Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_14 ID=scaffold_14-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: 2042280
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 64439 characters in sequence are not A, C, G, or T
File 7 of 7
Found at i:1758927 original size:38 final size:39
Alignment explanation
Indices: 1758876--1759061 Score: 111
Period size: 38 Copynumber: 4.8 Consensus size: 39
1758866 TTATAGTATC
*
1758876 ATATATT-ATAATTTTAGTAAATTCATATAAGAATATTG
1 ATATATTAAGAATTTTAGTAAATTCATATAAGAATATTG
* ** **
1758914 AT-TATTAAGAATTTTATTAAA-TCATATATTTTAAT-TAAA
1 ATATATTAAGAATTTTAGTAAATTCATATA--AGAATAT-TG
* * * * *
1758953 ATATATTTAATAATAATTATGTTAAATT-ATATTTTATAGTATT-
1 ATATA-TTAAGAAT-TTTA-G-TAAATTCATA--TAAGAATATTG
*
1758996 ATATATT-ATAATTTTAGTAAATTCATATAAGAATATTG
1 ATATATTAAGAATTTTAGTAAATTCATATAAGAATATTG
*
1759034 AT-TATTAAGAATTTTATTAAA-TCATATA
1 ATATATTAAGAATTTTAGTAAATTCATATA
1759062 TTTTAATTAA
Statistics
Matches: 113, Mismatches: 19, Indels: 33
0.68 0.12 0.20
Matches are distributed among these distances:
37 29 0.26
38 35 0.31
39 9 0.08
40 5 0.04
41 12 0.11
42 5 0.04
43 5 0.04
44 10 0.09
45 2 0.02
46 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (39 bp):
ATATATTAAGAATTTTAGTAAATTCATATAAGAATATTG
Found at i:1759297 original size:44 final size:45
Alignment explanation
Indices: 1759234--1759331 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 45
1759224 CTATTACACC
*
1759234 TCCATTCCATTCAACCAAACACA-AGA-ATACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGATATACTATTACGCCTCTAT
* * *
1759278 TCCATTACATTCAACCAAACAATTGATTTGCTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAATAGATATACTATTACGCCTCTAT
1759323 TCCATTACA
1 TCCATTACA
1759332 CCTCTATTCC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
43 1 0.02
44 22 0.46
45 25 0.52
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.32
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGATATACTATTACGCCTCTAT
Found at i:1759335 original size:16 final size:16
Alignment explanation
Indices: 1759316--1759363 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
1759306 TGCTATTACG
*
1759316 CCTCTATTCCATTACA
1 CCTCTATTCCAATACA
*
1759332 CCTCTATTCCAATACG
1 CCTCTATTCCAATACA
*
1759348 CTTCTATTCCAATACA
1 CCTCTATTCCAATACA
1759364 GTGAACCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.27, C:0.35, G:0.02, T:0.35
Consensus pattern (16 bp):
CCTCTATTCCAATACA
Found at i:1759781 original size:12 final size:12
Alignment explanation
Indices: 1759764--1759793 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1759754 CCTTAGACGC
1759764 CCGTGTGCTAGA
1 CCGTGTGCTAGA
*
1759776 CCGTGTGCTAGG
1 CCGTGTGCTAGA
1759788 CCGTGT
1 CCGTGT
1759794 AACTGCCTGA
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:0.10, C:0.27, G:0.37, T:0.27
Consensus pattern (12 bp):
CCGTGTGCTAGA
Found at i:1761038 original size:50 final size:49
Alignment explanation
Indices: 1760969--1761087 Score: 148
Period size: 50 Copynumber: 2.4 Consensus size: 49
1760959 GTACATGTAT
* * * ** * *
1760969 GCTCATACGAGCTGTGAATCGGTTTGCTCTCATGAGTTGTAAATTGGTAA
1 GCTCATACGAGTTGAGAATCGATAAGCTCTCATGAGTTG-AAATCGATAA
*
1761019 GCTCGTACGAGTTGAGAATCGATAAGCTCTCATGAGTTGAAATCGATAA
1 GCTCATACGAGTTGAGAATCGATAAGCTCTCATGAGTTGAAATCGATAA
*
1761068 ACTCATACGAGTTGAGAATC
1 GCTCATACGAGTTGAGAATC
1761088 AGTAAGTCTT
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
49 26 0.44
50 33 0.56
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (49 bp):
GCTCATACGAGTTGAGAATCGATAAGCTCTCATGAGTTGAAATCGATAA
Found at i:1761044 original size:25 final size:24
Alignment explanation
Indices: 1761016--1761087 Score: 92
Period size: 24 Copynumber: 2.9 Consensus size: 24
1761006 TGTAAATTGG
1761016 TAAGCTCGTACGAGTTGAGAATCGA
1 TAAGCTC-TACGAGTTGAGAATCGA
*
1761041 TAAGCTCTCATGAGTTGA-AATCGA
1 TAAGCTCT-ACGAGTTGAGAATCGA
*
1761065 TAAACTCATACGAGTTGAGAATC
1 TAAGCTC-TACGAGTTGAGAATC
1761088 AGTAAGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 21 0.51
25 20 0.49
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (24 bp):
TAAGCTCTACGAGTTGAGAATCGA
Found at i:1761067 original size:24 final size:24
Alignment explanation
Indices: 1760994--1761067 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 24
1760984 GAATCGGTTT
* *
1760994 GCTCTCATGAGTTGTAAATTGGTAA
1 GCTCTCATGAGTTG-AAATCGATAA
*
1761019 GCTCGT-ACGAGTTGAGAATCGATAA
1 GCTC-TCATGAGTTGA-AATCGATAA
1761044 GCTCTCATGAGTTGAAATCGATAA
1 GCTCTCATGAGTTGAAATCGATAA
1761068 ACTCATACGA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
24 11 0.26
25 30 0.71
26 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (24 bp):
GCTCTCATGAGTTGAAATCGATAA
Found at i:1762881 original size:24 final size:24
Alignment explanation
Indices: 1762833--1762879 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1762823 ACTGGTTATA
*
1762833 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGCATATTTG
*
1762857 GAGAGATTTGAGGAGAGCATATT
1 GAGAGAATTGAGGAG-GCATATT
1762880 GGGATTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.34, C:0.02, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGCATATTTG
Found at i:1763639 original size:27 final size:26
Alignment explanation
Indices: 1763609--1763857 Score: 275
Period size: 27 Copynumber: 9.3 Consensus size: 26
1763599 TTAATAGATG
* *
1763609 AAAATGATTGAAAGACCACCATAGGGT
1 AAAATGATCGAAATACC-CCATAGGGT
*
1763636 AAAATGATCGAAATACCCCTATAAGGT
1 AAAATGATCGAAATACCCC-ATAGGGT
* *
1763663 AAAATGATTGAAATACCCCCAAAGGGT
1 AAAATGATCGAAATA-CCCCATAGGGT
* ** *
1763690 AAAATTATCGAAATACCCTTTTAAGGT
1 AAAATGATCGAAATACCC-CATAGGGT
* * *
1763717 AAAATGACCGAAATACCCTTATACGGT
1 AAAATGATCGAAATACCC-CATAGGGT
*
1763744 AAAATGACCGAAATACCCTCATAGGGT
1 AAAATGATCGAAATACCC-CATAGGGT
* *
1763771 AAAATAACCGAAATACCCCCATAGGGT
1 AAAATGATCGAAATA-CCCCATAGGGT
1763798 AAAATG-TCTGAAATACCCCTATAGGGT
1 AAAATGATC-GAAATACCCC-ATAGGGT
1763825 AAAATGATCGAAATACCCCATAGGGT
1 AAAATGATCGAAATACCCCATAGGGT
1763851 AAAATGA
1 AAAATGA
1763858 CTGTTATGGC
Statistics
Matches: 194, Mismatches: 21, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
26 24 0.12
27 161 0.83
28 9 0.05
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (26 bp):
AAAATGATCGAAATACCCCATAGGGT
Found at i:1763689 original size:54 final size:54
Alignment explanation
Indices: 1763609--1763857 Score: 306
Period size: 54 Copynumber: 4.6 Consensus size: 54
1763599 TTAATAGATG
* * *
1763609 AAAATGATTGAAAGACCACCATAGGGTAAAATGATCGAAATACCCCTATAAGGT
1 AAAATGATCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCTATAAGGT
* * * * *
1763663 AAAATGATTGAAATACCCCCAAAGGGTAAAATTATCGAAATACCCTTTTAAGGT
1 AAAATGATCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCTATAAGGT
* ** * * *
1763717 AAAATGACCGAAATACCCTTATACGGTAAAATGACCGAAATA-CCCTCATAGGGT
1 AAAATGATCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCT-ATAAGGT
* * *
1763771 AAAATAACCGAAATACCCCCATAGGGTAAAATG-TCTGAAATACCCCTATAGGGT
1 AAAATGATCGAAATACCCCCATAGGGTAAAATGATC-GAAATACCCCTATAAGGT
1763825 AAAATGATCGAAATA-CCCCATAGGGTAAAATGA
1 AAAATGATCGAAATACCCCCATAGGGTAAAATGA
1763858 CTGTTATGGC
Statistics
Matches: 167, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
53 21 0.13
54 142 0.85
55 4 0.02
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (54 bp):
AAAATGATCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCTATAAGGT
Found at i:1764116 original size:26 final size:27
Alignment explanation
Indices: 1764087--1764148 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 27
1764077 GTAGCTTTAT
*
1764087 TGCGATATTGA-TACTGGCAGCTCTGC
1 TGCGATATTGATTACTGGAAGCTCTGC
** *
1764113 TGCGATGCT-ATTACTGGAAGCTTTGC
1 TGCGATATTGATTACTGGAAGCTCTGC
1764139 TGCGATATTG
1 TGCGATATTG
1764149 GTGTGTTGGC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 1 0.04
26 27 0.96
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.34
Consensus pattern (27 bp):
TGCGATATTGATTACTGGAAGCTCTGC
Found at i:1764287 original size:28 final size:29
Alignment explanation
Indices: 1764247--1764419 Score: 232
Period size: 28 Copynumber: 6.2 Consensus size: 29
1764237 TATTGCACTG
**
1764247 CACTG-TTACTGTATTGGGCTAAGGTACA
1 CACTGATTACTGTATTGGGCTAAGGCCCA
1764275 CACTGATT-CTGTATTGGGCTAAGGCCCA
1 CACTGATTACTGTATTGGGCTAAGGCCCA
* *
1764303 CAATGATT-CTGTATTGGGCTAACGCCCA
1 CACTGATTACTGTATTGGGCTAAGGCCCA
*
1764331 CACTGATT-TTGTATTGGGCTAAGGCCCA
1 CACTGATTACTGTATTGGGCTAAGGCCCA
* * *
1764359 AACT-ATTACTATATTGGGCTAAGGCCTA
1 CACTGATTACTGTATTGGGCTAAGGCCCA
1764387 CACTG-TTACTGTATTGGGCTAAGGCCCA
1 CACTGATTACTGTATTGGGCTAAGGCCCA
1764415 CACTG
1 CACTG
1764420 TACTGTCACT
Statistics
Matches: 128, Mismatches: 14, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
27 3 0.02
28 123 0.96
29 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (29 bp):
CACTGATTACTGTATTGGGCTAAGGCCCA
Found at i:1769710 original size:50 final size:50
Alignment explanation
Indices: 1769655--1769799 Score: 209
Period size: 50 Copynumber: 2.9 Consensus size: 50
1769645 TATTGAGATT
* *
1769655 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAG
** * *
1769705 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGATATGGCATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAG
** *
1769755 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCA
1769800 GTACAGAAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 83 1.00
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAG
Found at i:1770079 original size:16 final size:16
Alignment explanation
Indices: 1770053--1770094 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1770043 TTATTTAAGT
*
1770053 AAGCAAGTAAGTAAAC
1 AAGCGAGTAAGTAAAC
* *
1770069 AAGTGAGTAAGTAAAG
1 AAGCGAGTAAGTAAAC
1770085 AAGCGAGTAA
1 AAGCGAGTAA
1770095 AGATTCTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.52, C:0.07, G:0.26, T:0.14
Consensus pattern (16 bp):
AAGCGAGTAAGTAAAC
Found at i:1771970 original size:29 final size:29
Alignment explanation
Indices: 1771895--1771972 Score: 86
Period size: 32 Copynumber: 2.6 Consensus size: 29
1771885 AAGTCATGCA
* * *
1771895 TATATATAATATATGTATAACCACCCTCG
1 TATATATTATATATATACAACCACCCTCG
1771924 TATATCTATGTATATATATACAACC-CCACTCG
1 TATA--TAT-TATATATATACAACCACC-CTCG
1771956 TATATATTATATATATA
1 TATATATTATATATATA
1771973 ACACACATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
29 14 0.33
30 3 0.07
31 5 0.12
32 20 0.48
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (29 bp):
TATATATTATATATATACAACCACCCTCG
Found at i:1776743 original size:51 final size:51
Alignment explanation
Indices: 1776614--1776843 Score: 257
Period size: 50 Copynumber: 4.5 Consensus size: 51
1776604 GGTAAAGAGG
* * * *
1776614 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG-AGG
1 TCCCATGTAAGAGCATGTGTGGGACATGGCATGGGCACCGAGATGAGAAGA
** * * *
1776664 TCCCCCGTAAGAGCATGTGTGGGACATGGCGTGGGCACCGATATGAGAACA
1 TCCCATGTAAGAGCATGTGTGGGACATGGCATGGGCACCGAGATGAGAAGA
* ** * *
1776715 TCCCATGTAAGAGCTTGTGTGGGACATGGTGTTGGCACCGAGATGA-AAGG
1 TCCCATGTAAGAGCATGTGTGGGACATGGCATGGGCACCGAGATGAGAAGA
* * * *
1776765 TCCCCTGTAAGAGCATGTGTGAGACATGGCATGGGCACCGATATGAGAAAA
1 TCCCATGTAAGAGCATGTGTGGGACATGGCATGGGCACCGAGATGAGAAGA
* * *
1776816 TCTCATGTAAGACCATGTCTGGGACATG
1 TCCCATGTAAGAGCATGTGTGGGACATG
1776844 AATTTGGCAT
Statistics
Matches: 147, Mismatches: 31, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
50 81 0.55
51 66 0.45
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.21
Consensus pattern (51 bp):
TCCCATGTAAGAGCATGTGTGGGACATGGCATGGGCACCGAGATGAGAAGA
Found at i:1776791 original size:101 final size:101
Alignment explanation
Indices: 1776614--1776843 Score: 361
Period size: 101 Copynumber: 2.3 Consensus size: 101
1776604 GGTAAAGAGG
*
1776614 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCCCGTAAGAGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAAAGGTCCCCCGTAAGAGCA
* * *
1776679 TGTGTGGGACATGGCGTGGGCACCGATATGAGAACA
66 TGTGTGAGACATGGCATGGGCACCGATATGAGAAAA
* * * ** *
1776715 TCCCATGTAAGAGCTTGTGTGGGACATGGTGTTGGCACCGAGATGAAAGGTCCCCTGTAAGAGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAAAGGTCCCCCGTAAGAGCA
1776780 TGTGTGAGACATGGCATGGGCACCGATATGAGAAAA
66 TGTGTGAGACATGGCATGGGCACCGATATGAGAAAA
*
1776816 TCTCATGTAAGACCATGTCTGGGACATG
1 TCCCATGTAAGACCATGTCTGGGACATG
1776844 AATTTGGCAT
Statistics
Matches: 115, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 115 1.00
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.21
Consensus pattern (101 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAAAGGTCCCCCGTAAGAGCA
TGTGTGAGACATGGCATGGGCACCGATATGAGAAAA
Found at i:1783847 original size:29 final size:30
Alignment explanation
Indices: 1783788--1783845 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1783778 TTCGAACTTT
*
1783788 GGGGCAAAAACATAATTATGTAAAAGTTTA
1 GGGGCAAAAACATAATTATGCAAAAGTTTA
* *
1783818 GGGG-AAAAATCATAATTTTGCCAAAGTT
1 GGGGCAAAAA-CATAATTATGCAAAAGTT
1783846 AGAGTCGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (30 bp):
GGGGCAAAAACATAATTATGCAAAAGTTTA
Found at i:1784740 original size:10 final size:8
Alignment explanation
Indices: 1784720--1784753 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
1784710 TTTTAATATT
1784720 TTATTTAA
1 TTATTTAA
1784728 TTATTCCTAA
1 TTATT--TAA
1784738 TTATTTAA
1 TTATTTAA
1784746 TTATTTAA
1 TTATTTAA
1784754 CCTAATTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (8 bp):
TTATTTAA
Found at i:1784760 original size:31 final size:31
Alignment explanation
Indices: 1784703--1784761 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1784693 ATTTTTAATT
* **
1784703 CTAATTATTTTAATATTTTATTTAATTATTC
1 CTAATTATTTTAATATTTAACCTAATTATTC
1784734 CTAATTA-TTTAATTATTTAACCTAATTA
1 CTAATTATTTTAA-TATTTAACCTAATTA
1784762 CAGTTTCTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (31 bp):
CTAATTATTTTAATATTTAACCTAATTATTC
Found at i:1802770 original size:20 final size:20
Alignment explanation
Indices: 1802734--1802771 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1802724 CTAGGGTATG
*
1802734 GAAAAATTGAATTAAAGGCT
1 GAAAAATTGAATAAAAGGCT
1802754 GAAAAATAT-AATAAAAGG
1 GAAAAAT-TGAATAAAAGG
1802772 TTGTATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.58, C:0.03, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAAATTGAATAAAAGGCT
Found at i:1806143 original size:14 final size:14
Alignment explanation
Indices: 1806124--1806156 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1806114 TTTTTCCAAA
1806124 ACACACA-CTCACAC
1 ACACACACCT-ACAC
1806138 ACACACACCTACAC
1 ACACACACCTACAC
1806152 ACACA
1 ACACA
1806157 AACACATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.45, C:0.48, G:0.00, T:0.06
Consensus pattern (14 bp):
ACACACACCTACAC
Found at i:1810434 original size:17 final size:17
Alignment explanation
Indices: 1810409--1810441 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1810399 CCTTATTTTC
1810409 TGGAAACTTGCCTAATT
1 TGGAAACTTGCCTAATT
*
1810426 TGGATACTTGCCTAAT
1 TGGAAACTTGCCTAAT
1810442 CGAGACTGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (17 bp):
TGGAAACTTGCCTAATT
Found at i:1824058 original size:49 final size:50
Alignment explanation
Indices: 1823937--1824073 Score: 156
Period size: 49 Copynumber: 2.8 Consensus size: 50
1823927 AGGGAATGAG
* *
1823937 ATCCCATGTAAGACCATGTCTGAGACATGGCATGGGCACCGATATGAGAAC
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGATATGAGAAC
* * *
1823988 -TCCCATGTAAGACCATATCTGGGATATGGCATTGGTA-G-TATTG-GAAAC
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGATA-TGAG-AAC
* *
1824036 ATCCCATGTAATACCATGTCTGGGACATGGCTTTGGCA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
1824074 TGTTATTATC
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
47 3 0.04
48 6 0.08
49 32 0.44
50 32 0.44
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (50 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGATATGAGAAC
Found at i:1825847 original size:16 final size:15
Alignment explanation
Indices: 1825821--1825853 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
1825811 ATCTTTTAAA
1825821 TTTATCTAAATAAGT
1 TTTATCTAAATAAGT
1825836 TTTATACTAAATAAGT
1 TTTAT-CTAAATAAGT
1825852 TT
1 TT
1825854 GTAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (15 bp):
TTTATCTAAATAAGT
Found at i:1828286 original size:21 final size:21
Alignment explanation
Indices: 1828247--1828286 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1828237 TTTTGTTTGC
*
1828247 TTTAATAAGTTTTTCTTAAGA
1 TTTAATAAATTTTTCTTAAGA
1828268 TTTAATAAATTATTT-TTAA
1 TTTAATAAATT-TTTCTTAA
1828287 TTGGATTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTAATAAATTTTTCTTAAGA
Found at i:1836929 original size:62 final size:61
Alignment explanation
Indices: 1836834--1837001 Score: 203
Period size: 62 Copynumber: 2.7 Consensus size: 61
1836824 GGCCTCACGG
* * *
1836834 GCAAGGCACACGGGCGTGTGTCTGGGCTGTGTAACTCACTGTTTGTGGTACAAAACCATACT-
1 GCAAGG-ACACGGGCATGTGTCTGGGCCGTGTAACTCACTGTTTGTGGTACAAAACCACA-TA
* * *
1836896 GCCAAGGACACAGGCATGTGTCTGGGCCATGTAACTCACTGTTTGTGGTACAAGACCACATA
1 G-CAAGGACACGGGCATGTGTCTGGGCCGTGTAACTCACTGTTTGTGGTACAAAACCACATA
* * **
1836958 GGAAGGGACACGGGCATGTGCCCAGGCCGTGTAACTCACTGTTT
1 GCAA-GGACACGGGCATGTGTCTGGGCCGTGTAACTCACTGTTT
1837002 ATGCTTTGGA
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
61 3 0.03
62 83 0.91
63 5 0.05
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.23
Consensus pattern (61 bp):
GCAAGGACACGGGCATGTGTCTGGGCCGTGTAACTCACTGTTTGTGGTACAAAACCACATA
Found at i:1839088 original size:26 final size:26
Alignment explanation
Indices: 1839059--1839124 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
1839049 ACACACCAAT
* *
1839059 ATTGTAGCAAAGTTGCCAGTAATAGA
1 ATTGTAGCAAAGCTACCAGTAATAGA
* * *
1839085 ATTGCAGCGAAGCTACCAGTAATAGT
1 ATTGTAGCAAAGCTACCAGTAATAGA
*
1839111 ATATGTGGCAAAGC
1 AT-TGTAGCAAAGC
1839125 CACTAGTACA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
26 23 0.74
27 8 0.26
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (26 bp):
ATTGTAGCAAAGCTACCAGTAATAGA
Found at i:1839323 original size:27 final size:27
Alignment explanation
Indices: 1839293--1839370 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 27
1839283 TCATCTCTTA
*
1839293 GGGGTATAACAGTTATTTTACCCTATG
1 GGGGTATAACAGTCATTTTACCCTATG
** * *
1839320 GGGGTATTTCAGTCCTTTTACCCTTTG
1 GGGGTATAACAGTCATTTTACCCTATG
* ** *
1839347 AGGGTATTTCGGTCATTTTACCCT
1 GGGGTATAACAGTCATTTTACCCT
1839371 TCAAGGGTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.41
Consensus pattern (27 bp):
GGGGTATAACAGTCATTTTACCCTATG
Found at i:1839371 original size:27 final size:27
Alignment explanation
Indices: 1839307--1839450 Score: 148
Period size: 27 Copynumber: 5.3 Consensus size: 27
1839297 TATAACAGTT
* * *
1839307 ATTTTACCCTATGGGGGTATTTCAGTC
1 ATTTTACCCTTTGAGGGTATTTCGGTC
*
1839334 CTTTTACCCTTTGAGGGTATTTCGGTC
1 ATTTTACCCTTTGAGGGTATTTCGGTC
** * *
1839361 ATTTTACCCTTCAAGGGTATTTCCGCC
1 ATTTTACCCTTTGAGGGTATTTCGGTC
*
1839388 ATTTTACCTTTTG-GGCGTATTTCGGTC
1 ATTTTACCCTTTGAGG-GTATTTCGGTC
**
1839415 ATTTTACCC-TCCAGGGGTATTTCGGTC
1 ATTTTACCCTTTGA-GGGTATTTCGGTC
*
1839442 ATCTTACCC
1 ATTTTACCC
1839451 ACAAATCGCA
Statistics
Matches: 96, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
26 3 0.03
27 91 0.95
28 2 0.02
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.41
Consensus pattern (27 bp):
ATTTTACCCTTTGAGGGTATTTCGGTC
Found at i:1839449 original size:54 final size:54
Alignment explanation
Indices: 1839320--1839450 Score: 174
Period size: 54 Copynumber: 2.4 Consensus size: 54
1839310 TTACCCTATG
* *
1839320 GGGGTATTTCAGTCCTTTTACCCTTTGAGGGTATTTCGGTCATTTTACCCTTCA
1 GGGGTATTTCAGTCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCCTCCA
* * * *
1839374 AGGGTATTTCCGCCATTTTACCTTTTG-GGCGTATTTCGGTCATTTTACCCTCCA
1 GGGGTATTTCAGTCATTTTACCCTTTGAGG-GTATTTCGGTCATTTTACCCTCCA
* *
1839428 GGGGTATTTCGGTCATCTTACCC
1 GGGGTATTTCAGTCATTTTACCC
1839451 ACAAATCGCA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 2 0.03
54 63 0.97
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.40
Consensus pattern (54 bp):
GGGGTATTTCAGTCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCCTCCA
Found at i:1861131 original size:23 final size:23
Alignment explanation
Indices: 1861105--1861150 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1861095 ATGAATATAT
*
1861105 AGTTGCTAATTTTGATGGTATTA
1 AGTTGCTAATTTTGATGGAATTA
* *
1861128 AGTTTCTAATTTTGTTGGAATTA
1 AGTTGCTAATTTTGATGGAATTA
1861151 CCTCTTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.26, C:0.04, G:0.20, T:0.50
Consensus pattern (23 bp):
AGTTGCTAATTTTGATGGAATTA
Found at i:1864250 original size:25 final size:25
Alignment explanation
Indices: 1864220--1864270 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1864210 TGTATCATCC
1864220 ATTTCATGTTTCA-ATATATCATGTA
1 ATTTCAT-TTTCATATATATCATGTA
* *
1864245 ATTTCATTTTCATGTATTTCATGTA
1 ATTTCATTTTCATATATATCATGTA
1864270 A
1 A
1864271 AGACCTGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (25 bp):
ATTTCATTTTCATATATATCATGTA
Found at i:1864535 original size:25 final size:25
Alignment explanation
Indices: 1864412--1864537 Score: 82
Period size: 25 Copynumber: 5.1 Consensus size: 25
1864402 ATGCATGTAT
* * *
1864412 GCTCACACGAGCTGTGAATCGGTAT
1 GCTCATACGAGCTGAGAATCGGTAA
* *
1864437 GCTC-TCATGAGTTGTA-AATCGG-ATA
1 GCTCAT-ACGAGCTG-AGAATCGGTA-A
* *
1864462 GTTCATACGAGCTGAGAATTGGTAA
1 GCTCATACGAGCTGAGAATCGGTAA
* * *
1864487 GCTC-TCACGATCTG-CAATCAGTAA
1 GCTCAT-ACGAGCTGAGAATCGGTAA
*
1864511 GCTCATACAAGCTGAGAATCGGTAA
1 GCTCATACGAGCTGAGAATCGGTAA
1864536 GC
1 GC
1864538 CCTAATGACA
Statistics
Matches: 74, Mismatches: 18, Indels: 18
0.67 0.16 0.16
Matches are distributed among these distances:
24 20 0.27
25 52 0.70
26 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (25 bp):
GCTCATACGAGCTGAGAATCGGTAA
Found at i:1871967 original size:25 final size:26
Alignment explanation
Indices: 1871939--1872023 Score: 83
Period size: 25 Copynumber: 3.4 Consensus size: 26
1871929 ACGAGCGGTA
*
1871939 AATCGGTAAGCTCAT-TCTAGCTAAG
1 AATCGGTAAGCTCATATCGAGCTAAG
*
1871964 AATCAGTAAGCTC-TCA-CGAGCT--G
1 AATCGGTAAGCTCAT-ATCGAGCTAAG
*
1871987 CAATCGTTAAGCTCATAT-GAGCTAAG
1 -AATCGGTAAGCTCATATCGAGCTAAG
1872013 AATCGGTAAGC
1 AATCGGTAAGC
1872024 CCTAATGACA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
23 1 0.02
24 18 0.38
25 28 0.58
26 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (26 bp):
AATCGGTAAGCTCATATCGAGCTAAG
Found at i:1888538 original size:22 final size:21
Alignment explanation
Indices: 1888500--1888542 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1888490 GCAAACCCAT
*
1888500 CCCAATCCAACCAACACACCA
1 CCCAAACCAACCAACACACCA
1888521 CCCAAACCAACCCAACACACCA
1 CCCAAACCAA-CCAACACACCA
1888543 TGTGGGGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.44, C:0.53, G:0.00, T:0.02
Consensus pattern (21 bp):
CCCAAACCAACCAACACACCA
Found at i:1888755 original size:32 final size:32
Alignment explanation
Indices: 1888687--1888953 Score: 202
Period size: 32 Copynumber: 8.4 Consensus size: 32
1888677 GAATGACTAC
* * * *
1888687 AAGCCATAAGT-ACAGTAATGTGATTGGCACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
** *
1888718 AAGCCATCAGTATTAGTGATATGATCAGCACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
* * * * *
1888750 CAGCCATCAATAACGGTAACATGATCGGCACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
* * *
1888782 AAGCCATCAGTAGCAGTGTTATGATTGGCACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
* * * *
1888814 TAGCCATCAGTAACAGTGAAATGACCGACACA
1 AAGCCATCAGTAACAGTGATATGATCGGCACA
* * * *
1888846 CAGCCATCGGTAAC-GATAATATGATTGGCACA
1 AAGCCATCAGTAACAG-TGATATGATCGGCACA
* *
1888878 AAGCCATCAATAAC-GAT-ACTGTGATCGGCACA
1 AAGCCATCAGTAACAG-TGA-TATGATCGGCACA
* ** *
1888910 AAGCCATCAATAATGGT-ACTATGATCGACACA
1 AAGCCATCAGTAACAGTGA-TATGATCGGCACA
1888942 AAGCCATCAGTA
1 AAGCCATCAGTA
1888954 GTATCGTAGC
Statistics
Matches: 186, Mismatches: 46, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
31 12 0.06
32 173 0.93
33 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTGATATGATCGGCACA
Found at i:1888939 original size:96 final size:96
Alignment explanation
Indices: 1888698--1888950 Score: 278
Period size: 96 Copynumber: 2.6 Consensus size: 96
1888688 AGCCATAAGT
* *
1888698 ACAGTAATGTGATTGGCACAAAGCCATCAGTATTAGTGATATGATC-AGCACACAGCCATCAATA
1 ACAGTACTGTGATTGGCACAAAGCCATCAGTAATAGTGATATGATCGA-CACACAGCCATCAATA
* *
1888762 ACGGTAACATGATCGGCACAAAGCCATCAGTA
65 ACGATAACATGATCGGCACAAAGCCATCAATA
* ** * * * * * **
1888794 GCAGTGTTATGATTGGCACATAGCCATCAGTAACAGTGAAATGACCGACACACAGCCATCGGTAA
1 ACAGTACTGTGATTGGCACAAAGCCATCAGTAATAGTGATATGATCGACACACAGCCATCAATAA
* *
1888859 CGATAATATGATTGGCACAAAGCCATCAATA
66 CGATAACATGATCGGCACAAAGCCATCAATA
* * * *
1888890 AC-GATACTGTGATCGGCACAAAGCCATCAATAATGGT-ACTATGATCGACACAAAGCCATCA
1 ACAG-TACTGTGATTGGCACAAAGCCATCAGTAATAGTGA-TATGATCGACACACAGCCATCA
1888951 GTAGTATCGT
Statistics
Matches: 126, Mismatches: 28, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
95 2 0.02
96 123 0.98
97 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (96 bp):
ACAGTACTGTGATTGGCACAAAGCCATCAGTAATAGTGATATGATCGACACACAGCCATCAATAA
CGATAACATGATCGGCACAAAGCCATCAATA
Found at i:1888984 original size:26 final size:26
Alignment explanation
Indices: 1888955--1889026 Score: 126
Period size: 26 Copynumber: 2.8 Consensus size: 26
1888945 CCATCAGTAG
*
1888955 TATCGTAGCAAAGCTGCCAGCATAAA
1 TATCGCAGCAAAGCTGCCAGCATAAA
1888981 TATCGCAGCAAAGCTGCCAGCATAAA
1 TATCGCAGCAAAGCTGCCAGCATAAA
*
1889007 TATCGCAGCAAAACTGCCAG
1 TATCGCAGCAAAGCTGCCAG
1889027 TAATAGTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGCATAAA
Found at i:1889303 original size:27 final size:27
Alignment explanation
Indices: 1889254--1889368 Score: 153
Period size: 27 Copynumber: 4.3 Consensus size: 27
1889244 GGCAAAAATA
*
1889254 GTCA-TTTACCC-ACTAGGGCATTACG
1 GTCATTTTACCCTACAAGGGCATTACG
* * *
1889279 GTTATTTTACCCTATAAGGGTATTACG
1 GTCATTTTACCCTACAAGGGCATTACG
1889306 GTCATTTTACCCTACAAGGGCATTACG
1 GTCATTTTACCCTACAAGGGCATTACG
* * *
1889333 GTCATTTTACCCTACACGGGTATTATG
1 GTCATTTTACCCTACAAGGGCATTACG
1889360 GTCATTTTA
1 GTCATTTTA
1889369 TAAATATTGA
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
25 3 0.04
26 7 0.09
27 68 0.87
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCCTACAAGGGCATTACG
Found at i:1889334 original size:54 final size:53
Alignment explanation
Indices: 1889254--1889368 Score: 169
Period size: 54 Copynumber: 2.2 Consensus size: 53
1889244 GGCAAAAATA
* * *
1889254 GTCA-TTTACCCACTAGGGCATTACGGTTATTTTACCCTATAAGGGTATTACG
1 GTCATTTTACCCACAAGGGCATTACGGTCATTTTACCCTACAAGGGTATTACG
* *
1889306 GTCATTTTACCCTACAAGGGCATTACGGTCATTTTACCCTACACGGGTATTATG
1 GTCATTTTACCC-ACAAGGGCATTACGGTCATTTTACCCTACAAGGGTATTACG
1889360 GTCATTTTA
1 GTCATTTTA
1889369 TAAATATTGA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
52 4 0.07
53 7 0.12
54 45 0.80
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (53 bp):
GTCATTTTACCCACAAGGGCATTACGGTCATTTTACCCTACAAGGGTATTACG
Found at i:1892689 original size:23 final size:23
Alignment explanation
Indices: 1892659--1892704 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1892649 TAAGTTCAAC
1892659 ATATGAATATCATAAATATGATT
1 ATATGAATATCATAAATATGATT
1892682 ATATGAATATCATAAATATGATT
1 ATATGAATATCATAAATATGATT
1892705 GTTTTGCTTG
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:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (23 bp):
ATATGAATATCATAAATATGATT
Found at i:1898443 original size:17 final size:17
Alignment explanation
Indices: 1898409--1898460 Score: 86
Period size: 17 Copynumber: 3.0 Consensus size: 17
1898399 GTTGGGCCGA
*
1898409 AATGGGCTCTGTGAGCCC
1 AATGGGCT-TGTGGGCCC
1898427 AATGGGCTTGTGGGCCC
1 AATGGGCTTGTGGGCCC
1898444 AATGGGCTTGTGGGCCC
1 AATGGGCTTGTGGGCCC
1898461 CACACGGATG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 25 0.76
18 8 0.24
ACGTcount: A:0.13, C:0.25, G:0.38, T:0.23
Consensus pattern (17 bp):
AATGGGCTTGTGGGCCC
Found at i:1898785 original size:27 final size:27
Alignment explanation
Indices: 1898752--1898814 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
1898742 AGATGAAAGA
* *
1898752 GACTGAAATACCGCTATAGGGTAAAAT
1 GACTGAAATACCACCATAGGGTAAAAT
*
1898779 GATTGAAATACCACCATAGGGTAAAAT
1 GACTGAAATACCACCATAGGGTAAAAT
1898806 GACTGAAAT
1 GACTGAAAT
1898815 TGTAACACCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (27 bp):
GACTGAAATACCACCATAGGGTAAAAT
Found at i:1902392 original size:27 final size:26
Alignment explanation
Indices: 1902319--1902587 Score: 227
Period size: 27 Copynumber: 10.0 Consensus size: 26
1902309 GCTGTTACAA
*
1902319 AAATACCCCCATAGGGTAAAATAACTG
1 AAATA-CCCCATAGGGTAAAATGACTG
* *
1902346 AAATACCCTATAGGGTAAAATGATTG
1 AAATACCCCATAGGGTAAAATGACTG
* *
1902372 GAATACACCCATAGGGTAAAATGACTA
1 AAATAC-CCCATAGGGTAAAATGACTG
**
1902399 AAATACCCCCATAGGGTAAAATGACCA
1 AAATA-CCCCATAGGGTAAAATGACTG
* * *
1902426 AAATACTCCCATAAGGTAAAATAACCG
1 AAATAC-CCCATAGGGTAAAATGACTG
*
1902453 AAATATCCCCATAGGGTAAAATGACCG
1 AAATA-CCCCATAGGGTAAAATGACTG
** *
1902480 AAATACCTTTATAGGGTAAAATGACCG
1 AAATACC-CCATAGGGTAAAATGACTG
*** **
1902507 AAATACCTTTGTAGGGTAAAATGACAA
1 AAATACC-CCATAGGGTAAAATGACTG
1902534 AAATACCCTCATA-GGTCAAAATGACTG
1 AAATACCC-CATAGGGT-AAAATGACTG
** *
1902561 TTATACTCC-TAGGAGATAAAATGACTG
1 AAATACCCCATAGG-G-TAAAATGACTG
1902588 TTGTGGCCTT
Statistics
Matches: 205, Mismatches: 27, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
25 2 0.01
26 31 0.15
27 169 0.82
28 3 0.01
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.22
Consensus pattern (26 bp):
AAATACCCCATAGGGTAAAATGACTG
Found at i:1902525 original size:81 final size:80
Alignment explanation
Indices: 1902318--1902558 Score: 254
Period size: 81 Copynumber: 3.0 Consensus size: 80
1902308 GGCTGTTACA
* * ** *
1902318 AAAATACCCCCATAGGGTAAAATAACTGAAATACC-CTATAGGGTAAAATGATTGGAATACACCC
1 AAAATACCCCCATAGGGTAAAATGACCGAAATACCTCTATAGGGTAAAATGACAGAAATAC-CCC
*
1902382 ATAGGGTAAAATGACT
65 ATAGGGTAAAATGACC
* * * * *
1902398 AAAATACCCCCATAGGGTAAAATGACCAAAATA-CTCCCATAAGGTAAAATAACCGAAATATCCC
1 AAAATACCCCCATAGGGTAAAATGACCGAAATACCT-CTATAGGGTAAAATGACAGAAATA-CCC
1902462 CATAGGGTAAAATGACC
64 CATAGGGTAAAATGACC
* *** * * *
1902479 GAAATACCTTTATAGGGTAAAATGACCGAAATACCTTTGTAGGGTAAAATGACAAAAATACCCTC
1 AAAATACCCCCATAGGGTAAAATGACCGAAATACCTCTATAGGGTAAAATGACAGAAATACCC-C
1902544 ATA-GGTCAAAATGAC
65 ATAGGGT-AAAATGAC
1902559 TGTTATACTC
Statistics
Matches: 133, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
79 1 0.01
80 36 0.27
81 93 0.70
82 3 0.02
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (80 bp):
AAAATACCCCCATAGGGTAAAATGACCGAAATACCTCTATAGGGTAAAATGACAGAAATACCCCA
TAGGGTAAAATGACC
Found at i:1903024 original size:28 final size:28
Alignment explanation
Indices: 1902984--1903116 Score: 169
Period size: 28 Copynumber: 4.8 Consensus size: 28
1902974 ACTGTTACTA
* *
1902984 TATTGGGCTAAGGCCCACATTGATTTTG
1 TATTGGGCTAAGGCCCACACTGATTCTG
*
1903012 TATTGGCCTAAGGCCCACACTGATTCTG
1 TATTGGGCTAAGGCCCACACTGATTCTG
* * *
1903040 TATTGGGCTAAGGCCCACACTGCTACTA
1 TATTGGGCTAAGGCCCACACTGATTCTG
* * *
1903068 TCTTGGGCTAAGGCCTACACTG-TTATTG
1 TATTGGGCTAAGGCCCACACTGATT-CTG
1903096 TATTGGGCTAAGGCCCACACT
1 TATTGGGCTAAGGCCCACACT
1903117 ACACTATCAC
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
27 1 0.01
28 89 0.99
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (28 bp):
TATTGGGCTAAGGCCCACACTGATTCTG
Found at i:1903079 original size:56 final size:56
Alignment explanation
Indices: 1902973--1903124 Score: 182
Period size: 56 Copynumber: 2.7 Consensus size: 56
1902963 TATTGCACGG
* * * ** * *
1902973 CACTGTTACTATATTGGGCTAAGGCCCACATTGATTTTGTATTGGCCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCACACTGCTACTATCTTGGCCTAAGGCCCA
* *
1903029 CACTGATT-CTGTATTGGGCTAAGGCCCACACTGCTACTATCTTGGGCTAAGGCCTA
1 CACTG-TTACTGTATTGGGCTAAGGCCCACACTGCTACTATCTTGGCCTAAGGCCCA
* *
1903085 CACTGTTATTGTATTGGGCTAAGGCCCACACTAC-ACTATC
1 CACTGTTACTGTATTGGGCTAAGGCCCACACTGCTACTATC
1903125 ACTGAATAGG
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
55 8 0.10
56 73 0.88
57 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (56 bp):
CACTGTTACTGTATTGGGCTAAGGCCCACACTGCTACTATCTTGGCCTAAGGCCCA
Found at i:1903137 original size:33 final size:33
Alignment explanation
Indices: 1903100--1903178 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
1903090 TTATTGTATT
*
1903100 GGGCTAAGGCCCACACTACACTATCACTGAATA
1 GGGCTAAGGCCCACACTACACTATCACTAAATA
** *
1903133 GGGCTAAGGCCCACACTGTACTGTCACTAAATA
1 GGGCTAAGGCCCACACTACACTATCACTAAATA
* *
1903166 AGGCTCAGGCCCA
1 GGGCTAAGGCCCA
1903179 AACTGTTACT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (33 bp):
GGGCTAAGGCCCACACTACACTATCACTAAATA
Found at i:1903184 original size:33 final size:34
Alignment explanation
Indices: 1903101--1903189 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 34
1903091 TATTGTATTG
* ** * * *
1903101 GGCTAAGGCCCACACT-ACACTATCACTGAATAG
1 GGCTAAGGCCCAAACTGTTACTGTCACTAAATAA
*
1903134 GGCTAAGGCCCACACTG-TACTGTCACTAAATAA
1 GGCTAAGGCCCAAACTGTTACTGTCACTAAATAA
*
1903167 GGCTCAGGCCCAAACTGTTACTG
1 GGCTAAGGCCCAAACTGTTACTG
1903190 CATGTTGTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
33 43 0.90
34 5 0.10
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.20
Consensus pattern (34 bp):
GGCTAAGGCCCAAACTGTTACTGTCACTAAATAA
Found at i:1904633 original size:20 final size:20
Alignment explanation
Indices: 1904608--1904656 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1904598 TGATTCGGAA
1904608 AAGAGAAGAGGGGAAGAGAG
1 AAGAGAAGAGGGGAAGAGAG
1904628 AAGAGAAGAGGGGAAGAGAG
1 AAGAGAAGAGGGGAAGAGAG
1904648 AAGAGAAGA
1 AAGAGAAGA
1904657 TTCGGTAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (20 bp):
AAGAGAAGAGGGGAAGAGAG
Found at i:1911081 original size:25 final size:25
Alignment explanation
Indices: 1911049--1911138 Score: 117
Period size: 25 Copynumber: 3.6 Consensus size: 25
1911039 CACCAATATT
*
1911049 GCAGCAAAGCTACCAGAATAATAAC
1 GCAGCAAAGCTGCCAGAATAATAAC
*
1911074 GCAACAAAGCTGCCAGAATAATAAC
1 GCAGCAAAGCTGCCAGAATAATAAC
* * * *
1911099 TCAGCAAAGTTGCCAGTAACAGTAAC
1 GCAGCAAAGCTGCCAG-AATAATAAC
1911125 GCAGCAAAGCTGCC
1 GCAGCAAAGCTGCC
1911139 GGTAACAGTA
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
25 36 0.65
26 19 0.35
ACGTcount: A:0.42, C:0.26, G:0.19, T:0.13
Consensus pattern (25 bp):
GCAGCAAAGCTGCCAGAATAATAAC
Found at i:1911345 original size:27 final size:27
Alignment explanation
Indices: 1911314--1911605 Score: 304
Period size: 27 Copynumber: 10.9 Consensus size: 27
1911304 TCAACTCCTA
** *
1911314 AGGGTATAACAGTCATTTTACCCTTTG
1 AGGGTATTTCAGTCATTTTACCCTTCG
* * * *
1911341 GGGGTATTTCGGTCATTTTACACATCG
1 AGGGTATTTCAGTCATTTTACCCTTCG
* *
1911368 GGGGTATTTC-GATCATTTTACTCTTCG
1 AGGGTATTTCAG-TCATTTTACCCTTCG
1911395 AGGGTATTTCAGTCATTTTACCCTTCG
1 AGGGTATTTCAGTCATTTTACCCTTCG
* * *
1911422 AGGGTATTT-GGTTATTTTACCATTCG
1 AGGGTATTTCAGTCATTTTACCCTTCG
* * * *
1911448 AGGGTGTTTTATTCATTTTACCCTTGG
1 AGGGTATTTCAGTCATTTTACCCTTCG
1911475 AGGGTATTTC-GATCATTTTACCCTTCG
1 AGGGTATTTCAG-TCATTTTACCCTTCG
* *
1911502 AGGGTATTTCGGTTATTTTACCCTTCG
1 AGGGTATTTCAGTCATTTTACCCTTCG
* *
1911529 AGGGTATTTCGGTTATTTTACCCTTCG
1 AGGGTATTTCAGTCATTTTACCCTTCG
* * * *
1911556 AGCGTATTTCGGTCATTTTAACCTTCA
1 AGGGTATTTCAGTCATTTTACCCTTCG
*
1911583 AGGGTATTT-TGATCATTTTACCC
1 AGGGTATTTCAG-TCATTTTACCC
1911606 ACAAATTGCA
Statistics
Matches: 227, Mismatches: 32, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
26 24 0.11
27 201 0.89
28 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (27 bp):
AGGGTATTTCAGTCATTTTACCCTTCG
Found at i:1911563 original size:81 final size:81
Alignment explanation
Indices: 1911326--1911605 Score: 341
Period size: 81 Copynumber: 3.5 Consensus size: 81
1911316 GGTATAACAG
* * * * * * *
1911326 TCATTTTACCCTTTGGGGGTATTTCGGTCATTTTACACATCGGGGGTATTTCGATCATTTTACTC
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGATTATTTTACCC
1911391 TTCGAGGGTATTTC-A
66 TTCGAGGGTATTTCGA
* * * *
1911406 GTCATTTTACCCTTCGAGGGTATTT-GGTTATTTTACCATTCGAGGGTGTTT-TATTCATTTTAC
1 -TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGATT-ATTTTAC
*
1911469 CCTTGGAGGGTATTTCGA
64 CCTTCGAGGGTATTTCGA
* *
1911487 TCATTTTACCCTTCGAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTCGGTTATTTTACCC
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGATTATTTTACCC
* *
1911552 TTCGAGCGTATTTCGG
66 TTCGAGGGTATTTCGA
* * * *
1911568 TCATTTTAACCTTCAAGGGTATTTTGATCATTTTACCC
1 TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCC
1911606 ACAAATTGCA
Statistics
Matches: 171, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
79 2 0.01
80 65 0.38
81 102 0.60
82 2 0.01
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (81 bp):
TCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGATTATTTTACCC
TTCGAGGGTATTTCGA
Found at i:1915156 original size:45 final size:45
Alignment explanation
Indices: 1915096--1915205 Score: 125
Period size: 45 Copynumber: 2.4 Consensus size: 45
1915086 TAAATCAATC
* *
1915096 ACCCACCAAATACAACCAATTTACCCTCC-AAGCACAAAAAAAC-AT
1 ACCCTCCAAACACAACCAATTTACCCTCCGAA-CAC-AAAAAACTAT
* * **
1915141 AGCCTCCAAACACAACTAATTTACCCTCCGAACACAACCAACTAT
1 ACCCTCCAAACACAACCAATTTACCCTCCGAACACAAAAAACTAT
*
1915186 ACCCTCCAAACACAATCAAT
1 ACCCTCCAAACACAACCAAT
1915206 ATCCCTTCAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
44 5 0.09
45 47 0.87
46 2 0.04
ACGTcount: A:0.45, C:0.37, G:0.03, T:0.15
Consensus pattern (45 bp):
ACCCTCCAAACACAACCAATTTACCCTCCGAACACAAAAAACTAT
Found at i:1915192 original size:23 final size:22
Alignment explanation
Indices: 1915096--1915211 Score: 99
Period size: 23 Copynumber: 5.2 Consensus size: 22
1915086 TAAATCAATC
* * *
1915096 ACCCACCAAATACAACCAATTT
1 ACCCTCCAAACACAACCAATAT
* ** *
1915118 ACCCTCCAAGCACAAAAAAACAT
1 ACCCTCCAAACAC-AACCAATAT
* * *
1915141 AGCCTCCAAACACAACTAATTT
1 ACCCTCCAAACACAACCAATAT
*
1915163 ACCCTCCGAACACAACCAACTAT
1 ACCCTCCAAACACAACCAA-TAT
*
1915186 ACCCTCCAAACACAATCAATAT
1 ACCCTCCAAACACAACCAATAT
1915208 -CCCT
1 ACCCT
1915212 TCAACATATC
Statistics
Matches: 73, Mismatches: 19, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
21 4 0.05
22 34 0.47
23 35 0.48
ACGTcount: A:0.43, C:0.38, G:0.03, T:0.16
Consensus pattern (22 bp):
ACCCTCCAAACACAACCAATAT
Found at i:1919424 original size:22 final size:21
Alignment explanation
Indices: 1919394--1919593 Score: 121
Period size: 23 Copynumber: 8.7 Consensus size: 21
1919384 CTATCACCCC
1919394 CCAAACACAACCAATTTACTCT
1 CCAAACACAACCAATTTAC-CT
* *
1919416 CGAAACACAGCCAATTTACCCT
1 CCAAACACAACCAATTTA-CCT
1919438 CCAAACACAACCATATATATAACCT
1 CCAAACACAACCA-AT-T-T-ACCT
* *
1919463 CCGAACACAACCAAGTATACCTT
1 CCAAACACAACCAA-TTTACC-T
1919486 CCAAACACAACCAATTTACCCT
1 CCAAACACAACCAATTTA-CCT
*** * * *
1919508 TTGAACATAACCAAATGTACTT
1 CCAAACACAACC-AATTTACCT
* *
1919530 GCAAAACACCACCATATATATAACCT
1 -CCAAACACAACCA-AT-T-T-ACCT
* *
1919556 CCGAACACAACCAACTATACCCT
1 CCAAACACAACCAA-TTTA-CCT
1919579 CCAAACACAACCAAT
1 CCAAACACAACCAAT
1919594 ATACTCTTTA
Statistics
Matches: 136, Mismatches: 26, Indels: 32
0.70 0.13 0.16
Matches are distributed among these distances:
22 49 0.36
23 51 0.38
24 3 0.02
25 29 0.21
26 4 0.03
ACGTcount: A:0.42, C:0.34, G:0.04, T:0.19
Consensus pattern (21 bp):
CCAAACACAACCAATTTACCT
Found at i:1920096 original size:20 final size:21
Alignment explanation
Indices: 1920054--1920098 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
1920044 AATTACTTTA
1920054 AAAACACATTATAAATAACCT
1 AAAACACATTATAAATAACCT
* *
1920075 AAAACACATT-TAAATCATCT
1 AAAACACATTATAAATAACCT
1920095 AAAA
1 AAAA
1920099 ACTGCATACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAACACATTATAAATAACCT
Found at i:1920099 original size:21 final size:22
Alignment explanation
Indices: 1920052--1920100 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1920042 TTAATTACTT
1920052 TAAAAACACATTATAAATAACC
1 TAAAAACACATTATAAATAACC
* *
1920074 T-AAAACACATT-TAAATCATC
1 TAAAAACACATTATAAATAACC
1920094 TAAAAAC
1 TAAAAAC
1920101 TGCATACCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
21 15 0.62
22 1 0.04
ACGTcount: A:0.57, C:0.18, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAAAACACATTATAAATAACC
Found at i:1928927 original size:27 final size:27
Alignment explanation
Indices: 1928897--1928960 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
1928887 CCTCAATATT
*
1928897 TGTAAAATGATCGTAATGCCCCTGTAG
1 TGTAAAATGATCGCAATGCCCCTGTAG
*
1928924 TGTAAAATGATCGCAATGCCTCTGTAG
1 TGTAAAATGATCGCAATGCCCCTGTAG
*
1928951 GGTAAAATGA
1 TGTAAAATGA
1928961 CCGTTGATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (27 bp):
TGTAAAATGATCGCAATGCCCCTGTAG
Found at i:1929071 original size:24 final size:24
Alignment explanation
Indices: 1929040--1929173 Score: 132
Period size: 24 Copynumber: 5.6 Consensus size: 24
1929030 CCCTCGAGGT
* *
1929040 TAAATGATTGATTTATCTGTGATG
1 TAAATGACTGATTTGTCTGTGATG
* * * *
1929064 TAAGTGATTGATTTGTCCGAGATG
1 TAAATGACTGATTTGTCTGTGATG
*
1929088 TAAATGACTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATG
*
1929112 TAAATGACTGATTTGTTTGTGATTGG
1 TAAATGACTGATTTGTCTGTGA-T-G
1929138 T--ATGACTGATTTGTCTGTGAATTG
1 TAAATGACTGATTTGTCTGTG-A-TG
1929162 T--ATGACTGATTT
1 TAAATGACTGATTT
1929174 TGTGCATGAC
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
24 90 0.95
25 4 0.04
26 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.45
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATG
Found at i:1929304 original size:26 final size:26
Alignment explanation
Indices: 1929275--1929327 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1929265 TGTTACTGGT
*
1929275 AGCTTTGCTACGGTACTATTTTTGGC
1 AGCTTTGCTACGGTACTATTGTTGGC
1929301 AGCTTTGCTACGGTACTATTGTTGGC
1 AGCTTTGCTACGGTACTATTGTTGGC
1929327 A
1 A
1929328 ACTCTGTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.40
Consensus pattern (26 bp):
AGCTTTGCTACGGTACTATTGTTGGC
Found at i:1929436 original size:32 final size:32
Alignment explanation
Indices: 1929342--1929436 Score: 120
Period size: 32 Copynumber: 3.0 Consensus size: 32
1929332 TGTTGCGATG
* ** *
1929342 CTACTGACGGCTTTGTGCGGATCATATTACCA
1 CTACTGATGGCTTTGTGCCAATCATATTACTA
* *
1929374 TTACT-ATAGGCTGTGTGCCAATCATATTACTA
1 CTACTGAT-GGCTTTGTGCCAATCATATTACTA
1929406 CTACTGATGGCTTTGTGCCAATCATATTACT
1 CTACTGATGGCTTTGTGCCAATCATATTACT
1929437 GTACTTATGG
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
31 1 0.02
32 50 0.94
33 2 0.04
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (32 bp):
CTACTGATGGCTTTGTGCCAATCATATTACTA
Found at i:1938415 original size:17 final size:18
Alignment explanation
Indices: 1938379--1938416 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1938369 TGTTACTATG
1938379 TATTTTAGAATTAGAAAA
1 TATTTTAGAATTAGAAAA
1938397 TATTTTA-AATGTA-AAAA
1 TATTTTAGAAT-TAGAAAA
1938414 TAT
1 TAT
1938417 GATTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (18 bp):
TATTTTAGAATTAGAAAA
Found at i:1948477 original size:21 final size:21
Alignment explanation
Indices: 1948453--1948531 Score: 54
Period size: 21 Copynumber: 3.6 Consensus size: 21
1948443 TCGAACACTC
1948453 AATTTTAATTTCTTAACCTAA
1 AATTTTAATTTCTTAACCTAA
* * *
1948474 AATTATAAATTCTATTTATTA-CT-C
1 AATT-TTAATT-T-CTTA--ACCTAA
1948498 AATTTTAATTTCTTAACCTAA
1 AATTTTAATTTCTTAACCTAA
* *
1948519 AATTATAAATTCT
1 AATTTTAATTTCT
1948532 ATTTATTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
19 1 0.02
20 2 0.05
21 18 0.42
22 6 0.14
23 6 0.14
24 7 0.16
25 2 0.05
26 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTTTAATTTCTTAACCTAA
Found at i:1948490 original size:27 final size:27
Alignment explanation
Indices: 1948460--1948535 Score: 62
Period size: 27 Copynumber: 3.1 Consensus size: 27
1948450 CTCAATTTTA
1948460 ATTTCTTAACCTAAAATTATAAATTCT
1 ATTTCTTAACCTAAAATTATAAATTCT
* * *
1948487 ATTTATT-A-CT-CAATT-TTAA----
1 ATTTCTTAACCTAAAATTATAAATTCT
1948506 -TTTCTTAACCTAAAATTATAAATTCT
1 ATTTCTTAACCTAAAATTATAAATTCT
1948532 ATTT
1 ATTT
1948536 ATTTTAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 18
0.59 0.10 0.31
Matches are distributed among these distances:
18 5 0.15
19 1 0.03
20 2 0.06
21 4 0.12
22 3 0.09
23 3 0.09
24 4 0.12
25 2 0.06
26 1 0.03
27 9 0.26
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTCTTAACCTAAAATTATAAATTCT
Found at i:1948499 original size:45 final size:45
Alignment explanation
Indices: 1948449--1948538 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
1948439 ATTCTCGAAC
1948449 ACTCAATTTTAATTTCTTAACCTAAAATTATAAATTCTATTTATT
1 ACTCAATTTTAATTTCTTAACCTAAAATTATAAATTCTATTTATT
1948494 ACTCAATTTTAATTTCTTAACCTAAAATTATAAATTCTATTTATT
1 ACTCAATTTTAATTTCTTAACCTAAAATTATAAATTCTATTTATT
1948539 TTAAAATTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (45 bp):
ACTCAATTTTAATTTCTTAACCTAAAATTATAAATTCTATTTATT
Found at i:1950520 original size:23 final size:23
Alignment explanation
Indices: 1950490--1950536 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1950480 ACGTGTGTGT
1950490 TTGTGTTTTGGCAAAAAGAAAGA
1 TTGTGTTTTGGCAAAAAGAAAGA
1950513 TTGTGTTTTGGCAAAAAGAAAGA
1 TTGTGTTTTGGCAAAAAGAAAGA
1950536 T
1 T
1950537 AGTTGAGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (23 bp):
TTGTGTTTTGGCAAAAAGAAAGA
Found at i:1968117 original size:20 final size:21
Alignment explanation
Indices: 1968073--1968115 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1968063 AACAACTCAC
*
1968073 TTAGTTTAATGAATAAAAAGT
1 TTAGTTTAATCAATAAAAAGT
1968094 TTAGTTTAATCAATAAAAAGT
1 TTAGTTTAATCAATAAAAAGT
1968115 T
1 T
1968116 AGAATCTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.40
Consensus pattern (21 bp):
TTAGTTTAATCAATAAAAAGT
Found at i:1976425 original size:9 final size:9
Alignment explanation
Indices: 1976403--1976435 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1976393 TTATCACTTG
1976403 TTATATT-A
1 TTATATTAA
1976411 -TATATTAA
1 TTATATTAA
1976419 TTATATTAA
1 TTATATTAA
1976428 TTATATTA
1 TTATATTA
1976436 TAGTTACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 6 0.26
8 1 0.04
9 16 0.70
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTATATTAA
Found at i:1976816 original size:23 final size:23
Alignment explanation
Indices: 1976786--1976832 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1976776 ACGTGTGTGT
1976786 TTGTGTTTTGGCAAAAAGAAAGA
1 TTGTGTTTTGGCAAAAAGAAAGA
1976809 TTGTGTTTTGGCAAAAAGAAAGA
1 TTGTGTTTTGGCAAAAAGAAAGA
1976832 T
1 T
1976833 AGTTGANNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (23 bp):
TTGTGTTTTGGCAAAAAGAAAGA
Found at i:1982171 original size:27 final size:27
Alignment explanation
Indices: 1982141--1982204 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
1982131 CCTCAATATT
**
1982141 TGTAAAATGATCGTAATGCCCCTGTAG
1 TGTAAAATGATCACAATGCCCCTGTAG
1982168 TGTAAAATGATCACAATGCCCCTGTAG
1 TGTAAAATGATCACAATGCCCCTGTAG
*
1982195 GGTAAAATGA
1 TGTAAAATGA
1982205 CCGTTGATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (27 bp):
TGTAAAATGATCACAATGCCCCTGTAG
Found at i:1982315 original size:24 final size:24
Alignment explanation
Indices: 1982284--1982417 Score: 123
Period size: 24 Copynumber: 5.6 Consensus size: 24
1982274 CCCTCGAGGT
* *
1982284 TAAATGATTGATTTATCTGTGATG
1 TAAATGACTGATTTGTCTGTGATG
* * * *
1982308 TAAGTGATTGATTTGTCCGAGATG
1 TAAATGACTGATTTGTCTGTGATG
* *
1982332 TAAATGACAGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATG
*
1982356 TAAATGACTGATTTGTTTGTGATTGG
1 TAAATGACTGATTTGTCTGTGA-T-G
1982382 T--ATGACTGATTTGTCTGTGAATTG
1 TAAATGACTGATTTGTCTGTG-A-TG
1982406 T--ATGACTGATTT
1 TAAATGACTGATTT
1982418 TGTGGATGGC
Statistics
Matches: 93, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
24 88 0.95
25 4 0.04
26 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.44
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATG
Found at i:1982552 original size:26 final size:26
Alignment explanation
Indices: 1982523--1982579 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
1982513 ACTGGTAACG
1982523 TTGCTACGGTACTATTGTTGGCAGCT
1 TTGCTACGGTACTATTGTTGGCAGCT
1982549 TTGCTACGGTACTATTGTTGGCAGCT
1 TTGCTACGGTACTATTGTTGGCAGCT
1982575 TTGCT
1 TTGCT
1982580 GCGATGCTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.40
Consensus pattern (26 bp):
TTGCTACGGTACTATTGTTGGCAGCT
Found at i:1982711 original size:32 final size:32
Alignment explanation
Indices: 1982586--1982711 Score: 157
Period size: 32 Copynumber: 4.0 Consensus size: 32
1982576 TGCTGCGATG
* **
1982586 CTACTGACGGCTTTGTGCCGATCATATTACCG
1 CTACTGATGGCTTTGTGCCGATCATATTACTA
* * * *
1982618 TTACT-ATAGGCTGTGTGCTGATCATA-TACTT
1 CTACTGAT-GGCTTTGTGCCGATCATATTACTA
1982649 CTACTGATGGCTTTGTGCCGATCATATTACTA
1 CTACTGATGGCTTTGTGCCGATCATATTACTA
*
1982681 CTACTGATGGCTTTGTGCCAATCATATTACT
1 CTACTGATGGCTTTGTGCCGATCATATTACT
1982712 GTAGTTATGG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
31 24 0.30
32 56 0.70
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.37
Consensus pattern (32 bp):
CTACTGATGGCTTTGTGCCGATCATATTACTA
Found at i:1982723 original size:63 final size:63
Alignment explanation
Indices: 1982586--1982707 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
1982576 TGCTGCGATG
* ** **
1982586 CTACTGACGGCTTTGTGCCGATCATATTACCGTTACTATAGGCTGTGTGCTGATCATATACTT
1 CTACTGATGGCTTTGTGCCGATCATATTACCACTACTATAGGCTGTGTGCCAATCATATACTT
* *
1982649 CTACTGATGGCTTTGTGCCGATCATATTACTACTACTGAT-GGCTTTGTGCCAATCATAT
1 CTACTGATGGCTTTGTGCCGATCATATTACCACTACT-ATAGGCTGTGTGCCAATCATAT
1982708 TACTGTAGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 49 0.96
64 2 0.04
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (63 bp):
CTACTGATGGCTTTGTGCCGATCATATTACCACTACTATAGGCTGTGTGCCAATCATATACTT
Found at i:1988485 original size:17 final size:18
Alignment explanation
Indices: 1988459--1988499 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1988449 ACTTAATTAA
*
1988459 AATAAATAAATTATT-TT
1 AATAAATAAAATATTGTT
*
1988476 AATAATTAAAATATTGTT
1 AATAAATAAAATATTGTT
1988494 AATAAA
1 AATAAA
1988500 ATATTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
AATAAATAAAATATTGTT
Found at i:1993829 original size:21 final size:21
Alignment explanation
Indices: 1993804--1993846 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1993794 AACAACTCAC
1993804 TTAGTTTAATGAATAAAAAGT
1 TTAGTTTAATGAATAAAAAGT
*
1993825 TTAGTTTAATTAATAAAAAGT
1 TTAGTTTAATGAATAAAAAGT
1993846 T
1 T
1993847 AGAATCCCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.42
Consensus pattern (21 bp):
TTAGTTTAATGAATAAAAAGT
Found at i:2006597 original size:37 final size:38
Alignment explanation
Indices: 2006509--2006598 Score: 89
Period size: 37 Copynumber: 2.4 Consensus size: 38
2006499 ATATATAATT
*
2006509 AATATAAATGTAATTATGTTATATTATTTTAGATTATA
1 AATATAAATGTAATTATGTCATATTATTTTAGATTATA
* * * *
2006547 AAAATATAT-TAATTAT-TCATAATTGTTTGTATA-T-TA
1 AATATAAATGTAATTATGTCAT-ATTATTT-TAGATTATA
2006583 AATATAAATGTAATTA
1 AATATAAATGTAATTA
2006599 CATTACAAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
36 12 0.29
37 20 0.48
38 10 0.24
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (38 bp):
AATATAAATGTAATTATGTCATATTATTTTAGATTATA
Found at i:2011018 original size:20 final size:21
Alignment explanation
Indices: 2010975--2011019 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
2010965 AACAACTCAC
*
2010975 TTAGTTTAATGAATAAAAAGT
1 TTAGTTTAATCAATAAAAAGT
2010996 TTAGTTTAATCAATAAAAA-T
1 TTAGTTTAATCAATAAAAAGT
2011016 TTAG
1 TTAG
2011020 AATCTCACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (21 bp):
TTAGTTTAATCAATAAAAAGT
Found at i:2013008 original size:9 final size:9
Alignment explanation
Indices: 2012985--2013018 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
2012975 CTTATGTCTT
2012985 ATTATATT-
1 ATTATATTA
2012993 A-TATATTA
1 ATTATATTA
2013001 ATTATATTA
1 ATTATATTA
2013010 ATTATATTA
1 ATTATATTA
2013019 TATTTACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 6 0.25
8 2 0.08
9 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTATATTA
Found at i:2035852 original size:21 final size:21
Alignment explanation
Indices: 2035827--2035869 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2035817 AACAACTCAC
2035827 TTAGTTTAATGAATAAAAAGT
1 TTAGTTTAATGAATAAAAAGT
*
2035848 TTAGTTTAATTAATAAAAAGT
1 TTAGTTTAATGAATAAAAAGT
2035869 T
1 T
2035870 AGAATCCCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.42
Consensus pattern (21 bp):
TTAGTTTAATGAATAAAAAGT
Found at i:2038082 original size:9 final size:9
Alignment explanation
Indices: 2038060--2038092 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2038050 TTATCACTTG
2038060 TTATATT-A
1 TTATATTAA
2038068 -TATATTAA
1 TTATATTAA
2038076 TTATATTAA
1 TTATATTAA
2038085 TTATATTA
1 TTATATTA
2038093 TAGTTACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 6 0.26
8 1 0.04
9 16 0.70
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTATATTAA
Found at i:2040822 original size:14 final size:15
Alignment explanation
Indices: 2040803--2040833 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2040793 AGGACAGTTA
2040803 TAAGGGTT-GGGGTT
1 TAAGGGTTAGGGGTT
2040817 TAAGGGTTAGGGGTT
1 TAAGGGTTAGGGGTT
2040832 TA
1 TA
2040834 CGATTTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
TAAGGGTTAGGGGTT
Done.