Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 135 of 198
Found at i:43109867 original size:15 final size:15
Alignment explanation
Indices: 43109832--43109873 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
43109822 TTAAGAATTT
*
43109832 TATTAAATTAT-ATA
1 TATTTAATTATAATA
43109846 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
43109860 TATTTAATAATAAT
1 TATTTAATTATAAT
43109874 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:43110013 original size:18 final size:17
Alignment explanation
Indices: 43109985--43110019 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43109975 ATTATTAAGA
*
43109985 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
43110002 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
43110020 TTAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:43110102 original size:157 final size:157
Alignment explanation
Indices: 43109816--43110132 Score: 580
Period size: 157 Copynumber: 2.0 Consensus size: 157
43109806 ATAAGAATAT
* *
43109816 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAAAAATAATTATGTTT
*
43109881 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
* *
43109946 TAATAATTTACCAAAGCAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
43109973 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAAAAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAAAAATAATTATGTTT
43110038 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
43110103 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
43110130 TAA
1 TAA
43110133 GGGTATTCTA
Statistics
Matches: 154, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 154 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAAAAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:43110279 original size:16 final size:16
Alignment explanation
Indices: 43110255--43110306 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
43110245 GATTTGCTAT
*
43110255 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
43110271 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
43110287 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
43110303 TACA
1 TACA
43110307 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:43111690 original size:19 final size:18
Alignment explanation
Indices: 43111663--43111703 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
43111653 ACTAAAGGTG
43111663 TTTTCTTTTTTTATATTTA
1 TTTTC-TTTTTTATATTTA
*
43111682 TTTTGTTTTTTATATTTA
1 TTTTCTTTTTTATATTTA
43111700 TTTT
1 TTTT
43111704 TATTTCGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTTTATATTTA
Found at i:43111692 original size:18 final size:18
Alignment explanation
Indices: 43111669--43111703 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
43111659 GGTGTTTTCT
43111669 TTTTTTATATTTATTTTG
1 TTTTTTATATTTATTTTG
43111687 TTTTTTATATTTATTTT
1 TTTTTTATATTTATTTT
43111704 TATTTCGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTTTTATATTTATTTTG
Found at i:43113274 original size:73 final size:74
Alignment explanation
Indices: 43113170--43113308 Score: 226
Period size: 73 Copynumber: 1.9 Consensus size: 74
43113160 CAAACTTAAA
* * *
43113170 TTTTAAACGATCTCGGGAATTAAGAAGAGATCGTGTCCTAACTTACTGGGCATAAT-CCCTTTTT
1 TTTTAAACGATCTCGGGAATTAAGAAAAGATCATGTCCTAACTCACTGGGCATAATCCCCTTTTT
43113234 TCCTCAAAT
66 TCCTCAAAT
* *
43113243 TTTTAAACGATCTCGGGAATTAAGAAAAGATCATGTCCTAACTCATTGGGCATGATCCCCTTTTT
1 TTTTAAACGATCTCGGGAATTAAGAAAAGATCATGTCCTAACTCACTGGGCATAATCCCCTTTTT
43113308 T
66 T
43113309 TAAAAAATCT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
73 51 0.85
74 9 0.15
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Consensus pattern (74 bp):
TTTTAAACGATCTCGGGAATTAAGAAAAGATCATGTCCTAACTCACTGGGCATAATCCCCTTTTT
TCCTCAAAT
Found at i:43115954 original size:23 final size:23
Alignment explanation
Indices: 43115928--43115971 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
43115918 ACATTTCACG
*
43115928 AACATGTATGCGAACGTTAAACA
1 AACATGTATGCGAACGCTAAACA
* *
43115951 AACATGTTTGTGAACGCTAAA
1 AACATGTATGCGAACGCTAAA
43115972 TGAATCGAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (23 bp):
AACATGTATGCGAACGCTAAACA
Found at i:43119464 original size:89 final size:89
Alignment explanation
Indices: 43119289--43119788 Score: 344
Period size: 90 Copynumber: 5.6 Consensus size: 89
43119279 TCAAAATAAT
*
43119289 TGTATT-ATTTCTTTAGAATGTTTGTA-TTTTTTATATCTGTAAATTTAATGTAGT-CGT-TTAG
1 TGTATTAATTTC-TTAGAATGTTTGTATTTTTTTATATCTGTAAATTTAATTTAGTCCGTATTA-
** * * * *
43119350 GGTTTAAGGTTT-CATTATTATATTTTCG
64 TATGT-A-GTTTGAATT-TAAAATTTTCG
*
43119378 TGTATTAATTTCTTAGAATGTTTGTATTTTTTTATATCTGTAAATTTAATTTAATCCGTATTATA
1 TGTATTAATTTCTTAGAATGTTTGTATTTTTTTATATCTGTAAATTTAATTTAGTCCGTATTATA
*
43119443 TGTAGTTTGAATTGAAAATTTTCG
66 TGTAGTTTGAATTTAAAATTTTCG
* ** * * *
43119467 TGTATTAATTTTACTCA-TCTGTTTGTAGTTTGTTGAGTGT-T-TAAATTTAATTTAG-CCTGTA
1 TGTATTAA-TTT-CTTAGAATGTTTGTA-TTTTTTTA-TATCTGTAAATTTAATTTAGTCC-GTA
* *
43119528 TTATATATAGTTTGACTTTAAAATTTTCG
61 TTATATGTAGTTTGAATTTAAAATTTTCG
* * * * * * *** * * *
43119557 TGCATTAA-TT-TTACCCATCTGTTTTTAGTTTCTTGGGTGTTTAAATTTAATTTAGCCCGTATT
1 TGTATTAATTTCTTA--GA-ATGTTTGTATTTTTTTATATCTGTAAATTTAATTTAGTCCGTATT
43119620 ATATGTAGTTTGAATTTAAAATTTTCG
63 ATATGTAGTTTGAATTTAAAATTTTCG
* * * * *** * * *
43119647 TGTATTAA-TT-TTACCCATCTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTAGTCCGTGTT
1 TGTATTAATTTCTTA--GA-ATGTTTGTATTTTTTTATATCTGTAAATTTAATTTAGTCCGTATT
* * * * *
43119710 ATTTGTTGTTTGAATTTTATATTTTTG
63 ATATGTAGTTTGAATTTAAAATTTTCG
*
43119737 TGTATTAATATTC-TAGAATGTTTGTATTTTATTATATCTGTAAATTTAATTT
1 TGTATTAAT-TTCTTAGAATGTTTGTATTTTTTTATATCTGTAAATTTAATTT
43119789 GTTGTGTACT
Statistics
Matches: 341, Mismatches: 50, Indels: 40
0.79 0.12 0.09
Matches are distributed among these distances:
86 2 0.01
88 4 0.01
89 73 0.21
90 236 0.69
91 17 0.05
92 9 0.03
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (89 bp):
TGTATTAATTTCTTAGAATGTTTGTATTTTTTTATATCTGTAAATTTAATTTAGTCCGTATTATA
TGTAGTTTGAATTTAAAATTTTCG
Found at i:43119512 original size:90 final size:90
Alignment explanation
Indices: 43119418--43119745 Score: 478
Period size: 90 Copynumber: 3.6 Consensus size: 90
43119408 TTTATATCTG
* *
43119418 TAAATTTAATTTAATCCGTATTATATGTAGTTTGAATTGAAAATTTTCGTGTATTAATTTTACTC
1 TAAATTTAATTTAATCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCC
*
43119483 ATCTGTTTGTAGTTTGTTGAGTGTT
66 ATCTGTTTGTAGTTTGTTGGGTGTT
* * * *
43119508 TAAATTTAATTT-AGCCTGTATTATATATAGTTTGACTTTAAAATTTTCGTGCATTAATTTTACC
1 TAAATTTAATTTAATCC-GTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACC
* *
43119572 CATCTGTTTTTAGTTTCTTGGGTGTT
65 CATCTGTTTGTAGTTTGTTGGGTGTT
**
43119598 TAAATTTAATTTAGCCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCC
1 TAAATTTAATTTAATCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCC
43119663 ATCTGTTTGTAGTTTGTTGGGTGTT
66 ATCTGTTTGTAGTTTGTTGGGTGTT
* * * * * * *
43119688 TAAATTTAATTTAGTCCGTGTTATTTGTTGTTTGAATTTTATATTTTTGTGTATTAAT
1 TAAATTTAATTTAATCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAAT
43119746 ATTCTAGAAT
Statistics
Matches: 213, Mismatches: 23, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
89 3 0.01
90 208 0.98
91 2 0.01
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.52
Consensus pattern (90 bp):
TAAATTTAATTTAATCCGTATTATATGTAGTTTGAATTTAAAATTTTCGTGTATTAATTTTACCC
ATCTGTTTGTAGTTTGTTGGGTGTT
Found at i:43122437 original size:6 final size:5
Alignment explanation
Indices: 43122420--43122515 Score: 111
Period size: 6 Copynumber: 17.6 Consensus size: 5
43122410 TAATTTTTTT
43122420 TTTCA TTTCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCA TTTCA TTTCA
1 TTTCA TTTCA TTT-CA TTT-CA TTT-CA TTT-CA TTTCA TTTCA TTTCA
*
43122469 TTTCA TTTCA TTTACA TTTACA TTTACA TTTAAA TTTCA TTTCA TTT
1 TTTCA TTTCA TTT-CA TTT-CA TTT-CA TTT-CA TTTCA TTTCA TTT
43122516 AAATTTTATT
Statistics
Matches: 87, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
5 42 0.48
6 45 0.52
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56
Consensus pattern (5 bp):
TTTCA
Found at i:43122487 original size:49 final size:49
Alignment explanation
Indices: 43122420--43122515 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 49
43122410 TAATTTTTTT
* * * **
43122420 TTTCATTTCATTTCCATTTCCATTTCCATTTCCATTTCATTTCATTTCA
1 TTTCATTTCATTTACATTTACATTTACATTTAAATTTCATTTCATTTCA
43122469 TTTCATTTCATTTACATTTACATTTACATTTAAATTTCATTTCATTT
1 TTTCATTTCATTTACATTTACATTTACATTTAAATTTCATTTCATTT
43122516 AAATTTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56
Consensus pattern (49 bp):
TTTCATTTCATTTACATTTACATTTACATTTAAATTTCATTTCATTTCA
Found at i:43122555 original size:21 final size:21
Alignment explanation
Indices: 43122510--43122567 Score: 93
Period size: 20 Copynumber: 2.9 Consensus size: 21
43122500 AAATTTCATT
*
43122510 TCATTTAAATTTTATTTTTTC
1 TCATTTCAATTTTATTTTTTC
43122531 -CATTTCAATTTTATTTTTTC
1 TCATTTCAATTTTATTTTTTC
43122551 TCATTTCAATTTT-TTTT
1 TCATTTCAATTTTATTTT
43122568 CACATTAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 23 0.66
21 12 0.34
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (21 bp):
TCATTTCAATTTTATTTTTTC
Found at i:43122651 original size:17 final size:17
Alignment explanation
Indices: 43122621--43122674 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
43122611 CAGTTTTTGT
43122621 TTTCATTTCAATTTATAA
1 TTTCATTTC-ATTTATAA
43122639 TTT-ATTTTCATTTA-AA
1 TTTCA-TTTCATTTATAA
43122655 CTTTCATTTCATTTCATAA
1 -TTTCATTTCATTT-ATAA
43122674 T
1 T
43122675 CATTACAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.06
17 17 0.55
18 10 0.32
19 2 0.06
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTCATTTCATTTATAA
Found at i:43123030 original size:12 final size:11
Alignment explanation
Indices: 43123011--43123092 Score: 74
Period size: 12 Copynumber: 6.9 Consensus size: 11
43123001 ATTTTTCTTT
43123011 TTTCATTTCAA
1 TTTCATTTCAA
43123022 TTTCAATTTTCAA
1 TTTC-A-TTTCAA
43123035 TTTTCATTTCTAA
1 -TTTCATTTC-AA
* *
43123048 ATTCATTTCAT
1 TTTCATTTCAA
*
43123059 TTTCATTTCTCA
1 TTTCATTTC-AA
43123071 TTTCATTTCACA
1 TTTCATTTCA-A
*
43123083 TTGCATTTCA
1 TTTCATTTCA
43123093 TCTAAATTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
11 13 0.22
12 32 0.55
13 9 0.16
14 4 0.07
ACGTcount: A:0.24, C:0.20, G:0.01, T:0.55
Consensus pattern (11 bp):
TTTCATTTCAA
Found at i:43123031 original size:18 final size:17
Alignment explanation
Indices: 43123010--43123093 Score: 66
Period size: 18 Copynumber: 4.7 Consensus size: 17
43123000 AATTTTTCTT
43123010 TTTTCATTTCAATTTCAA
1 TTTTCATTTC-ATTTCAA
43123028 TTTTCAATTTTCATTTCTAA
1 TTTTC-A-TTTCATTTC-AA
*
43123048 -ATTCATTTCATTTTC-A
1 TTTTCATTTCA-TTTCAA
43123064 TTTCTCATTTCATTTCACA
1 TTT-TCATTTCATTTCA-A
*
43123083 -TTGCATTTCAT
1 TTTTCATTTCAT
43123094 CTAAATTTGT
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
16 1 0.02
17 18 0.33
18 20 0.36
19 10 0.18
20 6 0.11
ACGTcount: A:0.24, C:0.19, G:0.01, T:0.56
Consensus pattern (17 bp):
TTTTCATTTCATTTCAA
Found at i:43123132 original size:21 final size:21
Alignment explanation
Indices: 43123088--43123145 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
43123078 TCACATTGCA
* * **
43123088 TTTCATCTAAATTTGTTTTTT
1 TTTCATTTAAATTTATTTCAT
43123109 TTTCATTTAAATTTATTTCAT
1 TTTCATTTAAATTTATTTCAT
*
43123130 TTTCCATTTTAATTTA
1 TTT-CATTTAAATTTA
43123146 CGTTTTTTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTCATTTAAATTTATTTCAT
Found at i:43123154 original size:22 final size:19
Alignment explanation
Indices: 43123105--43123209 Score: 61
Period size: 22 Copynumber: 5.2 Consensus size: 19
43123095 TAAATTTGTT
*
43123105 TTTTTTTCATTTAAATTTA
1 TTTTTTTCATTTTAATTTA
43123124 TTTCATTTTCCATTTTAATTTA
1 TTT--TTTT-CATTTTAATTTA
*
43123146 CGTTTTTTTCATATTAATTT-
1 --TTTTTTTCATTTTAATTTA
* * *
43123166 TTGTCTT-ATTGTAATTTA
1 TTTTTTTCATTTTAATTTA
* *
43123184 TTTCATTTCAATTTATACTTTA
1 TTT-TTTTC-ATTT-TAATTTA
43123206 TTTT
1 TTTT
43123210 CATTTCATAT
Statistics
Matches: 64, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
17 8 0.12
18 7 0.11
19 5 0.08
21 17 0.27
22 24 0.38
24 3 0.05
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTTTTCATTTTAATTTA
Found at i:43123222 original size:11 final size:11
Alignment explanation
Indices: 43123208--43123285 Score: 50
Period size: 11 Copynumber: 6.8 Consensus size: 11
43123198 ATACTTTATT
43123208 TTCATTTCATA
1 TTCATTTCATA
*
43123219 TTCATTTAATA
1 TTCATTTCATA
* *
43123230 TTTTAGTTTCATT
1 -TTCA-TTTCATA
* *
43123243 TTAAATTCAT-
1 TTCATTTCATA
* *
43123253 TTCATATTTTATT
1 TTC--ATTTCATA
43123266 TTCATTTCATA
1 TTCATTTCATA
43123277 TTCATTTCA
1 TTCATTTCA
43123286 CTTTATTCAC
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
10 2 0.04
11 30 0.59
12 11 0.22
13 8 0.16
ACGTcount: A:0.27, C:0.13, G:0.01, T:0.59
Consensus pattern (11 bp):
TTCATTTCATA
Found at i:43123261 original size:18 final size:18
Alignment explanation
Indices: 43123240--43123278 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
43123230 TTTTAGTTTC
43123240 ATTTTAAATTCATTTCAT
1 ATTTTAAATTCATTTCAT
**
43123258 ATTTTATTTTCATTTCAT
1 ATTTTAAATTCATTTCAT
43123276 ATT
1 ATT
43123279 CATTTCACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTAAATTCATTTCAT
Found at i:43123284 original size:29 final size:29
Alignment explanation
Indices: 43123183--43123285 Score: 138
Period size: 29 Copynumber: 3.6 Consensus size: 29
43123173 ATTGTAATTT
*
43123183 ATTTCAT-TTCAATTT-ATACTTTATTTTC
1 ATTTCATATTC-ATTTCATATTTTATTTTC
* *
43123211 ATTTCATATTCATTTAATATTTTAGTTTC
1 ATTTCATATTCATTTCATATTTTATTTTC
* *
43123240 ATTTTAAATTCATTTCATATTTTATTTTC
1 ATTTCATATTCATTTCATATTTTATTTTC
43123269 ATTTCATATTCATTTCA
1 ATTTCATATTCATTTCA
43123286 CTTTATTCAC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
28 11 0.17
29 54 0.83
ACGTcount: A:0.27, C:0.13, G:0.01, T:0.59
Consensus pattern (29 bp):
ATTTCATATTCATTTCATATTTTATTTTC
Found at i:43123724 original size:22 final size:21
Alignment explanation
Indices: 43123661--43123724 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 21
43123651 GCATTAATAT
43123661 ATTTAATGTGTTTTAAATTAA
1 ATTTAATGTGTTTTAAATTAA
** * * **
43123682 ATATGCATGTATATTGTATTATA
1 AT-TTAATGTGTTTTAAATTA-A
43123705 ATTTAATGTGTTTTAAATTA
1 ATTTAATGTGTTTTAAATTA
43123725 GGAATAAGAA
Statistics
Matches: 29, Mismatches: 12, Indels: 3
0.66 0.27 0.07
Matches are distributed among these distances:
21 2 0.07
22 24 0.83
23 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.52
Consensus pattern (21 bp):
ATTTAATGTGTTTTAAATTAA
Found at i:43127318 original size:45 final size:45
Alignment explanation
Indices: 43127254--43127432 Score: 204
Period size: 45 Copynumber: 4.0 Consensus size: 45
43127244 TATGTGTACC
* * * *
43127254 GGGTACCATTGGTTATAAAGGTGGTTGTTGTGTGCTGATTCCACT
1 GGGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACT
* * * *
43127299 GGGTATCATTGATTATAAAGGTAGTTGTTGTGTGCTGATTCCAAT
1 GGGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACT
*
43127344 GGGTA-CTATTGATTATGAAGGTGGTTGCTATGTGCTGATTCCA-T
1 GGGTATC-ATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACT
* * *
43127388 CGAGTATCATTGACTATAAGGGTGG-TGCTATGTGCTGA-TCCACT
1 -GGGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACT
43127432 G
1 G
43127433 TATATCTGTT
Statistics
Matches: 118, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
43 5 0.04
44 16 0.14
45 96 0.81
46 1 0.01
ACGTcount: A:0.21, C:0.13, G:0.29, T:0.37
Consensus pattern (45 bp):
GGGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACT
Found at i:43129930 original size:12 final size:12
Alignment explanation
Indices: 43129896--43129924 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
43129886 ATTTTCAACT
43129896 AAAAAAGCAAAC
1 AAAAAAGCAAAC
43129908 AAAAAAGCAAAC
1 AAAAAAGCAAAC
43129920 AAAAA
1 AAAAA
43129925 TTCAAATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.79, C:0.14, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAGCAAAC
Found at i:43139981 original size:22 final size:22
Alignment explanation
Indices: 43139956--43139999 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
43139946 TTTAATATAT
43139956 TTTATCTAT-TAAATAATTTAAA
1 TTTAT-TATATAAATAATTTAAA
* *
43139978 TTTATTATATAATTTATTTAAA
1 TTTATTATATAAATAATTTAAA
43140000 ATATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTATTATATAAATAATTTAAA
Found at i:43140134 original size:21 final size:21
Alignment explanation
Indices: 43140108--43140163 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
43140098 TATTGTTTCT
*
43140108 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
43140129 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
43140150 AATCTCACCGCTAC
1 AATCTCACCGCTAC
43140164 CGCTGTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:43146641 original size:34 final size:34
Alignment explanation
Indices: 43146574--43146644 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
43146564 GCAAGATTTG
* * *
43146574 GAAAAGGAATAAAATATACTTTCCTTAAAAAAAA
1 GAAAAGGAAGAAAATATAATTTCCTAAAAAAAAA
*
43146608 GAAAAGGAAGAAAATATAATTTTC-AAAAGAAAAA
1 GAAAAGGAAGAAAATATAATTTCCTAAAA-AAAAA
43146642 GAA
1 GAA
43146645 TTATAAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 3 0.09
34 29 0.91
ACGTcount: A:0.62, C:0.06, G:0.13, T:0.20
Consensus pattern (34 bp):
GAAAAGGAAGAAAATATAATTTCCTAAAAAAAAA
Found at i:43160037 original size:24 final size:24
Alignment explanation
Indices: 43159991--43160038 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
43159981 TAGAAGATTA
*
43159991 AGTATTTATTAGTATATTATATTT
1 AGTATTTATTAGCATATTATATTT
43160015 AGTATTTATTAGCATAATT-TATTT
1 AGTATTTATTAGCAT-ATTATATTT
43160039 GACCTACGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.56
Consensus pattern (24 bp):
AGTATTTATTAGCATATTATATTT
Found at i:43162008 original size:24 final size:24
Alignment explanation
Indices: 43161964--43162009 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
43161954 TTTCTAGAAG
* *
43161964 ATTTAGTTTTTAGTTATATAATAT
1 ATTTAGTATTTAGTTACATAATAT
43161988 ATTTAGTATTTA-TTAGCATAAT
1 ATTTAGTATTTAGTTA-CATAAT
43162010 TTAGTTGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (24 bp):
ATTTAGTATTTAGTTACATAATAT
Found at i:43180399 original size:40 final size:41
Alignment explanation
Indices: 43180300--43180423 Score: 151
Period size: 40 Copynumber: 3.0 Consensus size: 41
43180290 AAATTACGTC
* * * * *
43180300 CATGGGTATTGAAGTACAAATAAGGGCACGTCTATGCAATT
1 CATGGGTATCGAAGTACAAACAGGGGCACGTATGTGCAATT
* * * *
43180341 CAAGGGTACCGATGTACAAACAGGGGTACGTATGTGCAATT
1 CATGGGTATCGAAGTACAAACAGGGGCACGTATGTGCAATT
*
43180382 -TTGGGTATCGAAGTACAAACAGGGGCACGTATGTGCAATT
1 CATGGGTATCGAAGTACAAACAGGGGCACGTATGTGCAATT
43180422 CA
1 CA
43180424 ACATATTTTT
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
40 35 0.52
41 32 0.48
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (41 bp):
CATGGGTATCGAAGTACAAACAGGGGCACGTATGTGCAATT
Found at i:43181762 original size:20 final size:21
Alignment explanation
Indices: 43181716--43181767 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
43181706 TGACGATTGC
*
43181716 TATC-AAGATTTGGGAAATAT
1 TATCAAAGATTTGGGAAAGAT
43181736 T-TGCAAAGATTT-GGAAAGAT
1 TAT-CAAAGATTTGGGAAAGAT
43181756 TATCAAAGATTT
1 TATCAAAGATTT
43181768 CTTAATCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 19 0.68
21 8 0.29
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (21 bp):
TATCAAAGATTTGGGAAAGAT
Found at i:43185239 original size:19 final size:18
Alignment explanation
Indices: 43185213--43185257 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
43185203 AAGCCACCAG
**
43185213 TACAGTATACTTTCCCCA
1 TACAGTATACTAACCCCA
*
43185231 TATCAGTATCCTAACCCCA
1 TA-CAGTATACTAACCCCA
43185250 TACAGTAT
1 TACAGTAT
43185258 GTCATGTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.31, C:0.31, G:0.07, T:0.31
Consensus pattern (18 bp):
TACAGTATACTAACCCCA
Found at i:43185405 original size:27 final size:27
Alignment explanation
Indices: 43185375--43185895 Score: 575
Period size: 27 Copynumber: 19.4 Consensus size: 27
43185365 TCATCTCCTA
** *
43185375 GGGGTATAACAGTCATTTTAACCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
43185402 GGGGTATTTCAATCATTCTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* **
43185429 AGGGTATTTTGGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
43185456 GGGGTATTTCAGTCATTTTAACCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
43185483 GGGGTATTTCAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
** *
43185510 GGGGTATTTTGGTCATTTTACCCTACG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
43185537 GGGGTATTTCAGTCATTTTACCCTACG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
43185564 AGGGTATTT-TGATTATTTTACCCTATA
1 GGGGTATTTCAG-TCATTTTACCCTATG
*
43185591 GGGGTATTTCGGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
43185618 GGAGTATTTTAGTCATTTTACCCTACG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
43185645 GGGGTATTTCAGTTATTTTACCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
43185672 GGGGTATTTC-GATTATTTTATCCTACG
1 GGGGTATTTCAG-TCATTTTACCCTATG
43185699 GGGGTATTTC-GATCA-TTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
* * *
43185725 GGGGTATTTCAATTATTTTATCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
43185752 GGGGTATTTCAGTCATTTTACTCTACG
1 GGGGTATTTCAGTCATTTTACCCTATG
** * * *
43185779 ATGGTATTTTAGTTATTTTATCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
43185806 AGGGTATTTCGGTTATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
43185833 GGGGTATTTCGGTCATTTTACCCTACG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
43185860 TGGGTATTT-TGTCATTTTATCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
43185886 GGGGTATTTC
1 GGGGTATTTC
43185896 GGGGTGTCAG
Statistics
Matches: 416, Mismatches: 72, Indels: 12
0.83 0.14 0.02
Matches are distributed among these distances:
26 44 0.11
27 371 0.89
28 1 0.00
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:43185469 original size:81 final size:81
Alignment explanation
Indices: 43185375--43185895 Score: 643
Period size: 81 Copynumber: 6.5 Consensus size: 81
43185365 TCATCTCCTA
** * * * * *
43185375 GGGGTATAACAGTCATTTTAACCTATGGGGGTATTTCAATCATTCTACCCTATGAGGGTATTTTG
1 GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCAATTATTTTACCCTATGGGGGTATTTCG
*
43185440 GTCATTTTACCCTATG
66 GTCATTTTACCCTACG
* * * *
43185456 GGGGTATTTCAGTCATTTTAACCTATGGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTTG
1 GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCAATTATTTTACCCTATGGGGGTATTTCG
43185521 GTCATTTTACCCTACG
66 GTCATTTTACCCTACG
* * ** *
43185537 GGGGTATTTCAGTCATTTTACCCTACGAGGGTATTTTGATTATTTTACCCTATAGGGGTATTTCG
1 GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCAATTATTTTACCCTATGGGGGTATTTCG
*
43185602 GTCATTTTACCCTATG
66 GTCATTTTACCCTACG
* * * * *
43185618 GGAGTATTTTAGTCATTTTACCCTACGGGGGTATTTCAGTTATTTTACCTTATGGGGGTATTTCG
1 GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCAATTATTTTACCCTATGGGGGTATTTCG
* * *
43185683 ATTATTTTATCCTACG
66 GTCATTTTACCCTACG
*
43185699 GGGGTATTTC-GATCA-TTTACCCTATGGGGGTATTTCAATTATTTTATCCTATGGGGGTATTTC
1 GGGGTATTTCAG-TCATTTTACCCTATGGGGGTATTTCAATTATTTTACCCTATGGGGGTATTTC
* *
43185762 AGTCATTTTACTCTACG
65 GGTCATTTTACCCTACG
** * * * * **
43185779 ATGGTATTTTAGTTATTTTATCCTATGAGGGTATTTCGGTTATTTTACCCTATGGGGGTATTTCG
1 GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCAATTATTTTACCCTATGGGGGTATTTCG
43185844 GTCATTTTACCCTACG
66 GTCATTTTACCCTACG
* * * *
43185860 TGGGTATTT-TGTCATTTTATCCTATAGGGGTATTTC
1 GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTC
43185896 GGGGTGTCAG
Statistics
Matches: 381, Mismatches: 56, Indels: 7
0.86 0.13 0.02
Matches are distributed among these distances:
80 89 0.23
81 292 0.77
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (81 bp):
GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCAATTATTTTACCCTATGGGGGTATTTCG
GTCATTTTACCCTACG
Found at i:43190505 original size:14 final size:14
Alignment explanation
Indices: 43190486--43190512 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43190476 CTAAGTTCAA
43190486 ATTTCTTTTCTCTC
1 ATTTCTTTTCTCTC
43190500 ATTTCTTTTCTCT
1 ATTTCTTTTCTCT
43190513 TTTTAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTCTTTTCTCTC
Found at i:43195180 original size:22 final size:21
Alignment explanation
Indices: 43195128--43195180 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
43195118 AAGTTAAAAG
*
43195128 CAAA-AAAAATAAAAAATGAT
1 CAAATAAAAATAAAAAATCAT
* *
43195148 CAAAGTCAAAATAAAAAGTCAT
1 CAAA-TAAAAATAAAAAATCAT
43195170 CCAAATAAAAA
1 -CAAATAAAAA
43195181 ATGATAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 4 0.15
22 18 0.69
23 4 0.15
ACGTcount: A:0.68, C:0.11, G:0.06, T:0.15
Consensus pattern (21 bp):
CAAATAAAAATAAAAAATCAT
Found at i:43196084 original size:7 final size:7
Alignment explanation
Indices: 43196067--43196106 Score: 55
Period size: 8 Copynumber: 5.6 Consensus size: 7
43196057 TTGAGTCAAA
43196067 AAAAATG
1 AAAAATG
43196074 -AAAATG
1 AAAAATG
43196080 AAAAATG
1 AAAAATG
43196087 AAAAAATG
1 -AAAAATG
43196095 AAAAAGTG
1 AAAAA-TG
43196103 AAAA
1 AAAA
43196107 TGGAGAGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.20
7 11 0.37
8 13 0.43
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:43196092 original size:15 final size:16
Alignment explanation
Indices: 43196074--43196106 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
43196064 AAAAAAAATG
43196074 AAAATGAAAAA-TGAA
1 AAAATGAAAAAGTGAA
43196089 AAAATGAAAAAGTGAA
1 AAAATGAAAAAGTGAA
43196105 AA
1 AA
43196107 TGGAGAGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (16 bp):
AAAATGAAAAAGTGAA
Found at i:43197503 original size:88 final size:88
Alignment explanation
Indices: 43197264--43198051 Score: 1134
Period size: 88 Copynumber: 9.0 Consensus size: 88
43197254 TGAAATCACA
* * * * *
43197264 AAGCCTTGCCTCCATGGGTTGCAGCGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTA-CT
1 AAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATC-
*
43197328 GACAGCGAAGCAGATCGAAGATACC
65 GACAGCGAAGCAGATCGAAGACA-C
* * *
43197353 AA-CCTTGCCTCCCTAGGTTGGAGT-GA-CTAGGTTGAAGATAGCAGATCTGGCCTTCCTGCATC
1 AAGCCTTGCCTCCCTCGGTTGTAGTGGAGC-AGGTTGAAGATAGCAGATCTTGCCTTCCTGCATC
**
43197415 GATGGCGAAGCAGATCGAAGACAC
65 GACAGCGAAGCAGATCGAAGACAC
43197439 AAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCG
1 AAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCG
*
43197504 ATAGCGAAGCAGATCGAAGACAC
66 ACAGCGAAGCAGATCGAAGACAC
* ** *
43197527 AAGCCTTGCCTCCTTCATTTGTAGCGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCG
1 AAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCG
* *
43197592 ACGGTGAAGCAGATCGAAGACAC
66 ACAGCGAAGCAGATCGAAGACAC
* * * *
43197615 AAGCCTTGCCTCCCTCAGTTGTAGTGGAGCAGGTTGAAGATAGCTGATCTTGCCTTCATGCATTG
1 AAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCG
43197680 ACAGCGAAGCAGATCGAAGACAC
66 ACAGCGAAGCAGATCGAAGACAC
* *
43197703 AAGCCTTGCCTCCCTCGTTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGTATCG
1 AAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCG
** * *
43197768 ATGGGGAAGCAGATTGAAGACAC
66 ACAGCGAAGCAGATCGAAGACAC
*
43197791 AAGCCTTGCCTCCCTCGGTTATAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCG
1 AAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCG
** * * *
43197856 ATGGTGAAGCATATCGAAGGCAC
66 ACAGCGAAGCAGATCGAAGACAC
* * * *
43197879 AAGCCTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGGCTTCCTACATCA
1 AAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCG
*
43197944 ACAGTGAAGCAGATCGAAGACAC
66 ACAGCGAAGCAGATCGAAGACAC
* ** *
43197967 AAGCCTTGCTTCCCTTAGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTAGCCTTCCTGCATCG
1 AAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCG
43198032 ACAGCGAAGCAGATCGAAGA
66 ACAGCGAAGCAGATCGAAGA
43198052 TACTAATTCT
Statistics
Matches: 631, Mismatches: 63, Indels: 11
0.90 0.09 0.02
Matches are distributed among these distances:
86 4 0.01
87 72 0.11
88 552 0.87
89 3 0.00
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (88 bp):
AAGCCTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCG
ACAGCGAAGCAGATCGAAGACAC
Found at i:43199430 original size:18 final size:20
Alignment explanation
Indices: 43199404--43199443 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
43199394 CCCCTTTTAC
43199404 ATATATTA-TTATA-TAAAT
1 ATATATTATTTATATTAAAT
*
43199422 ATATCTTATTTATATTAAAT
1 ATATATTATTTATATTAAAT
43199442 AT
1 AT
43199444 TTCATTCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 5 0.26
20 7 0.37
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATTATTTATATTAAAT
Found at i:43207076 original size:2 final size:2
Alignment explanation
Indices: 43207069--43207100 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
43207059 TGGTTAGTAT
43207069 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43207101 CACTATTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43209177 original size:7 final size:7
Alignment explanation
Indices: 43209165--43209202 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
43209155 ATAGACTCTT
43209165 AACCCTA
1 AACCCTA
43209172 AACCCTA
1 AACCCTA
43209179 AACCCTA
1 AACCCTA
*
43209186 AACCTTA
1 AACCCTA
43209193 AACCCTA
1 AACCCTA
43209200 AAC
1 AAC
43209203 TTTTTTAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (7 bp):
AACCCTA
Found at i:43209323 original size:80 final size:80
Alignment explanation
Indices: 43209190--43209350 Score: 277
Period size: 80 Copynumber: 2.0 Consensus size: 80
43209180 ACCCTAAACC
**
43209190 TTAAACCCTAAACTTTTTTAGATTAGCTATTGAAGTAAGTTTTGTTTCTCGCAATGTAAACATTC
1 TTAAACCCTAAACTCGTTTAGATTAGCTATTGAAGTAAGTTTTGTTTCTCGCAATGTAAACATTC
*
43209255 TTATAATGCAACTTA
66 TTACAATGCAACTTA
*
43209270 TTAAACCCTAAACTCGTTTAGATTAGCTATTGAAGTAAGTTTTGTTTCTCGCAATGTAAACGTTC
1 TTAAACCCTAAACTCGTTTAGATTAGCTATTGAAGTAAGTTTTGTTTCTCGCAATGTAAACATTC
*
43209335 TTACAATGCCACTTA
66 TTACAATGCAACTTA
43209350 T
1 T
43209351 CATTAGTTTG
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (80 bp):
TTAAACCCTAAACTCGTTTAGATTAGCTATTGAAGTAAGTTTTGTTTCTCGCAATGTAAACATTC
TTACAATGCAACTTA
Found at i:43209436 original size:15 final size:15
Alignment explanation
Indices: 43209416--43209444 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43209406 TATGCATACA
43209416 AAATACAAAAGACAG
1 AAATACAAAAGACAG
43209431 AAATACAAAAGACA
1 AAATACAAAAGACA
43209445 TAATAGTGAA
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:0.69, C:0.14, G:0.10, T:0.07
Consensus pattern (15 bp):
AAATACAAAAGACAG
Found at i:43221769 original size:38 final size:39
Alignment explanation
Indices: 43221708--43221792 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 39
43221698 CATATACACT
* * *
43221708 TTTTTATAACGTACATAC-T-TATATTTATATATTTTTG
1 TTTTTATAACGTACATACATATATATGTAAATATTTATG
*
43221745 TATTTTATAATC-TATATACATATATATGTAAATATTTATG
1 T-TTTTATAA-CGTACATACATATATATGTAAATATTTATG
43221785 TTTTTATA
1 TTTTTATA
43221793 TTTTATAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
37 1 0.03
38 14 0.35
39 9 0.22
40 16 0.40
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (39 bp):
TTTTTATAACGTACATACATATATATGTAAATATTTATG
Found at i:43227994 original size:45 final size:45
Alignment explanation
Indices: 43227937--43228435 Score: 612
Period size: 45 Copynumber: 11.1 Consensus size: 45
43227927 CAGATCAATG
* * *
43227937 AGATAGCAGATCTTATCTTCCTATATTGGCAGTGAAGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGA
* *
43227982 AGATGGCAGATCTTGTCTTCCTGTATTGGCAGCGAAATAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGA
*
43228027 AGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGA
* * *
43228072 AGATAGCAGGTCTTGTCTTCCTGTATTGGCAGCGAAGCAGA-CTAA
1 AGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GA
* * *
43228117 AGATAGCA-AGTCTTGTCTTCCTGCACTGACAGCGAAGTAGA-CTGA
1 AGATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GA
**
43228162 AGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATTAA
1 AGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGA
* * *
43228207 AAATAGCAGGTCTTGTCTTCCTGTATTGGCAGCAAAGTAGA-CTGA
1 AGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GA
*
43228252 AGATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGA
* * * * ** *
43228297 AGATAGTAGGTCTTGTATTCCTATATTGATAGCGAATTAGA-CTGA
1 AGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GA
* * *
43228342 AGATAGCAGGTCTTATCTTCCTGTATTGGCAGCGAAGTAGGTCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGA
* * * * * *
43228387 AGATAACAGATCTTATCTTCTTGTATTAGCAGCGAAGTATATCGG
1 AGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGA
43228432 AGAT
1 AGAT
43228436 TGCAAATCCT
Statistics
Matches: 391, Mismatches: 55, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
44 2 0.01
45 386 0.99
46 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (45 bp):
AGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGA
Found at i:43228524 original size:45 final size:43
Alignment explanation
Indices: 43228475--43228615 Score: 133
Period size: 45 Copynumber: 3.2 Consensus size: 43
43228465 GGAGCGGATC
43228475 GAAGATAGCAAACCTTATCCCTCTGAAGTTGCAGTAGGGCAGGTT
1 GAAGATAGCAAACCTTATCCCTCT-AAGTTGCAGT-GGGCAGGTT
** * **
43228520 GAAGATA-CAAGTCTTGTCTCCT-TAGAGTTGCAGTGGAGCAGACT
1 GAAGATAGCAAACCTTATC-CCTCTA-AGTTGCAGTGG-GCAGGTT
* * *
43228564 GAAGATAGTAAACCTTATCCCCCAAAAGTTGCAGTGGGGCAGGTT
1 GAAGATAGCAAACCTTATCCCTC-TAAGTTGCAGT-GGGCAGGTT
43228609 GAAGATA
1 GAAGATA
43228616 CAAGTCTTAT
Statistics
Matches: 76, Mismatches: 13, Indels: 14
0.74 0.13 0.14
Matches are distributed among these distances:
43 3 0.04
44 32 0.42
45 38 0.50
46 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.24
Consensus pattern (43 bp):
GAAGATAGCAAACCTTATCCCTCTAAGTTGCAGTGGGCAGGTT
Found at i:43228551 original size:44 final size:43
Alignment explanation
Indices: 43228500--43228649 Score: 138
Period size: 44 Copynumber: 3.4 Consensus size: 43
43228490 TATCCCTCTG
* **
43228500 AAGTTGCAGTAGGGCAGGTTGAAGATACAAGTCTTGTCTCCTTA
1 AAGTTGCAGT-GGGCAGGTTGAAGATACAAGTCTTATCTCCCAA
* ** * ** *
43228544 GAGTTGCAGTGGAGCAGACTGAAGATAGTAAACCTTATCCCCCAA
1 AAGTTGCAGTGG-GCAGGTTGAAGATA-CAAGTCTTATCTCCCAA
*
43228589 AAGTTGCAGTGGGGCAGGTTGAAGATACAAGTCTTATCTCCCAG
1 AAGTTGCAGT-GGGCAGGTTGAAGATACAAGTCTTATCTCCCAA
**
43228633 ACTTTGCAGTGGAGCAG
1 AAGTTGCAGTGG-GCAG
43228650 ACTAAAACCA
Statistics
Matches: 82, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
43 4 0.05
44 45 0.55
45 31 0.38
46 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.25
Consensus pattern (43 bp):
AAGTTGCAGTGGGCAGGTTGAAGATACAAGTCTTATCTCCCAA
Found at i:43228568 original size:89 final size:90
Alignment explanation
Indices: 43228462--43228652 Score: 271
Period size: 89 Copynumber: 2.1 Consensus size: 90
43228452 CTAAAGCAGT
* * **
43228462 AGTGGAGCGGA-TCGAAGATAGCAAACCTTATCCCTCTGAAGTTGCAGTAGGGCAGGTTGAAGAT
1 AGTGGAGCAGACTCGAAGATAGCAAACCTTATCCCCCAAAAGTTGCAGTAGGGCAGGTTGAAGAT
* *
43228526 ACAAGTCTTGTCTCCTTAGA-GTTGC
66 ACAAGTCTTATCTCC-CAGACGTTGC
* *
43228551 AGTGGAGCAGACT-GAAGATAGTAAACCTTATCCCCCAAAAGTTGCAGTGGGGCAGGTTGAAGAT
1 AGTGGAGCAGACTCGAAGATAGCAAACCTTATCCCCCAAAAGTTGCAGTAGGGCAGGTTGAAGAT
*
43228615 ACAAGTCTTATCTCCCAGACTTTGC
66 ACAAGTCTTATCTCCCAGACGTTGC
43228640 AGTGGAGCAGACT
1 AGTGGAGCAGACT
43228653 AAAACCACAA
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
88 3 0.03
89 87 0.96
90 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (90 bp):
AGTGGAGCAGACTCGAAGATAGCAAACCTTATCCCCCAAAAGTTGCAGTAGGGCAGGTTGAAGAT
ACAAGTCTTATCTCCCAGACGTTGC
Found at i:43230466 original size:39 final size:39
Alignment explanation
Indices: 43230422--43230507 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 39
43230412 ACATACACAC
* * * * *
43230422 TTTTTATAATGTACATACTTATAT-TTTATATATTTTTG
1 TTTTTATAATCTACATACATATATATGTAAATATTTATG
*
43230460 TATTTTATAATCTATATACATATATATGTAAATATTTATG
1 T-TTTTATAATCTACATACATATATATGTAAATATTTATG
43230500 TTTTTATA
1 TTTTTATA
43230508 TTTTATAATC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
38 1 0.03
39 27 0.68
40 12 0.30
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (39 bp):
TTTTTATAATCTACATACATATATATGTAAATATTTATG
Found at i:43232854 original size:22 final size:22
Alignment explanation
Indices: 43232826--43232868 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
43232816 GTTATGGTCC
43232826 TTACGAGTTCCTAGTGATGCCA
1 TTACGAGTTCCTAGTGATGCCA
43232848 TTACGAGTTCCTAGTGATGCC
1 TTACGAGTTCCTAGTGATGCC
43232869 TTTCTGACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (22 bp):
TTACGAGTTCCTAGTGATGCCA
Found at i:43237463 original size:24 final size:24
Alignment explanation
Indices: 43237387--43237463 Score: 100
Period size: 24 Copynumber: 3.2 Consensus size: 24
43237377 GGGTGTTACA
* *
43237387 TCCCGGTATTGGCTTACTTGAACT
1 TCCCGATATTGGCTCACTTGAACT
* *
43237411 TCCCAATATTGACTCACTTGAACT
1 TCCCGATATTGGCTCACTTGAACT
* *
43237435 TCCCGATATTGGCTCATTTGAGCT
1 TCCCGATATTGGCTCACTTGAACT
43237459 TCCCG
1 TCCCG
43237464 TTATACAGCC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (24 bp):
TCCCGATATTGGCTCACTTGAACT
Found at i:43237515 original size:25 final size:25
Alignment explanation
Indices: 43237455--43237548 Score: 98
Period size: 25 Copynumber: 3.8 Consensus size: 25
43237445 GGCTCATTTG
*
43237455 AGCTTCCCGTTATACAGCCCAGATA
1 AGCTTCCCGTTATACAGCTCAGATA
**
43237480 AGCTTTTCGTTATACAGCTCAGATA
1 AGCTTCCCGTTATACAGCTCAGATA
* ** * *
43237505 AGCTTCCCGTTACATGGCTCACATG
1 AGCTTCCCGTTATACAGCTCAGATA
* *
43237530 AGCTTACCGTTATATAGCT
1 AGCTTCCCGTTATACAGCT
43237549 TGAAAGAGCT
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.31
Consensus pattern (25 bp):
AGCTTCCCGTTATACAGCTCAGATA
Found at i:43241760 original size:17 final size:18
Alignment explanation
Indices: 43241729--43241763 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
43241719 GACTCTTAGC
43241729 TTTAATTTTTCATTTGTT
1 TTTAATTTTTCATTTGTT
*
43241747 TTTACTTTTT-ATTTGTT
1 TTTAATTTTTCATTTGTT
43241764 CCTTTACGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.74
Consensus pattern (18 bp):
TTTAATTTTTCATTTGTT
Found at i:43249662 original size:29 final size:29
Alignment explanation
Indices: 43249621--43249683 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
43249611 CTATCGACGC
* *
43249621 CACACAGCCGTGTGATGGGCTGTGT-TCGA
1 CACACAGCCGTGTGATAGGCAGTGTGT-GA
**
43249650 CACACAGTTGTGTGATAGGCAGTGTGTGA
1 CACACAGCCGTGTGATAGGCAGTGTGTGA
43249679 CACAC
1 CACAC
43249684 GATTTAGGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.32, T:0.24
Consensus pattern (29 bp):
CACACAGCCGTGTGATAGGCAGTGTGTGA
Found at i:43261820 original size:64 final size:64
Alignment explanation
Indices: 43261746--43261881 Score: 218
Period size: 64 Copynumber: 2.1 Consensus size: 64
43261736 AGCCTCTCGC
*
43261746 AATTAATTAATTAATCTAAATTTAACTCAAATAAAGTTATCTTCAACTACACCAAATTCAATTT
1 AATTATTTAATTAATCTAAATTTAACTCAAATAAAGTTATCTTCAACTACACCAAATTCAATTT
* * * * *
43261810 AATTATTTAATTAATCTAAATTTAACTCAAATCAAGTTATCTTCAGCTATATCATATTCAATTT
1 AATTATTTAATTAATCTAAATTTAACTCAAATAAAGTTATCTTCAACTACACCAAATTCAATTT
43261874 AATTATTT
1 AATTATTT
43261882 CTATTTAGCC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (64 bp):
AATTATTTAATTAATCTAAATTTAACTCAAATAAAGTTATCTTCAACTACACCAAATTCAATTT
Found at i:43264504 original size:304 final size:303
Alignment explanation
Indices: 43263919--43264519 Score: 954
Period size: 304 Copynumber: 2.0 Consensus size: 303
43263909 GATTAAAATA
* *
43263919 AACCTGACAAACCATTTGCAAAAACAAATGGGATTAGCACTGAAATAATTCATCATATACTTAAT
1 AACCTAACAAACCATTTGCAAAAACAAATGGGATTAGCACTAAAATAATTCATCATATACTTAAT
* * *
43263984 GCCCTTCAATAATTTAATCAAAATCGTTCATATATACATTTCATCGAATCAGTACCAAAAAGAGA
66 GCCCTTCAATAATTTAATCAAAATCATTCATATATACATTTCATCGAATCAATACCAAAAAGAAA
43264049 CATTCTTGTATGATCATTCTCTAGCATAAATATTTTAATGGATAAACACATGTATTAACAAATAA
131 CATTCTTGTATGATCATTCTCTAGCATAAATATTTTAATGGATAAACACATGTATTAACAAATAA
* *
43264114 TTTAAATATCAATCACAAATTTTAATAGCCCAATGAACTATAGTAACATAACTTGGTTACTCAGG
196 TTTAAATATCAATCACAAATTTTAATAGCCCAATGAACTATAGTAACATAACTCGGATACTCAGG
*
43264179 TAACTAGATCACAACAAAGAGCATCAAAATGCTAAACTATAGT
261 TAACTACATCACAACAAAGAGCATCAAAATGCTAAACTATAGT
* * * *
43264222 AACCTAACAAACCATTTGCAAAAAGTAGATTGGATTAGCACTAAAATAATTCATCATATACTTCA
1 AACCTAACAAACCATTTGCAAAAA-CAAATGGGATTAGCACTAAAATAATTCATCATATACTTAA
* * *
43264287 TGCCCTTCAATAATTTCATTAAAATCATTCATATATACATTTCATTGAATCAATACCAAAAAGAA
65 TGCCCTTCAATAATTTAATCAAAATCATTCATATATACATTTCATCGAATCAATACCAAAAAGAA
* * *
43264352 ACATTCTTGTATGATCATTCTCTAGCATAGATCTTTTAATGGATAAACACATGTATTAACAAATC
130 ACATTCTTGTATGATCATTCTCTAGCATAAATATTTTAATGGATAAACACATGTATTAACAAATA
* * * **
43264417 ATTTATAA-ATCAATCATAAATTTTAATAGCCTAGTGAACTATAGTAACATAACTCGGATACTTG
195 ATTTA-AATATCAATCACAAATTTTAATAGCCCAATGAACTATAGTAACATAACTCGGATACTCA
43264481 GGTAACTACATCAC-ACTAAAGAGCATCAAAATGCTAAAC
259 GGTAACTACATCACAAC-AAAGAGCATCAAAATGCTAAAC
43264520 AGAGGCACTA
Statistics
Matches: 272, Mismatches: 23, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
303 25 0.09
304 245 0.90
305 2 0.01
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (303 bp):
AACCTAACAAACCATTTGCAAAAACAAATGGGATTAGCACTAAAATAATTCATCATATACTTAAT
GCCCTTCAATAATTTAATCAAAATCATTCATATATACATTTCATCGAATCAATACCAAAAAGAAA
CATTCTTGTATGATCATTCTCTAGCATAAATATTTTAATGGATAAACACATGTATTAACAAATAA
TTTAAATATCAATCACAAATTTTAATAGCCCAATGAACTATAGTAACATAACTCGGATACTCAGG
TAACTACATCACAACAAAGAGCATCAAAATGCTAAACTATAGT
Found at i:43267668 original size:17 final size:17
Alignment explanation
Indices: 43267646--43267678 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
43267636 AATTTTTTTT
43267646 CTTTCA-TGTTCTTTCAA
1 CTTTCATTGTT-TTTCAA
43267663 CTTTCATTGTTTTTCA
1 CTTTCATTGTTTTTCA
43267679 TTCTCTTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.15, C:0.21, G:0.06, T:0.58
Consensus pattern (17 bp):
CTTTCATTGTTTTTCAA
Found at i:43268111 original size:20 final size:20
Alignment explanation
Indices: 43268073--43268115 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
43268063 ATAAATTGAA
43268073 TTTTTTTTATATTCAAAACAT
1 TTTTTTTTATATTCAAAAC-T
* *
43268094 TTTTTTTTGT-TTCCAAACT
1 TTTTTTTTATATTCAAAACT
43268113 TTT
1 TTT
43268116 ACAAAATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 7 0.35
21 9 0.45
ACGTcount: A:0.23, C:0.12, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTTTTTATATTCAAAACT
Found at i:43272301 original size:10 final size:9
Alignment explanation
Indices: 43272224--43272428 Score: 58
Period size: 9 Copynumber: 21.0 Consensus size: 9
43272214 TTTAATATTT
43272224 TTATAAAATA
1 TTATAAAA-A
43272234 TTA-AAAAA
1 TTATAAAAA
43272242 -TA-AAAAA
1 TTATAAAAA
*
43272249 TTGATATAAAC
1 TT-ATA-AAAA
43272260 TTATAAAAAAA
1 TTAT--AAAAA
* * *
43272271 CTATTAATA
1 TTATAAAAA
43272280 TTATAAAAA
1 TTATAAAAA
43272289 TTATAACAAA
1 TTATAA-AAA
43272299 TTAATAAAAA
1 TT-ATAAAAA
**
43272309 CAAT-AAAA
1 TTATAAAAA
43272317 TTAATAAAAACA
1 TT-AT-AAAA-A
* *
43272329 TATTTAAAAT
1 T-TATAAAAA
43272339 TCTATAAAAA
1 T-TATAAAAA
* *
43272349 ATATTAAAAT
1 TTA-TAAAAA
43272359 TCTATAAAAAAAA
1 T-TAT---AAAAA
* **
43272372 TCATAAGCA
1 TTATAAAAA
*
43272381 TTGTAAAAAA
1 TTAT-AAAAA
43272391 TTATAAAAA
1 TTATAAAAA
* *
43272400 GTATTAAAA
1 TTATAAAAA
43272409 TTAATATAAAA
1 TT-ATA-AAAA
43272420 TTATAAAAA
1 TTATAAAAA
43272429 AGAATCATAA
Statistics
Matches: 141, Mismatches: 33, Indels: 43
0.65 0.15 0.20
Matches are distributed among these distances:
7 7 0.05
8 6 0.04
9 48 0.34
10 38 0.27
11 30 0.21
12 6 0.04
13 6 0.04
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (9 bp):
TTATAAAAA
Found at i:43272338 original size:21 final size:21
Alignment explanation
Indices: 43272296--43272368 Score: 84
Period size: 20 Copynumber: 3.7 Consensus size: 21
43272286 AAATTATAAC
43272296 AAATT-AATAAAAACA-A-TA
1 AAATTCAATAAAAACATATTA
43272314 AAATT-AATAAAAACATATTTA
1 AAATTCAATAAAAACATA-TTA
*
43272335 AAATTCTATAAAAA-ATATTA
1 AAATTCAATAAAAACATATTA
*
43272355 AAATTCTATAAAAA
1 AAATTCAATAAAAA
43272369 AAATCATAAG
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
18 15 0.30
19 1 0.02
20 17 0.34
21 10 0.20
22 7 0.14
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATTCAATAAAAACATATTA
Found at i:43272366 original size:51 final size:51
Alignment explanation
Indices: 43272311--43272428 Score: 116
Period size: 51 Copynumber: 2.3 Consensus size: 51
43272301 AATAAAAACA
* * *
43272311 ATAAAATTAATAAAAACATAT-TTAAAATTCTATAAAAAATATTAAAATT-CT
1 ATAAAATTAATAAAAACAT-TGTAAAAAAT-TATAAAAAATATTAAAATTAAT
** * * *
43272362 ATAAAAAAAATCATAAGCATTGTAAAAAATTATAAAAAGTATTAAAATTAAT
1 ATAAAATTAAT-AAAAACATTGTAAAAAATTATAAAAAATATTAAAATTAAT
43272414 ATAAAATT-ATAAAAA
1 ATAAAATTAATAAAAA
43272429 AGAATCATAA
Statistics
Matches: 52, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
50 3 0.06
51 30 0.58
52 19 0.37
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (51 bp):
ATAAAATTAATAAAAACATTGTAAAAAATTATAAAAAATATTAAAATTAAT
Found at i:43272369 original size:21 final size:22
Alignment explanation
Indices: 43272312--43272370 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
43272302 ATAAAAACAA
* *
43272312 TAAAATT-AATAAAAACATATT
1 TAAAATTCTATAAAAAAATATT
43272333 TAAAATTCTAT-AAAAAATA-T
1 TAAAATTCTATAAAAAAATATT
43272353 TAAAATTCTATAAAAAAA
1 TAAAATTCTATAAAAAAA
43272371 ATCATAAGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.35
21 20 0.59
22 2 0.06
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAATTCTATAAAAAAATATT
Found at i:43272885 original size:11 final size:11
Alignment explanation
Indices: 43272871--43272908 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
43272861 AAAATTTTAT
43272871 AATTTTATATC
1 AATTTTATATC
43272882 AATTTTA-AT-
1 AATTTTATATC
*
43272891 ATTTTTATATC
1 AATTTTATATC
43272902 AATTTTA
1 AATTTTA
43272909 ATATTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 6 0.26
10 4 0.17
11 13 0.57
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (11 bp):
AATTTTATATC
Found at i:43272885 original size:19 final size:18
Alignment explanation
Indices: 43272863--43273055 Score: 79
Period size: 20 Copynumber: 9.9 Consensus size: 18
43272853 TTTTTTTTAA
43272863 AATTTTATAATTTTATAT
1 AATTTTATAATTTTATAT
*
43272881 CAATTTTAATATTTTTATAT
1 -AATTTT-ATAATTTTATAT
*
43272901 CAATTTTAATATTTTTAT-T
1 -AATTTT-ATAATTTTATAT
* * *
43272920 ATTTTTAAGAATGTTA-AT
1 AATTTT-ATAATTTTATAT
* *
43272938 GCAATTTTTTAATTTTAAAT
1 --AATTTTATAATTTTATAT
43272958 AATTTTTATTAATTATATATATTT
1 AA-TTTTA-TAATT-T-TATA--T
* *
43272982 AAATTTATTATATTT-TAT
1 AATTTTATAAT-TTTATAT
*
43273000 AATATTTATAAGTTTTTTAT
1 AAT-TTTATAA-TTTTATAT
* *
43273020 AATTTCAATAAGTTTATATT
1 AATTT-TATAATTTTATA-T
43273040 AATTTTAGT-ATTTTAT
1 AATTTTA-TAATTTTAT
43273056 TTTTTAATAT
Statistics
Matches: 136, Mismatches: 20, Indels: 36
0.71 0.10 0.19
Matches are distributed among these distances:
18 18 0.13
19 40 0.29
20 61 0.45
21 2 0.01
22 7 0.05
23 5 0.04
24 3 0.02
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (18 bp):
AATTTTATAATTTTATAT
Found at i:43272898 original size:20 final size:20
Alignment explanation
Indices: 43272863--43272918 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
43272853 TTTTTTTTAA
*
43272863 AATTTT-ATAATTTTATATC
1 AATTTTAATATTTTTATATC
43272882 AATTTTAATATTTTTATATC
1 AATTTTAATATTTTTATATC
43272902 AATTTTAATATTTTTAT
1 AATTTTAATATTTTTAT
43272919 TATTTTTAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 6 0.17
20 29 0.83
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
AATTTTAATATTTTTATATC
Found at i:43272916 original size:9 final size:9
Alignment explanation
Indices: 43272884--43272927 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
43272874 TTTATATCAA
43272884 TTTTAATAT
1 TTTTAATAT
*
43272893 TTTTATATCAA
1 TTTTA-AT-AT
43272904 TTTTAATAT
1 TTTTAATAT
*
43272913 TTTTATTAT
1 TTTTAATAT
43272922 TTTTAA
1 TTTTAA
43272928 GAATGTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 19 0.66
10 4 0.14
11 6 0.21
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTAATAT
Found at i:43273302 original size:23 final size:26
Alignment explanation
Indices: 43273256--43273302 Score: 64
Period size: 23 Copynumber: 1.9 Consensus size: 26
43273246 TAGTAAAGGG
*
43273256 TCTTAATTATTATTATTTTTACATTT
1 TCTTAATTATTATTATTTTGACATTT
43273282 TCTTAA-TATT-TT-TTTTGACAT
1 TCTTAATTATTATTATTTTGACAT
43273303 ATAAGCCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 4 0.20
26 6 0.30
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.64
Consensus pattern (26 bp):
TCTTAATTATTATTATTTTGACATTT
Found at i:43274805 original size:25 final size:25
Alignment explanation
Indices: 43274774--43274856 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 25
43274764 CAAACATGTA
43274774 AACGGGAAGCTCTTTCGAGCCATAT
1 AACGGGAAGCTCTTTCGAGCCATAT
* * *
43274799 AATGGGAAGCTCATGT-GAGCCATGT
1 AACGGGAAGCTC-TTTCGAGCCATAT
* * *
43274824 AACGAGAAGCTCATCCGAGCCATA-
1 AACGGGAAGCTCTTTCGAGCCATAT
*
43274848 ATCGGGAAG
1 AACGGGAAG
43274857 TTAAAATGAG
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
24 7 0.16
25 36 0.80
26 2 0.04
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (25 bp):
AACGGGAAGCTCTTTCGAGCCATAT
Found at i:43277400 original size:25 final size:25
Alignment explanation
Indices: 43277363--43277413 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
43277353 TGATCATTAA
*
43277363 TATCAATAGGCAATATTTCACTATC
1 TATCAATAAGCAATATTTCACTATC
43277388 TATCAATAAGCAATATTTCACTATC
1 TATCAATAAGCAATATTTCACTATC
43277413 T
1 T
43277414 CAATTTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (25 bp):
TATCAATAAGCAATATTTCACTATC
Found at i:43277845 original size:21 final size:21
Alignment explanation
Indices: 43277811--43277885 Score: 78
Period size: 23 Copynumber: 3.4 Consensus size: 21
43277801 CAACACATAA
* * *
43277811 GTGCTTGAAACGACATACGAG
1 GTGCCTGATACGACACACGAG
*
43277832 GTGTCTGATACGACACACACGAG
1 GTGCCTGATACG--ACACACGAG
43277855 GTGCCTGATACGACACACATGAG
1 GTGCCTGATACGACACAC--GAG
43277878 GTGCCTGA
1 GTGCCTGA
43277886 AATATGACAC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 15 0.33
23 30 0.67
ACGTcount: A:0.29, C:0.24, G:0.28, T:0.19
Consensus pattern (21 bp):
GTGCCTGATACGACACACGAG
Found at i:43277895 original size:23 final size:23
Alignment explanation
Indices: 43277869--43277929 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
43277859 CTGATACGAC
* *
43277869 ACACATGAGGTGCCTGAAATATG
1 ACACATAAAGTGCCTGAAATATG
* *
43277892 ACACATAAAGTGCTTGATATATG
1 ACACATAAAGTGCCTGAAATATG
43277915 ACACATAAAGTGCCT
1 ACACATAAAGTGCCT
43277930 AATCAGCAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (23 bp):
ACACATAAAGTGCCTGAAATATG
Found at i:43277896 original size:25 final size:23
Alignment explanation
Indices: 43277827--43277885 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
43277817 GAAACGACAT
*
43277827 ACGAGGTGTCTGATACGACACAC
1 ACGAGGTGCCTGATACGACACAC
43277850 ACGAGGTGCCTGATACGACACAC
1 ACGAGGTGCCTGATACGACACAC
*
43277873 ATGAGGTGCCTGA
1 ACGAGGTGCCTGA
43277886 AATATGACAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.29, C:0.25, G:0.29, T:0.17
Consensus pattern (23 bp):
ACGAGGTGCCTGATACGACACAC
Found at i:43279267 original size:23 final size:23
Alignment explanation
Indices: 43279233--43279276 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
43279223 AAGTATGTAT
43279233 ATATATTAATTACAAATGTATAC
1 ATATATTAATTACAAATGTATAC
* *
43279256 ATATATTTATTACACATGTAT
1 ATATATTAATTACAAATGTAT
43279277 TTATAATTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (23 bp):
ATATATTAATTACAAATGTATAC
Found at i:43281037 original size:56 final size:52
Alignment explanation
Indices: 43280964--43281163 Score: 169
Period size: 50 Copynumber: 3.9 Consensus size: 52
43280954 ACATTAAGGG
* * **
43280964 GATGAGA--TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGA
1 GATGAGAGGTCCCACGTAAGACCATGTTTGGGACATGGCATTGGCA-TACCGA
* *
43281015 GGTTATGAGAGGTCCCACGTAAGACCATGTTTGGGACATAGCGTTGGC--ACCGA
1 -G--ATGAGAGGTCCCACGTAAGACCATGTTTGGGACATGGCATTGGCATACCGA
* * *
43281068 GATGAGAGGTCCCCCGTAAAACCATGTTTGGGACATGGCATGGGCAT--CGA
1 GATGAGAGGTCCCACGTAAGACCATGTTTGGGACATGGCATTGGCATACCGA
* * ** * * * *
43281118 TATAAGAACTCCCATGTAAGACCATATATGGGATATGGCATTGGCA
1 GATGAGAGGTCCCACGTAAGACCATGTTTGGGACATGGCATTGGCA
43281164 GTACAGGAAA
Statistics
Matches: 120, Mismatches: 22, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
50 77 0.64
52 2 0.02
53 3 0.03
54 6 0.05
56 32 0.27
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (52 bp):
GATGAGAGGTCCCACGTAAGACCATGTTTGGGACATGGCATTGGCATACCGA
Found at i:43281142 original size:50 final size:50
Alignment explanation
Indices: 43280971--43281202 Score: 155
Period size: 50 Copynumber: 4.5 Consensus size: 50
43280961 GGGGATGAGA
* * **
43280971 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGC---ATCGA---TATAAGAAC
* * * * * * * **
43281027 TCCCACGTAAGACCATGTTTGGGACATAGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATAAGAAC
** * * *
43281077 TCCCCCGTAAAACCATGTTTGGGACATGGCATGGGCATCGATATAAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATAAGAAC
* * * * *
43281127 TCCCATGTAAGACCATATATGGGATATGGCATTGGCA--G-TACAGGAAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATAAG-AAC
*
43281175 ATCCCATGTAAGACTATGTCTGGGACAT
1 -TCCCATGTAAGACCATGTCTGGGACAT
43281203 AAATTTGGCA
Statistics
Matches: 144, Mismatches: 30, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
47 4 0.03
48 4 0.03
49 23 0.16
50 78 0.54
53 3 0.02
56 32 0.22
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATAAGAAC
Found at i:43281440 original size:20 final size:20
Alignment explanation
Indices: 43281415--43281453 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
43281405 TGAGTTATTT
43281415 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
43281435 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
43281454 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:43287748 original size:25 final size:25
Alignment explanation
Indices: 43287720--43287781 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
43287710 CAAACATGTA
*
43287720 AACGATAAGCTCTTTCAAGCCATAT
1 AACGAGAAGCTCTTTCAAGCCATAT
* * *
43287745 AACGGGAAGCTCTTTCGAGCCATGT
1 AACGAGAAGCTCTTTCAAGCCATAT
* *
43287770 AATGGGAAGCTC
1 AACGAGAAGCTC
43287782 ATCCGAGCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (25 bp):
AACGAGAAGCTCTTTCAAGCCATAT
Found at i:43287788 original size:25 final size:25
Alignment explanation
Indices: 43287737--43287793 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
43287727 AGCTCTTTCA
* * *
43287737 AGCCATATAACGGGAAGCTCTTTCG
1 AGCCATGTAACGGGAAGCTCATCCG
*
43287762 AGCCATGTAATGGGAAGCTCATCCG
1 AGCCATGTAACGGGAAGCTCATCCG
43287787 AGCCATG
1 AGCCATG
43287794 ATCAATAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (25 bp):
AGCCATGTAACGGGAAGCTCATCCG
Found at i:43288375 original size:21 final size:21
Alignment explanation
Indices: 43288351--43288392 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43288341 TGAATTTAAC
* *
43288351 CTCAATTTAATACAATTCATA
1 CTCAATTGAATACAATACATA
*
43288372 CTCAATTGAATCCAATACATA
1 CTCAATTGAATACAATACATA
43288393 TCTTTGGCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.21, G:0.02, T:0.33
Consensus pattern (21 bp):
CTCAATTGAATACAATACATA
Found at i:43292867 original size:18 final size:19
Alignment explanation
Indices: 43292833--43292868 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
43292823 TTTAAAAGAG
*
43292833 TTTAGATAAAAATATTAAA
1 TTTAAATAAAAATATTAAA
43292852 TTTAAATAAAAA-ATTAA
1 TTTAAATAAAAATATTAA
43292869 TCACGTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
TTTAAATAAAAATATTAAA
Found at i:43294813 original size:3 final size:3
Alignment explanation
Indices: 43294807--43294837 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
43294797 GCATCTCCAT
43294807 TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
43294838 ATTGTTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:43295171 original size:27 final size:27
Alignment explanation
Indices: 43295128--43295195 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
43295118 CTTGCCATGC
*
43295128 CAAAACCCAAACTAGATTCTAGTAATT
1 CAAAACCCAAACCAGATTCTAGTAATT
* * *
43295155 CAAAACCCTAACCAGATTTTGGTAATT
1 CAAAACCCAAACCAGATTCTAGTAATT
** *
43295182 TGAAATCCAAACCA
1 CAAAACCCAAACCA
43295196 CGAGGGCATA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.25
Consensus pattern (27 bp):
CAAAACCCAAACCAGATTCTAGTAATT
Found at i:43295337 original size:21 final size:21
Alignment explanation
Indices: 43295313--43295353 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
43295303 TCCATCGTGG
43295313 CTAGTTAACTG-GCCACATCAA
1 CTAGTTAAC-GAGCCACATCAA
43295334 CTAGTTAACGAGCCACATCA
1 CTAGTTAACGAGCCACATCA
43295354 CCTATCCCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (21 bp):
CTAGTTAACGAGCCACATCAA
Found at i:43299380 original size:32 final size:33
Alignment explanation
Indices: 43299344--43299416 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 33
43299334 TAACTTGTTC
43299344 ATATTATTTTTTAAATT-AT-TTTAAAAACATTT
1 ATATTATTTTTTAAATTAATATTTAAAAA-ATTT
* *
43299376 ATATTA-TTTTTAATTTAATATTTAATAAATTT
1 ATATTATTTTTTAAATTAATATTTAAAAAATTT
43299408 ATA-TATTTT
1 ATATTATTTT
43299417 GCATTTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
31 11 0.31
32 18 0.50
33 7 0.19
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (33 bp):
ATATTATTTTTTAAATTAATATTTAAAAAATTT
Found at i:43301247 original size:21 final size:22
Alignment explanation
Indices: 43301221--43301284 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
43301211 TTATGATAAT
*
43301221 TAAATAATATTTATTTTTATGA
1 TAAATATTATTTATTTTTATGA
**
43301243 T-AATATTATTTATCCTTATGA
1 TAAATATTATTTATTTTTATGA
43301264 TAAATATTATATTATGTTTTA
1 TAAATATTAT-TTAT-TTTTA
43301285 CTTTTGAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 18 0.53
22 9 0.26
23 4 0.12
24 3 0.09
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (22 bp):
TAAATATTATTTATTTTTATGA
Found at i:43302375 original size:23 final size:23
Alignment explanation
Indices: 43302346--43302399 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
43302336 AAAAAATAAT
* *
43302346 TTCAAGTTAA-TCGAATCAAGTTA
1 TTCAAGTTAACTCAAAT-AAGTAA
*
43302369 TTCAAGTCAACTCAAATAAGTAA
1 TTCAAGTTAACTCAAATAAGTAA
43302392 TTCAAGTT
1 TTCAAGTT
43302400 TCGAATTCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (23 bp):
TTCAAGTTAACTCAAATAAGTAA
Found at i:43302578 original size:19 final size:19
Alignment explanation
Indices: 43302533--43302604 Score: 101
Period size: 20 Copynumber: 3.7 Consensus size: 19
43302523 AAAATTAAAA
43302533 AAAAATTCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
43302552 CAAAAATTCAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
*
43302572 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
43302591 AAAAATTCCAAAAT
1 AAAAATT-CAAAAT
43302605 TTATATATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
18 4 0.08
19 19 0.40
20 25 0.52
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:43302611 original size:20 final size:19
Alignment explanation
Indices: 43302533--43302609 Score: 88
Period size: 19 Copynumber: 4.1 Consensus size: 19
43302523 AAAATTAAAA
43302533 AAAAATTCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
43302552 CAAAAATTCAAAATAATTT-T
1 -AAAAATTCAAAAT-ATTTAT
*
43302572 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
43302591 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
43302609 A
1 A
43302610 TATTTTTTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
18 11 0.21
19 23 0.43
20 19 0.36
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:43302642 original size:28 final size:30
Alignment explanation
Indices: 43302600--43302672 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 30
43302590 TAAAAATTCC
* * *
43302600 AAAATTTATATATTTTTTAA-AAT-TATAA
1 AAAATTTAAAAATTTTTCAAGAATATATAA
*
43302628 AAAATTTAAAAATTTCTCAAGAATATATAA
1 AAAATTTAAAAATTTTTCAAGAATATATAA
*
43302658 AAAAGTT-AAAATTTT
1 AAAATTTAAAAATTTT
43302673 AAAAATTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 16 0.43
29 10 0.27
30 11 0.30
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (30 bp):
AAAATTTAAAAATTTTTCAAGAATATATAA
Found at i:43302655 original size:45 final size:44
Alignment explanation
Indices: 43302568--43302656 Score: 101
Period size: 45 Copynumber: 2.0 Consensus size: 44
43302558 TTCAAAATAA
*
43302568 TTTTTAAAATTCAAAATATTTATAAAAATTCCAAAATTTATATAT
1 TTTTTAAAATTCAAAAAATTTATAAAAATTCCAAAA-TTATATAT
* *
43302613 TTTTTAAAATTATAAAAAATTTA-AAAATTTCTCAAGAA-TATATA
1 TTTTTAAAATT-CAAAAAATTTATAAAAATTC-CAA-AATTATATA
43302657 AAAAAGTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
45 24 0.63
46 12 0.32
47 2 0.05
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.43
Consensus pattern (44 bp):
TTTTTAAAATTCAAAAAATTTATAAAAATTCCAAAATTATATAT
Found at i:43318317 original size:23 final size:24
Alignment explanation
Indices: 43318277--43318322 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
43318267 AAAAATTTTC
43318277 TTTTTAGTTATTTTATTTTCCTTG
1 TTTTTAGTTATTTTATTTTCCTTG
43318301 TTTTTA-TT-TTTTAATTTTCCTT
1 TTTTTAGTTATTTT-ATTTTCCTT
43318323 TTAATTGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 11 0.52
24 6 0.29
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.74
Consensus pattern (24 bp):
TTTTTAGTTATTTTATTTTCCTTG
Found at i:43319035 original size:5 final size:5
Alignment explanation
Indices: 43319025--43319052 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
43319015 GTTTTTCAGT
43319025 TTTAG TTTAG TTTAG TTTAG TTTAG TTT
1 TTTAG TTTAG TTTAG TTTAG TTTAG TTT
43319053 TTATTTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (5 bp):
TTTAG
Found at i:43320479 original size:23 final size:24
Alignment explanation
Indices: 43320439--43320484 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
43320429 AAAAAGTTTA
43320439 TTTTTAGTTATTTTATTTTCCTTG
1 TTTTTAGTTATTTTATTTTCCTTG
43320463 TTTTTA-TT-TTTTAATTTTCCTT
1 TTTTTAGTTATTTT-ATTTTCCTT
43320485 TTAATTGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 11 0.52
24 6 0.29
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.74
Consensus pattern (24 bp):
TTTTTAGTTATTTTATTTTCCTTG
Found at i:43322638 original size:23 final size:24
Alignment explanation
Indices: 43322598--43322643 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
43322588 AAAAAGTTTA
43322598 TTTTTAGTTATTTTATTTTCCTTG
1 TTTTTAGTTATTTTATTTTCCTTG
43322622 TTTTTA-TT-TTTTAATTTTCCTT
1 TTTTTAGTTATTTT-ATTTTCCTT
43322644 TTAATTGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 11 0.52
24 6 0.29
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.74
Consensus pattern (24 bp):
TTTTTAGTTATTTTATTTTCCTTG
Found at i:43334089 original size:26 final size:26
Alignment explanation
Indices: 43334051--43334103 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
43334041 TTGGATAAAA
43334051 AGGGATTGATAAGTGCAGATTCCTCG
1 AGGGATTGATAAGTGCAGATTCCTCG
* * *
43334077 AGGGGTTGCTAAGTGCTGATTCCTCG
1 AGGGATTGATAAGTGCAGATTCCTCG
43334103 A
1 A
43334104 ATTATTAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (26 bp):
AGGGATTGATAAGTGCAGATTCCTCG
Found at i:43334220 original size:42 final size:42
Alignment explanation
Indices: 43334080--43334302 Score: 195
Period size: 42 Copynumber: 5.3 Consensus size: 42
43334070 TTCCTCGAGG
* * * * *
43334080 GGTTGCTAAGTGCTGATTCCTCGAATTA-TTAACTCTAAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATCACTGAA-TGTAAAGGT
* * ** * *
43334122 GGTTGCTAAGTGTTGATTCCACCGTTTCTTTGATTGTGAAAAG-
1 GGTTGCTAAGTGCTGATTCC-CCGTATCACTGAATGT-AAAGGT
* *
43334165 GGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATCACTGAATGTAAAGGT
* * *
43334207 TGTTGCTAAGTGCTGATTCCACCGTATC-TTTAATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCC-CCGTATCACTGAA-TGT-AAAGGT
* *
43334250 GGTTGCTATGTGCTGATTCCCCGTATCACTGAAT-TTAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATCACTGAATGTAAAGGT
43334291 GGTTGCTAAGTG
1 GGTTGCTAAGTG
43334303 TTGAATCCAC
Statistics
Matches: 143, Mismatches: 29, Indels: 19
0.75 0.15 0.10
Matches are distributed among these distances:
40 4 0.03
41 16 0.11
42 59 0.41
43 53 0.37
44 11 0.08
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCCCGTATCACTGAATGTAAAGGT
Found at i:43334224 original size:85 final size:84
Alignment explanation
Indices: 43334079--43334313 Score: 328
Period size: 85 Copynumber: 2.8 Consensus size: 84
43334069 ATTCCTCGAG
* * * * *
43334079 GGGTTGCTAAGTGCTGATTCCTCGAATTA-TTAACTCTAAAGGTGGTTGCTAAGTGTTGATTCCA
1 GGGTTGCTATGTGCTGATTCCCCGTATCACTGAA-T-TAAAGGTGGTTGCTAAGTGTTGATTCCA
* *
43334143 CCGTTTCTTTGATTGTGAAAA
64 CCGTATCTTTAATTGTGAAAA
* *
43334164 GGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGGTTGTTGCTAAGTGCTGATTCCAC
1 GGGTTGCTATGTGCTGATTCCCCGTATCACTGAAT-TAAAGGTGGTTGCTAAGTGTTGATTCCAC
*
43334229 CGTATCTTTAATTGTGAAAG
65 CGTATCTTTAATTGTGAAAA
* *
43334249 GGGTTGCTATGTGCTGATTCCCCGTATCACTGAATTTAAGGTGGTTGCTAAGTGTTGAATCCACC
1 GGGTTGCTATGTGCTGATTCCCCGTATCACTGAATTAAAGGTGGTTGCTAAGTGTTGATTCCACC
43334314 AAGTAACGGA
Statistics
Matches: 134, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
84 26 0.19
85 105 0.78
86 3 0.02
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (84 bp):
GGGTTGCTATGTGCTGATTCCCCGTATCACTGAATTAAAGGTGGTTGCTAAGTGTTGATTCCACC
GTATCTTTAATTGTGAAAA
Found at i:43337319 original size:44 final size:43
Alignment explanation
Indices: 43337271--43338369 Score: 351
Period size: 44 Copynumber: 25.0 Consensus size: 43
43337261 AAACCTAGGG
* *
43337271 AGGCAAGGCTGGTGTCTTCGACCTGCTTCGCTGTCAGTACAAGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTG-CAGTACAGGA
* * * * * * * * *
43337315 AGGCAAGATCTGCTATTTTCAACCTGCTCCACTGCA--ACCTAGGG
1 AGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGCAGTA-C-AGGA
*
43337359 AGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGCCAGTACAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTG-CAGTACAGGA
* * * * * ***
43337403 AGGCAAGATCTGCTATCTTC-AGTCTGCTCCACTGCAACCCAAGG-
1 AGGCAAG-GCTGGTGTCTTCGA-TCTGCTTCGCTGCAGTAC-AGGA
* * *
43337447 AGGCAAGGCTGGTGGCTTCGATCTGCTTCGATGCCAGTACAAGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTG-CAGTACAGGA
* * * * * * * *** *
43337491 AGGCAAGATCTGCTATTTTCAACCTGCTCCGCTGCAACCCAGGG
1 AGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGCAGTACAGGA
*
43337535 AGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGCTAGTACAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGC-AGTACAGGA
* * * * * * *** *
43337579 AGGCAAGATCTGCTATTTTCAACCTG-TTCCGCTGCAACCCAGGG
1 AGGCAAG-GCTGGTGTCTTCGATCTGCTT-CGCTGCAGTACAGGA
** * * *
43337623 AGGCAAGGCCAGTTTCTTCGATCAGCTTCGCTGCTGGTACAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGC-AGTACAGGA
* * * * ** *** *
43337667 AGGCAAGATCTGCTATCTTC-AGTCTGCTCCATTGCAACCCAGGG
1 AGGCAAG-GCTGGTGTCTTCGA-TCTGCTTCGCTGCAGTACAGGA
* *
43337711 AGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCGGTACAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTG-CAGTACAGGA
** * * * * *
43337755 AGGCAAGATTTGTTATCTTC-AGTCTGCTCCGCTAC-G-ACCTAGGG
1 AGGCAAG-GCTGGTGTCTTCGA-TCTGCTTCGCTGCAGTA-C-AGGA
*
43337799 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGATGCCAGTACAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTG-CAGTACAGGA
* * * * * * * *** *
43337843 AGGCAAGATCTGCTATTTTCAACCTGCTCCGCTGCAACCCAGGG
1 AGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGCAGTACAGGA
* *
43337887 AGGCAAGGCCGGTGTCTTCGATCTGCTTCACTGCTAGTACAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGC-AGTACAGGA
* * * * * * * *** *
43337931 AGGCAAGATCTGCTATTTTCAACCT-ATTCG-TCGCAACCCAGGG
1 AGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCT-GCAGTACAGGA
* *
43337974 AGGCAAGGCCGGTGTCTTCGATCTGCTTCGCTGCTGGTACAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGC-AGTACAGGA
** * * * * * * *** *
43338018 AGGCAAAATCTGCTATCTT-TAGGCTGCTCCACTGCAACCCAGGG
1 AGGC-AAGGCTGGTGTCTTCGA-TCTGCTTCGCTGCAGTACAGGA
*
43338062 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCTGTACAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTG-CAGTACAGGA
* ** * * * * *** *
43338106 AGGCAAGATCTTCTATCTTC-AGTCTACTCCACTGCAACCCAGGG
1 AGGCAAG-GCTGGTGTCTTCGA-TCTGCTTCGCTGCAGTACAGGA
* * * *
43338150 AGGCAAGGCTGATGTCTTCGATCTGCTTCACTGTCGGTATAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTG-CAGTACAGGA
* ** * * * * *** *
43338194 AGACAATATCTGCTAT-TCTCAACCTG-TTCCGCTGCAACCCAGGG
1 AGGCAA-GGCTGGTGTCT-TCGATCTGCTT-CGCTGCAGTACAGGA
* *
43338238 AGGCAAGGCTGGTGTCTTCGATATGCTTCGCTGCCTA-CACAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTG-C-AGTACAGGA
** * * * * * * *** *
43338282 AGGCAAAATCTGCTATCTTC-AGTTTGCTCCACTACAACCCAGGG
1 AGGC-AAGGCTGGTGTCTTCGA-TCTGCTTCGCTGCAGTACAGGA
* *
43338326 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGTTGTCGGTACAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTG-CAGTACAGGA
43338370 TGACAAGATC
Statistics
Matches: 718, Mismatches: 280, Indels: 114
0.65 0.25 0.10
Matches are distributed among these distances:
42 12 0.02
43 217 0.30
44 278 0.39
45 209 0.29
46 2 0.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (43 bp):
AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCAGTACAGGA
Found at i:43337397 original size:88 final size:88
Alignment explanation
Indices: 43337202--43338515 Score: 1637
Period size: 88 Copynumber: 14.9 Consensus size: 88
43337192 GGTTATTTCA
* * * * * *
43337202 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAAATTTGCTGTTTTTAGTCTGCTCCGCTGCAAACCT
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCTGCTCCACTGC-AACCC
43337267 AGGGAGGCAAGGCTGGTGTCTTCG
65 AGGGAGGCAAGGCTGGTGTCTTCG
* * * ** *
43337291 ACCTGCTTCGCTGTCAGTACAAGAAGGCAAGATCTGCTATTTTCAACCTGCTCCACTGCAACCTA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCTGCTCCACTGCAACCCA
*
43337356 GGGAGGCAAGGCTGGTGTCTTTG
66 GGGAGGCAAGGCTGGTGTCTTCG
*
43337379 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCCA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCTGCTCCACTGCAACCCA
* *
43337444 AGGAGGCAAGGCTGGTGGCTTCG
66 GGGAGGCAAGGCTGGTGTCTTCG
* * ** *
43337467 ATCTGCTTCGATGCCAGTACAAGAAGGCAAGATCTGCTATTTTCAACCTGCTCCGCTGCAACCCA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCTGCTCCACTGCAACCCA
*
43337532 GGGAGGCAAGGCTGGTGTCTTTG
66 GGGAGGCAAGGCTGGTGTCTTCG
* ** * *
43337555 ATCTGCTTCGCTGCTAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTGTTCCGCTGCAACCCA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCTGCTCCACTGCAACCCA
** *
43337620 GGGAGGCAAGGCCAGTTTCTTCG
66 GGGAGGCAAGGCTGGTGTCTTCG
* ** * *
43337643 ATCAGCTTCGCTGCTGGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCATTGCAACCCA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCTGCTCCACTGCAACCCA
43337708 GGGAGGCAAGGCTGGTGTCTTCG
66 GGGAGGCAAGGCTGGTGTCTTCG
* * * * * * * * * *
43337731 ATCTGCTTCACTGTCGGTACAGGAAGGCAAGATTTGTTATCTTCAGTCTGCTCCGCTACGACCTA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCTGCTCCACTGCAACCCA
43337796 GGGAGGCAAGGCTGGTGTCTTCG
66 GGGAGGCAAGGCTGGTGTCTTCG
* ** *
43337819 ATCTGCTTCGATGCCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTGCTCCGCTGCAACCCA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCTGCTCCACTGCAACCCA
*
43337884 GGGAGGCAAGGCCGGTGTCTTCG
66 GGGAGGCAAGGCTGGTGTCTTCG
* * ** ** **
43337907 ATCTGCTTCACTGCTAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTATTCGTC-GCAACCCA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCTGCTCCACTGCAACCCA
*
43337971 GGGAGGCAAGGCCGGTGTCTTCG
66 GGGAGGCAAGGCTGGTGTCTTCG
** * *
43337994 ATCTGCTTCGCTGCTGGTACAGGAAGGCAAAATCTGCTATCTTT-AGGCTGCTCCACTGCAACCC
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTAT-TTTCAGTCTGCTCCACTGCAACCC
43338058 AGGGAGGCAAGGCTGGTGTCTTCG
65 AGGGAGGCAAGGCTGGTGTCTTCG
* * * * *
43338082 ATCTGCTTCGCTGTCTGTACAGGAAGGCAAGATCTTCTATCTTCAGTCTACTCCACTGCAACCCA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCTGCTCCACTGCAACCCA
*
43338147 GGGAGGCAAGGCTGATGTCTTCG
66 GGGAGGCAAGGCTGGTGTCTTCG
* * * * * * * ** * *
43338170 ATCTGCTTCACTGTCGGTATAGGAAGACAATATCTGCTATTCTCAACCTGTTCCGCTGCAACCCA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCTGCTCCACTGCAACCCA
43338235 GGGAGGCAAGGCTGGTGTCTTCG
66 GGGAGGCAAGGCTGGTGTCTTCG
* * * * * *
43338258 ATATGCTTCGCTGCCTA-CACAGGAAGGCAAAATCTGCTATCTTCAGTTTGCTCCACTACAACCC
1 ATCTGCTTCGCTGCC-AGTACAGGAAGGCAAGATCTGCTATTTTCAGTCTGCTCCACTGCAACCC
43338322 AGGGAGGCAAGGCTGGTGTCTTCG
65 AGGGAGGCAAGGCTGGTGTCTTCG
* * * * * * * *
43338346 ATCTGCTTCGTTGTCGGTACAGGATGACAAGATCTGCTATCTTT-AGTCTACTCCATTGCAACCT
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTAT-TTTCAGTCTGCTCCACTGCAACCC
* *
43338410 AGGGAGGCAAGGCTTGTGTCTTTG
65 AGGGAGGCAAGGCTGGTGTCTTCG
* ** * * *
43338434 ATCTGCTTCACTGCTGGTACAAGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTACAACCCA
1 ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCTGCTCCACTGCAACCCA
*
43338499 GGGAGGCAAGACTGGTG
66 GGGAGGCAAGGCTGGTG
43338516 ATTTCACTGA
Statistics
Matches: 1059, Mismatches: 159, Indels: 15
0.86 0.13 0.01
Matches are distributed among these distances:
87 78 0.07
88 930 0.88
89 51 0.05
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.26
Consensus pattern (88 bp):
ATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATTTTCAGTCTGCTCCACTGCAACCCA
GGGAGGCAAGGCTGGTGTCTTCG
Found at i:43345892 original size:3 final size:3
Alignment explanation
Indices: 43345884--43345981 Score: 55
Period size: 3 Copynumber: 33.7 Consensus size: 3
43345874 AAAGAATTAA
*
43345884 AAT AAT AAT ACAT AAT AA- AAT AA- AAT AAT -GT AA- AA- AAT AA-
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
43345924 ACT AAT ACGAT AAT GAT ACT TAT AAT AAT AAT AGT AAT AAT AAT AAT
1 AAT AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
43345971 AGT ATT AAT AA
1 AAT AAT AAT AA
43345982 ATTAAAAAAA
Statistics
Matches: 72, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
2 10 0.14
3 56 0.78
4 3 0.04
5 3 0.04
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:43345963 original size:15 final size:15
Alignment explanation
Indices: 43345886--43345981 Score: 69
Period size: 15 Copynumber: 6.6 Consensus size: 15
43345876 AGAATTAAAA
43345886 TAATAATACATAATA-
1 TAATAATA-ATAATAG
*
43345901 AAATAA-AATAAT-G
1 TAATAATAATAATAG
*
43345914 TAA-AA-AATAA-AC
1 TAATAATAATAATAG
* *
43345926 TAATACGATAATGATAC
1 TAATA--ATAATAATAG
*
43345943 TTATAATAATAATAG
1 TAATAATAATAATAG
43345958 TAATAATAATAATAG
1 TAATAATAATAATAG
*
43345973 TATTAATAA
1 TAATAATAA
43345982 ATTAAAAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
12 10 0.15
13 8 0.12
14 1 0.02
15 36 0.55
16 4 0.06
17 6 0.09
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.31
Consensus pattern (15 bp):
TAATAATAATAATAG
Found at i:43346646 original size:16 final size:15
Alignment explanation
Indices: 43346609--43346647 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
43346599 AATAAAATCG
43346609 AAAGAA-AAAAAGAA
1 AAAGAAGAAAAAGAA
*
43346623 AAACAAGAAAAAGAA
1 AAAGAAGAAAAAGAA
43346638 AACAGAAGAA
1 AA-AGAAGAA
43346648 GCAAAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 5 0.24
15 10 0.48
16 6 0.29
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAGAAGAAAAAGAA
Found at i:43349664 original size:42 final size:42
Alignment explanation
Indices: 43349559--43349746 Score: 202
Period size: 43 Copynumber: 4.5 Consensus size: 42
43349549 AGATTCCCCG
* * ** *
43349559 AGGGGTTGCTAAGTGCTGATTACACCATATCTTTGATTGTGAA
1 AGGGGTTGCTAAGTGCTGATT-CCCCGTATCACTGAATGTGAA
* * *
43349602 AGGGGTTGCTATGTGTTGATTCCCCGTATCACTGAATAT-AA
1 AGGGGTTGCTAAGTGCTGATTCCCCGTATCACTGAATGTGAA
** *
43349643 AGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAA
1 AGG-GGTTGCTAAGTGCTGATTCC-CCGTATCACTGAATGTGAA
* *
43349687 AGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAAT-T-TA
1 AGGGGTTGCTAAGTGCTGATTCCCCGTATCACTGAATGTGAA
43349727 AGGTGGTTGCTAAGTGCTGA
1 AGG-GGTTGCTAAGTGCTGA
43349747 ATCCACCGAG
Statistics
Matches: 121, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
40 4 0.03
41 21 0.17
42 41 0.34
43 50 0.41
44 5 0.04
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (42 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGTATCACTGAATGTGAA
Found at i:43349707 original size:85 final size:84
Alignment explanation
Indices: 43349562--43349754 Score: 332
Period size: 85 Copynumber: 2.3 Consensus size: 84
43349552 TTCCCCGAGG
* * *
43349562 GGTTGCTAAGTGCTGATTACACCATATCTTTGATTGTGAAAGGGGTTGCTATGTGTTGATTCCCC
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCC
43349627 GTATCACTGAATATAAAGGT
66 GTATCACTGAAT-TAAAGGT
43349647 GGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCC
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCC
*
43349712 GTATCACTGAATTTAAGGT
66 GTATCACTGAATTAAAGGT
*
43349731 GGTTGCTAAGTGCTGAATCCACCG
1 GGTTGCTAAGTGCTGATTCCACCG
43349755 AGTAACGGAT
Statistics
Matches: 103, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
84 29 0.28
85 74 0.72
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (84 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTTGATTGTGAAAGGGGTTGCTATGTGCTGATTCCCC
GTATCACTGAATTAAAGGT
Found at i:43356824 original size:11 final size:11
Alignment explanation
Indices: 43356808--43356836 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
43356798 CCACATCAAC
43356808 AAATTATTTTA
1 AAATTATTTTA
43356819 AAATTATTTTA
1 AAATTATTTTA
43356830 AAATTAT
1 AAATTAT
43356837 CATCATCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:43357251 original size:5 final size:5
Alignment explanation
Indices: 43357241--43357277 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
43357231 TTTTTTTTAG
43357241 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
43357278 GCAGGTGAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:43361282 original size:20 final size:20
Alignment explanation
Indices: 43361259--43361327 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 20
43361249 TTTTTTTGGA
43361259 ATTGATCTGAAATTTTATAT
1 ATTGATCTGAAATTTTATAT
**
43361279 ATTGAGTGGGTAAATGCTTT-TCA-
1 ATTGA-TCTG-AAAT--TTTAT-AT
43361302 ATTGATCTGAAATTTTATAT
1 ATTGATCTGAAATTTTATAT
43361322 ATTGAT
1 ATTGAT
43361328 TTTTGGAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 4 0.11
20 12 0.32
21 6 0.16
22 6 0.16
23 6 0.16
24 4 0.11
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (20 bp):
ATTGATCTGAAATTTTATAT
Found at i:43365740 original size:39 final size:39
Alignment explanation
Indices: 43365697--43365773 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
43365687 GGAACTTCAC
43365697 TGATACACAACTTACCCTTAGCTCTCGAGGGAGCTTTGT
1 TGATACACAACTTACCCTTAGCTCTCGAGGGAGCTTTGT
* * *
43365736 TGATACACAACTTATCTTTAGCTCTCGGGGGAGCTTTG
1 TGATACACAACTTACCCTTAGCTCTCGAGGGAGCTTTG
43365774 CTAATACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.32
Consensus pattern (39 bp):
TGATACACAACTTACCCTTAGCTCTCGAGGGAGCTTTGT
Found at i:43379789 original size:19 final size:19
Alignment explanation
Indices: 43379765--43379804 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
43379755 TGGTTGCGAG
43379765 AAAGATTTCTTCTTTGTAC
1 AAAGATTTCTTCTTTGTAC
43379784 AAAGATTTCTTCTTTGTAC
1 AAAGATTTCTTCTTTGTAC
43379803 AA
1 AA
43379805 GTTGGGGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (19 bp):
AAAGATTTCTTCTTTGTAC
Found at i:43384217 original size:31 final size:32
Alignment explanation
Indices: 43384180--43384417 Score: 195
Period size: 31 Copynumber: 7.7 Consensus size: 32
43384170 CATCATCGGT
43384180 ACATAGTACCTGATA-AATTATAAACACTGGC
1 ACATAGTACCTGATACAATTATAAACACTGGC
* * *
43384211 ATATAGTGCCTGATACAA-TATAAACACTGGT
1 ACATAGTACCTGATACAATTATAAACACTGGC
* * * *
43384242 ACATAGTACGTGATA-AACTATAAACATTAGC
1 ACATAGTACCTGATACAATTATAAACACTGGC
* * * * * **
43384273 ACATAGTGCTTAATACAA-TATAAATATTGAT
1 ACATAGTACCTGATACAATTATAAACACTGGC
*
43384304 ACATAGTACCTGATA-AATTATAAACACTGAC
1 ACATAGTACCTGATACAATTATAAACACTGGC
* *
43384335 ACATAGTGCCTGATACAA-TATAAACA-TCGGT
1 ACATAGTACCTGATACAATTATAAACACT-GGC
* * *
43384366 ACATAGTATCTGATA-AATTATAAACTCCGGC
1 ACATAGTACCTGATACAATTATAAACACTGGC
* * * *
43384397 ATATAGTGCCTGCTATAATTA
1 ACATAGTACCTGATACAATTA
43384418 AACCCTAATG
Statistics
Matches: 164, Mismatches: 34, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
30 7 0.04
31 146 0.89
32 11 0.07
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (32 bp):
ACATAGTACCTGATACAATTATAAACACTGGC
Found at i:43384279 original size:62 final size:60
Alignment explanation
Indices: 43384177--43384408 Score: 293
Period size: 62 Copynumber: 3.8 Consensus size: 60
43384167 ATCCATCATC
*
43384177 GGTACATAGTACCTGATAAATTATAAACACTGGCATATAGTGCCTGATACAATATAAACACT
1 GGTACATAGTACCTGATAAATTATAAACACT-GCACATAGTGCCTGATACAATATAAACA-T
* * * * * *
43384239 GGTACATAGTACGTGATAAACTATAAACATTAGCACATAGTGCTTAATACAATATAAATATT
1 GGTACATAGTACCTGATAAATTATAAACACT-GCACATAGTGCCTGATACAATATAAACA-T
*
43384301 GATACATAGTACCTGATAAATTATAAACACTGACACATAGTGCCTGATACAATATAAACAT
1 GGTACATAGTACCTGATAAATTATAAACACTG-CACATAGTGCCTGATACAATATAAACAT
* * * *
43384362 CGGTACATAGTATCTGATAAATTATAAACTCCGGCATATAGTGCCTG
1 -GGTACATAGTACCTGATAAATTATAAAC-ACTGCACATAGTGCCTG
43384409 CTATAATTAA
Statistics
Matches: 146, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
61 2 0.01
62 142 0.97
63 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (60 bp):
GGTACATAGTACCTGATAAATTATAAACACTGCACATAGTGCCTGATACAATATAAACAT
Found at i:43389521 original size:125 final size:126
Alignment explanation
Indices: 43389305--43389835 Score: 739
Period size: 125 Copynumber: 4.2 Consensus size: 126
43389295 ATTTTCGCAG
* * *
43389305 TCGCGCCCACGTGTATGCGCTTTTACTACAGTAGGTCCTGGAA-AAATAATTTCGAGTTGACGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* *
43389369 TCTGAGCAAATAGTATAAAAAAT-GCTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAA
66 TCTGAGCAAATAGTAT-AAAAATCGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
* * * * * *
43389430 TCGTGCCCTCCTAGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTTGAGTTGACGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* *
43389495 TCTGAGCAAATAGTAT-AAAATCGCTTCTACCAGGATGCTTTATGAGAAGAATTTGTGAAA
66 TCTGAGCAAATAGTATAAAAATCGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
* * * *
43389555 TCGCACCCACGTGGACGCGCTTTTGCTACAGTAGGTCCT-GAAAAAATTATTTCGAGTTGACATT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* *** * * *
43389619 TCTGAGCAAATAGCATAAAAAAAACTTCAAGCAGGATGCTATTTGAGAAGAATTTCTGAAA
66 TCTGAGCAAATAGTATAAAAATCGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
* * *
43389680 TCGCGCCCTCGTGGACGTGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
* * *
43389745 TCTGAGCAAATAGTAT-AAAATCGCTTCTACCAGGATGTTTTATGAGAAGAATTTGTGAAA
66 TCTGAGCAAATAGTATAAAAATCGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
*
43389805 TCGCGCCCACGTGGACGCGCTTTTACTACAG
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAG
43389836 GAGCATGTTT
Statistics
Matches: 350, Mismatches: 52, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
124 41 0.12
125 236 0.67
126 73 0.21
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (126 bp):
TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
TCTGAGCAAATAGTATAAAAATCGCTTCAACCAGGATGCTATATGAGAAGAATTTGTGAAA
Found at i:43389716 original size:250 final size:250
Alignment explanation
Indices: 43389305--43389835 Score: 891
Period size: 250 Copynumber: 2.1 Consensus size: 250
43389295 ATTTTCGCAG
* * * *
43389305 TCGCGCCCACGTGTATGCGCTTTTACTACAGTAGGTCCTGGAAAAATAATTTCGAGTTGACGTTT
1 TCGCGCCCACGTGGACGCGCTTTTACTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACATTT
* ** * * *
43389370 CTGAGCAAATAGTATAAAAAATGCTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAATCGTG
66 CTGAGCAAATAGCATAAAAAAAACTTCAAGCAGGATGCTATATGAGAAGAATTTCTGAAATCGCG
*
43389435 CCCTCCTAGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTTGAGTTGACGTTTCTGA
131 CCCTCCTAGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGA
43389500 GCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAGAATTTGTGAAA
196 GCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAGAATTTGTGAAA
* * *
43389555 TCGCACCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACATTT
1 TCGCGCCCACGTGGACGCGCTTTTACTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACATTT
*
43389620 CTGAGCAAATAGCATAAAAAAAACTTCAAGCAGGATGCTATTTGAGAAGAATTTCTGAAATCGCG
66 CTGAGCAAATAGCATAAAAAAAACTTCAAGCAGGATGCTATATGAGAAGAATTTCTGAAATCGCG
* * *
43389685 CCCTCGTGGACGTGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGA
131 CCCTCCTAGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGA
*
43389750 GCAAATAGTATAAAATCGCTTCTACCAGGATGTTTTATGAGAAGAATTTGTGAAA
196 GCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAGAATTTGTGAAA
43389805 TCGCGCCCACGTGGACGCGCTTTTACTACAG
1 TCGCGCCCACGTGGACGCGCTTTTACTACAG
43389836 GAGCATGTTT
Statistics
Matches: 260, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
250 260 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (250 bp):
TCGCGCCCACGTGGACGCGCTTTTACTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACATTT
CTGAGCAAATAGCATAAAAAAAACTTCAAGCAGGATGCTATATGAGAAGAATTTCTGAAATCGCG
CCCTCCTAGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGA
GCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAGAATTTGTGAAA
Found at i:43390216 original size:29 final size:29
Alignment explanation
Indices: 43390184--43390243 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
43390174 TCAACATAAA
*
43390184 AGGTGCTCATATCTTGGAGGCAATGGTGC
1 AGGTGCTCATAGCTTGGAGGCAATGGTGC
*
43390213 AGGTGCTCGTAGCTTGGAGGCAATGGTGC
1 AGGTGCTCATAGCTTGGAGGCAATGGTGC
43390242 AG
1 AG
43390244 ACTTATCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.38, T:0.25
Consensus pattern (29 bp):
AGGTGCTCATAGCTTGGAGGCAATGGTGC
Found at i:43393075 original size:22 final size:21
Alignment explanation
Indices: 43393075--43393427 Score: 216
Period size: 22 Copynumber: 16.3 Consensus size: 21
43393065 GGTTTTAGGG
*
43393075 TTTAGGGTTTTTAAGTTTAGGG
1 TTTAGGGTTTTTAAG-TTAAGG
43393097 TTTAGGGTTTTTAAGTTTAAGG
1 TTTAGGGTTTTTAAG-TTAAGG
*
43393119 TTTAGGG-TTTTAAGTTTAGG
1 TTTAGGGTTTTTAAGTTAAGG
* * *
43393139 TTTATGGTTTTTAGGTTTAGGG
1 TTTAGGGTTTTTAAG-TTAAGG
*
43393161 TTTGGGGTTTTTAAGTTAAAGG
1 TTTAGGGTTTTTAAGTT-AAGG
* * *
43393183 -TTATGGTTTTTAGGTTTACGG
1 TTTAGGGTTTTTAAG-TTAAGG
43393204 TTT-GAGGTTTTTAAGTTAAGG
1 TTTAG-GGTTTTTAAGTTAAGG
* *
43393225 GTTAGGGTTTTTAGGGTT-AGTG
1 TTTAGGGTTTTTA-AGTTAAG-G
* * *
43393247 TTTGAGGTTTTTTTAGTTTAGGG
1 TTT-AGGGTTTTTAAG-TTAAGG
** *
43393270 TTTATAGTTTTTAGGTTTAAGG
1 TTTAGGGTTTTTAAG-TTAAGG
* *
43393292 TTTAGGGTTTTTAGGTTTAGGG
1 TTTAGGGTTTTTAAG-TTAAGG
* *
43393314 TTT-GTGGTTTTTAGGTTTAGGG
1 TTTAG-GGTTTTTAAG-TTAAGG
43393336 TTTGAGGG-TTTTAAGTTAAGG
1 TTT-AGGGTTTTTAAGTTAAGG
* * **
43393357 GTTAGCGGGTTTTTAGGTTTGGGG
1 TTTA--GGGTTTTTAAG-TTAAGG
* *
43393381 TTT-GTGTTTTTAAATTAAGG
1 TTTAGGGTTTTTAAGTTAAGG
* * *
43393401 GTTAGCGTTTTTAATTTAAGG
1 TTTAGGGTTTTTAAGTTAAGG
*
43393422 GTTAGG
1 TTTAGG
43393428 ATTAGGGTTA
Statistics
Matches: 262, Mismatches: 49, Indels: 41
0.74 0.14 0.12
Matches are distributed among these distances:
20 18 0.07
21 82 0.31
22 132 0.50
23 22 0.08
24 8 0.03
ACGTcount: A:0.18, C:0.01, G:0.32, T:0.50
Consensus pattern (21 bp):
TTTAGGGTTTTTAAGTTAAGG
Found at i:43393080 original size:7 final size:7
Alignment explanation
Indices: 43393068--43393170 Score: 54
Period size: 7 Copynumber: 14.4 Consensus size: 7
43393058 AAGTTAAGGT
43393068 TTTAGGG
1 TTTAGGG
43393075 TTTAGGG
1 TTTAGGG
*
43393082 TTTTTA-AG
1 --TTTAGGG
43393090 TTTAGGG
1 TTTAGGG
43393097 TTTAGGG
1 TTTAGGG
*
43393104 TTTTTA-AG
1 --TTTAGGG
*
43393112 TTTAAGG
1 TTTAGGG
43393119 TTTAGGG
1 TTTAGGG
*
43393126 TTTTA-AG
1 -TTTAGGG
43393133 TTTA-GG
1 TTTAGGG
*
43393139 TTTATGGTT
1 TTTA-GG-G
43393148 TTTA-GG
1 TTTAGGG
43393154 TTTAGGG
1 TTTAGGG
*
43393161 TTTGGGG
1 TTTAGGG
43393168 TTT
1 TTT
43393171 TTAAGTTAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
6 21 0.28
7 35 0.47
8 7 0.09
9 12 0.16
ACGTcount: A:0.17, C:0.00, G:0.32, T:0.51
Consensus pattern (7 bp):
TTTAGGG
Found at i:43393115 original size:15 final size:15
Alignment explanation
Indices: 43393047--43393099 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
43393037 AACTTAAGGG
*
43393047 TTAGGGTTTTAAAG-
1 TTAGGGTTTTTAAGT
* *
43393061 TTAAGG-TTTTAGGGT
1 TTAGGGTTTTTA-AGT
43393076 TTAGGGTTTTTAAGT
1 TTAGGGTTTTTAAGT
43393091 TTAGGGTTT
1 TTAGGGTTT
43393100 AGGGTTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 4 0.13
14 6 0.19
15 16 0.52
16 5 0.16
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (15 bp):
TTAGGGTTTTTAAGT
Found at i:43393121 original size:29 final size:29
Alignment explanation
Indices: 43393043--43393184 Score: 95
Period size: 29 Copynumber: 5.0 Consensus size: 29
43393033 ATTTAACTTA
*
43393043 AGGG-TTAGGGTTTTAAAG-TTAAGGTTTT
1 AGGGTTTAGGGTTTTTAAGTTTAAGG-TTT
43393071 AGGGTTTAGGG---TT---TTTAA-GTTT
1 AGGGTTTAGGGTTTTTAAGTTTAAGGTTT
43393093 AGGGTTTAGGGTTTTTAAGTTTAAGGTTT
1 AGGGTTTAGGGTTTTTAAGTTTAAGGTTT
* * * *
43393122 AGGGTTTTAAGTTTAGGTTTATGGTTTTTAGGTTT
1 AGGG-TTTAGGGTT---TTTA-AG-TTTAAGGTTT
* *
43393157 AGGGTTTGGGGTTTTTAAGTTAAAGGTT
1 AGGGTTTAGGGTTTTTAAGTTTAAGGTT
43393185 ATGGTTTTTA
Statistics
Matches: 88, Mismatches: 11, Indels: 29
0.69 0.09 0.23
Matches are distributed among these distances:
22 14 0.16
23 1 0.01
24 4 0.05
25 2 0.02
26 1 0.01
28 9 0.10
29 21 0.24
30 8 0.09
31 4 0.05
33 4 0.05
34 7 0.08
35 13 0.15
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (29 bp):
AGGGTTTAGGGTTTTTAAGTTTAAGGTTT
Found at i:43393121 original size:44 final size:43
Alignment explanation
Indices: 43393068--43393427 Score: 345
Period size: 44 Copynumber: 8.3 Consensus size: 43
43393058 AAGTTAAGGT
* * *
43393068 TTTAGGGTTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAAG
1 TTTAAGGTTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAGG
* * *
43393112 TTTAAGGTTTAGGG-TTTTAAGTTTAGGTTTATGGTTTTTAGG
1 TTTAAGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAGG
* * * *
43393154 TTTAGGGTTTGGGGTTTTTAAGTTAAAGGTTATGGTTTTTAGG
1 TTTAAGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAGG
*
43393197 TTTACGGTTT-GAGGTTTTTAAGTTAAGGGTTAGGGTTTTTAGG
1 TTTAAGGTTTAG-GGTTTTTAAGTTAAGGGTTAGGGTTTTTAGG
* * * * **
43393240 GTT-AGTGTTTGAGGTTTTTTTAGTTTAGGGTTTATAGTTTTTAGG
1 TTTAAG-GTTT-AGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAGG
* * *
43393285 TTTAAGGTTTAGGGTTTTTAGGTTTAGGGTTTGTGGTTTTTAGG
1 TTTAAGGTTTAGGGTTTTTAAGTTAAGGGTTAG-GGTTTTTAGG
*
43393329 TTTAGGGTTTGAGGG-TTTTAAGTTAAGGGTTAGCGGGTTTTTAGG
1 TTTAAGGTTT-AGGGTTTTTAAGTTAAGGGTTA--GGGTTTTTAGG
** * * * *
43393374 TTTGGGGTTT-GTGTTTTTAAATTAAGGGTTAGCGTTTTTA-A
1 TTTAAGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAGG
*
43393415 TTTAAGGGTTAGG
1 TTTAAGGTTTAGG
43393428 ATTAGGGTTA
Statistics
Matches: 264, Mismatches: 39, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
41 7 0.03
42 35 0.13
43 86 0.33
44 91 0.34
45 42 0.16
46 3 0.01
ACGTcount: A:0.18, C:0.01, G:0.32, T:0.49
Consensus pattern (43 bp):
TTTAAGGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAGG
Done.