Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 1 of 316
Found at i:624 original size:32 final size:32
Alignment explanation
Indices: 586--656 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
576 CCGAAACCGC
* *
586 GATATCCGCAGGGT-GGGATATACCTCAGCCGG
1 GATATCC-CAAGGTCGGGATATACCTAAGCCGG
* * *
618 GCTATCCTAAGTTCGGGATATACCTAAGCCGG
1 GATATCCCAAGGTCGGGATATACCTAAGCCGG
650 GATATCC
1 GATATCC
657 TCGGAATGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 3 0.09
32 29 0.91
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (32 bp):
GATATCCCAAGGTCGGGATATACCTAAGCCGG
Found at i:650 original size:16 final size:16
Alignment explanation
Indices: 600--654 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
590 TCCGCAGGGT
*
600 GGGATATACCTCAGCC
1 GGGATATACCTAAGCC
* *
616 GGGCTAT-CCTAAGTTC
1 GGGATATACCTAAG-CC
632 GGGATATACCTAAGCC
1 GGGATATACCTAAGCC
648 GGGATAT
1 GGGATAT
655 CCTCGGAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 5 0.16
16 21 0.66
17 6 0.19
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (16 bp):
GGGATATACCTAAGCC
Found at i:6932 original size:11 final size:11
Alignment explanation
Indices: 6912--6973 Score: 67
Period size: 11 Copynumber: 5.8 Consensus size: 11
6902 TGACAAAAAA
6912 ATTATT-TTTT
1 ATTATTATTTT
*
6922 AATATTATTTT
1 ATTATTATTTT
*
6933 -TTGTTATTTT
1 ATTATTATTTT
*
6943 -TTCTTTATTTT
1 ATT-ATTATTTT
6954 ATTATTATTTT
1 ATTATTATTTT
6965 ATTATTATT
1 ATTATTATT
6974 ATGTTGCTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
10 15 0.34
11 27 0.61
12 2 0.05
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:6975 original size:14 final size:13
Alignment explanation
Indices: 6912--6973 Score: 61
Period size: 13 Copynumber: 4.5 Consensus size: 13
6902 TGACAAAAAA
*
6912 ATTATTTTTTAAT
1 ATTATTTTTTATT
*
6925 ATTATTTTTTGTT
1 ATTATTTTTTATT
*
6938 ATTTTTTCTTTATTTT
1 ATTATTT-TTTA--TT
6954 ATTATTATTTTATT
1 ATTATT-TTTTATT
6968 ATTATT
1 ATTATT
6974 ATGTTGCTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
13 17 0.43
14 11 0.28
16 11 0.28
17 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (13 bp):
ATTATTTTTTATT
Found at i:7066 original size:30 final size:30
Alignment explanation
Indices: 7031--7088 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
7021 ATTTTTTTAA
7031 TAATTTTGTTATTATTTTAAAGAAATTTGT
1 TAATTTTGTTATTATTTTAAAGAAATTTGT
* *
7061 TAATTTTGTTATTATTTTAGAGATATTT
1 TAATTTTGTTATTATTTTAAAGAAATTT
7089 ACTTATTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (30 bp):
TAATTTTGTTATTATTTTAAAGAAATTTGT
Found at i:18460 original size:44 final size:45
Alignment explanation
Indices: 18395--18485 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
18385 ACCTCTATTC
* * *
18395 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
18439 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
18484 CA
1 CA
18486 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:18487 original size:16 final size:16
Alignment explanation
Indices: 18466--18534 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
18456 GATTAGCTAT
18466 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
18482 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
18499 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
18515 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
18531 TACA
1 TACA
18535 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:18508 original size:33 final size:32
Alignment explanation
Indices: 18466--18534 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
18456 GATTAGCTAT
18466 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
18499 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
18531 TACA
1 TACA
18535 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:21280 original size:52 final size:52
Alignment explanation
Indices: 21142--21314 Score: 186
Period size: 52 Copynumber: 3.3 Consensus size: 52
21132 CTATGGTCTT
* * *
21142 ACACAGATCACATTACACACCGATGCCATATCCCAGATATGATCTTATAC-GGA
1 ACACATATCACA-T-CACACCGATGCCATAGCCCAGATATGGTCTTATACAGGA
** *
21195 ATCACATTATCATGTCACACCGATGTCATAGCCCAGATATGGTCTTATACAGGA
1 A-CACA-TATCACATCACACCGATGCCATAGCCCAGATATGGTCTTATACAGGA
** * * **
21249 ACACATATCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACAGCC
1 ACACATATCACATCACACCGATGCCATAGCCCAGATATGGTCTTATACAGGA
*
21301 GCACATATCACATC
1 ACACATATCACATC
21315 TTTTTCGTCG
Statistics
Matches: 100, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
52 50 0.50
53 37 0.37
54 9 0.09
55 4 0.04
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (52 bp):
ACACATATCACATCACACCGATGCCATAGCCCAGATATGGTCTTATACAGGA
Found at i:35624 original size:22 final size:21
Alignment explanation
Indices: 35582--35625 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
35572 CACCATGTAG
* *
35582 TTCATCATGTTGATCCCAGAA
1 TTCACCATGTTGATCACAGAA
*
35603 TTCACCATGTTTGATCAGAGAA
1 TTCACCATG-TTGATCACAGAA
35625 T
1 T
35626 CATCTTGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (21 bp):
TTCACCATGTTGATCACAGAA
Found at i:37466 original size:154 final size:155
Alignment explanation
Indices: 37271--37586 Score: 607
Period size: 154 Copynumber: 2.0 Consensus size: 155
37261 ATCAGTCTAC
37271 GATGAAAAAGGAGATTTCGAAAATCACATAAAAACATAAACGACTGAGAAAATTTAGGTTTATCT
1 GATGAAAAAGGAGATTTCGAAAATCACATAAAAACATAAACGACTGAGAAAATTTAGGTTTATCT
37336 CTCTCACGAAAACTGTTTCCCTACTGTAGCGTGTATGTG-TTTTTTTTTTTTGGCCTCTCGTAAC
66 CTCTCACGAAAACTGTTTCCCTACTGTAGCGTGTATGTGTTTTTTTTTTTTTGGCCTCTCGTAAC
37400 CCAAAACTAAAAAATAGAGTAAAAA
131 CCAAAACTAAAAAATAGAGTAAAAA
37425 GATGAAAAAGGAGATTTCGAAAATCACATAAAAACATAAACGACTGAGAAAATTTAGGTTTATCT
1 GATGAAAAAGGAGATTTCGAAAATCACATAAAAACATAAACGACTGAGAAAATTTAGGTTTATCT
37490 CTCTCACGAAAACTGTTTCCCTACTGTAGCGTGTATGTGTTTTTTTTTTTTTTGGCCTCTCGTAA
66 CTCTCACGAAAACTGTTTCCCTACTGTAGCGTGTATGTG-TTTTTTTTTTTTTGGCCTCTCGTAA
37555 CCCAAAACTAAAAAATAGAGTAAAAA
130 CCCAAAACTAAAAAATAGAGTAAAAA
*
37581 GTTGAA
1 GATGAA
37587 GAGAGAGAAT
Statistics
Matches: 159, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
154 104 0.65
156 55 0.35
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (155 bp):
GATGAAAAAGGAGATTTCGAAAATCACATAAAAACATAAACGACTGAGAAAATTTAGGTTTATCT
CTCTCACGAAAACTGTTTCCCTACTGTAGCGTGTATGTGTTTTTTTTTTTTTGGCCTCTCGTAAC
CCAAAACTAAAAAATAGAGTAAAAA
Found at i:39958 original size:16 final size:16
Alignment explanation
Indices: 39933--39966 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
39923 TGCTCCGACC
39933 CAAGCCAACCCAATAA
1 CAAGCCAACCCAATAA
*
39949 CAAGCTAACCCAATAA
1 CAAGCCAACCCAATAA
39965 CA
1 CA
39967 CAGTACTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.35, G:0.06, T:0.09
Consensus pattern (16 bp):
CAAGCCAACCCAATAA
Found at i:42122 original size:71 final size:71
Alignment explanation
Indices: 42027--42169 Score: 250
Period size: 71 Copynumber: 2.0 Consensus size: 71
42017 CTAAAATATG
* **
42027 ATGGTATTCACGGGGCATTGGACAAGAATAAAAATGATTTAGATTTAGGTGGAATAGAAAGGTAA
1 ATGGTATTCACAGGGCATAAGACAAGAATAAAAATGATTTAGATTTAGGTGGAATAGAAAGGTAA
42092 ATGGTC
66 ATGGTC
*
42098 ATGGTATTCACAGGGCATAAGACAAGATTAAAAATGATTTAGATTTAGGTGGAATAGAAAGGTAA
1 ATGGTATTCACAGGGCATAAGACAAGAATAAAAATGATTTAGATTTAGGTGGAATAGAAAGGTAA
42163 ATGGTC
66 ATGGTC
42169 A
1 A
42170 ACCTTGCCAG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.27
Consensus pattern (71 bp):
ATGGTATTCACAGGGCATAAGACAAGAATAAAAATGATTTAGATTTAGGTGGAATAGAAAGGTAA
ATGGTC
Found at i:44369 original size:3 final size:3
Alignment explanation
Indices: 44358--44425 Score: 93
Period size: 3 Copynumber: 22.7 Consensus size: 3
44348 CAATAATACC
* * *
44358 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
44403 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
44426 AGTTAACAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 1 0.02
3 56 0.98
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:45891 original size:44 final size:44
Alignment explanation
Indices: 45842--45953 Score: 120
Period size: 43 Copynumber: 2.6 Consensus size: 44
45832 ACCTACTCTG
* * *
45842 CTGTAACCTCAGAGAGATAAGATCCTTTAT-TTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGAT-CTATATCTTCAATCCGCTCCA
* * * * * *
45886 CTGTAACTTCAGGGAGATAGGAT-TATGTCTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCTATATCTTCAATCCGCTCCA
45929 CTGTAACCTCAGGGAGATAAGATCT
1 CTGTAACCTCAGGGAGATAAGATCT
45954 GAAATTTCCA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
42 3 0.05
43 31 0.56
44 21 0.38
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (44 bp):
CTGTAACCTCAGGGAGATAAGATCTATATCTTCAATCCGCTCCA
Found at i:46443 original size:177 final size:174
Alignment explanation
Indices: 46140--46527 Score: 582
Period size: 177 Copynumber: 2.2 Consensus size: 174
46130 TTTTTTTTTT
* * * * * *
46140 GATCTGCTTTGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACTAGCTCCACTGCAATCGA
1 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTTCTTCAACCAGCTCCACTACAACCGA
** *
46205 TGGACGCAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTTTTGTCTT
66 AAGACGCAAGGCTTTGTTTTCAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTT
46270 CAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTC
131 CAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTC
* ** *
46314 GATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTA-TCACAACC
1 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCT-TCTTCAACCAGCTCCACT-ACAACC
* *
46378 GAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTTGTCAATGTAGGAAGGCAAGATCTTTT
64 GAAAGACGCAAGGCTTTGT-T-TTCAATCTGCTTCGC-TGTCAATGTAGGAAGGCAAGATCTTTT
46442 GTCTTCAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTC
126 GTCTTCAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTC
46491 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTG
1 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTG
46528 TAACTTCATT
Statistics
Matches: 192, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
174 40 0.21
175 28 0.15
176 14 0.07
177 110 0.57
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (174 bp):
GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTTCTTCAACCAGCTCCACTACAACCGA
AAGACGCAAGGCTTTGTTTTCAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTT
CAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTC
Found at i:46477 original size:89 final size:88
Alignment explanation
Indices: 46140--46526 Score: 575
Period size: 88 Copynumber: 4.4 Consensus size: 88
46130 TTTTTTTTTT
* * * ** * * * * *
46140 GATCTGCTTTGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTTAACTAGCTCCA-CTGCAATC
1 GATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATC-ACAACC
** *
46203 GATGGACGCAAGGCTTTGT-T-TTC
65 GAAAGAGGCAAGG-TTTGTGTCTTC
* *
46226 AATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCG
1 GATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCG
46291 AAAGAGGCAAGGTTTGTGTCTTC
66 AAAGAGGCAAGGTTTGTGTCTTC
46314 GATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCG
1 GATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCG
46379 AAAGAGGCAAGGTTTGTGTCTTC
66 AAAGAGGCAAGGTTTGTGTCTTC
46402 GATCTGCTTCGCTTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACC
1 GATCTGCTTCGC-TGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACC
46467 GAAAGAGGCAAGGTTTGTGTCTTC
65 GAAAGAGGCAAGGTTTGTGTCTTC
*
46491 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
1 GATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
46527 GTAACTTCAT
Statistics
Matches: 280, Mismatches: 16, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
86 39 0.14
87 28 0.10
88 125 0.45
89 88 0.31
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (88 bp):
GATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCG
AAAGAGGCAAGGTTTGTGTCTTC
Found at i:48252 original size:24 final size:23
Alignment explanation
Indices: 48225--48269 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
48215 CTCTTTTTCT
48225 TTTTATT-TTTTATTTTGATTTTGA
1 TTTTATTGTTTT-TTTTG-TTTTGA
*
48249 TTTTGTTGTTTTTTTTGTTTT
1 TTTTATTGTTTTTTTTGTTTT
48270 CCCTTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 11 0.58
25 4 0.21
ACGTcount: A:0.09, C:0.00, G:0.11, T:0.80
Consensus pattern (23 bp):
TTTTATTGTTTTTTTTGTTTTGA
Found at i:53380 original size:3 final size:3
Alignment explanation
Indices: 53369--53435 Score: 84
Period size: 3 Copynumber: 22.7 Consensus size: 3
53359 CAATAATACC
* * *
53369 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
53414 AAT -AT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
53436 AGTTAACAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 3 0.05
3 52 0.95
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:54893 original size:44 final size:44
Alignment explanation
Indices: 54844--54955 Score: 120
Period size: 43 Copynumber: 2.6 Consensus size: 44
54834 ACCTACTCTG
* * *
54844 CTGTAACCTCAGAGAGATAAGATCCTTTAT-TTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGAT-CTATATCTTCAATCCGCTCCA
* * * * * *
54888 CTGTAACTTCAGGGAGATAGGAT-TATGTCTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCTATATCTTCAATCCGCTCCA
54931 CTGTAACCTCAGGGAGATAAGATCT
1 CTGTAACCTCAGGGAGATAAGATCT
54956 GAAATTTCCA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
42 3 0.05
43 31 0.56
44 21 0.38
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (44 bp):
CTGTAACCTCAGGGAGATAAGATCTATATCTTCAATCCGCTCCA
Found at i:55445 original size:177 final size:174
Alignment explanation
Indices: 55142--55529 Score: 582
Period size: 177 Copynumber: 2.2 Consensus size: 174
55132 TTTTTTTTTT
* * * * * *
55142 GATCTGCTTTGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACTAGCTCCACTGCAATCGA
1 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTTCTTCAACCAGCTCCACTACAACCGA
** *
55207 TGGACGCAAGGCTTTGTTTTCAATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTTTTGTCTT
66 AAGACGCAAGGCTTTGTTTTCAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTT
55272 CAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTC
131 CAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTC
* ** *
55316 GATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTA-TCACAACC
1 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCT-TCTTCAACCAGCTCCACT-ACAACC
* *
55380 GAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTTGTCAATGTAGGAAGGCAAGATCTTTT
64 GAAAGACGCAAGGCTTTGT-T-TTCAATCTGCTTCGC-TGTCAATGTAGGAAGGCAAGATCTTTT
55444 GTCTTCAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTC
126 GTCTTCAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTC
55493 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTG
1 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTG
55530 TAACTTCATT
Statistics
Matches: 192, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
174 40 0.21
175 28 0.15
176 14 0.07
177 110 0.57
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (174 bp):
GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTTCTTCAACCAGCTCCACTACAACCGA
AAGACGCAAGGCTTTGTTTTCAATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTT
CAACCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTC
Found at i:55479 original size:89 final size:88
Alignment explanation
Indices: 55142--55528 Score: 575
Period size: 88 Copynumber: 4.4 Consensus size: 88
55132 TTTTTTTTTT
* * * ** * * * * *
55142 GATCTGCTTTGCTGTTAATGCAGGAAGGCAAGATCTGCT-TCTTTAACTAGCTCCA-CTGCAATC
1 GATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATC-ACAACC
** *
55205 GATGGACGCAAGGCTTTGT-T-TTC
65 GAAAGAGGCAAGG-TTTGTGTCTTC
* *
55228 AATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCG
1 GATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCG
55293 AAAGAGGCAAGGTTTGTGTCTTC
66 AAAGAGGCAAGGTTTGTGTCTTC
55316 GATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCG
1 GATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCG
55381 AAAGAGGCAAGGTTTGTGTCTTC
66 AAAGAGGCAAGGTTTGTGTCTTC
55404 GATCTGCTTCGCTTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACC
1 GATCTGCTTCGC-TGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACC
55469 GAAAGAGGCAAGGTTTGTGTCTTC
65 GAAAGAGGCAAGGTTTGTGTCTTC
*
55493 GATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
1 GATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
55529 GTAACTTCAT
Statistics
Matches: 280, Mismatches: 16, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
86 39 0.14
87 28 0.10
88 125 0.45
89 88 0.31
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (88 bp):
GATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCG
AAAGAGGCAAGGTTTGTGTCTTC
Found at i:57248 original size:24 final size:23
Alignment explanation
Indices: 57221--57265 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
57211 CTCTTTTTCT
57221 TTTTATT-TTTTATTTTGATTTTGA
1 TTTTATTGTTTT-TTTTG-TTTTGA
*
57245 TTTTGTTGTTTTTTTTGTTTT
1 TTTTATTGTTTTTTTTGTTTT
57266 CCCTTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 11 0.58
25 4 0.21
ACGTcount: A:0.09, C:0.00, G:0.11, T:0.80
Consensus pattern (23 bp):
TTTTATTGTTTTTTTTGTTTTGA
Found at i:62398 original size:3 final size:3
Alignment explanation
Indices: 62387--62457 Score: 99
Period size: 3 Copynumber: 23.7 Consensus size: 3
62377 CAATAATACC
* * *
62387 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
62432 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
62458 AGTTAACAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
2 1 0.02
3 59 0.98
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:64950 original size:125 final size:125
Alignment explanation
Indices: 64728--64976 Score: 498
Period size: 125 Copynumber: 2.0 Consensus size: 125
64718 AATTGCAGCC
64728 AAACTTTCTATATTTCCCCCTCTCATTTGATCTACAGACGTTACCTGAGCTTGTTCCTGTATGTT
1 AAACTTTCTATATTTCCCCCTCTCATTTGATCTACAGACGTTACCTGAGCTTGTTCCTGTATGTT
64793 TAGCTCATTAATTGTGTTATGCAAGAAAAGCAGGCTAAAAGGTGACATGCATGTAAAGAT
66 TAGCTCATTAATTGTGTTATGCAAGAAAAGCAGGCTAAAAGGTGACATGCATGTAAAGAT
64853 AAACTTTCTATATTTCCCCCTCTCATTTGATCTACAGACGTTACCTGAGCTTGTTCCTGTATGTT
1 AAACTTTCTATATTTCCCCCTCTCATTTGATCTACAGACGTTACCTGAGCTTGTTCCTGTATGTT
64918 TAGCTCATTAATTGTGTTATGCAAGAAAAGCAGGCTAAAAGGTGACATGCATGTAAAGA
66 TAGCTCATTAATTGTGTTATGCAAGAAAAGCAGGCTAAAAGGTGACATGCATGTAAAGA
64977 CTACTCAAAG
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 124 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (125 bp):
AAACTTTCTATATTTCCCCCTCTCATTTGATCTACAGACGTTACCTGAGCTTGTTCCTGTATGTT
TAGCTCATTAATTGTGTTATGCAAGAAAAGCAGGCTAAAAGGTGACATGCATGTAAAGAT
Found at i:69071 original size:16 final size:16
Alignment explanation
Indices: 69022--69075 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
69012 TCCGCAAAGT
69022 GGGATATACCTAAGCC
1 GGGATATACCTAAGCC
* **
69038 GGGCTAT-CCTAATTC
1 GGGATATACCTAAGCC
69053 GGGATATACCTAAGCC
1 GGGATATACCTAAGCC
69069 GGGATAT
1 GGGATAT
69076 CCTGAGAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
15 12 0.39
16 19 0.61
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (16 bp):
GGGATATACCTAAGCC
Found at i:69290 original size:42 final size:43
Alignment explanation
Indices: 69196--69290 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 43
69186 CGAACCGGGA
* * * *
69196 TGGGATATCAGAGGGATATCCCCGGAATTGATTATTCTAAGAG
1 TGGGATATGAGAGGGATAACCCCGGAATAGATTATTCCAAGAG
* *
69239 -GGGAAATGAGAGGGATAACCCTGGAATAGATTATTCCAAG-G
1 TGGGATATGAGAGGGATAACCCCGGAATAGATTATTCCAAGAG
69280 TGGGATATGAG
1 TGGGATATGAG
69291 CGGTATTTAC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.02
42 43 0.98
ACGTcount: A:0.33, C:0.12, G:0.32, T:0.24
Consensus pattern (43 bp):
TGGGATATGAGAGGGATAACCCCGGAATAGATTATTCCAAGAG
Found at i:70347 original size:43 final size:43
Alignment explanation
Indices: 70300--70386 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
70290 GGATATTACA
70300 AAAACTACCCTGCTAAGCAAAAACAAGAAAAGGTATGTCATCC
1 AAAACTACCCTGCTAAGCAAAAACAAGAAAAGGTATGTCATCC
*
70343 AAAACTACCCTGCTAAGCAAAAACAAGAAAAGGTATGTCGTCC
1 AAAACTACCCTGCTAAGCAAAAACAAGAAAAGGTATGTCATCC
70386 A
1 A
70387 GCTATGCTAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.16
Consensus pattern (43 bp):
AAAACTACCCTGCTAAGCAAAAACAAGAAAAGGTATGTCATCC
Found at i:71629 original size:13 final size:13
Alignment explanation
Indices: 71607--71644 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
71597 CCAAACACCG
71607 AAACAAAGCCCAA
1 AAACAAAGCCCAA
*
71620 AAACACAGCCC-A
1 AAACAAAGCCCAA
*
71632 AACCAAAGCCCAA
1 AAACAAAGCCCAA
71645 GCCCCTAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.55, C:0.37, G:0.08, T:0.00
Consensus pattern (13 bp):
AAACAAAGCCCAA
Found at i:71824 original size:21 final size:21
Alignment explanation
Indices: 71793--71850 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
71783 CAAATAGGTT
71793 AAAAATA-TGAACCGGACACC
1 AAAAATACTGAACCGGACACC
*
71813 AAAACA-ACTGAACCGGACACT
1 AAAA-ATACTGAACCGGACACC
71834 AAAAATACTGAACCGGA
1 AAAAATACTGAACCGGA
71851 ACGGAATATG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 6 0.18
21 28 0.82
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (21 bp):
AAAAATACTGAACCGGACACC
Found at i:76949 original size:11 final size:10
Alignment explanation
Indices: 76923--76971 Score: 53
Period size: 11 Copynumber: 4.6 Consensus size: 10
76913 TATTTTTTAA
76923 TATTATTTTT
1 TATTATTTTT
*
76933 TGTTATTTTCT
1 TATTATTTT-T
*
76944 TTTTATTTTGT
1 TATTATTTT-T
76955 TATTATTTTAT
1 TATTATTTT-T
76966 TATTAT
1 TATTAT
76972 ATTGCTACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
10 8 0.24
11 25 0.76
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (10 bp):
TATTATTTTT
Found at i:76968 original size:19 final size:19
Alignment explanation
Indices: 76925--76969 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
76915 TTTTTTAATA
76925 TTATT-TTTTGTTATTTTC
1 TTATTATTTTGTTATTTTC
*
76943 TTTTTATTTTGTTATTATT-
1 TTATTATTTTGTTATT-TTC
76962 TTATTATT
1 TTATTATT
76970 ATATTGCTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.17
19 17 0.74
20 2 0.09
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (19 bp):
TTATTATTTTGTTATTTTC
Found at i:76971 original size:22 final size:22
Alignment explanation
Indices: 76912--76994 Score: 71
Period size: 22 Copynumber: 3.9 Consensus size: 22
76902 GATAAAAGAA
*
76912 TTATT-TTTTAATATTATTTT-
1 TTATTATTTTATTATTATTTTG
* * *
76932 TTGTTATTTTCTTTTTATTTTG
1 TTATTATTTTATTATTATTTTG
*
76954 TTATTATTTTATTATTATATTG
1 TTATTATTTTATTATTATTTTG
* * * *
76976 CTACTATTTCATTGTTATT
1 TTATTATTTTATTATTATT
76995 GTTTGAATAT
Statistics
Matches: 48, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 4 0.08
21 12 0.25
22 32 0.67
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (22 bp):
TTATTATTTTATTATTATTTTG
Found at i:77039 original size:21 final size:21
Alignment explanation
Indices: 77015--77064 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
77005 GGTATAAAAC
* * *
77015 TTATTTTTTTTAATAATTTTG
1 TTATTTTTTTAAAGAAATTTG
*
77036 TTATTATTTTAAAGAAATTTG
1 TTATTTTTTTAAAGAAATTTG
*
77057 TTAATTTT
1 TTATTTTT
77065 GTTATTATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (21 bp):
TTATTTTTTTAAAGAAATTTG
Found at i:85956 original size:3 final size:3
Alignment explanation
Indices: 85948--85985 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
85938 AATTAACCTT
85948 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
85986 TTTTGCTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:87486 original size:15 final size:16
Alignment explanation
Indices: 87444--87489 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
87434 TTTTTCGTTT
87444 AAACATTGAAATTTGC
1 AAACATTGAAATTTGC
*
87460 AATATGATTGAAATTTGC
1 AA-A-CATTGAAATTTGC
87478 -AACATTGAAATT
1 AAACATTGAAATT
87490 AGCCTACTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 9 0.35
16 3 0.12
17 2 0.08
18 12 0.46
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (16 bp):
AAACATTGAAATTTGC
Found at i:88978 original size:20 final size:20
Alignment explanation
Indices: 88922--88991 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 20
88912 ATTAAATATA
*
88922 AAATATTAAAATATAATAAAT
1 AAATATTAAAACATAA-AAAT
88943 CAAATACATTTAAAAACATAAAAAT
1 -AAAT--A-TT-AAAACATAAAAAT
*
88968 AAATATTAAAACA-AGAAAT
1 AAATATTAAAACATAAAAAT
88987 AAATA
1 AAATA
88992 AAAAAATGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
19 10 0.24
20 6 0.14
21 2 0.05
22 5 0.12
24 5 0.12
25 6 0.14
26 8 0.19
ACGTcount: A:0.67, C:0.06, G:0.01, T:0.26
Consensus pattern (20 bp):
AAATATTAAAACATAAAAAT
Found at i:88997 original size:19 final size:20
Alignment explanation
Indices: 88954--88997 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
88944 AAATACATTT
*
88954 AAAAACATAAAAATAAATAT
1 AAAAACATAAAAATAAATAA
* *
88974 TAAAACA-AGAAATAAATAA
1 AAAAACATAAAAATAAATAA
88993 AAAAA
1 AAAAA
88998 TGAAACTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAACATAAAAATAAATAA
Found at i:99777 original size:35 final size:35
Alignment explanation
Indices: 99731--99835 Score: 192
Period size: 35 Copynumber: 3.0 Consensus size: 35
99721 GACGAGCTTG
*
99731 CTGCTTGCGAGCTGCGCAACTGACTACCGATTGCA
1 CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
99766 CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
1 CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
*
99801 CTGCTTGCGAGTTGCGCGACTGACTACCGATTGCA
1 CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
99836 AGGGCTGAGT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (35 bp):
CTGCTTGCGAGCTGCGCGACTGACTACCGATTGCA
Found at i:99834 original size:19 final size:19
Alignment explanation
Indices: 99778--99834 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
99768 GCTTGCGAGC
99778 TGCGCGACTGACTACCGAT
1 TGCGCGACTGACTACCGAT
**
99797 T--GC-ACTG-CTTGCGAGT
1 TGCGCGACTGACTACCGA-T
99813 TGCGCGACTGACTACCGAT
1 TGCGCGACTGACTACCGAT
99832 TGC
1 TGC
99835 AAGGGCTGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
15 5 0.17
16 6 0.21
17 2 0.07
18 2 0.07
19 9 0.31
20 5 0.17
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.25
Consensus pattern (19 bp):
TGCGCGACTGACTACCGAT
Found at i:99853 original size:33 final size:34
Alignment explanation
Indices: 99749--99853 Score: 115
Period size: 35 Copynumber: 3.1 Consensus size: 34
99739 GAGCTGCGCA
* * *
99749 ACTGACTACCGATTGCACTGCTTGCGAGCTGCGCG
1 ACTGACTACCGATTGCACGGCTT-CGAGTTGAGCG
* *
99784 ACTGACTACCGATTGCACTGCTTGCGAGTTGCGCG
1 ACTGACTACCGATTGCACGGCTT-CGAGTTGAGCG
*
99819 ACTGACTACCGATTGCAAGGGC-T-GAGTTGAGCG
1 ACTGACTACCGATTGC-ACGGCTTCGAGTTGAGCG
99852 AC
1 AC
99854 GGAAAGAGGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
33 11 0.17
35 51 0.78
36 3 0.05
ACGTcount: A:0.20, C:0.28, G:0.30, T:0.23
Consensus pattern (34 bp):
ACTGACTACCGATTGCACGGCTTCGAGTTGAGCG
Found at i:103164 original size:42 final size:42
Alignment explanation
Indices: 103103--103188 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
103093 TAAAGTTTAG
*
103103 GAAGAAATGGAAGTAATCCCTGCAAACTATCGTTTAATTAAT
1 GAAGAAATGGAAGTAATCCCTGCAAACTATCATTTAATTAAT
*
103145 GAAGAAATGGAAGTTATCCCTGCAAACTATCATTTAATTAAT
1 GAAGAAATGGAAGTAATCCCTGCAAACTATCATTTAATTAAT
103187 GA
1 GA
103189 GCAAAATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (42 bp):
GAAGAAATGGAAGTAATCCCTGCAAACTATCATTTAATTAAT
Found at i:109369 original size:35 final size:35
Alignment explanation
Indices: 109329--109480 Score: 196
Period size: 35 Copynumber: 4.1 Consensus size: 35
109319 GTACACTTGT
109329 GTACCTATCATATGGATAGCTTGGATCTAGATCTA
1 GTACCTATCATATGGATAGCTTGGATCTAGATCTA
109364 GTACCTATCATATGGATAGCTTGGATCTAGATCTA
1 GTACCTATCATATGGATAGCTTGGATCTAGATCTA
*
109399 GTTTGTTAAAACAACAATCATATGGATAGCTTGGATCTAGATCTA
1 ----G-T---AC--CTATCATATGGATAGCTTGGATCTAGATCTA
*
109444 GTACCTATCACATGGATAGCTTGGATCTAGATCTA
1 GTACCTATCATATGGATAGCTTGGATCTAGATCTA
109479 GT
1 GT
109481 TTGTTAAAAC
Statistics
Matches: 104, Mismatches: 3, Indels: 20
0.82 0.02 0.16
Matches are distributed among these distances:
35 66 0.63
37 2 0.02
39 1 0.01
40 2 0.02
41 1 0.01
43 2 0.02
45 30 0.29
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (35 bp):
GTACCTATCATATGGATAGCTTGGATCTAGATCTA
Found at i:109421 original size:45 final size:45
Alignment explanation
Indices: 109370--109495 Score: 164
Period size: 45 Copynumber: 3.0 Consensus size: 45
109360 TCTAGTACCT
109370 ATCATATGGATAGCTTGGATCTAGATCTAGTTTGTTAAAACAACA
1 ATCATATGGATAGCTTGGATCTAGATCTAGTTTGTTAAAACAACA
*
109415 ATCATATGGATAGCTTGGATCTAGATCTA----G-T---AC--CT
1 ATCATATGGATAGCTTGGATCTAGATCTAGTTTGTTAAAACAACA
*
109450 ATCACATGGATAGCTTGGATCTAGATCTAGTTTGTTAAAACAACA
1 ATCATATGGATAGCTTGGATCTAGATCTAGTTTGTTAAAACAACA
109495 A
1 A
109496 ACAATGTTAG
Statistics
Matches: 68, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
35 29 0.43
37 2 0.03
39 1 0.01
40 2 0.03
41 1 0.01
43 2 0.03
45 31 0.46
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (45 bp):
ATCATATGGATAGCTTGGATCTAGATCTAGTTTGTTAAAACAACA
Found at i:109468 original size:80 final size:80
Alignment explanation
Indices: 109335--109495 Score: 313
Period size: 80 Copynumber: 2.0 Consensus size: 80
109325 TTGTGTACCT
*
109335 ATCATATGGATAGCTTGGATCTAGATCTAGTACCTATCATATGGATAGCTTGGATCTAGATCTAG
1 ATCATATGGATAGCTTGGATCTAGATCTAGTACCTATCACATGGATAGCTTGGATCTAGATCTAG
109400 TTTGTTAAAACAACA
66 TTTGTTAAAACAACA
109415 ATCATATGGATAGCTTGGATCTAGATCTAGTACCTATCACATGGATAGCTTGGATCTAGATCTAG
1 ATCATATGGATAGCTTGGATCTAGATCTAGTACCTATCACATGGATAGCTTGGATCTAGATCTAG
109480 TTTGTTAAAACAACA
66 TTTGTTAAAACAACA
109495 A
1 A
109496 ACAATGTTAG
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (80 bp):
ATCATATGGATAGCTTGGATCTAGATCTAGTACCTATCACATGGATAGCTTGGATCTAGATCTAG
TTTGTTAAAACAACA
Found at i:123719 original size:17 final size:17
Alignment explanation
Indices: 123697--123731 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
123687 CTTTGGGCTG
* *
123697 TGATTTGAATGGGGTTT
1 TGATTTCAATGGGCTTT
123714 TGATTTCAATGGGCTTT
1 TGATTTCAATGGGCTTT
123731 T
1 T
123732 CCGGAACAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.29, T:0.49
Consensus pattern (17 bp):
TGATTTCAATGGGCTTT
Found at i:142617 original size:12 final size:12
Alignment explanation
Indices: 142602--142626 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
142592 TTGGATATTC
142602 ATATATTTTTAG
1 ATATATTTTTAG
142614 ATATATTTTTAG
1 ATATATTTTTAG
142626 A
1 A
142627 AATAACGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (12 bp):
ATATATTTTTAG
Found at i:144478 original size:51 final size:51
Alignment explanation
Indices: 144381--144493 Score: 122
Period size: 51 Copynumber: 2.2 Consensus size: 51
144371 TGGTACAGGT
* * * * *
144381 TAAATTTGTTAAATTAAGACTAAATTGATAAAAATGTGTAAATATTATGGG-
1 TAAATTTATTAAATCAAGACCAAATTGATAAAAATATATAAATATTA-GGGC
* *
144432 TAAATTTATTAAATCAATACCAAATTGAT-AGAATATATAAATTATTAGGGC
1 TAAATTTATTAAATCAAGACCAAATTGATAAAAATATATAAA-TATTAGGGC
*
144483 TGAATTTATTA
1 TAAATTTATTA
144494 TTACACCGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
50 12 0.23
51 40 0.77
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.38
Consensus pattern (51 bp):
TAAATTTATTAAATCAAGACCAAATTGATAAAAATATATAAATATTAGGGC
Found at i:145934 original size:21 final size:21
Alignment explanation
Indices: 145905--145954 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
145895 TGAATAGATT
*
145905 TAATATTTATTGTTTAAACAA
1 TAATATTTATTGTGTAAACAA
*
145926 TATTATTTATTGTGTAAACAA
1 TAATATTTATTGTGTAAACAA
145947 TAATATTT
1 TAATATTT
145955 TTAAAGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (21 bp):
TAATATTTATTGTGTAAACAA
Found at i:158345 original size:18 final size:18
Alignment explanation
Indices: 158318--158410 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
158308 CCCAACTACT
*
158318 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* *
158336 GTATATGTGAATAGTGCC
1 GTATACGTGAATAGTACC
**
158354 GTATACGTGAATAGTATT
1 GTATACGTGAATAGTACC
*
158372 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
158390 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
158408 GTA
1 GTA
158411 AACGGTCGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:158376 original size:36 final size:36
Alignment explanation
Indices: 158318--158410 Score: 150
Period size: 36 Copynumber: 2.6 Consensus size: 36
158308 CCCAACTACT
* *
158318 GTATACGTGAACAGTACCGTATATGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
**
158354 GTATACGTGAATAGTATTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
158390 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
158411 AACGGTCGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:159313 original size:22 final size:22
Alignment explanation
Indices: 159288--159336 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
159278 ACTTTCGCTC
159288 AATA-ATTAAATTTAGAAT-TAAT
1 AATATATTAAA-TTA-AATATAAT
159310 AATATATTAAATTAAATATAAT
1 AATATATTAAATTAAATATAAT
159332 AATAT
1 AATAT
159337 GATATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.12
22 16 0.64
23 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AATATATTAAATTAAATATAAT
Found at i:166758 original size:34 final size:34
Alignment explanation
Indices: 166715--166781 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
166705 GTGGATGATA
166715 ATCGAGATCTTATACTTGATACTTTGATAGTTTT
1 ATCGAGATCTTATACTTGATACTTTGATAGTTTT
166749 ATCGAGATCTTATACTTGATACTTTGATAGTTT
1 ATCGAGATCTTATACTTGATACTTTGATAGTTT
166782 GTCTTTCTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (34 bp):
ATCGAGATCTTATACTTGATACTTTGATAGTTTT
Found at i:175107 original size:44 final size:44
Alignment explanation
Indices: 175057--175146 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
175047 TTGCTAGATG
*
175057 CTGAATATTTTCAAATAGCTTATAGACTAAATTACTGTGACATA
1 CTGAATATTTTCAAATAGCTTATAGACTAAATTACAGTGACATA
175101 CTGAATATTTTCAAATAGCTTATAGACTAAATTACAGTGACATA
1 CTGAATATTTTCAAATAGCTTATAGACTAAATTACAGTGACATA
175145 CT
1 CT
175147 TTTATTGATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (44 bp):
CTGAATATTTTCAAATAGCTTATAGACTAAATTACAGTGACATA
Found at i:187151 original size:23 final size:23
Alignment explanation
Indices: 187099--187151 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
187089 GTATTATTAG
187099 AAAATAAAGTTATGATAAAATCA
1 AAAATAAAGTTATGATAAAATCA
* * *
187122 AATATAAAGTTA-GGTAAATTACA
1 AAAATAAAGTTATGATAAAAT-CA
187145 AAAATAA
1 AAAATAA
187152 TCATTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.26
Consensus pattern (23 bp):
AAAATAAAGTTATGATAAAATCA
Found at i:191595 original size:18 final size:20
Alignment explanation
Indices: 191572--191619 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
191562 TGAAATTGTA
191572 TAATAAATTAAAATTTA-TG
1 TAATAAATTAAAATTTATTG
* *
191591 T-ATAATTTTAAGATTTATTG
1 TAATAA-ATTAAAATTTATTG
191611 TAATAAATT
1 TAATAAATT
191620 TTTTATTTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 4 0.17
19 10 0.43
20 5 0.22
21 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (20 bp):
TAATAAATTAAAATTTATTG
Found at i:194937 original size:16 final size:16
Alignment explanation
Indices: 194904--194937 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
194894 GTAGAATGTT
* *
194904 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
194920 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
194936 AA
1 AA
194938 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:197341 original size:21 final size:21
Alignment explanation
Indices: 197315--197355 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
197305 AGACGAGCAA
* *
197315 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
197336 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
197356 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:199294 original size:16 final size:16
Alignment explanation
Indices: 199261--199294 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
199251 GGAGATTGTT
* *
199261 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
199277 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
199293 AA
1 AA
199295 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:202130 original size:15 final size:17
Alignment explanation
Indices: 202104--202160 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
202094 TAATAAACAC
202104 AATTATTTAAAA-ATTA
1 AATTATTTAAAATATTA
202120 AATTA-TTAAAATATT-
1 AATTATTTAAAATATTA
* * *
202135 AATTGTATAAATTATTA
1 AATTATTTAAAATATTA
*
202152 AACTATTTA
1 AATTATTTA
202161 TATGGTTGGT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 10 0.31
16 16 0.50
17 6 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
AATTATTTAAAATATTA
Found at i:202134 original size:24 final size:25
Alignment explanation
Indices: 202107--202160 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
202097 TAAACACAAT
202107 TATTTAAAAAT-TAAATTATTAAAA
1 TATTTAAAAATATAAATTATTAAAA
*** *
202131 TA-TTAATTGTATAAATTATTAAAC
1 TATTTAAAAATATAAATTATTAAAA
202155 TATTTA
1 TATTTA
202161 TATGGTTGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 5 0.21
24 16 0.67
25 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
TATTTAAAAATATAAATTATTAAAA
Found at i:205458 original size:28 final size:28
Alignment explanation
Indices: 205426--205481 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
205416 CATCATTTTA
* *
205426 TGTGTATGATCACACTAAATCAAAATTT
1 TGTGTATAATCACAATAAATCAAAATTT
*
205454 TGTGTATAATTACAATAAATCAAAATTT
1 TGTGTATAATCACAATAAATCAAAATTT
205482 CATATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (28 bp):
TGTGTATAATCACAATAAATCAAAATTT
Found at i:213549 original size:26 final size:26
Alignment explanation
Indices: 213519--213570 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
213509 CCCCCAAAGA
213519 AAGGGAAACACTTAAATCTATTGAAG
1 AAGGGAAACACTTAAATCTATTGAAG
213545 AAGGGAAACACTTAAATCTATTGAAG
1 AAGGGAAACACTTAAATCTATTGAAG
213571 GAGAGACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (26 bp):
AAGGGAAACACTTAAATCTATTGAAG
Found at i:215454 original size:14 final size:15
Alignment explanation
Indices: 215419--215457 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 15
215409 ACTCTAACTA
215419 AATTATTAATACATTT
1 AATT-TTAATACATTT
215435 ATATTTTAATA-ATTT
1 A-ATTTTAATACATTT
215450 AATTTTAA
1 AATTTTAA
215458 AAAATTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.32
15 5 0.23
16 7 0.32
17 3 0.14
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTTTAATACATTT
Found at i:216883 original size:13 final size:14
Alignment explanation
Indices: 216865--216918 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 14
216855 AGAGTAGTAT
216865 AAAGAT-AATCATG
1 AAAGATCAATCATG
*
216878 AAAGATCAATCTAGTAT
1 AAAGATCAATC-A-T-G
216895 AAAGAT-AATCATG
1 AAAGATCAATCATG
216908 AAAGATCAATC
1 AAAGATCAATC
216919 TAGTTACTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 12 0.35
14 9 0.26
15 2 0.06
16 5 0.15
17 6 0.18
ACGTcount: A:0.52, C:0.11, G:0.13, T:0.24
Consensus pattern (14 bp):
AAAGATCAATCATG
Found at i:216936 original size:30 final size:30
Alignment explanation
Indices: 216859--216922 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
216849 ATAGTAAGAG
216859 TAGTATAAAGATAATCATGAAAGATCAATC
1 TAGTATAAAGATAATCATGAAAGATCAATC
216889 TAGTATAAAGATAATCATGAAAGATCAATC
1 TAGTATAAAGATAATCATGAAAGATCAATC
216919 TAGT
1 TAGT
216923 TACTAACTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.28
Consensus pattern (30 bp):
TAGTATAAAGATAATCATGAAAGATCAATC
Found at i:217399 original size:63 final size:62
Alignment explanation
Indices: 217306--217427 Score: 158
Period size: 63 Copynumber: 2.0 Consensus size: 62
217296 AAAAAATTGC
* *
217306 CATGAATAAATCAATATGTAAATCCCACTTCAAC-CTGACTTCCAAAAATTATCTTAAAATCGG
1 CATGAAGAAATCAATATGTAAATCCCACTTCAACAC-AACTTCC-AAAATTATCTTAAAATCGG
* * *
217369 CATGAAGAAATCAATACT-TAAATCCGACTTCGACACAACTTTCAAAATTATCTTAAAAT
1 CATGAAGAAATCAATA-TGTAAATCCCACTTCAACACAACTTCCAAAATTATCTTAAAAT
217428 TTGTTGACTG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
62 16 0.31
63 34 0.65
64 2 0.04
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (62 bp):
CATGAAGAAATCAATATGTAAATCCCACTTCAACACAACTTCCAAAATTATCTTAAAATCGG
Found at i:219802 original size:6 final size:6
Alignment explanation
Indices: 219791--219820 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
219781 ACATCTTTCA
219791 TCATCC TCATCC TCATCC TCATCC TCATCC
1 TCATCC TCATCC TCATCC TCATCC TCATCC
219821 AACACAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
TCATCC
Found at i:228512 original size:11 final size:11
Alignment explanation
Indices: 228496--228520 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
228486 TTGATCGCCT
228496 CATTCTTTAAC
1 CATTCTTTAAC
228507 CATTCTTTAAC
1 CATTCTTTAAC
228518 CAT
1 CAT
228521 GGGTTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (11 bp):
CATTCTTTAAC
Found at i:240896 original size:31 final size:31
Alignment explanation
Indices: 240861--240924 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
240851 TTATAAAATG
*
240861 GTTATTAAACTATTCGAAAATTTTTATTTAA
1 GTTATCAAACTATTCGAAAATTTTTATTTAA
*
240892 GTTATCAAACTATTCGAAAGTTTTTATTTAA
1 GTTATCAAACTATTCGAAAATTTTTATTTAA
240923 GT
1 GT
240925 CATTGGGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (31 bp):
GTTATCAAACTATTCGAAAATTTTTATTTAA
Found at i:243011 original size:16 final size:17
Alignment explanation
Indices: 242987--243024 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
242977 AGTACAAATA
* *
242987 ATTTAAATATTT-CTTT
1 ATTTGAATATTTGATTT
243003 ATTTGAATATTTGATTT
1 ATTTGAATATTTGATTT
243020 ATTTG
1 ATTTG
243025 TTTTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (17 bp):
ATTTGAATATTTGATTT
Found at i:248449 original size:17 final size:17
Alignment explanation
Indices: 248429--248465 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
248419 AAATAGATTT
248429 TTAATTAAAAATTTTAA
1 TTAATTAAAAATTTTAA
*
248446 TTAATTAAAATTTTTAA
1 TTAATTAAAAATTTTAA
248463 TTA
1 TTA
248466 TTCTTTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAATTAAAAATTTTAA
Found at i:248632 original size:17 final size:17
Alignment explanation
Indices: 248612--248645 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
248602 AGGTTTAGGT
248612 TTAAAATTTTTAATTAA
1 TTAAAATTTTTAATTAA
**
248629 TTAATTTTTTTAATTAA
1 TTAAAATTTTTAATTAA
248646 AAATCTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAAAATTTTTAATTAA
Found at i:265296 original size:219 final size:211
Alignment explanation
Indices: 265058--265491 Score: 796
Period size: 214 Copynumber: 2.0 Consensus size: 211
265048 TATCTTGTTG
265058 ATATTATTATTAAAAAAAATATTAATGAATTTCAAATAAATTAATTTATATGAACCGTTTTGACA
1 ATATTATTATTAAAAAAAATATTAATGAATTTCAAATAAATTAATTTATATGAA-CGTTTTGACA
265123 TAAAATATATATATATATTTTGAACTAACGATGTTGAATTGTATGTTATGATGGTACTGATTATT
65 T--AATATATATAT-TA-TTTGAACTAACGATGTTGAATTGTATGTTATGATGGTACTGATTATT
265188 ATGATGTAAGTCTTATTAATAATGATTTCAATTTTGATATTTTATATTGTATGTGGTGATGATAT
126 ATGATGTAAGTCTTA-TAATAATGATTTCAATTTTGATATTTTATATTGTATGTGGTGATGATAT
265253 CGATTATTATGATGCAAGTATATT
190 CGA-TATT-TGATGCAAGTATATT
265277 ATATTATTATTAAAAAAAATATTAATGAATTTCAAATAAATTAATTTATATGAACGTTTTGACAT
1 ATATTATTATTAAAAAAAATATTAATGAATTTCAAATAAATTAATTTATATGAACGTTTTGACAT
265342 AATATATATATTATTTGAACTAACGATGTTGAATTGTATGTTATGATGGTACTGATTATTATGAT
66 AATATATATATTATTTGAACTAACGATGTTGAATTGTATGTTATGATGGTACTGATTATTATGAT
265407 GTAAGTCTTATAATAATGATTTCAATTTTGATATTTTATATTGTATGTGGTGATGATATCGATAT
131 GTAAGTCTTATAATAATGATTTCAATTTTGATATTTTATATTGTATGTGGTGATGATATCGATAT
265472 TTGATGCAAGTATATT
196 TTGATGCAAGTATATT
265488 ATAT
1 ATAT
265492 ATGATTCAAT
Statistics
Matches: 215, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
211 19 0.09
212 4 0.02
213 52 0.24
214 62 0.29
215 2 0.01
216 11 0.05
218 11 0.05
219 54 0.25
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.44
Consensus pattern (211 bp):
ATATTATTATTAAAAAAAATATTAATGAATTTCAAATAAATTAATTTATATGAACGTTTTGACAT
AATATATATATTATTTGAACTAACGATGTTGAATTGTATGTTATGATGGTACTGATTATTATGAT
GTAAGTCTTATAATAATGATTTCAATTTTGATATTTTATATTGTATGTGGTGATGATATCGATAT
TTGATGCAAGTATATT
Found at i:265496 original size:20 final size:20
Alignment explanation
Indices: 265462--265512 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
265452 TGTGGTGATG
* *
265462 ATATCGATATTTGATGCAAGT
1 ATATTGATATATGATGCAA-T
*
265483 ATATT-ATATATGATTCAAT
1 ATATTGATATATGATGCAAT
265502 ATATTGATATA
1 ATATTGATATA
265513 AATTGATTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 6 0.23
20 16 0.62
21 4 0.15
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (20 bp):
ATATTGATATATGATGCAAT
Found at i:266507 original size:22 final size:23
Alignment explanation
Indices: 266482--266525 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
266472 ATAATAATTT
266482 TTTTAAAAT-TATAATTAAAATA
1 TTTTAAAATATATAATTAAAATA
* *
266504 TTTTAAGATATATATTTAAAAT
1 TTTTAAAATATATAATTAAAAT
266526 TAATATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTTAAAATATATAATTAAAATA
Found at i:268864 original size:21 final size:20
Alignment explanation
Indices: 268835--268874 Score: 55
Period size: 19 Copynumber: 1.9 Consensus size: 20
268825 ATAATTTAAT
268835 TTATGATTATTAGTTAAAAATG
1 TTATGATTATT--TTAAAAATG
268857 TTAT-ATTATTTTAAAAAT
1 TTATGATTATTTTAAAAAT
268875 ATATCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
TTATGATTATTTTAAAAATG
Found at i:275092 original size:172 final size:171
Alignment explanation
Indices: 274789--275098 Score: 489
Period size: 172 Copynumber: 1.8 Consensus size: 171
274779 TAATGTCATC
* * *
274789 AACAATACATGACATAAAATCAAATAATTCTTGTACTGAAATAAATACTAAATCTTAAAACATCC
1 AACAATACATGACATAAAATCAAAGAATTCTTGTACTGAAATAAAGACTAAATCTTAAAACAACC
*
274854 AACCATCTTTCGATTTCCCAATCTGTGAAACTAAAGAACTATGGAACTCAAACCCAAGATAACTG
66 AACCATCTTTCGATTTCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAAGATAACTG
274919 CAGACATGGAGGAGAAACATGAACACAACATGTATGCCACT
131 CAGACATGGAGGAGAAACATGAACACAACATGTATGCCACT
* * * *
274960 AACAATACATGACAATACAATCAAAGAATGTC-TGTACTGAAATAAAGACTAAATCTTCAGATAA
1 AACAATACATGAC-ATAAAATCAAAGAAT-TCTTGTACTGAAATAAAGACTAAATCTTAAAACAA
* *
275024 CCAACCGTCTTTCGATTATCCCAATTTGTGAAACTAAAGAAATATGGAACTCAAACCC-AGATAA
64 CCAACCATCTTTCGATT-TCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAAGATAA
275088 CTGCAGACATG
128 CTGCAGACATG
275099 TCATAGAAAC
Statistics
Matches: 126, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
171 13 0.10
172 73 0.58
173 40 0.32
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.24
Consensus pattern (171 bp):
AACAATACATGACATAAAATCAAAGAATTCTTGTACTGAAATAAAGACTAAATCTTAAAACAACC
AACCATCTTTCGATTTCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAAGATAACTG
CAGACATGGAGGAGAAACATGAACACAACATGTATGCCACT
Found at i:275314 original size:148 final size:147
Alignment explanation
Indices: 274971--275387 Score: 529
Period size: 148 Copynumber: 2.8 Consensus size: 147
274961 ACAATACATG
* * *
274971 ACAATACAATCAAAGAATGTCTGTACTGAAATAAAGACTAAATCTTCAGATAACCAACCGTCTTT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGAATCTTCACATAACCAACCGTCTTT
* * *
275036 C-GATTATCCCAATTTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCAGACATGT
66 CAG-TTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCAAACACGT
*
275100 CATAGAAACACGCCACCA
130 CATACAAACACGCCACCA
* * * *
275118 ACAACACAATCAAAGAATATCTGTACTGAAATGAAGACTGTATCTTCACATAACCAACCATCTTT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGAATCTTCACATAACCAACCGTCTTT
* * * *
275183 CAGTTATCTCAATCTGTGAAACTAAAGAAATATGGAACCCAAACCCATATCA-TAG-AAACACGA
66 CAGTTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACT-GCAAACACG-
* * *
275246 ATACA-ACATATATGCCACCA
129 -T-CATACAAACACGCCACCA
* **
275266 ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGCATCTTCACATAACCGCCCGTCTCT
1 ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGAATCTTCACATAACCAACCGTCT-T
* * *
275331 TGA-TTATCCCAATCAGTGAAACTAAAGAAATATGGAACTCTAACCCAGATAACTGCA
65 TCAGTTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCA
275388 GACAACTGAG
Statistics
Matches: 231, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
146 6 0.03
147 104 0.45
148 114 0.49
149 7 0.03
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.23
Consensus pattern (147 bp):
ACAATACAATCAAAGAATGTCTGTACTGAAATGAAGACTGAATCTTCACATAACCAACCGTCTTT
CAGTTATCCCAATCTGTGAAACTAAAGAAATATGGAACTCAAACCCAGATAACTGCAAACACGTC
ATACAAACACGCCACCA
Found at i:275644 original size:19 final size:18
Alignment explanation
Indices: 275602--275644 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
275592 ATGCCAACAA
275602 ACAAA-AAAAAAAAAAAC
1 ACAAACAAAAAAAAAAAC
*
275619 ACAAACAAAAAACAAAAC
1 ACAAACAAAAAAAAAAAC
275637 ACAGAACA
1 ACA-AACA
275645 CAACAATAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 14 0.61
19 4 0.17
ACGTcount: A:0.79, C:0.19, G:0.02, T:0.00
Consensus pattern (18 bp):
ACAAACAAAAAAAAAAAC
Found at i:275647 original size:21 final size:21
Alignment explanation
Indices: 275597--275647 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
275587 CATATATGCC
275597 AACA-AACA-AAAAAAAAAAA
1 AACACAACACAAAAAAAAAAA
*
275616 AACACAA-ACAAAAAACAAAA
1 AACACAACACAAAAAAAAAAA
* *
275636 CACAGAACACAA
1 AACACAACACAA
275648 CAATAGCACA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 5 0.19
20 17 0.65
21 4 0.15
ACGTcount: A:0.78, C:0.20, G:0.02, T:0.00
Consensus pattern (21 bp):
AACACAACACAAAAAAAAAAA
Found at i:282969 original size:20 final size:21
Alignment explanation
Indices: 282944--282983 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
282934 CATCTGCTCA
*
282944 ACTCCACCTG-TTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
282964 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
282984 TGCTCGTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.28
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:294609 original size:17 final size:17
Alignment explanation
Indices: 294587--294620 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
294577 ATCCACTAAT
*
294587 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
294604 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
294621 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:299247 original size:17 final size:17
Alignment explanation
Indices: 299225--299258 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
299215 ATCCACTAAT
*
299225 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
299242 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
299259 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:301777 original size:15 final size:15
Alignment explanation
Indices: 301745--301789 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
301735 TAATTCTTTG
*
301745 ATTTATATTCATATAT
1 ATTTATA-TCATACAT
*
301761 ATTTATATCATCCAT
1 ATTTATATCATACAT
301776 ATTTAT-TCATACAT
1 ATTTATATCATACAT
301790 TCAAAGTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 7 0.27
15 12 0.46
16 7 0.27
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTATATCATACAT
Found at i:305898 original size:21 final size:20
Alignment explanation
Indices: 305840--305903 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 20
305830 CCTGATCAGT
305840 ATACGACACATAAGTGCCTG
1 ATACGACACATAAGTGCCTG
* * *
305860 AAACGACACACGAGGTGCCTG
1 ATACGACACA-TAAGTGCCTG
305881 ATACGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTG
305902 AT
1 AT
305904 CGGCAAAGCC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 9 0.25
21 27 0.75
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (20 bp):
ATACGACACATAAGTGCCTG
Found at i:306180 original size:14 final size:12
Alignment explanation
Indices: 306161--306204 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
306151 TATTCATAAA
306161 TTAATTCACTTTAT
1 TTAATTCA-TTT-T
306175 TTAATTCATTTT
1 TTAATTCATTTT
*
306187 TTAAATCCATTTT
1 TT-AATTCATTTT
306200 TTAAT
1 TTAAT
306205 CAAATTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 6 0.21
13 14 0.50
14 8 0.29
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAATTCATTTT
Found at i:307008 original size:29 final size:28
Alignment explanation
Indices: 306976--307032 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
306966 TTTTCTTCCC
306976 CTGTT-TTCGTCTCTTTCTCTGTTTCTTTT
1 CTGTTCTTCGTCTCTTT-TCTG-TTCTTTT
*
307005 CTGTTCTTCTTCTCTTTTCTGTTCTTTT
1 CTGTTCTTCGTCTCTTTTCTGTTCTTTT
307033 ATTTCATTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 7 0.27
29 9 0.35
30 10 0.38
ACGTcount: A:0.00, C:0.25, G:0.09, T:0.67
Consensus pattern (28 bp):
CTGTTCTTCGTCTCTTTTCTGTTCTTTT
Found at i:332879 original size:50 final size:50
Alignment explanation
Indices: 332825--332924 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
332815 ATTTTTCCTT
332825 AGTTTTTTTTCTTTATGGTTTTTAGAAAATTTGACTTCAAATAATTGGAC
1 AGTTTTTTTTCTTTATGGTTTTTAGAAAATTTGACTTCAAATAATTGGAC
332875 AGTTTTTTTTCTTTATGGTTTTTAGAAAATTTGACTTCAAATAATTGGAC
1 AGTTTTTTTTCTTTATGGTTTTTAGAAAATTTGACTTCAAATAATTGGAC
332925 TTATTTAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.50
Consensus pattern (50 bp):
AGTTTTTTTTCTTTATGGTTTTTAGAAAATTTGACTTCAAATAATTGGAC
Found at i:335808 original size:58 final size:59
Alignment explanation
Indices: 335699--335813 Score: 153
Period size: 58 Copynumber: 2.0 Consensus size: 59
335689 CAAAATTGAG
* * * * *
335699 TAGTTGAGTGATCATTTTGTAACTTTTTATAATTAGATTATCAAAAAAAATT-TACTAA
1 TAGTTAAGTGATCATTTTATAACTTTTCATAATTAGATCAGCAAAAAAAATTATACTAA
*
335757 TAGTTAAGTGATCATTTTATAACTTTTCATAATTAGA-CGGCAAAAAGAAATTATACT
1 TAGTTAAGTGATCATTTTATAACTTTTCATAATTAGATCAGCAAAAA-AAATTATACT
335814 TGATTAAGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
57 6 0.12
58 39 0.80
59 4 0.08
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (59 bp):
TAGTTAAGTGATCATTTTATAACTTTTCATAATTAGATCAGCAAAAAAAATTATACTAA
Found at i:336308 original size:17 final size:18
Alignment explanation
Indices: 336274--336319 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
336264 CCGTTATGTC
336274 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
336289 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
336306 CGCGACCGCGACCG
1 CGCGACCGCGACCG
336320 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:337403 original size:18 final size:18
Alignment explanation
Indices: 337366--337403 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
337356 CGATATCTCC
*
337366 TTTTTTTTTCTTTTTCTT
1 TTTTTTTTTCTTGTTCTT
*
337384 TTTTTTTTTC-TGTTCAT
1 TTTTTTTTTCTTGTTCTT
337401 TTT
1 TTT
337404 CTTGGTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTCTTGTTCTT
Found at i:344594 original size:12 final size:12
Alignment explanation
Indices: 344577--344603 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
344567 TTTGAATGAG
344577 TTTTAATTGAAT
1 TTTTAATTGAAT
344589 TTTTAATTGAAT
1 TTTTAATTGAAT
344601 TTT
1 TTT
344604 AACATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (12 bp):
TTTTAATTGAAT
Found at i:344603 original size:11 final size:11
Alignment explanation
Indices: 344564--344605 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
344554 TTGAACAAAC
*
344564 GAATTTGAA-T
1 GAATTTTAATT
*
344574 GAGTTTTAATT
1 GAATTTTAATT
344585 GAATTTTTAATT
1 GAA-TTTTAATT
344597 GAATTTTAA
1 GAATTTTAA
344606 CATAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 7 0.26
11 9 0.33
12 11 0.41
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (11 bp):
GAATTTTAATT
Found at i:354794 original size:12 final size:12
Alignment explanation
Indices: 354777--354803 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
354767 AATATTATTA
354777 TTTCATACAAAC
1 TTTCATACAAAC
354789 TTTCATACAAAC
1 TTTCATACAAAC
354801 TTT
1 TTT
354804 TTTTCGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (12 bp):
TTTCATACAAAC
Found at i:365284 original size:10 final size:10
Alignment explanation
Indices: 365264--365297 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
365254 TATAGGTTTG
365264 TTACTTTATTT
1 TTAC-TTATTT
365275 TTACTTA-TT
1 TTACTTATTT
365284 TTACTTATTT
1 TTACTTATTT
365294 TTAC
1 TTAC
365298 ATTTGAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
10 9 0.41
11 4 0.18
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.68
Consensus pattern (10 bp):
TTACTTATTT
Found at i:371301 original size:19 final size:19
Alignment explanation
Indices: 371277--371317 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
371267 AACATAATAT
371277 TTTATCATGGGTCAAGAGA
1 TTTATCATGGGTCAAGAGA
371296 TTTATCATGGGTCAAGAGA
1 TTTATCATGGGTCAAGAGA
371315 TTT
1 TTT
371318 TTGAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (19 bp):
TTTATCATGGGTCAAGAGA
Found at i:371927 original size:19 final size:20
Alignment explanation
Indices: 371887--371926 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
371877 TTTTTATAAA
371887 TATTAAAAAAGTTAAATTTT
1 TATTAAAAAAGTTAAATTTT
371907 TATTAAAAAAGTTAAATTTT
1 TATTAAAAAAGTTAAATTTT
371927 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TATTAAAAAAGTTAAATTTT
Found at i:371933 original size:20 final size:20
Alignment explanation
Indices: 371890--371933 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
371880 TTATAAATAT
* *
371890 TAAAAAAGTTAAATTTTTAT
1 TAAAAAAGTTAAATTTTAAG
371910 TAAAAAAGTTAAATTTTAAG
1 TAAAAAAGTTAAATTTTAAG
371930 TAAA
1 TAAA
371934 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (20 bp):
TAAAAAAGTTAAATTTTAAG
Found at i:371996 original size:32 final size:32
Alignment explanation
Indices: 371936--371997 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
371926 TAAGTAAATT
*
371936 AAAAATTATAAATCTTATAAAATATATTTTTA
1 AAAAATTATAAATATTATAAAATATATTTTTA
* *
371968 AAAAATTATATAATATTTTAATAT-TATTTT
1 AAAAATTATA-AATATTATAAAATATATTTT
371998 CAATATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 16 0.62
33 10 0.38
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
AAAAATTATAAATATTATAAAATATATTTTTA
Found at i:380431 original size:142 final size:140
Alignment explanation
Indices: 380280--380534 Score: 372
Period size: 142 Copynumber: 1.8 Consensus size: 140
380270 TTCTATTATG
* *
380280 TTAATTTAAAATATTGTTTATATCATTATATTTTTAATGGTTGAA-TTTTTACAT-AAATAAATA
1 TTAATTTAAAATACTGTTTATATCATTATATTTTTAATGGTTAAATTTTTTACATAAAATAAATA
* *
380343 ATTTTAAAAAATTAAATTATTATTTCAAAC-TTGAAATACATTATTTAATTTATGTCAATAAAAC
66 A--TT-AAAAATTAAA-T-TTATTACAAACTTTAAAATACATTATTTAATTTATGTCAATAAAAC
380407 AAATAAAATTGTATA
126 AAATAAAATTGTATA
*
380422 TTAATTTAAAATACTGTTTATTTCATTATATTTTTAATGGTTAAATTTTTTACATAAAATAAATA
1 TTAATTTAAAATACTGTTTATATCATTATATTTTTAATGGTTAAATTTTTTACATAAAATAAATA
* * *
380487 ATTAAAATTTTAATTTATTACAAACTTTAAAATACATTATTTTATTTA
66 ATTAAAAATTAAATTTATTACAAACTTTAAAATACATTATTTAATTTA
380535 CGTAAGTAAC
Statistics
Matches: 102, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
139 10 0.10
140 21 0.21
141 8 0.08
142 44 0.43
143 9 0.09
144 10 0.10
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (140 bp):
TTAATTTAAAATACTGTTTATATCATTATATTTTTAATGGTTAAATTTTTTACATAAAATAAATA
ATTAAAAATTAAATTTATTACAAACTTTAAAATACATTATTTAATTTATGTCAATAAAACAAATA
AAATTGTATA
Found at i:383155 original size:29 final size:31
Alignment explanation
Indices: 383123--383185 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
383113 TCAACAATTT
*
383123 AAAATTTAGTCTCTTTA-TTTTTAT-TATAA
1 AAAATTTAATCTCTTTACTTTTTATATATAA
* *
383152 AAAATTTAATCTTTTTACTTTTTATATTTAA
1 AAAATTTAATCTCTTTACTTTTTATATATAA
383183 AAA
1 AAA
383186 TATAAATCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.52
30 7 0.24
31 7 0.24
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (31 bp):
AAAATTTAATCTCTTTACTTTTTATATATAA
Found at i:384233 original size:18 final size:18
Alignment explanation
Indices: 384207--384299 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
384197 TACGACCGTT
384207 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
384225 TACGATACTATTCACATA
1 TACGGTACTATTCACGTA
384243 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
384261 TACAGTACTATTCACATA
1 TACGGTACTATTCACGTA
*
384279 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
384297 TAC
1 TAC
384300 AGTAGTTGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:384254 original size:36 final size:36
Alignment explanation
Indices: 384207--384303 Score: 169
Period size: 36 Copynumber: 2.7 Consensus size: 36
384197 TACGACCGTT
384207 TACGGTACTATTCACGTATAC-GATACTATTCACATA
1 TACGGTACTATTCACGTATACAG-TACTATTCACATA
384243 TACGGTACTATTCACGTATACAGTACTATTCACATA
1 TACGGTACTATTCACGTATACAGTACTATTCACATA
*
384279 TACGGTACTGTTCACGTATACAGTA
1 TACGGTACTATTCACGTATACAGTA
384304 GTTGGGATTG
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
36 58 0.98
37 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACAGTACTATTCACATA
Found at i:388424 original size:11 final size:11
Alignment explanation
Indices: 388397--388439 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
388387 TGACCTTTCC
388397 AAGGTATGGG-
1 AAGGTATGGGA
*
388407 TAGGTATGGGA
1 AAGGTATGGGA
*
388418 AAGGTATGGGC
1 AAGGTATGGGA
*
388429 AAGGCATGGGA
1 AAGGTATGGGA
388440 TAATAGCAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.30, C:0.05, G:0.47, T:0.19
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:389010 original size:15 final size:15
Alignment explanation
Indices: 388990--389018 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
388980 TATGAAAACT
388990 CTAATTTTTGAGAGA
1 CTAATTTTTGAGAGA
389005 CTAATTTTTGAGAG
1 CTAATTTTTGAGAG
389019 GCCATTATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (15 bp):
CTAATTTTTGAGAGA
Found at i:389043 original size:12 final size:12
Alignment explanation
Indices: 389026--389060 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
389016 GAGGCCATTA
389026 TAGAATTTTTCT
1 TAGAATTTTTCT
*
389038 TAGAATTTTACT
1 TAGAATTTTTCT
*
389050 TAGTATTTTTC
1 TAGAATTTTTC
389061 ATTAAGCTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (12 bp):
TAGAATTTTTCT
Found at i:393384 original size:21 final size:21
Alignment explanation
Indices: 393358--393398 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
393348 ATCTGCTCAA
* *
393358 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
393379 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
393399 TTGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:397171 original size:10 final size:10
Alignment explanation
Indices: 397152--397201 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
397142 TTTTTCGAAG
*
397152 GAAAAAAGAA
1 GAAAAGAGAA
397162 GAAAAGAGAA
1 GAAAAGAGAA
397172 GAAAAGAGAA
1 GAAAAGAGAA
* *
397182 -AGAGGAGAA
1 GAAAAGAGAA
397191 GAAAAGA-AA
1 GAAAAGAGAA
397200 GA
1 GA
397202 GTACCGGCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:397202 original size:17 final size:19
Alignment explanation
Indices: 397155--397197 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
397145 TTCGAAGGAA
397155 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
397173 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
397192 AAAAGA
1 AAAAGA
397198 AAGAGTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:397275 original size:10 final size:10
Alignment explanation
Indices: 397260--397288 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
397250 AGACTTTGAA
397260 GAAGAAGAAG
1 GAAGAAGAAG
397270 GAAGAAGAAG
1 GAAGAAGAAG
397280 GAAGAAGAA
1 GAAGAAGAA
397289 AGAAAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:397305 original size:11 final size:11
Alignment explanation
Indices: 397281--397314 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
397271 AAGAAGAAGG
* *
397281 AAGAAGAAAGA
1 AAGAAAAAAAA
397292 AAGAAAAAAAA
1 AAGAAAAAAAA
397303 AAGAAAAAAAA
1 AAGAAAAAAAA
397314 A
1 A
397315 TATATAACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:397436 original size:11 final size:12
Alignment explanation
Indices: 397416--397440 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
397406 AAAAAAAATC
397416 AAAGCAAAAAAA
1 AAAGCAAAAAAA
397428 AAAGCAAAAAAA
1 AAAGCAAAAAAA
397440 A
1 A
397441 GAAGGGAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAGCAAAAAAA
Found at i:397599 original size:23 final size:23
Alignment explanation
Indices: 397573--397649 Score: 104
Period size: 23 Copynumber: 3.3 Consensus size: 23
397563 GCAGCCCAGC
*
397573 AGAAAAAAAAAGGAAG-AAAAAGA
1 AGAAAAAAAAA-AAAGAAAAAAGA
397596 AGAAAAAAGAAAAAAGAAAAAAGA
1 AGAAAAAA-AAAAAAGAAAAAAGA
397620 A-AAAAAGAAAAAAAGAAAAAAGA
1 AGAAAAA-AAAAAAAGAAAAAAGA
397643 AGAAAAA
1 AGAAAAA
397650 GGGGGTTCAA
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
23 32 0.65
24 17 0.35
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (23 bp):
AGAAAAAAAAAAAAGAAAAAAGA
Found at i:397607 original size:7 final size:7
Alignment explanation
Indices: 397590--397648 Score: 82
Period size: 7 Copynumber: 7.9 Consensus size: 7
397580 AAAAGGAAGA
397590 AAAAGAAG
1 AAAA-AAG
397598 AAAAAAG
1 AAAAAAG
397605 AAAAAAG
1 AAAAAAG
397612 AAAAAAG
1 AAAAAAG
397619 AAAAAAAG
1 -AAAAAAG
397627 AAAAAAAG
1 -AAAAAAG
397635 AAAAAAG
1 AAAAAAG
397642 AAGAAAA
1 AA-AAAA
397649 AGGGGGTTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
7 26 0.53
8 23 0.47
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:397608 original size:15 final size:14
Alignment explanation
Indices: 397590--397648 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 14
397580 AAAAGGAAGA
397590 AAAAGAAGAAAAAAG
1 AAAA-AAGAAAAAAG
397605 AAAAAAGAAAAAAG
1 AAAAAAGAAAAAAG
397619 AAAAAAAGAAAAAAAG
1 -AAAAAAG-AAAAAAG
397635 AAAAAAGAAGAAAA
1 AAAAAAGAA-AAAA
397649 AGGGGGTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
14 12 0.29
15 22 0.54
16 7 0.17
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAAG
Found at i:397609 original size:30 final size:30
Alignment explanation
Indices: 397573--397648 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 30
397563 GCAGCCCAGC
*
397573 AGAAAAAA-AAAGGAAGAAAAAGAAG-AAAAA
1 AGAAAAAAGAAA-AAAGAAAAA-AAGAAAAAA
397603 AGAAAAAAGAAAAAAGAAAAAAAGAAAAAA
1 AGAAAAAAGAAAAAAGAAAAAAAGAAAAAA
397633 AGAAAAAAGAAGAAAA
1 AGAAAAAAGAA-AAAA
397649 AGGGGGTTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
29 3 0.07
30 32 0.76
31 7 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (30 bp):
AGAAAAAAGAAAAAAGAAAAAAAGAAAAAA
Found at i:398216 original size:18 final size:19
Alignment explanation
Indices: 398191--398246 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 19
398181 GAAATTTTCG
**
398191 AATTTTCGCGTTT-TCAAA
1 AATTTTCGCGTTTGAAAAA
* *
398209 AGTTTTCGTGTTTGAAAAA
1 AATTTTCGCGTTTGAAAAA
398228 AATTTTCGCGTTT-AAAAA
1 AATTTTCGCGTTTGAAAAA
398246 A
1 A
398247 TTTCTCGTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 17 0.55
19 14 0.45
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (19 bp):
AATTTTCGCGTTTGAAAAA
Found at i:398264 original size:37 final size:37
Alignment explanation
Indices: 398191--398264 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
398181 GAAATTTTCG
* * * *
398191 AATTTTCGCGTTTTCAAAAGTTTTCGTGTTTGAAAAA
1 AATTTTCGCGTTTTAAAAAATTTTCGTATTTCAAAAA
398228 AATTTTCGCG-TTTAAAAAATTTCTCGTATTTCAAAAA
1 AATTTTCGCGTTTTAAAAAATTT-TCGTATTTCAAAAA
398265 TTGTCGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 10 0.31
37 22 0.69
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (37 bp):
AATTTTCGCGTTTTAAAAAATTTTCGTATTTCAAAAA
Found at i:398365 original size:16 final size:16
Alignment explanation
Indices: 398314--398367 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
398304 CGTGCTTTTA
398314 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* *
398330 AAAAATCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
398348 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
398364 AAAA
1 AAAA
398368 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Done.