Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 2 of 28
Found at i:172628 original size:18 final size:19
Alignment explanation
Indices: 172596--172657 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 19
172586 ATAAAATTTT
**
172596 TTATTTAAATTTATTTTAA
1 TTATTTAAAAATATTTTAA
172615 TT-TTTAAAAATA-TTTAA
1 TTATTTAAAAATATTTTAA
** *
172632 TTATTTTTATATATTTTAA
1 TTATTTAAAAATATTTTAA
172651 TTGATTT
1 TT-ATTT
172658 GATTAATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
17 7 0.20
18 15 0.43
19 9 0.26
20 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTATTTAAAAATATTTTAA
Found at i:177755 original size:9 final size:9
Alignment explanation
Indices: 177741--177766 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
177731 AACAGCAAGT
177741 TAATTAACC
1 TAATTAACC
177750 TAATTAACC
1 TAATTAACC
177759 TAATTAAC
1 TAATTAAC
177767 TGTATAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (9 bp):
TAATTAACC
Found at i:183920 original size:123 final size:120
Alignment explanation
Indices: 183685--183923 Score: 293
Period size: 120 Copynumber: 2.0 Consensus size: 120
183675 AGGTATAAAC
* * *
183685 GAGTCTCATGGGTTGAATAATGAGGAAAAAAATGAGTTGATTAATGTAACAATTCGAAGTAAATG
1 GAGTCCCATGGGTTGAATAATAAAGAAAAAAATGAGTTGATTAATGTAACAATTCGAAGTAAATG
* * * * *
183750 GGGTATTTGAAGATGACTTTGAAAGTGATAGGCCAGTGAAAGTAATGGTAAGGAT
66 AGGCATCTGAAGATGACTTTGAAAATGATAGGACAGTGAAAGTAATGGTAAGGAT
* * *
183805 GAGTCCCATGGGTTGAGTAATAAAGAAGAAAATG-GATTGGTTAATGTAACAATCTTTCGAAGTA
1 GAGTCCCATGGGTTGAATAATAAAGAAAAAAATGAG-TTGATTAATGTAACAA---TTCGAAGTA
* * *
183869 AA-GAGGCATCTGAGGATGACTTTGAAAATGATAGGGATAGTGAAGGTAATGGTAA
62 AATGAGGCATCTGAAGATGACTTTGAAAATGATA-GGACAGTGAAAGTAATGGTAA
183924 AGATAAATCA
Statistics
Matches: 100, Mismatches: 14, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
119 1 0.01
120 44 0.44
122 26 0.26
123 29 0.29
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.27
Consensus pattern (120 bp):
GAGTCCCATGGGTTGAATAATAAAGAAAAAAATGAGTTGATTAATGTAACAATTCGAAGTAAATG
AGGCATCTGAAGATGACTTTGAAAATGATAGGACAGTGAAAGTAATGGTAAGGAT
Found at i:186277 original size:16 final size:16
Alignment explanation
Indices: 186256--186291 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
186246 TTCATTAAGG
*
186256 AAAGTTAAGTACAAGC
1 AAAGTTAAGAACAAGC
186272 AAAGTTAAGAACAAGC
1 AAAGTTAAGAACAAGC
186288 AAAG
1 AAAG
186292 AACCAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.56, C:0.11, G:0.19, T:0.14
Consensus pattern (16 bp):
AAAGTTAAGAACAAGC
Found at i:187942 original size:23 final size:23
Alignment explanation
Indices: 187915--187959 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
187905 TGCATTGAAC
*
187915 TTTGGGTTATAATCTCTT-AAGAA
1 TTTGGGATATAAT-TCTTGAAGAA
187938 TTTGGGATATAATTCTTGAAGA
1 TTTGGGATATAATTCTTGAAGA
187960 GATTGAGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (23 bp):
TTTGGGATATAATTCTTGAAGAA
Found at i:193800 original size:30 final size:31
Alignment explanation
Indices: 193735--193800 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
193725 GTTTTCAATC
*
193735 TCAAATTTCATCAATTCTTTTTCGAATTTCT
1 TCAAATTTCATCAATTCTTTTTCGAATTTCA
*
193766 TCAAATTTACATC-ATT-TTTTTC-ATTTTTCA
1 TCAAATTT-CATCAATTCTTTTTCGA-ATTTCA
193796 TCAAA
1 TCAAA
193801 ATCTTCATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 1 0.03
30 15 0.48
31 11 0.35
32 4 0.13
ACGTcount: A:0.29, C:0.18, G:0.02, T:0.52
Consensus pattern (31 bp):
TCAAATTTCATCAATTCTTTTTCGAATTTCA
Found at i:201676 original size:20 final size:20
Alignment explanation
Indices: 201651--201727 Score: 118
Period size: 20 Copynumber: 3.9 Consensus size: 20
201641 GTAATAAAAC
201651 AAAATGTATCGATACATTGA
1 AAAATGTATCGATACATTGA
*
201671 AAAATGTATCGATACATTCA
1 AAAATGTATCGATACATTGA
* * *
201691 TACATGTATCGATACTTTGA
1 AAAATGTATCGATACATTGA
201711 AAAATGTATCGATACAT
1 AAAATGTATCGATACAT
201728 CTGGGTAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (20 bp):
AAAATGTATCGATACATTGA
Found at i:202827 original size:32 final size:32
Alignment explanation
Indices: 202768--202868 Score: 111
Period size: 31 Copynumber: 3.2 Consensus size: 32
202758 CGACATTAGG
* *
202768 TTTAG-AAGGGTTGTCACCAACTCGTGTGGGC
1 TTTAGAAAGGGTTGTCACGAACTTGTGTGGGC
*
202799 TTTAGAGAA-GGTTG-CTACTAACTTGTGTGGGC
1 TTTAGA-AAGGGTTGTC-ACGAACTTGTGTGGGC
* *
202831 TTTA-AAAGGGTTGTCACGGACTTGTGTGGGT
1 TTTAGAAAGGGTTGTCACGAACTTGTGTGGGC
202862 TTTAGAA
1 TTTAGAA
202869 GAGGTTTCCA
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
30 2 0.03
31 29 0.49
32 26 0.44
33 2 0.03
ACGTcount: A:0.22, C:0.13, G:0.32, T:0.34
Consensus pattern (32 bp):
TTTAGAAAGGGTTGTCACGAACTTGTGTGGGC
Found at i:202854 original size:31 final size:31
Alignment explanation
Indices: 202768--202888 Score: 104
Period size: 32 Copynumber: 3.8 Consensus size: 31
202758 CGACATTAGG
* * *
202768 TTTAGAAGGGTTGTCACCAACTCGTGTGGGC
1 TTTAAAAGGGTTGTCACTAACTTGTGTGGGC
202799 TTTAGAGAA-GGTTG-CTACTAACTTGTGTGGGC
1 TTTA-A-AAGGGTTGTC-ACTAACTTGTGTGGGC
** *
202831 TTTAAAAGGGTTGTCACGGACTTGTGTGGGT
1 TTTAAAAGGGTTGTCACTAACTTGTGTGGGC
* *
202862 TTTAGAAGAGGTT-TCCACTGACTTGTG
1 TTTAAAAG-GGTTGT-CACTAACTTGTG
202889 GGCTTTGAAC
Statistics
Matches: 75, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
30 2 0.03
31 32 0.43
32 39 0.52
33 2 0.03
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (31 bp):
TTTAAAAGGGTTGTCACTAACTTGTGTGGGC
Found at i:202874 original size:63 final size:63
Alignment explanation
Indices: 202768--202888 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 63
202758 CGACATTAGG
* *
202768 TTTAGAAGGGTTGTCACCAACTCGTGTGGGCTTTAGAGAAGGTTGCTACTAACTTGTGTGGGC
1 TTTAAAAGGGTTGTCACCAACTCGTGTGGGCTTTAGAGAAGGTTGCCACTAACTTGTGTGGGC
** * * * *
202831 TTTAAAAGGGTTGTCACGGACTTGTGTGGGTTTTAGA-AGAGGTTTCCACTGACTTGTG
1 TTTAAAAGGGTTGTCACCAACTCGTGTGGGCTTTAGAGA-AGGTTGCCACTAACTTGTG
202889 GGCTTTGAAC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
62 1 0.02
63 48 0.98
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (63 bp):
TTTAAAAGGGTTGTCACCAACTCGTGTGGGCTTTAGAGAAGGTTGCCACTAACTTGTGTGGGC
Found at i:202940 original size:28 final size:28
Alignment explanation
Indices: 202792--203608 Score: 692
Period size: 28 Copynumber: 28.5 Consensus size: 28
202782 CACCAACTCG
* *
202792 TGTGGGCTTTAGAGAAGGTTGCTACTAACTT
1 TGTGGGCTTT-GA-AAGGGTGCCACTAAC-T
* * **
202823 GTGTGGGCTTTAAAAGGGTTGTCACGGACTT
1 -TGTGGGCTTTGAAAGGG-TGCCACTAAC-T
* * * *
202854 GTGTGGGTTTTAGAAGAGGTTTCCACTGACT
1 -TGTGGGCTTT-GAA-AGGGTGCCACTAACT
**
202885 TGTGGGCTTTGAACAAAGTGCCACTAACT
1 TGTGGGCTTTGAA-AGGGTGCCACTAACT
** *
202914 TGTCAGCTTTCAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTAACT
* *
202942 TGTGGGCTTTGAAAAGAAAGTGCCACTGACT
1 TGTGGGCTTTG-AAAG--GGTGCCACTAACT
* *
202973 TGTGGGCTTTGAAAAGGTGCCACTAACA
1 TGTGGGCTTTGAAAGGGTGCCACTAACT
* * * *
203001 TATGGGCTTTGAAAAGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTAACT
* * * *
203029 TGTGGACTTTCAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTAACT
** *
203057 TGTGGGCTTT-AAGAATGTGCCACTGACT
1 TGTGGGCTTTGAA-AGGGTGCCACTAACT
* *
203085 TGTGGGCTTTGAAAAGGATGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTAACT
*
203114 TGTGGGCTTTGAAAAGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTAACT
*
203142 TGTGGGC-TTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTAACT
* *
203169 TGTGGGCTTT-AAGAAGGTGCCACTAATT
1 TGTGGGCTTTGAA-AGGGTGCCACTAACT
* *
203197 TATGGGCTTTGAAAGAATGTGCCACTAACT
1 TGTGGGCTTTGAAAG--GGTGCCACTAACT
* *
203227 TGTGGGCTTTGAAAAGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTAACT
* * * *
203255 TGTAGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTAACT
* * * *
203283 TATGGGCTTTGAAAAGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTAACT
* *
203311 TGTGGGCTTTAAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTAACT
* ** *
203339 TGTGGGCTTT-AAGAAGAAGCCACTGACT
1 TGTGGGCTTTGAA-AGGGTGCCACTAACT
* * **
203367 TGTAGGCTTTGAAAAGGTTGCCACCGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTAACT
* * * *
203396 TATGGGCTTTGAACAGGGTGCCAATGATT
1 TGTGGGCTTTGAA-AGGGTGCCACTAACT
* *
203425 TGTGGGCTTTCAAAGGGTGTCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTAACT
* *
203453 TGTGGGCTTTAAAAAGGGTGCCACTGACT
1 TGTGGGCTTT-GAAAGGGTGCCACTAACT
* *
203482 TGTGGGCTTTGAAAAGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTAACT
* * * *
203510 TGTGGACTTT-ATAAGGATACCACTGACT
1 TGTGGGCTTTGA-AAGGGTGCCACTAACT
* * *
203538 TGTGGGCGTTGAGAA-GGTGCCATTGACT
1 TGTGGGCTTTGA-AAGGGTGCCACTAACT
203566 TGTGGGCTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTAACT
203595 TGTGGGCTTTGAAA
1 TGTGGGCTTTGAAA
203609 AGAGGTCGTA
Statistics
Matches: 644, Mismatches: 118, Indels: 50
0.79 0.15 0.06
Matches are distributed among these distances:
27 32 0.05
28 359 0.56
29 145 0.23
30 44 0.07
31 42 0.07
32 19 0.03
33 3 0.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTAACT
Found at i:203050 original size:56 final size:56
Alignment explanation
Indices: 202792--203608 Score: 822
Period size: 56 Copynumber: 14.2 Consensus size: 56
202782 CACCAACTCG
* * * *
202792 TGTGGGCTTTAGAGAAGGTTGCTACTAACTTGTGTGGGCTTT-AAAAGGGTTGTCACGGACTT
1 TGTGGGCTTT-GA-AAGGATGCCACTAAC-T-TGTGGGCTTTGAAAA-GG-TGCCACTGAC-T
* * * * * *
202854 GTGTGGGTTTTAGAAGAGGTTTCCACTGACTTGTGGGCTTTGAACAAAGTGCCACTAACT
1 -TGTGGGCTTT-GAA-AGGATGCCACTAACTTGTGGGCTTTGAA-AAGGTGCCACTGACT
** * *
202914 TGTCAGCTTTCAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAG---GTGCCACTGACT
* * *
202973 TGTGGGCTTTGAAAAGG-TGCCACTAACATATGGGCTTTGAAAAGGTGCCATTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* * * *
203029 TGTGGACTTTCAAAGGATGCCACTGACTTGTGGGCTTT-AAGAATGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAA-AAGGTGCCACTGACT
* *
203085 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTAACT
1 TGTGGGCTTTG-AAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* *
203142 TGTGGGC-TTGAAAGGATGCCACTAACTTGTGGGCTTT-AAGAAGGTGCCACTAATT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAA-AAGGTGCCACTGACT
* * * *
203197 TATGGGCTTTGAAAGAATGTGCCACTAACTTGTGGGCTTTGAAAAGATGCCACTAACT
1 TGTGGGCTTTGAAAGGA--TGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* * * * *
203255 TGTAGGCTTTGAAAAGATGCCACTGACTTATGGGCTTTGAAAAGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* **
203311 TGTGGGCTTTAAAAGGATGCCACTAACTTGTGGGCTTT-AAGAAGAAGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAA-AAGGTGCCACTGACT
* * ** * * * *
203367 TGTAGGCTTTGAAAAGGTTGCCACCGACTTATGGGCTTTGAACAGGGTGCCAATGATT
1 TGTGGGCTTTG-AAAGGATGCCACTAACTTGTGGGCTTTGAA-AAGGTGCCACTGACT
* * * *
203425 TGTGGGCTTTCAAAGGGTGTCACTAACTTGTGGGCTTTAAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAA-GGTGCCACTGACT
* * * *
203482 TGTGGGCTTTGAAAAGATGCCACTAACTTGTGGACTTT-ATAAGGATACCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGG-TGCCACTGACT
* * * *
203538 TGTGGGCGTTGAGAAGG-TGCCATTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGA-AAGGATGCCACTAACTTGTGGGCTTTGAAAA-GGTGCCACTGACT
203595 TGTGGGCTTTGAAA
1 TGTGGGCTTTGAAA
203609 AGAGGTCGTA
Statistics
Matches: 634, Mismatches: 96, Indels: 55
0.81 0.12 0.07
Matches are distributed among these distances:
54 2 0.00
55 57 0.09
56 206 0.32
57 189 0.30
58 74 0.12
59 53 0.08
60 6 0.01
61 17 0.03
62 5 0.01
63 25 0.04
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (56 bp):
TGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACT
Found at i:204945 original size:11 final size:11
Alignment explanation
Indices: 204918--204951 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
204908 TGGACCCTTA
*
204918 TTTTTTGTGTT
1 TTTTTTGTTTT
204929 TTTTTTGTTTT
1 TTTTTTGTTTT
*
204940 TTTTTTCTTTT
1 TTTTTTGTTTT
204951 T
1 T
204952 GAGAATGGCA
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:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:210173 original size:19 final size:19
Alignment explanation
Indices: 210149--210192 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
210139 AAATAGAAAA
*
210149 TGTATCGATACATGAGTGT
1 TGTATCGATACATAAGTGT
*
210168 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
210187 TGTATC
1 TGTATC
210193 AAGACAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.41
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:212763 original size:52 final size:52
Alignment explanation
Indices: 212630--212765 Score: 168
Period size: 52 Copynumber: 2.6 Consensus size: 52
212620 TTAAGTTTCT
* * *
212630 CAATTGTTCATAATCGAGGATACTCCAAC-CCCAGTTTTATTTTCAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACTCCCAGTTTTATTTCCAAAACAC
* * **
212681 CAATTTTCCTTTAATCGGGGATACTCCAACTCTGA-TTTTATTTCCAAAAACAC
1 CAATTTTTC-ATAATCGGGGATACTCCAACTCCCAGTTTTATTTCC-AAAACAC
*
212734 CAATTTTTCACAATCGGGGATACTCCAACTCC
1 CAATTTTTCATAATCGGGGATACTCCAACTCC
212766 GTTAATCATC
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
51 7 0.10
52 47 0.66
53 17 0.24
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.32
Consensus pattern (52 bp):
CAATTTTTCATAATCGGGGATACTCCAACTCCCAGTTTTATTTCCAAAACAC
Found at i:212816 original size:28 final size:27
Alignment explanation
Indices: 212749--212820 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
212739 TTTCACAATC
* *
212749 GGGGATACTCCAACTCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
* **
212776 GGGGATACTCCAACCCCGTTATTTTTGA
1 GGGGATACTCCAACCCCGTTAATCAT-A
212804 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
212821 AACTTTATTC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.25
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:212828 original size:107 final size:107
Alignment explanation
Indices: 212697--212899 Score: 246
Period size: 106 Copynumber: 1.9 Consensus size: 107
212687 TCCTTTAATC
* ** * *
212697 GGGGATACTCCAACTCTGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCAACTTTA-TTCCAAAAACACCAATTTCTCACAATCGGGGATACTCCAA
* *
212762 CTCCGTTAATCAT-CGGGGATACTCCAACCCCGTTATTTTTGA
65 CCCCGTTAATCATGAGGGGATACTCCAACCCCGTTATTTTTGA
* * *** *
212804 GGGGATACTCCAACCCCAACTTTATTCCTAAAATATTGATTTCTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCAACTTTATTCCAAAAACACCAATTTCTCACAATCGGGGATACTCCAAC
* **
212869 CCCGTTATTTTTGAGGGGATACTCCAACCCC
66 CCCGTTAATCATGAGGGGATACTCCAACCCC
212900 CGGCTTTATT
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
106 42 0.53
107 37 0.47
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCAACTTTATTCCAAAAACACCAATTTCTCACAATCGGGGATACTCCAAC
CCCGTTAATCATGAGGGGATACTCCAACCCCGTTATTTTTGA
Found at i:212856 original size:79 final size:79
Alignment explanation
Indices: 212773--213138 Score: 529
Period size: 79 Copynumber: 4.6 Consensus size: 79
212763 TCCGTTAATC
**
212773 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCAACTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
212838 ATTGATTTCTCATA
66 ATTGATTTCTCATA
212852 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCCGGCTTTATTCCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAA-CCCCGGCTTTATTCCTAAAA
212917 TATTGATTTCTCATA
65 TATTGATTTCTCATA
* * * * * *
212932 ATCGGCGATACTCCAACCCCGTTATTTCTGAGGGGATACTCTAACCCTGGCTTTATTTCTAATAT
1 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
*
212997 ATTAATTTCTCATA
66 ATTGATTTCTCATA
* * *
213011 ATCGGGGATACTCCAACCCCGTTATCTCTGAGGGGATACTCCAACCCCGGTTTTATTTCC--AAA
1 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGGCTTTA-TTCCTAAAA
* * *
213074 TCATCGATTTTTCACA
65 T-ATTGATTTCTCATA
** *
213090 ATCGGGGATACTCCAACCCCGTTATTTTCAAGAGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCG
213139 TTACTATCTC
Statistics
Matches: 259, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
78 3 0.01
79 179 0.69
80 77 0.30
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.32
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
ATTGATTTCTCATA
Found at i:212954 original size:159 final size:158
Alignment explanation
Indices: 212773--213137 Score: 527
Period size: 159 Copynumber: 2.3 Consensus size: 158
212763 TCCGTTAATC
212773 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCAACTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCAACTTTATTCCTAAAAT
* * *
212838 ATTGATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCCGG
66 ATTAATTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCTGAGGGGATACTCCAA-CCCCGG
* *
212903 CTTTA-TTCCTAAAAT-ATTGATTTCTCATA
130 CTTTATTTCC--AAATCATCGATTTCTCACA
* * * *** * *
212932 ATCGGCGATACTCCAACCCCGTTATTTCTGAGGGGATACTCTAACCCTGGCTTTATTTCTAATAT
1 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCAACTTTATTCCTAAAAT
*
212997 ATTAATTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCTGAGGGGATACTCCAACCCCGGT
66 ATTAATTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCTGAGGGGATACTCCAACCCCGGC
*
213062 TTTATTTCCAAATCATCGATTTTTCACA
131 TTTATTTCCAAATCATCGATTTCTCACA
** *
213090 ATCGGGGATACTCCAACCCCGTTATTTTCAAGAGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCC
213138 GTTACTATCT
Statistics
Matches: 182, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
157 4 0.02
158 62 0.34
159 116 0.64
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (158 bp):
ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCAACTTTATTCCTAAAAT
ATTAATTTCTCATAATCGGGGATACTCCAACCCCGTTATCTCTGAGGGGATACTCCAACCCCGGC
TTTATTTCCAAATCATCGATTTCTCACA
Found at i:223164 original size:51 final size:50
Alignment explanation
Indices: 223102--223216 Score: 167
Period size: 51 Copynumber: 2.3 Consensus size: 50
223092 AATTAACTAG
* * * *
223102 ATGTATAGATACATTGAATAATGTATTGATACATTTGGGTAACAAAATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATTTGGATAA-AAAATAGA
223153 ATGTATCGATACATTGAAAAATGTATCGATACATTTGGATAAAAAATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATTTGGATAAAAAATAGA
* *
223203 ATATATCAATACAT
1 ATGTATCGATACAT
223217 GTACTATTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 20 0.34
51 38 0.66
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (50 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATTTGGATAAAAAATAGA
Found at i:225133 original size:138 final size:137
Alignment explanation
Indices: 224982--225258 Score: 466
Period size: 138 Copynumber: 2.0 Consensus size: 137
224972 CTTAAATACC
* * *
224982 TGGAATGTTTTGAAATACATACCCTTAACGT-CTTTTTTAATTTACTTTGCTTATTTTTTGGATT
1 TGGAATGTTTTGAAATACATACCCTTAACATCCTTTTTT-ATTTACTTTGCTTATTATTTAGATT
* *
225046 AATTCTTGATCATAGGATTATTTGGATATATTTGTCCTATATTTTCTGATTCTATTGCTAATTAA
65 AATTCTTGATCATAGGATTATTTGGATATATTTGCCCTATATTTTCTGATTCTATCGCTAATTAA
225111 CTTGATATA
130 CTTGAT-TA
*
225120 TGGAATGTTTTGAAATACATACCCTTAGCATCCTTTTTTATTTACTTTGCTTATTATTTAGATTA
1 TGGAATGTTTTGAAATACATACCCTTAACATCCTTTTTTATTTACTTTGCTTATTATTTAGATTA
*
225185 ATTCTTGATCATAGGATTATTTGGATATATTTGCCCTATATTTTGTGATTCTATCGCTAATTAAC
66 ATTCTTGATCATAGGATTATTTGGATATATTTGCCCTATATTTTCTGATTCTATCGCTAATTAAC
225250 TTGATTA
131 TTGATTA
225257 TG
1 TG
225259 TGTTTAGATT
Statistics
Matches: 131, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
137 4 0.03
138 120 0.92
139 7 0.05
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.49
Consensus pattern (137 bp):
TGGAATGTTTTGAAATACATACCCTTAACATCCTTTTTTATTTACTTTGCTTATTATTTAGATTA
ATTCTTGATCATAGGATTATTTGGATATATTTGCCCTATATTTTCTGATTCTATCGCTAATTAAC
TTGATTA
Found at i:227591 original size:20 final size:19
Alignment explanation
Indices: 227536--227591 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
227526 AAAACCCTTA
*
227536 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
227556 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
227576 AATGTATCGATACATG
1 AAAGTATCGATACATG
227592 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:227679 original size:13 final size:13
Alignment explanation
Indices: 227661--227686 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
227651 TACACAAAAT
227661 ATGTATCGATACA
1 ATGTATCGATACA
227674 ATGTATCGATACA
1 ATGTATCGATACA
227687 CAAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:227708 original size:35 final size:32
Alignment explanation
Indices: 227643--227708 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
227633 TAGCCAAACT
*
227643 TGTATCGATACACAAAATATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
227675 TGTATCGATACACAAAAAAAATTGTATCGATACA
1 TGTATCGATACAC--AAAAAA-TGTATCGATACA
227709 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.43
34 5 0.17
35 12 0.40
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:228013 original size:32 final size:30
Alignment explanation
Indices: 227968--228026 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 30
227958 TAGATCAAAG
227968 TATTTTATATTTTTCTAGAGCT-TTTGTTCA
1 TATTTTATATTTTTCTA-AGCTCTTTGTTCA
227998 TATTGTTATTATTTTTCTAAGCTCTTTGT
1 TATT-TTA-TATTTTTCTAAGCTCTTTGT
228027 ATTTAATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 4 0.15
31 7 0.27
32 15 0.58
ACGTcount: A:0.19, C:0.10, G:0.10, T:0.61
Consensus pattern (30 bp):
TATTTTATATTTTTCTAAGCTCTTTGTTCA
Found at i:229942 original size:21 final size:21
Alignment explanation
Indices: 229909--229958 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
229899 TTGTAAGTTG
*
229909 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
229931 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
229952 AAATAAA
1 AAATAAA
229959 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:231776 original size:15 final size:15
Alignment explanation
Indices: 231756--231786 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
231746 TAAAAATATC
*
231756 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
231771 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
231786 C
1 C
231787 CAAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:233886 original size:13 final size:13
Alignment explanation
Indices: 233868--233905 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
233858 CATTTTTCTT
233868 TGTATCGATACAA
1 TGTATCGATACAA
*
233881 TGTATCGATACAC
1 TGTATCGATACAA
233894 TGTATCGATACA
1 TGTATCGATACA
233906 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:236370 original size:20 final size:19
Alignment explanation
Indices: 236315--236370 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
236305 AAAACCCTTA
*
236315 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
236335 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
236355 AATGTATCGATACATG
1 AAAGTATCGATACATG
236371 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:236458 original size:13 final size:13
Alignment explanation
Indices: 236440--236465 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
236430 TACACAAAAT
236440 ATGTATCGATACA
1 ATGTATCGATACA
236453 ATGTATCGATACA
1 ATGTATCGATACA
236466 CAAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:236487 original size:35 final size:32
Alignment explanation
Indices: 236422--236487 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
236412 TAGCCAAACT
*
236422 TGTATCGATACACAAAATATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
236454 TGTATCGATACACAAAAAAAATTGTATCGATACA
1 TGTATCGATACAC--AAAAAA-TGTATCGATACA
236488 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.43
34 5 0.17
35 12 0.40
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:240403 original size:58 final size:59
Alignment explanation
Indices: 240323--240468 Score: 163
Period size: 58 Copynumber: 2.5 Consensus size: 59
240313 TTTTTATCTC
* * * *
240323 ATTTTCCATGA-CTTAGGGACTTTCTTG-TAATTCTATATATCTTAGAGTCATTTAAGTA
1 ATTTTCCATGATC-TAGAGACTTTCATGCAAATTCTACATATCTTAGAGTCATTTAAGTA
* * * * *
240381 ATTTTCCATGATCCAGAGACTTTCATGCAAATTTTACATATCTTAGGGTCATTTAGGTC
1 ATTTTCCATGATCTAGAGACTTTCATGCAAATTCTACATATCTTAGAGTCATTTAAGTA
* *
240440 ATTTT-CAAGATCTACAGACTTTCATGCAA
1 ATTTTCCATGATCTAGAGACTTTCATGCAA
240469 TTTCATGCAT
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
58 43 0.58
59 31 0.42
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (59 bp):
ATTTTCCATGATCTAGAGACTTTCATGCAAATTCTACATATCTTAGAGTCATTTAAGTA
Found at i:240503 original size:58 final size:58
Alignment explanation
Indices: 240428--240597 Score: 179
Period size: 58 Copynumber: 2.9 Consensus size: 58
240418 ATATCTTAGG
* *
240428 GTCATTTAGGTCA-TTTTCAAGATCTACA-GACTTTCATGCAATTTCATGCATTTTGAT
1 GTCATTTAGGTCATTTTTCAAGATCTA-AGGACTTTAATGCAATTGCATGCATTTTGAT
* * * * * *
240485 GTCTTTTAGGTTATTTTTCATGATTTAAGGATTTTAATGCTATTGCATGCATTTTGAT
1 GTCATTTAGGTCATTTTTCAAGATCTAAGGACTTTAATGCAATTGCATGCATTTTGAT
* *
240543 GTCATTTAGGTCA-TTTTCTAA-AACTTAAGGA-TTTAATGCAATTTCATGTCATTTT
1 GTCATTTAGGTCATTTTTC-AAGATC-TAAGGACTTTAATGCAATTGCATG-CATTTT
240598 CTATAATCTA
Statistics
Matches: 93, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
57 33 0.35
58 60 0.65
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (58 bp):
GTCATTTAGGTCATTTTTCAAGATCTAAGGACTTTAATGCAATTGCATGCATTTTGAT
Found at i:240625 original size:39 final size:39
Alignment explanation
Indices: 240552--240654 Score: 129
Period size: 39 Copynumber: 2.7 Consensus size: 39
240542 TGTCATTTAG
* *
240552 GTCATTTTCTA-AAACTTAAGGA-TTTAATGCAATTTCAT
1 GTCATTTTCTATAATC-TAGGGACTTTAATGCAATTTCAT
*
240590 GTCATTTTCTATAATCTAGGGACTTTAATGTAATTTCAT
1 GTCATTTTCTATAATCTAGGGACTTTAATGCAATTTCAT
* * *
240629 GTGATTTTTTATGATCTAGGGACTTT
1 GTCATTTTCTATAATCTAGGGACTTT
240655 TGTACAATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
38 16 0.28
39 41 0.72
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.46
Consensus pattern (39 bp):
GTCATTTTCTATAATCTAGGGACTTTAATGCAATTTCAT
Found at i:240664 original size:39 final size:39
Alignment explanation
Indices: 240581--240674 Score: 113
Period size: 39 Copynumber: 2.4 Consensus size: 39
240571 GGATTTAATG
*
240581 CAATTTCATGTCATTTTCTATAATCTAGGGACTTTAATGT
1 CAATTTCATGTGATTTTCTATAATCTAGGGACTTT-ATGT
* *
240621 -AATTTCATGTGATTTTTTATGATCTAGGGACTTT-TGT
1 CAATTTCATGTGATTTTCTATAATCTAGGGACTTTATGT
*
240658 ACAATTTTATGTG-TTTT
1 -CAATTTCATGTGATTTT
240675 AATGTCATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
37 3 0.06
38 4 0.08
39 41 0.85
ACGTcount: A:0.24, C:0.11, G:0.15, T:0.50
Consensus pattern (39 bp):
CAATTTCATGTGATTTTCTATAATCTAGGGACTTTATGT
Found at i:249704 original size:21 final size:21
Alignment explanation
Indices: 249678--249743 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
249668 TTAGTTTCCA
249678 AAAATAACATTTTAAGACATT
1 AAAATAACATTTTAAGACATT
* *
249699 AAAATAATTATTTT---CCA--
1 AAAATAA-CATTTTAAGACATT
249716 AAAATAACATTTTAAGACATT
1 AAAATAACATTTTAAGACATT
249737 AAAATAA
1 AAAATAA
249744 AGAAATCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
16 5 0.14
17 7 0.20
19 4 0.11
21 14 0.40
22 5 0.14
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAATAACATTTTAAGACATT
Found at i:249708 original size:38 final size:38
Alignment explanation
Indices: 249666--249743 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
249656 ATTTTAGGAG
249666 AATTAGTTTCCAAAAATAACATTTTAAGACATTAAAAT
1 AATTAGTTTCCAAAAATAACATTTTAAGACATTAAAAT
*
249704 AATTATTTTCCAAAAATAACATTTTAAGACATTAAAAT
1 AATTAGTTTCCAAAAATAACATTTTAAGACATTAAAAT
249742 AA
1 AA
249744 AGAAATCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (38 bp):
AATTAGTTTCCAAAAATAACATTTTAAGACATTAAAAT
Found at i:250617 original size:22 final size:22
Alignment explanation
Indices: 250591--250642 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
250581 AGAAAAGTTT
250591 AACATTGATCAAATCAATTTT-A
1 AACATTGATCAAA-CAATTTTAA
* *
250613 AACA-TGCTTTAAACAATTTTAA
1 AACATTG-ATCAAACAATTTTAA
250635 AACATTGA
1 AACATTGA
250643 AATCAGATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
21 9 0.38
22 13 0.54
23 2 0.08
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (22 bp):
AACATTGATCAAACAATTTTAA
Found at i:258875 original size:79 final size:79
Alignment explanation
Indices: 258676--259030 Score: 502
Period size: 79 Copynumber: 4.5 Consensus size: 79
258666 AATAAAATCA
* * *
258676 GGGTTGGAGTATCCCCGCGAAAATAACAGGGTTGTAGTATCCCCGATTGTGAGAAATCAATATTT
1 GGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATTGTGAGAAATCAATATTT
*
258741 TAGGAATAAAGCC-
66 TAGAAATAAAGCCG
* *
258754 GGGTTGGAGTATCCCCTCGAAAATAAC-GTGGTTGGAGGATCCTCAATTGTGAGAAATCAATATT
1 GGGTTGGAGTATCCCCTCGAAAATAACAG-GGTTGGAGTATCCTCGATTGTGAGAAATCAATATT
*
258818 TTAGGAATAAAGCCG
65 TTAGAAATAAAGCCG
*
258833 GGGTTGGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCTCGATTGTGAGAAATCAATATTT
1 GGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATTGTGAGAAATCAATATTT
* *
258898 TAAAAATAAAACCG
66 TAGAAATAAAGCCG
* * * *
258912 GGGTTGTAGTATCCCCTC-AGAAATAACGGGGTTGGAGTATTCTCGATTGTGAGAAATCAATACT
1 GGGTTGGAGTATCCCCTCGA-AAATAACAGGGTTGGAGTATCCTCGATTGTGAGAAATCAATATT
** *
258976 TTAGAAATAGTGCCA
65 TTAGAAATAAAGCCG
*
258991 GGGTTGGAGTATCCCCTCGAAAATAA-TGGGTTGGAGTATC
1 GGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATC
259031 ACCGATGATT
Statistics
Matches: 248, Mismatches: 24, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
77 1 0.00
78 83 0.33
79 162 0.65
80 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.27
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATTGTGAGAAATCAATATTT
TAGAAATAAAGCCG
Found at i:259005 original size:158 final size:157
Alignment explanation
Indices: 258664--259036 Score: 525
Period size: 157 Copynumber: 2.4 Consensus size: 157
258654 CGGTGTTCTG
** * *
258664 GAAATAAAATCAGGGTTGGAGTATCCCCGCGAAAATAACAGGGTTGTAGTATCCCCGATTGTGAG
1 GAAATAAAGCCAGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAG
** * *
258729 AAATCAATATTTTAGGAATAAAGCCGGGTTGGAGTATCCCCTCGAAAATAACGTGGTTGGAGGAT
66 AAATCAATATTTTAAAAATAAAACCGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGGAT
*
258794 CCTCAATTGTGAGAAATCAATATTTTA
131 CCTCAATTGTGAGAAATCAATACTTTA
* * * *
258821 GGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCTCGATTGTGAG
1 GAAATAAAGCCAGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAG
* *
258886 AAATCAATATTTTAAAAATAAAACCGGGGTTGTAGTATCCCCTC-AGAAATAACGGGGTTGGAGT
66 AAATCAATATTTTAAAAATAAAACC-GGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGG
* *
258950 ATTCTCGATTGTGAGAAATCAATACTTTA
129 ATCCTCAATTGTGAGAAATCAATACTTTA
** * *
258979 GAAATAGTGCCAGGGTTGGAGTATCCCCTCGAAAATAA-TGGGTTGGAGTATCACCGAT
1 GAAATAAAGCCAGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGAT
259037 GATTAACGGG
Statistics
Matches: 189, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
157 97 0.51
158 92 0.49
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (157 bp):
GAAATAAAGCCAGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAG
AAATCAATATTTTAAAAATAAAACCGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGGAT
CCTCAATTGTGAGAAATCAATACTTTA
Found at i:259226 original size:51 final size:51
Alignment explanation
Indices: 259047--259228 Score: 249
Period size: 51 Copynumber: 3.6 Consensus size: 51
259037 GATTAACGGG
*
259047 GTTGGAGTATCTCCGATTATGAAAAATTGGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAATCGGA
* *
259098 GTTGGAGTATCCCCGATTAT-AGAAAATTGGTGTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTATGA-AAAATTGGTGTTTTGAAAATAAAATCGGA
** ** * * **
259149 GTTAAAGTATCATCGATTGTGGAAAATTGGTGTTTCAAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAATCGGA
259200 GTTGGAGTATCCCCGATTATGAAAAATTG
1 GTTGGAGTATCCCCGATTATGAAAAATTG
259229 AGAAACTTAA
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
50 1 0.01
51 109 0.99
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAATCGGA
Found at i:269788 original size:28 final size:28
Alignment explanation
Indices: 269754--269828 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
269744 AAAATAAAAT
** *
269754 CGGGGTTGGAGTATCCCCTTGGAAATAA
1 CGGGGTTGGAGTATCCCCGCGAAAATAA
269782 CGGGGTTGGAGTATCCCCGCGAAAATAA
1 CGGGGTTGGAGTATCCCCGCGAAAATAA
269810 CGGGGTTGGAGTATCCCCG
1 CGGGGTTGGAGTATCCCCG
269829 ATTGTGAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGCGAAAATAA
Found at i:269878 original size:79 final size:79
Alignment explanation
Indices: 269782--270064 Score: 449
Period size: 79 Copynumber: 3.6 Consensus size: 79
269772 TTGGAAATAA
*
269782 CGGGGTTGGAGTATCCCCGCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
269847 TTTAAGAATAAAGC
66 TTTAAGAATAAAGC
* * * * *
269861 CGGGGTTAGAGTATCCCCTCGAAAATAGCGTGGTTGGAGTATGCCCGATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
*
269926 TTTAGGAATAAAGC
66 TTTAAGAATAAAGC
*
269940 CGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
* *
270005 TTTAAAAATAAAAC
66 TTTAAGAATAAAGC
** *
270019 CGGGGTTGGAGTATCTTCTCGGAAATAACGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
270065 TCGAAAATAA
Statistics
Matches: 184, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 184 1.00
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
TTTAAGAATAAAGC
Found at i:270053 original size:28 final size:26
Alignment explanation
Indices: 270019--270117 Score: 128
Period size: 28 Copynumber: 3.6 Consensus size: 26
270009 AAAATAAAAC
270019 CGGGGTTGGAGTATCTTCTCGGAAATAA
1 CGGGGTTGGAGTATC--CTCGGAAATAA
*
270047 CGGGGTTGGAGTATCCCCTCGAAAATAA
1 CGGGGTTGGAGTAT--CCTCGGAAATAA
270075 CGGGGTTGGAGTATCCTC-GATAATTAA
1 CGGGGTTGGAGTATCCTCGGA-AA-TAA
270102 CGGGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
270118 CCGATTATGA
Statistics
Matches: 65, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
25 1 0.02
26 6 0.09
27 19 0.29
28 38 0.58
30 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.26
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCTCGGAAATAA
Found at i:270182 original size:51 final size:51
Alignment explanation
Indices: 270106--270287 Score: 274
Period size: 51 Copynumber: 3.6 Consensus size: 51
270096 AATTAACGGG
*
270106 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAATCGGA
* * *
270157 GTTGGAGTATCCCCGATTATAAAAAATTGGTGTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAATCGGA
* * **
270208 GTTGGAGTATCCCCAATTATGAAAAATTGGTGTTTCGAAAATAAAATTAGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAATCGGA
* *
270259 GTTGGAGTATCCCTGATTATGACAAATTG
1 GTTGGAGTATCCCCGATTATGAAAAATTG
270288 AGAAACTTAA
Statistics
Matches: 117, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 117 1.00
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAATCGGA
Found at i:273355 original size:23 final size:23
Alignment explanation
Indices: 273324--273367 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
273314 TAGACAATAG
273324 TTTTTAAAAAAT-AATTTTTTAT
1 TTTTTAAAAAATGAATTTTTTAT
*
273346 TTTTTAAAAAAATGAGTTTTTT
1 TTTTT-AAAAAATGAATTTTTT
273368 TGTTGTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 7 0.37
24 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (23 bp):
TTTTTAAAAAATGAATTTTTTAT
Found at i:273999 original size:13 final size:14
Alignment explanation
Indices: 273975--274004 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
273965 AAATATTAAT
273975 AAAAAT-ATTTTTA
1 AAAAATAATTTTTA
273988 AAAAATAATTTTTA
1 AAAAATAATTTTTA
274002 AAA
1 AAA
274005 TTTGTGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAAATAATTTTTA
Found at i:274481 original size:268 final size:268
Alignment explanation
Indices: 274004--274532 Score: 1031
Period size: 268 Copynumber: 2.0 Consensus size: 268
273994 AATTTTTAAA
274004 ATTTGTGAATAAAATCATAGAAACTCAAGATGTACTCAAGAATCAATTATGTTTGAGAAAAGCAT
1 ATTTGTGAATAAAATCATAGAAACTCAAGATGTACTCAAGAATCAATTATGTTTGAGAAAAGCAT
*
274069 TATCATCACATAATGTCTGTTTAAAATCAAAACTAATTAATTATGTACTATCTTCAAAACTTGAT
66 TATCATCACATAATGTCTGTTTAAAATCAAAACCAATTAATTATGTACTATCTTCAAAACTTGAT
274134 AAAAATAATTATAATTTCAGTATTTAAAAAAATTCTCATACAAGAATTTTGTGGAAAGCCTTTTG
131 AAAAATAATTATAATTTCAGTATTTAAAAAAATTCTCATACAAGAATTTTGTGGAAAGCCTTTTG
*
274199 TTTCAAAATAAAATGGGAATCTTTGAGGTTAGATAGTTTCTCCGGATTCTCCAATACATAGGCGA
196 TTTCAAAATAAAATGGGAATCTTTGAGGTTAGATAGATTCTCCGGATTCTCCAATACATAGGCGA
274264 ATAAAAAT
261 ATAAAAAT
*
274272 ATTTGTGAATAAAATCATAGAAACTCAAGATGTACTCAAGAATCAATTATGTTTGAGATAAGCAT
1 ATTTGTGAATAAAATCATAGAAACTCAAGATGTACTCAAGAATCAATTATGTTTGAGAAAAGCAT
274337 TATCATCACATAATGTCTGTTTAAAATCAAAACCAATTAATTATGTACTATCTTCAAAACTTGAT
66 TATCATCACATAATGTCTGTTTAAAATCAAAACCAATTAATTATGTACTATCTTCAAAACTTGAT
274402 AAAAATAATTATAATTTCAGTATTTAAAAAAATTCTCATACAAGAATTTTGTGGAAAGCCTTTTG
131 AAAAATAATTATAATTTCAGTATTTAAAAAAATTCTCATACAAGAATTTTGTGGAAAGCCTTTTG
274467 TTTCAAAATAAAATGGGAATCTTTGAGGTTAGATAGATTCTCCGGATTCTCCAATACATAGGCGA
196 TTTCAAAATAAAATGGGAATCTTTGAGGTTAGATAGATTCTCCGGATTCTCCAATACATAGGCGA
274532 A
261 A
274533 ATTTTTAAAA
Statistics
Matches: 258, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
268 258 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.34
Consensus pattern (268 bp):
ATTTGTGAATAAAATCATAGAAACTCAAGATGTACTCAAGAATCAATTATGTTTGAGAAAAGCAT
TATCATCACATAATGTCTGTTTAAAATCAAAACCAATTAATTATGTACTATCTTCAAAACTTGAT
AAAAATAATTATAATTTCAGTATTTAAAAAAATTCTCATACAAGAATTTTGTGGAAAGCCTTTTG
TTTCAAAATAAAATGGGAATCTTTGAGGTTAGATAGATTCTCCGGATTCTCCAATACATAGGCGA
ATAAAAAT
Found at i:275231 original size:5 final size:5
Alignment explanation
Indices: 275221--275345 Score: 53
Period size: 5 Copynumber: 23.4 Consensus size: 5
275211 ACCAAGTTTA
*
275221 CTTTT CTTTT C-TTT CTTTTT CTCATTT CTGTTT -TATTT -TTTC CTTTTT
1 CTTTT CTTTT CTTTT C-TTTT CT--TTT CT-TTT CT-TTT CTTTT C-TTTT
* **
275269 CTTTT CCTTT CTTTTT CTTTCT CTTTTT CCTTATT -TTTT -TCCT CATTTT
1 CTTTT CTTTT C-TTTT CTTT-T C-TTTT -CTT-TT CTTTT CTTTT C-TTTT
*
275318 CTTTT CTTTT CTTTT CTCTTG CTTTT CT
1 CTTTT CTTTT CTTTT CT-TTT CTTTT CT
275346 CTCTTTTTTT
Statistics
Matches: 94, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
4 10 0.11
5 46 0.49
6 27 0.29
7 11 0.12
ACGTcount: A:0.03, C:0.22, G:0.02, T:0.73
Consensus pattern (5 bp):
CTTTT
Found at i:275275 original size:12 final size:12
Alignment explanation
Indices: 275258--275333 Score: 63
Period size: 10 Copynumber: 6.4 Consensus size: 12
275248 CTGTTTTATT
275258 TTTTCCTTTTTC
1 TTTTCCTTTTTC
275270 TTTTCC--TTTC
1 TTTTCCTTTTTC
* *
275280 TTTTTCTTTCTC
1 TTTTCCTTTTTC
275292 TTTTTCCTTATTT-
1 -TTTTCCTT-TTTC
275305 TTTTCCTCATTTTC
1 TTTTCCT--TTTTC
275319 TTTT-C-TTTTC
1 TTTTCCTTTTTC
275329 TTTTC
1 TTTTC
275334 TCTTGCTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 17
0.71 0.05 0.23
Matches are distributed among these distances:
10 18 0.35
12 16 0.31
13 11 0.21
14 7 0.13
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTCCTTTTTC
Found at i:275290 original size:48 final size:48
Alignment explanation
Indices: 275221--275337 Score: 134
Period size: 48 Copynumber: 2.4 Consensus size: 48
275211 ACCAAGTTTA
*
275221 CTTTTCTTTTCTTTCTT-TTTCTCATTTCTGT-TTTA-TTTTTTCCT-TTTT
1 CTTTTCTTTTCTTT-TTCTTTCTC-TTT-T-TCCTTATTTTTTTCCTATTTT
*
275269 CTTTTCCTTTCTTTTTCTTTCTCTTTTTCCTTATTTTTTTCCTCATTTT
1 CTTTTCTTTTCTTTTTCTTTCTCTTTTTCCTTATTTTTTTCCT-ATTTT
275318 CTTTTCTTTTCTTTTCTCTT
1 CTTTTCTTTTCTTTT-TCTT
275338 GCTTTTCTCT
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
45 1 0.02
46 4 0.07
47 14 0.23
48 19 0.32
49 18 0.30
50 4 0.07
ACGTcount: A:0.03, C:0.22, G:0.01, T:0.74
Consensus pattern (48 bp):
CTTTTCTTTTCTTTTTCTTTCTCTTTTTCCTTATTTTTTTCCTATTTT
Found at i:275355 original size:49 final size:44
Alignment explanation
Indices: 275222--275355 Score: 130
Period size: 49 Copynumber: 2.9 Consensus size: 44
275212 CCAAGTTTAC
* *
275222 TTTTCTTTTCTTTCTTTTTC-TCATTTCTGT-TTTATTTTTTCCT
1 TTTTCTTTTCTTTCTTTTTCTTCTTTTCTCTCTTT-TTTTTTCCT
*
275265 TTTTCTTTTCCTTTCTTTTTCTTTCTCTTTTTC-CTTATTTTTTTCCT
1 TTTTCTTTT-CTTTCTTTTTC-TTCT-TTTCTCTCTT-TTTTTTTCCT
275312 CATTTTCTTTTCTTTTCTTTTCTCTTGCTTTTCTCTCTTTTTTT
1 --TTTTCTTTTC-TTTCTTTT-TCTT-CTTTTCTCTCTTTTTTT
275356 ATAATTTTTT
Statistics
Matches: 75, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
43 9 0.12
44 11 0.15
46 2 0.03
47 15 0.20
48 2 0.03
49 29 0.39
50 7 0.09
ACGTcount: A:0.03, C:0.22, G:0.01, T:0.74
Consensus pattern (44 bp):
TTTTCTTTTCTTTCTTTTTCTTCTTTTCTCTCTTTTTTTTTCCT
Found at i:278184 original size:116 final size:116
Alignment explanation
Indices: 278000--278427 Score: 427
Period size: 116 Copynumber: 3.7 Consensus size: 116
277990 ACTATGAGGA
* * * * * * *
278000 TCATTTTAGCAATATTCATGCATTTTAGGACTATATAGGTTATTTCACATAATCTAAAGTCATAT
1 TCATTTTAGCAATTTTCAT-CATTTAAGGACCATTTAGGTTATTTTACATAATCTAAGGTCATTT
*
278065 TAATAATTTTCATCATTTTAGGGCCATTTAAGTTATTTTATATAATCCATG-G
65 TAATAATTTTCATCATTTTAGGGCCATTTAAGTTATTTTATATAATCTA-GAG
* * * * * *
278117 TTATTTTAGTAATTTTTATCATTTAAGGACCATTTAGGTTATTTTATATAATTTAAGGTTATTTT
1 TCATTTTAGCAATTTTCATCATTTAAGGACCATTTAGGTTATTTTACATAATCTAAGGTCATTTT
**
278182 AATTAA-TTTCATCATTTTAAAGCCATTT-AGTTATTTTATATAATCTAGAG
66 AA-TAATTTTCATCATTTTAGGGCCATTTAAGTTATTTTATATAATCTAGAG
* * * * *
278232 TGATTTTAGCAATTTTCATCATTGAAAGG-CCATTTAAGTTTTTTTTACATAATCTAGGGTCATT
1 TCATTTTAGCAATTTTCATCATT-TAAGGACCATTT-AGGTTATTTTACATAATCTAAGGTCATT
* * ** * * * *
278296 TTAGTAATTTTTATTGTTTAAGGGCCAATTAGGTTATTTTACATAATCTAGAG
64 TTAATAATTTTCATCATTTTAGGGCCATTTAAGTTATTTTATATAATCTAGAG
* * * *
278349 TCATTTTAGTTAATTTT-ATCATTTAA-GAGCCATTTAAGTTATTTTACATAATCCATGGTCATT
1 TCATTTTAG-CAATTTTCATCATTTAAGGA-CCATTTAGGTTATTTTACATAATCTAAGGTCATT
***
278412 TTGGCAATTTTCATCA
64 TTAATAATTTTCATCA
278428 CCATAAGAAT
Statistics
Matches: 253, Mismatches: 49, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
114 1 0.00
115 49 0.19
116 139 0.55
117 58 0.23
118 6 0.02
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.47
Consensus pattern (116 bp):
TCATTTTAGCAATTTTCATCATTTAAGGACCATTTAGGTTATTTTACATAATCTAAGGTCATTTT
AATAATTTTCATCATTTTAGGGCCATTTAAGTTATTTTATATAATCTAGAG
Found at i:278333 original size:174 final size:174
Alignment explanation
Indices: 278069--278427 Score: 465
Period size: 174 Copynumber: 2.1 Consensus size: 174
278059 TCATATTAAT
** * * * *
278069 AATTTTCATCATTTTAGGGCCATTTAAGTTATTTTATATAATCCATGGTTATTTTAGTAATTTTT
1 AATTTTCATCATTGAAAGGCCATTTAAGTTATTTTACATAATCCAGGGTCATTTTAGTAATTTTT
* * * *
278134 ATCATTTAAGGACCATTTAGGTTATTTTATATAATTTA-AGGTTATTTTAATTAATTTCATCATT
66 ATCATTTAAGGACCAATTAGGTTATTTTACATAATCTAGA-GTCATTTTAATTAATTTCATCA-T
* * *
278198 TTAA-AGCCATTT-AGTTATTTTATATAATCTA-GAGTGATTTTAGC
129 TTAAGAGCCATTTAAGTTATTTTACATAATCCATG-GTCATTTTAGC
* *
278242 AATTTTCATCATTGAAAGGCCATTTAAGTTTTTTTTACATAATCTAGGGTCATTTTAGTAATTTT
1 AATTTTCATCATTGAAAGGCCATTTAAG-TTATTTTACATAATCCAGGGTCATTTTAGTAATTTT
** * * *
278307 TATTGTTTAAGGGCCAATTAGGTTATTTTACATAATCTAGAGTCATTTTAGTTAATTTTATCATT
65 TATCATTTAAGGACCAATTAGGTTATTTTACATAATCTAGAGTCATTTTAATTAATTTCATCATT
*
278372 TAAGAGCCATTTAAGTTATTTTACATAATCCATGGTCATTTTGGC
130 TAAGAGCCATTTAAGTTATTTTACATAATCCATGGTCATTTTAGC
278417 AATTTTCATCA
1 AATTTTCATCA
278428 CCATAAGAAT
Statistics
Matches: 160, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
173 30 0.19
174 91 0.57
175 38 0.24
176 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.48
Consensus pattern (174 bp):
AATTTTCATCATTGAAAGGCCATTTAAGTTATTTTACATAATCCAGGGTCATTTTAGTAATTTTT
ATCATTTAAGGACCAATTAGGTTATTTTACATAATCTAGAGTCATTTTAATTAATTTCATCATTT
AAGAGCCATTTAAGTTATTTTACATAATCCATGGTCATTTTAGC
Found at i:278410 original size:58 final size:56
Alignment explanation
Indices: 278038--278427 Score: 338
Period size: 58 Copynumber: 6.7 Consensus size: 56
278028 GACTATATAG
* * * * * *
278038 GTTATTTCACATAATCTAAAGTCATATTAATAATTTTCATCATTTTAGGGCCATTTAA
1 GTTATTTTACATAATCT-AGGTCATTTTAGTAATTTT-ATCATTTAAGAGCCATTTAA
* * * *
278096 GTTATTTTATATAATCCATGGTTATTTTAGTAATTTTTATCATTTAAG-GACCATTTAG
1 GTTATTTTACATAATCTA-GGTCATTTTAGTAA-TTTTATCATTTAAGAG-CCATTTAA
* * * * *
278154 GTTATTTTATATAATTTAAGGTTATTTTAATTAATTTCATCATTTTAA-AGCCATTT-A
1 GTTATTTTACATAATCT-AGGTCATTTT-AGTAATTTTATCA-TTTAAGAGCCATTTAA
* * * *
278211 GTTATTTTATATAATCTAGAGTGATTTTAGCAATTTTCATCATTGAA-AGGCCATTTAA
1 GTTATTTTACATAATCTAG-GTCATTTTAGTAATTTT-ATCATTTAAGA-GCCATTTAA
* ** * * *
278269 GTTTTTTTTACATAATCTAGGGTCATTTTAGTAATTTTTATTGTTTAAGGGCCAATTAG
1 G-TTATTTTACATAATCTA-GGTCATTTTAGTAA-TTTTATCATTTAAGAGCCATTTAA
278328 GTTATTTTACATAATCTAGAGTCATTTTAGTTAATTTTATCATTTAAGAGCCATTTAA
1 GTTATTTTACATAATCTAG-GTCATTTTAG-TAATTTTATCATTTAAGAGCCATTTAA
* * *
278386 GTTATTTTACATAATCCATGGTCATTTTGGCAATTTTCATCA
1 GTTATTTTACATAATCTA-GGTCATTTTAGTAATTTT-ATCA
278428 CCATAAGAAT
Statistics
Matches: 274, Mismatches: 39, Indels: 38
0.78 0.11 0.11
Matches are distributed among these distances:
56 13 0.05
57 43 0.16
58 154 0.56
59 59 0.22
60 5 0.02
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.47
Consensus pattern (56 bp):
GTTATTTTACATAATCTAGGTCATTTTAGTAATTTTATCATTTAAGAGCCATTTAA
Found at i:278622 original size:79 final size:78
Alignment explanation
Indices: 278505--278710 Score: 216
Period size: 79 Copynumber: 2.6 Consensus size: 78
278495 TGAGAGATCT
* * * * * * *
278505 AAGTCCTTAGGACCATGTTGGTATTTTCGTATCAAGACATGTACATTAGTACCTTTTTAGCAAGT
1 AAGTCCTTAAGAGCATGTTGGTATTTTCATATCGAGACATGTGCATTAG-ACCATTTCAGCAAGT
* *
278570 TT-ATTAAGAAATTC
65 TTCATCAA-AAATCC
* * *
278584 GAGTCCTTAAGAGCATGTTGATATTTTCATATCGAGACATGTGCATTAAGACCATTTCAGTAAGT
1 AAGTCCTTAAGAGCATGTTGGTATTTTCATATCGAGACATGTGCATT-AGACCATTTCAGCAAGT
*
278649 TTCGTCAAAAATCC
65 TTCATCAAAAATCC
* * * * *
278663 AAATCCTTACGAGCATATTGGCATCTTCATATCGAGACATGTGCATTA
1 AAGTCCTTAAGAGCATGTTGGTATTTTCATATCGAGACATGTGCATTA
278711 AGATTGTTTA
Statistics
Matches: 105, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
78 1 0.01
79 99 0.94
80 5 0.05
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (78 bp):
AAGTCCTTAAGAGCATGTTGGTATTTTCATATCGAGACATGTGCATTAGACCATTTCAGCAAGTT
TCATCAAAAATCC
Found at i:278846 original size:78 final size:78
Alignment explanation
Indices: 278731--278895 Score: 186
Period size: 78 Copynumber: 2.1 Consensus size: 78
278721 AGTGAGCTTC
* * * *
278731 ATGTTAAAACCGAGTCTCTAAGGTCATATTGGTATTTTCGTATCGATACATGTCCATTTGGGCCA
1 ATGTTAAAACCGAGTCTCTAAGGTCATATTAGCATTTTCGTATCGATACATGTCCATTAGAGCCA
*
278796 TTTAGGTAATGGT
66 ATTAGGTAATGGT
** * * * * * * * *
278809 ATGTTAAAATTGAGTTTCTAGGGTCATCTTAGCATTTTCTTGTCGATGCGTGTCCATTAGAGTCA
1 ATGTTAAAACCGAGTCTCTAAGGTCATATTAGCATTTTCGTATCGATACATGTCCATTAGAGCCA
*
278874 ATTAGGTAATGTT
66 ATTAGGTAATGGT
278887 ATGTTAAAA
1 ATGTTAAAA
278896 AACCGAGTGT
Statistics
Matches: 71, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (78 bp):
ATGTTAAAACCGAGTCTCTAAGGTCATATTAGCATTTTCGTATCGATACATGTCCATTAGAGCCA
ATTAGGTAATGGT
Found at i:281716 original size:21 final size:22
Alignment explanation
Indices: 281691--281740 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
281681 ATTTAGTATT
281691 CCCCTTAAAAAAAAT-TTTCTC
1 CCCCTTAAAAAAAATATTTCTC
*
281712 CCCCTT-AATAAAATATTTCTC
1 CCCCTTAAAAAAAATATTTCTC
*
281733 TCCCTTAA
1 CCCCTTAA
281741 CAAATTATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.28
21 17 0.68
22 1 0.04
ACGTcount: A:0.34, C:0.30, G:0.00, T:0.36
Consensus pattern (22 bp):
CCCCTTAAAAAAAATATTTCTC
Found at i:283647 original size:34 final size:35
Alignment explanation
Indices: 283609--283675 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
283599 CCTTACAACA
283609 CTATC-TTTC-AAGGCAAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCAAAGATAG-AACCTCTCTCT
*
283643 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCAAAGATAGAACCTCTC
283676 AATCACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.41
37 12 0.41
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCAAAGATAGAACCTCTCTCT
Found at i:284172 original size:13 final size:13
Alignment explanation
Indices: 284154--284179 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
284144 CTATTTATGA
284154 TGTATCGATACAC
1 TGTATCGATACAC
284167 TGTATCGATACAC
1 TGTATCGATACAC
284180 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:284250 original size:14 final size:14
Alignment explanation
Indices: 284227--284257 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
284217 GATTTTTAAC
284227 GATACATGAATAGT
1 GATACATGAATAGT
*
284241 GATACGTGAATAGT
1 GATACATGAATAGT
284255 GAT
1 GAT
284258 GAACAGTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (14 bp):
GATACATGAATAGT
Found at i:284264 original size:48 final size:45
Alignment explanation
Indices: 284193--284288 Score: 138
Period size: 48 Copynumber: 2.1 Consensus size: 45
284183 AATATGTATC
*
284193 GATACATGAATAGTGATGAACAGTGATTTTTAACGATACATGAATAGT
1 GATACATGAATAGTGATGAACAGTGA--TGTAACGATACATGAA-AGT
* *
284241 GATACGTGAATAGTGATGAACAGTGATGTATCGATACATGAAAGT
1 GATACATGAATAGTGATGAACAGTGATGTAACGATACATGAAAGT
284286 GAT
1 GAT
284289 GTATCGATAC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
45 6 0.13
46 14 0.31
48 25 0.56
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (45 bp):
GATACATGAATAGTGATGAACAGTGATGTAACGATACATGAAAGT
Found at i:284311 original size:22 final size:22
Alignment explanation
Indices: 284256--284311 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
284246 GTGAATAGTG
284256 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
284278 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
284299 ATGAACAGTGATG
1 ATGAACAGTGATG
284312 AATAGTGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:284318 original size:10 final size:10
Alignment explanation
Indices: 284299--284329 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
284289 GTATCGATAC
*
284299 ATGAACAGTG
1 ATGAATAGTG
284309 ATGAATAGTG
1 ATGAATAGTG
284319 ATGAATAGTG
1 ATGAATAGTG
284329 A
1 A
284330 AAAATGAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.29, T:0.26
Consensus pattern (10 bp):
ATGAATAGTG
Found at i:284418 original size:53 final size:53
Alignment explanation
Indices: 284354--284490 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
284344 CTACTTCCAA
284354 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
284407 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
284460 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
284491 TATGCAATTT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:284523 original size:20 final size:20
Alignment explanation
Indices: 284460--284530 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
284450 GCCAATGTCC
**
284460 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
284480 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
284500 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
284520 TGTATCGATAC
1 TGTATCGATAC
284531 TTTTTAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:284596 original size:21 final size:21
Alignment explanation
Indices: 284570--284610 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
284560 GTAAACCTTG
284570 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
284591 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
284611 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:289680 original size:21 final size:21
Alignment explanation
Indices: 289656--289696 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
289646 CTTCATCCGA
*
289656 GTCAACTTCTTCATCATCATG
1 GTCAACATCTTCATCATCATG
*
289677 GTCATCATCTTCATCATCAT
1 GTCAACATCTTCATCATCAT
289697 TAATGGTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.07, T:0.39
Consensus pattern (21 bp):
GTCAACATCTTCATCATCATG
Found at i:291369 original size:13 final size:13
Alignment explanation
Indices: 291351--291375 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
291341 TACAAGGAAC
291351 ATGTATCGATACA
1 ATGTATCGATACA
291364 ATGTATCGATAC
1 ATGTATCGATAC
291376 TAAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:292810 original size:20 final size:20
Alignment explanation
Indices: 292774--292811 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
292764 GTTTTAAATA
292774 AATTAATAAAATATTATATC
1 AATTAATAAAATATTATATC
*
292794 AATT-ATAATAATTTTATA
1 AATTAATAA-AATATTATA
292812 ATAAGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTAATAAAATATTATATC
Found at i:294749 original size:20 final size:20
Alignment explanation
Indices: 294699--294751 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
294689 AAATTTTTAG
* *
294699 AAATTTTTTTGAAAAAAATTC
1 AAATTTTTTT-ATAAAAATGC
*
294720 -CATTTATTTTATAAAAATGC
1 AAATTT-TTTTATAAAAATGC
294740 AAATTTTTTTAT
1 AAATTTTTTTAT
294752 CCTTCCCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.49
Consensus pattern (20 bp):
AAATTTTTTTATAAAAATGC
Found at i:301645 original size:16 final size:16
Alignment explanation
Indices: 301619--301694 Score: 66
Period size: 16 Copynumber: 4.7 Consensus size: 16
301609 CTCACTTAAA
301619 TTAAAATTAATCTCAAT
1 TTAAAA-TAATCTCAAT
301636 TTAAAATAATC-CAGAT
1 TTAAAATAATCTCA-AT
* *
301652 ATAAAAAAATCTGC-AT
1 TTAAAATAATCT-CAAT
* *
301668 TCAAAATAATCTAAAT
1 TTAAAATAATCTCAAT
*
301684 TTAAACTAATC
1 TTAAAATAATC
301695 GAAACTTGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
15 2 0.04
16 38 0.81
17 6 0.13
18 1 0.02
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (16 bp):
TTAAAATAATCTCAAT
Found at i:301804 original size:17 final size:16
Alignment explanation
Indices: 301752--301799 Score: 71
Period size: 17 Copynumber: 3.0 Consensus size: 16
301742 AAACTCAAAT
*
301752 TAATTTAAATTTATAA
1 TAATTTAAATTTAAAA
301768 TAAATTTAAATTTAAAA
1 T-AATTTAAATTTAAAA
301785 TAATTTAAA-TTAAAA
1 TAATTTAAATTTAAAA
301800 GATAACTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 6 0.20
16 9 0.30
17 15 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATTTAAATTTAAAA
Found at i:302381 original size:27 final size:27
Alignment explanation
Indices: 302318--302383 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
302308 ATATATAATA
* * * *
302318 ATTATATTTAAAATATTATATATTTAT
1 ATTATATTTAATAGATCATATATTCAT
*
302345 A-TAAATTTTAATAGATCATATATTCAT
1 ATTATA-TTTAATAGATCATATATTCAT
302372 ATTATATTTAAT
1 ATTATATTTAAT
302384 TCATTACTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
26 3 0.10
27 25 0.81
28 3 0.10
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (27 bp):
ATTATATTTAATAGATCATATATTCAT
Found at i:305517 original size:53 final size:54
Alignment explanation
Indices: 305441--305570 Score: 167
Period size: 53 Copynumber: 2.4 Consensus size: 54
305431 ACCTTATTCC
*
305441 ATTACAAATATACTATCACAAATTTTTGTC-CTATTTAAATTCTGTCACTATTTT
1 ATTACAAATATACTATCACAAATTTTTGTCTC-ATTTAAATTCCGTCACTATTTT
* * *
305495 ATTACAAATA-ACTATCATAAATTTTTGTCTCATTTAAATTCCGTCACTACTAT
1 ATTACAAATATACTATCACAAATTTTTGTCTCATTTAAATTCCGTCACTATTTT
* * *
305548 GTTGCAAA-ATTCTATCACAAATT
1 ATTACAAATATACTATCACAAATT
305571 GAAATTGTGT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
52 1 0.02
53 54 0.82
54 11 0.17
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (54 bp):
ATTACAAATATACTATCACAAATTTTTGTCTCATTTAAATTCCGTCACTATTTT
Found at i:307412 original size:20 final size:20
Alignment explanation
Indices: 307387--307438 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
307377 TCACAATTTA
307387 TATCGATACATTGTTCATTG
1 TATCGATACATTGTTCATTG
307407 TATCGATACATTGTTCATTG
1 TATCGATACATTGTTCATTG
307427 TATCGATACATT
1 TATCGATACATT
307439 TTGGGTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.44
Consensus pattern (20 bp):
TATCGATACATTGTTCATTG
Found at i:309949 original size:79 final size:79
Alignment explanation
Indices: 309859--310196 Score: 438
Period size: 79 Copynumber: 4.3 Consensus size: 79
309849 TTTCCGAAGC
*
309859 GATACTCCAACCCTAATTTTA-TTTCTAAAACACTAATTTTTCACAATCGGAGATACTCCAACCC
1 GATACTCCAACCCTGATTTTATTTTC-AAAACACTAATTTTTCACAATCGGAGATACTCCAACCC
309923 CGTTATTTTCGAGGG
65 CGTTATTTTCGAGGG
* * * * *
309938 AATACTCCAACCCGGGTTTTATTTTCAAAACACCAATTTTTCACAATCGGAGATACTCCAACCTC
1 GATACTCCAACCCTGATTTTATTTTCAAAACACTAATTTTTCACAATCGGAGATACTCCAACCCC
310003 GTTATTTTCGAGGG
66 GTTATTTTCGAGGG
*
310017 GATACTCCAA-CCTCGGTTTTATTTTCAAAACACTAATTTTTCACAATCAGG-GATACTCCAACC
1 GATACTCCAACCCT-GATTTTATTTTCAAAACACTAATTTTTCACAATC-GGAGATACTCCAACC
310080 CCGTTA-TTTCTGAGGG
64 CCGTTATTTTC-GAGGG
* * * * *
310096 GATACTCCAACCCCGATTTTATTTTCAAATCA-TCAATTTTTCACCATTGGGGATACTCCAACCC
1 GATACTCCAACCCTGATTTTATTTTCAAAACACT-AATTTTTCACAATCGGAGATACTCCAACCC
310160 CGTTA-TTTCTGAAGGG
65 CGTTATTTTC-G-AGGG
* *
310176 G-TACTCCGACCCTGTTTTTAT
1 GATACTCCAACCCTGATTTTAT
310197 CTCCAAAATA
Statistics
Matches: 233, Mismatches: 18, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
78 9 0.04
79 211 0.91
80 13 0.06
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (79 bp):
GATACTCCAACCCTGATTTTATTTTCAAAACACTAATTTTTCACAATCGGAGATACTCCAACCCC
GTTATTTTCGAGGG
Found at i:312167 original size:4 final size:4
Alignment explanation
Indices: 312158--312188 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
312148 TTTTGAGGTG
*
312158 TTTA TTTA TTTA TTTA TTCA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
312189 TGTTTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:321492 original size:21 final size:21
Alignment explanation
Indices: 321439--321495 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
321429 AACATGTCAT
*
321439 AAATGCATGAAGCATAGCTCA
1 AAATGCATGAATCATAGCTCA
321460 AAATGCATGAATCATAGCTCA
1 AAATGCATGAATCATAGCTCA
321481 AAATGCATGAATCAT
1 AAATGCATGAATCAT
321496 GGGCTGTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.23
Consensus pattern (21 bp):
AAATGCATGAATCATAGCTCA
Found at i:322412 original size:52 final size:52
Alignment explanation
Indices: 322334--322482 Score: 214
Period size: 52 Copynumber: 2.9 Consensus size: 52
322324 CGAAATATGA
322334 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
* * *
322386 AAATTTGCCTGCATGTATCGATACATTATAA-AATGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATT-TAATAGTGTATCGATACATCTAGGC
*
322438 AAATTTGCCTACATGTATCGATACA--TAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTTA-AT-AGTGTATCGATACA
322483 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
49 2 0.02
50 1 0.01
52 82 0.93
53 3 0.03
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGC
Found at i:322489 original size:13 final size:13
Alignment explanation
Indices: 322471--322495 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
322461 CATAGATCAG
322471 TGTATCGATACAA
1 TGTATCGATACAA
322484 TGTATCGATACA
1 TGTATCGATACA
322496 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:322573 original size:33 final size:33
Alignment explanation
Indices: 322536--322602 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
322526 AGTAGCTTAA
322536 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
322569 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
322602 A
1 A
322603 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:322576 original size:13 final size:13
Alignment explanation
Indices: 322558--322582 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
322548 CAAAAAAATA
322558 TGTATCGATACAT
1 TGTATCGATACAT
322571 TGTATCGATACA
1 TGTATCGATACA
322583 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:325048 original size:79 final size:79
Alignment explanation
Indices: 324953--325382 Score: 455
Period size: 79 Copynumber: 5.4 Consensus size: 79
324943 ATTCATGTTT
* * *
324953 TTATTTCCGAAGGGATACTCCAACCCCGGTTTTATTTTCAAAAAATCAATTTTTCACAATCGGAG
1 TTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTTCAAAACATCAATTTTTCACAATCGGAG
*
325018 ATACTCCAACCCTG
66 ATACTCCAACCCCG
* * ** * * *
325032 TTATTTTCGAAAGGATACTCCAATCTTGATTTTATTTCCAAAACACCAATTTTTCACAATC-AAG
1 TTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTTCAAAACATCAATTTTTCACAATCGGA-
*
325096 GATACTCAAACCCCG
65 GATACTCCAACCCCG
* * *
325111 TTATTTCCGAGGGGATACTCCAACCCC-AGTTTTA-TTTCTAAAACACCAATTTTTCACAATC-G
1 TTATTTTCGAAGGGATACTCCAACCCCGA-TTTTATTTTC-AAAACATCAATTTTTCACAATCGG
*
325173 AGGATACTCCAACCCTG
64 A-GATACTCCAACCCCG
* * * *
325190 TTATTTT-TAAGGAGATACTCCAACCTCGATTTTATTTCCAAAACGTCAA-TTTTCGACAATCGG
1 TTATTTTCGAAGG-GATACTCCAACCCCGATTTTATTTTCAAAACATCAATTTTTC-ACAATCGG
* *
325253 GGATATTCCAACCCCG
64 AGATACTCCAACCCCG
* ** * *
325269 TTA-TTTCTGAGGGGATACTCCAACTTCGATTTTATTTTCAAAACATCAATTTTTCACCATTTGG
1 TTATTTTC-GAAGGGATACTCCAACCCCGATTTTATTTTCAAAACATCAATTTTTCA-CAATCGG
325333 -GATACTCCAACCCCG
64 AGATACTCCAACCCCG
* *
325348 TTA-TTTCTAAGGGAGTACTCCAACCCCGTTTTTAT
1 TTATTTTCGAAGGGA-TACTCCAACCCCGATTTTAT
325383 CTCCAAAATA
Statistics
Matches: 293, Mismatches: 45, Indels: 26
0.80 0.12 0.07
Matches are distributed among these distances:
78 21 0.07
79 254 0.87
80 18 0.06
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (79 bp):
TTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTTCAAAACATCAATTTTTCACAATCGGAG
ATACTCCAACCCCG
Found at i:325208 original size:158 final size:155
Alignment explanation
Indices: 324953--325390 Score: 556
Period size: 158 Copynumber: 2.8 Consensus size: 155
324943 ATTCATGTTT
* *
324953 TTATTTCCGAAGGGATACTCCAACCCCGGTTTTATTTTCAAAAAATCAATTTTTCACAATCGGAG
1 TTATTTCCGAGGGGATACTCCAACCCC-GTTTTATTTTCAAAACATCAATTTTTCACAATCGG-G
* * * *
325018 ATACTCCAACCCTGTTATTTTCGAAAGGATACTCCAATCTTGATTTTATTTCCAAAACACCAATT
64 ATACTCCAACCCTGTTATTTT-TAAGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAA-T
325083 TTTC-ACAATCAAGGATACTCAAACCCCG
127 TTTCGACAATCAAGGATACTCAAACCCCG
*
325111 TTATTTCCGAGGGGATACTCCAACCCCAGTTTTA-TTTCTAAAACACCAATTTTTCACAATCGAG
1 TTATTTCCGAGGGGATACTCCAACCCC-GTTTTATTTTC-AAAACATCAATTTTTCACAATCG-G
**
325175 GATACTCCAACCCTGTTATTTTTAAGGAGATACTCCAACCTCGATTTTATTTCCAAAACGTCAAT
63 GATACTCCAACCCTGTTATTTTTAAGG-GATACTCCAACCTCGATTTTATTTCCAAAACACCAAT
** * *
325240 TTTCGACAATCGGGGATATTCCAACCCCG
127 TTTCGACAATCAAGGATACTCAAACCCCG
* ** * *
325269 TTATTTCTGAGGGGATACTCCAACTTCGATTTTATTTTCAAAACATCAATTTTTCACCATTTGGG
1 TTATTTCCGAGGGGATACTCCAACCCCG-TTTTATTTTCAAAACATCAATTTTTCA-CAATCGGG
* * * * *
325334 ATACTCCAACCCCGTTATTTCTAAGGGAGTACTCCAACCCCGTTTTTATCTCCAAAA
64 ATACTCCAACCCTGTTATTTTTAAGGGA-TACTCCAACCTCGATTTTATTTCCAAAA
325391 TATTAAATTT
Statistics
Matches: 247, Mismatches: 25, Indels: 16
0.86 0.09 0.06
Matches are distributed among these distances:
157 15 0.06
158 223 0.90
159 9 0.04
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (155 bp):
TTATTTCCGAGGGGATACTCCAACCCCGTTTTATTTTCAAAACATCAATTTTTCACAATCGGGAT
ACTCCAACCCTGTTATTTTTAAGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTC
GACAATCAAGGATACTCAAACCCCG
Found at i:327413 original size:18 final size:18
Alignment explanation
Indices: 327365--327415 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
327355 CAAATAAACG
* * *
327365 ATCATCATTTTCATCATC
1 ATCATCATTATCTTCATA
327383 ATCATCATTATCTTCATA
1 ATCATCATTATCTTCATA
327401 ATCAT-ATTCATCTTC
1 ATCATCATT-ATCTTC
327416 TTCATCACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 3 0.10
18 26 0.90
ACGTcount: A:0.29, C:0.25, G:0.00, T:0.45
Consensus pattern (18 bp):
ATCATCATTATCTTCATA
Found at i:332858 original size:21 final size:21
Alignment explanation
Indices: 332833--332884 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
332823 TAGCTACCAT
* *
332833 TTAAATGAAATGATGCATTTG
1 TTAAATGAAATGATGCACTTA
*
332854 TTAAATAAAATGATGCACTTA
1 TTAAATGAAATGATGCACTTA
*
332875 TTAGATGAAA
1 TTAAATGAAA
332885 GGATACATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (21 bp):
TTAAATGAAATGATGCACTTA
Found at i:337616 original size:21 final size:21
Alignment explanation
Indices: 337590--337663 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
337580 TAGCCACCAT
* * *
337590 TTGGATGAAAGAATGTAATTG
1 TTGGATCAAAGAATGCATTTG
*
337611 TTGGATCAAAAAATGCATTTG
1 TTGGATCAAAGAATGCATTTG
*
337632 TTGGATCAAATG-ATGCATTTA
1 TTGGATCAAA-GAATGCATTTG
*
337653 TTGGATGAAAG
1 TTGGATCAAAG
337664 GATATATCTT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
20 1 0.02
21 44 0.98
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.34
Consensus pattern (21 bp):
TTGGATCAAAGAATGCATTTG
Found at i:337727 original size:15 final size:16
Alignment explanation
Indices: 337709--337749 Score: 75
Period size: 15 Copynumber: 2.6 Consensus size: 16
337699 ATGAAAAGAC
337709 TTTTTAATTGAAATA-
1 TTTTTAATTGAAATAT
337724 TTTTTAATTGAAATAT
1 TTTTTAATTGAAATAT
337740 TTTTTAATTG
1 TTTTTAATTG
337750 TGTCTTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.60
16 10 0.40
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (16 bp):
TTTTTAATTGAAATAT
Found at i:339285 original size:33 final size:32
Alignment explanation
Indices: 339209--339288 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 32
339199 TAAAAAAATT
* *
339209 AAAAATAAAAATTATTTTATTTTATCTATACA
1 AAAAATAAAAATTATTTTATCTTACCTATACA
*
339241 AAAAATAAAAAATTATCTTTATCTTACCTATATA
1 AAAAAT-AAAAATTAT-TTTATCTTACCTATACA
*
339275 AGAAATAAAAATTA
1 AAAAATAAAAATTA
339289 ACTACAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
32 6 0.14
33 17 0.40
34 19 0.45
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (32 bp):
AAAAATAAAAATTATTTTATCTTACCTATACA
Found at i:340869 original size:22 final size:22
Alignment explanation
Indices: 340844--340894 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
340834 AACAAATATT
340844 TTTAATTTTAATAATATTTTAA
1 TTTAATTTTAATAATATTTTAA
* *
340866 TTTAATTTTGATAATGTTTTAA
1 TTTAATTTTAATAATATTTTAA
*
340888 TTGAATT
1 TTTAATT
340895 ATGATGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (22 bp):
TTTAATTTTAATAATATTTTAA
Found at i:340899 original size:22 final size:22
Alignment explanation
Indices: 340854--340899 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
340844 TTTAATTTTA
* *
340854 ATAATATTTTAATTTAATTTTG
1 ATAATATTTTAATTGAATTATG
*
340876 ATAATGTTTTAATTGAATTATG
1 ATAATATTTTAATTGAATTATG
340898 AT
1 AT
340900 GTTAACCCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (22 bp):
ATAATATTTTAATTGAATTATG
Found at i:342290 original size:50 final size:51
Alignment explanation
Indices: 342199--342300 Score: 154
Period size: 50 Copynumber: 2.0 Consensus size: 51
342189 TTTCACTTCT
*
342199 ATTATTATTTTATCTAACGCCTATCTAACGTTTCTATAAAATGTACCATTC
1 ATTATTATTTCATCTAACGCCTATCTAACGTTTCTATAAAATGTACCATTC
* *
342250 ATTATTATTTCATCTACAC-CC-ATCTGACGTTTCTATAAAATGTACTATTC
1 ATTATTATTTCATCTA-ACGCCTATCTAACGTTTCTATAAAATGTACCATTC
342300 A
1 A
342301 AAAATTGATT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
50 28 0.60
51 17 0.36
52 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (51 bp):
ATTATTATTTCATCTAACGCCTATCTAACGTTTCTATAAAATGTACCATTC
Found at i:342496 original size:15 final size:17
Alignment explanation
Indices: 342478--342514 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
342468 TAGATATATT
*
342478 TTAATA-TAT-TTTTTA
1 TTAATATTATATTTATA
342493 TTAATATTATATTTATA
1 TTAATATTATATTTATA
342510 TTAAT
1 TTAAT
342515 TTTTACATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 3 0.16
17 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTAATATTATATTTATA
Found at i:342694 original size:153 final size:153
Alignment explanation
Indices: 342405--342695 Score: 338
Period size: 154 Copynumber: 1.9 Consensus size: 153
342395 TATGTATGTA
* * *
342405 TTATTTTTTATATATTTAAAATATTATAAATTTATATGAATTATTAGATATTAATTATTTATTTA
1 TTATTTTTTATATATTTAAAATATTATAAATTTATATAAATTATTAGATACTAATAATTTATTTA
* * * *
342470 GATATATTTTAATATATTTTTTATTAATATTATATTTATATTAATTTTTACATTATGTTTTAATT
66 GATAAATTTTAATATATTTTATATTAATACTATATTTATATT-ATTTTTACATTATATTTTAATT
342535 ATTTTTTATTTATGATATTGAATT
130 ATTTTTTATTTATGATATTGAATT
* * * * *
342559 TTATTTTTT-TATCTTTAAAGTATTATAAA-TTATATAAATTTTTATATACTGATAATTTATTTT
1 TTATTTTTTATATATTTAAAATATTATAAATTTATATAAATTATTAGATACTAATAATTTA-TTT
** * * * *
342622 ATTTAAATTTTAATATGTTATTATATTCATACTATATGTTAT-TT-TTTTATCGCATTGTATTTT
65 AGATAAATTTTAATATATT-TTATATTAATACTATAT-TTATATTATTTT-T-ACATTATATTTT
342685 AATTATTTTTT
126 AATTATTTTTT
342696 CATATTGTGT
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
152 28 0.25
153 37 0.32
154 45 0.39
155 4 0.04
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (153 bp):
TTATTTTTTATATATTTAAAATATTATAAATTTATATAAATTATTAGATACTAATAATTTATTTA
GATAAATTTTAATATATTTTATATTAATACTATATTTATATTATTTTTACATTATATTTTAATTA
TTTTTTATTTATGATATTGAATT
Found at i:342878 original size:25 final size:26
Alignment explanation
Indices: 342837--342887 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
342827 ATTTAATATG
* *
342837 ATTTAACTTAAATTTTATAATTATTA
1 ATTTAACTTAAAATTTATAAATATTA
342863 ATTTAA-TTAAAATTTATAAATATTA
1 ATTTAACTTAAAATTTATAAATATTA
342888 GAAATTTTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTTAACTTAAAATTTATAAATATTA
Found at i:345380 original size:20 final size:17
Alignment explanation
Indices: 345355--345393 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 17
345345 TGGTGTTACA
345355 AATTAATCAAATATTAAATC
1 AATTAAT-AAA-ATT-AATC
345375 AATTAATAAAATTAATC
1 AATTAATAAAATTAATC
345392 AA
1 AA
345394 AAGTATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 3 0.16
19 3 0.16
20 7 0.37
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTAATAAAATTAATC
Found at i:353427 original size:19 final size:21
Alignment explanation
Indices: 353388--353428 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
353378 AATAACAGTT
*
353388 AAAATATTTATTTTATAATTA
1 AAAATATTTAGTTTATAATTA
353409 AAAATA-TTAGTTT-TAATTA
1 AAAATATTTAGTTTATAATTA
353428 A
1 A
353429 TATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 6 0.32
21 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AAAATATTTAGTTTATAATTA
Found at i:354353 original size:20 final size:20
Alignment explanation
Indices: 354325--354441 Score: 139
Period size: 20 Copynumber: 5.8 Consensus size: 20
354315 AAGTACCCAG
354325 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* * *
354345 ATATATCGATACA-TGTACGA
1 ATGTATCGATACATTCTTC-A
354365 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* * *
354385 ATATATCGATACA-TGTACGA
1 ATGTATCGATACATTCTTC-A
354405 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
*
354425 ATGTATTGATACATTCT
1 ATGTATCGATACATTCT
354442 GTCTTTTTAC
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
19 6 0.08
20 68 0.85
21 6 0.08
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:354380 original size:40 final size:40
Alignment explanation
Indices: 354325--354438 Score: 210
Period size: 40 Copynumber: 2.9 Consensus size: 40
354315 AAGTACCCAG
354325 ATGTATCGATACATTCTTCAATATATCGATACATGTACGA
1 ATGTATCGATACATTCTTCAATATATCGATACATGTACGA
354365 ATGTATCGATACATTCTTCAATATATCGATACATGTACGA
1 ATGTATCGATACATTCTTCAATATATCGATACATGTACGA
* *
354405 ATGTATCGATACATTCTTCAATGTATTGATACAT
1 ATGTATCGATACATTCTTCAATATATCGATACAT
354439 TCTGTCTTTT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (40 bp):
ATGTATCGATACATTCTTCAATATATCGATACATGTACGA
Found at i:359117 original size:22 final size:20
Alignment explanation
Indices: 359069--359118 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
359059 TAACATAACC
*
359069 ATAAA-TAATTTTTTATATT
1 ATAAATTAATTTTTTAAATT
359088 A-AATATTAATATTTTTAAATAT
1 ATAA-ATTAAT-TTTTTAAAT-T
359110 ATAAATTAA
1 ATAAATTAA
359119 CAAATAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 2 0.08
19 2 0.08
20 4 0.16
21 8 0.32
22 7 0.28
23 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAAATTAATTTTTTAAATT
Found at i:359726 original size:29 final size:30
Alignment explanation
Indices: 359663--359723 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
359653 TTAAAATTTA
*
359663 TATAA-AT-ATAAAATATTTTAAATATAAT
1 TATAATATGATAAAATATTATAAATATAAT
359691 TATAATATGATAAAATA-TATAAATATAA-
1 TATAATATGATAAAATATTATAAATATAAT
359719 TATAA
1 TATAA
359724 ATACTTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 10 0.33
29 12 0.40
30 8 0.27
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
TATAATATGATAAAATATTATAAATATAAT
Found at i:360097 original size:17 final size:17
Alignment explanation
Indices: 360043--360097 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 17
360033 TTAAATATTT
*
360043 TAAAATTTAT-ATAATA
1 TAAAATTTATAAAAATA
*
360059 TAAAATATTA-ATAAAT-
1 TAAAAT-TTATAAAAATA
360075 TAAAATTTATAAAAATA
1 TAAAATTTATAAAAATA
360092 TAAAAT
1 TAAAAT
360098 ATTTATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 3 0.09
16 17 0.53
17 12 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATTTATAAAAATA
Found at i:360593 original size:20 final size:20
Alignment explanation
Indices: 360568--360605 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
360558 AATAAAATAA
*
360568 ATATTTTTTAATTATTTATT
1 ATATTTATTAATTATTTATT
*
360588 ATATTTATTATTTATTTA
1 ATATTTATTAATTATTTA
360606 ATATTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATATTTATTAATTATTTATT
Found at i:360621 original size:18 final size:17
Alignment explanation
Indices: 360599--360648 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
360589 TATTTATTAT
360599 TTATTTAATATTAAAAA
1 TTATTTAATATTAAAAA
*
360616 TATATTTAATATTTAAAA
1 T-TATTTAATATTAAAAA
360634 TTATTTTAAT-TTAAA
1 TTA-TTTAATATTAAA
360649 TCGATTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 7 0.24
18 22 0.76
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATTTAATATTAAAAA
Found at i:361215 original size:17 final size:16
Alignment explanation
Indices: 361193--361237 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
361183 TATTTATGTA
*
361193 TAATTTATAATTTAATT
1 TAATTTATAATAT-ATT
*
361210 TAATTTAAAATATATT
1 TAATTTATAATATATT
361226 TAA-TTATAATAT
1 TAATTTATAATAT
361238 TTATTTGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 8 0.32
16 6 0.24
17 11 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATTTATAATATATT
Found at i:363069 original size:25 final size:27
Alignment explanation
Indices: 363037--363099 Score: 78
Period size: 25 Copynumber: 2.4 Consensus size: 27
363027 TTATATACAA
*
363037 ATTATATTAAATTATT-ATAAG-TTTT
1 ATTATATTAAATTATTAATAAGAATTT
* *
363062 ATTATATTTAA-TATTAATGAGAATTT
1 ATTATATTAAATTATTAATAAGAATTT
363088 ATTATATTAAAT
1 ATTATATTAAAT
363100 AATTTTTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 4 0.13
25 14 0.45
26 13 0.42
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (27 bp):
ATTATATTAAATTATTAATAAGAATTT
Found at i:366183 original size:12 final size:11
Alignment explanation
Indices: 366148--366174 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
366138 TTTAAATTTT
366148 AAAAAATGATA
1 AAAAAATGATA
366159 AAAAAATGATA
1 AAAAAATGATA
366170 AAAAA
1 AAAAA
366175 TATGGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (11 bp):
AAAAAATGATA
Found at i:368546 original size:27 final size:27
Alignment explanation
Indices: 368510--368581 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
368500 AAAGTCACTC
* *
368510 TTTGTATTTATCAAAAATAGTAG-TTCT
1 TTTGTGTTTATCAAAAATAAT-GCTTCT
368537 TTTGTGTTTATCAAAAATAATGCTTCT
1 TTTGTGTTTATCAAAAATAATGCTTCT
*
368564 TTTGTGTTTGTCAAAAAT
1 TTTGTGTTTATCAAAAAT
368582 GGTAACTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
26 1 0.02
27 40 0.98
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.49
Consensus pattern (27 bp):
TTTGTGTTTATCAAAAATAATGCTTCT
Found at i:371155 original size:21 final size:21
Alignment explanation
Indices: 371131--371172 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
371121 CAGACAAGTA
** *
371131 ATACTCCGCAACAGGTGGAGT
1 ATACTCCAAAACAGGTAGAGT
371152 ATACTCCAAAACAGGTAGAGT
1 ATACTCCAAAACAGGTAGAGT
371173 TTCAACAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (21 bp):
ATACTCCAAAACAGGTAGAGT
Found at i:373079 original size:27 final size:28
Alignment explanation
Indices: 373049--373127 Score: 87
Period size: 27 Copynumber: 2.9 Consensus size: 28
373039 CAAAAGCCAC
373049 CCTTTGTGTTTGTAAAAAATGA-TGGTT
1 CCTTTGTGTTTGTAAAAAATGAGTGGTT
373076 CCTTTGTGTTTG-ACAAAAAT-AGTGGTT
1 CCTTTGTGTTTGTA-AAAAATGAGTGGTT
* *
373103 -CTTATGTGTTTATCAAAAATG-GTGG
1 CCTT-TGTGTTTGTAAAAAATGAGTGG
373128 CTTGTTGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
26 5 0.11
27 40 0.89
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.42
Consensus pattern (28 bp):
CCTTTGTGTTTGTAAAAAATGAGTGGTT
Found at i:373615 original size:23 final size:21
Alignment explanation
Indices: 373572--373615 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
373562 CTGTGTAGCC
**
373572 AAAAAAATAACTTTATTTGAG
1 AAAAAAATAACTTTAAATGAG
373593 AAAAAAATTAAGCTTTAAATGAG
1 AAAAAAA-TAA-CTTTAAATGAG
373616 TTTTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 3 0.16
23 9 0.47
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.30
Consensus pattern (21 bp):
AAAAAAATAACTTTAAATGAG
Found at i:373931 original size:15 final size:15
Alignment explanation
Indices: 373911--373943 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
373901 TAATCAATTT
373911 TTTTGTTAAATTTAA
1 TTTTGTTAAATTTAA
*
373926 TTTTGTTTAATTTAA
1 TTTTGTTAAATTTAA
373941 TTT
1 TTT
373944 AAATAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (15 bp):
TTTTGTTAAATTTAA
Found at i:386049 original size:22 final size:20
Alignment explanation
Indices: 386008--386052 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
385998 ATTTTACTAC
386008 AAATTATTTTGTTATAAAAG
1 AAATTATTTTGTTATAAAAG
* *
386028 AAATTGATTTTTTCTATTAAAG
1 AAATT-ATTTTGT-TATAAAAG
386050 AAA
1 AAA
386053 GAATAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 6 0.29
22 10 0.48
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (20 bp):
AAATTATTTTGTTATAAAAG
Found at i:386111 original size:2 final size:2
Alignment explanation
Indices: 386106--386134 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
386096 TTACCTCATC
386106 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
386135 TTATGAACGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:386310 original size:39 final size:37
Alignment explanation
Indices: 386256--386332 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 37
386246 AAATTATGAT
* * *
386256 AAATACTTGTTATAAGTATATTTGTCCATATATTTAAAA
1 AAATACTTATTATAAG-ATACTTATCCA-ATATTTAAAA
*
386295 AAATACTTATTATAAGATACTTATCTAATATTTAAAA
1 AAATACTTATTATAAGATACTTATCCAATATTTAAAA
386332 A
1 A
386333 TTATAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 11 0.32
38 8 0.24
39 15 0.44
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (37 bp):
AAATACTTATTATAAGATACTTATCCAATATTTAAAA
Found at i:387292 original size:22 final size:22
Alignment explanation
Indices: 387264--387308 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
387254 GGGCTAAATT
387264 AGTGCCACATGTTGTCTCTATC
1 AGTGCCACATGTTGTCTCTATC
387286 AGTGCCACATGTTGTCTCTATC
1 AGTGCCACATGTTGTCTCTATC
387308 A
1 A
387309 CTAACAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.36
Consensus pattern (22 bp):
AGTGCCACATGTTGTCTCTATC
Found at i:390292 original size:21 final size:21
Alignment explanation
Indices: 390258--390316 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
390248 ATGACTAGGG
* *
390258 ATAAGGTATTGATACATTAA-
1 ATAAGATATTGATACATGAAT
*
390278 ACTAAGATATAGATACATGAAT
1 A-TAAGATATTGATACATGAAT
390300 ATAAGATATTGATACAT
1 ATAAGATATTGATACAT
390317 AAGGCATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.32
Consensus pattern (21 bp):
ATAAGATATTGATACATGAAT
Found at i:394376 original size:2 final size:2
Alignment explanation
Indices: 394369--394393 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
394359 ATTTAATTTG
394369 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
394394 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:396161 original size:14 final size:15
Alignment explanation
Indices: 396142--396174 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
396132 TTATGTCGTA
396142 TAAATA-TAATAACT
1 TAAATATTAATAACT
*
396156 TAAATATTATTAACT
1 TAAATATTAATAACT
396171 TAAA
1 TAAA
396175 GGAGTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAATATTAATAACT
Done.