Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold27
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: 2789374
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 115785 characters in sequence are not A, C, G, or T
File 2 of 16
Found at i:171379 original size:13 final size:14
Alignment explanation
Indices: 171359--171392 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
171349 TAGAACAACC
171359 AGAA-AGAAAAAAA
1 AGAAGAGAAAAAAA
171372 AG-AGAGAAAAAAA
1 AGAAGAGAAAAAAA
171385 AGAAGAGA
1 AGAAGAGA
171393 GCTATTCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 13 0.68
14 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AGAAGAGAAAAAAA
Found at i:171390 original size:16 final size:17
Alignment explanation
Indices: 171359--171393 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
171349 TAGAACAACC
171359 AGAAAGAAAAAAAAGAG
1 AGAAAGAAAAAAAAGAG
*
171376 AGAAA-AAAAAGAAGAG
1 AGAAAGAAAAAAAAGAG
171392 AG
1 AG
171394 CTATTCCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAAAAAAGAG
Found at i:175530 original size:8 final size:8
Alignment explanation
Indices: 175517--175552 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
175507 ATAGTTTAAG
175517 ATTATTTT
1 ATTATTTT
175525 ATTATTTT
1 ATTATTTT
175533 ATTATTTT
1 ATTATTTT
175541 ATTA-TTT
1 ATTATTTT
175548 ATTAT
1 ATTAT
175553 AATTGATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
ATTATTTT
Found at i:176176 original size:6 final size:6
Alignment explanation
Indices: 176167--176200 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
176157 CCATTGCCCA
*
176167 TGCCTG TGCCTG TGCCTA TGCCTG TGCCTG TGCC
1 TGCCTG TGCCTG TGCCTG TGCCTG TGCCTG TGCC
176201 CCTATCTGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.03, C:0.35, G:0.29, T:0.32
Consensus pattern (6 bp):
TGCCTG
Found at i:176182 original size:18 final size:18
Alignment explanation
Indices: 176161--176201 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
176151 GCTATGCCAT
176161 TGCCCATGCCTGTGCCTG
1 TGCCCATGCCTGTGCCTG
*
176179 TGCCTATGCCTGTGCCTG
1 TGCCCATGCCTGTGCCTG
176197 TGCCC
1 TGCCC
176202 CTATCTGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.05, C:0.39, G:0.27, T:0.29
Consensus pattern (18 bp):
TGCCCATGCCTGTGCCTG
Found at i:177257 original size:26 final size:26
Alignment explanation
Indices: 177191--177265 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 26
177181 AATAGAATTC
177191 AAATAATATATAAATTTATATATTATTAAT
1 AAATAA-A-ATAAATTTAT-T-TTATTAAT
*
177221 AAATTAAAT-AATATTATTTTATTAA-
1 AAATAAAATAAAT-TTATTTTATTAAT
177246 AAATAAAAATAAATTTATTT
1 AAAT-AAAATAAATTTATTT
177266 ATACTTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
25 4 0.10
26 17 0.43
27 7 0.17
28 6 0.15
29 1 0.03
30 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AAATAAAATAAATTTATTTTATTAAT
Found at i:185844 original size:14 final size:14
Alignment explanation
Indices: 185821--185874 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
185811 ATTAATTTTT
*
185821 AAAT-TAATTATCA
1 AAATATAATTATTA
185834 AAATATAATTATTTTA
1 AAATATAATTA--TTA
185850 AAATA-AATTATTA
1 AAATATAATTATTA
*
185863 AAATATTATTAT
1 AAATATAATTAT
185875 ATATTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
13 12 0.34
14 11 0.31
15 5 0.14
16 7 0.20
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATATAATTATTA
Found at i:185853 original size:29 final size:29
Alignment explanation
Indices: 185815--185874 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
185805 TTTATTATTA
* *
185815 ATTTTTAAATTAATTATCAAAATATAATT
1 ATTTTAAAATAAATTATCAAAATATAATT
* *
185844 ATTTTAAAATAAATTATTAAAATATTATT
1 ATTTTAAAATAAATTATCAAAATATAATT
185873 AT
1 AT
185875 ATATTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
ATTTTAAAATAAATTATCAAAATATAATT
Found at i:185880 original size:33 final size:32
Alignment explanation
Indices: 185807--185881 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 32
185797 GGTGATTTTT
*
185807 TATTATTA-AT-TTTTAAATTAATTATCAAAA
1 TATTATTATATATTTTAAATAAATTATCAAAA
*
185837 TA-TA--AT-TATTTTAAAATAAATTATTAAAA
1 TATTATTATATATTTT-AAATAAATTATCAAAA
185866 TATTATTATATATTTT
1 TATTATTATATATTTT
185882 TTACTTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
27 2 0.06
28 4 0.11
29 18 0.50
30 4 0.11
32 2 0.06
33 6 0.17
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (32 bp):
TATTATTATATATTTTAAATAAATTATCAAAA
Found at i:186027 original size:14 final size:14
Alignment explanation
Indices: 186008--186074 Score: 66
Period size: 13 Copynumber: 4.8 Consensus size: 14
185998 TTGATGTAAA
186008 AATAATAATATTTT
1 AATAATAATATTTT
186022 AATAAT-ATATTTT
1 AATAATAATATTTT
186035 AAAATAATAATATTTT
1 --AATAATAATATTTT
* * *
186051 GATACTAA-ATTTA
1 AATAATAATATTTT
*
186064 AATAGTAATAT
1 AATAATAATAT
186075 GATCAAAAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
13 17 0.39
14 14 0.32
15 6 0.14
16 7 0.16
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (14 bp):
AATAATAATATTTT
Found at i:186062 original size:29 final size:28
Alignment explanation
Indices: 186006--186074 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 28
185996 ACTTGATGTA
*
186006 AAAATAATAATATTTTAATAATATATTTT
1 AAAATAATAATATTTTAATAATA-AATTT
* *
186035 AAAATAATAATATTTTGATACTAAATTT
1 AAAATAATAATATTTTAATAATAAATTT
*
186063 -AAATAGTAATAT
1 AAAATAATAATAT
186075 GATCAAAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 11 0.31
28 4 0.11
29 21 0.58
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (28 bp):
AAAATAATAATATTTTAATAATAAATTT
Found at i:187633 original size:2 final size:2
Alignment explanation
Indices: 187626--187660 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
187616 GCATGGGATC
187626 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
187661 GCAAATTACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:192898 original size:20 final size:20
Alignment explanation
Indices: 192873--192925 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
192863 AAATTCCTAG
192873 ATGTATCGATACA-AAGATCA
1 ATGTATCGATACACAA-ATCA
*
192893 ATGTATCGATACACAAATTA
1 ATGTATCGATACACAAATCA
192913 ATGTATCGATACA
1 ATGTATCGATACA
192926 TTTCCTTGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
ATGTATCGATACACAAATCA
Found at i:198422 original size:156 final size:156
Alignment explanation
Indices: 198073--198422 Score: 416
Period size: 156 Copynumber: 2.2 Consensus size: 156
198063 ATACCTTTAA
* * *
198073 ACATGAAAGTATCCCGATAATCTTAAAGGACTTA-AAAATAATCATAAATGGGATGAACCTATCT
1 ACATGAAAGTATCTCGATAACCTTAAAGGAC-TACAAAATAATCACAAATGGGATGAACCTATCT
* * * *
198137 TAAATGCATACTTTTAGTATAAAAGCATCCAAGTGACAACATAAAACTTGGTTTTAGAAAAATTA
65 TAAATGCACACCTTTAGCATAAAAGCATCCAAGTGACAACATAAAACTTGGTTTAAGAAAAATTA
*
198202 TGAACATGCCCTTAGGGTATACCTTCG
130 TGAAAATGCCCTTAGGGTATACCTTCG
* * * * * * * *
198229 ACATTAAAATATCTTGGTAACTTTAAAAGACTTCAAAATGATCACAAATGGGATGAACCTATCTT
1 ACATGAAAGTATCTCGATAACCTTAAAGGACTACAAAATAATCACAAATGGGATGAACCTATCTT
* * ** * * *
198294 AAATGCACACCTTTGGCATAAAAGCATGCTGGTGACAACCTAAGATTTGGTTCTAAGAAAAATTA
66 AAATGCACACCTTTAGCATAAAAGCATCCAAGTGACAACATAAAACTTGGTT-TAAGAAAAATTA
* * *
198359 TGAAAATGCCTTTGGGGTATACCTTTG
130 TGAAAATGCCCTTAGGGTATACCTTCG
* *
198386 ATATGAAAGTATCTCGATAACCTTATAGGAC-ACAAAA
1 ACATGAAAGTATCTCGATAACCTTAAAGGACTACAAAA
198423 GAAATCTAGG
Statistics
Matches: 157, Mismatches: 35, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
155 1 0.01
156 99 0.63
157 57 0.36
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (156 bp):
ACATGAAAGTATCTCGATAACCTTAAAGGACTACAAAATAATCACAAATGGGATGAACCTATCTT
AAATGCACACCTTTAGCATAAAAGCATCCAAGTGACAACATAAAACTTGGTTTAAGAAAAATTAT
GAAAATGCCCTTAGGGTATACCTTCG
Found at i:199584 original size:79 final size:77
Alignment explanation
Indices: 199417--199874 Score: 334
Period size: 79 Copynumber: 5.8 Consensus size: 77
199407 GAGATAACAG
* * * * * * * * * *
199417 GGTTGGAATATCCCTGATGGTGGAAATCAGTGTTCTAGAAATAAAATCAATGTTGGAGTATCCCT
1 GGTTGGAGTATTCC-GATGGTGAAAATCGGTATTTTAGAAATAAAATCGAGGTTAGAGTATCCCC
199482 TCAAAAATAAC-A
65 TCAAAAATAACGA
** * * * * *
199494 GGGTTATAGTATAGCCGATGGTGAAAATTTGGTGTTTTAGAAATAAAATCGAGGTTAGAATATTC
1 -GGTTGGAGTAT-TCCGATGGTGAAAA-TCGGTATTTTAGAAATAAAATCGAGGTTAGAGTATCC
*
199559 CCTCAAAAATAATGA
63 CCTCAAAAATAACGA
* * * * *
199574 TGTTGGAGTATCTCCGATGGTAGAAAGTCGATATCTTAGAAATAAAATCGAGGTTGGAGTAT-CC
1 GGTTGGAGTAT-TCCGATGGT-GAAAATCGGTATTTTAGAAATAAAATCGAGGTTAGAGTATCCC
** *
199638 CTTGAAAATAACAA
64 CTCAAAAATAACGA
* * * * *
199652 GGTTGGAGTATTCTTGATAGTGGAGAAATCGGTGTTTTAGGAATAAAAT-TAGAGTTAGAGTATC
1 GGTTGGAGTATTC-CGATGGT-GA-AAATCGGTATTTTAGAAATAAAATCGAG-GTTAGAGTATC
*
199716 CCCTCAGAAATAACGA
62 CCCTCAAAAATAACGA
* * * * *
199732 GATTGGAGTATCCTCGATGGTGAAAAAAT-AGTATTTTAGAAATAAAAT-TAGGGTTGGAGTATC
1 GGTTGGAGTATTC-CGATGGTG--AAAATCGGTATTTTAGAAATAAAATCGA-GGTTAGAGTATC
* * *
199795 CCCTTAAAAATAATGG
62 CCCTCAAAAATAACGA
* * *
199811 GGTTGGAGTA-TCCTTGATGATGGAAAATCGATATTTTAGAAATAAAATCGAGGTTGGAGTATCC
1 GGTTGGAGTATTCC--GATGGT-GAAAATCGGTATTTTAGAAATAAAATCGAGGTTAGAGTATCC
199875 TTGATAATGG
Statistics
Matches: 300, Mismatches: 64, Indels: 31
0.76 0.16 0.08
Matches are distributed among these distances:
77 3 0.01
78 55 0.18
79 200 0.67
80 41 0.14
81 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.30
Consensus pattern (77 bp):
GGTTGGAGTATTCCGATGGTGAAAATCGGTATTTTAGAAATAAAATCGAGGTTAGAGTATCCCCT
CAAAAATAACGA
Found at i:199691 original size:158 final size:156
Alignment explanation
Indices: 199452--199874 Score: 446
Period size: 158 Copynumber: 2.7 Consensus size: 156
199442 ATCAGTGTTC
* **
199452 TAGAAATAAAATCAATGTTGGAGTATCCCTTCAAAAATAACAGGGTTATAGTATAGCC--GATG-
1 TAGAAATAAAATCAAGGTTGGAGTATCCCTT-AAAAATAACAGGGTTGGAGTAT--CCTTGATGT
* * *
199514 GTGAAAATTTGGTGTTTTAGAAATAAAATCGAGGTTAGAATATTCCCTCAAAAATAATGATG-TT
63 G-GAAAA-TCGGTGTTTTAGAAATAAAATCGAGGTTAGAATATCCCCTCAAAAATAACGA-GATT
* * *
199578 GGAGTAT-CTCCGATGGT-AGAAAGTCGATATCT
125 GGAGTATCCT-CGATGGTGAAAAAATAG-TATCT
* * * *
199610 TAGAAATAAAATCGAGGTTGGAGTATCCCTTGAAAATAACAAGGTTGGAGTATTCTTGATAGTGG
1 TAGAAATAAAATCAAGGTTGGAGTATCCCTTAAAAATAACAGGGTTGGAGTATCCTTGAT-GTGG
* * * *
199675 AGAAATCGGTGTTTTAGGAATAAAAT-TAGAGTTAGAGTATCCCCTCAGAAATAACGAGATTGGA
65 A-AAATCGGTGTTTTAGAAATAAAATCGAG-GTTAGAATATCCCCTCAAAAATAACGAGATTGGA
*
199739 GTATCCTCGATGGTGAAAAAATAGTATTT
128 GTATCCTCGATGGTGAAAAAATAGTATCT
* * **
199768 TAGAAATAAAATTAGGGTTGGAGTATCCCCTTAAAAATAATGGGGTTGGAGTATCCTTGATGATG
1 TAGAAATAAAATCAAGGTTGGAGTAT-CCCTTAAAAATAACAGGGTTGGAGTATCCTTGATG-TG
* * * *
199833 GAAAATCGATATTTTAGAAATAAAATCGAGGTTGGAGTATCC
64 GAAAATCGGTGTTTTAGAAATAAAATCGAGGTTAGAATATCC
199875 TTGATAATGG
Statistics
Matches: 222, Mismatches: 31, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
155 1 0.00
157 24 0.11
158 150 0.68
159 47 0.21
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (156 bp):
TAGAAATAAAATCAAGGTTGGAGTATCCCTTAAAAATAACAGGGTTGGAGTATCCTTGATGTGGA
AAATCGGTGTTTTAGAAATAAAATCGAGGTTAGAATATCCCCTCAAAAATAACGAGATTGGAGTA
TCCTCGATGGTGAAAAAATAGTATCT
Found at i:199867 original size:51 final size:52
Alignment explanation
Indices: 199811--199927 Score: 173
Period size: 52 Copynumber: 2.3 Consensus size: 52
199801 AAAATAATGG
*
199811 GGTTGGAGTATCCTTGATGATGG-AAAATCGATATTTTAGAAATAAAATCGA
1 GGTTGGAGTATCCTTGATAATGGAAAAATCGATATTTTAGAAATAAAATCGA
* * * *
199862 GGTTGGAGTATCCTTGATAATGGAAAAATTGATGTTTTAGGAATAAAATCGG
1 GGTTGGAGTATCCTTGATAATGGAAAAATCGATATTTTAGAAATAAAATCGA
*
199914 GGTTGAAGTATCCT
1 GGTTGGAGTATCCT
199928 CTTTAAAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 22 0.37
52 37 0.63
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (52 bp):
GGTTGGAGTATCCTTGATAATGGAAAAATCGATATTTTAGAAATAAAATCGA
Found at i:199900 original size:131 final size:130
Alignment explanation
Indices: 199729--200007 Score: 310
Period size: 131 Copynumber: 2.1 Consensus size: 130
199719 TCAGAAATAA
* * ** * *
199729 CGAGATTGGAGTATCCTCGATGGTGAAAAAATAGTATTTTAGAAATAAAATTAGGGTTGGAGTAT
1 CGAGGTTGGAGTATCCTTGATAATGAAAAAATAGTATTTTAGAAATAAAATCAGGGTTGAAGTAT
* * * * * *
199794 CCCCTTAAAAATAATGGGGTTGGAGTATCCTTGAT-GATGGAAAATCGATATTTTAGAAATAAAA
66 CCCCTTAAAAATAATAGGGTTCGAATATCCTCGATAG-TGAAAAATCGATATTTTAAAAATAAAA
199858 T
130 T
* * * * *
199859 CGAGGTTGGAGTATCCTTGATAATGGAAAAATTGATGTTTTAGGAATAAAATCGGGGTTGAAGTA
1 CGAGGTTGGAGTATCCTTGATAATGAAAAAATAG-TATTTTAGAAATAAAATCAGGGTTGAAGTA
* * * * *
199924 TCCTCTTTAAAATAATAGGGTTCGAATATCCTCGATAGTTAAAAATTGGTATTTTAAAAATAAAA
65 TCCCCTTAAAAATAATAGGGTTCGAATATCCTCGATAGTGAAAAATCGATATTTTAAAAATAAAA
199989 T
130 T
*
199990 -TAGGGTTGGAGTATCCTT
1 CGA-GGTTGGAGTATCCTT
200008 CAAAGATAAT
Statistics
Matches: 123, Mismatches: 23, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
130 29 0.24
131 93 0.76
132 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.33
Consensus pattern (130 bp):
CGAGGTTGGAGTATCCTTGATAATGAAAAAATAGTATTTTAGAAATAAAATCAGGGTTGAAGTAT
CCCCTTAAAAATAATAGGGTTCGAATATCCTCGATAGTGAAAAATCGATATTTTAAAAATAAAAT
Found at i:200056 original size:210 final size:209
Alignment explanation
Indices: 199651--200067 Score: 511
Period size: 210 Copynumber: 2.0 Consensus size: 209
199641 GAAAATAACA
* * * * *
199651 AGGTTGGAGTATTCTTGATAGTGGAGAAATCGGTGTTTTAGGAATAAAATTAGAGTTAGAGTATC
1 AGGTTGGAGTATCCTTGATAATGGAAAAATCGATGTTTTAGGAATAAAATCAGAGTTAGAGTATC
* * * * *
199716 CCCTCAGAAATAACGAGATTGGAGTATCCTCGATGGTGAAAAAATAGTATTTTAGAAATAAAATT
66 CCCTCAGAAATAAAGAGATTCGAATATCCTCGATAGTGAAAAAATAGTATTTTAAAAATAAAATT
* * *
199781 AGGGTTGGAGTATCCCCTTAAAAATAATGGGGTTGGAGTATCCTTGATGATGGAAAATCGATATT
131 AGGGTTGGAGTAT-CCCTTAAAAATAATGGGGTTAGAGTATCCCTGATGACGGAAAATCGATATT
199846 TTAGAAATAAAATCG
195 TTAGAAATAAAATCG
* * *
199861 AGGTTGGAGTATCCTTGATAATGGAAAAATTGATGTTTTAGGAATAAAATCGGGGTT-GAAGTAT
1 AGGTTGGAGTATCCTTGATAATGGAAAAATCGATGTTTTAGGAATAAAATCAGAGTTAG-AGTAT
* * * * * *
199925 CCTCTTTA-AAATAATAG-GGTTCGAATATCCTCGATAGTTAAAAATTGGTATTTTAAAAATAAA
65 CC-CCTCAGAAATAA-AGAGATTCGAATATCCTCGATAGTGAAAAAATAGTATTTTAAAAATAAA
* * *
199988 ATTAGGGTTGGAGTAT-CCTTCAAAGATAATGGGGTTATAGTATCCCTGAT-AGCGGAAAAATTG
128 ATTAGGGTTGGAGTATCCCTT-AAAAATAATGGGGTTAGAGTATCCCTGATGA-CGG-AAAATCG
200051 ATATTTTAGAAATAAAA
190 ATATTTTAGAAATAAAA
200068 ACATCAATGA
Statistics
Matches: 176, Mismatches: 25, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
208 5 0.03
209 28 0.16
210 139 0.79
211 4 0.02
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.32
Consensus pattern (209 bp):
AGGTTGGAGTATCCTTGATAATGGAAAAATCGATGTTTTAGGAATAAAATCAGAGTTAGAGTATC
CCCTCAGAAATAAAGAGATTCGAATATCCTCGATAGTGAAAAAATAGTATTTTAAAAATAAAATT
AGGGTTGGAGTATCCCTTAAAAATAATGGGGTTAGAGTATCCCTGATGACGGAAAATCGATATTT
TAGAAATAAAATCG
Found at i:202985 original size:50 final size:52
Alignment explanation
Indices: 202897--203026 Score: 167
Period size: 50 Copynumber: 2.6 Consensus size: 52
202887 GCTTGAATGT
* * * * *
202897 ATCGATACATTGAGAAATGTATCAATACATCTGGGTTAAGACCTAGAAT-CA
1 ATCGATACAATGAAAAATGTATCGATACATCTGAGTTAAAACCTAGAATGCA
* *
202948 ATCGATACAATGAAAAATATATCGAT-CATCTGAGTTAAAACCTAGAATGTA
1 ATCGATACAATGAAAAATGTATCGATACATCTGAGTTAAAACCTAGAATGCA
*
202999 A-AGATACAATGAAAAATGTATCGATACA
1 ATCGATACAATGAAAAATGTATCGATACA
203027 AATTGTAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
50 42 0.62
51 26 0.38
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (52 bp):
ATCGATACAATGAAAAATGTATCGATACATCTGAGTTAAAACCTAGAATGCA
Found at i:203875 original size:167 final size:167
Alignment explanation
Indices: 203609--203912 Score: 396
Period size: 167 Copynumber: 1.8 Consensus size: 167
203599 ATTTAATTGT
** *
203609 TAAACTTTTGAAAATTTCATTTCATACTTGATGAAAAACCAAGAAGATAAAAAAAGTTTTAAAAA
1 TAAACTTTTGAAAATTTCATTTCATACTCAACGAAAAACCAAGAAGATAAAAAAAGTTTTAAAAA
* * * * *
203674 TTTCTATACTCCTATGGAAGACGATAAGAATAATAAAAATCTTTAAAAATAACTAAAATGATGAT
66 TTTCTATACCCCTACGAAAGACGATAAGAATAATAAAAATCTTTAAAAATAACTAAAATAACGAT
203739 TTTAACTCTAAAAAAATGAAAATTTCAATTTAATCTC
131 TTTAACTCTAAAAAAATGAAAATTTCAATTTAATCTC
* * * * ** *
203776 TAAACTTTTGAAATTTTTATTTCATACTCAACGAAAAACTGAA-AGGATACGAAAGGTTTTAAAA
1 TAAACTTTTGAAAATTTCATTTCATACTCAACGAAAAAC-CAAGAAGATAAAAAAAGTTTTAAAA
* * * * *
203840 ATTTTTATACCCCTACGAAAGGTC-ATAAGAATAATAGAAATCTTTAAAAATGATTAAAATAACG
65 ATTTCTATACCCCTACGAAA-GACGATAAGAATAATAAAAATCTTTAAAAATAACTAAAATAACG
203904 ATTTTAACT
129 ATTTTAACT
203913 ATTTAATCCC
Statistics
Matches: 115, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
167 111 0.97
168 4 0.03
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.33
Consensus pattern (167 bp):
TAAACTTTTGAAAATTTCATTTCATACTCAACGAAAAACCAAGAAGATAAAAAAAGTTTTAAAAA
TTTCTATACCCCTACGAAAGACGATAAGAATAATAAAAATCTTTAAAAATAACTAAAATAACGAT
TTTAACTCTAAAAAAATGAAAATTTCAATTTAATCTC
Found at i:204019 original size:147 final size:147
Alignment explanation
Indices: 203766--204056 Score: 343
Period size: 147 Copynumber: 2.0 Consensus size: 147
203756 GAAAATTTCA
* * * * * *
203766 ATTTAATCTCTAAACTTTTGAAATTTTTATTTCATACTCAACGAAAAACTGAAAGGATACGAAAG
1 ATTTAATCCCTAAACTTTTAAAAATTTCATTTCATACTCAACGAAAAACTAAAAAGATACGAAAG
* * * * * *
203831 GTTTTAAAAATTTTTATACCCCTACGAAAGGTCATAAGAATAATAGAAATCTTTAAAAATGATTA
66 GTGTTAAAAATTTCTATACCCCTACGAAAGGCCATAAGAATAATAGAAATATTTAAAAATAACTA
203896 AAATAACGATTTTAACT
131 AAATAACGATTTTAACT
* * * * * *
203913 ATTTAATCCCTAAATTTTTAAAAATTTCATTTCGTATTTAACGAAGAACTAAAAAGATAC-TAAG
1 ATTTAATCCCTAAACTTTTAAAAATTTCATTTCATACTCAACGAAAAACTAAAAAGATACGAAAG
* * * *
203977 AGTGTTGAAAATTTCTATAGCCCTATGGAAA-GCCATAGGAATAATAGAAATATTTAAAAATAAC
66 -GTGTTAAAAATTTCTATACCCCTA-CGAAAGGCCATAAGAATAATAGAAATATTTAAAAATAAC
*
204041 TAAAATAATGATTTTA
129 TAAAATAACGATTTTA
204057 CTTCTAAATA
Statistics
Matches: 119, Mismatches: 23, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
146 3 0.03
147 112 0.94
148 4 0.03
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (147 bp):
ATTTAATCCCTAAACTTTTAAAAATTTCATTTCATACTCAACGAAAAACTAAAAAGATACGAAAG
GTGTTAAAAATTTCTATACCCCTACGAAAGGCCATAAGAATAATAGAAATATTTAAAAATAACTA
AAATAACGATTTTAACT
Found at i:205832 original size:146 final size:146
Alignment explanation
Indices: 205547--205820 Score: 388
Period size: 146 Copynumber: 1.9 Consensus size: 146
205537 ATATAAATGC
*
205547 AAACTCACAAAATAAATTGAAATCTTTAAAATTGATTTAATATCAATTAAACAATAATATTTGAA
1 AAACTCACAAAATAAATTGAAATCTTTAAAACTGATTTAATATCAATTAAACAATAATATTTGAA
** * * * *
205612 GAATATTGAAAATTATAAACTAAGAAAAATACTACTGAAGAAATTTACGGAGTATATATTTTGAA
66 GAATATTGAAAATTATAAACTAAGAAAAATACTACCAAAGAAATTTACGAAGTAAAAACTTTGAA
205677 AATAGGAAAAATTCTA
131 AATAGGAAAAATTCTA
* * * *
205693 AAACTCATAAGATAAATTG-AATTTTTCAAAACTGATTTAATATGAATTAAACAATAATATTTGA
1 AAACTCACAAAATAAATTGAAATCTTT-AAAACTGATTTAATATCAATTAAACAATAATATTTGA
* * * *
205757 AGAATTTTGAAAATTATAAACTTAGAAAAATCCTACCAAAGAAATTTATGAAGTAAAAAACTTT
65 AGAATATTGAAAATTATAAACTAAGAAAAATACTACCAAAGAAATTTACGAAGT-AAAAACTTT
205821 AAATTTTGAA
Statistics
Matches: 111, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
145 6 0.05
146 99 0.89
147 6 0.05
ACGTcount: A:0.51, C:0.08, G:0.09, T:0.32
Consensus pattern (146 bp):
AAACTCACAAAATAAATTGAAATCTTTAAAACTGATTTAATATCAATTAAACAATAATATTTGAA
GAATATTGAAAATTATAAACTAAGAAAAATACTACCAAAGAAATTTACGAAGTAAAAACTTTGAA
AATAGGAAAAATTCTA
Found at i:211354 original size:13 final size:13
Alignment explanation
Indices: 211336--211360 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
211326 TTTAAAAATA
211336 AAAATTTCTCTTC
1 AAAATTTCTCTTC
211349 AAAATTTCTCTT
1 AAAATTTCTCTT
211361 TTTTATTTGA
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:0.20, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAATTTCTCTTC
Found at i:213080 original size:67 final size:67
Alignment explanation
Indices: 212982--213619 Score: 534
Period size: 67 Copynumber: 9.5 Consensus size: 67
212972 GCCAATATAA
* ** * *
212982 AAGATCAATGATGGAGAATATGTGGTT-TTATCAACAACTGAAACAAACTGATAACGAGCTGGAG
1 AAGATC-ATGATGGGGAATATGTGGTTCCCATCAACAACTGAAACAAATTGATAACGAGCTAGAG
213046 TAG
65 TAG
** * * * * *
213049 AAGATCATGATGGGGAATATGTGGTTCTTATCAAC-AGTCGAAATAAATTGGTAACAAGTTAGAG
1 AAGATCATGATGGGGAATATGTGGTTCCCATCAACAACT-GAAACAAATTGATAACGAGCTAGAG
213113 TAG
65 TAG
** * * * * ** * * *
213116 AATTTCATGATGGGAAATATGTGGTTCCCATTAATAGCCAAAACAAACTGGTAAGGAGCTAGAGT
1 AAGATCATGATGGGGAATATGTGGTTCCCATCAACAACTGAAACAAATTGATAACGAGCTAGAGT
213181 AG
66 AG
* * * *
213183 AAGATCATGGTCGGGAATATGTGGTTCCCATTAATAGA-TGAAACAAATTGATAAC-ATGCTAGA
1 AAGATCATGATGGGGAATATGTGGTTCCCATCAACA-ACTGAAACAAATTGATAACGA-GCTAGA
213246 GTAG
64 GTAG
* * * ** * * *
213250 AAGATCATGATGGGGAATATGTGGTTTCCATCAATAGCCAAAATAAATTGATAAAGAGCTAAAGT
1 AAGATCATGATGGGGAATATGTGGTTCCCATCAACAACTGAAACAAATTGATAACGAGCTAGAGT
213315 A-
66 AG
* * * * ** * * *
213316 AAAATCATGATAGGAAATATGTGGTTCCCATCAATAGTTGAAATAAATTGATAACAAACTAGAGT
1 AAGATCATGATGGGGAATATGTGGTTCCCATCAACAACTGAAACAAATTGATAACGAGCTAGAGT
213381 AG
66 AG
* ** * * * *
213383 AAGATCATGAAGAAGAAGATGTGGTTCCCATCAACAACTGAAACAAATTGGTAATGAGCTGGAGT
1 AAGATCATGATGGGGAATATGTGGTTCCCATCAACAACTGAAACAAATTGATAACGAGCTAGAGT
213448 AG
66 AG
* * * * ** *
213450 AAGATCATGATGAGGAATGTGTGGTTCCCATCAACATCCGAAACAAACAGATAATGAGCTAGAGT
1 AAGATCATGATGGGGAATATGTGGTTCCCATCAACAACTGAAACAAATTGATAACGAGCTAGAGT
*
213515 AA
66 AG
* * * * * * * * *
213517 AAGATCATAATGGGAAATATGTGATTCCCATCAATAGCTAAAACAAACT-AGTAATGAGCTAAAG
1 AAGATCATGATGGGGAATATGTGGTTCCCATCAACAACTGAAACAAATTGA-TAACGAGCTAGAG
213581 TCA-
65 T-AG
* * *
213584 AAGATCAAGACGGGGAATATGTGGTTCCTATCAACA
1 AAGATCATGATGGGGAATATGTGGTTCCCATCAACA
213620 GCCAAAACAA
Statistics
Matches: 460, Mismatches: 101, Indels: 20
0.79 0.17 0.03
Matches are distributed among these distances:
66 78 0.17
67 380 0.83
68 2 0.00
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (67 bp):
AAGATCATGATGGGGAATATGTGGTTCCCATCAACAACTGAAACAAATTGATAACGAGCTAGAGT
AG
Found at i:213199 original size:134 final size:134
Alignment explanation
Indices: 213022--213630 Score: 620
Period size: 134 Copynumber: 4.6 Consensus size: 134
213012 TCAACAACTG
* * * * **
213022 AAACAAACTGATAACGAGCTGGAGTAGAAGATCATGATGGGGAATATGTGGTTCTTATCAACAGT
1 AAACAAACTGGTAATGAGCTAGAGTAGAAGATCATGATCGGGAATATGTGGTTCCCATCAACAGT
* * * ** *
213087 CGAAATAAATTGGTAACAAGTTAGAGTAGAATTTCATGATGGGAAATATGTGGTTCCCATTAATA
66 CGAAACAAATTGATAACAAGCTAGAGTAGAAGATCATGATGGGAAATATGTGGTTCCCATCAATA
213152 GCCA
131 GCCA
* * * *
213156 AAACAAACTGGTAAGGAGCTAGAGTAGAAGATCATGGTCGGGAATATGTGGTTCCCATTAATAGA
1 AAACAAACTGGTAATGAGCTAGAGTAGAAGATCATGATCGGGAATATGTGGTTCCCATCAACAG-
* * *
213221 T-GAAACAAATTGATAACATGCTAGAGTAGAAGATCATGATGGGGAATATGTGGTTTCCATCAAT
65 TCGAAACAAATTGATAACAAGCTAGAGTAGAAGATCATGATGGGAAATATGTGGTTCCCATCAAT
213285 AGCCA
130 AGCCA
* * * * * * * * *
213290 AAATAAATTGATAAAGAGCTAAAGTA-AAAATCATGATAGGAAATATGTGGTTCCCATCAATAGT
1 AAACAAACTGGTAATGAGCTAGAGTAGAAGATCATGATCGGGAATATGTGGTTCCCATCAACAGT
* * * * * * *
213354 TGAAATAAATTGATAACAAACTAGAGTAGAAGATCATGA-AGAAGAAGATGTGGTTCCCATCAAC
66 CGAAACAAATTGATAACAAGCTAGAGTAGAAGATCATGATGGGA-AATATGTGGTTCCCATCAAT
* **
213418 AACTG
130 AGCCA
* * *
213423 AAACAAATTGGTAATGAGCTGGAGTAGAAGATCATGAT-GAGGAATGTGTGGTTCCCATCAACA-
1 AAACAAACTGGTAATGAGCTAGAGTAGAAGATCATGATCG-GGAATATGTGGTTCCCATCAACAG
** ** * * *
213486 TCCGAAACAAACAGATAATGAGCTAGAGTAAAAGATCATAATGGGAAATATGTGATTCCCATCAA
65 T-CGAAACAAATTGATAACAAGCTAGAGTAGAAGATCATGATGGGAAATATGTGGTTCCCATCAA
*
213551 TAGCTA
129 TAGCCA
* * * *
213557 AAACAAACTAGTAATGAGCTAAAGTCA-AAGATCAAGA-CGGGGAATATGTGGTTCCTATCAACA
1 AAACAAACTGGTAATGAGCTAGAGT-AGAAGATCATGATC-GGGAATATGTGGTTCCCATCAACA
* *
213620 GCCAAAACAAA
64 GTCGAAACAAA
213631 CTAGTATTGA
Statistics
Matches: 390, Mismatches: 74, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
132 2 0.01
133 109 0.28
134 274 0.70
135 5 0.01
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (134 bp):
AAACAAACTGGTAATGAGCTAGAGTAGAAGATCATGATCGGGAATATGTGGTTCCCATCAACAGT
CGAAACAAATTGATAACAAGCTAGAGTAGAAGATCATGATGGGAAATATGTGGTTCCCATCAATA
GCCA
Found at i:213475 original size:267 final size:267
Alignment explanation
Indices: 212979--213620 Score: 718
Period size: 267 Copynumber: 2.4 Consensus size: 267
212969 TATGCCAATA
* * * * * * *
212979 TAAAAGATCAATGATGGAGAATATGTGGTTT-TATCAACAACTGAAACAAACTGATAACGAGCTG
1 TAAAAGATC-ATGATGGGGAATATGTGGTTTCCATCAATAGCTAAAACAAACTGATAAAGAGCTA
* * * **
213043 GAGTAGAAGATCATGATGGGGAATATGTGGTTCTTATCAACAGTCGAAATAAATTGGTAACAAGT
65 AAGTA-AAGATCATGATGGGGAATATGTGGTTCCTATCAACAGTCGAAATAAATTGATAACAAAC
** * * * * * *
213108 TAGAGTAGAATTTCATGATGGGAAATATGTGGTTCCCATTAATAGCCAAAACAAACTGGTAAGGA
129 TAGAGTAGAAGATCATGAAGAGAAAGATGTGGTTCCCATCAACAACCAAAACAAACTGGTAAGGA
* * * * **
213173 GCTAGAGTAGAAGATCATGGTCGGGAATATGTGGTTCCCATTAATAGATGAAACAAATTGATAA-
194 GCTAGAGTAGAAGATCATGATCGGGAATATGTGGTTCCCATCAACAGACGAAACAAACAGATAAT
213237 CATGCTAGAG
259 CA-GCTAGAG
* * * *
213247 TAGAAGATCATGATGGGGAATATGTGGTTTCCATCAATAGCCAAAATAAATTGATAAAGAGCTAA
1 TAAAAGATCATGATGGGGAATATGTGGTTTCCATCAATAGCTAAAACAAACTGATAAAGAGCTAA
* * * * * *
213312 AGTAAAAATCATGATAGGAAATATGTGGTTCCCATCAATAGTTGAAATAAATTGATAACAAACTA
66 AGTAAAGATCATGATGGGGAATATGTGGTTCCTATCAACAGTCGAAATAAATTGATAACAAACTA
** * *
213377 GAGTAGAAGATCATGAAGA-AGAAGATGTGGTTCCCATCAACAACTGAAACAAATTGGTAATGAG
131 GAGTAGAAGATCATGAAGAGA-AAGATGTGGTTCCCATCAACAACCAAAACAAACTGGTAAGGAG
* * **
213441 CTGGAGTAGAAGATCATGAT-GAGGAATGTGTGGTTCCCATCAACATCCGAAACAAACAGATAAT
195 CTAGAGTAGAAGATCATGATCG-GGAATATGTGGTTCCCATCAACAGACGAAACAAACAGATAAT
*
213505 GAGCTAGAG
259 CAGCTAGAG
* * * * *
213514 TAAAAGATCATAATGGGAAATATGTGATTCCCATCAATAGCTAAAACAAACT-AGTAATGAGCTA
1 TAAAAGATCATGATGGGGAATATGTGGTTTCCATCAATAGCTAAAACAAACTGA-TAAAGAGCTA
* *
213578 AAGTCAAAGATCAAGACGGGGAATATGTGGTTCCTATCAACAG
65 AAGT-AAAGATCATGATGGGGAATATGTGGTTCCTATCAACAG
213621 CCAAAACAAA
Statistics
Matches: 307, Mismatches: 61, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
266 3 0.01
267 236 0.77
268 68 0.22
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (267 bp):
TAAAAGATCATGATGGGGAATATGTGGTTTCCATCAATAGCTAAAACAAACTGATAAAGAGCTAA
AGTAAAGATCATGATGGGGAATATGTGGTTCCTATCAACAGTCGAAATAAATTGATAACAAACTA
GAGTAGAAGATCATGAAGAGAAAGATGTGGTTCCCATCAACAACCAAAACAAACTGGTAAGGAGC
TAGAGTAGAAGATCATGATCGGGAATATGTGGTTCCCATCAACAGACGAAACAAACAGATAATCA
GCTAGAG
Found at i:213668 original size:27 final size:27
Alignment explanation
Indices: 213619--213674 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
213609 TCCTATCAAC
*
213619 AGCCAAAACAAACTAGTATTGAGCTGG
1 AGCCAAAACAAACTAGTAGTGAGCTGG
*
213646 AGCCAAAACAATA-TGGTAGTGAGCTGG
1 AGCCAAAACAA-ACTAGTAGTGAGCTGG
213673 AG
1 AG
213675 TAGAAGATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (27 bp):
AGCCAAAACAAACTAGTAGTGAGCTGG
Found at i:213760 original size:66 final size:67
Alignment explanation
Indices: 213666--213899 Score: 305
Period size: 66 Copynumber: 3.5 Consensus size: 67
213656 ATATGGTAGT
* * *
213666 GAGCTGGAGTAGAAGATCATGATGGGGAATATGTGGTTCCCATCAACAGCCAAAACAAACTGATG
1 GAGCTAGAGTAGAAGATCATGATGGGGAATATGTGGTTCCCATCAACAACCAAAACAAACTGATA
213731 A-
66 AC
* *
213732 GAAGCTAGAGTA-AAGATCATGACGGGGAATATGTGGTTCCCATCAACAACCAAAACAAATTGAT
1 G-AGCTAGAGTAGAAGATCATGATGGGGAATATGTGGTTCCCATCAACAACCAAAACAAACTGAT
213796 AAC
65 AAC
* * * *
213799 GAGCTAGAGTAGAAGAGCATGATAGGGAATATGTGGTT-CCATCAACAACCAAAACAAACTAACA
1 GAGCTAGAGTAGAAGATCATGATGGGGAATATGTGGTTCCCATCAACAACCAAAACAAACTGATA
*
213863 GC
66 AC
* * *
213865 AAG-TTGAAGTAGAAGATCATGATGGAGAATATGTG
1 GAGCTAG-AGTAGAAGATCATGATGGGGAATATGTG
213900 ATTTTACAAT
Statistics
Matches: 147, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
65 2 0.01
66 112 0.76
67 33 0.22
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (67 bp):
GAGCTAGAGTAGAAGATCATGATGGGGAATATGTGGTTCCCATCAACAACCAAAACAAACTGATA
AC
Found at i:219406 original size:38 final size:38
Alignment explanation
Indices: 219355--219434 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 38
219345 TGTTTAATAA
219355 CTTTAGGAATTTAGTCACCTTTTTCTCTTTTACCTATT
1 CTTTAGGAATTTAGTCACCTTTTTCTCTTTTACCTATT
** *
219393 CTTTAGGAATTTAGTCGGCTTTTTCTCTTTTACTTATT
1 CTTTAGGAATTTAGTCACCTTTTTCTCTTTTACCTATT
219431 CTTT
1 CTTT
219435 CACTTTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.16, C:0.19, G:0.10, T:0.55
Consensus pattern (38 bp):
CTTTAGGAATTTAGTCACCTTTTTCTCTTTTACCTATT
Found at i:225416 original size:32 final size:30
Alignment explanation
Indices: 225358--225435 Score: 120
Period size: 32 Copynumber: 2.5 Consensus size: 30
225348 GAACAGTACG
*
225358 TGTATCGATACATTCTATTTTTTACCCAGA
1 TGTATCGATACATTTTATTTTTTACCCAGA
225388 TGTATCGATACATTTTATTTTTTTTACCCAGA
1 TGTATCGATACATTTTA--TTTTTTACCCAGA
*
225420 TGTATTGATACATTTT
1 TGTATCGATACATTTT
225436 TCAATGTATC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 16 0.36
32 28 0.64
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (30 bp):
TGTATCGATACATTTTATTTTTTACCCAGA
Found at i:228845 original size:33 final size:32
Alignment explanation
Indices: 228803--228866 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
228793 TACAAGCCAA
228803 TGTATCGATACAT-TGTGGGATGTATTGATACAT
1 TGTATCGATACATCT-TGGG-TGTATTGATACAT
*
228836 TGTATCGATACATCTTGTGTGTATTGATACA
1 TGTATCGATACATCTTGGGTGTATTGATACA
228867 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.41
33 16 0.55
34 1 0.03
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATTGATACAT
Found at i:228944 original size:20 final size:21
Alignment explanation
Indices: 228897--228951 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
228887 GCCAATGACT
*
228897 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
228918 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
228938 TGTATCGATACATT
1 TGTATCGATACATT
228952 GTATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:235070 original size:19 final size:20
Alignment explanation
Indices: 235027--235078 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
235017 CATTTGAAAA
*
235027 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCAT
235047 TGTATCGATACATGT-T-CAT
1 TGTATCGATACAT-TATGCAT
235066 TGTATCGATACAT
1 TGTATCGATACAT
235079 AAACAAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 15 0.50
20 14 0.47
21 1 0.03
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTATGCAT
Found at i:240788 original size:13 final size:13
Alignment explanation
Indices: 240770--240808 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
240760 ATAATCACCC
*
240770 TGTATCGATACAG
1 TGTATCGATACAA
240783 TGTATCGATACAA
1 TGTATCGATACAA
240796 TGTATCGATACAA
1 TGTATCGATACAA
240809 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:240819 original size:20 final size:20
Alignment explanation
Indices: 240794--240872 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
240784 GTATCGATAC
240794 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
240814 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
240839 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
240859 CATGTATCGATACA
1 AATGTATCGATACA
240873 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:244695 original size:21 final size:21
Alignment explanation
Indices: 244666--244710 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
244656 AAGTTTTCAT
*
244666 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
244686 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
244708 TTT
1 TTT
244711 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:246946 original size:13 final size:13
Alignment explanation
Indices: 246928--246953 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
246918 CAATTTTTTG
246928 TGTATCGATACAT
1 TGTATCGATACAT
246941 TGTATCGATACAT
1 TGTATCGATACAT
246954 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:248183 original size:20 final size:19
Alignment explanation
Indices: 248160--248233 Score: 87
Period size: 19 Copynumber: 3.7 Consensus size: 19
248150 CACACCCAGA
*
248160 TGTATCGATACATGCTGCTT
1 TGTATCGATACATG-TGCAT
*
248180 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTGCAT
248199 TGTATCGATACATG-GACAAAT
1 TGTATCGATACATGTG-C--AT
248220 TGTATCGATACATG
1 TGTATCGATACATG
248234 AAACTGGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.38
20 14 0.29
21 16 0.33
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATGTGCAT
Found at i:252338 original size:13 final size:13
Alignment explanation
Indices: 252320--252344 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
252310 CATTTTATGG
252320 TGTATCGATACAA
1 TGTATCGATACAA
252333 TGTATCGATACA
1 TGTATCGATACA
252345 TACTATGTGT
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):
TGTATCGATACAA
Found at i:252360 original size:32 final size:33
Alignment explanation
Indices: 252297--252364 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
252287 CGTTACAAGC
**
252297 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
252330 CAATGTATCGATACATACTAT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
252362 CAA
1 CAA
252365 GTTTGGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:252461 original size:20 final size:20
Alignment explanation
Indices: 252419--252468 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
252409 TCTTTTTCAA
*
252419 GTATCGATACAATGCAACAT
1 GTATCGATACAATGAAACAT
* **
252439 GTATCGATACAATTAAATGT
1 GTATCGATACAATGAAACAT
252459 GTATCGATAC
1 GTATCGATAC
252469 TTTTCAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACAATGAAACAT
Found at i:254792 original size:13 final size:13
Alignment explanation
Indices: 254774--254812 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
254764 ATAATCCCCC
*
254774 TGTATCGATACAG
1 TGTATCGATACAA
254787 TGTATCGATACAA
1 TGTATCGATACAA
254800 TGTATCGATACAA
1 TGTATCGATACAA
254813 AGAATGCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:261018 original size:13 final size:13
Alignment explanation
Indices: 261000--261024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
260990 CATTTTATGG
261000 TGTATCGATACAA
1 TGTATCGATACAA
261013 TGTATCGATACA
1 TGTATCGATACA
261025 TACTATGTGT
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):
TGTATCGATACAA
Found at i:261040 original size:32 final size:33
Alignment explanation
Indices: 260977--261044 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
260967 CGTTACAAGC
**
260977 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
261010 CAATGTATCGATACATACTAT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
261042 CAA
1 CAA
261045 GTTTGGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:261139 original size:20 final size:20
Alignment explanation
Indices: 261097--261146 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
261087 TTTTTTTCAA
*
261097 GTATCGATACAATGCAACAT
1 GTATCGATACAATGAAACAT
* **
261117 GTATCGATACAATTAAATGT
1 GTATCGATACAATGAAACAT
261137 GTATCGATAC
1 GTATCGATAC
261147 TTTTCAAGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACAATGAAACAT
Found at i:266676 original size:13 final size:13
Alignment explanation
Indices: 266658--266685 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
266648 ACATGCTGCT
266658 TTGTATCGATACA
1 TTGTATCGATACA
266671 TTGTATCGATACA
1 TTGTATCGATACA
266684 TT
1 TT
266686 CTCATTGTAT
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:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:266681 original size:33 final size:32
Alignment explanation
Indices: 266639--266703 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
266629 CACACCCAGA
*
266639 TGTATCGATACATGCTGCTTTGTATCGATACAT
1 TGTATCGATACATGCT-CATTGTATCGATACAT
*
266672 TGTATCGATACATTCTCATTGTATCGATACAT
1 TGTATCGATACATGCTCATTGTATCGATACAT
266704 GGACAAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGCTCATTGTATCGATACAT
Found at i:266793 original size:13 final size:13
Alignment explanation
Indices: 266777--266833 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
266767 TGGTACAATG
266777 TATCGATACATTA
1 TATCGATACATTA
*
266790 TATCGATACATGA
1 TATCGATACATTA
*
266803 -A--GA-A-A-TG
1 TATCGATACATTA
266810 TATCGATACATTA
1 TATCGATACATTA
266823 TATCGATACAT
1 TATCGATACAT
266834 GAAGAAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
8 2 0.06
9 1 0.03
10 4 0.12
11 1 0.03
12 2 0.06
13 24 0.71
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:266794 original size:33 final size:31
Alignment explanation
Indices: 266773--266853 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 31
266763 TATGTGGTAC
266773 AATGTATCGATACATTATATCGATACATGAAGA
1 AATGTATCGATACATTATATCGAT--ATGAAGA
266806 AATGTATCGATACATTATATCGATACATGAAGA
1 AATGTATCGATACATTATATCGAT--ATGAAGA
266839 AATGTATCGATACAT
1 AATGTATCGATACAT
266854 AGCTTGTAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (31 bp):
AATGTATCGATACATTATATCGATATGAAGA
Found at i:266815 original size:20 final size:20
Alignment explanation
Indices: 266790--266853 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
266780 CGATACATTA
266790 TATCGATACATGAAGAAATG
1 TATCGATACATGAAGAAATG
*
266810 TATCGATACAT-------TA
1 TATCGATACATGAAGAAATG
266823 TATCGATACATGAAGAAATG
1 TATCGATACATGAAGAAATG
266843 TATCGATACAT
1 TATCGATACAT
266854 AGCTTGTAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
13 12 0.34
20 23 0.66
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (20 bp):
TATCGATACATGAAGAAATG
Found at i:274435 original size:22 final size:21
Alignment explanation
Indices: 274380--274460 Score: 119
Period size: 21 Copynumber: 3.8 Consensus size: 21
274370 CAAATCCAAA
274380 TTCTCAAATTTCTTCAAATCT
1 TTCTCAAATTTCTTCAAATCT
* *
274401 TTCTCAAACTTC-TAACAATCT
1 TTCTCAAATTTCTTCA-AATCT
274422 TTCATCAAATTTCTTCAAATCT
1 TTC-TCAAATTTCTTCAAATCT
274444 TTCTCAAATTTCTTCAA
1 TTCTCAAATTTCTTCAA
274461 TTTCACAACA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.04
21 33 0.62
22 16 0.30
23 2 0.04
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (21 bp):
TTCTCAAATTTCTTCAAATCT
Found at i:275841 original size:33 final size:33
Alignment explanation
Indices: 275804--275870 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
275794 TGAGAGTTGA
* * *
275804 TCACTTCACTTTCGTAGTGCATGGATGAGCACT
1 TCACTTCACTTTCGCAGCGCATGGATGAGAACT
*
275837 TCACTTCACTTTCGCAGCGTATGGATGAGAACT
1 TCACTTCACTTTCGCAGCGCATGGATGAGAACT
275870 T
1 T
275871 TAGTTCTCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (33 bp):
TCACTTCACTTTCGCAGCGCATGGATGAGAACT
Found at i:276870 original size:20 final size:20
Alignment explanation
Indices: 276845--276964 Score: 124
Period size: 20 Copynumber: 6.7 Consensus size: 20
276835 TACCACTGTT
276845 TGTATCGATACATGGCACAA
1 TGTATCGATACATGGCACAA
276865 TGTATCGATACATGGCACAA
1 TGTATCGATACATGGCACAA
276885 TGTATCGATACAT-------
1 TGTATCGATACATGGCACAA
* *
276898 TGTATCTATACATGGCATAA
1 TGTATCGATACATGGCACAA
276918 TGTATCGATACAT-------
1 TGTATCGATACATGGCACAA
276931 TGTATCGATACATGGCACAA
1 TGTATCGATACATGGCACAA
276951 TGTATCGATACATG
1 TGTATCGATACATG
276965 AATTGTATTG
Statistics
Matches: 84, Mismatches: 2, Indels: 28
0.74 0.02 0.25
Matches are distributed among these distances:
13 25 0.30
20 59 0.70
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATGGCACAA
Found at i:276903 original size:13 final size:13
Alignment explanation
Indices: 276885--276943 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 13
276875 CATGGCACAA
276885 TGTATCGATACAT
1 TGTATCGATACAT
*
276898 TGTATCTATACA-
1 TGTATCGATACAT
*
276910 TG--GC-ATA-A-
1 TGTATCGATACAT
276918 TGTATCGATACAT
1 TGTATCGATACAT
276931 TGTATCGATACAT
1 TGTATCGATACAT
276944 GGCACAATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
8 3 0.08
9 3 0.08
10 2 0.05
11 3 0.08
12 3 0.08
13 24 0.63
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:276909 original size:33 final size:33
Alignment explanation
Indices: 276865--276963 Score: 180
Period size: 33 Copynumber: 3.0 Consensus size: 33
276855 CATGGCACAA
276865 TGTATCGATACATGGCACAATGTATCGATACAT
1 TGTATCGATACATGGCACAATGTATCGATACAT
* *
276898 TGTATCTATACATGGCATAATGTATCGATACAT
1 TGTATCGATACATGGCACAATGTATCGATACAT
276931 TGTATCGATACATGGCACAATGTATCGATACAT
1 TGTATCGATACATGGCACAATGTATCGATACAT
276964 GAATTGTATT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATGGCACAATGTATCGATACAT
Found at i:276955 original size:53 final size:53
Alignment explanation
Indices: 276845--276964 Score: 134
Period size: 53 Copynumber: 2.3 Consensus size: 53
276835 TACCACTGTT
** * *
276845 TGTATCGATACATGGCACAATGTATCGATACATGGCACAATGTATCGATACAT
1 TGTATCGATACATGGCACAATGTATCGATACATGGCACAATACATCGACACAA
* * * * * *
276898 TGTATCTATACATGGCATAATGTATCGATACATTGTATCGATACAT-GGCACAA
1 TGTATCGATACATGGCACAATGTATCGATACATGGCA-CAATACATCGACACAA
276951 TGTATCGATACATG
1 TGTATCGATACATG
276965 AATTGTATTG
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
53 50 0.91
54 5 0.09
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (53 bp):
TGTATCGATACATGGCACAATGTATCGATACATGGCACAATACATCGACACAA
Found at i:283068 original size:85 final size:85
Alignment explanation
Indices: 282897--283351 Score: 341
Period size: 85 Copynumber: 5.4 Consensus size: 85
282887 GAAGGGAGGT
* * *
282897 TGCCACCGACTTGTGTGGACTTTGGAAAAGGTTGCCACCGACTTGTGGGCTTTGAAAAGATGCCA
1 TGCCACTGACTTGTG-GG-CTTT-GAAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCA
* *
282962 CTAACTTGTGGGCTTTCAAAAGG
63 CTGACTTGTGGGCTTTGAAAAGG
*
282985 TACCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTCGAAAAGATGCCACT
1 TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTT-GAAAAGATGCCACT
* *
283049 GACTTATGGGATTTGAAAAGG
65 GACTTGTGGGCTTTGAAAAGG
* * * * * * * * *
283070 TGCAACTAATTTGTGGACTTGGAAAAAG-TGCCACTAATTTGTGGG-TTTGAAAAGGTGCCACTG
1 TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTG
283133 ACTTGTGGGCTTTG-AAAGG
66 ACTTGTGGGCTTTGAAAAGG
* * *
283152 ATGCCACTGACATGTGGGC-TT-AAAAGGATGCCAC-GAAGTTGTGGAC-TT-AAAAGGATGCCA
1 -TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTG-ACTTGTGGGCTTTGAAAA-GATGCCA
* * **
283212 CGGAGTTGTGTAC-TT-AAAAGG
63 CTGACTTGTGGGCTTTGAAAAGG
* * * * * *
283233 ATGCCA-TGGAGTTGTGGACTTT-AAAAGGGATGCCACAGAGTTGTGGACTTT-AAAAGGGTGCC
1 -TGCCACT-GACTTGTGGGCTTTGAAAA-GGATGCCACTGACTTGTGGGCTTTGAAAA-GATGCC
* * * *
283295 ACAGAGTTGTGGAC-TTAAAAATGG
62 ACTGACTTGTGGGCTTTGAAAA-GG
* * * *
283319 TGCCACAGAATTATGGAC-TT-AAAAGGATGCCAC
1 TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCAC
283352 GAAGTTGTGG
Statistics
Matches: 309, Mismatches: 43, Indels: 35
0.80 0.11 0.09
Matches are distributed among these distances:
80 1 0.00
81 30 0.10
82 42 0.14
83 67 0.22
84 56 0.18
85 92 0.30
86 6 0.02
87 2 0.01
88 13 0.04
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (85 bp):
TGCCACTGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTG
ACTTGTGGGCTTTGAAAAGG
Found at i:283129 original size:27 final size:28
Alignment explanation
Indices: 282897--283324 Score: 333
Period size: 28 Copynumber: 15.2 Consensus size: 28
282887 GAAGGGAGGT
*
282897 TGCCACCGACTTGTGTGGACTTTGGAAAAGG
1 TGCCACTGACTTGTG-GG-CTTT-GAAAAGG
* *
282928 TTGCCACCGACTTGTGGGCTTTGAAAAGA
1 -TGCCACTGACTTGTGGGCTTTGAAAAGG
* *
282957 TGCCACTAACTTGTGGGCTTTCAAAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGG
*
282985 TACCACTGACTTGTGGGCTTTGAAAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGG
*
283013 TGCCACTGACTTGTGGGCTTTCGAAAAGA
1 TGCCACTGACTTGTGGGCTTT-GAAAAGG
* *
283042 TGCCACTGACTTATGGGATTTGAAAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGG
* * * * * *
283070 TGCAACTAATTTGTGGACTTGGAAAAAG
1 TGCCACTGACTTGTGGGCTTTGAAAAGG
* *
283098 TGCCACTAATTTGTGGG-TTTGAAAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGG
283125 TGCCACTGACTTGTGGGCTTTG-AAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGG
*
283152 ATGCCACTGACATGTGGGC-TT-AAAAGG
1 -TGCCACTGACTTGTGGGCTTTGAAAAGG
* *
283179 ATGCCAC-GAAGTTGTGGAC-TT-AAAAGG
1 -TGCCACTG-ACTTGTGGGCTTTGAAAAGG
* * **
283206 ATGCCACGGAGTTGTGTAC-TT-AAAAGG
1 -TGCCACTGACTTGTGGGCTTTGAAAAGG
* *
283233 ATGCCA-TGGAGTTGTGGACTTT-AAAAGGG
1 -TGCCACT-GACTTGTGGGCTTTGAAAA-GG
* * *
283262 ATGCCACAGAGTTGTGGACTTT-AAAAGGG
1 -TGCCACTGACTTGTGGGCTTTGAAAA-GG
* * * *
283291 TGCCACAGAGTTGTGGAC-TTAAAAATGG
1 TGCCACTGACTTGTGGGCTTTGAAAA-GG
283319 TGCCAC
1 TGCCAC
283325 AGAATTATGG
Statistics
Matches: 349, Mismatches: 36, Indels: 26
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.00
27 99 0.28
28 168 0.48
29 60 0.17
30 4 0.01
31 2 0.01
32 15 0.04
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTGAAAAGG
Found at i:283350 original size:27 final size:27
Alignment explanation
Indices: 283119--283448 Score: 355
Period size: 27 Copynumber: 12.0 Consensus size: 27
283109 TGTGGGTTTG
* * *
283119 AAAAGG-TGCCACTGACTTGTGGGCTTT
1 AAAAGGATGCCACAGAGTTGTGGAC-TT
* * ** *
283146 GAAAGGATGCCACTGACATGTGGGCTT
1 AAAAGGATGCCACAGAGTTGTGGACTT
283173 AAAAGGATGCCAC-GAAGTTGTGGACTT
1 AAAAGGATGCCACAG-AGTTGTGGACTT
* *
283200 AAAAGGATGCCACGGAGTTGTGTACTT
1 AAAAGGATGCCACAGAGTTGTGGACTT
**
283227 AAAAGGATGCCATGGAGTTGTGGACTTT
1 AAAAGGATGCCACAGAGTTGTGGAC-TT
283255 AAAAGGGATGCCACAGAGTTGTGGACTTT
1 AAAA-GGATGCCACAGAGTTGTGGAC-TT
*
283284 AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAGGATGCCACAGAGTTGTGGACTT
* *
283311 AAAAATGG-TGCCACAGAATTATGGACTT
1 -AAAA-GGATGCCACAGAGTTGTGGACTT
*
283339 AAAAGGATGCCAC-GAAGTTGTGGACCT
1 AAAAGGATGCCACAG-AGTTGTGGACTT
283366 AAAAGGATGCCACAGAGTTGTGGACTT
1 AAAAGGATGCCACAGAGTTGTGGACTT
*
283393 AAAAGGATGCCA-TGTAGTTGTGGACTTT
1 AAAAGGATGCCACAG-AGTTGTGGAC-TT
* *
283421 AAAAGGGGTGCCACGGAGTTGTGGACTT
1 AAAA-GGATGCCACAGAGTTGTGGACTT
283449 TAATAGAAAA
Statistics
Matches: 268, Mismatches: 21, Indels: 27
0.85 0.07 0.09
Matches are distributed among these distances:
26 5 0.02
27 142 0.53
28 75 0.28
29 45 0.17
30 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.25
Consensus pattern (27 bp):
AAAAGGATGCCACAGAGTTGTGGACTT
Found at i:284798 original size:18 final size:19
Alignment explanation
Indices: 284771--284821 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
284761 TGATTTTGCC
284771 TTTCTATTTTTTTTTGT-GT
1 TTTCT-TTTTTTTTTGTGGT
*
284790 TTTCTTTTTCTTTTGTGGT
1 TTTCTTTTTTTTTTGTGGT
284809 TTTGCCTTTTTTT
1 TTT--CTTTTTTT
284822 CATTTTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 10 0.37
19 10 0.37
21 7 0.26
ACGTcount: A:0.02, C:0.10, G:0.12, T:0.76
Consensus pattern (19 bp):
TTTCTTTTTTTTTTGTGGT
Found at i:288005 original size:24 final size:24
Alignment explanation
Indices: 287973--288018 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
287963 CGATAAATGA
287973 GAATAAAGGTTAAAAGTATTTCTC
1 GAATAAAGGTTAAAAGTATTTCTC
**
287997 GAATAAAGGTTCGAAGTATTTC
1 GAATAAAGGTTAAAAGTATTTC
288019 CCCAAGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.33
Consensus pattern (24 bp):
GAATAAAGGTTAAAAGTATTTCTC
Found at i:292813 original size:59 final size:59
Alignment explanation
Indices: 292746--292863 Score: 168
Period size: 59 Copynumber: 2.0 Consensus size: 59
292736 AATTATCAAG
292746 AAATACTTGCATGAACATTAAACTCAAGGTAGATAAGATCGC-T-AAAGCTAGGAAAGAAT
1 AAATACTTGCATGAACATTAAACTCAAGGTAGATAAG--CGCATCAAAGCTAGGAAAGAAT
* * * *
292805 AAATACTTGCATGAACCTTAAACTCATGGTAGGTAAGGGCATCAAAGCTAGGAAAGAAT
1 AAATACTTGCATGAACATTAAACTCAAGGTAGATAAGCGCATCAAAGCTAGGAAAGAAT
292864 TAGAGAAGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
57 2 0.04
58 1 0.02
59 50 0.94
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.22
Consensus pattern (59 bp):
AAATACTTGCATGAACATTAAACTCAAGGTAGATAAGCGCATCAAAGCTAGGAAAGAAT
Found at i:297462 original size:20 final size:20
Alignment explanation
Indices: 297430--297487 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
297420 GGTCAAAACC
*
297430 TTGAAAAGTATCGATACACA
1 TTGAAATGTATCGATACACA
* *
297450 TTTAAATGTATCGATACAGA
1 TTGAAATGTATCGATACACA
* *
297470 TTGCATTGTATCGATACA
1 TTGAAATGTATCGATACA
297488 TTGTATCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (20 bp):
TTGAAATGTATCGATACACA
Found at i:297611 original size:13 final size:13
Alignment explanation
Indices: 297593--297618 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
297583 ACACACAGTA
297593 TGTATCGATACAT
1 TGTATCGATACAT
297606 TGTATCGATACAT
1 TGTATCGATACAT
297619 CATAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:301756 original size:13 final size:13
Alignment explanation
Indices: 301738--301763 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
301728 ACACACAGTA
301738 TGTATCGATACAT
1 TGTATCGATACAT
301751 TGTATCGATACAT
1 TGTATCGATACAT
301764 CATAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:301779 original size:33 final size:32
Alignment explanation
Indices: 301718--301782 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
301708 GTAGCCAAAC
**
301718 TTGTATCGATACACACAGTATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
301750 TTGTATCGATACATCATAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
301783 CTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:307754 original size:20 final size:20
Alignment explanation
Indices: 307722--307779 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
307712 GGTCAAAACC
*
307722 TTGAAAAGTATCGATACACA
1 TTGAAATGTATCGATACACA
* *
307742 TTTAAATGTATCGATACAGA
1 TTGAAATGTATCGATACACA
* *
307762 TTGCATTGTATCGATACA
1 TTGAAATGTATCGATACA
307780 TTGTATCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (20 bp):
TTGAAATGTATCGATACACA
Found at i:307903 original size:13 final size:13
Alignment explanation
Indices: 307885--307910 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
307875 ACACACAGTA
307885 TGTATCGATACAT
1 TGTATCGATACAT
307898 TGTATCGATACAT
1 TGTATCGATACAT
307911 CATAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:312048 original size:13 final size:13
Alignment explanation
Indices: 312030--312055 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
312020 ACACACAGTA
312030 TGTATCGATACAT
1 TGTATCGATACAT
312043 TGTATCGATACAT
1 TGTATCGATACAT
312056 CATAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:312071 original size:33 final size:32
Alignment explanation
Indices: 312010--312074 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
312000 GTAGCCAAAC
**
312010 TTGTATCGATACACACAGTATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
312042 TTGTATCGATACATCATAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
312075 CTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:318046 original size:20 final size:20
Alignment explanation
Indices: 318014--318071 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
318004 GGTCAAAACC
*
318014 TTGAAAAGTATCGATACACA
1 TTGAAATGTATCGATACACA
* *
318034 TTTAAATGTATCGATACAGA
1 TTGAAATGTATCGATACACA
* *
318054 TTGCATTGTATCGATACA
1 TTGAAATGTATCGATACA
318072 TTGTATCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (20 bp):
TTGAAATGTATCGATACACA
Found at i:318195 original size:13 final size:13
Alignment explanation
Indices: 318177--318202 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
318167 ACACACAGTA
318177 TGTATCGATACAT
1 TGTATCGATACAT
318190 TGTATCGATACAT
1 TGTATCGATACAT
318203 CATAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:322338 original size:13 final size:13
Alignment explanation
Indices: 322320--322345 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
322310 ACACACAGTA
322320 TGTATCGATACAT
1 TGTATCGATACAT
322333 TGTATCGATACAT
1 TGTATCGATACAT
322346 CATAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:322361 original size:33 final size:32
Alignment explanation
Indices: 322300--322364 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
322290 GTAGCCAAAC
**
322300 TTGTATCGATACACACAGTATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
322332 TTGTATCGATACATCATAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
322365 CTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:327852 original size:13 final size:13
Alignment explanation
Indices: 327834--327858 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
327824 CAGAATTCTT
327834 TGTATCGATACAC
1 TGTATCGATACAC
327847 TGTATCGATACA
1 TGTATCGATACA
327859 AAGGGATTAT
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:330080 original size:13 final size:13
Alignment explanation
Indices: 330062--330090 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
330052 ATATAGATTG
330062 CATTGTATCGATA
1 CATTGTATCGATA
330075 CATTGTATCGATA
1 CATTGTATCGATA
330088 CAT
1 CAT
330091 GACCAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:330103 original size:20 final size:21
Alignment explanation
Indices: 330078--330130 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
330068 ATCGATACAT
**
330078 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
330098 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
330119 TGTATCGATACA
1 TGTATCGATACA
330131 AGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:331077 original size:32 final size:32
Alignment explanation
Indices: 330992--331089 Score: 124
Period size: 32 Copynumber: 3.1 Consensus size: 32
330982 GGAGGAGATC
* * *
330992 TGAGAGGGTTGCCACCAACTTATGTGGGCTTT
1 TGAGAGGGTTGCCACCAACTTGTATGGGTTTT
331024 TGAGAGGGTTGCCACCAACTTGTATGGGTTTT
1 TGAGAGGGTTGCCACCAACTTGTATGGGTTTT
* ** * *
331056 TGAGAGGGTTTCCGTCGACTTGTGTGGGTTTT
1 TGAGAGGGTTGCCACCAACTTGTATGGGTTTT
331088 TG
1 TG
331090 GAAAAAGGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.15, C:0.15, G:0.34, T:0.36
Consensus pattern (32 bp):
TGAGAGGGTTGCCACCAACTTGTATGGGTTTT
Found at i:331200 original size:30 final size:29
Alignment explanation
Indices: 331126--331459 Score: 159
Period size: 29 Copynumber: 11.2 Consensus size: 29
331116 GGCTTTAAAA
* * *
331126 AAAAAGGTTACCACTGACTTGTATGGATTTCT
1 AAAAAGGGTGCCACTGACTTGTA--GACTT-T
* * *
331158 ACAAAGGTTGCCACTAACTTGTAGACTTT
1 AAAAAGGGTGCCACTGACTTGTAGACTTT
* *
331187 AAGAAAGGGTGCCATTGACTTGTAGGCTTT
1 AA-AAAGGGTGCCACTGACTTGTAGACTTT
** * *
331217 GGAAAGGGTGCCACTGACTTATGGACTTT
1 AAAAAGGGTGCCACTGACTTGTAGACTTT
* * * *
331246 GAAAAGGGTGTCATTGACTTGTATGGGCTTT
1 AAAAAGGGTGCCACTGACTTGTA--GACTTT
* * * *
331277 AAAAAGGGTGCCACTAAGTCGTGGACTTT
1 AAAAAGGGTGCCACTGACTTGTAGACTTT
* * * *
331306 AAAAAGGGTGCCATTGAGTCGTGGACTTT
1 AAAAAGGGTGCCACTGACTTGTAGACTTT
* * * * * ** *
331335 GAGAAGGGTACCACTAAGTCATCGACTTT
1 AAAAAGGGTGCCACTGACTTGTAGACTTT
* * * *
331364 AGAAAA-TGTACCACTGACTTATGGACTTT
1 A-AAAAGGGTGCCACTGACTTGTAGACTTT
* * * *
331393 GAAAAGGTTGCCA-TCGACTTTTGTGGGCTTT
1 AAAAAGGGTGCCACT-GAC--TTGTAGACTTT
* * *
331424 AAAAATAGGTGCCACTAACTTGTTGACTTT
1 AAAAA-GGGTGCCACTGACTTGTAGACTTT
*
331454 GAAAAG
1 AAAAAG
331460 AGTTGCCATC
Statistics
Matches: 233, Mismatches: 59, Indels: 23
0.74 0.19 0.07
Matches are distributed among these distances:
28 5 0.02
29 122 0.52
30 43 0.18
31 34 0.15
32 28 0.12
33 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (29 bp):
AAAAAGGGTGCCACTGACTTGTAGACTTT
Found at i:331282 original size:31 final size:31
Alignment explanation
Indices: 331091--331322 Score: 138
Period size: 29 Copynumber: 7.5 Consensus size: 31
331081 GGGTTTTTGG
* * *
331091 AAAAAGGTTGCCATCGACTTTTATGGGCTTT
1 AAAAAGGGTGCCATTGACTTGTATGGGCTTT
* * * **
331122 AAAAAAAAAGGTTACCACTGACTTGTATGGATTTCT
1 ----AAAAAGGGTGCCATTGACTTGTATGGGCTT-T
* * * * *
331158 ACAAAGGTTGCCACTAACTTGTA--GACTTT
1 AAAAAGGGTGCCATTGACTTGTATGGGCTTT
331187 AAGAAAGGGTGCCATTGACTTGTA--GGCTTT
1 AA-AAAGGGTGCCATTGACTTGTATGGGCTTT
** * *
331217 GGAAAGGGTGCCACTGAC-T-TATGGACTTT
1 AAAAAGGGTGCCATTGACTTGTATGGGCTTT
* *
331246 GAAAAGGGTGTCATTGACTTGTATGGGCTTT
1 AAAAAGGGTGCCATTGACTTGTATGGGCTTT
* * * * *
331277 AAAAAGGGTGCCACTAAGTCG--TGGACTTT
1 AAAAAGGGTGCCATTGACTTGTATGGGCTTT
331306 AAAAAGGGTGCCATTGA
1 AAAAAGGGTGCCATTGA
331323 GTCGTGGACT
Statistics
Matches: 159, Mismatches: 32, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
27 2 0.01
28 1 0.01
29 59 0.37
30 28 0.18
31 24 0.15
32 20 0.13
35 24 0.15
36 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (31 bp):
AAAAAGGGTGCCATTGACTTGTATGGGCTTT
Found at i:331302 original size:60 final size:60
Alignment explanation
Indices: 331126--331322 Score: 218
Period size: 60 Copynumber: 3.3 Consensus size: 60
331116 GGCTTTAAAA
* * * ** * * *
331126 AAAAAGGTTACCACTGACTTGTATGGATTTCTACAAAGGTTGCCACTAACTTGTAGACTTT
1 AAAAAGGGTGCCATTGACTTGTATGGGCTT-TAAAAAGGGTGCCACTAACTTGTGGACTTT
** * *
331187 AAGAAAGGGTGCCATTGACTTGTA--GGCTTTGGAAAGGGTGCCACTGACTTATGGACTTT
1 AA-AAAGGGTGCCATTGACTTGTATGGGCTTTAAAAAGGGTGCCACTAACTTGTGGACTTT
* * * *
331246 GAAAAGGGTGTCATTGACTTGTATGGGCTTTAAAAAGGGTGCCACTAAGTCGTGGACTTT
1 AAAAAGGGTGCCATTGACTTGTATGGGCTTTAAAAAGGGTGCCACTAACTTGTGGACTTT
331306 AAAAAGGGTGCCATTGA
1 AAAAAGGGTGCCATTGA
331323 GTCGTGGACT
Statistics
Matches: 112, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
58 20 0.18
59 25 0.22
60 47 0.42
61 2 0.02
62 18 0.16
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (60 bp):
AAAAAGGGTGCCATTGACTTGTATGGGCTTTAAAAAGGGTGCCACTAACTTGTGGACTTT
Found at i:331325 original size:29 final size:29
Alignment explanation
Indices: 331160--331524 Score: 194
Period size: 29 Copynumber: 12.3 Consensus size: 29
331150 GGATTTCTAC
* * * *
331160 AAAGGTTGCCACTAACTTGTAGACTTTAA
1 AAAGGGTGCCATTGACTTGTGGACTTTAA
**
331189 GAAAGGGTGCCATTGACTTGTAGG-CTTTGG
1 -AAAGGGTGCCATTGACTTGT-GGACTTTAA
* * *
331219 AAAGGGTGCCACTGACTTATGGACTTTGA
1 AAAGGGTGCCATTGACTTGTGGACTTTAA
* *
331248 AAAGGGTGTCATTGACTTGTATGGGCTTTAA
1 AAAGGGTGCCATTGACTTG--TGGACTTTAA
* * * *
331279 AAAGGGTGCCACTAAGTCGTGGACTTTAA
1 AAAGGGTGCCATTGACTTGTGGACTTTAA
* * *
331308 AAAGGGTGCCATTGAGTCGTGGACTTTGA
1 AAAGGGTGCCATTGACTTGTGGACTTTAA
* * * * * ** *
331337 GAAGGGTACCACTAAGTCATCGACTTTAGA
1 AAAGGGTGCCATTGACTTGTGGACTTTA-A
* * * * *
331367 AAA-TGTACCACTGACTTATGGACTTTGA
1 AAAGGGTGCCATTGACTTGTGGACTTTAA
* * *
331395 AAAGGTTGCCATCGACTTTTGTGGGCTTTAA
1 AAAGGGTGCCATTGAC--TTGTGGACTTTAA
* * * * *
331426 AAATAGGTGCCACTAACTTGTTGACTTTGA
1 AAA-GGGTGCCATTGACTTGTGGACTTTAA
* ** **
331456 AAAGAGTTGCCATCAACTTGTGTGGGGTTTAA
1 AAAG-GGTGCCATTGAC-T-TGTGGACTTTAA
* * *
331488 AAAGGGTACCATTGACTTGCGGACTTTGA
1 AAAGGGTGCCATTGACTTGTGGACTTTAA
331517 AAAGGGTG
1 AAAGGGTG
331525 ACACTAAGTC
Statistics
Matches: 253, Mismatches: 70, Indels: 25
0.73 0.20 0.07
Matches are distributed among these distances:
28 6 0.02
29 135 0.53
30 47 0.19
31 45 0.18
32 20 0.08
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (29 bp):
AAAGGGTGCCATTGACTTGTGGACTTTAA
Found at i:331454 original size:61 final size:60
Alignment explanation
Indices: 331360--331521 Score: 180
Period size: 61 Copynumber: 2.7 Consensus size: 60
331350 AAGTCATCGA
* * * ** * *
331360 CTTTAGAAAATGTACCACTGACTTATGGACTTTGAAAAGGTTGCCATCGACTTTTGTGGG
1 CTTTAAAAAAGGTACCACTAACTTGCGGACTTTGAAAAGGTTGCCATCAACTTGTGTGGG
* **
331420 CTTTAAAAATAGGTGCCACTAACTTGTTGACTTTGAAAAGAGTTGCCATCAACTTGTGTGGG
1 CTTTAAAAA-AGGTACCACTAACTTGCGGACTTTGAAAAG-GTTGCCATCAACTTGTGTGGG
* * * *
331482 GTTTAAAAAGGGTACCATTGACTTGCGGACTTTGAAAAGG
1 CTTTAAAAAAGGTACCACTAACTTGCGGACTTTGAAAAGG
331522 GTGACACTAA
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
60 9 0.11
61 49 0.58
62 27 0.32
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (60 bp):
CTTTAAAAAAGGTACCACTAACTTGCGGACTTTGAAAAGGTTGCCATCAACTTGTGTGGG
Found at i:338936 original size:15 final size:15
Alignment explanation
Indices: 338918--338952 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
338908 CGAGTCAACT
338918 TCATCATTATCATCA
1 TCATCATTATCATCA
*
338933 TCATCATTATCTTCA
1 TCATCATTATCATCA
338948 TCATC
1 TCATC
338953 TTTGATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:340675 original size:19 final size:19
Alignment explanation
Indices: 340630--340684 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
340620 ACTGCCACTT
340630 TCATGTATCGATACAATTG
1 TCATGTATCGATACAATTG
340649 TGCATGTATCGATACAA-TG
1 T-CATGTATCGATACAATTG
*
340668 ATCATGTATTGATACAA
1 -TCATGTATCGATACAA
340685 AGTATCATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (19 bp):
TCATGTATCGATACAATTG
Found at i:344816 original size:917 final size:917
Alignment explanation
Indices: 343041--344877 Score: 3307
Period size: 917 Copynumber: 2.0 Consensus size: 917
343031 TTAAGATGGC
343041 ATAGAGGTGCTTATTTTGTGAAAACAAGTTCACTGAACCTACCCCAATGAGAACTTCATTTGGTG
1 ATAGAGGTGCTTATTTTGTGAAAACAAGTTCACTGAACCTACCCCAATGAGAACTTCATTTGGTG
* *
343106 TTGTCACTTAAGTGTCCATGGAATATCTTTTCATGTTCCAGTCATATATAACAGTCCTTAGACCT
66 TTGTCACTTAAGTGTCCATGGAATATCTTCTCATGTTCCAATCATATATAACAGTCCTTAGACCT
* * *
343171 GTGATACTAGGTCATCTTGTATATAGAGTATCACACTTTGATTTATCTGAAACATGTCTATTGGG
131 GTGATACTAGGTCATCTTGTATATAGAGTATCACACTTTCATTTATCTGAAACACGTCTATAGGG
*
343236 ATAGATGCCTAAGCTAGGATACTTTGTGTATGGCATGAAGCATACTAAAATGGATGAGTGATCAA
196 ATAGATGACTAAGCTAGGATACTTTGTGTATGGCATGAAGCATACTAAAATGGATGAGTGATCAA
* *
343301 AAAAGGATTCACCAATCCTAGTGACAATTAGAGATATATCCAATTTATCTTCACTATGGTTAGTT
261 AAAAGGATTCACCAATCCTAGTGACAATTAGAGATATATCCAAATGATCTTCACTATGGTTAGTT
*
343366 GGGTTAATGTTTTTGGCCAGAGCATAATGAATTATAAGGAGTTGTTTCTCATAGATTCATGACTG
326 GGGTTAATGTTTTTGGCCAGAGCATAATGAATTATAAGGAATTGTTTCTCATAGATTCATGACTG
*
343431 TTAAGAATAAGTTGTAAGATCTGAAATGGATTGAAGTATGAGTAGACTTTGCATAATGCTCATGT
391 TTAAGAATAAGTTGTAAGATCTAAAATGGATTGAAGTATGAGTA-ACTTTGCATAATGCTCATGT
343496 TCAATCTAGGATATATGGTGAAAGGACCATACTACATTGCTAGGTTGGTTATTGAAAGATTTCAA
455 TCAATCTAGGATATATGGTGAAAGGACCATACTACATTGCTAGGTTGGTTATTGAAAGATTTCAA
343561 TGAGGTCACATTGACTCTTCAACATTTGGGTAGTCCTTATAGTTGCTAGATCCCATTCTTGATTT
520 TGAGGTCACATTGACTCTTCAACATTTGGGTAGTCCTTATAGTTGCTAGATCCCATTCTTGATTT
* *
343626 ATGAACATGATTAGTGAGATTAATTTTGTTTATTGCTAATATGTTCGGAACCCAATGGGTCATGC
585 ATGAACATGATTAGTGAGATTAATTATGTTCATTGCTAATATGTTCGGAACCCAATGGGTCATGC
*
343691 TCATTAAGATGGACTTGTTGAATTAAATCTCTGATATAATTAAGTATGATTGAATTAAATAAAAG
650 TCAATAAGATGGACTTGTTGAATTAAATCTCTGATATAATTAAGTATGATTGAATTAAATAAAAG
* * * *
343756 GTAATCAGGTGGAGGACTTAATTAAGTAGTTTAATTAAGATTTATTTTGAAGACAAAATTAGATT
715 GTAATCAGGTAGAGGACTTAATTAAATAGTTCAATTAAGATTTATTTTGAAGACAAAATTACATT
* *
343821 TGTGAAATCTAAATTTACTTTTTTAATTAAGACATGGTTGATAAGATTGTCTTATCCATATAATG
780 TGTGAAATCTAAATTTACTTGTCTAATTAAGACATGGTTGATAAGATTGTCTTATCCATATAATG
* * *
343886 TCCAAATTAGGACAAACCATGTTTGGGCGAATAAATCTCATCCTGGTGGAAATATGATTTCACCT
845 TCCAAATTAGGACAAACCATGTTTAGGCGAATAAATCTCATCCTGGTGGAAATAGGATTTCAACT
343951 ATACTAGA
910 ATACTAGA
343959 ATAGAGGTGCTTATTTTGTGAAAACAAGTTCACTGAACCTACCCCAATGAGAACTTCATTTGGTG
1 ATAGAGGTGCTTATTTTGTGAAAACAAGTTCACTGAACCTACCCCAATGAGAACTTCATTTGGTG
*
344024 TTGTCACTTAAGTGTCCATGGAATATCTTCTCATGTTCCAATCATATATAACAGTCCTTAGACTT
66 TTGTCACTTAAGTGTCCATGGAATATCTTCTCATGTTCCAATCATATATAACAGTCCTTAGACCT
*
344089 GTGATACTAGGTCATCTTGTATATAGAGTATCACACTTTCATTTATCTGAAACACGTTTATAGGG
131 GTGATACTAGGTCATCTTGTATATAGAGTATCACACTTTCATTTATCTGAAACACGTCTATAGGG
344154 ATAGATGACTAAGCTAGGATACTTTGTGTATGGCATGAAGCATACTAAAATGGATGAGTGATCAA
196 ATAGATGACTAAGCTAGGATACTTTGTGTATGGCATGAAGCATACTAAAATGGATGAGTGATCAA
*
344219 AAAAGGATTCACCAATCCTAGTGACAATTGGAGATATATCCAAAATGATCTTCACTATGGTTAGT
261 AAAAGGATTCACCAATCCTAGTGACAATTAGAGATATATCC-AAATGATCTTCACTATGGTTAGT
*
344284 TGGGTTAATGTTTTTGGCCAGAGCATAATGAATTATAAGGAATTGTTTCTCATAGATTCATTACT
325 TGGGTTAATGTTTTTGGCCAGAGCATAATGAATTATAAGGAATTGTTTCTCATAGATTCATGACT
* *
344349 GTTAATAATAAGTTGTAAGATCTAAAATGGATTGAAGTATGAGT-ACTTTGTATAATGCTCATGT
390 GTTAAGAATAAGTTGTAAGATCTAAAATGGATTGAAGTATGAGTAACTTTGCATAATGCTCATGT
* *
344413 TCAATCTAGGATATATGGTGAAAGGACCATACTACATTGGTAGGTTGGTTATTGAAAGGTTTCAA
455 TCAATCTAGGATATATGGTGAAAGGACCATACTACATTGCTAGGTTGGTTATTGAAAGATTTCAA
* *
344478 TGAGGTCACATTGACTTTTCAACATTTGGGTAGTCTTTATAGTTGCTAGATCCCATTCTTGATTT
520 TGAGGTCACATTGACTCTTCAACATTTGGGTAGTCCTTATAGTTGCTAGATCCCATTCTTGATTT
*
344543 ATGAACATGATTAGTGAGATTAATTATGTTCATTGCTAATATGTTCGGAACCTAATGGGTCATGC
585 ATGAACATGATTAGTGAGATTAATTATGTTCATTGCTAATATGTTCGGAACCCAATGGGTCATGC
*
344608 TCAATAAGATGGACTTGTTGAATTAAATCTCTGATTTAATTAAGTATGATTGAATTAAATAAAAG
650 TCAATAAGATGGACTTGTTGAATTAAATCTCTGATATAATTAAGTATGATTGAATTAAATAAAAG
* *
344673 GTAATTAGGTAGAGGACTTTATTAAATAGTTCAATTAAGATTTATTTTGAAGACAAAATTACATT
715 GTAATCAGGTAGAGGACTTAATTAAATAGTTCAATTAAGATTTATTTTGAAGACAAAATTACATT
*
344738 TGTTAAATCTAAATTTACTTGTCTAATTAAGACATGGTTGATAAGATTGTCTTATCCATATAATG
780 TGTGAAATCTAAATTTACTTGTCTAATTAAGACATGGTTGATAAGATTGTCTTATCCATATAATG
*
344803 TCCAAATTAGGACAAACCATGTTTAGGCGAATAAATCTTATCCTGGTGGAAATAGGATTTCAACT
845 TCCAAATTAGGACAAACCATGTTTAGGCGAATAAATCTCATCCTGGTGGAAATAGGATTTCAACT
344868 ATACTAGA
910 ATACTAGA
344876 AT
1 AT
344878 TTAATTGTGA
Statistics
Matches: 880, Mismatches: 38, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
917 462 0.52
918 292 0.33
919 126 0.14
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (917 bp):
ATAGAGGTGCTTATTTTGTGAAAACAAGTTCACTGAACCTACCCCAATGAGAACTTCATTTGGTG
TTGTCACTTAAGTGTCCATGGAATATCTTCTCATGTTCCAATCATATATAACAGTCCTTAGACCT
GTGATACTAGGTCATCTTGTATATAGAGTATCACACTTTCATTTATCTGAAACACGTCTATAGGG
ATAGATGACTAAGCTAGGATACTTTGTGTATGGCATGAAGCATACTAAAATGGATGAGTGATCAA
AAAAGGATTCACCAATCCTAGTGACAATTAGAGATATATCCAAATGATCTTCACTATGGTTAGTT
GGGTTAATGTTTTTGGCCAGAGCATAATGAATTATAAGGAATTGTTTCTCATAGATTCATGACTG
TTAAGAATAAGTTGTAAGATCTAAAATGGATTGAAGTATGAGTAACTTTGCATAATGCTCATGTT
CAATCTAGGATATATGGTGAAAGGACCATACTACATTGCTAGGTTGGTTATTGAAAGATTTCAAT
GAGGTCACATTGACTCTTCAACATTTGGGTAGTCCTTATAGTTGCTAGATCCCATTCTTGATTTA
TGAACATGATTAGTGAGATTAATTATGTTCATTGCTAATATGTTCGGAACCCAATGGGTCATGCT
CAATAAGATGGACTTGTTGAATTAAATCTCTGATATAATTAAGTATGATTGAATTAAATAAAAGG
TAATCAGGTAGAGGACTTAATTAAATAGTTCAATTAAGATTTATTTTGAAGACAAAATTACATTT
GTGAAATCTAAATTTACTTGTCTAATTAAGACATGGTTGATAAGATTGTCTTATCCATATAATGT
CCAAATTAGGACAAACCATGTTTAGGCGAATAAATCTCATCCTGGTGGAAATAGGATTTCAACTA
TACTAGA
Found at i:347771 original size:13 final size:13
Alignment explanation
Indices: 347753--347778 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
347743 CAATAAGCAG
347753 AAAAATAAAAAGA
1 AAAAATAAAAAGA
347766 AAAAATAAAAAGA
1 AAAAATAAAAAGA
347779 TCAAAGTCTA
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:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (13 bp):
AAAAATAAAAAGA
Found at i:348522 original size:52 final size:52
Alignment explanation
Indices: 348437--348561 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
348427 ATATGAAAAG
* *
348437 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
348489 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
348541 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
348562 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:348574 original size:52 final size:51
Alignment explanation
Indices: 348437--348581 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
348427 ATATGAAAAG
*
348437 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
348489 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
348541 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
348582 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:348588 original size:13 final size:13
Alignment explanation
Indices: 348570--348594 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
348560 CAAAGATCAG
348570 TGTATCGATACAA
1 TGTATCGATACAA
348583 TGTATCGATACA
1 TGTATCGATACA
348595 TGTGAGTAAT
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):
TGTATCGATACAA
Found at i:348678 original size:13 final size:13
Alignment explanation
Indices: 348660--348684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
348650 CAAAAAAATA
348660 TGTATCGATACAT
1 TGTATCGATACAT
348673 TGTATCGATACA
1 TGTATCGATACA
348685 ACATTTTATG
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:348680 original size:33 final size:33
Alignment explanation
Indices: 348638--348704 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
348628 AGTAGCTTAA
348638 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
348671 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
348704 A
1 A
348705 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:349586 original size:67 final size:68
Alignment explanation
Indices: 349460--349586 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 68
349450 ATTGGGTTTT
* * *
349460 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
349525 AGA
66 AGA
* * * * *
349528 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAATGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
349587 GAAAAGGGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
67 47 0.92
68 4 0.08
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:349808 original size:49 final size:49
Alignment explanation
Indices: 349599--350390 Score: 989
Period size: 49 Copynumber: 16.7 Consensus size: 49
349589 AAAGGGATGA
* *
349599 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
349651 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
349694 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
349742 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
349791 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
349840 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
349889 CAATATGCTGATTCAAGGCTAGCTATATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
349938 CAATATGCTGATTCAAGGCTAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
349987 CAATGTGCTGAGTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
350036 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
350079 CAATGTGCTGATTCAAGGCCAGCTACATTGGATTTAAAGAAGAAGTTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
350128 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
350171 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
350220 CAATATGCTGATTCAAGGCCAGCTATATTAGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
350263 CAATGTACTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
350312 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
350355 CAATGTACTGATTCAAGGCCAGCTACATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
350391 GAAGGGTTGC
Statistics
Matches: 661, Mismatches: 53, Indels: 60
0.85 0.07 0.08
Matches are distributed among these distances:
43 191 0.29
45 4 0.01
47 3 0.00
48 48 0.07
49 383 0.58
52 32 0.05
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:350102 original size:92 final size:92
Alignment explanation
Indices: 349599--350390 Score: 1115
Period size: 92 Copynumber: 8.4 Consensus size: 92
349589 AAAGGGATGA
* *
349599 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAATATGCTGATT
349664 CAAGGCCAGCTATATTGGACTTAAAGGTGC
63 CAAGGCCAGCTATATTGGACTTAAAGGTGC
* * *
349694 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGT-GAGGTGCCAATGTGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
*
349758 GGCCAGCTACATTGGACTTAAAGATGAAGGTGC
66 GGCCAGCTATATTGGACTT----A--AAGGTGC
* * * *
349791 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
*
349856 GGCCAGCTACATTGGACTTAAAGATAAAGGTGC
66 GGCCAGCTATATTGGAC-T-----TAAAGGTGC
* * *
349889 CAATATGCTGATTCAAGGCTAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
*
349954 GGCTAGCTATATTGGACTTAATGGTGAAGGTGC
66 GGCCAGCTATATTGGACTT-A-----AAGGTGC
* *
349987 CAATGTGCTGAGTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
350052 GGCCAGCTATATTGGACTTAAAGGTGC
66 GGCCAGCTATATTGGACTTAAAGGTGC
* *
350079 CAATGTGCTGATTCAAGGCCAGCTACATTGGATTTAAAGA-AGAAGTTGCCAATATGCTGATTCA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATGCTGATTCA
350143 AGGCCAGCTATATTGGACTTAAAGGTGC
65 AGGCCAGCTATATTGGACTTAAAGGTGC
*
350171 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGTTGCCAATATGCTGATTCA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATGCTGATTCA
*
350235 AGGCCAGCTATATTAGACTTAAAGGTGC
65 AGGCCAGCTATATTGGACTTAAAGGTGC
* *
350263 CAATGTACTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGTTGCCAATATGCTGATTCA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATGCTGATTCA
350327 AGGCCAGCTATATTGGACTTAAAGGTGC
65 AGGCCAGCTATATTGGACTTAAAGGTGC
* *
350355 CAATGTACTGATTCAAGGCCAGCTACATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
350391 GAAGGGTTGC
Statistics
Matches: 645, Mismatches: 32, Indels: 43
0.90 0.04 0.06
Matches are distributed among these distances:
91 39 0.06
92 309 0.48
93 1 0.00
95 40 0.06
97 48 0.07
98 205 0.32
99 1 0.00
100 1 0.00
104 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (92 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAAGGTGC
Found at i:350428 original size:33 final size:33
Alignment explanation
Indices: 350390--350461 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
350380 CATTGGGCTT
*
350390 AGAAGGGTTGCCATCGACTTGTGAGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGAGGGCTTTAG
*
350423 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGAGGGCTTTAG
*
350456 AAAAGG
1 AGAAGG
350462 TGAAAGATGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.24, C:0.15, G:0.36, T:0.25
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGAGGGCTTTAG
Found at i:350525 original size:34 final size:34
Alignment explanation
Indices: 350444--350799 Score: 371
Period size: 34 Copynumber: 10.3 Consensus size: 34
350434 CACCGACTTG
** * *
350444 TGTGGGCTTTAGAAAAGGTGAAAGATGCCACGAAGT
1 TGTGGGCTTTA-AAAA-GAAAAAGGTGCCACGGAGT
* *
350480 TGTGGAC-TTAAAAAGAACAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
* * *
350513 TATGGGCTTTAAAAGGGAAAAGAGTGCCACTGGAGT
1 TGTGGGCTTTAAAAAGAAAAAG-GTGCCAC-GGAGT
* *
350549 TGTGGGCTTTGAAAAG---AAGATGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
* * * *
350580 TGTGGAC-TTAGAAGGAAAAAGAGGGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGT
**
350614 TGTGGATTTTAAAAAGAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
*
350648 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAAT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
*
350682 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAA-AGAAAAAG-GTGCCACGGAGT
* * *
350719 TGTGGGCTTTGAAAAGAAATAGGTTGCCACGGAAT
1 TGTGGGCTTTAAAAAGAAAAAGG-TGCCACGGAGT
*
350754 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAA-AGAAAAAG-GTGCCACGGAGT
350790 TGTGGGCTTT
1 TGTGGGCTTT
350800 GAGACAAAAT
Statistics
Matches: 268, Mismatches: 38, Indels: 28
0.80 0.11 0.08
Matches are distributed among these distances:
30 5 0.02
31 11 0.04
32 6 0.02
33 25 0.09
34 84 0.31
35 55 0.21
36 60 0.22
37 22 0.08
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.22
Consensus pattern (34 bp):
TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
Found at i:350575 original size:100 final size:98
Alignment explanation
Indices: 350463--350768 Score: 341
Period size: 105 Copynumber: 3.0 Consensus size: 98
350453 TAGAAAAGGT
* * *
350463 GAAAGATGCCACGAAGTTGTGGACTTAAAAAGAACAAG-GTGCCACGGAGTTATGGGCTTTAAAA
1 GAAAGATGCCACGAAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
350527 GGGAAAAGAGTGCCACTGGAGTTGTGGGCTTTGAAAA
66 -GGAAAAG-GTGCCAC-GGAGTTGTGGGCTTT-AAAA
* * * **
350564 G-AAGATGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGGGCCACGGAGTTGTGGATTTTAAAA
1 GAAAGATGCCACGAAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAA
*
350628 AGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
65 AGGAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA
* *
350663 GAAAAAGGTGCCACGGAA-TTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCT
1 G--AAAGATGCCAC-GAAGTTGTGGAC-TT-AAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCT
*
350727 TTGAAAA-GAAATAGGTTGCCACGGAATTGTGGGCTTTAAAA
60 TT-AAAAGGAAA-AGG-TGCCACGGAGTTGTGGGCTTTAAAA
350768 G
1 G
350769 GGAAAAAGAG
Statistics
Matches: 174, Mismatches: 20, Indels: 18
0.82 0.09 0.08
Matches are distributed among these distances:
99 20 0.11
100 39 0.22
101 25 0.14
102 20 0.11
103 4 0.02
104 6 0.03
105 40 0.23
106 20 0.11
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.21
Consensus pattern (98 bp):
GAAAGATGCCACGAAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
GGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA
Found at i:350725 original size:71 final size:71
Alignment explanation
Indices: 350444--350799 Score: 366
Period size: 71 Copynumber: 5.1 Consensus size: 71
350434 CACCGACTTG
** * * *
350444 TGTGGGCTTTAGAAAAGGTGAAAGA-TGCCAC-GAAGTTGTGGAC-TT-AAAAAGAACAAG-GTG
1 TGTGGGCTTTA-AAAA-GAAAAAGAGTGCCACGGAA-TTGTGGGCTTTGAAAAGGAAAAAGAGTG
350504 CCACGGAGT
63 CCACGGAGT
* * * *
350513 TATGGGCTTTAAAAGGGAAAAGAGTGCCACTGGAGTTGTGGGCTTTGAAAA-G---AAGA-TGCC
1 TGTGGGCTTTAAAAAGAAAAAGAGTGCCAC-GGAATTGTGGGCTTTGAAAAGGAAAAAGAGTGCC
350573 ACGGAGT
65 ACGGAGT
* * * * * * * *
350580 TGTGGAC-TTAGAAGGAAAAAGAGGGCCACGGAGTTGT-GGATTTTAAAAAGAAAAAG-GTGCCA
1 TGTGGGCTTTAAAAAGAAAAAGAGTGCCACGGAATTGTGGGCTTTGAAAAGGAAAAAGAGTGCCA
350642 CGGAGT
66 CGGAGT
350648 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAATTGTGGGCTTTGAAAAGGGAAAAAGAGTGCC
1 TGTGGGCTTTAAAAAGAAAAAGAGTGCCACGGAATTGTGGGCTTTGAAAA-GGAAAAAGAGTGCC
350712 ACGGAGT
65 ACGGAGT
* *
350719 TGTGGGCTTTGAAAAGAAATAG-GTTGCCACGGAATTGTGGGCTTT-AAAAGGGAAAAAGAGTGC
1 TGTGGGCTTTAAAAAGAAAAAGAG-TGCCACGGAATTGTGGGCTTTGAAAA-GGAAAAAGAGTGC
350782 CACGGAGT
64 CACGGAGT
350790 TGTGGGCTTT
1 TGTGGGCTTT
350800 GAGACAAAAT
Statistics
Matches: 248, Mismatches: 23, Indels: 30
0.82 0.08 0.10
Matches are distributed among these distances:
64 9 0.04
65 9 0.04
66 19 0.08
67 25 0.10
68 42 0.17
69 38 0.15
70 12 0.05
71 73 0.29
72 21 0.08
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.22
Consensus pattern (71 bp):
TGTGGGCTTTAAAAAGAAAAAGAGTGCCACGGAATTGTGGGCTTTGAAAAGGAAAAAGAGTGCCA
CGGAGT
Found at i:351864 original size:26 final size:26
Alignment explanation
Indices: 351834--351887 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
351824 TGAAAAGGGG
*
351834 TTTTTCCTTCT-TTTGTTTTTTTTTTT
1 TTTTTCCTT-TGTTTGTTGTTTTTTTT
**
351860 TTTTTGGTTTGTTTGTTGTTTTTTTT
1 TTTTTCCTTTGTTTGTTGTTTTTTTT
351886 TT
1 TT
351888 GTGGAAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (26 bp):
TTTTTCCTTTGTTTGTTGTTTTTTTT
Found at i:358434 original size:13 final size:13
Alignment explanation
Indices: 358416--358442 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
358406 ACAATAAGCA
358416 AAAAAATAAAAAG
1 AAAAAATAAAAAG
358429 AAAAAATAAAAAG
1 AAAAAATAAAAAG
358442 A
1 A
358443 TCAAAGTCTA
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:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (13 bp):
AAAAAATAAAAAG
Found at i:359186 original size:52 final size:52
Alignment explanation
Indices: 359101--359225 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
359091 ATATGAAAAG
* *
359101 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
359153 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
359205 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
359226 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:359238 original size:52 final size:51
Alignment explanation
Indices: 359101--359245 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
359091 ATATGAAAAG
*
359101 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
359153 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
359205 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
359246 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:359252 original size:13 final size:13
Alignment explanation
Indices: 359234--359258 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
359224 CAAAGATCAG
359234 TGTATCGATACAA
1 TGTATCGATACAA
359247 TGTATCGATACA
1 TGTATCGATACA
359259 TGTGAGTAAT
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):
TGTATCGATACAA
Found at i:359343 original size:13 final size:13
Alignment explanation
Indices: 359325--359349 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
359315 CAAAAAAATA
359325 TGTATCGATACAT
1 TGTATCGATACAT
359338 TGTATCGATACA
1 TGTATCGATACA
359350 ACATTTTATG
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:359345 original size:33 final size:33
Alignment explanation
Indices: 359303--359369 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
359293 AGTAGCTTAA
359303 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
359336 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
359369 A
1 A
359370 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:372613 original size:11 final size:11
Alignment explanation
Indices: 372599--372637 Score: 62
Period size: 10 Copynumber: 3.5 Consensus size: 11
372589 AACAAAACAA
372599 AAAAAAAAACC
1 AAAAAAAAACC
372610 AAAAAAAAA-C
1 AAAAAAAAACC
372620 AAAAAAAAACCC
1 AAAAAAAAA-CC
372632 AAAAAA
1 AAAAAA
372638 CTAAGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.38
11 9 0.35
12 7 0.27
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACC
Found at i:372613 original size:12 final size:12
Alignment explanation
Indices: 372592--372637 Score: 60
Period size: 11 Copynumber: 4.0 Consensus size: 12
372582 ATACCTAAAC
*
372592 AAAACAAAAAAA
1 AAAACCAAAAAA
372604 AAAACC-AAAAA
1 AAAACCAAAAAA
372615 AAAA-CAAAAAA
1 AAAACCAAAAAA
*
372626 AAACCCAAAAAA
1 AAAACCAAAAAA
372638 CTAAGAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 1 0.03
11 17 0.57
12 12 0.40
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAACCAAAAAA
Found at i:373373 original size:19 final size:19
Alignment explanation
Indices: 373327--373380 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
373317 TTTCAACATT
373327 TTGTATCGATACA-AACAG
1 TTGTATCGATACATAACAG
*
373345 TAAATGTATCGATACATAACTG
1 T---TGTATCGATACATAACAG
373367 TTGTATCGATACAT
1 TTGTATCGATACAT
373381 GTATCGATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 1 0.03
19 13 0.42
21 12 0.39
22 5 0.16
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (19 bp):
TTGTATCGATACATAACAG
Found at i:373442 original size:20 final size:20
Alignment explanation
Indices: 373417--373471 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
373407 CTGCCAAGGA
*
373417 AATGTATCGATACATTATTC
1 AATGTATCGATACATTAATC
373437 AATGTATCGATACATTAATC
1 AATGTATCGATACATTAATC
**
373457 TTTGTATCGATACAT
1 AATGTATCGATACAT
373472 CTGGGAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTAATC
Found at i:377611 original size:28 final size:28
Alignment explanation
Indices: 377570--378428 Score: 747
Period size: 28 Copynumber: 30.0 Consensus size: 28
377560 ACGTTCATCT
* * *
377570 CTTT-AAAGCACATAAGTCAATGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
377597 CTTTTAAAGCCCATAAGTCAATGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
377625 CTTTCAAAGCCCACGAGTCAGTGGCAACTC
1 CTTTCAAAGCCCACAAGTCAGTGGC-AC-C
* * **
377655 TTTTCAAAGCCCACAAGTTAGTGGCATG
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
377683 CTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* **
377711 CTTTCGAAGCCCACAAGTCAGTGGCATT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
377739 CTTTCAGAGCCCACGACTCAATGGCAACTC
1 CTTTCAAAGCCCACAAGTCAGTGGC-AC-C
* * * *
377769 TTTTTAAAGCCCACAAGTTAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
377796 CTTTCAAAGCCCAAAAGTCAGTGGTACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
377824 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* ** *
377852 CTTTCAAAGCCCACGAGTTGGTGGTAACTC
1 CTTTCAAAGCCCACAAGTCAGTGG-CAC-C
* * * *
377882 TTTTCAAATCCCACAAGTTAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
377909 CTTTACAAAGCCTACAAGTCAGTGGCACC
1 CTTT-CAAAGCCCACAAGTCAGTGGCACC
377938 CTTTCAAA-CCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* *
377966 TTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
377994 CTTTCAAAGCCCACAAGTCAGTGGGATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
378022 TTTTCAAGGCCCACAAGTTAGTCGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
378050 ATTTCAAAGCCCATAAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
378078 CTTTCACAGCCAACAAGTCAGTGGCACTA
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* * * * *
378107 TTTTCAAAGCCCACAAGTTAGTAGTATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
378135 CTTTCAAATCACATAAGTC-GATGGCACC
1 CTTTCAAAGCCCACAAGTCAG-TGGCACC
* * *
378163 CTTTAAAAGCTCACAAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
378191 CTTTCACAGCCCACAAGTCAGTGGCACTT
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* * *
378220 TTTTCAAAGCCCATAAGTTAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* * *
378249 TTTTTAAAGCCCACACTAGTCGGTGGCAACTC
1 CTTTCAAAGCCCACA--AGTCAGTGGC-AC-C
* *
378281 TTTTCAAAGCCCACAAGTCGGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
378309 CTTTCAAAGCCCATACAAGTCGGTTGCAACTC
1 CTTTCAAAGCCC--ACAAGTCAGTGGC-AC-C
* * *
378341 TTTTCAAAGCCCACAAGTTAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
378369 CTTTCAAAGCCCACGAGTCAGTGGCAACTC
1 CTTTCAAAGCCCACAAGTCAGTGGC-AC-C
* *
378399 TTTTCAAAGCCCACACAAGTTAGTGGCACC
1 CTTTCAAAG-CC-CACAAGTCAGTGGCACC
378429 TTTTTTTTTA
Statistics
Matches: 679, Mismatches: 126, Indels: 51
0.79 0.15 0.06
Matches are distributed among these distances:
27 46 0.07
28 384 0.57
29 90 0.13
30 103 0.15
31 14 0.02
32 42 0.06
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACC
Found at i:377838 original size:141 final size:142
Alignment explanation
Indices: 377565--379432 Score: 1273
Period size: 141 Copynumber: 12.9 Consensus size: 142
377555 CTAGAACGTT
* * * * * * * *
377565 CATCTCTTT-AAAGCACATAAGTCAATGGCACCCTTTTAAAGCCCATAAGTCAATGGCA-TCCTT
1 CATC-CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTT
* *
377628 TCAAAGCCCACGAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA-TGC-TTTCAAA
65 TCAAAGCCCACAAGTCAGTGGC-ACTC-TTTCAAAGCCCACAAGTCAGTGGCACT-CTTTTCAAA
377691 GCCCACAAGTCAGTGG
127 GCCCACAAGTCAGTGG
* * * * * *
377707 CATCCTTTCGAAGCCCACAAGTCAGTGGCATTCTTTCAGAGCCCACGACTCAATGGCAACTCTTT
1 CATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGC-ACTCTTT
* * * *
377772 TTAAAGCCCACAAGTTAGTGGCA-TCTTTCAAAGCCCAAAAGTCAGTGGTACTC-TTTCAAAGCC
65 TCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCC
377835 CACAAGTCAGTGG
130 CACAAGTCAGTGG
* ** * * *
377848 CA-CTCTTTCAAAGCCCACGAGTTGGTGGTAACTCTTTTCAAATCCCACAAGTTAGTGGCA-TCT
1 CATC-CTTTCAAAGCCCACAAGTCAGTGG-CACTC-TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
377911 TTACAAAGCCTACAAGTCAGTGGCACCCTTTCAAA-CCCACAAGTCAGTGGCACTCTTTTCAAAG
63 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
377975 CCCACAAGTCAGTGG
128 CCCACAAGTCAGTGG
* * * * *
377990 CATCCTTTCAAAGCCCACAAGTCAGTGGGA-TCTTTTCAAGGCCCACAAGTTAGTCGCAC-CATT
1 CATCCTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACTCTTT
* * * * * *
378053 TCAAAGCCCATAAGTTAGTGGCACCCTTTCACAGCCAACAAGTCAGTGGCACTATTTTCAAAGCC
65 TCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCC
* *
378118 CACAAGTTAGTAG
130 CACAAGTCAGTGG
* * * * * * * * *
378131 TATCCTTTCAAATCACATAAGTC-GATGGCACCCTTTAAAAGCTCACAAGTTAGTGGCAC-CCTT
1 CATCCTTTCAAAGCCCACAAGTCAG-TGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTT
* * * * *
378194 TCACAGCCCACAAGTCAGTGGCACTTTTTTCAAAGCCCATAAGTTAGTGGCACTCTTTTTAAAGC
65 TCAAAGCCCACAAGTCAGTGGCAC-TCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
*
378259 CCACACTAGTCGGTGG
129 CCACA--AGTCAGTGG
* * * * *
378275 CAACTCTTTTCAAAGCCCACAAGTCGGTGGCACCCTTTCAAAGCCCATACAAGTCGGTTGCAACT
1 C-A-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCC--ACAAGTCAGTGGC-ACT
* *
378340 CTTTTCAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGCCCACGAGTCAGTGGCAACTCTTTTC
61 CTTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGC-ACTCTTTTC
*
378404 AAAGCCCACACAAGTTAGTGG
124 AAAG-CC-CACAAGTCAGTGG
* * * * * * *
378425 CA-CCTTTTTTTTTAAAAAAACACACTCAAGTCGGTGGCAACCCTTTTCAAA--TCACTATTGTC
1 CATCC------TTT--CAAAGC-C-CACAAGTCAGTGGC-ACTC-TTTCAAAGCCCAC-A-AGTC
* * * * * * * * * *
378487 --TGACATCGCTAGCATT-GAA-TCAAC-A-T-ATTGGCAC-CTTT-ATTAGCCCA-ATGTCACT
52 AGTGGCA-CTCT---TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCA-AAGCCCACAAGTCAGT
* * * *** * *
378542 GGC-CT-TGAATTAGCACATTGGTCCACTTTTCCCGTAGC
112 GGCACTCT---TT-TCA-A--AGCCCACAAGT-CAGT-GG
* **** * *
378580 CTAATGTCGCTAGCCTTGAATTGGCATAAGTTAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTG
1 C--A--TC-CT----TTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTG
** * *
378644 GCAC-CGATTCAAAGCCCACAAGTCAGTGGCAC-CGATTCAAAGCCCACAAGTCAGTGGCA-TCC
56 GCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
378706 TTTCAAAGCCCATAAGTTAGTGG
120 TTTCAAAGCCCACAAGTCAGTGG
* * * * * * * *
378729 CACTCTTTTCAAAGCTCGCAAGTCAGTGGCACCCTTTCAAACCCCCCAAGCCAGTGGCACTTTTT
1 CA-TCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTT
* *
378794 TCAAAGCCCACAAGTCGGTGGCAC-CTTTTCAAAGCCCATACAAGTCGGTGGCAACTCTTTTCAA
65 TCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCC--ACAAGTCAGTGGC-ACTCTTTTCAA
*
378858 AGCCCACAAGTTAGTGG
126 AGCCCACAAGTCAGTGG
* ** * * *
378875 CATCCTTTCAAAGCCCACGAGTTGGTGGCAACTCTTTTCAAATCCCAAAAGTCAGTGGCA-TCCT
1 CATCCTTTCAAAGCCCACAAGTCAGTGGC-ACTC-TTTCAAAGCCCACAAGTCAGTGGCACTCTT
378939 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAGC-C-TTTCAAA
64 TTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCA-CTCTTTTCAAA
379002 GCCCACAAGTCAGTGG
127 GCCCACAAGTCAGTGG
* * * * * *
379018 GA-CCTTTTCAAGGCCCACAAGTTAGTGGCACCCTTTCACAGCCCACAAGTCAGTGGCAC-CCTT
1 CATCC-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTT
* * * * * * * *
379081 TCACAGCCAACAACTCAGTCGCACTATTTTCAAAGCCCACAAGTCAGTGGTA-TCCTTTCAAATC
65 TCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
379145 CCACAAGTCAGTGG
129 CCACAAGTCAGTGG
* * * * * * *
379159 CACCCTTTAAAAGCTCACAAGTTAGTGGCACCCTTTCACAGCCCACAAGTCAGTGGCACTTTTTT
1 CATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTT
* * * * *
379224 CAAAGCCCATAAGTCAGTGACACTCTTTTTAAAGCCCACACTAGTCGGTGGCAACACTTTTCAAA
66 CAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACA--AGTCAGTGGC-ACTCTTTTCAAA
* *
379289 GCCCACAAGTCGGTGA
127 GCCCACAAGTCAGTGG
* * * * *
379305 CACCCTTCCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCATAAGTTAGTGGCA-TC
1 CATCCTTTCAAAG-CC-CACAAGTCAGTGGC-ACTC-TTTCAAAGCCCACAAGTCAGTGGCACTC
* * * *
379369 CTTTCAAAGCCCACGAGTCGGTGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCAC-CTTTT
62 TTTTCAAAGCCCACAAGTCAGTGGC-ACTC-TTTCAAAG-CC-CACAAGTCAGTGGCACTCTTTT
379433 TTAAAAAAAA
Statistics
Matches: 1363, Mismatches: 252, Indels: 216
0.74 0.14 0.12
Matches are distributed among these distances:
140 59 0.04
141 409 0.30
142 216 0.16
143 65 0.05
144 51 0.04
145 38 0.03
146 123 0.09
147 38 0.03
148 29 0.02
149 54 0.04
150 91 0.07
151 22 0.02
152 23 0.02
153 27 0.02
154 12 0.01
155 43 0.03
156 13 0.01
157 33 0.02
158 6 0.00
159 9 0.01
160 1 0.00
161 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (142 bp):
CATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTT
CAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCC
ACAAGTCAGTGG
Found at i:377855 original size:113 final size:113
Alignment explanation
Indices: 377569--379431 Score: 1305
Period size: 113 Copynumber: 16.3 Consensus size: 113
377559 AACGTTCATC
* * * * * * *
377569 TCTTT-AAAGCACATAAGTCAATGGCACCCTTTTAAAGCCCATAAGTCAATGGCA-TCCTTTCAA
1 TCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAA
*
377632 AGCCCACGAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA
65 AGCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA
* *
377681 TGCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCGAAGCCCACAAGTCAGTGGCATTCTTTCA
1 T-CTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCA
* * * * *
377745 GAGCCCACGACTCAATGGCAACTCTTTTTAAAGCCCACAAGTTAGTGGCA
64 AAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA
* *
377795 TCTTTCAAAGCCCAAAAGTCAGTGGTACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAA
1 TCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAA
* ** * *
377860 GCCCACGAGTTGGTGGTAACTCTTTTCAAATCCCACAAGTTAGTGGCA
66 GCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA
* *
377908 TCTTTACAAAGCCTACAAGTCAGTGGCACCCTTTCAAA-CCCACAAGTCAGTGGCACTCTTTTCA
1 TCTTT-CAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCA
* * *
377972 AAGCCCACAAGTCAGTGGC-A-TCCTTTCAAAGCCCACAAGTCAGTGGGA
64 AAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA
* * * * * *
378020 TCTTTTCAAGGCCCACAAGTTAGTCGCAC-CATTTCAAAGCCCATAAGTTAGTGGCACCCTTTCA
1 TC-TTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCA
* * * * *
378084 CAGCCAACAAGTCAGTGGC-ACTATTTTCAAAGCCCACAAGTTAGTAGTA
64 AAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA
* * * * * * * *
378133 TCCTTTCAAATCACATAAGTC-GATGGCACCCTTTAAAAGCTCACAAGTTAGTGGCACCCTTTCA
1 T-CTTTCAAAGCCCACAAGTCAG-TGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCA
* * *
378197 CAGCCCACAAGTCAGTGGC-ACTTTTTTCAAAGCCCATAAGTTAGTGGCA
64 AAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA
* * * *
378246 CTCTTTTTAAAGCCCACACTAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCGGTGGCACCCT
1 -TC-TTTCAAAGCCCACA--AGTCAGTGGC-ACTC-TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
378311 TTCAAAGCCCATACAAGTCGGTTGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA
60 TTCAAAGCCC--ACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA
* *
378367 TCCTTTCAAAGCCCACGAGTCAGTGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCACCTTT
1 T-CTTTCAAAGCCCACAAGTCAGTGGC-ACTC-TTTCAAAG-CC-CACAAGTCAGTGGCA-C---
* * * * * * * * *
378432 TTTTTTAAAAAAACACACTCAAGTCGGTGGCAACCCTTTTCAAA--TCACTA-TT-GTCTGACA
57 -TCTTT--CAAAGC-C-CACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAG--TGGCA
** * * * * * *
378492 TCGCTAGCATTGAA-TCAAC-A-T-ATTGGCAC-CTTT-ATTAGCCCA-ATGTCACTGG--C-C-
1 T--CTTTCA---AAGCCCACAAGTCAGTGGCACTCTTTCA-AAGCCCACAAGTCAGTGGCACTCT
* * * ** * *
378546 TTGAATTAG--CAC-A-T---TGGTCCACT-TTTCCCGTAG-CC-TAA--T-GTCGCTA
60 TTCAA--AGCCCACAAGTCAGTGG-CAACTCTTT-TCAAAGCCCACAAGTTAGTGGC-A
* * * * * * * *
378592 GCCTTGAATTG-GCATAAGTTAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCAC-CGATTC
1 TCTTTCAA-AGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTC
** *
378654 AAAGCCCACAAGTCAGTGGC-AC-CGATTCAAAGCCCACAAGTCAGTGGCA
63 AAAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA
* * * * *
378703 TCCTTTCAAAGCCCATAAGTTAGTGGCACTCTTTTCAAAGCTCGCAAGTCAGTGGCACCCTTTCA
1 T-CTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCA
* * * * **
378768 AACCCCCCAAGCCAGTGGC-ACTTTTTTCAAAGCCCACAAGTCGGTGGCA
64 AAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA
* * *
378817 CCTTTTCAAAGCCCATACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA-TCCT
1 TC-TTTCAAAGCCC--ACAAGTCAGTGGC-ACTC-TTTCAAAGCCCACAAGTCAGTGGCACT-CT
* ** * * *
378881 TTCAAAGCCCACGAGTTGGTGGCAACTCTTTTCAAATCCCAAAAGTCAGTGGCA
60 TTCAAAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA
378935 TCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAGC-CTTTC
1 T-CTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCA-CTCTTTC
* *
378999 AAAGCCCACAAGTCAGTGG-GAC-CTTTTCAAGGCCCACAAGTTAGTGGCA
63 AAAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA
* * * * * * * *
379048 CCCTTTCACAGCCCACAAGTCAGTGGCACCCTTTCACAGCCAACAACTCAGTCGCACTATTTTCA
1 -TCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCA
* * * *
379113 AAGCCCACAAGTCAGTGG-TA-TCCTTTCAAATCCCACAAGTCAGTGGCA
64 AAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA
* * * * * * *
379161 CCCTTTAAAAGCTCACAAGTTAGTGGCACCCTTTCACAGCCCACAAGTCAGTGGCACTTTTTTCA
1 -TCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCAC-TCTTTCA
* * * **
379226 AAGCCCATAAGTCAGTGAC-ACTCTTTTTAAAGCCCACACTAGTCGGTGGCAA
64 AAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACA--AGTTAGTGGC-A
* * * * * *
379278 CACTTTTCAAAGCCCACAAGTCGGTGACACCCTTCCAAAGCCCACACAAGTCGGTGGCAACTCTT
1 -TC-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAG-CC-CACAAGTCAGTGGC-ACTC-T
* * * * **
379343 TTCAAAGCCCATAAGTTAGTGGC-A-TCCTTTCAAAGCCCACGAGTCGGTGGCAA
60 TTCAAAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGC-A
*
379396 CTCTTTTCAAAGCCCACACAAGTTAGTGGCAC-CTTT
1 -TC-TTTCAAAG-CC-CACAAGTCAGTGGCACTCTTT
379432 TTTAAAAAAA
Statistics
Matches: 1415, Mismatches: 229, Indels: 207
0.76 0.12 0.11
Matches are distributed among these distances:
95 1 0.00
96 1 0.00
97 1 0.00
98 3 0.00
99 8 0.01
100 11 0.01
101 17 0.01
102 6 0.00
103 5 0.00
104 1 0.00
105 8 0.01
106 3 0.00
107 4 0.00
108 7 0.00
109 3 0.00
110 6 0.00
111 4 0.00
112 123 0.09
113 483 0.34
114 207 0.15
115 51 0.04
116 40 0.03
117 53 0.04
118 146 0.10
119 17 0.01
120 80 0.06
121 58 0.04
122 5 0.00
123 2 0.00
124 4 0.00
125 17 0.01
126 5 0.00
127 28 0.02
128 4 0.00
129 3 0.00
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (113 bp):
TCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAA
GCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCA
Found at i:378643 original size:28 final size:28
Alignment explanation
Indices: 378607--379431 Score: 769
Period size: 28 Copynumber: 28.6 Consensus size: 28
378597 GAATTGGCAT
*
378607 AAGTTAGTGGCATCCTTTCAAAGCCCAC
1 AAGTCAGTGGCATCCTTTCAAAGCCCAC
*
378635 AAGTCAGTGGCA-CCGATTCAAAGCCCAC
1 AAGTCAGTGGCATCC-TTTCAAAGCCCAC
*
378663 AAGTCAGTGGCA-CCGATTCAAAGCCCAC
1 AAGTCAGTGGCATCC-TTTCAAAGCCCAC
*
378691 AAGTCAGTGGCATCCTTTCAAAGCCCAT
1 AAGTCAGTGGCATCCTTTCAAAGCCCAC
* * * *
378719 AAGTTAGTGGCACTCTTTTCAAAGCTCGC
1 AAGTCAGTGGCA-TCCTTTCAAAGCCCAC
* * *
378748 AAGTCAGTGGCACCCTTTCAAACCCCCC
1 AAGTCAGTGGCATCCTTTCAAAGCCCAC
* **
378776 AAGCCAGTGGCACTTTTTTCAAAGCCCAC
1 AAGTCAGTGGCA-TCCTTTCAAAGCCCAC
*
378805 AAGTCGGTGGCA-CCTTTTCAAAGCCCATAC
1 AAGTCAGTGGCATCC-TTTCAAAGCCC--AC
* *
378835 AAGTCGGTGGCAACTCTTTTCAAAGCCCAC
1 AAGTCAGTGGC-A-TCCTTTCAAAGCCCAC
*
378865 AAGTTAGTGGCATCCTTTCAAAGCCCAC
1 AAGTCAGTGGCATCCTTTCAAAGCCCAC
* ** * * *
378893 GAGTTGGTGGCAACTCTTTTCAAATCCCAA
1 AAGTCAGTGGC-A-TCCTTTCAAAGCCCAC
378923 AAGTCAGTGGCATCCTTTCAAAGCCCAC
1 AAGTCAGTGGCATCCTTTCAAAGCCCAC
*
378951 AAGTCAGTGGCACTCTTTTCAAAGCCCAC
1 AAGTCAGTGGCA-TCCTTTCAAAGCCCAC
*
378980 AAGTCAGTGGCAGCCTTTCAAAGCCCAC
1 AAGTCAGTGGCATCCTTTCAAAGCCCAC
* *
379008 AAGTCAGTGGGA-CCTTTTCAAGGCCCAC
1 AAGTCAGTGGCATCC-TTTCAAAGCCCAC
* * *
379036 AAGTTAGTGGCACCCTTTCACAGCCCAC
1 AAGTCAGTGGCATCCTTTCAAAGCCCAC
* * *
379064 AAGTCAGTGGCACCCTTTCACAGCCAAC
1 AAGTCAGTGGCATCCTTTCAAAGCCCAC
* * **
379092 AACTCAGTCGCACTATTTTCAAAGCCCAC
1 AAGTCAGTGGCA-TCCTTTCAAAGCCCAC
* *
379121 AAGTCAGTGGTATCCTTTCAAATCCCAC
1 AAGTCAGTGGCATCCTTTCAAAGCCCAC
* * *
379149 AAGTCAGTGGCACCCTTTAAAAGCTCAC
1 AAGTCAGTGGCATCCTTTCAAAGCCCAC
* * *
379177 AAGTTAGTGGCACCCTTTCACAGCCCAC
1 AAGTCAGTGGCATCCTTTCAAAGCCCAC
** *
379205 AAGTCAGTGGCACTTTTTTCAAAGCCCAT
1 AAGTCAGTGGCA-TCCTTTCAAAGCCCAC
* * *
379234 AAGTCAGTGACACTCTTTTTAAAGCCCAC
1 AAGTCAGTGGCA-TCCTTTCAAAGCCCAC
* *
379263 ACTAGTCGGTGGCAACACTTTTCAAAGCCCAC
1 A--AGTCAGTGGCATC-C-TTTCAAAGCCCAC
* * * *
379295 AAGTCGGTGACACCCTTCCAAAGCCCACAC
1 AAGTCAGTGGCATCCTTTCAAAG-CC-CAC
* * *
379325 AAGTCGGTGGCAACTCTTTTCAAAGCCCAT
1 AAGTCAGTGGC-A-TCCTTTCAAAGCCCAC
*
379355 AAGTTAGTGGCATCCTTTCAAAGCCCAC
1 AAGTCAGTGGCATCCTTTCAAAGCCCAC
* * *
379383 GAGTCGGTGGCAACTCTTTTCAAAGCCCACAC
1 AAGTCAGTGGC-A-TCCTTTCAAAG-CC-CAC
*
379415 AAGTTAGTGGCA-CCTTT
1 AAGTCAGTGGCATCCTTT
379432 TTTAAAAAAA
Statistics
Matches: 660, Mismatches: 108, Indels: 57
0.80 0.13 0.07
Matches are distributed among these distances:
27 4 0.01
28 361 0.55
29 144 0.22
30 91 0.14
31 16 0.02
32 43 0.07
33 1 0.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (28 bp):
AAGTCAGTGGCATCCTTTCAAAGCCCAC
Found at i:380236 original size:20 final size:20
Alignment explanation
Indices: 380213--380312 Score: 121
Period size: 20 Copynumber: 5.0 Consensus size: 20
380203 AAGTACCCAG
*
380213 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTATCA
* *
380233 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTATCA
* * *
380253 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTATCA
380273 ATGTATCGATACATTCT-TCA
1 ATGTATCGATACATT-TATCA
380293 ATGTATCGATACATTCTATC
1 ATGTATCGATACATT-TATC
380313 TTTTTACCAA
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
20 68 0.96
21 3 0.04
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTATCA
Found at i:380454 original size:15 final size:15
Alignment explanation
Indices: 380434--380464 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
380424 TAGACACCTC
380434 ATTTTGTCCGGGTCA
1 ATTTTGTCCGGGTCA
380449 ATTTTGTCCGGGTCA
1 ATTTTGTCCGGGTCA
380464 A
1 A
380465 AACTTGGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (15 bp):
ATTTTGTCCGGGTCA
Found at i:381808 original size:55 final size:55
Alignment explanation
Indices: 380480--381819 Score: 2010
Period size: 55 Copynumber: 24.2 Consensus size: 55
380470 GGCTAGTAGG
380480 TCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA--TTGTCCAGTCC
1 TCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTT-T-CAGTCC
380535 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
* *
380590 CCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCATTCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
* *
380645 CCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
*
380700 TCAACGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
*
380755 CCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
380810 TCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA--TTGTCCAGTCC
1 TCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTT-T-CAGTCC
380865 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
*
380920 CCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
380975 TCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA--TTGTCCAGTCC
1 TCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTT-T-CAGTCC
*
381030 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAATCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
*
381085 CCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
*
381140 CCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
*
381195 TCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCC
1 TCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCC
* *
381250 TCAAAGAACAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCC
1 TCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCC
*
381305 CCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
* * *
381360 TCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGCTGGTGGCA-TTTTCCAGTCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCC
*
381415 TCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCC
1 TCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCC
* *
381470 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCCAGTCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
*
381525 TCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCC
* *
381581 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCCAGTCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
* **
381636 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
*** * *
381691 TCAAAGAGCAGGATGCTTTTTATTTTCAAAGCCTACACAAGTTGGTGGCACCTTTCAGTCC
1 TCAAAGAGCAGGA--C---ACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
* * * * * *
381752 TCAAAGAGCAGGACGCCTTTTAAAGCCCACACGAGTTGGTGGCACTTTTTACTCC
1 TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
* *
381807 TCAATGAGAAGGA
1 TCAAAGAGCAGGA
381820 TACACTTTAT
Statistics
Matches: 1197, Mismatches: 58, Indels: 60
0.91 0.04 0.05
Matches are distributed among these distances:
53 4 0.00
54 16 0.01
55 1049 0.88
56 74 0.06
57 7 0.01
59 1 0.00
60 3 0.00
61 43 0.04
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.20
Consensus pattern (55 bp):
TCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
Found at i:382421 original size:1 final size:1
Alignment explanation
Indices: 382415--382456 Score: 57
Period size: 1 Copynumber: 42.0 Consensus size: 1
382405 AAAGTGTTTG
* * *
382415 AAAAAAAAAAAAAAAATATAGAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
382457 TTTAAATGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.93, C:0.00, G:0.02, T:0.05
Consensus pattern (1 bp):
A
Found at i:382486 original size:20 final size:21
Alignment explanation
Indices: 382461--382516 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
382451 AAAAAATTTA
* *
382461 AATGTATTGATACATTT-TTG
1 AATGTATCGATACATTTGTGG
382481 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTGG
382502 AATGTATCGATACAT
1 AATGTATCGATACAT
382517 CCTACAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (21 bp):
AATGTATCGATACATTTGTGG
Done.