Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 224 of 320
Found at i:74526839 original size:50 final size:50
Alignment explanation
Indices: 74526785--74526908 Score: 167
Period size: 50 Copynumber: 2.5 Consensus size: 50
74526775 CACAGCTCAT
* ** *
74526785 ATGAGCTTTCCGTTATACAGCTCGCATGAGCTTCTTGATATTCAGCTTGC
1 ATGAGCTTTCCGTTATTCAGCTCGCATGAGCTTCCAGATATTCAGCTCGC
* * *
74526835 ATGAGCTTTCAGATATTCAGCTCGCATGAGCTTCCAGATATTCAGCTCGT
1 ATGAGCTTTCCGTTATTCAGCTCGCATGAGCTTCCAGATATTCAGCTCGC
* *
74526885 ATGAGCTTCCCATTATTCAGCTCG
1 ATGAGCTTTCCGTTATTCAGCTCG
74526909 GAGAAGCTTC
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (50 bp):
ATGAGCTTTCCGTTATTCAGCTCGCATGAGCTTCCAGATATTCAGCTCGC
Found at i:74526895 original size:192 final size:192
Alignment explanation
Indices: 74526529--74526883 Score: 658
Period size: 192 Copynumber: 1.8 Consensus size: 192
74526519 GATATAAATG
*
74526529 ATATGTCATTAGGGTTACCGATTTGGTCGGGCCCTGCATGTGTTGCAGACACACCACAGTTCATA
1 ATATGTCATTAGGGTTACCGATTTGGTCGGGCCCTGCATGTGTTGCAGACACACCACAGCTCATA
74526594 TGAGCTTCCCGTTATACAGCTCGCATGAGCTTCTTGATATTCAGCTCGCATGAGCTTTCAGATAT
66 TGAGCTTCCCGTTATACAGCTCGCATGAGCTTCTTGATATTCAGCTCGCATGAGCTTTCAGATAT
*
74526659 TCAGCTCGCATGAGCTTCCCATTATTCAGCTCGGAGAAGCTTCCCGTTTACAGCTCGTTTGA
131 TCAGCTCGCATGAGCTTCCCAATATTCAGCTCGGAGAAGCTTCCCGTTTACAGCTCGTTTGA
74526721 ATATGTCATTAGGGTTACCGATTTGGTCGGGCCCTGCATGTGTTGCAGACACACCACAGCTCATA
1 ATATGTCATTAGGGTTACCGATTTGGTCGGGCCCTGCATGTGTTGCAGACACACCACAGCTCATA
* *
74526786 TGAGCTTTCCGTTATACAGCTCGCATGAGCTTCTTGATATTCAGCTTGCATGAGCTTTCAGATAT
66 TGAGCTTCCCGTTATACAGCTCGCATGAGCTTCTTGATATTCAGCTCGCATGAGCTTTCAGATAT
74526851 TCAGCTCGCATGAGCTT-CCAGATATTCAGCTCG
131 TCAGCTCGCATGAGCTTCCCA-ATATTCAGCTCG
74526884 TATGAGCTTC
Statistics
Matches: 158, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
191 3 0.02
192 155 0.98
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (192 bp):
ATATGTCATTAGGGTTACCGATTTGGTCGGGCCCTGCATGTGTTGCAGACACACCACAGCTCATA
TGAGCTTCCCGTTATACAGCTCGCATGAGCTTCTTGATATTCAGCTCGCATGAGCTTTCAGATAT
TCAGCTCGCATGAGCTTCCCAATATTCAGCTCGGAGAAGCTTCCCGTTTACAGCTCGTTTGA
Found at i:74529396 original size:31 final size:31
Alignment explanation
Indices: 74529353--74529438 Score: 120
Period size: 31 Copynumber: 2.8 Consensus size: 31
74529343 TCAATCTCAG
*
74529353 CATAT-ACTGGGCCGAAGCCTTTACATTGTT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
* *
74529383 CATGTCACTGGGCCGAAGCCTTTTCATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATT
* *
74529414 CATATCACTGGTCTGAAGCCTTTAC
1 CATATCACTGGGCCGAAGCCTTTAC
74529439 TATAAACGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 4 0.08
31 44 0.92
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.34
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTACATTATT
Found at i:74529684 original size:25 final size:25
Alignment explanation
Indices: 74529656--74529725 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
74529646 CTCTTTTAAT
74529656 AACTGGGGCAAAGCCCTTTTCGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
74529681 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
74529706 AACTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
74529726 GCACTTCCTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:74529798 original size:20 final size:20
Alignment explanation
Indices: 74529773--74529829 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
74529763 TATATGAATT
* *
74529773 TATCATGTACATATTATACA
1 TATCATGTGCATATCATACA
74529793 TATCATGTGCATATCATACA
1 TATCATGTGCATATCATACA
74529813 TATCATGTGCATATCAT
1 TATCATGTGCATATCAT
74529830 GTCAAATCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.39
Consensus pattern (20 bp):
TATCATGTGCATATCATACA
Found at i:74529807 original size:11 final size:11
Alignment explanation
Indices: 74529791--74529841 Score: 63
Period size: 11 Copynumber: 4.9 Consensus size: 11
74529781 ACATATTATA
74529791 CATATCATGTG
1 CATATCATGTG
*
74529802 CATATCA--TA
1 CATATCATGTG
74529811 CATATCATGTG
1 CATATCATGTG
74529822 CATATCATGT-
1 CATATCATGTG
*
74529832 CAAATCATGT
1 CATATCATGT
74529842 ATATCAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 8 0.23
10 9 0.26
11 18 0.51
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (11 bp):
CATATCATGTG
Found at i:74529808 original size:31 final size:31
Alignment explanation
Indices: 74529773--74529842 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
74529763 TATATGAATT
74529773 TATCATGTACATAT-TATACATATCATGTGCA
1 TATCATGTACATATATATACATATCATGT-CA
* *
74529804 TATCA--TACATATCATGTGCATATCATGTCA
1 TATCATGTACATAT-ATATACATATCATGTCA
*
74529834 AATCATGTA
1 TATCATGTA
74529843 TATCAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
29 7 0.22
30 6 0.19
31 17 0.53
32 2 0.06
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (31 bp):
TATCATGTACATATATATACATATCATGTCA
Found at i:74536748 original size:31 final size:31
Alignment explanation
Indices: 74536710--74536787 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
74536700 AGCATATACA
* * *
74536710 GGGCCGAAGCCTTTACATTGCTCATGCCATT
1 GGGCCGAAGCCTTTACATTACTCATACCACT
* * *
74536741 GGGCCGAAGCCTTTTCATTATTCATATCACT
1 GGGCCGAAGCCTTTACATTACTCATACCACT
74536772 GGGCCGAAGCCTTTAC
1 GGGCCGAAGCCTTTAC
74536788 TGTAAACGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (31 bp):
GGGCCGAAGCCTTTACATTACTCATACCACT
Found at i:74537111 original size:11 final size:10
Alignment explanation
Indices: 74537095--74537149 Score: 60
Period size: 11 Copynumber: 5.5 Consensus size: 10
74537085 ATATATGAAT
74537095 TATCATGTCCA
1 TATCATGT-CA
*
74537106 TATCAT-ACA
1 TATCATGTCA
74537115 TATCATGTGCA
1 TATCATGT-CA
74537126 TATCATGTCA
1 TATCATGTCA
*
74537136 AATCATGT-A
1 TATCATGTCA
74537145 TATCA
1 TATCA
74537150 AAATCTCATG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 13 0.34
10 9 0.24
11 16 0.42
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (10 bp):
TATCATGTCA
Found at i:74539397 original size:27 final size:25
Alignment explanation
Indices: 74539346--74539398 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
74539336 TAGCTCGACT
*
74539346 ATAGAAACATGGGTAGTCCATCAGG
1 ATAGAAACATGGGTAGTCCACCAGG
*
74539371 ATAGTAAACAATGGGTAGTCCGCCAGG
1 ATAG-AAAC-ATGGGTAGTCCACCAGG
74539398 A
1 A
74539399 AATTAAGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (25 bp):
ATAGAAACATGGGTAGTCCACCAGG
Found at i:74541339 original size:26 final size:26
Alignment explanation
Indices: 74541304--74541368 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
74541294 TGGCTATCCG
*
74541304 GAGC-TCCTGATTAAAGGTTCTTCGT
1 GAGCTTCCTGATTAAAAGTTCTTCGT
*
74541329 GAGCTTCCTGATTAAAAGTTCTTTGT
1 GAGCTTCCTGATTAAAAGTTCTTCGT
* *
74541355 GAACTTCCTAATTA
1 GAGCTTCCTGATTA
74541369 TGGCTCTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
25 4 0.11
26 31 0.89
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (26 bp):
GAGCTTCCTGATTAAAAGTTCTTCGT
Found at i:74551452 original size:21 final size:22
Alignment explanation
Indices: 74551419--74551465 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
74551409 ATATAAAAGC
*
74551419 AAAATGATAGCAAAACAATGAA
1 AAAATGATAGCAAAACAATAAA
*
74551441 AAAAT-ATGGCAAAACAATAAA
1 AAAATGATAGCAAAACAATAAA
74551462 AAAA
1 AAAA
74551466 ACAACAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.68, C:0.09, G:0.11, T:0.13
Consensus pattern (22 bp):
AAAATGATAGCAAAACAATAAA
Found at i:74554646 original size:42 final size:42
Alignment explanation
Indices: 74554599--74554687 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
74554589 TTATGAGGAA
*
74554599 GTTGAAAATTTGCAGAATGATGATGATCTAAAGAGTACGTTG
1 GTTGAAAATTTGCAGAATGATGATGATCTAAAGAGTACGGTG
74554641 GTTGAAAATTTGCAGAATGATGATGATCTAAAGAGTACGGTG
1 GTTGAAAATTTGCAGAATGATGATGATCTAAAGAGTACGGTG
74554683 GTTGA
1 GTTGA
74554688 TTCGGAGTGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (42 bp):
GTTGAAAATTTGCAGAATGATGATGATCTAAAGAGTACGGTG
Found at i:74556194 original size:20 final size:19
Alignment explanation
Indices: 74556134--74556208 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 19
74556124 ATATATTTAG
* *
74556134 AATTTTTTTGAAATTTTTATA
1 AATTATTTTGAAA--TTTAAA
*
74556155 AA-TATTCTGAAATTTAAA
1 AATTATTTTGAAATTTAAA
*
74556173 AATTATTTTGAATATTTGAA
1 AATTATTTTGAA-ATTTAAA
74556193 AATTATTTTGAAATTT
1 AATTATTTTGAAATTT
74556209 TTATTGAAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
18 7 0.15
19 12 0.26
20 26 0.55
21 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.52
Consensus pattern (19 bp):
AATTATTTTGAAATTTAAA
Found at i:74556832 original size:19 final size:19
Alignment explanation
Indices: 74556810--74556853 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
74556800 TTGAGTCAAC
*
74556810 TCGATTAAGTAATTCGAGT
1 TCGAATAAGTAATTCGAGT
**
74556829 TCGAATCGGTAATTCGAGT
1 TCGAATAAGTAATTCGAGT
74556848 TCGAAT
1 TCGAAT
74556854 CGAGTTGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (19 bp):
TCGAATAAGTAATTCGAGT
Found at i:74556854 original size:19 final size:19
Alignment explanation
Indices: 74556818--74556855 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
74556808 ACTCGATTAA
74556818 GTAATTCGAGTTCGAATCG
1 GTAATTCGAGTTCGAATCG
74556837 GTAATTCGAGTTCGAATCG
1 GTAATTCGAGTTCGAATCG
74556856 AGTTGAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (19 bp):
GTAATTCGAGTTCGAATCG
Found at i:74556973 original size:21 final size:21
Alignment explanation
Indices: 74556942--74556995 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
74556932 TTGGATTCTC
74556942 TCAACAAAAATTGTAAAATAAT
1 TCAA-AAAAATTGTAAAATAAT
74556964 TCAAAAAAATTGTAAAATAAT
1 TCAAAAAAATTGTAAAATAAT
*
74556985 TCAAAATAATT
1 TCAAAAAAATT
74556996 TTCAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (21 bp):
TCAAAAAAATTGTAAAATAAT
Found at i:74557015 original size:10 final size:10
Alignment explanation
Indices: 74556950--74557052 Score: 70
Period size: 10 Copynumber: 10.2 Consensus size: 10
74556940 TCTCAACAAA
74556950 AATTGTAAAAT
1 AATT-TAAAAT
* *
74556961 AATTCAAAAA
1 AATTTAAAAT
74556971 AATTGTAAAAT
1 AATT-TAAAAT
*
74556982 AATTCAAAAT
1 AATTTAAAAT
*
74556992 AATTTTCAAA-
1 AA-TTTAAAAT
74557002 AATTTAAAAT
1 AATTTAAAAT
**
74557012 AATTTTTAA-
1 AATTTAAAAT
*
74557021 AATTCAAAAT
1 AATTTAAAAT
74557031 -ATTTATAAA-
1 AATTTA-AAAT
74557040 AATTTCAAAAT
1 AATTT-AAAAT
74557051 AA
1 AA
74557053 ATTCTAAAAA
Statistics
Matches: 70, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
9 16 0.23
10 34 0.49
11 20 0.29
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (10 bp):
AATTTAAAAT
Found at i:74557024 original size:19 final size:19
Alignment explanation
Indices: 74556961--74557062 Score: 98
Period size: 20 Copynumber: 5.1 Consensus size: 19
74556951 ATTGTAAAAT
* *
74556961 AATTCAAAAAAATTGTAAAA
1 AATTCAAAATAATT-TTAAA
74556981 TAATTCAAAATAATTTTCAAA
1 -AATTCAAAATAATTTT-AAA
* *
74557002 AATTTAAAATAATTTTTAA
1 AATTCAAAATAATTTTAAA
74557021 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTT-TAAA
*
74557040 AATTTCAAAATAAATTCTAAA
1 AA-TTCAAAAT-AATTTTAAA
74557061 AA
1 AA
74557063 ATATATAAAG
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
18 4 0.06
19 16 0.23
20 24 0.35
21 22 0.32
22 3 0.04
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.35
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:74557025 original size:39 final size:39
Alignment explanation
Indices: 74556982--74557061 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 39
74556972 ATTGTAAAAT
* *
74556982 AATTCAAAATAATTT-TCAAAAATTT-AAAATAATTTTTAA
1 AATTCAAAAT-ATTTAT-AAAAATTTCAAAATAAATTCTAA
74557021 AATTCAAAATATTTATAAAAATTTCAAAATAAATTCTAA
1 AATTCAAAATATTTATAAAAATTTCAAAATAAATTCTAA
74557060 AA
1 AA
74557062 AATATATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 25 0.68
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (39 bp):
AATTCAAAATATTTATAAAAATTTCAAAATAAATTCTAA
Found at i:74557049 original size:27 final size:27
Alignment explanation
Indices: 74556996--74557050 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
74556986 CAAAATAATT
*
74556996 TTCAAAAATTTAAAATAATTTTTAAAA
1 TTCAAAAATTTAAAATAATTTTCAAAA
74557023 TTCAAAATATTTATAAA-AA-TTTCAAAA
1 TTCAAAA-ATTTA-AAATAATTTTCAAAA
74557050 T
1 T
74557051 AAATTCTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 15 0.60
28 7 0.28
29 3 0.12
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (27 bp):
TTCAAAAATTTAAAATAATTTTCAAAA
Found at i:74557062 original size:21 final size:20
Alignment explanation
Indices: 74556950--74557064 Score: 106
Period size: 21 Copynumber: 5.7 Consensus size: 20
74556940 TCTCAACAAA
*
74556950 AATTGTAAAATAATTCAAAAA
1 AATTGTAAAA-AATTCAAAAT
74556971 AATTGTAAAATAATTCAAAAT
1 AATTGTAAAA-AATTCAAAAT
* * *
74556992 AATTTTCAAAAATTTAAAAT
1 AATTGTAAAAAATTCAAAAT
**
74557012 AATT-TTTAAAATTCAAAAT
1 AATTGTAAAAAATTCAAAAT
* * *
74557031 ATTTATAAAAATTTCAAAAT
1 AATTGTAAAAAATTCAAAAT
*
74557051 AAATTCTAAAAAAT
1 -AATTGTAAAAAAT
74557065 ATATAAAGTT
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 15 0.19
20 25 0.32
21 38 0.49
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (20 bp):
AATTGTAAAAAATTCAAAAT
Found at i:74565312 original size:42 final size:43
Alignment explanation
Indices: 74565231--74565386 Score: 172
Period size: 43 Copynumber: 3.7 Consensus size: 43
74565221 AAAACGCCAT
74565231 TATAGAACATGATCTTTAGCAACACTTTTCCTACAAATGCCGC
1 TATAGAACATGATCTTTAGCAACACTTTTCCTACAAATGCCGC
* ** *
74565274 TATAGAATATGATCTTTAG-GTCACTTTTCCTACAAATGCTGC
1 TATAGAACATGATCTTTAGCAACACTTTTCCTACAAATGCCGC
* ** * ** * *
74565316 TATAGAACATGATATTTAGCGGCGCTTTTATTACAAACGCCAC
1 TATAGAACATGATCTTTAGCAACACTTTTCCTACAAATGCCGC
* *
74565359 TAAAGAACATGATTTTTAGCAAC-CTTTT
1 TATAGAACATGATCTTTAGCAACACTTTT
74565387 TTTTTTTACA
Statistics
Matches: 95, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
42 42 0.44
43 53 0.56
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (43 bp):
TATAGAACATGATCTTTAGCAACACTTTTCCTACAAATGCCGC
Found at i:74565790 original size:21 final size:21
Alignment explanation
Indices: 74565764--74565811 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
74565754 ATTTTCTTGT
* *
74565764 TGCCTCTGCTGCCTTTGTTGC
1 TGCCTCTGCTGCCCTCGTTGC
*
74565785 TGCCTCTGCTTCCCTCGTTGC
1 TGCCTCTGCTGCCCTCGTTGC
74565806 TGCCTC
1 TGCCTC
74565812 CGCTTTAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.00, C:0.40, G:0.21, T:0.40
Consensus pattern (21 bp):
TGCCTCTGCTGCCCTCGTTGC
Found at i:74569155 original size:17 final size:17
Alignment explanation
Indices: 74569135--74569167 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
74569125 TTTTGCACCT
74569135 CCCACCATTTTCAACTC
1 CCCACCATTTTCAACTC
*
74569152 CCCACTATTTTCAACT
1 CCCACCATTTTCAACT
74569168 AAAAAAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.42, G:0.00, T:0.33
Consensus pattern (17 bp):
CCCACCATTTTCAACTC
Found at i:74573776 original size:21 final size:21
Alignment explanation
Indices: 74573752--74573791 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
74573742 TTACCTTCTA
*
74573752 AAGTTAAAAGTCAAAACTATC
1 AAGTTAAAAGGCAAAACTATC
74573773 AAGTTAAAAGGCAAAACTA
1 AAGTTAAAAGGCAAAACTA
74573792 CATTGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATC
Found at i:74580050 original size:21 final size:21
Alignment explanation
Indices: 74580024--74580067 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
74580014 CATCAAAAAG
74580024 ATAGAAAATTCTAGCTATCAC
1 ATAGAAAATTCTAGCTATCAC
74580045 ATAGAAAATTCTAGCTATCAC
1 ATAGAAAATTCTAGCTATCAC
74580066 AT
1 AT
74580068 CTGGAGCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (21 bp):
ATAGAAAATTCTAGCTATCAC
Found at i:74582370 original size:30 final size:30
Alignment explanation
Indices: 74582334--74582395 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
74582324 CAAGTAGCCG
*
74582334 AAGCTAGTTTAAATCGCACACTTAGTGTCA
1 AAGCTAGTTTAAATCGCACACTTAGTGCCA
74582364 AAGCTAGTTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTTAAATCGCACACTTAGTGCCA
74582394 AA
1 AA
74582396 ACTTCCGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (30 bp):
AAGCTAGTTTAAATCGCACACTTAGTGCCA
Found at i:74585848 original size:17 final size:19
Alignment explanation
Indices: 74585826--74585862 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
74585816 TACCTTGGTA
74585826 ATTGT-ATTT-TTTTTTAT
1 ATTGTAATTTGTTTTTTAT
74585843 ATTGTAAATTTGTTTTTTAT
1 ATTGT-AATTTGTTTTTTAT
74585863 CATATCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (19 bp):
ATTGTAATTTGTTTTTTAT
Found at i:74585962 original size:22 final size:22
Alignment explanation
Indices: 74585935--74585979 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
74585925 ATATAATTCG
74585935 TAATAAAGGTAATTTTAGTCTA
1 TAATAAAGGTAATTTTAGTCTA
74585957 TAATAAAGGTAATTTTAGTCTA
1 TAATAAAGGTAATTTTAGTCTA
74585979 T
1 T
74585980 GTATATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (22 bp):
TAATAAAGGTAATTTTAGTCTA
Found at i:74598893 original size:27 final size:27
Alignment explanation
Indices: 74598841--74598919 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
74598831 CCCTTCACGT
* *
74598841 TTCTTTTC-TTTCTTTCTTTT-TATCTA
1 TTCTCTTCTTTTC-TTCTTTTCTTTCTA
74598867 TTCTCTTCTTTTCTTCTTTTCTTTCTA
1 TTCTCTTCTTTTCTTCTTTTCTTTCTA
*
74598894 TTCCCTTCTTTTCTTCTTTTCTTTCT
1 TTCTCTTCTTTTCTTCTTTTCTTTCT
74598920 CTGTTTTGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
26 14 0.29
27 34 0.71
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (27 bp):
TTCTCTTCTTTTCTTCTTTTCTTTCTA
Found at i:74601470 original size:21 final size:20
Alignment explanation
Indices: 74601442--74601483 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
74601432 CAAAACTTGT
74601442 ATAACTATAATCAAA-CATTC
1 ATAACTATAAT-AAATCATTC
*
74601462 ATAATCTATCATAAATCATTC
1 ATAA-CTATAATAAATCATTC
74601483 A
1 A
74601484 AGCTCATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAACTATAATAAATCATTC
Found at i:74602935 original size:12 final size:11
Alignment explanation
Indices: 74602913--74602937 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
74602903 TTACCATCTC
74602913 TTTCCTTTTTT
1 TTTCCTTTTTT
74602924 TTTCCTTTTTT
1 TTTCCTTTTTT
74602935 TTT
1 TTT
74602938 GCCACAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCCTTTTTT
Found at i:74606723 original size:21 final size:21
Alignment explanation
Indices: 74606705--74606748 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
74606695 AGCTATGGTC
* *
74606705 GTGGTCGAGTAGGACATGGCA
1 GTGGTCGAGCAGGAAATGGCA
74606726 GTGGTCGAGCAGGAAATGGCA
1 GTGGTCGAGCAGGAAATGGCA
74606747 GT
1 GT
74606749 CGTGGAGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.14, G:0.43, T:0.18
Consensus pattern (21 bp):
GTGGTCGAGCAGGAAATGGCA
Found at i:74615217 original size:20 final size:20
Alignment explanation
Indices: 74615188--74615232 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
74615178 AATGACGGAC
74615188 TTTT-GGACTTTTAATTTTG-
1 TTTTGGGAC-TTTAATTTTGA
74615207 TTTTGGGACTTTAATTTTGA
1 TTTTGGGACTTTAATTTTGA
74615227 TTTTGG
1 TTTTGG
74615233 TATTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.16, C:0.04, G:0.20, T:0.60
Consensus pattern (20 bp):
TTTTGGGACTTTAATTTTGA
Found at i:74618196 original size:44 final size:43
Alignment explanation
Indices: 74618124--74618275 Score: 134
Period size: 43 Copynumber: 3.5 Consensus size: 43
74618114 ATGTGATATT
* * *
74618124 GTGTAAGACCACGTCTGGGACGTTGGCATCGACT-TCTGTTTTAC
1 GTGTAAGACCACGTCTAGGACATCGGCATCGA-TATCTG-TTTAC
* *
74618168 GTGTAAGACCATGTCTAGGACATCGGCATC-ATATCCGATTT-C
1 GTGTAAGACCACGTCTAGGACATCGGCATCGATATCTG-TTTAC
* * * *
74618210 GTGTAAGACC-CTGTCTGGGACA-CTGGCATCGATGTTTGATTAC
1 GTGTAAGACCAC-GTCTAGGACATC-GGCATCGATATCTGTTTAC
*
74618253 ATGTAAGACCACGTCTAGGACAT
1 GTGTAAGACCACGTCTAGGACAT
74618276 TAGCATTGTA
Statistics
Matches: 87, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
41 1 0.01
42 29 0.33
43 30 0.34
44 27 0.31
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (43 bp):
GTGTAAGACCACGTCTAGGACATCGGCATCGATATCTGTTTAC
Found at i:74618225 original size:42 final size:44
Alignment explanation
Indices: 74618164--74618275 Score: 124
Period size: 42 Copynumber: 2.6 Consensus size: 44
74618154 GACTTCTGTT
*
74618164 TTACGTGTAAGACCATGTCTAGGACATC-GGCATC-ATATCCGA
1 TTACGTGTAAGACCCTGTCTAGGACATCTGGCATCGATATCCGA
* * * **
74618206 TTTCGTGTAAGACCCTGTCTGGGACA-CTGGCATCGATGTTTGA
1 TTACGTGTAAGACCCTGTCTAGGACATCTGGCATCGATATCCGA
*
74618249 TTACATGTAAGACCAC-GTCTAGGACAT
1 TTACGTGTAAGACC-CTGTCTAGGACAT
74618276 TAGCATTGTA
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
41 1 0.02
42 29 0.51
43 26 0.46
44 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (44 bp):
TTACGTGTAAGACCCTGTCTAGGACATCTGGCATCGATATCCGA
Found at i:74623878 original size:68 final size:68
Alignment explanation
Indices: 74623804--74623940 Score: 195
Period size: 68 Copynumber: 2.0 Consensus size: 68
74623794 AATTGATAGC
* * * *
74623804 TAATCTACCCTAAAACCCAAATTCAAAGTTAGTTACAAACCCT-GAACTGAGTTAATCTTCTTGA
1 TAATCTACCATAAAACCCAAATTCAAAGTTAGTTACAAACCCTAAAAC-GAGTTAATATTCATGA
74623868 TTGG
65 TTGG
* * *
74623872 TAATCTACCATAAATCTCAAATTCAAAGTTAGTTACAAACCTTAAAACGAGTTAATATTCATGAT
1 TAATCTACCATAAAACCCAAATTCAAAGTTAGTTACAAACCCTAAAACGAGTTAATATTCATGAT
74623937 TGG
66 TGG
74623940 T
1 T
74623941 TTATTGATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 58 0.95
69 3 0.05
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (68 bp):
TAATCTACCATAAAACCCAAATTCAAAGTTAGTTACAAACCCTAAAACGAGTTAATATTCATGAT
TGG
Found at i:74633342 original size:39 final size:39
Alignment explanation
Indices: 74633280--74633419 Score: 181
Period size: 39 Copynumber: 3.6 Consensus size: 39
74633270 ATCATGATTT
* * *
74633280 GAAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
* * * *
74633319 GAAGCCCGTAGGCTAACTAAAGCAAACAAGTGTTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
* * * *
74633358 GAAGCCTGAAGGCTCATTGAAGCACACAAGTGCTAAATG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
74633397 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
74633420 TCATCAGAGC
Statistics
Matches: 83, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 83 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
Found at i:74633939 original size:9 final size:9
Alignment explanation
Indices: 74633925--74633953 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
74633915 TTGCCCCAAA
74633925 TTTTACAAT
1 TTTTACAAT
74633934 TTTTACAAT
1 TTTTACAAT
74633943 TTTTACAAT
1 TTTTACAAT
74633952 TT
1 TT
74633954 AGTCCCTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTACAAT
Found at i:74635262 original size:29 final size:30
Alignment explanation
Indices: 74635229--74635286 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
74635219 GATTCATCCA
*
74635229 TGGAAAATTAAGAAAA-AAA-AGGATAAATT
1 TGGAAAAATAA-AAAATAAAGAGGATAAATT
*
74635258 TGGAAAAATAAAAAATAAAGATGATAAAT
1 TGGAAAAATAAAAAATAAAGAGGATAAAT
74635287 AATAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.16
29 13 0.52
30 8 0.32
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.21
Consensus pattern (30 bp):
TGGAAAAATAAAAAATAAAGAGGATAAATT
Found at i:74636334 original size:26 final size:26
Alignment explanation
Indices: 74636305--74636355 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
74636295 CCCATTATAT
74636305 GGCTCTTCATGAGCTTCCTGATTAAA
1 GGCTCTTCATGAGCTTCCTGATTAAA
**
74636331 GGCTCTTTGTGAGCTTCCTGATTAA
1 GGCTCTTCATGAGCTTCCTGATTAA
74636356 TGACTGGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (26 bp):
GGCTCTTCATGAGCTTCCTGATTAAA
Found at i:74642830 original size:23 final size:24
Alignment explanation
Indices: 74642803--74642854 Score: 97
Period size: 23 Copynumber: 2.2 Consensus size: 24
74642793 TGAAGAGGTT
74642803 GATAGAGAAAATTAAAGAGACT-G
1 GATAGAGAAAATTAAAGAGACTGG
74642826 GATAGAGAAAATTAAAGAGACTGG
1 GATAGAGAAAATTAAAGAGACTGG
74642850 GATAG
1 GATAG
74642855 GGAAGTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.50, C:0.04, G:0.29, T:0.17
Consensus pattern (24 bp):
GATAGAGAAAATTAAAGAGACTGG
Found at i:74643953 original size:40 final size:38
Alignment explanation
Indices: 74643907--74644005 Score: 108
Period size: 40 Copynumber: 2.6 Consensus size: 38
74643897 ACGGTACTCT
* * *
74643907 ATGGTGTGTAGGGTTGAATGTGTTGATTTTATCCCCAT
1 ATGGTGTGTAGGGTTGAATGGGTCGATTTTATCCCCAC
* * **
74643945 ATTTGGTGTGTAGAGATGGGTGGGTCGATTTTATCCCCAC
1 A--TGGTGTGTAGGGTTGAATGGGTCGATTTTATCCCCAC
*
74643985 ATGGTGTGTTGGGTTGAATGG
1 ATGGTGTGTAGGGTTGAATGG
74644006 AGATGGTGTG
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
38 16 0.34
40 31 0.66
ACGTcount: A:0.17, C:0.10, G:0.34, T:0.38
Consensus pattern (38 bp):
ATGGTGTGTAGGGTTGAATGGGTCGATTTTATCCCCAC
Found at i:74650284 original size:8 final size:8
Alignment explanation
Indices: 74650270--74650302 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
74650260 ATTTAAGTAA
74650270 ATATTATT
1 ATATTATT
*
74650278 TTATTATT
1 ATATTATT
74650286 ATATTATT
1 ATATTATT
74650294 ATATT-TT
1 ATATTATT
74650301 AT
1 AT
74650303 TAATTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 4 0.17
8 19 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
ATATTATT
Found at i:74650453 original size:18 final size:18
Alignment explanation
Indices: 74650432--74650471 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
74650422 ATATTATAAT
*
74650432 ATAATAATATAACTAAAA
1 ATAATAATACAACTAAAA
*
74650450 ATAATAATACAACTAAAC
1 ATAATAATACAACTAAAA
74650468 ATAA
1 ATAA
74650472 AACAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (18 bp):
ATAATAATACAACTAAAA
Found at i:74650492 original size:14 final size:15
Alignment explanation
Indices: 74650453--74650495 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
74650443 ACTAAAAATA
* *
74650453 ATAATACAACTAAAC
1 ATAAAACAAATAAAC
74650468 ATAAAACAAATAAAC
1 ATAAAACAAATAAAC
*
74650483 -TAAAAGAAATAAA
1 ATAAAACAAATAAA
74650496 AGATAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.70, C:0.12, G:0.02, T:0.16
Consensus pattern (15 bp):
ATAAAACAAATAAAC
Found at i:74653286 original size:42 final size:42
Alignment explanation
Indices: 74653175--74653329 Score: 213
Period size: 42 Copynumber: 3.7 Consensus size: 42
74653165 TATCATACCA
* *
74653175 ATGCCATATCCCAGATATGGTCTTACATGTAA-TCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACG-AAGTCTCATATCG
* *
74653217 ATGCCAATAGCCCAGCTATGGTCTTACACGAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
* * *
74653260 ATGCCATATCCCAGATATGGTCTTACACGCAGTCTTATATTG
1 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
*
74653302 ATGTCATATCCCAGATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
74653330 ATAGTCTTTG
Statistics
Matches: 101, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
42 66 0.65
43 35 0.35
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
Found at i:74654802 original size:46 final size:45
Alignment explanation
Indices: 74654752--74654927 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
74654742 TGGTTGAGCA
74654752 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
74654798 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
74654845 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
74654891 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
74654928 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 68 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:74654908 original size:93 final size:93
Alignment explanation
Indices: 74654749--74654919 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
74654739 GGATGGTTGA
* *
74654749 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
74654814 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
74654842 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
74654907 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
74654920 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:74656485 original size:129 final size:129
Alignment explanation
Indices: 74656255--74656511 Score: 505
Period size: 129 Copynumber: 2.0 Consensus size: 129
74656245 AATATAATTA
74656255 AATCAATGCATTATTTACATAAGAACTTACCTCGATACAAAATAGTAGAAATAGGACCTACTCGT
1 AATCAATGCATTATTTACATAAGAACTTACCTCGATACAAAATAGTAGAAATAGGACCTACTCGT
74656320 CAAACACCTTGTTTTTCCTCCAATCTAGGTCCAAACCTTGTTTCTCTTGATAATCGAGCTTGAT
66 CAAACACCTTGTTTTTCCTCCAATCTAGGTCCAAACCTTGTTTCTCTTGATAATCGAGCTTGAT
74656384 AATCAATGCATTATTTACATAAGAACTTACCTCGATACAAAATAGTAGAAATAGGACCTACTCGT
1 AATCAATGCATTATTTACATAAGAACTTACCTCGATACAAAATAGTAGAAATAGGACCTACTCGT
*
74656449 CAAACACTTTGTTTTTCCTCCAATCTAGGTCCAAACCTTGTTTCTCTTGATAATCGAGCTTGA
66 CAAACACCTTGTTTTTCCTCCAATCTAGGTCCAAACCTTGTTTCTCTTGATAATCGAGCTTGA
74656512 AAAGTTTTGA
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 127 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (129 bp):
AATCAATGCATTATTTACATAAGAACTTACCTCGATACAAAATAGTAGAAATAGGACCTACTCGT
CAAACACCTTGTTTTTCCTCCAATCTAGGTCCAAACCTTGTTTCTCTTGATAATCGAGCTTGAT
Found at i:74668703 original size:2 final size:2
Alignment explanation
Indices: 74668698--74668728 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
74668688 TATTTTTTGT
74668698 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
74668729 AAGAATCCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:74669694 original size:66 final size:66
Alignment explanation
Indices: 74669588--74669712 Score: 187
Period size: 66 Copynumber: 1.9 Consensus size: 66
74669578 ATAATGCATT
* * * *
74669588 ATGTCAAAATTAACCCTTAACGTTTACATTTTTTATCAATTTGGCTCTTATTCTTTTTTTGGTAT
1 ATGTCAAAATTAACCCTTAACGTTTACATCTTTTATCAATTTAGCCCTTATTATTTTTTTGGTAT
74669653 A
66 A
* * *
74669654 ATGTCAAATTTTACCCTTAATGTTTACATCTTTTATCAATTTAGCCCTTATTATTTTTT
1 ATGTCAAAATTAACCCTTAACGTTTACATCTTTTATCAATTTAGCCCTTATTATTTTTT
74669713 AAAATTACTT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 52 1.00
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (66 bp):
ATGTCAAAATTAACCCTTAACGTTTACATCTTTTATCAATTTAGCCCTTATTATTTTTTTGGTAT
A
Found at i:74671240 original size:30 final size:31
Alignment explanation
Indices: 74671181--74671249 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
74671171 ACATAGCAAG
74671181 CAAATACCTCTAAAATAATAATAAAAATTAA
1 CAAATACCTCTAAAATAATAATAAAAATTAA
* * *
74671212 CAAATGCCTTTAAAATAATAA-CAAAATTAA
1 CAAATACCTCTAAAATAATAATAAAAATTAA
74671242 CAATATAC
1 CAA-ATAC
74671250 AATATCCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.26
Consensus pattern (31 bp):
CAAATACCTCTAAAATAATAATAAAAATTAA
Found at i:74672414 original size:3 final size:3
Alignment explanation
Indices: 74672365--74672396 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
74672355 TTAATAAATC
74672365 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
74672397 ATAATTAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:74674472 original size:22 final size:20
Alignment explanation
Indices: 74674434--74674474 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
74674424 GGATAAATAC
*
74674434 AAAAAAAAATAATTGAAAGA
1 AAAAAAAAATAAATGAAAGA
74674454 AAAAAAAACATTAAATGAAAG
1 AAAAAAAA-A-TAAATGAAAG
74674475 TTTGAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (20 bp):
AAAAAAAAATAAATGAAAGA
Found at i:74675445 original size:16 final size:16
Alignment explanation
Indices: 74675420--74675458 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
74675410 TGTAAAGTTA
*
74675420 CTAATAATATCAATTT
1 CTAATTATATCAATTT
74675436 CTAATTATATCAATTT
1 CTAATTATATCAATTT
74675452 CGTAATT
1 C-TAATT
74675459 TTCCTGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (16 bp):
CTAATTATATCAATTT
Found at i:74676451 original size:16 final size:16
Alignment explanation
Indices: 74676430--74676467 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
74676420 TCGAAGTACA
*
74676430 ATTTTATCATTATATT
1 ATTTTATAATTATATT
*
74676446 ATTTTATAATTCTATT
1 ATTTTATAATTATATT
74676462 ATTTTA
1 ATTTTA
74676468 GAGGAGACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTTATAATTATATT
Found at i:74679178 original size:13 final size:13
Alignment explanation
Indices: 74679160--74679184 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74679150 CCTCACACAG
74679160 CCGTGTCATGCGC
1 CCGTGTCATGCGC
74679173 CCGTGTCATGCG
1 CCGTGTCATGCG
74679185 TACACTGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.36, G:0.32, T:0.24
Consensus pattern (13 bp):
CCGTGTCATGCGC
Found at i:74683325 original size:23 final size:23
Alignment explanation
Indices: 74683299--74683349 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
74683289 TTCTGAGAGG
74683299 TTAAAACATAATTTTATC-ATTT
1 TTAAAACATAATTTTATCAATTT
***
74683321 ATTAATTTATAATTTTATCAATTT
1 -TTAAAACATAATTTTATCAATTT
74683345 TTAAA
1 TTAAA
74683350 GGAATTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAAAACATAATTTTATCAATTT
Found at i:74684456 original size:21 final size:21
Alignment explanation
Indices: 74684409--74684460 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
74684399 TGCGTATAAT
* * *
74684409 AAAATATATATACTAATACTA
1 AAAATAAATATACTAAGAATA
* *
74684430 ATAATAAATATACTAGGAATA
1 AAAATAAATATACTAAGAATA
74684451 AAAATAAATA
1 AAAATAAATA
74684461 AAATAATAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAATAAATATACTAAGAATA
Found at i:74685275 original size:21 final size:21
Alignment explanation
Indices: 74685245--74685284 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
74685235 ATATGTAATA
*
74685245 ATAGTGTTAGAAATATACAAT
1 ATAGTATTAGAAATATACAAT
74685266 ATAGTATTAGAAATATACA
1 ATAGTATTAGAAATATACA
74685285 TACAATAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (21 bp):
ATAGTATTAGAAATATACAAT
Found at i:74686068 original size:12 final size:13
Alignment explanation
Indices: 74686053--74686091 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
74686043 AAATGAGAGA
74686053 AAAGGGAG-AGGG
1 AAAGGGAGAAGGG
*
74686065 AAAGGGAGAAAGG
1 AAAGGGAGAAGGG
74686078 AAAGGGAGAAGGG
1 AAAGGGAGAAGGG
74686091 A
1 A
74686092 TTTCCAGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (13 bp):
AAAGGGAGAAGGG
Found at i:74695138 original size:16 final size:16
Alignment explanation
Indices: 74695093--74695140 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
74695083 TATTGCAACC
*
74695093 AAATTTATAATTAAACT
1 AAATTTATAA-TAAAAT
74695110 AAATTTA-AATAAAAT
1 AAATTTATAATAAAAT
*
74695125 ATATTTATAATAAAAT
1 AAATTTATAATAAAAT
74695141 TTAAAGAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 11 0.39
16 10 0.36
17 7 0.25
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTTATAATAAAAT
Found at i:74695588 original size:29 final size:32
Alignment explanation
Indices: 74695527--74695589 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 32
74695517 CAAGATGAAT
* **
74695527 TTATAAATTTTTTTAGAAAGGTCAAAATTTAA
1 TTATAAATTTTTTGAGAAAGGTCAAAACATAA
74695559 TTAT-AATTTTTTGAG-AA-GTCAAAACATAA
1 TTATAAATTTTTTGAGAAAGGTCAAAACATAA
74695588 TT
1 TT
74695590 TTACCATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 12 0.43
30 2 0.07
31 10 0.36
32 4 0.14
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (32 bp):
TTATAAATTTTTTGAGAAAGGTCAAAACATAA
Found at i:74698213 original size:24 final size:23
Alignment explanation
Indices: 74698173--74698233 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
74698163 TAACATAATT
74698173 ATTATT-ATATAAT-TTAATAAC
1 ATTATTAATATAATATTAATAAC
*
74698194 ATTATTAATATAATTATTAATAAT
1 ATTATTAATATAA-TATTAATAAC
74698218 A-T-TTAATATAATATTA
1 ATTATTAATATAATATTA
74698234 TTATTAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
21 11 0.31
22 15 0.42
23 2 0.06
24 8 0.22
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTATTAATATAATATTAATAAC
Found at i:74698217 original size:15 final size:14
Alignment explanation
Indices: 74698194--74698246 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 14
74698184 ATTTAATAAC
74698194 ATTATTAAT-ATA-
1 ATTATTAATAATAT
74698206 ATTATTAATAATAT
1 ATTATTAATAATAT
*
74698220 -TTAAT-ATAATATT
1 ATTATTAATAATA-T
*
74698233 ATTATTAAAAATAT
1 ATTATTAATAATAT
74698247 TTCAATGCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
12 15 0.45
13 8 0.24
14 5 0.15
15 5 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTATTAATAATAT
Found at i:74698931 original size:7 final size:7
Alignment explanation
Indices: 74698919--74698944 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
74698909 CCTCCATTAA
74698919 GCAGCTG
1 GCAGCTG
74698926 GCAGCTG
1 GCAGCTG
74698933 GCAGCTG
1 GCAGCTG
74698940 GCAGC
1 GCAGC
74698945 AGATATCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.31, G:0.42, T:0.12
Consensus pattern (7 bp):
GCAGCTG
Found at i:74702291 original size:46 final size:46
Alignment explanation
Indices: 74702224--74702313 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
74702214 ACAATTCTAC
*
74702224 TCAATGGGTCCAATACAAACAGCTATTTAATTGAATGGAATAAGAT
1 TCAATAGGTCCAATACAAACAGCTATTTAATTGAATGGAATAAGAT
* * *
74702270 TCAATAGGTTCAATACAAACAGCTATTTGATTGAGTGGAATAAG
1 TCAATAGGTCCAATACAAACAGCTATTTAATTGAATGGAATAAG
74702314 GGCTAGTTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (46 bp):
TCAATAGGTCCAATACAAACAGCTATTTAATTGAATGGAATAAGAT
Found at i:74705676 original size:23 final size:20
Alignment explanation
Indices: 74705635--74705689 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
74705625 AATAATAAAG
*
74705635 TAAATCATATATTATTTTTA
1 TAAATTATATATTATTTTTA
*
74705655 TAATATTATATATTATGATTTTT
1 TAA-ATTATATATTAT--TTTTA
74705678 TAAATT-TATATT
1 TAAATTATATATT
74705690 TTAATAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 3 0.10
21 17 0.57
22 3 0.10
23 7 0.23
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TAAATTATATATTATTTTTA
Found at i:74705726 original size:39 final size:39
Alignment explanation
Indices: 74705647--74705729 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
74705637 AATCATATAT
* * * *
74705647 TATTTTTATAATATTATATATTATGATTTTTTAAATTTA
1 TATTTTAATAATAATATATATTAAGATTTATTAAATTTA
74705686 TATTTTAATAATAAT-TATATTAAGAATGTTATTAAATTATA
1 TATTTTAATAATAATATATATTAAG-AT-TTATTAAATT-TA
74705727 TAT
1 TAT
74705730 GATTTTATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
38 8 0.22
39 15 0.41
40 9 0.24
41 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (39 bp):
TATTTTAATAATAATATATATTAAGATTTATTAAATTTA
Found at i:74707774 original size:28 final size:28
Alignment explanation
Indices: 74707737--74707790 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
74707727 TTTTGTAAAA
74707737 TTTATAAA-TTTAATTTTTATACTTTTAT
1 TTTATAAATTTTAA-TTTTATACTTTTAT
* *
74707765 TTTATCAATTTTAATTTTATTCTTTT
1 TTTATAAATTTTAATTTTATACTTTT
74707791 TGAATTTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTATAAATTTTAATTTTATACTTTTAT
Found at i:74707783 original size:15 final size:14
Alignment explanation
Indices: 74707737--74707784 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
74707727 TTTTGTAAAA
*
74707737 TTTATAAATTTAATT
1 TTTATAATTTTAA-T
*
74707752 TTTATACTTTT-AT
1 TTTATAATTTTAAT
74707765 TTTATCAATTTTAAT
1 TTTAT-AATTTTAAT
74707780 TTTAT
1 TTTAT
74707785 TCTTTTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 6 0.21
14 6 0.21
15 16 0.57
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTATAATTTTAAT
Found at i:74711439 original size:42 final size:43
Alignment explanation
Indices: 74711331--74711502 Score: 161
Period size: 43 Copynumber: 4.0 Consensus size: 43
74711321 AACATATACA
* * * * *
74711331 ATGCCAACGTCCTAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAATCAGATATCG
* *
74711374 ATGCC-ACTATCCCAGACAGGGTCTTACACGAAATCAGATA-CG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAATCAGATATCG
* * * * *
74711416 ATTCCAATGTCCCAGACATGGTCTTACACGCAAAACAGAAATTG
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AAATCAGATATCG
* *
74711460 ATGCCAACGTCTCAGACGTGGTCTTACACGCAGAA-CAGATATC
1 ATGCCAACGTCCCAGACATGGTCTTACACG-A-AATCAGATATC
74711503 AAAATTCCTA
Statistics
Matches: 104, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
42 28 0.27
43 39 0.38
44 35 0.34
45 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAATCAGATATCG
Found at i:74716110 original size:31 final size:31
Alignment explanation
Indices: 74716075--74716136 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
74716065 ATTTACTTAG
74716075 CCATATCGGTGTGAGGCTGCTTGGAGTTGAT
1 CCATATCGGTGTGAGGCTGCTTGGAGTTGAT
*
74716106 CCATATCGGTGTGAGGCTGGTTGGAGTTGAT
1 CCATATCGGTGTGAGGCTGCTTGGAGTTGAT
74716137 GCTGAGATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.16, C:0.15, G:0.37, T:0.32
Consensus pattern (31 bp):
CCATATCGGTGTGAGGCTGCTTGGAGTTGAT
Found at i:74725285 original size:2 final size:2
Alignment explanation
Indices: 74725278--74725305 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
74725268 TGCCACCAAT
74725278 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
74725306 CAAGGCACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:74726264 original size:193 final size:193
Alignment explanation
Indices: 74725935--74726320 Score: 763
Period size: 193 Copynumber: 2.0 Consensus size: 193
74725925 GCTGATATCT
74725935 ATTTCTGGTTTGATTGTATTCTCAAACTTTATAGCTTCTTTTTCCTCAGCATTCATGTAGAAGCA
1 ATTTCTGGTTTGATTGTATTCTCAAACTTTATAGCTTCTTTTTCCTCAGCATTCATGTAGAAGCA
74726000 GAAAATATAAATTCTGCTTTTTCTCTATGCCAATCCCGATAGGATAATTATCACACATTAGTCAC
66 GAAAATATAAATTCTGCTTTTTCTCTATGCCAATCCCGATAGGATAATTATCACACATTAGTCAC
*
74726065 ATGTTCCACTTCAATCATATCAAGCCGTACCGCCGACCAACGTTGCACCTATGCTTATGGACA
131 ATGTTCCACTTCAATCATATCAAGCCGTACCGCCGACCAAAGTTGCACCTATGCTTATGGACA
74726128 ATTTCTGGTTTGATTGTATTCTCAAACTTTATAGCTTCTTTTTCCTCAGCATTCATGTAGAAGCA
1 ATTTCTGGTTTGATTGTATTCTCAAACTTTATAGCTTCTTTTTCCTCAGCATTCATGTAGAAGCA
74726193 GAAAATATAAATTCTGCTTTTTCTCTATGCCAATCCCGATAGGATAATTATCACACATTAGTCAC
66 GAAAATATAAATTCTGCTTTTTCTCTATGCCAATCCCGATAGGATAATTATCACACATTAGTCAC
74726258 ATGTTCCACTTCAATCATATCAAGCCGTACCGCCGACCAAAGTTGCACCTATGCTTATGGACA
131 ATGTTCCACTTCAATCATATCAAGCCGTACCGCCGACCAAAGTTGCACCTATGCTTATGGACA
74726321 CGTGCTTGAA
Statistics
Matches: 192, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
193 192 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (193 bp):
ATTTCTGGTTTGATTGTATTCTCAAACTTTATAGCTTCTTTTTCCTCAGCATTCATGTAGAAGCA
GAAAATATAAATTCTGCTTTTTCTCTATGCCAATCCCGATAGGATAATTATCACACATTAGTCAC
ATGTTCCACTTCAATCATATCAAGCCGTACCGCCGACCAAAGTTGCACCTATGCTTATGGACA
Found at i:74741959 original size:29 final size:30
Alignment explanation
Indices: 74741926--74741994 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 30
74741916 AAAATTAAAT
74741926 AGTTGGGTGATC-ATTTTGTAACTTTTCAC
1 AGTTGGGTGATCTATTTTGTAACTTTTCAC
* *
74741955 AGTTGGGTG-GCTATTTTGTAACTTTTCAT
1 AGTTGGGTGATCTATTTTGTAACTTTTCAC
*
74741984 AGTTTGGTGAT
1 AGTTGGGTGAT
74741995 AAAAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.03
29 33 0.97
ACGTcount: A:0.19, C:0.10, G:0.25, T:0.46
Consensus pattern (30 bp):
AGTTGGGTGATCTATTTTGTAACTTTTCAC
Found at i:74744537 original size:29 final size:29
Alignment explanation
Indices: 74744497--74744552 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
74744487 ATAGGGATTT
* *
74744497 GATCAAATTAGTCCCTCTACTGTTAAATA
1 GATCAAATTAGTACCTCTACTATTAAATA
*
74744526 GATC-AATATAGTACCTGTACTATTAAA
1 GATCAAAT-TAGTACCTCTACTATTAAA
74744553 AAGAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (29 bp):
GATCAAATTAGTACCTCTACTATTAAATA
Found at i:74746436 original size:63 final size:63
Alignment explanation
Indices: 74746360--74746487 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
74746350 ATTATGTAAT
74746360 GACTCAAAGTGAAAATTTTGTTTATTTATGAAGTAAATTGATGGGTATTGTGTTTTTGGAACA
1 GACTCAAAGTGAAAATTTTGTTTATTTATGAAGTAAATTGATGGGTATTGTGTTTTTGGAACA
74746423 GACTCAAAGTGAAAATTTTGTTTATTTATGAAGTAAATTGATGGGTATTGTGTTTTTGGAACA
1 GACTCAAAGTGAAAATTTTGTTTATTTATGAAGTAAATTGATGGGTATTGTGTTTTTGGAACA
74746486 GA
1 GA
74746488 AGCTGGTGGG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.41
Consensus pattern (63 bp):
GACTCAAAGTGAAAATTTTGTTTATTTATGAAGTAAATTGATGGGTATTGTGTTTTTGGAACA
Found at i:74756332 original size:19 final size:20
Alignment explanation
Indices: 74756308--74756356 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
74756298 AAAAAATATA
*
74756308 AAAAAT-TAAAATTAATT-AT
1 AAAAATATAAAA-AAATTAAT
74756327 AAAAATATAAAAAAATTAAT
1 AAAAATATAAAAAAATTAAT
74756347 AAAAACTATA
1 AAAAA-TATA
74756357 CTCAAATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 10 0.38
20 12 0.46
21 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAATATAAAAAAATTAAT
Found at i:74756356 original size:29 final size:28
Alignment explanation
Indices: 74756299--74756356 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
74756289 TCTCTATTTA
* *
74756299 AAAAATATAAAAAATTAAAATTAATTAT
1 AAAAATATAAAAAATTAAAATAAACTAT
74756327 AAAAATATAAAAAAATTAATAA-AAACTAT
1 AAAAATAT-AAAAAATTAA-AATAAACTAT
74756356 A
1 A
74756357 CTCAAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 8 0.31
29 16 0.62
30 2 0.08
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (28 bp):
AAAAATATAAAAAATTAAAATAAACTAT
Found at i:74765654 original size:10 final size:10
Alignment explanation
Indices: 74765639--74765676 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
74765629 TTAAATTATA
74765639 AAAGATAATT
1 AAAGATAATT
74765649 AAAGATAATT
1 AAAGATAATT
*
74765659 AAAGATAAAT
1 AAAGATAATT
74765669 AAAGATAA
1 AAAGATAA
74765677 AAGCTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.24
Consensus pattern (10 bp):
AAAGATAATT
Found at i:74765684 original size:17 final size:17
Alignment explanation
Indices: 74765636--74765684 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 17
74765626 TAATTAAATT
*
74765636 ATAAAAGATAATTAAAG
1 ATAAAAGATAAATAAAG
74765653 ATAATTAAAGATAAATAAAG
1 AT-A--AAAGATAAATAAAG
*
74765673 ATAAAAGCTAAA
1 ATAAAAGATAAA
74765685 ATTAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 10 0.37
18 1 0.04
19 1 0.04
20 15 0.56
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.22
Consensus pattern (17 bp):
ATAAAAGATAAATAAAG
Found at i:74766019 original size:19 final size:20
Alignment explanation
Indices: 74765992--74766029 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
74765982 TAGAATATTA
74765992 TCATCTAT-ATAAATTTTTC
1 TCATCTATAATAAATTTTTC
* *
74766011 TCATTTATAATATATTTTT
1 TCATCTATAATAAATTTTT
74766030 TTTTTTGCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.58
Consensus pattern (20 bp):
TCATCTATAATAAATTTTTC
Found at i:74768290 original size:40 final size:40
Alignment explanation
Indices: 74768195--74768279 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
74768185 TTCTAACTTG
* *
74768195 AAAACCAACTGTTCAACTATTTATATGCAAGAAATTAACA
1 AAAATCAACAGTTCAACTATTTATATGCAAGAAATTAACA
* *
74768235 AAAATCAATAGTTCAA-TAATTTATATGCAATAAATTAACA
1 AAAATCAACAGTTCAACT-ATTTATATGCAAGAAATTAACA
74768275 AAAAT
1 AAAAT
74768280 AAGCGGTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.03
40 39 0.98
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (40 bp):
AAAATCAACAGTTCAACTATTTATATGCAAGAAATTAACA
Found at i:74775391 original size:20 final size:20
Alignment explanation
Indices: 74775366--74775410 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
74775356 ACATTAGTAT
74775366 TTTTATTCTGAATTTTAAGA
1 TTTTATTCTGAATTTTAAGA
*
74775386 TTTTATTCTGAATTTTAATA
1 TTTTATTCTGAATTTTAAGA
74775406 TTTTA
1 TTTTA
74775411 ATTTAGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTTATTCTGAATTTTAAGA
Found at i:74778331 original size:21 final size:21
Alignment explanation
Indices: 74778259--74778363 Score: 70
Period size: 21 Copynumber: 5.0 Consensus size: 21
74778249 CGTTAACTCA
*
74778259 TATGAGTTT-CAGTTAACCCT
1 TATGAGTTTCCATTTAACCCT
* * * * *
74778279 TACGGGTTT-CAGTTCAGCTCT
1 TATGAGTTTCCA-TTTAACCCT
* *
74778300 TATAAGCTTCCATTTAACCCT
1 TATGAGTTTCCATTTAACCCT
* *
74778321 TATGAGTTTCCATTTAGCTCT
1 TATGAGTTTCCATTTAACCCT
* * *
74778342 TATAAGCTTCCGTTTAACCCT
1 TATGAGTTTCCATTTAACCCT
74778363 T
1 T
74778364 TCAGGTTTCC
Statistics
Matches: 61, Mismatches: 22, Indels: 3
0.71 0.26 0.03
Matches are distributed among these distances:
20 9 0.15
21 50 0.82
22 2 0.03
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (21 bp):
TATGAGTTTCCATTTAACCCT
Found at i:74778393 original size:42 final size:42
Alignment explanation
Indices: 74778271--74778386 Score: 144
Period size: 42 Copynumber: 2.8 Consensus size: 42
74778261 TGAGTTTCAG
* * * *
74778271 TTAACCCTTACGGGTTTCAGTTCAGCTCTTATAAGCTTCCAT
1 TTAACCCTTTCAGGTTTCCGTTTAGCTCTTATAAGCTTCCAT
* * *
74778313 TTAACCCTTATGA-GTTTCCATTTAGCTCTTATAAGCTTCCGT
1 TTAACCCTT-TCAGGTTTCCGTTTAGCTCTTATAAGCTTCCAT
*
74778355 TTAACCCTTTCAGGTTTCCGTTTAGCACTTAT
1 TTAACCCTTTCAGGTTTCCGTTTAGCTCTTAT
74778387 GTGCTTCAGT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.03
42 60 0.97
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.41
Consensus pattern (42 bp):
TTAACCCTTTCAGGTTTCCGTTTAGCTCTTATAAGCTTCCAT
Found at i:74778975 original size:30 final size:30
Alignment explanation
Indices: 74778929--74779052 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
74778919 TTTTATTATG
*
74778929 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
74778960 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
74778990 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
74779020 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
74779050 CCA
1 CCA
74779053 TAAATATGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:74778984 original size:15 final size:15
Alignment explanation
Indices: 74778939--74779046 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
74778929 CCAATATCTC
74778939 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
74778954 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
74778969 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
74778984 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
74778999 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
74779014 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
74779029 GATACCCATATCTTT
1 GATACCCATATCTTT
74779044 GAT
1 GAT
74779047 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:74783669 original size:30 final size:30
Alignment explanation
Indices: 74783623--74783716 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
74783613 TTTTATTATG
*
74783623 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
74783654 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
74783684 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
74783714 CCA
1 CCA
74783717 TAAATATGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
30 51 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:74783678 original size:15 final size:15
Alignment explanation
Indices: 74783633--74783710 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
74783623 CCAATATCTC
74783633 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
74783648 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
74783663 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
74783678 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
74783693 GATACCCATATCTTT
1 GATACCCATATCTTT
74783708 GAT
1 GAT
74783711 TTTCCATAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:74790895 original size:15 final size:15
Alignment explanation
Indices: 74790872--74790905 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
74790862 TATTCCTTTT
74790872 AATTGAAATAAAATA
1 AATTGAAATAAAATA
* *
74790887 AATTTAAATATAATA
1 AATTGAAATAAAATA
74790902 AATT
1 AATT
74790906 ATTTTCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
AATTGAAATAAAATA
Found at i:74794248 original size:16 final size:16
Alignment explanation
Indices: 74794227--74794262 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
74794217 ATTTTTTGAA
74794227 TTATAATATAATAAAT
1 TTATAATATAATAAAT
* *
74794243 TTATAATATTATGAAT
1 TTATAATATAATAAAT
74794259 TTAT
1 TTAT
74794263 GTTTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTATAATATAATAAAT
Found at i:74799332 original size:6 final size:7
Alignment explanation
Indices: 74799310--74799335 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
74799300 ATTAAGCGAA
74799310 TTTAATT
1 TTTAATT
74799317 TTTAATT
1 TTTAATT
74799324 TTTAATT
1 TTTAATT
74799331 TTTAA
1 TTTAA
74799336 ACACAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTAATT
Found at i:74800281 original size:17 final size:17
Alignment explanation
Indices: 74800259--74800293 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
74800249 TCACTTGTAA
74800259 CCATTTCGTTATTCTGT
1 CCATTTCGTTATTCTGT
* *
74800276 CCATTTGGTTATTTTGT
1 CCATTTCGTTATTCTGT
74800293 C
1 C
74800294 AATAACATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.11, C:0.20, G:0.14, T:0.54
Consensus pattern (17 bp):
CCATTTCGTTATTCTGT
Found at i:74802484 original size:75 final size:75
Alignment explanation
Indices: 74802400--74802551 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
74802390 TCTGTCGTGA
74802400 GCCTATAAATTCTTTAAAGAGTTAGTATGGGTTGAAATCTCAGCAAGTGCAAATGTTAAGATTTC
1 GCCTATAAATTCTTTAAAGAGTTAGTATGGGTTGAAATCTCAGCAAGTGCAAATGTTAAGATTTC
74802465 TTTGATCTGT
66 TTTGATCTGT
74802475 GCCTATAAATTCTTTAAAGAGTTAGTATGGGTTGAAATCTCAGCAAGTGCAAATGTTAAGATTTC
1 GCCTATAAATTCTTTAAAGAGTTAGTATGGGTTGAAATCTCAGCAAGTGCAAATGTTAAGATTTC
74802540 TTTGATCTGT
66 TTTGATCTGT
74802550 GC
1 GC
74802552 TCGAGCTCTA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.37
Consensus pattern (75 bp):
GCCTATAAATTCTTTAAAGAGTTAGTATGGGTTGAAATCTCAGCAAGTGCAAATGTTAAGATTTC
TTTGATCTGT
Found at i:74805112 original size:14 final size:14
Alignment explanation
Indices: 74805095--74805127 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
74805085 ACTACACTTC
74805095 AAAGACTTCTTTCG
1 AAAGACTTCTTTCG
*
74805109 AAAGACTTCTTTTG
1 AAAGACTTCTTTCG
74805123 AAAGA
1 AAAGA
74805128 GTCAACCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (14 bp):
AAAGACTTCTTTCG
Found at i:74814327 original size:16 final size:17
Alignment explanation
Indices: 74814296--74814328 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
74814286 CCAAACAAAG
*
74814296 AAAAAAACACACACATA
1 AAAAAAACACAAACATA
74814313 AAAAAAACA-AAACATA
1 AAAAAAACACAAACATA
74814329 TCATCATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.76, C:0.18, G:0.00, T:0.06
Consensus pattern (17 bp):
AAAAAAACACAAACATA
Found at i:74816749 original size:62 final size:60
Alignment explanation
Indices: 74816631--74816766 Score: 195
Period size: 62 Copynumber: 2.2 Consensus size: 60
74816621 CACACTAGTA
74816631 GTCACCTAAATATTAGTAAATTTCTTTTTTGGTCACCCAACTCTGAAAAGCTACAAAATG
1 GTCACCTAAATATTAGTAAATTTCTTTTTTGGTCACCCAACTCTGAAAAGCTACAAAATG
* * *
74816691 GTCACCTAATTATTAGTAAATTTCTTTTTTTTGGTTACCCAAC-CATGAAAAGTTACAAAATG
1 GTCACCTAAATATTAGTAAATTTC--TTTTTTGGTCACCCAACTC-TGAAAAGCTACAAAATG
74816753 GTCA-CTAAACTATT
1 GTCACCTAAA-TATT
74816767 CAATTTTGTC
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
60 23 0.34
61 5 0.07
62 40 0.59
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (60 bp):
GTCACCTAAATATTAGTAAATTTCTTTTTTGGTCACCCAACTCTGAAAAGCTACAAAATG
Found at i:74816997 original size:60 final size:59
Alignment explanation
Indices: 74816930--74817045 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 59
74816920 CTAGCTAGTG
* * *
74816930 ACCAAAAAAGACAAAATT-GAATAATTGGGTGACGATTTTGTAACTTTTCATAGTTAAGTT
1 ACCAAAAAAG--AAAATTAGAATAATTAGATGACCATTTTGTAACTTTTCATAGTTAAGTT
* * *
74816990 ACCAAAAAAGAAATTTACTAATAGTTAGATGACCATTTTGTAACTTTTCATAGTTA
1 ACCAAAAAAGAAAATTA-GAATAATTAGATGACCATTTTGTAACTTTTCATAGTTA
74817046 GATGACCAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
58 5 0.10
60 43 0.90
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (59 bp):
ACCAAAAAAGAAAATTAGAATAATTAGATGACCATTTTGTAACTTTTCATAGTTAAGTT
Found at i:74817064 original size:60 final size:60
Alignment explanation
Indices: 74816959--74817075 Score: 175
Period size: 60 Copynumber: 1.9 Consensus size: 60
74816949 AATAATTGGG
* *
74816959 TGACGATTTTGTAACTTTTCATAGTTAAGTTACCAAAAAAGAAATTTACTAATAGTTAGA
1 TGACCATTTTGTAACTTTTCATAGTTAAGTGACCAAAAAAGAAATTTACTAATAGTTAGA
*
74817019 TGACCATTTTGTAACTTTTCATAGTT-AGATGACCAGATAAA-AAATTTACTAATAGTT
1 TGACCATTTTGTAACTTTTCATAGTTAAG-TGACCA-AAAAAGAAATTTACTAATAGTT
74817076 TAGGTGACTA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
59 2 0.04
60 46 0.88
61 4 0.08
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (60 bp):
TGACCATTTTGTAACTTTTCATAGTTAAGTGACCAAAAAAGAAATTTACTAATAGTTAGA
Found at i:74820375 original size:21 final size:21
Alignment explanation
Indices: 74820351--74820390 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
74820341 TGAAAATAAA
* *
74820351 TTTAAAAAATTATTATATATT
1 TTTAAAAAAATACTATATATT
74820372 TTTAAAAAAATACTATATA
1 TTTAAAAAAATACTATATA
74820391 AAAATTATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTAAAAAAATACTATATATT
Found at i:74823171 original size:11 final size:12
Alignment explanation
Indices: 74823142--74823174 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
74823132 AAAATGGGAA
*
74823142 AGAAAACTTAAG
1 AGAAAACTAAAG
74823154 AGAAAACTAAAG
1 AGAAAACTAAAG
74823166 -GAAAACTAA
1 AGAAAACTAA
74823175 GCAAAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.64, C:0.09, G:0.15, T:0.12
Consensus pattern (12 bp):
AGAAAACTAAAG
Found at i:74825618 original size:28 final size:27
Alignment explanation
Indices: 74825553--74825745 Score: 224
Period size: 28 Copynumber: 7.3 Consensus size: 27
74825543 ATAGCAATGG
* *
74825553 GCTAAGTGAAATAAGACCATGACA--T
1 GCTAAGTGAAATAAGTCCATGGCATGT
74825578 -CTAAGTGAAATAAGTCCATGGCAATGT
1 GCTAAGTGAAATAAGTCCATGGC-ATGT
* * *
74825605 GCTAAGTAAAATAAGACCGTGGCAATGT
1 GCTAAGTGAAATAAGTCCATGGC-ATGT
*
74825633 GCTAAGTGAAATAAGACCATGGCA--T
1 GCTAAGTGAAATAAGTCCATGGCATGT
74825658 -CTAAGTGAAATAAGTCCATGGCAATGT
1 GCTAAGTGAAATAAGTCCATGGC-ATGT
*
74825685 GCTAAGTGAAATAAGTCCACGGCA--T
1 GCTAAGTGAAATAAGTCCATGGCATGT
74825710 -CTAAGTGAAATAAGTCCATGGCATGGT
1 GCTAAGTGAAATAAGTCCATGGCAT-GT
74825737 GCTAAGTGA
1 GCTAAGTGA
74825746 GAAATTTCTT
Statistics
Matches: 146, Mismatches: 10, Indels: 21
0.82 0.06 0.12
Matches are distributed among these distances:
24 63 0.43
25 4 0.03
27 5 0.03
28 74 0.51
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.23
Consensus pattern (27 bp):
GCTAAGTGAAATAAGTCCATGGCATGT
Found at i:74825662 original size:52 final size:52
Alignment explanation
Indices: 74825554--74825745 Score: 241
Period size: 52 Copynumber: 3.7 Consensus size: 52
74825544 TAGCAATGGG
* *
74825554 CTAAGTGAAATAAGACCATGAC-A--T-CTAAGTGAAATAAGTCCATGGCAATGT
1 CTAAGTGAAATAAGTCCATGGCAATGTGCTAAGTGAAATAAGTCCATGGC-A--T
* * * *
74825605 GCTAAGTAAAATAAGACCGTGGCAATGTGCTAAGTGAAATAAGACCATGGCAT
1 -CTAAGTGAAATAAGTCCATGGCAATGTGCTAAGTGAAATAAGTCCATGGCAT
*
74825658 CTAAGTGAAATAAGTCCATGGCAATGTGCTAAGTGAAATAAGTCCACGGCAT
1 CTAAGTGAAATAAGTCCATGGCAATGTGCTAAGTGAAATAAGTCCATGGCAT
74825710 CTAAGTGAAATAAGTCCATGGC-ATGGTGCTAAGTGA
1 CTAAGTGAAATAAGTCCATGGCAAT-GTGCTAAGTGA
74825746 GAAATTTCTT
Statistics
Matches: 126, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
51 2 0.02
52 99 0.79
53 2 0.02
55 2 0.02
56 21 0.17
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (52 bp):
CTAAGTGAAATAAGTCCATGGCAATGTGCTAAGTGAAATAAGTCCATGGCAT
Found at i:74825671 original size:80 final size:80
Alignment explanation
Indices: 74825546--74825733 Score: 285
Period size: 80 Copynumber: 2.4 Consensus size: 80
74825536 TTAGACCATA
* *
74825546 GCAATGGGCTAAGTGAAATAAGACCATGACATCTAAGTGAAATAAGTCCATGGCAATGTGCTAAG
1 GCAATGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCATGGCAATGTGCTAAG
**
74825611 TAAAATAAGACCGTG
66 TAAAATAAGACCACG
74825626 GCAATGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCATGGCAATGTGCTAAG
1 GCAATGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCATGGCAATGTGCTAAG
* *
74825691 TGAAATAAGTCCACG
66 TAAAATAAGACCACG
*
74825706 GC-A--T-CTAAGTGAAATAAGTCCATGGCAT
1 GCAATGTGCTAAGTGAAATAAGACCATGGCAT
74825734 GGTGCTAAGT
Statistics
Matches: 101, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
76 23 0.23
77 1 0.01
79 1 0.01
80 76 0.75
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.22
Consensus pattern (80 bp):
GCAATGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGAAATAAGTCCATGGCAATGTGCTAAG
TAAAATAAGACCACG
Found at i:74825893 original size:50 final size:51
Alignment explanation
Indices: 74825769--74825915 Score: 219
Period size: 50 Copynumber: 2.9 Consensus size: 51
74825759 TGAACCTTAG
* * *
74825769 GAATAACATAACTTTGGACACAAGTGTGGTACTATGTGAAGGCTACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
*
74825820 GAATAAAATTGCTTTGGACACAAGTGTGGTACTATGTGAA-GCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
74825870 GAATAAAATAGCTTTGG-CTACAAG-GATGGTACTATGTGAAGGCCAC
1 GAATAAAATAGCTTTGGAC-ACAAGTG-TGGTACTATGTGAAGGCCAC
74825916 CGTGTATCTA
Statistics
Matches: 88, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
49 2 0.02
50 44 0.50
51 42 0.48
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.29
Consensus pattern (51 bp):
GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
Found at i:74833756 original size:51 final size:53
Alignment explanation
Indices: 74833660--74833778 Score: 179
Period size: 51 Copynumber: 2.3 Consensus size: 53
74833650 CCATAATGGT
* *
74833660 AACAGTAACAGTAACAGTAGCGGTACACAGAGTACCTCATCGGAACAAATCTGG
1 AACAGTAACAGTAACAGTAGAGGTA-ACAGAGTACCTCATCGGAACAAATCCGG
* *
74833714 AACAGTAACAGTAACAGTA-AGGT-ACAGAGTACCTCTTCGGAACTAATCCGG
1 AACAGTAACAGTAACAGTAGAGGTAACAGAGTACCTCATCGGAACAAATCCGG
74833765 AACAGTAACAGTAA
1 AACAGTAACAGTAA
74833779 AGCGACACTT
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 39 0.64
53 3 0.05
54 19 0.31
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (53 bp):
AACAGTAACAGTAACAGTAGAGGTAACAGAGTACCTCATCGGAACAAATCCGG
Found at i:74833926 original size:20 final size:20
Alignment explanation
Indices: 74833901--74833940 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
74833891 TCAGTACATA
74833901 TTTCAGCT-AATCATATATAT
1 TTTCAGCTCAAT-ATATATAT
*
74833921 TTTCAGTTCAATATATATAT
1 TTTCAGCTCAATATATATAT
74833941 ATCAATTCAC
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:0.35, C:0.12, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTCAGCTCAATATATATAT
Found at i:74835217 original size:16 final size:16
Alignment explanation
Indices: 74835196--74835240 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
74835186 TTATTTAACC
74835196 AATATAAAATAATATT
1 AATATAAAATAATATT
*
74835212 AATATATAATAATATT
1 AATATAAAATAATATT
* *
74835228 TAT-TTAAATAATA
1 AATATAAAATAATA
74835241 AGTAAATACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATATAAAATAATATT
Found at i:74839859 original size:22 final size:21
Alignment explanation
Indices: 74839831--74839897 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
74839821 CATTATATCA
74839831 ATATTTCATGTACCATCAACTC
1 ATATTTCATGTACCATCAA-TC
* *
74839853 ATATTTC-TTTATC-TC-A--
1 ATATTTCATGTACCATCAATC
74839869 ATATTTCATGTACCATCAATTC
1 ATATTTCATGTACCATCAA-TC
74839891 ATATTTC
1 ATATTTC
74839898 TTTATCTCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
16 7 0.20
17 4 0.11
18 2 0.06
19 2 0.06
20 2 0.06
21 4 0.11
22 14 0.40
ACGTcount: A:0.30, C:0.22, G:0.03, T:0.45
Consensus pattern (21 bp):
ATATTTCATGTACCATCAATC
Found at i:74839870 original size:38 final size:38
Alignment explanation
Indices: 74839823--74839906 Score: 150
Period size: 38 Copynumber: 2.2 Consensus size: 38
74839813 AGTTAATTCA
*
74839823 TTATATCAATATTTCATGTACCATCAACTCATATTTCT
1 TTATCTCAATATTTCATGTACCATCAACTCATATTTCT
*
74839861 TTATCTCAATATTTCATGTACCATCAATTCATATTTCT
1 TTATCTCAATATTTCATGTACCATCAACTCATATTTCT
74839899 TTATCTCA
1 TTATCTCA
74839907 CATAATTAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.30, C:0.21, G:0.02, T:0.46
Consensus pattern (38 bp):
TTATCTCAATATTTCATGTACCATCAACTCATATTTCT
Found at i:74841252 original size:2 final size:2
Alignment explanation
Indices: 74841245--74841281 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
74841235 ATGTGATGGA
*
74841245 TG TG TG TG TG TG TG TC TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
74841282 TTTTCCACGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.03, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:74851139 original size:3 final size:3
Alignment explanation
Indices: 74851131--74851155 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
74851121 ACCTAATTAA
74851131 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
74851156 AAATTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:74851492 original size:10 final size:10
Alignment explanation
Indices: 74851477--74851583 Score: 62
Period size: 9 Copynumber: 10.6 Consensus size: 10
74851467 GCATTTAATT
74851477 AATTTTTTAA
1 AATTTTTTAA
*
74851487 AA-TTTTAAA
1 AATTTTTTAA
*
74851496 ATTATTTTTTAT
1 A--ATTTTTTAA
*
74851508 AA-TTTTTAT
1 AATTTTTTAA
74851517 AATTTTTTAA
1 AATTTTTTAA
*
74851527 TA-TTTTTAA
1 AATTTTTTAA
*
74851536 TGA-TTTTTAA
1 -AATTTTTTAA
*
74851546 AATTTTTTTTAT
1 AA--TTTTTTAA
*
74851558 ATTTTTTTAAA
1 AATTTTTT-AA
74851569 AATTTTTT-A
1 AATTTTTTAA
74851578 AATTTT
1 AATTTT
74851584 AAAAATTAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
9 31 0.40
10 24 0.31
11 9 0.12
12 13 0.17
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:74851499 original size:22 final size:21
Alignment explanation
Indices: 74851473--74851551 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 21
74851463 GTTAGCATTT
74851473 AATTAATTTTTTAAAATTTTAA
1 AATT-ATTTTTTAAAATTTTAA
*
74851495 AATTATTTTTTATAATTTT--
1 AATTATTTTTTAAAATTTTAA
* * * *
74851514 TATAATTTTTTAATATTTT-T
1 AATTATTTTTTAAAATTTTAA
*
74851534 AATGA-TTTTTAAAATTTT
1 AATTATTTTTTAAAATTTT
74851552 TTTTATATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
19 27 0.56
20 3 0.06
21 14 0.29
22 4 0.08
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (21 bp):
AATTATTTTTTAAAATTTTAA
Found at i:74851503 original size:19 final size:19
Alignment explanation
Indices: 74851479--74851574 Score: 61
Period size: 22 Copynumber: 4.7 Consensus size: 19
74851469 ATTTAATTAA
*
74851479 TTTTTTAAAATTTTAAAATT
1 TTTTTTAAAATTTTATAA-T
*
74851499 ATTTTTTATAATTTTTATAA-
1 -TTTTTTA-AAATTTTATAAT
*
74851519 TTTTTTAATATTTT-TAAT
1 TTTTTTAAAATTTTATAAT
* *
74851537 GATTTTTAAAATTTTTTTTATAT
1 -TTTTTTAAAA--TTTTATA-AT
74851560 TTTTTTAAAAATTTT
1 TTTTTT-AAAATTTT
74851575 TTAAATTTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
17 3 0.05
18 5 0.08
19 15 0.25
21 15 0.25
22 16 0.27
23 6 0.10
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (19 bp):
TTTTTTAAAATTTTATAAT
Found at i:74851556 original size:12 final size:12
Alignment explanation
Indices: 74851539--74851576 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
74851529 TTTTTAATGA
74851539 TTTTTAAAATTT
1 TTTTTAAAATTT
*
74851551 TTTTT-ATATTT
1 TTTTTAAAATTT
*
74851562 TTTTAAAAATTT
1 TTTTTAAAATTT
74851574 TTT
1 TTT
74851577 AAATTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTTAAAATTT
Done.