Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008912.1 Hibiscus syriacus cultivar Beakdansim tig00112215_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: 3753803
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 18
Found at i:3147802 original size:14 final size:13
Alignment explanation
Indices: 3147775--3147825 Score: 57
Period size: 13 Copynumber: 3.5 Consensus size: 13
3147765 TTTATTGAAA
3147775 AACCGAAAAACCG
1 AACCGAAAAACCG
3147788 AACCGAAAAACCCG
1 AACCGAAAAA-CCG
3147802 AACCGTTAAAAAAACCG
1 AACCG----AAAAACCG
3147819 AACCGAA
1 AACCGAA
3147826 CCGATAAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
13 12 0.36
14 8 0.24
17 8 0.24
18 5 0.15
ACGTcount: A:0.53, C:0.29, G:0.14, T:0.04
Consensus pattern (13 bp):
AACCGAAAAACCG
Found at i:3147819 original size:17 final size:14
Alignment explanation
Indices: 3147775--3147825 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
3147765 TTTATTGAAA
3147775 AACCG-AAAAACCG
1 AACCGAAAAAACCG
*
3147788 AACCGAAAAACCCG
1 AACCGAAAAAACCG
3147802 AACCGTTAAAAAAACCG
1 AACCG---AAAAAACCG
3147819 AACCGAA
1 AACCGAA
3147826 CCGATAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 5 0.16
14 14 0.44
17 13 0.41
ACGTcount: A:0.53, C:0.29, G:0.14, T:0.04
Consensus pattern (14 bp):
AACCGAAAAAACCG
Found at i:3153933 original size:15 final size:15
Alignment explanation
Indices: 3153909--3153938 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3153899 ATGAGTTTAA
*
3153909 TTAGGTATATGAAAG
1 TTAGGAATATGAAAG
3153924 TTAGGAATATGAAAG
1 TTAGGAATATGAAAG
3153939 GGGTTGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (15 bp):
TTAGGAATATGAAAG
Found at i:3154144 original size:64 final size:63
Alignment explanation
Indices: 3154076--3154294 Score: 200
Period size: 64 Copynumber: 3.4 Consensus size: 63
3154066 TTGAAGGTGT
* * * *
3154076 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAAACTAA-ATACATCGAATGCAATTTGTG
1 ATCGATGCATAGGTAGTGCATCGATGCATC-CTATT-AA-TAAGAAACATCGAATGCAATTAGTG
3154139 C
63 C
*
3154140 ATCGATGCATCA-GTAGTGCATCGATACATCCTATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCTATTAATAA-GAAACATCGAATGCAATTAGTGC
* * * * *
3154204 ATCGATGCATAAGGCA-TGCATCGATGCATACC-AGTAATAATACAACATCGAATACATTTTA-T
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT-CCTATTAATAAGA-AACATCGAATGCA-ATTAGT
3154266 GC
62 GC
*
3154268 ACCGATGCATCA-GTAGTGCATCGATGC
1 ATCGATGCAT-AGGTAGTGCATCGATGC
3154295 CTACCTTCAT
Statistics
Matches: 131, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
62 3 0.02
63 5 0.04
64 115 0.88
65 8 0.06
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (63 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCCTATTAATAAGAAACATCGAATGCAATTAGTGC
Found at i:3154651 original size:18 final size:18
Alignment explanation
Indices: 3154616--3154651 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3154606 AAATTGGGTA
* *
3154616 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
3154634 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
3154652 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:3158570 original size:15 final size:15
Alignment explanation
Indices: 3158546--3158575 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3158536 ATGAGTTTAA
*
3158546 TTAGGTATATGAAAG
1 TTAGGAATATGAAAG
3158561 TTAGGAATATGAAAG
1 TTAGGAATATGAAAG
3158576 GGGTTGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (15 bp):
TTAGGAATATGAAAG
Found at i:3158781 original size:64 final size:63
Alignment explanation
Indices: 3158713--3158850 Score: 172
Period size: 64 Copynumber: 2.2 Consensus size: 63
3158703 TTGAAGGTGT
** * * *
3158713 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAAACTAA-ATACATCGAATGCAATTTGTG
1 ATCGATGCATCAGTAGTGCATCGATGCATC-CTATT-AA-TAAGAAACATCGAATGCAATTAGTG
3158776 C
63 C
*
3158777 ATCGATGCATCAGTGGTGCATCGATGCATCCTATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATCAGTAGTGCATCGATGCATCCTATTAATAA-GAAACATCGAATGCAATTAGTGC
3158841 ATCGATGCAT
1 ATCGATGCAT
3158851 AAGGCATGCA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
62 3 0.05
63 2 0.03
64 59 0.91
65 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (63 bp):
ATCGATGCATCAGTAGTGCATCGATGCATCCTATTAATAAGAAACATCGAATGCAATTAGTGC
Found at i:3158845 original size:18 final size:17
Alignment explanation
Indices: 3158822--3158886 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 17
3158812 AATAAGGAAA
3158822 CATCGAATGCAATTAGTG
1 CATCG-ATGCAATTAGTG
*
3158840 CATCGATGC-ATAAGGCATG
1 CATCGATGCAATTA-G--TG
3158859 CATCGAATGCAATTAGTG
1 CATCG-ATGCAATTAGTG
3158877 CATCGATGCA
1 CATCGATGCA
3158887 TAAGGCATGC
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
16 3 0.08
17 10 0.25
18 12 0.30
19 7 0.17
20 5 0.12
21 3 0.08
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (17 bp):
CATCGATGCAATTAGTG
Found at i:3158862 original size:19 final size:19
Alignment explanation
Indices: 3158838--3158907 Score: 92
Period size: 19 Copynumber: 3.7 Consensus size: 19
3158828 ATGCAATTAG
3158838 TGCATCGATGCATAAGGCA
1 TGCATCGATGCATAAGGCA
*
3158857 TGCATCGAATGCAATTA-G--
1 TGCATCG-ATGC-ATAAGGCA
3158875 TGCATCGATGCATAAGGCA
1 TGCATCGATGCATAAGGCA
3158894 TGCATCGATGCATA
1 TGCATCGATGCATA
3158908 CCAGTAATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
16 3 0.07
17 5 0.11
18 7 0.16
19 21 0.48
20 5 0.11
21 3 0.07
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCATAAGGCA
Found at i:3158863 original size:37 final size:37
Alignment explanation
Indices: 3158822--3158905 Score: 161
Period size: 37 Copynumber: 2.3 Consensus size: 37
3158812 AATAAGGAAA
3158822 CATCGAATGCAATTAGTGCATCGATGCATAAGGCATG
1 CATCGAATGCAATTAGTGCATCGATGCATAAGGCATG
3158859 CATCGAATGCAATTAGTGCATCGATGCATAAGGCATG
1 CATCGAATGCAATTAGTGCATCGATGCATAAGGCATG
3158896 CATCG-ATGCA
1 CATCGAATGCA
3158906 TACCAGTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 5 0.11
37 42 0.89
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (37 bp):
CATCGAATGCAATTAGTGCATCGATGCATAAGGCATG
Found at i:3158965 original size:101 final size:101
Alignment explanation
Indices: 3158758--3158951 Score: 252
Period size: 101 Copynumber: 1.9 Consensus size: 101
3158748 AAACTAAATA
* * * *
3158758 CATCGAATGCAATTTGTGCATCGATGCATCAGTGGTGCATCGATGCATCCTATTAATAAGGAAAC
1 CATCGAATGCAATTAGTGCATCGATGCATAAGTGATGCATCGATGCATCCTAGTAATAAGGAAAC
* *
3158823 ATCGAATGCAATTAGTGCATCGATGCATAAGGCATG
66 ATCGAATACAATTAGTGCACCGATGCATAAGGCATG
*
3158859 CATCGAATGCAATTAGTGCATCGATGCATAAG-GCATGCATCGATGCATACC-AGTAATAA-TAC
1 CATCGAATGCAATTAGTGCATCGATGCATAAGTG-ATGCATCGATGCAT-CCTAGTAATAAGGA-
*
3158921 AACATCGAATACATTTTA-TGCACCGATGCAT
63 AACATCGAATACA-ATTAGTGCACCGATGCAT
3158952 CAGTAGTGCA
Statistics
Matches: 81, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
100 2 0.02
101 74 0.91
102 5 0.06
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (101 bp):
CATCGAATGCAATTAGTGCATCGATGCATAAGTGATGCATCGATGCATCCTAGTAATAAGGAAAC
ATCGAATACAATTAGTGCACCGATGCATAAGGCATG
Found at i:3159325 original size:18 final size:18
Alignment explanation
Indices: 3159290--3159325 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3159280 AAATTGAGTA
* *
3159290 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
3159308 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
3159326 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:3162301 original size:21 final size:21
Alignment explanation
Indices: 3162275--3162318 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3162265 TATTCTCATT
*
3162275 GTTGATTATATATCTAGATGG
1 GTTGATTATATATCTAAATGG
* *
3162296 GTTGATTATGTGTCTAAATGG
1 GTTGATTATATATCTAAATGG
3162317 GT
1 GT
3162319 AGAAGCTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.27, T:0.43
Consensus pattern (21 bp):
GTTGATTATATATCTAAATGG
Found at i:3165056 original size:20 final size:20
Alignment explanation
Indices: 3165009--3165062 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
3164999 CTTTATCTAC
* *
3165009 TTTATTTATTTT-CTCATTA
1 TTTATTTATTTTATTCAGTA
3165028 -TTA-TTATTTTATTCAGTA
1 TTTATTTATTTTATTCAGTA
3165046 TTTATTTATTTTATTCA
1 TTTATTTATTTTATTCA
3165063 TTTATTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 7 0.23
18 8 0.27
19 3 0.10
20 12 0.40
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTATTTATTTTATTCAGTA
Found at i:3168974 original size:22 final size:22
Alignment explanation
Indices: 3168947--3168989 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3168937 GTAAGATTTA
* *
3168947 AAAGTCAAGTGGGAAGGTCCAT
1 AAAGTCAAATGGGAAGATCCAT
3168969 AAAGTCAAATGGGAAGATCCA
1 AAAGTCAAATGGGAAGATCCA
3168990 ATGAGATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.14, G:0.28, T:0.16
Consensus pattern (22 bp):
AAAGTCAAATGGGAAGATCCAT
Found at i:3171359 original size:97 final size:97
Alignment explanation
Indices: 3171190--3171384 Score: 227
Period size: 97 Copynumber: 2.0 Consensus size: 97
3171180 ATACAATAAC
* * * *
3171190 ATAGAATGCACTAGAAACAAAGACAGGGAATTGGTTACCCGATCTTAATGATCCTAGAGATCCCT
1 ATAGAATGCAATAGAAACAAAGACAGGAAATGGGTTACCCGATCTTAATGATCCTAGAGAACCCT
3171255 TGCATTCTAAAAATT-TGAATTCTTTAATTTGG
66 TGCATTCT-AAAATTCTGAATTCTTTAATTTGG
* * * *
3171287 ATAGAATGCAATAGAAACGAAA-ACATGAAATGGGTTATCTGATCTTAATGGTCCTAGCTA-AAC
1 ATAGAATGCAATAGAAAC-AAAGACAGGAAATGGGTTACCCGATCTTAATGATCCTAG--AGAAC
* * *
3171350 CTTTG-ATTCTGACATTCTGAATTCTTTAATTTGG
63 CCTTGCATTCTAAAATTCTGAATTCTTTAATTTGG
3171384 A
1 A
3171385 ATGAACTAGA
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
96 4 0.05
97 69 0.83
98 9 0.11
99 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (97 bp):
ATAGAATGCAATAGAAACAAAGACAGGAAATGGGTTACCCGATCTTAATGATCCTAGAGAACCCT
TGCATTCTAAAATTCTGAATTCTTTAATTTGG
Found at i:3172992 original size:22 final size:23
Alignment explanation
Indices: 3172949--3172992 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3172939 ATAAATTTAG
*
3172949 TTTTTTTAAATGTGATTTTAATT
1 TTTTTTTAAATGTGATTATAATT
* *
3172972 TTTTTTTATAT-TTATTATAAT
1 TTTTTTTAAATGTGATTATAAT
3172993 AGGCTTATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (23 bp):
TTTTTTTAAATGTGATTATAATT
Found at i:3174276 original size:21 final size:21
Alignment explanation
Indices: 3174250--3174306 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
3174240 TTTTACACTT
3174250 AGGGAACCGATTCCCTATGAG
1 AGGGAACCGATTCCCTATGAG
3174271 AGGGAACCGATTCCCTATGAG
1 AGGGAACCGATTCCCTATGAG
* *
3174292 ATGGTACCGATTCCC
1 AGGGAACCGATTCCC
3174307 CCACGCTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (21 bp):
AGGGAACCGATTCCCTATGAG
Found at i:3174523 original size:13 final size:13
Alignment explanation
Indices: 3174502--3174556 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
3174492 AAGTTCGATA
*
3174502 AATTCAAATACTT
1 AATTGAAATACTT
3174515 AATTGAAATACTT
1 AATTGAAATACTT
* *
3174528 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
3174542 AATTGAAATACTT
1 AATTGAAATACTT
3174555 AA
1 AA
3174557 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:3174638 original size:32 final size:33
Alignment explanation
Indices: 3174542--3174640 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
3174532 AACTCAACAT
* * *
3174542 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
3174575 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
3174608 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
3174640 A
1 A
3174641 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:3174659 original size:21 final size:21
Alignment explanation
Indices: 3174635--3174676 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3174625 ACTTCAAGTT
3174635 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
3174656 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
3174677 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:3186172 original size:43 final size:43
Alignment explanation
Indices: 3186123--3186205 Score: 157
Period size: 43 Copynumber: 1.9 Consensus size: 43
3186113 ATTGTACAAG
3186123 TATGAGCCAAATCAAGCAACATTAACACTTGTGTATTAATAAA
1 TATGAGCCAAATCAAGCAACATTAACACTTGTGTATTAATAAA
*
3186166 TATGAGCCAAATCAAGCAACGTTAACACTTGTGTATTAAT
1 TATGAGCCAAATCAAGCAACATTAACACTTGTGTATTAAT
3186206 TTTATGTTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (43 bp):
TATGAGCCAAATCAAGCAACATTAACACTTGTGTATTAATAAA
Found at i:3194095 original size:44 final size:45
Alignment explanation
Indices: 3194045--3194143 Score: 139
Period size: 44 Copynumber: 2.2 Consensus size: 45
3194035 CAACCCAATG
* * *
3194045 GTATCGATACCCTTC-AATGAGTATCGATACTACTATGTATAACA
1 GTATCGATACCCGTCTAAGGAGTATCGATACTAATATGTATAACA
* *
3194089 GTATCGATA-TCGTCTAAGGAGTATCGATACTAATATGTATACCA
1 GTATCGATACCCGTCTAAGGAGTATCGATACTAATATGTATAACA
3194133 GTATCGATACC
1 GTATCGATACC
3194144 GAACATGGTA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
43 3 0.06
44 44 0.94
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (45 bp):
GTATCGATACCCGTCTAAGGAGTATCGATACTAATATGTATAACA
Found at i:3194096 original size:24 final size:24
Alignment explanation
Indices: 3194064--3194142 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 24
3194054 CCCTTCAATG
3194064 AGTATCGATACTACTATGTATAAC
1 AGTATCGATACTACTATGTATAAC
* *
3194088 AGTATCGATA-T-C---GTCTAAGG
1 AGTATCGATACTACTATGTATAA-C
* *
3194108 AGTATCGATACTAATATGTATACC
1 AGTATCGATACTACTATGTATAAC
3194132 AGTATCGATAC
1 AGTATCGATAC
3194143 CGAACATGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 5 0.12
20 10 0.23
21 1 0.02
22 1 0.02
23 1 0.02
24 21 0.49
25 4 0.09
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (24 bp):
AGTATCGATACTACTATGTATAAC
Found at i:3196390 original size:28 final size:28
Alignment explanation
Indices: 3196339--3196393 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
3196329 AAAATTTAAT
* * *
3196339 TTTTTTTGAAAAACTATAGAATATATAG
1 TTTTTATGAAAAACAAAAGAATATATAG
*
3196367 TTTTTATGAAAAACAAAAGTATATATA
1 TTTTTATGAAAAACAAAAGAATATATA
3196394 TATATATATA
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:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (28 bp):
TTTTTATGAAAAACAAAAGAATATATAG
Found at i:3202605 original size:44 final size:44
Alignment explanation
Indices: 3202542--3202634 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
3202532 CCAACGATAT
* * * * *
3202542 CGATACCCTTCAATGAGTATCGATACTAGTATGTATAGTAGTAC
1 CGATACCCTCCAAGGAGTATCAATACTACTATATATAGTAGTAC
* *
3202586 CGATACCGTCCAAGGAGTATCAATACTACTATATATAGTAGTAT
1 CGATACCCTCCAAGGAGTATCAATACTACTATATATAGTAGTAC
3202630 CGATA
1 CGATA
3202635 TCGAACATGG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (44 bp):
CGATACCCTCCAAGGAGTATCAATACTACTATATATAGTAGTAC
Found at i:3206992 original size:15 final size:15
Alignment explanation
Indices: 3206970--3207012 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
3206960 TAGATAAGAA
3206970 ATAATAAATAAATAT
1 ATAATAAATAAATAT
3206985 -TAAATAAATAAATAT
1 AT-AATAAATAAATAT
*
3207000 ATAATAAAAAAAT
1 ATAATAAATAAAT
3207013 CAAAGGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAATAAATAAATAT
Found at i:3207036 original size:14 final size:14
Alignment explanation
Indices: 3207019--3207181 Score: 56
Period size: 13 Copynumber: 11.8 Consensus size: 14
3207009 AAATCAAAGG
3207019 AAAAAATAAAAT-A
1 AAAAAATAAAATAA
*
3207032 AAAAAATAAAA-AT
1 AAAAAATAAAATAA
** *
3207045 ATTAAAT-AAATCA
1 AAAAAATAAAATAA
**
3207058 AAGGAA-AAAAT-A
1 AAAAAATAAAATAA
*
3207070 AATAAAT-AAATAA
1 AAAAAATAAAATAA
* * *
3207083 AGATAACAAAATAA
1 AAAAAATAAAATAA
*
3207097 ATCAAAGA-AAAATAA
1 A--AAAAATAAAATAA
*
3207112 GAAAAATAAAAT-A
1 AAAAAATAAAATAA
* *
3207125 AAAATATTAAATAA
1 AAAAAATAAAATAA
3207139 ATCAAAGGGAA-AAAATAA
1 A--AAA---AATAAAATAA
*
3207157 ATAAAATAAAATAA
1 AAAAAATAAAATAA
*
3207171 TAAAAATAAAA
1 AAAAAATAAAA
3207182 ACTATTAAAT
Statistics
Matches: 107, Mismatches: 27, Indels: 31
0.65 0.16 0.19
Matches are distributed among these distances:
12 12 0.11
13 43 0.40
14 30 0.28
15 7 0.07
16 7 0.07
18 7 0.07
19 1 0.01
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (14 bp):
AAAAAATAAAATAA
Found at i:3207057 original size:43 final size:43
Alignment explanation
Indices: 3206975--3207162 Score: 206
Period size: 43 Copynumber: 4.3 Consensus size: 43
3206965 AAGAAATAAT
* * *
3206975 AAATAAATATTAAATAAATAAATATATAATAAAAAAATCAAAGGAAA
1 AAATAAA-A-TAAAAAAATAAA-A-ATATTAAATAAATCAAAGGAAA
3207022 AAATAAAATAAAAAAATAAAAATATTAAATAAATCAAAGGAAA
1 AAATAAAATAAAAAAATAAAAATATTAAATAAATCAAAGGAAA
* * **
3207065 AAAT-AAATAAATAAATAAAGATAACAAAATAAATCAAA-G-AA
1 AAATAAAATAAAAAAATAAAAAT-ATTAAATAAATCAAAGGAAA
3207106 AAATAAGAA-AAATAAAATAAAAATATTAAATAAATCAAAGGGAAA
1 AAATAA-AATAAA-AAAATAAAAATATTAAATAAATCAAA-GGAAA
3207151 AAAT-AAATAAAA
1 AAATAAAATAAAA
3207163 TAAAATAATA
Statistics
Matches: 122, Mismatches: 11, Indels: 20
0.80 0.07 0.13
Matches are distributed among these distances:
41 6 0.05
42 34 0.28
43 51 0.42
44 6 0.05
45 17 0.14
46 1 0.01
47 7 0.06
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (43 bp):
AAATAAAATAAAAAAATAAAAATATTAAATAAATCAAAGGAAA
Found at i:3207098 original size:4 final size:4
Alignment explanation
Indices: 3206968--3207083 Score: 73
Period size: 4 Copynumber: 28.8 Consensus size: 4
3206958 GTTAGATAAG
* * *
3206968 AAAT -AAT AAAT AAAT -ATT AAAT AAAT AAAT ATAT -AAT AAAA AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * *
3207013 CAAAGG AAA- AAAT AAAAT AAAA AAAT AAA- AATATT AAAT AAAT CAAAGG
1 -AAA-T AAAT AAAT -AAAT AAAT AAAT AAAT AA-A-T AAAT AAAT -AAA-T
3207062 AAA- AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAA
3207084 GATAACAAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 26
0.71 0.08 0.21
Matches are distributed among these distances:
3 15 0.17
4 55 0.62
5 17 0.19
6 2 0.02
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:3207138 original size:85 final size:84
Alignment explanation
Indices: 3206985--3207166 Score: 264
Period size: 85 Copynumber: 2.1 Consensus size: 84
3206975 AAATAAATAT
* *
3206985 TAAATAAATAAATATATAATAAAAAAATCAAAGGAAAAAATAAAATAAAAAAATAAAAATATTAA
1 TAAATAAATAAATAGATAACAAAAAAATCAAAGGAAAAAATAAAATAAAAAAATAAAAATATTAA
3207050 ATAAATCAAA-GGAAAAAA
66 ATAAATCAAAGGGAAAAAA
3207068 TAAATAAATAAATAAAGATAACAAAATAAATCAAA-G-AAAAATAAGAA-AAATAAAATAAAAAT
1 TAAATAAATAAAT--AGATAACAAAA-AAATCAAAGGAAAAAATAA-AATAAA-AAAATAAAAAT
3207130 ATTAAATAAATCAAAGGGAAAAAA
61 ATTAAATAAATCAAAGGGAAAAAA
3207154 TAAATAAAATAAA
1 TAAAT-AAATAAA
3207167 ATAATAAAAA
Statistics
Matches: 90, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
83 13 0.14
84 11 0.12
85 38 0.42
86 21 0.23
87 7 0.08
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (84 bp):
TAAATAAATAAATAGATAACAAAAAAATCAAAGGAAAAAATAAAATAAAAAAATAAAAATATTAA
ATAAATCAAAGGGAAAAAA
Found at i:3207206 original size:54 final size:53
Alignment explanation
Indices: 3207104--3207218 Score: 135
Period size: 54 Copynumber: 2.2 Consensus size: 53
3207094 TAAATCAAAG
* *
3207104 AAAAATAAGAAAAATAAAATAAAAATATTAAATAAATCAAAGGGAAAAAATAA
1 AAAAATAAGAAAAATAAAATAAAAATATTAAATAAATAAAAGGAAAAAAATAA
* ** *
3207157 ATAAAATAA-AATAATAAAAATAAAAACTATTAAAT-TTTAAAAGTAAAAAAATAA
1 A-AAAATAAGAAAAAT-AAAATAAAAA-TATTAAATAAATAAAAGGAAAAAAATAA
3207211 AAAAATAA
1 AAAAATAA
3207219 TAAGTAGTGA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
53 13 0.25
54 32 0.60
55 8 0.15
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (53 bp):
AAAAATAAGAAAAATAAAATAAAAATATTAAATAAATAAAAGGAAAAAAATAA
Found at i:3208526 original size:31 final size:30
Alignment explanation
Indices: 3208491--3208574 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 30
3208481 AACAAAAATC
3208491 AAATAATAATAAAAA-AAAGGAAATATTAATA
1 AAATAATAATAAAAATAAA--AAATATTAATA
*
3208522 AAATAATAAATAAAAATAAATAATATTAATA
1 AAATAAT-AATAAAAATAAAAAATATTAATA
*
3208553 TAATATATAATAAAAATAAAAA
1 AAATA-ATAATAAAAATAAAAA
3208575 TCATTTTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
31 34 0.72
32 10 0.21
33 3 0.06
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (30 bp):
AAATAATAATAAAAATAAAAAATATTAATA
Found at i:3208532 original size:18 final size:17
Alignment explanation
Indices: 3208522--3208575 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 17
3208512 AATATTAATA
3208522 AAATAATAAATAAAAAT
1 AAATAATAAATAAAAAT
*
3208539 AAATAATATTAATATAATAT
1 AAATAATA--AATA-AAAAT
3208559 ATAATAA-AAATAAAAAT
1 A-AATAATAAATAAAAAT
3208576 CATTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 12 0.39
18 4 0.13
19 4 0.13
20 6 0.19
21 5 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATAATAAATAAAAAT
Found at i:3208640 original size:37 final size:37
Alignment explanation
Indices: 3208599--3208902 Score: 196
Period size: 39 Copynumber: 8.1 Consensus size: 37
3208589 ATATATATAC
*
3208599 ATTTTTTAAATTTTTTTTCAAAACTATATATTAATAT
1 ATTTTTTAAATATTTTTTCAAAACTATATATTAATAT
* * *
3208636 A-TTTTCAAAAATTGTTTTTAAAAC--TATA-TAATAT
1 ATTTTTTAAATATT-TTTTCAAAACTATATATTAATAT
* * *
3208670 ATTTTTTCAAAAATATTTTCAAAACTATATATTATATAC
1 ATTTTTT-AAATATTTTTTCAAAACTATATATTA-ATAT
* * *
3208709 ATTTTTTAAAAATATTTTCAAAATTATATATT-ATAT
1 ATTTTTTAAATATTTTTTCAAAACTATATATTAATAT
* *
3208745 ATATTTTCAAACTATTTTTTAAAAAAACTATATATT-ATAT
1 AT-TTTTTAAA-TATTTTTT--CAAAACTATATATTAATAT
*
3208785 ATTTATTTTCAAA-ATGTTTTCAAAAACTATATATT-ATAT
1 A-TT-TTTT-AAATATTTTTTC-AAAACTATATATTAATAT
* *** *
3208824 ATATTTTCAAA-ACAATTTCAAAACTATATAAT-ATAT
1 AT-TTTTTAAATATTTTTTCAAAACTATATATTAATAT
* ** *
3208860 ATATTTTTAGAAAACCATTTTCAAAACTATATAATATATAT
1 AT-TTTTTA-AATA-TTTTTTCAAAACTATATATTA-ATAT
3208901 AT
1 AT
3208903 ATTCAAATAT
Statistics
Matches: 221, Mismatches: 25, Indels: 38
0.78 0.09 0.13
Matches are distributed among these distances:
34 7 0.03
35 17 0.08
36 44 0.20
37 31 0.14
38 37 0.17
39 48 0.22
40 24 0.11
41 10 0.05
42 3 0.01
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTTTTAAATATTTTTTCAAAACTATATATTAATAT
Found at i:3208654 original size:38 final size:37
Alignment explanation
Indices: 3208613--3208974 Score: 348
Period size: 38 Copynumber: 9.6 Consensus size: 37
3208603 TTTAAATTTT
*
3208613 TTTTCAAAACTATATATTA-ATATATTTTCAAAAATTG
1 TTTTCAAAACTATATATTATATATATTTTCAAAAA-TA
* *
3208650 TTTTTAAAACTATATA--ATATATTTTTTCAAAAATA
1 TTTTCAAAACTATATATTATATATATTTTCAAAAATA
* *
3208685 TTTTCAAAACTATATATTATATACATTTTTTAAAAATA
1 TTTTCAAAACTATATATTATATATA-TTTTCAAAAATA
* * *
3208723 TTTTCAAAATTATATATTATATATATTTTCAAACTATT
1 TTTTCAAAACTATATATTATATATATTTTCAAA-AATA
* *
3208761 TTTTAAAAAAACTATATATTATATATTTATTTTC-AAAATG
1 TTTT--CAAAACTATATATTATATA--TATTTTCAAAAATA
3208801 TTTTCAAAAACTATATATTATATATATTTTCAAAACA-A
1 TTTTC-AAAACTATATATTATATATATTTTCAAAA-ATA
* * *
3208839 -TTTCAAAACTATATAATATATATATTTTTAGAAAACCA
1 TTTTCAAAACTATATATTATATATATTTTCA-AAAA-TA
* * *
3208877 TTTTCAAAACTATATAATATATATATATTCAAATATCGA
1 TTTTCAAAACTATATATTATATATATTTTCAAAAAT--A
* *
3208916 TTTT--AAAGTATATA-T-TATATGTTTTCAAAAATCA
1 TTTTCAAAACTATATATTATATATATTTTCAAAAAT-A
3208950 TTTTCTAAAAACTATATATTATATA
1 TTTTC--AAAACTATATATTATATA
3208975 AAACCCGAAC
Statistics
Matches: 271, Mismatches: 30, Indels: 45
0.78 0.09 0.13
Matches are distributed among these distances:
34 5 0.02
35 31 0.11
36 40 0.15
37 50 0.18
38 56 0.21
39 53 0.20
40 27 0.10
41 2 0.01
42 7 0.03
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (37 bp):
TTTTCAAAACTATATATTATATATATTTTCAAAAATA
Found at i:3210284 original size:22 final size:22
Alignment explanation
Indices: 3210256--3210351 Score: 192
Period size: 22 Copynumber: 4.4 Consensus size: 22
3210246 AGTCGTTATG
3210256 GGTACACTCTCAAGGGTGTATC
1 GGTACACTCTCAAGGGTGTATC
3210278 GGTACACTCTCAAGGGTGTATC
1 GGTACACTCTCAAGGGTGTATC
3210300 GGTACACTCTCAAGGGTGTATC
1 GGTACACTCTCAAGGGTGTATC
3210322 GGTACACTCTCAAGGGTGTATC
1 GGTACACTCTCAAGGGTGTATC
3210344 GGTACACT
1 GGTACACT
3210352 GTGTGTAAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 74 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (22 bp):
GGTACACTCTCAAGGGTGTATC
Found at i:3211132 original size:20 final size:20
Alignment explanation
Indices: 3211107--3211150 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
3211097 AATAAACATT
3211107 AAATTCAAACTAATC-AAACC
1 AAATTCAAAC-AATCAAAACC
3211127 AAATTCAAACAATCAAAACC
1 AAATTCAAACAATCAAAACC
3211147 AAAT
1 AAAT
3211151 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.59, C:0.23, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATTCAAACAATCAAAACC
Found at i:3221027 original size:83 final size:85
Alignment explanation
Indices: 3220829--3221044 Score: 294
Period size: 85 Copynumber: 2.6 Consensus size: 85
3220819 TTTCAACATA
* * * * *
3220829 TTGATAGATAACCTTTCTCGCCTTGAGTTAAGCTGTAAATTTGATATGTCCTTGAGCTGAATGTA
1 TTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTA
* * *
3220894 ATCAAACTTGAATGTTTTGG
66 ATCAAACTTCAAAGGTTTGG
* * *
3220914 TTCACAGATAATCCTTCTCGCCTTGAGCTATGCCGTAAATTTGATATGCCCTTGAGCTGAATAG-
1 TTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAAT-GT
*
3220978 AATCGAAC-TCAAAGGTTT-G
65 AATCAAACTTCAAAGGTTTGG
3220997 TTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATG
1 TTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATG
3221045 TTGCGAGCAG
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
83 46 0.40
84 7 0.06
85 61 0.53
86 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (85 bp):
TTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTA
ATCAAACTTCAAAGGTTTGG
Found at i:3222705 original size:98 final size:99
Alignment explanation
Indices: 3222505--3222695 Score: 294
Period size: 98 Copynumber: 1.9 Consensus size: 99
3222495 TATAATCACC
* * *
3222505 TTTATCAGGCTAGCTGAATATTATCCATAAAGTCGGGGCTTTTAACCAATTTCTTTAGAGGGACA
1 TTTATCAGGCTAGCTGAATATTATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACA
* * *
3222570 GCTCAAGCTTTATTGTATAGATATTATAACAACA
66 GCTCAAACTTTATTGTATACATATAATAACAACA
* * *
3222604 TTTATTAGGCTAGCTGAATCTTATCTATAAAGTC-GGGCGTTTAACCAATTGCTCTAGAGGGACA
1 TTTATCAGGCTAGCTGAATATTATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACA
3222668 GCTCAAACTTTATTGTATACATATAATA
66 GCTCAAACTTTATTGTATACATATAATA
3222696 TTATAATTTA
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
98 52 0.63
99 31 0.37
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (99 bp):
TTTATCAGGCTAGCTGAATATTATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACA
GCTCAAACTTTATTGTATACATATAATAACAACA
Found at i:3223921 original size:150 final size:151
Alignment explanation
Indices: 3223649--3223929 Score: 388
Period size: 150 Copynumber: 1.9 Consensus size: 151
3223639 GATATAGGTG
* * *
3223649 TTTGAGGTGTCTTCAAGGCTGCAACTTCCCCATCCATTCTTAAACCCCACGGGCCAATCTCGGAT
1 TTTGAGGTGTCTTCAAAGCTGCAACTGCCCCATCCATTCTTAAACCCCACAGGCCAATCTCGGAT
*** **
3223714 TACATTCATGGAAGCTCTTCTACTTGGATTTATTTTTCCATCCTTTTGTGTCTTATGTTATTCAC
66 TACATTCATGGAAGCTCTTCTACCAAGATTTATTTTTCCATCCTTTTGTCACTTATGTTATTCAC
3223779 AGAAATTTTTTGTTGAAGCAA
131 AGAAATTTTTTGTTGAAGCAA
* * * *
3223800 TTTGAGGTGTCTTCAAAGCTGCATCTGCCCCATCCATTCTTAAA-CCCACAGGCCAGTGTTGGAT
1 TTTGAGGTGTCTTCAAAGCTGCAACTGCCCCATCCATTCTTAAACCCCACAGGCCAATCTCGGAT
* * *
3223864 TACATTCATGGAAGTTCTTCTGCCAAGATTTCA-TTTTCCATCCTTTTG-CACATTATGTTCTTC
66 TACATTCATGGAAGCTCTTCTACCAAGATTT-ATTTTTCCATCCTTTTGTCAC-TTATGTTATTC
3223927 ACA
129 ACA
3223930 TGAATTCTCT
Statistics
Matches: 113, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
149 1 0.01
150 70 0.62
151 42 0.37
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (151 bp):
TTTGAGGTGTCTTCAAAGCTGCAACTGCCCCATCCATTCTTAAACCCCACAGGCCAATCTCGGAT
TACATTCATGGAAGCTCTTCTACCAAGATTTATTTTTCCATCCTTTTGTCACTTATGTTATTCAC
AGAAATTTTTTGTTGAAGCAA
Found at i:3226759 original size:5 final size:6
Alignment explanation
Indices: 3226709--3226887 Score: 54
Period size: 6 Copynumber: 29.5 Consensus size: 6
3226699 AATATTAAAT
* * *
3226709 AAATAGA AATTAA AATTAA AAA-AA AAATCAA AGGA-AA AAATAA AAATAA
1 AAATA-A AAATAA AAATAA AAATAA AAAT-AA A-AATAA AAATAA AAATAA
* * * * *
3226758 AAATATT AAAT-A GATTAA AGGA-AA AAATAA AAAAATA AAAT-A AAATAA
1 AAATA-A AAATAA AAATAA A-AATAA AAATAA AAATA-A AAATAA AAATAA
* * * *
3226806 AGATAA AAA-AT AAATCAA AGGA-AA AAATAT AAA-AA AAATAA ATAA-AGCA
1 AAATAA AAATAA AAAT-AA A-AATAA AAATAA AAATAA AAATAA A-AATA--A
**
3226855 AAGGGAA AAAT-A AAATAA AAATAA AAATAA AAA
1 AA-ATAA AAATAA AAATAA AAATAA AAATAA AAA
3226888 CTGTTAAATT
Statistics
Matches: 126, Mismatches: 25, Indels: 43
0.65 0.13 0.22
Matches are distributed among these distances:
5 28 0.22
6 70 0.56
7 23 0.18
8 4 0.03
9 1 0.01
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:3226759 original size:36 final size:36
Alignment explanation
Indices: 3226709--3226887 Score: 101
Period size: 36 Copynumber: 4.7 Consensus size: 36
3226699 AATATTAAAT
* *
3226709 AAATAGAAATTAAAATTAAAAAAAAAATCAAAGGAAA
1 AAATA-AAAATAAAAATAAAAAAAAAATCAAAGGAAA
** * * *
3226746 AAATAAAAATAAAAATATTAAATAGATTAAAGGAAA
1 AAATAAAAATAAAAATAAAAAAAAAATCAAAGGAAA
* * * * **
3226782 AAATAAAAAAATAAAATAAAATAAAGATAAAAAATAAA
1 AAATAAAAATA-AAAATAAAAAAAAAAT-CAAAGGAAA
* * *
3226820 TCAAAGGAAAAAATATAAAA-AAAATAAATAAAGCAAAGGGAA
1 --AAA--TAAAAATA-AAAATAAAA-AAA-AAATCAAAGGAAA
3226862 AAAT-AAAATAAAAATAAAAATAAAAA
1 AAATAAAAATAAAAATAAAAA-AAAAA
3226888 CTGTTAAATT
Statistics
Matches: 107, Mismatches: 25, Indels: 21
0.70 0.16 0.14
Matches are distributed among these distances:
36 42 0.39
37 29 0.27
38 6 0.06
40 6 0.06
41 4 0.04
42 18 0.17
43 2 0.02
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (36 bp):
AAATAAAAATAAAAATAAAAAAAAAATCAAAGGAAA
Found at i:3226775 original size:48 final size:45
Alignment explanation
Indices: 3226709--3226845 Score: 111
Period size: 43 Copynumber: 3.2 Consensus size: 45
3226699 AATATTAAAT
*
3226709 AAATAGAAAT-TAAA-ATTAAAAAAAAAATCAAAGGAAAAAATAA
1 AAATAAAAATATAAAGATTAAAAAAAAAATCAAAGGAAAAAATAA
*
3226752 AAATAAAAATATTAAATAGATTAAAGGAAAAAAT---A--AAAAAAT-A
1 AAATAAAAATA-T-AA-AGATTAAA-AAAAAAATCAAAGGAAAAAATAA
* *
3226795 AAAT--AAA-ATAAAGA-TAAAAAATAAATCAAAGGAAAAAATAT
1 AAATAAAAATATAAAGATTAAAAAAAAAATCAAAGGAAAAAATAA
3226836 AAA-AAAAATA
1 AAATAAAAATA
3226846 AATAAAGCAA
Statistics
Matches: 74, Mismatches: 5, Indels: 30
0.68 0.05 0.28
Matches are distributed among these distances:
35 6 0.08
36 4 0.05
37 3 0.04
38 3 0.04
39 1 0.01
40 8 0.11
41 6 0.08
42 3 0.04
43 15 0.20
44 7 0.09
45 1 0.01
46 3 0.04
47 1 0.01
48 6 0.08
49 7 0.09
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (45 bp):
AAATAAAAATATAAAGATTAAAAAAAAAATCAAAGGAAAAAATAA
Found at i:3226814 original size:31 final size:30
Alignment explanation
Indices: 3226750--3226819 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
3226740 AGGAAAAAAT
* * * *
3226750 AAAAATAAAAATATTAAATAGATTAAAGGA
1 AAAAATAAAAAAATAAAATAAAATAAAGGA
*
3226780 AAAAATAAAAAAATAAAATAAAATAAAGATA
1 AAAAATAAAAAAATAAAATAAAATAAAG-GA
3226811 AAAAATAAA
1 AAAAATAAA
3226820 TCAAAGGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.19
Consensus pattern (30 bp):
AAAAATAAAAAAATAAAATAAAATAAAGGA
Found at i:3226837 original size:19 final size:18
Alignment explanation
Indices: 3226779--3226847 Score: 55
Period size: 17 Copynumber: 4.2 Consensus size: 18
3226769 AGATTAAAGG
3226779 AAAAA-ATAAA-AAA-AT
1 AAAAATATAAATAAAGAT
3226794 -AAAATA-AAATAAAGAT
1 AAAAATATAAATAAAGAT
3226810 AAAAA-ATAAATCAAAGGA-
1 AAAAATATAAAT-AAA-GAT
*
3226828 AAAAATATAAA-AAAAAT
1 AAAAATATAAATAAAGAT
3226845 AAA
1 AAA
3226848 TAAAGCAAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 16
0.72 0.02 0.26
Matches are distributed among these distances:
14 7 0.16
15 4 0.09
16 4 0.09
17 14 0.32
18 8 0.18
19 7 0.16
ACGTcount: A:0.80, C:0.01, G:0.04, T:0.14
Consensus pattern (18 bp):
AAAAATATAAATAAAGAT
Found at i:3226838 original size:32 final size:32
Alignment explanation
Indices: 3226813--3226879 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
3226803 TAAAGATAAA
*
3226813 AAATAAATCAAAGGAAAAAATATAAAAAAAAT
1 AAATAAAGCAAAGGAAAAAATATAAAAAAAAT
*
3226845 AAATAAAGCAAAGGGAAAAATA-AAATAAAAAT
1 AAATAAAGCAAAGGAAAAAATATAAA-AAAAAT
3226877 AAA
1 AAA
3226880 AATAAAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 3 0.09
32 29 0.91
ACGTcount: A:0.75, C:0.03, G:0.09, T:0.13
Consensus pattern (32 bp):
AAATAAAGCAAAGGAAAAAATATAAAAAAAAT
Found at i:3226844 original size:24 final size:23
Alignment explanation
Indices: 3226773--3226847 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 23
3226763 TTAAATAGAT
*
3226773 TAAAGGAAAAAATAAAAAAATAAAA
1 TAAAGGAAAAAAT-ATAAAA-AAAA
*
3226798 TAAA--ATAAAGATA-AAAAATAAA
1 TAAAGGA-AAAAATATAAAAA-AAA
3226820 TCAAAGGAAAAAATATAAAAAAAA
1 T-AAAGGAAAAAATATAAAAAAAA
3226844 TAAA
1 TAAA
3226848 TAAAGCAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
21 1 0.02
22 8 0.19
23 8 0.19
24 15 0.36
25 10 0.24
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.15
Consensus pattern (23 bp):
TAAAGGAAAAAATATAAAAAAAA
Found at i:3226850 original size:13 final size:13
Alignment explanation
Indices: 3226780--3226851 Score: 56
Period size: 14 Copynumber: 5.2 Consensus size: 13
3226770 GATTAAAGGA
*
3226780 AAAAATAAAAAAAT
1 AAAAA-AAATAAAT
*
3226794 AAAATAAAATAAAG
1 AAAA-AAAATAAAT
*
3226808 ATAAAAAATAAAT
1 AAAAAAAATAAAT
*
3226821 CAAAGGAAAAA-ATAT
1 -AAA--AAAAATAAAT
3226836 AAAAAAAATAAAT
1 AAAAAAAATAAAT
3226849 AAA
1 AAA
3226852 GCAAAGGGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
12 5 0.11
13 14 0.30
14 18 0.39
15 4 0.09
16 5 0.11
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.15
Consensus pattern (13 bp):
AAAAAAAATAAAT
Found at i:3226881 original size:12 final size:11
Alignment explanation
Indices: 3226687--3226887 Score: 51
Period size: 12 Copynumber: 16.8 Consensus size: 11
3226677 GTTAGATAAG
3226687 AAATAATAAAT-
1 AAATAA-AAATA
*
3226698 AAATATTAAAT-
1 AAATA-AAAATA
*
3226709 AAATAGAAATTA
1 AAATA-AAAATA
*
3226721 AAATTAAAAAAA
1 AAA-TAAAAATA
3226733 AAATCAAAGGAA-A
1 AAAT-AAA--AATA
3226746 AAATAAAAATAA
1 AAATAAAAAT-A
*
3226758 AAATATTAAATA
1 AAATA-AAAATA
* *
3226770 GATTAAAGGAA-A
1 AAATAAA--AATA
3226782 AAATAAAAAAATA
1 AAAT--AAAAATA
3226795 AAAT-AAAATA
1 AAATAAAAATA
3226805 AAGATAAAAA-A
1 AA-ATAAAAATA
3226816 TAAATCAAAGGAA-A
1 -AAAT-AAA--AATA
3226830 AAATATAAAA-A
1 AAATA-AAAATA
3226841 AAATAAATAA-A
1 AAATAAA-AATA
*
3226852 GCAAAGGGAAAAATA
1 --AAA--TAAAAATA
3226867 AAATAAAAATAA
1 AAATAAAAAT-A
3226879 AAATAAAAA
1 AAATAAAAA
3226888 CTGTTAAATT
Statistics
Matches: 148, Mismatches: 14, Indels: 55
0.68 0.06 0.25
Matches are distributed among these distances:
10 12 0.08
11 41 0.28
12 51 0.34
13 30 0.20
14 10 0.07
15 4 0.03
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.18
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:3228225 original size:30 final size:31
Alignment explanation
Indices: 3228191--3228248 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
3228181 ACCCTGGACC
*
3228191 AAAAACAAAAATCAAATAATAAA-AAAAGAA
1 AAAAACAAAAATAAAATAATAAATAAAAGAA
* **
3228221 AAAAATATTAATAAAATAATAAATAAAA
1 AAAAACAAAAATAAAATAATAAATAAAA
3228249 ATAAATAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (31 bp):
AAAAACAAAAATAAAATAATAAATAAAAGAA
Found at i:3228250 original size:6 final size:6
Alignment explanation
Indices: 3228191--3228286 Score: 56
Period size: 6 Copynumber: 15.8 Consensus size: 6
3228181 ACCCTGGACC
* * **
3228191 AAAAAC AAAAAT CAAATAAT AAAAA- AAGAA- AAAAAT ATTAAT -AAAAT
1 AAAAAT AAAAAT -AAA-AAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
** *
3228238 AATAAAT AAAAAT AAATAAT ATTAAT ATAAAAT -ATAAT AAAAAT AAAAA
1 AA-AAAT AAAAAT AAA-AAT AAAAAT A-AAAAT AAAAAT AAAAAT AAAAA
3228287 ACATTTTTAA
Statistics
Matches: 69, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
5 15 0.22
6 32 0.46
7 19 0.28
8 3 0.04
ACGTcount: A:0.75, C:0.02, G:0.01, T:0.22
Consensus pattern (6 bp):
AAAAAT
Found at i:3228253 original size:10 final size:10
Alignment explanation
Indices: 3228238--3228284 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
3228228 TTAATAAAAT
3228238 AATAAATAAA
1 AATAAATAAA
3228248 AATAAAT-AA
1 AATAAATAAA
* *
3228257 TATTAATATAA
1 AATAAATA-AA
3228268 AATATAATAAA
1 AATA-AATAAA
3228279 AATAAA
1 AATAAA
3228285 AAACATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
9 7 0.23
10 9 0.30
11 10 0.33
12 4 0.13
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AATAAATAAA
Found at i:3228256 original size:22 final size:20
Alignment explanation
Indices: 3228204--3228252 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
3228194 AACAAAAATC
3228204 AAATAATAAAAAAAGAAAAA
1 AAATAATAAAAAAAGAAAAA
* *
3228224 AATATTAATAAAATAATAAATAA
1 AA-A-TAATAAAAAAAGAAA-AA
3228247 AAATAA
1 AAATAA
3228253 ATAATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 2 0.08
21 4 0.17
22 14 0.58
23 4 0.17
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (20 bp):
AAATAATAAAAAAAGAAAAA
Found at i:3228262 original size:31 final size:31
Alignment explanation
Indices: 3228204--3228287 Score: 111
Period size: 31 Copynumber: 2.7 Consensus size: 31
3228194 AACAAAAATC
3228204 AAATAATAAA-AAAAGA-AAAAAATATTAATA
1 AAATAATAAATAAAA-ATAAAAAATATTAATA
*
3228234 AAATAATAAATAAAAATAAATAATATTAATA
1 AAATAATAAATAAAAATAAAAAATATTAATA
*
3228265 TAA-AATATAATAAAAATAAAAAA
1 AAATAATA-AATAAAAATAAAAAA
3228288 CATTTTTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
30 15 0.31
31 33 0.69
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (31 bp):
AAATAATAAATAAAAATAAAAAATATTAATA
Found at i:3228335 original size:36 final size:34
Alignment explanation
Indices: 3228289--3228640 Score: 131
Period size: 35 Copynumber: 9.9 Consensus size: 34
3228279 AATAAAAAAC
* *
3228289 ATTTTTAAAACTATATTATATACGTTTTTGAAAATT
1 ATTTTCAAAACTATATTATATA--TTTTTCAAAATT
* * * *
3228325 GTTTTCAAAACCACAATA-ATATATTTTCAAAAATT
1 ATTTTCAAAACTATATTATATAT-TTTTC-AAAATT
* *
3228360 ATTTTTAAAACTATATAATATAAATATTTTTCAAAACT
1 ATTTTCAAAACTATAT--TAT--ATATTTTTCAAAATT
* * * *
3228398 A---T--ATA-T-TA-TATACATTTTTTAAAAAT
1 ATTTTCAAAACTATATTATATATTTTTCAAAATT
3228424 ATTTTCAAAACTATATATTATATATTTTTTCAAAATAT
1 ATTTTCAAAAC--TATATTATATA-TTTTTCAAAAT-T
* * *
3228462 TTTTTAAAAACTATATTATATATATATTCAAAA-T
1 ATTTTCAAAACTATATTATATAT-TTTTCAAAATT
* * *
3228496 GTTTTCGAAAACTATATTTTATATATATATTCAAAA-C
1 ATTTTC-AAAACTATA--TTATATAT-TTTTCAAAATT
* * *
3228533 A-ATTCAAAACTATATAATATATATGTTTTTAGAAA-A
1 ATTTTCAAAACTATAT--TATATAT-TTTTCA-AAATT
3228569 ACGTTTTCAAAACTATATAATATATATATTTTCAAAAATT
1 A--TTTTCAAAACTATAT--TATATAT-TTTTC-AAAATT
* *
3228609 GATTTT-AAATC-ATATTTTATATGTTTTCAAAA
1 -ATTTTCAAAACTATATTATATAT-TTTTCAAAA
3228641 ACCGTTTTCT
Statistics
Matches: 245, Mismatches: 39, Indels: 66
0.70 0.11 0.19
Matches are distributed among these distances:
26 13 0.05
28 3 0.01
29 1 0.00
31 4 0.02
32 1 0.00
33 4 0.02
34 14 0.06
35 64 0.26
36 44 0.18
37 33 0.13
38 20 0.08
39 38 0.16
40 5 0.02
41 1 0.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (34 bp):
ATTTTCAAAACTATATTATATATTTTTCAAAATT
Found at i:3228390 original size:26 final size:26
Alignment explanation
Indices: 3228361--3228421 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
3228351 TCAAAAATTA
*
3228361 TTTTTAAAACTATATAATATAAATAT
1 TTTTTAAAACTATATAATATAAACAT
* * *
3228387 TTTTCAAAACTATATATTATATACAT
1 TTTTTAAAACTATATAATATAAACAT
3228413 TTTTTAAAA
1 TTTTTAAAA
3228422 ATATTTTCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (26 bp):
TTTTTAAAACTATATAATATAAACAT
Found at i:3228542 original size:35 final size:35
Alignment explanation
Indices: 3228388--3228605 Score: 143
Period size: 36 Copynumber: 5.9 Consensus size: 35
3228378 TATAAATATT
* * * *
3228388 TTTCAAAACTATATATTATATACATTTTTTAAAAATA
1 TTTCAAAACTATATATTATAT--ATATATTCAAAACA
* * *
3228425 TTTTCAAAACTATATATTATATATTTTTTCAAAATA
1 -TTTCAAAACTATATATTATATATATATTCAAAACA
* **
3228461 TTTTTTAAAA--ACTATATTATATATATATTCAAAATGT
1 --TTTCAAAACTA-TATATTATATATATATTCAAAA-CA
*
3228498 TTTCGAAAACTATATTTTATATATATATTCAAAACA
1 TTTC-AAAACTATATATTATATATATATTCAAAACA
* * * * * *
3228534 ATTCAAAACTATATAATATATATGTTTTTAGAAAAACGT
1 TTTCAAAACTATATATTATATAT-ATATT--CAAAAC-A
* *
3228573 TTTCAAAACTATATAATATATATATTTTCAAAA
1 TTTCAAAACTATATATTATATATATATTCAAAA
3228606 ATTGATTTTA
Statistics
Matches: 150, Mismatches: 20, Indels: 22
0.78 0.10 0.11
Matches are distributed among these distances:
35 21 0.14
36 47 0.31
37 29 0.19
38 31 0.21
39 22 0.15
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.44
Consensus pattern (35 bp):
TTTCAAAACTATATATTATATATATATTCAAAACA
Found at i:3228606 original size:37 final size:37
Alignment explanation
Indices: 3228387--3228669 Score: 235
Period size: 38 Copynumber: 7.6 Consensus size: 37
3228377 ATATAAATAT
* * *
3228387 TTTTCAAAACTATATATTATATACATTTTTTAAAAATA
1 TTTTCAAAACTATATATTATATATA-TTTTCAAAAATG
* *
3228425 TTTTCAAAACTATATATTATATATTTTTTCAAAATATT
1 TTTTCAAAACTATATATTATATATATTTTCAAAA-ATG
* *
3228463 TTTTAAAAAC--TATATTATATATATATTC-AAAATG
1 TTTTCAAAACTATATATTATATATATTTTCAAAAATG
* *
3228497 TTTTCGAAAACTATATTTTATATATATATTCAAAACA--
1 TTTTC-AAAACTATATATTATATATATTTTCAAAA-ATG
* * * * *
3228534 -ATTCAAAACTATATAATATATATGTTTTTAGAAAAACG
1 TTTTCAAAACTATATATTATATAT-ATTTT-CAAAAATG
*
3228572 TTTTCAAAACTATATAATATATATATTTTCAAAAATTG
1 TTTTCAAAACTATATATTATATATATTTTCAAAAA-TG
* * *
3228610 ATTTT-AAATC-ATAT-TT-TATATGTTTTCAAAAACCG
1 -TTTTCAAAACTATATATTATATATATTTTCAAAAA-TG
3228645 TTTTCTAAAAACTATATATTATATA
1 TTTTC--AAAACTATATATTATATA
3228670 CCCCGAACGA
Statistics
Matches: 200, Mismatches: 26, Indels: 36
0.76 0.10 0.14
Matches are distributed among these distances:
34 10 0.05
35 41 0.20
36 24 0.12
37 42 0.21
38 50 0.25
39 29 0.14
40 4 0.02
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.45
Consensus pattern (37 bp):
TTTTCAAAACTATATATTATATATATTTTCAAAAATG
Found at i:3229649 original size:18 final size:18
Alignment explanation
Indices: 3229626--3229664 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3229616 TCGAGATACA
*
3229626 CTTTTTACTCTATTTAAG
1 CTTTTTACTCCATTTAAG
*
3229644 CTTTTTCCTCCATTTAAG
1 CTTTTTACTCCATTTAAG
3229662 CTT
1 CTT
3229665 CAAAAGGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.23, G:0.05, T:0.54
Consensus pattern (18 bp):
CTTTTTACTCCATTTAAG
Found at i:3244216 original size:21 final size:20
Alignment explanation
Indices: 3244189--3244286 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
3244179 AATCAGTGTC
3244189 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
3244210 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
3244230 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3244250 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
3244271 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3244287 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3244239 original size:41 final size:41
Alignment explanation
Indices: 3244130--3244286 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
3244120 AAATGACCAA
* **
3244130 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
3244169 CAGAATCGCAAATC-AGTGTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
3244210 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
3244251 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
3244287 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:3244296 original size:20 final size:20
Alignment explanation
Indices: 3244273--3244443 Score: 107
Period size: 20 Copynumber: 8.6 Consensus size: 20
3244263 GCGAATATGA
3244273 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
3244293 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
3244313 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
** *
3244333 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTAACCAT
* * *
3244353 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* *
3244373 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
* **
3244393 AAATCGCAACGAG-AATCTGT
1 AAATCGCAACGCGTAA-CCAT
* *
3244413 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
3244433 AAATCGCAACG
1 AAATCGCAACG
3244444 AGAATCTGTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 127 0.97
21 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:3244338 original size:60 final size:58
Alignment explanation
Indices: 3244253--3244462 Score: 208
Period size: 60 Copynumber: 3.5 Consensus size: 58
3244243 CGATTTTCCA
* ** * *
3244253 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCGAAC-CGTAAATCGCAA-GCGTATCCGT
* ** *
3244313 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTTTCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCG-AACCGTAAATCGCAA-GCGTATCCGT
* *
3244373 AAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTGTAAATCGCAA-CGATAATCCGT
1 AAATCGCAACG-TGAATCCGTAAATCGCAACGCGAA-CCGTAAATCGCAAGCG-T-ATCCGT
* * *
3244433 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGTGAATCCGTAAATCGCAAC
3244463 ACTGAAATTT
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 120 0.96
61 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (58 bp):
AAATCGCAACGTGAATCCGTAAATCGCAACGCGAACCGTAAATCGCAAGCGTATCCGT
Found at i:3244444 original size:20 final size:20
Alignment explanation
Indices: 3244307--3244462 Score: 174
Period size: 20 Copynumber: 7.8 Consensus size: 20
3244297 CGCAATGCGT
*
3244307 ATCCGTAAATCGCAACG-TGT
1 ATCCGTAAATCGCAACGAT-A
*
3244327 ATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
* * *
3244347 TTCCGTATATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
3244367 ATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
3244387 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
*
3244407 ATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
3244427 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
* *
3244447 ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAAC
3244463 ACTGAAATTT
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 119 0.98
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGATA
Found at i:3244444 original size:40 final size:40
Alignment explanation
Indices: 3244273--3244462 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 40
3244263 GCGAATATGA
* *
3244273 AAATCGCAACGCGAA-CACATAAATCGCAATGCG-T-ATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAA--CGATAATCCGT
* * * *
3244313 AAATCGCAACGTGTATCCGTAAATCGCAACGCGT-TTCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGT
* * *
3244353 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
*
3244393 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
3244433 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
3244463 ACTGAAATTT
Statistics
Matches: 133, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 129 0.97
41 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:3245184 original size:24 final size:24
Alignment explanation
Indices: 3245145--3245191 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3245135 AAATTTGGTC
3245145 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
3245169 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
3245192 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:3247759 original size:33 final size:33
Alignment explanation
Indices: 3247672--3247869 Score: 188
Period size: 33 Copynumber: 5.8 Consensus size: 33
3247662 CAGAAATTAC
* *
3247672 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
3247705 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
* *
3247739 AATCGCAATGCGAAATGAAAATCGCAATGCG-A
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
* * *
3247771 AAT-G-AAAGTCGCAACAAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATG-CG-AA-ATGAAAATCGCAA--CG--A-GAA
* *
3247810 AATCGCAATGCGAAATGAAAATCGCAACGACAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
3247843 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
3247870 TGCGAAATGA
Statistics
Matches: 136, Mismatches: 16, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
30 3 0.02
31 3 0.02
32 5 0.04
33 67 0.49
34 30 0.22
35 2 0.01
36 2 0.01
38 12 0.09
39 6 0.04
40 3 0.02
41 3 0.02
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:3247791 original size:52 final size:52
Alignment explanation
Indices: 3247700--3247921 Score: 383
Period size: 52 Copynumber: 4.2 Consensus size: 52
3247690 AAATCCCAAC
*
3247700 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACAAGAGAATCGCAATGCGAA
*
3247753 ATGAAAATCGCAATGCGAAATGAAAGTCGCAACAAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACAAGAGAATCGCAATGCGAA
* *
3247805 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACAAGAGAATCGCAATGCGAA
3247857 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAA-AGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAC-AAGAGAATCGCAATGCGAA
3247909 ATGAAAATCGCAA
1 ATGAAAATCGCAA
3247922 CGAGAGAATC
Statistics
Matches: 162, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
52 145 0.90
53 17 0.10
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACAAGAGAATCGCAATGCGAA
Found at i:3247899 original size:33 final size:33
Alignment explanation
Indices: 3247758--3247943 Score: 204
Period size: 33 Copynumber: 5.5 Consensus size: 33
3247748 GCGAAATGAA
*
3247758 AATCGCAATGCGAAATGAAAGTCGCAAC-AAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAA-AG
3247791 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G
*
3247827 AAAATCGCAA--CGACA-G--AATCGCAATGCGAAATG
1 --AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G
3247860 AAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 --AATCGCAATGCGAAATGAAAATCGCAACGAAAG
*
3247895 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
3247928 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
3247944 TATAAACGCA
Statistics
Matches: 138, Mismatches: 4, Indels: 22
0.84 0.02 0.13
Matches are distributed among these distances:
33 101 0.73
35 8 0.06
36 13 0.09
38 16 0.12
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAG
Found at i:3247994 original size:19 final size:19
Alignment explanation
Indices: 3247950--3248047 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
3247940 AAATTATAAA
3247950 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3247969 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
3247989 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
3248005 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3248022 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3248041 CGCATTG
1 CGCATTG
3248048 AGATAGTCAT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 32 0.45
20 19 0.27
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:3248057 original size:19 final size:19
Alignment explanation
Indices: 3248016--3248059 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3248006 GTTGCGATTT
* **
3248016 TCATTTCGCATTGCGATTT
1 TCATTTCGCATTGAGATAG
3248035 TCATTTCGCATTGAGATAG
1 TCATTTCGCATTGAGATAG
3248054 TCATTT
1 TCATTT
3248060 TTGCCTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGAGATAG
Found at i:3248177 original size:14 final size:14
Alignment explanation
Indices: 3248158--3248194 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3248148 CATCAATTAC
3248158 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3248172 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3248186 ACAAATCAA
1 ACAAATCAA
3248195 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3250194 original size:14 final size:14
Alignment explanation
Indices: 3250175--3250231 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3250165 GCGAAATGAA
*
3250175 AATCGCAACGACAG
1 AATCGCAACGAAAG
3250189 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
3250206 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
3250222 AATCGCAACG
1 AATCGCAACG
3250232 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3250202 original size:33 final size:33
Alignment explanation
Indices: 3250156--3250248 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
3250146 GCGAAACCAA
*
3250156 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
3250189 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3250222 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3250249 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3250213 original size:19 final size:19
Alignment explanation
Indices: 3250119--3250253 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3250109 TAGTTTACTT
* *
3250119 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
3250139 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3250158 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3250177 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
3250191 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3250210 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
3250224 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3250243 TCGCAATGCGA
1 TCGCAACGCGA
3250254 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3250271 original size:19 final size:18
Alignment explanation
Indices: 3250249--3250377 Score: 85
Period size: 19 Copynumber: 7.3 Consensus size: 18
3250239 AAAATCGCAA
3250249 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
3250268 TGCGA--TTCTTT--CGT
1 TGCGATTTTGTTTCGCGT
* *
3250282 TGCGATTTTCATTTCGCAT
1 TGCGATTTT-GTTTCGCGT
*
3250301 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
3250315 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
3250334 TGCAATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
3250353 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
3250373 TGCGA
1 TGCGA
3250378 AAGTAAACTA
Statistics
Matches: 85, Mismatches: 14, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
14 18 0.21
16 6 0.07
17 6 0.07
19 42 0.49
20 13 0.15
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:3250284 original size:14 final size:14
Alignment explanation
Indices: 3250265--3250321 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3250255 TTTGGTTTCG
3250265 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
3250279 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
3250296 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
3250312 CGTTGCGATT
1 CGTTGCGATT
3250322 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:3250297 original size:33 final size:33
Alignment explanation
Indices: 3250249--3250336 Score: 140
Period size: 33 Copynumber: 2.7 Consensus size: 33
3250239 AAAATCGCAA
** *
3250249 TGCGATTTTGGTTTCGCGTTGCGATTCTTTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
*
3250282 TGCGATTTTCATTTCGCATTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
3250315 TGCGATTTTCATTTCGCGTTGC
1 TGCGATTTTCATTTCGCGTTGC
3250337 AATTTTGGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.09, C:0.20, G:0.24, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
Found at i:3250541 original size:93 final size:93
Alignment explanation
Indices: 3250425--3250893 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
3250415 ATGGATTGCA
*
3250425 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAAAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3250489 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3250517 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3250582 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3250610 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3250675 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3250703 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3250768 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3250796 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
3250861 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3250889 TTACT
1 TTACT
3250894 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 370 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:3252637 original size:19 final size:20
Alignment explanation
Indices: 3252593--3252654 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
3252583 CTTTGGTTGA
*
3252593 AATGAAAATCGCAACGAGAG
1 AATGACAATCGCAACGAGAG
** *
3252613 AATGACTGTCGCAACGCGA-
1 AATGACAATCGCAACGAGAG
3252632 AATGACAATCGCAACGAGAG
1 AATGACAATCGCAACGAGAG
3252652 AAT
1 AAT
3252655 CGCAACGCGA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGACAATCGCAACGAGAG
Found at i:3252657 original size:14 final size:14
Alignment explanation
Indices: 3252638--3252694 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3252628 GCGAAATGAC
3252638 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3252652 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3252671 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3252685 AATCGCAACG
1 AATCGCAACG
3252695 CGAAATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3252663 original size:33 final size:33
Alignment explanation
Indices: 3252591--3252711 Score: 170
Period size: 33 Copynumber: 3.5 Consensus size: 33
3252581 GTCTTTGGTT
3252591 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGC
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAACGC
*
3252630 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3252663 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
3252696 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
3252712 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
33 56 0.71
36 1 0.01
38 1 0.01
39 21 0.27
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3252676 original size:19 final size:19
Alignment explanation
Indices: 3252591--3252716 Score: 92
Period size: 19 Copynumber: 7.1 Consensus size: 19
3252581 GTCTTTGGTT
*
3252591 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
***
3252610 GAGAATGACTGTCGCAACGC
1 GA-AATGAAAATCGCAACGC
*
3252630 GAAATGACAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
3252647 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3252663 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
3252680 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
3252696 GAAATAAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
3252715 GA
1 GA
3252717 TTTTGGTTTC
Statistics
Matches: 84, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
14 20 0.24
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 37 0.44
20 15 0.18
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3252747 original size:14 final size:14
Alignment explanation
Indices: 3252728--3252784 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3252718 TTTGGTTTCG
3252728 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3252742 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3252761 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3252775 CGTTGCGATT
1 CGTTGCGATT
3252785 GTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3252766 original size:19 final size:19
Alignment explanation
Indices: 3252742--3252830 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
3252732 GCGATTCTCT
3252742 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3252761 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
3252775 CGTTGCGATTGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*** *
3252794 CGTTGCGACAGTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
3252814 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
3252831 ATCTCGTTGC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 25 0.45
20 15 0.27
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:3252822 original size:39 final size:33
Alignment explanation
Indices: 3252712--3252830 Score: 157
Period size: 33 Copynumber: 3.4 Consensus size: 33
3252702 AAAATCGCAA
**
3252712 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3252745 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
3252778 TGCGATTGTCATTTCGCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCGT
3252817 TGCGATTTTCATTT
1 TGCGATTTTCATTT
3252831 ATCTCGTTGC
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
33 50 0.66
35 1 0.01
36 1 0.01
37 1 0.01
39 23 0.30
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:3252964 original size:33 final size:33
Alignment explanation
Indices: 3252922--3252992 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3252912 AATACTAACT
3252922 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
3252955 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
3252988 TGAAA
1 TGAAA
3252993 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:3253226 original size:22 final size:22
Alignment explanation
Indices: 3253174--3253228 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3253164 TGGTTGTGAG
**
3253174 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3253196 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3253218 GGATTTCTTCG
1 GGATTTCTTCG
3253229 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3253403 original size:20 final size:20
Alignment explanation
Indices: 3253375--3253548 Score: 181
Period size: 20 Copynumber: 8.7 Consensus size: 20
3253365 CTTTAAATAT
3253375 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
3253395 CGTGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* * *
3253417 -TCGTTACGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
3253436 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3253456 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3253476 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3253496 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
3253516 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
3253536 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3253549 TCATATTCGC
Statistics
Matches: 124, Mismatches: 26, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.02
20 107 0.86
21 13 0.10
22 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3253540 original size:60 final size:60
Alignment explanation
Indices: 3253377--3253548 Score: 218
Period size: 60 Copynumber: 2.9 Consensus size: 60
3253367 TTAAATATCG
** ** * *
3253377 CGTTGCGATTTACGGATACGTGTTGCGATTTTATGTATTATCGTTACGATTTACCGATACG
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACCGATACA
* *** * *
3253438 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
*
3253498 CGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTT
3253549 TCATATTCGC
Statistics
Matches: 93, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 68 0.73
61 25 0.27
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
Found at i:3253564 original size:60 final size:60
Alignment explanation
Indices: 3253375--3253568 Score: 217
Period size: 60 Copynumber: 3.2 Consensus size: 60
3253365 CTTTAAATAT
** ** * *
3253375 CGCGTTGCGATTTACGGATACGTGTTGCGATTTTATGTATTATCGTTACGATTTACCGATA
1 CGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACAGATA
* *** * *
3253436 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
* * * * *
3253496 CACGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
*
3253556 CGCATTGCGATTT
1 CGCGTTGCGATTT
3253569 TGGAAAATCG
Statistics
Matches: 109, Mismatches: 24, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 82 0.75
61 27 0.25
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
Found at i:3253585 original size:21 final size:20
Alignment explanation
Indices: 3253535--3253632 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
3253525 ATTTATGTGT
* * * *
3253535 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
3253555 TCGCATTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
3253576 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
3253596 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
3253617 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
3253633 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:3253627 original size:41 final size:41
Alignment explanation
Indices: 3253535--3253691 Score: 119
Period size: 41 Copynumber: 3.9 Consensus size: 41
3253525 ATTTATGTGT
* *
3253535 TCGCGTTGCGATTTTCATATTCGCATTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
3253576 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
3253617 TCGCGTTGCGATTTTGGAAACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
3253657 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
3253692 TTGGTCATTT
Statistics
Matches: 90, Mismatches: 18, Indels: 18
0.71 0.14 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 53 0.59
42 5 0.06
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:3254515 original size:13 final size:13
Alignment explanation
Indices: 3254477--3254551 Score: 69
Period size: 13 Copynumber: 5.8 Consensus size: 13
3254467 CAGCTTGATG
* *
3254477 AGTCGAGCGACTA
1 AGTCGAGCCACCA
* *
3254490 AGCCGAACCACCA
1 AGTCGAGCCACCA
3254503 AGTCGAGCCACCA
1 AGTCGAGCCACCA
* *
3254516 AGCCGAGCCACCG
1 AGTCGAGCCACCA
** *
3254529 AGTCGAGCTGCTA
1 AGTCGAGCCACCA
3254542 AGTCGAGCCA
1 AGTCGAGCCA
3254552 AGCTGACTGA
Statistics
Matches: 47, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.29, C:0.35, G:0.27, T:0.09
Consensus pattern (13 bp):
AGTCGAGCCACCA
Found at i:3254518 original size:26 final size:26
Alignment explanation
Indices: 3254477--3254536 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
3254467 CAGCTTGATG
* *
3254477 AGTCGAGCGACTAAGCCGAACCACCA
1 AGTCGAGCCACCAAGCCGAACCACCA
* *
3254503 AGTCGAGCCACCAAGCCGAGCCACCG
1 AGTCGAGCCACCAAGCCGAACCACCA
3254529 AGTCGAGC
1 AGTCGAGC
3254537 TGCTAAGTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.37, G:0.27, T:0.07
Consensus pattern (26 bp):
AGTCGAGCCACCAAGCCGAACCACCA
Found at i:3254548 original size:26 final size:25
Alignment explanation
Indices: 3254476--3254551 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 25
3254466 GCAGCTTGAT
*
3254476 GAGTCGAGCGACTAAGCCGAACCACC
1 GAGTCGAGCG-CTAAGCCGAGCCACC
* * *
3254502 AAGTCGAGCCACCAAGCCGAGCCACC
1 GAGTCGAG-CGCTAAGCCGAGCCACC
*
3254528 GAGTCGAGCTGCTAAGTCGAGCCA
1 GAGTCGAGC-GCTAAGCCGAGCCA
3254552 AGCTGACTGA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
25 1 0.03
26 38 0.95
27 1 0.03
ACGTcount: A:0.29, C:0.34, G:0.28, T:0.09
Consensus pattern (25 bp):
GAGTCGAGCGCTAAGCCGAGCCACC
Found at i:3254630 original size:13 final size:13
Alignment explanation
Indices: 3254593--3254631 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
3254583 TTGACTTGTG
*
3254593 TTGACTTTGACAA
1 TTGACTTTGACCA
*
3254606 TTGATTTTGACCA
1 TTGACTTTGACCA
3254619 TTGACTTTGACCA
1 TTGACTTTGACCA
3254632 AAAAGTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGACTTTGACCA
Found at i:3256638 original size:43 final size:45
Alignment explanation
Indices: 3256590--3256687 Score: 137
Period size: 47 Copynumber: 2.2 Consensus size: 45
3256580 CATCGAAAAC
*
3256590 TATGAATT-GTT-CCTGATTTATATAATCATGGAATTTATCGGTT
1 TATGAATTGGTTACCTGATTTATACAATCATGGAATTTATCGGTT
* *
3256633 TATGAATTATGGTTACCTGATTTATGCAATCATGGAATTTATTGGTT
1 TATGAA-T-TGGTTACCTGATTTATACAATCATGGAATTTATCGGTT
3256680 TATGAATT
1 TATGAATT
3256688 ATGGTTACTT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
43 6 0.12
44 1 0.02
45 2 0.04
46 4 0.08
47 35 0.73
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (45 bp):
TATGAATTGGTTACCTGATTTATACAATCATGGAATTTATCGGTT
Found at i:3256655 original size:47 final size:47
Alignment explanation
Indices: 3256601--3256695 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
3256591 ATGAATTGTT
*
3256601 CCTGATTTATATAATCATGGAATTTATCGGTTTATGAATTATGGTTA
1 CCTGATTTATACAATCATGGAATTTATCGGTTTATGAATTATGGTTA
* *
3256648 CCTGATTTATGCAATCATGGAATTTATTGGTTTATGAATTATGGTTA
1 CCTGATTTATACAATCATGGAATTTATCGGTTTATGAATTATGGTTA
3256695 C
1 C
3256696 TTGAAATATG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.44
Consensus pattern (47 bp):
CCTGATTTATACAATCATGGAATTTATCGGTTTATGAATTATGGTTA
Found at i:3263651 original size:18 final size:17
Alignment explanation
Indices: 3263594--3263656 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
3263584 CAATTTAAAC
*
3263594 TATAATAAAAATATAAAAA
1 TATAATAAAAATAT--AAT
*
3263613 TACAAATAAAAATATAAT
1 TA-TAATAAAAATATAAT
*
3263631 TATAATAAAAATATATTT
1 TATAATAAAAATATA-AT
3263649 TATAATAA
1 TATAATAA
3263657 TTCATTATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
17 12 0.32
18 13 0.34
19 2 0.05
20 11 0.29
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
TATAATAAAAATATAAT
Found at i:3265854 original size:29 final size:30
Alignment explanation
Indices: 3265821--3265898 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 30
3265811 AATTTTGATA
*
3265821 TTATAATTTTTCTATATATTTT-AAA-ATTT
1 TTATAATTTTTCAATA-ATTTTGAAATATTT
***
3265850 TTAT-ATTTAAGAATAATTTTGAAATATTT
1 TTATAATTTTTCAATAATTTTGAAATATTT
*
3265879 TTATAATTTTTAAAATAATT
1 TTATAATTTTT-CAATAATT
3265899 ATGTATTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
27 5 0.13
28 10 0.26
29 12 0.32
30 4 0.11
31 7 0.18
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (30 bp):
TTATAATTTTTCAATAATTTTGAAATATTT
Found at i:3268357 original size:28 final size:28
Alignment explanation
Indices: 3268308--3268362 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
3268298 GTTTATACAA
*
3268308 AAATCAAAACTATGAATATAATTAAATC
1 AAATCAAAACTATGAATATAATAAAATC
3268336 AAATCAAAA-TCA-GAATATTAATAAAAT
1 AAATCAAAACT-ATGAATA-TAATAAAAT
3268363 ATGCAAACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.27
Consensus pattern (28 bp):
AAATCAAAACTATGAATATAATAAAATC
Found at i:3277377 original size:20 final size:19
Alignment explanation
Indices: 3277352--3277411 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 19
3277342 ATATTAAATT
3277352 AATATAATAAATAGAATAAA
1 AATATAATAAATA-AATAAA
3277372 AATATAATTAAGATATAA-AAA
1 AATATAA-TAA-ATA-AATAAA
* *
3277393 AATTTAATATATAAATAAA
1 AATATAATAAATAAATAAA
3277412 TAAGAAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 2 0.06
19 6 0.18
20 9 0.26
21 12 0.35
22 5 0.15
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
AATATAATAAATAAATAAA
Found at i:3277382 original size:34 final size:34
Alignment explanation
Indices: 3277316--3277382 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
3277306 TTCTTTTATT
* * *
3277316 TTAATATAATAAAGATAATGTATAATATATTAAA
1 TTAATATAATAAAGAGAATGAAAAATATATTAAA
*
3277350 TTAATATAATAAATAGAAT-AAAAATATAATTAA
1 TTAATATAATAAAGAGAATGAAAAATAT-ATTAA
3277383 GATATAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 6 0.21
34 22 0.79
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (34 bp):
TTAATATAATAAAGAGAATGAAAAATATATTAAA
Found at i:3277404 original size:17 final size:17
Alignment explanation
Indices: 3277379--3277412 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3277369 AAAAATATAA
3277379 TTAAGATATAAAAAAAT
1 TTAAGATATAAAAAAAT
* *
3277396 TTAATATATAAATAAAT
1 TTAAGATATAAAAAAAT
3277413 AAGAAATAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
TTAAGATATAAAAAAAT
Found at i:3277492 original size:16 final size:16
Alignment explanation
Indices: 3277467--3277505 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3277457 TAAGTATAAT
3277467 GAAT-TTATATAAATA
1 GAATATTATATAAATA
*
3277482 GAATATTATATAATTA
1 GAATATTATATAAATA
*
3277498 TAATATTA
1 GAATATTA
3277506 AAAATATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (16 bp):
GAATATTATATAAATA
Found at i:3282203 original size:64 final size:65
Alignment explanation
Indices: 3282126--3282281 Score: 201
Period size: 65 Copynumber: 2.4 Consensus size: 65
3282116 TACACTAGGG
* * * * *
3282126 GTGCATCGATACACTAATTACATTCGATGTTTCAAAGA-GCT-AGGAGTGCATCGATGCATGG-T
1 GTGCATCGGTACACTAAATGCATTCGATGTTTCAAA-ATACTCAAGAGTGCATCGATGCATGGCT
3282188 AT
65 -T
* * *
3282190 GTGTATCGGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTT
1 GTGCATCGGTACACTAAATGCATTCGATGTTTCAAAATACTCAAGAGTGCATCGATGCATGGCTT
3282255 GTGCATCGGTACACTAAATGCATTCGA
1 GTGCATCGGTACACTAAATGCATTCGA
3282282 AATAGGGTGC
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 1 0.01
64 32 0.41
65 45 0.57
66 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACACTAAATGCATTCGATGTTTCAAAATACTCAAGAGTGCATCGATGCATGGCTT
Found at i:3282956 original size:13 final size:13
Alignment explanation
Indices: 3282938--3282966 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3282928 GCATTTAAGT
3282938 TCAAACATCCAAA
1 TCAAACATCCAAA
3282951 TCAAACATCCAAA
1 TCAAACATCCAAA
3282964 TCA
1 TCA
3282967 TCAAATTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.31, G:0.00, T:0.17
Consensus pattern (13 bp):
TCAAACATCCAAA
Found at i:3282968 original size:22 final size:22
Alignment explanation
Indices: 3282939--3282986 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
3282929 CATTTAAGTT
3282939 CAAACATCCAAA-TCAAAC-ATC
1 CAAACAT-CAAATTCAAACAATC
3282960 CAAATCATCAAATTCAAACAATC
1 CAAA-CATCAAATTCAAACAATC
3282983 CAAA
1 CAAA
3282987 AACATATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.33
22 9 0.38
23 7 0.29
ACGTcount: A:0.54, C:0.29, G:0.00, T:0.17
Consensus pattern (22 bp):
CAAACATCAAATTCAAACAATC
Found at i:3284960 original size:23 final size:22
Alignment explanation
Indices: 3284926--3284999 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
3284916 CATAGCAGAG
*
3284926 TGCATCGATGCAGATTCAAGGAA
1 TGCATCGATGCACATTCAAGG-A
* *
3284949 TGCATCGGTGCATC-TTC-ATGA
1 TGCATCGATGCA-CATTCAAGGA
*
3284970 TGCATCAATGCACATTCAAGGGA
1 TGCATCGATGCACATTCAA-GGA
3284993 TGCATCG
1 TGCATCG
3285000 GTACACTATC
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
20 1 0.03
21 14 0.35
22 3 0.08
23 22 0.55
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:3288718 original size:20 final size:21
Alignment explanation
Indices: 3288679--3288718 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3288669 GAAGCTTTAA
* *
3288679 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
3288700 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
3288719 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:3290815 original size:64 final size:65
Alignment explanation
Indices: 3290747--3290899 Score: 168
Period size: 65 Copynumber: 2.4 Consensus size: 65
3290737 TACACTAGGG
* * *
3290747 GTGCATCGGTACACTAATTATATTCGATGTTT-TAAATAGCC-AGAAGTACATCGATGCATGG-T
1 GTGCATCGGTACACTAAATACATTCGATGTTTCAAAATAGCCAAG-AGTACATCGATGCATGGCT
3290809 CT
65 -T
* * * ** * *
3290811 GTGCATCGGTACACAAAATGCATTTGATGTTTCAAAATATTCAAGAGTGCATCGATGTATGGCTT
1 GTGCATCGGTACACTAAATACATTCGATGTTTCAAAATAGCCAAGAGTACATCGATGCATGGCTT
*
3290876 GTGCATCGGTACACTAAATGCATT
1 GTGCATCGGTACACTAAATACATT
3290900 TGAAATGGAG
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
64 27 0.36
65 45 0.60
66 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (65 bp):
GTGCATCGGTACACTAAATACATTCGATGTTTCAAAATAGCCAAGAGTACATCGATGCATGGCTT
Found at i:3296852 original size:4 final size:4
Alignment explanation
Indices: 3296843--3296867 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3296833 GTACTTTAAG
3296843 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
3296868 AATTCATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:3297521 original size:24 final size:24
Alignment explanation
Indices: 3297493--3297545 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
3297483 GTCGCGAGCT
3297493 TGAAGGTCATGAGTAATAGTAAGA
1 TGAAGGTCATGAGTAATAGTAAGA
3297517 TGAAGGTCATGAGTAATAGTAAGA
1 TGAAGGTCATGAGTAATAGTAAGA
3297541 TGAAG
1 TGAAG
3297546 AAGACGATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.42, C:0.04, G:0.30, T:0.25
Consensus pattern (24 bp):
TGAAGGTCATGAGTAATAGTAAGA
Found at i:3298249 original size:2 final size:2
Alignment explanation
Indices: 3298244--3298282 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3298234 ATTTTTTATT
3298244 TA TA TA 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 TA TA TA T
3298283 TTACTTTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3298336 original size:16 final size:17
Alignment explanation
Indices: 3298315--3298350 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3298305 TATAATTTCT
*
3298315 TTTATTTCT-TTTTTTA
1 TTTATTACTATTTTTTA
3298331 TTTATTACTATTTTTTA
1 TTTATTACTATTTTTTA
3298348 TTT
1 TTT
3298351 TAATACTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTACTATTTTTTA
Found at i:3298352 original size:18 final size:17
Alignment explanation
Indices: 3298314--3298358 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
3298304 TTATAATTTC
*
3298314 TTTTATTTCTTTTTTTA
1 TTTTATTACTTTTTTTA
3298331 -TTTATTACTATTTTTTA
1 TTTTATTACT-TTTTTTA
*
3298348 TTTTAATACTT
1 TTTTATTACTT
3298359 ATTATTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 8 0.33
17 8 0.33
18 8 0.33
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTACTTTTTTTA
Found at i:3305744 original size:23 final size:21
Alignment explanation
Indices: 3305693--3305752 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 21
3305683 TTTGGTGCAT
* *
3305693 AGGGAATCGA-TCCCCCCTTG
1 AGGGAACCGATTCCCCCATTG
3305713 AGGGAACCGATTCCCCCATTG
1 AGGGAACCGATTCCCCCATTG
3305734 AAGGGGAACCGATTCCCCC
1 -A-GGGAACCGATTCCCCC
3305753 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 9 0.26
21 9 0.26
22 1 0.03
23 16 0.46
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.17
Consensus pattern (21 bp):
AGGGAACCGATTCCCCCATTG
Found at i:3305779 original size:20 final size:20
Alignment explanation
Indices: 3305694--3305779 Score: 66
Period size: 21 Copynumber: 4.1 Consensus size: 20
3305684 TTGGTGCATA
* *
3305694 GGGAATCGA-TCCCCCCTTG
1 GGGAACCGATTCCCCCCTAG
*
3305713 AGGGAACCGATTCCCCCATTGAAG
1 -GGGAACCGATTCCCCC-CT--AG
*
3305737 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCC-TAG
* *
3305758 GGGAATCGATACCCCCCTAG
1 GGGAACCGATTCCCCCCTAG
3305778 GG
1 GG
3305780 TTCTGGTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
20 12 0.23
21 23 0.43
22 1 0.02
23 16 0.30
24 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.27, T:0.15
Consensus pattern (20 bp):
GGGAACCGATTCCCCCCTAG
Done.