Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 139 of 328
Found at i:40503654 original size:40 final size:40
Alignment explanation
Indices: 40503574--40503794 Score: 283
Period size: 40 Copynumber: 5.6 Consensus size: 40
40503564 TATTCGGACG
*
40503574 ATATCCGGGCTAAGTCCCGAAGGCA-TTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
40503613 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
*
40503653 ATATCCGGGCTAAGTCCCGAAGGC-GTTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCAG-TTGTGCTA-TTGACT
* ** *
40503693 ATATCCGGGCTAAGTCCCGAAAGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
* *
40503733 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAG-TCCCGAAGGCAGTTGTGCTA-TTGACT
*
40503773 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
40503795 TACTTGGGTT
Statistics
Matches: 163, Mismatches: 11, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.01
39 41 0.25
40 115 0.71
41 6 0.04
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
Found at i:40503708 original size:80 final size:79
Alignment explanation
Indices: 40503574--40503794 Score: 322
Period size: 80 Copynumber: 2.8 Consensus size: 79
40503564 TATTCGGACG
* *
40503574 ATATCCGGGCTAAGTCCCGAAGGCATTGTGCTAG-TGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCTTTGTGCGAGTTG-CTATATCCGGGCTAAGTCCCGAAGGCA
*
40503638 GTTGTGCTATTGACT
65 GTTGTGCTAGTGACT
* *
40503653 ATATCCGGGCTAAGTCCCGAAGGCGTTTGTGCGAGTTGCTATATCCGGGCTAAGTCCCGAAAGCT
1 ATATCCGGGCTAAGTCCCGAAGGC-TTTGTGCGAGTTGCTATATCCGGGCTAAGTCCCGAAGGCA
*
40503718 TTTGTGCTAGTGACT
65 GTTGTGCTAGTGACT
*
40503733 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAG-TCCCGAAGGC-TTTGTGCGAGTTGCTATATCCGGGCTAAGTCCCGAAGG
40503795 TACTTGGGTT
Statistics
Matches: 130, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
79 38 0.29
80 89 0.68
81 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27
Consensus pattern (79 bp):
ATATCCGGGCTAAGTCCCGAAGGCTTTGTGCGAGTTGCTATATCCGGGCTAAGTCCCGAAGGCAG
TTGTGCTAGTGACT
Found at i:40506334 original size:24 final size:24
Alignment explanation
Indices: 40506282--40506393 Score: 84
Period size: 25 Copynumber: 4.5 Consensus size: 24
40506272 GTACATGTAT
* * * *
40506282 GCTCATACGTGCTCTGAATCGGTAT
1 GCTCATACGAGCTAT-AATCGATAA
*
40506307 GCTCTTACGAGCTATAATCGATAA
1 GCTCATACGAGCTATAATCGATAA
*
40506331 GCTCATACGAGCTAAATAAT-GGTAA
1 GCTCATACGAGCT--ATAATCGATAA
* **
40506356 ACTCATACGAGCTGAATAA-CGGCAA
1 GCTCATACGAGCT--ATAATCGATAA
40506381 GCTCATACGAGCT
1 GCTCATACGAGCT
40506394 GAATATTGGT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
24 19 0.26
25 49 0.67
26 5 0.07
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (24 bp):
GCTCATACGAGCTATAATCGATAA
Found at i:40506407 original size:25 final size:25
Alignment explanation
Indices: 40506302--40506408 Score: 119
Period size: 25 Copynumber: 4.3 Consensus size: 25
40506292 GCTCTGAATC
* *
40506302 GGTATGCTCTTACGAGCT--ATAAT
1 GGTAAGCTCATACGAGCTGAATAAT
* *
40506325 CGATAAGCTCATACGAGCTAAATAAT
1 -GGTAAGCTCATACGAGCTGAATAAT
* *
40506351 GGTAAACTCATACGAGCTGAATAAC
1 GGTAAGCTCATACGAGCTGAATAAT
* *
40506376 GGCAAGCTCATACGAGCTGAATATT
1 GGTAAGCTCATACGAGCTGAATAAT
40506401 GGTAAGCT
1 GGTAAGCT
40506409 TTCTCGAGCT
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
24 15 0.22
25 49 0.71
26 5 0.07
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (25 bp):
GGTAAGCTCATACGAGCTGAATAAT
Found at i:40509308 original size:22 final size:22
Alignment explanation
Indices: 40509262--40509308 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
40509252 GGCCGGGGTA
* **
40509262 GAGGCCGTAGGGGGCTCAAGTT
1 GAGGCCGTAAGGGGCTCAAACT
40509284 GAGGCCGTAAGGGGCTCAAACT
1 GAGGCCGTAAGGGGCTCAAACT
40509306 GAG
1 GAG
40509309 TCCTCAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.43, T:0.15
Consensus pattern (22 bp):
GAGGCCGTAAGGGGCTCAAACT
Found at i:40521113 original size:46 final size:46
Alignment explanation
Indices: 40521026--40521153 Score: 143
Period size: 46 Copynumber: 2.7 Consensus size: 46
40521016 ACATCTCGTA
* * * *
40521026 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAG
1 GCCGATGCATGTCCAAGACATGTCTTACACTAGCCTACGTCTCAAG
* *
40521072 GCCGATGCATGTCCAAGACATGTCTTATACTAGCACT-CGTCTCAAT
1 GCCGATGCATGTCCAAGACATGTCTTACACTAGC-CTACGTCTCAAG
*
40521118 GCCAATGACATGTTCCAA-ACATGGTCTTACACTAGC
1 GCCGATG-CATG-TCCAAGACAT-GTCTTACACTAGC
40521154 TCTTATACTA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
46 44 0.63
47 9 0.13
48 17 0.24
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.27
Consensus pattern (46 bp):
GCCGATGCATGTCCAAGACATGTCTTACACTAGCCTACGTCTCAAG
Found at i:40528767 original size:46 final size:46
Alignment explanation
Indices: 40528714--40528889 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
40528704 TATTTGGGCA
40528714 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
40528760 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
40528807 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
40528853 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40528890 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:40528869 original size:93 final size:93
Alignment explanation
Indices: 40528710--40528881 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
40528700 AGGATATTTG
* *
40528710 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
40528775 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
40528803 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
40528868 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
40528882 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:40530742 original size:34 final size:34
Alignment explanation
Indices: 40530703--40530770 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
40530693 TACACAAACT
40530703 ACATAATAGCAACCACAATCAAGATAAAACTATC
1 ACATAATAGCAACCACAATCAAGATAAAACTATC
40530737 ACATAATAGCAACCACAATCAAGATAAAACTATC
1 ACATAATAGCAACCACAATCAAGATAAAACTATC
40530771 TCATGCAACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.53, C:0.24, G:0.06, T:0.18
Consensus pattern (34 bp):
ACATAATAGCAACCACAATCAAGATAAAACTATC
Found at i:40532783 original size:38 final size:38
Alignment explanation
Indices: 40532732--40532807 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
40532722 AATGACTCAA
40532732 AAATAATAATAAAATAATTTATTCAACTCTAAATTTAT
1 AAATAATAATAAAATAATTTATTCAACTCTAAATTTAT
*
40532770 AAATAATAATAAAATAATTTATTCAACTCTGAATTTAT
1 AAATAATAATAAAATAATTTATTCAACTCTAAATTTAT
40532808 GGTCTCGAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.39
Consensus pattern (38 bp):
AAATAATAATAAAATAATTTATTCAACTCTAAATTTAT
Found at i:40535750 original size:29 final size:29
Alignment explanation
Indices: 40535689--40535787 Score: 159
Period size: 28 Copynumber: 3.5 Consensus size: 29
40535679 ACAGTAAGTC
*
40535689 CGCACACTTAGTGCT-TA-ATATTCAAACC
1 CGCACACTTAGTGCTATACA-ATTCAAACT
40535717 CGCACACTTAGTGCTATACAATTCAAACT
1 CGCACACTTAGTGCTATACAATTCAAACT
40535746 CGCACACTTAGTGCTATACAATT-AAACT
1 CGCACACTTAGTGCTATACAATTCAAACT
40535774 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40535788 CAATCTCATT
Statistics
Matches: 68, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
28 34 0.50
29 33 0.49
30 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTATACAATTCAAACT
Found at i:40537609 original size:20 final size:20
Alignment explanation
Indices: 40537586--40537654 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
40537576 AAGGAGTACA
40537586 AAAAAAATATGAGAAAATAT
1 AAAAAAATATGAGAAAATAT
* * * *
40537606 AAAAAACTATGAGGAAGTGCT
1 AAAAAAATATGAGAAAAT-AT
40537627 AAAAAAA-ATGAGAAAATAT
1 AAAAAAATATGAGAAAATAT
40537646 AAAAAAATA
1 AAAAAAATA
40537655 AAAAAATACC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 8 0.21
20 24 0.62
21 7 0.18
ACGTcount: A:0.67, C:0.03, G:0.13, T:0.17
Consensus pattern (20 bp):
AAAAAAATATGAGAAAATAT
Found at i:40537660 original size:18 final size:18
Alignment explanation
Indices: 40537628--40537662 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40537618 GGAAGTGCTA
* *
40537628 AAAAAAATGAGAAAATAT
1 AAAAAAATAAAAAAATAT
40537646 AAAAAAATAAAAAAATA
1 AAAAAAATAAAAAAATA
40537663 CCAAAAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (18 bp):
AAAAAAATAAAAAAATAT
Found at i:40537763 original size:18 final size:17
Alignment explanation
Indices: 40537732--40537765 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40537722 TAATAAATTT
*
40537732 ATTTTTAAATTTATTAA
1 ATTTTTAAAATTATTAA
40537749 ATTTTTATAAATTATTA
1 ATTTTTA-AAATTATTA
40537766 TTAATGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTTAAAATTATTAA
Found at i:40546339 original size:17 final size:18
Alignment explanation
Indices: 40546319--40546353 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
40546309 TTAAATTAAA
40546319 AATTAAAC-AAAAATAAT
1 AATTAAACTAAAAATAAT
*
40546336 AATTAAACTAAAAGTAAT
1 AATTAAACTAAAAATAAT
40546354 TGAACGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AATTAAACTAAAAATAAT
Found at i:40549697 original size:40 final size:40
Alignment explanation
Indices: 40549635--40549851 Score: 280
Period size: 40 Copynumber: 5.5 Consensus size: 40
40549625 AAGCCAAGTA
* * * *
40549635 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
40549674 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
40549714 CCTTTGGGACTTAGCCCGGATATGGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40549754 CCTTCGGGACTTAGCTCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
40549794 CCTTCGGGACTTAGCCCAGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
40549834 CC-TCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40549852 TTATCATCCA
Statistics
Matches: 158, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
39 28 0.18
40 130 0.82
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40554848 original size:61 final size:61
Alignment explanation
Indices: 40554773--40554891 Score: 238
Period size: 61 Copynumber: 2.0 Consensus size: 61
40554763 GATATGGTAC
40554773 TTTTGAGTATGAATGATATGTTTAAATGGTGGTGTGGAATGGATATATATATATATATATA
1 TTTTGAGTATGAATGATATGTTTAAATGGTGGTGTGGAATGGATATATATATATATATATA
40554834 TTTTGAGTATGAATGATATGTTTAAATGGTGGTGTGGAATGGATATATATATATATAT
1 TTTTGAGTATGAATGATATGTTTAAATGGTGGTGTGGAATGGATATATATATATATAT
40554892 TGTAACAGCC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.43
Consensus pattern (61 bp):
TTTTGAGTATGAATGATATGTTTAAATGGTGGTGTGGAATGGATATATATATATATATATA
Found at i:40563218 original size:46 final size:48
Alignment explanation
Indices: 40563149--40563341 Score: 167
Period size: 52 Copynumber: 3.9 Consensus size: 48
40563139 TTGCACATTG
* * *
40563149 TCACATATCACACACCGAAGCCATAACCCTGCTATGGTCTTACGCGG-A
1 TCAC-TATCACACACCGATGCCATAACCCAGCTATGGTCTTACACGGAA
* ** *
40563197 TCAC-ATCACACACCGATGCCATATCCCAAATATGGTCTTATACGGAA
1 TCACTATCACACACCGATGCCATAACCCAGCTATGGTCTTACACGGAA
* *
40563244 TCACATTATCATATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGAGAA
1 TCAC--TATC--A-CACACCGATGCCATAACCCAGCTATGGTCTTACACG-GAA
* *
40563298 -CGCATATCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTA
1 TCAC-TATCACA---CACCGATGCCATAACCCAGCTATGGTCTTA
40563342 AACGAGCGCA
Statistics
Matches: 122, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
46 34 0.28
47 5 0.04
48 4 0.03
49 2 0.02
50 4 0.03
52 35 0.29
53 35 0.29
54 3 0.02
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.24
Consensus pattern (48 bp):
TCACTATCACACACCGATGCCATAACCCAGCTATGGTCTTACACGGAA
Found at i:40563356 original size:52 final size:52
Alignment explanation
Indices: 40563196--40563358 Score: 193
Period size: 52 Copynumber: 3.1 Consensus size: 52
40563186 TCTTACGCGG
* **
40563196 ATCACATCACACACCGATGCCATATCCCAAATATGGTCTTATACG-GAATCACATT
1 ATCACAT--CACACCGATGCCATAGCCCAGCTATGGTCTTATACGAGAA-CACA-T
* *
40563251 ATCATATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGAGAACGCAT
1 ATCACATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGAGAACACAT
** * **
40563303 ATCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGAGCGCACAT
1 ATCACATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGAGAACACAT
40563355 ATCA
1 ATCA
40563359 TATACTTTCC
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
52 50 0.53
53 36 0.38
54 3 0.03
55 6 0.06
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.23
Consensus pattern (52 bp):
ATCACATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGAGAACACAT
Found at i:40566372 original size:13 final size:13
Alignment explanation
Indices: 40566354--40566380 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40566344 GGTGTATTAA
40566354 AGGTTTCTCAATG
1 AGGTTTCTCAATG
40566367 AGGTTTCTCAATG
1 AGGTTTCTCAATG
40566380 A
1 A
40566381 TCACTTCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (13 bp):
AGGTTTCTCAATG
Found at i:40569227 original size:26 final size:26
Alignment explanation
Indices: 40569198--40569305 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
40569188 TGATACAAAT
40569198 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
40569224 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40569250 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
40569276 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40569302 TGAT
1 TGAT
40569306 TGGAATTTCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:40573984 original size:15 final size:15
Alignment explanation
Indices: 40573957--40574020 Score: 74
Period size: 15 Copynumber: 4.1 Consensus size: 15
40573947 TTGTACATAA
40573957 TTAAATATTTTTATT
1 TTAAATATTTTTATT
* *
40573972 TTGAATTTTTTTAGTT
1 TTAAATATTTTTA-TT
40573988 GATTAAATATTTTTATT
1 --TTAAATATTTTTATT
*
40574005 TTTAATATTTTTATT
1 TTAAATATTTTTATT
40574020 T
1 T
40574021 ACCTTATTGG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
15 26 0.63
16 2 0.05
17 2 0.05
18 11 0.27
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (15 bp):
TTAAATATTTTTATT
Found at i:40577725 original size:33 final size:33
Alignment explanation
Indices: 40577683--40577749 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
40577673 GAGTTTTTAA
40577683 CTGTTTCCACAAGGTGAAGGAGGTCTTCTCCAT
1 CTGTTTCCACAAGGTGAAGGAGGTCTTCTCCAT
*
40577716 CTGTTTCCACAAGGTGAATGAGGTCTTCTCCAT
1 CTGTTTCCACAAGGTGAAGGAGGTCTTCTCCAT
40577749 C
1 C
40577750 ATTACCTCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.31
Consensus pattern (33 bp):
CTGTTTCCACAAGGTGAAGGAGGTCTTCTCCAT
Found at i:40583186 original size:45 final size:45
Alignment explanation
Indices: 40583131--40583218 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
40583121 CCAAAACATG
*
40583131 TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTCATA
1 TGTCACATATATCACGAAATCAGACCACAACTCAATGAGTTCATA
* * * *
40583176 TGTCATATATATCATGAAATTAGACCACAATTCAATGAGTTCA
1 TGTCACATATATCACGAAATCAGACCACAACTCAATGAGTTCA
40583219 GATTACATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (45 bp):
TGTCACATATATCACGAAATCAGACCACAACTCAATGAGTTCATA
Found at i:40586772 original size:25 final size:25
Alignment explanation
Indices: 40586738--40586803 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
40586728 CTTGATTTAT
*
40586738 AGCTCATGTGAGCAATCATATTCAC
1 AGCTCATGTGAGCAATCACATTCAC
* *
40586763 AGCTCATGTGAGCAGTTACATTCAC
1 AGCTCATGTGAGCAATCACATTCAC
* **
40586788 AGATTGTGTGAGCAAT
1 AGCTCATGTGAGCAAT
40586804 TTAAGTCTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (25 bp):
AGCTCATGTGAGCAATCACATTCAC
Found at i:40593599 original size:39 final size:39
Alignment explanation
Indices: 40593559--40593735 Score: 300
Period size: 39 Copynumber: 4.5 Consensus size: 39
40593549 ATTCATTTTT
* * *
40593559 AAGCATATATCACATTACACATATAATCACATAACATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
40593598 AAGCATATATCACAATGCTCATATAATTACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
*
40593637 AAGCATATATCACAAAACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
40593676 AAGCATATATCACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
40593715 AAGCATATATCACAATACTCA
1 AAGCATATATCACAATACTCA
40593736 AAAACATGTT
Statistics
Matches: 129, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 129 1.00
ACGTcount: A:0.46, C:0.22, G:0.03, T:0.28
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:40593667 original size:17 final size:17
Alignment explanation
Indices: 40593640--40593706 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 17
40593630 AACATTCAAG
40593640 CATAT-ATCACAAAACT
1 CATATAATCACAAAACT
*
40593656 CATATAATCACATAACATT
1 CATATAATCACA-AA-ACT
* *
40593675 CAAGCATATATCACAATACT
1 C-A-TATA-ATCACAAAACT
40593695 CATATAATCACA
1 CATATAATCACA
40593707 TAACATTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
16 5 0.12
17 12 0.30
18 5 0.12
19 4 0.10
20 4 0.10
21 4 0.10
22 6 0.15
ACGTcount: A:0.48, C:0.24, G:0.01, T:0.27
Consensus pattern (17 bp):
CATATAATCACAAAACT
Found at i:40593796 original size:22 final size:22
Alignment explanation
Indices: 40593768--40593815 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
40593758 GGCGTTTGAG
40593768 CTATGAAACTTAAAAGTGGGCA
1 CTATGAAACTTAAAAGTGGGCA
40593790 CTATGAAACTTAAAAGTGGGCA
1 CTATGAAACTTAAAAGTGGGCA
40593812 CTAT
1 CTAT
40593816 CACCACTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.25
Consensus pattern (22 bp):
CTATGAAACTTAAAAGTGGGCA
Found at i:40596259 original size:2 final size:2
Alignment explanation
Indices: 40596252--40596285 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40596242 TTACATAAAC
40596252 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40596286 CATGTTACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40600267 original size:18 final size:18
Alignment explanation
Indices: 40600244--40600280 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
40600234 ACTGAACAGT
40600244 CAAAATAAGTAAATGTGA
1 CAAAATAAGTAAATGTGA
40600262 CAAAATAAGTAAATGTGA
1 CAAAATAAGTAAATGTGA
40600280 C
1 C
40600281 GAGTGAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.08, G:0.16, T:0.22
Consensus pattern (18 bp):
CAAAATAAGTAAATGTGA
Found at i:40608309 original size:10 final size:10
Alignment explanation
Indices: 40608296--40608326 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
40608286 AAATTAAATG
40608296 TCATGCAGGA
1 TCATGCAGGA
40608306 TCATGCAGGA
1 TCATGCAGGA
40608316 TCATGCAGGA
1 TCATGCAGGA
40608326 T
1 T
40608327 AAAATAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (10 bp):
TCATGCAGGA
Found at i:40609184 original size:34 final size:34
Alignment explanation
Indices: 40609118--40609185 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
40609108 GCTCAAGTAG
*** **
40609118 AACAATACAGTAGCATTTAATATGCTTTTAACAA
1 AACAATACAGTAGCAAACAATATGCTCATAACAA
*
40609152 AACAATACAGTTGCAAACAATATGCTCATAACAA
1 AACAATACAGTAGCAAACAATATGCTCATAACAA
40609186 TTCGATTCAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.47, C:0.18, G:0.09, T:0.26
Consensus pattern (34 bp):
AACAATACAGTAGCAAACAATATGCTCATAACAA
Found at i:40616745 original size:16 final size:16
Alignment explanation
Indices: 40616724--40616756 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
40616714 TTGTAACGAC
40616724 CCAAAAATCCTGAAAT
1 CCAAAAATCCTGAAAT
40616740 CCAAAAATCCTGAAAT
1 CCAAAAATCCTGAAAT
40616756 C
1 C
40616757 TTGAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.27, G:0.06, T:0.18
Consensus pattern (16 bp):
CCAAAAATCCTGAAAT
Found at i:40618242 original size:29 final size:28
Alignment explanation
Indices: 40618195--40618306 Score: 102
Period size: 29 Copynumber: 3.9 Consensus size: 28
40618185 TGAGTATAAT
* *
40618195 ATGATTTGGGCCTAATGGGCCATATGAA
1 ATGAATTGGGCCTAGTGGGCCATATGAA
*
40618223 AGTGAATTGGGCCTAGTGGGCCATAAGAA
1 A-TGAATTGGGCCTAGTGGGCCATATGAA
* * *
40618252 TATGAACTAGGCC-AGATGGGCCATTTG-A
1 -ATGAATTGGGCCTAG-TGGGCCATATGAA
* *
40618280 ATAAGATTGGGCCTAGTGGGCTATATG
1 ATGA-ATTGGGCCTAGTGGGCCATATG
40618307 CATGTATGTA
Statistics
Matches: 67, Mismatches: 12, Indels: 10
0.75 0.13 0.11
Matches are distributed among these distances:
27 3 0.04
28 19 0.28
29 44 0.66
30 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (28 bp):
ATGAATTGGGCCTAGTGGGCCATATGAA
Found at i:40621187 original size:16 final size:16
Alignment explanation
Indices: 40621166--40621198 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40621156 TTGTAATGCC
40621166 CCAAAAATCCCGAAAT
1 CCAAAAATCCCGAAAT
*
40621182 CCAAAAATCCTGAAAT
1 CCAAAAATCCCGAAAT
40621198 C
1 C
40621199 TTGAATTTTT
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:0.48, C:0.30, G:0.06, T:0.15
Consensus pattern (16 bp):
CCAAAAATCCCGAAAT
Found at i:40622526 original size:14 final size:14
Alignment explanation
Indices: 40622507--40622536 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40622497 TATCTTATAA
40622507 ATATGCGTGAATCT
1 ATATGCGTGAATCT
*
40622521 ATATGCGTTAATCT
1 ATATGCGTGAATCT
40622535 AT
1 AT
40622537 CTTGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (14 bp):
ATATGCGTGAATCT
Found at i:40625566 original size:2 final size:2
Alignment explanation
Indices: 40625559--40625595 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
40625549 GAGAAAATAA
40625559 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40625596 AAAGGAAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40628704 original size:109 final size:108
Alignment explanation
Indices: 40628512--40628708 Score: 241
Period size: 109 Copynumber: 1.8 Consensus size: 108
40628502 CATATACGAT
* * * *
40628512 TAATGTCATTACATTTGTACACAAAAGGTTCAATTAGATCAATGATAGTATTTATCAATTGTATA
1 TAATGTCATTACATTTGTACACAAAAGATTCAATTAGAACAATGATAGTACTTACCAATTGTATA
* ***
40628577 ATTCATTTGATTAGGTTCATAATTTAAGTCATGTGTTTACAAG
66 AGTCATCCAATTAGGTTCATAATTTAAGTCATGTGTTTACAAG
* * ** * *
40628620 TAATGTCATTATATTTGTACATAGATTGATTCAATTGGAACAATGATCGTACTTACCAATTGTAT
1 TAATGTCATTACATTTGTACACA-AAAGATTCAATTAGAACAATGATAGTACTTACCAATTGTAT
* *
40628685 AAGTCCTCCAATTATGTTCATAAT
65 AAGTCATCCAATTAGGTTCATAAT
40628709 AAAATTCGTG
Statistics
Matches: 72, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
108 21 0.29
109 51 0.71
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (108 bp):
TAATGTCATTACATTTGTACACAAAAGATTCAATTAGAACAATGATAGTACTTACCAATTGTATA
AGTCATCCAATTAGGTTCATAATTTAAGTCATGTGTTTACAAG
Found at i:40630777 original size:24 final size:25
Alignment explanation
Indices: 40630709--40630885 Score: 98
Period size: 27 Copynumber: 7.0 Consensus size: 25
40630699 AGTACGCATA
40630709 AACTTTGCATAGATAGTTCACACAC
1 AACTTTGCATAGATAGTTCACACAC
* *
40630734 AGAACTTTACATA-ATCAGTTCGCACAC
1 --AACTTTGCATAGAT-AGTTCACACAC
* *
40630761 -ACTTTGCACAGATAGTTCACACATAA
1 AACTTTGCATAGATAGTTCACAC--AC
* ** *
40630787 AACTTTACATA-ATCAGAACACGCAC
1 AACTTTGCATAGAT-AGTTCACACAC
* * * *
40630812 -ACTTTGCATGGACAATTCACACATAG
1 AACTTTGCATAGATAGTTCACAC--AC
*
40630838 AACTTTACATA-ATCAG-T-ACACAC
1 AACTTTGCATAGAT-AGTTCACACAC
40630861 ATACTTTGCATAGATAGTTCACACA
1 A-ACTTTGCATAGATAGTTCACACA
40630886 TAGAACTTTA
Statistics
Matches: 109, Mismatches: 26, Indels: 31
0.66 0.16 0.19
Matches are distributed among these distances:
23 2 0.02
24 40 0.37
25 11 0.10
26 13 0.12
27 43 0.39
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (25 bp):
AACTTTGCATAGATAGTTCACACAC
Found at i:40630918 original size:153 final size:153
Alignment explanation
Indices: 40630584--40630930 Score: 444
Period size: 153 Copynumber: 2.3 Consensus size: 153
40630574 TGTATATAAT
* * * * * *
40630584 ACTTTACATAATTAATATGCACATACTTTGCATAGACAGATCACATATAGAAATATACATAATTA
1 ACTTTACATAATCAATACGCACATACTTTGCATAGATAGTTCACACATAGAAATATACATAATCA
* * * * ** * *
40630649 GTACACATACACTTTGCATAGACAGTTCACACATAGAAGTTTATGTAATCAGTACGCATAAACTT
66 GAACACACACACTTTGCATAGACAATTCACACATAGAACTTTACATAATCAGTACACACAAACTT
40630714 TGCATAGATAGTTCACACACAGA
131 TGCATAGATAGTTCACACACAGA
* * * * *
40630737 ACTTTACATAATCAGTTCGCACACACTTTGCACAGATAGTTCACACATA-AAACTTTACATAATC
1 ACTTTACATAATCAATACGCACATACTTTGCATAGATAGTTCACACATAGAAA-TATACATAATC
* * *
40630801 AGAACACGCACACTTTGCATGGACAATTCACACATAGAACTTTACATAATCAGTACACACATACT
65 AGAACACACACACTTTGCATAGACAATTCACACATAGAACTTTACATAATCAGTACACACAAACT
*
40630866 TTGCATAGATAGTTCACACATAGA
130 TTGCATAGATAGTTCACACACAGA
* * *
40630890 ACTTTACATAATCAATACGTATATACTTTGCATTGATAGTT
1 ACTTTACATAATCAATACGCACATACTTTGCATAGATAGTT
40630931 ATGTTGGATC
Statistics
Matches: 163, Mismatches: 30, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
152 3 0.02
153 160 0.98
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (153 bp):
ACTTTACATAATCAATACGCACATACTTTGCATAGATAGTTCACACATAGAAATATACATAATCA
GAACACACACACTTTGCATAGACAATTCACACATAGAACTTTACATAATCAGTACACACAAACTT
TGCATAGATAGTTCACACACAGA
Found at i:40630928 original size:51 final size:51
Alignment explanation
Indices: 40630584--40630930 Score: 379
Period size: 51 Copynumber: 6.8 Consensus size: 51
40630574 TGTATATAAT
* * * * * * *
40630584 ACTTTACATAATTAATATGCACATACTTTGCATAGACAGATCACATATAGA
1 ACTTTACATAATCAGTACGCACACACTTTGCATAGATAGTTCACACATAGA
* * * * * *
40630635 AATATACATAATTAGTACACATACACTTTGCATAGACAGTTCACACATAGA
1 ACTTTACATAATCAGTACGCACACACTTTGCATAGATAGTTCACACATAGA
* ** * * *
40630686 AGTTTATGTAATCAGTACGCATAAACTTTGCATAGATAGTTCACACACAGA
1 ACTTTACATAATCAGTACGCACACACTTTGCATAGATAGTTCACACATAGA
* * *
40630737 ACTTTACATAATCAGTTCGCACACACTTTGCACAGATAGTTCACACATAAA
1 ACTTTACATAATCAGTACGCACACACTTTGCATAGATAGTTCACACATAGA
* * * * * *
40630788 ACTTTACATAATCAGAACACGCACACTTTGCATGGACAATTCACACATAGA
1 ACTTTACATAATCAGTACGCACACACTTTGCATAGATAGTTCACACATAGA
* *
40630839 ACTTTACATAATCAGTACACACATACTTTGCATAGATAGTTCACACATAGA
1 ACTTTACATAATCAGTACGCACACACTTTGCATAGATAGTTCACACATAGA
* * * * *
40630890 ACTTTACATAATCAATACGTATATACTTTGCATTGATAGTT
1 ACTTTACATAATCAGTACGCACACACTTTGCATAGATAGTT
40630931 ATGTTGGATC
Statistics
Matches: 249, Mismatches: 47, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 249 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (51 bp):
ACTTTACATAATCAGTACGCACACACTTTGCATAGATAGTTCACACATAGA
Found at i:40634518 original size:21 final size:21
Alignment explanation
Indices: 40634489--40634533 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
40634479 TTATTCATGA
*
40634489 ATTATATTAATACTTTGTATT
1 ATTACATTAATACTTTGTATT
40634510 ATTACATTAATACTTTGTATT
1 ATTACATTAATACTTTGTATT
40634531 ATT
1 ATT
40634534 GTTCTCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (21 bp):
ATTACATTAATACTTTGTATT
Found at i:40638097 original size:21 final size:20
Alignment explanation
Indices: 40638071--40638117 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
40638061 ACGAAAATAT
*
40638071 TAAAATATTAAAATATTAAAA
1 TAAAATATTAAAA-AATAAAA
*
40638092 TAAAATTTTAAAAAATAAAA
1 TAAAATATTAAAAAATAAAA
40638112 -AAAATA
1 TAAAATA
40638118 AAAATGGCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 5 0.22
20 6 0.26
21 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAATATTAAAAAATAAAA
Found at i:40638104 original size:8 final size:8
Alignment explanation
Indices: 40638064--40638093 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
40638054 CAAACAAACG
40638064 AAAATATT
1 AAAATATT
40638072 AAAATATT
1 AAAATATT
40638080 AAAATATT
1 AAAATATT
40638088 AAAATA
1 AAAATA
40638094 AAATTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAATATT
Found at i:40638119 original size:29 final size:29
Alignment explanation
Indices: 40638064--40638120 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
40638054 CAAACAAACG
* * * *
40638064 AAAATATTAAAATATTAAAATATTAAAAT
1 AAAATATTAAAAAATAAAAAAAATAAAAT
*
40638093 AAAATTTTAAAAAATAAAAAAAATAAAA
1 AAAATATTAAAAAATAAAAAAAATAAAA
40638121 ATGGCTAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (29 bp):
AAAATATTAAAAAATAAAAAAAATAAAAT
Found at i:40641221 original size:19 final size:20
Alignment explanation
Indices: 40641191--40641229 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
40641181 GAACATAATT
40641191 AAATTGAAAAAAAAAAGAAA
1 AAATTGAAAAAAAAAAGAAA
40641211 AAATT-AAAAAAAAAAGAAA
1 AAATTGAAAAAAAAAAGAAA
40641230 TATCTTTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (20 bp):
AAATTGAAAAAAAAAAGAAA
Found at i:40644485 original size:14 final size:14
Alignment explanation
Indices: 40644466--40644492 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40644456 TTATTGTGCA
40644466 AAAGAAATTATTTT
1 AAAGAAATTATTTT
40644480 AAAGAAATTATTT
1 AAAGAAATTATTT
40644493 AATCATAAAT
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:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
AAAGAAATTATTTT
Found at i:40654346 original size:42 final size:42
Alignment explanation
Indices: 40654285--40654398 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 42
40654275 TTTGACATTA
* * *
40654285 CTTGTAAGACCATATCTGGGATATGGCATCGATATGAGGAT-T
1 CTTGTAAGACCATAGCTGGGATATGGCATCGACACGA-GATCT
* * * *
40654327 TTTGTAAGACCATAGCTGGGCTATTAGCATCGACGCGAGATCT
1 CTTGTAAGACCATAGCTGGGATA-TGGCATCGACACGAGATCT
*
40654370 CATGTAAGACCATAGCTGGGATATGGCAT
1 CTTGTAAGACCATAGCTGGGATATGGCAT
40654399 TGTTATGGTA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
42 28 0.47
43 31 0.53
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (42 bp):
CTTGTAAGACCATAGCTGGGATATGGCATCGACACGAGATCT
Found at i:40655676 original size:10 final size:10
Alignment explanation
Indices: 40655649--40655708 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
40655639 TTAAATTCTA
40655649 AAAGATAAAT
1 AAAGATAAAT
40655659 ACAA-ATAAAT
1 A-AAGATAAAT
*
40655669 AAAGATAATT
1 AAAGATAAAT
*
40655679 AAGGAT-AAT
1 AAAGATAAAT
*
40655688 GAAAGATACAT
1 -AAAGATAAAT
*
40655699 AAAAATAAAT
1 AAAGATAAAT
40655709 CCTAAATTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
9 4 0.10
10 31 0.79
11 4 0.10
ACGTcount: A:0.65, C:0.03, G:0.10, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:40655741 original size:13 final size:13
Alignment explanation
Indices: 40655725--40655749 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40655715 TTTAAATCTA
40655725 AATAATTATCCTT
1 AATAATTATCCTT
40655738 AATAATTATCCT
1 AATAATTATCCT
40655750 AGTATAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
AATAATTATCCTT
Found at i:40656342 original size:15 final size:15
Alignment explanation
Indices: 40656318--40656353 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
40656308 ATCCTCCCTT
* *
40656318 TTTTTTATTTTTTTA
1 TTTTTAATTTATTTA
40656333 TTTTTAATTTATTTA
1 TTTTTAATTTATTTA
40656348 TTTTTA
1 TTTTTA
40656354 CTTAGGAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTAATTTATTTA
Found at i:40656509 original size:96 final size:97
Alignment explanation
Indices: 40656344--40656523 Score: 281
Period size: 96 Copynumber: 1.9 Consensus size: 97
40656334 TTTTAATTTA
* * * *
40656344 TTTATTTTTACTTAGGAATATATTGAGCCTTTTGACGCAAAGAGAGATGACAGCCAAGCACCCCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCAAAGAGAGATGACAGCCAAGCACCCCA
40656409 CCCCGATTACTCAGCCCAATACACTCCTAATT
66 CCCCGATTACTCAGCCCAATACACTCCTAATT
* * *
40656441 TTTATTTTT-CTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCGAGCACCTCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCAAAGAGAGATGACAGCCAAGCACCCCA
*
40656505 CCCCGGTTACTCAGCCCAA
66 CCCCGATTACTCAGCCCAA
40656524 CACATTTTTA
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
96 66 0.88
97 9 0.12
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (97 bp):
TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCAAAGAGAGATGACAGCCAAGCACCCCA
CCCCGATTACTCAGCCCAATACACTCCTAATT
Found at i:40657577 original size:16 final size:16
Alignment explanation
Indices: 40657556--40657604 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
40657546 TCATTAAGAC
* *
40657556 AAAATAATAAATAATT
1 AAAATAATAAAAAAAT
40657572 AAAATAAATAAAAAAAT
1 AAAAT-AATAAAAAAAT
*
40657589 AAAAAAATAAAGAAAA
1 AAAATAATAAA-AAAA
40657605 ATCAGGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (16 bp):
AAAATAATAAAAAAAT
Found at i:40657588 original size:8 final size:8
Alignment explanation
Indices: 40657556--40657604 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
40657546 TCATTAAGAC
*
40657556 AAAATAAT
1 AAAAAAAT
* *
40657564 AAATAATT
1 AAAAAAAT
40657572 AAAATAAAT
1 AAAA-AAAT
40657581 AAAAAAAT
1 AAAAAAAT
40657589 AAAAAAAT
1 AAAAAAAT
40657597 AAAGAAAA
1 AAA-AAAA
40657605 ATCAGGAGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
8 23 0.68
9 11 0.32
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (8 bp):
AAAAAAAT
Found at i:40660667 original size:29 final size:29
Alignment explanation
Indices: 40660631--40660689 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
40660621 TCATTAATTA
40660631 TAAATTCAGTTTTATCTTCATAAATTGAC
1 TAAATTCAGTTTTATCTTCATAAATTGAC
40660660 TAAATTCAGTTTTATCTTCATAAATTGAC
1 TAAATTCAGTTTTATCTTCATAAATTGAC
40660689 T
1 T
40660690 CAAAAGTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.46
Consensus pattern (29 bp):
TAAATTCAGTTTTATCTTCATAAATTGAC
Found at i:40664007 original size:10 final size:10
Alignment explanation
Indices: 40663986--40664037 Score: 68
Period size: 10 Copynumber: 5.1 Consensus size: 10
40663976 AATTAAATTC
40663986 TAAAAGATAAA
1 TAAAA-ATAAA
*
40663997 TACAAATAAA
1 TAAAAATAAA
*
40664007 TAAAAATAAT
1 TAAAAATAAA
*
40664017 TAAAGATAAA
1 TAAAAATAAA
40664027 TAAAAATAAA
1 TAAAAATAAA
40664037 T
1 T
40664038 CCTAAATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
10 31 0.89
11 4 0.11
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:40667995 original size:3 final size:3
Alignment explanation
Indices: 40667987--40668048 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
40667977 AAATAAACTC
40667987 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
40668035 TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TC
40668049 ACATCAAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:40669154 original size:29 final size:29
Alignment explanation
Indices: 40669095--40669156 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
40669085 TCATGTTTAG
* ****
40669095 AAATTTTAAAGAAAATTATTTTTTTTGAA
1 AAATTTTAAAGAAAATCATTTTTAAAAAA
40669124 AAATTTTAAAGAAAATCATTTTTAAAAAA
1 AAATTTTAAAGAAAATCATTTTTAAAAAA
40669153 AAAT
1 AAAT
40669157 AACTCGAACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (29 bp):
AAATTTTAAAGAAAATCATTTTTAAAAAA
Found at i:40680884 original size:2 final size:2
Alignment explanation
Indices: 40680877--40680919 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
40680867 ATACGAAGTC
40680877 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40680919 A
1 A
40680920 ATTCGTCATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40681731 original size:31 final size:29
Alignment explanation
Indices: 40681662--40681781 Score: 222
Period size: 29 Copynumber: 4.1 Consensus size: 29
40681652 CTATAATGAC
40681662 TTAGTTTCCAGTGGTGTCAAAAAATGCAA
1 TTAGTTTCCAGTGGTGTCAAAAAATGCAA
40681691 TTAGTTTCCAGTGGTGTCAAAAAATGCAA
1 TTAGTTTCCAGTGGTGTCAAAAAATGCAA
40681720 TTTCAGTTTCCAGTGGTGTCAAAAAATGCAA
1 -TT-AGTTTCCAGTGGTGTCAAAAAATGCAA
40681751 TTAGTTTCCAGTGGTGTCAAAAAATGCAA
1 TTAGTTTCCAGTGGTGTCAAAAAATGCAA
40681780 TT
1 TT
40681782 TCAGAACCTT
Statistics
Matches: 89, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
29 58 0.65
30 4 0.04
31 27 0.30
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (29 bp):
TTAGTTTCCAGTGGTGTCAAAAAATGCAA
Found at i:40681757 original size:60 final size:60
Alignment explanation
Indices: 40681664--40681785 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
40681654 ATAATGACTT
40681664 AGTTTCCAGTGGTGTCAAAAAATGCAATTAGTTTCCAGTGGTGTCAAAAAATGCAATTTC
1 AGTTTCCAGTGGTGTCAAAAAATGCAATTAGTTTCCAGTGGTGTCAAAAAATGCAATTTC
40681724 AGTTTCCAGTGGTGTCAAAAAATGCAATTAGTTTCCAGTGGTGTCAAAAAATGCAATTTC
1 AGTTTCCAGTGGTGTCAAAAAATGCAATTAGTTTCCAGTGGTGTCAAAAAATGCAATTTC
40681784 AG
1 AG
40681786 AACCTTGTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (60 bp):
AGTTTCCAGTGGTGTCAAAAAATGCAATTAGTTTCCAGTGGTGTCAAAAAATGCAATTTC
Found at i:40685478 original size:17 final size:17
Alignment explanation
Indices: 40685456--40685502 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
40685446 CTAAATCAAA
40685456 TATAAATAAAATATAAG
1 TATAAATAAAATATAAG
*
40685473 TATAAAT--AATATAAT
1 TATAAATAAAATATAAG
40685488 TAATAAATATAAATA
1 T-ATAAATA-AAATA
40685503 ATGTAATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 8 0.32
16 6 0.24
17 7 0.28
19 4 0.16
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
TATAAATAAAATATAAG
Found at i:40685493 original size:22 final size:22
Alignment explanation
Indices: 40685468--40685510 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40685458 TAAATAAAAT
*
40685468 ATAAGTATAAATAATATAATTA
1 ATAAATATAAATAATATAATTA
*
40685490 ATAAATATAAATAATGTAATT
1 ATAAATATAAATAATATAATT
40685511 CAAAAAGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (22 bp):
ATAAATATAAATAATATAATTA
Found at i:40686613 original size:78 final size:81
Alignment explanation
Indices: 40686468--40686649 Score: 221
Period size: 78 Copynumber: 2.3 Consensus size: 81
40686458 TCGAATGATG
* * * *
40686468 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
*
40686533 GTGCGAGTTAATA-AA
66 GTGCGAGTCAATATAA
* **
40686548 TCCGGGCTAAG-CCCGAAGGCATTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATT
*
40686610 CGTGCGAGTCACTATAA
65 CGTGCGAGTCAATATAA
**
40686627 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
40686650 TGAGCGATCG
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
77 1 0.01
78 47 0.53
79 29 0.33
80 11 0.12
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
GTGCGAGTCAATATAA
Found at i:40686642 original size:40 final size:40
Alignment explanation
Indices: 40686521--40686649 Score: 158
Period size: 40 Copynumber: 3.3 Consensus size: 40
40686511 GGACTAGGAT
* * *
40686521 CCGAAGGCATTCGTGCGAGTTAATAAATCCGGGCTAAG-C
1 CCGAAGGCATTCGTGCGAGTTACTAAACCCGGGCTTAGTC
*
40686560 CCGAAGGCATT-GTGCAAGTTACTAAACCCGGG-TTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAACCCGGGCTT-AGTC
* *
40686599 CCGAAGGCATTCGTGCGAGTCACTATAA-CCGGGCTTCGTC
1 CCGAAGGCATTCGTGCGAGTTACTA-AACCCGGGCTTAGTC
40686639 CCGAAGGCATT
1 CCGAAGGCATT
40686650 TGAGCGATCG
Statistics
Matches: 78, Mismatches: 7, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
37 1 0.01
38 20 0.26
39 23 0.29
40 30 0.38
41 4 0.05
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.22
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAACCCGGGCTTAGTC
Found at i:40693779 original size:39 final size:40
Alignment explanation
Indices: 40693679--40693859 Score: 167
Period size: 39 Copynumber: 4.6 Consensus size: 40
40693669 TCGAATGATG
* * *
40693679 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAA
* * * *
40693719 TCCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAA
40693759 TCCGGGCTAAG-CCCGAAGGCATT-GTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
* * * **
40693797 CCCGGGTTAAGTCCCGAAGGCATTC-TGCGAGTCGCTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AA
**
40693837 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
40693860 TGAGCGAGTC
Statistics
Matches: 116, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
38 22 0.19
39 52 0.45
40 35 0.30
41 7 0.06
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
Found at i:40704186 original size:16 final size:16
Alignment explanation
Indices: 40704115--40704186 Score: 92
Period size: 16 Copynumber: 4.6 Consensus size: 16
40704105 ACAACTGAAT
* *
40704115 TATT-CATTAAAGGTC
1 TATTCCATTACAGCTC
*
40704130 TATTCTATTACAGCTC
1 TATTCCATTACAGCTC
40704146 TATTCCATTACAGCTC
1 TATTCCATTACAGCTC
* *
40704162 TATTACATTACAGATC
1 TATTCCATTACAGCTC
40704178 TATTCCATT
1 TATTCCATT
40704187 CCCCCCAACC
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 4 0.08
16 45 0.92
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (16 bp):
TATTCCATTACAGCTC
Found at i:40714329 original size:68 final size:64
Alignment explanation
Indices: 40714219--40714369 Score: 162
Period size: 68 Copynumber: 2.3 Consensus size: 64
40714209 ATACAGATGG
* * * *
40714219 TATGTAGCTAGGTCACATGTATGGTGCTGAGTGCACATCATGT-GTACAAAAGAGCTACGAGACA
1 TATGTAGCTAGGTCGCATGGATGATGCTGAGTGCACACCATGTAG-ACAAAAGAGCTACG-G-CA
40714283 TTA
63 -TA
* * * *
40714286 TGATGTAGCTAGGTCGCATGGGTGATGCT-ATGTGTACACCATGTAGACAAGAGAGCTACGGGAT
1 T-ATGTAGCTAGGTCGCATGGATGATGCTGA-GTGCACACCATGTAGACAAAAGAGCTACGGCAT
40714350 A
64 A
40714351 TATGTAGCTAGGTCGCATG
1 TATGTAGCTAGGTCGCATG
40714370 CGTGGTTCCA
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
64 18 0.25
65 3 0.04
66 1 0.01
67 3 0.04
68 47 0.64
69 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.26
Consensus pattern (64 bp):
TATGTAGCTAGGTCGCATGGATGATGCTGAGTGCACACCATGTAGACAAAAGAGCTACGGCATA
Found at i:40714368 original size:64 final size:66
Alignment explanation
Indices: 40714288--40714411 Score: 171
Period size: 67 Copynumber: 1.9 Consensus size: 66
40714278 AGACATTATG
* * * *
40714288 ATGTAGCTAGGTCGCATGGGTGATGCTA-TG-TGTACACCATGTAGACAAGAGAGCTACGGGATA
1 ATGTAGCTAGGTCGCATGCGTGATGCCAGTGAAGGACACCATGTAGACAAGAGAGCTACGGGATA
40714351 T
66 T
* *
40714352 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTAC
1 ATGTAGCTAGGTCGCATGCGTGATGCCA-GTGAAGGACACCATGTAGACAAGAGAGCTAC
40714412 TAGATAAACT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 24 0.47
66 2 0.04
67 25 0.49
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (66 bp):
ATGTAGCTAGGTCGCATGCGTGATGCCAGTGAAGGACACCATGTAGACAAGAGAGCTACGGGATA
T
Found at i:40715131 original size:23 final size:23
Alignment explanation
Indices: 40715105--40715150 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
40715095 AATTGGCTAG
40715105 ACCAAAAATTTTAAAAATTTTAT
1 ACCAAAAATTTTAAAAATTTTAT
40715128 ACCAAAAATTTTAAAAATTTTAT
1 ACCAAAAATTTTAAAAATTTTAT
40715151 GGTAAGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (23 bp):
ACCAAAAATTTTAAAAATTTTAT
Found at i:40720523 original size:21 final size:22
Alignment explanation
Indices: 40720498--40720539 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
40720488 GCACTTTTTA
40720498 AAAATTTA-AAAA-ATTATAAAC
1 AAAATTTATAAAACATT-TAAAC
40720519 AAAATTTATAAAACATTTAAA
1 AAAATTTATAAAACATTTAAA
40720540 ATTATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 8 0.42
23 3 0.16
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATTTATAAAACATTTAAAC
Found at i:40730284 original size:32 final size:32
Alignment explanation
Indices: 40730243--40730304 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
40730233 CATCTATTTT
40730243 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
40730275 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
40730305 ACCAAAAGCT
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:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:40732085 original size:5 final size:5
Alignment explanation
Indices: 40732075--40732103 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
40732065 GGGAGAGTTC
40732075 TTTCT TTTCT TTTCT TTTCT TTT-T TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
40732104 AAATGGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTCT
Found at i:40734148 original size:31 final size:29
Alignment explanation
Indices: 40734113--40734174 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
40734103 ATGATATTGA
40734113 CAATTTATGAAAATTAAATCAAAAAAAAATT
1 CAATTT-TGAAAATTAAA-CAAAAAAAAATT
* ** *
40734144 CAATTTTTAAAATTGTACAAATAAAAATT
1 CAATTTTGAAAATTAAACAAAAAAAAATT
40734173 CA
1 CA
40734175 TAACATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 13 0.48
30 8 0.30
31 6 0.22
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.32
Consensus pattern (29 bp):
CAATTTTGAAAATTAAACAAAAAAAAATT
Found at i:40738936 original size:15 final size:14
Alignment explanation
Indices: 40738920--40738970 Score: 52
Period size: 15 Copynumber: 3.7 Consensus size: 14
40738910 TTTTTTTATA
40738920 AAATAATTATATTT
1 AAATAATTATATTT
**
40738934 -AA-AATTATATAA
1 AAATAATTATATTT
*
40738946 AAATAATTTCTATTT
1 AAATAA-TTATATTT
40738961 AAATAATTAT
1 AAATAATTAT
40738971 TAGTTAAGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
12 8 0.29
13 4 0.14
14 5 0.18
15 11 0.39
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATAATTATATTT
Found at i:40739059 original size:12 final size:12
Alignment explanation
Indices: 40739042--40739071 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
40739032 AAAACATAAT
40739042 TTGAAATATTTA
1 TTGAAATATTTA
40739054 TTGAAATATTTA
1 TTGAAATATTTA
40739066 TTGAAA
1 TTGAAA
40739072 GAAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (12 bp):
TTGAAATATTTA
Found at i:40739230 original size:20 final size:19
Alignment explanation
Indices: 40739205--40739248 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
40739195 TGGAGAATGA
40739205 TTTCTGAAAAATGATTTACT
1 TTTCTG-AAAATGATTTACT
*
40739225 TTTCTGGAAATGATTTACT
1 TTTCTGAAAATGATTTACT
40739244 TTTCT
1 TTTCT
40739249 AGTGTTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.50
Consensus pattern (19 bp):
TTTCTGAAAATGATTTACT
Found at i:40740415 original size:24 final size:24
Alignment explanation
Indices: 40740385--40740435 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
40740375 AATATTGTGA
*
40740385 TTTAACTCTTAATTTTTATAAAAT
1 TTTAACTCTTAATATTTATAAAAT
40740409 TTTAACTCTTAATATTTATAAAAT
1 TTTAACTCTTAATATTTATAAAAT
40740433 TTT
1 TTT
40740436 CTTTCCCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTAACTCTTAATATTTATAAAAT
Found at i:40744272 original size:14 final size:14
Alignment explanation
Indices: 40744253--40744279 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40744243 AAAAAAGCCT
40744253 GAAAAGCTTTTACG
1 GAAAAGCTTTTACG
40744267 GAAAAGCTTTTAC
1 GAAAAGCTTTTAC
40744280 AGGTTACCAG
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:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (14 bp):
GAAAAGCTTTTACG
Found at i:40745275 original size:16 final size:15
Alignment explanation
Indices: 40745249--40745283 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
40745239 TGATGTGAAT
40745249 AATATAAAATATTAA
1 AATATAAAATATTAA
*
40745264 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
40745280 AATA
1 AATA
40745284 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:40745454 original size:20 final size:20
Alignment explanation
Indices: 40745397--40745506 Score: 60
Period size: 22 Copynumber: 5.0 Consensus size: 20
40745387 AATACTACAT
40745397 AAATATGTACAT-ATATAAA
1 AAATATGTACATAATATAAA
** *
40745416 AAATAAATACGTGATAATATTAA
1 AAATATGTAC---ATAATATAAA
40745439 AAATATGTACATAATATAGTGTAAA
1 AAATATGTACAT-A-ATA---TAAA
**
40745464 AAATACATACATAATATAATTA
1 AAATATGTACATAATATAA--A
* *
40745486 AAATATATACATAAGATAAA
1 AAATATGTACATAATATAAA
40745506 A
1 A
40745507 TGTAAATATA
Statistics
Matches: 70, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
19 8 0.11
20 7 0.10
21 1 0.01
22 23 0.33
23 17 0.24
24 1 0.01
25 13 0.19
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.30
Consensus pattern (20 bp):
AAATATGTACATAATATAAA
Found at i:40745495 original size:22 final size:23
Alignment explanation
Indices: 40745434--40745504 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 23
40745424 ACGTGATAAT
*
40745434 ATTAAAAATATGTACATAATATA
1 ATTAAAAATATATACATAATATA
* *
40745457 GTGTAAAAAATACATACATAATATA
1 AT-T-AAAAATATATACATAATATA
*
40745482 ATT-AAAATATATACATAAGATA
1 ATTAAAAATATATACATAATATA
40745504 A
1 A
40745505 AATGTAAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 18 0.45
23 1 0.03
24 2 0.05
25 19 0.47
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (23 bp):
ATTAAAAATATATACATAATATA
Found at i:40745556 original size:25 final size:25
Alignment explanation
Indices: 40745520--40745637 Score: 95
Period size: 25 Copynumber: 4.9 Consensus size: 25
40745510 AAATATATAT
*
40745520 ATATATAAATAATATAGTATTAAAG
1 ATATATACATAATATAGTATTAAAG
* *
40745545 ATATATACATAAAATAGTA-TAATAT
1 ATATATACATAATATAGTATTAA-AG
* * *
40745570 ATATATACGTAATATAGAATT-TAG
1 ATATATACATAATATAGTATTAAAG
* *
40745594 A-ATATACCTAATATA-T-TAAAAG
1 ATATATACATAATATAGTATTAAAG
* *
40745616 A-ATATATATAATATAATATTAA
1 ATATATACATAATATAGTATTAA
40745638 GAAATAATAA
Statistics
Matches: 73, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
21 1 0.01
22 15 0.21
23 14 0.19
24 8 0.11
25 34 0.47
26 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.36
Consensus pattern (25 bp):
ATATATACATAATATAGTATTAAAG
Found at i:40746206 original size:30 final size:30
Alignment explanation
Indices: 40746172--40746302 Score: 226
Period size: 30 Copynumber: 4.4 Consensus size: 30
40746162 AATAGAGCAA
* *
40746172 GTGTGGCTAGTGGATTTGGTGGTGGAGAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
*
40746202 GTGTGGCTAATGGAGTTGGTGGTGGAAAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
*
40746232 GAGTGGCTAGTGGAGTTGGTGGTGGAAAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
40746262 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
40746292 GTGTGGCTAGT
1 GTGTGGCTAGT
40746303 TGAGAAAAGT
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 95 1.00
ACGTcount: A:0.20, C:0.04, G:0.49, T:0.27
Consensus pattern (30 bp):
GTGTGGCTAGTGGAGTTGGTGGTGGAAAAG
Found at i:40747069 original size:14 final size:14
Alignment explanation
Indices: 40747050--40747112 Score: 74
Period size: 14 Copynumber: 4.5 Consensus size: 14
40747040 GAGTTGATTT
* *
40747050 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
40747064 TTGAAAAAACAGAAA
1 TTG-AAAAACAGAAA
*
40747079 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
*
40747093 TT-AAAAACAGAAT
1 TTGAAAAACAGAAA
40747106 TTGAAAA
1 TTGAAAA
40747113 GACCTCATTG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.26
14 19 0.45
15 12 0.29
ACGTcount: A:0.62, C:0.05, G:0.13, T:0.21
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:40747085 original size:13 final size:13
Alignment explanation
Indices: 40747069--40747112 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
40747059 ATAAATTGAA
40747069 AAAACAGAAATTG
1 AAAACAGAAATTG
*
40747082 AAAAGCAGAAATTA
1 AAAA-CAGAAATTG
*
40747096 AAAACAGAATTTG
1 AAAACAGAAATTG
40747109 AAAA
1 AAAA
40747113 GACCTCATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.64, C:0.07, G:0.14, T:0.16
Consensus pattern (13 bp):
AAAACAGAAATTG
Found at i:40747288 original size:77 final size:75
Alignment explanation
Indices: 40747135--40747415 Score: 413
Period size: 77 Copynumber: 3.7 Consensus size: 75
40747125 TGGCCCGAGA
* * **
40747135 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGCAGAAATTGAAAA-CGCCTCAGCGT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATAG-CTCAGCAC
* **
40747199 GTGACCCGAGG
65 GTGAGCAAAGG
*
40747210 CTCAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAAAGCAGAAATTGAAAATAGCTCAGCA
1 CTCAACTCACCTCTCGCAATATGAGTTGA-T-TTTTGAAAAACAGAAATTGAAAATAGCTCAGCA
40747275 CGTGAGCAAAGG
64 CGTGAGCAAAGG
*
40747287 CTCAACTCACCTCTCACAATATGAGTTGATTCTTTTGAAAAACAGAAATTGAAAATAGCTCAGCA
1 CTCAACTCACCTCTCGCAATATGAGTTGA-T-TTTTGAAAAACAGAAATTGAAAATAGCTCAGCA
40747352 CGTGAGCAAAGG
64 CGTGAGCAAAGG
*
40747364 CTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-AAAA
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAA
40747416 GGCTCAACTC
Statistics
Matches: 193, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
74 4 0.02
75 47 0.24
76 2 0.01
77 139 0.72
78 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (75 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATAGCTCAGCACG
TGAGCAAAGG
Found at i:40747441 original size:54 final size:54
Alignment explanation
Indices: 40747359--40747470 Score: 179
Period size: 54 Copynumber: 2.1 Consensus size: 54
40747349 GCACGTGAGC
* *
40747359 AAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTA
1 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTA
* **
40747413 AAAGGCTCAACTCACCTCTCTCAATATGAGTTGATTTTTGAAAAGTAAAAATTA
1 AAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTA
40747467 AAAG
1 AAAG
40747471 CAGAGTTTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.29
Consensus pattern (54 bp):
AAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTA
Found at i:40747589 original size:16 final size:17
Alignment explanation
Indices: 40747556--40747590 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40747546 TGATATTTTG
*
40747556 AAAAGCAGAAATTGGAA
1 AAAAACAGAAATTGGAA
40747573 AAAAACAGAAATT-GAA
1 AAAAACAGAAATTGGAA
40747589 AA
1 AA
40747591 TACCTCAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.66, C:0.06, G:0.17, T:0.11
Consensus pattern (17 bp):
AAAAACAGAAATTGGAA
Found at i:40747715 original size:89 final size:91
Alignment explanation
Indices: 40747484--40747742 Score: 295
Period size: 89 Copynumber: 2.9 Consensus size: 91
40747474 AGTTTGAAAG
* * * * *
40747484 ACAGAATTTGAAAATACCTCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCAATATAAGTT-G
1 ACAGAAATTGAAAATACCTCAGC--GTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGG
40747548 ATATTTTGAAAAGCAGAAATTGGAAAAAA
64 ATATTTTGAAAAGCAGAAATT-GAAAAAA
* *
40747577 ACAGAAATTGAAAATACCTCAGCATGTCC-TGAGGCTCAATTCACCTCTCGCAATATGAGTTGGT
1 ACAGAAATTGAAAATACCTCAGCGTG-CCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGG-
* * *
40747641 TTTTTTTG-AAA-CATAAATT-AAAAAA
64 ATATTTTGAAAAGCAGAAATTGAAAAAA
*
40747666 AC-GAAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACTTCTCGCAATATGAGTT-G-
1 ACAG-AAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGGA
40747728 -A-TTTGAAAAGCAGAA
65 TATTTTGAAAAGCAGAA
40747743 TTTGTAAGGC
Statistics
Matches: 144, Mismatches: 15, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
84 4 0.03
85 3 0.02
86 4 0.03
88 4 0.03
89 59 0.41
91 38 0.26
92 5 0.03
93 27 0.19
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (91 bp):
ACAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGGAT
ATTTTGAAAAGCAGAAATTGAAAAAA
Found at i:40747870 original size:14 final size:14
Alignment explanation
Indices: 40747834--40747878 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
40747824 TTGATTTTTG
40747834 AAAAACAGAAATT-
1 AAAAACAGAAATTA
*
40747847 AAAAGCAGAAATTA
1 AAAAACAGAAATTA
*
40747861 AAAAATAGAAATTA
1 AAAAACAGAAATTA
40747875 AAAA
1 AAAA
40747879 TACCTCGGCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 12 0.43
14 16 0.57
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16
Consensus pattern (14 bp):
AAAAACAGAAATTA
Found at i:40747880 original size:13 final size:13
Alignment explanation
Indices: 40747834--40747878 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
40747824 TTGATTTTTG
40747834 AAAAACAGAAATT
1 AAAAACAGAAATT
*
40747847 AAAAGCAGAAATT
1 AAAAACAGAAATT
*
40747860 AAAAAATAGAAATT
1 -AAAAACAGAAATT
40747874 AAAAA
1 AAAAA
40747879 TACCTCGGCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16
Consensus pattern (13 bp):
AAAAACAGAAATT
Found at i:40747928 original size:100 final size:99
Alignment explanation
Indices: 40747655--40747950 Score: 407
Period size: 100 Copynumber: 3.0 Consensus size: 99
40747645 TTTGAAACAT
40747655 AAATTAAAAAAACGAAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACTTCTCGCAAT
1 AAATTAAAAAAA-G-AAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACTTCTCGCAAT
* * *
40747720 ATGAGTTGA--TTTGAAAAGCAGAATTTGTAAGGCAA
64 ATGAGTTGATTTTTGAAAAGCAGAAATT-AAAAGCAA
*
40747755 AAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACTTCTCGCAATA
1 AAATT-AAAAAAAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACTTCTCGCAATA
* *
40747820 TGAGTTGATTTTTGAAAAACAGAAATTAAAAGCAG
65 TGAGTTGATTTTTGAAAAGCAGAAATTAAAAGCAA
* * *** * *
40747855 AAATTAAAAAATAGAAATTAAAAATACCTCGGCGTGCCCCAAGGCTCAGCTCACCTCTCGCAATA
1 AAATTAAAAAA-AGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACTTCTCGCAATA
*
40747920 TGAGTTGATTTTTGAAAAGCATAAATTAAAA
65 TGAGTTGATTTTTGAAAAGCAGAAATTAAAA
40747951 TTACCTCAGC
Statistics
Matches: 176, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
99 64 0.36
100 91 0.52
101 21 0.12
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.25
Consensus pattern (99 bp):
AAATTAAAAAAAGAAATTGAAAATACCTCAGCGTGCCTTGAGGCTCAACTCACTTCTCGCAATAT
GAGTTGATTTTTGAAAAGCAGAAATTAAAAGCAA
Found at i:40747988 original size:73 final size:74
Alignment explanation
Indices: 40747869--40748026 Score: 246
Period size: 73 Copynumber: 2.1 Consensus size: 74
40747859 TAAAAAATAG
* *
40747869 AAATTAAAAATACCTCGGCGTGCCCCAAGGCTCAGCTCACCTCTCGCAATATGAGTTGA-TTTTT
1 AAATTAAAAATACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
40747933 GAAAAGCAT
66 GAAAAGCAT
* * **
40747942 AAATTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTAAAAATACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
40748007 GAAAAGCAT
66 GAAAAGCAT
40748016 AAATTGAAAAA
1 AAATT-AAAAA
40748027 ACGAAAATTG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
73 53 0.70
74 19 0.25
75 4 0.05
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (74 bp):
AAATTAAAAATACCTCAGCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
GAAAAGCAT
Found at i:40748125 original size:91 final size:89
Alignment explanation
Indices: 40747942--40748111 Score: 263
Period size: 91 Copynumber: 1.9 Consensus size: 89
40747932 TGAAAAGCAT
*
40747942 AAATTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTAAAATTACCTCAGCGTGTCCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTTTT
*
40748007 GAAAAGCATAAATTGAAAAAACGA
66 GAAAAGCAGAAATTGAAAAAACGA
40748031 AAATTGAAAA-TACCTCAGCGTGTGACCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTT
1 AAATT-AAAATTACCTCAGCGTGT--CCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGA-TT
40748095 TTTTG-AAAGACAGAAAT
62 TTTTGAAAAG-CAGAAAT
40748112 AAAAACATCA
Statistics
Matches: 74, Mismatches: 2, Indels: 7
0.89 0.02 0.08
Matches are distributed among these distances:
89 18 0.24
90 4 0.05
91 39 0.53
92 13 0.18
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (89 bp):
AAATTAAAATTACCTCAGCGTGTCCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTTTT
GAAAAGCAGAAATTGAAAAAACGA
Found at i:40755104 original size:16 final size:15
Alignment explanation
Indices: 40755079--40755112 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
40755069 GAAGTGAATC
40755079 ATATAAAATATTAAA
1 ATATAAAATATTAAA
*
40755094 ATATCAAAATATTAGA
1 ATAT-AAAATATTAAA
40755110 ATA
1 ATA
40755113 ATAATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (15 bp):
ATATAAAATATTAAA
Found at i:40755284 original size:20 final size:20
Alignment explanation
Indices: 40755227--40755286 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
40755217 AATACTACAT
40755227 AAATATGTACAT-ATATAAA
1 AAATATGTACATAATATAAA
** *
40755246 AAATAAATACGTGATAATATTAA
1 AAATATGTAC---ATAATATAAA
40755269 AAATATGTACATAATATA
1 AAATATGTACATAATATA
40755287 GTGTAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 2 0.06
23 14 0.45
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AAATATGTACATAATATAAA
Found at i:40755325 original size:22 final size:22
Alignment explanation
Indices: 40755227--40755360 Score: 71
Period size: 25 Copynumber: 5.9 Consensus size: 22
40755217 AATACTACAT
*
40755227 AAATATGTACAT-ATATAA--A
1 AAATATATACATAATATAATTA
* * *
40755246 AAATAAATACGTGATA-ATATTAA
1 AAATATATACATAATATA-ATT-A
* *
40755269 AAATATGTACATAATATAGTGTAAA
1 AAATATATACATAATATAAT-T--A
*
40755294 AAATACATACATAATATAATTA
1 AAATATATACATAATATAATTA
*
40755316 AAATATATACATAAGATAACATGTA
1 AAATATATACATAATAT-A-AT-TA
*
40755341 AATATATATATATAA-ATAAT
1 AA-ATATATACATAATATAAT
40755361 ATAGTATTAA
Statistics
Matches: 89, Mismatches: 14, Indels: 20
0.72 0.11 0.16
Matches are distributed among these distances:
19 10 0.11
20 4 0.04
22 16 0.18
23 17 0.19
24 6 0.07
25 25 0.28
26 11 0.12
ACGTcount: A:0.57, C:0.05, G:0.06, T:0.32
Consensus pattern (22 bp):
AAATATATACATAATATAATTA
Found at i:40755371 original size:15 final size:14
Alignment explanation
Indices: 40755339--40755404 Score: 57
Period size: 14 Copynumber: 4.7 Consensus size: 14
40755329 AGATAACATG
40755339 TAAATATATATATA
1 TAAATATATATATA
40755353 TAAATA-ATATAGTA
1 TAAATATATATA-TA
* *
40755367 TTAAAGATATATACA
1 -TAAATATATATATA
40755382 TAAA-ATAGTATA-A
1 TAAATATA-TATATA
*
40755395 TATATATATA
1 TAAATATATA
40755405 CGTAATATAG
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
13 14 0.32
14 19 0.43
15 6 0.14
16 5 0.11
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (14 bp):
TAAATATATATATA
Found at i:40755405 original size:25 final size:26
Alignment explanation
Indices: 40755263--40755414 Score: 95
Period size: 25 Copynumber: 6.0 Consensus size: 26
40755253 TACGTGATAA
* *
40755263 TATTAA-AAATATGTACATAATATAG
1 TATTAATATATATATACATAATATAG
* * * *
40755288 T-GTAAAAAATACATACATAATATA-
1 TATTAATATATATATACATAATATAG
* *
40755312 -ATTAA-A-ATATATACATAAGATAA
1 TATTAATATATATATACATAATATAG
* *
40755335 CATGTAAATATATATATATAAATAATATAG
1 TAT-T--A-ATATATATATACATAATATAG
* *
40755365 TATTAA-AGATATATACATAAAATAG
1 TATTAATATATATATACATAATATAG
*
40755390 TA-TAATATATATATACGTAATATAG
1 TATTAATATATATATACATAATATAG
40755415 AATTTAGAAT
Statistics
Matches: 100, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
22 14 0.14
23 1 0.01
24 11 0.11
25 52 0.52
26 1 0.01
27 2 0.02
28 1 0.01
29 2 0.02
30 16 0.16
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.34
Consensus pattern (26 bp):
TATTAATATATATATACATAATATAG
Found at i:40755477 original size:23 final size:25
Alignment explanation
Indices: 40755434--40755479 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40755424 TATACCTAAT
40755434 ATATTAAAAGAATATATATAATATA
1 ATATTAAAAGAATATATATAATATA
*
40755459 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
40755480 ACAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATATA
Found at i:40756026 original size:30 final size:30
Alignment explanation
Indices: 40755956--40756100 Score: 168
Period size: 30 Copynumber: 4.8 Consensus size: 30
40755946 TAGGTACAAG
* *
40755956 TGGTGGTGGAGCAAGTGTGGTTAGTGGAGT
1 TGGTGGTGGAGAAAGTGTGGCTAGTGGAGT
* * ** *
40755986 AGATAATGGAGAAAGTGTGGCTAGTGGATT
1 TGGTGGTGGAGAAAGTGTGGCTAGTGGAGT
* *
40756016 TGGTGGTGGAGAAGGTGTGGCTAATGGAGT
1 TGGTGGTGGAGAAAGTGTGGCTAGTGGAGT
*
40756046 TGGTGGTGGA-AAAGGAGTGGCTAGTGGAGT
1 TGGTGGTGGAGAAA-GTGTGGCTAGTGGAGT
40756076 TGGTGGTGGA-AAAGGTGTGGCTAGT
1 TGGTGGTGGAGAAA-GTGTGGCTAGT
40756101 TGAGAAAAGT
Statistics
Matches: 96, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
29 2 0.02
30 94 0.98
ACGTcount: A:0.23, C:0.03, G:0.47, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAGAAAGTGTGGCTAGTGGAGT
Found at i:40757644 original size:28 final size:27
Alignment explanation
Indices: 40757581--40757650 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
40757571 ATAGTGAGTC
40757581 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
40757608 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
40757636 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40757651 GTACAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:40764848 original size:28 final size:27
Alignment explanation
Indices: 40764785--40764854 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
40764775 ATAGTGAGTC
*
40764785 CGCACACTTAGTGCTATATAATTAACT
1 CGCACACTTAGTGCTATATAATAAACT
*
40764812 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAAT-AAACT
40764840 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40764855 GTACAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATAAACT
Found at i:40767767 original size:20 final size:19
Alignment explanation
Indices: 40767726--40767768 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
40767716 TAAAAAATAA
** *
40767726 TTAAAAATCATAAATTTTT
1 TTAAAAATCATAAAAATCT
40767745 TTAAAAATTCATAAAAATCT
1 TTAAAAA-TCATAAAAATCT
40767765 TTAA
1 TTAA
40767769 GGGTAAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAAAATCATAAAAATCT
Found at i:40771267 original size:22 final size:23
Alignment explanation
Indices: 40771242--40771284 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
40771232 GGTCGATGAG
40771242 AAAAAATAAATAT-AAATTATAA
1 AAAAAATAAATATAAAATTATAA
*
40771264 AAAAAGTAAATATAAAATTAT
1 AAAAAATAAATATAAAATTAT
40771285 TTTAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAAAATAAATATAAAATTATAA
Found at i:40771315 original size:20 final size:20
Alignment explanation
Indices: 40771278--40771325 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
40771268 AGTAAATATA
40771278 AAATTATTTTAAATATTTTT
1 AAATTATTTTAAATATTTTT
*
40771298 AAATATATTTTATA-ATTTTT
1 AAAT-TATTTTAAATATTTTT
40771318 AGAATTAT
1 A-AATTAT
40771326 AATTAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
AAATTATTTTAAATATTTTT
Found at i:40773275 original size:14 final size:14
Alignment explanation
Indices: 40773256--40773284 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40773246 ACGGGGCTAC
40773256 ACCAATAGTGGTGG
1 ACCAATAGTGGTGG
40773270 ACCAATAGTGGTGG
1 ACCAATAGTGGTGG
40773284 A
1 A
40773285 TCGCAGCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.21
Consensus pattern (14 bp):
ACCAATAGTGGTGG
Found at i:40774872 original size:56 final size:56
Alignment explanation
Indices: 40774811--40774921 Score: 143
Period size: 56 Copynumber: 2.0 Consensus size: 56
40774801 TTTTAAAATT
* * * *
40774811 TTATAACTTTTATTACTCAG-GGTTTGTTTAGGGTTACACACAAAATTAATGAAAAA
1 TTATAACCTCTATTACT-AGCGGTTTGCTTAAGGTTACACACAAAATTAATGAAAAA
* * *
40774867 TTATAACCTCTGTTGCTTGCGGTTTGCTTAAGGTTACACACAAAATTAATGAAAA
1 TTATAACCTCTATTACTAGCGGTTTGCTTAAGGTTACACACAAAATTAATGAAAA
40774922 TAATTATAGC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
55 1 0.02
56 46 0.98
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (56 bp):
TTATAACCTCTATTACTAGCGGTTTGCTTAAGGTTACACACAAAATTAATGAAAAA
Found at i:40777634 original size:49 final size:50
Alignment explanation
Indices: 40777576--40777721 Score: 204
Period size: 51 Copynumber: 2.9 Consensus size: 50
40777566 GTAGCCAAAA
* *
40777576 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA-T
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAAGT
* * * *
40777625 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGA-CCAAGT
* *
40777676 TATCGGGTACGCATAGTAGCCTACACTTAGTACTACACATGTGACC
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACC
40777722 TAGCTACATA
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
49 39 0.47
50 4 0.05
51 40 0.48
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (50 bp):
TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAAGT
Found at i:40777854 original size:68 final size:64
Alignment explanation
Indices: 40777710--40777868 Score: 158
Period size: 68 Copynumber: 2.4 Consensus size: 64
40777700 ACTTAGTACT
* * *
40777710 ACACATGTGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGGTGTACACATAGTATC
1 ACACATGTGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGATGTACACATAGCACC
* * ** * *
40777774 ACCCATGCGACCTAGCTACATCATAATGTCTTGTAGCTCTCTTGTAC-ACATGATGTGCACTTAG
1 ACACATGTGACCTAGCTACAT-AT-A--TCCCGTAGCTCTCTTGT-CTACATGATGTACACATAG
40777838 CACC
61 CACC
* *
40777842 ATACATGTGACCTAGCTAAATACTATC
1 ACACATGTGACCTAGCTACATA-TATC
40777869 TGTATCATCC
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
64 19 0.25
65 4 0.05
66 1 0.01
67 2 0.03
68 49 0.64
69 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (64 bp):
ACACATGTGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGATGTACACATAGCACC
Found at i:40778563 original size:30 final size:30
Alignment explanation
Indices: 40778529--40778588 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
40778519 CCTTAACTCG
40778529 AACTTTGGCAAATTTACAATTTTGCCCCTA
1 AACTTTGGCAAATTTACAATTTTGCCCCTA
* * *
40778559 AACTTTTGCATATTTACACTTTTGCCCCTA
1 AACTTTGGCAAATTTACAATTTTGCCCCTA
40778589 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (30 bp):
AACTTTGGCAAATTTACAATTTTGCCCCTA
Found at i:40778936 original size:52 final size:51
Alignment explanation
Indices: 40778854--40778957 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 51
40778844 ACCCTAGCTT
*
40778854 AAATTATTGTTAGAATAAGCTTAATCAAATTACCGAGATTCCAAAAACGTAA
1 AAATTATTGCTAGAATAAGCTTAATCAAATTACCGAGATTCC-AAAACGTAA
* *
40778906 AAATTATTGCTAGAATAAGCTTAATTAAATTACCGGGATTCCAAAACGTAA
1 AAATTATTGCTAGAATAAGCTTAATCAAATTACCGAGATTCCAAAACGTAA
40778957 A
1 A
40778958 GAACTTGAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 10 0.20
52 39 0.80
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.29
Consensus pattern (51 bp):
AAATTATTGCTAGAATAAGCTTAATCAAATTACCGAGATTCCAAAACGTAA
Found at i:40781347 original size:13 final size:13
Alignment explanation
Indices: 40781315--40781352 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
40781305 CAGTTAATTA
40781315 AATTAT-TTAATTT
1 AATTATATT-ATTT
40781328 AATTTATATTATTT
1 AA-TTATATTATTT
40781342 AATTATATTAT
1 AATTATATTAT
40781353 ACATTTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 11 0.48
14 10 0.43
15 2 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
AATTATATTATTT
Found at i:40784869 original size:14 final size:14
Alignment explanation
Indices: 40784831--40784873 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
40784821 CAAAATCTAC
40784831 AATATAATTAAA-T
1 AATATAATTAAATT
40784844 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
40784859 AA-ATAATTTAATT
1 AATATAATTAAATT
40784872 AA
1 AA
40784874 CTGTTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:40795651 original size:21 final size:21
Alignment explanation
Indices: 40795627--40795669 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40795617 CTCCTCTTTT
40795627 TGTCTATTTTCTTTGTGTTGC
1 TGTCTATTTTCTTTGTGTTGC
40795648 TGTCTATTTTCTTTGTGTTGC
1 TGTCTATTTTCTTTGTGTTGC
40795669 T
1 T
40795670 TTCTTTCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.05, C:0.14, G:0.19, T:0.63
Consensus pattern (21 bp):
TGTCTATTTTCTTTGTGTTGC
Found at i:40799150 original size:11 final size:11
Alignment explanation
Indices: 40799134--40799158 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40799124 TGGTTTTATT
40799134 TTTTTATTTTA
1 TTTTTATTTTA
40799145 TTTTTATTTTA
1 TTTTTATTTTA
40799156 TTT
1 TTT
40799159 GGTTAAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:40810314 original size:27 final size:27
Alignment explanation
Indices: 40810284--40810455 Score: 220
Period size: 27 Copynumber: 6.4 Consensus size: 27
40810274 ATACTAGACC
* *
40810284 CCCTTATGTGATAAAATAACTATTTTG
1 CCCTTATGTGGTAAAATGACTATTTTG
* * *
40810311 CCCTTATATAGTAAAATGACTGTTTTG
1 CCCTTATGTGGTAAAATGACTATTTTG
* *
40810338 -CCTTCATGTGGTAAAATGACTGTTTTA
1 CCCTT-ATGTGGTAAAATGACTATTTTG
* *
40810365 CCCTTATATGGTAAAATGACTGTTTTG
1 CCCTTATGTGGTAAAATGACTATTTTG
*
40810392 CCCTCATGTGGTAAAATGACTATTTTG
1 CCCTTATGTGGTAAAATGACTATTTTG
*
40810419 CCCTTATATGGTAAAATGACTATTTTG
1 CCCTTATGTGGTAAAATGACTATTTTG
*
40810446 CCCCTATGTG
1 CCCTTATGTG
40810456 ATATATGTTT
Statistics
Matches: 126, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
26 4 0.03
27 118 0.94
28 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (27 bp):
CCCTTATGTGGTAAAATGACTATTTTG
Found at i:40810455 original size:54 final size:54
Alignment explanation
Indices: 40810284--40810448 Score: 258
Period size: 54 Copynumber: 3.1 Consensus size: 54
40810274 ATACTAGACC
* * * *
40810284 CCCTTATGTGATAAAATAACTATTTTGCCCTTATATAGTAAAATGACTGTTTTG
1 CCCTCATGTGGTAAAATGACTATTTTGCCCTTATATGGTAAAATGACTGTTTTG
* * *
40810338 CCTTCATGTGGTAAAATGACTGTTTTACCCTTATATGGTAAAATGACTGTTTTG
1 CCCTCATGTGGTAAAATGACTATTTTGCCCTTATATGGTAAAATGACTGTTTTG
*
40810392 CCCTCATGTGGTAAAATGACTATTTTGCCCTTATATGGTAAAATGACTATTTTG
1 CCCTCATGTGGTAAAATGACTATTTTGCCCTTATATGGTAAAATGACTGTTTTG
40810446 CCC
1 CCC
40810449 CTATGTGATA
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 100 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (54 bp):
CCCTCATGTGGTAAAATGACTATTTTGCCCTTATATGGTAAAATGACTGTTTTG
Found at i:40813280 original size:22 final size:22
Alignment explanation
Indices: 40813255--40813298 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40813245 TAGTCATATA
40813255 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
40813277 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
40813299 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Done.