Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 178 of 185
Found at i:54055145 original size:12 final size:12
Alignment explanation
Indices: 54055128--54055153 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54055118 GAGAACAATC
54055128 TTTTTTAATATA
1 TTTTTTAATATA
54055140 TTTTTTAATATA
1 TTTTTTAATATA
54055152 TT
1 TT
54055154 AATTGATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTTAATATA
Found at i:54055790 original size:27 final size:27
Alignment explanation
Indices: 54055760--54055813 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
54055750 TAGGTAAAAG
*
54055760 ATGAGACCATTGA-TATGGAATTTGTGA
1 ATGAGACCATTGAGT-TGGAATTAGTGA
*
54055787 ATGAGATCATTGAGTTGGAATTAGTGA
1 ATGAGACCATTGAGTTGGAATTAGTGA
54055814 GATAAATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (27 bp):
ATGAGACCATTGAGTTGGAATTAGTGA
Found at i:54057421 original size:17 final size:17
Alignment explanation
Indices: 54057394--54057439 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 17
54057384 AAAGTTAAGG
54057394 GGGGAAATAAAAAGTTTT
1 GGGGAAAT-AAAAGTTTT
54057412 GGGG-AATAAAAG-TTT
1 GGGGAAATAAAAGTTTT
54057427 GAGGGAAAGTAAA
1 G-GGGAAA-TAAA
54057440 TAGGGAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.16
16 8 0.32
17 5 0.20
18 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.33, T:0.22
Consensus pattern (17 bp):
GGGGAAATAAAAGTTTT
Found at i:54057808 original size:9 final size:9
Alignment explanation
Indices: 54057794--54057830 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
54057784 TATAGTTTGA
54057794 TATTCGAAT
1 TATTCGAAT
54057803 TATTCGAAT
1 TATTCGAAT
*
54057812 TATTCGAGT
1 TATTCGAAT
54057821 TATTCGAAT
1 TATTCGAAT
54057830 T
1 T
54057831 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:54059397 original size:48 final size:48
Alignment explanation
Indices: 54059326--54059425 Score: 173
Period size: 48 Copynumber: 2.1 Consensus size: 48
54059316 ATATTTATTT
*
54059326 AATTAGAATAACTGCAACATTAAAACTTGGAACAAACTTTGTAATATA
1 AATTAGAATAACTGCAACATTAAAACTTGGAACAAACATTGTAATATA
* *
54059374 AATTAGATTAATTGCAACATTAAAACTTGGAACAAACATTGTAATATA
1 AATTAGAATAACTGCAACATTAAAACTTGGAACAAACATTGTAATATA
54059422 AATT
1 AATT
54059426 TTGCAATATA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.31
Consensus pattern (48 bp):
AATTAGAATAACTGCAACATTAAAACTTGGAACAAACATTGTAATATA
Found at i:54059458 original size:62 final size:62
Alignment explanation
Indices: 54059363--54059487 Score: 164
Period size: 62 Copynumber: 2.0 Consensus size: 62
54059353 TGGAACAAAC
* * * *
54059363 TTTGTAATATAAATTAGATTAATTGCAACATT-AAAACTTGGAACAAACATTGTAATATAAAT
1 TTTGCAATATAAATTAGAATAATTACAACATTAAAAAC-TAGAACAAACATTGTAATATAAAT
* *
54059425 TTTGCAATATAAATTA-AATACATTACAATATTAAAAACTAGAACAAACTTTGTAATATAAAT
1 TTTGCAATATAAATTAGAATA-ATTACAACATTAAAAACTAGAACAAACATTGTAATATAAAT
54059487 T
1 T
54059488 AGGTACATTG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
61 3 0.05
62 47 0.85
63 5 0.09
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (62 bp):
TTTGCAATATAAATTAGAATAATTACAACATTAAAAACTAGAACAAACATTGTAATATAAAT
Found at i:54062616 original size:30 final size:31
Alignment explanation
Indices: 54062561--54062618 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
54062551 CATCAGATTA
*
54062561 TTTTAACAGTTTTGTTTTTTGTTGTCAGTTT
1 TTTTAACAGTTTTATTTTTTGTTGTCAGTTT
54062592 TTTTAACAGTTTTATTTTTT-TTGTCAG
1 TTTTAACAGTTTTATTTTTTGTTGTCAG
54062619 AACTAGAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.16, C:0.07, G:0.14, T:0.64
Consensus pattern (31 bp):
TTTTAACAGTTTTATTTTTTGTTGTCAGTTT
Found at i:54063972 original size:24 final size:22
Alignment explanation
Indices: 54063949--54063992 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
54063939 TAGTTTATTA
*
54063949 ATATTTTGATTTGATTTTTAATT
1 ATATTTTGAATT-ATTTTTAATT
*
54063972 ATATTTTTAATTATTTTTAAT
1 ATATTTTGAATTATTTTTAAT
54063993 CATTTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (22 bp):
ATATTTTGAATTATTTTTAATT
Found at i:54066134 original size:24 final size:24
Alignment explanation
Indices: 54066098--54066152 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
54066088 TTCCCAATAT
* * *
54066098 ATGGCTATCCGGAGCTTCCCGTTA
1 ATGGCTCTACGGAGCTACCCGTTA
54066122 ATGGCTCTACGGAGCTACCCGTTA
1 ATGGCTCTACGGAGCTACCCGTTA
*
54066146 TTGGCTC
1 ATGGCTC
54066153 GAATGAGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.16, C:0.29, G:0.25, T:0.29
Consensus pattern (24 bp):
ATGGCTCTACGGAGCTACCCGTTA
Found at i:54066160 original size:24 final size:24
Alignment explanation
Indices: 54066108--54066161 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
54066098 ATGGCTATCC
* * *
54066108 GGAGCTTCCCGTTAATGGCTCTAC
1 GGAGCTACCCGTTAATGGCTCGAA
*
54066132 GGAGCTACCCGTTATTGGCTCGAA
1 GGAGCTACCCGTTAATGGCTCGAA
*
54066156 TGAGCT
1 GGAGCT
54066162 TCCTGATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (24 bp):
GGAGCTACCCGTTAATGGCTCGAA
Found at i:54066553 original size:15 final size:17
Alignment explanation
Indices: 54066535--54066571 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
54066525 AAATACATGG
54066535 AAATGA-TGATAT-ATA
1 AAATGATTGATATAATA
54066550 AAAT-ATTGATATAATA
1 AAATGATTGATATAATA
54066566 AAATGA
1 AAATGA
54066572 ACGATATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.05
15 10 0.53
16 7 0.37
17 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (17 bp):
AAATGATTGATATAATA
Found at i:54081939 original size:20 final size:18
Alignment explanation
Indices: 54081910--54081948 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
54081900 TATACACCTA
54081910 TATATATATGTACATATTTT
1 TATATATATG--CATATTTT
*
54081930 TATATTTATGCATATTTT
1 TATATATATGCATATTTT
54081948 T
1 T
54081949 TTCTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (18 bp):
TATATATATGCATATTTT
Found at i:54107238 original size:41 final size:41
Alignment explanation
Indices: 54107147--54107291 Score: 175
Period size: 41 Copynumber: 3.6 Consensus size: 41
54107137 AGGCTAAGCG
* **** *
54107147 CCTAGCAGGCTAAATGCCGGTGA-ATTTTTCAGACTATAAA
1 CCTAGCAGGCTAAGTGCCGGTGATAGGAATCAGGCTATAAA
* * *
54107187 TCTAGCAGGCTAAGTGCCGGTGATCGGAATCAGGTTATAAA
1 CCTAGCAGGCTAAGTGCCGGTGATAGGAATCAGGCTATAAA
* * *
54107228 CCTAGCAGGCTACGTGCCGGTGATATGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATAGGAATCAGGCTATAAA
54107269 CCTAGCAGGCTAAGTGCCGGTGA
1 CCTAGCAGGCTAAGTGCCGGTGA
54107292 ATATGTTAAA
Statistics
Matches: 88, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 21 0.24
41 67 0.76
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGATAGGAATCAGGCTATAAA
Found at i:54113929 original size:41 final size:41
Alignment explanation
Indices: 54113838--54113982 Score: 175
Period size: 41 Copynumber: 3.6 Consensus size: 41
54113828 AGGCTAAGCG
* **** *
54113838 CCTAGCAGGCTAAATGCCGGTGA-ATTTTTCAGACTATAAA
1 CCTAGCAGGCTAAGTGCCGGTGATAGGAATCAGGCTATAAA
* * *
54113878 TCTAGCAGGCTAAGTGCCGGTGATCGGAATCAGGTTATAAA
1 CCTAGCAGGCTAAGTGCCGGTGATAGGAATCAGGCTATAAA
* * *
54113919 CCTAGCAGGCTACGTGCCGGTGATATGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATAGGAATCAGGCTATAAA
54113960 CCTAGCAGGCTAAGTGCCGGTGA
1 CCTAGCAGGCTAAGTGCCGGTGA
54113983 ATATGTTAAA
Statistics
Matches: 88, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 21 0.24
41 67 0.76
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGATAGGAATCAGGCTATAAA
Found at i:54114767 original size:18 final size:18
Alignment explanation
Indices: 54114744--54114781 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
54114734 GGGTTTGTCA
54114744 TCATTATTATCCATATTT
1 TCATTATTATCCATATTT
*
54114762 TCATTATTATCCCTATTT
1 TCATTATTATCCATATTT
54114780 TC
1 TC
54114782 CGCTAGATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (18 bp):
TCATTATTATCCATATTT
Found at i:54116884 original size:103 final size:104
Alignment explanation
Indices: 54116705--54116969 Score: 426
Period size: 103 Copynumber: 2.6 Consensus size: 104
54116695 AACCGTTATT
* * *
54116705 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
54116770 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
54116808 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGG
54116872 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
54116912 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
54116970 TTATGTACAA
Statistics
Matches: 150, Mismatches: 9, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
102 1 0.01
103 83 0.55
104 65 0.43
105 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:54117331 original size:30 final size:29
Alignment explanation
Indices: 54117297--54117361 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
54117287 TAATCCACCA
54117297 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
54117327 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
54117357 CCCAA
1 CCCAA
54117362 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:54117335 original size:31 final size:30
Alignment explanation
Indices: 54117304--54117361 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
54117294 CCACCCAACT
54117304 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
54117334 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
54117362 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:54119686 original size:19 final size:19
Alignment explanation
Indices: 54119659--54119695 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54119649 TGTCAGGGTA
54119659 CACGCCAGCAAATCGCGTC
1 CACGCCAGCAAATCGCGTC
* *
54119678 CACGTCAGCAACTCGCGT
1 CACGCCAGCAAATCGCGT
54119696 TGACATGGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.41, G:0.22, T:0.14
Consensus pattern (19 bp):
CACGCCAGCAAATCGCGTC
Found at i:54119843 original size:12 final size:11
Alignment explanation
Indices: 54119826--54119858 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
54119816 AACAAATCCT
54119826 CTCTCATATTTC
1 CTCTCA-ATTTC
54119838 CTCTCAA-TTC
1 CTCTCAATTTC
54119848 CTCTCAATTTC
1 CTCTCAATTTC
54119859 TTTCCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 4 0.20
12 6 0.30
ACGTcount: A:0.18, C:0.36, G:0.00, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:54119902 original size:29 final size:29
Alignment explanation
Indices: 54119870--54119956 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
54119860 TTCCAAAATT
54119870 CTCTCAAATTCATATTTAATTTCAATTTC
1 CTCTCAAATTCATATTTAATTTCAATTTC
* * * *
54119899 CTCTCAATTTC--CTTCAA----AAATT-
1 CTCTCAAATTCATATTTAATTTCAATTTC
*
54119921 CTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAAATTCATATTTAATTTCAATTTC
54119950 CTCTCAA
1 CTCTCAA
54119957 TTTCCTTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 14
0.65 0.14 0.22
Matches are distributed among these distances:
22 9 0.21
23 4 0.10
24 4 0.10
27 4 0.10
28 4 0.10
29 17 0.40
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (29 bp):
CTCTCAAATTCATATTTAATTTCAATTTC
Found at i:54119909 original size:51 final size:51
Alignment explanation
Indices: 54119841--54119963 Score: 212
Period size: 51 Copynumber: 2.4 Consensus size: 51
54119831 ATATTTCCTC
* * *
54119841 TCAA-TTCCTCTCAATTTCTTTCCAAAATTCTCTCAAATTCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
54119891 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
54119942 TCAATTTCCTCTCAATTTCCTT
1 TCAATTTCCTCTCAATTTCCTT
54119964 TTTTAAAATA
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
50 4 0.06
51 65 0.94
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATT
Found at i:54122772 original size:38 final size:36
Alignment explanation
Indices: 54122699--54122809 Score: 177
Period size: 36 Copynumber: 3.0 Consensus size: 36
54122689 GGTAGCTTTA
*
54122699 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
54122735 GCTATACTTATCTGATCAAGTGAAAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTG--AAAAAGTGATAAGT
* *
54122773 GCTATATTTATCTGATCAAGTGATAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
54122809 G
1 G
54122810 GTAGCTTAGC
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
36 35 0.50
38 35 0.50
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.31
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:54124269 original size:23 final size:23
Alignment explanation
Indices: 54124236--54124297 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
54124226 TAAAAACCCT
*
54124236 AACCTTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
54124259 AATCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
54124282 AACCCTAACCTAATTT
1 AACCCTAACCTAATTT
54124298 TACATAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:54127575 original size:123 final size:122
Alignment explanation
Indices: 54127346--54127687 Score: 474
Period size: 123 Copynumber: 2.8 Consensus size: 122
54127336 CATGCTAATT
*
54127346 TAGCAAAAACGCGTCCACGAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAGAAG
1 TAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCT--AAG
*
54127411 CGATTTTATATTATTTGCTCAGAAACGTC-AAAAAAAATATTTCTTACATGACCTACTG
64 CGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATATTTCTTACATGACCTACTG
* * * * *
54127469 TAGCAAAAACGCG-CTGACGAGGCCGCGATTTTACAAATTCTTCTCAAATAACATCTTGCT-AGC
1 TAGCAAAAACGCGTC-CACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAAGC
* *
54127532 GATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCGTGACCTACTG
65 GATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-AA-TATTTCTTACATGACCTACTG
* * *
54127592 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAACTAGCATCCTACTAGAAG
1 TAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCT--AAG
**
54127657 CGATTTTATACTATTTTATCAGAAACGTCAA
64 CGATTTTATACTATTTGCTCAGAAACGTCAA
54127688 CTCGAAATTA
Statistics
Matches: 192, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
120 30 0.16
121 6 0.03
122 3 0.02
123 121 0.63
124 1 0.01
126 31 0.16
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (122 bp):
TAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAAGCG
ATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATATTTCTTACATGACCTACTG
Found at i:54136461 original size:17 final size:17
Alignment explanation
Indices: 54136436--54136469 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54136426 ATTATTTTAA
*
54136436 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
54136453 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
54136470 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:54136471 original size:15 final size:16
Alignment explanation
Indices: 54136436--54136474 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
54136426 ATTATTTTAA
*
54136436 ATTTTATTAAATCATAT
1 ATTTAATTAAATCA-AT
54136453 ATTTAATTAAATC-AT
1 ATTTAATTAAATCAAT
54136468 ATTTAAT
1 ATTTAAT
54136475 ATTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTAAATCAAT
Found at i:54136478 original size:17 final size:18
Alignment explanation
Indices: 54136440--54136479 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
54136430 TTTTAAATTT
*
54136440 TATTAAATCATATATTTA
1 TATTAAATCATATATTAA
54136458 -ATTAAATCATAT-TTAA
1 TATTAAATCATATATTAA
54136474 TATTAA
1 TATTAA
54136480 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATCATATATTAA
Found at i:54136655 original size:91 final size:91
Alignment explanation
Indices: 54136524--54136731 Score: 362
Period size: 91 Copynumber: 2.3 Consensus size: 91
54136514 TTGATTTTAG
*
54136524 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* *
54136589 ATTTAATATTAATTATTTTAAATTGTA
65 ATTTAATAATAATTATTTTAAATTATA
*
54136616 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
54136681 TTTAATAATAATTATTTTAAATTATA
66 TTTAATAATAATTATTTTAAATTATA
*
54136707 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
54136732 GGTATAATTA
Statistics
Matches: 111, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
91 95 0.86
92 16 0.14
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATAATAATTATTTTAAATTATA
Found at i:54136698 original size:47 final size:47
Alignment explanation
Indices: 54136556--54136699 Score: 147
Period size: 47 Copynumber: 3.1 Consensus size: 47
54136546 ATTATTAAGA
*
54136556 ATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATTAATT
* * * **
54136603 A-TTT-T-AAATTGTATA-AATTCATATAAGA--AAATTTATTATTAAGA
1 ATTTTATGAAATTATATATAATT-AT-TAA-ATTATATTTAATATTAATT
* *
54136647 ATTTTATGAAATTATATATTATTATTAAATTATATTTAATAATAATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATTAATT
54136694 ATTTTA
1 ATTTTA
54136700 AATTATACAA
Statistics
Matches: 75, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
43 3 0.04
44 24 0.32
45 8 0.11
46 8 0.11
47 29 0.39
48 3 0.04
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (47 bp):
ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATTAATT
Found at i:54136902 original size:16 final size:16
Alignment explanation
Indices: 54136881--54136922 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
54136871 TTATTAAATT
*
54136881 ATATATTTTAATTATA
1 ATATATTTTAATAATA
54136897 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
54136912 AT-TATGTTTAA
1 ATATAT-TTTAA
54136923 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:54136907 original size:15 final size:15
Alignment explanation
Indices: 54136872--54136913 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54136862 TTAAGAATTT
*
54136872 TATTAAATTAT-ATA
1 TATTTAATTATAATA
54136886 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
54136900 TATTTAATAATAAT
1 TATTTAATTATAAT
54136914 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:54137157 original size:16 final size:16
Alignment explanation
Indices: 54137136--54137173 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
54137126 TTGATTTGCT
*
54137136 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
54137152 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
54137168 AATACA
1 ATTACA
54137174 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:54137613 original size:15 final size:15
Alignment explanation
Indices: 54137574--54137621 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
54137564 ATGTCAGCAC
54137574 TTTAAATATA--AAGA
1 TTTAAATATACCAA-A
*
54137588 TTAAAATTATACCAAA
1 TTTAAA-TATACCAAA
54137604 TTTAAATATACCAAA
1 TTTAAATATACCAAA
54137619 TTT
1 TTT
54137622 TATGAAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 5 0.17
15 16 0.55
16 6 0.21
17 2 0.07
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (15 bp):
TTTAAATATACCAAA
Found at i:54139102 original size:21 final size:19
Alignment explanation
Indices: 54139078--54139124 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
54139068 GCTAATAAAA
*
54139078 TTTAAAACTTTTTTCTCAAAT
1 TTTAAAACTTTATT-TC-AAT
*
54139099 TTTATAACTTTATTTCAAT
1 TTTAAAACTTTATTTCAAT
54139118 TTTAAAA
1 TTTAAAA
54139125 TAAAAATTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 9 0.39
20 2 0.09
21 12 0.52
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAAAACTTTATTTCAAT
Found at i:54139267 original size:11 final size:11
Alignment explanation
Indices: 54139238--54139267 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
54139228 TGCCTTCTGA
54139238 TTTTTTTTCTT
1 TTTTTTTTCTT
*
54139249 TTTCTTTTCTT
1 TTTTTTTTCTT
54139260 TTTTTTTT
1 TTTTTTTT
54139268 AAAATTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:54140650 original size:19 final size:20
Alignment explanation
Indices: 54140602--54140651 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
54140592 TTTTTTTACT
* *
54140602 TTTTAAATT-TATTATTAAT
1 TTTTAAATTATTTTATTAAA
54140621 TTTTAAA-TATTTTA-TAAA
1 TTTTAAATTATTTTATTAAA
54140639 TTTTAAATTATTT
1 TTTTAAATTATTT
54140652 GTTGACGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTAAATTATTTTATTAAA
Found at i:54147980 original size:21 final size:21
Alignment explanation
Indices: 54147955--54147997 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
54147945 TATAAATTTT
54147955 TATGATTAAAGTTACAAATTA
1 TATGATTAAAGTTACAAATTA
54147976 TATGATTAAAGTTACAAATTA
1 TATGATTAAAGTTACAAATTA
54147997 T
1 T
54147998 TTGCATCGTG
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:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (21 bp):
TATGATTAAAGTTACAAATTA
Found at i:54151165 original size:14 final size:14
Alignment explanation
Indices: 54151146--54151174 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54151136 TTGACTCCTA
54151146 CTACTTTCACCCTG
1 CTACTTTCACCCTG
54151160 CTACTTTCACCCTG
1 CTACTTTCACCCTG
54151174 C
1 C
54151175 AAGGTGCTGT
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:0.14, C:0.45, G:0.07, T:0.34
Consensus pattern (14 bp):
CTACTTTCACCCTG
Found at i:54152400 original size:15 final size:16
Alignment explanation
Indices: 54152372--54152406 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
54152362 CATTTTAGTC
54152372 ATCACTTTTAAAAATA
1 ATCACTTTTAAAAATA
*
54152388 ATCA-TTTTGAAAATA
1 ATCACTTTTAAAAATA
54152403 ATCA
1 ATCA
54152407 AAGTTTGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (16 bp):
ATCACTTTTAAAAATA
Found at i:54179572 original size:31 final size:30
Alignment explanation
Indices: 54179513--54179578 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
54179503 TTTGTTAGTT
* *
54179513 AAATTTGACTATCACCATTTAAAGAGAGTC
1 AAATTTGACAATCACCATTTAAAAAGAGTC
* *
54179543 AAATTTGACAATCAATCTTTTAAAAAGAGTC
1 AAATTTGACAATC-ACCATTTAAAAAGAGTC
*
54179574 GAATT
1 AAATT
54179579 GATGTTGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 12 0.40
31 18 0.60
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (30 bp):
AAATTTGACAATCACCATTTAAAAAGAGTC
Found at i:54181280 original size:29 final size:30
Alignment explanation
Indices: 54181216--54181287 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
54181206 ACAACTGGAC
*
54181216 TTAAATTTTGAAATATAAAAAGTAAAGGGA
1 TTAAATTTTGAAATATAAAAAGTAAAGGAA
* *
54181246 CTAAATTTCTGAAA-ATAAAAA-TAGAGGAA
1 TTAAATTT-TGAAATATAAAAAGTAAAGGAA
54181275 TTAAATTTT-AAAT
1 TTAAATTTTGAAAT
54181288 TTATGAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 3 0.08
28 1 0.03
29 13 0.36
30 14 0.39
31 5 0.14
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (30 bp):
TTAAATTTTGAAATATAAAAAGTAAAGGAA
Found at i:54182454 original size:29 final size:29
Alignment explanation
Indices: 54182396--54182456 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
54182386 TTAACCTTAT
* * *
54182396 TTTATTCTCTTTAATAGTATAAAAACTAA
1 TTTATTCTATTTAATAATATAAAAAATAA
54182425 TTTATTCTATTTAATAATA-AAATAAATAA
1 TTTATTCTATTTAATAATATAAA-AAATAA
54182454 TTT
1 TTT
54182457 GATTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 3 0.11
29 25 0.89
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.48
Consensus pattern (29 bp):
TTTATTCTATTTAATAATATAAAAAATAA
Found at i:54186301 original size:29 final size:31
Alignment explanation
Indices: 54186255--54186312 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
54186245 ATTTGAATTT
*
54186255 TAAAATATAAAAAGTAAATAGACTAAATTAC
1 TAAAATATAAAAAGTAAAAAGACTAAATTAC
54186286 TAAAA-ATAAAAA-TAAAAAGACTAAATT
1 TAAAATATAAAAAGTAAAAAGACTAAATT
54186313 TCACATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 14 0.54
30 7 0.27
31 5 0.19
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (31 bp):
TAAAATATAAAAAGTAAAAAGACTAAATTAC
Found at i:54186933 original size:114 final size:111
Alignment explanation
Indices: 54186700--54186933 Score: 269
Period size: 113 Copynumber: 2.1 Consensus size: 111
54186690 GATTCACAAA
*
54186700 AAGCGCCGCAAAAAAATAAGGCCAACGACGTCGTTTATTGAGTTTTTGGGCCATTAGCGGCGTTT
1 AAGCGCCGCAAAAAAATAAGGCCAACGACGCCGTTTATTGAGTTTTTGGGCCATTAGCGGCGTTT
*
54186765 TTACAAAAGCGCCCTAATGCTCCTGTCTTTAGCGGCGTTTTCTGAG
66 TTACAAAAGCGCCCTAATGATCCTGTCTTTAGCGGCGTTTTCTGAG
* * * * *
54186811 AAGCGCCGCAAAAAACCTAAGGGCAACGACGCCGTTTTCTTTG-TTTTTTGGGCCTTTAGCGGCG
1 AAGCGCCGCAAAAAA-ATAAGGCCAACGACGCCG-TTT-ATTGAGTTTTTGGGCCATTAGCGGCG
* * * * *
54186875 TTTTCT-TAAAAGTGCCGCTAATGAT-TTGTTTTTTAGCGGCGTTTTTCTG-T
63 TTTT-TACAAAAGCGCC-CTAATGATCCTG-TCTTTAGCGGCG-TTTTCTGAG
54186925 AAGCGCCGC
1 AAGCGCCGC
54186934 TAATAGTAAT
Statistics
Matches: 104, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
111 15 0.14
112 15 0.14
113 36 0.35
114 31 0.30
115 7 0.07
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (111 bp):
AAGCGCCGCAAAAAAATAAGGCCAACGACGCCGTTTATTGAGTTTTTGGGCCATTAGCGGCGTTT
TTACAAAAGCGCCCTAATGATCCTGTCTTTAGCGGCGTTTTCTGAG
Found at i:54187296 original size:28 final size:28
Alignment explanation
Indices: 54187256--54187312 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
54187246 AATTTGATAT
54187256 ATAGTTCGACTAAATTAATATATAAATC
1 ATAGTTCGACTAAATTAATATATAAATC
54187284 ATAGTTCGACTAAATTAATATATAAATC
1 ATAGTTCGACTAAATTAATATATAAATC
54187312 A
1 A
54187313 AACAAAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (28 bp):
ATAGTTCGACTAAATTAATATATAAATC
Found at i:54187341 original size:18 final size:21
Alignment explanation
Indices: 54187295--54187343 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 21
54187285 TAGTTCGACT
54187295 AAATTAATATATAAATCAAAC
1 AAATTAATATATAAATCAAAC
* *
54187316 AAAGTAATATA-AAA-C-ACC
1 AAATTAATATATAAATCAAAC
54187334 AAATTAATAT
1 AAATTAATAT
54187344 CGTGATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 11 0.44
19 1 0.04
20 3 0.12
21 10 0.40
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATTAATATATAAATCAAAC
Found at i:54187627 original size:15 final size:16
Alignment explanation
Indices: 54187609--54187639 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
54187599 GCTTTAAGAC
54187609 TTAGGGTT-TAGGGGT
1 TTAGGGTTATAGGGGT
54187624 TTAGGGTTATAGGGGT
1 TTAGGGTTATAGGGGT
54187640 CGTGTTAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.16, C:0.00, G:0.45, T:0.39
Consensus pattern (16 bp):
TTAGGGTTATAGGGGT
Found at i:54187955 original size:21 final size:21
Alignment explanation
Indices: 54187931--54188009 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
54187921 TCGAATGTAA
54187931 GGGTTTGTGGTTTGGAGTTTG
1 GGGTTTGTGGTTTGGAGTTTG
* * *
54187952 GGGTTTGTGTTTTTGAGTTTA
1 GGGTTTGTGGTTTGGAGTTTG
* * *
54187973 GAGTTTAAT-GTTTGGGGTTTG
1 GGGTTT-GTGGTTTGGAGTTTG
* *
54187994 GGGTTAGGGGTTTGGA
1 GGGTTTGTGGTTTGGA
54188010 AATTTAAGGG
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
21 41 0.98
22 1 0.02
ACGTcount: A:0.10, C:0.00, G:0.43, T:0.47
Consensus pattern (21 bp):
GGGTTTGTGGTTTGGAGTTTG
Found at i:54188912 original size:231 final size:230
Alignment explanation
Indices: 54188418--54188934 Score: 777
Period size: 230 Copynumber: 2.2 Consensus size: 230
54188408 AAGTTGTGAA
* *
54188418 GAAAACGGCGCCGTTTTCTTATTACATTTAGTGGCGTTTTATACAAAACGCCGCAACTATGTTTT
1 GAAAACGACGCCGTTTTCTTATTACATTTAGTGGCGTTTTA-ATAAAACGCCGCAACTATGTTTT
* * * ** *
54188483 CTTTGTTACGGGAACGGCGTCGTTTTCCATTGTTATTAGTGGCGTTACACCCAAAACGCCGCAAA
65 CTTTGTTACAGAAACGGCATCGTTTTCCAAGGATATTAGTGGCGTTACACCCAAAACGCCGCAAA
*
54188548 TATATTTTAAAGATTACACGAGTTTGCGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCATT
130 TATATTTTAAAGATTACACGAGTTTGCGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCACT
* *
54188613 TATATATAAACGTCGCAAACTCGAAATGGTGTTACG
195 TATATATAAACGCCGCAAAATCGAAATGGTGTTACG
* * *
54188649 AAAAATGACGCCGTTTTCTTATTACATTTAGTGGCGTTTTAGATAAAACGCCGCAAGTATGTTTT
1 GAAAACGACGCCGTTTTCTTATTACATTTAGTGGCGTTTTA-ATAAAACGCCGCAACTATGTTTT
*
54188714 CTTTGTTACAGAAACGGCATCGTTTT-CAAGGATATTTGTGGCGTTACACCCAAAACGCCGCAAA
65 CTTTGTTACAGAAACGGCATCGTTTTCCAAGGATATTAGTGGCGTTACACCCAAAACGCCGCAAA
* * *
54188778 TATATTTTAAAGATTACAGGAGTTTGCTTTAAACGACTGCGTTTGACCTTATATTTAGTGGCGCT
130 TATATTTTAAAGATTACACGAGTTTGCGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCACT
54188843 TATATATAAACGCCGCAAAATCGAAATGGTGTTACG
195 TATATATAAACGCCGCAAAATCGAAATGGTGTTACG
* *** *
54188879 GAAAACGACGCCGTTTACTTAGTTGGTTTTAGTGGCGCTTTT-ATTAAACGCCGCAA
1 GAAAACGACGCCGTTTTCTTA-TTACATTTAGTGGCG-TTTTAATAAAACGCCGCAA
54188935 ATTTGCATTA
Statistics
Matches: 258, Mismatches: 26, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
230 160 0.62
231 94 0.36
232 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (230 bp):
GAAAACGACGCCGTTTTCTTATTACATTTAGTGGCGTTTTAATAAAACGCCGCAACTATGTTTTC
TTTGTTACAGAAACGGCATCGTTTTCCAAGGATATTAGTGGCGTTACACCCAAAACGCCGCAAAT
ATATTTTAAAGATTACACGAGTTTGCGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCACTT
ATATATAAACGCCGCAAAATCGAAATGGTGTTACG
Found at i:54189286 original size:19 final size:19
Alignment explanation
Indices: 54189264--54189307 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
54189254 CAGACATCTC
*
54189264 CCCCAAATCCCTAAAATTT
1 CCCCAAATCCCTAAAAGTT
* *
54189283 CCCCTAATCCCTAACAGTT
1 CCCCAAATCCCTAAAAGTT
54189302 CCCCAA
1 CCCCAA
54189308 CGTAGTCCAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.43, G:0.02, T:0.23
Consensus pattern (19 bp):
CCCCAAATCCCTAAAAGTT
Found at i:54191381 original size:39 final size:39
Alignment explanation
Indices: 54191324--54192878 Score: 289
Period size: 37 Copynumber: 40.9 Consensus size: 39
54191314 TACAATTTCT
54191324 TAACTTATATAATATTAAGATAACTTATATAATATTACA
1 TAACTTATATAATATTAAGATAACTTATATAATATTACA
* * * * *
54191363 TAACTTATATCATGTTAAGATAA--AAAATCGA-ATTACA
1 TAACTTATATAATATTAAGATAACTTATAT-AATATTACA
* * * *
54191400 TAACTTATATAATATTAATATTACTTTTATAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTATATAATATT-ACA
* ** * * *
54191440 TCAAATT-T-CGA-ATT-ACATAACTTATACAATAATA-A
1 T-AACTTATATAATATTAAGATAACTTATATAATATTACA
* * * * *
54191475 GGTAAAATT-TCT-A-ATT-ACATAACTTATACAATATTAAGA
1 --T-AACTTATATAATATTAAGATAACTTATATAATATT-ACA
* ** *
54191514 TAAAATT-T-CGA-ATT-ACATAACTTATATAATATTACA
1 T-AACTTATATAATATTAAGATAACTTATATAATATTACA
* * **
54191550 TAACTTACGTACAATATTAAGATAAAATT-T-CGA-ATTACA
1 TAACTTA--TATAATATTAAGAT-AACTTATATAATATTACA
* * * *
54191589 TAAGTTATATAATATTAAGATTACTTTTATAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTATATAATATT-ACA
* ** *
54191629 TCAAATT-T-CGA-ATT-ACATAACTTATATAATATTACA
1 T-AACTTATATAATATTAAGATAACTTATATAATATTACA
* * **
54191665 TAACTTACGTACAATATTAAGATAAAATT-T-CGA-ATTACA
1 TAACTTA--TATAATATTAAGAT-AACTTATATAATATTACA
* * * *
54191704 TAAGTTATATAATATTAAGATTACTTTTATAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTATATAATATT-ACA
* ** *
54191744 TCAAATT-T-CGA-ATT-ACATAACTTATATAATATTACA
1 T-AACTTATATAATATTAAGATAACTTATATAATATTACA
* * **
54191780 TAACTTACGTACAATATTAAGATAAAATT-T-CGA-ATTACA
1 TAACTTA--TATAATATTAAGAT-AACTTATATAATATTACA
* * * *
54191819 TAAGTTATATAATATTAAGATTACTTTTATAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTATATAATATT-ACA
* ** *
54191859 TCAAATT-T-CGA-ATT-ACATAACTTATATAATATTACA
1 T-AACTTATATAATATTAAGATAACTTATATAATATTACA
* * **
54191895 TAACTTACGTACAATATTAAGATAAAATT-T-CGA-ATTACA
1 TAACTTA--TATAATATTAAGAT-AACTTATATAATATTACA
* * * *
54191934 TAAGTTATATAATATTAAGATTACTTTTATAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTATATAATATT-ACA
* ** *
54191974 TCAAATT-T-CGA-ATT-ACATAACTTATATAATATTACA
1 T-AACTTATATAATATTAAGATAACTTATATAATATTACA
* * **
54192010 TAACTTACGTACAATATTAAGATAAAATT-T-CGA-ATTACA
1 TAACTTA--TATAATATTAAGAT-AACTTATATAATATTACA
* * * *
54192049 TAAGTTATATAATATTAAGATTACTTTTATAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTATATAATATT-ACA
* ** *
54192089 TCAAATT-T-CGA-ATT-ACATAACTTATATAATATTACA
1 T-AACTTATATAATATTAAGATAACTTATATAATATTACA
* * **
54192125 TAACTTACGTACAATATTAAGATAAAATT-T-CGA-ATTACA
1 TAACTTA--TATAATATTAAGAT-AACTTATATAATATTACA
* * * *
54192164 TAAGTTATATAATATTAAGATTACTTTTATAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTATATAATATT-ACA
* ** *
54192204 TCAAATT-T-CGA-ATT-ACATAACTTATATAATATTACA
1 T-AACTTATATAATATTAAGATAACTTATATAATATTACA
* * **
54192240 TAACTTACGTACAATATTAAGATAAAATT-T-CGA-ATTACA
1 TAACTTA--TATAATATTAAGAT-AACTTATATAATATTACA
* * * *
54192279 TAAGTTATATAATATTAAGATTACTTTTATAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTATATAATATT-ACA
* ** *
54192319 TCAAATT-T-CGA-ATT-ACATAACTTATATAATATTACA
1 T-AACTTATATAATATTAAGATAACTTATATAATATTACA
* * **
54192355 TAACTTACGTACAATATTAAGATAAAATT-T-CGA-ATTACA
1 TAACTTA--TATAATATTAAGAT-AACTTATATAATATTACA
* *
54192394 TAACTTATATAATATT-ACATAACTTATACAATATTA-A
1 TAACTTATATAATATTAAGATAACTTATATAATATTACA
* ** * * * *
54192431 GGTAAGATT-T-CGA-ATT-ACATAACTCATACAATATTAAGA
1 --TAA-CTTATATAATATTAAGATAACTTATATAATATT-ACA
* * *
54192470 TTACTTATATAATATTAAGATAAAATT-TCT-A-ATTACA
1 TAACTTATATAATATTAAGAT-AACTTATATAATATTACA
* * *
54192507 TAACTTACATAA-ATT-ACATAACTTATACAATATTA-A
1 TAACTTATATAATATTAAGATAACTTATATAATATTACA
* ** * * * *
54192543 GGTAAGATT-T-CGA-ATT-ACATAACTCATACAATATTAAGA
1 --TAA-CTTATATAATATTAAGATAACTTATATAATATT-ACA
* * *
54192582 TTACTTATATAATATTAAGATAAAATT-TCT-A-ATTACA
1 TAACTTATATAATATTAAGAT-AACTTATATAATATTACA
* * *
54192619 TAACTTACATAA-ATT-ACATAACTTATACAATATTA-A
1 TAACTTATATAATATTAAGATAACTTATATAATATTACA
* ** * * * *
54192655 GGTAAGATT-T-CGA-ATT-ACATAACTCATACAATATTAAGA
1 --TAA-CTTATATAATATTAAGATAACTTATATAATATT-ACA
* * * *
54192694 TTACTTATATAATATTAAGATTACTTTTATAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTATATAATATT-ACA
* * * * * *
54192734 TCAAATT-T-TGA-ATT-ACATAACTTATATAATTTTCCG
1 T-AACTTATATAATATTAAGATAACTTATATAATATTACA
* * * *
54192770 TAACTTATAT-A-ATT-ACATAACTCATACAATATTAAGA
1 TAACTTATATAATATTAAGATAACTTATATAATATT-ACA
* * *
54192807 TTACTTATATAATATTAAGATAAAATT-TCT-A-ATTACA
1 TAACTTATATAATATTAAGAT-AACTTATATAATATTACA
* * *
54192844 TAACTTACATAA-ATT-ACATAACTTATACAATATTA
1 TAACTTATATAATATTAAGATAACTTATATAATATTA
54192879 AGGTAAGATT
Statistics
Matches: 1101, Mismatches: 263, Indels: 306
0.66 0.16 0.18
Matches are distributed among these distances:
34 12 0.01
35 53 0.05
36 92 0.08
37 469 0.43
38 72 0.07
39 197 0.18
40 98 0.09
41 76 0.07
42 32 0.03
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (39 bp):
TAACTTATATAATATTAAGATAACTTATATAATATTACA
Found at i:54191457 original size:57 final size:56
Alignment explanation
Indices: 54191343--54191470 Score: 168
Period size: 57 Copynumber: 2.3 Consensus size: 56
54191333 TAATATTAAG
* *
54191343 ATAACTTATATAATATTACATAACTTATATCATGTTAAGATAAAAAATCGAATTAC
1 ATAACTTATATAATATTACATAACTTATATAATATTAAGATAAAAAATCGAATTAC
* * **
54191399 ATAACTTATATAATATTA-ATATTACTTTTATAATATTAAGATCAAATTTCGAATTAC
1 ATAACTTATATAATATTACATA--ACTTATATAATATTAAGATAAAAAATCGAATTAC
*
54191456 ATAACTTATACAATA
1 ATAACTTATATAATA
54191471 ATAAGGTAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
55 3 0.05
56 18 0.29
57 42 0.67
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (56 bp):
ATAACTTATATAATATTACATAACTTATATAATATTAAGATAAAAAATCGAATTAC
Found at i:54191645 original size:115 final size:115
Alignment explanation
Indices: 54191504--54193083 Score: 1984
Period size: 115 Copynumber: 13.9 Consensus size: 115
54191494 TAACTTATAC
*
54191504 AATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
1 AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
54191569 AGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
66 AGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
54191619 AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
1 AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
54191684 AGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
66 AGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
54191734 AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
1 AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
54191799 AGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
66 AGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
54191849 AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
1 AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
54191914 AGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
66 AGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
54191964 AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
1 AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
54192029 AGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
66 AGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
54192079 AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
1 AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
54192144 AGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
66 AGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
54192194 AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
1 AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
54192259 AGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
66 AGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
54192309 AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
1 AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
* * * * *
54192374 AGATAAAATTTCGAATTACATAACTTATATAATATT-ACATAACTTATAC
66 AGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
* * * * * *
54192423 AATATTAAGGT-AAGATTTCGAATTACATAACTCATACAATATTAAGATTACTTA--TATAATAT
1 AATATTAAGATCAA-ATTTCGAATTACATAACTTATATAATATT-ACATAACTTACGTACAATAT
* * * * * * *
54192485 TAAGATAAAATTTCTAATTACATAACTTACATAA-ATT-ACATAACTTATAC
64 TAAGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
* * * * * *
54192535 AATATTAAGGT-AAGATTTCGAATTACATAACTCATACAATATTAAGATTACTTA--TATAATAT
1 AATATTAAGATCAA-ATTTCGAATTACATAACTTATATAATATT-ACATAACTTACGTACAATAT
* * * * * * *
54192597 TAAGATAAAATTTCTAATTACATAACTTACATAA-ATT-ACATAACTTATAC
64 TAAGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
* * * * * *
54192647 AATATTAAGGT-AAGATTTCGAATTACATAACTCATACAATATTAAGATTACTTA--TATAATAT
1 AATATTAAGATCAA-ATTTCGAATTACATAACTTATATAATATT-ACATAACTTACGTACAATAT
* ** ** * * * * * *
54192709 TAAGATTACTTTTATAATATTAAGATCAAATT-T-TGA-ATT-ACATAACTTATAT
64 TAAGATAAAATTT-CGA-ATT-ACAT-AAGTTATATAATATTAAGATTACTTTTAT
* ** * ** * * * * *
54192761 AATTTTCCG-T-AACTTATATAATTACATAACTCATACAATATTAAGATTACTTA--TATAATAT
1 AATATTAAGATCAAATT-TCGAATTACATAACTTATATAATATT-ACATAACTTACGTACAATAT
* * * * * * *
54192822 TAAGATAAAATTTCTAATTACATAACTTACATAA-ATT-ACATAACTTATAC
64 TAAGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
* * * * * *
54192872 AATATTAAGGT-AAGATTTCGAATTACATAACTCATACAATATTAAGATTACTTA--TATAATAT
1 AATATTAAGATCAA-ATTTCGAATTACATAACTTATATAATATT-ACATAACTTACGTACAATAT
* * * * * * *
54192934 TAAGATAAAATTTCTAATTACATAACTTACATAA-ATT-ACATAACTTATAC
64 TAAGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
* * * * * *
54192984 AATATTAAGGT-AAGATTTCGAATTACATAACTCATACAATATTAAGATTACTTA--TATAATAT
1 AATATTAAGATCAA-ATTTCGAATTACATAACTTATATAATATT-ACATAACTTACGTACAATAT
* * *
54193046 TAAGATAAAATTTCTAATTACATAACTTACATAA-ATTA
64 TAAGATAAAATTTCGAATTACATAAGTTATATAATATTA
54193084 CATAACTTAC
Statistics
Matches: 1407, Mismatches: 46, Indels: 26
0.95 0.03 0.02
Matches are distributed among these distances:
109 4 0.00
110 3 0.00
111 26 0.02
112 398 0.28
113 100 0.07
114 72 0.05
115 800 0.57
116 4 0.00
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (115 bp):
AATATTAAGATCAAATTTCGAATTACATAACTTATATAATATTACATAACTTACGTACAATATTA
AGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATTACTTTTAT
Found at i:54192516 original size:9 final size:9
Alignment explanation
Indices: 54192502--54192531 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
54192492 AAATTTCTAA
54192502 TTACATAAC
1 TTACATAAC
*
54192511 TTACATAAA
1 TTACATAAC
54192520 TTACATAAC
1 TTACATAAC
54192529 TTA
1 TTA
54192532 TACAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (9 bp):
TTACATAAC
Found at i:54192628 original size:9 final size:9
Alignment explanation
Indices: 54192614--54192643 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
54192604 AAATTTCTAA
54192614 TTACATAAC
1 TTACATAAC
*
54192623 TTACATAAA
1 TTACATAAC
54192632 TTACATAAC
1 TTACATAAC
54192641 TTA
1 TTA
54192644 TACAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (9 bp):
TTACATAAC
Found at i:54192853 original size:9 final size:9
Alignment explanation
Indices: 54192839--54192868 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
54192829 AAATTTCTAA
54192839 TTACATAAC
1 TTACATAAC
*
54192848 TTACATAAA
1 TTACATAAC
54192857 TTACATAAC
1 TTACATAAC
54192866 TTA
1 TTA
54192869 TACAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (9 bp):
TTACATAAC
Found at i:54192965 original size:9 final size:9
Alignment explanation
Indices: 54192951--54192980 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
54192941 AAATTTCTAA
54192951 TTACATAAC
1 TTACATAAC
*
54192960 TTACATAAA
1 TTACATAAC
54192969 TTACATAAC
1 TTACATAAC
54192978 TTA
1 TTA
54192981 TACAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (9 bp):
TTACATAAC
Found at i:54193077 original size:9 final size:9
Alignment explanation
Indices: 54193063--54193403 Score: 280
Period size: 9 Copynumber: 39.1 Consensus size: 9
54193053 AAATTTCTAA
54193063 TTACATAAC
1 TTACATAAC
*
54193072 TTACATAAA
1 TTACATAAC
54193081 TTACATAAC
1 TTACATAAC
*
54193090 TTACATAAA
1 TTACATAAC
*
54193099 TTAAATAAC
1 TTACATAAC
*
54193108 TTGCATAAC
1 TTACATAAC
*
54193117 TTAAATAAC
1 TTACATAAC
54193126 TTACATAAC
1 TTACATAAC
54193135 --ACATAACC
1 TTACATAA-C
* *
54193143 TT-CCTAGC
1 TTACATAAC
* *
54193151 TTACATTAT
1 TTACATAAC
*
54193160 TTTC-TAA-
1 TTACATAAC
54193167 TTACATAAC
1 TTACATAAC
*
54193176 TTACATAAA
1 TTACATAAC
54193185 TTACATAAC
1 TTACATAAC
*
54193194 TTACATAAA
1 TTACATAAC
*
54193203 TTAAATAAC
1 TTACATAAC
*
54193212 TTGCATAAC
1 TTACATAAC
*
54193221 TTAAATAAC
1 TTACATAAC
54193230 TTACATAAC
1 TTACATAAC
54193239 --ACATAACC
1 TTACATAA-C
* *
54193247 TT-CCTAGC
1 TTACATAAC
* *
54193255 TTACATTAT
1 TTACATAAC
*
54193264 TTAGATAA-
1 TTACATAAC
*
54193272 -TACATAGC
1 TTACATAAC
*
54193280 CTACATAAC
1 TTACATAAC
54193289 TTACATAAC
1 TTACATAAC
*
54193298 TTACATAAA
1 TTACATAAC
*
54193307 TTAAATAAC
1 TTACATAAC
54193316 TTACATAAC
1 TTACATAAC
54193325 TTACATAAC
1 TTACATAAC
*
54193334 TCACATAA-
1 TTACATAAC
*
54193342 -TACACAAC
1 TTACATAAC
54193350 TTACATAAC
1 TTACATAAC
54193359 TTACATAA-
1 TTACATAAC
54193367 -TACATAAC
1 TTACATAAC
* *
54193375 ATT-CCTATC
1 -TTACATAAC
*
54193384 ATATCATAAC
1 TTA-CATAAC
54193394 TTACATAAC
1 TTACATAAC
54193403 T
1 T
54193404 CATTTATAGT
Statistics
Matches: 258, Mismatches: 55, Indels: 38
0.74 0.16 0.11
Matches are distributed among these distances:
7 32 0.12
8 14 0.05
9 205 0.79
10 7 0.03
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.33
Consensus pattern (9 bp):
TTACATAAC
Found at i:54193189 original size:104 final size:104
Alignment explanation
Indices: 54193056--54193341 Score: 484
Period size: 104 Copynumber: 2.8 Consensus size: 104
54193046 TAAGATAAAA
54193056 TTTCTAATTACATAACTTACATAAATTACATAACTTACATAAATTAAATAACTTGCATAACTTAA
1 TTTCTAATTACATAACTTACATAAATTACATAACTTACATAAATTAAATAACTTGCATAACTTAA
54193121 ATAACTTACATAACACATAACCTTCCTAGCTTACATTAT
66 ATAACTTACATAACACATAACCTTCCTAGCTTACATTAT
54193160 TTTCTAATTACATAACTTACATAAATTACATAACTTACATAAATTAAATAACTTGCATAACTTAA
1 TTTCTAATTACATAACTTACATAAATTACATAACTTACATAAATTAAATAACTTGCATAACTTAA
54193225 ATAACTTACATAACACATAACCTTCCTAGCTTACATTAT
66 ATAACTTACATAACACATAACCTTCCTAGCTTACATTAT
** * * * *
54193264 TTAGATAA-TACATAGCCTACATAACTTACATAACTTACATAAATTAAATAACTTACATAACTTA
1 TT-TCTAATTACATAACTTACATAAATTACATAACTTACATAAATTAAATAACTTGCATAACTTA
* *
54193328 CATAACTCACATAA
65 AATAACTTACATAA
54193342 TACACAACTT
Statistics
Matches: 173, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
104 170 0.98
105 3 0.02
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.34
Consensus pattern (104 bp):
TTTCTAATTACATAACTTACATAAATTACATAACTTACATAAATTAAATAACTTGCATAACTTAA
ATAACTTACATAACACATAACCTTCCTAGCTTACATTAT
Found at i:54195374 original size:21 final size:21
Alignment explanation
Indices: 54195348--54195418 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
54195338 CTACAACTTA
* *
54195348 AAGCAGAGGCGGCGGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
54195369 AAGCAGCGGCTGTAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
54195390 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
54195411 AAGCAGAG
1 AAGCAGAG
54195419 CAGAGCAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.30, C:0.18, G:0.48, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:54195824 original size:42 final size:42
Alignment explanation
Indices: 54195778--54195976 Score: 276
Period size: 42 Copynumber: 4.7 Consensus size: 42
54195768 AAAAAACGCT
* * *
54195778 GCTAAAG-ACAATGCTCTTTAGTGGCGTTTCTTTCAAAGCGCC
1 GCTAAAGAAC-ATGGTCTTTAGCGGCGTTTTTTTCAAAGCGCC
* * *
54195820 GCTAAAGAACATGGTTTTTAGCGGTG-TTTTTTCTAAGCGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCAAAGCGCC
* *
54195861 GCTAAAGAACATGGTCTTTAGCGGCATTTTTTTTATAAGCGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCA-AAGCGCC
*
54195904 GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCAAAGCGCC
*
54195946 GCTAAAGAACATGGTCTTTAGTGGCGTTTTT
1 GCTAAAGAACATGGTCTTTAGCGGCGTTTTT
54195977 GTTTGTAAAC
Statistics
Matches: 139, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
41 36 0.26
42 62 0.45
43 41 0.29
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (42 bp):
GCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCAAAGCGCC
Found at i:54204354 original size:10 final size:11
Alignment explanation
Indices: 54204339--54204367 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
54204329 GCCAAAGATG
54204339 TGAATTGAAT-
1 TGAATTGAATA
54204349 TGAATTGAATA
1 TGAATTGAATA
54204360 TGAATTGA
1 TGAATTGA
54204368 TGTTAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (11 bp):
TGAATTGAATA
Found at i:54204723 original size:24 final size:25
Alignment explanation
Indices: 54204685--54204737 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
54204675 CAGCTCGAAA
** *
54204685 GAGCATCCCGTTA-TTAGCTCTCAT
1 GAGCATCCCAATATTTAGCTCTCAC
*
54204709 GAGCATCCCAATATTTGGCTCTCAC
1 GAGCATCCCAATATTTAGCTCTCAC
54204734 GAGC
1 GAGC
54204738 TTTCCGTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (25 bp):
GAGCATCCCAATATTTAGCTCTCAC
Found at i:54204934 original size:24 final size:24
Alignment explanation
Indices: 54204842--54204960 Score: 78
Period size: 24 Copynumber: 4.8 Consensus size: 24
54204832 CTCTTATGAG
* * *
54204842 CTTCCCGATATACGGCTCTCCGGAG
1 CTTCCCGAT-TATGGCTCTCCAGAA
* * * *
54204867 CTTCCCGATTAAAGGTTCTTTCATGAG
1 CTTCCCGATT-ATGGCTC-TCCA-GAA
*
54204894 CTTCCTGATTAATGGCTCTCCAGAA
1 CTTCCCGATT-ATGGCTCTCCAGAA
* **
54204919 CTTCCCGA-TATTGGCTCGCTTGAA
1 CTTCCCGATTA-TGGCTCTCCAGAA
54204943 CTTCCCGATTATGGCTCT
1 CTTCCCGATTATGGCTCT
54204961 TATAAGCTTC
Statistics
Matches: 75, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
23 1 0.01
24 26 0.35
25 25 0.33
26 5 0.07
27 18 0.24
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.33
Consensus pattern (24 bp):
CTTCCCGATTATGGCTCTCCAGAA
Found at i:54205984 original size:7 final size:7
Alignment explanation
Indices: 54205974--54206039 Score: 53
Period size: 7 Copynumber: 8.6 Consensus size: 7
54205964 AAAGTTAAAA
54205974 TATATAT
1 TATATAT
54205981 TATAATAT
1 TAT-ATAT
54205989 TATAATAT
1 TAT-ATAT
*
54205997 TATATCT
1 TATATAT
54206004 TA-ATTAT
1 TATA-TAT
54206011 TAAGTATAT
1 T-A-TATAT
54206020 ATATTATAT
1 -TA-TATAT
54206029 TATATAT
1 TATATAT
54206036 TATA
1 TATA
54206040 ATAAGTAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
6 1 0.02
7 20 0.40
8 18 0.36
9 9 0.18
10 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (7 bp):
TATATAT
Found at i:54205990 original size:8 final size:8
Alignment explanation
Indices: 54205977--54206042 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
54205967 GTTAAAATAT
54205977 ATATTATA
1 ATATTATA
54205985 ATATTATA
1 ATATTATA
54205993 ATATTAT-
1 ATATTATA
*
54206000 ATCTTA-A
1 ATATTATA
*
54206007 TTATTA-A
1 ATATTATA
*
54206014 GTATATATATT
1 --ATAT-TATA
54206025 ATATTAT-
1 ATATTATA
54206032 ATATTATA
1 ATATTATA
54206040 ATA
1 ATA
54206043 AGTAAATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
7 17 0.36
8 21 0.45
9 7 0.15
10 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (8 bp):
ATATTATA
Found at i:54206009 original size:27 final size:26
Alignment explanation
Indices: 54205974--54206042 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 26
54205964 AAAGTTAAAA
54205974 TATATATTATAATATTATAATATTATAT
1 TATATATTATAATA-TAT-ATATTATAT
54206002 CT-TA-ATTATTAAGTATATATATTATAT
1 -TATATATTA-TAA-TATATATATTATAT
54206029 TATATATTATAATA
1 TATATATTATAATA
54206043 AGTAAATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 12 0.33
29 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (26 bp):
TATATATTATAATATATATATTATAT
Found at i:54206052 original size:30 final size:32
Alignment explanation
Indices: 54205984--54206052 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
54205974 TATATATTAT
* *
54205984 AATATTATAATATTATATCTTAATTATTAAGTA
1 AATA-TATAATATTATATATTAATTAATAAGTA
* *
54206017 TATATATTATATTATATATT-A-TAATAAGTA
1 AATATATAATATTATATATTAATTAATAAGTA
54206047 AATATA
1 AATATA
54206053 ATAAATAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 13 0.42
31 1 0.03
32 14 0.45
33 3 0.10
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (32 bp):
AATATATAATATTATATATTAATTAATAAGTA
Found at i:54206145 original size:14 final size:14
Alignment explanation
Indices: 54206122--54206158 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
54206112 ATAAGGAAAC
54206122 AGAG-AAGAAAAAG
1 AGAGAAAGAAAAAG
54206135 AGAGAAAGAAAAAG
1 AGAGAAAGAAAAAG
54206149 -GAGAAA-AAAA
1 AGAGAAAGAAAA
54206159 TTAAGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 10 0.43
14 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AGAGAAAGAAAAAG
Found at i:54206152 original size:15 final size:13
Alignment explanation
Indices: 54206122--54206158 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
54206112 ATAAGGAAAC
54206122 AGAGAAGAAAAAG
1 AGAGAAGAAAAAG
54206135 AGAGAAAGAAAAAG
1 AGAG-AAGAAAAAG
54206149 -GAGAA-AAAAA
1 AGAGAAGAAAAA
54206159 TTAAGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.22
12 2 0.09
13 7 0.30
14 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AGAGAAGAAAAAG
Found at i:54208740 original size:25 final size:25
Alignment explanation
Indices: 54208711--54208763 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
54208701 TTAGCGCGCG
* * **
54208711 CTCTGATTATTAGCACGTTGGTGCT
1 CTCTGATTACTAACACGTCAGTGCT
54208736 CTCTGATTACTAACACGTCAGTGCT
1 CTCTGATTACTAACACGTCAGTGCT
54208761 CTC
1 CTC
54208764 CATTTAGCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (25 bp):
CTCTGATTACTAACACGTCAGTGCT
Found at i:54208793 original size:22 final size:22
Alignment explanation
Indices: 54208768--54208810 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
54208758 GCTCTCCATT
54208768 TAGCACATCT-GTGCTCTCTGTA
1 TAGCAC-TCTAGTGCTCTCTGTA
*
54208790 TAGCACTTTAGTGCTCTCTGT
1 TAGCACTCTAGTGCTCTCTGT
54208811 TCATTAGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.40
Consensus pattern (22 bp):
TAGCACTCTAGTGCTCTCTGTA
Found at i:54211795 original size:21 final size:21
Alignment explanation
Indices: 54211771--54211842 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
54211761 CCGTAAGGGT
54211771 TGAACGGAAGCTCATAAGAGC
1 TGAACGGAAGCTCATAAGAGC
** * *
54211792 TGAAC-GAAAATCGATAAGGGT
1 TGAACGGAAGCTC-ATAAGAGC
* * *
54211813 TAAACAGAAGCTCAAAAGAGC
1 TGAACGGAAGCTCATAAGAGC
54211834 TGAACGGAA
1 TGAACGGAA
54211843 ACCCATTAGG
Statistics
Matches: 37, Mismatches: 12, Indels: 4
0.70 0.23 0.08
Matches are distributed among these distances:
20 5 0.14
21 27 0.73
22 5 0.14
ACGTcount: A:0.44, C:0.15, G:0.26, T:0.14
Consensus pattern (21 bp):
TGAACGGAAGCTCATAAGAGC
Found at i:54211810 original size:42 final size:42
Alignment explanation
Indices: 54211757--54211858 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
54211747 TGCTAAGTAG
* * *
54211757 AAACCCGTAAGGGTTGAACGGAAGCTCATAAGAGCTGAACGA
1 AAACCCATAAGGGTTGAACAGAAGCTCAAAAGAGCTGAACGA
* * * *
54211799 AAATCGATAAGGGTTAAACAGAAGCTCAAAAGAGCTGAACGG
1 AAACCCATAAGGGTTGAACAGAAGCTCAAAAGAGCTGAACGA
*
54211841 AAACCCATTAGGGTTGAA
1 AAACCCATAAGGGTTGAA
54211859 TTGAAACTCA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.41, C:0.17, G:0.26, T:0.16
Consensus pattern (42 bp):
AAACCCATAAGGGTTGAACAGAAGCTCAAAAGAGCTGAACGA
Found at i:54220838 original size:18 final size:19
Alignment explanation
Indices: 54220795--54220844 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
54220785 AATCAATAAA
54220795 ATTTTAATTTTATTTAATT
1 ATTTTAATTTTATTTAATT
** *
54220814 -TGATAATTTT-TTTACTT
1 ATTTTAATTTTATTTAATT
54220831 ATTTTAATTTTATT
1 ATTTTAATTTTATT
54220845 ATGTAAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
17 6 0.25
18 16 0.67
19 2 0.08
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTTTAATTTTATTTAATT
Found at i:54221750 original size:22 final size:21
Alignment explanation
Indices: 54221702--54221751 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
54221692 ATCCTTATTC
54221702 TTTTTA-TTTTCTTTAAACAT
1 TTTTTATTTTTCTTTAAACAT
54221722 TTTTTATTTTTCATTTAAA-AT
1 TTTTTATTTTTC-TTTAAACAT
54221743 TTTCTTATT
1 TTT-TTATT
54221752 CTCATTCTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.22
21 10 0.37
22 11 0.41
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTTATTTTTCTTTAAACAT
Found at i:54221756 original size:21 final size:20
Alignment explanation
Indices: 54221702--54221757 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 20
54221692 ATCCTTATTC
54221702 TTTTTATTTTC-TTTAAACAT
1 TTTTTATTTTCATTTAAA-AT
54221722 TTTTTATTTTTCATTTAAAAT
1 TTTTTA-TTTTCATTTAAAAT
*
54221743 TTTCTTATTCTCATT
1 TTT-TTATTTTCATT
54221758 CTAGAATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.19
21 17 0.53
22 9 0.28
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTATTTTCATTTAAAAT
Found at i:54231649 original size:33 final size:33
Alignment explanation
Indices: 54231612--54231696 Score: 138
Period size: 33 Copynumber: 2.6 Consensus size: 33
54231602 GTATTAAAAG
54231612 AAAGAATAAAGAAAAAGAAATAGAAAGACATGC
1 AAAGAATAAAGAAAAAGAAATAGAAAGACATGC
54231645 AAAGAATAAAGAAAAAGAAATAGAAAGACATGC
1 AAAGAATAAAGAAAAAGAAATAGAAAGACATGC
*
54231678 -AA-AATTAAGAAAGAAGAAA
1 AAAGAATAAAGAAA-AAGAAA
54231697 GACTCACGGC
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
31 9 0.18
32 8 0.16
33 33 0.66
ACGTcount: A:0.68, C:0.05, G:0.18, T:0.09
Consensus pattern (33 bp):
AAAGAATAAAGAAAAAGAAATAGAAAGACATGC
Found at i:54232348 original size:5 final size:5
Alignment explanation
Indices: 54232338--54232378 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
54232328 TCTTAGATTT
54232338 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA T
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA T
54232379 CTAAATTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:54249428 original size:17 final size:17
Alignment explanation
Indices: 54249406--54249439 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
54249396 TGGCTTCTGT
54249406 CCCTGTCCCTGCTGAAC
1 CCCTGTCCCTGCTGAAC
54249423 CCCTGTCCCTGCTGAAC
1 CCCTGTCCCTGCTGAAC
54249440 TCCTTATCCC
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:0.47, G:0.18, T:0.24
Consensus pattern (17 bp):
CCCTGTCCCTGCTGAAC
Found at i:54257052 original size:5 final size:5
Alignment explanation
Indices: 54257042--54257097 Score: 76
Period size: 5 Copynumber: 10.8 Consensus size: 5
54257032 AAGTGAGTTG
* *
54257042 TTATA TTATA TTATTA TAATA TTATA TTATA TTATTA TAATA TTATA TTATA
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTA-TA TTATA TTATA TTATA
54257094 TTAT
1 TTAT
54257098 TATATATATA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
5 37 0.82
6 8 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:54257058 original size:8 final size:8
Alignment explanation
Indices: 54257045--54257102 Score: 64
Period size: 8 Copynumber: 7.0 Consensus size: 8
54257035 TGAGTTGTTA
54257045 TATTATAT
1 TATTATAT
*
54257053 TATTATAA
1 TATTATAT
54257061 TATTATAT
1 TATTATAT
54257069 TA-TATTAT
1 TATTA-TAT
*
54257077 TATAATATT
1 TATTATA-T
54257086 ATATTATAT
1 -TATTATAT
54257095 TATTATAT
1 TATTATAT
54257103 ATATAAAGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
7 2 0.05
8 31 0.74
9 3 0.07
10 6 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTATAT
Found at i:54257066 original size:21 final size:21
Alignment explanation
Indices: 54257042--54257106 Score: 121
Period size: 21 Copynumber: 3.0 Consensus size: 21
54257032 AAGTGAGTTG
54257042 TTATATTATATTATTATAATA
1 TTATATTATATTATTATAATA
54257063 TTATATTATATTATTATAATA
1 TTATATTATATTATTATAATA
54257084 TTATATTATATTATTATATATA
1 TTATATTATATTATTATA-ATA
54257106 T
1 T
54257107 AAAGCAAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 39 0.91
22 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATATTATATTATTATAATA
Found at i:54257384 original size:12 final size:13
Alignment explanation
Indices: 54257355--54257386 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
54257345 TGTAGCTTAT
54257355 ATTGAATTAGTGG
1 ATTGAATTAGTGG
54257368 A-TGAATTAGT-G
1 ATTGAATTAGTGG
54257379 ATTGAATT
1 ATTGAATT
54257387 GATGGAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 15 0.83
13 1 0.06
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (13 bp):
ATTGAATTAGTGG
Found at i:54257909 original size:10 final size:11
Alignment explanation
Indices: 54257884--54257916 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
54257874 TATTTATTTA
54257884 AAAAATAAAAT
1 AAAAATAAAAT
*
54257895 AAAAATAAAGT
1 AAAAATAAAAT
54257906 -AAAATAAAAT
1 AAAAATAAAAT
54257916 A
1 A
54257917 TTATGGAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:54258273 original size:27 final size:25
Alignment explanation
Indices: 54258217--54258274 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
54258207 ACTTTAGCGC
**
54258217 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTCAGT
54258242 GCTCTCTGA-TATTTAGCACGTCAGT
1 GCTCTCTGATTA-TTAGCACGTCAGT
54258267 GCTCTCTG
1 GCTCTCTG
54258275 TTCAGCACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 2 0.07
25 28 0.93
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTCAGT
Found at i:54264239 original size:26 final size:26
Alignment explanation
Indices: 54264208--54264267 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
54264198 GAAGCTCCGG
*
54264208 AGAGCCATTAATTAGAAAGCTCACAA
1 AGAGCCATTAATCAGAAAGCTCACAA
* * *
54264234 AGAGCCTTTAATCAGGAAGCTCACGA
1 AGAGCCATTAATCAGAAAGCTCACAA
54264260 AGAGCCAT
1 AGAGCCAT
54264268 ATATCGGGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATCAGAAAGCTCACAA
Found at i:54264584 original size:20 final size:20
Alignment explanation
Indices: 54264559--54264598 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
54264549 AGCAATTACA
54264559 CAATTC-ACATATATAATATT
1 CAATTCAACATATA-AATATT
54264579 CAATTCAAACATATAAATAT
1 CAATTC-AACATATAAATAT
54264599 AAACAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTCAACATATAAATATT
Found at i:54266867 original size:21 final size:20
Alignment explanation
Indices: 54266833--54266872 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
54266823 TTAAATCATC
*
54266833 AAAATTAAAATTGAGTGGTAG
1 AAAATCAAAATTGA-TGGTAG
*
54266854 AAAATCAAAGTTGATGGTA
1 AAAATCAAAATTGATGGTA
54266873 CATTTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.03, G:0.23, T:0.28
Consensus pattern (20 bp):
AAAATCAAAATTGATGGTAG
Found at i:54270997 original size:17 final size:17
Alignment explanation
Indices: 54270975--54271020 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
54270965 AAAAATATTA
54270975 TAATTTTTCTTA-ATTTT
1 TAATTTTT-TTAGATTTT
54270992 TAATTTTTTTAGATTTT
1 TAATTTTTTTAGATTTT
54271009 TCAAGTTTTTTT
1 T-AA-TTTTTTT
54271021 TTGCTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.12
17 14 0.54
18 2 0.08
19 7 0.27
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (17 bp):
TAATTTTTTTAGATTTT
Found at i:54276306 original size:17 final size:17
Alignment explanation
Indices: 54276284--54276317 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54276274 ATCCACTAAT
*
54276284 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
54276301 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
54276318 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:54280946 original size:17 final size:17
Alignment explanation
Indices: 54280924--54280957 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54280914 ATCCACTAAT
*
54280924 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
54280941 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
54280958 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:54283425 original size:92 final size:91
Alignment explanation
Indices: 54283325--54283865 Score: 282
Period size: 92 Copynumber: 5.9 Consensus size: 91
54283315 TTTTCAACTA
* * *
54283325 TAGAGTATGGTGTTGTAATAATATTTTTTTTATTTTTCAGAATAATTATAATAATTCA-TATTTA
1 TAGAGTATGATGATGTAATAATATTTTTTTTATTTTTTAGAATAATTATAATAATT-AGTATTTA
*
54283389 CTTTATTTCATTTTCGAGGCATTTGAGT
65 -TTTATTTCATTTTCGAGGCATTTGAGC
* * * * * * *
54283417 TTGGGTATGATGATGCAATAAT-TTTTTTAAATTTTTTTTTGGAATAATTATAATAATAATTATT
1 TAGAGTATGATGATGTAATAATATTTTTT---TTATTTTTTAGAATAATTATAATAATTAGTATT
* * * *
54283481 TA-TTATATTCTATTTTTGGGGCCTTTGGGC
63 TATTTAT-TTC-ATTTTCGAGGCATTTGAGC
*** * * * *
54283511 TAGAGTCCAATGCTGTAATAATATTTTTATTATTTTTTAGAATAACTATCATAATTAGTATTTAT
1 TAGAGTATGATGATGTAATAATATTTTTTTTATTTTTTAGAATAATTATAATAATTAGTATTTA-
* * *
54283576 TTTATTTCATTTCCG-GAGCACTTGTGC
65 TTTATTTCATTTTCGAG-GCATTTGAGC
* ** * * * * * * * * *
54283603 CAGAGCCTGGTGTTGCAATATTATATTTATTATTTTCT-GAAATAGTTACAATAATTAGTATTTA
1 TAGAGTATGATGATGTAATAATATTTTTTTTATTTTTTAG-AATAATTATAATAATTAGTATTTA
54283667 TTTTATTTCATTTTCG-GGCAATTTGA-C
65 -TTTATTTCATTTTCGAGGC-ATTTGAGC
* * * * * * * * * *
54283694 TTGTGTCTGGTGGTGCAAT-AT-TTTTATTTTATTTTATGGAACAATTATAATAGTTA-T-TTTA
1 TAGAGTATGATGATGTAATAATATTTT-TTTTATTTTTTAGAATAATTATAATAATTAGTATTTA
* * * *
54283755 TTTTATTTTATTTTC-AGGGCACTTGGGT
65 -TTTATTTCATTTTCGA-GGCATTTGAGC
* * * * * * *
54283783 TTGAGTCA-G-TGAAGCAATAATATTTTTTTTAATTTTTTTTGGAGTAATTATAACAATTAGAAT
1 TAGAGT-ATGATGATGTAATAATATTTTTTTT-A--TTTTTTAGAATAATTATAATAATTAGTAT
54283846 TTATTTTATTTCATTTTCGA
62 TTA-TTTATTTCATTTTCGA
54283866 CACTTACATT
Statistics
Matches: 345, Mismatches: 78, Indels: 49
0.73 0.17 0.10
Matches are distributed among these distances:
88 29 0.08
89 19 0.06
90 28 0.08
91 26 0.08
92 150 0.43
93 7 0.02
94 80 0.23
95 6 0.02
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.50
Consensus pattern (91 bp):
TAGAGTATGATGATGTAATAATATTTTTTTTATTTTTTAGAATAATTATAATAATTAGTATTTAT
TTATTTCATTTTCGAGGCATTTGAGC
Found at i:54284018 original size:80 final size:80
Alignment explanation
Indices: 54283925--54284098 Score: 210
Period size: 80 Copynumber: 2.2 Consensus size: 80
54283915 TTATAATAAA
**
54283925 TATTTATTTTATTTAA-TTTCTAGGGCACTTGGGCTTGAGTTAGGTGGTGCAATAAATTTTTT-A
1 TATTTATTTTATTTAATTTTC-AGGGCACTTGAACTTGAGTTAGGTGGTGCAAT-AATTTTTTCA
*
54283988 -TTTTCTAGAATAATTAT
64 TTTTTC-AGAACAATTAT
* * * * *
54284005 TATTTATTCTATTTCATTTTCGGGGCACTTGAACTTGAGTTTGGTGTTGCAATAATTTTTTCATT
1 TATTTATTTTATTTAATTTTCAGGGCACTTGAACTTGAGTTAGGTGGTGCAATAATTTTTTCATT
*
54284070 TTTCGGAACAATTAT
66 TTTCAGAACAATTAT
*
54284085 TACTTATTTTATTT
1 TATTTATTTTATTT
54284099 TTTTTCCGAA
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
79 8 0.10
80 63 0.79
81 9 0.11
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.51
Consensus pattern (80 bp):
TATTTATTTTATTTAATTTTCAGGGCACTTGAACTTGAGTTAGGTGGTGCAATAATTTTTTCATT
TTTCAGAACAATTAT
Found at i:54284114 original size:80 final size:80
Alignment explanation
Indices: 54283958--54284114 Score: 176
Period size: 80 Copynumber: 2.0 Consensus size: 80
54283948 GGCACTTGGG
* *
54283958 CTTGAGTTAGGTGGTGCAATAAATTTTTTATTTTCTAGAATAATTATTATTTATTCTATTTCATT
1 CTTGAGTTAGGTGGTGCAATAAATTTTTTATTTTCTAGAACAATTATTACTTATTCTATTTCATT
***
54284023 TTCGGGGCACTTGAA
66 TTCGAAACACTTGAA
* * * * *
54284038 CTTGAGTTTGGTGTTGCAAT-AATTTTTTCATTTT-TCGGAACAATTATTACTTATTTTATTT-T
1 CTTGAGTTAGGTGGTGCAATAAATTTTTT-ATTTTCT-AGAACAATTATTACTTATTCTATTTCA
54284100 TTTTCCGAAACACTT
64 TTTT-CGAAACACTT
54284115 AGGCCAGAGT
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
79 13 0.20
80 51 0.80
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (80 bp):
CTTGAGTTAGGTGGTGCAATAAATTTTTTATTTTCTAGAACAATTATTACTTATTCTATTTCATT
TTCGAAACACTTGAA
Found at i:54284279 original size:90 final size:88
Alignment explanation
Indices: 54284166--54284366 Score: 234
Period size: 90 Copynumber: 2.2 Consensus size: 88
54284156 TATAATAAAT
* *
54284166 ATTATTTTATTTTATTTCATTTTC-GGTGTATTTGGGCTAGAGTCTAGTGTT-A-G-AAT-AATA
1 ATTA-TTTATTTTATTTCATTTTCAGG-GCA-TTAGGCTAGAGT-T--TGTTGATGCAATAAATA
*
54284226 TTTTTTTATTTTCTGAAA-GAATTATAATT
60 TTTTTTTATTTTCTGAAATG-ATTATAATA
*
54284255 ATTATAATTATTTTATTTCATTTTCAGGGCATTAGGCTTGAGTTTGTTGATGCAATAAATATTTT
1 ATTAT--TTATTTTATTTCATTTTCAGGGCATTAGGCTAGAGTTTGTTGATGCAATAAATATTTT
*
54284320 TTTATTTTTTGAAATGATTATAATA
64 TTTATTTTCTGAAATGATTATAATA
54284345 ATTATTTATTTTATTTCATTTT
1 ATTATTTATTTTATTTCATTTT
54284367 TTGAATATTT
Statistics
Matches: 99, Mismatches: 5, Indels: 17
0.82 0.04 0.14
Matches are distributed among these distances:
86 4 0.04
87 1 0.01
88 20 0.20
89 17 0.17
90 54 0.55
91 3 0.03
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.54
Consensus pattern (88 bp):
ATTATTTATTTTATTTCATTTTCAGGGCATTAGGCTAGAGTTTGTTGATGCAATAAATATTTTTT
TATTTTCTGAAATGATTATAATA
Found at i:54306772 original size:23 final size:22
Alignment explanation
Indices: 54306721--54306772 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
54306711 CCTCGTCTTT
*
54306721 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
54306743 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
54306766 TTCTTTT
1 TTCTTTT
54306773 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:54306787 original size:18 final size:18
Alignment explanation
Indices: 54306766--54306804 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
54306756 TTTCTTCAAC
* *
54306766 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
54306784 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
54306802 TTC
1 TTC
54306805 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:54310601 original size:23 final size:22
Alignment explanation
Indices: 54310550--54310601 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
54310540 CCTCGTCTTT
*
54310550 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
54310572 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
54310595 TTCTTTT
1 TTCTTTT
54310602 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:54310616 original size:18 final size:18
Alignment explanation
Indices: 54310595--54310633 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
54310585 TTTCTTCAAC
* *
54310595 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
54310613 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
54310631 TTC
1 TTC
54310634 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:54314430 original size:23 final size:22
Alignment explanation
Indices: 54314379--54314430 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
54314369 CCTCGTCTTT
*
54314379 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
54314401 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
54314424 TTCTTTT
1 TTCTTTT
54314431 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:54314445 original size:18 final size:18
Alignment explanation
Indices: 54314424--54314462 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
54314414 TTTCTTCAAC
* *
54314424 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
54314442 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
54314460 TTC
1 TTC
54314463 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:54318259 original size:23 final size:22
Alignment explanation
Indices: 54318208--54318259 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
54318198 CCTCGTCTTT
*
54318208 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
54318230 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
54318253 TTCTTTT
1 TTCTTTT
54318260 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:54318274 original size:18 final size:18
Alignment explanation
Indices: 54318253--54318291 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
54318243 TTTCTTCAAC
* *
54318253 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
54318271 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
54318289 TTC
1 TTC
54318292 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:54322088 original size:23 final size:22
Alignment explanation
Indices: 54322037--54322088 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
54322027 CCTCGTCTTT
*
54322037 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
54322059 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
54322082 TTCTTTT
1 TTCTTTT
54322089 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:54322103 original size:18 final size:18
Alignment explanation
Indices: 54322082--54322120 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
54322072 TTTCTTCAAC
* *
54322082 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
54322100 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
54322118 TTC
1 TTC
54322121 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:54336811 original size:48 final size:48
Alignment explanation
Indices: 54336759--54336932 Score: 224
Period size: 48 Copynumber: 3.6 Consensus size: 48
54336749 TATGTGTGCT
*
54336759 AGTGTAAGACCATGTCTAGG-ACATGGCATCGGCCACGATATGAGAGCC
1 AGTGTAAGACCATGT-TTGGAACATGGCATCGGCCACGATATGAGAGCC
* * * * * *
54336807 AGTGTAAGACCATGTTTGGAACATGGTATCGGCGATGTTGTGAGAGCT
1 AGTGTAAGACCATGTTTGGAACATGGCATCGGCCACGATATGAGAGCC
* * * *
54336855 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGACATGTGAGCC
1 AGTGTAAGACCATGTTTGGAACATGGCATCGGCCACGATATGAGAGCC
*
54336903 AGTATAAGACCATGTTTGGAACATGGCATC
1 AGTGTAAGACCATGTTTGGAACATGGCATC
54336933 AGCAATTCAT
Statistics
Matches: 106, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
47 3 0.03
48 103 0.97
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTTTGGAACATGGCATCGGCCACGATATGAGAGCC
Found at i:54341356 original size:50 final size:51
Alignment explanation
Indices: 54341281--54341404 Score: 196
Period size: 50 Copynumber: 2.5 Consensus size: 51
54341271 TGGCAACCAG
* *
54341281 TGATAAGTGATAGCTTCGGCTACACTTATCTGAACAAGGACAAGTGA-AAC
1 TGATAAGTGATAGCTTCGGCTACACTTATCTGAACAAGGACAAATGACAAA
*
54341331 TGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGACAAA
1 TGATAAGTGATAGCTTCGGCTACACTTATCTGAACAAGGACAAATGACAAA
* *
54341382 TGAAAAGTGGTAGCTTCGGCTAC
1 TGATAAGTGATAGCTTCGGCTAC
54341405 CTGATTAGTG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 45 0.66
51 23 0.34
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (51 bp):
TGATAAGTGATAGCTTCGGCTACACTTATCTGAACAAGGACAAATGACAAA
Found at i:54341420 original size:31 final size:31
Alignment explanation
Indices: 54341382--54341497 Score: 142
Period size: 31 Copynumber: 3.7 Consensus size: 31
54341372 AAATGACAAA
*
54341382 TGAAAAGTGGTAGCTTCGGCTACCTGATTAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
* * *
54341413 TGAAAAGTGGTTGCTTTGGCTACCTGACCAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
* * * *
54341444 TGAAAAATGGTAGCTCCGACTACCTGATCAA
1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
* *
54341475 TGAATAGTGGTAGCTTTGGCTAC
1 TGAAAAGTGGTAGCTTCGGCTAC
54341498 AAGTGACAAG
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 69 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (31 bp):
TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
Found at i:54341628 original size:48 final size:47
Alignment explanation
Indices: 54341566--54341738 Score: 259
Period size: 48 Copynumber: 3.7 Consensus size: 47
54341556 TGCTTCTGTA
54341566 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATCAGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATC-GTG
*
54341614 TAAGACCATAGCTGGGCTATGGCATTGATATGTGATATGTGATCCGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGAT-CGTG
*
54341662 TAAGACCATAGCTAGGCTATGGCATCGATATGTGA-A--T-AT-GTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATCGTG
54341704 TAAGACCATAGCTGGGCTATGGCATC-ATTATGTGA
1 TAAGACCATAGCTGGGCTATGGCATCGA-TATGTGA
54341739 AGATGTATAA
Statistics
Matches: 119, Mismatches: 4, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
41 1 0.01
42 35 0.29
44 2 0.02
45 1 0.01
47 1 0.01
48 78 0.66
49 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (47 bp):
TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATCGTG
Found at i:54341709 original size:42 final size:42
Alignment explanation
Indices: 54341611--54341756 Score: 161
Period size: 42 Copynumber: 3.3 Consensus size: 42
54341601 TATGTGATCA
* *
54341611 GTGTAAGACCATAGCTGGGCTATGGCATTGA-TATGTGATATGTGAT
1 GTGTAAGACCATAGCTAGGCTATGGCA-TCATTATGTGA-A---GAT
*
54341657 CCGTGTAAGACCATAGCTAGGCTATGGCATCGA-TATGTGAATAT
1 --GTGTAAGACCATAGCTAGGCTATGGCATC-ATTATGTGAAGAT
*
54341701 GTGTAAGACCATAGCTGGGCTATGGCATCATTATGTGAAGAT
1 GTGTAAGACCATAGCTAGGCTATGGCATCATTATGTGAAGAT
*
54341743 GTATAAGACCATAG
1 GTGTAAGACCATAG
54341757 TTGAACTATG
Statistics
Matches: 90, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
41 1 0.01
42 51 0.57
44 2 0.02
47 2 0.02
48 34 0.38
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.29
Consensus pattern (42 bp):
GTGTAAGACCATAGCTAGGCTATGGCATCATTATGTGAAGAT
Found at i:54341766 original size:42 final size:41
Alignment explanation
Indices: 54341662--54341772 Score: 134
Period size: 42 Copynumber: 2.7 Consensus size: 41
54341652 GTGATCCGTG
* * *
54341662 TAAGACCATAGCT-AGGCTATGGCATCGATATGTGAATATGTG
1 TAAGACCATAGCTGA-ACTATGGCATC-ATATGTGAAGATGTA
**
54341704 TAAGACCATAGCTGGGCTATGGCATCATTATGTGAAGATGTA
1 TAAGACCATAGCTGAACTATGGCATCA-TATGTGAAGATGTA
*
54341746 TAAGACCATAGTTGAACTATGGCATCA
1 TAAGACCATAGCTGAACTATGGCATCA
54341773 AGAAAATGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
41 1 0.02
42 60 0.98
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28
Consensus pattern (41 bp):
TAAGACCATAGCTGAACTATGGCATCATATGTGAAGATGTA
Found at i:54342715 original size:75 final size:75
Alignment explanation
Indices: 54342590--54342752 Score: 236
Period size: 75 Copynumber: 2.2 Consensus size: 75
54342580 ACGACTTGGA
* * * *
54342590 GACACGGGCGTGTGGCCCGGCCGTGTGGTTAGATTTTCATACTAATGTCATAAAGAAAAAGTTAC
1 GACACGGGCGTGTGGCCCGACCGTATGGTTAGATTTGCATACTAACGTCATAAAGAAAAAGTTAC
54342655 ACGTCCTGAG
66 ACGTCCTGAG
* * * * *
54342665 GACACGGGCGTGTGGCCCGATCGTATGGTTCGATTTGCATGCTAACGTCATAAATAGAAAGTTAC
1 GACACGGGCGTGTGGCCCGACCGTATGGTTAGATTTGCATACTAACGTCATAAAGAAAAAGTTAC
*
54342730 ACTTCCTGAG
66 ACGTCCTGAG
54342740 GACACGGGCGTGT
1 GACACGGGCGTGT
54342753 CAAAGACACA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (75 bp):
GACACGGGCGTGTGGCCCGACCGTATGGTTAGATTTGCATACTAACGTCATAAAGAAAAAGTTAC
ACGTCCTGAG
Found at i:54345004 original size:40 final size:40
Alignment explanation
Indices: 54344949--54345178 Score: 268
Period size: 40 Copynumber: 5.8 Consensus size: 40
54344939 TCCATACATA
54344949 CGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACT
1 CGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACT
54344989 CGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACT
1 CGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACT
* *
54345029 CGCACGAATGCCTTCGGGACTTAACCCGGATTTAGTATCT
1 CGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACT
* * * * *
54345069 CGCACAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCT
1 CGCACGAATGCCTTCGGGACTTAACCCGG-ATTTAATAACT
* ** * * *
54345109 CGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTT
1 CGCACGAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-T
* * *
54345150 AGCAC-AAAGCCTTCGGGACTTAGCCCGGA
1 CGCACGAATGCCTTCGGGACTTAACCCGGA
54345179 CAGCATTCAA
Statistics
Matches: 169, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 5 0.03
40 152 0.90
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACT
Found at i:54345187 original size:41 final size:41
Alignment explanation
Indices: 54345110--54345187 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
54345100 TTTGTATCTC
* * *
54345110 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
54345151 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
54345188 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:54362684 original size:53 final size:53
Alignment explanation
Indices: 54362502--54362708 Score: 198
Period size: 53 Copynumber: 3.8 Consensus size: 53
54362492 ATTAGGGTTT
* * * * * *
54362502 AAGGATACCAAGTAAGACCATGCCAAGGCATGACATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * * * * * *
54362556 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * ** *
54362611 AAAGATCCCATGTAAGACCATGCCAAGGTATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* * *
54362664 AAGGATACCACGTAAGACCATGTCAAGACATGGAAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
54362709 TAAAAAGGAA
Statistics
Matches: 120, Mismatches: 31, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
53 44 0.37
54 37 0.31
55 39 0.32
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:54388613 original size:29 final size:29
Alignment explanation
Indices: 54388550--54388617 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
54388540 TAATCAACCA
54388550 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
54388579 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
54388608 CGCACACTTA
1 CGCACACTTA
54388618 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:54388758 original size:29 final size:30
Alignment explanation
Indices: 54388719--54388797 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
54388709 CTTAATAATC
54388719 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
54388749 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
54388778 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
54388798 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:54396080 original size:44 final size:43
Alignment explanation
Indices: 54396017--54396271 Score: 118
Period size: 44 Copynumber: 5.6 Consensus size: 43
54396007 TGATCTATAA
* * * * *
54396017 TACTGTAA-CTTTAGAGAGATAAGATCCTTTGTTTTAATCTGCTC
1 TACTGTAATC-TTAGGGAGATAAGATAC-TAGCTTCAATCTGCTC
* *
54396061 TACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGCTT
1 TACTGTAATCTTAGGGAGATAAGA-TACTAGCTTCAATCTGCTC
* * * *
54396105 TGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATATGATCTAC
1 TACTGTAATCTTAGGGAGATAAGA-TACTAGCTTCAATC-----TG--CT-C
* * * * * * *
54396157 TATACTGTAAGT-TCAGAGAGATAAGATCCTTTGTTTTAATCCGCTC
1 --TACTGTAA-TCTTAGGGAGATAAGATAC-TAGCTTCAATCTGCTC
* * *
54396203 CACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTC
1 TACTGTAATCTTAGGGAGATAAGA-TACTAGCTTCAATCTGCTC
** * *
54396247 CGCTGTAATCTCAAGGAGATAAGAT
1 TACTGTAATCTTAGGGAGATAAGAT
54396272 TTCTGGCTTC
Statistics
Matches: 164, Mismatches: 31, Indels: 33
0.72 0.14 0.14
Matches are distributed among these distances:
43 2 0.01
44 118 0.72
45 5 0.03
46 1 0.01
47 2 0.01
49 3 0.02
51 2 0.01
53 2 0.01
54 28 0.17
55 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (43 bp):
TACTGTAATCTTAGGGAGATAAGATACTAGCTTCAATCTGCTC
Done.