Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_pilon, whole genome shotgun sequence
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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 29
Found at i:5064712 original size:21 final size:22
Alignment explanation
Indices: 5064676--5064716 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5064666 TTAAGTTTTT
*
5064676 TATTTTTATTTTTTAAAAATAA
1 TATTTTTATTTATTAAAAATAA
5064698 TATTTTTA-TTATTAAAAAT
1 TATTTTTATTTATTAAAAAT
5064717 TTTAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTTTTATTTATTAAAAATAA
Found at i:5068170 original size:43 final size:43
Alignment explanation
Indices: 5068062--5068334 Score: 393
Period size: 43 Copynumber: 6.3 Consensus size: 43
5068052 AGTAAGAGTC
* * *
5068062 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACC
1 TGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACA
* * *
5068105 TGGGGGGAACTGTAAGGTTTACCCTTGTACACAGCAAAGGGACT
1 T-GGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACA
*
5068149 TGGGGGAATTGTAAGGCTTACCCTTGCACACAGCAAAGGGACA
1 TGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACA
* *
5068192 TGGGGGAATTGTAAGGTTTACCCTTGCACACAGCAAAGGGACA
1 TGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACA
* * *
5068235 TGGGGGAACTGTAAGGCTTACCCTTGCACACAGTAAAAGGACC
1 TGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACA
* * *
5068278 TGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACC
1 TGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACA
*
5068321 TGGGGAAACTGTAA
1 TGGGGGAACTGTAA
5068335 CGGTAATTAA
Statistics
Matches: 210, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
43 172 0.82
44 38 0.18
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (43 bp):
TGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACA
Found at i:5072897 original size:232 final size:233
Alignment explanation
Indices: 5072491--5072947 Score: 907
Period size: 232 Copynumber: 2.0 Consensus size: 233
5072481 TGATGCTATT
5072491 TTTGTATACCCTGTTTGGGTATACGTGATCGGGAGCAATTATATCTTCATGTGTGGTTTGAGATG
1 TTTGTATACCCTGTTTGGGTATACGTGATCGGGAGCAATTATATCTTCATGTGTGGTTTGAGATG
5072556 AAAACCGAGTATGAACTTATCTGTTTATATTTATTTTTTGCTGTATTAAGCGGCTTTATATTCTG
66 AAAACCGAGTATGAACTTATCTGTTTATATTTATTTTTTGCTGTATTAAGCGGCTTTATATTCTG
5072621 TGAGCAGGATTATGGCCTTGACTTTGATGATCTTGATCATCCTGTTAAGC-ATTCCAGTGCAGAT
131 TGAGCAGGATTATGGCCTTGACTTTGATGATCTTGATCATCCTGTTAAGCAATTCCAGTGCAGAT
5072685 GCGGCAGTACGTTTTGCAGGGACATGAAACTTCTGCTA
196 GCGGCAGTACGTTTTGCAGGGACATGAAACTTCTGCTA
5072723 TTTGTATACCCTGTTTGGGTATACGTGATCGGGAGCAATTATATCTTCATGTGTGGTTTGAGATG
1 TTTGTATACCCTGTTTGGGTATACGTGATCGGGAGCAATTATATCTTCATGTGTGGTTTGAGATG
5072788 AAAACCGAGTATGAACTTATCTGTTTATATTTATTTTTTGCTGTATTAAGCGGCTTTATATTCTG
66 AAAACCGAGTATGAACTTATCTGTTTATATTTATTTTTTGCTGTATTAAGCGGCTTTATATTCTG
5072853 TGAGCAGGATTATGGCCTTGACTTTGATGATCTTGATCATCCTGTTAAGCAATTCCAGTGCAGAT
131 TGAGCAGGATTATGGCCTTGACTTTGATGATCTTGATCATCCTGTTAAGCAATTCCAGTGCAGAT
5072918 GCGGCAGTACGTTTTGCAGGGACATGAAAC
196 GCGGCAGTACGTTTTGCAGGGACATGAAAC
5072948 GTTCAACTAG
Statistics
Matches: 224, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
232 180 0.80
233 44 0.20
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (233 bp):
TTTGTATACCCTGTTTGGGTATACGTGATCGGGAGCAATTATATCTTCATGTGTGGTTTGAGATG
AAAACCGAGTATGAACTTATCTGTTTATATTTATTTTTTGCTGTATTAAGCGGCTTTATATTCTG
TGAGCAGGATTATGGCCTTGACTTTGATGATCTTGATCATCCTGTTAAGCAATTCCAGTGCAGAT
GCGGCAGTACGTTTTGCAGGGACATGAAACTTCTGCTA
Found at i:5073708 original size:27 final size:24
Alignment explanation
Indices: 5073659--5073712 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 24
5073649 TTAAATGATA
5073659 AACGAACATAAAAGAACACAAACG
1 AACGAACATAAAAGAACACAAACG
*
5073683 AACGAACATAATAAATGAACATAAACG
1 AACGAACAT-A-AAA-GAACACAAACG
5073710 AAC
1 AAC
5073713 ACAATAACGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 9 0.35
25 1 0.04
26 3 0.12
27 13 0.50
ACGTcount: A:0.61, C:0.19, G:0.11, T:0.09
Consensus pattern (24 bp):
AACGAACATAAAAGAACACAAACG
Found at i:5073994 original size:27 final size:24
Alignment explanation
Indices: 5073945--5073998 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 24
5073935 TTAAATGATA
5073945 AACGAACATAAAAGAACACAAACG
1 AACGAACATAAAAGAACACAAACG
*
5073969 AACGAACATAATAAATGAACATAAACG
1 AACGAACAT-A-AAA-GAACACAAACG
5073996 AAC
1 AAC
5073999 ACAATAAACG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 9 0.35
25 1 0.04
26 3 0.12
27 13 0.50
ACGTcount: A:0.61, C:0.19, G:0.11, T:0.09
Consensus pattern (24 bp):
AACGAACATAAAAGAACACAAACG
Found at i:5073999 original size:23 final size:23
Alignment explanation
Indices: 5073969--5074012 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5073959 AACACAAACG
* *
5073969 AACGAACATAATAAATGAACATA
1 AACGAACACAATAAACGAACATA
5073992 AACGAACACAATAAACGAACA
1 AACGAACACAATAAACGAACA
5074013 ACACAAACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.18, G:0.09, T:0.11
Consensus pattern (23 bp):
AACGAACACAATAAACGAACATA
Found at i:5074142 original size:287 final size:286
Alignment explanation
Indices: 5073590--5074163 Score: 1121
Period size: 287 Copynumber: 2.0 Consensus size: 286
5073580 ATAAACGAGC
5073590 AAAAGTTTTTTTGTTCATGTTCGTTCATTAAGGAATATAGCTTGTTCATGTTTGTTCATTTAAAT
1 AAAAGTTTTTTTGTTCATGTTCGTTCATTAAGGAATATAGCTTGTTCATGTTTGTTCATTTAAAT
5073655 GATAAACGAACATAAAAGAACACAAACGAACGAACATAATAAATGAACATAAACGAACACAATAA
66 GATAAACGAACATAAAAGAACACAAACGAACGAACATAATAAATGAACATAAACGAACACAATAA
5073720 CGAACAACACAAACACAAAAAATAAACTTATTCGAACACAACAAATGAATGTAAAAAAAAGTAAA
131 CGAACAACACAAACACAAAAAATAAACTTATTCGAACACAACAAATGAATGTAAAAAAAAGTAAA
5073785 CAACAAGAATAACAACTTAAAACTCATTAATATAACCTGCAACTTTAGAGTTAATTTATTTGAAT
196 CAACAAGAATAACAACTTAAAACTCATTAATATAACCTGCAACTTTAGAGTTAATTTATTTGAAT
5073850 ACGACAAAAATATACAGAAATCATAA
261 ACGACAAAAATATACAGAAATCATAA
5073876 AAAAGTTTTTTTGTTCATGTTCGTTCATTAAGGAATATAGCTTGTTCATGTTTGTTCATTTAAAT
1 AAAAGTTTTTTTGTTCATGTTCGTTCATTAAGGAATATAGCTTGTTCATGTTTGTTCATTTAAAT
5073941 GATAAACGAACATAAAAGAACACAAACGAACGAACATAATAAATGAACATAAACGAACACAATAA
66 GATAAACGAACATAAAAGAACACAAACGAACGAACATAATAAATGAACATAAACGAACACAAT-A
*
5074006 ACGAACAACACAAACACAAAAAATAAACTTATTTGAACACAACAAATGAATGTAAAAAAAAGTAA
130 ACGAACAACACAAACACAAAAAATAAACTTATTCGAACACAACAAATGAATGTAAAAAAAAGTAA
5074071 ACAACAAGAATAACAACTTAAAACTCATTAATATAACCTGCAACTTTAGAGTTAATTTATTTGAA
195 ACAACAAGAATAACAACTTAAAACTCATTAATATAACCTGCAACTTTAGAGTTAATTTATTTGAA
*
5074136 TACGACAAAAATATACAGAAATTATAA
260 TACGACAAAAATATACAGAAATCATAA
5074163 A
1 A
5074164 TAAGATATAT
Statistics
Matches: 285, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
286 128 0.45
287 157 0.55
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (286 bp):
AAAAGTTTTTTTGTTCATGTTCGTTCATTAAGGAATATAGCTTGTTCATGTTTGTTCATTTAAAT
GATAAACGAACATAAAAGAACACAAACGAACGAACATAATAAATGAACATAAACGAACACAATAA
CGAACAACACAAACACAAAAAATAAACTTATTCGAACACAACAAATGAATGTAAAAAAAAGTAAA
CAACAAGAATAACAACTTAAAACTCATTAATATAACCTGCAACTTTAGAGTTAATTTATTTGAAT
ACGACAAAAATATACAGAAATCATAA
Found at i:5074943 original size:26 final size:27
Alignment explanation
Indices: 5074896--5074950 Score: 103
Period size: 26 Copynumber: 2.1 Consensus size: 27
5074886 AATGATTTTA
5074896 ATCAATGCATCCATATAAATACTCATT
1 ATCAATGCATCCATATAAATACTCATT
5074923 ATCAATGCAT-CATATAAATACTCATT
1 ATCAATGCATCCATATAAATACTCATT
5074949 AT
1 AT
5074951 TTATACATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.35
Consensus pattern (27 bp):
ATCAATGCATCCATATAAATACTCATT
Found at i:5076197 original size:2 final size:2
Alignment explanation
Indices: 5076190--5076227 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5076180 TATAATAATC
5076190 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5076228 TTACAGATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5080145 original size:147 final size:147
Alignment explanation
Indices: 5079878--5080167 Score: 580
Period size: 147 Copynumber: 2.0 Consensus size: 147
5079868 ACATGTATTG
5079878 TCTGAGTTTTATTTAATAATTTAATCTTTGACTCCGACCCTGAAAGCATTCACCCGATCCTGTCC
1 TCTGAGTTTTATTTAATAATTTAATCTTTGACTCCGACCCTGAAAGCATTCACCCGATCCTGTCC
5079943 CAAAAGTTTACATAACTTTTCTTTCTTCCTAAACTTATATTCTGCAAGGTGATGACAATTTGTGG
66 CAAAAGTTTACATAACTTTTCTTTCTTCCTAAACTTATATTCTGCAAGGTGATGACAATTTGTGG
5080008 TTTCTTGGCAGCTGTAT
131 TTTCTTGGCAGCTGTAT
5080025 TCTGAGTTTTATTTAATAATTTAATCTTTGACTCCGACCCTGAAAGCATTCACCCGATCCTGTCC
1 TCTGAGTTTTATTTAATAATTTAATCTTTGACTCCGACCCTGAAAGCATTCACCCGATCCTGTCC
5080090 CAAAAGTTTACATAACTTTTCTTTCTTCCTAAACTTATATTCTGCAAGGTGATGACAATTTGTGG
66 CAAAAGTTTACATAACTTTTCTTTCTTCCTAAACTTATATTCTGCAAGGTGATGACAATTTGTGG
5080155 TTTCTTGGCAGCT
131 TTTCTTGGCAGCT
5080168 AAGCAACCTT
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 143 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (147 bp):
TCTGAGTTTTATTTAATAATTTAATCTTTGACTCCGACCCTGAAAGCATTCACCCGATCCTGTCC
CAAAAGTTTACATAACTTTTCTTTCTTCCTAAACTTATATTCTGCAAGGTGATGACAATTTGTGG
TTTCTTGGCAGCTGTAT
Found at i:5085456 original size:86 final size:86
Alignment explanation
Indices: 5085311--5085483 Score: 346
Period size: 86 Copynumber: 2.0 Consensus size: 86
5085301 AATACTGCAT
5085311 ATGTAAGAACAGCAAATTGGACATGGAATTCCTTGATTTCTTTTCAAGTCAGTATGTCCTCAATT
1 ATGTAAGAACAGCAAATTGGACATGGAATTCCTTGATTTCTTTTCAAGTCAGTATGTCCTCAATT
5085376 TTATATGATTCATCTTGAATG
66 TTATATGATTCATCTTGAATG
5085397 ATGTAAGAACAGCAAATTGGACATGGAATTCCTTGATTTCTTTTCAAGTCAGTATGTCCTCAATT
1 ATGTAAGAACAGCAAATTGGACATGGAATTCCTTGATTTCTTTTCAAGTCAGTATGTCCTCAATT
5085462 TTATATGATTCATCTTGAATG
66 TTATATGATTCATCTTGAATG
5085483 A
1 A
5085484 ACCAAATTAA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (86 bp):
ATGTAAGAACAGCAAATTGGACATGGAATTCCTTGATTTCTTTTCAAGTCAGTATGTCCTCAATT
TTATATGATTCATCTTGAATG
Found at i:5086534 original size:17 final size:18
Alignment explanation
Indices: 5086498--5086536 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5086488 CCCAAATATT
* *
5086498 TTTTACAATCTATCATAG
1 TTTTACAATATATAATAG
5086516 TTTTA-AATATATAATAG
1 TTTTACAATATATAATAG
5086533 TTTT
1 TTTT
5086537 CAAGCGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (18 bp):
TTTTACAATATATAATAG
Found at i:5093783 original size:35 final size:36
Alignment explanation
Indices: 5093743--5093842 Score: 123
Period size: 35 Copynumber: 2.8 Consensus size: 36
5093733 GTAATGCCTT
5093743 GTTTGGTAAATGTTTTTTTG-AAAATGATTTTCAAA
1 GTTTGGTAAATGTTTTTTTGAAAAATGATTTTCAAA
* *
5093778 GTTTGGTAAATGTTTCTTTGAAAAATAGTTTTTCAAA
1 GTTTGGTAAATGTTTTTTTGAAAAAT-GATTTTCAAA
* * * *
5093815 GTATGATAGATG-TTTGTTGAAAAATGAT
1 GTTTGGTAAATGTTTTTTTGAAAAATGAT
5093843 AATGGGATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 21 0.38
36 16 0.29
37 18 0.33
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (36 bp):
GTTTGGTAAATGTTTTTTTGAAAAATGATTTTCAAA
Found at i:5093828 original size:37 final size:35
Alignment explanation
Indices: 5093749--5093842 Score: 109
Period size: 37 Copynumber: 2.6 Consensus size: 35
5093739 CCTTGTTTGG
* *
5093749 TAAATGTTTTTTTG-AAAATGATTTTCAAAGTTTGG
1 TAAATG-TTTTTTGAAAAATGATTTTCAAAGTATGA
*
5093784 TAAATGTTTCTTTGAAAAATAGTTTTTCAAAGTATGA
1 TAAATGTTT-TTTGAAAAAT-GATTTTCAAAGTATGA
* *
5093821 TAGATGTTTGTTGAAAAATGAT
1 TAAATGTTTTTTGAAAAATGAT
5093843 AATGGGATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
34 3 0.06
35 12 0.24
36 14 0.28
37 21 0.42
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (35 bp):
TAAATGTTTTTTGAAAAATGATTTTCAAAGTATGA
Found at i:5103731 original size:72 final size:73
Alignment explanation
Indices: 5103590--5103735 Score: 285
Period size: 72 Copynumber: 2.0 Consensus size: 73
5103580 CACTTAGGAG
5103590 AGAATTAGGTTTAACTGACCTATCTTCACTTAGTGGTTTAAAATAATTTTAGCACTTTTAAGAAT
1 AGAATTAGGTTTAACTGACCTATCTTCACTTAGTGGTTTAAAATAATTTTAGCACTTTTAAGAAT
5103655 AAATGAAA
66 AAATGAAA
5103663 AGAATTAGGTTTAACTGACCTATCTTCACTTAGT-GTTTAAAATAATTTTAGCACTTTTAAGAAT
1 AGAATTAGGTTTAACTGACCTATCTTCACTTAGTGGTTTAAAATAATTTTAGCACTTTTAAGAAT
5103727 AAATGAAA
66 AAATGAAA
5103735 A
1 A
5103736 ATGCTTATAA
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 39 0.53
73 34 0.47
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (73 bp):
AGAATTAGGTTTAACTGACCTATCTTCACTTAGTGGTTTAAAATAATTTTAGCACTTTTAAGAAT
AAATGAAA
Found at i:5104022 original size:21 final size:21
Alignment explanation
Indices: 5103996--5104035 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5103986 CCCCCTTTGA
*
5103996 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
5104017 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
5104036 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:5107675 original size:36 final size:36
Alignment explanation
Indices: 5107624--5107744 Score: 172
Period size: 36 Copynumber: 3.4 Consensus size: 36
5107614 GGCAACCAAC
5107624 TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTTT
1 TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTTT
* * *
5107660 TTTTAAAAATGATTTTCAAAGTTTGGTAAGTGTTTC
1 TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTTT
* *
5107696 TTTGAAAAATAGTTTTTCAAAGTTTGGTAGATG-TTT
1 TTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTTT
*
5107732 GTTGAAAAATGAT
1 TTTGAAAAATGAT
5107745 AATGGGATAA
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
35 2 0.03
36 53 0.72
37 19 0.26
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.45
Consensus pattern (36 bp):
TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTTT
Found at i:5109923 original size:28 final size:28
Alignment explanation
Indices: 5109892--5109964 Score: 98
Period size: 26 Copynumber: 2.7 Consensus size: 28
5109882 TTTCATCGTT
*
5109892 TCAATTATCCTTT-TCTTTTTTTATACAC
1 TCAATT-TTCTTTATCTTTTTTTATACAC
*
5109920 TCAATTTTCTTTATC--TTTTTGTACAC
1 TCAATTTTCTTTATCTTTTTTTATACAC
5109946 TCAATTTTCTTTATCTTTT
1 TCAATTTTCTTTATCTTTT
5109965 CACTTTTTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
26 25 0.62
27 5 0.12
28 10 0.25
ACGTcount: A:0.19, C:0.19, G:0.01, T:0.60
Consensus pattern (28 bp):
TCAATTTTCTTTATCTTTTTTTATACAC
Found at i:5109945 original size:26 final size:26
Alignment explanation
Indices: 5109909--5109964 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
5109899 TCCTTTTCTT
5109909 TTTTTATACACTCAATTTTCTTTATC
1 TTTTTATACACTCAATTTTCTTTATC
*
5109935 TTTTTGTACACTCAATTTTCTTTATC
1 TTTTTATACACTCAATTTTCTTTATC
5109961 TTTT
1 TTTT
5109965 CACTTTTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.20, C:0.18, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTTTATACACTCAATTTTCTTTATC
Found at i:5110005 original size:23 final size:23
Alignment explanation
Indices: 5109979--5110059 Score: 54
Period size: 23 Copynumber: 3.3 Consensus size: 23
5109969 TTTTCATATT
5109979 TTAAATATTAGTAAATATATAAA
1 TTAAATATTAGTAAATATATAAA
* * * **
5110002 TTAATTGAATATAGGATAAGTTTCATATT
1 TTAAAT--AT-TA-G-TAAATAT-ATAAA
*
5110031 TTAAATATTAGTGAATATATAAA
1 TTAAATATTAGTAAATATATAAA
5110054 TTAAAT
1 TTAAAT
5110060 TGAATATAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 12
0.64 0.17 0.19
Matches are distributed among these distances:
23 14 0.34
24 4 0.10
25 3 0.07
26 4 0.10
27 3 0.07
28 5 0.12
29 8 0.20
ACGTcount: A:0.48, C:0.01, G:0.09, T:0.42
Consensus pattern (23 bp):
TTAAATATTAGTAAATATATAAA
Found at i:5110063 original size:18 final size:16
Alignment explanation
Indices: 5110042--5110076 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
5110032 TAAATATTAG
5110042 TGAATATATAAATTAAAT
1 TGAATATA-AAA-TAAAT
5110060 TGAATATAAAATAAAT
1 TGAATATAAAATAAAT
5110076 T
1 T
5110077 TTAGAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 3 0.18
18 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (16 bp):
TGAATATAAAATAAAT
Found at i:5110087 original size:53 final size:52
Alignment explanation
Indices: 5109978--5110089 Score: 152
Period size: 53 Copynumber: 2.1 Consensus size: 52
5109968 TTTTTCATAT
** * * *
5109978 TTTAAATATTAGTAAATATATAAATTAATTGAATATAGGATAAGTTTCATAT
1 TTTAAATATTAGTAAATATATAAATTAATTGAATATAAAATAAATTTCAGAG
* *
5110030 TTTAAATATTAGTGAATATATAAATTAAATTGAATATAAAATAAATTTTAGAG
1 TTTAAATATTAGTAAATATATAAATT-AATTGAATATAAAATAAATTTCAGAG
5110083 TTTAAAT
1 TTTAAAT
5110090 TATAAAGTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
52 25 0.48
53 27 0.52
ACGTcount: A:0.48, C:0.01, G:0.09, T:0.42
Consensus pattern (52 bp):
TTTAAATATTAGTAAATATATAAATTAATTGAATATAAAATAAATTTCAGAG
Found at i:5112951 original size:28 final size:28
Alignment explanation
Indices: 5112902--5112956 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
5112892 CTTTGTTTAA
* * *
5112902 ATTATGTTGTCGAGCCAATGCTTGAAAC
1 ATTATGCTGTCAAGACAATGCTTGAAAC
*
5112930 ATTATGCTGTCAAGACAGTGCTTGAAA
1 ATTATGCTGTCAAGACAATGCTTGAAA
5112957 GCAACGGCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (28 bp):
ATTATGCTGTCAAGACAATGCTTGAAAC
Found at i:5117603 original size:20 final size:19
Alignment explanation
Indices: 5117578--5117645 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
5117568 GGCTGCTGGA
5117578 AACCGGTTTAACTGGTTTTC
1 AACCGGTTTAACTGG-TTTC
*
5117598 AACCGGTTCTGACTGGTTTC
1 AACCGGTT-TAACTGGTTTC
* * * *
5117618 AACCGGTTTGACCGGTCTG
1 AACCGGTTTAACTGGTTTC
5117637 AACCGGTTT
1 AACCGGTTT
5117646 GACCGGTCTG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
19 17 0.40
20 20 0.47
21 6 0.14
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.34
Consensus pattern (19 bp):
AACCGGTTTAACTGGTTTC
Found at i:5117633 original size:9 final size:9
Alignment explanation
Indices: 5117599--5117658 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 9
5117589 CTGGTTTTCA
5117599 ACCGGTTCTG
1 ACCGGTT-TG
* *
5117609 ACTGGTTTCA
1 ACCGGTTT-G
5117619 ACCGGTTTG
1 ACCGGTTTG
*
5117628 ACCGGTCTG
1 ACCGGTTTG
5117637 AACCGGTTTG
1 -ACCGGTTTG
*
5117647 ACCGGTCTG
1 ACCGGTTTG
5117656 ACC
1 ACC
5117659 CGACCCGACC
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
9 20 0.49
10 21 0.51
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:5117640 original size:19 final size:19
Alignment explanation
Indices: 5117598--5117656 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
5117588 ACTGGTTTTC
* * *
5117598 AACCGGTTCTGACTGGTTTC
1 AACCGGTT-TGACCGGTCTG
5117618 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
5117637 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
5117656 A
1 A
5117657 CCCGACCCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 28 0.78
20 8 0.22
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:5117676 original size:17 final size:17
Alignment explanation
Indices: 5117654--5117709 Score: 103
Period size: 17 Copynumber: 3.3 Consensus size: 17
5117644 TTGACCGGTC
5117654 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
5117671 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
*
5117688 TGACCCGACCCGACTGT
1 TGACCCGACCCGACCGT
5117705 TGACC
1 TGACC
5117710 GTTGACCGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:5124930 original size:19 final size:18
Alignment explanation
Indices: 5124906--5124974 Score: 84
Period size: 19 Copynumber: 3.7 Consensus size: 18
5124896 CCGGTTTTCA
5124906 ACCGGTTCTGACCGGTTTG
1 ACCGG-TCTGACCGGTTTG
* *
5124925 ACCGGTTTCAACCGGTTTG
1 ACCGGTCT-GACCGGTTTG
*
5124944 ACCGGTCTGAGACGGTTTG
1 ACCGGTCTGA-CCGGTTTG
5124963 ACCGGTCTGACC
1 ACCGGTCTGACC
5124975 CGACCCGACC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
18 4 0.10
19 38 0.90
ACGTcount: A:0.14, C:0.28, G:0.30, T:0.28
Consensus pattern (18 bp):
ACCGGTCTGACCGGTTTG
Found at i:5124968 original size:9 final size:9
Alignment explanation
Indices: 5124886--5124974 Score: 79
Period size: 9 Copynumber: 9.3 Consensus size: 9
5124876 GCTGCTGGAA
*
5124886 ACCGGTTTA
1 ACCGGTTTG
*
5124895 ACCGGTTTTCA
1 ACCGG-TTT-G
5124906 ACCGGTTCTG
1 ACCGGTT-TG
5124916 ACCGGTTTG
1 ACCGGTTTG
*
5124925 ACCGGTTTCA
1 ACCGGTTT-G
5124935 ACCGGTTTG
1 ACCGGTTTG
*
5124944 ACCGGTCTG
1 ACCGGTTTG
*
5124953 AGACGGTTTG
1 A-CCGGTTTG
*
5124963 ACCGGTCTG
1 ACCGGTTTG
5124972 ACC
1 ACC
5124975 CGACCCGACC
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
9 33 0.49
10 27 0.40
11 7 0.10
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:5125008 original size:17 final size:17
Alignment explanation
Indices: 5125000--5125037 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
5124990 CCGTTGACCC
5125000 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
*
5125017 GACCCGACCCGATCGTT
1 GACCCGACCCGACCGTT
5125034 GACC
1 GACC
5125038 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:5125016 original size:22 final size:23
Alignment explanation
Indices: 5124970--5125044 Score: 98
Period size: 24 Copynumber: 3.2 Consensus size: 23
5124960 TTGACCGGTC
*
5124970 TGACCCGACCCGACCGTTGACCGT
1 TGACCCGACCCGACCG-CGACCGT
5124994 TGACCCGACCCGACC-CGACCGT
1 TGACCCGACCCGACCGCGACCGT
* *
5125016 TGACCCGACCCGATCGTTGACCGT
1 TGACCCGACCCGACCG-CGACCGT
5125040 TGACC
1 TGACC
5125045 GTTGACCGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
22 20 0.43
24 26 0.57
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.16
Consensus pattern (23 bp):
TGACCCGACCCGACCGCGACCGT
Found at i:5125042 original size:7 final size:7
Alignment explanation
Indices: 5125030--5125071 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
5125020 CCGACCCGAT
5125030 CGTTGAC
1 CGTTGAC
5125037 CGTTGAC
1 CGTTGAC
5125044 CGTTGAC
1 CGTTGAC
5125051 CGTTGAC
1 CGTTGAC
5125058 CGTTGAC
1 CGTTGAC
5125065 CGTTGAC
1 CGTTGAC
5125072 TTTCTTTGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (7 bp):
CGTTGAC
Found at i:5128824 original size:29 final size:29
Alignment explanation
Indices: 5128789--5129096 Score: 137
Period size: 29 Copynumber: 10.2 Consensus size: 29
5128779 TTATTGAATT
*
5128789 TATTTTATTCTTATATTAACTAAAATATA
1 TATTTTATTCTTATCTTAACTAAAATATA
*
5128818 TATTTTAATCTTATCTTAACTTATAAA-ATA
1 TATTTTATTCTTATCTTAAC-TA-AAATATA
* * * *
5128848 TATTTTATTCCTACCTTAAATTTAAA-ATA
1 TATTTTATTCTTATCTT-AACTAAAATATA
* *** *
5128877 TATTTTATTTTTATCTTAACTTGTTACATA
1 TATTTTATTCTTATCTTAAC-TAAAATATA
* * * * *
5128907 TATTATATTATTAACTTAAATTATTAA-ATA
1 TATTTTATTCTTATCTT-AACTA-AAATATA
* *
5128937 TATTATATTCTTAAT-TTAAATTATTAAATAT-
1 TATTTTATTCTT-ATCTT-AACTA--AAATATA
5128968 TA-TTTATTCTTATCTTAACTTGAAAATATA
1 TATTTTATTCTTATCTTAAC-T-AAAATATA
* **
5128998 TATTTTATT-TTAATTTTAAAAAAAATATATTAATA
1 TATTTTATTCTT-ATCTT--AACTAA-A-A-T-ATA
* *
5129033 TATTTTATTCTTATTTTAATTTAAAA-ATA
1 TATTTTATTCTTATCTTAA-CTAAAATATA
* * * *
5129062 TATTTTATTTTTATCTTAATTATAATTTA
1 TATTTTATTCTTATCTTAACTAAAATATA
5129091 TATTTT
1 TATTTT
5129097 TATCTTAATT
Statistics
Matches: 220, Mismatches: 34, Indels: 50
0.72 0.11 0.16
Matches are distributed among these distances:
28 7 0.03
29 78 0.35
30 75 0.34
31 28 0.13
32 4 0.02
33 6 0.03
34 3 0.01
35 17 0.08
36 2 0.01
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.55
Consensus pattern (29 bp):
TATTTTATTCTTATCTTAACTAAAATATA
Found at i:5128851 original size:30 final size:30
Alignment explanation
Indices: 5128743--5129096 Score: 246
Period size: 30 Copynumber: 11.8 Consensus size: 30
5128733 TTAAAATCAC
*
5128743 ATCTTAACATTAAAAAATATATTTTATT-TT
1 ATCTTAAC-TTATAAAATATATTTTATTCTT
** *
5128773 -T-TTAACTTATTGAATTTATTTTATTCTT
1 ATCTTAACTTATAAAATATATTTTATTCTT
* *
5128801 ATATTAAC-TA-AAATATATATTTTAATCTT
1 ATCTTAACTTATAAA-ATATATTTTATTCTT
*
5128830 ATCTTAACTTATAAAATATATTTTATTCCT
1 ATCTTAACTTATAAAATATATTTTATTCTT
* * *
5128860 ACCTTAAATT-TAAAATATATTTTATTTTT
1 ATCTTAACTTATAAAATATATTTTATTCTT
* * * * *
5128889 ATCTTAACTTGTTACATATATTATATTATT
1 ATCTTAACTTATAAAATATATTTTATTCTT
* * * *
5128919 AACTTAAATTATTAAATATATTATATTCTT
1 ATCTTAACTTATAAAATATATTTTATTCTT
* *
5128949 AAT-TTAAATTATTAAATAT-TATTTATTCTT
1 -ATCTTAACTTATAAAATATAT-TTTATTCTT
5128979 ATCTTAACTTGA-AAATATATATTTTATT-TT
1 ATCTTAACTT-ATAAA-ATATATTTTATTCTT
* ** *
5129009 AATTTTAAAAAAAATATATTAATATATTTTATTCTT
1 -ATCTT----AACTTATA-AAATATATTTTATTCTT
* * *
5129045 ATTTTAATTTA-AAAATATATTTTATTTTT
1 ATCTTAACTTATAAAATATATTTTATTCTT
**
5129074 ATCTTAA-TTATAATTTATATTTT
1 ATCTTAACTTATAAAATATATTTT
5129097 TATCTTAATT
Statistics
Matches: 261, Mismatches: 41, Indels: 45
0.75 0.12 0.13
Matches are distributed among these distances:
27 15 0.06
28 11 0.04
29 83 0.32
30 103 0.39
31 23 0.09
32 1 0.00
34 1 0.00
35 21 0.08
36 3 0.01
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (30 bp):
ATCTTAACTTATAAAATATATTTTATTCTT
Found at i:5128853 original size:59 final size:58
Alignment explanation
Indices: 5128755--5129096 Score: 207
Period size: 59 Copynumber: 5.7 Consensus size: 58
5128745 CTTAACATTA
** * *
5128755 AAAAATATATTTT-ATTTT-T-TTAACTTATTGAATTTATTTTATTCTTATATTAACT
1 AAAAATATATTTTAATTTTATCTTAACTTATAAAATATATTTTATTCTTATATTAATT
* * **
5128810 AAAATATATATTTTAATCTTATCTTAACTTATAAAATATATTTTATTCCTACCTTAAATT
1 AAAA-ATATATTTTAATTTTATCTTAACTTATAAAATATATTTTATTCTTATATT-AATT
* * * * * * *
5128870 TAAAATATATTTTATTTTTATCTTAACTTGTTACATATATTATATTATTA-ACTTAAATT
1 AAAAATATATTTTAATTTTATCTTAACTTATAAAATATATTTTATTCTTATA-TT-AATT
* * * * *
5128929 ATTAAATATATTAT-ATTCTTAAT-TTAAATTATTAAATAT-TATTTATTCTTATCTTAACTT
1 A-AAAATATATTTTAATT-TT-ATCTTAACTTATAAAATATAT-TTTATTCTTATATTAA-TT
* ** * *
5128989 GAAAATATATATTTT-ATTTTAATTTTAAAAAAAATATATTAATATATTTTATTCTTATTTTAAT
1 -AAAA-ATATATTTTAATTTT-ATCTT----AACTTATA-AAATATATTTTATTCTTATATTAA-
5129053 TT
57 TT
* **
5129055 AAAAATATATTTTATTTTTATCTTAA-TTATAATTTATATTTT
1 AAAAATATATTTTAATTTTATCTTAACTTATAAAATATATTTT
5129097 TATCTTAATT
Statistics
Matches: 224, Mismatches: 41, Indels: 41
0.73 0.13 0.13
Matches are distributed among these distances:
55 4 0.02
56 9 0.04
57 4 0.02
58 9 0.04
59 80 0.36
60 52 0.23
61 16 0.07
64 13 0.06
65 14 0.06
66 22 0.10
67 1 0.00
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.55
Consensus pattern (58 bp):
AAAAATATATTTTAATTTTATCTTAACTTATAAAATATATTTTATTCTTATATTAATT
Found at i:5129034 original size:35 final size:35
Alignment explanation
Indices: 5128994--5129087 Score: 104
Period size: 35 Copynumber: 2.7 Consensus size: 35
5128984 AACTTGAAAA
5128994 TATATATTTTATTTTAATTTTAA-AAAAAATATAT
1 TATATATTTTATTTTAATTTTAATAAAAAATATAT
*
5129028 TAATATATTTTATTCTT-ATTTTAATTTAAAAATATAT
1 T-ATATATTTTATT-TTAATTTTAA-TAAAAAATATAT
* * *
5129065 TTTAT-TTTTATCTTAATTATAAT
1 TATATATTTTATTTTAATTTTAAT
5129088 TTATATTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
34 4 0.08
35 31 0.61
36 5 0.10
37 11 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (35 bp):
TATATATTTTATTTTAATTTTAATAAAAAATATAT
Found at i:5129080 original size:24 final size:24
Alignment explanation
Indices: 5129038--5129104 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
5129028 TAATATATTT
*
5129038 TATTCTTATTTTAAT-TTAAAAATA
1 TATT-TTATTTTTATCTTAAAAATA
**
5129062 TATTTTATTTTTATCTTAATTATA
1 TATTTTATTTTTATCTTAAAAATA
5129086 -ATTTATATTTTTATCTTAA
1 TATTT-TATTTTTATCTTAA
5129105 TTTTAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 13 0.34
24 25 0.66
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTTTATTTTTATCTTAAAAATA
Found at i:5129093 original size:66 final size:68
Alignment explanation
Indices: 5128945--5129094 Score: 170
Period size: 66 Copynumber: 2.3 Consensus size: 68
5128935 TATATTATAT
*
5128945 TCTTAATT-TAAATTAT-TAAATATTATTTATTCTTATCTTAACTTGAAAATATATATTTTATTT
1 TCTTAATTATAAATTATATTAATATTATTTATTCTTATCTTAACTTGAAAATATATATTTTATTT
5129008 TAA
66 TAA
* * * * *
5129011 TTTTAA--AAAAAATATATTAATA-TATTTTATTCTTATTTTAA-TTTAAAA-ATATATTTTATT
1 TCTTAATTATAAATTATATTAATATTA-TTTATTCTTATCTTAACTTGAAAATATATATTTTATT
*
5129071 TTTA
65 TTAA
*
5129075 TCTTAATTATAATTTATATT
1 TCTTAATTATAAATTATATT
5129095 TTTATCTTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
64 20 0.29
65 14 0.21
66 34 0.50
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (68 bp):
TCTTAATTATAAATTATATTAATATTATTTATTCTTATCTTAACTTGAAAATATATATTTTATTT
TAA
Found at i:5133377 original size:18 final size:18
Alignment explanation
Indices: 5133346--5133434 Score: 115
Period size: 18 Copynumber: 4.9 Consensus size: 18
5133336 GCGTAGAATT
*
5133346 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
* * *
5133364 TATCACGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
* *
5133382 TGTCCCGAATGACCACTG
1 TGTCCCGAAGGACCACTA
5133400 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
5133418 TGTCCCGAATGACCACT
1 TGTCCCGAAGGACCACT
5133435 TTTTAAGAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:5134649 original size:149 final size:149
Alignment explanation
Indices: 5134392--5134693 Score: 577
Period size: 149 Copynumber: 2.0 Consensus size: 149
5134382 AAGTGCCCCA
* *
5134392 TAGAATTGCACTGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
*
5134457 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAATAATATACA
66 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
5134522 TATGTCCCGAAGAACCGCG
131 TATGTCCCGAAGAACCGCG
5134541 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
5134606 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
66 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
5134671 TATGTCCCGAAGAACCGCG
131 TATGTCCCGAAGAACCGCG
5134690 TAGA
1 TAGA
5134694 CCCTCGACTC
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (149 bp):
TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
TATGTCCCGAAGAACCGCG
Found at i:5135590 original size:18 final size:18
Alignment explanation
Indices: 5135569--5135603 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5135559 TCCCATCTAG
5135569 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
5135587 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
5135604 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:5136210 original size:21 final size:21
Alignment explanation
Indices: 5136186--5136230 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5136176 TCTTGTTCGT
* *
5136186 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5136207 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5136228 TTG
1 TTG
5136231 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:5139386 original size:23 final size:23
Alignment explanation
Indices: 5139360--5139404 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5139350 CACCACAGCT
*
5139360 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
5139383 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
5139405 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:5139642 original size:149 final size:149
Alignment explanation
Indices: 5139383--5139686 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
5139373 CGAAGTGCCC
*
5139383 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
5139448 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
5139513 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
5139532 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
5139597 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
5139662 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
5139681 CGTAGA
1 CGTAGA
5139687 CCCTCGACTC
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:5140300 original size:5 final size:5
Alignment explanation
Indices: 5140290--5140318 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5140280 TTCATATAAC
5140290 TCATT TCATT TCATT TCATT TCATT TCAT
1 TCATT TCATT TCATT TCATT TCATT TCAT
5140319 ATCTATCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (5 bp):
TCATT
Found at i:5140595 original size:18 final size:18
Alignment explanation
Indices: 5140574--5140608 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5140564 TCCCATCTAG
5140574 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
5140592 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
5140609 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:5141215 original size:21 final size:21
Alignment explanation
Indices: 5141191--5141235 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5141181 TCTTGTTCGT
* *
5141191 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5141212 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5141233 TTG
1 TTG
5141236 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:5145779 original size:7 final size:7
Alignment explanation
Indices: 5145770--5145820 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
5145760 GATCCTAACT
*
5145770 TATCACT
1 TATCACA
5145777 TAT-ACA
1 TATCACA
5145783 TATCACA
1 TATCACA
5145790 TATCACA
1 TATCACA
*
5145797 TATTACA
1 TATCACA
5145804 TATCACA
1 TATCACA
5145811 TATCACA
1 TATCACA
5145818 TAT
1 TAT
5145821 ACCATTTCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
6 5 0.12
7 35 0.88
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (7 bp):
TATCACA
Found at i:5145830 original size:21 final size:20
Alignment explanation
Indices: 5145770--5145822 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
5145760 GATCCTAACT
*
5145770 TATCACTTATACATATCACA
1 TATCACATATACATATCACA
5145790 TATCACATATTACATATCACA
1 TATCACATA-TACATATCACA
5145811 TATCACATATAC
1 TATCACATATAC
5145823 CATTTCACGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.34
Consensus pattern (20 bp):
TATCACATATACATATCACA
Found at i:5146002 original size:18 final size:18
Alignment explanation
Indices: 5145979--5146049 Score: 106
Period size: 18 Copynumber: 3.9 Consensus size: 18
5145969 GCGTAGAATT
*
5145979 TGTCCCGTATGACCACTA
1 TGTCCCGAATGACCACTA
* *
5145997 TGTCCCGAAGGACCACTG
1 TGTCCCGAATGACCACTA
5146015 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
*
5146033 TGTCCCGAATGATCACT
1 TGTCCCGAATGACCACT
5146050 CCTTAAGAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:5148230 original size:20 final size:20
Alignment explanation
Indices: 5148192--5148231 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5148182 TGATCTAACA
*
5148192 AATATATTTAGCTATTAGAT
1 AATATATTTAGCTAGTAGAT
*
5148212 AATATATTTAGCTGGTAGAT
1 AATATATTTAGCTAGTAGAT
5148232 CACATGGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (20 bp):
AATATATTTAGCTAGTAGAT
Found at i:5158272 original size:20 final size:20
Alignment explanation
Indices: 5158227--5158272 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
5158217 AAAATTGTTA
* *
5158227 ATATTTTATAACCATTTGAT
1 ATATTTAATAAACATTTGAT
* *
5158247 AAATTTAATAAACATTTTAT
1 ATATTTAATAAACATTTGAT
5158267 ATATTT
1 ATATTT
5158273 TAAAAGTTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (20 bp):
ATATTTAATAAACATTTGAT
Found at i:5160377 original size:200 final size:200
Alignment explanation
Indices: 5160034--5160425 Score: 757
Period size: 200 Copynumber: 2.0 Consensus size: 200
5160024 TTGTGATCAT
5160034 ACATTTATGAAATTAGCTAAAAGATATAACATGTAAGACATACTTTCAAAGACACATTTGATGCG
1 ACATTTATGAAATTAGCTAAAAGATATAACATGTAAGACATACTTTCAAAGACACATTTGATGCG
5160099 ATATACCTTTGTTTTACGGGACATAAAAATATTATAATAATTTTAGACATATATTATTCCAAAAA
66 ATATACCTTTGTTTTACGGGACATAAAAATATTATAATAATTTTAGACATATATTATTCCAAAAA
5160164 AAAAATTTAAGGTGGTATTTCAATAAGAAAACACCATAATTTCAGTAATATTTGAATTAAAAAAA
131 AAAAATTTAAGGTGGTATTTCAATAAGAAAACACCATAATTTCAGTAATATTTGAATTAAAAAAA
5160229 TTTAG
196 TTTAG
5160234 ACATTTATGAAATTAGCTAAAAGATATAACATGTAAGACATACTTTCAAAGACACATTTGATGCG
1 ACATTTATGAAATTAGCTAAAAGATATAACATGTAAGACATACTTTCAAAGACACATTTGATGCG
*
5160299 ATATACCTTTGTTTTACGGGACATAAAAATATTATAATAATTTTAGACATATATTATTCCCAAAA
66 ATATACCTTTGTTTTACGGGACATAAAAATATTATAATAATTTTAGACATATATTATTCCAAAAA
* *
5160364 AAAATTTTAAGGTGGTATTTCAATAAGAAAACACCATAATTTCAGTAATATTTGGATTAAAA
131 AAAAATTTAAGGTGGTATTTCAATAAGAAAACACCATAATTTCAGTAATATTTGAATTAAAA
5160426 TTAATAATTT
Statistics
Matches: 189, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 189 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (200 bp):
ACATTTATGAAATTAGCTAAAAGATATAACATGTAAGACATACTTTCAAAGACACATTTGATGCG
ATATACCTTTGTTTTACGGGACATAAAAATATTATAATAATTTTAGACATATATTATTCCAAAAA
AAAAATTTAAGGTGGTATTTCAATAAGAAAACACCATAATTTCAGTAATATTTGAATTAAAAAAA
TTTAG
Found at i:5173987 original size:77 final size:79
Alignment explanation
Indices: 5173906--5174061 Score: 298
Period size: 77 Copynumber: 2.0 Consensus size: 79
5173896 AATGTAAACA
5173906 TTTAGTTACATGATGTAAAATTTTAATATATTTTTACAT-AATTATGTAAAA-TTAATATTAATT
1 TTTAGTTACATGATGTAAAATTTTAATATATTTTTACATAAATTATGTAAAATTTAATATTAATT
5173969 AAAATTAAAATAAT
66 AAAATTAAAATAAT
5173983 TTTAGTTACATGATGTAAAATTTTAATATATTTTTACATAAATTATGTAAAATTTAATATTAATT
1 TTTAGTTACATGATGTAAAATTTTAATATATTTTTACATAAATTATGTAAAATTTAATATTAATT
5174048 AAAATTAAAATAAT
66 AAAATTAAAATAAT
5174062 ACATGATATA
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
77 39 0.51
78 12 0.16
79 26 0.34
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.46
Consensus pattern (79 bp):
TTTAGTTACATGATGTAAAATTTTAATATATTTTTACATAAATTATGTAAAATTTAATATTAATT
AAAATTAAAATAAT
Found at i:5179330 original size:56 final size:56
Alignment explanation
Indices: 5179268--5179398 Score: 262
Period size: 56 Copynumber: 2.3 Consensus size: 56
5179258 ATGTATTATA
5179268 GATTTTACGAAAGATATCGAGATATCTTTTGAGACTCTAATGCTGATTGGATAATG
1 GATTTTACGAAAGATATCGAGATATCTTTTGAGACTCTAATGCTGATTGGATAATG
5179324 GATTTTACGAAAGATATCGAGATATCTTTTGAGACTCTAATGCTGATTGGATAATG
1 GATTTTACGAAAGATATCGAGATATCTTTTGAGACTCTAATGCTGATTGGATAATG
5179380 GATTTTACGAAAGATATCG
1 GATTTTACGAAAGATATCG
5179399 GGAGTTGCTC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 75 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (56 bp):
GATTTTACGAAAGATATCGAGATATCTTTTGAGACTCTAATGCTGATTGGATAATG
Found at i:5181410 original size:21 final size:21
Alignment explanation
Indices: 5181384--5181430 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
5181374 TAATTTTCAA
5181384 ACATTATTGCACCTAATTTTG
1 ACATTATTGCACCTAATTTTG
5181405 ACATTATTGCACCTAATTTTG
1 ACATTATTGCACCTAATTTTG
5181426 ACATT
1 ACATT
5181431 GCAATATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.43
Consensus pattern (21 bp):
ACATTATTGCACCTAATTTTG
Found at i:5184770 original size:9 final size:9
Alignment explanation
Indices: 5184756--5184785 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
5184746 GATCTCCCTT
5184756 TCATCGTTG
1 TCATCGTTG
5184765 TCATCGTTG
1 TCATCGTTG
5184774 TCATCGTTG
1 TCATCGTTG
5184783 TCA
1 TCA
5184786 ACGCTTCTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (9 bp):
TCATCGTTG
Found at i:5185971 original size:23 final size:21
Alignment explanation
Indices: 5185949--5185991 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5185939 CCTATTTAAT
5185949 TTTTAAACATTATTGCACCTAA
1 TTTT-AACATTATTGCACCTAA
* *
5185971 TTTTGACATTGTTGCACCTAA
1 TTTTAACATTATTGCACCTAA
5185992 ACTTGAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (21 bp):
TTTTAACATTATTGCACCTAA
Found at i:5185997 original size:21 final size:21
Alignment explanation
Indices: 5185955--5185997 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5185945 TAATTTTTAA
**
5185955 ACATTATTGCACCTAATTTTG
1 ACATTATTGCACCTAAACTTG
*
5185976 ACATTGTTGCACCTAAACTTG
1 ACATTATTGCACCTAAACTTG
5185997 A
1 A
5185998 ACCAATTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (21 bp):
ACATTATTGCACCTAAACTTG
Found at i:5200921 original size:15 final size:14
Alignment explanation
Indices: 5200888--5200922 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
5200878 ATGTATCTTC
*
5200888 TTAGGAGATAAGTT
1 TTAGGAGATAAGGT
5200902 TTAGGAGATAAGAGT
1 TTAGGAGATAAG-GT
5200917 TTAGGA
1 TTAGGA
5200923 AGAAGAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.31, T:0.31
Consensus pattern (14 bp):
TTAGGAGATAAGGT
Found at i:5210738 original size:2 final size:2
Alignment explanation
Indices: 5210731--5210764 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5210721 CATTTTCTTT
5210731 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
5210765 CACAGGTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5212802 original size:15 final size:15
Alignment explanation
Indices: 5212782--5212812 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5212772 TTAGATCAAT
5212782 ACCCAACCTTATCCC
1 ACCCAACCTTATCCC
5212797 ACCCAACCTTATCCC
1 ACCCAACCTTATCCC
5212812 A
1 A
5212813 AAATTTCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.52, G:0.00, T:0.19
Consensus pattern (15 bp):
ACCCAACCTTATCCC
Found at i:5215020 original size:17 final size:17
Alignment explanation
Indices: 5214998--5215036 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
5214988 GGGTTCAAAT
* *
5214998 TCGAGTTTGAGCTTGAA
1 TCGAGTTCGAGCTTCAA
5215015 TCGAGTTCGAGCTTCAA
1 TCGAGTTCGAGCTTCAA
5215032 TCGAG
1 TCGAG
5215037 CTCAAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (17 bp):
TCGAGTTCGAGCTTCAA
Found at i:5215062 original size:11 final size:11
Alignment explanation
Indices: 5215021--5215063 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
5215011 TGAATCGAGT
*
5215021 TCGAGCTTCAA
1 TCGAGCTCCAA
*
5215032 TCGAGCTCAAAA
1 TCGAGCTC-CAA
*
5215044 TTGAGCTCCAA
1 TCGAGCTCCAA
5215055 TCGAGCTCC
1 TCGAGCTCC
5215064 TGATTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (11 bp):
TCGAGCTCCAA
Found at i:5215122 original size:31 final size:31
Alignment explanation
Indices: 5215087--5215161 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
5215077 GCTCGAGCAT
5215087 TTTCGAGTTCGAGTCGAGTTTCAATAATATA
1 TTTCGAGTTCGAGTCGAGTTTCAATAATATA
*
5215118 TTTCGAGTTCGAGTCGAGTTTCTATAATATA
1 TTTCGAGTTCGAGTCGAGTTTCAATAATATA
5215149 TTTCGAGTTCGAG
1 TTTCGAGTTCGAG
5215162 CTGAGCTTGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (31 bp):
TTTCGAGTTCGAGTCGAGTTTCAATAATATA
Found at i:5217181 original size:30 final size:29
Alignment explanation
Indices: 5217133--5217242 Score: 84
Period size: 30 Copynumber: 3.8 Consensus size: 29
5217123 ATATTCTATC
5217133 AATTTAAATTT-A-AT-TATAAATTAATA
1 AATTTAAATTTCATATATATAAATTAATA
* * *
5217159 AATTTAACTCTTCATATATAT-AATCATATT
1 AATTTAAAT-TTCATATATATAAATTA-ATA
* *
5217189 AATTTAAATTTAATTATATATAAATTAAAA
1 AATTTAAATTTCA-TATATATAAATTAATA
* * *
5217219 AAATTAATTGTTCATATTTATAAA
1 AATTTAAAT-TTCATATATATAAA
5217243 CTCTAGTAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
26 8 0.12
27 2 0.03
28 1 0.02
29 9 0.14
30 37 0.58
31 7 0.11
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (29 bp):
AATTTAAATTTCATATATATAAATTAATA
Found at i:5225444 original size:22 final size:22
Alignment explanation
Indices: 5225418--5225468 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
5225408 GATTTTTGCT
5225418 AATTTTTTAAATAATGATTTCA
1 AATTTTTTAAATAATGATTTCA
5225440 AATTTTTTAAATAATGATTTCA
1 AATTTTTTAAATAATGATTTCA
5225462 AATTTTT
1 AATTTTT
5225469 GATAGGAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (22 bp):
AATTTTTTAAATAATGATTTCA
Found at i:5232654 original size:23 final size:23
Alignment explanation
Indices: 5232623--5232680 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
5232613 ATATAAATGT
*
5232623 ACCGAAGTGCCACGTAGAATTGC
1 ACCGTAGTGCCACGTAGAATTGC
*
5232646 ACCGTAGTGCCGCGTAGAATTGC
1 ACCGTAGTGCCACGTAGAATTGC
5232669 ACCGTAGTGCCA
1 ACCGTAGTGCCA
5232681 TATAATAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.19
Consensus pattern (23 bp):
ACCGTAGTGCCACGTAGAATTGC
Found at i:5235435 original size:68 final size:68
Alignment explanation
Indices: 5235299--5235435 Score: 222
Period size: 68 Copynumber: 2.0 Consensus size: 68
5235289 TGTCTCAATC
* *
5235299 CATAAAAGACAAAATCAAAAACAAAATCCTGAACTTCCGCACGAACAGATAACCAGAAACAGCAT
1 CATAAAAGACAAAATCAAAAACAAAATCCTGAACTTCCACACGAACAGATAACAAGAAACAGCAT
5235364 CCG
66 CCG
* *
5235367 CATAAAAGACAAAATCAAAAACAAAATCCTGAACTTCCACACGAACAGAGT-ACAAGAATCAGCT
1 CATAAAAGACAAAATCAAAAACAAAATCCTGAACTTCCACACGAACAGA-TAACAAGAAACAGCA
5235431 TCCG
65 TCCG
5235435 C
1 C
5235436 CTTAAACGCC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 63 0.98
69 1 0.02
ACGTcount: A:0.49, C:0.26, G:0.12, T:0.13
Consensus pattern (68 bp):
CATAAAAGACAAAATCAAAAACAAAATCCTGAACTTCCACACGAACAGATAACAAGAAACAGCAT
CCG
Found at i:5249590 original size:14 final size:14
Alignment explanation
Indices: 5249571--5249600 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5249561 ATTTGATGTA
5249571 TGAGAGAAAGGGTT
1 TGAGAGAAAGGGTT
5249585 TGAGAGAAAGGGTT
1 TGAGAGAAAGGGTT
5249599 TG
1 TG
5249601 CGGAGGAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.23
Consensus pattern (14 bp):
TGAGAGAAAGGGTT
Found at i:5253315 original size:19 final size:19
Alignment explanation
Indices: 5253291--5253341 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
5253281 ATCAACTAAA
5253291 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
5253310 TCGCAATGCGATCGATAAT
1 TCGCAATGCGATCGATAAT
* *
5253329 TTGCAACGCGATC
1 TCGCAATGCGATC
5253342 TCCGGTATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (19 bp):
TCGCAATGCGATCGATAAT
Found at i:5253442 original size:21 final size:20
Alignment explanation
Indices: 5253415--5253482 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
5253405 CATATTCGCA
5253415 TTGCGATAGTCCAAGTTCGAG
1 TTGCGATAGTCCAAGTTCG-G
* ** *
5253436 TTACGATTTTCCAAATTC-G
1 TTGCGATAGTCCAAGTTCGG
*
5253455 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCG-G
5253476 TTGCGAT
1 TTGCGAT
5253483 TCGAGTTACG
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
19 14 0.39
21 22 0.61
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCCAAGTTCGG
Found at i:5253460 original size:40 final size:40
Alignment explanation
Indices: 5253415--5253562 Score: 125
Period size: 52 Copynumber: 3.4 Consensus size: 40
5253405 CATATTCGCA
5253415 TTGCGATAGTCCAAGTTCGAGTTACGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGAGTTACGATTTTCCAAATTCG
*
5253455 TTGCGATAGTCGAAGTTCGCGTTGCGATTCGAGTTACGATTTTCCAAATTCG
1 TTGCGATAGTCCAA-----------G-TTCGAGTTACGATTTTCCAAATTCG
* * * *
5253507 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCG
1 TTGCGATAGTCCAAGTTCGAGTTACGA-TT-TTCCAAATTCG
5253549 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
5253563 AATCGCAACG
Statistics
Matches: 89, Mismatches: 5, Indels: 26
0.74 0.04 0.22
Matches are distributed among these distances:
40 23 0.26
41 3 0.03
42 23 0.26
51 1 0.01
52 39 0.44
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (40 bp):
TTGCGATAGTCCAAGTTCGAGTTACGATTTTCCAAATTCG
Found at i:5253508 original size:52 final size:52
Alignment explanation
Indices: 5253430--5253535 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
5253420 ATAGTCCAAG
5253430 TTCGAGTTACGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGA
1 TTCGAGTTACGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGA
5253482 TTCGAGTTACGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGA
1 TTCGAGTTACGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGA
5253534 TT
1 TT
5253536 TATTCTAAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (52 bp):
TTCGAGTTACGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGA
Found at i:5253663 original size:6 final size:6
Alignment explanation
Indices: 5253652--5253676 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5253642 GACACGTATT
5253652 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
5253677 GACGAGACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:5259429 original size:36 final size:37
Alignment explanation
Indices: 5259389--5259464 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 37
5259379 TTTTTATACT
5259389 TTTAATTTTGTAAA-AAAATTATATAAATATTATA-AA
1 TTTAATTTTGTAAAGAAAA-TATATAAATATTATACAA
* *
5259425 TTTAATTTTTTAAAGAAAATATATAAATATTTTACAA
1 TTTAATTTTGTAAAGAAAATATATAAATATTATACAA
5259462 TTT
1 TTT
5259465 GTAATATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 27 0.75
37 9 0.25
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAGAAAATATATAAATATTATACAA
Found at i:5262990 original size:24 final size:26
Alignment explanation
Indices: 5262956--5263004 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
5262946 ACTTTTCAAA
5262956 TTATATCGTATACATGTATG-TATAT
1 TTATATCGTATACATGTATGATATAT
**
5262981 TTATA-CGTATGTATGTATGATATA
1 TTATATCGTATACATGTATGATATA
5263005 ACGTCGGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (26 bp):
TTATATCGTATACATGTATGATATAT
Found at i:5263008 original size:20 final size:20
Alignment explanation
Indices: 5262969--5263008 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5262959 TATCGTATAC
*
5262969 ATGTATGTATATTTATACGT
1 ATGTATGTATATATATACGT
5262989 ATGTATGTATGATATA-ACGT
1 ATGTATGTAT-ATATATACGT
5263009 CGGCCTCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (20 bp):
ATGTATGTATATATATACGT
Found at i:5267309 original size:80 final size:80
Alignment explanation
Indices: 5267176--5267336 Score: 322
Period size: 80 Copynumber: 2.0 Consensus size: 80
5267166 CGTATATTTT
5267176 CTCAATCTCTGGTAAGCTTCCATCAAATCCATGAGCTTAAATTCAGTTGTCTTAGCACTGGGTAA
1 CTCAATCTCTGGTAAGCTTCCATCAAATCCATGAGCTTAAATTCAGTTGTCTTAGCACTGGGTAA
5267241 ATTTCAAAAAAAGAG
66 ATTTCAAAAAAAGAG
5267256 CTCAATCTCTGGTAAGCTTCCATCAAATCCATGAGCTTAAATTCAGTTGTCTTAGCACTGGGTAA
1 CTCAATCTCTGGTAAGCTTCCATCAAATCCATGAGCTTAAATTCAGTTGTCTTAGCACTGGGTAA
5267321 ATTTCAAAAAAAGAG
66 ATTTCAAAAAAAGAG
5267336 C
1 C
5267337 ATCTCGTATA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (80 bp):
CTCAATCTCTGGTAAGCTTCCATCAAATCCATGAGCTTAAATTCAGTTGTCTTAGCACTGGGTAA
ATTTCAAAAAAAGAG
Found at i:5269079 original size:50 final size:50
Alignment explanation
Indices: 5269004--5269101 Score: 196
Period size: 50 Copynumber: 2.0 Consensus size: 50
5268994 GATATGGGTC
5269004 CATGCGAAAAATAACTATTTACACACACAAGTATCATAATGATTCGAAAA
1 CATGCGAAAAATAACTATTTACACACACAAGTATCATAATGATTCGAAAA
5269054 CATGCGAAAAATAACTATTTACACACACAAGTATCATAATGATTCGAA
1 CATGCGAAAAATAACTATTTACACACACAAGTATCATAATGATTCGAA
5269102 CATATGGTTA
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:0.47, C:0.18, G:0.10, T:0.24
Consensus pattern (50 bp):
CATGCGAAAAATAACTATTTACACACACAAGTATCATAATGATTCGAAAA
Found at i:5270589 original size:55 final size:55
Alignment explanation
Indices: 5270522--5270825 Score: 418
Period size: 55 Copynumber: 5.5 Consensus size: 55
5270512 AGTCTAATCC
* * *
5270522 CTATTCCTTCAGGGAGTATA-AGACTCGATCAATCTTCAATAAACGGGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAATAAACGGGTCCGCTCT
* * *
5270577 CTATCTGC-TCAGGGAGTATAGAACTCGAACAATCTTC-ATAAAATGGGTCCGCTCT
1 CTAT-TCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAT-AAACGGGTCCGCTCT
* **
5270632 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGAATCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGGGTCCGCTCT
*
5270687 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAAACAGGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAT-AAACGGGTCCGCTCT
* *
5270743 CTATTCCTTCAGAGAGTATAGAACTCGGAA-AATCTTCAATAAACAGGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGAACTC-GAACAATCTTCAATAAACGGGTCCGCTCT
*
5270798 CTATTCCTTCAGAGAGTATAGGACTCGA
1 CTATTCCTTCAGAGAGTATAGAACTCGA
5270826 TCTTCATAAA
Statistics
Matches: 226, Mismatches: 16, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
54 6 0.03
55 165 0.73
56 52 0.23
57 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (55 bp):
CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGGGTCCGCTCT
Found at i:5270777 original size:111 final size:109
Alignment explanation
Indices: 5270522--5270825 Score: 425
Period size: 111 Copynumber: 2.8 Consensus size: 109
5270512 AGTCTAATCC
* * * *
5270522 CTATTCCTTCAGGGAGTATA-AGACTCGATCAATCTTCAATAAACGGGTCCGCTCCCTATCTGC-
1 CTATTCCTTCAGAGAGTATAGA-ACTCGA-AAATCTTCAATAAACGAGTCCGCTCCCTAT-TCCT
* **
5270585 TCAGGGAGTATAGAACTCGAACAATCTTCATAAAATGGGTCCGCTCT
63 TCAGAGAGTATAGAACTCGAACAATCTTCATAAAACAGGTCCGCTCT
* * *
5270632 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGAATCCGCTCTCTATTCCTTC
1 CTATTCCTTCAGAGAGTATAGAACTCGAA-AATCTTCAATAAACGAGTCCGCTCCCTATTCCTTC
5270697 AGAGAGTATAGAACTCGAACAATCTTCAATAAAACAGGTCCGCTCT
65 AGAGAGTATAGAACTCGAACAATCTTC-ATAAAACAGGTCCGCTCT
5270743 CTATTCCTTCAGAGAGTATAGAACTCGGAAAATCTTCAATAAAC-AGGTCCGCTCCCTATTCCTT
1 CTATTCCTTCAGAGAGTATAGAACTC-GAAAATCTTCAATAAACGA-GTCCGCTCCCTATTCCTT
*
5270807 CAGAGAGTATAGGACTCGA
64 CAGAGAGTATAGAACTCGA
5270826 TCTTCATAAA
Statistics
Matches: 174, Mismatches: 14, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
109 2 0.01
110 79 0.45
111 90 0.52
112 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (109 bp):
CTATTCCTTCAGAGAGTATAGAACTCGAAAATCTTCAATAAACGAGTCCGCTCCCTATTCCTTCA
GAGAGTATAGAACTCGAACAATCTTCATAAAACAGGTCCGCTCT
Found at i:5270804 original size:166 final size:164
Alignment explanation
Indices: 5270522--5270825 Score: 445
Period size: 166 Copynumber: 1.8 Consensus size: 164
5270512 AGTCTAATCC
* * * *
5270522 CTATTCCTTCAGGGAGTATAAGACTCGATCAATCTTCAATAAACGGGTCCGCTCCCTATCTGCTC
1 CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACAGGTCCGCTCCCTATCTCCTC
* *
5270587 AGGGAGTATAGAACTCGAACAATCTTCATAAAATGGGTCCGCTCTCTATTCCTTCAGAGAGTATA
66 AGAGAGTATAGAACTCGAACAATCTTCATAAAA-GGGTCCGCTCCCTATTCCTTCAGAGAGTATA
5270652 GAACTCGAACAATCTTCAACAAACGAATCCGCTCT
130 GAACTCGAACAATCTTCAACAAACGAATCCGCTCT
*
5270687 CTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAATAAAACAGGTCCGCTCTCTAT-TCC
1 CTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAAT-AAACAGGTCCGCTCCCTATCTCC
5270750 TTCAGAGAGTATAGAACTCGGAA-AATCTTCAATAAACA-GGTCCGCTCCCTATTCCTTCAGAGA
64 -TCAGAGAGTATAGAACTC-GAACAATCTTC-ATAAA-AGGGTCCGCTCCCTATTCCTTCAGAGA
*
5270813 GTATAGGACTCGA
125 GTATAGAACTCGA
5270826 TCTTCATAAA
Statistics
Matches: 125, Mismatches: 8, Indels: 11
0.87 0.06 0.08
Matches are distributed among these distances:
164 2 0.02
165 37 0.30
166 77 0.62
167 8 0.06
168 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (164 bp):
CTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACAGGTCCGCTCCCTATCTCCTC
AGAGAGTATAGAACTCGAACAATCTTCATAAAAGGGTCCGCTCCCTATTCCTTCAGAGAGTATAG
AACTCGAACAATCTTCAACAAACGAATCCGCTCT
Found at i:5270881 original size:37 final size:36
Alignment explanation
Indices: 5270840--5270911 Score: 126
Period size: 37 Copynumber: 2.0 Consensus size: 36
5270830 CATAAAATGA
5270840 GTTTGCTTCACTAATCTTCCGTGAAGGCTTACAGATG
1 GTTTGCTTCACTAATCTTCCGTGAAGGCTTA-AGATG
*
5270877 GTTTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
1 GTTTGCTTCACTAATCTTCCGTGAAGGCTTAAGAT
5270912 TGACCTGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 4 0.12
37 30 0.88
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (36 bp):
GTTTGCTTCACTAATCTTCCGTGAAGGCTTAAGATG
Found at i:5272213 original size:18 final size:17
Alignment explanation
Indices: 5272186--5272271 Score: 61
Period size: 18 Copynumber: 4.8 Consensus size: 17
5272176 TGAACCCCTC
5272186 TTTTATTTTTCTTTATT
1 TTTTATTTTTCTTTATT
5272203 TTTTCATTTTTCTCTT-TT
1 TTTT-ATTTTTCT-TTATT
* *
5272221 TGTT-TTTCTCTTTCATT
1 TTTTATTTTTCTTT-ATT
*
5272238 TTGTT-TTTCTTCTTCTTTT
1 TT-TTATTT-TTCTT-TATT
5272257 TTTTCATTTTTCTTT
1 TTTT-ATTTTTCTTT
5272272 TCTTCATTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
15 2 0.04
16 6 0.11
17 7 0.13
18 21 0.38
19 15 0.27
20 4 0.07
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTATTTTTCTTTATT
Found at i:5272220 original size:15 final size:14
Alignment explanation
Indices: 5272201--5272297 Score: 78
Period size: 15 Copynumber: 6.9 Consensus size: 14
5272191 TTTTTCTTTA
5272201 TTTTTTCATTTTTC
1 TTTTTTCATTTTTC
*
5272215 TCTTTTT-GTTTTTC
1 T-TTTTTCATTTTTC
*
5272229 -TCTTTCATTTTGT-
1 TTTTTTCATTTT-TC
*
5272242 TTTTCTTC-TTCTT-
1 TTTT-TTCATTTTTC
5272255 TTTTTTCATTTTTC
1 TTTTTTCATTTTTC
5272269 TTTTCTTCATTTTTC
1 TTTT-TTCATTTTTC
*
5272284 TTCTTCTCATTTTT
1 TT-TTTTCATTTTT
5272298 ATTATTTTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 17
0.74 0.08 0.19
Matches are distributed among these distances:
12 7 0.10
13 13 0.19
14 17 0.25
15 28 0.42
16 2 0.03
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (14 bp):
TTTTTTCATTTTTC
Found at i:5272267 original size:40 final size:40
Alignment explanation
Indices: 5272223--5272322 Score: 109
Period size: 39 Copynumber: 2.5 Consensus size: 40
5272213 TCTCTTTTTG
5272223 TTTTTCTCTTTCATTTTGTTTTTCTTCTTCT-TTTTT-TTCA
1 TTTTTCTCTTTCATTTT-TTTTTCTTCTTCTATTTTTATT-A
**
5272263 TTTTTCT-TTTC-TTCATTTTTCTTCTTCTCATTTTTATTA
1 TTTTTCTCTTTCATTTTTTTTTCTTCTTCT-ATTTTTATTA
* *
5272302 TTTTTTTCATTCATTTTTTTT
1 TTTTTCTCTTTCATTTTTTTT
5272323 ATTTTTTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
37 13 0.27
38 2 0.04
39 16 0.33
40 12 0.24
41 6 0.12
ACGTcount: A:0.08, C:0.16, G:0.01, T:0.75
Consensus pattern (40 bp):
TTTTTCTCTTTCATTTTTTTTTCTTCTTCTATTTTTATTA
Found at i:5272281 original size:22 final size:22
Alignment explanation
Indices: 5272241--5272283 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5272231 TTTCATTTTG
*
5272241 TTTTTCTTCTTCTTTTTTTTCA
1 TTTTTCTTCTTCTTATTTTTCA
5272263 TTTTTCTT-TTCTTCATTTTTC
1 TTTTTCTTCTTCTT-ATTTTTC
5272284 TTCTTCTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTTCTTCTTCTTATTTTTCA
Found at i:5272282 original size:37 final size:37
Alignment explanation
Indices: 5272241--5272319 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 37
5272231 TTTCATTTTG
**
5272241 TTTTTCTTCTTCTTTTTTTTCATT-TTTCTTTTC-TTCA
1 TTTTTCTTCTTCTCATTTTT-ATTATTT-TTTTCATTCA
5272278 TTTTTCTTCTTCTCATTTTTATTATTTTTTTCATTCA
1 TTTTTCTTCTTCTCATTTTTATTATTTTTTTCATTCA
5272315 TTTTT
1 TTTTT
5272320 TTTATTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
36 8 0.21
37 30 0.79
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (37 bp):
TTTTTCTTCTTCTCATTTTTATTATTTTTTTCATTCA
Found at i:5272282 original size:61 final size:59
Alignment explanation
Indices: 5272190--5272351 Score: 136
Period size: 61 Copynumber: 2.6 Consensus size: 59
5272180 CCCCTCTTTT
* * *
5272190 ATTTTTCTTTATTTTTTCATTTTTCTCTTTTTGTTTTTCTC-TTTCATT-TTGTTTTTCTTC-TT
1 ATTTTT-TTTA-TTTTTC--TTTTCTCTTTTTCTTCTTCTCATTT--TTATTATTTTT-TTCATT
5272252 C
59 C
5272253 -TTTTTTTTCATTTTTCTTTTCTTCATTTTTCTTCTTCTCATTTTTATTATTTTTTTCATTC
1 ATTTTTTTT-ATTTTTCTTTTC-TC-TTTTTCTTCTTCTCATTTTTATTATTTTTTTCATTC
*
5272314 ATTTTTTTTATTTTTTTATTTTCTCTTTTAT-TTCTTCT
1 ATTTTTTTTA--TTTTTCTTTTCTCTTTT-TCTTCTTCT
5272352 TCAAGCAAAA
Statistics
Matches: 85, Mismatches: 4, Indels: 22
0.77 0.04 0.20
Matches are distributed among these distances:
59 5 0.06
60 7 0.08
61 43 0.51
62 20 0.24
63 10 0.12
ACGTcount: A:0.09, C:0.15, G:0.01, T:0.75
Consensus pattern (59 bp):
ATTTTTTTTATTTTTCTTTTCTCTTTTTCTTCTTCTCATTTTTATTATTTTTTTCATTC
Found at i:5272342 original size:22 final size:21
Alignment explanation
Indices: 5272236--5272342 Score: 56
Period size: 22 Copynumber: 4.8 Consensus size: 21
5272226 TTCTCTTTCA
*
5272236 TTTTGTTTTTCTTCTTCTTTT-T
1 TTTTTTTTTTC-TCTT-TTTTAT
** *
5272258 TTTCATTTTTCT-TTTCTTCAT
1 TTTTTTTTTTCTCTTT-TTTAT
* * *
5272279 TTTTCTTCTTCTCATTTTTAT
1 TTTTTTTTTTCTCTTTTTTAT
*
5272300 TATTTTTTTCATTCATTTTTTTTAT
1 T-TTTTTTT--TTC-TCTTTTTTAT
5272325 TTTTTTATTTTCTCTTTT
1 TTTTTT-TTTTCTCTTTT
5272343 ATTTCTTCTT
Statistics
Matches: 64, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
19 1 0.02
20 4 0.06
21 16 0.25
22 21 0.33
23 3 0.05
24 8 0.12
25 11 0.17
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.77
Consensus pattern (21 bp):
TTTTTTTTTTCTCTTTTTTAT
Found at i:5274833 original size:156 final size:158
Alignment explanation
Indices: 5274549--5274862 Score: 614
Period size: 156 Copynumber: 2.0 Consensus size: 158
5274539 TCAATGGTTT
5274549 GCCTGGGATTGGTGGCGCCAAGATTGGAGTACTCGACAAATATCTTTTCACTGCTTCAAAAGATC
1 GCCTGGGATTGGTGGCGCCAAGATTGGAGTACTCGACAAATATCTTTTCACTGCTTCAAAAGATC
5274614 TTTGACAATCCTCATTCCGTTCCCCTGAGTTATTCTTGCGAAGAAGGCGAAATATGGGATCACAC
66 TTTGACAATCCTCATTCCGTTCCCCTGAGTTATTCTTGCGAAGAAGGCGAAATATGGGATCACAC
5274679 TTTTCCGTCAGTTG-G-AATAAATCGAG
131 TTTTCCGTCAGTTGTGAAATAAATCGAG
5274705 GCCTGGGATTGGTGGCGCCAAGATTGGAGTACTCGACAAATATCTTTTCACTGCTTCAAAAGATC
1 GCCTGGGATTGGTGGCGCCAAGATTGGAGTACTCGACAAATATCTTTTCACTGCTTCAAAAGATC
5274770 TTTGACAATCCTCATTCCGTTCCCCTGAGTTATTCTTGCGAAGAAGGCGAAATATGGGATCACAC
66 TTTGACAATCCTCATTCCGTTCCCCTGAGTTATTCTTGCGAAGAAGGCGAAATATGGGATCACAC
5274835 TTTTCCGTCAGTTGTGAAATAAATCGAG
131 TTTTCCGTCAGTTGTGAAATAAATCGAG
5274863 CTATATAATT
Statistics
Matches: 156, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
156 144 0.92
157 1 0.01
158 11 0.07
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (158 bp):
GCCTGGGATTGGTGGCGCCAAGATTGGAGTACTCGACAAATATCTTTTCACTGCTTCAAAAGATC
TTTGACAATCCTCATTCCGTTCCCCTGAGTTATTCTTGCGAAGAAGGCGAAATATGGGATCACAC
TTTTCCGTCAGTTGTGAAATAAATCGAG
Found at i:5282201 original size:45 final size:45
Alignment explanation
Indices: 5282140--5282284 Score: 218
Period size: 45 Copynumber: 3.2 Consensus size: 45
5282130 TTGTTATTCA
* *
5282140 CAAAAAATAAATCCTAACCACATGATATCTAATTCGTATGCTTATT
1 CAAAAAATAAA-CCTAACCGCATGATATCTAATTCGCATGCTTATT
*
5282186 TAAAAAATAAACCTAACCGCATGATATCTAATTCGCATGCTTATT
1 CAAAAAATAAACCTAACCGCATGATATCTAATTCGCATGCTTATT
*
5282231 CAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCATTTATT
1 CAAAAAATAAACCTAACCGCATGATATCTAATTCGCATGC--TTATT
*
5282278 CGAAAAA
1 CAAAAAA
5282285 CGAAAATAAA
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
45 70 0.77
46 10 0.11
47 11 0.12
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (45 bp):
CAAAAAATAAACCTAACCGCATGATATCTAATTCGCATGCTTATT
Found at i:5290811 original size:77 final size:77
Alignment explanation
Indices: 5290621--5290824 Score: 281
Period size: 76 Copynumber: 2.7 Consensus size: 77
5290611 GTTGTACAAG
* * * *
5290621 GGGGGGAATCGGTACCCCCT-TGGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 GGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
**
5290684 CAAAACTGTTTA
66 CAAAACCATTTA
*
5290696 GGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 GGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
5290760 CCAAAACCATTTA
66 -CAAAACCATTTA
* * *
5290773 -GGGGGAATCGGTTCCTCCTATGGGGGGGAATCAGTTCCCTCTGAGCAATCTG
1 GGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTG
5290825 TAATTTTTGG
Statistics
Matches: 115, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
75 24 0.21
76 54 0.47
77 37 0.32
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.24
Consensus pattern (77 bp):
GGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
CAAAACCATTTA
Found at i:5293419 original size:21 final size:21
Alignment explanation
Indices: 5293393--5293432 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5293383 CAGAACCCCA
*
5293393 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
5293414 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
5293433 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:5297325 original size:22 final size:21
Alignment explanation
Indices: 5297283--5297322 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5297273 GAGTTTGTTT
*
5297283 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
5297304 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
5297323 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:5299372 original size:75 final size:76
Alignment explanation
Indices: 5299246--5299452 Score: 283
Period size: 75 Copynumber: 2.7 Consensus size: 76
5299236 GTTGTACAAG
* * * *
5299246 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG-C
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAGCC
**
5299309 AAAACTGTTTA
66 AAAACCATTTA
* * *
5299320 GGGGGAATCGGTTCCTCCTATGGGGGGAATTGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAGCC
5299385 AAAACCATTTA
66 AAAACCATTTA
* * *
5299396 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTGTAATT
1 GGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
5299453 TTTGGCTTTG
Statistics
Matches: 116, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
74 17 0.15
75 38 0.33
76 31 0.27
77 30 0.26
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAGCC
AAAACCATTTA
Found at i:5302545 original size:45 final size:47
Alignment explanation
Indices: 5302493--5302581 Score: 155
Period size: 45 Copynumber: 1.9 Consensus size: 47
5302483 TCGAATAAAT
5302493 GCATGCGAACTAGATATCATGCGGTTAGG-TTTATTTTT-TGAACAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
*
5302538 GCATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
5302582 TAACAAAGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 28 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
Found at i:5312296 original size:26 final size:26
Alignment explanation
Indices: 5312266--5312350 Score: 84
Period size: 26 Copynumber: 3.3 Consensus size: 26
5312256 AAATAATAAT
*
5312266 AAAAATGAGAAGAAGGAAGAGAAGGA
1 AAAAATGAGAAGAAGGAAAAGAAGGA
* *
5312292 AAAAATGAGAAAAAAGGAAAATGATGGA
1 AAAAATGAG-AAGAAGGAAAA-GAAGGA
* * *
5312320 AAAAACGAAAAGAA-AAAAAGAA-GA
1 AAAAATGAGAAGAAGGAAAAGAAGGA
5312344 AAAAATG
1 AAAAATG
5312351 GAAAATGAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
24 8 0.17
25 2 0.04
26 13 0.27
27 13 0.27
28 12 0.25
ACGTcount: A:0.68, C:0.01, G:0.25, T:0.06
Consensus pattern (26 bp):
AAAAATGAGAAGAAGGAAAAGAAGGA
Found at i:5312310 original size:18 final size:18
Alignment explanation
Indices: 5312287--5312330 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5312277 GAAGGAAGAG
5312287 AAGGAAAA-AATGAGAAAA
1 AAGGAAAATAATG-GAAAA
*
5312305 AAGGAAAATGATGGAAAA
1 AAGGAAAATAATGGAAAA
*
5312323 AACGAAAA
1 AAGGAAAA
5312331 GAAAAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.68, C:0.02, G:0.23, T:0.07
Consensus pattern (18 bp):
AAGGAAAATAATGGAAAA
Found at i:5312337 original size:25 final size:26
Alignment explanation
Indices: 5312318--5312372 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
5312308 GAAAATGATG
5312318 GAAAAAA-CGAAAA-GAAAAAAAGAA
1 GAAAAAATCGAAAATGAAAAAAAGAA
*
5312342 GAAAAAATGGAAAATGAAAAAAAGAGA
1 GAAAAAATCGAAAATGAAAAAAAGA-A
5312369 GAAA
1 GAAA
5312373 TAAAAGGAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 7 0.26
25 5 0.19
26 10 0.37
27 5 0.19
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.04
Consensus pattern (26 bp):
GAAAAAATCGAAAATGAAAAAAAGAA
Found at i:5313738 original size:36 final size:37
Alignment explanation
Indices: 5313649--5313758 Score: 143
Period size: 36 Copynumber: 3.0 Consensus size: 37
5313639 TCAAAACAGG
* * * *
5313649 TCAATCTTAAGCCTTTA-TGAAAGAGCAGTGAAGCAAT
1 TCAATCTTAAGCCTTCACAG-AAGAGTAGTGAAGCAAA
*
5313686 TCAAACTTAAGCCTTCACAGAAGAGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAA
*
5313723 TC-ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAA
5313759 CTCGTTTGTT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
36 32 0.49
37 32 0.49
38 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (37 bp):
TCAATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAA
Found at i:5313844 original size:55 final size:55
Alignment explanation
Indices: 5313776--5314243 Score: 571
Period size: 55 Copynumber: 8.6 Consensus size: 55
5313766 GTTGAAGATT
* * ** **
5313776 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTC
5313831 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTCA-TGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-ATTGAAGATTGTTC
* * *
5313886 GAGTTCTACACTCTCTGAAGGAATAGAGAGCGGACACGTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTC
*
5313941 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGCTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTAT-TGAAGATTGTTC
* * * *
5313996 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACTCGTTTGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTC
* * * *
5314047 GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATT-TTCC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTT-C
5314102 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGCTTTATTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCG-TTTATTGAAGATTGTTC
* * * **
5314158 AAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTATT-AAGATTGTTC
1 GAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGAC-CCGTTTATTGAAGATTGTTC
*
5314213 GAG-TCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTTC-TATACTCT-CTGAAGGAATAGAGAGC
5314244 AGGCTCGTCA
Statistics
Matches: 366, Mismatches: 34, Indels: 26
0.86 0.08 0.06
Matches are distributed among these distances:
51 43 0.12
52 1 0.00
53 2 0.01
54 2 0.01
55 265 0.72
56 50 0.14
57 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (55 bp):
GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTC
Found at i:5314263 original size:217 final size:216
Alignment explanation
Indices: 5313776--5314243 Score: 624
Period size: 217 Copynumber: 2.1 Consensus size: 216
5313766 GTTGAAGATT
* * ** *
5313776 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGT-TCGTTGAAGATTGTTCGAGTTCTAT
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACTCGTAT-GTTGAAGA---TT-GAGTCCTAT
*
5313840 ACTCTCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTCGAGTTCTACACTCTCTGAA
61 ACTCTCTGAAAGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTCGAGTTCTACACTCTCTGAA
* *
5313905 GGAATAGAGAGCGGACACGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGA
126 GGAATAGAGAGCGGACACGTTTATTGAAGATTGTTCAAGTTCTATACTCTCTGAAGGAATAGAGA
* * *
5313970 GCGGACCCGTTTTATGAAGATTGCTC
191 GCAGACACATTTTATGAAGATTGCTC
*
5313996 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACTCGTTTGTTGAAGATTGAGTCCTATACTCT
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACTCGTATGTTGAAGATTGAGTCCTATACTCT
* * *
5314061 CTGAAAGAATAGGGAGCGGACCTGTTT-ATTGAAGATT-TTCCGAGTTCTATACTCTCTGAAGGA
66 CTGAAAGAATAGAGAGCGGACCCGTTTCA-TGAAGATTGTT-CGAGTTCTACACTCTCTGAAGGA
* *
5314124 ATAGAGAGCGGACCCGCTTTATTGAAGATTGTTCAAG-TCTTATACTCTCTGAATGAATAGAGAG
129 ATAGAGAGCGGACACG-TTTATTGAAGATTGTTCAAGTTC-TATACTCTCTGAAGGAATAGAGAG
* *
5314188 CAGACACATTTTATTAAGATTGTTC
192 CAGACACATTTTATGAAGATTGCTC
5314213 GAG-TCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTTC-TATACTCT-CTGAAGGAATAGGGAGC
5314244 AGGCTCGTCA
Statistics
Matches: 223, Mismatches: 18, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
215 3 0.01
216 87 0.39
217 89 0.40
220 43 0.19
221 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (216 bp):
GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACTCGTATGTTGAAGATTGAGTCCTATACTCT
CTGAAAGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTCGAGTTCTACACTCTCTGAAGGAAT
AGAGAGCGGACACGTTTATTGAAGATTGTTCAAGTTCTATACTCTCTGAAGGAATAGAGAGCAGA
CACATTTTATGAAGATTGCTC
Found at i:5326246 original size:65 final size:65
Alignment explanation
Indices: 5326108--5326238 Score: 185
Period size: 63 Copynumber: 2.0 Consensus size: 65
5326098 ATAAAATAAG
* * * * *
5326108 CATTACATTTTGGATTTCATTAAAAAGAAATATTGATATTTAATTATCATTAAGGGTTAATATGA
1 CATTAAATTTTGGATTTCATTAAAAAGAAATATTGACACTTAACTATCATTAAGGGCTAATATGA
* *
5326173 CATTAAATTTTGGGTTTCGTT-AAAA-AAATATTGACACTTAACTATCATTAAGGGCTAATATGA
1 CATTAAATTTTGGATTTCATTAAAAAGAAATATTGACACTTAACTATCATTAAGGGCTAATATGA
5326236 CAT
1 CAT
5326239 ATTAAATTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 37 0.63
64 4 0.07
65 18 0.31
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (65 bp):
CATTAAATTTTGGATTTCATTAAAAAGAAATATTGACACTTAACTATCATTAAGGGCTAATATGA
Found at i:5338269 original size:32 final size:34
Alignment explanation
Indices: 5338233--5338316 Score: 91
Period size: 37 Copynumber: 2.4 Consensus size: 34
5338223 TAAATACGAA
*
5338233 ATAAATAAACAACAT-AA-AAAATAAAAAAAATG
1 ATAAATAAACAAAATGAACAAAATAAAAAAAATG
* *
5338265 ATAAAGTAAAATAGAAATGAACAAAATAAATAAAATG
1 ATAAA-T-AAACA-AAATGAACAAAATAAAAAAAATG
5338302 ATAAAATAAACAAAA
1 AT-AAATAAACAAAA
5338317 ATAAAACATA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
32 5 0.12
33 1 0.02
34 4 0.10
35 6 0.14
36 6 0.14
37 17 0.40
38 3 0.07
ACGTcount: A:0.73, C:0.05, G:0.06, T:0.17
Consensus pattern (34 bp):
ATAAATAAACAAAATGAACAAAATAAAAAAAATG
Found at i:5338309 original size:17 final size:17
Alignment explanation
Indices: 5338250--5338316 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
5338240 AACAACATAA
*
5338250 AAAATAAAAAAAATGAT
1 AAAATAAATAAAATGAT
* *
5338267 AAAGTAAAATAGAAATGAAC
1 AAAAT-AAATA-AAATG-AT
5338287 AAAATAAATAAAATGAT
1 AAAATAAATAAAATGAT
*
5338304 AAAATAAACAAAA
1 AAAATAAATAAAA
5338317 ATAAAACATA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
17 17 0.41
18 9 0.22
19 10 0.24
20 5 0.12
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.16
Consensus pattern (17 bp):
AAAATAAATAAAATGAT
Found at i:5338347 original size:41 final size:41
Alignment explanation
Indices: 5338285--5338362 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 41
5338275 ATAGAAATGA
*
5338285 ACAAAATAAATAAAATGATAAA-ATAAACAAAAATAAAACAT
1 ACAAAATAAATAAAATGATAAACAAAAAC-AAAATAAAACAT
5338326 ACAAAATAAA-AAAA-GCAATAAACAAAAACAAAATAAA
1 ACAAAATAAATAAAATG--ATAAACAAAAACAAAATAAA
5338363 TAAAAAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
39 1 0.03
40 4 0.12
41 23 0.70
42 5 0.15
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.13
Consensus pattern (41 bp):
ACAAAATAAATAAAATGATAAACAAAAACAAAATAAAACAT
Found at i:5338535 original size:6 final size:7
Alignment explanation
Indices: 5338518--5338566 Score: 62
Period size: 7 Copynumber: 6.9 Consensus size: 7
5338508 AACAAATAAT
5338518 AAAAAAG
1 AAAAAAG
5338525 AAAAAAG
1 AAAAAAG
5338532 AAAAAAG
1 AAAAAAG
5338539 AAAAATAG
1 AAAAA-AG
*
5338547 AAAAAAC
1 AAAAAAG
* *
5338554 AAATAAT
1 AAAAAAG
5338561 AAAAAA
1 AAAAAA
5338567 CCAAAATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
7 30 0.81
8 7 0.19
ACGTcount: A:0.84, C:0.02, G:0.08, T:0.06
Consensus pattern (7 bp):
AAAAAAG
Found at i:5338536 original size:15 final size:15
Alignment explanation
Indices: 5338518--5338595 Score: 67
Period size: 14 Copynumber: 5.4 Consensus size: 15
5338508 AACAAATAAT
5338518 AAAAAAGAAAAA-AG
1 AAAAAAGAAAAATAG
5338532 AAAAAAGAAAAATAG
1 AAAAAAGAAAAATAG
*
5338547 AAAAAACAAATAAT--
1 AAAAAAGAAA-AATAG
**
5338561 AAAAAACCAAAAT-G
1 AAAAAAGAAAAATAG
*
5338575 AAAAATAGTAAAATA-
1 AAAAA-AGAAAAATAG
5338590 AAAAAA
1 AAAAAA
5338596 ATAAAGTATA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
13 3 0.05
14 27 0.49
15 22 0.40
16 3 0.05
ACGTcount: A:0.79, C:0.04, G:0.08, T:0.09
Consensus pattern (15 bp):
AAAAAAGAAAAATAG
Found at i:5338555 original size:43 final size:44
Alignment explanation
Indices: 5338505--5338596 Score: 132
Period size: 43 Copynumber: 2.1 Consensus size: 44
5338495 AACATGTAAG
* *
5338505 AAAAACAAATAATAAAAAAGAAAAAAGAAAAA-AGAAAAATAGA
1 AAAAACAAATAATAAAAAACAAAAAAGAAAAATAGAAAAATAAA
* * *
5338548 AAAAACAAATAATAAAAAACCAAAATGAAAAATAGTAAAATAAA
1 AAAAACAAATAATAAAAAACAAAAAAGAAAAATAGAAAAATAAA
5338592 AAAAA
1 AAAAA
5338597 TAAAGTATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 29 0.67
44 14 0.33
ACGTcount: A:0.79, C:0.04, G:0.07, T:0.10
Consensus pattern (44 bp):
AAAAACAAATAATAAAAAACAAAAAAGAAAAATAGAAAAATAAA
Found at i:5338579 original size:13 final size:14
Alignment explanation
Indices: 5338505--5338567 Score: 65
Period size: 14 Copynumber: 4.4 Consensus size: 14
5338495 AACATGTAAG
5338505 AAAAACAAATAATA
1 AAAAACAAATAATA
* * *
5338519 AAAAAGAAAAAAGA
1 AAAAACAAATAATA
*
5338533 AAAAAGAAA-AATAGA
1 AAAAACAAATAAT--A
5338548 AAAAACAAATAATA
1 AAAAACAAATAATA
5338562 AAAAAC
1 AAAAAC
5338568 CAAAATGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
13 2 0.05
14 27 0.66
15 9 0.22
16 3 0.07
ACGTcount: A:0.81, C:0.05, G:0.06, T:0.08
Consensus pattern (14 bp):
AAAAACAAATAATA
Found at i:5338600 original size:14 final size:13
Alignment explanation
Indices: 5338505--5338596 Score: 58
Period size: 14 Copynumber: 6.6 Consensus size: 13
5338495 AACATGTAAG
* *
5338505 AAAAACAAATAAT
1 AAAAAAAAAAAAT
*
5338518 AAAAAAGAAAAAAG
1 AAAAAA-AAAAAAT
*
5338532 AAAAAAGAAAAAT
1 AAAAAAAAAAAAT
5338545 AGAAAAAACAAATAAT
1 A-AAAAAA-AAA-AAT
**
5338561 AAAAAACCAAAAT
1 AAAAAAAAAAAAT
**
5338574 GAAAAATAGTAAAAT
1 -AAAAA-AAAAAAAT
5338589 AAAAAAAA
1 AAAAAAAA
5338597 TAAAGTATAT
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
13 15 0.25
14 28 0.46
15 14 0.23
16 4 0.07
ACGTcount: A:0.79, C:0.04, G:0.07, T:0.10
Consensus pattern (13 bp):
AAAAAAAAAAAAT
Found at i:5339845 original size:28 final size:30
Alignment explanation
Indices: 5339790--5339845 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
5339780 AATATAATTT
5339790 ATATAATATATATTTCAAAATAGTTTTTTA
1 ATATAATATATATTTCAAAATAGTTTTTTA
*
5339820 ATATAATATATATTTTAAAA-AGTTTT
1 ATATAATATATATTTCAAAATAGTTTT
5339846 CAAAACTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (30 bp):
ATATAATATATATTTCAAAATAGTTTTTTA
Found at i:5339855 original size:24 final size:24
Alignment explanation
Indices: 5339828--5339874 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5339818 TAATATAATA
*
5339828 TATATTTTAAAAAGTTTTCAAAAC
1 TATATGTTAAAAAGTTTTCAAAAC
* *
5339852 TATATGTTATATAGTTTTCAAAA
1 TATATGTTAAAAAGTTTTCAAAA
5339875 TGTTTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (24 bp):
TATATGTTAAAAAGTTTTCAAAAC
Found at i:5339928 original size:38 final size:37
Alignment explanation
Indices: 5339871--5340158 Score: 226
Period size: 38 Copynumber: 7.8 Consensus size: 37
5339861 TATAGTTTTC
5339871 AAAATG-TTTTAAAA--A-ATATTATATAAGTTTTCAA
1 AAAATGTTTTTAAAACTATATATTATATAA-TTTTCAA
*
5339905 AAAATGTTTTTAAAATTATATATTATATAATTTTC-A
1 AAAATGTTTTTAAAACTATATATTATATAATTTTCAA
* *
5339941 AAAATGTTTTAAAAAATTATATATTATATAATTTTTCAA
1 AAAATGTTTT-TAAAACTATATATTATATAA-TTTTCAA
*
5339980 AAAATATTTTTAAAACTATATATTATATAATTTTTCCAA
1 AAAATGTTTTTAAAACTATATATTATATAA-TTTT-CAA
*
5340019 AATAT-TTTTTAAAACTATATA-T-TAT-ATTTT-AA
1 AAAATGTTTTTAAAACTATATATTATATAATTTTCAA
** * *
5340051 AAATAT-TTTCAAAAAACTATATAATATATAAATTTTC-G
1 AAA-ATGTTT-TTAAAACTATATATTATAT-AATTTTCAA
* *
5340089 AAAATCGTTTTCTGAAAATTATATATTATAT--TTCGTCAA
1 AAAAT-GTTTT-T-AAAACTATATATTATATAATT-TTCAA
** *
5340128 AAAACATTTTCACAAACTATATATATATATA
1 AAAATGTTTTTA-AAACTATATAT-TATATA
5340159 TATATATATA
Statistics
Matches: 211, Mismatches: 19, Indels: 43
0.77 0.07 0.16
Matches are distributed among these distances:
32 4 0.02
33 5 0.02
34 21 0.10
35 10 0.05
36 18 0.09
37 40 0.19
38 74 0.35
39 24 0.11
40 15 0.07
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (37 bp):
AAAATGTTTTTAAAACTATATATTATATAATTTTCAA
Found at i:5340087 original size:72 final size:75
Alignment explanation
Indices: 5339965--5340158 Score: 202
Period size: 72 Copynumber: 2.6 Consensus size: 75
5339955 AATTATATAT
* * * * * *
5339965 TATATAATTTTTC-AAAAAATATTTT-TAAAACTATATATTATATAATTTTTCCAAAAT-ATTTT
1 TATATTATATTTCTAAAAAACATTTTCAAAAACTATATAATATATAAATTTTCCAAAATCATTTT
*
5340027 -TTAAAACTA
66 CTGAAAACTA
* * *
5340036 TATATTATATTT-T-AAAAATATTTTCAAAAAACTATATAATATATAAATTTTCGAAAATCGTTT
1 TATATTATATTTCTAAAAAACATTTTC-AAAAACTATATAATATATAAATTTTCCAAAATCATTT
*
5340099 TCTGAAAATTA
65 TCTGAAAACTA
*
5340110 TATATTATATTTCGTCAAAAAACATTTTCACAAACTATATATATATATA
1 TATATTATATTTC-T-AAAAAACATTTTCAAAAACTATATA-ATATATA
5340159 TATATATATA
Statistics
Matches: 102, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
70 11 0.11
71 10 0.10
72 28 0.27
73 4 0.04
74 19 0.19
76 1 0.01
77 11 0.11
78 18 0.18
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.44
Consensus pattern (75 bp):
TATATTATATTTCTAAAAAACATTTTCAAAAACTATATAATATATAAATTTTCCAAAATCATTTT
CTGAAAACTA
Found at i:5340150 original size:2 final size:2
Alignment explanation
Indices: 5340145--5340187 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
5340135 TTTCACAAAC
5340145 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5340186 TA
1 TA
5340188 CAAAATAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5340155 original size:110 final size:108
Alignment explanation
Indices: 5339928--5340155 Score: 241
Period size: 110 Copynumber: 2.1 Consensus size: 108
5339918 AATTATATAT
* * * *
5339928 TATATA-ATTTTCAAAAATGTTTTAAAAAATTATATATTATATAATTTTTCAAAAAATATTTTTA
1 TATATATATTTTCAAAAATATTTTAAAAAACTATATAATATATAAATTTTCAAAAAATATTTTTA
** * * *
5339992 AAACTATATATTATATAATTTTTCCAAAATATTTTTTAAAACTA
66 AAACTATATATTATAT-ATTCGTCCAAAAAAATTTTCAAAACTA
* *
5340036 TATATTATATTTT-AAAAATATTTTCAAAAAACTATATAATATATAAATTTTC-GAAAATCGTTT
1 TATA-TATATTTTCAAAAATATTTT-AAAAAACTATATAATATATAAATTTTCAAAAAAT-ATTT
*
5340099 TCTGAAAATTATATATTATAT-TTCGT-CAAAAAACATTTTCACAAACTA
63 T-T-AAAACTATATATTATATATTCGTCCAAAAAA-ATTTTCA-AAACTA
5340147 TATATATAT
1 TATATATAT
5340156 ATATATATAT
Statistics
Matches: 100, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
108 4 0.04
109 23 0.23
110 46 0.46
111 11 0.11
112 16 0.16
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (108 bp):
TATATATATTTTCAAAAATATTTTAAAAAACTATATAATATATAAATTTTCAAAAAATATTTTTA
AAACTATATATTATATATTCGTCCAAAAAAATTTTCAAAACTA
Found at i:5347733 original size:36 final size:36
Alignment explanation
Indices: 5347690--5347763 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
5347680 TGCATATGGC
5347690 AATATAAATCATTGTAGGTTCGTGCATATGTATCGA
1 AATATAAATCATTGTAGGTTCGTGCATATGTATCGA
5347726 AATATAAATCATTGTAGGTTCGTGCATATGTATCGA
1 AATATAAATCATTGTAGGTTCGTGCATATGTATCGA
5347762 AA
1 AA
5347764 AAAAGGTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (36 bp):
AATATAAATCATTGTAGGTTCGTGCATATGTATCGA
Done.