Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 141 of 163
Found at i:38260657 original size:16 final size:15
Alignment explanation
Indices: 38260638--38260667 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
38260628 ACATATTTAA
38260638 ATTTATTATTTATTAT
1 ATTTATTA-TTATTAT
38260654 ATTTATTATTATTA
1 ATTTATTATTATTA
38260668 ATTAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTATTATTATTAT
Found at i:38260839 original size:31 final size:30
Alignment explanation
Indices: 38260766--38260854 Score: 101
Period size: 31 Copynumber: 3.0 Consensus size: 30
38260756 TTGATTTAAT
**
38260766 GTGCAATTATATATATG-AACTTTAATTTG
1 GTGCAATTATATACGTGAAACTTTAATTTG
*
38260795 GTGCAATTATATACGTGAAACTCTAATTGTG
1 GTGCAATTATATACGTGAAACTTTAATT-TG
* *
38260826 GTTCAAATT-TATACTTGAAACTTTAATTT
1 GTGC-AATTATATACGTGAAACTTTAATTT
38260855 TGATTTAATC
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 15 0.29
30 10 0.20
31 22 0.43
32 4 0.08
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (30 bp):
GTGCAATTATATACGTGAAACTTTAATTTG
Found at i:38262858 original size:29 final size:29
Alignment explanation
Indices: 38262826--38262918 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
38262816 TATGGATACC
*
38262826 CGGGGGCAAAATGGTAATTTTGGTAAAAT
1 CGGGGGAAAAATGGTAATTTTGGTAAAAT
*
38262855 CGGGGTTAAAAATGG-AATTTT-G-AAAGATT
1 CGGGG-GAAAAATGGTAATTTTGGTAAA-A-T
* * *
38262884 CAGGGGTAAAATGGTAATTTTTGGTGAAAT
1 CGGGGGAAAAATGGTAA-TTTTGGTAAAAT
38262914 CGGGG
1 CGGGG
38262919 TTAAAAACGA
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
27 3 0.06
28 9 0.18
29 18 0.36
30 16 0.32
31 2 0.04
32 2 0.04
ACGTcount: A:0.33, C:0.05, G:0.32, T:0.29
Consensus pattern (29 bp):
CGGGGGAAAAATGGTAATTTTGGTAAAAT
Found at i:38262869 original size:30 final size:30
Alignment explanation
Indices: 38262833--38262987 Score: 110
Period size: 30 Copynumber: 5.2 Consensus size: 30
38262823 ACCCGGGGGC
38262833 AAAATGGTAATTTTGGTAAAATCGGGGTTA
1 AAAATGGTAATTTTGGTAAAATCGGGGTTA
38262863 AAAATGG-AATTTT-G-AAAGATTCAGGGG-T-
1 AAAATGGTAATTTTGGTAAA-A-TC-GGGGTTA
*
38262891 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGGTAA-TTTTGGTAAAATCGGGGTTA
* * * ** *
38262922 AAAA-CGAAATTTTAG-AAGCTTCGGGGGT-
1 AAAATGGTAATTTTGGTAA-AATCGGGGTTA
* * *
38262950 AAAATGGTAAATTTTGGTGAAATCGAGGCTA
1 AAAATGGT-AATTTTGGTAAAATCGGGGTTA
38262981 AAAATGG
1 AAAATGG
38262988 GATTTAGGAA
Statistics
Matches: 95, Mismatches: 16, Indels: 27
0.69 0.12 0.20
Matches are distributed among these distances:
27 3 0.03
28 14 0.15
29 28 0.29
30 34 0.36
31 14 0.15
32 2 0.02
ACGTcount: A:0.37, C:0.05, G:0.28, T:0.30
Consensus pattern (30 bp):
AAAATGGTAATTTTGGTAAAATCGGGGTTA
Found at i:38262921 original size:59 final size:58
Alignment explanation
Indices: 38262828--38262992 Score: 215
Period size: 59 Copynumber: 2.8 Consensus size: 58
38262818 TGGATACCCG
* *
38262828 GGGGCAAAATGGTAATTTTGGTAAAATCGGGGTTAAAAATGGAATTTT-GAAAGATTCA
1 GGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAG-AAGATTCA
* * * *
38262886 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAACGAAATTTTAGAAGCTTCG
1 GGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCA
* * *
38262945 GGGGTAAAATGGTAAATTTTGGTGAAATCGAGGCTAAAAATGGGATTT
1 GGGGTAAAATGGT-AATTTTGGTGAAATCGGGGTTAAAAATGGAATTT
38262993 AGGAAAGTTT
Statistics
Matches: 93, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
58 14 0.15
59 76 0.82
60 3 0.03
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.30
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCA
Found at i:38263024 original size:59 final size:59
Alignment explanation
Indices: 38262828--38263024 Score: 213
Period size: 59 Copynumber: 3.4 Consensus size: 59
38262818 TGGATACCCG
* * *
38262828 GGGGCAAAATGGTAA-TTTTGGTAAAATCGGGGTTAAAAATGGAATTTTGAAAGATTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTAGAAAGATTCA
* * * *
38262886 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAACGAAATTTTAG-AAGCTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAA-TTTAGAAAGATTCA
* * * * **
38262945 GGGGTAAAATGGTAAATTTTGGTGAAATCGAGGCTAAAAATGGGATTTAGGAAAG-TTTT
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTA-GAAAGATTCA
*
38263004 GGGGTCAAAAT-GTGATTTTTG
1 GGGGT-AAAATGGTAATTTTTG
38263025 AAAGTTTTGG
Statistics
Matches: 117, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
58 18 0.15
59 87 0.74
60 12 0.10
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTAGAAAGATTCA
Found at i:38263061 original size:30 final size:30
Alignment explanation
Indices: 38262996--38263205 Score: 332
Period size: 30 Copynumber: 7.0 Consensus size: 30
38262986 GGGATTTAGG
* *
38262996 AAAGTTTTGGGGTCAAAATGTGATTTTTG-
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
38263025 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
38263055 AAAGTTTTAGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
38263085 AAAGTTTTGGGGTCAAAATATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
38263115 AAAGTTTTGGGGTCAAAATATAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
38263145 AAAGTTTTGGGGTCAAAATGTAATTTTAGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
**
38263175 AAAGTTTCAGGGTCAAAATGTAATTTCTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTT-TGGA
38263206 CAATTTATGG
Statistics
Matches: 169, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
29 27 0.16
30 139 0.82
31 3 0.02
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (30 bp):
AAAGTTTTGGGGTCAAAATGTAATTTTGGA
Found at i:38263903 original size:21 final size:21
Alignment explanation
Indices: 38263877--38263924 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
38263867 CTTATTCTTT
38263877 TTCTTC-TATTTTGTTCTTTTA
1 TTCTTCATATTTTGTT-TTTTA
*
38263898 TTCTTCATTTTTTGTTTTTTA
1 TTCTTCATATTTTGTTTTTTA
38263919 TT-TTCA
1 TTCTTCA
38263925 AAACCTTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.16
21 13 0.52
22 8 0.32
ACGTcount: A:0.10, C:0.12, G:0.04, T:0.73
Consensus pattern (21 bp):
TTCTTCATATTTTGTTTTTTA
Found at i:38263962 original size:24 final size:23
Alignment explanation
Indices: 38263907--38263962 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
38263897 ATTCTTCATT
38263907 TTTTGTTTTTTATTTTCAAAACC
1 TTTTGTTTTTTATTTTCAAAACC
**
38263930 TTTCCTTTTATTGATTTTC-AAACC
1 TTTTGTTTT-TT-ATTTTCAAAACC
38263954 TTTTGTTTT
1 TTTTGTTTT
38263963 CCTTTTTGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 7 0.26
24 14 0.52
25 6 0.22
ACGTcount: A:0.18, C:0.14, G:0.05, T:0.62
Consensus pattern (23 bp):
TTTTGTTTTTTATTTTCAAAACC
Found at i:38265033 original size:17 final size:16
Alignment explanation
Indices: 38265013--38265071 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 16
38265003 ATTTTTATTT
*
38265013 AAATTTAAATTCAAAGC
1 AAATTTAAATT-AAAAC
*
38265030 AAATTTAAATATAAAAT
1 AAATTTAAAT-TAAAAC
* *
38265047 AAATTTAAATTTAAAT
1 AAATTTAAATTAAAAC
*
38265063 AAAATTAAA
1 AAATTTAAA
38265072 AATTAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
16 13 0.35
17 23 0.62
18 1 0.03
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (16 bp):
AAATTTAAATTAAAAC
Found at i:38265077 original size:23 final size:23
Alignment explanation
Indices: 38265030--38265082 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
38265020 AATTCAAAGC
*
38265030 AAATTTAAATATAAAATAAATTT
1 AAATTTAAATATAAAATAAAATT
*
38265053 AAATTTAAATA-AAATTAAAAATT
1 AAATTTAAATATAAAAT-AAAATT
38265076 -AATTTAA
1 AAATTTAA
38265083 CTCTAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATTTAAATATAAAATAAAATT
Found at i:38265100 original size:28 final size:28
Alignment explanation
Indices: 38265042--38265100 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
38265032 ATTTAAATAT
* **
38265042 AAAATAAATTTAAATTTAAATAAAATTA
1 AAAATAAATTTAAATCTAAATAAAACGA
* * *
38265070 AAAATTAATTTAACTCTAAATTAAACGA
1 AAAATAAATTTAAATCTAAATAAAACGA
38265098 AAA
1 AAA
38265101 GTCCAAACCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (28 bp):
AAAATAAATTTAAATCTAAATAAAACGA
Found at i:38265496 original size:68 final size:68
Alignment explanation
Indices: 38265371--38266103 Score: 1126
Period size: 68 Copynumber: 10.8 Consensus size: 68
38265361 GTTCTTCAGG
* * * * * * * *
38265371 GAGATAAAGACTTTGCTATCCACTTTACTTCAATTTCGATGAGATGATGTCGCTCTTATTTCAAT
1 GAGATAAAGAC-GTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCAAT
*
38265436 TTTA
65 TTCA
* * *
38265440 GAGATGGAA-ACGTGTTATCCACTCTATTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAAT
1 GAGAT-AAAGACGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCAAT
38265504 TTCA
65 TTCA
* *
38265508 GAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTTCTTCAATT
1 GAGATAAAGACGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCAATT
*
38265573 TTA
66 TCA
** *
38265576 GAGATAAAGATATGTTATCCACTCTTCTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCAATT
1 GAGATAAAGACGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCAATT
38265641 TCA
66 TCA
*
38265644 GAGATAAAGATGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCAATT
1 GAGATAAAGACGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCAATT
38265709 TCA
66 TCA
* * *
38265712 GAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTACTCTTACTTCAATT
1 GAGATAAAGACGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCAATT
38265777 TCA
66 TCA
*
38265780 GAGATAAAGATGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCAATT
1 GAGATAAAGACGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCAATT
38265845 TCA
66 TCA
* *
38265848 AAGATAAAGATGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCAATT
1 GAGATAAAGACGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCAATT
38265913 TCA
66 TCA
* * *
38265916 GAGATGAAGACGCGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATT
1 GAGATAAAGACGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCAATT
38265981 TCA
66 TCA
** *
38265984 GAGACGAAGACGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTTTTACTTCAATT
1 GAGATAAAGACGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCAATT
38266049 TCA
66 TCA
* * *
38266052 GAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTG
1 GAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCGAGGGGATGACGTTG
38266104 AGACCTGCAG
Statistics
Matches: 616, Mismatches: 45, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
67 2 0.00
68 576 0.94
69 36 0.06
70 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (68 bp):
GAGATAAAGACGTGTTATCCACTCTACTTCAATTTCGAGGGGATGACGTTGCTCTTACTTCAATT
TCA
Found at i:38274865 original size:29 final size:30
Alignment explanation
Indices: 38274822--38274915 Score: 97
Period size: 29 Copynumber: 3.2 Consensus size: 30
38274812 TACTCGGGGG
38274822 AAAAATGGTAATTTTGGTGAAATCGAGGTT
1 AAAAATGGTAATTTTGGTGAAATCGAGGTT
* * *
38274852 AAAAATGG-AATTTT-G-AAAGATTCGGGGGT
1 AAAAATGGTAATTTTGGTGAA-A-TCGAGGTT
*
38274881 -AAAATGGTAATTTTCGGTGAAATTGAGGTT
1 AAAAATGGTAATTTT-GGTGAAATCGAGGTT
38274911 AAAAA
1 AAAAA
38274916 AAGAATTTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
27 2 0.04
28 9 0.18
29 18 0.36
30 13 0.26
31 6 0.12
32 2 0.04
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.31
Consensus pattern (30 bp):
AAAAATGGTAATTTTGGTGAAATCGAGGTT
Found at i:38274998 original size:59 final size:57
Alignment explanation
Indices: 38274818--38275005 Score: 225
Period size: 59 Copynumber: 3.2 Consensus size: 57
38274808 TGGATACTCG
* * **
38274818 GGGGAAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAGATTCG
1 GGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTAGAAAG-TTTT
* **
38274876 GGGGTAAAATGGTAATTTTCGGTGAAATTGAGGTTAAAAAAAGAATTTTAG-AAGTTTT
1 GGGGTAAAATGGTAATTTT-GGTGAAATCGAGGTTAAAAATGGAA-TTTAGAAAGTTTT
* *
38274934 GGGGGTAAAATGGTAAATTTTGGTGAAATCGAGGCTAAAAATGGGATTTAGGAAAGTTTT
1 -GGGGTAAAATGGT-AATTTTGGTGAAATCGAGGTTAAAAATGGAATTTA-GAAAGTTTT
38274994 GGGGTCAAAATG
1 GGGGT-AAAATG
38275006 TGATTTTTGA
Statistics
Matches: 111, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
58 24 0.22
59 64 0.58
60 23 0.21
ACGTcount: A:0.37, C:0.03, G:0.30, T:0.30
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTAGAAAGTTTT
Found at i:38275109 original size:30 final size:30
Alignment explanation
Indices: 38274986--38275110 Score: 207
Period size: 30 Copynumber: 4.2 Consensus size: 30
38274976 GGGATTTAGG
* *
38274986 AAAGTTTTGGGGTCAAAATGTGATTTTTG-
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
38275015 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
38275045 AAAGGTTTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
*
38275075 AAAGTTCTGGGGTCAAAATGTAATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGA
38275105 AAAGTT
1 AAAGTT
38275111 AAAGGACTAA
Statistics
Matches: 90, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 27 0.30
30 63 0.70
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (30 bp):
AAAGTTTTGGGGTCAAAATGTAATTTTGGA
Found at i:38275579 original size:21 final size:21
Alignment explanation
Indices: 38275553--38275600 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
38275543 CTTATTCTTT
38275553 TTCTTC-TATTTTGTTCTTTTA
1 TTCTTCATATTTTGTT-TTTTA
*
38275574 TTCTTCATTTTTTGTTTTTTA
1 TTCTTCATATTTTGTTTTTTA
38275595 TT-TTCA
1 TTCTTCA
38275601 AAACCTTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.16
21 13 0.52
22 8 0.32
ACGTcount: A:0.10, C:0.12, G:0.04, T:0.73
Consensus pattern (21 bp):
TTCTTCATATTTTGTTTTTTA
Found at i:38275638 original size:24 final size:23
Alignment explanation
Indices: 38275583--38275638 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
38275573 ATTCTTCATT
38275583 TTTTGTTTTTTATTTTCAAAACC
1 TTTTGTTTTTTATTTTCAAAACC
**
38275606 TTTCCTTTTATTGATTTTC-AAACC
1 TTTTGTTTT-TT-ATTTTCAAAACC
38275630 TTTTGTTTT
1 TTTTGTTTT
38275639 CCTTTTTGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 7 0.26
24 14 0.52
25 6 0.22
ACGTcount: A:0.18, C:0.14, G:0.05, T:0.62
Consensus pattern (23 bp):
TTTTGTTTTTTATTTTCAAAACC
Found at i:38276702 original size:6 final size:6
Alignment explanation
Indices: 38276693--38276760 Score: 68
Period size: 6 Copynumber: 11.3 Consensus size: 6
38276683 TTTAATTTTT
* **
38276693 ATTTAA ATTTAA ATTCAA A-GCAA ATTTAA ATAATTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA ATTTAA ATTTAA
*
38276742 A-ATAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
38276761 AAAATTAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
5 8 0.15
6 38 0.73
8 6 0.12
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:38276730 original size:31 final size:31
Alignment explanation
Indices: 38276695--38276754 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
38276685 TAATTTTTAT
*
38276695 TTAAATTTAAATTCAAAGCAAATTTAAATAA
1 TTAAATTTAAATTCAAAACAAATTTAAATAA
* *
38276726 TTAAATTTAAATTTAAAATAAATTTAAAT
1 TTAAATTTAAATTCAAAACAAATTTAAAT
38276755 TTAAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (31 bp):
TTAAATTTAAATTCAAAACAAATTTAAATAA
Found at i:38276749 original size:17 final size:16
Alignment explanation
Indices: 38276696--38276769 Score: 80
Period size: 17 Copynumber: 4.6 Consensus size: 16
38276686 AATTTTTATT
*
38276696 TAAATTTAAATTCAAA
1 TAAATTTAAATTTAAA
* *
38276712 GCAAATTTAAA--TAAT
1 -TAAATTTAAATTTAAA
38276727 TAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
38276744 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
*
38276760 TAAAATTAAA
1 TAAATTTAAA
38276770 AATTAATTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
14 9 0.19
15 2 0.04
16 13 0.27
17 24 0.50
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:38276787 original size:28 final size:28
Alignment explanation
Indices: 38276734--38276788 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
38276724 AATTAAATTT
* *
38276734 AAATTTAAAATAAATTTAAATTTAAATA
1 AAATTAAAAATAAATTTAAATCTAAATA
* *
38276762 AAATTAAAAATTAATTTAACTCTAAAT
1 AAATTAAAAATAAATTTAAATCTAAAT
38276789 TAAACGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (28 bp):
AAATTAAAAATAAATTTAAATCTAAATA
Found at i:38276798 original size:28 final size:28
Alignment explanation
Indices: 38276740--38276798 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
38276730 ATTTAAATTT
* **
38276740 AAAATAAATTTAAATTTAAATAAAATTA
1 AAAATAAATTTAAATCTAAATAAAACGA
* * *
38276768 AAAATTAATTTAACTCTAAATTAAACGA
1 AAAATAAATTTAAATCTAAATAAAACGA
38276796 AAA
1 AAA
38276799 GTCCAAGCCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (28 bp):
AAAATAAATTTAAATCTAAATAAAACGA
Found at i:38277385 original size:6 final size:6
Alignment explanation
Indices: 38277365--38277423 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
38277355 TTAAATGGGT
* * *
38277365 TTTAAA TTT-AT TTTAAA TTTAAA TTTACTTA TTTAAA TTT-AC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
*
38277413 TTTAAG TTTAA
1 TTTAAA TTTAA
38277424 TCAAATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:38277400 original size:14 final size:14
Alignment explanation
Indices: 38277381--38277408 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38277371 TTTATTTTAA
38277381 ATTTAAATTTACTT
1 ATTTAAATTTACTT
38277395 ATTTAAATTTACTT
1 ATTTAAATTTACTT
38277409 TAAATTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTAAATTTACTT
Found at i:38278596 original size:18 final size:18
Alignment explanation
Indices: 38278548--38278599 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
38278538 TTTGGTTTTA
*
38278548 AAAAAGAAAATAAA-GAG
1 AAAAAGAAAAAAAAGGAG
*
38278565 AAAAAGATAAAAAAGGAG
1 AAAAAGAAAAAAAAGGAG
38278583 -AAAAGAAAGAAAAAGGA
1 AAAAAGAAA-AAAAAGGA
38278600 AGGGAAATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 19 0.63
18 11 0.37
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAAAAAAGGAG
Found at i:38279329 original size:30 final size:30
Alignment explanation
Indices: 38279289--38279419 Score: 203
Period size: 30 Copynumber: 4.4 Consensus size: 30
38279279 GTAGGTCCCT
*
38279289 AAAC-TTTCCAAAATTACATTTTGACCCCA
1 AAACTTTTCCAAAATTACATTTTGACACCA
*
38279318 AAACTTTTCCAAAATTACGTTTTGACACCA
1 AAACTTTTCCAAAATTACATTTTGACACCA
*
38279348 AAACTTTTCCAAAATTACGTTTTGACACCA
1 AAACTTTTCCAAAATTACATTTTGACACCA
* *
38279378 AAACTTTTCTAAAATTACATTTTGACCCCA
1 AAACTTTTCCAAAATTACATTTTGACACCA
38279408 AAAC-TTTCCAAA
1 AAACTTTTCCAAA
38279420 GTTCTATTTT
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
29 11 0.12
30 84 0.88
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (30 bp):
AAACTTTTCCAAAATTACATTTTGACACCA
Found at i:38279350 original size:19 final size:19
Alignment explanation
Indices: 38279326--38279380 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 19
38279316 CAAAACTTTT
38279326 CCAAAATTACGTTTTGACA
1 CCAAAATTACGTTTTGACA
38279345 CC-AAA--AC-TTTT----
1 CCAAAATTACGTTTTGACA
38279356 CCAAAATTACGTTTTGACA
1 CCAAAATTACGTTTTGACA
38279375 CCAAAA
1 CCAAAA
38279381 CTTTTCTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 2 0.07
12 3 0.11
14 2 0.07
15 8 0.29
16 2 0.07
18 3 0.11
19 8 0.29
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (19 bp):
CCAAAATTACGTTTTGACA
Found at i:38284932 original size:38 final size:38
Alignment explanation
Indices: 38284835--38285466 Score: 419
Period size: 38 Copynumber: 16.8 Consensus size: 38
38284825 AAGCACCAAC
***
38284835 ATCATTTCCTATCCTCTTGAAATTGAAGT-AGAGTTGG
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAGAGCAAG
** *
38284872 ATAACAAGTCTTTAT-CTC-TGAAATTGAAGTAAGAGCAAG
1 AT--CATTTC-CTATCCTCTTGAAATTGAAGTAAGAGCAAG
* * *
38284911 ATCATTTCCTATCTTCTTGAAATTGAAGTAA-AGACTGGAT
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAGAG-C--AAG
** *
38284951 ATCAAGT-CTTTACCTC-TGAAATTGAAGTAAGAGCAAG
1 ATCATTTCCTAT-CCTCTTGAAATTGAAGTAAGAGCAAG
* * *
38284988 ATCATTTCCTA-CACTCTTGAAATTGAGGT-AGAGCTGGAT
1 ATCATTTCCTATC-CTCTTGAAATTGAAGTAAGAGC--AAG
** *
38285027 ATCAAGTCTGTAT-CTC-TGAAATTGAAGTAAGAGCAAG
1 ATCATTTC-CTATCCTCTTGAAATTGAAGTAAGAGCAAG
***
38285064 ATCATTTCCTATCCTCTTGAAATTGAAGT-AGAGTTGG
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAGAGCAAG
* * * *
38285101 ATAATAAGTCTTTAT-CTC-TGAAATTGAAGTAAGAGTAAG
1 ATCAT--TTC-CTATCCTCTTGAAATTGAAGTAAGAGCAAG
* * *
38285140 ATCTTTTCCTATCCTCTTGAAATTGAAGTAA-AGCTGGAT
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAGAGC--AAG
** * *
38285179 ATCAAGTCTTTATCC-CTCTGAAATTGAAATAAGAGCAAG
1 ATCATTTC-CTATCCTCT-TGAAATTGAAGTAAGAGCAAG
**
38285218 ATCATTTCCTATCCTCTTGAAATTGAAGTAA-AGCTGG
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAGAGCAAG
** * *
38285255 ATAACAAGTCTTTAT-CTC-TGAAATTGAAGTAAGGGCAAG
1 AT--CATTTC-CTATCCTCTTGAAATTGAAGTAAGAGCAAG
* *
38285294 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGATTG-GAT
1 ATCATTTCCTATCCTCTTGAAATTGAAGT-AAGA--GCAAG
** *
38285334 ATCAAGTCTTTAT-CTC-TGAAATTGAAGTAAGAGCAAG
1 ATCATTTC-CTATCCTCTTGAAATTGAAGTAAGAGCAAG
38285371 ATCATTTCCTATCCTCTTGAAATTGAAGTAA-AGC---
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAGAGCAAG
*
38285405 -TC---T-GTAT-CTC-TGAAATTGAAGTAAGAGCAAG
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAGAGCAAG
38285436 ATCATTTCCTATCCTCTTGAAATTGAAGTAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAA
38285467 AGCTGGATAA
Statistics
Matches: 455, Mismatches: 83, Indels: 113
0.70 0.13 0.17
Matches are distributed among these distances:
27 14 0.03
28 6 0.01
29 3 0.01
30 1 0.00
32 2 0.00
33 2 0.00
35 1 0.00
36 20 0.04
37 79 0.17
38 165 0.36
39 105 0.23
40 50 0.11
41 7 0.02
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (38 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAAGAGCAAG
Found at i:38285071 original size:76 final size:76
Alignment explanation
Indices: 38284835--38285513 Score: 1026
Period size: 76 Copynumber: 9.0 Consensus size: 76
38284825 AAGCACCAAC
* * *
38284835 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
38284900 GTAAGAGCAAG
66 GTAAGAGCAAG
* *
38284911 ATCATTTCCTATCTTCTTGAAATTGAAGTAAAGACTGGATATCAAGTCTTTACCTCTGAAATTGA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAG-CTGGATATCAAGTCTTTATCTCTGAAATTGA
38284976 AGTAAGAGCAAG
65 AGTAAGAGCAAG
* * *
38284988 ATCATTTCCTA-CACTCTTGAAATTGAGGTAGAGCTGGATATCAAGTCTGTATCTCTGAAATTGA
1 ATCATTTCCTATC-CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGA
38285052 AGTAAGAGCAAG
65 AGTAAGAGCAAG
* *
38285064 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAAT-AAGTCTTTATCTCTGAAATTGA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGAT-ATCAAGTCTTTATCTCTGAAATTGA
*
38285128 AGTAAGAGTAAG
65 AGTAAGAGCAAG
*
38285140 ATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCCCTCTGAAATTG
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT--CTCTGAAATTG
*
38285205 AAATAAGAGCAAG
64 AAGTAAGAGCAAG
*
38285218 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
*
38285283 GTAAGGGCAAG
66 GTAAGAGCAAG
*
38285294 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGATTGGATATCAAGTCTTTATCTCTGAAATTGA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAG-CTGGATATCAAGTCTTTATCTCTGAAATTGA
38285359 AGTAAGAGCAAG
65 AGTAAGAGCAAG
*
38285371 ATCATTTCCTATCCTCTTGAAATTGAAGTAAA----G----C---TCTGTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
38285425 GTAAGAGCAAG
66 GTAAGAGCAAG
* *
38285436 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAGTT-AT
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGA-
38285500 AGTAAGAGCAAG
65 AGTAAGAGCAAG
38285512 AT
1 AT
38285514 GAATTTTCAA
Statistics
Matches: 554, Mismatches: 29, Indels: 40
0.89 0.05 0.06
Matches are distributed among these distances:
65 62 0.11
68 1 0.00
69 1 0.00
72 1 0.00
73 1 0.00
75 3 0.01
76 270 0.49
77 143 0.26
78 72 0.13
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (76 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAG
Found at i:38285448 original size:65 final size:65
Alignment explanation
Indices: 38285344--38285470 Score: 254
Period size: 65 Copynumber: 2.0 Consensus size: 65
38285334 ATCAAGTCTT
38285344 TATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTCTG
1 TATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTCTG
38285409 TATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCT
1 TATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCT
38285471 GGATAACAAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (65 bp):
TATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTCTG
Found at i:38285883 original size:6 final size:6
Alignment explanation
Indices: 38285863--38285921 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
38285853 TTAAATGGGT
* * *
38285863 TTTAAA TTT-AT TTTAAA TTTAAA TTTACTTA TTTAAA TTT-AC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
*
38285911 TTTAAG TTTAA
1 TTTAAA TTTAA
38285922 TCAAATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:38285898 original size:14 final size:14
Alignment explanation
Indices: 38285879--38285906 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38285869 TTTATTTTAA
38285879 ATTTAAATTTACTT
1 ATTTAAATTTACTT
38285893 ATTTAAATTTACTT
1 ATTTAAATTTACTT
38285907 TAAATTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTAAATTTACTT
Found at i:38287096 original size:18 final size:17
Alignment explanation
Indices: 38287050--38287100 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
38287040 TTGGTTTTAA
*
38287050 AAAAGAAAATAAA-GAG
1 AAAAGAAAAAAAAGGAG
*
38287066 AGAAAGATAAAAAAGGAG
1 A-AAAGAAAAAAAAGGAG
38287084 AAAAGAAAGAAAAAGGA
1 AAAAGAAA-AAAAAGGA
38287101 AGGGAATCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 1 0.03
17 16 0.55
18 12 0.41
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.04
Consensus pattern (17 bp):
AAAAGAAAAAAAAGGAG
Found at i:38287390 original size:5 final size:5
Alignment explanation
Indices: 38287380--38287411 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
38287370 AGTACCCGCG
38287380 GACCC GACCC GACCC GACCC GACCC GAACCC G
1 GACCC GACCC GACCC GACCC GACCC G-ACCC G
38287412 CCTCTAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.22, C:0.56, G:0.22, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:38287826 original size:30 final size:30
Alignment explanation
Indices: 38287786--38287861 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
38287776 CTCTGTAGGT
**
38287786 CCCT-AAACTTTCCAAAAATTATGTTTTGA
1 CCCTAAAACTTTCCAAAAATTACATTTTGA
* *
38287815 CCCTAAAACTTTTCTAAAATTACATTTTGA
1 CCCTAAAACTTTCCAAAAATTACATTTTGA
*
38287845 CCCCAAAACTTTCCAAA
1 CCCTAAAACTTTCCAAA
38287862 GTTTCATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (30 bp):
CCCTAAAACTTTCCAAAAATTACATTTTGA
Found at i:38287870 original size:29 final size:30
Alignment explanation
Indices: 38287790--38287871 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
38287780 GTAGGTCCCT
** *
38287790 AAAC-TTTCCAAAAATTATGTTTTGACCCTA
1 AAACTTTTCC-AAAATTACATTTTGACCCCA
*
38287820 AAACTTTTCTAAAATTACATTTTGACCCCA
1 AAACTTTTCCAAAATTACATTTTGACCCCA
* *
38287850 AAAC-TTTCCAAAGTTTCATTTT
1 AAACTTTTCCAAAATTACATTTT
38287872 TAGCCCTGAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 15 0.34
30 25 0.57
31 4 0.09
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (30 bp):
AAACTTTTCCAAAATTACATTTTGACCCCA
Found at i:38294023 original size:29 final size:30
Alignment explanation
Indices: 38293959--38294025 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
38293949 ATCTCAAAAC
*
38293959 TATACATGAACTATGGTTTAATATGCAATTG
1 TATACATGAACTATGATTT-ATATGCAATTG
* * *
38293990 TATACATGAACTTTGATTT-TGTGCAATTT
1 TATACATGAACTATGATTTATATGCAATTG
38294019 TATACAT
1 TATACAT
38294026 AAAATTATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 15 0.47
31 17 0.53
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.43
Consensus pattern (30 bp):
TATACATGAACTATGATTTATATGCAATTG
Found at i:38294039 original size:29 final size:29
Alignment explanation
Indices: 38293982--38294038 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
38293972 TGGTTTAATA
* *
38293982 TGCAATTGTATACATGAACTTTGATTTTG
1 TGCAATTGTATACATAAAATTTGATTTTG
*
38294011 TGCAATTTTATACATAAAATTATGATTT
1 TGCAATTGTATACATAAAATT-TGATTT
38294039 GATCCAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (29 bp):
TGCAATTGTATACATAAAATTTGATTTTG
Found at i:38304799 original size:20 final size:19
Alignment explanation
Indices: 38304747--38304799 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
38304737 TTATATATTC
*
38304747 TTTATAATTTTTTTAATTTT
1 TTTAT-ATTTTTTGAATTTT
* *
38304767 TTATAAATATTTTGAATTTAT
1 TT-TATATTTTTTGAATTT-T
38304788 TTTATATTTTTT
1 TTTATATTTTTT
38304800 TGGTGAGAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTATATTTTTTGAATTTT
Found at i:38305436 original size:2 final size:2
Alignment explanation
Indices: 38305431--38305455 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38305421 CATCCACTTT
38305431 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
38305456 TTGTTACCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38310026 original size:2 final size:2
Alignment explanation
Indices: 38310019--38310046 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38310009 ATAAAGAATA
38310019 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38310047 TCAAGGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38311558 original size:15 final size:15
Alignment explanation
Indices: 38311538--38311567 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38311528 GTACAACTCT
*
38311538 CACTTGTATTGATAC
1 CACTTGCATTGATAC
38311553 CACTTGCATTGATAC
1 CACTTGCATTGATAC
38311568 AAATGCACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (15 bp):
CACTTGCATTGATAC
Found at i:38312479 original size:11 final size:12
Alignment explanation
Indices: 38312450--38312482 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
38312440 TTTTTGTCTC
38312450 AATTAATTTTGA
1 AATTAATTTTGA
*
38312462 GATTAATTTT-A
1 AATTAATTTTGA
38312473 AATTAATTTT
1 AATTAATTTT
38312483 TCTTTGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (12 bp):
AATTAATTTTGA
Found at i:38312658 original size:22 final size:22
Alignment explanation
Indices: 38312602--38312658 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
38312592 AATAAAACCA
*
38312602 AAAATTTAA-ATT-TTTTAAAT
1 AAAATTTAATTTTGTTTTAAAT
*
38312622 AAAATTTGATTTTGTTTTAAAT
1 AAAATTTAATTTTGTTTTAAAT
*
38312644 -AATTTTAATTATTGT
1 AAAATTTAATT-TTGT
38312659 GGGGTAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 8 0.27
21 10 0.33
22 12 0.40
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.54
Consensus pattern (22 bp):
AAAATTTAATTTTGTTTTAAAT
Found at i:38316535 original size:3 final size:3
Alignment explanation
Indices: 38316529--38316562 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
38316519 AATAAAATAG
38316529 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
38316563 ATACTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:38317189 original size:13 final size:14
Alignment explanation
Indices: 38317156--38317190 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
38317146 TTTAGTCCAA
38317156 TTGGACTTGTAAAC
1 TTGGACTTGTAAAC
*
38317170 TTAGACTTGT-AAC
1 TTGGACTTGTAAAC
38317183 TTGGACTT
1 TTGGACTT
38317191 TATTTGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (14 bp):
TTGGACTTGTAAAC
Found at i:38328515 original size:6 final size:6
Alignment explanation
Indices: 38328504--38328530 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
38328494 TTTTAGCTTA
38328504 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
38328531 GGTTGGTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:38329490 original size:16 final size:17
Alignment explanation
Indices: 38329469--38329503 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
38329459 TTTTGATTTG
38329469 TTTTTAAA-TATTTTAA
1 TTTTTAAAGTATTTTAA
38329485 TTTTTAAATGTATTTTAA
1 TTTTTAAA-GTATTTTAA
38329503 T
1 T
38329504 AATGTGACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TTTTTAAAGTATTTTAA
Found at i:38330235 original size:20 final size:20
Alignment explanation
Indices: 38330184--38330235 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
38330174 GATCTGGATT
* *
38330184 TTCTGCCGATAAAACTTCAC
1 TTCTACCGATACAACTTCAC
* *
38330204 TTCTATCGATACAACTTCAG
1 TTCTACCGATACAACTTCAC
38330224 TTCTACCGATAC
1 TTCTACCGATAC
38330236 CTTGAAGGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.33
Consensus pattern (20 bp):
TTCTACCGATACAACTTCAC
Found at i:38330496 original size:20 final size:20
Alignment explanation
Indices: 38330459--38330514 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
38330449 TTGGCCTGAG
* *
38330459 ACTTCTACCGGTAGAACTTC
1 ACTTCTACCGATACAACTTC
* *
38330479 ACTTTTACCGATACAACTTT
1 ACTTCTACCGATACAACTTC
*
38330499 AGTTCTACCGATACAA
1 ACTTCTACCGATACAA
38330515 GTATGCTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (20 bp):
ACTTCTACCGATACAACTTC
Found at i:38330527 original size:20 final size:21
Alignment explanation
Indices: 38330480--38330534 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
38330470 TAGAACTTCA
*
38330480 CTTTTACCGATACAACTTTAG
1 CTTTTACCGATACAACTATAG
* *
38330501 -TTCTACCGATACAAGTAT-G
1 CTTTTACCGATACAACTATAG
*
38330520 CTTTTACCGAAACAA
1 CTTTTACCGATACAA
38330535 TGAAACTACA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.33
Consensus pattern (21 bp):
CTTTTACCGATACAACTATAG
Found at i:38332269 original size:23 final size:23
Alignment explanation
Indices: 38332210--38332270 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
38332200 AACCCGACCT
*
38332210 ATTGACTTTGATCGAACCGAATC
1 ATTGACTTTGATCGAACCGAACC
* * *
38332233 ATTTAATTTGATCGAATCGAACC
1 ATTGACTTTGATCGAACCGAACC
*
38332256 ATTGACTTTAATCGA
1 ATTGACTTTGATCGA
38332271 TCGTTGACCG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (23 bp):
ATTGACTTTGATCGAACCGAACC
Found at i:38335049 original size:22 final size:23
Alignment explanation
Indices: 38335024--38335073 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
38335014 AAATTGATGC
38335024 AAAAAAATAATTAAATTA-TTTA
1 AAAAAAATAATTAAATTAGTTTA
* * **
38335046 AAAATAATTATTATTTTAGTTTA
1 AAAAAAATAATTAAATTAGTTTA
38335069 AAAAA
1 AAAAA
38335074 TCATAAAAGA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
AAAAAAATAATTAAATTAGTTTA
Found at i:38335060 original size:17 final size:18
Alignment explanation
Indices: 38335026--38335061 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
38335016 ATTGATGCAA
38335026 AAAAATAATTAAATTATTT
1 AAAAATAATT-AATTATTT
38335045 AAAAATAATT-ATTATTT
1 AAAAATAATTAATTATTT
38335062 TAGTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
19 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAAATAATTAATTATTT
Found at i:38336176 original size:32 final size:31
Alignment explanation
Indices: 38336128--38336195 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
38336118 TTATTTTTAA
*
38336128 TTTTTTAAAATATTTTTGTATTGTTATATAT
1 TTTTTTAAAATATTTTTGTATTGTTATATAC
* *
38336159 TTTTTTCAACAAT-TTTTTTTATTTTTATATAC
1 TTTTTT-AA-AATATTTTTGTATTGTTATATAC
38336191 TTTTT
1 TTTTT
38336196 AGATTTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 6 0.19
32 23 0.72
33 3 0.09
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.68
Consensus pattern (31 bp):
TTTTTTAAAATATTTTTGTATTGTTATATAC
Found at i:38336202 original size:23 final size:22
Alignment explanation
Indices: 38336176--38336218 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
38336166 AACAATTTTT
*
38336176 TTTATTTTTATATACTTTTTAGA
1 TTTATTATTATATA-TTTTTAGA
38336199 TTTATTATTATATATTTTTA
1 TTTATTATTATATATTTTTA
38336219 AAATAGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTATTATTATATATTTTTAGA
Found at i:38337372 original size:28 final size:29
Alignment explanation
Indices: 38337320--38337374 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
38337310 TATTAGCGTA
38337320 TTTTTATTTTGTTCACTTAAATTTATTTT
1 TTTTTATTTTGTTCACTTAAATTTATTTT
*
38337349 TTTTTATTTTAG-TCAC-TAACTTTATT
1 TTTTTATTTT-GTTCACTTAAATTTATT
38337375 GAAATTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 9 0.38
29 14 0.58
30 1 0.04
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (29 bp):
TTTTTATTTTGTTCACTTAAATTTATTTT
Found at i:38345326 original size:43 final size:43
Alignment explanation
Indices: 38345265--38345357 Score: 186
Period size: 43 Copynumber: 2.2 Consensus size: 43
38345255 TTCAATGCAC
38345265 TCGAATTCATATCCTCCTATATTGACAACAATGTTCATACCAA
1 TCGAATTCATATCCTCCTATATTGACAACAATGTTCATACCAA
38345308 TCGAATTCATATCCTCCTATATTGACAACAATGTTCATACCAA
1 TCGAATTCATATCCTCCTATATTGACAACAATGTTCATACCAA
38345351 TCGAATT
1 TCGAATT
38345358 AAGACTCAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.33
Consensus pattern (43 bp):
TCGAATTCATATCCTCCTATATTGACAACAATGTTCATACCAA
Found at i:38350305 original size:12 final size:12
Alignment explanation
Indices: 38350288--38350312 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38350278 ATATAGGGTC
38350288 AGAATTTAGACT
1 AGAATTTAGACT
38350300 AGAATTTAGACT
1 AGAATTTAGACT
38350312 A
1 A
38350313 TGACATTACA
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:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (12 bp):
AGAATTTAGACT
Found at i:38354096 original size:17 final size:19
Alignment explanation
Indices: 38354076--38354110 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
38354066 ATTGCTGAGA
38354076 GTATTGTT-T-TTATTTTG
1 GTATTGTTATATTATTTTG
38354093 GTATTGTTATATTATTTT
1 GTATTGTTATATTATTTT
38354111 AGATTTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (19 bp):
GTATTGTTATATTATTTTG
Found at i:38354665 original size:21 final size:21
Alignment explanation
Indices: 38354635--38354692 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
38354625 ATTCAATTAG
* *
38354635 ATATT-TTTATTTTTATGATT
1 ATATTATTTATTTTTATAATA
*
38354655 ATATTATTTATATTTATAATA
1 ATATTATTTATTTTTATAATA
*
38354676 ATTTTATTTATTTTTAT
1 ATATTATTTATTTTTAT
38354693 TTTTTACCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 5 0.16
21 27 0.84
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
ATATTATTTATTTTTATAATA
Found at i:38357881 original size:30 final size:31
Alignment explanation
Indices: 38357828--38357890 Score: 110
Period size: 30 Copynumber: 2.0 Consensus size: 31
38357818 TAGTGCTGTC
38357828 AACCCTTTCCTTTTTGCTTAATTACTGTTATT
1 AACCCTTTCCTTTTT-CTTAATTACTGTTATT
38357860 AACCCTTTCCTTTTT-TTAATTACTGTTATT
1 AACCCTTTCCTTTTTCTTAATTACTGTTATT
38357890 A
1 A
38357891 GTACATATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 16 0.52
32 15 0.48
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.54
Consensus pattern (31 bp):
AACCCTTTCCTTTTTCTTAATTACTGTTATT
Found at i:38358180 original size:22 final size:23
Alignment explanation
Indices: 38358150--38358199 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 23
38358140 AATATATTTA
38358150 TATATAAATAA-AAATTA-TAAAAT
1 TATATAAATAATAAA--AGTAAAAT
38358173 TATA-AAATAATAAAAGTAAAAT
1 TATATAAATAATAAAAGTAAAAT
38358195 TATAT
1 TATAT
38358200 CTTGGTCCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
21 1 0.04
22 16 0.67
23 7 0.29
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
TATATAAATAATAAAAGTAAAAT
Found at i:38372530 original size:14 final size:15
Alignment explanation
Indices: 38372511--38372540 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
38372501 TTTAATTTTG
38372511 TTATTTAA-ATAATA
1 TTATTTAAGATAATA
38372525 TTATTTAAGATAATA
1 TTATTTAAGATAATA
38372540 T
1 T
38372541 AAGTACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TTATTTAAGATAATA
Found at i:38377266 original size:56 final size:56
Alignment explanation
Indices: 38377175--38377521 Score: 302
Period size: 56 Copynumber: 5.9 Consensus size: 56
38377165 CTTCAGGACA
* * *
38377175 CACACGGGCTGGGCACACGGGCGTGTGCTATACCGTGTGTGTATACTATTTTGTTG
1 CACACGGGCTGGGCATACGGGCGTGTGCTAAACCATGTGTGTATACTATTTTGTTG
* * * * * * *
38377231 CATACGGGTTGGGCATATGGGCGTGTG-TCAGACCGTGTGTGCATACTGTTTGTGGATTAAAG
1 CACACGGGCTGGGCATACGGGCGTGTGCT-AAACCATGTGTGTATACTATTT-T-G-TT---G
* * * *
38377293 TACAGGGGACACGTGGGCTTGGAACACGGGCGTGTGCT-AACCGTGTGTGTATACTATTTTGTTG
1 CACACGGG---C-TGGGC-----ATACGGGCGTGTGCTAAACCATGTGTGTATACTATTTTGTTG
* *
38377357 CACACGGGCTGGGCATACGGGCATGTGCTAAATCATGTGTGTATACTATTTTGTTG
1 CACACGGGCTGGGCATACGGGCGTGTGCTAAACCATGTGTGTATACTATTTTGTTG
* *
38377413 CACACGGGCTGGGCATACGGGCATGTGCTAAATCATGTGTGTATACTATTTTGTTG
1 CACACGGGCTGGGCATACGGGCGTGTGCTAAACCATGTGTGTATACTATTTTGTTG
* * * * * * **
38377469 CACATGAGCTGGGCACACGGGCGTGTGCCAGACCATATGAATATACTATTTTG
1 CACACGGGCTGGGCATACGGGCGTGTGCTAAACCATGTGTGTATACTATTTTG
38377522 CAATTATAGA
Statistics
Matches: 241, Mismatches: 32, Indels: 36
0.78 0.10 0.12
Matches are distributed among these distances:
55 14 0.06
56 165 0.68
57 1 0.00
58 1 0.00
59 2 0.01
60 5 0.02
61 1 0.00
62 6 0.02
64 7 0.03
66 5 0.02
67 2 0.01
68 1 0.00
69 1 0.00
70 18 0.07
71 11 0.05
72 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.30
Consensus pattern (56 bp):
CACACGGGCTGGGCATACGGGCGTGTGCTAAACCATGTGTGTATACTATTTTGTTG
Found at i:38378361 original size:450 final size:450
Alignment explanation
Indices: 38377520--38378415 Score: 1443
Period size: 450 Copynumber: 2.0 Consensus size: 450
38377510 TATACTATTT
* * *
38377520 TGCAATTATAGATGTAGTGGTCACACGGGCCAACACATGGTCGTGTGCTAGGGCATGTAGACCAT
1 TGCAATTATAGATGCAGTGGTCACACGGGCCAACACATGATCGTGTGCTAGAGCATGTAGACCAT
* * *
38377585 GTTTTCGATCGAAACACTATATAAAGCGATTGTAAGTTGACCGTAGCACTTAAATGATCTAAACT
66 GTTTTCGACCGAAACACTATATAAAACGACTGTAAGTTGACCGTAGCACTTAAATGATCTAAACT
* * * *
38377650 GAATTGCGAGAGAGTTATTAGATAAGTTCTTGATTCTGATTATATGGGCATATGATTGATTTTCT
131 AAATTGCGAGAGAGTTATTAGATAAGTGCTTGATTCTGATTATAAGGGCATATGATTGATTTGCT
* * * * *
38377715 ATGTTCTACTAATATTTGATATATCTGATATGCTTATATATATATATATGTATGTATTTGAAATT
196 ATGTTCTACCAATATCTGATATATCTGATATGCGTATACATATATATATATATGTATTTGAAATT
* *
38377780 TATGAATTCAATATCTATTCTGCATTTGCATGAGGTTTGGGGATTGTGAAGTGAATGAAGTACTG
261 TATGAATTCAATATCTATTCTGCATTTGCATGAGGGTTGGGGATTGTGAAGTGAAAGAAGTACTG
* * **
38377845 AATTGAACTGATTTGGTAGTTTAACCACTAGAAATTATAATTGATTTGGTAGTGAAACTGTAAAC
326 AATTGAACTAATTTGGTAGTTTAACCACTAGAAATTATAACTGAACTGGTAGTGAAACTGTAAAC
*
38377910 AC-TACAATGTGTTAGACTGACACTCTATGGTGTGTAAGGTTGGACATTGGTGTGTTAAAC
391 ACGGA-AATGTGTTAGACTGACACTCTATGGTGTGTAAGGTTGGACATTGGTGTGTTAAAC
* * * **
38377970 TGCAATTATAGGTGCAGTGGTCACATGGGCCAACACATGATCGTGTGTTAGATTATGTAGACCAT
1 TGCAATTATAGATGCAGTGGTCACACGGGCCAACACATGATCGTGTGCTAGAGCATGTAGACCAT
* * *
38378035 GTTTTTGACCGAAACACTATATAAAACGACTGTAAGTTGACCGTAGCACTTGAATTATCTAAACT
66 GTTTTCGACCGAAACACTATATAAAACGACTGTAAGTTGACCGTAGCACTTAAATGATCTAAACT
*
38378100 AAATTGCGAGAGAGTTATTAGATAAGTGCTTGATTCTGATTATAAGGGCATATGATTTATTTGCT
131 AAATTGCGAGAGAGTTATTAGATAAGTGCTTGATTCTGATTATAAGGGCATATGATTGATTTGCT
*
38378165 ATGTTCTACCAATATCTGATATATCTGATATGCGTATGCATATATATATATATGTATTTGAAATT
196 ATGTTCTACCAATATCTGATATATCTGATATGCGTATACATATATATATATATGTATTTGAAATT
* *
38378230 TATGAATTCAATATCTGTTCTGCATTTGCATGAGGGTTGGGGATTGTGAAGTGAAAGAAGTATTG
261 TATGAATTCAATATCTATTCTGCATTTGCATGAGGGTTGGGGATTGTGAAGTGAAAGAAGTACTG
* * *
38378295 AATTGAGCTAATTTGGTGGTTTAACCACTTGAAATTATAACTGAACTGGTAGTGAAACTGTAAAC
326 AATTGAACTAATTTGGTAGTTTAACCACTAGAAATTATAACTGAACTGGTAGTGAAACTGTAAAC
38378360 ACGGAAATGTGTTAGACTGACACTCTATGGTGTGTAAGGTTGGACATTGGTGTGTT
391 ACGGAAATGTGTTAGACTGACACTCTATGGTGTGTAAGGTTGGACATTGGTGTGTT
38378416 GGGCTGGACA
Statistics
Matches: 408, Mismatches: 37, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
450 407 1.00
451 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (450 bp):
TGCAATTATAGATGCAGTGGTCACACGGGCCAACACATGATCGTGTGCTAGAGCATGTAGACCAT
GTTTTCGACCGAAACACTATATAAAACGACTGTAAGTTGACCGTAGCACTTAAATGATCTAAACT
AAATTGCGAGAGAGTTATTAGATAAGTGCTTGATTCTGATTATAAGGGCATATGATTGATTTGCT
ATGTTCTACCAATATCTGATATATCTGATATGCGTATACATATATATATATATGTATTTGAAATT
TATGAATTCAATATCTATTCTGCATTTGCATGAGGGTTGGGGATTGTGAAGTGAAAGAAGTACTG
AATTGAACTAATTTGGTAGTTTAACCACTAGAAATTATAACTGAACTGGTAGTGAAACTGTAAAC
ACGGAAATGTGTTAGACTGACACTCTATGGTGTGTAAGGTTGGACATTGGTGTGTTAAAC
Found at i:38384294 original size:30 final size:28
Alignment explanation
Indices: 38384248--38384320 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 28
38384238 GTATATTTGG
*
38384248 AATTTAATCCTAATTTTTT-ATTTTCAAA
1 AATTTAATCCTAATTTTTTGAATTT-AAA
*
38384276 AATTTAATCTCTCTATTTTTTGAATTTAAA
1 AATTTAATC-CT-AATTTTTTGAATTTAAA
* *
38384306 AATTTAGTTCTAATT
1 AATTTAATCCTAATT
38384321 GTTAATACCG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 12 0.32
29 4 0.11
30 17 0.46
31 4 0.11
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.53
Consensus pattern (28 bp):
AATTTAATCCTAATTTTTTGAATTTAAA
Found at i:38384681 original size:43 final size:44
Alignment explanation
Indices: 38384588--38384681 Score: 102
Period size: 43 Copynumber: 2.2 Consensus size: 44
38384578 ATCTCAAATT
* * * **
38384588 TTAACAAAGTAAAGGGACCACAATTGAAATTTAACTTTTTATAA
1 TTAAAAAAGTAAAGGGACCAAAATTGAAAATTAACTCATTATAA
* * *
38384632 TT-AAAAAGTAGAGGGACTAAAATTGAAAATTAAC-CATTATTA
1 TTAAAAAAGTAAAGGGACCAAAATTGAAAATTAACTCATTATAA
38384674 TTAAAAAA
1 TTAAAAAA
38384682 AACCCCCAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
42 7 0.17
43 32 0.78
44 2 0.05
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.30
Consensus pattern (44 bp):
TTAAAAAAGTAAAGGGACCAAAATTGAAAATTAACTCATTATAA
Found at i:38387786 original size:16 final size:16
Alignment explanation
Indices: 38387767--38387804 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
38387757 GTTCGGATGA
38387767 AAAATTTTAGGT-TTTT
1 AAAATTTTA-GTATTTT
*
38387783 AAAATCTTAGTATTTT
1 AAAATTTTAGTATTTT
38387799 AAAATT
1 AAAATT
38387805 CATAAATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (16 bp):
AAAATTTTAGTATTTT
Found at i:38388496 original size:9 final size:10
Alignment explanation
Indices: 38388477--38388501 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
38388467 TAACTTTACA
38388477 TTTTAATTTT
1 TTTTAATTTT
38388487 TTTTAATTTT
1 TTTTAATTTT
38388497 TTTTA
1 TTTTA
38388502 GTTCTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTAATTTT
Found at i:38388628 original size:10 final size:11
Alignment explanation
Indices: 38388613--38388666 Score: 51
Period size: 10 Copynumber: 4.9 Consensus size: 11
38388603 TTTAATTAAT
38388613 TTTTTAAAA-A
1 TTTTTAAAATA
38388623 TTTTTAAAATA
1 TTTTTAAAATA
38388634 TTTTTATATATATA
1 TTTTTA-A-A-ATA
*
38388648 TTTTT-TAAT-
1 TTTTTAAAATA
38388657 TTTTTAAAAT
1 TTTTTAAAAT
38388667 TTAAAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 5 0.14
10 14 0.38
11 8 0.22
12 1 0.03
13 1 0.03
14 8 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTTAAAATA
Found at i:38392103 original size:60 final size:58
Alignment explanation
Indices: 38392022--38392264 Score: 240
Period size: 58 Copynumber: 4.0 Consensus size: 58
38392012 TTGGTACTTG
* *
38392022 AACTTGATA-TTTTTTCGTAATTTTGTACCTAAACATTTTTTTGACTCAATTTGATACCTA
1 AACTTGACATTTTTTTC-TAATTTGGTA-CTAAAC-TTTTTTTGACTCAATTTGATACCTA
* *
38392082 AACTTGACATTTTTTTCTAATTTGGTAGCTAAACTTTTTTT-ACTCAATTTGGTATCTA
1 AACTTGACATTTTTTTCTAATTTGGTA-CTAAACTTTTTTTGACTCAATTTGATACCTA
* *
38392140 AACTTGACACTTTTTCCTAATTTGGTACTGAAACTTTTTTTGGA-TCCAATTTGATACCTA
1 AACTTGACATTTTTTTCTAATTTGGTACT-AAACTTTTTTT-GACT-CAATTTGATACCTA
* * * * * * *
38392200 AACTTGGCATTTTTTCCCCTAATTTGGCTCCTAAGCTTTGTTTTAGATTCAATTTGGTATCTA
1 AACTTGACATTTTTT--TCTAATTTGG-TACTAAACTTT-TTTT-GACTCAATTTGATACCTA
38392263 AA
1 AA
38392265 TTTATTAAAT
Statistics
Matches: 157, Mismatches: 16, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
57 2 0.01
58 51 0.32
59 8 0.05
60 49 0.31
61 7 0.04
62 16 0.10
63 23 0.15
64 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (58 bp):
AACTTGACATTTTTTTCTAATTTGGTACTAAACTTTTTTTGACTCAATTTGATACCTA
Found at i:38392114 original size:31 final size:31
Alignment explanation
Indices: 38392054--38392175 Score: 105
Period size: 31 Copynumber: 4.0 Consensus size: 31
38392044 TTGTACCTAA
*
38392054 ACATTTTTTTGACTCAATTTGATACCTAAACTTG
1 ACATTTTTTT--CTCAATTTGGTA-CTAAACTTG
38392088 ACATTTTTTTCT-AATTTGGTAGCTAAAC-T-
1 ACATTTTTTTCTCAATTTGGTA-CTAAACTTG
*
38392117 ---TTTTTTACTCAATTTGGTATCTAAACTTG
1 ACATTTTTTTCTCAATTTGGTA-CTAAACTTG
* *
38392146 ACACTTTTTCCT-AATTTGGTACTGAAACTT
1 ACATTTTTTTCTCAATTTGGTACT-AAACTT
38392176 TTTTTGGATC
Statistics
Matches: 75, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
26 8 0.11
27 15 0.20
28 1 0.01
30 3 0.04
31 29 0.39
32 9 0.12
34 10 0.13
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (31 bp):
ACATTTTTTTCTCAATTTGGTACTAAACTTG
Found at i:38392130 original size:27 final size:27
Alignment explanation
Indices: 38392040--38392204 Score: 95
Period size: 31 Copynumber: 5.7 Consensus size: 27
38392030 ATTTTTTCGT
*
38392040 AATTTTGTACCTAAACATTTTTTTGACTC
1 AATTTGGTACCTAAAC-TTTTTTT-ACTC
* *
38392069 AATTTGATACCTAAACTTGACATTTTT-TTC
1 AATTTGGTACCTAAACTT----TTTTTACTC
*
38392099 TAATTTGGTAGCTAAACTTTTTTTACTC
1 -AATTTGGTACCTAAACTTTTTTTACTC
* *
38392127 AATTTGGTATCTAAACTTGACACTTTTTCCT-
1 AATTTGGTACCTAAACTT-----TTTTTACTC
38392158 AATTTGGTA-CTGAAACTTTTTTTGGA-TCC
1 AATTTGGTACCT-AAACTTTTTTT--ACT-C
*
38392187 AATTTGATACCTAAACTT
1 AATTTGGTACCTAAACTT
38392205 GGCATTTTTT
Statistics
Matches: 109, Mismatches: 10, Indels: 34
0.71 0.07 0.22
Matches are distributed among these distances:
26 5 0.05
27 23 0.21
28 4 0.04
29 28 0.26
30 6 0.06
31 31 0.28
32 12 0.11
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (27 bp):
AATTTGGTACCTAAACTTTTTTTACTC
Found at i:38392148 original size:58 final size:59
Alignment explanation
Indices: 38392022--38392264 Score: 260
Period size: 60 Copynumber: 4.0 Consensus size: 59
38392012 TTGGTACTTG
* * *
38392022 AACTTGATATTTTTTCGTAATTTTGTACCTAAACATTTTTTTGACTCAATTTGATACCTA
1 AACTTGACATTTTTTCCTAATTTGGTACCTAAAC-TTTTTTTGACTCAATTTGATACCTA
* * * *
38392082 AACTTGACATTTTTTTCTAATTTGGTAGCTAAACTTTTTTT-ACTCAATTTGGTATCTA
1 AACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTTGACTCAATTTGATACCTA
*
38392140 AACTTGACACTTTTTCCTAATTTGGTA-CTGAAACTTTTTTTGGA-TCCAATTTGATACCTA
1 AACTTGACATTTTTTCCTAATTTGGTACCT-AAACTTTTTTT-GACT-CAATTTGATACCTA
* * * * *
38392200 AACTTGGCATTTTTTCCCCTAATTTGGCT-CCTAAGCTTTGTTTTAGATTCAATTTGGTATCTA
1 AACTTGACATTTTTT--CCTAATTTGG-TACCTAAACTTT-TTTT-GACTCAATTTGATACCTA
38392263 AA
1 AA
38392265 TTTATTAAAT
Statistics
Matches: 156, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
57 2 0.01
58 51 0.33
59 8 0.05
60 55 0.35
62 16 0.10
63 23 0.15
64 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (59 bp):
AACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTTGACTCAATTTGATACCTA
Found at i:38392446 original size:31 final size:31
Alignment explanation
Indices: 38392411--38392543 Score: 105
Period size: 31 Copynumber: 4.4 Consensus size: 31
38392401 TAAATAAAAA
*
38392411 TTAGGTATCAAATTAGAAAAAAGAGTCAAGT
1 TTAGGTACCAAATTAGAAAAAAGAGTCAAGT
* ***
38392442 TTAGGTACCAAATTGGACCCCAA-A---AAGT
1 TTAGGTACCAAATTAGA-AAAAAGAGTCAAGT
* * *
38392470 TTAAGTACCAAGTTA-AAAAAAGTGTCAAGT
1 TTAGGTACCAAATTAGAAAAAAGAGTCAAGT
** * *
38392500 TTAGGTATTAAATTAGAAAAAAGTGTCAAAT
1 TTAGGTACCAAATTAGAAAAAAGAGTCAAGT
*
38392531 TTAAGTACCAAAT
1 TTAGGTACCAAAT
38392544 CAAATAAAAA
Statistics
Matches: 76, Mismatches: 20, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
26 2 0.03
27 1 0.01
28 16 0.21
30 15 0.20
31 40 0.53
32 2 0.03
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.27
Consensus pattern (31 bp):
TTAGGTACCAAATTAGAAAAAAGAGTCAAGT
Found at i:38392568 original size:89 final size:89
Alignment explanation
Indices: 38392411--38392586 Score: 210
Period size: 89 Copynumber: 2.0 Consensus size: 89
38392401 TAAATAAAAA
* * *** ***
38392411 TTAGGTATCAAATTAGAAAAAAGAGTCAAGTTTAGGTACCAAATTGGACCCCAAAAAGTTTAAGT
1 TTAGGTATCAAATTAGAAAAAAGAGTCAAATTTAAGTACCAAATCAAACAAAAAAAAGTTTAAGT
* * *
38392476 ACCAAGTTAAAAAAAGTGTCAAGT
66 ACCAAATAAAAAAAAGTATCAAGT
* * *
38392500 TTAGGTATTAAATTAGAAAAAAGTGTCAAATTTAAGTACCAAATCAAATAAAAAAAAGTTT-AGA
1 TTAGGTATCAAATTAGAAAAAAGAGTCAAATTTAAGTACCAAATCAAACAAAAAAAAGTTTAAG-
38392564 TACCAAATAAAAAAAAGTATCAA
65 TACCAAATAAAAAAAAGTATCAA
38392587 ATTCAGAAAC
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
88 2 0.03
89 70 0.97
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (89 bp):
TTAGGTATCAAATTAGAAAAAAGAGTCAAATTTAAGTACCAAATCAAACAAAAAAAAGTTTAAGT
ACCAAATAAAAAAAAGTATCAAGT
Found at i:38392723 original size:14 final size:16
Alignment explanation
Indices: 38392704--38392737 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
38392694 CAAATTTGAT
38392704 ATTTAA-TTT-ATATA
1 ATTTAATTTTGATATA
38392718 ATTTAATTTTGATATA
1 ATTTAATTTTGATATA
38392734 ATTT
1 ATTT
38392738 GGTACGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 3 0.17
16 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
ATTTAATTTTGATATA
Found at i:38394749 original size:14 final size:14
Alignment explanation
Indices: 38394730--38394760 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38394720 CCCCAGTCGC
38394730 CATTACCACATCAG
1 CATTACCACATCAG
*
38394744 CATTACCACGTCAG
1 CATTACCACATCAG
38394758 CAT
1 CAT
38394761 CCATGTCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.35, G:0.10, T:0.23
Consensus pattern (14 bp):
CATTACCACATCAG
Found at i:38403964 original size:17 final size:17
Alignment explanation
Indices: 38403942--38403975 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38403932 TTAGAATTGG
*
38403942 ATTGAAAAAATTATTTA
1 ATTGAAAAAATAATTTA
38403959 ATTGAAAAAATAATTTA
1 ATTGAAAAAATAATTTA
38403976 TTTAAATTAA
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):
ATTGAAAAAATAATTTA
Found at i:38410328 original size:18 final size:18
Alignment explanation
Indices: 38410303--38410339 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
38410293 AAAGTAAAAA
*
38410303 ATAAAATTTTAC-ATTAT
1 ATAAAAATTTACAATTAT
38410320 ATAAAAATTTACAATTAT
1 ATAAAAATTTACAATTAT
38410338 AT
1 AT
38410340 GAGATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAAAAATTTACAATTAT
Found at i:38413539 original size:59 final size:59
Alignment explanation
Indices: 38413424--38413739 Score: 526
Period size: 59 Copynumber: 5.3 Consensus size: 59
38413414 GGATACCCGA
* ** *
38413424 GGGGTAAAATGGTAATTTTTGGTGTAAATTAGGGTTAAAAATGGAATTCTAGAAGCTTCG
1 GGGGTAAAATGGTAATTTTCGGTG-AAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCG
* * *
38413484 GGGGTAAAATGGTAATTTTCGGTAAAATCGGGGTTAAAAATAGAATTTTAAAAGCTTCG
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCG
38413543 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAAATGGAATTTTAGAAGCTTCG
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTT-AAAAATGGAATTTTAGAAGCTTCG
38413603 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCG
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCG
38413662 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCG
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCG
*
38413721 GGGGTTAAAAT-ATAATTTT
1 GGGG-TAAAATGGTAATTTT
38413740 GGAAAAGTTT
Statistics
Matches: 243, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
59 158 0.65
60 85 0.35
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCG
Found at i:38413635 original size:119 final size:118
Alignment explanation
Indices: 38413424--38413739 Score: 526
Period size: 119 Copynumber: 2.7 Consensus size: 118
38413414 GGATACCCGA
* ** *
38413424 GGGGTAAAATGGTAATTTTTGGTGTAAATTAGGGTTAAAAATGGAATTCTAGAAGCTTCGGGGGT
1 GGGGTAAAATGGTAATTTTCGGTG-AAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCGGGGGT
38413489 AAAATGGTAATTTTCGGTAAAATCGGGGTTAAAAATAGAATTTTAAAAGCTTCG
65 AAAATGGTAATTTTCGGTAAAATCGGGGTTAAAAATAGAATTTTAAAAGCTTCG
38413543 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAAATGGAATTTTAGAAGCTTCGGGGGT
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTT-AAAAATGGAATTTTAGAAGCTTCGGGGGT
* * *
38413608 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCG
65 AAAATGGTAATTTTCGGTAAAATCGGGGTTAAAAATAGAATTTTAAAAGCTTCG
38413662 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCGGGGGTT
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCGGGGG-T
*
38413727 AAAAT-ATAATTTT
65 AAAATGGTAATTTT
38413740 GGAAAAGTTT
Statistics
Matches: 187, Mismatches: 8, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
118 44 0.24
119 143 0.76
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (118 bp):
GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTCGGGGGTA
AAATGGTAATTTTCGGTAAAATCGGGGTTAAAAATAGAATTTTAAAAGCTTCG
Found at i:38413755 original size:30 final size:30
Alignment explanation
Indices: 38413721--38413935 Score: 376
Period size: 30 Copynumber: 7.2 Consensus size: 30
38413711 AGAAGCTTCG
*
38413721 GGGGTTAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
*
38413751 GGGGTCAAAATATAATTTTAGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
*
38413781 GGGGTCAAAATATAATTTTAGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
38413811 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
*
38413841 GGAGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
38413871 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
* *
38413901 AGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
38413931 GGGGT
1 GGGGT
38413936 TGAAATAATT
Statistics
Matches: 177, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 177 1.00
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
GGGGTCAAAATATAATTTTGGAAAAGTTTT
Found at i:38414275 original size:161 final size:162
Alignment explanation
Indices: 38414040--38414356 Score: 435
Period size: 161 Copynumber: 2.0 Consensus size: 162
38414030 ACTAATTCGA
* * * *
38414040 AAACTTTGAAAAATCTTTGGACCAATTTTGTAATTAACTAAGAGTTAATTTAAGGACTAAATTAA
1 AAACCTTGAAAAATCTTTGGACCAATTTCGTAATTAAATAAGAGCTAATTTAAGGACTAAATTAA
* * * *
38414105 AATAAATTAAAAATAGAAGGGACTAAATGCAGAAATAAGCTAA-AAATTGACACGTGGCAACCTC
66 AACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAATAAA-TGACACGTGGCAACCTC
**
38414169 TGGTGCAGTCAAACAGTCAAAGGACTAGTTTAT
130 TGGCACAGTCAAACAGTCAAAGGACTAGTTTAT
* * * *
38414202 AAACCTTGAAAAAT-TATTGGGCCAATTTCGTAATTAAAATAA-AGCTGATTT-GGGATTAAATT
1 AAACCTTGAAAAATCT-TTGGACCAATTTCGTAATT-AAATAAGAGCTAATTTAAGGACTAAATT
* *
38414264 AAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAATACATGACACGTGGCAACCT
64 AAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAATAAATGACACGTGGCAACCT
38414329 CTGGCACAGTCAAACAGTCAAAGGACTA
129 CTGGCACAGTCAAACAGTCAAAGGACTA
38414357 AATTATAATC
Statistics
Matches: 136, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
161 92 0.68
162 39 0.29
163 5 0.04
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (162 bp):
AAACCTTGAAAAATCTTTGGACCAATTTCGTAATTAAATAAGAGCTAATTTAAGGACTAAATTAA
AACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAATAAATGACACGTGGCAACCTCT
GGCACAGTCAAACAGTCAAAGGACTAGTTTAT
Found at i:38414440 original size:161 final size:160
Alignment explanation
Indices: 38414091--38414441 Score: 388
Period size: 161 Copynumber: 2.2 Consensus size: 160
38414081 GAGTTAATTT
* * * *
38414091 AAGGACTAAATTAAAATAAATTAAAAATAGAAGGGACTAAATGCAGAAATAAGCTAAAAATTGAC
1 AAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAATTGAC
** ** **
38414156 ACGTGGCAACCTCTGGTGCAGTCAAACAGTCAAAGGACTAGTTTATAAACCTTGAAAAATTATTG
66 ACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTATAAACCTT-AAAAATTACAG
* * * * **
38414221 GGCCAATTTCGTAATTAAAATAAAGCTGATT
130 GGCAAATTTCGCAAATAAAATAAAGATGAAG
** * * *
38414252 TGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAATACA-TGA
1 AAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAA-AAATTGA
*
38414316 CACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTATAATCCAATT-AAAATTAC
65 CACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTATAAACC--TTAAAAATTAC
38414380 AGGGCAAATTT-GCAAATAATTAA-AAAGATGCAAG
128 AGGGCAAATTTCGCAAATAA--AATAAAGATG-AAG
* *
38414414 AAGGACTAAATTGAAGCAAA-TAAAAATA
1 AAGGACTAAATTAAAACAAATTAAAAATA
38414442 CGGAAGGATC
Statistics
Matches: 157, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
160 6 0.04
161 129 0.82
162 20 0.13
163 2 0.01
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (160 bp):
AAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAATTGAC
ACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTATAAACCTTAAAAATTACAGG
GCAAATTTCGCAAATAAAATAAAGATGAAG
Found at i:38415106 original size:15 final size:15
Alignment explanation
Indices: 38415086--38415120 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38415076 TATAAAATAT
* *
38415086 TTATTATTATTACTG
1 TTATTATTATCACTA
38415101 TTATTATTATCACTA
1 TTATTATTATCACTA
38415116 TTATT
1 TTATT
38415121 GTTGTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.60
Consensus pattern (15 bp):
TTATTATTATCACTA
Found at i:38415126 original size:24 final size:24
Alignment explanation
Indices: 38415090--38415145 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
38415080 AAATATTTAT
*
38415090 TATTATTACTGTTATT-ATTATCAC
1 TATTATTACTGTTATTAATGAT-AC
**
38415114 TATTATTGTTGTTATTAATGATAC
1 TATTATTACTGTTATTAATGATAC
38415138 TATTATTA
1 TATTATTA
38415146 ACCATCCTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (24 bp):
TATTATTACTGTTATTAATGATAC
Found at i:38415847 original size:17 final size:18
Alignment explanation
Indices: 38415827--38415896 Score: 65
Period size: 17 Copynumber: 3.9 Consensus size: 18
38415817 TCTATTTGGT
*
38415827 TTTTTTATT-AATTTAAA
1 TTTTTAATTAAATTTAAA
38415844 -TTTTAATTAAATTTAAA
1 TTTTTAATTAAATTTAAA
* **
38415861 -TTTAAAGCAAATTTAAA
1 TTTTTAATTAAATTTAAA
38415878 TTTTTACATTTAAATTTAA
1 TTTTTA-A-TTAAATTTAA
38415897 CCATGAATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
16 7 0.17
17 22 0.52
18 4 0.10
19 1 0.02
20 8 0.19
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (18 bp):
TTTTTAATTAAATTTAAA
Found at i:38415852 original size:16 final size:17
Alignment explanation
Indices: 38415836--38415896 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
38415826 TTTTTTTATT
38415836 AATTTAAATTTTAATTA
1 AATTTAAATTTTAATTA
* **
38415853 AATTTAAATTTAAAGCA
1 AATTTAAATTTTAATTA
38415870 AATTTAAATTTTTACATTTA
1 AATTTAAA-TTTTA-A-TTA
38415890 AATTTAA
1 AATTTAA
38415897 CCATGAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
17 22 0.63
18 4 0.11
19 1 0.03
20 8 0.23
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (17 bp):
AATTTAAATTTTAATTA
Found at i:38415859 original size:6 final size:6
Alignment explanation
Indices: 38415836--38415896 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
38415826 TTTTTTTATT
* **
38415836 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-GCA AATTTA AATTTTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA--TTTA
*
38415884 CATTTA AATTTA A
1 AATTTA AATTTA A
38415897 CCATGAATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
5 7 0.16
6 31 0.72
8 5 0.12
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:38416271 original size:38 final size:38
Alignment explanation
Indices: 38416219--38416780 Score: 357
Period size: 38 Copynumber: 15.8 Consensus size: 38
38416209 AAGACTTTGC
* *
38416219 TATCCAACTTTACTTCAATTTCAAGAGGAT-AAACTTGC
1 TATCC-ACTCTACTTCAATTTCAAGAGGATGAAACTTGT
*
38416257 TATCCAACTCTACTTCAATTTCAGGAGGATG--AC--G-
1 TATCC-ACTCTACTTCAATTTCAAGAGGATGAAACTTGT
* * *
38416291 T-TGCTCT-TACTTCAATTTC-AGA-GATGAAGACATGT
1 TATCCACTCTACTTCAATTTCAAGAGGATGAA-ACTTGT
*
38416326 TATCCACTCTACTTCAATTTCAAGGGGATG--AC--G-
1 TATCCACTCTACTTCAATTTCAAGAGGATGAAACTTGT
* * *
38416359 T-TGCTCT-TACTTCAATTTC-AGA-GATGAAGACATGT
1 TATCCACTCTACTTCAATTTCAAGAGGATGAA-ACTTGT
*
38416394 TATCCACTCTACTTCAATTTCAAGGGGATG--AC--G-
1 TATCCACTCTACTTCAATTTCAAGAGGATGAAACTTGT
* * * *
38416427 T-TGCTCT-TACTTCAATTTC-AGA-GATGTAGACGTGT
1 TATCCACTCTACTTCAATTTCAAGAGGATG-AAACTTGT
* *
38416462 TATCCACTCTACTTTAATTTCAAGGGGATG--AC--G-
1 TATCCACTCTACTTCAATTTCAAGAGGATGAAACTTGT
* * * *
38416495 T-TGCTCT-TACTTCAATTTC-GGA-GATGAAGACCTGT
1 TATCCACTCTACTTCAATTTCAAGAGGATGAA-ACTTGT
* * *
38416530 TATCCACTCTACTTCAATTTCAAGGGGATGGAGACGTGT
1 TATCCACTCTACTTCAATTTCAAGAGGAT-GAAACTTGT
38416569 TATCCACTCTACTTCAATTTCAAG-GG--G--AC--GT
1 TATCCACTCTACTTCAATTTCAAGAGGATGAAACTTGT
* **
38416600 CAT-TGCTCTTACTTCAATTTC-AGA-GATGAAGACGTT-T
1 TATCCACTC-TACTTCAATTTCAAGAGGATGAA-AC-TTGT
38416637 TATCCACTCTACTTCAATTTCAAG-GGATGAAGACGTT-T
1 TATCCACTCTACTTCAATTTCAAGAGGATGAA-AC-TTGT
*
38416675 TATCCACTCTACTTCAATTTCAAG-GGATGAAGACGTGT
1 TATCCACTCTACTTCAATTTCAAGAGGATGAA-ACTTGT
* *
38416713 TATCC-CTCTACTTCAATTTCAAGGGGATGAAGACGTGT
1 TATCCACTCTACTTCAATTTCAAGAGGATGAA-ACTTGT
38416751 TATCCACTCTACTTCAATTTCAAG-GGATGA
1 TATCCACTCTACTTCAATTTCAAGAGGATGA
38416781 CGTTGAGACC
Statistics
Matches: 427, Mismatches: 39, Indels: 116
0.73 0.07 0.20
Matches are distributed among these distances:
29 16 0.04
30 13 0.03
31 63 0.15
32 23 0.05
33 7 0.02
34 8 0.02
35 8 0.02
36 22 0.05
37 83 0.19
38 120 0.28
39 62 0.15
40 2 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (38 bp):
TATCCACTCTACTTCAATTTCAAGAGGATGAAACTTGT
Found at i:38416302 original size:31 final size:31
Alignment explanation
Indices: 38416267--38416521 Score: 162
Period size: 31 Copynumber: 7.7 Consensus size: 31
38416257 TATCCAACTC
38416267 TACTTCAATTTCAGGAGGATGACGTTGCTCT
1 TACTTCAATTTCAGGAGGATGACGTTGCTCT
* * * *
38416298 TACTTCAATTTCAGAGATGAAGACATGTTATCCACT
1 TACTTCAATTTCAG-GAGGATGAC--G-T-TGCTCT
38416334 CTACTTCAATTTCAAGG-GGATGACGTTGCTCT
1 -TACTTCAATTTC-AGGAGGATGACGTTGCTCT
* * * *
38416366 TACTTCAATTTCAGAGATGAAGACATGTTATCCACT
1 TACTTCAATTTCAG-GAGGATGAC--G-T-TGCTCT
38416402 CTACTTCAATTTCAAGG-GGATGACGTTGCTCT
1 -TACTTCAATTTC-AGGAGGATGACGTTGCTCT
* * *
38416434 TACTTCAATTTCAGAGATG-TAGACGTGTTATCCACT
1 TACTTCAATTTCAG-GAGGAT-GAC--G-T-TGCTCT
*
38416470 CTACTTTAATTTCAAGG-GGATGACGTTGCTCT
1 -TACTTCAATTTC-AGGAGGATGACGTTGCTCT
38416502 TACTTCAATTTC-GGA-GATGA
1 TACTTCAATTTCAGGAGGATGA
38416522 AGACCTGTTA
Statistics
Matches: 174, Mismatches: 24, Indels: 54
0.69 0.10 0.21
Matches are distributed among these distances:
29 7 0.04
30 4 0.02
31 52 0.30
32 28 0.16
33 3 0.02
34 6 0.03
35 3 0.02
36 26 0.15
37 39 0.22
38 6 0.03
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (31 bp):
TACTTCAATTTCAGGAGGATGACGTTGCTCT
Found at i:38416355 original size:68 final size:68
Alignment explanation
Indices: 38416228--38416785 Score: 569
Period size: 68 Copynumber: 8.0 Consensus size: 68
38416218 CTATCCAACT
* *
38416228 TTACTTCAATTTCAAGAGGAT-AA-ACTTGCTATCCAACTCTACTTCAATTTC-AGGAGGATGAC
1 TTACTTCAATTTC-AGA-GATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGG-GGATGAC
38416290 GTTGCTC
62 GTTGCTC
*
38416297 TTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
1 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
38416362 CTC
66 CTC
*
38416365 TTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
1 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
38416430 CTC
66 CTC
* *
38416433 TTACTTCAATTTCAGAGATGTAGACGTGTTATCCACTCTACTTTAATTTCAAGGGGATGACGTTG
1 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
38416498 CTC
66 CTC
* *
38416501 TTACTTCAATTTCGGAGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGATGGAGACG
1 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT---GAC-
* *
38416566 TGTTATCCAC
62 -G-T-TGCTC
* ** * * ** *
38416576 TCTACTTCAATTTCA-AG--G-GGACGTCAT-TGCTCT-TACTTCAATTTCAGAGATGAAGACGT
1 T-TACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCA-AGGGGATGACG-
* *
38416635 TTTATCCAC
63 --T-TGCTC
* * *
38416644 TCTACTTCAATTTCAAGGGATGAAGACGTTTTATCCACTCTACTTCAATTTCAAGGGATGAAGAC
1 T-TACTTCAATTTC-AGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGG--GATGAC
* *
38416709 GTGTTATCCC
62 --GTT-GCTC
*
38416719 TCTACTTCAATTTCAAGGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAA-GGGATGACG
1 T-TACTTCAATTTC-A-GAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
38416783 TTG
63 TTG
38416786 AGACCTGCAG
Statistics
Matches: 428, Mismatches: 34, Indels: 53
0.83 0.07 0.10
Matches are distributed among these distances:
66 1 0.00
67 3 0.01
68 247 0.58
69 26 0.06
70 14 0.03
71 14 0.03
72 6 0.01
73 13 0.03
74 8 0.02
75 40 0.09
76 55 0.13
78 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (68 bp):
TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
CTC
Found at i:38416580 original size:107 final size:106
Alignment explanation
Indices: 38416219--38416780 Score: 528
Period size: 107 Copynumber: 5.3 Consensus size: 106
38416209 AAGACTTTGC
* * *
38416219 TATCCAACTTTACTTCAATTTCAAGAGGAT-AA-ACTTGCTATCCAACTCTACTTCAATTTC-AG
1 TATCC-ACTCTACTTCAATTTCAAG-GGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAG
* * *
38416281 GAGGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGT
63 G-GGAAGACGTTGCTCTTACTTCAATTTCGGAGATGAAGACGTGT
* * * **
38416326 TATCCACTCTACTTCAATTTCAAGGG--GATGAC--G-T-TGCTCT-TACTTCAATTTCAGAGAT
1 TATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCA-AGGG
* * * ** *
38416384 GAAGACATGTTATCCACTCTACTTCAATTTC-AAGGGGATGAC--G-
65 GAAGAC--G-T-TGCTCT-TACTTCAATTTCGGAGATGAAGACGTGT
* * * * *
38416427 T-TGCTCT-TACTTCAATTTC-AGAGATGTAGACGTGTTATCCACTCTACTTTAATTTCAAGGGG
1 TATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGG
* *
38416489 ATGACGTTGCTCTTACTTCAATTTCGGAGATGAAGACCTGT
66 AAGACGTTGCTCTTACTTCAATTTCGGAGATGAAGACGTGT
*
38416530 TATCCACTCTACTTCAATTTCAAGGGGATGGAGACGTGTTATCCACTCTACTTCAATTTCAAGGG
1 TATCCACTCTACTTCAATTTCAA-GGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGG
* * * * *
38416595 GACGTCATTGCTCTTACTTCAATTTCAGAGATGAAGACGTTT
65 GAAGACGTTGCTCTTACTTCAATTTCGGAGATGAAGACGTGT
*
38416637 TATCCACTCTACTTCAATTTCAAGGGATGAAGACGTTTTATCCACTCTACTTCAATTTCAAGGGA
1 TATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGG-
* * *
38416702 TGAAGACGTGTTATCCCTCTACTTCAATTTCAAGGGGATGAAGACGTGT
65 -GAAGAC--GTT-GCTCT-TACTTCAATTTC--GGAGATGAAGACGTGT
38416751 TATCCACTCTACTTCAATTTCAAGGGATGA
1 TATCCACTCTACTTCAATTTCAAGGGATGA
38416781 CGTTGAGACC
Statistics
Matches: 372, Mismatches: 51, Indels: 57
0.77 0.11 0.12
Matches are distributed among these distances:
98 3 0.01
99 36 0.10
100 26 0.07
101 6 0.02
102 6 0.02
103 4 0.01
104 27 0.07
105 40 0.11
106 58 0.16
107 102 0.27
108 4 0.01
110 2 0.01
111 3 0.01
112 12 0.03
114 43 0.12
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (106 bp):
TATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGG
AAGACGTTGCTCTTACTTCAATTTCGGAGATGAAGACGTGT
Found at i:38416591 original size:175 final size:178
Alignment explanation
Indices: 38416298--38416785 Score: 628
Period size: 175 Copynumber: 2.8 Consensus size: 178
38416288 ACGTTGCTCT
* *
38416298 TACTTCAATTTC-AGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGG--GATGA-C-
1 TACTTCAATTTCAAGGGA-GAAGAC--GTTATCCACTCTACTTCAATTTC-AGGGATGAAGACCT
* * * *
38416358 GTT-GCTCT-TACTTCAATTTC-A-GAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGG
62 GTTATCCCTCTACTTCAATTTCAAGGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGG
*
38416419 GGATGACGTTGCTCTTACTTCAATTTCAGAGATGTAGACGTGTTATCCACTC
127 GGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTC
* * * *
38416471 TACTTTAATTTCAAGGG-GATGACG-T-TGCTCT-TACTTCAATTTC-GGAGATGAAGACCTGTT
1 TACTTCAATTTCAAGGGAGAAGACGTTATCCACTCTACTTCAATTTCAGG-GATGAAGACCTGTT
*
38416531 ATCCACTCTACTTCAATTTCAAGGGGATGGAGACGTGTTATCCACTCTACTTCAATTTCAAGGGG
65 ATCC-CTCTACTTCAATTTCAAGGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGG
* * * *
38416596 ACGTCATTGCTCTTACTTCAATTTCAGAGATGAAGACGTTTTATCCACTC
129 ATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTC
*
38416646 TACTTCAATTTCAAGGGATGAAGACGTTTTATCCACTCTACTTCAATTTCAAGGGATGAAGACGT
1 TACTTCAATTTCAAGGGA-GAAGACG--TTATCCACTCTACTTCAATTTC-AGGGATGAAGACCT
38416711 GTTATCCCTCTACTTCAATTTCAAGGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAA-G
62 GTTATCCCTCTACTTCAATTTCAAGGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGG
38416775 GGATGACGTTG
127 GGATGACGTTG
38416786 AGACCTGCAG
Statistics
Matches: 270, Mismatches: 25, Indels: 32
0.83 0.08 0.10
Matches are distributed among these distances:
165 2 0.01
166 1 0.00
167 12 0.04
168 8 0.03
169 2 0.01
170 4 0.01
171 1 0.00
172 7 0.03
173 23 0.09
174 4 0.01
175 100 0.37
177 6 0.02
180 1 0.00
181 13 0.05
182 67 0.25
183 17 0.06
184 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (178 bp):
TACTTCAATTTCAAGGGAGAAGACGTTATCCACTCTACTTCAATTTCAGGGATGAAGACCTGTTA
TCCCTCTACTTCAATTTCAAGGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT
GACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTC
Found at i:38428746 original size:59 final size:58
Alignment explanation
Indices: 38428676--38428933 Score: 392
Period size: 59 Copynumber: 4.4 Consensus size: 58
38428666 TGGATACCCG
* **
38428676 GGGGGCAAAATGGTAATTTTGGTGTAAATTAGGGTTAAAAATGGAATTTTAGAAGCTTC
1 GGGGGTAAAATGGTAATTTTGGTG-AAATCGGGGTTAAAAATGGAATTTTAGAAGCTTC
* *
38428735 GGGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATAGAATTTTAGAAGCTTC
1 GGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTC
*
38428794 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTT
1 GGGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTC
*
38428853 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACGGAATTTTAGAAGCTTC
1 GGGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTC
*
38428912 GGGGGTCAAAAT-ATAATTTTGG
1 GGGGGT-AAAATGGTAATTTTGG
38428934 AAAAGTTTTG
Statistics
Matches: 185, Mismatches: 11, Indels: 7
0.91 0.05 0.03
Matches are distributed among these distances:
58 6 0.03
59 167 0.90
60 12 0.06
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.31
Consensus pattern (58 bp):
GGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGCTTC
Found at i:38428752 original size:29 final size:29
Alignment explanation
Indices: 38428711--38428923 Score: 155
Period size: 29 Copynumber: 7.2 Consensus size: 29
38428701 AAATTAGGGT
38428711 TAAAAATGGAATTTTAGAAGCTTCGGGGG
1 TAAAAATGGAATTTTAGAAGCTTCGGGGG
* ** *
38428740 T-AAAATGGTAATTTTTGGTAA-AATCGGGGT
1 TAAAAATGG-AA-TTTTAG-AAGCTTCGGGGG
*
38428770 TAAAAATAGAATTTTAGAAGCTTCGGGGG
1 TAAAAATGGAATTTTAGAAGCTTCGGGGG
* ** ** *
38428799 T-AAAATGGTAATTTTCGGTGAAATCGGGGT
1 TAAAAATGG-AATTTTAGAAG-CTTCGGGGG
*
38428829 TAAAAATGGAATTTTAGAAGCTTTGGGGG
1 TAAAAATGGAATTTTAGAAGCTTCGGGGG
* ** ** *
38428858 T-AAAATGGTAATTTTCGGTGAAATCGGGGT
1 TAAAAATGG-AATTTTAGAAG-CTTCGGGGG
*
38428888 TAAAAACGGAATTTTAGAAGCTTCGGGGG
1 TAAAAATGGAATTTTAGAAGCTTCGGGGG
*
38428917 TCAAAAT
1 TAAAAAT
38428924 ATAATTTTGG
Statistics
Matches: 134, Mismatches: 39, Indels: 22
0.69 0.20 0.11
Matches are distributed among these distances:
28 22 0.16
29 48 0.36
30 43 0.32
31 21 0.16
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.31
Consensus pattern (29 bp):
TAAAAATGGAATTTTAGAAGCTTCGGGGG
Found at i:38428901 original size:30 final size:30
Alignment explanation
Indices: 38428682--38428902 Score: 123
Period size: 30 Copynumber: 7.4 Consensus size: 30
38428672 CCCGGGGGGC
**
38428682 AAAATGGTAATTTT-GGTGTAAATTAGGGTTA
1 AAAATGG-AATTTTCGGTG-AAATCGGGGTTA
* ** ** *
38428713 AAAATGGAATTTTAGAAG-CTTCGGGGGT-
1 AAAATGGAATTTTCGGTGAAATCGGGGTTA
* *
38428741 AAAATGGTAATTTTTGGTAAAATCGGGGTTA
1 AAAATGG-AATTTTCGGTGAAATCGGGGTTA
* * ** ** *
38428772 AAAATAGAATTTTAGAAG-CTTCGGGGGT-
1 AAAATGGAATTTTCGGTGAAATCGGGGTTA
38428800 AAAATGGTAATTTTCGGTGAAATCGGGGTTA
1 AAAATGG-AATTTTCGGTGAAATCGGGGTTA
* ** ** * *
38428831 AAAATGGAATTTTAGAAG-CTTTGGGGGT-
1 AAAATGGAATTTTCGGTGAAATCGGGGTTA
38428859 AAAATGGTAATTTTCGGTGAAATCGGGGTTA
1 AAAATGG-AATTTTCGGTGAAATCGGGGTTA
*
38428890 AAAACGGAATTTT
1 AAAATGGAATTTT
38428903 AGAAGCTTCG
Statistics
Matches: 136, Mismatches: 44, Indels: 21
0.68 0.22 0.10
Matches are distributed among these distances:
28 20 0.15
29 41 0.30
30 47 0.35
31 28 0.21
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (30 bp):
AAAATGGAATTTTCGGTGAAATCGGGGTTA
Found at i:38428917 original size:30 final size:30
Alignment explanation
Indices: 38428707--38428922 Score: 146
Period size: 30 Copynumber: 7.3 Consensus size: 30
38428697 GTGTAAATTA
38428707 GGGTTAAAAATGGAATTTTAGAAGCTTCGG
1 GGGTTAAAAATGGAATTTTAGAAGCTTCGG
* **
38428737 GGG-T-AAAATGGTAATTTTTGGTAA-AATC-G
1 GGGTTAAAAATGG-AA-TTTTAG-AAGCTTCGG
*
38428766 GGGTTAAAAATAGAATTTTAGAAGCTTCGG
1 GGGTTAAAAATGGAATTTTAGAAGCTTCGG
* ** **
38428796 GGG-T-AAAATGGTAATTTTCGGTGAAATC-G
1 GGGTTAAAAATGG-AATTTTAGAAG-CTTCGG
*
38428825 GGGTTAAAAATGGAATTTTAGAAGCTTTGG
1 GGGTTAAAAATGGAATTTTAGAAGCTTCGG
* ** **
38428855 GGG-T-AAAATGGTAATTTTCGGTGAAATC-G
1 GGGTTAAAAATGG-AATTTTAGAAG-CTTCGG
*
38428884 GGGTTAAAAACGGAATTTTAGAAGCTTCGG
1 GGGTTAAAAATGGAATTTTAGAAGCTTCGG
*
38428914 GGGTCAAAA
1 GGGTTAAAA
38428923 TATAATTTTG
Statistics
Matches: 137, Mismatches: 32, Indels: 34
0.67 0.16 0.17
Matches are distributed among these distances:
28 22 0.16
29 43 0.31
30 51 0.37
31 21 0.15
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (30 bp):
GGGTTAAAAATGGAATTTTAGAAGCTTCGG
Found at i:38428960 original size:32 final size:30
Alignment explanation
Indices: 38428913--38429083 Score: 297
Period size: 30 Copynumber: 5.6 Consensus size: 30
38428903 AGAAGCTTCG
38428913 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
38428943 GGGGTCAAAAAATATAATTTTGGAAAAGTTTT
1 GGGGTC--AAAATATAATTTTGGAAAAGTTTT
*
38428975 GGGGTTAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
38429005 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
38429035 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
**
38429065 GGGGTTGAAATATAATTTT
1 GGGGTCAAAATATAATTTT
38429084 TAGACAATTT
Statistics
Matches: 135, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
30 106 0.79
32 29 0.21
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.37
Consensus pattern (30 bp):
GGGGTCAAAATATAATTTTGGAAAAGTTTT
Found at i:38429406 original size:161 final size:162
Alignment explanation
Indices: 38429176--38429492 Score: 451
Period size: 161 Copynumber: 2.0 Consensus size: 162
38429166 ACTAATTCGA
* * * * *
38429176 AAACTTTGAAAAATTTTTGGACCAATTTTGTAATTAACTAAGAGTTAATTTAAGGACTAAATTAA
1 AAACCTTGAAAAATTATTGGACCAATTTCGTAATTAAATAAGAGCTAATTTAAGGACTAAATTAA
* *
38429241 AATAAATTAAAAATAGAAGGGACTAAATGCAGAAATAAGCCAA-AAATTGACACGTGGCAACCTC
66 AATAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAATAAA-TGACACGTGGCAACCTC
**
38429305 TGGTGCAGTCAAACAGTCAAAGGACTAGTTTAT
130 TGGCACAGTCAAACAGTCAAAGGACTAGTTTAT
* * * *
38429338 AAACCTTGAAAAATTATTGGGCCAATTTCGTAATTAAAATAA-AGCTGATTT-GGGATTAAATTA
1 AAACCTTGAAAAATTATTGGACCAATTTCGTAATT-AAATAAGAGCTAATTTAAGGACTAAATTA
* *
38429401 AAATAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAATACATGACACGTGGCAACCTC
65 AAATAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAATAAATGACACGTGGCAACCTC
*
38429466 TGGCACAGTCAAACAGTTAAAGGACTA
130 TGGCACAGTCAAACAGTCAAAGGACTA
38429493 AATTATAATC
Statistics
Matches: 137, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
161 92 0.67
162 40 0.29
163 5 0.04
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (162 bp):
AAACCTTGAAAAATTATTGGACCAATTTCGTAATTAAATAAGAGCTAATTTAAGGACTAAATTAA
AATAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAATAAATGACACGTGGCAACCTCT
GGCACAGTCAAACAGTCAAAGGACTAGTTTAT
Found at i:38429576 original size:161 final size:160
Alignment explanation
Indices: 38429227--38429561 Score: 390
Period size: 161 Copynumber: 2.1 Consensus size: 160
38429217 GAGTTAATTT
* *
38429227 AAGGACTAAATTAAAATAAATTAAAAATAGAAGGGACTAAATGCAGAAATAAGCCAAAAATTGAC
1 AAGGACTAAATTAAAATAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAATTGAC
** ** **
38429292 ACGTGGCAACCTCTGGTGCAGTCAAACAGTCAAAGGACTAGTTTATAAACCTTGAAAAATTATTG
66 ACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTATAAACCTT-AAAAATTACAG
* * * **
38429357 GGCCAATTTCGTAATTAAAATAAAGCTGATT
130 GGCAAATTTCGAAATTAAAATAAAGATGAAG
** * * *
38429388 TGGGATTAAATTAAAATAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAATACA-TGA
1 AAGGACTAAATTAAAATAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAA-AAATTGA
* *
38429452 CACGTGGCAACCTCTGGCACAGTCAAACAGTTAAAGGACTAAATTATAATCCAATT-AAAATTAC
65 CACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTATAAACC--TTAAAAATTAC
*
38429516 AGGGCAAATTT-GCAAATTATTAA-AAAGATGCAAG
128 AGGGCAAATTTCG-AAATTA-AAATAAAGATG-AAG
38429550 AAGGACTAAATT
1 AAGGACTAAATT
38429562 GAAGCAAATA
Statistics
Matches: 144, Mismatches: 24, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
160 1 0.01
161 127 0.88
162 14 0.10
163 2 0.01
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (160 bp):
AAGGACTAAATTAAAATAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAATTGAC
ACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTATAAACCTTAAAAATTACAGG
GCAAATTTCGAAATTAAAATAAAGATGAAG
Found at i:38430256 original size:15 final size:15
Alignment explanation
Indices: 38430236--38430270 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38430226 TATAAAATAT
* *
38430236 TTATTATTATTACTG
1 TTATTATTATCACTA
38430251 TTATTATTATCACTA
1 TTATTATTATCACTA
38430266 TTATT
1 TTATT
38430271 GTTGTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.60
Consensus pattern (15 bp):
TTATTATTATCACTA
Found at i:38430276 original size:24 final size:24
Alignment explanation
Indices: 38430240--38430295 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
38430230 AAATATTTAT
*
38430240 TATTATTACTGTTATT-ATTATCAC
1 TATTATTACTGTTATTAATGAT-AC
**
38430264 TATTATTGTTGTTATTAATGATAC
1 TATTATTACTGTTATTAATGATAC
38430288 TATTATTA
1 TATTATTA
38430296 ACCATCCTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (24 bp):
TATTATTACTGTTATTAATGATAC
Found at i:38431003 original size:17 final size:18
Alignment explanation
Indices: 38430981--38431024 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
38430971 GTTTTTTATT
38430981 AATTTAAATTTAA-AATA
1 AATTTAAATTTAACAATA
* *
38430998 AATTTAAATTTAACCATG
1 AATTTAAATTTAACAATA
38431016 AATTTAAAT
1 AATTTAAAT
38431025 CTTGTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (18 bp):
AATTTAAATTTAACAATA
Found at i:38433169 original size:279 final size:279
Alignment explanation
Indices: 38432660--38433225 Score: 952
Period size: 279 Copynumber: 2.0 Consensus size: 279
38432650 GAAAGGGGCT
* * * ** * *
38432660 TCCTTAGTGCTCAGATCTATCGAGTCAGTATTCCTCTCATACAAAACATCCTTGGCTAGCTAAAT
1 TCCTT-GTACTCAGATCTATCGAGTCAATATTCCTCCCATACAAAACATCCCCGACTAACTAAAT
*
38432725 TGCTGACAATACCTTGGTCCCAACCTTTATGTCTCGATTTATCGACACGGCAGATCGTGATTGCA
65 TGCTGACAATACCTTGGTCCCAACCTTTATGTCTCGATTTATCGACACAGCAGATCGTGATTGCA
38432790 GATCACCAAATATATGAATGCAATCATCAAAGGAAAAAGACACGCCTTAATTCTGTCAAGGAAGT
130 GATCACCAAATATATGAATGCAATCATCAAAGGAAAAAGACACGCCTTAATTCTGTCAAGGAAGT
* *
38432855 TCAAGCCAAGAACAAAATCATAGTCATTTAAACGAATTACCTTAAAATCTTCCTTGCCCTTCCAC
195 TCAAGCCAAGAACAAAATCATAGTCATCTAAACGAATTACCTCAAAATCTTCCTTGCCCTTCCAC
38432920 TCGTCGATTTGTAGCTTCAC
260 TCGTCGATTTGTAGCTTCAC
* *
38432940 TCCTTGTACTCAGATCTATCGAGTCAATATTCCTCCCATACAAAACATCCCCGATTAACTAGATT
1 TCCTTGTACTCAGATCTATCGAGTCAATATTCCTCCCATACAAAACATCCCCGACTAACTAAATT
*
38433005 GCTGACAATACCTTGGTCCCAACCTTTATGTCTCGATTTATCGACACATCAGATCGTGATTGCAG
66 GCTGACAATACCTTGGTCCCAACCTTTATGTCTCGATTTATCGACACAGCAGATCGTGATTGCAG
* * *
38433070 ATCACCAAATATATGAATGCAATCGTCAAAGGAAAAAGACATGCTTTAATTCTGTCAAGGAAGTT
131 ATCACCAAATATATGAATGCAATCATCAAAGGAAAAAGACACGCCTTAATTCTGTCAAGGAAGTT
*
38433135 CAAGCCAAGAACAAAATCATAGTCATCTAAACGAATTACCTCAAAATCTTCCTTGCCCTTCCATT
196 CAAGCCAAGAACAAAATCATAGTCATCTAAACGAATTACCTCAAAATCTTCCTTGCCCTTCCACT
* *
38433200 CGTCGATTTGTAGTTTTAC
261 CGTCGATTTGTAGCTTCAC
38433219 TCCTTGT
1 TCCTTGT
38433226 GTTACTCCCA
Statistics
Matches: 267, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
279 262 0.98
280 5 0.02
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (279 bp):
TCCTTGTACTCAGATCTATCGAGTCAATATTCCTCCCATACAAAACATCCCCGACTAACTAAATT
GCTGACAATACCTTGGTCCCAACCTTTATGTCTCGATTTATCGACACAGCAGATCGTGATTGCAG
ATCACCAAATATATGAATGCAATCATCAAAGGAAAAAGACACGCCTTAATTCTGTCAAGGAAGTT
CAAGCCAAGAACAAAATCATAGTCATCTAAACGAATTACCTCAAAATCTTCCTTGCCCTTCCACT
CGTCGATTTGTAGCTTCAC
Found at i:38441811 original size:36 final size:36
Alignment explanation
Indices: 38441764--38441836 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
38441754 CCGGCAGTTG
38441764 AACCGGGTTTTATTTAAAAGGCTTAATTAATGATTT
1 AACCGGGTTTTATTTAAAAGGCTTAATTAATGATTT
* *
38441800 AACCGGGTTTTATTTAGAAGGCTTAATTCATGATTT
1 AACCGGGTTTTATTTAAAAGGCTTAATTAATGATTT
38441836 A
1 A
38441837 GCCCCTGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.41
Consensus pattern (36 bp):
AACCGGGTTTTATTTAAAAGGCTTAATTAATGATTT
Found at i:38442414 original size:12 final size:11
Alignment explanation
Indices: 38442389--38442427 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
38442379 AAACATTTTA
*
38442389 TTTTTAAACTT
1 TTTTTAAAATT
38442400 TTTTTAAAATAT
1 TTTTTAAAAT-T
*
38442412 TTTTTATAATT
1 TTTTTAAAATT
38442423 TTTTT
1 TTTTT
38442428 TTACATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTAAAATT
Found at i:38442500 original size:15 final size:15
Alignment explanation
Indices: 38442482--38442516 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38442472 CAATTATCGT
*
38442482 TTTTTTTTTTGTAAA
1 TTTTTTTTTTATAAA
*
38442497 TTTTATTTTTATAAA
1 TTTTTTTTTTATAAA
38442512 TTTTT
1 TTTTT
38442517 CATAGTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTTTTTTTATAAA
Found at i:38445778 original size:30 final size:30
Alignment explanation
Indices: 38445744--38445808 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
38445734 ATACAAATTT
38445744 ATTGTTGAAAGAATGAAGACAATATGTTTA
1 ATTGTTGAAAGAATGAAGACAATATGTTTA
38445774 ATTGTTGAAAGAATGAAGACAATATGTTTA
1 ATTGTTGAAAGAATGAAGACAATATGTTTA
38445804 ATTGT
1 ATTGT
38445809 GGGGAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (30 bp):
ATTGTTGAAAGAATGAAGACAATATGTTTA
Found at i:38456229 original size:68 final size:66
Alignment explanation
Indices: 38456039--38456230 Score: 199
Period size: 69 Copynumber: 2.8 Consensus size: 66
38456029 TTTTTTCGAT
* *
38456039 GAGAATAACATGAAATCACAGTTTCATACAATCATTTCTCATAGTAAATAATATCTATTAAAAAG
1 GAGAATGACATGAAATCACAGTTTCATACTATC-TTT-TCATAGTAAATAATATCTATTAAAAAG
38456104 GAA
64 GAA
* * * * * * *
38456107 TAGGGATGTCATAAAATCATAGTTTCATA-TAATCTCTTCTCATAATAAAAAATATCTATTAAAA
1 GA-GAATGACATGAAATCACAGTTTCATACT-ATCT-TT-TCATAGTAAATAATATCTATTAAAA
38456171 A-GAGA
62 AGGA-A
*
38456176 GAGAATGACATGAAATCACAATTTCATACCGTATCTTTTCATAGTAAATAATATC
1 GAGAATGACATGAAATCACAGTTTCATA-C-TATCTTTTCATAGTAAATAATATC
38456231 ATCTCATTAA
Statistics
Matches: 100, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
68 40 0.40
69 55 0.55
70 4 0.04
71 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (66 bp):
GAGAATGACATGAAATCACAGTTTCATACTATCTTTTCATAGTAAATAATATCTATTAAAAAGGA
A
Found at i:38459564 original size:30 final size:29
Alignment explanation
Indices: 38459540--38459872 Score: 233
Period size: 30 Copynumber: 11.3 Consensus size: 29
38459530 CAAAAATTAT
*
38459540 CATTTT-ACCCCTAAACTTCCCAAAATTC
1 CATTTTAACCCCGAAACTTCCCAAAATTC
* *
38459568 CATTTTGACCCCAAAACTT-CCAACAATTAC
1 CATTTTAACCCCGAAACTTCCCAA-AATT-C
**
38459598 CATTTT-ACCCTTAAACTTCCCAAAATTC
1 CATTTTAACCCCGAAACTTCCCAAAATTC
38459626 CATTTTAAACCCC-AAAGCTTCCCAAAATTC
1 CATTTT-AACCCCGAAA-CTTCCCAAAATTC
*
38459656 CATTTTTAACCCCGAAGCTTCCCAAAATTC
1 CA-TTTTAACCCCGAAACTTCCCAAAATTC
* *
38459686 CATTTTTGACCCCGAAACTT-CCAAAAGTAC
1 CA-TTTTAACCCCGAAACTTCCCAAAA-TTC
* *
38459716 CATTTT-ACCCCCAAACTTTCCAAAATTC
1 CATTTTAACCCCGAAACTTCCCAAAATTC
** * *
38459744 CATTTTTAACTTCG--ATTTCATCAAAAATTAC
1 CA-TTTTAACCCCGAAACTTC--CCAAAATT-C
* *
38459775 CATTTT-ACCCCTAAACTTTCCAAAATTC
1 CATTTTAACCCCGAAACTTCCCAAAATTC
* *
38459803 CATTTATAACCTCG--ATTTCACCAAAAATTAC
1 CATTT-TAACCCCGAAACTTC-CC-AAAATT-C
**
38459834 CATTTT-ACCCTC-AAACTTTTCAAAATTC
1 CATTTTAACCC-CGAAACTTCCCAAAATTC
*
38459862 CTTTTTTAACC
1 C-ATTTTAACC
38459873 TCGATTTCAC
Statistics
Matches: 246, Mismatches: 31, Indels: 54
0.74 0.09 0.16
Matches are distributed among these distances:
28 46 0.19
29 78 0.32
30 101 0.41
31 21 0.09
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (29 bp):
CATTTTAACCCCGAAACTTCCCAAAATTC
Found at i:38459647 original size:88 final size:84
Alignment explanation
Indices: 38459540--38459813 Score: 277
Period size: 88 Copynumber: 3.1 Consensus size: 84
38459530 CAAAAATTAT
*
38459540 CATTTT-ACCCCTAAACTTCCCAAAATTCCA-TTTTGACCCCAAAACTTCCAACAATTACCATTT
1 CATTTTAACCCC-AAACTTCCCAAAATTCCATTTTTAACCCC-AAACTTCCAA-AATTACCATTT
*
38459603 TACCCTTAAACTTCCCAAAATTC
63 TACCCCTAAACTT-CCAAAATTC
*
38459626 CATTTTAAACCCCAAAGCTTCCCAAAATTCCATTTTTAACCCCGAAGCTTCCCAAAATT-CCATT
1 CATTTT-AACCCCAAA-CTTCCCAAAATTCCATTTTTAACCCC-AAACTT-CCAAAATTACCA-T
* *
38459690 TTTGACCCCGAAACTTCCAAAAGTAC
61 TTT-ACCCCTAAACTTCCAAAA-TTC
* * ** * *
38459716 CATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACTTC-GATTTCATCAAAAATTACCATTT
1 CATTTTAACCCCAAACTTCCCAAAATTCCATTTTTAACCCCAAACTTC--C-AAAATTACCATTT
38459780 TACCCCTAAACTTTCCAAAATTC
63 TACCCCTAAAC-TTCCAAAATTC
38459803 CATTTATAACC
1 CATTT-TAACC
38459814 TCGATTTCAC
Statistics
Matches: 158, Mismatches: 16, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
85 1 0.01
86 8 0.05
87 20 0.13
88 68 0.43
89 39 0.25
90 22 0.14
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (84 bp):
CATTTTAACCCCAAACTTCCCAAAATTCCATTTTTAACCCCAAACTTCCAAAATTACCATTTTAC
CCCTAAACTTCCAAAATTC
Found at i:38459778 original size:59 final size:59
Alignment explanation
Indices: 38459495--38460024 Score: 555
Period size: 59 Copynumber: 9.0 Consensus size: 59
38459485 CTAGTCCCCG
*** * *
38459495 AACTTTCCAAAATTCCA-TTTTAACCTTAATTTCATCAAAAATTATCATTTTACCCCTA
1 AACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTA
* * * * * *
38459553 AACTTCCCAAAATTCCA-TTTTGACCCCAAAACTT--CCAACAATTACCATTTTACCCTTA
1 AACTTTCCAAAATTCCATTTTTAACCCC--GATTTCACCAAAAATTACCATTTTACCCCTA
* * * * *
38459611 AACTTCCCAAAATTCCATTTTAAACCCCAAAGCTTC-CC-AAAATT-CCATTTTTAACCCCGA
1 AACTTTCCAAAATTCCATTTTTAACCCC-GA-TTTCACCAAAAATTACCA-TTTT-ACCCCTA
* * * * * *
38459671 AGCTTCCCAAAATTCCATTTTTGACCCCGAAACTT--CC-AAAAGTACCATTTTACCCCCA
1 AACTTTCCAAAATTCCATTTTTAACCCCG--ATTTCACCAAAAATTACCATTTTACCCCTA
** *
38459729 AACTTTCCAAAATTCCATTTTTAACTTCGATTTCATCAAAAATTACCATTTTACCCCTA
1 AACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTA
* *
38459788 AACTTTCCAAAATTCCATTTATAACCTCGATTTCACCAAAAATTACCATTTTA-CCCTCA
1 AACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCT-A
* * * * * *
38459847 AACTTTTCAAAATTCCTTTTTTAACCTCGATTTCACCAAAAATTACCATTTTGCCTCTG
1 AACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTA
* *
38459906 AACTTTCTAAAA-TCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTGCCCCTA
1 AACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTA
*
38459964 AACTTTCCAAAA-TCCTATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCTCTA
1 AACTTTCCAAAATTCC-ATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTA
38460023 AA
1 AA
38460025 GTCAAAAATT
Statistics
Matches: 409, Mismatches: 47, Indels: 31
0.84 0.10 0.06
Matches are distributed among these distances:
56 3 0.01
58 157 0.38
59 203 0.50
60 45 0.11
61 1 0.00
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (59 bp):
AACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTA
Found at i:38459903 original size:29 final size:30
Alignment explanation
Indices: 38459737--38460020 Score: 133
Period size: 29 Copynumber: 9.7 Consensus size: 30
38459727 CAAACTTTCC
* *
38459737 AAAATT-CCATTTTTAACTTCGATTTCATCA
1 AAAATTACCA-TTTTAACCTCGATTTCACCA
* **
38459767 AAAATTACCATTTTACCCCTAAACTTT--CC-
1 AAAATTACCATTTTA-ACCTCGA-TTTCACCA
38459796 AAAATT-CCATTTATAACCTCGATTTCACCA
1 AAAATTACCATTT-TAACCTCGATTTCACCA
* * *
38459826 AAAATTACCATTTTACCCTCAAACTTT--TC-
1 AAAATTACCATTTTAACCTC-GA-TTTCACCA
*
38459855 AAAATT-CCTTTTTTAACCTCGATTTCACCA
1 AAAATTACC-ATTTTAACCTCGATTTCACCA
* *
38459885 AAAATTACCATTTT-GCCTCTGAACTTT---CT
1 AAAATTACCATTTTAACCTC-G-A-TTTCACCA
*
38459914 AAAA-T-CCATTTTTAACCCCGATTTCACCA
1 AAAATTACCA-TTTTAACCTCGATTTCACCA
** **
38459943 AAAATTACCATTTTGCCCCTAAACTTT--CC-
1 AAAATTACCATTTT-AACCTCGA-TTTCACCA
*
38459972 AAAA-T-CCTATTTTTAACCCCGATTTCACCA
1 AAAATTACC-A-TTTTAACCTCGATTTCACCA
38460002 AAAATTACCATTTT-ACCTC
1 AAAATTACCATTTTAACCTC
38460021 TAAAGTCAAA
Statistics
Matches: 188, Mismatches: 32, Indels: 69
0.65 0.11 0.24
Matches are distributed among these distances:
26 3 0.02
27 15 0.08
28 24 0.13
29 57 0.30
30 51 0.27
31 24 0.13
32 14 0.07
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAATTACCATTTTAACCTCGATTTCACCA
Found at i:38473542 original size:18 final size:18
Alignment explanation
Indices: 38473516--38473551 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38473506 CCACCAAAAA
38473516 TAAAATATACATTTAAAT
1 TAAAATATACATTTAAAT
* *
38473534 TAAATTATATATTTAAAT
1 TAAAATATACATTTAAAT
38473552 ATTATATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATATACATTTAAAT
Found at i:38475375 original size:27 final size:27
Alignment explanation
Indices: 38475345--38475428 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
38475335 ATGTATAAAC
38475345 CTCTAAATTCCATGGCGATTCTTCAAT
1 CTCTAAATTCCATGGCGATTCTTCAAT
*** * * * *
38475372 CTCTGCCTTTCC-TTGC-ATAT-ATAAAC
1 CTCT-AAATTCCATGGCGAT-TCTTCAAT
38475398 CTCTAAATTCCATGGCGATTCTTCAAT
1 CTCTAAATTCCATGGCGATTCTTCAAT
38475425 CTCT
1 CTCT
38475429 GCCGGAACCA
Statistics
Matches: 38, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
25 4 0.11
26 13 0.34
27 17 0.45
28 4 0.11
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.38
Consensus pattern (27 bp):
CTCTAAATTCCATGGCGATTCTTCAAT
Found at i:38475406 original size:53 final size:53
Alignment explanation
Indices: 38475326--38475431 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
38475316 TAAAGGAGTT
*
38475326 TTTCCTTGCATGTATAAACCTCTAAATTCCATGGCGATTCTTCAATCTCTGCC
1 TTTCCTTGCATATATAAACCTCTAAATTCCATGGCGATTCTTCAATCTCTGCC
38475379 TTTCCTTGCATATATAAACCTCTAAATTCCATGGCGATTCTTCAATCTCTGCC
1 TTTCCTTGCATATATAAACCTCTAAATTCCATGGCGATTCTTCAATCTCTGCC
38475432 GGAACCATTA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.24, C:0.28, G:0.10, T:0.38
Consensus pattern (53 bp):
TTTCCTTGCATATATAAACCTCTAAATTCCATGGCGATTCTTCAATCTCTGCC
Done.