Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012649.1 Kokia drynarioides strain JFW-HI SEQ_127659, whole genome shotgun sequence
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: 205193
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 229 characters in sequence are not A, C, G, or T
Found at i:8680 original size:28 final size:28
Alignment explanation
Indices: 8625--8680 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
8615 GACCAATTCA
* *
8625 AAAAGTATAAGATTAAAATTAATCAAAT
1 AAAAGTACAAGATTAAAATTAATAAAAT
*
8653 AAAAGTACAAGGATT-AAATTTATAAAAT
1 AAAAGTACAA-GATTAAAATTAATAAAAT
8681 TTACAACGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.59, C:0.04, G:0.09, T:0.29
Consensus pattern (28 bp):
AAAAGTACAAGATTAAAATTAATAAAAT
Found at i:10769 original size:27 final size:28
Alignment explanation
Indices: 10725--10785 Score: 97
Period size: 27 Copynumber: 2.2 Consensus size: 28
10715 AAATAAGACT
*
10725 TTTTTGATACTCGAAGGCAAAATGGTAA
1 TTTTGGATACTCGAAGGCAAAATGGTAA
*
10753 TTTTGGATTCTCG-AGGCAAAATGGTAA
1 TTTTGGATACTCGAAGGCAAAATGGTAA
10780 TTTTGG
1 TTTTGG
10786 GAAAATTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 20 0.65
28 11 0.35
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.36
Consensus pattern (28 bp):
TTTTGGATACTCGAAGGCAAAATGGTAA
Found at i:10915 original size:29 final size:29
Alignment explanation
Indices: 10883--11109 Score: 98
Period size: 30 Copynumber: 7.7 Consensus size: 29
10873 TGGCATTCGG
*
10883 GGGTAAAATGGTAATTTTTGAAAGTTTTA
1 GGGTAAAATGGTAATTTTTGAAAGTTTGA
* *
10912 GGGTCAAAAATGG-AATTTTTGGAGGTTTGA
1 GGGT--AAAATGGTAATTTTTGAAAGTTTGA
* ** *
10942 GTGTAAAA-GTGTAATTTTAAAAAATTTCGA
1 GGGTAAAATG-GTAATTTTTGAAAGTTT-GA
* *
10972 GGTTGAAAATGG-AATTTTTGGAAA-TTCG-
1 GGGT-AAAATGGTAATTTTT-GAAAGTTTGA
11000 GGGATAAAAAAT-GTAATTTTTGAAAGTTTCGA
1 GGG-T--AAAATGGTAATTTTTGAAAGTTT-GA
* * * *
11032 GGTTAAAAATAG-AATTTTTGGATGTTTG-
1 GGGT-AAAATGGTAATTTTTGAAAGTTTGA
* *
11060 GGGCTAAATAT-ATAATTTTCGAAAGTTTCGA
1 GGG-TAAA-ATGGTAATTTTTGAAAGTTT-GA
*
11091 -AGTCAAAATGG-AATTTTTG
1 GGGT-AAAATGGTAATTTTTG
11110 GACAGTTTAG
Statistics
Matches: 148, Mismatches: 28, Indels: 44
0.67 0.13 0.20
Matches are distributed among these distances:
27 1 0.01
28 12 0.08
29 47 0.32
30 67 0.45
31 18 0.12
32 3 0.02
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.37
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTGAAAGTTTGA
Found at i:10948 original size:59 final size:58
Alignment explanation
Indices: 10859--11122 Score: 230
Period size: 59 Copynumber: 4.5 Consensus size: 58
10849 AATAGGGATA
* * * * *
10859 AAAAATGGAAGTTTTGGCA-TTCGGGGGTAAAATGGTAATTTTTGAAAGTTT-TAGGGTC
1 AAAAATGGAATTTTTGGAAGTTTGGGGATAAAAT-GTAATTTTTGAAAGTTTCGA-GGTC
* * ** * *
10917 AAAAATGGAATTTTTGGAGGTTTGAGTG-TAAAAGTGTAATTTTAAAAAATTTCGAGGTT
1 AAAAATGGAATTTTTGGAAGTTTG-GGGATAAAA-TGTAATTTTTGAAAGTTTCGAGGTC
* * * *
10976 GAAAATGGAATTTTTGGAAATTCGGGGATAAAAAATGTAATTTTTGAAAGTTTCGAGGTT
1 AAAAATGGAATTTTTGGAAGTTTGGGGAT--AAAATGTAATTTTTGAAAGTTTCGAGGTC
* * * * * *
11036 AAAAATAGAATTTTTGGATGTTTGGGGCTAAATATATAATTTTCGAAAGTTTCGAAGTC
1 AAAAATGGAATTTTTGGAAGTTTGGGGATAAA-ATGTAATTTTTGAAAGTTTCGAGGTC
*
11095 -AAAATGGAATTTTTGGACAGTTTAGGGA
1 AAAAATGGAATTTTTGGA-AGTTTGGGGA
11123 CCTACAGAGC
Statistics
Matches: 165, Mismatches: 32, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
58 37 0.22
59 75 0.45
60 49 0.30
61 4 0.02
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAAGTTTGGGGATAAAATGTAATTTTTGAAAGTTTCGAGGTC
Found at i:10997 original size:30 final size:30
Alignment explanation
Indices: 10887--11053 Score: 112
Period size: 30 Copynumber: 5.6 Consensus size: 30
10877 ATTCGGGGGT
* *
10887 AAAATGGTAATTTTT-GAAAGTTT-TAGGGTCA
1 AAAATGG-AATTTTTGGAAA-TTTCGA-GGTTA
**
10918 AAAATGGAATTTTTGGAGGTTT-GA-GTGTA
1 AAAATGGAATTTTTGGAAATTTCGAGGT-TA
* * *** *
10947 AAAGTGTAATTTTAAAAAATTTCGAGGTTG
1 AAAATGGAATTTTTGGAAATTTCGAGGTTA
* *
10977 AAAATGGAATTTTTGGAAA-TTCGGGGATAA
1 AAAATGGAATTTTTGGAAATTTCGAGG-TTA
*
11007 AAAATGTAATTTTT-GAAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAA-TTTCGAGGTTA
*
11037 AAAATAGAATTTTTGGA
1 AAAATGGAATTTTTGGA
11054 TGTTTGGGGC
Statistics
Matches: 103, Mismatches: 25, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
28 2 0.02
29 26 0.25
30 56 0.54
31 19 0.18
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAATTTCGAGGTTA
Found at i:11047 original size:119 final size:117
Alignment explanation
Indices: 10860--11111 Score: 289
Period size: 119 Copynumber: 2.1 Consensus size: 117
10850 ATAGGGATAA
* * * * *
10860 AAAATGGAAGTTTTGG-CATTCGGGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAAATG
1 AAAATGGAATTTTTGGAAATTCGGGGATAAAATGGTAATTTTTGAAAGTTTGAGGGTCAAAAATA
* * * *
10924 GAATTTTTGGAGGTTTGAGTG-TAAA-AGTGTAATTTTAAAAAATTTCGAGGTTG
66 GAATTTTTGGAGGTTTG-GGGCTAAATA-TATAATTTTAAAAAATTTCGAAG-TC
*
10977 AAAATGGAATTTTTGGAAATTCGGGGATAAAAAAT-GTAATTTTTGAAAGTTTCGA-GGTTAAAA
1 AAAATGGAATTTTTGGAAATTCGGGGAT--AAAATGGTAATTTTTGAAAGTTT-GAGGGTCAAAA
* ** *
11040 ATAGAATTTTTGGATGTTTGGGGCTAAATATATAATTTTCGAAAGTTTCGAAGTC
63 ATAGAATTTTTGGAGGTTTGGGGCTAAATATATAATTTTAAAAAATTTCGAAGTC
11095 AAAATGGAATTTTTGGA
1 AAAATGGAATTTTTGGA
11112 CAGTTTAGGG
Statistics
Matches: 115, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
117 15 0.13
118 29 0.25
119 64 0.56
120 7 0.06
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (117 bp):
AAAATGGAATTTTTGGAAATTCGGGGATAAAATGGTAATTTTTGAAAGTTTGAGGGTCAAAAATA
GAATTTTTGGAGGTTTGGGGCTAAATATATAATTTTAAAAAATTTCGAAGTC
Found at i:12280 original size:3 final size:3
Alignment explanation
Indices: 12274--12309 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
12264 AATTTGTTAT
12274 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12310 ATGATACTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:13017 original size:6 final size:6
Alignment explanation
Indices: 12991--13059 Score: 72
Period size: 6 Copynumber: 11.8 Consensus size: 6
12981 GTTTAAAATT
* **
12991 ATTTCAA ATTTAA A-CTAA ATTTAA ATTTAA A-ACAA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
13038 ATTTAA A-GTAA ATTTAA ATTTA
1 ATTTAA ATTTAA ATTTAA ATTTA
13060 GAAATAAATC
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
5 11 0.22
6 36 0.71
7 4 0.08
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:13032 original size:23 final size:23
Alignment explanation
Indices: 13006--13059 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
12996 AAATTTAAAC
13006 TAAATTTAAATTTAAAACAAATT
1 TAAATTTAAATTTAAAACAAATT
**
13029 TAAATTTAAATTTAAAGTAAATT
1 TAAATTTAAATTTAAAACAAATT
13052 TAAATTTA
1 TAAATTTA
13060 GAAATAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TAAATTTAAATTTAAAACAAATT
Found at i:13049 original size:17 final size:18
Alignment explanation
Indices: 13029--13073 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
13019 AAAACAAATT
*
13029 TAAATTTAAATTTA-AAG
1 TAAATTTAAATTTAGAAA
13046 TAAATTTAAATTTAGAAA
1 TAAATTTAAATTTAGAAA
*
13064 TAAATCTAAA
1 TAAATTTAAA
13074 AATTAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (18 bp):
TAAATTTAAATTTAGAAA
Found at i:13067 original size:23 final size:23
Alignment explanation
Indices: 13006--13067 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
12996 AAATTTAAAC
* **
13006 TAAATTTAAATTTAAAACAAATT
1 TAAATTTAAATATAAAGTAAATT
*
13029 TAAATTTAAATTTAAAGTAAATT
1 TAAATTTAAATATAAAGTAAATT
13052 TAAATTTAGAA-ATAAA
1 TAAATTTA-AATATAAA
13068 TCTAAAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 33 0.94
24 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (23 bp):
TAAATTTAAATATAAAGTAAATT
Found at i:13073 original size:18 final size:17
Alignment explanation
Indices: 12976--13038 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
12966 ATTTTAAAGT
* *
12976 TTTAAGTTTAAAAT-TA
1 TTTAAATTTAAAATAAA
*
12992 TTTCAAATTTAAACTAAA
1 TTT-AAATTTAAAATAAA
*
13010 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
13027 TTTAAATTTAAA
1 TTTAAATTTAAA
13039 TTTAAAGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
16 3 0.08
17 33 0.82
18 4 0.10
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:14009 original size:70 final size:67
Alignment explanation
Indices: 13883--14015 Score: 167
Period size: 70 Copynumber: 1.9 Consensus size: 67
13873 ATAAACAATA
* * * * * *
13883 TAATGGTTTTGTCTTTTAACTTAATGGGTAAACATTTATCAAAATGTCATAATTTTACTTTTTAA
1 TAATGGTTTTGACTTTCAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
13948 CT
66 CT
* *
13950 TAATGGTTTTGACTTTCAACTTTAGAAAGGGTAAACATTTATCAAAACGACGTAGTTTTACCTTT
1 TAATGGTTTTGACTTTCAAC-TT--AAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTT
14015 T
63 T
14016 CTTATTCGGA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
67 18 0.33
68 2 0.04
70 35 0.64
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.44
Consensus pattern (67 bp):
TAATGGTTTTGACTTTCAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
CT
Found at i:15093 original size:70 final size:71
Alignment explanation
Indices: 14868--15144 Score: 371
Period size: 71 Copynumber: 3.9 Consensus size: 71
14858 TCTAAAATTA
* * * * *
14868 ACTGAAACATACACCAAACATTTGGTGATCATCTTTGAATGTCATGGTTTAATATCAGAGACATC
1 ACTGAAACAGACACCAAACACTTGATGATCATCTTTAAATGTCATGATTTAATATCAGAGACATC
*
14933 TGTCTA
66 TGTCTC
* * *
14939 ACTGAAACAGACACCAAACACTTGATGATCATATTTGAATGTCATGATTTAATATCAGAGATATC
1 ACTGAAACAGACACCAAACACTTGATGATCATCTTTAAATGTCATGATTTAATATCAGAGACATC
15004 TGTCTC
66 TGTCTC
* *
15010 ACTGAAACCGACACCAAACACTTGATGA-CAATTTTTAAATGTCATG-TTTAATATCAGAGACAT
1 ACTGAAACAGACACCAAACACTTGATGATC-ATCTTTAAATGTCATGATTTAATATCAGAGACAT
*
15073 TTGTCTC
65 CTGTCTC
* * * *
15080 ACTAAAACAGACACCAAACATTTAGTTG-TCATCTTTAAATGTCATGATTTAATATCAGAAACAT
1 ACTGAAACAGACACCAAACACTT-GATGATCATCTTTAAATGTCATGATTTAATATCAGAGACAT
15144 C
65 C
15145 ACTTACAATA
Statistics
Matches: 183, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
70 58 0.32
71 125 0.68
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (71 bp):
ACTGAAACAGACACCAAACACTTGATGATCATCTTTAAATGTCATGATTTAATATCAGAGACATC
TGTCTC
Found at i:15123 original size:141 final size:142
Alignment explanation
Indices: 14868--15138 Score: 386
Period size: 141 Copynumber: 1.9 Consensus size: 142
14858 TCTAAAATTA
* * * *
14868 ACTGAAACATACACCAAACATTTGGTGATCATCTTTGAATGTCATGGTTTAATATCAGAGACATC
1 ACTGAAACAGACACCAAACACTTGATGATCATCTTTAAATGTCATGGTTTAATATCAGAGACATC
* *
14933 TGTCTAACTGAAACAGACACCAAACACTTGATGATCATATTTGAATGTCATGATTTAATATCAGA
66 TGTCTAACTAAAACAGACACCAAACACTTGATGATCATATTTAAATGTCATGATTTAATATCAGA
14998 GATATCTGTCTC
131 GATATCTGTCTC
* *
15010 ACTGAAACCGACACCAAACACTTGATGA-CAATTTTTAAATGTCAT-GTTTAATATCAGAGACAT
1 ACTGAAACAGACACCAAACACTTGATGATC-ATCTTTAAATGTCATGGTTTAATATCAGAGACAT
* * * * *
15073 TTGTCTCACTAAAACAGACACCAAACATTTAGTTG-TCATCTTTAAATGTCATGATTTAATATCA
65 CTGTCTAACTAAAACAGACACCAAACACTT-GATGATCATATTTAAATGTCATGATTTAATATCA
15137 GA
129 GA
15139 AACATCACTT
Statistics
Matches: 114, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
141 74 0.65
142 40 0.35
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (142 bp):
ACTGAAACAGACACCAAACACTTGATGATCATCTTTAAATGTCATGGTTTAATATCAGAGACATC
TGTCTAACTAAAACAGACACCAAACACTTGATGATCATATTTAAATGTCATGATTTAATATCAGA
GATATCTGTCTC
Found at i:16493 original size:71 final size:70
Alignment explanation
Indices: 16411--16673 Score: 294
Period size: 71 Copynumber: 3.7 Consensus size: 70
16401 AAACATAAAC
* *
16411 CAAACATTTGGTAGCCATATTTAAATGTCATGATTTAATATCAGAGACATCTGTCTAACTGAAAC
1 CAAACACTTGGTAGCCATATTTGAATGTCATGATTTAATATCAGAGACATCTGTCTAACTGAAAC
*
16476 AAACA
66 AGACA
* ** * * * *
16481 TCAAACACTTGGTGGTTATCTTTGAATGTCATGATTTAATATCAAACACATCTGTCTAACTGAAT
1 -CAAACACTTGGTAGCCATATTTGAATGTCATGATTTAATATCAGAGACATCTGTCTAACTGAAA
16546 CAGACA
65 CAGACA
* * * * *
16552 CTAAACACTTGGTAACCATCTTTGAATGTCATGGTTTAATATTAGAGACATCTGTTTAACT-AGA
1 C-AAACACTTGGTAGCCATATTTGAATGTCATGATTTAATATCAGAGACATCTGTCTAACTGA-A
*
16616 ATAGACA
64 ACAGACA
* * * * *
16623 CCAAACGCTTGATGGCCATATTTGAATGTCATGGTTTAATTTCAGAGACAT
1 -CAAACACTTGGTAGCCATATTTGAATGTCATGATTTAATATCAGAGACAT
16674 TTGTTACAAT
Statistics
Matches: 161, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
70 2 0.01
71 158 0.98
72 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (70 bp):
CAAACACTTGGTAGCCATATTTGAATGTCATGATTTAATATCAGAGACATCTGTCTAACTGAAAC
AGACA
Found at i:18648 original size:225 final size:222
Alignment explanation
Indices: 18114--18720 Score: 937
Period size: 225 Copynumber: 2.7 Consensus size: 222
18104 GCAAGCAGTA
* * *
18114 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACAAAACACTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGTTAA
* *
18179 TTTTGAATGCTACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGATT
66 TTTTGAATGCTACGGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
** * * *
18244 GTCACGTAACTATCTTTAATACTTCTCAAACTTTCACTTAATGATTTTTTTTTTTTTTTTGTGTT
131 GTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCAATTAATGATTTTTTTTTTTTTGTTGTGTT
* *
18309 TATCCACCTGCTTGTCCCCTCCTTCCC
196 TATCCACCTGCTTGCCCCCTCATTCCC
* * *
18336 TCTTGTACTAAGCCAATAATGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGTCAA
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGTTAA
18401 TTTTGAATGCTACGGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
66 TTTTGAATGCTACGGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
*
18466 GTCTCGTGGCTGTCTTTAATACTTCTCAAACTTTCAATTAAT-ATTTTTTTTCCGATTTTTGTTG
131 GTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCAATTAATGATTTTTTTT----TTTTTGTTG
**
18530 TGTTTATCCATTTGCTTGCCCCCTCATTCCC
192 TGTTTATCCACCTGCTTGCCCCCTCATTCCC
* * *
18561 TCTTCTACTAAACCAAAAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGTTAG
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGTTAA
* * * *
18626 TTTTGAATGCTATGGTTTAATGTCAGAGGTATCTCTCTTACAGTAAAAAGCACAAAAGATGGCTT
66 TTTTGAATGCTACGGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
*
18691 GTCACGTGGTTGTCTTTAATACTTCTCAAA
131 GTCACGTGGCTGTCTTTAATACTTCTCAAA
18721 AGGTGGCCAT
Statistics
Matches: 351, Mismatches: 30, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
221 9 0.03
222 159 0.45
225 183 0.52
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (222 bp):
TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGTTAA
TTTTGAATGCTACGGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
GTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCAATTAATGATTTTTTTTTTTTTGTTGTGTT
TATCCACCTGCTTGCCCCCTCATTCCC
Found at i:18904 original size:197 final size:198
Alignment explanation
Indices: 18532--18917 Score: 560
Period size: 197 Copynumber: 2.0 Consensus size: 198
18522 TTTTGTTGTG
** *
18532 TTTATCCATTTGCTTGCCCCCTCATTCCCTCTTCTACTAAACCAAAAAGGAATCTAAAACTAATT
1 TTTATCCACCTGCTTGCCCCCTCAGTCCCTCTTCTACTAAACCAAAAAGGAATCTAAAACTAATT
* *** * **
18597 GAAACAGACACCAAACACTTGGTGGTTAGTTTTGAATGCTATGGTTTAATGTCAGAGGTATCTCT
66 GAAACAGACACCAAACACTTGGTGGTTAGTTTTGAATGCCACAATTTAATGTCAAAGACATCTCT
* * *
18662 CTTACAGTAAAAAGCACAAAAGATGGCTTGTCACGTGGTTGTCTTTAATACTTCTCAAAAGGTGG
131 CTTACAATAAAAAGCACAAAAGATGGCTTGTCACATGGCTGTCTTTAATACTTCTCAAAAGGTGG
18727 CCA
196 CCA
* * * * *
18730 TTTATCCACCTGCTTG-CCCCTCCGTCTCTCTTGTACTAAACCAATAAGGAATTTAAAACTAATT
1 TTTATCCACCTGCTTGCCCCCTCAGTCCCTCTTCTACTAAACCAAAAAGGAATCTAAAACTAATT
* *
18794 GAAACAGACACCAAACACTTGGTGGTTATTTTTGAATGCCACAATTTAATGTCAAAGACATTTCT
66 GAAACAGACACCAAACACTTGGTGGTTAGTTTTGAATGCCACAATTTAATGTCAAAGACATCTCT
*
18859 GTTACAATAAAAAGCACAAAAGATGGGC-TGTCACATGGCTGTCTTTAATACTTCTCAAA
131 CTTACAATAAAAAGCACAAAAGAT-GGCTTGTCACATGGCTGTCTTTAATACTTCTCAAA
18918 CTTTAACTTA
Statistics
Matches: 166, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
197 149 0.90
198 17 0.10
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (198 bp):
TTTATCCACCTGCTTGCCCCCTCAGTCCCTCTTCTACTAAACCAAAAAGGAATCTAAAACTAATT
GAAACAGACACCAAACACTTGGTGGTTAGTTTTGAATGCCACAATTTAATGTCAAAGACATCTCT
CTTACAATAAAAAGCACAAAAGATGGCTTGTCACATGGCTGTCTTTAATACTTCTCAAAAGGTGG
CCA
Found at i:19270 original size:427 final size:423
Alignment explanation
Indices: 18307--19394 Score: 1556
Period size: 427 Copynumber: 2.6 Consensus size: 423
18297 TTTTTTTGTG
* * * *
18307 TTTATCCACCTGCTTGTCCCCTCCTTCCCTCTTGTACTAAGCCAATAATGAATCTAAAACTAATT
1 TTTATCCACCTGCTT-CCCCCTCCTTCCCTCTTGTACTAAACCAATAAGGAATTTAAAACTAATT
* *
18372 GAAACAGACACCAAACACTTGGTGGTCAATTTTGAATGCTACGGTTTAATGTCAGAGGCATCTCT
65 GAAACAGACACCAAACACTTGGTGGT-ATTTTTGAATGCTACGATTTAATGTCAGAGGCATCTCT
*
18437 GTTACAATAAAAAGCACAAAAGATGGCTTGTCTCGTGGCTGTCTTTAATACTTCTCAAACTTTCA
129 GTTACAATAAAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAACTTT-A
* * * ** *
18502 A-TTAA--TATTTTTTTTCCGATTTTTGTTGTGTTTATCCATTTGCTTGCCCCCTCATTCCCTCT
193 ACTTAATGTTTTTTTTTTTCGATTTTTGTTGTATTTATCCACCTGCTAGCCCCCTCATTCCCTCT
* * *
18564 TCTACTAAACCAAAAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGTTAGTTT
258 TCTACTAAACCAAAAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGCGATCAGTTT
** * * *
18629 TGAATGCTATGGTTTAATGTCAGAGGTATCTCTCTTACAGTAAAAAGCACAAAAGATGGCTTGTC
323 TGAATGCTACAGTTTAATGTCAGAGGCATCTCTCTTACAATAAAAAGCACAAAAGATGGCTTATC
*
18694 ACGTGGTTGTCTTTAATACTTCTCAAAAGGTGGCCA
388 ACGTGGTTATCTTTAATACTTCTCAAAAGGTGGCCA
* * *
18730 TTTATCCACCTGCTTGCCCCTCCGTCTCTCTTGTACTAAACCAATAAGGAATTTAAAACTAATTG
1 TTTATCCACCTGCTTCCCCCTCCTTCCCTCTTGTACTAAACCAATAAGGAATTTAAAACTAATTG
* * * * *
18795 AAACAGACACCAAACACTTGGTGGTTATTTTTGAATGCCACAATTTAATGTCAAAGACATTTCTG
66 AAACAGACACCAAACACTTGGTGG-TATTTTTGAATGCTACGATTTAATGTCAGAGGCATCTCTG
*
18860 TTACAATAAAAAGCACAAAAGATGGGC-TGTCACATGGCTGTCTTTAATACTTCTCAAACTTTAA
130 TTACAATAAAAAGCACAAAAGAT-GGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTAA
* * *
18924 CTTAATGTTTTTTTTTTTTGATTTTTGTTGTATTTATCTACCTGCTAGCCCACCTCATTCCCTTT
194 CTTAATGTTTTTTTTTTTCGATTTTTGTTGTATTTATCCACCTGCTAGCCC-CCTCATTCCCTCT
* ** * *
18989 TGTACTAAATTAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACTCTTGGCGATCAGTTT
258 TCTACTAAACCAAAAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGCGATCAGTTT
* * *
19054 TGAATGTTACAGTTTAATGTCAGAGGCATCTCTGC-TACAATAAAAAAGTACAAAATATGGCTTA
323 TGAATGCTACAGTTTAATGTCAGAGGCATCTCT-CTTACAAT-AAAAAGCACAAAAGATGGCTTA
19118 TCACGTGGTTATCTTTAATACTTCTCAAAAGGTGGCCA
386 TCACGTGGTTATCTTTAATACTTCTCAAAAGGTGGCCA
* *
19156 TTTATCCACGTGCTTACCCCCTCATTCCCTCTTGTACTAAACCAATAAGGAATTTAAAACTAATT
1 TTTATCCACCTGCTT-CCCCCTCCTTCCCTCTTGTACTAAACCAATAAGGAATTTAAAACTAATT
*
19221 GAAACAGACACCAAACAGTTGGTGGCTATTTTTGAATGCTACGATTTAATGTCAGAGGCATCTCT
65 GAAACAGACACCAAACACTTGGTGG-TATTTTTGAATGCTACGATTTAATGTCAGAGGCATCTCT
* ** * * * *
19286 GTTACAATAAAAAACACAAAAGATAACTTGTCATGTAGTTGTCTTTAATACTTCTCAAACTTTCA
129 GTTACAATAAAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTAA
* *
19351 CTTAATGTTTTTTTTTTTCCAATTTTTATTGTATTTATCCACCT
194 CTTAATGTTTTTTTTTTT-CGATTTTTGTTGTATTTATCCACCT
19395 ACTGAAAGAA
Statistics
Matches: 589, Mismatches: 65, Indels: 17
0.88 0.10 0.03
Matches are distributed among these distances:
421 2 0.00
422 160 0.27
423 19 0.03
424 36 0.06
425 103 0.17
426 72 0.12
427 176 0.30
428 21 0.04
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (423 bp):
TTTATCCACCTGCTTCCCCCTCCTTCCCTCTTGTACTAAACCAATAAGGAATTTAAAACTAATTG
AAACAGACACCAAACACTTGGTGGTATTTTTGAATGCTACGATTTAATGTCAGAGGCATCTCTGT
TACAATAAAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTAACT
TAATGTTTTTTTTTTTCGATTTTTGTTGTATTTATCCACCTGCTAGCCCCCTCATTCCCTCTTCT
ACTAAACCAAAAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGCGATCAGTTTTGA
ATGCTACAGTTTAATGTCAGAGGCATCTCTCTTACAATAAAAAGCACAAAAGATGGCTTATCACG
TGGTTATCTTTAATACTTCTCAAAAGGTGGCCA
Found at i:21173 original size:59 final size:57
Alignment explanation
Indices: 21088--21205 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 57
21078 AAAATACTAG
21088 TTTTGAAGCAAAAATAGTCAACATTTTGGACTTATTATATTGATGGAAAAATATATTAA
1 TTTTGAAGCAAAAATAGTCAACATTTTGGAC-TATTATATTGATGG-AAAATATATTAA
*
21147 TTTTGAAGCAAAAATAGTCAAGATTTTGGACTATTATATTGATGGAAAATATATTAA
1 TTTTGAAGCAAAAATAGTCAACATTTTGGACTATTATATTGATGGAAAATATATTAA
21204 TT
1 TT
21206 AAAATCGTAA
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
57 14 0.24
58 14 0.24
59 30 0.52
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (57 bp):
TTTTGAAGCAAAAATAGTCAACATTTTGGACTATTATATTGATGGAAAATATATTAA
Found at i:21560 original size:6 final size:6
Alignment explanation
Indices: 21542--21605 Score: 87
Period size: 6 Copynumber: 10.8 Consensus size: 6
21532 TTTATTTGAG
* *
21542 GGGTGA GGGGTGA GGGTGA GGGTGA GGGTGA GGGTGA GGGTGG GGGTGG
1 GGGTGA -GGGTGA GGGTGA GGGTGA GGGTGA GGGTGA GGGTGA GGGTGA
21591 GGGTG- GGGTG- GGGTG
1 GGGTGA GGGTGA GGGTG
21606 GGGAAGGGGC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
5 10 0.18
6 40 0.71
7 6 0.11
ACGTcount: A:0.09, C:0.00, G:0.73, T:0.17
Consensus pattern (6 bp):
GGGTGA
Found at i:22226 original size:197 final size:196
Alignment explanation
Indices: 21835--23438 Score: 1033
Period size: 197 Copynumber: 8.0 Consensus size: 196
21825 TTTTTGTTCT
* * *
21835 ATTTATCCACCTGCTT--CCACTCCTTCCCTCTTGTACTAAATCAATAAGGAATCTAAAACTAAT
1 ATTTATCCACCTGTTTGCCCCCTCCTTCCCTCTTGTACTAAACCAATAAGGAAT-TAAAACTAAT
* * * * * * *
21898 TGAAACAGACACCAAATACTTGGTGGTCAGTTTTGACTGCTACGATTTAATGTCAGAGGCATCTT
65 TGAAACAGACACCAAACACTTGGTGCT-ATTTTTGAATGCAACAATTTAATGTCAGAGGCATCTC
*
21963 TGTTACAATAAAAAAGCACAAAAAATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAAAGGT
129 TGTTACAAT-AAAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAAAGGT
22028 GGCC
193 GGCC
* * *
22032 ATTTATCCCCCTGTTTGCCTCCTCCTTCCCTTTTGTACTAAACCAATAAGGAATTGAAAACTAAT
1 ATTTATCCACCTGTTTGCCCCCTCCTTCCCTCTTGTACTAAACCAATAAGGAATT-AAAACTAAT
**
22097 TGAAACAGACGTCAAACACTTGGTAGCTATTTTTGAATG-AACAATTTAATGTCAGAGGCATCTC
65 TGAAACAGACACCAAACACTTGGT-GCTATTTTTGAATGCAACAATTTAATGTCAGAGGCATCTC
* * *
22161 TGTTAGAATAAAAAGCATAAAAGATAGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAAAGGTG
129 TGTTACAATAAAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAAAGGTG
*
22226 GTC
194 GCC
*
22229 ATTTATCCACCTGTTTGCCCCCTCCTAT-CCTCTTGTACTAAACCAATAAGGAGTTAAAACTAAT
1 ATTTATCCACCTGTTTGCCCCCTCCT-TCCCTCTTGTACTAAACCAATAAGGAATTAAAACTAAT
* * * * *
22293 TGAAACAGATACCAAACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGACATTTC
65 TGAAACAGACACCAAACACTTGGT-GCTATTTTTGAATGCAACAATTTAATGTCAGAGGCATCTC
* * *** *
22358 TGTTACAATAAAAAGCACAAAAGATGGCTTGTCACATGGTTGTCTTTAATACTTCTCAAACTTTA
129 TGTTACAATAAAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAAAGGTG
* *
22423 ACTTA
194 GC--C
* ** ** * ***** * * *
22428 ATTTTTTTTTTATATTTTTGTTGTAT-TTATCCACTCGTTTCTTGTTCTAAACCAATAATGAATC
1 A---TTTATCCACCTGTTTGCCCCCTCCT-T-C-C-C---TCTTGTACTAAACCAATAAGGAAT-
* ** * * * *
22492 TAAAACTAATTGAAATATTCACCAAACATTTGGTGGCTATTTTTGAATGCCACATTTTAATGTTA
55 TAAAACTAATTGAAACAGACACCAAACACTTGGT-GCTATTTTTGAATGCAACAATTTAATGTCA
* ** *
22557 GAGGCATCTCTGTTACAATAAAAAGCACAAAAGAAGAG-TTGTCACGTGATTGCCTTTAATACTT
119 GAGGCATCTCTGTTACAATAAAAAGCACAAAAGATG-GCTTGTCACGTGGCTGTCTTTAATACTT
*** ** *
22621 CTCAAACTTTCACTTA
183 CTCAAAAGGTGGC--C
**** ***** * * *
22637 ATGTT-T-TTGTTGTTGTTGTATTTATCCACTTTCTTCTTGTTCTAAACCAATAAGGAATCTAAA
1 AT-TTATCCACCTG-T-TTG-CCCCCT-C-CTTCCCTCTTGTACTAAACCAATAAGGAAT-TAAA
* * *
22700 ACTAATTGAAACAGACACCAAACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATATCAGAGG
59 ACTAATTGAAACAGACACCAAACACTTGGT-GCTATTTTTGAATGCAACAATTTAATGTCAGAGG
* * * * * ** *
22765 CATTTCTGTTACAATAAAAAGCACAAAAAATGGCTTATTACGTGGTTACCTTTAATAGTTCTCAA
123 CATCTCTGTTACAATAAAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAA
*** ** *
22830 ACTTTCACTTA
188 AAGGTGGC--C
* ***** ***** * * *
22841 ATTTTTTTTTTTG-TTGTATTTATCCACTCGCTTATTG-ATCTAAACCAATAAGGAATCTAAAAC
1 ATTTATCCACCTGTTTG-CCCCCTCC-TTC-CCTCTTGTA-CTAAACCAATAAGGAAT-TAAAAC
* * ** *
22904 TAATTGAAACAGACACCAAACACTTGGTGACTATTTTTGAATACCACGGTTTAATGTCAGAGACA
61 TAATTGAAACAGACACCAAACACTTGGTG-CTATTTTTGAATGCAACAATTTAATGTCAGAGGCA
* * * *
22969 TCTCTGTTACAATAAAAAGCACAAAAAATGACTTGTCACGTGGTTGTCTTTAATACTTCTCAAAC
125 TCTCTGTTACAATAAAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAAA
** ** *
23034 TTTCACTTA
190 GGTGGC--C
* ** ** **** * * * * *
23043 ATTTTTTTTTTATTTTGTTGTATTTATCC-ACTTGCTTCTTGTACTAAACCAATAAAGAATCAAA
1 A---TTTATCCA-CCTG-T-T-TGCCCCCTCCTTCCCTCTTGTACTAAACCAATAAGGAAT-TAA
* * **
23107 AACTAATTGAAACAGACACC-AACACATGGTGGCTATTTTTGAATGCCACGGTTTAATGTCAGAG
58 AACTAATTGAAACAGACACCAAACACTTGGT-GCTATTTTTGAATGCAACAATTTAATGTCAGAG
* * * * * *
23171 GCATCTCTATTACAATAAAAAGCACAAAAGATGGCTTATTACGTCGTTGCCTTTAATACTTCTCA
122 GCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCA
*** ** *
23236 AACTTTCACTTG
187 AAAGGTGGC--C
***** **** * * * *
23248 ATTT-TTTTTTTGTAGTATTTATCC-ACTTGCTTCTTGTACTAAACCAATAAAGAATCTAAAACT
1 ATTTATCCACCTGT--T-TGCCCCCTCCTTCCCTCTTGTACTAAACCAATAAGGAAT-TAAAACT
* * * *
23311 AATTGCAACAGACACCAAATACTTAGTGGCTATTTTTGAATGTC-ACAATTTAATGTCATAGGCA
62 AATTGAAACAGACACCAAACACTTGGT-GCTATTTTTGAATG-CAACAATTTAATGTCAGAGGCA
* *
23375 TCTCTGTTATAATAAAAAGCACAAAATATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAA
125 TCTCTGTTACAATAAAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAA
23439 TTTTCACTTA
Statistics
Matches: 1206, Mismatches: 154, Indels: 90
0.83 0.11 0.06
Matches are distributed among these distances:
196 44 0.04
197 195 0.16
198 32 0.03
199 73 0.06
200 70 0.06
201 104 0.09
202 182 0.15
203 3 0.00
204 156 0.13
205 124 0.10
206 53 0.04
207 7 0.01
208 27 0.02
209 132 0.11
210 3 0.00
211 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (196 bp):
ATTTATCCACCTGTTTGCCCCCTCCTTCCCTCTTGTACTAAACCAATAAGGAATTAAAACTAATT
GAAACAGACACCAAACACTTGGTGCTATTTTTGAATGCAACAATTTAATGTCAGAGGCATCTCTG
TTACAATAAAAAGCACAAAAGATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAAAGGTGGC
C
Found at i:22622 original size:406 final size:398
Alignment explanation
Indices: 21863--23689 Score: 1802
Period size: 406 Copynumber: 4.5 Consensus size: 398
21853 ACTCCTTCCC
* *
21863 TCTTGTACTAAATCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAATACTTGGTGG-TCA
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCT-A
* * * *
21927 GTTTTGACTGCTAC-GATTTAATGTCAGAGGCATCTT-TGTTACAATAAAAAAGCACAAAAAATG
65 TTTTTGAATGCCACAG-TTTAATGTCAGAGGCAT-TTCTGTTACAAT-AAAAAGCACAAAAGATG
* * * * *** ** * * ***** **
21990 GCTTGTCACGTGGCTGTCTTTAATACTTCTCAAAAGGTGGC--CATTTATCCCCCTGTT-TGCCT
127 GCTTATTACGTGGTTGCCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTTGTTGT-ATT
** * * **
22052 CCTCC-TTCCCTT-TTGTACTAAACCAATAAGGAAT-TGAAAACTAATTGAAACAGACGTCAAAC
191 TATCCACTCGCTTCTTGTACTAAACCAATAAGGAATCT-AAAACTAATTGAAACAGACACCAAAC
* * *
22114 ACTTGGTAGCTATTTTTGAATG-AACAATTTAATGTCAGAGGCATCTCTGTTAGAATAAAAAGCA
255 ACTTGGTGGCTATTTTTGAATGCCACAATTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCA
* * * * ** *
22178 TAAAAGATAGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAAAGGTGGTCATTTATCCACCTGT
320 CAAAAGA-AGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAAA-CT-ATCATTTTTTTA-TTGT
***** *
22243 -TTG-CCCCCTCCTATCC
381 GTTGTATTTATCCTATCT
* *
22259 TCTTGTACTAAACCAATAAGGAGT-TAAAACTAATTGAAACAGATACCAAACACTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
*
22323 TTTTGAATGCCACAGTTTAATGTCAGAGACATTTCTGTTACAATAAAAAGCACAAAAGATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* * * * *
22388 GTCACATGGTTGTCTTTAATACTTCTCAAACTTTAACTTAATTTTTTTTTTATATTTTTGTTGTA
131 ATTACGTGGTTGCCTTTAATACTTCTCAAACTTTCACTTAA-----TTTTT-T-TTTTTGTTGTA
* * * * **
22453 TTTATCCACTCGTTTCTTGTTCTAAACCAATAATGAATCTAAAACTAATTGAAATATTCACCAAA
189 TTTATCCACTCGCTTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAA
* * *
22518 CATTTGGTGGCTATTTTTGAATGCCACATTTTAATGTTAGAGGCATCTCTGTTACAATAAAAAGC
254 CACTTGGTGGCTATTTTTGAATGCCACAATTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGC
* ** * * *
22583 ACAAAAGAAGAGTTGTCACGTGATTGCCTTTAATACTTCTC-AAACTTTCACTTAATGTTTTTGT
319 ACAAAAGAAG-CTTGTCACGTGGCTGTCTTTAATACTTCTCAAAACTATCA--T--T-TTTTTAT
*
22647 TGTTGTTGTATTTATCCACTTTCT
378 TG-TGTTGTATTTAT-C-CTATCT
*
22671 TCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* *
22736 TTTTGAATGCCACAGTTTAATATCAGAGGCATTTCTGTTACAATAAAAAGCACAAAAAATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* *
22801 ATTACGTGGTTACCTTTAATAGTTCTCAAACTTTCACTTAATTTTTTTTTTTGTTGTATTTATCC
131 ATTACGTGGTTGCCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTTGTTGTATTTATCC
*
22866 ACTCGCTTATTG-ATCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTG
196 ACTCGCTTCTTGTA-CTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTG
* * ** *
22930 GTGACTATTTTTGAATACCACGGTTTAATGTCAGAGACATCTCTGTTACAATAAAAAGCACAAAA
260 GTGGCTATTTTTGAATGCCACAATTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAA
* ** *
22995 -AATGACTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTATTTT
325 GAA-G-CTTGTCACGTGGCTGTCTTTAATACTTCTCAAA-----AC-T-ATCATTTTTTTATTGT
23059 GTTGTATTTATCC-ACTTGCT
381 GTTGTATTTATCCTA--T-CT
* * *
23079 TCTTGTACTAAACCAATAAAGAATCAAAAACTAATTGAAACAGACACC-AACACATGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * *
23143 TTTTGAATGCCACGGTTTAATGTCAGAGGCATCTCTATTACAATAAAAAGCACAAAAGATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* * *
23208 ATTACGTCGTTGCCTTTAATACTTCTCAAACTTTCACTTGA-TTTTTTTTTTGTAGTATTTATCC
131 ATTACGTGGTTGCCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTTGTTGTATTTATCC
* * * * *
23272 ACTTGCTTCTTGTACTAAACCAATAAAGAATCTAAAACTAATTGCAACAGACACCAAATACTTAG
196 ACTCGCTTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGG
* * * *
23337 TGGCTATTTTTGAATGTCACAATTTAATGTCATAGGCATCTCTGTTATAATAAAAAGCACAAAAT
261 TGGCTATTTTTGAATGCCACAATTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAG
* **
23402 ATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAATTTTCACTTAATGTTTTTTTTTTTCTGA
326 A-AGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAA-----AC-T-A----TCATTTTTT-T-A
*
23467 TTTTTGTTGTATTTATCCTCCTACTTACCTCCTCCTT
377 -TTGTGTTGTATTTA---T-C--C-TA-----T-C-T
* * *
23504 CCCTCTTGTACTAAACCAATAAGGAATTTAAAACTAATTGCAACAGACACCAAACACTTGGTGGT
1 ---TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGC
* * * *
23569 TATTTTTGAATGCCACGGGTTAATGTCAGAAGCATCTCTGTTACAATAAAAAGCACAAAAGATGG
63 TATTTTTGAATGCCACAGTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAGCACAAAAGATGG
* * * **
23634 CTTGTCACGTGGCTATCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTT
128 CTTATTACGTGGTTGCCTTTAATACTTCTCAAACTTTCACTTAAT-TTTTTTTTTT
23690 TTAGATTTTT
Statistics
Matches: 1214, Mismatches: 147, Indels: 105
0.83 0.10 0.07
Matches are distributed among these distances:
394 52 0.04
395 71 0.06
396 25 0.02
401 4 0.00
403 11 0.01
404 6 0.00
405 69 0.06
406 410 0.34
407 123 0.10
408 67 0.06
409 10 0.01
410 11 0.01
411 2 0.00
412 30 0.02
413 150 0.12
414 1 0.00
416 1 0.00
417 1 0.00
419 1 0.00
421 1 0.00
424 3 0.00
425 1 0.00
428 44 0.04
429 110 0.09
431 10 0.01
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (398 bp):
TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
TTTTGAATGCCACAGTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAGCACAAAAGATGGCTT
ATTACGTGGTTGCCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTTGTTGTATTTATCC
ACTCGCTTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGG
TGGCTATTTTTGAATGCCACAATTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAG
AAGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAAACTATCATTTTTTTATTGTGTTGTATTTA
TCCTATCT
Found at i:22958 original size:202 final size:202
Alignment explanation
Indices: 21863--23689 Score: 1959
Period size: 204 Copynumber: 8.9 Consensus size: 202
21853 ACTCCTTCCC
* *
21863 TCTTGTACTAAATCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAATACTTGGTGG-TCA
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCT-A
* * * *
21927 GTTTTGACTGCTAC-GATTTAATGTCAGAGGCATCTTTGTTACAATAAAAAAGCACAAAAAATGG
65 TTTTTGAATGCCACAG-TTTAATGTCAGAGGCATCTCTGTTACAAT-AAAAAGCACAAAAAATGG
* *** ** * * ***** ** *
21991 CTTGTCACGTGGCTGTCTTTAATACTTCTCAAAAGGTGGC--CATTTATCCCCCTGTT-TGCCTC
128 CTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTTGTTGT-ATTT
* * *
22053 CTCC-TTCCCT
192 ATCCACTCGCT
** *
22063 T-TTGTACTAAACCAATAAGGAAT-TGAAAACTAATTGAAACAGACGTCAAACACTTGGTAGCTA
1 TCTTGTACTAAACCAATAAGGAATCT-AAAACTAATTGAAACAGACACCAAACACTTGGTGGCTA
* * * * * *
22126 TTTTTGAATG-AACAATTTAATGTCAGAGGCATCTCTGTTAGAATAAAAAGCATAAAAGATAGCT
65 TTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAAATGGCT
* *** ** * * ***** *****
22190 TGTCACGTGGCTGTCTTTAATACTTCTCAAAAGGT--GGTCATTTATCCACCTGTT-TGCCCCCT
130 TGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTTGTTGT-ATTTAT
22252 CCTA-TC-C-
194 CC-ACTCGCT
* *
22259 TCTTGTACTAAACCAATAAGGAGT-TAAAACTAATTGAAACAGATACCAAACACTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * *
22323 TTTTGAATGCCACAGTTTAATGTCAGAGACATTTCTGTTACAATAAAAAGCACAAAAGATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAAATGGCTT
* *
22388 GTCACATGGTTGTCTTTAATACTTCTCAAACTTTAACTTAATTTTTTTTTTATATTTTTGTTGTA
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAA-----TTTTT-T-TTTTTGTTGTA
*
22453 TTTATCCACTCGTT
189 TTTATCCACTCGCT
* * * ** *
22467 TCTTGTTCTAAACCAATAATGAATCTAAAACTAATTGAAATATTCACCAAACATTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* *
22532 TTTTGAATGCCACATTTTAATGTTAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGAA-GAG-
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAA-AATG-GC
* * *
22595 TTGTCACGTGATTGCCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTGTTGTTGTTGTATTT
129 TTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAT-TTTTT-TTTTTGTTGTATTT
**
22660 ATCCACTTTCT
192 ATCCACTCGCT
*
22671 TCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* *
22736 TTTTGAATGCCACAGTTTAATATCAGAGGCATTTCTGTTACAATAAAAAGCACAAAAAATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAAATGGCTT
* * ** *
22801 ATTACGTGGTTACCTTTAATAGTTCTCAAACTTTCACTTAATTTTTTTTTTTGTTGTATTTATCC
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTTGTTGTATTTATCC
22866 ACTCGCT
196 ACTCGCT
* *
22873 TATTG-ATCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGACTA
1 TCTTGTA-CTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTA
* * * *
22937 TTTTTGAATACCACGGTTTAATGTCAGAGACATCTCTGTTACAATAAAAAGCACAAAAAATGACT
65 TTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAAATGGCT
23002 TGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTATTTTGTTGTATT
130 TGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAA---TTTTTTT-TTTTGTTGTATT
*
23067 TATCCACTTGCT
191 TATCCACTCGCT
* * *
23079 TCTTGTACTAAACCAATAAAGAATCAAAAACTAATTGAAACAGACACC-AACACATGGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * *
23143 TTTTGAATGCCACGGTTTAATGTCAGAGGCATCTCTATTACAATAAAAAGCACAAAAGATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAAATGGCTT
* * * * * *
23208 ATTACGTCGTTGCCTTTAATACTTCTCAAACTTTCACTTGA-TTTTTTTTTTGTAGTATTTATCC
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTTGTTGTATTTATCC
*
23272 ACTTGCT
196 ACTCGCT
* * * *
23279 TCTTGTACTAAACCAATAAAGAATCTAAAACTAATTGCAACAGACACCAAATACTTAGTGGCTAT
1 TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * * * *
23344 TTTTGAATGTCACAATTTAATGTCATAGGCATCTCTGTTATAATAAAAAGCACAAAATATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAAATGGCTT
* *
23409 GTCACGTGGCTGTCTTTAATACTTCTCAAATTTTCACTTAATGTTTTTTTTTTTCTGATTTTTGT
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAA--------TTTTT-T--TTTTTGT
*
23474 TGTATTTATCCTCCTACTTACCTCCTCCTT
185 TGTATTTA---T-C--C--A-CT-C-GC-T
* * *
23504 CCCTCTTGTACTAAACCAATAAGGAATTTAAAACTAATTGCAACAGACACCAAACACTTGGTGGT
1 ---TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGC
* * * *
23569 TATTTTTGAATGCCACGGGTTAATGTCAGAAGCATCTCTGTTACAATAAAAAGCACAAAAGATGG
63 TATTTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAAATGG
* *
23634 CTTGTCACGTGGCTATCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTT
128 CTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAT-TTTTTTTTTT
23690 TTAGATTTTT
Statistics
Matches: 1408, Mismatches: 156, Indels: 108
0.84 0.09 0.06
Matches are distributed among these distances:
196 45 0.03
197 176 0.12
198 32 0.02
199 63 0.04
200 71 0.05
201 111 0.08
202 178 0.13
203 8 0.01
204 180 0.13
205 122 0.09
206 75 0.05
207 2 0.00
208 21 0.01
209 128 0.09
210 6 0.00
211 1 0.00
213 14 0.01
216 1 0.00
217 1 0.00
218 5 0.00
219 1 0.00
220 2 0.00
221 5 0.00
222 2 0.00
224 1 0.00
225 1 0.00
228 156 0.11
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (202 bp):
TCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAAATGGCTT
GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTTGTTGTATTTATCC
ACTCGCT
Found at i:23308 original size:812 final size:805
Alignment explanation
Indices: 21641--23689 Score: 2288
Period size: 812 Copynumber: 2.5 Consensus size: 805
21631 CCTCCTTCCC
* * * * *
21641 TCTTCTACTAAACCAATAAGGAATCTAAAACTAATTAAAACAGACACAAAACACTTGTGGTTATT
1 TCTTGTACTAAACCAATAAAGAATCTAAAACTAATTGAAACAGACACCAAACACTTGTGGCTATT
*
21706 TTTGAATGCCACGATTTAAT-TACAGAGGCATCTCTATTACAATAAAAAGCACAAAAGATGGCTT
66 TTTGAATGCCAC-ATTTAATGT-CAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* * *
21770 GTCACGTGGCTATCTTTAATACTTCTCAAACTTTCACTTAATATTTTTTTTTCGATTTTTGTTCT
129 GTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTT-A-A--TGTTTTT-GATTTTTGTTGT
*
21835 ATTTATCCACCTGCTTCCACTCCTTCCCTCTTGTACTAAATCAATAAGGAATCTAAAACTAATTG
189 ATTTATCCA----CTT---CTCCTT--CTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTG
* * * *
21900 AAACAGACACCAAATACTTGGTGGTCAGTTTTGACTGCTACGATTTAATGTCAGAGGCATCTT-T
245 AAACAGACACCAAACACTTGGTGGT-ATTTTTGAATGCCACG-TTTAATGTCAGAGGCAT-TTCT
* *** *
21964 GTTACAATAAAAAAGCACAAAAAATGGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAAAGGTG
307 GTTACAAT-AAAAAGCACAAAAAATGGCTTGTCACGTGGCTATCTTTAATACTTCTCAAACTTTC
* * * ***** * * *
22029 GC--CATTTATCCCCCTGTTTGCCTCCTCCTTCCCTTTTGTACTAAACCAATAAGGAATTGAAAA
371 ACTTAATTTTTTTTTTTGTTTGACTCATCCCTCCCTTTTGTACTAAACCAATAAGGAATTGAAAA
** *
22092 CTAATTGAAACAGACGTCAAACACTTGGTAGCTATTTTTGAATGAACAATTTAATGTCAGAGGCA
436 CTAATTGAAACAGACACCAAACACTTGGTAGCTATTTTTGAATGAACAATTTAATGTCAGAGACA
* * *
22157 TCTCTGTTAGAATAAAAAGCATAAAAGATAGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAAA
501 TCTCTGTTACAATAAAAAGCACAAAAAATAGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAAA
* ** * * * * *
22222 GGTGGTCATTTATCCACCTGTTTGCCCCCTCCTATCCTCTTGTACTAAACCAATAAGGAGTTAAA
566 CGTAATCATTTATCCACCTGTTTGCACCCTACTATCCTCTTGTACTAAACCAATAAAGAATAAAA
* *
22287 ACTAATTGAAACAGATACCAAACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGA
631 ACTAATTGAAACAGACACCAAACACATGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGA
* * * * *
22352 CATTTCTGTTACAATAAAAAGCACAAAAGATGGCTTGTCACATGGTTGTCTTTAATACTTCTCAA
696 CATCTCTATTACAATAAAAAGCACAAAAGATGGCTTATCACATCGTTGCCTTTAATACTTCTCAA
* *
22417 ACTTTAACTTAATTTTTTTTTTATATTTTTGTTGTATTTATCCACTCGTT
761 ACTTTAACTTAA-----TTTTTATATTTTTGTAGTATTTATCCACTCGCT
* * * ** *
22467 TCTTGTTCTAAACCAATAATGAATCTAAAACTAATTGAAATATTCACCAAACATTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAAGAATCTAAAACTAATTGAAACAGACACCAAACACTT-GTGGCTAT
* *
22532 TTTTGAATGCCACATTTTAATGTTAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGAAGAG-T
65 TTTTGAATGCCACA-TTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATG-GCT
** * *
22596 TGTCACGTGATTGCCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTG-TTGTTGTTGTATTT
128 TGTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTGATTTTTGTTGTATTT
*
22660 ATCCACTT-T-C-T-TCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAA
193 ATCCACTTCTCCTTCTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAA
*
22721 ACACTTGGTGGCTATTTTTGAATGCCACAGTTTAATATCAGAGGCATTTCTGTTACAATAAAAAG
258 ACACTTGGTGG-TATTTTTGAATGCCAC-GTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAG
* * * * *
22786 CACAAAAAATGGCTTATTACGTGGTTACCTTTAATAGTTCTCAAACTTTCACTTAATTTTTTTTT
321 CACAAAAAATGGCTTGTCACGTGGCTATCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTT
* * *
22851 TTG-TTGTATTTATCCACTCGCTTATTG-ATCTAAACCAATAAGGAATCT-AAAACTAATTGAAA
386 TTGTTTG-ACTCATCC-CTCCCTT-TTGTA-CTAAACCAATAAGGAAT-TGAAAACTAATTGAAA
**
22913 CAGACACCAAACACTTGGT-GACTATTTTTGAAT-ACCACGGTTTAATGTCAGAGACATCTCTGT
446 CAGACACCAAACACTTGGTAG-CTATTTTTGAATGA--ACAATTTAATGTCAGAGACATCTCTGT
*
22976 TACAATAAAAAGCACAAAAAAT-GACTTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCAC
508 TACAATAAAAAGCACAAAAAATAG-CTTGTCACGTGGCTGTCTTTAATACTTCTCAAA-----AC
* ** * ** ** ** * *
23040 TTAATTTTTTTTTTATTTTGTTGTATTTATCC-ACT-TGCTTCTTGTACTAAACCAATAAAGAAT
567 GTAATCATTTATCCA-CCTG-T-T-TGCACCCTACTAT-CCTCTTGTACTAAACCAATAAAGAAT
*
23103 CAAAAACTAATTGAAACAGACACC-AACACATGGTGGCTATTTTTGAATGCCACGGTTTAATGTC
627 -AAAAACTAATTGAAACAGACACCAAACACATGGTGGCTATTTTTGAATGCCACAGTTTAATGTC
* * *
23167 AGAGGCATCTCTATTACAATAAAAAGCACAAAAGATGGCTTATTACGTCGTTGCCTTTAATACTT
691 AGAGACATCTCTATTACAATAAAAAGCACAAAAGATGGCTTATCACATCGTTGCCTTTAATACTT
* * *
23232 CTCAAACTTTCACTTGA-TTTT-T-TTTTTGTAGTATTTATCCACTTGCT
756 CTCAAACTTTAACTTAATTTTTATATTTTTGTAGTATTTATCCACTCGCT
* *
23279 TCTTGTACTAAACCAATAAAGAATCTAAAACTAATTGCAACAGACACCAAATACTTAGTGGCTAT
1 TCTTGTACTAAACCAATAAAGAATCTAAAACTAATTGAAACAGACACCAAACACTT-GTGGCTAT
* * * *
23344 TTTTGAATGTCACAATTTAATGTCATAGGCATCTCTGTTATAATAAAAAGCACAAAATATGGCTT
65 TTTTGAATGCCAC-ATTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
*
23409 GTCACGTGGCTGTCTTTAATACTTCTCAAATTTTCACTTAATGTTTTTTTTTTTCTGATTTTTGT
129 GTCACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTTAATG-------TTTT-TGATTTTTGT
*
23474 TGTATTTATCCTCCTACTTACCTCCTCCTTCCCTCTTGTACTAAACCAATAAGGAATTTAAAACT
186 TGTATTTA---TCC-AC-T---T-CTCCTT--CTCTTGTACTAAACCAATAAGGAATCTAAAACT
* * *
23539 AATTGCAACAGACACCAAACACTTGGTGGTTATTTTTGAATGCCACGGGTTAATGTCAGAAGCAT
240 AATTGAAACAGACACCAAACACTTGGTGG-TATTTTTGAATGCCAC-GTTTAATGTCAGAGGCAT
* *
23604 CTCTGTTACAATAAAAAGCACAAAAGATGGCTTGTCACGTGGCTATCTTTAATACTTCTCAAACT
303 TTCTGTTACAATAAAAAGCACAAAAAATGGCTTGTCACGTGGCTATCTTTAATACTTCTCAAACT
23669 TTCACTTAATGTTTTTTTTTT
368 TTCACTTAAT-TTTTTTTTTT
23690 TTAGATTTTT
Statistics
Matches: 1036, Mismatches: 131, Indels: 101
0.82 0.10 0.08
Matches are distributed among these distances:
807 49 0.05
808 98 0.09
809 13 0.01
810 8 0.01
811 66 0.06
812 249 0.24
813 3 0.00
814 4 0.00
817 11 0.01
818 2 0.00
819 6 0.01
820 138 0.13
821 55 0.05
822 1 0.00
823 6 0.01
824 3 0.00
825 3 0.00
826 50 0.05
827 98 0.09
828 2 0.00
829 1 0.00
831 1 0.00
832 1 0.00
833 1 0.00
836 157 0.15
837 10 0.01
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (805 bp):
TCTTGTACTAAACCAATAAAGAATCTAAAACTAATTGAAACAGACACCAAACACTTGTGGCTATT
TTTGAATGCCACATTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTTGT
CACGTGGCTGTCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTGATTTTTGTTGTATTTATC
CACTTCTCCTTCTCTTGTACTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACA
CTTGGTGGTATTTTTGAATGCCACGTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAGCACAA
AAAATGGCTTGTCACGTGGCTATCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTTTTGTT
TGACTCATCCCTCCCTTTTGTACTAAACCAATAAGGAATTGAAAACTAATTGAAACAGACACCAA
ACACTTGGTAGCTATTTTTGAATGAACAATTTAATGTCAGAGACATCTCTGTTACAATAAAAAGC
ACAAAAAATAGCTTGTCACGTGGCTGTCTTTAATACTTCTCAAAACGTAATCATTTATCCACCTG
TTTGCACCCTACTATCCTCTTGTACTAAACCAATAAAGAATAAAAACTAATTGAAACAGACACCA
AACACATGGTGGCTATTTTTGAATGCCACAGTTTAATGTCAGAGACATCTCTATTACAATAAAAA
GCACAAAAGATGGCTTATCACATCGTTGCCTTTAATACTTCTCAAACTTTAACTTAATTTTTATA
TTTTTGTAGTATTTATCCACTCGCT
Found at i:23676 original size:228 final size:228
Alignment explanation
Indices: 23279--23719 Score: 722
Period size: 228 Copynumber: 1.9 Consensus size: 228
23269 TCCACTTGCT
*
23279 TCTTGTACTAAACCAATAAAGAATCTAAAACTAATTGCAACAGACACCAAATACTTAGTGGCTAT
1 TCTTGTACTAAACCAATAAAGAATCTAAAACTAATTGCAACAGACACCAAACACTTAGTGGCTAT
* * * * * *
23344 TTTTGAATGTCACAATTTAATGTCATAGGCATCTCTGTTATAATAAAAAGCACAAAATATGGCTT
66 TTTTGAATGCCACAAGTTAATGTCAGAAGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
* *
23409 GTCACGTGGCTGTCTTTAATACTTCTCAAATTTTCACTTAATGTTTTTTTTTTTCT-GATTTTTG
131 GTCACGTGGCTATCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTTT-TAGATTTTTG
*
23473 TTGTATTTATCCTCCTACTTACCTCCTCCTTCCC
195 TTGTATTTATCCACCTACTTACCTCCTCCTTCCC
* * * *
23507 TCTTGTACTAAACCAATAAGGAATTTAAAACTAATTGCAACAGACACCAAACACTTGGTGGTTAT
1 TCTTGTACTAAACCAATAAAGAATCTAAAACTAATTGCAACAGACACCAAACACTTAGTGGCTAT
**
23572 TTTTGAATGCCACGGGTTAATGTCAGAAGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
66 TTTTGAATGCCACAAGTTAATGTCAGAAGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
23637 GTCACGTGGCTATCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTTTTAGATTTTTGT
131 GTCACGTGGCTATCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTTTTAGATTTTTGT
23702 TGTATTTATCCACCTACT
196 TGTATTTATCCACCTACT
23720 GAAAGAAAAA
Statistics
Matches: 196, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
227 1 0.01
228 195 0.99
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (228 bp):
TCTTGTACTAAACCAATAAAGAATCTAAAACTAATTGCAACAGACACCAAACACTTAGTGGCTAT
TTTTGAATGCCACAAGTTAATGTCAGAAGCATCTCTGTTACAATAAAAAGCACAAAAGATGGCTT
GTCACGTGGCTATCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTTTTAGATTTTTGT
TGTATTTATCCACCTACTTACCTCCTCCTTCCC
Found at i:26384 original size:6 final size:6
Alignment explanation
Indices: 26373--26406 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
26363 AATTTTCTAT
*
26373 GGGAGG GGGAGG GGGAGG GGGAGG GGGTGG GGGA
1 GGGAGG GGGAGG GGGAGG GGGAGG GGGAGG GGGA
26407 TCTGCCCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.15, C:0.00, G:0.82, T:0.03
Consensus pattern (6 bp):
GGGAGG
Found at i:27532 original size:206 final size:205
Alignment explanation
Indices: 26424--27637 Score: 1778
Period size: 206 Copynumber: 5.9 Consensus size: 205
26414 CCTCATTCCC
* * * * * *
26424 TCTTGTACTAAACCAATAAAGAATCTAAAATTAATTGAAACAGACACCAAATATTTGGTGGTTAT
1 TCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* *
26489 TTTTGAATGCCACATTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAACACAAAAAATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAGCACAAAAAATGGCTT
** * *
26554 GTCACAAGTTTGTCTTTAATAGTTCTCAAACTTTCACTTAATTTTTTTTTTAATTTTTGTTGTAT
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAA--TTTTTTTT-ATTTTTGTTGTAT
26619 TTATCCACTCGCT
193 TTATCCACTCGCT
* * * *
26632 TCATGTTCTAAACCAATAAAGAATCTAAAATTAATTGAAACAGACACCAAATACTTGGTGGCTAT
1 TCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * * *
26697 TTTTGAATGCC-CAAGTTTAATGT-TGTAGGCATCTCTGTTACAATAAAAAGCACAAAATATGGT
66 TTTTGAATGCCAC-AGTTTAATGTCAG-AGGCATTTCTGTTACAATAAAAAGCACAAAAAATGGC
* *
26760 TTGTCACGTGGTTATCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTATTTTTGTTTTATT
129 TTGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTATTTTTGTTGTATT
26825 TATCCACTCGCT
194 TATCCACTCGCT
* *
26837 TATTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGACTAT
1 TCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * * *
26902 TTTTGAATGCTACAGTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAGTATAAAAAATGACTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAGCACAAAAAATGGCTT
*
26967 GTCACGTGGTTGTCTTTAATAGTTCTCAAACTTTCACTTAATATATTTTTTTAATTTTTGTTGTA
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTT-A-AT-TTTTTTT-ATTTTTGTTGTA
*
27032 TTTATCCACTCACT
192 TTTATCCACTCGCT
* *
27046 TCTTGTTCTAAACCAATAATGAATCTTAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
1 TCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* ** * * * *
27111 TTTTGAATGCCATAGTTTAATGTCAGAGATATTTTTGTTATAATAAAAAACACAAAAGATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAGCACAAAAAATGGCTT
*
27176 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAA----TATT-TTTTTGTTGTATTTA
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTATTTTTGTTGTATTTA
27236 TCCACTCGCT
196 TCCACTCGCT
* * *
27246 TATTGTTCTAAACCAATAAGAAATTTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
1 TCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* *
27311 TTTTGAATGCCACAGTTTAATGTCAGAGGCATCTT-TGTTACAATAAAAAGCACAAAAGACGGCT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCAT-TTCTGTTACAATAAAAAGCACAAAAAATGGCT
* * * * *
27375 TGTAACGTAGTTGCCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTGTTGTTGTTGTATT
130 TGTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAT-TTTTTTTATTTTTGTTGTATT
*
27440 TATCCACTTGCT
194 TATCCACTCGCT
27452 TCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
1 TCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
*
27517 TTTTGAATCCCACAGTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAGCACAAAAAATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAGCACAAAAAATGGCTT
* *
27582 GTCACGTGGTTGCCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTTTTT
131 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAAT-TTTTTTTATTTTT
27638 TTAATTTTTG
Statistics
Matches: 911, Mismatches: 79, Indels: 34
0.89 0.08 0.03
Matches are distributed among these distances:
200 178 0.20
201 2 0.00
202 3 0.00
205 179 0.20
206 207 0.23
207 5 0.01
208 160 0.18
209 177 0.19
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (205 bp):
TCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
TTTTGAATGCCACAGTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAGCACAAAAAATGGCTT
GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTATTTTTGTTGTATTTA
TCCACTCGCT
Found at i:27610 original size:615 final size:617
Alignment explanation
Indices: 26424--27670 Score: 1869
Period size: 615 Copynumber: 2.0 Consensus size: 617
26414 CCTCATTCCC
* * * *
26424 TCTTGTACTAAACCAATAAAGAATCTAAAATTAATTGAAACAGACACCAAATATTTGGTGGTTAT
1 TCTTGTACTAAACCAATAAAGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* *
26489 TTTTGAATGCCACATTTTAATGTCAGAGGCATTTCTGTTACAATAAAAAACACAAAAAATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGACATTTCTGTTACAATAAAAAACACAAAAAATGGCTT
* * *
26554 GTCACAAGTTTGTCTTTAATAGTTCTCAAACTTTCACTTAATTTTTTTTTTAATTTTTGTTGTAT
131 GTCACAAGGTTGTCTTTAATACTTCTCAAACTTTCACTTAA-----TTATT-ATTTTTGTTGTAT
* *
26619 TTATCCACTCGCTTCATGTTCTAAACCAATAAAGAATCTAAAATTAATTGAAACAGACACCAAAT
190 TTATCCACTCGCTTCATGTTCTAAACCAATAAAGAATCTAAAACTAATTGAAACAGACACCAAAC
*
26684 ACTTGGTGGCTATTTTTGAATGCCCAAGTTTAATGTTGTAGGCATCTCTGTTACAATAAAAAGCA
255 ACTTGGTGGCTATTTTTGAATGCCCAAGTTTAATGTAGTAGGCATCTCTGTTACAATAAAAAGCA
* * * * * *
26749 CAAAATATGGTTTGTCACGTGGTTATCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTATT
320 CAAAAGACGGCTTGTAACGTAGTTACCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTATT
* *
26814 TTTGTTTTATTTATCCACTCGCTTATTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACA
385 GTTGTTGTATTTATCCACTCGCTTATTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACA
* *
26879 GACACCAAACACTTGGTGACTATTTTTGAATGCTACAGTTTAATGTCAGAGGCATTTCTGTTACA
450 GACACCAAACACTTGGTGACTATTTTTGAATCCCACAGTTTAATGTCAGAGGCATTTCTGTTACA
* * * *
26944 ATAAAAAGTATAAAAAATGACTTGTCACGTGGTTGTCTTTAATAGTTCTCAAACTTTCACTTAA-
515 ATAAAAAGCACAAAAAATGACTTGTCACGTGGTTGCCTTTAATACTTCTCAAACTTTCACTTAAT
*
27008 TATATTTTTTTAATTTTTGTTGTATTTATCCACTCACT
580 TATATTTTTTTAATTTTTGTTGTATTTATCCAATCACT
* * *
27046 TCTTGTTCTAAACCAATAATGAATCTTAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
1 TCTTGTACTAAACCAATAAAGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
* * * * *
27111 TTTTGAATGCCATAGTTTAATGTCAGAGATATTTTTGTTATAATAAAAAACACAAAAGATGGCTT
66 TTTTGAATGCCACAGTTTAATGTCAGAGACATTTCTGTTACAATAAAAAACACAAAAAATGGCTT
**
27176 GTCACGTGGTTGTCTTTAATACTTCTCAAACTTTCACTTAA-TATT-TTTTTGTTGTATTTATCC
131 GTCACAAGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTATTATTTTTGTTGTATTTATCC
*
27239 ACTCGCTT-ATTGTTCTAAACCAAT-AAGAAATTTAAAACTAATTGAAACAGACACCAAACACTT
196 ACTCGCTTCA-TGTTCTAAACCAATAAAG-AATCTAAAACTAATTGAAACAGACACCAAACACTT
*
27302 GGTGGCTATTTTTGAATG-CCACAGTTTAATGTCAG-AGGCATCTTTGTTACAATAAAAAGCACA
259 GGTGGCTATTTTTGAATGCCCA-AGTTTAATGT-AGTAGGCATCTCTGTTACAATAAAAAGCACA
* *
27365 AAAGACGGCTTGTAACGTAGTTGCCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTGTTG
322 AAAGACGGCTTGTAACGTAGTTACCTTTAATACTTCTCAAACTTTCACTTAAT-TTTTTTTATTG
* *
27430 TTGTTGTATTTATCCACTTGCTTCTTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAG
386 TTGTTGTATTTATCCACTCGCTTATTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAG
*
27495 ACACCAAACACTTGGTGGCTATTTTTGAATCCCACAGTTTAATGTCAGAGGCATTTCTGTTACAA
451 ACACCAAACACTTGGTGACTATTTTTGAATCCCACAGTTTAATGTCAGAGGCATTTCTGTTACAA
*
27560 TAAAAAGCACAAAAAATGGCTTGTCACGTGGTTGCCTTTAATACTTCTCAAACTTTCACTTAATG
516 TAAAAAGCACAAAAAATGACTTGTCACGTGGTTGCCTTTAATACTTCTCAAACTTTCACTTAA--
* * *
27625 TTTTTTTTTTTTTTTAATTTTTGTTGTATTTATCCAATCTCT
579 ---TTATATTTTTTTAATTTTTGTTGTATTTATCCAATCACT
27667 TCTT
1 TCTT
27671 NNNNNNNNNN
Statistics
Matches: 566, Mismatches: 48, Indels: 23
0.89 0.08 0.04
Matches are distributed among these distances:
613 7 0.01
614 173 0.31
615 192 0.34
616 3 0.01
621 38 0.07
622 153 0.27
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (617 bp):
TCTTGTACTAAACCAATAAAGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGGCTAT
TTTTGAATGCCACAGTTTAATGTCAGAGACATTTCTGTTACAATAAAAAACACAAAAAATGGCTT
GTCACAAGGTTGTCTTTAATACTTCTCAAACTTTCACTTAATTATTATTTTTGTTGTATTTATCC
ACTCGCTTCATGTTCTAAACCAATAAAGAATCTAAAACTAATTGAAACAGACACCAAACACTTGG
TGGCTATTTTTGAATGCCCAAGTTTAATGTAGTAGGCATCTCTGTTACAATAAAAAGCACAAAAG
ACGGCTTGTAACGTAGTTACCTTTAATACTTCTCAAACTTTCACTTAATTTTTTTTATTGTTGTT
GTATTTATCCACTCGCTTATTGTTCTAAACCAATAAGGAATCTAAAACTAATTGAAACAGACACC
AAACACTTGGTGACTATTTTTGAATCCCACAGTTTAATGTCAGAGGCATTTCTGTTACAATAAAA
AGCACAAAAAATGACTTGTCACGTGGTTGCCTTTAATACTTCTCAAACTTTCACTTAATTATATT
TTTTTAATTTTTGTTGTATTTATCCAATCACT
Found at i:28089 original size:208 final size:208
Alignment explanation
Indices: 27721--29204 Score: 1578
Period size: 208 Copynumber: 7.1 Consensus size: 208
27711 NNNNNNNNNN
27721 TTTCACTTAATGTTTTTTTTTTTTTTAAATTTTTGTTGTATTTATCCACTCGC-TCATTGTTCTA
1 TTTCACTTAATG-TTTTTTTTTTTTT-AATTTTTGTTG----TAT-CACTCGCTTC-TTGTTCTA
* * *
27785 GATCAATAAGGAATCTAAAAC-TAATTGAAACAGACACCAAACACTTGGT-AGCTATTTTTGAAT
58 AACCAATAAGGAATCT-AAACTTAATTGAAACAGACACCAAACACTTGGTGA-TTATTTTTGAAT
* * * *
27848 GCCAAAGTTTAATGTCAGAGGCATATTTGTTACAATAAAAAGCACAAAAGATGACTTGTCACATG
121 GCCACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTGTCACGTG
** *
27913 ACTATCTTTAATACTTCTCAAAC
186 GTTGTCTTTAATACTTCTCAAAC
* *
27936 TTTCACTTAATGCTTTTTTTTTTTTTAATTTTTGTTGTA-CAATCGCTTCTTGTTTTAAACCAAT
1 TTTCACTTAATG-TTTTTTTTTTTTTAATTTTTGTTGTATCACTCGCTTCTTGTTCTAAACCAAT
* *
28000 AAGGAATCTACACTTAATTGAAACAGACACCAAACACTTGGTGTTTATTTTTGAATGCCACAGTT
65 AAGGAATCTAAACTTAATTGAAACAGACACCAAACACTTGGTGATTATTTTTGAATGCCACAGTT
* * * * * *
28065 TAAAGTCAAAGGCATCTCTGTTACAATAAAAAGCACAAAAGAGGGCTTGTCATGTGGTTGCCTTT
130 TAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTGTCACGTGGTTGTCTTT
28130 AATACTTCTCAAAC
195 AATACTTCTCAAAC
* * *
28144 TTTCACTTAATGCTTTTTTTTTTTTTTAATTTTTGTTGTATTTATCCAATCTCTTCTTGTTTTAA
1 TTTCACTTAATG--TTTTTTTTTTTTTAATTTTTGTTG----TAT-CACTCGCTTCTTGTTCTAA
* *
28209 ACCAATAAAGAATCTAAACTTAATTGAAACAGACACCAAACACTTGGTGATTATTTTTGAATGTC
59 ACCAATAAGGAATCTAAACTTAATTGAAACAGACACCAAACACTTGGTGATTATTTTTGAATGCC
* * * * *
28274 ACAATTTAATGTCAGAGGCATATCTGTTACAATAAAAAGCACAAAAGATGGCTTGTCACATGATT
124 ACAGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTGTCACGTGGTT
*
28339 ATCTTTAATACTTCTCAAAC
189 GTCTTTAATACTTCTCAAAC
* * * *
28359 TTTCACTTAATGCTTTTTTTTTTTT--TTTTTGTATTTATTCAATCGCTTCTTGTTTTAAACCAA
1 TTTCACTTAATGTTTTTTTTTTTTTAATTTTTGT-TGTA-TCACTCGCTTCTTGTTCTAAACCAA
* * *
28422 TAAGGAATATAAACTTAATTGAAACAAACACCAAACACTTGGTGATTATTTTTGAATGCGACAGT
64 TAAGGAATCTAAACTTAATTGAAACAGACACCAAACACTTGGTGATTATTTTTGAATGCCACAGT
* * * *
28487 TTAAAGTCAGAGGCATCTCTGTTACAATAAAAAGTACAAAAGATGGCTTGTCACGTGGTTGCCTT
129 TTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTGTCACGTGGTTGTCTT
*
28552 TAATACTTCTTAAAC
194 TAATACTTCTCAAAC
* * * * * * * * * * * * * * *
28567 TTTCACTT-AT-ATATATATTTTTT--GTTGTATT-AATCCACTTGTTTATTGTACTAAGCTATT
1 TTTCACTTAATGTTTTTTTTTTTTTAATTTTTGTTGTAT-CACTCGCTTCTTGTTCTAAACCAAT
* * * *
28627 AAGAAATCTAAAAC-TAATTGAAACAGAAACCAAACACTTGATGATTATTTTTGAATGTCACAGT
65 AAGGAATCT-AAACTTAATTGAAACAGACACCAAACACTTGGTGATTATTTTTGAATGCCACAGT
* *
28691 TTAATGTCAGAGGCATCTCTGTTACAATAAAAAACACAAAATAT-AGCTTGTCACGTGGTTGTCT
129 TTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGA-CTTGTCACGTGGTTGTCT
*
28755 TTAATACTTTTCAAAC
193 TTAATACTTCTCAAAC
* * *
28771 TTTCACTTAAT-TTTTTTTTTGTTGT-A------TT-TATCCACTTGCTTATTGTTCTAAACCAA
1 TTTCACTTAATGTTTTTTTTT-TTTTAATTTTTGTTGTAT-CACTCGCTTCTTGTTCTAAACCAA
* * * **
28827 TAAAGAATCTAAAATTAATTGAAATAGACACCAAACACTTGGTGGCTATTTTTGAATGCCACAGT
64 TAAGGAATCTAAACTTAATTGAAACAGACACCAAACACTTGGTGATTATTTTTGAATGCCACAGT
* * * * * *
28892 TTAATGTCAAAGGCATATTTGTTACAATAAAAAGCACAAAAGACGACTTATCACGTGGTTGCCTT
129 TTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTGTCACGTGGTTGTCTT
28957 TAATACTTCTCAAAC
194 TAATACTTCTCAAAC
* * * * * *
28972 TTTCACTTAATG-TTTTTTTATTTTACTTTTGCTGTATTTATCCACTTGTTTCTTGTACTAAACC
1 TTTCACTTAATGTTTTTTTTTTTTTAATTTT--TGT-TGTAT-CACTCGCTTCTTGTTCTAAACC
* * * ** * * * *
29036 AATAAAGAATTTAAAAC-TAATTGAAATAGACACCAAGTACTTGGTGGTCATTTTTGAATTCTAC
62 AATAAGGAATCT-AAACTTAATTGAAACAGACACCAAACACTTGGTGATTATTTTTGAATGCCAC
* * * ** * * *
29100 -GATTTAATGTTAGAGGCATCTTTATTACAATAAAAAATACAAAAGATGATTTATTACGTGGTTG
126 AG-TTTAATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTGTCACGTGGTTG
*
29164 TTTTTAATACTTCTCAAAC
190 TCTTTAATACTTCTCAAAC
*
29183 TTTCACTTATTGTTTTTTTTTT
1 TTTCACTTAATGTTTTTTTTTT
29205 GTTGTATTTA
Statistics
Matches: 1092, Mismatches: 142, Indels: 73
0.84 0.11 0.06
Matches are distributed among these distances:
200 6 0.01
201 163 0.15
202 1 0.00
203 1 0.00
204 148 0.14
205 12 0.01
206 16 0.01
207 5 0.00
208 317 0.29
209 28 0.03
210 4 0.00
211 163 0.15
212 12 0.01
213 14 0.01
214 11 0.01
215 191 0.17
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (208 bp):
TTTCACTTAATGTTTTTTTTTTTTTAATTTTTGTTGTATCACTCGCTTCTTGTTCTAAACCAATA
AGGAATCTAAACTTAATTGAAACAGACACCAAACACTTGGTGATTATTTTTGAATGCCACAGTTT
AATGTCAGAGGCATCTCTGTTACAATAAAAAGCACAAAAGATGACTTGTCACGTGGTTGTCTTTA
ATACTTCTCAAAC
Found at i:28507 original size:423 final size:418
Alignment explanation
Indices: 27721--29204 Score: 1839
Period size: 423 Copynumber: 3.6 Consensus size: 418
27711 NNNNNNNNNN
* *
27721 TTTCACTTAATGTTTTTTTTTTTTTTAAATTTTTGTTGTATTTATCCACTCGC-TCATTGTTCTA
1 TTTCACTTAATG--TTTTTTTTTTTT-AATTTTTGTTGTATTTATCCACTTGCTTC-TTGTACTA
* * * *
27785 GATCAATAAGGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGT-AGCTATTTTTGAATG
62 AACCAATAAAGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGA-TTATTTTTGAATG
* * *
27849 CCA-AAGTTTAATGTCAGAGGCATATTTGTTACAATAAAAAGCACAAAAGATGACTTGTCACATG
126 TCACAA-TTTAATGTCAGAGGCATATCTGTTACAATAAAAAACACAAAAGATGACTTGTCACATG
* *
27913 ACTATCTTTAATACTTCTCAAACTTTCACTTAATGCTTTTTTTTTTTTTAATTTTTGT-TGTA-C
190 ATTATCTTTAATACTTCTCAAACTTTCACTTAATG--TTTTTTTTTTTT--TTTTTGTATTTATC
*
27976 AATCGCTTCTTGTTTTAAACCAATAAGGAATCTACACTTAATTGAAACAGACACCAAACACTTGG
251 AATCGCTTCTTGTTTTAAACCAATAAGGAATCTAAACTTAATTGAAACAGACACCAAACACTTGG
*
28041 TGTTTATTTTTGAATGCCACAGTTTAAAGTCAAAGGCATCTCTGTTACAATAAAAAGCACAAAAG
316 TGATTATTTTTGAATGCCACAGTTTAAAGTCAAAGGCATCTCTGTTACAATAAAAAGCACAAAAG
* *
28106 AGGGCTTGTCATGTGGTTGCCTTTAATACTTCTCAAAC
381 ACGGCTTGTCACGTGGTTGCCTTTAATACTTCTCAAAC
* **
28144 TTTCACTTAATGCTTTTTTTTTTTTTTAATTTTTGTTGTATTTATCCAATCT-CTTCTTGTTTTA
1 TTTCACTTAATG---TTTTTTTTTTTTAATTTTTGTTGTATTTATCCACT-TGCTTCTTGTACTA
28208 AACCAATAAAGAATCT-AAACTTAATTGAAACAGACACCAAACACTTGGTGATTATTTTTGAATG
62 AACCAATAAAGAATCTAAAAC-TAATTGAAACAGACACCAAACACTTGGTGATTATTTTTGAATG
* *
28272 TCACAATTTAATGTCAGAGGCATATCTGTTACAATAAAAAGCACAAAAGATGGCTTGTCACATGA
126 TCACAATTTAATGTCAGAGGCATATCTGTTACAATAAAAAACACAAAAGATGACTTGTCACATGA
28337 TTATCTTTAATACTTCTCAAACTTTCACTTAATGCTTTTTTTTTTTTTTTTTGTATTTATTCAAT
191 TTATCTTTAATACTTCTCAAACTTTCACTTAATG-TTTTTTTTTTTTTTTTTGTATTTA-TCAAT
* *
28402 CGCTTCTTGTTTTAAACCAATAAGGAATATAAACTTAATTGAAACAAACACCAAACACTTGGTGA
254 CGCTTCTTGTTTTAAACCAATAAGGAATCTAAACTTAATTGAAACAGACACCAAACACTTGGTGA
* * * *
28467 TTATTTTTGAATGCGACAGTTTAAAGTCAGAGGCATCTCTGTTACAATAAAAAGTACAAAAGATG
319 TTATTTTTGAATGCCACAGTTTAAAGTCAAAGGCATCTCTGTTACAATAAAAAGCACAAAAGACG
*
28532 GCTTGTCACGTGGTTGCCTTTAATACTTCTTAAAC
384 GCTTGTCACGTGGTTGCCTTTAATACTTCTCAAAC
* * * * * * * *
28567 TTTCACTT-A-------TATATATATTTTTTGTTGTATTAATCCACTTGTTTATTGTACT-AAGC
1 TTTCACTTAATGTTTTTTTTTTTTAATTTTTGTTGTATTTATCCACTTGCTTCTTGTACTAAACC
* * * *
28623 TATTAAGAAATCTAAAACTAATTGAAACAGAAACCAAACACTTGATGATTATTTTTGAATGTCAC
66 AATAAAG-AATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGATTATTTTTGAATGTCAC
* * * * * *
28688 AGTTTAATGTCAGAGGCATCTCTGTTACAATAAAAAACACAAAATAT-AGCTTGTCACGTGGTTG
130 AATTTAATGTCAGAGGCATATCTGTTACAATAAAAAACACAAAAGATGA-CTTGTCACATGATTA
* * * *
28752 TCTTTAATACTTTTCAAACTTTCACTTAA------TTTTTTTTTTGTTGTATTTATCCACTTGCT
194 TCTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTTTTTTTTTGTATTTAT-CAATCGCT
* * * * * **
28811 TATTGTTCTAAACCAATAAAGAATCTAAAATTAATTGAAATAGACACCAAACACTTGGTGGCTAT
258 TCTTGTTTTAAACCAATAAGGAATCTAAACTTAATTGAAACAGACACCAAACACTTGGTGATTAT
* * * *
28876 TTTTGAATGCCACAGTTTAATGTCAAAGGCATATTTGTTACAATAAAAAGCACAAAAGACGACTT
323 TTTTGAATGCCACAGTTTAAAGTCAAAGGCATCTCTGTTACAATAAAAAGCACAAAAGACGGCTT
*
28941 ATCACGTGGTTGCCTTTAATACTTCTCAAAC
388 GTCACGTGGTTGCCTTTAATACTTCTCAAAC
* * * *
28972 TTTCACTTAATGTTTTTTTATTTT-ACTTTTGCTGTATTTATCCACTTGTTTCTTGTACTAAACC
1 TTTCACTTAATGTTTTTTTTTTTTAATTTTTGTTGTATTTATCCACTTGCTTCTTGTACTAAACC
* * ** * *
29036 AATAAAGAATTTAAAACTAATTGAAATAGACACCAAGTACTTGGTGGTCATTTTTGAAT-TCTAC
66 AATAAAGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGATTATTTTTGAATGTC-AC
* * * * * * * * * * * *
29100 GATTTAATGTTAGAGGCATCTTTATTACAATAAAAAATACAAAAGATGATTTATTACGTGGTTGT
130 AATTTAATGTCAGAGGCATATCTGTTACAATAAAAAACACAAAAGATGACTTGTCACATGATTAT
* *
29165 TTTTAATACTTCTCAAACTTTCACTTATTGTTTTTTTTTT
195 CTTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTT
29205 GTTGTATTTA
Statistics
Matches: 928, Mismatches: 102, Indels: 67
0.85 0.09 0.06
Matches are distributed among these distances:
404 1 0.00
405 175 0.19
406 1 0.00
411 11 0.01
412 318 0.34
413 16 0.02
418 6 0.01
420 7 0.01
421 3 0.00
422 17 0.02
423 354 0.38
424 19 0.02
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (418 bp):
TTTCACTTAATGTTTTTTTTTTTTAATTTTTGTTGTATTTATCCACTTGCTTCTTGTACTAAACC
AATAAAGAATCTAAAACTAATTGAAACAGACACCAAACACTTGGTGATTATTTTTGAATGTCACA
ATTTAATGTCAGAGGCATATCTGTTACAATAAAAAACACAAAAGATGACTTGTCACATGATTATC
TTTAATACTTCTCAAACTTTCACTTAATGTTTTTTTTTTTTTTTTTGTATTTATCAATCGCTTCT
TGTTTTAAACCAATAAGGAATCTAAACTTAATTGAAACAGACACCAAACACTTGGTGATTATTTT
TGAATGCCACAGTTTAAAGTCAAAGGCATCTCTGTTACAATAAAAAGCACAAAAGACGGCTTGTC
ACGTGGTTGCCTTTAATACTTCTCAAAC
Found at i:29685 original size:34 final size:34
Alignment explanation
Indices: 29642--29709 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
29632 GGTAGTGAGG
29642 GGCTTTAGCCCCTCCCTCCAAATAGAAAATTGTT
1 GGCTTTAGCCCCTCCCTCCAAATAGAAAATTGTT
29676 GGCTTTAGCCCCTCCCTCCAAATAGAAAATTGTT
1 GGCTTTAGCCCCTCCCTCCAAATAGAAAATTGTT
29710 TCTTTAGTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (34 bp):
GGCTTTAGCCCCTCCCTCCAAATAGAAAATTGTT
Found at i:31910 original size:65 final size:64
Alignment explanation
Indices: 31796--31920 Score: 162
Period size: 65 Copynumber: 1.9 Consensus size: 64
31786 AAATAATTTG
* * * *
31796 AAAAATAATAAGAGCTGAATTGACAAAAATGTAAACATTAAGGGTTAAATTTGACATTATACCA
1 AAAAAGAATAAGAGCTCAATTGACAAAAATGCAAACATTAAGGGCTAAATTTGACATTATACCA
* * *
31860 AAAAAGAATAAGAGC-CAATTTGATAAAAGATGCAATCATTAAGGGCTAAATTTGATATTAT
1 AAAAAGAATAAGAGCTCAA-TTGACAAAA-ATGCAAACATTAAGGGCTAAATTTGACATTAT
31921 GCATTATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
63 2 0.04
64 22 0.42
65 28 0.54
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.27
Consensus pattern (64 bp):
AAAAAGAATAAGAGCTCAATTGACAAAAATGCAAACATTAAGGGCTAAATTTGACATTATACCA
Found at i:32174 original size:28 final size:27
Alignment explanation
Indices: 32143--32204 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
32133 TATACTTTTT
32143 AAATAATTTTATT-AAATTTAATTATTAA
1 AAATAATTTTATTGAAATTTAA--ATTAA
* *
32171 AAAT-ATTTTTTTGAATTTTAAATTAA
1 AAATAATTTTATTGAAATTTAAATTAA
32197 AAATAATT
1 AAATAATT
32205 GAATGTTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 9 0.30
27 10 0.33
28 11 0.37
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
AAATAATTTTATTGAAATTTAAATTAA
Found at i:32187 original size:27 final size:26
Alignment explanation
Indices: 32143--32201 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
32133 TATACTTTTT
32143 AAATAATTTTATTAAA-TTTAATTATTAA
1 AAAT-ATTTTATTAAATTTTAA--ATTAA
* *
32171 AAATATTTTTTTGAATTTTAAATTAA
1 AAATATTTTATTAAATTTTAAATTAA
32197 AAATA
1 AAATA
32202 ATTGAATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 10 0.36
27 9 0.32
28 9 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (26 bp):
AAATATTTTATTAAATTTTAAATTAA
Found at i:44114 original size:17 final size:17
Alignment explanation
Indices: 44091--44165 Score: 98
Period size: 17 Copynumber: 4.4 Consensus size: 17
44081 CCAAACTCAT
44091 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
44109 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
44126 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
44143 TTTAAAGTTATTATAAA
1 TTTAAATTTATTTTAAA
44160 TTTAAA
1 TTTAAA
44166 ATAAATAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
17 37 0.73
18 14 0.27
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:44148 original size:35 final size:34
Alignment explanation
Indices: 44091--44165 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 34
44081 CCAAACTCAT
* * *
44091 TTTAAATTTATTTTAAGATTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAGATTAAAGTTATTAT-AAA
44126 TTTAAATTTATTTTAA-ATTTAAAGTTATTATAAA
1 TTTAAATTTATTTTAAGA-TTAAAGTTATTATAAA
44160 TTTAAA
1 TTTAAA
44166 ATAAATAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
34 10 0.28
35 26 0.72
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTTTAAGATTAAAGTTATTATAAA
Found at i:44887 original size:3 final size:3
Alignment explanation
Indices: 44879--44921 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
44869 TTAATGACAC
*
44879 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA -AA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
44922 CATTAATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:45929 original size:30 final size:30
Alignment explanation
Indices: 45854--46133 Score: 295
Period size: 29 Copynumber: 9.5 Consensus size: 30
45844 AAACTGTTCG
* * *
45854 AAAATTCTATTTTT-ACCCTC-GAACTTCTA
1 AAAATTCCATTTTTGACCC-CAAAACTTCCA
45883 AAAATTCCATTTTTTGACCCCAAAACTTCCA
1 AAAATTCCA-TTTTTGACCCCAAAACTTCCA
45914 AAAATTCCATTTTTGACCCCAAAACTTCCA
1 AAAATTCCATTTTTGACCCCAAAACTTCCA
* * * * *
45944 AAAATTACGTTTTT-ACCCCCACACTTCTA
1 AAAATTCCATTTTTGACCCCAAAACTTCCA
* ** *
45973 AAAAATCCA-TTTTGACATCGAAACTTCCA
1 AAAATTCCATTTTTGACCCCAAAACTTCCA
*
46002 AAAATTCCA-TTTTAACCCCAAAACTTCCA
1 AAAATTCCATTTTTGACCCCAAAACTTCCA
* *
46031 AAAATTCTATTTTTGACCCCAACACTTCCA
1 AAAATTCCATTTTTGACCCCAAAACTTCCA
** *
46061 AAAATTCCATTTTT-ACCCCCGAACTTTCA
1 AAAATTCCATTTTTGACCCCAAAACTTCCA
* * *
46090 AAAATACCATTTCTGACCCCGAAACTTCCAA
1 AAAATTCCATTTTTGACCCCAAAACTTCC-A
46121 AAAATT-CATTTTT
1 AAAATTCCATTTTT
46134 ATGCTCGAAC
Statistics
Matches: 208, Mismatches: 36, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
28 4 0.02
29 91 0.44
30 87 0.42
31 26 0.12
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAATTCCATTTTTGACCCCAAAACTTCCA
Found at i:46143 original size:59 final size:58
Alignment explanation
Indices: 45854--46217 Score: 307
Period size: 59 Copynumber: 6.2 Consensus size: 58
45844 AAACTGTTCG
* * *
45854 AAAATTCTATTTTT-ACCCTCG-AACTTCTAAAAATTCCATTTTTTGACCCCAAAACTTCCA
1 AAAATTCCATTTTTGACCC-CGAAACTTCCAAAAATTCCA-TTTTT-ACCCC-GAACTTCCA
* * * * *
45914 AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACGTTTTTACCCCCACACTTCTA
1 AAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCCGA-ACTTCCA
* ** * *
45973 AAAAATCCA-TTTTGACATCGAAACTTCCAAAAATTCCATTTTAACCCCAAAACTTCCA
1 AAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCC-GAACTTCCA
* *
46031 AAAATTCTATTTTTGACCCC-AACACTTCCAAAAATTCCATTTTTACCCCCGAACTTTCA
1 AAAATTCCATTTTTGACCCCGAA-ACTTCCAAAAATTCCATTTTTA-CCCCGAACTTCCA
* * * * *
46090 AAAATACCATTTCTGACCCCGAAACTTCCAAAAAATT-CATTTTTATGCTCGAACCTCC-
1 AAAATTCCATTTTTGACCCCGAAACTTCC-AAAAATTCCATTTTTA-CCCCGAACTTCCA
* * * *
46148 AAAATCTCCATTTTCGACCTCGAAAC-TCTC-AAAATTACC-CTTTTACCCCCGAA-TATCTA
1 AAAAT-TCCATTTTTGACCCCGAAACTTC-CAAAAATT-CCATTTTTA-CCCCGAACT-TCCA
46207 AAAATTCCATT
1 AAAATTCCATT
46218 CTTAACCTTG
Statistics
Matches: 248, Mismatches: 41, Indels: 32
0.77 0.13 0.10
Matches are distributed among these distances:
57 6 0.02
58 74 0.30
59 118 0.48
60 32 0.13
61 18 0.07
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCA
Found at i:48210 original size:29 final size:30
Alignment explanation
Indices: 48166--48223 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
48156 GGGGGTGGGA
*
48166 TGAGAGGAGGGTAAAAGTTTTAGGGGAAAG
1 TGAGAGGAGAGTAAAAGTTTTAGGGGAAAG
*
48196 TGAGA-GAGAGTAAAAGTTTTGGGGGAAA
1 TGAGAGGAGAGTAAAAGTTTTAGGGGAAA
48224 ATAAAAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.41, T:0.21
Consensus pattern (30 bp):
TGAGAGGAGAGTAAAAGTTTTAGGGGAAAG
Found at i:48241 original size:19 final size:20
Alignment explanation
Indices: 48207--48247 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
48197 GAGAGAGAGT
*
48207 AAAAGTTTTGGGGGAAAATA
1 AAAAGTTTTGGAGGAAAATA
48227 AAAAGTTTT-GAGGAAAATA
1 AAAAGTTTTGGAGGAAAATA
48246 AA
1 AA
48248 TGGGGGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (20 bp):
AAAAGTTTTGGAGGAAAATA
Found at i:54218 original size:29 final size:30
Alignment explanation
Indices: 54174--54525 Score: 136
Period size: 29 Copynumber: 12.1 Consensus size: 30
54164 TATTTTCTTT
* *
54174 AAAAATTCCATTTTGACCCTCAAGCTTTTC
1 AAAAATTACATTTTGACCCTCAAACTTTTC
*
54204 AAAAATTACA-TTTGACCCTTAAACTTTTC
1 AAAAATTACATTTTGACCCTCAAACTTTTC
* *
54233 -AAAATTATATTTTGACCC-CTAAACTTCTC
1 AAAAATTACATTTTGACCCTC-AAACTTTTC
* * * *
54262 TAAAA-TATCATTTTAACCGT-AAACTTATC
1 AAAAATTA-CATTTTGACCCTCAAACTTTTC
* * * * *
54291 CAAAATTATGATTTTG-CACC-CGAA-TATCC
1 AAAAATTA-CATTTTGAC-CCTCAAACTTTTC
* * *
54320 AAAAAATTACATTTTTACCCCCAAAC--ATC
1 -AAAAATTACATTTTGACCCTCAAACTTTTC
* * *
54349 CAAAATTACTATTTTG-CCCTCGAA-TATTC
1 AAAAATTAC-ATTTTGACCCTCAAACTTTTC
** * **
54378 AAAAATTACCATTTT--CCCTTGAAC-ATAA
1 AAAAATTA-CATTTTGACCCTCAAACTTTTC
* * *
54406 AAAAATTACCATTTT-ACCCTCGAAC-ATCC
1 AAAAATTA-CATTTTGACCCTCAAACTTTTC
* * *
54435 AAAAATTACCATTTT-ACCCTCGAAC-ATCC
1 AAAAATTA-CATTTTGACCCTCAAACTTTTC
*
54464 AAAAATTACCATTTTG-CCC-CAAA-TTTCC
1 AAAAATTA-CATTTTGACCCTCAAACTTTTC
* * * *
54492 AAAAATCACATTTTCAACCTCAAATTTTTC
1 AAAAATTACATTTTGACCCTCAAACTTTTC
54522 AAAA
1 AAAA
54526 GTTTGATTTT
Statistics
Matches: 257, Mismatches: 42, Indels: 46
0.74 0.12 0.13
Matches are distributed among these distances:
27 6 0.02
28 61 0.24
29 138 0.54
30 52 0.20
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCTCAAACTTTTC
Found at i:54420 original size:57 final size:57
Alignment explanation
Indices: 54350--54506 Score: 194
Period size: 57 Copynumber: 2.8 Consensus size: 57
54340 CCAAACATCC
* *
54350 AAAATTACTATTTTGCCCTCGAATATTCAAAAATTACCATTTTCCCTTGAACATAAA
1 AAAATTACCATTTTGCCCTCGAATATTCAAAAATTACCATTTTCCCTCGAACATAAA
* * * **
54407 AAAATTACCATTTTACCCTCGAACATCCAAAAATTACCATTTTACCCTCGAACATCCA
1 AAAATTACCATTTTGCCCTCGAATATTCAAAAATTACCATTTT-CCCTCGAACATAAA
* *
54465 AAAATTACCATTTTGCCC-CAAAT-TTCCAAAAATCA-CATTTTC
1 AAAATTACCATTTTGCCCTCGAATATT-CAAAAATTACCATTTTC
54507 AACCTCAAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
55 1 0.01
56 7 0.08
57 50 0.58
58 28 0.33
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (57 bp):
AAAATTACCATTTTGCCCTCGAATATTCAAAAATTACCATTTTCCCTCGAACATAAA
Found at i:54494 original size:28 final size:29
Alignment explanation
Indices: 54288--54482 Score: 202
Period size: 29 Copynumber: 6.8 Consensus size: 29
54278 CCGTAAACTT
** *
54288 ATCC-AAAATTATGATTTTGCACC-CGAAT
1 ATCCAAAAATTACCATTTTGC-CCTCGAAC
* * *
54316 ATCCAAAAAATTA-CATTTTTACCCCCAAAC
1 ATCC-AAAAATTACCA-TTTTGCCCTCGAAC
* *
54346 ATCC-AAAATTACTATTTTGCCCTCGAAT
1 ATCCAAAAATTACCATTTTGCCCTCGAAC
* *
54374 ATTCAAAAATTACCATTTT-CCCTTGAAC
1 ATCCAAAAATTACCATTTTGCCCTCGAAC
** *
54402 ATAAAAAAATTACCATTTTACCCTCGAAC
1 ATCCAAAAATTACCATTTTGCCCTCGAAC
*
54431 ATCCAAAAATTACCATTTTACCCTCGAAC
1 ATCCAAAAATTACCATTTTGCCCTCGAAC
54460 ATCCAAAAATTACCATTTTGCCC
1 ATCCAAAAATTACCATTTTGCCC
54483 CAAATTTCCA
Statistics
Matches: 141, Mismatches: 19, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
28 48 0.34
29 74 0.52
30 19 0.13
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.31
Consensus pattern (29 bp):
ATCCAAAAATTACCATTTTGCCCTCGAAC
Found at i:56466 original size:24 final size:24
Alignment explanation
Indices: 56428--56538 Score: 132
Period size: 24 Copynumber: 4.6 Consensus size: 24
56418 AGTTCATTAC
*
56428 GTTTACGCTCGTCAGCTAATGTAT
1 GTTTACACTCGTCAGCTAATGTAT
* * *
56452 GTTTACACTCATCAGTTAATGTAA
1 GTTTACACTCGTCAGCTAATGTAT
* *
56476 GTTTACACTCGTCAGTTAGTGTAT
1 GTTTACACTCGTCAGCTAATGTAT
* * *
56500 GTTTACGCTCGTCAACTAATGTAC
1 GTTTACACTCGTCAGCTAATGTAT
*
56524 GTTTACACACGTCAG
1 GTTTACACTCGTCAG
56539 TTATTCAGAT
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (24 bp):
GTTTACACTCGTCAGCTAATGTAT
Found at i:56499 original size:48 final size:48
Alignment explanation
Indices: 56428--56541 Score: 147
Period size: 48 Copynumber: 2.4 Consensus size: 48
56418 AGTTCATTAC
* * **
56428 GTTTACGCTCGTCAGCTAATGTATGTTTACACTCATCAGTTAATGTAA
1 GTTTACACTCGTCAGTTAATGTATGTTTACACTCATCAACTAATGTAA
* * * *
56476 GTTTACACTCGTCAGTTAGTGTATGTTTACGCTCGTCAACTAATGTAC
1 GTTTACACTCGTCAGTTAATGTATGTTTACACTCATCAACTAATGTAA
*
56524 GTTTACACACGTCAGTTA
1 GTTTACACTCGTCAGTTA
56542 TTCAGATATA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (48 bp):
GTTTACACTCGTCAGTTAATGTATGTTTACACTCATCAACTAATGTAA
Found at i:63015 original size:81 final size:81
Alignment explanation
Indices: 62924--63085 Score: 324
Period size: 81 Copynumber: 2.0 Consensus size: 81
62914 TCATCTTAAA
62924 ATTTTTTCAATTTTTAAAATAACCATCCACTCCCATAAAAACAATTTCACTCAAAATAAATAAAT
1 ATTTTTTCAATTTTTAAAATAACCATCCACTCCCATAAAAACAATTTCACTCAAAATAAATAAAT
62989 AAAACCATCAATAGTT
66 AAAACCATCAATAGTT
63005 ATTTTTTCAATTTTTAAAATAACCATCCACTCCCATAAAAACAATTTCACTCAAAATAAATAAAT
1 ATTTTTTCAATTTTTAAAATAACCATCCACTCCCATAAAAACAATTTCACTCAAAATAAATAAAT
63070 AAAACCATCAATAGTT
66 AAAACCATCAATAGTT
63086 TAAAACAACT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (81 bp):
ATTTTTTCAATTTTTAAAATAACCATCCACTCCCATAAAAACAATTTCACTCAAAATAAATAAAT
AAAACCATCAATAGTT
Found at i:63927 original size:16 final size:16
Alignment explanation
Indices: 63894--63943 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
63884 AAATTTTTTC
63894 AAATT-GAGT-AAATA
1 AAATTCGAGTCAAATA
*
63908 AAATTCGAGTCAAATG
1 AAATTCGAGTCAAATA
*
63924 AAATTCGAGTCAAATC
1 AAATTCGAGTCAAATA
63940 AAAT
1 AAAT
63944 CAAGTGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 5 0.16
15 4 0.12
16 23 0.72
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (16 bp):
AAATTCGAGTCAAATA
Found at i:64217 original size:21 final size:21
Alignment explanation
Indices: 64161--64212 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
64151 CTTTCTTTAT
*
64161 ATATTTTTTAGAATTTATTTTG
1 ATATTTTTTA-AAATTATTTTG
64183 A-ATTTTTTAAAATTATTTTG
1 ATATTTTTTAAAATTATTTTG
64203 ATTATTTTTT
1 A-TATTTTTT
64213 TAATTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 11 0.41
21 8 0.30
22 8 0.30
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (21 bp):
ATATTTTTTAAAATTATTTTG
Found at i:71439 original size:47 final size:47
Alignment explanation
Indices: 71381--71565 Score: 217
Period size: 47 Copynumber: 3.9 Consensus size: 47
71371 TTGCACTATC
* * * * * *
71381 TAGTGGTTCGACCACATATATTTGTTTTAACAGCATAATTGCAAATA
1 TAGTGGCTCGACCACATATATTTGTTCTAGCAGCTTGACTGCAAATA
* * * * *
71428 TAATGGCTCGACCACAAATATTTGTTCTGGCATCTTGACTACAAATA
1 TAGTGGCTCGACCACATATATTTGTTCTAGCAGCTTGACTGCAAATA
*
71475 TAGTGGCTCGACCACATATATTTGTTCTAGCAGCTTGACTGAAAATA
1 TAGTGGCTCGACCACATATATTTGTTCTAGCAGCTTGACTGCAAATA
* * * * *
71522 TAGTGGCTTGACCACATATATTTGATCTGGCAGTTTAACTGCAA
1 TAGTGGCTCGACCACATATATTTGTTCTAGCAGCTTGACTGCAA
71566 CTCTGGTGGC
Statistics
Matches: 115, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 115 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (47 bp):
TAGTGGCTCGACCACATATATTTGTTCTAGCAGCTTGACTGCAAATA
Found at i:71543 original size:94 final size:94
Alignment explanation
Indices: 71381--71553 Score: 247
Period size: 94 Copynumber: 1.8 Consensus size: 94
71371 TTGCACTATC
* * * *
71381 TAGTGGTTCGACCACATATATTTGTTTTAACAGCATAATTGCAAATATAATGGCTCGACCACAAA
1 TAGTGGCTCGACCACATATATTTGTTCTAACAGCATAACTGAAAATATAATGGCTCGACCACAAA
*
71446 TATTTGTTCTGGCATCTTGACTACAAATA
66 TATTTGATCTGGCATCTTGACTACAAATA
* * * * * *
71475 TAGTGGCTCGACCACATATATTTGTTCTAGCAGCTTGACTGAAAATATAGTGGCTTGACCACATA
1 TAGTGGCTCGACCACATATATTTGTTCTAACAGCATAACTGAAAATATAATGGCTCGACCACAAA
71540 TATTTGATCTGGCA
66 TATTTGATCTGGCA
71554 GTTTAACTGC
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
94 68 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (94 bp):
TAGTGGCTCGACCACATATATTTGTTCTAACAGCATAACTGAAAATATAATGGCTCGACCACAAA
TATTTGATCTGGCATCTTGACTACAAATA
Found at i:72845 original size:14 final size:16
Alignment explanation
Indices: 72814--72851 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
72804 TTTTTAAAAT
72814 TTAAATAAATATTTAA
1 TTAAATAAATATTTAA
72830 TTAAATAAA-A-TTAA
1 TTAAATAAATATTTAA
*
72844 TTAGATAA
1 TTAAATAA
72852 TTTACCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.52
15 1 0.05
16 9 0.43
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TTAAATAAATATTTAA
Found at i:77590 original size:42 final size:41
Alignment explanation
Indices: 77519--77600 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 41
77509 TAGTCTATGT
* *
77519 ACTTGTATCGGTAGAAGCATGACTTGTATCGATAGATGTCTC
1 ACTTGTATCGGTAGAAGCATGACTGGTATCG-TAGAAGTCTC
*
77561 ACTTGTATCGGTAGAA-CTATTA-TAGGTATCGTAGAAGTCT
1 ACTTGTATCGGTAGAAGC-ATGACT-GGTATCGTAGAAGTCT
77601 ATACTGTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
41 10 0.29
42 25 0.71
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (41 bp):
ACTTGTATCGGTAGAAGCATGACTGGTATCGTAGAAGTCTC
Found at i:79707 original size:37 final size:34
Alignment explanation
Indices: 79665--79772 Score: 112
Period size: 37 Copynumber: 3.0 Consensus size: 34
79655 TAAAATAAAC
79665 ATTAAATTAAATTAAA-TATTAAAATAATCACTTTAA
1 ATTAAATTAAATTAAACTATTAAAATAAT-A--TTAA
*
79701 TATTAAATT-AATAAAATACTATTAAAATAAGTATTAA
1 -ATTAAATTAAAT-TAA-ACTATTAAAATAA-TATTAA
79738 ATTAAATTTAATATTAAACTATTAAAATAATATTA
1 ATTAAA-TTAA-ATTAAACTATTAAAATAATATTA
79773 TTTTTGGAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
36 14 0.23
37 29 0.47
38 4 0.06
39 14 0.23
40 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.40
Consensus pattern (34 bp):
ATTAAATTAAATTAAACTATTAAAATAATATTAA
Found at i:79713 original size:11 final size:11
Alignment explanation
Indices: 79697--79772 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
79687 AATAATCACT
79697 TTAATATTAAA
1 TTAATATTAAA
79708 TTAATA--AAA
1 TTAATATTAAA
*
79717 -TACTATTAAA
1 TTAATATTAAA
*
79727 ATAAGTATTAAA
1 TTAA-TATTAAA
79739 TTAA-ATTTAATA
1 TTAATA-TTAA-A
79751 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
79764 ATAATATTA
1 TTAATATTA
79773 TTTTTGGAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 4 0.08
11 17 0.33
12 15 0.29
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:81028 original size:16 final size:16
Alignment explanation
Indices: 81007--81037 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
80997 CTATGCATGC
*
81007 AAAATATGAAAGACAA
1 AAAATACGAAAGACAA
81023 AAAATACGAAAGACA
1 AAAATACGAAAGACA
81038 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.10, G:0.13, T:0.10
Consensus pattern (16 bp):
AAAATACGAAAGACAA
Found at i:82598 original size:8 final size:8
Alignment explanation
Indices: 82585--82609 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
82575 TCAGCTCATT
82585 TCATCACA
1 TCATCACA
82593 TCATCACA
1 TCATCACA
82601 TCATCACA
1 TCATCACA
82609 T
1 T
82610 AACATATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.28
Consensus pattern (8 bp):
TCATCACA
Found at i:83506 original size:3 final size:3
Alignment explanation
Indices: 83500--83528 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
83490 ATTTTAACCT
83500 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
83529 TAATATAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:84501 original size:22 final size:22
Alignment explanation
Indices: 84476--84523 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
84466 TCTCATTTAT
84476 ATTTAAATATATATTAGATTAG
1 ATTTAAATATATATTAGATTAG
*** *
84498 ATTTTCGTATATATTAGATTGG
1 ATTTAAATATATATTAGATTAG
84520 ATTT
1 ATTT
84524 TTATGCAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.50
Consensus pattern (22 bp):
ATTTAAATATATATTAGATTAG
Found at i:84524 original size:22 final size:22
Alignment explanation
Indices: 84483--84524 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
84473 TATATTTAAA
84483 TATATATTAGATTAGATTTTCG
1 TATATATTAGATTAGATTTTCG
*
84505 TATATATTAGATTGGATTTT
1 TATATATTAGATTAGATTTT
84525 TATGCAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.52
Consensus pattern (22 bp):
TATATATTAGATTAGATTTTCG
Found at i:85797 original size:18 final size:18
Alignment explanation
Indices: 85774--85808 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
85764 GAGTTAAACG
*
85774 AATCGAGTTATTCGAGTT
1 AATCGAATTATTCGAGTT
*
85792 AATCGAATTATTTGAGT
1 AATCGAATTATTCGAGT
85809 CAACTCAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (18 bp):
AATCGAATTATTCGAGTT
Found at i:85934 original size:22 final size:22
Alignment explanation
Indices: 85892--85938 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
85882 AACTATAATA
*
85892 TTTTACATTTTTACCCCAAACAT
1 TTTTACATTTTTACCCAAAAC-T
85915 TTTTAC-TTTTCT-CCCAAAACT
1 TTTTACATTTT-TACCCAAAACT
85936 TTT
1 TTT
85939 ACTCCTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 4 0.18
22 11 0.50
23 7 0.32
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTACATTTTTACCCAAAACT
Found at i:85962 original size:29 final size:30
Alignment explanation
Indices: 85914--85972 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
85904 ACCCCAAACA
*
85914 TTTTTACTTTTCTCCCAAAACTTTTACTCC
1 TTTTCACTTTTCTCCCAAAACTTTTACTCC
*
85944 TTTTCACTTTTC-CCTAAAACTTTTACTCC
1 TTTTCACTTTTCTCCCAAAACTTTTACTCC
85973 CCTCCCATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.20, C:0.31, G:0.00, T:0.49
Consensus pattern (30 bp):
TTTTCACTTTTCTCCCAAAACTTTTACTCC
Found at i:86673 original size:20 final size:20
Alignment explanation
Indices: 86648--86687 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
86638 CAAGAAGATA
86648 ATTGAAGCAAGTAAAGAACC
1 ATTGAAGCAAGTAAAGAACC
86668 ATTGAAGCAAGTAAAGAACC
1 ATTGAAGCAAGTAAAGAACC
86688 TAATCTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.20, T:0.15
Consensus pattern (20 bp):
ATTGAAGCAAGTAAAGAACC
Found at i:89567 original size:11 final size:11
Alignment explanation
Indices: 89551--89576 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
89541 ATCAAGTCCA
89551 TTTTTTTTTCT
1 TTTTTTTTTCT
89562 TTTTTTTTTCT
1 TTTTTTTTTCT
89573 TTTT
1 TTTT
89577 CACTCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:102774 original size:18 final size:17
Alignment explanation
Indices: 102733--102774 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
102723 TTATAAGTCT
*
102733 ATAATTTTTTATATTAT
1 ATAATTTTTTATATTAC
*
102750 ATTATTTTTATATATTAC
1 ATAATTTTT-TATATTAC
102768 ATAATTT
1 ATAATTT
102775 ATAACATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
ATAATTTTTTATATTAC
Found at i:117009 original size:19 final size:19
Alignment explanation
Indices: 116974--117010 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
116964 AAAGTAGTGA
116974 AAATTTATTTTCTTAGAAT
1 AAATTTATTTTCTTAGAAT
116993 AAATTCTATTTTC-TAGAA
1 AAATT-TATTTTCTTAGAA
117011 ATTATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (19 bp):
AAATTTATTTTCTTAGAAT
Found at i:119737 original size:22 final size:23
Alignment explanation
Indices: 119709--119751 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
119699 AAATAAATTT
119709 TTAAATT-CTAAAAATAAAAAGA
1 TTAAATTACTAAAAATAAAAAGA
*
119731 TTAAATTATTAAAAATAAAAA
1 TTAAATTACTAAAAATAAAAA
119752 TAAGAGAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
TTAAATTACTAAAAATAAAAAGA
Found at i:120219 original size:31 final size:31
Alignment explanation
Indices: 120193--120252 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
120183 TTTAATTTTC
*
120193 TTAAAAATAATAAAAGTATAATTTAATAATT
1 TTAAAAATAATAAAAATATAATTTAATAATT
** *
120224 TTAAAAATTTTAAAAATATAATCTAATAA
1 TTAAAAATAATAAAAATATAATTTAATAA
120253 AATAATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (31 bp):
TTAAAAATAATAAAAATATAATTTAATAATT
Found at i:120286 original size:24 final size:23
Alignment explanation
Indices: 120259--120304 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
120249 ATAAAATAAT
* *
120259 AAAATTATATTTTTTATTTTCATA
1 AAAATTATA-ATTTAATTTTCATA
120283 AAAATTATAATTTAATTTTCAT
1 AAAATTATAATTTAATTTTCAT
120305 TGACAAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
AAAATTATAATTTAATTTTCATA
Found at i:121669 original size:27 final size:27
Alignment explanation
Indices: 121619--121670 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
121609 TATAAACATT
*
121619 AAATATTAAATTTATATTATTTCTATA
1 AAATATTAAATTTATACTATTTCTATA
*
121646 AAATATTATATTTA-ACTATATTCTA
1 AAATATTAAATTTATACTAT-TTCTA
121671 AAACGTGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (27 bp):
AAATATTAAATTTATACTATTTCTATA
Found at i:122447 original size:25 final size:25
Alignment explanation
Indices: 122419--122490 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
122409 ATAATAAATT
122419 TTTTTAATTTGATACTTAAATTTGA
1 TTTTTAATTTGATACTTAAATTTGA
*
122444 -TTTTGATGTTG--A--T-AATTT--
1 TTTTTAAT-TTGATACTTAAATTTGA
122462 TTTTTAATTTGATACTTAAATTTGA
1 TTTTTAATTTGATACTTAAATTTGA
122487 TTTT
1 TTTT
122491 GATTTTAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 18
0.64 0.04 0.32
Matches are distributed among these distances:
18 3 0.08
19 6 0.17
20 6 0.17
21 1 0.03
22 1 0.03
23 6 0.17
24 6 0.17
25 7 0.19
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.60
Consensus pattern (25 bp):
TTTTTAATTTGATACTTAAATTTGA
Found at i:122473 original size:43 final size:43
Alignment explanation
Indices: 122412--122493 Score: 155
Period size: 43 Copynumber: 1.9 Consensus size: 43
122402 ATATTATATA
122412 ATAAATTTTTTTAATTTGATACTTAAATTTGATTTTGATGTTG
1 ATAAATTTTTTTAATTTGATACTTAAATTTGATTTTGATGTTG
*
122455 ATAATTTTTTTTAATTTGATACTTAAATTTGATTTTGAT
1 ATAAATTTTTTTAATTTGATACTTAAATTTGATTTTGAT
122494 TTTAATCGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.57
Consensus pattern (43 bp):
ATAAATTTTTTTAATTTGATACTTAAATTTGATTTTGATGTTG
Found at i:125273 original size:98 final size:98
Alignment explanation
Indices: 125114--125300 Score: 277
Period size: 98 Copynumber: 1.9 Consensus size: 98
125104 TTGGATTCAT
* * * * *
125114 TCGGTTTTAATTTAGGGAAATTGTTTTTGTTTATTCGTGATGATTATCAAAATACCTTTATATAA
1 TCGGTTTGAATTTAGGAAAATTGTTTCTGCTTATTCGTGATAATTATCAAAATACCTTTATATAA
* *
125179 TATTCTTTTTAAATATATAATAATTGGATTTGA
66 TATTATTTTAAAATATATAATAATTGGATTTGA
* *
125212 TCGGTTTGGATTTAGGAAAATTGTTTCTGCTTGTTCGTGATAATTATCAAAATACAC-TTATATA
1 TCGGTTTGAATTTAGGAAAATTGTTTCTGCTTATTCGTGATAATTATCAAAATAC-CTTTATATA
125276 ATATTATTTTAAAATATATAATAAT
65 ATATTATTTTAAAATATATAATAAT
125301 AAAATTTATA
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
98 78 0.99
99 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.47
Consensus pattern (98 bp):
TCGGTTTGAATTTAGGAAAATTGTTTCTGCTTATTCGTGATAATTATCAAAATACCTTTATATAA
TATTATTTTAAAATATATAATAATTGGATTTGA
Found at i:136082 original size:16 final size:16
Alignment explanation
Indices: 136043--136084 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
136033 TGTGTAAAAA
136043 AAACAT-AAATATAAAT
1 AAACATGAAA-ATAAAT
*
136059 AGACATGAAAATAAAT
1 AAACATGAAAATAAAT
*
136075 AAAGATGAAA
1 AAACATGAAA
136085 TAAGAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (16 bp):
AAACATGAAAATAAAT
Found at i:136773 original size:21 final size:19
Alignment explanation
Indices: 136733--136776 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
136723 AATACTTAAA
* *
136733 AAAAATTAAAACTTTGTTT
1 AAAAATAAAAACTTTCTTT
136752 AAAAATAAAAACTTTTTCTTT
1 AAAAATAAAAAC--TTTCTTT
136773 AAAA
1 AAAA
136777 TGATTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
21 10 0.48
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (19 bp):
AAAAATAAAAACTTTCTTT
Found at i:136904 original size:19 final size:20
Alignment explanation
Indices: 136880--136923 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
136870 CATAATTAAA
136880 AAAAATGAAAAC-TTTCTTT
1 AAAAATGAAAACTTTTCTTT
**
136899 AAAAATTTAAACTTTTTCTTT
1 AAAAATGAAAAC-TTTTCTTT
136920 AAAA
1 AAAA
136924 TGACTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (20 bp):
AAAAATGAAAACTTTTCTTT
Found at i:137033 original size:142 final size:143
Alignment explanation
Indices: 136683--137182 Score: 612
Period size: 142 Copynumber: 3.5 Consensus size: 143
136673 TTGTTTTAAA
* ** *
136683 AAAATCACTATTTTATTTAAAAA-TAAAAAATTTATTTCAAAATACTTAAAAAAAATTAAAACTT
1 AAAATCACTATTTTACTTAAAAATTAAAACTTTTATTTCAAAATAATTAAAAAAAATTAAAACTT
** * *
136747 TGTTTAAAAATAAAAACTTTTTCTTTAAAATGATTAAAAAAAACAGTTTTTTATTTTTTAAAATC
66 TGTTTAAAAATTTAAACTTTTTCTTTAAAATGACT-AAAAAAA-AGATTTTTA-TTTTTAAAATC
136812 TAAACTTTTTTTTAATG
128 TAAA-TTTTTTTTAATG
* * * * * * * *
136829 AAATTCACTACTTTAATTAAAAATTCAAACTTTTGTTTCGACATAATTAAAAAAAATGAAAACTT
1 AAAATCACTATTTTACTTAAAAATTAAAACTTTTATTTCAAAATAATTAAAAAAAATTAAAACTT
* * *
136894 TCTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAATAGATTTTTATTTTTAAAA-ATAT
66 TGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAAAAGATTTTTATTTTTAAAATCTA-
136958 AA-TTTTTTTAATG
130 AATTTTTTTTAATG
* **
136971 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTTGAAATAATTAAAAAAAATTAAAACTT
1 AAAATCACTATTTTACTTAAAAATTAAAACTTTTATTTCAAAATAATTAAAAAAAATTAAAACTT
* * **
137036 TGTTTAAAAATTTAAAATTTTTCCTTAAAATGACTAAAAAAAATCTTTTTATTTTTAAAATCTAA
66 TGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAAAAGATTTTTATTTTTAAAATCTAA
137101 ACTTTTTTTTTTAA-G
131 A---TTTTTTTTAATG
* * ** *
137116 AAAATCACTATTTTTCTTAAAAATTAAAATTTTTATTTCAAAATTGTTAAAAAAAAATCAAAACT
1 AAAATCACTATTTTACTTAAAAATTAAAACTTTTATTTCAAAATAATT-AAAAAAAATTAAAACT
137181 TT
65 TT
137183 TCCCAAGATC
Statistics
Matches: 306, Mismatches: 40, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
142 125 0.41
143 4 0.01
144 11 0.04
145 50 0.16
146 52 0.17
147 64 0.21
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (143 bp):
AAAATCACTATTTTACTTAAAAATTAAAACTTTTATTTCAAAATAATTAAAAAAAATTAAAACTT
TGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAAAAGATTTTTATTTTTAAAATCTAA
ATTTTTTTTAATG
Found at i:137628 original size:3 final size:3
Alignment explanation
Indices: 137620--137662 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
137610 CATGAAACCC
* * * *
137620 TAA TAA TAA TGA TAA TAA TAA TAA TAG TAT TGA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
137663 TTGGGTCCTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:137653 original size:21 final size:21
Alignment explanation
Indices: 137620--137662 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
137610 CATGAAACCC
137620 TAATAATAATGATAATAATAA
1 TAATAATAATGATAATAATAA
* *
137641 TAATAGTATTGATAATAATAA
1 TAATAATAATGATAATAATAA
137662 T
1 T
137663 TTGGGTCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (21 bp):
TAATAATAATGATAATAATAA
Found at i:139940 original size:61 final size:61
Alignment explanation
Indices: 139865--139983 Score: 229
Period size: 61 Copynumber: 2.0 Consensus size: 61
139855 CCTTGAAGTT
*
139865 CATCCACGATCGTAATCTAGTCCGGTAAGTTTGTATTGTTAAATTCCTATATATATATATA
1 CATCCACGATCGTAATCTAGTCCGGTAAGTTTGTACTGTTAAATTCCTATATATATATATA
139926 CATCCACGATCGTAATCTAGTCCGGTAAGTTTGTACTGTTAAATTCCTATATATATAT
1 CATCCACGATCGTAATCTAGTCCGGTAAGTTTGTACTGTTAAATTCCTATATATATAT
139984 TGCATATTCT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (61 bp):
CATCCACGATCGTAATCTAGTCCGGTAAGTTTGTACTGTTAAATTCCTATATATATATATA
Found at i:140194 original size:52 final size:51
Alignment explanation
Indices: 140095--140272 Score: 284
Period size: 52 Copynumber: 3.4 Consensus size: 51
140085 AAACGAAAAG
* * * *
140095 GGTCCGATAATTATGTGTCATCGTGAGTATATAAATTCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCTTGAGTATATAAA-TCTTTATGGATTATGA
*
140147 GGTCAGATGACTATGTGTCATCTTGAGTATATAAATCATTTATGGATTATGA
1 GGTCCGATGACTATGTGTCATCTTGAGTATATAAATC-TTTATGGATTATGA
140199 GGTCCGATGACTATGTGTCATCTTGAGTATATAAATCCTTTATGGATTATGA
1 GGTCCGATGACTATGTGTCATCTTGAGTATATAAAT-CTTTATGGATTATGA
140251 GGTCCGATGACTATGTGTCATC
1 GGTCCGATGACTATGTGTCATC
140273 ATTATGGATT
Statistics
Matches: 118, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
51 2 0.02
52 115 0.97
53 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.38
Consensus pattern (51 bp):
GGTCCGATGACTATGTGTCATCTTGAGTATATAAATCTTTATGGATTATGA
Found at i:140295 original size:33 final size:35
Alignment explanation
Indices: 140238--140305 Score: 113
Period size: 33 Copynumber: 2.0 Consensus size: 35
140228 TATAAATCCT
140238 TTATGGATTATGAGGTCCGATGACTATGTGTCATCA
1 TTATGGATTATGA-GTCCGATGACTATGTGTCATCA
140274 TTATGGATTAT-A-TCCGATGACTATGTGTCATC
1 TTATGGATTATGAGTCCGATGACTATGTGTCATC
140306 GTGAGTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 20 0.62
35 1 0.03
36 11 0.34
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (35 bp):
TTATGGATTATGAGTCCGATGACTATGTGTCATCA
Found at i:140332 original size:85 final size:88
Alignment explanation
Indices: 140181--140357 Score: 270
Period size: 85 Copynumber: 2.0 Consensus size: 88
140171 GAGTATATAA
* * **
140181 ATCATTTATGGATTATGAGGTCCGATGACTATGTGTCATCTTGAGTATATAAATCCTTTATGGAT
1 ATCATTTATGGATTATGA-GTCCGATGACTATGTGTCATCGTGAGTATAAAAATCCTTTACAGAT
*
140246 TATGAGGTCCGATGACTATGTGTC
65 TATGAGGTCCGATGACTATGTATC
140270 ATCA-TTATGGATTAT-A-TCCGATGACTATGTGTCATCGTGAGTATAAAAATCCTTTACAGATT
1 ATCATTTATGGATTATGAGTCCGATGACTATGTGTCATCGTGAGTATAAAAATCCTTTACAGATT
*
140332 ATGAGTTCCGATGACTATGTATC
66 ATGAGGTCCGATGACTATGTATC
140355 ATC
1 ATC
140358 GTGACTATAT
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
85 66 0.80
87 1 0.01
88 11 0.13
89 4 0.05
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (88 bp):
ATCATTTATGGATTATGAGTCCGATGACTATGTGTCATCGTGAGTATAAAAATCCTTTACAGATT
ATGAGGTCCGATGACTATGTATC
Found at i:140357 original size:52 final size:52
Alignment explanation
Indices: 140286--140421 Score: 186
Period size: 52 Copynumber: 2.6 Consensus size: 52
140276 ATGGATTATA
* *
140286 TCCGATGACTATGTGTCATCGTGAGTATA-AAAATCCTTTACAGATTATGAGT
1 TCCGATGACTATGTGTCATCGTGAGTATATAAAA-CCTTTACAGATTAAGAGG
* * * *
140338 TCCGATGACTATGTATCATCGTGACTATATGAAACCTTTACAGGTTAAGAGG
1 TCCGATGACTATGTGTCATCGTGAGTATATAAAACCTTTACAGATTAAGAGG
*
140390 TCCGATGACTATGTGTTATCGTGAGTAT-TAAA
1 TCCGATGACTATGTGTCATCGTGAGTATATAAA
140422 TGAAAATGAA
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
51 3 0.04
52 67 0.92
53 3 0.04
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (52 bp):
TCCGATGACTATGTGTCATCGTGAGTATATAAAACCTTTACAGATTAAGAGG
Found at i:140398 original size:137 final size:137
Alignment explanation
Indices: 140152--140405 Score: 377
Period size: 137 Copynumber: 1.9 Consensus size: 137
140142 TATGAGGTCA
* * ** *
140152 GATGACTATGTGTCATCTTGAGTATATAAATCATTTATGGATTATGAGGTCCGATGACTATGTGT
1 GATGACTATGTGTCATCGTGAGTATAAAAATCATTTACAGATTATGAGGTCCGATGACTATGTAT
* * * *
140217 CATCTTGAGTATATAAATCCTTTATGGATTATGAGGTCCGATGACTATGTGTCATCATTATGGAT
66 CATCGTGACTATATAAATCCTTTAAGGATTAAGAGGTCCGATGACTATGTGTCATCATTATGGAT
140282 TATATCC
131 TATATCC
* *
140289 GATGACTATGTGTCATCGTGAGTATAAAAATCCTTTACAGATTATGAGTTCCGATGACTATGTAT
1 GATGACTATGTGTCATCGTGAGTATAAAAATCATTTACAGATTATGAGGTCCGATGACTATGTAT
140354 CATCGTGACTATATGAAA-CCTTTACAGG-TTAAGAGGTCCGATGACTATGTGT
66 CATCGTGACTATAT-AAATCCTTTA-AGGATTAAGAGGTCCGATGACTATGTGT
140406 TATCGTGAGT
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
137 99 0.95
138 5 0.05
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (137 bp):
GATGACTATGTGTCATCGTGAGTATAAAAATCATTTACAGATTATGAGGTCCGATGACTATGTAT
CATCGTGACTATATAAATCCTTTAAGGATTAAGAGGTCCGATGACTATGTGTCATCATTATGGAT
TATATCC
Found at i:141076 original size:21 final size:21
Alignment explanation
Indices: 141050--141102 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
141040 GTGATTGAGA
141050 GTATCGGTAGATTCTGTACTT
1 GTATCGGTAGATTCTGTACTT
141071 GTATCGGTAGATTCTGTACTT
1 GTATCGGTAGATTCTGTACTT
141092 GTATCGGTAGA
1 GTATCGGTAGA
141103 AGTTGCAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.40
Consensus pattern (21 bp):
GTATCGGTAGATTCTGTACTT
Found at i:142375 original size:3 final size:3
Alignment explanation
Indices: 142369--142416 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
142359 GTACGTGTGA
142369 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
142417 AGTTTAATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:142437 original size:13 final size:14
Alignment explanation
Indices: 142419--142448 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
142409 ATTATTATAG
142419 TTTAATTA-GATTT
1 TTTAATTAGGATTT
142432 TTTAATTAGGATTT
1 TTTAATTAGGATTT
142446 TTT
1 TTT
142449 GTGATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (14 bp):
TTTAATTAGGATTT
Found at i:147314 original size:17 final size:17
Alignment explanation
Indices: 147284--147318 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
147274 AATACATGAG
*
147284 TAAATAATTTTTTGGGT
1 TAAATAATTATTTGGGT
*
147301 TAAATTATTATTTGGGT
1 TAAATAATTATTTGGGT
147318 T
1 T
147319 TTAAATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (17 bp):
TAAATAATTATTTGGGT
Found at i:152827 original size:3 final size:3
Alignment explanation
Indices: 152821--152845 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
152811 CATCATCGTC
152821 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
152846 GAATGTGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:160687 original size:24 final size:24
Alignment explanation
Indices: 160654--160709 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
160644 TATATTGTTG
* *
160654 TTTTGGTGCTGTTTT-TTATGTTAT
1 TTTTGTTGCTGTTTTGAT-TGTTAT
160678 TTTTGTTGCTGTTTTGATTGTTAT
1 TTTTGTTGCTGTTTTGATTGTTAT
160702 TTTTGTTG
1 TTTTGTTG
160710 TTTGGTTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.07, C:0.04, G:0.21, T:0.68
Consensus pattern (24 bp):
TTTTGTTGCTGTTTTGATTGTTAT
Found at i:169067 original size:15 final size:17
Alignment explanation
Indices: 169047--169080 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
169037 AATTTTTGGA
169047 TGATTTT-AGTTT-AAT
1 TGATTTTAAGTTTCAAT
169062 TGATTTTAAGTTTCAAT
1 TGATTTTAAGTTTCAAT
169079 TG
1 TG
169081 TTCAAGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 5 0.29
17 5 0.29
ACGTcount: A:0.26, C:0.03, G:0.15, T:0.56
Consensus pattern (17 bp):
TGATTTTAAGTTTCAAT
Found at i:180406 original size:3 final size:3
Alignment explanation
Indices: 180398--180424 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
180388 TTTGAATGCT
180398 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
180425 ACTTCCTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:181783 original size:18 final size:19
Alignment explanation
Indices: 181754--181849 Score: 103
Period size: 18 Copynumber: 5.3 Consensus size: 19
181744 GAAAGAGGAA
181754 CCAAAGAAAGAAGGTGAAG
1 CCAAAGAAAGAAGGTGAAG
*
181773 CCAAA-AAAGAAGATGAA-
1 CCAAAGAAAGAAGGTGAAG
*
181790 CAAAAGAAAGAAGGTGAAG
1 CCAAAGAAAGAAGGTGAAG
* *
181809 CC-AAGAAGGAAGATGAA-
1 CCAAAGAAAGAAGGTGAAG
*
181826 -CAGAAGAAAGAAGGAGAAG
1 CCA-AAGAAAGAAGGTGAAG
181845 CCAAA
1 CCAAA
181850 AAGGAAGAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
16 1 0.02
17 4 0.06
18 47 0.76
19 8 0.13
20 2 0.03
ACGTcount: A:0.57, C:0.10, G:0.28, T:0.04
Consensus pattern (19 bp):
CCAAAGAAAGAAGGTGAAG
Found at i:181797 original size:36 final size:36
Alignment explanation
Indices: 181746--181857 Score: 170
Period size: 36 Copynumber: 3.1 Consensus size: 36
181736 CCAGAGAAGA
* * *
181746 AAGAGGAACCAAAGAAAGAAGGTGAAGCCAAAAAAG
1 AAGATGAACAAAAGAAAGAAGGTGAAGCCAAAAAGG
*
181782 AAGATGAACAAAAGAAAGAAGGTGAAGCCAAGAAGG
1 AAGATGAACAAAAGAAAGAAGGTGAAGCCAAAAAGG
* *
181818 AAGATGAACAGAAGAAAGAAGGAGAAGCCAAAAAGG
1 AAGATGAACAAAAGAAAGAAGGTGAAGCCAAAAAGG
181854 AAGA
1 AAGA
181858 AGAAGGTAAG
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.58, C:0.09, G:0.29, T:0.04
Consensus pattern (36 bp):
AAGATGAACAAAAGAAAGAAGGTGAAGCCAAAAAGG
Found at i:181869 original size:36 final size:35
Alignment explanation
Indices: 181757--181874 Score: 155
Period size: 36 Copynumber: 3.3 Consensus size: 35
181747 AGAGGAACCA
* *
181757 AAGAAAGAAGGTGAAGCCAAAAAAGAAGATGAACAA
1 AAGAAAGAAGGTGAAGCCAAAAAGGAAGATGAA-AG
*
181793 AAGAAAGAAGGTGAAGCCAAGAAGGAAGATGAACAG
1 AAGAAAGAAGGTGAAGCCAAAAAGGAAGATGAA-AG
* * *
181829 AAGAAAGAAGGAGAAGCCAAAAAGGAAGAAGAAGG
1 AAGAAAGAAGGTGAAGCCAAAAAGGAAGATGAAAG
181864 TAAGAAAGAAG
1 -AAGAAAGAAG
181875 AGGAAACCAA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
35 1 0.01
36 73 0.99
ACGTcount: A:0.58, C:0.07, G:0.31, T:0.04
Consensus pattern (35 bp):
AAGAAAGAAGGTGAAGCCAAAAAGGAAGATGAAAG
Found at i:181869 original size:72 final size:72
Alignment explanation
Indices: 181734--181887 Score: 186
Period size: 72 Copynumber: 2.1 Consensus size: 72
181724 CCAGCAAAAG
* *
181734 AACCAGAGAAGAAAGAGGAACCAAAGAAAGAAGGTGAAGCCAAAAAAGAAGATGAACAAAAGAAA
1 AACCA-AGAAGAAAGAGGAACCAAAGAAAGAAGGAGAAGCCAAAAAAGAAGAAGAACAAAAGAAA
181799 GAAG-GTGA
65 GAAGAG-GA
* * * * ***
181807 AGCCAAGAAGGAAGATGAA-CAGAAGAAAGAAGGAGAAGCCAAAAAGGAAGAAGAAGGTAAGAAA
1 AACCAAGAAGAAAGAGGAACCA-AAGAAAGAAGGAGAAGCCAAAAAAGAAGAAGAACAAAAGAAA
181871 GAAGAGGA
65 GAAGAGGA
181879 AACCAAGAA
1 AACCAAGAA
181888 AGATGGTGAG
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
71 2 0.03
72 62 0.90
73 5 0.07
ACGTcount: A:0.58, C:0.09, G:0.29, T:0.03
Consensus pattern (72 bp):
AACCAAGAAGAAAGAGGAACCAAAGAAAGAAGGAGAAGCCAAAAAAGAAGAAGAACAAAAGAAAG
AAGAGGA
Found at i:181874 original size:18 final size:18
Alignment explanation
Indices: 181757--181890 Score: 85
Period size: 18 Copynumber: 7.4 Consensus size: 18
181747 AGAGGAACCA
**
181757 AAGAAAGAAGGTGAAGCC
1 AAGAAAGAAGAAGAAGCC
* * *
181775 AAAAAAGAAGATGAA-CAA
1 AAGAAAGAAGAAGAAGC-C
**
181793 AAGAAAGAAGGTGAAGCC
1 AAGAAAGAAGAAGAAGCC
* * *
181811 AAGAAGGAAGATGAA-CAG
1 AAGAAAGAAGAAGAAGC-C
*
181829 AAGAAAGAAGGAGAAGCC
1 AAGAAAGAAGAAGAAGCC
**
181847 AA-AAAGGAAGAAGAAGGT
1 AAGAAA-GAAGAAGAAGCC
* *
181865 AAGAAAGAAGAGGAAACC
1 AAGAAAGAAGAAGAAGCC
181883 AAGAAAGA
1 AAGAAAGA
181891 TGGTGAGAAG
Statistics
Matches: 90, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
17 5 0.06
18 80 0.89
19 5 0.06
ACGTcount: A:0.59, C:0.07, G:0.30, T:0.04
Consensus pattern (18 bp):
AAGAAAGAAGAAGAAGCC
Found at i:197786 original size:58 final size:59
Alignment explanation
Indices: 197686--197883 Score: 239
Period size: 58 Copynumber: 3.4 Consensus size: 59
197676 AAGGTCCCTA
* * * *
197686 AACTGTCCAAAAATTCAATTTTTAACCCCAAAACTTTCAAAAATTATATTTTTACCCTCG
1 AACTATCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTACATTTTTACCC-CG
*
197746 AACT-TCCAAAAATTCCATTTTT-ACCCCAAAACTTCCAAAAATTACATTTTTACCCCTA
1 AACTATCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTACATTTTTACCCC-G
* *
197804 AACT-TCC-AAAATTCCATTTTTGACCTCAAAAC-TCTCAAAAATTACCA-TTTTACCCCCG
1 AACTATCCAAAAATTCCATTTTTAACCCCAAAACTTC-CAAAAATTA-CATTTTTA-CCCCG
197862 AA-TATCCAAAAATTCCATTTTT
1 AACTATCCAAAAATTCCATTTTT
197884 TTATCTCGAT
Statistics
Matches: 125, Mismatches: 6, Indels: 15
0.86 0.04 0.10
Matches are distributed among these distances:
57 18 0.14
58 66 0.53
59 37 0.30
60 4 0.03
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (59 bp):
AACTATCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTACATTTTTACCCCG
Found at i:197871 original size:29 final size:29
Alignment explanation
Indices: 197685--197883 Score: 199
Period size: 29 Copynumber: 6.8 Consensus size: 29
197675 GAAGGTCCCT
* *
197685 AAACTGTCCAAAAATTCAATTTTTAACCCCA
1 AAACT-TCCAAAAATTCCATTTTT-ACCCCC
* ** *
197716 AAACTTTCAAAAATTATATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *
197745 GAACTTCCAAAAATTCCATTTTTACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *
197774 AAACTTCCAAAAATTACATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *
197803 AAACTTCC-AAAATTCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
197832 AAAC-TCTCAAAAATTACCA-TTTTACCCCC
1 AAACTTC-CAAAAATT-CCATTTTTACCCCC
*
197861 GAA-TATCCAAAAATTCCATTTTT
1 AAACT-TCCAAAAATTCCATTTTT
197884 TTATCTCGAT
Statistics
Matches: 141, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
28 18 0.13
29 88 0.62
30 27 0.19
31 8 0.06
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:198016 original size:28 final size:27
Alignment explanation
Indices: 197956--198016 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
197946 CTAAATTTTC
197956 CCAAAATTACATTTTACCCTCGAGAAT
1 CCAAAATTACATTTTACCCTCGAGAAT
* * * *
197983 CTAAAATTACCATTTTGCCCTTGAGTAT
1 CCAAAATTA-CATTTTACCCTCGAGAAT
198011 CCAAAA
1 CCAAAA
198017 AGTCTCATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.31
Consensus pattern (27 bp):
CCAAAATTACATTTTACCCTCGAGAAT
Done.