Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold409
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: 3905031
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 17 of 25
Found at i:2575800 original size:28 final size:28
Alignment explanation
Indices: 2575756--2575834 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
2575746 CAAATGAGGA
*
2575756 CTTT-AAAGAGGTTCCACTGACTCATAGG
1 CTTTAAAAG-GGTGCCACTGACTCATAGG
* *
2575784 CTTTAAAAGGGTGCCACTGACTTATTGG
1 CTTTAAAAGGGTGCCACTGACTCATAGG
2575812 CTTTGAAAAGGGTGCCACTGACT
1 CTTT-AAAAGGGTGCCACTGACT
2575835 TGTGGGCTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 24 0.52
29 22 0.48
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (28 bp):
CTTTAAAAGGGTGCCACTGACTCATAGG
Found at i:2575858 original size:29 final size:29
Alignment explanation
Indices: 2575760--2575850 Score: 121
Period size: 29 Copynumber: 3.1 Consensus size: 29
2575750 TGAGGACTTT
* * *
2575760 AAAGAGGTTCCACTGACTCATAGGCTTT-A
1 AAAG-GGTGCCACTGACTTATGGGCTTTGA
*
2575789 AAAGGGTGCCACTGACTTATTGGCTTTGA
1 AAAGGGTGCCACTGACTTATGGGCTTTGA
*
2575818 AAAGGGTGCCACTGACTTGTGGGCTTTGA
1 AAAGGGTGCCACTGACTTATGGGCTTTGA
2575847 AAAG
1 AAAG
2575851 AATGCCACCA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
28 20 0.36
29 36 0.64
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (29 bp):
AAAGGGTGCCACTGACTTATGGGCTTTGA
Found at i:2575891 original size:31 final size:31
Alignment explanation
Indices: 2575856--2575939 Score: 159
Period size: 31 Copynumber: 2.7 Consensus size: 31
2575846 AAAAGAATGC
*
2575856 CACCAACTCGTGTGGACTTTGACTGCGGTGA
1 CACCAACTCATGTGGACTTTGACTGCGGTGA
2575887 CACCAACTCATGTGGACTTTGACTGCGGTGA
1 CACCAACTCATGTGGACTTTGACTGCGGTGA
2575918 CACCAACTCATGTGGACTTTGA
1 CACCAACTCATGTGGACTTTGA
2575940 AAAGGATTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (31 bp):
CACCAACTCATGTGGACTTTGACTGCGGTGA
Found at i:2575965 original size:33 final size:35
Alignment explanation
Indices: 2575928--2576049 Score: 95
Period size: 37 Copynumber: 3.4 Consensus size: 35
2575918 CACCAACTCA
*
2575928 TGTGGACTTTGAAAAGGAT-TATGCCAC-AACTTC
1 TGTGGACTTTGAAAAGGATGGATGCCACAAACTTC
* * *
2575961 TGTGGACTTTGGAAACAGTATGGCTGCCACAAACTTG
1 TGTGGACTTT-GAAA-AGGATGGATGCCACAAACTTC
* * * * *
2575998 TGTGAACTTTGAAAAAGGTTTGGTTGCCACCAACTTA
1 TGTGGACTTTG-AAAAGG-ATGGATGCCACAAACTTC
* *
2576035 TGTAGACTTTAAAAA
1 TGTGGACTTTGAAAA
2576050 TGATTTGGTT
Statistics
Matches: 70, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
33 10 0.14
34 4 0.06
35 4 0.06
36 13 0.19
37 39 0.56
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (35 bp):
TGTGGACTTTGAAAAGGATGGATGCCACAAACTTC
Found at i:2576026 original size:37 final size:37
Alignment explanation
Indices: 2575949--2576086 Score: 124
Period size: 37 Copynumber: 3.8 Consensus size: 37
2575939 AAAAGGATTA
* * * * *
2575949 TGCCA-CAACTTCTGTGGACTTTGGAAACA-GTATGGC
1 TGCCACCAACTTGTGTGAACTTT-GAAAAAGGTTTGGT
*
2575985 TGCCACAAACTTGTGTGAACTTTGAAAAAGGTTTGGT
1 TGCCACCAACTTGTGTGAACTTTGAAAAAGGTTTGGT
* *
2576022 TGCCACCAACTTATGT-AGACTTT-AAAAATGATTTGGT
1 TGCCACCAACTTGTGTGA-ACTTTGAAAAA-GGTTTGGT
* *
2576059 TGCCACCTACTTGTGTGAA-TTTTAAAAA
1 TGCCACCAACTTGTGTGAACTTTGAAAAA
2576087 TGATTTAGTT
Statistics
Matches: 85, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
36 19 0.22
37 65 0.76
38 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (37 bp):
TGCCACCAACTTGTGTGAACTTTGAAAAAGGTTTGGT
Found at i:2576087 original size:37 final size:37
Alignment explanation
Indices: 2575985--2576092 Score: 130
Period size: 37 Copynumber: 2.9 Consensus size: 37
2575975 ACAGTATGGC
* * *
2575985 TGCCACAAACTTGTGTGAACTTTGAAAAA-GGTTTGGT
1 TGCCACCAACTTGTGTGAA-TTTTAAAAATGATTTGGT
* *
2576022 TGCCACCAACTTATGT-AGACTTTAAAAATGATTTGGT
1 TGCCACCAACTTGTGTGA-ATTTTAAAAATGATTTGGT
*
2576059 TGCCACCTACTTGTGTGAATTTTAAAAATGATTT
1 TGCCACCAACTTGTGTGAATTTTAAAAATGATTT
2576093 AGTTTCTGTG
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
36 8 0.13
37 51 0.85
38 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.36
Consensus pattern (37 bp):
TGCCACCAACTTGTGTGAATTTTAAAAATGATTTGGT
Found at i:2578977 original size:21 final size:21
Alignment explanation
Indices: 2578953--2578997 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
2578943 AGGGGTTTAT
2578953 TACAACATTCGGCGTTTGACC
1 TACAACATTCGGCGTTTGACC
2578974 TACAACATTCGGCGTTTGACC
1 TACAACATTCGGCGTTTGACC
2578995 TAC
1 TAC
2578998 CCCAAACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (21 bp):
TACAACATTCGGCGTTTGACC
Found at i:2580200 original size:61 final size:61
Alignment explanation
Indices: 2580095--2580283 Score: 173
Period size: 61 Copynumber: 3.1 Consensus size: 61
2580085 GACACCTTTG
* * ** * * * *
2580095 TCATCTTTAAGCCTAA-ATCACTGGCCTTGAATTAGCATACTGGCACCTTTATCATTCTTC
1 TCATCTTCAAGCCCAATATCACTAACCATGAATCAACATATTGGCACCTTTATCATTCTTC
* * *
2580155 TCATCTTCAAGCCCGATATCACTATCCATGAATCAACATATTGGCACCTTTATTATTCTTC
1 TCATCTTCAAGCCCAATATCACTAACCATGAATCAACATATTGGCACCTTTATCATTCTTC
* * * * * * * * * * *
2580216 CCATCTTTAAGTCCAATGTCACTAACCTTGAATCAATACATTGGCACTTTTCTCATCCTTA
1 TCATCTTCAAGCCCAATATCACTAACCATGAATCAACATATTGGCACCTTTATCATTCTTC
2580277 TCATCTT
1 TCATCTT
2580284 TAAGTCCGGT
Statistics
Matches: 103, Mismatches: 25, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
60 13 0.13
61 90 0.87
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.37
Consensus pattern (61 bp):
TCATCTTCAAGCCCAATATCACTAACCATGAATCAACATATTGGCACCTTTATCATTCTTC
Found at i:2580284 original size:61 final size:61
Alignment explanation
Indices: 2580135--2580290 Score: 186
Period size: 61 Copynumber: 2.6 Consensus size: 61
2580125 ATTAGCATAC
* * * * *
2580135 TGGCACCTTTATCATTCTTCTCATCTTCAAGCCCGATATCACTATCCATGAATCAACATAT
1 TGGCACCTTTATCATTCTTCTCATCTTTAAGTCCAATATCACTAACCATGAATCAACACAT
* * * * *
2580196 TGGCACCTTTATTATTCTTCCCATCTTTAAGTCCAATGTCACTAACCTTGAATCAATACAT
1 TGGCACCTTTATCATTCTTCTCATCTTTAAGTCCAATATCACTAACCATGAATCAACACAT
* * * *
2580257 TGGCACTTTTCTCATCCTTATCATCTTTAAGTCC
1 TGGCACCTTTATCATTCTTCTCATCTTTAAGTCC
2580291 GGTGTTACAG
Statistics
Matches: 79, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 79 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.38
Consensus pattern (61 bp):
TGGCACCTTTATCATTCTTCTCATCTTTAAGTCCAATATCACTAACCATGAATCAACACAT
Found at i:2580984 original size:20 final size:20
Alignment explanation
Indices: 2580943--2580993 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2580933 TATGATTTGA
*
2580943 ATCGATACAATTAGTAAATGT
1 ATCGATAC-ATAAGTAAATGT
*
2580964 ATCGATACATAAGTGAATGT
1 ATCGATACATAAGTAAATGT
*
2580984 ATTGATACAT
1 ATCGATACAT
2580994 GCCTGAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (20 bp):
ATCGATACATAAGTAAATGT
Found at i:2581063 original size:20 final size:20
Alignment explanation
Indices: 2581038--2581093 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
2581028 TCTGGAAAAA
2581038 AAATGTATCGATACATAAGT
1 AAATGTATCGATACATAAGT
2581058 AAATGTATCGATACATAAGT
1 AAATGTATCGATACATAAGT
2581078 AAATGTATCGATACAT
1 AAATGTATCGATACAT
2581094 GCTCACAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (20 bp):
AAATGTATCGATACATAAGT
Found at i:2581109 original size:22 final size:20
Alignment explanation
Indices: 2581041--2581136 Score: 81
Period size: 20 Copynumber: 4.7 Consensus size: 20
2581031 GGAAAAAAAA
* *
2581041 TGTATCGATACATAAGT-AAA
1 TGTATCGATACATTA-TCAAT
* *
2581061 TGTATCGATACATAAGT-AAA
1 TGTATCGATACATTA-TCAAT
2581081 TGTATCGATACATGCTCA-CAAT
1 TGTATCGATACAT--T-ATCAAT
*
2581103 TGTATCGATACATTATCTAT
1 TGTATCGATACATTATCAAT
2581123 TGTATCGATACATT
1 TGTATCGATACATT
2581137 TTGGGTTTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.01
20 51 0.75
22 15 0.22
23 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATTATCAAT
Found at i:2590615 original size:13 final size:13
Alignment explanation
Indices: 2590597--2590622 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2590587 TACACCAAGT
2590597 ATGTATCGATACA
1 ATGTATCGATACA
2590610 ATGTATCGATACA
1 ATGTATCGATACA
2590623 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2590620 original size:32 final size:33
Alignment explanation
Indices: 2590579--2590642 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2590569 TAGCCAAACT
* **
2590579 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2590611 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2590643 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2595971 original size:158 final size:157
Alignment explanation
Indices: 2595189--2596195 Score: 616
Period size: 158 Copynumber: 6.4 Consensus size: 157
2595179 CCTAATCACA
* * * * * * * *
2595189 AAAAGAATGGACATTATTACGAAAATCCATGTTTATCTTATTTGATGGATTAACTTTTATTCTTA
1 AAAAGAATAGAGATTATTATGAGAATCCATGTTTGTCTTATTTGATGGATGAACTTTGATTCTAA
* * * * * **
2595254 GGAAAATAATGGAAGGAAAAGCTATTCTTGCAAACCAGAGCATTAATATCGTGTATCCCAACGAG
66 GGAAAATTATGGAAAGAAAAGCT-TTCTTGCAAACCAAAGCATTAATATCATATATCCCAATAAG
* *
2595319 GAAAAGGTGTTTATGGTTCCCAAT-ATA
130 GAAAACGTGTTTATGGTTCCCAATCATG
* * * * * * *
2595346 AAAAAAATGGAGATTATTTTAAGAATTCATGTTTGTCTTGTTTGATTGATGAACTTTGATTCTAA
1 AAAAGAATAGAGATTATTATGAGAATCCATGTTTGTCTTATTTGATGGATGAACTTTGATTCTAA
* * ** * ** *
2595411 AGTAAATGGTGAAAAGAAAAGCACTTT-TTGCGAAATAAAAGCATGAATATCATATATCCCAATA
66 GGAAAATTATGGAAAGAAAAG--CTTTCTTGC-AAACCAAAGCATTAATATCATATATCCCAATA
* * * * * **
2595475 AGGAGAATGCGTTTACGGTGCCCAATC-CC
128 AGGAAAACGTGTTTATGGTTCCCAATCATG
* * * * * * *
2595504 AAAAGGAGAGGAGATTATTATGTGAATTCTTGTTTGTTTTATTTGA-GGAATGAACTTTGATTCC
1 AAAAGAATA-GAGATTATTATGAGAATCCATGTTTGTCTTATTTGATGG-ATGAACTTTGATTCT
* * * *
2595568 ATA-G-AAATTGATGGAAAGAAAAGCTTTTCTTTTG-AAATCAAAGCATCAACATCATTTATCCC
64 A-AGGAAAATT-ATGGAAAGAAAAGC-TTTC--TTGCAAACCAAAGCATTAATATCATATATCCC
* * * * *
2595630 AA-ATAGTATAACATGTTTATAG-TCTCTAATCATG
124 AATA-AGGAAAACGTGTTTATGGTTC-CCAATCATG
* * ** * ** * * *
2595664 AAAAGAATGGGGATTATTACAAAAATCCAAATCTT-TCTTATTTAATAGATGAACTATGA--CT-
1 AAAAGAATAGAGATTATTATGAGAATCCATGT-TTGTCTTATTTGATGGATGAACTTTGATTCTA
* * * * * * * * *
2595725 TGCAAAA-TGTGGGAAGAAAAGCTTTTCTTGTGAAGCCAAAGCTTTAATATCCTATATCCCAATG
65 AGGAAAATTATGGAAAGAAAAGC-TTTCTTG-CAAACCAAAGCATTAATATCATATATCCCAATA
* ** * * *
2595789 AGTAAAACAAGTTTGTAGTGCCCAATCATG
128 AGGAAAACGTGTTTATGGTTCCCAATCATG
* * * *
2595819 AAAACAATAGAGATTATTATGGGAATCCATATTTGTCTTATTCGATGGATGAACTTTGATTCTAA
1 AAAAGAATAGAGATTATTATGAGAATCCATGTTTGTCTTATTTGATGGATGAACTTTGATTCTAA
* * * *
2595884 GGAAAATTATGGAAGGAAAACCTTGTCTTGCAAACCAAAGCATTAATATCATGTGTCCCAATAAG
66 GGAAAATTATGGAAAGAAAAGCTT-TCTTGCAAACCAAAGCATTAATATCATATATCCCAATAAG
* *
2595949 GAGAATGTGTTTATGGTTCCCAAT-ATTG
130 GAAAACGTGTTTATGGTTCCCAATCA-TG
* * * *
2595977 AAAAGAAGAGAGATTATTATGAGAATCCATGTTTGTCTTATTT-ACCGGACGAACTTTGGTTCTA
1 AAAAGAATAGAGATTATTATGAGAATCCATGTTTGTCTTATTTGA-TGGATGAACTTTGATTCTA
* * * * ** * *
2596041 AAGAAAA-TAGAGGAAAGAAATGCTTTTCTTGCAAAACAAAAGCACCAATATCGTATATCCTAAT
65 AGGAAAATTA-TGGAAAGAAAAGC-TTTCTTGC-AAACCAAAGCATTAATATCATATATCCCAAT
* * * * * **
2596105 GACGAAAACATGCTTATGGTGT-TCAATC-CC
127 AAGGAAAACGTGTTTATGGT-TCCCAATCATG
* * * * *
2596135 AAAAGGAACT-G-GATTATTACGAGAATCCTTGTTTATTTTATTTGAAGGATGAACTTTGATT
1 AAAA-GAA-TAGAGATTATTATGAGAATCCATGTTTGTCTTATTTGATGGATGAACTTTGATT
2596196 TTACGAAATT
Statistics
Matches: 643, Mismatches: 168, Indels: 77
0.72 0.19 0.09
Matches are distributed among these distances:
153 3 0.00
154 2 0.00
155 107 0.17
156 2 0.00
157 82 0.13
158 235 0.37
159 198 0.31
160 11 0.02
161 3 0.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (157 bp):
AAAAGAATAGAGATTATTATGAGAATCCATGTTTGTCTTATTTGATGGATGAACTTTGATTCTAA
GGAAAATTATGGAAAGAAAAGCTTTCTTGCAAACCAAAGCATTAATATCATATATCCCAATAAGG
AAAACGTGTTTATGGTTCCCAATCATG
Found at i:2600422 original size:20 final size:20
Alignment explanation
Indices: 2600372--2600446 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
2600362 TTTTCACAAT
* * *
2600372 TTGTATCAATACACTGTTCA
1 TTGTATCGATACATTGCTCA
2600392 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGCTCA
* *
2600412 TTGTATTGATACATT-TTACA
1 TTGTATCGATACATTGCT-CA
*
2600432 ATGTATCGATACATT
1 TTGTATCGATACATT
2600447 CAGGCATTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.02
20 46 0.98
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACATTGCTCA
Found at i:2602880 original size:79 final size:78
Alignment explanation
Indices: 2602749--2603316 Score: 332
Period size: 79 Copynumber: 7.2 Consensus size: 78
2602739 TTTTCATCTC
* * * * **
2602749 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCAATTTTTCGTAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCTGGCTTTATTTCTAAAACATTAA-TTTTCACAATCGGGGATACTCCAAC
* *
2602814 CTCGTTATTTCCAA
65 CCCGTTATTTCCGA
*
2602828 GGGGATACTCCAACCCTGGCTTTATTTCTAAAATATTAATTTCTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCTGGCTTTATTTCTAAAACATTAATTT-TCACAATCGGGGATACTCCAAC
* *
2602893 CCCATTATTTTCGA
65 CCCGTTATTTCCGA
* ** *** *
2602907 AGGGATACTCCAACTCC-GATTTTATTTCTAAAACACCCATTTTCCATAATCGGGGATACTCCAA
1 GGGGATACTCCAAC-CCTGGCTTTATTTCTAAAACATTAATTTT-CACAATCGGGGATACTCCAA
**
2602971 CTACGATTTTATTTCC-A
64 CCCCG---TTATTTCCGA
**** * * *** * * * * *
2602988 AAACACTAATTTTTCACAA-TC-GGGGATA-CTCT-AACCCTGTTA-TTT--C-ATTGGGGATAC
1 GGGGA-T-A---CTC-CAACCCTGGCTTTATTTCTAAAACAT-TAATTTTCACAATCGGGGATAC
*
2603045 TCCAACCCCATTATTTCCGA
59 TCCAACCCCGTTATTTCCGA
* * *
2603065 GGGGATACTCCAA-CCTCGGCTTTATTTCTAAAATATTAATTTCTCACAATCAGGGATACTCTAA
1 GGGGATACTCCAACCCT-GGCTTTATTTCTAAAACATTAATTT-TCACAATCGGGGATACTCCAA
* ** *
2603129 CCCCATTATTTTTGT
64 CCCCGTTATTTCCGA
* * * * * * *
2603144 GGGGATACTCCAACCCCGGCCTTATTTCTAAAGCATTGATTTCCCACAATCAGGGATACTCTAAC
1 GGGGATACTCCAACCCTGGCTTTATTTCTAAAACATTAATTT-TCACAATCGGGGATACTCCAAC
**
2603209 CCCGTTATTTTTGA
65 CCCGTTATTTCCGA
* * *** ** * *
2603223 GGGGAAACTCCAACACTAATTTTATTT-TCAAAACACCAATTTTCTATAATCAGGGATACTCCAA
1 GGGGATACTCCAACCCTGGCTTTATTTCT-AAAACATTAATTTTC-ACAATCGGGGATACTCCAA
*
2603287 CCCTGTTATTTCCGA
64 CCCCGTTATTTCCGA
2603302 GGGGATACTCCAACC
1 GGGGATACTCCAACC
2603317 TCGATTTTAT
Statistics
Matches: 373, Mismatches: 90, Indels: 52
0.72 0.17 0.10
Matches are distributed among these distances:
71 4 0.01
72 2 0.01
73 4 0.01
74 5 0.01
75 6 0.02
76 10 0.03
77 2 0.01
78 7 0.02
79 298 0.80
80 4 0.01
81 3 0.01
82 8 0.02
83 7 0.02
84 4 0.01
85 4 0.01
86 2 0.01
87 3 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (78 bp):
GGGGATACTCCAACCCTGGCTTTATTTCTAAAACATTAATTTTCACAATCGGGGATACTCCAACC
CCGTTATTTCCGA
Found at i:2602967 original size:51 final size:51
Alignment explanation
Indices: 2602908--2603018 Score: 168
Period size: 51 Copynumber: 2.2 Consensus size: 51
2602898 TATTTTCGAA
* * * *
2602908 GGGATACTCCAACTCCGATTTTATTTCTAAAACACCCATTTTCCATAATCG
1 GGGATACTCCAACTACGATTTTATTTCCAAAACACCAATTTTCCACAATCG
* *
2602959 GGGATACTCCAACTACGATTTTATTTCCAAAACACTAATTTTTCACAATCG
1 GGGATACTCCAACTACGATTTTATTTCCAAAACACCAATTTTCCACAATCG
2603010 GGGATACTC
1 GGGATACTC
2603019 TAACCCTGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGATACTCCAACTACGATTTTATTTCCAAAACACCAATTTTCCACAATCG
Found at i:2603041 original size:28 final size:28
Alignment explanation
Indices: 2603009--2603079 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
2602999 TTTCACAATC
* ** **
2603009 GGGGATACTCTAACCCTGTTATTTCATT
1 GGGGATACTCCAACCCCATTATTTCAGA
*
2603037 GGGGATACTCCAACCCCATTATTTCCGA
1 GGGGATACTCCAACCCCATTATTTCAGA
2603065 GGGGATACTCCAACC
1 GGGGATACTCCAACC
2603080 TCGGCTTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (28 bp):
GGGGATACTCCAACCCCATTATTTCAGA
Found at i:2603105 original size:107 final size:107
Alignment explanation
Indices: 2602958--2603160 Score: 284
Period size: 107 Copynumber: 1.9 Consensus size: 107
2602948 TTCCATAATC
* * *
2602958 GGGGATACTCCAACTACGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCTAAC
1 GGGGATACTCCAACTACGACTTTATTTCCAAAACACTAATTTCTCACAATCAGGGATACTCTAAC
**
2603023 CCTGTTATTTCAT-TGGGGATACTCCAACCCCATTATTTCCGA
66 CCCATTATTT-ATGTGGGGATACTCCAACCCCATTATTTCCGA
* * * *
2603065 GGGGATACTCCAACCT-CGGCTTTATTTCTAAAATATTAATTTCTCACAATCAGGGATACTCTAA
1 GGGGATACTCCAA-CTACGACTTTATTTCCAAAACACTAATTTCTCACAATCAGGGATACTCTAA
*
2603129 CCCCATTATTTTTGTGGGGATACTCCAACCCC
65 CCCCATTATTTATGTGGGGATACTCCAACCCC
2603161 GGCCTTATTT
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
106 1 0.01
107 81 0.96
108 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (107 bp):
GGGGATACTCCAACTACGACTTTATTTCCAAAACACTAATTTCTCACAATCAGGGATACTCTAAC
CCCATTATTTATGTGGGGATACTCCAACCCCATTATTTCCGA
Found at i:2607152 original size:15 final size:15
Alignment explanation
Indices: 2607134--2607176 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2607124 TAGAAGAGAG
2607134 AAAAAAAGAAAGAA-A
1 AAAAAAAGAAA-AAGA
*
2607149 AAAAAAGGAAAAAGA
1 AAAAAAAGAAAAAGA
2607164 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
2607177 TAGTTAGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAGA
Found at i:2607161 original size:21 final size:22
Alignment explanation
Indices: 2607136--2607176 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2607126 GAAGAGAGAA
*
2607136 AAAAAGAAAGAAAA-AAAAAGG
1 AAAAAGAAAAAAAAGAAAAAGG
2607157 AAAAAGAAAAAAAAGAAAAA
1 AAAAAGAAAAAAAAGAAAAA
2607177 TAGTTAGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAGAAAAAGG
Found at i:2608902 original size:154 final size:155
Alignment explanation
Indices: 2608688--2608983 Score: 389
Period size: 154 Copynumber: 1.9 Consensus size: 155
2608678 CACTAGGTCT
* * * * *
2608688 GCTTTTATGCCGAAGGTGGGTATTTAGGATAGTTTTATCCCGTTTAAAATCCTTTTTAAGTCCTT
1 GCTTTTATGCCGAAAGTGGATATTTAGGATAGGTTCATCCCGTTTAAAATCCTTTTTAAGTCATT
* * * * * * * *
2608753 TAGGGGTATC-AGGTACTTTTACGTCAAAGGTATCTCGTAAGGGCATTTTTGTAATTTTTTAGAA
66 TAGGGGTATCGA-GTACGTCTACGTCAAAGGTATCCCCTAAGGGCATCTTCGTAATTTTTGAAAA
2608817 CCAACTCCTAGGTCATCATTGGGTTC
130 CCAACTCCTAGGTCATCATTGGGTTC
* *
2608843 GCTTTTATG-CTAAAGTGGATATTTAGGATAGGTTCATCCCTTTTAAAATCCTTTTTAAGTCATT
1 GCTTTTATGCCGAAAGTGGATATTTAGGATAGGTTCATCCCGTTTAAAATCCTTTTTAAGTCATT
* * * * *
2608907 TAGGGGTATCGAGTACGTCTATGTCGAATGTATCCCCTTAGGTCATCTTCGTAATTTTTGAAAAC
66 TAGGGGTATCGAGTACGTCTACGTCAAAGGTATCCCCTAAGGGCATCTTCGTAATTTTTGAAAAC
2608972 CAACTCCTAGGT
131 CAACTCCTAGGT
2608984 TGTCACCCCG
Statistics
Matches: 120, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
154 110 0.92
155 10 0.08
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (155 bp):
GCTTTTATGCCGAAAGTGGATATTTAGGATAGGTTCATCCCGTTTAAAATCCTTTTTAAGTCATT
TAGGGGTATCGAGTACGTCTACGTCAAAGGTATCCCCTAAGGGCATCTTCGTAATTTTTGAAAAC
CAACTCCTAGGTCATCATTGGGTTC
Found at i:2613860 original size:22 final size:23
Alignment explanation
Indices: 2613835--2613877 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2613825 AAGAAAAAAA
* *
2613835 AACCTTTGTTT-CTTTTTATATG
1 AACCTTTATTTCCTTTCTATATG
2613857 AACCTTTATTTCCTTTCTATA
1 AACCTTTATTTCCTTTCTATA
2613878 ATTATCTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.21, C:0.19, G:0.05, T:0.56
Consensus pattern (23 bp):
AACCTTTATTTCCTTTCTATATG
Found at i:2614780 original size:6 final size:6
Alignment explanation
Indices: 2614771--2614822 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
2614761 TCTTTGTAAA
* *
2614771 AAAAAG AAAAAG AAGAAG -AAAAG AAAAAGG AAAAAG -CAAAG AAGAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA-G AAAAAG AAAAAG AA-AAAG
2614819 AAAA
1 AAAA
2614823 TCAAGAAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 8 0.21
6 18 0.47
7 12 0.32
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2614798 original size:18 final size:18
Alignment explanation
Indices: 2614768--2614822 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
2614758 TTTTCTTTGT
2614768 AAAA-AAAAG-AAAAAGA
1 AAAAGAAAAGAAAAAAGA
* *
2614784 AGAAGAAAAGAAAAAGGA
1 AAAAGAAAAGAAAAAAGA
* *
2614802 AAAAGCAAAGAAGAAAGA
1 AAAAGAAAAGAAAAAAGA
2614820 AAA
1 AAA
2614823 TCAAGAAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
16 3 0.10
17 5 0.16
18 23 0.74
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAAAAAAGA
Found at i:2615646 original size:114 final size:113
Alignment explanation
Indices: 2615446--2615665 Score: 350
Period size: 114 Copynumber: 1.9 Consensus size: 113
2615436 AAAACTGTGT
* * *
2615446 GTAGCTAACCTAATTCAAATGTATCGATACATTAACCCCAATGGCTATAATTATATCGATACATT
1 GTAGCTAACCTAATTCAAATGAATCGATACATTAACCCCAACGGCTATAATTACATCGATACATT
2615511 ATGAATTGTATTGACACATTGAGCCCAACGACTAGAATTTCATCTGAAA
66 ATGAATTGTATTGACACATTGAGCCCAA-GACTAGAATTTCATCTGAAA
* * * * *
2615560 GTAGCTACCCTAATTCAATTGAATTGATACATTAACCCTAACGGCTATAATTGCATCGATACATT
1 GTAGCTAACCTAATTCAAATGAATCGATACATTAACCCCAACGGCTATAATTACATCGATACATT
*
2615625 ATGAATTGTATTGACACATTGAGCCCAAGGCTAGAATTTCA
66 ATGAATTGTATTGACACATTGAGCCCAAGACTAGAATTTCA
2615666 AATGCATTGT
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
113 12 0.12
114 85 0.88
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (113 bp):
GTAGCTAACCTAATTCAAATGAATCGATACATTAACCCCAACGGCTATAATTACATCGATACATT
ATGAATTGTATTGACACATTGAGCCCAAGACTAGAATTTCATCTGAAA
Found at i:2616131 original size:35 final size:31
Alignment explanation
Indices: 2616084--2616181 Score: 124
Period size: 31 Copynumber: 3.0 Consensus size: 31
2616074 AAGTGATTGA
*
2616084 GAGGTTCTATCTTAGCCTTTGTAAAAGATAGG
1 GAGGTTCTATCTTAGCCTATG-AAAAGATAGG
* *
2616116 AAGAAGGTTTTATCTTAGCCTATAAAAAGATAGG
1 --G-AGGTTCTATCTTAGCCTATGAAAAGATAGG
*
2616150 GAGGTTCTATCTTAGCCTGTGAAAAGATAGG
1 GAGGTTCTATCTTAGCCTATGAAAAGATAGG
2616181 G
1 G
2616182 TTGTAAGGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
31 28 0.49
32 1 0.02
34 11 0.19
35 17 0.30
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.31
Consensus pattern (31 bp):
GAGGTTCTATCTTAGCCTATGAAAAGATAGG
Found at i:2622033 original size:19 final size:20
Alignment explanation
Indices: 2621988--2622038 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
2621978 CTCACCCAGA
2621988 TGTATCGATACATATTGCTT
1 TGTATCGATACATATTGCTT
*
2622008 AGTATCGATACATGA-T-CTT
1 TGTATCGATACAT-ATTGCTT
2622027 TGTATCGATACA
1 TGTATCGATACA
2622039 CCATAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.50
20 13 0.46
21 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTGCTT
Found at i:2622149 original size:52 final size:53
Alignment explanation
Indices: 2622086--2622194 Score: 157
Period size: 52 Copynumber: 2.1 Consensus size: 53
2622076 AACCTAATTC
* * * *
2622086 AATTGTATCGATACATGGTAAATTTTATCTATACA-TTTAGCTGAACGGCTAT
1 AATTGTATCGATACATGATAAATTATATCGATACATTTTAGCTGAACGGCTAG
* *
2622138 AATTGTATCGATACATTATAAATTATATCGATACATTTTAGCTTAACGGCTAG
1 AATTGTATCGATACATGATAAATTATATCGATACATTTTAGCTGAACGGCTAG
2622191 AATT
1 AATT
2622195 TCAAGTGCAT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
52 31 0.62
53 19 0.38
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.39
Consensus pattern (53 bp):
AATTGTATCGATACATGATAAATTATATCGATACATTTTAGCTGAACGGCTAG
Found at i:2622666 original size:35 final size:34
Alignment explanation
Indices: 2622617--2622710 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 34
2622607 AGTGATTGAG
2622617 AGGTTCTATCTTAGCCTTTGTAAAAGATAGGGAGA
1 AGGTTCTATCTTAGCCTTTGTAAAAGATAGGG-GA
* * *
2622652 AGGTTTTATATTAGCCTATG-AAAAGAT-GGGGA
1 AGGTTCTATCTTAGCCTTTGTAAAAGATAGGGGA
2622684 A-GTTCTATCTTAG-C-TTGTGAAAAGATA
1 AGGTTCTATCTTAGCCTTTGT-AAAAGATA
2622711 TGATTGTAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
29 2 0.04
30 1 0.02
31 17 0.34
32 3 0.06
33 3 0.06
34 7 0.14
35 17 0.34
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (34 bp):
AGGTTCTATCTTAGCCTTTGTAAAAGATAGGGGA
Found at i:2624331 original size:35 final size:35
Alignment explanation
Indices: 2624258--2624387 Score: 90
Period size: 35 Copynumber: 3.8 Consensus size: 35
2624248 CATCATTGGA
*
2624258 CTATA-CTGATCAAA---TTTTCATCATTGTTTGG
1 CTATATCTGATCAAACTCTTTTCATCATTGTTTAG
* * * *
2624289 TTGTATCTGGTCAAACTCTTTTTATCATTGTTTAG
1 CTATATCTGATCAAACTCTTTTCATCATTGTTTAG
* ** *
2624324 CTATATCTGATCAAGCTCTTCCCATCATTATTT-G
1 CTATATCTGATCAAACTCTTTTCATCATTGTTTAG
* ** * *
2624358 ACAATAAATGGTCAAACTCTTTCCATCATT
1 -CTATATCTGATCAAACTCTTTTCATCATT
2624388 CGTTAACTGT
Statistics
Matches: 75, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
31 3 0.04
32 8 0.11
34 1 0.01
35 63 0.84
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (35 bp):
CTATATCTGATCAAACTCTTTTCATCATTGTTTAG
Found at i:2624473 original size:47 final size:47
Alignment explanation
Indices: 2624421--2624810 Score: 354
Period size: 47 Copynumber: 8.3 Consensus size: 47
2624411 CTTTTTACCT
* * * * * * *
2624421 CATTTGATTGTATTAGCGTTAAGACTTGGTTAATCTCTTTCCACCCA
1 CATTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCCA
* * * *
2624468 CATTTGACTATATTGGCATTAGGACCTAGTCAAACTTTTTCCACCCT
1 CATTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCCA
2624515 CATTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCA-CCA
1 CATTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCCA
* * * * * *
2624561 TCATTTGACTATATTGGCATTAGAACCTGGCCAAAGTCTTTCTACCCT
1 -CATTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCCA
* * * ** *
2624609 TATTTGATTGTATTGGCATTAGGACCTAGTCAAACTCTTTTTACCCT
1 CATTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCCA
* ** ** * *
2624656 CGTTTGACTGTATTGGTGTTAGGAGTTGGTCAAACTCTTTCTACCCT
1 CATTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCCA
** * * * * * *
2624703 TGTGTGACTATATTGGCATTAGGACCT-ATCAAACTTTTTCTACCCT
1 CATTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCCA
* * * **
2624749 CATTTGACTGTATTGGCATTAGCACCTAGTTAAACTC-TTCTCACCTT
1 CATTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTC-CACCCA
2624796 CATTTGACTGTATTG
1 CATTTGACTGTATTG
2624811 ATGTTAGCCT
Statistics
Matches: 282, Mismatches: 57, Indels: 8
0.81 0.16 0.02
Matches are distributed among these distances:
46 44 0.16
47 236 0.84
48 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (47 bp):
CATTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCCA
Found at i:2624579 original size:94 final size:94
Alignment explanation
Indices: 2624418--2624810 Score: 396
Period size: 94 Copynumber: 4.2 Consensus size: 94
2624408 ATTCTTTTTA
* * * * * * *
2624418 CCTCATTTGATTGTATTAGCGTTAAGACTTGGTTAATCTCTTTCCACCCA-CATTTGACTATATT
1 CCTCATTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCA-CCATCATTTGACTATATT
*
2624482 GGCATTAGGACCTAGTCAAACTTTTTCCAC
65 GGCATTAGGACCTAGTCAAACTCTTTCCAC
2624512 CCTCATTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCATCATTTGACTATATTG
1 CCTCATTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCATCATTTGACTATATTG
* * * * *
2624577 GCATTAGAACCTGGCCAAAGTCTTTCTAC
66 GCATTAGGACCTAGTCAAACTCTTTCCAC
* * * ** * * *
2624606 CCTTATTTGATTGTATTGGCATTAGGACCTAGTCAAACTCTTTTTACCCTCGTTTGACTGTATTG
1 CCTCATTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCATCATTTGACTATATTG
** ** * *
2624671 GTGTTAGGAGTTGGTCAAACTCTTTCTAC
66 GCATTAGGACCTAGTCAAACTCTTTCCAC
** * * * * * * *
2624700 CCTTGTGTGACTATATTGGCATTAGGACCT-ATCAAACTTTTTCTACCCTCATTTGACTGTATTG
1 CCTCATTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCATCATTTGACTATATTG
* *
2624764 GCATTAGCACCTAGTTAAACTC-TTCTCAC
66 GCATTAGGACCTAGTCAAACTCTTTC-CAC
*
2624793 CTTCATTTGACTGTATTG
1 CCTCATTTGACTGTATTG
2624811 ATGTTAGCCT
Statistics
Matches: 248, Mismatches: 49, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
92 3 0.01
93 63 0.25
94 182 0.73
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (94 bp):
CCTCATTTGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCATCATTTGACTATATTG
GCATTAGGACCTAGTCAAACTCTTTCCAC
Found at i:2624678 original size:141 final size:140
Alignment explanation
Indices: 2624455--2624817 Score: 467
Period size: 141 Copynumber: 2.6 Consensus size: 140
2624445 CTTGGTTAAT
* * *
2624455 CTCTTTCCACCCACATTTGACTATATTGGCATTAGGACCTAGTCAAACT-TTTTCCACCCTCATT
1 CTCTTTCTACCCTCATTTGACTGTATTGGCATTAGGACCTAGTCAAACTCTTTT-CACCCTCATT
** *
2624519 TGACTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCATCATTTGACTATATTGGCATTAG
65 TGACTGTATTGGTGTTAGGACCTGGTCAAACTCTTTCCACCATCATGTGACTATATTGGCATTAG
*
2624584 AACCTGGCCAAA
130 AACCT-ACCAAA
* * * * *
2624596 GTCTTTCTACCCTTATTTGATTGTATTGGCATTAGGACCTAGTCAAACTCTTTTTACCCTCGTTT
1 CTCTTTCTACCCTCATTTGACTGTATTGGCATTAGGACCTAGTCAAACTCTTTTCACCCTCATTT
** * * ** *
2624661 GACTGTATTGGTGTTAGGAGTTGGTCAAACTCTTTCTACCCTTGTGTGACTATATTGGCATTAGG
66 GACTGTATTGGTGTTAGGACCTGGTCAAACTCTTTCCACCATCATGTGACTATATTGGCATTAGA
*
2624726 ACCTATCAAA
131 ACCTACCAAA
* * * * *
2624736 CTTTTTCTACCCTCATTTGACTGTATTGGCATTAGCACCTAGTTAAACTCTTCTCACCTTCATTT
1 CTCTTTCTACCCTCATTTGACTGTATTGGCATTAGGACCTAGTCAAACTCTTTTCACCCTCATTT
*
2624801 GACTGTATTGATGTTAG
66 GACTGTATTGGTGTTAG
2624818 CCTTGATCAA
Statistics
Matches: 190, Mismatches: 31, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
140 75 0.39
141 111 0.58
142 4 0.02
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (140 bp):
CTCTTTCTACCCTCATTTGACTGTATTGGCATTAGGACCTAGTCAAACTCTTTTCACCCTCATTT
GACTGTATTGGTGTTAGGACCTGGTCAAACTCTTTCCACCATCATGTGACTATATTGGCATTAGA
ACCTACCAAA
Found at i:2625049 original size:43 final size:41
Alignment explanation
Indices: 2624950--2625070 Score: 116
Period size: 43 Copynumber: 2.9 Consensus size: 41
2624940 CTTATTATCC
* * * *
2624950 TTCGTTGACTTGTCGGTTCATTCTTGGTTAACTTTTTATCT
1 TTCGTTGACTTATCGGTTCAATCTCGGTTAACTTTTTACCT
* ** *
2624991 TTCGTTTACCCATCGGTTTAATCTCGGTTAAATCTTTTTACCT
1 TTCGTTGACTTATCGGTTCAATCTCGGTT-AA-CTTTTTACCT
* * * *
2625034 TTTGTTGACTTATCGGCTCAATCTCAGTCAACTTTTT
1 TTCGTTGACTTATCGGTTCAATCTCGGTTAACTTTTT
2625071 TATCCTTTGC
Statistics
Matches: 62, Mismatches: 16, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
41 28 0.45
42 4 0.06
43 30 0.48
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.49
Consensus pattern (41 bp):
TTCGTTGACTTATCGGTTCAATCTCGGTTAACTTTTTACCT
Found at i:2626944 original size:12 final size:11
Alignment explanation
Indices: 2626927--2626977 Score: 57
Period size: 12 Copynumber: 4.3 Consensus size: 11
2626917 GAAACTCAGC
2626927 AAAAAAAGAGAA
1 AAAAAAAGA-AA
2626939 AAAAAAAGAAA
1 AAAAAAAGAAA
2626950 GAAAAAAAGAGAA
1 -AAAAAAAGA-AA
*
2626963 AAGAACAAGAAA
1 AA-AAAAAGAAA
2626975 AAA
1 AAA
2626978 TAGGAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
11 3 0.09
12 24 0.69
13 8 0.23
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:2626952 original size:14 final size:14
Alignment explanation
Indices: 2626927--2626963 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2626917 GAAACTCAGC
2626927 AAAAAAAG--AGAA
1 AAAAAAAGAAAGAA
2626939 AAAAAAAGAAAGAA
1 AAAAAAAGAAAGAA
*
2626953 AAAAAGAGAAA
1 AAAAAAAGAAA
2626964 AGAACAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 8 0.36
14 14 0.64
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAGAA
Found at i:2626959 original size:24 final size:25
Alignment explanation
Indices: 2626927--2626974 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
2626917 GAAACTCAGC
2626927 AAAAAAAGAGAAAA-AAAAAGAAAG
1 AAAAAAAGAGAAAAGAAAAAGAAAG
*
2626951 AAAAAAAGAGAAAAGAACAAGAAA
1 AAAAAAAGAGAAAAGAAAAAGAAA
2626975 AAATAGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (25 bp):
AAAAAAAGAGAAAAGAAAAAGAAAG
Found at i:2628684 original size:154 final size:153
Alignment explanation
Indices: 2628497--2628954 Score: 449
Period size: 155 Copynumber: 3.0 Consensus size: 153
2628487 CATCGAGTCC
* * * * *
2628497 GCTTTTATGTCGAAAGTGGGTATTTAGGGTAGGTTCATCCCGTTTAAAATCTTTTTTAAGTCCTT
1 GCTTTTATGCCAAAAGTGGGTATTTAGGATAGGTTCATCCCATTTAAAATC-TTTTTAAGTCTTT
* * *
2628562 TAGGGTATCGGGTACTTTTGCATCAAAAGTATCCCCCAGGGGTATTTTCGTAATTTTTCAAAACC
65 TAGGGTATCGGGTACTTTTGCATCAAAGGTATCCCACAGGGGCATTTTCGTAATTTTTCAAAACC
* *
2628627 AACTCCTAAGTCATCACTGGGTTT
130 AACTCCTAGGTCATCACTGGGTCT
* * ** *
2628651 GCTTTTATGCTAAAAGTGGATATTTAGGATAGGTTCATCCTTTTTAAAATCCCTTTTAAGTCTTT
1 GCTTTTATGCCAAAAGTGGGTATTTAGGATAGGTTCATCCCATTTAAAAT-CTTTTTAAGTCTTT
* * ** * *
2628716 TAGGGGTATCAGGTACTTCTATG--TCAATGGTATCCCTTAAGGGCATCTTCGTAATTTTTCAAA
65 TA-GGGTATCGGGTACTT-T-TGCATCAAAGGTATCCCACAGGGGCATTTTCGTAATTTTTCAAA
** *
2628779 ACCAACTCCTAGGTTGTCACCGGGTCT
127 ACCAACTCCTAGGTCATCACTGGGTCT
* * * * * * * *
2628806 GCTTTTATGCCGAAGGTGGGTCTTTAAGATAGGTTCATCTCATTTATAATCTTTCTAAATCTTTT
1 GCTTTTATGCCAAAAGTGGGTATTTAGGATAGGTTCATCCCATTTAAAATCTTTTTAAGTCTTTT
* * *
2628871 AGGGTTACCGAGATAC-TTT-CATGTCAAAGGTATACCCACAGAGGCATTTTCGTAATTTTT-AA
66 AGGG-TATCG-GGTACTTTTGCA--TCAAAGGTAT-CCCACAGGGGCATTTTCGTAATTTTTCAA
* * *
2628933 AATCGAGTCCTAGGTCATCACT
126 AACCAACTCCTAGGTCATCACT
2628955 CTTACACCAA
Statistics
Matches: 243, Mismatches: 50, Indels: 21
0.77 0.16 0.07
Matches are distributed among these distances:
152 1 0.00
153 4 0.02
154 73 0.30
155 141 0.58
156 22 0.09
157 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (153 bp):
GCTTTTATGCCAAAAGTGGGTATTTAGGATAGGTTCATCCCATTTAAAATCTTTTTAAGTCTTTT
AGGGTATCGGGTACTTTTGCATCAAAGGTATCCCACAGGGGCATTTTCGTAATTTTTCAAAACCA
ACTCCTAGGTCATCACTGGGTCT
Found at i:2635866 original size:20 final size:20
Alignment explanation
Indices: 2635840--2635893 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
2635830 CTACCACTAT
2635840 TTGTATCGATACATGGTAT-AA
1 TTGTATCGATACAT-G-ATGAA
*
2635861 -TGTATCAATACATGATGAA
1 TTGTATCGATACATGATGAA
2635880 TTGTATCGATACAT
1 TTGTATCGATACAT
2635894 TGCTTGTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 2 0.07
19 3 0.10
20 24 0.83
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:2641328 original size:13 final size:13
Alignment explanation
Indices: 2641310--2641349 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
2641300 ACAACATTCC
2641310 TTGTATCGATACA
1 TTGTATCGATACA
2641323 TTGTATCGATACA
1 TTGTATCGATACA
*
2641336 TTTTATCGATACA
1 TTGTATCGATACA
2641349 T
1 T
2641350 GGGTTACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2643851 original size:20 final size:20
Alignment explanation
Indices: 2643804--2643939 Score: 84
Period size: 20 Copynumber: 6.7 Consensus size: 20
2643794 ACATTATGCT
**
2643804 TTGTATCGATACATGTTC-A
1 TTGTATCGATACATGGACAA
*
2643823 TTGTGTCGATACATGGACAA
1 TTGTATCGATACATGGACAA
2643843 TTGTATCGATACAT-GA-AA
1 TTGTATCGATACATGGACAA
* * * ** *
2643861 TTGGTAGTAGCTACCCTACCACTAT
1 TT-GTA-TCGATA-CAT-GGAC-AA
2643886 TTGTATCGATACATGGTACAA
1 TTGTATCGATACATGG-ACAA
*
2643907 -TGTATCGATACAT-GATGAA
1 TTGTATCGATACATGGA-CAA
2643926 TTGTATCGATACAT
1 TTGTATCGATACAT
2643940 TGCTTGTAAC
Statistics
Matches: 90, Mismatches: 16, Indels: 21
0.71 0.13 0.17
Matches are distributed among these distances:
18 5 0.06
19 23 0.26
20 44 0.49
21 3 0.03
22 4 0.04
23 5 0.06
24 3 0.03
25 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:2657145 original size:21 final size:20
Alignment explanation
Indices: 2657098--2657151 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
2657088 CATTTGAGAC
*
2657098 ATGTATCGATACATTCACTG
1 ATGTATCGATACATTCACTA
*
2657118 ATGTATCAATACATTCACTA
1 ATGTATCGATACATTCACTA
2657138 ATTGTATCGATACA
1 A-TGTATCGATACA
2657152 AATTGTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:2657450 original size:341 final size:341
Alignment explanation
Indices: 2656827--2657514 Score: 1358
Period size: 341 Copynumber: 2.0 Consensus size: 341
2656817 TATAGACATG
2656827 AATTTTGACCCTATATGATGCAAAAAACCTATTTGAACCAAGCATTAGATATGTTATGGAAAATG
1 AATTTTGACCCTATATGATGCAAAAAACCTATTTGAACCAAGCATTAGATATGTTATGGAAAATG
*
2656892 AGGAAAAAGTCATAACATGTGAAAAATGACCAACATGTATCGATACATTGAAAAATGTATCGATA
66 AGGAAAAAGTCATAAAATGTGAAAAATGACCAACATGTATCGATACATTGAAAAATGTATCGATA
2656957 CATTTATATCAAAAACCCAAAATGTATCTATACAAAGCAAATTGTATCAATACATATAGAATGTA
131 CATTTATATCAAAAACCCAAAATGTATCTATACAAAGCAAATTGTATCAATACATATAGAATGTA
2657022 TCGACATATTTACTTATGTATCGTTACAATTTTTTTTACAGAACTCGACATGTTCTTGTGTCGAT
196 TCGACATATTTACTTATGTATCGTTACAATTTTTTTTACAGAACTCGACATGTTCTTGTGTCGAT
2657087 ACATTTGAGACATGTATCGATACATTCACTGATGTATCAATACATTCACTAATTGTATCGATACA
261 ACATTTGAGACATGTATCGATACATTCACTGATGTATCAATACATTCACTAATTGTATCGATACA
2657152 AATTGTAGAAATTTGA
326 AATTGTAGAAATTTGA
2657168 AATTTTGACCCTATATGATGCAAAAAACCTATTTGAACCAAGCATTAGATATGTTATGGAAAATG
1 AATTTTGACCCTATATGATGCAAAAAACCTATTTGAACCAAGCATTAGATATGTTATGGAAAATG
2657233 AGGAAAAAGTCATAAAATGTGAAAAATGACCAACATGTATCGATACATTGAAAAATGTATCGATA
66 AGGAAAAAGTCATAAAATGTGAAAAATGACCAACATGTATCGATACATTGAAAAATGTATCGATA
*
2657298 CATTTATATCAAAAACCCAAAATGTATCTATACAAAGCAAATTGTATCGATACATATAGAATGTA
131 CATTTATATCAAAAACCCAAAATGTATCTATACAAAGCAAATTGTATCAATACATATAGAATGTA
2657363 TCGACATATTTACTTATGTATCGTTACAATTTTTTTTACAGAACTCGACATGTTCTTGTGTCGAT
196 TCGACATATTTACTTATGTATCGTTACAATTTTTTTTACAGAACTCGACATGTTCTTGTGTCGAT
2657428 ACATTTGAGACATGTATCGATACATTCACTGATGTATCAATACATTCACTAATTGTATCGATACA
261 ACATTTGAGACATGTATCGATACATTCACTGATGTATCAATACATTCACTAATTGTATCGATACA
2657493 AATTGTAGAAATTTGA
326 AATTGTAGAAATTTGA
2657509 AATTTT
1 AATTTT
2657515 TTACCGTTGG
Statistics
Matches: 345, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
341 345 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (341 bp):
AATTTTGACCCTATATGATGCAAAAAACCTATTTGAACCAAGCATTAGATATGTTATGGAAAATG
AGGAAAAAGTCATAAAATGTGAAAAATGACCAACATGTATCGATACATTGAAAAATGTATCGATA
CATTTATATCAAAAACCCAAAATGTATCTATACAAAGCAAATTGTATCAATACATATAGAATGTA
TCGACATATTTACTTATGTATCGTTACAATTTTTTTTACAGAACTCGACATGTTCTTGTGTCGAT
ACATTTGAGACATGTATCGATACATTCACTGATGTATCAATACATTCACTAATTGTATCGATACA
AATTGTAGAAATTTGA
Found at i:2657486 original size:21 final size:20
Alignment explanation
Indices: 2657439--2657492 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
2657429 CATTTGAGAC
*
2657439 ATGTATCGATACATTCACTG
1 ATGTATCGATACATTCACTA
*
2657459 ATGTATCAATACATTCACTA
1 ATGTATCGATACATTCACTA
2657479 ATTGTATCGATACA
1 A-TGTATCGATACA
2657493 AATTGTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:2660988 original size:22 final size:22
Alignment explanation
Indices: 2660963--2661023 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
2660953 AAAGGTTAAA
*
2660963 AAAATAAAAAAATCAAGA-CAAG
1 AAAATAAAAAAA-CAAAATCAAG
* * *
2660985 AAAATATATAAAGAAAATCAAG
1 AAAATAAAAAAACAAAATCAAG
*
2661007 AAAATAAAAAAAAAAAA
1 AAAATAAAAAAACAAAA
2661024 GGTCTAGATG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.77, C:0.05, G:0.07, T:0.11
Consensus pattern (22 bp):
AAAATAAAAAAACAAAATCAAG
Found at i:2661955 original size:28 final size:28
Alignment explanation
Indices: 2661862--2661957 Score: 104
Period size: 28 Copynumber: 3.4 Consensus size: 28
2661852 TTTATGTCAT
*
2661862 ATCCCTAGTGGAGTCTAGACAACCTATA
1 ATCCCTAGTGGAGTCTGGACAACCTATA
* * * *
2661890 AT-CCTCAATGGAGTTTGGACAACCTGTG
1 ATCCCT-AGTGGAGTCTGGACAACCTATA
* * *
2661918 ATCCCCAGTGGAGCCTGGACAACCTACA
1 ATCCCTAGTGGAGTCTGGACAACCTATA
2661946 ATCCCTAGTGGA
1 ATCCCTAGTGGA
2661958 ATTAGGAAAA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
27 3 0.06
28 48 0.91
29 2 0.04
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (28 bp):
ATCCCTAGTGGAGTCTGGACAACCTATA
Found at i:2662356 original size:12 final size:13
Alignment explanation
Indices: 2662307--2662375 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
2662297 GAAACTATCA
*
2662307 TCAAGAACTTTTA
1 TCAAGAACTTTTG
** *
2662320 TTGAGAACGTTTG
1 TCAAGAACTTTTG
2662333 TCGAA-AAC-TTTG
1 TC-AAGAACTTTTG
2662345 TCAAGAA-TTTTG
1 TCAAGAACTTTTG
*
2662357 TCAAGAACTTGTG
1 TCAAGAACTTTTG
2662370 TCAAGA
1 TCAAGA
2662376 CCCTTTCATC
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
11 2 0.04
12 19 0.42
13 23 0.51
14 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (13 bp):
TCAAGAACTTTTG
Found at i:2662373 original size:13 final size:12
Alignment explanation
Indices: 2662323--2662375 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 12
2662313 ACTTTTATTG
2662323 AGAACGTTTGTCGA
1 AGAAC-TTTGTC-A
2662337 A-AACTTTGTCA
1 AGAACTTTGTCA
*
2662348 AGAATTTTGTCA
1 AGAACTTTGTCA
2662360 AGAACTTGTGTCA
1 AGAACTT-TGTCA
2662373 AGA
1 AGA
2662376 CCCTTTCATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 2 0.06
12 21 0.60
13 11 0.31
14 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (12 bp):
AGAACTTTGTCA
Found at i:2662456 original size:11 final size:12
Alignment explanation
Indices: 2662428--2662461 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2662418 AAACTTGTGA
*
2662428 CAAAAATTTTAT
1 CAAAAACTTTAT
2662440 CAAAAACTTTAT
1 CAAAAACTTTAT
*
2662452 CAAAATCTTT
1 CAAAAACTTT
2662462 TCCAAAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (12 bp):
CAAAAACTTTAT
Found at i:2662815 original size:28 final size:27
Alignment explanation
Indices: 2662775--2662827 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
2662765 TCAAATCCTT
2662775 TCAAAGCCTATAAGTCAGTGGCACCTCC
1 TCAAAGCCTATAA-TCAGTGGCACCTCC
*
2662803 TCAAAGTCC-ATAATTAGTGGCACCT
1 TCAAAG-CCTATAATCAGTGGCACCT
2662828 ACATATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 11 0.48
28 10 0.43
29 2 0.09
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (27 bp):
TCAAAGCCTATAATCAGTGGCACCTCC
Found at i:2663569 original size:20 final size:20
Alignment explanation
Indices: 2663523--2663572 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2663513 TACTATGCAA
* ** *
2663523 ATGTATCGGTACATGAGTTT
1 ATGTATCGATACATGAACTC
*
2663543 ATATATCGATACATGAACTC
1 ATGTATCGATACATGAACTC
2663563 ATGTATCGAT
1 ATGTATCGAT
2663573 GCTAGACCAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATGAACTC
Found at i:2669169 original size:16 final size:17
Alignment explanation
Indices: 2669150--2669182 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2669140 ATATAATATT
2669150 TTGATTTCTGTT-TTTC
1 TTGATTTCTGTTATTTC
*
2669166 TTGATTTTTGTTATTTC
1 TTGATTTCTGTTATTTC
2669183 ACTATTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.09, C:0.09, G:0.12, T:0.70
Consensus pattern (17 bp):
TTGATTTCTGTTATTTC
Found at i:2669837 original size:15 final size:15
Alignment explanation
Indices: 2669817--2669846 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2669807 TTAAGAGTGT
2669817 TTAGGCCTTGACCCC
1 TTAGGCCTTGACCCC
2669832 TTAGGCCTTGACCCC
1 TTAGGCCTTGACCCC
2669847 AGCCTAGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.40, G:0.20, T:0.27
Consensus pattern (15 bp):
TTAGGCCTTGACCCC
Found at i:2672399 original size:16 final size:16
Alignment explanation
Indices: 2672380--2672413 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2672370 TTTTATGTTC
2672380 TATATTTATACACATA
1 TATATTTATACACATA
*
2672396 TATATTTATAGACATA
1 TATATTTATACACATA
2672412 TA
1 TA
2672414 CATATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (16 bp):
TATATTTATACACATA
Found at i:2682429 original size:20 final size:20
Alignment explanation
Indices: 2682384--2682437 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
2682374 GTTACAAGCA
* *
2682384 ATGTATCGATAGAATTCATC
1 ATGTATCGATACAATTCACC
*
2682404 AAGTATCGATACAATGT-ACC
1 ATGTATCGATACAAT-TCACC
2682424 ATGTATCGATACAA
1 ATGTATCGATACAA
2682438 ACAGTGGTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:2682491 original size:20 final size:20
Alignment explanation
Indices: 2682466--2682520 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
2682456 CTACCAGTTT
***
2682466 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTAAA
*
2682486 CATGTATTGATACAA-TAAA
1 CATGTATCGATACAATTAAA
2682505 CATGTATCGATACAAT
1 CATGTATCGATACAAT
2682521 GTATCGATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTAAA
Found at i:2696799 original size:13 final size:13
Alignment explanation
Indices: 2696781--2696808 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2696771 TACAAAAGAT
2696781 CAATGTATCGATA
1 CAATGTATCGATA
2696794 CAATGTATCGATA
1 CAATGTATCGATA
2696807 CA
1 CA
2696809 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2696871 original size:13 final size:13
Alignment explanation
Indices: 2696853--2696885 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
2696843 AGCTTCGTAG
2696853 CGATACATTGTAT
1 CGATACATTGTAT
2696866 CGATACATTGTAT
1 CGATACATTGTAT
2696879 CGATACA
1 CGATACA
2696886 ACACTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:2697880 original size:49 final size:49
Alignment explanation
Indices: 2697555--2699692 Score: 2136
Period size: 49 Copynumber: 43.4 Consensus size: 49
2697545 ATATGCGGCT
* ** * *
2697555 AGCGATATTGGGCTCGAAGATGCGAAGAATGACAATGTGCTGATTCATGGCC
1 AGCGATATTGGACTTAAAGAT--GAAG-ATGCCAATGTGCTGATTCAAGGCC
* * * * * **
2697607 AACGACATTAGACTTGAAGAAG-A-ATGCCAATGTGCTGAGACAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * * * **
2697654 AGCGACATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTAATTCACGGTT
1 AGCGATATTGGACTTAAAGAT--G---AA-GATGCCAATGTGCTGATTCAAGGCC
* * * * *
2697709 AGCGACATTAGACTTGAAGATGAGAATAATGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGAT--GAA-GATGCCAATGTGCTGATTCAAGGCC
* * ** ** *
2697761 AACGCCA-ATGGGTTTTAAAGATGACGAAGGCGCCAATATGCTTGATTCAAGGCC
1 -A-GCGATATTGGACTTAAAGAT---GAAGATGCCAATGTGC-TGATTCAAGGCC
* * * * * *
2697815 AACGATATCGAACTTAAAAATGAAGGTGCCAATGTGTTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * *
2697864 AGCGACATTGGTCTTAAAAATGACAG-TGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGA-AGATGCCAATGTGCTGATTCAAGGCC
* ** * * *
2697913 AACGATACCGGACTTAAAAATAAAGATGCCAATGTACTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * * ** * *
2697962 AACGACATTGGTCTTAAAAATGTCAAAGGCGCCAATATACTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATG---AAGATGCCAATGTGCTGATTCAAGGCC
* * * *
2698014 AGTGATATTGGACTTAAAGATGAAGATGTCAATGTGCTAATTCAAGGTC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * *
2698063 AGCGACATTGGACTT--AGATGATGGTGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
*** * *
2698110 AGCGATACCAGACTTAAAGATGAAAATGCCAATGGGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* *
2698159 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * * *
2698208 AGCGACATTGGTCTTAAAGATGACGGTGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
** * *
2698257 AGCGATACCGGACTTAAAAATGAAGATGCCAATGTGCTGATTCAAGGCT
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* ** *
2698306 AGTGATATTGGACTTAAAGATGAAGATGTTAATGTGCTGATTCAAGGTC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * * *
2698355 AGCAACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
** * *
2698404 AGCGATACCGGACTTAAAGATGAAGATGCTAATGTGTTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * * * *
2698453 AACGACATTGGTCTTAAAGATGACGGTGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
** * *
2698502 AGCGATACCGGACTTAAAAATGAAGATGCCAATGTGCTGATTCAAGGCT
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * ** * *
2698551 AGTGATATTGGACTTAAAGATAAAGATGTTAATGTGCTAATTCAAGGTC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * * *
2698600 AGCAACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* ** * *
2698649 AACGATACCGGACTTAAAAATAAAGATGCCAATGTGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * * ** *
2698698 AACGACATTGGTCTTAAAAATGTCAAAGGCGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATG---AAGATGCCAATGTGCTGATTCAAGGCC
* * * *
2698750 AGTGATATTGGACTTAAAGATGAAGATGTCAATGTGCTAATTCAAGGTC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * *
2698799 AGCGACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * *
2698848 AGCGATACTAGACTTAAAGATGAAGATGCCAATGGGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* *
2698897 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * * *
2698946 AGCGACATTGGTCTTAAAGATGACGGTGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * *
2698995 AGTGATATCGGACTTAAAAATGAAGATGCCAATGTGCTGATTCAAGGCT
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * *
2699044 AGTGATATTGGACTTAAAGATGAAGATGTTC-ATGTGCTGATTCAAGGTC
1 AGCGATATTGGACTTAAAGATGAAGATG-CCAATGTGCTGATTCAAGGCC
* * *
2699093 AGTGACATTGGACTT----A--AAGATGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
**
2699136 AGCGATACCGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * *
2699185 AGTGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * * * *
2699234 AGCGACATTGGTCTTAAAGATGACGGTGCCAATATGCTAATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * * *
2699283 AGCGATACTGGACTTAAAAATAAAAATGCTAATGTGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * *
2699332 AGTGATATTGGACTTAAAGATGAAGATGTCAATGTGCTGATTCAAGGTC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * * *
2699381 AGCAACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* *
2699430 AGCGATACTGGACTTAAAGATGAAGATGCTAATGTGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* *
2699479 AGCGACATTGGACTTAAAGATGACAAAGATGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATG---AAGATGCCAATGTGCTGATTCAAGGCC
* * *
2699531 AGCGATATTGGACTTAAAGATAAAGATGTCAATGTGCTGATTCAAGGTC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
* * * *
2699580 AGCGACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
*** *
2699629 AGCGATACCAGACTT----A--AAGATGCCAATATGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
*
2699672 AACGATATTGGACTTAGAAGA
1 AGCGATATTGGACTTA-AAGA
2699693 AGATGTCACC
Statistics
Matches: 1710, Mismatches: 337, Indels: 82
0.80 0.16 0.04
Matches are distributed among these distances:
42 1 0.00
43 69 0.04
45 2 0.00
47 74 0.04
48 3 0.00
49 1291 0.75
50 17 0.01
52 164 0.10
53 33 0.02
54 18 0.01
55 38 0.02
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (49 bp):
AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCC
Found at i:2699767 original size:28 final size:29
Alignment explanation
Indices: 2699710--2700070 Score: 259
Period size: 29 Copynumber: 12.5 Consensus size: 29
2699700 ACCAACTTGA
* **
2699710 GTGGGCTTTTGAAAGGGTT-GCACCAACTT
1 GTGGGCTTTTGAAA-GGTTACCACTGACTT
*
2699739 GTGTGCTTTTG-AAGGTTACCACTGACTT
1 GTGGGCTTTTGAAAGGTTACCACTGACTT
* *
2699767 GTGGGCTTTTGAAAAGATACCACTGACTT
1 GTGGGCTTTTGAAAGGTTACCACTGACTT
* **
2699796 GTGGGC-TTTGAAAAAGGGTGTCACTGACTT
1 GTGGGCTTTTG--AAAGGTTACCACTGACTT
* * *
2699826 GTGGGCTTTCGAAAAGATT-CCACGGACTT
1 GTGGGCTTTTG-AAAGGTTACCACTGACTT
*
2699855 GTGGGCTTTTG-AAGGTTGCCACTGACTT
1 GTGGGCTTTTGAAAGGTTACCACTGACTT
* * * * **
2699883 GTGGGCTTTGGAAAAGATGCCAGGGACTT
1 GTGGGCTTTTGAAAGGTTACCACTGACTT
* * * *
2699912 GTGGGCTTTGGAAAAGGGTACCCCTAACTT
1 GTGGGCTTTTG-AAAGGTTACCACTGACTT
* * * * * *
2699942 ATGGGCTTTGGAAAAGATGCCA-GGACTT
1 GTGGGCTTTTGAAAGGTTACCACTGACTT
*
2699970 GTGGGCTTTTG-AAGGTTGCCACTGACTT
1 GTGGGCTTTTGAAAGGTTACCACTGACTT
* * * * * *
2699998 GTGGGCTTTGGAAAAGATGCCCCGGACTT
1 GTGGGCTTTTGAAAGGTTACCACTGACTT
* * *
2700027 GTGGGCTTTGGAAAAGGGTGCCACTGACTT
1 GTGGGCTTTTG-AAAGGTTACCACTGACTT
*
2700057 GTGGGCTTTGGAAA
1 GTGGGCTTTTGAAA
2700071 AAGGTGCCAC
Statistics
Matches: 269, Mismatches: 52, Indels: 22
0.78 0.15 0.06
Matches are distributed among these distances:
27 17 0.06
28 70 0.26
29 107 0.40
30 72 0.27
31 3 0.01
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.30
Consensus pattern (29 bp):
GTGGGCTTTTGAAAGGTTACCACTGACTT
Found at i:2699797 original size:29 final size:29
Alignment explanation
Indices: 2699757--2700102 Score: 374
Period size: 29 Copynumber: 11.9 Consensus size: 29
2699747 TTGAAGGTTA
* *
2699757 CCACTGACTTGTGGGCTTTTGAAAAGATA
1 CCACTGACTTGTGGGCTTTGGAAAAGATG
* *
2699786 CCACTGACTTGTGGGCTTTGAAAAAGGGTG
1 CCACTGACTTGTGGGCTTTGGAAAA-GATG
* * *
2699816 TCACTGACTTGTGGGCTTTCGAAAAGATT
1 CCACTGACTTGTGGGCTTTGGAAAAGATG
* * * *
2699845 CCACGGACTTGTGGGCTTTTG-AAGGTTG
1 CCACTGACTTGTGGGCTTTGGAAAAGATG
2699873 CCACTGACTTGTGGGCTTTGGAAAAGATG
1 CCACTGACTTGTGGGCTTTGGAAAAGATG
** * *
2699902 CCAGGGACTTGTGGGCTTTGGAAAAGGGTA
1 CCACTGACTTGTGGGCTTTGGAAAA-GATG
* * *
2699932 CCCCTAACTTATGGGCTTTGGAAAAGATG
1 CCACTGACTTGTGGGCTTTGGAAAAGATG
* * * *
2699961 CCA-GGACTTGTGGGCTTTTG-AAGGTTG
1 CCACTGACTTGTGGGCTTTGGAAAAGATG
2699988 CCACTGACTTGTGGGCTTTGGAAAAGATG
1 CCACTGACTTGTGGGCTTTGGAAAAGATG
* * *
2700017 CCCCGGACTTGTGGGCTTTGGAAAAGGGTG
1 CCACTGACTTGTGGGCTTTGGAAAA-GATG
*
2700047 CCACTGACTTGTGGGCTTTGGAAAAAGGTG
1 CCACTGACTTGTGGGCTTTGG-AAAAGATG
* * *
2700077 CCACTAACTTATGGGCTTTAGAAAAG
1 CCACTGACTTGTGGGCTTTGGAAAAG
2700103 GTGAGGAATG
Statistics
Matches: 261, Mismatches: 49, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
27 8 0.03
28 51 0.20
29 108 0.41
30 90 0.34
31 4 0.02
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.28
Consensus pattern (29 bp):
CCACTGACTTGTGGGCTTTGGAAAAGATG
Found at i:2699840 original size:59 final size:58
Alignment explanation
Indices: 2699757--2700103 Score: 434
Period size: 59 Copynumber: 5.9 Consensus size: 58
2699747 TTGAAGGTTA
* * *
2699757 CCACTGACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTTGAAAAAGGGTG
1 CCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGGGCTTTG-AAAAGGGTG
* * * *
2699816 TCACTGACTTGTGGGCTTTCGAAAAGATTCCACGGACTTGTGGGCTTTTG--AAGGTTG
1 CCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGGGC-TTTGAAAAGGGTG
* *
2699873 CCACTGACTTGTGGGCTTTGGAAAAGATGCCAGGGACTTGTGGGCTTTGGAAAAGGGTA
1 CCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGGGCTTT-GAAAAGGGTG
* * * *
2699932 CCCCTAACTTATGGGCTTTGGAAAAGATGCCA-GGACTTGTGGGCTTTTG--AAGGTTG
1 CCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGGGC-TTTGAAAAGGGTG
*
2699988 CCACTGACTTGTGGGCTTTGGAAAAGATGCCCCGGACTTGTGGGCTTTGGAAAAGGGTG
1 CCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGGGCTTT-GAAAAGGGTG
* ** *
2700047 CCACTGACTTGTGGGCTTTGGAAAAAGGTGCCACTAACTTATGGGCTTTAGAAAAGG
1 CCACTGACTTGTGGGCTTTGG-AAAAGATGCCACGGACTTGTGGGCTTT-GAAAAGG
2700104 TGAGGAATGT
Statistics
Matches: 251, Mismatches: 27, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
56 39 0.16
57 61 0.24
58 13 0.05
59 105 0.42
60 33 0.13
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.28
Consensus pattern (58 bp):
CCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGGGCTTTGAAAAGGGTG
Found at i:2700010 original size:115 final size:116
Alignment explanation
Indices: 2699735--2700095 Score: 535
Period size: 116 Copynumber: 3.1 Consensus size: 116
2699725 GGTTGCACCA
* * * * *
2699735 ACTTGTGTGCTTTTGAAGGTTACCACTGACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGG
* * * *
2699800 GCTTTGAAAAAGGGTGTCACTGACTTGTGGGCTTTCGAAAAGATTCCACGG
66 GCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGG
*
2699851 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCAGGGACTTGTGG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGG
* * * *
2699916 GCTTTGGAAAAGGGTACCCCTAACTTATGGGCTTTGGAAAAGATGCCA-GG
66 GCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGG
*
2699966 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCCCGGACTTGTGG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGG
* **
2700031 GCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAAGGTGCCACTA
66 GCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGG-AAAAGATGCCACGG
*
2700083 ACTTATGGGCTTT
1 ACTTGTGGGCTTT
2700096 AGAAAAGGTG
Statistics
Matches: 219, Mismatches: 24, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
115 98 0.45
116 109 0.50
117 12 0.05
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (116 bp):
ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACTTGTGG
GCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGG
Found at i:2701027 original size:19 final size:20
Alignment explanation
Indices: 2701003--2701054 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
2700993 TACCCAAACT
2701003 TGTATCGATACAC-AAAATA
1 TGTATCGATACACAAAAATA
2701022 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC-AAAAATA
2701043 TGTATCGATACA
1 TGTATCGATACA
2701055 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 13 0.42
21 18 0.58
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (20 bp):
TGTATCGATACACAAAAATA
Found at i:2705089 original size:15 final size:15
Alignment explanation
Indices: 2705069--2705099 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2705059 TAAAAATGTC
*
2705069 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2705084 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2705099 C
1 C
2705100 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2707199 original size:13 final size:13
Alignment explanation
Indices: 2707181--2707218 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2707171 CATTTTTCTT
2707181 TGTATCGATACAA
1 TGTATCGATACAA
*
2707194 TGTATCGATACAC
1 TGTATCGATACAA
2707207 TGTATCGATACA
1 TGTATCGATACA
2707219 GGGGGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2707373 original size:20 final size:20
Alignment explanation
Indices: 2707330--2707375 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2707320 AAATCTTTTG
2707330 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
2707351 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
2707371 CAAAA
1 CAAAA
2707376 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:2709703 original size:20 final size:19
Alignment explanation
Indices: 2709648--2709703 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
2709638 AAAACCCTTA
*
2709648 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
2709668 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
2709688 AATGTATCGATACATG
1 AAAGTATCGATACATG
2709704 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:2709791 original size:13 final size:13
Alignment explanation
Indices: 2709773--2709798 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2709763 TATACAAAAT
2709773 ATGTATCGATACA
1 ATGTATCGATACA
2709786 ATGTATCGATACA
1 ATGTATCGATACA
2709799 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2709796 original size:32 final size:33
Alignment explanation
Indices: 2709755--2709819 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
2709745 TAGCCAAACT
*
2709755 TGTATCGATATAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
2709787 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
2709820 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 12 0.40
34 18 0.60
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:2711501 original size:17 final size:17
Alignment explanation
Indices: 2711475--2711521 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2711465 ATTCGGACCC
*
2711475 TTTTTGTTG-TTGTTTTG
1 TTTTTTTTGTTTG-TTTG
2711492 TTTTTTTTGTTTGTTTG
1 TTTTTTTTGTTTGTTTG
2711509 TTTGTTTTT-TTTG
1 TTT-TTTTTGTTTG
2711522 CGGAGGATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (17 bp):
TTTTTTTTGTTTGTTTG
Found at i:2711505 original size:21 final size:20
Alignment explanation
Indices: 2711475--2711521 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
2711465 ATTCGGACCC
2711475 TTTTTGTTG-TTGTTTTGTTT
1 TTTTTGTTGTTTG-TTTGTTT
2711495 TTTTTGTTTGTTTGTTTGTTT
1 TTTTTG-TTGTTTGTTTGTTT
2711516 TTTTTG
1 TTTTTG
2711522 CGGAGGATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 6 0.24
21 16 0.64
22 3 0.12
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (20 bp):
TTTTTGTTGTTTGTTTGTTT
Found at i:2724630 original size:16 final size:16
Alignment explanation
Indices: 2724606--2724639 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2724596 GAAACATGTT
*
2724606 AAGATCACATAAACAG
1 AAGAGCACATAAACAG
2724622 AAGAGCACATAAACAG
1 AAGAGCACATAAACAG
2724638 AA
1 AA
2724640 AAGGAAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.18, G:0.15, T:0.09
Consensus pattern (16 bp):
AAGAGCACATAAACAG
Found at i:2725491 original size:19 final size:18
Alignment explanation
Indices: 2725467--2725561 Score: 75
Period size: 19 Copynumber: 5.7 Consensus size: 18
2725457 AGTGATACAT
2725467 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
2725486 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
2725499 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
2725518 TGTATCGGTAC--A--T-
1 TGTATCGATACAAACTTA
*
2725531 TGTATCAATACAACACTTA
1 TGTATCGATACAA-ACTTA
2725550 TGTATCGATACA
1 TGTATCGATACA
2725562 GTTACGGTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 24
0.68 0.05 0.27
Matches are distributed among these distances:
13 20 0.33
14 2 0.03
16 4 0.07
18 2 0.03
19 32 0.53
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:2725501 original size:32 final size:32
Alignment explanation
Indices: 2725460--2725561 Score: 177
Period size: 32 Copynumber: 3.2 Consensus size: 32
2725450 GCTTCGTAGT
*
2725460 GATACATTGTATCGATACAAAACTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
2725492 GATACATTGTATCGATACAACACTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
* *
2725524 GGTACATTGTATCAATACAACACTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
2725556 GATACA
1 GATACA
2725562 GTTACGGTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (32 bp):
GATACATTGTATCGATACAACACTTATGTATC
Found at i:2725504 original size:13 final size:13
Alignment explanation
Indices: 2725486--2725510 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2725476 ACAAAACTTA
2725486 TGTATCGATACAT
1 TGTATCGATACAT
2725499 TGTATCGATACA
1 TGTATCGATACA
2725511 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2726370 original size:47 final size:47
Alignment explanation
Indices: 2726295--2726389 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 47
2726285 CGAAGATGCA
* ** * *
2726295 AAGAATGACAATGTGCTGATTCATGGCCAGTGACATTAGACTTGAAG
1 AAGAATGACAATGTACTGAGACAAGGCCAGTGACATTAGACTTAAAG
* *
2726342 AAGAATGCCAATGTACTGAGACAAGGCCAGTGACATTAGGCTTAAAG
1 AAGAATGACAATGTACTGAGACAAGGCCAGTGACATTAGACTTAAAG
2726389 A
1 A
2726390 TGGGAAAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (47 bp):
AAGAATGACAATGTACTGAGACAAGGCCAGTGACATTAGACTTAAAG
Found at i:2726671 original size:49 final size:49
Alignment explanation
Indices: 2726454--2727086 Score: 605
Period size: 49 Copynumber: 12.8 Consensus size: 49
2726444 ATGAGAAGAA
* * ** **
2726454 TGCCAATGTGCTGATTCAAGGCCAACGGCATTGGGTTTTAAAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATT-GGACTTAAAGAT---GAAGG
* * *
2726507 CGCCAATATGCTTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGG
1 TGCCAATATGC-TGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * *
2726557 TGCCAATCTGCTGATTCAAGG-CAGCGACATTGGTCTTAAAGATGATGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
*** * * *
2726605 TGCCAATATGCTGATTCAAGGCCAGCGATACCAGACATAAAAATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * * *
2726654 TGCCAATGTGCTAATTCAAGGCCAACGACATTGGTCTTAAAAATGTCAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGG
* * * *
2726706 CGCCAATATGCTGATTCAAGGCTAGTGATATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * * *
2726755 TGTCAATGTGTTGATTCAAGGTCAGCGACATTGGACTTAAAGATGATGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* *** *
2726804 TGCCAATATGCTGATTCAAGGCCAACGATACCAGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * *
2726853 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGG
* * * *
2726905 CGCCAATATGTTGATTCAAGACCAGCGATATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * *
2726954 TGTCAATGTGCTGATTCAAGGTCAGCGACATTGGACTTAAAGATGATGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * **
2727003 TGCCAATATGCTAATTCAAGGCCAACGATACCGGACTT-AA-A-G-A--
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
*
2727046 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
2727087 AGAAGATGCC
Statistics
Matches: 472, Mismatches: 99, Indels: 27
0.79 0.17 0.05
Matches are distributed among these distances:
43 35 0.07
44 2 0.00
46 1 0.00
47 1 0.00
48 44 0.09
49 257 0.54
50 14 0.03
52 81 0.17
53 19 0.04
54 18 0.04
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
Found at i:2726770 original size:150 final size:147
Alignment explanation
Indices: 2726508--2727097 Score: 631
Period size: 150 Copynumber: 4.0 Consensus size: 147
2726498 TGACGAAGGC
* * *
2726508 GCCAATATGCTTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGGTGCCAATCTGCTGATT
1 GCCAATGTGC-TGATTCAAGGCCAACGACATCGGACTTAAAGATGAAGGTGCCAATATGCTGATT
* * * * **
2726573 CAAGG-CAGCGACATTGGTCTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATACC
65 CAAGGCCAACGACATTGGACTTAAAGATGAAGGTGCCAATATGTTGATTCAAGGCCAGCGATATT
* * *
2726637 AGACATAAAAATGAAGAT
130 GGACTTAAAGATGAAGAT
* * * * *
2726655 GCCAATGTGCTAATTCAAGGCCAACGACATTGGTCTTAAAAATGTCAAAGGCGCCAATATGCTGA
1 GCCAATGTGCTGATTCAAGGCCAACGACATCGGACTTAAAGATG---AAGGTGCCAATATGCTGA
* ** * * * * * *
2726720 TTCAAGGCTAGTGATATTGGACTTAAAGATGAAGATGTCAATGTGTTGATTCAAGGTCAGCGACA
63 TTCAAGGCCAACGACATTGGACTTAAAGATGAAGGTGCCAATATGTTGATTCAAGGCCAGCGATA
* *
2726785 TTGGACTTAAAGATGATGGT
128 TTGGACTTAAAGATGAAGAT
* * * * * *
2726805 GCCAATATGCTGATTCAAGGCCAACGATACCAGACTTAAAGATGAAGATGCCAATGTGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAACGACATCGGACTTAAAGATGAAGGTGCCAATATGCTGATTC
* *
2726870 AAGGCCAACGACATTGGACTTAAAGATGACAAAGGCGCCAATATGTTGATTCAAGACCAGCGATA
66 AAGGCCAACGACATTGGACTTAAAGATG---AAGGTGCCAATATGTTGATTCAAGGCCAGCGATA
2726935 TTGGACTTAAAGATGAAGAT
128 TTGGACTTAAAGATGAAGAT
* * * * * *
2726955 GTCAATGTGCTGATTCAAGGTCAGCGACATTGGACTTAAAGATGATGGTGCCAATATGCTAATTC
1 GCCAATGTGCTGATTCAAGGCCAACGACATCGGACTTAAAGATGAAGGTGCCAATATGCTGATTC
* ** * *
2727020 AAGGCCAACGATACCGGACTT-AA-A-G-A--TGCCAATATGCTGATTCAAGGCCAACGATATTG
66 AAGGCCAACGACATTGGACTTAAAGATGAAGGTGCCAATATGTTGATTCAAGGCCAGCGATATTG
2727079 GACTTAAA-A-GAAGAT
131 GACTTAAAGATGAAGAT
2727094 GCCA
1 GCCA
2727098 CCAACTTGTG
Statistics
Matches: 366, Mismatches: 70, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
139 9 0.02
140 1 0.00
141 37 0.10
143 1 0.00
146 29 0.08
147 52 0.14
148 1 0.00
149 25 0.07
150 211 0.58
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (147 bp):
GCCAATGTGCTGATTCAAGGCCAACGACATCGGACTTAAAGATGAAGGTGCCAATATGCTGATTC
AAGGCCAACGACATTGGACTTAAAGATGAAGGTGCCAATATGTTGATTCAAGGCCAGCGATATTG
GACTTAAAGATGAAGAT
Found at i:2726798 original size:199 final size:197
Alignment explanation
Indices: 2726448--2727087 Score: 948
Period size: 199 Copynumber: 3.2 Consensus size: 197
2726438 TTGAAGATGA
* ** * *
2726448 GAAGAATGCCAATGTGCTGATTCAAGGCCAACGGCATTGGGTTTTAAAGATGACGAAGGCGCCAA
1 GAAG-ATGCCAATGTGCTGATTCAAGGCCAACGACATT-GGACTTAAAAATGACAAAGGCGCCAA
* * * * *
2726513 TATGCTTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGGTGCCAATCTGCTGATTCAAGG
64 TATGC-TGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGTCAATGTGCTGATTCAAGG
* *
2726578 -CAGCGACATTGGTCTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATACCAGACA
128 TCAGCGACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAACGATACCAGAC-
2726642 TAAAAAT
192 T-AAAAT
* * *
2726649 GAAGATGCCAATGTGCTAATTCAAGGCCAACGACATTGGTCTTAAAAATGTCAAAGGCGCCAATA
1 GAAGATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAAATGACAAAGGCGCCAATA
* * *
2726714 TGCTGATTCAAGGCTAGTGATATTGGACTTAAAGATGAAGATGTCAATGTGTTGATTCAAGGTCA
66 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGTCAATGTGCTGATTCAAGGTCA
2726779 GCGACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAACGATACCAGACTTAA
131 GCGACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAACGATACCAGAC-TAA
2726844 AGAT
195 A-AT
*
2726848 GAAGATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGCGCCAATA
1 GAAGATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAAATGACAAAGGCGCCAATA
* *
2726913 TGTTGATTCAAGACCAGCGATATTGGACTTAAAGATGAAGATGTCAATGTGCTGATTCAAGGTCA
66 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGTCAATGTGCTGATTCAAGGTCA
* *
2726978 GCGACATTGGACTTAAAGATGATGGTGCCAATATGCTAATTCAAGGCCAACGATACCGGACT---
131 GCGACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAACGATACCAGACTAAA
2727040 -T
196 AT
* * *
2727041 AAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAA
1 GAAGATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAA
2727088 GAAGATGCCA
Statistics
Matches: 405, Mismatches: 32, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
193 44 0.11
198 55 0.14
199 271 0.67
200 31 0.08
201 4 0.01
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (197 bp):
GAAGATGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAAATGACAAAGGCGCCAATA
TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGTCAATGTGCTGATTCAAGGTCA
GCGACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAACGATACCAGACTAAA
AT
Found at i:2727064 original size:43 final size:43
Alignment explanation
Indices: 2727003--2727086 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
2726993 AAGATGATGG
2727003 TGCCAATATGCTAATTCAAGGCCAACGATACCGGACTTAAAGA
1 TGCCAATATGCTAATTCAAGGCCAACGATACCGGACTTAAAGA
* **
2727046 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAA
1 TGCCAATATGCTAATTCAAGGCCAACGATACCGGACTTAAA
2727087 AGAAGATGCC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (43 bp):
TGCCAATATGCTAATTCAAGGCCAACGATACCGGACTTAAAGA
Found at i:2727131 original size:31 final size:31
Alignment explanation
Indices: 2727093--2727339 Score: 118
Period size: 29 Copynumber: 8.5 Consensus size: 31
2727083 TAAAAGAAGA
2727093 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAA-GGT
2727125 TG-CACCAACTTGTGT--GCTTTTG-AAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGT
** * *
2727152 TGCCACTGAC-T-TGTGGGCTTTTGAAAAGA
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGT
* ** * *
2727181 TACCACTGAC-T-TGTGGGCTTTGGAAAAGGG
1 TGCCACCAACTTGTGTGGGCTTTTG-AAAGGT
* * * * *
2727211 TGTCACTAAC-T-TGTGGGCTTTGGAAAAGA
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGT
**
2727240 TGCCACGGAC-T-TGTGGGCTTTT-AAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGT
* ** * * *
2727268 TGCCACTAAC-T-TGTGCACTTTGGAAAAGA
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGT
2727297 TGCCA-CAGAC-T-TGTGGGCTTTT-AAAGGT
1 TGCCACCA-ACTTGTGTGGGCTTTTGAAAGGT
**
2727325 TGCCACTGACTTGTG
1 TGCCACCAACTTGTG
2727340 GGCTTTGGAA
Statistics
Matches: 171, Mismatches: 34, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
26 3 0.02
27 6 0.04
28 47 0.27
29 74 0.43
30 26 0.15
31 13 0.08
32 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.31
Consensus pattern (31 bp):
TGCCACCAACTTGTGTGGGCTTTTGAAAGGT
Found at i:2727175 original size:57 final size:56
Alignment explanation
Indices: 2727106--2727434 Score: 282
Period size: 57 Copynumber: 5.7 Consensus size: 56
2727096 CACCAACTTG
* * * * * *
2727106 TGTGGGCTTTTGAAAGGGTTGCACCAACTTGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTGGAAA-AGATGCACCAACTTGTGGGCTTTTAAAGGTTGCCACTAACT
* * ** * * *
2727163 TGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTTGGAAAAGGGTGTCACTAACT
1 TGTGGGCTTTGGAAAAGAT-GCACCAACTTGTGGGCTTT--TAAAGGTTGCCACTAACT
**
2727222 TGTGGGCTTTGGAAAAGATGCCACGGACTTGTGGGCTTTTAAAGGTTGCCACTAACT
1 TGTGGGCTTTGGAAAAGATG-CACCAACTTGTGGGCTTTTAAAGGTTGCCACTAACT
** *
2727279 TGTGCACTTTGGAAAAGATGC-CACAGACTTGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTGGAAAAGATGCAC-CA-ACTTGTGGGCTTTTAAAGGTTGCCACTAACT
** * * ** * *
2727336 TGTGGGCTTTGGAAAAGATGCCACGGACTTATGGTCGTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGGAAAAGATG-CACCAACTTGTGGGC-TT-TTAAAGGTTGCCACTAACT
* **
2727395 TGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTT
1 TGTGGGCTTTGGAAAA-GATG-CACCAACTTGTGGGCTTT
2727435 GAAAAAGGTG
Statistics
Matches: 225, Mismatches: 36, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
55 1 0.00
56 3 0.01
57 119 0.53
58 3 0.01
59 83 0.37
60 16 0.07
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (56 bp):
TGTGGGCTTTGGAAAAGATGCACCAACTTGTGGGCTTTTAAAGGTTGCCACTAACT
Found at i:2727194 original size:29 final size:29
Alignment explanation
Indices: 2727152--2727441 Score: 332
Period size: 29 Copynumber: 10.0 Consensus size: 29
2727142 TTTTGAAGGT
*
2727152 TGCCACTGACTTGTGGGCTTTTGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
* *
2727181 TACCACTGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAA-GA
* *
2727211 TGTCACTAACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
* * * *
2727240 TGCCACGGACTTGTGGGCTTT-TAAAGGT
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
* **
2727268 TGCCACTAACTTGTGCACTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
* * * *
2727297 TGCCACAGACTTGTGGGCTTT-TAAAGGT
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
2727325 TGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAAGA
* * * * *
2727354 TGCCACGGACTTATGGTCGTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAA-GA
*
2727384 TGCCACTGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAA-GA
*
2727414 TGCCACTGACTTGTGGGCTTTGAAAAAG
1 TGCCACTGACTTGTGGGCTTTGGAAAAG
2727442 GTGAGGAATG
Statistics
Matches: 216, Mismatches: 41, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
28 45 0.21
29 93 0.43
30 78 0.36
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (29 bp):
TGCCACTGACTTGTGGGCTTTGGAAAAGA
Found at i:2727572 original size:13 final size:13
Alignment explanation
Indices: 2727554--2727581 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2727544 TACAAAAGAT
2727554 CAATGTATCGATA
1 CAATGTATCGATA
2727567 CAATGTATCGATA
1 CAATGTATCGATA
2727580 CA
1 CA
2727582 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2727660 original size:19 final size:18
Alignment explanation
Indices: 2727636--2727693 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
2727626 TGATACATTC
2727636 TATCGATACAAAACTTATG
1 TATCGATAC-AAACTTATG
2727655 TATCGATAC--A--T-TG
1 TATCGATACAAACTTATG
2727668 TATCGATACAACACTTATG
1 TATCGATACAA-ACTTATG
2727687 TATCGAT
1 TATCGAT
2727694 GCAATTACGG
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.33
14 1 0.03
16 2 0.06
18 1 0.03
19 18 0.55
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TATCGATACAAACTTATG
Found at i:2727671 original size:13 final size:13
Alignment explanation
Indices: 2727653--2727677 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2727643 ACAAAACTTA
2727653 TGTATCGATACAT
1 TGTATCGATACAT
2727666 TGTATCGATACA
1 TGTATCGATACA
2727678 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2727672 original size:32 final size:32
Alignment explanation
Indices: 2727627--2727693 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
2727617 GCTTTATAAT
2727627 GATACATTCTATCGATACAAAACTTATGTATC
1 GATACATTCTATCGATACAAAACTTATGTATC
* *
2727659 GATACATTGTATCGATACAACACTTATGTATC
1 GATACATTCTATCGATACAAAACTTATGTATC
2727691 GAT
1 GAT
2727694 GCAATTACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
GATACATTCTATCGATACAAAACTTATGTATC
Found at i:2728730 original size:49 final size:49
Alignment explanation
Indices: 2728438--2729457 Score: 947
Period size: 49 Copynumber: 20.5 Consensus size: 49
2728428 CGAAGAATGA
* * * *
2728438 CAATGTCCTGATTCATA-GCCAGCAACATTGGACTTGAAGAAGAA--TGC
1 CAATGTGCTGATTCA-AGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
** * *
2728485 CAATGTGCTGAGACAAGG-CAGCAACATTAGG-CTTAAAGATGGGAAAAAGGATGT
1 CAATGTGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGAT--G---AAGG-TGC
* * ** * * *
2728539 CAATGTGTTGATTCACGGTTAGCGACATTAGACTTGAAGATGAGAAGAATGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT--GAAG-GTGC
* ** ***
2728591 CAATGTGCTGATTCAAGGCCAACGACATTGGGTTTTAAAGATGATGAAGCAAC
1 CAATGTGCTGATTCAAGGCCAGCGACATT-GGACTT-AA-A-GATGAAGGTGC
* * * *
2728644 CAATATGCTTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGGTGC
1 CAATGTGC-TGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * *
2728694 TAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGATGACA-GTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-AGGTGC
* ** * * *
2728743 CAATATGCTGATTCAAGGCCAGCGACACCGGATTTAAAAATGAAGTTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * ** * * *
2728792 CAATGTGCTAATTCAAGTCCAATGACATTCGTCTTAAAAATGTCAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG---AAGGTGC
* * * * *
2728844 CAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAGATGAAGATGT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * *
2728893 CAATGTGCTAATTCAAGGCCAGCGACATTGGACATAAAGATGATGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * ** *
2728942 CAATATGCTGATTCAAGGCCAGCGATACCGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* *
2728991 CAACGTGCTGTTTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * *
2729040 CAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGATGACGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * * ** * * *
2729089 CAATATGTTGATTCAA-GCCGAGCGATACCGGACATAAAAATGAAGATGC
1 CAATGTGCTGATTCAAGGCC-AGCGACATTGGACTTAAAGATGAAGGTGC
* * * * *
2729138 CAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAGATGAAGATGT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* *
2729187 CAATGTGCTGATTCAAGGTCAGCGACATTGGACTTAAAGATGATGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * * ** *
2729236 CAATATGTTGATTCAAGGCCAGCGATACCGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* **
2729285 CAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACAAAGGCAC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG---AAGGTGC
* * * *
2729337 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * *
2729386 CAATGTGCTGATTCAAGGTCAGCGACATTAGACTTAAAGATGACGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* *
2729435 CAATATGCTGATTTAAGGCCAGC
1 CAATGTGCTGATTCAAGGCCAGC
2729458 AATACCAGAC
Statistics
Matches: 784, Mismatches: 161, Indels: 54
0.78 0.16 0.05
Matches are distributed among these distances:
46 18 0.02
47 15 0.02
48 4 0.01
49 534 0.68
50 18 0.02
51 3 0.00
52 114 0.15
53 15 0.02
54 41 0.05
55 19 0.02
56 3 0.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
Found at i:2729577 original size:29 final size:28
Alignment explanation
Indices: 2729522--2729774 Score: 105
Period size: 29 Copynumber: 8.8 Consensus size: 28
2729512 TAGAAGAAGA
2729522 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
1 TGCCACCAACTTGTGT--GCTTTTG-AA-GGT
2729554 TG-CACCAACTTGTGTGCTTTTGAAGGT
1 TGCCACCAACTTGTGTGCTTTTGAAGGT
** * * * *
2729581 TGCCACTGACTTGTGGGCTTTTAAAAAGA
1 TGCCACCAACTTGTGTGCTTTT-GAAGGT
* ** * *
2729610 TACCACTGACTTGTAG-GCTTTGGAAAAGGG
1 TGCCACCAACTTGT-GTGCTTTTG--AAGGT
* ** * * * *
2729640 TGTCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACCAACTTGTGTGCTTTTG-AAGGT
*** *
2729669 TGCCACGGGCTTGTGGGCTTTTGAAGGT
1 TGCCACCAACTTGTGTGCTTTTGAAGGT
** * * * *
2729697 TGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACCAACTTGTGTGCTTTTG-AAGGT
** *
2729726 TGCCACGTACTTGTGGGCTTTTGAAGGT
1 TGCCACCAACTTGTGTGCTTTTGAAGGT
* *
2729754 TGCCACCGACTTGTGGGCTTT
1 TGCCACCAACTTGTGTGCTTT
2729775 GGAAAAGATG
Statistics
Matches: 181, Mismatches: 33, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
27 5 0.03
28 63 0.35
29 75 0.41
30 23 0.13
31 13 0.07
32 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (28 bp):
TGCCACCAACTTGTGTGCTTTTGAAGGT
Found at i:2729622 original size:57 final size:57
Alignment explanation
Indices: 2729561--2729863 Score: 417
Period size: 57 Copynumber: 5.2 Consensus size: 57
2729551 GGTTGCACCA
* ** * *
2729561 ACTTGTGTGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTAAAAAGATACCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGG
* * * *
2729618 ACTTGTAGGCTTTGGAAAAGGGTGTCACTGACTTGTGGGCTTTGGAAAAGATGCCACGG
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGG
* *
2729677 GCTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGT
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGG
*
2729734 ACTTGTGGGCTTTTGAAGGTTGCCACCGACTTGTGGGCTTTGGAAAAGATGCCACGG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGG
* * **
2729791 ACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGGATGCCACTA
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTGACTTGTGGGCTTTGGAAAA-GATGCCACGG
2729851 ACTTGTGGGCTTT
1 ACTTGTGGGCTTT
2729864 GGAAAAGGTG
Statistics
Matches: 218, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
57 119 0.55
59 78 0.36
60 21 0.10
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (57 bp):
ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGG
Found at i:2729649 original size:30 final size:30
Alignment explanation
Indices: 2729576--2729871 Score: 367
Period size: 29 Copynumber: 10.1 Consensus size: 30
2729566 TGTGCTTTTG
* *
2729576 AAGGTTGCCACTGACTTGTGGGCTTT-TAA
1 AAGGATGCCACTGACTTGTGGGCTTTGGAA
* * *
2729605 AAAGATACCACTGACTTGTAGGCTTTGGAA
1 AAGGATGCCACTGACTTGTGGGCTTTGGAA
* *
2729635 AAGGGTGTCACTGACTTGTGGGCTTTGGAA
1 AAGGATGCCACTGACTTGTGGGCTTTGGAA
* * *
2729665 AA-GATGCCACGGGCTTGTGGGCTTTTG--
1 AAGGATGCCACTGACTTGTGGGCTTTGGAA
*
2729692 AAGGTTGCCACTGACTTGTGGGCTTTGGAA
1 AAGGATGCCACTGACTTGTGGGCTTTGGAA
*
2729722 AA-GATGCCAC-GTACTTGTGGGCTTTTG--
1 AAGGATGCCACTG-ACTTGTGGGCTTTGGAA
* *
2729749 AAGGTTGCCACCGACTTGTGGGCTTTGGAA
1 AAGGATGCCACTGACTTGTGGGCTTTGGAA
*
2729779 AA-GATGCCACGGACTTGTGGGCTTTGGAA
1 AAGGATGCCACTGACTTGTGGGCTTTGGAA
*
2729808 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
1 AAGGATGCCACTGACTTGTGGGCTTTGGAA
*
2729838 AAGGATGCCACTAACTTGTGGGCTTTGGAA
1 AAGGATGCCACTGACTTGTGGGCTTTGGAA
2729868 AAGG
1 AAGG
2729872 TGAGGAATGT
Statistics
Matches: 228, Mismatches: 29, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
27 4 0.02
28 43 0.19
29 91 0.40
30 90 0.39
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.28
Consensus pattern (30 bp):
AAGGATGCCACTGACTTGTGGGCTTTGGAA
Found at i:2729739 original size:116 final size:116
Alignment explanation
Indices: 2729561--2729871 Score: 448
Period size: 116 Copynumber: 2.7 Consensus size: 116
2729551 GGTTGCACCA
* ** * * *
2729561 ACTTGTGTGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTAAAAAGATACCACTGACTTGTAG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTAACTTGTGG
* *
2729626 GCTTTGGAAAAGGGTGTCACTGACTTGTGGGCTTTGGAAAAGATGCCACGG
66 GCTTTGGAAAAGGGTGCCACCGACTTGTGGGCTTTGGAAAAGATGCCACGG
*
2729677 GCTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGT-ACTTGTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCAC-TAACTTGTG
* *
2729741 GGCTTTTG--AAGGTTGCCACCGACTTGTGGGCTTTGGAAAAGATGCCACGG
65 GGCTTTGGAAAAGGGTGCCACCGACTTGTGGGCTTTGGAAAAGATGCCACGG
* *
2729791 ACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGGATGCCACTAACTTG
1 ACTTGTGGGCTTTTG--AAGGTTGCCACTGACTTGTGGGCTTTGGAAAA-GATGCCACTAACTTG
2729856 TGGGCTTTGGAAAAGG
63 TGGGCTTTGGAAAAGG
2729872 TGAGGAATGT
Statistics
Matches: 174, Mismatches: 14, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
114 52 0.30
116 95 0.55
117 23 0.13
119 4 0.02
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.30
Consensus pattern (116 bp):
ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTAACTTGTGG
GCTTTGGAAAAGGGTGCCACCGACTTGTGGGCTTTGGAAAAGATGCCACGG
Found at i:2730000 original size:13 final size:13
Alignment explanation
Indices: 2729984--2730008 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2729974 ACAAAAGATC
2729984 AATGTATCGATAA
1 AATGTATCGATAA
2729997 AATGTATCGATA
1 AATGTATCGATA
2730009 CATTTGAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
AATGTATCGATAA
Found at i:2730073 original size:13 final size:13
Alignment explanation
Indices: 2730055--2730106 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
2730045 AGCTTCGTAG
2730055 CGATACATTGTAT
1 CGATACATTGTAT
2730068 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
2730087 CGATACATTGTAT
1 CGATACATTGTAT
2730100 CGATACA
1 CGATACA
2730107 AAACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:2730087 original size:19 final size:19
Alignment explanation
Indices: 2730063--2730125 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
2730053 AGCGATACAT
2730063 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
2730082 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
2730095 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
2730114 TGTATCGATACA
1 TGTATCGATACA
2730126 GTTACAGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:2730096 original size:32 final size:32
Alignment explanation
Indices: 2730055--2730125 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
2730045 AGCTTCGTAG
2730055 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
2730087 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
2730119 CGATACA
1 CGATACA
2730126 GTTACAGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:2735780 original size:37 final size:37
Alignment explanation
Indices: 2735730--2735813 Score: 159
Period size: 37 Copynumber: 2.3 Consensus size: 37
2735720 GCCACAATCG
*
2735730 TGCATTTGTGACATTCATAACCTTTCATTTTGCATGA
1 TGCATTTGTGACATTCATAACATTTCATTTTGCATGA
2735767 TGCATTTGTGACATTCATAACATTTCATTTTGCATGA
1 TGCATTTGTGACATTCATAACATTTCATTTTGCATGA
2735804 TGCATTTGTG
1 TGCATTTGTG
2735814 CTTCATCTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (37 bp):
TGCATTTGTGACATTCATAACATTTCATTTTGCATGA
Found at i:2736219 original size:28 final size:27
Alignment explanation
Indices: 2736179--2736423 Score: 316
Period size: 28 Copynumber: 8.8 Consensus size: 27
2736169 CCTCACCTTC
2736179 CAAAGCCCACAAGTCAGTGGCACTTTTT
1 CAAAGCCCACAAGTCAGTGGCAC-TTTT
*
2736207 CAAAGCCCACAAGTCAGTGGCAAC-CTT
1 CAAAGCCCACAAGTCAGTGGC-ACTTTT
2736234 CAAAGCCCACAAGTCAGTGGCATCTTTT
1 CAAAGCCCACAAGTCAGTGGCA-CTTTT
*
2736262 CAAAAGCCCACAAGTCAGTGGCACCTTT
1 C-AAAGCCCACAAGTCAGTGGCACTTTT
2736290 CAAAGCCCACAAGTCAGTGGCAAC-TTT
1 CAAAGCCCACAAGTCAGTGGC-ACTTTT
2736317 CGAAAGCCCACAAGTCAGTGGCATCTTTT
1 C-AAAGCCCACAAGTCAGTGGCA-CTTTT
*
2736346 CAAAAGCCCACAAGTTAGTGGCACATTTT
1 C-AAAGCCCACAAGTCAGTGGCAC-TTTT
* * *
2736375 CAAAGCCCATAAATCAGTGGCAAC-CTT
1 CAAAGCCCACAAGTCAGTGGC-ACTTTT
*
2736402 CAAAGCCCACAAGGCAGTGGCA
1 CAAAGCCCACAAGTCAGTGGCA
2736424 ACCTTCAAAA
Statistics
Matches: 195, Mismatches: 12, Indels: 22
0.85 0.05 0.10
Matches are distributed among these distances:
26 2 0.01
27 69 0.35
28 70 0.36
29 54 0.28
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (27 bp):
CAAAGCCCACAAGTCAGTGGCACTTTT
Found at i:2736262 original size:55 final size:56
Alignment explanation
Indices: 2736173--2736443 Score: 347
Period size: 55 Copynumber: 4.9 Consensus size: 56
2736163 GACATTCCTC
*
2736173 ACCTTCCAAAGCCCACAAGTCAGTGGCACTTTTTC-AAAGCCCACAAGTCAGTGGCA
1 ACCTT-CAAAGCCCACAAGTCAGTGGCACATTTTCAAAAGCCCACAAGTCAGTGGCA
2736229 ACCTTCAAAGCCCACAAGTCAGTGGCATC-TTTTCAAAAGCCCACAAGTCAGTGGC-
1 ACCTTCAAAGCCCACAAGTCAGTGGCA-CATTTTCAAAAGCCCACAAGTCAGTGGCA
* *
2736284 ACCTTTCAAAGCCCACAAGTCAGTGGCA-ACTTTCGAAAGCCCACAAGTCAGTGGCA
1 ACC-TTCAAAGCCCACAAGTCAGTGGCACATTTTCAAAAGCCCACAAGTCAGTGGCA
* * * * *
2736340 TCTTTTCAAAAGCCCACAAGTTAGTGGCACATTTTC-AAAGCCCATAAATCAGTGGCA
1 AC-CTTC-AAAGCCCACAAGTCAGTGGCACATTTTCAAAAGCCCACAAGTCAGTGGCA
* ** *
2736397 ACCTTCAAAGCCCACAAGGCAGTGGCA-ACCTTCAAAAGCACACAAGT
1 ACCTTCAAAGCCCACAAGTCAGTGGCACATTTTCAAAAGCCCACAAGT
2736444 TGGTGTAACC
Statistics
Matches: 189, Mismatches: 17, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
54 4 0.02
55 83 0.44
56 57 0.30
57 40 0.21
58 5 0.03
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.20
Consensus pattern (56 bp):
ACCTTCAAAGCCCACAAGTCAGTGGCACATTTTCAAAAGCCCACAAGTCAGTGGCA
Found at i:2736323 original size:84 final size:84
Alignment explanation
Indices: 2736180--2736443 Score: 415
Period size: 84 Copynumber: 3.2 Consensus size: 84
2736170 CTCACCTTCC
*
2736180 AAAGCCCACAAGTCAGTGGCACTTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACA
1 AAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACA
2736245 AGTCAGTGGCATCTTTTCA
66 AGTCAGTGGCATCTTTTCA
* *
2736264 AAAGCCCACAAGTCAGTGGCAC-CTTTCAAAGCCCACAAGTCAGTGGCAACTTTCGAAAGCCCAC
1 AAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCAACCTTC-AAAGCCCAC
2736328 AAGTCAGTGGCATCTTTTCA
65 AAGTCAGTGGCATCTTTTCA
* * *
2736348 AAAGCCCACAAGTTAGTGGCACATTTTCAAAGCCCATAAATCAGTGGCAACCTTCAAAGCCCACA
1 AAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACA
* * *
2736413 AGGCAGTGGCAAC-CTTCA
66 AGTCAGTGGCATCTTTTCA
*
2736431 AAAGCACACAAGT
1 AAAGCCCACAAGT
2736444 TGGTGTAACC
Statistics
Matches: 167, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
83 46 0.28
84 93 0.56
85 28 0.17
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.19
Consensus pattern (84 bp):
AAAGCCCACAAGTCAGTGGCACATTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAGCCCACA
AGTCAGTGGCATCTTTTCA
Found at i:2736459 original size:112 final size:113
Alignment explanation
Indices: 2736172--2736486 Score: 349
Period size: 112 Copynumber: 2.8 Consensus size: 113
2736162 AGACATTCCT
* * * *
2736172 CACCTTCCAAAGCCCACAAGTCAGTGGC-ACTTTTTC-AAAGCCCACAAGTCAGTGGCAA-CC-T
1 CACCTTTCAAAGCCCACAAGGCAGTGGCAAC--CTTCAAAAGCACACAAGTCAGTGG-AACCCTT
* *
2736233 TC-AAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGG
63 TCAAAAGCCCACAAGTTAGTGGCATCTTTTCAAAAGCCCACAAATCAGTGG
* * * * * * *
2736283 CACCTTTCAAAGCCCACAAGTCAGTGGCAACTTTCGAAAGCCCACAAGTCAGTGGCATCTTTTCA
1 CACCTTTCAAAGCCCACAAGGCAGTGGCAACCTTCAAAAGCACACAAGTCAGTGGAACCCTTTCA
*
2736348 AAAGCCCACAAGTTAGTGGCA-CATTTTC-AAAGCCCATAAATCAGTGG
66 AAAGCCCACAAGTTAGTGGCATC-TTTTCAAAAGCCCACAAATCAGTGG
** *
2736395 CAACC-TTCAAAGCCCACAAGGCAGTGGCAACCTTCAAAAGCACACAAGTTGGTGTAACCCTTTC
1 C-ACCTTTCAAAGCCCACAAGGCAGTGGCAACCTTCAAAAGCACACAAGTCAGTGGAACCCTTTC
*
2736459 AAAAGCACACACAAGTTGGTGGCATCTT
65 AAAAGC-C-CACAAGTTAGTGGCATCTT
2736487 CTTCTAAGTC
Statistics
Matches: 177, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
110 5 0.03
111 47 0.27
112 79 0.45
113 29 0.16
114 16 0.09
115 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (113 bp):
CACCTTTCAAAGCCCACAAGGCAGTGGCAACCTTCAAAAGCACACAAGTCAGTGGAACCCTTTCA
AAAGCCCACAAGTTAGTGGCATCTTTTCAAAAGCCCACAAATCAGTGG
Found at i:2736558 original size:49 final size:49
Alignment explanation
Indices: 2736486--2736717 Score: 374
Period size: 49 Copynumber: 4.7 Consensus size: 49
2736476 GGTGGCATCT
* *
2736486 TCTTCTAAGTCCAATATTTCTGGCCTTGAATCAGCATATTGGCACCTTCA
1 TCTT-TAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
2736536 TCTTTAAGTCTAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCTTCA
*
2736585 TCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGTACCTTCA
1 TCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
2736634 TCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTAGCACCTTCA
1 TCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCTTCA
**
2736683 TCTTTAAGTCCAATATCACTGGCCTTGAATCAGCA
1 TCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCA
2736718 TATTAGCATC
Statistics
Matches: 169, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 165 0.98
50 4 0.02
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (49 bp):
TCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCTTCA
Found at i:2736723 original size:49 final size:49
Alignment explanation
Indices: 2736486--2736885 Score: 356
Period size: 49 Copynumber: 8.0 Consensus size: 49
2736476 GGTGGCATCT
** *
2736486 TCTTCTAAGTCCAATATTTCTGGCCTTGAATCAGCATATTGGCACCTTCA
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
2736536 TCTTTAAGTCTAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
2736585 TCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGTACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * *
2736634 TCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTAGCACCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * *
2736683 TCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTAGCATCCATAACA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CC-T-TCA
* * * * * *
2736735 TTCCTT--GGCACAATGTCGTTGGCCTTGAATCAGCACATTAGCATTCTTCTCA
1 -TCTTTAAGTC-CAATATCGCTGGCCTTGAATCAGCACATTGGCA--CCT-TCA
* * * * * * * *
2736787 TCTTCAAGTCTAATGTCGCTGACCGTGAATCAGCATATTGACATTCTTTACA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--CCTT-CA
* * ** *
2736839 GCTTTAAGCCCAATATCATTGGTCC-TGAATCAGCATATTGGCACCTT
1 TCTTTAAGTCCAATATCGCTGG-CCTTGAATCAGCACATTGGCACCTT
2736886 TATCGCTCTT
Statistics
Matches: 296, Mismatches: 44, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
49 172 0.58
50 9 0.03
51 7 0.02
52 98 0.33
53 10 0.03
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (49 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCA
Found at i:2737568 original size:13 final size:13
Alignment explanation
Indices: 2737550--2737576 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2737540 ACCAAGAAAA
2737550 TGTATCGATACAT
1 TGTATCGATACAT
2737563 TGTATCGATACAT
1 TGTATCGATACAT
2737576 T
1 T
2737577 AATCTTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2742614 original size:165 final size:165
Alignment explanation
Indices: 2742416--2743007 Score: 812
Period size: 165 Copynumber: 3.6 Consensus size: 165
2742406 TTTCTTTAGG
* * * *
2742416 GGATTTTTCTTAGTTTTTGATTGTTACAATTCATCAAATATATTTATTTATTTCATATTAAATCA
1 GGATTTTTCTTAGTTTTTAATTTTTAAAATTCATAAAATATATTTATTTATTTCATATTAAATCA
* * * ** **
2742481 ATTTTTAAAAATTTATTTAATTTCATGAGTTTTGATTTTTTTCTTGAAATTTTAATGTTTCCGAA
66 ATTTTCAAAAATTCATTTATTTTCATGAGTTTTGATTTTTTTCTTGAAATTTTCCTGTTTCAAAA
* * *
2742546 ATACGGAGTTTTCCACTCCATAAATGTTTTCGGGA
131 ATACGGAGTTTTCTACTCCGTAAATATTTTCGGGA
* * *
2742581 GGATTTTTTTTGGTTTTTAATTTTTAAAATTCATAAAACATATTTATTTATTTCATATTAAATCA
1 GGATTTTTCTTAGTTTTTAATTTTTAAAATTCATAAAATATATTTATTTATTTCATATTAAATCA
* ** ** *
2742646 GTTTTCAAAAATTCATTTATTTTCATGAGTTTTGAATTTTTCCCTTGAAATTTTCCCATTTCTAA
66 ATTTTCAAAAATTCATTTATTTTCATGAGTTTTG-ATTTTTTTCTTGAAATTTTCCTGTTTCAAA
*
2742711 AATACGGAGTTTTCTACTCCGTAAATATTTTCGGAA
130 AATACGGAGTTTTCTACTCCGTAAATATTTTCGGGA
* * * * *
2742747 AGATTTTTCTTGGTTTTTAATTTTGAAAATT-ATAAAATTTATTTATTTATTTCATATTAAATTA
1 GGATTTTTCTTAGTTTTTAATTTTTAAAATTCATAAAATATATTTATTTATTTCATATTAAATCA
* * * *
2742811 GTTTTCAAAAATTTATTTATTTTCATGAGTTTTAAATTTTTTTCTTAAAATTTTCCTGTTTCAAA
66 ATTTTCAAAAATTCATTTATTTTCATGAGTTTT-GATTTTTTTCTTGAAATTTTCCTGTTTCAAA
2742876 AATACGGAGTTTTCTACTCCGTAAATATTTTCGGG-
130 AATACGGAGTTTTCTACTCCGTAAATATTTTCGGGA
* *
2742911 GGATTTTTATTAGTTTTTAATTTTT-AAATTCATAAAATATATTTATTTAATTCATATTAAATCA
1 GGATTTTTCTTAGTTTTTAATTTTTAAAATTCATAAAATATATTTATTTATTTCATATTAAATCA
* *
2742975 ATGTTCAAAAATTCATTTATTTTCATGAATTTT
66 ATTTTCAAAAATTCATTTATTTTCATGAGTTTT
2743008 CAAAAATTCG
Statistics
Matches: 375, Mismatches: 49, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
163 5 0.01
164 80 0.21
165 208 0.55
166 82 0.22
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.51
Consensus pattern (165 bp):
GGATTTTTCTTAGTTTTTAATTTTTAAAATTCATAAAATATATTTATTTATTTCATATTAAATCA
ATTTTCAAAAATTCATTTATTTTCATGAGTTTTGATTTTTTTCTTGAAATTTTCCTGTTTCAAAA
ATACGGAGTTTTCTACTCCGTAAATATTTTCGGGA
Found at i:2743548 original size:10 final size:11
Alignment explanation
Indices: 2743511--2743605 Score: 72
Period size: 11 Copynumber: 8.5 Consensus size: 11
2743501 TAGGAACAAT
*
2743511 TAGAGAGAAAA
1 TAGAAAGAAAA
*
2743522 TAGAGAACAAAA
1 TAGA-AAGAAAA
*
2743534 CAGAAAGAAAA
1 TAGAAAGAAAA
2743545 -AG-AAGAAAAA
1 TAGAAAG-AAAA
2743555 TAGAGAAGAAAA
1 TAGA-AAGAAAA
*
2743567 TTGAAAGAAAA
1 TAGAAAGAAAA
2743578 -AG-AAGAAAAA
1 TAGAAAG-AAAA
*
2743588 TAAAGAAGAAAA
1 TAGA-AAGAAAA
2743600 TAGAAA
1 TAGAAA
2743606 ACTAGCTAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
9 6 0.09
10 11 0.16
11 22 0.33
12 22 0.33
13 6 0.09
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.07
Consensus pattern (11 bp):
TAGAAAGAAAA
Found at i:2743556 original size:33 final size:33
Alignment explanation
Indices: 2743518--2743605 Score: 140
Period size: 33 Copynumber: 2.7 Consensus size: 33
2743508 AATTAGAGAG
* *
2743518 AAAATAGAGAACAAAACAGAAAGAAAAAGAAGA
1 AAAATAGAGAAGAAAATAGAAAGAAAAAGAAGA
*
2743551 AAAATAGAGAAGAAAATTGAAAGAAAAAGAAGA
1 AAAATAGAGAAGAAAATAGAAAGAAAAAGAAGA
*
2743584 AAAATAAAGAAGAAAATAGAAA
1 AAAATAGAGAAGAAAATAGAAA
2743606 ACTAGCTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (33 bp):
AAAATAGAGAAGAAAATAGAAAGAAAAAGAAGA
Found at i:2743561 original size:13 final size:12
Alignment explanation
Indices: 2743511--2743603 Score: 69
Period size: 12 Copynumber: 8.3 Consensus size: 12
2743501 TAGGAACAAT
2743511 TAGAG-AGAAAA
1 TAGAGAAGAAAA
*
2743522 TAGAGAACAAAA
1 TAGAGAAGAAAA
*
2743534 CAGA-AAG-AAA
1 TAGAGAAGAAAA
2743544 -A-AGAAGAAAAA
1 TAGAGAAG-AAAA
2743555 TAGAGAAGAAAA
1 TAGAGAAGAAAA
*
2743567 TTGA-AAG-AAA
1 TAGAGAAGAAAA
2743577 -A-AGAAGAAAAA
1 TAGAGAAG-AAAA
*
2743588 TAAAGAAGAAAA
1 TAGAGAAGAAAA
2743600 TAGA
1 TAGA
2743604 AAACTAGCTA
Statistics
Matches: 65, Mismatches: 6, Indels: 21
0.71 0.07 0.23
Matches are distributed among these distances:
8 2 0.03
9 7 0.11
10 6 0.09
11 16 0.25
12 24 0.37
13 10 0.15
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.08
Consensus pattern (12 bp):
TAGAGAAGAAAA
Found at i:2744390 original size:34 final size:35
Alignment explanation
Indices: 2744352--2744418 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
2744342 CCTTACAACA
2744352 CTATC-TTTC-AAGGCTAAGATAAAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGAT-AAAACCTCTCTCT
*
2744386 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAAAACCTCTC
2744419 AATCACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
36 13 0.45
37 11 0.38
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAAAACCTCTCTCT
Found at i:2744916 original size:26 final size:22
Alignment explanation
Indices: 2744859--2744901 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2744849 TTAAATAGTG
2744859 TGAACAGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
*
2744881 TAAACAGTGATGTATCGATAC
1 TGAACAGTGATGTATCGATAC
2744902 TGTGATGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAACAGTGATGTATCGATACA
Found at i:2744979 original size:10 final size:10
Alignment explanation
Indices: 2744960--2744990 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2744950 GTATCGATAC
2744960 ATGAACAGTG
1 ATGAACAGTG
*
2744970 ATGAATAGTG
1 ATGAACAGTG
2744980 ATGAACAGTG
1 ATGAACAGTG
2744990 A
1 A
2744991 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:2745036 original size:13 final size:13
Alignment explanation
Indices: 2745018--2745042 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2745008 TGCCAATGCT
2745018 ATGTATCGATACA
1 ATGTATCGATACA
2745031 ATGTATCGATAC
1 ATGTATCGATAC
2745043 TTAGCAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2745163 original size:21 final size:21
Alignment explanation
Indices: 2745123--2745163 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2745113 GTCAACCTTG
*
2745123 TGTATTGATACCAATAGTATA
1 TGTATTGATACCAACAGTATA
2745144 TGTATTGATA-CAACACGTAT
1 TGTATTGATACCAACA-GTAT
2745164 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (21 bp):
TGTATTGATACCAACAGTATA
Found at i:2746684 original size:155 final size:156
Alignment explanation
Indices: 2746481--2746836 Score: 470
Period size: 155 Copynumber: 2.3 Consensus size: 156
2746471 TATCGGGTGT
* * * *
2746481 TTTTACATCGAAGGTATCCCATAGGGGCATTTTCATGATTTCTT-AAAACTAACTCCTAGGTCAT
1 TTTTACATCGAAGGTATCCCCTAGGGGTATTTTCATAATTT-TTCAAAACCAACTCCTAGGTCAT
* * *
2746545 CACCGGGTTTGCTTTTATACCGAAGGTAGATATTT-AGAATAGGTTCATCCCTTTTAAAATCGTT
65 CACCGGGTCTGCTTTTATACCAAAGGTAGATATTTAAG-ATAGGTTCATCCCTTTTAAAA-CCTT
* * *
2746609 -TTTAAG-TCTTTTAGAGGTA-TCGAGTAC
128 CGTCAAGCCCTTTTAGAGGTACT-GAGTAC
* * *
2746636 TTTTACATCGAAGGTATCCCCTAGGGGTACTTTCGTAATTTTTCAAAACCAACTCCTAGGTCGTC
1 TTTTACATCGAAGGTATCCCCTAGGGGTATTTTCATAATTTTTCAAAACCAACTCCTAGGTCATC
*
2746701 ACCGGGTCTGCTTTTATGCCAAAGGTAGATATTTAAGATAGGTTCATCCCTTTTAAAACCTTCGT
66 ACCGGGTCTGCTTTTATACCAAAGGTAGATATTTAAGATAGGTTCATCCCTTTTAAAACCTTCGT
*
2746766 CAAGCCCTTTTAGGGGTACTGAGTAC
131 CAAGCCCTTTTAGAGGTACTGAGTAC
* * *
2746792 TTTTACGTCGAAGGTATCCTTCTAGAGGTATTTTCATAATTTTTC
1 TTTTACATCGAAGGTATCC-CCTAGGGGTATTTTCATAATTTTTC
2746837 TTGAATCGAG
Statistics
Matches: 175, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
154 5 0.03
155 111 0.63
156 37 0.21
157 22 0.13
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (156 bp):
TTTTACATCGAAGGTATCCCCTAGGGGTATTTTCATAATTTTTCAAAACCAACTCCTAGGTCATC
ACCGGGTCTGCTTTTATACCAAAGGTAGATATTTAAGATAGGTTCATCCCTTTTAAAACCTTCGT
CAAGCCCTTTTAGAGGTACTGAGTAC
Found at i:2749350 original size:16 final size:18
Alignment explanation
Indices: 2749331--2749364 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2749321 AGCCTTTTCC
2749331 TTTT-CTATTTTT-TTTT
1 TTTTGCTATTTTTGTTTT
2749347 TTTTGCTATTTTTGTTTT
1 TTTTGCTATTTTTGTTTT
2749365 GCTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 8 0.50
18 4 0.25
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.82
Consensus pattern (18 bp):
TTTTGCTATTTTTGTTTT
Found at i:2749358 original size:14 final size:13
Alignment explanation
Indices: 2749340--2749374 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
2749330 CTTTTCTATT
2749340 TTTTTTTTTTTGC
1 TTTTTTTTTTTGC
*
2749353 TATTTTTGTTTTGC
1 T-TTTTTTTTTTGC
2749367 TTTTTTTT
1 TTTTTTTT
2749375 CTTGTTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.03, C:0.06, G:0.09, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTTTGC
Found at i:2759750 original size:12 final size:12
Alignment explanation
Indices: 2759685--2759791 Score: 57
Period size: 12 Copynumber: 8.7 Consensus size: 12
2759675 TTTTATAATT
2759685 TATTATTAAAATA
1 TATTATT-AAATA
2759698 TGATATATTAAATA
1 T-AT-TATTAAATA
2759712 T-TT-TTAAATA
1 TATTATTAAATA
2759722 TATTTGTAATTATAATA
1 TA--T-T-ATTA-AATA
2759739 TATTATTAAATA
1 TATTATTAAATA
*
2759751 CT-TTTTTGAAATA
1 -TATTATT-AAATA
2759764 TA--A-T-AATA
1 TATTATTAAATA
2759772 TATTATTAAATA
1 TATTATTAAATA
*
2759784 TAATATTA
1 TATTATTA
2759792 TTCTTAAAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 33
0.68 0.03 0.30
Matches are distributed among these distances:
8 6 0.08
10 10 0.13
11 2 0.03
12 21 0.28
13 12 0.16
14 10 0.13
15 5 0.07
16 3 0.04
17 6 0.08
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.50
Consensus pattern (12 bp):
TATTATTAAATA
Done.