0.07
ACGTcount: A:0.38, C:0.20, G:0.29, T:0.13
Consensus pattern (19 bp):
AGGCACCGAAGTGCAATAG
Found at i:12335837 original size:9 final size:9
Alignment explanation
Indices: 12335823--12335865 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
12335813 AACCCAAAAT
12335823 AAAAAATAA
1 AAAAAATAA
12335832 AAAAAATAA
1 AAAAAATAA
12335841 AAAAAATGAA
1 AAAAAAT-AA
* *
12335851 GAAAAAGAA
1 AAAAAATAA
12335860 AAAAAA
1 AAAAAA
12335866 CCTAACCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 23 0.77
10 7 0.23
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (9 bp):
AAAAAATAA
Found at i:12335845 original size:19 final size:19
Alignment explanation
Indices: 12335823--12335865 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
12335813 AACCCAAAAT
*
12335823 AAAAAAT-AAAAAAAATAA
1 AAAAAATGAAAAAAAAGAA
*
12335841 AAAAAATGAAGAAAAAGAA
1 AAAAAATGAAAAAAAAGAA
12335860 AAAAAA
1 AAAAAA
12335866 CCTAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (19 bp):
AAAAAATGAAAAAAAAGAA
Found at i:12339881 original size:26 final size:26
Alignment explanation
Indices: 12339851--12339909 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
12339841 TTTACCACAA
*
12339851 GTAAAAT-TGTCAAAGTTTTA-TAAGG
1 GTAAAATCT-TCAAAATTTTACTAAGG
12339876 GATAAAATCTTCAAAATTTTACTAAGG
1 G-TAAAATCTTCAAAATTTTACTAAGG
12339903 GTAAAAT
1 GTAAAAT
12339910 AGGCATGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 1 0.03
26 22 0.73
27 7 0.23
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (26 bp):
GTAAAATCTTCAAAATTTTACTAAGG
Found at i:12349353 original size:17 final size:18
Alignment explanation
Indices: 12349331--12349369 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
12349321 ATCAAAGGAT
12349331 ATAAACTTACT-T-CTAAC
1 ATAAACTTA-TATGCTAAC
12349348 ATAAACTTATATGCTAAC
1 ATAAACTTATATGCTAAC
12349366 ATAA
1 ATAA
12349370 TTCCAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.05
17 10 0.50
18 9 0.45
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.33
Consensus pattern (18 bp):
ATAAACTTATATGCTAAC
Found at i:12351093 original size:16 final size:17
Alignment explanation
Indices: 12351072--12351104 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12351062 GACCTTTAGT
*
12351072 TTTGATTCC-ATAGCTA
1 TTTGATACCTATAGCTA
12351088 TTTGATACCTATAGCTA
1 TTTGATACCTATAGCTA
12351105 CTAGAACCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (17 bp):
TTTGATACCTATAGCTA
Found at i:12351229 original size:5 final size:5
Alignment explanation
Indices: 12351219--12351245 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12351209 TATTCCAACC
12351219 ATAAA ATAAA ATAAA ATAAA ATAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA AT
12351246 TTTATTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:12351544 original size:38 final size:38
Alignment explanation
Indices: 12351493--12351569 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
12351483 TCAACTTGCT
*
12351493 CGTCTACTCCTTTCGACATCTCAACTGGCACCTTTGAA
1 CGTCTACTCCTTTCGACATCTCAACTGGCACCTTCGAA
*
12351531 CGTCTACTCCTTTCGACATCTCAACTGGGACCTTCGAA
1 CGTCTACTCCTTTCGACATCTCAACTGGCACCTTCGAA
12351569 C
1 C
12351570 ACTAGCTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.21, C:0.35, G:0.14, T:0.30
Consensus pattern (38 bp):
CGTCTACTCCTTTCGACATCTCAACTGGCACCTTCGAA
Found at i:12352435 original size:22 final size:22
Alignment explanation
Indices: 12352405--12352446 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12352395 TCTCAATTCT
*
12352405 TTTACTCTTTATATATTTAAAA
1 TTTAATCTTTATATATTTAAAA
* *
12352427 TTTAATCTTTTTATTTTTAA
1 TTTAATCTTTATATATTTAA
12352447 TTTCAAGAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTAATCTTTATATATTTAAAA
Found at i:12355825 original size:33 final size:32
Alignment explanation
Indices: 12355765--12355826 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
12355755 TCTTTAAATA
* * **
12355765 AAAAACATAAAATTTTAAAAATTATATTTTTC
1 AAAAACAAAAAATTTGAAAAAAAATATTTTTC
12355797 AAAAACAAAAAATTATGAAAAAAAATATTT
1 AAAAACAAAAAATT-TGAAAAAAAATATTT
12355827 AAAATTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 13 0.52
33 12 0.48
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (32 bp):
AAAAACAAAAAATTTGAAAAAAAATATTTTTC
Found at i:12359652 original size:26 final size:27
Alignment explanation
Indices: 12359623--12359678 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
12359613 TTTCCATAGG
*
12359623 ACCAATTTTTGTA-AA-CATTTCATACA
1 ACCAA-TTTTGTATAACCAATTCATACA
*
12359649 ACC-ATTTTGTATAACCAATTCATATA
1 ACCAATTTTGTATAACCAATTCATACA
12359675 ACCA
1 ACCA
12359679 TTAGTCATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
24 7 0.28
25 3 0.12
26 15 0.60
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (27 bp):
ACCAATTTTGTATAACCAATTCATACA
Found at i:12359664 original size:13 final size:13
Alignment explanation
Indices: 12359638--12359680 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
12359628 TTTTTGTAAA
*
12359638 CATTTCATACAAC
1 CATTTCATATAAC
**
12359651 CATTTTGTATAAC
1 CATTTCATATAAC
*
12359664 CAATTCATATAAC
1 CATTTCATATAAC
12359677 CATT
1 CATT
12359681 AGTCATCTAG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.37
Consensus pattern (13 bp):
CATTTCATATAAC
Found at i:12359679 original size:26 final size:24
Alignment explanation
Indices: 12359629--12359680 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
12359619 TAGGACCAAT
*
12359629 TTTTGTAAACATTTCATACAACCA
1 TTTTGTAAACAATTCATACAACCA
*
12359653 TTTTGTATAACCAATTCATATAACCA
1 TTTTGTA-AA-CAATTCATACAACCA
12359679 TT
1 TT
12359681 AGTCATCTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.29
25 2 0.08
26 15 0.62
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.40
Consensus pattern (24 bp):
TTTTGTAAACAATTCATACAACCA
Found at i:12364389 original size:14 final size:14
Alignment explanation
Indices: 12364370--12364441 Score: 64
Period size: 14 Copynumber: 5.4 Consensus size: 14
12364360 TATATAACCA
12364370 TTTCATATATCTAT
1 TTTCATATATCTAT
* *
12364384 TTTCATATAACCGA-
1 TTTCATAT-ATCTAT
*
12364398 -TTCATAAATC-A-
1 TTTCATATATCTAT
12364409 TTTCATATATCTAT
1 TTTCATATATCTAT
12364423 TTTCATATAT-TCAT
1 TTTCATATATCT-AT
12364437 TTTCA
1 TTTCA
12364442 CCCAATGAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
11 1 0.02
12 11 0.23
13 8 0.17
14 25 0.52
15 3 0.06
ACGTcount: A:0.32, C:0.17, G:0.01, T:0.50
Consensus pattern (14 bp):
TTTCATATATCTAT
Found at i:12364418 original size:27 final size:27
Alignment explanation
Indices: 12364353--12364418 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 27
12364343 TCCAATGTTC
*
12364353 CATTTCATATATAACCATTTCATATAT
1 CATTTCATATATAACCATTTCATAAAT
12364380 CTATTT--TCATATAACCGA-TTCATAAAT
1 C-ATTTCAT-ATATAACC-ATTTCATAAAT
12364407 CATTTCATATAT
1 CATTTCATATAT
12364419 CTATTTTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
26 5 0.15
27 22 0.67
28 6 0.18
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.44
Consensus pattern (27 bp):
CATTTCATATATAACCATTTCATAAAT
Found at i:12371280 original size:45 final size:45
Alignment explanation
Indices: 12371212--12371302 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
12371202 GAACTATGTG
* *
12371212 ATCTGAATTCATTAAGTTGTGGTCTAAGTTCATGATATATATGAC
1 ATCTGAACTCATTAAGTTATGGTCTAAGTTCATGATATATATGAC
* * * * *
12371257 ATCTGAACTCATTGAGTTATGGTCTGAGTTTATGATGTATGTGAC
1 ATCTGAACTCATTAAGTTATGGTCTAAGTTCATGATATATATGAC
12371302 A
1 A
12371303 CATGTTTTGG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.40
Consensus pattern (45 bp):
ATCTGAACTCATTAAGTTATGGTCTAAGTTCATGATATATATGAC
Found at i:12378760 original size:44 final size:44
Alignment explanation
Indices: 12378536--12378760 Score: 186
Period size: 46 Copynumber: 5.0 Consensus size: 44
12378526 TATGTGAGCC
* * **
12378536 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAAATGCT
1 AGTGTAAGACATGTCTGGGACATGCATTGG-CACA-GA-GATGTGCT
* * * * *
12378583 AGTGTAATACATATTTGGGACATGCATTGGCATTGAGACGA-GAGCT
1 AGTGTAAGACATGTCTGGGACATGCATTGGCA--CAGA-GATGTGCT
* * ** * *
12378629 TGTGTGAGACATGTCTGGGACATGCATCAGC-CTCGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATTGGCAC-AGAGATGT--GCT
12378675 AGTGTAAGACATGTCTGGGACATGCATTGGCTAC-GAGATGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATTGGC-ACAGAGATGTGCT
* *
12378719 ACTGTAAGACATGTCTGGGACATGCATTGGCACAGATATGTG
1 AGTGTAAGACATGTCTGGGACATGCATTGGCACAGAGATGTG
12378761 AGAGCCAGTG
Statistics
Matches: 142, Mismatches: 27, Indels: 21
0.75 0.14 0.11
Matches are distributed among these distances:
43 4 0.03
44 42 0.30
46 65 0.46
47 29 0.20
48 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATTGGCACAGAGATGTGCT
Found at i:12378767 original size:92 final size:91
Alignment explanation
Indices: 12378538--12378784 Score: 252
Period size: 92 Copynumber: 2.7 Consensus size: 91
12378528 TGTGAGCCAG
* * * * *
12378538 TGTAAGACATGTCTGGGACATGCATCGGCCACATTATG-AAATGCTAGTGTAATACATATTTGGG
1 TGTAAGACATGTCTGGGACATGCATCGGCCAGA-TATGTGAA-GCCAGTGTAAGACATATCTGGG
**
12378602 ACATGCATTGGCATTGAGACGAGAGCTTG
64 ACATGCATTGGCA-TGAGACGAGAGCTAC
* * * * *
12378631 TGTGAGACATGTCTGGGACATGCATCAGCCTCGAGATGT-AAGCCAGTGTAAGACATGTCTGGGA
1 TGTAAGACATGTCTGGGACATGCATCGGCC-AGATATGTGAAGCCAGTGTAAGACATATCTGGGA
*
12378695 CATGCATTGGC-T-ACGA-GATGTGCTAC
65 CATGCATTGGCATGA-GACGA-GAGCTAC
*
12378721 TGTAAGACATGTCTGGGACATGCATTGGCACAGATATGTGAGAGCCAGTGTAAGACCATATCTG
1 TGTAAGACATGTCTGGGACATGCATCGGC-CAGATATGTGA-AGCCAGTGTAAGA-CATATCTG
12378785 AGATATGGCA
Statistics
Matches: 128, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
89 3 0.02
90 39 0.30
91 2 0.02
92 43 0.34
93 40 0.31
94 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (91 bp):
TGTAAGACATGTCTGGGACATGCATCGGCCAGATATGTGAAGCCAGTGTAAGACATATCTGGGAC
ATGCATTGGCATGAGACGAGAGCTAC
Found at i:12378842 original size:26 final size:26
Alignment explanation
Indices: 12378813--12378863 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
12378803 GATATGTGTA
*
12378813 AGATTTCTCAATTATCCTCTGGTATG
1 AGATTTCCCAATTATCCTCTGGTATG
* *
12378839 AGATTTCCCGATTATCCTCTTGTAT
1 AGATTTCCCAATTATCCTCTGGTAT
12378864 TCCAAGTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.43
Consensus pattern (26 bp):
AGATTTCCCAATTATCCTCTGGTATG
Found at i:12385097 original size:31 final size:31
Alignment explanation
Indices: 12385059--12385120 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
12385049 AGCTATATGT
12385059 TTTGGAACTATACTGTAATTTGAAAATAAAA
1 TTTGGAACTATACTGTAATTTGAAAATAAAA
12385090 TTTGGAACTATACTGTAATTTGAAAATAAAA
1 TTTGGAACTATACTGTAATTTGAAAATAAAA
12385121 GTGTATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (31 bp):
TTTGGAACTATACTGTAATTTGAAAATAAAA
Found at i:12385111 original size:18 final size:18
Alignment explanation
Indices: 12385059--12385111 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
12385049 AGCTATATGT
12385059 TTTGGAACTATACTGTAA
1 TTTGGAACTATACTGTAA
**
12385077 TTT-GAA--A-A-TAAAA
1 TTTGGAACTATACTGTAA
12385090 TTTGGAACTATACTGTAA
1 TTTGGAACTATACTGTAA
12385108 TTTG
1 TTTG
12385112 AAAATAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 10
0.65 0.10 0.25
Matches are distributed among these distances:
13 6 0.23
14 4 0.15
15 1 0.04
16 1 0.04
17 4 0.15
18 10 0.38
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.40
Consensus pattern (18 bp):
TTTGGAACTATACTGTAA
Found at i:12386100 original size:39 final size:39
Alignment explanation
Indices: 12385917--12386101 Score: 266
Period size: 39 Copynumber: 4.8 Consensus size: 39
12385907 TGAGGTCTGC
* *
12385917 AGGC-TTTATGCTGGTATTATATCCGGGATAAGTCCTGA
1 AGGCATTTATGCTGGTATTATATCCGGGCTAAGTCCCGA
* * *
12385955 AGGCATTTGTGCTGGTGTTATATCCGGGCTACGTCCCGA
1 AGGCATTTATGCTGGTATTATATCCGGGCTAAGTCCCGA
* * *
12385994 AGGCATTTGTGCTGGTGTTATATCCGGGATAAGTCCCGA
1 AGGCATTTATGCTGGTATTATATCCGGGCTAAGTCCCGA
*
12386033 AGGCATTTATGCTGGTATTATATCCGGGCTAAAGTCCCGC
1 AGGCATTTATGCTGGTATTATATCCGGGCT-AAGTCCCGA
12386073 AGGC-TTTATGCTGGTATTATATCCGGGCT
1 AGGCATTTATGCTGGTATTATATCCGGGCT
12386102 TAAAGTCCTG
Statistics
Matches: 134, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
38 4 0.03
39 118 0.88
40 12 0.09
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.32
Consensus pattern (39 bp):
AGGCATTTATGCTGGTATTATATCCGGGCTAAGTCCCGA
Found at i:12386267 original size:18 final size:18
Alignment explanation
Indices: 12386244--12386279 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
12386234 AAGTTGGTCA
12386244 GGTATGTATTATATACTT
1 GGTATGTATTATATACTT
12386262 GGTATGTATTATATACTT
1 GGTATGTATTATATACTT
12386280 TTATATGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.50
Consensus pattern (18 bp):
GGTATGTATTATATACTT
Found at i:12387824 original size:22 final size:22
Alignment explanation
Indices: 12387796--12387839 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
12387786 CATTTTGAGA
12387796 ATGGCATGTATAGGGACTTGGT
1 ATGGCATGTATAGGGACTTGGT
12387818 ATGGCATGTATAGGGACTTGGT
1 ATGGCATGTATAGGGACTTGGT
12387840 CTTTTTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.36, T:0.32
Consensus pattern (22 bp):
ATGGCATGTATAGGGACTTGGT
Found at i:12390681 original size:8 final size:8
Alignment explanation
Indices: 12390639--12390663 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12390629 ATATAGACTG
12390639 AATAAAAT
1 AATAAAAT
12390647 AATAAAAT
1 AATAAAAT
12390655 AATAAAAT
1 AATAAAAT
12390663 A
1 A
12390664 TCTTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:12390972 original size:30 final size:31
Alignment explanation
Indices: 12390917--12390975 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
12390907 CACCCTTAAA
* * *
12390917 ATATTTGCACTATTAGTCCTTCAAATTTTTC
1 ATATTTACACTATTAATCCCTCAAATTTTTC
12390948 ATATTTACACT-TTAATCCCTCAAATTTT
1 ATATTTACACTATTAATCCCTCAAATTTT
12390976 AAGTATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.29, C:0.20, G:0.03, T:0.47
Consensus pattern (31 bp):
ATATTTACACTATTAATCCCTCAAATTTTTC
Found at i:12390983 original size:30 final size:31
Alignment explanation
Indices: 12390916--12390985 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
12390906 CCACCCTTAA
* * *
12390916 AATATTTGCACTATTAGTCCTTCAAATTTTT
1 AATATTTACACTATTAATCCCTCAAATTTTT
*
12390947 CATATTTACACT-TTAATCCCTCAAA-TTTT
1 AATATTTACACTATTAATCCCTCAAATTTTT
12390976 AAGTATTTAC
1 AA-TATTTAC
12390986 TCTTGGGCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 5 0.15
30 18 0.55
31 10 0.30
ACGTcount: A:0.31, C:0.19, G:0.04, T:0.46
Consensus pattern (31 bp):
AATATTTACACTATTAATCCCTCAAATTTTT
Found at i:12391677 original size:45 final size:45
Alignment explanation
Indices: 12391613--12391702 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
12391603 CATACATAAA
* *
12391613 TCGTGATAGTGTGACGACTCTTGACGATTTTAAACTGTGTTTTTC
1 TCGTGATAGTGTGACGACTCCTGACAATTTTAAACTGTGTTTTTC
12391658 TCGTGATAGTGTGACGACTCCTGACAATTTTAAACTGTGTTTTTC
1 TCGTGATAGTGTGACGACTCCTGACAATTTTAAACTGTGTTTTTC
12391703 ATATAGTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (45 bp):
TCGTGATAGTGTGACGACTCCTGACAATTTTAAACTGTGTTTTTC
Found at i:12394060 original size:26 final size:26
Alignment explanation
Indices: 12394027--12394082 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
12394017 CCTAGCCTCT
12394027 TTTTCAATAAACTAGGGCATAAGCCC
1 TTTTCAATAAACTAGGGCATAAGCCC
*
12394053 TTTTCAATAAACTGGGGCATAAGCCC
1 TTTTCAATAAACTAGGGCATAAGCCC
12394079 TTTT
1 TTTT
12394083 GCACTTCCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.32
Consensus pattern (26 bp):
TTTTCAATAAACTAGGGCATAAGCCC
Found at i:12394194 original size:16 final size:17
Alignment explanation
Indices: 12394161--12394196 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
12394151 TATCATGTGC
12394161 ATATCATATCAACCACGT
1 ATATCATATC-ACCACGT
12394179 ATATCATATC-CCACGT
1 ATATCATATCACCACGT
12394195 AT
1 AT
12394197 CAAATTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.31
Consensus pattern (17 bp):
ATATCATATCACCACGT
Found at i:12408733 original size:48 final size:48
Alignment explanation
Indices: 12408658--12408885 Score: 209
Period size: 48 Copynumber: 4.9 Consensus size: 48
12408648 CACATGGTAG
* * * * * *
12408658 GATGCCAATGCAATATCCCAGATATGGTCTTACATGGGATCACATTTT
1 GATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCACATATC
* ** *
12408706 GATGCCAATGCCATGTCCTAGACATGGTCTTGCATGGGATCGTAGATC
1 GATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCACATATC
*
12408754 GATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCACATATC
1 GATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCACATATC
* * ** * *
12408802 GATGCCGAT---A-G--CTCAG-CTATGGTCTTACACGAAATTACATATT
1 GATGCCAATGCCATGTCCT-AGAC-ATGGTCTTACATGGGATCACATATC
* * *
12408845 GATGCCAAAGCCATGTCCCAGACATGGTCTTACATTGGATC
1 GATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATC
12408886 GCACATAACC
Statistics
Matches: 141, Mismatches: 30, Indels: 18
0.75 0.16 0.10
Matches are distributed among these distances:
42 3 0.02
43 28 0.20
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 104 0.74
49 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (48 bp):
GATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCACATATC
Found at i:12412625 original size:40 final size:41
Alignment explanation
Indices: 12412563--12412665 Score: 131
Period size: 41 Copynumber: 2.6 Consensus size: 41
12412553 AACCCAAGTA
* * *
12412563 CCTTCGGGATTTA-ACCGGATATAG-CAAATCGCAC-AAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-AATAGCACAAAATG
*
12412602 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAAATG
*
12412643 CCTTCGGGTCTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
12412666 CATCCGAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
39 12 0.21
40 16 0.29
41 28 0.50
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (41 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAAATG
Found at i:12420023 original size:41 final size:40
Alignment explanation
Indices: 12419920--12420113 Score: 307
Period size: 40 Copynumber: 4.8 Consensus size: 40
12419910 ATAGAAAATC
* *
12419920 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTC
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
12419960 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
* *
12420000 GCACAAAATGCCTTCGGGTCTTAGCCCGGATATCGTCACTA
1 GCAC-AAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
* *
12420041 GCACAAATGCCTTCGGGACTTAACCCGGATATAGCCACTA
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
*
12420081 GCACAAAGTGCCTTCGGGTCTTAGCCCGGATAT
1 GCACAAA-TGCCTTCGGGACTTAGCCCGGATAT
12420114 CATCCGAATA
Statistics
Matches: 142, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
40 81 0.57
41 61 0.43
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTA
Found at i:12420114 original size:81 final size:80
Alignment explanation
Indices: 12419890--12420114 Score: 326
Period size: 81 Copynumber: 2.8 Consensus size: 80
12419880 AACCCAAGTA
* * * * * *
12419890 CCTTCGGGATTTAA-CCGGATATAGAAAATCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAACCCGGATATAGACACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATCG
*
12419954 TAACTCGCACAAATG
66 TAACTAGCACAAATG
* *
12419969 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAATGCCTTCGGGTCTTAGCCCGGATATC
1 CCTTCGGGACTTAACCCGGATATAGACACTAGCAC-AAATGCCTTCGGGTCTTAGCCCGGATATC
*
12420034 GTCACTAGCACAAATG
65 GTAACTAGCACAAATG
*
12420050 CCTTCGGGACTTAACCCGGATATAGCCACTAGCACAAAGTGCCTTCGGGTCTTAGCCCGGATATC
1 CCTTCGGGACTTAACCCGGATATAGACACTAGCACAAA-TGCCTTCGGGTCTTAGCCCGGATATC
12420115 ATCCGAATAA
Statistics
Matches: 131, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
79 12 0.09
80 19 0.15
81 100 0.76
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGACACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATCG
TAACTAGCACAAATG
Found at i:12420936 original size:14 final size:14
Alignment explanation
Indices: 12420914--12420956 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
12420904 TTTCATTTTG
12420914 TAACATAAAATTAT
1 TAACATAAAATTAT
*
12420928 TAGCATAAAA-TAT
1 TAACATAAAATTAT
* *
12420941 TAACACAAAATAAT
1 TAACATAAAATTAT
12420955 TA
1 TA
12420957 TAATATGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.30
Consensus pattern (14 bp):
TAACATAAAATTAT
Found at i:12420950 original size:13 final size:13
Alignment explanation
Indices: 12420914--12420952 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
12420904 TTTCATTTTG
12420914 TAACATAAAATTAT
1 TAACATAAAA-TAT
*
12420928 TAGCATAAAATAT
1 TAACATAAAATAT
*
12420941 TAACACAAAATA
1 TAACATAAAATA
12420953 ATTATAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (13 bp):
TAACATAAAATAT
Found at i:12422341 original size:40 final size:40
Alignment explanation
Indices: 12422296--12422376 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
12422286 CAAGTCTATT
*
12422296 AGGGAATGACAAAGTATATGCTCCTACAAGTAATGCAGCA
1 AGGGAAAGACAAAGTATATGCTCCTACAAGTAATGCAGCA
12422336 AGGGAAAGACAAAGTATATGCTCCTACAAGTAATGCAGCA
1 AGGGAAAGACAAAGTATATGCTCCTACAAGTAATGCAGCA
12422376 A
1 A
12422377 CTCTTTCTCC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (40 bp):
AGGGAAAGACAAAGTATATGCTCCTACAAGTAATGCAGCA
Found at i:12451729 original size:46 final size:45
Alignment explanation
Indices: 12451664--12451789 Score: 148
Period size: 46 Copynumber: 2.8 Consensus size: 45
12451654 ATATCTCGAG
* *
12451664 GCCGATGCATGTCCTAGACATGTATTACACTAGCTCTCGTCTCAAT-T
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCG--T-AATGT
* * *
12451711 -TCGATGCATGTCCCAGACATGTCTTACACTGGTTCTCGTAATGT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTAATGT
*
12451755 GGCCAATGCATGTCCCAGACATGTCTTACACTAGC
1 -GCCGATGCATGTCCCAGACATGTCTTACACTAGC
12451790 ACACATATCA
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
43 3 0.04
44 2 0.03
46 62 0.93
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTAATGT
Found at i:12461020 original size:26 final size:26
Alignment explanation
Indices: 12460991--12461044 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
12460981 TATAGCTCTC
12460991 TAATATGATGTAAATCATGTGAAAAG
1 TAATATGATGTAAATCATGTGAAAAG
**
12461017 TAATATGATGTAAATTGTGTGAAAAG
1 TAATATGATGTAAATCATGTGAAAAG
12461043 TA
1 TA
12461045 GGCTAGATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.33
Consensus pattern (26 bp):
TAATATGATGTAAATCATGTGAAAAG
Found at i:12462499 original size:28 final size:29
Alignment explanation
Indices: 12462447--12462501 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
12462437 ACGGGGGGTT
12462447 TTCACACGGCCAAGCACACGCCCGTGTCC
1 TTCACACGGCCAAGCACACGCCCGTGTCC
* *
12462476 TTCACATGGCCTAG-ACACGCCCGTGT
1 TTCACACGGCCAAGCACACGCCCGTGT
12462502 GGTGGCCCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.20, C:0.40, G:0.22, T:0.18
Consensus pattern (29 bp):
TTCACACGGCCAAGCACACGCCCGTGTCC
Found at i:12466339 original size:21 final size:21
Alignment explanation
Indices: 12466315--12466364 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
12466305 AGCATTTTGA
12466315 TACATTTTCTTTAAATCATTG
1 TACATTTTCTTTAAATCATTG
12466336 TACATTTTCTTTAAATCATTG
1 TACATTTTCTTTAAATCATTG
12466357 TACATTTT
1 TACATTTT
12466365 GGTATTTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.04, T:0.54
Consensus pattern (21 bp):
TACATTTTCTTTAAATCATTG
Found at i:12468630 original size:26 final size:26
Alignment explanation
Indices: 12468594--12468644 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
12468584 TCGCAACCCG
12468594 ACTGACACTAGCATTTCTAGGATATA
1 ACTGACACTAGCATTTCTAGGATATA
*
12468620 ACTGGCACTAGCATTTCTAGGATAT
1 ACTGACACTAGCATTTCTAGGATAT
12468645 CTCGGAGGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (26 bp):
ACTGACACTAGCATTTCTAGGATATA
Found at i:12477252 original size:11 final size:11
Alignment explanation
Indices: 12477238--12477267 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12477228 TGTGTTGATT
12477238 CTCCAACCGTC
1 CTCCAACCGTC
12477249 CTCCAACCGTC
1 CTCCAACCGTC
*
12477260 TTCCAACC
1 CTCCAACC
12477268 TCTATGAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.20, C:0.53, G:0.07, T:0.20
Consensus pattern (11 bp):
CTCCAACCGTC
Found at i:12484317 original size:43 final size:44
Alignment explanation
Indices: 12484209--12484317 Score: 127
Period size: 43 Copynumber: 2.5 Consensus size: 44
12484199 GCAAACGTCT
*
12484209 CAGACGTGGTCTTACATGT-AATCAAATATTGATGCCACTATCC
1 CAGACATGGTCTTACATGTAAATCAAATATTGATGCCACTATCC
* * * *
12484252 CAGACAGGGTCTTACACG-AAATCAAATA-TGATGTCGA-TGTCC
1 CAGACATGGTCTTACATGTAAATCAAATATTGATG-CCACTATCC
*
12484294 CAGACATGGTTTTACATGTAAATC
1 CAGACATGGTCTTACATGTAAATC
12484318 GTAAGTCGAT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
42 24 0.44
43 31 0.56
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.28
Consensus pattern (44 bp):
CAGACATGGTCTTACATGTAAATCAAATATTGATGCCACTATCC
Found at i:12487906 original size:42 final size:44
Alignment explanation
Indices: 12487835--12487925 Score: 118
Period size: 42 Copynumber: 2.1 Consensus size: 44
12487825 TCTTATATGT
* *
12487835 AATCAAATATTGATGCCACTGTCCTAGAC-AGCGTCTTACACG-A
1 AATCAAATATCGATGCCACTGTCCCAGACAAG-GTCTTACACGTA
12487878 AATCAAATA-CGATGCCGA-TGTCCCAGACAAGGTCTTACACGTA
1 AATCAAATATCGATGCC-ACTGTCCCAGACAAGGTCTTACACGTA
12487921 AATCA
1 AATCA
12487926 TAAGTTGATG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
42 25 0.58
43 18 0.42
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.23
Consensus pattern (44 bp):
AATCAAATATCGATGCCACTGTCCCAGACAAGGTCTTACACGTA
Found at i:12492380 original size:26 final size:26
Alignment explanation
Indices: 12492351--12492468 Score: 125
Period size: 25 Copynumber: 4.6 Consensus size: 26
12492341 TCGGGTTGCA
*
12492351 AAGGCTTTCCAAATAACTTTGCCACT
1 AAGGCTTTCCAGATAACTTTGCCACT
* *
12492377 AAGGCTTTCCAAATAA-TATGCCAC-
1 AAGGCTTTCCAGATAACTTTGCCACT
* ** *
12492401 ATAGGCTTTTCAGATAAC-TCACCACA
1 A-AGGCTTTCCAGATAACTTTGCCACT
*
12492427 AAGGCTTTCCAGATAACTTTGTCACT
1 AAGGCTTTCCAGATAACTTTGCCACT
*
12492453 AAGGCTTCCCAGATAA
1 AAGGCTTTCCAGATAA
12492469 TAAGCCACAT
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
24 1 0.01
25 39 0.51
26 36 0.47
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (26 bp):
AAGGCTTTCCAGATAACTTTGCCACT
Found at i:12492476 original size:76 final size:76
Alignment explanation
Indices: 12492349--12492496 Score: 226
Period size: 76 Copynumber: 1.9 Consensus size: 76
12492339 ACTCGGGTTG
* * *
12492349 CAAAGGCTTTCCAAATAACTTTGCCACTAAGGCTTTCCAAATAATATGCCACATAG-GCTTTTCA
1 CAAAGGCTTTCCAAATAACTTTGCCACTAAGGCTTCCCAAATAATAAGCCACATAGACCTTTT-A
12492413 GATAACTCACCA
65 GATAACTCACCA
* * *
12492425 CAAAGGCTTTCCAGATAACTTTGTCACTAAGGCTTCCCAGATAATAAGCCACATAGACCTTTTAG
1 CAAAGGCTTTCCAAATAACTTTGCCACTAAGGCTTCCCAAATAATAAGCCACATAGACCTTTTAG
12492490 ATAACTC
66 ATAACTC
12492497 GGAACTAAGG
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
76 60 0.92
77 5 0.08
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (76 bp):
CAAAGGCTTTCCAAATAACTTTGCCACTAAGGCTTCCCAAATAATAAGCCACATAGACCTTTTAG
ATAACTCACCA
Found at i:12492477 original size:51 final size:51
Alignment explanation
Indices: 12492352--12492477 Score: 114
Period size: 51 Copynumber: 2.5 Consensus size: 51
12492342 CGGGTTGCAA
* * ** *
12492352 AGGCTTTCCAAATAACTTTGCCACTAAGGCTTTCCAAATAATATGCCACAT
1 AGGCTTCCCAGATAACTAAGCCACAAAGGCTTTCCAAATAATATGCCACAT
** * * * *
12492403 AGGCTTTTCAGATAACTCA-CCACAAAGGCTTTCCAGATAACTTTGTCAC-T
1 AGGCTTCCCAGATAACTAAGCCACAAAGGCTTTCCAAATAA-TATGCCACAT
12492453 AAGGCTTCCCAGATAA-TAAGCCACA
1 -AGGCTTCCCAGATAACTAAGCCACA
12492478 TAGACCTTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
50 22 0.36
51 39 0.64
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.27
Consensus pattern (51 bp):
AGGCTTCCCAGATAACTAAGCCACAAAGGCTTTCCAAATAATATGCCACAT
Found at i:12506774 original size:18 final size:19
Alignment explanation
Indices: 12506751--12506789 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
12506741 TGAATTAAAG
*
12506751 TTTATAATTTTTTAA-AAT
1 TTTATAAATTTTTAATAAT
12506769 TTTATAAATTTTTAATAAT
1 TTTATAAATTTTTAATAAT
12506788 TT
1 TT
12506790 ATTTAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATAAATTTTTAATAAT
Found at i:12510206 original size:27 final size:30
Alignment explanation
Indices: 12510145--12510207 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 30
12510135 AAGTCAAAAG
12510145 TATTTTTTATATTTAAATATTTAATATTAT
1 TATTTTTTATATTTAAATATTTAATATTAT
* *
12510175 AATTTTTTA-ATTT-AA-ATTTAATATTTT
1 TATTTTTTATATTTAAATATTTAATATTAT
12510202 TATTTT
1 TATTTT
12510208 AAATAAACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 16 0.53
28 2 0.07
29 4 0.13
30 8 0.27
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (30 bp):
TATTTTTTATATTTAAATATTTAATATTAT
Found at i:12513538 original size:6 final size:6
Alignment explanation
Indices: 12513527--12513568 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
12513517 TCCAAGTTTC
* *
12513527 CATTTT CATTTT CATTTT CATTTT CATTTC CATTTC CATTTT
1 CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT
12513569 TGGAAACCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (6 bp):
CATTTT
Found at i:12513550 original size:18 final size:18
Alignment explanation
Indices: 12513523--12513568 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
12513513 GGATTCCAAG
*
12513523 TTTCCATTTTCATTTTCA
1 TTTCCATTTTCATTTCCA
*
12513541 TTTTCATTTTCATTTCCA
1 TTTCCATTTTCATTTCCA
12513559 TTTCCATTTT
1 TTTCCATTTT
12513569 TGGAAACCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTCCATTTTCATTTCCA
Found at i:12517897 original size:49 final size:49
Alignment explanation
Indices: 12517796--12517927 Score: 171
Period size: 49 Copynumber: 2.7 Consensus size: 49
12517786 ATGGATGTGT
* * *
12517796 GCTAGTGTAAGACATGTCTGGGATAT-GCATCGACCTCGAGATATGCAA
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGAGAGATGCAA
* *
12517844 GCTAGTGTAAGACCTGCCTGGGACATGGCATCGACACT-GATAGATG-AGA
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGAGAGATGCA-A
*
12517893 GCTAGTGTAAGACCTGTCTGGGACATGACATCGAC
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGAC
12517928 TTATATGTGT
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
48 24 0.32
49 48 0.65
50 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (49 bp):
GCTAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGAGAGATGCAA
Found at i:12517967 original size:97 final size:97
Alignment explanation
Indices: 12517796--12517972 Score: 214
Period size: 97 Copynumber: 1.8 Consensus size: 97
12517786 ATGGATGTGT
* * *
12517796 GCTAGTGTAAGACATGTCTGGGATATGCATCGACCTCGAGATATGCAAGCTAGTGTAAGACCTGC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATATGCAAGCCAGTGTAAGACCTAC
*
12517861 CTGGGACATGGCATCGACACTGATAGATGAGA
66 CTGGAACATGGCATCGACACTGATAGATGAGA
* * * * **
12517893 GCTAGTGTAAGACCTGTCTGGGACATGACATCGA-CT-TATATGTGTGAGCCAGTGTAAGACCAT
1 GCTAGTGTAAGACATGTCTGGGACATG-CATCGACCTCGAGATATGCAAGCCAGTGTAAGACC-T
**
12517956 ATTTGGAACATGGCATC
64 ACCTGGAACATGGCATC
12517973 AGCATCATAC
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
96 19 0.29
97 41 0.62
98 6 0.09
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (97 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATATGCAAGCCAGTGTAAGACCTAC
CTGGAACATGGCATCGACACTGATAGATGAGA
Found at i:12521810 original size:15 final size:15
Alignment explanation
Indices: 12521783--12521826 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
12521773 TATAGTATCA
12521783 TATCTTGGGATTTCTC
1 TATCTT-GGATTTCTC
*
12521799 TATCTTGGATTTCTT
1 TATCTTGGATTTCTC
*
12521814 TA-CTTGGTTTTCT
1 TATCTTGGATTTCT
12521827 TGTTATCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 10 0.38
15 10 0.38
16 6 0.23
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (15 bp):
TATCTTGGATTTCTC
Found at i:12522005 original size:26 final size:26
Alignment explanation
Indices: 12521975--12522027 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
12521965 ATTTACGTGT
*
12521975 AAGGATTTGACATCGGCAAAGGAATA
1 AAGGATTTGACATAGGCAAAGGAATA
12522001 AAGGATTTGACATAGGCAAAGGAATA
1 AAGGATTTGACATAGGCAAAGGAATA
12522027 A
1 A
12522028 GTGGTGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.45, C:0.09, G:0.26, T:0.19
Consensus pattern (26 bp):
AAGGATTTGACATAGGCAAAGGAATA
Found at i:12532712 original size:10 final size:10
Alignment explanation
Indices: 12532699--12532738 Score: 80
Period size: 10 Copynumber: 4.0 Consensus size: 10
12532689 CTAAGAACTC
12532699 TTGAAGGGAG
1 TTGAAGGGAG
12532709 TTGAAGGGAG
1 TTGAAGGGAG
12532719 TTGAAGGGAG
1 TTGAAGGGAG
12532729 TTGAAGGGAG
1 TTGAAGGGAG
12532739 ATCTTCAGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.50, T:0.20
Consensus pattern (10 bp):
TTGAAGGGAG
Found at i:12535271 original size:255 final size:255
Alignment explanation
Indices: 12534821--12535473 Score: 1164
Period size: 255 Copynumber: 2.6 Consensus size: 255
12534811 AAATGGAGTA
*
12534821 ATTAGCTGAAATTGCATTCGAGGTAAGTCCGTGTGACTAAATATCCATGTGATTGTTAATATACT
1 ATTAGCTGAAATTGCATTCGAGGTAAGTCCGTGTGACTAAATATGCATGTGATTGTTAATATACT
*
12534886 TGAAATCTATCTTGATTTAGTTATATTGAA-TATATGTTGATGATATTGAGTATGATGAAAGTGA
66 TGAAATCTATCTTGCTTTAGTTATATTGAATTATATGTTGATGATATTGAGTATGATGAAAGTGA
12534950 TGCCAAACGTTAATAATATTCATGTGATGATAGAATACATTAGAAATTTGATGGAATATGATATC
131 TGCCAAACGTTAATAATATTCATGTGATGATAGAATACATTAGAAATTTGATGGAATATGATATC
**
12535015 CCATAGAAACGAGTAAGTTGTATGTAAATAATGCAACTTAGTTATATTTATAAATTGAAT
196 CCATAGAAACGAGTAAGTTGTACATAAATAATGCAACTTAGTTATATTTATAAATTGAAT
*
12535075 ATTAGCTGAAATTGCATTCGAGGTAAGTCTGTGTGACTAAATATGCATGTGATTGTTAATATACT
1 ATTAGCTGAAATTGCATTCGAGGTAAGTCCGTGTGACTAAATATGCATGTGATTGTTAATATACT
*
12535140 TGAAATCTATCTTGCTTTGGTTATATTGAATTATATGTTGATGATATTGAGTATGATGAAAGTGA
66 TGAAATCTATCTTGCTTTAGTTATATTGAATTATATGTTGATGATATTGAGTATGATGAAAGTGA
*
12535205 TGCCAAACGTTAATAATATTTATGTGATGATAGAATACATTAGAAATTTGATGGAATATGATATC
131 TGCCAAACGTTAATAATATTCATGTGATGATAGAATACATTAGAAATTTGATGGAATATGATATC
* *
12535270 CCATAGAAACGAGTAAGTTGTACATAAATAATGCAACTTAGTTGTATTTATACATTGAAT
196 CCATAGAAACGAGTAAGTTGTACATAAATAATGCAACTTAGTTATATTTATAAATTGAAT
* ** *
12535330 GTTAGCCAAAATTGCATTCGAGGTAAGTCCGTGTGACTAGATATGCATGTGATTGTTAATATACT
1 ATTAGCTGAAATTGCATTCGAGGTAAGTCCGTGTGACTAAATATGCATGTGATTGTTAATATACT
*
12535395 TGAAACCTATCTTGCTTTAGTTATATTGAATTATATGTTGATGATATTGAGTATGATGAAAGTGA
66 TGAAATCTATCTTGCTTTAGTTATATTGAATTATATGTTGATGATATTGAGTATGATGAAAGTGA
*
12535460 TGCCAAACATTAAT
131 TGCCAAACGTTAAT
12535474 TGTAATACCC
Statistics
Matches: 381, Mismatches: 17, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
254 91 0.24
255 290 0.76
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (255 bp):
ATTAGCTGAAATTGCATTCGAGGTAAGTCCGTGTGACTAAATATGCATGTGATTGTTAATATACT
TGAAATCTATCTTGCTTTAGTTATATTGAATTATATGTTGATGATATTGAGTATGATGAAAGTGA
TGCCAAACGTTAATAATATTCATGTGATGATAGAATACATTAGAAATTTGATGGAATATGATATC
CCATAGAAACGAGTAAGTTGTACATAAATAATGCAACTTAGTTATATTTATAAATTGAAT
Found at i:12535654 original size:22 final size:23
Alignment explanation
Indices: 12535629--12535674 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
12535619 CAACCAAATC
12535629 AATTCA-ACATATTT-TGAAGATA
1 AATTCATACATATTTAT-AAGATA
*
12535651 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
12535674 A
1 A
12535675 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:12535680 original size:23 final size:23
Alignment explanation
Indices: 12535636--12535680 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12535626 ATCAATTCAA
*
12535636 CATATTTTGAAGATAAATTCATG
1 CATATTTTGAAGATAAAGTCATG
*
12535659 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TGAAGATAAAGTCAT
12535681 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (23 bp):
CATATTTTGAAGATAAAGTCATG
Found at i:12536158 original size:15 final size:15
Alignment explanation
Indices: 12536140--12536179 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
12536130 TGCTGCTGTC
12536140 CAAACTGTTTTTGTG
1 CAAACTGTTTTTGTG
12536155 CAAACTGTTTTTGTG
1 CAAACTGTTTTTGTG
*
12536170 CAAGCTGTTT
1 CAAACTGTTT
12536180 ATTACCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (15 bp):
CAAACTGTTTTTGTG
Found at i:12539705 original size:51 final size:51
Alignment explanation
Indices: 12539624--12539724 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
12539614 CCCAAACGGC
12539624 ATAACTAGAAACTCATAATGCCCGTACCTGGTTCTAAAGGCTGTTTTTGGT
1 ATAACTAGAAACTCATAATGCCCGTACCTGGTTCTAAAGGCTGTTTTTGGT
*
12539675 ATAATTAGAAACTCATAATGCCCGTACCTGGTTCTAAAGGCTGTTTTTGG
1 ATAACTAGAAACTCATAATGCCCGTACCTGGTTCTAAAGGCTGTTTTTGG
12539725 CACATCTGAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (51 bp):
ATAACTAGAAACTCATAATGCCCGTACCTGGTTCTAAAGGCTGTTTTTGGT
Found at i:12543605 original size:48 final size:48
Alignment explanation
Indices: 12543514--12543729 Score: 171
Period size: 47 Copynumber: 4.6 Consensus size: 48
12543504 GATGTGTGCT
* ** *
12543514 AGTGTAAGACC-TGTCTGGGACAT-GCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAACAAGACGAGAGCC
* * *
12543560 AGTGTAAGACCATGTCTGGAACATGGCATCGGCAATAAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAACAAGACGAGAGCC
* ** ****
12543608 AGTGTAAGA-CATGTCTGGGACACGGCATCGG---CTTGAC-ATGTTTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAACAAGACGA-GAGCC
* * * *
12543652 AGTGTAAGACC-TGTCTAGGACATGGCATCGACACCGATAGATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAAC-A-AGACGAGAGCC
*
12543701 AGTGTAAGACC-TGTCCGGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
12543730 AGCCTCGATA
Statistics
Matches: 133, Mismatches: 27, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
43 1 0.01
44 31 0.23
45 1 0.01
46 11 0.08
47 32 0.24
48 26 0.20
49 30 0.23
50 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCAACAAGACGAGAGCC
Found at i:12543721 original size:93 final size:92
Alignment explanation
Indices: 12543560--12543729 Score: 229
Period size: 93 Copynumber: 1.8 Consensus size: 92
12543550 TATGAGAGCC
* * *
12543560 AGTGTAAGACCATGTCTGGAACATGGCATCGGCAATAAGACGAGAGCTAGTGTAAGACATGTCTG
1 AGTGTAAGACCATGTCTGGAACATGGCATCGACAATAAGACGAGAGCCAGTGTAAGACATGTCCG
12543625 GGACACGGCATCGGCTTGACATGTTTT
66 GGACACGGCATCGGCTTGACATGTTTT
* *
12543652 AGTGTAAGACC-TGTCTAGG-ACATGGCATCGACACCGAT-AGATGAGAGCCAGTGTAAGACCTG
1 AGTGTAAGACCATGTCT-GGAACATGGCATCGACA---ATAAGACGAGAGCCAGTGTAAGACATG
*
12543714 TCCGGGACATGGCATC
62 TCCGGGACACGGCATC
12543730 AGCCTCGATA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
91 18 0.26
92 13 0.19
93 35 0.51
94 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (92 bp):
AGTGTAAGACCATGTCTGGAACATGGCATCGACAATAAGACGAGAGCCAGTGTAAGACATGTCCG
GGACACGGCATCGGCTTGACATGTTTT
Found at i:12543739 original size:49 final size:48
Alignment explanation
Indices: 12543514--12543739 Score: 166
Period size: 49 Copynumber: 4.8 Consensus size: 48
12543504 GATGTGTGCT
* *
12543514 AGTGTAAGACCTGTCTGGGACAT-GCATCGGCCAC-AT-TATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATC-GCCTCGATAGATGAGAGCC
* * * * *
12543560 AGTGTAAGACCATGTCTGGAACATGGCATCG--GCAATAAGACGAGAGCT
1 AGTGTAAGACC-TGTCTGGGACATGGCATCGCCTCGAT-AGATGAGAGCC
* * * * * ****
12543608 AGTGTAAGACATGTCTGGGACACGGCATCGGCTTG--ACAT--GTTTT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGCCTCGATAGATGAGAGCC
*
12543652 AGTGTAAGACCTGTCTAGGACATGGCATCGACAC-CGATAGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCG-C-CTCGATAGATGAGAGCC
*
12543701 AGTGTAAGACCTGTCCGGGACATGGCATCAGCCTCGATA
1 AGTGTAAGACCTGTCTGGGACATGGCATC-GCCTCGATA
12543740 TCAGTGTAAG
Statistics
Matches: 137, Mismatches: 28, Indels: 27
0.71 0.15 0.14
Matches are distributed among these distances:
44 29 0.21
45 2 0.01
46 16 0.12
47 32 0.23
48 23 0.17
49 34 0.25
50 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.22
Consensus pattern (48 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGCCTCGATAGATGAGAGCC
Found at i:12545895 original size:29 final size:29
Alignment explanation
Indices: 12545854--12545941 Score: 151
Period size: 29 Copynumber: 3.1 Consensus size: 29
12545844 GTGAGCATGA
12545854 ATAT-AATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
* *
12545882 ATATAAATGTGATTTGGGCCTAAAGGGTC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
12545911 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
12545940 AT
1 AT
12545942 GTGAATATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
28 4 0.07
29 51 0.93
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.32
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTAATGGGCC
Found at i:12546599 original size:13 final size:13
Alignment explanation
Indices: 12546581--12546612 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
12546571 GGTGTGTAAC
12546581 GGATGGATTATTG
1 GGATGGATTATTG
12546594 GGATGGATTATTG
1 GGATGGATTATTG
12546607 GGATGG
1 GGATGG
12546613 GATTGCACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.34
Consensus pattern (13 bp):
GGATGGATTATTG
Found at i:12548197 original size:27 final size:27
Alignment explanation
Indices: 12548166--12548303 Score: 204
Period size: 27 Copynumber: 5.1 Consensus size: 27
12548156 TTAGTTTACC
12548166 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * *
12548193 AAATTACTAAAATACACTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
12548220 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
12548247 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
12548274 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
12548301 AAA
1 AAA
12548304 NNNNNNNNNN
Statistics
Matches: 96, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 96 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:12548241 original size:54 final size:54
Alignment explanation
Indices: 12548166--12548303 Score: 258
Period size: 54 Copynumber: 2.6 Consensus size: 54
12548156 TTAGTTTACC
12548166 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACACTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACACTTGGTTTATA
*
12548220 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACACTTGGTTTATA
*
12548274 AAATTACCAAAATACCCCTAGTTTGTAAAA
1 AAATTACCAAAATACCCCTGGTTTGTAAAA
12548304 NNNNNNNNNN
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 82 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACACTTGGTTTATA
Found at i:12548503 original size:27 final size:27
Alignment explanation
Indices: 12548446--12548524 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
12548436 NNNNNNNNNA
* * * *
12548446 TTTTACCCTCGATTTACAGAATTA-CTA
1 TTTTACCCTCAATTTAAAAAATTATC-G
* *
12548473 TTTTACGCTTAATTTAAAAAATTATCG
1 TTTTACCCTCAATTTAAAAAATTATCG
* *
12548500 TTTTACCCTCGATTTACAAAATTAT
1 TTTTACCCTCAATTTAAAAAATTAT
12548525 TGAAATACCC
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
27 40 0.98
28 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (27 bp):
TTTTACCCTCAATTTAAAAAATTATCG
Found at i:12548549 original size:27 final size:27
Alignment explanation
Indices: 12548526--12548875 Score: 522
Period size: 27 Copynumber: 13.0 Consensus size: 27
12548516 CAAAATTATT
*
12548526 GAAATACCCCTGTAGGATAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
12548553 AAAATACCCCTATAGGGTAGAATTATC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
12548580 GAAATACCCCTATAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
12548607 GAAATGCCCCTGTAGGGTAGAATTATC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
12548634 GCAATACCCTTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
12548661 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
12548688 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
12548715 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
*
12548742 GAAATACCCCTGTAGGGTAGAATTATC
1 GAAATACCCCTGTAGGGTAGAATTACC
*
12548769 GCAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
*
12548796 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
12548823 AAAATACCCCTGTAGGGTGGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * * *
12548850 GAGATA-CCTTGTGGGGTAAAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
12548876 ATTTTGCCCC
Statistics
Matches: 292, Mismatches: 31, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
26 16 0.05
27 276 0.95
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTACC
Found at i:12549353 original size:22 final size:22
Alignment explanation
Indices: 12549301--12549365 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
12549291 TTAAAGCCTT
* *
12549301 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
12549323 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
12549345 CTGATTATGGTTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
12549366 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:12549553 original size:27 final size:26
Alignment explanation
Indices: 12549522--12549594 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 26
12549512 TATTCTGTTA
* * *
12549522 AGTGGCTTTGCCACATTATCTATTTCT
1 AGTGGCTATGCCACAATATCT-GTTCT
*
12549549 GGTGGCTATGCCACAAATATCTGTTCT
1 AGTGGCTATGCCAC-AATATCTGTTCT
*
12549576 AGTGGCTCTGCCACAATAT
1 AGTGGCTATGCCACAATAT
12549595 TTGTATCTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
26 5 0.13
27 28 0.72
28 6 0.15
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (26 bp):
AGTGGCTATGCCACAATATCTGTTCT
Found at i:12549807 original size:31 final size:31
Alignment explanation
Indices: 12549761--12549871 Score: 150
Period size: 31 Copynumber: 3.5 Consensus size: 31
12549751 TTGCATTCAA
* *
12549761 ATTCTGATTTTTGATTCTGTTACCTAATAATG
1 ATTCTGA-TTCTGATTCTGTTACCTAATACTG
* *
12549793 ATTCTGATTTTGATTCTGTTACCTTATACTG
1 ATTCTGATTCTGATTCTGTTACCTAATACTG
* * *
12549824 ATTCTGATTCTGATTCTCTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTACCTAATACTG
12549855 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
12549872 AATTCTGATA
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
31 65 0.90
32 7 0.10
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.50
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTTACCTAATACTG
Found at i:12549889 original size:18 final size:17
Alignment explanation
Indices: 12549868--12549901 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12549858 CTGATTCTGA
12549868 TTCTAATTCTGATAATGT
1 TTCTAATTCTG-TAATGT
*
12549886 TTCTTATTCTGTAATG
1 TTCTAATTCTGTAATG
12549902 GGTTAAAGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (17 bp):
TTCTAATTCTGTAATGT
Found at i:12549895 original size:6 final size:6
Alignment explanation
Indices: 12549791--12549880 Score: 67
Period size: 6 Copynumber: 14.7 Consensus size: 6
12549781 TACCTAATAA
* * *
12549791 TGATTC TGATTT TGATTC TG-TTACC TTATAC TGATTC TGATTC TGATTC
1 TGATTC TGATTC TGATTC TGATT--C TGATTC TGATTC TGATTC TGATTC
* * * *
12549840 T-CTCACC TAATTC TGATTC TGATTC TGATTC TAATTC TGAT
1 TGAT--TC TGATTC TGATTC TGATTC TGATTC TGATTC TGAT
12549881 AATGTTTCTT
Statistics
Matches: 65, Mismatches: 13, Indels: 12
0.72 0.14 0.13
Matches are distributed among these distances:
5 3 0.05
6 56 0.86
7 4 0.06
8 2 0.03
ACGTcount: A:0.20, C:0.19, G:0.12, T:0.49
Consensus pattern (6 bp):
TGATTC
Found at i:12551855 original size:27 final size:27
Alignment explanation
Indices: 12551825--12552237 Score: 547
Period size: 27 Copynumber: 15.3 Consensus size: 27
12551815 TTTAGTTTAC
12551825 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* * *
12551852 AAAATTACTAAAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
12551879 AAAATCACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* **
12551906 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCCTGGTTTGT
*
12551933 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* * *
12551960 AAAATTACTAAAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
12551987 AAAATCACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
12552014 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* **
12552041 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCCTGGTTTGT
* *
12552068 AAAATCACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* * * **
12552095 AAAATTACTAAAATACCCTTTGTTAAT
1 AAAATTACCAAAATACCCCTGGTTTGT
**
12552122 AAAATTACCAAAATACCATTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
12552149 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
** *
12552176 AAAATTATAAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* *
12552203 AAAATTACCAAAATATCCCTGATTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
12552230 GAAATTAC
1 AAAATTAC
12552238 TGAAAACCCT
Statistics
Matches: 330, Mismatches: 56, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 330 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGGTTTGT
Found at i:12551891 original size:54 final size:54
Alignment explanation
Indices: 12551819--12552318 Score: 554
Period size: 54 Copynumber: 9.3 Consensus size: 54
12551809 GAATACTTTA
* *
12551819 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTG
1 GTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
*
12551873 GTTTATAAAATCACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
1 GTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
* * *
12551927 GTTTACAAAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCCTTG
1 GTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
* * *
12551981 GTTTATAAAATCACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTA
1 GTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
* * ** * * *
12552035 GTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATCACCAAAATACCCCTA
1 GTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
* * * * ** *
12552089 GTTTGTAAAATTACTAAAATACCCTTTGTTAATAAAATTACCAAAATACCATTG
1 GTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
* ** * *
12552143 GTTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTATAAAAATACCCCTA
1 GTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
* * * * ** *
12552197 GTTTGTAAAATTACCAAAATATCCCTGATTTGTGAAATTACTGAAA-ACCCTCG
1 GTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
*** * *** ** *
12552250 ACCTGTAAAATTATTGAAATA-CCCTCGACTTGTAAAATTACCAAAGTACCCTTG
1 GTTTATAAAATTACCAAAATACCCCT-GGTTTGTAAAATTACCAAAATACCCTTG
* *
12552304 ATTTACAAAATTACC
1 GTTTATAAAATTACC
12552319 GTTTTACCCT
Statistics
Matches: 380, Mismatches: 64, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
52 4 0.01
53 34 0.09
54 342 0.90
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.31
Consensus pattern (54 bp):
GTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
Found at i:12552283 original size:27 final size:27
Alignment explanation
Indices: 12551825--12552301 Score: 197
Period size: 27 Copynumber: 17.7 Consensus size: 27
12551815 TTTAGTTTAC
* **
12551825 AAAATTACCAAAATACCC-CTGGTTTGT
1 AAAATTACTAAAATACCCTC-GACTTGT
* ** *
12551852 AAAATTACTAAAATACCCTTGGTTTAT
1 AAAATTACTAAAATACCCTCGACTTGT
* * **
12551879 AAAATCACCAAAATACCC-CTGGTTTGT
1 AAAATTACTAAAATACCCTC-GACTTGT
* * ** **
12551906 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTACTAAAATACCCTCGACTTGT
* * *
12551933 AAAATTACCAAAATACCC-CTAGTTTGT
1 AAAATTACTAAAATACCCTCGA-CTTGT
* ** *
12551960 AAAATTACTAAAATACCCTTGGTTTAT
1 AAAATTACTAAAATACCCTCGACTTGT
* * **
12551987 AAAATCACCAAAATACCC-CTGGTTTGT
1 AAAATTACTAAAATACCCTC-GACTTGT
* * *
12552014 AAAATTACCAAAATACCC-CTAGTTTGT
1 AAAATTACTAAAATACCCTCGA-CTTGT
* * ** **
12552041 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTACTAAAATACCCTCGACTTGT
* * * *
12552068 AAAATCACCAAAATACCC-CTAGTTTGT
1 AAAATTACTAAAATACCCTCGA-CTTGT
* *
12552095 AAAATTACTAAAATACCCTTTG--TTAAT
1 AAAATTACTAAAATACCC-TCGACTT-GT
* * * **
12552122 AAAATTACCAAAATACCATTGGTTTGT
1 AAAATTACTAAAATACCCTCGACTTGT
* **
12552149 AAAATTACCAAAATACCC-CTGGTTTGT
1 AAAATTACTAAAATACCCTC-GACTTGT
* *
12552176 AAAATTA-TAAAAATACCC-CTAGTTTGT
1 AAAATTACT-AAAATACCCTCGA-CTTGT
* *
12552203 AAAATTACCAAAATATCCCT-GATTTGT
1 AAAATTACTAAAATA-CCCTCGACTTGT
* * *
12552230 GAAATTACTGAAA-ACCCTCGACCTGT
1 AAAATTACTAAAATACCCTCGACTTGT
* *
12552256 AAAATTATTGAAATACCCTCGACTTGT
1 AAAATTACTAAAATACCCTCGACTTGT
* *
12552283 AAAATTACCAAAGTACCCT
1 AAAATTACTAAAATACCCT
12552302 TGATTTACAA
Statistics
Matches: 362, Mismatches: 66, Indels: 44
0.77 0.14 0.09
Matches are distributed among these distances:
25 4 0.01
26 22 0.06
27 330 0.91
28 6 0.02
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
AAAATTACTAAAATACCCTCGACTTGT
Found at i:12552313 original size:27 final size:26
Alignment explanation
Indices: 12552266--12552354 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 26
12552256 AAAATTATTG
* **
12552266 AAATACCCTCGACTTGTAAAATTACC
1 AAATACCCTCGATTTACAAAATTACC
*
12552292 AAAGTACCCTTGATTTACAAAATTACC
1 AAA-TACCCTCGATTTACAAAATTACC
***
12552319 GTTTTACCCTCGATTTACAAAATTACC
1 -AAATACCCTCGATTTACAAAATTACC
12552346 GAAATACCC
1 -AAATACCC
12552355 CTGTAGGGTA
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
26 3 0.06
27 47 0.94
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.29
Consensus pattern (26 bp):
AAATACCCTCGATTTACAAAATTACC
Found at i:12552369 original size:27 final size:27
Alignment explanation
Indices: 12552339--12552560 Score: 304
Period size: 27 Copynumber: 8.3 Consensus size: 27
12552329 CGATTTACAA
12552339 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
12552366 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
12552393 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
12552420 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
**
12552447 AATTATAGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
12552474 GATTATCGCAATACCCCTGCAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
12552501 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
12552528 AATTACC-AAGATACCTC-GTGGGGTAA
1 AATTACCGAA-ATACCCCTGTAGGGTAG
12552554 AATTACC
1 AATTACC
12552561 ATTTTGCCCC
Statistics
Matches: 174, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
26 15 0.09
27 159 0.91
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:12553057 original size:6 final size:6
Alignment explanation
Indices: 12553046--12553136 Score: 62
Period size: 6 Copynumber: 14.8 Consensus size: 6
12553036 TTACCTAATA
* * * *
12553046 CTGATT CTGATT TTGATT CCG-TT ACCTGATA CTGATT CTAATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT CTGATT
* *
12553095 CTG-TCAC CTAATT CTGATT CTGATT CTGATT CT-AGTT CTGAT
1 CTGAT--T CTGATT CTGATT CTGATT CTGATT CTGA-TT CTGAT
12553137 AATGTTTCTT
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
5 4 0.06
6 54 0.83
7 5 0.08
8 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (6 bp):
CTGATT
Found at i:12553061 original size:31 final size:31
Alignment explanation
Indices: 12553028--12553128 Score: 130
Period size: 31 Copynumber: 3.3 Consensus size: 31
12553018 TTCTGGTTTT
*
12553028 TGATTCTATTACCTAATACTGATTCTGATTT
1 TGATTCTATTACCTAATACTGATTCTGATTC
** * *
12553059 TGATTCCGTTACCTGATACTGATTCTAATTC
1 TGATTCTATTACCTAATACTGATTCTGATTC
* * *
12553090 TGATTCTGTCACCTAATTCTGATTCTGATTC
1 TGATTCTATTACCTAATACTGATTCTGATTC
12553121 TGATTCTA
1 TGATTCTA
12553129 GTTCTGATAA
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.23, C:0.20, G:0.12, T:0.46
Consensus pattern (31 bp):
TGATTCTATTACCTAATACTGATTCTGATTC
Found at i:12559743 original size:21 final size:24
Alignment explanation
Indices: 12559699--12559745 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
12559689 ATCGAAACAT
12559699 TTCACAAATAATTCACTAACATCA
1 TTCACAAATAATTCACTAACATCA
*
12559723 TTCACACATAA-TCA-T-ACATCA
1 TTCACAAATAATTCACTAACATCA
12559744 TT
1 TT
12559746 ACAGAGTCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 1 0.05
23 3 0.14
24 10 0.45
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.32
Consensus pattern (24 bp):
TTCACAAATAATTCACTAACATCA
Found at i:12562068 original size:27 final size:27
Alignment explanation
Indices: 12562034--12562110 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 27
12562024 GGGAAAAATA
* *
12562034 GTCATTTTACCCTACATGGGTATGTCG
1 GTCATTTTACACTACAAGGGTATGTCG
*
12562061 GTCATTTTACACTACAAGGGTATTTCG
1 GTCATTTTACACTACAAGGGTATGTCG
*
12562088 GTAATTTTACACTACAAGGGTAT
1 GTCATTTTACACTACAAGGGTAT
12562111 TTCAATAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (27 bp):
GTCATTTTACACTACAAGGGTATGTCG
Found at i:12562111 original size:27 final size:26
Alignment explanation
Indices: 12562051--12562602 Score: 474
Period size: 27 Copynumber: 20.7 Consensus size: 26
12562041 TACCCTACAT
* * * *
12562051 GGGTATGTCGGTCATTTTACACTACAA
1 GGGTATTTCGGTAATTTTACA-AACGA
* *
12562078 GGGTATTTCGGTAATTTTACACTACAA
1 GGGTATTTCGGTAATTTTACA-AACGA
** **
12562105 GGGTATTTCAATAATTTTACAAATAA
1 GGGTATTTCGGTAATTTTACAAACGA
* *
12562131 GGGATGTTTCGGTAATTTTACAAATTGA
1 GGG-TATTTCGGTAATTTTACAAA-CGA
* *
12562159 GGGTATTTCGATAATTTTATAAATCGA
1 GGGTATTTCGGTAATTTTACAAA-CGA
12562186 GGGTATTTCGGTAATTTTACAAATCGA
1 GGGTATTTCGGTAATTTTACAAA-CGA
* * * **
12562213 GGGTGTTTCAGTAATTTCACAAATTA
1 GGGTATTTCGGTAATTTTACAAACGA
* *
12562239 GGGGTATTTCAGTAATTTTACAAATTGA
1 -GGGTATTTCGGTAATTTTACAAA-CGA
* * *
12562267 GGGTATTTCAGTAATTTCACAATCGA
1 GGGTATTTCGGTAATTTTACAAACGA
* * *
12562293 TGGTATTTTGGTAATTTTACAAATCCA
1 GGGTATTTCGGTAATTTTACAAA-CGA
*
12562320 TGGTATTTCGGTAATTTTACAAATCGA
1 GGGTATTTCGGTAATTTTACAAA-CGA
* * * *
12562347 GCGTATTTTGATAATTTTACAAATAGA
1 GGGTATTTCGGTAATTTTACAAA-CGA
** *
12562374 GGGTATTTTAGTAATTTTACAATCGA
1 GGGTATTTCGGTAATTTTACAAACGA
* *
12562400 GGGTATTTCAGTAATTTTACGAATCGA
1 GGGTATTTCGGTAATTTTAC-AAACGA
* * *
12562427 GGGTATTTCGATAATTTCACAATCGA
1 GGGTATTTCGGTAATTTTACAAACGA
* ** *
12562453 AGGTATTTTAGTAATTTTACAAATTGA
1 GGGTATTTCGGTAATTTTACAAA-CGA
* * *
12562480 GGGTATTTTGGTAATTTCACAATCGA
1 GGGTATTTCGGTAATTTTACAAACGA
*
12562506 AGGTATTTCGGTAATTTTACAAATCGA
1 GGGTATTTCGGTAATTTTACAAA-CGA
** * *
12562533 GGGTATTTTAGTAATTTCACAATCGA
1 GGGTATTTCGGTAATTTTACAAACGA
*
12562559 GAGTATTTCGGTAATTTTACAAATCGA
1 GGGTATTTCGGTAATTTTACAAA-CGA
* *
12562586 GGGTATTCCAGTAATTT
1 GGGTATTTCGGTAATTT
12562603 CTCTTTATTA
Statistics
Matches: 438, Mismatches: 78, Indels: 18
0.82 0.15 0.03
Matches are distributed among these distances:
26 113 0.26
27 318 0.73
28 7 0.02
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (26 bp):
GGGTATTTCGGTAATTTTACAAACGA
Found at i:12562325 original size:53 final size:53
Alignment explanation
Indices: 12562077--12562603 Score: 605
Period size: 53 Copynumber: 9.9 Consensus size: 53
12562067 TTACACTACA
* * * * *
12562077 AGGGTATTTCGGTAATTTTAC-ACTACAAGGGTATTTCAATAATTTTACAAAT-A
1 AGGGTATTTCGGTAATTTTACAAAT-CGAGGGTATTTCAGTAATTTCAC-AATCG
* * * *
12562130 AGGGATGTTTCGGTAATTTTACAAATTGAGGGTATTTC-GATAATTTTATAAATCG
1 AGGG-TATTTCGGTAATTTTACAAATCGAGGGTATTTCAG-TAATTTCA-CAATCG
* *
12562185 AGGGTATTTCGGTAATTTTACAAATCGAGGGTGTTTCAGTAATTTCACAAAT-T
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTCAC-AATCG
* *
12562238 AGGGGTATTTCAGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAATCG
1 A-GGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAATCG
* * * * * *
12562292 ATGGTATTTTGGTAATTTTACAAATCCATGGTATTTCGGTAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTCAC-AATCG
* * * * * *
12562346 AGCGTATTTTGATAATTTTACAAATAGAGGGTATTTTAGTAATTTTACAATCG
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAATCG
* *
12562399 AGGGTATTTCAGTAATTTTACGAATCGAGGGTATTTC-GATAATTTCACAATCG
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAG-TAATTTCACAATCG
* ** * **
12562452 AAGGTATTTTAGTAATTTTACAAATTGAGGGTATTTTGGTAATTTCACAATCG
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAATCG
* *
12562505 AAGGTATTTCGGTAATTTTACAAATCGAGGGTATTTTAGTAATTTCACAATCG
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAATCG
* *
12562558 AGAGTATTTCGGTAATTTTACAAATCGAGGGTATTCCAGTAATTTC
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTC
12562604 TCTTTATTAT
Statistics
Matches: 408, Mismatches: 54, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
52 1 0.00
53 232 0.57
54 168 0.41
55 7 0.02
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (53 bp):
AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTCACAATCG
Found at i:12562334 original size:80 final size:81
Alignment explanation
Indices: 12562077--12562602 Score: 606
Period size: 80 Copynumber: 6.6 Consensus size: 81
12562067 TTACACTACA
* * * *
12562077 AGGGTATTTCGGTAATTTTAC-ACTACAAGGGTATTTCAATAATTTTACAAAT-AAGGG-ATGTT
1 AGGGTATTTCGGTAATTTTACAAAT-CGAGGGTATTTCAGTAATTTTACAAATCGAGGGTAT-TT
* *
12562139 TCGGTAATTTTACAAATTG
64 T-AGTAATTTTACAAATCG
* * * * *
12562158 AGGGTATTTCGATAATTTTATAAATCGAGGGTATTTCGGTAATTTTACAAATCGAGGGTGTTTCA
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTTA
* *
12562223 GTAATTTCACAAAT-T
66 GTAATTTTACAAATCG
* * * *
12562238 AGGGGTATTTCAGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCAC-AATCGATGGTATTTT
1 A-GGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTT
* *
12562302 GGTAATTTTACAAATCC
65 AGTAATTTTACAAATCG
* * * *
12562319 ATGGTATTTCGGTAATTTTACAAATCGAGCGTATTT-TGATAATTTTACAAATAGAGGGTATTTT
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAG-TAATTTTACAAATCGAGGGTATTTT
12562383 AGTAATTTTAC-AATCG
65 AGTAATTTTACAAATCG
* * * *
12562399 AGGGTATTTCAGTAATTTTACGAATCGAGGGTATTTC-GATAATTTCAC-AATCGAAGGTATTTT
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAG-TAATTTTACAAATCGAGGGTATTTT
*
12562462 AGTAATTTTACAAATTG
65 AGTAATTTTACAAATCG
* * * *
12562479 AGGGTATTTTGGTAATTTCAC-AATCGAAGGTATTTCGGTAATTTTACAAATCGAGGGTATTTTA
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTTA
*
12562543 GTAATTTCAC-AATCG
66 GTAATTTTACAAATCG
* *
12562558 AGAGTATTTCGGTAATTTTACAAATCGAGGGTATTCCAGTAATTT
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAGTAATTT
12562603 CTCTTTATTA
Statistics
Matches: 377, Mismatches: 56, Indels: 25
0.82 0.12 0.05
Matches are distributed among these distances:
79 69 0.18
80 178 0.47
81 121 0.32
82 8 0.02
83 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (81 bp):
AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTTA
GTAATTTTACAAATCG
Found at i:12568857 original size:43 final size:43
Alignment explanation
Indices: 12568804--12568928 Score: 139
Period size: 43 Copynumber: 2.9 Consensus size: 43
12568794 ATTGAGATAT
* * * *
12568804 GATTACATGTAAGACTATGTCTGGGACATTGGCATTGTATTGA
1 GATTTCATGTAAGACCATGTCTAGGACATTGGCATTGTATTCA
* *
12568847 GATTTCATGTAAGACCATGTCTCA-GACATTGGCATCGTTAATCA
1 GATTTCATGTAAGACCATGTCT-AGGACATTGGCATTG-TATTCA
* *
12568891 -ATTTCATGTAAGACCATATCTAGGATA-TGGCATTGTAT
1 GATTTCATGTAAGACCATGTCTAGGACATTGGCATTGTAT
12568929 GAGCTTATGT
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
41 2 0.03
42 8 0.12
43 55 0.80
44 4 0.06
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (43 bp):
GATTTCATGTAAGACCATGTCTAGGACATTGGCATTGTATTCA
Done.