Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 98 of 205
Found at i:28715162 original size:18 final size:18
Alignment explanation
Indices: 28715114--28715154 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
28715104 TTTGGTTAAA
28715114 AATTAACCGAATTAACTG
1 AATTAACCGAATTAACTG
* *
28715132 AATTAACCAAATTACCTG
1 AATTAACCGAATTAACTG
28715150 AATTA
1 AATTA
28715155 CTCGAATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.29
Consensus pattern (18 bp):
AATTAACCGAATTAACTG
Found at i:28715229 original size:17 final size:17
Alignment explanation
Indices: 28715170--28715232 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
28715160 ATTGAATCAC
*
28715170 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
** * *
28715187 TACATAAGCCTTTGAATCAC
1 TACATAA---TTAAAAACAT
28715207 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
28715224 TACATAATT
1 TACATAATT
28715233 TTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 22 0.65
20 12 0.35
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:28715442 original size:17 final size:18
Alignment explanation
Indices: 28715420--28715457 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
28715410 TTTTAGTTTT
28715420 ATTGGGTTGGGTTGG-TA
1 ATTGGGTTGGGTTGGATA
28715437 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGATA
28715455 ATT
1 ATT
28715458 TTATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGATA
Found at i:28715883 original size:62 final size:59
Alignment explanation
Indices: 28715769--28715887 Score: 150
Period size: 62 Copynumber: 2.0 Consensus size: 59
28715759 GTACAAACTG
* ****
28715769 TTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTTGAATATTTTAATAGTAAATTA
1 TTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTGAATAAGACAATAG-AAATTA
28715829 TTTTTATATT-TTGTCCAATTTAATAAAATAAAAGTTCTTTTGAATAAGACAATAGAAAT
1 TTTTTATATTGTT-T-C-ATTTAATAAAATAAAAGTTCTTTTGAATAAGACAATAGAAAT
28715888 AATGCAACAT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
59 2 0.04
60 11 0.22
61 5 0.10
62 33 0.65
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.47
Consensus pattern (59 bp):
TTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTGAATAAGACAATAGAAATTA
Found at i:28717882 original size:64 final size:64
Alignment explanation
Indices: 28717781--28717910 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 64
28717771 TTAGATTTGG
28717781 ATTTAACCACGTGGTAGTTAATCCCGTTCATGATGCTATATTGTTTCAATACACCGAAAAAACT
1 ATTTAACCACGTGGTAGTTAATCCCGTTCATGATGCTATATTGTTTCAATACACCGAAAAAACT
*
28717845 ATTTAACCACGTGGTAGTTAATCCTGTTCATGATGCTATATTGTTTCAATACACCGAAAAAACT
1 ATTTAACCACGTGGTAGTTAATCCCGTTCATGATGCTATATTGTTTCAATACACCGAAAAAACT
28717909 AT
1 AT
28717911 CCTTACTAGA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (64 bp):
ATTTAACCACGTGGTAGTTAATCCCGTTCATGATGCTATATTGTTTCAATACACCGAAAAAACT
Found at i:28718921 original size:13 final size:13
Alignment explanation
Indices: 28718903--28718930 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28718893 CTAAACTTCT
28718903 CTAATTTTTCTTG
1 CTAATTTTTCTTG
28718916 CTAATTTTTCTTG
1 CTAATTTTTCTTG
28718929 CT
1 CT
28718931 GTAACTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.18, G:0.07, T:0.61
Consensus pattern (13 bp):
CTAATTTTTCTTG
Found at i:28719141 original size:125 final size:126
Alignment explanation
Indices: 28718986--28719346 Score: 386
Period size: 125 Copynumber: 2.9 Consensus size: 126
28718976 AAGGGTAAGT
* **
28718986 AAGAACTATTGTAGAAAAAGAGCGTCCACGTAGAAACTTTTTTCAGTAATTTTGCTAATGGTGCA
1 AAGAACTACTGTAGAAAAAGAGCGTCCACGTAGAAACTTTTTTCAGTAATTTTGCTAACAGTGCA
* * *
28719051 TCCTGCTTGAAGCGTTTTTTATATTAACTTTTCAGAACCATCTTCTCATAATT-ATTTTTC
66 TCCTGCTTGAAGCGTTTTTTACATTAACTTTTCAAAACCATCTTCTCAAAATTAATTTTTC
* * *
28719111 AAGAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
1 AAGAACTACTGTAGAAAAAGAGCGTCCACGTAGAAACTTTTTTCAGTAATTTTGCTAACAGTGCA
** **
28719176 TCCTGCTTGAAGCGTTTTTTACATTATTTTTTCAAAACTGTCTTCTCAAAATTAATTTTTC
66 TCCTGCTTGAAGCGTTTTTTACATTAACTTTTCAAAACCATCTTCTCAAAATTAATTTTTC
* * * * * * * * * ** * * *
28719237 CAGAAACTATTATAAAAAAAGAACATCCACAT-GAGAGCTTTTTTTTAGTGCTTTTGCTGAGAAT
1 AAG-AACTACTGTAGAAAAAGAGCGTCCACGTAGA-AAC-TTTTTTCAGTAATTTTGCTAACAGT
* * **
28719301 GCATCCTGCTTGAAGTGTTTTTGT-CACTATTTTTTCAAAACCATCT
63 GCATCCTGCTTGAAGCGTTTTT-TACATTAACTTTTCAAAACCATCT
28719347 CATTATTATT
Statistics
Matches: 201, Mismatches: 30, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
125 105 0.52
126 10 0.05
127 25 0.12
128 60 0.30
129 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (126 bp):
AAGAACTACTGTAGAAAAAGAGCGTCCACGTAGAAACTTTTTTCAGTAATTTTGCTAACAGTGCA
TCCTGCTTGAAGCGTTTTTTACATTAACTTTTCAAAACCATCTTCTCAAAATTAATTTTTC
Found at i:28719509 original size:34 final size:33
Alignment explanation
Indices: 28719472--28719550 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
28719462 TTATTTTTAA
28719472 AAAAACCTAAACCCTAATTTAATTAA-TTTTCTT
1 AAAAACCTAAACCCTAATTTAATTAATTTTTC-T
*
28719505 AAAAACCTTAAA-CCTAATTTGATTAATTTTTCT
1 AAAAACC-TAAACCCTAATTTAATTAATTTTTCT
*
28719538 AAAATCCTAAACC
1 AAAAACCTAAACC
28719551 TTGATTTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
32 4 0.10
33 28 0.68
34 9 0.22
ACGTcount: A:0.43, C:0.19, G:0.01, T:0.37
Consensus pattern (33 bp):
AAAAACCTAAACCCTAATTTAATTAATTTTTCT
Found at i:28719569 original size:27 final size:27
Alignment explanation
Indices: 28719523--28719605 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 27
28719513 TAAACCTAAT
*
28719523 TTGATTAATTTTTCTAAAATC-CTAAACC
1 TTGATTTA-TTTT-TAAAATCTCTAAACC
28719551 TTGATTTATTGTTTAAAATCTCTAAATCC
1 TTGATTTATT-TTTAAAATCTCTAAA-CC
*
28719580 -TGATTTATTTATAAAATCTCTAAACC
1 TTGATTTATTTTTAAAATCTCTAAACC
28719606 CTAAACAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
26 2 0.04
27 23 0.46
28 23 0.46
29 2 0.04
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.45
Consensus pattern (27 bp):
TTGATTTATTTTTAAAATCTCTAAACC
Found at i:28727470 original size:2 final size:2
Alignment explanation
Indices: 28727465--28727499 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
28727455 AATATATATA
28727465 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
28727500 ATTCAAACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28728234 original size:48 final size:48
Alignment explanation
Indices: 28728179--28728272 Score: 188
Period size: 48 Copynumber: 2.0 Consensus size: 48
28728169 GCCAGCCTCA
28728179 GTTTGGCTTCCAAGAAAATCACAAGATATAATAAGATTGAAGCGTTCG
1 GTTTGGCTTCCAAGAAAATCACAAGATATAATAAGATTGAAGCGTTCG
28728227 GTTTGGCTTCCAAGAAAATCACAAGATATAATAAGATTGAAGCGTT
1 GTTTGGCTTCCAAGAAAATCACAAGATATAATAAGATTGAAGCGTT
28728273 GAGTTTCGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (48 bp):
GTTTGGCTTCCAAGAAAATCACAAGATATAATAAGATTGAAGCGTTCG
Found at i:28730391 original size:318 final size:319
Alignment explanation
Indices: 28729796--28730433 Score: 1127
Period size: 318 Copynumber: 2.0 Consensus size: 319
28729786 AATGCATGCT
* *
28729796 TTTATATGTGTTTCATCTATGGCACCAATACAATCCTTTAAAATAAATAATGAGATAAAAGTTAG
1 TTTATATGTGTTCCATCTATGGCACCAATACAATCCTTTAAAATAAATAATAAGATAAAAGTTAG
*
28729861 AAATAATTTATATTTTAAAAATATAAAAATTGTGTAAATTTTACCTTAAAGTGATGCCAATATCT
66 AAATAATTTATATTTTAAAAATATAAAAATTGTGTAAATTTTACCTTAAAATGATGCCAATATCT
*
28729926 AGTATCATGTCGAATATGGTTCGGTACTTCCTCGAGTTGACCTTCAGTGGGTTTAATCGTGTCTA
131 AGTATCATGTCGAATATGGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCGTGTCTA
**
28729991 TTCCCATTCGAGCAAATATATGCAACATATCAGTAAAAATTTGACTAACAGTTTCCCCAGATCGT
196 TTCCCATTCGAGCAAATATATGCAACATATCAGTAAAAATTCAACTAACAGTTTCCCCAGATCGT
*
28730056 TGAAATCGCTTTGTTGCATTTGAATTTGATTCTCTATTTCCAAGAATATACAATGATAA
261 TGAAATCGCTCTGTTGCATTTGAATTTGATTCTCTATTTCCAAGAATATACAATGATAA
*
28730115 TTTATGTGTGTTCCATCTATGGTC-CCAATACAATCCTTTAAAATAAATAATAAGAT-AAAGTTA
1 TTTATATGTGTTCCATCTATGG-CACCAATACAATCCTTTAAAATAAATAATAAGATAAAAGTTA
28730178 GAAATAATTTATATTTTAAAAATATAAAAATTGTGTAAATTTTACCTTAAAATGATGCCAATATC
65 GAAATAATTTATATTTTAAAAATATAAAAATTGTGTAAATTTTACCTTAAAATGATGCCAATATC
* * *
28730243 TTGTATCATGTCGAATATGGTTCGGTATTTCCTCGAATTGACCTTTAGTGGGTTTAATCGTGTCT
130 TAGTATCATGTCGAATATGGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCGTGTCT
*
28730308 ATTCCCATTCGAGCAAATATATGTAACATATCAGTAAAAATTCAACTAACAGTTTCCCCAGATCG
195 ATTCCCATTCGAGCAAATATATGCAACATATCAGTAAAAATTCAACTAACAGTTTCCCCAGATCG
* *
28730373 TTGAAATCGCTCTGTTGCATTTGAATTTGATTCTCTATTTCTAAGAATGTACAATGATAA
260 TTGAAATCGCTCTGTTGCATTTGAATTTGATTCTCTATTTCCAAGAATATACAATGATAA
28730433 T
1 T
28730434 GCTAACTTCT
Statistics
Matches: 304, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
318 252 0.83
319 51 0.17
320 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (319 bp):
TTTATATGTGTTCCATCTATGGCACCAATACAATCCTTTAAAATAAATAATAAGATAAAAGTTAG
AAATAATTTATATTTTAAAAATATAAAAATTGTGTAAATTTTACCTTAAAATGATGCCAATATCT
AGTATCATGTCGAATATGGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCGTGTCTA
TTCCCATTCGAGCAAATATATGCAACATATCAGTAAAAATTCAACTAACAGTTTCCCCAGATCGT
TGAAATCGCTCTGTTGCATTTGAATTTGATTCTCTATTTCCAAGAATATACAATGATAA
Found at i:28737860 original size:17 final size:17
Alignment explanation
Indices: 28737838--28737891 Score: 81
Period size: 17 Copynumber: 3.2 Consensus size: 17
28737828 CAAATATGGA
*
28737838 ATGTAATCTTCGAAGAT
1 ATGTAATCTTAGAAGAT
* *
28737855 ATGTAATCTTGGATGAT
1 ATGTAATCTTAGAAGAT
28737872 ATGTAATCTTAGAAGAT
1 ATGTAATCTTAGAAGAT
28737889 ATG
1 ATG
28737892 ATTCTGTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.37
Consensus pattern (17 bp):
ATGTAATCTTAGAAGAT
Found at i:28737904 original size:24 final size:23
Alignment explanation
Indices: 28737876--28737922 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
28737866 GATGATATGT
28737876 AATCTTAGAAGATATGATTCTGTA
1 AATCTTAG-AGATATGATTCTGTA
* *
28737900 AATCTTAGAGATTTGATTTTGTA
1 AATCTTAGAGATATGATTCTGTA
28737923 GATTGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (23 bp):
AATCTTAGAGATATGATTCTGTA
Found at i:28739326 original size:9 final size:9
Alignment explanation
Indices: 28739314--28739350 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
28739304 ATCAAGATTT
28739314 GAAATCTTG
1 GAAATCTTG
28739323 GAAATCTTG
1 GAAATCTTG
28739332 GAAATCTTG
1 GAAATCTTG
28739341 GAAATCTTG
1 GAAATCTTG
28739350 G
1 G
28739351 TCCAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.32
Consensus pattern (9 bp):
GAAATCTTG
Found at i:28742137 original size:30 final size:30
Alignment explanation
Indices: 28742101--28742175 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
28742091 TGGTTGACCC
* *
28742101 ATCCCTTTTCATAATTCGATAACCGAAGTT
1 ATCCCTTTTCATAATTCGACAACCGAAGCT
* * * *
28742131 ATCCCTTTTTATAGTTTGACAGCCGAAGCT
1 ATCCCTTTTCATAATTCGACAACCGAAGCT
28742161 ATCCC-TTTCATAATT
1 ATCCCTTTTCATAATT
28742176 TGATGGTAGT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 8 0.22
30 29 0.78
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGACAACCGAAGCT
Found at i:28742193 original size:29 final size:30
Alignment explanation
Indices: 28742161--28742353 Score: 103
Period size: 30 Copynumber: 6.5 Consensus size: 30
28742151 AGCCGAAGCT
28742161 ATCCC-TTTCATAATTTGATGGTAGTCACC
1 ATCCCTTTTCATAATTTGATGGTAGTCACC
*** ** *
28742190 ATCCCTTTTCATTGCTCAATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTAGTCACC
** * *
28742220 ATCCCTTTTCATAATTTGATACCT-G-AAGCT
1 ATCCCTTTTCATAATTTGAT-GGTAGTCA-CC
* * ** ** *
28742250 ATCCCTTTTCATAAATCGACAGCCG-AATCC
1 ATCCCTTTTCATAATTTGATGGTAGTCA-CC
*
28742280 ATCCCTTTTCAT-ATTTCGATGGTCGTCACC
1 ATCCCTTTTCATAATTT-GATGGTAGTCACC
* * *
28742310 ATCCCTTTTCAT--TGTTGACGGTCGTCAAC
1 ATCCCTTTTCATAAT-TTGATGGTAGTCACC
28742339 ATCCCTTTTCATAAT
1 ATCCCTTTTCATAAT
28742354 CGATAACTGA
Statistics
Matches: 124, Mismatches: 31, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
29 32 0.26
30 89 0.72
31 3 0.02
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.37
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTGATGGTAGTCACC
Found at i:28742312 original size:30 final size:29
Alignment explanation
Indices: 28742278--28742351 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 29
28742268 ACAGCCGAAT
28742278 CCATCCCTTTTCATATTTCGATGGTCGTCA
1 CCATCCCTTTTCATATTT-GATGGTCGTCA
*
28742308 CCATCCCTTTTCAT-TGTTGACGGTCGTCA
1 CCATCCCTTTTCATAT-TTGATGGTCGTCA
*
28742337 ACATCCCTTTTCATA
1 CCATCCCTTTTCATA
28742352 ATCGATAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 24 0.60
30 16 0.40
ACGTcount: A:0.18, C:0.31, G:0.12, T:0.39
Consensus pattern (29 bp):
CCATCCCTTTTCATATTTGATGGTCGTCA
Found at i:28742333 original size:119 final size:119
Alignment explanation
Indices: 28742099--28742379 Score: 372
Period size: 119 Copynumber: 2.4 Consensus size: 119
28742089 GATGGTTGAC
* * ** * *
28742099 CCATCCCTTTTCATAATTCGATAACC-GAAGTTATCCCTTTTTATAGTTTGACAGCCGAAGCTAT
1 CCATCCCTTTTCATAATTCGAT-ACCTGAAGCTATCCCTTTTCATAAATCGACAGCCGAAGCCAT
*
28742163 CCCTTTCATAATTTGATGGTAGTCACCATCCCTTTTCATTGCTCAATGGTCGTCA
65 CCCTTTCATAATTTGATGGTAGTCACCATCCCTTTTCATTGCTCAACGGTCGTCA
* *
28742218 CCATCCCTTTTCATAATTTGATACCTGAAGCTATCCCTTTTCATAAATCGACAGCCGAATCCATC
1 CCATCCCTTTTCATAATTCGATACCTGAAGCTATCCCTTTTCATAAATCGACAGCCGAAGCCATC
* **
28742283 CCTTTTCAT-ATTTCGATGGTCGTCACCATCCCTTTTCATTG-TTGACGGTCGTCA
66 CC-TTTCATAATTT-GATGGTAGTCACCATCCCTTTTCATTGCTCAACGGTCGTCA
* * *
28742337 ACATCCCTTTTCATAA-TCGATAACTGAAGCTATCCTTTTTCAT
1 CCATCCCTTTTCATAATTCGATACCTGAAGCTATCCCTTTTCAT
28742380 TTGCTGATGA
Statistics
Matches: 143, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
118 27 0.19
119 84 0.59
120 32 0.22
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.37
Consensus pattern (119 bp):
CCATCCCTTTTCATAATTCGATACCTGAAGCTATCCCTTTTCATAAATCGACAGCCGAAGCCATC
CCTTTCATAATTTGATGGTAGTCACCATCCCTTTTCATTGCTCAACGGTCGTCA
Found at i:28744859 original size:25 final size:27
Alignment explanation
Indices: 28744820--28744889 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 27
28744810 TTGTACATGT
** *
28744820 ATGCTCACATAAGCTGT-A-AATTAGA
1 ATGCTCACACGAGCTGTGATAATGAGA
* *
28744845 ATGCTCACACGAGCTGTGATAATGGGC
1 ATGCTCACACGAGCTGTGATAATGAGA
*
28744872 CTGCTCACACGAGCTGTG
1 ATGCTCACACGAGCTGTG
28744890 GGTCGAAACG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
25 15 0.41
26 1 0.03
27 21 0.57
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (27 bp):
ATGCTCACACGAGCTGTGATAATGAGA
Found at i:28749458 original size:18 final size:18
Alignment explanation
Indices: 28749435--28749491 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
28749425 TCAGTGAAAA
*
28749435 TGGGCTCACACGCCTATG
1 TGGGCTCACACGCCCATG
28749453 TGGGCTCACACGCCCATG
1 TGGGCTCACACGCCCATG
* * *
28749471 TGGGCCCACGCGCCCGTG
1 TGGGCTCACACGCCCATG
28749489 TGG
1 TGG
28749492 CCCACTCGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.12, C:0.37, G:0.33, T:0.18
Consensus pattern (18 bp):
TGGGCTCACACGCCCATG
Found at i:28752163 original size:14 final size:13
Alignment explanation
Indices: 28752140--28752172 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
28752130 ATAGGATTGT
28752140 ATTTAGTGAAAGG
1 ATTTAGTGAAAGG
28752153 ATTTGAGTGAAAGG
1 ATTT-AGTGAAAGG
28752167 ATTTAG
1 ATTTAG
28752173 CTCAAAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.33
Consensus pattern (13 bp):
ATTTAGTGAAAGG
Found at i:28755645 original size:24 final size:23
Alignment explanation
Indices: 28755617--28755663 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
28755607 GATGATATGC
28755617 AATCTTAGA-AGTTATGATTTTGTA
1 AATCTTAGAGA-TT-TGATTTTGTA
28755641 AATCTTAGAGATTTGATTTTGTA
1 AATCTTAGAGATTTGATTTTGTA
28755664 GATTGCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.45
24 11 0.50
25 1 0.05
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (23 bp):
AATCTTAGAGATTTGATTTTGTA
Found at i:28755661 original size:23 final size:24
Alignment explanation
Indices: 28755617--28755663 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
28755607 GATGATATGC
28755617 AATCTTAGAAGTTATGATTTTGTA
1 AATCTTAGAAGTTATGATTTTGTA
28755641 AATCTTAG-AGATT-TGATTTTGTA
1 AATCTTAGAAG-TTATGATTTTGTA
28755664 GATTGCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (24 bp):
AATCTTAGAAGTTATGATTTTGTA
Found at i:28756599 original size:34 final size:34
Alignment explanation
Indices: 28756544--28756609 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
28756534 AATTATTGGA
*
28756544 AATTAATTAAAAAACATAAAATTTTATAAAAAAT
1 AATTAATTAAAAAACACAAAATTTTATAAAAAAT
* *
28756578 AATTGATTAAAAACCACAAAATTTTATAAAAA
1 AATTAATTAAAAAACACAAAATTTTATAAAAA
28756610 CAATTGTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (34 bp):
AATTAATTAAAAAACACAAAATTTTATAAAAAAT
Found at i:28760885 original size:25 final size:25
Alignment explanation
Indices: 28760839--28760886 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
28760829 TTTAGTTTGA
* *
28760839 TTAATTAATAAAATTTATATATAAT
1 TTAATTAATAAAATTGACATATAAT
* *
28760864 TTAATTAATGAAATTGGCATATA
1 TTAATTAATAAAATTGACATATA
28760887 TCTTAAGATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (25 bp):
TTAATTAATAAAATTGACATATAAT
Found at i:28762278 original size:248 final size:248
Alignment explanation
Indices: 28761840--28762342 Score: 970
Period size: 248 Copynumber: 2.0 Consensus size: 248
28761830 AAAATATGAT
*
28761840 TTATTTTATTTTATAAATAATATATGACACGCTTAATGTTTAATAAAACATGGAAAAAGGAAAGA
1 TTATTTTATTTTATAAATAATATATGACACGCTTAATGTTTAATAAAACATGGAAAAAAGAAAGA
*
28761905 AAATGTGAATTCTGTCATCTTTTTCATTAGAACCGAAAACCAAAGGGGGAAAGGGTTCTCGCTCA
66 AAATGTGAATTCTGTCATCTTTTTCATTAAAACCGAAAACCAAAGGGGGAAAGGGTTCTCGCTCA
28761970 TGACAAGCTTAACCTTGCTAATTGGTAAGTTGTTTTTAGTCTGTTTCTTATAATTTTTATGTTTT
131 TGACAAGCTTAACCTTGCTAATTGGTAAGTTGTTTTTAGTCTGTTTCTTATAATTTTTATGTTTT
28762035 TGGAATCTTAGGAGCTTGATCTATCTAACCCAGGGTGTAACTCCCCAAAATTC
196 TGGAATCTTAGGAGCTTGATCTATCTAACCCAGGGTGTAACTCCCCAAAATTC
**
28762088 TTATTTTATTTTATAAATAATATATGACACTTTTAATGTTTAATAAAACATGGAAAAAAGAAAGA
1 TTATTTTATTTTATAAATAATATATGACACGCTTAATGTTTAATAAAACATGGAAAAAAGAAAGA
28762153 AAATGTGAATTCTGTCATCTTTTTCATTAAAACCGAAAACCAAAGGGGGAAAGGGTTCTCGCTCA
66 AAATGTGAATTCTGTCATCTTTTTCATTAAAACCGAAAACCAAAGGGGGAAAGGGTTCTCGCTCA
28762218 TGACAAGCTTAACCTTGCTAATTGGTAAGTTGTTTTTAGTCTGTTTCTTATAATTTTTATGTTTT
131 TGACAAGCTTAACCTTGCTAATTGGTAAGTTGTTTTTAGTCTGTTTCTTATAATTTTTATGTTTT
28762283 TGGAATCTTAGGAGCTTGATCTATCTAACCCAGGGTGTAACTCCCCAAAATTC
196 TGGAATCTTAGGAGCTTGATCTATCTAACCCAGGGTGTAACTCCCCAAAATTC
28762336 TTATTTT
1 TTATTTT
28762343 TGTTATTGTG
Statistics
Matches: 251, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
248 251 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.37
Consensus pattern (248 bp):
TTATTTTATTTTATAAATAATATATGACACGCTTAATGTTTAATAAAACATGGAAAAAAGAAAGA
AAATGTGAATTCTGTCATCTTTTTCATTAAAACCGAAAACCAAAGGGGGAAAGGGTTCTCGCTCA
TGACAAGCTTAACCTTGCTAATTGGTAAGTTGTTTTTAGTCTGTTTCTTATAATTTTTATGTTTT
TGGAATCTTAGGAGCTTGATCTATCTAACCCAGGGTGTAACTCCCCAAAATTC
Found at i:28764858 original size:18 final size:18
Alignment explanation
Indices: 28764823--28764867 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
28764813 TCAATAAGTG
*
28764823 ACGTTTTGAAAATTAATA
1 ACGTTTTGAAAATGAATA
28764841 ACGTTTTGAAAGA-GAATA
1 ACGTTTTGAAA-ATGAATA
28764859 AC-TTTTGAA
1 ACGTTTTGAA
28764868 TACGAATCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 7 0.28
18 17 0.68
19 1 0.04
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.36
Consensus pattern (18 bp):
ACGTTTTGAAAATGAATA
Found at i:28771597 original size:40 final size:40
Alignment explanation
Indices: 28771552--28771680 Score: 115
Period size: 40 Copynumber: 3.2 Consensus size: 40
28771542 AATCAGTCTA
28771552 GCTTGAATATAATCCGTTTTGGGTTGATTATATTTTGCCT
1 GCTTGAATATAATCCGTTTTGGGTTGATTATATTTTGCCT
* * * *
28771592 GCTTGAATTATTGAAAT-TGTGTTTGTGCTG-TTATA---GGCCT
1 GCTTGAA-TA-T--AATCCGT-TTTGGGTTGATTATATTTTGCCT
* *
28771632 CGCTTGAATTTAATCCGTGTTGGGTTGATTATATTTTGCCT
1 -GCTTGAATATAATCCGTTTTGGGTTGATTATATTTTGCCT
28771673 GCTTGAAT
1 GCTTGAAT
28771681 TATTGAAATT
Statistics
Matches: 68, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
37 9 0.13
38 7 0.10
39 1 0.01
40 20 0.29
41 13 0.19
42 1 0.01
43 7 0.10
44 10 0.15
ACGTcount: A:0.19, C:0.12, G:0.22, T:0.46
Consensus pattern (40 bp):
GCTTGAATATAATCCGTTTTGGGTTGATTATATTTTGCCT
Found at i:28771655 original size:81 final size:81
Alignment explanation
Indices: 28771552--28771714 Score: 308
Period size: 81 Copynumber: 2.0 Consensus size: 81
28771542 AATCAGTCTA
*
28771552 GCTTGAATATAATCCGTTTTGGGTTGATTATATTTTGCCTGCTTGAATTATTGAAATTGTGTTTG
1 GCTTGAATATAATCCGTGTTGGGTTGATTATATTTTGCCTGCTTGAATTATTGAAATTGTGTTTG
28771617 TGCTGTTATAGGCCTC
66 TGCTGTTATAGGCCTC
*
28771633 GCTTGAATTTAATCCGTGTTGGGTTGATTATATTTTGCCTGCTTGAATTATTGAAATTGTGTTTG
1 GCTTGAATATAATCCGTGTTGGGTTGATTATATTTTGCCTGCTTGAATTATTGAAATTGTGTTTG
28771698 TGCTGTTATAGGCCTC
66 TGCTGTTATAGGCCTC
28771714 G
1 G
28771715 GTAAGATGCT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.45
Consensus pattern (81 bp):
GCTTGAATATAATCCGTGTTGGGTTGATTATATTTTGCCTGCTTGAATTATTGAAATTGTGTTTG
TGCTGTTATAGGCCTC
Found at i:28771707 original size:43 final size:43
Alignment explanation
Indices: 28771579--28771707 Score: 139
Period size: 43 Copynumber: 3.1 Consensus size: 43
28771569 TTTGGGTTGA
28771579 TTATATTTTGCCTGCTTGAATTATTGAAATTGTGTTTGTGCTG
1 TTATATTTTGCCTGCTTGAATTATTGAAATTGTGTTTGTGCTG
* * * *
28771622 TTATA---GGCCTCGCTTGAA-T-TT--AATCCGTG-TTGGGTTG
1 TTATATTTTGCCT-GCTTGAATTATTGAAAT-TGTGTTTGTGCTG
28771659 ATTATATTTTGCCTGCTTGAATTATTGAAATTGTGTTTGTGCTG
1 -TTATATTTTGCCTGCTTGAATTATTGAAATTGTGTTTGTGCTG
28771703 TTATA
1 TTATA
28771708 GGCCTCGGTA
Statistics
Matches: 67, Mismatches: 8, Indels: 22
0.69 0.08 0.23
Matches are distributed among these distances:
37 9 0.13
38 8 0.12
39 2 0.03
40 12 0.18
41 12 0.18
42 2 0.03
43 13 0.19
44 9 0.13
ACGTcount: A:0.19, C:0.11, G:0.22, T:0.48
Consensus pattern (43 bp):
TTATATTTTGCCTGCTTGAATTATTGAAATTGTGTTTGTGCTG
Found at i:28773021 original size:6 final size:6
Alignment explanation
Indices: 28773010--28773035 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28773000 GTTGCTCCAG
28773010 CAATGA CAATGA CAATGA CAATGA CA
1 CAATGA CAATGA CAATGA CAATGA CA
28773036 TATACAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.15
Consensus pattern (6 bp):
CAATGA
Found at i:28773963 original size:27 final size:27
Alignment explanation
Indices: 28773917--28774149 Score: 304
Period size: 27 Copynumber: 8.6 Consensus size: 27
28773907 TAAGATTTTG
*
28773917 CCACAAAGGCAGTTCGTTCAGAGTACA
1 CCACAAAGGCAGTTCTTTCAGAGTACA
*
28773944 CCACAAAGGCAATTCTTTCAGAGTACA
1 CCACAAAGGCAGTTCTTTCAGAGTACA
* *
28773971 CCACAAAGGAAATTCTTTCAGAGTACA
1 CCACAAAGGCAGTTCTTTCAGAGTACA
* *
28773998 CCACAAAGGCAGTTCTTTTAGAGTACG
1 CCACAAAGGCAGTTCTTTCAGAGTACA
* * * * **
28774025 CCACCAATGCAATTCTTTTAGAGTATG
1 CCACAAAGGCAGTTCTTTCAGAGTACA
*
28774052 CCACAAAGGTAGTTCTTTCAGAGTACA
1 CCACAAAGGCAGTTCTTTCAGAGTACA
* *
28774079 CCACAAAGGTAGTACTTTCAGAGTACA
1 CCACAAAGGCAGTTCTTTCAGAGTACA
* * *
28774106 CCACAAAGGTAATTCTTTCAGAGTACG
1 CCACAAAGGCAGTTCTTTCAGAGTACA
28774133 CCACAAAGGCAGTTCTT
1 CCACAAAGGCAGTTCTT
28774150 AGTTGTCGTG
Statistics
Matches: 182, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 182 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (27 bp):
CCACAAAGGCAGTTCTTTCAGAGTACA
Found at i:28774147 original size:81 final size:81
Alignment explanation
Indices: 28773917--28774149 Score: 340
Period size: 81 Copynumber: 2.9 Consensus size: 81
28773907 TAAGATTTTG
* *
28773917 CCACAAAGGCAGTTCGTTCAGAGTACACCACAAAGGCAATTCTTTCAGAGTACACCACAAAGGAA
1 CCACAAAGGCAGTTCTTTCAGAGTACACCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGAA
*
28773982 ATTCTTTCAGAGTACA
66 GTTCTTTCAGAGTACA
* * * * * * *
28773998 CCACAAAGGCAGTTCTTTTAGAGTACGCCACCAATGCAATTCTTTTAGAGTATGCCACAAAGGTA
1 CCACAAAGGCAGTTCTTTCAGAGTACACCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGAA
28774063 GTTCTTTCAGAGTACA
66 GTTCTTTCAGAGTACA
* * * *
28774079 CCACAAAGGTAGTACTTTCAGAGTACACCACAAAGGTAATTCTTTCAGAGTACGCCACAAAGGCA
1 CCACAAAGGCAGTTCTTTCAGAGTACACCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGAA
28774144 GTTCTT
66 GTTCTT
28774150 AGTTGTCGTG
Statistics
Matches: 132, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 132 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (81 bp):
CCACAAAGGCAGTTCTTTCAGAGTACACCACAAAGGCAATTCTTTCAGAGTACGCCACAAAGGAA
GTTCTTTCAGAGTACA
Found at i:28777470 original size:11 final size:11
Alignment explanation
Indices: 28777442--28777482 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
28777432 TAAAATTTAA
28777442 TTAAAAA-ATT
1 TTAAAAATATT
*
28777452 ATAAAAATATT
1 TTAAAAATATT
*
28777463 TTATAAATATT
1 TTAAAAATATT
28777474 TTAAAAATA
1 TTAAAAATA
28777483 CATAAAATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 6 0.23
11 20 0.77
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:28777503 original size:12 final size:12
Alignment explanation
Indices: 28777486--28777510 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28777476 AAAAATACAT
28777486 AAAATTCTATAA
1 AAAATTCTATAA
28777498 AAAATTCTATAA
1 AAAATTCTATAA
28777510 A
1 A
28777511 TATTTTATGT
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTCTATAA
Found at i:28777529 original size:17 final size:17
Alignment explanation
Indices: 28777507--28777556 Score: 68
Period size: 16 Copynumber: 2.9 Consensus size: 17
28777497 AAAAATTCTA
28777507 TAAATATTTTATGTTAT
1 TAAATATTTTATGTTAT
28777524 TAAATATTTT-T-TATAT
1 TAAATATTTTATGT-TAT
28777540 TAAATATTTTAATGTTA
1 TAAATATTTT-ATGTTA
28777557 AATATTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.03
16 14 0.48
17 10 0.34
18 3 0.10
19 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (17 bp):
TAAATATTTTATGTTAT
Found at i:28777542 original size:16 final size:16
Alignment explanation
Indices: 28777507--28777564 Score: 66
Period size: 15 Copynumber: 3.6 Consensus size: 16
28777497 AAAAATTCTA
28777507 TAAATATTTTATGT-TAT
1 TAAATATTTT-T-TATAT
28777524 TAAATATTTTTTATAT
1 TAAATATTTTTTATAT
* *
28777540 TAAATA-TTTTAATGT
1 TAAATATTTTTTATAT
28777555 TAAATATTTT
1 TAAATATTTT
28777565 AATGTTAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
15 14 0.38
16 13 0.35
17 10 0.27
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TAAATATTTTTTATAT
Found at i:28777557 original size:15 final size:15
Alignment explanation
Indices: 28777523--28777574 Score: 77
Period size: 15 Copynumber: 3.4 Consensus size: 15
28777513 TTTTATGTTA
* *
28777523 TTAAATATTTTTTATA
1 TTAAATA-TTTTAATG
28777539 TTAAATATTTTAATG
1 TTAAATATTTTAATG
28777554 TTAAATATTTTAATG
1 TTAAATATTTTAATG
28777569 TTAAAT
1 TTAAAT
28777575 TAATTATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
15 27 0.79
16 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (15 bp):
TTAAATATTTTAATG
Found at i:28783150 original size:3 final size:3
Alignment explanation
Indices: 28783142--28783186 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
28783132 TAGTCATTCT
*
28783142 ATA ATA ATA ATA ATA ATA ATA AAA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28783187 CGCAAAATAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:28790431 original size:31 final size:31
Alignment explanation
Indices: 28790395--28790459 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
28790385 ATTAATCTAG
*
28790395 TGACTTAAATAAAAACTTTTGAATAGTTCAA
1 TGACTTAAATAAAAACTTTCGAATAGTTCAA
* *
28790426 TGACTTAAATGAAAACTTTCGAATAGTTTAA
1 TGACTTAAATAAAAACTTTCGAATAGTTCAA
28790457 TGA
1 TGA
28790460 TCAAATTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.35
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCGAATAGTTCAA
Found at i:28794817 original size:28 final size:30
Alignment explanation
Indices: 28794769--28794833 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
28794759 ACTTACCTCA
*
28794769 TGTTTACTGTCCCAACGAACT-CTA-TTTG
1 TGTTTACTGTCCCAACAAACTCCTATTTTG
* *
28794797 TGTTTACTGTCCTAGCAAACTGCCTATTTTG
1 TGTTTACTGTCCCAACAAACT-CCTATTTTG
28794828 TGTTTA
1 TGTTTA
28794834 TTGTTGTCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 18 0.58
30 3 0.10
31 10 0.32
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (30 bp):
TGTTTACTGTCCCAACAAACTCCTATTTTG
Found at i:28795402 original size:98 final size:98
Alignment explanation
Indices: 28795233--28795623 Score: 746
Period size: 98 Copynumber: 4.0 Consensus size: 98
28795223 ACAATAAAAT
*
28795233 TTTAAAAGAACATCAACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
28795298 TCTAGAATCCCAAACTCGGAATATTTCCTTTAC
66 TCTAGAATCCCAAACTCGGAATATTTCCTTTAC
28795331 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
28795396 TCTAGAATCCCAAACTCGGAATATTTCCTTTAC
66 TCTAGAATCCCAAACTCGGAATATTTCCTTTAC
28795429 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
28795494 TCTAGAATCCCAAACTCGGAATATTTCCTTTAC
66 TCTAGAATCCCAAACTCGGAATATTTCCTTTAC
*
28795527 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
* *
28795592 TTTAAAATCCCAAACTCGGAATATTTCCTTTA
66 TCTAGAATCCCAAACTCGGAATATTTCCTTTA
28795624 TTATTTTTAA
Statistics
Matches: 289, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 289 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
TCTAGAATCCCAAACTCGGAATATTTCCTTTAC
Found at i:28795917 original size:15 final size:15
Alignment explanation
Indices: 28795899--28795931 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28795889 CAAATGCTAT
28795899 AATAATAAATACAAC
1 AATAATAAATACAAC
*
28795914 AATAATAAATACATC
1 AATAATAAATACAAC
28795929 AAT
1 AAT
28795932 GACATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:28796387 original size:19 final size:19
Alignment explanation
Indices: 28796363--28796400 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28796353 TGTAAAATAT
28796363 TTTGAAAATATATGTATAC
1 TTTGAAAATATATGTATAC
28796382 TTTGAAAATATATGTATAC
1 TTTGAAAATATATGTATAC
28796401 GGAAAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (19 bp):
TTTGAAAATATATGTATAC
Found at i:28796405 original size:17 final size:18
Alignment explanation
Indices: 28796366--28796406 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
28796356 AAAATATTTT
*
28796366 GAAAATATATGTATACTTT
1 GAAAATATATGTATAC-TG
28796385 GAAAATATATGTATAC-G
1 GAAAATATATGTATACTG
28796402 GAAAA
1 GAAAA
28796407 ATGTTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
19 16 0.76
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.32
Consensus pattern (18 bp):
GAAAATATATGTATACTG
Found at i:28797840 original size:33 final size:33
Alignment explanation
Indices: 28797802--28797882 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
28797792 ACAATTGTCT
*
28797802 TAGTGGACTATCT-TTGTCATGTGTTTATTGTCCC
1 TAGTGGACTATCTCTTGTC-TGTGTTTACTG-CCC
* *
28797836 -AGTGGAGTATCTCTTTTCTGTGTTTACTGCCC
1 TAGTGGACTATCTCTTGTCTGTGTTTACTGCCC
*
28797868 TAGCGGACTATCTCT
1 TAGTGGACTATCTCT
28797883 GTGGATGCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 3 0.08
33 33 0.82
34 4 0.10
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (33 bp):
TAGTGGACTATCTCTTGTCTGTGTTTACTGCCC
Found at i:28799965 original size:50 final size:50
Alignment explanation
Indices: 28799887--28800079 Score: 197
Period size: 50 Copynumber: 3.7 Consensus size: 50
28799877 TTTCTTGTAC
* * * **
28799887 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATTAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACATCTCATATTAG
* * * * * * **
28799937 TGCCCATGCTATGTCCCTGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACATCTCATATTAG
* *
28799987 TGCCAACGCCATGTCCCAGACATGGTTTTACATGGGACATCTCATAACCTTAATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACATCTCAT-A--TT-A-G
28800042 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
28800080 TCTCTTTACC
Statistics
Matches: 113, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
50 76 0.67
53 1 0.01
55 1 0.01
56 35 0.31
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACATCTCATATTAG
Found at i:28800021 original size:100 final size:105
Alignment explanation
Indices: 28799887--28800084 Score: 244
Period size: 100 Copynumber: 1.9 Consensus size: 105
28799877 TTTCTTGTAC
* * * ** * *
28799887 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCAT-A-TT-A-G-TGCCCATGCT
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACATCTCATAACTTAATGATGCCAATGCC
*
28799947 ATGTCCCTGACATGGTCTTACAGGGGACCTCTCATCTCGG
66 ATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
28799987 TGCCAACGCCATGTCCCAGACATGGTTTTACATGGGACATCTCATAACCTTAATGATGCCAATGC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACATCTCATAA-CTTAATGATGCCAATGC
* *
28800052 CATGTCCCAGACATGGTCTTACATGGGATCTCT
65 CATGTCCCAGACATGGTCTTACAGGGGACCTCT
28800085 TTACCCAAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
100 38 0.47
101 1 0.01
103 2 0.03
104 1 0.01
105 1 0.01
106 37 0.46
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (105 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACATCTCATAACTTAATGATGCCAATGCC
ATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:28806015 original size:31 final size:28
Alignment explanation
Indices: 28805971--28806033 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 28
28805961 AGCGTAAAGG
*
28805971 CTAAATTTTAATTTTAT-CAAATTTAGTCT
1 CTAAATTTTAATTTT-TGAAAATTTAGT-T
28806000 CTAAACTTTTCAATTTTTGAAAATTTAGTT
1 CTAAA-TTTT-AATTTTTGAAAATTTAGTT
28806030 CTAA
1 CTAA
28806034 TCAAATGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.17
30 10 0.33
31 15 0.50
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (28 bp):
CTAAATTTTAATTTTTGAAAATTTAGTT
Found at i:28810098 original size:37 final size:36
Alignment explanation
Indices: 28810047--28810122 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
28810037 ACAGCAAAAA
*
28810047 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATATTATCTTAATAGTATT-ATATT-AATTTAATAT
*
28810083 TAATACTTATCTTAATAGTATTTTATTAATTTAATAT
1 TAATA-TTATCTTAATAGTATTATATTAATTTAATAT
28810120 TAA
1 TAA
28810123 AGTGATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 13 0.37
37 20 0.57
38 2 0.06
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (36 bp):
TAATATTATCTTAATAGTATTATATTAATTTAATAT
Found at i:28811577 original size:90 final size:90
Alignment explanation
Indices: 28811401--28811640 Score: 250
Period size: 90 Copynumber: 2.6 Consensus size: 90
28811391 CAGTTTAAAT
* * * * * * * *
28811401 ATTTTGTGAATTCATCAAGTCTGTCTCAATA-GAACCACCAGCCAAAGCATGGGATATGAATTCA
1 ATTTAGTGAATTCATCAAGTCCGTCTTAACATG-ACCA-C--CCAAACCCTGGGTTATGAAATCA
* * *
28811465 TTAAGAATATTTAGTGGCTCATCCTATAA
62 TTAAGAACATCTAGTAGCTCATCCTATAA
* * *
28811494 ATTTAGT-AGGTTTATCAAGTCCGTCTTAATATGACCACCCAAACCCTGGGTTATGAAATCATTA
1 ATTTAGTGA-ATTCATCAAGTCCGTCTTAACATGACCACCCAAACCCTGGGTTATGAAATCATTA
* *
28811558 AGAGCATCTAGTAGTTCATCCTATAA
65 AGAACATCTAGTAGCTCATCCTATAA
* * *
28811584 ATTTAGTGAATTCATTAAGTTCGTCTTAACATGACCACCCAAACTCTGGGTTATGAA
1 ATTTAGTGAATTCATCAAGTCCGTCTTAACATGACCACCCAAACCCTGGGTTATGAA
28811641 CTTATTAAAA
Statistics
Matches: 124, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
90 92 0.74
91 1 0.01
92 2 0.02
93 28 0.23
94 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (90 bp):
ATTTAGTGAATTCATCAAGTCCGTCTTAACATGACCACCCAAACCCTGGGTTATGAAATCATTAA
GAACATCTAGTAGCTCATCCTATAA
Found at i:28814944 original size:22 final size:23
Alignment explanation
Indices: 28814917--28814964 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
28814907 CCCATGCCAC
28814917 AGTCCAAAA-AACAATAATAA-AA
1 AGTCCAAAATAACAA-AATAATAA
*
28814939 AGTCCAAAATACCAAAATAATAA
1 AGTCCAAAATAACAAAATAATAA
28814962 AGT
1 AGT
28814965 GTAAAACGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.62, C:0.15, G:0.06, T:0.17
Consensus pattern (23 bp):
AGTCCAAAATAACAAAATAATAA
Found at i:28815381 original size:30 final size:27
Alignment explanation
Indices: 28815320--28815382 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 27
28815310 CCAAGCCACA
**
28815320 AGATAATGTGGACAAGCTGCCAAATAC
1 AGATAATGTGGACAAGCCACCAAATAC
28815347 AGATACATGTGGACAAGCCACCAGAATCAC
1 AGATA-ATGTGGACAAGCCACCA-AAT-AC
28815377 AGATAA
1 AGATAA
28815383 ACTGCCAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 5 0.16
28 15 0.48
29 4 0.13
30 7 0.23
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.16
Consensus pattern (27 bp):
AGATAATGTGGACAAGCCACCAAATAC
Found at i:28819437 original size:24 final size:24
Alignment explanation
Indices: 28819405--28819524 Score: 150
Period size: 24 Copynumber: 5.0 Consensus size: 24
28819395 AGGCATTCCC
*
28819405 GAATACGCCACAAAGGCACTTGCA
1 GAATACGCCACAAAGGCACTTACA
*
28819429 GAATACGCCACAAAGGCACATACA
1 GAATACGCCACAAAGGCACTTACA
* *
28819453 GAATACGCCATAAATGCACTTACA
1 GAATACGCCACAAAGGCACTTACA
* * *
28819477 AAATACACCACAAAGGAACTTACA
1 GAATACGCCACAAAGGCACTTACA
* * *
28819501 AAATACGCCATAATGGCACTTACA
1 GAATACGCCACAAAGGCACTTACA
28819525 TAATCACGTG
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 82 1.00
ACGTcount: A:0.44, C:0.27, G:0.14, T:0.15
Consensus pattern (24 bp):
GAATACGCCACAAAGGCACTTACA
Found at i:28829986 original size:36 final size:36
Alignment explanation
Indices: 28829939--28830011 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
28829929 CTCATTTGAT
28829939 TTGTACCTAATGACTTATTAATGCAAGCATAACATA
1 TTGTACCTAATGACTTATTAATGCAAGCATAACATA
28829975 TTGTACCTAATGACTTATTAATGCAAGCATAACATA
1 TTGTACCTAATGACTTATTAATGCAAGCATAACATA
28830011 T
1 T
28830012 ATGCATACTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (36 bp):
TTGTACCTAATGACTTATTAATGCAAGCATAACATA
Found at i:28841443 original size:260 final size:261
Alignment explanation
Indices: 28840982--28841507 Score: 921
Period size: 260 Copynumber: 2.0 Consensus size: 261
28840972 ATTCATACGA
*
28840982 ACTTACCTGGCTAAATTGTAAAAATTTCAAAGTACAAGGGCATTTTTACCATTCTCCTCGATTTT
1 ACTTACCTGGCTAAATTGTAAAAATGTCAAAGTACAAGGGCATTTTTACCATTCTCCTCGATTTT
* *
28841047 CCATCCGATCTTGATCTAAATTAATAATTTCATTCAATCTATTAATTTAGACAGTAAAAAATGTA
66 CCATCCAATCTTGATCTAAATTAATAATTTCAATCAATCTATTAATTTAGACAGTAAAAAATGTA
*
28841112 TTTTATGCAATTTAGTCATTATTTACATTTTTAAAAAATTACCCCTAAAGTTTTACTTTTGTTCA
131 TTTAATGCAATTTAGTCATTATTTACATTTTTAAAAAATTACCCCTAAAGTTTTACTTTTGTTCA
* *
28841177 ATTTAGTCCCTAAGCCTAAAACATGCAATTTAACCATTTTTACCC-AAAATTGAGCTTAGTCGAA
196 ATTTAGTCCCTAAGCCAAAAACATGCAATTTAACCATTTTTACCCAAAAATTGAGCCTAGTCGAA
28841241 T
261 T
*
28841242 ACTTACCTGGCTAAATTGTAGAAATGTCAAAGTAC-AGGAGCATTTTTACCATTCTCCTCGATTT
1 ACTTACCTGGCTAAATTGTAAAAATGTCAAAGTACAAGG-GCATTTTTACCATTCTCCTCGATTT
*
28841306 TCCATCCAATCTTGATCTAATTTAATAATTTCAATCAATCTATTAATTTAGACAGTAAAAAATGT
65 TCCATCCAATCTTGATCTAAATTAATAATTTCAATCAATCTATTAATTTAGACAGTAAAAAATGT
* *
28841371 ATTTAATGCAATTTAGTCATTTTTTACATTTTTACAAAATTACCCCTAAAGTTTTACTTTTGTTC
130 ATTTAATGCAATTTAGTCATTATTTACATTTTTAAAAAATTACCCCTAAAGTTTTACTTTTGTTC
* *
28841436 AATTTAGTCCCTGAGCCAAAAACATGCAATTTAACCATTTTTACCCAAAAATTGAGCCTATTCGA
195 AATTTAGTCCCTAAGCCAAAAACATGCAATTTAACCATTTTTACCCAAAAATTGAGCCTAGTCGA
28841501 AT
260 AT
28841503 ACTTA
1 ACTTA
28841508 TTGCATCCAA
Statistics
Matches: 252, Mismatches: 12, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
259 3 0.01
260 226 0.90
261 23 0.09
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.38
Consensus pattern (261 bp):
ACTTACCTGGCTAAATTGTAAAAATGTCAAAGTACAAGGGCATTTTTACCATTCTCCTCGATTTT
CCATCCAATCTTGATCTAAATTAATAATTTCAATCAATCTATTAATTTAGACAGTAAAAAATGTA
TTTAATGCAATTTAGTCATTATTTACATTTTTAAAAAATTACCCCTAAAGTTTTACTTTTGTTCA
ATTTAGTCCCTAAGCCAAAAACATGCAATTTAACCATTTTTACCCAAAAATTGAGCCTAGTCGAA
T
Found at i:28843414 original size:21 final size:21
Alignment explanation
Indices: 28843390--28843432 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28843380 TGGAATTTTT
*
28843390 AAGTTAAACAAATTTTTGAAA
1 AAGTTAAACAAAGTTTTGAAA
* *
28843411 AAGTTAAATAGAGTTTTGAAA
1 AAGTTAAACAAAGTTTTGAAA
28843432 A
1 A
28843433 CTGTAACTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (21 bp):
AAGTTAAACAAAGTTTTGAAA
Found at i:28846812 original size:40 final size:42
Alignment explanation
Indices: 28846727--28846817 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 42
28846717 AACAAAGTAG
* *
28846727 TATCTAAATATTAATTGAGTAAAAGTAAAGTTAAACAATTACAA
1 TATCTAAATATTAATTAAGT--AAGTAAACTTAAACAATTACAA
* *
28846771 TATCTAAATATTAATTAAGT-A-TAAACTTAAATATTTACAA
1 TATCTAAATATTAATTAAGTAAGTAAACTTAAACAATTACAA
28846811 TATCTAA
1 TATCTAA
28846818 TACAAATTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 23 0.53
41 1 0.02
44 19 0.44
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (42 bp):
TATCTAAATATTAATTAAGTAAGTAAACTTAAACAATTACAA
Found at i:28864465 original size:62 final size:62
Alignment explanation
Indices: 28864360--28864546 Score: 196
Period size: 62 Copynumber: 3.0 Consensus size: 62
28864350 CATGACTCAT
* * * * * * *
28864360 ACGGCTTGGGTACACGCCCATGTCCCTAATCATGTTGTTTTATATCACAAACAGTGAGTTAC
1 ACGGCTTGGGTACAAGCCCGTGTCCCTAGTCGTGTGGTCTTATACCACAAACAGTGAGTTAC
* * * * *
28864422 ACGGCTTGGGTACATGCCCGTGTCCCTGGCCGTGTGGTCTTATACCACAAACAGTAAGGTAC
1 ACGGCTTGGGTACAAGCCCGTGTCCCTAGTCGTGTGGTCTTATACCACAAACAGTGAGTTAC
* * * * * *
28864484 ACGGCCTGAGCACAAGCCTGTGTCCCAAGTCGTGTGGTCTTGA-CCCACAAACAGTGAGTTAC
1 ACGGCTTGGGTACAAGCCCGTGTCCCTAGTCGTGTGGTCTT-ATACCACAAACAGTGAGTTAC
28864546 A
1 A
28864547 GGGCCTGGAC
Statistics
Matches: 102, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
62 101 0.99
63 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (62 bp):
ACGGCTTGGGTACAAGCCCGTGTCCCTAGTCGTGTGGTCTTATACCACAAACAGTGAGTTAC
Found at i:28864552 original size:62 final size:62
Alignment explanation
Indices: 28864399--28864566 Score: 178
Period size: 62 Copynumber: 2.7 Consensus size: 62
28864389 TCATGTTGTT
* * * * * **
28864399 TTATATCACAAACAGTGAGTTACACGGCTTGGGTACATGCCCGTGTCCCTGGCCGTGTGGTC
1 TTATACCACAAACAGTGAGTTACACGGCCTGAGCACAAGCCCGTGTCCCAAGCCGTGTGGTC
* * * *
28864461 TTATACCACAAACAGTAAGGTACACGGCCTGAGCACAAGCCTGTGTCCCAAGTCGTGTGGTC
1 TTATACCACAAACAGTGAGTTACACGGCCTGAGCACAAGCCCGTGTCCCAAGCCGTGTGGTC
* * *
28864523 TTGA-CCCACAAACAGTGAGTTACAGGGCCTG-GACACACGCCCGT
1 TT-ATACCACAAACAGTGAGTTACACGGCCTGAG-CACAAGCCCGT
28864567 ATCCATGGCT
Statistics
Matches: 87, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
61 1 0.01
62 85 0.98
63 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.22
Consensus pattern (62 bp):
TTATACCACAAACAGTGAGTTACACGGCCTGAGCACAAGCCCGTGTCCCAAGCCGTGTGGTC
Found at i:28866075 original size:16 final size:16
Alignment explanation
Indices: 28866056--28866091 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28866046 ATTTGTTTTT
*
28866056 GTTCTGTATTCAGGTA
1 GTTCTGTATTCAGCTA
*
28866072 GTTCTGTATTTAGCTA
1 GTTCTGTATTCAGCTA
28866088 GTTC
1 GTTC
28866092 ATATTCTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.14, G:0.22, T:0.47
Consensus pattern (16 bp):
GTTCTGTATTCAGCTA
Found at i:28866349 original size:16 final size:17
Alignment explanation
Indices: 28866328--28866361 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
28866318 AAACACAACA
28866328 TTTTTAT-ATTTAAAAT
1 TTTTTATAATTTAAAAT
28866344 TTTTTATAATTTAAAAT
1 TTTTTATAATTTAAAAT
28866361 T
1 T
28866362 AAATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTATAATTTAAAAT
Found at i:28866859 original size:20 final size:20
Alignment explanation
Indices: 28866818--28866855 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
28866808 TTGAAGTTAC
*
28866818 AAATTATATAAAATAACTAT
1 AAATTATATAAAATAAATAT
*
28866838 AAATTATA-ACAATAAATA
1 AAATTATATAAAATAAATA
28866856 ATAATTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATTATATAAAATAAATAT
Found at i:28870322 original size:50 final size:50
Alignment explanation
Indices: 28870218--28870313 Score: 124
Period size: 50 Copynumber: 2.0 Consensus size: 50
28870208 ACATTAAGGG
* * *
28870218 AATGAGA--TCCCATGTAAAACCATGTCTGGGACACGGCGTTGGCTCCAA
1 AATGAGATGTCCCATGTAAAACCATGTCTGGGACACGGCATGGGCACCAA
* * *
28870266 AATGAGATGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACC
1 AATGAGATGTCCCATGTAAAACCATGTCTGGGACACGGCATGGGCACC
28870314 GATGTGAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
48 7 0.17
50 33 0.82
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (50 bp):
AATGAGATGTCCCATGTAAAACCATGTCTGGGACACGGCATGGGCACCAA
Found at i:28876495 original size:23 final size:23
Alignment explanation
Indices: 28876440--28876516 Score: 118
Period size: 23 Copynumber: 3.3 Consensus size: 23
28876430 AGTGTTATTG
28876440 ATCAGTGGTAGCTTCGGCTACATT
1 ATCAGTGGTAGCTTCGGCTACA-T
* *
28876464 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
28876487 ATCAGTGGTAGCTTCGTCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28876510 ATCAGTG
1 ATCAGTG
28876517 TGGCACTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 28 0.58
24 20 0.42
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:28880520 original size:42 final size:42
Alignment explanation
Indices: 28880382--28880776 Score: 335
Period size: 42 Copynumber: 9.3 Consensus size: 42
28880372 CGATGGATTT
* * * *
28880382 AGCACTTAGCAACCACCTT-AAATTCAGTGATACGGGGAATC
1 AGCACATAGCAACCACCTTCACATTCAATAATACGGGGAATC
* *
28880423 AGCACATAGCAACC-CCTTTCACAGTCTAA-GATACGGTGGAATC
1 AGCACATAGCAACCACC-TTCACATTC-AATAATACGG-GGAATC
* * * *
28880466 ACCACTTTGCAACCACCTTCATATTCAATAATACGGGGAATC
1 AGCACATAGCAACCACCTTCACATTCAATAATACGGGGAATC
* *
28880508 AGCACATAGCAACC-CCGTTCACAGTCTAA-GATACGGTGGAATC
1 AGCACATAGCAACCACC-TTCACATTC-AATAATACGG-GGAATC
* * * *
28880551 ACCACTTGGCAACCACCTTCATATTCAATAATACGGGGAATC
1 AGCACATAGCAACCACCTTCACATTCAATAATACGGGGAATC
* *
28880593 AGCACATAGCAACC-CCGTTCACAGTCTAA-GATACGGTGGAATC
1 AGCACATAGCAACCACC-TTCACATTC-AATAATACGG-GGAATC
* * * *
28880636 ACCACTTGGCAACCACCTTCATATTCAATAATACGGGGAATC
1 AGCACATAGCAACCACCTTCACATTCAATAATACGGGGAATC
* *
28880678 AGCACATAGCAACC-CCTTTC-CAATTCAAAAATACGGTGGCATC
1 AGCACATAGCAACCACC-TTCAC-ATTCAATAATACGG-GGAATC
* * *
28880721 AGCACATAGCAACCACC-TCTAGAGTCAGTAA-ATCGGGGAATC
1 AGCACATAGCAACCACCTTC-ACATTCAATAATA-CGGGGAATC
*
28880763 AGCACTTAGCAACC
1 AGCACATAGCAACC
28880777 CCTCGGGGAA
Statistics
Matches: 285, Mismatches: 46, Indels: 45
0.76 0.12 0.12
Matches are distributed among these distances:
40 2 0.01
41 21 0.07
42 131 0.46
43 123 0.43
44 8 0.03
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (42 bp):
AGCACATAGCAACCACCTTCACATTCAATAATACGGGGAATC
Found at i:28880779 original size:85 final size:85
Alignment explanation
Indices: 28880384--28880779 Score: 575
Period size: 85 Copynumber: 4.7 Consensus size: 85
28880374 ATGGATTTAG
* * *
28880384 CACTTAGCAACCACCTT-AAATTCAGTGATACGGGGAATCAGCACATAGCAACCCCTTTCACAGT
1 CACTTAGCAACCACCTTCATATTCAATAATACGGGGAATCAGCACATAGCAACCCCTTTCACAGT
28880448 CTAAGATACGGTGGAATCAC
66 CTAAGATACGGTGGAATCAC
* *
28880468 CACTTTGCAACCACCTTCATATTCAATAATACGGGGAATCAGCACATAGCAACCCCGTTCACAGT
1 CACTTAGCAACCACCTTCATATTCAATAATACGGGGAATCAGCACATAGCAACCCCTTTCACAGT
28880533 CTAAGATACGGTGGAATCAC
66 CTAAGATACGGTGGAATCAC
* *
28880553 CACTTGGCAACCACCTTCATATTCAATAATACGGGGAATCAGCACATAGCAACCCCGTTCACAGT
1 CACTTAGCAACCACCTTCATATTCAATAATACGGGGAATCAGCACATAGCAACCCCTTTCACAGT
28880618 CTAAGATACGGTGGAATCAC
66 CTAAGATACGGTGGAATCAC
* *
28880638 CACTTGGCAACCACCTTCATATTCAATAATACGGGGAATCAGCACATAGCAACCCCTTTC-CAAT
1 CACTTAGCAACCACCTTCATATTCAATAATACGGGGAATCAGCACATAGCAACCCCTTTCAC-AG
* * * *
28880702 TCAAAAATACGGTGGCATCAG
65 TCTAAGATACGGTGGAATCAC
* * * * *
28880723 CACATAGCAACCACC-TCTAGAGTCAGTAA-ATCGGGGAATCAGCACTTAGCAACCCCT
1 CACTTAGCAACCACCTTC-ATATTCAATAATA-CGGGGAATCAGCACATAGCAACCCCT
28880780 CGGGGAATCA
Statistics
Matches: 290, Mismatches: 18, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
84 20 0.07
85 270 0.93
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (85 bp):
CACTTAGCAACCACCTTCATATTCAATAATACGGGGAATCAGCACATAGCAACCCCTTTCACAGT
CTAAGATACGGTGGAATCAC
Found at i:28888202 original size:43 final size:42
Alignment explanation
Indices: 28888144--28888298 Score: 181
Period size: 43 Copynumber: 3.6 Consensus size: 42
28888134 TAAATTCAGT
28888144 GATACGGGGAATCAGCACATAGCAACCCCTTTCACAATCAAA
1 GATACGGGGAATCAGCACATAGCAACCCCTTTCACAATCAAA
* ** * * *
28888186 GATACGGTAGAATCAGCAGTTAGCAACAACCTTT-ATATTCAATA
1 GATACGG-GGAATCAGCACATAGCAAC-CCCTTTCACAATCAA-A
28888230 -ATACGGGGAATCAGCACATAGCAACCCCTTTC-CAATTCAAA
1 GATACGGGGAATCAGCACATAGCAACCCCTTTCACAA-TCAAA
*
28888271 AATACGGTGGAATCAGCACATAGCAACC
1 GATACGG-GGAATCAGCACATAGCAACC
28888299 ACCTCTAGAG
Statistics
Matches: 94, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
41 7 0.07
42 33 0.35
43 48 0.51
44 6 0.06
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (42 bp):
GATACGGGGAATCAGCACATAGCAACCCCTTTCACAATCAAA
Found at i:28888252 original size:42 final size:40
Alignment explanation
Indices: 28888116--28888339 Score: 180
Period size: 43 Copynumber: 5.3 Consensus size: 40
28888106 CGATGGATTT
* * * *
28888116 AGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAATC
1 AGCACATAGCAA-CACCTTTAATTCAATAATACGGGGAATC
* * *
28888157 AGCACATAGCAACCCCTTTCACAATCAA-AGATACGGTAGAATC
1 AGCACATAGCAACACCTTT-A-ATTCAATA-ATACGG-GGAATC
**
28888200 AGCAGTTAGCAACAACCTTTATATTCAATAATACGGGGAATC
1 AGCACATAGCAAC-ACCTTTA-ATTCAATAATACGGGGAATC
* *
28888242 AGCACATAGCAACCCCTTTCCAATTCAAAAATACGGTGGAATC
1 AGCACATAGCAACACCTTT--AATTCAATAATACGG-GGAATC
* * * *
28888285 AGCACATAGCAACCACCTCTAGAGTCAGTAATTCGGGGAATC
1 AGCACATAGCAA-CACCTTTA-ATTCAATAATACGGGGAATC
* *
28888327 AACACTTAGCAAC
1 AGCACATAGCAAC
28888340 CCCTCGGGGA
Statistics
Matches: 147, Mismatches: 25, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
40 5 0.03
41 18 0.12
42 56 0.38
43 57 0.39
44 11 0.07
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (40 bp):
AGCACATAGCAACACCTTTAATTCAATAATACGGGGAATC
Found at i:28888270 original size:85 final size:85
Alignment explanation
Indices: 28888116--28888343 Score: 307
Period size: 85 Copynumber: 2.7 Consensus size: 85
28888106 CGATGGATTT
*
28888116 AGCACTTAGCAACCACC-TTAAATTCAGTGATACGGGGAATCAGCACATAGCAACCCCTTTCACA
1 AGCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCCTTTCACA
*
28888180 ATCAAAGATACGGTAGAATC
66 ATCAAAAATACGGTAGAATC
* * * *
28888200 AGCAGTTAGCAACAACCTTTATATTCAATAATACGGGGAATCAGCACATAGCAACCCCTTTC-CA
1 AGCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCCTTTCACA
*
28888264 ATTCAAAAATACGGTGGAATC
66 A-TCAAAAATACGGTAGAATC
* * * * * * *
28888285 AGCACATAGCAACCACCTCTAGAGTCAGTAATTCGGGGAATCAACACTTAGCAACCCCT
1 AGCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCCT
28888344 CGGGGAATCT
Statistics
Matches: 125, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
84 18 0.14
85 107 0.86
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.21
Consensus pattern (85 bp):
AGCACTTAGCAACCACCTTTAAATTCAGTAATACGGGGAATCAGCACATAGCAACCCCTTTCACA
ATCAAAAATACGGTAGAATC
Found at i:28892599 original size:50 final size:50
Alignment explanation
Indices: 28892510--28892624 Score: 126
Period size: 50 Copynumber: 2.3 Consensus size: 50
28892500 GATCACATGA
* * * * *
28892510 AAGACCATGTCTGGGACATGGCGTTGGCGTCGAGATGAGAAGTCCCCCGT
1 AAGACCATGTCTGGGACATGGCATGGGCCTCGAGATGAGAACTCCCACGT
* *
28892560 AAGACCATGTTTGGGACATGGCATGGGCACT-GATG-TGAGAACTCCCATGT
1 AAGACCATGTCTGGGACATGGCATGGGC-CTCGA-GATGAGAACTCCCACGT
*
28892610 AAGACCATATCTGGG
1 AAGACCATGTCTGGG
28892625 CTATGACATT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
50 52 0.96
51 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (50 bp):
AAGACCATGTCTGGGACATGGCATGGGCCTCGAGATGAGAACTCCCACGT
Found at i:28907102 original size:16 final size:16
Alignment explanation
Indices: 28907069--28907102 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28907059 GTAAATTCTC
*
28907069 AAAAAGATATGAAAAG
1 AAAAAGATAGGAAAAG
*
28907085 AAAAAGATAGGAACAG
1 AAAAAGATAGGAAAAG
28907101 AA
1 AA
28907103 GAGAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.21, T:0.09
Consensus pattern (16 bp):
AAAAAGATAGGAAAAG
Found at i:28910530 original size:200 final size:201
Alignment explanation
Indices: 28910180--28910631 Score: 728
Period size: 200 Copynumber: 2.2 Consensus size: 201
28910170 TTGCCATCTA
* * *
28910180 TTTTTTAATAATAGTTTTCCAAGACTTAAATGCGAAAAACACATCACTTTTCTGCTTCAGGAAGA
1 TTTTTCAATAATAGTTTTCCAAGACTTAAATGCGGAAAACACATCAC-TTTCTACTTCAGGAAGA
*
28910245 ATGCCCAAACTTTTCTAGAAAAATCATCAATAAAAGTTAGCATATAATTAGCTCCACCTCTCGAA
65 ACGCCCAAACTTTTCTAGAAAAATCATCAATAAAAGTTAGCATATAATTAGCTCCACCTCTCGAA
*
28910310 AGCACTCTAGATGGCCTCCACAGATCAGAATGAATATACTCCAGCGTTCCCTTCATGTTATGGC-
130 AGCACTCTAGATGGCCTCCACAGATCAGAATGAATATACTCCAACGTTCCCTTCATGTTATGGCT
28910374 TTTTCTG
195 TTTTCTG
*
28910381 TTTTTCAATAATAGTTTTCCAAGACTTAAATGCGGAAAACACATCACTTTCTACTTTAGGAAGAA
1 TTTTTCAATAATAGTTTTCCAAGACTTAAATGCGGAAAACACATCACTTTCTACTTCAGGAAGAA
* *
28910446 CGCCCAAACTTTTCTAGAAAAATCATCAATAAAAGTTAGCATATAATTAGGTTCACCTCTC-AAA
66 CGCCCAAACTTTTCTAGAAAAATCATCAATAAAAGTTAGCATATAATTAGCTCCACCTCTCGAAA
* * *
28910510 GGCACTCTAGATGGCCTCCACAGATCAGAATTAATATACTCCAATGTTCCCTTCCTGTTATGGCT
131 -GCACTCTAGATGGCCTCCACAGATCAGAATGAATATACTCCAACGTTCCCTTCATGTTATGGCT
*
28910575 TTTTTTG
195 TTTTCTG
* * * *
28910582 TTTTTCAATAAGAGTATTCCAAGACTTAAATGTGGAAGACACATCACTTT
1 TTTTTCAATAATAGTTTTCCAAGACTTAAATGCGGAAAACACATCACTTT
28910632 TCAGAATTAA
Statistics
Matches: 233, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
199 3 0.01
200 133 0.57
201 97 0.42
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.32
Consensus pattern (201 bp):
TTTTTCAATAATAGTTTTCCAAGACTTAAATGCGGAAAACACATCACTTTCTACTTCAGGAAGAA
CGCCCAAACTTTTCTAGAAAAATCATCAATAAAAGTTAGCATATAATTAGCTCCACCTCTCGAAA
GCACTCTAGATGGCCTCCACAGATCAGAATGAATATACTCCAACGTTCCCTTCATGTTATGGCTT
TTTCTG
Found at i:28913199 original size:33 final size:33
Alignment explanation
Indices: 28913144--28913235 Score: 95
Period size: 28 Copynumber: 2.9 Consensus size: 33
28913134 TAACAATCTA
* * *
28913144 GGCCTGAGCCCTATTCAGTAACAGTATAGTGTG
1 GGCCTTAGCCCAATACAGTAACAGTATAGTGTG
* *
28913177 GGCCTTAGCCTAATACATTAAC-----AGTGTG
1 GGCCTTAGCCCAATACAGTAACAGTATAGTGTG
*
28913205 GGCCTTAGCCCAATACAGTAATAGTATAGTG
1 GGCCTTAGCCCAATACAGTAACAGTATAGTG
28913236 CAATAATACA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
28 25 0.54
33 21 0.46
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (33 bp):
GGCCTTAGCCCAATACAGTAACAGTATAGTGTG
Found at i:28913361 original size:26 final size:26
Alignment explanation
Indices: 28913332--28913412 Score: 117
Period size: 26 Copynumber: 3.1 Consensus size: 26
28913322 AACACACCAA
28913332 TATCGCAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
* *
28913358 TATCGCAGCAAAGCTACCACTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
* * *
28913384 TATTGCAACAAAGCTGCTAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
28913410 TAT
1 TAT
28913413 ACTTTCTCCA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAACAG
Found at i:28913596 original size:27 final size:27
Alignment explanation
Indices: 28913576--28914096 Score: 436
Period size: 27 Copynumber: 19.4 Consensus size: 27
28913566 GGGTATAACA
28913576 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
28913603 GTCATTTTATCCTATGA-GGTATCTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
28913629 GTCATTTTATCCTAT-AGGGGTATCTCG
1 GTCATTTTACCCTATGA-GGGTATTTCG
* *
28913656 ATCATTTTACCCAATGAGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
28913683 GTCA-TTTACCCTATGGGGGTATCTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
28913709 ATCATTTTACCCTATAAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
28913736 GTCATTTTACCCTATGGGGGTATTCCA
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
28913763 GTTATTTTACCTTAT-AGGGGTATTTCA
1 GTCATTTTACCCTATGA-GGGTATTTCG
** *
28913790 GTCATGCTACTCTAT-AGGGGTA-TTCTG
1 GTCATTTTACCCTATGA-GGGTATTTC-G
* * * *
28913817 ATCATTTTATCCTATTAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * * *
28913844 ATTATTTTACTCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *** * *
28913871 GTTATTCTATATTATGGGGGTATTTCA
1 GTCATTTTACCCTATGAGGGTATTTCG
*
28913898 GTCATTTTA-CC-ATGTAGGGGTATTTCT
1 GTCATTTTACCCTATG-A-GGGTATTTCG
28913925 GTCATTTTACCCTATG-GGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * *
28913951 GTCATTTTACCGTATGGGGGTATTTCT
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
28913978 ATCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* * * *
28914005 ATCTTTTTATCCTATG-GGCATATTTCG
1 GTCATTTTACCCTATGAGG-GTATTTCG
* *
28914032 GTCATTCTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGAGGGTATTTCG
* *
28914059 GTCATTTTATCCTGT-AGGGATATTT-G
1 GTCATTTTACCCTATGAGGG-TATTTCG
28914085 GATCATTTTACC
1 G-TCATTTTACC
28914097 TATTTTGTGG
Statistics
Matches: 403, Mismatches: 74, Indels: 34
0.79 0.14 0.07
Matches are distributed among these distances:
25 4 0.01
26 79 0.20
27 309 0.77
28 8 0.02
29 3 0.01
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGAGGGTATTTCG
Found at i:28914386 original size:20 final size:19
Alignment explanation
Indices: 28914345--28914386 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
28914335 AGCCCAATGA
**
28914345 GCCCACATGGCCCATTTTG
1 GCCCACATGGCCCATTACG
28914364 GCCCACCATGGCCCATTACG
1 GCCCA-CATGGCCCATTACG
28914384 GCC
1 GCC
28914387 AAAGCCCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.17, C:0.43, G:0.21, T:0.19
Consensus pattern (19 bp):
GCCCACATGGCCCATTACG
Found at i:28921435 original size:41 final size:41
Alignment explanation
Indices: 28921378--28921483 Score: 185
Period size: 41 Copynumber: 2.6 Consensus size: 41
28921368 AATGAGATAA
* *
28921378 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
28921419 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
*
28921460 TTCGGACTTTACGTCTAGCAGGCT
1 TTCAGACTTTACGTCTAGCAGGCT
28921484 AATTGCCAGT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
Found at i:28929297 original size:92 final size:92
Alignment explanation
Indices: 28929137--28929444 Score: 327
Period size: 92 Copynumber: 3.3 Consensus size: 92
28929127 CTGGCGTGTT
* * *
28929137 ATAGCTCTTATGAGCAA--TACGTCATGTTATCAAGGGAGAATATTTAGCCTACAAGCTTTTCAC
1 ATAGCTCTTATGAGCAATCTA-G-CGTGTTATCGAGGGAGAATATTTAGCCTACAAGCTTTACAC
* *
28929200 CATGTGTATC-CGACATGTTATCGGTTGGA
64 TATGTGTATCTAG-CATGTTATCGGTTGGA
* * * **
28929229 ATAGCTCTTATTAGTAATCTAGCGTGTTAT-TAGGAGAGAATATTTAGCCTACGGGCTTTACACT
1 ATAGCTCTTATGAGCAATCTAGCGTGTTATCGAGG-GAGAATATTTAGCCTACAAGCTTTACACT
* *
28929293 ATGTGTATCTATCATGTTATCGTTTGGA
65 ATGTGTATCTAGCATGTTATCGGTTGGA
* * * * * *
28929321 ATAGATGTTATGAGCAATTTGGCATGTTATCGAGGGAGAATATTTAGCCTACAAGCTTTGCACTA
1 ATAGCTCTTATGAGCAATCTAGCGTGTTATCGAGGGAGAATATTTAGCCTACAAGCTTTACACTA
** **
28929386 TGTCAATCTAGCATGTTATTAGTTGGA
66 TGTGTATCTAGCATGTTATCGGTTGGA
* * *
28929413 ATAACTCTTATGAGCAAACTAACGTGTTATCG
1 ATAGCTCTTATGAGCAATCTAGCGTGTTATCG
28929445 GATGGTTACC
Statistics
Matches: 175, Mismatches: 36, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
91 3 0.02
92 166 0.95
93 4 0.02
94 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (92 bp):
ATAGCTCTTATGAGCAATCTAGCGTGTTATCGAGGGAGAATATTTAGCCTACAAGCTTTACACTA
TGTGTATCTAGCATGTTATCGGTTGGA
Found at i:28933110 original size:16 final size:16
Alignment explanation
Indices: 28933078--28933112 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28933068 GTAGATCGGC
*
28933078 AAATGCCGAAATCCTG
1 AAATGCCGAAAACCTG
*
28933094 AAATGCCGAAAAGCTG
1 AAATGCCGAAAACCTG
28933110 AAA
1 AAA
28933113 GTACAGCTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (16 bp):
AAATGCCGAAAACCTG
Found at i:28933520 original size:27 final size:27
Alignment explanation
Indices: 28933443--28933557 Score: 115
Period size: 27 Copynumber: 4.3 Consensus size: 27
28933433 CAAAAAGGTT
* *
28933443 GTAAAATTACCAAAATACCCCCAAAGG
1 GTAAAATTACCAAAATACCCCCGATGG
* * *
28933470 GTAAAATTATCGAAATACCCTCGATGG
1 GTAAAATTACCAAAATACCCCCGATGG
**
28933497 GTAAAATTACCAAAATACCTTCGATGG
1 GTAAAATTACCAAAATACCCCCGATGG
* * * *
28933524 ATAAAATTATCGAAATACCTCCG-TAGG
1 GTAAAATTACCAAAATACCCCCGAT-GG
28933551 GTAAAAT
1 GTAAAAT
28933558 AACTGTTATA
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
26 1 0.01
27 73 0.99
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (27 bp):
GTAAAATTACCAAAATACCCCCGATGG
Found at i:28937690 original size:179 final size:180
Alignment explanation
Indices: 28937382--28937733 Score: 611
Period size: 179 Copynumber: 1.9 Consensus size: 180
28937372 TTTGCATAAA
*
28937382 TTTTAAGGAATCCTTAGTTAAATAGTAGCATAGAAATATGCATAATTTTTTCTAAGTGACAAATC
1 TTTTAAGGAATCCTTAGTTAAACAGTAGCATAGAAATA-GCAT-ATTTTTTCTAAGTGACAAATC
*
28937447 TAAGATCTCGAAAGAGCTTATGATTTAGCTTCCAAGTTCATAAATGGTTGAGTTGCCATAGAATT
64 TAAGATCTCGAAAGAGCTTATGATTTAGATTCCAAGTTCATAAATGGTTGAGTTGCCATAGAATT
*
28937512 TTTCCTAGACATTGTTAAACATGATAAGGAATGAATTGAATTATGAACATTT
129 TTTCCAAGACATTGTTAAACATGATAAGGAATGAATTGAATTATGAACATTT
28937564 TTTTAAGGAATCCTTAGTTAAACAGT-GACATAGAAATCA-CAT-TTTTTTCTAAGTGACAAATC
1 TTTTAAGGAATCCTTAGTTAAACAGTAG-CATAGAAAT-AGCATATTTTTTCTAAGTGACAAATC
*
28937626 TAAGATCTCGAAAGAGCTTATGATTTAGATTCCAAGTTCATAAATGGTTGAGTTGCCGTAGAATT
64 TAAGATCTCGAAAGAGCTTATGATTTAGATTCCAAGTTCATAAATGGTTGAGTTGCCATAGAATT
28937691 TTTCCAAGACATTGTTAAACATGATAAGGAATGAATTGAATTA
129 TTTCCAAGACATTGTTAAACATGATAAGGAATGAATTGAATTA
28937734 AAAGTTGTAG
Statistics
Matches: 164, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
179 125 0.76
181 4 0.02
182 34 0.21
183 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (180 bp):
TTTTAAGGAATCCTTAGTTAAACAGTAGCATAGAAATAGCATATTTTTTCTAAGTGACAAATCTA
AGATCTCGAAAGAGCTTATGATTTAGATTCCAAGTTCATAAATGGTTGAGTTGCCATAGAATTTT
TCCAAGACATTGTTAAACATGATAAGGAATGAATTGAATTATGAACATTT
Found at i:28951857 original size:50 final size:50
Alignment explanation
Indices: 28951796--28951990 Score: 223
Period size: 50 Copynumber: 3.9 Consensus size: 50
28951786 ATGTTCGCTT
* * * *
28951796 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCTCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACATCCGGTA
* * *
28951846 CACGTAGTAGCCTGCACATAATACTACACACGTGATCGA-AACTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATAAC-ATCCGGTA
* * * * *
28951897 CGCATAGTAGCCTGCTCATAGTACTACACATGCGACC-TATCATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACA-TCCGGTA
* *
28951947 CACATAGTAGCCTGCACATAGTACTTCACACGTGACCATCACAT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACAT
28951991 TCACTTTTAC
Statistics
Matches: 118, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
49 1 0.01
50 77 0.65
51 40 0.34
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.24
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACATCCGGTA
Found at i:28951924 original size:101 final size:101
Alignment explanation
Indices: 28951798--28951981 Score: 280
Period size: 101 Copynumber: 1.8 Consensus size: 101
28951788 GTTCGCTTCA
* * *
28951798 CATAGTAGCCTGCACATAGTACTACACATGTGACC-ATTACCTCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-CTCCGATACACATAGTAGCCTGCA
28951862 CATAATACTACACACGTGATCGAAACTATCCGGTACG
65 CATAATACTACACACGTGATCGAAACTATCCGGTACG
* * *
28951899 CATAGTAGCCTGCTCATAGTACTACACATGCGACCTATCATTCCGGTACACATAGTAGCCTGCAC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCACTCCGATACACATAGTAGCCTGCAC
* *
28951964 ATAGTACTTCACACGTGA
66 ATAATACTACACACGTGA
28951982 CCATCACATT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 71 0.96
102 3 0.04
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCACTCCGATACACATAGTAGCCTGCAC
ATAATACTACACACGTGATCGAAACTATCCGGTACG
Found at i:28954828 original size:42 final size:42
Alignment explanation
Indices: 28954748--28954829 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
28954738 CGTTTTCTCT
* **
28954748 ATGCCATAGTCCAACTATGGTCTTAAACATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTAAACATATGCACATATTG
*
28954790 ATGCCATAGCCCAACTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAACTATGGTCTTAAACA-TATGCACATAT
28954830 CACACCGATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTAAACATATGCACATATTG
Found at i:28957557 original size:51 final size:51
Alignment explanation
Indices: 28957495--28957678 Score: 203
Period size: 51 Copynumber: 3.6 Consensus size: 51
28957485 CTTCACATAA
* * * *
28957495 TAGCCTACACATAGTACTACACATGTGCCCATTACCATCCGATACACGTAG
1 TAGCCTGCACATAGTACTACACACGTGACCATTACCATCCGGTACACGTAG
** * * * *
28957546 TAGCCTGCACATAGTACTACACACGTGATTGA-AACTATCTGGTACACATAG
1 TAGCCTGCACATAGTACTACACACGTGA-CCATTACCATCCGGTACACGTAG
* * *
28957597 TAGCCTGCACATAGTACTACACATGCGACC--TATCATTCCGGTACACGTAG
1 TAGCCTGCACATAGTACTACACACGTGACCATTACCA-TCCGGTACACGTAG
*
28957647 TAGCCTGCACATAGTACTCCACACGTGACCAT
1 TAGCCTGCACATAGTACTACACACGTGACCAT
28957679 CACATTCACT
Statistics
Matches: 107, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
49 2 0.02
50 39 0.36
51 65 0.61
52 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (51 bp):
TAGCCTGCACATAGTACTACACACGTGACCATTACCATCCGGTACACGTAG
Found at i:28957670 original size:101 final size:101
Alignment explanation
Indices: 28957488--28957674 Score: 286
Period size: 101 Copynumber: 1.8 Consensus size: 101
28957478 ATGTTCGCTT
* *
28957488 CACATAATAGCCTACACATAGTACTACACATGTGCCCATTACCATCCGATACACGTAGTAGCCTG
1 CACATAATAGCCTACACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTG
28957553 CACATAGTACTACACACGTGATTGAAACTATCTGGTA
65 CACATAGTACTACACACGTGATTGAAACTATCTGGTA
* * * *
28957590 CACATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTG
1 CACATAATAGCCTACACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTG
*
28957654 CACATAGTACTCCACACGTGA
65 CACATAGTACTACACACGTGA
28957675 CCATCACATT
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
100 4 0.05
101 40 0.52
102 33 0.43
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.24
Consensus pattern (101 bp):
CACATAATAGCCTACACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTGC
ACATAGTACTACACACGTGATTGAAACTATCTGGTA
Found at i:28965749 original size:27 final size:27
Alignment explanation
Indices: 28965718--28965895 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28965708 TAAATTGTAC
28965718 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
28965745 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28965771 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28965799 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
28965827 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28965854 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28965881 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28965896 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:28965832 original size:82 final size:81
Alignment explanation
Indices: 28965719--28965874 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28965709 AAATTGTACA
* *
28965719 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
28965783 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28965800 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
28965865 TGCGAGTTGA
65 TGCGAATTGA
28965875 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28965886 original size:82 final size:81
Alignment explanation
Indices: 28965715--28965895 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
28965705 GATTAAATTG
* *
28965715 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28965780 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28965796 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28965860 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28965878 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28965896 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28973343 original size:12 final size:12
Alignment explanation
Indices: 28973326--28973351 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28973316 CATTCCGAAG
28973326 TATATATATACA
1 TATATATATACA
28973338 TATATATATACA
1 TATATATATACA
28973350 TA
1 TA
28973352 AGTATGCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATATACA
Found at i:28973864 original size:27 final size:27
Alignment explanation
Indices: 28973833--28974010 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28973823 TAAATTGTAC
28973833 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
28973860 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28973886 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28973914 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
28973942 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28973969 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28973996 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28974011 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:28973947 original size:82 final size:81
Alignment explanation
Indices: 28973834--28973989 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28973824 AAATTGTACA
* *
28973834 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
28973898 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28973915 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
28973980 TGCGAGTTGA
65 TGCGAATTGA
28973990 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28974001 original size:82 final size:81
Alignment explanation
Indices: 28973830--28974010 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
28973820 GATTAAATTG
* *
28973830 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28973895 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28973911 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28973975 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28973993 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28974011 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28977301 original size:50 final size:50
Alignment explanation
Indices: 28977213--28977311 Score: 121
Period size: 50 Copynumber: 2.0 Consensus size: 50
28977203 GGACATTTAA
28977213 AGATGTTAACAAATCAACCCAGCAATTCAGTTTCTGC-TTTCTTTCCCTNG
1 AGATGTTAACAAATCAACCCAGCAATTCAGTTTCTGCTTTTCTTTCCCT-G
* * * * *
28977263 AGATGTTAGCAAATCAGCCCAGCACTTGA-TTTCTTGCTTTTTTTTCCCT
1 AGATGTTAACAAATCAACCCAGCAATTCAGTTTC-TGCTTTTCTTTCCCT
28977312 AATGAGTCCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 4 0.10
50 28 0.67
51 10 0.24
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.37
Consensus pattern (50 bp):
AGATGTTAACAAATCAACCCAGCAATTCAGTTTCTGCTTTTCTTTCCCTG
Found at i:28977733 original size:11 final size:11
Alignment explanation
Indices: 28977708--28977742 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
28977698 AACTTTATTA
28977708 TCTTTTATGTTT
1 TCTTTTAT-TTT
28977720 TCTTTTATTTT
1 TCTTTTATTTT
28977731 TCTTTTATTTT
1 TCTTTTATTTT
28977742 T
1 T
28977743 ATCTTGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 15 0.65
12 8 0.35
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.80
Consensus pattern (11 bp):
TCTTTTATTTT
Found at i:28978783 original size:39 final size:39
Alignment explanation
Indices: 28978740--28978819 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
28978730 TCATAATTTA
*
28978740 TCCTGGTTTAGAAAGTGAGGTTGAAAGATAGGTGAGTAT
1 TCCTGGTTTAGAAAGCGAGGTTGAAAGATAGGTGAGTAT
28978779 TCCTGGTTTAGAAAGCGAGGTTGAAAGATAGGTGAGTAT
1 TCCTGGTTTAGAAAGCGAGGTTGAAAGATAGGTGAGTAT
28978818 TC
1 TC
28978820 ATTGATTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (39 bp):
TCCTGGTTTAGAAAGCGAGGTTGAAAGATAGGTGAGTAT
Found at i:28982120 original size:27 final size:27
Alignment explanation
Indices: 28982089--28982151 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
28982079 TTAGAGTGTG
28982089 CCACAAAGGCATTCC-CTTCATAGATCA
1 CCACAAAGGC-TTCCTCTTCATAGATCA
* *
28982116 CCACAAATGCTTCCTTTTTCATAGATCA
1 CCACAAAGGCTTCC-TCTTCATAGATCA
28982144 CCACAAAG
1 CCACAAAG
28982152 ACATCCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 4 0.13
27 9 0.29
28 18 0.58
ACGTcount: A:0.33, C:0.32, G:0.10, T:0.25
Consensus pattern (27 bp):
CCACAAAGGCTTCCTCTTCATAGATCA
Found at i:28982158 original size:28 final size:28
Alignment explanation
Indices: 28982105--28982161 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
28982095 AGGCATTCCC
*
28982105 TTCATAGATCACCACAAATGCTTCCTTT
1 TTCATAGATCACCACAAATGCATCCTTT
28982133 TTCATAGATCACCACAAA-GACATCCTTT
1 TTCATAGATCACCACAAATG-CATCCTTT
28982161 T
1 T
28982162 CCAGCATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.33
Consensus pattern (28 bp):
TTCATAGATCACCACAAATGCATCCTTT
Found at i:28985628 original size:101 final size:102
Alignment explanation
Indices: 28985513--28985735 Score: 249
Period size: 101 Copynumber: 2.2 Consensus size: 102
28985503 GCATGGACTG
* ** *
28985513 TGTGTAGGCCACTATGTGAAAGTGAAAG-TGAT-GGTCACGTGTGTAGTACTATGTGTAGGCTAC
1 TGTGTAGGCTACTATGTGAAACAGAAAGCT--TCGATCACGTGTGTAGTACTATGTGTAGGCTAC
*
28985576 TACGTGTA-CTAGA-A-TGATAGGTCGCATGTGTAGTACAA
64 TACGTGTATC-AGATAGTGAT-GGTCACATGTGTAGTACAA
* * * * * *
28985614 TGTGTAAGCTACTATGCGTACCAGATAGCTTCGATCACGTGTGTAGTACTATGTTTAGGCTACTA
1 TGTGTAGGCTACTATGTGAAACAGAAAGCTTCGATCACGTGTGTAGTACTATGTGTAGGCTACTA
* *
28985679 CGTGTATCGGATAGTGATGGTCACATGTGTAGTACTA
66 CGTGTATCAGATAGTGATGGTCACATGTGTAGTACAA
*
28985716 TGTGCAGGCTACTATGTGAA
1 TGTGTAGGCTACTATGTGAA
28985736 CCGGTATCAT
Statistics
Matches: 100, Mismatches: 17, Indels: 9
0.79 0.13 0.07
Matches are distributed among these distances:
100 1 0.01
101 59 0.59
102 36 0.36
103 4 0.04
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (102 bp):
TGTGTAGGCTACTATGTGAAACAGAAAGCTTCGATCACGTGTGTAGTACTATGTGTAGGCTACTA
CGTGTATCAGATAGTGATGGTCACATGTGTAGTACAA
Found at i:28985676 original size:51 final size:49
Alignment explanation
Indices: 28985544--28985729 Score: 185
Period size: 51 Copynumber: 3.7 Consensus size: 49
28985534 GTGAAAGTGA
* *
28985544 TGGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACTAGA-ATGAT
1 TGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGATA-G-T
* * * * * *
28985594 AGGTCGCATGTGTAGTACAATGTGTAAGCTACTATGCGTACCAGATAGCT
1 TGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGATAG-T
* * * * *
28985644 TCGATCACGTGTGTAGTACTATGTTTAGGCTACTACGTGTATCGGATAGT
1 T-GGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGATAGT
*
28985694 GATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 --TGGTCACATGTGTAGTACTATGTGTAGGCTACTA
28985730 TGTGAACCGG
Statistics
Matches: 108, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
50 40 0.37
51 67 0.62
52 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (49 bp):
TGGTCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGATAGT
Found at i:28985979 original size:16 final size:16
Alignment explanation
Indices: 28985958--28985989 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28985948 TGATTGAAAG
*
28985958 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
28985974 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
28985990 GCGACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:28997380 original size:47 final size:47
Alignment explanation
Indices: 28997324--28997468 Score: 131
Period size: 47 Copynumber: 3.1 Consensus size: 47
28997314 ATAAGAAATT
* *
28997324 TTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TTTAATATTAAGAATTTTATGAAATTATATATAATTATTAAATTATA
** * *
28997371 TTTAATATTAATTA-TTT-T-AAATTGTATA-AATTCATATAAGA--AAA
1 TTTAATATTAAGAATTTTATGAAATTATATATAATT-AT-TAA-ATTATA
* * *
28997415 TTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TTTAATATTAAGAATTTTATGAAATTATATATAATTATTAAATTATA
*
28997462 TGTAATA
1 TTTAATA
28997469 ATAATTATTT
Statistics
Matches: 74, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
43 3 0.04
44 23 0.31
45 8 0.11
46 8 0.11
47 29 0.39
48 3 0.04
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (47 bp):
TTTAATATTAAGAATTTTATGAAATTATATATAATTATTAAATTATA
Found at i:28997452 original size:91 final size:91
Alignment explanation
Indices: 28997305--28997512 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
28997295 TTGATTTTAG
* *
28997305 TAAATTCATATAAGAAATTTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAAA-ATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
28997370 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
28997397 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
28997462 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
28997488 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
28997513 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 91 0.84
92 17 0.16
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:28997481 original size:26 final size:28
Alignment explanation
Indices: 28997427--28997487 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
28997417 TATTATCAAG
* *
28997427 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
28997455 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
28997481 AATTATA
1 AATTATA
28997488 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:28997487 original size:44 final size:43
Alignment explanation
Indices: 28997345--28997487 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
28997335 GAATTTTATG
* *
28997345 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
28997389 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
28997436 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
28997480 AAATTATA
1 AAATTATA
28997488 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:28997593 original size:59 final size:57
Alignment explanation
Indices: 28997529--28997935 Score: 196
Period size: 59 Copynumber: 6.8 Consensus size: 57
28997519 ATTATTTTAA
*
28997529 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTGTTTCAAATTAT
1 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTGATT--AATTAT
** * * ** * *
28997588 ATTTTA-TAGTGTCATATATTATGAGTTTAGTAAATTCATATAAGAATTATAATT-ATTAA-GA-
1 ATTTTATTA-AATCATATATT-TTA-ATTA--AAA-T-ATAT-TTAATAATAATTGATTAATTAT
28997649 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATT-ATTTCAAATTAT
1 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTGA-TT--AATTAT
* * * ** * *
28997708 ATTTTA-TAGTATCATATATTATGATTTTAGTAAAT-TCATAAAAGAAT-ATTGATT-ATTAAGA
1 ATTTTATTA-AATCATATATT-TTA-ATTA--AAATAT-ATTTAATAATAATTGATTAATT-A-T
28997769 ATTTTATTAAAAT-ATATATTTTAATTAAAATATATTTAATAATAATT-ATGTTAAATTAT
1 ATTTTATT-AAATCATATATTTTAATTAAAATATATTTAATAATAATTGA--TT-AATTAT
* * * * * *
28997828 ATTTTA-TAGTATCATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTGATT-ATTAAGA
1 ATTTTATTA-AATCATATATT-TTAATT-A--AAATAT-ATTTAATAATAATTGATTAATT-A-T
* *
28997889 ATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATT
1 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATT
28997936 ATGTTAAAAT
Statistics
Matches: 260, Mismatches: 44, Indels: 89
0.66 0.11 0.23
Matches are distributed among these distances:
54 10 0.04
55 6 0.02
56 1 0.00
57 29 0.11
58 16 0.06
59 59 0.23
60 19 0.07
61 55 0.21
62 18 0.07
63 31 0.12
64 1 0.00
65 6 0.02
66 9 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.48
Consensus pattern (57 bp):
ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTGATTAATTAT
Found at i:28997805 original size:16 final size:17
Alignment explanation
Indices: 28997769--28997803 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
28997759 ATTATTAAGA
28997769 ATTTTATTAAAATATAT
1 ATTTTATTAAAATATAT
28997786 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
28997804 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:28997928 original size:15 final size:15
Alignment explanation
Indices: 28997893--28997934 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28997883 TTAAGAATTT
*
28997893 TATTAAATTAT-ATA
1 TATTTAATTATAATA
28997907 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
28997921 TATTTAATAATAAT
1 TATTTAATTATAAT
28997935 TATGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:28997943 original size:120 final size:119
Alignment explanation
Indices: 28997528--28997937 Score: 691
Period size: 120 Copynumber: 3.4 Consensus size: 119
28997518 AATTATTTTA
*
28997528 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTGTTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
* *
28997593 ATAGTGTCATATATTATGAGTTTAGTAAATTCATATAAGAAT-TATAATTATTAAG
66 ATAGTATCATATATTATGA-TTTAGTAAATTCATATAAGAATAT-TGATTATTAAG
28997648 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
*
28997713 ATAGTATCATATATTATGATTTTAGTAAATTCATAAAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGA-TTTAGTAAATTCATATAAGAATATTGATTATTAAG
28997768 AATTTTATTAAAAT-ATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATT
1 AATTTTATT-AAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATT
28997831 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
64 TTATAGTATCATATATTATGATTT-AGTAAATTCATATAAGAATATTGATTATTAAG
* *
28997888 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT
28997938 GTTAAAATAT
Statistics
Matches: 278, Mismatches: 7, Indels: 10
0.94 0.02 0.03
Matches are distributed among these distances:
119 7 0.03
120 264 0.95
121 7 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.48
Consensus pattern (119 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
ATAGTATCATATATTATGATTTAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:28998147 original size:16 final size:16
Alignment explanation
Indices: 28998123--28998155 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28998113 TTGATTTGCT
*
28998123 ATTATGCCTCTATTCC
1 ATTACGCCTCTATTCC
28998139 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
28998155 A
1 A
28998156 ATACAGCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.33, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:29022352 original size:30 final size:29
Alignment explanation
Indices: 29022318--29022390 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
29022308 TGATCATCAG
* *
29022318 CATCCCTTTTCATAATTTGATAGCCGAAGT
1 CATCCCTTTTCATAA-TCGATAGCCGAAGC
*
29022348 CATCCCTTTTCATGATCGATAGCCGAAGC
1 CATCCCTTTTCATAATCGATAGCCGAAGC
29022377 CATCCCTTTTCATA
1 CATCCCTTTTCATA
29022391 GTTCAATGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 25 0.64
30 14 0.36
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.34
Consensus pattern (29 bp):
CATCCCTTTTCATAATCGATAGCCGAAGC
Found at i:29022380 original size:29 final size:30
Alignment explanation
Indices: 29022198--29022390 Score: 124
Period size: 30 Copynumber: 6.5 Consensus size: 30
29022188 ATGGTTAACA
* * * *
29022198 CATCTCTTTTCTTTATTCGATAGCCGAGGC
1 CATCCCTTTTCATAATTCGATAGCCGAAGC
* * *
29022228 TATCCCTTTTCGTAATTCGATAGCCAAAGC
1 CATCCCTTTTCATAATTCGATAGCCGAAGC
* * * ** *
29022258 TATCCCTTTTCATAATTTGATGGTTGTCA-C
1 CATCCCTTTTCATAATTCGATAGCCG-AAGC
** * * ***
29022288 CAT-CCTATTTCATGGTTCAATGATCATCAG-
1 CATCCCT-TTTCATAATTCGAT-AGCCGAAGC
* *
29022318 CATCCCTTTTCATAATTTGATAGCCGAAGT
1 CATCCCTTTTCATAATTCGATAGCCGAAGC
*
29022348 CATCCCTTTTCATGA-TCGATAGCCGAAGC
1 CATCCCTTTTCATAATTCGATAGCCGAAGC
29022377 CATCCCTTTTCATA
1 CATCCCTTTTCATA
29022391 GTTCAATGGT
Statistics
Matches: 122, Mismatches: 35, Indels: 13
0.72 0.21 0.08
Matches are distributed among these distances:
29 32 0.26
30 86 0.70
31 4 0.03
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.37
Consensus pattern (30 bp):
CATCCCTTTTCATAATTCGATAGCCGAAGC
Found at i:29022416 original size:29 final size:29
Alignment explanation
Indices: 29022376--29022451 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
29022366 ATAGCCGAAG
*
29022376 CCATCCCTTTTCATAGTTCAATGGTCATCA
1 CCATCCCTTTTCATAATT-AATGGTCATCA
* * **
29022406 CCATCCCTTTCCATAATTTATGGTTGTCA
1 CCATCCCTTTTCATAATTAATGGTCATCA
29022435 CCATCCCTTTTCATAAT
1 CCATCCCTTTTCATAAT
29022452 CGATAGACAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 24 0.60
30 16 0.40
ACGTcount: A:0.22, C:0.30, G:0.08, T:0.39
Consensus pattern (29 bp):
CCATCCCTTTTCATAATTAATGGTCATCA
Found at i:29043477 original size:20 final size:21
Alignment explanation
Indices: 29043449--29043487 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
29043439 TGTAAACTTA
29043449 AGTGCTTAAATT-ATATTTTT
1 AGTGCTTAAATTGATATTTTT
*
29043469 AGTGGTTAAATTGATATTT
1 AGTGCTTAAATTGATATTT
29043488 AGGCTTGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (21 bp):
AGTGCTTAAATTGATATTTTT
Found at i:29047122 original size:28 final size:28
Alignment explanation
Indices: 29047089--29047230 Score: 133
Period size: 28 Copynumber: 5.1 Consensus size: 28
29047079 AGGCATTCCC
*
29047089 TTCATAGATTGCCATAAATGCTTCCTTT
1 TTCATAGATTGCCATAAAGGCTTCCTTT
* *
29047117 TTCATAGATTTCCATAAAGGCTTCCATT
1 TTCATAGATTGCCATAAAGGCTTCCTTT
* * *
29047145 TTCATAAATCT-CTACAAAGGCTTCCTTT
1 TTCATAGAT-TGCCATAAAGGCTTCCTTT
* *** *
29047173 TTCATAAACCACCACAAAGGCTTCCTTT
1 TTCATAGATTGCCATAAAGGCTTCCTTT
* * * *
29047201 TTAAGAGATCGCCATGAAGGCTTCCTTT
1 TTCATAGATTGCCATAAAGGCTTCCTTT
29047229 TT
1 TT
29047231 TGGCGTTTTT
Statistics
Matches: 95, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
28 94 0.99
29 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.37
Consensus pattern (28 bp):
TTCATAGATTGCCATAAAGGCTTCCTTT
Found at i:29047150 original size:56 final size:56
Alignment explanation
Indices: 29047072--29047230 Score: 144
Period size: 56 Copynumber: 2.9 Consensus size: 56
29047062 TTTAAAGTGT
* * * **
29047072 ACCACAAAGGCATTCC--CTTCATAGATTGCCATAAATGCTTCCTTTTTCATAGATT
1 ACCACAAAGGC-TTCCATTTTCATAGATTGCCATAAAGGCTTCCTTTTTCATAAACC
* * * * *
29047127 TCCATAAAGGCTTCCATTTTCATAAATCT-CTACAAAGGCTTCCTTTTTCATAAACC
1 ACCACAAAGGCTTCCATTTTCATAGAT-TGCCATAAAGGCTTCCTTTTTCATAAACC
* * * * *
29047183 ACCACAAAGGCTTCCTTTTTAAGAGATCGCCATGAAGGCTTCCTTTTT
1 ACCACAAAGGCTTCCATTTTCATAGATTGCCATAAAGGCTTCCTTTTT
29047231 TGGCGTTTTT
Statistics
Matches: 80, Mismatches: 20, Indels: 7
0.75 0.19 0.07
Matches are distributed among these distances:
54 4 0.05
55 9 0.11
56 66 0.82
57 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (56 bp):
ACCACAAAGGCTTCCATTTTCATAGATTGCCATAAAGGCTTCCTTTTTCATAAACC
Found at i:29050372 original size:22 final size:21
Alignment explanation
Indices: 29050347--29050395 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
29050337 AAGTCATGTA
29050347 ATTTATCAAACCCAATAA-ATAT
1 ATTTATCAAACCCAA-AATAT-T
* *
29050369 ATTTATTATACCCAAAATATT
1 ATTTATCAAACCCAAAATATT
29050390 ATTTAT
1 ATTTAT
29050396 TTATTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTTATCAAACCCAAAATATT
Found at i:29053074 original size:3 final size:3
Alignment explanation
Indices: 29053068--29053092 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29053058 TTAACAATAA
29053068 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
29053093 CTTTTCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Done.