Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold38
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: 2073527
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 10 of 15
Found at i:1359409 original size:20 final size:20
Alignment explanation
Indices: 1359366--1359448 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 20
1359356 GGAATATGTA
*
1359366 ATTATATTATATTTATATATTTT
1 ATTATATTATAATT-T-TA-TTT
1359389 ATTATATTATAATTTTATTT
1 ATTATATTATAATTTTATTT
**
1359409 AAAATATTATATATATTT-TTT
1 ATTATATTATA-AT-TTTATTT
1359430 A-TATATTAATAA-TTTATTT
1 ATTATATT-ATAATTTTATTT
1359449 TAAATAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
18 3 0.06
19 3 0.06
20 18 0.35
21 11 0.21
22 4 0.08
23 13 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTATATTATAATTTTATTT
Found at i:1359430 original size:41 final size:41
Alignment explanation
Indices: 1359369--1359454 Score: 113
Period size: 40 Copynumber: 2.1 Consensus size: 41
1359359 ATATGTAATT
1359369 ATATTATATTTATATATTTTATTATATT-ATAATTTTATTTAAA
1 ATATTATA-TTATATATTTTA-TATATTAATAA-TTTATTTAAA
* *
1359412 ATATTATA-TATATTTTTTATATATTAATAATTTATTTTAA
1 ATATTATATTATATATTTTATATATTAATAATTTATTTAAA
1359452 ATA
1 ATA
1359455 AATTTTAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
40 18 0.45
41 14 0.35
43 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (41 bp):
ATATTATATTATATATTTTATATATTAATAATTTATTTAAA
Found at i:1359449 original size:20 final size:19
Alignment explanation
Indices: 1359383--1359450 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 19
1359373 TATATTTATA
1359383 TATTTTATTATATTATAATTT
1 TATTTTA-TATATTATAA-TT
* *
1359404 TATTTAAAATATTATATATAT
1 TATTTTATATATTATA-AT-T
1359425 T-TTTTATATATTAATAATT
1 TATTTTATATATT-ATAATT
1359444 TATTTTA
1 TATTTTA
1359451 AATAAATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
19 2 0.05
20 25 0.64
21 12 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTATATATTATAATT
Found at i:1362170 original size:13 final size:13
Alignment explanation
Indices: 1362152--1362176 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1362142 TTTTTAAAAA
1362152 TAAATAAAAATAT
1 TAAATAAAAATAT
1362165 TAAATAAAAATA
1 TAAATAAAAATA
1362177 ATTGATATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAATAAAAATAT
Found at i:1362456 original size:71 final size:71
Alignment explanation
Indices: 1362340--1362473 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 71
1362330 TGGTGTCTTG
** *
1362340 AGTCAAAGATGTCAGACATGTCGGAGAGTTAAAGTTCTGCAATTCTTATATATATATATATATAT
1 AGTCAAAGATGTCAGACATGTCACAGAGTTAAAGGTCTGCAATTCTTATATATATATATATATAT
1362405 ATGTGT
66 ATGTGT
* * *
1362411 AGTCAGAGATGTCAGACATGTCACTGAGTTAAAGGTCTGCAATTCTTTTATATATATATATAT
1 AGTCAAAGATGTCAGACATGTCACAGAGTTAAAGGTCTGCAATTCTTATATATATATATATAT
1362474 GTATATAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (71 bp):
AGTCAAAGATGTCAGACATGTCACAGAGTTAAAGGTCTGCAATTCTTATATATATATATATATAT
ATGTGT
Found at i:1362812 original size:9 final size:9
Alignment explanation
Indices: 1362794--1362855 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 9
1362784 AGGTGGATTT
*
1362794 GGTGGCGGA
1 GGTGGTGGA
*
1362803 GTTGGTGGA
1 GGTGGTGGA
*
1362812 GGTGCTGGA
1 GGTGGTGGA
**
1362821 GGTGGTGTT
1 GGTGGTGGA
* *
1362830 GGAGGAGGA
1 GGTGGTGGA
*
1362839 GCTGGTGGA
1 GGTGGTGGA
1362848 GGTGGTGG
1 GGTGGTGG
1362856 GTTTGGAGGT
Statistics
Matches: 38, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.11, C:0.05, G:0.61, T:0.23
Consensus pattern (9 bp):
GGTGGTGGA
Found at i:1362839 original size:27 final size:29
Alignment explanation
Indices: 1362809--1362872 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 29
1362799 CGGAGTTGGT
1362809 GGAGGTGCTGGAGGTGGT-G-TTGGAGGA
1 GGAGGTGCTGGAGGTGGTGGTTTGGAGGA
* * *
1362836 GGAGCTGGTGGAGGTGGTGGGTTTGGAGGT
1 GGAGGTGCTGGAGGTGGT-GGTTTGGAGGA
1362866 GGAGGTG
1 GGAGGTG
1362873 GATTAGGAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 16 0.53
29 1 0.03
30 13 0.43
ACGTcount: A:0.12, C:0.03, G:0.61, T:0.23
Consensus pattern (29 bp):
GGAGGTGCTGGAGGTGGTGGTTTGGAGGA
Found at i:1362845 original size:36 final size:36
Alignment explanation
Indices: 1362782--1362851 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
1362772 CCTAACAAAG
* * *
1362782 GGAGGTGGATTTGGTGGCGGAGTTGGTGGAGGTGCT
1 GGAGGTGGATTTGGAGGAGGAGCTGGTGGAGGTGCT
1362818 GGAGGTGG-TGTTGGAGGAGGAGCTGGTGGAGGTG
1 GGAGGTGGAT-TTGGAGGAGGAGCTGGTGGAGGTG
1362852 GTGGGTTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 1 0.03
36 29 0.97
ACGTcount: A:0.13, C:0.04, G:0.59, T:0.24
Consensus pattern (36 bp):
GGAGGTGGATTTGGAGGAGGAGCTGGTGGAGGTGCT
Found at i:1362851 original size:24 final size:24
Alignment explanation
Indices: 1362793--1362851 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
1362783 GAGGTGGATT
* * * *
1362793 TGGTGGCGGAGTTGGTGGAGGTGC
1 TGGTGGAGGTGTTGGAGGAGGAGC
* *
1362817 TGGAGGTGGTGTTGGAGGAGGAGC
1 TGGTGGAGGTGTTGGAGGAGGAGC
1362841 TGGTGGAGGTG
1 TGGTGGAGGTG
1362852 GTGGGTTTGG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.12, C:0.05, G:0.59, T:0.24
Consensus pattern (24 bp):
TGGTGGAGGTGTTGGAGGAGGAGC
Found at i:1362924 original size:30 final size:29
Alignment explanation
Indices: 1362890--1363101 Score: 172
Period size: 30 Copynumber: 7.1 Consensus size: 29
1362880 AGGTGGGCAT
* * *
1362890 GGTGGTGGTGTTGGTGGAGGGTTTGGTAAA
1 GGTGGTGGT-TTGGTGGTGGGATTGGAAAA
* *
1362920 GGTGGTGGATTTGGTGGTGGGATTGGTAAG
1 GGTGGTGG-TTTGGTGGTGGGATTGGAAAA
* * * *
1362950 GGTGGAGGCATTGGTGGTGGAATAGGAAAA
1 GGTGGTGG-TTTGGTGGTGGGATTGGAAAA
*
1362980 GGTGGTGGATTTGGTGGTGGGGTTGGAAAA
1 GGTGGTGG-TTTGGTGGTGGGATTGGAAAA
* * * * *
1363010 GGCGGTGGAGTGGGTGGCGGAATTGGAAAA
1 GGTGGTGG-TTTGGTGGTGGGATTGGAAAA
* * *
1363040 GGTGGTGGATTTGGAGGTGGCATTGGAAAG
1 GGTGGTGG-TTTGGTGGTGGGATTGGAAAA
* * *
1363070 GGTGGTGGATTTGGAGGTGGCATTGGCAAA
1 GGTGGTGG-TTTGGTGGTGGGATTGGAAAA
1363100 GG
1 GG
1363102 GGGAGGAATT
Statistics
Matches: 150, Mismatches: 31, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
30 149 0.99
31 1 0.01
ACGTcount: A:0.19, C:0.03, G:0.51, T:0.26
Consensus pattern (29 bp):
GGTGGTGGTTTGGTGGTGGGATTGGAAAA
Found at i:1362954 original size:60 final size:60
Alignment explanation
Indices: 1362890--1363305 Score: 230
Period size: 60 Copynumber: 6.8 Consensus size: 60
1362880 AGGTGGGCAT
* ** * *
1362890 GGTGGTGGTGTTGGTGGAGGGTTTGGTAAAGGTGGTGGATTTGGTGGTGGGATTGGTAAG
1 GGTGGTGGAGTTGGTGGAGGAATTGGAAAAGGTGGTGGATTTGGTGGTGGGATTGGAAAG
* * * * *
1362950 GGTGGAGGCA-TTGGTGGTGGAATAGGAAAAGGTGGTGGATTTGGTGGTGGGGTTGGAAAA
1 GGTGGTGG-AGTTGGTGGAGGAATTGGAAAAGGTGGTGGATTTGGTGGTGGGATTGGAAAG
* * * * *
1363010 GGCGGTGGAGTGGGTGGCGGAATTGGAAAAGGTGGTGGATTTGGAGGTGGCATTGGAAAG
1 GGTGGTGGAGTTGGTGGAGGAATTGGAAAAGGTGGTGGATTTGGTGGTGGGATTGGAAAG
* * * * * * * * * * * * *
1363070 GGTGGTGGATTTGGAGGTGGCATTGGCAAAGGGGGAGGAATTGGCGGAGGAATAGGAAAA
1 GGTGGTGGAGTTGGTGGAGGAATTGGAAAAGGTGGTGGATTTGGTGGTGGGATTGGAAAG
* * * * * * * * * *
1363130 GGAGGAGGA-TTCGGAGGTGGTATTGGTAAGGGAGGAGGCCATGGAATTGGTAGTGGGATCGGCA
1 GGTGGTGGAGTT-GGTGGAGGAATTGG-AA--AAGGTGG---TGGATTTGGTGGTGGGATTGG-A
1363194 AAG
58 AAG
* * * * * * * * *
1363197 GG-GGAGGCA-TTGGAGGTGGAATTGGAAAGGGTGGTGGGTTCGGTGGAGGAATTGGCAAG
1 GGTGGTGG-AGTTGGTGGAGGAATTGGAAAAGGTGGTGGATTTGGTGGTGGGATTGGAAAG
* * * * *
1363256 GGTGGTGGCA-TTGGAGGTGGGATTGGAAAAGGTGGTGGATTCGGTAGTGG
1 GGTGGTGG-AGTTGGTGGAGGAATTGGAAAAGGTGGTGGATTTGGTGGTGG
1363306 TGCCGGAGGT
Statistics
Matches: 279, Mismatches: 65, Indels: 24
0.76 0.18 0.07
Matches are distributed among these distances:
59 8 0.03
60 218 0.78
61 1 0.00
63 9 0.03
65 2 0.01
66 33 0.12
67 8 0.03
ACGTcount: A:0.22, C:0.04, G:0.51, T:0.23
Consensus pattern (60 bp):
GGTGGTGGAGTTGGTGGAGGAATTGGAAAAGGTGGTGGATTTGGTGGTGGGATTGGAAAG
Found at i:1363017 original size:90 final size:90
Alignment explanation
Indices: 1362890--1363149 Score: 236
Period size: 90 Copynumber: 2.9 Consensus size: 90
1362880 AGGTGGGCAT
* * * * * * * * * *
1362890 GGTGGTGG-TGTTGGTGGAGGGTTTGGTAAAGGTGGTGGATTTGGTGGTGGGATTGGTAAGGGTG
1 GGTGGTGGAT-TTGGTGGTGGGGTTGGAAAAGGCGGTGGAGTGGGTGGCGGAATTGGAAAAGGTG
*
1362954 GAGGCA-TTGGTGGTGGAATAGGAAAA
65 GAGG-ATTTGGAGGTGGAATAGGAAAA
1362980 GGTGGTGGATTTGGTGGTGGGGTTGGAAAAGGCGGTGGAGTGGGTGGCGGAATTGGAAAAGGTGG
1 GGTGGTGGATTTGGTGGTGGGGTTGGAAAAGGCGGTGGAGTGGGTGGCGGAATTGGAAAAGGTGG
* * * *
1363045 TGGATTTGGAGGTGGCATTGGAAAG
66 AGGATTTGGAGGTGGAATAGGAAAA
* ** * * * * * * * * *
1363070 GGTGGTGGATTTGGAGGTGGCATTGGCAAAGGGGGAGGAATTGGCGGAGGAATAGGAAAAGGAGG
1 GGTGGTGGATTTGGTGGTGGGGTTGGAAAAGGCGGTGGAGTGGGTGGCGGAATTGGAAAAGGTGG
*
1363135 AGGATTCGGAGGTGG
66 AGGATTTGGAGGTGG
1363150 TATTGGTAAG
Statistics
Matches: 139, Mismatches: 29, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
89 1 0.01
90 137 0.99
91 1 0.01
ACGTcount: A:0.22, C:0.03, G:0.52, T:0.24
Consensus pattern (90 bp):
GGTGGTGGATTTGGTGGTGGGGTTGGAAAAGGCGGTGGAGTGGGTGGCGGAATTGGAAAAGGTGG
AGGATTTGGAGGTGGAATAGGAAAA
Found at i:1363083 original size:18 final size:18
Alignment explanation
Indices: 1363021--1363084 Score: 50
Period size: 18 Copynumber: 3.9 Consensus size: 18
1363011 GCGGTGGAGT
* *
1363021 GGGTGGCGGAATTGGAAA
1 GGGTGGTGGATTTGGAAA
*
1363039 AGGTGGTGGATTTGG--A
1 GGGTGGTGGATTTGGAAA
*
1363055 -GGT-G-GCA-TTGGAAA
1 GGGTGGTGGATTTGGAAA
1363069 GGGTGGTGGATTTGGA
1 GGGTGGTGGATTTGGA
1363085 GGTGGCATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
12 4 0.11
13 2 0.06
14 2 0.06
15 6 0.17
16 2 0.06
17 2 0.06
18 17 0.49
ACGTcount: A:0.22, C:0.03, G:0.50, T:0.25
Consensus pattern (18 bp):
GGGTGGTGGATTTGGAAA
Found at i:1363155 original size:90 final size:90
Alignment explanation
Indices: 1362965--1363287 Score: 281
Period size: 90 Copynumber: 3.5 Consensus size: 90
1362955 AGGCATTGGT
* * * * * * * * * *
1362965 GGTGGAATAGGAAAAGGTGGTGGATTTGGTGGTGGGGTTGGAAAAGGCGGTGGAGTGGGTGGCGG
1 GGTGGAATTGGAAAGGGTGGTGGATTTGGAGGTGGGATTGGAAAAGGGGGAGGAATTGGAGGAGG
*
1363030 AATTGGAAAAGGTGGTGGATTTGGA
66 AATTGGAAAAGGTGGTGGATTCGGA
* * * *
1363055 GGTGGCATTGGAAAGGGTGGTGGATTTGGAGGTGGCATTGGCAAAGGGGGAGGAATTGGCGGAGG
1 GGTGGAATTGGAAAGGGTGGTGGATTTGGAGGTGGGATTGGAAAAGGGGGAGGAATTGGAGGAGG
* * *
1363120 AATAGGAAAAGGAGGAGGATTCGGA
66 AATTGGAAAAGGTGGTGGATTCGGA
* * * * * * *
1363145 GGTGGTATTGGTAAGGGAGGAGGCCATGGAATTGGTA-GTGGGATCGGCAAAGGGGGAGGCATTG
1 GGTGGAATTGG-AA-AG-GGTGG---TGGATTTGG-AGGTGGGATTGGAAAAGGGGGAGGAATTG
* * * *
1363209 GAGGTGGAATTGGAAAGGGTGGTGGGTTCGGT
59 GAGGAGGAATTGGAAAAGGTGGTGGATTCGGA
* *
1363241 GGAGGAATTGGCAAGGGTGGTGGCA-TTGGAGGTGGGATTGGAAAAGG
1 GGTGGAATTGGAAAGGGTGGTGG-ATTTGGAGGTGGGATTGGAAAAGG
1363288 TGGTGGATTC
Statistics
Matches: 185, Mismatches: 39, Indels: 18
0.76 0.16 0.07
Matches are distributed among these distances:
89 1 0.01
90 104 0.56
91 3 0.02
92 1 0.01
93 8 0.04
94 1 0.01
95 1 0.01
96 65 0.35
97 1 0.01
ACGTcount: A:0.24, C:0.05, G:0.50, T:0.21
Consensus pattern (90 bp):
GGTGGAATTGGAAAGGGTGGTGGATTTGGAGGTGGGATTGGAAAAGGGGGAGGAATTGGAGGAGG
AATTGGAAAAGGTGGTGGATTCGGA
Found at i:1363164 original size:30 final size:30
Alignment explanation
Indices: 1362926--1363167 Score: 137
Period size: 30 Copynumber: 8.1 Consensus size: 30
1362916 TAAAGGTGGT
* * * *
1362926 GGATTTGGTGGTGGGATTGGTAAGGGTGGA
1 GGATTTGGAGGTGGCATTGGAAAGGGAGGA
* * * * * *
1362956 GGCA-TTGGTGGTGGAATAGGAAAAGGTGGT
1 GG-ATTTGGAGGTGGCATTGGAAAGGGAGGA
* ** * * *
1362986 GGATTTGGTGGTGGGGTTGGAAAAGGCGGT
1 GGATTTGGAGGTGGCATTGGAAAGGGAGGA
* * * * * * * *
1363016 GGAGTGGGTGGCGGAATTGGAAAAGGTGGT
1 GGATTTGGAGGTGGCATTGGAAAGGGAGGA
* *
1363046 GGATTTGGAGGTGGCATTGGAAAGGGTGGT
1 GGATTTGGAGGTGGCATTGGAAAGGGAGGA
1363076 GGATTTGGAGGTGGCATTGGCAAAGGG-GGA
1 GGATTTGGAGGTGGCATTGG-AAAGGGAGGA
* * * * * *
1363106 GGAATTGGCGGAGGAATAGGAAAAGGAGGA
1 GGATTTGGAGGTGGCATTGGAAAGGGAGGA
* * *
1363136 GGATTCGGAGGTGGTATTGGTAAGGGAGGA
1 GGATTTGGAGGTGGCATTGGAAAGGGAGGA
1363166 GG
1 GG
1363168 CCATGGAATT
Statistics
Matches: 172, Mismatches: 36, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
29 6 0.03
30 159 0.92
31 7 0.04
ACGTcount: A:0.24, C:0.03, G:0.51, T:0.22
Consensus pattern (30 bp):
GGATTTGGAGGTGGCATTGGAAAGGGAGGA
Found at i:1363249 original size:30 final size:30
Alignment explanation
Indices: 1363214--1363300 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
1363204 CATTGGAGGT
*
1363214 GGAATTGGAAAGGGTGGTGGGTTCGGTGGA
1 GGAATTGGAAAGGGTGGTGGATTCGGTGGA
* * *
1363244 GGAATTGGCAAGGGTGGTGGCATT-GGAGGT
1 GGAATTGGAAAGGGTGGTGG-ATTCGGTGGA
* *
1363274 GGGATTGGAAAAGGTGGTGGATTCGGT
1 GGAATTGGAAAGGGTGGTGGATTCGGT
1363301 AGTGGTGCCG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
29 3 0.06
30 42 0.89
31 2 0.04
ACGTcount: A:0.21, C:0.05, G:0.51, T:0.24
Consensus pattern (30 bp):
GGAATTGGAAAGGGTGGTGGATTCGGTGGA
Found at i:1363356 original size:42 final size:42
Alignment explanation
Indices: 1363267--1363359 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
1363257 GTGGTGGCAT
* *
1363267 TGGAGGTGGGATTGGAAAAGGTGGTGGATTCGGTAGTGGTGC
1 TGGAGGTGGCATTGGAAAAGGTGGTGGATTCGGTAGTGGAGC
* * * * *
1363309 CGGAGGTGGCTTTGGCAAAGGTGGTGGTTTTGG-AGGTGGAGC
1 TGGAGGTGGCATTGGAAAAGGTGGTGGATTCGGTA-GTGGAGC
1363351 TGGAGGTGG
1 TGGAGGTGG
1363360 TGGTGGTTTC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.02
42 41 0.98
ACGTcount: A:0.16, C:0.06, G:0.52, T:0.26
Consensus pattern (42 bp):
TGGAGGTGGCATTGGAAAAGGTGGTGGATTCGGTAGTGGAGC
Found at i:1363362 original size:30 final size:30
Alignment explanation
Indices: 1363328--1363407 Score: 124
Period size: 30 Copynumber: 2.7 Consensus size: 30
1363318 CTTTGGCAAA
*
1363328 GGTGGTGGTTTTGGAGGTGGAGCTGGAGGT
1 GGTGGTGGTTTTGGAGGTGGAGCTGGAGGC
*
1363358 GGTGGTGGTTTCGGAGGTGGAGCTGGAGGC
1 GGTGGTGGTTTTGGAGGTGGAGCTGGAGGC
* *
1363388 GGCGGTGGTTATGGAGGTGG
1 GGTGGTGGTTTTGGAGGTGG
1363408 TGGGGGTGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.10, C:0.06, G:0.57, T:0.26
Consensus pattern (30 bp):
GGTGGTGGTTTTGGAGGTGGAGCTGGAGGC
Found at i:1363833 original size:8 final size:8
Alignment explanation
Indices: 1363766--1363840 Score: 50
Period size: 8 Copynumber: 9.6 Consensus size: 8
1363756 TAATACCGAT
*
1363766 TAAATAAA
1 TAAATATA
1363774 TAAAT-TA
1 TAAATATA
*
1363781 TAAAAATA
1 TAAATATA
1363789 TAAA-ATCA
1 TAAATAT-A
*
1363797 -AAAAATA
1 TAAATATA
*
1363804 TAAATAAA
1 TAAATATA
* *
1363812 TTATATAAA
1 -TAAATATA
1363821 TAAATATA
1 TAAATATA
1363829 TAAATA-A
1 TAAATATA
1363836 TAAAT
1 TAAAT
1363841 TTAATTTTAC
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
7 17 0.31
8 31 0.56
9 7 0.13
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (8 bp):
TAAATATA
Found at i:1365322 original size:26 final size:27
Alignment explanation
Indices: 1365293--1365376 Score: 75
Period size: 26 Copynumber: 3.1 Consensus size: 27
1365283 TTATTTATAT
1365293 TATAATTTAT-TTTATATTAATTTTGA
1 TATAATTTATATTTATATTAATTTTGA
* * *
1365319 TATATTTTATATTTTTATT-ATTTTTA
1 TATAATTTATATTTATATTAATTTTGA
* *
1365345 TTTAATGTATATATTTTATATT-ATTTTTA
1 TATAAT-T-TATA-TTTATATTAATTTTGA
1365374 TAT
1 TAT
1365377 TTTATAAGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
26 19 0.40
27 8 0.17
28 4 0.09
29 16 0.34
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (27 bp):
TATAATTTATATTTATATTAATTTTGA
Found at i:1365328 original size:38 final size:37
Alignment explanation
Indices: 1365286--1365382 Score: 110
Period size: 37 Copynumber: 2.6 Consensus size: 37
1365276 TAAATGTTTA
* *
1365286 TTTATATTATAATTTATTTTATA-TTAATTTTGATATAT
1 TTTATATTATTATTTATTTTATATTTAA-TGT-ATATAT
*
1365324 TTTATATTTTTA-TTATTTT-TATTTAATGTATATAT
1 TTTATATTATTATTTATTTTATATTTAATGTATATAT
*
1365359 TTTATATTATTTTTATATTTTATA
1 TTTATATTATTATT-TATTTTATA
1365383 AGTATATCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
35 16 0.32
36 5 0.10
37 17 0.34
38 12 0.24
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (37 bp):
TTTATATTATTATTTATTTTATATTTAATGTATATAT
Found at i:1365340 original size:9 final size:9
Alignment explanation
Indices: 1365299--1365379 Score: 53
Period size: 9 Copynumber: 8.8 Consensus size: 9
1365289 ATATTATAAT
1365299 TTATTTTATA
1 TTATTTT-TA
*
1365309 TTAATTTTGA
1 TT-ATTTTTA
1365319 -TATATTTTA
1 TTAT-TTTTA
1365328 -TATTTTTA
1 TTATTTTTA
1365336 TTATTTTTA
1 TTATTTTTA
* *
1365345 TT-TAATGTA
1 TTAT-TTTTA
1365354 TATATTTTATA
1 T-TATTTT-TA
1365365 TTATTTTTA
1 TTATTTTTA
1365374 -TATTTT
1 TTATTTT
1365380 ATAAGTATAT
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
8 14 0.24
9 24 0.41
10 11 0.19
11 9 0.16
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.69
Consensus pattern (9 bp):
TTATTTTTA
Found at i:1365363 original size:18 final size:18
Alignment explanation
Indices: 1365286--1365382 Score: 67
Period size: 18 Copynumber: 5.3 Consensus size: 18
1365276 TAAATGTTTA
* *
1365286 TTTATATTAT-AATTTAT
1 TTTATATTATGTATATAT
*
1365303 TTTATATTAATTTTGATATAT
1 TTTATATT-A-TGT-ATATAT
*
1365324 TTTATATT-TTTAT-TAT
1 TTTATATTATGTATATAT
1365340 TTT-TATTTAATGTATATAT
1 TTTATA-TT-ATGTATATAT
* *
1365359 TTTATATTATTTTTATAT
1 TTTATATTATGTATATAT
1365377 TTTATA
1 TTTATA
1365383 AGTATATCAT
Statistics
Matches: 66, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
15 2 0.03
16 8 0.12
17 10 0.15
18 22 0.33
19 9 0.14
20 2 0.03
21 13 0.20
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATATTATGTATATAT
Found at i:1365675 original size:24 final size:25
Alignment explanation
Indices: 1365648--1365701 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
1365638 TTTTTTTATG
**
1365648 ATATCATATTTATT-ATAAT-TATAA
1 ATATCATAAATATTAATAATATA-AA
*
1365672 ATATAATAAATATTAATAATATAAA
1 ATATCATAAATATTAATAATATAAA
1365697 ATATC
1 ATATC
1365702 GAAACAAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 11 0.46
25 11 0.46
26 2 0.08
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (25 bp):
ATATCATAAATATTAATAATATAAA
Found at i:1365921 original size:19 final size:19
Alignment explanation
Indices: 1365860--1365921 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
1365850 AAAGATTTTC
*
1365860 TTTAA-TTATTATAATATTT
1 TTTAATTTAATATAA-ATTT
* *
1365879 TTTAAATTTAATA-AAAATA
1 TTT-AATTTAATATAAATTT
*
1365898 ATTAATTTAATATAAATTT
1 TTTAATTTAATATAAATTT
1365917 TTTAA
1 TTTAA
1365922 CTGAAATATA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 9 0.27
19 15 0.45
20 4 0.12
21 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAATTTAATATAAATTT
Found at i:1366309 original size:19 final size:19
Alignment explanation
Indices: 1366269--1366306 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
1366259 TGATTTATTA
1366269 ATTATTATATATTAAAAAT
1 ATTATTATATATTAAAAAT
*
1366288 ATTATTA-A-ATTAAATAT
1 ATTATTATATATTAAAAAT
1366305 AT
1 AT
1366307 ATTTTTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 1 0.06
19 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTATTATATATTAAAAAT
Found at i:1366477 original size:2 final size:2
Alignment explanation
Indices: 1366470--1366498 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1366460 GCAGCCAGCT
1366470 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1366499 ATCTGCCTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1371887 original size:21 final size:21
Alignment explanation
Indices: 1371870--1371912 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1371860 TCAATTTATT
*
1371870 ATTATATAAATCATATTTAAA
1 ATTATAAAAATCATATTTAAA
1371891 ATTATAAAAAT-ATA--TAAA
1 ATTATAAAAATCATATTTAAA
1371909 ATTA
1 ATTA
1371913 ATTTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
20 3 0.14
21 10 0.48
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTATAAAAATCATATTTAAA
Found at i:1371956 original size:2 final size:2
Alignment explanation
Indices: 1371949--1371979 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1371939 ATCTTTCTTT
*
1371949 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1371980 TCTTTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1372443 original size:32 final size:33
Alignment explanation
Indices: 1372395--1372459 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1372385 ATGTATTTAA
* *
1372395 AATATTTTATAATTATATAAATTTTAATATATT
1 AATAATTTATAATTATATAAATTTTAAAATATT
*
1372428 AATAATTTAT-ATTATATTAATTTTAAAATATT
1 AATAATTTATAATTATATAAATTTTAAAATATT
1372460 TATAGATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 20 0.69
33 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
AATAATTTATAATTATATAAATTTTAAAATATT
Found at i:1372500 original size:13 final size:13
Alignment explanation
Indices: 1372482--1372525 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
1372472 TCGTAGTTTT
*
1372482 TATTATTTTTATA
1 TATTATATTTATA
1372495 TATTATATTTATA
1 TATTATATTTATA
*
1372508 TAATTATATATA-A
1 T-ATTATATTTATA
1372521 TATTA
1 TATTA
1372526 CTGGATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 4 0.14
13 15 0.54
14 9 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TATTATATTTATA
Found at i:1372775 original size:13 final size:14
Alignment explanation
Indices: 1372742--1372777 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1372732 ATATTATTTT
1372742 TATATAAAT-TTAA
1 TATATAAATATTAA
1372755 T-TATAAATATTAA
1 TATATAAATATTAA
1372768 TATA-AAATAT
1 TATATAAATAT
1372778 ATTTTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 7 0.33
13 12 0.57
14 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATAAATATTAA
Found at i:1375162 original size:15 final size:15
Alignment explanation
Indices: 1375131--1375176 Score: 58
Period size: 14 Copynumber: 3.0 Consensus size: 15
1375121 TGATTTCAAC
1375131 TAAAAATAATATAAATT
1 TAAAAA-AAT-TAAATT
1375148 TAAAAAAATTAAATT
1 TAAAAAAATTAAATT
*
1375163 T-TAAAAATTAAATT
1 TAAAAAAATTAAATT
1375177 AATTTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 12 0.43
15 7 0.25
16 3 0.11
17 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAAAAATTAAATT
Found at i:1381507 original size:33 final size:33
Alignment explanation
Indices: 1381465--1381530 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
1381455 TCCTTAATAA
*
1381465 CCATATCTTTATTCACTTCAGATTTCAATCTTT
1 CCATATCTTTATTCACTTCAGACTTCAATCTTT
1381498 CCATATCTTTATTCACTTCAGACTTCAATCTTT
1 CCATATCTTTATTCACTTCAGACTTCAATCTTT
1381531 TTTCCAACTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.26, G:0.03, T:0.47
Consensus pattern (33 bp):
CCATATCTTTATTCACTTCAGACTTCAATCTTT
Found at i:1382789 original size:22 final size:20
Alignment explanation
Indices: 1382761--1382804 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1382751 AAAATTAAAA
*
1382761 TATTATTTTTATTATTAATATT
1 TATTA-TTTTATAATTAA-ATT
1382783 TATTATTTTATAATTAAATT
1 TATTATTTTATAATTAAATT
1382803 TA
1 TA
1382805 AATAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 11 0.52
22 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTATTTTATAATTAAATT
Found at i:1387520 original size:20 final size:20
Alignment explanation
Indices: 1387495--1387532 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1387485 TTTATGAACT
**
1387495 TATTTAAATTTTTTAATTAG
1 TATTTAAAAATTTTAATTAG
1387515 TATTTAAAAATTTTAATT
1 TATTTAAAAATTTTAATT
1387533 CAAATTCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
TATTTAAAAATTTTAATTAG
Found at i:1391521 original size:13 final size:14
Alignment explanation
Indices: 1391498--1391534 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
1391488 AAAGAAAACA
1391498 TTTCACTTTTTTCTT
1 TTTC-CTTTTTTCTT
1391513 TTT-CTTTTTTCTT
1 TTTCCTTTTTTCTT
1391526 TTTCCTTTT
1 TTTCCTTTT
1391535 CTCCTCCGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 13 0.62
14 5 0.24
15 3 0.14
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTCCTTTTTTCTT
Found at i:1391806 original size:18 final size:19
Alignment explanation
Indices: 1391785--1391827 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1391775 ATTTATAAAT
1391785 ATAATAAAT-ATTATCATA
1 ATAATAAATAATTATCATA
*
1391803 ATAAT-TATAATTATCATA
1 ATAATAAATAATTATCATA
*
1391821 ATTATAA
1 ATAATAA
1391828 TTTTTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAATAAATAATTATCATA
Found at i:1395305 original size:16 final size:16
Alignment explanation
Indices: 1395269--1395306 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1395259 ATGTTATCCC
1395269 ATATTTATTAAATTTT
1 ATATTTATTAAATTTT
* *
1395285 A-ATTTTTTTAATTTT
1 ATATTTATTAAATTTT
1395300 ATATTTA
1 ATATTTA
1395307 AATTTATTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 2
0.78 0.13 0.09
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATATTTATTAAATTTT
Found at i:1396508 original size:29 final size:30
Alignment explanation
Indices: 1396444--1396516 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
1396434 AAAAGTCAAG
*
1396444 AATTTATTTAACTATAAATTAAAAATAAAA
1 AATTTATTTAAATATAAATTAAAAATAAAA
*
1396474 AGTTTATTTAAATAT-AA-TAAAAATATAAA
1 AATTTATTTAAATATAAATTAAAAATA-AAA
*
1396503 AATTTAATTAAATA
1 AATTTATTTAAATA
1396517 AAGTGATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 8 0.21
29 17 0.45
30 13 0.34
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (30 bp):
AATTTATTTAAATATAAATTAAAAATAAAA
Found at i:1397638 original size:2 final size:2
Alignment explanation
Indices: 1397633--1397674 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1397623 ATATATCTTT
1397633 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1397675 AAGATATAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1399083 original size:15 final size:14
Alignment explanation
Indices: 1399063--1399114 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
1399053 TTTTAAATAT
1399063 AATTATAATATAAAA
1 AATTATAA-ATAAAA
*
1399078 AATTATAAA-AATAT
1 AATTATAAATAA-AA
1399092 AA-TATAAATAAATA
1 AATTATAAATAAA-A
1399106 AATTATAAA
1 AATTATAAA
1399115 ATTTAATACG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 9 0.29
14 8 0.26
15 14 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATTATAAATAAAA
Found at i:1399086 original size:27 final size:25
Alignment explanation
Indices: 1399049--1399114 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 25
1399039 ATAAATGTAT
*
1399049 AAAATTTTAAATATAATTATAATATAA
1 AAAATTATAAATATAA-TATAA-ATAA
1399076 AAAATTATAAAAATATAATATAAATAA
1 AAAATTAT--AAATATAATATAAATAA
1399103 ATAAATTATAAA
1 A-AAATTATAAA
1399115 ATTTAATACG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
26 3 0.09
27 12 0.34
28 12 0.34
29 8 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AAAATTATAAATATAATATAAATAA
Found at i:1399097 original size:28 final size:29
Alignment explanation
Indices: 1399057--1399115 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
1399047 ATAAAATTTT
1399057 AAATATAATTATAATATAAA-AAATTATAA
1 AAATATAATTATAA-ATAAATAAATTATAA
1399086 AAATATAA-TATAAATAAATAAATTATAA
1 AAATATAATTATAAATAAATAAATTATAA
1399114 AA
1 AA
1399116 TTTAATACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 5 0.17
28 16 0.55
29 8 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (29 bp):
AAATATAATTATAAATAAATAAATTATAA
Found at i:1399121 original size:27 final size:27
Alignment explanation
Indices: 1399057--1399122 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
1399047 ATAAAATTTT
1399057 AAATATAATTATAATATAAA-AAATTATAA
1 AAATATAA-TATAA-ATAAATAAATTAT-A
1399086 AAATATAATATAAATAAATAAATTATA
1 AAATATAATATAAATAAATAAATTATA
*
1399113 AAATTTAATA
1 AAATATAATA
1399123 CGAAGAAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 15 0.43
28 12 0.34
29 8 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
AAATATAATATAAATAAATAAATTATA
Found at i:1400496 original size:23 final size:22
Alignment explanation
Indices: 1400470--1400516 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
1400460 TGTAATTATT
1400470 TTTAAAAAATAATATTTAATAAA
1 TTTAAAAAATAATATTT-ATAAA
***
1400493 TTTAAATTTTAATATTTATAAA
1 TTTAAAAAATAATATTTATAAA
1400515 TT
1 TT
1400517 ATTTTTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTAAAAAATAATATTTATAAA
Found at i:1400536 original size:18 final size:20
Alignment explanation
Indices: 1400479--1400529 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
1400469 TTTTAAAAAA
*
1400479 TAATATTTAATAAATTTAAATTT
1 TAATATTT-ATAAA-TT-ATTTT
1400502 TAATATTTATAAATTATTTT
1 TAATATTTATAAATTATTTT
*
1400522 TTATATTT
1 TAATATTT
1400530 TAATTATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 11 0.42
21 2 0.08
22 5 0.19
23 8 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TAATATTTATAAATTATTTT
Found at i:1400816 original size:11 final size:11
Alignment explanation
Indices: 1400800--1400841 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
1400790 AAAAATAATA
1400800 TTAAATAATTT
1 TTAAATAATTT
*
1400811 TTAAATAATTA
1 TTAAATAATTT
*
1400822 TTAAATAAATT
1 TTAAATAATTT
*
1400833 TTAACTAAT
1 TTAAATAAT
1400842 GATTATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAAATAATTT
Found at i:1400826 original size:22 final size:22
Alignment explanation
Indices: 1400792--1400846 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1400782 TATTCAATAA
*
1400792 AAATAA-TATTAAATAATTTTT
1 AAATAATTATTAAATAAATTTT
1400813 AAATAATTATTAAATAAATTTT
1 AAATAATTATTAAATAAATTTT
* *
1400835 AACTAATGATTA
1 AAATAATTATTA
1400847 TAAAAACTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AAATAATTATTAAATAAATTTT
Found at i:1401491 original size:22 final size:22
Alignment explanation
Indices: 1401466--1401509 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1401456 AATAATTTTT
1401466 TTAAAAAATTTATATA-ATTAAA
1 TTAAAAAATTT-TATACATTAAA
*
1401488 TTAAATAATTTTATACATTAAA
1 TTAAAAAATTTTATACATTAAA
1401510 AATTTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAAAAAATTTTATACATTAAA
Found at i:1402945 original size:19 final size:19
Alignment explanation
Indices: 1402921--1402965 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1402911 AACACATAAA
*
1402921 TTTTTTTCTTTCTTT-TTTC
1 TTTTTTTC-TCCTTTCTTTC
1402940 TTTTTTTCTCCTTTCTTTC
1 TTTTTTTCTCCTTTCTTTC
1402959 TTTTTTT
1 TTTTTTT
1402966 TAGCCCTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTCTCCTTTCTTTC
Found at i:1403382 original size:31 final size:32
Alignment explanation
Indices: 1403327--1403386 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
1403317 ATAAAATAAA
*
1403327 ATAAATTATTAATATATAAAAAATATAAACAT
1 ATAAATTATTAATATACAAAAAATATAAACAT
1403359 ATAATATT-TTAA-ATACAAAAAATATAAA
1 ATAA-ATTATTAATATACAAAAAATATAAA
1403387 AATGAATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 15 0.58
32 8 0.31
33 3 0.12
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (32 bp):
ATAAATTATTAATATACAAAAAATATAAACAT
Found at i:1403456 original size:11 final size:10
Alignment explanation
Indices: 1403401--1403466 Score: 57
Period size: 11 Copynumber: 6.6 Consensus size: 10
1403391 AATACATAAT
*
1403401 TTTTTTTTTAC
1 TTTTTCTTT-C
*
1403412 TTTTTCATT-
1 TTTTTCTTTC
1403421 TTTTTCATTT-
1 TTTTTC-TTTC
*
1403431 TTTTT-TCTC
1 TTTTTCTTTC
1403440 TTTTTCTTTC
1 TTTTTCTTTC
1403450 TTCTTTCTTTC
1 TT-TTTCTTTC
1403461 TTTTTC
1 TTTTTC
1403467 AGCTGAATCA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
8 2 0.04
9 11 0.24
10 16 0.35
11 17 0.37
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:1403614 original size:28 final size:28
Alignment explanation
Indices: 1403542--1403614 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 28
1403532 TATATGTTAG
*
1403542 ATATAATTTT-TTTAATATAAATATAAT
1 ATATAATTTTATTTATTATAAATATAAT
* * *
1403569 TTAATAATTTTTAATTATTATTCAATATAA-
1 AT-ATAA-TTTTATTTATTA-TAAATATAAT
1403599 ATATAATTTTATTTAT
1 ATATAATTTTATTTAT
1403615 ATTTTATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
27 1 0.03
28 13 0.36
29 8 0.22
30 6 0.17
31 8 0.22
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (28 bp):
ATATAATTTTATTTATTATAAATATAAT
Found at i:1403659 original size:35 final size:35
Alignment explanation
Indices: 1403552--1403662 Score: 138
Period size: 35 Copynumber: 3.1 Consensus size: 35
1403542 ATATAATTTT
1403552 TTTAATATAAATATAA-TTTAATAATTTTTAATTATTA
1 TTTAATATAAATATAATTTTAATAA-TTTTAA--ATTA
* *
1403589 TTCAATATAAATATAATTTTATTTATATTTT--ATTA
1 TTTAATATAAATATAATTTTA-ATA-ATTTTAAATTA
1403624 TTTAATATAAATATAATTTTAATAATTTTAAATTA
1 TTTAATATAAATATAATTTTAATAATTTTAAATTA
1403659 TTTA
1 TTTA
1403663 TTATTTATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
33 5 0.08
34 2 0.03
35 32 0.49
37 15 0.23
38 4 0.06
39 6 0.09
40 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (35 bp):
TTTAATATAAATATAATTTTAATAATTTTAAATTA
Found at i:1404178 original size:21 final size:19
Alignment explanation
Indices: 1404141--1404204 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 19
1404131 ATTTAAATAT
1404141 TTAAAT-TATTATATTTATA
1 TTAAATATA-TATATTTATA
1404160 TTAAATATCATACTATTTAT-
1 TTAAATAT-ATA-TATTTATA
*
1404180 TTAAATGTATAT-TTT-TA
1 TTAAATATATATATTTATA
1404197 TTAAATAT
1 TTAAATAT
1404205 TTACTATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 1 0.03
17 10 0.26
18 1 0.03
19 9 0.23
20 10 0.26
21 8 0.21
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (19 bp):
TTAAATATATATATTTATA
Found at i:1404621 original size:2 final size:2
Alignment explanation
Indices: 1404616--1404644 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1404606 GAAACCATAA
1404616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1404645 AACTTCTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1405633 original size:21 final size:21
Alignment explanation
Indices: 1405607--1405659 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1405597 TACTACTGAT
1405607 TTTAATTTTATCATTACAATA
1 TTTAATTTTATCATTACAATA
* *
1405628 TTTAATTTCATCATTATAATA
1 TTTAATTTTATCATTACAATA
**
1405649 ACTAATTTTAT
1 TTTAATTTTAT
1405660 TATCAAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAATTTTATCATTACAATA
Found at i:1405850 original size:20 final size:19
Alignment explanation
Indices: 1405827--1405877 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
1405817 TTAACCAGTT
1405827 TATTTAAATAAAATTTTAAA
1 TATTTAAATAAAATTTT-AA
**
1405847 TATTTTAAA-ATGATTTTAA
1 TA-TTTAAATAAAATTTTAA
1405866 T-TTTAAATAAAA
1 TATTTAAATAAAA
1405878 ATTATATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
17 6 0.24
18 2 0.08
19 3 0.12
20 8 0.32
21 6 0.24
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TATTTAAATAAAATTTTAA
Found at i:1406834 original size:13 final size:14
Alignment explanation
Indices: 1406809--1406848 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
1406799 TTAAAAAAAT
1406809 TTTATTAATAATTA
1 TTTATTAATAATTA
1406823 TTTATT-ATAATTA
1 TTTATTAATAATTA
1406836 -TTA-TAA-AATTA
1 TTTATTAATAATTA
1406847 TT
1 TT
1406849 AAGTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 6 0.25
12 5 0.21
13 7 0.29
14 6 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATTAATAATTA
Found at i:1406847 original size:11 final size:12
Alignment explanation
Indices: 1406804--1406849 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
1406794 AAAAGTTAAA
1406804 AAAATT-TTATT
1 AAAATTATTATT
1406815 AATAATTATTTATT
1 AA-AATTA-TTATT
*
1406829 ATAATTATTA-T
1 AAAATTATTATT
1406840 AAAATTATTA
1 AAAATTATTA
1406850 AGTATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 12 0.40
12 7 0.23
13 5 0.17
14 6 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AAAATTATTATT
Found at i:1410258 original size:19 final size:19
Alignment explanation
Indices: 1410222--1410259 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1410212 TATTAAAATC
*
1410222 ATATTCATATTTTTTTATT
1 ATATTCATATTTTATTATT
1410241 ATATT-ATATTTTAATTATT
1 ATATTCATATTTT-ATTATT
1410260 TTTTATCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
ATATTCATATTTTATTATT
Found at i:1410651 original size:19 final size:19
Alignment explanation
Indices: 1410620--1410662 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1410610 GTCTACAAAA
1410620 TTTTGTCCAAATT-GTCATG
1 TTTTGTCCAAATTGGT-ATG
1410639 TTTTAGTCC-AATTGGTATG
1 TTTT-GTCCAAATTGGTATG
1410658 TTTTG
1 TTTTG
1410663 GATAAGGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.05
19 15 0.68
20 6 0.27
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.51
Consensus pattern (19 bp):
TTTTGTCCAAATTGGTATG
Found at i:1410819 original size:19 final size:19
Alignment explanation
Indices: 1410795--1410831 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1410785 AATTATAATA
1410795 CATAAAAATAAATAAATTT
1 CATAAAAATAAATAAATTT
1410814 CATAAAAATAAATAAATT
1 CATAAAAATAAATAAATT
1410832 ATTATATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
CATAAAAATAAATAAATTT
Found at i:1411190 original size:33 final size:32
Alignment explanation
Indices: 1411115--1411191 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
1411105 TATATTCATA
1411115 TTATATTTATATAAATTTTGATAAATTAATAAT
1 TTATATTTATATAAATTTTGATAAATTAAT-AT
*
1411148 TTATA-TTATATAAATTTTGATATATTTAAT-T
1 TTATATTTATATAAATTTTGATA-AATTAATAT
1411179 TATATATTTATAT
1 T-TATATTTATAT
1411192 TATATTTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
31 2 0.05
32 21 0.52
33 17 0.43
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (32 bp):
TTATATTTATATAAATTTTGATAAATTAATAT
Found at i:1411195 original size:38 final size:32
Alignment explanation
Indices: 1411115--1411183 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
1411105 TATATTCATA
1411115 TTATATTTATATAAATTTTGATAAATTAATAAT
1 TTATA-TTATATAAATTTTGATAAATTAATAAT
*
1411148 TTATATTATATAAATTTTGATATATT--TAAT
1 TTATATTATATAAATTTTGATAAATTAATAAT
1411178 TTATAT
1 TTATAT
1411184 ATTTATATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 10 0.29
32 20 0.57
33 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (32 bp):
TTATATTATATAAATTTTGATAAATTAATAAT
Found at i:1411203 original size:38 final size:38
Alignment explanation
Indices: 1411097--1411204 Score: 105
Period size: 38 Copynumber: 2.8 Consensus size: 38
1411087 AATATATTTG
* * *
1411097 ATAATTTATATATTCATATTATATTTA-TATAAATTTT
1 ATAATTTATATATTTATATTATATTTATTTTAAATATT
* ** *
1411134 GATAAATTA-ATAATTTATATTATATAAATTTTGATATATT
1 -ATAATTTATAT-ATTTATATTATATTTATTTT-AAATATT
1411174 -TAATTTATATATTTATATTATATTTATTTTA
1 ATAATTTATATATTTATATTATATTTATTTTA
1411205 TTTTTTGAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
37 3 0.05
38 44 0.79
39 4 0.07
40 5 0.09
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (38 bp):
ATAATTTATATATTTATATTATATTTATTTTAAATATT
Found at i:1412152 original size:2 final size:2
Alignment explanation
Indices: 1412145--1412177 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1412135 TTGCGTTACT
*
1412145 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1412178 TATGTTACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1418199 original size:18 final size:18
Alignment explanation
Indices: 1418169--1418214 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1418159 GTACTACTTA
1418169 TTTAATATTAAAA-TATT
1 TTTAATATTAAAATTATT
1418186 TTTAATATTTAAAATTA-T
1 TTTAATA-TTAAAATTATT
1418204 TTTAAT-TTAAA
1 TTTAATATTAAA
1418215 TCTTTCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.19
17 7 0.26
18 13 0.48
19 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAATATTAAAATTATT
Found at i:1418480 original size:28 final size:27
Alignment explanation
Indices: 1418449--1418530 Score: 76
Period size: 28 Copynumber: 3.0 Consensus size: 27
1418439 ATTTTTATAA
1418449 ATAAAAATATTTTTATTTAAATTTAATT
1 ATAAAAATATTTTTATTTAAATTTAA-T
* * *
1418477 ATAAAAATATATTAATATTATA-TTAAT
1 ATAAAAATATTTTTAT-TTAAATTTAAT
** *
1418504 ATATTAATATTTTTATTAATAATTTAA
1 ATAAAAATATTTTTATTTA-AATTTAA
1418531 GCTTTTTTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
26 2 0.05
27 14 0.33
28 22 0.52
29 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
ATAAAAATATTTTTATTTAAATTTAAT
Found at i:1418498 original size:19 final size:19
Alignment explanation
Indices: 1418474--1418514 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1418464 TTTAAATTTA
1418474 ATTATAAAAATATATTAAT
1 ATTATAAAAATATATTAAT
**
1418493 ATTATATTAATATATTAAT
1 ATTATAAAAATATATTAAT
1418512 ATT
1 ATT
1418515 TTTATTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTATAAAAATATATTAAT
Found at i:1418530 original size:20 final size:19
Alignment explanation
Indices: 1418482--1418524 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
1418472 TAATTATAAA
1418482 AATATATTAATATTATATT
1 AATATATTAATATTATATT
*
1418501 AATATATTAATATTTTTATT
1 AATATATTAATA-TTATATT
1418521 AATA
1 AATA
1418525 ATTTAAGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AATATATTAATATTATATT
Found at i:1420195 original size:21 final size:21
Alignment explanation
Indices: 1420177--1420233 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
1420167 ATTTTTTTAT
1420177 AAAAAAATTATTTCCTTTTCA
1 AAAAAAATTATTTCCTTTTCA
* ** *
1420198 AATAAAATTATTTAATTATTTA
1 AAAAAAATTATTTCCTT-TTCA
1420220 AAAAAACATTATTT
1 AAAAAA-ATTATTT
1420234 TTTTTAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 14 0.48
22 8 0.28
23 7 0.24
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAAAAATTATTTCCTTTTCA
Found at i:1420864 original size:12 final size:13
Alignment explanation
Indices: 1420836--1420882 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 13
1420826 ATATTTTATT
**
1420836 TATTTATTATTTA
1 TATTTATTAAATA
1420849 TATTT-TTAAATA
1 TATTTATTAAATA
1420861 TATTTCATTAAATA
1 TATTT-ATTAAATA
*
1420875 TATATATT
1 TATTTATT
1420883 TTATAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 10 0.34
13 8 0.28
14 11 0.38
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTTATTAAATA
Found at i:1423835 original size:18 final size:17
Alignment explanation
Indices: 1423780--1423835 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 17
1423770 TAATTTTATA
*
1423780 AAAATAATATAATAAAT
1 AAAATAATATATTAAAT
1423797 ACAAATAATATATTTAAAT
1 A-AAATAATATA-TTAAAT
*
1423816 AAAATAAAATATTAATAT
1 AAAATAATATATTAA-AT
1423834 AA
1 AA
1423836 TACATTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 5 0.15
18 23 0.68
19 6 0.18
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATAATATATTAAAT
Found at i:1424452 original size:135 final size:135
Alignment explanation
Indices: 1424198--1424465 Score: 362
Period size: 135 Copynumber: 2.0 Consensus size: 135
1424188 GTATTAAATG
* *
1424198 TGATAAACTTGACTTGAAATGACCTGAGTTGAATTGACTTAAACTAAAAAATATCTCAAAATTTG
1 TGATAAACTTGACTTGAAATGACCTGAATTGAATTGACTTAAACTAAAAAATATCTCAAAATTTA
* *
1424263 AAACATAAATTAACTTAACTAACTCGATTTTAAATCAACTAAATTCACTTAATTAATATATCAAG
66 AAACATAAATTAACTTAACTAACTCGATATGAAATCAACTAAATTCACTTAATTAATATATCAAG
1424328 ACCTT
131 ACCTT
* * *
1424333 TGATAGACTTGACTTGAAATGA-CTCGAATTGAATTGATTTAAAGTAAAAAATATCTCAAAATTT
1 TGATAAACTTGACTTGAAATGACCT-GAATTGAATTGACTTAAACTAAAAAATATCTCAAAATTT
* * * ** *
1424397 AAAACATAAATTAA-TTCAACTAATTTGATATGAAATTAACTCGATTC-GTTGAATTAATATATC
65 AAAACATAAATTAACTT-AACTAACTCGATATGAAATCAACTAAATTCACTT-AATTAATATATC
*
1424460 GAGACC
128 AAGACC
1424466 AAGCTTAGAT
Statistics
Matches: 116, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
134 6 0.05
135 110 0.95
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (135 bp):
TGATAAACTTGACTTGAAATGACCTGAATTGAATTGACTTAAACTAAAAAATATCTCAAAATTTA
AAACATAAATTAACTTAACTAACTCGATATGAAATCAACTAAATTCACTTAATTAATATATCAAG
ACCTT
Found at i:1424970 original size:29 final size:28
Alignment explanation
Indices: 1424916--1424972 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
1424906 TAAAAGATAC
* *
1424916 TTTTTTTTAAATATTATATATAAATAAA
1 TTTTTTTTAAATATTAAAAATAAATAAA
1424944 TTTTTATTTAATATATTAAAAAT-AATAAA
1 TTTTT-TTTAA-ATATTAAAAATAAATAAA
1424973 AAATAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.20
29 11 0.44
30 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTTTTTTAAATATTAAAAATAAATAAA
Found at i:1425476 original size:55 final size:55
Alignment explanation
Indices: 1425349--1425478 Score: 192
Period size: 55 Copynumber: 2.4 Consensus size: 55
1425339 AATATCAAAT
1425349 ATAAATATATTTAATTTTTAATAAATTTTTTTATGAATTTAAAAGATTTATGAAA
1 ATAAATATATTTAATTTTTAATAAATTTTTTTATGAATTTAAAAGATTTATGAAA
* * *
1425404 ATAAATATGTTCAATTTTTTATAAATTTTTTTATGAATTTAAAAGATTTATGAAGA
1 ATAAATATATTTAATTTTTAATAAATTTTTTTATGAATTTAAAAGATTTATGAA-A
*
1425460 AT-TATAT-TTTATATTTTTA
1 ATAAATATATTTA-ATTTTTA
1425479 TTTATATGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
54 3 0.04
55 61 0.91
56 3 0.04
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.52
Consensus pattern (55 bp):
ATAAATATATTTAATTTTTAATAAATTTTTTTATGAATTTAAAAGATTTATGAAA
Found at i:1436617 original size:2 final size:2
Alignment explanation
Indices: 1436610--1436656 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1436600 TTTAATTGTT
1436610 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1436652 TA TA T
1 TA TA T
1436657 TCAGGCTGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1440784 original size:19 final size:20
Alignment explanation
Indices: 1440760--1440806 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
1440750 TAATTAAAAA
1440760 ATAATATAATAAAAATATAT
1 ATAATATAATAAAAATATAT
* *
1440780 A-AATAT-ATTAAAATTTAT
1 ATAATATAATAAAAATATAT
1440798 ATAATATAA
1 ATAATATAA
1440807 ATTATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 11 0.48
19 10 0.43
20 2 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAATATAATAAAAATATAT
Found at i:1440800 original size:33 final size:29
Alignment explanation
Indices: 1440763--1440830 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 29
1440753 TTAAAAAATA
1440763 ATATAATAAAAATATATAAATATATTAAAATTT
1 ATATAATAAAAAT-TAT-AA-AT-TTAAAATTT
* *
1440796 ATATAATATAAATTATTAATTTAAAATTT
1 ATATAATAAAAATTATAAATTTAAAATTT
1440825 ATATAA
1 ATATAA
1440831 AATATTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 15 0.45
30 2 0.06
31 1 0.03
32 3 0.09
33 12 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATAATAAAAATTATAAATTTAAAATTT
Found at i:1440826 original size:15 final size:16
Alignment explanation
Indices: 1440787--1440830 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
1440777 TATAAATATA
1440787 TTAAAATTTATATAAT
1 TTAAAATTTATATAAT
*
1440803 AT-AAA-TTAT-TAAT
1 TTAAAATTTATATAAT
1440816 TTAAAATTTATATAA
1 TTAAAATTTATATAA
1440831 AATATTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
13 5 0.22
14 7 0.30
15 7 0.30
16 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAAATTTATATAAT
Found at i:1441163 original size:12 final size:12
Alignment explanation
Indices: 1441143--1441187 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1441133 ATTGAGTGAA
*
1441143 GAAAGAGAGAAG
1 GAAAAAGAGAAG
1441155 GAAAAAGAGAA-
1 GAAAAAGAGAAG
*
1441166 GAAAAAGAAAAG
1 GAAAAAGAGAAG
*
1441178 GAAAGAGAGA
1 GAAAAAGAGA
1441188 GAAAGAAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (12 bp):
GAAAAAGAGAAG
Found at i:1441169 original size:11 final size:11
Alignment explanation
Indices: 1441140--1441191 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
1441130 TAGATTGAGT
*
1441140 GAAGAAAGAGA
1 GAAGAAAAAGA
1441151 GAAGGAAAAAGA
1 GAA-GAAAAAGA
1441163 GAAGAAAAAGA
1 GAAGAAAAAGA
* *
1441174 AAAG-GAAAGA
1 GAAGAAAAAGA
1441184 GAGAGAAA
1 GA-AGAAA
1441192 GAAAGGGTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
10 6 0.18
11 16 0.48
12 11 0.33
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (11 bp):
GAAGAAAAAGA
Found at i:1441169 original size:23 final size:23
Alignment explanation
Indices: 1441140--1441193 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
1441130 TAGATTGAGT
*
1441140 GAAGAAAGAGAGAAGGAAAAAGA
1 GAAGAAAGAGAAAAGGAAAAAGA
* *
1441163 GAAGAAAAAGAAAAGGAAAGAGA
1 GAAGAAAGAGAAAAGGAAAAAGA
1441186 G-AGAAAGA
1 GAAGAAAGA
1441194 AAGGGTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
GAAGAAAGAGAAAAGGAAAAAGA
Found at i:1441717 original size:21 final size:22
Alignment explanation
Indices: 1441663--1441722 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
1441653 TTTTTTTGAA
* * *
1441663 TTTTTATATATATATTTTAAAT
1 TTTTTATATTTTTAATTTAAAT
*
1441685 TTTTTATTTTTTTAATTTAAAT
1 TTTTTATATTTTTAATTTAAAT
1441707 TTTTT-TATTTTTAATT
1 TTTTTATATTTTTAATT
1441723 ATATTTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
21 10 0.30
22 23 0.70
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTATATTTTTAATTTAAAT
Found at i:1441722 original size:15 final size:15
Alignment explanation
Indices: 1441683--1441722 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1441673 TATATTTTAA
*
1441683 ATTTTTTATTTTTTT
1 ATTTTTAATTTTTTT
* *
1441698 AATTTAAATTTTTTT
1 ATTTTTAATTTTTTT
1441713 ATTTTTAATT
1 ATTTTTAATT
1441723 ATATTTAAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTTTTAATTTTTTT
Found at i:1441761 original size:53 final size:52
Alignment explanation
Indices: 1441647--1441757 Score: 131
Period size: 51 Copynumber: 2.1 Consensus size: 52
1441637 TTTAGGGTGT
* *
1441647 TTTAAATTTTTTTGAATTTTTATATATATATTTTAAATTTTTTATTTTTTTAA
1 TTTAAATTTTTTT-AATTTTTATATATATATTTTAAATTTTATATTTTTTAAA
1441700 TTTAAATTTTTTT-ATTTTTA-AT-TATA-TTTAAATTATTAAATATTTTTTAAAA
1 TTTAAATTTTTTTAATTTTTATATATATATTTTAAATT-TT--ATATTTTTT-AAA
1441752 TTTAAA
1 TTTAAA
1441758 ATTTAATAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
48 8 0.15
49 6 0.12
50 2 0.04
51 15 0.29
52 8 0.15
53 13 0.25
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (52 bp):
TTTAAATTTTTTTAATTTTTATATATATATTTTAAATTTTATATTTTTTAAA
Found at i:1445895 original size:11 final size:10
Alignment explanation
Indices: 1445854--1445930 Score: 61
Period size: 10 Copynumber: 7.4 Consensus size: 10
1445844 TAAATAATAA
1445854 TTTATGATATAT
1 TTTAT-ATAT-T
*
1445866 TTTA-ATATA
1 TTTATATATT
1445875 TTTATATATT
1 TTTATATATT
1445885 TTTAGTATATT
1 TTTA-TATATT
1445896 TTTAT-T-TT
1 TTTATATATT
*
1445904 ATATTATATTATA
1 -T-TTATA-TATT
1445917 TTTATATATT
1 TTTATATATT
1445927 TTTA
1 TTTA
1445931 AATTATATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
8 2 0.04
9 6 0.11
10 24 0.44
11 15 0.28
12 6 0.11
13 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (10 bp):
TTTATATATT
Found at i:1445937 original size:31 final size:31
Alignment explanation
Indices: 1445810--1445938 Score: 88
Period size: 31 Copynumber: 4.1 Consensus size: 31
1445800 ATATTAGGAT
* *
1445810 TATTTATTATA-TTATATATGTTTATAAATTT
1 TATTTATTATATTTATATATATTT-TAAATTA
** *
1445841 TAATAAATAATAATTTATGATATATTTT-AA-TA
1 T-ATTTATTAT-ATTTAT-ATATATTTTAAATTA
* **
1445873 TATTTA-TATATTTTTAGTATATTTTTATTTTA
1 TATTTATTATATTTATA-TATA-TTTTAAATTA
1445905 TATTATATTATATTTATATAT-TTTTAAATTA
1 TATT-TATTATATTTATATATATTTTAAATTA
1445936 TAT
1 TAT
1445939 AATCATAAAT
Statistics
Matches: 74, Mismatches: 14, Indels: 20
0.69 0.13 0.19
Matches are distributed among these distances:
28 1 0.01
29 9 0.12
30 6 0.08
31 15 0.20
32 14 0.19
33 8 0.11
34 14 0.19
35 7 0.09
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (31 bp):
TATTTATTATATTTATATATATTTTAAATTA
Found at i:1446802 original size:24 final size:25
Alignment explanation
Indices: 1446745--1446795 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
1446735 AAAAAAATTA
* *
1446745 AAATAATATTAAATTTTAATTTATTT
1 AAATTATATTTAATTTT-ATTTATTT
1446771 AAATTATATTTAATTTTA-TTATTT
1 AAATTATATTTAATTTTATTTATTT
1446795 A
1 A
1446796 TTTTATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 1 0.04
26 15 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
AAATTATATTTAATTTTATTTATTT
Found at i:1446807 original size:24 final size:25
Alignment explanation
Indices: 1446756--1446812 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
1446746 AATAATATTA
*
1446756 AATTTTAATTTATTTAAATTATATTT
1 AATTTT-ATTTATTTAAATTATAATT
**
1446782 AATTTTA-TTATTTATTTTATAATT
1 AATTTTATTTATTTAAATTATAATT
*
1446806 AAATTTA
1 AATTTTA
1446813 AATAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 20 0.74
25 1 0.04
26 6 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
AATTTTATTTATTTAAATTATAATT
Found at i:1447851 original size:3 final size:3
Alignment explanation
Indices: 1447843--1447914 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
1447833 ATTTATAAAC
1447843 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1447891 ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
1447915 CAGATATAAC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1448482 original size:2 final size:2
Alignment explanation
Indices: 1448475--1448504 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1448465 TCCCATACAG
1448475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1448505 TAAAATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1448996 original size:26 final size:26
Alignment explanation
Indices: 1448930--1448996 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 26
1448920 TTTTTATAAA
* ** *
1448930 TTTAAATTATTATTTAATAATAAAAT
1 TTTAAATTTTTAAATAATAAAAAAAT
**
1448956 TTT-AATTATAAAAATAATAAAAAAAT
1 TTTAAATT-TTTAAATAATAAAAAAAT
1448982 TTTAAATTTTTAAAT
1 TTTAAATTTTTAAAT
1448997 GGTACTTGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
25 4 0.13
26 23 0.74
27 4 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TTTAAATTTTTAAATAATAAAAAAAT
Found at i:1453477 original size:20 final size:20
Alignment explanation
Indices: 1453438--1453477 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1453428 CGAAGATTTC
***
1453438 AGTTTTGGGTTTTCTTTTGT
1 AGTTTTGGGTTTTAGATTGT
1453458 AGTTTTGGGTTTTAGATTGT
1 AGTTTTGGGTTTTAGATTGT
1453478 TAATGGGCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.03, G:0.28, T:0.60
Consensus pattern (20 bp):
AGTTTTGGGTTTTAGATTGT
Found at i:1453716 original size:19 final size:18
Alignment explanation
Indices: 1453682--1453717 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1453672 TGATTATAAT
*
1453682 ATAATAAAATATACGAAC
1 ATAATAAAACATACGAAC
1453700 ATAATATAAACATACGAA
1 ATAATA-AAACATACGAA
1453718 TTGTCCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.61, C:0.11, G:0.06, T:0.22
Consensus pattern (18 bp):
ATAATAAAACATACGAAC
Found at i:1454548 original size:24 final size:24
Alignment explanation
Indices: 1454521--1454567 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
1454511 AAAATAAACC
1454521 AAAAAATATATAAAAATCA-AATT
1 AAAAAATATATAAAAATCATAATT
*
1454544 AAAAAATATCTAAAAATCATAATT
1 AAAAAATATATAAAAATCATAATT
1454568 TTTGTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAAAATATATAAAAATCATAATT
Found at i:1454604 original size:27 final size:26
Alignment explanation
Indices: 1454574--1454653 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 26
1454564 AATTTTTGTA
1454574 AAATTAACCAAAAAATATCTAAAAATC
1 AAATTAA-CAAAAAATATCTAAAAATC
*
1454601 AAATT--GAAAAAAT-T-TAAAAATC
1 AAATTAACAAAAAATATCTAAAAATC
*
1454623 AAATCAA-ATTGAAAAATATCTAAAAATC
1 AAATTAACA---AAAAATATCTAAAAATC
1454651 AAA
1 AAA
1454654 ATTTCTGTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
22 12 0.27
23 2 0.05
24 7 0.16
26 6 0.14
27 6 0.14
28 11 0.25
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.24
Consensus pattern (26 bp):
AAATTAACAAAAAATATCTAAAAATC
Found at i:1454610 original size:22 final size:23
Alignment explanation
Indices: 1454584--1454653 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 23
1454574 AAATTAACCA
1454584 AAAAATATCTAAAAATCAAATTG
1 AAAAATATCTAAAAATCAAATTG
*
1454607 AAAAA-ATTTAAAAATCAAATCAAATTG
1 AAAAATATCT---AA--AAATCAAATTG
1454634 AAAAATATCTAAAAATCAAA
1 AAAAATATCTAAAAATCAAA
1454654 ATTTCTGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
22 3 0.08
23 13 0.33
25 4 0.10
27 16 0.41
28 3 0.08
ACGTcount: A:0.64, C:0.09, G:0.03, T:0.24
Consensus pattern (23 bp):
AAAAATATCTAAAAATCAAATTG
Found at i:1454639 original size:62 final size:62
Alignment explanation
Indices: 1454510--1454640 Score: 169
Period size: 62 Copynumber: 2.1 Consensus size: 62
1454500 GCTTTCCAAA
**
1454510 AAAAATAAACCAAAAAATATATAAAAATCAAATTAAAAAATATCTAAAAATCATAATTTTTG
1 AAAAATAAACCAAAAAATATATAAAAATCAAATTAAAAAATATCTAAAAATCATAATAATTG
* * *
1454572 TAAAATTAACCAAAAAATATCTAAAAATCAAATTGAAAAAAT-T-TAAAAATCA-AATCAAATTG
1 AAAAATAAACCAAAAAATATATAAAAATCAAATT-AAAAAATATCTAAAAATCATAAT--AATTG
1454634 AAAAATA
1 AAAAATA
1454641 TCTAAAAATC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
60 3 0.05
61 9 0.15
62 40 0.68
63 7 0.12
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.26
Consensus pattern (62 bp):
AAAAATAAACCAAAAAATATATAAAAATCAAATTAAAAAATATCTAAAAATCATAATAATTG
Found at i:1454641 original size:89 final size:89
Alignment explanation
Indices: 1454534--1454714 Score: 301
Period size: 89 Copynumber: 2.0 Consensus size: 89
1454524 AAATATATAA
* *
1454534 AAATCAAATTAAAAAATATCTAAAAATCATAATTTTTGTAAAATTAACCAAAAAATATCTAAAAA
1 AAATCAAATTAAAAAATATCTAAAAATCAAAATTTCTGTAAAATTAACCAAAAAA-ATCTAAAAA
* *
1454599 TCAAA-TTGAAAAAATTTAAAAATC
65 TCAAATTTAAAAAAATCTAAAAATC
*
1454623 AAATCAAATTGAAAAATATCTAAAAATCAAAATTTCTGTAAAATTAACCAAAAAAATCTAAAAAT
1 AAATCAAATTAAAAAATATCTAAAAATCAAAATTTCTGTAAAATTAACCAAAAAAATCTAAAAAT
1454688 CAAATTTAAAAAAATCTAAAAATC
66 CAAATTTAAAAAAATCTAAAAATC
1454712 AAA
1 AAA
1454715 ATTTTTGTTG
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
88 14 0.16
89 72 0.84
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (89 bp):
AAATCAAATTAAAAAATATCTAAAAATCAAAATTTCTGTAAAATTAACCAAAAAAATCTAAAAAT
CAAATTTAAAAAAATCTAAAAATC
Found at i:1454647 original size:28 final size:27
Alignment explanation
Indices: 1454596--1454653 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
1454586 AAATATCTAA
*
1454596 AAATCAAATTGAAAAAATTTAAAAATC
1 AAATCAAATTGAAAAAATCTAAAAATC
1454623 AAATCAAATTGAAAAATATCTAAAAATC
1 AAATCAAATTGAAAAA-ATCTAAAAATC
1454651 AAA
1 AAA
1454654 ATTTCTGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.64, C:0.09, G:0.03, T:0.24
Consensus pattern (27 bp):
AAATCAAATTGAAAAAATCTAAAAATC
Found at i:1454983 original size:10 final size:11
Alignment explanation
Indices: 1454925--1454988 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
1454915 TTAAAAAAAT
1454925 ATTTTATTAAA
1 ATTTTATTAAA
*
1454936 ATTTAATTATAA
1 ATTTTATTA-AA
* *
1454948 AATATATT-AA
1 ATTTTATTAAA
* * *
1454958 ATATTAATATA
1 ATTTTATTAAA
1454969 ATTTT-TTAAA
1 ATTTTATTAAA
1454979 ATTTTATTAA
1 ATTTTATTAA
1454989 TTATAAATAA
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
10 14 0.37
11 17 0.45
12 7 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTTATTAAA
Found at i:1456038 original size:14 final size:14
Alignment explanation
Indices: 1456019--1456047 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1456009 ATCTGTATCT
1456019 GGACTATGTTACTC
1 GGACTATGTTACTC
1456033 GGACTATGTTACTC
1 GGACTATGTTACTC
1456047 G
1 G
1456048 AACTCAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (14 bp):
GGACTATGTTACTC
Found at i:1456157 original size:181 final size:181
Alignment explanation
Indices: 1455853--1456191 Score: 599
Period size: 181 Copynumber: 1.9 Consensus size: 181
1455843 TGAATCCCGT
*
1455853 GACTATGTTACTCGGACTCAAATATGAGTATCAGATACAAGTATATATTTGACATAAATATATAT
1 GACTATGTTACTCGAACTCAAATATGAGTATCAGATACAAGTATATATTTGACATAAATATATAT
* * *
1455918 AATTTTTTAAAAGTTTTTTTTCCAAATATTTGGAGGATCCTTGGAGGATCATGTTCCCACTCCCA
66 AATATTTTAAAAGTTTTTTTTCCAAATATTTGGAGGATCCGTGGAGGATCATGTTCCCACACCCA
1455983 TGTCCCCATACCCAAG-TCCGGATATGATCTGTATCTGGACTATGTTACTCG
131 TGTCCCCATACCCAAGCT-CGGATATGATCTGTATCTGGACTATGTTACTCG
* *
1456034 GACTATGTTACTCGAACTCAAATATGAGTATCAGATACAGGTATGTATTTGACATAAATATATAT
1 GACTATGTTACTCGAACTCAAATATGAGTATCAGATACAAGTATATATTTGACATAAATATATAT
1456099 AATATTTTAAAAGTTTTTTTTCCAAATATTTGGAGGATCCGTGGAGGATCATGTTCCCACACCCA
66 AATATTTTAAAAGTTTTTTTTCCAAATATTTGGAGGATCCGTGGAGGATCATGTTCCCACACCCA
*
1456164 TGTCCCCATACCCACGCTCGGATATGAT
131 TGTCCCCATACCCAAGCTCGGATATGAT
1456192 TTGGACATTG
Statistics
Matches: 150, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
181 149 0.99
182 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (181 bp):
GACTATGTTACTCGAACTCAAATATGAGTATCAGATACAAGTATATATTTGACATAAATATATAT
AATATTTTAAAAGTTTTTTTTCCAAATATTTGGAGGATCCGTGGAGGATCATGTTCCCACACCCA
TGTCCCCATACCCAAGCTCGGATATGATCTGTATCTGGACTATGTTACTCG
Found at i:1456841 original size:220 final size:219
Alignment explanation
Indices: 1456416--1457008 Score: 791
Period size: 220 Copynumber: 2.7 Consensus size: 219
1456406 TAATGTGAAC
*
1456416 ATTTGAAAATATGTAGAGCCCAGATGGAGCACATGCAAGCTTCAAAAGACTTAACGCATCTGCAA
1 ATTTGAAAATATGTAGAGCCCAAATGGAGCACATGCAAGCTTCAAAA-ACTTAACGCATCTGCAA
* * *
1456481 CGATGGACACAT-AGGTTTTCCACACTAGTAACTGTATCAACTATCGAACATTAAAGTAGAAACC
65 CGATGGACACATCA-GTTTTCCAGACTAGTAACTGTATCAACCATCGAACATTAAAGTAGATACC
* * * *
1456545 TGACTTATGTCTGGTGATATGATATTATTTCAGCTAAACATCAAGACTACAATGTTTTCAAGACT
129 TGACTTATGTCTGGTGATATGACATCATTTCAACTAAACATCAAGACTACAATGTTTCCAAGACT
** * *
1456610 CGTAGAATTCCTGTTACAAAG-TGCAA
194 CAAAGAATTCCTATCAC-AAGTTGCAA
** *
1456636 ATTTGAAACCATGTAGGGCCCAAATGGAGCACATGCAAGCTTCAAAAACTTAACTGCATCTGCAA
1 ATTTGAAAATATGTAGAGCCCAAATGGAGCACATGCAAGCTTCAAAAACTTAAC-GCATCTGCAA
* * * *
1456701 CGATGGACACACTCAGTTTTCCAGACTTGTAACTGTATCAACCATTGAAAATTAAAGCAGATACC
65 CGATGGACACA-TCAGTTTTCCAGACTAGTAACTGTATCAACCATCGAACATTAAAGTAGATACC
* * * *
1456766 TGACTTATGTCTGGAGATATGACATCATTTCAACTAAATATCAAGGGC-ACAATGTTTCCGAGA-
129 TGACTTATGTCTGGTGATATGACATCATTTCAACTAAACATCAA-GACTACAATGTTTCCAAGAC
1456829 TCAAAGAATTCCTATCACAAGTTGCAA
193 TCAAAGAATTCCTATCACAAGTTGCAA
* * ** *
1456856 ATATGAAAATATGTAGTGCCCAAATGGAGCACATGCAAGCTTTGAAAACTTAGCGCATCTGCAAC
1 ATTTGAAAATATGTAGAGCCCAAATGGAGCACATGCAAGCTTCAAAAACTTAACGCATCTGCAAC
* * * *
1456921 GATGGACACGTTCAATTTTCCAGACTAGTAACTGTATCAACCATCG-ACGTTGAAGTAGATACCT
66 GATGGACAC-ATCAGTTTTCCAGACTAGTAACTGTATCAACCATCGAACATTAAAGTAGATACCT
*
1456985 GACTTATGTCTGGTGATATAACAT
130 GACTTATGTCTGGTGATATGACAT
1457009 TACTCTTAAC
Statistics
Matches: 327, Mismatches: 40, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
218 36 0.11
219 62 0.19
220 130 0.40
221 96 0.29
222 3 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (219 bp):
ATTTGAAAATATGTAGAGCCCAAATGGAGCACATGCAAGCTTCAAAAACTTAACGCATCTGCAAC
GATGGACACATCAGTTTTCCAGACTAGTAACTGTATCAACCATCGAACATTAAAGTAGATACCTG
ACTTATGTCTGGTGATATGACATCATTTCAACTAAACATCAAGACTACAATGTTTCCAAGACTCA
AAGAATTCCTATCACAAGTTGCAA
Found at i:1459371 original size:22 final size:22
Alignment explanation
Indices: 1459343--1459387 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1459333 TTAATCTAAT
1459343 GATTAGAAGAGTATTAGAGTTG
1 GATTAGAAGAGTATTAGAGTTG
*
1459365 GATTAGAAGAGTATTAGATTTG
1 GATTAGAAGAGTATTAGAGTTG
1459387 G
1 G
1459388 CATGTGAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (22 bp):
GATTAGAAGAGTATTAGAGTTG
Found at i:1459562 original size:38 final size:38
Alignment explanation
Indices: 1459520--1459593 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
1459510 ACTTATGCTA
*
1459520 ATCCATAAGCAAATCTTATTAAAATATACATTAAAATG
1 ATCCATAAGCAAATCTTATTAAAATATACAATAAAATG
* * *
1459558 ATCCATGAGCAAATCTTATTGAAATGTACAATAAAA
1 ATCCATAAGCAAATCTTATTAAAATATACAATAAAA
1459594 CATTTATGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (38 bp):
ATCCATAAGCAAATCTTATTAAAATATACAATAAAATG
Found at i:1460150 original size:27 final size:29
Alignment explanation
Indices: 1460096--1460150 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
1460086 AGATATCTTC
**
1460096 AAATTTATATAATATAAATTAACGTATCA
1 AAATTTATATAATATAAATTAAAATATCA
*
1460125 AAATTTATATAA-A-ATATTAAAATATC
1 AAATTTATATAATATAAATTAAAATATC
1460151 TTAAATACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 10 0.43
28 1 0.04
29 12 0.52
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (29 bp):
AAATTTATATAATATAAATTAAAATATCA
Found at i:1465188 original size:2 final size:2
Alignment explanation
Indices: 1465181--1465221 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1465171 CCAAGCGCTG
* *
1465181 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1465222 TGTCTTGTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1466061 original size:14 final size:13
Alignment explanation
Indices: 1466042--1466107 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 13
1466032 TTATGTTATG
1466042 TTATATTTAAATTA
1 TTATATTT-AATTA
1466056 TTATATTT-ATT-
1 TTATATTTAATTA
*
1466067 TTATAATTATATTA
1 TTATATTTA-ATTA
1466081 TTATA--TAATATA
1 TTATATTTAAT-TA
*
1466093 TTATA-TAAATTA
1 TTATATTTAATTA
1466105 TTA
1 TTA
1466108 ATTATTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
11 9 0.20
12 17 0.38
13 6 0.13
14 13 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTATATTTAATTA
Found at i:1466065 original size:25 final size:25
Alignment explanation
Indices: 1466037--1466125 Score: 83
Period size: 25 Copynumber: 3.5 Consensus size: 25
1466027 TTTTTTTATG
*
1466037 TTATGTTATATTTAAATTATTATAT
1 TTATATTATATTTAAATTATTATAT
* * *
1466062 TTATTTTATAATTATATTATTATAT
1 TTATATTATATTTAAATTATTATAT
*
1466087 AATATATTATA--TAAATTATTAATTAT
1 -TTATATTATATTTAAATTATT-A-TAT
*
1466113 TGATATTATATTT
1 TTATATTATATTT
1466126 TTTATGATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
24 8 0.16
25 31 0.61
26 11 0.22
27 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
TTATATTATATTTAAATTATTATAT
Found at i:1467717 original size:12 final size:12
Alignment explanation
Indices: 1467692--1467748 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
1467682 TTTAAACAAG
*
1467692 ATTTA-TTTTGA
1 ATTTATTTTTAA
1467703 ATTTATTTTTAA
1 ATTTATTTTTAA
* *
1467715 ATTTCTTCTTAA
1 ATTTATTTTTAA
*
1467727 TTTTATTTTATAA
1 ATTTATTTT-TAA
*
1467740 ATTAATTTT
1 ATTTATTTT
1467749 ATTTTAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
11 5 0.14
12 21 0.58
13 10 0.28
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (12 bp):
ATTTATTTTTAA
Found at i:1467785 original size:20 final size:19
Alignment explanation
Indices: 1467728--1467786 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
1467718 TCTTCTTAAT
* *
1467728 TTTATTTTATAAATTAAT-
1 TTTATTTTAAAAATAAATA
* *
1467746 TTTATTTTAACATTATAATA
1 TTTATTTTAAAAATA-AATA
1467766 TTTATTTTAAAAAATAAATA
1 TTTATTTT-AAAAATAAATA
1467786 T
1 T
1467787 AATATTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
18 11 0.34
19 3 0.09
20 13 0.41
21 5 0.16
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTATTTTAAAAATAAATA
Found at i:1468324 original size:13 final size:13
Alignment explanation
Indices: 1468298--1468334 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1468288 AGGATATGTT
1468298 ATTAATTT-TATA
1 ATTAATTTATATA
1468310 ATTAATTTATATA
1 ATTAATTTATATA
*
1468323 ATTAATTAATAT
1 ATTAATTTATAT
1468335 TTAATAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTAATTTATATA
Found at i:1468610 original size:144 final size:148
Alignment explanation
Indices: 1468427--1468703 Score: 490
Period size: 148 Copynumber: 1.9 Consensus size: 148
1468417 AAAATTTTCA
1468427 AAAATTGAAACAATAAGGCAATGACAAAAGAAAAAAAAGTTGAAACATTACTT-G-GTGTGTATA
1 AAAATTGAAACAATAAGGCAATGACAAAAGAAAAAAAAGTTGAAACATTACTTGGTGTGTGTATA
*
1468490 TA-A-ATATATATAATATTAATTTACAAGATTTAATTTTTCCATTTTGTCTATATTAAGTGTACT
66 TATATATATATATAATATTAATTTACAAGATTTAATTTTTCCATTTTGTCTACATTAAGTGTACT
1468553 TTGCACAAAAGAATTCCG
131 TTGCACAAAAGAATTCCG
* *
1468571 AAAATTGAAACAATAAGGCAATGACAAAAGAAAATAAAGTTGAAACATTCCTTGGTGTGTGTATA
1 AAAATTGAAACAATAAGGCAATGACAAAAGAAAAAAAAGTTGAAACATTACTTGGTGTGTGTATA
*
1468636 TATATATATATATAATATTAATTTACAAGATTTAATTTTTCCATTTTGTCTCCATTAAGTGTACT
66 TATATATATATATAATATTAATTTACAAGATTTAATTTTTCCATTTTGTCTACATTAAGTGTACT
1468701 TTG
131 TTG
1468704 GACAGGCAAA
Statistics
Matches: 125, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
144 51 0.41
145 1 0.01
146 11 0.09
147 1 0.01
148 61 0.49
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (148 bp):
AAAATTGAAACAATAAGGCAATGACAAAAGAAAAAAAAGTTGAAACATTACTTGGTGTGTGTATA
TATATATATATATAATATTAATTTACAAGATTTAATTTTTCCATTTTGTCTACATTAAGTGTACT
TTGCACAAAAGAATTCCG
Found at i:1472333 original size:15 final size:15
Alignment explanation
Indices: 1472313--1472342 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1472303 TTTAACCATT
*
1472313 TTTTTGGTTTTTTTA
1 TTTTTGATTTTTTTA
1472328 TTTTTGATTTTTTTA
1 TTTTTGATTTTTTTA
1472343 GAGATTTTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (15 bp):
TTTTTGATTTTTTTA
Found at i:1472558 original size:32 final size:30
Alignment explanation
Indices: 1472504--1472581 Score: 77
Period size: 32 Copynumber: 2.5 Consensus size: 30
1472494 TCAAATTATT
* * **
1472504 AATTAATAATAAAATAAT-TTATTTAAATTT
1 AATTAAAAATAATA-AATATTATTTAAATAA
*
1472534 AATTATAAAATATATAAATATTATTTTAATAA
1 AATTA-AAAATA-ATAAATATTATTTAAATAA
1472566 AATTAAAAATAATAAA
1 AATTAAAAATAATAAA
1472582 ATAAATTTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 10 0.25
31 14 0.35
32 16 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
AATTAAAAATAATAAATATTATTTAAATAA
Found at i:1473395 original size:38 final size:37
Alignment explanation
Indices: 1473344--1473419 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 37
1473334 TTAAATCATG
*
1473344 AATATATAAATATTTTAAAATTT-T-TATATATAATATA
1 AATATATAAATA--TTAAAATTTATATAAATATAATATA
*
1473381 AATATTTAACATATTAAAATTTATATAAATATAATATA
1 AATATATAA-ATATTAAAATTTATATAAATATAATATA
1473419 A
1 A
1473420 TTTAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 9 0.26
37 9 0.26
38 16 0.47
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (37 bp):
AATATATAAATATTAAAATTTATATAAATATAATATA
Done.