Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold127
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: 3416254
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 147187 characters in sequence are not A, C, G, or T
File 4 of 10
Found at i:1048552 original size:25 final size:25
Alignment explanation
Indices: 1048523--1048582 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
1048513 TTAATTAGTA
*
1048523 TAAAATATTAATAATTCAAT-AAAT
1 TAAAATATTAATAATTAAATAAAAT
1048547 TGAAAA-ATTCAATAATTAAATAAAAT
1 T-AAAATATT-AATAATTAAATAAAAT
1048573 TAAAAT-TTAA
1 TAAAATATTAA
1048583 GAGAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
24 6 0.19
25 20 0.65
26 5 0.16
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (25 bp):
TAAAATATTAATAATTAAATAAAAT
Found at i:1049411 original size:30 final size:30
Alignment explanation
Indices: 1049354--1049412 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1049344 GTCTTTTGAA
*
1049354 AATATTTACAAAAAGATACATCTAATTTTT
1 AATATTTACAAAAAGATACAACTAATTTTT
* * *
1049384 AATATTTACAAATAGA-GCAACTAAATTTT
1 AATATTTACAAAAAGATACAACTAATTTTT
1049413 GAAAACAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.37
Consensus pattern (30 bp):
AATATTTACAAAAAGATACAACTAATTTTT
Found at i:1055796 original size:13 final size:14
Alignment explanation
Indices: 1055772--1055800 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1055762 AATCGAAGGG
1055772 AAATGAAGAGAGAA
1 AAATGAAGAGAGAA
1055786 AAATG-AGAGAGAA
1 AAATGAAGAGAGAA
1055799 AA
1 AA
1055801 GAAGAGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.07
Consensus pattern (14 bp):
AAATGAAGAGAGAA
Found at i:1057259 original size:21 final size:21
Alignment explanation
Indices: 1057230--1057300 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
1057220 TTGCACCCAT
*
1057230 GGCCGTGTGACCTATCCACAA
1 GGCCGTGTGACCCATCCACAA
* *
1057251 GGCTGTGTGACCCATCCGCAA
1 GGCCGTGTGACCCATCCACAA
* *
1057272 GGCCGTGTGACCCATGCACAC
1 GGCCGTGTGACCCATCCACAA
*
1057293 GACCGTGT
1 GGCCGTGT
1057301 AGCCTATCTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.20, C:0.34, G:0.28, T:0.18
Consensus pattern (21 bp):
GGCCGTGTGACCCATCCACAA
Found at i:1059874 original size:9 final size:9
Alignment explanation
Indices: 1059856--1059892 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
1059846 TATAATTTGA
1059856 TATTCGAAT
1 TATTCGAAT
*
1059865 TATTCAAAT
1 TATTCGAAT
*
1059874 TATTCGAGT
1 TATTCGAAT
1059883 TATTCGAAT
1 TATTCGAAT
1059892 T
1 T
1059893 TGAAAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:1063200 original size:58 final size:58
Alignment explanation
Indices: 1063110--1063227 Score: 218
Period size: 58 Copynumber: 2.0 Consensus size: 58
1063100 TCATGTTCCT
*
1063110 AAATTTGCATTGATTTGCTTTGGCTGATAAATATATATATTTTCATCCCAGTTGTTAA
1 AAATTTGCATTGATTTGCTTTGGCTGATAAATATATATATTTTCATCCCAATTGTTAA
*
1063168 AAATTTGCATTGATTTGCTTTGGCTGATAAATATATATTTTTTCATCCCAATTGTTAA
1 AAATTTGCATTGATTTGCTTTGGCTGATAAATATATATATTTTCATCCCAATTGTTAA
1063226 AA
1 AA
1063228 TACAAAACGA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.45
Consensus pattern (58 bp):
AAATTTGCATTGATTTGCTTTGGCTGATAAATATATATATTTTCATCCCAATTGTTAA
Found at i:1074877 original size:117 final size:117
Alignment explanation
Indices: 1074671--1074900 Score: 408
Period size: 117 Copynumber: 2.0 Consensus size: 117
1074661 ATGTGGATAT
1074671 AACATCTGTTAATTGAAATTGGATTGAAGCATACATCACTAGCAAAACTTTGGTACCATAATTAA
1 AACATCTGTTAATTGAAATTGGATTGAAGCATACATCACTAGCAAAACTTTGGTACCATAATTAA
* *
1074736 GTTGCTGTTCATATTGCCTTGAAATCAATCTATCATGAAAGAATCAAACTTC
66 GTTGCTCTTCATATTGCCTCGAAATCAATCTATCATGAAAGAATCAAACTTC
* *
1074788 AACATCTGTTAATTGAAATTGGATTGGAGCATACATCACTAGCAAAA-TTCTGGTGCCATAATTA
1 AACATCTGTTAATTGAAATTGGATTGAAGCATACATCACTAGCAAAACTT-TGGTACCATAATTA
1074852 AGTTGCTCTTCATATTGCCTCGAAATCAATCTATCATGAAAGAATCAAA
65 AGTTGCTCTTCATATTGCCTCGAAATCAATCTATCATGAAAGAATCAAA
1074901 GCATCAAGGT
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
116 2 0.02
117 106 0.98
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (117 bp):
AACATCTGTTAATTGAAATTGGATTGAAGCATACATCACTAGCAAAACTTTGGTACCATAATTAA
GTTGCTCTTCATATTGCCTCGAAATCAATCTATCATGAAAGAATCAAACTTC
Found at i:1075903 original size:18 final size:19
Alignment explanation
Indices: 1075880--1075922 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
1075870 TATATTTTTA
1075880 AAAAAATTATAAAAAAT-T
1 AAAAAATTATAAAAAATAT
*
1075898 AAAAAATTCTAAAAAATAT
1 AAAAAATTATAAAAAATAT
1075917 AAAAAA
1 AAAAAA
1075923 AGTTAAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAAATTATAAAAAATAT
Found at i:1075923 original size:10 final size:9
Alignment explanation
Indices: 1075877--1075928 Score: 52
Period size: 10 Copynumber: 5.4 Consensus size: 9
1075867 TTTTATATTT
1075877 TTAAAAAAA
1 TTAAAAAAA
1075886 TTATAAAAAA
1 TTA-AAAAAA
1075896 TT-AAAAAA
1 TTAAAAAAA
*
1075904 TTCTAAAAAA
1 TT-AAAAAAA
1075914 TATAAAAAAA
1 T-TAAAAAAA
1075924 GTTAA
1 -TTAA
1075929 GATTTCAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
8 8 0.22
9 3 0.08
10 24 0.65
11 2 0.05
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:1076404 original size:66 final size:66
Alignment explanation
Indices: 1076322--1076451 Score: 251
Period size: 66 Copynumber: 2.0 Consensus size: 66
1076312 ACCCCAAATC
1076322 TAAGACCATATCACCAAATTCGCATTCACCAGTCATACATTTACAAAATAGCTTTTCGCTTTCAT
1 TAAGACCATATCACCAAATTCGCATTCACCAGTCATACATTTACAAAATAGCTTTTCGCTTTCAT
1076387 T
66 T
*
1076388 TAAGACCATATCACCAAATTCGCATTCACCCGTCATACATTTACAAAATAGCTTTTCGCTTTCA
1 TAAGACCATATCACCAAATTCGCATTCACCAGTCATACATTTACAAAATAGCTTTTCGCTTTCA
1076452 ATCTGTTGTT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.32
Consensus pattern (66 bp):
TAAGACCATATCACCAAATTCGCATTCACCAGTCATACATTTACAAAATAGCTTTTCGCTTTCAT
T
Found at i:1089823 original size:14 final size:13
Alignment explanation
Indices: 1089775--1089824 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
1089765 ATTGGTCATA
1089775 GAGAGA-ATTGAG
1 GAGAGATATTGAG
* *
1089787 GAGGGATATT-TG
1 GAGAGATATTGAG
1089799 GAGAGAT-TTGAG
1 GAGAGATATTGAG
1089811 GAGAGAATATTGAG
1 GAGAG-ATATTGAG
1089825 ATTTGGGGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 2 0.07
12 18 0.60
13 5 0.17
14 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.40, T:0.24
Consensus pattern (13 bp):
GAGAGATATTGAG
Found at i:1090948 original size:27 final size:26
Alignment explanation
Indices: 1090917--1091143 Score: 238
Period size: 27 Copynumber: 8.4 Consensus size: 26
1090907 CCCCAAAATA
* *
1090917 GGTAAAATAACCAAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCC-CATAG
** *
1090944 GGTAAAATGATTGAAATACCCATATAG
1 GGTAAAATGACCGAAATACCC-CATAG
* *
1090971 GGTAAAATGACCAAAATACCCCTATAA
1 GGTAAAATGACCGAAATACCCC-ATAG
*
1090998 GGTAAAATGACCGAAATACTCCCATAA
1 GGTAAAATGACCGAAATAC-CCCATAG
* * *
1091025 GGTAAAATAACTGAAATAACCTCATAG
1 GGTAAAATGACCGAAAT-ACCCCATAG
*
1091052 GGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
* * *
1091079 GGTAAAATAACCAAAATAACACCATAG
1 GGTAAAATGACCGAAAT-ACCCCATAG
*
1091106 GGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
1091133 GGTAAAATGAC
1 GGTAAAATGAC
1091144 TGTTAGACCC
Statistics
Matches: 165, Mismatches: 29, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
26 2 0.01
27 157 0.95
28 6 0.04
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.19
Consensus pattern (26 bp):
GGTAAAATGACCGAAATACCCCATAG
Found at i:1091002 original size:54 final size:54
Alignment explanation
Indices: 1090917--1091140 Score: 292
Period size: 54 Copynumber: 4.1 Consensus size: 54
1090907 CCCCAAAATA
* * *
1090917 GGTAAAATAACCAAAATACCCTCATAGGGTAAAATGATTGAAATACCCATATAG
1 GGTAAAATAACCAAAATAACCTCATAGGGTAAAATGATCGAAATACCCACATAG
* * * * *
1090971 GGTAAAATGACCAAAAT-ACCCCTATAAGGTAAAATGACCGAAATACTCC-CATAA
1 GGTAAAATAACCAAAATAACCTC-ATAGGGTAAAATGATCGAAATAC-CCACATAG
** *
1091025 GGTAAAATAACTGAAATAACCTCATAGGGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATAACCAAAATAACCTCATAGGGTAAAATGATCGAAATACCCACATAG
*
1091079 GGTAAAATAACCAAAATAACAC-CATAGGGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATAACCAAAATAAC-CTCATAGGGTAAAATGATCGAAATACCCACATAG
1091133 GGTAAAAT
1 GGTAAAAT
1091141 GACTGTTAGA
Statistics
Matches: 148, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
53 5 0.03
54 136 0.92
55 7 0.05
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (54 bp):
GGTAAAATAACCAAAATAACCTCATAGGGTAAAATGATCGAAATACCCACATAG
Found at i:1091052 original size:81 final size:79
Alignment explanation
Indices: 1090916--1091143 Score: 287
Period size: 81 Copynumber: 2.8 Consensus size: 79
1090906 ACCCCAAAAT
1090916 AGGTAAAATAACCAAAATACCCTCATAGGGTAAAATGATTGAAATACCCAT-ATAGGGTAAAATG
1 AGGTAAAATAACCAAAATACCC-CATAGGGTAAAATGA-TGAAATACCC-TCATAGGGTAAAATG
*
1090980 ACCAAAATACCCCTATA
63 ACCAAAATACCCCCATA
* * * * *
1090997 AGGTAAAATGACCGAAATACTCCCATAAGGTAAAATAACTGAAATAACCTCATAGGGTAAAATGA
1 AGGTAAAATAACCAAAATAC-CCCATAGGGTAAAATGA-TGAAATACCCTCATAGGGTAAAATGA
* *
1091062 TCGAAATACCCCCATA
64 CCAAAATACCCCCATA
* * *
1091078 GGGTAAAATAACCAAAATAACACCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGA
1 AGGTAAAATAACCAAAAT-ACCCCATAGGGTAAAATGAT-GAAATACCCTCATAGGGTAAAATGA
1091143 C
64 C
1091144 TGTTAGACCC
Statistics
Matches: 125, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
80 2 0.02
81 119 0.95
82 4 0.03
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.19
Consensus pattern (79 bp):
AGGTAAAATAACCAAAATACCCCATAGGGTAAAATGATGAAATACCCTCATAGGGTAAAATGACC
AAAATACCCCCATA
Found at i:1096472 original size:63 final size:63
Alignment explanation
Indices: 1096365--1096522 Score: 210
Period size: 63 Copynumber: 2.5 Consensus size: 63
1096355 TCTTCATAGC
* * * *
1096365 AAACACACATTCTAACCACATATATATATATAATTCATAACATTAAGTTCAGCT-AAAAAAATTT
1 AAACATACATTCGAACCAC--ATATATATATAATTCATAACATTAAATTCAACTCAAAAAAA-TT
1096429 G
63 G
* * *
1096430 TAACATACATTCGAACCTCATATATATATAATTCATAACATTAAATTCAACTCAAAGAAATTG
1 AAACATACATTCGAACCACATATATATATAATTCATAACATTAAATTCAACTCAAAAAAATTG
*
1096493 AAACATACATTCGAACCACATGTATATATA
1 AAACATACATTCGAACCACATATATATATA
1096523 TATATATTAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
63 61 0.74
64 6 0.07
65 15 0.18
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.30
Consensus pattern (63 bp):
AAACATACATTCGAACCACATATATATATAATTCATAACATTAAATTCAACTCAAAAAAATTG
Found at i:1101520 original size:75 final size:74
Alignment explanation
Indices: 1101395--1101810 Score: 263
Period size: 75 Copynumber: 5.8 Consensus size: 74
1101385 TATCCGTTAT
* * * * *
1101395 CGGTGGATTCAGCACTTAACAACCGCCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAACACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCA-
1101460 ATTTAAGATA
65 ATTTAAGATA
* * ****
1101470 CGGTGGGATCAACACTTAGCAACCACCAATGATTCGGGGAATCAGTACTTAGCAAGCCCTCGGGG
1 CGGTGGAATCAACACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAA-CCC-CTTTC
* * *
1101535 GA-TTCAG-CA
64 AATTTAAGATA
* * * * ** * * *
1101544 C-TTAGCAA-C-CCCCTT--C-A-CATTTAA-GATACGGTGCAATCAGCACTTAGCAACCAC---
1 CGGT-GGAATCAACACTTAGCAACCA-CCAATGATTCGG-GGAATCAGCACTTAGCAACCCCTTT
*
1101598 CAA--TGA-AT-
63 CAATTTAAGATA
*
1101606 CGG-GGAATCAACACTTAGCAACC-CC-----TTGGGGGAATCAGCACTTAGCAACCCCCTTT-A
1 CGGTGGAATCAACACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAA-CCCCTTTCA
1101663 TATTTAAAGATA
65 -ATTT-AAGATA
* * *
1101675 CTGTGGAATCAGCACTTAGCAACCACCAATGAGTT-GGGGAATCAGCACTTAGCAACCCCCTTCA
1 CGGTGGAATCAACACTTAGCAACCACCAATGA-TTCGGGGAATCAGCACTTAGCAACCCCTTTC-
*
1101739 AATTTAAAATA
64 AATTTAAGATA
* * *
1101750 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTT
1 CGGTGGAATCAACACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTT
1101811 GGGGGAATCA
Statistics
Matches: 260, Mismatches: 47, Indels: 68
0.69 0.13 0.18
Matches are distributed among these distances:
60 17 0.07
61 9 0.03
62 2 0.01
63 7 0.03
64 2 0.01
65 1 0.00
66 2 0.01
67 3 0.01
68 12 0.05
69 21 0.08
70 20 0.08
71 2 0.01
72 4 0.02
73 2 0.01
74 5 0.02
75 119 0.46
76 28 0.11
77 4 0.02
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (74 bp):
CGGTGGAATCAACACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAA
TTTAAGATA
Found at i:1101550 original size:102 final size:102
Alignment explanation
Indices: 1101430--1101733 Score: 459
Period size: 102 Copynumber: 3.0 Consensus size: 102
1101420 CCAATGAGTC
* *
1101430 GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGATCAACACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
* *
1101495 CCAATGATTCGGGGAATCAGTACTTAGCAAGCCCTCG
66 CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTCG
* * *
1101532 GGGGATTCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGCAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
* * *
1101597 CCAATGAATCGGGGAATCAACACTTAGCAACCCCTTG
66 CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTCG
* *
1101634 GGGGAATCAGCACTTAGCAACCCCCTTT-ATATTTAAAGATACTGTGGAATCAGCACTTAGCAAC
1 GGGGAATCAGCACTTAGCAA-CCCCTTTCACATTT-AAGATACGGTGGAATCAGCACTTAGCAAC
1101698 CACCAATGAGTT-GGGGAATCAGCACTTAGCAACCCC
64 CACCAATGA-TTCGGGGAATCAGCACTTAGCAACCCC
1101734 CTTCAAATTT
Statistics
Matches: 182, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
102 116 0.64
103 65 0.36
104 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.21
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTCG
Found at i:1101621 original size:33 final size:33
Alignment explanation
Indices: 1101578--1101833 Score: 158
Period size: 33 Copynumber: 7.5 Consensus size: 33
1101568 GATACGGTGC
1101578 AATCAGCACTTAGCAACCACCAATGAATCGGGG
1 AATCAGCACTTAGCAACCACCAATGAATCGGGG
* *
1101611 AATCAACACTTAGCAACC-CC--T---TGGGGG
1 AATCAGCACTTAGCAACCACCAATGAATCGGGG
* * *
1101638 AATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACTGTGG
1 AATCAGCACTTAGCAACCACC---A-A--T-GA-AT-C-GGGG
* *
1101681 AATCAGCACTTAGCAACCACCAATGAGTTGGGG
1 AATCAGCACTTAGCAACCACCAATGAATCGGGG
* *
1101714 AATCAGCACTTAGCAACCCCCTTCAAATTTAAAATACGGTGG
1 AATCAGCACTTAGCAA-CCAC--C-AA--T-GAAT-CGG-GG
*
1101756 AATCAGCACTTAGCAACCACCAATGAATAGGGG
1 AATCAGCACTTAGCAACCACCAATGAATCGGGG
*
1101789 AATCAGCACTTAGCAACC-CC--T---TGGGGG
1 AATCAGCACTTAGCAACCACCAATGAATCGGGG
1101816 AATCAGCACTTAGCAACC
1 AATCAGCACTTAGCAACC
1101834 CCTTTTTATA
Statistics
Matches: 180, Mismatches: 18, Indels: 56
0.71 0.07 0.22
Matches are distributed among these distances:
27 45 0.25
28 2 0.01
30 2 0.01
32 4 0.02
33 56 0.31
34 5 0.03
35 4 0.02
36 4 0.02
37 3 0.02
38 2 0.01
39 3 0.02
40 3 0.02
41 6 0.03
42 18 0.10
43 23 0.13
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (33 bp):
AATCAGCACTTAGCAACCACCAATGAATCGGGG
Found at i:1101729 original size:76 final size:75
Alignment explanation
Indices: 1101634--1101808 Score: 296
Period size: 75 Copynumber: 2.3 Consensus size: 75
1101624 CAACCCCTTG
* * *
1101634 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACTGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCAAATTTAAA-ATACGGTGGAATCAGCACTTAGCAACC
* *
1101699 ACCAATGAGTT
65 ACCAATGAATA
1101710 GGGGAATCAGCACTTAGCAACCCCCTTCAAATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCAAATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
1101775 CCAATGAATA
66 CCAATGAATA
1101785 GGGGAATCAGCACTTAGCAACCCC
1 GGGGAATCAGCACTTAGCAACCCC
1101809 TTGGGGGAAT
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
75 59 0.63
76 35 0.37
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (75 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCAAATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
CCAATGAATA
Found at i:1101819 original size:27 final size:27
Alignment explanation
Indices: 1101785--1101837 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
1101775 CCAATGAATA
1101785 GGGGAATCAGCACTTAGCAACCCCTTG
1 GGGGAATCAGCACTTAGCAACCCCTTG
1101812 GGGGAATCAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACTTAGCAACCCCTT
1101838 TTTATATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.30, G:0.25, T:0.19
Consensus pattern (27 bp):
GGGGAATCAGCACTTAGCAACCCCTTG
Found at i:1123820 original size:102 final size:102
Alignment explanation
Indices: 1123704--1123889 Score: 309
Period size: 102 Copynumber: 1.8 Consensus size: 102
1123694 CCAATGAGTC
* **
1123704 GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGATCAACACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGCAATCAACACTTAGCAACCA
*
1123769 CCAATGATTCAGGGAATCAGTACTTAGCAAGCCCTCG
66 CCAATGAATCAGGGAATCAGTACTTAGCAAGCCCTCG
* *
1123806 GGGGATTCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGCAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGCAATCAACACTTAGCAACCA
*
1123871 CCAATGAATCGGGGAATCA
66 CCAATGAATCAGGGAATCA
1123890 ACACATAGCA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 77 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGCAATCAACACTTAGCAACCA
CCAATGAATCAGGGAATCAGTACTTAGCAAGCCCTCG
Found at i:1123980 original size:75 final size:75
Alignment explanation
Indices: 1123806--1123981 Score: 298
Period size: 75 Copynumber: 2.3 Consensus size: 75
1123796 CAAGCCCTCG
* * *
1123806 GGGGATTCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGCAATCAGCACTTAGCAACCA
1 GGGGAATCAACACTTAGCAACCCCTTTCACATTTAAGATACGGTGCAATCAGCACTTAGCAACCA
1123871 CCAATGAATC
66 CCAATGAATC
* *
1123881 GGGGAATCAACACATAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAACACTTAGCAACCCCTTTCACATTTAAGATACGGTGCAATCAGCACTTAGCAACCA
1123946 CCAATGAATC
66 CCAATGAATC
*
1123956 GGGGAATCAAGACTTAGCAACCCCTT
1 GGGGAATCAACACTTAGCAACCCCTT
1123982 GGGGGAATCA
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 94 1.00
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (75 bp):
GGGGAATCAACACTTAGCAACCCCTTTCACATTTAAGATACGGTGCAATCAGCACTTAGCAACCA
CCAATGAATC
Found at i:1123995 original size:177 final size:177
Alignment explanation
Indices: 1123681--1124009 Score: 543
Period size: 177 Copynumber: 1.9 Consensus size: 177
1123671 GTGGATTCAT
* * * *
1123681 CACTTAGCAACCGCCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACG
1 CACTTAGCAACCACCAATGAATCGGGGAATCAACACATAGCAACCCCTTTCACATTTAAGATACG
* * *
1123746 GTGGGATCAACACTTAGCAACCACCAATGATTCAGGGAATCAGTACTTAGCAAGCCCTCGGGGGA
66 GTGGAATCAACACTTAGCAACCACCAATGAATCAGGGAATCAGTACTTAGCAACCCCTCGGGGGA
*
1123811 TTCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGCAATCAG
131 ATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGCAATCAG
1123858 CACTTAGCAACCACCAATGAATCGGGGAATCAACACATAGCAACCCCTTTCACATTTAAGATACG
1 CACTTAGCAACCACCAATGAATCGGGGAATCAACACATAGCAACCCCTTTCACATTTAAGATACG
* * *
1123923 GTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAAG-ACTTAGCAACCCCTTGGGGG
66 GTGGAATCAACACTTAGCAACCACCAATGAATCAGGGAATC-AGTACTTAGCAACCCCTCGGGGG
1123987 AATCAGCACTTAGCAACCCCCTT
130 AATCAGCACTTAGCAACCCCCTT
1124010 TATATTCAAT
Statistics
Matches: 140, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
177 138 0.99
178 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.20
Consensus pattern (177 bp):
CACTTAGCAACCACCAATGAATCGGGGAATCAACACATAGCAACCCCTTTCACATTTAAGATACG
GTGGAATCAACACTTAGCAACCACCAATGAATCAGGGAATCAGTACTTAGCAACCCCTCGGGGGA
ATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGCAATCAG
Found at i:1149115 original size:76 final size:75
Alignment explanation
Indices: 1148989--1149149 Score: 250
Period size: 76 Copynumber: 2.1 Consensus size: 75
1148979 GCGGATTCAA
* * * *
1148989 CACTTAGCAACCACCAGTGATTCGGGGAATTATCACTTAGCAACCCCTTTCACATTCAATGATAC
1 CACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTTCACATTCAA-GATAC
1149054 GGTGGAATCAG
65 GGTGGAATCAG
* *
1149065 CACTTAGCAACCACCAATGAATCGGGGAGTCAACACTTAGCAACCCCTTTCACATTTAAGATACG
1 CACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTTCACATTCAAGATACG
*
1149130 GTGGGATCAG
66 GTGGAATCAG
1149140 CACTTAGCAA
1 CACTTAGCAA
1149150 NNNNNNNNNN
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
75 25 0.32
76 53 0.68
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.23
Consensus pattern (75 bp):
CACTTAGCAACCACCAATGAATCGGGGAATCAACACTTAGCAACCCCTTTCACATTCAAGATACG
GTGGAATCAG
Found at i:1153900 original size:67 final size:63
Alignment explanation
Indices: 1153793--1154013 Score: 282
Period size: 63 Copynumber: 3.4 Consensus size: 63
1153783 TCTTCATAGC
* * **
1153793 AAACACACATTCGAACCACATATATATATAATTCACAACATTAAATTCAGCTCGCAGAAATTG
1 AAACATACATTCGAACCACATATATATATAATTCATAACATTAAATTCAGCTCAAAGAAATTG
* * *
1153856 AAACATATATTCGAACCACATGTATGTATATATAATTCATAACATTAAGTTCAGCT-AAAAAAAT
1 AAACATACATTCGAACCACA--TA--TATATATAATTCATAACATTAAATTCAGCTCAAAGAAA-
1153920 TTG
61 TTG
* * **
1153923 TAACATACATTTGAACGTCATATATATATAATTCATAACATTAAATTCAGCTCAAAGAAATTG
1 AAACATACATTCGAACCACATATATATATAATTCATAACATTAAATTCAGCTCAAAGAAATTG
*
1153986 AAACATACATTCGAACCACATGTATATA
1 AAACATACATTCGAACCACATATATATA
1154014 CATATTATAC
Statistics
Matches: 133, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
63 73 0.55
64 6 0.05
65 4 0.03
66 4 0.03
67 46 0.35
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (63 bp):
AAACATACATTCGAACCACATATATATATAATTCATAACATTAAATTCAGCTCAAAGAAATTG
Found at i:1160127 original size:33 final size:33
Alignment explanation
Indices: 1160086--1160226 Score: 147
Period size: 33 Copynumber: 4.2 Consensus size: 33
1160076 ATCCCTCCAA
* *
1160086 CACACCAATGCTCAGAAGAGCTAATCCAACCAG
1 CACACCAATGCTCATAAGAGCTAATCCAACCAT
* * *
1160119 CACGCCAATGCCACATAAGAGTTAATCCAACCAT
1 CACACCAATG-CTCATAAGAGCTAATCCAACCAT
* * * *
1160153 CATACTAGTGCTCATAAGAGCTAATCCAACTAT
1 CACACCAATGCTCATAAGAGCTAATCCAACCAT
* * * *
1160186 CACACCAGTGTTCATAAGAGCTAGTCCAACCAA
1 CACACCAATGCTCATAAGAGCTAATCCAACCAT
*
1160219 CAGACCAA
1 CACACCAA
1160227 ATAGAAAGTA
Statistics
Matches: 87, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
33 62 0.71
34 25 0.29
ACGTcount: A:0.38, C:0.30, G:0.13, T:0.18
Consensus pattern (33 bp):
CACACCAATGCTCATAAGAGCTAATCCAACCAT
Found at i:1164755 original size:25 final size:27
Alignment explanation
Indices: 1164722--1164784 Score: 78
Period size: 25 Copynumber: 2.4 Consensus size: 27
1164712 ATAAACCTAT
*
1164722 ATATATTATATA-ATAA-AACCCACGC
1 ATATATTATATATACAACAACCCACGC
*
1164747 ATATATTATATATACAACAACCCACTC
1 ATATATTATATATACAACAACCCACGC
*
1164774 AAATA-TATATA
1 ATATATTATATA
1164785 CTATATAACG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.36
26 9 0.27
27 12 0.36
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (27 bp):
ATATATTATATATACAACAACCCACGC
Found at i:1169393 original size:22 final size:19
Alignment explanation
Indices: 1169352--1169394 Score: 50
Period size: 22 Copynumber: 2.1 Consensus size: 19
1169342 CCATTATGGA
*
1169352 TAAATTGATGAATTAGGCT
1 TAAATTGATGAATTAAGCT
1169371 TAAATTTGATAGATATTAAGCT
1 TAAA-TTGAT-GA-ATTAAGCT
1169393 TA
1 TA
1169395 GATCATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 5 0.25
21 2 0.10
22 9 0.45
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (19 bp):
TAAATTGATGAATTAAGCT
Found at i:1173287 original size:27 final size:28
Alignment explanation
Indices: 1173230--1173287 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
1173220 GATTATATCG
*
1173230 CATTATTTGTTATTTGGTAGTTTCACTA
1 CATTATTTGTTATTTGGTAGTTTCACCA
* *
1173258 CATTA-TTGATTA-TTGGTGGTTTTACCA
1 CATTATTTG-TTATTTGGTAGTTTCACCA
1173285 CAT
1 CAT
1173288 CGAGCTCTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 18 0.69
28 8 0.31
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (28 bp):
CATTATTTGTTATTTGGTAGTTTCACCA
Found at i:1173397 original size:19 final size:19
Alignment explanation
Indices: 1173373--1173422 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
1173363 TAGAATCTCA
1173373 CATGTGCATTTGTGATGAT
1 CATGTGCATTTGTGATGAT
1173392 CATGTGCATTTGTGATGAT
1 CATGTGCATTTGTGATGAT
1173411 CATGTGCATTTG
1 CATGTGCATTTG
1173423 AAATTCCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.20, C:0.12, G:0.26, T:0.42
Consensus pattern (19 bp):
CATGTGCATTTGTGATGAT
Found at i:1181974 original size:26 final size:26
Alignment explanation
Indices: 1181918--1181976 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
1181908 AGGTTATTCC
* ** *
1181918 TTATTTTTGAAATAATTTTTCTTTCC
1 TTATTTTTGAAATAATTTTGCAATCA
1181944 TTATTTTTGAAATAATTTTGCAAT-A
1 TTATTTTTGAAATAATTTTGCAATCA
1181969 TGTATTTT
1 T-TATTTT
1181977 AAAAACAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 1 0.04
26 27 0.96
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (26 bp):
TTATTTTTGAAATAATTTTGCAATCA
Found at i:1186957 original size:14 final size:14
Alignment explanation
Indices: 1186938--1186964 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1186928 GGTCAGGATG
1186938 TAATGTAAAATTTA
1 TAATGTAAAATTTA
1186952 TAATGTAAAATTT
1 TAATGTAAAATTT
1186965 GTTCCAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
TAATGTAAAATTTA
Found at i:1197602 original size:23 final size:22
Alignment explanation
Indices: 1197549--1197606 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 22
1197539 AATCTTCAAG
1197549 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
1197568 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
*
1197590 GATTTTGCAATCTTAGA
1 GA-TATGCAATCTTAGA
1197607 GATTTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 13 0.38
22 8 0.24
23 13 0.38
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:1197616 original size:22 final size:23
Alignment explanation
Indices: 1197572--1197616 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1197562 AGATATGATA
*
1197572 TGCAATCTTAGAAGATATGATTT
1 TGCAATCTTAGAAGATATAATTT
*
1197595 TGCAATCTTAG-AGATTTAATTT
1 TGCAATCTTAGAAGATATAATTT
1197617 GTAGATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (23 bp):
TGCAATCTTAGAAGATATAATTT
Found at i:1200286 original size:44 final size:44
Alignment explanation
Indices: 1200041--1200287 Score: 125
Period size: 44 Copynumber: 5.7 Consensus size: 44
1200031 GACTTGATGC
* * * *
1200041 AATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCATTACTTT
1 AATCCGCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTT
* ** * * * *
1200085 AATCCGTTCCACCACAACCTC-GAGGAGATAGGAT-TATCGACTTC
1 AATCCGCTCCACTGCAACTTCAG-GGAGATAAGATCTAT-TACTTT
* * * * *
1200129 AATCTGCTCCACTGCAACCTCAAGGAGATAAGATTTGTT--TTCT
1 AATCCGCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTT-T
* * * * * *
1200172 CAGTCTGCTCGACTGTAACTTCAGGGAGATAAGACCCTA-TGC---
1 -AATCCGCTCCACTGCAACTTCAGGGAGATAAGA-TCTATTACTTT
* * ** *
1200214 GATCCACTCTGCTGCAAC-TCTAGAGAGATAAGATCTATTACTTT
1 AATCCGCTCCACTGCAACTTC-AGGGAGATAAGATCTATTACTTT
*
1200258 AATCCGCTCCACTACAACTTCAGGGAGATA
1 AATCCGCTCCACTGCAACTTCAGGGAGATA
1200288 GGATTATCGG
Statistics
Matches: 144, Mismatches: 44, Indels: 30
0.66 0.20 0.14
Matches are distributed among these distances:
40 5 0.03
41 24 0.17
42 2 0.01
43 3 0.02
44 105 0.73
45 5 0.03
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (44 bp):
AATCCGCTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTT
Found at i:1200635 original size:130 final size:131
Alignment explanation
Indices: 1200325--1200742 Score: 640
Period size: 131 Copynumber: 3.2 Consensus size: 131
1200315 ACACTTGAAT
* * * * *
1200325 ATAAGATTCACCGTCTTCGATCTGCTCTGCTACTGCTTAGGGAGACAATATCTGTAGTTTCCAAC
1 ATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAAC
* * * *
1200390 CTATTCCACTGCTGCTCAGGGACATAGGACTTGCGGCTTAAATCTGTTTCCCTACTCCTGGGGAA
66 CTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTATTTCCCTACTCTTGGGGAA
1200455 G
131 G
* * *
1200456 ATAAGATTTGCCGTCTTCGATCTGCACCGCTACTGCTTAGGGAGACAAGATCTGCAATTTTCAAC
1 ATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAAC
* * *
1200521 CTATTCCAATGTTGGTCAGGGACATAGGACTGGTGGCTTAAATCT-TTTCCCTACTCTTGGGGAA
66 CTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTATTTCCCTACTCTTGGGGAA
1200585 G
131 G
** * *
1200586 ATAAGATTTTCCGTCTTCGATCTACTCCGCTACTGCTTAGGGAGGCAAGATCTGCAATTTCCAAC
1 ATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAAC
* *
1200651 CTACTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTATTTTCCTACTCTTGGGGAA
66 CTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTATTTCCCTACTCTTGGGGAA
1200716 G
131 G
1200717 ATAAGATTCGCCGTCTTCGATCTGCT
1 ATAAGATTCGCCGTCTTCGATCTGCT
1200743 TCACTGTCGA
Statistics
Matches: 259, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
130 120 0.46
131 139 0.54
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (131 bp):
ATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAAC
CTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTATTTCCCTACTCTTGGGGAA
G
Found at i:1200881 original size:87 final size:87
Alignment explanation
Indices: 1200732--1201087 Score: 577
Period size: 87 Copynumber: 4.1 Consensus size: 87
1200722 ATTCGCCGTC
* * * * *
1200732 TTCGATCTGCTTCACTGTCGACGCAAGAGGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1200797 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* * * *
1200819 TTTGATCTGCTTCGCTATCAATGCAGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCGA
1 TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1200884 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
*
1200906 TTCGATCTGCTTCGCTGTCAATGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
1200971 CCGATGGAGGCAAGTCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* *
1200993 TTCGATCTGTTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
1201058 CCGATGGAGGCAAGGCTTTATT
66 CCGATGGAGGCAAGGCTTTGTT
*
1201080 TTCAATCT
1 TTCGATCT
1201088 TCACTGATCT
Statistics
Matches: 248, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 248 1.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.29
Consensus pattern (87 bp):
TTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
CCGATGGAGGCAAGGCTTTGTT
Found at i:1203048 original size:35 final size:35
Alignment explanation
Indices: 1203002--1203071 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1202992 AATACCATCG
1203002 GCATATGATGACATTGACGCATGCAGTAGCCTCTA
1 GCATATGATGACATTGACGCATGCAGTAGCCTCTA
1203037 GCATATGATGACATTGACGCATGCAGTAGCCTCTA
1 GCATATGATGACATTGACGCATGCAGTAGCCTCTA
1203072 TCCATTTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (35 bp):
GCATATGATGACATTGACGCATGCAGTAGCCTCTA
Found at i:1203286 original size:14 final size:13
Alignment explanation
Indices: 1203246--1203286 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
1203236 CCTTGGCCTC
1203246 TTCTTTTCCTTTT
1 TTCTTTTCCTTTT
1203259 TTCTTTTCTCTTTT
1 TTCTTTTC-CTTTT
*
1203273 TTCATTTTCATTTT
1 TTC-TTTTCCTTTT
1203287 GACTTTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 8 0.32
14 12 0.48
15 5 0.20
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76
Consensus pattern (13 bp):
TTCTTTTCCTTTT
Found at i:1209007 original size:22 final size:24
Alignment explanation
Indices: 1208952--1209013 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 24
1208942 ATTGGGCTGA
*
1208952 TTGGGTTGGGGCTAGGCTTAATGGGT
1 TTGGGTTTGGGCTAGGCTTAAT--GT
*
1208978 TTAGGTTTGGGCTAGG-TTAAT-T
1 TTGGGTTTGGGCTAGGCTTAATGT
1209000 TTGGGTTTGGGCTA
1 TTGGGTTTGGGCTA
1209014 ACTGGGCTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 14 0.42
25 5 0.15
26 14 0.42
ACGTcount: A:0.13, C:0.06, G:0.40, T:0.40
Consensus pattern (24 bp):
TTGGGTTTGGGCTAGGCTTAATGT
Found at i:1209846 original size:28 final size:28
Alignment explanation
Indices: 1209792--1209846 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
1209782 AATGACTCCC
* *
1209792 AATTTTTGTTTTTTTTAAAGTCGACAACT
1 AATTTTTGTTTTTTTCAAAATC-ACAACT
1209821 AATTTTTGTTTTTTTCCAAAAT-ACAA
1 AATTTTTGTTTTTTT-CAAAATCACAA
1209847 ATGGTTTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.17
29 15 0.65
30 4 0.17
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (28 bp):
AATTTTTGTTTTTTTCAAAATCACAACT
Found at i:1212735 original size:17 final size:17
Alignment explanation
Indices: 1212713--1212748 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1212703 TTGCAACTCA
1212713 ATATCCTAATAACATTG
1 ATATCCTAATAACATTG
1212730 ATATCCTAATAACATTG
1 ATATCCTAATAACATTG
1212747 AT
1 AT
1212749 TAAACTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.36
Consensus pattern (17 bp):
ATATCCTAATAACATTG
Found at i:1214375 original size:14 final size:16
Alignment explanation
Indices: 1214351--1214383 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1214341 ATAAACGTAG
1214351 AAAAAAGAAAA-ATAC
1 AAAAAAGAAAACATAC
1214366 AAAAAA-AAAACATAC
1 AAAAAAGAAAACATAC
1214381 AAA
1 AAA
1214384 TTTAATATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.82, C:0.09, G:0.03, T:0.06
Consensus pattern (16 bp):
AAAAAAGAAAACATAC
Found at i:1216337 original size:20 final size:20
Alignment explanation
Indices: 1216299--1216338 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1216289 AATTTATAAG
*
1216299 GAATAAAATTAAATTAAAGA
1 GAATAAAATTAAATGAAAGA
1216319 GAATAAAATTCAAA-GAAAGA
1 GAATAAAATT-AAATGAAAGA
1216339 TTTAAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.20
Consensus pattern (20 bp):
GAATAAAATTAAATGAAAGA
Found at i:1219969 original size:24 final size:24
Alignment explanation
Indices: 1219942--1219999 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1219932 GATTATCTTC
* *
1219942 TTCATCTTTACCTCGA-CCTCTGTA
1 TTCATCTTCAACTCGACCCTC-GTA
* *
1219966 TTCATCATCAACTCGACCCTCGTC
1 TTCATCTTCAACTCGACCCTCGTA
1219990 TTCATCTTCA
1 TTCATCTTCA
1220000 TCTGCACCCC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.19, C:0.36, G:0.07, T:0.38
Consensus pattern (24 bp):
TTCATCTTCAACTCGACCCTCGTA
Found at i:1221417 original size:88 final size:88
Alignment explanation
Indices: 1221324--1221496 Score: 294
Period size: 88 Copynumber: 2.0 Consensus size: 88
1221314 TTAATTGTAT
*
1221324 ATATTTTACTGAA-TTTATTAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGA
1 ATATTTTAC-CAATTTTATTAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGA
1221388 CATGAAAATTAATATTCTTTTGAA
65 CATGAAAATTAATATTCTTTTGAA
* *
1221412 ATATTTTACCAATTTTGTTAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGAT
1 ATATTTTACCAATTTTATTAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGAC
*
1221477 ATGGAAATTAATATTCTTTT
66 ATGAAAATTAATATTCTTTT
1221497 TGGAAAGAAT
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 2 0.03
88 78 0.98
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (88 bp):
ATATTTTACCAATTTTATTAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGAC
ATGAAAATTAATATTCTTTTGAA
Found at i:1224169 original size:5 final size:5
Alignment explanation
Indices: 1224153--1224218 Score: 78
Period size: 5 Copynumber: 12.8 Consensus size: 5
1224143 GTAGTACATT
* * * *
1224153 TCATA TCTTA TCATA TCATA TCTTA TCATA TCTCATA TCATA ACATA ACATA
1 TCATA TCATA TCATA TCATA TCATA TCATA --TCATA TCATA TCATA TCATA
1224205 TCATA TCATA TCAT
1 TCATA TCATA TCAT
1224219 GTCCTACCCC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
5 48 0.91
7 5 0.09
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (5 bp):
TCATA
Found at i:1224735 original size:123 final size:124
Alignment explanation
Indices: 1224515--1224760 Score: 458
Period size: 123 Copynumber: 2.0 Consensus size: 124
1224505 TTTTCTTTAC
1224515 GAAATATAGCATAGCATATAGCTTTTACACAACCAAACTTACTTAAAATATTTTTCCTAAGCTTA
1 GAAATATAGCATAGCATATAGCTTTTACACAACCAAACTTACTTAAAATATTTTTCCTAAGCTTA
1224580 CCCTTGTGTATAAACAGCTAAAACTTACTCTTTTCCGGGCTTATATGACACCCACGAAT
66 CCCTTGTGTATAAACAGCTAAAACTTACTCTTTTCCGGGCTTATATGACACCCACGAAT
* *
1224639 GAAATATAGCATAGCATATAGCTTTTACACAACC-AAGTTACTTAAAATATTTTTTCTAAGCTTA
1 GAAATATAGCATAGCATATAGCTTTTACACAACCAAACTTACTTAAAATATTTTTCCTAAGCTTA
*
1224703 CCCTTGTGTATAAACAGCTAAAACTTACTCTTTTCCGGGCTTATATGATACCCACGAA
66 CCCTTGTGTATAAACAGCTAAAACTTACTCTTTTCCGGGCTTATATGACACCCACGAA
1224761 CCCAATTTTT
Statistics
Matches: 119, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
123 85 0.71
124 34 0.29
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (124 bp):
GAAATATAGCATAGCATATAGCTTTTACACAACCAAACTTACTTAAAATATTTTTCCTAAGCTTA
CCCTTGTGTATAAACAGCTAAAACTTACTCTTTTCCGGGCTTATATGACACCCACGAAT
Found at i:1236980 original size:26 final size:26
Alignment explanation
Indices: 1236950--1237008 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
1236940 TACCTACACT
1236950 AGTTTCAGAATATCATAACATATATC
1 AGTTTCAGAATATCATAACATATATC
* *
1236976 AGTTTCAGAATATCATAGCATGTATC
1 AGTTTCAGAATATCATAACATATATC
1237002 AGTTTCA
1 AGTTTCA
1237009 AATCACTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (26 bp):
AGTTTCAGAATATCATAACATATATC
Found at i:1242092 original size:5 final size:5
Alignment explanation
Indices: 1242084--1242110 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1242074 TTATCATCTC
1242084 TCATA TCATA TCATA TCATA TCATA TC
1 TCATA TCATA TCATA TCATA TCATA TC
1242111 CTTCCTCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (5 bp):
TCATA
Found at i:1247450 original size:18 final size:18
Alignment explanation
Indices: 1247427--1247461 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1247417 GCACTAACAT
*
1247427 AAAAATGTAATGACAATA
1 AAAAATGCAATGACAATA
1247445 AAAAATGCAATGACAAT
1 AAAAATGCAATGACAAT
1247462 GTATGCTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (18 bp):
AAAAATGCAATGACAATA
Found at i:1250433 original size:11 final size:11
Alignment explanation
Indices: 1250417--1250445 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1250407 CTCTTTAGTG
1250417 TGGTTGCCACT
1 TGGTTGCCACT
1250428 TGGTTGCCACT
1 TGGTTGCCACT
1250439 TGGTTGC
1 TGGTTGC
1250446 AATGAAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.24, G:0.31, T:0.38
Consensus pattern (11 bp):
TGGTTGCCACT
Found at i:1261593 original size:17 final size:17
Alignment explanation
Indices: 1261573--1261607 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1261563 AATAGAATAA
1261573 TTTAAAAAATTTAAAAT
1 TTTAAAAAATTTAAAAT
*
1261590 TTTAAAAACTTTAAAAT
1 TTTAAAAAATTTAAAAT
1261607 T
1 T
1261608 AACTTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAAAAATTTAAAAT
Found at i:1266461 original size:59 final size:60
Alignment explanation
Indices: 1266363--1266479 Score: 175
Period size: 59 Copynumber: 2.0 Consensus size: 60
1266353 CTCCAAGGAT
* **
1266363 TAACTTGGACAAAAAAAAAGGTCAAGTCCCAATGTGGGAATAATTGTCAAGTTCAAGGTC
1 TAACTTGGACAAAAAAAAAGGTCAAGCCCCAATGTGGGAATAATTACCAAGTTCAAGGTC
*
1266423 TAACTTGGA-TAAAAAAAA-GTCCAAGCCCCAATGTGGGAATAATTACCAAGTTCAAGG
1 TAACTTGGACAAAAAAAAAGGT-CAAGCCCCAATGTGGGAATAATTACCAAGTTCAAGG
1266480 CCTAGTTTAG
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 2 0.04
59 41 0.79
60 9 0.17
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (60 bp):
TAACTTGGACAAAAAAAAAGGTCAAGCCCCAATGTGGGAATAATTACCAAGTTCAAGGTC
Found at i:1266493 original size:59 final size:59
Alignment explanation
Indices: 1266363--1266538 Score: 165
Period size: 59 Copynumber: 2.9 Consensus size: 59
1266353 CTCCAAGGAT
* * * ** *
1266363 TAACTTGGACAAAAAAAAAGGTCAAGTCCCAATGTGGGAATAATTGTCAAGTTCAAGGTC
1 TAACTTAGATAAAAAAAAA-GTCAAGCCCCAATGTGGGAATAATTACCAAGTTCAAGGCC
*
1266423 TAACTTGGAT-AAAAAAAAGTCCAAGCCCCAATGTGGGAATAATTACCAAGTTCAAGGCC
1 TAACTTAGATAAAAAAAAAGT-CAAGCCCCAATGTGGGAATAATTACCAAGTTCAAGGCC
** * * * ** *
1266482 TAGTTTAGATAATAATAAAAAATTCAGGCTCCAATGTGACAAAAATTACCAAGTTCA
1 TAACTTAGAT-A-AA-AAAAAAGTCAAGCCCCAATGTGGGAATAATTACCAAGTTCA
1266539 GGTCACAAAA
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
58 2 0.02
59 49 0.51
60 9 0.09
62 30 0.31
63 7 0.07
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (59 bp):
TAACTTAGATAAAAAAAAAGTCAAGCCCCAATGTGGGAATAATTACCAAGTTCAAGGCC
Found at i:1271409 original size:56 final size:50
Alignment explanation
Indices: 1271199--1271438 Score: 212
Period size: 50 Copynumber: 4.7 Consensus size: 50
1271189 GATAATAATA
* * ** * * * *
1271199 TGCCAAAGCCATGTCCCAGACATGGTATTACATGGGATGTTTCTTGT-AC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * ** ** * *
1271248 TGCCAATGCCATATCCCAGGTATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * * **
1271298 TACCTATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
*
1271348 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCACAATCTCAATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT--C-ATCTC-A-G
*
1271403 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGG
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGG
1271439 AATCTTTTTA
Statistics
Matches: 153, Mismatches: 31, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
49 37 0.24
50 75 0.49
52 1 0.01
53 5 0.03
54 1 0.01
55 1 0.01
56 33 0.22
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
Found at i:1278080 original size:18 final size:18
Alignment explanation
Indices: 1278031--1278080 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
1278021 TAATAAAATC
1278031 ATATTTTTATATTTAATA
1 ATATTTTTATATTTAATA
**
1278049 GCATTTTTATATTTAATA
1 ATATTTTTATATTTAATA
1278067 TATATTTTTA-ATTT
1 -ATATTTTTATATTT
1278081 CAAAACACAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
ATATTTTTATATTTAATA
Found at i:1280801 original size:28 final size:28
Alignment explanation
Indices: 1280770--1280825 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1280760 TAAATTGGAG
1280770 GTCCTTAAATGGTAATTAGACCATTGGT
1 GTCCTTAAATGGTAATTAGACCATTGGT
1280798 GTCCTTAAATGGTAATTAGACCATTGGT
1 GTCCTTAAATGGTAATTAGACCATTGGT
1280826 TAACTTGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (28 bp):
GTCCTTAAATGGTAATTAGACCATTGGT
Found at i:1282477 original size:101 final size:102
Alignment explanation
Indices: 1282365--1282549 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
1282355 GAAGTGATGG
*
1282365 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGAT-GGTCACATGTGTAGT
*
1282428 ACTATGTGCAGGCTACTATGCATACCGGATAGCTTCGA
65 ACTACGTGCAGGCTACTATGCATACCGGATAGCTTCGA
* * * *
1282466 TCACGTGTGTAGTACTTTGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCACATGTGTATTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
1282531 CTACGTGCAGGCTACTATG
66 CTACGTGCAGGCTACTATG
1282550 TGAACCGGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 39 0.51
102 33 0.43
103 4 0.05
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
CTACGTGCAGGCTACTATGCATACCGGATAGCTTCGA
Found at i:1282508 original size:51 final size:50
Alignment explanation
Indices: 1282365--1282557 Score: 183
Period size: 51 Copynumber: 3.8 Consensus size: 50
1282355 GAAGTGATGG
* *
1282365 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-ATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GATAGA
* * * ** * *
1282415 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCATACCGGATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-ATAGA
* * *
1282466 TCACGTGTGTAGTACTTTGTGCAGGCTACTACGTGTATCGGATAG-TGATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGAT-A-GA
* * * * *
1282517 TCACATGTGTATTACTACGTGCAGGCTACTATGTGAACCGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG
1282558 TATAATTTAT
Statistics
Matches: 114, Mismatches: 25, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
49 1 0.01
50 37 0.32
51 76 0.67
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.30
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGATAGA
Found at i:1283468 original size:40 final size:40
Alignment explanation
Indices: 1283413--1283489 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
1283403 TCTCTGACTT
1283413 GGGTCACACGGCCAAGCCACACACCCATGTGCTAGGTGCA
1 GGGTCACACGGCCAAGCCACACACCCATGTGCTAGGTGCA
* * * *
1283453 GGGTCACTCGGCCAAGCCACACGCTCGTGTGCTAGGT
1 GGGTCACACGGCCAAGCCACACACCCATGTGCTAGGT
1283490 CGTGTGAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.21, C:0.34, G:0.30, T:0.16
Consensus pattern (40 bp):
GGGTCACACGGCCAAGCCACACACCCATGTGCTAGGTGCA
Found at i:1285502 original size:42 final size:42
Alignment explanation
Indices: 1285429--1285532 Score: 138
Period size: 42 Copynumber: 2.5 Consensus size: 42
1285419 ATGAGTTTTC
* * **
1285429 GTTCAACTCTAATGGGTTTCCGTTAAGCTCTTTTGAGCTTCT
1 GTTCAACCCTTATGGGTTTCCGTTAAGCTCTTACGAGCTTCT
*
1285471 GTTTAACCCTTATGGGTTTCCGTTCAA-CTCTTACGAGCTTCT
1 GTTCAACCCTTATGGGTTTCCGTT-AAGCTCTTACGAGCTTCT
*
1285513 GTTCAACCCTTACGGGTTTC
1 GTTCAACCCTTATGGGTTTC
1285533 TATTTATCAC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 52 0.96
43 2 0.04
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.40
Consensus pattern (42 bp):
GTTCAACCCTTATGGGTTTCCGTTAAGCTCTTACGAGCTTCT
Found at i:1285533 original size:21 final size:21
Alignment explanation
Indices: 1285467--1285533 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
1285457 TCTTTTGAGC
* *
1285467 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTCAACCCTTACGGGT
* * * *
1285488 TTCCGTTCAACTCTTACGAGC
1 TTCTGTTCAACCCTTACGGGT
1285509 TTCTGTTCAACCCTTACGGGT
1 TTCTGTTCAACCCTTACGGGT
1285530 TTCT
1 TTCT
1285534 ATTTATCACT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.15, C:0.27, G:0.16, T:0.42
Consensus pattern (21 bp):
TTCTGTTCAACCCTTACGGGT
Found at i:1287437 original size:25 final size:25
Alignment explanation
Indices: 1287375--1287437 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
1287365 TAATCAGGAA
* *
1287375 GCTCTTTCGAGCCATAAAATGGGAT
1 GCTCTTACGAGCTATAAAATGGGAT
* *
1287400 GCTCATAAGAGCTA-AATAATGGGAT
1 GCTCTTACGAGCTATAA-AATGGGAT
*
1287425 GCTCTTGCGAGCT
1 GCTCTTACGAGCT
1287438 GTGGTGTGTC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
24 2 0.07
25 28 0.93
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (25 bp):
GCTCTTACGAGCTATAAAATGGGAT
Found at i:1287544 original size:21 final size:21
Alignment explanation
Indices: 1287518--1287560 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1287508 ATCGAATTTC
1287518 TTAGGTTCAAACGAGACTTAG
1 TTAGGTTCAAACGAGACTTAG
1287539 TTAGGTTCAAACGAGACTTAG
1 TTAGGTTCAAACGAGACTTAG
1287560 T
1 T
1287561 ACTTTTCCAA
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:0.23, T:0.30
Consensus pattern (21 bp):
TTAGGTTCAAACGAGACTTAG
Found at i:1289131 original size:21 final size:21
Alignment explanation
Indices: 1289107--1289147 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1289097 TTAGGGTCAT
1289107 AATAAT-TAATAAAAGTATTAA
1 AATAATATAAT-AAAGTATTAA
*
1289128 AATAATATAATCAAGTATTA
1 AATAATATAATAAAGTATTA
1289148 TTATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (21 bp):
AATAATATAATAAAGTATTAA
Found at i:1292389 original size:23 final size:24
Alignment explanation
Indices: 1292354--1292401 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1292344 TATTTTAAGA
* *
1292354 TTATATTTCTATATTTG-TTTAAT
1 TTATATTTATATAATTGTTTTAAT
*
1292377 TTATTTTTATATAATTGTTTTAAT
1 TTATATTTATATAATTGTTTTAAT
1292401 T
1 T
1292402 CAATCAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (24 bp):
TTATATTTATATAATTGTTTTAAT
Found at i:1293146 original size:18 final size:18
Alignment explanation
Indices: 1293125--1293159 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1293115 TTTTAATTTT
*
1293125 TTTTAAATTTTTTAAAAA
1 TTTTAAATTTTATAAAAA
1293143 TTTTAAATTTTATAAAA
1 TTTTAAATTTTATAAAA
1293160 TTAATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTAAATTTTATAAAAA
Found at i:1294209 original size:27 final size:27
Alignment explanation
Indices: 1294171--1294257 Score: 129
Period size: 27 Copynumber: 3.2 Consensus size: 27
1294161 GCCACAAGCA
*
1294171 GCACCAAAGGTGCCTGTGGCAGAGGCG
1 GCACCAAAGGTGCCTGTGCCAGAGGCG
*
1294198 GCACCAAAGGTGCCTGTGTCAGAGGCG
1 GCACCAAAGGTGCCTGTGCCAGAGGCG
** *
1294225 GCACCAAAGGTGCCACTGCCACAGGCG
1 GCACCAAAGGTGCCTGTGCCAGAGGCG
1294252 GCACCA
1 GCACCA
1294258 CTTGTATTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.24, C:0.31, G:0.34, T:0.10
Consensus pattern (27 bp):
GCACCAAAGGTGCCTGTGCCAGAGGCG
Found at i:1294302 original size:3 final size:3
Alignment explanation
Indices: 1294289--1294319 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1294279 CCGTCCAGCT
*
1294289 GAA GGA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1294320 GATGAGGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1294430 original size:24 final size:26
Alignment explanation
Indices: 1294393--1294442 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
1294383 AAAATAATGG
1294393 ATTATCTTGTTATTATGTTTTT-TTGT
1 ATTATCTTGTTATTAT-TTTTTGTTGT
1294419 ATTAT-TT-TTATTATTTTTTGTTGT
1 ATTATCTTGTTATTATTTTTTGTTGT
1294443 TAGTTTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 5 0.22
24 11 0.48
25 2 0.09
26 5 0.22
ACGTcount: A:0.16, C:0.02, G:0.10, T:0.72
Consensus pattern (26 bp):
ATTATCTTGTTATTATTTTTTGTTGT
Found at i:1294712 original size:37 final size:37
Alignment explanation
Indices: 1294586--1294723 Score: 102
Period size: 37 Copynumber: 3.7 Consensus size: 37
1294576 AACTAATATT
**
1294586 ATTATTATGGTTAGTTATTAGGATTAGTAAAAACCCTA
1 ATTATTATGGTTAGTTATTATTATTAGT-AAAACCCTA
* * *** * *
1294624 ATTATTAT-TTTAGTTAGTATGATTGTTAGTTTTTA-CATT
1 ATTATTATGGTTAGTTA-T-T-ATTATTAG-TAAAACCCTA
* *
1294663 A-TATTATTGTTAGTTATTATTTTTAGTAAAACCCTA
1 ATTATTATGGTTAGTTATTATTATTAGTAAAACCCTA
*
1294699 ATTATTATGGTTAGTTAGTATTATT
1 ATTATTATGGTTAGTTATTATTATT
1294724 TTGAGTATAA
Statistics
Matches: 74, Mismatches: 19, Indels: 15
0.69 0.18 0.14
Matches are distributed among these distances:
35 2 0.03
36 10 0.14
37 28 0.38
38 16 0.22
39 11 0.15
40 6 0.08
41 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (37 bp):
ATTATTATGGTTAGTTATTATTATTAGTAAAACCCTA
Found at i:1294744 original size:76 final size:77
Alignment explanation
Indices: 1294585--1294750 Score: 196
Period size: 76 Copynumber: 2.2 Consensus size: 77
1294575 AAACTAATAT
* *
1294585 TATTATTATGGTTAGTTATTAGGATTAGTAAAAACCCTAATTATTATTTTAGTTAGTATGATTGT
1 TATTATTATTGTTAGTTATTAGGATTAGTAAAAACCCTAATTATTATGTTAGTTAGTATGATTGT
* * * *
1294650 TAGTTTTTACAT
66 TAGTTATAAAAC
*** *
1294662 TA-TATTATTGTTAGTTATTATTTTTAGT-AAAACCCTAATTATTATGGTTAGTTAGTATTATT-
1 TATTATTATTGTTAGTTATTAGGATTAGTAAAAACCCTAATTATTAT-GTTAGTTAGTATGATTG
1294724 TTGAG-TATAAAAC
65 TT-AGTTATAAAAC
1294737 TATTATTATTGTTA
1 TATTATTATTGTTA
1294751 TTGTGTTAGT
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
75 25 0.33
76 49 0.64
77 2 0.03
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.51
Consensus pattern (77 bp):
TATTATTATTGTTAGTTATTAGGATTAGTAAAAACCCTAATTATTATGTTAGTTAGTATGATTGT
TAGTTATAAAAC
Found at i:1300406 original size:152 final size:149
Alignment explanation
Indices: 1299755--1300811 Score: 1042
Period size: 152 Copynumber: 7.0 Consensus size: 149
1299745 ACTTCAAAAA
* ** * *
1299755 AAATTTAGTAAAAAACCCTTATTTCGGCCCTTTATTCGTA-TTTTTTCCCGAATTTTATTACTTT
1 AAATTTA-TAAAAAACCCTTATTTCGGCCATTTGCTCATATTTTTTTCCCAAATTTTATTACTTT
*
1299819 -AAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
65 AAAAAAATATATTATTTTCT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
* * *
1299883 AATTAAATTTAGTGTTTTTTTAAAT
129 -ATT-AATTAATTGTTTTTTT--AG
* * * * * * *
1299908 AAATTTA-AAAAAACCCTTATTTCGCCCCTTTGCTCGTATATTTTTACCGATTTTTATTACTTTC
1 AAATTTATAAAAAACCCTTATTTCGGCCATTTGCTCATATTTTTTTCCCAAATTTTATTACTTT-
*
1299972 AATAAAAA-ATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATG
65 AA-AAAAATATATTATTTTCT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT
* *
1300036 TATTAATTAGGTCTGTTTTTTTAAAA
128 TATTAATTA-AT-TGTTTTTTT--AG
* * * * **
1300062 AAAATTAGTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCCGATTTTATTACTTT
1 AAATTTA-TAAAAAACCCTTATTTCGGCCATTTGCTCATATTTTTTTCCCAAATTTTATTACTTT
* *
1300127 -AAAAAATATA--A-----TATTTTATTATTTTAAATTATTTTAGTACATTATATTTGAAATTTA
65 AAAAAAATATATTATTTTCTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT-
* * * *
1300184 AATAAATTTAGTGTGTTTTTTAAAT
129 -ATTAA-TTAAT-TGTTTTTT-TAG
* *
1300209 AAATTT-TAAAAAAATCCTTATTTCGGCCCA-TTGCTCATATTTTTTTCTCAAATTTTATTACTT
1 AAATTTAT-AAAAAACCCTTATTTCGG-CCATTTGCTCATATTTTTTTCCCAAATTTTATTACTT
* * *
1300272 TCAATAAAAATATATTATTTTAGTATTTTATTAGTTTA-ATTTATTTTAGTATATTATGTTTGAA
64 T-AA-AAAAATATATTATTTT-CTATTTTATTATTTTACA-TTATTTTAGTACATTATGTTTGAA
* *
1300336 ATGTATTAATTAATTCTTTTTTTA-
125 ATTTATTAATTAATTGTTTTTTTAG
* * *
1300360 AAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTT
1 AAATTTA-TAAAAAACCCTTATTTCGGCCATTTGCTCATATTTTTTTCCCAAATTTTATTACTTT
* * * *
1300425 AAAAAAGTATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTATATTATGTTTTAAATTT
65 AAAAAAATATATTATTTTCT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
* *
1300490 ATTAATTTAGTGTATTTTTTAG
129 ATTAATTAATTGT-TTTTTTAG
* * * *
1300512 ATAAATTAAAAAAAACTCTTATTTCGGCCCTTTGCTCATATTTTTTTCCCAAATTTTATTACTTT
1 A-AATTTATAAAAAACCCTTATTTCGGCCATTTGCTCATATTTTTTTCCCAAATTTTATTACTTT
1300577 CAATAAAAATATATTATTTTCGTATTTTATT-TTTTACATTATTTTAGTACATTATGTTTGAAAT
65 -AA-AAAAATATATTATTTTC-TATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
* * *
1300641 GTGTTAATTAATTATTTTTTT--
127 TTATTAATTAATTGTTTTTTTAG
* * * * * **
1300662 AAATTTAGTAAAAAA-CCTTACTTCGACCCTTTGTTCGTATTTTTTTCTCCGCATTTTATTACTT
1 AAATTTA-TAAAAAACCCTTATTTCGGCCATTTGCTCATATTTTTTTC-CCAAATTTTATTACTT
* *
1300726 T-AGAAAATATCA-TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAACT
64 TAAAAAAATAT-ATTATTTTCT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
* *
1300789 TTATTAATTTAGTGTGTTTTTTA
127 TTATTAATTAATTGT-TTTTTTA
1300812 AATATACAAT
Statistics
Matches: 770, Mismatches: 89, Indels: 93
0.81 0.09 0.10
Matches are distributed among these distances:
145 1 0.00
146 88 0.11
147 31 0.04
148 59 0.08
149 51 0.07
150 85 0.11
151 48 0.06
152 132 0.17
153 71 0.09
154 105 0.14
155 10 0.01
156 50 0.06
157 39 0.05
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.51
Consensus pattern (149 bp):
AAATTTATAAAAAACCCTTATTTCGGCCATTTGCTCATATTTTTTTCCCAAATTTTATTACTTTA
AAAAAATATATTATTTTCTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAT
TAATTAATTGTTTTTTTAG
Found at i:1300667 original size:453 final size:445
Alignment explanation
Indices: 1299755--1300812 Score: 1248
Period size: 453 Copynumber: 2.3 Consensus size: 445
1299745 ACTTCAAAAA
* *
1299755 AAATTTAGTAAAAAACCCTTATTTCGGCCCTTTATTCGTA-TTTTTTCCCGAATTTTATTACTTT
1 AAATTTAG-AAAAAA-CCTTATTTCGGCCCTTTGTTCGTATTTTTTTCTCGAATTTTATTACTTT
1299819 AAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTA
64 AAAAAATATA-TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT-
* * *
1299884 ATTAAATTTAGTGTTTTTTTAAATAAATTTAAAAAAACCCTTATTTCGCCCCTTTGCTCGTATAT
127 ATT-AATTAAGTCTTTTTTT-AATAAATTTAAAAAAACCCTTATTTCGCCCATTTGCTCGTATAT
* *
1299949 TTTTACCGATTTTTATTACTTTCAATAAAAAATATTATTTTCTAATTTTATTATTTTACATTATT
190 TTTTACCGAATTTTATTACTTTCAATAAAAAATACTATTTTCTAATTTTATTATTTTACATTATT
*
1300014 TTAGTACATTATGTTTGAAATGTATTAATTAGGTCTGTTTTTTTAAAAAAAATTAGTAAAAAACC
255 TTAGTACATTATGTTTGAAATGTATTAATTAGG-CTGTTTTTTTAAAAAAAATTAGAAAAAAACC
* * **
1300079 CTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCCGATTTTATTACTTTAAAAAATATAATATTTT
319 CTTATTTCGGCCCTTTGCTCATATTTTTTTCCCAAATTTTATTACTTTAAAAAATATAATATTTT
* * *
1300144 ATTATTTTAAATTATTTTAGTACATTATATTTGAAATTTAAATAAATTTAGTGTGTTTTTTAAAT
384 ATTATTTTAAATTATTTTAGTACATTATATTTGAAATGT-AATAAATTTAATGTATTTTTT--AT
* * * *
1300209 AAATTTTA-AAAAAATCCTTATTTCGGCCCATTGCTCATATTTTTTTCTCAAATTTTATTACTTT
1 AAA-TTTAGAAAAAA-CCTTATTTCGGCCCTTTGTTCGTATTTTTTTCTCGAATTTTATTACTTT
* * *
1300273 CAATAAAA-ATATATTATTTTAGTATTTTATTAGTTTA-ATTTATTTTAGTATATTATGTTTGAA
64 -AA-AAAATATATATT-TTCTA--ATTTTATTATTTTACA-TTATTTTAGTACATTATGTTTGAA
* * * *
1300336 ATGTATTAATTAATTCTTTTTTT-A-AAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGT
123 ATTTATTAATTAAGTCTTTTTTTAATAAATTTA--AAAAAACCCTTATTTCGCCCATTTGCTCGT
* * *
1300399 ATTTTTTTCCCGAATTTTATTACTTT-AA-AAAAGTATACTATTTTCTAATTTTATTATTTTACA
186 ATATTTTTACCGAATTTTATTACTTTCAATAAAA-AATACTATTTTCTAATTTTATTATTTTACA
* * * * *
1300462 TTATTTTAGTATATTATGTTTTAAATTTATTAATTTA-G-TGTATTTTTT-AGATAAATTA-AAA
250 TTATTTTAGTACATTATGTTTGAAATGTATTAA-TTAGGCTGT-TTTTTTAAAAAAAATTAGAAA
*
1300523 AAAACTCTTATTTCGGCCCTTTGCTCATATTTTTTTCCCAAATTTTATTACTTTCAATAAAAATA
313 AAAACCCTTATTTCGGCCCTTTGCTCATATTTTTTTCCCAAATTTTATTACTTT--A-AAAAATA
* * * * *
1300588 TATTATTTTCGTATTTTATTTTTTACATTATTTTAGTACATTATGTTTGAAATGT-GTTAA-TTA
375 TAATA-TTT--TA--TTA--TTTTAAATTATTTTAGTACATTATATTTGAAATGTAATAAATTTA
1300651 AT-TATTTTTT-T
433 ATGTATTTTTTAT
* * *
1300662 AAATTTAGTAAAAAACCTTACTTCGACCCTTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTT
1 AAATTTAG-AAAAAACCTTATTTCGGCCCTTTGTTCGTATTTTTTTCT-CGAATTTTATTACTTT
* *
1300727 AGAAAATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAACTTTA
64 AAAAAATAT-ATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTA
* *
1300792 TTAATTTAGTGTGTTTTTTAA
128 TTAATTAAGTCT-TTTTTTAA
1300813 ATATACAATT
Statistics
Matches: 516, Mismatches: 57, Indels: 63
0.81 0.09 0.10
Matches are distributed among these distances:
450 51 0.10
451 59 0.11
452 33 0.06
453 139 0.27
454 110 0.21
455 26 0.05
456 17 0.03
457 43 0.08
458 6 0.01
460 32 0.06
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.51
Consensus pattern (445 bp):
AAATTTAGAAAAAACCTTATTTCGGCCCTTTGTTCGTATTTTTTTCTCGAATTTTATTACTTTAA
AAAATATATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTA
ATTAAGTCTTTTTTTAATAAATTTAAAAAAACCCTTATTTCGCCCATTTGCTCGTATATTTTTAC
CGAATTTTATTACTTTCAATAAAAAATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTA
CATTATGTTTGAAATGTATTAATTAGGCTGTTTTTTTAAAAAAAATTAGAAAAAAACCCTTATTT
CGGCCCTTTGCTCATATTTTTTTCCCAAATTTTATTACTTTAAAAAATATAATATTTTATTATTT
TAAATTATTTTAGTACATTATATTTGAAATGTAATAAATTTAATGTATTTTTTAT
Found at i:1301157 original size:9 final size:10
Alignment explanation
Indices: 1301143--1301260 Score: 67
Period size: 10 Copynumber: 11.0 Consensus size: 10
1301133 AAAATTTACC
1301143 TTCTTT-TTT
1 TTCTTTCTTT
1301152 TTCTTTCTTT
1 TTCTTTCTTT
* *
1301162 TTCCTTCCTT
1 TTCTTTCTTT
**
1301172 CCCTCTTCTTCT
1 TTCT-TTCTT-T
1301184 TCTCCTTTCTTT
1 T-T-CTTTCTTT
*
1301196 TTCTTTCTTC
1 TTCTTTCTTT
*
1301206 TCCTTTCCTTT
1 TTCTTT-CTTT
1301217 TTCTTTCTCTCCTT
1 TTC-TT-TCT--TT
*
1301231 TTCTTTCTTC
1 TTCTTTCTTT
* *
1301241 TCCTTTCCTT
1 TTCTTTCTTT
1301251 TTCTTTCTTT
1 TTCTTTCTTT
1301261 CTTTCTTCTC
Statistics
Matches: 81, Mismatches: 18, Indels: 19
0.69 0.15 0.16
Matches are distributed among these distances:
9 6 0.07
10 40 0.49
11 10 0.12
12 10 0.12
13 8 0.10
14 7 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:1301192 original size:28 final size:28
Alignment explanation
Indices: 1301161--1301276 Score: 73
Period size: 28 Copynumber: 4.2 Consensus size: 28
1301151 TTTCTTTCTT
1301161 TTTCCTTCCTTCCCTCTTC-TTCTTCTCC
1 TTTCCTT-CTTCCCTCTTCTTTCTTCTCC
* ** *
1301189 TTT-CTTTTTCTTTCTTC-TCCTT-TCC
1 TTTCCTTCTTCCCTCTTCTTTCTTCTCC
* *
1301214 TTTTTCTT-TCTCTCCTTTTCTTTCTTCTCC
1 -TTTCCTTCT-TC-CCTCTTCTTTCTTCTCC
**
1301244 TTTCCTT-TTCTTTCTTTCTTTCTTCTCC
1 TTTCCTTCTTCCCTC-TTCTTTCTTCTCC
1301272 TTTCC
1 TTTCC
1301277 CTCTCCTTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 14
0.73 0.13 0.15
Matches are distributed among these distances:
25 3 0.04
26 16 0.23
27 9 0.13
28 27 0.39
29 11 0.16
30 3 0.04
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTCCTTCTTCCCTCTTCTTTCTTCTCC
Found at i:1301205 original size:20 final size:20
Alignment explanation
Indices: 1301180--1301275 Score: 108
Period size: 20 Copynumber: 4.7 Consensus size: 20
1301170 TTCCCTCTTC
1301180 TTCTTCTCCTTTCTTTTTCT
1 TTCTTCTCCTTTCTTTTTCT
1301200 TTCTTCTCCTTTCCTTTTTCT
1 TTCTTCTCCTTT-CTTTTTCT
1301221 TTC-TCTCCTTTTCTTTCTTC-
1 TTCTTCTCC-TTTCTTT-TTCT
*
1301241 TCCTT-TCCTTTTCTTTCTTTCT
1 TTCTTCTCC-TTTC-TT-TTTCT
1301263 TTCTTCTCCTTTC
1 TTCTTCTCCTTTC
1301276 CCTCTCCTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 14
0.80 0.02 0.17
Matches are distributed among these distances:
20 31 0.47
21 23 0.35
22 9 0.14
23 3 0.05
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (20 bp):
TTCTTCTCCTTTCTTTTTCT
Found at i:1301220 original size:14 final size:15
Alignment explanation
Indices: 1301198--1301276 Score: 74
Period size: 15 Copynumber: 5.1 Consensus size: 15
1301188 CTTTCTTTTT
1301198 CTTTCTTCTCCTTTC
1 CTTTCTTCTCCTTTC
*
1301213 CTTTTTCTTTCTCTCCTTTT
1 C--TTTC--T-TCTCCTTTC
1301233 CTTTCTTCTCCTTTC
1 CTTTCTTCTCCTTTC
1301248 CTTTTCTT-T-CTTT-
1 C-TTTCTTCTCCTTTC
1301261 CTTTCTTCTCCTTTC
1 CTTTCTTCTCCTTTC
1301276 C
1 C
1301277 CTCTCCTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 18
0.73 0.03 0.25
Matches are distributed among these distances:
12 6 0.11
13 2 0.04
14 8 0.15
15 12 0.23
16 7 0.13
17 4 0.08
18 4 0.08
19 1 0.02
20 9 0.17
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
CTTTCTTCTCCTTTC
Found at i:1301229 original size:15 final size:16
Alignment explanation
Indices: 1301192--1301274 Score: 61
Period size: 17 Copynumber: 5.2 Consensus size: 16
1301182 CTTCTCCTTT
1301192 CTTTTTCTTTCTTCTC
1 CTTTTTCTTTCTTCTC
1301208 CTTTCCTT-TTTCTTTCTC
1 CTTT--TTCTTTC-TTCTC
*
1301226 TCCTTTTCTTTCTTCTC
1 -CTTTTTCTTTCTTCTC
*
1301243 C--TTTCCTT-TTCT-
1 CTTTTTCTTTCTTCTC
1301255 -TTCTTTCTTTCTTCTC
1 CTT-TTTCTTTCTTCTC
1301271 CTTT
1 CTTT
1301275 CCCTCTCCTT
Statistics
Matches: 53, Mismatches: 3, Indels: 22
0.68 0.04 0.28
Matches are distributed among these distances:
13 4 0.08
14 12 0.23
15 4 0.08
16 6 0.11
17 13 0.25
18 11 0.21
19 3 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (16 bp):
CTTTTTCTTTCTTCTC
Found at i:1302335 original size:21 final size:21
Alignment explanation
Indices: 1302311--1302531 Score: 442
Period size: 21 Copynumber: 10.5 Consensus size: 21
1302301 TTCTTTATAT
1302311 ATTTTTAGAATTTTTTTTGAA
1 ATTTTTAGAATTTTTTTTGAA
1302332 ATTTTTAGAATTTTTTTTGAA
1 ATTTTTAGAATTTTTTTTGAA
1302353 ATTTTTAGAATTTTTTTTGAA
1 ATTTTTAGAATTTTTTTTGAA
1302374 ATTTTTAGAATTTTTTTTGAA
1 ATTTTTAGAATTTTTTTTGAA
1302395 ATTTTTAGAATTTTTTTTGAA
1 ATTTTTAGAATTTTTTTTGAA
1302416 ATTTTTAGAATTTTTTTTGAA
1 ATTTTTAGAATTTTTTTTGAA
1302437 ATTTTTAGAATTTTTTTTGAA
1 ATTTTTAGAATTTTTTTTGAA
1302458 ATTTTTAGAATTTTTTTTGAA
1 ATTTTTAGAATTTTTTTTGAA
1302479 ATTTTTAGAATTTTTTTTGAA
1 ATTTTTAGAATTTTTTTTGAA
1302500 ATTTTTAGAATTTTTTTTGAA
1 ATTTTTAGAATTTTTTTTGAA
1302521 ATTTTTAGAAT
1 ATTTTTAGAAT
1302532 CTTTAAAAAT
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 200 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (21 bp):
ATTTTTAGAATTTTTTTTGAA
Found at i:1302599 original size:20 final size:19
Alignment explanation
Indices: 1302555--1302630 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 19
1302545 TAAATGTTGG
*
1302555 AATTTTTATAAATATTTTT
1 AATTTTTAAAAATATTTTT
1302574 AA-TTTTAAAAATTATTTTT
1 AATTTTTAAAAA-TATTTTT
* *
1302593 AATTTTTGAAAAACATTTTG
1 AATTTTT-AAAAATATTTTT
*
1302613 AATTTTTTAAAATTATTT
1 AA-TTTTTAAAAATATTT
1302631 GAATTTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
18 8 0.17
19 11 0.23
20 19 0.40
21 10 0.21
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (19 bp):
AATTTTTAAAAATATTTTT
Found at i:1302617 original size:39 final size:38
Alignment explanation
Indices: 1302554--1302638 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 38
1302544 ATAAATGTTG
* * *
1302554 GAATTTTTATAAATATTTTTAA-TTTTAAAAATTATTTT
1 GAATTTTTAAAAACATTTTGAATTTTTAAAAATTA-TTT
* *
1302592 TAATTTTTGAAAAACATTTTGAATTTTTTAAAATTATTT
1 GAATTTTT-AAAAACATTTTGAATTTTTAAAAATTATTT
1302631 GAATTTTT
1 GAATTTTT
1302639 TTTATTTTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
38 7 0.18
39 21 0.54
40 11 0.28
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (38 bp):
GAATTTTTAAAAACATTTTGAATTTTTAAAAATTATTT
Found at i:1302631 original size:19 final size:20
Alignment explanation
Indices: 1302325--1302639 Score: 97
Period size: 21 Copynumber: 15.7 Consensus size: 20
1302315 TTAGAATTTT
* * *
1302325 TTTTGAAATTTTTAGAATTTT
1 TTTTGAATTTTTTA-AAATTA
* * *
1302346 TTTTGAAATTTTTAGAATTTT
1 TTTTGAATTTTTTA-AAATTA
* * *
1302367 TTTTGAAATTTTTAGAATTTT
1 TTTTGAATTTTTTA-AAATTA
* * *
1302388 TTTTGAAATTTTTAGAATTTT
1 TTTTGAATTTTTTA-AAATTA
* * *
1302409 TTTTGAAATTTTTAGAATTTT
1 TTTTGAATTTTTTA-AAATTA
* * *
1302430 TTTTGAAATTTTTAGAATTTT
1 TTTTGAATTTTTTA-AAATTA
* * *
1302451 TTTTGAAATTTTTAGAATTTT
1 TTTTGAATTTTTTA-AAATTA
* * *
1302472 TTTTGAAATTTTTAGAATTTT
1 TTTTGAATTTTTTA-AAATTA
* * *
1302493 TTTTGAAATTTTTAGAATTTT
1 TTTTGAATTTTTTA-AAATTA
* * *
1302514 TTTTGAAATTTTTAGAA-TC
1 TTTTGAATTTTTTAAAATTA
** * * *
1302533 TTTAAAAATATAT-AAA-T-
1 TTTTGAATTTTTTAAAATTA
* *
1302550 GTTGGAA-TTTTTATAAA-TA
1 TTTTGAATTTTTTA-AAATTA
* *
1302569 TTTTTAA-TTTTAAAAATTA
1 TTTTGAATTTTTTAAAATTA
* * **
1302588 TTTTTAATTTTTGAAAAACA
1 TTTTGAATTTTTTAAAATTA
1302608 TTTTGAATTTTTTAAAATTA
1 TTTTGAATTTTTTAAAATTA
1302628 -TTTGAATTTTTT
1 TTTTGAATTTTTT
1302640 TTATTTTTGT
Statistics
Matches: 265, Mismatches: 24, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
16 3 0.01
17 4 0.02
18 10 0.04
19 40 0.15
20 26 0.10
21 182 0.69
ACGTcount: A:0.32, C:0.01, G:0.08, T:0.59
Consensus pattern (20 bp):
TTTTGAATTTTTTAAAATTA
Found at i:1302756 original size:19 final size:19
Alignment explanation
Indices: 1302732--1302793 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1302722 ATTCAACTCG
1302732 ATTCAAACTCGAATTACTT
1 ATTCAAACTCGAATTACTT
* * * * *
1302751 ATTCAAA-TTGACTCAAATA
1 ATTCAAACTCGAAT-TACTT
1302770 ATTTCAAACTCGAATTACTT
1 A-TTCAAACTCGAATTACTT
1302790 ATTC
1 ATTC
1302794 GAATTGACTC
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
18 4 0.13
19 13 0.43
20 9 0.30
21 4 0.13
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTCAAACTCGAATTACTT
Found at i:1302783 original size:39 final size:39
Alignment explanation
Indices: 1302733--1302812 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
1302723 TTCAACTCGA
1302733 TTCAAACTCGAATTACTTATTCAAATTGACTCAAATAAT
1 TTCAAACTCGAATTACTTATTCAAATTGACTCAAATAAT
*
1302772 TTCAAACTCGAATTACTTATTCGAATTGACTCAAATAAT
1 TTCAAACTCGAATTACTTATTCAAATTGACTCAAATAAT
1302811 TT
1 TT
1302813 AACTAACTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (39 bp):
TTCAAACTCGAATTACTTATTCAAATTGACTCAAATAAT
Found at i:1303641 original size:17 final size:17
Alignment explanation
Indices: 1303619--1303653 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1303609 AATACATTAA
1303619 TTAATT-AATTAATTTTC
1 TTAATTAAATT-ATTTTC
1303636 TTAATTAAATTATTTTC
1 TTAATTAAATTATTTTC
1303653 T
1 T
1303654 CTACCCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (17 bp):
TTAATTAAATTATTTTC
Found at i:1304334 original size:24 final size:24
Alignment explanation
Indices: 1304297--1304351 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
1304287 ACAATAGTTC
* *
1304297 ATTCTTCCTTATTTTTTAT-TTCTT
1 ATTCTTCCTCA-TTTCTATCTTCTT
*
1304321 ATTCTTCGTCATTTCTATCTTCTT
1 ATTCTTCCTCATTTCTATCTTCTT
*
1304345 TTTCTTC
1 ATTCTTC
1304352 TTTTTTGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.11, C:0.22, G:0.02, T:0.65
Consensus pattern (24 bp):
ATTCTTCCTCATTTCTATCTTCTT
Found at i:1306174 original size:16 final size:16
Alignment explanation
Indices: 1306153--1306184 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1306143 TGATTGAAAG
*
1306153 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
1306169 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
1306185 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:1308250 original size:62 final size:61
Alignment explanation
Indices: 1308149--1308323 Score: 181
Period size: 62 Copynumber: 2.8 Consensus size: 61
1308139 GCTGTCGACG
* * *
1308149 CCACACGGCC-AGGCACACGAGTGTGTGCCCAGGCTGTGTAACTCATTGTTTGTGGTACAAGA
1 CCACAC-GCCAAGG-ACACGGGCGTGTGCCCAGGCCGTGTAACTCATTGTTTGTGGTACAAGA
* *
1308211 CCACACGCCCAAGGACACGGGCGTGTGCCCAGGCCGTGTAAGTCACTGTTTGTGGTACAAGA
1 CCACACG-CCAAGGACACGGGCGTGTGCCCAGGCCGTGTAACTCATTGTTTGTGGTACAAGA
* * * * * * * **
1308273 TCACACAGGCAGGGGCACAGGCATGTGTCCAGTTCGTGTAACTCATTGTTT
1 CCACAC-GCCAAGGACACGGGCGTGTGCCCAGGCCGTGTAACTCATTGTTT
1308324 ATGCTTCGAA
Statistics
Matches: 94, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
61 1 0.01
62 89 0.95
63 4 0.04
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.22
Consensus pattern (61 bp):
CCACACGCCAAGGACACGGGCGTGTGCCCAGGCCGTGTAACTCATTGTTTGTGGTACAAGA
Found at i:1321627 original size:31 final size:31
Alignment explanation
Indices: 1321592--1321650 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
1321582 ATGTGTATGA
* * *
1321592 TTGAATCAAAATTAAAGTTGCATGTATACAT
1 TTGAACCAAAATCAAAGTTGCATATATACAT
* *
1321623 TTGAACCACAATCAAAGTTTCATATATA
1 TTGAACCAAAATCAAAGTTGCATATATA
1321651 TAATTACACC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (31 bp):
TTGAACCAAAATCAAAGTTGCATATATACAT
Found at i:1326365 original size:30 final size:29
Alignment explanation
Indices: 1326267--1326365 Score: 76
Period size: 30 Copynumber: 3.3 Consensus size: 29
1326257 AGTATATTGC
* *
1326267 CAGTCACT-AACTTTTATTAAAATAATAAAG
1 CAGTCACTAAAC-TTTA-GAAAATAAAAAAG
* * * **
1326297 CAGACACTAAACTTT-GAAAAGTGACAACT
1 CAGTCACTAAACTTTAGAAAA-TAAAAAAG
*
1326326 CAATCACTAAACTTTACGAAAATAAAAAAG
1 CAGTCACTAAACTTTA-GAAAATAAAAAAG
1326356 CAGTCACTAA
1 CAGTCACTAA
1326366 CAGACATTTT
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
28 4 0.08
29 17 0.33
30 23 0.44
31 8 0.15
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.24
Consensus pattern (29 bp):
CAGTCACTAAACTTTAGAAAATAAAAAAG
Found at i:1328730 original size:28 final size:29
Alignment explanation
Indices: 1328686--1328753 Score: 97
Period size: 28 Copynumber: 2.4 Consensus size: 29
1328676 TTTTCCATTT
*
1328686 TCCTCCACTCT-TATCATAGCAGTCGTTC
1 TCCTTCACTCTCTATCATAGCAGTCGTTC
*
1328714 TCCTTCACTCTCT-TCATAGTAGTCGTTC
1 TCCTTCACTCTCTATCATAGCAGTCGTTC
1328742 TCCTTC-CTCTCT
1 TCCTTCACTCTCT
1328754 GTCCATCAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 6 0.16
28 30 0.81
29 1 0.03
ACGTcount: A:0.13, C:0.37, G:0.09, T:0.41
Consensus pattern (29 bp):
TCCTTCACTCTCTATCATAGCAGTCGTTC
Found at i:1330125 original size:21 final size:21
Alignment explanation
Indices: 1330101--1330143 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1330091 TAATTATCTT
*
1330101 ATAATTGC-TCATTGATTTGTA
1 ATAATTGCAT-ATTAATTTGTA
1330122 ATAATTGCATATTAATTTGTA
1 ATAATTGCATATTAATTTGTA
1330143 A
1 A
1330144 ATTTTTGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.47
Consensus pattern (21 bp):
ATAATTGCATATTAATTTGTA
Found at i:1331502 original size:45 final size:45
Alignment explanation
Indices: 1331416--1331509 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 45
1331406 AGAATGGTCT
*
1331416 GCTAAGAGAGAGAAAATTACACAAACTACAAGGACTGATTATATG
1 GCTAAGAGAGAGAAAATTACACAAACTACAAGGACTAATTATATG
* * **
1331461 GCTAAGAGAGAGGAAATTGCACAAACTATGTA-GACTAATTATATG
1 GCTAAGAGAGAGAAAATTACACAAACTA-CAAGGACTAATTATATG
1331506 GCTA
1 GCTA
1331510 GAAATATTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 42 0.98
46 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.22
Consensus pattern (45 bp):
GCTAAGAGAGAGAAAATTACACAAACTACAAGGACTAATTATATG
Found at i:1334081 original size:136 final size:137
Alignment explanation
Indices: 1333903--1334177 Score: 516
Period size: 136 Copynumber: 2.0 Consensus size: 137
1333893 AAATGATGAA
1333903 CCTTAGTTTACTTGGGTAATATGTCAATATATCCCTCCGATACCATCACCACTCCGAACCCCCGT
1 CCTTAGTTTAC-TGGGTAATATGTCAATATATCCCTCCGATACCATCACCACTCCGAACCCCCGT
*
1333968 AATACACCAAAACACGAATGTATTTTATCCCCCGTTCAATTCAAAACAAACATCAAAATTCAATA
65 AATACACCAAAACACGAATGTATTTTATACCCCGTTCAATTCAAAACAAACATCAAAATTCAATA
1334033 TTATAACT
130 TTATAACT
1334041 CCTTAGTTTAC-GGGTAATATGTCAATATATCCCTCCGATACCATCACCACTCCGAACCCCCGTA
1 CCTTAGTTTACTGGGTAATATGTCAATATATCCCTCCGATACCATCACCACTCCGAACCCCCGTA
*
1334105 ATACACCAAAACACGAATGTATTTTATATCCCGTTCAATTCAAAACAAACATCAAAATTCAATAT
66 ATACACCAAAACACGAATGTATTTTATACCCCGTTCAATTCAAAACAAACATCAAAATTCAATAT
1334170 TATAACT
131 TATAACT
1334177 C
1 C
1334178 AGATAATGAT
Statistics
Matches: 135, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
136 124 0.92
138 11 0.08
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (137 bp):
CCTTAGTTTACTGGGTAATATGTCAATATATCCCTCCGATACCATCACCACTCCGAACCCCCGTA
ATACACCAAAACACGAATGTATTTTATACCCCGTTCAATTCAAAACAAACATCAAAATTCAATAT
TATAACT
Found at i:1334212 original size:2 final size:2
Alignment explanation
Indices: 1334205--1334233 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1334195 CAATAGTGGA
1334205 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1334234 CACATCATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1336684 original size:2 final size:2
Alignment explanation
Indices: 1336677--1336705 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1336667 CAATAGTGGA
1336677 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1336706 CACATCATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1339403 original size:21 final size:21
Alignment explanation
Indices: 1339377--1339418 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1339367 GTCCAATGTG
*
1339377 GCTAGTTAACTGGTCACGTCA
1 GCTAGTTAACGGGTCACGTCA
1339398 GCTAGTTAACGGGTCACGTCA
1 GCTAGTTAACGGGTCACGTCA
1339419 CCTATCCCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (21 bp):
GCTAGTTAACGGGTCACGTCA
Found at i:1343369 original size:28 final size:26
Alignment explanation
Indices: 1343318--1343372 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 26
1343308 TATTTTAAAA
1343318 AATTATAATAAAAAATAAATATTAAT
1 AATTATAATAAAAAATAAATATTAAT
1343344 AATTATAGTATAAATAAATAAA-ATTAAT
1 AATTATA--ATAAA-AAATAAATATTAAT
1343372 A
1 A
1343373 CACAAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 7 0.27
28 12 0.46
29 7 0.27
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
AATTATAATAAAAAATAAATATTAAT
Found at i:1345626 original size:40 final size:40
Alignment explanation
Indices: 1345568--1345705 Score: 104
Period size: 40 Copynumber: 3.5 Consensus size: 40
1345558 ACCCACTAGT
**
1345568 TTGACACCCAATGCCTCATCAGATAATTCGAAGTAATAAA
1 TTGACACCCAATGCCTCATCAGATAAACCGAAGTAATAAA
* * * *
1345608 TTGACATCCAGTGTCTCATCAGCTAAACCGAAG---TAAA
1 TTGACACCCAATGCCTCATCAGATAAACCGAAGTAATAAA
* * * * *
1345645 TTGGCACCCAGTGCCTCATC-GAATTAATCTGAAGTAGTAAA
1 TTGACACCCAATGCCTCATCAG-A-TAAACCGAAGTAATAAA
* * *
1345686 TTAAAACCCAATGTCTCATC
1 TTGACACCCAATGCCTCATC
1345706 GACTCGAAGT
Statistics
Matches: 76, Mismatches: 17, Indels: 9
0.75 0.17 0.09
Matches are distributed among these distances:
36 1 0.01
37 21 0.28
38 8 0.11
40 27 0.36
41 19 0.25
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (40 bp):
TTGACACCCAATGCCTCATCAGATAAACCGAAGTAATAAA
Found at i:1345908 original size:24 final size:24
Alignment explanation
Indices: 1345863--1345909 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1345853 TATATATACC
1345863 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
1345887 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
1345910 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:1346650 original size:30 final size:32
Alignment explanation
Indices: 1346610--1346677 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
1346600 TTTCTTTTAT
* *
1346610 TATATTTACTT-ATTA-TAATATATAATATAA
1 TATATATACTTAATTATTAAGATATAATATAA
*
1346640 TATATATACTTAATTATTAAGATATAATATTA
1 TATATATACTTAATTATTAAGATATAATATAA
1346672 TA-ATAT
1 TATATAT
1346678 TAATATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 10 0.30
31 8 0.24
32 15 0.45
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (32 bp):
TATATATACTTAATTATTAAGATATAATATAA
Found at i:1360716 original size:47 final size:47
Alignment explanation
Indices: 1360662--1360798 Score: 274
Period size: 47 Copynumber: 2.9 Consensus size: 47
1360652 TTAGTTTGGT
1360662 AATGAACAGTTTTCTTGTATGGATTTGTTTAGGTCTTCCTCTTGGAA
1 AATGAACAGTTTTCTTGTATGGATTTGTTTAGGTCTTCCTCTTGGAA
1360709 AATGAACAGTTTTCTTGTATGGATTTGTTTAGGTCTTCCTCTTGGAA
1 AATGAACAGTTTTCTTGTATGGATTTGTTTAGGTCTTCCTCTTGGAA
1360756 AATGAACAGTTTTCTTGTATGGATTTGTTTAGGTCTTCCTCTT
1 AATGAACAGTTTTCTTGTATGGATTTGTTTAGGTCTTCCTCTT
1360799 TTCCAATTCA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 90 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.46
Consensus pattern (47 bp):
AATGAACAGTTTTCTTGTATGGATTTGTTTAGGTCTTCCTCTTGGAA
Found at i:1380057 original size:3 final size:3
Alignment explanation
Indices: 1380049--1380078 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1380039 TTCATGTATA
1380049 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1380079 CCATAGCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:1380496 original size:23 final size:23
Alignment explanation
Indices: 1380465--1380509 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1380455 TGTAGATGTC
*
1380465 TGAATTTAAAGG-GAGAGGAGAGA
1 TGAAATTAAAGGTGAGA-GAGAGA
1380488 TGAAATTAAAGGTGAGAGAGAG
1 TGAAATTAAAGGTGAGAGAGAG
1380510 TGTTGTCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.38, T:0.18
Consensus pattern (23 bp):
TGAAATTAAAGGTGAGAGAGAGA
Found at i:1385976 original size:21 final size:20
Alignment explanation
Indices: 1385927--1385963 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1385917 ATACAAAAGG
1385927 AAAA-TCAAAATAATTTTCA
1 AAAATTCAAAATAATTTTCA
1385946 AAAATTCAAAATAATTTT
1 AAAATTCAAAATAATTTT
1385964 TTAAATTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATTCAAAATAATTTTCA
Found at i:1385995 original size:19 final size:19
Alignment explanation
Indices: 1385945--1386002 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
1385935 AATAATTTTC
* *
1385945 AAAAATTCAAAATAATTTTT
1 AAAAATTCCAAAT-ATTTAT
* * *
1385965 TAAATTTTCAAATATTTAT
1 AAAAATTCCAAATATTTAT
1385984 AAAAATTCCAAA-ATTTAT
1 AAAAATTCCAAATATTTAT
1386002 A
1 A
1386003 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
18 7 0.23
19 14 0.47
20 9 0.30
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAAATTCCAAATATTTAT
Found at i:1386808 original size:373 final size:373
Alignment explanation
Indices: 1386058--1387178 Score: 1968
Period size: 374 Copynumber: 3.0 Consensus size: 373
1386048 TATAAAGTTC
* *
1386058 AAAATTTAAAATAATAATTTTGGAACATAAATAAGTTAATTAATAATTCAAGTTTATCATACTAA
1 AAAAATTAAAATAATAAATTTGGAACATAAATAAGTTAATTAATAATTCAAGTTTATCATACTAA
* *
1386123 AGTATTTTTTTTTCTTATTTTGCTTTGAAAAAGTTTTCAAATATATACGGCTTCAAATTTGTGTG
66 AGTATTTTTTTTTCTTATTTTGCTTTGAAAAAGTTTTCAAATATATATGGCTTCAAATTTATGTG
1386188 CTCTAACATGGAATTAGTTATACTATGATAAGATTTTAATTTGACATGTTTAATTTTTTAATTTA
131 CTCTAACATGGAATTAGTTATACTATGATAAGATTTTAATTTGACATGTTTAATTTTTTAATTTA
* *
1386253 ACTCAAATAATTTCACTCGATTTTAAATTTCATTTGAATCGACTCAATTTGAAAAATTTTTAAAC
196 ACTCAAATAATTTCACTCGATTTTAAATTTCATTTGAATCGACTCAATTCGAAAAAATTTTAAAC
1386318 TGAGTTAGGATGATAAAATAGAACTTGTCAACTCGATTAAATCGAAATTTTTTACTCGATTCGAT
261 TGAGTTAGGATGATAAAATAGAACTTGTCAACTCGATTAAATCGAAATTTTTTACTCGATTCGAT
1386383 CGAAAGCTCACCCCTACTCGTTAACCAAGTTACCCCCCATCCATTAAA
326 CGAAAGCTCACCCCTACTCGTTAACCAAGTTACCCCCCATCCATTAAA
*
1386431 AAAAATTAAAATAATAAATTTGGAACATAAATAAGTTAATTAATAATTCAAGTTTATCATATTAA
1 AAAAATTAAAATAATAAATTTGGAACATAAATAAGTTAATTAATAATTCAAGTTTATCATACTAA
*
1386496 AGTATTTTTTTTTCTTATTTTGCTTTGAAAAAGTTTTCAAATATATATGGCTTCAAATTTTTGTG
66 AGTATTTTTTTTTCTTATTTTGCTTTGAAAAAGTTTTCAAATATATATGGCTTCAAATTTATGTG
1386561 CTCTAACATGGAATTAGTTATACTATGATAAGATTTTAATTTGACATGTTTAATTTTTTTAATTT
131 CTCTAACATGGAATTAGTTATACTATGATAAGATTTTAATTTGACATGTTTAA-TTTTTTAATTT
1386626 AACTCAAATAATTTCACTCGATTTTAAATTTCATTTGAATCGACTCAATTCGAAAAAATTTTAAA
195 AACTCAAATAATTTCACTCGATTTTAAATTTCATTTGAATCGACTCAATTCGAAAAAATTTTAAA
*
1386691 CTGAGTTAGGATGATAAAATAGAACTTGTCAACTCGATTAAATCAAAATTTTTTACTCGATTCGA
260 CTGAGTTAGGATGATAAAATAGAACTTGTCAACTCGATTAAATCGAAATTTTTTACTCGATTCGA
1386756 TCGAAAGCTCACCCCTACTCGTTAACCAAGTTACCCCCCATCCATTAAA
325 TCGAAAGCTCACCCCTACTCGTTAACCAAGTTACCCCCCATCCATTAAA
*
1386805 AAAAATCTAAAATGATAAATTTGGAACATAAATAAGTTAATTAATAATTCAAGTTTATCATACTA
1 AAAAAT-TAAAATAATAAATTTGGAACATAAATAAGTTAATTAATAATTCAAGTTTATCATACTA
*
1386870 AAGTA-TTTTTTTTCTTA------TTTGAAAAAGTTTTCAAATATATATGGTTTCAAATTTATGT
65 AAGTATTTTTTTTTCTTATTTTGCTTTGAAAAAGTTTTCAAATATATATGGCTTCAAATTTATGT
* *
1386928 GCTCTAACATGGAATTAGTTATACTATGATAATATTTTAATTTGACATGTTTAATTTTATAATTT
130 GCTCTAACATGGAATTAGTTATACTATGATAAGATTTTAATTTGACATGTTTAATTTTTTAATTT
* * *
1386993 AACTCAAACAATTTCACTCGATTTTAAATTTCATTTGAATCGACTCAATTCGAAAAAAATTCAAA
195 AACTCAAATAATTTCACTCGATTTTAAATTTCATTTGAATCGACTCAATTCGAAAAAATTTTAAA
* * *
1387058 CCGAGTTAGGATGATAAAATAGAACTTGTCAACTCGACTAACTCGAAATTTTTTCACTCGATTCG
260 CTGAGTTAGGATGATAAAATAGAACTTGTCAACTCGATTAAATCGAAATTTTTT-ACTCGATTCG
*
1387123 ATTGAAAGCTCACCCCTACTCGTTAACCAAGTTAACCCCCCTATCCATTAAA
324 ATCGAAAGCTCACCCCTACTCGTTAACCAAGTT-ACCCCCC-ATCCATTAAA
1387175 AAAA
1 AAAA
1387179 TACCTTAGTC
Statistics
Matches: 721, Mismatches: 22, Indels: 13
0.95 0.03 0.02
Matches are distributed among these distances:
367 122 0.17
368 134 0.19
369 7 0.01
370 14 0.02
373 178 0.25
374 205 0.28
375 61 0.08
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (373 bp):
AAAAATTAAAATAATAAATTTGGAACATAAATAAGTTAATTAATAATTCAAGTTTATCATACTAA
AGTATTTTTTTTTCTTATTTTGCTTTGAAAAAGTTTTCAAATATATATGGCTTCAAATTTATGTG
CTCTAACATGGAATTAGTTATACTATGATAAGATTTTAATTTGACATGTTTAATTTTTTAATTTA
ACTCAAATAATTTCACTCGATTTTAAATTTCATTTGAATCGACTCAATTCGAAAAAATTTTAAAC
TGAGTTAGGATGATAAAATAGAACTTGTCAACTCGATTAAATCGAAATTTTTTACTCGATTCGAT
CGAAAGCTCACCCCTACTCGTTAACCAAGTTACCCCCCATCCATTAAA
Found at i:1390206 original size:18 final size:19
Alignment explanation
Indices: 1390175--1390210 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1390165 TGTCCATGTT
*
1390175 ATATATTATTAAAAATAAA
1 ATATATTATAAAAAATAAA
1390194 ATAT-TTATAAAAAATAA
1 ATATATTATAAAAAATAA
1390211 TTTTCTATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATATATTATAAAAAATAAA
Found at i:1398427 original size:60 final size:60
Alignment explanation
Indices: 1398334--1398452 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
1398324 TTGTTTTTTA
*
1398334 TAATTATTTTAAAATTAATGTGTTAGTAATTTAGGATTATGTTATAAATTATTATGTTTG
1 TAATTATTTTAAAATTAATGTATTAGTAATTTAGGATTATGTTATAAATTATTATGTTTG
* * *
1398394 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAATGTATTAGTAATTTAGGATTATGTTATAAATTATTATGTTT
1398453 AGTTTAGTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATGTATTAGTAATTTAGGATTATGTTATAAATTATTATGTTTG
Found at i:1398850 original size:116 final size:117
Alignment explanation
Indices: 1398714--1398968 Score: 374
Period size: 116 Copynumber: 2.2 Consensus size: 117
1398704 GAGTTTTGTG
* * *
1398714 ATTTTTTAGTAATATAATTTTTTTAAAAATAATTTTATAGTTATTTTGTTATTAATTTATGATTA
1 ATTTTTTAGTAATGT-ATTTTTTTAAAAACAATTTTATAGTTATTTTGTTAGTAATTTATGATTA
* *
1398779 GGTTTTATAAATTGTTAGTGTTTA-TTTATGTGTTTAGTGATTTTTTT-A-GTAA
65 GGTTATATAAATTGTTAGTATTTAGTTTA-GTGTTTAGTGATTTTTTTAATGT-A
1398831 ATTTTTTAGTAATGTATTTTTTTAAAAACAATTTTATAGTTATTTTGTTAGTAATTTATGATTAG
1 ATTTTTTAGTAATGTATTTTTTTAAAAACAATTTTATAGTTATTTTGTTAGTAATTTATGATTAG
* *
1398896 GTTATATCAATTGTTAGTATTTAGTTTAGTGTTTTGTGATTTTTTTAATGTA
66 GTTATATAAATTGTTAGTATTTAGTTTAGTGTTTAGTGATTTTTTTAATGTA
*
1398948 ATTTTTATA-TAATGTAATTTT
1 ATTTTT-TAGTAATGTATTTTT
1398969 ATTTGATTTT
Statistics
Matches: 126, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
116 85 0.67
117 37 0.29
118 4 0.03
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.58
Consensus pattern (117 bp):
ATTTTTTAGTAATGTATTTTTTTAAAAACAATTTTATAGTTATTTTGTTAGTAATTTATGATTAG
GTTATATAAATTGTTAGTATTTAGTTTAGTGTTTAGTGATTTTTTTAATGTA
Found at i:1399897 original size:169 final size:168
Alignment explanation
Indices: 1399614--1399921 Score: 607
Period size: 169 Copynumber: 1.8 Consensus size: 168
1399604 AGGTGATGAA
1399614 TTTTTATTTTGTTATAGTTATTTATTTTGTTAATAATTAATGGGATTAGGTTACAAATTGTTAGT
1 TTTTTATTTTGTTATAGTTATTTATTTTGTTAATAATTAATGGGATTAGGTTACAAATTGTTAGT
1399679 GTTTAGTGTAGGGTTTTGTGATTTTTTAGTAATGTAATTTTAAAAAAAATAATTTTATAGTTATT
66 GTTTAGTGTAGGGTTTTGTGATTTTTTAGTAATGTAATTTTAAAAAAAATAATTTTATAGTTATT
1399744 TTGTTAGTAGTTTATGATTAGGTTATAAATTGTTAGTG
131 TTGTTAGTAGTTTATGATTAGGTTATAAATTGTTAGTG
1399782 TTTTGTATTTTGTTATAGTTATTTATTTTGTTAATAATTAATGGGATTAGGTTACAAATTGTTAG
1 TTTT-TATTTTGTTATAGTTATTTATTTTGTTAATAATTAATGGGATTAGGTTACAAATTGTTAG
1399847 TGTTTAGTGTAGGGTTTTGTGATTTTTTAGTAATGTAATTTTAAAAAAAATAATTTTATAGTTAT
65 TGTTTAGTGTAGGGTTTTGTGATTTTTTAGTAATGTAATTTTAAAAAAAATAATTTTATAGTTAT
1399912 TTTGTTAGTA
130 TTTGTTAGTA
1399922 NNNNNNNNNN
Statistics
Matches: 139, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
168 4 0.03
169 135 0.97
ACGTcount: A:0.29, C:0.01, G:0.18, T:0.53
Consensus pattern (168 bp):
TTTTTATTTTGTTATAGTTATTTATTTTGTTAATAATTAATGGGATTAGGTTACAAATTGTTAGT
GTTTAGTGTAGGGTTTTGTGATTTTTTAGTAATGTAATTTTAAAAAAAATAATTTTATAGTTATT
TTGTTAGTAGTTTATGATTAGGTTATAAATTGTTAGTG
Found at i:1402032 original size:33 final size:33
Alignment explanation
Indices: 1401975--1402040 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1401965 TCTACTCTTT
* * *
1401975 CCGGCTCATATCCACTATCATACTTCACTCCTC
1 CCGGCCCATACCCACCATCATACTTCACTCCTC
*
1402008 CCGGCCCATACCCACCATCGTACTTCACTCCTC
1 CCGGCCCATACCCACCATCATACTTCACTCCTC
1402041 TCAACTCAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.20, C:0.47, G:0.08, T:0.26
Consensus pattern (33 bp):
CCGGCCCATACCCACCATCATACTTCACTCCTC
Found at i:1402319 original size:76 final size:75
Alignment explanation
Indices: 1402233--1402455 Score: 292
Period size: 71 Copynumber: 3.0 Consensus size: 75
1402223 AATAATTTCA
* *
1402233 TATTTATGTAATGAATTTTTTTCCATTTTATTTATCAATTTTATGGGTTCTTTTGCAATTTAAAT
1 TATTTATGTAATGACTTTTTTACCATTTTATTTATCAATTTTATGGGTT-TTTTGCAATTTAAAT
*
1402298 AGTCAACTTTG
65 AGTAAACTTTG
* *
1402309 TATTTATGTAATGACTTTTTTGCCATTTTATTTATCAATTTTA----TTTATTGCAATTTAAATA
1 TATTTATGTAATGACTTTTTTACCATTTTATTTATCAATTTTATGGGTTTTTTGCAATTTAAATA
1402370 GTAAACTTTG
66 GTAAACTTTG
* * * * *
1402380 TATTTATGTAATGACTTTTTCACTATTTCAGTTATCAATTTTATGGGTTTTTTTACAATTTAAAT
1 TATTTATGTAATGACTTTTTTACCATTTTATTTATCAATTTTATGGG-TTTTTTGCAATTTAAAT
*
1402445 AAATAAACTTT
65 -AGTAAACTTT
1402456 AGACTAACTT
Statistics
Matches: 129, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
71 62 0.48
72 2 0.02
76 56 0.43
77 9 0.07
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (75 bp):
TATTTATGTAATGACTTTTTTACCATTTTATTTATCAATTTTATGGGTTTTTTGCAATTTAAATA
GTAAACTTTG
Found at i:1406557 original size:13 final size:13
Alignment explanation
Indices: 1406539--1406565 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1406529 CACAAACGAT
1406539 AAAATTTTCACAC
1 AAAATTTTCACAC
1406552 AAAATTTTCACAC
1 AAAATTTTCACAC
1406565 A
1 A
1406566 TATAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:1410413 original size:38 final size:38
Alignment explanation
Indices: 1410362--1410489 Score: 184
Period size: 38 Copynumber: 3.4 Consensus size: 38
1410352 AAACAATTAA
* *
1410362 CATGCTTAACATGTTTTCAGTTCAATAGTAGCATTAGG
1 CATGCTTAACATGTATTCAGTTCAATAGTAGCAGTAGG
* *
1410400 CATGCTTAACATGTATTCAGTTCAATAGTAACAGTAGA
1 CATGCTTAACATGTATTCAGTTCAATAGTAGCAGTAGG
* ** *
1410438 TATGCTTAACATGTATTGGGTTCAATAGTAGTAGTAGG
1 CATGCTTAACATGTATTCAGTTCAATAGTAGCAGTAGG
1410476 CATGCTTAACATGT
1 CATGCTTAACATGT
1410490 GTTTCGTAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 79 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (38 bp):
CATGCTTAACATGTATTCAGTTCAATAGTAGCAGTAGG
Found at i:1411413 original size:16 final size:16
Alignment explanation
Indices: 1411369--1411411 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1411359 GAATTATGAT
* * *
1411369 GAAAAGAATAGGAAAA
1 GAAAAGAAAAAGAGAA
1411385 GAAAAGAAAAAGAGAA
1 GAAAAGAAAAAGAGAA
1411401 GAAATAGAAAA
1 GAAA-AGAAAA
1411412 GATGGAAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (16 bp):
GAAAAGAAAAAGAGAA
Found at i:1412092 original size:24 final size:24
Alignment explanation
Indices: 1412060--1412105 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1412050 CGTGAGTAAA
*
1412060 ATTAGAAAAATAGAAAA-TTACTTT
1 ATTAAAAAAAT-GAAAACTTACTTT
1412084 ATTAAAAAAATGAAAACTTACT
1 ATTAAAAAAATGAAAACTTACT
1412106 CATAGTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (24 bp):
ATTAAAAAAATGAAAACTTACTTT
Found at i:1414158 original size:49 final size:49
Alignment explanation
Indices: 1414092--1414226 Score: 198
Period size: 49 Copynumber: 2.8 Consensus size: 49
1414082 AATAATAACA
* * * *
1414092 TGCCAAAGCCATGTCCCAAAGATGGTCTTACATGGGATGTTTCTTGCAC
1 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGATGTTTCTTGCAC
* * * *
1414141 TGCCAATGTCATATCCCAGATATGATCTTACATGAGATGTTTCTTGTAC
1 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGATGTTTCTTGCAC
1414190 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGA
1 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGA
1414227 GTTCTCATAT
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 75 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (49 bp):
TGCCAATGCCATATCCCAGATATGGTCTTACATGGGATGTTTCTTGCAC
Done.