Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008228.1 Hibiscus syriacus cultivar Beakdansim tig00110864_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: 3739947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 20
Found at i:3349022 original size:45 final size:45
Alignment explanation
Indices: 3348956--3349042 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
3348946 TTGCGTTGGT
**
3348956 CAACAATGGAGGGTTTGTTTCACTTATATCAACCGCGAAGCCGGC
1 CAACAATGGAGGGTTCATTTCACTTATATCAACCGCGAAGCCGGC
* *
3349001 CAACAATGGAGGGTTCATTTCACTTATATGAATCGCGAAGCC
1 CAACAATGGAGGGTTCATTTCACTTATATCAACCGCGAAGCC
3349043 AATAACCTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (45 bp):
CAACAATGGAGGGTTCATTTCACTTATATCAACCGCGAAGCCGGC
Found at i:3351136 original size:3 final size:3
Alignment explanation
Indices: 3351128--3351243 Score: 148
Period size: 3 Copynumber: 38.3 Consensus size: 3
3351118 GTTTTTTAAT
* *
3351128 TTA TTA TTA TTT TTA TTA TT- TTA TCTA TTTA TTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA
*
3351174 TT- TTA TTA TTA TT- TTA TTA TTC TTA TTA TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
3351218 TTA TTTA TTA TTA TTA TTA TTA TTA T
1 TTA -TTA TTA TTA TTA TTA TTA TTA T
3351244 AAATTTATTA
Statistics
Matches: 100, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
2 6 0.06
3 83 0.83
4 10 0.10
5 1 0.01
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3351140 original size:16 final size:16
Alignment explanation
Indices: 3351128--3351243 Score: 148
Period size: 16 Copynumber: 7.2 Consensus size: 16
3351118 GTTTTTTAAT
3351128 TTATTATTATT-TTTA
1 TTATTATTATTATTTA
3351143 TTATT-TTATCTATTTA
1 TTATTATTAT-TATTTA
* *
3351159 TTACTATTATTATTATT
1 TTATTATTATTATT-TA
*
3351176 TTATTATTATTTTATTA
1 TTATTATTATTAT-TTA
*
3351193 TTCTTATTATTATTTA
1 TTATTATTATTATTTA
3351209 TTATTATTATTATTTA
1 TTATTATTATTATTTA
3351225 TTATTATTATTA-TTA
1 TTATTATTATTATTTA
3351240 TTAT
1 TTAT
3351244 AAATTTATTA
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
14 4 0.05
15 13 0.15
16 42 0.48
17 28 0.32
18 1 0.01
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTATTATTATTTA
Found at i:3351148 original size:19 final size:18
Alignment explanation
Indices: 3351128--3351243 Score: 130
Period size: 19 Copynumber: 6.4 Consensus size: 18
3351118 GTTTTTTAAT
3351128 TTATTATTATTTTTATTA
1 TTATTATTATTTTTATTA
*
3351146 TT-TTATCTATTTATTACTA
1 TTATTAT-TATTT-TTATTA
3351165 TTATTATTA-TTTTATTA
1 TTATTATTATTTTTATTA
* *
3351182 TTATT-TTATTATTCTTA
1 TTATTATTATTTTTATTA
*
3351199 TTATTATTTATTATTATTA
1 TTATTA-TTATTTTTATTA
*
3351218 TTATTTATTATTATTATTA
1 TTA-TTATTATTTTTATTA
3351237 TTATTAT
1 TTATTAT
3351244 AAATTTATTA
Statistics
Matches: 86, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
16 3 0.03
17 25 0.29
18 13 0.15
19 38 0.44
20 7 0.08
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTATTATTTTTATTA
Found at i:3351242 original size:28 final size:27
Alignment explanation
Indices: 3351128--3351243 Score: 141
Period size: 28 Copynumber: 4.3 Consensus size: 27
3351118 GTTTTTTAAT
3351128 TTATTATTATT-TTTATTATTTTATCTA
1 TTATTATTATTATTTATTATTTTAT-TA
*
3351155 TTTATTACTATTA-TTATTATTTTATTA
1 -TTATTATTATTATTTATTATTTTATTA
*
3351182 TTATT-TTATTA-TTCTTATTATTATTTA
1 TTATTATTATTATTTATTATT-TTA-TTA
3351209 TTATTATTATTATTTATTATTATTATTA
1 TTATTATTATTATTTATTATT-TTATTA
3351237 TTATTAT
1 TTATTAT
3351244 AAATTTATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
25 12 0.15
26 8 0.10
27 10 0.13
28 38 0.48
29 11 0.14
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (27 bp):
TTATTATTATTATTTATTATTTTATTA
Found at i:3352933 original size:2 final size:2
Alignment explanation
Indices: 3352926--3352963 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3352916 ATATCATGCT
3352926 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3352964 CTTCATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3355315 original size:34 final size:34
Alignment explanation
Indices: 3355219--3355316 Score: 117
Period size: 34 Copynumber: 2.8 Consensus size: 34
3355209 CAATTTACTT
* *
3355219 TTTTTATTTTTGCATTTCTACATCTTTGTATTTGCA
1 TTTTCATTTTTGCATTT-TA-ATCTTTGTATTTACA
* *
3355255 TTTGCATTTTTGCATTTTTA-CGTTTGTATTTACA
1 TTTTCATTTTTGCATTTTAATC-TTTGTATTTACA
*
3355289 TTTTCATTTTTGCATTTGAATCTTTGTA
1 TTTTCATTTTTGCATTTTAATCTTTGTA
3355317 AAATTATATT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
33 1 0.02
34 35 0.66
35 2 0.04
36 15 0.28
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.60
Consensus pattern (34 bp):
TTTTCATTTTTGCATTTTAATCTTTGTATTTACA
Found at i:3357188 original size:14 final size:14
Alignment explanation
Indices: 3357156--3357205 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
3357146 ATCAAAAAAG
3357156 AGAAAAAAAG-AGA
1 AGAAAAAAAGAAGA
*
3357169 TGAAAAAGAAGAAGA
1 AGAAAAA-AAGAAGA
*
3357184 A-AAAAAAGGAAAGA
1 AGAAAAAAAG-AAGA
3357198 AGAAAAAA
1 AGAAAAAA
3357206 TGAATCAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 8 0.27
14 13 0.43
15 9 0.30
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (14 bp):
AGAAAAAAAGAAGA
Found at i:3358303 original size:18 final size:18
Alignment explanation
Indices: 3358262--3358297 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3358252 GCAAGTGGTC
*
3358262 CAAGAAGCCAGAAAGTCT
1 CAAGAAGACAGAAAGTCT
3358280 CAAGAAGACAGAAAGTCT
1 CAAGAAGACAGAAAGTCT
3358298 GGAGAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.11
Consensus pattern (18 bp):
CAAGAAGACAGAAAGTCT
Found at i:3359021 original size:43 final size:43
Alignment explanation
Indices: 3358960--3359133 Score: 258
Period size: 43 Copynumber: 4.0 Consensus size: 43
3358950 GCCAAATCTA
* *
3358960 CTCATCAATTGCTCCAACCAATCACCATTCAGTTTTTGCACAT
1 CTCATCAATTGCTCCAACCGATCACCATTCAGTTCTTGCACAT
* *
3359003 CTCATCAATTGCTCCAACCGATCACCATTCAGCTCTTGTACAT
1 CTCATCAATTGCTCCAACCGATCACCATTCAGTTCTTGCACAT
* *
3359046 CTCATCAATTGCTTCAACCGATCACCATTCAGTTATTGCACAT
1 CTCATCAATTGCTCCAACCGATCACCATTCAGTTCTTGCACAT
* ** *
3359089 CTTATCAATTGCTCCAACCGATCATTATTCAGTTCTTACACAT
1 CTCATCAATTGCTCCAACCGATCACCATTCAGTTCTTGCACAT
3359132 CT
1 CT
3359134 GCCTTCAAAG
Statistics
Matches: 117, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 117 1.00
ACGTcount: A:0.27, C:0.32, G:0.08, T:0.33
Consensus pattern (43 bp):
CTCATCAATTGCTCCAACCGATCACCATTCAGTTCTTGCACAT
Found at i:3360779 original size:54 final size:54
Alignment explanation
Indices: 3360707--3360922 Score: 299
Period size: 54 Copynumber: 4.0 Consensus size: 54
3360697 CTGACCAGAA
* *
3360707 ATCTGTGCAGAAGCCACAGGAAAGGATGAATGTATTGACAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAAC
* * * *
3360761 ATATGAGCAGAAGTCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACAAAC
1 ATCTGAGCAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAAC
* * * *
3360815 ATCTGAGCAGAAGTCACAGGAAATGATGAATGTTTTGTTAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAAC
* * *
3360869 ATCTGTGCAGAAGCCACAAG-AAGAGATGAATGCATTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACAGGAAAG-GATGAATGTATTGTCAAATGTTTTACGAAC
3360923 CAGTGATTAT
Statistics
Matches: 143, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
53 2 0.01
54 141 0.99
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.26
Consensus pattern (54 bp):
ATCTGAGCAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAAC
Found at i:3362082 original size:37 final size:36
Alignment explanation
Indices: 3361991--3362160 Score: 110
Period size: 36 Copynumber: 4.7 Consensus size: 36
3361981 TTCAAATAGT
** **
3361991 AATTTATCTCACTTGAGATTA-TTTTTCTTAAAACA-
1 AATTTATCTCACTTGAGA-TAGTTTCACTCGAAACAC
* ** *
3362026 AATTGCATCTCGTTTGAGATAGTTTCACTCGAAATATC
1 AATT-TATCTCACTTGAGATAGTTTCACTCGAAACA-C
* * ** ** *
3362064 AATTTATCTCACTCGAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCACTTGAGATAGTTTCACTCGAAACAC
* * * *
3362100 AATTTGTCTCGCTTGCGACAGTTTCACTCGAAACAAC
1 AATTTATCTCACTTGAGATAGTTTCACTCGAAAC-AC
*
3362137 AATTTATCTCACTTGAGATTGTTT
1 AATTTATCTCACTTGAGATAGTTT
3362161 TTCTTAAAAA
Statistics
Matches: 95, Mismatches: 35, Indels: 8
0.69 0.25 0.06
Matches are distributed among these distances:
35 6 0.06
36 44 0.46
37 41 0.43
38 4 0.04
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (36 bp):
AATTTATCTCACTTGAGATAGTTTCACTCGAAACAC
Found at i:3362110 original size:73 final size:73
Alignment explanation
Indices: 3361991--3362207 Score: 305
Period size: 73 Copynumber: 3.0 Consensus size: 73
3361981 TTCAAATAGT
* * *
3361991 AATTTATCTCACTTGAGATTATTTTTCTTAAAAC-AAA-TTGCATCTCGTTTGAGATAGTTTCAC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTG--TCTCGCTTGAGACAGTTTCAC
* *
3362054 TCGAAATATC
64 TCGAAACAAC
* *
3362064 AATTTATCTCACTCGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGCGACAGTTTCACTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
3362129 GAAACAAC
66 GAAACAAC
*
3362137 AATTTATCTCACTTGAGATTGTTTTTCTTAAAA-AAAGATTCGTCTCGCTTGAGACAGTTTCACT
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-ATTTGTCTCGCTTGAGACAGTTTCACT
*
3362201 AGAAACA
65 CGAAACA
3362208 GAAATTTCCA
Statistics
Matches: 130, Mismatches: 11, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
72 3 0.02
73 121 0.93
74 3 0.02
75 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.38
Consensus pattern (73 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
GAAACAAC
Found at i:3362134 original size:36 final size:35
Alignment explanation
Indices: 3362094--3362214 Score: 107
Period size: 36 Copynumber: 3.3 Consensus size: 35
3362084 GTTTTTCTTA
*
3362094 AAACAAAATTTGTCTCGCTTGCGACAGTTTCACTCG
1 AAACAAAATTTGTCTCGCTTGAGACAGTTTCACT-G
* * ** ** *
3362130 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTT
1 AAACAA-AATTTGTCTCGCTTGAGACAGTTTCACTG
* *
3362166 AAAAAAAGATTCGTCTCGCTTGAGACAGTTTCACTAG
1 AAACAAA-ATTTGTCTCGCTTGAGACAGTTTCACT-G
3362203 AAACAGAAATTT
1 AAACA-AAATTT
3362215 CCATCACTCG
Statistics
Matches: 62, Mismatches: 19, Indels: 7
0.70 0.22 0.08
Matches are distributed among these distances:
35 1 0.02
36 31 0.50
37 28 0.45
38 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (35 bp):
AAACAAAATTTGTCTCGCTTGAGACAGTTTCACTG
Found at i:3362451 original size:20 final size:17
Alignment explanation
Indices: 3362402--3362443 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
3362392 TCTGAAGAGA
3362402 AAGAAGAAGTTCATAAT
1 AAGAAGAAGTTCATAAT
3362419 AAGAAGAAGTTCATAAT
1 AAGAAGAAGTTCATAAT
3362436 AAGAAGAA
1 AAGAAGAA
3362444 CTTGTTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.57, C:0.05, G:0.19, T:0.19
Consensus pattern (17 bp):
AAGAAGAAGTTCATAAT
Found at i:3362534 original size:140 final size:140
Alignment explanation
Indices: 3362282--3362566 Score: 480
Period size: 140 Copynumber: 2.0 Consensus size: 140
3362272 GAAGAGGCAT
*
3362282 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCCCAGAAGGAGATAAA
1 AAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCCCAGAAGGAGATAAA
* * * *
3362347 TCAGCACCAATATTTCCAGAGGAAGTTCATTATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGT
66 TCAGCACCAACATTTCCAGAGGAAATTCATAATGAGAAGAACTCATCTAAAGAGAAAGAAGAAGT
3362412 TCATAATAAG
131 TCATAATAAG
3362422 AAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCCCAGAAGGAGATAAA
1 AAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCCCAGAAGGAGATAAA
* * *
3362487 TCATCACCAACATTTCCAGAGGAAATTCATAATGAGAAGAACTCATCTAAAGAGGAATAAGAAGT
66 TCAGCACCAACATTTCCAGAGGAAATTCATAATGAGAAGAACTCATCTAAAGAGAAAGAAGAAGT
* *
3362552 TCATAGTGAG
131 TCATAATAAG
3362562 AAGAA
1 AAGAA
3362567 CTTGTTCAAC
Statistics
Matches: 135, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
140 135 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (140 bp):
AAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCCCAGAAGGAGATAAA
TCAGCACCAACATTTCCAGAGGAAATTCATAATGAGAAGAACTCATCTAAAGAGAAAGAAGAAGT
TCATAATAAG
Found at i:3362639 original size:123 final size:122
Alignment explanation
Indices: 3362419--3362825 Score: 636
Period size: 123 Copynumber: 3.3 Consensus size: 122
3362409 AGTTCATAAT
*
3362419 AAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCCCAGAAGGAGAT
1 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGATTCTAT-CCAGAAGGAGAT
* *
3362484 AAATCATCACCAACATTTCCAGAGGAAATTCATAATGAGAAGAACTCATCTAAAGAGG
65 AAATCAGCACCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTAAAGAGG
* *
3362542 AATAAGAAGTTCATAGTGAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCCTAGAAGGAGAT
1 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCC-AGAAGGAGAT
*
3362607 AAATCAGCACCACCATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTAAAGAGG
65 AAATCAGCACCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTAAAGAGG
*
3362665 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGAT
1 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATC-CAGAAGGAGAT
* * * ** *
3362730 AGATCAGCATCAACTTTTCCAGATAAAGTTCATAATGAGAAGAACTTATCTGAAA-AGG
65 AAATCAGCACCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCT-AAAGAGG
* *
3362788 AAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTT
1 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
3362826 GCCTTAATTC
Statistics
Matches: 263, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
122 2 0.01
123 257 0.98
124 4 0.02
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.26
Consensus pattern (122 bp):
AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCCAGAAGGAGATA
AATCAGCACCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTAAAGAGG
Found at i:3363210 original size:3 final size:3
Alignment explanation
Indices: 3363202--3363299 Score: 173
Period size: 3 Copynumber: 33.3 Consensus size: 3
3363192 GTTTATTTAT
*
3363202 TTA TTA TTA TTA TTA TT- TTA TTA CTA TTA TTA TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3363248 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3363296 TTA T
1 TTA T
3363300 AAATTTATTA
Statistics
Matches: 91, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
2 4 0.04
3 87 0.96
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3363803 original size:16 final size:16
Alignment explanation
Indices: 3363760--3363804 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3363750 CAACAGAGAG
3363760 CAAAACGCAACAACAAC
1 CAAAAC-CAACAACAAC
** *
3363777 CACGACAAACAACAAC
1 CAAAACCAACAACAAC
3363793 CAAAACCAACAA
1 CAAAACCAACAA
3363805 TCATCAAAGA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.60, C:0.36, G:0.04, T:0.00
Consensus pattern (16 bp):
CAAAACCAACAACAAC
Found at i:3364337 original size:13 final size:13
Alignment explanation
Indices: 3364319--3364343 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3364309 TTTTTATAAG
3364319 TTTTAATTTTGTC
1 TTTTAATTTTGTC
3364332 TTTTAATTTTGT
1 TTTTAATTTTGT
3364344 TTTATTATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTTAATTTTGTC
Found at i:3365149 original size:25 final size:23
Alignment explanation
Indices: 3365121--3365180 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 23
3365111 GATGTCATTT
3365121 TTTAATATATTAAATAAATAAATAC
1 TTTAATATATT-AATAAA-AAATAC
* *
3365146 TTTAATTATAATTCATAAAAATTAC
1 TTTAA-TAT-ATTAATAAAAAATAC
3365171 TTTAA-ATATT
1 TTTAATATATT
3365181 TTTCTTCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
22 3 0.10
23 2 0.06
25 15 0.48
26 8 0.26
27 3 0.10
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAATATATTAATAAAAAATAC
Found at i:3376295 original size:182 final size:180
Alignment explanation
Indices: 3375954--3376600 Score: 832
Period size: 182 Copynumber: 3.6 Consensus size: 180
3375944 ATCGATACAA
* * * * * **
3375954 ATAAAAATATATCGATCTATAACAGTATAACAGGTAAAAATATGATCAAACCGGTTTCATTATGA
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA-CAAACCAGTCTCAAAATGA
* * * * *
3376019 AAAAACCGGTAAAGCGCTACCTAATATGTTGAAAGTATCGATTCTATTGAAATAAGTATCGACAC
65 CAAAACCGGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATACT-TTGATATAAGTATCGACAC
*
3376084 TTTTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTCT
129 TTTTGGAATTTAAAAGAGAAGCAGTAATAG-GCCTATAAAGTGTCGATACTTT
* *
3376137 ATAAAATTGTATCGATCCATAACAGTATAACAGGTAAAAATATGATCAAACCAGTCTCAAAATGA
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA-CAAACCAGTCTCAAAATGA
* * * * *
3376202 CAAAACCGATAAAGAGCTACCGGATATGTTGAAAGTGTTGATACTTTGCTATAAGTATCGACACT
65 CAAAACCGGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATACTTTGATATAAGTATCGACACT
*
3376267 TTTGGAATTTAAAAGAGAAGCAGTAATAGTGCCTATAAAGTGTCGATATTTT
130 TTTGGAATTTAAAAGAGAAGCAGTAATAG-GCCTATAAAGTGTCGATACTTT
* * * *
3376319 ATAAAAATGTATTGGTCCATAACAATATAAAAGGTAAAAATATGACAAAACCGGTCTCAAAATGA
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAC-AAACCAGTCTCAAAATGA
* * * *
3376384 CAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATTGACACT
65 CAAAACCGGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATACTTTGATATAAGTATCGACACT
* *
3376449 TTTAGAATTTAAAAGATAAGC---AATA-----AT--AGTG-CTGATACTTT
130 TTTGGAATTTAAAAGAGAAGCAGTAATAGGCCTATAAAGTGTC-GATACTTT
* * *
3376490 ATAAAAATGTATCGATCCATAACAACATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGA
1 ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAACCA-GTCTCAAAATGA
3376555 C-AAACCGGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATACTTT
65 CAAAACCGGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATACTTT
3376601 AATAAATAAG
Statistics
Matches: 416, Mismatches: 45, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
170 48 0.12
171 65 0.16
173 2 0.00
179 4 0.01
181 1 0.00
182 201 0.48
183 95 0.23
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (180 bp):
ATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAACCAGTCTCAAAATGAC
AAAACCGGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATACTTTGATATAAGTATCGACACTT
TTGGAATTTAAAAGAGAAGCAGTAATAGGCCTATAAAGTGTCGATACTTT
Found at i:3378885 original size:9 final size:9
Alignment explanation
Indices: 3378861--3378905 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
3378851 TTGGCAAGGC
*
3378861 GGCAGAGGA
1 GGCAGTGGA
*
3378870 GGAAGTGGA
1 GGCAGTGGA
3378879 GGCAGTGGA
1 GGCAGTGGA
* *
3378888 TGTAGTGGA
1 GGCAGTGGA
3378897 GGCAGTGGA
1 GGCAGTGGA
3378906 AGCTATGGAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.27, C:0.07, G:0.53, T:0.13
Consensus pattern (9 bp):
GGCAGTGGA
Found at i:3378914 original size:18 final size:18
Alignment explanation
Indices: 3378873--3378916 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
3378863 CAGAGGAGGA
*
3378873 AGTGGAGGCAGTGGATGT
1 AGTGGAGGCAGTGGAAGT
3378891 AGTGGAGGCAGTGGAAGCT
1 AGTGGAGGCAGTGGAAG-T
3378910 A-TGGAGG
1 AGTGGAGG
3378917 AAGAGAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.25, C:0.07, G:0.50, T:0.18
Consensus pattern (18 bp):
AGTGGAGGCAGTGGAAGT
Found at i:3379227 original size:66 final size:66
Alignment explanation
Indices: 3379096--3379227 Score: 156
Period size: 66 Copynumber: 2.0 Consensus size: 66
3379086 AAGGGGGAAG
* * * *
3379096 TGGGTGGAAGAATAGATGGAGTGGTGAAAGAAGTTATGTAGTTGAGGGGTGAAGTTAAGATGGTG
1 TGGGTGGAAGAATAGATGGAGTGGTGAAAGAAGATATGGAGTTGAGGGGTGAACTTAAGAGGGTG
3379161 A
66 A
* * * * * * * *
3379162 TGGGTGGAATATTTGATGGAGTGGTGAAGGAAGATGTGGATTTGAGGGGTGAACTTACGGGGGTG
1 TGGGTGGAAGAATAGATGGAGTGGTGAAAGAAGATATGGAGTTGAGGGGTGAACTTAAGAGGGTG
3379227 A
66 A
3379228 AGGGAGTGGT
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.28, C:0.02, G:0.44, T:0.27
Consensus pattern (66 bp):
TGGGTGGAAGAATAGATGGAGTGGTGAAAGAAGATATGGAGTTGAGGGGTGAACTTAAGAGGGTG
A
Found at i:3379354 original size:18 final size:18
Alignment explanation
Indices: 3379331--3379388 Score: 98
Period size: 18 Copynumber: 3.2 Consensus size: 18
3379321 GAAAAAATAT
*
3379331 GAAGAAGAAAAGATAGAG
1 GAAGAAGAAAAGATGGAG
*
3379349 GAAGAAGGAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
3379367 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
3379385 GAAG
1 GAAG
3379389 TGAGAAGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.55, C:0.00, G:0.40, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:3383924 original size:199 final size:199
Alignment explanation
Indices: 3383597--3384666 Score: 1547
Period size: 199 Copynumber: 5.4 Consensus size: 199
3383587 AAAAATGAAC
* * * * * **
3383597 CGATCCTAAAAATATCAAAACTGATAATTATAATGTAATAGGTAAATTTACAATGTAACCAATAT
1 CGATCCCAAAAACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTAACCGGTAT
** *
3383662 ATTTATACCGGTTTTATGAGAGAATAGGTCAACATAATGTATCGACACTTTTTAAATTTGTGTCA
66 AAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGTATCGACACTTTTGAAATTTGTGTCA
*
3383727 ATACATTTTGTCCAGAATGAATGCCAAACTAGGTGCACGCATAAAGTGTCAATACATTTAAAATT
131 ATACATTTTGTCCAGAATGAATGCCAAACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATT
3383792 GTAT
196 GTAT
* * * * *
3383796 CGATTCCAAAAACATCGAAACCGATAATTACAATGTAATAGATAAGTTTACAATGTAACTGGTAG
1 CGATCCCAAAAACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTAACCGGTAT
* *
3383861 AAATATCCCGGTTTTATGAGAGAATAAGTCAACATAATGTATCGACACTTTTGAAATTTGTGTCA
66 AAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGTATCGACACTTTTGAAATTTGTGTCA
*
3383926 ATACATTTTTTCCAGAATGAATGCCAAACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATT
131 ATACATTTTGTCCAGAATGAATGCCAAACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATT
3383991 GTAT
196 GTAT
3383995 CGATCCCAAAAACAT------CG---A--A-AATGTAATAGGTAAATTTACAATGTAACCGGTAT
1 CGATCCCAAAAACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTAACCGGTAT
* * * * * * *
3384048 AAATAAACCAGTTTTATGAGAGATTAGGTCTACAGAATGTATTGACACTTTTGAAATTTGTGTCG
66 AAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGTATCGACACTTTTGAAATTTGTGTCA
* * *
3384113 ATACTTTTTGCCCAGAATGAATGACAAACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATT
131 ATACATTTTGTCCAGAATGAATGCCAAACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATT
3384178 GTAT
196 GTAT
* * *
3384182 TGATCCCAAAAACATCGAAACCGATAATTACAATGTAATAGTTAAATTTACAATGTAACCGATAT
1 CGATCCCAAAAACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTAACCGGTAT
** * * *
3384247 AAATATACCAATTTTATGAGAGAATAAGTCAATATAATGTATCGACAGTTTTGAAATTTGTGTCA
66 AAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGTATCGACACTTTTGAAATTTGTGTCA
*
3384312 ATACATTTTGCCCAGAATGAATGCCAAACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATT
131 ATACATTTTGTCCAGAATGAATGCCAAACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATT
* *
3384377 TTAA
196 GTAT
** * * * *
3384381 CGATCCCAAAAACATCGAAAATGATAATTACAATGTAATATGTAAATTTACAATGTAGCCAGTAC
1 CGATCCCAAAAACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTAACCGGTAT
*
3384446 AAATATACC-ATGTTTATGAGAGAATAGGTC-ACATAATGTATCGACACTTTTGAAATTTGTGTC
66 AAATATACCGGT-TTTATGAGAGAATAGGTCAACATAATGTATCGACACTTTTGAAATTTGTGTC
* * * *
3384509 GATATATTTTGTCCAGAATGAATGCCAGACTAGGTGTACGCATAAAGTGTCGATACATTTAAAAT
130 AATACATTTTGTCCAGAATGAATGCCAAACTAGGTGCACGCATAAAGTGTCGATACATTTAAAAT
3384574 TGTAT
195 TGTAT
* * *
3384579 CAATCCCAAAAACATCGAAACTGATAATTACAATGTAATAGGTAAATTTACAATTTAACCGGTAT
1 CGATCCCAAAAACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTAACCGGTAT
3384644 AAATATACCGGTTTTATGAGAGA
66 AAATATACCGGTTTTATGAGAGA
3384667 TTAGTTTTGA
Statistics
Matches: 776, Mismatches: 81, Indels: 29
0.88 0.09 0.03
Matches are distributed among these distances:
187 165 0.21
188 1 0.00
190 1 0.00
193 4 0.01
196 1 0.00
198 175 0.23
199 429 0.55
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (199 bp):
CGATCCCAAAAACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTAACCGGTAT
AAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGTATCGACACTTTTGAAATTTGTGTCA
ATACATTTTGTCCAGAATGAATGCCAAACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATT
GTAT
Found at i:3384341 original size:386 final size:385
Alignment explanation
Indices: 3383628--3384666 Score: 1569
Period size: 386 Copynumber: 2.7 Consensus size: 385
3383618 TGATAATTAT
* ** *
3383628 AATGTAATAGGTAAATTTACAATGTAACCAATATATTTATACCGGTTTTATGAGAGAATAGGTCA
1 AATGTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCAGTTTTATGAGAGAATAGGTC-
* * *
3383693 ACATAATGTATCGACACTTTTTAAATTTGTGTCAATACATTTTGTCCAGAATGAATGCCAAACTA
65 ACATAATGTATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACTA
* *
3383758 GGTGCACGCATAAAGTGTCAATACATTTAAAATTGTATCGATTCCAAAAACATCGAAACCGATAA
130 GGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAA
* * * *
3383823 TTACAATGTAATAGATAAGTTTACAATGTAACTGGTAGAAATATCCCGGTTTTATGAGAGAATAA
195 TTACAATGTAATAGATAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAA
**
3383888 GTCAACATAATGTATCGACACTTTTGAAATTTGTGTCAATACATTTTTTCCAGAATGAATGCCAA
260 GTCAACATAATGTATCGACACTTTTGAAATTTGTGTCAATACATTTTGCCCAGAATGAATGCCAA
*
3383953 ACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAA
325 ACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTAACGATCCCAAAAACATCGAA
* * *
3384014 AATGTAATAGGTAAATTTACAATGTAACCGGTATAAATAAACCAGTTTTATGAGAGATTAGGTCT
1 AATGTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCAGTTTTATGAGAGAATAGGTC-
* * * *
3384079 ACAGAATGTATTGACACTTTTGAAATTTGTGTCGATACTTTTTGCCCAGAATGAATGACAAACTA
65 ACATAATGTATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACTA
*
3384144 GGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATTGATCCCAAAAACATCGAAACCGATAA
130 GGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAA
* * **
3384209 TTACAATGTAATAGTTAAATTTACAATGTAACCGATATAAATATACCAATTTTATGAGAGAATAA
195 TTACAATGTAATAGATAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAA
* *
3384274 GTCAATATAATGTATCGACAGTTTTGAAATTTGTGTCAATACATTTTGCCCAGAATGAATGCCAA
260 GTCAACATAATGTATCGACACTTTTGAAATTTGTGTCAATACATTTTGCCCAGAATGAATGCCAA
*
3384339 ACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATTTTAACGATCCCAAAAACATCGAA
325 ACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTAACGATCCCAAAAACATCGAA
* *
3384400 AATGATAATTACAATGTAATATGTAAATTTACAATGTAGCCAGTACAAATATACCA-TGTTTATG
1 AATG-TAA-T---A-G------GTAAATTTACAATGTAACCAGTATAAATATACCAGT-TTTATG
3384464 AGAGAATAGGTCACATAATGTATCGACACTTTTGAAATTTGTGTCGATA-TATTTTGTCCAGAAT
53 AGAGAATAGGTCACATAATGTATCGACACTTTTGAAATTTGTGTCGATACT-TTTTGTCCAGAAT
* * *
3384528 GAATGCCAGACTAGGTGTACGCATAAAGTGTCGATACATTTAAAATTGTATCAATCCCAAAAACA
117 GAATGCCAAACTAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACA
* * *
3384593 TCGAAACTGATAATTACAATGTAATAGGTAAATTTACAATTTAACCGGTATAAATATACCGGTTT
182 TCGAAACCGATAATTACAATGTAATAGATAAATTTACAATGTAACCGGTATAAATATACCGGTTT
3384658 TATGAGAGA
247 TATGAGAGA
3384667 TTAGTTTTGA
Statistics
Matches: 588, Mismatches: 51, Indels: 17
0.90 0.08 0.03
Matches are distributed among these distances:
386 358 0.61
387 3 0.01
388 1 0.00
391 1 0.00
392 1 0.00
396 1 0.00
397 176 0.30
398 47 0.08
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (385 bp):
AATGTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCAGTTTTATGAGAGAATAGGTCA
CATAATGTATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACTAG
GTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCGAAACCGATAAT
TACAATGTAATAGATAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAAG
TCAACATAATGTATCGACACTTTTGAAATTTGTGTCAATACATTTTGCCCAGAATGAATGCCAAA
CTAGGTGCACGCATAAAGTGTCGATACATTTAAAATTGTAACGATCCCAAAAACATCGAA
Found at i:3385942 original size:47 final size:45
Alignment explanation
Indices: 3385862--3385971 Score: 125
Period size: 47 Copynumber: 2.4 Consensus size: 45
3385852 TATAAAATCC
3385862 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
3385907 CTTACCATTTAAATTCCATAAGCT-GATAAGTTTATTTTATCAATATA
1 CTTACCATTT--ATCCCATAAGCTCG-TAAGCTTATTTTACCAAAATA
* *
3385954 CTTGCCA-TTATTCCATAA
1 CTTACCATTTATCCCATAA
3385972 CCATATACCA
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
44 9 0.16
45 10 0.18
46 3 0.05
47 35 0.61
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:3386873 original size:255 final size:255
Alignment explanation
Indices: 3386422--3386932 Score: 995
Period size: 255 Copynumber: 2.0 Consensus size: 255
3386412 ATGTCAATTT
3386422 ATAAAAAATGATATAAAATCATGTCGATATAAACAAGGTCGACTTATCGCAAGTCTTCCTGATGA
1 ATAAAAAATGATATAAAATCATGTCGATATAAACAAGGTCGACTTATCGCAAGTCTTCCTGATGA
3386487 TGTATAAAACATCCATGTATAATTTCATGCATGTATTGCACTCACCTTGACACTTTATGTCTTTC
66 TGTATAAAACATCCATGTATAATTTCATGCATGTATTGCACTCACCTTGACACTTTATGTCTTTC
3386552 AAAATATATGAGCCTCACTATTGATCCACAATAAACCCTCTTGATTTGCTTCAATCGCAAATCAA
131 AAAATATATGAGCCTCACTATTGATCCACAATAAACCCTCTTGATTTGCTTCAATCGCAAATCAA
*
3386617 TCATAATTTGTATAATTCACAAATTCATAATGATATATATATTAGTATTGTACTAACATA
196 TCATAATTTATATAATTCACAAATTCATAATGATATATATATTAGTATTGTACTAACATA
3386677 ATAAAAAATGATATAAAATCATGTCGATATAAACAAGGTCGACTTATCGCAAGTCTTCCTGATGA
1 ATAAAAAATGATATAAAATCATGTCGATATAAACAAGGTCGACTTATCGCAAGTCTTCCTGATGA
3386742 TGTATAAAACATCCATGTATAATTTCATGCATGTATTGCACTCACCTTGACACTTTATGTCTTTC
66 TGTATAAAACATCCATGTATAATTTCATGCATGTATTGCACTCACCTTGACACTTTATGTCTTTC
*
3386807 AAAATATATTAGCCTCACTATTGATCCACAATAAACCCTCTTGATTTGCTTCAATCGCAAATCAA
131 AAAATATATGAGCCTCACTATTGATCCACAATAAACCCTCTTGATTTGCTTCAATCGCAAATCAA
*
3386872 TCATAATTTATATAATTCACAAATTCATAATGATATATATGTTAGTATTGTACTAACATA
196 TCATAATTTATATAATTCACAAATTCATAATGATATATATATTAGTATTGTACTAACATA
3386932 A
1 A
3386933 ACATATCCCA
Statistics
Matches: 253, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
255 253 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (255 bp):
ATAAAAAATGATATAAAATCATGTCGATATAAACAAGGTCGACTTATCGCAAGTCTTCCTGATGA
TGTATAAAACATCCATGTATAATTTCATGCATGTATTGCACTCACCTTGACACTTTATGTCTTTC
AAAATATATGAGCCTCACTATTGATCCACAATAAACCCTCTTGATTTGCTTCAATCGCAAATCAA
TCATAATTTATATAATTCACAAATTCATAATGATATATATATTAGTATTGTACTAACATA
Found at i:3393914 original size:21 final size:21
Alignment explanation
Indices: 3393890--3393969 Score: 90
Period size: 23 Copynumber: 3.8 Consensus size: 21
3393880 TTGGTGCAGA
*
3393890 GGGAATCGATACCCCCTGAAG
1 GGGAACCGATACCCCCTGAAG
*
3393911 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC--TGAAG
* *
3393934 GGGAACCGATTCCCCCT-TAG
1 GGGAACCGATACCCCCTGAAG
*
3393954 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
3393970 ACGGGGTCTG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.31
21 15 0.29
23 21 0.40
ACGTcount: A:0.24, C:0.33, G:0.26, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCCCTGAAG
Found at i:3393936 original size:23 final size:23
Alignment explanation
Indices: 3393890--3393951 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
3393880 TTGGTGCAGA
* *
3393890 GGGAATCGATACCCCC--TGAAG
1 GGGAACCGATTCCCCCTTTGAAG
3393911 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
3393934 GGGAACCGATTCCCCCTT
1 GGGAACCGATTCCCCCTT
3393952 AGGGGAATCG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.38
23 23 0.62
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:3395048 original size:15 final size:16
Alignment explanation
Indices: 3395023--3395053 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3395013 GCCAACACAT
3395023 CAGGATTAGATAATGA
1 CAGGATTAGATAATGA
3395039 CAGG-TTAGATAATGA
1 CAGGATTAGATAATGA
3395054 AAAACAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
CAGGATTAGATAATGA
Found at i:3397784 original size:15 final size:15
Alignment explanation
Indices: 3397764--3397810 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
3397754 TTTCTCAAAG
*
3397764 CTCTTCTCAACCAAC
1 CTCTTCTTAACCAAC
3397779 CTCTTCTTAACGACAAC
1 CTCTTCTTAAC--CAAC
3397796 CTTCTTCTTAACCAA
1 C-TCTTCTTAACCAA
3397811 TCGCTTCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.36
16 3 0.11
17 5 0.18
18 10 0.36
ACGTcount: A:0.28, C:0.38, G:0.02, T:0.32
Consensus pattern (15 bp):
CTCTTCTTAACCAAC
Found at i:3401794 original size:15 final size:15
Alignment explanation
Indices: 3401774--3401804 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3401764 ATGTATCGAC
3401774 ACATAAAGTTTCCAA
1 ACATAAAGTTTCCAA
3401789 ACATAAAGTTTCCAA
1 ACATAAAGTTTCCAA
3401804 A
1 A
3401805 AAAGTGTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (15 bp):
ACATAAAGTTTCCAA
Found at i:3402284 original size:199 final size:199
Alignment explanation
Indices: 3401914--3402453 Score: 787
Period size: 199 Copynumber: 2.7 Consensus size: 199
3401904 GTAAACAAAT
* ** * * *
3401914 GTGTCGATACATTTATTAAA-AGTATCAATCCCCAAAATATCAAAACCGATAATTATAATATAAT
1 GTGTCGATACATTTA--AAATTGTATCAATCCAAAAAATATCGAAACTGATAATTATAATGTAAT
* * * *
3401978 AAGTAAATTTACAATGTAACCGGTAGAAATATACCAGTTTTATGAGAAAATAGGTATTCATAATG
64 AGGTAACTTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTATACATAATG
* * * *
3402043 TATCGACACTTTTTAAATTTGTATTGATACTTTTTGTCCAGAATGAATGCCCAACAAGGTGCACA
129 TATCGACACTTTTTAAATTTGTATCGATACATTTTATCCAGAATGAATGCCCAACAAGATGCACA
3402108 CATAAA
194 CATAAA
* *
3402114 GTGTCGATACATTTAAAATTGTATCAATCCTAAAAATATCGAAATTGATAATTATAATGTAATAG
1 GTGTCGATACATTTAAAATTGTATCAATCCAAAAAATATCGAAACTGATAATTATAATGTAATAG
* * *
3402179 GTAACTTTACAATGTAACCGGTAGAAATATACCGGTTATATGAGCAAATAGGTCTACATAATGTA
66 GTAACTTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTATACATAATGTA
* * **
3402244 TCGACACTTTTTAAATTTGTGTCGATACATTTTATCCAGAATGAATGCCCAACGAGATGCATGCA
131 TCGACACTTTTTAAATTTGTATCGATACATTTTATCCAGAATGAATGCCCAACAAGATGCACACA
3402309 TAAA
196 TAAA
* * * *
3402313 GTGTCAATATATTTAAAATTGTATCAAT-CAAAAAACATTGAAACTGATAATTATAATGTAATAG
1 GTGTCGATACATTTAAAATTGTATCAATCCAAAAAATATCGAAACTGATAATTATAATGTAATAG
* *
3402377 GTAACTTTACAATGTAACCGGTAAAAATATACTGGTTTTATGAGAAAATAGGTATACATAATGTA
66 GTAACTTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTATACATAATGTA
3402442 TCGACACTTTTT
131 TCGACACTTTTT
3402454 GTCCAGAATG
Statistics
Matches: 306, Mismatches: 33, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
198 107 0.35
199 184 0.60
200 15 0.05
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (199 bp):
GTGTCGATACATTTAAAATTGTATCAATCCAAAAAATATCGAAACTGATAATTATAATGTAATAG
GTAACTTTACAATGTAACCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTATACATAATGTA
TCGACACTTTTTAAATTTGTATCGATACATTTTATCCAGAATGAATGCCCAACAAGATGCACACA
TAAA
Found at i:3402602 original size:177 final size:177
Alignment explanation
Indices: 3402273--3402631 Score: 506
Period size: 177 Copynumber: 2.0 Consensus size: 177
3402263 TGTCGATACA
* * *
3402273 TTTTATCCAGAATGAATGCCCAACGAGATGCATGCATAAAGTGTCAATATATTTAAAATTGTATC
1 TTTTATCCAGAATGAATGCCCAACGAGATGCAAGCATAAAGTGTCAATACATTTAAAATTGTAAC
** * *
3402338 AATCAAAAAACATTGAAACTGATAATTATAATGTAATAGGTAACTTTACAATGTAACCGGTAAAA
66 AATCAAAAAACATCAAAACCGATAATTATAATGTAATAGGTAACTTTACAATGTAACCAGTAAAA
** * *
3402403 ATATACTGGTTTTATGAGAAAATAGGT-ATACATAATGTATCGACACT
131 ATATACCAGTTTAATGAGAAAATAGGTCA-ACATAATATATCGACACT
* * *
3402450 TTTTGTCCAGAATGAATGCCCAACGAGGTGCAAGCATAAAGTGTCGATACATTTAAAATTGTAAC
1 TTTTATCCAGAATGAATGCCCAACGAGATGCAAGCATAAAGTGTCAATACATTTAAAATTGTAAC
* * * *
3402515 GATCCCAAAAACATCAAAACCGATAATTATAATGTAATAGGTAACTTTACAATGTAACTAGTAGA
66 AAT-CAAAAAACATCAAAACCGATAATTATAATGTAATAGGTAACTTTACAATGTAACCAGTAAA
* *
3402580 AATATACCAG-TTAATTAGAAAATAGGTCAACATAATATATCGATACT
130 AATATACCAGTTTAATGAGAAAATAGGTCAACATAATATATCGACACT
3402627 TTTTA
1 TTTTA
3402632 AATTGTGTCA
Statistics
Matches: 159, Mismatches: 21, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
177 96 0.60
178 63 0.40
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (177 bp):
TTTTATCCAGAATGAATGCCCAACGAGATGCAAGCATAAAGTGTCAATACATTTAAAATTGTAAC
AATCAAAAAACATCAAAACCGATAATTATAATGTAATAGGTAACTTTACAATGTAACCAGTAAAA
ATATACCAGTTTAATGAGAAAATAGGTCAACATAATATATCGACACT
Found at i:3402782 original size:197 final size:199
Alignment explanation
Indices: 3402438--3402849 Score: 600
Period size: 198 Copynumber: 2.1 Consensus size: 199
3402428 GTATACATAA
* * * *
3402438 TGTATCGACACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCAAGCATAAAGTGTCGATACATT
1 TGTATCAATACTTTTTGTCCAGAATAAATGCCAAACGAGGTGCAAGCATAAAGTGTCGATACATT
* * *
3402503 TAAAATTGTAACGATCCCAAAAACATCAAAACCGATAATTATAATGTAATAGGTAACTTTACAAT
66 TAAAATAGTAACGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAAT
* *
3402568 GTAACTAGTAGAAATATACCAGT-TAATTAGAAAATAGGTCAACATAATATATCGATACTTTTTA
131 GTAACCAGTAGAAATATACCAGTATAATTAAAAAATAGGTCAACATAATATATCGATACTTTTTA
3402632 AA-T
196 AATT
* *
3402635 TGTGTCAATACTTTTTGTCCAGAATAAAAT-CCAAACGAGGTGCATGCATAAAGTGTCGATACAT
1 TGTATCAATACTTTTTGTCCAGAAT-AAATGCCAAACGAGGTGCAAGCATAAAGTGTCGATACAT
* *
3402699 TTATTAAA-AGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTA-
65 TTA--AAATAGTAACGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTAC
* * * *
3402762 AATTTAACCGGTAGAAATATACCGGTATAATTAAAAAATAGGTCAACATAATATTTCGATACTTT
128 AATGTAACCAGTAGAAATATACCAGTATAATTAAAAAATAGGTCAACATAATATATCGATACTTT
3402827 TTAAATT
193 TTAAATT
*
3402834 TGTATCAATATTTTTT
1 TGTATCAATACTTTTT
3402850 TAAAATTACA
Statistics
Matches: 191, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
197 79 0.41
198 94 0.49
199 18 0.09
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (199 bp):
TGTATCAATACTTTTTGTCCAGAATAAATGCCAAACGAGGTGCAAGCATAAAGTGTCGATACATT
TAAAATAGTAACGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAAT
GTAACCAGTAGAAATATACCAGTATAATTAAAAAATAGGTCAACATAATATATCGATACTTTTTA
AATT
Found at i:3405193 original size:23 final size:23
Alignment explanation
Indices: 3405145--3405194 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
3405135 ACATACTTTA
* *
3405145 TTATATAAGCGCTACTTATTACG
1 TTATATAAGCGCTACCTAATACG
* *
3405168 TTATATAATCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
3405191 TTAT
1 TTAT
3405195 TGTGCTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:3405291 original size:158 final size:158
Alignment explanation
Indices: 3404999--3405855 Score: 1425
Period size: 158 Copynumber: 5.4 Consensus size: 158
3404989 AGTAAGTAAT
* * * * * *
3404999 TACCTATTACGTTACAT-ATGCTCTACGTAATATGTTATTATGCTTGATAATGTTTCTAGTAATT
1 TACCTATTACGTTATATAAT-CGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAAT
3405063 AACC-TGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTA
65 AACCGT-TTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTA
* *
3405127 AGTAATTAACATACTTTATTATATAAGCGC
129 AGTAATTAACCTATTTTATTATATAAGCGC
*
3405157 TACTTATTACGTTATATAATCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATA
1 TACCTATTACGTTATATAATCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATA
*
3405222 ACCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAG
66 ACCGTTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAG
3405287 TAATTAACCTATTTTATTATATAAGCGC
131 TAATTAACCTATTTTATTATATAAGCGC
* *
3405315 TATCTATTACGTTATATAATCGCTACCTAATATGTTATTGTGCTTGAT-ATGTTTCCAATAAATA
1 TACCTATTACGTTATATAATCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATA
*
3405379 ACCGTTTATATTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAG
66 ACCGTTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAG
3405444 TAATTAACCTATTTTATTATATAAGCGC
131 TAATTAACCTATTTTATTATATAAGCGC
*
3405472 TACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATA
1 TACCTATTACGTTATATAATCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATA
* * *
3405537 TCCGTTTATGTTATCCTTGGTAATATTTTAGACGTTTACCTAATATGTTGTAATAACAAATTAAG
66 ACCGTTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAG
* *
3405602 TAATTATCCTATTTTATTATATAAGCAC
131 TAATTAACCTATTTTATTATATAAGCGC
* *
3405630 TACATATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATA
1 TACCTATTACGTTATATAATCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATA
* *
3405695 ACTGTTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATATTGTAATAACAAATTAAG
66 ACCGTTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAG
3405760 TAATTAACCTATTTTATTATATAAGCGC
131 TAATTAACCTATTTTATTATATAAGCGC
* * *
3405788 TACCTATTACGTTATATAAGT-GTTACCTAATATGTTATTGTGCTTGATAATATTTCCAGTAATT
1 TACCTATTACGTTATATAA-TCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAAT
3405852 AACC
65 AACC
3405856 TATTTTAATA
Statistics
Matches: 657, Mismatches: 38, Indels: 8
0.93 0.05 0.01
Matches are distributed among these distances:
157 152 0.23
158 503 0.77
159 2 0.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (158 bp):
TACCTATTACGTTATATAATCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATA
ACCGTTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAG
TAATTAACCTATTTTATTATATAAGCGC
Found at i:3405351 original size:23 final size:23
Alignment explanation
Indices: 3405303--3405352 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
3405293 ACCTATTTTA
* *
3405303 TTATATAAGCGCTATCTATTACG
1 TTATATAAGCGCTACCTAATACG
* *
3405326 TTATATAATCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
3405349 TTAT
1 TTAT
3405353 TGTGCTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:3405476 original size:23 final size:23
Alignment explanation
Indices: 3405450--3405500 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
3405440 TAAGTAATTA
**
3405450 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
3405473 ACCTATTACGTTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
3405496 ACCTA
1 ACCTA
3405501 ATATGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:3405508 original size:23 final size:23
Alignment explanation
Indices: 3405460--3405509 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
3405450 ACCTATTTTA
*
3405460 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
*
3405483 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
3405506 TTAT
1 TTAT
3405510 TGTGCTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:3405620 original size:315 final size:315
Alignment explanation
Indices: 3405002--3405855 Score: 1426
Period size: 315 Copynumber: 2.7 Consensus size: 315
3404992 AAGTAATTAC
* * * * * *
3405002 CTATTACGTTACAT-ATGCTCTACGTAATATGTTATTATGCTTGATAATGTTTCTAGTAATTAAC
1 CTATTACGTTATATAAT-CGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATAAC
3405066 C-TGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
65 CGT-TTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGT
* * * *
3405130 AATTAACATACTTTATTATATAAGCGCTACTTATTACGTTATATAATCGCTACCTAATATGTTAT
129 AATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTAT
*
3405195 TGTGCTTGATAATGTTTCCAGTAAATAACCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTA
194 TGTGCTTGATAATGTTTCCAGTAAATAACCGGTTATGTTATCCTTGGTAACATTTTAGACGTTTA
*
3405260 CCTAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTTATTATATAAGCGCTA
259 CCTAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTTATTATATAAGCACTA
*
3405317 TCTATTACGTTATATAATCGCTACCTAATATGTTATTGTGCTTGAT-ATGTTTCCAATAAATAAC
1 -CTATTACGTTATATAATCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATAAC
*
3405381 CGTTTATATTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTA
65 CGTTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTA
3405446 ATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATT
130 ATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATT
* * *
3405511 GTGCTTGATAATGTTTCCAGTAAATATCCGTTTATGTTATCCTTGGTAATATTTTAGACGTTTAC
195 GTGCTTGATAATGTTTCCAGTAAATAACCGGTTATGTTATCCTTGGTAACATTTTAGACGTTTAC
*
3405576 CTAATATGTTGTAATAACAAATTAAGTAATTATCCTATTTTATTATATAAGCACTA
260 CTAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTTATTATATAAGCACTA
*
3405632 CATATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATAAC
1 C-TATTACGTTATATAATCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATAAC
* *
3405697 TGTTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATATTGTAATAACAAATTAAGTA
65 CGTTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTA
* *
3405762 ATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGTGTTACCTAATATGTTATT
130 ATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATT
* *
3405827 GTGCTTGATAATATTTCCAGTAATTAACC
195 GTGCTTGATAATGTTTCCAGTAAATAACC
3405856 TATTTTAATA
Statistics
Matches: 506, Mismatches: 28, Indels: 8
0.93 0.05 0.01
Matches are distributed among these distances:
314 1 0.00
315 296 0.58
316 207 0.41
317 2 0.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (315 bp):
CTATTACGTTATATAATCGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAAATAACC
GTTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTAATAACAAATTAAGTAA
TTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTG
TGCTTGATAATGTTTCCAGTAAATAACCGGTTATGTTATCCTTGGTAACATTTTAGACGTTTACC
TAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTTATTATATAAGCACTA
Found at i:3405666 original size:23 final size:23
Alignment explanation
Indices: 3405618--3405667 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
3405608 TCCTATTTTA
*
3405618 TTATATAAGCACTACATATTACG
1 TTATATAAGCACTACATAATACG
* * *
3405641 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCACTACATAATACG
3405664 TTAT
1 TTAT
3405668 TGTGCTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (23 bp):
TTATATAAGCACTACATAATACG
Found at i:3405802 original size:23 final size:23
Alignment explanation
Indices: 3405776--3405825 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
3405766 ACCTATTTTA
*
3405776 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
* * *
3405799 TTATATAAGTGTTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
3405822 TTAT
1 TTAT
3405826 TGTGCTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:3405904 original size:87 final size:87
Alignment explanation
Indices: 3405758--3405931 Score: 276
Period size: 87 Copynumber: 2.0 Consensus size: 87
3405748 TAACAAATTA
* * ** * *
3405758 AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGTGTTACCTAATATGT
1 AGTAATTAACCTATTTTAATATATAAGCGCTACCTATTACATTATATAAACGGTACCTAATATGC
*
3405823 TATTGTGCTTGATAATATTTCC
66 TATTGTACTTGATAATATTTCC
*
3405845 AGTAATTAACCTATTTTAATATATAAGCGTTACCTATTACATTATATAAACGGTACCTAATATGC
1 AGTAATTAACCTATTTTAATATATAAGCGCTACCTATTACATTATATAAACGGTACCTAATATGC
3405910 TATTGTACTTGATAATATTTCC
66 TATTGTACTTGATAATATTTCC
3405932 GGTTAAATGA
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 79 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.42
Consensus pattern (87 bp):
AGTAATTAACCTATTTTAATATATAAGCGCTACCTATTACATTATATAAACGGTACCTAATATGC
TATTGTACTTGATAATATTTCC
Found at i:3407445 original size:83 final size:85
Alignment explanation
Indices: 3407348--3407511 Score: 278
Period size: 83 Copynumber: 2.0 Consensus size: 85
3407338 TATTTTGAAA
* *
3407348 AAAAGGTGATATTTTGGTAATTATTTCAAAAAAGTGATATTTTGGTAATTATTTCGAAAAA-GTG
1 AAAAGGTGATATTTTGATAATTATTTCAAAAAAGTGATATTTTGGTAATTATTTCAAAAAAGGTG
*
3407412 ATATTTTGGTAATTATTTCG
66 ATATTTTCGTAATTATTTCG
*
3407432 AAAA-GTGATATTTTGATAATTATTTCGAAAAAGTGATATTTTGGTAATTATTTCAAAAAAGGTG
1 AAAAGGTGATATTTTGATAATTATTTCAAAAAAGTGATATTTTGGTAATTATTTCAAAAAAGGTG
3407496 ATATTTTCGTAATTAT
66 ATATTTTCGTAATTAT
3407512 AAAAAAATTT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
83 53 0.71
84 22 0.29
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.43
Consensus pattern (85 bp):
AAAAGGTGATATTTTGATAATTATTTCAAAAAAGTGATATTTTGGTAATTATTTCAAAAAAGGTG
ATATTTTCGTAATTATTTCG
Found at i:3407454 original size:55 final size:55
Alignment explanation
Indices: 3407347--3407511 Score: 269
Period size: 55 Copynumber: 2.9 Consensus size: 55
3407337 ATATTTTGAA
3407347 AAAAAGGTGATATTTTGGTAATTATTTCAAAAAAGTGATATTTTGGTAATTATTTCG
1 AAAAA-GTGATATTTTGGTAATTATTTCAAAAAAGTGATATTTT-GTAATTATTTCG
*
3407404 AAAAAGTGATATTTTGGTAATTATTTC-GAAAAGTGATATTTTGATAATTATTTCG
1 AAAAAGTGATATTTTGGTAATTATTTCAAAAAAGTGATATTTTG-TAATTATTTCG
3407459 AAAAAGTGATATTTTGGTAATTATTTCAAAAAAGGTGATATTTTCGTAATTAT
1 AAAAAGTGATATTTTGGTAATTATTTCAAAAAA-GTGATATTTT-GTAATTAT
3407512 AAAAAAATTT
Statistics
Matches: 102, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
54 1 0.01
55 52 0.51
56 26 0.25
57 22 0.22
58 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (55 bp):
AAAAAGTGATATTTTGGTAATTATTTCAAAAAAGTGATATTTTGTAATTATTTCG
Found at i:3407518 original size:28 final size:28
Alignment explanation
Indices: 3407346--3407511 Score: 262
Period size: 28 Copynumber: 5.9 Consensus size: 28
3407336 AATATTTTGA
3407346 AAAAAAGGTGATATTTTGGTAATTATTTC
1 AAAAAA-GTGATATTTTGGTAATTATTTC
3407375 AAAAAAGTGATATTTTGGTAATTATTTC
1 AAAAAAGTGATATTTTGGTAATTATTTC
*
3407403 GAAAAAGTGATATTTTGGTAATTATTTC
1 AAAAAAGTGATATTTTGGTAATTATTTC
* *
3407431 -GAAAAGTGATATTTTGATAATTATTTC
1 AAAAAAGTGATATTTTGGTAATTATTTC
*
3407458 GAAAAAGTGATATTTTGGTAATTATTTC
1 AAAAAAGTGATATTTTGGTAATTATTTC
*
3407486 AAAAAAGGTGATATTTTCGTAATTAT
1 AAAAAA-GTGATATTTTGGTAATTAT
3407512 AAAAAAATTT
Statistics
Matches: 128, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
27 25 0.20
28 79 0.62
29 24 0.19
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (28 bp):
AAAAAAGTGATATTTTGGTAATTATTTC
Found at i:3407529 original size:83 final size:82
Alignment explanation
Indices: 3407345--3407533 Score: 238
Period size: 83 Copynumber: 2.3 Consensus size: 82
3407335 AAATATTTTG
* *
3407345 AAAAAAAGGTGATATTTTGGTAATTATTTCAAAAAAGTGATATTTTGGTAATTATTTCGAAAAAG
1 AAAAAAA-GTAATATTTT-GTAATTATTTCAAAAAAGTGATATTTTGGTAATTATTTCAAAAAAG
*
3407410 TGATATTTTGGTAATTATT
64 TGATATTTTCGTAATTATT
*** * *
3407429 TCGAAAAGTGATATTTTGATAATTATTTCGAAAAAGTGATATTTTGGTAATTATTTCAAAAAAGG
1 AAAAAAAGTAATATTTTG-TAATTATTTCAAAAAAGTGATATTTTGGTAATTATTTCAAAAAA-G
3407494 TGATATTTTCGTAATTA-T
64 TGATATTTTCGTAATTATT
*
3407512 AAAAAAATTTAAT-TTTTGTAAT
1 AAAAAAA-GTAATATTTTGTAAT
3407534 AGTTGACTGT
Statistics
Matches: 91, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
82 5 0.05
83 62 0.68
84 24 0.26
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (82 bp):
AAAAAAAGTAATATTTTGTAATTATTTCAAAAAAGTGATATTTTGGTAATTATTTCAAAAAAGTG
ATATTTTCGTAATTATT
Found at i:3415392 original size:17 final size:19
Alignment explanation
Indices: 3415367--3415401 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
3415357 TCTTTTCTTA
3415367 CATTCTTTATTTT-CAAAT
1 CATTCTTTATTTTGCAAAT
3415385 CATT-TTTATTTTGCAAA
1 CATTCTTTATTTTGCAAA
3415402 CTATGCTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.14, G:0.03, T:0.54
Consensus pattern (19 bp):
CATTCTTTATTTTGCAAAT
Found at i:3421129 original size:21 final size:22
Alignment explanation
Indices: 3421105--3421158 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 22
3421095 ATATGCCTTA
3421105 GGGTATCGGTACCACCTA-AGG
1 GGGTATCGGTACCACCTATAGG
* *
3421126 GGGTATC-G-A-TACCTATGGG
1 GGGTATCGGTACCACCTATAGG
3421145 GGGTATCGGTACCA
1 GGGTATCGGTACCA
3421159 TCCGAGCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
18 5 0.19
19 10 0.38
20 2 0.08
21 8 0.31
22 1 0.04
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.22
Consensus pattern (22 bp):
GGGTATCGGTACCACCTATAGG
Found at i:3423939 original size:23 final size:22
Alignment explanation
Indices: 3423888--3423951 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
3423878 GTACCATCAG
*
3423888 GGGGTATCGATACCCATTCAAA
1 GGGGTATCGATACCTATTCAAA
*
3423910 GATGGTATCGATACCTATTCAAA
1 G-GGGTATCGATACCTATTCAAA
*
3423933 TGGGGTATTGATACTCTAT
1 -GGGGTATCGATAC-CTAT
3423952 GCACAAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 29 0.83
24 5 0.14
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (22 bp):
GGGGTATCGATACCTATTCAAA
Found at i:3432175 original size:19 final size:19
Alignment explanation
Indices: 3432151--3432196 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
3432141 TCGATTTCAA
3432151 TATAATTATATTATTATAT
1 TATAATTATATTATTATAT
* * *
3432170 TATAATTACATTTTTATGT
1 TATAATTATATTATTATAT
3432189 TAT-ATTAT
1 TATAATTAT
3432197 TATAATTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
TATAATTATATTATTATAT
Found at i:3432265 original size:17 final size:17
Alignment explanation
Indices: 3432245--3432277 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3432235 ATTAAACCCA
3432245 AAGGCCCAATTACAACC
1 AAGGCCCAATTACAACC
3432262 AAGGCCCAATTACAAC
1 AAGGCCCAATTACAAC
3432278 AAAACCCGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.33, G:0.12, T:0.12
Consensus pattern (17 bp):
AAGGCCCAATTACAACC
Found at i:3432484 original size:20 final size:20
Alignment explanation
Indices: 3432459--3432508 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
3432449 AACCACCCGA
3432459 AACCCTAGGGTACTCATTGT
1 AACCCTAGGGTACTCATTGT
3432479 AACCCTAGGGTACTCATTGT
1 AACCCTAGGGTACTCATTGT
3432499 AACCCTAGGG
1 AACCCTAGGG
3432509 CTATTCTGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (20 bp):
AACCCTAGGGTACTCATTGT
Found at i:3445062 original size:35 final size:35
Alignment explanation
Indices: 3445016--3445082 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
3445006 AAGTTATTTG
3445016 AATCAAGCCTTCACAAAAGAGTAATGAAGCAATGA
1 AATCAAGCCTTCACAAAAGAGTAATGAAGCAATGA
3445051 AATCAAGCCTTCACAAAAGAGTAATGAAGCAA
1 AATCAAGCCTTCACAAAAGAGTAATGAAGCAA
3445083 GATCAGATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.49, C:0.18, G:0.16, T:0.16
Consensus pattern (35 bp):
AATCAAGCCTTCACAAAAGAGTAATGAAGCAATGA
Found at i:3452721 original size:2 final size:2
Alignment explanation
Indices: 3452714--3452738 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3452704 ACAAATATTA
3452714 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
3452739 AGAACTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3454368 original size:93 final size:92
Alignment explanation
Indices: 3454152--3454403 Score: 315
Period size: 93 Copynumber: 2.7 Consensus size: 92
3454142 TCGTGATCTT
** * *
3454152 TCTACTAGAAACATTGGTCCCTCGAGTGAGGCGTCGCTGATTCGAAATATCCTGAATCGAGCAAA
1 TCTACTAGAAATGTTGGTCCCTCGAGTGAGGTGTCGCTGATTCGAAAT-GCCTGAATCGAGCAAA
* *
3454217 GGTTGAACAAGTTCTTCATTATGAGTTC
65 GGTCGAACAAGTTCTTCATTATGAATTC
* ** * * * * * *
3454245 TCTACTGGAAATGTTAATCTCTCAATTGAGGTGTCACTGATTTGAAATGCCTTGAATCGAGTAAA
1 TCTACTAGAAATGTTGGTCCCTCGAGTGAGGTGTCGCTGATTCGAAATGCC-TGAATCGAGCAAA
3454310 GGTCGAACAAGTTCTTCATTATGAATTC
65 GGTCGAACAAGTTCTTCATTATGAATTC
* * *
3454338 TCTACTAGAAATGTTGGTCCCTTGAGTGAGGTGTCGCTGATTCAAAATGTCATGAATCGAGCAAA
1 TCTACTAGAAATGTTGGTCCCTCGAGTGAGGTGTCGCTGATTCGAAATG-CCTGAATCGAGCAAA
3454403 G
65 G
3454404 AAAATGTTAA
Statistics
Matches: 130, Mismatches: 27, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
92 2 0.02
93 127 0.98
94 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (92 bp):
TCTACTAGAAATGTTGGTCCCTCGAGTGAGGTGTCGCTGATTCGAAATGCCTGAATCGAGCAAAG
GTCGAACAAGTTCTTCATTATGAATTC
Found at i:3454676 original size:74 final size:74
Alignment explanation
Indices: 3454519--3454783 Score: 239
Period size: 74 Copynumber: 3.5 Consensus size: 74
3454509 AGGGAAACAT
** * ** * * *
3454519 TCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATTTCTTGTTTTG
1 TCTCAAGCGAGACAAAACTTGTTTTAAGAAAAA-AATCTCAAGTGAGATAAAATTTC-TGTTTCG
* *
3454584 AGTAAAAATTG
64 AGTAAAAACTA
* * * *
3454595 TCCCAAGC-ATGAC-GAAGTTTTTTTAAGAAAAAAATCTCAAGTGAGATAAAAATTTCTGTTTCG
1 TCTCAAGCGA-GACAAAACTTGTTTTAAGAAAAAAATCTCAAGTGAGAT-AAAATTTCTGTTTCG
*
3454658 AGTGAAAACTA
64 AGTAAAAACTA
* * * *
3454669 TCTCAAGCGAGACAAAACTTGTTTTAAGTAAAACAATCTCAAGTAAGATAAAATTTATGTTTCAA
1 TCTCAAGCGAGACAAAACTTGTTTTAAG-AAAAAAATCTCAAGTGAGATAAAATTTCTGTTTCGA
*
3454734 G-CAAAACTA
65 GTAAAAACTA
** * *
3454743 TCTCAAGCGAGATGAATCTAGTTTTAAGAAAAACAATCTCA
1 TCTCAAGCGAGACAAAACTTGTTTTAAGAAAAA-AATCTCA
3454784 TGTTTAGAGT
Statistics
Matches: 156, Mismatches: 27, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
73 4 0.03
74 74 0.47
75 51 0.33
76 27 0.17
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (74 bp):
TCTCAAGCGAGACAAAACTTGTTTTAAGAAAAAAATCTCAAGTGAGATAAAATTTCTGTTTCGAG
TAAAAACTA
Found at i:3454740 original size:38 final size:38
Alignment explanation
Indices: 3454619--3454783 Score: 133
Period size: 36 Copynumber: 4.4 Consensus size: 38
3454609 AAGTTTTTTT
* * *
3454619 AAGAAAAA-AATCTCAAGTGAGATAAAAATTTCTGTTTC
1 AAGAAAAACAATCTCAAGCGAGAT-AAAATCTATGTTTC
* * * * *
3454657 GAGTGAAAACTATCTCAAGCGAGACAAAA-CT-TGTTTT
1 AAG-AAAAACAATCTCAAGCGAGATAAAATCTATGTTTC
* ** *
3454694 AAGTAAAACAATCTCAAGTAAGATAAAATTTATGTTTC
1 AAGAAAAACAATCTCAAGCGAGATAAAATCTATGTTTC
* * * *
3454732 AAGCAAAACTATCTCAAGCGAGAT-GAATCTA-GTTTT
1 AAGAAAAACAATCTCAAGCGAGATAAAATCTATGTTTC
3454768 AAGAAAAACAATCTCA
1 AAGAAAAACAATCTCA
3454784 TGTTTAGAGT
Statistics
Matches: 99, Mismatches: 24, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
36 38 0.38
37 13 0.13
38 28 0.28
39 8 0.08
40 12 0.12
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (38 bp):
AAGAAAAACAATCTCAAGCGAGATAAAATCTATGTTTC
Found at i:3454851 original size:38 final size:37
Alignment explanation
Indices: 3454784--3455419 Score: 342
Period size: 38 Copynumber: 17.1 Consensus size: 37
3454774 AACAATCTCA
* * * ** *
3454784 TGTTTAGAGTAAAAATATCTAAAATGAGATAAAACCTT
1 TGTTTAGAGTGAAACTATCTCAAGCGAGAT-AAATCTT
* * *
3454822 TGCTTCGAGTGAAACTATCTCAAGCGAGATTAATC-T
1 TGTTTAGAGTGAAACTATCTCAAGCGAGATAAATCTT
** * *
3454858 TGTTTTA-AGAAAAACAATCTCAAGTGAGATAAATCTT
1 TG-TTTAGAGTGAAACTATCTCAAGCGAGATAAATCTT
* * *
3454895 CTGTTTAGAGTGAAACTATCTCAAGCAATATGAATC-T
1 -TGTTTAGAGTGAAACTATCTCAAGCGAGATAAATCTT
* **
3454932 TGTTTTAAGAAAAAAATGCAAAACTATCTCAAGCGAGACGAATCTT
1 TG-TTT-AG-----AGTG--AAACTATCTCAAGCGAGATAAATCTT
* * * *
3454978 TGCTTCGAGTGAAAATATCTCAAGCGAGATGAATC-T
1 TGTTTAGAGTGAAACTATCTCAAGCGAGATAAATCTT
* * **
3455014 TGTTTTA-AG-AAAACAATCTCAATTGAGATAAATCTT
1 TG-TTTAGAGTGAAACTATCTCAAGCGAGATAAATCTT
* *
3455050 CTGTTTAGAGTGAAACTATCTTAAGCGAGATGAATC-T
1 -TGTTTAGAGTGAAACTATCTCAAGCGAGATAAATCTT
* ** * *
3455087 TGTTTTA-AG-AAAAAAATCTCAAGTGAAATAAATCTTT
1 TG-TTTAGAGTGAAACTATCTCAAGCGAGATAAATC-TT
* *
3455124 TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTT
1 TGTTTAGAGTGAAACTATCTCAAGCGAGATAAATCTT
* ** * *
3455161 AT-TTTA-AG-AAAAAAATCTCAAGTGATATAAATCTT
1 -TGTTTAGAGTGAAACTATCTCAAGCGAGATAAATCTT
* * *
3455196 TTTTTCGAGTGAAACTATCTCAAGCGA-AAAGAATC-T
1 TGTTTAGAGTGAAACTATCTCAAGCGAGATA-AATCTT
** * *
3455232 TGTTTTA-AGAAAAACAATCTCAAGTC-AGATAAAGCTT
1 TG-TTTAGAGTGAAACTATCTCAAG-CGAGATAAATCTT
* * *
3455269 CTGTTTCGAGTGAAACTATCTCAAGCAAGATGAATC-T
1 -TGTTTAGAGTGAAACTATCTCAAGCGAGATAAATCTT
** * *
3455306 TGTTTTA-AGAAAAACAATCTCAAGTGAGATAAATCTT
1 TG-TTTAGAGTGAAACTATCTCAAGCGAGATAAATCTT
* * * *
3455343 CTATTTCGAGTGAAACTATCTCAAGTGAGATGAATC-T
1 -TGTTTAGAGTGAAACTATCTCAAGCGAGATAAATCTT
* * *
3455380 TGTTTTA-AG-AAAAATAGTCTCAAGTGAGATAAATCTT
1 TG-TTTAGAGTGAAACTA-TCTCAAGCGAGATAAATCTT
3455417 TGT
1 TGT
3455420 ATTAAATGAG
Statistics
Matches: 451, Mismatches: 104, Indels: 88
0.70 0.16 0.14
Matches are distributed among these distances:
34 1 0.00
35 66 0.15
36 116 0.26
37 100 0.22
38 135 0.30
39 3 0.01
43 3 0.01
44 1 0.00
45 23 0.05
46 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (37 bp):
TGTTTAGAGTGAAACTATCTCAAGCGAGATAAATCTT
Found at i:3454887 original size:74 final size:74
Alignment explanation
Indices: 3454808--3455416 Score: 834
Period size: 74 Copynumber: 8.2 Consensus size: 74
3454798 ATATCTAAAA
* * *
3454808 TGAGATAAAACCTT-TGCTTCGAGTGAAACTATCTCAAGCGAGATTAATCTTGTTTTAAGAAAAA
1 TGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAA
3454872 CAATCTCAAG
65 CAATCTCAAG
* * *
3454882 TGAGATAAATCTTCTGTTTAGAGTGAAACTATCTCAAGCAATATGAATCTTGTTTTAAGAAAAAA
1 TGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAG--AAAA
3454947 ATGCAAAACTATCTCAAG
64 A--C---A--ATCTCAAG
* ** * *
3454965 CGAGACGAATCTT-TGCTTCGAGTGAAAATATCTCAAGCGAGATGAATCTTGTTTTAAG-AAAAC
1 TGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAAC
*
3455028 AATCTCAAT
66 AATCTCAAG
* *
3455037 TGAGATAAATCTTCTGTTTAGAGTGAAACTATCTTAAGCGAGATGAATCTTGTTTTAAGAAAAA-
1 TGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAAC
3455101 AATCTCAAG
66 AATCTCAAG
* * *
3455110 TGAAATAAATCTTTTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTATTTTAAGAAAAA-
1 TGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAAC
3455174 AATCTCAAG
66 AATCTCAAG
* * * *
3455183 TGATATAAATCTT-TTTTTCGAGTGAAACTATCTCAAGCGAAAAGAATCTTGTTTTAAGAAAAAC
1 TGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAAC
3455247 AATCTCAAG
66 AATCTCAAG
* * *
3455256 TCAGATAAAGCTTCTGTTTCGAGTGAAACTATCTCAAGCAAGATGAATCTTGTTTTAAGAAAAAC
1 TGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAAC
3455321 AATCTCAAG
66 AATCTCAAG
* * *
3455330 TGAGATAAATCTTCTATTTCGAGTGAAACTATCTCAAGTGAGATGAATCTTGTTTTAAGAAAAAT
1 TGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAAC
*
3455395 AGTCTCAAG
66 AATCTCAAG
3455404 TGAGATAAATCTT
1 TGAGATAAATCTT
3455417 TGTATTAAAT
Statistics
Matches: 474, Mismatches: 47, Indels: 28
0.86 0.09 0.05
Matches are distributed among these distances:
72 63 0.13
73 154 0.32
74 187 0.39
76 5 0.01
77 1 0.00
78 1 0.00
79 4 0.01
81 1 0.00
82 40 0.08
83 18 0.04
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (74 bp):
TGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAAC
AATCTCAAG
Found at i:3454945 original size:170 final size:161
Alignment explanation
Indices: 3454622--3455393 Score: 706
Period size: 146 Copynumber: 4.9 Consensus size: 161
3454612 TTTTTTTAAG
* * * * *
3454622 AAAAAAATCTCAAGTGAGATAAAAATTTCTGTTTCGAGTGAAAACTATCTCAAGCGAGACAAAAC
1 AAAAATATCTCAAGTGAGATAAAAACTT-TGCTTCGAGTG-AAACTATCTCAAGCGAGATAAATC
* * **
3454687 TTGTTTTAAGTAAAACAATCTCAAGTAAGATAAAAT-TTATGTTTCA-AGCAAAACTATCTCAAG
64 TTGTTTTAAG-AAAACAATCTCAAGTGAGAT-AAATCTTCTGTTT-AGAGTGAAACTATCTCAAG
* *
3454750 CGAGATGAATCTAGTTTTAAGAAAAACAATCTCATGTTTAGAGT
126 CGAGATGAATCTTGTTTTAAGAAAAA-AATCTCA----T---GC
* * * *
3454794 AAAAATATCTAAAATGAGATAAAACCTTTGCTTCGAGTGAAACTATCTCAAGCGAGATTAATCTT
1 AAAAATATCTCAAGTGAGATAAAAACTTTGCTTCGAGTGAAACTATCTCAAGCGAGATAAATCTT
* *
3454859 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTAGAGTGAAACTATCTCAAGCAAT
66 GTTTTAAG-AAAACAATCTCAAGTGAGATAAATCTTCTGTTTAGAGTGAAACTATCTCAAGCGAG
3454924 ATGAATCTTGTTTTAAG-AAAAAA----ATGC
130 ATGAATCTTGTTTTAAGAAAAAAATCTCATGC
* * ** * * *
3454951 AAAACTATCTCAAGCGAGA-CGAATCTTTGCTTCGAGTGAAAATATCTCAAGCGAGATGAATCTT
1 AAAAATATCTCAAGTGAGATAAAAACTTTGCTTCGAGTGAAACTATCTCAAGCGAGATAAATCTT
* *
3455015 GTTTTAAGAAAACAATCTCAATTGAGATAAATCTTCTGTTTAGAGTGAAACTATCTTAAGCGAGA
66 GTTTTAAGAAAACAATCTCAAGTGAGATAAATCTTCTGTTTAGAGTGAAACTATCTCAAGCGAGA
3455080 TGAATCTTGTTTTAAG-----------A---
131 TGAATCTTGTTTTAAGAAAAAAATCTCATGC
* * * *
3455097 AAAAA-ATCTCAAGTGAAAT-AAATCTTTTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCT
1 AAAAATATCTCAAGTGAGATAAAAAC-TTTGCTTCGAGTGAAACTATCTCAAGCGAGATAAATCT
* * * * * *
3455160 TATTTTAAGAAAAAAATCTCAAGTGATATAAATCTT-TTTTTCGAGTGAAACTATCTCAAGCGAA
65 TGTTTTAAGAAAACAATCTCAAGTGAGATAAATCTTCTGTTTAGAGTGAAACTATCTCAAGCGAG
*
3455224 AAGAATCTTGTTTTAAG---AAAA----A--C
130 ATGAATCTTGTTTTAAGAAAAAAATCTCATGC
* * * * *
3455247 ----A-ATCTCAAGTCAGAT-AAAGCTTCTGTTTCGAGTGAAACTATCTCAAGCAAGATGAATCT
1 AAAAATATCTCAAGTGAGATAAAAACTT-TGCTTCGAGTGAAACTATCTCAAGCGAGATAAATCT
* * *
3455306 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTATTTCGAGTGAAACTATCTCAAGTGA
65 TGTTTTAAG-AAAACAATCTCAAGTGAGATAAATCTTCTGTTTAGAGTGAAACTATCTCAAGCGA
3455371 GATGAATCTTGTTTTAAGAAAAA
129 GATGAATCTTGTTTTAAGAAAAA
3455394 TAGTCTCAAG
Statistics
Matches: 528, Mismatches: 57, Indels: 51
0.83 0.09 0.08
Matches are distributed among these distances:
145 57 0.11
146 132 0.25
147 25 0.05
148 41 0.08
149 2 0.00
151 2 0.00
155 69 0.13
156 48 0.09
157 16 0.03
160 1 0.00
164 1 0.00
168 2 0.00
169 9 0.02
170 90 0.17
171 10 0.02
172 23 0.04
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (161 bp):
AAAAATATCTCAAGTGAGATAAAAACTTTGCTTCGAGTGAAACTATCTCAAGCGAGATAAATCTT
GTTTTAAGAAAACAATCTCAAGTGAGATAAATCTTCTGTTTAGAGTGAAACTATCTCAAGCGAGA
TGAATCTTGTTTTAAGAAAAAAATCTCATGC
Found at i:3455076 original size:73 final size:73
Alignment explanation
Indices: 3454951--3455416 Score: 668
Period size: 73 Copynumber: 6.4 Consensus size: 73
3454941 AAAAAAATGC
* * ** * *
3454951 AAAACTATCTCAAGCGAGACGAATCTT-TGCTTCGAGTGAAAATATCTCAAGCGAGATGAATCTT
1 AAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTT
3455015 GTTTTAAG
66 GTTTTAAG
* * *
3455023 AAAACAATCTCAATTGAGATAAATCTTCTGTTTAGAGTGAAACTATCTTAAGCGAGATGAATCTT
1 AAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTT
3455088 GTTTTAAG
66 GTTTTAAG
* * *
3455096 AAAAAAATCTCAAGTGAAATAAATCTTTTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTT
1 AAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTT
*
3455161 ATTTTAAG
66 GTTTTAAG
* * * * *
3455169 AAAAAAATCTCAAGTGATATAAATCTT-TTTTTCGAGTGAAACTATCTCAAGCGAAAAGAATCTT
1 AAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTT
3455233 GTTTTAAG
66 GTTTTAAG
* * *
3455241 AAAAACAATCTCAAGTCAGATAAAGCTTCTGTTTCGAGTGAAACTATCTCAAGCAAGATGAATCT
1 -AAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCT
3455306 TGTTTTAAG
65 TGTTTTAAG
* *
3455315 AAAAACAATCTCAAGTGAGATAAATCTTCTATTTCGAGTGAAACTATCTCAAGTGAGATGAATCT
1 -AAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCT
3455380 TGTTTTAAG
65 TGTTTTAAG
3455389 AAAA-ATAGTCTCAAGTGAGATAAATCTT
1 AAAACA-A-TCTCAAGTGAGATAAATCTT
3455417 TGTATTAAAT
Statistics
Matches: 355, Mismatches: 34, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
72 64 0.18
73 161 0.45
74 130 0.37
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (73 bp):
AAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTT
GTTTTAAG
Found at i:3455251 original size:146 final size:146
Alignment explanation
Indices: 3454794--3455417 Score: 811
Period size: 146 Copynumber: 4.2 Consensus size: 146
3454784 TGTTTAGAGT
* * * * * * *
3454794 AAAAATATCTAAAATGAGATAAAACCTTTGCTTCGAGTGAAACTATCTCAAGCGAGATTAATCTT
1 AAAAAAATCTCAAGTGAGATAAATCTTTTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTT
* * * *
3454859 GTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTAGAGTGAAACTATCTCAAGCAAT
66 GTTTTAAGAAAAA-AATCTCAAGTGAGATAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAG
3454924 ATGAATCTTGTTTTAAG
130 ATGAATCTTGTTTTAAG
* ** * *
3454941 AAAAAAATGCAAAACTATCTCAAGCGAGACGAATC-TTTGCTTCGAGTGAAAATATCTCAAGCGA
1 -----AA---AAAA--ATCTCAAGTGAGATAAATCTTTTGTTTCGAGTGAAACTATCTCAAGCGA
* * * *
3455005 GATGAATCTTGTTTTAAGAAAACAATCTCAATTGAGATAAATCTTCTGTTTAGAGTGAAACTATC
56 GATGAATCTTGTTTTAAGAAAAAAATCTCAAGTGAGATAAATCTTCTATTTCGAGTGAAACTATC
*
3455070 TTAAGCGAGATGAATCTTGTTTTAAG
121 TCAAGCGAGATGAATCTTGTTTTAAG
*
3455096 AAAAAAATCTCAAGTGAAATAAATCTTTTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTT
1 AAAAAAATCTCAAGTGAGATAAATCTTTTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTT
* * * *
3455161 ATTTTAAGAAAAAAATCTCAAGTGATATAAATCTT-TTTTTCGAGTGAAACTATCTCAAGCGAAA
66 GTTTTAAGAAAAAAATCTCAAGTGAGATAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGA
*
3455225 AGAATCTTGTTTTAAG
131 TGAATCTTGTTTTAAG
* * * *
3455241 AAAAACAATCTCAAGTCAGATAAAGCTTCTGTTTCGAGTGAAACTATCTCAAGCAAGATGAATCT
1 AAAAA-AATCTCAAGTGAGATAAATCTTTTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCT
*
3455306 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTATTTCGAGTGAAACTATCTCAAGTGA
65 TGTTTTAAGAAAAA-AATCTCAAGTGAGATAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGA
3455371 GATGAATCTTGTTTTAAG
129 GATGAATCTTGTTTTAAG
*
3455389 AAAAATAGTCTCAAGTGAGATAAATCTTT
1 AAAAA-AATCTCAAGTGAGATAAATCTTT
3455418 GTATTAAATG
Statistics
Matches: 418, Mismatches: 45, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
145 60 0.14
146 135 0.32
147 25 0.06
148 65 0.16
150 2 0.00
152 2 0.00
155 67 0.16
156 49 0.12
157 13 0.03
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (146 bp):
AAAAAAATCTCAAGTGAGATAAATCTTTTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTT
GTTTTAAGAAAAAAATCTCAAGTGAGATAAATCTTCTATTTCGAGTGAAACTATCTCAAGCGAGA
TGAATCTTGTTTTAAG
Found at i:3458234 original size:29 final size:31
Alignment explanation
Indices: 3458177--3458234 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
3458167 CAACAAGACT
3458177 AGACAAAATGAAATCAATGTTAGTAAAAACA
1 AGACAAAATGAAATCAATGTTAGTAAAAACA
* *
3458208 AGACAAAAT-AATTCAA-GTTAGTTAAAA
1 AGACAAAATGAAATCAATGTTAGTAAAAA
3458235 TGATTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 6 0.24
31 9 0.36
ACGTcount: A:0.57, C:0.09, G:0.12, T:0.22
Consensus pattern (31 bp):
AGACAAAATGAAATCAATGTTAGTAAAAACA
Found at i:3464442 original size:30 final size:31
Alignment explanation
Indices: 3464403--3464467 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
3464393 TTTATATCGT
*
3464403 ATAGGCATATCA-TTTCCATACCTTTATCAC
1 ATAGACATATCATTTTCCATACCTTTATCAC
3464433 ATAGACATATCATTTTCCATACCTTTATCAC
1 ATAGACATATCATTTTCCATACCTTTATCAC
3464464 ATAG
1 ATAG
3464468 CTCAAATAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (31 bp):
ATAGACATATCATTTTCCATACCTTTATCAC
Found at i:3469516 original size:22 final size:22
Alignment explanation
Indices: 3469488--3469530 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3469478 ATTATACGGT
*
3469488 ATGAATAGTACCGTGAACAGTA
1 ATGAATAGTACCATGAACAGTA
* *
3469510 ATGAATATTTCCATGAACAGT
1 ATGAATAGTACCATGAACAGT
3469531 GCTATAGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (22 bp):
ATGAATAGTACCATGAACAGTA
Found at i:3470162 original size:23 final size:22
Alignment explanation
Indices: 3470136--3470214 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 22
3470126 AACTCGTATA
3470136 AATTACACCGAATTGCCACGTAG
1 AATTACACCGAA-TGCCACGTAG
* *
3470159 AATTTATC-CCGAAGGACCGCGTAG
1 AA-TTA-CACCGAATG-CCACGTAG
* *
3470183 AAATGCACCGAAGTGCCACGTAG
1 AATTACACCGAA-TGCCACGTAG
3470206 AATTACACC
1 AATTACACC
3470215 ATAGTGCCAT
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
22 1 0.02
23 23 0.53
24 18 0.42
25 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (22 bp):
AATTACACCGAATGCCACGTAG
Found at i:3470501 original size:30 final size:31
Alignment explanation
Indices: 3470462--3470526 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
3470452 TTTATATCGT
*
3470462 ATAGGCATATCA-TTTCCATACCTTTATCAC
1 ATAGACATATCATTTTCCATACCTTTATCAC
3470492 ATAGACATATCATTTTCCATACCTTTATCAC
1 ATAGACATATCATTTTCCATACCTTTATCAC
3470523 ATAG
1 ATAG
3470527 CTCATATAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (31 bp):
ATAGACATATCATTTTCCATACCTTTATCAC
Found at i:3470951 original size:20 final size:20
Alignment explanation
Indices: 3470926--3470979 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
3470916 CAAAATTCTC
3470926 ATGCATCGATGCACCCTTTA
1 ATGCATCGATGCACCCTTTA
3470946 ATGCATCGATGCACCCTTTA
1 ATGCATCGATGCACCCTTTA
3470966 ATGCATCGATGCAC
1 ATGCATCGATGCAC
3470980 ATTCACATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (20 bp):
ATGCATCGATGCACCCTTTA
Found at i:3471002 original size:31 final size:31
Alignment explanation
Indices: 3470967--3471046 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
3470957 CACCCTTTAA
3470967 TGCATCGATGCACATTCACATTTGGTCTTAG
1 TGCATCGATGCACATTCACATTTGGTCTTAG
3470998 TGCATCGATGCACATTCACATTTGGTCTTAG
1 TGCATCGATGCACATTCACATTTGGTCTTAG
* *
3471029 TGCATCGGTGCCCATTCA
1 TGCATCGATGCACATTCA
3471047 TAGTGCATCG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (31 bp):
TGCATCGATGCACATTCACATTTGGTCTTAG
Found at i:3473150 original size:15 final size:15
Alignment explanation
Indices: 3473130--3473167 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
3473120 ACAGAGTGCC
3473130 TACAAATATGTTCCT
1 TACAAATATGTTCCT
3473145 TACAAATATGTTCCT
1 TACAAATATGTTCCT
*
3473160 TAAAAATA
1 TACAAATA
3473168 GTGGGATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (15 bp):
TACAAATATGTTCCT
Found at i:3478129 original size:19 final size:19
Alignment explanation
Indices: 3478101--3478138 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3478091 GGGAAGGATT
3478101 TTTTTAAATTTTTAATAATA
1 TTTTTAAATTTTTAA-AATA
3478121 TTTTT-AATTTTTAAAATA
1 TTTTTAAATTTTTAAAATA
3478139 AAAAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 9 0.50
20 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTAAATTTTTAAAATA
Found at i:3484401 original size:20 final size:19
Alignment explanation
Indices: 3484365--3484400 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3484355 GGGAAAGGAT
3484365 TTTTTAATTTTTAATAATA
1 TTTTTAATTTTTAATAATA
3484384 TTTTT-ATTTTTAA-AATA
1 TTTTTAATTTTTAATAATA
3484401 AAAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 8 0.47
19 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTAATTTTTAATAATA
Found at i:3485012 original size:29 final size:29
Alignment explanation
Indices: 3484979--3485108 Score: 224
Period size: 29 Copynumber: 4.5 Consensus size: 29
3484969 AGACCCCGGA
* *
3484979 TATAAATATAATAATTAAAGGATTCTAAT
1 TATAAATATAAAAATTAAAGAATTCTAAT
3485008 TATAAATATAAAAATTAAAGAATTCTAAT
1 TATAAATATAAAAATTAAAGAATTCTAAT
* *
3485037 TATAAATATAATAATTAAAGGATTCTAAT
1 TATAAATATAAAAATTAAAGAATTCTAAT
3485066 TATAAATATAAAAATTAAAGAATTCTAAT
1 TATAAATATAAAAATTAAAGAATTCTAAT
3485095 TATAAATATAAAAA
1 TATAAATATAAAAA
3485109 CCGAGGGCCC
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 95 1.00
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (29 bp):
TATAAATATAAAAATTAAAGAATTCTAAT
Found at i:3485050 original size:58 final size:58
Alignment explanation
Indices: 3484979--3485105 Score: 254
Period size: 58 Copynumber: 2.2 Consensus size: 58
3484969 AGACCCCGGA
3484979 TATAAATATAATAATTAAAGGATTCTAATTATAAATATAAAAATTAAAGAATTCTAAT
1 TATAAATATAATAATTAAAGGATTCTAATTATAAATATAAAAATTAAAGAATTCTAAT
3485037 TATAAATATAATAATTAAAGGATTCTAATTATAAATATAAAAATTAAAGAATTCTAAT
1 TATAAATATAATAATTAAAGGATTCTAATTATAAATATAAAAATTAAAGAATTCTAAT
3485095 TATAAATATAA
1 TATAAATATAA
3485106 AAACCGAGGG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 69 1.00
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (58 bp):
TATAAATATAATAATTAAAGGATTCTAATTATAAATATAAAAATTAAAGAATTCTAAT
Found at i:3489556 original size:39 final size:39
Alignment explanation
Indices: 3489502--3489578 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
3489492 GGTAGTAGGA
*
3489502 TTAAAATAGTTTGCATACTTATTCTTCCTTACATTCTCG
1 TTAAAAGAGTTTGCATACTTATTCTTCCTTACATTCTCG
* *
3489541 TTAAAAGAGTTTGCATACTTATTCTTTCTTGCATTCTC
1 TTAAAAGAGTTTGCATACTTATTCTTCCTTACATTCTC
3489579 ATTCACTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (39 bp):
TTAAAAGAGTTTGCATACTTATTCTTCCTTACATTCTCG
Found at i:3490628 original size:20 final size:20
Alignment explanation
Indices: 3490605--3490657 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3490595 ATGATAATTT
3490605 GGTATCGATACTGAT-GTAGA
1 GGTATCGATACTGATAGTA-A
**
3490625 GGTATCGATACCAATAGTAA
1 GGTATCGATACTGATAGTAA
*
3490645 GGTACCGATACTG
1 GGTATCGATACTG
3490658 TAAGTGACGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (20 bp):
GGTATCGATACTGATAGTAA
Found at i:3491187 original size:15 final size:15
Alignment explanation
Indices: 3491160--3491197 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3491150 TTATGTAAAA
*
3491160 ATGTTCTATGTGAAT
1 ATGTTCTAGGTGAAT
3491175 ATGTTCTAGGTGAAT
1 ATGTTCTAGGTGAAT
*
3491190 GTGTTCTA
1 ATGTTCTA
3491198 TGGTTAAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.45
Consensus pattern (15 bp):
ATGTTCTAGGTGAAT
Found at i:3491857 original size:13 final size:13
Alignment explanation
Indices: 3491839--3491863 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3491829 TTCATTATGA
3491839 AATATGAATTTTC
1 AATATGAATTTTC
3491852 AATATGAATTTT
1 AATATGAATTTT
3491864 TTTATGAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
AATATGAATTTTC
Found at i:3493233 original size:40 final size:40
Alignment explanation
Indices: 3493185--3493290 Score: 194
Period size: 40 Copynumber: 2.6 Consensus size: 40
3493175 CCTTACCTTG
* *
3493185 GGTATCGATACTATAAGAACAATATCGATACCGTTCATGT
1 GGTATCGATACTGTAAGAACAATATCGATACCATTCATGT
3493225 GGTATCGATACTGTAAGAACAATATCGATACCATTCATGT
1 GGTATCGATACTGTAAGAACAATATCGATACCATTCATGT
3493265 GGTATCGATACTGTAAGAACAATATC
1 GGTATCGATACTGTAAGAACAATATC
3493291 AGTACTTTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (40 bp):
GGTATCGATACTGTAAGAACAATATCGATACCATTCATGT
Found at i:3498889 original size:3 final size:3
Alignment explanation
Indices: 3498881--3498914 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
3498871 CATGTTTAGT
3498881 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
3498915 GCTATTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3499566 original size:11 final size:11
Alignment explanation
Indices: 3499552--3499582 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3499542 TTTTGATGGG
3499552 TTTTTTTTTGT
1 TTTTTTTTTGT
*
3499563 TTTTTGTTTGT
1 TTTTTTTTTGT
3499574 TTTTTTTTT
1 TTTTTTTTT
3499583 TTGCAAAGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:3499576 original size:17 final size:17
Alignment explanation
Indices: 3499551--3499585 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3499541 ATTTTGATGG
*
3499551 GTTTTTTTTTGTTTTTT
1 GTTTGTTTTTGTTTTTT
*
3499568 GTTTGTTTTTTTTTTTT
1 GTTTGTTTTTGTTTTTT
3499585 G
1 G
3499586 CAAAGACGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (17 bp):
GTTTGTTTTTGTTTTTT
Found at i:3501613 original size:70 final size:69
Alignment explanation
Indices: 3501460--3501616 Score: 154
Period size: 70 Copynumber: 2.2 Consensus size: 69
3501450 GACAGGAAAA
* * *
3501460 TTTATTTAATTTTAAAATAAATAGGGCCTAAAAAGTAATTAAACCATAAAAATAAGAGATTAAGG
1 TTTA-TTAATTTTAAAATAAATAGGGCCTAAAAAGTAATTAAACCAGAAAAATAAGAGATCAAAG
3501525 GTTAT
65 GTTAT
* * * * * * ** *
3501530 TTCAGTAATTTTTAAAATTTAA-AGGTCTTAAAAAGTAATTAAACCAGACAAATTTGAGGTCAAA
1 TTTATTAA-TTTTAAAA-TAAATAGGGCCTAAAAAGTAATTAAACCAGAAAAATAAGAGATCAAA
*
3501594 GTTTAAT
64 GGTT-AT
3501601 TTTATTAATTTTAAAA
1 TTTATTAATTTTAAAA
3501617 CTTACAGTAT
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
69 3 0.04
70 55 0.80
71 11 0.16
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.36
Consensus pattern (69 bp):
TTTATTAATTTTAAAATAAATAGGGCCTAAAAAGTAATTAAACCAGAAAAATAAGAGATCAAAGG
TTAT
Found at i:3502755 original size:60 final size:60
Alignment explanation
Indices: 3502627--3502757 Score: 164
Period size: 58 Copynumber: 2.2 Consensus size: 60
3502617 GTCGGGGGAG
* **
3502627 GGGGAAGGGG-GAGTTGAGAGTGAAAGAATATTTTTTTTTTTGTTTCAAACAATGAAATC
1 GGGGAAGGGGAGAGTTGAGAGTGAAAGAACATAATTTTTTTTGTTTCAAACAATGAAATC
3502686 GAGGG-AGGGGAGAGTTGAGAGT-AAA-AACATAATTTTTTTTGTTTCAGAA-AATGAAAGGTC
1 G-GGGAAGGGGAGAGTTGAGAGTGAAAGAACATAATTTTTTTTGTTTCA-AACAATGAAA--TC
3502746 GGGGAAGGGGAG
1 GGGGAAGGGGAG
3502758 GGGGAGTTGA
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
58 25 0.40
59 14 0.22
60 24 0.38
ACGTcount: A:0.34, C:0.05, G:0.34, T:0.28
Consensus pattern (60 bp):
GGGGAAGGGGAGAGTTGAGAGTGAAAGAACATAATTTTTTTTGTTTCAAACAATGAAATC
Found at i:3507587 original size:31 final size:31
Alignment explanation
Indices: 3507552--3507616 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
3507542 TATGGGTGTC
3507552 AATGAATAGAGCATTCAACGAACTATTCATA
1 AATGAATAGAGCATTCAACGAACTATTCATA
*
3507583 AATGAATAGAGCATTCAACGAACTATTCGTA
1 AATGAATAGAGCATTCAACGAACTATTCATA
3507614 AAT
1 AAT
3507617 TGTTTGTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (31 bp):
AATGAATAGAGCATTCAACGAACTATTCATA
Found at i:3508401 original size:2 final size:2
Alignment explanation
Indices: 3508396--3508428 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3508386 AAAAGGCTTA
3508396 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3508429 AAAAGTGACC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3515198 original size:18 final size:18
Alignment explanation
Indices: 3515175--3515212 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3515165 ACCGGTTACA
3515175 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
3515193 ACCCGACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
3515211 AC
1 AC
3515213 TGTTGACCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.47, G:0.21, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:3515219 original size:7 final size:7
Alignment explanation
Indices: 3515205--3515235 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3515195 CCGACCTGAC
3515205 CCGTTGA
1 CCGTTGA
*
3515212 CTGTTGA
1 CCGTTGA
3515219 CCGTTGA
1 CCGTTGA
3515226 CCGTTGA
1 CCGTTGA
3515233 CCG
1 CCG
3515236 GGTGCTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.13, C:0.29, G:0.29, T:0.29
Consensus pattern (7 bp):
CCGTTGA
Found at i:3515275 original size:30 final size:30
Alignment explanation
Indices: 3515235--3515293 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
3515225 ACCGTTGACC
*
3515235 GGGTGCTATTCTGGTAATTATTTGGAAAAA
1 GGGTGATATTCTGGTAATTATTTGGAAAAA
*
3515265 GGGTGATATTCTGGTAATTATTTTGAAAA
1 GGGTGATATTCTGGTAATTATTTGGAAAA
3515294 GGTGCTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.05, G:0.25, T:0.39
Consensus pattern (30 bp):
GGGTGATATTCTGGTAATTATTTGGAAAAA
Found at i:3515405 original size:30 final size:29
Alignment explanation
Indices: 3515248--3515424 Score: 103
Period size: 29 Copynumber: 6.1 Consensus size: 29
3515238 TGCTATTCTG
* * * * *
3515248 GTAATTATTTGGAAAAAGGGTGATATTCTG
1 GTAATTATTTTG-AAAATGATGATATTTTA
* * * *
3515278 GTAATTATTTTGAAAA-GGTGCTAATTTC
1 GTAATTATTTTGAAAATGATGATATTTTA
* *
3515306 GTAATT-TTTT-AAAATAAAT-ATAATTTA
1 GTAATTATTTTGAAAAT-GATGATATTTTA
* * **
3515333 ATAAATT-TTTTTAAAAAAATGATATTTTA
1 GT-AATTATTTTGAAAATGATGATATTTTA
* *
3515362 GTAATTATTTTGAAAATGGTGATATTTTG
1 GTAATTATTTTGAAAATGATGATATTTTA
* * *
3515391 GTAATTTTTTTTGAAAATGATGCTATTTTC
1 GTAA-TTATTTTGAAAATGATGATATTTTA
3515421 GTAA
1 GTAA
3515425 AATGGTTGTT
Statistics
Matches: 118, Mismatches: 22, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
26 4 0.03
27 11 0.09
28 30 0.25
29 37 0.31
30 36 0.31
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.46
Consensus pattern (29 bp):
GTAATTATTTTGAAAATGATGATATTTTA
Found at i:3516135 original size:24 final size:24
Alignment explanation
Indices: 3516104--3516207 Score: 136
Period size: 24 Copynumber: 4.3 Consensus size: 24
3516094 TATATGGTTT
* *
3516104 TTGACCTGGATCTTGATATGATAC
1 TTGACCTGGATTTTTATATGATAC
*
3516128 TTGTCCTGGATTTTTATATGATAC
1 TTGACCTGGATTTTTATATGATAC
3516152 TTGACCTGGATTTTTATATGATAC
1 TTGACCTGGATTTTTATATGATAC
* * * * *
3516176 TTGACATGGATTCTGATCTGCTAC
1 TTGACCTGGATTTTTATATGATAC
3516200 TTGACCTG
1 TTGACCTG
3516208 AATTATGTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.42
Consensus pattern (24 bp):
TTGACCTGGATTTTTATATGATAC
Found at i:3522406 original size:13 final size:13
Alignment explanation
Indices: 3522388--3522413 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3522378 CAACCCGACT
3522388 CGACCCGTTGACC
1 CGACCCGTTGACC
3522401 CGACCCGTTGACC
1 CGACCCGTTGACC
3522414 GGGTGCTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.46, G:0.23, T:0.15
Consensus pattern (13 bp):
CGACCCGTTGACC
Found at i:3522456 original size:29 final size:28
Alignment explanation
Indices: 3522414--3522478 Score: 103
Period size: 29 Copynumber: 2.3 Consensus size: 28
3522404 CCCGTTGACC
3522414 GGGTGCTATTCTGGTAATTATTTGGAATA
1 GGGTGCTATTCTGGTAATTATTTGGAA-A
*
3522443 GGGTGCTATTCTGGTAATTATTTTGAAA
1 GGGTGCTATTCTGGTAATTATTTGGAAA
*
3522471 AGGTGCTA
1 GGGTGCTA
3522479 ATTTCGTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 8 0.24
29 26 0.76
ACGTcount: A:0.25, C:0.08, G:0.28, T:0.40
Consensus pattern (28 bp):
GGGTGCTATTCTGGTAATTATTTGGAAA
Found at i:3522554 original size:29 final size:29
Alignment explanation
Indices: 3522496--3522582 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
3522486 ATTTTTAAAA
* * *
3522496 AAAAAAAAGATAATTTAGTAA--A-TTTA
1 AAAAAAATGATATTTTAGTAATTATTTTG
3522522 AAAAAAATGATATTTTAGTAATTATTTTG
1 AAAAAAATGATATTTTAGTAATTATTTTG
* * * *
3522551 AAAATAGTGATGTTTTGGTAATT-TTTTG
1 AAAAAAATGATATTTTAGTAATTATTTTG
3522579 AAAA
1 AAAA
3522583 TGATGCTATT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
26 19 0.37
28 10 0.20
29 22 0.43
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (29 bp):
AAAAAAATGATATTTTAGTAATTATTTTG
Found at i:3522599 original size:28 final size:29
Alignment explanation
Indices: 3522529--3522583 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
3522519 TTAAAAAAAA
3522529 TGATATTTTAGTAATTATTTTGAAAATAG
1 TGATATTTTAGTAATTATTTTGAAAATAG
* *
3522558 TGATGTTTTGGTAATT-TTTTGAAAAT
1 TGATATTTTAGTAATTATTTTGAAAAT
3522584 GATGCTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (29 bp):
TGATATTTTAGTAATTATTTTGAAAATAG
Found at i:3523311 original size:12 final size:13
Alignment explanation
Indices: 3523296--3523354 Score: 54
Period size: 12 Copynumber: 4.8 Consensus size: 13
3523286 TATCTGGTTT
3523296 TTGACCTGGAT-C
1 TTGACCTGGATAC
**
3523308 TTGATAT-GATAC
1 TTGACCTGGATAC
3523320 TTGACCTGGAT-C
1 TTGACCTGGATAC
**
3523332 TTGATAT-GATAC
1 TTGACCTGGATAC
3523344 TTGACCTGGAT
1 TTGACCTGGAT
3523355 TTTTATATGA
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
11 6 0.17
12 23 0.66
13 6 0.17
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (13 bp):
TTGACCTGGATAC
Found at i:3523379 original size:24 final size:24
Alignment explanation
Indices: 3523296--3523378 Score: 139
Period size: 24 Copynumber: 3.5 Consensus size: 24
3523286 TATCTGGTTT
3523296 TTGACCTGGATCTTGATATGATAC
1 TTGACCTGGATCTTGATATGATAC
3523320 TTGACCTGGATCTTGATATGATAC
1 TTGACCTGGATCTTGATATGATAC
* *
3523344 TTGACCTGGATTTTTATATGATAC
1 TTGACCTGGATCTTGATATGATAC
*
3523368 TTGACATGGAT
1 TTGACCTGGAT
3523379 TCTAATCTGC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.40
Consensus pattern (24 bp):
TTGACCTGGATCTTGATATGATAC
Found at i:3523392 original size:24 final size:24
Alignment explanation
Indices: 3523311--3523396 Score: 93
Period size: 24 Copynumber: 3.6 Consensus size: 24
3523301 CTGGATCTTG
* *
3523311 ATATGATACTTGACCTGGA-TCTTG
1 ATATGATACTTGACATGGATTC-TA
* * *
3523335 ATATGATACTTGACCTGGATTTTT
1 ATATGATACTTGACATGGATTCTA
3523359 ATATGATACTTGACATGGATTCTA
1 ATATGATACTTGACATGGATTCTA
* *
3523383 ATCTGCTACTTGAC
1 ATATGATACTTGAC
3523397 CTGAATTATG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
24 53 0.98
25 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (24 bp):
ATATGATACTTGACATGGATTCTA
Found at i:3523393 original size:48 final size:48
Alignment explanation
Indices: 3523296--3523399 Score: 138
Period size: 48 Copynumber: 2.2 Consensus size: 48
3523286 TATCTGGTTT
* *
3523296 TTGACCTGGATCTTGATATGATACTTGACCTGGATCTTGATATGATAC
1 TTGACCTGGATCTTGATATGATACTTGACATGGATCTTAATATGATAC
* * * *
3523344 TTGACCTGGATTTTTATATGATACTTGACATGGAT-TCTAATCTGCTAC
1 TTGACCTGGATCTTGATATGATACTTGACATGGATCT-TAATATGATAC
3523392 TTGACCTG
1 TTGACCTG
3523400 AATTATGTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
47 1 0.02
48 48 0.98
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.39
Consensus pattern (48 bp):
TTGACCTGGATCTTGATATGATACTTGACATGGATCTTAATATGATAC
Found at i:3526192 original size:13 final size:12
Alignment explanation
Indices: 3526169--3526230 Score: 52
Period size: 13 Copynumber: 4.9 Consensus size: 12
3526159 CATTGACTAG
3526169 AAATATTAAATA
1 AAATATTAAATA
*
3526181 AAATATTTAAATG
1 AAATA-TTAAATA
*** *
3526194 AAACGGTAACTA
1 AAATATTAAATA
3526206 GAAATATTAAATA
1 -AAATATTAAATA
3526219 AAATATTTAAAT
1 AAATA-TTAAAT
3526231 GAGACGATAA
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
12 14 0.38
13 23 0.62
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.32
Consensus pattern (12 bp):
AAATATTAAATA
Found at i:3526206 original size:38 final size:38
Alignment explanation
Indices: 3526164--3526242 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
3526154 ATTAGCATTG
*
3526164 ACTAGAAATATTAAATAAAATATTTAAATGAAACGGTA
1 ACTAGAAATATTAAATAAAATATTTAAATGAAACGATA
*
3526202 ACTAGAAATATTAAATAAAATATTTAAATGAGACGATA
1 ACTAGAAATATTAAATAAAATATTTAAATGAAACGATA
3526240 ACT
1 ACT
3526243 GTGTTGTGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.29
Consensus pattern (38 bp):
ACTAGAAATATTAAATAAAATATTTAAATGAAACGATA
Found at i:3538229 original size:13 final size:13
Alignment explanation
Indices: 3538211--3538235 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3538201 CAACAAAGTC
3538211 CTTTTTTTCTTTT
1 CTTTTTTTCTTTT
3538224 CTTTTTTTCTTT
1 CTTTTTTTCTTT
3538236 CGAACTTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
CTTTTTTTCTTTT
Found at i:3542433 original size:34 final size:34
Alignment explanation
Indices: 3542399--3542473 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
3542389 AATAACAATA
*
3542399 AAAATAAAA-ATTAGCATGTTAGTACAAATGAAT
1 AAAATAAAAGATTAGAATGTTAGTACAAATGAAT
* *
3542432 AAAATAAAAGATTAGAATGTTAGTTCGAATG-AT
1 AAAATAAAAGATTAGAATGTTAGTACAAATGAAT
3542465 AAAATAAAA
1 AAAATAAAA
3542474 TAAATGTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 20 0.53
34 18 0.47
ACGTcount: A:0.56, C:0.04, G:0.13, T:0.27
Consensus pattern (34 bp):
AAAATAAAAGATTAGAATGTTAGTACAAATGAAT
Found at i:3544431 original size:220 final size:219
Alignment explanation
Indices: 3544069--3544845 Score: 950
Period size: 220 Copynumber: 3.5 Consensus size: 219
3544059 ATGATATTAC
* * * *
3544069 TCCTTTTCGTTGAGGAAAT-TGTGTCAATCTGGAGATAATTTGGAGACAACACAGTTCCTTCGTG
1 TCCTTCTCGTTGAGGAAATCAG-GTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCGCG
* * ** *
3544133 TTGAGAAAGTCTGATTGTCTGAGGATGA-ATTTGC-TCATTTGCGTTGAGGAGATCGGGTCGATA
65 TTGAGGAAGTCTGATTGTCTGAGGATGACACTT-CTTC-TTCACGTTGAGGAGATCGGGTCAATA
*
3544196 TGGAAA-ATATTTGGTGTTGAAGATAGCAATGCTCATCCATGTTGAAGAGATCTAGTCATTTTCA
128 TGGAAATA-ATTTGGTGTTGAAGAT-GCAATGCTCATCCATGTTGAAGAGATCTGGTCATTTTCA
3544260 GGTAAATTATTTGTTGAAGATGACGATGT
191 GGTAAATTATTTGTTGAAGATGACGATGT
* * * * *
3544289 TCCTTCTCGTTGAGGAAATCAAGTCAATCTGGAGATAATTTAGTGACAAAATGGTTCCTTCGCGT
1 TCCTTCTCGTTGAGGAAATCAGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCGCGT
* * *
3544354 TGAGGAAGTCTGATTGTCTGAGGATGACACTTCTTCTTTACGTTGAGGGGATCGGGTCAATCTGG
66 TGAGGAAGTCTGATTGTCTGAGGATGACACTTCTTCTTCACGTTGAGGAGATCGGGTCAATATGG
* * * *
3544419 AAATAATTTGGTGTTGAAGATGACACTGTTCATCCATGTTGAAGAGATCTGGTCACTTTCAGATA
131 AAATAATTTGGTGTTGAAGATG-CAATGCTCATCCATGTTGAAGAGATCTGGTCATTTTCAGGTA
* *
3544484 AATTATTTGTTGAAGATGATGTTGT
195 AATTATTTGTTGAAGATGACGATGT
* * * ** *
3544509 TCCTTCTCGTTGAGGAAATCGGGTCAATCTAGAGATAATTTGGTGACAACACGGTTTATTCTCGT
1 TCCTTCTCGTTGAGGAAATCAGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCGCGT
* * * * * *
3544574 TGAGGAAGTTTGATTGTCTGAGGATGACACTTCTTCTTCGCATTGAGGAGATCGAGTCAATTTAG
66 TGAGGAAGTCTGATTGTCTGAGGATGACACTTCTTCTTCACGTTGAGGAGATCGGGTCAATATGG
* * * * ** *
3544639 AAATATTTTGATGTTAAAGATGAAACTGCTCATCTGTGTTGAAGAGATCTGGTCGTTTTCAGGTA
131 AAATAATTTGGTGTTGAAGATGCAA-TGCTCATCCATGTTGAAGAGATCTGGTCATTTTCAGGTA
* ** * *
3544704 AATTGTTTACTGGAGATAACGATGT
195 AATTATTTGTTGAAGATGACGATGT
* * * * *
3544729 TCCTTATCGTTGAAGAAATCAGGTCAATTTGGAGATAATTTGGAGACAACACGGTTCCTTTGCTT
1 TCCTTCTCGTTGAGGAAATCAGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCGCGT
* * * *
3544794 TGAGGAATTCTGATTGTCTGAAGATGACACTGCTCCTTCACGTTGAGGAGAT
66 TGAGGAAGTCTGATTGTCTGAGGATGACACTTCTTCTTCACGTTGAGGAGAT
3544846 ATGGTCATAA
Statistics
Matches: 476, Mismatches: 75, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
219 2 0.00
220 468 0.98
221 6 0.01
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (219 bp):
TCCTTCTCGTTGAGGAAATCAGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCGCGT
TGAGGAAGTCTGATTGTCTGAGGATGACACTTCTTCTTCACGTTGAGGAGATCGGGTCAATATGG
AAATAATTTGGTGTTGAAGATGCAATGCTCATCCATGTTGAAGAGATCTGGTCATTTTCAGGTAA
ATTATTTGTTGAAGATGACGATGT
Found at i:3547884 original size:2 final size:2
Alignment explanation
Indices: 3547879--3547908 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3547869 TTATTGTGTG
3547879 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3547909 ATTATATTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3553256 original size:32 final size:33
Alignment explanation
Indices: 3553196--3553288 Score: 111
Period size: 32 Copynumber: 2.8 Consensus size: 33
3553186 CATAACAATA
*
3553196 AAAATAAAAT-TTAGCATGTTAGTACGAATGAT
1 AAAATAAAATATTAGAATGTTAGTACGAATGAT
3553228 -AAATAAAATATTAGAATGTTAGCT-CGAATGAT
1 AAAATAAAATATTAGAATGTTAG-TACGAATGAT
3553260 AAAATAAAATAAATGTTAGAATGTTAGTA
1 AAAATAAAAT--A--TTAGAATGTTAGTA
3553289 GGTTAGTGAC
Statistics
Matches: 52, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
31 9 0.17
32 19 0.37
33 10 0.19
35 1 0.02
36 1 0.02
37 12 0.23
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.31
Consensus pattern (33 bp):
AAAATAAAATATTAGAATGTTAGTACGAATGAT
Found at i:3555223 original size:170 final size:169
Alignment explanation
Indices: 3554941--3555285 Score: 496
Period size: 170 Copynumber: 2.0 Consensus size: 169
3554931 ATTTTAAGAT
* * *
3554941 TTTTTCGATTGGTTTCCAACTTCTAATTAAATTCGAATTTAAATATGAATGACAGGATACCTATA
1 TTTTTCGATCGGTTTCCAACTTCTAATTAAATTCGAATTTAAATATGAATGACAGGATACATACA
* *
3555006 AAAATAAAATTAAGAATTAAGAATGTTGAAAATAATGAAATAAAATTGCCAAAAAAGTAAA-AAA
66 AAAATAAAATTAAAAATTAAGAATGCTGAAAATAATGAAATAAAATTGCC---AAAGTAAACAAA
*
3555070 AAT-ATTAAATTAAAAATATTGGTTTCCTCTCATGAGCGCTA
128 AATGATTAAATTAAAAATATGGGTTTCCTCTCATGAGCGCTA
* * * ** **
3555111 TTTTTCGATCGGTTTTCAACTTTTAATTAAATTCGAATTTAATTATGAATGGTATTATACATACA
1 TTTTTCGATCGGTTTCCAACTTCTAATTAAATTCGAATTTAAATATGAATGACAGGATACATACA
* *
3555176 AAAATAAAATTAAAAATTAAGAATGCTGAAAATAATGAAATAAAATTGCCAAATTAAACTAGAAA
66 AAAATAAAATTAAAAATTAAGAATGCTGAAAATAATGAAATAAAATTGCCAAAGTAAAC-AAAAA
*
3555241 TGATTAAATTAAAAATATGGGTTTCCTCTCATGAGCGTTA
130 TGATTAAATTAAAAATATGGGTTTCCTCTCATGAGCGCTA
3555281 TTTTT
1 TTTTT
3555286 AACGTTGTTA
Statistics
Matches: 156, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
167 7 0.04
169 5 0.03
170 144 0.92
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.35
Consensus pattern (169 bp):
TTTTTCGATCGGTTTCCAACTTCTAATTAAATTCGAATTTAAATATGAATGACAGGATACATACA
AAAATAAAATTAAAAATTAAGAATGCTGAAAATAATGAAATAAAATTGCCAAAGTAAACAAAAAT
GATTAAATTAAAAATATGGGTTTCCTCTCATGAGCGCTA
Found at i:3560093 original size:10 final size:11
Alignment explanation
Indices: 3560074--3560105 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
3560064 TCATATACAC
3560074 AATTAT-TTTT
1 AATTATATTTT
3560084 AATT-TATTTT
1 AATTATATTTT
3560094 AATTATATTTT
1 AATTATATTTT
3560105 A
1 A
3560106 TAATATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.05
10 12 0.60
11 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
AATTATATTTT
Found at i:3561891 original size:21 final size:21
Alignment explanation
Indices: 3561867--3561912 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3561857 GGAAGAGATA
*
3561867 AAGGAAGAGCAAGAAATCATC
1 AAGGAACAGCAAGAAATCATC
**
3561888 AAGGCTCAGCAAGAAATCATC
1 AAGGAACAGCAAGAAATCATC
3561909 AAGG
1 AAGG
3561913 CTCAAAGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (21 bp):
AAGGAACAGCAAGAAATCATC
Found at i:3561924 original size:24 final size:21
Alignment explanation
Indices: 3561874--3561916 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3561864 ATAAAGGAAG
3561874 AGCAAGAAATCATCAAGGCTC
1 AGCAAGAAATCATCAAGGCTC
3561895 AGCAAGAAATCATCAAGGCTC
1 AGCAAGAAATCATCAAGGCTC
3561916 A
1 A
3561917 AAGGCAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.14
Consensus pattern (21 bp):
AGCAAGAAATCATCAAGGCTC
Found at i:3565761 original size:8 final size:7
Alignment explanation
Indices: 3565739--3565793 Score: 71
Period size: 7 Copynumber: 8.3 Consensus size: 7
3565729 GTAGAAGGTT
3565739 GAAAGGG
1 GAAAGGG
3565746 GAAAGGG
1 GAAAGGG
3565753 GAAAGGG
1 GAAAGGG
*
3565760 GGAAGGG
1 GAAAGGG
3565767 G-AAGGG
1 GAAAGGG
3565773 G-AAGGG
1 GAAAGGG
3565779 G-AAGGG
1 GAAAGGG
*
3565785 GAAGGGG
1 GAAAGGG
3565792 GA
1 GA
3565794 GGGAGAGGGG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
6 18 0.40
7 27 0.60
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (7 bp):
GAAAGGG
Found at i:3565769 original size:6 final size:6
Alignment explanation
Indices: 3565741--3565808 Score: 84
Period size: 6 Copynumber: 10.8 Consensus size: 6
3565731 AGAAGGTTGA
3565741 AAGGGG AAAGGGG AAAGGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG
1 AAGGGG -AAGGGG -AA-GGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG
*
3565792 GA-GGG AGAGGGG AAGGG
1 AAGGGG A-AGGGG AAGGG
3565809 AGCACGCGGG
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
5 3 0.05
6 34 0.61
7 15 0.27
8 4 0.07
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:3568002 original size:12 final size:12
Alignment explanation
Indices: 3567985--3568009 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3567975 TATAAGGTAA
3567985 TTTTTTTATAAT
1 TTTTTTTATAAT
3567997 TTTTTTTATAAT
1 TTTTTTTATAAT
3568009 T
1 T
3568010 ATATATGATT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTTATAAT
Found at i:3568166 original size:22 final size:23
Alignment explanation
Indices: 3568141--3568190 Score: 93
Period size: 22 Copynumber: 2.2 Consensus size: 23
3568131 TATATTATTT
3568141 AAATTATTTACGTTTATGTGTA-
1 AAATTATTTACGTTTATGTGTAG
3568163 AAATTATTTACGTTTATGTGTAG
1 AAATTATTTACGTTTATGTGTAG
3568186 AAATT
1 AAATT
3568191 TTATTGTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.34, C:0.04, G:0.14, T:0.48
Consensus pattern (23 bp):
AAATTATTTACGTTTATGTGTAG
Found at i:3571249 original size:14 final size:14
Alignment explanation
Indices: 3571230--3571262 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3571220 TATAAAATAA
3571230 TAATTCTTGTAGTT
1 TAATTCTTGTAGTT
*
3571244 TAATTCTTGTTGTT
1 TAATTCTTGTAGTT
3571258 TAATT
1 TAATT
3571263 TACATTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.06, G:0.12, T:0.61
Consensus pattern (14 bp):
TAATTCTTGTAGTT
Done.