Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 23 of 335
Found at i:8605871 original size:26 final size:26
Alignment explanation
Indices: 8605840--8605890 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
8605830 TACTTATTTA
8605840 TATAATAT-ATATATAATATAATATAC
1 TATAATATAATA-ATAATATAATATAC
*
8605866 TATAATATAATAATAATTTAATATA
1 TATAATATAATAATAATATAATATA
8605891 TATTTTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAATAATAATATAATATAC
Found at i:8608491 original size:29 final size:31
Alignment explanation
Indices: 8608425--8608492 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 31
8608415 ATAACAAAAT
*
8608425 ACAATATAAATAACTAAAATATAATATTTTAA
1 ACAA-ATAAATAACTAAAATATAATATTTAAA
* *
8608457 AC--ATAAATCATTAAAATAT-A-ATTTAAA
1 ACAAATAAATAACTAAAATATAATATTTAAA
8608484 ACAAATAAA
1 ACAAATAAA
8608493 ATGACTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
27 8 0.26
28 1 0.03
29 20 0.65
32 2 0.06
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (31 bp):
ACAAATAAATAACTAAAATATAATATTTAAA
Found at i:8613567 original size:35 final size:35
Alignment explanation
Indices: 8613521--8613591 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
8613511 CACGATAACA
8613521 TCATGTGATAATTTCCTCTCCCAAGCTTTTTGGCT
1 TCATGTGATAATTTCCTCTCCCAAGCTTTTTGGCT
8613556 TCATGTGATAATTTCCTCTCCCAAGCTTTTTGGCT
1 TCATGTGATAATTTCCTCTCCCAAGCTTTTTGGCT
8613591 T
1 T
8613592 TTCTCGTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.17, C:0.25, G:0.14, T:0.44
Consensus pattern (35 bp):
TCATGTGATAATTTCCTCTCCCAAGCTTTTTGGCT
Found at i:8626110 original size:12 final size:12
Alignment explanation
Indices: 8626093--8626117 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8626083 GCAGTAGCCC
8626093 CAGTACCAGCAG
1 CAGTACCAGCAG
8626105 CAGTACCAGCAG
1 CAGTACCAGCAG
8626117 C
1 C
8626118 GATAGTGGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.36, G:0.24, T:0.08
Consensus pattern (12 bp):
CAGTACCAGCAG
Found at i:8634691 original size:13 final size:13
Alignment explanation
Indices: 8634673--8634699 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8634663 AGCTTCCAAG
8634673 ATATTAAGTTCCC
1 ATATTAAGTTCCC
8634686 ATATTAAGTTCCC
1 ATATTAAGTTCCC
8634699 A
1 A
8634700 ATCCGAGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (13 bp):
ATATTAAGTTCCC
Found at i:8639080 original size:2 final size:2
Alignment explanation
Indices: 8639073--8639097 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8639063 CTTATATCTC
8639073 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
8639098 ACACACACTA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:8641110 original size:24 final size:25
Alignment explanation
Indices: 8641083--8641131 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
8641073 AGAAAAAGCT
8641083 AAGAAACATAGTTACATG-CCTTGA
1 AAGAAACATAGTTACATGCCCTTGA
8641107 AAGAAACATAGTTACATGCCCTTGA
1 AAGAAACATAGTTACATGCCCTTGA
8641132 CATTGCAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (25 bp):
AAGAAACATAGTTACATGCCCTTGA
Found at i:8643778 original size:2 final size:2
Alignment explanation
Indices: 8643771--8643803 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
8643761 ATTTAAAATT
8643771 TA TA TA 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
8643804 TGTTGAGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8645800 original size:15 final size:15
Alignment explanation
Indices: 8645782--8645828 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
8645772 TAAAAAATAA
8645782 TATAAATTTAACACT
1 TATAAATTTAACACT
*
8645797 TATAAAATTTAACGC-
1 TAT-AAATTTAACACT
* *
8645812 TAAAAATTTAATACT
1 TATAAATTTAACACT
8645827 TA
1 TA
8645829 ATTTTCAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 9 0.35
15 7 0.27
16 10 0.38
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (15 bp):
TATAAATTTAACACT
Found at i:8645819 original size:14 final size:16
Alignment explanation
Indices: 8645785--8645828 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 16
8645775 AAAATAATAT
8645785 AAATTTAACACTTATA
1 AAATTTAACACTTATA
*
8645801 AAATTTAACGC-TA-A
1 AAATTTAACACTTATA
*
8645815 AAATTTAATACTTA
1 AAATTTAACACTTA
8645829 ATTTTCAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 10 0.42
15 4 0.17
16 10 0.42
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (16 bp):
AAATTTAACACTTATA
Found at i:8646411 original size:24 final size:24
Alignment explanation
Indices: 8646383--8646431 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
8646373 TATATTTCAA
* *
8646383 ATTTTT-AGCTTCCATATATATAC
1 ATTTTTAAACTTCCATACATATAC
*
8646406 ATTTTTAAATTTCCATACATATAC
1 ATTTTTAAACTTCCATACATATAC
8646430 AT
1 AT
8646432 ATACAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.35, C:0.16, G:0.02, T:0.47
Consensus pattern (24 bp):
ATTTTTAAACTTCCATACATATAC
Found at i:8646825 original size:20 final size:20
Alignment explanation
Indices: 8646782--8646825 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
8646772 AAATCCCTTC
* * * *
8646782 AAAGTAAATTCCTTGGATTG
1 AAAGGAAATTCCTTGAAATA
8646802 AAAGGAAATTCCTTGAAATA
1 AAAGGAAATTCCTTGAAATA
8646822 AAAG
1 AAAG
8646826 ATAAGAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (20 bp):
AAAGGAAATTCCTTGAAATA
Found at i:8646868 original size:3 final size:3
Alignment explanation
Indices: 8646860--8646911 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
8646850 AGTTTAGTTT
8646860 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
8646908 ATA A
1 ATA A
8646912 AAGACATCAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:8648107 original size:10 final size:9
Alignment explanation
Indices: 8648091--8648244 Score: 62
Period size: 9 Copynumber: 17.7 Consensus size: 9
8648081 TGGTTTACAC
8648091 ATAAAAATT
1 ATAAAAATT
8648100 ATTAAAAA-T
1 A-TAAAAATT
*
8648109 A-AAAAAAT
1 ATAAAAATT
8648117 ATAAAAATT
1 ATAAAAATT
*
8648126 AT--TAA-T
1 ATAAAAATT
*
8648132 AAAAAAATT
1 ATAAAAATT
8648141 ATAGAAAA-T
1 ATA-AAAATT
*
8648150 ATAAATATT
1 ATAAAAATT
8648159 A-AAAAA--
1 ATAAAAATT
*
8648165 ATGAAAATTT
1 AT-AAAAATT
* *
8648175 GTATAAACTT
1 ATA-AAAATT
8648185 ATAAAATATT
1 ATAAAA-ATT
*
8648195 A-AAAGATT
1 ATAAAAATT
*
8648203 ATAAAAAAT
1 ATAAAAATT
8648212 ATTAAAAA-T
1 A-TAAAAATT
8648221 AT-AAAATT
1 ATAAAAATT
* *
8648229 CTAATATATT
1 ATAA-AAATT
8648239 ATAAAA
1 ATAAAA
8648245 TAATTTATAT
Statistics
Matches: 107, Mismatches: 19, Indels: 38
0.65 0.12 0.23
Matches are distributed among these distances:
6 3 0.03
7 11 0.10
8 22 0.21
9 37 0.35
10 34 0.32
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:8648127 original size:26 final size:26
Alignment explanation
Indices: 8648091--8648226 Score: 88
Period size: 26 Copynumber: 5.2 Consensus size: 26
8648081 TGGTTTACAC
8648091 ATAAAAATTATTAAAAATAAAAAAAT
1 ATAAAAATTATTAAAAATAAAAAAAT
8648117 ATAAAAATTATT---AATAAAAAAATT
1 ATAAAAATTATTAAAAATAAAAAAA-T
* *
8648141 ATAGAAAA-TA-TAAATATTAAAAAA-
1 ATA-AAAATTATTAAAAATAAAAAAAT
* * * *
8648165 ATGAAAATT-TGTATAAACTTATAAAAT
1 ATAAAAATTAT-TA-AAAATAAAAAAAT
* *
8648192 ATTAAAAGATTATAAAAAATATTAAAAAT
1 A-TAAAA-ATTATTAAAAATA-AAAAAAT
8648221 ATAAAA
1 ATAAAA
8648227 TTCTAATATA
Statistics
Matches: 84, Mismatches: 12, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
23 15 0.18
24 9 0.11
25 6 0.07
26 29 0.35
27 1 0.01
28 13 0.15
29 10 0.12
30 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (26 bp):
ATAAAAATTATTAAAAATAAAAAAAT
Found at i:8648156 original size:24 final size:23
Alignment explanation
Indices: 8648100--8648173 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 23
8648090 CATAAAAATT
*
8648100 ATTAAAAATAAAAAAATATAAAA
1 ATTATAAATAAAAAAATATAAAA
*
8648123 ATTATTAATAAAAAAATTATAGAAA
1 ATTATAAATAAAAAAA-TATA-AAA
*
8648148 A-TATAAATATTAAAAAA-ATGAAA
1 ATTATAAATA--AAAAAATATAAAA
8648171 ATT
1 ATT
8648174 TGTATAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
23 18 0.43
24 14 0.33
25 4 0.10
26 6 0.14
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (23 bp):
ATTATAAATAAAAAAATATAAAA
Found at i:8648212 original size:20 final size:18
Alignment explanation
Indices: 8648187--8648226 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 18
8648177 ATAAACTTAT
8648187 AAAATATTAAAAGATTATAA
1 AAAATATTAAAA-A-TATAA
8648207 AAAATATTAAAAATATAA
1 AAAATATTAAAAATATAA
8648225 AA
1 AA
8648227 TTCTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 1 0.05
20 12 0.60
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAATATTAAAAATATAA
Found at i:8648308 original size:22 final size:21
Alignment explanation
Indices: 8648257--8648307 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
8648247 ATTTATATAA
8648257 TTTATAAAACATATTTAAAAT
1 TTTATAAAACATATTTAAAAT
8648278 TTTATAAAAGCATA-TTAAAAT
1 TTTATAAAA-CATATTTAAAAT
8648299 TCTT-TAAAA
1 T-TTATAAAA
8648308 ATCGTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (21 bp):
TTTATAAAACATATTTAAAAT
Found at i:8656777 original size:25 final size:25
Alignment explanation
Indices: 8656743--8656793 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
8656733 TCCTTGAGAA
*
8656743 TATTGAAATTAAGTCGTCTTCATGT
1 TATTGAAATTAAGTAGTCTTCATGT
*
8656768 TATTGAAATTAAGTATTCTTCATGT
1 TATTGAAATTAAGTAGTCTTCATGT
8656793 T
1 T
8656794 CACTTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (25 bp):
TATTGAAATTAAGTAGTCTTCATGT
Found at i:8668853 original size:20 final size:21
Alignment explanation
Indices: 8668824--8668873 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
8668814 AATTAATTGA
8668824 AAAATAATTTGTATA-AAAAT
1 AAAATAATTTGTATACAAAAT
* * *
8668844 AAATTAATTTTTTTACAAAAT
1 AAAATAATTTGTATACAAAAT
8668865 AAAATAATT
1 AAAATAATT
8668874 AATATTGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAATAATTTGTATACAAAAT
Found at i:8670386 original size:12 final size:12
Alignment explanation
Indices: 8670345--8670387 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
8670335 CTTTTAGAAA
*
8670345 TAATATTAAT-T
1 TAATATTTATAT
* *
8670356 TAATATATATAA
1 TAATATTTATAT
8670368 TAATATTTATAT
1 TAATATTTATAT
8670380 TAATATTT
1 TAATATTT
8670388 TTCTAGCACA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 8 0.31
12 18 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TAATATTTATAT
Found at i:8682926 original size:30 final size:30
Alignment explanation
Indices: 8682890--8682952 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
8682880 TAAATATAAG
**
8682890 AAAAAATATTTTGTATACATTAGGATTTTT
1 AAAAAATATTTTGTATACATTAAAATTTTT
*
8682920 AAAAAATATTTTGTATATATTAAAATTTTT
1 AAAAAATATTTTGTATACATTAAAATTTTT
8682950 AAA
1 AAA
8682953 CTCTACACGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (30 bp):
AAAAAATATTTTGTATACATTAAAATTTTT
Found at i:8685133 original size:2 final size:2
Alignment explanation
Indices: 8685126--8685152 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8685116 CTCTATAATG
8685126 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
8685153 TGCAAGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8688599 original size:2 final size:2
Alignment explanation
Indices: 8688594--8688650 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
8688584 TGTGTGTGAA
*
8688594 AG AG AG AG AG AG AG TG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
8688636 AG A- AG AG A- AG AG AG A
1 AG AG AG AG AG AG AG AG A
8688651 CCTGCTCTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02
Consensus pattern (2 bp):
AG
Found at i:8694008 original size:29 final size:29
Alignment explanation
Indices: 8693966--8694026 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
8693956 CTTACAACGG
*
8693966 TTGAAACTGTTGAGCATGTACTGCTATAT
1 TTGAAACTGTTGAGCACGTACTGCTATAT
8693995 TTGAAACTGTTGAGCACGTACTGCTATAT
1 TTGAAACTGTTGAGCACGTACTGCTATAT
8694024 TTG
1 TTG
8694027 CCCGATTGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (29 bp):
TTGAAACTGTTGAGCACGTACTGCTATAT
Found at i:8695939 original size:86 final size:86
Alignment explanation
Indices: 8695791--8695962 Score: 274
Period size: 86 Copynumber: 2.0 Consensus size: 86
8695781 ATTGTTCAAT
* * * *
8695791 CTGTACCAAGTTCAATGAGTTCACTAGTTATGTAGATGTCATATTGTGATATGCGGTGTGCTCAT
1 CTGTACCAAGTTCAATGAGTTCACAAGTTATGTAGATGCCATATTGTGATATGAGGTATGCTCAT
*
8695856 GGTTTGACCCTGCATATAGCA
66 GGTATGACCCTGCATATAGCA
8695877 CTGTACCAAGTT-AAGTGAGTTCACAAGTTATGTAGATGCCATATTGTGATATGAGGTATGCTCA
1 CTGTACCAAGTTCAA-TGAGTTCACAAGTTATGTAGATGCCATATTGTGATATGAGGTATGCTCA
*
8695941 TGGTATGACGCTGCATATAGCA
65 TGGTATGACCCTGCATATAGCA
8695963 GGAACCTAGT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
85 2 0.03
86 77 0.97
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (86 bp):
CTGTACCAAGTTCAATGAGTTCACAAGTTATGTAGATGCCATATTGTGATATGAGGTATGCTCAT
GGTATGACCCTGCATATAGCA
Found at i:8702914 original size:9 final size:9
Alignment explanation
Indices: 8702900--8702929 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
8702890 CTCATAACAA
8702900 AAAAAAAAT
1 AAAAAAAAT
8702909 AAAAAAAAT
1 AAAAAAAAT
*
8702918 AAAAACAAT
1 AAAAAAAAT
8702927 AAA
1 AAA
8702930 TTTTTCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:8703698 original size:13 final size:14
Alignment explanation
Indices: 8703680--8703712 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
8703670 CAATATATCT
8703680 ATTATTTAA-CTAA
1 ATTATTTAAGCTAA
*
8703693 ATTATTTAAGGTAA
1 ATTATTTAAGCTAA
8703707 ATTATT
1 ATTATT
8703713 CTCTTGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (14 bp):
ATTATTTAAGCTAA
Found at i:8714451 original size:24 final size:25
Alignment explanation
Indices: 8714399--8714451 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
8714389 ATTTAATTAC
*
8714399 CAAATTGAAACAAAAAATCAATACT
1 CAAATTGAAACAAAAAATCAAAACT
*
8714424 -AAATT-AAACATTAAAAT-AAAACT
1 CAAATTGAAACA-AAAAATCAAAACT
8714447 CAAAT
1 CAAAT
8714452 AACAAATAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.23
Consensus pattern (25 bp):
CAAATTGAAACAAAAAATCAAAACT
Found at i:8721113 original size:18 final size:18
Alignment explanation
Indices: 8721060--8721113 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
8721050 TGGTGAATCC
8721060 ATTTTTA-A-GTTA-ATA
1 ATTTTTATATGTTATATA
* *
8721075 ATTTTT-TATGTTATGTT
1 ATTTTTATATGTTATATA
8721092 ATTTTTATATGTTATATA
1 ATTTTTATATGTTATATA
8721110 ATTT
1 ATTT
8721114 ATAACACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 7 0.23
16 4 0.13
17 7 0.23
18 13 0.42
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (18 bp):
ATTTTTATATGTTATATA
Found at i:8738140 original size:21 final size:22
Alignment explanation
Indices: 8738109--8738151 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
8738099 AATTAATAAA
*
8738109 CATATTTAAAATTTTATAAAAT
1 CATATTTAAAATTCTATAAAAT
8738131 CATA-TTAAAATTCTATAAAAT
1 CATATTTAAAATTCTATAAAAT
8738152 GAAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (22 bp):
CATATTTAAAATTCTATAAAAT
Found at i:8738175 original size:9 final size:9
Alignment explanation
Indices: 8738153--8738192 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
8738143 CTATAAAATG
8738153 AAAAATATT
1 AAAAATATT
*
8738162 AAAAAATGTT
1 -AAAAATATT
*
8738172 AAAAATGTT
1 AAAAATATT
8738181 AAAAATATT
1 AAAAATATT
8738190 AAA
1 AAA
8738193 TATTGCTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (9 bp):
AAAAATATT
Found at i:8738723 original size:10 final size:10
Alignment explanation
Indices: 8738701--8738802 Score: 51
Period size: 9 Copynumber: 10.7 Consensus size: 10
8738691 TTAAAAAAAA
8738701 TTTATACAT-T
1 TTTATA-ATAT
8738711 TTTATAATAT
1 TTTATAATAT
8738721 TTT-TGATATAT
1 TTTAT-A-ATAT
*
8738732 TTTATTA-AT
1 TTTATAATAT
*
8738741 TTTATAA-AA
1 TTTATAATAT
** *
8738750 AATATAATTT
1 TTTATAATAT
8738760 TTTATAAT-T
1 TTTATAATAT
*
8738769 TAT-TAAT-T
1 TTTATAATAT
8738777 TTTATAACT-T
1 TTTATAA-TAT
8738787 TTTATAATA-
1 TTTATAATAT
8738796 TTTATAA
1 TTTATAA
8738803 GTTTATATCG
Statistics
Matches: 73, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
8 7 0.10
9 31 0.42
10 27 0.37
11 7 0.10
12 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (10 bp):
TTTATAATAT
Found at i:8738794 original size:19 final size:18
Alignment explanation
Indices: 8738751--8738824 Score: 69
Period size: 19 Copynumber: 3.9 Consensus size: 18
8738741 TTTATAAAAA
8738751 ATATAATTTTTTATAATTT
1 ATATAA-TTTTTATAATTT
8738770 AT-TAATTTTTATAACTTT
1 ATATAATTTTTATAA-TTT
* *
8738788 TTATAATATTTATAAGTTT
1 ATATAATTTTTATAA-TTT
* *
8738807 ATATCGATTTTAATAATT
1 ATAT-AATTTTTATAATT
8738825 CTTTTATACT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
17 9 0.20
18 7 0.16
19 21 0.47
20 8 0.18
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (18 bp):
ATATAATTTTTATAATTT
Found at i:8739452 original size:23 final size:22
Alignment explanation
Indices: 8739417--8739459 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
8739407 GACATGAGCG
8739417 AATTAGAGCTGAAACAAAAAAAC
1 AATTAGAGCTG-AACAAAAAAAC
* *
8739440 AATTGGAGTTGAACAAAAAA
1 AATTAGAGCTGAACAAAAAA
8739460 GGCCTACTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.58, C:0.09, G:0.16, T:0.16
Consensus pattern (22 bp):
AATTAGAGCTGAACAAAAAAAC
Found at i:8757777 original size:122 final size:122
Alignment explanation
Indices: 8757636--8757884 Score: 417
Period size: 122 Copynumber: 2.0 Consensus size: 122
8757626 AAAATACAAA
* *
8757636 AAAAAAAACTAACACAAATATTAGTAGTCATATATTAGATACTCTAGACTACAGTGGTATTTCAG
1 AAAAAAAACTAACAAAAATATTAGTAGTCATATATTAGATACTCTAGACTACAGTGGTATCTCAG
* *
8757701 TTCCTGGAAGTAGTGAAACTTACCTGTACCTAGCAACAGTACTACCTTTTGCATATT
66 TTCCTGGAAGTAGTGAAACTTACCTGTACCTAGCAACAGTACTACCTTCTACATATT
* *
8757758 AAAAAAAACTAACAAAAATATTATTAGTCATATATTAGATACTCTAGACTATAGTGGTATCTCAG
1 AAAAAAAACTAACAAAAATATTAGTAGTCATATATTAGATACTCTAGACTACAGTGGTATCTCAG
* *
8757823 TTCCTGGAAGTAGTGAAACTTACCTGTACCTAGCAATAGTACTGCCTTCTACATATT
66 TTCCTGGAAGTAGTGAAACTTACCTGTACCTAGCAACAGTACTACCTTCTACATATT
*
8757880 CAAAA
1 AAAAA
8757885 GCAAAACACC
Statistics
Matches: 118, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
122 118 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (122 bp):
AAAAAAAACTAACAAAAATATTAGTAGTCATATATTAGATACTCTAGACTACAGTGGTATCTCAG
TTCCTGGAAGTAGTGAAACTTACCTGTACCTAGCAACAGTACTACCTTCTACATATT
Found at i:8760341 original size:22 final size:22
Alignment explanation
Indices: 8760315--8760360 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
8760305 GTGTTGGATT
*
8760315 TATAATATGGATAAATTGCAAC
1 TATAATATGGAGAAATTGCAAC
8760337 TATAATATGGAGAAATTGCAAC
1 TATAATATGGAGAAATTGCAAC
8760359 TA
1 TA
8760361 ACTTGAGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (22 bp):
TATAATATGGAGAAATTGCAAC
Found at i:8762161 original size:12 final size:12
Alignment explanation
Indices: 8762123--8762163 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
8762113 AACATTTAAA
8762123 ATATT-AAAAAT
1 ATATTAAAAAAT
*
8762134 AAATTAAAAAATT
1 ATATTAAAAAA-T
8762147 ATATTAAAAAAT
1 ATATTAAAAAAT
8762159 ATATT
1 ATATT
8762164 TTATAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 4 0.15
12 11 0.42
13 11 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATATTAAAAAAT
Found at i:8763387 original size:13 final size:14
Alignment explanation
Indices: 8763371--8763406 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
8763361 CAATCTCATA
8763371 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
8763384 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
8763397 TCTC-ATTTCA
1 TCTCAATTTCA
8763407 TTCCAATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:8763396 original size:18 final size:19
Alignment explanation
Indices: 8763358--8763398 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
8763348 TGGTTCATGT
8763358 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
8763377 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
8763395 TTTC
1 TTTC
8763399 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:8763588 original size:21 final size:21
Alignment explanation
Indices: 8763562--8763646 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
8763552 TGATCAGTAT
*
8763562 ACGACACATAAAGTGCCTAAA
1 ACGACACACAAAGTGCCTAAA
* * * *
8763583 ACGACACACGAGGTGCCTGAT
1 ACGACACACAAAGTGCCTAAA
* *
8763604 ACGACACACGAGGTGCCTGAAA
1 ACGACACACAAAGTGCCT-AAA
*
8763626 TACGACACATAAAGTGCCTAA
1 -ACGACACACAAAGTGCCTAA
8763647 TCGGTAAAGC
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 34 0.65
22 3 0.06
23 15 0.29
ACGTcount: A:0.39, C:0.26, G:0.21, T:0.14
Consensus pattern (21 bp):
ACGACACACAAAGTGCCTAAA
Found at i:8763612 original size:23 final size:22
Alignment explanation
Indices: 8763560--8763634 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 22
8763550 CCTGATCAGT
** *
8763560 ATACGACACATAAAGTGCCT-A
1 ATACGACACACGAGGTGCCTGA
*
8763581 AAACGACACACGAGGTGCCTG-
1 ATACGACACACGAGGTGCCTGA
8763602 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCTG-A
8763625 ATACGACACA
1 ATACGACACA
8763635 TAAAGTGCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 36 0.78
23 10 0.22
ACGTcount: A:0.39, C:0.27, G:0.21, T:0.13
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTGA
Found at i:8765460 original size:53 final size:53
Alignment explanation
Indices: 8765393--8765526 Score: 207
Period size: 53 Copynumber: 2.5 Consensus size: 53
8765383 ACAAGTGTGC
* *
8765393 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTGATAATGTGACT
* *
8765446 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTGATAATGTGACT
*
8765499 CCGTATAAGACCAT-GTCTGGGATATGGC
1 CCGTATAAGACCATAG-CTGGGCTATGGC
8765527 TTCGTATGAT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
52 1 0.01
53 74 0.99
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTGATAATGTGACT
Found at i:8767857 original size:46 final size:46
Alignment explanation
Indices: 8767677--8767857 Score: 247
Period size: 46 Copynumber: 3.9 Consensus size: 46
8767667 TTGACATGAA
* * * * * *
8767677 GCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTT
*** *
8767723 GCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
*
8767769 GCCATGGTATCTTTCTACCATGGTCTTACACATTTCATATCAGGTT
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
8767815 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
8767858 AGAGCACACT
Statistics
Matches: 121, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 4 0.03
46 117 0.97
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
Found at i:8770002 original size:11 final size:11
Alignment explanation
Indices: 8769986--8770037 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
8769976 TATACTAAAT
8769986 AAATAATAATA
1 AAATAATAATA
*
8769997 AAATAAT-ATT
1 AAATAATAATA
* *
8770007 AAATATCTCATA
1 AAATA-ATAATA
*
8770019 AAATATTAATA
1 AAATAATAATA
8770030 AAATAATA
1 AAATAATA
8770038 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:8770621 original size:20 final size:20
Alignment explanation
Indices: 8770596--8770647 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
8770586 CCCCAAAAGG
* *
8770596 GTTAACTGAAACTCATATGA
1 GTTAACAGAAACTCATACGA
* *
8770616 GTTAACAGAAGCTCGTACGA
1 GTTAACAGAAACTCATACGA
8770636 GTTAAACAGAAA
1 GTT-AACAGAAA
8770648 GCAAACACGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (20 bp):
GTTAACAGAAACTCATACGA
Found at i:8773038 original size:15 final size:15
Alignment explanation
Indices: 8773013--8773070 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
8773003 TCATATATAT
8773013 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
8773029 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
8773044 AATAATTTCAATCAA
1 TATAAATTCAATCAA
8773059 TATAAATTCAAT
1 TATAAATTCAAT
8773071 AAAACAGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:8773055 original size:30 final size:28
Alignment explanation
Indices: 8773016--8773074 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
8773006 TATATATTAT
8773016 ATAATTCAATCAATATAAATTCAATCAAA
1 ATAATTCAATCAATATAAATTCAAT-AAA
8773045 ATAATTTCAATCAATATAAATTCAATAAA
1 ATAA-TTCAATCAATATAAATTCAATAAA
8773074 A
1 A
8773075 CAGATATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATTCAATCAATATAAATTCAATAAA
Found at i:8773674 original size:18 final size:18
Alignment explanation
Indices: 8773653--8773689 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
8773643 AATAATAACT
*
8773653 ATAATAAAAATTTATTTA
1 ATAACAAAAATTTATTTA
*
8773671 ATAACAAATATTTATTTA
1 ATAACAAAAATTTATTTA
8773689 A
1 A
8773690 CACTTGTGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAACAAAAATTTATTTA
Found at i:8774133 original size:30 final size:30
Alignment explanation
Indices: 8774079--8774135 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
8774069 GAGTCGTTAC
8774079 AATTATATAATATTATTATTTAACATATAT
1 AATTATATAATATTATTATTTAACATATAT
8774109 AATTAATATAATATT-TT-TTATAACATA
1 AATT-ATATAATATTATTATT-TAACATA
8774136 AGATATTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
29 2 0.08
30 13 0.52
31 10 0.40
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTATATAATATTATTATTTAACATATAT
Found at i:8774513 original size:3 final size:3
Alignment explanation
Indices: 8774505--8774543 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
8774495 AAAAACACAC
8774505 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
8774544 AATGATAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:8792633 original size:3 final size:3
Alignment explanation
Indices: 8792627--8792655 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
8792617 TATTATAAAA
8792627 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
8792656 AAAAAGGGAA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:8796151 original size:19 final size:21
Alignment explanation
Indices: 8796095--8796156 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
8796085 ATTGGGTAGA
8796095 TCAGCTCTTACGAGCTTTTGT
1 TCAGCTCTTACGAGCTTTTGT
* *
8796116 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTACGAGCTTTTGT
8796137 TCAGCT-TT-CGAGCTTTTGT
1 TCAGCTCTTACGAGCTTTTGT
8796156 T
1 T
8796157 GGTGTATTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.27
20 2 0.05
21 25 0.68
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTTTGT
Found at i:8798698 original size:21 final size:21
Alignment explanation
Indices: 8798656--8798698 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
8798646 TGTTTATGTC
*
8798656 TTTTATCAATTTAATTTTTAT
1 TTTTATCAATTTAATTTATAT
*
8798677 TTTTAT-AGTTTAATTTGATAT
1 TTTTATCAATTTAATTT-ATAT
8798698 T
1 T
8798699 AAATATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTTATCAATTTAATTTATAT
Found at i:8799381 original size:27 final size:27
Alignment explanation
Indices: 8799328--8799381 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
8799318 TTTGCATCTG
* *
8799328 AATAATTGTATTAATTTTTGTAAAAAA
1 AATAATTGTATTAATATTTATAAAAAA
*
8799355 AATAATTGTATTAATAATTTATGAAAA
1 AATAATTGTATTAAT-ATTTATAAAAA
8799382 TTAAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (27 bp):
AATAATTGTATTAATATTTATAAAAAA
Found at i:8799427 original size:18 final size:18
Alignment explanation
Indices: 8799389--8799426 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
8799379 AAATTAAATT
8799389 AAATTAAAATTTTATATA
1 AAATTAAAATTTTATATA
8799407 AAATTAAAATTTT-TATA
1 AAATTAAAATTTTATATA
8799424 AAA
1 AAA
8799427 AAATTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTAAAATTTTATATA
Found at i:8799428 original size:19 final size:18
Alignment explanation
Indices: 8799389--8799428 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
8799379 AAATTAAATT
*
8799389 AAATTAAAATTTTATATA
1 AAATTAAAATTTTATAAA
8799407 AAATTAAAATTTTTATAAA
1 AAATTAAAA-TTTTATAAA
8799426 AAA
1 AAA
8799429 ATTATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTAAAATTTTATAAA
Found at i:8799448 original size:32 final size:32
Alignment explanation
Indices: 8799394--8799459 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
8799384 AAATTAAATT
* ** *
8799394 AAAATTTTATATAAAATTAAAATTTTTATAAA
1 AAAATTATATATAAAACCAAAATTGTTATAAA
* *
8799426 AAAATTATATATTAAACCAAAATTGTTATGAA
1 AAAATTATATATAAAACCAAAATTGTTATAAA
8799458 AA
1 AA
8799460 TTTGAGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (32 bp):
AAAATTATATATAAAACCAAAATTGTTATAAA
Found at i:8807152 original size:60 final size:59
Alignment explanation
Indices: 8807079--8807217 Score: 167
Period size: 60 Copynumber: 2.3 Consensus size: 59
8807069 CAGTTTTAAC
*
8807079 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCTCT-TAC-AGTAAC-AGAGTATAT
1 TGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAGCC-CTATACAAGT--CGAGA-TATAT
* * *
8807140 TGGGCCTAGCCCATATTAGTATCAATCTGGGCCGTAGCCCTATACAAGTCGAGATATAT
1 TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATACAAGTCGAGATATAT
*
8807199 TGGGCCTTGCCCATATCAA
1 TGGGCCTAGCCCATATCAA
8807218 CACAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
59 24 0.35
60 35 0.51
61 9 0.13
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (59 bp):
TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATACAAGTCGAGATATAT
Found at i:8808546 original size:18 final size:18
Alignment explanation
Indices: 8808516--8808571 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
8808506 GAAAATCGGC
8808516 AAGAGGAGAAAGAAAAGAG
1 AAGAGG-GAAAGAAAAGAG
* *
8808535 AAGAGGGAAAGAGATGAG
1 AAGAGGGAAAGAAAAGAG
* *
8808553 -AGAAGGAAAGAAAATAG
1 AAGAGGGAAAGAAAAGAG
8808570 AA
1 AA
8808572 AATAGAATTG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 13 0.43
18 11 0.37
19 6 0.20
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.04
Consensus pattern (18 bp):
AAGAGGGAAAGAAAAGAG
Found at i:8810651 original size:44 final size:45
Alignment explanation
Indices: 8810561--8810689 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
8810551 GACAGAACGA
*
8810561 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
8810607 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
8810651 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
8810690 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:8815268 original size:18 final size:18
Alignment explanation
Indices: 8815245--8815303 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 18
8815235 GACAAAAGGA
*
8815245 GAAAGAAAAGAGAAGAGG
1 GAAAGAAAAGAGAAGAAG
* *
8815263 GAAAGAGATGAG-AGAAG
1 GAAAGAAAAGAGAAGAAG
*
8815280 GAAAGAAAATAGAA-AAG
1 GAAAGAAAAGAGAAGAAG
*
8815297 GAGAGAA
1 GAAAGAA
8815304 TTGTTCAGCT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
17 22 0.67
18 11 0.33
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (18 bp):
GAAAGAAAAGAGAAGAAG
Found at i:8816913 original size:39 final size:39
Alignment explanation
Indices: 8816859--8817039 Score: 290
Period size: 39 Copynumber: 4.6 Consensus size: 39
8816849 AACACAAATG
* *
8816859 CCTTCGGGTCTTAGCCCGGATATAGCACCAGCACGAATA
1 CCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATA
* *
8816898 CCTTCGGGACTTAGCCCGAATATAACACTAGCACGAATA
1 CCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATA
*
8816937 CCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATA
* *
8816976 CCTTCGGGACTTAGCCCGGACATAACACCAGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATA
*
8817015 CCTTTGGGACTTAGCCCGGATATAA
1 CCTTCGGGACTTAGCCCGGATATAA
8817040 ATCTCACACA
Statistics
Matches: 132, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 132 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGATATAACACCAGCACGAATA
Found at i:8817550 original size:2 final size:2
Alignment explanation
Indices: 8817543--8817568 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8817533 ATTCCAATAT
8817543 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
8817569 ATTTTCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:8822679 original size:75 final size:75
Alignment explanation
Indices: 8822560--8822731 Score: 214
Period size: 75 Copynumber: 2.4 Consensus size: 75
8822550 CATGGCAAAG
** *
8822560 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
8822619 CCATACTGAGC
65 CCATACTGAGC
8822630 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
8822695 CATACTGAGT
66 CATACTGAGC
***
8822705 TAAAAAAATGTAGGTATGGTATT-TCAA
1 T-GTGAAATGTAGGTATGGTATTATCAA
8822732 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 1 0.01
75 47 0.53
76 18 0.20
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.34
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACTGAGC
Found at i:8822698 original size:35 final size:35
Alignment explanation
Indices: 8822563--8822729 Score: 176
Period size: 35 Copynumber: 4.6 Consensus size: 35
8822553 GGCAAAGTGT
* **
8822563 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
8822598 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
8822633 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
*
8822673 GAAATGTAGGTATGGCATTTCCCATACTGAGTTAAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTT-AA
*
8822709 AAAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
8822730 AATGAGGAAA
Statistics
Matches: 117, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
35 65 0.56
36 21 0.18
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:8826076 original size:1 final size:1
Alignment explanation
Indices: 8826070--8826100 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
8826060 CCATGCAAAC
*
8826070 AAAAAAAAAAAAAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8826101 GCCAAACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:8828857 original size:14 final size:14
Alignment explanation
Indices: 8828838--8828864 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8828828 ATACTTTATT
8828838 TATATACACATATA
1 TATATACACATATA
8828852 TATATACACATAT
1 TATATACACATAT
8828865 GGATGTCACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (14 bp):
TATATACACATATA
Found at i:8835660 original size:23 final size:22
Alignment explanation
Indices: 8835629--8835678 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
8835619 TTACGGAATT
*
8835629 AAAACAATTAAAATTCATTAGTA
1 AAAATAATTAAAATTCA-TAGTA
* * *
8835652 AAAATAATTTAATTTCATATTA
1 AAAATAATTAAAATTCATAGTA
8835674 AAAAT
1 AAAAT
8835679 TTCAATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATAATTAAAATTCATAGTA
Found at i:8836532 original size:19 final size:19
Alignment explanation
Indices: 8836508--8836545 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
8836498 AAGAAAAAAA
8836508 AAGTTAAATTTACGTAAAT
1 AAGTTAAATTTACGTAAAT
8836527 AAGTTAAATTTACGTAAAT
1 AAGTTAAATTTACGTAAAT
8836546 CTTCTTCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (19 bp):
AAGTTAAATTTACGTAAAT
Found at i:8836595 original size:20 final size:20
Alignment explanation
Indices: 8836570--8836612 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
8836560 CCTAAATTGC
* *
8836570 TTATTTATAAGATTATTATT
1 TTATTTATAAAACTATTATT
8836590 TTATTTATAAAACTATTATT
1 TTATTTATAAAACTATTATT
8836610 TTA
1 TTA
8836613 ATAAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TTATTTATAAAACTATTATT
Found at i:8836752 original size:24 final size:24
Alignment explanation
Indices: 8836706--8836753 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
8836696 AATTTAAATG
* **
8836706 ATTTTTATTTTTTAAAGTTTTTAA
1 ATTTTAATTTTTTAAAGAATTTAA
*
8836730 ATTTTAATTTTTTTAAGAATTTAA
1 ATTTTAATTTTTTAAAGAATTTAA
8836754 GACTAAATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTTAATTTTTTAAAGAATTTAA
Found at i:8837445 original size:10 final size:11
Alignment explanation
Indices: 8837407--8837450 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 11
8837397 AATAAGGTTT
8837407 ATTTTATTTT-
1 ATTTTATTTTA
8837417 ATTTTATTTTA
1 ATTTTATTTTA
*
8837428 A--TTGTTTTA
1 ATTTTATTTTA
8837437 ATTTT-TTTTA
1 ATTTTATTTTA
8837447 ATTT
1 ATTT
8837451 AATCACTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
9 8 0.27
10 19 0.63
11 3 0.10
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (11 bp):
ATTTTATTTTA
Found at i:8837445 original size:19 final size:19
Alignment explanation
Indices: 8837413--8837449 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
8837403 GTTTATTTTA
8837413 TTTTATTTTATTTTAATTG
1 TTTTATTTTATTTTAATTG
8837432 TTTTAATTTT-TTTTAATT
1 TTTT-ATTTTATTTTAATT
8837450 TAATCACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (19 bp):
TTTTATTTTATTTTAATTG
Found at i:8837445 original size:24 final size:24
Alignment explanation
Indices: 8837408--8837453 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
8837398 ATAAGGTTTA
*
8837408 TTTTATTTTATTTTATTTTAATTG
1 TTTTATTTTATTTTAATTTAATTG
8837432 TTTTAATTTT-TTTTAATTTAAT
1 TTTT-ATTTTATTTTAATTTAAT
8837454 CACTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (24 bp):
TTTTATTTTATTTTAATTTAATTG
Found at i:8848899 original size:13 final size:13
Alignment explanation
Indices: 8848881--8848912 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
8848871 ATAGTTTAAT
8848881 AATAAAATAAAGA
1 AATAAAATAAAGA
8848894 AATAAAATAAAGA
1 AATAAAATAAAGA
8848907 AATAAA
1 AATAAA
8848913 TGAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (13 bp):
AATAAAATAAAGA
Found at i:8849262 original size:15 final size:15
Alignment explanation
Indices: 8849239--8849286 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
8849229 TATCAAATTT
8849239 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
8849254 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
8849269 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
8849283 ATAT
1 ATAT
8849287 ATTATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:8851919 original size:15 final size:14
Alignment explanation
Indices: 8851901--8851931 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
8851891 TTAATTTATT
8851901 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
8851916 TAATAATAATCTAA
1 TAATAATAATCTAA
8851930 TA
1 TA
8851932 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:8851942 original size:21 final size:20
Alignment explanation
Indices: 8851918--8851986 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
8851908 AATGCTAATA
8851918 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
8851939 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
8851958 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
8851979 ATAATAAT
1 ATAATAAT
8851987 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:8853015 original size:46 final size:46
Alignment explanation
Indices: 8852962--8853137 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
8852952 TGGTTGAGCA
8852962 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
8853008 TCTGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
8853053 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
8853101 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
8853138 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:8853118 original size:93 final size:93
Alignment explanation
Indices: 8852959--8853130 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
8852949 GGATGGTTGA
* * *
8852959 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
8853024 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
8853052 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
8853117 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
8853131 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:8854711 original size:23 final size:23
Alignment explanation
Indices: 8854684--8854741 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
8854674 TAATATTTCG
8854684 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
8854707 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
*
8854730 GGTCTGTTTGGG
1 GGTGTGTTTGGG
8854742 AGGAATCCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.07, C:0.05, G:0.41, T:0.47
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATATTCT
Found at i:8854867 original size:18 final size:19
Alignment explanation
Indices: 8854846--8854886 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
8854836 AATGAAATGA
8854846 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
8854864 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
8854883 GAAA
1 GAAA
8854887 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:8859657 original size:15 final size:15
Alignment explanation
Indices: 8859634--8859677 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
8859624 TATCAAATTT
8859634 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
8859649 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
8859664 ATATTGATTGAAAT
1 ATATTGATTGAAAT
8859678 ATGTATTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:8860336 original size:18 final size:19
Alignment explanation
Indices: 8860315--8860355 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
8860305 AATGAAATGA
8860315 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
8860333 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
8860352 GAAA
1 GAAA
8860356 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:8863074 original size:141 final size:141
Alignment explanation
Indices: 8862820--8863104 Score: 543
Period size: 141 Copynumber: 2.0 Consensus size: 141
8862810 TTTCTATTGA
* *
8862820 AAAAGAGTACATGATTGTGATGTGTATTGATCCCACTGCAAAGTAGAGTAGATAGTGGACTAGTA
1 AAAAGAGTACATGATTGTGATGTGTACTGATCCCAATGCAAAGTAGAGTAGATAGTGGACTAGTA
*
8862885 TTACAACCTTCTTGAACTTGCCATATTTTTTTATCACTTTCAAGAAGATACAAATTGCATGTATA
66 TTACAACCTTCTTGAACTTGCCATATTCTTTTATCACTTTCAAGAAGATACAAATTGCATGTATA
8862950 ACAGAGTTTTC
131 ACAGAGTTTTC
8862961 AAAAGAGTACATGATTGTGATGTGTACTGATCCCAATGCAAAGTAGAGTAGATAGTGGACTAGTA
1 AAAAGAGTACATGATTGTGATGTGTACTGATCCCAATGCAAAGTAGAGTAGATAGTGGACTAGTA
8863026 TTACAACCTTCTTGAACTTGCCATATTCTTTTATCACTTTCAAGAAGATACAAATTGCATGTATA
66 TTACAACCTTCTTGAACTTGCCATATTCTTTTATCACTTTCAAGAAGATACAAATTGCATGTATA
8863091 ACAGAGTTTTC
131 ACAGAGTTTTC
8863102 AAA
1 AAA
8863105 GTGGGACCGT
Statistics
Matches: 141, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
141 141 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (141 bp):
AAAAGAGTACATGATTGTGATGTGTACTGATCCCAATGCAAAGTAGAGTAGATAGTGGACTAGTA
TTACAACCTTCTTGAACTTGCCATATTCTTTTATCACTTTCAAGAAGATACAAATTGCATGTATA
ACAGAGTTTTC
Found at i:8866425 original size:19 final size:20
Alignment explanation
Indices: 8866401--8866441 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
8866391 TTGTAAAACA
* *
8866401 ATTAAAT-GAAAGTTTAATT
1 ATTAAATAGAAACTATAATT
8866420 ATTAAATAGAAACTATAATT
1 ATTAAATAGAAACTATAATT
8866440 AT
1 AT
8866442 AAAGAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (20 bp):
ATTAAATAGAAACTATAATT
Found at i:8866586 original size:19 final size:19
Alignment explanation
Indices: 8866558--8866607 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
8866548 TATATAATTT
*
8866558 ATATTTTAAAAAA-TATTA
1 ATATTATAAAAAATTATTA
8866576 ATTATTATAAAAAATTATTA
1 A-TATTATAAAAAATTATTA
*
8866596 ATATGATAAAAA
1 ATATTATAAAAA
8866608 TAATTTCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 1 0.04
19 21 0.75
20 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATATTATAAAAAATTATTA
Found at i:8867333 original size:15 final size:16
Alignment explanation
Indices: 8867313--8867342 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8867303 TAAAAATATA
8867313 ATATAA-ATTTATAAT
1 ATATAACATTTATAAT
8867328 ATATAACATTTATAA
1 ATATAACATTTATAA
8867343 AAAATTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATAACATTTATAAT
Found at i:8867760 original size:24 final size:23
Alignment explanation
Indices: 8867732--8867792 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
8867722 GCTTATAATA
* *
8867732 TAATTTTTATAAATTGTATAAAAG
1 TAATTTTTTTAAA-TATATAAAAG
*
8867756 TAATTTTTTTGACATATATAAAAG
1 TAATTTTTTT-AAATATATAAAAG
8867780 TAATTTTTTTAAA
1 TAATTTTTTTAAA
8867793 ATTAGATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 2 0.06
24 28 0.88
25 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (23 bp):
TAATTTTTTTAAATATATAAAAG
Found at i:8869612 original size:16 final size:16
Alignment explanation
Indices: 8869576--8869610 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
8869566 AAATATCATT
8869576 ATTTATATTAGAAATA
1 ATTTATATTAGAAATA
8869592 ATTTATATTAG-AATA
1 ATTTATATTAGAAATA
8869607 ATTT
1 ATTT
8869611 TAAAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (16 bp):
ATTTATATTAGAAATA
Found at i:8870086 original size:24 final size:23
Alignment explanation
Indices: 8870054--8870100 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
8870044 AAATTTATAT
*
8870054 TTTATATATAATTATATTAAATTA
1 TTTAAATATAA-TATATTAAATTA
* *
8870078 TTTAAATATCATATATTTAATTA
1 TTTAAATATAATATATTAAATTA
8870101 ATTTTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTAAATATAATATATTAAATTA
Found at i:8870093 original size:40 final size:40
Alignment explanation
Indices: 8870002--8870095 Score: 97
Period size: 40 Copynumber: 2.4 Consensus size: 40
8869992 ATGTTTATTT
* *
8870002 TTTAAAA-A-ATATTTTATATATTATCAATTTATAAATAA
1 TTTAAAATATATATTTTATATATAATCAATATATAAATAA
* * *
8870040 TTTAAAATTTATATTTTATATATAAT-TATAT-TAAATTA
1 TTTAAAATATATATTTTATATATAATCAATATATAAATAA
8870078 TTTAAATATCATATATTT
1 TTTAAA-AT-ATATATTT
8870096 AATTAATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
38 19 0.41
39 5 0.11
40 22 0.48
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (40 bp):
TTTAAAATATATATTTTATATATAATCAATATATAAATAA
Found at i:8873805 original size:22 final size:21
Alignment explanation
Indices: 8873780--8873827 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
8873770 AATTTTTTTC
8873780 AAATATATAAAATTATATATTT
1 AAATATATAAAATT-TATATTT
* * *
8873802 AAATTTGTAAAGTTTATATTT
1 AAATATATAAAATTTATATTT
*
8873823 TAATA
1 AAATA
8873828 ATTATTATTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (21 bp):
AAATATATAAAATTTATATTT
Found at i:8875861 original size:22 final size:23
Alignment explanation
Indices: 8875833--8875893 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
8875823 AAATCGAAGA
* *
8875833 ATATATATAATTTTATATA-AAT
1 ATATATATATTTTTATATATAAC
*
8875855 ATATATA-ATTTTTATCTATAAC
1 ATATATATATTTTTATATATAAC
*
8875877 ATGTATATATTTTTATA
1 ATATATATATTTTTATA
8875894 CATTCTATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 9 0.28
22 15 0.47
23 8 0.25
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (23 bp):
ATATATATATTTTTATATATAAC
Found at i:8875888 original size:23 final size:21
Alignment explanation
Indices: 8875832--8875892 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 21
8875822 AAAATCGAAG
*
8875832 AATATATATAATTTTA-TATA
1 AATATATATATTTTTATTATA
8875852 AATATATATAATTTTTATCTATA
1 AATATATAT-ATTTTTAT-TATA
*
8875875 ACATGTATATATTTTTAT
1 A-ATATATATATTTTTAT
8875893 ACATTCTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 9 0.26
21 6 0.17
23 13 0.37
24 7 0.20
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (21 bp):
AATATATATATTTTTATTATA
Found at i:8880009 original size:14 final size:14
Alignment explanation
Indices: 8879990--8880017 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8879980 TTGTTTATTA
8879990 GGAAAATATTTTTT
1 GGAAAATATTTTTT
8880004 GGAAAATATTTTTT
1 GGAAAATATTTTTT
8880018 TAGTTTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (14 bp):
GGAAAATATTTTTT
Found at i:8880458 original size:14 final size:15
Alignment explanation
Indices: 8880439--8880467 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8880429 TTCAGGAAAT
8880439 TATTTT-CTGGCAAA
1 TATTTTACTGGCAAA
8880453 TATTTTACTGGCAAA
1 TATTTTACTGGCAAA
8880468 CAAATAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (15 bp):
TATTTTACTGGCAAA
Found at i:8889603 original size:55 final size:55
Alignment explanation
Indices: 8889519--8889637 Score: 213
Period size: 55 Copynumber: 2.2 Consensus size: 55
8889509 TTTGGGGCAC
8889519 CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTGTTGACTGTGATTAAT
1 CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTGTTGACTGTGATTAAT
*
8889574 CTATTCCCTTTTTATTCATTTTGTATTCCAGTAATGTTTGTTGACTGTGATTAAT
1 CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTGTTGACTGTGATTAAT
*
8889629 -AATTCCCTT
1 CTATTCCCTT
8889638 CAAATTTTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
54 8 0.13
55 54 0.87
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.51
Consensus pattern (55 bp):
CTATTCCCTTTTTATTCATTTTGTATTCCAGCAATGTTTGTTGACTGTGATTAAT
Found at i:8890297 original size:88 final size:87
Alignment explanation
Indices: 8890146--8890309 Score: 247
Period size: 88 Copynumber: 1.9 Consensus size: 87
8890136 TCACCAGACC
* *
8890146 TTAACCACCTAAGCAGTAGGGTAACAGGCTGAAAATATAGATCTTATCACCCTAAGCAATAGGGA
1 TTAACCACCTAAGCAGTACGGTAACAAGCTGAAAATATAGATCTTATCACCCTAAGCAATAGGGA
8890211 AACAGATCAAAGGCAACGAGCT
66 AACAGATCAAAGGCAACGAGCT
* * ** *
8890233 TTAACCCCCTAAGTAGTACGGTAACAAGCTGAAGTTTATAGATCTTATCACCCTAAGCAGTAGGG
1 TTAACCACCTAAGCAGTACGGTAACAAGCTGAA-AATATAGATCTTATCACCCTAAGCAATAGGG
*
8890298 AAGCAGATCAAA
65 AAACAGATCAAA
8890310 AGACGGCGAA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
87 29 0.43
88 39 0.57
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (87 bp):
TTAACCACCTAAGCAGTACGGTAACAAGCTGAAAATATAGATCTTATCACCCTAAGCAATAGGGA
AACAGATCAAAGGCAACGAGCT
Found at i:8890740 original size:43 final size:42
Alignment explanation
Indices: 8890682--8890831 Score: 133
Period size: 43 Copynumber: 3.5 Consensus size: 42
8890672 GAGCTTCAAC
* * *
8890682 CCCCTAAGCAATAGGGTAACAAGCCAAATTTTCAAACCTTAAA
1 CCCCTAAGCAGTAGGGTAACAAGTC-AATTTACAAACCTTAAA
* * * *
8890725 CCCCTAAGCAGTAGGGTAACAGGTTGAATTTACAGATC-TAAA
1 CCCCTAAGCAGTAGGGTAACAAG-TCAATTTACAAACCTTAAA
* ** * *
8890767 CCCCTAAGCAGTAGGGAAAC-AGATCAATGATGGCAAGCCTTAAC
1 CCCCTAAGCAGTAGGGTAACAAG-TCAAT--TTACAAACCTTAAA
8890811 CCCCTAAGCAGTAGGGTAACA
1 CCCCTAAGCAGTAGGGTAACA
8890832 GGCTGAAAAT
Statistics
Matches: 84, Mismatches: 18, Indels: 8
0.76 0.16 0.07
Matches are distributed among these distances:
41 5 0.06
42 23 0.27
43 34 0.40
44 22 0.26
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (42 bp):
CCCCTAAGCAGTAGGGTAACAAGTCAATTTACAAACCTTAAA
Found at i:8891784 original size:23 final size:25
Alignment explanation
Indices: 8891758--8891804 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
8891748 TATCATTCAT
*
8891758 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
8891781 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
8891805 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:8892178 original size:46 final size:46
Alignment explanation
Indices: 8892065--8892291 Score: 305
Period size: 46 Copynumber: 5.0 Consensus size: 46
8892055 TTTGACGTGA
* * * * * *
8892065 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
8892111 TG-CATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
8892156 TGCCATGGTATCTTTAAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
8892202 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
8892248 TGCCATGGTATCTTTCAACCATGGTCTTACATATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
8892292 AGAGCACACT
Statistics
Matches: 163, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
44 4 0.02
45 34 0.21
46 125 0.77
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:8894732 original size:46 final size:44
Alignment explanation
Indices: 8894673--8894787 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
8894663 ACAGGACAGA
* *
8894673 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
8894719 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
8894763 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
8894788 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:8894768 original size:44 final size:45
Alignment explanation
Indices: 8894673--8894806 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
8894663 ACAGGACAGA
* *
8894673 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
8894719 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
8894763 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
8894807 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:8899235 original size:24 final size:25
Alignment explanation
Indices: 8899180--8899235 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
8899170 GTATGTTATG
* *
8899180 TATATATTATGTATATGCTTTTAAA
1 TATATATTATATATATGATTTTAAA
* *
8899205 TAT-TATTATATATCT-ATTTTCAA
1 TATATATTATATATATGATTTTAAA
8899228 TATATATT
1 TATATATT
8899236 TATGTAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 9 0.35
24 14 0.54
25 3 0.12
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (25 bp):
TATATATTATATATATGATTTTAAA
Found at i:8899409 original size:2 final size:2
Alignment explanation
Indices: 8899369--8899396 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8899359 TATTATTATC
8899369 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
8899397 TTCTTTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8903734 original size:30 final size:30
Alignment explanation
Indices: 8903671--8903734 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
8903661 ATCTAAAATT
* *
8903671 TTTATATATATTTAAAAAAATATATATCTA
1 TTTATATATATTTAAAAAAATAAATATCAA
8903701 TTTATA-ATATTTAAATAAAATAAATAAT-AA
1 TTTATATATATTTAAA-AAAATAAAT-ATCAA
8903731 TTTA
1 TTTA
8903735 AAAATTAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 9 0.30
30 19 0.63
31 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (30 bp):
TTTATATATATTTAAAAAAATAAATATCAA
Found at i:8908346 original size:45 final size:47
Alignment explanation
Indices: 8908239--8908350 Score: 118
Period size: 50 Copynumber: 2.3 Consensus size: 47
8908229 CACACTTATT
* * * *
8908239 GAAAAGAGGCAAACACAATCTTCCTAGGATAATGAAGAAAAGAAAACGTT
1 GAAAAGA-G-AAAAACAATCTTCCTAGAAAAATGAAGAAAAGAAAACG-A
8908289 GAAAAGGGAGAAAAACAATCTTCCTAGAAAAATGAAGAAAAGAAAAC-A
1 GAAAA--GAGAAAAACAATCTTCCTAGAAAAATGAAGAAAAGAAAACGA
*
8908337 GCAAAAGAAAAAAA
1 G-AAAAGAGAAAAA
8908351 ACTAACCATA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
47 7 0.13
48 1 0.02
49 4 0.07
50 39 0.72
51 1 0.02
52 2 0.04
ACGTcount: A:0.58, C:0.12, G:0.19, T:0.12
Consensus pattern (47 bp):
GAAAAGAGAAAAACAATCTTCCTAGAAAAATGAAGAAAAGAAAACGA
Found at i:8911461 original size:53 final size:53
Alignment explanation
Indices: 8911380--8911530 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
8911370 CTTACACGGT
* *
8911380 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
8911435 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
8911488 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
8911531 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:8918977 original size:53 final size:53
Alignment explanation
Indices: 8918896--8919046 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
8918886 CTTACACGGT
* *
8918896 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
8918951 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
8919004 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
8919047 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:8922730 original size:13 final size:13
Alignment explanation
Indices: 8922681--8922730 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
8922671 CAAAAAAAAT
*
8922681 AAAATTAAAAAGA
1 AAAATTAAAATGA
8922694 TAAAA--AAAATGA
1 -AAAATTAAAATGA
8922706 AAAATT-AAATGA
1 AAAATTAAAATGA
*
8922718 AAGATTAAAATGA
1 AAAATTAAAATGA
8922731 TTTTTTGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 4 0.13
12 17 0.55
13 6 0.19
14 4 0.13
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (13 bp):
AAAATTAAAATGA
Found at i:8944258 original size:8 final size:9
Alignment explanation
Indices: 8944232--8944256 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
8944222 TATATAATAC
8944232 ATTAAAAAT
1 ATTAAAAAT
8944241 ATTAAAAAT
1 ATTAAAAAT
8944250 ATTAAAA
1 ATTAAAA
8944257 TAAATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:8944429 original size:11 final size:11
Alignment explanation
Indices: 8944416--8944464 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
8944406 ACATAATAGT
*
8944416 AAAATAGTAAT
1 AAAATAGTAAA
8944427 AAAATAGTAAA
1 AAAATAGTAAA
* *
8944438 AAAAAAGTAAG
1 AAAATAGTAAA
*
8944449 AAAATACTAAA
1 AAAATAGTAAA
8944460 AAAAT
1 AAAAT
8944465 GCAATTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.18
Consensus pattern (11 bp):
AAAATAGTAAA
Found at i:8944446 original size:22 final size:22
Alignment explanation
Indices: 8944416--8944463 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
8944406 ACATAATAGT
* * *
8944416 AAAATAGTAATAAAATAGTAAA
1 AAAAAAGTAAGAAAATACTAAA
8944438 AAAAAAGTAAGAAAATACTAAA
1 AAAAAAGTAAGAAAATACTAAA
8944460 AAAA
1 AAAA
8944464 TGCAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (22 bp):
AAAAAAGTAAGAAAATACTAAA
Found at i:8947899 original size:34 final size:34
Alignment explanation
Indices: 8947861--8947931 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
8947851 CCGAAAAGTG
8947861 AAAATCTAGCTGGACTTAGAGCTTGAAAACTAAA
1 AAAATCTAGCTGGACTTAGAGCTTGAAAACTAAA
8947895 AAAATCTAGCTGGACTTAGAGCTTGAAAACTAAA
1 AAAATCTAGCTGGACTTAGAGCTTGAAAACTAAA
8947929 AAA
1 AAA
8947932 GAAAATAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (34 bp):
AAAATCTAGCTGGACTTAGAGCTTGAAAACTAAA
Found at i:8953742 original size:7 final size:7
Alignment explanation
Indices: 8953730--8953761 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
8953720 AGCCCAAGGC
8953730 TTTTTTA
1 TTTTTTA
8953737 TTTTTTA
1 TTTTTTA
8953744 TTTTTTA
1 TTTTTTA
8953751 TTTTTT-
1 TTTTTTA
8953757 TTTTT
1 TTTTT
8953762 ACTATTTCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (7 bp):
TTTTTTA
Found at i:8971353 original size:55 final size:54
Alignment explanation
Indices: 8971234--8971355 Score: 156
Period size: 55 Copynumber: 2.2 Consensus size: 54
8971224 ATTTTGAAGT
* * *
8971234 ACATATTTTTAATTATAAAAATGCAATGCACGTTTTTAATTATAAAATTGTAAT
1 ACATATTTTTAATTATAAAAATGCAATACACGTTTTTAATTATAAAAATGTAAC
* *
8971288 ACAAATTTTTTAATTATAAAAATGCAGTACA-GATTTTTAATTATAAAAATGTAAC
1 ACATA-TTTTTAATTATAAAAATGCAATACACG-TTTTTAATTATAAAAATGTAAC
*
8971343 CCATACTTTTTAA
1 ACATA-TTTTTAA
8971356 ACATTAAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
54 5 0.09
55 53 0.91
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (54 bp):
ACATATTTTTAATTATAAAAATGCAATACACGTTTTTAATTATAAAAATGTAAC
Found at i:8971355 original size:28 final size:27
Alignment explanation
Indices: 8971233--8971338 Score: 131
Period size: 27 Copynumber: 3.9 Consensus size: 27
8971223 AATTTTGAAG
8971233 TACATATTTTTAATTATAAAAATGCAA
1 TACATATTTTTAATTATAAAAATGCAA
* ** * *
8971260 TGCACGTTTTTAATTATAAAATTGTAA
1 TACATATTTTTAATTATAAAAATGCAA
* *
8971287 TACAAATTTTTTAATTATAAAAATGCAG
1 TACATA-TTTTTAATTATAAAAATGCAA
*
8971315 TACAGATTTTTAATTATAAAAATG
1 TACATATTTTTAATTATAAAAATG
8971339 TAACCCATAC
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
27 43 0.65
28 23 0.35
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.42
Consensus pattern (27 bp):
TACATATTTTTAATTATAAAAATGCAA
Found at i:8986961 original size:2 final size:2
Alignment explanation
Indices: 8986954--8986978 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8986944 CCATTTATGA
8986954 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
8986979 CACATTCATC
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
Done.