Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold150
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1854615
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 196055 characters in sequence are not A, C, G, or T
File 7 of 6
Found at i:1739907 original size:31 final size:31
Alignment explanation
Indices: 1739869--1739930 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1739859 GATTTTCATA
1739869 GGGTACGTTTTCTCCAGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCAGGAGAAAACGTACCC
*
1739900 GGGTACGTTTTCTCCTGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCAGGAGAAAACGTACCC
1739931 TGGAGATTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (31 bp):
GGGTACGTTTTCTCCAGGAGAAAACGTACCC
Found at i:1739957 original size:16 final size:16
Alignment explanation
Indices: 1739938--1739971 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1739928 CCCTGGAGAT
1739938 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
1739954 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
1739970 TG
1 TG
1739972 ATACCCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.24, G:0.26, T:0.44
Consensus pattern (16 bp):
TGGGTACGTTTTCTCC
Found at i:1764543 original size:11 final size:11
Alignment explanation
Indices: 1764527--1764556 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1764517 CAAAATACCT
1764527 AGAGTAAACCC
1 AGAGTAAACCC
1764538 AGAGTAAACCC
1 AGAGTAAACCC
*
1764549 AAAGTAAA
1 AGAGTAAA
1764557 TCCCGAGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.53, C:0.20, G:0.17, T:0.10
Consensus pattern (11 bp):
AGAGTAAACCC
Found at i:1764564 original size:22 final size:22
Alignment explanation
Indices: 1764529--1764573 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1764519 AAATACCTAG
1764529 AGTAAACCCAGAGTAAACCCAA
1 AGTAAACCCAGAGTAAACCCAA
**
1764551 AGTAAATCCC-GAGTGGACCCAA
1 AGTAAA-CCCAGAGTAAACCCAA
1764573 A
1 A
1764574 TTTTCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.44, C:0.27, G:0.18, T:0.11
Consensus pattern (22 bp):
AGTAAACCCAGAGTAAACCCAA
Found at i:1775413 original size:31 final size:31
Alignment explanation
Indices: 1775375--1775433 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1775365 TCGTTCGTCT
1775375 GCAATTTTGGGGGTTTTAAAGATGTAAGTCA
1 GCAATTTTGGGGGTTTTAAAGATGTAAGTCA
*
1775406 GCAATTTTGGGGGTTTTAAAGATTTAAG
1 GCAATTTTGGGGGTTTTAAAGATGTAAG
1775434 CAATTTATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.37
Consensus pattern (31 bp):
GCAATTTTGGGGGTTTTAAAGATGTAAGTCA
Found at i:1776289 original size:2 final size:2
Alignment explanation
Indices: 1776282--1776311 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1776272 CCTCCTAATA
*
1776282 CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1776312 TGCCATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:1776846 original size:70 final size:70
Alignment explanation
Indices: 1776762--1776898 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 70
1776752 GTCATGTCAA
* * *
1776762 CTATTTCTTTATTAATAATTCGTCAACTTTTCTATAAATAGTCTAGTGAAGATCAGCTTTATTTA
1 CTATTTCTTAATTAATAATTCGTCAACGTTTCTATAAATAGTCTAGTGAAGATCAGCTTTATATA
1776827 CATTG
66 CATTG
1776832 CTATTTCTTAATTAATAATTCGTCAACGTTTCTATAAATAGTCTAGTGAAGATCAGCTTTATATA
1 CTATTTCTTAATTAATAATTCGTCAACGTTTCTATAAATAGTCTAGTGAAGATCAGCTTTATATA
1776897 CA
66 CA
1776899 CTGCCATTCT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (70 bp):
CTATTTCTTAATTAATAATTCGTCAACGTTTCTATAAATAGTCTAGTGAAGATCAGCTTTATATA
CATTG
Found at i:1778857 original size:22 final size:22
Alignment explanation
Indices: 1778827--1778881 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1778817 TTATCGTGCC
* * *
1778827 ATCGAATCATCGTCATTGCGCT
1 ATCGCATCATCGTCATAGCACT
*
1778849 ATCGCATCATCGTTATAGCACT
1 ATCGCATCATCGTCATAGCACT
1778871 ATCGCATCATC
1 ATCGCATCATC
1778882 ATAATCGCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (22 bp):
ATCGCATCATCGTCATAGCACT
Found at i:1778891 original size:22 final size:22
Alignment explanation
Indices: 1778847--1778891 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1778837 CGTCATTGCG
* *
1778847 CTATCGCATCATCGTTATAGCA
1 CTATCGCATCATCATAATAGCA
*
1778869 CTATCGCATCATCATAATCGCA
1 CTATCGCATCATCATAATAGCA
1778891 C
1 C
1778892 AATCACAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.31, G:0.11, T:0.29
Consensus pattern (22 bp):
CTATCGCATCATCATAATAGCA
Found at i:1781046 original size:10 final size:10
Alignment explanation
Indices: 1780967--1781104 Score: 70
Period size: 10 Copynumber: 13.7 Consensus size: 10
1780957 AGTGCCATTT
1780967 TTTACTGATAA
1 TTTACTGAT-A
1780978 TTT-CTGATA
1 TTTACTGATA
1780987 TTTACTGATAA
1 TTTACTGAT-A
*
1780998 TTTTACTGCT-
1 -TTTACTGATA
*
1781008 GTTACTGATA
1 TTTACTGATA
* * * *
1781018 ATTGCTGTTG
1 TTTACTGATA
*
1781028 GTT-CTGATA
1 TTTACTGATA
1781037 TTTACTGATA
1 TTTACTGATA
*
1781047 TTTACTGATGCT
1 TTTACTGAT--A
*
1781059 TTTGCTG-TGA
1 TTTACTGAT-A
**
1781069 GCT-CTGATA
1 TTTACTGATA
*
1781078 ATTACTGATA
1 TTTACTGATA
*
1781088 TTTACTGAGA
1 TTTACTGATA
1781098 TTTACTG
1 TTTACTG
1781105 TTGGTACTGA
Statistics
Matches: 97, Mismatches: 21, Indels: 19
0.71 0.15 0.14
Matches are distributed among these distances:
9 22 0.23
10 56 0.58
11 5 0.05
12 14 0.14
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (10 bp):
TTTACTGATA
Found at i:1781772 original size:2 final size:2
Alignment explanation
Indices: 1781767--1781798 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1781757 GGATAAATAA
1781767 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1781799 NTAATATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1792875 original size:2 final size:2
Alignment explanation
Indices: 1792868--1792910 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1792858 TACAACAGCA
1792868 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1792910 A
1 A
1792911 TTATTTTCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1798140 original size:197 final size:196
Alignment explanation
Indices: 1797805--1798197 Score: 777
Period size: 197 Copynumber: 2.0 Consensus size: 196
1797795 AATTAAAAAA
1797805 TTGTTTAAAAATAATTGAAAATCAAATACATTTCATAGTAATAATTACCTTACATGGATCTGTGT
1 TTGTTTAAAAATAATTGAAAATCAAATACATTTCATAGTAATAATTACCTTACATGGATCTGTGT
1797870 CATAGTTAAGGATGACAACCTAAATTTGAAAGACGTATTTCACGTTATCATTCTATTCTTCATTC
66 CATAGTTAAGGATGACAACCTAAATTTGAAAGACGTATTTCACGTTATCATTCTATTCTTCATTC
1797935 AAATATAATTTTTGGAAATAACTTTAAAACGGCAATGCAGGGCACATATAAAGAGAACAAGAAAG
131 AAATATAATTTTTGGAAATAACTTTAAAACGGCAATGCAGGGCACATATAAAGAGAACAAGAAAG
1798000 G
196 G
1798001 NTTGTTTAAAAATAATTGAAAATCAAATACATTTCATAGTAATAATTACCTTACATGGATCTGTG
1 -TTGTTTAAAAATAATTGAAAATCAAATACATTTCATAGTAATAATTACCTTACATGGATCTGTG
1798066 TCATAGTTAAGGATGACAACCTAAATTTGAAAGACGTATTTCACGTTATCATTCTATTCTTCATT
65 TCATAGTTAAGGATGACAACCTAAATTTGAAAGACGTATTTCACGTTATCATTCTATTCTTCATT
1798131 CAAATATAATTTTTGGAAATAACTTTAAAACGGCAATGCAGGGCACATATAAAGAGAACAAGAAA
130 CAAATATAATTTTTGGAAATAACTTTAAAACGGCAATGCAGGGCACATATAAAGAGAACAAGAAA
1798196 GG
195 GG
1798198 AATTTATCTA
Statistics
Matches: 196, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
197 196 1.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.32
Consensus pattern (196 bp):
TTGTTTAAAAATAATTGAAAATCAAATACATTTCATAGTAATAATTACCTTACATGGATCTGTGT
CATAGTTAAGGATGACAACCTAAATTTGAAAGACGTATTTCACGTTATCATTCTATTCTTCATTC
AAATATAATTTTTGGAAATAACTTTAAAACGGCAATGCAGGGCACATATAAAGAGAACAAGAAAG
G
Found at i:1801001 original size:1 final size:1
Alignment explanation
Indices: 1800990--1801020 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
1800980 TCTAAACTCA
*
1800990 CCCCCCACCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1801021 TTAAAAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.03, C:0.97, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1804702 original size:15 final size:15
Alignment explanation
Indices: 1804676--1804724 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1804666 CAACGCGTCA
1804676 TTGCACTAACACAACT
1 TTGCA-TAACACAACT
* *
1804692 TTGCATAACACACCG
1 TTGCATAACACAACT
*
1804707 TTGCTCTAACACAACT
1 TTGC-ATAACACAACT
1804723 TT
1 TT
1804725 AAGGAAACTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.29
Consensus pattern (15 bp):
TTGCATAACACAACT
Found at i:1807701 original size:19 final size:19
Alignment explanation
Indices: 1807665--1807704 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1807655 TCTCAGATGC
* **
1807665 TGGAGGAGGTTAGGGTTTT
1 TGGAGCAGGTTAAAGTTTT
1807684 TGGAGCAGGTTAAAGTTTT
1 TGGAGCAGGTTAAAGTTTT
1807703 TG
1 TG
1807705 TTGCAGGTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.03, G:0.40, T:0.38
Consensus pattern (19 bp):
TGGAGCAGGTTAAAGTTTT
Found at i:1807994 original size:177 final size:177
Alignment explanation
Indices: 1807660--1808185 Score: 623
Period size: 177 Copynumber: 3.0 Consensus size: 177
1807650 CGAACTCTCA
* * * *
1807660 GATGCTGGAGGAGGTTAGGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTG-CCT-TACAT-
1 GATGCAGGAGGAGGTAAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCTA-ATG
* * ** * *
1807722 AGCAATATCTAAGTTACTGCTGGTCCGCACTTCACCAAACTTGCATGGATGATGTGTCTTATGAT
65 A-CAATATCTTAGTTACTACTGGTCCTAACTTCACCAAACTTGCATGTATGATGAGTCTTATGAT
* * * * *
1807787 ACTGATACACCAGGCAGGCTTGAGTGCTGAATCTGAGCTATAGGTTTCG
129 ACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGGTTTCG
* *
1807836 GATGCAGGAGGATGTAAAGGTTTTTGGAGCTGGTTAAAGTTTCTGTTGCAGGTGCCCTCTAATGA
1 GATGCAGGAGGAGGTAAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCTAATGA
* ** * * * *
1807901 TAATATCTTAGTTACTACTGGTCCTAACTTCATTAAACTTGTATGTATGATGCGTCTTATTATAG
66 CAATATCTTAGTTACTACTGGTCCTAACTTCACCAAACTTGCATGTATGATGAGTCTTATGATAC
* *
1807966 TGATGCACCTGACAGGCTTAAATGCTGAATCTGAGCCACAGGTTTCG
131 TGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGGTTTCG
** * * ** *** *
1808013 GATGCCTGAGGAGGTTAAGATTTTAAGAGCTGGTTAAAGTTTTTGAAACAGGTGCCCTCTGATGA
1 GATGCAGGAGGAGGTAAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCTAATGA
* * *
1808078 CGATATCTTAGTTATTACTGGTCCTAACTTCACCAATCTTGCAT-TGAT-AT-AGTCTTATGATA
66 CAATATCTTAGTTACTACTGGTCCTAACTTCACCAAACTTGCATGT-ATGATGAGTCTTATGATA
*
1808140 CTGATGCACCTGACAGGCTTGAATGCTGAATCAGAGCCATAGGTTT
130 CTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGGTTT
1808186 ATGATTCTTG
Statistics
Matches: 296, Mismatches: 50, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
175 52 0.18
176 51 0.17
177 190 0.64
178 3 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (177 bp):
GATGCAGGAGGAGGTAAAGGTTTTTGGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCTAATGA
CAATATCTTAGTTACTACTGGTCCTAACTTCACCAAACTTGCATGTATGATGAGTCTTATGATAC
TGATGCACCTGACAGGCTTGAATGCTGAATCTGAGCCATAGGTTTCG
Found at i:1809740 original size:16 final size:16
Alignment explanation
Indices: 1809719--1809749 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1809709 AGGTGGTGTC
1809719 ATAAAGGTGATGCCTA
1 ATAAAGGTGATGCCTA
1809735 ATAAAGGTGATGCCT
1 ATAAAGGTGATGCCT
1809750 CGTCTCGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (16 bp):
ATAAAGGTGATGCCTA
Found at i:1810832 original size:32 final size:32
Alignment explanation
Indices: 1810791--1810884 Score: 152
Period size: 32 Copynumber: 2.9 Consensus size: 32
1810781 TTCAGGCAAA
*
1810791 GGGGTCATTTTTCTAAGTAGAATAATGACCGG
1 GGGGTCATTTTTCTACGTAGAATAATGACCGG
* *
1810823 GGGGTCATTTTTCTGCGTTGAATAATGACCGG
1 GGGGTCATTTTTCTACGTAGAATAATGACCGG
*
1810855 GGGGTCATTTTTCTACGTAGAAAAATGACC
1 GGGGTCATTTTTCTACGTAGAATAATGACC
1810885 CCCGGTCATT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.32
Consensus pattern (32 bp):
GGGGTCATTTTTCTACGTAGAATAATGACCGG
Found at i:1817847 original size:21 final size:20
Alignment explanation
Indices: 1817805--1817851 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1817795 GAAAACTATA
*
1817805 GTAATTATAGTTTACGAGTC
1 GTAACTATAGTTTACGAGTC
1817825 GTTAACTATAGTTTACG-GTTC
1 G-TAACTATAGTTTACGAG-TC
1817846 GTAACT
1 GTAACT
1817852 GTAATTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (20 bp):
GTAACTATAGTTTACGAGTC
Found at i:1818854 original size:2 final size:2
Alignment explanation
Indices: 1818847--1818876 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1818837 TTAGTGTTGT
*
1818847 TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1818877 CCGGTATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1818927 original size:2 final size:2
Alignment explanation
Indices: 1818920--1818944 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1818910 TGGGGGTCAN
1818920 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1818945 ATCGTACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1819165 original size:2 final size:2
Alignment explanation
Indices: 1819158--1819198 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1819148 TTAGATGCAT
1819158 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1819199 TGAGCTATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1822120 original size:50 final size:50
Alignment explanation
Indices: 1822042--1822205 Score: 237
Period size: 50 Copynumber: 3.3 Consensus size: 50
1822032 ACATTGTTAT
* *
1822042 ACTGTTATATT-TCCACCTAGACATTATGAAT-TGTTATTATCTGTA-ATCAC
1 ACTGTTATATTGT-CTCCTAGACATTATG-ATGTGTTATAATCTGTATA-CAC
1822092 A-TAGTTATATTGTCTCCTAGACATTATGATGTGTTATAATCTGTATACAC
1 ACT-GTTATATTGTCTCCTAGACATTATGATGTGTTATAATCTGTATACAC
*
1822142 ACTGTTATATTGTCTCCTAGATATTATGATGTGTTATAATCTGTATACAC
1 ACTGTTATATTGTCTCCTAGACATTATGATGTGTTATAATCTGTATACAC
1822192 ACTGTTATATTGTC
1 ACTGTTATATTGTC
1822206 CGCCGTGATC
Statistics
Matches: 106, Mismatches: 3, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
49 3 0.03
50 100 0.94
51 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (50 bp):
ACTGTTATATTGTCTCCTAGACATTATGATGTGTTATAATCTGTATACAC
Found at i:1822451 original size:2 final size:2
Alignment explanation
Indices: 1822441--1822494 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1822431 TCCCCCCCCC
*
1822441 CT CT AT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1822483 CT CT CT CT CT CT
1 CT CT CT CT CT CT
1822495 GATATACATA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1822846 original size:45 final size:45
Alignment explanation
Indices: 1822782--1822873 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
1822772 AATGATCTTA
*
1822782 TTTAATCAGATTGTCAAAAATCGAACTTTGGAAAACAACTGCACT
1 TTTAATCAGATTATCAAAAATCGAACTTTGGAAAACAACTGCACT
*
1822827 TTTAATCAGATTATCAAAAATTGAACTTTGGAAAACAACTGCACT
1 TTTAATCAGATTATCAAAAATCGAACTTTGGAAAACAACTGCACT
1822872 TT
1 TT
1822874 AAATATGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (45 bp):
TTTAATCAGATTATCAAAAATCGAACTTTGGAAAACAACTGCACT
Found at i:1823191 original size:2 final size:2
Alignment explanation
Indices: 1823184--1823226 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1823174 TTTGCATCGA
1823184 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1823226 C
1 C
1823227 ATTGGATGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1824350 original size:24 final size:24
Alignment explanation
Indices: 1824318--1824365 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1824308 TCAAAGTGTT
1824318 TGAAACGTTTGTGAATTAACAGAG
1 TGAAACGTTTGTGAATTAACAGAG
1824342 TGAAACGTTTGTGAATTAACAGAG
1 TGAAACGTTTGTGAATTAACAGAG
1824366 AATCCAAGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (24 bp):
TGAAACGTTTGTGAATTAACAGAG
Found at i:1828461 original size:1 final size:1
Alignment explanation
Indices: 1828457--1828487 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
1828447 TTTGTCAAGC
1828457 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1828488 GGGAAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1831021 original size:101 final size:100
Alignment explanation
Indices: 1830843--1831121 Score: 409
Period size: 101 Copynumber: 2.7 Consensus size: 100
1830833 GGAGTGGCAG
*
1830843 CCATGTAGAGCTGGAATATACAACCCAGTAAGTGTACCCCACTACAGAGCTAAAGTTACACATAG
1 CCATGTAGAGCTGGAATATACAACACAGTAAGTGTA-CCCACTACAGAGCTAAAGTTACACATAG
* *
1830908 AGTAAAGGAAGAGGAAATACACAACATAGAGGCCAA
65 AGTAAAGAAAGAGGAAAAACACAACATAGAGGCCAA
1830944 CCATGTAGAGCTGGAATATACAACACAGTAAGTGTACTCCACTACAGAGCTAAAGTTACACATAG
1 CCATGTAGAGCTGGAATATACAACACAGTAAGTGTAC-CCACTACAGAGCTAAAGTTACACATAG
1831009 AGTAAAGAAAGAGGAAAAACACAACATAGAGGCCAA
65 AGTAAAGAAAGAGGAAAAACACAACATAGAGGCCAA
* * * *
1831045 CCATGTAAAGCTGGAATATACAACATATGTAGTAGATTTAGCCCATTACAGAGCT--AGTTACAC
1 CCATGTAGAGCTGGAATATACAACACA-GTA--AG-TGTA-CCCACTACAGAGCTAAAGTTACAC
*
1831108 ATAGAGTAGAGAAA
61 ATAGAGTAAAGAAA
1831122 AACACTATAA
Statistics
Matches: 164, Mismatches: 8, Indels: 10
0.90 0.04 0.05
Matches are distributed among these distances:
100 1 0.01
101 121 0.74
102 3 0.02
103 21 0.13
104 2 0.01
105 15 0.09
106 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.18
Consensus pattern (100 bp):
CCATGTAGAGCTGGAATATACAACACAGTAAGTGTACCCACTACAGAGCTAAAGTTACACATAGA
GTAAAGAAAGAGGAAAAACACAACATAGAGGCCAA
Found at i:1831805 original size:11 final size:11
Alignment explanation
Indices: 1831789--1831828 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
1831779 CAATTCCCTT
1831789 GTAAACCTAAA
1 GTAAACCTAAA
*
1831800 GTAAACCTTAA
1 GTAAACCTAAA
*
1831811 GTAAACCCAAA
1 GTAAACCTAAA
1831822 GTAAACC
1 GTAAACC
1831829 CCGAGTAGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.10, T:0.17
Consensus pattern (11 bp):
GTAAACCTAAA
Found at i:1831829 original size:11 final size:11
Alignment explanation
Indices: 1831789--1831843 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
1831779 CAATTCCCTT
*
1831789 GTAAACCTAAA
1 GTAAACCCAAA
**
1831800 GTAAACCTTAA
1 GTAAACCCAAA
1831811 GTAAACCCAAA
1 GTAAACCCAAA
**
1831822 GTAAACCCCGA
1 GTAAACCCAAA
*
1831833 GTAGACCCAAA
1 GTAAACCCAAA
1831844 TTTTCCATGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.47, C:0.25, G:0.13, T:0.15
Consensus pattern (11 bp):
GTAAACCCAAA
Found at i:1831835 original size:22 final size:22
Alignment explanation
Indices: 1831789--1831843 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1831779 CAATTCCCTT
* **
1831789 GTAAACCTAAAGTAAACCTTAA
1 GTAAACCCAAAGTAAACCCCAA
*
1831811 GTAAACCCAAAGTAAACCCCGA
1 GTAAACCCAAAGTAAACCCCAA
*
1831833 GTAGACCCAAA
1 GTAAACCCAAA
1831844 TTTTCCATGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.47, C:0.25, G:0.13, T:0.15
Consensus pattern (22 bp):
GTAAACCCAAAGTAAACCCCAA
Found at i:1836906 original size:13 final size:14
Alignment explanation
Indices: 1836881--1836916 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1836871 AAAGTTATGT
1836881 ATAGAATATATAG-A
1 ATAGAA-ATATAGAA
1836895 ATAGAAATATAGAA
1 ATAGAAATATAGAA
1836909 ATAGAAAT
1 ATAGAAAT
1836917 GGAATCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (14 bp):
ATAGAAATATAGAA
Found at i:1840485 original size:27 final size:26
Alignment explanation
Indices: 1840452--1840504 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
1840442 CCTAAACTTA
1840452 TTCAGTTAATATTATAATATATTTAT
1 TTCAGTTAATATTATAATATATTTAT
*
1840478 NTTCAGTTAATATTATAATTTATTTAT
1 -TTCAGTTAATATTATAATATATTTAT
1840505 CTTTTTCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (26 bp):
TTCAGTTAATATTATAATATATTTAT
Found at i:1845330 original size:2 final size:2
Alignment explanation
Indices: 1845325--1845364 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1845315 ACTATTAAAC
1845325 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1845365 ATAAAAAGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1849460 original size:113 final size:113
Alignment explanation
Indices: 1849311--1849537 Score: 445
Period size: 113 Copynumber: 2.0 Consensus size: 113
1849301 ATCCTATAAA
*
1849311 AGGCTTTTATAGGATTTAAAATCCTATGAATGACCATGTTGGGATATTTTATCCCAGAGGATAAA
1 AGGCTTTTATAGGATTTAAAATCCTATGAATCACCATGTTGGGATATTTTATCCCAGAGGATAAA
1849376 AAGTCCTCTAAATATATCATCTTGATTGATTGTATGTTGGGGTTAACT
66 AAGTCCTCTAAATATATCATCTTGATTGATTGTATGTTGGGGTTAACT
1849424 AGGCTTTTATAGGATTTAAAATCCTATGAATCACCATGTTGGGATATTTTATCCCAGAGGATAAA
1 AGGCTTTTATAGGATTTAAAATCCTATGAATCACCATGTTGGGATATTTTATCCCAGAGGATAAA
1849489 AAGTCCTCTAAATATATCATCTTGATTGATTGTATGTTGGGGTTAACT
66 AAGTCCTCTAAATATATCATCTTGATTGATTGTATGTTGGGGTTAACT
1849537 A
1 A
1849538 AACACTTATG
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 113 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (113 bp):
AGGCTTTTATAGGATTTAAAATCCTATGAATCACCATGTTGGGATATTTTATCCCAGAGGATAAA
AAGTCCTCTAAATATATCATCTTGATTGATTGTATGTTGGGGTTAACT
Found at i:1850029 original size:273 final size:267
Alignment explanation
Indices: 1849537--1850085 Score: 938
Period size: 273 Copynumber: 2.0 Consensus size: 267
1849527 GGGGTTAACT
* *
1849537 AAACACTTATGATTCAATTGTCTGATCATATAGTCTAGTAAAAGCAATATTCAAACAACCAATGT
1 AAACTCTTATGATTCAATTGTCTGATCATATAGTCTAGTAAAAGCAATATTCAAAAAACCAATGT
*
1849602 ATTAATTTATTAGATAATGTCATTTTATCCATCGAATGAATTACACGTGCTAAATTATATGTACC
66 ATTAATTTATTAGATAATGTCATTATATCCATCGAATGAATTACACGTGCTAAATTATATGTACC
1849667 ATCAATAACATATTCTTCTTGAAATGACTTAATAGAGCTTATAACAATAAGATCTAACAAATTCT
131 ATCAATAACATATTCTTCTTGAAATGACTTAATAGAGCTTATAACAATAAGATCTAACAAATTCT
*
1849732 GAGAAAATAAATACCAAGAATTACCAATTCTATTGAATATTAAT-AAAAGTATTTCTGTTTATGT
196 GAGAAAATAAATACCAAAAATTACCAATTCTATTGAATATTAATGAAAA-TATTTCTGTTTATGT
1849796 AAACCCAC
260 AAACCCAC
1849804 AAACTCTTATGATTCAATTGTCTGATCATATAGTCTAGTAAAAGCAATACTAGTATTCAAAAAAC
1 AAACTCTTATGATTCAATTGTCTGATCATATAGTCTAGTAAAAGC---A--A-TATTCAAAAAAC
* *
1849869 CAATGTATTAATTTATTAGATAATGTCATTATATCCATCTAATGAATTACATGTGCTAAATTATA
60 CAATGTATTAATTTATTAGATAATGTCATTATATCCATCGAATGAATTACACGTGCTAAATTATA
* * *
1849934 TGTACTATCGATAACATATTCTTCTTGAAATGACTTAATAGAGCTTATAACAATAAGATTTAACA
125 TGTACCATCAATAACATATTCTTCTTGAAATGACTTAATAGAGCTTATAACAATAAGATCTAACA
1849999 AATTCTGAGAAAATAAATACCAAAAATTACCAATTCTATTGAATATTAATGAAAATATTTCTGTT
190 AATTCTGAGAAAATAAATACCAAAAATTACCAATTCTATTGAATATTAATGAAAATATTTCTGTT
*
1850064 TATGTAAACCCAT
255 TATGTAAACCCAC
1850077 AAACTCTTA
1 AAACTCTTA
1850086 CTTTTCACTG
Statistics
Matches: 265, Mismatches: 10, Indels: 8
0.94 0.04 0.03
Matches are distributed among these distances:
267 44 0.17
270 1 0.00
272 1 0.00
273 215 0.81
274 4 0.02
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.35
Consensus pattern (267 bp):
AAACTCTTATGATTCAATTGTCTGATCATATAGTCTAGTAAAAGCAATATTCAAAAAACCAATGT
ATTAATTTATTAGATAATGTCATTATATCCATCGAATGAATTACACGTGCTAAATTATATGTACC
ATCAATAACATATTCTTCTTGAAATGACTTAATAGAGCTTATAACAATAAGATCTAACAAATTCT
GAGAAAATAAATACCAAAAATTACCAATTCTATTGAATATTAATGAAAATATTTCTGTTTATGTA
AACCCAC
Found at i:1851577 original size:40 final size:37
Alignment explanation
Indices: 1851532--1851608 Score: 109
Period size: 40 Copynumber: 2.0 Consensus size: 37
1851522 CATTAGTTAA
* *
1851532 AAAATCATCTCTCTTCTTTTATTACGCATATACATGTAT
1 AAAATCATCTCCCTTCTTTCATTACG--TATACATGTAT
1851571 NAAAATCATCTCCCTTCTTTCATTACGTATACATGTAT
1 -AAAATCATCTCCCTTCTTTCATTACGTATACATGTAT
1851609 GATATGTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 11 0.31
40 24 0.69
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.42
Consensus pattern (37 bp):
AAAATCATCTCCCTTCTTTCATTACGTATACATGTAT
Found at i:1853135 original size:2 final size:2
Alignment explanation
Indices: 1853128--1853164 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1853118 TGTTCAACAA
1853128 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1853165 CTAATGAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1853242 original size:2 final size:2
Alignment explanation
Indices: 1853235--1853277 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1853225 TGTTCAACAA
1853235 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1853277 C
1 C
1853278 CTAATGAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1853280 original size:113 final size:107
Alignment explanation
Indices: 1853103--1853321 Score: 384
Period size: 113 Copynumber: 2.0 Consensus size: 107
1853093 TGTATTTTTA
1853103 ACCAGTGAACCCTAATGTTCAACAACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCTA
1 ACCAGTGAACCCTAATGTTCAACAACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCTA
1853168 ATGAATGATTTCGGTTTGTTTCAAAGTTAATTATGAACATGT
66 ATGAATGATTTCGGTTTGTTTCAAAGTTAATTATGAACATGT
1853210 ACCAGTGAACCCTAATGTTCAACAACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT
1 ACCAGTGAACCCTAATGTTCAACAA------CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT
1853275 CTCCTAATGAATGATTTCGGTTTGTTTCAAAGTTAATTATGAACATG
60 CTCCTAATGAATGATTTCGGTTTGTTTCAAAGTTAATTATGAACATG
1853322 ATTATATATA
Statistics
Matches: 106, Mismatches: 0, Indels: 6
0.95 0.00 0.05
Matches are distributed among these distances:
107 25 0.24
113 81 0.76
ACGTcount: A:0.22, C:0.29, G:0.10, T:0.39
Consensus pattern (107 bp):
ACCAGTGAACCCTAATGTTCAACAACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCTA
ATGAATGATTTCGGTTTGTTTCAAAGTTAATTATGAACATGT
Done.