Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 182 of 187
Found at i:54673771 original size:29 final size:29
Alignment explanation
Indices: 54673738--54673834 Score: 110
Period size: 29 Copynumber: 3.4 Consensus size: 29
54673728 ACTTTTTTAA
54673738 TTTTTTAAATTTTAAAATATTTAAAATAC
1 TTTTTTAAATTTTAAAATATTTAAAATAC
*
54673767 TTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAAATTTTAAAATA--TTTAAAATAC
* **
54673798 TTTTTT-ATTTTTTTAAT-TTTAAAATA-
1 TTTTTTAAATTTTAAAATATTTAAAATAC
*
54673824 TTTTTAAAATT
1 TTTTTTAAATT
54673835 ATTTTTAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
26 5 0.08
27 12 0.20
29 18 0.31
30 8 0.14
31 16 0.27
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTTTAAATTTTAAAATATTTAAAATAC
Found at i:54673792 original size:11 final size:11
Alignment explanation
Indices: 54673776--54673843 Score: 51
Period size: 11 Copynumber: 6.6 Consensus size: 11
54673766 CTTTTTTTAA
54673776 TTTTAAAATAT
1 TTTTAAAATAT
54673787 TTTTAAAATACT
1 TTTTAAAATA-T
54673799 TTTT----TAT
1 TTTTAAAATAT
**
54673806 TTTT-TTA-AT
1 TTTTAAAATAT
54673815 -TTTAAAATAT
1 TTTTAAAATAT
54673825 TTTTAAAATTAT
1 TTTTAAAA-TAT
54673837 TTTTAAA
1 TTTTAAA
54673844 TTTTAAATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
7 5 0.11
8 5 0.11
9 3 0.06
10 2 0.04
11 17 0.36
12 15 0.32
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:54673839 original size:12 final size:11
Alignment explanation
Indices: 54673814--54673843 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
54673804 ATTTTTTTAA
54673814 TTTTAAAATAT
1 TTTTAAAATAT
54673825 TTTTAAAATTAT
1 TTTTAAAA-TAT
54673837 TTTTAAA
1 TTTTAAA
54673844 TTTTAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:54673840 original size:37 final size:37
Alignment explanation
Indices: 54673695--54673857 Score: 157
Period size: 38 Copynumber: 4.5 Consensus size: 37
54673685 AATAAATATA
* *
54673695 TTTA-TTTTTTAATTTTAAAATATTTTTTACATTACTTT
1 TTTATTTTTTTAATTTTAAAATA-TTTTTAAAATAC-TT
*
54673733 TTTAATTTTTTAAATTTTAAAATA--TTTAAAATAC--
1 TTT-ATTTTTTTAATTTTAAAATATTTTTAAAATACTT
54673767 ----TTTTTTTAATTTTAAAATATTTTTAAAATACTTT
1 TTTATTTTTTTAATTTTAAAATATTTTTAAAATAC-TT
54673801 TTTATTTTTTTAATTTTAAAATATTTTTAAAATTA-TT
1 TTTATTTTTTTAATTTTAAAATATTTTTAAAA-TACTT
** *
54673838 TTTAAATTTTAAATTTTAAA
1 TTTATTTTTTTAATTTTAAA
54673858 TAAAATGGGC
Statistics
Matches: 106, Mismatches: 7, Indels: 25
0.77 0.05 0.18
Matches are distributed among these distances:
29 18 0.17
31 10 0.09
37 27 0.25
38 31 0.29
39 3 0.03
40 17 0.16
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (37 bp):
TTTATTTTTTTAATTTTAAAATATTTTTAAAATACTT
Found at i:54673840 original size:68 final size:68
Alignment explanation
Indices: 54673696--54673850 Score: 217
Period size: 68 Copynumber: 2.3 Consensus size: 68
54673686 ATAAATATAT
* *
54673696 TTATTTTTTAATTTTAAAATATTTTTTACATTACTTTTTTAATTTTTTAAATTTTAAAATATTTA
1 TTATTTTTTAATTTTAAAATATTTTTTAAAATACTTTTTTAATTTTTTAAATTTTAAAATATTTA
54673761 AAA
66 AAA
*
54673764 -TACTTTTTTTAATTTTAAAATA-TTTTTAAAATACTTTTTT-ATTTTTTTAATTTTAAAATATT
1 TTA--TTTTTTAATTTTAAAATATTTTTTAAAATACTTTTTTAATTTTTTAAATTTTAAAATA--
54673826 TTTAAAA
62 TTTAAAA
*
54673833 TTATTTTTAAATTTTAAA
1 TTATTTTTTAATTTTAAA
54673851 TTTTAAATAA
Statistics
Matches: 78, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
67 21 0.27
68 30 0.38
69 25 0.32
70 2 0.03
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (68 bp):
TTATTTTTTAATTTTAAAATATTTTTTAAAATACTTTTTTAATTTTTTAAATTTTAAAATATTTA
AAA
Found at i:54677140 original size:31 final size:31
Alignment explanation
Indices: 54677061--54677137 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
54677051 ATCCCATAAT
* *
54677061 TTAAATTAAAACTTTTGAATAATTTAGTAAC
1 TTAAATTAAAACTTTTAAAAAATTTAGTAAC
* *
54677092 TTAAGTAAAAACTTTTAAAAAATTTAGTAAC
1 TTAAATTAAAACTTTTAAAAAATTTAGTAAC
*
54677123 -TAAATTATAACTTTT
1 TTAAATTAAAACTTTT
54677138 TAATTAAGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 12 0.31
31 27 0.69
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (31 bp):
TTAAATTAAAACTTTTAAAAAATTTAGTAAC
Found at i:54678167 original size:31 final size:29
Alignment explanation
Indices: 54678129--54678205 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
54678119 CTAACGGCTC
* *
54678129 AGTGACTAAAATGTTACAACATGATAACATA
1 AGTGACTAAAATGTAAC-ACATCA-AACATA
* **
54678160 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACATCAAACATA
54678189 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
54678206 TTGAGTCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 3 0.08
31 15 0.38
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.25
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACATCAAACATA
Found at i:54685337 original size:13 final size:13
Alignment explanation
Indices: 54685319--54685344 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54685309 TTGTGGATGC
54685319 CACTCCCAATAAT
1 CACTCCCAATAAT
54685332 CACTCCCAATAAT
1 CACTCCCAATAAT
54685345 GTTATATTCA
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:0.38, G:0.00, T:0.23
Consensus pattern (13 bp):
CACTCCCAATAAT
Found at i:54687229 original size:17 final size:17
Alignment explanation
Indices: 54687203--54687236 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54687193 CAAAGGTAAA
54687203 AAAAGAAAAAAAAAAGG
1 AAAAGAAAAAAAAAAGG
* *
54687220 AAAAGGAAAAAGAAAGG
1 AAAAGAAAAAAAAAAGG
54687237 GTTGTTTTTT
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAAAAAGG
Found at i:54689768 original size:3 final size:3
Alignment explanation
Indices: 54689760--54689787 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54689750 AACTGATTCA
54689760 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
54689788 GACTCAGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:54697736 original size:15 final size:15
Alignment explanation
Indices: 54697702--54697735 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
54697692 TTTGCTGAAA
*
54697702 TTTTTGGTGTTTCTT
1 TTTTTGGTGTATCTT
54697717 TTTTTGGT-TATCTT
1 TTTTTGGTGTATCTT
54697731 TTTTT
1 TTTTT
54697736 TTTCTTTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.03, C:0.06, G:0.15, T:0.76
Consensus pattern (15 bp):
TTTTTGGTGTATCTT
Found at i:54698035 original size:2 final size:2
Alignment explanation
Indices: 54698028--54698112 Score: 152
Period size: 2 Copynumber: 42.5 Consensus size: 2
54698018 CCTTTTGTAA
* *
54698028 TG TG TG TG TG TG TG TG TG TA TG TG TG TT TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
54698070 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
54698112 T
1 T
54698113 TTTATTCATA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.01, C:0.00, G:0.47, T:0.52
Consensus pattern (2 bp):
TG
Found at i:54703391 original size:23 final size:21
Alignment explanation
Indices: 54703357--54703408 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 21
54703347 TAATAACTTA
54703357 GAATTTTTTTAT-ATTCTTTTT
1 GAATTTTTTTATAATT-TTTTT
54703378 GAATTATTATTTATAATTTTTTT
1 GAATT-TT-TTTATAATTTTTTT
54703401 GAATTTTT
1 GAATTTTT
54703409 AGAATCAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 6 0.21
22 4 0.14
23 15 0.54
24 3 0.11
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (21 bp):
GAATTTTTTTATAATTTTTTT
Found at i:54704882 original size:2 final size:2
Alignment explanation
Indices: 54704875--54704910 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
54704865 CTACCCTTAC
54704875 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54704911 TCTTTCTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54713936 original size:41 final size:41
Alignment explanation
Indices: 54713777--54713928 Score: 277
Period size: 41 Copynumber: 3.7 Consensus size: 41
54713767 TTAAAGTCTA
*
54713777 ATTCAGTTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
54713818 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
54713859 ATTCAGTTCACCAGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
54713900 ATTCAATTCACCGGCACTTAGCCTGCTAG
1 ATTCAGTTCACCGGCACTTAGCCTGCTAG
54713929 ACATATAGTC
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 107 1.00
ACGTcount: A:0.21, C:0.29, G:0.20, T:0.30
Consensus pattern (41 bp):
ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:54713951 original size:41 final size:41
Alignment explanation
Indices: 54713781--54713951 Score: 245
Period size: 41 Copynumber: 4.2 Consensus size: 41
54713771 AGTCTAATTC
* *
54713781 AGTTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTC
1 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTA
*
54713822 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTC
1 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTA
*
54713863 AGTTCACCAGCACTTAGCCTGCTAGGCTTATAGCCTGATTCA
1 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT-A
* * * *
54713905 A-TTCACCGGCACTTAGCCTGCTAGACATATAGTCTGAATA
1 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTA
*
54713945 ATTTCAC
1 AGTTCAC
54713952 TGACAATAAA
Statistics
Matches: 120, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
40 2 0.02
41 117 0.98
42 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.30
Consensus pattern (41 bp):
AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTA
Found at i:54714758 original size:2 final size:2
Alignment explanation
Indices: 54714751--54714777 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
54714741 TCGATCTAGC
54714751 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
54714778 ATTTCATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54715802 original size:13 final size:13
Alignment explanation
Indices: 54715784--54715808 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54715774 ACCAACGATA
54715784 AAATTTTCACACG
1 AAATTTTCACACG
54715797 AAATTTTCACAC
1 AAATTTTCACAC
54715809 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:54721384 original size:24 final size:24
Alignment explanation
Indices: 54721357--54721431 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
54721347 ATGGCAAATT
54721357 GTGAAAAGTAGGTATGGTGTTTCA
1 GTGAAAAGTAGGTATGGTGTTTCA
* **
54721381 GTGAAGAA-AACCATACTGG-G-TT--
1 GTGAA-AAGTA-GGTA-TGGTGTTTCA
54721403 GTGAAAAGTAGGTATGGTGTTTCA
1 GTGAAAAGTAGGTATGGTGTTTCA
54721427 GTGAA
1 GTGAA
54721432 GAAAACCATA
Statistics
Matches: 37, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
20 3 0.08
21 5 0.14
22 8 0.22
24 13 0.35
25 5 0.14
26 3 0.08
ACGTcount: A:0.32, C:0.07, G:0.32, T:0.29
Consensus pattern (24 bp):
GTGAAAAGTAGGTATGGTGTTTCA
Found at i:54721408 original size:46 final size:46
Alignment explanation
Indices: 54721353--54721491 Score: 242
Period size: 46 Copynumber: 3.0 Consensus size: 46
54721343 ATCCATGGCA
54721353 AATTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTG
1 AATTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTG
**
54721399 GGTTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTG
1 AATTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTG
* *
54721445 AATTGTGAAAAGTAGGTATGGTATTTCAGTGAAGGAAACCATACTG
1 AATTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTG
54721491 A
1 A
54721492 GTTATAGCAT
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.28
Consensus pattern (46 bp):
AATTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTG
Found at i:54721817 original size:2 final size:2
Alignment explanation
Indices: 54721810--54721852 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
54721800 TAGATTGACG
54721810 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54721852 T
1 T
54721853 GTTTGGAGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54724931 original size:20 final size:21
Alignment explanation
Indices: 54724901--54724942 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
54724891 TTATACTATA
54724901 TCAGTAATTTT-ATCTTGAATT
1 TCAGTAATTTTAAT-TTGAATT
54724922 TCAG-AATTTTAATTTGAATT
1 TCAGTAATTTTAATTTGAATT
54724942 T
1 T
54724943 TATTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (21 bp):
TCAGTAATTTTAATTTGAATT
Found at i:54727690 original size:22 final size:22
Alignment explanation
Indices: 54727663--54727711 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
54727653 GAGTTAACTC
54727663 TTTTTC-TTTCTGCTCG-TTCTAT
1 TTTTTCGTTT-TGCTCGTTTC-AT
*
54727685 TTTTTCGTTTTGCTTGTTTCAT
1 TTTTTCGTTTTGCTCGTTTCAT
54727707 TTTTT
1 TTTTT
54727712 GGTGCTAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.04, C:0.16, G:0.10, T:0.69
Consensus pattern (22 bp):
TTTTTCGTTTTGCTCGTTTCAT
Found at i:54730335 original size:13 final size:13
Alignment explanation
Indices: 54730317--54730341 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54730307 TTTATTAGTG
54730317 AAAGAGTACATAT
1 AAAGAGTACATAT
54730330 AAAGAGTACATA
1 AAAGAGTACATA
54730342 CAAATTAGTT
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:0.56, C:0.08, G:0.16, T:0.20
Consensus pattern (13 bp):
AAAGAGTACATAT
Found at i:54730422 original size:20 final size:20
Alignment explanation
Indices: 54730360--54730422 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 20
54730350 TTTCTAATAT
54730360 ATAATTATGTTCAACCTTTA
1 ATAATTATGTTCAACCTTTA
* *
54730380 ATTGATATTA--TTCAA-ATAATA
1 A-T-A-ATTATGTTCAACCT-TTA
54730401 ATAATTATGTTCAACCTTTA
1 ATAATTATGTTCAACCTTTA
54730421 AT
1 AT
54730423 TATGTTCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
18 4 0.12
19 1 0.03
20 12 0.38
21 10 0.31
22 1 0.03
23 4 0.12
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (20 bp):
ATAATTATGTTCAACCTTTA
Found at i:54731151 original size:15 final size:15
Alignment explanation
Indices: 54731131--54731176 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
54731121 TTTTTTTTGC
54731131 TTCGTGTGTTCTAAA
1 TTCGTGTGTTCTAAA
*
54731146 TTCGTGAGTT-TAAA
1 TTCGTGTGTTCTAAA
54731160 CTAT-GTGTGTTCTAAA
1 -T-TCGTGTGTTCTAAA
54731176 T
1 T
54731177 GTTGCAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 4 0.15
15 17 0.65
16 5 0.19
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.46
Consensus pattern (15 bp):
TTCGTGTGTTCTAAA
Found at i:54732390 original size:36 final size:36
Alignment explanation
Indices: 54732343--54732415 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
54732333 CTTATTAAAA
54732343 CTTAGATGGGGAATACTTAGGAGTCCATCGTTCTAT
1 CTTAGATGGGGAATACTTAGGAGTCCATCGTTCTAT
54732379 CTTAGATGGGGAATACTTAGGAGTCCATCGTTCTAT
1 CTTAGATGGGGAATACTTAGGAGTCCATCGTTCTAT
54732415 C
1 C
54732416 CTGTAAGGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (36 bp):
CTTAGATGGGGAATACTTAGGAGTCCATCGTTCTAT
Found at i:54734458 original size:15 final size:15
Alignment explanation
Indices: 54734423--54734474 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
54734413 TTAAGAATTT
*
54734423 TATTAAATTAT-ATA
1 TATTTAATTATAATA
54734437 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
54734451 TATTTAATAATAAT-
1 TATTTAATTATAATA
54734465 TATGTTAATT
1 TAT-TTAATT
54734475 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:54734466 original size:54 final size:54
Alignment explanation
Indices: 54734402--54734587 Score: 151
Period size: 54 Copynumber: 3.2 Consensus size: 54
54734392 ATTCATATAG
*
54734402 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTT
* * * *
54734456 AATAATAATTATGT--TAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATAT
1 AATAATAATTAT-TAAGAATTT-TA--TTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT
**
54734519 AAG
53 -TT
* *
54734522 AATATTAATTATTAAGAATTTTATTAAATTATGTATTTTAATTATAATATATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTT
54734576 AATAATAATTAT
1 AATAATAATTAT
54734588 GTTTAAATAT
Statistics
Matches: 100, Mismatches: 16, Indels: 32
0.68 0.11 0.22
Matches are distributed among these distances:
53 5 0.05
54 24 0.24
55 5 0.05
56 4 0.04
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 9 0.09
62 1 0.01
63 3 0.03
64 4 0.04
65 5 0.05
66 13 0.13
67 5 0.05
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (54 bp):
AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTT
Found at i:54734559 original size:120 final size:119
Alignment explanation
Indices: 54734315--54734595 Score: 451
Period size: 120 Copynumber: 2.4 Consensus size: 119
54734305 NNNNNNCATC
* * * *
54734315 ATATA-TTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTTCCTTTATAGTATCATATAT
1 ATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAATTTACTTTACAGTATCATATAT
54734378 TATGATTTGAGTAAATTCATATAGAATATTAATTATTAAGAATTTTATTAAATT
66 TATGATTTGAGTAAATTCATATAGAATATTAATTATTAAGAATTTTATTAAATT
* *
54734432 ATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTATATTTTACAGTATCATATA
1 ATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAATT-TACTTTACAGTATCATATA
54734496 TTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
65 TTATGATTTGAGTAAATTCATAT-AGAATATTAATTATTAAGAATTTTATTAAATT
* *
54734552 ATGTATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 ATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAAT
54734596 ATGATTAAAT
Statistics
Matches: 151, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
117 5 0.03
118 32 0.21
119 41 0.27
120 70 0.46
121 3 0.02
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (119 bp):
ATATATTTTAATTATAATATATTTAATAATAATTATGTTCAAATTTACTTTACAGTATCATATAT
TATGATTTGAGTAAATTCATATAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:54734818 original size:45 final size:40
Alignment explanation
Indices: 54734719--54734828 Score: 114
Period size: 45 Copynumber: 2.6 Consensus size: 40
54734709 TTTTCCATTA
*
54734719 TGCTATTACACCTCTATTCCATT-CAATCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACAATCAAAAACAAGAT
* * * *
54734758 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACAATCAA--AAACA--AGA-T
*
54734803 TGCTATTACACCTCTATTTCATTACA
1 TGCTATTACACCTCTATTCCATTACA
54734829 CCTCTAATCC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
39 21 0.37
40 6 0.11
42 4 0.07
44 2 0.04
45 24 0.42
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.35
Consensus pattern (40 bp):
TGCTATTACACCTCTATTCCATTACAATCAAAAACAAGAT
Found at i:54734828 original size:16 final size:16
Alignment explanation
Indices: 54734807--54734852 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
54734797 TTGATTTGCT
* *
54734807 ATTACACCTCTATTTC
1 ATTACACCTCTAATCC
54734823 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
54734839 AATACACCTCTAAT
1 ATTACACCTCTAAT
54734853 ACAATATAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:54734857 original size:16 final size:16
Alignment explanation
Indices: 54734809--54734858 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
54734799 GATTTGCTAT
* * *
54734809 TACACCTCTATTTCAT
1 TACACCTCTAATACAA
*
54734825 TACACCTCTAATCCAA
1 TACACCTCTAATACAA
54734841 TACACCTCTAATACAA
1 TACACCTCTAATACAA
54734857 TA
1 TA
54734859 TAGCGAACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (16 bp):
TACACCTCTAATACAA
Found at i:54735393 original size:102 final size:102
Alignment explanation
Indices: 54735217--54735423 Score: 414
Period size: 102 Copynumber: 2.0 Consensus size: 102
54735207 TAGGAGTCGG
54735217 TTACGCACAAAGAAGGTATTAACACCCTCGTGACGCCCAAAATTGGTATCTCGTTAAACGTGCGT
1 TTACGCACAAAGAAGGTATTAACACCCTCGTGACGCCCAAAATTGGTATCTCGTTAAACGTGCGT
54735282 TGTCTTAATTTTCAAAAATATAAGTTCAATTTAATAT
66 TGTCTTAATTTTCAAAAATATAAGTTCAATTTAATAT
54735319 TTACGCACAAAGAAGGTATTAACACCCTCGTGACGCCCAAAATTGGTATCTCGTTAAACGTGCGT
1 TTACGCACAAAGAAGGTATTAACACCCTCGTGACGCCCAAAATTGGTATCTCGTTAAACGTGCGT
54735384 TGTCTTAATTTTCAAAAATATAAGTTCAATTTAATAT
66 TGTCTTAATTTTCAAAAATATAAGTTCAATTTAATAT
54735421 TTA
1 TTA
54735424 ATCGTGATCC
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 105 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.33
Consensus pattern (102 bp):
TTACGCACAAAGAAGGTATTAACACCCTCGTGACGCCCAAAATTGGTATCTCGTTAAACGTGCGT
TGTCTTAATTTTCAAAAATATAAGTTCAATTTAATAT
Found at i:54735747 original size:19 final size:19
Alignment explanation
Indices: 54735720--54735775 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 19
54735710 AAAATAAAAA
54735720 TATTTAAAAATGCCAATAG
1 TATTTAAAAATGCCAATAG
*
54735739 TATTAAAAACGAAATGCCAATAG
1 TATT--TAA--AAATGCCAATAG
54735762 TATTTAAAAATGCC
1 TATTTAAAAATGCC
54735776 GAGTTCAGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
19 11 0.35
21 4 0.13
23 16 0.52
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.29
Consensus pattern (19 bp):
TATTTAAAAATGCCAATAG
Found at i:54735754 original size:23 final size:24
Alignment explanation
Indices: 54735727--54735771 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
54735717 AAATATTTAA
54735727 AAATGCCAATAGTA-TTAAAAACG
1 AAATGCCAATAGTATTTAAAAACG
54735750 AAATGCCAATAGTATTTAAAAA
1 AAATGCCAATAGTATTTAAAAA
54735772 TGCCGAGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.24
Consensus pattern (24 bp):
AAATGCCAATAGTATTTAAAAACG
Found at i:54735908 original size:35 final size:35
Alignment explanation
Indices: 54735867--54735943 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
54735857 TTTGTCTAAG
54735867 CCGACCCGAGAAAATATTCCTAAGCCCGACCCAAC
1 CCGACCCGAGAAAATATTCCTAAGCCCGACCCAAC
* *
54735902 CCGACCCGAGAAAATATTCCTAAGCCCGGCCCAGC
1 CCGACCCGAGAAAATATTCCTAAGCCCGACCCAAC
*
54735937 ACGACCC
1 CCGACCC
54735944 ATTTTTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.31, C:0.42, G:0.17, T:0.10
Consensus pattern (35 bp):
CCGACCCGAGAAAATATTCCTAAGCCCGACCCAAC
Found at i:54736897 original size:46 final size:44
Alignment explanation
Indices: 54736845--54736953 Score: 134
Period size: 46 Copynumber: 2.4 Consensus size: 44
54736835 TTTTTAAATC
*
54736845 TAGTATTATTTAATATTTAAGCT-TAAC-ATTGTTTTAAATTTATCAT
1 TAGTATTATTTAATATTTAA--TAT-ACTATTATTTTAAA-TTATCAT
54736891 TAGTATTATTTTAATATTTAATATACTATTATTTTAAATTATCAT
1 TAGTATTA-TTTAATATTTAATATACTATTATTTTAAATTATCAT
*
54736936 TAATATTATTTAA-ATTTA
1 TAGTATTATTTAATATTTA
54736954 TCATACATCA
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
43 5 0.09
44 5 0.09
45 17 0.29
46 19 0.33
47 12 0.21
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.54
Consensus pattern (44 bp):
TAGTATTATTTAATATTTAATATACTATTATTTTAAATTATCAT
Found at i:54736975 original size:45 final size:45
Alignment explanation
Indices: 54736880--54737006 Score: 134
Period size: 45 Copynumber: 2.8 Consensus size: 45
54736870 ACATTGTTTT
* * *
54736880 AAATTTATCATTAGTATTATTTTAATATTTAAT-ATACTATTATTTT
1 AAATTTATCATTAATATTATTTTAA-ATTT-ATCATACTATAATTTG
54736926 AAA-TTATCATTAATATTA-TTTAAATTTATCATACATCATAATTTG
1 AAATTTATCATTAATATTATTTTAAATTTATCATAC-T-ATAATTTG
* * *
54736971 AAATTTATCATGTACTATAATTTTAAACTTATCATA
1 AAATTTATCAT-TAATATTATTTTAAATTTATCATA
54737007 TCATTATTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
42 2 0.03
43 8 0.12
44 6 0.09
45 23 0.33
46 10 0.14
47 6 0.09
48 14 0.20
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (45 bp):
AAATTTATCATTAATATTATTTTAAATTTATCATACTATAATTTG
Found at i:54736977 original size:24 final size:21
Alignment explanation
Indices: 54736877--54737006 Score: 84
Period size: 24 Copynumber: 5.7 Consensus size: 21
54736867 TTAACATTGT
* *
54736877 TTTAAATTTATCATTAGTATTAT
1 TTTAAATTTATCA-TACTA-TAA
*
54736900 TTTAATATTTAAT-ATACTATTAT
1 TTTAA-ATTT-ATCATACTA-TAA
* *
54736923 TTTAAA-TTATCATTAATATTA
1 TTTAAATTTATCA-TACTATAA
54736944 TTTAAATTTATCATACATCATAA
1 TTTAAATTTATCATAC-T-ATAA
54736967 TTTGAAATTTATCATGTACTATAA
1 TTT-AAATTTATCA--TACTATAA
*
54736991 TTTTAAACTTATCATA
1 -TTTAAATTTATCATA
54737007 TCATTATTTA
Statistics
Matches: 89, Mismatches: 7, Indels: 23
0.75 0.06 0.19
Matches are distributed among these distances:
20 2 0.02
21 12 0.13
22 14 0.16
23 24 0.27
24 28 0.31
25 6 0.07
26 3 0.03
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTAAATTTATCATACTATAA
Found at i:54737213 original size:28 final size:27
Alignment explanation
Indices: 54737182--54737243 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
54737172 TACAATATTA
*
54737182 TTATTATATGTATATAATCTGTATTTTT
1 TTATTATATGAATAT-ATCTGTATTTTT
* * *
54737210 TTATTCTATGAATATATTTTTATTTTT
1 TTATTATATGAATATATCTGTATTTTT
*
54737237 ATATTAT
1 TTATTAT
54737244 TATAACTATG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 15 0.54
28 13 0.46
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (27 bp):
TTATTATATGAATATATCTGTATTTTT
Found at i:54740133 original size:10 final size:10
Alignment explanation
Indices: 54740112--54740187 Score: 61
Period size: 10 Copynumber: 7.8 Consensus size: 10
54740102 TATTTTTTAA
54740112 ATATATTA--
1 ATATATTATT
54740120 ATATATTATT
1 ATATATTATT
* *
54740130 ATATAATATA
1 ATATATTATT
* *
54740140 ATATAATATA
1 ATATATTATT
*
54740150 ATATAATA-T
1 ATATATTATT
54740159 ATTATATTA-T
1 A-TATATTATT
54740169 ATTATATTATT
1 A-TATATTATT
54740180 ATATATTA
1 ATATATTA
54740188 AACAAACAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
8 8 0.13
9 1 0.02
10 49 0.82
11 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
ATATATTATT
Found at i:54740140 original size:5 final size:5
Alignment explanation
Indices: 54740118--54740184 Score: 71
Period size: 5 Copynumber: 13.4 Consensus size: 5
54740108 TTAAATATAT
* * * *
54740118 TAATA TATTA TTATA TAATA TAATA TAATA TAATA TAATA TATTA TATTA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
* * *
54740168 TATTA TATTA TTATA TA
1 TAATA TAATA TAATA TA
54740185 TTAAACAAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 54 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (5 bp):
TAATA
Found at i:54740418 original size:22 final size:22
Alignment explanation
Indices: 54740379--54740426 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
54740369 AAATAAAAGA
54740379 AAAAGAAACAAAAGAAGA-ACAG
1 AAAAGAAACAAAAGAAGAGAC-G
*
54740401 AAAAGAAAC-AGAGAAAGAGACG
1 AAAAGAAACAAAAG-AAGAGACG
54740423 AAAA
1 AAAA
54740427 CAGGGGAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 3 0.13
22 18 0.78
23 2 0.09
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAAGAAACAAAAGAAGAGACG
Found at i:54740811 original size:22 final size:24
Alignment explanation
Indices: 54740783--54740827 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
54740773 ATATGGTAAG
54740783 AAATTAAG-TAGAAAAG-AAGTAT
1 AAATTAAGCTAGAAAAGTAAGTAT
54740805 AAATTAAGCTAGAAAAGTAAGTA
1 AAATTAAGCTAGAAAAGTAAGTA
54740828 AGCTTAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.38
23 8 0.38
24 5 0.24
ACGTcount: A:0.58, C:0.02, G:0.18, T:0.22
Consensus pattern (24 bp):
AAATTAAGCTAGAAAAGTAAGTAT
Found at i:54742419 original size:2 final size:2
Alignment explanation
Indices: 54742412--54742445 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
54742402 TCCTCTGAAC
54742412 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54742446 CAATCTACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54746600 original size:28 final size:27
Alignment explanation
Indices: 54746549--54746615 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
54746539 TAAGATAAAT
*
54746549 TATA-TTTATATTCATCTAATTATTAG
1 TATATTTTATATTAATCTAATTATTAG
* *
54746575 TATATTTTATTTTAATCATAATTATTAT
1 TATATTTTATATTAATC-TAATTATTAG
*
54746603 TGATATTTAATAT
1 T-ATATTTTATAT
54746616 CTTTATTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.12
27 10 0.30
28 10 0.30
29 9 0.27
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (27 bp):
TATATTTTATATTAATCTAATTATTAG
Found at i:54747142 original size:19 final size:19
Alignment explanation
Indices: 54747106--54747143 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
54747096 CATGAGGTTG
*
54747106 TTTATAAATTATTTATAAT
1 TTTATAAATTATTAATAAT
54747125 TTTAT-AATTAATTAATAAT
1 TTTATAAATT-ATTAATAAT
54747144 AAATTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTATAAATTATTAATAAT
Found at i:54752210 original size:23 final size:23
Alignment explanation
Indices: 54752183--54752281 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
54752173 ATAAGTGCCA
* *
54752183 CACTGATATGTAGCCGAAGCCAC
1 CACTGATACGTAGCCGAAGCTAC
54752206 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
54752229 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
*
54752252 CACTGATATGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
54752275 CACTGAT
1 CACTGAT
54752282 NNNNNNNNNN
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 73 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.19
Consensus pattern (23 bp):
CACTGATACGTAGCCGAAGCTAC
Found at i:54758586 original size:54 final size:54
Alignment explanation
Indices: 54758527--54758643 Score: 145
Period size: 49 Copynumber: 2.2 Consensus size: 54
54758517 GTAATCTAAT
* *
54758527 TATTTATTTTCAATACATAAGATAATATTTATTTTAAAACAAATCC-AAAAATAA
1 TATTTATTTTC-ATACATAAGATAATATTTACTTTAAAACAAACCCAAAAAATAA
* * *
54758581 TATTTA--TT--TACATTAGATAATATTTACTTTGAAGCAAACCCAAAAAATAA
1 TATTTATTTTCATACATAAGATAATATTTACTTTAAAACAAACCCAAAAAATAA
54758631 TATTTATTTTCAT
1 TATTTATTTTCAT
54758644 TTAAAAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
49 28 0.53
50 14 0.26
52 4 0.08
54 7 0.13
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.41
Consensus pattern (54 bp):
TATTTATTTTCATACATAAGATAATATTTACTTTAAAACAAACCCAAAAAATAA
Found at i:54758604 original size:49 final size:50
Alignment explanation
Indices: 54758540--54758644 Score: 149
Period size: 49 Copynumber: 2.1 Consensus size: 50
54758530 TTATTTTCAA
* * *
54758540 TACATAAGATAATATTTATTTTAAAACAAATCC-AAAAATAATATTTATT
1 TACATTAGATAATATTTACTTTAAAACAAACCCAAAAAATAATATTTATT
* *
54758589 TACATTAGATAATATTTACTTTGAAGCAAACCCAAAAAATAATATTTATT
1 TACATTAGATAATATTTACTTTAAAACAAACCCAAAAAATAATATTTATT
*
54758639 TTCATT
1 TACATT
54758645 TAAAAAAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
49 28 0.57
50 21 0.43
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (50 bp):
TACATTAGATAATATTTACTTTAAAACAAACCCAAAAAATAATATTTATT
Found at i:54759984 original size:17 final size:18
Alignment explanation
Indices: 54759950--54759985 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
54759940 AAATTACAAA
54759950 AAAATTCTAAATATTTAT
1 AAAATTCTAAATATTTAT
54759968 AAAATTCTAAA-ATTTAT
1 AAAATTCTAAATATTTAT
54759985 A
1 A
54759986 TTTTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATTCTAAATATTTAT
Found at i:54760016 original size:25 final size:24
Alignment explanation
Indices: 54759950--54760016 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 24
54759940 AAATTACAAA
*
54759950 AAAATTCTAAATATTTATAAAATTCT
1 AAAATT-TAAA-ATTTTTAAAATTCT
** *
54759976 AAAATTTATATTTTTTTTAAATTCT
1 AAAATTTA-AAATTTTTAAAATTCT
54760001 AGAAATTTAAAATTTT
1 A-AAATTTAAAATTTT
54760017 AATTTTTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
25 19 0.58
26 14 0.42
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (24 bp):
AAAATTTAAAATTTTTAAAATTCT
Found at i:54762594 original size:8 final size:8
Alignment explanation
Indices: 54762570--54762712 Score: 51
Period size: 8 Copynumber: 17.0 Consensus size: 8
54762560 TATAGGAAAC
54762570 TTTTAAAA
1 TTTTAAAA
54762578 TGATTTAAAA
1 T--TTTAAAA
54762588 TTTTAAAA
1 TTTTAAAA
54762596 TTTTAGAAA
1 TTTTA-AAA
54762605 ----AAAA
1 TTTTAAAA
*
54762609 TTAAATAAAA
1 TT--TTAAAA
*
54762619 TTATAAAA
1 TTTTAAAA
54762627 TTATTTAAAA
1 -T-TTTAAAA
* * *
54762637 ATTCAATA
1 TTTTAAAA
54762645 TTTTAAAA
1 TTTTAAAA
54762653 TTTTTAAAA
1 -TTTTAAAA
**
54762662 AATTAAAA
1 TTTTAAAA
*
54762670 TTATGAAAA
1 TT-TTAAAA
**
54762679 TTCAAAAAA
1 TT-TTAAAA
*
54762688 TATTAAAA
1 TTTTAAAA
54762696 TTATTAAAA
1 TT-TTAAAA
*
54762705 ATTTAAAA
1 TTTTAAAA
54762713 ACATATAATT
Statistics
Matches: 101, Mismatches: 20, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
4 3 0.03
5 1 0.01
8 46 0.46
9 31 0.31
10 20 0.20
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.39
Consensus pattern (8 bp):
TTTTAAAA
Found at i:54762669 original size:43 final size:42
Alignment explanation
Indices: 54762622--54762712 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 42
54762612 AATAAAATTA
* * *
54762622 TAAAATTATTTAAAAATTC-AATATTTTAAAATTTTTAAAAAAT
1 TAAAATTA--TAAAAATTCAAAAATATTAAAATTATTAAAAAAT
* *
54762665 TAAAATTATGAAAATTCAAAAAATATTAAAATTATTAAAAATT
1 TAAAATTATAAAAATTC-AAAAATATTAAAATTATTAAAAAAT
54762708 TAAAA
1 TAAAA
54762713 ACATATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 8 0.20
43 33 0.80
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.38
Consensus pattern (42 bp):
TAAAATTATAAAAATTCAAAAATATTAAAATTATTAAAAAAT
Found at i:54762678 original size:26 final size:25
Alignment explanation
Indices: 54762614--54762751 Score: 100
Period size: 26 Copynumber: 5.2 Consensus size: 25
54762604 AAAAATTAAA
*
54762614 TAAAATTA-TAAAATTATTTAAAAAT
1 TAAAATTATTAAAATT-TTAAAAAAT
*
54762639 TCAATATT-TTAAAATTTTTAAAAAAT
1 T-AAAATTATTAAAA-TTTTAAAAAAT
* **
54762665 TAAAATTATGAAAATTCAAAAAATAT
1 TAAAATTATTAAAATTTTAAAAA-AT
*
54762691 TAAAATTATTAAAAATTTAAAAACAT
1 TAAAATTATTAAAATTTTAAAAA-AT
** *
54762717 ATAATTTTTATTAAAATTGTTAAAAATT
1 -TAA-AATTATTAAAATT-TTAAAAAAT
54762745 ATAAAAT
1 -TAAAAT
54762752 ATAAAAAGAA
Statistics
Matches: 88, Mismatches: 17, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
25 13 0.15
26 47 0.53
27 6 0.07
28 15 0.17
29 7 0.08
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (25 bp):
TAAAATTATTAAAATTTTAAAAAAT
Found at i:54762766 original size:37 final size:37
Alignment explanation
Indices: 54762666--54762767 Score: 93
Period size: 37 Copynumber: 2.8 Consensus size: 37
54762656 TTAAAAAATT
* *
54762666 AAAATTATGAAAAT-TCAAAAAATATTAAAATTATTA
1 AAAATTATAAAAATATAAAAAAATATTAAAATTATTA
* **** *
54762702 AAAATT-TAAAAACATATAATTTTTATTAAAATTGTTA
1 AAAATTATAAAAATATA-AAAAAATATTAAAATTATTA
54762739 AAAATTAT-AAAATATAAAAAGAATATTAA
1 AAAATTATAAAAATATAAAAA-AATATTAA
54762768 TTATAATATT
Statistics
Matches: 49, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
35 5 0.10
36 9 0.18
37 34 0.69
38 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (37 bp):
AAAATTATAAAAATATAAAAAAATATTAAAATTATTA
Found at i:54764921 original size:47 final size:47
Alignment explanation
Indices: 54764852--54764945 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
54764842 TATCTCAAAG
54764852 TTGTGTATTTTTAATTCTACCAATGCCACATATTTATAGGGAGAAAT
1 TTGTGTATTTTTAATTCTACCAATGCCACATATTTATAGGGAGAAAT
54764899 TTGTGTATTTTTAATTCTACCAATGCCACATATTTATAGGGAGAAAT
1 TTGTGTATTTTTAATTCTACCAATGCCACATATTTATAGGGAGAAAT
54764946 AGAAGAATCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (47 bp):
TTGTGTATTTTTAATTCTACCAATGCCACATATTTATAGGGAGAAAT
Found at i:54767423 original size:17 final size:17
Alignment explanation
Indices: 54767385--54767675 Score: 261
Period size: 17 Copynumber: 16.8 Consensus size: 17
54767375 AAACTAAAGT
*
54767385 TTTTTTAAACACGAGAA
1 TTTTTAAAACACGAGAA
54767402 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGAGAA
*
54767420 TTTTTAAAATACG-GAA
1 TTTTTAAAACACGAGAA
*
54767436 ATTTTAGAAACACG-GAAA
1 TTTTTA-AAACACGAG-AA
* *
54767454 TTTTTTAAAACACGACAT
1 -TTTTTAAAACACGAGAA
*
54767472 TTTTTGAAACACGAGAA
1 TTTTTAAAACACGAGAA
*
54767489 TTTTTAAAACA-GGGAA
1 TTTTTAAAACACGAGAA
*
54767505 ATTTTAGAAACACG-GAAA
1 TTTTTA-AAACACGAG-AA
* *
54767523 TTTTTTTAAAACACGACAT
1 --TTTTTAAAACACGAGAA
*
54767542 TTTTTGAAACACGAGAA
1 TTTTTAAAACACGAGAA
*
54767559 TTTTTAAAACA-GGGAA
1 TTTTTAAAACACGAGAA
* *
54767575 ATTTTAGAAACACGAAAA
1 TTTTTA-AAACACGAGAA
* *
54767593 TTTTTAAAACACGACATT
1 TTTTTAAAACACGAGA-A
*
54767611 TTTTTGAAACACGAGAA
1 TTTTTAAAACACGAGAA
*
54767628 TTTTTAAAACA-GGGAA
1 TTTTTAAAACACGAGAA
* *
54767644 ATTTTAGAAACACGAAAA
1 TTTTTA-AAACACGAGAA
54767662 TTTTTAAAACACGA
1 TTTTTAAAACACGA
54767676 CATTTTTTGA
Statistics
Matches: 222, Mismatches: 36, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
16 35 0.16
17 110 0.50
18 59 0.27
19 13 0.06
20 5 0.02
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (17 bp):
TTTTTAAAACACGAGAA
Found at i:54767496 original size:69 final size:68
Alignment explanation
Indices: 54767384--54767688 Score: 502
Period size: 69 Copynumber: 4.4 Consensus size: 68
54767374 AAAACTAAAG
* * * * *
54767384 TTTTTTTAAACACGAGAATTTTTGAAAACACGAGAATTTTTAAAATACGGAAATTTTAGAAACAC
1 TTTTTTAAAACACGACATTTTTTG-AAACACGAGAATTTTTAAAACAGGGAAATTTTAGAAACAC
54767449 GGAAA
65 -GAAA
54767454 TTTTTTAAAACACGACATTTTTTGAAACACGAGAATTTTTAAAACAGGGAAATTTTAGAAACACG
1 TTTTTTAAAACACGACATTTTTTGAAACACGAGAATTTTTAAAACAGGGAAATTTTAGAAACAC-
54767519 GAAA
65 GAAA
54767523 TTTTTTTAAAACACGACATTTTTTGAAACACGAGAATTTTTAAAACAGGGAAATTTTAGAAACAC
1 -TTTTTTAAAACACGACATTTTTTGAAACACGAGAATTTTTAAAACAGGGAAATTTTAGAAACAC
54767588 GAAA
65 GAAA
*
54767592 ATTTTTAAAACACGACATTTTTTTGAAACACGAGAATTTTTAAAACAGGGAAATTTTAGAAACAC
1 TTTTTTAAAACACGACA-TTTTTTGAAACACGAGAATTTTTAAAACAGGGAAATTTTAGAAACAC
54767657 GAAA
65 GAAA
*
54767661 ATTTTTAAAACACGACATTTTTTGAAAC
1 TTTTTTAAAACACGACATTTTTTGAAAC
54767689 TCGAATTTTT
Statistics
Matches: 227, Mismatches: 6, Indels: 6
0.95 0.03 0.03
Matches are distributed among these distances:
68 27 0.12
69 115 0.51
70 85 0.37
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (68 bp):
TTTTTTAAAACACGACATTTTTTGAAACACGAGAATTTTTAAAACAGGGAAATTTTAGAAACACG
AAA
Found at i:54767688 original size:34 final size:33
Alignment explanation
Indices: 54767385--54767693 Score: 312
Period size: 34 Copynumber: 8.9 Consensus size: 33
54767375 AAACTAAAGT
* *
54767385 TTTTTTAAACACGAGAATTTTTGAAAACACGAGAA
1 TTTTTAAAACACGA-AATTTTTG-AAACACGAAAA
* * *
54767420 TTTTTAAAATACGGAAATTTTAGAAACACGGAAAT
1 TTTTTAAAACAC-GAAATTTTTGAAACAC-GAAAA
* *
54767455 TTTTTAAAACACGACATTTTTTGAAACACGAGAA
1 TTTTTAAAACACGA-AATTTTTGAAACACGAAAA
* * *
54767489 TTTTTAAAACAGGGAAATTTTAGAAACACGGAAATT
1 TTTTTAAAACA-CGAAATTTTTGAAACAC-GAAA-A
* *
54767525 TTTTTAAAACACGACATTTTTTGAAACACGAGAA
1 TTTTTAAAACACGA-AATTTTTGAAACACGAAAA
* *
54767559 TTTTTAAAACAGGGAAATTTTAGAAACACGAAAA
1 TTTTTAAAACA-CGAAATTTTTGAAACACGAAAA
* *
54767593 TTTTTAAAACACGACATTTTTTTGAAACACGAGAA
1 TTTTTAAAACACGA-A-ATTTTTGAAACACGAAAA
* *
54767628 TTTTTAAAACAGGGAAATTTTAGAAACACGAAAA
1 TTTTTAAAACA-CGAAATTTTTGAAACACGAAAA
* *
54767662 TTTTTAAAACACGACATTTTTTGAAACTCGAA
1 TTTTTAAAACACGA-AATTTTTGAAACACGAA
54767694 TTTTTTCTTT
Statistics
Matches: 226, Mismatches: 36, Indels: 25
0.79 0.13 0.09
Matches are distributed among these distances:
33 4 0.02
34 113 0.50
35 82 0.36
36 27 0.12
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (33 bp):
TTTTTAAAACACGAAATTTTTGAAACACGAAAA
Found at i:54768628 original size:12 final size:12
Alignment explanation
Indices: 54768613--54768654 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
54768603 TGTTTTTTTC
54768613 TTTTTCTTCTC-
1 TTTTTCTTCTCT
*
54768624 TTTTTCTTTCCCT
1 TTTTTC-TTCTCT
*
54768637 TTTTTTTTCTCT
1 TTTTTCTTCTCT
54768649 TTTTTC
1 TTTTTC
54768655 CTTTCTCTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
11 6 0.24
12 14 0.56
13 5 0.20
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTCTTCTCT
Found at i:54768653 original size:11 final size:11
Alignment explanation
Indices: 54768605--54768653 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
54768595 TTTGTTTTTG
54768605 TTTTTT-TCTT
1 TTTTTTCTCTT
*
54768615 TTTCTTCTCTT
1 TTTTTTCTCTT
*
54768626 TTTCTTTCCCTTT
1 TTT-TTTCTC-TT
54768639 TTTTTTCTCTT
1 TTTTTTCTCTT
54768650 TTTT
1 TTTT
54768654 CCTTTCTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
10 5 0.16
11 13 0.41
12 9 0.28
13 5 0.16
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTCTCTT
Found at i:54769331 original size:29 final size:29
Alignment explanation
Indices: 54769244--54769373 Score: 138
Period size: 29 Copynumber: 4.4 Consensus size: 29
54769234 TATAGGGCCA
*
54769244 AAATGTAATTCCTAGAAAA-TTTAAGGG-TC
1 AAATGTAATT--TAGAAAAGTTTAAGGGTTG
* *
54769273 AAAGTGAAATTTTGAGAAAGTTTAAGGGTTG
1 AAA-TGTAATTTAGA-AAAGTTTAAGGGTTG
*
54769304 AAATGTAATTTAGAAAAGTTTAGGGGTTG
1 AAATGTAATTTAGAAAAGTTTAAGGGTTG
* ***
54769333 AAATGTAATTTAGAAAAGTTTAGGGGCCA
1 AAATGTAATTTAGAAAAGTTTAAGGGTTG
54769362 AAATGTAATTTA
1 AAATGTAATTTA
54769374 TATTTTTTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
28 3 0.03
29 58 0.66
30 23 0.26
31 4 0.05
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (29 bp):
AAATGTAATTTAGAAAAGTTTAAGGGTTG
Found at i:54769351 original size:58 final size:58
Alignment explanation
Indices: 54769237--54769373 Score: 152
Period size: 58 Copynumber: 2.3 Consensus size: 58
54769227 AGGAAAATAT
*
54769237 AGGGCCAAAATGTAATTCCTAGAAAATTTAAGGGTCAAAGTGAAATTTTGAGAAAGTTTA
1 AGGGCCAAAATGTAATT--TAGAAAATTTAAGGGTCAAAGTGAAATTTAGAGAAAGTTTA
*** * * *
54769297 AGGGTTGAAATGTAATTTAGAAAAGTTTAGGGGTTGAAA-TGTAATTTAGA-AAAGTTTA
1 AGGGCCAAAATGTAATTTAGAAAA-TTTAAGGG-TCAAAGTGAAATTTAGAGAAAGTTTA
*
54769355 GGGGCCAAAATGTAATTTA
1 AGGGCCAAAATGTAATTTA
54769374 TATTTTTTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
58 30 0.47
59 16 0.25
60 18 0.28
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (58 bp):
AGGGCCAAAATGTAATTTAGAAAATTTAAGGGTCAAAGTGAAATTTAGAGAAAGTTTA
Found at i:54770375 original size:25 final size:25
Alignment explanation
Indices: 54770310--54770382 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
54770300 GAGCTTATCA
* *
54770310 TTATTCAACTCGAAAAAACTTACTG
1 TTATTCAGCTCGAAAGAACTTACTG
54770335 TTATTCAGCTCGAAAGAACTTACTG
1 TTATTCAGCTCGAAAGAACTTACTG
*
54770360 TTATTCAGCTCGAAAGAGCTTAC
1 TTATTCAGCTCGAAAGAACTTAC
54770383 CGTTTATAGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.32
Consensus pattern (25 bp):
TTATTCAGCTCGAAAGAACTTACTG
Found at i:54772410 original size:140 final size:140
Alignment explanation
Indices: 54772158--54772464 Score: 524
Period size: 140 Copynumber: 2.2 Consensus size: 140
54772148 CACGGCCCAG
54772158 CACACGGCCTGGCACACGGGCGTGTGGTTTGGCCTTGTGACCCAAGTCAGTGAGTTACACGGGCT
1 CACACGGCCTGGCACACGGGCGTGTGGTTTGGCCTTGTGACCCAAGTCAGTGAGTTACACGGGCT
* *
54772223 GGGACACGACCGTGTGATCCTATTTTGAATACCAACACGACCTAAGACACAGGTGTGTCTCTTGG
66 GGGACACGACCATGTGATCCTATTTTGAATACCAACACGACCTAAGACACAGGTGTGTCTATTGG
54772288 CCGTGTGAGT
131 CCGTGTGAGT
*
54772298 CACACTGCCTGGCACACGGGCGTGTGGTTTGGCCTTGTGACCCAAGTCAGTGAGTTACACGGGCT
1 CACACGGCCTGGCACACGGGCGTGTGGTTTGGCCTTGTGACCCAAGTCAGTGAGTTACACGGGCT
* * *
54772363 GGGACACGGCCATGTGCTCTTATTTTGAATACCAACACGACCTAAGACACAGGTGTGTCTATTGG
66 GGGACACGACCATGTGATCCTATTTTGAATACCAACACGACCTAAGACACAGGTGTGTCTATTGG
54772428 CCGTGTGAGT
131 CCGTGTGAGT
* * *
54772438 CACACGGCTTGGCCACATGGCCGTGTG
1 CACACGGCCTGG-CACACGGGCGTGTG
54772465 ACCCCTACAG
Statistics
Matches: 156, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
140 144 0.92
141 12 0.08
ACGTcount: A:0.20, C:0.26, G:0.30, T:0.24
Consensus pattern (140 bp):
CACACGGCCTGGCACACGGGCGTGTGGTTTGGCCTTGTGACCCAAGTCAGTGAGTTACACGGGCT
GGGACACGACCATGTGATCCTATTTTGAATACCAACACGACCTAAGACACAGGTGTGTCTATTGG
CCGTGTGAGT
Found at i:54774111 original size:14 final size:14
Alignment explanation
Indices: 54774094--54774124 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
54774084 ATTAATTTTT
54774094 AAATAATAATAAGA
1 AAATAATAATAAGA
54774108 AAATAATAATAAGA
1 AAATAATAATAAGA
54774122 AAA
1 AAA
54774125 AAGGAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (14 bp):
AAATAATAATAAGA
Found at i:54774200 original size:28 final size:29
Alignment explanation
Indices: 54774159--54774231 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 29
54774149 AAAATACAAT
*
54774159 TTACATTTTGGCCC-CACTATTTCTAAAA
1 TTACATTTTAGCCCTCACTATTTCTAAAA
* *
54774187 TTACATTTTAGCCCCTCACTTTTTTTAAAA
1 TTACATTTTAG-CCCTCACTATTTCTAAAA
54774217 TTACATTTTAGCCCT
1 TTACATTTTAGCCCT
54774232 GGGAGTTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 10 0.25
29 7 0.17
30 23 0.57
ACGTcount: A:0.26, C:0.25, G:0.05, T:0.44
Consensus pattern (29 bp):
TTACATTTTAGCCCTCACTATTTCTAAAA
Found at i:54774819 original size:32 final size:32
Alignment explanation
Indices: 54774783--54774849 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
54774773 AAGAAAAAAA
*
54774783 AGAG-AAATGAGAAAAGAAAAAAAGAAGAGAGG
1 AGAGAAAAAGAGAAAAG-AAAAAAGAAGAGAGG
* * *
54774815 AGAGAAAAAGAGAAACGAAGAATGAAGAGAGG
1 AGAGAAAAAGAGAAAAGAAAAAAGAAGAGAGG
54774847 AGA
1 AGA
54774850 AGAGAGGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 20 0.67
33 10 0.33
ACGTcount: A:0.63, C:0.01, G:0.33, T:0.03
Consensus pattern (32 bp):
AGAGAAAAAGAGAAAAGAAAAAAGAAGAGAGG
Found at i:54775222 original size:16 final size:17
Alignment explanation
Indices: 54775177--54775224 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
54775167 GGAGGCCTGT
54775177 CCAACAGTAGCCCAACA
1 CCAACAGTAGCCCAACA
*
54775194 CCAACAGTTGCCCAAC-
1 CCAACAGTAGCCCAACA
* *
54775210 CCAGCAGTGGCCCAA
1 CCAACAGTAGCCCAA
54775225 AGTAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.42, G:0.17, T:0.08
Consensus pattern (17 bp):
CCAACAGTAGCCCAACA
Found at i:54777587 original size:30 final size:30
Alignment explanation
Indices: 54777553--54777631 Score: 103
Period size: 29 Copynumber: 2.7 Consensus size: 30
54777543 AAGCTTACAA
*
54777553 AAAAAATTCAAAATAATT-TTTA-TTTTTT
1 AAAAAATTCAAAATAATTATATAGTTTTTT
54777581 ATAAAAATTCAAAA-AATTATATAGTTTTTT
1 A-AAAAATTCAAAATAATTATATAGTTTTTT
*
54777611 AAAAAATTCTAAATAA-TATAT
1 AAAAAATTCAAAATAATTATAT
54777632 CTAGAAAGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
28 5 0.11
29 31 0.69
30 9 0.20
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (30 bp):
AAAAAATTCAAAATAATTATATAGTTTTTT
Found at i:54779063 original size:26 final size:26
Alignment explanation
Indices: 54779047--54779102 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 26
54779037 ATATAAAATC
54779047 ATAAAAAAAATTTAAAAATAACAAAA
1 ATAAAAAAAATTTAAAAATAACAAAA
*
54779073 ATAAAAAAAATTTAAAAACTAAAAAAA
1 ATAAAAAAAATTTAAAAA-TAACAAAA
54779100 ATA
1 ATA
54779103 TATTATAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.20
Consensus pattern (26 bp):
ATAAAAAAAATTTAAAAATAACAAAA
Found at i:54779067 original size:17 final size:18
Alignment explanation
Indices: 54779032--54779079 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
54779022 AGAAAATCTC
54779032 AAAAAATATAAAATCATAA
1 AAAAAATATAAAA-CATAA
*
54779051 AAAAAATTTAAAA-ATAA
1 AAAAAATATAAAACATAA
*
54779068 CAAAAATA-AAAA
1 AAAAAATATAAAA
54779080 AAATTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 4 0.15
17 10 0.38
19 12 0.46
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (18 bp):
AAAAAATATAAAACATAA
Found at i:54779081 original size:18 final size:17
Alignment explanation
Indices: 54779060--54779102 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
54779050 AAAAAAATTT
54779060 AAAAATAACAAAAATAAA
1 AAAAATAA-AAAAATAAA
* *
54779078 AAAAATTTAAAAACTAAA
1 AAAAA-TAAAAAAATAAA
54779096 AAAAATA
1 AAAAATA
54779103 TATTATAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 18 0.86
19 2 0.10
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAAATAAAAAAATAAA
Found at i:54783204 original size:22 final size:23
Alignment explanation
Indices: 54783178--54783230 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
54783168 TAAATAACAA
54783178 AATATTAAAAATATTTT-TAATT
1 AATATTAAAAATATTTTATAATT
* *
54783200 AATATT-TATATATTTTATAATT
1 AATATTAAAAATATTTTATAATT
54783222 AA-ATTAAAA
1 AATATTAAAA
54783231 TTTTAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATATTAAAAATATTTTATAATT
Found at i:54786129 original size:31 final size:31
Alignment explanation
Indices: 54786087--54786145 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
54786077 CTTGACAACC
* *
54786087 TAGTGACTTAAATGAAAACTTTTGAATAAAT
1 TAGTAACTTAAATGAAAAATTTTGAATAAAT
54786118 TAGTAACTTAAATGAAAAATTTTGAATA
1 TAGTAACTTAAATGAAAAATTTTGAATA
54786146 GCTCAATGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (31 bp):
TAGTAACTTAAATGAAAAATTTTGAATAAAT
Found at i:54786481 original size:2 final size:2
Alignment explanation
Indices: 54786474--54786504 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
54786464 GGAATTGGGG
54786474 GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
54786505 CGAACTCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:54787172 original size:6 final size:6
Alignment explanation
Indices: 54787163--54787187 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
54787153 GCTCAGTCGA
54787163 AAGCTC AAGCTC AAGCTC AAGCTC A
1 AAGCTC AAGCTC AAGCTC AAGCTC A
54787188 TGCCCAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.16, T:0.16
Consensus pattern (6 bp):
AAGCTC
Found at i:54792065 original size:24 final size:22
Alignment explanation
Indices: 54792034--54792089 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 22
54792024 CAAGAGAATC
*
54792034 ATAAATAAACA-TATTTATTAGAT
1 ATAAATAAACAGCATTTA-TA-AT
54792057 ATAAAATAATACAGCATTTATAAT
1 AT-AAATAA-ACAGCATTTATAAT
54792081 ATAAATAAA
1 ATAAATAAA
54792090 TGAATTGAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 1 0.03
23 8 0.28
24 10 0.34
25 5 0.17
26 5 0.17
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (22 bp):
ATAAATAAACAGCATTTATAAT
Found at i:54793143 original size:18 final size:19
Alignment explanation
Indices: 54793115--54793152 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
54793105 TTTATAATAC
*
54793115 TTTATATTATTATGTTATT
1 TTTATATTATTATGTAATT
54793134 TTTATA-TATTATGTAATT
1 TTTATATTATTATGTAATT
54793152 T
1 T
54793153 AGGACACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTATATTATTATGTAATT
Found at i:54793766 original size:11 final size:11
Alignment explanation
Indices: 54793746--54793853 Score: 56
Period size: 11 Copynumber: 10.4 Consensus size: 11
54793736 ATAAAAATTA
54793746 AAAAATTATTTT
1 AAAAA-TATTTT
54793758 AAAAATATTTT
1 AAAAATATTTT
54793769 --AAA-A--TT
1 AAAAATATTTT
* * *
54793775 AAAAAAAATTA
1 AAAAATATTTT
54793786 AAAAAGTATTTT
1 AAAAA-TATTTT
*
54793798 AAAAAAATTTT
1 AAAAATATTTT
54793809 --AAA-A-TTT
1 AAAAATATTTT
54793816 AAAAA-ATTTAAT
1 AAAAATATTT--T
*
54793828 AAAAGTATTTT
1 AAAAATATTTT
*
54793839 AAAAGTATTTT
1 AAAAATATTTT
54793850 AAAA
1 AAAA
54793854 TTAAAAAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 25
0.72 0.06 0.23
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 5 0.06
9 11 0.14
10 2 0.03
11 33 0.42
12 18 0.23
13 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:54793803 original size:41 final size:40
Alignment explanation
Indices: 54793720--54793863 Score: 207
Period size: 40 Copynumber: 3.5 Consensus size: 40
54793710 ACCAAAAATT
*
54793720 TATTTTAAAAATTAAAATAAAAATTAAAAAATTATTTTAAAAA
1 TATTTT-AAAATT-AAA-AAAAATTAAAAAAGTATTTTAAAAA
54793763 TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
* * * *
54793803 AATTTTAAAATTTAAAAAATTTAATAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAAATTAA-AAAAGTATTTTAAAAA
54793844 TATTTTAAAATTAAAAAAAA
1 TATTTTAAAATTAAAAAAAA
54793864 AATAAAAATA
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
40 45 0.49
41 35 0.38
42 6 0.07
43 6 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:54800125 original size:107 final size:105
Alignment explanation
Indices: 54799940--54800364 Score: 593
Period size: 107 Copynumber: 4.0 Consensus size: 105
54799930 TGGATTGAGA
* * * * * * * * *
54799940 TTTAAGAGGATATTTGGCTATTTAGTCAAATGAGAAATTGAAACACAGCACGTTAGGGTACGTTT
1 TTTAA-AGGATATTTGGCTATTTGGTCGAACGAAAAATCGAAACCCAGCACATTAGGGCACATTT
*
54800005 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAATT
65 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAT
*
54800046 TTTAATAGGATATTTGGCTATTTGGTTGAACGAAAAAATCGAAACCCAGCACATTAGGGCACATT
1 TTTAA-AGGATATTTGGCTATTTGGTCGAACG-AAAAATCGAAACCCAGCACATTAGGGCACATT
*
54800111 TTCTCGAATTTCCAAAAGCAAAATATTGTCC-TACTTTGAAAT
64 TTCTCGAATTTCCAAACGCAAAATATTG-CCTTACTTTGAAAT
* * *
54800153 TTTAGAAGGATATTTGGCTATTTGGTCGAACGAAAAAATTGAAACCCAGCACATTAGGACACGTT
1 TTTA-AAGGATATTTGGCTATTTGGTCGAACG-AAAAATCGAAACCCAGCACATTAGGGCACATT
*
54800218 TTCTCGAATTTCCAAACGCAAAATATTGCCTTCCTTTGAAAT
64 TTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAT
* *
54800260 TTTAAAAGGACATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACATTAGGGCACATTT
1 TTT-AAAGGATATTTGGCTATTTGGTCGAACGAAAAATCGAAACCCAGCACATTAGGGCACATTT
*
54800325 TCTCGAATTTCCAAACGCAAAATATTGTCTTA-TTTAGAAA
65 TCTCGAATTTCCAAACGCAAAATATTGCCTTACTTT-GAAA
54800365 AAAAAATTCT
Statistics
Matches: 287, Mismatches: 26, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
105 3 0.01
106 92 0.32
107 188 0.66
108 4 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (105 bp):
TTTAAAGGATATTTGGCTATTTGGTCGAACGAAAAATCGAAACCCAGCACATTAGGGCACATTTT
CTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAT
Found at i:54800435 original size:20 final size:21
Alignment explanation
Indices: 54800392--54800436 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
54800382 GTATGATGTT
*
54800392 AATATGCATAATGGAACAATA
1 AATATGCATAATGAAACAATA
54800413 AATATG-ATAATGTAAACAA-A
1 AATATGCATAATG-AAACAATA
54800433 AATA
1 AATA
54800437 ATATGAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.58, C:0.07, G:0.11, T:0.24
Consensus pattern (21 bp):
AATATGCATAATGAAACAATA
Found at i:54800466 original size:21 final size:21
Alignment explanation
Indices: 54800426--54800466 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
54800416 ATGATAATGT
*
54800426 AAACAAAAATAATATGAGAAA
1 AAACAAAAATAATATAAGAAA
54800447 AAACAAAAAATAATA-AAGAA
1 AAAC-AAAAATAATATAAGAA
54800467 CAAATCAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (21 bp):
AAACAAAAATAATATAAGAAA
Found at i:54800698 original size:7 final size:7
Alignment explanation
Indices: 54800658--54800685 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
54800648 TGTGAATTAT
54800658 AAAAATA
1 AAAAATA
54800665 AAAAATA
1 AAAAATA
54800672 AAAAATA
1 AAAAATA
54800679 AAAAATA
1 AAAAATA
54800686 TATATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:54800722 original size:2 final size:2
Alignment explanation
Indices: 54800715--54800741 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
54800705 TTAAAATGTA
54800715 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
54800742 AGTGTGTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54802676 original size:88 final size:86
Alignment explanation
Indices: 54802570--54802866 Score: 247
Period size: 88 Copynumber: 3.4 Consensus size: 86
54802560 TTATCGTTTT
* * *
54802570 AATCCGCTCCACTGCAACTTCAGGGAGACAAGATTAATAGCTTCAATCAGCTCCACTGCAACTTC
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGATT-AT-GCTTCAATCAGCTCCACTGCAACTTC
**
54802635 AGGGAGATAAGATTGGTATCTTC
64 AGGGAGATAAGATTAATATCTTC
* * * * * *
54802658 AACCTGCTCCACTACAACTTTAGGGAGATAAGGCTTAT-CTTCAGTCTGCTCCACTTCAAC-TCT
1 AATCTGCTCCACTACAACTTCAGGGAGATAA-GATTATGCTTCAATCAGCTCCACTGCAACTTC-
* * * *
54802721 AAGGAGATAAGACTTATTATGGTGC
64 AGGGAGATAAGA-TTAATAT-CTTC
* * * ** * * * *
54802746 GATCTGCTCTACTGCAACTTCAAAGAGATAAGATTCATCGTTTTAATCCGCTCCATTGCAACTTC
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGATT-AT-GCTTCAATCAGCTCCACTGCAACTTC
* * *
54802811 AGTGAGATAGGATTAATAACTTC
64 AGGGAGATAAGATTAATATCTTC
* *
54802834 AATTTGCTCCACTATAACTTCAGGGAGATAAGA
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGA
54802867 CTGGATGCGA
Statistics
Matches: 159, Mismatches: 42, Indels: 16
0.73 0.19 0.07
Matches are distributed among these distances:
85 2 0.01
86 30 0.19
87 8 0.05
88 84 0.53
89 8 0.05
90 25 0.16
91 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (86 bp):
AATCTGCTCCACTACAACTTCAGGGAGATAAGATTATGCTTCAATCAGCTCCACTGCAACTTCAG
GGAGATAAGATTAATATCTTC
Found at i:54802710 original size:42 final size:42
Alignment explanation
Indices: 54802570--54803037 Score: 216
Period size: 44 Copynumber: 10.8 Consensus size: 42
54802560 TTATCGTTTT
* *
54802570 AATCCGCTCCACTGCAACTTCAGGGAGACAAGA-TTAATAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-AT--CTTC
* *
54802614 AATCAGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACT--TATCTTC
* * * *
54802658 AACCTGCTCCACTACAACTTTAGGGAGATAAGGCTTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATCTTC
* * * *
54802700 AGTCTGCTCCACTTCAAC-TCTAAGGAGATAAGACTTATTATGGTGC
1 AATCTGCTCCACTGCAACTTC-AGGGAGATAAGACTTA-TCT--T-C
* * ** *
54802746 GATCTGCTCTACTGCAACTTCAAAGAGATAAGA-TTCATCGTTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-ATC--TTC
* * * *
54802790 AATCCGCTCCATTGCAACTTCAGTGAGATAGGA-TTAATAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-AT--CTTC
* ** * *
54802834 AATTTGCTCCACTATAACTTCAGGGAGATAAGACTGGA--TGC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TATCTTC
* * * * *
54802875 GATCTGCTCTACTGCAACTTCAGAGAGATAATATCTGTAGT-TTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TA-TCTTC
* ** * * ** * *
54802919 AACCCACTCTACTGTAACTTTTGTGGAGATAGGA-TTGGCTTCTTC
1 AATCTGCTCCACTGCAACTTCAG-GGAGATAAGACTT---ATCTTC
** *** *
54802964 TGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGATGC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATCTTC
* * *
54803005 GATCTGCTCTACTGCAACTTCAGAGAGATAAGA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA
54803038 TCTGTGGTTT
Statistics
Matches: 320, Mismatches: 80, Indels: 51
0.71 0.18 0.11
Matches are distributed among these distances:
41 60 0.19
42 41 0.13
43 3 0.01
44 151 0.47
45 31 0.10
46 30 0.09
47 4 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (42 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATCTTC
Found at i:54803038 original size:41 final size:41
Alignment explanation
Indices: 54802849--54803038 Score: 139
Period size: 41 Copynumber: 4.5 Consensus size: 41
54802839 GCTCCACTAT
*
54802849 AACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGC
1 AACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGC
* * * *** * ** *
54802890 AACTTCAGAGAGATAATATCTGTAGTTTTAACCCACTCTACTGT
1 AACTTCAGGGAGATAAGAT-TG--GATGCGATCTGCTCTACTGC
** * * * *
54802934 AACTTTTGTGGAGATAGGATTGGCTTCTTCTG-TCTGCTCCACTGC
1 AACTTCAG-GGAGATAAGATTGG---ATGC-GATCTGCTCTACTGC
54802979 AACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGC
1 AACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGC
*
54803020 AACTTCAGAGAGATAAGAT
1 AACTTCAGGGAGATAAGAT
54803039 CTGTGGTTTT
Statistics
Matches: 109, Mismatches: 31, Indels: 18
0.69 0.20 0.11
Matches are distributed among these distances:
40 1 0.01
41 48 0.44
42 3 0.03
44 33 0.30
45 24 0.22
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (41 bp):
AACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGC
Found at i:54803060 original size:130 final size:129
Alignment explanation
Indices: 54802743--54803083 Score: 418
Period size: 130 Copynumber: 2.6 Consensus size: 129
54802733 CTTATTATGG
* * * * *
54802743 TGCGATCTGCTCTACTGCAACTTCAAAGAGATAAGAT-TCATCGTTTTAATCCGCTCCATTGCAA
1 TGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCT-GTAGTTTTAATCCGCTCTACTGCAA
* *
54802807 CTTCAGTGAGATAGGATTAATAACTTCAATTTGCTCCACTATAACTTCAGGGAGATAAGACTGGA
65 CTTCAGTGAGATAGGATTAATAACTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGACTGGA
* * * *
54802872 TGCGATCTGCTCTACTGCAACTTCAGAGAGATAATATCTGTAGTTTTAACCCACTCTACTGTAAC
1 TGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAGTTTTAATCCGCTCTACTGCAAC
** ** * ** * *
54802937 TTTTGTGGAGATAGGATTGGCT-TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGG
66 TTCAGT-GAGATAGGATT-AATAACTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGACTGG
54803001 A
129 A
* *
54803002 TGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGTTCTACTGCAA-
1 TGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAGTTTTAATCCGCTCTACTGCAAC
*
54803066 TCTCAGGGAGATAGGATT
66 T-TCAGTGAGATAGGATT
54803084 TGTGGCTTAA
Statistics
Matches: 179, Mismatches: 29, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
129 70 0.39
130 108 0.60
131 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (129 bp):
TGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAGTTTTAATCCGCTCTACTGCAAC
TTCAGTGAGATAGGATTAATAACTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGACTGGA
Found at i:54803181 original size:44 final size:44
Alignment explanation
Indices: 54803133--54803720 Score: 173
Period size: 44 Copynumber: 13.4 Consensus size: 44
54803123 AGATTCGTCG
* *
54803133 TCTTCGATCTGTTCCACTACTGCTTAGGGAGATAGGATCTGCAA
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAA
* * * * * *
54803177 TCTTCAACCTACTCCACTGCTGCTCAGGGGGATAGGA-CT--AA
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAA
** * * * **
54803218 TGGCTTAAAT-TAGCTTCC-CTACTACCTT-GAGAAGATAAGAT-TCACCG
1 T--CTTCGATCT-GC-TCCACTACT-GCTTAG-GGAGATAGGATCT-ACAA
*
54803265 TCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAA
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAA
* * * * ****
54803309 TCTTCGACCTACTCCACTACTGCTCAGAGAGATAAGG--CTGGTG
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGAT-AGGATCTACAA
* ** * * * * **
54803352 GCTTAAATCTGTTTCC-CTACTACATT-GGGAAGATAAGATCCACCG
1 TCTTCGATCTG-CTCCACTACTGC-TTAGGG-AGATAGGATCTACAA
* *
54803397 TCTTCGATTTGCTCCACTACTGCTTAGGGAGACAGGATCTACAA
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAA
* * * * * * *
54803441 TCTTCGACCTACTCCACTGCTGCTCAAGAAGATAAGG--CT--GA
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGAT-AGGATCTACAA
** * * **
54803482 TGGCTTAAATCTGCTTCC-CTACTACCTT-GGGAAGATAAGAT-TCACCG
1 T--CTTCGATCTGC-TCCACTACT-GCTTAGGG-AGATAGGATCT-ACAA
* * *
54803529 TCTTCAATTTGCTCCACTACTGCTTAGGGAGACAGGATCTACAA
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAA
* * * * *
54803573 TCTTCAACCTACTCCACTGCTGCTCT-GGGAGATAGGA-CT--GA
1 TCTTCGATCTGCTCCACTACTGCT-TAGGGAGATAGGATCTACAA
** * * **
54803614 TGGCTTAAATCTGCTTCC-CTACTACCTT-GGGAAGATAAGATTCT-CTG
1 T--CTTCGATCTGC-TCCACTACT-GCTTAGGG-AGATAGGA-TCTACAA
* * *
54803661 TCTTCGATCTGCTCCACTACTGCTTAAGGAGACAAGATCTACAA
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAA
* *
54803705 TCTTCGACCTACTCCA
1 TCTTCGATCTGCTCCA
54803721 TTGCTACTCA
Statistics
Matches: 385, Mismatches: 111, Indels: 96
0.65 0.19 0.16
Matches are distributed among these distances:
41 7 0.02
42 1 0.00
43 68 0.18
44 230 0.60
45 73 0.19
46 3 0.01
47 3 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (44 bp):
TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACAA
Found at i:54803762 original size:132 final size:132
Alignment explanation
Indices: 54803086--54803744 Score: 975
Period size: 132 Copynumber: 5.0 Consensus size: 132
54803076 ATAGGATTTG
* * * ** *
54803086 TGGCTTAAATATGTTTCCCTACTACCTTGGAAAGATAAGATTCGTCGTCTTCGATCTGTTCCACT
1 TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACT
* * * * *
54803151 ACTGCTTAGGGAGATAGGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGGGAT-AGGAC
66 ACTGCTTAGGGAGACAGGATCTACAATCTTCGACCTACTCCACTGCTGCTCAAGGAGATAAGG-C
*
54803215 TAA
130 TGA
*
54803218 TGGCTTAAAT-TAGCTTCCCTACTACCTTGAGAAGATAAGATTCACCGTCTTCGATCTGCTCCAC
1 TGGCTTAAATCT-GCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCAC
*
54803282 TACTGCTTAGGGAGACAGGATCTACAATCTTCGACCTACTCCACTACTGCTC-AGAGAGATAAGG
65 TACTGCTTAGGGAGACAGGATCTACAATCTTCGACCTACTCCACTGCTGCTCAAG-GAGATAAGG
*
54803346 CTGG
129 CTGA
* * * *
54803350 TGGCTTAAATCTGTTTCCCTACTACATTGGGAAGATAAGATCCACCGTCTTCGATTTGCTCCACT
1 TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACT
*
54803415 ACTGCTTAGGGAGACAGGATCTACAATCTTCGACCTACTCCACTGCTGCTCAAGAAGATAAGGCT
66 ACTGCTTAGGGAGACAGGATCTACAATCTTCGACCTACTCCACTGCTGCTCAAGGAGATAAGGCT
54803480 GA
131 GA
* *
54803482 TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCAATTTGCTCCACT
1 TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACT
* **
54803547 ACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCTGGGAGAT-AGGAC
66 ACTGCTTAGGGAGACAGGATCTACAATCTTCGACCTACTCCACTGCTGCTCAAGGAGATAAGG-C
54803611 TGA
130 TGA
* *
54803614 TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCTCTGTCTTCGATCTGCTCCACT
1 TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACT
* * * *
54803679 ACTGCTTAAGGAGACAAGATCTACAATCTTCGACCTACTCCATTGCTACTCAAGGAGATAAGGCT
66 ACTGCTTAGGGAGACAGGATCTACAATCTTCGACCTACTCCACTGCTGCTCAAGGAGATAAGGCT
54803744 G
131 G
54803745 GTGCTTTCGA
Statistics
Matches: 479, Mismatches: 41, Indels: 14
0.90 0.08 0.03
Matches are distributed among these distances:
131 5 0.01
132 465 0.97
133 9 0.02
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (132 bp):
TGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACT
ACTGCTTAGGGAGACAGGATCTACAATCTTCGACCTACTCCACTGCTGCTCAAGGAGATAAGGCT
GA
Found at i:54804129 original size:24 final size:24
Alignment explanation
Indices: 54804097--54804154 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
54804087 CGGATTGCCC
54804097 CCACTGTAATCTTCAA-AGTCAAAT
1 CCACTGTAATCTTCAAGAGTC-AAT
*
54804121 CCACTGTAATCTTCAAGATTCAAT
1 CCACTGTAATCTTCAAGAGTCAAT
*
54804145 CCACTATAAT
1 CCACTGTAAT
54804155 TTTGGGACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31
Consensus pattern (24 bp):
CCACTGTAATCTTCAAGAGTCAAT
Found at i:54804796 original size:106 final size:106
Alignment explanation
Indices: 54804611--54804938 Score: 494
Period size: 106 Copynumber: 3.1 Consensus size: 106
54804601 TAGTTATTTC
* ** **
54804611 AATGAAAAATATTATCACAATGGACAAGATAAAATTTTATTGAGAATAAAGCTCGAAATGAATAA
1 AATGAAAAAGATTATCACAATGGACAAGATGGAATTTTATTGAGAGCAAAGCTCGAAATGAATAA
*
54804676 ATTAACCAAAATAGCAAATTTTGCTAAGACGAACTGAATAA
66 ATTAAACAAAATAGCAAATTTTGCTAAGACGAACTGAATAA
* *
54804717 AATGAAAAAGATTATCACAATGGACAACATGGAATTTTATTAAGAGCAAAGCTCGAAATGAATAA
1 AATGAAAAAGATTATCACAATGGACAAGATGGAATTTTATTGAGAGCAAAGCTCGAAATGAATAA
* *
54804782 ATTAAACAAAATAGCAAATTTTGCTATGATGAACTGAATAA
66 ATTAAACAAAATAGCAAATTTTGCTAAGACGAACTGAATAA
* *
54804823 GATGAAAAAGATTATCACAATGGACAAGATGGAATTTTATTGAGAGCAAAGCTTGAAATGAATAA
1 AATGAAAAAGATTATCACAATGGACAAGATGGAATTTTATTGAGAGCAAAGCTCGAAATGAATAA
* * *
54804888 ATTAATCAAAATAGAAAATTTTGCTAAGATCCGAAATGAATAA
66 ATTAAACAAAATAGCAAATTTTGCTAAGA--CGAACTGAATAA
*
54804931 GATGAAAA
1 AATGAAAA
54804939 CAAGTACCCC
Statistics
Matches: 201, Mismatches: 19, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
106 183 0.91
108 18 0.09
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (106 bp):
AATGAAAAAGATTATCACAATGGACAAGATGGAATTTTATTGAGAGCAAAGCTCGAAATGAATAA
ATTAAACAAAATAGCAAATTTTGCTAAGACGAACTGAATAA
Found at i:54805227 original size:20 final size:20
Alignment explanation
Indices: 54805199--54805248 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
54805189 CACATTGGCC
*
54805199 TCTCATTTTCCTTTTTCTTT
1 TCTCTTTTTCCTTTTTCTTT
**
54805219 TCTCTTTTTTGTTTTTCTTT
1 TCTCTTTTTCCTTTTTCTTT
*
54805239 TCTTTTTTTC
1 TCTCTTTTTC
54805249 GTCTTTTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (20 bp):
TCTCTTTTTCCTTTTTCTTT
Found at i:54810031 original size:107 final size:106
Alignment explanation
Indices: 54809852--54810211 Score: 544
Period size: 106 Copynumber: 3.4 Consensus size: 106
54809842 GAGATTTAAG
* * *
54809852 AGGATATTTGGTTATTTGGTCAAACGAGAAATCGAAACCCAACACGTTAGGGCACGTTTTCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACATTAGGGCACGTTTTCTCGA
*
54809917 ATTTCTAAACGCAAAATATTACCTTACTTTGAAATTTTA-A
66 ATTTCTAAACGCAAAATATTGCCTTACTTTGAAATTTTAGA
* *
54809957 TAGGATATTTGGCTATTTGGTTGAACGAAAAAATCGAAACCCAACACATTAGGGCACGTTTTCTC
1 -AGGATATTTGGCTATTTGGTCGAACG-AGAAATCGAAACCCAACACATTAGGGCACGTTTTCTC
* *
54810022 GAATTTCTAAACGCAAAATATTGCTTTATTTTGAAATTTTAGA
64 GAATTTCTAAACGCAAAATATTGCCTTACTTTGAAATTTTAGA
* * * *
54810065 AGGATATTTGGCTATTTGGTCGAATGAGAAATTGAAACCCAGCACATTAGGACACGTTTTCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACATTAGGGCACGTTTTCTCGA
* *
54810130 ATTT-TCAAACTCAAAATATTGTCTTACTTTGAAATTTTAGA
66 ATTTCT-AAACGCAAAATATTGCCTTACTTTGAAATTTTAGA
*
54810171 ATGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCA
54810212 GTANNNNNNN
Statistics
Matches: 230, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
105 1 0.00
106 131 0.57
107 97 0.42
108 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (106 bp):
AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAACACATTAGGGCACGTTTTCTCGA
ATTTCTAAACGCAAAATATTGCCTTACTTTGAAATTTTAGA
Found at i:54822597 original size:34 final size:34
Alignment explanation
Indices: 54822554--54822622 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
54822544 ACAGCATGTA
54822554 AGAATTCTACCTGCTAATGTTGATAATAGAAGTT
1 AGAATTCTACCTGCTAATGTTGATAATAGAAGTT
54822588 AGAATTCTACCTGCTAATGTTGATAATAGAAGTT
1 AGAATTCTACCTGCTAATGTTGATAATAGAAGTT
54822622 A
1 A
54822623 ATGAACTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (34 bp):
AGAATTCTACCTGCTAATGTTGATAATAGAAGTT
Found at i:54825702 original size:2 final size:2
Alignment explanation
Indices: 54825695--54825722 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54825685 TAGTTTCTTA
54825695 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54825723 GTCAAAGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54825973 original size:17 final size:17
Alignment explanation
Indices: 54825943--54825975 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
54825933 CGTCGATATG
54825943 TTTATATTTAATAATTT
1 TTTATATTTAATAATTT
54825960 TTTAT-TTTATATAATT
1 TTTATATTTA-ATAATT
54825976 AATTTAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATTTAATAATTT
Found at i:54832384 original size:36 final size:36
Alignment explanation
Indices: 54832336--54832408 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
54832326 TAAATTCGCC
*
54832336 TAAGTCAGCCTATGTAACACCCCTTACCCTACTTGA
1 TAAGTCAACCTATGTAACACCCCTTACCCTACTTGA
*
54832372 TAAGTCAACCTATGTAACACCCCTTACTCTACTTGA
1 TAAGTCAACCTATGTAACACCCCTTACCCTACTTGA
54832408 T
1 T
54832409 TGTTGGGTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.32, G:0.10, T:0.30
Consensus pattern (36 bp):
TAAGTCAACCTATGTAACACCCCTTACCCTACTTGA
Found at i:54836564 original size:22 final size:22
Alignment explanation
Indices: 54836502--54836573 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
54836492 GATGTTCAAA
* **
54836502 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
54836524 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
54836546 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
54836568 CATGAG
1 CATGAG
54836574 GGTATGGGTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:54838625 original size:27 final size:27
Alignment explanation
Indices: 54838581--54838644 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
54838571 ACATACAAAA
54838581 GAAATTTCAAATCTAATTACCAAATTAT
1 GAAA-TTCAAATCTAATTACCAAATTAT
54838609 GAAATTCAACATC-AATTACCAAATTAT
1 GAAATTCAA-ATCTAATTACCAAATTAT
54838636 -AAATTCAAA
1 GAAATTCAAA
54838645 CTTAATCCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
25 1 0.03
26 8 0.23
27 19 0.54
28 7 0.20
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.31
Consensus pattern (27 bp):
GAAATTCAAATCTAATTACCAAATTAT
Found at i:54841594 original size:21 final size:22
Alignment explanation
Indices: 54841554--54841606 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
54841544 TTTCTAAGAA
*
54841554 ATTAAAAAAATATAAAATTATC
1 ATTAAAATAATATAAAATTATC
*
54841576 ATTAAAATAAT-TAATATTATC
1 ATTAAAATAATATAAAATTATC
54841597 ATTAAAATAA
1 ATTAAAATAA
54841607 ATGTTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (22 bp):
ATTAAAATAATATAAAATTATC
Found at i:54842412 original size:28 final size:30
Alignment explanation
Indices: 54842381--54842438 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
54842371 TTGTCTCATA
* *
54842381 TACTTTATATTATTACA-A-TTGTATTGTT
1 TACTGTATATTATTAAAGATTTGTATTGTT
*
54842409 TACTGTGTATTATTAAAGATTTGTATTGTT
1 TACTGTATATTATTAAAGATTTGTATTGTT
54842439 GAGAATATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.56
29 1 0.04
30 10 0.40
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.55
Consensus pattern (30 bp):
TACTGTATATTATTAAAGATTTGTATTGTT
Found at i:54845682 original size:16 final size:16
Alignment explanation
Indices: 54845661--54845691 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54845651 AAATAAAGTA
54845661 TAATAAAACAAATAGG
1 TAATAAAACAAATAGG
*
54845677 TAATAAAAGAAATAG
1 TAATAAAACAAATAG
54845692 AAAGCCATGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.03, G:0.13, T:0.19
Consensus pattern (16 bp):
TAATAAAACAAATAGG
Found at i:54848077 original size:40 final size:40
Alignment explanation
Indices: 54848033--54848111 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
54848023 GACTATTAAA
*
54848033 AATGTGATGTTTTGATACATCGAGACAAAATGTGAATTGT
1 AATGTGATGTTTTGATACATCGAGACAAAATGAGAATTGT
54848073 AATGTGATGTTTTGATACATCGAGACAAAATGAGAATTG
1 AATGTGATGTTTTGATACATCGAGACAAAATGAGAATTG
54848112 CATGTCAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.33
Consensus pattern (40 bp):
AATGTGATGTTTTGATACATCGAGACAAAATGAGAATTGT
Found at i:54848328 original size:44 final size:44
Alignment explanation
Indices: 54848265--54848421 Score: 190
Period size: 44 Copynumber: 3.6 Consensus size: 44
54848255 GAGGAAGATT
* * * *
54848265 TGGCAACTTGTCTATGAATTTGGTGGTTTCATCCAAAACCTACG
1 TGGCAGCTTGTCTACGAATTTGGTGGTTTCATCCACAACCTACA
* * *
54848309 TGGCAGCTTGTCTACGAATTTGGTAGCTTCATCCACAACCTATA
1 TGGCAGCTTGTCTACGAATTTGGTGGTTTCATCCACAACCTACA
**
54848353 TGGCAGCTTGTCTATTAATTTGGTGGTTT-ATCCACAACCTACA
1 TGGCAGCTTGTCTACGAATTTGGTGGTTTCATCCACAACCTACA
* * * *
54848396 TGACAGTTTGTCTGCAAATTTGGTGG
1 TGGCAGCTTGTCTACGAATTTGGTGG
54848422 CTTAGTCCAC
Statistics
Matches: 96, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
43 34 0.35
44 62 0.65
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (44 bp):
TGGCAGCTTGTCTACGAATTTGGTGGTTTCATCCACAACCTACA
Found at i:54848431 original size:87 final size:88
Alignment explanation
Indices: 54848265--54848432 Score: 232
Period size: 87 Copynumber: 1.9 Consensus size: 88
54848255 GAGGAAGATT
* * *
54848265 TGGCAACTTGTCTATGAATTTGGTGGTTTCATCCAAAACCTACGTGGCAGCTTGTCTACGAATTT
1 TGGCAACTTGTCTATGAATTTGGTGGTTTCATCCAAAACCTACATGACAGCTTGTCTACAAATTT
54848330 GGTAGCTTCATCCACAACCTATA
66 GGTAGCTTCATCCACAACCTATA
* * * * *
54848353 TGGCAGCTTGTCTATTAATTTGGTGGTTT-ATCCACAACCTACATGACAGTTTGTCTGCAAATTT
1 TGGCAACTTGTCTATGAATTTGGTGGTTTCATCCAAAACCTACATGACAGCTTGTCTACAAATTT
*
54848417 GGTGGCTT-AGTCCACA
66 GGTAGCTTCA-TCCACA
54848433 TATATATTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
86 1 0.01
87 42 0.60
88 27 0.39
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (88 bp):
TGGCAACTTGTCTATGAATTTGGTGGTTTCATCCAAAACCTACATGACAGCTTGTCTACAAATTT
GGTAGCTTCATCCACAACCTATA
Found at i:54852765 original size:23 final size:23
Alignment explanation
Indices: 54852739--54852784 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
54852729 TACTTGTATA
54852739 ATTTTGCCCATTTTTTCGTATGG
1 ATTTTGCCCATTTTTTCGTATGG
54852762 ATTTTGCCCATTTTTTCGTATGG
1 ATTTTGCCCATTTTTTCGTATGG
54852785 TATAGTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.17, G:0.17, T:0.52
Consensus pattern (23 bp):
ATTTTGCCCATTTTTTCGTATGG
Found at i:54853127 original size:106 final size:106
Alignment explanation
Indices: 54853002--54853205 Score: 390
Period size: 106 Copynumber: 1.9 Consensus size: 106
54852992 ATATAGACAC
*
54853002 AAAATTCGGCTAATGGAATTATAATGTATATGTATTACGATATGATGTTTTATAATAGTAAAATA
1 AAAATTCGGCTAATAGAATTATAATGTATATGTATTACGATATGATGTTTTATAATAGTAAAATA
54853067 TGTTTAGTTAGTTGGTTAAGTGGTACACATGTAAAATATGT
66 TGTTTAGTTAGTTGGTTAAGTGGTACACATGTAAAATATGT
*
54853108 AAAATTCGGCTAATAGAATTATAATGTATATTTATTACGATATGATGTTTTATAATAGTAAAATA
1 AAAATTCGGCTAATAGAATTATAATGTATATGTATTACGATATGATGTTTTATAATAGTAAAATA
54853173 TGTTTAGTTAGTTGGTTAAGTGGTACACATGTA
66 TGTTTAGTTAGTTGGTTAAGTGGTACACATGTA
54853206 TGAATATTAT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 96 1.00
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.40
Consensus pattern (106 bp):
AAAATTCGGCTAATAGAATTATAATGTATATGTATTACGATATGATGTTTTATAATAGTAAAATA
TGTTTAGTTAGTTGGTTAAGTGGTACACATGTAAAATATGT
Found at i:54857853 original size:57 final size:57
Alignment explanation
Indices: 54857779--54857887 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
54857769 GATCCTATCC
54857779 TGATATAGCCCTCCCGAAGAATATGTGTGAAAA-AGATCTAGCCCGAACGGGTGATCT
1 TGATATAGCCCTCCCGAAGAATATGTG-GAAAATAGATCTAGCCCGAACGGGTGATCT
* * *
54857836 TGATATAGCCCTCCCGAAGAATATGTGGAAAATGGATTTAGCCCGGACGGGT
1 TGATATAGCCCTCCCGAAGAATATGTGGAAAATAGATCTAGCCCGAACGGGT
54857888 AATCCGAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
56 5 0.10
57 43 0.90
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (57 bp):
TGATATAGCCCTCCCGAAGAATATGTGGAAAATAGATCTAGCCCGAACGGGTGATCT
Found at i:54858122 original size:67 final size:67
Alignment explanation
Indices: 54858014--54858145 Score: 237
Period size: 67 Copynumber: 2.0 Consensus size: 67
54858004 GTTTATATTA
* * *
54858014 CAGGGGATTTAGCTTGTACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
54858079 TG
66 TG
54858081 CAGGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
54858146 GAATTGAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (67 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
TG
Found at i:54858849 original size:2 final size:2
Alignment explanation
Indices: 54858844--54858882 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
54858834 ATTTAAAATC
54858844 TA TA TA TA TA 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 TA TA TA TA TA T
54858883 TTAGGATTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54870161 original size:24 final size:20
Alignment explanation
Indices: 54870107--54870150 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
54870097 TTAAACCTCT
54870107 TAGGACTCTCATTTTATAGA
1 TAGGACTCTCATTTTATAGA
*
54870127 TAGGACTCTCATTTTGTAGA
1 TAGGACTCTCATTTTATAGA
54870147 TAGG
1 TAGG
54870151 CACTAATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (20 bp):
TAGGACTCTCATTTTATAGA
Found at i:54872603 original size:11 final size:12
Alignment explanation
Indices: 54872573--54872602 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
54872563 TAACATTTTT
*
54872573 TAAAAAATTATA
1 TAAAAAATGATA
54872585 TAAAAAATGATA
1 TAAAAAATGATA
54872597 TAAAAA
1 TAAAAA
54872603 TTAATACGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (12 bp):
TAAAAAATGATA
Found at i:54876198 original size:19 final size:21
Alignment explanation
Indices: 54876174--54876213 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
54876164 TTTGGTTTGA
54876174 AAATTTT-AA-TAAAAAAATT
1 AAATTTTAAATTAAAAAAATT
54876193 AAATTTTAAATTAAAAAAATT
1 AAATTTTAAATTAAAAAAATT
54876214 GAGTTATTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 2 0.11
21 10 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATTTTAAATTAAAAAAATT
Found at i:54891905 original size:23 final size:21
Alignment explanation
Indices: 54891863--54891906 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
54891853 ATAAATTGTA
*
54891863 AAAATATACATGAATTTTAAT
1 AAAATATACATAAATTTTAAT
54891884 AAAATATACAAATAAATTTTAAT
1 AAAATATAC--ATAAATTTTAAT
54891907 TTTATGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
23 11 0.55
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAATATACATAAATTTTAAT
Found at i:54896447 original size:24 final size:24
Alignment explanation
Indices: 54896419--54896470 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
54896409 TTAGTAAGCC
* *
54896419 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
54896443 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
54896467 AAAT
1 AAAT
54896471 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Done.