Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 4 of 410
Found at i:1029260 original size:87 final size:87
Alignment explanation
Indices: 1029157--1029368 Score: 345
Period size: 87 Copynumber: 2.4 Consensus size: 87
1029147 TAATTTTTAC
* *
1029157 TTTTCCAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCA
*
1029222 ATTTCTACTTTCCAATTTA-TGT
66 ATTTCTACTTTCCAA-TTACTAT
* *
1029244 TTTTCAAAAATCAACTCATATTGCGAGACGTGAGCTGAGCCTCGGGGCACGCTGAGGTATTTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCA
1029309 ATTTCTACTTTCCAATTACTAT
66 ATTTCTACTTTCCAATTACTAT
* *
1029331 TTTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGA
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1029369 ACCTTTTAAT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
86 3 0.03
87 112 0.97
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (87 bp):
TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCA
ATTTCTACTTTCCAATTACTAT
Found at i:1030145 original size:22 final size:22
Alignment explanation
Indices: 1030120--1030175 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
1030110 AACCATGAAG
1030120 CAACCCCATACCCCCACTACAA
1 CAACCCCATACCCCCACTACAA
*
1030142 CAACCCCATACCCCTACTACAA
1 CAACCCCATACCCCCACTACAA
**
1030164 CAGTCCCATACC
1 CAACCCCATACC
1030176 TTCACAGTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.34, C:0.52, G:0.02, T:0.12
Consensus pattern (22 bp):
CAACCCCATACCCCCACTACAA
Found at i:1030757 original size:20 final size:21
Alignment explanation
Indices: 1030712--1030757 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
1030702 GTGGCCGGAG
1030712 CTCT-CCC-CTCCCTTCTCTT
1 CTCTCCCCGCTCCCTTCTCTT
* *
1030731 CTTTCCCCGCTCCC-TCTTTT
1 CTCTCCCCGCTCCCTTCTCTT
1030751 CTCTCCC
1 CTCTCCC
1030758 TCATCTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.14
20 14 0.64
21 5 0.23
ACGTcount: A:0.00, C:0.57, G:0.02, T:0.41
Consensus pattern (21 bp):
CTCTCCCCGCTCCCTTCTCTT
Found at i:1031245 original size:3 final size:3
Alignment explanation
Indices: 1031232--1031275 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
1031222 TTATTTCCAA
*
1031232 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
1031276 GTATACATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1031340 original size:26 final size:27
Alignment explanation
Indices: 1031307--1031371 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
1031297 GTGAATATTG
*
1031307 TATA-TATTTATATATAATATTATTTT
1 TATATTATTTATATATAATATTATTAT
*
1031333 TA-ATTATTGTAT-TTTAATATTATTAT
1 TATATTATT-TATATATAATATTATTAT
*
1031359 TATATTATATATA
1 TATATTATTTATA
1031372 CTTCTTCGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 1 0.03
26 23 0.72
27 8 0.25
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
TATATTATTTATATATAATATTATTAT
Found at i:1031522 original size:21 final size:22
Alignment explanation
Indices: 1031477--1031537 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
1031467 TTTTTTACTA
*
1031477 TTATATTT-ATTATTA-TATTAT
1 TTAT-TTTCATTATTATTATTAG
1031498 TTATTTTCATTATTATTATT-G
1 TTATTTTCATTATTATTATTAG
*
1031519 TTATTTTCATCATTATTAT
1 TTATTTTCATTATTATTAT
1031538 ACATATATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.08
21 29 0.81
22 4 0.11
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (22 bp):
TTATTTTCATTATTATTATTAG
Found at i:1044757 original size:74 final size:70
Alignment explanation
Indices: 1044562--1044813 Score: 219
Period size: 74 Copynumber: 3.6 Consensus size: 70
1044552 AATTCATGTT
* * ** * *
1044562 TTCAAACATTAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGTCACACGCTGAGGT-A-TT--
1 TTCAAAAATCAACTCATATTGCGAGAGGTGAGTCGAGCCTCAAG--ACACGCTGAGGTAATTTCA
1044623 -TTTA-G
64 ATTTATG
* ** * * * * * *
1044628 TTTATAAAATTGACACATATTGCGAGAGGTGAGTCAAGCCTCAGGTCACGCTGAGGTATTTTTAA
1 TTCA-AAAATCAACTCATATTGCGAGAGGTGAGTCGAGCCTCAAGACACGCTGAGGTAATTTCAA
*
1044693 TTCCTGTTG
65 TT--T-ATG
* * *
1044702 TTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
1 -TTCAAAAATCAACTCATATTGCGAGAGGTGAGTCGAGCCTCAAGACACGCTGAGGTAATTTCAA
1044767 TTTATG
65 TTTATG
*
1044773 TTCCAAAATCAACTCATATTGCGAGAGGTGAGTCGAGCCTC
1 TTCAAAAATCAACTCATATTGCGAGAGGTGAGTCGAGCCTC
1044814 GGGGTACGCC
Statistics
Matches: 148, Mismatches: 27, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
65 11 0.07
66 3 0.02
67 35 0.24
70 40 0.27
71 2 0.01
72 2 0.01
74 52 0.35
75 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (70 bp):
TTCAAAAATCAACTCATATTGCGAGAGGTGAGTCGAGCCTCAAGACACGCTGAGGTAATTTCAAT
TTATG
Found at i:1044811 original size:70 final size:73
Alignment explanation
Indices: 1044643--1044813 Score: 222
Period size: 74 Copynumber: 2.4 Consensus size: 73
1044633 AAAATTGACA
* * * * * *
1044643 CATATTGCGAGAGGTGAGTCAAGCCTCAGGTCACGCTGAGGTATTTTTAATTCCTGTTGTTTCAA
1 CATATTGCGAGAGGTGAGTCGAGCCTCAAGACACGCTGAGGTAATTTCAATT-CTGATGTTTCAA
*
1044708 AAATCAGCT
65 AAATCAACT
* * *
1044717 CATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATT-T-ATG-TTCCAA
1 CATATTGCGAGAGGTGAGTCGAGCCTCAAGACACGCTGAGGTAATTTCAATTCTGATGTTTCAAA
1044779 AATCAACT
66 AATCAACT
1044787 CATATTGCGAGAGGTGAGTCGAGCCTC
1 CATATTGCGAGAGGTGAGTCGAGCCTC
1044814 GGGGTACGCC
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
70 38 0.44
71 2 0.02
72 1 0.01
74 45 0.52
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (73 bp):
CATATTGCGAGAGGTGAGTCGAGCCTCAAGACACGCTGAGGTAATTTCAATTCTGATGTTTCAAA
AATCAACT
Found at i:1044828 original size:70 final size:72
Alignment explanation
Indices: 1044643--1044841 Score: 224
Period size: 70 Copynumber: 2.7 Consensus size: 72
1044633 AAAATTGACA
* * *
1044643 CATATTGCGAGAGGTGAGTCAAGCCTCAGGTCACGCTGAGGTATTTTTAATTCCTGTTGTTTCAA
1 CATATTGCGAGAGGTGAGTCGAGCCTCAGGT-ACGCTGAGGTATTTTCAATT-CTGATGTTTCAA
*
1044708 AAATCAGCT
64 AAATCAACT
* ** * * *
1044717 CATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATT-T-ATG-TTCCAA
1 CATATTGCGAGAGGTGAGTCGAGCCTC-AGGTACGCTGAGGTATTTTCAATTCTGATGTTTCAAA
1044779 AATCAACT
65 AATCAACT
* *
1044787 CATATTGCGAGAGGTGAGTCGAGCCTCGGGGTACGCCGAGGTATTTTCAAATTCT
1 CATATTGCGAGAGGTGAGTCGAGCCTC-AGGTACGCTGAGGTATTTTC-AATTCT
1044842 CTTGTTCAAA
Statistics
Matches: 104, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
70 52 0.50
71 6 0.06
72 2 0.02
74 42 0.40
75 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (72 bp):
CATATTGCGAGAGGTGAGTCGAGCCTCAGGTACGCTGAGGTATTTTCAATTCTGATGTTTCAAAA
ATCAACT
Found at i:1044828 original size:144 final size:137
Alignment explanation
Indices: 1044532--1044833 Score: 336
Period size: 144 Copynumber: 2.1 Consensus size: 137
1044522 GATATGTTTT
* * * *
1044532 GGGTACTCTGAGGTATCTTTAATTCATGTTTTCAAACATTAACTCATATTGCGAGAAATGAGTTG
1 GGGTACGCTGAGGTATTTTTAATTCATGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTG
* * * * **
1044597 AGCCTCAGGTCACACGCTGAGGTATTTTTAGTTTATAAAATTGACACATATTGCGAGAGGTGAGT
66 AGCCTCAAG-CACACGCTGAGGTAATTTCAATTTATAAAATCAACACATATTGCGAGAGGTGAGT
1044662 CAAGCCTC
130 CAAGCCTC
* * * **
1044670 AGGTCACGCTGAGGTATTTTTAATTCCTGTTGTTTCAAAAATCAGCTCATATTGCGAGAGGTGAG
1 GGGT-ACGCTGAGGTATTTTTAATTCATG-T-TTTCAAAAATCAACTCATATTGCGAGAAATGAG
* *
1044735 TTGAGCCTCAAG-ACACGTTGAGGTAATTTCAATTTATGTTCCAAAATCAACTCATATTGCGAGA
63 TTGAGCCTCAAGCACACGCTGAGGTAATTTCAATTTA---T--AAAATCAACACATATTGCGAGA
*
1044799 GGTGAGTCGAGCCTC
123 GGTGAGTCAAGCCTC
*
1044814 GGGGTACGCCGAGGTATTTT
1 -GGGTACGCTGAGGTATTTT
1044834 CAAATTCTCT
Statistics
Matches: 135, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
138 3 0.02
139 41 0.30
140 1 0.01
141 39 0.29
142 1 0.01
144 47 0.35
145 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (137 bp):
GGGTACGCTGAGGTATTTTTAATTCATGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTG
AGCCTCAAGCACACGCTGAGGTAATTTCAATTTATAAAATCAACACATATTGCGAGAGGTGAGTC
AAGCCTC
Found at i:1045013 original size:87 final size:87
Alignment explanation
Indices: 1044871--1045076 Score: 342
Period size: 87 Copynumber: 2.4 Consensus size: 87
1044861 TAATTTTTAC
* * * *
1044871 TTTTCCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACTCTGAGGTATTTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGACACGCTGAGGTATTTTCA
*
1044936 ATTTCTACTTTCCAATTTA-TGT
66 ATTTCTACTTTCCAA-TTACTAT
1044958 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGACACGCTGAGGTATTTTCA
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGACACGCTGAGGTATTTTCA
1045023 ATTTCTACTTTCCAATTACTAT
66 ATTTCTACTTTCCAATTACTAT
*
1045045 TTTTCAAGAATCAACTCATATTGCGAGAGGTG
1 TTTTCAAAAATCAACTCATATTGCGAGAGGTG
1045077 GGTTGAACCT
Statistics
Matches: 112, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
86 3 0.03
87 109 0.97
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (87 bp):
TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGACACGCTGAGGTATTTTCA
ATTTCTACTTTCCAATTACTAT
Found at i:1045867 original size:22 final size:22
Alignment explanation
Indices: 1045842--1045896 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1045832 GAAGCAACCT
1045842 CATACCCCCACTACAACAGCCC
1 CATACCCCCACTACAACAGCCC
*
1045864 CATACCCCCACTACAACAGTCC
1 CATACCCCCACTACAACAGCCC
*
1045886 CATACCTCCAC
1 CATACCCCCAC
1045897 AGTCCTCGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.31, C:0.53, G:0.04, T:0.13
Consensus pattern (22 bp):
CATACCCCCACTACAACAGCCC
Found at i:1046898 original size:26 final size:27
Alignment explanation
Indices: 1046865--1046929 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
1046855 GTGAATATTG
*
1046865 TATA-TATTTATATATAATATTATTTT
1 TATATTATTTATATATAATATTATTAT
*
1046891 TA-ATTATTGTAT-TTTAATATTATTAT
1 TATATTATT-TATATATAATATTATTAT
*
1046917 TATATTATATATA
1 TATATTATTTATA
1046930 CTTCTTCGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 1 0.03
26 23 0.72
27 8 0.25
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
TATATTATTTATATATAATATTATTAT
Found at i:1047069 original size:21 final size:21
Alignment explanation
Indices: 1047056--1047095 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1047046 ATTATATTAT
1047056 TTATTTTCACTATTATTATTG
1 TTATTTTCACTATTATTATTG
1047077 TTATTTTCA-TCATTATTAT
1 TTATTTTCACT-ATTATTAT
1047096 ACATATATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.25, C:0.10, G:0.03, T:0.62
Consensus pattern (21 bp):
TTATTTTCACTATTATTATTG
Found at i:1047093 original size:24 final size:24
Alignment explanation
Indices: 1047043--1047095 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 24
1047033 TATTATATTT
*
1047043 ATTATTA-TATTATTTATTTTCAC
1 ATTATTATTATTAGTTATTTTCAC
1047066 --TATTATTATT-GTTATTTTCATC
1 ATTATTATTATTAGTTATTTTCA-C
1047088 ATTATTAT
1 ATTATTAT
1047096 ACATATATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 14 0.56
22 5 0.20
24 6 0.24
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (24 bp):
ATTATTATTATTAGTTATTTTCAC
Found at i:1058831 original size:16 final size:17
Alignment explanation
Indices: 1058810--1058849 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1058800 TTAAATTAAT
1058810 TTAAATTATTTT-TCAA
1 TTAAATTATTTTCTCAA
*
1058826 TTAAATAATTTTCTCAA
1 TTAAATTATTTTCTCAA
*
1058843 TTCAATT
1 TTAAATT
1058850 CTAATCCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAATTATTTTCTCAA
Found at i:1060309 original size:15 final size:15
Alignment explanation
Indices: 1060291--1060331 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1060281 AACCTAACCC
1060291 AAAAAAAAACAAAGA
1 AAAAAAAAACAAAGA
1060306 AAAAAAAGAA-AAAGA
1 AAAAAAA-AACAAAGA
1060321 AAAAGAAAAAC
1 AAAA-AAAAAC
1060332 CTACCCCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAACAAAGA
Found at i:1060347 original size:16 final size:18
Alignment explanation
Indices: 1060326--1060365 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
1060316 AAAGAAAAAG
1060326 AAAAACCT-A-CCCCAAA
1 AAAAACCTAACCCCCAAA
1060342 AAAAACCTAACCCCCCAAA
1 AAAAACCTAA-CCCCCAAA
1060361 AAAAA
1 AAAAA
1060366 AGAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 1 0.05
19 12 0.57
ACGTcount: A:0.60, C:0.35, G:0.00, T:0.05
Consensus pattern (18 bp):
AAAAACCTAACCCCCAAA
Found at i:1060943 original size:2 final size:2
Alignment explanation
Indices: 1060938--1060968 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1060928 TAAATACTAT
*
1060938 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1060969 TTTAAATACC
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:1062974 original size:12 final size:12
Alignment explanation
Indices: 1062954--1062989 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1062944 ATTCATTTAA
1062954 CATTCATGCATT
1 CATTCATGCATT
*
1062966 CATTTATGCATT
1 CATTCATGCATT
*
1062978 CATTCATTCATT
1 CATTCATGCATT
1062990 GCATATTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:1070020 original size:71 final size:69
Alignment explanation
Indices: 1069826--1070086 Score: 314
Period size: 70 Copynumber: 3.7 Consensus size: 69
1069816 GAGTTAAGCC
* *
1069826 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTG-TTTT--AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
1069891 GAGGTAT
63 GAGGTAT
* * ** * *
1069898 TTTCAATTTTTGTGTTTTAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTG
1 TTTTAATTTTTGT-TTTAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCGGGGCACGCTG
1069962 AGGTAT
64 AGGTAT
1069968 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG
1 TTTTAATTTTTGTTTT--AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG
1070033 AGGTA-
64 AGGTAT
* ** * *
1070038 TTTT--TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 TTTTAATTTTTGTTTTAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
1070087 TTTAATTTTT
Statistics
Matches: 165, Mismatches: 19, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
66 31 0.19
68 9 0.05
69 4 0.02
70 60 0.36
71 45 0.27
72 16 0.10
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (69 bp):
TTTTAATTTTTGTTTTAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAG
GTAT
Found at i:1070136 original size:190 final size:197
Alignment explanation
Indices: 1069916--1070428 Score: 587
Period size: 190 Copynumber: 2.6 Consensus size: 197
1069906 TTTGTGTTTT
* * * *
1069916 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTTGT
* *
1069981 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTT-TTT
66 TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTATTT
**
1070045 ATGTTTT-AA-A-TT-G-ACTCATATTGCGAGAGGT-GAGTT-AAGCCTTTTAATTT-TTGTTTT
131 ATGTTTTCAATAGTTAGAACTCATATTGCGAGAGGTAG-GTTGAA-CCTTTTAATTTCTACTTTT
1070102 TCAA
194 TCAA
* *
1070106 AATCAACTCATATTGCTAGAGGTGAGTTGAGCCTC-GGGCACGCTGAGGTATTTTCAATTTTTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTTGT
* ** *
1070170 GTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAA
66 -TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTT--A
*
1070235 TTTCTGTTTTCAATTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTAGGTTGAACCTTTT
128 TTTATGTTTTCAA--TA----GTT--AG----AACTCATATTGCGAGAGGTAGGTTGAACCTTTT
1070300 AATTTCTACTTTTTCAA
181 AATTTCTACTTTTTCAA
* *
1070317 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTTGT
* * * *
1070382 TGTCAAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGG
66 TTTC---AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
1070429 TCATACGTCG
Statistics
Matches: 269, Mismatches: 26, Indels: 32
0.82 0.08 0.10
Matches are distributed among these distances:
189 25 0.09
190 88 0.33
193 9 0.03
194 2 0.01
197 1 0.00
202 2 0.01
205 1 0.00
210 32 0.12
211 48 0.18
212 26 0.10
214 35 0.13
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35
Consensus pattern (197 bp):
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTTGT
TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTATTT
ATGTTTTCAATAGTTAGAACTCATATTGCGAGAGGTAGGTTGAACCTTTTAATTTCTACTTTTTC
AA
Found at i:1070206 original size:71 final size:71
Alignment explanation
Indices: 1070086--1070250 Score: 244
Period size: 71 Copynumber: 2.3 Consensus size: 71
1070076 GAGTTAAGCC
** *
1070086 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTC-GGGCACGC
1 TTTTCAATTTTTGTTTTT-AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
1070149 TGAGGTA
65 TGAGGTA
*
1070156 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC
1 TTTTCAATTTTTGT-TTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
1070221 TGAGGTA
65 TGAGGTA
* *
1070228 TTTTCAATTTCTGTTTTCAATTT
1 TTTTCAATTTTTGTTTTTAATTT
1070251 ACGTTGTTCA
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
70 4 0.05
71 51 0.59
72 31 0.36
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (71 bp):
TTTTCAATTTTTGTTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCT
GAGGTA
Found at i:1070587 original size:165 final size:166
Alignment explanation
Indices: 1070315--1070790 Score: 719
Period size: 165 Copynumber: 2.9 Consensus size: 166
1070305 CTACTTTTTC
1070315 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
* * *
1070380 GTTGTCAAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGGTCATACGTCGAGGTAT
66 GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGTCGAGGTAT
*
1070445 TTTCAATTTCCGTTTTTCAATTTTTGCCTTTC-AAA
131 TTTCAATTTCCGTTTTTCAATTTCTGCCTTTCAAAA
*
1070480 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACGCGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
* * *
1070545 GTTGTCAAAAAAGTCAACTCGTATTACGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTAT
66 GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGTCGAGGTAT
*
1070610 TTTCAATTTCCATTTTTCAATTTCTGCCTTTCAAAAAAA
131 TTTCAATTTCCGTTTTTCAATTTCTGCCTTTC---AAAA
* *
1070649 AAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
* * * ** * *
1070714 GTTTTC--AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG--ACACGTTGAGGTAT
66 GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGTCGAGGTAT
*
1070775 TTTCAATTTCTGTTTT
131 TTTCAATTTCCGTTTT
1070791 CAAAAAATCA
Statistics
Matches: 284, Mismatches: 23, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
165 180 0.63
167 34 0.12
169 70 0.25
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (166 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGTCGAGGTAT
TTTCAATTTCCGTTTTTCAATTTCTGCCTTTCAAAA
Found at i:1070888 original size:77 final size:75
Alignment explanation
Indices: 1070646--1071153 Score: 377
Period size: 72 Copynumber: 6.5 Consensus size: 75
1070636 CCTTTCAAAA
* * ** *
1070646 AAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGACA-CGCTGAGGTAATTTCAAT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCAGCGCTGAGGTATTTTCAAT
*
1070710 TTCTGTTTTC
66 TTCTATTTTC
* ** ** * *
1070720 --AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG-ACA-CGTTGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCAGCGCTGAGGTATTTTCAA
*
1070781 TTTCTGTTTTC
65 TTTCTATTTTC
* * *
1070792 -AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCA-GCGCTGAGGTATTTTCAA
1070856 TTTCTATCTTTC
65 TTTCTAT-TTTC
* * * *
1070868 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTCAGATCACACACTGAGGTATTTTTT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT-GGCTCA-GCGCTGAGGTA--TTTT
*
1070932 CAATTTATATTTTTC
62 CAATTTCTA-TTTTC
* * * * *
1070947 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTTACA-TG-TCGAGGTATTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCT-CAGCGCT-GAGGTATTTTC
** *
1071010 AAAATCTGTTTTTC
63 AATTTCT-ATTTTC
* *
1071024 AAATTCTGTTTTTAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGA
1 -AA----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCA-GCGCTGA
* *
1071089 GCTATTTTCAATTTCTGTTTTTTTTTC
54 GGTATTTTCAATTTC-----TATTTTC
1071116 AAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGC
1 AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC
1071154 TTTTTAATTT
Statistics
Matches: 351, Mismatches: 47, Indels: 64
0.76 0.10 0.14
Matches are distributed among these distances:
72 63 0.18
73 35 0.10
75 21 0.06
76 7 0.02
77 59 0.17
78 3 0.01
79 56 0.16
80 5 0.01
81 7 0.02
82 29 0.08
86 2 0.01
87 3 0.01
88 51 0.15
89 1 0.00
91 2 0.01
92 6 0.02
93 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (75 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCAGCGCTGAGGTATTTTCAAT
TTCTATTTTC
Found at i:1070970 original size:79 final size:76
Alignment explanation
Indices: 1070646--1071363 Score: 427
Period size: 88 Copynumber: 9.0 Consensus size: 76
1070636 CCTTTCAAAA
* ** *
1070646 AAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTC-G-GGACACGCTGAGGTAATTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
1070709 TTTCTGTTTTC
66 TTTCTGTTTTC
* ** * *
1070720 --AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA-A-GACACGTTGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
1070781 TTTCTGTTTTC
66 TTTCTGTTTTC
* * ** * ** *
1070792 -AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
*
1070856 TTTCTATCTTTC
66 TTTCTGT-TTTC
* *
1070868 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTA--TTTTC
* *
1070933 AATTTATATTTTTC
64 AATTTCT-GTTTTC
* * * * * *
1070947 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTTACATG-TCGAGGTATTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCT-GAGGTATTTTCA
**
1071011 AAATCTGTTTTTC
65 ATTTCTG-TTTTC
* ** * **
1071024 AAATTCTGTTTTTAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGA
1 -AA----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGA
*
1071089 GCTATTTTCAATTTCTGTTTTTTTTTC
55 GGTATTTTCAATTTCTG-----TTTTC
* * * * * *
1071116 AAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTA-ATTTCTGCGAGAGTTGAGTT
1 AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC--CTCAGA--TC-AC-A-CGCTGAGGT
*
1071180 GAGTCTTTTAATTTCTGTTTTTC
58 -A-T-TTTCAATTTCTG-TTTTC
* **
1071203 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCCAG-TCACA-TATCGAGGTATTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-CAGATCACACGCT-GAGGTATTTTC
**
1071264 AAAATCTGCTTTTC
64 AATTTCTG-TTTTC
** * *
1071278 AAGTTAAGTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGA
1 ------A-----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGA
*
1071343 GCTATTTTCAATTTCTGTTTT
55 GGTATTTTCAATTTCTGTTTT
1071364 TAATGTCTGT
Statistics
Matches: 504, Mismatches: 83, Indels: 101
0.73 0.12 0.15
Matches are distributed among these distances:
72 64 0.13
73 32 0.06
75 36 0.07
76 5 0.01
77 63 0.12
78 7 0.01
79 64 0.13
80 2 0.00
81 7 0.01
82 30 0.06
83 1 0.00
84 31 0.06
85 7 0.01
86 1 0.00
87 11 0.02
88 120 0.24
89 3 0.01
90 1 0.00
91 13 0.03
92 6 0.01
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (76 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
TTTCTGTTTTC
Found at i:1071024 original size:14 final size:14
Alignment explanation
Indices: 1071005--1071043 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1070995 TGTCGAGGTA
1071005 TTTTCAAAATCTGT
1 TTTTCAAAATCTGT
*
1071019 TTTTCAAATTCTGT
1 TTTTCAAAATCTGT
*
1071033 TTTTAAAAATC
1 TTTTCAAAATC
1071044 AACTCATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (14 bp):
TTTTCAAAATCTGT
Found at i:1071171 original size:30 final size:30
Alignment explanation
Indices: 1071135--1071196 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
1071125 CAACTCATAT
1071135 TGCGAGAGGTGAGTTGAG-CTTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTC-TTTTAATTTC
*
1071165 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
1071195 TG
1 TG
1071197 TTTTTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (30 bp):
TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
Found at i:1071297 original size:254 final size:247
Alignment explanation
Indices: 1070788--1071364 Score: 754
Period size: 254 Copynumber: 2.3 Consensus size: 247
1070778 CAATTTCTGT
* * *
1070788 TTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATTTT
1 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTT
*
1070853 CAATTTC----TATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCA
66 CAATTTCTGTTTTTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCA
* *
1070914 CACACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGAGT
131 CACACTGAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCACATTGCGAGAGGTGAGT
* ** * * * **
1070979 TGAGCCTCGGGTTACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAATTCTG
195 TGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAAG
** * *
1071032 TTTTTAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTT
1 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTT
* *
1071097 CAATTTCTGTTTTTTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTA-A
66 CAATTTCTGTTTTTCTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC--TTCAGA
* * * * * * *
1071161 TTTCTGCGAGAGTTGAGTTGAGTCTTTT-AATTTCTGTTTTTC-AAAAATCAACTCATATTGCGA
128 --TC-AC-ACA-CTGAGGT-A-TCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGCGA
*
1071224 GAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAGTTAAG
186 GAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAAG
1071286 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTT
1 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTT
1071351 CAATTTCTGTTTTT
66 CAATTTCTGTTTTT
1071365 AATGTCTGTT
Statistics
Matches: 287, Mismatches: 32, Indels: 18
0.85 0.09 0.05
Matches are distributed among these distances:
244 65 0.23
248 13 0.05
249 30 0.10
250 1 0.00
251 3 0.01
252 2 0.01
253 1 0.00
254 149 0.52
255 5 0.02
256 13 0.05
257 5 0.02
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (247 bp):
TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTT
CAATTTCTGTTTTTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCA
CACACTGAGGTATCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGCGAGAGGTGAGTT
GAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAAG
Found at i:1072025 original size:15 final size:15
Alignment explanation
Indices: 1072007--1072041 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1071997 AACCTAACCC
1072007 AAAAAAAA-AACAAAG
1 AAAAAAAAGAA-AAAG
1072022 AAAAAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
1072037 AAAAA
1 AAAAA
1072042 CCTACCCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.89, C:0.03, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:1072056 original size:16 final size:16
Alignment explanation
Indices: 1072037--1072073 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1072027 AAAGAAAAAG
*
1072037 AAAAACCTACCCCAAA
1 AAAAACCTAACCCAAA
1072053 AAAAACCTAACCCAAA
1 AAAAACCTAACCCAAA
1072069 AAAAA
1 AAAAA
1072074 GAAGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.65, C:0.30, G:0.00, T:0.05
Consensus pattern (16 bp):
AAAAACCTAACCCAAA
Found at i:1072653 original size:2 final size:2
Alignment explanation
Indices: 1072648--1072684 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1072638 TAAATACTAT
*
1072648 TA TA TA CA TA TA TA TA TA TA TA TA TA 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 T
1072685 TTTAAATACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1080283 original size:2 final size:2
Alignment explanation
Indices: 1080276--1080305 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1080266 TCTGTTTATG
1080276 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
1080306 ATTTACCTAC
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):
TA
Found at i:1080598 original size:19 final size:19
Alignment explanation
Indices: 1080574--1080611 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1080564 TTGAGATTGC
1080574 CAACCTATTTGCCTGAAAT
1 CAACCTATTTGCCTGAAAT
1080593 CAACCTATTTGCCTGAAAT
1 CAACCTATTTGCCTGAAAT
1080612 TATTCATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (19 bp):
CAACCTATTTGCCTGAAAT
Found at i:1080705 original size:6 final size:7
Alignment explanation
Indices: 1080687--1080712 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1080677 CACTCCCTTT
1080687 TAAAAAA
1 TAAAAAA
1080694 TAAAAAA
1 TAAAAAA
1080701 TAAAAAA
1 TAAAAAA
1080708 TAAAA
1 TAAAA
1080713 TTTCAAAGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:1082756 original size:19 final size:19
Alignment explanation
Indices: 1082734--1082777 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1082724 CCCATGCATT
1082734 TGCATTGCATTGCATCATG
1 TGCATTGCATTGCATCATG
*
1082753 TGCATTGCATTGCATCATT
1 TGCATTGCATTGCATCATG
1082772 TGCATT
1 TGCATT
1082778 AGATTTTCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.41
Consensus pattern (19 bp):
TGCATTGCATTGCATCATG
Found at i:1084717 original size:2 final size:2
Alignment explanation
Indices: 1084710--1084737 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1084700 ACTTAATTAT
1084710 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
1084738 CGATTTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1090928 original size:15 final size:15
Alignment explanation
Indices: 1090907--1090949 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1090897 ATCATCGGAA
1090907 GAAGAAGAGGAGGAG
1 GAAGAAGAGGAGGAG
* * *
1090922 GAGGAAGAAGAAGAG
1 GAAGAAGAGGAGGAG
1090937 GAAGAAGAAGGAG
1 GAAGAAG-AGGAG
1090950 AACCTGGAGT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (15 bp):
GAAGAAGAGGAGGAG
Found at i:1090939 original size:12 final size:12
Alignment explanation
Indices: 1090903--1090946 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
1090893 AATCATCATC
1090903 GGAAGAAGAAGA
1 GGAAGAAGAAGA
*
1090915 GG-AG--GAGGA
1 GGAAGAAGAAGA
1090924 GGAAGAAGAAGA
1 GGAAGAAGAAGA
1090936 GGAAGAAGAAG
1 GGAAGAAGAAG
1090947 GAGAACCTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 6 0.22
10 2 0.07
11 2 0.07
12 17 0.63
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (12 bp):
GGAAGAAGAAGA
Found at i:1090946 original size:18 final size:18
Alignment explanation
Indices: 1090904--1090951 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
1090894 ATCATCATCG
* *
1090904 GAAGAAGAAGAGGAGGAG
1 GAAGAAGAAGAAGAGGAA
*
1090922 GAGGAAGAAGAAGAGGAA
1 GAAGAAGAAGAAGAGGAA
*
1090940 GAAGAAGGAGAA
1 GAAGAAGAAGAA
1090952 CCTGGAGTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (18 bp):
GAAGAAGAAGAAGAGGAA
Found at i:1113111 original size:13 final size:13
Alignment explanation
Indices: 1113093--1113131 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1113083 GCTTTAGAAT
1113093 TTGGGTTTTTAAG
1 TTGGGTTTTTAAG
1113106 TTGGGTTTTTAAG
1 TTGGGTTTTTAAG
1113119 TTGGGTTTTTAAG
1 TTGGGTTTTTAAG
1113132 ATAATCTCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
TTGGGTTTTTAAG
Found at i:1113701 original size:14 final size:14
Alignment explanation
Indices: 1113676--1113711 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1113666 TAAATCATTT
1113676 TAAAAAAT-AAAAA
1 TAAAAAATGAAAAA
1113689 TAAAAAATGAAAAA
1 TAAAAAATGAAAAA
*
1113703 TATAAAATG
1 TAAAAAATG
1113712 TTCATAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (14 bp):
TAAAAAATGAAAAA
Found at i:1116398 original size:13 final size:14
Alignment explanation
Indices: 1116375--1116407 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1116365 ATATTACATT
*
1116375 AATATATAATTTAA
1 AATATATAATTAAA
1116389 AATATA-AATTAAA
1 AATATATAATTAAA
1116402 AATATA
1 AATATA
1116408 GCAAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATATATAATTAAA
Found at i:1122199 original size:18 final size:17
Alignment explanation
Indices: 1122172--1122205 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1122162 CAACAATTCA
*
1122172 TCAACCAACTCCACCAT
1 TCAACCAACTCAACCAT
1122189 TCAATCCAACTCAACCA
1 TCAA-CCAACTCAACCA
1122206 CGAATGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.18
Consensus pattern (17 bp):
TCAACCAACTCAACCAT
Found at i:1123022 original size:12 final size:12
Alignment explanation
Indices: 1123007--1123033 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1122997 ATAAATGAAA
1123007 ATATATGTATGT
1 ATATATGTATGT
1123019 ATATATGTATGT
1 ATATATGTATGT
1123031 ATA
1 ATA
1123034 CGGGGAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (12 bp):
ATATATGTATGT
Found at i:1127470 original size:27 final size:25
Alignment explanation
Indices: 1127381--1127701 Score: 234
Period size: 26 Copynumber: 12.4 Consensus size: 25
1127371 TATATTCTGT
* **
1127381 TTTTAAATTTTTT-TAT-TTGTTGG
1 TTTTAAATTTTTTATATATTATTTA
* * *
1127404 TTTTAAACTCTTTTACATATTATCTA
1 TTTTAAA-TTTTTTATATATTATTTA
* * *
1127430 TATTGAATTTTTATATATATTGTTTA
1 TTTTAAATTTTT-TATATATTATTTA
* *
1127456 TTTTTAAA-TTTTTATTTATTATCTA
1 -TTTTAAATTTTTTATATATTATTTA
* * * *
1127481 TTTTAATTTTTTTATATAATGTTCA
1 TTTTAAATTTTTTATATATTATTTA
* *
1127506 TTTTAAACTCTTTTTATACATCATTTA
1 TTTTAAA-T-TTTTTATATATTATTTA
* *
1127533 CTTTAAAATTTTTTATGTATTATTTA
1 -TTTTAAATTTTTTATATATTATTTA
*
1127559 TTTTAAATTATTTTTACATATTATTTA
1 TTTTAAA-T-TTTTTATATATTATTTA
1127586 TTTTAAATTTTTTCCCATATATTATTTA
1 TTTTAAATTTTTT---ATATATTATTTA
* * *
1127614 TTTTAAATATTTGTGTATATTATCTA
1 TTTTAAAT-TTTTTATATATTATTTA
* * *
1127640 TTTTAAAGTTTTATATATATTACTTG
1 TTTTAAA-TTTTTTATATATTATTTA
* *
1127666 GTTTAAATTATTTTATATGTTATTTA
1 TTTTAAATT-TTTTATATATTATTTA
*
1127692 CTTTAAATTT
1 TTTTAAATTT
1127702 CTTTTACATT
Statistics
Matches: 230, Mismatches: 51, Indels: 32
0.73 0.16 0.10
Matches are distributed among these distances:
23 7 0.03
24 11 0.05
25 48 0.21
26 94 0.41
27 41 0.18
28 25 0.11
29 4 0.02
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (25 bp):
TTTTAAATTTTTTATATATTATTTA
Found at i:1127843 original size:26 final size:26
Alignment explanation
Indices: 1127795--1127859 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
1127785 TTAAACTTTA
*
1127795 TATGTCATTTTAATTTTTTTATAAAT
1 TATGTTATTTTAATTTTTTTATAAAT
*
1127821 TA-GTTATTTTAGATTTTTTTATATAT
1 TATGTTATTTTA-ATTTTTTTATAAAT
*
1127847 TATTTTATTTTAA
1 TATGTTATTTTAA
1127860 ATTGTTTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.24
26 18 0.53
27 8 0.24
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.65
Consensus pattern (26 bp):
TATGTTATTTTAATTTTTTTATAAAT
Found at i:1127854 original size:27 final size:26
Alignment explanation
Indices: 1127801--1127880 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 26
1127791 TTTATATGTC
* *
1127801 ATTTTAATTTTTTTATAAATTA-GTT
1 ATTTTAATTTTTTTATATATTATTTT
1127826 ATTTTAGATTTTTTTATATATTATTTT
1 ATTTTA-ATTTTTTTATATATTATTTT
* *
1127853 ATTTTAAATTGTTTTGTATATTAATTTT
1 ATTTT-AATTTTTTTATATATT-ATTTT
1127881 TTAAAATTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
25 6 0.13
26 15 0.32
27 20 0.43
28 6 0.13
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (26 bp):
ATTTTAATTTTTTTATATATTATTTT
Found at i:1129713 original size:14 final size:14
Alignment explanation
Indices: 1129694--1129721 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1129684 CTATAACAAC
1129694 ATTATGATGAATTA
1 ATTATGATGAATTA
1129708 ATTATGATGAATTA
1 ATTATGATGAATTA
1129722 GTAAATTAAT
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:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
ATTATGATGAATTA
Found at i:1130163 original size:15 final size:15
Alignment explanation
Indices: 1130143--1130172 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1130133 CATATACAAA
1130143 TAATTATATTTATCC
1 TAATTATATTTATCC
1130158 TAATTATATTTATCC
1 TAATTATATTTATCC
1130173 GGTATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTATATTTATCC
Found at i:1132891 original size:18 final size:18
Alignment explanation
Indices: 1132868--1132921 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
1132858 TATCCTAAAA
1132868 AAATTAGATAAAAATATC
1 AAATTAGATAAAAATATC
1132886 AAATT--AT-AAAA-A--
1 AAATTAGATAAAAATATC
1132898 AAATTAGATAAAAATATC
1 AAATTAGATAAAAATATC
1132916 AAATTA
1 AAATTA
1132922 TACATCAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
12 5 0.17
14 3 0.10
15 8 0.27
16 3 0.10
18 11 0.37
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (18 bp):
AAATTAGATAAAAATATC
Found at i:1132900 original size:30 final size:30
Alignment explanation
Indices: 1132864--1132923 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1132854 GTAATATCCT
1132864 AAAAAAATTAGATAAAAATATCAAATTATA
1 AAAAAAATTAGATAAAAATATCAAATTATA
1132894 AAAAAAATTAGATAAAAATATCAAATTATA
1 AAAAAAATTAGATAAAAATATCAAATTATA
1132924 CATCAACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (30 bp):
AAAAAAATTAGATAAAAATATCAAATTATA
Found at i:1137063 original size:26 final size:26
Alignment explanation
Indices: 1137027--1137110 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
1137017 CATGAAATTC
1137027 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
1137053 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
1137079 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
1137105 TTATCA
1 TTATCA
1137111 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:1139313 original size:35 final size:35
Alignment explanation
Indices: 1139261--1139365 Score: 165
Period size: 35 Copynumber: 3.0 Consensus size: 35
1139251 TTTTTTTCTT
* *
1139261 TTTATTCCGTCACGGCTGGAGTCATGGGCACGACG
1 TTTATTCTGTCACGGCTGGAGTCGTGGGCACGACG
* *
1139296 TTTATTCTGTCATGGCTGGAGTCGTGGGCACGATG
1 TTTATTCTGTCACGGCTGGAGTCGTGGGCACGACG
*
1139331 CTTATTCTGTCACGGCTGGAGTCGTGGGCACGACG
1 TTTATTCTGTCACGGCTGGAGTCGTGGGCACGACG
1139366 CTGGGCGTGA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.29
Consensus pattern (35 bp):
TTTATTCTGTCACGGCTGGAGTCGTGGGCACGACG
Found at i:1146750 original size:1 final size:1
Alignment explanation
Indices: 1146744--1146842 Score: 63
Period size: 1 Copynumber: 99.0 Consensus size: 1
1146734 CATGTTCCAC
* ** * * * * **** *
1146744 AAAAAAAAAAAGAAAAAAAAGCAAAAAAACAAAAAAAAAAGAAGAAAAATAATTCGAAAAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
1146809 AAAAAAAAGAAAAAAGAAAAAAGAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1146843 GTTTGATGAT
Statistics
Matches: 73, Mismatches: 25, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.85, C:0.03, G:0.09, T:0.03
Consensus pattern (1 bp):
A
Found at i:1146761 original size:9 final size:9
Alignment explanation
Indices: 1146747--1146843 Score: 81
Period size: 9 Copynumber: 10.0 Consensus size: 9
1146737 GTTCCACAAA
1146747 AAAAAAAAG
1 AAAAAAAAG
1146756 AAAAAAAAG
1 AAAAAAAAG
*
1146765 CAAAAAAACAA
1 -AAAAAAA-AG
1146776 AAAAAAAAG
1 AAAAAAAAG
1146785 AAGAAAAATAATTCG
1 -A-AAAAA-AA---G
1146800 AAAAAAAAG
1 AAAAAAAAG
1146809 AAAAAAAAG
1 AAAAAAAAG
1146818 --AAAAAAG
1 AAAAAAAAG
*
1146825 AAAAAAGAAA
1 AAAAAA-AAG
1146835 AAAAAAAAG
1 AAAAAAAAG
1146844 TTTGATGATT
Statistics
Matches: 73, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
7 7 0.10
9 26 0.36
10 23 0.32
11 6 0.08
12 4 0.05
13 5 0.07
14 1 0.01
15 1 0.01
ACGTcount: A:0.84, C:0.03, G:0.10, T:0.03
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1147613 original size:35 final size:35
Alignment explanation
Indices: 1147567--1147672 Score: 167
Period size: 35 Copynumber: 3.0 Consensus size: 35
1147557 TTTTTTCTTT
* *
1147567 TTATTCCGTCACGGCTGGAGTCATGGGCACGACGC
1 TTATTCTGTCACGGCTGGAGTCGTGGGCACGACGC
*
1147602 TTATTCTGTCACGGCTGGAGTTGTGGGCACGACGC
1 TTATTCTGTCACGGCTGGAGTCGTGGGCACGACGC
* *
1147637 TTATTCTGTCACGGCTGGAGTCGTGGGAATGACGC
1 TTATTCTGTCACGGCTGGAGTCGTGGGCACGACGC
1147672 T
1 T
1147673 GGGCGCGACA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.16, C:0.24, G:0.33, T:0.27
Consensus pattern (35 bp):
TTATTCTGTCACGGCTGGAGTCGTGGGCACGACGC
Found at i:1153806 original size:26 final size:26
Alignment explanation
Indices: 1153759--1153841 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
1153749 CATGAAATTC
1153759 TTATCATGAAA-ATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
1153784 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
1153810 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
1153836 TTATCA
1 TTATCA
1153842 ATTTGTATCA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
25 11 0.20
26 44 0.80
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:1154631 original size:4 final size:4
Alignment explanation
Indices: 1154622--1154667 Score: 74
Period size: 4 Copynumber: 11.5 Consensus size: 4
1154612 TGAAACAAAA
* *
1154622 ATGT ATGT ATGA ATGT ATGT ATGT ATGT TTGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1154668 AAGGAGAGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:1156614 original size:3 final size:3
Alignment explanation
Indices: 1156606--1156653 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
1156596 AACCGTAGGT
1156606 AGA AGA AGA AGA AGA A-A AGGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA
1156651 AGA
1 AGA
1156654 GCAAAGCTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1165852 original size:105 final size:105
Alignment explanation
Indices: 1165707--1166550 Score: 1291
Period size: 105 Copynumber: 8.0 Consensus size: 105
1165697 TACATTTTTA
* * * **
1165707 AAATAAAATAAAAAATAAAAAGGTTGATACATTAGATCAAGCTGAGATGGCTATGTCAAAAGAAC
1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTCGGAAGAAC
*
1165772 AAATACTTAGCTTCGTCCAAAGGAATTACATTTGATCATC
66 AAATACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC
* *
1165812 AAATAAAATAAAAAATAAAAATGTTGACACATTGGGTCAAGCT-AGGATGGCTATGTCGGAAGAG
1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGA-GATGGCTATGTCGGAAGAA
*
1165876 CAAATACTTAGCTTCGTCCAAAGGAATTACATTTGATCATC
65 CAAATACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC
*
1165917 AAATAAAATAAAAAATAAAAAGGTTGACACATTAGGTCAAGCTGAGATGGCTATGTCGGAAGAAC
1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTCGGAAGAAC
*
1165982 AAATACTTAGCTTCGTCCGAAGGGATTACATTTGATCATC
66 AAATACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC
* * *
1166022 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCT-AGGATGGTTATCTCGGAAGAG
1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGA-GATGGCTATGTCGGAAGAA
* *
1166086 CAAATACTTAGCTTCGTCCGAAGGGATTACATTTGATCACC
65 CAAATACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC
* *
1166127 AAATAAAATAAAAAATAAAAAGGTTGACACATTAGGTCAAGCT-AGGATGGCTATCTCGGAAGAA
1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGA-GATGGCTATGTCGGAAGAA
* * *
1166191 CAAATACTTAGCTTCATCCGAAGGAACTACATTTGATCACC
65 CAAATACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC
1166232 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTCGGAAGAA-
1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTCGGAAGAAC
*
1166296 AAAGTACTTAGCTTCGTCCAAAGGAATTACATTTGATCATC
66 AAA-TACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC
* * * *
1166337 AAATAAAATAAAAAATAATAAGGTCGACACATTGGGTCAAGCTGAGATGGTTATGTGGGAAGAAC
1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTCGGAAGAAC
* * * * *
1166402 AAGTACTTAGGTTCATCCGAAGGGATTACATTTGACCATC
66 AAATACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC
*
1166442 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTTGGAAGAAC
1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTCGGAAGAAC
** * **
1166507 AAATACTTAGCTTCACCCGAAGGGATTACATTCAATCATC
66 AAATACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC
1166547 AAAT
1 AAAT
1166551 TGGTCCCGTA
Statistics
Matches: 684, Mismatches: 49, Indels: 12
0.92 0.07 0.02
Matches are distributed among these distances:
104 5 0.01
105 675 0.99
106 4 0.01
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (105 bp):
AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTCGGAAGAAC
AAATACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC
Found at i:1170745 original size:84 final size:84
Alignment explanation
Indices: 1170604--1170771 Score: 291
Period size: 84 Copynumber: 2.0 Consensus size: 84
1170594 ATCACAAGTG
*
1170604 CGAATATGATCATTATATGGAAGGGATTTGATGGTGAGAGGGTGTTCGGGATGAAAAGGATGCTC
1 CGAATATGATCATTATATGGAAGGGATTTGATGGTGAGAGGGTGTTCAGGATGAAAAGGATGCTC
*
1170669 AAAATTTACGGAGTTGTAA
66 AAAATTTACAGAGTTGTAA
* * *
1170688 CGAATATGATCATTGTATGGAAGGGATTTGATGGTGAGAGTGTGTTCAGGATGAAAAGGATGCTT
1 CGAATATGATCATTATATGGAAGGGATTTGATGGTGAGAGGGTGTTCAGGATGAAAAGGATGCTC
1170753 AAAATTTACAGAGTTGTAA
66 AAAATTTACAGAGTTGTAA
1170772 AATAATTTAA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.33, C:0.07, G:0.31, T:0.30
Consensus pattern (84 bp):
CGAATATGATCATTATATGGAAGGGATTTGATGGTGAGAGGGTGTTCAGGATGAAAAGGATGCTC
AAAATTTACAGAGTTGTAA
Found at i:1176046 original size:25 final size:25
Alignment explanation
Indices: 1175991--1176046 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
1175981 ATTTGTAATA
*
1175991 ATAATATATACACAATATGGTATTT
1 ATAATATATACACAATATGGTATAT
* * *
1176016 AAAATATATATATATATAT-GTATAT
1 ATAATATATACACA-ATATGGTATAT
1176041 ATAATA
1 ATAATA
1176047 GTATTTAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (25 bp):
ATAATATATACACAATATGGTATAT
Found at i:1176114 original size:38 final size:39
Alignment explanation
Indices: 1175988--1176114 Score: 118
Period size: 38 Copynumber: 3.3 Consensus size: 39
1175978 ATAATTTGTA
* * *
1175988 ATAATA-ATATATACACAATATGGTATTTAAAATATATAT
1 ATAATATATATATACACTA-ATGGTATTAAAAATATATAC
* * * *
1176027 AT-ATATATGTATATA-TAATAGTATTTAAGAATATATAC
1 ATAATATATATATACACTAATGGTA-TTAAAAATATATAC
* * *
1176065 ATAAGAAATATATA-ACTAATGGCATTAAAAATATATAC
1 ATAATATATATATACACTAATGGTATTAAAAATATATAC
1176103 ATAATATATATA
1 ATAATATATATA
1176115 AAATACCTAA
Statistics
Matches: 69, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
37 5 0.07
38 41 0.59
39 23 0.33
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (39 bp):
ATAATATATATATACACTAATGGTATTAAAAATATATAC
Found at i:1177489 original size:74 final size:72
Alignment explanation
Indices: 1177391--1177551 Score: 173
Period size: 72 Copynumber: 2.2 Consensus size: 72
1177381 GAAACTTAAC
* ** * *
1177391 TTGAAAAGCAAATTTTGAAAATACCTCAATATGTGA-CTCAAGGCTCAAATCACCTCTCGCAATA
1 TTGAAAAACAAAAATTGAAAATACCTC-A-ACGTGACCT-AAGGCTCAAATCACCTCTAGCAATA
1177455 TGAGTTGAAA
63 TGAGTTGAAA
* * * *
1177465 TT-AAAACACAAAAATTGAAAATACCTCAGCGTGACCTGAGGCTCGACTCACCTCTAGCAATATG
1 TTGAAAA-ACAAAAATTGAAAATACCTCAACGTGACCTAAGGCTCAAATCACCTCTAGCAATATG
**
1177529 AGTTGATT
65 AGTTGAAA
1177537 TTGAAAAACAAAAAT
1 TTGAAAAACAAAAAT
1177552 AAAAAGGCTT
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
72 43 0.59
73 11 0.15
74 19 0.26
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (72 bp):
TTGAAAAACAAAAATTGAAAATACCTCAACGTGACCTAAGGCTCAAATCACCTCTAGCAATATGA
GTTGAAA
Found at i:1177940 original size:145 final size:145
Alignment explanation
Indices: 1177677--1178381 Score: 808
Period size: 145 Copynumber: 4.7 Consensus size: 145
1177667 ATTAAAAGGT
* * * *
1177677 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGA-AAACAAAAATTGAAATTACCTCAGCGTGT
** * *
1177742 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-AATTAAAACACAAAAATTGAAAATACCT
65 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACACAGAAATTGAAAATACCT
1177806 CAGCGTG-CCCGAGGC
130 CAGCGTGTCCCGAGGC
* * *
1177821 TCAACTCACCTCTAGCAATATGAGTTGATTTTTTGAAAGACAAAAATTGAAAATACCTCAGCATG
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAA-ACAAAAATTGAAATTACCTCAGCGTG
* ** *
1177886 TCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAA-ACAGAAATTGAAATTACC
64 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACACAGAAATTGAAAATACC
1177950 TCAGCGTGTCCCGAGGC
129 TCAGCGTGTCCCGAGGC
** * * *
1177967 TCAACTCACCTCTCGCAATATGAGTTGA-AATTAAAACACAAAAATTGAAAATACCTCAGCGTGC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA-ACAAAAATTGAAATTACCTCAGCGTGT
* *
1178031 CCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTGAAAGACA-AAATTGAAAATACC
65 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAACACAGAAATTGAAAATACC
* **
1178095 TCAGCATGTCTTGAGGC
129 TCAGCGTGTCCCGAGGC
** * *
1178112 TCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAACGTGTC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAAAAATTGAAATTACCTCAGCGTGTC
* * *
1178177 CCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTTGAAAAACAAAAATTGAAAAACGG
66 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTG--AAAC------------ACAG
*
1178242 AAATTGAAAATACCTCAGCGTGTGACCTGAGGC
115 AAATTGAAAATACCTCAGCGTGT--CCCGAGGC
* * * *
1178275 TCAACTCGCCGCTCGCAATACGAGTTGATTTTTTTGACAACAAAAATTGAAATTACCTCAGCGTG
1 TCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAACAAAAATTGAAATTACCTCAGCGTG
*
1178340 TCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTT
64 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1178382 TTTTTGAAAA
Statistics
Matches: 479, Mismatches: 55, Indels: 35
0.84 0.10 0.06
Matches are distributed among these distances:
144 90 0.19
145 206 0.43
146 55 0.11
148 3 0.01
160 2 0.00
161 22 0.05
163 35 0.07
165 66 0.14
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (145 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAAAAATTGAAATTACCTCAGCGTGTC
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACACAGAAATTGAAAATACCTC
AGCGTGTCCCGAGGC
Found at i:1177981 original size:72 final size:73
Alignment explanation
Indices: 1177677--1178237 Score: 715
Period size: 72 Copynumber: 7.7 Consensus size: 73
1177667 ATTAAAAGGT
* * * * *
1177677 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAA-ACAGAAATTGAAATTACCTCATCGTG
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGA-AACACAAAAATTGAAAATACCTCAGCGTG
*
1177741 TCCTGAGGC
65 TCCCGAGGC
** *
1177750 TCAACTCACCTCTCGCAATATGAGTTGA-AATTAAAACACAAAAATTGAAAATACCTCAGCGTG-
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACACAAAAATTGAAAATACCTCAGCGTGT
1177813 CCCGAGGC
66 CCCGAGGC
* * *
1177821 TCAACTCACCTCTAGCAATATGAGTTGATTTTTTGAAAGACAAAAATTGAAAATACCTCAGCATG
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAACACAAAAATTGAAAATACCTCAGCGTG
**
1177886 TCTTGAGGC
65 TCCCGAGGC
** * *
1177895 TCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAA-ACAGAAATTGAAATTACCTCAGCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACACAAAAATTGAAAATACCTCAGCGTGT
1177959 CCCGAGGC
66 CCCGAGGC
** *
1177967 TCAACTCACCTCTCGCAATATGAGTTGA-AATTAAAACACAAAAATTGAAAATACCTCAGCGTG-
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACACAAAAATTGAAAATACCTCAGCGTGT
1178030 CCCTGAGGC
66 CCC-GAGGC
* * *
1178039 TCAACTCACCTCTAGCAATATGAGTTGATTTTTTGAAAGAC-AAAATTGAAAATACCTCAGCATG
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAACACAAAAATTGAAAATACCTCAGCGTG
**
1178103 TCTTGAGGC
65 TCCCGAGGC
** * * *
1178112 TCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAA-ACAGAAATTGAAATTACCTCAACGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACACAAAAATTGAAAATACCTCAGCGTGT
1178176 CCCGAGGC
66 CCCGAGGC
* *
1178184 TCAACTCACCTCTAGCAATATGAGTTGATTTTTTTGAAAAACAAAAATTGAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAACACAAAAATTGAAAA
1178238 ACGGAAATTG
Statistics
Matches: 422, Mismatches: 53, Indels: 24
0.85 0.11 0.05
Matches are distributed among these distances:
71 46 0.11
72 198 0.47
73 118 0.28
74 48 0.11
75 12 0.03
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.28
Consensus pattern (73 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACACAAAAATTGAAAATACCTCAGCGTGT
CCCGAGGC
Found at i:1178086 original size:217 final size:218
Alignment explanation
Indices: 1177687--1178381 Score: 1000
Period size: 217 Copynumber: 3.1 Consensus size: 218
1177677 TCAACCCACC
* * *
1177687 TCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTGTCCTGAGGCTC
1 TCTCGCAATATGAGTTGATTTTTGA-AAACAGAAATTGAAATTACCTCAACGTGTCCCGAGGCTC
1177752 AACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCC-
65 AACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCT
1177816 GAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTGAAAGACAAAAATTGAAAATACCTCA
130 GAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTGAAAGACAAAAATTGAAAATACCTCA
1177881 GCATGTCTTGAGGCTCAACTCATT
195 GCATGTCTTGAGGCTCAACTCATT
*
1177905 TCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCA
1 TCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCCCGAGGCTCA
1177970 ACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCTG
66 ACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCTG
1178035 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTGAAAGAC-AAAATTGAAAATACCTCAG
131 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTGAAAGACAAAAATTGAAAATACCTCAG
1178099 CATGTCTTGAGGCTCAACTCATT
196 CATGTCTTGAGGCTCAACTCATT
1178122 TCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCCCGAGGCTCA
1 TCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCCCGAGGCTCA
* ** *
1178187 ACTCACCTCTAGCAATATGAGTTGATTTTTTTGAAAAACAAAAATTGAAAAACGGAAATTGAAAA
66 ACTCACCTCTCGCAATATGAGTTGA---AATT--AAAAC---------ACAA---AAATTGAAAA
* * * * * *
1178252 TACCTCAGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATACGAGTTGATTTTTTTGACA-AC
114 TACCTCAGC--GTGCCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTTTGAAAGAC
* * * **
1178316 AAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACC
176 AAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATT
*
1178359 TCTCGCAATATGAATTGATTTTT
1 TCTCGCAATATGAGTTGATTTTT
1178382 TTTTTGAAAA
Statistics
Matches: 435, Mismatches: 20, Indels: 25
0.91 0.04 0.05
Matches are distributed among these distances:
217 231 0.53
218 70 0.16
220 2 0.00
222 5 0.01
231 3 0.01
234 19 0.04
236 37 0.09
237 68 0.16
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (218 bp):
TCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAACGTGTCCCGAGGCTCA
ACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCTG
AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTGAAAGACAAAAATTGAAAATACCTCAG
CATGTCTTGAGGCTCAACTCATT
Found at i:1178236 original size:14 final size:14
Alignment explanation
Indices: 1178217--1178251 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1178207 GTTGATTTTT
1178217 TTGAAAAACAAAAA
1 TTGAAAAACAAAAA
**
1178231 TTGAAAAACGGAAA
1 TTGAAAAACAAAAA
1178245 TTGAAAA
1 TTGAAAA
1178252 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.06, G:0.14, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAAAAA
Found at i:1178304 original size:91 final size:88
Alignment explanation
Indices: 1178146--1178326 Score: 254
Period size: 91 Copynumber: 2.0 Consensus size: 88
1178136 TTGATTTTTG
* * *
1178146 AAAACAGAAATTGAAATTACCTCAACGTGTCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAACGTGTCCCGAGGCTCAACTCACCGCTAGCAATACGAGTTG
1178211 ATTTTTTTGAAAAACAAAAATTGA
66 ATTTTTTTG-AAAACAAAAATTGA
* * * * *
1178235 AAAACGGAAATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATACGAGT
1 AAAACAGAAATTGAAAATACCTCAACGTGT--CCCGAGGCTCAACTCACCGCTAGCAATACGAGT
*
1178300 TGATTTTTTTGACAACAAAAATTGA
64 TGATTTTTTTGAAAACAAAAATTGA
1178325 AA
1 AA
1178327 TTACCTCAGC
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
89 27 0.33
90 15 0.19
91 39 0.48
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (88 bp):
AAAACAGAAATTGAAAATACCTCAACGTGTCCCGAGGCTCAACTCACCGCTAGCAATACGAGTTG
ATTTTTTTGAAAACAAAAATTGA
Found at i:1178350 original size:165 final size:161
Alignment explanation
Indices: 1178081--1178383 Score: 453
Period size: 165 Copynumber: 1.9 Consensus size: 161
1178071 TTGAAAGACA
* *** *
1178081 AAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTG
1 AAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATTTTTG
* *
1178146 AAAACAGAAATTGAAATTACCTCAACGTGTCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTG
66 AAAACAAAAATTGAAATTACCTCAACGTGTCCCGAGGCTCAACTCACCTCTAGCAATATGAATTG
1178211 ATTTTTTTGAAAAACAAAAATTGAAAAACGG
131 ATTTTTTTGAAAAACAAAAATTGAAAAACGG
* *
1178242 AAATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATACGAGTTGATTTT
1 AAATTGAAAATACCTCAGCATGT--CCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGA--TT
* * * *
1178307 TTTGACAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
62 TTTGAAAACAAAAATTGAAATTACCTCAACGTGTCCCGAGGCTCAACTCACCTCTAGCAATATGA
1178372 ATTGATTTTTTT
127 ATTGATTTTTTT
1178384 TTTGAAAAAC
Statistics
Matches: 125, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
161 22 0.18
163 30 0.24
165 73 0.58
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (161 bp):
AAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATTTTTG
AAAACAAAAATTGAAATTACCTCAACGTGTCCCGAGGCTCAACTCACCTCTAGCAATATGAATTG
ATTTTTTTGAAAAACAAAAATTGAAAAACGG
Found at i:1178385 original size:76 final size:75
Alignment explanation
Indices: 1178242--1178383 Score: 223
Period size: 74 Copynumber: 1.9 Consensus size: 75
1178232 TGAAAAACGG
* *
1178242 AAATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATACGAGTTGATTTT
1 AAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCGCTCGCAATACGAATTGATTTT
1178307 TTTGACAACAA
65 TTTGACAACAA
* * *
1178318 AAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTT
1 AAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCGCTCGCAATACGAATTGATTTTT
1178382 TT
66 TT
1178384 TTTGAAAAAC
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
74 39 0.64
76 22 0.36
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (75 bp):
AAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCGCTCGCAATACGAATTGATTTTT
TTGACAACAA
Found at i:1178451 original size:59 final size:60
Alignment explanation
Indices: 1178345--1178464 Score: 170
Period size: 59 Copynumber: 2.0 Consensus size: 60
1178335 GCGTGTCCTG
* * ****
1178345 AGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTTTTTGAAAAACAGAAATT-AAA
1 AGGCTCAACTCACCTCTCACAATATGAATTGAATTTTTTGAAAAAAAACAGAAATTGAAA
*
1178404 AGGCTCAACTCACCTCTCACAATATGAGTTGAATTTTTTGAAAAAAAACAGAAATTGAAA
1 AGGCTCAACTCACCTCTCACAATATGAATTGAATTTTTTGAAAAAAAACAGAAATTGAAA
1178464 A
1 A
1178465 TACCTCAACG
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 49 0.92
60 4 0.08
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (60 bp):
AGGCTCAACTCACCTCTCACAATATGAATTGAATTTTTTGAAAAAAAACAGAAATTGAAA
Found at i:1183255 original size:17 final size:17
Alignment explanation
Indices: 1183235--1183384 Score: 210
Period size: 17 Copynumber: 8.5 Consensus size: 17
1183225 AATGATATGT
1183235 AATCTTAGATATGATAC
1 AATCTTAGATATGATAC
* * *
1183252 AATCTTAAATACGATTGC
1 AATCTTAGATATGA-TAC
1183270 AATCTTAGATATGATAC
1 AATCTTAGATATGATAC
1183287 AATCTTAGATATGATAC
1 AATCTTAGATATGATAC
*
1183304 AATCTTAGATATGATTGC
1 AATCTTAGATATGA-TAC
1183322 AATCTTAGATATGATAC
1 AATCTTAGATATGATAC
*
1183339 AATCTTAGATATGATTGC
1 AATCTTAGATATGA-TAC
1183357 AATCTTAGATATGATATAC
1 AATCTTAGATATG--ATAC
1183376 AATCTTAGA
1 AATCTTAGA
1183385 AGATATGATT
Statistics
Matches: 118, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
17 61 0.52
18 45 0.38
19 11 0.09
20 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (17 bp):
AATCTTAGATATGATAC
Found at i:1183275 original size:35 final size:35
Alignment explanation
Indices: 1183235--1183384 Score: 214
Period size: 35 Copynumber: 4.3 Consensus size: 35
1183225 AATGATATGT
* * *
1183235 AATCTTAGATATGA-TACAATCTTAAATACGATTGC
1 AATCTTAGATATGATTACAATCTTAGATATGA-TAC
1183270 AATCTTAGATATGA-TACAATCTTAGATATGATAC
1 AATCTTAGATATGATTACAATCTTAGATATGATAC
*
1183304 AATCTTAGATATGATTGCAATCTTAGATATGATAC
1 AATCTTAGATATGATTACAATCTTAGATATGATAC
*
1183339 AATCTTAGATATGATTGCAATCTTAGATATGATATAC
1 AATCTTAGATATGATTACAATCTTAGATATG--ATAC
1183376 AATCTTAGA
1 AATCTTAGA
1183385 AGATATGATT
Statistics
Matches: 108, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
34 16 0.15
35 79 0.73
37 13 0.12
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (35 bp):
AATCTTAGATATGATTACAATCTTAGATATGATAC
Found at i:1183291 original size:52 final size:52
Alignment explanation
Indices: 1183235--1183384 Score: 246
Period size: 52 Copynumber: 2.8 Consensus size: 52
1183225 AATGATATGT
* *
1183235 AATCTTAGATATGATACAATCTTAAATACGATTGCAATCTTAGATATGATAC
1 AATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGATATGATAC
1183287 AATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGATATGATAC
1 AATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGATATGATAC
* *
1183339 AATCTTAGATATGATTGCAATCTTAGATATGATATACAATCTTAGA
1 AATCTTAGATATGA-TACAATCTTAGATATGAT-TGCAATCTTAGA
1183385 AGATATGATT
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
52 64 0.70
53 17 0.18
54 11 0.12
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (52 bp):
AATCTTAGATATGATACAATCTTAGATATGATTGCAATCTTAGATATGATAC
Found at i:1183889 original size:18 final size:17
Alignment explanation
Indices: 1183865--1183924 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
1183855 CCAATATATT
1183865 TTATATTTTTTATATAA
1 TTATATTTTTTATATAA
*
1183882 TTAT-TATTCTTATA-AA
1 TTATAT-TTTTTATATAA
1183898 -TATATTTTTTATTATATA
1 TTATATTTTTTA-TATA-A
1183916 TTATATTTT
1 TTATATTTT
1183925 AAATTTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
15 8 0.23
16 6 0.17
17 12 0.34
18 1 0.03
19 8 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATATTTTTTATATAA
Found at i:1183909 original size:15 final size:16
Alignment explanation
Indices: 1183866--1183924 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 16
1183856 CAATATATTT
1183866 TATATTTTTTATATAA
1 TATATTTTTTATATAA
1183882 T-TATTATTCTTATA-AA
1 TATATT-TT-TTATATAA
1183898 TATATTTTTTATTATATA
1 TATATTTTTTA-TATA-A
1183916 TTATATTTT
1 -TATATTTT
1183925 AAATTTATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
15 7 0.19
16 10 0.28
17 10 0.28
18 1 0.03
19 8 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATTTTTTATATAA
Found at i:1183949 original size:26 final size:26
Alignment explanation
Indices: 1183901--1183950 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1183891 TTATAAATAT
* * * *
1183901 ATTTTTTATTATATATTATATTTTAA
1 ATTTATTATTAAATATCACATTTTAA
1183927 ATTTATTATTAAATATCACATTTT
1 ATTTATTATTAAATATCACATTTT
1183951 TTTATATGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTATTATTAAATATCACATTTTAA
Found at i:1186243 original size:17 final size:17
Alignment explanation
Indices: 1186221--1186253 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1186211 GCTGATGGGA
*
1186221 TTTGGGGTTAGGGTTAT
1 TTTGGGCTTAGGGTTAT
1186238 TTTGGGCTTAGGGTTA
1 TTTGGGCTTAGGGTTA
1186254 GGTTAATCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.03, G:0.39, T:0.45
Consensus pattern (17 bp):
TTTGGGCTTAGGGTTAT
Found at i:1187170 original size:143 final size:139
Alignment explanation
Indices: 1186869--1187173 Score: 445
Period size: 143 Copynumber: 2.2 Consensus size: 139
1186859 GAAAAGTAGA
* *
1186869 TTTTGGAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGCTTTTTGAAAACA
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACA
* *
1186934 TGAATTAAAATAGAAATTGGAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACTTCTCGCAAT
66 TAAATTAAAACAGAAATTGGAAATACCTCAGCA-GTGAGCCGAGGCTCAACTCACTTCTCGCAAT
1186999 ATGAGTTAAT
130 ATGAGTTAAT
* *
1187009 TTTTGAAAAACAGGAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAC
*
1187074 ATAAATTGAAAAAAACAGAAATT-GAAATTACCTCAGC-GTG-TCCTGAGGCTCAACTCACTTCT
65 ATAAATT----AAAACAGAAATTGGAAA-TACCTCAGCAGTGAGCC-GAGGCTCAACTCACTTCT
*
1187136 CGCAATATGAGTTGAT
124 CGCAATATGAGTTAAT
1187152 TTTTGAAAAACAGAAATTAAAA
1 TTTTGAAAAACAGAAATTAAAA
1187174 AAACAGAAAC
Statistics
Matches: 149, Mismatches: 9, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
140 56 0.38
141 10 0.07
142 2 0.01
143 57 0.38
144 4 0.03
145 20 0.13
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (139 bp):
TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACA
TAAATTAAAACAGAAATTGGAAATACCTCAGCAGTGAGCCGAGGCTCAACTCACTTCTCGCAATA
TGAGTTAAT
Found at i:1187334 original size:176 final size:172
Alignment explanation
Indices: 1187030--1187516 Score: 655
Period size: 176 Copynumber: 2.8 Consensus size: 172
1187020 AGGAATTAAA
*
1187030 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAAACAGAAA
1 AGGCTCAACTCTCCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATT----AAAACAGAAA
* *
1187095 TTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAA
62 TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAA
* *
1187160 AACAGAAATTAAAAAAACAGAAACTGAAAATACCTCAGCATGTGAGCTG
126 AACAGAAATTAAAAAAA-AG-AACTAAAAATACCTCAGCATGTGAGCCG
* * *
1187209 AGGCTCAACTCTCCTCTCGCAATATGAGTTGATTTTGGAAAAGTAGAAATTAAAGACAGAAATTG
1 AGGCTCAACTCTCCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTAAA-ACAGAAATTG
* **
1187274 AAATTACCTCAGCGTGTCCCGAGACTCAACTCACCTCTCGCAATATGAGTTGACTTTTGAAAAGT
65 AAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTGAAAAAC
* * * *
1187339 ATAAATT--AAACAAGAATTAAAAATTCCTCAGCATGTGAGCCG
129 AGAAATTAAAAAAAAGAACTAAAAATACCTCAGCATGTGAGCCG
* *
1187381 AGGCTCAACTCAT-CTCTCGCAATATGAGTTGATTTTTGAAAAAAATAAATT-AAACAGGAATTT
1 AGGCTCAACTC-TCCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTAAAACA-GAAATT
* *
1187444 AAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT-AAAAAC
64 GAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAAC
1187507 AGAAA-TAAAA
129 AGAAATTAAAA
1187517 CATCAAAATA
Statistics
Matches: 276, Mismatches: 27, Indels: 20
0.85 0.08 0.06
Matches are distributed among these distances:
167 1 0.00
168 8 0.03
169 5 0.02
170 3 0.01
171 58 0.21
172 69 0.25
173 3 0.01
174 4 0.01
175 3 0.01
176 75 0.27
179 47 0.17
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.26
Consensus pattern (172 bp):
AGGCTCAACTCTCCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTAAAACAGAAATTGA
AATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAG
AAATTAAAAAAAAGAACTAAAAATACCTCAGCATGTGAGCCG
Found at i:1187336 original size:86 final size:86
Alignment explanation
Indices: 1187030--1187500 Score: 574
Period size: 86 Copynumber: 5.4 Consensus size: 86
1187020 AGGAATTAAA
1187030 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAAACAGAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATT---AAAAACAGAAA
*
1187095 TTGAAATTACCTCAGCGTGTCCTG
63 TTGAAATTACCTCAGCGTGTCCCG
* * * *
1187119 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAAAACAGAAAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATT--AAAAACAGAAAT
* ** *
1187184 TGAAAATACCTCAGCATGTGAGCTG
64 TGAAATTACCTCAGC--GTGTCCCG
* * * * *
1187209 AGGCTCAACTCTCCTCTCGCAATATGAGTTGATTTTGGAAAAGTAGAAATTAAAGACAGAAATTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTAAAAACAGAAATTG
1187274 AAATTACCTCAGCGTGTCCCG
66 AAATTACCTCAGCGTGTCCCG
* * * *
1187295 AGACTCAACTCACCTCTCGCAATATGAGTTGACTTTTGAAAAGTATAAATTAAACA-AG-AATTA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTAAAAACAGAAATT-
* **
1187358 AAAATT-CCTCAGCATGTGAGCCG
65 GAAATTACCTCAGC--GTGTCCCG
* * *
1187381 AGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTGAAAAAAATAAATT--AAACAGGAATTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTAAAAACA-GAAATT
* *
1187444 AAAAATACCTCAGCGTGTCCCG
65 GAAATTACCTCAGCGTGTCCCG
1187466 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1187501 AAAAACAGAA
Statistics
Matches: 335, Mismatches: 38, Indels: 22
0.85 0.10 0.06
Matches are distributed among these distances:
84 13 0.04
85 48 0.14
86 113 0.34
87 10 0.03
88 51 0.15
89 48 0.14
90 52 0.16
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (86 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTAAAAACAGAAATTG
AAATTACCTCAGCGTGTCCCG
Found at i:1188268 original size:7 final size:7
Alignment explanation
Indices: 1188253--1188306 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
1188243 TTAATTATCA
*
1188253 TTATAGT
1 TTATGGT
1188260 TTATGGT
1 TTATGGT
1188267 TTATGGT
1 TTATGGT
* *
1188274 TTAAGAT
1 TTATGGT
*
1188281 ATATGGT
1 TTATGGT
*
1188288 TTAGGGT
1 TTATGGT
*
1188295 TTAAGGT
1 TTATGGT
1188302 TTATG
1 TTATG
1188307 AGTTAACTAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (7 bp):
TTATGGT
Found at i:1188285 original size:21 final size:21
Alignment explanation
Indices: 1188261--1188345 Score: 89
Period size: 21 Copynumber: 3.9 Consensus size: 21
1188251 CATTATAGTT
*
1188261 TATGGTTTATGGTTTAAGATA
1 TATGGTTTAGGGTTTAAGATA
* *
1188282 TATGGTTTAGGGTTTAAGGTT
1 TATGGTTTAGGGTTTAAGATA
**
1188303 TATGAGTTAACTATAGTTTAAGATA
1 TATG-GTT---TAGGGTTTAAGATA
1188328 TATGGTTTAGGGTTTAAG
1 TATGGTTTAGGGTTTAAG
1188346 GTTTAGGAGT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
21 31 0.61
22 3 0.06
24 3 0.06
25 14 0.27
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (21 bp):
TATGGTTTAGGGTTTAAGATA
Found at i:1188324 original size:46 final size:46
Alignment explanation
Indices: 1188272--1188361 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
1188262 ATGGTTTATG
*
1188272 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTATGAGTTAACTATA
1 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAACTATA
1188318 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAACTA
1 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAACTA
1188362 GTATTTGAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (46 bp):
GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGGAGTTAACTATA
Found at i:1188417 original size:7 final size:7
Alignment explanation
Indices: 1188388--1188516 Score: 55
Period size: 7 Copynumber: 18.1 Consensus size: 7
1188378 GATGAATTAT
1188388 GGGTTTA
1 GGGTTTA
*
1188395 GGGATTA
1 GGGTTTA
* *
1188402 TGATTTA
1 GGGTTTA
1188409 GGGTTTA
1 GGGTTTA
*
1188416 GGGGTTA
1 GGGTTTA
1188423 GGG-TTA
1 GGGTTTA
*
1188429 GAGTTTA
1 GGGTTTA
* *
1188436 AGGTGTAA
1 GGGT-TTA
*
1188444 GGGTTTG
1 GGGTTTA
*
1188451 GGGTTAA
1 GGGTTTA
** *
1188458 AAGTTAA
1 GGGTTTA
1188465 GGGTTTA
1 GGGTTTA
*
1188472 GAGTTTA
1 GGGTTTA
*
1188479 GTGTTTA
1 GGGTTTA
*
1188486 TGGG-ATA
1 -GGGTTTA
*
1188493 GGGGTTAA
1 -GGGTTTA
1188501 GAGGTTTA
1 G-GGTTTA
*
1188509 GGGCTTA
1 GGGTTTA
1188516 G
1 G
1188517 ATTAATTAGT
Statistics
Matches: 87, Mismatches: 30, Indels: 10
0.69 0.24 0.08
Matches are distributed among these distances:
6 5 0.06
7 68 0.78
8 14 0.16
ACGTcount: A:0.23, C:0.01, G:0.40, T:0.36
Consensus pattern (7 bp):
GGGTTTA
Found at i:1194302 original size:25 final size:24
Alignment explanation
Indices: 1194274--1194328 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1194264 AATTAAACAT
*
1194274 AATATAATATT-TTAACATAGAAATA
1 AATATAAT-TTATTAAAATA-AAATA
*
1194299 AATATTATTTAATTAAAATAAAATA
1 AATATAATTT-ATTAAAATAAAATA
1194324 AATAT
1 AATAT
1194329 TTAAAAGGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 2 0.08
25 17 0.65
26 7 0.27
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
AATATAATTTATTAAAATAAAATA
Found at i:1194378 original size:43 final size:44
Alignment explanation
Indices: 1194330--1194547 Score: 234
Period size: 43 Copynumber: 5.1 Consensus size: 44
1194320 AATAAATATT
* *
1194330 TAAAAGGTCAT-ATTTTTAACGGCGTTTTTAGGAAAAGCGCCGC
1 TAAAAGGTCATGATCTTTAGCGGCGTTTTTAGGAAAAGCGCCGC
* * *
1194373 TAAAA-GTCATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAAGGTCATGATCTTTAGCGGCGTTTTTAGGAAAAGCGCCGC
* * * * *
1194416 T-AAAGGTCCTGGTCTTTAGCGACGTTTTTTA-AAAAAGCGCTGC
1 TAAAAGGTCATGATCTTTAGCGGCG-TTTTTAGGAAAAGCGCCGC
* *
1194459 TAAAA-GTCATGACCTTTAGCGGCGTTTGTAGGAAAAGCGCCGC
1 TAAAAGGTCATGATCTTTAGCGGCGTTTTTAGGAAAAGCGCCGC
* * * *
1194502 -GAAAGGTCTTGGTCTTTAGCGGCGTTTTTA-TAAAAGCGCCGC
1 TAAAAGGTCATGATCTTTAGCGGCGTTTTTAGGAAAAGCGCCGC
1194544 TAAA
1 TAAA
1194548 GACCAGGACC
Statistics
Matches: 141, Mismatches: 27, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
42 27 0.19
43 107 0.76
44 7 0.05
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (44 bp):
TAAAAGGTCATGATCTTTAGCGGCGTTTTTAGGAAAAGCGCCGC
Found at i:1194497 original size:86 final size:85
Alignment explanation
Indices: 1194352--1194564 Score: 311
Period size: 86 Copynumber: 2.5 Consensus size: 85
1194342 TTTTTAACGG
* * *
1194352 CGTTTTTAGGAAAAGCGCCGCTAAAAGTCATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
1 CGTTTTTA-AAAAAGCGCCGCTAAAAGTCATGACCTTTAGCGGCGTTTGTAGGAAAAGCGCCGCG
1194417 AAAGGTCCTGGTCTTTAGCGA
65 AAAGGTCCTGGTCTTTAGCGA
*
1194438 CGTTTTTTAAAAAAGCGCTGCTAAAAGTCATGACCTTTAGCGGCGTTTGTAGGAAAAGCGCCGCG
1 CG-TTTTTAAAAAAGCGCCGCTAAAAGTCATGACCTTTAGCGGCGTTTGTAGGAAAAGCGCCGCG
* *
1194503 AAAGGTCTTGGTCTTTAGCGG
65 AAAGGTCCTGGTCTTTAGCGA
* * *
1194524 CGTTTTTATAAAAGCGCCGCT-AAAGACCAGGACCTTTAGCG
1 CGTTTTTAAAAAAGCGCCGCTAAAAG-TCATGACCTTTAGCG
1194565 ACGCTTTTCC
Statistics
Matches: 115, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
84 4 0.03
85 30 0.26
86 75 0.65
87 6 0.05
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (85 bp):
CGTTTTTAAAAAAGCGCCGCTAAAAGTCATGACCTTTAGCGGCGTTTGTAGGAAAAGCGCCGCGA
AAGGTCCTGGTCTTTAGCGA
Found at i:1206516 original size:11 final size:11
Alignment explanation
Indices: 1206502--1206528 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1206492 AATATTAAAA
1206502 ATATATAGAAC
1 ATATATAGAAC
1206513 ATATATAGAAC
1 ATATATAGAAC
1206524 ATATA
1 ATATA
1206529 CAATACATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (11 bp):
ATATATAGAAC
Found at i:1206656 original size:21 final size:20
Alignment explanation
Indices: 1206632--1206673 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 20
1206622 TATATAATAG
1206632 TATTAGAAATATACAATATAA
1 TATTAGAAATATAC-ATATAA
1206653 TATTAGAAATATACATATAA
1 TATTAGAAATATACATATAA
1206673 T
1 T
1206674 GGTATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
TATTAGAAATATACATATAA
Found at i:1206686 original size:44 final size:42
Alignment explanation
Indices: 1206617--1206798 Score: 148
Period size: 44 Copynumber: 4.0 Consensus size: 42
1206607 ACACACATAT
* * *
1206617 ATATATATATAATAGTATTAGAAATATACAATATAATATTAGAA
1 ATATATATATAAT-GTATAAAAAATATATAATATAATATTA-AA
*
1206661 ATATACATATAATGGTATAAAAAATATATAACTAATAATATTAAA
1 ATATATATATAAT-GTATAAAAAATATATAA-T-ATAATATTAAA
* * *
1206706 ATATATATAATAATATATATAAAATATATTTATATAATATTAAAA
1 ATATATAT-ATAATGTATAAAAAATATA-TAATATAATATT-AAA
* * * *
1206751 ATTTATTTACATAACATATATGAAAACATATATAATATAATATTAAA
1 A--TATATATAT-A-ATGTAT-AAAAAATATATAATATAATATTAAA
1206798 A
1 A
1206799 CATTTACATA
Statistics
Matches: 114, Mismatches: 14, Indels: 17
0.79 0.10 0.12
Matches are distributed among these distances:
44 34 0.30
45 27 0.24
46 18 0.16
47 10 0.09
48 17 0.15
49 8 0.07
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (42 bp):
ATATATATATAATGTATAAAAAATATATAATATAATATTAAA
Found at i:1206725 original size:14 final size:14
Alignment explanation
Indices: 1206706--1206744 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1206696 TAATATTAAA
1206706 ATATATATAATAAT
1 ATATATATAATAAT
*
1206720 ATATATAAAAT-AT
1 ATATATATAATAAT
*
1206733 ATTTATATAATA
1 ATATATATAATA
1206745 TTAAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATATAATAAT
Found at i:1206734 original size:21 final size:22
Alignment explanation
Indices: 1206617--1206815 Score: 108
Period size: 23 Copynumber: 8.8 Consensus size: 22
1206607 ACACACATAT
1206617 ATATATATATAATAGTAT-TAGAA
1 ATATATATATAATA-TATATA-AA
* *
1206640 ATATACAATATAATAT-TA-GAA
1 ATATA-TATATAATATATATAAA
* * *
1206661 ATATACATATAATGGTATAAAAA
1 ATATATATATAAT-ATATATAAA
1206684 ATATATA-ACTAATA-ATATTAAA
1 ATATATATA-TAATATATA-TAAA
1206706 ATATATATAATAATATATATAAA
1 ATATATAT-ATAATATATATAAA
1206729 ATATATTTATATAATAT-TA-AAA
1 ATATA--TATATAATATATATAAA
* * * *
1206751 ATTTATTTACATAACATATATGAA
1 A--TATATATATAATATATATAAA
*
1206775 A-ACATATATAATATAATATTAAA
1 ATATATATATAATAT-ATA-TAAA
* * *
1206798 ACATTTACATAATATATA
1 ATATATATATAATATATA
1206816 CACATATGAT
Statistics
Matches: 137, Mismatches: 20, Indels: 38
0.70 0.10 0.19
Matches are distributed among these distances:
20 7 0.05
21 20 0.15
22 29 0.21
23 43 0.31
24 35 0.26
25 3 0.02
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (22 bp):
ATATATATATAATATATATAAA
Found at i:1206751 original size:22 final size:22
Alignment explanation
Indices: 1206695--1206798 Score: 88
Period size: 22 Copynumber: 4.5 Consensus size: 22
1206685 TATATAACTA
*
1206695 ATAATATT-AAAATATATATA-
1 ATAATATTAAAAATATATTTAT
1206715 ATAATATATATAAAATATATTTAT
1 ATAATAT-TA-AAAATATATTTAT
* *
1206739 ATAATATTAAAAATTTATTTAC
1 ATAATATTAAAAATATATTTAT
*
1206761 ATAACATATATGAAAACATATA-TAAT
1 AT-A-ATAT-T-AAAA-ATATATTTAT
1206787 ATAATATTAAAA
1 ATAATATTAAAA
1206799 CATTTACATA
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
20 7 0.10
21 1 0.01
22 17 0.25
23 15 0.22
24 15 0.22
25 2 0.03
26 8 0.12
27 4 0.06
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (22 bp):
ATAATATTAAAAATATATTTAT
Found at i:1206809 original size:24 final size:24
Alignment explanation
Indices: 1206737--1206813 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 24
1206727 AAATATATTT
*
1206737 ATATAATATTAAAAATTTATTTACATA
1 ATATAATATT-AAAA--CATTTACATA
* * *
1206764 ACAT-ATATGAAAACA--TATATA
1 ATATAATATTAAAACATTTACATA
1206785 ATATAATATTAAAACATTTACATA
1 ATATAATATTAAAACATTTACATA
1206809 ATATA
1 ATATA
1206814 TACACATATG
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
21 8 0.20
22 10 0.25
23 1 0.03
24 10 0.25
25 4 0.10
26 4 0.10
27 3 0.08
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (24 bp):
ATATAATATTAAAACATTTACATA
Found at i:1207019 original size:3 final size:3
Alignment explanation
Indices: 1207013--1207084 Score: 117
Period size: 3 Copynumber: 24.0 Consensus size: 3
1207003 TACTATGATG
1207013 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
***
1207061 ATA ATA ATA GGG ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
1207085 TTGATATATA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1208099 original size:46 final size:46
Alignment explanation
Indices: 1208032--1208120 Score: 169
Period size: 46 Copynumber: 1.9 Consensus size: 46
1208022 TCCCTCTAAC
1208032 TTAAATCTGCTCTGCTATTGCTGAAAAATCCCTAATTTCTATCATT
1 TTAAATCTGCTCTGCTATTGCTGAAAAATCCCTAATTTCTATCATT
*
1208078 TTAAATCTGCTCTGCTATTGCTGAAAAATCTCTAATTTCTATC
1 TTAAATCTGCTCTGCTATTGCTGAAAAATCCCTAATTTCTATC
1208121 GTTTCTTGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (46 bp):
TTAAATCTGCTCTGCTATTGCTGAAAAATCCCTAATTTCTATCATT
Found at i:1212658 original size:21 final size:21
Alignment explanation
Indices: 1212609--1212658 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1212599 TACCAGTCTT
*
1212609 CTTCTAACTGCCTCATTGTTG
1 CTTCTAATTGCCTCATTGTTG
* *
1212630 CTTCTAATTGCTTCATTTTTG
1 CTTCTAATTGCCTCATTGTTG
1212651 CTTCTAAT
1 CTTCTAAT
1212659 ACCAGTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.16, C:0.24, G:0.10, T:0.50
Consensus pattern (21 bp):
CTTCTAATTGCCTCATTGTTG
Found at i:1215130 original size:21 final size:21
Alignment explanation
Indices: 1215081--1215130 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1215071 TTCAAGTCTT
* *
1215081 CTTCTAACTGCCTCCTTGTTG
1 CTTCTAATTGCCTCATTGTTG
* *
1215102 CTTCTAATTGCTTCATTTTTG
1 CTTCTAATTGCCTCATTGTTG
1215123 CTTCTAAT
1 CTTCTAAT
1215131 ACCAGTTGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.14, C:0.26, G:0.10, T:0.50
Consensus pattern (21 bp):
CTTCTAATTGCCTCATTGTTG
Found at i:1216240 original size:21 final size:21
Alignment explanation
Indices: 1216214--1216256 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1216204 ATTGTTTTAG
1216214 GTGCTGAAGGAAGACACTGGA
1 GTGCTGAAGGAAGACACTGGA
1216235 GTGCTGAAGGAAGACACTGGA
1 GTGCTGAAGGAAGACACTGGA
1216256 G
1 G
1216257 ATGGATGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.40, T:0.14
Consensus pattern (21 bp):
GTGCTGAAGGAAGACACTGGA
Found at i:1218481 original size:16 final size:16
Alignment explanation
Indices: 1218460--1218508 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
1218450 AACTATAATT
1218460 TATTAAATAAAATTTA
1 TATTAAATAAAATTTA
*
1218476 TATTAATTAAAATATTA
1 TATTAAATAAAAT-TTA
*
1218493 TTTTAAA-AAATATTTA
1 TATTAAATAAA-ATTTA
1218509 ATTTCAAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 18 0.64
17 10 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTAAATAAAATTTA
Found at i:1221147 original size:26 final size:26
Alignment explanation
Indices: 1221118--1221178 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
1221108 ATAAAACTTA
1221118 AACCCTGAACCCTAAATCCAAACTCG-
1 AACCCT-AACCCTAAATCCAAACTCGT
* * *
1221144 AACCCATAATCTTAAATCTAAACTCGT
1 AACCC-TAACCCTAAATCCAAACTCGT
1221171 AACCCTAA
1 AACCCTAA
1221179 ATCTTTGAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 24 0.80
27 6 0.20
ACGTcount: A:0.41, C:0.33, G:0.05, T:0.21
Consensus pattern (26 bp):
AACCCTAACCCTAAATCCAAACTCGT
Found at i:1221191 original size:15 final size:15
Alignment explanation
Indices: 1221171--1221211 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1221161 CTAAACTCGT
*
1221171 AACCCTAAATCTTTG
1 AACCCTAAATCATTG
*
1221186 AACCCTAAACCATTG
1 AACCCTAAATCATTG
*
1221201 AACCTTAAATC
1 AACCCTAAATC
1221212 CCGAATCTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.39, C:0.29, G:0.05, T:0.27
Consensus pattern (15 bp):
AACCCTAAATCATTG
Found at i:1221308 original size:38 final size:38
Alignment explanation
Indices: 1221263--1221340 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
1221253 TTGAACCATG
1221263 AATCTTAAATTTTGAAACCAAACCCTGAATCTCAAAAA
1 AATCTTAAATTTTGAAACCAAACCCTGAATCTCAAAAA
*
1221301 AATCTTAAATTTTGAAACTAAACCCTGAATCTCAAAAA
1 AATCTTAAATTTTGAAACCAAACCCTGAATCTCAAAAA
1221339 AA
1 AA
1221341 ATTAACTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.27
Consensus pattern (38 bp):
AATCTTAAATTTTGAAACCAAACCCTGAATCTCAAAAA
Found at i:1221354 original size:37 final size:38
Alignment explanation
Indices: 1221267--1221354 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 38
1221257 ACCATGAATC
* *
1221267 TTAAATTTTGAAACCAAACCCTGAATCTCAAAAAAATC
1 TTAAATTATGAAACCAAACCCTGAATCTCAAAAAAATA
* *
1221305 TTAAATTTTGAAACTAAACCCTGAATCTCAAAAAAA-A
1 TTAAATTATGAAACCAAACCCTGAATCTCAAAAAAATA
*
1221342 TTAACTTATGAAA
1 TTAAATTATGAAA
1221355 AAAAAATGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
37 11 0.24
38 35 0.76
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (38 bp):
TTAAATTATGAAACCAAACCCTGAATCTCAAAAAAATA
Found at i:1225293 original size:9 final size:9
Alignment explanation
Indices: 1225279--1225346 Score: 75
Period size: 9 Copynumber: 7.6 Consensus size: 9
1225269 ATAAGTATAA
1225279 AATTAACCG
1 AATTAACCG
1225288 AATTAACCG
1 AATTAACCG
*
1225297 AATTAATCG
1 AATTAACCG
*
1225306 AATT-ACCTA
1 AATTAACC-G
*
1225315 AATTACCCG
1 AATTAACCG
*
1225324 AATTAACCA
1 AATTAACCG
*
1225333 AATTAAACG
1 AATTAACCG
1225342 AATTA
1 AATTA
1225347 TTTGTATAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
8 2 0.04
9 44 0.92
10 2 0.04
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:1225302 original size:18 final size:18
Alignment explanation
Indices: 1225278--1225346 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
1225268 AATAAGTATA
1225278 AAATTAACCGAATTAACC
1 AAATTAACCGAATTAACC
* *
1225296 GAATTAATCGAATT-ACC
1 AAATTAACCGAATTAACC
*
1225313 TAAATTACCCGAATTAACC
1 -AAATTAACCGAATTAACC
*
1225332 AAATTAAACGAATTA
1 AAATTAACCGAATTA
1225347 TTTGTATAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
17 3 0.07
18 36 0.86
19 3 0.07
ACGTcount: A:0.48, C:0.19, G:0.07, T:0.26
Consensus pattern (18 bp):
AAATTAACCGAATTAACC
Found at i:1225325 original size:36 final size:36
Alignment explanation
Indices: 1225278--1225346 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
1225268 AATAAGTATA
* *
1225278 AAATTAACCGAATTAACCGAATTAATCGAATTACCT
1 AAATTAACCGAATTAACCAAATTAAACGAATTACCT
*
1225314 AAATTACCCGAATTAACCAAATTAAACGAATTA
1 AAATTAACCGAATTAACCAAATTAAACGAATTA
1225347 TTTGTATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.48, C:0.19, G:0.07, T:0.26
Consensus pattern (36 bp):
AAATTAACCGAATTAACCAAATTAAACGAATTACCT
Found at i:1226188 original size:4 final size:4
Alignment explanation
Indices: 1226181--1226218 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
1226171 ATAAATAAAA
*
1226181 ATGT ATGT ATGT ATGT ATGC ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1226219 ATATACGGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.03, G:0.24, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:1229021 original size:22 final size:22
Alignment explanation
Indices: 1228995--1229038 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1228985 CACGTAAATG
1228995 AAAGTTATTGCATAATAACATT
1 AAAGTTATTGCATAATAACATT
1229017 AAAGTTATTGCATAATAACATT
1 AAAGTTATTGCATAATAACATT
1229039 TCTTAGTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (22 bp):
AAAGTTATTGCATAATAACATT
Found at i:1229912 original size:17 final size:16
Alignment explanation
Indices: 1229890--1229922 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1229880 TCAAATTAAA
1229890 ATTATATTAATTAAAAT
1 ATTATATTAA-TAAAAT
1229907 ATTATATTAATAAAAT
1 ATTATATTAATAAAAT
1229923 GTTTAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTATATTAATAAAAT
Found at i:1230004 original size:16 final size:14
Alignment explanation
Indices: 1229963--1230014 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
1229953 ATAATATCTT
1229963 ATTAAATAAA-AAA
1 ATTAAATAAATAAA
*
1229976 ATTCAATAAATAAA
1 ATTAAATAAATAAA
*
1229990 ATTAAATATATATAA
1 ATTAAATAAATA-AA
*
1230005 ATTTAATAAA
1 ATTAAATAAA
1230015 ATATTAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 9 0.28
14 13 0.41
15 10 0.31
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
ATTAAATAAATAAA
Found at i:1230018 original size:16 final size:15
Alignment explanation
Indices: 1229963--1230024 Score: 58
Period size: 14 Copynumber: 4.2 Consensus size: 15
1229953 ATAATATCTT
1229963 ATTAAATAAA-A-AA
1 ATTAAATAAATATAA
*
1229976 ATTCAATAAATA-AA
1 ATTAAATAAATATAA
*
1229990 ATTAAATATATATAA
1 ATTAAATAAATATAA
*
1230005 ATTTAATAAAATATTAA
1 ATTAAAT-AAATA-TAA
1230022 ATT
1 ATT
1230025 CCCTAATTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 9 0.22
14 13 0.32
15 8 0.20
16 4 0.10
17 6 0.15
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTAAATAAATATAA
Found at i:1230812 original size:105 final size:105
Alignment explanation
Indices: 1230669--1230933 Score: 431
Period size: 105 Copynumber: 2.5 Consensus size: 105
1230659 TATATTTTTA
* * * * *
1230669 AAATAAAATAAAAAAATAAAAAGTTTAACACATTGGGTCAAGCTGAGATGACTATGTTGGAAGAG
1 AAATAAAAT-AAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTTAGAAGAA
* *
1230734 CAAATACTTAGCTTCGTATGAAGGGATTACATTCGATCATC
65 CAAATACTTAACTTCGTACGAAGGGATTACATTCGATCATC
*
1230775 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGACATGGCTATGTTAGAAGAAC
1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTTAGAAGAAC
* *
1230840 AAATACTTAACTTCGTCCGAAGGGATTACATTTGATCATC
66 AAATACTTAACTTCGTACGAAGGGATTACATTCGATCATC
1230880 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTAT
1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTAT
1230934 TGTAACGCCC
Statistics
Matches: 148, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
105 139 0.94
106 9 0.06
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.25
Consensus pattern (105 bp):
AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTTAGAAGAAC
AAATACTTAACTTCGTACGAAGGGATTACATTCGATCATC
Found at i:1231303 original size:26 final size:26
Alignment explanation
Indices: 1231267--1231375 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
1231257 TGATACAAAT
*
1231267 TGATAATAGGTTAGGTAAATATTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
1231293 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
1231319 TGATAAT-GGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
1231344 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
1231370 TGATAA
1 TGATAA
1231376 GAATTTCATG
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
25 24 0.30
26 56 0.70
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:1231332 original size:51 final size:52
Alignment explanation
Indices: 1231267--1231375 Score: 175
Period size: 51 Copynumber: 2.1 Consensus size: 52
1231257 TGATACAAAT
1231267 TGATAATAGGTTAGGTAAATATTCCATGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATATTCCATGATAATAGGTTAGGTAAATGTTCCA
* * * *
1231319 TGATAAT-GGTTAGGTAAATGTTTCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATATTCCATGATAATAGGTTAGGTAAATGTTCCA
1231370 TGATAA
1 TGATAA
1231376 GAATTTCATG
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
51 46 0.87
52 7 0.13
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.37
Consensus pattern (52 bp):
TGATAATAGGTTAGGTAAATATTCCATGATAATAGGTTAGGTAAATGTTCCA
Found at i:1233451 original size:26 final size:26
Alignment explanation
Indices: 1233392--1233526 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
1233382 TGATACAAAT
1233392 TGATAATAGGTTAGGTAAATGTT-CA
1 TGATAATAGGTTAGGTAAATGTTCCA
1233417 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
1233443 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
1233469 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
1233495 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
1233521 TGATAA
1 TGATAA
1233527 GAATTTCATG
Statistics
Matches: 107, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
25 23 0.21
26 84 0.79
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:1235038 original size:26 final size:26
Alignment explanation
Indices: 1235009--1235061 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1234999 TTTACAGTTT
1235009 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
1235035 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
1235061 T
1 T
1235062 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Done.