Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 137 of 226
Found at i:45697701 original size:16 final size:15
Alignment explanation
Indices: 45697676--45697706 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
45697666 AATGATCATC
45697676 CTCATTTTCTTTCTT
1 CTCATTTTCTTTCTT
45697691 CTCACTTTTCTTTCTT
1 CTCA-TTTTCTTTCTT
45697707 ACCAAGCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (15 bp):
CTCATTTTCTTTCTT
Found at i:45705817 original size:18 final size:18
Alignment explanation
Indices: 45705794--45705854 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
45705784 CAAGGTCACG
45705794 ATCAATAGCGTCACTATC
1 ATCAATAGCGTCACTATC
*
45705812 ATCAATAGCGTCACTAGC
1 ATCAATAGCGTCACTATC
**
45705830 ATCAATATTGTCACTATC
1 ATCAATAGCGTCACTATC
45705848 ATCAATA
1 ATCAATA
45705855 TTGATATCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.30
Consensus pattern (18 bp):
ATCAATAGCGTCACTATC
Found at i:45705855 original size:18 final size:18
Alignment explanation
Indices: 45705803--45705869 Score: 86
Period size: 18 Copynumber: 3.9 Consensus size: 18
45705793 GATCAATAGC
**
45705803 GTCACTATCATCAATAGC
1 GTCACTATCATCAATATT
*
45705821 GTCACTAGCATCAATATT
1 GTCACTATCATCAATATT
45705839 GTCACTATCATCAATATT
1 GTCACTATCATCAATATT
45705857 G--A-TATCATCAATA
1 GTCACTATCATCAATA
45705870 AGAAAAACCT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
15 11 0.24
16 1 0.02
18 33 0.73
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (18 bp):
GTCACTATCATCAATATT
Found at i:45707299 original size:21 final size:20
Alignment explanation
Indices: 45707259--45707329 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
45707249 GTTAATTTCA
*
45707259 TTTTTAAT-ATTATT-TAAT
1 TTTTTAATAATTTTTATAAT
* *
45707277 TTTTTATTTTATTTTTATAAT
1 TTTTTA-ATAATTTTTATAAT
*
45707298 TTAATTAATAATTTTTATAAT
1 TT-TTTAATAATTTTTATAAT
*
45707319 TTTTTTATAAT
1 TTTTTAATAAT
45707330 AGCTGGTAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
18 6 0.14
19 1 0.02
20 12 0.29
21 20 0.48
22 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTAATAATTTTTATAAT
Found at i:45717693 original size:14 final size:14
Alignment explanation
Indices: 45717674--45717708 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
45717664 TTGAGTACAT
45717674 AAATATTATATACC
1 AAATATTATATACC
* *
45717688 AAATATTGTCTACC
1 AAATATTATATACC
45717702 AAATATT
1 AAATATT
45717709 TTAGCTAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (14 bp):
AAATATTATATACC
Found at i:45719321 original size:43 final size:44
Alignment explanation
Indices: 45719214--45719331 Score: 132
Period size: 43 Copynumber: 2.7 Consensus size: 44
45719204 CTCGTACAAC
* * * *
45719214 GCCAACGTCCCAAACGTGGTCTTACATG-TAATCACAAATCGAT
1 GCCAACGTCCCAGACATGGTCTTACACGAAAATCACAAATCGAT
* * * * *
45719257 GCCACCGTCCTAGATAGGGTCTTACACGAAAAT-ACAAGTCGAT
1 GCCAACGTCCCAGACATGGTCTTACACGAAAATCACAAATCGAT
*
45719300 GCCAACGTCCCAGGCATGGTCTTACACGAAAA
1 GCCAACGTCCCAGACATGGTCTTACACGAAAA
45719332 CACTTATCAG
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
43 57 0.95
44 3 0.05
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.20
Consensus pattern (44 bp):
GCCAACGTCCCAGACATGGTCTTACACGAAAATCACAAATCGAT
Found at i:45721430 original size:18 final size:18
Alignment explanation
Indices: 45721404--45721440 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
45721394 TCAGAAAGAC
*
45721404 CACCGCTATCCTTATATA
1 CACCACTATCCTTATATA
45721422 CACCACTATCCTTATATA
1 CACCACTATCCTTATATA
45721440 C
1 C
45721441 TTAAGTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.35, G:0.03, T:0.32
Consensus pattern (18 bp):
CACCACTATCCTTATATA
Found at i:45726041 original size:42 final size:42
Alignment explanation
Indices: 45725975--45726064 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
45725965 ACGGCCTAGC
* * * * *
45725975 ACACAGCCTGGCACACGGGCGTGTGTGGCAACGCAAAGAGTT
1 ACACGGCCTGACACACGGACGTGTGGGGCAACCCAAAGAGTT
* * **
45726017 ACACGGCCTGACACATGGACGTGTGGGGCATCCCAGTGAGTT
1 ACACGGCCTGACACACGGACGTGTGGGGCAACCCAAAGAGTT
45726059 ACACGG
1 ACACGG
45726065 GTGAGGACAC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.24, C:0.27, G:0.33, T:0.16
Consensus pattern (42 bp):
ACACGGCCTGACACACGGACGTGTGGGGCAACCCAAAGAGTT
Found at i:45726672 original size:25 final size:25
Alignment explanation
Indices: 45726624--45726672 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
45726614 TACTCCACAA
* * *
45726624 AGGCTTTCTATTCAGAATAAGCCAT
1 AGGCTTTCCACTCAGAACAAGCCAT
*
45726649 AGGCTTTCCACTCAGAACATGCCA
1 AGGCTTTCCACTCAGAACAAGCCA
45726673 CAAAGGCGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (25 bp):
AGGCTTTCCACTCAGAACAAGCCAT
Found at i:45730344 original size:12 final size:12
Alignment explanation
Indices: 45730327--45730351 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45730317 AAAGAAAATC
45730327 TCTTTTTTTTTT
1 TCTTTTTTTTTT
45730339 TCTTTTTTTTTT
1 TCTTTTTTTTTT
45730351 T
1 T
45730352 TTGTTGAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:45732125 original size:21 final size:21
Alignment explanation
Indices: 45732084--45732136 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
45732074 TTTGGTTGAA
*
45732084 AAATTATTTAATTGAGAAATT
1 AAATTAATTAATTGAGAAATT
* * **
45732105 AATTTAGTTAATTGATTAATT
1 AAATTAATTAATTGAGAAATT
45732126 AAATTAATTAA
1 AAATTAATTAA
45732137 ATAAAATAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (21 bp):
AAATTAATTAATTGAGAAATT
Found at i:45732742 original size:22 final size:22
Alignment explanation
Indices: 45732692--45732742 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
45732682 TCCTTTTCAT
* *
45732692 AATCT-AAGCTTAATTCCTATC
1 AATCTCAAGCCTAATTCCAATC
*
45732713 AATTTCAAGCCTAATT-CAATC
1 AATCTCAAGCCTAATTCCAATC
45732734 AAATCTCAA
1 -AATCTCAA
45732743 TCAGGGAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (22 bp):
AATCTCAAGCCTAATTCCAATC
Found at i:45741694 original size:29 final size:30
Alignment explanation
Indices: 45741637--45741715 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
45741627 TAATTTTTAG
45741637 GGGTTCT-AAAAAATAA-TTTGTACAAGAT
1 GGGTTCTGAAAAAATAATTTTGTACAAGAT
***
45741665 GGGTTCTGAAAAAATAATTTTGT-GGGGAT
1 GGGTTCTGAAAAAATAATTTTGTACAAGAT
* *
45741694 GGGCTCTGAAAAAGTAATTTTG
1 GGGTTCTGAAAAAATAATTTTG
45741716 ACGATATGGG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
28 7 0.16
29 32 0.73
30 5 0.11
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.33
Consensus pattern (30 bp):
GGGTTCTGAAAAAATAATTTTGTACAAGAT
Found at i:45741724 original size:29 final size:29
Alignment explanation
Indices: 45741644--45741725 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
45741634 TAGGGGTTCT
* *
45741644 AAAAAATAA-TTTGTACAAGATGGGTTCTG
1 AAAAAATAATTTTG-ACGAGATGGGCTCTG
** *
45741673 AAAAAATAATTTTGTGGGGATGGGCTCTG
1 AAAAAATAATTTTGACGAGATGGGCTCTG
* *
45741702 AAAAAGTAATTTTGACGATATGGG
1 AAAAAATAATTTTGACGAGATGGG
45741726 TTGAGTTTTG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
29 38 0.90
30 4 0.10
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.30
Consensus pattern (29 bp):
AAAAAATAATTTTGACGAGATGGGCTCTG
Found at i:45742279 original size:13 final size:13
Alignment explanation
Indices: 45742261--45742285 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45742251 TAATGTTTTG
45742261 ATTTTTCGTGTTA
1 ATTTTTCGTGTTA
45742274 ATTTTTCGTGTT
1 ATTTTTCGTGTT
45742286 TCAAATTTCT
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:0.12, C:0.08, G:0.16, T:0.64
Consensus pattern (13 bp):
ATTTTTCGTGTTA
Found at i:45745779 original size:25 final size:24
Alignment explanation
Indices: 45745734--45745785 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
45745724 GTCATTAGAG
45745734 TTATCGATTTCAGCTCTTATGAGC
1 TTATCGATTTCAGCTCTTATGAGC
*
45745758 TTATCGATCTTTAGCT-TGTATGAGC
1 TTATCGAT-TTCAGCTCT-TATGAGC
45745783 TTA
1 TTA
45745786 CCCTTATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.44
Consensus pattern (24 bp):
TTATCGATTTCAGCTCTTATGAGC
Found at i:45745829 original size:24 final size:24
Alignment explanation
Indices: 45745768--45745829 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
45745758 TTATCGATCT
*
45745768 TTAGCTTGTATGAGCTTACCCTTA
1 TTAGCTCGTATGAGCTTACCCTTA
* * *
45745792 TTCAGCTCGGATGAGGTTACCGTT-
1 TT-AGCTCGTATGAGCTTACCCTTA
45745816 TATAGCTCGTATGA
1 T-TAGCTCGTATGA
45745830 ACATACATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
24 13 0.42
25 18 0.58
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (24 bp):
TTAGCTCGTATGAGCTTACCCTTA
Found at i:45752108 original size:25 final size:25
Alignment explanation
Indices: 45752054--45752143 Score: 85
Period size: 25 Copynumber: 3.6 Consensus size: 25
45752044 AGTTATCGAT
* ** *
45752054 TTCAGCTCTTATGAGCTTATTGATA
1 TTCAGCTCGTATGAGCTTACCGTTA
*
45752079 CTCAGCTCGTATGAGCTTACCGTTA
1 TTCAGCTCGTATGAGCTTACCGTTA
* * *
45752104 TTCAGCTTGGAAGAGCTTACCGTT-
1 TTCAGCTCGTATGAGCTTACCGTTA
45752128 TAT-AGCTCGTATGAGC
1 T-TCAGCTCGTATGAGC
45752144 ATACATGTAC
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
24 11 0.21
25 41 0.79
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (25 bp):
TTCAGCTCGTATGAGCTTACCGTTA
Found at i:45752492 original size:42 final size:42
Alignment explanation
Indices: 45752433--45752521 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
45752423 TACTTTCGTC
*
45752433 CACACGGGCAGAGACACGGGCATGTGTCTCAGCCGTGTATGA
1 CACACGGGCAGAGACACGGGCATATGTCTCAGCCGTGTATGA
45752475 CACACGGGCAGAGACACGGGCATATGTCTCAGCCGTGTATGA
1 CACACGGGCAGAGACACGGGCATATGTCTCAGCCGTGTATGA
45752517 CACAC
1 CACAC
45752522 AGCTAGGTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.26, C:0.28, G:0.30, T:0.16
Consensus pattern (42 bp):
CACACGGGCAGAGACACGGGCATATGTCTCAGCCGTGTATGA
Found at i:45753554 original size:11 final size:11
Alignment explanation
Indices: 45753530--45753621 Score: 52
Period size: 11 Copynumber: 8.3 Consensus size: 11
45753520 AATGCTTATC
45753530 TTAACATTAA-A
1 TTAA-ATTAATA
45753541 TTAAATTAATA
1 TTAAATTAATA
45753552 TTAAATTAATA
1 TTAAATTAATA
*
45753563 --AAA-TACTA
1 TTAAATTAATA
*
45753571 TCAAGA-TAAGTA
1 TTAA-ATTAA-TA
45753583 TTAAATTAA-A
1 TTAAATTAATA
45753593 TCTAATATTAAACTA
1 T-TAA-ATT-AA-TA
*
45753608 TTAAAATAATA
1 TTAAATTAATA
45753619 TTA
1 TTA
45753622 TTTTTAGAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 22
0.72 0.04 0.24
Matches are distributed among these distances:
8 4 0.06
9 3 0.05
10 9 0.14
11 28 0.42
12 13 0.20
13 4 0.06
14 3 0.05
15 2 0.03
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.38
Consensus pattern (11 bp):
TTAAATTAATA
Found at i:45753554 original size:16 final size:16
Alignment explanation
Indices: 45753530--45753560 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
45753520 AATGCTTATC
45753530 TTAACATTAAATTAAA
1 TTAACATTAAATTAAA
*
45753546 TTAATATTAAATTAA
1 TTAACATTAAATTAA
45753561 TAAAATACTA
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:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAACATTAAATTAAA
Found at i:45755122 original size:27 final size:26
Alignment explanation
Indices: 45755084--45755137 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 26
45755074 CCTGAAATAA
45755084 ATATAAATCCT-CCATAACACACCAAT
1 ATATAAATCCTCCCA-AACACACCAAT
45755110 ATATAATATCCTCCCAAACACACCAAT
1 ATATAA-ATCCTCCCAAACACACCAAT
45755137 A
1 A
45755138 AGGCATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 6 0.23
27 17 0.65
28 3 0.12
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.22
Consensus pattern (26 bp):
ATATAAATCCTCCCAAACACACCAAT
Found at i:45759069 original size:16 final size:18
Alignment explanation
Indices: 45759048--45759085 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
45759038 ATTTGAATAT
*
45759048 TAATTTGAAT-ATATTA-
1 TAATTTAAATAATATTAC
45759064 TAATTTAAATAATATTAC
1 TAATTTAAATAATATTAC
45759082 TAAT
1 TAAT
45759086 AATTCTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 6 0.32
18 4 0.21
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
TAATTTAAATAATATTAC
Found at i:45760867 original size:55 final size:55
Alignment explanation
Indices: 45760794--45760902 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
45760784 CTACTTTAAG
45760794 ATTTAAGGTTTGGAATGTTAGTATTGTATTTATAAATAGATTATTTTAAAGATTA
1 ATTTAAGGTTTGGAATGTTAGTATTGTATTTATAAATAGATTATTTTAAAGATTA
*
45760849 ATTTAAGGTTTGGAATGTTAGTATTGTATTTATAAGTAGATTATTTTAAAGATT
1 ATTTAAGGTTTGGAATGTTAGTATTGTATTTATAAATAGATTATTTTAAAGATT
45760903 TCATATAAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (55 bp):
ATTTAAGGTTTGGAATGTTAGTATTGTATTTATAAATAGATTATTTTAAAGATTA
Found at i:45763219 original size:32 final size:32
Alignment explanation
Indices: 45763178--45763241 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
45763168 AAATTAACTA
45763178 AGTAATAAAAATAAAAAGTAAAAACTCCAATG
1 AGTAATAAAAATAAAAAGTAAAAACTCCAATG
45763210 AGTAATAAAAATAAAAAGTAAAAACTCCAATG
1 AGTAATAAAAATAAAAAGTAAAAACTCCAATG
45763242 CACGATTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.19
Consensus pattern (32 bp):
AGTAATAAAAATAAAAAGTAAAAACTCCAATG
Found at i:45764749 original size:27 final size:27
Alignment explanation
Indices: 45764719--45764771 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
45764709 AAAATAATTA
*
45764719 AAATCCAA-TATTTTAATAATTTAAGTT
1 AAATCCAATTATTTT-ATAATTAAAGTT
**
45764746 AAATTTAATTATTTTATAATTAAAGT
1 AAATCCAATTATTTTATAATTAAAGT
45764772 ATTAATTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (27 bp):
AAATCCAATTATTTTATAATTAAAGTT
Found at i:45765168 original size:32 final size:32
Alignment explanation
Indices: 45765128--45765191 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
45765118 AAAAAAAAGA
45765128 TTAACCAATTTTGGAAGAAAAACTTTGATTTG
1 TTAACCAATTTTGGAAGAAAAACTTTGATTTG
45765160 TTAACCAATTTTGGAAGAAAAACTTTGATTTG
1 TTAACCAATTTTGGAAGAAAAACTTTGATTTG
45765192 GTGTTTGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (32 bp):
TTAACCAATTTTGGAAGAAAAACTTTGATTTG
Found at i:45766094 original size:11 final size:11
Alignment explanation
Indices: 45766078--45766104 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
45766068 GAGATTGTCA
45766078 CACAATTAAAG
1 CACAATTAAAG
45766089 CACAATTAAAG
1 CACAATTAAAG
45766100 CACAA
1 CACAA
45766105 ATTTGGAGGG
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:0.56, C:0.22, G:0.07, T:0.15
Consensus pattern (11 bp):
CACAATTAAAG
Found at i:45776897 original size:9 final size:9
Alignment explanation
Indices: 45776870--45776906 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
45776860 TGAGTTTTTG
45776870 AATTCGAAT
1 AATTCGAAT
* *
45776879 AACTCAAAT
1 AATTCGAAT
45776888 AATTCGAAT
1 AATTCGAAT
45776897 AATTCGAAT
1 AATTCGAAT
45776906 A
1 A
45776907 TCAAACTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:45778374 original size:39 final size:39
Alignment explanation
Indices: 45778275--45778374 Score: 137
Period size: 39 Copynumber: 2.6 Consensus size: 39
45778265 CATATTCACT
* * * *
45778275 TTTAAGAATATATCACATTACACATATAATCACATGACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
45778314 TTTAAACATATATCATAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
45778353 TTTAAGCATATATTACAATACT
1 TTTAAGCATATATCACAATACT
45778375 AAAAAACATG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:45779475 original size:14 final size:14
Alignment explanation
Indices: 45779456--45779482 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45779446 GAACCTTATT
45779456 ATCATGTTAAAATC
1 ATCATGTTAAAATC
45779470 ATCATGTTAAAAT
1 ATCATGTTAAAAT
45779483 AAGTTGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.37
Consensus pattern (14 bp):
ATCATGTTAAAATC
Found at i:45784772 original size:31 final size:30
Alignment explanation
Indices: 45784712--45784806 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
45784702 CTTTTTCTAG
* * *
45784712 TTGA-TCAGCTCGATCTTGGCTTATTGAGC
1 TTGATTCAGCTCAATCTTAGCTCATTGAGC
* *
45784741 TTGATTCAGCTCACAT-TTCAGTTCCTTGAGC
1 TTGATTCAGCTCA-ATCTT-AGCTCATTGAGC
**
45784772 TCAATTCAGCTCAATCTTAGCTCATTGAGC
1 TTGATTCAGCTCAATCTTAGCTCATTGAGC
45784802 TTGAT
1 TTGAT
45784807 GCTATTTTAT
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
29 4 0.08
30 24 0.47
31 23 0.45
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (30 bp):
TTGATTCAGCTCAATCTTAGCTCATTGAGC
Found at i:45784802 original size:30 final size:30
Alignment explanation
Indices: 45784716--45784802 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 30
45784706 TTCTAGTTGA
* * * **
45784716 TCAGCTCGATCTTGGCTTATTGAGCTTGAT
1 TCAGCTCAATCTTAGCTCATTGAGCTCAAT
* *
45784746 TCAGCTCACAT-TTCAGTTCCTTGAGCTCAAT
1 TCAGCTCA-ATCTT-AGCTCATTGAGCTCAAT
45784777 TCAGCTCAATCTTAGCTCATTGAGCT
1 TCAGCTCAATCTTAGCTCATTGAGCT
45784803 TGATGCTATT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
30 22 0.49
31 23 0.51
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (30 bp):
TCAGCTCAATCTTAGCTCATTGAGCTCAAT
Found at i:45787133 original size:29 final size:29
Alignment explanation
Indices: 45787074--45787229 Score: 154
Period size: 29 Copynumber: 5.4 Consensus size: 29
45787064 TACCCGTCCT
* * *
45787074 TTTTCATATTCGATGGTCGA-AACCATTCA
1 TTTTCATAATCGATGGTC-ATCACCATCCA
45787103 TTTTCATTAATCGATGGTCATCA-CATCCA
1 TTTTCA-TAATCGATGGTCATCACCATCCA
* * *
45787132 TTTTCATAGTTGATGGTCATCACCATCCC
1 TTTTCATAATCGATGGTCATCACCATCCA
* * * *
45787161 TTTTCATATTCGATAGTCGTCACCATCCT
1 TTTTCATAATCGATGGTCATCACCATCCA
* * * *
45787190 TTTTCATATTTGATGGTCGTCACCATCCC
1 TTTTCATAATCGATGGTCATCACCATCCA
45787219 TTTTCATAATC
1 TTTTCATAATC
45787230 AACAGCGGAA
Statistics
Matches: 108, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
28 14 0.13
29 82 0.76
30 12 0.11
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (29 bp):
TTTTCATAATCGATGGTCATCACCATCCA
Found at i:45787165 original size:58 final size:58
Alignment explanation
Indices: 45787103--45787229 Score: 184
Period size: 58 Copynumber: 2.2 Consensus size: 58
45787093 AAACCATTCA
*
45787103 TTTTCATTAATCGATGGTCATCA-CATCCATTTTCATAGTTGATGGTCATCACCATCCC
1 TTTTCA-TAATCGATAGTCATCACCATCCATTTTCATAGTTGATGGTCATCACCATCCC
* * * * *
45787161 TTTTCATATTCGATAGTCGTCACCATCCTTTTTCATATTTGATGGTCGTCACCATCCC
1 TTTTCATAATCGATAGTCATCACCATCCATTTTCATAGTTGATGGTCATCACCATCCC
45787219 TTTTCATAATC
1 TTTTCATAATC
45787230 AACAGCGGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 13 0.21
58 48 0.79
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.41
Consensus pattern (58 bp):
TTTTCATAATCGATAGTCATCACCATCCATTTTCATAGTTGATGGTCATCACCATCCC
Found at i:45787246 original size:29 final size:29
Alignment explanation
Indices: 45787214--45787284 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
45787204 GGTCGTCACC
*
45787214 ATCCCTTTTCATAATCAACAGCGGAAGTT
1 ATCCCTTTTCATAATCAACAGCGGAAGCT
* * *
45787243 ATCCCTTTTCATAATTAATAGTGGAAGCT
1 ATCCCTTTTCATAATCAACAGCGGAAGCT
*
45787272 ATCTCTTTTCATA
1 ATCCCTTTTCATA
45787285 TTTGATGGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (29 bp):
ATCCCTTTTCATAATCAACAGCGGAAGCT
Found at i:45791237 original size:21 final size:21
Alignment explanation
Indices: 45791211--45791252 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
45791201 ATCATCATTT
45791211 CTTTGATGTCAATCTCCAAAG
1 CTTTGATGTCAATCTCCAAAG
45791232 CTTTGATGTCAATCTCCAAAG
1 CTTTGATGTCAATCTCCAAAG
45791253 ATTGGCGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (21 bp):
CTTTGATGTCAATCTCCAAAG
Found at i:45793075 original size:24 final size:24
Alignment explanation
Indices: 45793025--45793076 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
45793015 AATCAATGTC
* *
45793025 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
45793049 AAATATATTATACTAATAAATATT
1 AAATATATTATACTAATAAATACT
45793073 AAAT
1 AAAT
45793077 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:45797369 original size:24 final size:24
Alignment explanation
Indices: 45797342--45797398 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
45797332 AAACCTAATT
* *
45797342 CTAATCAATGTCT-AATATATTATG
1 CTAATAAATGT-TAAATATATTATA
45797366 CTAATAAATGTTAAATATATTATA
1 CTAATAAATGTTAAATATATTATA
45797390 CTAATAAAT
1 CTAATAAAT
45797399 ACTAAATCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 1 0.03
24 29 0.97
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (24 bp):
CTAATAAATGTTAAATATATTATA
Found at i:45797404 original size:24 final size:24
Alignment explanation
Indices: 45797355--45797405 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
45797345 ATCAATGTCT
* **
45797355 AATATATTATGCTAATAAATGTTA
1 AATATATTATACTAATAAATACTA
45797379 AATATATTATACTAATAAATACTA
1 AATATATTATACTAATAAATACTA
45797403 AAT
1 AAT
45797406 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (24 bp):
AATATATTATACTAATAAATACTA
Found at i:45799569 original size:25 final size:25
Alignment explanation
Indices: 45799535--45799583 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
45799525 TATACATCCC
* * *
45799535 CATTTGTTATGAACCTCATTTTATG
1 CATTTATTATCAACATCATTTTATG
45799560 CATTTATTATCAACATCATTTTAT
1 CATTTATTATCAACATCATTTTAT
45799584 TAAAGCTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.49
Consensus pattern (25 bp):
CATTTATTATCAACATCATTTTATG
Found at i:45800944 original size:14 final size:14
Alignment explanation
Indices: 45800925--45800951 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45800915 AAATGATAAC
45800925 AACATAATAGTAAT
1 AACATAATAGTAAT
45800939 AACATAATAGTAA
1 AACATAATAGTAA
45800952 AATGGTAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.26
Consensus pattern (14 bp):
AACATAATAGTAAT
Found at i:45804012 original size:15 final size:14
Alignment explanation
Indices: 45803992--45804022 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
45803982 AAAGATACAA
45803992 TATTTTTAATTCTTT
1 TATTTTTAATT-TTT
45804007 TATTTTTAATTTTT
1 TATTTTTAATTTTT
45804021 TA
1 TA
45804023 ATTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTTTAATTTTT
Found at i:45804022 original size:23 final size:26
Alignment explanation
Indices: 45803994--45804044 Score: 72
Period size: 23 Copynumber: 2.1 Consensus size: 26
45803984 AGATACAATA
45803994 TTTTTAATT-CTTTTA-TT-TTTAAT
1 TTTTTAATTACTTTTATTTGTTTAAT
*
45804017 TTTTTAATTATTTTTATTTGTTTAAT
1 TTTTTAATTACTTTTATTTGTTTAAT
45804043 TT
1 TT
45804045 CTTTTTAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
24 5 0.21
25 2 0.08
26 8 0.33
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (26 bp):
TTTTTAATTACTTTTATTTGTTTAAT
Found at i:45804029 original size:18 final size:19
Alignment explanation
Indices: 45804005--45804057 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
45803995 TTTTAATTCT
45804005 TTTATTTTTAATTTTTTAA
1 TTTATTTTTAATTTTTTAA
45804024 -TTATTTTT-ATTTGTTTAA
1 TTTATTTTTAATTT-TTTAA
*
45804042 TTTCTTTTTAACTTTT
1 TTTATTTTTAA-TTTT
45804058 AGGTTGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 4 0.14
18 13 0.45
19 7 0.24
20 2 0.07
21 3 0.10
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTATTTTTAATTTTTTAA
Found at i:45807439 original size:13 final size:13
Alignment explanation
Indices: 45807367--45807443 Score: 52
Period size: 12 Copynumber: 6.0 Consensus size: 13
45807357 GTTTTTGGAG
45807367 TTATAATTTTTAT
1 TTATAATTTTTAT
* **
45807380 TAACGA-TTTT-T
1 TTATAATTTTTAT
*
45807391 TTATAATATTT-T
1 TTATAATTTTTAT
* *
45807403 TTAGAATTTTTGGAA
1 TTATAATTTTT--AT
45807418 TTATAATTTTTAT
1 TTATAATTTTTAT
*
45807431 TTATTATTTTTAT
1 TTATAATTTTTAT
45807444 AAAATTTAAC
Statistics
Matches: 47, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
11 4 0.09
12 17 0.36
13 16 0.34
15 10 0.21
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (13 bp):
TTATAATTTTTAT
Found at i:45819689 original size:30 final size:30
Alignment explanation
Indices: 45819653--45819731 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
45819643 TTTCAATATT
45819653 TTAAAAGTATAATGATTAAAATTAAT-CAA
1 TTAAAAGTATAATGATTAAAATTAATCCAA
* * *
45819682 GTTAAAAGTACAAAGATTAAAGTTAATCCAA
1 -TTAAAAGTATAATGATTAAAATTAATCCAA
* *
45819713 TTCAAA-TATAATGAATAAA
1 TTAAAAGTATAATGATTAAA
45819732 TTCATAACAT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 10 0.24
30 28 0.68
31 3 0.07
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.30
Consensus pattern (30 bp):
TTAAAAGTATAATGATTAAAATTAATCCAA
Found at i:45819850 original size:2 final size:2
Alignment explanation
Indices: 45819843--45819881 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
45819833 AGATATAGTA
45819843 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
45819882 AAGTGAGGCA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:45837501 original size:22 final size:22
Alignment explanation
Indices: 45837462--45837503 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
45837452 CCAACAACCA
45837462 AAATTTGAAAAAAGTCATTACT
1 AAATTTGAAAAAAGTCATTACT
*
45837484 AAATTTTAAATAAA-TCATTA
1 AAATTTGAAA-AAAGTCATTA
45837504 ATATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (22 bp):
AAATTTGAAAAAAGTCATTACT
Found at i:45837619 original size:16 final size:16
Alignment explanation
Indices: 45837590--45837630 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
45837580 TAGAATCGGC
* *
45837590 ATATTAATATTATTTA
1 ATATTAAAAATATTTA
*
45837606 ATCTTAAAAATATTTA
1 ATATTAAAAATATTTA
45837622 ATATTAAAA
1 ATATTAAAA
45837631 TAATACAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTAAAAATATTTA
Found at i:45863580 original size:18 final size:19
Alignment explanation
Indices: 45863548--45863590 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
45863538 CTCTTCCTCT
*
45863548 TATTTTCTTTCTTTCTTTC
1 TATTTTCTTTCTTTCCTTC
45863567 T-TTTTC-TTCTTTTCCTTC
1 TATTTTCTTTC-TTTCCTTC
45863585 TATTTT
1 TATTTT
45863591 ATTATTCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.14
18 13 0.62
19 5 0.24
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTCTTTCTTTCCTTC
Found at i:45864954 original size:22 final size:22
Alignment explanation
Indices: 45864926--45864971 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
45864916 TTGTACTTGG
45864926 TCTGTTCTGCGATCTTATCTGA
1 TCTGTTCTGCGATCTTATCTGA
* *
45864948 TCTGTTCTGTGATTTTATCTGA
1 TCTGTTCTGCGATCTTATCTGA
45864970 TC
1 TC
45864972 CGTTGCTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (22 bp):
TCTGTTCTGCGATCTTATCTGA
Found at i:45865862 original size:13 final size:13
Alignment explanation
Indices: 45865844--45865869 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45865834 TGGCTAAAAA
45865844 ATTTACTAAAGTT
1 ATTTACTAAAGTT
45865857 ATTTACTAAAGTT
1 ATTTACTAAAGTT
45865870 TAGCAATTGC
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:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
ATTTACTAAAGTT
Found at i:45878503 original size:21 final size:21
Alignment explanation
Indices: 45878479--45878518 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
45878469 TGTATAAAAC
45878479 TTTTACAAAA-AAAAAAAGACA
1 TTTT-CAAAATAAAAAAAGACA
*
45878500 TTTTCAAAATAAATAAAGA
1 TTTTCAAAATAAAAAAAGA
45878519 GTTTTCCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (21 bp):
TTTTCAAAATAAAAAAAGACA
Found at i:45882267 original size:12 final size:12
Alignment explanation
Indices: 45882250--45882274 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45882240 TCATTGAATA
45882250 TGGCTAGAAGTC
1 TGGCTAGAAGTC
45882262 TGGCTAGAAGTC
1 TGGCTAGAAGTC
45882274 T
1 T
45882275 CTCGACTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (12 bp):
TGGCTAGAAGTC
Found at i:45883047 original size:12 final size:13
Alignment explanation
Indices: 45883026--45883069 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
45883016 TGATTAGGTC
*
45883026 AAATAAATTATTA
1 AAATAAATTATAA
45883039 AAA-AAATTATAA
1 AAATAAATTATAA
45883051 AAATAAATTA-AA
1 AAATAAATTATAA
*
45883063 AATTAAA
1 AAATAAA
45883070 AATAGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAATTATAA
Found at i:45883405 original size:28 final size:26
Alignment explanation
Indices: 45883352--45883408 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 26
45883342 TTAAGAAAAA
*
45883352 AAAGGAAATAAATAAAAAAGGTAAAG
1 AAAGGAAATAAATAAAAAAAGTAAAG
45883378 AAAGAGAAATAAGATAAAAGAAAG-AAAG
1 AAAG-GAAATAA-ATAAAA-AAAGTAAAG
45883406 AAA
1 AAA
45883409 TAAAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 4 0.15
27 7 0.26
28 13 0.48
29 3 0.11
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (26 bp):
AAAGGAAATAAATAAAAAAAGTAAAG
Found at i:45883420 original size:24 final size:20
Alignment explanation
Indices: 45883374--45883419 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 20
45883364 TAAAAAAGGT
*
45883374 AAAGAAAGAGAAATAAGATA
1 AAAGAAAGAGAAATAAAATA
45883394 AAAGAAAGAAAGAAATAAAATTA
1 AAAGAAAG--AGAAATAAAA-TA
45883417 AAA
1 AAA
45883420 AATTAAGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
22 9 0.41
23 5 0.23
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (20 bp):
AAAGAAAGAGAAATAAAATA
Found at i:45885565 original size:17 final size:16
Alignment explanation
Indices: 45885543--45885576 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
45885533 TGGGATGGCA
45885543 TTTGTTTGATGTTTATT
1 TTTGTTTG-TGTTTATT
*
45885560 TTTGTTTGTTTTTATT
1 TTTGTTTGTGTTTATT
45885576 T
1 T
45885577 CATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGTTTGTGTTTATT
Found at i:45891215 original size:11 final size:11
Alignment explanation
Indices: 45891199--45891224 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
45891189 TGGTCGAAAA
45891199 ATTTTAATTTT
1 ATTTTAATTTT
45891210 ATTTTAATTTT
1 ATTTTAATTTT
45891221 ATTT
1 ATTT
45891225 ATGTTCAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTTAATTTT
Found at i:45896775 original size:12 final size:13
Alignment explanation
Indices: 45896750--45896778 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
45896740 GACGCTTTAT
45896750 CTATGTCTCCCAC
1 CTATGTCTCCCAC
45896763 CTATGTC-CCCAC
1 CTATGTCTCCCAC
45896775 CTAT
1 CTAT
45896779 CATCCTAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.17, C:0.45, G:0.07, T:0.31
Consensus pattern (13 bp):
CTATGTCTCCCAC
Found at i:45897673 original size:22 final size:22
Alignment explanation
Indices: 45897645--45897690 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
45897635 AGATGTGGAC
45897645 TGCCCTAGCTTAGTATGAATTT
1 TGCCCTAGCTTAGTATGAATTT
*
45897667 TGCCCTAGTTTAGTATGAATTT
1 TGCCCTAGCTTAGTATGAATTT
45897689 TG
1 TG
45897691 GTTAACTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (22 bp):
TGCCCTAGCTTAGTATGAATTT
Found at i:45898086 original size:20 final size:20
Alignment explanation
Indices: 45898057--45898202 Score: 114
Period size: 20 Copynumber: 7.3 Consensus size: 20
45898047 TATGTGAATA
* *
45898057 TACTTCGGTACTCTTGTTTG
1 TACTTCGATACTCTTGTATG
* * * * *
45898077 TACTTTGGTACCCATGTTTG
1 TACTTCGATACTCTTGTATG
*
45898097 TACTTCAATACTCTTGTATG
1 TACTTCGATACTCTTGTATG
* * *
45898117 TATTTAGATACTCCTGTATG
1 TACTTCGATACTCTTGTATG
* * * * *
45898137 TACTTCGGTATTCCTATTTG
1 TACTTCGATACTCTTGTATG
45898157 TACTTCGATACTCTTGTATG
1 TACTTCGATACTCTTGTATG
* * *
45898177 TACTTC-ATACCCCTGTTTG
1 TACTTCGATACTCTTGTATG
45898196 TACTTCG
1 TACTTCG
45898203 GTATTCCTAT
Statistics
Matches: 98, Mismatches: 27, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
19 16 0.16
20 82 0.84
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.46
Consensus pattern (20 bp):
TACTTCGATACTCTTGTATG
Found at i:45900651 original size:16 final size:17
Alignment explanation
Indices: 45900622--45900653 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
45900612 ACTAGGACAA
45900622 AAAGAAATAGAAAAATG
1 AAAGAAATAGAAAAATG
45900639 AAAGAAA-AGAAAAAT
1 AAAGAAATAGAAAAAT
45900654 AATGATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (17 bp):
AAAGAAATAGAAAAATG
Found at i:45900965 original size:68 final size:69
Alignment explanation
Indices: 45900860--45901007 Score: 185
Period size: 69 Copynumber: 2.2 Consensus size: 69
45900850 AAAAAAAAAA
* * * *
45900860 GGGAAG-ACATACTCCTTGTTTCTTTAAACAAGGGAGAATGACCT-CTATTGTGTTTCTTAAAAA
1 GGGAAGAACATGCTCCTTATTTCTCTAAACAAGGGAGAACGACCTACTATTGTGTTTCTTAAAAA
45900923 TAGT
66 TAGT
* * *
45900927 GGGAAGAACATGCTCTTTATTTCTCTAAA-AAGGTGAGAACGACCTATTTTTGTGTTTCTTAAAA
1 GGGAAGAACATGCTCCTTATTTCTCTAAACAAGG-GAGAACGACCTACTATTGTGTTTCTTAAAA
*
45900991 TTAGT
65 ATAGT
*
45900996 AGGAAGAACATG
1 GGGAAGAACATG
45901008 TTTTTATGTA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
67 10 0.14
68 28 0.41
69 31 0.45
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (69 bp):
GGGAAGAACATGCTCCTTATTTCTCTAAACAAGGGAGAACGACCTACTATTGTGTTTCTTAAAAA
TAGT
Found at i:45901991 original size:16 final size:16
Alignment explanation
Indices: 45901945--45901996 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
45901935 GTAAAGGTTG
*
45901945 TTCTAAACAAGAGTTA
1 TTCTCAACAAGAGTTA
**
45901961 TT-TCATACATTAGTTA
1 TTCTCA-ACAAGAGTTA
*
45901977 TTCTCAACAAGAGTTG
1 TTCTCAACAAGAGTTA
45901993 TTCT
1 TTCT
45901997 TAAATTATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 2 0.07
16 23 0.82
17 3 0.11
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (16 bp):
TTCTCAACAAGAGTTA
Found at i:45905329 original size:9 final size:9
Alignment explanation
Indices: 45905317--45905402 Score: 136
Period size: 9 Copynumber: 9.6 Consensus size: 9
45905307 TCAATTTGGG
45905317 TAATTCGGT
1 TAATTCGGT
*
45905326 TAATTCGGG
1 TAATTCGGT
*
45905335 TAATTTGGT
1 TAATTCGGT
*
45905344 TAATTCGGG
1 TAATTCGGT
45905353 TAATTCGGT
1 TAATTCGGT
*
45905362 TAATTCGGA
1 TAATTCGGT
45905371 TAATTCGGT
1 TAATTCGGT
45905380 TAATTCGGT
1 TAATTCGGT
45905389 TAATTCGGT
1 TAATTCGGT
45905398 TAATT
1 TAATT
45905403 TTTAACCAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 69 1.00
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.43
Consensus pattern (9 bp):
TAATTCGGT
Found at i:45905335 original size:18 final size:18
Alignment explanation
Indices: 45905309--45905402 Score: 152
Period size: 18 Copynumber: 5.2 Consensus size: 18
45905299 GTAGTGATTC
*
45905309 AATTTGGGTAATTCGGTT
1 AATTCGGGTAATTCGGTT
*
45905327 AATTCGGGTAATTTGGTT
1 AATTCGGGTAATTCGGTT
45905345 AATTCGGGTAATTCGGTT
1 AATTCGGGTAATTCGGTT
*
45905363 AATTCGGATAATTCGGTT
1 AATTCGGGTAATTCGGTT
*
45905381 AATTCGGTTAATTCGGTT
1 AATTCGGGTAATTCGGTT
45905399 AATT
1 AATT
45905403 TTTAACCAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 71 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (18 bp):
AATTCGGGTAATTCGGTT
Found at i:45905502 original size:28 final size:29
Alignment explanation
Indices: 45905466--45905645 Score: 105
Period size: 28 Copynumber: 5.8 Consensus size: 29
45905456 CGAATTAACC
45905466 GAAAAAATTTCGG-TCGGTTAATTTTTTT
1 GAAAAAATTTCGGTTCGGTTAATTTTTTT
* ****
45905494 GAAAAAATTTCGGTTCGGTTAACCGACCGAATTAACC
1 GAAAAAATTTCGGTTCGGTT-----A---ATTTTTTT
45905531 GAAAAAATTTCGG-TCGGTTAATTTTTTT
1 GAAAAAATTTCGGTTCGGTTAATTTTTTT
* ****
45905559 GAAAAAATTTCGGTTCGGTTAACCGACCGAATTAACC
1 GAAAAAATTTCGGTTCGGTT-----A---ATTTTTTT
45905596 GAAAAAATTTCGG-TCGGTTAATTTTTTT
1 GAAAAAATTTCGGTTCGGTTAATTTTTTT
45905624 GAAAAAATTTCGGTTCGGTTAA
1 GAAAAAATTTCGGTTCGGTTAA
45905646 CGGTTAAAGA
Statistics
Matches: 113, Mismatches: 20, Indels: 37
0.66 0.12 0.22
Matches are distributed among these distances:
28 45 0.40
29 20 0.18
31 2 0.02
34 2 0.02
36 12 0.11
37 32 0.28
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (29 bp):
GAAAAAATTTCGGTTCGGTTAATTTTTTT
Found at i:45905536 original size:37 final size:36
Alignment explanation
Indices: 45905494--45905616 Score: 127
Period size: 37 Copynumber: 3.6 Consensus size: 36
45905484 TAATTTTTTT
45905494 GAAAAAATTTCGGTTCGGTTAACCGACCGAATTAACC
1 GAAAAAATTTCGG-TCGGTTAACCGACCGAATTAACC
* ****
45905531 GAAAAAATTTCGGTCGGTT-----A---ATTTTTTT
1 GAAAAAATTTCGGTCGGTTAACCGACCGAATTAACC
45905559 GAAAAAATTTCGGTTCGGTTAACCGACCGAATTAACC
1 GAAAAAATTTCGG-TCGGTTAACCGACCGAATTAACC
45905596 GAAAAAATTTCGGTCGGTTAA
1 GAAAAAATTTCGGTCGGTTAA
45905617 TTTTTTTGAA
Statistics
Matches: 67, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
28 16 0.24
29 6 0.09
31 1 0.01
34 1 0.01
36 14 0.21
37 29 0.43
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (36 bp):
GAAAAAATTTCGGTCGGTTAACCGACCGAATTAACC
Found at i:45905541 original size:65 final size:65
Alignment explanation
Indices: 45905442--45905646 Score: 410
Period size: 65 Copynumber: 3.2 Consensus size: 65
45905432 TTTTGGTTAA
45905442 TTCGGTTAACCGACCGAATTAACCGAAAAAATTTCGGTCGGTTAATTTTTTTGAAAAAATTTCGG
1 TTCGGTTAACCGACCGAATTAACCGAAAAAATTTCGGTCGGTTAATTTTTTTGAAAAAATTTCGG
45905507 TTCGGTTAACCGACCGAATTAACCGAAAAAATTTCGGTCGGTTAATTTTTTTGAAAAAATTTCGG
1 TTCGGTTAACCGACCGAATTAACCGAAAAAATTTCGGTCGGTTAATTTTTTTGAAAAAATTTCGG
45905572 TTCGGTTAACCGACCGAATTAACCGAAAAAATTTCGGTCGGTTAATTTTTTTGAAAAAATTTCGG
1 TTCGGTTAACCGACCGAATTAACCGAAAAAATTTCGGTCGGTTAATTTTTTTGAAAAAATTTCGG
45905637 TTCGGTTAAC
1 TTCGGTTAAC
45905647 GGTTAAAGAT
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 140 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (65 bp):
TTCGGTTAACCGACCGAATTAACCGAAAAAATTTCGGTCGGTTAATTTTTTTGAAAAAATTTCGG
Found at i:45906702 original size:45 final size:45
Alignment explanation
Indices: 45906638--45906725 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
45906628 GACAATGTTG
* *
45906638 TGAGAGACAAATGCTAGAAACTAAGTAAAAGAGACATTTATATTA
1 TGAGAGACAAATGCTAGAAACTAAGTAAAAGAGAAATATATATTA
* *
45906683 TGAGAGACAAATGTTAGAAACTAATTAAAAGAGAAATATATAT
1 TGAGAGACAAATGCTAGAAACTAAGTAAAAGAGAAATATATAT
45906726 GATCGTTAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (45 bp):
TGAGAGACAAATGCTAGAAACTAAGTAAAAGAGAAATATATATTA
Found at i:45907275 original size:13 final size:13
Alignment explanation
Indices: 45907257--45907281 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45907247 TTTACAAGAG
45907257 TTTATAATTAGAT
1 TTTATAATTAGAT
45907270 TTTATAATTAGA
1 TTTATAATTAGA
45907282 AACATTTTCT
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:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTATAATTAGAT
Found at i:45914691 original size:19 final size:19
Alignment explanation
Indices: 45914669--45914705 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
45914659 ACCACTGTCA
*
45914669 CCCAACGTAATCAAATTTG
1 CCCAACATAATCAAATTTG
*
45914688 CCCACCATAATCAAATTT
1 CCCAACATAATCAAATTT
45914706 ATTATTAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.30, G:0.05, T:0.27
Consensus pattern (19 bp):
CCCAACATAATCAAATTTG
Found at i:45916384 original size:22 final size:22
Alignment explanation
Indices: 45916324--45916384 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
45916314 GCACTAATGA
*
45916324 ACAGAGAGCACTAAAGTGCTAT
1 ACAGAGAGCACTAATGTGCTAT
45916346 ACAGAGAGCAC-ATATGTGCTA-
1 ACAGAGAGCACTA-ATGTGCTAT
*
45916367 ATCGGAGAGCACTAATGT
1 A-CAGAGAGCACTAATGT
45916385 TTTAATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 2 0.06
22 31 0.91
23 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.20
Consensus pattern (22 bp):
ACAGAGAGCACTAATGTGCTAT
Found at i:45925979 original size:41 final size:41
Alignment explanation
Indices: 45925919--45926014 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
45925909 ACAGGGGCCT
* * * *
45925919 GTATGTGCAATTTAGGGGTACCGAAGTACAATCAGGGGCAC
1 GTATGTACAATTCAAGGGTACCGAAGTACAATCAGGGACAC
* * *
45925960 GTATGTATAATTCAAGGGTATCGGAGTACAATCAGGGACAC
1 GTATGTACAATTCAAGGGTACCGAAGTACAATCAGGGACAC
45926001 GTATGTACAATTCA
1 GTATGTACAATTCA
45926015 GGGAATAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (41 bp):
GTATGTACAATTCAAGGGTACCGAAGTACAATCAGGGACAC
Found at i:45926010 original size:20 final size:21
Alignment explanation
Indices: 45925944--45926018 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
45925934 GGGTACCGAA
*
45925944 GTACAA-TCAGGGGCACGTAT
1 GTACAATTCAGGGACACGTAT
* * *
45925964 GTATAATTCAAGGGTA-TCGGA-
1 GTACAATTC-AGGG-ACACGTAT
45925985 GTACAA-TCAGGGACACGTAT
1 GTACAATTCAGGGACACGTAT
45926005 GTACAATTCAGGGA
1 GTACAATTCAGGGA
45926019 ATAATTAACT
Statistics
Matches: 42, Mismatches: 7, Indels: 11
0.70 0.12 0.18
Matches are distributed among these distances:
18 1 0.02
19 7 0.17
20 13 0.31
21 14 0.33
22 7 0.17
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (21 bp):
GTACAATTCAGGGACACGTAT
Found at i:45929938 original size:18 final size:19
Alignment explanation
Indices: 45929915--45929953 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
45929905 ATTTTTAAAT
45929915 ATTTAAT-ATTTTATTTAA
1 ATTTAATGATTTTATTTAA
*
45929933 ATTTAATGTTTTTATTTAA
1 ATTTAATGATTTTATTTAA
45929952 AT
1 AT
45929954 AAACTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTTAATGATTTTATTTAA
Found at i:45932603 original size:14 final size:14
Alignment explanation
Indices: 45932584--45932610 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45932574 CATGATAAAA
45932584 TAAAATACAAGTGG
1 TAAAATACAAGTGG
45932598 TAAAATACAAGTG
1 TAAAATACAAGTG
45932611 TGCAAGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (14 bp):
TAAAATACAAGTGG
Found at i:45948832 original size:104 final size:103
Alignment explanation
Indices: 45948539--45948909 Score: 591
Period size: 105 Copynumber: 3.6 Consensus size: 103
45948529 TAGCCGTTAT
** *
45948539 TGGTGGATCCCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
45948604 AATCAGCACATAGCAACCCCCTTTTTATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
45948642 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
45948707 AATCAGCACATAGCAACCCCCCTTTTCATTTCAAAGATA
66 AATCAGCACATAGCAA-CCCCCTTTTCATTTCAAAGATA
45948746 TGGTGGATATCGCACTTAGCACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
*
45948811 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATA
* * * * * **
45948851 TGGTGGATCA-CGCACATGGCACCACCCATAAATCAGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
45948910 TTTATATACA
Statistics
Matches: 252, Mismatches: 12, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
103 78 0.31
104 85 0.34
105 88 0.35
106 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (103 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATA
Found at i:45958411 original size:25 final size:25
Alignment explanation
Indices: 45958383--45958432 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
45958373 AAAAAATTTC
45958383 CTATTATTATTATTA-TTT-ATTTTTA
1 CTATT-TTATT-TTATTTTCATTTTTA
45958408 CTATTTTATTTTATTTTCATTTTTA
1 CTATTTTATTTTATTTTCATTTTTA
45958433 TTTTTGCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 3 0.13
24 8 0.35
25 12 0.52
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (25 bp):
CTATTTTATTTTATTTTCATTTTTA
Found at i:45958435 original size:6 final size:6
Alignment explanation
Indices: 45958386--45958437 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
45958376 AAATTTCCTA
* *
45958386 TTATTA TTATTAT TTATTT TTACTATT TTA-TT TTATTT TCATTT TTATTT
1 TTATTT TTATT-T TTATTT TTA-T-TT TTATTT TTATTT TTATTT TTATTT
45958436 TT
1 TT
45958438 GCAGGAAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 5 0.13
6 23 0.59
7 6 0.15
8 5 0.13
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (6 bp):
TTATTT
Found at i:45962255 original size:63 final size:63
Alignment explanation
Indices: 45962177--45962302 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
45962167 TTGTATATAA
45962177 TTGTTTGTGTATATGTGTTTAATAAACATTGTTGATAAAGATAAGATATAAATGTGATCAAAG
1 TTGTTTGTGTATATGTGTTTAATAAACATTGTTGATAAAGATAAGATATAAATGTGATCAAAG
45962240 TTGTTTGTGTATATGTGTTTAATAAACATTGTTGATAAAGATAAGATATAAATGTGATCAAAG
1 TTGTTTGTGTATATGTGTTTAATAAACATTGTTGATAAAGATAAGATATAAATGTGATCAAAG
45962303 ACTTGAATGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.40
Consensus pattern (63 bp):
TTGTTTGTGTATATGTGTTTAATAAACATTGTTGATAAAGATAAGATATAAATGTGATCAAAG
Found at i:45966847 original size:2 final size:2
Alignment explanation
Indices: 45966840--45966866 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45966830 CCTGACAATG
45966840 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 T
45966867 GTGCAGGGCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45968408 original size:12 final size:12
Alignment explanation
Indices: 45968393--45968420 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
45968383 TGAGTCTCTT
45968393 TCTCTCTCTCCC
1 TCTCTCTCTCCC
45968405 TCTCTCTCTCCC
1 TCTCTCTCTCCC
45968417 TCTC
1 TCTC
45968421 ATCCCCACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (12 bp):
TCTCTCTCTCCC
Found at i:45969893 original size:9 final size:9
Alignment explanation
Indices: 45969879--45969904 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
45969869 GAGTGCAATA
45969879 CTAAATTGC
1 CTAAATTGC
45969888 CTAAATTGC
1 CTAAATTGC
45969897 CTAAATTG
1 CTAAATTG
45969905 AAGAAGTTTA
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:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (9 bp):
CTAAATTGC
Found at i:45973109 original size:18 final size:18
Alignment explanation
Indices: 45973086--45973120 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
45973076 TTTCAGTACT
45973086 TTGTTCATTTCATGCACC
1 TTGTTCATTTCATGCACC
*
45973104 TTGTTCTTTTCATGCAC
1 TTGTTCATTTCATGCAC
45973121 ACTATTAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.26, G:0.11, T:0.49
Consensus pattern (18 bp):
TTGTTCATTTCATGCACC
Found at i:45974787 original size:12 final size:12
Alignment explanation
Indices: 45974770--45974794 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45974760 GACACTTTAT
45974770 TTCACTTGGAAA
1 TTCACTTGGAAA
45974782 TTCACTTGGAAA
1 TTCACTTGGAAA
45974794 T
1 T
45974795 CAAAGGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TTCACTTGGAAA
Found at i:45976480 original size:2 final size:2
Alignment explanation
Indices: 45976473--45976504 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
45976463 ATTGGTTGAG
*
45976473 AT AT AT AT AT AT CT 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
45976505 TTTGGTTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45976551 original size:23 final size:23
Alignment explanation
Indices: 45976524--45976573 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
45976514 TTGATTACAT
45976524 TTTCTAGGTTGCTTTTGGTGCTA
1 TTTCTAGGTTGCTTTTGGTGCTA
** *
45976547 TTTCTTTGTTGCTTTTGGTGTTA
1 TTTCTAGGTTGCTTTTGGTGCTA
45976570 TTTC
1 TTTC
45976574 ATTGTTGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.06, C:0.12, G:0.22, T:0.60
Consensus pattern (23 bp):
TTTCTAGGTTGCTTTTGGTGCTA
Found at i:45976578 original size:23 final size:23
Alignment explanation
Indices: 45976531--45976609 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
45976521 CATTTTCTAG
*
45976531 GTTGCTTTTGGTGCTATTTCTTT
1 GTTGCTTTTGGTGCTATTTCATT
*
45976554 GTTGCTTTTGGTGTTATTTCATT
1 GTTGCTTTTGGTGCTATTTCATT
* *
45976577 GTTGTTTTTTTGTGCTATTTCATT
1 GTTG-CTTTTGGTGCTATTTCATT
* *
45976601 ATTGTTTTT
1 GTTGCTTTT
45976610 AATGTTGTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
23 30 0.61
24 19 0.39
ACGTcount: A:0.08, C:0.09, G:0.19, T:0.65
Consensus pattern (23 bp):
GTTGCTTTTGGTGCTATTTCATT
Found at i:45976595 original size:24 final size:24
Alignment explanation
Indices: 45976536--45976609 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
45976526 TCTAGGTTGC
* *
45976536 TTTTGGTGCTATTTCTTTGTTG-C
1 TTTTGGTGCTATTTCATTGTTGTT
*
45976559 TTTTGGTGTTATTTCATTGTTGTT
1 TTTTGGTGCTATTTCATTGTTGTT
* *
45976583 TTTTTGTGCTATTTCATTATTGTT
1 TTTTGGTGCTATTTCATTGTTGTT
45976607 TTT
1 TTT
45976610 AATGTTGTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 20 0.45
24 24 0.55
ACGTcount: A:0.08, C:0.08, G:0.18, T:0.66
Consensus pattern (24 bp):
TTTTGGTGCTATTTCATTGTTGTT
Found at i:45983241 original size:30 final size:30
Alignment explanation
Indices: 45983205--45983264 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
45983195 TAACATGTAT
*
45983205 ATGCCTCTAAAATAATAATAAAATTAACAA
1 ATGCCTCTAAAATAATAACAAAATTAACAA
45983235 ATGCCTCTAAAATAATAACAAAATTAACAA
1 ATGCCTCTAAAATAATAACAAAATTAACAA
45983265 TAAAAAAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.57, C:0.15, G:0.03, T:0.25
Consensus pattern (30 bp):
ATGCCTCTAAAATAATAACAAAATTAACAA
Found at i:45986260 original size:18 final size:19
Alignment explanation
Indices: 45986237--45986285 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
45986227 AATCGTGTAG
*
45986237 TTCATTTTCAAAAT-ATTA
1 TTCATTTTCAAAATCACTA
*
45986255 TTCATTTAC-AAATCACTA
1 TTCATTTTCAAAATCACTA
*
45986273 TTCAATTTCAAAA
1 TTCATTTTCAAAA
45986286 CATTTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 4 0.16
18 18 0.72
19 3 0.12
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (19 bp):
TTCATTTTCAAAATCACTA
Found at i:45996524 original size:40 final size:40
Alignment explanation
Indices: 45996469--45996550 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
45996459 AAGCATGTTC
45996469 ACATGCCACTAATTCTGTTAATTGAAAGTATGCAAGGCAT
1 ACATGCCACTAATTCTGTTAATTGAAAGTATGCAAGGCAT
45996509 ACATGCCACTAATTCTGTTAATTGAAAGTATGCAAGGCAT
1 ACATGCCACTAATTCTGTTAATTGAAAGTATGCAAGGCAT
45996549 AC
1 AC
45996551 CCCGATAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (40 bp):
ACATGCCACTAATTCTGTTAATTGAAAGTATGCAAGGCAT
Found at i:45998163 original size:32 final size:32
Alignment explanation
Indices: 45998115--45998182 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
45998105 CCATTACCTA
* * *
45998115 TTATATGTGGATGCCTTTGTGGCTATCTGATG
1 TTATATATGGACGCCTTTGTGGCTATCTAATG
*
45998147 TTATATATGGACGCCTTTGTGGCTATTTAATG
1 TTATATATGGACGCCTTTGTGGCTATCTAATG
45998179 TTAT
1 TTAT
45998183 GGATGCCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.46
Consensus pattern (32 bp):
TTATATATGGACGCCTTTGTGGCTATCTAATG
Found at i:45998196 original size:28 final size:29
Alignment explanation
Indices: 45998152--45998208 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
45998142 TGATGTTATA
*
45998152 TATGGACGCCTTTGTGGCTA-TTTAATGT
1 TATGGACGCCTTCGTGGCTACTTTAATGT
* *
45998180 TATGGATGCCTTCGTGGCTACTTTTATGT
1 TATGGACGCCTTCGTGGCTACTTTAATGT
45998209 ATAGACTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.44
Consensus pattern (29 bp):
TATGGACGCCTTCGTGGCTACTTTAATGT
Found at i:46026752 original size:48 final size:50
Alignment explanation
Indices: 46026692--46026788 Score: 135
Period size: 51 Copynumber: 2.0 Consensus size: 50
46026682 TAAGCTAAAT
46026692 TAAATTACAT-A-AACAACCAAAATTGATAATTAATTCCAAGCATAATTC
1 TAAATTACATAACAACAACCAAAATTGATAATTAATTCCAAGCATAATTC
* * * *
46026740 TAAATTATATAAACAACAACCAAAATTGGTCATTAGTTCCAAGCATAAT
1 TAAATTACAT-AACAACAACCAAAATTGATAATTAATTCCAAGCATAAT
46026789 GTATATCAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
48 9 0.21
50 1 0.02
51 32 0.76
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.29
Consensus pattern (50 bp):
TAAATTACATAACAACAACCAAAATTGATAATTAATTCCAAGCATAATTC
Found at i:46027283 original size:15 final size:15
Alignment explanation
Indices: 46027263--46027293 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
46027253 AACAAACCCC
46027263 AAATCATCCAAATTG
1 AAATCATCCAAATTG
46027278 AAATCATCCAAATTG
1 AAATCATCCAAATTG
46027293 A
1 A
46027294 CAACAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (15 bp):
AAATCATCCAAATTG
Found at i:46032246 original size:14 final size:15
Alignment explanation
Indices: 46032227--46032255 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46032217 ATTCCACATA
46032227 CAAAAA-CATATTTC
1 CAAAAAGCATATTTC
46032241 CAAAAAGCATATTTC
1 CAAAAAGCATATTTC
46032256 TTAAAACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.28
Consensus pattern (15 bp):
CAAAAAGCATATTTC
Found at i:46049700 original size:26 final size:25
Alignment explanation
Indices: 46049669--46049722 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
46049659 TATGATTTTA
*
46049669 ATTGTGTCTTAAATATGTCTTAGTTT
1 ATTGTGTCTTAAACATGTCTT-GTTT
* *
46049695 ATTGTGTTTTTAACATGTCTTGTTT
1 ATTGTGTCTTAAACATGTCTTGTTT
46049720 ATT
1 ATT
46049723 ATATTTTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.20, C:0.07, G:0.15, T:0.57
Consensus pattern (25 bp):
ATTGTGTCTTAAACATGTCTTGTTT
Found at i:46057378 original size:2 final size:2
Alignment explanation
Indices: 46057371--46057414 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
46057361 TTATTTAGTG
46057371 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
46057413 TA
1 TA
46057415 AGTGGAAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46059086 original size:57 final size:59
Alignment explanation
Indices: 46058976--46059122 Score: 201
Period size: 57 Copynumber: 2.5 Consensus size: 59
46058966 ATTGACGGTA
*
46058976 AAAAGGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTG
1 AAAATGATCTAGCCCGGACGGGTGATCC-AT-CTGATATAGCCCTCCCGAAGAATATGTG-G
*
46059038 AAAATGATCTAGCCCGGATGGGTGAT-C-T-TGATATAGCCCTCCCGAAGAATATGTGG
1 AAAATGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
* *
46059094 AAAATGGATTTAGCCCGGACGGGTAATCC
1 AAAAT-GATCTAGCCCGGACGGGTGATCC
46059123 GAATTAGGGT
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
56 6 0.08
57 45 0.58
58 1 0.01
59 1 0.01
61 1 0.01
62 24 0.31
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.23
Consensus pattern (59 bp):
AAAATGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:46059352 original size:67 final size:67
Alignment explanation
Indices: 46059244--46059375 Score: 219
Period size: 67 Copynumber: 2.0 Consensus size: 67
46059234 GTTTATATTA
* * *
46059244 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCACTATAAGAAATGAGGTTCGCAGGAGTGTGCTCTCT
46059309 TG
66 TG
* *
46059311 CAGGGGATTTAGCCTGGATTGGTAATCCCACTATAAGAAATGAGGTTTGCAGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCACTATAAGAAATGAGGTTCGCAGGAGTGTGCTCTCT
46059376 GAATTGGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (67 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCACTATAAGAAATGAGGTTCGCAGGAGTGTGCTCTCT
TG
Found at i:46059566 original size:26 final size:27
Alignment explanation
Indices: 46059503--46059566 Score: 62
Period size: 26 Copynumber: 2.4 Consensus size: 27
46059493 GATAAGTACT
46059503 TAAAATAATGAAATTAAACTTGAAATACA
1 TAAAAT-ATGAAATT-AACTTGAAATACA
* *
46059532 TAGAA-ATGATAATT-ACTTGATATAC-
1 TAAAATATGA-AATTAACTTGAAATACA
46059557 TAAAATATGA
1 TAAAATATGA
46059567 CATGGAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
25 4 0.13
26 14 0.47
27 4 0.13
28 4 0.13
29 4 0.13
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.31
Consensus pattern (27 bp):
TAAAATATGAAATTAACTTGAAATACA
Found at i:46062725 original size:20 final size:20
Alignment explanation
Indices: 46062700--46062738 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
46062690 TACTTTCTTC
46062700 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
46062720 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
46062739 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:46063056 original size:50 final size:50
Alignment explanation
Indices: 46062940--46063125 Score: 177
Period size: 50 Copynumber: 3.7 Consensus size: 50
46062930 GATAATAACA
* *
46062940 TGCCAAAT-CCATGTCCCAGACATGGTCTTACATGGGATGTT-TCCTGTAC--
1 TGCC-AATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGG
* * *
46062989 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
** *
46063039 TGCCAATGCCATGTCCCAGACATGGTCTT--ATGGAGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-G-GGAGTTCTCATATCGG
* * * *
46063089 TGTCAACGCCATGTCCTAGACATGGTCTTACGTGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
46063126 CCTATCATAA
Statistics
Matches: 114, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
48 9 0.08
49 35 0.31
50 68 0.60
51 1 0.01
52 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
Found at i:46063127 original size:50 final size:50
Alignment explanation
Indices: 46062948--46063181 Score: 168
Period size: 50 Copynumber: 4.6 Consensus size: 50
46062938 CATGCCAAAT
* ** * * * *
46062948 CCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTAC--TGCCAATG
1 CCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATAT-CGGTGCCAACG
* * * * ** *
46062997 CCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCGGTGCCAACG
* * *
46063047 CCATGTCCCAGACATGGTCTTATG-GAGGACCTCTCATCTCGGTGTCAACG
1 CCATGTCCCAGACATGGTCTTACGTG-GGACCTCTCATATCGGTGCCAACG
* * ** * *
46063097 CCATGTCCTAGACATGGTCTTACGTGGGACCTATCATAACCTCAATAATTCCAATG
1 CCATGTCCCAGACATGGTCTTACGTGGGACCTCTCAT-A--TC---GGTGCCAACG
46063153 CCATGTCCCAGACATGGTCTTACGTGGGA
1 CCATGTCCCAGACATGGTCTTACGTGGGA
46063182 TCTCATTCCT
Statistics
Matches: 147, Mismatches: 28, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
48 1 0.01
49 32 0.22
50 78 0.53
51 1 0.01
53 2 0.01
56 33 0.22
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATATCGGTGCCAACG
Found at i:46074196 original size:28 final size:28
Alignment explanation
Indices: 46074156--46074210 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
46074146 ACTTTGAATT
46074156 AAACCAAAGAATAACAATCAAAATAATC
1 AAACCAAAGAATAACAATCAAAATAATC
46074184 AAACCAAAGAATAACAATCAAAATAAT
1 AAACCAAAGAATAACAATCAAAATAAT
46074211 AATTCATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.65, C:0.16, G:0.04, T:0.15
Consensus pattern (28 bp):
AAACCAAAGAATAACAATCAAAATAATC
Found at i:46074205 original size:14 final size:14
Alignment explanation
Indices: 46074160--46074205 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
46074150 TGAATTAAAC
46074160 CAAAGAATAACAAT
1 CAAAGAATAACAAT
*
46074174 C-AA-AATAATCAAAC
1 CAAAGAATAA-C-AAT
46074188 CAAAGAATAACAAT
1 CAAAGAATAACAAT
46074202 CAAA
1 CAAA
46074206 ATAATAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
12 5 0.19
13 3 0.12
14 10 0.38
15 3 0.12
16 5 0.19
ACGTcount: A:0.65, C:0.17, G:0.04, T:0.13
Consensus pattern (14 bp):
CAAAGAATAACAAT
Found at i:46074702 original size:34 final size:32
Alignment explanation
Indices: 46074641--46074714 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 32
46074631 GACTCCTTTA
* * *
46074641 TAATTTATAAAACTTTAAACTATTAATAATAAAAT
1 TAATTT-T-AAACCTTAAAATAATAAT-ATAAAAT
46074676 TACATTTTAAACCTTAAAATAATAATATAAAAT
1 TA-ATTTTAAACCTTAAAATAATAATATAAAAT
46074709 TAATTT
1 TAATTT
46074715 ATTTCTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
32 4 0.11
33 9 0.26
34 15 0.43
35 3 0.09
36 4 0.11
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.41
Consensus pattern (32 bp):
TAATTTTAAACCTTAAAATAATAATATAAAAT
Found at i:46081005 original size:20 final size:22
Alignment explanation
Indices: 46080967--46081006 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
46080957 AATAATTATC
46080967 ATTTCTATGTATTTCAAGTATA
1 ATTTCTATGTATTTCAAGTATA
*
46080989 ATTTC-ATG-ATTTTAAGTA
1 ATTTCTATGTATTTCAAGTA
46081007 CTTATCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 3 0.18
22 5 0.29
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (22 bp):
ATTTCTATGTATTTCAAGTATA
Found at i:46082129 original size:2 final size:2
Alignment explanation
Indices: 46082122--46082165 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
46082112 ATATTCATTC
46082122 AT AT AT AT 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 AT AT AT AT
46082164 AT
1 AT
46082166 TCCTCCTCCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46083265 original size:8 final size:8
Alignment explanation
Indices: 46083252--46083276 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
46083242 ATATATACTA
46083252 AATAAAAT
1 AATAAAAT
46083260 AATAAAAT
1 AATAAAAT
46083268 AATAAAAT
1 AATAAAAT
46083276 A
1 A
46083277 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:46096772 original size:76 final size:76
Alignment explanation
Indices: 46096495--46096776 Score: 318
Period size: 76 Copynumber: 3.7 Consensus size: 76
46096485 TGACATTAGA
* * * * ** *
46096495 TGTGCCCTGCACTAGTCGAATAAATTGACAAAGACTTGCA-CAAAATGATAGTCAGATTAACTGA
1 TGTGCCCAGCACTAGTCGAATAAATCGACAAAGATTTGCATC-TAGCGCTAGTCAGATTAACTGA
46096559 CAATATTAATTG
65 CAATATTAATTG
* * * ** *
46096571 TGTGCCCAACACTAGTCGAATAAATTGACAAAGATTT--ATGCCTAGCACTACACATATTAACTG
1 TGTGCCCAGCACTAGTCGAATAAATCGACAAAGATTTGCAT--CTAGCGCTAGTCAGATTAACTG
** *
46096634 ATGATATTAATTA
64 ACAATATTAATTG
* * *
46096647 TGTGCCCAGCACTAGTCGAATAAATGGACAAAGATTTGCACCTAACGCTAGTCAGATTAACTGAC
1 TGTGCCCAGCACTAGTCGAATAAATCGACAAAGATTTGCATCTAGCGCTAGTCAGATTAACTGAC
46096712 AATATTAATTG
66 AATATTAATTG
** *
46096723 TGTGCCCAGCTGTAGTTGAATAAATCGACAAAGATTTGCATCTAGCGCTAGTCA
1 TGTGCCCAGCACTAGTCGAATAAATCGACAAAGATTTGCATCTAGCGCTAGTCA
46096777 TATAAACCAA
Statistics
Matches: 170, Mismatches: 31, Indels: 10
0.81 0.15 0.05
Matches are distributed among these distances:
74 1 0.01
76 167 0.98
77 1 0.01
78 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (76 bp):
TGTGCCCAGCACTAGTCGAATAAATCGACAAAGATTTGCATCTAGCGCTAGTCAGATTAACTGAC
AATATTAATTG
Found at i:46107269 original size:5 final size:5
Alignment explanation
Indices: 46107259--46107304 Score: 60
Period size: 5 Copynumber: 9.2 Consensus size: 5
46107249 TCCTTACTTA
46107259 TATTT TATTT T-TGTT TA-TT TATTT TATTT TATGTT TATTT TATTT T
1 TATTT TATTT TAT-TT TATTT TATTT TATTT TAT-TT TATTT TATTT T
46107305 TAGTCCTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
4 5 0.14
5 27 0.73
6 5 0.14
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:46107295 original size:20 final size:20
Alignment explanation
Indices: 46107259--46107304 Score: 76
Period size: 19 Copynumber: 2.3 Consensus size: 20
46107249 TCCTTACTTA
46107259 TATTTTATTTTTGTTTA-TT
1 TATTTTATTTTTGTTTATTT
46107278 TATTTTATTTTATGTTTATTT
1 TATTTTATTTT-TGTTTATTT
46107299 TATTTT
1 TATTTT
46107305 TAGTCCTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 11 0.44
20 6 0.24
21 8 0.32
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.78
Consensus pattern (20 bp):
TATTTTATTTTTGTTTATTT
Found at i:46107297 original size:11 final size:11
Alignment explanation
Indices: 46107262--46107306 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
46107252 TTACTTATAT
46107262 TTTATTTT-TG
1 TTTATTTTATG
46107272 TTTA-TTTAT-
1 TTTATTTTATG
46107281 TTTATTTTATG
1 TTTATTTTATG
*
46107292 TTTATTTTATT
1 TTTATTTTATG
46107303 TTTA
1 TTTA
46107307 GTCCTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
9 7 0.23
10 10 0.32
11 14 0.45
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (11 bp):
TTTATTTTATG
Found at i:46109459 original size:47 final size:46
Alignment explanation
Indices: 46109390--46109479 Score: 171
Period size: 47 Copynumber: 1.9 Consensus size: 46
46109380 AAATGAGGTT
46109390 TTAGTTTACTCTTATTCTTATTATTTAGTAAAAAAATAAAAAAAAAG
1 TTAGTTTACTCTTATTCTTATTATTTAGT-AAAAAATAAAAAAAAAG
46109437 TTAGTTTACTCTTATTCTTATTATTTAGTAAAAAATAAAAAAA
1 TTAGTTTACTCTTATTCTTATTATTTAGTAAAAAATAAAAAAA
46109480 TAATGTGATT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 14 0.33
47 29 0.67
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.42
Consensus pattern (46 bp):
TTAGTTTACTCTTATTCTTATTATTTAGTAAAAAATAAAAAAAAAG
Found at i:46116659 original size:21 final size:21
Alignment explanation
Indices: 46116630--46116685 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
46116620 GAATGACAAA
*
46116630 TCAGATTTTTCTTCTTAATTT
1 TCAGCTTTTTCTTCTTAATTT
*
46116651 TCAGCTTTTTCTTCTTGATTT
1 TCAGCTTTTTCTTCTTAATTT
46116672 TCAGCTTTTTCTTC
1 TCAGCTTTTTCTTC
46116686 CTAAAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.12, C:0.20, G:0.07, T:0.61
Consensus pattern (21 bp):
TCAGCTTTTTCTTCTTAATTT
Done.