Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 9 of 199
Found at i:2914149 original size:11 final size:11
Alignment explanation
Indices: 2914133--2914163 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2914123 GTGAAATATG
*
2914133 AAAATTAAATT
1 AAAATTAAATC
2914144 AAAATTAAATC
1 AAAATTAAATC
2914155 AAAATTAAA
1 AAAATTAAA
2914164 GTTTGATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAATTAAATC
Found at i:2915737 original size:151 final size:148
Alignment explanation
Indices: 2915467--2915920 Score: 630
Period size: 151 Copynumber: 3.0 Consensus size: 148
2915457 TTTTTTATTG
* *
2915467 AAAGTAATAAAATCCGGTAAAAAATACGAACATA-GGCCGAAATAAGTTTTTTTTTAAATTTATT
1 AAAGTAATAAAAT-CGGTAAAAAATACGAACAAAGGGCCGAAATAAG-ATTTTTTTAAATTTATT
2915531 TAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAT
64 T-AAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAT
*
2915596 TAGAAAATATTATATTTTTTA
128 TAGAAAATAATATATTTTTTA
*
2915617 AAAGTAATAAAATCTGGTGGAAAAATACGAACAAAGGGCCGAAATAATGATTTTTTTAAAATTTA
1 AAAGTAATAAAATC-GGT-AAAAAATACGAACAAAGGGCCGAAATAA-GATTTTTTT-AAATTTA
* * *
2915682 TTTAAAAA-ACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATATAAAATAATAAAA
62 TTTAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA
*
2915746 -TACGAAAATAATATATTTTTATTC
127 TTA-GAAAATAATATA-TTTT-TTA
** *
2915770 AAAGTAATAAAATC-CAAAAAAATACGAATAAAGGGCCGAAATAAGAAATTTTTTTAAATTTATT
1 AAAGTAATAAAATCGGTAAAAAATACGAACAAAGGGCCGAAATAAG--ATTTTTTTAAATTTATT
* *
2915834 TAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATTAGAAAATT
64 TAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATT
* *
2915899 AGAAAATAGTAT-TTATTTA
129 AGAAAATAATATATTTTTTA
2915918 AAA
1 AAA
2915921 ACACTCTTTT
Statistics
Matches: 272, Mismatches: 20, Indels: 26
0.86 0.06 0.08
Matches are distributed among these distances:
148 5 0.02
149 5 0.02
150 59 0.22
151 147 0.54
152 29 0.11
153 27 0.10
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (148 bp):
AAAGTAATAAAATCGGTAAAAAATACGAACAAAGGGCCGAAATAAGATTTTTTTAAATTTATTTA
AAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAG
AAAATAATATATTTTTTA
Found at i:2922764 original size:135 final size:135
Alignment explanation
Indices: 2922522--2922793 Score: 535
Period size: 135 Copynumber: 2.0 Consensus size: 135
2922512 AACTTCAATT
2922522 CAAGATTTGATCCGTATGAAACAAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTC
1 CAAGATTTGATCCGTATGAAACAAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTC
2922587 CCTATGAACCAAACCAACTAAACTGAATGATAGTCATAGCCTGACTTTTTGACTAGGTTATTAAG
66 CCTATGAACCAAACCAACTAAACTGAATGATAGTCATAGCCTGACTTTTTGACTAGGTTATTAAG
2922652 AAACC
131 AAACC
2922657 CAAGATTTGATCCGTATGAAACAAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTC
1 CAAGATTTGATCCGTATGAAACAAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTC
*
2922722 CCTATGACCCAAACCAACTAAACTGAATGATAGTCATAGCCTGACTTTTTGACTAGGTTATTAAG
66 CCTATGAACCAAACCAACTAAACTGAATGATAGTCATAGCCTGACTTTTTGACTAGGTTATTAAG
2922787 AAACC
131 AAACC
2922792 CA
1 CA
2922794 TTGTTTTTAG
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 136 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (135 bp):
CAAGATTTGATCCGTATGAAACAAACCAACTAAATCGGATGCATATCCCCAGTTTAGGCTCAGTC
CCTATGAACCAAACCAACTAAACTGAATGATAGTCATAGCCTGACTTTTTGACTAGGTTATTAAG
AAACC
Found at i:2923687 original size:39 final size:39
Alignment explanation
Indices: 2923644--2923805 Score: 211
Period size: 39 Copynumber: 4.2 Consensus size: 39
2923634 TGCCATACAC
*
2923644 TTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCAT
1 TTGCTGAGGATACATTGAACCCATCTGGCCAGCTGGCAT
* * *
2923683 TTGCTGAGGATACATTGAACCCATCTGGGCC-CCCGGCAC
1 TTGCTGAGGATACATTGAACCCATCT-GGCCAGCTGGCAT
* *
2923722 TTGCTGAGGATACATTGAACCCATCTGGCCCGTTGGCAT
1 TTGCTGAGGATACATTGAACCCATCTGGCCAGCTGGCAT
* * *
2923761 TTGCTGAGGATACATGGAACTCATCTGGCCCA-CAGGCAT
1 TTGCTGAGGATACATTGAACCCATCTGG-CCAGCTGGCAT
2923800 TTGCTG
1 TTGCTG
2923806 TGGAAGCATG
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
38 4 0.04
39 97 0.91
40 6 0.06
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.25
Consensus pattern (39 bp):
TTGCTGAGGATACATTGAACCCATCTGGCCAGCTGGCAT
Found at i:2923728 original size:78 final size:78
Alignment explanation
Indices: 2923641--2923805 Score: 251
Period size: 78 Copynumber: 2.1 Consensus size: 78
2923631 GGTTGCCATA
*
2923641 CACTTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCATTTGCTGAGGATACATTGAACCCA
1 CACTTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCATTTGCTGAGGATACATGGAACCCA
*
2923706 TCTGGGCCC-CCGG
66 TCT-GGCCCACAGG
* * * *
2923719 CACTTGCTGAGGATACATTGAACCCATCTGGCCCGTTGGCATTTGCTGAGGATACATGGAACTCA
1 CACTTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCATTTGCTGAGGATACATGGAACCCA
2923784 TCTGGCCCACAGG
66 TCTGGCCCACAGG
*
2923797 CATTTGCTG
1 CACTTGCTG
2923806 TGGAAGCATG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
77 5 0.06
78 74 0.94
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.24
Consensus pattern (78 bp):
CACTTGCTGAGGATACATCGAACCCATCTGGCCAGCTGGCATTTGCTGAGGATACATGGAACCCA
TCTGGCCCACAGG
Found at i:2926517 original size:205 final size:205
Alignment explanation
Indices: 2926058--2926673 Score: 1151
Period size: 205 Copynumber: 3.0 Consensus size: 205
2926048 AATATGCAAG
*
2926058 TAGAAACTGAACATAAAGAAACCACAACTTGCATTATATCTTTAGTAGGGGATTTAGCAGCGTGA
1 TAGAAACTGAACATAAAGAAACCACAACTTGCATTATATCTTTAGTAGAGGATTTAGCAGCGTGA
* *
2926123 AACTTCATAAACTTTCGAAAAGACTTTTCATTTTGAGAGCTGGAAAAACACAAGTTTACACAAAA
66 AACTTCATAAACTTTCGAAAAGACTTTTCATTATGAGAGCTGGAAAAACATAAGTTTACAC-AAA
*
2926188 AAAACGGGTTCACCATCCAATGAATTTGAGCATTGCCAACCAGATTTTTTCGCAAACGCCAGTTA
130 AAAACTGGTTCACCATCCAATGAATTTGAGCATTGCCAACCAGATTTTTTCGCAAACGCCAGTTA
2926253 TATTAAGACTT
195 TATTAAGACTT
2926264 TAGAAACTGAACATAAAGAAACCACAACTTGCATTATATCTTTAGTAGAGGATTTAGCAGCGTGA
1 TAGAAACTGAACATAAAGAAACCACAACTTGCATTATATCTTTAGTAGAGGATTTAGCAGCGTGA
2926329 AACTTCATAAACTTTCGAAAAGACTTTTCATTATGAGAGCTGGAAAAACATAAGTTTACACAAAA
66 AACTTCATAAACTTTCGAAAAGACTTTTCATTATGAGAGCTGGAAAAACATAAGTTTACACAAAA
*
2926394 AAACTGGTTCACCATCCAATGAATTTGAGCATTGCCAACCAGATTTTTTCGCAAATGCCAGTTAT
131 AAACTGGTTCACCATCCAATGAATTTGAGCATTGCCAACCAGATTTTTTCGCAAACGCCAGTTAT
2926459 ATTAAGACTT
196 ATTAAGACTT
2926469 TAGAAACTGAACATAAAGAAACCACAACTTGCATTATATCTTTAGTAGAGGATTTAGCAGCGTGA
1 TAGAAACTGAACATAAAGAAACCACAACTTGCATTATATCTTTAGTAGAGGATTTAGCAGCGTGA
*
2926534 AACTTCATAAACTTTCGAAAAGAATTTTCATTATGAGAGCTGGAAAAACATAAGTTTACACAAAA
66 AACTTCATAAACTTTCGAAAAGACTTTTCATTATGAGAGCTGGAAAAACATAAGTTTACACAAAA
* *
2926599 AAACTGGTTCACCATCCAATGAATTTGAGCATTCCCAACCAGATTTTTTTGCAAACGCCAGTTAT
131 AAACTGGTTCACCATCCAATGAATTTGAGCATTGCCAACCAGATTTTTTCGCAAACGCCAGTTAT
2926664 ATTAAGACTT
196 ATTAAGACTT
2926674 AGGTAGTCAC
Statistics
Matches: 401, Mismatches: 9, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
205 278 0.69
206 123 0.31
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (205 bp):
TAGAAACTGAACATAAAGAAACCACAACTTGCATTATATCTTTAGTAGAGGATTTAGCAGCGTGA
AACTTCATAAACTTTCGAAAAGACTTTTCATTATGAGAGCTGGAAAAACATAAGTTTACACAAAA
AAACTGGTTCACCATCCAATGAATTTGAGCATTGCCAACCAGATTTTTTCGCAAACGCCAGTTAT
ATTAAGACTT
Found at i:2934054 original size:17 final size:18
Alignment explanation
Indices: 2934032--2934071 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2934022 GTTTAGAAAT
*
2934032 TATTTTTATTAT-AGTAA
1 TATTTTTATAATAAGTAA
*
2934049 TATTTTTATAATAATTAA
1 TATTTTTATAATAAGTAA
2934067 TATTT
1 TATTT
2934072 AGAAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TATTTTTATAATAAGTAA
Found at i:2934989 original size:17 final size:17
Alignment explanation
Indices: 2934967--2935002 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2934957 TCTTTAGTGA
2934967 TATCAAAGAATAACTAT
1 TATCAAAGAATAACTAT
2934984 TATCAAAGAATAACTAT
1 TATCAAAGAATAACTAT
2935001 TA
1 TA
2935003 CATGCAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.31
Consensus pattern (17 bp):
TATCAAAGAATAACTAT
Found at i:2937442 original size:23 final size:23
Alignment explanation
Indices: 2937415--2937487 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
2937405 AGTGTTATTG
2937415 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
2937438 TTCAGTGGTAGCTACAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2937461 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2937484 ATCA
1 ATCA
2937488 ATGTGGCACT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2939238 original size:49 final size:49
Alignment explanation
Indices: 2939163--2939264 Score: 195
Period size: 49 Copynumber: 2.1 Consensus size: 49
2939153 AATCATATTT
*
2939163 TAAATATTGAAAATTTGAAATTGAACCACCGAAATGAACATCAATAATA
1 TAAATATTGAAAATTTGAAATCGAACCACCGAAATGAACATCAATAATA
2939212 TAAATATTGAAAATTTGAAATCGAACCACCGAAATGAACATCAATAATA
1 TAAATATTGAAAATTTGAAATCGAACCACCGAAATGAACATCAATAATA
2939261 TAAA
1 TAAA
2939265 CATCAATAGG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.25
Consensus pattern (49 bp):
TAAATATTGAAAATTTGAAATCGAACCACCGAAATGAACATCAATAATA
Found at i:2945621 original size:104 final size:104
Alignment explanation
Indices: 2945441--2945811 Score: 536
Period size: 104 Copynumber: 3.6 Consensus size: 104
2945431 AACCGTTATT
* * * *
2945441 GGTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCAGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
*
2945506 ATCAGCACATAGCAACCCTCTTTTTCATTTCAAAGATAC
66 ATCAGCACATAGCAACCCTCTTTTACATTTCAAAGATAC
2945545 GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
*
2945610 ATCAGCACATAGCAACCCT-TTTTCACATTTCAAAGATAT
66 ATCAGCACATAGCAACCCTCTTTT-ACATTTCAAAGATAC
* *
2945649 GGTGGATCA-CGCACATAGCACCACCAATGAACCGGGGAATCAACACTTAGCAACCCCTCGGGGG
1 GGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
* * *
2945713 AATCAGCACATAGCAACCCCCTTTCACATTT-AAAAATAC
65 AATCAGCACATAGCAACCCTCTTTTACATTTCAAAGATAC
* **
2945752 GGTGGA-CTCAGCACTTAGCAACCACCAAT-AAGTAGGGGAATCAGCACTTAGCAACCCCTC
1 GGTGGATATC-GCACTTAGC-ACCACCAATGAA-CCGGGGAATCAGCACTTAGCAACCCCTC
2945812 TATATGTAAT
Statistics
Matches: 243, Mismatches: 17, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
102 1 0.00
103 26 0.11
104 212 0.87
105 4 0.02
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCTCTTTTACATTTCAAAGATAC
Found at i:2946174 original size:31 final size:30
Alignment explanation
Indices: 2946143--2946200 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2946133 CCACTCAACT
2946143 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
2946173 TTTTGCATAATTACATTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
2946201 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:0.22, G:0.07, T:0.40
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:2947076 original size:42 final size:42
Alignment explanation
Indices: 2947016--2947117 Score: 168
Period size: 42 Copynumber: 2.4 Consensus size: 42
2947006 GGCTGTTACA
*
2947016 CATAAGGGTTAAACTGAAGCTTAAAAGAGCTGAACGAAAACC
1 CATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACGAAAACC
* *
2947058 CATAAGGGTTAAATTGAAGCTCAAAAGAGCTGAACGGAAACC
1 CATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACGAAAACC
*
2947100 CATAAAGGTTAAACTGAA
1 CATAAGGGTTAAACTGAA
2947118 ACTCGTATGA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.18
Consensus pattern (42 bp):
CATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACGAAAACC
Found at i:2947118 original size:21 final size:21
Alignment explanation
Indices: 2947053--2947119 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2947043 AGCTGAACGA
* *
2947053 AAACCCATAAGGGTTAAATTG
1 AAACCCATAAAGGTTAAACTG
* * * * *
2947074 AAGCTCA-AAAGAGCTGAACGG
1 AAACCCATAAAG-GTTAAACTG
2947095 AAACCCATAAAGGTTAAACTG
1 AAACCCATAAAGGTTAAACTG
2947116 AAAC
1 AAAC
2947120 TCGTATGAGT
Statistics
Matches: 32, Mismatches: 12, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
20 3 0.09
21 25 0.78
22 4 0.12
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.16
Consensus pattern (21 bp):
AAACCCATAAAGGTTAAACTG
Found at i:2947241 original size:24 final size:24
Alignment explanation
Indices: 2947209--2947256 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2947199 TACTTGGGTA
2947209 ATTTGCCGTCAATTCATCCTTTGC
1 ATTTGCCGTCAATTCATCCTTTGC
2947233 ATTTGCCGTCAATTCATCCTTTGC
1 ATTTGCCGTCAATTCATCCTTTGC
2947257 CACAAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.29, G:0.12, T:0.42
Consensus pattern (24 bp):
ATTTGCCGTCAATTCATCCTTTGC
Found at i:2947400 original size:45 final size:46
Alignment explanation
Indices: 2947315--2947402 Score: 124
Period size: 45 Copynumber: 1.9 Consensus size: 46
2947305 TTTTCAATTC
* * * *
2947315 ATAATTTAACAATATTTCATTTTTTTAACAATATGCTAAATACATA
1 ATAATTTAACAACATTCCATTTTTTCAACAATATACTAAATACATA
*
2947361 ATAATTTAACAACATTCCA-TTTTTCAACAATATATTAAATAC
1 ATAATTTAACAACATTCCATTTTTTCAACAATATACTAAATAC
2947403 GTAACATCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 20 0.54
46 17 0.46
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.41
Consensus pattern (46 bp):
ATAATTTAACAACATTCCATTTTTTCAACAATATACTAAATACATA
Found at i:2949217 original size:29 final size:28
Alignment explanation
Indices: 2949173--2949251 Score: 81
Period size: 32 Copynumber: 2.8 Consensus size: 28
2949163 TTTCTTTCCT
*
2949173 TATATA-CTAAATAAAATAATAAAATAA
1 TATATATCTAATTAAAATAATAAAATAA
*
2949200 TAATATATCTCATTAAAATATTAATAAAATAA
1 T-ATATATCTAATT-AAA-A-TAATAAAATAA
*
2949232 TATTTATCTAATT-AAATAAT
1 TATATATCTAATTAAAATAAT
2949252 TATAAAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
27 5 0.12
28 6 0.14
29 6 0.14
30 3 0.07
31 11 0.26
32 12 0.28
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (28 bp):
TATATATCTAATTAAAATAATAAAATAA
Found at i:2949246 original size:31 final size:32
Alignment explanation
Indices: 2949180--2949260 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
2949170 CCTTATATAC
* *
2949180 TAAATAAAATAATAAAATAATAATATATCTCAT
1 TAAAT-AATTAATAAAATAATAATATATCTAAT
*
2949213 TAAA-ATATTAATAAAATAAT-ATTTATCTAAT
1 TAAATA-ATTAATAAAATAATAATATATCTAAT
2949244 TAAATAATT-ATAAAATA
1 TAAATAATTAATAAAATA
2949261 TCATCAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
30 8 0.19
31 17 0.40
32 14 0.33
33 4 0.09
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (32 bp):
TAAATAATTAATAAAATAATAATATATCTAAT
Found at i:2951229 original size:18 final size:19
Alignment explanation
Indices: 2951203--2951241 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2951193 TACATATAAT
*
2951203 TACACTAAA-CTAAATTTA
1 TACACTAAATCAAAATTTA
*
2951221 TACATTAAATCAAAATTTA
1 TACACTAAATCAAAATTTA
2951240 TA
1 TA
2951242 TATAATTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (19 bp):
TACACTAAATCAAAATTTA
Found at i:2953752 original size:11 final size:11
Alignment explanation
Indices: 2953716--2953759 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
2953706 TCTGGAAAGT
2953716 AAATAACAAAT-
1 AAATAA-AAATA
2953727 AAATAAAAATAA
1 AAATAAAAAT-A
2953739 AAATAAAAATA
1 AAATAAAAATA
*
2953750 AAACAAAAAT
1 AAATAAAAAT
2953760 GAAGTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 4 0.13
11 16 0.53
12 10 0.33
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:2953758 original size:6 final size:6
Alignment explanation
Indices: 2953727--2953752 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2953717 AATAACAAAT
2953727 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
2953753 CAAAAATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:2966804 original size:2 final size:2
Alignment explanation
Indices: 2966797--2966823 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2966787 TATGTGCCTA
2966797 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
2966824 TAAACGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2972011 original size:34 final size:34
Alignment explanation
Indices: 2971968--2972034 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
2971958 AAACACCGAT
2971968 AACACAGCCAAAGCAATAAGGTTTACAGAAAGGA
1 AACACAGCCAAAGCAATAAGGTTTACAGAAAGGA
*
2972002 AACACAGCCAAAGCAATAAGGTTTACAGGAAGG
1 AACACAGCCAAAGCAATAAGGTTTACAGAAAGG
2972035 TATTATCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (34 bp):
AACACAGCCAAAGCAATAAGGTTTACAGAAAGGA
Found at i:2973892 original size:28 final size:27
Alignment explanation
Indices: 2973826--2973893 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
2973816 AACTTAGGTG
*
2973826 CCAAATTGGAAC-AAAAAAAATCAAGTA
1 CCAAATT-GAACAAAAAAAAAACAAGTA
* *
2973853 CCAAAGTGGAACAAAAAAAAAACTAGATA
1 CCAAA-TTGAACAAAAAAAAAACAAG-TA
2973882 CCAAATTGAACA
1 CCAAATTGAACA
2973894 TTAAAACTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 9 0.26
28 18 0.53
29 7 0.21
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.13
Consensus pattern (27 bp):
CCAAATTGAACAAAAAAAAAACAAGTA
Found at i:2973899 original size:28 final size:28
Alignment explanation
Indices: 2973789--2973899 Score: 66
Period size: 28 Copynumber: 3.9 Consensus size: 28
2973779 CTACTTGATT
* **
2973789 TAGATACTAAATTGAACATTGAAGCCAAAC
1 TAGATACCAAATTGAACATT-AA-AAAAAC
* *
2973819 TTAGGTGCCAAATTGGAACA--AAAAAAATC
1 -TAGATACCAAATT-GAACATTAAAAAAA-C
* * **
2973848 AAG-TACCAAAGTGGAACAAAAAAAAAAC
1 TAGATACCAAA-TTGAACATTAAAAAAAC
2973876 TAGATACCAAATTGAACATTAAAA
1 TAGATACCAAATTGAACATTAAAA
2973900 CTAATCTCGG
Statistics
Matches: 62, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
27 11 0.18
28 19 0.31
29 17 0.27
31 10 0.16
32 5 0.08
ACGTcount: A:0.53, C:0.14, G:0.14, T:0.19
Consensus pattern (28 bp):
TAGATACCAAATTGAACATTAAAAAAAC
Found at i:2975613 original size:30 final size:30
Alignment explanation
Indices: 2975577--2975637 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2975567 CTAGCGACTT
* *
2975577 TAATGAGATATTCTCATTTTTTGTAGGGGG
1 TAATGAGATATTCCCATTTTATGTAGGGGG
2975607 TAATGAGATATTCCCATTTTATGTAGGGGG
1 TAATGAGATATTCCCATTTTATGTAGGGGG
2975637 T
1 T
2975638 GCTCTTTCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (30 bp):
TAATGAGATATTCCCATTTTATGTAGGGGG
Found at i:2979514 original size:10 final size:10
Alignment explanation
Indices: 2979485--2979523 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
2979475 AACAAAGTAT
2979485 ATAAATTTTA
1 ATAAATTTTA
2979495 GATAAATTTTA
1 -ATAAATTTTA
*
2979506 ATAATTTTTA
1 ATAAATTTTA
*
2979516 AAAAATTT
1 ATAAATTT
2979524 CAAATAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (10 bp):
ATAAATTTTA
Found at i:2983030 original size:36 final size:38
Alignment explanation
Indices: 2982990--2983068 Score: 99
Period size: 36 Copynumber: 2.1 Consensus size: 38
2982980 AATTAACTAG
*
2982990 TAATTAAATAATTAAAATTTGAAGAAAA-AA-TTAATT
1 TAATTAAATAATTAAAATTTCAAGAAAATAAGTTAATT
* * *
2983026 TAATTAAGTAATTATAATTTCATGAAAATAAGTTAATT
1 TAATTAAATAATTAAAATTTCAAGAAAATAAGTTAATT
*
2983064 AAATT
1 TAATT
2983069 TATTTCTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
36 24 0.67
37 2 0.06
38 10 0.28
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.39
Consensus pattern (38 bp):
TAATTAAATAATTAAAATTTCAAGAAAATAAGTTAATT
Found at i:2984065 original size:22 final size:21
Alignment explanation
Indices: 2984037--2984084 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
2984027 ATAACTGAAT
*
2984037 TAAATATAGATTTAAAATTATA
1 TAAATATAAATTTAAAA-TATA
*
2984059 TAAATATAAATTTAAAATATT
1 TAAATATAAATTTAAAATATA
2984080 TAAAT
1 TAAAT
2984085 TTAATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TAAATATAAATTTAAAATATA
Found at i:2986303 original size:21 final size:21
Alignment explanation
Indices: 2986279--2986406 Score: 75
Period size: 21 Copynumber: 6.1 Consensus size: 21
2986269 CGTGTTTGCT
2986279 TTCAGTTTAGCTCTTATGAGC
1 TTCAGTTTAGCTCTTATGAGC
* * *
2986300 TTCA-ATTAACT-TATATGAGT
1 TTCAGTTTAGCTCT-TATGAGC
* * *
2986320 TTCAGTTTAACCCCTT-TGAGT
1 TTCAGTTT-AGCTCTTATGAGC
* * *
2986341 TTTAATTTAGCTCTTTTGAGC
1 TTCAGTTTAGCTCTTATGAGC
* * * *
2986362 TTTAGTTTAACTCTTATGGGTT
1 TTCAGTTTAGCTCTTATGAG-C
*
2986384 TTC-GTTCAGCTCTTATGAGC
1 TTCAGTTTAGCTCTTATGAGC
2986404 TTC
1 TTC
2986407 CATTTAACCT
Statistics
Matches: 80, Mismatches: 21, Indels: 13
0.70 0.18 0.11
Matches are distributed among these distances:
19 1 0.01
20 23 0.29
21 50 0.62
22 5 0.06
23 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.47
Consensus pattern (21 bp):
TTCAGTTTAGCTCTTATGAGC
Found at i:2986385 original size:42 final size:42
Alignment explanation
Indices: 2986339--2986427 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
2986329 ACCCCTTTGA
* * *
2986339 GTTTTAATTTAGCTCTTTTGAGCTT-TAGTTTAA-CTCTTATGG
1 GTTTTAATTCAGCTCTTATGAGCTTCCA-TTTAACCT-TTATGG
**
2986381 GTTTTCGTTCAGCTCTTATGAGCTTCCATTTAACCTTTATGG
1 GTTTTAATTCAGCTCTTATGAGCTTCCATTTAACCTTTATGG
2986423 GTTTT
1 GTTTT
2986428 CGTTTAGCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 37 0.93
43 3 0.08
ACGTcount: A:0.17, C:0.16, G:0.17, T:0.51
Consensus pattern (42 bp):
GTTTTAATTCAGCTCTTATGAGCTTCCATTTAACCTTTATGG
Found at i:2986428 original size:42 final size:43
Alignment explanation
Indices: 2986349--2986448 Score: 125
Period size: 42 Copynumber: 2.4 Consensus size: 43
2986339 GTTTTAATTT
* *
2986349 AGCTCTTTTGAGCTT-TAGTTTAACTCTTATGGGTTTTCGTTC
1 AGCTCTTATGAGCTTCCAGTTTAACTCTTATGGGTTTTCGTTC
*
2986391 AGCTCTTATGAGCTTCCA-TTTAAC-CTTTATGGGTTTTCGTTT
1 AGCTCTTATGAGCTTCCAGTTTAACTC-TTATGGGTTTTCGTTC
* *
2986433 AGCACTTATGTGCTTC
1 AGCTCTTATGAGCTTC
2986449 TGTGCAACCT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
41 1 0.02
42 49 0.96
43 1 0.02
ACGTcount: A:0.16, C:0.19, G:0.18, T:0.47
Consensus pattern (43 bp):
AGCTCTTATGAGCTTCCAGTTTAACTCTTATGGGTTTTCGTTC
Found at i:2986433 original size:21 final size:21
Alignment explanation
Indices: 2986366--2986442 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
2986356 TTGAGCTTTA
2986366 GTTTAACTCTTATGGGTTTTC
1 GTTTAACTCTTATGGGTTTTC
* * * * *
2986387 GTTCAGCTCTTATGAGCTTCC
1 GTTTAACTCTTATGGGTTTTC
*
2986408 ATTTAAC-CTTTATGGGTTTTC
1 GTTTAACTC-TTATGGGTTTTC
* *
2986429 GTTTAGCACTTATG
1 GTTTAACTCTTATG
2986443 TGCTTCTGTG
Statistics
Matches: 41, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
20 1 0.02
21 39 0.95
22 1 0.02
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.47
Consensus pattern (21 bp):
GTTTAACTCTTATGGGTTTTC
Found at i:2986458 original size:42 final size:42
Alignment explanation
Indices: 2986375--2986461 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 42
2986365 AGTTTAACTC
* **
2986375 TTATGGGTTTTCGTTCAGCTCTTATGAGCTTCCATTTAACCT
1 TTATGGGTTTTCGTTCAGCACTTATGAGCTTCCATGCAACCT
* * **
2986417 TTATGGGTTTTCGTTTAGCACTTATGTGCTTCTGTGCAACCT
1 TTATGGGTTTTCGTTCAGCACTTATGAGCTTCCATGCAACCT
2986459 TTA
1 TTA
2986462 GGCTTTTGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (42 bp):
TTATGGGTTTTCGTTCAGCACTTATGAGCTTCCATGCAACCT
Found at i:2994271 original size:11 final size:11
Alignment explanation
Indices: 2994251--2994288 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
2994241 AAAATAATAA
2994251 AGAAACAGAGG
1 AGAAACAGAGG
*
2994262 AGAAAGAGAGG
1 AGAAACAGAGG
*
2994273 AGAAACAGGGG
1 AGAAACAGAGG
2994284 AGAAA
1 AGAAA
2994289 GAAAGAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.55, C:0.05, G:0.39, T:0.00
Consensus pattern (11 bp):
AGAAACAGAGG
Found at i:2994955 original size:13 final size:14
Alignment explanation
Indices: 2994937--2994965 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2994927 GTACTACAAG
2994937 ATTATTTT-TTTAA
1 ATTATTTTATTTAA
2994950 ATTATTTTATTTAA
1 ATTATTTTATTTAA
2994964 AT
1 AT
2994966 GTCTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTATTTTATTTAA
Found at i:2995001 original size:5 final size:5
Alignment explanation
Indices: 2994993--2995023 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
2994983 GAGTTATTTA
*
2994993 AAAAT AAAAT AAAAT AAAGT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
2995024 TTATGGAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:2995347 original size:25 final size:25
Alignment explanation
Indices: 2995311--2995390 Score: 108
Period size: 25 Copynumber: 3.2 Consensus size: 25
2995301 ACTTTAGCTC
* *
2995311 GCTCTCTAATTATTAGCGCGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
2995336 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
**
2995361 GCTCTCTGA-TATTTAGCACGTCAGT
1 GCTCTCTGATTA-TTAGCACGTTGGT
2995386 GCTCT
1 GCTCT
2995391 TTGTTTAGCA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 2 0.04
25 48 0.96
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.39
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTGGT
Found at i:2995400 original size:22 final size:22
Alignment explanation
Indices: 2995372--2995417 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2995362 CTCTCTGATA
* *
2995372 TTTAGCACGTCAGTGCTCTTTG
1 TTTAGCACATCAGTGCTCTCTG
*
2995394 TTTAGCACATCTGTGCTCTCTG
1 TTTAGCACATCAGTGCTCTCTG
2995416 TT
1 TT
2995418 CATTAGTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (22 bp):
TTTAGCACATCAGTGCTCTCTG
Found at i:2996142 original size:175 final size:175
Alignment explanation
Indices: 2995851--2996201 Score: 648
Period size: 175 Copynumber: 2.0 Consensus size: 175
2995841 ACTTGAAATA
* *
2995851 TTTTGGTATATATATGAAATGAATTAATGGAACTATACGTATGTTTGCAAATATGGTTGGTAAGT
1 TTTTGGTATATATATGAAATGAATTAATGAAACTATACGTATGTTTGCAAATATGGTTGGTAAAT
2995916 TAAAATACTATGTATAAATGTTTTAATTAAACAATATCTAGCTATAACCGTTTTGACACCAAATG
66 TAAAATACTATGTATAAATGTTTTAATTAAACAATATCTAGCTATAACCGTTTTGACACCAAATG
* *
2995981 TAATAGTCTTATACCGGGTCTGTACGATTAGGCCAGGTATATGGT
131 TAATAGTCTTATACCGGGTCTGTACGATTAGACCAGGTATAGGGT
2996026 TTTTGGTATATATATGAAATGAATTAATGAAACTATACGTATGTTTGCAAATATGGTTGGTAAAT
1 TTTTGGTATATATATGAAATGAATTAATGAAACTATACGTATGTTTGCAAATATGGTTGGTAAAT
2996091 TAAAATACTATGTATAAATGTTTTAATTAAACAATATCTAGCTATAACCGTTTTGACACCAAATG
66 TAAAATACTATGTATAAATGTTTTAATTAAACAATATCTAGCTATAACCGTTTTGACACCAAATG
* *
2996156 TAATAGTCTTATACTGGGTTTGTACGATTAGACCAGGTATAGGGT
131 TAATAGTCTTATACCGGGTCTGTACGATTAGACCAGGTATAGGGT
2996201 T
1 T
2996202 GTTACAGGTC
Statistics
Matches: 170, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
175 170 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (175 bp):
TTTTGGTATATATATGAAATGAATTAATGAAACTATACGTATGTTTGCAAATATGGTTGGTAAAT
TAAAATACTATGTATAAATGTTTTAATTAAACAATATCTAGCTATAACCGTTTTGACACCAAATG
TAATAGTCTTATACCGGGTCTGTACGATTAGACCAGGTATAGGGT
Found at i:2996787 original size:25 final size:26
Alignment explanation
Indices: 2996741--2996790 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
2996731 TAGAAATTTA
2996741 GTTAAAAAGATTAAGTAATTTTTTTGT
1 GTTAAAAAGA-TAAGTAATTTTTTTGT
**
2996768 GTTAAAAAG-TAAGTTTTTTTTTT
1 GTTAAAAAGATAAGTAATTTTTTT
2996791 TGAGAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
27 9 0.43
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (26 bp):
GTTAAAAAGATAAGTAATTTTTTTGT
Found at i:3010069 original size:24 final size:21
Alignment explanation
Indices: 3010036--3010078 Score: 59
Period size: 24 Copynumber: 1.9 Consensus size: 21
3010026 TGTCATGTCA
3010036 TTTTTAATTAATATCTTAAATGT
1 TTTTTAATTAA-AT-TTAAATGT
3010059 TTTTATAATTAAATTTAAAT
1 TTTT-TAATTAAATTTAAAT
3010079 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 6 0.32
24 7 0.37
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTTAATTAAATTTAAATGT
Found at i:3029335 original size:2 final size:2
Alignment explanation
Indices: 3029328--3029357 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3029318 TCGTTAAGCC
3029328 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3029358 CCCTTGCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3036587 original size:5 final size:5
Alignment explanation
Indices: 3036577--3036606 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3036567 CACTTTCCAT
*
3036577 ACCCA ACCCA ACTCA ACCCA ACCCA ACCCA
1 ACCCA ACCCA ACCCA ACCCA ACCCA ACCCA
3036607 TACACATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.40, C:0.57, G:0.00, T:0.03
Consensus pattern (5 bp):
ACCCA
Found at i:3045522 original size:52 final size:52
Alignment explanation
Indices: 3045431--3045530 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 52
3045421 ATGTCATAAT
* *
3045431 TATTACTTATCTCTTAATTAATTTAAATATTAAGCGATAAATAATAAAAATA
1 TATTACTTATCTCTTAATTAATTTAAATAATAAGAGATAAATAATAAAAATA
* * *
3045483 TATTA-TTATTTCTTGAATTAA-TTAAATTAATATGAGATAAATAGTAAA
1 TATTACTTATCTCTT-AATTAATTTAAA-TAATAAGAGATAAATAATAAA
3045531 TATAAAAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
51 13 0.32
52 28 0.68
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (52 bp):
TATTACTTATCTCTTAATTAATTTAAATAATAAGAGATAAATAATAAAAATA
Found at i:3045553 original size:20 final size:20
Alignment explanation
Indices: 3045528--3045567 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3045518 GATAAATAGT
3045528 AAATAT-AAAAGAAGCTTTTG
1 AAATATGAAAAGAAG-TTTTG
*
3045548 AAATATGAAGAGAAGTTTTG
1 AAATATGAAAAGAAGTTTTG
3045568 GTACTTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (20 bp):
AAATATGAAAAGAAGTTTTG
Found at i:3045643 original size:13 final size:13
Alignment explanation
Indices: 3045625--3045650 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3045615 GTCAACTAAT
3045625 AATATGAAGACAC
1 AATATGAAGACAC
3045638 AATATGAAGACAC
1 AATATGAAGACAC
3045651 GTGGCAACCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
AATATGAAGACAC
Found at i:3050340 original size:14 final size:15
Alignment explanation
Indices: 3050301--3050340 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3050291 ATCAACAAAT
*
3050301 AATTTAAAAATTATA
1 AATTCAAAAATTATA
3050316 AATTCAAAAAATTA-A
1 AATTC-AAAAATTATA
3050331 AATTCAAAAA
1 AATTCAAAAA
3050341 ATATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 10 0.43
16 8 0.35
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (15 bp):
AATTCAAAAATTATA
Found at i:3050341 original size:15 final size:16
Alignment explanation
Indices: 3050306--3050342 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
3050296 CAAATAATTT
3050306 AAAAATTATAAATTCA
1 AAAAATTATAAATTCA
3050322 AAAAATTA-AAATTCA
1 AAAAATTATAAATTCA
3050337 AAAAAT
1 AAAAAT
3050343 ATTAAAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAATTATAAATTCA
Found at i:3050931 original size:18 final size:18
Alignment explanation
Indices: 3050910--3050944 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3050900 AATAATAAAT
3050910 TTAA-ATTTTATATTAATA
1 TTAATATTTT-TATTAATA
3050928 TTAATATTTTTATTAAT
1 TTAATATTTTTATTAAT
3050945 GATTCACAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATATTTTTATTAATA
Found at i:3069834 original size:26 final size:25
Alignment explanation
Indices: 3069758--3069837 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
3069748 ATTATTATTG
*
3069758 TTAAATTATATTTAATAATAATTTTA
1 TTAAATTATATTT-ATAATAATCTTA
* *
3069784 TTAAAATATGA-TTA-AAT-TTCTTA
1 TTAAATTAT-ATTTATAATAATCTTA
*
3069807 TTAAATTATATTTAGTAATAATCCTA
1 TTAAATTATATTTA-TAATAATCTTA
3069833 TTAAA
1 TTAAA
3069838 ATTTAATAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
22 1 0.02
23 15 0.35
24 3 0.07
25 4 0.09
26 19 0.44
27 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (25 bp):
TTAAATTATATTTATAATAATCTTA
Found at i:3070041 original size:16 final size:16
Alignment explanation
Indices: 3070022--3070066 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3070012 ATTATAACTT
3070022 TATTTCATTACAGCTC
1 TATTTCATTACAGCTC
* *
3070038 TATTCCGTTACAGCTC
1 TATTTCATTACAGCTC
3070054 TA-TTCTATTACAG
1 TATTTC-ATTACAG
3070067 TGAACTAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 2 0.08
16 22 0.92
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (16 bp):
TATTTCATTACAGCTC
Found at i:3077078 original size:94 final size:95
Alignment explanation
Indices: 3076969--3077157 Score: 299
Period size: 94 Copynumber: 2.0 Consensus size: 95
3076959 TTATAATAAT
*
3076969 TGAGAAAAAAAGTACCTGCTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGG
1 TGAGAAAAAAAGTACCTACTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGG
* *
3077034 AAGCGCACAGAGGGAATGAAAGAGGAAGCA
66 AAGCACACAGAGGCAATGAAAGAGGAAGCA
* ** *
3077064 TGAG-AAAAAGGTACCTACTGCAAGAATGGTATTGCCAGCTCTAGAACTTCAAAAACAAAAAGGG
1 TGAGAAAAAAAGTACCTACTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGG
*
3077128 AAGCACGCAGAGGCAATGAAAGAGGAAGCA
66 AAGCACACAGAGGCAATGAAAGAGGAAGCA
3077158 CTCAGGCTAA
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 82 0.95
95 4 0.05
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (95 bp):
TGAGAAAAAAAGTACCTACTGCAAGAATGGTATCACCAACTCTAGAACTTCAAAAACAAAAAGGG
AAGCACACAGAGGCAATGAAAGAGGAAGCA
Found at i:3077526 original size:29 final size:29
Alignment explanation
Indices: 3077493--3077550 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3077483 AAAATAAAAG
3077493 TAAGTCAAATAGTCAAAACCAACTTGGTT
1 TAAGTCAAATAGTCAAAACCAACTTGGTT
3077522 TAAGTCAAATAGTCAAAACCAACTTGGTT
1 TAAGTCAAATAGTCAAAACCAACTTGGTT
3077551 CTTTGTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (29 bp):
TAAGTCAAATAGTCAAAACCAACTTGGTT
Found at i:3080656 original size:22 final size:21
Alignment explanation
Indices: 3080638--3080680 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3080628 AGGATAAAAT
3080638 TGAAAAGATAAAAAAATAAAGA
1 TGAAAA-ATAAAAAAATAAAGA
* *
3080660 TGATAAATAATAAAATAAAGA
1 TGAAAAATAAAAAAATAAAGA
3080681 AAATATCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.19
Consensus pattern (21 bp):
TGAAAAATAAAAAAATAAAGA
Found at i:3083216 original size:199 final size:199
Alignment explanation
Indices: 3082861--3083268 Score: 543
Period size: 199 Copynumber: 2.1 Consensus size: 199
3082851 TACATGGGAG
* * *
3082861 TGTGATTTGGTCGTGTGTCCCCTATATCTTTAAAATTGCAAAACAAAATGCTCAAGTATTTTCAC
1 TGTGGTTTGGTCGTCTATCCCCTATATCTTTAAAATTGCAAAACAAAATGCTCAAGTATTTTCAC
*
3082926 GCGAGCAGGCACACAGACGTCTGTCTCAGTCGTATATGGCACACAACCTGGTACACAGGCATGTG
66 GCGAGCAGGCACACAGACGTCTGTCTCAGTCGTATATGGCACACAACCTGGCACACAGGCATGTG
* * * *
3082991 ACTTGACCGTGTGGCCCCTGCACCTAATTAATGTAAATTAAATTATTCACACAACTTAGCACACG
131 ACTTGACCATGTGGCCCCTACACCTAATTAAAGTAAATTAAAATATTCACACAACTTAGCACACG
*
3083056 GGCA
196 AGCA
* * * *
3083060 TGTGGTTTGGTCGTCTATCCCCTGTATCTTTAAAATTGCAAAACAGAATGTTCAGGTATTTTCAC
1 TGTGGTTTGGTCGTCTATCCCCTATATCTTTAAAATTGCAAAACAAAATGCTCAAGTATTTTCAC
* * * ** *
3083125 ATG-GA-CAGGCACACGGACGTCTGTCTCAGTCGTATGTGGCACGCGGCCTGGCACAC-GAGCGT
66 --GCGAGCAGGCACACAGACGTCTGTCTCAGTCGTATATGGCACACAACCTGGCACACAG-GCAT
* * * * *
3083187 GTGACTTGACCATGTGGCTCTTACACCTAATTAAAGTAAATTAAAATGTTCACACAGCTTAGCAT
128 GTGACTTGACCATGTGGCCCCTACACCTAATTAAAGTAAATTAAAATATTCACACAACTTAGCAC
*
3083252 ACTAGCA
193 ACGAGCA
3083259 TGTGGTTTGG
1 TGTGGTTTGG
3083269 CCGTGTGACC
Statistics
Matches: 181, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
198 1 0.01
199 177 0.98
200 2 0.01
201 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (199 bp):
TGTGGTTTGGTCGTCTATCCCCTATATCTTTAAAATTGCAAAACAAAATGCTCAAGTATTTTCAC
GCGAGCAGGCACACAGACGTCTGTCTCAGTCGTATATGGCACACAACCTGGCACACAGGCATGTG
ACTTGACCATGTGGCCCCTACACCTAATTAAAGTAAATTAAAATATTCACACAACTTAGCACACG
AGCA
Found at i:3088506 original size:26 final size:26
Alignment explanation
Indices: 3088477--3088527 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3088467 TGGATAATCA
3088477 TTAATC-AGGAAGCTCACAAAGAGCCT
1 TTAATCGA-GAAGCTCACAAAGAGCCT
* *
3088503 TTAATCGAGAATCTCACTAAGAGCC
1 TTAATCGAGAAGCTCACAAAGAGCC
3088528 ATATATCGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (26 bp):
TTAATCGAGAAGCTCACAAAGAGCCT
Found at i:3088535 original size:26 final size:26
Alignment explanation
Indices: 3088489--3088551 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 26
3088479 AATCAGGAAG
* *
3088489 CTCACAAAGAGCCTTTAATCGAGAAT-
1 CTCACTAAGAGCCTATAATCG-GAATA
*
3088515 CTCACTAAGAGCC-ATATATCGGGATA
1 CTCACTAAGAGCCTATA-ATCGGAATA
3088541 CTCA-TAAGAGC
1 CTCACTAAGAGC
3088552 TGCAGTGTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 12 0.38
26 20 0.62
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (26 bp):
CTCACTAAGAGCCTATAATCGGAATA
Found at i:3088623 original size:24 final size:25
Alignment explanation
Indices: 3088602--3088668 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
3088592 GGATGCTCCG
* *
3088602 AAGAGCTAT-TAACGGGAAGCTCGC
1 AAGAGCCATATAACGGGAAGCTCGA
*
3088626 AAGAACCATATAACGGGAAGCTCGA
1 AAGAGCCATATAACGGGAAGCTCGA
*
3088651 AAGAGCCATATATCGGGA
1 AAGAGCCATATAACGGGA
3088669 TGTTTATGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 7 0.19
25 30 0.81
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.15
Consensus pattern (25 bp):
AAGAGCCATATAACGGGAAGCTCGA
Found at i:3089034 original size:10 final size:10
Alignment explanation
Indices: 3089009--3089075 Score: 53
Period size: 11 Copynumber: 6.4 Consensus size: 10
3088999 TATACAAATG
*
3089009 AATTTAACATC
1 AATTTAATA-C
3089020 AATTTAATAC
1 AATTTAATAC
*
3089030 AATTTACATTC
1 AATTTA-ATAC
3089041 AATTTAATAC
1 AATTTAATAC
* *
3089051 AAGTTACATTC
1 AATTTA-ATAC
* *
3089062 AATTCAATCC
1 AATTTAATAC
3089072 AATT
1 AATT
3089076 CACATCTTAG
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
10 22 0.48
11 24 0.52
ACGTcount: A:0.43, C:0.16, G:0.01, T:0.39
Consensus pattern (10 bp):
AATTTAATAC
Found at i:3089035 original size:21 final size:21
Alignment explanation
Indices: 3089009--3089080 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
3088999 TATACAAATG
3089009 AATTTAACA-TCAATTTAATAC
1 AATTT-ACATTCAATTTAATAC
3089030 AATTTACATTCAATTTAATAC
1 AATTTACATTCAATTTAATAC
* * *
3089051 AAGTTACATTCAATTCAATCC
1 AATTTACATTCAATTTAATAC
*
3089072 AATTCACAT
1 AATTTACAT
3089081 CTTAGGCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
20 3 0.07
21 42 0.93
ACGTcount: A:0.43, C:0.18, G:0.01, T:0.38
Consensus pattern (21 bp):
AATTTACATTCAATTTAATAC
Found at i:3096558 original size:59 final size:59
Alignment explanation
Indices: 3096462--3096573 Score: 215
Period size: 59 Copynumber: 1.9 Consensus size: 59
3096452 AAAAAATTAT
3096462 TTTTTTCGTGTTAGAATCAGATATAAATATACAAAAAAAATAAAAAAAATTTCCTTTTC
1 TTTTTTCGTGTTAGAATCAGATATAAATATACAAAAAAAATAAAAAAAATTTCCTTTTC
*
3096521 TTTTTTCGTGTTAGAATCAGATATAAATATACGAAAAAAATAAAAAAAATTTC
1 TTTTTTCGTGTTAGAATCAGATATAAATATACAAAAAAAATAAAAAAAATTTC
3096574 TTGGGTGTCG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (59 bp):
TTTTTTCGTGTTAGAATCAGATATAAATATACAAAAAAAATAAAAAAAATTTCCTTTTC
Found at i:3096650 original size:105 final size:103
Alignment explanation
Indices: 3096521--3096747 Score: 318
Period size: 105 Copynumber: 2.2 Consensus size: 103
3096511 TTTCCTTTTC
* *
3096521 TTTTTTCGTGTTAGAATCAGATATAAATATACGAAAAAAATAAAAAAAATTTCTTGGGTG-TCGG
1 TTTTTTCGTGTCAGAATCAAATATAAATATACGAAAAAAATAAAAAAAA-TT-TTGGGTGCT-GG
3096585 CCATTG-A-GGCCAGCACCCAGTACAAATTTAAAAAAAATT-AT
63 CC--TGCATGGCCAGCACCCAGTACAAA-TTAAAAAAAATTCAT
3096626 TTTTTTCGTGTCAGAATCAAATATAAATATACGAAAAAAATAAAAAAAATTTTGGGTGCTGGCCT
1 TTTTTTCGTGTCAGAATCAAATATAAATATACGAAAAAAATAAAAAAAATTTTGGGTGCTGGCCT
* *
3096691 GCCAATGGCCGGCACCCAGTACAAATTAAAAAAAATTCTT
66 G-C-ATGGCCAGCACCCAGTACAAATTAAAAAAAATTCAT
3096731 TTTTTTCGTGTCAGAAT
1 TTTTTTCGTGTCAGAAT
3096748 TAGAATTTTT
Statistics
Matches: 112, Mismatches: 4, Indels: 12
0.88 0.03 0.09
Matches are distributed among these distances:
101 2 0.02
103 11 0.10
104 16 0.14
105 83 0.74
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (103 bp):
TTTTTTCGTGTCAGAATCAAATATAAATATACGAAAAAAATAAAAAAAATTTTGGGTGCTGGCCT
GCATGGCCAGCACCCAGTACAAATTAAAAAAAATTCAT
Found at i:3097284 original size:104 final size:102
Alignment explanation
Indices: 3096986--3097319 Score: 455
Period size: 105 Copynumber: 3.2 Consensus size: 102
3096976 CTGGGTGCTG
*
3096986 GCACCCAAATTTTTTTTATTTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAATT
1 GCACCCAAATTTTTTTTATTTTTTTCGTATATTTATATCTGATTCT-ACAC--AAAAAAA-TATT
* * *
3097051 TTTTTTTAAAATTGTACTGGGTACCGGCCATTGACAAGCCA
62 TTTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCA
* * **
3097092 GCACCCAAA-TTTTTTTATTTTTTTCGTATATTTATATCTGATTCT---GATATGAAT-TTTTTT
1 GCACCCAAATTTTTTTTATTTTTTTCGTATATTTATATCTGATTCTACACAAAAAAATATTTTTT
3097152 TTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCA
66 TTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCA
* *
3097189 GCACCCAAATTTTTTTTAAAATTTTTTCGTATATTTATATCTGATTCTAACACAAAAAAATACTT
1 GCACCCAAATTTTTTTT--ATTTTTTTCGTATATTTATATCTGATTCT-ACACAAAAAAATATTT
3097254 TTTTTT-AATTTGTACTGGGTGCCGGCCATTGACAGGCCA
63 TTTTTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCA
3097293 GCACCCAAAATTTTTTTTCATTTTTTT
1 GCACCC-AAATTTTTTTT-ATTTTTTT
3097320 TTCTTTTTTC
Statistics
Matches: 203, Mismatches: 16, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
97 49 0.24
98 7 0.03
99 4 0.02
100 28 0.14
104 51 0.25
105 55 0.27
106 9 0.04
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (102 bp):
GCACCCAAATTTTTTTTATTTTTTTCGTATATTTATATCTGATTCTACACAAAAAAATATTTTTT
TTTAAATTTGTACTGGGTGCCGGCCATTGACAGGCCA
Found at i:3100745 original size:25 final size:25
Alignment explanation
Indices: 3100711--3100762 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
3100701 GTTGTCTTCT
3100711 TTGTAATCACATTTGAAAGGAGACC
1 TTGTAATCACATTTGAAAGGAGACC
3100736 TTGTAATCACATTTGAAAGGAGACC
1 TTGTAATCACATTTGAAAGGAGACC
3100761 TT
1 TT
3100763 TATTTATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (25 bp):
TTGTAATCACATTTGAAAGGAGACC
Found at i:3110528 original size:62 final size:62
Alignment explanation
Indices: 3110450--3110574 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
3110440 AAAAGACTAC
3110450 TACTACAGAAAACTAATCGTTAAATGCTTGGGACATATAATTTTGGCATTCTGACCTTTAAG
1 TACTACAGAAAACTAATCGTTAAATGCTTGGGACATATAATTTTGGCATTCTGACCTTTAAG
3110512 TACTACAGAAAACTAATCGTTAAATGCTTGGGACATATAATTTTGGCATTCTGACCTTTAAG
1 TACTACAGAAAACTAATCGTTAAATGCTTGGGACATATAATTTTGGCATTCTGACCTTTAAG
3110574 T
1 T
3110575 CCCTGCTCTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (62 bp):
TACTACAGAAAACTAATCGTTAAATGCTTGGGACATATAATTTTGGCATTCTGACCTTTAAG
Found at i:3116162 original size:24 final size:24
Alignment explanation
Indices: 3116134--3116185 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3116124 TTAGTAAGTC
* *
3116134 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3116158 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3116182 AAAT
1 AAAT
3116186 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3122440 original size:61 final size:62
Alignment explanation
Indices: 3122317--3122440 Score: 146
Period size: 61 Copynumber: 2.0 Consensus size: 62
3122307 AAATTACAGA
* * * * *
3122317 ATCTAATTAAAAATTTTTAAAAAATTTCAAAGGTTTAATAATAATTTTTAAAACTTTTGAGG
1 ATCTAATTAAAAATTTTCAAAAAATTTCAAAGGTATAAGAATAATTTTCAAAACTTTGGAGG
* *
3122379 ATCT-ATTTAAAATTTTCAAAAAATTTTAAAGGTATAACGAA-AATTTTCAAATA-TTTGGAGG
1 ATCTAATTAAAAATTTTCAAAAAATTTCAAAGGTATAA-GAATAATTTTCAAA-ACTTTGGAGG
3122440 A
1 A
3122441 ACCAAGACCC
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
61 46 0.87
62 7 0.13
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.40
Consensus pattern (62 bp):
ATCTAATTAAAAATTTTCAAAAAATTTCAAAGGTATAAGAATAATTTTCAAAACTTTGGAGG
Found at i:3129856 original size:42 final size:43
Alignment explanation
Indices: 3129767--3129865 Score: 146
Period size: 42 Copynumber: 2.3 Consensus size: 43
3129757 TCGTCGCTAA
* * *
3129767 CTTTAGCAGCGCTTTTCCCACAAACGTCGCTAAAGACCAAGAT
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
**
3129810 CTTTAGCGGCGCTTTTCCC-CCTACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
3129852 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
3129866 AAAAAACAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 33 0.65
43 18 0.35
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.24
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:3130981 original size:111 final size:111
Alignment explanation
Indices: 3130765--3131059 Score: 330
Period size: 111 Copynumber: 2.6 Consensus size: 111
3130755 AAAGTAGCAC
* *
3130765 TTTAACACTTCAATTTATAGCGATAAAACATCTCAATTTGCAGCAACTAAACACTTCAATTTGCA
1 TTTAACACCTCAATTTACAGCGATAAAACATCTCAATTTGCAGCAACTAAACACTTCAATTTGCA
** ** *
3130830 GCACTTAAACACTTCAATTTGCAGTACTTAAACATATCAATTAACA
66 GCACTTAAACACTTCAATTAACAACACTTAAACACATCAATTAACA
* *
3130876 TTTATACACCTCAA-TTACAGCGATAAAACATCTCAATTTTCAGCAACTAAATACTTCAATTTGC
1 TTTA-ACACCTCAATTTACAGCGATAAAACATCTCAATTTGCAGCAACTAAACACTTCAATTTGC
* * *
3130940 AGCACTTAAACA-TATCAATTAACAACATTTATACACCTCAATTACAGCGA
65 AGCACTTAAACACT-TCAATTAACAACACTTAAACACATCAATTA-A-C-A
** * * *
3130990 TAAAACATCTCAATTTCCAGCAACTAAATAC-T-TCAATTTGCAGC-ACTTAAACACTTCAATTT
1 TTTAACACCTCAATTTACAGCGA-TAAA-ACATCTCAATTTGCAGCAAC-TAAACACTTCAATTT
3131052 GCAGCACT
63 GCAGCACT
3131060 ATCAAATTTC
Statistics
Matches: 156, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
110 1 0.01
111 85 0.54
112 9 0.06
113 11 0.07
114 43 0.28
115 5 0.03
116 2 0.01
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.31
Consensus pattern (111 bp):
TTTAACACCTCAATTTACAGCGATAAAACATCTCAATTTGCAGCAACTAAACACTTCAATTTGCA
GCACTTAAACACTTCAATTAACAACACTTAAACACATCAATTAACA
Found at i:3131002 original size:91 final size:88
Alignment explanation
Indices: 3130820--3131050 Score: 367
Period size: 91 Copynumber: 2.6 Consensus size: 88
3130810 ACTAAACACT
* * *
3130820 TCAATTTGCAGC-ACTTAAACACTTCAATTTGCAGTACTTAAACATATCAATTAACATTTATACA
1 TCAATTTCCAGCAAC-TAAATACTTCAATTTGCAGCACTTAAACATATCAATTAACATTTATACA
3130884 CCTCAATTACAGCGATAAAACATC
65 CCTCAATTACAGCGATAAAACATC
*
3130908 TCAATTTTCAGCAACTAAATACTTCAATTTGCAGCACTTAAACATATCAATTAACAACATTTATA
1 TCAATTTCCAGCAACTAAATACTTCAATTTGCAGCACTTAAACATATCAATT---AACATTTATA
3130973 CACCTCAATTACAGCGATAAAACATC
63 CACCTCAATTACAGCGATAAAACATC
3130999 TCAATTTCCAGCAACTAAATACTTCAATTTGCAGCACTTAAACACT-TCAATT
1 TCAATTTCCAGCAACTAAATACTTCAATTTGCAGCACTTAAACA-TATCAATT
3131051 TGCAGCACTA
Statistics
Matches: 134, Mismatches: 4, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
88 46 0.34
89 2 0.01
91 85 0.63
92 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (88 bp):
TCAATTTCCAGCAACTAAATACTTCAATTTGCAGCACTTAAACATATCAATTAACATTTATACAC
CTCAATTACAGCGATAAAACATC
Found at i:3131058 original size:23 final size:23
Alignment explanation
Indices: 3130760--3131059 Score: 182
Period size: 23 Copynumber: 13.3 Consensus size: 23
3130750 AATGGAAAGT
* **
3130760 AGCACTTTAACACTTCAATTTAT
1 AGCACTTAAACACTTCAATTTGC
*
3130783 AGCGA-TAAAACA-TCTCAATTTGC
1 AGC-ACTTAAACACT-TCAATTTGC
3130806 AGCAAC-TAAACACTTCAATTTGC
1 AGC-ACTTAAACACTTCAATTTGC
3130829 AGCACTTAAACACTTCAATTTGC
1 AGCACTTAAACACTTCAATTTGC
*
3130852 AGTACTTAAACA-TATCAA-TT--
1 AGCACTTAAACACT-TCAATTTGC
* * * * *
3130872 AACATTTATACACCTCAA-TTAC
1 AGCACTTAAACACTTCAATTTGC
* *
3130894 AGCGA-TAAAACA-TCTCAATTTTC
1 AGC-ACTTAAACACT-TCAATTTGC
*
3130917 AGCAAC-TAAATACTTCAATTTGC
1 AGC-ACTTAAACACTTCAATTTGC
**
3130940 AGCACTTAAACA-TATCAATTAAC
1 AGCACTTAAACACT-TCAATTTGC
* * * * *
3130963 AACATTTATACACCTCAA-TTAC
1 AGCACTTAAACACTTCAATTTGC
* *
3130985 AGCGA-TAAAACA-TCTCAATTTCC
1 AGC-ACTTAAACACT-TCAATTTGC
*
3131008 AGCAAC-TAAATACTTCAATTTGC
1 AGC-ACTTAAACACTTCAATTTGC
3131031 AGCACTTAAACACTTCAATTTGC
1 AGCACTTAAACACTTCAATTTGC
3131054 AGCACT
1 AGCACT
3131060 ATCAAATTTC
Statistics
Matches: 215, Mismatches: 39, Indels: 46
0.72 0.13 0.15
Matches are distributed among these distances:
20 14 0.07
22 36 0.17
23 161 0.75
24 4 0.02
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30
Consensus pattern (23 bp):
AGCACTTAAACACTTCAATTTGC
Found at i:3131478 original size:41 final size:39
Alignment explanation
Indices: 3131395--3131478 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 39
3131385 GCACAATACA
* **
3131395 ATATAAAAAGCATATATAAATATATGAATGTAGAGGCAT
1 ATATAAAAAGCATATATAAATATATGAATGTACAGAAAT
*
3131434 ATATAAAAAGCATATATAAATATATGTATGTCACAGAAACT
1 ATATAAAAAGCATATATAAATATATGAATGT-ACAGAAA-T
3131475 ATAT
1 ATAT
3131479 TCATTTATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 30 0.77
40 4 0.10
41 5 0.13
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (39 bp):
ATATAAAAAGCATATATAAATATATGAATGTACAGAAAT
Found at i:3133754 original size:146 final size:142
Alignment explanation
Indices: 3133428--3133788 Score: 508
Period size: 146 Copynumber: 2.5 Consensus size: 142
3133418 TATTGCTTAT
* *
3133428 TTATAAAATTCCGCAAAATTTTTTTCATTTTGAACAAAACGAC-CCGGTTTTGCTATTTTAAATT
1 TTATAAAATACCGC-AAATTTTTTTCATTTTGAACAAAACGACGCC-GTTTTGCTATTCTAAATT
* *
3133492 TTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTATAAAAACGCCGCTATTGCTTACC
64 TTTTTTATTTTTTTATAAATTGATTTATTCTTTACGGCGTTATAAAAACACCGCTATTGCTTACC
*
3133557 TTTAGCGGCGCTTC
129 TTTAGCGACGCTTC
* ** * *
3133571 TTAAAAAATGTCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTTTCTATTCTAAATTTT
1 TTATAAAATACCGCAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTATTCTAAATTTT
* *
3133636 TTTTATTTTTTTATAAATTGATTTATTCTTTACGGCGTTTTTCTGGAAAACACCGCTATTGCTTA
66 TTTTATTTTTTTATAAATTGATTTATTCTTTACGGCG---TTAT-AAAAACACCGCTATTGCTTA
3133701 CCTTTAGCGACGCTTC
127 CCTTTAGCGACGCTTC
* * **
3133717 TTATAAAACACCGCAAATTTTTTTTATTTTGAACAAAACGACGTTGTTTTGCTATTCTAAAATTT
1 TTATAAAATACCGCAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTATTCT-AAATTT
3133782 TTTTTAT
65 TTTTTAT
3133789 AATAATTTAT
Statistics
Matches: 192, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
142 81 0.42
143 13 0.07
145 3 0.02
146 82 0.43
147 13 0.07
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.45
Consensus pattern (142 bp):
TTATAAAATACCGCAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTATTCTAAATTTT
TTTTATTTTTTTATAAATTGATTTATTCTTTACGGCGTTATAAAAACACCGCTATTGCTTACCTT
TAGCGACGCTTC
Found at i:3133823 original size:98 final size:97
Alignment explanation
Indices: 3133702--3133885 Score: 287
Period size: 98 Copynumber: 1.9 Consensus size: 97
3133692 TATTGCTTAC
* * * **
3133702 CTTTAGCGACGCTTCTTATAAAACACCGCAAATTTTTTTTATTTTGAACAAAACGACGTTGTTTT
1 CTTTAGCGACGCTTCTTAAAAAACACCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
3133767 GCTATTCTAAAATTTTTTTTATAATAATTTATT
66 GCTATTCT-AAATTTTTTTTATAATAATTTATT
* * *
3133800 CTTTAGCGGCGCTTGTTAAAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
1 CTTTAGCGACGCTTCTTAAAAAACACCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
3133865 GCTATTCTAAATTTTTTTTAT
66 GCTATTCTAAATTTTTTTTAT
3133886 TTTTTTATAA
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
97 13 0.17
98 65 0.83
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.43
Consensus pattern (97 bp):
CTTTAGCGACGCTTCTTAAAAAACACCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
GCTATTCTAAATTTTTTTTATAATAATTTATT
Found at i:3133918 original size:244 final size:244
Alignment explanation
Indices: 3133556--3134312 Score: 877
Period size: 244 Copynumber: 3.0 Consensus size: 244
3133546 TATTGCTTAC
* *
3133556 CTTTAGCGGCGCTTCTTAAAAAATGTCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
1 CTTTAGCGGCGCTTCTTAAAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
*
3133621 TCTATTCTAAATTTTTTTTATTTTTTTATAAATTGATTTATTCTTTACGGCGTTTTTCTGGAAAA
66 GCTATTCTAAATTTTTTTTATTTTTTTATAAATTGATTTATTCTTTACGGCGTTTTTCTGGAAAA
* * *
3133686 CACCGCTATTGCTTACCTTTAGCGACGCTTCTTATAAAACACCGCAAATTTTTTTTATTTTGAAC
131 CACCGCTATTGCTTACCTTTAGCGACGCTTCTTATAAAACACCGCAAAATTTTATCATTTTGAAC
*** *
3133751 AAAACGACGTTGTTTTGCTATTCTAAAATTTTTTTTATAATAATTTATT
196 AAAACGACGCCATTTTGCTATTCTAAAAATTTTTTTATAATAATTTATT
*
3133800 CTTTAGCGGCGCTTGTTAAAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
1 CTTTAGCGGCGCTTCTTAAAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
* *
3133865 GCTATTCTAAATTTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTCTGGAAAG
66 GCTATTCTAAATTTTTTTTATTTTTTTATAAATTGATTTATTCTTTACGGCGTTTTTCTGGAAAA
* * * *
3133930 CGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCCTCAAAATTTTATCATTTTGAAC
131 CACCGCTATTGCTTACCTTTAGCGACGCTTCTTATAAAACACCGCAAAATTTTATCATTTTGAAC
*
3133995 AAAGCGACGCCATTTTGCTATTCTAAAAATTTTTTTATTTTTTTATAAATTAATTTATTCTTTGC
196 AAAACGACGCCATTTTGCTATTCT-AAAA-------ATTTTTTTAT-AA-T-A---A-----T--
3134060 GAAAACGCTGCTATT
240 --------T--TATT
* *
3134075 GCTTACCTTTAGCGGCGCTTCTTATAAAATGCCGCAAAATTTTTTCATTTTGAACAAAACGACGC
1 -C-T----TTAGCGGCGCTTCTTAAAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGC
* * * *
3134140 CGTTTTGCTATTCTAAATTTTTTTTATTTTTTTATAAACTGATTTATTCTTTGCGGCATTTTTAT
60 CGTTTTGCTATTCTAAATTTTTTTTATTTTTTTATAAATTGATTTATTCTTTACGGCGTTTTTCT
* * * * * * *
3134205 AGAAAACGCCGCTATTGCTTATCTTTAGCGGCGCTTCTTAAAAAACGCCGCAAAATTTTTTCATT
125 GGAAAACACCGCTATTGCTTACCTTTAGCGACGCTTCTTATAAAACACCGCAAAATTTTATCATT
* *
3134270 TTGAGCAAAACGACGCCGTTTTGCTATTCT-AAAATTTTTTTAT
190 TTGAACAAAACGACGCCATTTTGCTATTCTAAAAATTTTTTTAT
3134313 TTTTTTATAA
Statistics
Matches: 443, Mismatches: 33, Indels: 46
0.85 0.06 0.09
Matches are distributed among these distances:
244 202 0.46
245 4 0.01
252 9 0.02
253 2 0.00
254 1 0.00
255 1 0.00
258 1 0.00
263 1 0.00
272 10 0.02
273 1 0.00
275 4 0.01
276 1 0.00
277 1 0.00
279 3 0.01
281 202 0.46
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (244 bp):
CTTTAGCGGCGCTTCTTAAAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
GCTATTCTAAATTTTTTTTATTTTTTTATAAATTGATTTATTCTTTACGGCGTTTTTCTGGAAAA
CACCGCTATTGCTTACCTTTAGCGACGCTTCTTATAAAACACCGCAAAATTTTATCATTTTGAAC
AAAACGACGCCATTTTGCTATTCTAAAAATTTTTTTATAATAATTTATT
Found at i:3133971 original size:146 final size:146
Alignment explanation
Indices: 3133800--3135095 Score: 2050
Period size: 146 Copynumber: 9.0 Consensus size: 146
3133790 ATAATTTATT
* *
3133800 CTTTAGCGGCGCTTGTTAAAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
1 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
* *
3133865 GCTATTCTAAATTTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTCTGGAAAG
66 GCTATTCTAAAATTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTCTGGAAAA
3133930 CGCCGCTATTGCTTAC
131 CGCCGCTATTGCTTAC
* * * *
3133946 CTTTAGCGGCGCTTCTTATAAAACGCCTCAAAATTTTATCATTTTGAACAAAGCGACGCCATTTT
1 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
*
3134011 GCTATTCTAAAAATTTTTTTATTTTTTTATAAATTAATTTATTCTTT-----G-----C--GAAA
66 GCTATTCT-AAAATTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTCTGGAAA
*
3134064 ACGCTGCTATTGCTTAC
130 ACGCCGCTATTGCTTAC
*
3134081 CTTTAGCGGCGCTTCTTATAAAATGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
1 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
* * * * *
3134146 GCTATTCTAAATTTTTTTTATTTTTTTATAAACTGATTTATTCTTTGCGGCATTTTTATAGAAAA
66 GCTATTCTAAAATTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTCTGGAAAA
*
3134211 CGCCGCTATTGCTTAT
131 CGCCGCTATTGCTTAC
* *
3134227 CTTTAGCGGCGCTTCTTAAAAAACGCCGCAAAATTTTTTCATTTTGAGCAAAACGACGCCGTTTT
1 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
*
3134292 GCTATTCTAAAATTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCATTTTTCTGGAAAA
66 GCTATTCTAAAATTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTCTGGAAAA
3134357 CGCCGCTATTGCTTAC
131 CGCCGCTATTGCTTAC
* * * *
3134373 TTTTAGCGGCGCTTCTTATAAAACACCGTAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTT
1 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
* * *
3134438 GCTATTCT-AAATTTTTTTATTTTTTTATAAATTAATTTATTCTTTGCGGCGTTTTTATAGAAAA
66 GCTATTCTAAAATTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTCTGGAAAA
3134502 CGCCGCTATTGCTTAC
131 CGCCGCTATTGCTTAC
*
3134518 CTTTAGCGGCGCTTCTTAAAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
1 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
*
3134583 GCTATTCTAAAAATTTTTTATTTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTCTGGAAA
66 GCTATTCTAAAATTTTTTTA-TTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTCTGGAAA
3134648 ACGCCGCTATTGCTTAC
130 ACGCCGCTATTGCTTAC
* *
3134665 CTTTAGCGGCGCTTCTTAAAAAACGCCGTAAAA-TTTTTCATTTTGAACAAAACGACGCCGTTTT
1 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
* *
3134729 GCTATTCT-AAA-TTTTTTATTTTTTTTATAAATTGATTTATTCTTTGCAGCGTTTTTCGGGAAA
66 GCTATTCTAAAATTTTTTTA-TTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTCTGGAAA
*
3134792 ATGCCGCTATTGCTTAC
130 ACGCCGCTATTGCTTAC
*
3134809 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACCACGCCGTTTT
1 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
* * *
3134874 GCTATTCTAAAAATTTTTTATTTTTTTTATAAATTGATTTATTCTTTGCAGCGTTTTTCGGGAAA
66 GCTATTCTAAAATTTTTTTA-TTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTCTGGAAA
*
3134939 ACGCTGCTATTGCTTAC
130 ACGCCGCTATTGCTTAC
*
3134956 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACCCCGTTTT
1 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
* *
3135021 GCTATTCT-AAATTTTTTTATTTTTTTAATAAATTGATTTATTCTTTGCGGCGTTTTTATAGAAA
66 GCTATTCTAAAATTTTTTTATTTTTTT-ATAAATTGATTTATTCTTTGCGGCGTTTTTCTGGAAA
3135085 ACGCCGCTATT
130 ACGCCGCTATT
3135096 TCATTTTGAA
Statistics
Matches: 1065, Mismatches: 66, Indels: 38
0.91 0.06 0.03
Matches are distributed among these distances:
134 35 0.03
135 87 0.08
137 1 0.00
142 1 0.00
144 97 0.09
145 184 0.17
146 396 0.37
147 264 0.25
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.43
Consensus pattern (146 bp):
CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
GCTATTCTAAAATTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTCTGGAAAA
CGCCGCTATTGCTTAC
Found at i:3134536 original size:291 final size:292
Alignment explanation
Indices: 3133800--3135095 Score: 2102
Period size: 291 Copynumber: 4.5 Consensus size: 292
3133790 ATAATTTATT
* *
3133800 CTTTAGCGGCGCTTGTTAAAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
1 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
* * *
3133865 GCTATTCTAAATTTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTCTGGAAAG
66 GCTATTCTAAA-TTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTATAGAAAA
* * *
3133930 CGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCCTCAAAATTTTATCATTTTGAAC
130 CGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTAAAAAACGCCGCAAAATTTTTTCATTTTGAAC
* * *
3133995 AAAGCGACGCCATTTTGCTATTCTAAAAATTTTTT-TATTTTTTTATAAATTAATTTATTCTTT-
195 AAAACGACGCCGTTTTGCTATTCTAAAAATTTTTTAT-TTTTTTTATAAATTGATTTATTCTTTG
*
3134058 ----G-----C--GAAAACGCTGCTATTGCTTAC
259 CGGCGTTTTTCTGGAAAACGCCGCTATTGCTTAC
*
3134081 CTTTAGCGGCGCTTCTTATAAAATGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
1 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
* *
3134146 GCTATTCTAAATTTTTTTTATTTTTTTATAAACTGATTTATTCTTTGCGGCATTTTTATAGAAAA
66 GCTATTCTAAA-TTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTATAGAAAA
* *
3134211 CGCCGCTATTGCTTATCTTTAGCGGCGCTTCTTAAAAAACGCCGCAAAATTTTTTCATTTTGAGC
130 CGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTAAAAAACGCCGCAAAATTTTTTCATTTTGAAC
*
3134276 AAAACGACGCCGTTTTGCTATTCTAAAATTTTTTTA-TTTTTTTATAAATTGATTTATTCTTTGC
195 AAAACGACGCCGTTTTGCTATTCTAAAAATTTTTTATTTTTTTTATAAATTGATTTATTCTTTGC
*
3134340 GGCATTTTTCTGGAAAACGCCGCTATTGCTTAC
260 GGCGTTTTTCTGGAAAACGCCGCTATTGCTTAC
* * * *
3134373 TTTTAGCGGCGCTTCTTATAAAACACCGTAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTT
1 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
*
3134438 GCTATTCTAAATTTTTTTATTTTTTTATAAATTAATTTATTCTTTGCGGCGTTTTTATAGAAAAC
66 GCTATTCTAAATTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTATAGAAAAC
3134503 GCCGCTATTGCTTACCTTTAGCGGCGCTTCTTAAAAAACGCCGCAAAATTTTTTCATTTTGAACA
131 GCCGCTATTGCTTACCTTTAGCGGCGCTTCTTAAAAAACGCCGCAAAATTTTTTCATTTTGAACA
3134568 AAACGACGCCGTTTTGCTATTCTAAAAATTTTTTATTTTTTTTATAAATTGATTTATTCTTTGCG
196 AAACGACGCCGTTTTGCTATTCTAAAAATTTTTTATTTTTTTTATAAATTGATTTATTCTTTGCG
3134633 GCGTTTTTCTGGAAAACGCCGCTATTGCTTAC
261 GCGTTTTTCTGGAAAACGCCGCTATTGCTTAC
* *
3134665 CTTTAGCGGCGCTTCTTAAAAAACGCCGTAAAA-TTTTTCATTTTGAACAAAACGACGCCGTTTT
1 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
* ***
3134729 GCTATTCTAAA-TTTTTTATTTTTTTTATAAATTGATTTATTCTTTGCAGCGTTTTTCGGGAAAA
66 GCTATTCTAAATTTTTTTA-TTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTATAGAAAA
* *
3134793 TGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAAC
130 CGCCGCTATTGCTTACCTTTAGCGGCGCTTCTTAAAAAACGCCGCAAAATTTTTTCATTTTGAAC
*
3134858 AAAACCACGCCGTTTTGCTATTCTAAAAATTTTTTATTTTTTTTATAAATTGATTTATTCTTTGC
195 AAAACGACGCCGTTTTGCTATTCTAAAAATTTTTTATTTTTTTTATAAATTGATTTATTCTTTGC
* * *
3134923 AGCGTTTTTCGGGAAAACGCTGCTATTGCTTAC
260 GGCGTTTTTCTGGAAAACGCCGCTATTGCTTAC
*
3134956 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACCCCGTTTT
1 CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
3135021 GCTATTCTAAATTTTTTTATTTTTTTAATAAATTGATTTATTCTTTGCGGCGTTTTTATAGAAAA
66 GCTATTCTAAATTTTTTTATTTTTTT-ATAAATTGATTTATTCTTTGCGGCGTTTTTATAGAAAA
3135086 CGCCGCTATT
130 CGCCGCTATT
3135096 TCATTTTGAA
Statistics
Matches: 943, Mismatches: 54, Indels: 24
0.92 0.05 0.02
Matches are distributed among these distances:
280 25 0.03
281 214 0.23
290 8 0.01
291 418 0.44
292 228 0.24
293 50 0.05
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.43
Consensus pattern (292 bp):
CTTTAGCGGCGCTTCTTATAAAACGCCGCAAAATTTTTTCATTTTGAACAAAACGACGCCGTTTT
GCTATTCTAAATTTTTTTATTTTTTTATAAATTGATTTATTCTTTGCGGCGTTTTTATAGAAAAC
GCCGCTATTGCTTACCTTTAGCGGCGCTTCTTAAAAAACGCCGCAAAATTTTTTCATTTTGAACA
AAACGACGCCGTTTTGCTATTCTAAAAATTTTTTATTTTTTTTATAAATTGATTTATTCTTTGCG
GCGTTTTTCTGGAAAACGCCGCTATTGCTTAC
Found at i:3135541 original size:22 final size:22
Alignment explanation
Indices: 3135496--3135541 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3135486 CTTAACTCTT
*
3135496 AACCCCTAACATCTAATCCCTA
1 AACCCCTAACATCTAAACCCTA
*
3135518 AACCCCTAA-ACTCTAAACCTTA
1 AACCCCTAACA-TCTAAACCCTA
3135540 AA
1 AA
3135542 TCCCAATCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (22 bp):
AACCCCTAACATCTAAACCCTA
Found at i:3135555 original size:21 final size:21
Alignment explanation
Indices: 3135531--3135606 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
3135521 CCCTAAACTC
3135531 TAAACCTTAAATCCCAATCCT
1 TAAACCTTAAATCCCAATCCT
* * *
3135552 TAAACCAT-AATCCCTAATTCA
1 TAAACCTTAAATCCC-AATCCT
* *
3135573 TAATCCCTAAAT-CCATACTCCT
1 TAAACCTTAAATCCCA-A-TCCT
3135595 TAAACCTTAAAT
1 TAAACCTTAAAT
3135607 ATGAACTCTT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
20 7 0.17
21 20 0.48
22 15 0.36
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAACCTTAAATCCCAATCCT
Found at i:3135563 original size:14 final size:14
Alignment explanation
Indices: 3135546--3135600 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
3135536 CTTAAATCCC
*
3135546 AATCCTTAAACCAT
1 AATCCCTAAACCAT
**
3135560 AATCCCTAATTCAT
1 AATCCCTAAACCAT
3135574 AATCCCTAAATCCAT
1 AATCCCTAAA-CCAT
* *
3135589 ACTCCTTAAACC
1 AATCCCTAAACC
3135601 TTAAATATGA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
14 22 0.67
15 11 0.33
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.29
Consensus pattern (14 bp):
AATCCCTAAACCAT
Found at i:3135838 original size:15 final size:15
Alignment explanation
Indices: 3135814--3135844 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3135804 AACCCCTAAT
3135814 CCATAATCCCTAAAC
1 CCATAATCCCTAAAC
*
3135829 CCATACTCCCTAAAC
1 CCATAATCCCTAAAC
3135844 C
1 C
3135845 TTAAAATATG
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:0.35, C:0.45, G:0.00, T:0.19
Consensus pattern (15 bp):
CCATAATCCCTAAAC
Found at i:3135978 original size:245 final size:245
Alignment explanation
Indices: 3135540--3136197 Score: 1115
Period size: 245 Copynumber: 2.7 Consensus size: 245
3135530 CTAAACCTTA
* * * * *
3135540 AATCCC-AATCCTTAAA-CCATAATCCCTAATTCATAATCCCTAAATCCATACTCCTTAAACCTT
1 AATCCCTAAACCTTAAATCC-TAACCCCTAATCCATAATCCCTAAACCCATACTCCCTAAACCTT
*
3135603 -AAATATGAACTCTTAAACCGGCTTTAAATCTTAAATTAATCATATACCCTAAACTAAAAACCCT
65 AAAATATGAACTCCTAAACCGGCTTTAAATCTTAAATTAATCATATACCCTAAACTAAAAACCCT
3135667 AAACAAATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAA
130 AAACAAATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAA
3135732 TAATTAATCTAAACCCAAAACCCTAACTCGACCCCTGAATCCCTAACTTTT
195 TAATTAATCTAAACCCAAAACCCTAACTCGACCCCTGAATCCCTAACTTTT
3135783 AATCCCTAAACCTTAAATCCTAACCCCTAATCCATAATCCCTAAACCCATACTCCCTAAACCTTA
1 AATCCCTAAACCTTAAATCCTAACCCCTAATCCATAATCCCTAAACCCATACTCCCTAAACCTTA
*
3135848 AAATATGAACTCCTAAACCGGTTTTAAATCTTAAATTAATCATATACCCTAAACTAAAAACCCTA
66 AAATATGAACTCCTAAACCGGCTTTAAATCTTAAATTAATCATATACCCTAAACTAAAAACCCTA
3135913 AACAAATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAT
131 AACAAATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAT
3135978 AATTAATCTAAACCCAAAACCCTAACTCGACCCCTGAATCCCTAACTTTT
196 AATTAATCTAAACCCAAAACCCTAACTCGACCCCTGAATCCCTAACTTTT
3136028 AATCTCTAAACCCCTAAACCTTAAATCCTAACCCCTAATCCATAATCCCTAAACCCATACTCCCT
1 AA----T----CCCTAAACCTTAAATCCTAACCCCTAATCCATAATCCCTAAACCCATACTCCCT
* * *
3136093 AAACCTTAAAATATGAACTCCTAAACCGGCCTTAAATCTTAAATAAATCATATACCCTAAACCAA
58 AAACCTTAAAATATGAACTCCTAAACCGGCTTTAAATCTTAAATTAATCATATACCCTAAACTAA
*
3136158 AAACCCTAAACAAATTTATTATTATCTCATTTACAATTAT
123 AAACCCTAAACAAATTTATTATTATCTCTTTTACAATTAT
3136198 TTTAAATAAT
Statistics
Matches: 392, Mismatches: 12, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
243 6 0.02
244 49 0.12
245 182 0.46
249 1 0.00
253 154 0.39
ACGTcount: A:0.42, C:0.25, G:0.02, T:0.30
Consensus pattern (245 bp):
AATCCCTAAACCTTAAATCCTAACCCCTAATCCATAATCCCTAAACCCATACTCCCTAAACCTTA
AAATATGAACTCCTAAACCGGCTTTAAATCTTAAATTAATCATATACCCTAAACTAAAAACCCTA
AACAAATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAT
AATTAATCTAAACCCAAAACCCTAACTCGACCCCTGAATCCCTAACTTTT
Found at i:3136078 original size:21 final size:21
Alignment explanation
Indices: 3136027--3136079 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
3136017 CCCTAACTTT
* *
3136027 TAATCTCTAAACCCCTAAACCT
1 TAATCCCT-AACCCCTAAACCA
*
3136049 TAAAT-CCTAACCCCTAATCCA
1 T-AATCCCTAACCCCTAAACCA
3136070 TAATCCCTAA
1 TAATCCCTAA
3136080 ACCCATACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 3 0.12
21 17 0.65
22 3 0.12
23 3 0.12
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (21 bp):
TAATCCCTAACCCCTAAACCA
Found at i:3136091 original size:15 final size:15
Alignment explanation
Indices: 3136027--3136097 Score: 56
Period size: 15 Copynumber: 4.9 Consensus size: 15
3136017 CCCTAACTTT
* *
3136027 TAATCTCTAAACCCC
1 TAATCCCTAAACCCA
* * *
3136042 TAAACCTTAAATCC-
1 TAATCCCTAAACCCA
* *
3136056 TAACCCCT-AATCCA
1 TAATCCCTAAACCCA
3136070 TAATCCCTAAACCCA
1 TAATCCCTAAACCCA
*
3136085 TACTCCCTAAACC
1 TAATCCCTAAACC
3136098 TTAAAATATG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
13 5 0.11
14 13 0.29
15 27 0.60
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (15 bp):
TAATCCCTAAACCCA
Found at i:3136510 original size:73 final size:72
Alignment explanation
Indices: 3136389--3136560 Score: 254
Period size: 73 Copynumber: 2.4 Consensus size: 72
3136379 CTGAGCATTA
* *
3136389 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCTCATAAAACGGCGTCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGACGTCGTTGGGCTTAG
3136454 GTTTTTTT
66 G-TTTTTT
* * * * *
3136462 GCGGCGCTTTCTTAGAAACGTCGCTAAATCCCCGAAAGCTCGGGAAACGACGTCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGACGTCGTTGGGCTTAG
3136527 GTTTTTT
66 GTTTTTT
* *
3136534 GTGGCGCTTTCTCAAAAACGCCGCTAA
1 GCGGCGCTTTCTTAAAAACGCCGCTAA
3136561 TGCTTATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 29 0.33
73 59 0.67
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.27
Consensus pattern (72 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGACGTCGTTGGGCTTAG
GTTTTTT
Found at i:3145953 original size:12 final size:13
Alignment explanation
Indices: 3145936--3145972 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
3145926 GAACCGGACA
3145936 CGAACCGAA-CTC
1 CGAACCGAAGCTC
3145948 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
3145960 CGAACCGTAGCTC
1 CGAACCGAAGCTC
3145973 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:3148662 original size:22 final size:22
Alignment explanation
Indices: 3148635--3148678 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3148625 AAATTCCATT
3148635 TTTTCATA-AATTTTTTTTTAAA
1 TTTTCA-ACAATTTTTTTTTAAA
3148657 TTTTCAACAATTTTTTTTTAAA
1 TTTTCAACAATTTTTTTTTAAA
3148679 AAAAGTCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTCAACAATTTTTTTTTAAA
Found at i:3156037 original size:54 final size:51
Alignment explanation
Indices: 3155961--3156067 Score: 160
Period size: 54 Copynumber: 2.0 Consensus size: 51
3155951 TTCCGAAAGG
* * *
3155961 TTCTCGTCCATTTGTCCTTCACGACATTCACCCTTCTGTTGAGAATGTGGTTCT
1 TTCTCATCCACTTGTCCTTCACGACATTCACCC-T-T-TTGAGAATGTGATTCT
3156015 TTCTCATCCACTTGTCCTTCACGACATTCACCCTTTTGAGAATGTGATTCT
1 TTCTCATCCACTTGTCCTTCACGACATTCACCCTTTTGAGAATGTGATTCT
3156066 TT
1 TT
3156068 AAGCTATCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
51 17 0.34
52 1 0.02
53 1 0.02
54 31 0.62
ACGTcount: A:0.17, C:0.28, G:0.14, T:0.41
Consensus pattern (51 bp):
TTCTCATCCACTTGTCCTTCACGACATTCACCCTTTTGAGAATGTGATTCT
Found at i:3158932 original size:20 final size:20
Alignment explanation
Indices: 3158904--3158941 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3158894 AATTTAATTT
3158904 TTTCCTTTTATTTT-TTTAAC
1 TTTCCTTTT-TTTTCTTTAAC
*
3158924 TTTCTTTTTTTTTCTTTA
1 TTTCCTTTTTTTTCTTTA
3158942 TTTTCCGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTCCTTTTTTTTCTTTAAC
Found at i:3161011 original size:20 final size:20
Alignment explanation
Indices: 3160986--3161051 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
3160976 TTTTTTACTA
*
3160986 TTATAATCAAATATCTGTTT
1 TTATAATCAAATATCTATTT
*
3161006 TTATAA-CAAA-ATTTAATTACT
1 TTATAATCAAATATCT-ATT--T
3161027 ATTATAATCAAATATCTATTT
1 -TTATAATCAAATATCTATTT
3161048 TTAT
1 TTAT
3161052 GACAAAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
18 3 0.08
19 6 0.16
20 10 0.27
21 2 0.05
22 6 0.16
23 7 0.19
24 3 0.08
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (20 bp):
TTATAATCAAATATCTATTT
Found at i:3161026 original size:42 final size:42
Alignment explanation
Indices: 3160980--3161064 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
3160970 TTCAATTTTT
*
3160980 TTACTATTATAATCAAATATCTGTTTTTATAACAAAATTTAA
1 TTACTATTATAATCAAATATCTATTTTTATAACAAAATTTAA
*
3161022 TTACTATTATAATCAAATATCTATTTTTATGACAAAATTTAA
1 TTACTATTATAATCAAATATCTATTTTTATAACAAAATTTAA
3161064 T
1 T
3161065 GCCCAGAACT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.46
Consensus pattern (42 bp):
TTACTATTATAATCAAATATCTATTTTTATAACAAAATTTAA
Found at i:3170322 original size:25 final size:26
Alignment explanation
Indices: 3170268--3170322 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
3170258 TTAACTATTT
* * * *
3170268 AAAAAAATTAATTATCAAATTTAGTT
1 AAAAAAAGTAATGATCAAATTGAGTA
3170294 AAAAAAAGTAATGATCAAATTGA-TA
1 AAAAAAAGTAATGATCAAATTGAGTA
3170319 AAAA
1 AAAA
3170323 TATAAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (26 bp):
AAAAAAAGTAATGATCAAATTGAGTA
Found at i:3172105 original size:18 final size:18
Alignment explanation
Indices: 3172084--3172157 Score: 68
Period size: 17 Copynumber: 4.3 Consensus size: 18
3172074 ATTTTAGATT
3172084 TTTTTAATATTTTTTATA
1 TTTTTAATATTTTTTATA
3172102 TTTTTAA-ATTTTTT-TA
1 TTTTTAATATTTTTTATA
* *
3172118 -TTTT-ATGAGTTATTATTA
1 TTTTTAAT-ATTTTTTA-TA
*
3172136 TTTTTAAT-TTTTTAATA
1 TTTTTAATATTTTTTATA
3172153 TTTTT
1 TTTTT
3172158 GTTTTTATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
14 1 0.02
15 4 0.09
16 7 0.16
17 14 0.31
18 13 0.29
19 4 0.09
20 2 0.04
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTTAATATTTTTTATA
Found at i:3173361 original size:31 final size:28
Alignment explanation
Indices: 3173318--3173413 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 28
3173308 TCTTTAAATG
*
3173318 TGTACAATTGAATCAAAATCAAAGCTTCA
1 TGTATAATTGAATCAAAATCAAAG-TTCA
*
3173347 TGTATACATATGAATCACAAATCAAATTTCA
1 TGTATA-AT-TGAATCA-AAATCAAAGTTCA
* *
3173378 TGTGTATAATTG-AGCCAAATCAAAGTTCA
1 --TGTATAATTGAATCAAAATCAAAGTTCA
3173407 TGTATAA
1 TGTATAA
3173414 ATTTGATATT
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
27 7 0.12
29 17 0.30
30 4 0.07
31 13 0.23
32 10 0.18
33 6 0.11
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (28 bp):
TGTATAATTGAATCAAAATCAAAGTTCA
Found at i:3178537 original size:28 final size:31
Alignment explanation
Indices: 3178506--3178576 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 31
3178496 TGTGCCAAGA
*
3178506 AAAAATAAAAAAAAAAC-T-AAAAAAT-TTC
1 AAAAATAAAAAAAAAACTTAAAAAAATCATC
** *
3178534 AAAAATATCAGAAAAACTTAAAAAAATCATC
1 AAAAATAAAAAAAAAACTTAAAAAAATCATC
*
3178565 AAAAATGAAAAA
1 AAAAATAAAAAA
3178577 TTGGAAAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
28 14 0.44
29 1 0.03
30 7 0.22
31 10 0.31
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.17
Consensus pattern (31 bp):
AAAAATAAAAAAAAAACTTAAAAAAATCATC
Found at i:3183126 original size:39 final size:39
Alignment explanation
Indices: 3183082--3183213 Score: 171
Period size: 39 Copynumber: 3.4 Consensus size: 39
3183072 ATAATAAATA
* *
3183082 TTTTTATTTTTTTAATTTTAAAATACTTTTAAAATACTT
1 TTTTTATTTTTTAAATTTTAAAATATTTTTAAAATACTT
*
3183121 TTTTTAAATTTTTTAAATTTT--AATTTTTTTAAAATAC-T
1 TTTTT--ATTTTTTAAATTTTAAAATATTTTTAAAATACTT
*
3183159 TTTTAATTTTTTAAATTTTTAAAATATTTTTAAAATACTT
1 TTTTTATTTTTTAAA-TTTTAAAATATTTTTAAAATACTT
*
3183199 TTTTTAATTTTTAAA
1 TTTTTATTTTTTAAA
3183214 ATAAATTTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
36 10 0.12
37 4 0.05
38 5 0.06
39 34 0.43
40 14 0.17
41 13 0.16
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (39 bp):
TTTTTATTTTTTAAATTTTAAAATATTTTTAAAATACTT
Found at i:3183134 original size:9 final size:9
Alignment explanation
Indices: 3183120--3183192 Score: 71
Period size: 9 Copynumber: 8.0 Consensus size: 9
3183110 TTAAAATACT
3183120 TTTTTTAAA
1 TTTTTTAAA
3183129 TTTTTTAAA
1 TTTTTTAAA
*
3183138 --TTTTAAT
1 TTTTTTAAA
3183145 TTTTTTAAAA
1 TTTTTT-AAA
3183155 TACTTTTT-AA
1 T--TTTTTAAA
3183165 TTTTTTAAA
1 TTTTTTAAA
*
3183174 TTTTTAAAA
1 TTTTTTAAA
3183183 TATTTTTAAA
1 T-TTTTTAAA
3183193 ATACTTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
7 6 0.11
8 5 0.09
9 24 0.45
10 13 0.25
12 5 0.09
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:3183189 original size:11 final size:11
Alignment explanation
Indices: 3183097--3183201 Score: 56
Period size: 11 Copynumber: 10.4 Consensus size: 11
3183087 ATTTTTTTAA
*
3183097 TTTTAAAATAC
1 TTTTAAAATAT
3183108 TTTTAAAATACTT
1 TTTTAAAATA--T
*
3183121 TTTTTAAAT-T
1 TTTTAAAATAT
3183131 TTTT--AA-A-
1 TTTTAAAATAT
*
3183138 TTTT--AATTT
1 TTTTAAAATAT
3183147 TTTTAAAATACT
1 TTTTAAAATA-T
3183159 TTTT--AAT-T
1 TTTTAAAATAT
3183167 TTTT--AA-AT
1 TTTTAAAATAT
3183175 TTTTAAAATAT
1 TTTTAAAATAT
3183186 TTTTAAAATACT
1 TTTTAAAATA-T
3183198 TTTT
1 TTTT
3183202 TTAATTTTTA
Statistics
Matches: 77, Mismatches: 4, Indels: 25
0.73 0.04 0.24
Matches are distributed among these distances:
7 6 0.08
8 14 0.18
9 4 0.05
10 10 0.13
11 25 0.32
12 10 0.13
13 8 0.10
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:3183222 original size:21 final size:21
Alignment explanation
Indices: 3183184--3183223 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3183174 TTTTTAAAAT
**
3183184 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
3183205 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
3183224 GGTGTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:3186475 original size:16 final size:17
Alignment explanation
Indices: 3186442--3186482 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3186432 AAAATAAAAA
*
3186442 ATAAAAAA-TTGAAGGG
1 ATAAAAAACTAGAAGGG
3186458 ATAAAAAACTAGAA-GG
1 ATAAAAAACTAGAAGGG
*
3186474 ATGAAAAAC
1 ATAAAAAAC
3186483 ATAATTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.61, C:0.05, G:0.20, T:0.15
Consensus pattern (17 bp):
ATAAAAAACTAGAAGGG
Found at i:3192706 original size:14 final size:14
Alignment explanation
Indices: 3192668--3192706 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3192658 TGTTTTTGAG
3192668 TTTATGATATTTTAT
1 TTTAT-ATATTTTAT
* *
3192683 TCTATTTATTTTAT
1 TTTATATATTTTAT
3192697 TTTATATATT
1 TTTATATATT
3192707 ATGTTATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTATATATTTTAT
Found at i:3196981 original size:42 final size:40
Alignment explanation
Indices: 3196921--3197031 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 40
3196911 GATTTATGTA
* * *
3196921 TAAGACCACGTCTAGGACATCGGCATTATATTTGATTTCGTG
1 TAAGACCACGTCTGGGACAT-GGCATTATA-TTGATTACATG
*
3196963 TAAGACC-CTGTCTGGGACAATGGCATCGATATTGATTACATG
1 TAAGACCAC-GTCTGGGAC-ATGGCAT-TATATTGATTACATG
*
3197005 TAAGACCACGTCTGGGACGTTGGCATT
1 TAAGACCACGTCTGGGAC-ATGGCATT
3197032 GTACGAGTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
41 1 0.02
42 51 0.88
43 6 0.10
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (40 bp):
TAAGACCACGTCTGGGACATGGCATTATATTGATTACATG
Found at i:3199678 original size:46 final size:46
Alignment explanation
Indices: 3199611--3199787 Score: 300
Period size: 46 Copynumber: 3.8 Consensus size: 46
3199601 AGTGTGGAAC
*
3199611 GTAGGTATGGTATTTCAGTAAAGAAAACTATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
*
3199657 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAGAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* *
3199703 GTAGGTATGGTATTTCAGTAACGAAAACCATGCTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* *
3199749 GTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGTT
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
3199788 ATAGCATTGT
Statistics
Matches: 122, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 122 1.00
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.29
Consensus pattern (46 bp):
GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
Found at i:3201867 original size:20 final size:20
Alignment explanation
Indices: 3201823--3201867 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3201813 TAATAACAAT
*
3201823 AATATTTTAAATTTAAAACA
1 AATATTTTAAATTTAAAAAA
* *
3201843 TATATTTTAATTTTAAAAAA
1 AATATTTTAAATTTAAAAAA
3201863 AATAT
1 AATAT
3201868 AATTATATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTTTAAATTTAAAAAA
Found at i:3202382 original size:21 final size:21
Alignment explanation
Indices: 3202356--3202398 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3202346 TCAAAAATGA
3202356 TTTTT-GAAAAATTGATTAATT
1 TTTTTGGAAAAATTGA-TAATT
*
3202377 TTTTTGGAAAAGTTGATAATT
1 TTTTTGGAAAAATTGATAATT
3202398 T
1 T
3202399 GTTATGTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (21 bp):
TTTTTGGAAAAATTGATAATT
Found at i:3231921 original size:16 final size:16
Alignment explanation
Indices: 3231900--3231930 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3231890 ATGTAATTAT
*
3231900 ATAAAAAAAGTTAAAG
1 ATAAAAAAAATTAAAG
3231916 ATAAAAAAAATTAAA
1 ATAAAAAAAATTAAA
3231931 ATCTTGTACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (16 bp):
ATAAAAAAAATTAAAG
Found at i:3236942 original size:93 final size:93
Alignment explanation
Indices: 3236783--3236974 Score: 264
Period size: 93 Copynumber: 2.1 Consensus size: 93
3236773 TATTTCATAA
* *
3236783 TTCTTTGATATTTAAGAAGTATTCTGTCAATTCTGAACAACCAAGACCATATAACAAACCAGCAT
1 TTCTTTGATATTTAAGAAGTATTCTATCAATTCTCAACAACCAAGACCATATAACAAACCAGCAT
* *
3236848 ATTTCTCAGTCG-ACCAACTAAAGAAGTT
66 ATTTCTCAGCCGAACC-ACTAAAGAAATT
* * *
3236876 TTCTTTGAT-TTATTAGAGAGTATTCTATCCATTCTCAAC-ACCAAGACCATATAACACACCAGC
1 TTCTTTGATATT-TAAGA-AGTATTCTATCAATTCTCAACAACCAAGACCATATAACAAACCAGC
*
3236939 ATATTTCTCGGCCGAACCACTAAAGAAATT
64 ATATTTCTCAGCCGAACCACTAAAGAAATT
3236969 TTCTTT
1 TTCTTT
3236975 CAGTTTCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
92 2 0.02
93 65 0.74
94 21 0.24
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (93 bp):
TTCTTTGATATTTAAGAAGTATTCTATCAATTCTCAACAACCAAGACCATATAACAAACCAGCAT
ATTTCTCAGCCGAACCACTAAAGAAATT
Found at i:3238458 original size:17 final size:17
Alignment explanation
Indices: 3238436--3238470 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3238426 TGTTTATGGA
3238436 TATTA-TTTATTATTTAT
1 TATTATTTTA-TATTTAT
3238453 TATTATTTTATATTTAT
1 TATTATTTTATATTTAT
3238470 T
1 T
3238471 TTTGTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTATTTTATATTTAT
Found at i:3245090 original size:6 final size:6
Alignment explanation
Indices: 3245079--3245104 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3245069 AACCTTTTCT
3245079 TTTATA TTTATA TTTATA TTTATA TT
1 TTTATA TTTATA TTTATA TTTATA TT
3245105 GAATTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:3249700 original size:17 final size:17
Alignment explanation
Indices: 3249668--3249748 Score: 80
Period size: 17 Copynumber: 4.8 Consensus size: 17
3249658 AGAAATTGTG
3249668 ATAATTATACATTTATAA
1 ATAATTATA-ATTTATAA
3249686 ATAATTATAATTTATTAA
1 ATAATTATAATTTA-TAA
* *
3249704 A-AATTA-AACTTGTAA
1 ATAATTATAATTTATAA
*
3249719 A-AATTACACATTTA-AA
1 ATAATTATA-ATTTATAA
3249735 ATAATTATAATTTA
1 ATAATTATAATTTA
3249749 ATTTAAAATT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
15 9 0.17
16 13 0.24
17 19 0.35
18 13 0.24
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (17 bp):
ATAATTATAATTTATAA
Found at i:3249705 original size:49 final size:49
Alignment explanation
Indices: 3249626--3249757 Score: 135
Period size: 50 Copynumber: 2.7 Consensus size: 49
3249616 TTTAAAGTTT
* * * * *
3249626 CACATTTAAAAATAA-AATAATTGAA-ATAAAATAGAAATTGTGATAATTA
1 CACATTT-AAAATAATTATAATTTAATTTAAAATA-AAATTGTAAAAATTA
* * *
3249675 TACATTTATAAATAATTATAATTT-ATTAAAAATTAAACTTGTAAAAATTA
1 CACATTTA-AAATAATTATAATTTAATTTAAAA-TAAAATTGTAAAAATTA
3249725 CACATTTAAAATAATTATAATTTAATTTAAAAT
1 CACATTTAAAATAATTATAATTTAATTTAAAAT
3249758 TATTAATTAA
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
48 1 0.01
49 29 0.43
50 36 0.53
51 2 0.03
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.38
Consensus pattern (49 bp):
CACATTTAAAATAATTATAATTTAATTTAAAATAAAATTGTAAAAATTA
Found at i:3251653 original size:8 final size:8
Alignment explanation
Indices: 3251640--3251664 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3251630 CGTTTTAGTG
3251640 TGTGTATA
1 TGTGTATA
3251648 TGTGTATA
1 TGTGTATA
3251656 TGTGTATA
1 TGTGTATA
3251664 T
1 T
3251665 ATGTGTGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (8 bp):
TGTGTATA
Found at i:3264073 original size:35 final size:35
Alignment explanation
Indices: 3264027--3264102 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
3264017 TTCTTGCAAA
* *
3264027 GCTTTTTGAACTTTTTGTGTGAATATACTTTTGTT
1 GCTTTTTGAACTATTTGAGTGAATATACTTTTGTT
*
3264062 GCTTTTTGAACTATTTGAGTGAATATATTTTTGTT
1 GCTTTTTGAACTATTTGAGTGAATATACTTTTGTT
3264097 G-TTTTT
1 GCTTTTT
3264103 ACTAGAAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 5 0.13
35 33 0.87
ACGTcount: A:0.18, C:0.07, G:0.17, T:0.58
Consensus pattern (35 bp):
GCTTTTTGAACTATTTGAGTGAATATACTTTTGTT
Found at i:3269382 original size:15 final size:16
Alignment explanation
Indices: 3269356--3269385 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3269346 CGAATCTCAG
3269356 CTCTTGTTTCTCTTCT
1 CTCTTGTTTCTCTTCT
3269372 CTCTT-TTTCTCTTC
1 CTCTTGTTTCTCTTC
3269386 GAACAACGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.63
Consensus pattern (16 bp):
CTCTTGTTTCTCTTCT
Found at i:3271903 original size:18 final size:18
Alignment explanation
Indices: 3271865--3271900 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3271855 TTATTATTTT
*
3271865 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
3271883 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
3271901 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:3271939 original size:16 final size:16
Alignment explanation
Indices: 3271893--3271942 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
3271883 TAAAATTTAA
3271893 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
**
3271910 A-A--AATAATAAATT
1 ATATTAATAATTTATT
3271923 ATATTAATAATTTATT
1 ATATTAATAATTTATT
3271939 ATAT
1 ATAT
3271943 GACTAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
16 14 0.54
17 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:3271950 original size:29 final size:30
Alignment explanation
Indices: 3271875--3271939 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
3271865 TAAAATTTAC
*
3271875 TATTAAAATAA-AATTTAAATATTAAATAATT
1 TATTAAAATAATAAATT--ATATTAAATAATT
3271906 TATTAAAATAATAAATTATATT-AATAATT
1 TATTAAAATAATAAATTATATTAAATAATT
3271935 TATTA
1 TATTA
3271940 TATGACTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 12 0.38
30 5 0.16
31 11 0.34
32 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TATTAAAATAATAAATTATATTAAATAATT
Found at i:3272622 original size:14 final size:14
Alignment explanation
Indices: 3272603--3272630 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3272593 TGTAGAACTT
3272603 TTTTAGAATTTTTA
1 TTTTAGAATTTTTA
3272617 TTTTAGAATTTTTA
1 TTTTAGAATTTTTA
3272631 ATATATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (14 bp):
TTTTAGAATTTTTA
Found at i:3272646 original size:18 final size:17
Alignment explanation
Indices: 3272623--3272685 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 17
3272613 TTTATTTTAG
*
3272623 AATTTTTAATATATATTT
1 AATTTTTAAAATAT-TTT
3272641 AATTTTTTAAAATATTTT
1 AA-TTTTTAAAATATTTT
*
3272659 GATTTTTTAAAATTATTTT
1 -AATTTTTAAAA-TATTTT
3272678 GAATTTTT
1 -AATTTTT
3272686 TCTGAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
18 14 0.36
19 25 0.64
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
AATTTTTAAAATATTTT
Done.