Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold47
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: 2157611
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 149227 characters in sequence are not A, C, G, or T
File 15 of 15
Found at i:2050546 original size:43 final size:43
Alignment explanation
Indices: 2050228--2050547 Score: 361
Period size: 43 Copynumber: 7.0 Consensus size: 43
2050218 GCAACCCCTC
*
2050228 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA----C--CTT
* * *
2050277 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
*
2050320 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA----C--CTT
* * *
2050369 TAAGTCCAATGTAGCTGGCCTTCAATCAGCACATTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
*
2050412 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA----C--CTT
* * * *
2050461 TAAGTCCAATGTAGCTAGCCTTGAATCAGTACATTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
2050504 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
2050547 T
1 T
2050548 TCCATCTTTA
Statistics
Matches: 234, Mismatches: 25, Indels: 30
0.81 0.09 0.10
Matches are distributed among these distances:
43 119 0.51
45 3 0.01
47 2 0.01
49 110 0.47
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (43 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
Found at i:2050579 original size:52 final size:55
Alignment explanation
Indices: 2050501--2051009 Score: 303
Period size: 49 Copynumber: 9.8 Consensus size: 55
2050491 ACATTGGCAC
*
2050501 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * *
2050553 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
2050608 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGACATCTTTATCACTTTTCTCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG--A-C---ATC-C-TTT-T--TC-TC
2050673 AT
54 AT
* *
2050675 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCA-CC----T-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * *
2050724 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----------C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
2050767 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATT-AGCA-CC----T-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGA-CATCCTTTTTCTCAT
* * * * *
2050816 CTTTAAGCCCAATGTAGTTGGCCTTGAATCAGCACATTGGCA----------C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* *
2050859 CTTTAAGTCCAATATAGCTGGCATTGAATCAGCATATTGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
2050911 CTTTAAGTTCAATGTAGCTGGCTTTGAATCAGCACATTGACATCTTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * * * *
2050966 CTTTAAGCCCAATATCGTTGGTCGTGAATCAACATATTGGCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATC
2051010 TTTATCACTT
Statistics
Matches: 371, Mismatches: 51, Indels: 67
0.76 0.10 0.14
Matches are distributed among these distances:
43 75 0.20
45 2 0.01
47 1 0.00
49 79 0.21
50 1 0.00
51 1 0.00
52 75 0.20
53 3 0.01
54 10 0.03
55 70 0.19
57 1 0.00
58 1 0.00
59 1 0.00
60 1 0.00
61 4 0.01
62 1 0.00
63 3 0.01
64 2 0.01
66 2 0.01
67 38 0.10
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.35
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
Found at i:2050636 original size:55 final size:53
Alignment explanation
Indices: 2050501--2050651 Score: 196
Period size: 55 Copynumber: 2.8 Consensus size: 53
2050491 ACATTGGCAC
*
2050501 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTCCAT
* * *
2050553 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCC-TTTTC-CAT
* * * * *
2050608 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGACATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATC
2050652 TTTATCACTT
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
52 38 0.45
53 2 0.02
54 5 0.06
55 39 0.46
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACATCCTTTTCCAT
Found at i:2050725 original size:49 final size:49
Alignment explanation
Indices: 2050669--2050949 Score: 334
Period size: 49 Copynumber: 5.9 Consensus size: 49
2050659 CTTTTCTCAT
* *
2050669 CTTCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
2050718 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
2050766 ---C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCAC
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
2050810 CTTCATCTTTAAGCCCAATGTAGTTGGCCTTGAATCAGCACATTGGCA-
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
2050858 ---C--CTTTAAGTCCAATATAGCTGGCATTGAATCAGCATATTGGCAC
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
2050902 CTTTTCCATCTTTAAGTTCAATGTAGCTGGCTTTGAATCAGCACATTG
1 C--TT-CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
2050950 ACATCTTTTT
Statistics
Matches: 197, Mismatches: 20, Indels: 27
0.81 0.08 0.11
Matches are distributed among these distances:
43 76 0.39
45 2 0.01
47 1 0.01
49 82 0.42
50 1 0.01
52 35 0.18
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (49 bp):
CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:2050771 original size:116 final size:119
Alignment explanation
Indices: 2050550--2050771 Score: 270
Period size: 116 Copynumber: 1.9 Consensus size: 119
2050540 GCACCTTTTC
* *
2050550 CATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAG
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCC---TTCTCATCTTTAAG
* * * *
2050615 CCCAATATCGTTGGCCGTGAATCAACATATTGACATCTTTATCACTTTTCTCATCTT
63 CCCAATATAGCTGGCCGTGAATCAACACATTGACACCTTTATCACTTTTCTCATCTT
* * * *
2050672 CATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCA-CC-T-TCATCTTTAAGTCC
1 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTCTCATCTTTAAGCCC
* * * *
2050734 AATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTA
66 AATATAGCTGGCCGTGAATCAACACATTGACACCTTTA
2050772 AGTCCAATAT
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
116 43 0.50
117 1 0.01
121 2 0.02
122 40 0.47
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (119 bp):
CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTCTCATCTTTAAGCCC
AATATAGCTGGCCGTGAATCAACACATTGACACCTTTATCACTTTTCTCATCTT
Found at i:2050785 original size:43 final size:43
Alignment explanation
Indices: 2050724--2050905 Score: 238
Period size: 43 Copynumber: 4.1 Consensus size: 43
2050714 GCACCTTCAT
*
2050724 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
2050767 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCACCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C
* * *
2050814 ATCTTTAAGCCCAATGTAGTTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
2050859 CTTTAAGTCCAATATAGCTGGCATTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
2050902 CTTT
1 CTTT
2050906 TCCATCTTTA
Statistics
Matches: 120, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
43 81 0.68
45 1 0.01
47 1 0.01
49 37 0.31
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:2050832 original size:92 final size:92
Alignment explanation
Indices: 2050675--2050949 Score: 460
Period size: 92 Copynumber: 3.0 Consensus size: 92
2050665 TCATCTTCAT
*
2050675 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
2050740 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
2050767 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCACCTTCATCTTTAAGCCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
*
2050832 GTTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
2050859 CTTTAAGTCCAATATAGCTGGCATTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAAT
*
2050924 GTAGCTGGCTTTGAATCAGCACATTG
63 GTAGCTGGCCTTGAATCAGCACATTG
2050950 ACATCTTTTT
Statistics
Matches: 170, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
92 130 0.76
94 2 0.01
95 38 0.22
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (92 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:2050982 original size:358 final size:358
Alignment explanation
Indices: 2050320--2051094 Score: 1352
Period size: 358 Copynumber: 2.2 Consensus size: 358
2050310 TTGGCACCTC
* *
2050320 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
* *
2050385 GGCCTTCAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
66 GGCCTTCAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGC
* * *
2050450 ACCTTCTTCTTTAAGTCCAATGTAGCTAGCCTTGAATCAGTACATTGGCACCTTTAAGTCCAATA
131 ACCTTCATCTTTAAGCCCAATGTAGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATA
*
2050515 TAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGA
196 TAGCTGGCATTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGA
2050580 ATCAGCACATTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATAT
261 ATCAGCACATTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATAT
2050645 TGACATCTTTATCACTTTTCTCATCTTCATCTT
326 TGACATCTTTATCACTTTTCTCATCTTCATCTT
*
2050678 TAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
*
2050743 GGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGC
66 GGCCTTCAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGC
* *
2050808 ACCTTCATCTTTAAGCCCAATGTAGTTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATA
131 ACCTTCATCTTTAAGCCCAATGTAGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATA
*
2050873 TAGCTGGCATTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCTTTGA
196 TAGCTGGCATTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGA
* *
2050938 ATCAGCACATTGACATCTTTTTTCTCATCTTTAAGCCCAATATCGTTGGTCGTGAATCAACATAT
261 ATCAGCACATTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATAT
*
2051003 TGGCATCTTTATCACTTTTCTCATCTTCATCTT
326 TGACATCTTTATCACTTTTCTCATCTTCATCTT
* * * * * *
2051036 TAAGTCCAATGTCGCTGGCCTTGAATCGGCACATTGGCACCTTTATCTTTACGTCCAAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
2051095 ATCGCTAGCC
Statistics
Matches: 395, Mismatches: 22, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
358 395 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (358 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
GGCCTTCAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGC
ACCTTCATCTTTAAGCCCAATGTAGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATA
TAGCTGGCATTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGA
ATCAGCACATTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATAT
TGACATCTTTATCACTTTTCTCATCTTCATCTT
Found at i:2065298 original size:21 final size:22
Alignment explanation
Indices: 2065269--2065310 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2065259 AAATTAATAA
*
2065269 AACTGAAATTTATATTATTTTT
1 AACTGAAATATATATTATTTTT
*
2065291 AACT-AAATATATTTTATTTT
1 AACTGAAATATATATTATTTT
2065311 AGTCAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (22 bp):
AACTGAAATATATATTATTTTT
Found at i:2067906 original size:17 final size:17
Alignment explanation
Indices: 2067884--2067917 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2067874 AGCATATAAA
2067884 CCGGAAATAATGTAATT
1 CCGGAAATAATGTAATT
2067901 CCGGAAATAATGTAATT
1 CCGGAAATAATGTAATT
2067918 TTATGATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (17 bp):
CCGGAAATAATGTAATT
Found at i:2069235 original size:2 final size:2
Alignment explanation
Indices: 2069228--2069261 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2069218 TACATACTAG
2069228 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2069262 GTTGTAGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2071132 original size:6 final size:6
Alignment explanation
Indices: 2071121--2071152 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2071111 ATTAGAGTGT
*
2071121 ATTGTA ATTGTA ATTGTA ACTGTA ATTGTA AT
1 ATTGTA ATTGTA ATTGTA ATTGTA ATTGTA AT
2071153 AAAGACTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (6 bp):
ATTGTA
Found at i:2071356 original size:2 final size:2
Alignment explanation
Indices: 2071349--2071411 Score: 90
Period size: 2 Copynumber: 31.5 Consensus size: 2
2071339 GCATCATTTT
* *
2071349 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2071391 TA TG TA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
2071412 TATTGAGGTC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2082385 original size:2 final size:2
Alignment explanation
Indices: 2082380--2082410 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2082370 TTCACTCCTG
2082380 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2082411 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2082415 original size:2 final size:2
Alignment explanation
Indices: 2082410--2082437 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2082400 TCTCTCTCTC
2082410 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
2082438 ATTATTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2083306 original size:2 final size:2
Alignment explanation
Indices: 2083301--2083333 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2083291 TCTCTCTCTC
*
2083301 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2083334 GACACACACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2088774 original size:16 final size:15
Alignment explanation
Indices: 2088734--2088798 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 15
2088724 AAGTAAAATT
*
2088734 TAAAATTTATAGTTTGA
1 TAAAATTTA-AATTT-A
* *
2088751 TTAAATTTAATTTATA
1 TAAAATTTAAATT-TA
2088767 TAAAATTTAAAATTTA
1 TAAAATTT-AAATTTA
2088783 TAAAATTTAAACTTTA
1 TAAAATTTAAA-TTTA
2088799 CCTAAATCTG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
15 3 0.07
16 25 0.61
17 13 0.32
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (15 bp):
TAAAATTTAAATTTA
Found at i:2095228 original size:3 final size:3
Alignment explanation
Indices: 2095222--2095249 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2095212 TTTGTTGTTG
2095222 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
2095250 ATAAGTTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:2095785 original size:22 final size:21
Alignment explanation
Indices: 2095741--2095783 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
2095731 TCGAGTCTCC
2095741 AGATTAACTTTTTCTAGATTTT
1 AGATTAACTTTTTC-AGATTTT
2095763 AGATTAACCTTTTTC-GATTTT
1 AGATTAA-CTTTTTCAGATTTT
2095784 TAACCACTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 7 0.35
23 7 0.35
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (21 bp):
AGATTAACTTTTTCAGATTTT
Found at i:2096711 original size:33 final size:34
Alignment explanation
Indices: 2096669--2096737 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
2096659 GAAAGCCAAA
2096669 ATGTCAACTT-AAAGGTCTAGTCAAAGAAAGAGC
1 ATGTCAACTTAAAAGGTCTAGTCAAAGAAAGAGC
* *
2096702 ATGTCAACTTAAAAGGTTTAGTCAAAGAAGGAGC
1 ATGTCAACTTAAAAGGTCTAGTCAAAGAAAGAGC
2096736 AT
1 AT
2096738 TGTGAATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 10 0.30
34 23 0.70
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.23
Consensus pattern (34 bp):
ATGTCAACTTAAAAGGTCTAGTCAAAGAAAGAGC
Found at i:2097371 original size:14 final size:13
Alignment explanation
Indices: 2097352--2097387 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
2097342 CTTCCATAAT
*
2097352 AAAAAAAAGAAAG
1 AAAAAAAAAAAAG
2097365 AAAAAAAGAAAAAG
1 AAAAAAA-AAAAAG
2097379 AAAAAAAAA
1 AAAAAAAAA
2097388 TTGCTTCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:2098274 original size:22 final size:22
Alignment explanation
Indices: 2098227--2098275 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
2098217 TCAACATTAT
*
2098227 TTTTAACCTAAAATAATCTCAG
1 TTTTAACCTAAAATAATCTCAA
* *
2098249 TTTTAA-CTCAAATAGTCTCGAA
1 TTTTAACCTAAAATAATCTC-AA
2098271 TTTTA
1 TTTTA
2098276 TTGTATCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (22 bp):
TTTTAACCTAAAATAATCTCAA
Found at i:2123812 original size:110 final size:106
Alignment explanation
Indices: 2123627--2123943 Score: 312
Period size: 110 Copynumber: 2.9 Consensus size: 106
2123617 AATTCTTTTT
* * *
2123627 TTTTTTGCATAAATTACATAGCATTCCGGCA-CAAAGGGATTGGCCTCGAAATAAATCATTATCT
1 TTTTTTGCAT-AATTACATAG-ATTCAGGCACCAAA-GGATTGGCCTCGAAATAGATCATTGTCT
* *
2123691 AGAGTCTTAAAGTGGCATATGATTGCCCTTTATATAAGAGAATCCA
63 AGAGT-TTAAAGTGGCGTATGA-TGCCCTTTACATAAGAGAATCCA
* * * * *
2123737 TTTTTCGCATAACTTACATAGTATTCGGGCACCAAAGGATTGGCCCCGAAATAGATTATTGTCTG
1 TTTTTTGCATAA-TTACATAG-ATTCAGGCACCAAAGGATTGGCCTCGAAATAGATCATTGTCTA
* * * ** * * *
2123802 GAATTGTAAAGTGGTGTACGAACCCCTTGTACATAGGATAATTCA
64 GAGTT-TAAAGTGGCGTATGATGCCCTT-TACATAAGAGAATCCA
* * * * *
2123847 TTTTTTGCATTAATTACATAGATTCAGGCACCAAATGATTGGCTTAGAAATAGGTCATTGTTTAG
1 TTTTTTGCA-TAATTACATAGATTCAGGCACCAAAGGATTGGCCTCGAAATAGATCATTGTCTAG
2123912 AGTTATAAAGTGGCGTATGAATGCCCTTTACA
65 AGTT-TAAAGTGGCGTATG-ATGCCCTTTACA
2123944 AAGGATAATT
Statistics
Matches: 167, Mismatches: 34, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
109 62 0.37
110 98 0.59
111 7 0.04
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (106 bp):
TTTTTTGCATAATTACATAGATTCAGGCACCAAAGGATTGGCCTCGAAATAGATCATTGTCTAGA
GTTTAAAGTGGCGTATGATGCCCTTTACATAAGAGAATCCA
Found at i:2133735 original size:70 final size:70
Alignment explanation
Indices: 2133617--2133754 Score: 231
Period size: 70 Copynumber: 2.0 Consensus size: 70
2133607 AAGAGCTGCC
*
2133617 TTGAACCAGCCTAACCTTATACTTGGGGAATAAGCCTACTAAGCTTGTAAGTCGAAACCCCAATC
1 TTGAACCAGCCTAACCTTATACTTGGGGAATAAGCCTACTAAGCTTGTAAGCCGAAACCCCAATC
2133682 ATGCG
66 ATGCG
* * * *
2133687 TTGAGCCAGCCTAACCTTATACTTGGGGAGTAAGCCTACTAAGCTTGTAAGCCGAAATCCTAATC
1 TTGAACCAGCCTAACCTTATACTTGGGGAATAAGCCTACTAAGCTTGTAAGCCGAAACCCCAATC
2133752 ATG
66 ATG
2133755 TAAAGACCCA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (70 bp):
TTGAACCAGCCTAACCTTATACTTGGGGAATAAGCCTACTAAGCTTGTAAGCCGAAACCCCAATC
ATGCG
Found at i:2134207 original size:28 final size:28
Alignment explanation
Indices: 2134176--2134546 Score: 111
Period size: 28 Copynumber: 13.6 Consensus size: 28
2134166 ACATGAATCG
* *
2134176 AAGCCCACACTAGTTGGCACACAAGTCT
1 AAGCCCACATTAGTTGGCACACAAGTCA
* * * ** *
2134204 AAGCCCACATTTGCTAGCACGTAAGTCG
1 AAGCCCACATTAGTTGGCACACAAGTCA
* *
2134232 AAGCCCACA--CG-T-GCTAGCACGAGTCA
1 AAGCCCACATTAGTTGGC-A-CACAAGTCA
2134258 AAGCCCACATTCA-TTGG--CACAAGTCA
1 AAGCCCACATT-AGTTGGCACACAAGTCA
*
2134284 AAGCCCACATTCA-TTGGCACACAAGTCT
1 AAGCCCACATT-AGTTGGCACACAAGTCA
** * * *
2134312 AAGCCTTCATTCA-CTGGCATATAAGTCA
1 AAGCCCACATT-AGTTGGCACACAAGTCA
** * *
2134340 AAGCTTACACTT-G--CGAACACAAGTCA
1 AAGCCCACA-TTAGTTGGCACACAAGTCA
* * *
2134366 AAGCCTACACTT-GTTAG--CATAAGTCA
1 AAGCCCACA-TTAGTTGGCACACAAGTCA
*
2134392 AAGCCCACATCCA-TTGGCACACAAGT--
1 AAGCCCACAT-TAGTTGGCACACAAGTCA
* ** *
2134418 AAGCCTACACAAGTTGGCACTCAAGTCA
1 AAGCCCACATTAGTTGGCACACAAGTCA
* * * *
2134446 AAGCCCATATTAGCTAGCATTCAC-A-TTA
1 AAGCCCACATTAGTTGGCA--CACAAGTCA
* * * *
2134474 AAGCCTATATTATTTGGCAC-CTGAGTCA
1 AAGCCCACATTAGTTGGCACAC-AAGTCA
* * *
2134502 AAGCCCACACTAGTTGGAAC-CTAAGTTA
1 AAGCCCACATTAGTTGGCACAC-AAGTCA
* *
2134530 AAGCCGACACTAGTTGG
1 AAGCCCACATTAGTTGG
2134547 TATCTAAGTG
Statistics
Matches: 259, Mismatches: 59, Indels: 50
0.70 0.16 0.14
Matches are distributed among these distances:
24 2 0.01
25 5 0.02
26 101 0.39
27 1 0.00
28 143 0.55
29 4 0.02
30 3 0.01
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (28 bp):
AAGCCCACATTAGTTGGCACACAAGTCA
Found at i:2134277 original size:26 final size:26
Alignment explanation
Indices: 2134248--2134412 Score: 113
Period size: 26 Copynumber: 6.2 Consensus size: 26
2134238 ACACGTGCTA
*
2134248 GCACGAGTCAAAGCCCACATTCATTG
1 GCACAAGTCAAAGCCCACATTCATTG
2134274 GCACAAGTCAAAGCCCACATTCATTG
1 GCACAAGTCAAAGCCCACATTCATTG
* ** *
2134300 GCACACAAGTCTAAGCCTTCATTCACTG
1 G--CACAAGTCAAAGCCCACATTCATTG
* **
2134328 GCATATAAGTCAAAGCTTACA--C-TTG
1 GC--ACAAGTCAAAGCCCACATTCATTG
* * *
2134353 CGAACACAAGTCAAAGCCTACACTT-GTTA
1 -G--CACAAGTCAAAGCCCACA-TTCATTG
* *
2134382 GCATAAGTCAAAGCCCACATCCATTG
1 GCACAAGTCAAAGCCCACATTCATTG
2134408 GCACA
1 GCACA
2134413 CAAGTAAGCC
Statistics
Matches: 108, Mismatches: 19, Indels: 24
0.72 0.13 0.16
Matches are distributed among these distances:
25 3 0.03
26 66 0.61
28 37 0.34
29 2 0.02
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (26 bp):
GCACAAGTCAAAGCCCACATTCATTG
Found at i:2134365 original size:108 final size:108
Alignment explanation
Indices: 2134176--2134417 Score: 272
Period size: 108 Copynumber: 2.2 Consensus size: 108
2134166 ACATGAATCG
* ** * *
2134176 AAGCCCACACT-AGTTGGCACACAAGTCTAAGCCCACATTTGCTAGCACGTAAGTCGAAGCCCAC
1 AAGCCCACATTCA-TTGGCACACAAGTCTAAGCCCACATTCACTAGCACATAAGTCAAAGCCCAC
* * * *
2134240 ACGTGCTAGCACGAGTCAAAGCCCACA-TTCATTGGCACAAGTCA
65 ACGTGCGAACACAAGTCAAAGCCCACACTT-ATTAGCACAAGTCA
** * * **
2134284 AAGCCCACATTCATTGGCACACAAGTCTAAGCCTTCATTCACTGGCATATAAGTCAAAGCTTACA
1 AAGCCCACATTCATTGGCACACAAGTCTAAGCCCACATTCACTAGCACATAAGTCAAAGCCCACA
* * * *
2134349 CTTGCGAACACAAGTCAAAGCCTACACTTGTTAGCATAAGTCA
66 CGTGCGAACACAAGTCAAAGCCCACACTTATTAGCACAAGTCA
*
2134392 AAGCCCACATCCATTGGCACACAAGT
1 AAGCCCACATTCATTGGCACACAAGT
2134418 AAGCCTACAC
Statistics
Matches: 112, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
108 109 0.97
109 3 0.03
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (108 bp):
AAGCCCACATTCATTGGCACACAAGTCTAAGCCCACATTCACTAGCACATAAGTCAAAGCCCACA
CGTGCGAACACAAGTCAAAGCCCACACTTATTAGCACAAGTCA
Found at i:2134553 original size:28 final size:28
Alignment explanation
Indices: 2134487--2134579 Score: 96
Period size: 28 Copynumber: 3.3 Consensus size: 28
2134477 CCTATATTAT
* * *
2134487 TTGGCACCTGAGTCAAAGCCCACACTAG
1 TTGGAACCTAAGTGAAAGCCCACACTAG
* *
2134515 TTGGAACCTAAGTTAAAGCCGACACTAG
1 TTGGAACCTAAGTGAAAGCCCACACTAG
* * *
2134543 TTGGTATCTAAGTGAAAACCCACACTAG
1 TTGGAACCTAAGTGAAAGCCCACACTAG
* *
2134571 CTGGCACCT
1 TTGGAACCT
2134580 CGTAGGGAGG
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (28 bp):
TTGGAACCTAAGTGAAAGCCCACACTAG
Found at i:2135519 original size:17 final size:16
Alignment explanation
Indices: 2135484--2135523 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
2135474 GAAAAAAATG
2135484 GGAA-GAAAAAAAGAA
1 GGAAGGAAAAAAAGAA
2135499 --AAGGAAAAAAAGAAA
1 GGAAGGAAAAAAAG-AA
2135514 GGAAGGAAAA
1 GGAAGGAAAA
2135524 GATAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
13 2 0.10
14 9 0.43
15 2 0.10
17 8 0.38
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (16 bp):
GGAAGGAAAAAAAGAA
Found at i:2135525 original size:14 final size:13
Alignment explanation
Indices: 2135488--2135517 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
2135478 AAAATGGGAA
2135488 GAAAAAAAGAAAAG
1 GAAAAAAAG-AAAG
2135502 GAAAAAAAGAAAG
1 GAAAAAAAGAAAG
2135515 GAA
1 GAA
2135518 GGAAAAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
GAAAAAAAGAAAG
Found at i:2136488 original size:114 final size:114
Alignment explanation
Indices: 2136318--2136543 Score: 249
Period size: 114 Copynumber: 2.0 Consensus size: 114
2136308 TGGGATTTAA
* * * * * *
2136318 TTGCATTAATTACGTAGTATTCGGGTACCAAAAGATTAGCCTCGAAATAGATCATTGTCTAAAGT
1 TTGCATAAATTACATAGCATTCGGGCACCAAAAGATTAGCCTCGAAAAAAATCATTGTCTAAAGT
* * * *
2136383 CATAAA-TAGTATATGAACGCCTTTTATATAGGACAATTCTTTTTTTTTT
66 CATAAAGTAGCATACGAACGCCCTTTATATAGGACAA-TCTATTTTTTTT
** * * *
2136432 TTGCATAAATTACATAGCATTCGGGCACCAAGGGATTGGCC-CTGAAAAAAATCATTGTTTAGAG
1 TTGCATAAATTACATAGCATTCGGGCACCAAAAGATTAGCCTC-GAAAAAAATCATTGTCTAAAG
** * *
2136496 TTGTAAAGTGGCATACGAATGCCCTTTATATAGGACAATCTATTTTTT
65 TCATAAAGTAGCATACGAACGCCCTTTATATAGGACAATCTATTTTTT
2136544 ACGTAAATTA
Statistics
Matches: 91, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
113 1 0.01
114 65 0.71
115 25 0.27
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (114 bp):
TTGCATAAATTACATAGCATTCGGGCACCAAAAGATTAGCCTCGAAAAAAATCATTGTCTAAAGT
CATAAAGTAGCATACGAACGCCCTTTATATAGGACAATCTATTTTTTTT
Found at i:2136737 original size:109 final size:110
Alignment explanation
Indices: 2136428--2136776 Score: 362
Period size: 110 Copynumber: 3.2 Consensus size: 110
2136418 ATTCTTTTTT
* * * *
2136428 TTTTTTGCATAAATTACATAGCATTCGGGCACCAAGGGATTGGCCCTGAAAAAAATCATTGTTTA
1 TTTTTTGCATAAATTACATAGCATTCGGACACCAAAGGATTGGCTCTGAAATAAATCATTGTTTA
* * *
2136493 GAGTTGTAAAGTGGCATACGAATGCCCTTTATATAGGACAA-TCTA
66 GAGTTATAAAGTGGCGTACGAATGCCCTTTATATAGGATAATTC-A
* * * * * * * * * *
2136538 TTTTTTACGTAAATTACATAGTATTCGAACACTAAAGGATTTG-TCCCGAAATAGATTATTTTTT
1 TTTTTTGCATAAATTACATAGCATTCGGACACCAAAGGATTGGCT-CTGAAATAAATCATTGTTT
* * * *
2136602 AGAATCATAAAGTGGTGTACGAATGCCCTTTATATAGGTTAATTCA
65 AGAGTTATAAAGTGGCGTACGAATGCCCTTTATATAGGATAATTCA
* * * * **
2136648 TTTTGTGCATTAATTACATAG-ATTCGGACACCAAAGGATTGGCTTTGAAATATATCATTGTCAA
1 TTTTTTGCATAAATTACATAGCATTCGGACACCAAAGGATTGGCTCTGAAATAAATCATTGTTTA
* * * *
2136712 GGGTTATAAAGTGGCGTGCGAATGCCCTTTACACAGGATAATTCA
66 GAGTTATAAAGTGGCGTACGAATGCCCTTTATATAGGATAATTCA
* *
2136757 TTTTTGGCATAAAGTACATA
1 TTTTTTGCATAAATTACATA
2136777 ATACTTGGGC
Statistics
Matches: 189, Mismatches: 47, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
109 84 0.44
110 103 0.54
111 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (110 bp):
TTTTTTGCATAAATTACATAGCATTCGGACACCAAAGGATTGGCTCTGAAATAAATCATTGTTTA
GAGTTATAAAGTGGCGTACGAATGCCCTTTATATAGGATAATTCA
Found at i:2137134 original size:3 final size:3
Alignment explanation
Indices: 2137128--2137171 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
2137118 CCTTTTTTTA
* *
2137128 AAT AAT AAT AAT AAT AAT AAA AAT AAT AA- AAT AAA AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2137172 CTTTTTTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:2138861 original size:14 final size:14
Alignment explanation
Indices: 2138836--2138869 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2138826 CAATAAGCTT
2138836 TTTGTA-TATATCA
1 TTTGTATTATATCA
2138849 TTTGTATTATATCA
1 TTTGTATTATATCA
2138863 TTTGTAT
1 TTTGTAT
2138870 CATTTTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (14 bp):
TTTGTATTATATCA
Found at i:2139649 original size:20 final size:20
Alignment explanation
Indices: 2139584--2139658 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
2139574 GCCAAGAAAA
* * *
2139584 TGTATCGATACATTAATAAA
1 TGTATCGATACATTTATCAT
2139604 TGTATCGATACAATTT-TCAAAT
1 TGTATCGATAC-ATTTATC--AT
*
2139626 TGTATTGATACATTTATCAT
1 TGTATCGATACATTTATCAT
*
2139646 TGTATCAATACAT
1 TGTATCGATACAT
2139659 CTACTTTGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
20 25 0.56
21 7 0.16
22 13 0.29
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTTATCAT
Found at i:2144218 original size:13 final size:13
Alignment explanation
Indices: 2144200--2144263 Score: 68
Period size: 13 Copynumber: 5.4 Consensus size: 13
2144190 ACATTTCTTC
2144200 ATGTATCGATACA
1 ATGTATCGATACA
2144213 ATGTATCGATAC-
1 ATGTATCGATACA
*
2144225 A--T-T-G-TACC
1 ATGTATCGATACA
2144233 ATGTATCGATACA
1 ATGTATCGATACA
2144246 ATGTATCGATACA
1 ATGTATCGATACA
*
2144259 TTGTA
1 ATGTA
2144264 CCATGTATCG
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 3 0.07
8 2 0.05
9 1 0.02
10 2 0.05
11 1 0.02
12 2 0.05
13 32 0.74
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2144222 original size:33 final size:33
Alignment explanation
Indices: 2144180--2144279 Score: 168
Period size: 33 Copynumber: 3.0 Consensus size: 33
2144170 GTCACAAGCT
2144180 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
2144213 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
2144246 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
2144279 A
1 A
2144280 ATAGTGATAG
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
33 63 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:2144238 original size:20 final size:20
Alignment explanation
Indices: 2144213--2144278 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
2144203 TATCGATACA
2144213 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
2144233 ATGTATCGATAC-----A--
1 ATGTATCGATACATTGTACC
2144246 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
2144266 ATGTATCGATACA
1 ATGTATCGATACA
2144279 AATAGTGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 12 0.31
15 1 0.03
18 1 0.03
20 25 0.64
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGTACC
Found at i:2144333 original size:21 final size:21
Alignment explanation
Indices: 2144308--2144363 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 21
2144298 CTGCTAATTT
**
2144308 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGAA
*
2144329 CATGTTTCGATAC-A-TTGAA
1 CATGTATCGATACAATTTGAA
2144348 CATGTATCGATACAAT
1 CATGTATCGATACAAT
2144364 GTATCGATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 15 0.52
20 2 0.07
21 12 0.41
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
CATGTATCGATACAATTTGAA
Found at i:2144367 original size:13 final size:13
Alignment explanation
Indices: 2144349--2144375 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2144339 TACATTGAAC
2144349 ATGTATCGATACA
1 ATGTATCGATACA
2144362 ATGTATCGATACA
1 ATGTATCGATACA
2144375 A
1 A
2144376 AACAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2146291 original size:2 final size:2
Alignment explanation
Indices: 2146284--2146312 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2146274 AAACATATTG
2146284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2146313 ATTACACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2149299 original size:2 final size:2
Alignment explanation
Indices: 2149294--2149319 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2149284 AGGATATATA
2149294 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
2149320 CGCGTGTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2150066 original size:1 final size:1
Alignment explanation
Indices: 2150060--2150084 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2150050 ACCCCGCCCC
2150060 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
2150085 AGAGGGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:2151509 original size:6 final size:6
Alignment explanation
Indices: 2151481--2151548 Score: 55
Period size: 7 Copynumber: 10.5 Consensus size: 6
2151471 TCGAGGTATG
* * *
2151481 AGGTTT AGGGTTT AAGATT AGGTTT AGGTTT AAGGTTT AGGGTTG AGGTTT
1 AGGTTT A-GGTTT AGGTTT AGGTTT AGGTTT -AGGTTT A-GGTTT AGGTTT
*
2151532 AAGGTTCG AGGTTT AGG
1 -AGGTT-T AGGTTT AGG
2151549 ATTTGGGGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
6 22 0.45
7 27 0.55
ACGTcount: A:0.22, C:0.01, G:0.37, T:0.40
Consensus pattern (6 bp):
AGGTTT
Found at i:2151516 original size:13 final size:13
Alignment explanation
Indices: 2151481--2151597 Score: 69
Period size: 14 Copynumber: 8.7 Consensus size: 13
2151471 TCGAGGTATG
2151481 AGGTTTAGGGTTTA
1 AGGTTTA-GGTTTA
*
2151495 A-GATTAGGTTT-
1 AGGTTTAGGTTTA
2151506 AGGTTTAAGGTTTA
1 AGGTTT-AGGTTTA
* *
2151520 GGGTTGAGGTTTA
1 AGGTTTAGGTTTA
*
2151533 AGGTTCGAGGTTT-
1 AGGTT-TAGGTTTA
*
2151546 AGGATTTGGGGTTTA
1 AGG-TTT-AGGTTTA
* *
2151561 AAGTTTAAAGTTTA
1 AGGTTT-AGGTTTA
* *
2151575 AAGTTTAAGATTTA
1 AGGTTT-AGGTTTA
2151589 AGGTTTAGG
1 AGGTTTAGG
2151598 ATATAGGGTT
Statistics
Matches: 81, Mismatches: 15, Indels: 15
0.73 0.14 0.14
Matches are distributed among these distances:
11 1 0.01
12 8 0.10
13 26 0.32
14 44 0.54
15 2 0.02
ACGTcount: A:0.26, C:0.01, G:0.32, T:0.41
Consensus pattern (13 bp):
AGGTTTAGGTTTA
Found at i:2151544 original size:20 final size:19
Alignment explanation
Indices: 2151474--2151544 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
2151464 TCAGGGTTCG
*
2151474 AGGTATGAGGTTTAGGGTTTA
1 AGGT-TGAGGTTGA-GGTTTA
* *
2151495 AGATT-AGGTTTAGGTTTA
1 AGGTTGAGGTTGAGGTTTA
*
2151513 AGGTTTAGGGTTGAGGTTTA
1 AGGTTGA-GGTTGAGGTTTA
2151533 AGGTTCGAGGTT
1 AGGTT-GAGGTT
2151545 TAGGATTTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
18 10 0.23
19 8 0.19
20 21 0.49
21 4 0.09
ACGTcount: A:0.23, C:0.01, G:0.37, T:0.39
Consensus pattern (19 bp):
AGGTTGAGGTTGAGGTTTA
Found at i:2151568 original size:7 final size:7
Alignment explanation
Indices: 2151556--2151595 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
2151546 AGGATTTGGG
2151556 GTTTAAA
1 GTTTAAA
2151563 GTTTAAA
1 GTTTAAA
2151570 GTTTAAA
1 GTTTAAA
2151577 GTTT-AA
1 GTTTAAA
*
2151583 GATTTAAG
1 G-TTTAAA
2151591 GTTTA
1 GTTTA
2151596 GGATATAGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 3 0.10
7 25 0.83
8 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (7 bp):
GTTTAAA
Found at i:2151611 original size:22 final size:21
Alignment explanation
Indices: 2151585--2151640 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
2151575 AAGTTTAAGA
2151585 TTTAAGGTTTAGGATATAG-GG
1 TTTAAGGTTTAGGAT-TAGAGG
* * *
2151606 TTTTAAGGCTTAGCATTTGAGG
1 -TTTAAGGTTTAGGATTAGAGG
2151628 TTTAAGGTTTAGG
1 TTTAAGGTTTAGG
2151641 GCTTAAGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.25, C:0.04, G:0.30, T:0.41
Consensus pattern (21 bp):
TTTAAGGTTTAGGATTAGAGG
Found at i:2155500 original size:40 final size:41
Alignment explanation
Indices: 2155456--2155546 Score: 121
Period size: 40 Copynumber: 2.2 Consensus size: 41
2155446 CTTTTAAAAC
* *
2155456 AAGAGTTTCTTTTTTCTTAACGTGC-CCCACCTTATCAAAT
1 AAGAGTTTCTGTTTTCTTAACGTGCTCACACCTTATCAAAT
* * *
2155496 AAGAGCTTCTGTTTTCTTAACGTGCTCACGCCTTATTAAAT
1 AAGAGTTTCTGTTTTCTTAACGTGCTCACACCTTATCAAAT
*
2155537 AAGAATTTCT
1 AAGAGTTTCT
2155547 AATTTAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 23 0.53
41 20 0.47
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (41 bp):
AAGAGTTTCTGTTTTCTTAACGTGCTCACACCTTATCAAAT
Found at i:2155908 original size:14 final size:14
Alignment explanation
Indices: 2155891--2156244 Score: 108
Period size: 14 Copynumber: 25.7 Consensus size: 14
2155881 GGATTTTATA
2155891 GTTTGGGGTTTGAG
1 GTTTGGGGTTTGAG
*
2155905 GTTTGGGGTTAG-G
1 GTTTGGGGTTTGAG
*** *
2155918 GTTTAAAGTTTAAG
1 GTTTGGGGTTTGAG
** *
2155932 GTTTTAAGGTTTAAAG
1 G-TTTGGGGTTT-GAG
* *
2155948 TTTTGAGGTTT-AG
1 GTTTGGGGTTTGAG
* * *
2155961 AGTTTAGAGTTTGGG
1 -GTTTGGGGTTTGAG
*
2155976 GTTTGGGGGTT-AG
1 GTTTGGGGTTTGAG
*
2155989 CATTTGGGGGTTT-AG
1 -GTTT-GGGGTTTGAG
*
2156004 GTTTCGGGTTTCG-G
1 GTTTGGGGTTT-GAG
* *
2156018 GTTGGGGGTTTGGG
1 GTTTGGGGTTTGAG
*
2156032 GTTTGGGATTT-AG
1 GTTTGGGGTTTGAG
* *
2156045 GGTTGACGGTTTG-G
1 GTTTG-GGGTTTGAG
* *
2156059 TGTTGGGGGTTTGGG
1 -GTTTGGGGTTTGAG
* *
2156074 GTTCGGGGTTCGAG
1 GTTTGGGGTTTGAG
* *
2156088 GTTCGGGGTTCGA-
1 GTTTGGGGTTTGAG
* * *
2156101 GTTCGGGGTTCGGG
1 GTTTGGGGTTTGAG
* *
2156115 GTTCGCGG-TTGAG
1 GTTTGGGGTTTGAG
*
2156128 GTTTGGGGTTTGGG
1 GTTTGGGGTTTGAG
* *
2156142 GTCT-GGGTCTG-G
1 GTTTGGGGTTTGAG
* * *
2156154 GTCTGGGGTCTGGG
1 GTTTGGGGTTTGAG
* *
2156168 GTTTAGGGGTCTGGG
1 GTTT-GGGGTTTGAG
* *
2156183 GTCTGGGGTTTGGG
1 GTTTGGGGTTTGAG
*
2156197 GTCTGGGGTTT--G
1 GTTTGGGGTTTGAG
2156209 GTTTGGGGTTT--G
1 GTTTGGGGTTTGAG
* *
2156221 GTTTGGGGTTCGGG
1 GTTTGGGGTTTGAG
*
2156235 GTTCGGGGTT
1 GTTTGGGGTT
2156245 CGGGGTCGGG
Statistics
Matches: 268, Mismatches: 51, Indels: 42
0.74 0.14 0.12
Matches are distributed among these distances:
12 27 0.10
13 57 0.21
14 137 0.51
15 44 0.16
16 3 0.01
ACGTcount: A:0.08, C:0.06, G:0.48, T:0.38
Consensus pattern (14 bp):
GTTTGGGGTTTGAG
Found at i:2155943 original size:15 final size:15
Alignment explanation
Indices: 2155919--2155965 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2155909 GGGGTTAGGG
* *
2155919 TTTAAAGTTTAAGGT
1 TTTAAGGTTTAAAGT
2155934 TTTAAGGTTTAAAGT
1 TTTAAGGTTTAAAGT
* *
2155949 TTTGAGGTTTAGAGT
1 TTTAAGGTTTAAAGT
2155964 TT
1 TT
2155966 AGAGTTTGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (15 bp):
TTTAAGGTTTAAAGT
Found at i:2155959 original size:22 final size:22
Alignment explanation
Indices: 2155917--2155972 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
2155907 TTGGGGTTAG
2155917 GGTTTAAAG-TTTAAGGTTTTAA
1 GGTTTAAAGTTTTAAGGTTTT-A
*
2155939 GGTTTAAAGTTTTGAGG-TTTA
1 GGTTTAAAGTTTTAAGGTTTTA
*
2155960 GAGTTTAGAGTTT
1 G-GTTTAAAGTTT
2155973 GGGGTTTGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 2 0.07
22 22 0.73
23 6 0.20
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (22 bp):
GGTTTAAAGTTTTAAGGTTTTA
Found at i:2155986 original size:8 final size:7
Alignment explanation
Indices: 2155969--2157598 Score: 1270
Period size: 7 Copynumber: 234.3 Consensus size: 7
2155959 AGAGTTTAGA
2155969 GTTTGGG
1 GTTTGGG
2155976 GTTTGGG
1 GTTTGGG
* * *
2155983 GGTTAGC
1 GTTTGGG
*
2155990 ATTTGGGG
1 GTTT-GGG
*
2155998 GTTT-AG
1 GTTTGGG
*
2156004 GTTTCGG
1 GTTTGGG
*
2156011 GTTTCGG
1 GTTTGGG
*
2156018 GTTGGGG
1 GTTTGGG
2156025 GTTTGGG
1 GTTTGGG
2156032 GTTTGGG
1 GTTTGGG
* *
2156039 ATTTAGG
1 GTTTGGG
*
2156046 G-TTGACG
1 GTTTG-GG
*
2156053 GTTTGGT
1 GTTTGGG
*
2156060 GTTGGGG
1 GTTTGGG
2156067 GTTTGGG
1 GTTTGGG
*
2156074 GTTCGGG
1 GTTTGGG
* *
2156081 GTTCGAG
1 GTTTGGG
*
2156088 GTTCGGG
1 GTTTGGG
* *
2156095 G-TTCGA
1 GTTTGGG
*
2156101 GTTCGGG
1 GTTTGGG
*
2156108 GTTCGGG
1 GTTTGGG
* *
2156115 GTTCGCG
1 GTTTGGG
*
2156122 G-TTGAG
1 GTTTGGG
2156128 GTTTGGG
1 GTTTGGG
2156135 GTTTGGG
1 GTTTGGG
*
2156142 GTCT-GG
1 GTTTGGG
*
2156148 GTCT-GG
1 GTTTGGG
*
2156154 GTCTGGG
1 GTTTGGG
*
2156161 GTCTGGG
1 GTTTGGG
2156168 GTTTAGGG
1 GTTT-GGG
*
2156176 GTCTGGG
1 GTTTGGG
*
2156183 GTCTGGG
1 GTTTGGG
2156190 GTTTGGG
1 GTTTGGG
*
2156197 GTCTGGG
1 GTTTGGG
2156204 GTTT--G
1 GTTTGGG
2156209 GTTTGGG
1 GTTTGGG
2156216 GTTT--G
1 GTTTGGG
2156221 GTTTGGG
1 GTTTGGG
*
2156228 GTTCGGG
1 GTTTGGG
*
2156235 GTTCGGG
1 GTTTGGG
*
2156242 GTTCGGG
1 GTTTGGG
*
2156249 G--TCGG
1 GTTTGGG
*
2156254 GTTCGGG
1 GTTTGGG
*
2156261 GTTCGGG
1 GTTTGGG
*
2156268 GTTCGGG
1 GTTTGGG
*
2156275 GTTCGGG
1 GTTTGGG
*
2156282 GTTCGGG
1 GTTTGGG
*
2156289 GTTCGGG
1 GTTTGGG
*
2156296 GTTCGGG
1 GTTTGGG
*
2156303 GTTCGGG
1 GTTTGGG
*
2156310 GTTCGGG
1 GTTTGGG
*
2156317 GTTCGGG
1 GTTTGGG
*
2156324 GTTCGGG
1 GTTTGGG
*
2156331 G-TTCGG
1 GTTTGGG
*
2156337 G-TTCGG
1 GTTTGGG
*
2156343 G-TTCGG
1 GTTTGGG
*
2156349 G-TTCGG
1 GTTTGGG
*
2156355 G-TTCGG
1 GTTTGGG
**
2156361 GTTCAGG
1 GTTTGGG
**
2156368 GTTCAGG
1 GTTTGGG
**
2156375 GTTCAGG
1 GTTTGGG
**
2156382 G-TTCAG
1 GTTTGGG
**
2156388 GTTCAGG
1 GTTTGGG
**
2156395 GTTCAGG
1 GTTTGGG
**
2156402 GTTCAGG
1 GTTTGGG
**
2156409 GTTCAGG
1 GTTTGGG
**
2156416 GTTCAGG
1 GTTTGGG
**
2156423 GTTCAGG
1 GTTTGGG
*
2156430 GTTTAGG
1 GTTTGGG
*
2156437 GTTTAGG
1 GTTTGGG
*
2156444 GTTT-AG
1 GTTTGGG
*
2156450 GTTTAGG
1 GTTTGGG
*
2156457 GTTTAGG
1 GTTTGGG
*
2156464 GTTTCGG
1 GTTTGGG
*
2156471 GTTTCGG
1 GTTTGGG
*
2156478 GTTTCGG
1 GTTTGGG
*
2156485 GTTTCGG
1 GTTTGGG
*
2156492 GTTTCGG
1 GTTTGGG
*
2156499 GTTTCGG
1 GTTTGGG
*
2156506 GTTTCGG
1 GTTTGGG
*
2156513 GTTTCGG
1 GTTTGGG
*
2156520 GTTTCGG
1 GTTTGGG
*
2156527 GTTTCGG
1 GTTTGGG
*
2156534 GTTTCGG
1 GTTTGGG
*
2156541 GTTTCGG
1 GTTTGGG
*
2156548 GTTTCGG
1 GTTTGGG
*
2156555 GTTTCGG
1 GTTTGGG
*
2156562 GTTTCGG
1 GTTTGGG
2156569 GTTTGGG
1 GTTTGGG
*
2156576 GTTTCGG
1 GTTTGGG
2156583 GTTTGGG
1 GTTTGGG
2156590 GTTTGGG
1 GTTTGGG
2156597 GTTT-GG
1 GTTTGGG
*
2156603 GTTTTGG
1 GTTTGGG
2156610 GTTTGGG
1 GTTTGGG
2156617 GTTTGGG
1 GTTTGGG
2156624 GTTTGGG
1 GTTTGGG
*
2156631 GTTGGGGG
1 GTT-TGGG
2156639 GTTTGGG
1 GTTTGGG
2156646 GTTTGGG
1 GTTTGGG
2156653 GTTTGGG
1 GTTTGGG
2156660 GTTTGGG
1 GTTTGGG
2156667 GTTTTGGG
1 G-TTTGGG
2156675 GTTTGGG
1 GTTTGGG
2156682 GTTTGGG
1 GTTTGGG
2156689 GTTT-GG
1 GTTTGGG
2156695 GTTTGGG
1 GTTTGGG
2156702 GTTTGGG
1 GTTTGGG
2156709 GTTTGGG
1 GTTTGGG
2156716 GTTTGGG
1 GTTTGGG
2156723 GTTTGGG
1 GTTTGGG
2156730 G-TTGGG
1 GTTTGGG
2156736 GTTTGGG
1 GTTTGGG
2156743 GTTTGGG
1 GTTTGGG
2156750 GTTTGGG
1 GTTTGGG
2156757 GTTTGGG
1 GTTTGGG
2156764 GTTTGGG
1 GTTTGGG
2156771 GTTTGGG
1 GTTTGGG
*
2156778 GGTTGGG
1 GTTTGGG
2156785 G-TTGGG
1 GTTTGGG
2156791 GTTTGGG
1 GTTTGGG
* *
2156798 TTTTAGG
1 GTTTGGG
*
2156805 GTTTAGG
1 GTTTGGG
*
2156812 GTTTAGG
1 GTTTGGG
*
2156819 GTTTAGG
1 GTTTGGG
*
2156826 GTTTAGG
1 GTTTGGG
*
2156833 GTTTAGG
1 GTTTGGG
*
2156840 GTTTAGG
1 GTTTGGG
*
2156847 GTTTAGG
1 GTTTGGG
*
2156854 GTTTAGG
1 GTTTGGG
*
2156861 GTTTAGG
1 GTTTGGG
*
2156868 GTTTAGG
1 GTTTGGG
*
2156875 GTTTAGG
1 GTTTGGG
*
2156882 GTTTAGG
1 GTTTGGG
2156889 GTTT-GG
1 GTTTGGG
2156895 GTTT-GG
1 GTTTGGG
*
2156901 GTTTAGG
1 GTTTGGG
2156908 GTTTGGG
1 GTTTGGG
2156915 GTTTGGG
1 GTTTGGG
2156922 GTTTGGG
1 GTTTGGG
2156929 GTTTGGGG
1 GTTT-GGG
2156937 GTTTGGG
1 GTTTGGG
2156944 GTTTGGG
1 GTTTGGG
2156951 GTTTGGG
1 GTTTGGG
2156958 GTTTGGG
1 GTTTGGG
2156965 GTTTGGG
1 GTTTGGG
2156972 GTTTGGG
1 GTTTGGG
2156979 GTTTGGG
1 GTTTGGG
*
2156986 GTTGGGGG
1 GTT-TGGG
2156994 GTTTGGGG
1 GTTT-GGG
2157002 GTTTGGG
1 GTTTGGG
2157009 GTTTGGG
1 GTTTGGG
2157016 GTTTGGG
1 GTTTGGG
*
2157023 TTTTGGG
1 GTTTGGG
2157030 GTTTTGGG
1 G-TTTGGG
2157038 GTTTTGGG
1 G-TTTGGG
2157046 GTTTGGG
1 GTTTGGG
2157053 GTTTGGG
1 GTTTGGG
2157060 GTTTTGGG
1 G-TTTGGG
2157068 GTTTGGG
1 GTTTGGG
2157075 GTTTGGG
1 GTTTGGG
2157082 GTTTGGG
1 GTTTGGG
2157089 GTTTGGG
1 GTTTGGG
*
2157096 GTTGGGG
1 GTTTGGG
2157103 GTTTGGG
1 GTTTGGG
2157110 GTTTGGG
1 GTTTGGG
2157117 GTTTGGG
1 GTTTGGG
2157124 GTTTGGG
1 GTTTGGG
2157131 G-TTGGG
1 GTTTGGG
2157137 GTTTGGG
1 GTTTGGG
2157144 GTTTGGG
1 GTTTGGG
2157151 GTTTGGG
1 GTTTGGG
2157158 GTTT--G
1 GTTTGGG
*
2157163 GTTTACGG
1 GTTT-GGG
*
2157171 GTTTAGG
1 GTTTGGG
*
2157178 GTTTAGG
1 GTTTGGG
*
2157185 GTTTAGG
1 GTTTGGG
*
2157192 GTTTAGG
1 GTTTGGG
*
2157199 GTTTAGG
1 GTTTGGG
2157206 GTTT-GG
1 GTTTGGG
*
2157212 G-TTAGG
1 GTTTGGG
2157218 GTTT-GG
1 GTTTGGG
*
2157224 GTTTAGG
1 GTTTGGG
*
2157231 GTGTTAGG
1 GT-TTGGG
2157239 GTTTGGTAG
1 GTTTGG--G
*
2157248 GGTTGGTTAG
1 GTTTGG---G
*
2157258 GTTTAGG
1 GTTTGGG
*
2157265 GTTTAGG
1 GTTTGGG
*
2157272 GTTT-AG
1 GTTTGGG
*
2157278 GTTTAGG
1 GTTTGGG
* *
2157285 GTGTAGG
1 GTTTGGG
*
2157292 GTTTAGG
1 GTTTGGG
2157299 GTGTTGGG
1 GT-TTGGG
*
2157307 G-TTGAG
1 GTTTGGG
*
2157313 GTTTAGG
1 GTTTGGG
*
2157320 GTTGGAGG
1 GTTTG-GG
*
2157328 GTTTAGG
1 GTTTGGG
*
2157335 GTTTAGG
1 GTTTGGG
*
2157342 GTTTAGG
1 GTTTGGG
2157349 G-TTGAGG
1 GTTTG-GG
*
2157356 GTTTAGG
1 GTTTGGG
*
2157363 GTTTAGG
1 GTTTGGG
*
2157370 GTTTAGG
1 GTTTGGG
2157377 GTTTAGGG
1 GTTT-GGG
2157385 G--TGAGG
1 GTTTG-GG
*
2157391 GTTTAGG
1 GTTTGGG
*
2157398 GTTT-AG
1 GTTTGGG
*
2157404 GTTTAGG
1 GTTTGGG
*
2157411 GTTTAGG
1 GTTTGGG
*
2157418 GTTTAGG
1 GTTTGGG
*
2157425 GTTAGGG
1 GTTTGGG
*
2157432 GTTTAGG
1 GTTTGGG
2157439 GTTTAGGG
1 GTTT-GGG
*
2157447 GTTTAGG
1 GTTTGGG
*
2157454 GTTTAGG
1 GTTTGGG
* *
2157461 GTGT-GT
1 GTTTGGG
*
2157467 GTTAGGG
1 GTTTGGG
* *
2157474 TTTTAGG
1 GTTTGGG
*
2157481 GTTTAGG
1 GTTTGGG
*
2157488 GTTTAGG
1 GTTTGGG
*
2157495 GTTTAGG
1 GTTTGGG
*
2157502 GTTTAGG
1 GTTTGGG
* *
2157509 GTGT-GA
1 GTTTGGG
2157515 GTTTAGAGG
1 GTTT-G-GG
2157524 GTTGTAGGG
1 GTT-T-GGG
*
2157533 TTTTGGG
1 GTTTGGG
2157540 GTTTAGGGG
1 GTTT--GGG
2157549 GTTTGGG
1 GTTTGGG
2157556 GTTTGGG
1 GTTTGGG
2157563 G-TTGGG
1 GTTTGGG
2157569 GTTTGGG
1 GTTTGGG
2157576 GTTTGGG
1 GTTTGGG
2157583 GTTTGGG
1 GTTTGGG
2157590 GTTTGGG
1 GTTTGGG
2157597 GT
1 GT
2157599 GGTTGGGTGG
Statistics
Matches: 1441, Mismatches: 122, Indels: 120
0.86 0.07 0.07
Matches are distributed among these distances:
5 21 0.01
6 150 0.10
7 1136 0.79
8 103 0.07
9 21 0.01
10 10 0.01
ACGTcount: A:0.05, C:0.04, G:0.51, T:0.40
Consensus pattern (7 bp):
GTTTGGG
Found at i:2156180 original size:22 final size:21
Alignment explanation
Indices: 2156132--2156221 Score: 80
Period size: 19 Copynumber: 4.4 Consensus size: 21
2156122 GTTGAGGTTT
2156132 GGGGTTTGGGGTCT-GGGTCT
1 GGGGTTTGGGGTCTGGGGTCT
* *
2156152 -GGGTCTGGGGTCTGGGGTTT
1 GGGGTTTGGGGTCTGGGGTCT
* *
2156172 AGGGGTCTGGGGTCTGGGGTTT
1 -GGGGTTTGGGGTCTGGGGTCT
* * *
2156194 GGGGTCTGGGGT-T-TGGTTT
1 GGGGTTTGGGGTCTGGGGTCT
2156213 GGGGTTTGG
1 GGGGTTTGG
2156222 TTTGGGGTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
19 25 0.40
20 6 0.10
21 12 0.19
22 20 0.32
ACGTcount: A:0.01, C:0.08, G:0.56, T:0.36
Consensus pattern (21 bp):
GGGGTTTGGGGTCTGGGGTCT
Found at i:2156217 original size:12 final size:12
Alignment explanation
Indices: 2156186--2156230 Score: 63
Period size: 12 Copynumber: 3.6 Consensus size: 12
2156176 GTCTGGGGTC
*
2156186 TGGGGTTTGGGGTC
1 TGGGGTTT--GGTT
2156200 TGGGGTTTGGTT
1 TGGGGTTTGGTT
2156212 TGGGGTTTGGTT
1 TGGGGTTTGGTT
2156224 TGGGGTT
1 TGGGGTT
2156231 CGGGGTTCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 22 0.73
14 8 0.27
ACGTcount: A:0.00, C:0.02, G:0.53, T:0.44
Consensus pattern (12 bp):
TGGGGTTTGGTT
Done.