Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 12 of 290
Found at i:3552457 original size:55 final size:52
Alignment explanation
Indices: 3552349--3552641 Score: 183
Period size: 49 Copynumber: 5.6 Consensus size: 52
3552339 ATTAGGGTTT
* * * * *
3552349 AAGGATACCATGTAAGACGATGCCAAGGCATGGCAATTGGTAAGGTT-TCTAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACAT-G-TATTGATAA-GTTCT-TAAGGC
* *
3552404 AAGGAAATCATGTAAGACCATGTCAAGACATGTCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGT-ATTGATAAGTT-CT-TAAGGC
* * * * *
3552459 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGTATTGGTGAGTTCTTAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACAT-GTATTGATAAGTTCTTAAGGC
* * * * *
3552512 AAGGATACCATGTAAGACCATGTCGAGACATGGCAATGGTAAGTT-TCAA---
1 AAGGATACCATGTAAGACCATGTCAAGACAT-GTATTGATAAGTTCTTAAGGC
* * * * * * *
3552561 AAGGATACCACGTAAGACCATGACAAGTCATGGCAATGGTAAGTT-TCAA---
1 AAGGATACCATGTAAGACCATGTCAAGACAT-GTATTGATAAGTTCTTAAGGC
* *
3552610 AAGGATACCATGTAAGACCATGACAAGTCATG
1 AAGGATACCATGTAAGACCATGTCAAGACATG
3552642 GAAATGGTAA
Statistics
Matches: 204, Mismatches: 28, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
48 1 0.00
49 75 0.37
52 7 0.03
53 42 0.21
54 10 0.05
55 63 0.31
56 6 0.03
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (52 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGTATTGATAAGTTCTTAAGGC
Found at i:3552555 original size:108 final size:110
Alignment explanation
Indices: 3552356--3552652 Score: 300
Period size: 108 Copynumber: 2.8 Consensus size: 110
3552346 TTTAAGGATA
* *
3552356 CCATGTAAGACGATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
* *
3552421 CCATGTCAAGACATGTCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* * *
3552466 CCATGTAAGACCATGCCAAGGCATGG-TATTGGTGA-G-TTCTTAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
* * * * *
3552528 ACCATGTCGAGACATGGCAATGGTAAGTTTC-AAAAGG---A--TA
65 ACCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* * * *
3552568 CCACGTAAGACCATGACAAGTCATGGCAA-TGGTAA-GTTTC-AA---AAGGATACCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
* * * *
3552627 CCATGACAAGTCATGGAAATGGTAAG
66 CCATGTCAAGACATGGCAATGATAAG
3552653 GTACCCGTGT
Statistics
Matches: 163, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
98 39 0.24
101 2 0.01
102 30 0.18
103 4 0.02
104 1 0.01
107 8 0.05
108 47 0.29
109 7 0.04
110 25 0.15
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:3552581 original size:49 final size:49
Alignment explanation
Indices: 3552466--3552652 Score: 239
Period size: 49 Copynumber: 3.7 Consensus size: 49
3552456 GGCAAAGGTC
* * * * * *
3552466 CCATGTAAGACCATGCCAAGGCATGGTATTGGTGAGTTCTTAAGGCAAGGATA
1 CCATGTAAGACCATGACAAGTCATGGCAATGGTAAGTT-TCAA---AAGGATA
* * *
3552519 CCATGTAAGACCATGTCGAGACATGGCAATGGTAAGTTTCAAAAGGATA
1 CCATGTAAGACCATGACAAGTCATGGCAATGGTAAGTTTCAAAAGGATA
*
3552568 CCACGTAAGACCATGACAAGTCATGGCAATGGTAAGTTTCAAAAGGATA
1 CCATGTAAGACCATGACAAGTCATGGCAATGGTAAGTTTCAAAAGGATA
*
3552617 CCATGTAAGACCATGACAAGTCATGGAAATGGTAAG
1 CCATGTAAGACCATGACAAGTCATGGCAATGGTAAG
3552653 GTACCCGTGT
Statistics
Matches: 121, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
49 86 0.71
52 3 0.02
53 32 0.26
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (49 bp):
CCATGTAAGACCATGACAAGTCATGGCAATGGTAAGTTTCAAAAGGATA
Found at i:3552865 original size:16 final size:16
Alignment explanation
Indices: 3552844--3552874 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3552834 ATAAATTTGA
3552844 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
3552860 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
3552875 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:3565488 original size:20 final size:20
Alignment explanation
Indices: 3565430--3565495 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
3565420 ATAATTTTAT
* * *
3565430 TTTAGGGTTTAGGTTTTAAGA
1 TTTATGGTTAAGG-TTTAAGG
*
3565451 TTTAATGTTTAAGGTTTAAGG
1 TTT-ATGGTTAAGGTTTAAGG
* *
3565472 TTTATGGTTATGGTTTAATG
1 TTTATGGTTAAGGTTTAAGG
3565492 TTTA
1 TTTA
3565496 GTATTTTGGG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 18 0.49
21 12 0.32
22 7 0.19
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (20 bp):
TTTATGGTTAAGGTTTAAGG
Found at i:3565509 original size:21 final size:21
Alignment explanation
Indices: 3565483--3565523 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3565473 TTATGGTTAT
*
3565483 GGTTTAATGTTTAGTATTTTG
1 GGTTTAAGGTTTAGTATTTTG
* *
3565504 GGTTTAGGGTTTAGTGTTTT
1 GGTTTAAGGTTTAGTATTTT
3565524 AAAGCTTATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (21 bp):
GGTTTAAGGTTTAGTATTTTG
Found at i:3565614 original size:22 final size:23
Alignment explanation
Indices: 3565579--3565621 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3565569 GTCTTAGTGT
3565579 TTAGGGTTTTAAGGGTCAGGGTA
1 TTAGGGTTTTAAGGGTCAGGGTA
*
3565602 TTAGGG-TTTAAGGGTTAGGG
1 TTAGGGTTTTAAGGGTCAGGG
3565622 ATTTTGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.21, C:0.02, G:0.42, T:0.35
Consensus pattern (23 bp):
TTAGGGTTTTAAGGGTCAGGGTA
Found at i:3565746 original size:7 final size:7
Alignment explanation
Indices: 3565736--3565797 Score: 79
Period size: 7 Copynumber: 8.9 Consensus size: 7
3565726 GGTGTATAGC
3565736 TTAGGGT
1 TTAGGGT
3565743 TTAGGGT
1 TTAGGGT
*
3565750 TTAAGGT
1 TTAGGGT
* *
3565757 ATATGGT
1 TTAGGGT
3565764 TTAGGGT
1 TTAGGGT
* *
3565771 CTAAGGT
1 TTAGGGT
3565778 TTAGGGT
1 TTAGGGT
3565785 TTAGGGT
1 TTAGGGT
3565792 TTAGGG
1 TTAGGG
3565798 ATAAAATTTG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.19, C:0.02, G:0.39, T:0.40
Consensus pattern (7 bp):
TTAGGGT
Found at i:3565764 original size:21 final size:21
Alignment explanation
Indices: 3565714--3565794 Score: 92
Period size: 21 Copynumber: 3.9 Consensus size: 21
3565704 TTGTAACATA
* * *
3565714 TATAGGGCTTAGGGTGTATAGC
1 TATAGGGTTTAGGGTTTA-AGG
3565736 T-TAGGGTTTAGGGTTTAAGG
1 TATAGGGTTTAGGGTTTAAGG
* *
3565756 TATATGGTTTAGGGTCTAAGG
1 TATAGGGTTTAGGGTTTAAGG
*
3565777 TTTAGGGTTTAGGGTTTA
1 TATAGGGTTTAGGGTTTA
3565795 GGGATAAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
20 3 0.06
21 46 0.92
22 1 0.02
ACGTcount: A:0.21, C:0.04, G:0.36, T:0.40
Consensus pattern (21 bp):
TATAGGGTTTAGGGTTTAAGG
Found at i:3569049 original size:43 final size:43
Alignment explanation
Indices: 3568833--3569119 Score: 186
Period size: 43 Copynumber: 6.7 Consensus size: 43
3568823 CGTTTTCAGC
* * * * * * * *
3568833 AAAAGCGCCACTAAAGCTCACGTTCTATAGCAGCCTTTTTAGT
1 AAAAGCACCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGT
* **
3568876 AAAAGCATCGCTAAAGGTCATGTTCTATAGCAACGTTTGTGG-
1 AAAAGCACCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGT
** * * * *
3568918 GGAAGCACCGCTAAAGGTTACGCTCTATAGCGGCATTTGT-GT
1 AAAAGCACCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGT
*** * * * * * *
3568960 GAAAAGTGTCGCTAAAGGTCATGTTCCACAACGGTGGTTGTAGT
1 -AAAAGCACCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGT
3569004 AAAAGCACCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGT
1 AAAAGCACCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGT
*** * * * * * *
3569047 AAAAATGCCACTAAAAGTCATGTTCTATTGTGACACTTT-TGGGT
1 AAAAGCACCGCTAAAGGTCATGTTCTATAGCGGC-GTTTGT-GGT
**
3569091 -AAAGCACCGCTAAATATCATGTTCTATAG
1 AAAAGCACCGCTAAAGGTCATGTTCTATAG
3569120 TGGCATTGTA
Statistics
Matches: 182, Mismatches: 57, Indels: 10
0.73 0.23 0.04
Matches are distributed among these distances:
41 1 0.01
42 31 0.17
43 142 0.78
44 8 0.04
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (43 bp):
AAAAGCACCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGT
Found at i:3570034 original size:14 final size:14
Alignment explanation
Indices: 3570015--3570047 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
3570005 ATTCAACAAG
3570015 GCATATCATTACTT
1 GCATATCATTACTT
3570029 GCATATCATTACTT
1 GCATATCATTACTT
3570043 GCATA
1 GCATA
3570048 CATGTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (14 bp):
GCATATCATTACTT
Found at i:3571400 original size:41 final size:45
Alignment explanation
Indices: 3571295--3571412 Score: 149
Period size: 44 Copynumber: 2.7 Consensus size: 45
3571285 ATGTGTTTTT
*
3571295 TGTAAGACCACGTCTGGGACATTGGCATCG-A-CTTATGATTTACG
1 TGTAAGACCACGTCTGGGACATTGGCATCGTATCTTA-GATTTACA
*
3571339 TGTAAGACCACGTTTGGGACATT-GCATCGTATC-TA-ATTT-CA
1 TGTAAGACCACGTCTGGGACATTGGCATCGTATCTTAGATTTACA
* *
3571380 TGTAAGACCACGTCTAGGACATTGGCATTGTAT
1 TGTAAGACCACGTCTGGGACATTGGCATCGTAT
3571413 GAGTTTTTCG
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
41 22 0.33
42 12 0.18
43 6 0.09
44 25 0.38
45 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (45 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGTATCTTAGATTTACA
Found at i:3583440 original size:29 final size:29
Alignment explanation
Indices: 3583383--3583484 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
3583373 TACCTGTATT
* *
3583383 TGGCCCATTAAGG-CC-AATCATATTTATA
1 TGGCCCATT-AGGCCCAAATCACATATATA
* *
3583411 TAGCCCATTAGGCCCAAATCACCTATATA
1 TGGCCCATTAGGCCCAAATCACATATATA
* *
3583440 TGGCCGATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATATATA
*
3583469 TGGCCCGTTAGGCCCA
1 TGGCCCATTAGGCCCA
3583485 GTCACATTCA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
27 3 0.05
28 10 0.16
29 49 0.79
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATATATA
Found at i:3586875 original size:12 final size:12
Alignment explanation
Indices: 3586860--3586892 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3586850 AGTTGGAGAT
*
3586860 AAAGTATTTTTA
1 AAAGTATCTTTA
3586872 AAAGTATCTTTA
1 AAAGTATCTTTA
3586884 AAAGTATCT
1 AAAGTATCT
3586893 CTATGGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (12 bp):
AAAGTATCTTTA
Found at i:3592839 original size:46 final size:46
Alignment explanation
Indices: 3592690--3592965 Score: 210
Period size: 46 Copynumber: 5.9 Consensus size: 46
3592680 TTGGGTCTTT
* * * *
3592690 TGTATGCTAG-GTAAGACATGTCTGGGACATGCATCGGCCACATTA
1 TGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGTGA
* * *
3592735 TG-AGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCAT--TGA
1 TGTA-AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGTGA
* * * *
3592781 GGCGAGAGCTAGTGTAAGACATGTCTTGGACATGCATCTGCCTCGTGA
1 TG-TA-AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGTGA
*
3592829 TGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGA
1 TGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGTGA
* *
3592875 TGT--GTTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CACG-GATA
1 TGTAAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGTG--A
* * * *
3592921 TGGAGAGCAAGTATAAGACCATGTCTGGGACATGGCGTCGGCCTC
1 TGTA-AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTC
3592966 AATTTCGATA
Statistics
Matches: 189, Mismatches: 25, Indels: 29
0.78 0.10 0.12
Matches are distributed among these distances:
44 13 0.07
45 24 0.13
46 67 0.35
47 26 0.14
48 26 0.14
49 31 0.16
50 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.24
Consensus pattern (46 bp):
TGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGTGA
Found at i:3592944 original size:140 final size:138
Alignment explanation
Indices: 3592690--3592954 Score: 338
Period size: 140 Copynumber: 1.9 Consensus size: 138
3592680 TTGGGTCTTT
* *
3592690 TGTATGCTAGGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCA
1 TGTAAGCTAGGTAAGACATGTCTGGGACATGCATCGGCCACATGAT-AGAGCCAGTGTAAGACCA
* ** * * *
3592755 TGTTTGGGACATGGCATCGGCATTGAGGCGAGAGCTAGTGTAAGACATGTCTTGGACATGCATCT
65 TGTCTGGGACATGGCATCGGCACGGAGGCGAGAGCAAGTATAAGACATGTCTGGGACATGCATCT
3592820 GCCTCGTGA
130 GCCTCGTGA
* * **
3592829 TGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GAT-GTGTTAGTGTAAGACC
1 TGTAAGCTAG-GTAAGACATGTCTGGGACATGCATCGGCCAC-ATGATAGAGCCAGTGTAAGACC
*
3592892 ATGTCTGGGACATGGCATCGGCACGGATATG-GAGAGCAAGTATAAGACCATGTCTGGGACATG
64 ATGTCTGGGACATGGCATCGGCACGG--AGGCGAGAGCAAGTATAAGA-CATGTCTGGGACATG
3592955 GCGTCGGCCT
Statistics
Matches: 108, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
138 36 0.33
139 23 0.21
140 48 0.44
141 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (138 bp):
TGTAAGCTAGGTAAGACATGTCTGGGACATGCATCGGCCACATGATAGAGCCAGTGTAAGACCAT
GTCTGGGACATGGCATCGGCACGGAGGCGAGAGCAAGTATAAGACATGTCTGGGACATGCATCTG
CCTCGTGA
Found at i:3592953 original size:94 final size:92
Alignment explanation
Indices: 3592695--3592954 Score: 266
Period size: 94 Copynumber: 2.8 Consensus size: 92
3592685 TCTTTTGTAT
*
3592695 GCTAG-GTAAGACATGTCTGGGACATGCATCGGCCAC-ATTAT-GAGAGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGG-CACGA-TATGGAGAGCAAGTGTAAGACCATG
* * *
3592757 TTTGGGACATGGCATCGGCATTGAGGCGAGA
64 TCTGGGACAT-GCATCGGCA-TGACGAGAGA
* * * * *
3592788 GCTAGTGTAAGACATGTCTTGGACATGCATCTGCCTCG-TGATGTA-AGCTAGTGTAAGA-CATG
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-GGCACGAT-ATGGAGAGCAAGTGTAAGACCATG
*
3592850 TCTGGGACATGCATCGGC-T-ACGAGATGT
64 TCTGGGACATGCATCGGCATGACGAGA-GA
* *
3592878 GTTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATATGGAGAGCAAGTATAAGACCAT
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCAC-GATATGGAGAGCAAGTGTAAGACCAT
3592943 GTCTGGGACATG
63 GTCTGGGACATG
3592955 GCGTCGGCCT
Statistics
Matches: 139, Mismatches: 16, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
89 4 0.03
90 13 0.09
91 16 0.12
92 18 0.13
93 31 0.22
94 55 0.40
95 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (92 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCACGATATGGAGAGCAAGTGTAAGACCATGTC
TGGGACATGCATCGGCATGACGAGAGA
Found at i:3592987 original size:49 final size:49
Alignment explanation
Indices: 3592700--3593059 Score: 190
Period size: 49 Copynumber: 7.6 Consensus size: 49
3592690 TGTATGCTAG
* *
3592700 GTAAGA-CATGTCTGGGACAT-GCATCGGC-CACATTAT-GAGAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCAC-CAATATCGAGAGCAAGT
* *** ** *
3592746 GTAAGACCATGTTTGGGACATGGCATCGGCATTGA-GGCGAGAGCTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCACCAATATCGAGAGCAAGT
* * * *
3592794 GTAAGA-CATGTCTTGGACAT-GCATCTGC-CTC-GTGAT-GTA-AGCTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCAC-CAAT-ATCG-AGAGCAAGT
* * * **
3592840 GTAAGA-CATGTCTGGGACAT-GCATCGGCTA-CGAGAT---GTGTTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGC-ACCAATATCGAGAGCAAGT
** *
3592884 GTAAGACCATGTCTGGGACATGGCATCGGCACGGATATGGAGAGCAAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCACCAATATCGAGAGCAAGT
* * * *
3592933 ATAAGACCATGTCTGGGACATGGCGTCGGC-CTCAATTTCGATAGTC-AGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCAC-CAATATCGAGAG-CAAGT
** ** * *
3592982 GTAAGACCATGTCTAAGACATGGCATC-G-ACTTGATGAAC-A-AGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCAC-CAAT-ATCGAGAGCAAGT
*
3593029 GTAAGACCGTGTCTGGGACATGGCATCGGCA
1 GTAAGACCATGTCTGGGACATGGCATCGGCA
3593060 TTATACCTTA
Statistics
Matches: 244, Mismatches: 45, Indels: 47
0.73 0.13 0.14
Matches are distributed among these distances:
44 11 0.05
45 15 0.06
46 63 0.26
47 55 0.23
48 31 0.13
49 68 0.28
50 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGGCATCGGCACCAATATCGAGAGCAAGT
Found at i:3596868 original size:28 final size:28
Alignment explanation
Indices: 3596822--3596891 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
3596812 ATGAAAATTT
* * * *
3596822 CACTAAGCGTGCGAGTTTGGTTAACGAG
1 CACTAAGTGTGTGAGTTTGATTAACGAC
* *
3596850 CACTAAGTGTGTGATTTTGATTATCGAC
1 CACTAAGTGTGTGAGTTTGATTAACGAC
*
3596878 CACTAAGTATGTGA
1 CACTAAGTGTGTGA
3596892 AGGAAAATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (28 bp):
CACTAAGTGTGTGAGTTTGATTAACGAC
Found at i:3602694 original size:21 final size:21
Alignment explanation
Indices: 3602667--3602728 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
3602657 TATAATGAGT
3602667 ATATCATAGCATATCATGTAC
1 ATATCATAGCATATCATGTAC
* * * *
3602688 ATCTCATAACAGATCATGTGC
1 ATATCATAGCATATCATGTAC
3602709 ATATCAT-GTCATATCATGTA
1 ATATCATAG-CATATCATGTA
3602729 TAACAATATC
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.34
Consensus pattern (21 bp):
ATATCATAGCATATCATGTAC
Found at i:3602721 original size:10 final size:10
Alignment explanation
Indices: 3602667--3602727 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
3602657 TATAATGAGT
3602667 ATATCATAG-C
1 ATATCAT-GTC
3602677 ATATCATGTAC
1 ATATCATGT-C
* **
3602688 ATCTCATAAC
1 ATATCATGTC
*
3602698 AGATCATGTGC
1 ATATCATGT-C
3602709 ATATCATGTC
1 ATATCATGTC
3602719 ATATCATGT
1 ATATCATGT
3602728 ATAACAATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
9 1 0.03
10 23 0.57
11 16 0.40
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (10 bp):
ATATCATGTC
Found at i:3603432 original size:27 final size:27
Alignment explanation
Indices: 3603372--3603434 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3603362 GCATATTCGA
3603372 CATTTTACCATACAAGGGTATTACGGT
1 CATTTTACCATACAAGGGTATTACGGT
* * *
3603399 CACTTTACCCTACAGGGGCT-TTACGGT
1 CATTTTACCATACAAGGG-TATTACGGT
*
3603426 CTTTTTACC
1 CATTTTACC
3603435 TATTAGGGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 29 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (27 bp):
CATTTTACCATACAAGGGTATTACGGT
Found at i:3603508 original size:27 final size:27
Alignment explanation
Indices: 3603478--3603530 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3603468 GGGTGTTTTG
3603478 GTAAATCTACAAACCAAGGGTATTTCA
1 GTAAATCTACAAACCAAGGGTATTTCA
* * * *
3603505 GTAATTTTATAAACCAATGGTATTTC
1 GTAAATCTACAAACCAAGGGTATTTC
3603531 TATAATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (27 bp):
GTAAATCTACAAACCAAGGGTATTTCA
Found at i:3603536 original size:27 final size:27
Alignment explanation
Indices: 3603488--3603573 Score: 93
Period size: 27 Copynumber: 3.1 Consensus size: 27
3603478 GTAAATCTAC
*
3603488 AAACCAAGGGTATTTC-AGTAATTTTAT
1 AAACCAAAGGTATTTCTA-TAATTTTAT
* *
3603515 AAACCAATGGTATTTCTATAATTTTTAG
1 AAACCAAAGGTATTTCTATAA-TTTTAT
* *
3603543 AAAGTCAAAGGTATTTCTATAATTTTGT
1 AAA-CCAAAGGTATTTCTATAATTTTAT
3603571 AAA
1 AAA
3603574 TCAGGGGTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
27 18 0.36
28 16 0.32
29 16 0.32
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (27 bp):
AAACCAAAGGTATTTCTATAATTTTAT
Found at i:3603592 original size:27 final size:27
Alignment explanation
Indices: 3603562--3603707 Score: 127
Period size: 27 Copynumber: 5.4 Consensus size: 27
3603552 GGTATTTCTA
**
3603562 TAATTTTGTAAATCAGGGGTATTTTGG
1 TAATTTTACAAATCAGGGGTATTTTGG
* * *
3603589 TAATTTTACAAAT-TGACGGTATTTCGG
1 TAATTTTACAAATCAG-GGGTATTTTGG
* * *
3603616 TAATTTCACAAACCAGTGGTATTTTGG
1 TAATTTTACAAATCAGGGGTATTTTGG
3603643 TAATTTTACAAA-CTAGGGGTATTTTGG
1 TAATTTTACAAATC-AGGGGTATTTTGG
* ** *
3603670 TAATTCTACCCTAT-AGGGGTATTTTAG
1 TAATTTTA-CAAATCAGGGGTATTTTGG
*
3603697 TAATTTCACAA
1 TAATTTTACAA
3603708 TCGAGGGTAA
Statistics
Matches: 94, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
26 3 0.03
27 88 0.94
28 3 0.03
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.40
Consensus pattern (27 bp):
TAATTTTACAAATCAGGGGTATTTTGG
Found at i:3603736 original size:27 final size:27
Alignment explanation
Indices: 3603706--3603824 Score: 150
Period size: 27 Copynumber: 4.4 Consensus size: 27
3603696 GTAATTTCAC
*
3603706 AATCGAGGGTAAAACGATAATTCTGTA
1 AATCGAGGGTAAAACGATAATTCTATA
3603733 AATCGAGGGTAAAAC-AGTAATTCTATA
1 AATCGAGGGTAAAACGA-TAATTCTATA
* * *
3603760 AATTGAGAGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGATAATTCTATA
* * *
3603787 AATCGAGGGTAAAACGGTAATTTTTTA
1 AATCGAGGGTAAAACGATAATTCTATA
*
3603814 AATCGAAGGTA
1 AATCGAGGGTA
3603825 CTTTGGTAAT
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
26 1 0.01
27 80 0.99
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACGATAATTCTATA
Found at i:3614605 original size:40 final size:39
Alignment explanation
Indices: 3614561--3614693 Score: 167
Period size: 40 Copynumber: 3.3 Consensus size: 39
3614551 CGGTTATTTG
* * *
3614561 TGGCACTTAATGTGCAATATGACCTAGCTTCAGCTATATA
1 TGGCACTTAGTGTGCGAT-TGACATAGCTTCAGCTATATA
*
3614601 TGGCACTTAGTGTTCGATTCGACATAGCTTCAGCTATATA
1 TGGCACTTAGTGTGCGATT-GACATAGCTTCAGCTATATA
* * *
3614641 TGCCACTTAGTGTGCGATTTGAGATAGCTTCAGCTATGTA
1 TGGCACTTAGTGTGCGA-TTGACATAGCTTCAGCTATATA
*
3614681 CGGCACTTAGTGT
1 TGGCACTTAGTGT
3614694 ACGAGATATC
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 1 0.01
40 78 0.96
41 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.34
Consensus pattern (39 bp):
TGGCACTTAGTGTGCGATTGACATAGCTTCAGCTATATA
Found at i:3614727 original size:28 final size:28
Alignment explanation
Indices: 3614682--3614737 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
3614672 AGCTATGTAC
*
3614682 GGCACTTAGTGTACGAGATATCGAGTAT
1 GGCACTTAGTGTACGAGACATCGAGTAT
*
3614710 GGCACTTAGTGTGA-GAGACATTGAGTAT
1 GGCACTTAGTGT-ACGAGACATCGAGTAT
3614738 TCAACAGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.29, C:0.12, G:0.30, T:0.29
Consensus pattern (28 bp):
GGCACTTAGTGTACGAGACATCGAGTAT
Found at i:3637115 original size:2 final size:2
Alignment explanation
Indices: 3637110--3637934 Score: 1650
Period size: 2 Copynumber: 412.5 Consensus size: 2
3637100 TTCATATATA
3637110 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637152 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637194 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637236 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637278 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637320 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637362 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637404 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637446 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637488 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637530 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637572 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637614 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637656 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637698 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637740 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637782 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637824 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637866 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3637908 TG TG TG 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 T
3637935 TTTGGTAATG
Statistics
Matches: 823, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 823 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3639007 original size:10 final size:10
Alignment explanation
Indices: 3638992--3639043 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
3638982 AAAATTTAGG
3638992 ATTTATTTTT
1 ATTTATTTTT
*
3639002 ATTTATCTTT
1 ATTTATTTTT
* *
3639012 AATTATCTTT
1 ATTTATTTTT
* *
3639022 AATTATTTGT
1 ATTTATTTTT
3639032 ATTTATCTTTT
1 ATTTAT-TTTT
3639043 A
1 A
3639044 GAATTTAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
10 31 0.89
11 4 0.11
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:3644707 original size:10 final size:10
Alignment explanation
Indices: 3644694--3644746 Score: 72
Period size: 10 Copynumber: 5.3 Consensus size: 10
3644684 AGGATTTACT
3644694 TTTATTTATC
1 TTTATTTATC
*
3644704 TTTAATTATC
1 TTTATTTATC
*
3644714 TTTAATTATC
1 TTTATTTATC
3644724 TTTATTTAT-
1 TTTATTTATC
3644733 TTGTATTTATC
1 TT-TATTTATC
3644744 TTT
1 TTT
3644747 TAGAATTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
9 2 0.05
10 35 0.90
11 2 0.05
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTATTTATC
Found at i:3645498 original size:17 final size:18
Alignment explanation
Indices: 3645470--3645503 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3645460 TATTCTCCAT
3645470 TTTAATTTTCGTAATTTA
1 TTTAATTTTCGTAATTTA
3645488 TTTAA-TTTCGTAATTT
1 TTTAATTTTCGTAATTT
3645504 CTATTCGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (18 bp):
TTTAATTTTCGTAATTTA
Found at i:3648236 original size:79 final size:79
Alignment explanation
Indices: 3648060--3648284 Score: 244
Period size: 79 Copynumber: 2.8 Consensus size: 79
3648050 TTTGAATGAT
* * * *
3648060 ATCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCCGGACTAAGATCCGAAGGCA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATATCCGGGCTAAGACCCGAAGGCA
*
3648123 TTTGTGCGAGATACAT
64 TTTGTGCGAGATACAA
* *
3648139 ATTCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAG-CCCGAAGGCA
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA-TCCGGGCTAAGACCCGAAGGCA
*
3648201 TTTGTGCGAGTTACTAA
64 TTTGTGCGAGATAC-AA
* * * * * *
3648218 ATCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATATCCGGGCTAAGACCCGAAGGCATT
3648283 TG
66 TG
3648285 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
78 24 0.20
79 73 0.59
80 25 0.20
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACAA
Found at i:3648298 original size:40 final size:40
Alignment explanation
Indices: 3648062--3648284 Score: 226
Period size: 40 Copynumber: 5.6 Consensus size: 40
3648052 TGAATGATAT
* * * *
3648062 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
3648102 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-ATAT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
* * * *
3648141 TCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
3648181 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
3648219 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
3648260 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
3648285 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 14, Indels: 16
0.84 0.07 0.08
Matches are distributed among these distances:
39 73 0.45
40 78 0.48
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:3648306 original size:79 final size:79
Alignment explanation
Indices: 3648153--3648317 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
3648143 GGACTAAGAT
* * **
3648153 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
3648218 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
3648232 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
3648295 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
3648311 CCGAAGG
1 CCGAAGG
3648318 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:3650566 original size:23 final size:23
Alignment explanation
Indices: 3650525--3650639 Score: 90
Period size: 23 Copynumber: 4.9 Consensus size: 23
3650515 AAGCTCCTCA
*
3650525 TGAGCTGATGAACAATAAGCTCTAT
1 TGAGCTGA--AACAGTAAGCTCTAT
3650550 TGAGCTGAAACAGTAAGCTCTAT
1 TGAGCTGAAACAGTAAGCTCTAT
* *
3650573 CGAGCT-AAATAGTAAGCTC-AT
1 TGAGCTGAAACAGTAAGCTCTAT
** * ** * *
3650594 ACAAGCTAAAATGGTAAGCTCCAA
1 -TGAGCTGAAACAGTAAGCTCTAT
3650618 TGAGCTGAAAACAGTAAGCTCT
1 TGAGCTG-AAACAGTAAGCTCT
3650640 TACGAGCTAA
Statistics
Matches: 74, Mismatches: 12, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.03
22 17 0.23
23 35 0.47
24 12 0.16
25 8 0.11
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (23 bp):
TGAGCTGAAACAGTAAGCTCTAT
Found at i:3652950 original size:8 final size:8
Alignment explanation
Indices: 3652937--3652972 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
3652927 CAAAAATATG
3652937 TATACATA
1 TATACATA
3652945 TATACATA
1 TATACATA
*
3652953 TATGCATA
1 TATACATA
*
3652961 TATAAATA
1 TATACATA
3652969 TATA
1 TATA
3652973 TACACAGGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (8 bp):
TATACATA
Found at i:3654196 original size:35 final size:35
Alignment explanation
Indices: 3654157--3654273 Score: 91
Period size: 35 Copynumber: 3.3 Consensus size: 35
3654147 ACACATACAC
*
3654157 TTATATGCATACACTCATAAGTCAAAGTATAACAA
1 TTATATACATACACTCATAAGTCAAAGTATAACAA
* * *
3654192 TTATATACAT-CTTTA-TCAT-ACT-AAA-TACACATACAC
1 TTATATACATAC---ACTCATAAGTCAAAGT--ATA-ACAA
* *
3654228 TTATGTGCATACACTCATAAGTCAAAGTATAACAA
1 TTATATACATACACTCATAAGTCAAAGTATAACAA
3654263 TTATATACATA
1 TTATATACATA
3654274 TTTATATCAA
Statistics
Matches: 60, Mismatches: 11, Indels: 22
0.65 0.12 0.24
Matches are distributed among these distances:
33 1 0.02
34 5 0.08
35 29 0.48
36 19 0.32
37 5 0.08
38 1 0.02
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (35 bp):
TTATATACATACACTCATAAGTCAAAGTATAACAA
Found at i:3654211 original size:71 final size:71
Alignment explanation
Indices: 3654127--3654278 Score: 286
Period size: 71 Copynumber: 2.1 Consensus size: 71
3654117 CCAAGCCAAA
3654127 ACATCTTTATCATACTAAATACACATACACTTATATGCATACACTCATAAGTCAAAGTATAACAA
1 ACATCTTTATCATACTAAATACACATACACTTATATGCATACACTCATAAGTCAAAGTATAACAA
3654192 TTATAT
66 TTATAT
*
3654198 ACATCTTTATCATACTAAATACACATACACTTATGTGCATACACTCATAAGTCAAAGTATAACAA
1 ACATCTTTATCATACTAAATACACATACACTTATATGCATACACTCATAAGTCAAAGTATAACAA
3654263 TTATAT
66 TTATAT
*
3654269 ACATATTTAT
1 ACATCTTTAT
3654279 ATCAACGGTC
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 79 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.34
Consensus pattern (71 bp):
ACATCTTTATCATACTAAATACACATACACTTATATGCATACACTCATAAGTCAAAGTATAACAA
TTATAT
Found at i:3657551 original size:53 final size:53
Alignment explanation
Indices: 3657447--3657554 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
3657437 ACTTGTATAA
** *
3657447 GCTATTTTGAGGTCTTAAATCCAAGGATGGCACATTGATATTCGGTGTAAACT
1 GCTATTTTGAGGTCTTAAATCCAAGGATGGCACATTGATATTCAATATAAACT
3657500 GCTATTTTGAGGTCTTAAATCCAAGGATGGCACATTGATATTCAATATAAACT
1 GCTATTTTGAGGTCTTAAATCCAAGGATGGCACATTGATATTCAATATAAACT
3657553 GC
1 GC
3657555 CATCAAACTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (53 bp):
GCTATTTTGAGGTCTTAAATCCAAGGATGGCACATTGATATTCAATATAAACT
Found at i:3658039 original size:26 final size:26
Alignment explanation
Indices: 3658010--3658060 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
3658000 GGTTTAAATT
* * * *
3658010 CTTACAAAATTAAAATTAGAGATTAC
1 CTTAAAAAACTAAAATCAGAAATTAC
3658036 CTTAAAAAACTAAAATCAGAAATTA
1 CTTAAAAAACTAAAATCAGAAATTA
3658061 AATTCATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (26 bp):
CTTAAAAAACTAAAATCAGAAATTAC
Found at i:3658241 original size:51 final size:51
Alignment explanation
Indices: 3658165--3658825 Score: 1322
Period size: 51 Copynumber: 13.0 Consensus size: 51
3658155 GAATCATGAC
3658165 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
1 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
3658216 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
1 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
3658267 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
1 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
3658318 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
1 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
3658369 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
1 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
3658420 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
1 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
3658471 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
1 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
3658522 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
1 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
3658573 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
1 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
3658624 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
1 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
3658675 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
1 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
3658726 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
1 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
3658777 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAA
1 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAA
3658826 ATAGTTGTTG
Statistics
Matches: 610, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 610 1.00
ACGTcount: A:0.30, C:0.16, G:0.04, T:0.51
Consensus pattern (51 bp):
GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
Found at i:3661075 original size:24 final size:24
Alignment explanation
Indices: 3661043--3661090 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3661033 GACACTCCAA
3661043 AACATATATATATATATGATTAAG
1 AACATATATATATATATGATTAAG
3661067 AACATATATATATATATGATTAAG
1 AACATATATATATATATGATTAAG
3661091 CGTCAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (24 bp):
AACATATATATATATATGATTAAG
Found at i:3661559 original size:21 final size:21
Alignment explanation
Indices: 3661498--3661562 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
3661488 AGATCCTGAA
* *
3661498 TTTTCGTAATATTGTCAAAAC
1 TTTTAGTAATATTGTCAAATC
* *
3661519 TTTTACG-ATTATTGCCAAATC
1 TTTTA-GTAATATTGTCAAATC
*
3661540 TTTTAGTAATCTTGTCAAATC
1 TTTTAGTAATATTGTCAAATC
3661561 TT
1 TT
3661563 GAAACCAACC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.46
Consensus pattern (21 bp):
TTTTAGTAATATTGTCAAATC
Found at i:3665336 original size:90 final size:90
Alignment explanation
Indices: 3665173--3665363 Score: 231
Period size: 90 Copynumber: 2.1 Consensus size: 90
3665163 GGCTATTACA
* ** * ** * * * *
3665173 TAACCTGCAACACTGGTGGTTCATCCACCTATTTTCTGGCTGCTCTTATCTGCAATTTTGTTGTG
1 TAACCTGCAACACTGGTGGTTCATCCACCCACATTCTGACAACTCTCATCTACAATTATGTTATG
* *
3665238 TATCCACAACCATCTGGCAACATTT
66 CATCCACAACCATCTGGCAACATAT
*
3665263 TAACCTGCAACATTGGTGGTTCATCCACCCACATTCTGACAACTCTCATCTACAATTATGTTATG
1 TAACCTGCAACACTGGTGGTTCATCCACCCACATTCTGACAACTCTCATCTACAATTATGTTATG
*
3665328 CA-CTCACAACCATCTGGCAACGTAT
66 CATC-CACAACCATCTGGCAACATAT
*
3665353 TAAACTGCAAC
1 TAACCTGCAAC
3665364 TTTTGTGGCT
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
89 1 0.01
90 84 0.99
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (90 bp):
TAACCTGCAACACTGGTGGTTCATCCACCCACATTCTGACAACTCTCATCTACAATTATGTTATG
CATCCACAACCATCTGGCAACATAT
Found at i:3667715 original size:20 final size:20
Alignment explanation
Indices: 3667686--3667725 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3667676 AAGAAGAAAG
* *
3667686 GAAAACAAAAGGAAAAATAA
1 GAAAAAAAAAGAAAAAATAA
3667706 GAAAAAAAAAGAAAAAATAA
1 GAAAAAAAAAGAAAAAATAA
3667726 TGTAAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.80, C:0.03, G:0.12, T:0.05
Consensus pattern (20 bp):
GAAAAAAAAAGAAAAAATAA
Found at i:3667717 original size:10 final size:10
Alignment explanation
Indices: 3667671--3667722 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
3667661 CAAACATTAT
*
3667671 AAAAGAAGAAG
1 AAAAGAA-AAA
* *
3667682 AAAGGAAAAC
1 AAAAGAAAAA
*
3667692 AAAAGGAAAA
1 AAAAGAAAAA
*
3667702 ATAAGAAAAA
1 AAAAGAAAAA
3667712 AAAAGAAAAA
1 AAAAGAAAAA
3667722 A
1 A
3667723 TAATGTAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
10 27 0.82
11 6 0.18
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:3676446 original size:42 final size:42
Alignment explanation
Indices: 3676387--3676529 Score: 196
Period size: 42 Copynumber: 3.4 Consensus size: 42
3676377 GTAGGACCAT
*
3676387 ACCATATCTGGGATATGGCATCTATATGAGATTTCGTGTAAG
1 ACCATATCTGGGATATGGCATCGATATGAGATTTCGTGTAAG
* *
3676429 ACCATATCTAGGATATGGCATCGATATGAGACTTCGTGTAAG
1 ACCATATCTGGGATATGGCATCGATATGAGATTTCGTGTAAG
* * * * * *
3676471 ACCATAGCTGAGCTATTGGCATCGATACGAGATTACATGTAAG
1 ACCATATCTGGGATA-TGGCATCGATATGAGATTTCGTGTAAG
3676514 ACCATATCTGGGATAT
1 ACCATATCTGGGATAT
3676530 AACATTGGTA
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 51 0.59
43 35 0.41
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (42 bp):
ACCATATCTGGGATATGGCATCGATATGAGATTTCGTGTAAG
Found at i:3677130 original size:20 final size:20
Alignment explanation
Indices: 3677105--3677159 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
3677095 TGATTTTAGG
3677105 ATTTATTTTCATTTATC-TAT
1 ATTTATTTTCATTTATCAT-T
*
3677125 ATTTATCTTT-AATTATCATT
1 ATTTAT-TTTCATTTATCATT
*
3677145 ATTTATTTGCATTTA
1 ATTTATTTTCATTTA
3677160 GCTTTTAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 2 0.07
20 23 0.79
21 4 0.14
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTATTTTCATTTATCATT
Found at i:3677917 original size:17 final size:18
Alignment explanation
Indices: 3677889--3677922 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3677879 TATTCTCCAT
3677889 TTTAATTTTCGCAATTTA
1 TTTAATTTTCGCAATTTA
3677907 TTTAA-TTTCGCAATTT
1 TTTAATTTTCGCAATTT
3677923 CAATTCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAATTTTCGCAATTTA
Found at i:3680925 original size:15 final size:14
Alignment explanation
Indices: 3680907--3680983 Score: 70
Period size: 15 Copynumber: 5.3 Consensus size: 14
3680897 TTTTCTTAAT
3680907 TTTTATTCATTATTA
1 TTTTATTCATT-TTA
3680922 TTTTATTTCATTTTA
1 TTTTA-TTCATTTTA
3680937 TTATTATT--TTTTA
1 TT-TTATTCATTTTA
*
3680950 TTTTACTTTATTTTA
1 TTTTA-TTCATTTTA
3680965 TTATTTATT-ATTTTA
1 -T-TTTATTCATTTTA
3680980 TTTT
1 TTTT
3680984 TGGATATTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
12 3 0.05
13 12 0.22
14 1 0.02
15 23 0.42
16 12 0.22
17 4 0.07
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTATTCATTTTA
Found at i:3680929 original size:5 final size:5
Alignment explanation
Indices: 3680919--3680983 Score: 60
Period size: 5 Copynumber: 12.4 Consensus size: 5
3680909 TTATTCATTA
* *
3680919 TTATT TTATT TCATT TTATT ATTATTTT TTATT TTACT TTATT TTATT
1 TTATT TTATT TTATT TTATT -TTA--TT TTATT TTATT TTATT TTATT
*
3680967 ATT-TA TTATT TTATT TT
1 -TTATT TTATT TTATT TT
3680984 TGGATATTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
4 2 0.04
5 37 0.76
6 5 0.10
7 3 0.06
8 2 0.04
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (5 bp):
TTATT
Found at i:3680940 original size:28 final size:26
Alignment explanation
Indices: 3680909--3680982 Score: 89
Period size: 28 Copynumber: 2.8 Consensus size: 26
3680899 TTCTTAATTT
3680909 TTATTCATTATTATTTTATTTCATTTTA
1 TTATT-ATTATTATTTTATTT-ATTTTA
*
3680937 TTATTATTTTTTATTTTACTTTATTTTA
1 TTATTA-TTATTATTTTA-TTTATTTTA
3680965 TTA-T-TTATTATTTTATTT
1 TTATTATTATTATTTTATTT
3680983 TTGGATATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
24 3 0.07
25 10 0.24
27 2 0.05
28 24 0.57
29 3 0.07
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (26 bp):
TTATTATTATTATTTTATTTATTTTA
Found at i:3680964 original size:53 final size:53
Alignment explanation
Indices: 3680879--3680982 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 53
3680869 CAACCTTTAC
*
3680879 TTTTATTTTTTTTTTTACTTTTCTTAATTTTTATTCA-TTATTATTTTATTTCA
1 TTTTATTTTATTTTTTACTTTTCTTAATTTTTATT-ATTTATTATTTTATTTCA
*
3680932 TTTTATTATTATTTTTTA-TTTTACTTTA-TTTTATTATTTATTATTTTATTT
1 TTTTATT-TTATTTTTTACTTTT-CTTAATTTTTATTATTTATTATTTTATTT
3680983 TTGGATATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
52 1 0.02
53 32 0.70
54 13 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (53 bp):
TTTTATTTTATTTTTTACTTTTCTTAATTTTTATTATTTATTATTTTATTTCA
Found at i:3680992 original size:25 final size:25
Alignment explanation
Indices: 3680916--3680979 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 25
3680906 TTTTTATTCA
3680916 TTATTATTTTA-TTTCATTTTATTATTAT
1 TTATTATTTTACTTT-A--TTA-TATTAT
* *
3680944 TTTTTATTTTACTTTATTTTATTAT
1 TTATTATTTTACTTTATTATATTAT
3680969 TTATTATTTTA
1 TTATTATTTTA
3680980 TTTTTGGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 16 0.50
26 2 0.06
28 11 0.34
29 3 0.09
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (25 bp):
TTATTATTTTACTTTATTATATTAT
Found at i:3685404 original size:10 final size:10
Alignment explanation
Indices: 3685389--3685448 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
3685379 TAATTTTAGG
3685389 ATTTAT-TTT
1 ATTTATCTTT
3685398 CATTTATCTTT
1 -ATTTATCTTT
3685409 ATTTATCTTT
1 ATTTATCTTT
*
3685419 AATTATCTTT
1 ATTTATCTTT
3685429 ATTTAT-TTGT
1 ATTTATCTT-T
3685439 ATTTATCTTT
1 ATTTATCTTT
3685449 TAGAATTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:3689757 original size:46 final size:46
Alignment explanation
Indices: 3689695--3690705 Score: 1837
Period size: 46 Copynumber: 22.0 Consensus size: 46
3689685 AGTGTGCTCT
3689695 CTGATA-GAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
3689741 CTGATATGAAACGTGTAAGACCATGGTTGAAACATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3689787 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3689833 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3689879 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3689925 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3689971 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3690017 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3690063 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3690109 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3690155 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3690201 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3690247 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3690293 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3690339 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3690385 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3690431 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3690477 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3690523 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3690569 CTGATATGAAATGTGTAAGACCAAGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * ** * *
3690615 GTGACGAGGAAATGAATAAGACCATGGTTGAATGATAACATGGCAAC
1 CTGA-TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
3690662 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
3690706 TCATGTCGAA
Statistics
Matches: 941, Mismatches: 21, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
45 1 0.00
46 901 0.96
47 39 0.04
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:3696213 original size:42 final size:42
Alignment explanation
Indices: 3696160--3696312 Score: 182
Period size: 42 Copynumber: 3.6 Consensus size: 42
3696150 CTGAGATTAC
* * *
3696160 GTAAGACCATATCTGGGATATGGCATCTATATAAGATTTCTT
1 GTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCAT
* * * *
3696202 GTAAGATCATATCTAGGATATGGCATCGATATGAGACTTCGT
1 GTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCAT
* * * *
3696244 GTAAGACCATAGCT-GGACTATTAGCATCGATACGAGATTACAT
1 GTAAGACCATATCTGGGA-TA-TGGCATCGATATGAGATTTCAT
3696287 GTAAGACCATATCTGGGATATGGCAT
1 GTAAGACCATATCTGGGATATGGCAT
3696313 TGGTACGGTA
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
41 3 0.03
42 55 0.59
43 32 0.34
44 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (42 bp):
GTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCAT
Found at i:3697257 original size:17 final size:18
Alignment explanation
Indices: 3697225--3697258 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3697215 TAATCATGGT
*
3697225 ATGCTTGGTGAATGTGAA
1 ATGCTTGGTAAATGTGAA
3697243 ATGCTTGG-AAATGTGA
1 ATGCTTGGTAAATGTGA
3697259 TTTATGGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.32
Consensus pattern (18 bp):
ATGCTTGGTAAATGTGAA
Found at i:3698402 original size:4 final size:5
Alignment explanation
Indices: 3698370--3698446 Score: 50
Period size: 6 Copynumber: 14.4 Consensus size: 5
3698360 AAACAAGCAA
*
3698370 AAAAG AAAAAG AACAAG -GAAG TAAAAG -AAAG AAAAG AAAAG AAAAG
1 AAAAG -AAAAG AA-AAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG
* *
3698416 AGGAAG AAGAAG AAGAAG AAGAAG AAGAG AA
1 A-AAAG AA-AAG AA-AAG AA-AAG AAAAG AA
3698447 CTAATGTGAA
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
4 7 0.12
5 21 0.35
6 32 0.53
ACGTcount: A:0.70, C:0.01, G:0.27, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:3698406 original size:9 final size:10
Alignment explanation
Indices: 3698372--3698443 Score: 50
Period size: 9 Copynumber: 7.7 Consensus size: 10
3698362 ACAAGCAAAA
3698372 AAGAA-AAAG
1 AAGAAGAAAG
* *
3698381 AACAAGGAAG
1 AAGAAGAAAG
3698391 TAA-AAGAAAG
1 -AAGAAGAAAG
3698401 AA-AAGAAAAG
1 AAGAAG-AAAG
*
3698411 AA-AAG-AGG
1 AAGAAGAAAG
3698419 AAGAAG-AAG
1 AAGAAGAAAG
3698428 AAGAAG-AAG
1 AAGAAGAAAG
3698437 AAGAAGA
1 AAGAAGA
3698444 GAACTAATGT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
8 4 0.08
9 29 0.55
10 18 0.34
11 2 0.04
ACGTcount: A:0.69, C:0.01, G:0.28, T:0.01
Consensus pattern (10 bp):
AAGAAGAAAG
Found at i:3698426 original size:3 final size:3
Alignment explanation
Indices: 3698398--3698443 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
3698388 AAGTAAAAGA
*
3698398 AAG AA- AAG AA- AAG AA- AAG AGG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3698443 A
1 A
3698444 GAACTAATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3698973 original size:34 final size:33
Alignment explanation
Indices: 3698935--3699044 Score: 108
Period size: 34 Copynumber: 3.4 Consensus size: 33
3698925 TAAAAGATAT
*
3698935 TTTTATATATAAAGAATATAAATTATTTTTACTA
1 TTTTAAATATAAA-AATATAAATTATTTTTACTA
* *
3698969 TTTTAAATATAAAATATTTAAAAGATATTTTTA-TA
1 TTTTAAATATAAAA-ATAT-AAA-TTATTTTTACTA
3699004 ---T--ATA-AAAAATATAAATTATTTTTACTA
1 TTTTAAATATAAAAATATAAATTATTTTTACTA
3699031 TTTTAAATATAAAA
1 TTTTAAATATAAAA
3699045 TATTTATTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
26 8 0.13
27 5 0.08
28 3 0.05
29 4 0.07
30 4 0.07
32 4 0.07
33 5 0.08
34 15 0.25
35 5 0.08
36 8 0.13
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (33 bp):
TTTTAAATATAAAAATATAAATTATTTTTACTA
Found at i:3698979 original size:36 final size:35
Alignment explanation
Indices: 3698939--3699041 Score: 96
Period size: 28 Copynumber: 3.1 Consensus size: 35
3698929 AGATATTTTT
3698939 ATATATAAAGAATATAAATTATTTTTACTATTTTAA
1 ATATATAAA-AATATAAATTATTTTTACTATTTTAA
* * ** *
3698975 ATATA-AAATATTTAAA--A--GATA-T-TTTTAT
1 ATATATAAAAATATAAATTATTTTTACTATTTTAA
3699003 ATATA-AAAAATATAAATTATTTTTACTATTTTAA
1 ATATATAAAAATATAAATTATTTTTACTATTTTAA
3699037 ATATA
1 ATATA
3699042 AAATATTTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 14
0.68 0.13 0.19
Matches are distributed among these distances:
28 19 0.37
29 1 0.02
30 3 0.06
32 3 0.06
33 1 0.02
34 16 0.31
35 3 0.06
36 5 0.10
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (35 bp):
ATATATAAAAATATAAATTATTTTTACTATTTTAA
Found at i:3698996 original size:62 final size:62
Alignment explanation
Indices: 3698925--3699050 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
3698915 TTTTTTTTTC
*
3698925 TAAAAGATATTTTTATATATAAAGAATATAAATTATTTTTACTATTTTAAATATAAAATATT
1 TAAAAGATATTTTTATATATAAAAAATATAAATTATTTTTACTATTTTAAATATAAAATATT
3698987 TAAAAGATATTTTTATATATAAAAAATATAAATTATTTTTACTATTTTAAATATAAAATATT
1 TAAAAGATATTTTTATATATAAAAAATATAAATTATTTTTACTATTTTAAATATAAAATATT
3699049 TA
1 TA
3699051 TTTTTACATC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (62 bp):
TAAAAGATATTTTTATATATAAAAAATATAAATTATTTTTACTATTTTAAATATAAAATATT
Found at i:3699018 original size:28 final size:28
Alignment explanation
Indices: 3698925--3699018 Score: 80
Period size: 28 Copynumber: 3.1 Consensus size: 28
3698915 TTTTTTTTTC
*
3698925 TAAAAGATATTTTTATATATAAAGAATA
1 TAAAAGATATTTTTATATATAAAAAATA
** * * *
3698953 TAAATTATTTTTACTATTTTAAATATAAAATATT
1 TAAA--A--GATA-T-TTTTATATATAAAAAATA
3698987 TAAAAGATATTTTTATATATAAAAAATA
1 TAAAAGATATTTTTATATATAAAAAATA
3699015 TAAA
1 TAAA
3699019 TTATTTTTAC
Statistics
Matches: 49, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
28 23 0.47
29 1 0.02
30 3 0.06
32 3 0.06
33 1 0.02
34 18 0.37
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (28 bp):
TAAAAGATATTTTTATATATAAAAAATA
Found at i:3699461 original size:38 final size:37
Alignment explanation
Indices: 3699379--3699460 Score: 139
Period size: 38 Copynumber: 2.2 Consensus size: 37
3699369 TTGTCTAAAA
3699379 ACATTTTTACTAATTCTCTTTATAAAATATGTTTATT
1 ACATTTTTACTAATTCTCTTTATAAAATATGTTTATT
3699416 ACATTTTTACTAACTTCTCTTTATAAAATATGTTTA-T
1 ACATTTTTACTAA-TTCTCTTTATAAAATATGTTTATT
*
3699453 ACTTTTTT
1 ACATTTTT
3699461 TTATTTACTA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
37 21 0.49
38 22 0.51
ACGTcount: A:0.30, C:0.12, G:0.02, T:0.55
Consensus pattern (37 bp):
ACATTTTTACTAATTCTCTTTATAAAATATGTTTATT
Found at i:3701342 original size:24 final size:24
Alignment explanation
Indices: 3701282--3701354 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
3701272 AAGAATTTTT
* *
3701282 CATAAAAGCTTTCCAGAGAATTCG
1 CATAAACGCCTTCCAGAGAATTCG
3701306 CTATTAAACGCCTTCCAGAGAATTCG
1 C-A-TAAACGCCTTCCAGAGAATTCG
3701332 CATAAACGCCTTCCAGAGAATTC
1 CATAAACGCCTTCCAGAGAATTC
3701355 TCCACAAAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
24 22 0.49
25 2 0.04
26 21 0.47
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (24 bp):
CATAAACGCCTTCCAGAGAATTCG
Found at i:3702991 original size:16 final size:16
Alignment explanation
Indices: 3702970--3703026 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
3702960 TTAAAATAAA
3702970 TTTATATTTTATTATT
1 TTTATATTTTATTATT
3702986 TTTATA-TTTA-TA-T
1 TTTATATTTTATTATT
* *
3702999 TTTATAGTTT-TTATAA
1 TTTATATTTTATTAT-T
3703015 TTT-TATTTTATT
1 TTTATATTTTATT
3703027 TAATAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
13 7 0.21
14 7 0.21
15 9 0.26
16 11 0.32
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTATATTTTATTATT
Found at i:3703080 original size:25 final size:25
Alignment explanation
Indices: 3703052--3703105 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
3703042 AATTATTTTA
3703052 TTTTCATAATTATATAATTTTT-AAT
1 TTTTCATAATTATA-AATTTTTAAAT
*
3703077 TTTTTATAATTATAAATTTTTAAAT
1 TTTTCATAATTATAAATTTTTAAAT
3703102 TTTT
1 TTTT
3703106 GAGAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTTCATAATTATAAATTTTTAAAT
Found at i:3703631 original size:15 final size:16
Alignment explanation
Indices: 3703611--3703643 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3703601 GTCTCGATTT
3703611 TAATTT-ACACATAAA
1 TAATTTGACACATAAA
*
3703626 TAATTTGACATATAAA
1 TAATTTGACACATAAA
3703642 TA
1 TA
3703644 TTATAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (16 bp):
TAATTTGACACATAAA
Found at i:3706394 original size:33 final size:33
Alignment explanation
Indices: 3706350--3706429 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
3706340 TGTTTGTTCC
*
3706350 AAGTTTTTTCCAATAAATCTAATTGAAATTACA
1 AAGTTTGTTCCAATAAATCTAATTGAAATTACA
*
3706383 AAGTTTGTTCCAATAAATCTAATTTAAATTACA
1 AAGTTTGTTCCAATAAATCTAATTGAAATTACA
*
3706416 AAGTTTGATCCAAT
1 AAGTTTGTTCCAAT
3706430 TTTGATGCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.39
Consensus pattern (33 bp):
AAGTTTGTTCCAATAAATCTAATTGAAATTACA
Found at i:3709188 original size:38 final size:40
Alignment explanation
Indices: 3709106--3709189 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 40
3709096 AAATCTTAAC
* *
3709106 AAATAAAAAATATTTGTCAAACAATTCAAAAAAACCCAAT
1 AAATAAAAAATATTTGTCAAACAATTCAAAAAAACCAAAA
* *
3709146 AAATAAAAAA-A-TTGTCAAATAATTCAAAAACAA-TAAAA
1 AAATAAAAAATATTTGTCAAACAATTCAAAAA-AACCAAAA
3709184 AAATAA
1 AAATAA
3709190 CATTTATAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
38 26 0.67
39 3 0.08
40 10 0.26
ACGTcount: A:0.65, C:0.11, G:0.02, T:0.21
Consensus pattern (40 bp):
AAATAAAAAATATTTGTCAAACAATTCAAAAAAACCAAAA
Found at i:3710206 original size:22 final size:22
Alignment explanation
Indices: 3710178--3710222 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3710168 GTATGTGAGA
3710178 TACTTGAGGATAAAATCAGTGC
1 TACTTGAGGATAAAATCAGTGC
3710200 TACTTGAGGATAAAATCAGTGC
1 TACTTGAGGATAAAATCAGTGC
3710222 T
1 T
3710223 TCTTTTGGAA
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:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (22 bp):
TACTTGAGGATAAAATCAGTGC
Found at i:3716978 original size:23 final size:23
Alignment explanation
Indices: 3716945--3716991 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3716935 AATGACCACA
* *
3716945 AAAAGGTTTCTATAATCCATGCT
1 AAAAGGATTCTACAATCCATGCT
*
3716968 AAAAGGATTCTCCAATCCATGCT
1 AAAAGGATTCTACAATCCATGCT
3716991 A
1 A
3716992 TCTTGGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (23 bp):
AAAAGGATTCTACAATCCATGCT
Found at i:3724309 original size:126 final size:126
Alignment explanation
Indices: 3724124--3724461 Score: 462
Period size: 126 Copynumber: 2.7 Consensus size: 126
3724114 AATAGTGTCT
* * * * *
3724124 GCTTCAAGCAGGATGCACTTTCAGCAAAATTTTTAGAAAAAGCTCTCATATGGACGCTCTTTTGC
1 GCTTCAAGCAGGATGCACTGTCAGCAAAATTTCTAGAAAAAACTCCCATGTGGACGCTCTTTTGC
* * * *
3724189 TACAGCAGTTCATAGAAAAATAATTCTGAGTAAACATTTCTGAACAAATAATGTCGAAAAC
66 TACAGTAGTTCGTAGAAAAATAATTCTGAGTAAACATTTCTAAACAAATAATGTCAAAAAC
** * *
3724250 GCTTCAAGCAGGATGCACTGTCAGCAAAATTTCTAGAAAAAACTCCCATGTAAATGCTCTTTTAC
1 GCTTCAAGCAGGATGCACTGTCAGCAAAATTTCTAGAAAAAACTCCCATGTGGACGCTCTTTTGC
* * * *
3724315 TACAGTAGTTCGTAGAAAAATAATTCTGAGTAGACGTTTCTAAACAAGTAGTGTCAAAAAC
66 TACAGTAGTTCGTAGAAAAATAATTCTGAGTAAACATTTCTAAACAAATAATGTCAAAAAC
* * * * *
3724376 GCTTCAAGTAGGATGCACTGTTAGCAAAATTTC-AAAAAAAAGCTCCCACGTGGACGTTCTTTTG
1 GCTTCAAGCAGGATGCACTGTCAGCAAAATTTCTAGAAAAAA-CTCCCATGTGGACGCTCTTTTG
3724440 CTACAGTAGTTCGTAGAAAAAT
65 CTACAGTAGTTCGTAGAAAAAT
3724462 GAGGCTATAA
Statistics
Matches: 185, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
125 7 0.04
126 178 0.96
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (126 bp):
GCTTCAAGCAGGATGCACTGTCAGCAAAATTTCTAGAAAAAACTCCCATGTGGACGCTCTTTTGC
TACAGTAGTTCGTAGAAAAATAATTCTGAGTAAACATTTCTAAACAAATAATGTCAAAAAC
Found at i:3728584 original size:7 final size:7
Alignment explanation
Indices: 3728574--3728609 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
3728564 CATAATACAT
3728574 AATACTA
1 AATACTA
3728581 AATACTA
1 AATACTA
3728588 AATACTA
1 AATACTA
*
3728595 AATACGA
1 AATACTA
3728602 AATGACTA
1 AAT-ACTA
3728610 CTTTATTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 23 0.88
8 3 0.12
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.25
Consensus pattern (7 bp):
AATACTA
Found at i:3729459 original size:48 final size:46
Alignment explanation
Indices: 3729391--3729525 Score: 146
Period size: 48 Copynumber: 2.8 Consensus size: 46
3729381 ATACAAACAT
* * *
3729391 CATAAATGAAAAAAAAATCAAGCAGTATTGAAATTGTAATTATAA-TTG
1 CATAAATGAAAAAAATATCAA-TAGTATTGAAATT-TAATTA-AATTTA
* *
3729439 CATAAATGAATAAAATATCAAATAATATTGTAAATTTAATTAAATTTA
1 CATAAATGAAAAAAATATC-AATAGTATTG-AAATTTAATTAAATTTA
*
3729487 CATAAATTAAAAAAATATCGAATAGTATTGAAAATTTAA
1 CATAAATGAAAAAAATATC-AATAGTATTG-AAATTTAA
3729526 AATTATCACT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
47 2 0.03
48 65 0.88
49 7 0.09
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (46 bp):
CATAAATGAAAAAAATATCAATAGTATTGAAATTTAATTAAATTTA
Found at i:3730420 original size:30 final size:30
Alignment explanation
Indices: 3730385--3730442 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
3730375 TAGGTACTTC
* *
3730385 CACACGGGT-GATCCACATGCCCGTGTGTGA
1 CACACGGGTAGA-CCACACGCCCATGTGTGA
3730415 CACACGGGTAGACCACACGCCCATGTGT
1 CACACGGGTAGACCACACGCCCATGTGT
3730443 CATGGCTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (30 bp):
CACACGGGTAGACCACACGCCCATGTGTGA
Found at i:3737855 original size:4 final size:4
Alignment explanation
Indices: 3737848--3737884 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
3737838 CTTAAAAAAA
3737848 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
3737885 TTAGTATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:3738717 original size:30 final size:30
Alignment explanation
Indices: 3738683--3738742 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
3738673 TAGACACTTC
3738683 CACACGGGT-GATCCACACACCCGTGTGTCA
1 CACACGGGTAGA-CCACACACCCGTGTGTCA
*
3738713 CACACGGGTAGACCACACGCCCGTGTGTCA
1 CACACGGGTAGACCACACACCCGTGTGTCA
3738743 TGGCCGTGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 26 0.93
31 2 0.07
ACGTcount: A:0.23, C:0.37, G:0.25, T:0.15
Consensus pattern (30 bp):
CACACGGGTAGACCACACACCCGTGTGTCA
Found at i:3745418 original size:49 final size:50
Alignment explanation
Indices: 3745351--3745495 Score: 123
Period size: 53 Copynumber: 2.8 Consensus size: 50
3745341 CTAGGCATCA
* * * *
3745351 AGTGCTAAGCCTGTAGGCTAACATC-CCTTC-GAAACACACTTCGGCACTG
1 AGTGCCAAGCCCGAAGGCTAACATCTCC-CCAGAAACACACTTCGGCACTG
* * *
3745400 AGTGCCAAGCCCGAAGGCTTTACATCTGTCCCCATAAACACACTTCGGCATTG
1 AGTGCCAAGCCCGAAGGC-TAACATC--TCCCCAGAAACACACTTCGGCACTG
* * *
3745453 AGTGCCAAGCACGAAGGCTTTACATCCGCCCCTAGAAACACAC
1 AGTGCCAAGCCCGAAGGC-TAACAT-CTCCCC-AGAAACACAC
3745496 CTAGATTACT
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
49 15 0.19
50 6 0.08
52 5 0.06
53 52 0.66
54 1 0.01
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.20
Consensus pattern (50 bp):
AGTGCCAAGCCCGAAGGCTAACATCTCCCCAGAAACACACTTCGGCACTG
Found at i:3745449 original size:53 final size:53
Alignment explanation
Indices: 3745381--3745495 Score: 178
Period size: 53 Copynumber: 2.2 Consensus size: 53
3745371 ACATCCCTTC
* *
3745381 GAAACACACTTCGGCACTGAGTGCCAAGCCCGAAGGCTTTACATCTGTCCCC-A
1 GAAACACACTTCGGCACTGAGTGCCAAGCACGAAGGCTTTACATCCG-CCCCTA
* *
3745434 TAAACACACTTCGGCATTGAGTGCCAAGCACGAAGGCTTTACATCCGCCCCTA
1 GAAACACACTTCGGCACTGAGTGCCAAGCACGAAGGCTTTACATCCGCCCCTA
3745487 GAAACACAC
1 GAAACACAC
3745496 CTAGATTACT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
52 4 0.07
53 52 0.93
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.18
Consensus pattern (53 bp):
GAAACACACTTCGGCACTGAGTGCCAAGCACGAAGGCTTTACATCCGCCCCTA
Found at i:3751252 original size:42 final size:42
Alignment explanation
Indices: 3751193--3751276 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
3751183 CCTATAAACG
3751193 ATTGAGTCCTAATTCTAGCATTTACCACTTTTCTTATTAACA
1 ATTGAGTCCTAATTCTAGCATTTACCACTTTTCTTATTAACA
3751235 ATTGAGTCCTAATTCTAGCATTTACCACTTTTCTTATTAACA
1 ATTGAGTCCTAATTCTAGCATTTACCACTTTTCTTATTAACA
3751277 GAAATTTCCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (42 bp):
ATTGAGTCCTAATTCTAGCATTTACCACTTTTCTTATTAACA
Found at i:3759023 original size:43 final size:43
Alignment explanation
Indices: 3758952--3759040 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
3758942 TATCTAGAGT
3758952 TACGAAACTACAAATTAAGATTCGTGAATTGTCCCAGAAACTA
1 TACGAAACTACAAATTAAGATTCGTGAATTGTCCCAGAAACTA
* *
3758995 TACGGAACTCCAAATTAAGA-TCTGTGAATTGTCCCAGAAACTA
1 TACGAAACTACAAATTAAGATTC-GTGAATTGTCCCAGAAACTA
3759038 TAC
1 TAC
3759041 TCATATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 2 0.05
43 41 0.95
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (43 bp):
TACGAAACTACAAATTAAGATTCGTGAATTGTCCCAGAAACTA
Found at i:3759802 original size:49 final size:49
Alignment explanation
Indices: 3759746--3759919 Score: 267
Period size: 49 Copynumber: 3.5 Consensus size: 49
3759736 CTGGTACGTA
3759746 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
* * * ** * *
3759795 TAGTAGCCTACACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCCGGTACACG
3759845 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
*
3759894 TAGTAGCTTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
3759920 CGTGACCTCA
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
49 67 0.61
50 42 0.39
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
Found at i:3759908 original size:99 final size:99
Alignment explanation
Indices: 3759746--3759927 Score: 346
Period size: 99 Copynumber: 1.8 Consensus size: 99
3759736 CTGGTACGTA
3759746 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTACACTTA
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTACACTTA
3759811 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGTGACCTAACCATCTGATACACG
* *
3759845 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCTTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTACACTTA
3759910 GTACTACACACGTGACCT
66 GTACTACACACGTGACCT
3759928 CACAATAGAT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 81 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTACACTTA
GTACTACACACGTGACCTAACCATCTGATACACG
Found at i:3768820 original size:12 final size:12
Alignment explanation
Indices: 3768803--3768827 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3768793 ATGTAAGTGA
3768803 TCTTGATGATTT
1 TCTTGATGATTT
3768815 TCTTGATGATTT
1 TCTTGATGATTT
3768827 T
1 T
3768828 TACTTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:3769619 original size:47 final size:46
Alignment explanation
Indices: 3769551--3769859 Score: 224
Period size: 47 Copynumber: 6.6 Consensus size: 46
3769541 TTTGTGCGCT
* *
3769551 AGTGTAAGACATGTTTGGGACATGCTTCAGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCC
* ** *
3769597 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAGCCAGA-CGTG-G-GCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCAT---CAGCCACATTATGAGAGCC
* * * *
3769645 AGTGTAAGACATGTTTGGGACATGCTTCAGCCATATTATGAGTGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCC
* * * *
3769691 AGAGTAAGACATGTCTGGGACATGCATCGGCCTCGACA-GA-GATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAG-C-C-ACATTATGAGAGCC
* * * * * *
3769738 AGTGTAAGACGTGTCTGGGACACGCATCGGTCA-AGTGT-TGTG-G-T
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACA-T-TATGAGAGCC
3769782 AGTGTAAGACATGTCTGGGACATGCATCAG-CATGCATATATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCA--CAT-TATGAGAGCC
*
3769830 AGTATAAGAGCATGTCTGGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
3769860 GACATTTTAT
Statistics
Matches: 205, Mismatches: 35, Indels: 42
0.73 0.12 0.15
Matches are distributed among these distances:
43 10 0.05
44 30 0.15
45 5 0.02
46 45 0.22
47 60 0.29
48 24 0.12
49 17 0.08
50 7 0.03
51 7 0.03
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCC
Found at i:3770145 original size:19 final size:19
Alignment explanation
Indices: 3770121--3770163 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
3770111 TATTTATTTA
3770121 TATGCAACTTACTAAGCTT
1 TATGCAACTTACTAAGCTT
3770140 TATGCAACTTACTAAGCTT
1 TATGCAACTTACTAAGCTT
3770159 TATGC
1 TATGC
3770164 TTACTCTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (19 bp):
TATGCAACTTACTAAGCTT
Found at i:3770168 original size:16 final size:17
Alignment explanation
Indices: 3770127--3770168 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
3770117 TTTATATGCA
3770127 ACTTACTAAGCTTTATG
1 ACTTACTAAGCTTTATG
3770144 CAACTTACTAAGCTTTATG
1 --ACTTACTAAGCTTTATG
3770163 -CTTACT
1 ACTTACT
3770169 CTCTTTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.26
19 17 0.74
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (17 bp):
ACTTACTAAGCTTTATG
Found at i:3775774 original size:11 final size:11
Alignment explanation
Indices: 3775758--3775782 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3775748 TTCAGCTGAT
3775758 GAAAATGAAGA
1 GAAAATGAAGA
3775769 GAAAATGAAGA
1 GAAAATGAAGA
3775780 GAA
1 GAA
3775783 TTCTAGATAT
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:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (11 bp):
GAAAATGAAGA
Found at i:3776338 original size:64 final size:64
Alignment explanation
Indices: 3776064--3776319 Score: 485
Period size: 64 Copynumber: 4.0 Consensus size: 64
3776054 TTGACACTTT
3776064 GTAAATATTTATAAAAATATTTATGGCTAGGTTTATAACTCTGAGATCTCGATACTTTTTTTTC
1 GTAAATATTTATAAAAATATTTATGGCTAGGTTTATAACTCTGAGATCTCGATACTTTTTTTTC
3776128 GTAAATATTTATAAAAATATTTATGGCTAGGTTTATAACTCTGAGATCTCGATACTTTTTTTTC
1 GTAAATATTTATAAAAATATTTATGGCTAGGTTTATAACTCTGAGATCTCGATACTTTTTTTTC
3776192 GTAAATATTTATAAAAATATTTATGGCTAGGTTTATAACTCTGAGATCTCGATACTTTTTTTTC
1 GTAAATATTTATAAAAATATTTATGGCTAGGTTTATAACTCTGAGATCTCGATACTTTTTTTTC
* * *
3776256 GTAAATATTTATAAAAATATTTATGGCTCGGTTTATAACTCTGAGATCACCATACTTTTTTTTC
1 GTAAATATTTATAAAAATATTTATGGCTAGGTTTATAACTCTGAGATCTCGATACTTTTTTTTC
3776320 TCAATTTCTT
Statistics
Matches: 189, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 189 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (64 bp):
GTAAATATTTATAAAAATATTTATGGCTAGGTTTATAACTCTGAGATCTCGATACTTTTTTTTC
Found at i:3781536 original size:69 final size:68
Alignment explanation
Indices: 3781463--3781591 Score: 195
Period size: 69 Copynumber: 1.9 Consensus size: 68
3781453 TCTTTAAACT
* *
3781463 TAATCACTTTAATATTAAATTAATATAATATTTATCAAGATAAAAATTAAATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAATAAAATA-CTATCAAGATAAAAATTAAATTAAATTTAATATT
3781528 AAGA
65 AAGA
* * **
3781532 TAATCACTTTAATATTAAATTAATAAAATACTATTAGGATAAGTATTAAATTAAATTTAA
1 TAATCACTTTAATATTAAATTAATAAAATACTATCAAGATAAAAATTAAATTAAATTTAA
3781592 CATCAAACTA
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
68 25 0.46
69 29 0.54
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (68 bp):
TAATCACTTTAATATTAAATTAATAAAATACTATCAAGATAAAAATTAAATTAAATTTAATATTA
AGA
Found at i:3781555 original size:20 final size:18
Alignment explanation
Indices: 3781456--3781556 Score: 61
Period size: 20 Copynumber: 5.6 Consensus size: 18
3781446 AAGGCTCTCT
3781456 TTAAACTTAATCACTTTAATA
1 TTAAA-TTAAT-A-TTTAATA
3781477 TTAAATTAATA--TAATA
1 TTAAATTAATATTTAATA
* * * * *
3781493 TT-TATCAAGA-TAAAAA
1 TTAAATTAATATTTAATA
3781509 TTAAATTAA-ATTTAATA
1 TTAAATTAATATTTAATA
3781526 TTAAGA-TAATCACTTTAATA
1 TTAA-ATTAAT-A-TTTAATA
3781546 TTAAATTAATA
1 TTAAATTAATA
3781557 AAATACTATT
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
15 5 0.08
16 13 0.21
17 15 0.24
18 1 0.02
19 4 0.06
20 20 0.32
21 5 0.08
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (18 bp):
TTAAATTAATATTTAATA
Found at i:3784314 original size:48 final size:48
Alignment explanation
Indices: 3784260--3784436 Score: 209
Period size: 48 Copynumber: 3.7 Consensus size: 48
3784250 TATGTGTGCA
3784260 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
*
3784308 AGTGTAAGACCATGTCTGGGACATGGCATC-G--ACATTGAGATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATT---ATGAGAGCC
* ** * *
3784356 AGTGTAAGACCATGTCTGGGATATGGCATCGGCCTTGA-CATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCC-ACATTATGAGAGCC
* * *
3784404 AATGTAAAACCATGTCTGGGACATGACATCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
3784437 ATTTTACCCT
Statistics
Matches: 111, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
45 5 0.05
47 1 0.01
48 103 0.93
49 1 0.01
52 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
Found at i:3784382 original size:96 final size:96
Alignment explanation
Indices: 3784260--3784439 Score: 263
Period size: 96 Copynumber: 1.9 Consensus size: 96
3784250 TATGTGTGCA
* * *
3784260 AGTGTAAGACCATGTCTGGGACATGGCATCGGCC-ACATTATGAGAGCCAGTGTAAGACCATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTACA-CATGAGAGCCAATGTAAAACCATGTC
*
3784324 TGGGACATGGCATCGACATTGAGATGAGAGCT
65 TGGGACATGACATCGACATTGAGATGAGAGCT
* ** *
3784356 AGTGTAAGACCATGTCTGGGATATGGCATCGGCCTTGACATGTGAGCCAATGTAAAACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTACACATGAGAGCCAATGTAAAACCATGTCT
*
3784421 GGGACATGACATCGGCATT
66 GGGACATGACATCGACATT
3784440 TTACCCTCTT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
96 73 0.99
97 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (96 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTACACATGAGAGCCAATGTAAAACCATGTCT
GGGACATGACATCGACATTGAGATGAGAGCT
Found at i:3786344 original size:29 final size:28
Alignment explanation
Indices: 3786308--3786385 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
3786298 TCATGAGATT
3786308 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
3786338 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
3786365 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
3786386 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:3786660 original size:173 final size:174
Alignment explanation
Indices: 3786338--3786664 Score: 557
Period size: 173 Copynumber: 1.9 Consensus size: 174
3786328 AAATTGTACA
* *
3786338 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* *
3786403 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
*
3786468 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCTTG
131 TTTTGGACAGCGAAAAAGGTAAGTGTGCGAACTTGAAATGCTTG
* * * *
3786512 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
*
3786577 TGTGC-AACCCAGTATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
3786641 TTTTGGACAGCGAAAAAGGTAAGT
131 TTTTGGACAGCGAAAAAGGTAAGT
3786665 ACCTTGAGTT
Statistics
Matches: 143, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
173 79 0.55
174 64 0.45
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGAAAAAGGTAAGTGTGCGAACTTGAAATGCTTG
Found at i:3799248 original size:48 final size:46
Alignment explanation
Indices: 3799126--3799445 Score: 261
Period size: 48 Copynumber: 6.7 Consensus size: 46
3799116 ACATGTTGAG
* * *
3799126 GCCGATGCCATGTCCTAGACA-GGTCTTACAATGGCT-TGCATATCCCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAT----AT
* *
3799175 GCCGAT-ACATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATGT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATAT
* * * *
3799220 GGCTGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAT
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAT--AT
* * * *
3799269 GCCGATGCCATGTCCTAGACATGGTCTTACACTAGCACACATATCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAT--AT
* * *
3799317 GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTGATTACATT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA-TATA-T
* * * * * *
3799365 GCCGATGCAATATCCCAAACATGGTCTTATACTGGCTCTCATGTTGT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATAT
* *
3799412 GGCCAATGCCATGTCCCCGACATGGTCTTACACT
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACT
3799446 AGCACACATA
Statistics
Matches: 224, Mismatches: 35, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
46 5 0.02
47 19 0.08
48 188 0.84
49 12 0.05
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (46 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATAT
Found at i:3799387 original size:144 final size:143
Alignment explanation
Indices: 3799182--3799458 Score: 362
Period size: 144 Copynumber: 1.9 Consensus size: 143
3799172 GAGGCCGATA
* * * *
3799182 CATGTCCCAGACATGTCTTACACTGGCTCTCATAATGTGGCTGATGCCATGTCCCAGACATGGTC
1 CATGTCCCAGACATGTCTTACACTGGCTCTCATAATGTGGCCGATGCAATATCCCAAACATGGTC
* *
3799247 TTACACTAGCACACATATCAAT-GCCGATGCCATGTCCTAGACATGGTCTTACACTAGCACACAT
66 TTACACTAGCACACATAT-AATGGCCAATGCCATGTCCCAGACATGGTCTTACACTAGCACACAT
3799311 ATCAATGCTGATGC
130 ATCAATGCTGATGC
*
3799325 CATGTCCCAGACATGGTCTTACACTGGCTCTGATTACAT-T-GCCGATGCAATATCCCAAACATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTCTCA-TA-ATGTGGCCGATGCAATATCCCAAACATG
* * * * * ** *
3799388 GTCTTATACTGGCTCTCATGTTGTGGCCAATGCCATGTCCCCGACATGGTCTTACACTAGCACAC
63 GTCTTACACTAGCACACATATAATGGCCAATGCCATGTCCCAGACATGGTCTTACACTAGCACAC
3799453 ATATCA
128 ATATCA
3799459 CCCAAATGTC
Statistics
Matches: 115, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
143 15 0.13
144 95 0.83
145 3 0.03
146 2 0.02
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (143 bp):
CATGTCCCAGACATGTCTTACACTGGCTCTCATAATGTGGCCGATGCAATATCCCAAACATGGTC
TTACACTAGCACACATATAATGGCCAATGCCATGTCCCAGACATGGTCTTACACTAGCACACATA
TCAATGCTGATGC
Found at i:3802740 original size:20 final size:19
Alignment explanation
Indices: 3802704--3802754 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
3802694 AAGGGCCATT
*
3802704 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
3802723 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
3802743 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
3802755 GTTACTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:3803590 original size:92 final size:94
Alignment explanation
Indices: 3803494--3803716 Score: 240
Period size: 95 Copynumber: 2.4 Consensus size: 94
3803484 GGGATATGCA
* * * * * *
3803494 AGCCATTGTAAGACTTGTCTGGGACATGGCATTGG-CTTG-ACAT-G-TGTCAGTGTAAGACCTG
1 AGCCAGTGTAAGACCTGTCTGGAACATGGCATCGGCCTCGAACATAGAAGTCAGTGTAAGA-CTG
3803555 TCTGGGACATGGCATCGACGCCGATGGAGAG
65 TCT-GGACATGGCATCGACGCCGATGGAGAG
*
3803586 AGCCAGTGTAAGACCTGTCTGGAACATGGCATCGGCCTCGATATATAGAAGTCAGTGTAAGACTG
1 AGCCAGTGTAAGACCTGTCTGGAACATGGCATCGGCCTCGA-ACATAGAAGTCAGTGTAAGACTG
*** * *
3803651 TCTGGACATGGCATCGACTTAGAT-GTGTG
65 TCTGGACATGGCATCGACGCCGATGGAGAG
* * *
3803680 AGCTAGTGTAAGACCATGTTTGGAACAAGGCATCGGC
1 AGCCAGTGTAAGACC-TGTCTGGAACATGGCATCGGC
3803717 ATTGTACCCT
Statistics
Matches: 110, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
92 31 0.28
93 3 0.03
94 17 0.15
95 40 0.36
96 7 0.06
97 12 0.11
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (94 bp):
AGCCAGTGTAAGACCTGTCTGGAACATGGCATCGGCCTCGAACATAGAAGTCAGTGTAAGACTGT
CTGGACATGGCATCGACGCCGATGGAGAG
Found at i:3803605 original size:48 final size:49
Alignment explanation
Indices: 3803541--3803668 Score: 165
Period size: 48 Copynumber: 2.7 Consensus size: 49
3803531 TGACATGTGT
*
3803541 CAGTGTAAGACCTGTCTGGGACATGGCATCGACGC-CGATGGAGAG-AGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATAGAGAGAAGC
* * * * *
3803589 CAGTGTAAGACCTGTCTGGAACATGGCATCGGCCTCGATATATAGAAGT
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGAGAGAAGC
3803638 CAGTGTAAGA-CTGTCT-GGACATGGCATCGAC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC
3803669 TTAGATGTGT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
47 14 0.20
48 44 0.63
49 12 0.17
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.21
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGAGAGAAGC
Found at i:3803704 original size:95 final size:97
Alignment explanation
Indices: 3803539--3803716 Score: 254
Period size: 95 Copynumber: 1.9 Consensus size: 97
3803529 CTTGACATGT
*
3803539 GTCAGTGTAAGACCTGTCTGGGACATGGCATCGACGCCGATGGAGAGAGCCAGTGTAAGACCTGT
1 GTCAGTGTAAGACCTGTCTGGGACATGGCATCGACGCAGATGGAGAGAGCCAGTGTAAGACCTGT
*
3803604 CTGGAACATGGCATCGGCCTCGATATATAGAA
66 CTGGAACAAGGCATCGGCCTCGATATATAGAA
** * * *
3803636 GTCAGTGTAAGA-CTGTCT-GGACATGGCATCGACTTAGAT-GTGTGAGCTAGTGTAAGACCATG
1 GTCAGTGTAAGACCTGTCTGGGACATGGCATCGACGCAGATGGAGAGAGCCAGTGTAAGACC-TG
*
3803698 TTTGGAACAAGGCATCGGC
65 TCTGGAACAAGGCATCGGC
3803717 ATTGTACCCT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
94 17 0.24
95 37 0.51
96 6 0.08
97 12 0.17
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (97 bp):
GTCAGTGTAAGACCTGTCTGGGACATGGCATCGACGCAGATGGAGAGAGCCAGTGTAAGACCTGT
CTGGAACAAGGCATCGGCCTCGATATATAGAA
Found at i:3809626 original size:65 final size:65
Alignment explanation
Indices: 3809520--3809714 Score: 356
Period size: 65 Copynumber: 3.0 Consensus size: 65
3809510 AATTTTATCA
* *
3809520 TTCTAGATCAAGAAACCGAGATCCGGGCTTAAAT-TAGAAAGTACAAGGTTATAGACTAAAGCGG
1 TTCTAGATCAAGAAACCGAGATTCGGGCTTAAATCGA-AAAGTACAAGGTTATAGACTAAAGCGG
3809584 C
65 C
3809585 TTCTAGATCAAGAAACCGAGATTCGGGCTTAAATCGAAAAGTACAAGGTTATAGACTAAAGCGGC
1 TTCTAGATCAAGAAACCGAGATTCGGGCTTAAATCGAAAAGTACAAGGTTATAGACTAAAGCGGC
3809650 TTCTAGATCAAGAAACCGAGATTCGGGCTTAAATCGAAAAGTACAAGGTTATAGACTAAAGCGGC
1 TTCTAGATCAAGAAACCGAGATTCGGGCTTAAATCGAAAAGTACAAGGTTATAGACTAAAGCGGC
3809715 GTAATTAGCC
Statistics
Matches: 127, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
65 126 0.99
66 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (65 bp):
TTCTAGATCAAGAAACCGAGATTCGGGCTTAAATCGAAAAGTACAAGGTTATAGACTAAAGCGGC
Found at i:3810170 original size:46 final size:47
Alignment explanation
Indices: 3810114--3810237 Score: 166
Period size: 46 Copynumber: 2.7 Consensus size: 47
3810104 TTTATGTGCT
* * *
3810114 AGTGTAAGACATGCCTGGGACATGCGTCGGCCACATTATGA-G-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCC-CATTAAGACGAAGCC
3810160 AGTGTAAGACATGTCTGGGACATGCATCGG--CATTAAGACGAAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCCATTAAGACG-AAGCC
*
3810206 AGTGTAAGACAAGTCTGGGACATGCATCGGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCC
3810238 TTGAGATATG
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
43 7 0.10
44 1 0.01
46 61 0.88
ACGTcount: A:0.29, C:0.22, G:0.30, T:0.19
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCCATTAAGACGAAGCC
Found at i:3810272 original size:48 final size:46
Alignment explanation
Indices: 3810156--3810283 Score: 150
Period size: 46 Copynumber: 2.7 Consensus size: 46
3810146 ACATTATGAG
3810156 AGCCAGTGTAAGA-CATGTCTGGGACATGCATCGGCATTAAGACGAA
1 AGCCAGTGTAAGACCAT-TCTGGGACATGCATCGGCATTAAGACGAA
* * * * * *
3810202 AGCCAGTGTAAGACAAGTCTGGGACATGCATCGGCCTTGAGATATGCA
1 AGCCAGTGTAAGACCATTCTGGGACATGCATCGGCATT-A-AGACGAA
*
3810250 AGCCAGTGTAATACCATTCTGGGACATGACATCG
1 AGCCAGTGTAAGACCATTCTGGGACATG-CATCG
3810284 ACACCGATAG
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
46 33 0.48
47 2 0.03
48 29 0.42
49 5 0.07
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.21
Consensus pattern (46 bp):
AGCCAGTGTAAGACCATTCTGGGACATGCATCGGCATTAAGACGAA
Found at i:3810360 original size:19 final size:17
Alignment explanation
Indices: 3810318--3810353 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3810308 GACCTAGGAC
3810318 ATGGCATCGACCTCGAT
1 ATGGCATCGACCTCGAT
3810335 ATGGCATCGACCTCGAT
1 ATGGCATCGACCTCGAT
3810352 AT
1 AT
3810354 ATGGCATGGC
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:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (17 bp):
ATGGCATCGACCTCGAT
Found at i:3810362 original size:24 final size:24
Alignment explanation
Indices: 3810335--3810381 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
3810325 CGACCTCGAT
3810335 ATGGCATCGACCTCGATATATGGC
1 ATGGCATCGACCTCGATATATGGC
*
3810359 ATGGCATTGACCTCGATATATGG
1 ATGGCATCGACCTCGATATATGG
3810382 AAGTCAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (24 bp):
ATGGCATCGACCTCGATATATGGC
Found at i:3810799 original size:20 final size:21
Alignment explanation
Indices: 3810771--3810809 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
3810761 TTTGTGATGA
* *
3810771 ACTTGTGAT-TATAGATATAT
1 ACTTATGATGTATAAATATAT
3810791 ACTTATGATGTATAAATAT
1 ACTTATGATGTATAAATAT
3810810 GTATCTTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (21 bp):
ACTTATGATGTATAAATATAT
Found at i:3817562 original size:48 final size:48
Alignment explanation
Indices: 3817502--3817721 Score: 210
Period size: 48 Copynumber: 4.6 Consensus size: 48
3817492 ACGCCGTGTT
* * *
3817502 CCAAACATGGTCTTACACTGGCTCACATGTCAAGGCTGATGCGATGTC
1 CCAAACATGGTCTTACACTGGCTCACATCTCAAGGCCGATGCCATGTC
* * * * *
3817550 CCAAACAAGGTCTTACACTAGCTTACGTCTCAATGCCGATGCCATGTC
1 CCAAACATGGTCTTACACTGGCTCACATCTCAAGGCCGATGCCATGTC
* * * **
3817598 CCAAACATGGTATTACACTGGCTCTCATAAT-GTGGCCGATGCCATGTC
1 CCAAACATGGTCTTACACTGGCTCACAT-CTCAAGGCCGATGCCATGTC
* * * ** *
3817646 CCAGAGATGGTCTTACACTGGCTCTCAT-TACATTGCCGATGCCATGTT
1 CCAAACATGGTCTTACACTGGCTCACATCT-CAAGGCCGATGCCATGTC
* * *
3817694 CTAAACATGGTCTTACACTAGCACACAT
1 CCAAACATGGTCTTACACTGGCTCACAT
3817722 ATCACCCAAA
Statistics
Matches: 139, Mismatches: 30, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
46 1 0.01
48 137 0.99
49 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (48 bp):
CCAAACATGGTCTTACACTGGCTCACATCTCAAGGCCGATGCCATGTC
Found at i:3822009 original size:20 final size:20
Alignment explanation
Indices: 3821984--3822021 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3821974 TTGTTATTTT
3821984 TTGAAAGTT-AAGTGATTGAG
1 TTGAAAGTTGAA-TGATTGAG
3822004 TTGAAAGTTGAATGATTG
1 TTGAAAGTTGAATGATTG
3822022 TTTTGTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (20 bp):
TTGAAAGTTGAATGATTGAG
Found at i:3823868 original size:43 final size:42
Alignment explanation
Indices: 3823821--3823936 Score: 146
Period size: 42 Copynumber: 2.7 Consensus size: 42
3823811 TCCTAGAGGT
*
3823821 GGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACAA
1 GGTCTTACACGTAATCAAATATCGATGCCA-TGTCCCAGACAA
* *
3823864 GGTCTTACACGAAATCAAATAT-GATGCCGATGTCCCAGACAT
1 GGTCTTACACGTAATCAAATATCGATGCC-ATGTCCCAGACAA
*
3823906 GGTCTTACACGTAAATCTCAA-ATCGATGCCA
1 GGTCTTACACGT-AATC-AAATATCGATGCCA
3823937 ACAACCCAGA
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
42 28 0.44
43 28 0.44
44 8 0.12
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (42 bp):
GGTCTTACACGTAATCAAATATCGATGCCATGTCCCAGACAA
Found at i:3823903 original size:42 final size:43
Alignment explanation
Indices: 3823821--3823974 Score: 154
Period size: 43 Copynumber: 3.6 Consensus size: 43
3823811 TCCTAGAGGT
* *
3823821 GGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACAA
1 GGTCTTACACGAAATCAAATATCGATGCCACTGTCCCAGACAA
*
3823864 GGTCTTACACGAAATCAAATAT-GATGCCGA-TGTCCCAGACAT
1 GGTCTTACACGAAATCAAATATCGATGCC-ACTGTCCCAGACAA
* ** ***
3823906 GGTCTTACACGTAAATCTCAA-ATCGATGCCAAC-AACCCAGATGT
1 GGTCTTACACG-AAATC-AAATATCGATGCC-ACTGTCCCAGACAA
*
3823950 GGTCTTACACGAAATCACATATCGA
1 GGTCTTACACGAAATCAAATATCGA
3823975 AAATCCTATG
Statistics
Matches: 94, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
42 29 0.31
43 38 0.40
44 27 0.29
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (43 bp):
GGTCTTACACGAAATCAAATATCGATGCCACTGTCCCAGACAA
Found at i:3823946 original size:44 final size:43
Alignment explanation
Indices: 3823855--3823974 Score: 118
Period size: 44 Copynumber: 2.8 Consensus size: 43
3823845 ATGCCACTGT
* * * ***
3823855 CCCAGACAAGGTCTTACACGAAA--TCAAATATGATGCCGATGT
1 CCCAGACATGGTCTTACACGAAATCTCAAAT-CGATGCCAACAA
3823897 CCCAGACATGGTCTTACACGTAAATCTCAAATCGATGCCAACAA
1 CCCAGACATGGTCTTACACG-AAATCTCAAATCGATGCCAACAA
** * *
3823941 CCCAGATGTGGTCTTACACGAAATCACATATCGA
1 CCCAGACATGGTCTTACACGAAATCTCAAATCGA
3823975 AAATCCTATG
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
42 19 0.29
43 15 0.23
44 25 0.38
45 6 0.09
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.22
Consensus pattern (43 bp):
CCCAGACATGGTCTTACACGAAATCTCAAATCGATGCCAACAA
Found at i:3826747 original size:22 final size:22
Alignment explanation
Indices: 3826722--3826809 Score: 106
Period size: 23 Copynumber: 3.8 Consensus size: 22
3826712 CGAGCTAATG
*
3826722 AACAGTAATCTCTATCGAGCTG-
1 AACAGTAAGCTCTAT-GAGCTGA
3826744 AACAGTAAGCTCATATGAGCTGA
1 AACAGTAAGCTC-TATGAGCTGA
*
3826767 AACGGTAAGCTCTAGTGAGCTGA
1 AACAGTAAGCTCTA-TGAGCTGA
3826790 TAACAGTAAGCTCTTATGAG
1 -AACAGTAAGCTC-TATGAG
3826810 TTGATATATT
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
22 19 0.33
23 22 0.38
24 15 0.26
25 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (22 bp):
AACAGTAAGCTCTATGAGCTGA
Found at i:3826809 original size:24 final size:23
Alignment explanation
Indices: 3826713--3826815 Score: 104
Period size: 23 Copynumber: 4.4 Consensus size: 23
3826703 AGGTCCTCCC
* *
3826713 GAGCTAATGAACAGTAATCTCTAT
1 GAGCTGAT-AACAGTAAGCTCTAT
3826737 CGAGCTG--AACAGTAAGCTCATAT
1 -GAGCTGATAACAGTAAGCTC-TAT
*
3826760 GAGCTGA-AACGGTAAGCTCTAGT
1 GAGCTGATAACAGTAAGCTCTA-T
3826783 GAGCTGATAACAGTAAGCTCTTAT
1 GAGCTGATAACAGTAAGCTC-TAT
*
3826807 GAGTTGATA
1 GAGCTGATA
3826816 TATTGGTAAG
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
22 19 0.28
23 22 0.32
24 20 0.29
25 7 0.10
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (23 bp):
GAGCTGATAACAGTAAGCTCTAT
Found at i:3832549 original size:23 final size:23
Alignment explanation
Indices: 3832523--3832566 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3832513 ACTCCCCAAA
*
3832523 GTAATAATGTAATATTAGTAACT
1 GTAATAATATAATATTAGTAACT
3832546 GTAATAATATAATATTAGTAA
1 GTAATAATATAATATTAGTAA
3832567 TAAAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (23 bp):
GTAATAATATAATATTAGTAACT
Found at i:3832568 original size:17 final size:17
Alignment explanation
Indices: 3832546--3832579 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3832536 ATTAGTAACT
*
3832546 GTAATAATATAATATTA
1 GTAATAAAATAATATTA
3832563 GTAATAAAATAATATTA
1 GTAATAAAATAATATTA
3832580 TTATTATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
GTAATAAAATAATATTA
Done.