Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 158 of 226
Found at i:49031009 original size:6 final size:6
Alignment explanation
Indices: 49030998--49031023 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
49030988 AATTATCAAG
49030998 TAGTAA TAGTAA TAGTAA TAGTAA TA
1 TAGTAA TAGTAA TAGTAA TAGTAA TA
49031024 TAAGGTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (6 bp):
TAGTAA
Found at i:49039982 original size:21 final size:22
Alignment explanation
Indices: 49039956--49040024 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 22
49039946 CTATATGAGT
49039956 GGTGTCGCTTCAAACAATAGAA
1 GGTGTCGCTTCAAACAATAGAA
*
49039978 -GTGTCGCTTCAAGCAACATAAGAAA
1 GGTGTCGCTTCAAAC-A-AT-AG-AA
49040003 TGGTGTCGCTTCAAACAATAGA
1 -GGTGTCGCTTCAAACAATAGA
49040025 TGTGGGGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
21 13 0.33
22 1 0.03
23 3 0.08
24 4 0.10
25 4 0.10
26 1 0.03
27 13 0.33
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (22 bp):
GGTGTCGCTTCAAACAATAGAA
Found at i:49047521 original size:23 final size:22
Alignment explanation
Indices: 49047470--49047521 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
49047460 CCTCGTCTTT
*
49047470 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
49047492 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
49047515 TTCTTTT
1 TTCTTTT
49047522 TCAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:49047530 original size:12 final size:12
Alignment explanation
Indices: 49047479--49047533 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
49047469 TTTCTTTTGT
49047479 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
49047492 -TCATTTTC-TC
1 TTCTTTTTCAAC
49047502 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
49047515 TTCTTTTTCAAT
1 TTCTTTTTCAAC
49047527 TTCTTTT
1 TTCTTTT
49047534 CTGTTTCACA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 1 0.03
11 4 0.12
12 22 0.65
13 7 0.21
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:49047540 original size:17 final size:18
Alignment explanation
Indices: 49047515--49047552 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
49047505 TTTCTTCAAC
* *
49047515 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
49047532 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
49047550 TTC
1 TTC
49047553 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Found at i:49052163 original size:26 final size:26
Alignment explanation
Indices: 49052140--49052206 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
49052130 ATGTCCCAAC
49052140 CCACAGCTCGTGTGAGTAAACCCATT
1 CCACAGCTCGTGTGAGTAAACCCATT
**
49052166 CCACAGCTCGTGTGAGTAGGCCCATT
1 CCACAGCTCGTGTGAGTAAACCCATT
49052192 CCACAGCTCGTGTGA
1 CCACAGCTCGTGTGA
49052207 ACATTATTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.22
Consensus pattern (26 bp):
CCACAGCTCGTGTGAGTAAACCCATT
Found at i:49059319 original size:27 final size:28
Alignment explanation
Indices: 49059289--49059342 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
49059279 AAAAGCCTTT
49059289 TTTTTTAA-ATTTACCGAAATGGGCCGG
1 TTTTTTAATATTTACCGAAATGGGCCGG
* *
49059316 TTTTTTAATTATTTATCGGAATGGGCC
1 TTTTTTAA-TATTTACCGAAATGGGCC
49059343 ATTTTCCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
29 15 0.65
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (28 bp):
TTTTTTAATATTTACCGAAATGGGCCGG
Found at i:49062084 original size:15 final size:15
Alignment explanation
Indices: 49062059--49062098 Score: 71
Period size: 15 Copynumber: 2.6 Consensus size: 15
49062049 ATATAATTTT
49062059 TAAATATATAAAAAAA
1 TAAATA-ATAAAAAAA
49062075 TAAATAATAAAAAAA
1 TAAATAATAAAAAAA
49062090 TAAATAATA
1 TAAATAATA
49062099 GTTTATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAATAATAAAAAAA
Found at i:49072625 original size:97 final size:97
Alignment explanation
Indices: 49072518--49072850 Score: 639
Period size: 97 Copynumber: 3.4 Consensus size: 97
49072508 TTAAATTATG
*
49072518 TATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATATCCAAATTTAAGATTAAATCTG
1 TATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATATCCAAATTTAAGATTAAATCTT
49072583 CATATTTTAATTAAAATATAATTCGGTACTTA
66 CATATTTTAATTAAAATATAATTCGGTACTTA
49072615 TATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATATCCAAATTTAAGATTAAATCTT
1 TATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATATCCAAATTTAAGATTAAATCTT
49072680 CATATTTTAATTAAAATATAATTCGGTACTTA
66 CATATTTTAATTAAAATATAATTCGGTACTTA
*
49072712 TATAAACAATCAATCAAGTTTCAATTTCGATGCTTATATAATATCCAAATTTAAGATTAAATCTT
1 TATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATATCCAAATTTAAGATTAAATCTT
*
49072777 CATATTTTAATTAAAATATAATTCAGTACTTA
66 CATATTTTAATTAAAATATAATTCGGTACTTA
49072809 TATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAAT
1 TATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAAT
49072851 TGTTATTAAA
Statistics
Matches: 232, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 232 1.00
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (97 bp):
TATAAACAATCAATCAAGTTCCAATTTCGATGCTTATATAATATCCAAATTTAAGATTAAATCTT
CATATTTTAATTAAAATATAATTCGGTACTTA
Found at i:49072955 original size:11 final size:11
Alignment explanation
Indices: 49072939--49072965 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
49072929 TTATAAAATG
49072939 ACAATATCTCA
1 ACAATATCTCA
49072950 ACAATATCTCA
1 ACAATATCTCA
49072961 ACAAT
1 ACAAT
49072966 TGATAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (11 bp):
ACAATATCTCA
Found at i:49076138 original size:92 final size:91
Alignment explanation
Indices: 49075981--49076189 Score: 260
Period size: 92 Copynumber: 2.3 Consensus size: 91
49075971 TTGATTTTAG
* * * *
49075981 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTGTTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* **
49076046 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTAAA
*
49076073 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
49076137 TATGTAATAATTATTATTTTAAATTAAA
64 TATGTAATAATTATTATTTTAAATTAAA
* * * *
49076165 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
49076190 GTTATAATTA
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 69 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTAAA
Found at i:49076311 original size:66 final size:62
Alignment explanation
Indices: 49076241--49076451 Score: 174
Period size: 66 Copynumber: 3.4 Consensus size: 62
49076231 TAAATTATTT
49076241 AATATTAATTATTTCAAATTTTCATTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTA-AGTATCATATATTATGATTT-AGTAAATTCATATAA
49076306 G
62 G
* * * **
49076307 AATATTAATTA-TTAAGAGTTTTA-TTAA--ATTATATATT-TTAATTA-T-AA-T-ATAT-TT
1 AATATTAATTATTTAA-A-TTTTATTTAAGTATCATATATTATGATTTAGTAAATTCATATAAG
*
49076361 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTAAGTAAATTCATATA
1 AATATTAATTAT-TTAAATTT-TA-TTTA-AGTATCATATATTATGATTT-AGTAAATTCATATA
49076425 AG
61 AG
*
49076427 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
49076452 AAATTATATA
Statistics
Matches: 113, Mismatches: 13, Indels: 39
0.68 0.08 0.24
Matches are distributed among these distances:
53 3 0.03
54 13 0.12
55 5 0.04
56 6 0.05
57 3 0.03
58 1 0.01
59 10 0.09
60 8 0.07
61 10 0.09
62 1 0.01
63 3 0.03
64 6 0.05
65 11 0.10
66 28 0.25
67 5 0.04
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (62 bp):
AATATTAATTATTTAAATTTTATTTAAGTATCATATATTATGATTTAGTAAATTCATATAAG
Found at i:49076363 original size:15 final size:15
Alignment explanation
Indices: 49076328--49076379 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
49076318 TTAAGAGTTT
*
49076328 TATTAAATTAT-ATA
1 TATTTAATTATAATA
49076342 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
49076356 TATTTAATAATAAT-
1 TATTTAATTATAATA
49076370 TATGTTAATT
1 TAT-TTAATT
49076380 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:49076370 original size:54 final size:53
Alignment explanation
Indices: 49076307--49076492 Score: 142
Period size: 54 Copynumber: 3.2 Consensus size: 53
49076297 TTCATATAAG
* *
49076307 AATATTAATTATTAAGAGTTTTATTAAATTATATATTTTAATTATAATATATTT
1 AATAATAATTATTAAGA-TTTTATTAAATTATATATTTTAATTATAATATATTC
* *
49076361 AATAATAATTATGTTA-ATTTATATTTTACAGTATCATATATTATGATTTAAGTA-AATTCATAT
1 AATAATAATTAT-TAAGATTT-TA--TTA-A--AT--TATA-TAT--TTTAATTATAA-T-ATAT
**
49076424 AAG
52 -TC
*
49076427 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTC
1 AATAATAATTATTAAG-ATTTTATTAAATTATATATTTTAATTATAATATATTC
49076481 AATAATAATTAT
1 AATAATAATTAT
49076493 GTTTAAATAT
Statistics
Matches: 103, Mismatches: 11, Indels: 36
0.69 0.07 0.24
Matches are distributed among these distances:
53 3 0.03
54 25 0.24
55 6 0.06
56 11 0.11
57 3 0.03
58 3 0.03
59 6 0.06
61 6 0.06
62 3 0.03
63 3 0.03
64 11 0.11
65 6 0.06
66 13 0.13
67 4 0.04
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (53 bp):
AATAATAATTATTAAGATTTTATTAAATTATATATTTTAATTATAATATATTC
Found at i:49076403 original size:120 final size:120
Alignment explanation
Indices: 49076205--49076500 Score: 458
Period size: 120 Copynumber: 2.5 Consensus size: 120
49076195 AATTATTTTA
* * *
49076205 AATTTTATTAAATCATATATTTTAAATA-AAT-TATTTAATATTAATTAT-TTCAAATTTTCATT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTTTCATT
* *
49076267 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTAAGTAAATTCATATAAGAATATTAATTATTAAG
*
49076323 AGTTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTAT-ATT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTT-TCA-T
49076386 TTACAGTATCATATATTATGATTTAAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTACAGTATCATATATTATGATTTAAGTAAATTCATATAAGAATATTAATTATTAAG
*
49076443 AATTTTATTAAATTATATATTTTAATTATAATATATTCAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
49076501 ATGATTAAAT
Statistics
Matches: 163, Mismatches: 8, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
118 25 0.15
119 9 0.06
120 122 0.75
121 4 0.02
122 3 0.02
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTTTCATTT
ACAGTATCATATATTATGATTTAAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:49076706 original size:150 final size:154
Alignment explanation
Indices: 49076432--49076741 Score: 484
Period size: 150 Copynumber: 2.0 Consensus size: 154
49076422 ATAAGAATAT
* * * *
49076432 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTCAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATT--ATAATAATAATGTTT
* *
49076497 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
64 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
49076562 T-A-A-TTACCAAAACAAATTTCTGC
129 TAACATTTACCAAAACAAATTTATGC
* *
49076585 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATGGGTT-TAATAATAATGTTTAA
1 TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTATAATAATAATGTTTAA
49076649 ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
66 ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
49076714 ATCATTTACCAAAACAAATTTATGC
131 A-CATTTACCAAAACAAATTTATGC
49076739 TAA
1 TAA
49076742 GGGCATTCTA
Statistics
Matches: 144, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
150 77 0.53
151 1 0.01
153 44 0.31
154 22 0.15
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (154 bp):
TAATTATTAAGAATTTTATGAAATTATATATTTTAATTAAAATAGATTATAATAATAATGTTTAA
ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
ACATTTACCAAAACAAATTTATGC
Found at i:49076886 original size:16 final size:16
Alignment explanation
Indices: 49076865--49076900 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
49076855 GATTTGCTAT
49076865 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
49076881 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
49076897 TACA
1 TACA
49076901 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:49079892 original size:9 final size:9
Alignment explanation
Indices: 49079878--49079912 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
49079868 TCTCTTCTTA
49079878 TTTTTAATT
1 TTTTTAATT
49079887 TTTTTAA-T
1 TTTTTAATT
49079895 TTTTTATATT
1 TTTTTA-ATT
49079905 TTTTTAAT
1 TTTTTAAT
49079913 AATTTGCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 7 0.29
9 10 0.42
10 7 0.29
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTAATT
Found at i:49079905 original size:18 final size:17
Alignment explanation
Indices: 49079878--49079912 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
49079868 TCTCTTCTTA
49079878 TTTTTAATTTTTTTAAT
1 TTTTTAATTTTTTTAAT
49079895 TTTTTATATTTTTTTAAT
1 TTTTTA-ATTTTTTTAAT
49079913 AATTTGCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTAATTTTTTTAAT
Found at i:49081260 original size:12 final size:12
Alignment explanation
Indices: 49081243--49081267 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49081233 ATTTCATTCC
49081243 ACATATATATAT
1 ACATATATATAT
49081255 ACATATATATAT
1 ACATATATATAT
49081267 A
1 A
49081268 AACACATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ACATATATATAT
Found at i:49081646 original size:24 final size:25
Alignment explanation
Indices: 49081608--49081947 Score: 154
Period size: 22 Copynumber: 14.6 Consensus size: 25
49081598 GCATATATAC
* *
49081608 AAAATTGGACTGCATTTGTACATAA
1 AAAATTGGACAGCATTTATACATAA
*
49081633 AAAATT-GACAGCA--TATACATAT
1 AAAATTGGACAGCATTTATACATAA
* * * * *
49081655 ATAATTGGACTGCATTTCTAGATCA
1 AAAATTGGACAGCATTTATACATAA
*
49081680 AAAATT-GACAGCA--TATACATAT
1 AAAATTGGACAGCATTTATACATAA
* * * *
49081702 ATAATTGGACTGCATTTATACGTCA
1 AAAATTGGACAGCATTTATACATAA
* *
49081727 AAAAGT-GACAGCA--TATACATAT
1 AAAATTGGACAGCATTTATACATAA
* * * *
49081749 ATAATTGGACTGCATTTATACGTCA
1 AAAATTGGACAGCATTTATACATAA
*
49081774 AAAAGT-GACAGCA--TATACAT--
1 AAAATTGGACAGCATTTATACATAA
* * * *
49081794 -ATATTTGACAGCA--TATACACAT
1 AAAATTGGACAGCATTTATACATAA
* * * *
49081816 ATAATTGGACTGCATTTATACGTTA
1 AAAATTGGACAGCATTTATACATAA
*
49081841 AAAATT-GACAGCA--TATACATAT
1 AAAATTGGACAGCATTTATACATAA
* * * *
49081863 ATAATTGGACTGC-CTTATACATCA
1 AAAATTGGACAGCATTTATACATAA
*
49081887 AAAATT-GACAGCA--TATACATAT
1 AAAATTGGACAGCATTTATACATAA
* * * *
49081909 ATAATTGGACTGCATTTGTACAT-C
1 AAAATTGGACAGCATTTATACATAA
*
49081933 AAAATTTGACAGCAT
1 AAAATTGGACAGCAT
49081948 ATACATTCAT
Statistics
Matches: 226, Mismatches: 67, Indels: 45
0.67 0.20 0.13
Matches are distributed among these distances:
19 3 0.01
20 13 0.06
22 61 0.27
23 43 0.19
24 54 0.24
25 52 0.23
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (25 bp):
AAAATTGGACAGCATTTATACATAA
Found at i:49081661 original size:47 final size:47
Alignment explanation
Indices: 49081594--49081797 Score: 304
Period size: 47 Copynumber: 4.4 Consensus size: 47
49081584 CCAAAATTTG
* * * * *
49081594 GACAGCATAT--ATACAAAATTGGACTGCATTTGTACATAAAAAATT
1 GACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAAGT
* * *
49081639 GACAGCATATACATATATAATTGGACTGCATTTCTAGATCAAAAATT
1 GACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAAGT
*
49081686 GACAGCATATACATATATAATTGGACTGCATTTATACGTCAAAAAGT
1 GACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAAGT
*
49081733 GACAGCATATACATATATAATTGGACTGCATTTATACGTCAAAAAGT
1 GACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAAGT
49081780 GACAGCATATACATATAT
1 GACAGCATATACATATAT
49081798 TTGACAGCAT
Statistics
Matches: 148, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 10 0.07
47 138 0.93
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.30
Consensus pattern (47 bp):
GACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAAGT
Found at i:49081804 original size:20 final size:20
Alignment explanation
Indices: 49081779--49081817 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
49081769 CGTCAAAAAG
*
49081779 TGACAGCATATACATATATT
1 TGACAGCATATACACATATT
49081799 TGACAGCATATACACATAT
1 TGACAGCATATACACATAT
49081818 AATTGGACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (20 bp):
TGACAGCATATACACATATT
Found at i:49081808 original size:67 final size:67
Alignment explanation
Indices: 49081732--49081864 Score: 239
Period size: 67 Copynumber: 2.0 Consensus size: 67
49081722 CGTCAAAAAG
*
49081732 TGACAGCATATACATATATAATTGGACTGCATTTATACGTCAAAAAGTGACAGCATATACATATA
1 TGACAGCATATACACATATAATTGGACTGCATTTATACGTCAAAAAGTGACAGCATATACATATA
49081797 TT
66 TT
* *
49081799 TGACAGCATATACACATATAATTGGACTGCATTTATACGTTAAAAATTGACAGCATATACATATA
1 TGACAGCATATACACATATAATTGGACTGCATTTATACGTCAAAAAGTGACAGCATATACATATA
49081864 T
66 T
49081865 AATTGGACTG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.32
Consensus pattern (67 bp):
TGACAGCATATACACATATAATTGGACTGCATTTATACGTCAAAAAGTGACAGCATATACATATA
TT
Found at i:49081808 original size:114 final size:113
Alignment explanation
Indices: 49081684--49081910 Score: 391
Period size: 114 Copynumber: 2.0 Consensus size: 113
49081674 AGATCAAAAA
*
49081684 TTGACAGCATATACATATATAATTGGACTGCATTTATACGTCAAAAAGTGACAGCATATACATAT
1 TTGACAGCATATACACATATAATTGGACTGCATTTATACGTCAAAAAGTGACAGCATATACATAT
* *
49081749 ATAATTGGACTGCATTTATACGTCAAAAAGTGACAGCATATACATATAT
66 ATAATTGGACTGC-CTTATACATCAAAAAGTGACAGCATATACATATAT
* *
49081798 TTGACAGCATATACACATATAATTGGACTGCATTTATACGTTAAAAATTGACAGCATATACATAT
1 TTGACAGCATATACACATATAATTGGACTGCATTTATACGTCAAAAAGTGACAGCATATACATAT
*
49081863 ATAATTGGACTGCCTTATACATCAAAAATTGACAGCATATACATATAT
66 ATAATTGGACTGCCTTATACATCAAAAAGTGACAGCATATACATATAT
49081911 AATTGGACTG
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
113 32 0.30
114 75 0.70
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (113 bp):
TTGACAGCATATACACATATAATTGGACTGCATTTATACGTCAAAAAGTGACAGCATATACATAT
ATAATTGGACTGCCTTATACATCAAAAAGTGACAGCATATACATATAT
Found at i:49081811 original size:161 final size:160
Alignment explanation
Indices: 49081637--49081953 Score: 519
Period size: 161 Copynumber: 2.0 Consensus size: 160
49081627 ACATAAAAAA
* *
49081637 TTGACAGCATATACATATATAATTGGACTGCATTTCTA-GATCAAAAATTGACAGCATATACATA
1 TTGACAGCATATACACATATAATTGGACTGCATTTATACG-TCAAAAATTGACAGCATATACATA
* *
49081701 TATAATTGGACTGCATTTATACGTCAAAAAGTGACAGCATATACATATATAATTGGACTGCATTT
65 TATAATTGGACTGC-CTTATACATCAAAAAGTGACAGCATATACATATATAATTGGACTGCATTT
*
49081766 ATACGTCAAAAAGTGACAGCATATACATATAT
129 ATACATCAAAAAGTGACAGCATATACATATAT
*
49081798 TTGACAGCATATACACATATAATTGGACTGCATTTATACGTTAAAAATTGACAGCATATACATAT
1 TTGACAGCATATACACATATAATTGGACTGCATTTATACGTCAAAAATTGACAGCATATACATAT
* *
49081863 ATAATTGGACTGCCTTATACATCAAAAATTGACAGCATATACATATATAATTGGACTGCATTTGT
66 ATAATTGGACTGCCTTATACATCAAAAAGTGACAGCATATACATATATAATTGGACTGCATTTAT
**
49081928 ACATCAAAATTTGACAGCATATACAT
131 ACATCAAAAAGTGACAGCATATACAT
49081954 TCATTTACTC
Statistics
Matches: 145, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
160 71 0.49
161 73 0.50
162 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (160 bp):
TTGACAGCATATACACATATAATTGGACTGCATTTATACGTCAAAAATTGACAGCATATACATAT
ATAATTGGACTGCCTTATACATCAAAAAGTGACAGCATATACATATATAATTGGACTGCATTTAT
ACATCAAAAAGTGACAGCATATACATATAT
Found at i:49081898 original size:46 final size:47
Alignment explanation
Indices: 49081798--49081953 Score: 251
Period size: 47 Copynumber: 3.3 Consensus size: 47
49081788 ATACATATAT
* * *
49081798 TTGACAGCATATACACATATAATTGGACTGCATTTATACGTTAAAAA
1 TTGACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAA
*
49081845 TTGACAGCATATACATATATAATTGGACTGC-CTTATACATCAAAAA
1 TTGACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAA
* *
49081891 TTGACAGCATATACATATATAATTGGACTGCATTTGTACATCAAAAT
1 TTGACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAA
49081938 TTGACAGCATATACAT
1 TTGACAGCATATACAT
49081954 TCATTTACTC
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
46 43 0.43
47 58 0.57
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (47 bp):
TTGACAGCATATACATATATAATTGGACTGCATTTATACATCAAAAA
Found at i:49082239 original size:14 final size:15
Alignment explanation
Indices: 49082215--49082249 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
49082205 TATACACATT
49082215 ACCATATAAATACTA
1 ACCATATAAATACTA
49082230 ACCATA-AAATACTA
1 ACCATATAAATACTA
49082244 ATCCAT
1 A-CCAT
49082250 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:49082987 original size:43 final size:43
Alignment explanation
Indices: 49082899--49083022 Score: 137
Period size: 43 Copynumber: 2.9 Consensus size: 43
49082889 AGCTAGTACA
* *** * *
49082899 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATA-CCG
1 ATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACA-AGTCG
49082942 ATGCC-ACTGTCCCAGACAG-GGTCTTACACAAAAACACAAGTCG
1 ATGCCGAC-GTCCCAGAC-GTGGTCTTACACAAAAACACAAGTCG
*
49082985 ATGCCGACGTCCCAGACGTGGTCTTACACGAAAACACA
1 ATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACA
49083023 TATCAGAGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
42 4 0.06
43 63 0.90
44 3 0.04
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (43 bp):
ATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACAAGTCG
Found at i:49087221 original size:18 final size:19
Alignment explanation
Indices: 49087186--49087222 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
49087176 ATAAATTTTA
49087186 AAATTCAAAATATTTATAT
1 AAATTCAAAATATTTATAT
*
49087205 AAATTCCAAAT-TTTATAT
1 AAATTCAAAATATTTATAT
49087223 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATTCAAAATATTTATAT
Found at i:49090389 original size:38 final size:38
Alignment explanation
Indices: 49090338--49090413 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
49090328 CAAAATCCTC
49090338 CCTATCTACAAGTAAGACTTGGTTTTCTTTTTATCCAA
1 CCTATCTACAAGTAAGACTTGGTTTTCTTTTTATCCAA
*
49090376 CCTATCTATAAGTAAGACTTGGTTTTCTTTTTATCCAA
1 CCTATCTACAAGTAAGACTTGGTTTTCTTTTTATCCAA
49090414 GTTTTCATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (38 bp):
CCTATCTACAAGTAAGACTTGGTTTTCTTTTTATCCAA
Found at i:49096919 original size:24 final size:24
Alignment explanation
Indices: 49096888--49096933 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
49096878 ATGAAACAAT
*
49096888 AATAAAATGAGA-GATTAAATTTA
1 AATAAAATAAGAGGATTAAATTTA
*
49096911 AATAGAAATAAGAGGATTGAATT
1 AATA-AAATAAGAGGATTAAATT
49096934 GAAGCGCGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 7 0.37
25 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.28
Consensus pattern (24 bp):
AATAAAATAAGAGGATTAAATTTA
Found at i:49098142 original size:50 final size:50
Alignment explanation
Indices: 49098061--49098801 Score: 383
Period size: 50 Copynumber: 14.8 Consensus size: 50
49098051 GTGATGTCAA
* * * * *
49098061 GGAAGTAAGATTTACTGTTGTAGG-TTCAATCTGTTCCACTGCACTGCCAG
1 GGAAGTAAGATTCACCGCTGT-GGCTTTAATCTGTTCCACTGCAATGCCAG
** * ** ***
49098111 GGAAGTAAGATTTGCCGCTGTGGCTTTAATCTTTTTAACTGCAATGTTGG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTGTTCCACTGCAATGCCAG
** * * ** **
49098161 GGAAGCGAGATTTACCGATGTGGCTTTAATCTACTCCACTGCACCGCCAG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTGTTCCACTGCAATGCCAG
* * * * ** *
49098211 GGAAGTAGGATTCGCCACTGTGGCTTTAATCTTTTGAACTGCAATGTC-G
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTGTTCCACTGCAATGCCAG
** * * *** * *
49098260 GAGAAGCGAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCACCACTAA
1 G-GAAGTAAGATTCACCGCTGTGGCTTTAATCTGTTCCACTGCAATGCCAG
* * * * * ** * ** *
49098311 AGAAGTAGGATTCGCCGCTGTGGCTTTAACCTTTTTAACTACAATATCGG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTGTTCCACTGCAATGCCAG
** * * * * * *
49098361 GGAAGCGATATTCACCGATGTGGCTTTAATCTGCTCCACTACACTGCCAA
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTGTTCCACTGCAATGCCAG
* * * * ** * *
49098411 GGAAGTAGGATTCGCCGCTATGGCTTTAATCTTTTTAACTGCAATGTCGG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTGTTCCACTGCAATGCCAG
* * * * ** *
49098461 GGAAGCGAA-ATTCACCGATATGGCTTTAATCTGCTCCACTGCACCGACAG
1 GGAAG-TAAGATTCACCGCTGTGGCTTTAATCTGTTCCACTGCAATGCCAG
* * * * ** *
49098511 AGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGCAATGTCAG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTGTTCCACTGCAATGCCAG
** * * *
49098561 GGAAGCGAGATTCACCGATGTGGCTTTAATCTGCTCCACTGC-ATCGCTAG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTGTTCCACTGCAAT-GCCAG
* * ** * * ** * *
49098611 AGAAGTAGGATTCGTCGCTGTGGCTTTAACCTTTTTAACTGCAATGTCGG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTGTTCCACTGCAATGCCAG
** * * ** * *
49098661 GGAAGCGAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCACCGCTAA
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTGTTCCACTGCAATGCCAG
* ** * ** * * *
49098711 GGAAGTAGGATTTGCCGCTGTGGCTTTAATCTTTTTAACTGCAACGTCGG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTGTTCCACTGCAATGCCAG
** * * *
49098761 GGAAGCGAGATTCATCGATGTGACTTTAATCTGTTCCACTG
1 GGAAGTAAGATTCACCGCTGTGGCTTTAATCTGTTCCACTG
49098802 TAATCTCAGG
Statistics
Matches: 483, Mismatches: 201, Indels: 14
0.69 0.29 0.02
Matches are distributed among these distances:
49 7 0.01
50 473 0.98
51 3 0.01
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (50 bp):
GGAAGTAAGATTCACCGCTGTGGCTTTAATCTGTTCCACTGCAATGCCAG
Found at i:49098210 original size:100 final size:100
Alignment explanation
Indices: 49098088--49098801 Score: 1077
Period size: 100 Copynumber: 7.1 Consensus size: 100
49098078 TTGTAGGTTC
* * * *
49098088 AATCTGTTCCACTGCACTGCCAGGGAAGTAAGATTTGCCGCTGTGGCTTTAATCTTTTTAACTGC
1 AATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGC
* *
49098153 AATGTTGGGGAAGCGAGATTTACCGATGTGGCTTT
66 AATGTCGGGGAAGCGAGATTCACCGATGTGGCTTT
* * *
49098188 AATCTACTCCACTGCACCGCCAGGGAAGTAGGATTCGCCACTGTGGCTTTAATCTTTTGAACTGC
1 AATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGC
*
49098253 AATGTCGGAGAAGCGAGATTCACCGATGTGGCTTT
66 AATGTCGGGGAAGCGAGATTCACCGATGTGGCTTT
* * ** * *
49098288 AATCTGCTCCACTGCACCACTAAAGAAGTAGGATTCGCCGCTGTGGCTTTAACCTTTTTAACTAC
1 AATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGC
* *
49098353 AATATCGGGGAAGCGATATTCACCGATGTGGCTTT
66 AATGTCGGGGAAGCGAGATTCACCGATGTGGCTTT
* * * *
49098388 AATCTGCTCCACTACACTGCCAAGGAAGTAGGATTCGCCGCTATGGCTTTAATCTTTTTAACTGC
1 AATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGC
* *
49098453 AATGTCGGGGAAGCGAAATTCACCGATATGGCTTT
66 AATGTCGGGGAAGCGAGATTCACCGATGTGGCTTT
* *
49098488 AATCTGCTCCACTGCACCGACAGAGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGC
1 AATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGC
*
49098553 AATGTCAGGGAAGCGAGATTCACCGATGTGGCTTT
66 AATGTCGGGGAAGCGAGATTCACCGATGTGGCTTT
* * * * *
49098588 AATCTGCTCCACTGCATCGCTAGAGAAGTAGGATTCGTCGCTGTGGCTTTAACCTTTTTAACTGC
1 AATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGC
49098653 AATGTCGGGGAAGCGAGATTCACCGATGTGGCTTT
66 AATGTCGGGGAAGCGAGATTCACCGATGTGGCTTT
* * *
49098688 AATCTGCTCCACTGCACCGCTAAGGAAGTAGGATTTGCCGCTGTGGCTTTAATCTTTTTAACTGC
1 AATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGC
* * *
49098753 AACGTCGGGGAAGCGAGATTCATCGATGTGACTTT
66 AATGTCGGGGAAGCGAGATTCACCGATGTGGCTTT
*
49098788 AATCTGTTCCACTG
1 AATCTGCTCCACTG
49098802 TAATCTCAGG
Statistics
Matches: 556, Mismatches: 58, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 556 1.00
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.30
Consensus pattern (100 bp):
AATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGCTGTGGCTTTAATCTTTTTAACTGC
AATGTCGGGGAAGCGAGATTCACCGATGTGGCTTT
Found at i:49098847 original size:46 final size:46
Alignment explanation
Indices: 49098789--49099041 Score: 152
Period size: 46 Copynumber: 5.7 Consensus size: 46
49098779 TGTGACTTTA
*
49098789 ATCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGTAATTATTCG
1 ATCTATTCCACTGTAATCTCAGGGAGATAAGATCTGTAATTATTCG
* * * *
49098835 GTCTATTCCACTGTAATATCAGGGAGATAAGACCTG-----ATGCG
1 ATCTATTCCACTGTAATCTCAGGGAGATAAGATCTGTAATTATTCG
* * * * *
49098876 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTATT-TT-A
1 ATCTATTCCACTGTAATC-TCAGGGAGATAAGAT-CTGTAATTATTCG
** * * * * * * ** *
49098920 ATCCGTTCTACTGTATTCTCAAGGAAATAGGA--T-TACTGGCTTCA
1 ATCTATTCCACTGTAATCTCAGGGAGATAAGATCTGTAAT-TATTCG
** * * *
49098964 ATCTGCTCCGCTATAATCTCAGGGAGATAAGATCTGTAATTCTTCG
1 ATCTATTCCACTGTAATCTCAGGGAGATAAGATCTGTAATTATTCG
*
49099010 GTCTATTCCACTGTAATCTCAGGGAGATAAGA
1 ATCTATTCCACTGTAATCTCAGGGAGATAAGA
49099042 CCTGATGCGA
Statistics
Matches: 152, Mismatches: 41, Indels: 28
0.69 0.19 0.13
Matches are distributed among these distances:
41 33 0.22
42 2 0.01
43 2 0.01
44 46 0.30
45 2 0.01
46 64 0.42
47 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (46 bp):
ATCTATTCCACTGTAATCTCAGGGAGATAAGATCTGTAATTATTCG
Found at i:49099093 original size:175 final size:175
Alignment explanation
Indices: 49098788--49099169 Score: 665
Period size: 175 Copynumber: 2.2 Consensus size: 175
49098778 ATGTGACTTT
* *
49098788 AATCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGTAATTATTCGGTCTATTCCACTGTAATA
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTATTCGGTCTATTCCACTGTAATA
*
49098853 TCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTT
66 TCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAAAGAGATAAGATCCTTTATTT
* *
49098918 TAATCCGTTCTACTGTATTCTCAAGGAAATAGGATTACTGGCTTC
131 TAATCCGTTCCACTGTAATCTCAAGGAAATAGGATTACTGGCTTC
* * *
49098963 AATCTGCTCCGCTATAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTATTCGGTCTATTCCACTGTAATA
*
49099028 TCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAAAGAGATAAGATCTTTTATTT
66 TCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAAAGAGATAAGATCCTTTATTT
* *
49099093 TAATTCGTTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTC
131 TAATCCGTTCCACTGTAATCTCAAGGAAATAGGATTACTGGCTTC
49099138 AATCTGCTCCGCTGTAATCTCAGGGAGATAAG
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAG
49099170 GTTCACGATT
Statistics
Matches: 195, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
175 195 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (175 bp):
AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTATTCGGTCTATTCCACTGTAATA
TCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAAAGAGATAAGATCCTTTATTT
TAATCCGTTCCACTGTAATCTCAAGGAAATAGGATTACTGGCTTC
Found at i:49100450 original size:15 final size:15
Alignment explanation
Indices: 49100441--49100469 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
49100431 CTTTTTTATT
49100441 TTTTCATTTTTCATG
1 TTTTCATTTTTCATG
49100456 TTTTCATTTTTCAT
1 TTTTCATTTTTCAT
49100470 CATTTTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTTCATTTTTCATG
Found at i:49100467 original size:7 final size:7
Alignment explanation
Indices: 49100440--49100469 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
49100430 ACTTTTTTAT
49100440 TTTTTCA
1 TTTTTCA
49100447 TTTTTCA
1 TTTTTCA
49100454 TGTTTTCA
1 T-TTTTCA
49100462 TTTTTCA
1 TTTTTCA
49100469 T
1 T
49100470 CATTTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (7 bp):
TTTTTCA
Found at i:49106376 original size:18 final size:18
Alignment explanation
Indices: 49106353--49106389 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
49106343 AAATATGTAG
49106353 ATAAATATATAA-ACTAAT
1 ATAAATA-ATAATACTAAT
49106371 ATAAATAATAATACTAAT
1 ATAAATAATAATACTAAT
49106389 A
1 A
49106390 ATAATGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAATAATAATACTAAT
Found at i:49107196 original size:6 final size:6
Alignment explanation
Indices: 49107185--49107218 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
49107175 CCGAACAAAG
49107185 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
49107219 TCCCCCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:49107925 original size:2 final size:2
Alignment explanation
Indices: 49107918--49107942 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49107908 AGTTTGTTCT
49107918 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
49107943 TAATTTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49109709 original size:28 final size:27
Alignment explanation
Indices: 49109669--49109722 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
49109659 GGCTGCTATT
*
49109669 TCCTTTTTCATTTCCCCTTTTTTTCTC
1 TCCTTTTTCATTTCCCCTCTTTTTCTC
* *
49109696 TCCTTTTTATATTTTCCCTCTTTTTCT
1 TCCTTTTT-CATTTCCCCTCTTTTTCT
49109723 TCCCTACTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.06, C:0.30, G:0.00, T:0.65
Consensus pattern (27 bp):
TCCTTTTTCATTTCCCCTCTTTTTCTC
Found at i:49112104 original size:26 final size:27
Alignment explanation
Indices: 49112071--49112122 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
49112061 TGAGTTGAGA
49112071 AGTTTATTTAATT-AAGAAATTAATTT
1 AGTTTATTTAATTAAAGAAATTAATTT
*
49112097 AGTTTATTTAATTAAATAAATTAATT
1 AGTTTATTTAATTAAAGAAATTAATT
49112123 GATTAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (27 bp):
AGTTTATTTAATTAAAGAAATTAATTT
Found at i:49131313 original size:19 final size:19
Alignment explanation
Indices: 49131289--49131336 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
49131279 TTCTTTTATC
49131289 TTTCTTCTTATCGTTT-CTT
1 TTTCTTCTTAT-GTTTACTT
49131308 TTTCTTCTT-TGTTTACCTT
1 TTTCTTCTTATGTTTA-CTT
49131327 TTTCTT-TTAT
1 TTTCTTCTTAT
49131337 TTCCTACCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.15
18 3 0.12
19 19 0.73
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTCTTCTTATGTTTACTT
Found at i:49132029 original size:54 final size:54
Alignment explanation
Indices: 49131855--49132033 Score: 173
Period size: 54 Copynumber: 3.3 Consensus size: 54
49131845 TGACAGGCTG
* * * * * * * *
49131855 TGTGTCAAACCGTGTAACTCTTTGTCTTAAGTCACATGGGT-GCGTGCTAAGCCG
1 TGTGACAAACCGTGTAACTCTCTGACTTGAGTCACA-CGGTCGTGTGCTAGGCCA
** * * *
49131909 TGTCCCAAACAGTGTAACTCTCTGACTTGAGTCACACGGGCGTATG-TCAGGCCA
1 TGTGACAAACCGTGTAACTCTCTGACTTGAGTCACACGGTCGTGTGCT-AGGCCA
* **
49131963 TGTGTCTGACCGTGTAACTCTCTGACTTGAGTCACACGGTCGTGTGCTAGGCCA
1 TGTGACAAACCGTGTAACTCTCTGACTTGAGTCACACGGTCGTGTGCTAGGCCA
*
49132017 TATGACAAACCGTGTAA
1 TGTGACAAACCGTGTAA
49132034 GGCATTGACA
Statistics
Matches: 99, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
53 3 0.03
54 95 0.96
55 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (54 bp):
TGTGACAAACCGTGTAACTCTCTGACTTGAGTCACACGGTCGTGTGCTAGGCCA
Found at i:49136478 original size:18 final size:18
Alignment explanation
Indices: 49136453--49136495 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
49136443 TTGGGCTAAG
49136453 TGGG-CCACACGGGCGTA
1 TGGGCCCACACGGGCGTA
*
49136470 TGGGCCCACATGGGCGTA
1 TGGGCCCACACGGGCGTA
*
49136488 TGGACCCA
1 TGGGCCCA
49136496 TTTTTACCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.19, C:0.30, G:0.37, T:0.14
Consensus pattern (18 bp):
TGGGCCCACACGGGCGTA
Found at i:49141666 original size:3 final size:3
Alignment explanation
Indices: 49141658--49141773 Score: 198
Period size: 3 Copynumber: 39.0 Consensus size: 3
49141648 CAGAGAAGTG
49141658 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
49141706 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
49141754 GAA AAA GAA AAA GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA GAA
49141774 CCTCACTAAT
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
2 2 0.02
3 104 0.98
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:49142289 original size:129 final size:130
Alignment explanation
Indices: 49142024--49142300 Score: 315
Period size: 129 Copynumber: 2.1 Consensus size: 130
49142014 TTCGAATTTA
* * * *
49142024 AGAAGAAATTGTTCATGATCATAAATTAATGAACTTAGGCTATGATCGTAAATCAACGAACCTTA
1 AGAAGAAAATGTTCATGATCATAAATCAATGAACATAGGCTATGATCCTAAATCAACGAACCTTA
* ** * *
49142089 ATAATAGCACTCATGATCGTAAATTAACAAGCTGGTTGGAGTTGCGATCGTAAATCAACTAACTT
66 ATAATAGCAATCATGATCGTAAACCAACAAGCTGGTTGAAGTTGCGATCGTAAATCAACTAACTC
* * * * * * *
49142154 AGAAGAAAATGTTCATGATCGTAAATCAGTGAACATAGGTTGTGATCCTAAAT-AGCGAGCCTTG
1 AGAAGAAAATGTTCATGATCATAAATCAATGAACATAGGCTATGATCCTAAATCAACGAACCTTA
* * * ** * * *
49142218 ATAATATCAATCGTGATTGTAAACCAATGAGTTGTTTGAAGTTGTGATCGTAAAT-AAGCTAACT
66 ATAATAGCAATCATGATCGTAAACCAACAAGCTGGTTGAAGTTGCGATCGTAAATCAA-CTAACT
49142282 C
130 C
49142283 AGAAGAAAATGTTCATGA
1 AGAAGAAAATGTTCATGA
49142301 CCGTTAATAA
Statistics
Matches: 122, Mismatches: 24, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
128 2 0.02
129 75 0.61
130 45 0.37
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (130 bp):
AGAAGAAAATGTTCATGATCATAAATCAATGAACATAGGCTATGATCCTAAATCAACGAACCTTA
ATAATAGCAATCATGATCGTAAACCAACAAGCTGGTTGAAGTTGCGATCGTAAATCAACTAACTC
Found at i:49144754 original size:13 final size:13
Alignment explanation
Indices: 49144736--49144760 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49144726 TAACTAAAAC
49144736 AACACATAAATAA
1 AACACATAAATAA
49144749 AACACATAAATA
1 AACACATAAATA
49144761 TCATATAAAT
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:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (13 bp):
AACACATAAATAA
Found at i:49145509 original size:41 final size:41
Alignment explanation
Indices: 49145424--49145594 Score: 123
Period size: 41 Copynumber: 4.2 Consensus size: 41
49145414 AAACAATATT
* * * * * *
49145424 ACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGTTTTAG-TAC
1 ACCGGCACTTAGCCTGCTAGACATAAAGTCTGATAT-GTTTC
* *
49145465 ACCGACACTTAGCCTGCTAGACATAAAGTCTGATGTGTTTC
1 ACCGGCACTTAGCCTGCTAGACATAAAGTCTGATATGTTTC
* * * * *
49145506 ACCGGCAAC-AAGCTTGCTAGACGTAAAGTTTGGTATGTTTC
1 ACCGGC-ACTTAGCCTGCTAGACATAAAGTCTGATATGTTTC
* * * * *
49145547 ACCGGCA-TCAAGCCTACTAGACGTAATGTCTGGTATGTTTC
1 ACCGGCACT-TAGCCTGCTAGACATAAAGTCTGATATGTTTC
*
49145588 ATCGGCA
1 ACCGGCA
49145595 TCAAGCCTCC
Statistics
Matches: 107, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
40 2 0.02
41 103 0.96
42 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (41 bp):
ACCGGCACTTAGCCTGCTAGACATAAAGTCTGATATGTTTC
Found at i:49145595 original size:41 final size:41
Alignment explanation
Indices: 49145475--49145621 Score: 177
Period size: 41 Copynumber: 3.5 Consensus size: 41
49145465 ACCGACACTT
* * * *
49145475 AGCCTGCTAGACATAAAGTCTGATGTGTTTCACCGGCAACA
1 AGCCTGCTAGACGTAAAGTCTGGTATGTTTCACCGGCATCA
* *
49145516 AGCTTGCTAGACGTAAAGTTTGGTATGTTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGGTATGTTTCACCGGCATCA
* * *
49145557 AGCCTACTAGACGTAATGTCTGGTATGTTTCATCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGGTATGTTTCACCGGCATCA
*
49145598 AGCCTCCTGCTAGACGTAATGTCT
1 AG---CCTGCTAGACGTAAAGTCT
49145622 AGATTACTTC
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
41 73 0.80
44 18 0.20
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGGTATGTTTCACCGGCATCA
Found at i:49150885 original size:28 final size:28
Alignment explanation
Indices: 49150846--49150985 Score: 156
Period size: 28 Copynumber: 5.0 Consensus size: 28
49150836 AAAATAGGAT
* *
49150846 AAAACTATAAAATCTGAAAAATAGTGTC
1 AAAACTGTAAAATCTGAAAAATAGTGGC
* *
49150874 AAAACTGCAAAATCT-AAAAACCAGTGGC
1 AAAACTGTAAAATCTGAAAAA-TAGTGGC
* *
49150902 AAAACTGTAAAATCTAAAAAATAATGGC
1 AAAACTGTAAAATCTGAAAAATAGTGGC
* * *
49150930 AAAATTGTAAAATTTGAAAAAAAAGTGGC
1 AAAACTGTAAAATCTG-AAAAATAGTGGC
* *
49150959 AAAAGTGTAAAATCTGAAAAGTAGTGG
1 AAAACTGTAAAATCTGAAAAATAGTGG
49150986 ACACACGGTT
Statistics
Matches: 93, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
27 5 0.05
28 59 0.63
29 29 0.31
ACGTcount: A:0.53, C:0.10, G:0.16, T:0.21
Consensus pattern (28 bp):
AAAACTGTAAAATCTGAAAAATAGTGGC
Found at i:49150906 original size:56 final size:57
Alignment explanation
Indices: 49150846--49150985 Score: 174
Period size: 56 Copynumber: 2.5 Consensus size: 57
49150836 AAAATAGGAT
* * **
49150846 AAAACTATAAAATCTGAAAAATAGTGTCAAAACTGCAAAATCT-AAAAACCAGTGGC
1 AAAACTGTAAAATCTGAAAAATAGTGGCAAAACTGCAAAATCTGAAAAAAAAGTGGC
* * * * *
49150902 AAAACTGTAAAATCTAAAAAATAATGGCAAAATTGTAAAATTTGAAAAAAAAGTGGC
1 AAAACTGTAAAATCTGAAAAATAGTGGCAAAACTGCAAAATCTGAAAAAAAAGTGGC
* *
49150959 AAAAGTGTAAAATCTGAAAAGTAGTGG
1 AAAACTGTAAAATCTGAAAAATAGTGG
49150986 ACACACGGTT
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
56 36 0.51
57 34 0.49
ACGTcount: A:0.53, C:0.10, G:0.16, T:0.21
Consensus pattern (57 bp):
AAAACTGTAAAATCTGAAAAATAGTGGCAAAACTGCAAAATCTGAAAAAAAAGTGGC
Found at i:49157930 original size:18 final size:18
Alignment explanation
Indices: 49157903--49157995 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
49157893 TACGACCGTT
*
49157903 TACGGTACTATTCACGTA
1 TACGGCACTATTCACGTA
49157921 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
*
49157939 TATGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
* * *
49157957 TACAGAACTATTCACATA
1 TACGGCACTATTCACGTA
* *
49157975 TACGGTACTGTTCACGTA
1 TACGGCACTATTCACGTA
49157993 TAC
1 TAC
49157996 AGTAGTTGGG
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (18 bp):
TACGGCACTATTCACGTA
Found at i:49171985 original size:20 final size:21
Alignment explanation
Indices: 49171907--49171990 Score: 81
Period size: 20 Copynumber: 4.2 Consensus size: 21
49171897 ATTTCAACAT
*
49171907 GTATCGATACCTATAC-TGAA
1 GTATCGATACCTTTACTTGAA
*
49171927 GTATCGACACCTTTACTAT-AA
1 GTATCGATACCTTTACT-TGAA
49171948 -TATCGATA-CTTTGA-TTGAA
1 GTATCGATACCTTT-ACTTGAA
*
49171967 GTATCGATACCTTT-CTTGAG
1 GTATCGATACCTTTACTTGAA
49171987 GTAT
1 GTAT
49171991 AAATATTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
18 1 0.02
19 7 0.13
20 38 0.72
21 6 0.11
22 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (21 bp):
GTATCGATACCTTTACTTGAA
Found at i:49181502 original size:31 final size:29
Alignment explanation
Indices: 49181467--49181525 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
49181457 AGAGGTGGGA
*
49181467 TGGGAAATGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAA-GAATAAAAATTTTA-GGGAAAAG
* *
49181498 TGGGAGAGAGTAAAAATTTTAGGGAAAA
1 TGGGAAAGAATAAAAATTTTAGGGAAAA
49181526 TAAAATGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.28
30 12 0.48
31 6 0.24
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.22
Consensus pattern (29 bp):
TGGGAAAGAATAAAAATTTTAGGGAAAAG
Found at i:49181655 original size:29 final size:30
Alignment explanation
Indices: 49181614--49181670 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
49181604 GGGTTGGGAG
*
49181614 GGGAAGGGAGTAAAAGTTTTGGGGGAAAGT
1 GGGAAGGGAGTAAAAGTTTTGAGGGAAAGT
49181644 GGGAA-GGAGTAAAAGTTTTGAGGGAAA
1 GGGAAGGGAGTAAAAGTTTTGAGGGAAA
49181671 AGTAAAAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.44, T:0.19
Consensus pattern (30 bp):
GGGAAGGGAGTAAAAGTTTTGAGGGAAAGT
Found at i:49188718 original size:20 final size:21
Alignment explanation
Indices: 49188678--49188739 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 21
49188668 TAATTTACTT
* *
49188678 AAAGCTTT-ACAATGTTGTAAG
1 AAAG-TTTAACAATCTTATAAG
49188699 AAAG-TTAACAATCTTATAAG
1 AAAGTTTAACAATCTTATAAG
* *
49188719 -AAGTTTAATAATTTTATAAG
1 AAAGTTTAACAATCTTATAAG
49188739 A
1 A
49188740 TATTCAAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 5 0.15
20 25 0.74
21 4 0.12
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
AAAGTTTAACAATCTTATAAG
Found at i:49188804 original size:20 final size:20
Alignment explanation
Indices: 49188779--49188839 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
49188769 ATAATAAAGC
49188779 TGTAAGAAATTTTGTAATTT
1 TGTAAGAAATTTTGTAATTT
* **
49188799 TGTAAGAGATTTAATAATTT
1 TGTAAGAAATTTTGTAATTT
*
49188819 TGTCA-AAATTTTAGTAATTT
1 TGTAAGAAATTTT-GTAATTT
49188839 T
1 T
49188840 TGTTGTAATG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
19 5 0.15
20 28 0.85
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (20 bp):
TGTAAGAAATTTTGTAATTT
Found at i:49193615 original size:30 final size:30
Alignment explanation
Indices: 49193571--49193664 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
49193561 ATTTTTTATG
*
49193571 CCAATATCTTGATACCCATATCTTTGATTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
49193602 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
49193632 CCATTATTTGATAACCATATATTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
49193662 CCA
1 CCA
49193665 TAAATACGGA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 52 0.88
31 7 0.12
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:49193626 original size:15 final size:15
Alignment explanation
Indices: 49193574--49193627 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
49193564 TTTTATGCCA
49193574 ATATC-TTGATACCC
1 ATATCTTTGATACCC
**
49193588 ATATCTTTGATTTTCC
1 ATATCTTTGA-TACCC
*
49193604 A-ATATTTGATACCC
1 ATATCTTTGATACCC
49193618 ATATCTTTGA
1 ATATCTTTGA
49193628 CTTTCCATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
14 9 0.29
15 18 0.58
16 4 0.13
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.44
Consensus pattern (15 bp):
ATATCTTTGATACCC
Found at i:49193641 original size:15 final size:16
Alignment explanation
Indices: 49193586--49193666 Score: 71
Period size: 15 Copynumber: 5.3 Consensus size: 16
49193576 ATCTTGATAC
* *
49193586 CCATATCTTTGATTTT
1 CCATATATTTGACTTT
**
49193602 CCA-ATATTTGA-TAC
1 CCATATATTTGACTTT
*
49193616 CCATATCTTTGACTTT
1 CCATATATTTGACTTT
**
49193632 CCAT-TATTTGA-TAA
1 CCATATATTTGACTTT
49193646 CCATATATTTGACTTT
1 CCATATATTTGACTTT
49193662 CCATA
1 CCATA
49193667 AATACGGATG
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
14 9 0.18
15 27 0.54
16 14 0.28
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (16 bp):
CCATATATTTGACTTT
Found at i:49198293 original size:29 final size:29
Alignment explanation
Indices: 49198254--49198336 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
49198244 TTAATATCTC
*
49198254 GATACCCATATCTTTGATTTTCCAATATTT
1 GATA-CCATATCTTTGACTTTCCAATATTT
*
49198284 GATACCATATCTTTGACTTTCCACTATTT
1 GATACCATATCTTTGACTTTCCAATATTT
*
49198313 GATAACCATATATTTGACTTTCCA
1 GAT-ACCATATCTTTGACTTTCCA
49198337 TAAATACGGA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
29 26 0.53
30 23 0.47
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (29 bp):
GATACCATATCTTTGACTTTCCAATATTT
Found at i:49199391 original size:41 final size:41
Alignment explanation
Indices: 49199305--49199458 Score: 202
Period size: 41 Copynumber: 3.7 Consensus size: 41
49199295 AAAACATCGT
* *
49199305 TAAAGAACATGATCTTTAGCGGCGTTTTTCCTTAAGCGCCGC
1 TAAAGAACATGTTCTTTAGCGGCG-TTTTCTTTAAGCGCCGC
* * *
49199347 TAAAGATCATGGTCTTTAGCGGCGTTTTCTTTAAGCGCCTC
1 TAAAGAACATGTTCTTTAGCGGCGTTTTCTTTAAGCGCCGC
*
49199388 TAAAGAACATGTTCTTTAGCGACGTTTT-TTATATGAGCGCCGC
1 TAAAGAACATGTTCTTTAGCGGCGTTTTCTT-TA--AGCGCCGC
*
49199431 TAAAGAACATGTTCTTTAGCGGTGTTTT
1 TAAAGAACATGTTCTTTAGCGGCGTTTT
49199459 TTCTAAGAAC
Statistics
Matches: 99, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
40 2 0.02
41 42 0.42
42 22 0.22
43 33 0.33
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (41 bp):
TAAAGAACATGTTCTTTAGCGGCGTTTTCTTTAAGCGCCGC
Found at i:49199450 original size:84 final size:83
Alignment explanation
Indices: 49199305--49199458 Score: 227
Period size: 84 Copynumber: 1.8 Consensus size: 83
49199295 AAAACATCGT
* * *
49199305 TAAAGAACATGATCTTTAGCGGCGTTTTTCCTTAAGCGCCGCTAAAGATCATGGTCTTTAGCGGC
1 TAAAGAACATGATCTTTAGCGACGTTTTTCATTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGC
49199370 GTTTTCTTTAAGCGCCTC
66 GTTTTCTTTAAGCGCCTC
* * * *
49199388 TAAAGAACATGTTCTTTAGCGACGTTTTTTATATGAGCGCCGCTAAAGAACATGTTCTTTAGCGG
1 TAAAGAACATGATCTTTAGCGACGTTTTTCAT-TAAGCGCCGCTAAAGAACATGGTCTTTAGCGG
*
49199453 TGTTTT
65 CGTTTT
49199459 TTCTAAGAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
83 28 0.45
84 34 0.55
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (83 bp):
TAAAGAACATGATCTTTAGCGACGTTTTTCATTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGC
GTTTTCTTTAAGCGCCTC
Found at i:49199490 original size:30 final size:30
Alignment explanation
Indices: 49199433--49199490 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
49199423 AGCGCCGCTA
***
49199433 AAGAACATGTTCTTTAGCGGTGTTTTTTCT
1 AAGAACATGTTCTTTAGCGGCACTTTTTCT
49199463 AAGAACATGTTCTTTAGCGGCACTTTTT
1 AAGAACATGTTCTTTAGCGGCACTTTTT
49199491 TACAAAAACG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (30 bp):
AAGAACATGTTCTTTAGCGGCACTTTTTCT
Found at i:49199917 original size:21 final size:21
Alignment explanation
Indices: 49199872--49199920 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
49199862 CTTTTGAACC
*
49199872 TCTGCTTCTCTCGCTGCAGCC
1 TCTGCTTCTCTCGCTGCAGCA
*
49199893 TCTGTTTCTCTCGCTGTC-GCA
1 TCTGCTTCTCTCGCTG-CAGCA
49199914 TCTGCTT
1 TCTGCTT
49199921 TTGAACCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.04, C:0.37, G:0.18, T:0.41
Consensus pattern (21 bp):
TCTGCTTCTCTCGCTGCAGCA
Found at i:49205352 original size:9 final size:9
Alignment explanation
Indices: 49205326--49205468 Score: 160
Period size: 9 Copynumber: 15.8 Consensus size: 9
49205316 ATTTGCACGG
49205326 GTAAGTTAT
1 GTAAGTTAT
* *
49205335 TTAATTTAT
1 GTAAGTTAT
49205344 GTAAGTTAT
1 GTAAGTTAT
49205353 GTAAGTTAT
1 GTAAGTTAT
49205362 GTAAGTTAT
1 GTAAGTTAT
* *
49205371 TTAATTTAT
1 GTAAGTTAT
*
49205380 GTAGGTTAT
1 GTAAGTTAT
* *
49205389 GTAAGTCCAC
1 GTAAGT-TAT
* *
49205399 GGAATTTAT
1 GTAAGTTAT
49205408 GTAAGTTAT
1 GTAAGTTAT
49205417 GTAAGTTAT
1 GTAAGTTAT
* *
49205426 TTAATTTAT
1 GTAAGTTAT
49205435 GTAAGTTAT
1 GTAAGTTAT
49205444 GTAAGTTAT
1 GTAAGTTAT
* *
49205453 TTAATTTAT
1 GTAAGTTAT
49205462 GTAAGTT
1 GTAAGTT
49205469 TCTATATATG
Statistics
Matches: 107, Mismatches: 26, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
9 102 0.95
10 5 0.05
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.48
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:49205370 original size:27 final size:27
Alignment explanation
Indices: 49205326--49205621 Score: 203
Period size: 27 Copynumber: 10.7 Consensus size: 27
49205316 ATTTGCACGG
* * * *
49205326 GTAAGTTATTTAATTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTATTTAATTTAT
49205353 GTAAGTTATGTAAGTTATTTAATTTAT
1 GTAAGTTATGTAAGTTATTTAATTTAT
* * ***
49205380 GTAGGTTATGTAAGTCCACGGAATTTAT
1 GTAAGTTATGTAAGT-TATTTAATTTAT
49205408 GTAAGTTATGTAAGTTATTTAATTTAT
1 GTAAGTTATGTAAGTTATTTAATTTAT
49205435 GTAAGTTATGTAAGTTATTTAATTTAT
1 GTAAGTTATGTAAGTTATTTAATTTAT
* * *
49205462 GTAAGTTTCTATATATGTT-TATATATTGTAT
1 GTAAG--T-TATGTAAGTTATTTA-ATT-TAT
* * *
49205493 GTTAGTTAT-TATGTTATTATATAAGTTAT
1 GTAAGTTATGTAAGTTA-T-T-TAATTTAT
* *
49205522 TTAAGTTAT-TATGTTATTATATAAAGTATTAT
1 GTAAGTTATGTAAGTTA-T-T-T-AA-T-TTAT
* *
49205554 GTAATTTAT-TATGTTA-TT-A--TAT
1 GTAAGTTATGTAAGTTATTTAATTTAT
*
49205576 GTAAGTTATGTAAGGTATTTAATTTAT
1 GTAAGTTATGTAAGTTATTTAATTTAT
*
49205603 GTAAGTTATGCAAGCTTAT
1 GTAAGTTATGTAAG-TTAT
49205622 ATACAAGTTA
Statistics
Matches: 220, Mismatches: 30, Indels: 37
0.77 0.10 0.13
Matches are distributed among these distances:
22 11 0.05
23 5 0.02
24 2 0.01
25 1 0.00
26 1 0.00
27 99 0.45
28 29 0.13
29 30 0.14
30 15 0.07
31 9 0.04
32 18 0.08
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.50
Consensus pattern (27 bp):
GTAAGTTATGTAAGTTATTTAATTTAT
Found at i:49205521 original size:20 final size:20
Alignment explanation
Indices: 49205496--49205594 Score: 67
Period size: 20 Copynumber: 4.8 Consensus size: 20
49205486 ATTGTATGTT
*
49205496 AGTTATTATGTTATTATATA
1 AGTTATTAAGTTATTATATA
* *
49205516 AGTTATTTAAGTTATTATGTT
1 AGTTA-TTAAGTTATTATATA
*
49205537 A-TTATATAAAG-TATTATGTA
1 AGTTAT-T-AAGTTATTATATA
* *
49205557 ATTTATTATGTTATTATATGTA
1 AGTTATTAAGTTATTATA--TA
*
49205579 AGTTATGTAAGGTATT
1 AGTTAT-TAAGTTATT
49205595 TAATTTATGT
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
19 3 0.05
20 25 0.40
21 20 0.32
22 7 0.11
23 7 0.11
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (20 bp):
AGTTATTAAGTTATTATATA
Found at i:49205568 original size:32 final size:29
Alignment explanation
Indices: 49205490--49205594 Score: 129
Period size: 29 Copynumber: 3.4 Consensus size: 29
49205480 TTATATATTG
*
49205490 TATGTTAGTTATTATGTTATTATATAAGT
1 TATGTAAGTTATTATGTTATTATATAAGT
*
49205519 TATTTAAGTTATTATGTTATTATATAAAGTAT
1 TATGTAAGTTATTATGTTATTATAT-AAG--T
*
49205551 TATGTAATTTATTATGTTATTATATGTAAGT
1 TATGTAAGTTATTATGTTATTATA--TAAGT
*
49205582 TATGTAAGGTATT
1 TATGTAAGTTATT
49205595 TAATTTATGT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
29 23 0.35
30 3 0.05
31 12 0.18
32 23 0.35
33 3 0.05
34 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (29 bp):
TATGTAAGTTATTATGTTATTATATAAGT
Found at i:49205587 original size:9 final size:9
Alignment explanation
Indices: 49205573--49205612 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
49205563 TATGTTATTA
49205573 TATGTAAGT
1 TATGTAAGT
*
49205582 TATGTAAGG
1 TATGTAAGT
* *
49205591 TATTTAATT
1 TATGTAAGT
49205600 TATGTAAGT
1 TATGTAAGT
49205609 TATG
1 TATG
49205613 CAAGCTTATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (9 bp):
TATGTAAGT
Found at i:49205875 original size:62 final size:62
Alignment explanation
Indices: 49205790--49205909 Score: 159
Period size: 62 Copynumber: 1.9 Consensus size: 62
49205780 AGAAAACTTA
* * *** *
49205790 TAAAATTAATACAAATAAATTTTATTTCTCCCAAATTTAGAACACTTATTTAGAAAACGAAG
1 TAAAATTAATACAAATAAATTTTAATACAAACAAATTTAGAAAACTTATTTAGAAAACGAAG
* * *
49205852 TAAATTTAATACTAATAAATTTTAATACAAATAAATTTAGAAAACTTATTTAGAAAAC
1 TAAAATTAATACAAATAAATTTTAATACAAACAAATTTAGAAAACTTATTTAGAAAAC
49205910 TTATATAGGT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 49 1.00
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (62 bp):
TAAAATTAATACAAATAAATTTTAATACAAACAAATTTAGAAAACTTATTTAGAAAACGAAG
Found at i:49205877 original size:16 final size:16
Alignment explanation
Indices: 49205852--49205889 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
49205842 GAAAACGAAG
*
49205852 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
49205867 TAAATTTTAATACAAA
1 TAAATTTTAATACAAA
49205883 TAAATTT
1 TAAATTT
49205890 AGAAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:49205904 original size:13 final size:13
Alignment explanation
Indices: 49205886--49205913 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
49205876 ATACAAATAA
49205886 ATTTAGAAAACTT
1 ATTTAGAAAACTT
49205899 ATTTAGAAAACTT
1 ATTTAGAAAACTT
49205912 AT
1 AT
49205914 ATAGGTATTA
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:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAGAAAACTT
Found at i:49206952 original size:27 final size:29
Alignment explanation
Indices: 49206898--49206952 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
49206888 TAATTATCAC
*
49206898 AACAATAAACTTAATAATAATTGATAAAGT
1 AACAATAAACTTAATAATAAAT-ATAAAGT
*
49206928 AACAATCAACTTAAT-ATAAAT-TAAA
1 AACAATAAACTTAATAATAAATATAAA
49206953 TCAGAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
29 5 0.22
30 14 0.61
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.29
Consensus pattern (29 bp):
AACAATAAACTTAATAATAAATATAAAGT
Found at i:49207020 original size:24 final size:24
Alignment explanation
Indices: 49206993--49207038 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
49206983 AGTAACAGTT
49206993 ACAGGAAGCACAGTTACAGGAAGC
1 ACAGGAAGCACAGTTACAGGAAGC
49207017 ACAGGAAGCACAGTTACAGGAA
1 ACAGGAAGCACAGTTACAGGAA
49207039 TTTTACAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.20, G:0.28, T:0.09
Consensus pattern (24 bp):
ACAGGAAGCACAGTTACAGGAAGC
Found at i:49207038 original size:15 final size:15
Alignment explanation
Indices: 49206987--49207020 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
49206977 TGGTAAAGTA
49206987 ACAGTTACAGGAAGC
1 ACAGTTACAGGAAGC
49207002 ACAGTTACAGGAAGC
1 ACAGTTACAGGAAGC
49207017 ACAG
1 ACAG
49207021 GAAGCACAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.21, G:0.26, T:0.12
Consensus pattern (15 bp):
ACAGTTACAGGAAGC
Found at i:49209427 original size:7 final size:7
Alignment explanation
Indices: 49209415--49209496 Score: 53
Period size: 7 Copynumber: 11.6 Consensus size: 7
49209405 CCCCTAAACT
49209415 CATAACC
1 CATAACC
49209422 CATAACC
1 CATAACC
*
49209429 CCTAACC
1 CATAACC
49209436 C-TAAACC
1 CAT-AACC
49209443 CATAAACC
1 CAT-AACC
*
49209451 CTTAACC
1 CATAACC
*
49209458 C-CAACC
1 CATAACC
* *
49209464 CTTAAAC
1 CATAACC
*
49209471 CATAATC
1 CATAACC
49209478 CATAAGCC
1 CATAA-CC
49209486 TC-TAACC
1 -CATAACC
49209493 CATA
1 CATA
49209497 TCCCTTAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
6 7 0.11
7 41 0.67
8 12 0.20
9 1 0.02
ACGTcount: A:0.39, C:0.41, G:0.01, T:0.18
Consensus pattern (7 bp):
CATAACC
Found at i:49209444 original size:21 final size:22
Alignment explanation
Indices: 49209400--49209471 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
49209390 AACATTAATT
*
49209400 ATAAACCCCTAA-ACTCATAACCC
1 ATAAACCCCTAACCCT-A-AACCC
49209423 AT-AACCCCTAACCCTAAACCC
1 ATAAACCCCTAACCCTAAACCC
* *
49209444 ATAAACCCTTAACCC-CAACCC
1 ATAAACCCCTAACCCTAAACCC
*
49209465 TTAAACC
1 ATAAACC
49209472 ATAATCCATA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
21 18 0.42
22 21 0.49
23 4 0.09
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (22 bp):
ATAAACCCCTAACCCTAAACCC
Found at i:49209446 original size:28 final size:28
Alignment explanation
Indices: 49209406--49209493 Score: 99
Period size: 28 Copynumber: 3.1 Consensus size: 28
49209396 AATTATAAAC
*
49209406 CCCTAAACTCATAACCCATAACCCCTAA
1 CCCTAAACCCATAACCCATAACCCCTAA
*
49209434 CCCTAAACCCATAAACCCTTAACCCC-AA
1 CCCTAAACCCAT-AACCCATAACCCCTAA
* *
49209462 CCCTTAAA-CCATAATCCATAAGCCTCTAA
1 CCC-TAAACCCATAACCCATAA-CCCCTAA
49209491 CCC
1 CCC
49209494 ATATCCCTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
27 7 0.14
28 23 0.45
29 21 0.41
ACGTcount: A:0.38, C:0.43, G:0.01, T:0.18
Consensus pattern (28 bp):
CCCTAAACCCATAACCCATAACCCCTAA
Found at i:49209656 original size:7 final size:7
Alignment explanation
Indices: 49209636--49209691 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
49209626 ATTAACTACA
49209636 AACCCCT
1 AACCCCT
49209643 AAACCCCT
1 -AACCCCT
49209651 AACCCC-
1 AACCCCT
**
49209657 AACCATT
1 AACCCCT
*
49209664 AACCCTT
1 AACCCCT
49209671 AACCCCT
1 AACCCCT
*
49209678 AAACCCTT
1 -AACCCCT
49209686 AACCCC
1 AACCCC
49209692 AATCCTTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
6 4 0.10
7 23 0.57
8 13 0.32
ACGTcount: A:0.34, C:0.50, G:0.00, T:0.16
Consensus pattern (7 bp):
AACCCCT
Found at i:49215636 original size:50 final size:50
Alignment explanation
Indices: 49215570--49215669 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
49215560 AATGAGTTAG
49215570 AAGAGTTCTGAATGTTCTCATATGAAAATGTCAAACTATTCAATGAGAGA
1 AAGAGTTCTGAATGTTCTCATATGAAAATGTCAAACTATTCAATGAGAGA
49215620 AAGAGTTCTGAATGTTCTCATATGAAAATGTCAAACTATTCAATGAGAGA
1 AAGAGTTCTGAATGTTCTCATATGAAAATGTCAAACTATTCAATGAGAGA
49215670 CTAAAAAGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (50 bp):
AAGAGTTCTGAATGTTCTCATATGAAAATGTCAAACTATTCAATGAGAGA
Found at i:49215986 original size:15 final size:16
Alignment explanation
Indices: 49215957--49215986 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49215947 TTTTTCTTTT
49215957 AAATAAATGTATGTCA
1 AAATAAATGTATGTCA
49215973 AAATAAAT-TATGTC
1 AAATAAATGTATGTC
49215987 TAGGAGATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (16 bp):
AAATAAATGTATGTCA
Found at i:49216324 original size:15 final size:16
Alignment explanation
Indices: 49216306--49216335 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
49216296 TAATAACTAA
49216306 TATATAAT-TATATTT
1 TATATAATATATATTT
49216321 TATATAATATATATT
1 TATATAATATATATT
49216336 AATTGTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:49217240 original size:17 final size:18
Alignment explanation
Indices: 49217204--49217240 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
49217194 TTTTCAATTT
*
49217204 ATTGAATTTTTTATGCAA
1 ATTGAATTTTTTATGAAA
49217222 ATTGAATTTTTTA-GAAA
1 ATTGAATTTTTTATGAAA
49217239 AT
1 AT
49217241 ATTAGTTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.49
Consensus pattern (18 bp):
ATTGAATTTTTTATGAAA
Found at i:49223261 original size:86 final size:82
Alignment explanation
Indices: 49223103--49223331 Score: 271
Period size: 86 Copynumber: 2.7 Consensus size: 82
49223093 TGAGTTTTTG
* * *
49223103 GGGCCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGCTCGGGCATTTAGCGGCGTTTTTGAAA
1 GGGCCGTTAGCGGCGTTTTTAAAGAAACGCCGCTAATGCTCGGGCCTTTAGCGGCGTTTTTGAAA
*
49223168 ATGCGCCGCTAATGATT
66 ATGCGCCGCTAATGATC
* * * *
49223185 GGTCCTTTAGCGGTGTTCGTTTTTATAGAAACGCCGCTAATGCTCGGGCCTTTAGCGGTGTTTTT
1 GGGCCGTTAGC-G-G--CGTTTTTAAAGAAACGCCGCTAATGCTCGGGCCTTTAGCGGCGTTTTT
* *
49223250 GACGAA-GCGCCGCTAATGCTC
62 GA-AAATGCGCCGCTAATGATC
* * * * *
49223271 GGGCCGTTAGCGGCGTTTTTAAAGAATCGCTGTTAATGCTGGGGCCTTTAGCGGCATTTTT
1 GGGCCGTTAGCGGCGTTTTTAAAGAAACGCCGCTAATGCTCGGGCCTTTAGCGGCGTTTTT
49223332 AAAGAAACAC
Statistics
Matches: 125, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
82 51 0.41
83 1 0.01
84 2 0.02
85 1 0.01
86 68 0.54
87 2 0.02
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (82 bp):
GGGCCGTTAGCGGCGTTTTTAAAGAAACGCCGCTAATGCTCGGGCCTTTAGCGGCGTTTTTGAAA
ATGCGCCGCTAATGATC
Found at i:49223335 original size:41 final size:41
Alignment explanation
Indices: 49223103--49223337 Score: 274
Period size: 41 Copynumber: 5.6 Consensus size: 41
49223093 TGAGTTTTTG
49223103 GGGCCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGCTC
* * * *
49223144 GGGCATTTAGCGGCGTTTTTGAAA-ATGCGCCGCTAATGATT
1 GGGCCTTTAGCGGCGTTTTT-AAAGAAGCGCCGCTAATGCTC
* * *
49223185 GGTCCTTTAGCGGTGTTCGTTTTTATAGAAACGCCGCTAATGCTC
1 GGGCCTTTAGC-G-G--CGTTTTTAAAGAAGCGCCGCTAATGCTC
* * *
49223230 GGGCCTTTAGCGGTGTTTTTGACGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGCTC
* * * * *
49223271 GGGCCGTTAGCGGCGTTTTTAAAGAATCGCTGTTAATGCTG
1 GGGCCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGCTC
*
49223312 GGGCCTTTAGCGGCATTTTTAAAGAA
1 GGGCCTTTAGCGGCGTTTTTAAAGAA
49223338 ACACTGCAAA
Statistics
Matches: 161, Mismatches: 27, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
41 122 0.76
42 4 0.02
43 2 0.01
44 3 0.02
45 30 0.19
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGCTC
Found at i:49223802 original size:7 final size:7
Alignment explanation
Indices: 49223792--49223900 Score: 65
Period size: 7 Copynumber: 15.1 Consensus size: 7
49223782 AAGGTTTATT
49223792 GGTTAGG
1 GGTTAGG
49223799 GGTTAGG
1 GGTTAGG
*
49223806 GGTTAGA
1 GGTTAGG
**
49223813 GGTTAAA
1 GGTTAGG
**
49223820 ATTTAGG
1 GGTTAGG
*
49223827 GGTTTAAG
1 GG-TTAGG
* *
49223835 GTTTATTG
1 GGTTA-GG
*
49223843 GTTTAGG
1 GGTTAGG
49223850 GGTTAGG
1 GGTTAGG
*
49223857 TGTTAGG
1 GGTTAGG
*
49223864 GATTTAGG
1 G-GTTAGG
*
49223872 GGTGAGG
1 GGTTAGG
*
49223879 GGTTTGG
1 GGTTAGG
49223886 GGTTAGG
1 GGTTAGG
*
49223893 AGTTAGG
1 GGTTAGG
49223900 G
1 G
49223901 ATTTAGTGTT
Statistics
Matches: 76, Mismatches: 23, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
7 59 0.78
8 17 0.22
ACGTcount: A:0.19, C:0.00, G:0.46, T:0.35
Consensus pattern (7 bp):
GGTTAGG
Found at i:49223816 original size:21 final size:21
Alignment explanation
Indices: 49223792--49223915 Score: 65
Period size: 22 Copynumber: 5.7 Consensus size: 21
49223782 AAGGTTTATT
*
49223792 GGTTAGGGGTTAGGGGTTAGA
1 GGTTAGGGTTTAGGGGTTAGA
***
49223813 GGTTAAAATTTAGGGGTTTA-A
1 GGTTAGGGTTTAGGGG-TTAGA
*
49223834 GGTTTATTGGTTTAGGGGTTAG-
1 GG-TTA-GGGTTTAGGGGTTAGA
* *
49223856 GTGTTAGGGATTTAGGGGTGAGG
1 G-GTTAGGG-TTTAGGGGTTAGA
* * *
49223879 GGTTTGGGGTTAGGAGTTAG-
1 GGTTAGGGTTTAGGGGTTAGA
*
49223899 GGATTTAGTGTTTAGGG
1 GG--TTAGGGTTTAGGG
49223916 AGTCAAGGGT
Statistics
Matches: 77, Mismatches: 17, Indels: 17
0.69 0.15 0.15
Matches are distributed among these distances:
20 2 0.03
21 26 0.34
22 39 0.51
23 10 0.13
ACGTcount: A:0.19, C:0.00, G:0.44, T:0.36
Consensus pattern (21 bp):
GGTTAGGGTTTAGGGGTTAGA
Found at i:49224604 original size:16 final size:16
Alignment explanation
Indices: 49224583--49224615 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
49224573 ACTTAGTAAT
49224583 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
49224599 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
49224615 T
1 T
49224616 TGTATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (16 bp):
TAAAAGATACAATTAA
Found at i:49224713 original size:15 final size:16
Alignment explanation
Indices: 49224693--49224728 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
49224683 GATATTTTAG
*
49224693 AATATAAATGTAAA-T
1 AATATAAATATAAATT
49224708 AATATAAATATAAATT
1 AATATAAATATAAATT
49224724 AATAT
1 AATAT
49224729 TTAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AATATAAATATAAATT
Found at i:49232648 original size:15 final size:15
Alignment explanation
Indices: 49232628--49232661 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
49232618 TGAACGACGG
49232628 AATTCAAAGTTATTT
1 AATTCAAAGTTATTT
49232643 AATTCAAAGTTATTT
1 AATTCAAAGTTATTT
49232658 AATT
1 AATT
49232662 TACGTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (15 bp):
AATTCAAAGTTATTT
Found at i:49233068 original size:66 final size:66
Alignment explanation
Indices: 49232962--49233114 Score: 297
Period size: 66 Copynumber: 2.3 Consensus size: 66
49232952 GACACTTTTT
*
49232962 TAACTTTTATAATATTAAGATAAAATTTCTAACCACACATCAATTTCTAATTACATAAAATTAAG
1 TAACTTATATAATATTAAGATAAAATTTCTAACCACACATCAATTTCTAATTACATAAAATTAAG
49233027 A
66 A
49233028 TAACTTATATAATATTAAGATAAAATTTCTAACCACACATCAATTTCTAATTACATAAAATTAAG
1 TAACTTATATAATATTAAGATAAAATTTCTAACCACACATCAATTTCTAATTACATAAAATTAAG
49233093 A
66 A
49233094 TAACTTATATAATATTAAGAT
1 TAACTTATATAATATTAAGAT
49233115 TACTTATATA
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 86 1.00
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.37
Consensus pattern (66 bp):
TAACTTATATAATATTAAGATAAAATTTCTAACCACACATCAATTTCTAATTACATAAAATTAAG
A
Found at i:49233110 original size:20 final size:20
Alignment explanation
Indices: 49233082--49233192 Score: 115
Period size: 20 Copynumber: 5.8 Consensus size: 20
49233072 TTCTAATTAC
*
49233082 ATAAAATTAAGATAACTTAT
1 ATAATATTAAGATAACTTAT
*
49233102 ATAATATTAAGATTACTTAT
1 ATAATATTAAGATAACTTAT
* *
49233122 ATAGTATTAAGACAA-TT-T
1 ATAATATTAAGATAACTTAT
* *
49233140 CT-AT-TT-ACATAACTTAT
1 ATAATATTAAGATAACTTAT
49233157 ATAATTATTAAGATAACTTAT
1 ATAA-TATTAAGATAACTTAT
*
49233178 ATAATATTAATATAA
1 ATAATATTAAGATAA
49233193 AATTTCTAAC
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
15 4 0.05
16 4 0.05
17 3 0.04
18 3 0.04
19 3 0.04
20 42 0.58
21 14 0.19
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (20 bp):
ATAATATTAAGATAACTTAT
Found at i:49233165 original size:21 final size:21
Alignment explanation
Indices: 49233141--49233192 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
49233131 AGACAATTTC
*
49233141 TATTTACATAACTTATATAAT
1 TATTAACATAACTTATATAAT
*
49233162 TATTAAGATAACTTATATAA-
1 TATTAACATAACTTATATAAT
*
49233182 TATTAATATAA
1 TATTAACATAA
49233193 AATTTCTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (21 bp):
TATTAACATAACTTATATAAT
Found at i:49233205 original size:55 final size:53
Alignment explanation
Indices: 49233093--49233210 Score: 148
Period size: 55 Copynumber: 2.2 Consensus size: 53
49233083 TAAAATTAAG
* * *
49233093 ATAACTTATATAATATTAAGATTACTTATATAGTATTAAGACAATTTCTATTTAC
1 ATAACTTATATAATATTAAGATAACTTATATAATATTAAGAAAATTTCTA--TAC
*
49233148 ATAACTTATATAATTATTAAGATAACTTATATAATATTAATATAAAATTTCTA-AC
1 ATAACTTATATAA-TATTAAGATAACTTATATAATATT-A-AGAAAATTTCTATAC
49233203 ATAACTTA
1 ATAACTTA
49233211 CATAGGTTAC
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
55 23 0.41
56 22 0.39
57 1 0.02
58 10 0.18
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (53 bp):
ATAACTTATATAATATTAAGATAACTTATATAATATTAAGAAAATTTCTATAC
Found at i:49233253 original size:25 final size:25
Alignment explanation
Indices: 49233225--49233278 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
49233215 GGTTACATTC
*
49233225 TACACAACTTACATAAC-ATACATAA
1 TACACAACTGACATAACTA-ACATAA
* *
49233250 TACATAACTGGCATAACTAACATAA
1 TACACAACTGACATAACTAACATAA
49233275 TACA
1 TACA
49233279 TAGCTTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.50, C:0.22, G:0.04, T:0.24
Consensus pattern (25 bp):
TACACAACTGACATAACTAACATAA
Found at i:49233379 original size:9 final size:9
Alignment explanation
Indices: 49233367--49233447 Score: 50
Period size: 9 Copynumber: 9.7 Consensus size: 9
49233357 CATACATAAT
*
49233367 ACATAACTG
1 ACATAACTA
49233376 ACATAACTA
1 ACATAACTA
49233385 ACATAA-T-
1 ACATAACTA
* *
49233392 ACATAGCTT
1 ACATAACTA
49233401 ACATAA-T-
1 ACATAACTA
* *
49233408 ACACAACTT
1 ACATAACTA
*
49233417 ACATAGC-A
1 ACATAACTA
49233425 TACATAA-TA
1 -ACATAACTA
49233434 A-ATAACTA
1 ACATAACTA
49233442 ACATAA
1 ACATAA
49233448 AATACAACTT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
7 14 0.25
8 8 0.14
9 34 0.61
ACGTcount: A:0.52, C:0.20, G:0.04, T:0.25
Consensus pattern (9 bp):
ACATAACTA
Found at i:49233379 original size:16 final size:16
Alignment explanation
Indices: 49233358--49233488 Score: 83
Period size: 16 Copynumber: 8.1 Consensus size: 16
49233348 CTTACATGGC
49233358 ATACATAA--TACATA
1 ATACATAACTTACATA
*
49233372 ACTGACATAACTAACATA
1 A-T-ACATAACTTACATA
*
49233390 ATACATAGCTTACATA
1 ATACATAACTTACATA
*
49233406 ATACACAACTTACATA
1 ATACATAACTTACATA
*
49233422 GCATACATAA--TAAATA
1 --ATACATAACTTACATA
**
49233438 ACTAACATAAAATACA-A
1 A-T-ACATAACTTACATA
* *
49233455 CTTACATAGCTTACATA
1 -ATACATAACTTACATA
*
49233472 ATACGTAACTTACATA
1 ATACATAACTTACATA
49233488 A
1 A
49233489 CTTATATAAT
Statistics
Matches: 90, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
14 2 0.02
15 2 0.02
16 66 0.73
17 4 0.04
18 16 0.18
ACGTcount: A:0.50, C:0.19, G:0.04, T:0.27
Consensus pattern (16 bp):
ATACATAACTTACATA
Found at i:49233411 original size:66 final size:66
Alignment explanation
Indices: 49233310--49233504 Score: 214
Period size: 66 Copynumber: 2.9 Consensus size: 66
49233300 TAACTTATAT
* * ** *
49233310 ATAACTCACATAACTTACATAGTTTACATTCTACACAACTTACATGGCATACATAATACATAACT
1 ATAACTAACATAA--TACATAGCTTACATAATACACAACTTACATAGCATACATAATACATAACT
*
49233375 GAC
64 AAC
*
49233378 ATAACTAACATAATACATAGCTTACATAATACACAACTTACATAGCATACATAATAAATAACTAA
1 ATAACTAACATAATACATAGCTTACATAATACACAACTTACATAGCATACATAATACATAACTAA
49233443 C
66 C
* * ** * * *
49233444 ATAA-AATACA-ACTTACATAGCTTACATAATACGTAACTTACATAACTTATATAATACATAA
1 ATAACTA-ACATA-ATACATAGCTTACATAATACACAACTTACATAGCATACATAATACATAA
49233505 ATTTCCAGGC
Statistics
Matches: 110, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 96 0.87
68 12 0.11
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (66 bp):
ATAACTAACATAATACATAGCTTACATAATACACAACTTACATAGCATACATAATACATAACTAA
C
Found at i:49233430 original size:41 final size:40
Alignment explanation
Indices: 49233359--49233488 Score: 152
Period size: 41 Copynumber: 3.2 Consensus size: 40
49233349 TTACATGGCA
* * * *
49233359 TACATAATACATAACTGACATAACTAACATAATACATAGCT
1 TACATAATACACAACTTACATAGCT-ACATAATACATAACT
*
49233400 TACATAATACACAACTTACATAGCATACATAATAAATAACT
1 TACATAATACACAACTTACATAGC-TACATAATACATAACT
* * * *
49233441 AACATAAAATACAACTTACATAGCTTACATAATACGTAACT
1 TACATAATACACAACTTACATAGC-TACATAATACATAACT
49233482 TACATAA
1 TACATAA
49233489 CTTATATAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
41 75 0.99
42 1 0.01
ACGTcount: A:0.50, C:0.19, G:0.04, T:0.27
Consensus pattern (40 bp):
TACATAATACACAACTTACATAGCTACATAATACATAACT
Found at i:49233440 original size:25 final size:25
Alignment explanation
Indices: 49233391--49233446 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
49233381 ACTAACATAA
* *
49233391 TACATAGCTTACATAATACACAACT
1 TACATAGCATACATAATAAACAACT
*
49233416 TACATAGCATACATAATAAATAACT
1 TACATAGCATACATAATAAACAACT
*
49233441 AACATA
1 TACATA
49233447 AAATACAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.50, C:0.20, G:0.04, T:0.27
Consensus pattern (25 bp):
TACATAGCATACATAATAAACAACT
Found at i:49233452 original size:25 final size:25
Alignment explanation
Indices: 49233400--49233453 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
49233390 ATACATAGCT
* * **
49233400 TACATAATACACAACTTACATAGCA
1 TACATAATAAACAACTAACATAAAA
*
49233425 TACATAATAAATAACTAACATAAAA
1 TACATAATAAACAACTAACATAAAA
49233450 TACA
1 TACA
49233454 ACTTACATAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.56, C:0.19, G:0.02, T:0.24
Consensus pattern (25 bp):
TACATAATAAACAACTAACATAAAA
Found at i:49233470 original size:25 final size:26
Alignment explanation
Indices: 49233435--49233497 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
49233425 TACATAATAA
*
49233435 ATAACTAACATAAAATAC-AACTTAC
1 ATAACTTACATAAAATACGAACTTAC
*
49233460 ATAGCTTACAT--AATACGTAACTTAC
1 ATAACTTACATAAAATACG-AACTTAC
*
49233485 ATAACTTATATAA
1 ATAACTTACATAA
49233498 TACATAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
23 5 0.17
25 25 0.83
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.30
Consensus pattern (26 bp):
ATAACTTACATAAAATACGAACTTAC
Found at i:49233498 original size:25 final size:25
Alignment explanation
Indices: 49233453--49233500 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
49233443 CATAAAATAC
*
49233453 AACTTACATAGCTTACATAATACGT
1 AACTTACATAACTTACATAATACGT
*
49233478 AACTTACATAACTTATATAATAC
1 AACTTACATAACTTACATAATAC
49233501 ATAAATTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACGT
Found at i:49238990 original size:66 final size:66
Alignment explanation
Indices: 49238884--49239046 Score: 193
Period size: 66 Copynumber: 2.5 Consensus size: 66
49238874 CAAATTACAC
* ** * **
49238884 AACTTAAAGCGGAGGCAGCATTGAGAAAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCGGCT
1 AACTTAAAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAACT
49238948 AA
65 AA
* * *
49238950 AACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAACTG
1 AACTTAAAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAACTA
*
49239015 T
66 A
* * *
49239016 AGCTTAAAGCAGAGGCTGCAGCGAGGGAAGC
1 AACTTAAAGCAGAGGCAGCAGCGAGAGAAGC
49239047 AGAGCAGCGT
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
66 78 0.95
67 4 0.05
ACGTcount: A:0.39, C:0.17, G:0.28, T:0.15
Consensus pattern (66 bp):
AACTTAAAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAACTA
A
Found at i:49239502 original size:43 final size:43
Alignment explanation
Indices: 49239387--49239590 Score: 232
Period size: 43 Copynumber: 4.7 Consensus size: 43
49239377 CATTTTTAAA
* * *
49239387 AAAAACGCCACTAAAGGTCATGGTC-TTATGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTA-GCGGCGTTTGTCGG
* * * * **
49239430 AAAAGCGCCGCTAAA-GACCTGGGTGTTTAGCAGCGTTTGTTTG
1 AAAAGCGCCGCTAAAGGTCAT-GGTCTTTAGCGGCGTTTGTCGG
* *
49239473 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGTGTTTGTCAG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGG
* *
49239516 ATAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCATTTGTCGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGG
* **
49239559 GAAAGCGCAACTAAAGGTCATGGTCTTTAGCG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCG
49239591 ATGTTTTTTT
Statistics
Matches: 135, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
42 3 0.02
43 126 0.93
44 6 0.04
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGG
Found at i:49243184 original size:19 final size:19
Alignment explanation
Indices: 49243160--49243201 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
49243150 ATAGAATACG
49243160 ACATAACA-ATAATATATAA
1 ACATAACAGA-AATATATAA
*
49243179 ACATAACAGAGATATATAA
1 ACATAACAGAAATATATAA
49243198 ACAT
1 ACAT
49243202 GTAAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.24
Consensus pattern (19 bp):
ACATAACAGAAATATATAA
Found at i:49243941 original size:28 final size:28
Alignment explanation
Indices: 49243909--49243966 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
49243899 ATTCTCAATC
* *
49243909 TTCAATCCCCATTTTTC-AATTTTATATT
1 TTCAATCCCCAATCTTCAAATTTTA-ATT
*
49243937 TTCAATCTCCAATCTTCAAATTTTAATT
1 TTCAATCCCCAATCTTCAAATTTTAATT
49243965 TT
1 TT
49243967 TAATATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.28, C:0.21, G:0.00, T:0.52
Consensus pattern (28 bp):
TTCAATCCCCAATCTTCAAATTTTAATT
Found at i:49244532 original size:26 final size:26
Alignment explanation
Indices: 49244484--49244533 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
49244474 ATCGCACGTG
* *
49244484 TTTAATTTTTAATTTTGTGTTGTTGA
1 TTTAATTTTTAATTTTATATTGTTGA
49244510 TTTAATTATTTAA-TTTATATTGTT
1 TTTAATT-TTTAATTTTATATTGTT
49244534 TCATGACTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (26 bp):
TTTAATTTTTAATTTTATATTGTTGA
Found at i:49245002 original size:21 final size:21
Alignment explanation
Indices: 49244974--49245028 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
49244964 AACAGCGGTG
*
49244974 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
* * *
49244995 GTGGTGAGATTGGGTGCTGTA
1 GCGGTGAGATTAGGTACTGTA
*
49245016 GCAGTGAGATTAG
1 GCGGTGAGATTAG
49245029 AAACAACGGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.07, G:0.40, T:0.31
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:49249038 original size:23 final size:23
Alignment explanation
Indices: 49249007--49249070 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 23
49248997 CATAAGCACT
49249007 AAACTAAAT-AACTTAATTCAACTC
1 AAAC-AAATAAAC-TAATTCAACTC
49249031 AAACAAATAAACTAATTCAACTC
1 AAACAAATAAACTAATTCAACTC
*
49249054 -AACAAACTAATCTAATT
1 AAACAAA-TAAACTAATT
49249071 AGCCCGTACA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 6 0.16
23 24 0.65
24 7 0.19
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (23 bp):
AAACAAATAAACTAATTCAACTC
Found at i:49252951 original size:16 final size:14
Alignment explanation
Indices: 49252918--49252949 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
49252908 TAATCAAAAC
49252918 TATACTAGAATATA
1 TATACTAGAATATA
49252932 TATACTAGAATATA
1 TATACTAGAATATA
49252946 TATA
1 TATA
49252950 TATAACCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (14 bp):
TATACTAGAATATA
Found at i:49253825 original size:31 final size:31
Alignment explanation
Indices: 49253761--49253826 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
49253751 TTTTAAGAAT
* ** *
49253761 GCCATACGGCCACAGTCTGTCACACGGCTTA
1 GCCATACGGCCACAATCTGTCACACAACCTA
* *
49253792 GCCATACTGCCACAATCTGTCACATAACCTA
1 GCCATACGGCCACAATCTGTCACACAACCTA
49253823 GCCA
1 GCCA
49253827 CACAGTCGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.36, G:0.17, T:0.20
Consensus pattern (31 bp):
GCCATACGGCCACAATCTGTCACACAACCTA
Found at i:49267018 original size:17 final size:17
Alignment explanation
Indices: 49266976--49267020 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
49266966 TTTCCTTTCC
49266976 TCTCTCTTTATCTCTTCT
1 TCTCTCTTT-TCTCTTCT
*
49266994 TCTTTCTTTTCTC-TCT
1 TCTCTCTTTTCTCTTCT
49267010 TCTCCTCTTTT
1 TCT-CTCTTTT
49267021 TATAACTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.25
17 10 0.42
18 8 0.33
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.64
Consensus pattern (17 bp):
TCTCTCTTTTCTCTTCT
Found at i:49268867 original size:63 final size:63
Alignment explanation
Indices: 49268719--49268873 Score: 150
Period size: 63 Copynumber: 2.5 Consensus size: 63
49268709 AAACACATGG
* * * * * * *
49268719 GCATGTGTCTAAGCCGTGTAACTCACTGACTTCGTATTAGAGTCACATAGGCATGACACACGT
1 GCATATGTCCAAGCCATATAACTCACTGACTTCGTATTAGAGTCACAGAGGCAAGACACACGA
* * * * * * *
49268782 GCATGTTTCCAGGCCGTGTAACTCACTGGCTTCGTATTATAGTCACACGA-GCAAGACACACGA
1 GCATATGTCCAAGCCATATAACTCACTGACTTCGTATTAGAGTCACA-GAGGCAAGACACACGA
* *
49268845 GCGTATGTCCAAGCCATATAACTAACTGA
1 GCATATGTCCAAGCCATATAACTCACTGA
49268874 TTTTAGATTT
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
63 74 0.99
64 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (63 bp):
GCATATGTCCAAGCCATATAACTCACTGACTTCGTATTAGAGTCACAGAGGCAAGACACACGA
Found at i:49275866 original size:20 final size:20
Alignment explanation
Indices: 49275841--49275878 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
49275831 CGTGCTCATA
*
49275841 AACAATTGGGTCAATGACTT
1 AACAATTGAGTCAATGACTT
*
49275861 AACAATTGAGTCCATGAC
1 AACAATTGAGTCAATGAC
49275879 CTAAAAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (20 bp):
AACAATTGAGTCAATGACTT
Found at i:49275913 original size:29 final size:29
Alignment explanation
Indices: 49275880--49275937 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
49275870 GTCCATGACC
* *
49275880 TAAAAATGAACAACATACCTGCGTGCTCA
1 TAAAAATGAACAACATACCTACATGCTCA
49275909 TAAAAATGAACAACATACCTACATGCTCA
1 TAAAAATGAACAACATACCTACATGCTCA
49275938 ACAGTCGCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.21
Consensus pattern (29 bp):
TAAAAATGAACAACATACCTACATGCTCA
Found at i:49276534 original size:25 final size:25
Alignment explanation
Indices: 49276506--49276559 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
49276496 TGTAGTGGCA
*
49276506 AGGTGGCGACACAGGTGTGGCAAGG
1 AGGTGGCGACACAGGTGTGGCAAAG
* *
49276531 AGGTGGCGTCACAGGTGTGGTAAAG
1 AGGTGGCGACACAGGTGTGGCAAAG
49276556 AGGT
1 AGGT
49276560 CAGAGGTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.13, G:0.46, T:0.17
Consensus pattern (25 bp):
AGGTGGCGACACAGGTGTGGCAAAG
Done.