Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 81 of 82
Found at i:31007775 original size:3 final size:3
Alignment explanation
Indices: 31007769--31007793 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31007759 ATTTTTTATT
31007769 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
31007794 CAAAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:31018925 original size:75 final size:75
Alignment explanation
Indices: 31018801--31018940 Score: 174
Period size: 75 Copynumber: 1.9 Consensus size: 75
31018791 TTCTAGAGCC
* *
31018801 AAAATGCCTATGGTCAGGTCATCCTCAGTGCCCGTGAAAGTTCGCGATTTCAAAGAAAAAATGGA
1 AAAATGCCTATGGTCAGGTCATCCTCAGTGCCCGTGAAAGTTAGAGATTTCAAAGAAAAAATGGA
31018866 GGCTGCACAG
66 GGCTGCACAG
* * * * * * * *
31018876 AAAATGCCTATGGT-TGGATCTTCTTCTGTGCCCTTGAAAGTTAGAGATTTGAAAGAGAAAGTGG
1 AAAATGCCTATGGTCAGG-TCATCCTCAGTGCCCGTGAAAGTTAGAGATTTCAAAGAAAAAATGG
31018940 A
65 A
31018941 AACTGTGCAT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
74 2 0.04
75 52 0.96
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (75 bp):
AAAATGCCTATGGTCAGGTCATCCTCAGTGCCCGTGAAAGTTAGAGATTTCAAAGAAAAAATGGA
GGCTGCACAG
Found at i:31025095 original size:18 final size:18
Alignment explanation
Indices: 31025072--31025109 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
31025062 CTGGTCTTTC
31025072 ACTCTCGCCATTAATTCT
1 ACTCTCGCCATTAATTCT
31025090 ACTCTCGCCATTAATTCT
1 ACTCTCGCCATTAATTCT
31025108 AC
1 AC
31025110 CATCTACGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.34, G:0.05, T:0.37
Consensus pattern (18 bp):
ACTCTCGCCATTAATTCT
Found at i:31030170 original size:18 final size:18
Alignment explanation
Indices: 31030149--31030185 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
31030139 AAAGGCTTGT
31030149 TGCTTGCTCTCAGCTTCC
1 TGCTTGCTCTCAGCTTCC
31030167 TGCTTGCTCTCAGCTTCC
1 TGCTTGCTCTCAGCTTCC
31030185 T
1 T
31030186 CTCTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.38, G:0.16, T:0.41
Consensus pattern (18 bp):
TGCTTGCTCTCAGCTTCC
Found at i:31033733 original size:28 final size:28
Alignment explanation
Indices: 31033701--31033756 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
31033691 TCTGCTCTGA
*
31033701 CACCAATTGTTACGGTCCACACCAACCC
1 CACCAATTGTCACGGTCCACACCAACCC
31033729 CACCAATTGTCACGGTCCACACCAACCC
1 CACCAATTGTCACGGTCCACACCAACCC
31033757 TTGTAAGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.45, G:0.11, T:0.16
Consensus pattern (28 bp):
CACCAATTGTCACGGTCCACACCAACCC
Found at i:31034496 original size:270 final size:270
Alignment explanation
Indices: 31034000--31034498 Score: 576
Period size: 270 Copynumber: 1.8 Consensus size: 270
31033990 ACAATTTGGA
* * * * *
31034000 ATTCACATCTACGCGAGGACCATGACATCTTCCCTCACTTCAATAAGGGCCTACTATCCTCAGTG
1 ATTCACATCCACGCGAGGACCATGACATCCTCCCTCACTTCAACAAGGGCCCACTATCCTCAGTA
* * * * * *
31034065 GCACATCGCTAGTACTCAAAGTCCACTCTGATACCAATTGTCATGATCCACACCAACCCATGTGA
66 GCACATAGCTAGCACTCAAAGTCCACTCTAATAACAATTGTCACGATCCACACCAACCCATCTGA
* *
31034130 GATATTGTTCGCTTTGGCCCATTGACCTCACAATTTTGTCCCACAAAAAGTGCCTCACAAGTTAA
131 GATATTATCCGCTTTGGCCCATTGACCTCACAATTTTGTCCCACAAAAAGTGCCTCACAAGTTAA
* * ** *
31034195 AAGTTGTATGAATTCTTATGTTTCTAATATCACTCTAGGACTATAACACCCCTTTTTATATCTCG
196 AAGTGGTATCAACCCTTATATTTCTAATATCACTCTAGGACTATAACACCCCTTTTTATATCTCG
31034260 ACGATGTGGG
261 ACGATGTGGG
* ** *
31034270 ATTCACGTCCACGCGAGGACTGTGACATCCT-CCTCTACTTCAACAAGGGCCCACTGTCCTCAGT
1 ATTCACATCCACGCGAGGACCATGACATCCTCCCTC-ACTTCAACAAGGGCCCACTATCCTCAGT
* *** * * * **
31034334 AGCATATAGCTAGCACTCAAAGTTTGCTCTAATAACAATTGTCACGGTCCATACTAACCTTTCTG
65 AGCACATAGCTAGCACTCAAAGTCCACTCTAATAACAATTGTCACGATCCACACCAACCCATCTG
* * * *
31034399 ATG-TATTATCCGCTTTGGCCCGTTGGCCTCGCAGTTTTGTCCCAC-AAAAG-GCACTTCACAAG
130 A-GATATTATCCGCTTTGGCCCATTGACCTCACAATTTTGTCCCACAAAAAGTGC-C-TCACAAG
* * *
31034461 TTGAAGGTGGTGTCAACCCTTATA-TTCTCAATATCACT
192 TTAAAAGTGGTATCAACCCTTATATTTCT-AATATCACT
31034499 TTAATACATA
Statistics
Matches: 186, Mismatches: 38, Indels: 10
0.79 0.16 0.04
Matches are distributed among these distances:
268 2 0.01
269 14 0.08
270 169 0.91
271 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (270 bp):
ATTCACATCCACGCGAGGACCATGACATCCTCCCTCACTTCAACAAGGGCCCACTATCCTCAGTA
GCACATAGCTAGCACTCAAAGTCCACTCTAATAACAATTGTCACGATCCACACCAACCCATCTGA
GATATTATCCGCTTTGGCCCATTGACCTCACAATTTTGTCCCACAAAAAGTGCCTCACAAGTTAA
AAGTGGTATCAACCCTTATATTTCTAATATCACTCTAGGACTATAACACCCCTTTTTATATCTCG
ACGATGTGGG
Found at i:31042752 original size:13 final size:13
Alignment explanation
Indices: 31042734--31042765 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
31042724 TTATATATAT
31042734 ATATATAAAATAA
1 ATATATAAAATAA
*
31042747 ATATATATAATAA
1 ATATATAAAATAA
31042760 ATATAT
1 ATATAT
31042766 TTTCACTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATATAAAATAA
Found at i:31052205 original size:32 final size:32
Alignment explanation
Indices: 31052164--31052226 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
31052154 AACATTGATC
31052164 AATTCCCACTTCCTCCTCCGACCACCTGATGT
1 AATTCCCACTTCCTCCTCCGACCACCTGATGT
31052196 AATTCCCACTTCCTCCTCCGACCACCTGATG
1 AATTCCCACTTCCTCCTCCGACCACCTGATG
31052227 GGATCTACTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.19, C:0.44, G:0.10, T:0.27
Consensus pattern (32 bp):
AATTCCCACTTCCTCCTCCGACCACCTGATGT
Found at i:31053207 original size:26 final size:26
Alignment explanation
Indices: 31053171--31053222 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
31053161 TATTACAAGA
31053171 TATATAACATGATAAGTTGACGTGAT
1 TATATAACATGATAAGTTGACGTGAT
*
31053197 TATATATCATGATAAGTTGACGTGAT
1 TATATAACATGATAAGTTGACGTGAT
31053223 CGACGTCAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.37
Consensus pattern (26 bp):
TATATAACATGATAAGTTGACGTGAT
Found at i:31069466 original size:2 final size:2
Alignment explanation
Indices: 31069461--31069494 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
31069451 TGAGTGTGTG
*
31069461 AT AT AT AT AT AT AT AT GT 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
31069495 CAAAATTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31071726 original size:30 final size:31
Alignment explanation
Indices: 31071685--31071802 Score: 149
Period size: 30 Copynumber: 4.0 Consensus size: 31
31071675 AATCAAGTTC
31071685 TTATA-TTTTATTTTGAACT-AAATAAACTT
1 TTATATTTTTATTTTGAACTCAAATAAACTT
31071714 TTATATTTTTATTTTGAA-TCAAATAAA-TCT
1 TTATATTTTTATTTTGAACTCAAATAAACT-T
* * *
31071744 TTATATTTTTATTTTGAAC-CGAATCAATTT
1 TTATATTTTTATTTTGAACTCAAATAAACTT
*
31071774 TTATATTTTTATTTT-AAATCAAATAAACT
1 TTATATTTTTATTTTGAACTCAAATAAACT
31071803 CTTCTAACTA
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
29 9 0.12
30 67 0.87
31 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (31 bp):
TTATATTTTTATTTTGAACTCAAATAAACTT
Found at i:31071776 original size:60 final size:60
Alignment explanation
Indices: 31071685--31071805 Score: 181
Period size: 60 Copynumber: 2.0 Consensus size: 60
31071675 AATCAAGTTC
* *
31071685 TTATATTTTATTTTGAACTAAATAAACTTTTATATTTTTATTTTGAATCAAATAAA-TCT
1 TTATATTTTATTTTGAACCAAATAAACTTTTATATTTTTATTTTAAATCAAATAAACTCT
* * *
31071744 TTATATTTTTATTTTGAACCGAATCAATTTTTATATTTTTATTTTAAATCAAATAAACTCT
1 TTATA-TTTTATTTTGAACCAAATAAACTTTTATATTTTTATTTTAAATCAAATAAACTCT
31071805 T
1 T
31071806 CTAACTAATG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 5 0.09
60 46 0.84
61 4 0.07
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (60 bp):
TTATATTTTATTTTGAACCAAATAAACTTTTATATTTTTATTTTAAATCAAATAAACTCT
Found at i:31072041 original size:13 final size:14
Alignment explanation
Indices: 31072027--31072076 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
31072017 CTAATAATAA
31072027 TTAATTATAAAAAT
1 TTAATTATAAAAAT
*
31072041 TTATTTGATAAAAAT
1 TTAATT-ATAAAAAT
** *
31072056 AAAAATATAAAAAT
1 TTAATTATAAAAAT
31072070 TTAATTA
1 TTAATTA
31072077 AATATAATAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 17 0.63
15 10 0.37
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
TTAATTATAAAAAT
Found at i:31072105 original size:28 final size:29
Alignment explanation
Indices: 31072053--31072107 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
31072043 ATTTGATAAA
*
31072053 AATAAAAATATAAAAATTTAATTAAATAT
1 AATAAAAATATAAAAACTTAATTAAATAT
* *
31072082 AATAAAAA-ATAAATACTTATTTAAAT
1 AATAAAAATATAAAAACTTAATTAAAT
31072108 TTTTTACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (29 bp):
AATAAAAATATAAAAACTTAATTAAATAT
Found at i:31087963 original size:38 final size:38
Alignment explanation
Indices: 31087907--31088189 Score: 222
Period size: 38 Copynumber: 7.8 Consensus size: 38
31087897 ATTTTGTTCT
* *
31087907 GTCTCAAATTTACAACTTAATTTATAATTTAAAATTTC
1 GTCTCAAACTTACAACTTAATTTATAATTCAAAATTTC
** * * *
31087945 GTCTCAAACTTATGACTTAATATGTACTTCAAAA-TT-
1 GTCTCAAACTTACAACTTAATTTATAATTCAAAATTTC
*
31087981 -T-T-AAACTTACAACTTAATATT-TAATTCAAAATCTC
1 GTCTCAAACTTACAACTTAAT-TTATAATTCAAAATTTC
* * *
31088016 GTTTCAAACTTACAACTTAATTTATAATTTAAAATCTC
1 GTCTCAAACTTACAACTTAATTTATAATTCAAAATTTC
** * *
31088054 GTCTCAAACTTACGGCTTAATATGTAATTCAAAA--T-
1 GTCTCAAACTTACAACTTAATTTATAATTCAAAATTTC
* *
31088089 -T-TCAAACTTA-AGACTTAATTTATAGTTCAAAAATTC
1 GTCTCAAACTTACA-ACTTAATTTATAATTCAAAATTTC
* * * *
31088125 ATCTCAAACTTACAACTTAATCTATAATT--TAA---G
1 GTCTCAAACTTACAACTTAATTTATAATTCAAAATTTC
* *
31088158 GTCTCAAACTTGCAACTTAATTTGTAATTCAA
1 GTCTCAAACTTACAACTTAATTTATAATTCAA
31088190 GGTGCAATCT
Statistics
Matches: 196, Mismatches: 33, Indels: 35
0.74 0.12 0.13
Matches are distributed among these distances:
33 73 0.37
34 4 0.02
35 2 0.01
36 4 0.02
37 6 0.03
38 106 0.54
39 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (38 bp):
GTCTCAAACTTACAACTTAATTTATAATTCAAAATTTC
Found at i:31088035 original size:109 final size:109
Alignment explanation
Indices: 31087908--31088156 Score: 360
Period size: 109 Copynumber: 2.3 Consensus size: 109
31087898 TTTTGTTCTG
* * * *
31087908 TCTCAAATTTACAACTTAATTTATAATTTAAAATTTCGTCTCAAACTTATGACTTAATATGTACT
1 TCTCAAACTTACAACTTAATTTATAATTTAAAATCTCGTCTCAAACTTACGACTTAATATGTAAT
* *
31087973 TCAAAATTTTAAACTTACA-ACTTAATATT-TAATTC-AAAATCTCG
66 TCAAAATTTCAAACTTA-AGACTTAAT-TTATAATTCAAAAAT-TCA
* *
31088017 TTTCAAACTTACAACTTAATTTATAATTTAAAATCTCGTCTCAAACTTACGGCTTAATATGTAAT
1 TCTCAAACTTACAACTTAATTTATAATTTAAAATCTCGTCTCAAACTTACGACTTAATATGTAAT
*
31088082 TCAAAATTTCAAACTTAAGACTTAATTTATAGTTCAAAAATTCA
66 TCAAAATTTCAAACTTAAGACTTAATTTATAATTCAAAAATTCA
*
31088126 TCTCAAACTTACAACTTAATCTATAATTTAA
1 TCTCAAACTTACAACTTAATTTATAATTTAA
31088157 GGTCTCAAAC
Statistics
Matches: 126, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
108 3 0.02
109 118 0.94
110 5 0.04
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (109 bp):
TCTCAAACTTACAACTTAATTTATAATTTAAAATCTCGTCTCAAACTTACGACTTAATATGTAAT
TCAAAATTTCAAACTTAAGACTTAATTTATAATTCAAAAATTCA
Found at i:31088153 original size:71 final size:70
Alignment explanation
Indices: 31087908--31088153 Score: 214
Period size: 71 Copynumber: 3.4 Consensus size: 70
31087898 TTTTGTTCTG
* * * * * * *
31087908 TCTCAAATTTACAACTTAATTTATAATTTAAAATTTCGTCTCAAACTTATGACTTAATATGTACT
1 TCTCAAACTTACAACTTAATATATAATTCAAAA-TT--T-TCAAACTTAAGACTTAATTTATAAT
31087973 TCAAAATT-
62 TCAAAATTC
*
31087981 T-T-AAACTTACAACTTAATATTTAATTCAAAATCTCGTTTCAAACTTACA-ACTTAATTTATAA
1 TCTCAAACTTACAACTTAATATATAATTCAAAA--T--TTTCAAACTTA-AGACTTAATTTATAA
*
31088043 TTTAAAATCTC
61 TTCAAAAT-TC
** * *
31088054 GTCTCAAACTTACGGCTTAATATGTAATTCAAAA-TTTCAAACTTAAGACTTAATTTATAGTTCA
1 -TCTCAAACTTACAACTTAATATATAATTCAAAATTTTCAAACTTAAGACTTAATTTATAATTC-
31088118 AAAATTC
64 AAAATTC
*
31088125 ATCTCAAACTTACAACTTAATCTATAATT
1 -TCTCAAACTTACAACTTAATATATAATT
31088154 TAAGGTCTCA
Statistics
Matches: 142, Mismatches: 20, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
70 1 0.01
71 102 0.72
72 9 0.06
73 1 0.01
74 2 0.01
75 1 0.01
76 26 0.18
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (70 bp):
TCTCAAACTTACAACTTAATATATAATTCAAAATTTTCAAACTTAAGACTTAATTTATAATTCAA
AATTC
Found at i:31088163 original size:33 final size:33
Alignment explanation
Indices: 31088126--31088192 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
31088116 CAAAAATTCA
*
31088126 TCTCAAACTTACAACTTAATCTATAATTTAAGG
1 TCTCAAACTTACAACTTAATCTATAATTCAAGG
* * *
31088159 TCTCAAACTTGCAACTTAATTTGTAATTCAAGG
1 TCTCAAACTTACAACTTAATCTATAATTCAAGG
31088192 T
1 T
31088193 GCAATCTCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (33 bp):
TCTCAAACTTACAACTTAATCTATAATTCAAGG
Found at i:31088165 original size:71 final size:71
Alignment explanation
Indices: 31087983--31088186 Score: 205
Period size: 71 Copynumber: 2.8 Consensus size: 71
31087973 TCAAAATTTT
* *
31087983 AAACTTACAACTTAATATTTAATTCAAAATCTCGTTTCAAACTTACAACTTAATTTATAATTTAA
1 AAACTTACAACTTAATATATAATTCAAAA--TC---TCAAACTTACAACTTAATTTATAATTAAA
*
31088048 AATCTCGTCTC
61 AATCTCATCTC
** * * *
31088059 AAACTTACGGCTTAATATGTAATTCAAAATTTCAAACTTA-AGACTTAATTTATAGTTCAAAAAT
1 AAACTTACAACTTAATATATAATTCAAAATCTCAAACTTACA-ACTTAATTTATAATT-AAAAAT
31088123 -TCATCTC
64 CTCATCTC
* * ** * *
31088130 AAACTTACAACTTAATCTATAATTTAAGGTCTCAAACTTGCAACTTAATTTGTAATT
1 AAACTTACAACTTAATATATAATTCAAAATCTCAAACTTACAACTTAATTTATAATT
31088187 CAAGGTGCAA
Statistics
Matches: 107, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
70 1 0.01
71 73 0.68
72 6 0.06
74 1 0.01
76 26 0.24
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (71 bp):
AAACTTACAACTTAATATATAATTCAAAATCTCAAACTTACAACTTAATTTATAATTAAAAATCT
CATCTC
Found at i:31103298 original size:2 final size:2
Alignment explanation
Indices: 31103291--31103321 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
31103281 AAGGAAAGAT
*
31103291 AG AG AG AG AG AG AG AG AG AG AG TG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
31103322 AACGAAGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.03
Consensus pattern (2 bp):
AG
Found at i:31110514 original size:24 final size:24
Alignment explanation
Indices: 31110482--31110529 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
31110472 ATTTGGCTTC
*
31110482 TGTTTGATCCTTAGTGTGCTGTAG
1 TGTTTGATCCTTAGTGTGCAGTAG
*
31110506 TGTTTGATCCTTTGTGTGCAGTAG
1 TGTTTGATCCTTAGTGTGCAGTAG
31110530 ATACTGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.12, C:0.12, G:0.29, T:0.46
Consensus pattern (24 bp):
TGTTTGATCCTTAGTGTGCAGTAG
Found at i:31113924 original size:2 final size:2
Alignment explanation
Indices: 31113873--31113904 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31113863 TGGCTGTTAT
31113873 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
31113905 GTAGGTAGTN
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31116253 original size:24 final size:23
Alignment explanation
Indices: 31116221--31116265 Score: 81
Period size: 24 Copynumber: 1.9 Consensus size: 23
31116211 CTGCTGCAAA
31116221 TCTTCTCACCGGAATATTCTAGC
1 TCTTCTCACCGGAATATTCTAGC
31116244 TCTTCCTCACCGGAATATTCTA
1 TCTT-CTCACCGGAATATTCTA
31116266 ATGCTGCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.22, C:0.31, G:0.11, T:0.36
Consensus pattern (23 bp):
TCTTCTCACCGGAATATTCTAGC
Found at i:31118517 original size:20 final size:21
Alignment explanation
Indices: 31118482--31118531 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
31118472 TGGTTATCTG
31118482 AATTTATATAAATTAT-ATAA
1 AATTTATATAAATTATAATAA
**
31118502 AATTTATATACTTTATCAAATAA
1 AATTTATATAAATTAT--AATAA
31118525 AATTTAT
1 AATTTAT
31118532 TCATGGTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 14 0.56
23 11 0.44
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTTATATAAATTATAATAA
Found at i:31119638 original size:21 final size:20
Alignment explanation
Indices: 31119606--31119644 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
31119596 AGAAAGAAGA
*
31119606 AAAGACTCAGGCTGCAGCTG
1 AAAGAATCAGGCTGCAGCTG
31119626 AAAGAATCAAGGCTGCAGC
1 AAAGAATC-AGGCTGCAGC
31119645 ATTGAGTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.36, C:0.23, G:0.28, T:0.13
Consensus pattern (20 bp):
AAAGAATCAGGCTGCAGCTG
Found at i:31129480 original size:39 final size:39
Alignment explanation
Indices: 31129425--31129515 Score: 164
Period size: 39 Copynumber: 2.3 Consensus size: 39
31129415 TAGTAATTCT
*
31129425 CATTAAGCAACATATTCATTTAGGCATATCATGAATATCC
1 CATTAAACAA-ATATTCATTTAGGCATATCATGAATATCC
31129465 CATTAAACAAATATTCATTTAGGCATATCATGAATATCC
1 CATTAAACAAATATTCATTTAGGCATATCATGAATATCC
31129504 CATTAAACAAAT
1 CATTAAACAAAT
31129516 TAACATGAAG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 41 0.82
40 9 0.18
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.32
Consensus pattern (39 bp):
CATTAAACAAATATTCATTTAGGCATATCATGAATATCC
Found at i:31183134 original size:50 final size:50
Alignment explanation
Indices: 31183080--31183177 Score: 196
Period size: 50 Copynumber: 2.0 Consensus size: 50
31183070 CAGTAATGAG
31183080 TGTTGAATAGTTTTAACTGCAAATTACTTTATGACCTAAATTGGCATTAT
1 TGTTGAATAGTTTTAACTGCAAATTACTTTATGACCTAAATTGGCATTAT
31183130 TGTTGAATAGTTTTAACTGCAAATTACTTTATGACCTAAATTGGCATT
1 TGTTGAATAGTTTTAACTGCAAATTACTTTATGACCTAAATTGGCATT
31183178 CTCCAGAATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (50 bp):
TGTTGAATAGTTTTAACTGCAAATTACTTTATGACCTAAATTGGCATTAT
Found at i:31203628 original size:2 final size:2
Alignment explanation
Indices: 31203621--31203645 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31203611 ATAATGGGCT
31203621 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
31203646 GAGGTACAAA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:31223207 original size:35 final size:35
Alignment explanation
Indices: 31223161--31223230 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
31223151 GTTGTATAAG
31223161 ATAAAACATCTGTCAGGTGATACATGGAACAGTGC
1 ATAAAACATCTGTCAGGTGATACATGGAACAGTGC
*
31223196 ATAAAACATCTGTCAGGTGATACATGGAAGAGTGC
1 ATAAAACATCTGTCAGGTGATACATGGAACAGTGC
31223231 TGAAAGCTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (35 bp):
ATAAAACATCTGTCAGGTGATACATGGAACAGTGC
Found at i:31223744 original size:127 final size:127
Alignment explanation
Indices: 31223518--31223772 Score: 465
Period size: 127 Copynumber: 2.0 Consensus size: 127
31223508 GGTCTTGGGC
* *
31223518 CAACCTTTGCTTCCCAGTACGAAAAGACTGAGCTAAGGATTAGGCCTAATTCACCCAAATGCTAG
1 CAACCTTTGCTTCCCAGTACGAAAAGACTGAGATAAGGATTAGGCCTAATTCACCCAAATACTAG
*
31223583 AAAAATATCATACAGCCTTACCGCTAGATTCTGTTAAAAGAGTCATCCATTCAACCGTTGCT
66 AAAAATATCATACAGCCTCACCGCTAGATTCTGTTAAAAGAGTCATCCATTCAACCGTTGCT
* *
31223645 CAACCTTTGCTTCCCTGTACGAAAAGACTGAGATAAGGATTAGGCCTAATTGACCCAAATACTAG
1 CAACCTTTGCTTCCCAGTACGAAAAGACTGAGATAAGGATTAGGCCTAATTCACCCAAATACTAG
31223710 AAAAATATCATACAGCCTCACCGCTAGATTCTGTTAAAAGAGTCATCCATTCAACCGTTGCT
66 AAAAATATCATACAGCCTCACCGCTAGATTCTGTTAAAAGAGTCATCCATTCAACCGTTGCT
31223772 C
1 C
31223773 TGTTTTGTCT
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 123 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (127 bp):
CAACCTTTGCTTCCCAGTACGAAAAGACTGAGATAAGGATTAGGCCTAATTCACCCAAATACTAG
AAAAATATCATACAGCCTCACCGCTAGATTCTGTTAAAAGAGTCATCCATTCAACCGTTGCT
Found at i:31235036 original size:15 final size:15
Alignment explanation
Indices: 31235000--31235029 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31234990 AAATTATCTT
*
31235000 AAAATTATTTGGATA
1 AAAATTATTTGAATA
31235015 AAAATTATTTGAATA
1 AAAATTATTTGAATA
31235030 TACATTACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
AAAATTATTTGAATA
Found at i:31246709 original size:41 final size:41
Alignment explanation
Indices: 31246652--31246735 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
31246642 TTAACTATAG
* *
31246652 CAAAGTTGTGAAAGTTGAATCGGTAAAACATTTGTTTAAGT
1 CAAAGTTGTGAAAGTTGAATCAGAAAAACATTTGTTTAAGT
* *
31246693 CAAAGTTGTGAAAGTTGAATCAGAAAAACTTTTGTTTATGT
1 CAAAGTTGTGAAAGTTGAATCAGAAAAACATTTGTTTAAGT
31246734 CA
1 CA
31246736 CTTGATTGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (41 bp):
CAAAGTTGTGAAAGTTGAATCAGAAAAACATTTGTTTAAGT
Found at i:31260008 original size:14 final size:14
Alignment explanation
Indices: 31259989--31260024 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
31259979 AGAGAGAGAG
31259989 AGAAGTTCTTTGCT
1 AGAAGTTCTTTGCT
31260003 AGAAGTTCTTTGCT
1 AGAAGTTCTTTGCT
31260017 AGAAGTTC
1 AGAAGTTC
31260025 ATGCTCGACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (14 bp):
AGAAGTTCTTTGCT
Found at i:31260268 original size:24 final size:24
Alignment explanation
Indices: 31260220--31260273 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
31260210 TGGTGGTGGT
* * *
31260220 GGTGGAATAGGTGGAGGTGTCGGA
1 GGTGGAAAAGGTGGAGGGGTAGGA
*
31260244 GGTGGAAAAGGTGGTGGGGTAGGA
1 GGTGGAAAAGGTGGAGGGGTAGGA
*
31260268 GTTGGA
1 GGTGGA
31260274 GGTGGAGCTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.02, G:0.56, T:0.20
Consensus pattern (24 bp):
GGTGGAAAAGGTGGAGGGGTAGGA
Found at i:31260296 original size:24 final size:24
Alignment explanation
Indices: 31260269--31260352 Score: 72
Period size: 24 Copynumber: 3.8 Consensus size: 24
31260259 GGGGTAGGAG
*
31260269 TTGGAGGTGGAGCTGGCGGAGGGC
1 TTGGTGGTGGAGCTGGCGGAGGGC
*
31260293 TTGGTGGTGGA---GGTGGA--GC
1 TTGGTGGTGGAGCTGGCGGAGGGC
* * *
31260312 -TGGGGGTGGTGCTGGAGGAGGGC
1 TTGGTGGTGGAGCTGGCGGAGGGC
*
31260335 TTGGTGGTGGAGGTGGCG
1 TTGGTGGTGGAGCTGGCG
31260353 CAGGTGGTGG
Statistics
Matches: 45, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
18 8 0.18
19 2 0.04
21 10 0.22
23 2 0.04
24 23 0.51
ACGTcount: A:0.10, C:0.08, G:0.61, T:0.21
Consensus pattern (24 bp):
TTGGTGGTGGAGCTGGCGGAGGGC
Found at i:31260299 original size:42 final size:42
Alignment explanation
Indices: 31260253--31260434 Score: 161
Period size: 42 Copynumber: 4.3 Consensus size: 42
31260243 AGGTGGAAAA
* *
31260253 GGTGGTGG-GGTAGGAGTTGGAGGTGGAGCTGGCGGAGGGCTT
1 GGTGGTGGAGGT-GGAGCTGGAGGTGGAGCTGGAGGAGGGCTT
* *
31260295 GGTGGTGGAGGTGGAGCTGGGGGTGGTGCTGGAGGAGGGCTT
1 GGTGGTGGAGGTGGAGCTGGAGGTGGAGCTGGAGGAGGGCTT
* * * *** * ****
31260337 GGTGGTGGAGGTGGCGCAGGTGGTGGTTTTGGAGGTGGAAAA
1 GGTGGTGGAGGTGGAGCTGGAGGTGGAGCTGGAGGAGGGCTT
* * * *
31260379 GGTGGAGG-TGTAGGAGTTGGAGGTGGTGCTGGAGGAGGGCTT
1 GGTGGTGGAGGT-GGAGCTGGAGGTGGAGCTGGAGGAGGGCTT
31260421 GGTGGTGGAGGTGG
1 GGTGGTGGAGGTGG
31260435 TGCAGGTGGT
Statistics
Matches: 108, Mismatches: 29, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
41 2 0.02
42 101 0.94
43 5 0.05
ACGTcount: A:0.13, C:0.05, G:0.59, T:0.23
Consensus pattern (42 bp):
GGTGGTGGAGGTGGAGCTGGAGGTGGAGCTGGAGGAGGGCTT
Found at i:31260374 original size:30 final size:30
Alignment explanation
Indices: 31260306--31260459 Score: 86
Period size: 30 Copynumber: 5.3 Consensus size: 30
31260296 GTGGTGGAGG
* * * * **
31260306 TGGAGCTGGGGGTGGTGCTGGAGGAGGGCT
1 TGGAGGTGGAGGTGGTGCAGGTGGAGGTTT
* * *
31260336 TGGTGGTGGAGGTGGCGCAGGTGGTGGTTT
1 TGGAGGTGGAGGTGGTGCAGGTGGAGGTTT
** *
31260366 TGGAGGTGGA------AAAGGTGGAGGTGT
1 TGGAGGTGGAGGTGGTGCAGGTGGAGGTTT
* * * * **
31260390 AGGAGTTGGAGGTGGTGCTGGAGGAGGGCT
1 TGGAGGTGGAGGTGGTGCAGGTGGAGGTTT
* *
31260420 TGGTGGTGGAGGTGGTGCAGGTGGTGGTTT
1 TGGAGGTGGAGGTGGTGCAGGTGGAGGTTT
31260450 TGGAGGTGGA
1 TGGAGGTGGA
31260460 AAAGGTGGAG
Statistics
Matches: 87, Mismatches: 31, Indels: 12
0.67 0.24 0.09
Matches are distributed among these distances:
24 18 0.21
30 69 0.79
ACGTcount: A:0.13, C:0.05, G:0.57, T:0.25
Consensus pattern (30 bp):
TGGAGGTGGAGGTGGTGCAGGTGGAGGTTT
Found at i:31260447 original size:84 final size:84
Alignment explanation
Indices: 31260307--31260488 Score: 337
Period size: 84 Copynumber: 2.2 Consensus size: 84
31260297 TGGTGGAGGT
* *
31260307 GGAGCTGGGGGTGGTGCTGGAGGAGGGCTTGGTGGTGGAGGTGGCGCAGGTGGTGGTTTTGGAGG
1 GGAGTTGGAGGTGGTGCTGGAGGAGGGCTTGGTGGTGGAGGTGGCGCAGGTGGTGGTTTTGGAGG
31260372 TGGAAAAGGTGGAGGTGTA
66 TGGAAAAGGTGGAGGTGTA
*
31260391 GGAGTTGGAGGTGGTGCTGGAGGAGGGCTTGGTGGTGGAGGTGGTGCAGGTGGTGGTTTTGGAGG
1 GGAGTTGGAGGTGGTGCTGGAGGAGGGCTTGGTGGTGGAGGTGGCGCAGGTGGTGGTTTTGGAGG
31260456 TGGAAAAGGTGGAGGTGTA
66 TGGAAAAGGTGGAGGTGTA
31260475 GGAGTTGGAGGTGG
1 GGAGTTGGAGGTGG
31260489 AGCCGGTGGT
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 95 1.00
ACGTcount: A:0.15, C:0.04, G:0.57, T:0.24
Consensus pattern (84 bp):
GGAGTTGGAGGTGGTGCTGGAGGAGGGCTTGGTGGTGGAGGTGGCGCAGGTGGTGGTTTTGGAGG
TGGAAAAGGTGGAGGTGTA
Found at i:31260454 original size:126 final size:126
Alignment explanation
Indices: 31260190--31260455 Score: 363
Period size: 126 Copynumber: 2.1 Consensus size: 126
31260180 GACCCTTGGA
* * *
31260190 GGTGGTTTTGGTGGAGGTGCTGGTGGTGGTGGTGGAATAGGTGGAGGTGTCGGAGGTGGAAAAGG
1 GGTGGTTTTGGAGGAGGTGCTGGTGGTGGAGGTGGAACAGGTGGAGGTGTCGGAGGTGGAAAAGG
* * *
31260255 TGGTGGGGTAGGAGTTGGAGGTGGAGCTGGCGGAGGGCTTGGTGGTGGAGGTGGAGCTGGG
66 TGGAGGGGTAGGAGTTGGAGGTGGAGCTGGAGGAGGGCTTGGTGGTGGAGGTGGAGCAGGG
** ** * * *
31260316 GGTGGTGCTGGAGGAGG-GCTTGGTGGTGGAGGTGGCGCAGGTGGTGGTTTTGGAGGTGGAAAAG
1 GGTGGTTTTGGAGGAGGTGC-TGGTGGTGGAGGTGGAACAGGTGGAGGTGTCGGAGGTGGAAAAG
* * * *
31260380 GTGGAGGTGTAGGAGTTGGAGGTGGTGCTGGAGGAGGGCTTGGTGGTGGAGGTGGTGCAGGT
65 GTGGAGGGGTAGGAGTTGGAGGTGGAGCTGGAGGAGGGCTTGGTGGTGGAGGTGGAGCAGGG
31260442 GGTGGTTTTGGAGG
1 GGTGGTTTTGGAGG
31260456 TGGAAAAGGT
Statistics
Matches: 120, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
125 2 0.02
126 118 0.98
ACGTcount: A:0.13, C:0.05, G:0.58, T:0.24
Consensus pattern (126 bp):
GGTGGTTTTGGAGGAGGTGCTGGTGGTGGAGGTGGAACAGGTGGAGGTGTCGGAGGTGGAAAAGG
TGGAGGGGTAGGAGTTGGAGGTGGAGCTGGAGGAGGGCTTGGTGGTGGAGGTGGAGCAGGG
Found at i:31260455 original size:42 final size:42
Alignment explanation
Indices: 31260274--31260447 Score: 170
Period size: 42 Copynumber: 4.1 Consensus size: 42
31260264 AGGAGTTGGA
* * * *
31260274 GGTGGAGCTGGCGGAGGGCTTGGTGGTGGAGGTGGAGCTGGG
1 GGTGGTGCTGGAGGAGGGCTTGGTGGTGGAGGTGGAGCAGGT
*
31260316 GGTGGTGCTGGAGGAGGGCTTGGTGGTGGAGGTGGCGCAGGT
1 GGTGGTGCTGGAGGAGGGCTTGGTGGTGGAGGTGGAGCAGGT
** * **** * * ** *
31260358 GGTGGTTTTGGAGGTGGAAAAGGTGGAGG-TGTAGGAGTTGGA
1 GGTGGTGCTGGAGGAGGGCTTGGTGGTGGAGGT-GGAGCAGGT
*
31260400 GGTGGTGCTGGAGGAGGGCTTGGTGGTGGAGGTGGTGCAGGT
1 GGTGGTGCTGGAGGAGGGCTTGGTGGTGGAGGTGGAGCAGGT
31260442 GGTGGT
1 GGTGGT
31260448 TTTGGAGGTG
Statistics
Matches: 99, Mismatches: 31, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
41 2 0.02
42 95 0.96
43 2 0.02
ACGTcount: A:0.12, C:0.06, G:0.59, T:0.23
Consensus pattern (42 bp):
GGTGGTGCTGGAGGAGGGCTTGGTGGTGGAGGTGGAGCAGGT
Found at i:31260497 original size:30 final size:30
Alignment explanation
Indices: 31260449--31260508 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
31260439 GGTGGTGGTT
*
31260449 TTGGAGGTGGAAAAGGTGGAGGTGTAGGAG
1 TTGGAGGTGGAGAAGGTGGAGGTGTAGGAG
** * *
31260479 TTGGAGGTGGAGCCGGTGGTGGTGTTGGAG
1 TTGGAGGTGGAGAAGGTGGAGGTGTAGGAG
31260509 GAGGATTAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.18, C:0.03, G:0.55, T:0.23
Consensus pattern (30 bp):
TTGGAGGTGGAGAAGGTGGAGGTGTAGGAG
Found at i:31260530 original size:30 final size:29
Alignment explanation
Indices: 31260496--31260638 Score: 84
Period size: 30 Copynumber: 5.0 Consensus size: 29
31260486 TGGAGCCGGT
*
31260496 GGTGGTGTTGGAGGAGGATTAGGTGGTGGA
1 GGTGGTGCTGGAGGAGG-TTAGGTGGTGGA
* * *
31260526 GGTGGTGC---AGGTGG--AGGTGCTGGT
1 GGTGGTGCTGGAGGAGGTTAGGTGGTGGA
*** * *
31260550 GGTGGCATTGGAGGTGGTAAAGGTGGTGGTA
1 GGTGGTGCTGGAGGAGGT-TAGGTGGTGG-A
31260581 --TAGGTGCTGGAGGAGGATTAGGTGGTGGA
1 GGT-GGTGCTGGAGGAGG-TTAGGTGGTGGA
* *
31260610 GGTGGTGCAGGTGGAGGTTTAGGTGGTGG
1 GGTGGTGCTGGAGGAGG-TTAGGTGGTGG
31260639 TGCCGGTGCA
Statistics
Matches: 85, Mismatches: 17, Indels: 22
0.69 0.14 0.18
Matches are distributed among these distances:
24 13 0.15
27 11 0.13
29 2 0.02
30 57 0.67
31 2 0.02
ACGTcount: A:0.15, C:0.03, G:0.55, T:0.26
Consensus pattern (29 bp):
GGTGGTGCTGGAGGAGGTTAGGTGGTGGA
Found at i:31260531 original size:84 final size:84
Alignment explanation
Indices: 31260307--31260513 Score: 263
Period size: 84 Copynumber: 2.5 Consensus size: 84
31260297 TGGTGGAGGT
* * * * * * * *
31260307 GGAGCTGGGGGTGGTGCTGGAGGAGGGCTTGGTGGTGGAGGTGGCGCAGGTGGTGGTTTTGGAGG
1 GGAGTTGGAGGTGGAGCCGGAGGAGGGCTTGGAGGAGGAGGTGGTGCAGGAGGTGGTTTTGGAGG
31260372 TGGAAAAGGTGGAGGTGTA
66 TGGAAAAGGTGGAGGTGTA
* * * * *
31260391 GGAGTTGGAGGTGGTGCTGGAGGAGGGCTTGGTGGTGGAGGTGGTGCAGGTGGTGGTTTTGGAGG
1 GGAGTTGGAGGTGGAGCCGGAGGAGGGCTTGGAGGAGGAGGTGGTGCAGGAGGTGGTTTTGGAGG
31260456 TGGAAAAGGTGGAGGTGTA
66 TGGAAAAGGTGGAGGTGTA
* *
31260475 GGAGTTGGAGGTGGAGCCGGTGGTGGTG-TTGGAGGAGGA
1 GGAGTTGGAGGTGGAGCCGGAGGAGG-GCTTGGAGGAGGA
31260514 TTAGGTGGTG
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
84 112 0.99
85 1 0.01
ACGTcount: A:0.15, C:0.05, G:0.57, T:0.23
Consensus pattern (84 bp):
GGAGTTGGAGGTGGAGCCGGAGGAGGGCTTGGAGGAGGAGGTGGTGCAGGAGGTGGTTTTGGAGG
TGGAAAAGGTGGAGGTGTA
Found at i:31260543 original size:24 final size:24
Alignment explanation
Indices: 31260421--31260767 Score: 70
Period size: 24 Copynumber: 15.0 Consensus size: 24
31260411 AGGAGGGCTT
*
31260421 GGTGGTGGAGGTGGTGCAGGTGGT
1 GGTGGTGGAGGTGGTGCAGGTGGA
** ***
31260445 GGTTTTGGAGGTGGAAAAGGTGGA
1 GGTGGTGGAGGTGGTGCAGGTGGA
*
31260469 GGT-GTAGGA-GT--TGGAGGTGGA
1 GGTGGT-GGAGGTGGTGCAGGTGGA
** * * * *
31260490 GCCGGTGGTGGTGTTGGAGGAGGATTA
1 GGTGGTGGAGGTGGTGCAGGTGG---A
31260517 GGTGGTGGAGGTGGTGCAGGTGGA
1 GGTGGTGGAGGTGGTGCAGGTGGA
* * *
31260541 GGTGCTGGTGGT-G-GCA-TTGGA
1 GGTGGTGGAGGTGGTGCAGGTGGA
** **
31260562 GGTGGTAAAGGTGGT---GGTATA
1 GGTGGTGGAGGTGGTGCAGGTGGA
* * *
31260583 GGTGCTGGAGG-AG-G-A--T-TA
1 GGTGGTGGAGGTGGTGCAGGTGGA
31260601 GGTGGTGGAGGTGGTGCAGGTGGA
1 GGTGGTGGAGGTGGTGCAGGTGGA
* * * *
31260625 GGT-TTAGGTGGTGGTGCCGGTGCA
1 GGTGGT-GGAGGTGGTGCAGGTGGA
* * *
31260649 GGTGGTGGA-GTCGGAGGAGGTGCA
1 GGTGGTGGAGGT-GGTGCAGGTGGA
* * * ***
31260673 GGTGGTGGTGCTGGTGGAGGTCTT
1 GGTGGTGGAGGTGGTGCAGGTGGA
* *
31260697 GGTGGTGGAGGAGGCCT-C-GGAGGA
1 GGTGGTGGAGGTGG--TGCAGGTGGA
* * *
31260721 GGTGCTGGTGCG-GGTGCTGGTGGA
1 GGTGGTGGAG-GTGGTGCAGGTGGA
** *
31260745 GGTTTTGGAGGTGGTGCTGGTGG
1 GGTGGTGGAGGTGGTGCAGGTGG
31260768 TGGACTAGGT
Statistics
Matches: 228, Mismatches: 66, Indels: 58
0.65 0.19 0.16
Matches are distributed among these distances:
18 12 0.05
19 2 0.01
20 2 0.01
21 33 0.14
22 9 0.04
23 10 0.04
24 138 0.61
25 3 0.01
26 1 0.00
27 18 0.08
ACGTcount: A:0.13, C:0.06, G:0.56, T:0.25
Consensus pattern (24 bp):
GGTGGTGGAGGTGGTGCAGGTGGA
Found at i:31260647 original size:30 final size:30
Alignment explanation
Indices: 31260583--31260653 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
31260573 TGGTGGTATA
* * **
31260583 GGTGCTGGAGGAGGATTAGGTGGTGGAGGT
1 GGTGCAGGTGGAGGATTAGGTGGTGGAGCC
* *
31260613 GGTGCAGGTGGAGGTTTAGGTGGTGGTGCC
1 GGTGCAGGTGGAGGATTAGGTGGTGGAGCC
31260643 GGTGCAGGTGG
1 GGTGCAGGTGG
31260654 TGGAGTCGGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.13, C:0.07, G:0.56, T:0.24
Consensus pattern (30 bp):
GGTGCAGGTGGAGGATTAGGTGGTGGAGCC
Found at i:31260802 original size:12 final size:12
Alignment explanation
Indices: 31260721--31260803 Score: 64
Period size: 12 Copynumber: 6.9 Consensus size: 12
31260711 CCTCGGAGGA
31260721 GGTGCTGGTGCG-
1 GGTGCTGGTG-GT
*
31260733 GGTGCTGGTGGA
1 GGTGCTGGTGGT
** *
31260745 GGTTTTGGAGGT
1 GGTGCTGGTGGT
31260757 GGTGCTGGTGGT
1 GGTGCTGGTGGT
*
31260769 GG-ACTAGGTGGT
1 GGTGCT-GGTGGT
*
31260781 GGT-TTCGGTGGT
1 GGTGCT-GGTGGT
31260793 GGTGCTGGTGG
1 GGTGCTGGTGG
31260804 AGGAATTGGA
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
11 3 0.05
12 52 0.93
13 1 0.02
ACGTcount: A:0.05, C:0.08, G:0.55, T:0.31
Consensus pattern (12 bp):
GGTGCTGGTGGT
Found at i:31266104 original size:15 final size:15
Alignment explanation
Indices: 31266084--31266153 Score: 67
Period size: 15 Copynumber: 4.9 Consensus size: 15
31266074 CTCTCCATTA
31266084 TATTTAAATTTAATT
1 TATTTAAATTTAATT
31266099 TATTTAAATTTAA--
1 TATTTAAATTTAATT
* *
31266112 -A-TAAAAATTAATT
1 TATTTAAATTTAATT
*
31266125 ACATTTAAATTTAATT
1 -TATTTAAATTTAATT
*
31266141 TATTTAAGTTTAA
1 TATTTAAATTTAA
31266154 ACATAATATC
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
11 8 0.18
12 1 0.02
15 25 0.57
16 10 0.23
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (15 bp):
TATTTAAATTTAATT
Found at i:31266111 original size:21 final size:21
Alignment explanation
Indices: 31266085--31266154 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
31266075 TCTCCATTAT
31266085 ATTTAAATTTAATTTATTTAA
1 ATTTAAATTTAATTTATTTAA
** * * *
31266106 ATTTAAATAAAAATTAATTAC
1 ATTTAAATTTAATTTATTTAA
31266127 ATTTAAATTTAATTTATTTAA
1 ATTTAAATTTAATTTATTTAA
*
31266148 GTTTAAA
1 ATTTAAA
31266155 CATAATATCC
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (21 bp):
ATTTAAATTTAATTTATTTAA
Found at i:31270324 original size:18 final size:19
Alignment explanation
Indices: 31270284--31270325 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
31270274 TTGATTTGTT
* * *
31270284 AAATTATTAATTATACATT
1 AAATTATAAAATATACATA
31270303 AAATTATAAAATA-ACATA
1 AAATTATAAAATATACATA
31270321 AAATT
1 AAATT
31270326 TAATTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTATAAAATATACATA
Found at i:31291214 original size:16 final size:16
Alignment explanation
Indices: 31291193--31291229 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
31291183 TGGACAATGG
31291193 CATCTGAAATGCATTA
1 CATCTGAAATGCATTA
31291209 CATCTGAAATGCATTA
1 CATCTGAAATGCATTA
31291225 CATCT
1 CATCT
31291230 TGTTGGCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (16 bp):
CATCTGAAATGCATTA
Found at i:31301066 original size:14 final size:14
Alignment explanation
Indices: 31301047--31301107 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
31301037 AAGATTTCGT
31301047 AAAAAACTCTTAAA
1 AAAAAACTCTTAAA
*
31301061 AAAAAACTTTTTTAAA
1 AAAAAAC--TCTTAAA
*
31301077 AAATAAAATC-TAAA
1 AAA-AAACTCTTAAA
31301091 AAAAAA--CTTAAA
1 AAAAAACTCTTAAA
31301103 AAAAA
1 AAAAA
31301108 CTCCAATTAG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
11 1 0.03
12 9 0.22
13 3 0.08
14 14 0.35
15 1 0.03
16 9 0.22
17 3 0.08
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAAACTCTTAAA
Found at i:31312584 original size:60 final size:60
Alignment explanation
Indices: 31312491--31312611 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 60
31312481 TGCAAACAAG
* *
31312491 ATAGTTAATATAGACAAACCTTTATTTACATTACAAACACGATAGTTCATAACTTAACAC
1 ATAGTTAATACAGACAAACCTTTATTTACATTACAAACACGATAGTTCATAACCTAACAC
31312551 ATAGTTAATACAGACAAACCTTTATTTACATTACAAACACGATAGTTCATAACCTAACAC
1 ATAGTTAATACAGACAAACCTTTATTTACATTACAAACACGATAGTTCATAACCTAACAC
31312611 A
1 A
31312612 CTTCTTCTAC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.30
Consensus pattern (60 bp):
ATAGTTAATACAGACAAACCTTTATTTACATTACAAACACGATAGTTCATAACCTAACAC
Found at i:31314919 original size:93 final size:92
Alignment explanation
Indices: 31314815--31314999 Score: 361
Period size: 93 Copynumber: 2.0 Consensus size: 92
31314805 TTTTTTTTTA
31314815 TTTATATGCTATATAAAATTATTTTTTTTATGAATCTTTTGATTGTTGTTTAAATGCAATGTATT
1 TTTATATGCTATATAAAATTATTTTTTTTATGAATCTTTTGATTGTTGTTTAAATGCAATGTATT
31314880 AATTTAAAAAAAATTTAATCTTTATTC
66 AATTTAAAAAAAATTTAATCTTTATTC
31314907 NTTTATATGCTATATAAAATTATTTTTTTTATGAATCTTTTGATTGTTGTTTAAATGCAATGTAT
1 -TTTATATGCTATATAAAATTATTTTTTTTATGAATCTTTTGATTGTTGTTTAAATGCAATGTAT
31314972 TAATTTAAAAAAAATTTAATCTTTATTC
65 TAATTTAAAAAAAATTTAATCTTTATTC
31315000 CTTTTTGCTT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.52
Consensus pattern (92 bp):
TTTATATGCTATATAAAATTATTTTTTTTATGAATCTTTTGATTGTTGTTTAAATGCAATGTATT
AATTTAAAAAAAATTTAATCTTTATTC
Found at i:31337685 original size:20 final size:21
Alignment explanation
Indices: 31337657--31337695 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31337647 ATTTATTTAA
31337657 TTTA-ATTTTCTTTTTTTTCC
1 TTTATATTTTCTTTTTTTTCC
*
31337677 TTTATTTTTTCTTTTTTTT
1 TTTATATTTTCTTTTTTTT
31337696 GGGTTGGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTATATTTTCTTTTTTTTCC
Found at i:31337686 original size:12 final size:10
Alignment explanation
Indices: 31337662--31337695 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
31337652 TTTAATTTAA
31337662 TTTTCTTTTT
1 TTTTCTTTTT
*
31337672 TTTCCTTTATT
1 TTTTCTTT-TT
31337683 TTTTCTTTTT
1 TTTTCTTTTT
31337693 TTT
1 TTT
31337696 GGGTTGGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:31340231 original size:2 final size:2
Alignment explanation
Indices: 31340224--31340280 Score: 77
Period size: 2 Copynumber: 30.0 Consensus size: 2
31340214 TTTTGATAGT
31340224 TA TA TA TA TA TA TA TA -A TA -A TA TA -A 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
31340263 TA TA TA T- TA GTA TA TA TA
1 TA TA TA TA TA -TA TA TA TA
31340281 AACGNTTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.08
2 44 0.88
3 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:31340508 original size:2 final size:2
Alignment explanation
Indices: 31340501--31340563 Score: 76
Period size: 2 Copynumber: 32.0 Consensus size: 2
31340491 TTGATAATAC
*
31340501 AT AT AT AT -T AT AT AT AT -T AA AT AT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* *
31340542 AT AG AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
31340564 TCAAGATCCG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
1 2 0.04
2 48 0.92
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:31340529 original size:275 final size:275
Alignment explanation
Indices: 31340011--31340544 Score: 993
Period size: 275 Copynumber: 1.9 Consensus size: 275
31340001 TTATTCTTTT
31340011 TTTTTTTTTTTTTGCTTTCTCTTTTGTTTTGTTTTTATATTGAAACTCGTGTCACGTTATTCTTA
1 TTTTTTTTTTTTTGCTTTCTCTTTTGTTTTGTTTTTATATTGAAACTCGTGTCACGTTATTCTTA
31340076 ACACACATGTTGCAATCATACCTTATAAAATTCTTTGTGATAAATGAAGCAAAATGGAATTTTGC
66 ACACACATGTTGCAATCATACCTTATAAAATTCTTTGTGATAAATGAAGCAAAATGGAATTTTGC
31340141 CCGCCTGATAATATGTTTTGTCTTTCACTCTAGGACAGGAACTTGCGAGCATCTATTGTTTCTTT
131 CCGCCTGATAATATGTTTTGTCTTTCACTCTAGGACAGGAACTTGCGAGCATCTATTGTTTCTTT
* *
31340206 CTTCTTTGTTTTGATAGTTATATATATATATATAATAATATAATATATATATATA-TATATATAT
196 CTTCTTTGTTTTGATAATCATATATATATATATAATAATATAATATATATATATACTATATATAT
31340270 TAGTATATATAAACG
261 TAGTATATATAAACG
31340285 NTTTTTTTTTTTTTGCTTTCTCTTTTGTTTTGTTTTTATATTGAAACTCGTGTCACGTTATTCTT
1 -TTTTTTTTTTTTTGCTTTCTCTTTTGTTTTGTTTTTATATTGAAACTCGTGTCACGTTATTCTT
31340350 AACACACATGTTGCAATCATACCTTATAAAATTCTTTGTGATAAATGAAGCAAAATGGAATTTTG
65 AACACACATGTTGCAATCATACCTTATAAAATTCTTTGTGATAAATGAAGCAAAATGGAATTTTG
31340415 CCCGCCTGATAATATGTTTTGTCTTTCACTCTAGGACAGGAACTTGCGAGCATCTATTGTTTCTT
130 CCCGCCTGATAATATGTTTTGTCTTTCACTCTAGGACAGGAACTTGCGAGCATCTATTGTTTCTT
*
31340480 TCTTCTTTGTTTTGATAATACATATATATTATATATATTAA-AT-ATATATATATATACTATATA
195 TCTTCTTTGTTTTGATAAT-CATATATA-TATATATAATAATATAATATATATATATACTATATA
31340543 TA
258 TA
31340545 GATATATATA
Statistics
Matches: 253, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
275 225 0.89
276 17 0.07
277 11 0.04
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.46
Consensus pattern (275 bp):
TTTTTTTTTTTTTGCTTTCTCTTTTGTTTTGTTTTTATATTGAAACTCGTGTCACGTTATTCTTA
ACACACATGTTGCAATCATACCTTATAAAATTCTTTGTGATAAATGAAGCAAAATGGAATTTTGC
CCGCCTGATAATATGTTTTGTCTTTCACTCTAGGACAGGAACTTGCGAGCATCTATTGTTTCTTT
CTTCTTTGTTTTGATAATCATATATATATATATAATAATATAATATATATATATACTATATATAT
TAGTATATATAAACG
Found at i:31340533 original size:19 final size:19
Alignment explanation
Indices: 31340501--31340555 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
31340491 TTGATAATAC
31340501 ATATATATTATATATATTAA
1 ATATATA-TATATATATTAA
* *
31340521 ATATATATATATATACTAT
1 ATATATATATATATATTAA
*
31340540 ATATAGATATATATAT
1 ATATATATATATATAT
31340556 AGATATATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 24 0.77
20 7 0.23
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
ATATATATATATATATTAA
Found at i:31351926 original size:2 final size:2
Alignment explanation
Indices: 31351886--31351916 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31351876 TTGATCAGAG
31351886 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 A
31351917 ACAAATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31355367 original size:2 final size:2
Alignment explanation
Indices: 31355360--31355426 Score: 62
Period size: 2 Copynumber: 33.0 Consensus size: 2
31355350 TGTACTATGC
* ** ** **
31355360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AN NN NN NN AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
31355403 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
31355427 GGGGGTAAGA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 58 0.97
3 2 0.03
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:31381883 original size:23 final size:23
Alignment explanation
Indices: 31381833--31381885 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
31381823 TTACTTTCCT
*
31381833 TGTATTATGGATATTAAATAAAG
1 TGTATTTTGGATATTAAATAAAG
* *
31381856 TGTATTTTGGGTATATAAATATAG
1 TGTATTTTGGATAT-TAAATAAAG
31381880 -GTATTT
1 TGTATTT
31381886 CATCACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (23 bp):
TGTATTTTGGATATTAAATAAAG
Found at i:31394357 original size:3 final size:3
Alignment explanation
Indices: 31394349--31394376 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
31394339 GAGAAACTGT
31394349 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
31394377 TGGAGAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:31396614 original size:16 final size:15
Alignment explanation
Indices: 31396593--31396622 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
31396583 GCCCATCTTG
31396593 GAAATTTTCAACAGTT
1 GAAATTTTC-ACAGTT
31396609 GAAATTTTCACAGT
1 GAAATTTTCACAGT
31396623 CATAGCTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (15 bp):
GAAATTTTCACAGTT
Found at i:31404120 original size:18 final size:18
Alignment explanation
Indices: 31404093--31404137 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
31404083 GGCTATACTA
*
31404093 ATCAATTTTTCAAAGGCT
1 ATCAACTTTTCAAAGGCT
31404111 ATCAACTTTTCAAAGGCT
1 ATCAACTTTTCAAAGGCT
31404129 ATCAACTTT
1 ATCAACTTT
31404138 CTCTAACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (18 bp):
ATCAACTTTTCAAAGGCT
Found at i:31409233 original size:24 final size:24
Alignment explanation
Indices: 31409205--31409250 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
31409195 AGTGGATGAC
* *
31409205 GATGAGGATGACGACGAGGACGAG
1 GATGAGGAAGACGACGACGACGAG
*
31409229 GATGATGAAGACGACGACGACG
1 GATGAGGAAGACGACGACGACG
31409251 GTGAAGGAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.15, G:0.41, T:0.09
Consensus pattern (24 bp):
GATGAGGAAGACGACGACGACGAG
Found at i:31409235 original size:21 final size:21
Alignment explanation
Indices: 31409202--31409248 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
31409192 GTCAGTGGAT
* * *
31409202 GACGATGAGGATGACGACGAG
1 GACGAGGAGGATGAAGACGAC
*
31409223 GACGAGGATGATGAAGACGAC
1 GACGAGGAGGATGAAGACGAC
31409244 GACGA
1 GACGA
31409249 CGGTGAAGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.15, G:0.40, T:0.09
Consensus pattern (21 bp):
GACGAGGAGGATGAAGACGAC
Found at i:31409244 original size:18 final size:18
Alignment explanation
Indices: 31409202--31409245 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
31409192 GTCAGTGGAT
* *
31409202 GACGATGAGGATGACGAC
1 GACGACGAGGATGACGAA
* *
31409220 GAGGACGAGGATGATGAA
1 GACGACGAGGATGACGAA
31409238 GACGACGA
1 GACGACGA
31409246 CGACGGTGAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.14, G:0.41, T:0.09
Consensus pattern (18 bp):
GACGACGAGGATGACGAA
Found at i:31426041 original size:36 final size:36
Alignment explanation
Indices: 31425991--31426086 Score: 138
Period size: 36 Copynumber: 2.7 Consensus size: 36
31425981 GAAAACGTTG
*
31425991 TCCAATCTGAAAGAAACGTGAGATTCAACATCGCTA
1 TCCAATCTGGAAGAAACGTGAGATTCAACATCGCTA
* ** * *
31426027 TGCAATCTGGAAGAAACAAGAGATTCAACTTCTCTA
1 TCCAATCTGGAAGAAACGTGAGATTCAACATCGCTA
31426063 TCCAATCTGGAAGAAACGTGAGAT
1 TCCAATCTGGAAGAAACGTGAGAT
31426087 CTACTTCTGT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.23
Consensus pattern (36 bp):
TCCAATCTGGAAGAAACGTGAGATTCAACATCGCTA
Found at i:31454635 original size:3 final size:3
Alignment explanation
Indices: 31454627--31454668 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
31454617 TGGTCCACAT
*
31454627 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31454669 GAGTGAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:31457462 original size:8 final size:8
Alignment explanation
Indices: 31457449--31457510 Score: 56
Period size: 8 Copynumber: 7.8 Consensus size: 8
31457439 CAAAAAAACA
31457449 TATATATG
1 TATATATG
31457457 TATATATG
1 TATATATG
31457465 TATATA--
1 TATATATG
*
31457471 TATATATC
1 TATATATG
*
31457479 TATATATT
1 TATATATG
*
31457487 TATATGTGTG
1 TATA--TATG
*
31457497 TATGTATG
1 TATATATG
31457505 TATATA
1 TATATA
31457511 CAAACATAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
6 6 0.14
8 33 0.75
10 5 0.11
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.52
Consensus pattern (8 bp):
TATATATG
Found at i:31457474 original size:14 final size:14
Alignment explanation
Indices: 31457451--31457493 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
31457441 AAAAAACATA
*
31457451 TATATGTATATATG
1 TATATATATATATG
*
31457465 TATATATATATATC
1 TATATATATATATG
*
31457479 TATATATTTATATG
1 TATATATATATATG
31457493 T
1 T
31457494 GTGTATGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.53
Consensus pattern (14 bp):
TATATATATATATG
Found at i:31457510 original size:2 final size:2
Alignment explanation
Indices: 31457448--31457491 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
31457438 TCAAAAAAAC
* * * *
31457448 AT AT AT AT GT AT AT AT GT AT AT AT AT AT AT CT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31457490 AT
1 AT
31457492 GTGTGTATGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (2 bp):
AT
Found at i:31458506 original size:21 final size:21
Alignment explanation
Indices: 31458480--31458519 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
31458470 TTTTCTTATC
31458480 TTCTTGACCTTGTAAGACCTT
1 TTCTTGACCTTGTAAGACCTT
31458501 TTCTTGACCTTGTAAGACC
1 TTCTTGACCTTGTAAGACC
31458520 CCGTTCGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (21 bp):
TTCTTGACCTTGTAAGACCTT
Found at i:31463581 original size:10 final size:11
Alignment explanation
Indices: 31463556--31463599 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
31463546 ATTAAGGTAT
31463556 TATTTTTTTTC
1 TATTTTTTTTC
31463567 TATTTTTTTTC
1 TATTTTTTTTC
*
31463578 -ATTTTATTTTT
1 TATTTT-TTTTC
31463589 TATCTTTTTTT
1 TAT-TTTTTTT
31463600 GTACTTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 5 0.17
11 15 0.52
12 6 0.21
13 3 0.10
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (11 bp):
TATTTTTTTTC
Found at i:31464008 original size:19 final size:18
Alignment explanation
Indices: 31463977--31464023 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
31463967 CATCTCTCAT
31463977 TTTTTTTATTTGATTTAA
1 TTTTTTTATTTGATTTAA
* *
31463995 TTTTTTTCTCTTGATTTTA
1 TTTTTTTAT-TTGATTTAA
*
31464014 TTTATTTATT
1 TTTTTTTATT
31464024 ATTATTCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (18 bp):
TTTTTTTATTTGATTTAA
Found at i:31468685 original size:5 final size:5
Alignment explanation
Indices: 31468675--31468709 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
31468665 ATCTTCTTTT
31468675 CCATC CCATC CCATC CCATC CCATC CCATC CCATC
1 CCATC CCATC CCATC CCATC CCATC CCATC CCATC
31468710 GCACTCAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.20, C:0.60, G:0.00, T:0.20
Consensus pattern (5 bp):
CCATC
Found at i:31476752 original size:2 final size:2
Alignment explanation
Indices: 31476741--31476772 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
31476731 ATCCAATTTC
31476741 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31476773 GCACACAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31486276 original size:2 final size:2
Alignment explanation
Indices: 31486269--31486295 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31486259 TTTCTTCGTT
31486269 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
31486296 GTGTGCAACT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:31487050 original size:3 final size:3
Alignment explanation
Indices: 31487042--31487076 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
31487032 TGTCAATGAC
31487042 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
31487077 TATTATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:31509680 original size:30 final size:30
Alignment explanation
Indices: 31509646--31509750 Score: 106
Period size: 30 Copynumber: 3.6 Consensus size: 30
31509636 AATTATTAAT
*
31509646 TATAAAAATTTATTTAATTTAAAATAAAAA
1 TATAAAAATTTATTTAATATAAAATAAAAA
* * * *
31509676 TATAAAAACTTACTTGATGTAAAATAAAAA
1 TATAAAAATTTATTTAATATAAAATAAAAA
** * *
31509706 TATATGAATTTAATTAA-ATATAATAAAAA
1 TATAAAAATTTATTTAATATAAAATAAAAA
*
31509735 -ATAAAAATTAATTTAA
1 TATAAAAATTTATTTAA
31509751 ATATTTTTAA
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
28 12 0.20
29 10 0.17
30 38 0.63
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (30 bp):
TATAAAAATTTATTTAATATAAAATAAAAA
Found at i:31510686 original size:20 final size:20
Alignment explanation
Indices: 31510663--31510705 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
31510653 TTCTTTTTAC
*
31510663 TTTGCTTTGCTTTCTGGGTT
1 TTTGCTTTGCTTTCTGAGTT
* * *
31510683 TTTGTTTTGGTTTTTGAGTT
1 TTTGCTTTGCTTTCTGAGTT
31510703 TTT
1 TTT
31510706 TGTCTAATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.02, C:0.07, G:0.23, T:0.67
Consensus pattern (20 bp):
TTTGCTTTGCTTTCTGAGTT
Found at i:31519002 original size:2 final size:2
Alignment explanation
Indices: 31518995--31519030 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
31518985 ATTTAGAAAC
31518995 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
31519031 ATCGAATAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31528947 original size:17 final size:18
Alignment explanation
Indices: 31528927--31528968 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
31528917 TTTTAAATTT
31528927 TTTCTTTTTCAACTGGG-
1 TTTCTTTTTCAACTGGGA
* *
31528944 TTTCCTTTTTTACCTGGGA
1 TTT-CTTTTTCAACTGGGA
31528963 TTTCTT
1 TTTCTT
31528969 ATTTATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 3 0.14
18 15 0.71
19 3 0.14
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (18 bp):
TTTCTTTTTCAACTGGGA
Found at i:31531439 original size:23 final size:23
Alignment explanation
Indices: 31531395--31531436 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
31531385 GTGTAAATGA
31531395 TAAAAATATTTTATATTAAAATT
1 TAAAAATATTTTATATTAAAATT
31531418 TAAAAAT-TTTTA-ATTAAAA
1 TAAAAATATTTTATATTAAAA
31531437 AATAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAAAATATTTTATATTAAAATT
Found at i:31531442 original size:21 final size:23
Alignment explanation
Indices: 31531394--31531443 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
31531384 TGTGTAAATG
*
31531394 ATAAAAATATTTTATATTAAAAT
1 ATAAAAATATTTTATATTAAAAA
*
31531417 TTAAAAAT-TTTTA-ATTAAAAA
1 ATAAAAATATTTTATATTAAAAA
31531438 ATAAAA
1 ATAAAA
31531444 GAAATTNNNN
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.50
22 5 0.21
23 7 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATAAAAATATTTTATATTAAAAA
Found at i:31531818 original size:45 final size:45
Alignment explanation
Indices: 31531758--31531857 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 45
31531748 ATTAAATTTA
* *
31531758 AATAATAATAAATAATATTCTTTATTACATTCATTATAATCAAAT
1 AATAATAATAAATAATAATCTTTATAACATTCATTATAATCAAAT
* * * * *
31531803 AATAATATTAAATAATAATCTTTATAATATTTATTATAGTTAAAT
1 AATAATAATAAATAATAATCTTTATAACATTCATTATAATCAAAT
*
31531848 AATATTAATA
1 AATAATAATA
31531858 TATTAAATTA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (45 bp):
AATAATAATAAATAATAATCTTTATAACATTCATTATAATCAAAT
Found at i:31531865 original size:18 final size:19
Alignment explanation
Indices: 31531826--31531871 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
31531816 AATAATCTTT
*
31531826 ATAATATTTATTATAGTTAA
1 ATAATA-TTAATATAGTTAA
31531846 ATAATATTAATATA-TTAA
1 ATAATATTAATATAGTTAA
*
31531864 ATTATATT
1 ATAATATT
31531872 TAAATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 11 0.46
19 7 0.29
20 6 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
ATAATATTAATATAGTTAA
Found at i:31540256 original size:90 final size:90
Alignment explanation
Indices: 31540103--31540286 Score: 323
Period size: 90 Copynumber: 2.0 Consensus size: 90
31540093 TCGTACTACT
*
31540103 TAGTCTTTTAATGCGAGGGTGTTAAGGAAACCACAACTATCTCTTCTTTCTTCTCTGCCTATGGT
1 TAGTCTTTTAATGCGAGGGTGTCAAGGAAACCACAACTATCTCTTCTTTCTTCTCTGCCTATGGT
31540168 GAACACTTGTAAAGTCAACATGAAA
66 GAACACTTGTAAAGTCAACATGAAA
* * * *
31540193 TAGTCTTTTAATGCGAGGGTGTCAAGGATACCACAACTATCTGTTGTTTCTTTTCTGCCTATGGT
1 TAGTCTTTTAATGCGAGGGTGTCAAGGAAACCACAACTATCTCTTCTTTCTTCTCTGCCTATGGT
31540258 GAACACTTGTAAAGTCAACATGAAA
66 GAACACTTGTAAAGTCAACATGAAA
31540283 TAGT
1 TAGT
31540287 TTGCGTGCCA
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (90 bp):
TAGTCTTTTAATGCGAGGGTGTCAAGGAAACCACAACTATCTCTTCTTTCTTCTCTGCCTATGGT
GAACACTTGTAAAGTCAACATGAAA
Found at i:31545446 original size:2 final size:2
Alignment explanation
Indices: 31545439--31545508 Score: 122
Period size: 2 Copynumber: 35.0 Consensus size: 2
31545429 GGTATTATTC
* *
31545439 AT AT AT AT GT AT AT GT 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
31545481 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
31545509 TGAAAATCAG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31568925 original size:29 final size:29
Alignment explanation
Indices: 31568875--31568931 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
31568865 ATAAGCCAGA
* *
31568875 TAAATTCATGCTAGTACGAATTGTCAACG
1 TAAATTCATGCTAGTACAAATTGACAACG
*
31568904 TAAATTCATGCTCA-TATAAATTGACAAC
1 TAAATTCATGCT-AGTACAAATTGACAAC
31568932 ATCATCTTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.32
Consensus pattern (29 bp):
TAAATTCATGCTAGTACAAATTGACAACG
Found at i:31576159 original size:26 final size:25
Alignment explanation
Indices: 31576109--31576172 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 25
31576099 AATAAACATG
* *
31576109 ATTATAGGAATTAGAAATCACCATA
1 ATTATAGGGATTTGAAATCACCATA
*
31576134 ATTATAGGGATTTGAGAATCATCATA
1 ATTATAGGGATTTGA-AATCACCATA
31576160 ATTATAGGGATTT
1 ATTATAGGGATTT
31576173 TATTGTCTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
25 13 0.37
26 22 0.63
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (25 bp):
ATTATAGGGATTTGAAATCACCATA
Found at i:31583847 original size:2 final size:2
Alignment explanation
Indices: 31583840--31583864 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31583830 AAATGGAGAA
31583840 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
31583865 AAAAAAAGTA
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:31589431 original size:53 final size:53
Alignment explanation
Indices: 31589366--31589474 Score: 173
Period size: 53 Copynumber: 2.1 Consensus size: 53
31589356 AATCAAGTTC
* * *
31589366 AATTTCTATTGTTGACGTTTGAATAGGAATAATATCCCATTGTACTAAATAAT
1 AATTTCTATTGTTGACATTTGAAGAGGAATAATAACCCATTGTACTAAATAAT
* *
31589419 AATTTCTGTTGTTGACATTTGGAGAGGAATAATAACCCATTGTACTAAATAAT
1 AATTTCTATTGTTGACATTTGAAGAGGAATAATAACCCATTGTACTAAATAAT
31589472 AAT
1 AAT
31589475 AACAACAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.38
Consensus pattern (53 bp):
AATTTCTATTGTTGACATTTGAAGAGGAATAATAACCCATTGTACTAAATAAT
Found at i:31623830 original size:30 final size:30
Alignment explanation
Indices: 31623770--31623860 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 30
31623760 CTACGGCTTT
* * * *
31623770 GACTGCGGCCACGGCTATGGCT-TCGACTAC
1 GACTACGGCCAGGGCTACGGCTGTAG-CTAC
31623800 GACTACGGCCAGGGCTACGGCTGTAGCTAC
1 GACTACGGCCAGGGCTACGGCTGTAGCTAC
* * *
31623830 GGCTTCGGCCAGGACTACGGCTGTAGCTAC
1 GACTACGGCCAGGGCTACGGCTGTAGCTAC
31623860 G
1 G
31623861 GCTTCGGCTG
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
30 51 0.96
31 2 0.04
ACGTcount: A:0.18, C:0.31, G:0.33, T:0.19
Consensus pattern (30 bp):
GACTACGGCCAGGGCTACGGCTGTAGCTAC
Found at i:31623861 original size:30 final size:30
Alignment explanation
Indices: 31623796--31623868 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
31623786 ATGGCTTCGA
* * *
31623796 CTACGACTACGGCCAGGGCTACGGCTGTAG
1 CTACGGCTTCGGCCAGGACTACGGCTGTAG
31623826 CTACGGCTTCGGCCAGGACTACGGCTGTAG
1 CTACGGCTTCGGCCAGGACTACGGCTGTAG
31623856 CTACGGCTTCGGC
1 CTACGGCTTCGGC
31623869 TGTAGCTACG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.16, C:0.32, G:0.33, T:0.19
Consensus pattern (30 bp):
CTACGGCTTCGGCCAGGACTACGGCTGTAG
Found at i:31624256 original size:33 final size:33
Alignment explanation
Indices: 31624201--31624289 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 33
31624191 ACCACTGAAT
* *
31624201 CCACCATCCCTAATACCACCACGCCCGCCAAAA
1 CCACCATCCCTCATACCACCACGCCCACCAAAA
* ** * *
31624234 CCACCATCTCTCATACTGCCACGGCCACCAAAG
1 CCACCATCCCTCATACCACCACGCCCACCAAAA
*
31624267 CCACCATCCCTCATTCCACCACG
1 CCACCATCCCTCATACCACCACG
31624290 ACCAGTGAAG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.28, C:0.51, G:0.08, T:0.13
Consensus pattern (33 bp):
CCACCATCCCTCATACCACCACGCCCACCAAAA
Found at i:31636149 original size:2 final size:2
Alignment explanation
Indices: 31636142--31636248 Score: 135
Period size: 2 Copynumber: 52.5 Consensus size: 2
31636132 TTGATTGTGG
31636142 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
* ** **
31636184 TA TA CTA TA GT- TCG TA GG TA NG TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA -TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31636226 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
31636249 CCAATGTTCT
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
1 1 0.01
2 87 0.95
3 4 0.04
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:31641203 original size:24 final size:25
Alignment explanation
Indices: 31641170--31641220 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
31641160 AATACTTTTT
* *
31641170 AATATAAAAAAT-TATAAAAATAAA
1 AATATAAAAAATCTAAAAAAAAAAA
*
31641194 AATATTAAAAATCTAAAAAAAAAAA
1 AATATAAAAAATCTAAAAAAAAAAA
31641219 AA
1 AA
31641221 GTCATTTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (25 bp):
AATATAAAAAATCTAAAAAAAAAAA
Found at i:31649070 original size:22 final size:22
Alignment explanation
Indices: 31649040--31649081 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
31649030 ATGTTAGTCA
*
31649040 TATGCAATCATCATATGAAATG
1 TATGAAATCATCATATGAAATG
*
31649062 TATGAAATCGTCATATGAAA
1 TATGAAATCATCATATGAAA
31649082 ATGAAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (22 bp):
TATGAAATCATCATATGAAATG
Found at i:31649478 original size:26 final size:26
Alignment explanation
Indices: 31649442--31649491 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
31649432 ATAAAAATAA
31649442 AATAATAAATT-ATATTTTTAATTAAT
1 AATAATAAATTAAT-TTTTTAATTAAT
*
31649468 AATAATTAATTAATTTTTTAATTA
1 AATAATAAATTAATTTTTTAATTA
31649492 TAAAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
AATAATAAATTAATTTTTTAATTAAT
Found at i:31649564 original size:17 final size:17
Alignment explanation
Indices: 31649494--31649564 Score: 52
Period size: 17 Copynumber: 3.9 Consensus size: 17
31649484 TTTAATTATA
*
31649494 AAAAATATTTTTTTAAAT
1 AAAAATA-TTATTTAAAT
* *
31649512 AAAAATGTAAATATTTAATT
1 AAAAA--T-ATTATTTAAAT
* **
31649532 AAACATATTAAGTAAAT
1 AAAAATATTATTTAAAT
31649549 AAAAATATTATTTAAA
1 AAAAATATTATTTAAA
31649565 AATTTTAAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 7
0.68 0.19 0.12
Matches are distributed among these distances:
17 20 0.51
18 6 0.15
20 12 0.31
21 1 0.03
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.39
Consensus pattern (17 bp):
AAAAATATTATTTAAAT
Found at i:31681046 original size:24 final size:25
Alignment explanation
Indices: 31681011--31681069 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 25
31681001 GTTAGTTTAT
* *
31681011 TTTTTAT-TTTTTTTAA-AAAATTA
1 TTTTTATAATTTTATAATAAAATTA
31681034 TTTTTATAATTTTATAATAAAATTA
1 TTTTTATAATTTTATAATAAAATTA
31681059 -TTTTATAATTT
1 TTTTTATAATTT
31681070 AATTTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 7 0.22
24 18 0.56
25 7 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTTATAATTTTATAATAAAATTA
Found at i:31681078 original size:25 final size:26
Alignment explanation
Indices: 31681022--31681078 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
31681012 TTTTATTTTT
* *
31681022 TTTAAAAAATTATTTTTATAATTTTA
1 TTTATAAAATTATTTTTATAATTTAA
*
31681048 -TAATAAAATTA-TTTTATAATTTAA
1 TTTATAAAATTATTTTTATAATTTAA
31681072 TTTATAA
1 TTTATAA
31681079 TTTAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTATAAAATTATTTTTATAATTTAA
Found at i:31681172 original size:22 final size:23
Alignment explanation
Indices: 31681147--31681217 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 23
31681137 AATATTATTG
31681147 ATAATTAAATTATTAAATTTTT-
1 ATAATTAAATTATTAAATTTTTA
31681169 ATAATTAAA-TATATAAATTTATTAA
1 ATAATTAAATTAT-TAAATTT-TT-A
*
31681194 ATTAATTAAAATTATTAATTTTTT
1 A-TAATT-AAATTATTAAATTTTT
31681218 TAGCTCATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
21 3 0.07
22 16 0.39
23 2 0.05
25 1 0.02
26 7 0.17
27 9 0.22
28 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATAATTAAATTATTAAATTTTTA
Found at i:31682746 original size:3 final size:3
Alignment explanation
Indices: 31682738--31682766 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
31682728 ATCAAATCCT
31682738 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
31682767 GTATATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:31683714 original size:16 final size:18
Alignment explanation
Indices: 31683693--31683732 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
31683683 AAAAAAAAAT
31683693 AAATTA-TT-TTTTTTTA
1 AAATTACTTGTTTTTTTA
31683709 AAATTACTTGTTTTTTTA
1 AAATTACTTGTTTTTTTA
31683727 AGAATT
1 A-AATT
31683733 TCAAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.29
17 2 0.10
18 9 0.43
19 4 0.19
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (18 bp):
AAATTACTTGTTTTTTTA
Found at i:31717997 original size:5 final size:5
Alignment explanation
Indices: 31717987--31718021 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
31717977 GAAGTAGCTG
31717987 CTATA CTATA CTATA CTATA CTATA CTATA CTATA
1 CTATA CTATA CTATA CTATA CTATA CTATA CTATA
31718022 TATGTGAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
CTATA
Found at i:31722100 original size:12 final size:12
Alignment explanation
Indices: 31722083--31722119 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
31722073 ACAAGTAAGA
31722083 TAAAATTGTTGC
1 TAAAATTGTTGC
31722095 TAAAATTGTTGC
1 TAAAATTGTTGC
31722107 TAAAATTGTTGC
1 TAAAATTGTTGC
31722119 T
1 T
31722120 TAATATTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.43
Consensus pattern (12 bp):
TAAAATTGTTGC
Found at i:31746894 original size:16 final size:16
Alignment explanation
Indices: 31746873--31746905 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31746863 TGAGAAAATA
31746873 TTTTAAA-AATATATTT
1 TTTTAAATAAT-TATTT
31746889 TTTTAAATAATTATTT
1 TTTTAAATAATTATTT
31746905 T
1 T
31746906 CAATTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAAATAATTATTT
Found at i:31746940 original size:48 final size:49
Alignment explanation
Indices: 31746880--31746976 Score: 128
Period size: 48 Copynumber: 2.0 Consensus size: 49
31746870 ATATTTTAAA
* * *
31746880 AATATATTTTTTTAAATAATT-ATTTTCAATTTA-TTATTATTATTATTAT
1 AATATATTTTTTTAAAT--TTAAATTTAAAATTATTTATTATTATTATTAT
31746929 AATA-ATTTTTTTAAATTTAAATTTAAAATTATTTATTATTATTATTAT
1 AATATATTTTTTTAAATTTAAATTTAAAATTATTTATTATTATTATTAT
31746977 TAAATTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
46 2 0.05
47 9 0.21
48 28 0.65
49 4 0.09
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (49 bp):
AATATATTTTTTTAAATTTAAATTTAAAATTATTTATTATTATTATTAT
Found at i:31749974 original size:5 final size:5
Alignment explanation
Indices: 31749964--31749988 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31749954 CGATCTTCGC
31749964 AGTTG AGTTG AGTTG AGTTG AGTTG
1 AGTTG AGTTG AGTTG AGTTG AGTTG
31749989 GCCAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
AGTTG
Found at i:31760617 original size:5 final size:5
Alignment explanation
Indices: 31760607--31760634 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
31760597 CCCACTAGGA
31760607 GATGG GATGG GATGG GATGG GATGG GAT
1 GATGG GATGG GATGG GATGG GATGG GAT
31760635 TGTGACCCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.57, T:0.21
Consensus pattern (5 bp):
GATGG
Found at i:31770421 original size:2 final size:2
Alignment explanation
Indices: 31770414--31770442 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31770404 TTACCCATAC
31770414 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 A
31770443 CATACATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31770580 original size:2 final size:2
Alignment explanation
Indices: 31770575--31770603 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31770565 CCCCTACTAC
31770575 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 A
31770604 CATACATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31771563 original size:3 final size:3
Alignment explanation
Indices: 31771557--31771581 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31771547 TATACTACTC
31771557 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
31771582 ATGTTAAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31774565 original size:30 final size:32
Alignment explanation
Indices: 31774495--31774565 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 32
31774485 ATTTTTATTT
*
31774495 TTATTTTTTAAAAATAATTGATTAAGTTAATC
1 TTATTTTTTAAAAATAATTGATTAAGTTAATA
* * *
31774527 TTAATTTTT-AAAAT-TTTTATTAA-TTAATTA
1 TTATTTTTTAAAAATAATTGATTAAGTTAA-TA
31774557 TTATTTTTT
1 TTATTTTTT
31774566 TATGAAGGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 4 0.12
30 16 0.48
31 5 0.15
32 8 0.24
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (32 bp):
TTATTTTTTAAAAATAATTGATTAAGTTAATA
Found at i:31782357 original size:4 final size:4
Alignment explanation
Indices: 31782348--31782377 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
31782338 TTTGAACTCC
31782348 CACT CACT CACT CACT CACT CACT CACT CA
1 CACT CACT CACT CACT CACT CACT CACT CA
31782378 TAGTGATCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.50, G:0.00, T:0.23
Consensus pattern (4 bp):
CACT
Found at i:31786081 original size:2 final size:2
Alignment explanation
Indices: 31786074--31786098 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31786064 AACTGTGAGC
31786074 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 G
31786099 CATCGCTGTC
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:31786972 original size:5 final size:5
Alignment explanation
Indices: 31786959--31786991 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
31786949 TACAAGGCAT
*
31786959 GTGGT GTGGC GTGGC GTGGC GTGGC GTGGC GTG
1 GTGGC GTGGC GTGGC GTGGC GTGGC GTGGC GTG
31786992 TATGCATGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.61, T:0.24
Consensus pattern (5 bp):
GTGGC
Done.