Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 141 of 189
Found at i:42877239 original size:15 final size:16
Alignment explanation
Indices: 42877184--42877244 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
42877174 CTATAGTCTC
*
42877184 CTATAGTGTCACAA-T
1 CTATAGTTTCACAAGT
* *
42877199 TTATAGTTTTCACAATT
1 CTATAG-TTTCACAAGT
*
42877216 CTATTGTTTCA-AAGT
1 CTATAGTTTCACAAGT
42877231 CTATAGTTTTCACA
1 CTATAG-TTTCACA
42877245 TTTAAACAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
15 13 0.36
16 17 0.47
17 6 0.17
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (16 bp):
CTATAGTTTCACAAGT
Found at i:42878710 original size:20 final size:20
Alignment explanation
Indices: 42878687--42878728 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
42878677 CATAAATTAA
* *
42878687 TTAATTAAATAAAATTTTAT
1 TTAAGTAAATAAAATTATAT
42878707 TTAAGTAAATAAAATTATAT
1 TTAAGTAAATAAAATTATAT
42878727 TT
1 TT
42878729 CACTTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAAGTAAATAAAATTATAT
Found at i:42886940 original size:17 final size:16
Alignment explanation
Indices: 42886914--42886945 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
42886904 TGATAGATCT
42886914 CCGACGAGCTTCCAAA
1 CCGACGAGCTTCCAAA
42886930 CCGATCGAGCTTCCAA
1 CCGA-CGAGCTTCCAA
42886946 TAATCTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.38, G:0.19, T:0.16
Consensus pattern (16 bp):
CCGACGAGCTTCCAAA
Found at i:42894887 original size:43 final size:43
Alignment explanation
Indices: 42894837--42894923 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
42894827 CCATAAGTTA
*
42894837 ACCTATACATGTCATTATAACCTTGATTACGACATCAAAATCT
1 ACCTATACATGTCATTATAACCTTGATCACGACATCAAAATCT
42894880 ACCTATACATGTCATTATAACCTTGATCACGACATCAAAATCT
1 ACCTATACATGTCATTATAACCTTGATCACGACATCAAAATCT
42894923 A
1 A
42894924 AAAATATAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (43 bp):
ACCTATACATGTCATTATAACCTTGATCACGACATCAAAATCT
Found at i:42896271 original size:138 final size:138
Alignment explanation
Indices: 42896020--42896278 Score: 308
Period size: 138 Copynumber: 1.9 Consensus size: 138
42896010 AGGCCTACTC
* * * *
42896020 ACACAAGCTGACGGTCAAAATGTAAGCTACATGATGCTACTCACACAAGTTGATAAATATCTGTG
1 ACACAAGCTGACGGTCAAAATGAAAGCTACATGATGCTACTCACACAAGCTGATAAATATCTATA
** * * **
42896085 ACTAAAGCCGAACCTCAACCATCGGTAGGACATTCAGGACCAGCACCCGAAACATGGTAACCTGG
66 ACTAAAGAAGAACCTCAACCATCAGTAGAACATTCAGGACCAAAACCCGAAACATGGTAACCTGG
42896150 GTCTGCTT
131 GTCTGCTT
* * * * *
42896158 ACACAAGCTGACGGTCAGAATGAAAGTTACATGATGCTGCTCACACAAGCTGATGAGTAT-TCAT
1 ACACAAGCTGACGGTCAAAATGAAAGCTACATGATGCTACTCACACAAGCTGATAAATATCT-AT
* * *
42896222 AAC-AAATGTAAG-ACCTTAGCCATCAGTAGAACATTCAGGACCAAAACCCGCAACATG
65 AACTAAA-G-AAGAACCTCAACCATCAGTAGAACATTCAGGACCAAAACCCGAAACATG
42896279 AAAGCCTTAA
Statistics
Matches: 100, Mismatches: 18, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
137 4 0.04
138 95 0.95
139 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (138 bp):
ACACAAGCTGACGGTCAAAATGAAAGCTACATGATGCTACTCACACAAGCTGATAAATATCTATA
ACTAAAGAAGAACCTCAACCATCAGTAGAACATTCAGGACCAAAACCCGAAACATGGTAACCTGG
GTCTGCTT
Found at i:42897507 original size:20 final size:19
Alignment explanation
Indices: 42897483--42897527 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
42897473 TAATTAAAAC
42897483 TAGACACAATTAATTAAGT
1 TAGACACAATTAATTAAGT
* *
42897502 TAAGACGCAATTAATTCAGT
1 T-AGACACAATTAATTAAGT
42897522 TAGACA
1 TAGACA
42897528 AGACATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (19 bp):
TAGACACAATTAATTAAGT
Found at i:42902182 original size:17 final size:17
Alignment explanation
Indices: 42902160--42902193 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
42902150 ACACGAGCGT
42902160 GTCTCTTGGCCATGTGA
1 GTCTCTTGGCCATGTGA
42902177 GTCTCTTGGCCATGTGA
1 GTCTCTTGGCCATGTGA
42902194 CCCCTGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.29, T:0.35
Consensus pattern (17 bp):
GTCTCTTGGCCATGTGA
Found at i:42904886 original size:20 final size:22
Alignment explanation
Indices: 42904833--42904888 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
42904823 GTAACAAAAT
* * *
42904833 CATACCAAGGGCATCATAGATG
1 CATAACAAGGGCACCAAAGATG
*
42904855 CATAACAGGGGCACCAAAG-TG
1 CATAACAAGGGCACCAAAGATG
42904876 CA-AACAAGGGCAC
1 CATAACAAGGGCAC
42904889 TGAAGTTCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 10 0.34
21 4 0.14
22 15 0.52
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (22 bp):
CATAACAAGGGCACCAAAGATG
Found at i:42912557 original size:14 final size:14
Alignment explanation
Indices: 42912538--42912584 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
42912528 AAATGCAAAG
42912538 TATGAAGTGAAATA
1 TATGAAGTGAAATA
* * *
42912552 TATGAAATG-AGTT
1 TATGAAGTGAAATA
*
42912565 TATGAAGTGAAATG
1 TATGAAGTGAAATA
42912579 TATGAA
1 TATGAA
42912585 ATGAGTTTAG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (14 bp):
TATGAAGTGAAATA
Found at i:42912569 original size:27 final size:27
Alignment explanation
Indices: 42912538--42912593 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
42912528 AAATGCAAAG
42912538 TATGAAGTGAAATATATGAAATGAGTT
1 TATGAAGTGAAATATATGAAATGAGTT
*
42912565 TATGAAGTGAAATGTATGAAATGAGTT
1 TATGAAGTGAAATATATGAAATGAGTT
42912592 TA
1 TA
42912594 GCAACAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (27 bp):
TATGAAGTGAAATATATGAAATGAGTT
Found at i:42914100 original size:20 final size:20
Alignment explanation
Indices: 42914075--42914127 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
42914065 AATCAAGTGC
* *
42914075 AAATGATTTTAACCATGTCA
1 AAATGATTTTAAACAAGTCA
*
42914095 AAATGATTTCAAACAAGTCA
1 AAATGATTTTAAACAAGTCA
*
42914115 AAATCATTTTAAA
1 AAATGATTTTAAA
42914128 ATAATTTTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (20 bp):
AAATGATTTTAAACAAGTCA
Found at i:42925918 original size:50 final size:50
Alignment explanation
Indices: 42925807--42926103 Score: 310
Period size: 50 Copynumber: 5.8 Consensus size: 50
42925797 ATTTGGGTAA
* * *
42925807 AGAGATCCCATGGAAGACCATGTCTGGGACATGGCTTTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* *
42925863 AGAGGTCCCATGTAAGACCATGTCTGAGACATGTCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
42925913 AGAGGTCCCATGGCAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
42925963 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
42926013 AGAACTCCCATGTAAGACCATATTTGGGATATGGCATTGGCA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** ** *
42926062 AAACATCCCATGTAAGACCATGTCTGTAACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
42926104 TGTTATTATC
Statistics
Matches: 207, Mismatches: 33, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
48 1 0.00
49 37 0.18
50 127 0.61
53 3 0.01
55 2 0.01
56 37 0.18
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:42929080 original size:55 final size:54
Alignment explanation
Indices: 42928958--42929153 Score: 200
Period size: 54 Copynumber: 3.6 Consensus size: 54
42928948 AAATATTGTT
* * * * * * *
42928958 AAATGACTGAATTACCCCCAGAGGGTAAAATGATCGAATTACCCTCGAAGGTTA
1 AAATGACCGAAATACCCCTAAAGGGTAAAATGATCAAATTACCCCCGAAGGGTA
* * *
42929012 AAATGACTGAAATA-CCCTACAAGGGTAAATTGACCAAATTACCCCCCGAAGGGTA
1 AAATGACCGAAATACCCCTA-AAGGGTAAAATGATCAAATTA-CCCCCGAAGGGTA
* * *
42929067 AAATGACCGAAATACCCCTAAAGGGTAAAATGATGAAATT-GCCCCTATAGGGTA
1 AAATGACCGAAATACCCCTAAAGGGTAAAATGATCAAATTACCCCCGA-AGGGTA
* *
42929121 AAATGACCGTAATAACCCC-ATAGGGTAAAATGA
1 AAATGACCGAAAT-ACCCCTAAAGGGTAAAATGA
42929154 CTGAAATACA
Statistics
Matches: 121, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
53 9 0.07
54 61 0.50
55 46 0.38
56 5 0.04
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (54 bp):
AAATGACCGAAATACCCCTAAAGGGTAAAATGATCAAATTACCCCCGAAGGGTA
Found at i:42929149 original size:109 final size:108
Alignment explanation
Indices: 42928958--42929154 Score: 238
Period size: 109 Copynumber: 1.8 Consensus size: 108
42928948 AAATATTGTT
* * * * *
42928958 AAATGACTGAATTACCCCCAGAGGGTAAAATGATCGAATTACCCTCGAAGGTTAAAATGACTGAA
1 AAATGACCGAAATACCCCCAAAGGGTAAAATGATCGAATTACCCTCGAAGGGTAAAATGACCGAA
*
42929023 ATACCCTACAAGGGTAAATTGACCAAATTACCCCCCGAAGGGTA
66 ATACCC-ACAAGGGTAAAATGACCAAATTACCCCCCGAAGGGTA
* * *
42929067 AAATGACCGAAATACCCCTAAAGGGTAAAATGAT-GAAATTGCCC-CTATAGGGTAAAATGACCG
1 AAATGACCGAAATACCCCCAAAGGGTAAAATGATCG-AATTACCCTCGA-AGGGTAAAATGACCG
*
42929130 TAATAACCC-CATAGGGTAAAATGAC
64 AAAT-ACCCACA-AGGGTAAAATGAC
42929155 TGAAATACAC
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
108 5 0.07
109 65 0.88
110 4 0.05
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (108 bp):
AAATGACCGAAATACCCCCAAAGGGTAAAATGATCGAATTACCCTCGAAGGGTAAAATGACCGAA
ATACCCACAAGGGTAAAATGACCAAATTACCCCCCGAAGGGTA
Found at i:42929203 original size:27 final size:27
Alignment explanation
Indices: 42928958--42929193 Score: 162
Period size: 27 Copynumber: 8.7 Consensus size: 27
42928948 AAATATTGTT
* * *
42928958 AAATGACTGAATTACCCCCAGAGGGTA
1 AAATGACTGAAATACCCCTATAGGGTA
* * *
42928985 AAATGA-TCGAATTACCCTCGA-AGGTTA
1 AAATGACT-GAAATACCC-CTATAGGGTA
*
42929012 AAATGACTGAAATA-CCCTACAAGGGTA
1 AAATGACTGAAATACCCCTA-TAGGGTA
* * *
42929039 AATTGAC-CAAATTACCCCCCGA-AGGGTA
1 AAATGACTGAAA-TA--CCCCTATAGGGTA
* *
42929067 AAATGACCGAAATACCCCTAAAGGGTA
1 AAATGACTGAAATACCCCTATAGGGTA
*
42929094 AAATGA-TGAAATTGCCCCTATAGGGTA
1 AAATGACTGAAA-TACCCCTATAGGGTA
* *
42929121 AAATGACCGTAATAACCCC-ATAGGGTA
1 AAATGACTGAAAT-ACCCCTATAGGGTA
* * * *
42929148 AAATGACTGAAATACACGTGTAAGGTA
1 AAATGACTGAAATACCCCTATAGGGTA
* *
42929175 AAATGACTGTAATGCCCCT
1 AAATGACTGAAATACCCCT
42929194 CGTGGGTAAA
Statistics
Matches: 167, Mismatches: 27, Indels: 30
0.75 0.12 0.13
Matches are distributed among these distances:
25 2 0.01
26 18 0.11
27 116 0.69
28 24 0.14
29 3 0.02
30 4 0.02
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.21
Consensus pattern (27 bp):
AAATGACTGAAATACCCCTATAGGGTA
Found at i:42929235 original size:24 final size:24
Alignment explanation
Indices: 42929199--42929308 Score: 91
Period size: 24 Copynumber: 4.6 Consensus size: 24
42929189 CCCCTCGTGG
* *
42929199 GTAAATGATTGATTTGTCCATGAT
1 GTAAATGACTGATTTGTCTATGAT
* *
42929223 GTATATGACTGATTTGTCTTTGAT
1 GTAAATGACTGATTTGTCTATGAT
* *
42929247 TTAAATGACTGGTTTGTCTATGATT
1 GTAAATGACTGATTTGTCTATGA-T
*
42929272 GGT--ATGA-TCGATTTGTCTGTGAT
1 -GTAAATGACT-GATTTGTCTATGAT
* *
42929295 TTGAATGACTGATT
1 GTAAATGACTGATT
42929309 CTGAGTATTG
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
22 1 0.01
23 2 0.03
24 62 0.91
25 2 0.03
26 1 0.01
ACGTcount: A:0.24, C:0.08, G:0.23, T:0.45
Consensus pattern (24 bp):
GTAAATGACTGATTTGTCTATGAT
Found at i:42929254 original size:48 final size:48
Alignment explanation
Indices: 42929200--42929308 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 48
42929190 CCCTCGTGGG
* *
42929200 TAAATGATTGATTTGTCCATGA-TGTATATGA-CTGATTTGTCTTTGATT
1 TAAATGACTGATTTGTCCATGATTG-ATATGATC-GATTTGTCTGTGATT
* * *
42929248 TAAATGACTGGTTTGTCTATGATTGGTATGATCGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCCATGATTGATATGATCGATTTGTCTGTGATT
*
42929296 TGAATGACTGATT
1 TAAATGACTGATT
42929309 CTGAGTATTG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 49 0.94
49 3 0.06
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (48 bp):
TAAATGACTGATTTGTCCATGATTGATATGATCGATTTGTCTGTGATT
Found at i:42929494 original size:32 final size:32
Alignment explanation
Indices: 42929453--42929655 Score: 275
Period size: 32 Copynumber: 6.4 Consensus size: 32
42929443 CCTTCGATGC
* *
42929453 TACTGATGGCTTTGTGCTAATCATATTACCAT
1 TACTGATGGCTTTGTGCCAATCATATTACCGT
*
42929485 TACTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCAATCATATTACCGT
*
42929517 TACTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCAATCATATTACCGT
* *
42929549 TATTGATGGCTTTATGCCAATCATATTACCGT
1 TACTGATGGCTTTGTGCCAATCATATTACCGT
* * * *
42929581 TACTGATGG-TTGTGTGCCGATCATATCACTGC
1 TACTGATGGCTT-TGTGCCAATCATATTACCGT
*
42929613 TACTGATGGCTTTGTGCCAATCATATTACTG-
1 TACTGATGGCTTTGTGCCAATCATATTACCGT
*
42929644 TACTTATGGCTT
1 TACTGATGGCTT
42929656 GTAGCCATTC
Statistics
Matches: 154, Mismatches: 15, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
31 13 0.08
32 139 0.90
33 2 0.01
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCAATCATATTACCGT
Found at i:42930359 original size:16 final size:17
Alignment explanation
Indices: 42930327--42930359 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
42930317 ATTCTAGAAG
42930327 GGTTTTCAATGAAAACAT
1 GGTTTTCAA-GAAAACAT
42930345 GGTTTTCAA-AAAACA
1 GGTTTTCAAGAAAACA
42930360 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (17 bp):
GGTTTTCAAGAAAACAT
Found at i:42933718 original size:27 final size:27
Alignment explanation
Indices: 42933687--42933753 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
42933677 GTAGAGCATG
42933687 CAGTCATTTTATAACATAGGGGCATAA
1 CAGTCATTTTATAACATAGGGGCATAA
* *
42933714 CAGTCATTTTACT-ACGTGGGGGCATAA
1 CAGTCATTTTA-TAACATAGGGGCATAA
42933741 CAGTCATTTTATA
1 CAGTCATTTTATA
42933754 TCAGTTTGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
26 1 0.03
27 34 0.94
28 1 0.03
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (27 bp):
CAGTCATTTTATAACATAGGGGCATAA
Found at i:42937423 original size:20 final size:19
Alignment explanation
Indices: 42937395--42937445 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
42937385 AATCAAGTGC
*
42937395 AAATGATTTTAACCATGTCA
1 AAATAATTTTAACCA-GTCA
* *
42937415 AAATAATTTCAATCAGTCA
1 AAATAATTTTAACCAGTCA
*
42937434 AAATCATTTTAA
1 AAATAATTTTAA
42937446 AATGATTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (19 bp):
AAATAATTTTAACCAGTCA
Found at i:42943584 original size:42 final size:42
Alignment explanation
Indices: 42943530--42943623 Score: 136
Period size: 42 Copynumber: 2.2 Consensus size: 42
42943520 TGGCACACGC
* *
42943530 CCGTGTAACTCTCAAAA-CTGGCCCACATGCCCGTGTGCTAGG
1 CCGTGTAACTCTCAAAATC-AGCCCACACGCCCGTGTGCTAGG
*
42943572 CCGTGTAACTCTCGAAATCAGCCCACACGCCCGTGTGCTAGG
1 CCGTGTAACTCTCAAAATCAGCCCACACGCCCGTGTGCTAGG
*
42943614 CCATGTAACT
1 CCGTGTAACT
42943624 AACTAACTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
42 46 0.98
43 1 0.02
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.21
Consensus pattern (42 bp):
CCGTGTAACTCTCAAAATCAGCCCACACGCCCGTGTGCTAGG
Found at i:42946167 original size:24 final size:25
Alignment explanation
Indices: 42946125--42946171 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
42946115 CAAAATTTCT
42946125 TAACAAAACTTTAATACAACCTTAC
1 TAACAAAACTTTAATACAACCTTAC
*
42946150 TAACGAAAC-TTAATACAACCTT
1 TAACAAAACTTTAATACAACCTT
42946172 CATAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (25 bp):
TAACAAAACTTTAATACAACCTTAC
Found at i:42953627 original size:20 final size:20
Alignment explanation
Indices: 42953595--42953632 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42953585 AATATTTTAA
*
42953595 ATATATGATTATAGGTTTGT
1 ATATATGATTATAAGTTTGT
42953615 ATATATAGA-TATAAGTTT
1 ATATAT-GATTATAAGTTT
42953633 ATGTAGCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (20 bp):
ATATATGATTATAAGTTTGT
Found at i:42954139 original size:61 final size:61
Alignment explanation
Indices: 42954042--42954166 Score: 187
Period size: 61 Copynumber: 2.0 Consensus size: 61
42954032 ATGTGTGACA
* * *
42954042 TACGGCCTGGCAACATAGTTGTGTGTCCTCTATTAGTTTCTTTGCATACAAGTGAGGGTGT
1 TACGGCCTGGCAACACAGCTGTGTGTCCTCTATTAGTTTCTTTGCATACAAGTGAGGGAGT
* * * *
42954103 TACGGGCTGGCGACACAGCTGTGTGTCCTCTGTTAGTTTCTTTGCATACAAGTTAGGGAGT
1 TACGGCCTGGCAACACAGCTGTGTGTCCTCTATTAGTTTCTTTGCATACAAGTGAGGGAGT
42954164 TAC
1 TAC
42954167 ATGTCCCTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.34
Consensus pattern (61 bp):
TACGGCCTGGCAACACAGCTGTGTGTCCTCTATTAGTTTCTTTGCATACAAGTGAGGGAGT
Found at i:42966167 original size:45 final size:45
Alignment explanation
Indices: 42966103--42966191 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
42966093 AATAGATACT
* * *
42966103 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
*
42966148 CGGTGGAATCAACACATAGCAACCACTTTACTAATCAATGATGT
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGT
42966192 TCAGTTCACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:42966309 original size:51 final size:50
Alignment explanation
Indices: 42966198--42966388 Score: 211
Period size: 51 Copynumber: 3.8 Consensus size: 50
42966188 ATGTTCAGTT
* * * * *
42966198 CACATAGTAGCCTGCACATAGGTACTATACATGTGACCATTACCATTCAGTA
1 CACATAGTAGCCTGCACATA-GTACTACACATGTGACCA-AACTATACGGTA
* * *
42966250 CACGTAGTAGCCTGCACATAGTACTACACATGTGATCGAAACTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGA-CCAAACTATACGGTA
* * * * * * *
42966301 CGCATAGTAGCCAGCACATAGTACTAGACATGCGACCTATCTTTACGGTA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCAAACTATACGGTA
*
42966351 CACGTAGTAGCCTGCACATAGTACTACACATGTGACCA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCA
42966389 TCACTTTCAC
Statistics
Matches: 115, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
50 42 0.37
51 52 0.45
52 21 0.18
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGACCAAACTATACGGTA
Found at i:42966365 original size:101 final size:102
Alignment explanation
Indices: 42966200--42966385 Score: 286
Period size: 101 Copynumber: 1.8 Consensus size: 102
42966190 GTTCAGTTCA
* * *
42966200 CATAGTAGCCTGCACATAGGTACTATACATGTGACCATTACCATTCAGTACACGTAGTAGCCTGC
1 CATAGTAGCCAGCACATAGGTACTAGACATGCGACCA-TACCATTCAGTACACGTAGTAGCCTGC
42966265 ACATAGTACTACACATGTGATCGAAACTATCCGGTACG
65 ACATAGTACTACACATGTGATCGAAACTATCCGGTACG
* * *
42966303 CATAGTAGCCAGCACATA-GTACTAGACATGCGACC-TATCTTTACGGTACACGTAGTAGCCTGC
1 CATAGTAGCCAGCACATAGGTACTAGACATGCGACCATACCATT-CAGTACACGTAGTAGCCTGC
42966366 ACATAGTACTACACATGTGA
65 ACATAGTACTACACATGTGA
42966386 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
100 5 0.07
101 39 0.51
102 15 0.20
103 17 0.22
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (102 bp):
CATAGTAGCCAGCACATAGGTACTAGACATGCGACCATACCATTCAGTACACGTAGTAGCCTGCA
CATAGTACTACACATGTGATCGAAACTATCCGGTACG
Found at i:42970296 original size:50 final size:50
Alignment explanation
Indices: 42970189--42970342 Score: 191
Period size: 50 Copynumber: 3.0 Consensus size: 50
42970179 GGGGACGAGA
* **
42970189 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGATGTTATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGG---TACCGA-G--ATGAGAGG
42970245 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATGAGAGG
* * * *
42970295 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATGAGA
42970343 ACTCTCATGT
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
50 52 0.57
52 1 0.01
53 4 0.04
56 34 0.37
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATGAGAGG
Found at i:42970366 original size:50 final size:50
Alignment explanation
Indices: 42970245--42970373 Score: 132
Period size: 50 Copynumber: 2.6 Consensus size: 50
42970235 TTATGAGAGG
* * * * **
42970245 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGTACCGAGATGAGAGG
1 TCCCACGTAAGAACATATCTGGGACATGGCATGGGCACCGAGATGAGAAC
* * * *
42970295 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCACGTAAGAACATATCTGGGACATGGCATGGGCACCGAGATGAGAAC
* * * *
42970345 TCTCATGTACGAACATATCTGGGATATGG
1 TCCCACGTAAGAACATATCTGGGACATGG
42970374 TATTTGCAAT
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
TCCCACGTAAGAACATATCTGGGACATGGCATGGGCACCGAGATGAGAAC
Found at i:42970667 original size:20 final size:20
Alignment explanation
Indices: 42970631--42970669 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
42970621 TGAGTTATTT
*
42970631 AAGTAAGCAAGTGAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
42970651 AAGTAAG-AGAGTAAGTAAA
1 AAGTAAGCA-AGTAAGTAAA
42970670 GAAGAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.54, C:0.05, G:0.26, T:0.15
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:42970691 original size:27 final size:27
Alignment explanation
Indices: 42970659--42970712 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
42970649 ACAAGTAAGA
42970659 GAGTAAGTAAAGAAGAAAGTAAAGATC
1 GAGTAAGTAAAGAAGAAAGTAAAGATC
42970686 GAGTAAGTAAAGAAGAAAGTAAAGATC
1 GAGTAAGTAAAGAAGAAAGTAAAGATC
42970713 ATGATACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.26, T:0.15
Consensus pattern (27 bp):
GAGTAAGTAAAGAAGAAAGTAAAGATC
Found at i:42970695 original size:15 final size:13
Alignment explanation
Indices: 42970651--42970710 Score: 63
Period size: 12 Copynumber: 4.7 Consensus size: 13
42970641 GTGAGTAAAC
42970651 AAGT-AAGAGAGT
1 AAGTAAAGAGAGT
*
42970663 AAGTAAAGA-AGA
1 AAGTAAAGAGAGT
42970675 AAGTAAAGATCGAGT
1 AAGTAAAGA--GAGT
*
42970690 AAGTAAAGA-AGA
1 AAGTAAAGAGAGT
42970702 AAGTAAAGA
1 AAGTAAAGA
42970711 TCATGATACT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 26 0.63
13 4 0.10
15 11 0.27
ACGTcount: A:0.58, C:0.02, G:0.27, T:0.13
Consensus pattern (13 bp):
AAGTAAAGAGAGT
Found at i:42973995 original size:18 final size:20
Alignment explanation
Indices: 42973974--42974017 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
42973964 AAAGGAAGAC
42973974 AGAAAAAGA-AATCAAAAA-
1 AGAAAAAGAGAATCAAAAAG
*
42973992 AGAAAAAGAGAATGAAAAAG
1 AGAAAAAGAGAATCAAAAAG
42974012 AGAAAA
1 AGAAAA
42974018 GATTGAGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.39
19 8 0.35
20 6 0.26
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (20 bp):
AGAAAAAGAGAATCAAAAAG
Found at i:42975815 original size:33 final size:34
Alignment explanation
Indices: 42975778--42975849 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
42975768 GAGCTAGTTT
42975778 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
* *
42975811 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
42975845 ATTAA
1 ATTAA
42975850 TTTGTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 30 0.83
34 6 0.17
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
Found at i:42989572 original size:27 final size:27
Alignment explanation
Indices: 42989541--42989718 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42989531 TAAATTGTAC
42989541 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42989568 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42989594 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42989622 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42989650 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42989677 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42989704 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42989719 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:42989655 original size:82 final size:81
Alignment explanation
Indices: 42989542--42989697 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42989532 AAATTGTACA
* *
42989542 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42989606 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42989623 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42989688 TGCGAGTTGA
65 TGCGAATTGA
42989698 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:42989709 original size:82 final size:81
Alignment explanation
Indices: 42989538--42989718 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42989528 GATTAAATTG
* *
42989538 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42989603 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42989619 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42989683 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42989701 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42989719 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:43003732 original size:27 final size:27
Alignment explanation
Indices: 43003701--43003878 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
43003691 TAAATTGTAC
43003701 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
43003728 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43003754 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
43003782 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
43003810 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43003837 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
43003864 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43003879 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:43003815 original size:82 final size:81
Alignment explanation
Indices: 43003702--43003857 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
43003692 AAATTGTACA
* *
43003702 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
43003766 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
43003783 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
43003848 TGCGAGTTGA
65 TGCGAATTGA
43003858 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:43003869 original size:82 final size:81
Alignment explanation
Indices: 43003698--43003878 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
43003688 GATTAAATTG
* *
43003698 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
43003763 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
43003779 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
43003843 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
43003861 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
43003879 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:43007700 original size:19 final size:20
Alignment explanation
Indices: 43007672--43007727 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
43007662 CTATCGAATC
43007672 AAAA-TTGTAATTACA-A-AA
1 AAAACTTGTAATTA-ATACAA
43007690 AAAACTTGTAATTAATACAA
1 AAAACTTGTAATTAATACAA
43007710 AGAAACTTGTAATTAATA
1 A-AAACTTGTAATTAATA
43007728 TATATTCTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.15
19 10 0.29
20 3 0.09
21 16 0.47
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (20 bp):
AAAACTTGTAATTAATACAA
Found at i:43008033 original size:13 final size:13
Alignment explanation
Indices: 43008015--43008041 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43008005 CATAAAAAGC
43008015 AAACTTTTACAAA
1 AAACTTTTACAAA
43008028 AAACTTTTACAAA
1 AAACTTTTACAAA
43008041 A
1 A
43008042 GTTTTTCAGA
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:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
AAACTTTTACAAA
Found at i:43009423 original size:26 final size:26
Alignment explanation
Indices: 43009394--43009443 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
43009384 CACCAATATC
*
43009394 ATAGCAAAGCTGCCAGTAATAGTATT
1 ATAGCAAAGCTGCCAGTAACAGTATT
*
43009420 ATAGCGAAGCTGCCAGTAACAGTA
1 ATAGCAAAGCTGCCAGTAACAGTA
43009444 AATGCGACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (26 bp):
ATAGCAAAGCTGCCAGTAACAGTATT
Found at i:43009659 original size:27 final size:26
Alignment explanation
Indices: 43009629--43009768 Score: 158
Period size: 27 Copynumber: 5.3 Consensus size: 26
43009619 GGGTATAATA
43009629 GTCATTTTACCCTATTGGGGTATTTCG
1 GTCATTTTACCCTA-TGGGGTATTTCG
*
43009656 GTCATTTTACCTTATGAGGGT-TTTCG
1 GTCATTTTACCCTATG-GGGTATTTCG
*
43009682 GTCATTTCACCCTATGGAGGTATTTCG
1 GTCATTTTACCCTATGG-GGTATTTCG
*
43009709 GTCATTTTACCTTATAGGGGTATTT-G
1 GTCATTTTACCCTAT-GGGGTATTTCG
* * *
43009735 ATCATTTTATCCTAAGAGGGTATTTCG
1 GTCATTTTACCCTATG-GGGTATTTCG
*
43009762 ATCATTT
1 GTCATTT
43009769 ATTGACCTCT
Statistics
Matches: 98, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
25 2 0.02
26 44 0.45
27 50 0.51
28 2 0.02
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (26 bp):
GTCATTTTACCCTATGGGGTATTTCG
Found at i:43009740 original size:53 final size:53
Alignment explanation
Indices: 43009630--43009768 Score: 169
Period size: 53 Copynumber: 2.6 Consensus size: 53
43009620 GGTATAATAG
*
43009630 TCATTTTACCCTATTGG-GGTATTTCGGTCATTTTACCTTATGAGGGTTTTCGG
1 TCATTTTACCCTA-TGGAGGTATTTCGGTCATTTTACCTTATGAGGGTTTTCGA
*
43009683 TCATTTCACCCTATGGAGGTATTTCGGTCATTTTACCTTAT-AGGGGTATTT-GA
1 TCATTTTACCCTATGGAGGTATTTCGGTCATTTTACCTTATGA-GGGT-TTTCGA
* * *
43009736 TCATTTTATCCTA-AGAGGGTATTTCGATCATTT
1 TCATTTTACCCTATGGA-GGTATTTCGGTCATTT
43009769 ATTGACCTCT
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
52 6 0.08
53 67 0.88
54 3 0.04
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.44
Consensus pattern (53 bp):
TCATTTTACCCTATGGAGGTATTTCGGTCATTTTACCTTATGAGGGTTTTCGA
Found at i:43009769 original size:26 final size:27
Alignment explanation
Indices: 43009645--43009770 Score: 104
Period size: 26 Copynumber: 4.7 Consensus size: 27
43009635 TTACCCTATT
*
43009645 GGGGTATTTCGGTCATTT-TACCTTAT
1 GGGGTATTTCGGTCATTTATACCTTAA
* * *
43009671 GAGGGT-TTTCGGTCATTT-CACCCTAT
1 G-GGGTATTTCGGTCATTTATACCTTAA
43009697 GGAGGTATTTCGGTCATTT-TACCTTATA
1 GG-GGTATTTCGGTCATTTATACCTTA-A
*
43009725 GGGGTATTT-GATCATTT-TATCC-TAA
1 GGGGTATTTCGGTCATTTATA-CCTTAA
*
43009750 GAGGGTATTTCGATCATTTAT
1 G-GGGTATTTCGGTCATTTAT
43009771 TGACCTCTCG
Statistics
Matches: 86, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
25 3 0.03
26 42 0.49
27 38 0.44
28 3 0.03
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (27 bp):
GGGGTATTTCGGTCATTTATACCTTAA
Found at i:43022181 original size:6 final size:6
Alignment explanation
Indices: 43022157--43022195 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
43022147 TGGGGAAAAT
* *
43022157 AAATGA AAAATA AAA-TA AAATTA AAATTA AAATTA AAAT
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAAT
43022196 GATCCCTACT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (6 bp):
AAATTA
Found at i:43023056 original size:14 final size:15
Alignment explanation
Indices: 43023030--43023063 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
43023020 TCTTTCATAA
43023030 ATTAAAAATTTAAGT
1 ATTAAAAATTTAAGT
*
43023045 GTTAAAAA-TTAAGT
1 ATTAAAAATTTAAGT
43023059 ATTAA
1 ATTAA
43023064 TTTTTTATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (15 bp):
ATTAAAAATTTAAGT
Found at i:43023422 original size:16 final size:16
Alignment explanation
Indices: 43023401--43023436 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
43023391 TATCAAACTC
43023401 ATTTAAAATATTAAAT
1 ATTTAAAATATTAAAT
43023417 ATTTAAAATATTAAAT
1 ATTTAAAATATTAAAT
43023433 ATTT
1 ATTT
43023437 TAAACATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTAAAATATTAAAT
Found at i:43027737 original size:19 final size:20
Alignment explanation
Indices: 43027713--43027755 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
43027703 TAATAAATAA
43027713 TAAATTTT-AGAAAAATTAT
1 TAAATTTTAAGAAAAATTAT
*
43027732 TAAATTTTAATAAAAATTAT
1 TAAATTTTAAGAAAAATTAT
43027752 TAAA
1 TAAA
43027756 AATTAGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TAAATTTTAAGAAAAATTAT
Found at i:43028050 original size:9 final size:9
Alignment explanation
Indices: 43028002--43028095 Score: 64
Period size: 9 Copynumber: 10.1 Consensus size: 9
43027992 CTTTATAAAA
43028002 TTTTATAATT
1 TTTTAT-ATT
43028012 GTTTTA-ATAT
1 -TTTTATAT-T
* *
43028022 TTCTATATA
1 TTTTATATT
*
43028031 TTTTACAATT
1 TTTTA-TATT
43028041 TTTTATATT
1 TTTTATATT
* *
43028050 TTTTACAAT
1 TTTTATATT
43028059 TTTTATATT
1 TTTTATATT
* *
43028068 TCTTCTATT
1 TTTTATATT
*
43028077 TTTAATATT
1 TTTTATATT
*
43028086 TTTAATATT
1 TTTTATATT
43028095 T
1 T
43028096 GATTTTTTTA
Statistics
Matches: 65, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
9 50 0.77
10 10 0.15
11 5 0.08
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (9 bp):
TTTTATATT
Found at i:43028067 original size:18 final size:18
Alignment explanation
Indices: 43028002--43028088 Score: 79
Period size: 18 Copynumber: 4.7 Consensus size: 18
43027992 CTTTATAAAA
43028002 TTTTATAATTGTTTTA-ATAT
1 TTTTAT-ATT-TTTTACA-AT
* *
43028022 TTCTATATATTTTACAATT
1 TTTTATATTTTTTACAA-T
43028041 TTTTATATTTTTTACAAT
1 TTTTATATTTTTTACAAT
* *
43028059 TTTTATATTTCTT-CTAT
1 TTTTATATTTTTTACAAT
43028076 TTTTAATATTTTT
1 TTTT-ATATTTTT
43028089 AATATTTGAT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
17 7 0.12
18 26 0.46
19 19 0.33
20 5 0.09
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.67
Consensus pattern (18 bp):
TTTTATATTTTTTACAAT
Found at i:43028068 original size:27 final size:25
Alignment explanation
Indices: 43027999--43028107 Score: 69
Period size: 27 Copynumber: 4.1 Consensus size: 25
43027989 CGACTTTATA
*
43027999 AAATTTTATAATTGTTTTAATATTTCTAT
1 AAATTTT-TAATT-TTTT-ATATTT-TTT
* *
43028028 ATATTTTACAATTTTTTATATTTTTT
1 AAATTTT-TAATTTTTTATATTTTTT
* *
43028054 ACAATTTTTATATTTCTTCTA-TTTTT
1 A-AATTTTTA-ATTTTTTATATTTTTT
* *
43028080 AATATTTTTAATATTTGAT-TTTTTT
1 AA-ATTTTTAATTTTTTATATTTTTT
43028105 AAA
1 AAA
43028108 ATTTAATAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
24 1 0.02
25 13 0.20
26 17 0.26
27 19 0.29
28 4 0.06
29 11 0.17
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (25 bp):
AAATTTTTAATTTTTTATATTTTTT
Found at i:43028597 original size:21 final size:21
Alignment explanation
Indices: 43028550--43028598 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
43028540 TGATAATCTA
*
43028550 AAAAATATATTAAAAATTAAT
1 AAAAATATATTAAAAAATAAT
*
43028571 AAAAATATTTTAAAAAATAA-
1 AAAAATATATTAAAAAATAAT
43028591 AACAAATA
1 AA-AAATA
43028599 CAAACAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAATATATTAAAAAATAAT
Found at i:43030455 original size:43 final size:43
Alignment explanation
Indices: 43030403--43030675 Score: 289
Period size: 43 Copynumber: 6.3 Consensus size: 43
43030393 GTTTTTAGAA
* *
43030403 ACAAACGCCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACCAGGACCTTTAGCGACGCTTTTCCC
* *
43030446 ACAAACGCCGCTAAAGACTAGGACCTTTAGCGACGCTTTTCTC
1 ACAAACGCCGCTAAAGACCAGGACCTTTAGCGACGCTTTTCCC
* * *
43030489 ACAAACGCCGCTAAAAACCAAGACCTTTAGCGACGATTTTCCC
1 ACAAACGCCGCTAAAGACCAGGACCTTTAGCGACGCTTTTCCC
** * * * *
43030532 ACAAGTGCCGCTAAAGACCAGGACTTTTAGCGGCACTTTTTCC
1 ACAAACGCCGCTAAAGACCAGGACCTTTAGCGACGCTTTTCCC
* * * * *
43030575 ACAAATGCTGCTAAAGACCCA-AACCTATAGCGACGCTTTTTCC
1 ACAAACGCCGCTAAAGA-CCAGGACCTTTAGCGACGCTTTTCCC
* * * ****
43030618 ACAAACGCCGCTATA-ACTCAAGACCTTTAGCAACGCTTTGATT
1 ACAAACGCCGCTAAAGAC-CAGGACCTTTAGCGACGCTTTTCCC
43030661 ACAAACGCCGCTAAA
1 ACAAACGCCGCTAAA
43030676 AGTACTATTA
Statistics
Matches: 191, Mismatches: 36, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
41 1 0.01
42 3 0.02
43 184 0.96
44 3 0.02
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGACCAGGACCTTTAGCGACGCTTTTCCC
Found at i:43030560 original size:129 final size:129
Alignment explanation
Indices: 43030409--43030648 Score: 360
Period size: 129 Copynumber: 1.9 Consensus size: 129
43030399 AGAAACAAAC
* * * *
43030409 GCCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGA-CTAGGACCTT
1 GCCGCTAAAGACCAGGACTTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGACCCA-AACCTA
43030473 TAGCGACGC-TTTTCTCACAAACGCCGCTAAAAAC-CAAGACCTTTAGCGACGATTTTCCCACAA
65 TAGCGACGCTTTTTC-CACAAACGCCGCT-AAAACTCAAGACCTTTAGCGACGATTTTCCCACAA
43030536 GT
128 GT
* * *
43030538 GCCGCTAAAGACCAGGACTTTTAGCGGCACTTTTTCCACAAATGCTGCTAAAGACCCAAACCTAT
1 GCCGCTAAAGACCAGGACTTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGACCCAAACCTAT
*
43030603 AGCGACGCTTTTTCCACAAACGCCGCTATAACTCAAGACCTTTAGC
66 AGCGACGCTTTTTCCACAAACGCCGCTAAAACTCAAGACCTTTAGC
43030649 AACGCTTTGA
Statistics
Matches: 100, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
128 4 0.04
129 89 0.89
130 7 0.07
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (129 bp):
GCCGCTAAAGACCAGGACTTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGACCCAAACCTAT
AGCGACGCTTTTTCCACAAACGCCGCTAAAACTCAAGACCTTTAGCGACGATTTTCCCACAAGT
Found at i:43030671 original size:129 final size:129
Alignment explanation
Indices: 43030403--43030675 Score: 354
Period size: 129 Copynumber: 2.1 Consensus size: 129
43030393 GTTTTTAGAA
* * *
43030403 ACAAACGCCGCTAAAGACCAGGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACTAGG
1 ACAAACGCCGCTAAAGACCAGGACTTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGACCAGA
* * **
43030468 ACCTTTAGCGACGCTTTTCTCACAAACGCCGCTAAAAACCAAGACCTTTAGCGACGATTTTCCC
66 ACCTATAGCGACGCTTTTCTCACAAACGCCGCTAAAAACCAAGACCTTTAGCAACGATTTGACC
** * * *
43030532 ACAAGTGCCGCTAAAGACCAGGACTTTTAGCGGCACTTTTTCCACAAATGCTGCTAAAGACCCA-
1 ACAAACGCCGCTAAAGACCAGGACTTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGA-CCAG
* *
43030596 AACCTATAGCGACGCTTTT-TCCACAAACGCCGCT-ATAACTCAAGACCTTTAGCAACGCTTTGA
65 AACCTATAGCGACGCTTTTCT-CACAAACGCCGCTAAAAAC-CAAGACCTTTAGCAACGATTTGA
**
43030659 TT
128 CC
43030661 ACAAACGCCGCTAAA
1 ACAAACGCCGCTAAA
43030676 AGTACTATTA
Statistics
Matches: 123, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
128 5 0.04
129 116 0.94
130 2 0.02
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (129 bp):
ACAAACGCCGCTAAAGACCAGGACTTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGACCAGA
ACCTATAGCGACGCTTTTCTCACAAACGCCGCTAAAAACCAAGACCTTTAGCAACGATTTGACC
Found at i:43030939 original size:15 final size:15
Alignment explanation
Indices: 43030919--43030949 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43030909 AGGGATATGG
43030919 ATCATCTTCATCTTC
1 ATCATCTTCATCTTC
*
43030934 ATCATCTTCTTCTTC
1 ATCATCTTCATCTTC
43030949 A
1 A
43030950 CTTTCAACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.32, G:0.00, T:0.48
Consensus pattern (15 bp):
ATCATCTTCATCTTC
Found at i:43035392 original size:12 final size:12
Alignment explanation
Indices: 43035375--43035403 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
43035365 GAATTTTGGG
43035375 ATAAAAAAATAT
1 ATAAAAAAATAT
43035387 ATAAAAAAATAT
1 ATAAAAAAATAT
43035399 ATAAA
1 ATAAA
43035404 CACAAAGCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAAAAATAT
Found at i:43036146 original size:7 final size:7
Alignment explanation
Indices: 43036133--43036171 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
43036123 CTCTTAGCCT
43036133 CTAACCC
1 CTAACCC
*
43036140 TTAACCC
1 CTAACCC
43036147 CTAACCC
1 CTAACCC
**
43036154 CTAACTA
1 CTAACCC
43036161 CTAACCC
1 CTAACCC
43036168 CTAA
1 CTAA
43036172 ACCTTATTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAACCC
Found at i:43036238 original size:13 final size:13
Alignment explanation
Indices: 43036213--43036250 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
43036203 AATTAATCTA
43036213 AACCCTAAACCCT
1 AACCCTAAACCCT
43036226 AACCC-AAATCCCT
1 AACCCTAAA-CCCT
*
43036239 AACCCTTAACCC
1 AACCCTAAACCC
43036251 CTAAACCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 3 0.14
13 17 0.77
14 2 0.09
ACGTcount: A:0.37, C:0.47, G:0.00, T:0.16
Consensus pattern (13 bp):
AACCCTAAACCCT
Found at i:43036365 original size:7 final size:7
Alignment explanation
Indices: 43036353--43036384 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
43036343 CTCTTAATCT
43036353 CTAACCC
1 CTAACCC
*
43036360 CTAACCA
1 CTAACCC
43036367 CTAACCC
1 CTAACCC
43036374 CTAACCC
1 CTAACCC
43036381 CTAA
1 CTAA
43036385 ATCACAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.34, C:0.50, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAACCC
Found at i:43036530 original size:14 final size:14
Alignment explanation
Indices: 43036485--43036521 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
43036475 ATCCTAAATT
43036485 AACCATATACCTTA
1 AACCATATACCTTA
*
43036499 AACCATATACCCTA
1 AACCATATACCTTA
43036513 AACCATATA
1 AACCATATA
43036522 TATTAAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (14 bp):
AACCATATACCTTA
Found at i:43036901 original size:41 final size:40
Alignment explanation
Indices: 43036777--43036964 Score: 138
Period size: 41 Copynumber: 4.7 Consensus size: 40
43036767 AAATATTTTT
* *
43036777 GCGGCGCTTTTTTAAAAACGCCGCTAAAAGCCTA--AGCATTA
1 GCGGCG-TTTTTAAAAAACGCCGCT-AAAG-ATATGAGCATTA
* * * * * * *
43036818 GCGGCGCTTTTTCAAAAACGCTGCTAATGCT-CGGGCTTTTA
1 GCGGCG-TTTTTAAAAAACGCCGCTAAAGATATGAGC-ATTA
43036859 GCGGCGTTTTTAAAAAAGCGCCGCTAAAGATATGAGCATTA
1 GCGGCGTTTTTAAAAAA-CGCCGCTAAAGATATGAGCATTA
* * *
43036900 GCGGCG-TTTT---GAACGCCGCTAAAGATCTGAGCATCA
1 GCGGCGTTTTTAAAAAACGCCGCTAAAGATATGAGCATTA
* *
43036936 GCGACACTTTTTAAAAAACGCCGCTAAAG
1 GCGGC-GTTTTTAAAAAACGCCGCTAAAG
43036965 CCCCGAAAGG
Statistics
Matches: 119, Mismatches: 18, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
36 25 0.21
37 2 0.02
38 4 0.03
39 2 0.02
40 19 0.16
41 64 0.54
42 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (40 bp):
GCGGCGTTTTTAAAAAACGCCGCTAAAGATATGAGCATTA
Found at i:43037046 original size:39 final size:40
Alignment explanation
Indices: 43037000--43037136 Score: 161
Period size: 40 Copynumber: 3.5 Consensus size: 40
43036990 TTTGGCTTAG
** *
43037000 ATTTTTAGCGGCGTTTTTCAAAAAATGCCGCTAATGGTC-
1 ATTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCA
* **
43037039 ATTTTTAGCGGCGCTTTTCTGAAAGCGCCGCTAATGCTCA
1 ATTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCA
* ** *
43037079 ATCTTTAGCGGCGTTTTAT-GTAAAGCGCCGCTAATGCTCG
1 ATTTTTAGCGGCGTTTT-TCAAAAAGCGCCGCTAATGCTCA
43037119 ATTTTTAGCGGCGTTTTT
1 ATTTTTAGCGGCGTTTTT
43037137 GTCCAAACGC
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 34 0.40
40 49 0.58
41 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (40 bp):
ATTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCA
Found at i:43042343 original size:27 final size:27
Alignment explanation
Indices: 43042294--43042373 Score: 110
Period size: 27 Copynumber: 3.0 Consensus size: 27
43042284 ACAGTCATAC
* *
43042294 ATAACATTA-AGCAT-ACAGTCATTTT
1 ATAACATAAGAGCATAATAGTCATTTT
43042319 ATAACATAAGAGCATAATAGTCATTTT
1 ATAACATAAGAGCATAATAGTCATTTT
* *
43042346 ATAACATAGGGGCATAATAGTCATTTT
1 ATAACATAAGAGCATAATAGTCATTTT
43042373 A
1 A
43042374 GTCATTTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 8 0.16
26 5 0.10
27 36 0.73
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (27 bp):
ATAACATAAGAGCATAATAGTCATTTT
Found at i:43042382 original size:63 final size:63
Alignment explanation
Indices: 43042310--43042436 Score: 193
Period size: 63 Copynumber: 2.0 Consensus size: 63
43042300 TTAAGCATAC
*
43042310 AGTCATTTTATAACATAAGAGCATAA-TAGTCATTTTATAACATAGGGGCATAATAGTCATTTT
1 AGTCATTTTATAACATAAGAGCATAACCA-TCATTTTATAACATAGGGGCATAATAGTCATTTT
* * * *
43042373 AGTCATTTTATAACATATGGGCATAACCATTATTTTATAACATAGGGGTATAATAGTCATTTT
1 AGTCATTTTATAACATAAGAGCATAACCATCATTTTATAACATAGGGGCATAATAGTCATTTT
43042436 A
1 A
43042437 CCACGTGAGG
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
63 57 0.98
64 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (63 bp):
AGTCATTTTATAACATAAGAGCATAACCATCATTTTATAACATAGGGGCATAATAGTCATTTT
Found at i:43042434 original size:27 final size:28
Alignment explanation
Indices: 43042372--43042468 Score: 85
Period size: 27 Copynumber: 3.6 Consensus size: 28
43042362 ATAGTCATTT
*
43042372 TAGTCATTTTATAACATATGGGCATAAC
1 TAGTCATTTTATAACATAGGGGCATAAC
* * *
43042400 CA-TTATTTTATAACATAGGGGTATAA-
1 TAGTCATTTTATAACATAGGGGCATAAC
** *
43042426 TAGTCATTTTACCACGT-GAGGGCATAAC
1 TAGTCATTTTATAACATAG-GGGCATAAC
*
43042454 -AATCATTTTATAACA
1 TAGTCATTTTATAACA
43042469 GTTTGGGGGT
Statistics
Matches: 52, Mismatches: 14, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
26 2 0.04
27 49 0.94
28 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (28 bp):
TAGTCATTTTATAACATAGGGGCATAAC
Found at i:43052136 original size:33 final size:33
Alignment explanation
Indices: 43052080--43052152 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
43052070 ATACAACATG
* *
43052080 CAGTAACAGTCTGGGCCTGAGCCCTATTCAGTAA
1 CAGT-ACAGTCTGGGCCTGAGCCCAATACAGTAA
* * *
43052114 CAGTACAGTTTGGGTCTTAGCCCAATACAGTAA
1 CAGTACAGTCTGGGCCTGAGCCCAATACAGTAA
*
43052147 TAGTAC
1 CAGTAC
43052153 GTGCAATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 29 0.88
34 4 0.12
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (33 bp):
CAGTACAGTCTGGGCCTGAGCCCAATACAGTAA
Found at i:43052281 original size:26 final size:26
Alignment explanation
Indices: 43052251--43052331 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 26
43052241 AACACACTAA
*
43052251 TATCGCAGCAAACCTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
* * *
43052277 TATCGTAGCGAAGCTACCAGT-ATCAG
1 TATCGCAGCAAAGCTGCCAGTAAT-AG
* * * *
43052303 TATTGCACCAAAGCTGCCAATAACAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
43052329 TAT
1 TAT
43052332 ATGTGGCAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
25 2 0.05
26 39 0.93
27 1 0.02
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAATAG
Found at i:43052837 original size:20 final size:20
Alignment explanation
Indices: 43052808--43052862 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
43052798 AAGCCCATTG
43052808 GCCC-ACACGGCCCATCTTA
1 GCCCAACACGGCCCATCTTA
43052827 GCCCAACACGGCCCATCTTA
1 GCCCAACACGGCCCATCTTA
43052847 GCCCAACACGGCCCAT
1 GCCCAACACGGCCCAT
43052863 TACGGCCCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 4 0.11
20 31 0.89
ACGTcount: A:0.24, C:0.47, G:0.16, T:0.13
Consensus pattern (20 bp):
GCCCAACACGGCCCATCTTA
Found at i:43053516 original size:21 final size:21
Alignment explanation
Indices: 43053490--43053545 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
43053480 AACAGCGGTG
*
43053490 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
43053511 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
43053532 GCCGTGAGATTAGA
1 GCGGTGAGATTAGA
43053546 AACAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.11, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:43054654 original size:16 final size:16
Alignment explanation
Indices: 43054635--43054669 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
43054625 TAAAATATGT
43054635 AATATTTAATATTTTA
1 AATATTTAATATTTTA
43054651 AATATTTAATATTTTA
1 AATATTTAATATTTTA
43054667 AAT
1 AAT
43054670 GAGTTTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AATATTTAATATTTTA
Found at i:43055023 original size:14 final size:15
Alignment explanation
Indices: 43055006--43055040 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
43054996 ACAGTAAAAA
43055006 TTTAATACTTA-ATT
1 TTTAATACTTATATT
*
43055020 TTTAACACTTATATT
1 TTTAATACTTATATT
43055035 TTTAAT
1 TTTAAT
43055041 TTATGAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAATACTTATATT
Found at i:43058452 original size:25 final size:25
Alignment explanation
Indices: 43058388--43058471 Score: 89
Period size: 25 Copynumber: 3.3 Consensus size: 25
43058378 TACTAATTTC
**
43058388 AGCTCGTGAGAGCTTACCGATTCCC
1 AGCTCGTGAGAGCTTACCGATTCAT
*
43058413 AGCTC-TCGTATGAGCTTACCGATTTAT
1 AGCTCGT-G-A-GAGCTTACCGATTCAT
* *
43058440 AGCTCGTGAGAGCATACCAATTCAT
1 AGCTCGTGAGAGCTTACCGATTCAT
43058465 AGCTCGT
1 AGCTCGT
43058472 ATGAGCATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
24 1 0.02
25 26 0.53
26 2 0.04
27 19 0.39
28 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (25 bp):
AGCTCGTGAGAGCTTACCGATTCAT
Found at i:43058469 original size:52 final size:49
Alignment explanation
Indices: 43058361--43058477 Score: 135
Period size: 52 Copynumber: 2.3 Consensus size: 49
43058351 GCAGACACAC
* * * *
43058361 CACAGCTCATATGAGCTTACTAATTTCAGCTCGTGAGAGCTTACCGATT
1 CACAGCTCGTATGAGCTTACCAATTTCAGCTCGTGAGAGCATACCAATT
* * *
43058410 CCCAGCTCTCGTATGAGCTTACCGATTTATAGCTCGTGAGAGCATACCAATT
1 CACAG--CTCGTATGAGCTTACCAATTT-CAGCTCGTGAGAGCATACCAATT
*
43058462 CATAGCTCGTATGAGC
1 CACAGCTCGTATGAGC
43058478 ATACATGTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
49 4 0.07
50 11 0.20
51 18 0.32
52 23 0.41
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (49 bp):
CACAGCTCGTATGAGCTTACCAATTTCAGCTCGTGAGAGCATACCAATT
Found at i:43058477 original size:25 final size:25
Alignment explanation
Indices: 43058417--43058481 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
43058407 ATTCCCAGCT
* * *
43058417 CTCGTATGAGCTTACCGATTTATAG
1 CTCGTATGAGCATACCAATTCATAG
43058442 CTCGTGA-GAGCATACCAATTCATAG
1 CTCGT-ATGAGCATACCAATTCATAG
43058467 CTCGTATGAGCATAC
1 CTCGTATGAGCATAC
43058482 ATGTATAGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.03
25 33 0.94
26 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (25 bp):
CTCGTATGAGCATACCAATTCATAG
Found at i:43062870 original size:17 final size:17
Alignment explanation
Indices: 43062844--43062889 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
43062834 GGAGGTGTTG
*
43062844 CACGCGCAGGAGCGCAA
1 CACGCACAGGAGCGCAA
*
43062861 CACGCACAGGAGCGGAA
1 CACGCACAGGAGCGCAA
43062878 CACGCACAGGAG
1 CACGCACAGGAG
43062890 AAGGCCCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.35, T:0.00
Consensus pattern (17 bp):
CACGCACAGGAGCGCAA
Found at i:43063740 original size:44 final size:43
Alignment explanation
Indices: 43063692--43063829 Score: 113
Period size: 42 Copynumber: 3.2 Consensus size: 43
43063682 GTGCTGAGGA
*
43063692 AGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGG
1 AGGCAAGATTTG-TATCTTTAACCAGCTCCACTGCAACCGATGG
* ** * * * * *
43063736 AGGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAA-CGCA-GG
1 AGGCAA-GATTTGTATCTTTAACCAGCTCCACTG-CAACCG-ATGG
43063778 AAGGCAAGATTTGTTATCTTTAACCAGCTCCACTGCAACCGATGG
1 -AGGCAAGATTTG-TATCTTTAACCAGCTCCACTGCAACCGATGG
43063823 AGGCAAG
1 AGGCAAG
43063830 GCTTTGCTTT
Statistics
Matches: 68, Mismatches: 17, Indels: 18
0.66 0.17 0.17
Matches are distributed among these distances:
42 20 0.29
43 11 0.16
44 18 0.26
45 19 0.28
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (43 bp):
AGGCAAGATTTGTATCTTTAACCAGCTCCACTGCAACCGATGG
Found at i:43063960 original size:86 final size:87
Alignment explanation
Indices: 43063688--43063981 Score: 439
Period size: 87 Copynumber: 3.4 Consensus size: 87
43063678 TCTAGTGCTG
43063688 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
43063753 CGATCTGCTTCGCTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
* * *
43063775 AGGAAGGCAAGATTTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGCTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* * *
43063840 CGATCTACTTCGCTATTAACGT
66 CGATCTGCTTCGCTGTTAACGC
* * * * * **
43063862 AGGAAGGGAAGATCTGTTATCTTTAACTAGCTCCACTACAACCAAT-GAGGTGAGGCTTTGTTTT
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
43063926 CGATCTGCTTCGCTGTTAACGC
66 CGATCTGCTTCGCTGTTAACGC
* *
43063948 AAGAAGGCAAGATCTGCT-CCTTTAACCAGCTCCA
1 AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCA
43063982 GCTCCTTTAA
Statistics
Matches: 185, Mismatches: 22, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
85 14 0.08
86 49 0.26
87 122 0.66
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (87 bp):
AGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
CGATCTGCTTCGCTGTTAACGC
Found at i:43068710 original size:22 final size:22
Alignment explanation
Indices: 43068682--43068803 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
43068672 TTCCACATCC
43068682 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
43068704 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
43068728 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
43068751 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
43068775 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
43068798 ATCACA
1 ATCACA
43068804 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:43068717 original size:47 final size:47
Alignment explanation
Indices: 43068654--43069105 Score: 651
Period size: 47 Copynumber: 9.6 Consensus size: 47
43068644 CCCTTCGGGA
* * *
43068654 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
43068701 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43068748 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
43068795 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
43068842 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
43068889 CTTACCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
43068936 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43068983 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
43069032 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
43069079 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
43069106 TATTCAAATA
Statistics
Matches: 377, Mismatches: 24, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
46 1 0.00
47 328 0.87
48 1 0.00
49 47 0.12
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:43070469 original size:85 final size:85
Alignment explanation
Indices: 43070361--43070528 Score: 327
Period size: 85 Copynumber: 2.0 Consensus size: 85
43070351 CTAACACTAA
*
43070361 TATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCCATAACA
1 TATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCAATAACA
43070426 TCTTGTCCACCCATGCTCTT
66 TCTTGTCCACCCATGCTCTT
43070446 TATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCAATAACA
1 TATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCAATAACA
43070511 TCTTGTCCACCCATGCTC
66 TCTTGTCCACCCATGCTC
43070529 ATGGCCGGCC
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (85 bp):
TATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTTAGCAATAACA
TCTTGTCCACCCATGCTCTT
Found at i:43087150 original size:11 final size:10
Alignment explanation
Indices: 43087132--43087194 Score: 63
Period size: 11 Copynumber: 5.8 Consensus size: 10
43087122 ACAAATCGAA
43087132 ACACCACCAT
1 ACACCACCAT
43087142 ACAACCACCAT
1 AC-ACCACCAT
*
43087153 ATCACCACCAC
1 A-CACCACCAT
43087164 ACCACCACCAT
1 A-CACCACCAT
*
43087175 AGCACCACCGT
1 A-CACCACCAT
43087186 ATCACCACC
1 A-CACCACC
43087195 CTTGTAACAC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
10 2 0.04
11 42 0.93
12 1 0.02
ACGTcount: A:0.37, C:0.51, G:0.03, T:0.10
Consensus pattern (10 bp):
ACACCACCAT
Found at i:43087194 original size:22 final size:22
Alignment explanation
Indices: 43087133--43087183 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
43087123 CAAATCGAAA
* * *
43087133 CACCACCATACAACCACCATAT
1 CACCACCACACCACCACCATAG
43087155 CACCACCACACCACCACCATAG
1 CACCACCACACCACCACCATAG
43087177 CACCACC
1 CACCACC
43087184 GTATCACCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.37, C:0.53, G:0.02, T:0.08
Consensus pattern (22 bp):
CACCACCACACCACCACCATAG
Found at i:43098560 original size:33 final size:33
Alignment explanation
Indices: 43098518--43098640 Score: 111
Period size: 33 Copynumber: 3.4 Consensus size: 33
43098508 CGGTAGATTT
*
43098518 AGCACTTAGCAACCACCAGTGATTCGGGGAATC
1 AGCACTTAGCAACCACCAATGATTCGGGGAATC
** *
43098551 AGCACTTAGCAACCCCTTTCACATTCAAAAATACGGTGGAATC
1 AGCACTTAGCAA---C---CAC---CAATGATTCGG-GGAATC
43098594 AGCACTTAGCAACCACCAATGATTCGGGGAATC
1 AGCACTTAGCAACCACCAATGATTCGGGGAATC
*
43098627 AACACTTAGCAACC
1 AGCACTTAGCAACC
43098641 CCTTGGGGGA
Statistics
Matches: 72, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
33 31 0.43
34 8 0.11
36 1 0.01
37 3 0.04
39 3 0.04
40 1 0.01
42 7 0.10
43 18 0.25
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (33 bp):
AGCACTTAGCAACCACCAATGATTCGGGGAATC
Found at i:43098771 original size:51 final size:51
Alignment explanation
Indices: 43098695--43098924 Score: 243
Period size: 51 Copynumber: 4.5 Consensus size: 51
43098685 TACCGGTTCA
*
43098695 CATAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCTGGTACG
1 CATAGTAGCCTGCACATAGTACTACACATGTGATCGAAGCTATCTGGTACG
* * * * * * **
43098746 CATAGTAGCCTGTAGATAGTACTACACATGTGA-CCATCA-TTATCCGATATA
1 CATAGTAGCCTGCACATAGTACTACACATGTGATCGA--AGCTATCTGGTACG
*
43098797 CGTAGTAGCCTGCACATAGTACTACACATGTGATCGAAGCTATCTGGTACG
1 CATAGTAGCCTGCACATAGTACTACACATGTGATCGAAGCTATCTGGTACG
* ** ** * *
43098848 CATAGTAGCTTGCACATAGTACTACACATGCCA-CCTATC-ATTCTGGTACA
1 CATAGTAGCCTGCACATAGTACTACACATGTGATCGAAGCTA-TCTGGTACG
*
43098898 CGTAGTAGCCTGCACATAGTACTACAC
1 CATAGTAGCCTGCACATAGTACTACAC
43098925 GCGTGACCAT
Statistics
Matches: 146, Mismatches: 28, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
49 1 0.01
50 39 0.27
51 103 0.71
52 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (51 bp):
CATAGTAGCCTGCACATAGTACTACACATGTGATCGAAGCTATCTGGTACG
Found at i:43098873 original size:102 final size:101
Alignment explanation
Indices: 43098697--43098930 Score: 353
Period size: 102 Copynumber: 2.3 Consensus size: 101
43098687 CCGGTTCACA
* *
43098697 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCTGGTACGCATAGTAGCCTGTAGA
1 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCTGGTACGCATAGTAGCCTGCACA
** *
43098762 TAGTACTACACATGTGACC-ATCATTATCCGATATACG
66 TAGTACTACACATGCCACCTATCA-T-TCCGATACACG
* *
43098799 TAGTAGCCTGCACATAGTACTACACATGTGATCGAAGCTATCTGGTACGCATAGTAGCTTGCACA
1 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCTGGTACGCATAGTAGCCTGCACA
* *
43098864 TAGTACTACACATGCCACCTATCATTCTGGTACACG
66 TAGTACTACACATGCCACCTATCATTCCGATACACG
*
43098900 TAGTAGCCTGCACATAGTACTACACGCGTGA
1 TAGTAGCCTGCACATAGTACTACACACGTGA
43098931 CCATCACTTT
Statistics
Matches: 120, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
101 37 0.31
102 79 0.66
103 4 0.03
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (101 bp):
TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCTGGTACGCATAGTAGCCTGCACA
TAGTACTACACATGCCACCTATCATTCCGATACACG
Found at i:43099214 original size:30 final size:30
Alignment explanation
Indices: 43099164--43099222 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
43099154 AAAATCACAC
43099164 TTTGAAAAATTTACATTTTTGCCCCTAGAG
1 TTTGAAAAATTTACATTTTTGCCCCTAGAG
43099194 TTTGACAAAA-TTACGA-TTTTGCCCCTAGA
1 TTTGA-AAAATTTAC-ATTTTTGCCCCTAGA
43099223 CTCGTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (30 bp):
TTTGAAAAATTTACATTTTTGCCCCTAGAG
Found at i:43100610 original size:45 final size:45
Alignment explanation
Indices: 43100555--43100650 Score: 174
Period size: 45 Copynumber: 2.1 Consensus size: 45
43100545 CCATAAAATT
*
43100555 TTCATAATTTTTGGTTTAGCCAATAAGTACAATTTATTCTTTAAA
1 TTCATCATTTTTGGTTTAGCCAATAAGTACAATTTATTCTTTAAA
*
43100600 TTCATCATTTTTGGTTTAGCCAATAAGTACAGTTTATTCTTTAAA
1 TTCATCATTTTTGGTTTAGCCAATAAGTACAATTTATTCTTTAAA
43100645 TTCATC
1 TTCATC
43100651 CCTATTCTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (45 bp):
TTCATCATTTTTGGTTTAGCCAATAAGTACAATTTATTCTTTAAA
Found at i:43100762 original size:15 final size:15
Alignment explanation
Indices: 43100742--43100774 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
43100732 ATTTGTTTCT
*
43100742 ATTGAAAATAGACTC
1 ATTGAAAATAGAATC
43100757 ATTGAAAATAGAATC
1 ATTGAAAATAGAATC
43100772 ATT
1 ATT
43100775 AAGGATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.30
Consensus pattern (15 bp):
ATTGAAAATAGAATC
Found at i:43105098 original size:61 final size:61
Alignment explanation
Indices: 43105002--43105230 Score: 269
Period size: 61 Copynumber: 3.8 Consensus size: 61
43104992 TTGACAGAAA
* * * *
43105002 TCACCACAAAGGCTTACCTTTCAAGAGTTTTGCCACAAAGGCTATCCTTTACATCCAGTAC
1 TCACCACAAAGGCTTTCCTGTCAAGAGTTTTGCCACAAAGGTTATCCTTTACATCTAGTAC
* * * * * *
43105063 TCTCTACAATGGCTTTCCTGTCCAGAGTTTAGCCACAAAGGTTGTCCTTTACATCTAGTAC
1 TCACCACAAAGGCTTTCCTGTCAAGAGTTTTGCCACAAAGGTTATCCTTTACATCTAGTAC
* * * * * ** *
43105124 TCACCACAAAGGCTTTTCTGTCCAGAGTGTTGCCACAAATGTTGTATTTTATATCTAGTAC
1 TCACCACAAAGGCTTTCCTGTCAAGAGTTTTGCCACAAAGGTTATCCTTTACATCTAGTAC
* * *
43105185 TCGCCACAAAGGCTTTCCTATCAAAAGTTTTGCCACAAAGGTTATC
1 TCACCACAAAGGCTTTCCTGTCAAGAGTTTTGCCACAAAGGTTATC
43105231 TTTCTCCTAG
Statistics
Matches: 139, Mismatches: 29, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 139 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (61 bp):
TCACCACAAAGGCTTTCCTGTCAAGAGTTTTGCCACAAAGGTTATCCTTTACATCTAGTAC
Found at i:43105484 original size:18 final size:19
Alignment explanation
Indices: 43105449--43105484 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
43105439 TGGGACATTG
*
43105449 ATTTTGGATTTTACTTTGT
1 ATTTTGGATTTGACTTTGT
43105468 ATTTTGG-TTTGACTTTG
1 ATTTTGGATTTGACTTTG
43105485 CATGATTGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.14, C:0.06, G:0.19, T:0.61
Consensus pattern (19 bp):
ATTTTGGATTTGACTTTGT
Found at i:43106371 original size:20 final size:20
Alignment explanation
Indices: 43106300--43106372 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
43106290 CCAATTTGGG
* * *
43106300 GACAAGCCACCAGTATTGCA
1 GACAAGCTACCAGTAATGTA
* * * *
43106320 GATAAACTGCCAGTAATGTG
1 GACAAGCTACCAGTAATGTA
43106340 GACAAG-TCACCAGTAATGTA
1 GACAAGCT-ACCAGTAATGTA
43106360 GACAAGCTACCAG
1 GACAAGCTACCAG
43106373 ATTTGTGGAC
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 1 0.03
20 38 0.95
21 1 0.03
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (20 bp):
GACAAGCTACCAGTAATGTA
Found at i:43106415 original size:28 final size:29
Alignment explanation
Indices: 43106359--43106416 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
43106349 CCAGTAATGT
43106359 AGACAAGCTACCAGATTTGTGGACAAGCC
1 AGACAAGCTACCAGATTTGTGGACAAGCC
* * *
43106388 AGACAAGTTGCCAGA-TTGTGGAGAAGCC
1 AGACAAGCTACCAGATTTGTGGACAAGCC
43106416 A
1 A
43106417 CCAATAATGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (29 bp):
AGACAAGCTACCAGATTTGTGGACAAGCC
Found at i:43106447 original size:68 final size:69
Alignment explanation
Indices: 43106327--43106456 Score: 163
Period size: 68 Copynumber: 1.9 Consensus size: 69
43106317 GCAGATAAAC
* * * * *
43106327 TGCCAGTAATGTGGACAAGTCACCAGTAATGTAGACAAGCTACCAGATTTGTGGACAAGCCAGAC
1 TGCCAGTAATGTGGACAAGCCACCAATAATGCAAACAAGCTACCAGAATTGTGGACAAGCCAGAC
43106392 AAGT
66 AAGT
* * * * *
43106396 TGCCAG-ATTGTGGAGAAGCCACCAATAATGCAAACAAGCTGCTAGAATTGTGGACTAGCCA
1 TGCCAGTAATGTGGACAAGCCACCAATAATGCAAACAAGCTACCAGAATTGTGGACAAGCCA
43106457 TTAGTAATGT
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
68 45 0.88
69 6 0.12
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.20
Consensus pattern (69 bp):
TGCCAGTAATGTGGACAAGCCACCAATAATGCAAACAAGCTACCAGAATTGTGGACAAGCCAGAC
AAGT
Found at i:43108802 original size:22 final size:22
Alignment explanation
Indices: 43108771--43108813 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
43108761 TACACCAAAA
*
43108771 TAGGCTTTTAGCGGCATTTTTT
1 TAGGCCTTTAGCGGCATTTTTT
*
43108793 TAGGCCTTTAGCGGCGTTTTT
1 TAGGCCTTTAGCGGCATTTTT
43108814 AAGCGCCACT
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:0.12, C:0.16, G:0.26, T:0.47
Consensus pattern (22 bp):
TAGGCCTTTAGCGGCATTTTTT
Found at i:43108947 original size:43 final size:43
Alignment explanation
Indices: 43108899--43109112 Score: 268
Period size: 43 Copynumber: 5.0 Consensus size: 43
43108889 AAAAATGCCA
*
43108899 CTAAAGATCATGGCCTTTAGCAGCGCTTTTATCACAAACGCCG
1 CTAAAGATCATGACCTTTAGCAGCGCTTTTATCACAAACGCCG
* * * *
43108942 CTAAAGATCATGACCTTTAGCGGCGCTTTTACCACAAGCGCCA
1 CTAAAGATCATGACCTTTAGCAGCGCTTTTATCACAAACGCCG
* * *
43108985 CTAAAGATCACGACCTTTAGCGGCTCTTTTATCACAAACGCCG
1 CTAAAGATCATGACCTTTAGCAGCGCTTTTATCACAAACGCCG
* * * * * *
43109028 CTAAAGGTCATGATCTTCAGCAACGCTTTTGTCACAAACGCTG
1 CTAAAGATCATGACCTTTAGCAGCGCTTTTATCACAAACGCCG
*
43109071 CTAAAGAACATGACCTTTAGC-GACGCTTTTTATCACAAACGC
1 CTAAAGATCATGACCTTTAGCAG-CGC-TTTTATCACAAACGC
43109113 TAGTGACGCT
Statistics
Matches: 144, Mismatches: 25, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
43 130 0.90
44 14 0.10
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (43 bp):
CTAAAGATCATGACCTTTAGCAGCGCTTTTATCACAAACGCCG
Found at i:43113560 original size:41 final size:41
Alignment explanation
Indices: 43113508--43113787 Score: 280
Period size: 41 Copynumber: 6.8 Consensus size: 41
43113498 GCCACTATTT
*
43113508 CCCTGAGCATTAGCGGCGCTTTTCAAAAAACGCCGCTAAAGA
1 CCCTAAGCATTAGCGGCGCTTTTCAAAAAACGCCGCTAAA-A
* **
43113550 CCC-AATCATTAGCAACGC-TTTCTAAAAAACGCCGCTAAAA
1 CCCTAAGCATTAGCGGCGCTTTTC-AAAAAACGCCGCTAAAA
* * * * * * *
43113590 CCATGAGTATTAGCGGAGCTTCTCCAAAAACACCGCTAAAGA
1 CCCTAAGCATTAGCGGCGCTTTTCAAAAAACGCCGCTAAA-A
* * * * *
43113632 CCC-GATCATTAGCGACGCTTTTTAAAAAACACCGCTAAAA
1 CCCTAAGCATTAGCGGCGCTTTTCAAAAAACGCCGCTAAAA
* * *
43113672 CCCTAAGCATTAGCGGCGCCTATTC-AAAAACACCGCTAAAT
1 CCCTAAGCATTAGCGGCG-CTTTTCAAAAAACGCCGCTAAAA
* *
43113713 CCCTAAGCATTAGCGGTGCTTTACAAAAAACGCCGCTAAAA
1 CCCTAAGCATTAGCGGCGCTTTTCAAAAAACGCCGCTAAAA
* * *
43113754 CCCTGAGCATTAGCGGTGCTTTTTAAAAAACGCC
1 CCCTAAGCATTAGCGGCGCTTTTCAAAAAACGCC
43113788 ACTGAAGCCC
Statistics
Matches: 195, Mismatches: 36, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
40 15 0.08
41 167 0.86
42 13 0.07
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (41 bp):
CCCTAAGCATTAGCGGCGCTTTTCAAAAAACGCCGCTAAAA
Found at i:43113603 original size:82 final size:82
Alignment explanation
Indices: 43113508--43113784 Score: 344
Period size: 82 Copynumber: 3.4 Consensus size: 82
43113498 GCCACTATTT
* *
43113508 CCCTGAGCATTAGCGGCGCTTTTCAAAAAACGCCGCTAAAGACCCAATCATTAGCAACGCTTTCT
1 CCCTGAGCATTAGCGGCGCTTTTCAAAAAACACCGCTAAAGACCCAATCATTAGCGACGCTTTCT
43113573 AAAAAACGCCGCTAAAA
66 AAAAAACGCCGCTAAAA
* * * * * * *
43113590 CCATGAGTATTAGCGGAGCTTCTCCAAAAACACCGCTAAAGACCCGATCATTAGCGACGCTTTTT
1 CCCTGAGCATTAGCGGCGCTTTTCAAAAAACACCGCTAAAGACCCAATCATTAGCGACGCTTTCT
*
43113655 AAAAAACACCGCTAAAA
66 AAAAAACGCCGCTAAAA
* * * * **
43113672 CCCTAAGCATTAGCGGCGCCTATTC-AAAAACACCGCTAAA-TCCCTAAGCATTAGCGGTGCTTT
1 CCCTGAGCATTAGCGGCG-CTTTTCAAAAAACACCGCTAAAGACCC-AATCATTAGCGACGCTTT
43113735 AC-AAAAAACGCCGCTAAAA
64 -CTAAAAAACGCCGCTAAAA
* *
43113754 CCCTGAGCATTAGCGGTGCTTTTTAAAAAAC
1 CCCTGAGCATTAGCGGCGCTTTTCAAAAAAC
43113785 GCCACTGAAG
Statistics
Matches: 164, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
81 7 0.04
82 153 0.93
83 4 0.02
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (82 bp):
CCCTGAGCATTAGCGGCGCTTTTCAAAAAACACCGCTAAAGACCCAATCATTAGCGACGCTTTCT
AAAAAACGCCGCTAAAA
Found at i:43113683 original size:123 final size:123
Alignment explanation
Indices: 43113508--43113784 Score: 330
Period size: 123 Copynumber: 2.3 Consensus size: 123
43113498 GCCACTATTT
* * *
43113508 CCCTGAGCATTAGCGGCGCTTTTCAAAAAACGCCGCTAAAGACCCAATCATTAGCAACG-CT-TT
1 CCCTGAGCATTAGCGGCGCTTTTTAAAAAACACCGCTAAAGACCCAAGCATTAGCAACGCCTATT
* * * *
43113571 CTAAAAAACGCCGCTAAAACCATGAGTATTAGCGGAGCTTCT-CCAAAAACACCGCTAAAGA
66 C--AAAAACACCGCTAAAACCATAAGCATTAGCGGAGCTT-TACAAAAAACACCGCTAAA-A
* * **
43113632 CCC-GATCATTAGCGACGCTTTTTAAAAAACACCGCTAAA-ACCCTAAGCATTAGCGGCGCCTAT
1 CCCTGAGCATTAGCGGCGCTTTTTAAAAAACACCGCTAAAGACCC-AAGCATTAGCAACGCCTAT
* * * *
43113695 TCAAAAACACCGCTAAATCCCTAAGCATTAGCGGTGCTTTACAAAAAACGCCGCTAAAA
65 TCAAAAACACCGCTAAAACCATAAGCATTAGCGGAGCTTTACAAAAAACACCGCTAAAA
*
43113754 CCCTGAGCATTAGCGGTGCTTTTTAAAAAAC
1 CCCTGAGCATTAGCGGCGCTTTTTAAAAAAC
43113785 GCCACTGAAG
Statistics
Matches: 130, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
122 9 0.07
123 113 0.87
124 5 0.04
125 3 0.02
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (123 bp):
CCCTGAGCATTAGCGGCGCTTTTTAAAAAACACCGCTAAAGACCCAAGCATTAGCAACGCCTATT
CAAAAACACCGCTAAAACCATAAGCATTAGCGGAGCTTTACAAAAAACACCGCTAAAA
Found at i:43116851 original size:28 final size:28
Alignment explanation
Indices: 43116743--43116857 Score: 140
Period size: 30 Copynumber: 4.0 Consensus size: 28
43116733 ATACAATATG
* * * *
43116743 CAGTAACAGTCTGGGCCTGAGCCCTATT
1 CAGTAACAGTGTGGGCCTTAGCCCAATA
*
43116771 CAGTAGTACAGTGTGGGCCTTAGCCCATTA
1 CAGTA--ACAGTGTGGGCCTTAGCCCAATA
*
43116801 TAGTAACAGTGTGTGGGCCTTAGCCCAATA
1 CAGTAACA--GTGTGGGCCTTAGCCCAATA
43116831 CAGTAACAGTGTGGGCCTTAGCCCAAT
1 CAGTAACAGTGTGGGCCTTAGCCCAAT
43116858 GCAGCAATGC
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
28 27 0.36
30 48 0.64
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.25
Consensus pattern (28 bp):
CAGTAACAGTGTGGGCCTTAGCCCAATA
Found at i:43116985 original size:26 final size:26
Alignment explanation
Indices: 43116956--43117035 Score: 90
Period size: 26 Copynumber: 3.1 Consensus size: 26
43116946 ACACACCAAT
*
43116956 ATCGCAGCAAAGTTGCCAGTAATAGC
1 ATCGCAGCAAAGCTGCCAGTAATAGC
* * *
43116982 ATCGCAGTAGAGCTGCCAGT-ATCAGT
1 ATCGCAGCAAAGCTGCCAGTAAT-AGC
* *
43117008 ATCGCAGCAAAGCTACCAGTAACAGC
1 ATCGCAGCAAAGCTGCCAGTAATAGC
43117034 AT
1 AT
43117036 ATGTTGCAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
25 2 0.05
26 40 0.93
27 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.19
Consensus pattern (26 bp):
ATCGCAGCAAAGCTGCCAGTAATAGC
Found at i:43117643 original size:27 final size:27
Alignment explanation
Indices: 43117272--43117654 Score: 399
Period size: 27 Copynumber: 14.1 Consensus size: 27
43117262 TATAACAGTT
43117272 ATTTTACCCTATGGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * * *
43117299 ATTTTACCTTATAGAGGTATTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * * *
43117326 ATTCTACCCTGTGGGGGTATTTAGGCC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* **
43117353 ATTTTACCCTATGAGGGTATTTTAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * ***
43117380 ATTCTACCCTATGAGGGTATTTTAATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
43117407 ATTTTACCCTATAGGGGGTATTTCGGTC
1 ATTTTACCCTAT-GGGGGTATTTCGGTC
* *
43117435 ATTCTACCCTATGGGGGTATTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
43117462 ATTTTACCCTATAGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* ** *
43117489 ATTTTACCCTATGGGGCTATTTCAATT
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
43117516 ATTTTACCCTATGGGGATATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
43117543 ATTTTACCCTATAGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *** *
43117570 ATTCTACCTTATAAAGGTATTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
43117597 ATTTTACCCTGTGGGAGTAATTT-GGTC
1 ATTTTACCCTATGGGGGT-ATTTCGGTC
* * *
43117624 ATTTTACCCTGTGGGGGTAATTCGGCC
1 ATTTTACCCTATGGGGGTATTTCGGTC
43117651 ATTT
1 ATTT
43117655 ATTGACCTCT
Statistics
Matches: 296, Mismatches: 57, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
26 3 0.01
27 267 0.90
28 26 0.09
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGGTC
Found at i:43118334 original size:21 final size:21
Alignment explanation
Indices: 43118292--43118334 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
43118282 CAACAACAAC
*
43118292 CTCCCCAAATCCTAATATTCT
1 CTCCCCAAATCCTAATACTCT
*
43118313 CTCCTCAAATCTCTAAT-CTCT
1 CTCCCCAAATC-CTAATACTCT
43118334 C
1 C
43118335 CAAATATCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.26, C:0.40, G:0.00, T:0.35
Consensus pattern (21 bp):
CTCCCCAAATCCTAATACTCT
Found at i:43120874 original size:27 final size:27
Alignment explanation
Indices: 43120675--43120872 Score: 227
Period size: 27 Copynumber: 7.3 Consensus size: 27
43120665 GTAATGGGCA
43120675 TAAAATGACCGAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * * *
43120702 TAAAATGACTGAAATGCCTTTGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* **
43120729 TAAAATAAGGGAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
*
43120756 TAAAATGACCGAAATACCC-CTAAAGGG
1 TAAAATGACCGAAATACCCTC-GAAGGG
* * *
43120783 TAAAATTACCAAAATACCCTCGAAGAG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * *
43120810 TAAACTGACCAAAATACCCTCGAAAGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * *
43120837 TAAAATGACTGAAATACCCTTGATGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
43120864 TAAAATGAC
1 TAAAATGAC
43120873 TGTTATACCC
Statistics
Matches: 141, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
26 1 0.01
27 139 0.99
28 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.19
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCTCGAAGGG
Found at i:43121273 original size:28 final size:28
Alignment explanation
Indices: 43121229--43121290 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
43121219 ACTGCATTGT
*
43121229 ACTGTTACTGTATTGGGCTAAGGCCCAC
1 ACTGTTACTGTACTGGGCTAAGGCCCAC
*
43121257 ACTGTTACTGTACTGGGCTAATGCCCAC
1 ACTGTTACTGTACTGGGCTAAGGCCCAC
43121285 ACTGTT
1 ACTGTT
43121291 GCTATATAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.31
Consensus pattern (28 bp):
ACTGTTACTGTACTGGGCTAAGGCCCAC
Found at i:43121302 original size:28 final size:27
Alignment explanation
Indices: 43121229--43121308 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 27
43121219 ACTGCATTGT
43121229 ACTGTTACTGTATTGGGCTAAGGCCCAC
1 ACTGTTACTGTA-TGGGCTAAGGCCCAC
*
43121257 ACTGTTACTGTACTGGGCTAATGCCCAC
1 ACTGTTACTGTA-TGGGCTAAGGCCCAC
* * *
43121285 ACTGTTGCTATATAGGGCTCAGGC
1 ACTGTTACTGTAT-GGGCTAAGGC
43121309 TTAGACTGCT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 44 0.98
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (27 bp):
ACTGTTACTGTATGGGCTAAGGCCCAC
Found at i:43127562 original size:34 final size:35
Alignment explanation
Indices: 43127503--43127585 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 35
43127493 TAGCCTTTGG
* * *
43127503 TTCTTTCCTCTTTTCTTTGTGGCCGAATATTGCCT
1 TTCTTTCCTCTTCTCTCTGTGGCCGAATACTGCCT
* *
43127538 TTCTTTCTTCTTCTCTCT-TGGCCGAATACTGTCT
1 TTCTTTCCTCTTCTCTCTGTGGCCGAATACTGCCT
*
43127572 TTCTCTCCCTCTTC
1 TTCT-TTCCTCTTC
43127586 ATCTATTCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 18 0.45
35 22 0.55
ACGTcount: A:0.07, C:0.31, G:0.11, T:0.51
Consensus pattern (35 bp):
TTCTTTCCTCTTCTCTCTGTGGCCGAATACTGCCT
Found at i:43128250 original size:27 final size:27
Alignment explanation
Indices: 43128209--43128444 Score: 228
Period size: 27 Copynumber: 8.7 Consensus size: 27
43128199 GTAATGGGCC
** **
43128209 TAAAATGACCAAAATACCCTTGAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
* *
43128236 TAAAATGACTGAAATACCCTCAAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
43128263 TAAAATGACTGAAATACCCCCGAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
* * *
43128290 TAAAATGACTAAAATGCCCCAGAAAGGG
1 TAAAATGACTGAAATACCCCCG-AAGGG
* *
43128318 TAAAATGA-TCGAAATACCCCCAAAGGA
1 TAAAATGACT-GAAATACCCCCGAAGGG
* * *
43128345 TAAAATTACTAAAATACCCTCGAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
* *
43128372 TAAACTGA-TCG-AATACCCTCGAAGGG
1 TAAAATGACT-GAAATACCCCCGAAGGG
* *
43128398 TAAAATGA-TCAAAATACCCCCGAAGAG
1 TAAAATGACT-GAAATACCCCCGAAGGG
**
43128425 TAAAATGACTGTTATACCCC
1 TAAAATGACTGAAATACCCC
43128445 TAGGAGTTGA
Statistics
Matches: 174, Mismatches: 29, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
26 25 0.14
27 126 0.72
28 23 0.13
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCCCGAAGGG
Found at i:43128349 original size:82 final size:80
Alignment explanation
Indices: 43128209--43128444 Score: 262
Period size: 82 Copynumber: 2.9 Consensus size: 80
43128199 GTAATGGGCC
* * * *
43128209 TAAAATGACCAAAATACCCTTGAAGGGTAAAATGA-CTGAAATACCCTCAAAGGGTAAAATGACT
1 TAAAATGACTAAAATACCC-CGAAGGGTAAAATGATC-GAAATACCCCCAAAGGATAAAATGACT
43128273 GAAATACCCCCGAAGGG
64 GAAATACCCCCGAAGGG
* *
43128290 TAAAATGACTAAAATGCCCCAGAAAGGGTAAAATGATCGAAATACCCCCAAAGGATAAAATTACT
1 TAAAATGACTAAAATACCCC-G-AAGGGTAAAATGATCGAAATACCCCCAAAGGATAAAATGACT
* *
43128355 AAAATACCCTCGAAGGG
64 GAAATACCCCCGAAGGG
* ** * *
43128372 TAAACTGA-TCGAATACCCTCGAAGGGTAAAATGATCAAAATACCCCCGAA-GAGTAAAATGACT
1 TAAAATGACTAAAATACCC-CGAAGGGTAAAATGATCGAAATACCCCCAAAGGA-TAAAATGACT
**
43128435 GTTATACCCC
64 GAAATACCCC
43128445 TAGGAGTTGA
Statistics
Matches: 131, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
79 2 0.02
80 42 0.32
81 26 0.20
82 60 0.46
83 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (80 bp):
TAAAATGACTAAAATACCCCGAAGGGTAAAATGATCGAAATACCCCCAAAGGATAAAATGACTGA
AATACCCCCGAAGGG
Found at i:43128649 original size:26 final size:26
Alignment explanation
Indices: 43128620--43128682 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
43128610 GATACTGGCT
*
43128620 GCTTTGCTGCGTTACTGTTACTAGTA
1 GCTTTGCTGCGTTACTATTACTAGTA
** * * *
43128646 GCTTAACTGCATTACTATTATTGGTA
1 GCTTTGCTGCGTTACTATTACTAGTA
*
43128672 ACTTTGCTGCG
1 GCTTTGCTGCG
43128683 ATATTGCTGT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (26 bp):
GCTTTGCTGCGTTACTATTACTAGTA
Found at i:43141970 original size:9 final size:9
Alignment explanation
Indices: 43141956--43141981 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
43141946 CCGTACACCT
43141956 GCAACAAAC
1 GCAACAAAC
43141965 GCAACAAAC
1 GCAACAAAC
43141974 GCAACAAA
1 GCAACAAA
43141982 GGCAGCAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.31, G:0.12, T:0.00
Consensus pattern (9 bp):
GCAACAAAC
Found at i:43156707 original size:25 final size:25
Alignment explanation
Indices: 43156679--43156727 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
43156669 ACCAATGAAC
*
43156679 CGGGGAATCAGCACTTAGCAACCCT
1 CGGGGAATCAGCACATAGCAACCCT
43156704 CGGGGAATCAGCACATAGCAACCC
1 CGGGGAATCAGCACATAGCAACCC
43156728 CCTTTTCACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.33, G:0.24, T:0.12
Consensus pattern (25 bp):
CGGGGAATCAGCACATAGCAACCCT
Found at i:43156787 original size:102 final size:103
Alignment explanation
Indices: 43156542--43156804 Score: 415
Period size: 102 Copynumber: 2.6 Consensus size: 103
43156532 TAACCGTTAT
* **
43156542 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAA-CCCTCGGGGG
43156607 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
*
43156646 TGGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCTC-GGGG
1 TGGTGGATCA-CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCTCGGGGG
43156709 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
65 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
* **
43156749 TGGTGGATCACGCACATAGCACCACC-ATGAATCGGGGAATCAGCACACAGCAACCC
1 TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCC
43156805 CTTTATATAC
Statistics
Matches: 148, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
102 52 0.35
103 46 0.31
104 50 0.34
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (103 bp):
TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:43163632 original size:104 final size:105
Alignment explanation
Indices: 43163452--43163719 Score: 441
Period size: 104 Copynumber: 2.6 Consensus size: 105
43163442 TAACCGTTAT
* **
43163452 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
43163517 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* *
43163556 TGGTGGATATCGCACTTAGCACCACCAATAAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
43163621 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* **
43163661 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
43163720 TTATATACAA
Statistics
Matches: 152, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
104 81 0.53
105 70 0.46
106 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.19
Consensus pattern (105 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:43172343 original size:44 final size:44
Alignment explanation
Indices: 43172274--43172394 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 44
43172264 AAGATGGCGA
* * *
43172274 ATCTCATCTCTCTAAAGTTGCAGTGGAGCAGATTGAAGCTGATA-
1 ATCTCATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAG-TAATAG
* * *
43172318 ATC-CTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAG
1 ATCTC-ATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGTAATAG
* *
43172362 ATCTCATCTCTCTGAAGTTGCAGTAGAGTAGAT
1 ATCTCATCTCTCTGAAGTTGCAGTGGAGCAGAT
43172395 CACATCAGAG
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
43 5 0.08
44 57 0.90
45 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (44 bp):
ATCTCATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGTAATAG
Found at i:43173015 original size:9 final size:9
Alignment explanation
Indices: 43173001--43173026 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
43172991 CCGTACACCT
43173001 GCAACAAAC
1 GCAACAAAC
43173010 GCAACAAAC
1 GCAACAAAC
43173019 GCAACAAA
1 GCAACAAA
43173027 GGCAGCAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.31, G:0.12, T:0.00
Consensus pattern (9 bp):
GCAACAAAC
Found at i:43183408 original size:66 final size:66
Alignment explanation
Indices: 43183302--43183438 Score: 274
Period size: 66 Copynumber: 2.1 Consensus size: 66
43183292 TCTACATTAA
43183302 GATTGCCTCATGATGGTTTGAACACTTCTAAAACCAAAACAGAACCACACAATCAACTAACCGAA
1 GATTGCCTCATGATGGTTTGAACACTTCTAAAACCAAAACAGAACCACACAATCAACTAACCGAA
43183367 T
66 T
43183368 GATTGCCTCATGATGGTTTGAACACTTCTAAAACCAAAACAGAACCACACAATCAACTAACCGAA
1 GATTGCCTCATGATGGTTTGAACACTTCTAAAACCAAAACAGAACCACACAATCAACTAACCGAA
43183433 T
66 T
43183434 GATTG
1 GATTG
43183439 AGTTTTGGTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 71 1.00
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.22
Consensus pattern (66 bp):
GATTGCCTCATGATGGTTTGAACACTTCTAAAACCAAAACAGAACCACACAATCAACTAACCGAA
T
Done.