Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 92 of 316
Found at i:27946294 original size:14 final size:14
Alignment explanation
Indices: 27946275--27946301 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27946265 CAAAATCGAT
27946275 AAAATTTTCATATC
1 AAAATTTTCATATC
27946289 AAAATTTTCATAT
1 AAAATTTTCATAT
27946302 GACCTTCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATTTTCATATC
Found at i:27950004 original size:29 final size:30
Alignment explanation
Indices: 27949949--27950028 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
27949939 AATCTCAACA
* ***
27949949 TATACTGGGCTGAAGCCTTTTGTTAAA-CAG
1 TATACTGGGCCGAAGCCTTTCCATAAATC-G
27949979 T-TACTGGGCCGAAGCCTTTCCATAAATCG
1 TATACTGGGCCGAAGCCTTTCCATAAATCG
*
27950008 TATCACTGGGTCGAAGCCTTT
1 TAT-ACTGGGCCGAAGCCTTT
27950029 ACTGTAAACG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
29 23 0.55
30 3 0.07
31 16 0.38
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (30 bp):
TATACTGGGCCGAAGCCTTTCCATAAATCG
Found at i:27950269 original size:24 final size:23
Alignment explanation
Indices: 27950242--27950291 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
27950232 GCCTAGCCTC
27950242 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAACT--GGCAAAGCCCT
*
27950266 TTTTGATAAACTGGCAAAGCCCT
1 TTTTAATAAACTGGCAAAGCCCT
27950289 TTT
1 TTT
27950292 GCACTTCCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 14 0.58
24 6 0.25
25 4 0.17
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (23 bp):
TTTTAATAAACTGGCAAAGCCCT
Found at i:27950361 original size:21 final size:21
Alignment explanation
Indices: 27950337--27950397 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
27950327 TATAATGAGT
*
27950337 ATATCATGGCATATCATGTGA
1 ATATCATGACATATCATGTGA
** * *
27950358 ATATCAAAACGTATCATGTGC
1 ATATCATGACATATCATGTGA
*
27950379 ATATCATGTCATATCATGT
1 ATATCATGACATATCATGT
27950398 ATAATAACAA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (21 bp):
ATATCATGACATATCATGTGA
Found at i:27950397 original size:10 final size:10
Alignment explanation
Indices: 27950337--27950397 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
27950327 TATAATGAGT
*
27950337 ATATCATGGC
1 ATATCATGTC
*
27950347 ATATCATGTGA
1 ATATCATGT-C
***
27950358 ATATCAAAAC
1 ATATCATGTC
*
27950368 GTATCATGTGC
1 ATATCATGT-C
27950379 ATATCATGTC
1 ATATCATGTC
27950389 ATATCATGT
1 ATATCATGT
27950398 ATAATAACAA
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
10 23 0.61
11 15 0.39
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (10 bp):
ATATCATGTC
Found at i:27950465 original size:25 final size:25
Alignment explanation
Indices: 27950437--27950484 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
27950427 ATAATTAAAC
* * *
27950437 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
27950462 CCTAGGGGCAAAATAGTCATTTT
1 CCTAGGGGCAAAATAGTCATTTT
27950485 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:27969423 original size:18 final size:18
Alignment explanation
Indices: 27969402--27969511 Score: 105
Period size: 18 Copynumber: 6.1 Consensus size: 18
27969392 AGTCACTCTT
27969402 TAACAGTCAGTTATTCAG
1 TAACAGTCAGTTATTCAG
* * *
27969420 TAACTA-TAAATTATTCAA
1 TAAC-AGTCAGTTATTCAG
* *
27969438 TAACAGTCAATTTTTCAG
1 TAACAGTCAGTTATTCAG
** *
27969456 TAGTAGTCAGTTATCCAG
1 TAACAGTCAGTTATTCAG
* *
27969474 TAACAATTAGTTATTCAG
1 TAACAGTCAGTTATTCAG
*
27969492 TAGCAGTCAGTTATTCAG
1 TAACAGTCAGTTATTCAG
27969510 TA
1 TA
27969512 CCTTTATTTA
Statistics
Matches: 71, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
17 1 0.01
18 69 0.97
19 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (18 bp):
TAACAGTCAGTTATTCAG
Found at i:27969464 original size:54 final size:54
Alignment explanation
Indices: 27969406--27969511 Score: 140
Period size: 54 Copynumber: 2.0 Consensus size: 54
27969396 ACTCTTTAAC
* * *
27969406 AGTCAGTTATTCAGTAACTATAAATTATTCAATAACAGTCAATTTTTCAGTAGT
1 AGTCAGTTATCCAGTAACAATAAATTATTCAATAACAGTCAATTATTCAGTAGT
* * * * *
27969460 AGTCAGTTATCCAGTAACAATTAGTTATTCAGTAGCAGTCAGTTATTCAGTA
1 AGTCAGTTATCCAGTAACAATAAATTATTCAATAACAGTCAATTATTCAGTA
27969512 CCTTTATTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (54 bp):
AGTCAGTTATCCAGTAACAATAAATTATTCAATAACAGTCAATTATTCAGTAGT
Found at i:27971405 original size:47 final size:47
Alignment explanation
Indices: 27971346--27971464 Score: 193
Period size: 47 Copynumber: 2.5 Consensus size: 47
27971336 TTGGCACTAG
*
27971346 GACAAGGATACCATGTAAGACCATGTTTGGAACGTGGCATTTGGTAA
1 GACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAA
27971393 GACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAA
1 GACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAA
* * * *
27971440 GATAAGGACATCATGTAAAACCATG
1 GACAAGGATACCATGTAAGACCATG
27971465 CCAAGGCATG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.24
Consensus pattern (47 bp):
GACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAA
Found at i:27971570 original size:55 final size:54
Alignment explanation
Indices: 27971452--27971639 Score: 186
Period size: 55 Copynumber: 3.5 Consensus size: 54
27971442 TAAGGACATC
* * * ***
27971452 ATGTAAAACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGG-AAAGGAAAT
1 ATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGCAAAGGTCCT
** *
27971505 CATGTAAGACCATGTAAAGACATGGCATTGATGACTTACTATAAGGCAAAGGTCCT
1 -ATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGGCAAAGGTCCT
* *
27971561 ATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC-AAGGATACC-
1 ATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGCAAAGG-T-CCT
* **
27971614 AAGTAAGACCATATCAAGACATGGCA
1 ATGTAAGACCATGCCAAGACATGGCA
27971640 ATGGTAAGTT
Statistics
Matches: 112, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
52 4 0.04
53 30 0.27
54 33 0.29
55 39 0.35
56 6 0.05
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (54 bp):
ATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGCAAAGGTCCT
Found at i:27971651 original size:53 final size:54
Alignment explanation
Indices: 27971451--27971650 Score: 199
Period size: 53 Copynumber: 3.7 Consensus size: 54
27971441 ATAAGGACAT
* * * * * *
27971451 CATGTAAAACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAAT
1 CATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGATAC
* * *
27971505 CATGTAAGACCATGTAAAGACATGGCATTGATGACTTACTATAAGGCAAAGG-T-C
1 CATGTAAGACCATGTCAAGACATGGCATTGATAAGTT-CTATAAGGC-AAGGATAC
* * * *
27971559 CTATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATAC
1 C-ATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGATAC
* * * *
27971613 CAAGTAAGACCATATCAAGACATGGCAATGGTAAGTTC
1 CATGTAAGACCATGTCAAGACATGGCATTGATAAGTTC
27971651 AAAAAGGAAA
Statistics
Matches: 121, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
52 4 0.03
53 39 0.32
54 35 0.29
55 39 0.32
56 4 0.03
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (54 bp):
CATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGATAC
Found at i:27971665 original size:108 final size:109
Alignment explanation
Indices: 27971452--27971661 Score: 262
Period size: 108 Copynumber: 1.9 Consensus size: 109
27971442 TAAGGACATC
* *
27971452 ATGTAAAACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAATCATGTAAGACCA
1 ATGTAAAACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAACCAAGTAAGACCA
* * * * * *
27971517 TGTAAAGACATGGCATTGATGACTTACTATAAGGCAAAGGTCCT
66 TATAAAGACATGGCAATGATAACTTACAAAAAGGAAAAGGTCCT
* * * * *
27971561 ATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATACCAAGTAAGACCA
1 ATGTAAAACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAACCAAGTAAGACCA
* * *
27971625 TATCAAGACATGGCAATGGTAAGTT-CAAAAAGGAAAA
66 TATAAAGACATGGCAATGATAACTTACAAAAAGGAAAA
27971662 AGGTTCCCGA
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
107 9 0.11
108 42 0.49
109 34 0.40
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (109 bp):
ATGTAAAACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGAAAGGAAACCAAGTAAGACCA
TATAAAGACATGGCAATGATAACTTACAAAAAGGAAAAGGTCCT
Found at i:27973800 original size:13 final size:12
Alignment explanation
Indices: 27973784--27973822 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
27973774 TTTCCTATTA
27973784 TGTTTCTTTTCTT
1 TGTTTC-TTTCTT
27973797 TGTTTCATTTCTT
1 TGTTTC-TTTCTT
*
27973810 TTTTTCTTTCTT
1 TGTTTCTTTCTT
27973822 T
1 T
27973823 ATTTACTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.77
Consensus pattern (12 bp):
TGTTTCTTTCTT
Found at i:27979363 original size:68 final size:64
Alignment explanation
Indices: 27979254--27979484 Score: 189
Period size: 68 Copynumber: 3.5 Consensus size: 64
27979244 TACAGATGGT
* * * * * *
27979254 ATGTAGCTAGGTCACATGTATTATGCTAAGTGTACATCATGT-GTATAAGAGAGCTACGAGATAC
1 ATGTAGCTAGGTCACATGTGTGATACGAAGTGTACACCATGTAG-ACAAGAGAGCTACGAGATA-
27979318 A
64 A
* *
27979319 ATGCGGTAGCTAGGTCACATGTGTGATACG-AGATGTATACCATGTAGACAAGAGAGCTACGGGA
1 AT---GTAGCTAGGTCACATGTGTGATACGAAG-TGTACACCATGTAGACAAGAGAGCTACGAGA
27979383 TAA
62 TAA
* * * * * * *
27979386 ATGTAGCTAGGTCGCATGTGTGGTTCCAGGTGAAGGACACCATGTAGATAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCACATGTGTGATACGAAGT---GTACACCATGTAGACAAGAGAGCTACGAGAT
27979451 AA
63 AA
* * * *
27979453 A-GTGGCTAGGTCACATGGGTGGTACTAAGTGT
1 ATGTAGCTAGGTCACATGTGTGATACGAAGTGT
27979485 TCATGTTCAC
Statistics
Matches: 133, Mismatches: 24, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
63 1 0.01
64 22 0.17
65 3 0.02
66 23 0.17
67 35 0.26
68 48 0.36
69 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.25
Consensus pattern (64 bp):
ATGTAGCTAGGTCACATGTGTGATACGAAGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:27983311 original size:40 final size:40
Alignment explanation
Indices: 27983088--27983297 Score: 309
Period size: 40 Copynumber: 5.3 Consensus size: 40
27983078 TCCTCGTTCA
* * * *
27983088 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
27983127 AATGCCTTCGGGACTTAACCCGGATTT-GATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAG-TAACTCGCACG
27983167 AATGCCTTCGGGACTTAACCCGGATTT-GATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAG-TAACTCGCACG
*
27983207 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
* *
27983247 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
*
27983287 AAGGCCTTCGG
1 AATGCCTTCGG
27983298 ATCTTAGTCC
Statistics
Matches: 159, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
38 1 0.01
39 33 0.21
40 125 0.79
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
Found at i:27983334 original size:80 final size:80
Alignment explanation
Indices: 27983091--27983350 Score: 260
Period size: 80 Copynumber: 3.3 Consensus size: 80
27983081 TCGTTCAAAT
* * * * * *
27983091 GCCTTCGGGACATAGCCCGG-TTTTAGTAACTCACAC-AATGCCTTCGGGACTTAACCCGGATTT
1 GCCTTCGGGACTTAACCCGGATTTGA-TAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATAT
* * *
27983154 GATAACTCGCACGAAT
65 AATAACTAGCACGAAA
* * *
27983170 GCCTTCGGGACTTAACCCGGATTTGATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTGATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
27983235 ATAACTCGCACGAAT
66 ATAACTAGCACGAAA
* **
27983250 GCCTTCGGGACTTAACCCGGATTT-AGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATA
1 GCCTTCGGGACTTAACCCGGATTTGA-TAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATA
* *
27983313 TATTCACTTAGCAC-AAA
64 TAATAAC-TAGCACGAAA
* *
27983330 GCCTTCGGAACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
27983351 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
79 31 0.19
80 123 0.77
81 5 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATTTGATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
ATAACTAGCACGAAA
Found at i:27983334 original size:120 final size:118
Alignment explanation
Indices: 27983086--27983350 Score: 311
Period size: 120 Copynumber: 2.2 Consensus size: 118
27983076 GCTCCTCGTT
* * *
27983086 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAA-GCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCTTCGGGACTTAACCCGGA
* * * *
27983151 TTTGATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCA
65 TTTGATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATGATAACTAGCA
* * *
27983205 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 C-AAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACAC-AATGCCTTCGGGACTTAACCCGG
* ** *
27983270 ATTT-AGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATAT-ATTCACTTAGCA
64 ATTTGA-TAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATGA-TAAC-TAGCA
*
27983326 CAAAGCCTTCGGAACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
27983351 CAGCATTCAA
Statistics
Matches: 123, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
119 37 0.30
120 81 0.66
121 5 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (118 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCTTCGGGACTTAACCCGGAT
TTGATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATGATAACTAGCA
Found at i:27983359 original size:41 final size:41
Alignment explanation
Indices: 27983282--27983359 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
27983272 TTAGTATCTC
* * * *
27983282 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGAACTTAGCCCGGACACATTCACTTA
27983323 GCACAAA-GCCTTCGGAACTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTCGGAACTTAGCCCGGACA-CATTCA
27983360 ATTAATCATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 20 0.62
41 12 0.38
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGAACTTAGCCCGGACACATTCACTTA
Found at i:27990092 original size:40 final size:40
Alignment explanation
Indices: 27990009--27990218 Score: 309
Period size: 40 Copynumber: 5.3 Consensus size: 40
27989999 TCCTCGTTCA
* * * *
27990009 AATGCCTTCGGGACATAGCCC-GATTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTGA-TAACTCGCACG
27990048 AATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCACG
27990088 AATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCACG
*
27990128 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCACG
* *
27990168 AATGCCTTCGGGACTTAACCCGGATTT-AGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTGA-TAACTCGCACG
*
27990208 AAGGCCTTCGG
1 AATGCCTTCGG
27990219 ATCTTAGTCC
Statistics
Matches: 160, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 29 0.18
40 131 0.82
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCACG
Found at i:27990255 original size:80 final size:80
Alignment explanation
Indices: 27990012--27990271 Score: 260
Period size: 80 Copynumber: 3.3 Consensus size: 80
27990002 TCGTTCAAAT
* * * * * *
27990012 GCCTTCGGGACATAGCCC-GATTTTAGTAACTCACAC-AATGCCTTCGGGACTTAACCCGGATTT
1 GCCTTCGGGACTTAACCCGGATTTGA-TAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATAT
* * *
27990075 GATAACTCGCACGAAT
65 AATAACTAGCACGAAA
* * *
27990091 GCCTTCGGGACTTAACCCGGATTTGATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTGATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
27990156 ATAACTCGCACGAAT
66 ATAACTAGCACGAAA
* **
27990171 GCCTTCGGGACTTAACCCGGATTT-AGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATA
1 GCCTTCGGGACTTAACCCGGATTTGA-TAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATA
* *
27990234 TATTCACTTAGCAC-AAA
64 TAATAAC-TAGCACGAAA
* *
27990251 GCCTTCGGAACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
27990272 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
79 29 0.18
80 125 0.79
81 5 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATTTGATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
ATAACTAGCACGAAA
Found at i:27990255 original size:120 final size:119
Alignment explanation
Indices: 27990007--27990271 Score: 306
Period size: 120 Copynumber: 2.2 Consensus size: 119
27989997 GCTCCTCGTT
* *
27990007 CAAATGCCTTCGGGACATAGCCC-GATTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGG
1 CAAA-GCCTTCGGGACTTAGCCCGGATTTTAATAACTCACACAATGCCTTCGGGACTTAACCCGG
* * * *
27990071 ATTTGATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCA
65 ATTTGATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATGATAACTAGCA
* * *
27990126 CGAATGCCTTCGGGACTTAACCCGGA-TTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCG
1 C-AAAGCCTTCGGGACTTAGCCCGGATTTTAATAACTCACAC-AATGCCTTCGGGACTTAACCCG
* ** *
27990190 GATTT-AGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATAT-ATTCACTTAGCA
64 GATTTGA-TAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATGA-TAAC-TAGCA
*
27990247 CAAAGCCTTCGGAACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
27990272 CAGCATTCAA
Statistics
Matches: 123, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
119 35 0.28
120 83 0.67
121 5 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (119 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTTAATAACTCACACAATGCCTTCGGGACTTAACCCGGA
TTTGATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATGATAACTAGCA
Found at i:27990280 original size:41 final size:41
Alignment explanation
Indices: 27990203--27990280 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
27990193 TTAGTATCTC
* * * *
27990203 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGAACTTAGCCCGGACACATTCACTTA
27990244 GCACAAA-GCCTTCGGAACTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTCGGAACTTAGCCCGGACA-CATTCA
27990281 ATTAATCATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 20 0.62
41 12 0.38
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGAACTTAGCCCGGACACATTCACTTA
Found at i:27997023 original size:40 final size:40
Alignment explanation
Indices: 27996932--27997141 Score: 300
Period size: 40 Copynumber: 5.3 Consensus size: 40
27996922 TCCTCGTTCA
* * * *
27996932 AATGCCTTCGGGACATAGCCCGG-TTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTGA-TAACTCGCACG
27996971 AATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCACG
27997011 AATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCACG
* *
27997051 AATGCCTTCGGGACTTAACCCGGATTTAAGAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCACG
* *
27997091 AATGCCTTCGGGACTTAACCCGGATTT-AGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTGA-TAACTCGCACG
*
27997131 AAGGCCTTCGG
1 AATGCCTTCGG
27997142 ATTTTAGTCC
Statistics
Matches: 158, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
39 31 0.20
40 127 0.80
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCACG
Found at i:27997178 original size:80 final size:80
Alignment explanation
Indices: 27996935--27997194 Score: 233
Period size: 80 Copynumber: 3.3 Consensus size: 80
27996925 TCGTTCAAAT
* * * * * *
27996935 GCCTTCGGGACATAGCCCGG-TTTTAGTAACTCACAC-AATGCCTTCGGGACTTAACCCGGATTT
1 GCCTTCGGGACTTAACCCGGATTTGA-TAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATAT
* * * *
27996998 GATAACTCGCACGAAT
65 AAGAACTAGCACGAAA
* * *
27997014 GCCTTCGGGACTTAACCCGGATTTGATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTGATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
27997079 AGAACTCGCACGAAT
66 AGAACTAGCACGAAA
* * **
27997094 GCCTTCGGGACTTAACCCGGATTT-AGTATCTCGCACAAAGGCCTTC-GGATTTTAGTCCGGATA
1 GCCTTCGGGACTTAACCCGGATTTGA-TAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATA
***
27997157 TATTCACTTAGCAC-AAA
64 TAAGAAC-TAGCACGAAA
* *
27997174 GCCTTCGGAACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
27997195 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
79 31 0.20
80 120 0.77
81 5 0.03
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATTTGATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
AGAACTAGCACGAAA
Found at i:27997178 original size:120 final size:119
Alignment explanation
Indices: 27996930--27997194 Score: 297
Period size: 120 Copynumber: 2.2 Consensus size: 119
27996920 GCTCCTCGTT
* *
27996930 CAAATGCCTTCGGGACATAGCCCGG-TTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGG
1 CAAA-GCCTTCGGGACTTAGCCCGGATTTAAGTAACTCACACAATGCCTTCGGGACTTAACCCGG
* * * *
27996994 ATTTGATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCA
65 ATTTGATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATGATAACTAGCA
* * *
27997049 CGAATGCCTTCGGGACTTAACCCGGATTTAAG-AACTCGCACGAATGCCTTCGGGACTTAACCCG
1 C-AAAGCCTTCGGGACTTAGCCCGGATTTAAGTAACTCACAC-AATGCCTTCGGGACTTAACCCG
* * ** *
27997113 GATTT-AGTATCTCGCACAAAGGCCTTC-GGATTTTAGTCCGGATAT-ATTCACTTAGCA
64 GATTTGA-TAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATGA-TAAC-TAGCA
*
27997170 CAAAGCCTTCGGAACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
27997195 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
119 32 0.26
120 85 0.70
121 5 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (119 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
TTTGATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATGATAACTAGCA
Found at i:27997203 original size:41 final size:41
Alignment explanation
Indices: 27997126--27997203 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 41
27997116 TTAGTATCTC
** * * *
27997126 GCACAAAGGCCTTCGGATTTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGAACTTAGCCCGGACACATTCACTTA
27997167 GCACAAA-GCCTTCGGAACTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTCGGAACTTAGCCCGGACA-CATTCA
27997204 ATTAATCATG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 19 0.61
41 12 0.39
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGAACTTAGCCCGGACACATTCACTTA
Found at i:28003654 original size:51 final size:51
Alignment explanation
Indices: 28003507--28003643 Score: 166
Period size: 51 Copynumber: 2.7 Consensus size: 51
28003497 CTACCATCAA
* * * *
28003507 ATCTCTAAGAATATAATATCATATCTTCTATGATTCCATATCTTAGATAAG
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
* * ** * * * *
28003558 ATATGTAATCTTATAAAATAATATCTTATAAGATTCCATATCATATCTAAG
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
28003609 ATCTCTAAGATTATAATATCATATCTTCTAAGATT
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATT
28003644 AGTTACCATA
Statistics
Matches: 67, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (51 bp):
ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
Found at i:28007299 original size:51 final size:51
Alignment explanation
Indices: 28007152--28007288 Score: 166
Period size: 51 Copynumber: 2.7 Consensus size: 51
28007142 CTACCATCAA
* * * *
28007152 ATCTCTAAGAATATAATATCATATCTTCTATGATTCCATATCTTAGATAAG
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
* * ** * * * *
28007203 ATATGTAATCTTATAAAATAATATCTTATAAGATTCCATATCATATCTAAG
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
28007254 ATCTCTAAGATTATAATATCATATCTTCTAAGATT
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATT
28007289 AGTTACCATA
Statistics
Matches: 67, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (51 bp):
ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
Found at i:28008416 original size:40 final size:40
Alignment explanation
Indices: 28008193--28008402 Score: 309
Period size: 40 Copynumber: 5.3 Consensus size: 40
28008183 TCCTCGTTCA
* * * *
28008193 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
28008232 AATGCCTTCGGGACTTAACCCGGATTT-GATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAG-TAACTCGCACG
28008272 AATGCCTTCGGGACTTAACCCGGATTT-GATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAG-TAACTCGCACG
*
28008312 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
* *
28008352 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
*
28008392 AAGGCCTTCGG
1 AATGCCTTCGG
28008403 ATCTTAGTCC
Statistics
Matches: 159, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
38 1 0.01
39 33 0.21
40 125 0.79
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACG
Found at i:28008439 original size:80 final size:80
Alignment explanation
Indices: 28008196--28008455 Score: 260
Period size: 80 Copynumber: 3.3 Consensus size: 80
28008186 TCGTTCAAAT
* * * * * *
28008196 GCCTTCGGGACATAGCCCGG-TTTTAGTAACTCACAC-AATGCCTTCGGGACTTAACCCGGATTT
1 GCCTTCGGGACTTAACCCGGATTTGA-TAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATAT
* * *
28008259 GATAACTCGCACGAAT
65 AATAACTAGCACGAAA
* * *
28008275 GCCTTCGGGACTTAACCCGGATTTGATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATTTGATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
* *
28008340 ATAACTCGCACGAAT
66 ATAACTAGCACGAAA
* **
28008355 GCCTTCGGGACTTAACCCGGATTT-AGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATA
1 GCCTTCGGGACTTAACCCGGATTTGA-TAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATA
* *
28008418 TATTCACTTAGCAC-AAA
64 TAATAAC-TAGCACGAAA
* *
28008435 GCCTTCGGAACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
28008456 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
79 31 0.19
80 123 0.77
81 5 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATTTGATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATA
ATAACTAGCACGAAA
Found at i:28008439 original size:120 final size:118
Alignment explanation
Indices: 28008191--28008455 Score: 311
Period size: 120 Copynumber: 2.2 Consensus size: 118
28008181 GCTCCTCGTT
* * *
28008191 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAA-GCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCTTCGGGACTTAACCCGGA
* * * *
28008256 TTTGATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTGATAACTCGCA
65 TTTGATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATGATAACTAGCA
* * *
28008310 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 C-AAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACAC-AATGCCTTCGGGACTTAACCCGG
* ** *
28008375 ATTT-AGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATAT-ATTCACTTAGCA
64 ATTTGA-TAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATGA-TAAC-TAGCA
*
28008431 CAAAGCCTTCGGAACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
28008456 CAGCATTCAA
Statistics
Matches: 123, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
119 37 0.30
120 81 0.66
121 5 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (118 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAATAACTCACACAATGCCTTCGGGACTTAACCCGGAT
TTGATAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATGATAACTAGCA
Found at i:28008464 original size:41 final size:41
Alignment explanation
Indices: 28008387--28008464 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
28008377 TTAGTATCTC
* * * *
28008387 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGAACTTAGCCCGGACACATTCACTTA
28008428 GCACAAA-GCCTTCGGAACTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTCGGAACTTAGCCCGGACA-CATTCA
28008465 ATTAATCATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 20 0.62
41 12 0.38
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGAACTTAGCCCGGACACATTCACTTA
Found at i:28033205 original size:40 final size:40
Alignment explanation
Indices: 28033169--28033261 Score: 159
Period size: 40 Copynumber: 2.3 Consensus size: 40
28033159 CAGCTATTTG
*
28033169 TGGCACTTAGTGTTCGATTCGACATAGCTTCGGCTATATA
1 TGGCACTTAGTGTACGATTCGACATAGCTTCGGCTATATA
*
28033209 TGGCACTTAGTGTACGATTCGACATAGCTTTGGCTATATA
1 TGGCACTTAGTGTACGATTCGACATAGCTTCGGCTATATA
*
28033249 TTGCACTTAGTGT
1 TGGCACTTAGTGT
28033262 GTGATATGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (40 bp):
TGGCACTTAGTGTACGATTCGACATAGCTTCGGCTATATA
Found at i:28033277 original size:40 final size:40
Alignment explanation
Indices: 28033171--28033305 Score: 139
Period size: 40 Copynumber: 3.4 Consensus size: 40
28033161 GCTATTTGTG
*
28033171 GCACTTAGTGT-TCGATTCGACATAGCTTCGGCTATATATG
1 GCACTTAGTGTGT-GATTCGACATAGCTTCGGCTATATATA
** * *
28033211 GCACTTAGTGTACGATTCGACATAGCTTTGGCTATATATT
1 GCACTTAGTGTGTGATTCGACATAGCTTCGGCTATATATA
** * * *
28033251 GCACTTAGTGTGTGATAT-GAGTTAGCTTCAGCTATGTACA
1 GCACTTAGTGTGTGAT-TCGACATAGCTTCGGCTATATATA
*
28033291 GAACTTAGTGTGTGA
1 GCACTTAGTGTGTGA
28033306 GATATCGAGT
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
40 79 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (40 bp):
GCACTTAGTGTGTGATTCGACATAGCTTCGGCTATATATA
Found at i:28057918 original size:40 final size:40
Alignment explanation
Indices: 28057859--28057995 Score: 168
Period size: 40 Copynumber: 3.4 Consensus size: 40
28057849 CGGCTATTTG
28057859 TGGCACTTAGTGTGTGATTCGACATAGCTTC-GACTATATA
1 TGGCACTTAGTGTGTGATTCGACATAGCTTCAG-CTATATA
* * *
28057899 TGGCATTTAGTGTGCGATTCGACATAGCTTCAGCTCTATA
1 TGGCACTTAGTGTGTGATTCGACATAGCTTCAGCTATATA
* * * *
28057939 TTGCACTTAGTGTGTGATTTGAGATAGCTTCAGCTATGTA
1 TGGCACTTAGTGTGTGATTCGACATAGCTTCAGCTATATA
** *
28057979 CAGAACTTAGTGTGTGA
1 TGGCACTTAGTGTGTGA
28057996 GATATTAAGT
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 82 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (40 bp):
TGGCACTTAGTGTGTGATTCGACATAGCTTCAGCTATATA
Found at i:28060299 original size:29 final size:32
Alignment explanation
Indices: 28060267--28060361 Score: 106
Period size: 34 Copynumber: 2.9 Consensus size: 32
28060257 TATTTTAAAT
28060267 CTAATCTAAAAATG-AAAA-GAA-AAGAAAAC
1 CTAATCTAAAAATGAAAAACGAAGAAGAAAAC
*
28060296 CTAATCTAAAAATATGAAAAACTAAGAAGAAAAC
1 CTAATCT-AAAA-ATGAAAAACGAAGAAGAAAAC
* *
28060330 CTAATCTAAAAATATGAAAAACTAAGGAGAAA
1 CTAATCT-AAAA-ATGAAAAACGAAGAAGAAA
28060362 TGTTCAACCA
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
29 7 0.12
30 4 0.07
31 3 0.05
32 4 0.07
33 2 0.03
34 39 0.66
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.17
Consensus pattern (32 bp):
CTAATCTAAAAATGAAAAACGAAGAAGAAAAC
Found at i:28060326 original size:34 final size:34
Alignment explanation
Indices: 28060288--28060361 Score: 139
Period size: 34 Copynumber: 2.2 Consensus size: 34
28060278 ATGAAAAGAA
28060288 AAGAAAACCTAATCTAAAAATATGAAAAACTAAG
1 AAGAAAACCTAATCTAAAAATATGAAAAACTAAG
28060322 AAGAAAACCTAATCTAAAAATATGAAAAACTAAG
1 AAGAAAACCTAATCTAAAAATATGAAAAACTAAG
*
28060356 GAGAAA
1 AAGAAA
28060362 TGTTCAACCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.16
Consensus pattern (34 bp):
AAGAAAACCTAATCTAAAAATATGAAAAACTAAG
Found at i:28067831 original size:20 final size:20
Alignment explanation
Indices: 28067765--28067831 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
28067755 ATTTTAGTAA
*
28067765 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
28067785 ACATGACATGTATGCTATGC
1 ACATGATATGTATGATATGC
28067805 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
28067825 ACATGAT
1 ACATGAT
28067832 GTATTCATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:28067940 original size:23 final size:24
Alignment explanation
Indices: 28067881--28068008 Score: 224
Period size: 24 Copynumber: 5.4 Consensus size: 24
28067871 AAGGAAGTGC
28067881 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28067905 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28067929 AAAA-GGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28067952 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
28067975 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28067999 AAAAGTGGCT
1 AAAAG-GGCT
28068009 AGGCCTCTAG
Statistics
Matches: 100, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
22 3 0.03
23 38 0.38
24 55 0.55
25 4 0.04
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:28068250 original size:31 final size:31
Alignment explanation
Indices: 28068215--28068278 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
28068205 CGTTTACAGT
28068215 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
28068246 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
28068277 AA
1 AA
28068279 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:28076265 original size:20 final size:20
Alignment explanation
Indices: 28076165--28076275 Score: 134
Period size: 20 Copynumber: 5.5 Consensus size: 20
28076155 ACAAGAGTAG
* *
28076165 CGAAGTGCAGACAAAGGCA-
1 CGAAGTGCAAACAGAGGCAC
* *
28076184 CAAATGTGCAAACAGGGGCAC
1 CGAA-GTGCAAACAGAGGCAC
*
28076205 TGAAGTGCAAACAGAGGCAC
1 CGAAGTGCAAACAGAGGCAC
28076225 CGAAGTGCAAACAGAGGCAC
1 CGAAGTGCAAACAGAGGCAC
*
28076245 CGAAGTGAAAACAGAGGCAC
1 CGAAGTGCAAACAGAGGCAC
* *
28076265 CAAAGTACAAA
1 CGAAGTGCAAA
28076276 TCCCATACAA
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
19 3 0.04
20 73 0.94
21 2 0.03
ACGTcount: A:0.43, C:0.22, G:0.28, T:0.07
Consensus pattern (20 bp):
CGAAGTGCAAACAGAGGCAC
Found at i:28091253 original size:11 final size:10
Alignment explanation
Indices: 28091236--28091273 Score: 60
Period size: 11 Copynumber: 3.8 Consensus size: 10
28091226 AATTTCATGA
28091236 TTTTTATTTT
1 TTTTTATTTT
28091246 TGTTTTATTTT
1 T-TTTTATTTT
28091257 TTTTT-TTTT
1 TTTTTATTTT
28091266 TTTTTATT
1 TTTTTATT
28091274 ATTATAGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.35
10 7 0.27
11 10 0.38
ACGTcount: A:0.08, C:0.00, G:0.03, T:0.89
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:28091264 original size:19 final size:19
Alignment explanation
Indices: 28091236--28091288 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
28091226 AATTTCATGA
28091236 TTTTTATTTTTGTTTTATT
1 TTTTTATTTTTGTTTTATT
* *
28091255 TTTTTTTTTTTTTTTTATT
1 TTTTTATTTTTGTTTTATT
* *
28091274 ATTATAGTTTTTGTT
1 TTTTTA-TTTTTGTT
28091289 CACACGACCG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (19 bp):
TTTTTATTTTTGTTTTATT
Found at i:28094882 original size:32 final size:32
Alignment explanation
Indices: 28094846--28094907 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
28094836 AGCTTTTGGT
28094846 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
*
28094878 TTTTTCGTGTTGTCAAAGAGTTGAACAATG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATG
28094908 AAAATAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
Found at i:28103101 original size:6 final size:6
Alignment explanation
Indices: 28103090--28103163 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
28103080 GGGATCACTA
28103090 ACTAAT ACTAAT -CTAAT -CT-A- ACTAAT ACTAAT -CTAAT ACTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
*
28103133 A-GAAT ACTAAT -CTAAT ACTCTAAT ACTAAT A
1 ACTAAT ACTAAT ACTAAT A--CTAAT ACTAAT A
28103164 GAATAGAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
4 3 0.05
5 22 0.38
6 27 0.47
8 6 0.10
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (6 bp):
ACTAAT
Found at i:28103107 original size:5 final size:5
Alignment explanation
Indices: 28103087--28103148 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
28103077 GCCGGGATCA
28103087 CTAA- CTAAT ACTAAT CTAAT CTAA- CTAAT ACTAAT CTAAT ACTAAT
1 CTAAT CTAAT -CTAAT CTAAT CTAAT CTAAT -CTAAT CTAAT -CTAAT
**
28103133 AGAAT ACTAAT CTAAT
1 CTAAT -CTAAT CTAAT
28103149 ACTCTAATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
4 8 0.17
5 22 0.46
6 18 0.38
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.34
Consensus pattern (5 bp):
CTAAT
Found at i:28103125 original size:11 final size:11
Alignment explanation
Indices: 28103086--28103162 Score: 94
Period size: 11 Copynumber: 7.5 Consensus size: 11
28103076 AGCCGGGATC
28103086 ACTAA-CTAAT
1 ACTAATCTAAT
28103096 ACTAATCTAAT
1 ACTAATCTAAT
28103107 -CTAA-CTAAT
1 ACTAATCTAAT
28103116 ACTAATCTAAT
1 ACTAATCTAAT
**
28103127 ACTAATAGAAT
1 ACTAATCTAAT
28103138 ACTAATCTAAT
1 ACTAATCTAAT
28103149 AC---TCTAAT
1 ACTAATCTAAT
28103157 ACTAAT
1 ACTAAT
28103163 AGAATAGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
8 8 0.14
9 5 0.09
10 13 0.23
11 31 0.54
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (11 bp):
ACTAATCTAAT
Found at i:28103141 original size:22 final size:21
Alignment explanation
Indices: 28103086--28103162 Score: 108
Period size: 20 Copynumber: 3.8 Consensus size: 21
28103076 AGCCGGGATC
28103086 ACTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
28103107 -CTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
28103127 ACTAA-TAGAATACTAATCTAAT
1 ACTAACT--AATACTAATCTAAT
28103149 ACT--CTAATACTAAT
1 ACTAACTAATACTAAT
28103163 AGAATAGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.17
20 21 0.40
21 5 0.10
22 17 0.33
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (21 bp):
ACTAACTAATACTAATCTAAT
Found at i:28103177 original size:14 final size:14
Alignment explanation
Indices: 28103160--28103187 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28103150 CTCTAATACT
28103160 AATAGAATAGAAAA
1 AATAGAATAGAAAA
28103174 AATAGAATAGAAAA
1 AATAGAATAGAAAA
28103188 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:28132332 original size:16 final size:16
Alignment explanation
Indices: 28132311--28132342 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28132301 GCCCAATAAC
*
28132311 CTAAACTACCAGCCCA
1 CTAAACTAACAGCCCA
28132327 CTAAACTAACAGCCCA
1 CTAAACTAACAGCCCA
28132343 TTACACAAAA
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:0.41, C:0.41, G:0.06, T:0.12
Consensus pattern (16 bp):
CTAAACTAACAGCCCA
Found at i:28134137 original size:40 final size:40
Alignment explanation
Indices: 28134086--28134282 Score: 304
Period size: 40 Copynumber: 4.9 Consensus size: 40
28134076 ATAACCGCAA
* * * *
28134086 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* * *
28134126 GCACGAATGCCTTCGGGTCTTAGCTCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
28134166 GCATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
28134206 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
28134246 GCACAAATGCCTTCGGGTCTTAGCCCAGATATATCAA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAA
28134283 ATGCTCATGC
Statistics
Matches: 142, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:28138525 original size:11 final size:11
Alignment explanation
Indices: 28138509--28138535 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
28138499 TAGAAATTAG
28138509 TTTGTGAAACT
1 TTTGTGAAACT
28138520 TTTGTGAAACT
1 TTTGTGAAACT
28138531 TTTGT
1 TTTGT
28138536 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:28140070 original size:92 final size:92
Alignment explanation
Indices: 28139934--28140127 Score: 286
Period size: 92 Copynumber: 2.1 Consensus size: 92
28139924 TTGATTTTAG
* *
28139934 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
*
28139998 TAT-TAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
28140025 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
28140090 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
28140118 CAAATTCATA
1 TAAATTCATA
28140128 AACTATAATC
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
91 17 0.18
92 43 0.46
93 30 0.32
94 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:28140175 original size:48 final size:52
Alignment explanation
Indices: 28140105--28140203 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
28140095 AATAATTATT
28140105 ATTTTAAATTATACAAATTCATA-AACT-A-T-AATCATATTAGTTATAATA
1 ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
* * **
28140153 ATTTTAAATTTTATTAAA-TCATATATTTAATTAAATCATATTAGTTATAAT
1 ATTTTAAATTATA-CAAATTCATATAACTAATTAAATCATATTAGTTATAAT
28140204 CATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 17 0.40
49 5 0.12
50 1 0.02
51 1 0.02
52 18 0.43
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (52 bp):
ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
Found at i:28140185 original size:17 final size:17
Alignment explanation
Indices: 28140160--28140193 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28140150 ATAATTTTAA
*
28140160 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
28140177 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
28140194 TAGTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:28140210 original size:17 final size:16
Alignment explanation
Indices: 28140165--28140212 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
28140155 TTTAAATTTT
28140165 ATTAAATCATATATTTA
1 ATTAAATCATATA-TTA
28140182 ATTAAATC--ATATTA
1 ATTAAATCATATATTA
*
28140196 GTTATAATCATATATTA
1 ATTA-AATCATATATTA
28140213 TGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
17 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTAAATCATATATTA
Found at i:28140284 original size:18 final size:17
Alignment explanation
Indices: 28140253--28140287 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28140243 ATTATTAAGA
28140253 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
28140270 ATTTTAATTATATTATAT
1 ATTTT-ATTAAATTATAT
28140288 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:28140353 original size:129 final size:129
Alignment explanation
Indices: 28140200--28140432 Score: 414
Period size: 129 Copynumber: 1.8 Consensus size: 129
28140190 ATATTAGTTA
*
28140200 TAATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TAATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
* *
28140265 TATATATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTTACAGTATCATATT
66 TATATATTTTAATTAAAATATATTT-ATAATAATTATGTTATTTTATATTTTACAGTATCATATT
*
28140330 TAATAATA-ATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 TAATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
28140394 TATATATTTTAATTAAAATATATTTATAATAATTATGTT
66 TATATATTTTAATTAAAATATATTTATAATAATTATGTT
28140433 TAAATATGAT
Statistics
Matches: 99, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
128 14 0.14
129 78 0.79
130 7 0.07
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (129 bp):
TAATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
TATATATTTTAATTAAAATATATTTATAATAATTATGTTATTTTATATTTTACAGTATCATATT
Found at i:28140410 original size:18 final size:17
Alignment explanation
Indices: 28140382--28140416 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28140372 ATTATTAAGA
*
28140382 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
28140399 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
28140417 TTATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:28140416 original size:16 final size:17
Alignment explanation
Indices: 28140382--28140423 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
28140372 ATTATTAAGA
28140382 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA-TATAT
28140399 ATTTTAATTAAA-ATAT
1 ATTTTAATTAAATATAT
28140415 ATTTATAAT
1 ATTT-TAAT
28140424 AATTATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.35
17 9 0.39
18 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTAATTAAATATAT
Found at i:28140526 original size:143 final size:147
Alignment explanation
Indices: 28140370--28140640 Score: 478
Period size: 143 Copynumber: 1.9 Consensus size: 147
28140360 ATAAGAATAT
*
28140370 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATT-TATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
28140434 AAATATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAA-AATAATTTA
66 AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
28140496 CCAAAACAAATTTCTGC
131 CCAAAACAAATTTCTGC
28140513 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
28140578 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAAT--ATAATCTTATTAAAATTTAAATAACAATAA
28140641 CAATAATCAT
Statistics
Matches: 120, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
143 48 0.40
144 42 0.35
145 2 0.02
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
CCAAAACAAATTTCTGC
Found at i:28140553 original size:18 final size:17
Alignment explanation
Indices: 28140525--28140559 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28140515 ATTATTAAGA
*
28140525 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
28140542 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
28140560 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:28140770 original size:44 final size:45
Alignment explanation
Indices: 28140721--28140815 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
28140711 TTACACCTCT
* *
28140721 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
28140765 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
28140810 ATTACA
1 ATTACA
28140816 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:28140815 original size:16 final size:16
Alignment explanation
Indices: 28140794--28140826 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28140784 TTGATTTGCT
*
28140794 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
28140810 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
28140826 A
1 A
28140827 ATCCAATACA
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:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:28140836 original size:21 final size:21
Alignment explanation
Indices: 28140807--28140849 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
28140797 ACACCTCTAT
*
28140807 TCCATTACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
28140828 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
28140849 T
1 T
28140850 ACAGCGAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:28142380 original size:22 final size:23
Alignment explanation
Indices: 28142336--28142383 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
28142326 AAAATACGAC
* * *
28142336 AAATATACGAAAATATAATATAA
1 AAATATAAGAAAATAAAAAATAA
28142359 AAATATAAG-AAATAAAAAATAA
1 AAATATAAGAAAATAAAAAATAA
28142381 AAA
1 AAA
28142384 ATTAGAGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (23 bp):
AAATATAAGAAAATAAAAAATAA
Found at i:28143004 original size:21 final size:21
Alignment explanation
Indices: 28142991--28143030 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
28142981 ATTATATTGT
28142991 TTATTTTCACTATTATTATTA
1 TTATTTTCACTATTATTATTA
28143012 TTATTTTCA-TCATTATTAT
1 TTATTTTCACT-ATTATTAT
28143031 ACATATATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTTTCACTATTATTATTA
Found at i:28143028 original size:24 final size:24
Alignment explanation
Indices: 28142978--28143030 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 24
28142968 TATTATATTT
*
28142978 ATTATTA-TATTGTTTATTTTCAC
1 ATTATTATTATTGATTATTTTCAC
28143001 --TATTATTATT-ATTATTTTCATC
1 ATTATTATTATTGATTATTTTCA-C
28143023 ATTATTAT
1 ATTATTAT
28143031 ACATATATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 14 0.56
22 5 0.20
24 6 0.24
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (24 bp):
ATTATTATTATTGATTATTTTCAC
Found at i:28162103 original size:70 final size:70
Alignment explanation
Indices: 28161988--28162162 Score: 212
Period size: 70 Copynumber: 2.5 Consensus size: 70
28161978 CTTTCCAAGG
*
28161988 AAAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTT-
1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAAGACACGTCGAGGTATTTTTAATTTA
*
28162051 TTTTTT
65 TGTTTT
* ** * *
28162057 AAAAATCAACTTATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGTCGAGGTATTTTTAGTTTA
1 -AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGTCGAGGTATTTTTAATTTA
28162122 TGTTTT
65 TGTTTT
** * *
28162128 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
28162163 TTTAATTTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
69 30 0.33
70 54 0.59
71 7 0.08
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGTCGAGGTATTTTTAATTTAT
GTTTT
Found at i:28162283 original size:75 final size:73
Alignment explanation
Indices: 28162180--28162515 Score: 417
Period size: 72 Copynumber: 4.5 Consensus size: 73
28162170 TTTGTTTTTC
*
28162180 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTT-AATTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT-ATTTTCAATTTC
28162244 TGTTGTTAAAA
65 TGTT-TT-AAA
** * *
28162255 AAAATCAACTCATATTGCGAGAAATGAGTTGAACCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
*
28162320 GTTTT-CA
66 GTTTTAAA
* * ** ** *
28162327 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAAACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
28162392 GTTTTCAAA
66 GTTTT-AAA
* * * *
28162401 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGTCTC-GGTTCACATGCTGAAGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAATT
28162465 TCTGTTTTTAAA
63 TCTG-TTTTAAA
*
28162477 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
28162516 ATTACCCACT
Statistics
Matches: 227, Mismatches: 26, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
72 64 0.28
74 40 0.18
75 58 0.26
76 60 0.26
77 5 0.02
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (73 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
GTTTTAAA
Found at i:28162535 original size:76 final size:74
Alignment explanation
Indices: 28162180--28162515 Score: 419
Period size: 76 Copynumber: 4.5 Consensus size: 74
28162170 TTTGTTTTTC
*
28162180 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTT-AATTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT-ATTTTCAATTTC
*
28162244 TGTTGTTAAAA
65 TGTT-TTTAAA
** * *
28162255 AAAATCAACTCATATTGCGAGAAATGAGTTGAACCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
*
28162320 G-TTTT-CA
66 GTTTTTAAA
* * ** ** *
28162327 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAAACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
*
28162392 GTTTTCAAA
66 GTTTTTAAA
* * * *
28162401 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGTCTC-GGTTCACATGCTGAAGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAATT
28162465 TCTGTTTTTAAA
63 TCTGTTTTTAAA
*
28162477 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
28162516 ATTACCCACT
Statistics
Matches: 225, Mismatches: 29, Indels: 12
0.85 0.11 0.05
Matches are distributed among these distances:
72 60 0.27
73 5 0.02
74 39 0.17
75 56 0.25
76 64 0.28
77 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (74 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
GTTTTTAAA
Found at i:28162939 original size:88 final size:87
Alignment explanation
Indices: 28162737--28162982 Score: 289
Period size: 88 Copynumber: 2.8 Consensus size: 87
28162727 TGTTTTAATT
*
28162737 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACGCCGAGGTATTTTCAATTAAGC-
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACA--CCGAGGTATTTTCAATT--TCT
* * *
28162801 CTTTTGATTTCTGTTTTTCAAAAAAA
62 GTTTTCATTTATGTTTTTCAAAAAAA
* *
28162827 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACCGAGGTATTTTCCATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCGAGGTATTTTCAATTTCTGTTT
* *
28162892 TCATTATTATGTTTTT-GAAAGAA
66 TCA-T-TTATGTTTTTCAAAAAAA
* ** * ** *
28162915 TCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCGAGGTATTTTCAATTTCTGTTT
28162980 TCA
66 TCA
28162983 AAATTCAACT
Statistics
Matches: 136, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
86 1 0.01
87 5 0.04
88 81 0.60
89 9 0.07
90 40 0.29
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (87 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCGAGGTATTTTCAATTTCTGTTT
TCATTTATGTTTTTCAAAAAAA
Found at i:28163099 original size:73 final size:72
Alignment explanation
Indices: 28162915--28163167 Score: 391
Period size: 73 Copynumber: 3.5 Consensus size: 72
28162905 TTTGAAAGAA
* *
28162915 TCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
28162980 TCAAAAT
66 TCAAAAT
*
28162987 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTG-TT
28163052 TTCAAAAT
65 TTCAAAAT
** * *
28163060 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTG
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
*
28163125 TCAAAAAAA
66 TC--AAAAT
28163134 TCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCA
1 TCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCA
28163168 GTTCACATGT
Statistics
Matches: 167, Mismatches: 10, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
72 63 0.38
73 71 0.43
74 33 0.20
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (72 bp):
TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
TCAAAAT
Found at i:28163903 original size:16 final size:16
Alignment explanation
Indices: 28163882--28163913 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28163872 GCCCAATAAC
*
28163882 CTAAACTACCAGCCCA
1 CTAAACTAACAGCCCA
28163898 CTAAACTAACAGCCCA
1 CTAAACTAACAGCCCA
28163914 TTACACAAAA
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:0.41, C:0.41, G:0.06, T:0.12
Consensus pattern (16 bp):
CTAAACTAACAGCCCA
Found at i:28164473 original size:22 final size:23
Alignment explanation
Indices: 28164429--28164476 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
28164419 AAAATACGAC
* * *
28164429 AAATATATGAAAATATAATATAA
1 AAATATAAGAAAATAAAAAATAA
28164452 AAATATAAG-AAATAAAAAATAA
1 AAATATAAGAAAATAAAAAATAA
28164474 AAA
1 AAA
28164477 AAATTAGAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (23 bp):
AAATATAAGAAAATAAAAAATAA
Found at i:28164605 original size:16 final size:17
Alignment explanation
Indices: 28164582--28164628 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
28164572 CTCCCCCCTG
28164582 CCCTCTCTTCTTTC-CT
1 CCCTCTCTTCTTTCTCT
*
28164598 CGCTCTC-TCTTTTCTCT
1 CCCTCTCTTC-TTTCTCT
28164615 CCCTCCTCTTCTTT
1 CCCT-CTCTTCTTT
28164629 TTTTTTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 2 0.08
16 10 0.40
17 5 0.20
18 6 0.24
19 2 0.08
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (17 bp):
CCCTCTCTTCTTTCTCT
Found at i:28164607 original size:18 final size:19
Alignment explanation
Indices: 28164584--28164628 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
28164574 CCCCCCTGCC
*
28164584 CTCTCTTCTTTC-CTCGCT
1 CTCTCTTCTTTCTCTCCCT
28164602 CTCTC-T-TTTCTCTCCCT
1 CTCTCTTCTTTCTCTCCCT
28164619 C-CTCTTCTTT
1 CTCTCTTCTTT
28164629 TTTTTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
16 7 0.30
17 8 0.35
18 8 0.35
ACGTcount: A:0.00, C:0.44, G:0.02, T:0.53
Consensus pattern (19 bp):
CTCTCTTCTTTCTCTCCCT
Found at i:28165137 original size:18 final size:18
Alignment explanation
Indices: 28165114--28165150 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28165104 ATTATATTGT
28165114 TTATTTTCA-CTATTATTA
1 TTATTTTCATC-ATTATTA
28165132 TTATTTTCATCATTATTA
1 TTATTTTCATCATTATTA
28165150 T
1 T
28165151 ACATATATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTTTCATCATTATTA
Found at i:28173266 original size:19 final size:20
Alignment explanation
Indices: 28173229--28173266 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
28173219 TATAATAAAA
*
28173229 ATATTTCTTTTAATTATTTC
1 ATATTTCTTTTAATCATTTC
*
28173249 ATATTT-TTTTTATCATTT
1 ATATTTCTTTTAATCATTT
28173267 TTAAATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (20 bp):
ATATTTCTTTTAATCATTTC
Found at i:28178188 original size:6 final size:6
Alignment explanation
Indices: 28178165--28178202 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
28178155 ATTTTGTAAC
*
28178165 TAATTT T-ATTT TATTTT TAATTT TAATTT TATATTT TA
1 TAATTT TAATTT TAATTT TAATTT TAATTT TA-ATTT TA
28178203 GTTAGATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 5 0.18
6 17 0.61
7 6 0.21
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TAATTT
Found at i:28178200 original size:13 final size:13
Alignment explanation
Indices: 28178171--28178221 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
28178161 TAACTAATTT
*
28178171 TATTTTATTTTTA
1 TATTTTAATTTTA
28178184 -ATTTTAATTTTA
1 TATTTTAATTTTA
* **
28178196 TATTTTAGTTAGA
1 TATTTTAATTTTA
28178209 TATTTTTAATTTT
1 TA-TTTTAATTTT
28178222 GTATGAATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
12 11 0.38
13 11 0.38
14 7 0.24
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (13 bp):
TATTTTAATTTTA
Found at i:28183240 original size:19 final size:19
Alignment explanation
Indices: 28183185--28183240 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
28183175 ATTAATAAGC
*
28183185 AATTTAAAATTATAAAAAA
1 AATTCAAAATTATAAAAAA
*
28183204 ATATTCAAAA-AATAAAAATA
1 A-ATTCAAAATTATAAAAA-A
28183224 AATTCAAAATTATAAAA
1 AATTCAAAATTATAAAA
28183241 CGTTCAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (19 bp):
AATTCAAAATTATAAAAAA
Found at i:28188984 original size:16 final size:17
Alignment explanation
Indices: 28188952--28188985 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28188942 CCACGCAAGA
28188952 ATTATAATAAGCTTCAT
1 ATTATAATAAGCTTCAT
*
28188969 ATTATATTAA-CTTCAT
1 ATTATAATAAGCTTCAT
28188985 A
1 A
28188986 GCCCCCTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (17 bp):
ATTATAATAAGCTTCAT
Found at i:28193999 original size:3 final size:3
Alignment explanation
Indices: 28193991--28194024 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
28193981 CTATTAGCTT
28193991 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28194025 AAAAACCCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28195767 original size:21 final size:22
Alignment explanation
Indices: 28195741--28195783 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
28195731 CACTTCACAT
28195741 AGGGGC-ACACGTCT-GTGTGAG
1 AGGGGCAACAC-TCTCGTGTGAG
28195762 AGGGGCAACACTCTCGTGTGAG
1 AGGGGCAACACTCTCGTGTGAG
28195784 CATTCTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.21, C:0.21, G:0.40, T:0.19
Consensus pattern (22 bp):
AGGGGCAACACTCTCGTGTGAG
Found at i:28196933 original size:47 final size:48
Alignment explanation
Indices: 28196864--28197128 Score: 203
Period size: 46 Copynumber: 5.7 Consensus size: 48
28196854 AGGTGCCATG
* * *
28196864 CCATGTCCTAGACACGGTCTTACACTGGCTCAT-ATCTC-AAGTCGAT
1 CCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAGCCGAT
* * *
28196910 CCCATGTCCCAAACATGGTCTTACACTGACT-ATCATCTCGTAGCCGAT
1 -CCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAGCCGAT
* * * * *
28196958 GCATGTCCCAAACAT-GTCTTACACTGGCTTA-CGTCTCGAGGCCGAT
1 CCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAGCCGAT
* * * * * *
28197004 GCATGCCCCAGACAT-GTCTTACACTAGC-CCTCGTCTC-AATACCGAT
1 CCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAA-GCCGAT
* * **
28197050 GCCATGTCCCAGACATGGTCTTACATTGGCTC-TCATAAT-GTGGCCGA-
1 -CCATGTCCCAGACATGGTCTTACACTGGCTCATCAT-CTCGAAGCCGAT
*
28197097 CGCATGTCCCAGACAT-GTCTTACACTAGCTCA
1 C-CATGTCCCAGACATGGTCTTACACTGGCTCA
28197129 CACATGAATA
Statistics
Matches: 177, Mismatches: 29, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
45 1 0.01
46 77 0.44
47 73 0.41
48 24 0.14
49 2 0.01
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.26
Consensus pattern (48 bp):
CCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAGCCGAT
Found at i:28197741 original size:18 final size:18
Alignment explanation
Indices: 28197718--28197756 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
28197708 CATTTTCTTC
28197718 CATAAGAACTTAAAAAAA
1 CATAAGAACTTAAAAAAA
28197736 CATAAGAACTTAAAAAAA
1 CATAAGAACTTAAAAAAA
28197754 CAT
1 CAT
28197757 CACAAATCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.64, C:0.13, G:0.05, T:0.18
Consensus pattern (18 bp):
CATAAGAACTTAAAAAAA
Found at i:28204731 original size:61 final size:61
Alignment explanation
Indices: 28204636--28204762 Score: 245
Period size: 61 Copynumber: 2.1 Consensus size: 61
28204626 ATATAATTAT
*
28204636 ATATTAATAATTATCATCTTCTTTTTAAACTAAAAACATTTATTCTAGAAGCCTTTGTGAA
1 ATATTAATAATTATCATCTTCTTTTTAAACTAAAAACATTTATTCTAGAAGCCTTTATGAA
28204697 ATATTAATAATTATCATCTTCTTTTTAAACTAAAAACATTTATTCTAGAAGCCTTTATGAA
1 ATATTAATAATTATCATCTTCTTTTTAAACTAAAAACATTTATTCTAGAAGCCTTTATGAA
28204758 ATATT
1 ATATT
28204763 TACAAAATGA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.43
Consensus pattern (61 bp):
ATATTAATAATTATCATCTTCTTTTTAAACTAAAAACATTTATTCTAGAAGCCTTTATGAA
Found at i:28212770 original size:21 final size:20
Alignment explanation
Indices: 28212741--28212786 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
28212731 CGAAACGCAA
28212741 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
28212762 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
28212782 T-AACC
1 TCAACC
28212787 ATCCCAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:28215218 original size:27 final size:27
Alignment explanation
Indices: 28215187--28215364 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28215177 TAAATTGTAC
28215187 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
28215214 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28215240 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28215268 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
28215296 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28215323 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28215350 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28215365 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:28215301 original size:82 final size:81
Alignment explanation
Indices: 28215188--28215343 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28215178 AAATTGTACA
* *
28215188 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
28215252 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28215269 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
28215334 TGCGAGTTGA
65 TGCGAATTGA
28215344 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:28215355 original size:82 final size:81
Alignment explanation
Indices: 28215184--28215364 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
28215174 GATTAAATTG
* *
28215184 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28215249 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28215265 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28215329 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28215347 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28215365 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:28223291 original size:27 final size:27
Alignment explanation
Indices: 28223260--28223437 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
28223250 TAAATTGTAC
28223260 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
28223287 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28223313 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
28223341 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
28223369 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28223396 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28223423 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28223438 GACTCAATAT
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 108 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:28223374 original size:82 final size:81
Alignment explanation
Indices: 28223261--28223416 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
28223251 AAATTGTACA
*
28223261 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
28223325 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28223342 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
28223407 TGCGAGTTGA
65 TGCGAATTGA
28223417 TTATATAGCA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28223428 original size:82 final size:81
Alignment explanation
Indices: 28223257--28223437 Score: 238
Period size: 82 Copynumber: 2.2 Consensus size: 81
28223247 GATTAAATTG
*
28223257 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
28223322 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28223338 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
28223402 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28223420 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28223438 GACTCAATAT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 18 0.21
82 67 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28227107 original size:46 final size:44
Alignment explanation
Indices: 28227042--28227167 Score: 137
Period size: 46 Copynumber: 2.8 Consensus size: 44
28227032 ACAAAGATGA
* *
28227042 GTGCTAGTGTAAGACATGTCTGGGACATGCTTCGGCCT-CGAGAC
1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGAC
** *
28227086 GTAAGCCAGTGTAAGACATGTCTGGGATGTGCATCGGCTACGAGAT
1 GT--GCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGAC
**
28227132 GTGTTAGTGTAAGACCATGTCTGGGACATGGCATCG
1 GTGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCG
28227168 ACACATATAT
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
44 12 0.18
45 14 0.21
46 42 0.62
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (44 bp):
GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGAC
Found at i:28228138 original size:10 final size:10
Alignment explanation
Indices: 28228123--28228160 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
28228113 GCTCGTTTCC
*
28228123 AGCTCACTCG
1 AGCTCAATCG
28228133 AGCTCAAGTC-
1 AGCTCAA-TCG
28228143 AGCTCAATCG
1 AGCTCAATCG
28228153 AGCTCAAT
1 AGCTCAAT
28228161 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:28228147 original size:20 final size:20
Alignment explanation
Indices: 28228122--28228159 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28228112 AGCTCGTTTC
*
28228122 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
28228142 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
28228160 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:28228166 original size:20 final size:20
Alignment explanation
Indices: 28228123--28228183 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
28228113 GCTCGTTTCC
* * *
28228123 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
28228143 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
28228163 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
28228183 A
1 A
28228184 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:28228177 original size:11 final size:10
Alignment explanation
Indices: 28228133--28228179 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
28228123 AGCTCACTCG
*
28228133 AGCTCAAGTC
1 AGCTCAATTC
28228143 AGCTCAA-TC
1 AGCTCAATTC
*
28228152 GAGCTCAATTT
1 -AGCTCAATTC
28228163 AGCTACAATTC
1 AGCT-CAATTC
28228174 AGCTCA
1 AGCTCA
28228180 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:28229627 original size:40 final size:37
Alignment explanation
Indices: 28229560--28229653 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 37
28229550 TTGGAGTAAC
*
28229560 AAAAAAAATAAAAAAAATCGAAAAAAAATTGA-TTGAA
1 AAAAAAAATAAAAAAAATCGAAAAAAAATCGAGTT-AA
28229597 AAAAAAAATTCAAAAAAAAGT-GAAAAAAAAATCGAGTTAA
1 AAAAAAAA-T-AAAAAAAA-TCG-AAAAAAAATCGAGTTAA
*
28229637 AAAAAAGAAGAAAAAAA
1 AAAAAA-AATAAAAAAA
28229654 CAAAAGTGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
37 8 0.16
38 1 0.02
39 16 0.33
40 20 0.41
41 4 0.08
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (37 bp):
AAAAAAAATAAAAAAAATCGAAAAAAAATCGAGTTAA
Found at i:28232238 original size:10 final size:10
Alignment explanation
Indices: 28232223--28232260 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
28232213 GCTCGTTTCC
*
28232223 AGCTCACTCG
1 AGCTCAATCG
28232233 AGCTCAAGTC-
1 AGCTCAA-TCG
28232243 AGCTCAATCG
1 AGCTCAATCG
28232253 AGCTCAAT
1 AGCTCAAT
28232261 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:28232247 original size:20 final size:20
Alignment explanation
Indices: 28232222--28232259 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28232212 AGCTCGTTTC
*
28232222 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
28232242 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
28232260 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:28232266 original size:20 final size:20
Alignment explanation
Indices: 28232223--28232283 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
28232213 GCTCGTTTCC
* * *
28232223 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
28232243 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
28232263 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
28232283 A
1 A
28232284 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:28232277 original size:11 final size:10
Alignment explanation
Indices: 28232233--28232279 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
28232223 AGCTCACTCG
*
28232233 AGCTCAAGTC
1 AGCTCAATTC
28232243 AGCTCAA-TC
1 AGCTCAATTC
*
28232252 GAGCTCAATTT
1 -AGCTCAATTC
28232263 AGCTACAATTC
1 AGCT-CAATTC
28232274 AGCTCA
1 AGCTCA
28232280 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:28236474 original size:13 final size:13
Alignment explanation
Indices: 28236456--28236489 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
28236446 TTTATTTAGG
28236456 TTATATATAAATA
1 TTATATATAAATA
28236469 -T-TATATAAATA
1 TTATATATAAATA
28236480 TTATATATAA
1 TTATATATAA
28236490 TTATAAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 10 0.53
12 2 0.11
13 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TTATATATAAATA
Found at i:28236475 original size:11 final size:11
Alignment explanation
Indices: 28236459--28236486 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
28236449 ATTTAGGTTA
28236459 TATATAAATAT
1 TATATAAATAT
28236470 TATATAAATAT
1 TATATAAATAT
28236481 TATATA
1 TATATA
28236487 TAATTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TATATAAATAT
Found at i:28238432 original size:23 final size:23
Alignment explanation
Indices: 28238406--28238493 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 23
28238396 GCTTTACTGA
* *
28238406 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
28238429 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
28238450 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* * *
28238472 T-AGGCACTTTATGTGTCATATT
1 TCAGGCACCTCATGTGTCGTATT
28238494 GTGATCAGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
21 34 0.62
22 3 0.05
23 18 0.33
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.39
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:28238453 original size:21 final size:21
Alignment explanation
Indices: 28238418--28238478 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 21
28238408 AGGCACTTTA
28238418 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
28238441 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* *
28238462 TGTGTCGTTTTAGGCAC
1 TGTGTCGTATCAGGCAC
28238479 TTTATGTGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 27 0.75
23 9 0.25
ACGTcount: A:0.13, C:0.25, G:0.28, T:0.34
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:28241774 original size:17 final size:17
Alignment explanation
Indices: 28241752--28241785 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28241742 TTGATTATCG
28241752 ACAGTTAAATAAAGTGA
1 ACAGTTAAATAAAGTGA
*
28241769 ACAGTTGAATAAAGTGA
1 ACAGTTAAATAAAGTGA
28241786 CGATCAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.21, T:0.24
Consensus pattern (17 bp):
ACAGTTAAATAAAGTGA
Found at i:28244701 original size:24 final size:23
Alignment explanation
Indices: 28244674--28244723 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
28244664 TTTATTTAGG
28244674 TTATATATAAATA-T-TATATAA
1 TTATATATAAATATTATATATAA
28244695 TTATTATATAAATATTATATATAA
1 TTA-TATATAAATATTATATATAA
28244719 TTATA
1 TTATA
28244724 AACCATCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 3 0.12
22 10 0.38
23 3 0.12
24 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTATATATAAATATTATATATAA
Found at i:28244718 original size:13 final size:11
Alignment explanation
Indices: 28244677--28244715 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
28244667 ATTTAGGTTA
28244677 TATATAAATAT
1 TATATAAATAT
*
28244688 TATATAATTAT
1 TATATAAATAT
28244699 TATATAAATAT
1 TATATAAATAT
28244710 TATATA
1 TATATA
28244716 TAATTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TATATAAATAT
Found at i:28244750 original size:3 final size:3
Alignment explanation
Indices: 28244742--28244782 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
28244732 TTATGTTTTA
* *
28244742 TAT TAT TAT TAT TAT TAT TAT TAG TAT TGT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
28244783 AATGAAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:28246665 original size:23 final size:23
Alignment explanation
Indices: 28246635--28246706 Score: 80
Period size: 21 Copynumber: 3.3 Consensus size: 23
28246625 GCTTTACTGA
* *
28246635 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
28246658 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
28246679 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
28246701 T-AGGCA
1 TCAGGCA
28246707 TTTTATGTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 25 0.57
22 1 0.02
23 18 0.41
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:28246682 original size:21 final size:22
Alignment explanation
Indices: 28246647--28246706 Score: 88
Period size: 21 Copynumber: 2.8 Consensus size: 22
28246637 AGGCACTTTA
28246647 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAGGCACCTCG
28246670 TGTGTCGTA-TCAGGCACCTCG
1 TGTGTCGTATTCAGGCACCTCG
*
28246691 TGTGTCGT-TTTAGGCA
1 TGTGTCGTATTCAGGCA
28246707 TTTTATGTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
21 26 0.74
23 9 0.26
ACGTcount: A:0.13, C:0.23, G:0.28, T:0.35
Consensus pattern (22 bp):
TGTGTCGTATTCAGGCACCTCG
Found at i:28253201 original size:46 final size:47
Alignment explanation
Indices: 28253088--28253219 Score: 117
Period size: 46 Copynumber: 2.8 Consensus size: 47
28253078 TCCACATTAT
* * *
28253088 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGAC
1 GAGAGCTAATGTAAGA-CATGTCTGGGACATGGCATCGACATCGAGAC
* * * * * *
28253136 GAGTGCTAGTGTCAGACATGTCTGGGACAT-GCTTCGGCCTCGAGAC
1 GAGAGCTAATGTAAGACATGTCTGGGACATGGCATCGACATCGAGAC
* * *
28253182 GTA-AGCTAATGTAAGACATGTTTAGGACGT-GCATCGAC
1 G-AGAGCTAATGTAAGACATGTCTGGGACATGGCATCGAC
28253220 TACGAGATGT
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
46 40 0.59
47 15 0.22
48 13 0.19
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (47 bp):
GAGAGCTAATGTAAGACATGTCTGGGACATGGCATCGACATCGAGAC
Found at i:28261639 original size:67 final size:66
Alignment explanation
Indices: 28261527--28261696 Score: 166
Period size: 67 Copynumber: 2.5 Consensus size: 66
28261517 ATTCCATTGG
* * * *
28261527 GACAATAAACATGGGGTGTGTTGTATAAGACCATAGCCTATCTATGGCAGCATAA-AGAG-TC-C
1 GACAGTAAACA-GGGGTATGTTGTGTAAGACCATAGCCTAGCTATGGCAGCA-AAGAGAGTTCAC
28261589 GTCGA
64 -T-GA
* * * *
28261594 GACAGTAAATACGGGGTATGTTGTGTAAGACCATAGCTTGGCTATGGTAGCAAAGAGAGTTCACT
1 GACAGTAAACA-GGGGTATGTTGTGTAAGACCATAGCCTAGCTATGGCAGCAAAGAGAGTTCACT
*
28261659 GG
65 GA
* *
28261661 GATAGTAAACAGGAGGTATGTTGTGTAAGACTATAG
1 GACAGTAAACAGG-GGTATGTTGTGTAAGACCATAG
28261697 TCGACTATGA
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
66 4 0.05
67 78 0.91
68 3 0.03
69 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (66 bp):
GACAGTAAACAGGGGTATGTTGTGTAAGACCATAGCCTAGCTATGGCAGCAAAGAGAGTTCACTG
A
Found at i:28265407 original size:27 final size:27
Alignment explanation
Indices: 28265351--28265420 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
28265341 GTGTTTCCAA
* *
28265351 ACACTAAACATGGGGTAGTTAGCTAGG
1 ACACTAAACAAGGGGTAGTTAGCGAGG
*
28265378 ACACTAAACAAGGGGTAGTTTGTCGA-G
1 ACACTAAACAAGGGGTAGTTAG-CGAGG
* *
28265405 ACATTAAACACGGGGT
1 ACACTAAACAAGGGGT
28265421 CTGTCAGGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 35 0.95
28 2 0.05
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (27 bp):
ACACTAAACAAGGGGTAGTTAGCGAGG
Found at i:28270237 original size:19 final size:19
Alignment explanation
Indices: 28270197--28270237 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28270187 TAGCTGTATA
*
28270197 ATTATTATTTTAATAAATT
1 ATTATTATTTTAATAAAGT
28270216 ATTATTACTTTTAAT-AAGT
1 ATTATTA-TTTTAATAAAGT
28270235 ATT
1 ATT
28270238 GATAAGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTATTATTTTAATAAAGT
Found at i:28271389 original size:20 final size:20
Alignment explanation
Indices: 28271364--28271413 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
28271354 ATGTTAGTCC
* *
28271364 CATGAATAGTGGGGTCAACT
1 CATGAATAGTGGAGTCAAAT
*
28271384 CATGAACAGTGGAGTCAAAT
1 CATGAATAGTGGAGTCAAAT
28271404 CATGAATAGT
1 CATGAATAGT
28271414 TATAACATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (20 bp):
CATGAATAGTGGAGTCAAAT
Done.