Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 4 of 253
Found at i:1006564 original size:18 final size:18
Alignment explanation
Indices: 1006511--1006619 Score: 150
Period size: 18 Copynumber: 6.1 Consensus size: 18
1006501 AATCTTACAT
1006511 ATATGATATGCAATCTTAG
1 ATATGAT-TGCAATCTTAG
*
1006530 ATATGA-TACAATCTTAG
1 ATATGATTGCAATCTTAG
*
1006547 ATATGATTGCAGTCTTAG
1 ATATGATTGCAATCTTAG
*
1006565 ATATGA-TACAATCTTAG
1 ATATGATTGCAATCTTAG
1006582 ATATGATTGCAATCTTAG
1 ATATGATTGCAATCTTAG
*
1006600 ATATGATATACAATCTTAG
1 ATATGAT-TGCAATCTTAG
1006619 A
1 A
1006620 AGATATGATT
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
17 31 0.39
18 32 0.40
19 17 0.21
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (18 bp):
ATATGATTGCAATCTTAG
Found at i:1006567 original size:35 final size:35
Alignment explanation
Indices: 1006511--1006619 Score: 182
Period size: 35 Copynumber: 3.0 Consensus size: 35
1006501 AATCTTACAT
1006511 ATATGATATGCAATCTTAGATATGATACAATCTTAG
1 ATATGAT-TGCAATCTTAGATATGATACAATCTTAG
*
1006547 ATATGATTGCAGTCTTAGATATGATACAATCTTAG
1 ATATGATTGCAATCTTAGATATGATACAATCTTAG
1006582 ATATGATTGCAATCTTAGATATGATATACAATCTTAG
1 ATATGATTGCAATCTTAGATATG--ATACAATCTTAG
1006619 A
1 A
1006620 AGATATGATT
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
35 49 0.71
36 7 0.10
37 13 0.19
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (35 bp):
ATATGATTGCAATCTTAGATATGATACAATCTTAG
Found at i:1008940 original size:22 final size:23
Alignment explanation
Indices: 1008909--1008951 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1008899 GGTTTTGCCA
1008909 ATTTAGGGTTCTGATTGTTTTTT
1 ATTTAGGGTTCTGATTGTTTTTT
* *
1008932 ATTT-GGGTTTTGGTTGTTTT
1 ATTTAGGGTTCTGATTGTTTT
1008952 ATGACCAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.09, C:0.02, G:0.26, T:0.63
Consensus pattern (23 bp):
ATTTAGGGTTCTGATTGTTTTTT
Found at i:1010241 original size:25 final size:26
Alignment explanation
Indices: 1010204--1010255 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
1010194 TCAAACATGC
1010204 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* * *
1010230 ATTTCGGT-AATTTATCTCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
1010255 A
1 A
1010256 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:1011770 original size:26 final size:25
Alignment explanation
Indices: 1011731--1011811 Score: 135
Period size: 26 Copynumber: 3.2 Consensus size: 25
1011721 AGACATATTC
1011731 ATCATGAACATTTACCTAACCCATT
1 ATCATGAACATTTACCTAACCCATT
1011756 ATCATGAAACATTTACCTAACCCATT
1 ATCATG-AACATTTACCTAACCCATT
*
1011782 ATCATGGAACATTTACCTAACCTATT
1 ATCAT-GAACATTTACCTAACCCATT
1011808 ATCA
1 ATCA
1011812 ATTTGTATCA
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
25 6 0.11
26 46 0.87
27 1 0.02
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (25 bp):
ATCATGAACATTTACCTAACCCATT
Found at i:1020204 original size:21 final size:20
Alignment explanation
Indices: 1020166--1020208 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1020156 ATCCCAATCC
1020166 CATGCATCAGATAATAACAA
1 CATGCATCAGATAATAACAA
1020186 CATGCATGCAG-TAAATAACAA
1 CATGCAT-CAGAT-AATAACAA
1020207 CA
1 CA
1020209 GCAAACATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.49, C:0.21, G:0.12, T:0.19
Consensus pattern (20 bp):
CATGCATCAGATAATAACAA
Found at i:1020255 original size:24 final size:25
Alignment explanation
Indices: 1020219--1020268 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1020209 GCAAACATGC
1020219 ATTTAGGTCAATTTAACCCTAGGGT
1 ATTTAGGTCAATTTAACCCTAGGGT
* * *
1020244 ATTTCGGT-AATTTATCTCTAGGGT
1 ATTTAGGTCAATTTAACCCTAGGGT
1020268 A
1 A
1020269 AAACTGTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (25 bp):
ATTTAGGTCAATTTAACCCTAGGGT
Found at i:1021780 original size:26 final size:26
Alignment explanation
Indices: 1021751--1021834 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
1021741 TATGAAATTC
1021751 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
1021777 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
1021803 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
1021829 TTATCA
1 TTATCA
1021835 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:1027125 original size:26 final size:26
Alignment explanation
Indices: 1027094--1027201 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
1027084 TGAAATGCCC
*
1027094 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
1027120 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
1027146 ACCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
1027172 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
1027198 ATCA
1 ATCA
1027202 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:1027820 original size:16 final size:16
Alignment explanation
Indices: 1027799--1027834 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1027789 TGAATTACTG
1027799 ATTACAACTCTATTCA
1 ATTACAACTCTATTCA
* *
1027815 ATTACAGCTCTATTCC
1 ATTACAACTCTATTCA
1027831 ATTA
1 ATTA
1027835 TAGTGAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTACAACTCTATTCA
Found at i:1050338 original size:131 final size:130
Alignment explanation
Indices: 1050019--1050349 Score: 353
Period size: 130 Copynumber: 2.5 Consensus size: 130
1050009 ATGTTTGGCG
* * * * * *
1050019 ATTCGCGGAATCGTACCCTAACGTACTGGGTTGCAATTTCGCATTTGCTCAAAATAATCGAATAT
1 ATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCGAATAT
* * * * * * **
1050084 CACTTCAAAATTTCACTTATGTCTTTTAAAATCCCTTAAACGAAGGTGATGTGCGATATTTGGCA
66 CCCTTCAAAATTTCACTCAGGTCTTTAAAAATCCCTTAAACGAAGGTAATCTGCGATATTTAACA
* * * * * *
1050149 ATTCGTGGAATTGTGCCCTAACGTGTTGGGTTGCAATTGCTCGTTTGCTT-AAAGCAATCAAATA
1 ATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCTCGTTTG-TTCAAAACAATCGAATA
* *
1050213 TCCCTTCAAAATTTCACTCAGGTCTTCTAAAAATCCTTTGAAACGAAGGTAATACT-CGATGTTT
65 TCCCTTCAAAATTTCACTCAGGTCTT-TAAAAATCCCTT-AAACGAAGGTAAT-CTGCGATATTT
*
1050277 AATA
127 AACA
* * **
1050281 ATTCG-GGAATCATGCCCTATCGTGCTGGGTTGTGATTTCTCGTTTGTTCAAAACAATCGAATAT
1 ATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCGAATAT
*
1050345 TCCTT
66 CCCTT
1050350 TAGGTTTTCA
Statistics
Matches: 163, Mismatches: 33, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
130 75 0.46
131 62 0.38
132 25 0.15
133 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (130 bp):
ATTCGCGGAATCGTGCCCTAACGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAACAATCGAATAT
CCCTTCAAAATTTCACTCAGGTCTTTAAAAATCCCTTAAACGAAGGTAATCTGCGATATTTAACA
Found at i:1056345 original size:21 final size:21
Alignment explanation
Indices: 1056321--1056362 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1056311 ATATTTACTT
1056321 ATTATATAAGTA-TATTATTAA
1 ATTATAT-AGTATTATTATTAA
*
1056342 ATTATATATTATTATTATTAA
1 ATTATATAGTATTATTATTAA
1056363 GTAAAAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTATATAGTATTATTATTAA
Found at i:1056534 original size:10 final size:10
Alignment explanation
Indices: 1056519--1056550 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
1056509 TTAATGAAAT
1056519 AAAGAAAGAA
1 AAAGAAAGAA
1056529 AAAGAATAGAA
1 AAAGAA-AGAA
1056540 AAAGAAAGAA
1 AAAGAAAGAA
1056550 A
1 A
1056551 GGATGAAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:1058304 original size:2 final size:2
Alignment explanation
Indices: 1058261--1058285 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1058251 ACAGTTTTTA
1058261 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1058286 AGATTTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1061663 original size:68 final size:68
Alignment explanation
Indices: 1061544--1061676 Score: 187
Period size: 68 Copynumber: 2.0 Consensus size: 68
1061534 CATGTTTAAA
* *
1061544 ATGTCTATCTTAGTCATGTTATCGAAATTTAATATTTTGGTTACGCCTCCATTAAATCACTAATG
1 ATGTCTATCTTAGTCATGTTATCCAAATTTAATATTTTGGTCACGCCTCCATTAAATCACTAATG
1061609 CTG
66 CTG
* * ** *
1061612 ATGTCTATTTTAGTCATGTTA-CCAAATTTTAATATTTTGGTCATGTTTCCATTAAATCATTAAT
1 ATGTCTATCTTAGTCATGTTATCCAAA-TTTAATATTTTGGTCACGCCTCCATTAAATCACTAAT
1061676 G
65 G
1061677 GTGACCTTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
67 4 0.07
68 53 0.93
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (68 bp):
ATGTCTATCTTAGTCATGTTATCCAAATTTAATATTTTGGTCACGCCTCCATTAAATCACTAATG
CTG
Found at i:1063209 original size:19 final size:20
Alignment explanation
Indices: 1063168--1063208 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
1063158 TATAACATAT
1063168 AATTTACAACAAAAAATTAA
1 AATTTACAACAAAAAATTAA
1063188 AATTTA-AACAATAAAATTAA
1 AATTTACAACAA-AAAATTAA
1063208 A
1 A
1063209 TATGTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (20 bp):
AATTTACAACAAAAAATTAA
Found at i:1064703 original size:13 final size:14
Alignment explanation
Indices: 1064687--1064728 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
1064677 TTTCAATTTT
1064687 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
1064700 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
1064715 ATTTTAAATAATAT
1 ATTTT-AATAATAT
1064729 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:1064713 original size:16 final size:16
Alignment explanation
Indices: 1064691--1064727 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1064681 AATTTTATTT
1064691 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
1064708 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
1064723 TAATA
1 TAATA
1064728 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:1064780 original size:15 final size:15
Alignment explanation
Indices: 1064760--1064816 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
1064750 AATCAATATT
1064760 AATATTTTAATAATA
1 AATATTTTAATAATA
*
1064775 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
1064794 AATATATTAATAATA
1 AATATTTTAATAATA
1064809 AATATTTT
1 AATATTTT
1064817 GTAGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:1066788 original size:20 final size:21
Alignment explanation
Indices: 1066758--1066799 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
1066748 TATAACATAT
1066758 AATTTACAACAATAAAATTAA
1 AATTTACAACAATAAAATTAA
1066779 AATTTA-AACAATAAAATTAA
1 AATTTACAACAATAAAATTAA
1066799 A
1 A
1066800 TATGTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
AATTTACAACAATAAAATTAA
Found at i:1068798 original size:69 final size:68
Alignment explanation
Indices: 1068678--1068810 Score: 187
Period size: 69 Copynumber: 1.9 Consensus size: 68
1068668 ATGTTTAAAA
* * *
1068678 ATGTCTATCTTAGTCATGTTATCGAAATTTAATATTTTGGCCACGCCTCCGTTAAATCATTAATG
1 ATGTCTATCTTAGTCACGTTATCCAAATTTAATATTTTGGCCACGCCTCCGTTAAATCACTAATG
1068743 GTG
66 GTG
* * *
1068746 ATGTCTATTTTAGTCAACGTTA-CCAAATTTTAATATTTTGGTCACGCTTCCGTTAAATCACTAA
1 ATGTCTATCTTAGTC-ACGTTATCCAAA-TTTAATATTTTGGCCACGCCTCCGTTAAATCACTAA
1068810 T
64 T
1068811 CACTAATGGT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
68 18 0.32
69 39 0.68
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (68 bp):
ATGTCTATCTTAGTCACGTTATCCAAATTTAATATTTTGGCCACGCCTCCGTTAAATCACTAATG
GTG
Found at i:1069197 original size:29 final size:29
Alignment explanation
Indices: 1069155--1069212 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1069145 AACCCTATCC
1069155 TTAAAAATGCCACCGATGCCATTATTGAA
1 TTAAAAATGCCACCGATGCCATTATTGAA
1069184 TTAAAAATGCCACCGATGCCATTATTGAA
1 TTAAAAATGCCACCGATGCCATTATTGAA
1069213 GCAACAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (29 bp):
TTAAAAATGCCACCGATGCCATTATTGAA
Found at i:1070007 original size:20 final size:20
Alignment explanation
Indices: 1069966--1070007 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1069956 TATAATTTAC
*
1069966 AACAATAAAATTAAAATTTA
1 AACAATAAAATTAAAATGTA
1069986 AACAATAAAA-TAAATATGTA
1 AACAATAAAATTAAA-ATGTA
1070006 AA
1 AA
1070008 AAAAATCGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (20 bp):
AACAATAAAATTAAAATGTA
Found at i:1071386 original size:68 final size:68
Alignment explanation
Indices: 1071265--1071402 Score: 172
Period size: 68 Copynumber: 2.0 Consensus size: 68
1071255 ATGTTTAAAA
* * * *
1071265 ATGTTTATCTTAGTCATGTTACTGAAATTTAATATTTTGGCCACGCCTTCGTTAAATCACTAATG
1 ATGTCTATCTTAGTCACGTTACTCAAATTTAATATTTTAGCCACGCCTTCGTTAAATCACTAATG
1071330 GTG
66 GTG
* * * *
1071333 ATGTCTATTTTAGTCACGTTAC-CAAATTTTAATATTTTAGTCACG-TTTCCGTTAAATTACTAA
1 ATGTCTATCTTAGTCACGTTACTCAAA-TTTAATATTTTAGCCACGCCTT-CGTTAAATCACTAA
1071396 TGGTG
64 TGGTG
1071401 AT
1 AT
1071403 ATTTTTTAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
67 5 0.08
68 55 0.92
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (68 bp):
ATGTCTATCTTAGTCACGTTACTCAAATTTAATATTTTAGCCACGCCTTCGTTAAATCACTAATG
GTG
Found at i:1073383 original size:12 final size:12
Alignment explanation
Indices: 1073353--1073385 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1073343 TATATATTTT
1073353 AAAATT-ATATA
1 AAAATTAATATA
1073364 AAAA-TAATATA
1 AAAATTAATATA
1073375 AAAATTAATAT
1 AAAATTAATAT
1073386 GGGCGGGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:1074586 original size:17 final size:17
Alignment explanation
Indices: 1074564--1074597 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1074554 ATCCACTAAT
*
1074564 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1074581 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1074598 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1079216 original size:17 final size:17
Alignment explanation
Indices: 1079194--1079227 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1079184 ATCCACTAAT
*
1079194 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1079211 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1079228 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1079700 original size:13 final size:13
Alignment explanation
Indices: 1079682--1079706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1079672 CTCTAATCTT
1079682 TGTTTTGTGATTG
1 TGTTTTGTGATTG
1079695 TGTTTTGTGATT
1 TGTTTTGTGATT
1079707 TGGGCGAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.28, T:0.64
Consensus pattern (13 bp):
TGTTTTGTGATTG
Found at i:1082181 original size:20 final size:21
Alignment explanation
Indices: 1082151--1082192 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
1082141 TATAACATAT
1082151 AATTTACAACAATAAAATTAA
1 AATTTACAACAATAAAATTAA
1082172 AATTTA-AACAATAAAATTAA
1 AATTTACAACAATAAAATTAA
1082192 A
1 A
1082193 TATGTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
AATTTACAACAATAAAATTAA
Found at i:1083592 original size:68 final size:68
Alignment explanation
Indices: 1083471--1083607 Score: 170
Period size: 68 Copynumber: 2.0 Consensus size: 68
1083461 ATGTTTAAAA
* * * *
1083471 ATGTTTATCTTAGTCATGTTACTGAAATTTAATATTTTGGCCACGCCTTCGTTAAATCACTAATG
1 ATGTCTATCTTAGTCACGTTACTCAAATTTAATATTTTAGCCACGCCTTCGTTAAATCACTAATG
1083536 GTG
66 GTG
* * * *
1083539 ATGTCTATTTTAGTCACGTTAC-CAAATTTTAATATTTTAGTCACG-TTTCCGTTAAATTACTAA
1 ATGTCTATCTTAGTCACGTTACTCAAA-TTTAATATTTTAGCCACGCCTT-CGTTAAATCACTAA
1083602 TGGTG
64 TGGTG
1083607 A
1 A
1083608 CATTTTTTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
67 5 0.08
68 54 0.92
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (68 bp):
ATGTCTATCTTAGTCACGTTACTCAAATTTAATATTTTAGCCACGCCTTCGTTAAATCACTAATG
GTG
Found at i:1088057 original size:15 final size:16
Alignment explanation
Indices: 1088008--1088050 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1087998 TTTTTATGAA
*
1088008 ATTTTTATAATTTTACT
1 ATTTTTATAA-TTTATT
1088025 -TTTTTATAATTTATT
1 ATTTTTATAATTTATT
1088040 ATTTTTA-AATT
1 ATTTTTATAATT
1088051 ATTTATTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTTATAATTTATT
Found at i:1089682 original size:19 final size:19
Alignment explanation
Indices: 1089651--1089700 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1089641 TAAAAAGTGC
*
1089651 AAGTGCATACTGGCACACG
1 AAGTGCATCCTGGCACACG
* *
1089670 AAGTGTATCCTGGCACATG
1 AAGTGCATCCTGGCACACG
*
1089689 AGGTGCATCCTG
1 AAGTGCATCCTG
1089701 ACGCATAAGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (19 bp):
AAGTGCATCCTGGCACACG
Found at i:1091372 original size:27 final size:26
Alignment explanation
Indices: 1091312--1091373 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
1091302 ATTTTATTTT
*
1091312 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAAAATTAAG
* * *
1091338 ATAATTATTAGGATTATTAAAATTTAGG
1 AT-TTTATTAGGATAATTAAAA-TTAAG
1091366 ATTTTATT
1 ATTTTATT
1091374 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 21 0.72
28 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.48
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAAAATTAAG
Found at i:1095163 original size:23 final size:23
Alignment explanation
Indices: 1095137--1095181 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1095127 CCCAATCTTT
*
1095137 CTTTTTTTTTATTTATTATTTTC
1 CTTTCTTTTTATTTATTATTTTC
*
1095160 CTTTCTTTTTATTTTTTATTTT
1 CTTTCTTTTTATTTATTATTTT
1095182 TTATTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (23 bp):
CTTTCTTTTTATTTATTATTTTC
Found at i:1095175 original size:7 final size:7
Alignment explanation
Indices: 1095141--1095204 Score: 58
Period size: 7 Copynumber: 8.6 Consensus size: 7
1095131 ATCTTTCTTT
1095141 TTTTTTA
1 TTTTTTA
*
1095148 TTTATTA
1 TTTTTTA
1095155 TTTTCCTT-
1 TTTT--TTA
1095163 TCTTTTTA
1 T-TTTTTA
1095171 TTTTTTA
1 TTTTTTA
1095178 TTTTTTA
1 TTTTTTA
*
1095185 TTTTATTT
1 TTTT-TTA
1095193 TTATTTTA
1 TT-TTTTA
1095201 TTTT
1 TTTT
1095205 AGTTAAATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
7 30 0.64
8 10 0.21
9 7 0.15
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTA
Found at i:1095195 original size:11 final size:11
Alignment explanation
Indices: 1095173--1095204 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
1095163 TCTTTTTATT
1095173 TTTTATTTTTTA
1 TTTTA-TTTTTA
1095185 TTTTATTTTTA
1 TTTTATTTTTA
1095196 TTTTATTTT
1 TTTTATTTT
1095205 AGTTAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:1095199 original size:23 final size:22
Alignment explanation
Indices: 1095138--1095204 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 22
1095128 CCAATCTTTC
*
1095138 TTTTTTTTTA-TTTATTATTTTCC
1 TTTTTTTTTATTTTATT-TTTT-A
*
1095161 TTTCTTTTTATTTTTTATTTTTTA
1 TTT-TTTTT-TATTTTATTTTTTA
1095185 TTTTATTTTTATTTTATTTT
1 TTTT-TTTTTATTTTATTTT
1095205 AGTTAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 14 0.38
24 12 0.32
25 5 0.14
26 6 0.16
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTTTTTATTTTATTTTTTA
Found at i:1095200 original size:30 final size:30
Alignment explanation
Indices: 1095132--1095204 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
1095122 GGCAACCCAA
* *
1095132 TCTTTCTTTTTTTTTATTTATTATTTTCCTT
1 TCTTT-TTATTTTTTATTTATTATTTTCATT
*
1095163 TCTTTTTATTTTTTATTTTTTATTTT-ATT
1 TCTTTTTATTTTTTATTTATTATTTTCATT
*
1095192 TTTATTTTATTTT
1 TCT-TTTTATTTT
1095205 AGTTAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 4 0.11
30 28 0.76
31 5 0.14
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (30 bp):
TCTTTTTATTTTTTATTTATTATTTTCATT
Found at i:1096537 original size:15 final size:14
Alignment explanation
Indices: 1096515--1096560 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
1096505 AATAAAATTT
1096515 AAAAAAAAAGAAAA
1 AAAAAAAAAGAAAA
*
1096529 AATAAAAAAATAAAA
1 AA-AAAAAAAGAAAA
*
1096544 AAAAGAAGAAGAAAA
1 AAAA-AAAAAGAAAA
1096559 AA
1 AA
1096561 GTAAGTACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.87, C:0.00, G:0.09, T:0.04
Consensus pattern (14 bp):
AAAAAAAAAGAAAA
Found at i:1107074 original size:20 final size:20
Alignment explanation
Indices: 1107037--1107076 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1107027 GAGACGTTGG
*
1107037 AATGACTTCAATTCTCAAGA
1 AATGACTTCAAATCTCAAGA
1107057 AATGA-TTCAAATCATCAAGA
1 AATGACTTCAAATC-TCAAGA
1107077 TCTTTAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.28
Consensus pattern (20 bp):
AATGACTTCAAATCTCAAGA
Found at i:1122960 original size:16 final size:18
Alignment explanation
Indices: 1122925--1122961 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1122915 ATGTAATCAG
1122925 GAAAAGAAAAGTAAACAA
1 GAAAAGAAAAGTAAACAA
*
1122943 GAAAA-AAAAG-AAAGAA
1 GAAAAGAAAAGTAAACAA
1122959 GAA
1 GAA
1122962 CCGATTCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 5 0.28
18 5 0.28
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.03
Consensus pattern (18 bp):
GAAAAGAAAAGTAAACAA
Found at i:1134559 original size:7 final size:7
Alignment explanation
Indices: 1134531--1134574 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
1134521 ATTTAAAATT
1134531 TATAAAA
1 TATAAAA
1134538 TATTAAAA
1 TA-TAAAA
1134546 GTATAAAA
1 -TATAAAA
*
1134554 TATAAAT
1 TATAAAA
*
1134561 TATAAAT
1 TATAAAA
1134568 TATAAAA
1 TATAAAA
1134575 AAGAGCTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 21 0.64
8 10 0.30
9 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (7 bp):
TATAAAA
Found at i:1136507 original size:11 final size:11
Alignment explanation
Indices: 1136491--1136544 Score: 83
Period size: 11 Copynumber: 5.0 Consensus size: 11
1136481 TAGAATATAC
1136491 CCCATACCTTG
1 CCCATACCTTG
1136502 CCCATACCTTG
1 CCCATACCTTG
*
1136513 CCCATACCTTT
1 CCCATACCTTG
*
1136524 CCCATACC-TA
1 CCCATACCTTG
1136534 CCCATACCTTG
1 CCCATACCTTG
1136545 GAAATGTCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
10 9 0.23
11 30 0.77
ACGTcount: A:0.20, C:0.46, G:0.06, T:0.28
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:1137104 original size:18 final size:18
Alignment explanation
Indices: 1137083--1137133 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
1137073 CATTTACGGT
1137083 ACTATTCACGTATACGAC
1 ACTATTCACGTATACGAC
**
1137101 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGAC
*
1137119 ACTGTTCACGTATAC
1 ACTATTCACGTATAC
1137134 AGTAGTTGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.31
Consensus pattern (18 bp):
ACTATTCACGTATACGAC
Found at i:1141190 original size:11 final size:11
Alignment explanation
Indices: 1141170--1141223 Score: 74
Period size: 11 Copynumber: 5.0 Consensus size: 11
1141160 TAGAATATAC
*
1141170 CCCATTCCTTG
1 CCCATACCTTG
1141181 CCCATACCTTG
1 CCCATACCTTG
*
1141192 CCCATACCTTT
1 CCCATACCTTG
*
1141203 CCCATACC-TA
1 CCCATACCTTG
1141213 CCCATACCTTG
1 CCCATACCTTG
1141224 GAAAGGTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
10 9 0.24
11 29 0.76
ACGTcount: A:0.19, C:0.46, G:0.06, T:0.30
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:1151554 original size:23 final size:22
Alignment explanation
Indices: 1151509--1151554 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
1151499 CAACCAATCC
*
1151509 AATTCAGCATATTTTCAAGATA
1 AATTCAGCATATTTTCAAAATA
1151531 AATTCATGCATATTTAT-AAAATA
1 AATTCA-GCATATTT-TCAAAATA
1151554 A
1 A
1151555 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (22 bp):
AATTCAGCATATTTTCAAAATA
Found at i:1153138 original size:17 final size:17
Alignment explanation
Indices: 1153116--1153149 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1153106 TTCATTCTGA
*
1153116 CATTATCTCACAAAATT
1 CATTATATCACAAAATT
*
1153133 CATTATATCTCAAAATT
1 CATTATATCACAAAATT
1153150 TACAAATCCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (17 bp):
CATTATATCACAAAATT
Found at i:1164463 original size:30 final size:31
Alignment explanation
Indices: 1164427--1164495 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
1164417 GGTTTCATTT
* *
1164427 CAGTCACTCAAC-TTTTGAAAAA-TAACAAAA
1 CAGTCACT-AACGTTATAAAAAAGTAACAAAA
*
1164457 CAGTCACTAACGTTATAAAAAAGTGACAAAA
1 CAGTCACTAACGTTATAAAAAAGTAACAAAA
1164488 CAGTCACT
1 CAGTCACT
1164496 GACTAACAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 16 0.47
31 15 0.44
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.22
Consensus pattern (31 bp):
CAGTCACTAACGTTATAAAAAAGTAACAAAA
Found at i:1164553 original size:21 final size:21
Alignment explanation
Indices: 1164529--1164569 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1164519 TTAACAGAAC
1164529 AGCTAATGTGGCAAGTTAACT
1 AGCTAATGTGGCAAGTTAACT
* *
1164550 AGCTGATGTGGCCAGTTAAC
1 AGCTAATGTGGCAAGTTAAC
1164570 ATGCCACGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (21 bp):
AGCTAATGTGGCAAGTTAACT
Found at i:1164634 original size:3 final size:3
Alignment explanation
Indices: 1164626--1164665 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
1164616 TTTAACAGAG
*
1164626 GAA GAA GAA GAA GAA AAA GAA GAA GAA GAAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA GAA GAA
1164666 CAGTTACTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1165569 original size:3 final size:3
Alignment explanation
Indices: 1165561--1165713 Score: 272
Period size: 3 Copynumber: 51.3 Consensus size: 3
1165551 GCCAGTAATT
*
1165561 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1165609 TTC TTC TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
1165656 TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
1165704 TTC TTT TTC T
1 TTC TTC TTC T
1165714 CTAGCCCTAA
Statistics
Matches: 143, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
2 2 0.01
3 141 0.99
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1166246 original size:17 final size:18
Alignment explanation
Indices: 1166224--1166258 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1166214 AATTATTTTC
1166224 CTAAA-TATTATTTTTAT
1 CTAAATTATTATTTTTAT
1166241 CTAAATTATTATTTTTAT
1 CTAAATTATTATTTTTAT
1166259 TATTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (18 bp):
CTAAATTATTATTTTTAT
Found at i:1166281 original size:27 final size:27
Alignment explanation
Indices: 1166229--1166283 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1166219 TTTTCCTAAA
* *
1166229 TATTATTTTTATCTAAATTATTATTTT
1 TATTATTTTTATCTAAAATATCATTTT
1166256 TATTATTTTTAT-TAAAAATATCATTTT
1 TATTATTTTTATCT-AAAATATCATTTT
1166283 T
1 T
1166284 TCCTAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (27 bp):
TATTATTTTTATCTAAAATATCATTTT
Found at i:1166310 original size:45 final size:46
Alignment explanation
Indices: 1166226--1166317 Score: 118
Period size: 45 Copynumber: 2.0 Consensus size: 46
1166216 TTATTTTCCT
* *
1166226 AAATATTATTTTTATCTAAATTATTATTTTTATTATTTTTAT-TAA
1 AAATATCATTTTTATCTAAATTACTATTTTTATTATTTTTATCTAA
*
1166271 AAATATCATTTTT-TCCTAAATT-CTATTTTTATTGTTTTTTATCTAA
1 AAATATCATTTTTAT-CTAAATTACTATTTTTATT-ATTTTTATCTAA
1166317 A
1 A
1166318 TTATTATCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
44 11 0.27
45 26 0.63
46 4 0.10
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.60
Consensus pattern (46 bp):
AAATATCATTTTTATCTAAATTACTATTTTTATTATTTTTATCTAA
Found at i:1168512 original size:35 final size:35
Alignment explanation
Indices: 1168473--1168540 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1168463 AGGAAAGTAG
* *
1168473 GGTCAAATCCTCAAAGATTGGATTGCTACAACTAA
1 GGTCAAATCCTCAAAGACTAGATTGCTACAACTAA
**
1168508 GGTCAAATCCTCAGCGACTAGATTGCTACAACT
1 GGTCAAATCCTCAAAGACTAGATTGCTACAACT
1168541 TCTTGTTCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (35 bp):
GGTCAAATCCTCAAAGACTAGATTGCTACAACTAA
Found at i:1172175 original size:97 final size:95
Alignment explanation
Indices: 1172010--1172201 Score: 228
Period size: 97 Copynumber: 2.0 Consensus size: 95
1172000 TAAACTAAAT
* * * **
1172010 CCTAAGCACTTAAAAATAAAAAATCCTAAACCCTAATTCCATAAACCCTAATATTAACACTACTC
1 CCTAAACACTTAAAAATAAAAAATCCTAAACCCTAATTCCATAAACCCTAACACTAACACTAAAC
*
1172075 ACTTAAAAATT-TAAAAACCCT-AAACCCTAA
66 ACTT-AAAATTATAAAAA-ACTAAAACCCTAA
* ** *
1172105 CCTAAACACTTAAAAAATAAAAAATCCATAAACCTTAATTTTATAAACCCTAACCCTAAC-CTTA
1 CCTAAACACTT-AAAAATAAAAAATCC-TAAACCCTAATTCCATAAACCCTAACACTAACAC-TA
1172169 AACACTTAAAATTATAAAAAACTAAAACCCTAA
63 AACACTTAAAATTATAAAAAACTAAAACCCTAA
1172202 TTTTACTAGA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
95 10 0.12
96 24 0.29
97 48 0.59
ACGTcount: A:0.51, C:0.24, G:0.01, T:0.24
Consensus pattern (95 bp):
CCTAAACACTTAAAAATAAAAAATCCTAAACCCTAATTCCATAAACCCTAACACTAACACTAAAC
ACTTAAAATTATAAAAAACTAAAACCCTAA
Found at i:1172197 original size:59 final size:60
Alignment explanation
Indices: 1172084--1172206 Score: 171
Period size: 60 Copynumber: 2.1 Consensus size: 60
1172074 CACTTAAAAA
*
1172084 TTTAAAAACCCTAAACCCTAACCTAAACACTTAAAAAATAAAAAATCCATAAACCTTAAT
1 TTTAAAAACCCTAAACCCTAACCTAAACACTTAAAAAATAAAAAATCCATAAACCCTAAT
* * *
1172144 TTTATAAACCCT-AACCCTAACCTTAAACACTTAAAATTATAAAAAA-CTA-AAACCCTAAT
1 TTTAAAAACCCTAAACCCTAACC-TAAACACTTAAAA-AATAAAAAATCCATAAACCCTAAT
1172203 TTTA
1 TTTA
1172207 CTAGAAAACA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
59 23 0.40
60 26 0.46
61 8 0.14
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (60 bp):
TTTAAAAACCCTAAACCCTAACCTAAACACTTAAAAAATAAAAAATCCATAAACCCTAAT
Found at i:1174793 original size:18 final size:16
Alignment explanation
Indices: 1174770--1174804 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1174760 ATAAAAAATA
1174770 TTAATTAAAATATATAAT
1 TTAATT-AAATA-ATAAT
1174788 TTAATTAAATAATAAT
1 TTAATTAAATAATAAT
1174804 T
1 T
1174805 AGTGATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 5 0.29
18 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAATTAAATAATAAT
Found at i:1178903 original size:29 final size:30
Alignment explanation
Indices: 1178868--1178925 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
1178858 TGTGGTCCAA
1178868 TGTGCAATGTTATACATG-AAATTTGATTT
1 TGTGCAATGTTATACATGTAAATTTGATTT
* *
1178897 TGTGCAATTTTATACATGTTAATTTGATT
1 TGTGCAATGTTATACATGTAAATTTGATT
1178926 CAATTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (30 bp):
TGTGCAATGTTATACATGTAAATTTGATTT
Found at i:1184161 original size:149 final size:154
Alignment explanation
Indices: 1183830--1184240 Score: 589
Period size: 149 Copynumber: 2.7 Consensus size: 154
1183820 TTTCTTCGTC
* * * * *
1183830 GGTTTTATATCAATTTTAGGTACCAAAACAGTACTCTATCTTATCCCATTCGATTGGATTGGATT
1 GGTTTCATATCATTTTTAGGTGCCAAAACAGTACTCTATATTATCCCATTCGATTTGATTGGATT
* * *
1183895 TGAATTCTAGTTTATTTAACTTTTTAAAATTTATTTTTTATATATTCAAAAAGATTTGTACTATG
66 TGAATTCGAGTTTATTAAACTTTTTAAAATTTATTTTTTACATATTCAAAAAGATTTGTACTATG
1183960 TTTATATGCGAAATGTGCATATGAGGATT
131 -TTATAT----AATGTGCATATGAGGATT
*
1183989 GGTTTCATATCATTTTTAGGTGCCAAAACAGTACTCTATATTATCCCATTAGATTTGATTGGATT
1 GGTTTCATATCATTTTTAGGTGCCAAAACAGTACTCTATATTATCCCATTCGATTTGATTGGATT
* *
1184054 TAAATTCGAGTTTATTAAACTTTTTAAAACTTATTTTTTACATATTC-AAAAGATTTGTACTATG
66 TGAATTCGAGTTTATTAAACTTTTTAAAATTTATTTTTTACATATTCAAAAAGATTTGTACTATG
1184118 -T-T-T-ATGTGCATATGAGGATT
131 TTATATAATGTGCATATGAGGATT
* * * *
1184138 GGTTTCATATCATTTTTAAGTGCCAAAACAGTAATCTTTGTTATCCCATTCGATTTGATTGGATT
1 GGTTTCATATCATTTTTAGGTGCCAAAACAGTACTCTATATTATCCCATTCGATTTGATTGGATT
* *
1184203 TGAATTCGAGTTTATTAAATTTTTTAAAGTTTATTTTT
66 TGAATTCGAGTTTATTAAACTTTTTAAAATTTATTTTT
1184241 GGGTAAATTG
Statistics
Matches: 232, Mismatches: 20, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
149 111 0.48
154 1 0.00
155 1 0.00
156 1 0.00
158 17 0.07
159 101 0.44
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (154 bp):
GGTTTCATATCATTTTTAGGTGCCAAAACAGTACTCTATATTATCCCATTCGATTTGATTGGATT
TGAATTCGAGTTTATTAAACTTTTTAAAATTTATTTTTTACATATTCAAAAAGATTTGTACTATG
TTATATAATGTGCATATGAGGATT
Found at i:1186076 original size:99 final size:99
Alignment explanation
Indices: 1185905--1186083 Score: 340
Period size: 99 Copynumber: 1.8 Consensus size: 99
1185895 AGACTTGGAC
* *
1185905 AGAGGTTGAGGGAGAGGAAGATGCAGAGAAAGATGAGAAGAAAAAGAAGAAATGCATAGAGAATG
1 AGAGGTTGAGGGAGAAGAAGATGCAGAGAAAGATGAGAAGAAAAAGAAGAAATGCACAGAGAATG
1185970 CCCAATCATCTTTTTATTACACCAACAAGGAGAA
66 CCCAATCATCTTTTTATTACACCAACAAGGAGAA
1186004 AGAGGTTGAGGGAGAAGAAGATGCAGAGAAAGATGAGAAGAAAAAGAAGAAATGCACAGAGAATG
1 AGAGGTTGAGGGAGAAGAAGATGCAGAGAAAGATGAGAAGAAAAAGAAGAAATGCACAGAGAATG
1186069 CCCAATCATCTTTTT
66 CCCAATCATCTTTTT
1186084 TTTCGACCCT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
99 78 1.00
ACGTcount: A:0.45, C:0.11, G:0.28, T:0.16
Consensus pattern (99 bp):
AGAGGTTGAGGGAGAAGAAGATGCAGAGAAAGATGAGAAGAAAAAGAAGAAATGCACAGAGAATG
CCCAATCATCTTTTTATTACACCAACAAGGAGAA
Found at i:1186522 original size:30 final size:30
Alignment explanation
Indices: 1186488--1186547 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1186478 TTGTTATTGT
* *
1186488 ATTAACTTATATTTTTATA-TATTTTCAAAG
1 ATTAAATTA-ATTTTTATACTATTTTAAAAG
*
1186518 ATTAAATTAATTTTTTTACTATTTTAAAAG
1 ATTAAATTAATTTTTATACTATTTTAAAAG
1186548 GTCAAAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.53
Consensus pattern (30 bp):
ATTAAATTAATTTTTATACTATTTTAAAAG
Found at i:1190995 original size:5 final size:5
Alignment explanation
Indices: 1190985--1191012 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1190975 CAGGAAAACC
1190985 AAAGA AAAGA AAAGA AAAGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAA
1191013 TCTAACATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:1191546 original size:20 final size:20
Alignment explanation
Indices: 1191521--1191560 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1191511 GATAAAAATG
1191521 ATAACTCAAGGAAGAATAGC
1 ATAACTCAAGGAAGAATAGC
1191541 ATAACTCAAGGAAGAATAGC
1 ATAACTCAAGGAAGAATAGC
1191561 TACCAACACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.20, T:0.15
Consensus pattern (20 bp):
ATAACTCAAGGAAGAATAGC
Found at i:1196059 original size:21 final size:20
Alignment explanation
Indices: 1196034--1196076 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1196024 TTCGAACCGA
1196034 TTTTAT-AATCTTTTAAGTAAT
1 TTTTATGAAT-TTTTAA-TAAT
1196055 TTTTATGAATTTTTAATAAT
1 TTTTATGAATTTTTAATAAT
1196075 TT
1 TT
1196077 ATTTAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 12 0.57
22 3 0.14
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTTATGAATTTTTAATAAT
Found at i:1198766 original size:156 final size:157
Alignment explanation
Indices: 1198475--1198785 Score: 432
Period size: 156 Copynumber: 2.0 Consensus size: 157
1198465 TTTCTTCGTC
* * *
1198475 GGTTTTATATCAATTTTAGGTACCAAAACAGTAATCTATGTTATCCCATTCGATTGAATTGGATT
1 GGTTTTATATCAATTTTAGGTACCAAAACAGTAAACTATATTATCCCATACGATTGAATTGGATT
* * * *
1198540 TGAACTGGAGTTTATTTAACTTTTTAAACCTTTTTTTTATATATTCAAAAGATTTATACTATGTT
66 TGAACTCGAGTTAATTAAACTTTTTAAACCTTTTTTTTATATATTCAAAAAATTTATACTATGTT
*
1198605 TATATGCAAAATGTGCATATGAGGATT
131 TATATGCAAAATGTGCATATAAGGATT
* * *
1198632 GGTTTTATATCATTTTTAGGTATCC-AAACAGTAAACTATATTAT-CC-TAGGATTGGATTGGAT
1 GGTTTTATATCAATTTTAGGTA-CCAAAACAGTAAACTATATTATCCCATACGATTGAATTGGAT
* * * *
1198694 TTGAATTCGAGTTAATTAAATTTTTTAAA-GTTTATCTTTTATATATTCAAAAAATTTGTACTAT
65 TTGAACTCGAGTTAATTAAACTTTTTAAACCTTT-T-TTTTATATATTCAAAAAATTTATACTAT
1198758 GTTTATATGCAAAATGTGCATATAAGGA
128 GTTTATATGCAAAATGTGCATATAAGGA
1198786 CAAGAATCAC
Statistics
Matches: 136, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
154 3 0.02
155 38 0.28
156 55 0.40
157 38 0.28
158 2 0.01
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (157 bp):
GGTTTTATATCAATTTTAGGTACCAAAACAGTAAACTATATTATCCCATACGATTGAATTGGATT
TGAACTCGAGTTAATTAAACTTTTTAAACCTTTTTTTTATATATTCAAAAAATTTATACTATGTT
TATATGCAAAATGTGCATATAAGGATT
Found at i:1201428 original size:37 final size:37
Alignment explanation
Indices: 1201373--1201446 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
1201363 GCATGCAACG
*
1201373 TGATTGTATTTCTTGACTACAACCCAAGGGCTAAAGC
1 TGATCGTATTTCTTGACTACAACCCAAGGGCTAAAGC
*
1201410 TGATCGTATTTCTTGACTACAACCCCAGGGCTAAAGC
1 TGATCGTATTTCTTGACTACAACCCAAGGGCTAAAGC
1201447 AAAACTGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (37 bp):
TGATCGTATTTCTTGACTACAACCCAAGGGCTAAAGC
Found at i:1252409 original size:26 final size:26
Alignment explanation
Indices: 1252380--1252486 Score: 187
Period size: 26 Copynumber: 4.1 Consensus size: 26
1252370 TGGTACAAAT
1252380 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
1252406 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1252432 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
1252458 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1252484 TGA
1 TGA
1252487 CGGGCATTTC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:1256592 original size:41 final size:41
Alignment explanation
Indices: 1256503--1256657 Score: 143
Period size: 41 Copynumber: 3.8 Consensus size: 41
1256493 CACAGTCGTA
* * * **
1256503 TGGTAGGCCTTGTGGCAGACCGCGTAGGTCACACGACTATG
1 TGGTAAGCCTTGTGGCAGACCGTGTAGGTCACACGGCCGTG
*
1256544 TGTTAAGCCTTGTGGCAGACCGTGTAGGTCACACGGCCGTG
1 TGGTAAGCCTTGTGGCAGACCGTGTAGGTCACACGGCCGTG
* * * * * *
1256585 TGGTAAGCCCTATGGGAAACAGTATAGGTCACACGG-CGTG
1 TGGTAAGCCTTGTGGCAGACCGTGTAGGTCACACGGCCGTG
* * * * *
1256625 TGGTAGGCCATGTGGTAGATCGTGT-GGCCACAC
1 TGGTAAGCCTTGTGGCAGACCGTGTAGGTCACAC
1256658 AGCCTGGTCA
Statistics
Matches: 92, Mismatches: 22, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 7 0.08
40 21 0.23
41 64 0.70
ACGTcount: A:0.21, C:0.23, G:0.34, T:0.23
Consensus pattern (41 bp):
TGGTAAGCCTTGTGGCAGACCGTGTAGGTCACACGGCCGTG
Found at i:1256730 original size:22 final size:22
Alignment explanation
Indices: 1256705--1256754 Score: 93
Period size: 21 Copynumber: 2.3 Consensus size: 22
1256695 GTGGGCCCAT
1256705 TTTGGGCAATTTGTTGGCCCCG
1 TTTGGGCAATTTGTTGGCCCCG
1256727 TTT-GGCAATTTGTTGGCCCCG
1 TTTGGGCAATTTGTTGGCCCCG
1256748 TTTGGGC
1 TTTGGGC
1256755 TAAAAGTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.08, C:0.22, G:0.32, T:0.38
Consensus pattern (22 bp):
TTTGGGCAATTTGTTGGCCCCG
Found at i:1265456 original size:18 final size:18
Alignment explanation
Indices: 1265433--1265478 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1265423 GAAGAAGTGA
*
1265433 AAGATACACCCAAAACAG
1 AAGATACACCCAAAAAAG
*
1265451 AAGATAAACCCAAAAAAG
1 AAGATACACCCAAAAAAG
*
1265469 AAGATCCACC
1 AAGATACACC
1265479 AAAGCCCAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.57, C:0.26, G:0.11, T:0.07
Consensus pattern (18 bp):
AAGATACACCCAAAAAAG
Found at i:1265965 original size:2 final size:2
Alignment explanation
Indices: 1265958--1265987 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1265948 GGAGATAAGA
1265958 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1265988 TAATTTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1267764 original size:20 final size:20
Alignment explanation
Indices: 1267737--1267793 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
1267727 TTTAAAATAT
1267737 AAATTTTGGAATTTTTAT-AA
1 AAATTTTGGAATTTTT-TGAA
*
1267757 ATATTTT-GAATTTTTTGAA
1 AAATTTTGGAATTTTTTGAA
1267776 AAATATTTGGAATTTTTT
1 AAAT-TTTGGAATTTTTT
1267794 CTATTTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 1 0.03
19 13 0.41
20 9 0.28
21 9 0.28
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (20 bp):
AAATTTTGGAATTTTTTGAA
Found at i:1267769 original size:19 final size:19
Alignment explanation
Indices: 1267734--1267792 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 19
1267724 TTCTTTAAAA
1267734 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
1267752 TATAAATATTTTGAATTTTT
1 TATAAATATTTGGAA-TTTT
*
1267772 TGAAAAATATTTGGAATTTT
1 T-ATAAATATTTGGAATTTT
1267792 T
1 T
1267793 TCTATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.20
19 6 0.17
20 10 0.29
21 12 0.34
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:1268171 original size:57 final size:57
Alignment explanation
Indices: 1268105--1268218 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
1268095 TGGTTAAGGA
1268105 AGTCAACTTATTATAATAGTATTATGGGAAGGTAAAATATACATGTTCCAGCACCAT
1 AGTCAACTTATTATAATAGTATTATGGGAAGGTAAAATATACATGTTCCAGCACCAT
* * *
1268162 AGTCAACTTATTATGATAGTATTATGGGAAGGTAATATATGCATGTTCCAGCACCAT
1 AGTCAACTTATTATAATAGTATTATGGGAAGGTAAAATATACATGTTCCAGCACCAT
1268219 TCTTTTTAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (57 bp):
AGTCAACTTATTATAATAGTATTATGGGAAGGTAAAATATACATGTTCCAGCACCAT
Found at i:1279596 original size:27 final size:27
Alignment explanation
Indices: 1279572--1279690 Score: 132
Period size: 27 Copynumber: 4.4 Consensus size: 27
1279562 GGATTACCTA
* *
1279572 ATGTTTATTGTCCCGGCAGACTACCCT
1 ATGTTTATTGTCCTGGCAGACTACCCC
* * **
1279599 GTGTTTATTGTCCTAGTGGACTACCCC
1 ATGTTTATTGTCCTGGCAGACTACCCC
* *
1279626 ATTTTTATTGTCCTGACAGACTACCCC
1 ATGTTTATTGTCCTGGCAGACTACCCC
*
1279653 ATGTTTATTGTCCTGGC-GAACTACCGC
1 ATGTTTATTGTCCTGGCAG-ACTACCCC
*
1279680 ATTTTTATTGT
1 ATGTTTATTGT
1279691 TCCAGTGGAC
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
26 1 0.01
27 74 0.99
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (27 bp):
ATGTTTATTGTCCTGGCAGACTACCCC
Found at i:1279638 original size:54 final size:54
Alignment explanation
Indices: 1279575--1279690 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
1279565 TTACCTAATG
* ** * *
1279575 TTTATTGTCCCGGCAGACTACCCTGTGTTTATTGTCCTAGTGGACTACCCCATT
1 TTTATTGTCCCGACAGACTACCCCATGTTTATTGTCCTAGCGAACTACCCCATT
* * *
1279629 TTTATTGTCCTGACAGACTACCCCATGTTTATTGTCCTGGCGAACTACCGCATT
1 TTTATTGTCCCGACAGACTACCCCATGTTTATTGTCCTAGCGAACTACCCCATT
1279683 TTTATTGT
1 TTTATTGT
1279691 TCCAGTGGAC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.18, C:0.26, G:0.17, T:0.39
Consensus pattern (54 bp):
TTTATTGTCCCGACAGACTACCCCATGTTTATTGTCCTAGCGAACTACCCCATT
Found at i:1280106 original size:3 final size:3
Alignment explanation
Indices: 1280100--1280177 Score: 74
Period size: 3 Copynumber: 27.0 Consensus size: 3
1280090 ATCTAAGATT
* ** *
1280100 TTA TTA TTA TTA TTAA TTA TTA GTA TGG TT- TTA -TA TTA -AA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1280143 TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1280178 AGTTAAAGAT
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
2 7 0.11
3 51 0.84
4 3 0.05
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1283329 original size:22 final size:23
Alignment explanation
Indices: 1283284--1283329 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1283274 TGTGATGACG
1283284 TTATCTTATAAATATGCATGAAT
1 TTATCTTATAAATATGCATGAAT
1283307 TTATCTTGA-AAATATG-ATGAAT
1 TTATCTT-ATAAATATGCATGAAT
1283329 T
1 T
1283330 GATTTGGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.32
23 14 0.64
24 1 0.05
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (23 bp):
TTATCTTATAAATATGCATGAAT
Found at i:1286053 original size:23 final size:23
Alignment explanation
Indices: 1286024--1286194 Score: 211
Period size: 23 Copynumber: 7.4 Consensus size: 23
1286014 CCCTTTAATA
*
1286024 AATGTTATGCAAACCCCTTAGTG
1 AATGTTATGCGAACCCCTTAGTG
*
1286047 AATGTTATGCGAACCCCTTAATG
1 AATGTTATGCGAACCCCTTAGTG
* * *
1286070 AATGTTGTGCGAACCCCTTACTA
1 AATGTTATGCGAACCCCTTAGTG
**
1286093 AATGTTATGCGAACATCTTAGTG
1 AATGTTATGCGAACCCCTTAGTG
*
1286116 AATGTTATGTGAA-CCCTTCAGTG
1 AATGTTATGCGAACCCCTT-AGTG
*
1286139 AATGTTATGCGAACCCCTTAGTA
1 AATGTTATGCGAACCCCTTAGTG
* *
1286162 AATATTATGTGAACCCCTT-GATG
1 AATGTTATGCGAACCCCTTAG-TG
1286185 AATGTTATGC
1 AATGTTATGC
1286195 AAATCTTGTT
Statistics
Matches: 125, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.03
23 116 0.93
24 5 0.04
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (23 bp):
AATGTTATGCGAACCCCTTAGTG
Found at i:1286141 original size:69 final size:69
Alignment explanation
Indices: 1286012--1286194 Score: 235
Period size: 69 Copynumber: 2.6 Consensus size: 69
1286002 GTACCGCACG
* *
1286012 ACCCCTTTAATAAATGTTATGCAAACCCCTTAGTGAATGTTATGCGAACCCCTTAATGAATGTTG
1 ACCCC-TTAATAAATGTTATGCGAACCCCTTAGTGAATGTTATGCGAACCCCTTAATGAATGTTA
1286077 TGCGA
65 TGCGA
* ** * *
1286082 ACCCCTTACTAAATGTTATGCGAACATCTTAGTGAATGTTATGTGAA-CCCTTCAGTGAATGTTA
1 ACCCCTTAATAAATGTTATGCGAACCCCTTAGTGAATGTTATGCGAACCCCTT-AATGAATGTTA
1286146 TGCGA
65 TGCGA
* * *
1286151 ACCCCTTAGTAAATATTATGTGAACCCCTT-GATGAATGTTATGC
1 ACCCCTTAATAAATGTTATGCGAACCCCTTAG-TGAATGTTATGC
1286195 AAATCTTGTT
Statistics
Matches: 98, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
68 6 0.06
69 87 0.89
70 5 0.05
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (69 bp):
ACCCCTTAATAAATGTTATGCGAACCCCTTAGTGAATGTTATGCGAACCCCTTAATGAATGTTAT
GCGA
Found at i:1286861 original size:17 final size:17
Alignment explanation
Indices: 1286826--1286858 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1286816 TTAAGATAAG
*
1286826 TATTAAATTTAATTTAA
1 TATTAAATTTAATTAAA
1286843 TATTAAATTT-ATTAAA
1 TATTAAATTTAATTAAA
1286859 ATAATATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAAATTTAATTAAA
Found at i:1288668 original size:25 final size:25
Alignment explanation
Indices: 1288634--1288682 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1288624 TGATCCTTTT
* *
1288634 AACTATTATGTGAACCCTTTTGTAA
1 AACTATTATGCGAACCCTTATGTAA
*
1288659 AACTGTTATGCGAACCCTTATGTA
1 AACTATTATGCGAACCCTTATGTA
1288683 TAATGTACTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (25 bp):
AACTATTATGCGAACCCTTATGTAA
Found at i:1288760 original size:25 final size:25
Alignment explanation
Indices: 1288695--1288762 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
1288685 ATGTACTGCA
* * *
1288695 AACATTCATACGAACCCTCATTCTG
1 AACATTCATGCGAACCTTCAATCTG
* * *
1288720 AACACTCATGTGAACCTTCAATGTG
1 AACATTCATGCGAACCTTCAATCTG
*
1288745 AACATTCATGCCAACCTT
1 AACATTCATGCGAACCTT
1288763 ATCTACGAGC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.32, C:0.29, G:0.10, T:0.28
Consensus pattern (25 bp):
AACATTCATGCGAACCTTCAATCTG
Found at i:1289285 original size:47 final size:47
Alignment explanation
Indices: 1289221--1289347 Score: 139
Period size: 47 Copynumber: 2.7 Consensus size: 47
1289211 CAACAGTTTT
* *
1289221 TCTGCTTGACCAGTGGTTTATCCACAATGTATTTTAGTCAGCAACCA
1 TCTGCTCGACTAGTGGTTTATCCACAATGTATTTTAGTCAGCAACCA
* * * * * **
1289268 TCTGTTTGATTAGTGGTTTATCCATGAA-ATATTTTAGTCAGCAGTCA
1 TCTGCTCGACTAGTGGTTTATCCA-CAATGTATTTTAGTCAGCAACCA
* *
1289315 TTTGCTCGACTAGTGGTTCATCCACAATGTATT
1 TCTGCTCGACTAGTGGTTTATCCACAATGTATT
1289348 AACAGCTTTT
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
46 2 0.03
47 60 0.94
48 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (47 bp):
TCTGCTCGACTAGTGGTTTATCCACAATGTATTTTAGTCAGCAACCA
Found at i:1295248 original size:18 final size:18
Alignment explanation
Indices: 1295225--1295267 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1295215 AAACCATTAA
1295225 GCATCAAAACATGCTAAC
1 GCATCAAAACATGCTAAC
*
1295243 GCATCAAAACATGTTAAC
1 GCATCAAAACATGCTAAC
*
1295261 ACATCAA
1 GCATCAA
1295268 GGGAGTACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.47, C:0.26, G:0.09, T:0.19
Consensus pattern (18 bp):
GCATCAAAACATGCTAAC
Found at i:1299553 original size:21 final size:22
Alignment explanation
Indices: 1299527--1299573 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1299517 CTCTGCTCAA
*
1299527 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
1299548 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
1299570 ACTC
1 ACTC
1299574 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:1313785 original size:12 final size:12
Alignment explanation
Indices: 1313765--1313793 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1313755 TCTGTGTGTG
1313765 TTTCCTTTTTTT
1 TTTCCTTTTTTT
1313777 TTT-CTTTTTTT
1 TTTCCTTTTTTT
1313788 TTTCCT
1 TTTCCT
1313794 CTTTGTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTCCTTTTTTT
Found at i:1314535 original size:31 final size:31
Alignment explanation
Indices: 1314473--1314542 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1314463 TTATTATTCC
* *
1314473 ATTTGGTACTTATATTTAGTTTTAATGTTTA
1 ATTTGGTACTTATATTTAGTTTCAATATTTA
1314504 ATTTGGTACTTGAGT-TTT-GTTTCAATATTTA
1 ATTTGGTACTT-A-TATTTAGTTTCAATATTTA
*
1314535 ATTCGGTA
1 ATTTGGTA
1314543 TATAAACTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 29 0.85
32 4 0.12
33 1 0.03
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.54
Consensus pattern (31 bp):
ATTTGGTACTTATATTTAGTTTCAATATTTA
Found at i:1325566 original size:3 final size:3
Alignment explanation
Indices: 1325558--1325596 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1325548 TGTACTTGTT
1325558 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1325597 ACTCAGATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1327249 original size:12 final size:12
Alignment explanation
Indices: 1327232--1327259 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1327222 AGTTAATTTT
1327232 AAAATTGAAAAG
1 AAAATTGAAAAG
1327244 AAAATTGAAAAG
1 AAAATTGAAAAG
1327256 AAAA
1 AAAA
1327260 AAACTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (12 bp):
AAAATTGAAAAG
Found at i:1327731 original size:15 final size:15
Alignment explanation
Indices: 1327690--1327732 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1327680 TTCTATGTAA
* *
1327690 AAATATATTAAATAT
1 AAATATATAAAAAAT
* *
1327705 ATATAAATAAAAAAT
1 AAATATATAAAAAAT
1327720 AAATATATAAAAA
1 AAATATATAAAAA
1327733 CCTCAAAAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATATATAAAAAAT
Found at i:1333762 original size:30 final size:29
Alignment explanation
Indices: 1333718--1333805 Score: 74
Period size: 29 Copynumber: 2.9 Consensus size: 29
1333708 TAGGTCGGCC
*
1333718 ATAT-TTTTTTTTTAAAAATTTATATTTGT
1 ATATATTTTTATTTAAAAATTTATATTT-T
*
1333747 AT-TATTTTTAATTT-AATATTTAATAATTTT
1 ATATATTTTT-ATTTAAAAATTT-AT-ATTTT
1333777 ATATATTTTTATTTATTAAAATTATATAT
1 ATATATTTTTATTTA--AAAATT-TATAT
1333806 ATAATCATCT
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
28 1 0.02
29 13 0.28
30 12 0.26
31 11 0.23
32 2 0.04
33 7 0.15
34 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (29 bp):
ATATATTTTTATTTAAAAATTTATATTTT
Found at i:1333790 original size:15 final size:15
Alignment explanation
Indices: 1333718--1333790 Score: 51
Period size: 15 Copynumber: 4.8 Consensus size: 15
1333708 TAGGTCGGCC
* *
1333718 ATATTTTTTTTTTAA
1 ATATTTTTATTTTAT
* *
1333733 AAATTTATATTTGTAT
1 ATATTTTTATTT-TAT
*
1333749 -TATTTTTAATTTA-
1 ATATTTTTATTTTAT
*
1333762 ATATTTAATAATTTTAT
1 ATATTT--TTATTTTAT
1333779 ATATTTTTATTT
1 ATATTTTTATTT
1333791 ATTAAAATTA
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
14 7 0.16
15 22 0.51
16 8 0.19
17 6 0.14
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (15 bp):
ATATTTTTATTTTAT
Found at i:1338579 original size:2 final size:2
Alignment explanation
Indices: 1338572--1338601 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1338562 ACCTCCTTAA
1338572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1338602 CGTAAAGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1348039 original size:20 final size:20
Alignment explanation
Indices: 1347987--1348039 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
1347977 CTATACCTTT
1347987 GAAA-TTTAAAAAAGGAAAA
1 GAAATTTTAAAAAAGGAAAA
** *
1348006 -AAATTGAAAAAAAAGAAAA
1 GAAATTTTAAAAAAGGAAAA
1348025 GAAATTTTAATAAAA
1 GAAATTTTAA-AAAA
1348040 ATACCCATGG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 3 0.12
19 12 0.46
20 7 0.27
21 4 0.15
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (20 bp):
GAAATTTTAAAAAAGGAAAA
Found at i:1349448 original size:17 final size:16
Alignment explanation
Indices: 1349437--1349478 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1349427 TAAATATAAT
1349437 TTTATAAAAAATTTAAGA
1 TTTATAAAAAA-TTAA-A
1349455 -TTA-AAAAAATTAAA
1 TTTATAAAAAATTAAA
1349469 TTTATAAAAA
1 TTTATAAAAA
1349479 CAAAAATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.05
15 7 0.32
16 11 0.50
17 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
TTTATAAAAAATTAAA
Found at i:1357394 original size:16 final size:17
Alignment explanation
Indices: 1357370--1357414 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
1357360 TCGATCAAAC
1357370 TAATTTTTTAATTTTAA
1 TAATTTTTTAATTTTAA
* *
1357387 T-TTTTTTTAAATTTAA
1 TAATTTTTTAATTTTAA
1357403 TAATTTTTTAAT
1 TAATTTTTTAAT
1357415 CTAATCAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TAATTTTTTAATTTTAA
Found at i:1357399 original size:17 final size:17
Alignment explanation
Indices: 1357373--1357411 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
1357363 ATCAAACTAA
1357373 TTTTTTAATTT-TAATT
1 TTTTTTAATTTATAATT
1357389 TTTTTTAAATTTAATAATT
1 TTTTTT-AATTT-ATAATT
1357408 TTTT
1 TTTT
1357412 AATCTAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 5 0.25
19 9 0.45
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTTAATTTATAATT
Found at i:1376393 original size:21 final size:22
Alignment explanation
Indices: 1376352--1376393 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
1376342 ATAAAAAATC
1376352 TATTTAGAAAAAAGGTCAAATTT
1 TATTTAGAAAAAAGG-CAAATTT
1376375 TATTTA-AAATAAAGG-AAAT
1 TATTTAGAAA-AAAGGCAAAT
1376394 ATTTCCACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.22
22 3 0.17
23 11 0.61
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.33
Consensus pattern (22 bp):
TATTTAGAAAAAAGGCAAATTT
Found at i:1377623 original size:50 final size:51
Alignment explanation
Indices: 1377524--1377623 Score: 118
Period size: 49 Copynumber: 2.0 Consensus size: 51
1377514 GAATGACACG
* *
1377524 TGAATTTATTTTTAACAATTCTTTAAAAAAAATTTAAAAATCTTAAAATTT
1 TGAATTTATTTTTAACAATTCTTTAAAAAAAATATAAAAATCATAAAATTT
*
1377575 TGAA-TTATTTTTAA-AATT-TTGTTAAAAAAATATAAGAAA-CATATAAATT
1 TGAATTTATTTTTAACAATTCTT-TAAAAAAAATATAA-AAATCATA-AAATT
1377624 ATAAAACTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
48 2 0.05
49 19 0.44
50 18 0.42
51 4 0.09
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (51 bp):
TGAATTTATTTTTAACAATTCTTTAAAAAAAATATAAAAATCATAAAATTT
Found at i:1380941 original size:21 final size:21
Alignment explanation
Indices: 1380917--1380958 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1380907 ATATTTACTT
1380917 ATTATATAAGTA-TATTATTAA
1 ATTATAT-AGTATTATTATTAA
*
1380938 ATTATATATTATTATTATTAA
1 ATTATATAGTATTATTATTAA
1380959 GTAAAAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTATATAGTATTATTATTAA
Found at i:1381130 original size:10 final size:10
Alignment explanation
Indices: 1381115--1381146 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
1381105 TTAATGAAAT
1381115 AAAGAAAGAA
1 AAAGAAAGAA
1381125 AAAGAATAGAA
1 AAAGAA-AGAA
1381136 AAAGAAAGAA
1 AAAGAAAGAA
1381146 A
1 A
1381147 GGATGAAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:1383290 original size:46 final size:46
Alignment explanation
Indices: 1383238--1383347 Score: 202
Period size: 46 Copynumber: 2.4 Consensus size: 46
1383228 AGTGTGCTCT
1383238 CTGATATGAAATGTGTAAGACCATGGTTGAAAGAGACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGAGACCATGGCAAC
*
1383284 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGAGACCATGGCAAC
*
1383330 CTGATATGAAACGTGTAA
1 CTGATATGAAATGTGTAA
1383348 AGATACCATG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.24
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGAGACCATGGCAAC
Found at i:1383355 original size:33 final size:33
Alignment explanation
Indices: 1383313--1383380 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
1383303 ACCATGGTTG
*
1383313 AAAGATACCATGGCAACCTGATATGAAACGTGT
1 AAAGATACCATGGCAACCTAATATGAAACGTGT
*
1383346 AAAGATACCATGGCAACCTAATATGAAATGTGT
1 AAAGATACCATGGCAACCTAATATGAAACGTGT
1383379 AA
1 AA
1383381 GACCATGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (33 bp):
AAAGATACCATGGCAACCTAATATGAAACGTGT
Found at i:1383388 original size:30 final size:32
Alignment explanation
Indices: 1383313--1383388 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 32
1383303 ACCATGGTTG
*
1383313 AAAGATACCATGGCAACCTGATATGAAACGTGT
1 AAAGA-ACCATGGCAACCTAATATGAAACGTGT
*
1383346 AAAGATACCATGGCAACCTAATATGAAATGTGT
1 AAAGA-ACCATGGCAACCTAATATGAAACGTGT
1383379 -AAG-ACCATGG
1 AAAGAACCATGG
1383389 TTGAAAGATA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
30 7 0.17
32 3 0.07
33 31 0.76
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (32 bp):
AAAGAACCATGGCAACCTAATATGAAACGTGT
Found at i:1383398 original size:79 final size:79
Alignment explanation
Indices: 1383267--1383419 Score: 279
Period size: 79 Copynumber: 1.9 Consensus size: 79
1383257 ACCATGGTTG
*
1383267 AAAGAGACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCT
1 AAAGAGACCATGGCAACCTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCT
1383332 GATATGAAACGTGT
66 GATATGAAACGTGT
* *
1383346 AAAGATACCATGGCAACCTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGT
1 AAAGAGACCATGGCAACCTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCT
1383411 GATATGAAA
66 GATATGAAA
1383420 TGAATAAGAC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 71 1.00
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.22
Consensus pattern (79 bp):
AAAGAGACCATGGCAACCTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCT
GATATGAAACGTGT
Found at i:1383519 original size:138 final size:138
Alignment explanation
Indices: 1383346--1383634 Score: 542
Period size: 138 Copynumber: 2.1 Consensus size: 138
1383336 TGAAACGTGT
* *
1383346 AAAGATACCATGGCAACCTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGT
1 AAAGATACCATGGCAACCTAATATGAAATGCGTAAGACCATGGTTGAAAGATACCATGGCAACCT
1383411 GATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGAC
66 GATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGAC
1383476 CATGGTTG
131 CATGGTTG
* *
1383484 AAAGATACCATTGCAACCTGATATGAAATGCGTAAGACCATGGTTGAAAGATACCATGGCAACCT
1 AAAGATACCATGGCAACCTAATATGAAATGCGTAAGACCATGGTTGAAAGATACCATGGCAACCT
1383549 GATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGAC
66 GATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGAC
1383614 CATGGTTG
131 CATGGTTG
1383622 AAAGATACCATGG
1 AAAGATACCATGG
1383635 TAACATGACA
Statistics
Matches: 146, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 146 1.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (138 bp):
AAAGATACCATGGCAACCTAATATGAAATGCGTAAGACCATGGTTGAAAGATACCATGGCAACCT
GATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGAC
CATGGTTG
Found at i:1383644 original size:46 final size:46
Alignment explanation
Indices: 1383346--1383634 Score: 461
Period size: 46 Copynumber: 6.3 Consensus size: 46
1383336 TGAAACGTGT
* **
1383346 AAAGATACCATGGCAACCTAATATGAAATGTGTAAGACCATGGTTG
1 AAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTG
*
1383392 AAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTG
1 AAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTG
* * *
1383438 AAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTG
1 AAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTG
* **
1383484 AAAGATACCATTGCAACCTGATATGAAATGCGTAAGACCATGGTTG
1 AAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTG
1383530 AAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTG
1 AAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTG
* * *
1383576 AAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTG
1 AAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTG
1383622 AAAGATACCATGG
1 AAAGATACCATGG
1383635 TAACATGACA
Statistics
Matches: 225, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 225 1.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
AAAGATACCATGGCAACCTGATATGAAATGAATAAGACCATGGTTG
Found at i:1387024 original size:13 final size:14
Alignment explanation
Indices: 1387006--1387035 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1386996 TTTGTTCAAA
1387006 TTTTATA-TTTAAT
1 TTTTATATTTTAAT
1387019 TTTTATATTTTAAT
1 TTTTATATTTTAAT
1387033 TTT
1 TTT
1387036 GATACCTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTATATTTTAAT
Found at i:1389952 original size:2 final size:2
Alignment explanation
Indices: 1389945--1389980 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1389935 ATATTTTATT
1389945 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1389981 AATTGCTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1390115 original size:13 final size:13
Alignment explanation
Indices: 1390097--1390122 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1390087 ATTAGTATAA
1390097 ATAAAATATAAAT
1 ATAAAATATAAAT
1390110 ATAAAATATAAAT
1 ATAAAATATAAAT
1390123 TAATAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAAATATAAAT
Found at i:1391093 original size:20 final size:20
Alignment explanation
Indices: 1391068--1391129 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
1391058 TTTAGAAAAT
*
1391068 TTTAAAAATATATAAATTTA
1 TTTAAAAATATATAAAATTA
*
1391088 TTTAAAAA-ATTTAAAATTA
1 TTTAAAAATATATAAAATTA
* * *
1391107 TTAAAAAATATACAAAATAA
1 TTTAAAAATATATAAAATTA
1391127 TTT
1 TTT
1391130 TTTTAAAATC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTAAAAATATATAAAATTA
Found at i:1391102 original size:19 final size:19
Alignment explanation
Indices: 1391068--1391118 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
1391058 TTTAGAAAAT
*
1391068 TTTAAAAATATATAAATTTA
1 TTTAAAAA-ATATAAAATTA
*
1391088 TTTAAAAAATTTAAAATTA
1 TTTAAAAAATATAAAATTA
1391107 -TTAAAAAATATA
1 TTTAAAAAATATA
1391119 CAAAATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 11 0.39
19 9 0.32
20 8 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTAAAAAATATAAAATTA
Found at i:1395111 original size:21 final size:22
Alignment explanation
Indices: 1395061--1395111 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1395051 TAGATTAACG
* *
1395061 ATAATTATTTGCGTTAAATATT
1 ATAATTATATGCGCTAAATATT
*
1395083 ATAA-TATATGTGCTAAAT-TT
1 ATAATTATATGCGCTAAATATT
1395103 ATAATTATA
1 ATAATTATA
1395112 CACGTAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 6 0.24
21 15 0.60
22 4 0.16
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (22 bp):
ATAATTATATGCGCTAAATATT
Found at i:1395557 original size:35 final size:35
Alignment explanation
Indices: 1395517--1395590 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
1395507 TAATTAAGGA
* *
1395517 ACATTCAAGTGTAATTCAGCCTGCAGATGAACAAG
1 ACATTCAAGTGTAATTCAGCCTGCAAAAGAACAAG
**
1395552 ACATTCAAGTGTGCTTCAGCCTGCAAAAGAACAAG
1 ACATTCAAGTGTAATTCAGCCTGCAAAAGAACAAG
1395587 ACAT
1 ACAT
1395591 ATCAGTTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (35 bp):
ACATTCAAGTGTAATTCAGCCTGCAAAAGAACAAG
Found at i:1395893 original size:44 final size:44
Alignment explanation
Indices: 1395845--1395936 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 44
1395835 ATGAATTTAA
* * *
1395845 TTTAATCGTTTTAT-TTTTTATTTTGAAGGAAATAATATTA-CATT
1 TTTAATCGATTTATCTTTTT-TTTT-AAGCAAATAAAATTATCATT
* *
1395889 TTTAATTGATTTATCTTTTTTTTTAAGCAAATAAAATTATTATT
1 TTTAATCGATTTATCTTTTTTTTTAAGCAAATAAAATTATCATT
1395933 TTTA
1 TTTA
1395937 GTTTAAGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 13 0.32
44 23 0.56
45 5 0.12
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (44 bp):
TTTAATCGATTTATCTTTTTTTTTAAGCAAATAAAATTATCATT
Found at i:1408984 original size:25 final size:24
Alignment explanation
Indices: 1408945--1408992 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1408935 AATAATAATA
*
1408945 ATAATAAGTAGTATAAAAGTAAAAC
1 ATAATAAATAGTATAAAA-TAAAAC
* *
1408970 ATAATAAATATTATATAATAAAA
1 ATAATAAATAGTATAAAATAAAA
1408993 TATATGGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (24 bp):
ATAATAAATAGTATAAAATAAAAC
Found at i:1409096 original size:20 final size:20
Alignment explanation
Indices: 1409049--1409113 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
1409039 TATATGTAAA
*
1409049 AATAATATGTATAAATAA-AT
1 AATAATATATATAAA-AATAT
*
1409069 ATATAATATATGTAAAAATAT
1 A-ATAATATATATAAAAATAT
*
1409090 AATAATATATATATAAATAAT
1 AATAATATATATAAAAAT-AT
1409111 AAT
1 AAT
1409114 TATGAGAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
20 18 0.47
21 20 0.53
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
AATAATATATATAAAAATAT
Found at i:1409105 original size:31 final size:34
Alignment explanation
Indices: 1409039--1409105 Score: 86
Period size: 36 Copynumber: 2.0 Consensus size: 34
1409029 AATGAAAATT
1409039 TATATGTAAAAATAATATGTATAAATAAATATATAA
1 TATATGTAAAAATAATA--TATAAATAAATATATAA
*
1409075 TATATGTAAAAAT-ATA-AT-AATATATATATAA
1 TATATGTAAAAATAATATATAAATAAATATATAA
1409106 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 12 0.40
32 2 0.07
35 3 0.10
36 13 0.43
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.37
Consensus pattern (34 bp):
TATATGTAAAAATAATATATAAATAAATATATAA
Done.