Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 170 of 193
Found at i:53011051 original size:16 final size:18
Alignment explanation
Indices: 53011027--53011061 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
53011017 TTTAATTTTT
53011027 ATATGATTTTTTAT-TAA
1 ATATGATTTTTTATATAA
53011044 ATAT-ATTTTTTATATAA
1 ATATGATTTTTTATATAA
53011061 A
1 A
53011062 CATAGGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATATGATTTTTTATATAA
Found at i:53012603 original size:15 final size:16
Alignment explanation
Indices: 53012585--53012614 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53012575 TTTTCTAATT
53012585 CAAATCG-ATTAAAAC
1 CAAATCGAATTAAAAC
53012600 CAAATCGAATTAAAA
1 CAAATCGAATTAAAA
53012615 ATATTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.17, G:0.07, T:0.20
Consensus pattern (16 bp):
CAAATCGAATTAAAAC
Found at i:53014022 original size:6 final size:6
Alignment explanation
Indices: 53014013--53014039 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
53014003 AAAAGAAAAC
53014013 ATACAT ATACAT ATACAT ATACAT ATA
1 ATACAT ATACAT ATACAT ATACAT ATA
53014040 TATTGAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:53019176 original size:8 final size:8
Alignment explanation
Indices: 53019159--53019200 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
53019149 TTAATTTTTT
53019159 TAAAATTA
1 TAAAATTA
*
53019167 TAAAAATA
1 TAAAATTA
53019175 T-AAATTA
1 TAAAATTA
*
53019182 TTAAAATAA
1 -TAAAATTA
53019191 TAAAATTA
1 TAAAATTA
53019199 TA
1 TA
53019201 TTTCAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 5 0.18
8 18 0.64
9 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TAAAATTA
Found at i:53019181 original size:15 final size:17
Alignment explanation
Indices: 53019159--53019200 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
53019149 TTAATTTTTT
53019159 TAAAATTATAAAAAT-A
1 TAAAATTATAAAAATAA
*
53019175 T-AAATTATTAAAATAA
1 TAAAATTATAAAAATAA
53019191 TAAAATTATA
1 TAAAATTATA
53019201 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 12 0.55
16 3 0.14
17 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATTATAAAAATAA
Found at i:53019608 original size:20 final size:20
Alignment explanation
Indices: 53019570--53019608 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53019560 AATTATATAT
* *
53019570 ATATATATATTAATTTTTAG
1 ATATAAATATTAATATTTAG
*
53019590 ATATAAATATTTATATTTA
1 ATATAAATATTAATATTTA
53019609 TATTATAACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
ATATAAATATTAATATTTAG
Found at i:53024030 original size:19 final size:19
Alignment explanation
Indices: 53024006--53024045 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
53023996 TCTTGTTGAA
53024006 TTCCAATAAGGACAAGGTT
1 TTCCAATAAGGACAAGGTT
53024025 TTCCAATAAGGACAAGGTT
1 TTCCAATAAGGACAAGGTT
53024044 TT
1 TT
53024046 TCAGACGTAG
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:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (19 bp):
TTCCAATAAGGACAAGGTT
Found at i:53026297 original size:38 final size:37
Alignment explanation
Indices: 53026255--53026329 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 37
53026245 ACAACATTTG
*
53026255 CTGGTTGTTGGTCCGTTGTGCTTTGTTGTGGTTGTATA
1 CTGGTTGTTGGTCCATTGTGCTTTGTTGTGGTT-TATA
53026293 CTGGTTGTTGGTCCATTGTGCTTTGTTGTGGTTTATA
1 CTGGTTGTTGGTCCATTGTGCTTTGTTGTGGTTTATA
53026330 AAAGACTAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 4 0.11
38 32 0.89
ACGTcount: A:0.07, C:0.11, G:0.32, T:0.51
Consensus pattern (37 bp):
CTGGTTGTTGGTCCATTGTGCTTTGTTGTGGTTTATA
Found at i:53038213 original size:19 final size:20
Alignment explanation
Indices: 53038191--53038232 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
53038181 AAAAAATATC
53038191 TTTTTCATAT-TAATAA-AAG
1 TTTTT-ATATATAATAATAAG
*
53038210 TTTTTATGTATAATAATAAG
1 TTTTTATATATAATAATAAG
53038230 TTT
1 TTT
53038233 AAAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 3 0.15
19 11 0.55
20 6 0.30
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (20 bp):
TTTTTATATATAATAATAAG
Found at i:53038260 original size:18 final size:18
Alignment explanation
Indices: 53038234--53038268 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53038224 AATAAGTTTA
53038234 AAAAAAAATTTAATAAAT
1 AAAAAAAATTTAATAAAT
* *
53038252 AAAACAAATTTTATAAA
1 AAAAAAAATTTAATAAA
53038269 ACGAATTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAAAAATTTAATAAAT
Found at i:53039606 original size:51 final size:51
Alignment explanation
Indices: 53039530--53039632 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
53039520 TGTTAAAGAG
*
53039530 GATCAAGAGGAGAGGTTGGAACTGAGAGTGGATATTGGAATTGGGGATAAT
1 GATCAAGAGGAGAGGTTGGAACTGAGAGTGGATACTGGAATTGGGGATAAT
53039581 GATCAAGAGGAGAGGTTGGAACTGAGAGTGGATACTGGAATTGGGGATAAT
1 GATCAAGAGGAGAGGTTGGAACTGAGAGTGGATACTGGAATTGGGGATAAT
53039632 G
1 G
53039633 CAGTTGTAGA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.33, C:0.05, G:0.40, T:0.22
Consensus pattern (51 bp):
GATCAAGAGGAGAGGTTGGAACTGAGAGTGGATACTGGAATTGGGGATAAT
Found at i:53044863 original size:13 final size:13
Alignment explanation
Indices: 53044842--53044874 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
53044832 TTTGATTCTT
53044842 TATTAAATTTTAA
1 TATTAAATTTTAA
*
53044855 TATTCAATTTTAA
1 TATTAAATTTTAA
53044868 T-TTAAAT
1 TATTAAAT
53044875 AAAAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTAAATTTTAA
Found at i:53052578 original size:68 final size:68
Alignment explanation
Indices: 53052501--53052652 Score: 232
Period size: 68 Copynumber: 2.2 Consensus size: 68
53052491 AATCGAGTTA
* * *
53052501 AGCTCAAGCTTAAATACATATGAGCTTAATTGAACTTGAGTACAAAAATTGATAAATGAGCTTAA
1 AGCTCAAGCTTAAATACATATGAGCTTAATTGAACTTGAGAACAAAAATTGATAAATAAACTTAA
53052566 TCG
66 TCG
* * *
53052569 AGCTCAAGCTTAAAAACATATGAGCTTAATTGAGCTTGAGAATAAAAATTGATAAATAAACTTAA
1 AGCTCAAGCTTAAATACATATGAGCTTAATTGAACTTGAGAACAAAAATTGATAAATAAACTTAA
53052634 TCG
66 TCG
* *
53052637 AACTCAAGCTTGAATA
1 AGCTCAAGCTTAAATA
53052653 ACTCAATTAT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 75 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (68 bp):
AGCTCAAGCTTAAATACATATGAGCTTAATTGAACTTGAGAACAAAAATTGATAAATAAACTTAA
TCG
Found at i:53052615 original size:32 final size:32
Alignment explanation
Indices: 53052511--53052616 Score: 86
Period size: 32 Copynumber: 3.2 Consensus size: 32
53052501 AGCTCAAGCT
* * *
53052511 TAAATACATATGAGCTTAATTGAACTTGAGTA
1 TAAAAACATATGAGCTTAATTGAGCTTGAGAA
* * * ** **
53052543 CAAAAATTGATAAATGAGCTTAATCGAGCTCAAGCT
1 TAAAAA--CAT--ATGAGCTTAATTGAGCTTGAGAA
53052579 TAAAAACATATGAGCTTAATTGAGCTTGAGAA
1 TAAAAACATATGAGCTTAATTGAGCTTGAGAA
53052611 TAAAAA
1 TAAAAA
53052617 TTGATAAATA
Statistics
Matches: 54, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
32 28 0.52
34 4 0.07
36 22 0.41
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.28
Consensus pattern (32 bp):
TAAAAACATATGAGCTTAATTGAGCTTGAGAA
Found at i:53058972 original size:21 final size:23
Alignment explanation
Indices: 53058922--53058973 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
53058912 AATTTTTACA
53058922 AATTTTTTAAAATATAAATTTTG
1 AATTTTTTAAAATATAAATTTTG
* *
53058945 AAATTTTTAAAA-AT-TATTTTG
1 AATTTTTTAAAATATAAATTTTG
*
53058966 ATTTTTTT
1 AATTTTTT
53058974 GTAATTTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 12 0.48
22 2 0.08
23 11 0.44
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (23 bp):
AATTTTTTAAAATATAAATTTTG
Found at i:53062167 original size:50 final size:50
Alignment explanation
Indices: 53062123--53062241 Score: 202
Period size: 50 Copynumber: 2.4 Consensus size: 50
53062113 AATTTAAGGA
*
53062123 TTTATTGGTTGGTTTCACCATTTAACTCTCTTCAACTATTAATTTCACGTG
1 TTTA-TGGTTGGTTTCACCATTTAACTCTCTTCAACTATTAATTTCAAGTG
*
53062174 TTTATGGTTGGTTTCACCATTTAACTCTCTTCAACTATTAATTTCACGTG
1 TTTATGGTTGGTTTCACCATTTAACTCTCTTCAACTATTAATTTCAAGTG
*
53062224 TTTATGATTGGTTTCACC
1 TTTATGGTTGGTTTCACC
53062242 GTAAACTTTT
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
50 63 0.94
51 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (50 bp):
TTTATGGTTGGTTTCACCATTTAACTCTCTTCAACTATTAATTTCAAGTG
Found at i:53065952 original size:2 final size:2
Alignment explanation
Indices: 53065945--53065979 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
53065935 TATTACATTA
53065945 AT AT AT AT A- 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 AT
53065980 TAGTATAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53067031 original size:41 final size:41
Alignment explanation
Indices: 53066986--53067095 Score: 195
Period size: 41 Copynumber: 2.7 Consensus size: 41
53066976 TATGGGAAAA
*
53066986 CGCCGCTATTGCTCTGACCTTTAGTGGCGCTTTTCCATAAG
1 CGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCCATAAG
53067027 CGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCCATAAG
1 CGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCCATAAG
*
53067068 CGCCGCTATTGCTCT-ACCTTTTGCGGCG
1 CGCCGCTATTGCTCTGACCTTTAGCGGCG
53067096 TTTATGTAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
40 12 0.18
41 55 0.82
ACGTcount: A:0.13, C:0.32, G:0.23, T:0.33
Consensus pattern (41 bp):
CGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTTCCATAAG
Found at i:53070456 original size:19 final size:19
Alignment explanation
Indices: 53070409--53070456 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
53070399 ATAAGTTAAT
**
53070409 AATTATAAAAATATTTAAA
1 AATTATAAAAATAACTAAA
* *
53070428 AATAAT-AAAATAACTCAA
1 AATTATAAAAATAACTAAA
53070446 AATTATAAAAA
1 AATTATAAAAA
53070457 GTCAACAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (19 bp):
AATTATAAAAATAACTAAA
Found at i:53070741 original size:5 final size:5
Alignment explanation
Indices: 53070731--53070755 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53070721 TAATAATTAT
53070731 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
53070756 AAACATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:53073483 original size:21 final size:19
Alignment explanation
Indices: 53073457--53073496 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
53073447 TTGAATTTCC
53073457 ACAAAAAATAAACATAAAAAA
1 ACAAAAAATAAA-A-AAAAAA
*
53073478 ACAAAAAGTAAAAAAAAAA
1 ACAAAAAATAAAAAAAAAA
53073497 TGGAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 11 0.61
ACGTcount: A:0.82, C:0.07, G:0.03, T:0.07
Consensus pattern (19 bp):
ACAAAAAATAAAAAAAAAA
Found at i:53074952 original size:13 final size:13
Alignment explanation
Indices: 53074931--53074973 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
53074921 TTTTTTACCT
53074931 AAATAATACAAAA
1 AAATAATACAAAA
*
53074944 AAATTATACACCAAA
1 AAATAATACA--AAA
*
53074959 ATATAATACAAAA
1 AAATAATACAAAA
53074972 AA
1 AA
53074974 TAAAATTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 13 0.54
15 11 0.46
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.19
Consensus pattern (13 bp):
AAATAATACAAAA
Found at i:53075536 original size:16 final size:16
Alignment explanation
Indices: 53075495--53075530 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
53075485 TTAGTATTTT
*
53075495 TTTAAAAAATTTATTA
1 TTTAAATAATTTATTA
*
53075511 TTTAAATAATTTTTTA
1 TTTAAATAATTTATTA
53075527 TTTA
1 TTTA
53075531 TTTAATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTAAATAATTTATTA
Found at i:53085331 original size:10 final size:11
Alignment explanation
Indices: 53085315--53085339 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53085305 ATAATTATGG
53085315 TTTTTTTTAAA
1 TTTTTTTTAAA
53085326 TTTTTTTTAAA
1 TTTTTTTTAAA
53085337 TTT
1 TTT
53085340 ATACTTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTTTAAA
Found at i:53097325 original size:23 final size:22
Alignment explanation
Indices: 53097286--53097329 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
53097276 TAAAGTATGT
*
53097286 AAAAATAGAAATAAATATATAA
1 AAAAATACAAATAAATATATAA
*
53097308 AAAAATACAGAATGAATATATA
1 AAAAATACA-AATAAATATATA
53097330 TATATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (22 bp):
AAAAATACAAATAAATATATAA
Found at i:53097479 original size:22 final size:23
Alignment explanation
Indices: 53097444--53097487 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
53097434 ATTAAAAATA
53097444 TAAAAATTTGTAAAAAATATATT
1 TAAAAATTTGTAAAAAATATATT
* *
53097467 TAAAACTTT-TAAAAATTATAT
1 TAAAAATTTGTAAAAAATATAT
53097488 ATATAAGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TAAAAATTTGTAAAAAATATATT
Found at i:53097565 original size:20 final size:18
Alignment explanation
Indices: 53097536--53097591 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
53097526 AAAAATGGTG
*
53097536 AAAATCATTAAAATTTTTCA
1 AAAAT-ATTAAAATTTAT-A
53097556 AAAATGATTAAAATTTATA
1 AAAAT-ATTAAAATTTATA
53097575 AAAATATTTAAAATTTA
1 AAAATA-TTAAAATTTA
53097592 CAAATTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 1 0.03
19 16 0.48
20 16 0.48
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (18 bp):
AAAATATTAAAATTTATA
Found at i:53098208 original size:16 final size:16
Alignment explanation
Indices: 53098187--53098256 Score: 63
Period size: 16 Copynumber: 4.4 Consensus size: 16
53098177 GTTTGGTTCA
53098187 TGTAATGGAATAAGAC
1 TGTAATGGAATAAGAC
* * *
53098203 TGTAATAGAATAAAAT
1 TGTAATGGAATAAGAC
* *
53098219 TGTAATGAAATAAGGC
1 TGTAATGGAATAAGAC
53098235 TGTAACT-GAAT-AGAGC
1 TGTAA-TGGAATAAGA-C
53098251 TGTAAT
1 TGTAAT
53098257 CAGTAATTTA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
15 3 0.07
16 38 0.90
17 1 0.02
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (16 bp):
TGTAATGGAATAAGAC
Found at i:53098255 original size:32 final size:32
Alignment explanation
Indices: 53098187--53098256 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
53098177 GTTTGGTTCA
* *
53098187 TGTAATGGAATAAGACTGTAATAGAATAAAAT
1 TGTAATGAAATAAGACTGTAATAGAATAAAAC
* * *
53098219 TGTAATGAAATAAGGCTGTAACT-GAATAGAGC
1 TGTAATGAAATAAGACTGTAA-TAGAATAAAAC
53098251 TGTAAT
1 TGTAAT
53098257 CAGTAATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 31 0.97
33 1 0.03
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (32 bp):
TGTAATGAAATAAGACTGTAATAGAATAAAAC
Found at i:53100156 original size:31 final size:31
Alignment explanation
Indices: 53100118--53100277 Score: 102
Period size: 31 Copynumber: 5.3 Consensus size: 31
53100108 TTAATGTAAC
*
53100118 ATTTGGTACCTAAACTTGACATTTTTTCCTA
1 ATTTGGTACTTAAACTTGACATTTTTTCCTA
** *
53100149 ATTTGGTA-TATAAACTT--TTTTTTTTACTCA
1 ATTTGGTACT-TAAACTTGACATTTTTTCCT-A
* ** * *
53100179 ATTTGGTAATTGGACTTGACACTTTTTCTTA
1 ATTTGGTACTTAAACTTGACATTTTTTCCTA
53100210 ATTTGGTACTTAAACTT----TTTTTGGATCC-A
1 ATTTGGTACTTAAACTTGACATTTTT---TCCTA
* * * *
53100239 AATTGGCACTTGAACTTGACTTTTTTTCCTA
1 ATTTGGTACTTAAACTTGACATTTTTTCCTA
53100270 ATTTGGTA
1 ATTTGGTA
53100278 TCTAAGCTTT
Statistics
Matches: 95, Mismatches: 21, Indels: 26
0.67 0.15 0.18
Matches are distributed among these distances:
27 4 0.04
29 23 0.24
30 19 0.20
31 38 0.40
32 6 0.06
33 5 0.05
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.49
Consensus pattern (31 bp):
ATTTGGTACTTAAACTTGACATTTTTTCCTA
Found at i:53100265 original size:60 final size:61
Alignment explanation
Indices: 53100130--53100291 Score: 186
Period size: 60 Copynumber: 2.7 Consensus size: 61
53100120 TTGGTACCTA
** * *
53100130 AACTTGACATTTTTTCCTAATTTGGTATATAAACTTTTTTTTTTACTCAATTTGGTAATTG
1 AACTTGACATTTTTTCCTAATTTGGTATATAAACTTTTTTTGATACTCAAATTGGCAATTG
* * * *
53100191 GACTTGACACTTTTTCTTAATTTGGTACT-TAAACTTTTTTTGGAT-C-CAAATTGGCACTTG
1 AACTTGACATTTTTTCCTAATTTGGTA-TATAAACTTTTTTT-GATACTCAAATTGGCAATTG
* * *
53100251 AACTTGACTTTTTTTCCTAATTTGGTATCTAAGCTTTTTTT
1 AACTTGACATTTTTTCCTAATTTGGTATATAAACTTTTTTT
53100292 TAAGATTCAA
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
59 1 0.01
60 45 0.53
61 37 0.44
62 2 0.02
ACGTcount: A:0.23, C:0.14, G:0.12, T:0.51
Consensus pattern (61 bp):
AACTTGACATTTTTTCCTAATTTGGTATATAAACTTTTTTTGATACTCAAATTGGCAATTG
Found at i:53106620 original size:3 final size:3
Alignment explanation
Indices: 53106612--53106637 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
53106602 AGAGTCAACT
53106612 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
53106638 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:53107364 original size:14 final size:14
Alignment explanation
Indices: 53107328--53107368 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
53107318 CACTTTTGAG
*
53107328 AAGTG-TTTTTAAA
1 AAGTGATTTTGAAA
53107341 AAGTGA-TTTGAAA
1 AAGTGATTTTGAAA
53107354 AAGTGATTTTGAAA
1 AAGTGATTTTGAAA
53107368 A
1 A
53107369 TTTTGGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.37
Consensus pattern (14 bp):
AAGTGATTTTGAAA
Found at i:53107901 original size:2 final size:2
Alignment explanation
Indices: 53107889--53107921 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
53107879 TCAAGACTTC
53107889 AT AT AT A- 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
53107922 GCAAAACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53108273 original size:16 final size:17
Alignment explanation
Indices: 53108248--53108279 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
53108238 GGGTTAAATA
53108248 AAAAATTTAAAATTAAG
1 AAAAATTTAAAATTAAG
53108265 AAAAA-TTAAAATTAA
1 AAAAATTTAAAATTAA
53108280 TTTTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
AAAAATTTAAAATTAAG
Found at i:53110725 original size:17 final size:17
Alignment explanation
Indices: 53110703--53110761 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
53110693 CTAGAAATTT
*
53110703 ATAAATTTATGATTTTG
1 ATAAATTTATAATTTTG
* * * *
53110720 ATAAATTCAAAAGTTCG
1 ATAAATTTATAATTTTG
*
53110737 GTAAATTTATAATTTTG
1 ATAAATTTATAATTTTG
53110754 ATAAATTT
1 ATAAATTT
53110762 CATTTATGAT
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (17 bp):
ATAAATTTATAATTTTG
Found at i:53114065 original size:31 final size:31
Alignment explanation
Indices: 53114027--53114106 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
53114017 TTTTTTGTCC
53114027 AATTTGGTACTTAAACTTGACACTTTTTTTT
1 AATTTGGTACTTAAACTTGACACTTTTTTTT
*
53114058 AATTTGGTA-TCTAAACTTGATACTTTTTTTT
1 AATTTGGTACT-TAAACTTGACACTTTTTTTT
*
53114089 AAGTTGGTACTTAAACTT
1 AATTTGGTACTTAAACTT
53114107 TTTCGGATCC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
30 1 0.02
31 43 0.96
32 1 0.02
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (31 bp):
AATTTGGTACTTAAACTTGACACTTTTTTTT
Found at i:53114393 original size:58 final size:58
Alignment explanation
Indices: 53114303--53114418 Score: 135
Period size: 58 Copynumber: 2.0 Consensus size: 58
53114293 ATTATATTTA
* * * *
53114303 ATAAATTCAGGTACTAAATTAAATCTAAAAAAAGCTAGGCACCAAATTAGGAAAAAAT
1 ATAAATTCAAGTACCAAATTAAATCTAAAAAAAGCTAAGCACCAAATTAAGAAAAAAT
** ** *
53114361 ATAAAGTTCAAGTACCAAATTGGATC-AAAAAAATTTAAGTACCAAATTAAGAAAAAAT
1 ATAAA-TTCAAGTACCAAATTAAATCTAAAAAAAGCTAAGCACCAAATTAAGAAAAAAT
53114419 GTCAAGTTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
58 32 0.67
59 16 0.33
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.23
Consensus pattern (58 bp):
ATAAATTCAAGTACCAAATTAAATCTAAAAAAAGCTAAGCACCAAATTAAGAAAAAAT
Found at i:53114417 original size:27 final size:29
Alignment explanation
Indices: 53114343--53114418 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 29
53114333 AAAGCTAGGC
53114343 ACCAAATTAGGAAAAAATATAAAGTTCAAGT
1 ACCAAATTAGG-AAAAA-ATAAAGTTCAAGT
* *
53114374 ACCAAATT-GGATCAAAA-AAA-TTTAAGT
1 ACCAAATTAGGA-AAAAATAAAGTTCAAGT
*
53114401 ACCAAATTAAGAAAAAAT
1 ACCAAATTAGGAAAAAAT
53114419 GTCAAGTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
27 18 0.47
28 5 0.13
29 2 0.05
30 5 0.13
31 8 0.21
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.22
Consensus pattern (29 bp):
ACCAAATTAGGAAAAAATAAAGTTCAAGT
Found at i:53115319 original size:19 final size:19
Alignment explanation
Indices: 53115274--53115321 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
53115264 TAAATTTAGC
53115274 TTAAATTCAATAGTCATATT
1 TTAAATT-AATAGTCATATT
53115294 TTAAATTAATA-TCATATT
1 TTAAATTAATAGTCATATT
*
53115312 ATTTAATTAA
1 -TTAAATTAA
53115322 ATTCTTCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.27
19 12 0.46
20 7 0.27
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (19 bp):
TTAAATTAATAGTCATATT
Found at i:53119413 original size:29 final size:30
Alignment explanation
Indices: 53119381--53119442 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
53119371 TTCCAAATTT
53119381 TAATATTTTTAAT-ATTTTTTTCA-TTTATA
1 TAAT-TTTTTAATAATTTTTTTCACTTTATA
**
53119410 TAATTTTTTTGTAATTTTTTTCACTTTTATA
1 TAATTTTTTAATAATTTTTTTCAC-TTTATA
53119441 TA
1 TA
53119443 TGTTTACAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 6 0.21
29 14 0.50
31 8 0.29
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (30 bp):
TAATTTTTTAATAATTTTTTTCACTTTATA
Found at i:53135565 original size:6 final size:6
Alignment explanation
Indices: 53135554--53135593 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
53135544 AGGTGGCTAC
*
53135554 AAAATG AAAATG AAAATA AAAATG AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
53135594 CATTCCTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:53148078 original size:6 final size:6
Alignment explanation
Indices: 53148067--53148099 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
53148057 TTTAAGAAAT
*
53148067 GCTGCG GCTGCG GCTGCG GCTGCT GCTGCG GCT
1 GCTGCG GCTGCG GCTGCG GCTGCG GCTGCG GCT
53148100 TCTGAGGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.33, G:0.45, T:0.21
Consensus pattern (6 bp):
GCTGCG
Found at i:53152669 original size:6 final size:6
Alignment explanation
Indices: 53152658--53152690 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
53152648 TTTAAGAAAT
*
53152658 GCTGCG GCTGCG GCTGCG GCTGCT GCTGCG GCT
1 GCTGCG GCTGCG GCTGCG GCTGCG GCTGCG GCT
53152691 TCTGAGGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.33, G:0.45, T:0.21
Consensus pattern (6 bp):
GCTGCG
Found at i:53153002 original size:21 final size:20
Alignment explanation
Indices: 53152976--53153015 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
53152966 TTGTTGAAAA
53152976 CATAGA-GAGATTGAGGATTGT
1 CATAGATGAGA-TGA-GATTGT
53152997 CATAGATGAGATGAGATTG
1 CATAGATGAGATGAGATTG
53153016 GGTTTTGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.35, C:0.05, G:0.33, T:0.28
Consensus pattern (20 bp):
CATAGATGAGATGAGATTGT
Found at i:53165374 original size:17 final size:17
Alignment explanation
Indices: 53165352--53165386 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
53165342 AGACCCTGTG
53165352 TTAATCTACTAGCTAAT
1 TTAATCTACTAGCTAAT
53165369 TTAATCTACTAGCTAAT
1 TTAATCTACTAGCTAAT
53165386 T
1 T
53165387 AAGCATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (17 bp):
TTAATCTACTAGCTAAT
Found at i:53166400 original size:13 final size:13
Alignment explanation
Indices: 53166384--53166408 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53166374 AATTAGAAAC
53166384 GCTAATTAATGGT
1 GCTAATTAATGGT
53166397 GCTAATTAATGG
1 GCTAATTAATGG
53166409 ATTTATTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (13 bp):
GCTAATTAATGGT
Found at i:53173284 original size:14 final size:14
Alignment explanation
Indices: 53173265--53173303 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
53173255 ATAGTAAACA
53173265 TTCAAAATCACTTT
1 TTCAAAATCACTTT
53173279 TTC-AAATCACTTT
1 TTCAAAATCACTTT
*
53173292 TT-AAAAACACTT
1 TTCAAAATCACTT
53173304 CTCAAAAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 20 0.87
14 3 0.13
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (14 bp):
TTCAAAATCACTTT
Found at i:53174046 original size:3 final size:3
Alignment explanation
Indices: 53174040--53174065 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
53174030 AATAATAATA
53174040 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
53174066 AGTTGACTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:53177120 original size:16 final size:16
Alignment explanation
Indices: 53177099--53177133 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
53177089 ACTTTATCAA
53177099 CAACTTGTTCAAGTTC
1 CAACTTGTTCAAGTTC
*
53177115 CAACTTGTTCCAGTTC
1 CAACTTGTTCAAGTTC
53177131 CAA
1 CAA
53177134 GCTGATGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (16 bp):
CAACTTGTTCAAGTTC
Found at i:53182213 original size:21 final size:21
Alignment explanation
Indices: 53182189--53182229 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53182179 ATACATGAAA
53182189 TTAAAAAAAATAACTCTTAAT
1 TTAAAAAAAATAACTCTTAAT
* *
53182210 TTAAAGAAAATAACTTTTAA
1 TTAAAAAAAATAACTCTTAA
53182230 CTTGGTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.34
Consensus pattern (21 bp):
TTAAAAAAAATAACTCTTAAT
Found at i:53184151 original size:3 final size:3
Alignment explanation
Indices: 53184143--53184169 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
53184133 TACTGCTATC
53184143 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
53184170 GCAATTGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:53189472 original size:19 final size:19
Alignment explanation
Indices: 53189450--53189487 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
53189440 AATAAAATAG
*
53189450 TAGTAACATAATAATAAAA
1 TAGTAACAAAATAATAAAA
*
53189469 TAGTAACAAAATAGTAAAA
1 TAGTAACAAAATAATAAAA
53189488 AAAACAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.24
Consensus pattern (19 bp):
TAGTAACAAAATAATAAAA
Found at i:53195542 original size:23 final size:23
Alignment explanation
Indices: 53195515--53195559 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
53195505 AGCATTTCCC
* *
53195515 AAAAATATATATAATAATAAATTT
1 AAAAAT-TACATAAAAATAAATTT
53195539 AAAAATTACATAAAAATAAAT
1 AAAAATTACATAAAAATAAAT
53195560 AAATATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAATTACATAAAAATAAATTT
Found at i:53195762 original size:90 final size:88
Alignment explanation
Indices: 53195663--53195871 Score: 222
Period size: 90 Copynumber: 2.3 Consensus size: 88
53195653 TAACAATGTA
* * *
53195663 CTTTTTTTTTACACTCAATTATGTAGTTGAAATTTTAAAATACATCAAAAAAACCCTCAAACTTT
1 CTTTTTTTTT-CACTCAATTAGGTACTTGAAATTTCAAAATACATC-AAAAAACCC-CAAACTTT
**
53195728 TTT-AAAAAAAGCAATTAAGTTCCTC
63 TTTCAAAAAAAGCAATTAAGCCCCTC
* * * * *** *
53195753 CTTTTTTTTTGCATTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAATGTCCAAATTTTTT
1 CTTTTTTTTT-CACTCAATTAGGTACTTGAAATTTCAAAATACATCAAAAAACCCCAAACTTTTT
* *
53195818 TCAAAAATAGCAATTAAGCCCCTG
65 TCAAAAAAAGCAATTAAGCCCCTC
* *
53195842 CTTTTTTTTTTACTCAATTGGGTACTTGAA
1 CTTTTTTTTTCACTCAATTAGGTACTTGAA
53195872 CTGTCAATTG
Statistics
Matches: 100, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
88 28 0.28
89 34 0.34
90 38 0.38
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (88 bp):
CTTTTTTTTTCACTCAATTAGGTACTTGAAATTTCAAAATACATCAAAAAACCCCAAACTTTTTT
CAAAAAAAGCAATTAAGCCCCTC
Found at i:53195892 original size:88 final size:88
Alignment explanation
Indices: 53195720--53195890 Score: 238
Period size: 88 Copynumber: 2.0 Consensus size: 88
53195710 AAAAAACCCT
** *
53195720 CAAACTTTTTTAAAAAAAGCAATTAAGTTCCTCCTTTTTTTTTGCATTCAATTGGGTACTTGAAC
1 CAAACTTTTTTAAAAAAAGCAATTAAGCCCCTCCTTTTTTTTTGCACTCAATTGGGTACTTGAAC
*
53195785 TTTCAAAATGCATCAAAAATGTC
66 TGTCAAAATGCATCAAAAATGTC
* * * *
53195808 CAAATTTTTTTCAAAAATAGCAATTAAGCCCCTGCTTTTTTTTT-TACTCAATTGGGTACTTGAA
1 CAAACTTTTTT-AAAAAAAGCAATTAAGCCCCTCCTTTTTTTTTGCACTCAATTGGGTACTTGAA
*
53195872 CTGTC-AATTGCATCAAAAA
65 CTGTCAAAATGCATCAAAAA
53195891 ATCATTTAGC
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
87 13 0.18
88 32 0.44
89 28 0.38
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.39
Consensus pattern (88 bp):
CAAACTTTTTTAAAAAAAGCAATTAAGCCCCTCCTTTTTTTTTGCACTCAATTGGGTACTTGAAC
TGTCAAAATGCATCAAAAATGTC
Found at i:53196081 original size:21 final size:22
Alignment explanation
Indices: 53196052--53196102 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
53196042 TTTAATAAAA
*
53196052 ATATTAAAATTAG-AAAAAATT
1 ATATAAAAATTAGTAAAAAATT
*
53196073 ATATAAAAA-TCGTAAAAAATT
1 ATATAAAAATTAGTAAAAAATT
53196094 ATA-AAAAAT
1 ATATAAAAAT
53196103 GGAAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (22 bp):
ATATAAAAATTAGTAAAAAATT
Found at i:53196089 original size:19 final size:20
Alignment explanation
Indices: 53196066--53196132 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 20
53196056 TAAAATTAGA
53196066 AAAAATTATATAAAAATCGT
1 AAAAATTATATAAAAATCGT
53196086 AAAAAATTATA-AAAAAT-G-
1 -AAAAATTATATAAAAATCGT
* * * *
53196104 GAAATTTTTAT-AAAATCAT
1 AAAAATTATATAAAAATCGT
53196123 AAAAATTATA
1 AAAAATTATA
53196133 AAATGCATCA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
17 12 0.33
19 8 0.22
20 6 0.17
21 10 0.28
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.31
Consensus pattern (20 bp):
AAAAATTATATAAAAATCGT
Found at i:53196131 original size:17 final size:19
Alignment explanation
Indices: 53196111--53196146 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
53196101 ATGGAAATTT
53196111 TTATAAAAT-CAT-AAAAA
1 TTATAAAATGCATCAAAAA
53196128 TTATAAAATGCATCAAAAA
1 TTATAAAATGCATCAAAAA
53196147 GGTCCTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.28
Consensus pattern (19 bp):
TTATAAAATGCATCAAAAA
Found at i:53197156 original size:18 final size:18
Alignment explanation
Indices: 53197133--53197170 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
53197123 AATTGCTTGG
*
53197133 TTTTTAGTACTATAATTT
1 TTTTTAGTACGATAATTT
53197151 TTTTTAGTACGATAATTT
1 TTTTTAGTACGATAATTT
53197169 TT
1 TT
53197171 AAGTCAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (18 bp):
TTTTTAGTACGATAATTT
Found at i:53200449 original size:19 final size:19
Alignment explanation
Indices: 53200419--53200466 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
53200409 ATTCATGAAA
53200419 TTAAAAAA-AACTCTTAAT
1 TTAAAAAATAACTCTTAAT
*
53200437 TTAAAAAATAACTTTTAAT
1 TTAAAAAATAACTCTTAAT
*
53200456 TTAAATAATAA
1 TTAAAAAATAA
53200467 ATATTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAAAAAATAACTCTTAAT
Found at i:53201420 original size:18 final size:18
Alignment explanation
Indices: 53201388--53201441 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
53201378 CTGAGATGAG
53201388 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
53201404 AATAAATTTAATTAATTA
1 AATAAATTTAATTAATTA
*
53201422 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
53201440 AA
1 AA
53201442 ATTGTAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
16 9 0.26
17 5 0.15
18 20 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:53201451 original size:18 final size:18
Alignment explanation
Indices: 53201413--53201451 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
53201403 AAATAAATTT
*
53201413 AATTAATTAAAAATTTTA
1 AATTAATTAAAAATTTAA
53201431 AATTAATT-AAAATTGTAA
1 AATTAATTAAAAATT-TAA
53201449 AAT
1 AAT
53201452 AAAAACTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
AATTAATTAAAAATTTAA
Found at i:53203183 original size:12 final size:12
Alignment explanation
Indices: 53203166--53203190 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53203156 ATACCCTGCT
53203166 AAGAAAACATAA
1 AAGAAAACATAA
53203178 AAGAAAACATAA
1 AAGAAAACATAA
53203190 A
1 A
53203191 TTTCCTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.08
Consensus pattern (12 bp):
AAGAAAACATAA
Found at i:53205148 original size:17 final size:16
Alignment explanation
Indices: 53205113--53205143 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
53205103 AATTGGCTAA
53205113 AATTTATTAAAAAAAC
1 AATTTATTAAAAAAAC
53205129 AATTT-TTAAAAAAAC
1 AATTTATTAAAAAAAC
53205144 CCAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (16 bp):
AATTTATTAAAAAAAC
Found at i:53206613 original size:16 final size:16
Alignment explanation
Indices: 53206592--53206623 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53206582 TTTTTTCTGT
53206592 TTATAACCTTTAAAAA
1 TTATAACCTTTAAAAA
*
53206608 TTATAACTTTTAAAAA
1 TTATAACCTTTAAAAA
53206624 ATTGTCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
TTATAACCTTTAAAAA
Found at i:53207900 original size:29 final size:30
Alignment explanation
Indices: 53207867--53207923 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
53207857 ATGGTTTTTA
*
53207867 TTTTAAATTA-ATTT-TAAAATTTTAAAACG
1 TTTT-AATTATATTTCTAAAATATTAAAACG
53207896 TTTTAATTATATTTCTAAAATATTAAAA
1 TTTTAATTATATTTCTAAAATATTAAAA
53207924 TTATATCGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 5 0.20
29 8 0.32
30 12 0.48
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (30 bp):
TTTTAATTATATTTCTAAAATATTAAAACG
Found at i:53210192 original size:22 final size:22
Alignment explanation
Indices: 53210167--53210211 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
53210157 TATTGTCTAC
* *
53210167 TTTAACAAAATTTTTAATGTGG
1 TTTAACAAAATTTTCAATATGG
*
53210189 TTTAATAAAATTTTCAATATGG
1 TTTAACAAAATTTTCAATATGG
53210211 T
1 T
53210212 ACTTCTACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (22 bp):
TTTAACAAAATTTTCAATATGG
Found at i:53213752 original size:19 final size:19
Alignment explanation
Indices: 53213730--53213774 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
53213720 TTATATTAGG
53213730 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
53213749 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
53213768 ATTTAAT
1 ATTTAAT
53213775 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:53214584 original size:15 final size:16
Alignment explanation
Indices: 53214564--53214593 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53214554 CTTCCCTATT
53214564 TTCTA-TTTCTTTTAG
1 TTCTATTTTCTTTTAG
53214579 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
53214594 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAG
Found at i:53214598 original size:22 final size:22
Alignment explanation
Indices: 53214559--53214619 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
53214549 TTCGACTTCC
* *
53214559 CTATTTTCTATTT-CTTTTAGTT
1 CTATTTTCT-TTTATTTTTAATT
53214581 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
*
53214603 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTATTTTT
53214620 CCTTAGATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.13, C:0.11, G:0.03, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAATT
Found at i:53216106 original size:18 final size:17
Alignment explanation
Indices: 53216076--53216113 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
53216066 AAAATTTTTA
53216076 AATTTTTTTAATT-AAT
1 AATTTTTTTAATTAAAT
53216092 AATTTTTTTAAAATTAAAT
1 AATTTTTTT--AATTAAAT
53216111 AAT
1 AAT
53216114 CAAAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.47
18 4 0.21
19 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTTTTTTAATTAAAT
Found at i:53216258 original size:12 final size:12
Alignment explanation
Indices: 53216237--53216269 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
53216227 AAGGGTTGGG
53216237 TTTTTT-TTTCT
1 TTTTTTCTTTCT
53216248 TTTTTTCTTTCT
1 TTTTTTCTTTCT
*
53216260 TGTTTTCTTT
1 TTTTTTCTTT
53216270 GAGCAAAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (12 bp):
TTTTTTCTTTCT
Found at i:53221980 original size:20 final size:19
Alignment explanation
Indices: 53221954--53222006 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 19
53221944 TTAAAATTTG
53221954 AATTTAATGATAATATAAA
1 AATTTAATGATAATATAAA
**
53221973 ATATTTAATGGTATAATATATT
1 A-ATTTAAT-G-ATAATATAAA
53221995 AATTTAATGATA
1 AATTTAATGATA
53222007 TGATAGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 4 0.14
20 8 0.28
21 8 0.28
22 9 0.31
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (19 bp):
AATTTAATGATAATATAAA
Found at i:53224752 original size:147 final size:147
Alignment explanation
Indices: 53224359--53224783 Score: 464
Period size: 147 Copynumber: 2.9 Consensus size: 147
53224349 TCTTTTCTAA
* * * * *
53224359 ATTAACTTTATCTTCCACAA-CCAAGGAATCAACCCTTTCAGTGACATCCTCCTTAAGTTCAGAC
1 ATTAACTTTATCTTCCACAACCCCA-GAATCATCCATTTCAGTAACATCCTCCTTAAGTTCAGAT
* * *
53224423 GTCAGGTTATATTCCTTGATTGCATTTTCAGCATCTCCAATGTTCGATGAAATGCCACACTGAAC
65 GTCAGGTTATCTTCCTTAATTGCATTTTCAGCATCTCCAATGTTCGATGAAATGCCAGACTGAAC
* * *
53224488 CATTGTCCACTTGGCTAC
130 TATTGTACACTTCGCTAC
* * * * ** *
53224506 ATTAGCCTCATCTGT-TATGACCCCAGAATCATCCATTTC-GATAACTTCCTCCTTAAGTTCAGA
1 ATTAACTTTATCT-TCCACAACCCCAGAATCATCCATTTCAG-TAACATCCTCCTTAAGTTCAGA
* ** * *
53224569 TGTTAGGTTATCTTCCTTAATTGCACCTTCAGCATCTCCAATGTTAGATGAAATGTCAGACTGAA
64 TGTCAGGTTATCTTCCTTAATTGCATTTTCAGCATCTCCAATGTTCGATGAAATGCCAGACTGAA
* *
53224634 CTATTGTAGAGTTCGCTAC
129 CTATTGTACACTTCGCTAC
* * * * *
53224653 ATTAACTTTAACTTCCACAACCCCAGAATCATCCATTTCAGTAACCTCTTCCTCAAGTTGAGATG
1 ATTAACTTTATCTTCCACAACCCCAGAATCATCCATTTCAGTAACATCCTCCTTAAGTTCAGATG
* * * *
53224718 TCAGGTTATCTTCCTTAATTACGTTTTCTA-CATCT-AAATTGTTCGATGAAATGCCAGATTGAA
66 TCAGGTTATCTTCCTTAATTGCATTTTC-AGCATCTCCAA-TGTTCGATGAAATGCCAGACTGAA
53224781 CTA
129 CTA
53224784 CAGTCGACTT
Statistics
Matches: 226, Mismatches: 45, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
146 4 0.02
147 216 0.96
148 6 0.03
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (147 bp):
ATTAACTTTATCTTCCACAACCCCAGAATCATCCATTTCAGTAACATCCTCCTTAAGTTCAGATG
TCAGGTTATCTTCCTTAATTGCATTTTCAGCATCTCCAATGTTCGATGAAATGCCAGACTGAACT
ATTGTACACTTCGCTAC
Found at i:53225945 original size:30 final size:31
Alignment explanation
Indices: 53225911--53225991 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 31
53225901 GTTACATTTA
53225911 ACAAAACAATCACTCAACTT-T-GAAAAAGTG
1 ACAAAACAATCACTCAACTTATCG-AAAAGTG
* * * *
53225941 ACAAAACAGTCACTAAAGTTATCGAAGAGTG
1 ACAAAACAATCACTCAACTTATCGAAAAGTG
*
53225972 ACAAAACAATC-CTCTACTTA
1 ACAAAACAATCACTCAACTTA
53225992 CTATTCAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
30 23 0.56
31 17 0.41
32 1 0.02
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (31 bp):
ACAAAACAATCACTCAACTTATCGAAAAGTG
Found at i:53226837 original size:30 final size:31
Alignment explanation
Indices: 53226767--53226838 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
53226757 AAGCCAAGAG
*
53226767 GACTGTTTTGTCACTTTTCGATAACTTTAGT
1 GACTGTTTTGTCACTTTTCGATAACTTGAGT
* * *
53226798 GATTGTTTTGTCACATTTTC-A-AAGTTGATT
1 GACTGTTTTGTCAC-TTTTCGATAACTTGAGT
53226828 GACTGTTTTGT
1 GACTGTTTTGT
53226839 TAAATATAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 16 0.46
31 14 0.40
32 5 0.14
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.50
Consensus pattern (31 bp):
GACTGTTTTGTCACTTTTCGATAACTTGAGT
Found at i:53229303 original size:14 final size:15
Alignment explanation
Indices: 53229269--53229306 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
53229259 AAAAAAAATC
53229269 AAATTCAA-AGATCA
1 AAATTCAATAGATCA
*
53229283 AATTTCAATAGAT-A
1 AAATTCAATAGATCA
53229297 AAATTCAATA
1 AAATTCAATA
53229307 AGAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (15 bp):
AAATTCAATAGATCA
Found at i:53234299 original size:30 final size:25
Alignment explanation
Indices: 53234222--53234290 Score: 111
Period size: 25 Copynumber: 2.7 Consensus size: 25
53234212 AAAAATATTT
53234222 AAAATTTTATATTAACTTTTTATAACA
1 AAAATTTTAT-TTAA-TTTTTATAACA
53234249 AAAATTTTATTTAATTTTTATAACA
1 AAAATTTTATTTAATTTTTATAACA
*
53234274 AAAATTTTATTTTATTT
1 AAAATTTTATTTAATTT
53234291 AATTTTTATC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 27 0.66
26 4 0.10
27 10 0.24
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
AAAATTTTATTTAATTTTTATAACA
Found at i:53234315 original size:35 final size:30
Alignment explanation
Indices: 53234225--53234299 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
53234215 AATATTTAAA
53234225 ATTTTATATTAACTTTTTATAAC-AAAA----
1 ATTTTAT-TTAA-TTTTTATAACAAAAATTTT
53234252 ATTTTATTTAATTTTTATAACAAAAATTTT
1 ATTTTATTTAATTTTTATAACAAAAATTTT
53234282 ATTTTATTTAATTTTTAT
1 ATTTTATTTAATTTTTAT
53234300 CACCTACCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
25 10 0.23
26 8 0.19
27 7 0.16
30 18 0.42
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (30 bp):
ATTTTATTTAATTTTTATAACAAAAATTTT
Found at i:53235131 original size:17 final size:16
Alignment explanation
Indices: 53235109--53235145 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
53235099 CATACTTTTT
*
53235109 AAAAATGTTTTTGATAA
1 AAAAATATTTTTGA-AA
53235126 AAAAATATTTTTGAAA
1 AAAAATATTTTTGAAA
53235142 AAAA
1 AAAA
53235146 GTTAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (16 bp):
AAAAATATTTTTGAAA
Found at i:53235229 original size:33 final size:31
Alignment explanation
Indices: 53235174--53235252 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
53235164 TTTTTGACCA
*
53235174 AAAAAATATTTTTTTCAAAATATTTTTAGTGT
1 AAAAAATATTTTTTTCAAAATATTTTTA-TCT
* *
53235206 CAAAAATATTTTATTT-AGTAATATTTTTATCT
1 AAAAAATATTTT-TTTCA-AAATATTTTTATCT
53235238 AAAAAATATTTTTTT
1 AAAAAATATTTTTTT
53235253 GTCTTAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 3 0.07
32 25 0.61
33 13 0.32
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (31 bp):
AAAAAATATTTTTTTCAAAATATTTTTATCT
Found at i:53235247 original size:17 final size:16
Alignment explanation
Indices: 53235174--53235250 Score: 61
Period size: 17 Copynumber: 4.8 Consensus size: 16
53235164 TTTTTGACCA
53235174 AAAAAATATTTTT-TT
1 AAAAAATATTTTTATT
*
53235189 -CAAAATATTTTTAGTGT
1 AAAAAATATTTTTA-T-T
*
53235206 CAAAAATA-TTTTATT
1 AAAAAATATTTTTATT
* **
53235221 TAGTAATATTTTTATCT
1 AAAAAATATTTTTAT-T
53235238 AAAAAATATTTTT
1 AAAAAATATTTTT
53235251 TTGTCTTAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
14 11 0.23
15 6 0.12
16 8 0.17
17 17 0.35
18 6 0.12
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (16 bp):
AAAAAATATTTTTATT
Found at i:53235261 original size:19 final size:19
Alignment explanation
Indices: 53235229--53235269 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
53235219 TTTAGTAATA
53235229 TTTTTATCTAAAAAATATT
1 TTTTTATCTAAAAAATATT
* *
53235248 TTTTTGTCTTAAAAATATT
1 TTTTTATCTAAAAAATATT
53235267 TTT
1 TTT
53235270 GAGAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTTATCTAAAAAATATT
Found at i:53235268 original size:17 final size:17
Alignment explanation
Indices: 53235190--53235270 Score: 58
Period size: 17 Copynumber: 4.7 Consensus size: 17
53235180 TATTTTTTTC
* *
53235190 AAAATATTTTTAGTGTCA
1 AAAATATTTTT-GTCTTA
*
53235208 AAAATA-TTTTAT-TTA
1 AAAATATTTTTGTCTTA
** * *
53235223 GTAATATTTTTATCTAA
1 AAAATATTTTTGTCTTA
53235240 AAAATATTTTTTTGTCTTA
1 AAAATA--TTTTTGTCTTA
53235259 AAAATATTTTTG
1 AAAATATTTTTG
53235271 AGAAATAATG
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
15 6 0.12
16 7 0.14
17 16 0.32
18 6 0.12
19 15 0.30
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (17 bp):
AAAATATTTTTGTCTTA
Found at i:53237099 original size:19 final size:18
Alignment explanation
Indices: 53237014--53237100 Score: 54
Period size: 19 Copynumber: 4.7 Consensus size: 18
53237004 AATATAGAAA
*
53237014 AAAATTATAAAAGTTTAT
1 AAAATTATAAAAGATTAT
*
53237032 AAAATCTA-AGAAA-ACTATT
1 AAAAT-TATA-AAAGATTA-T
* *
53237051 GAAAA-TATAAAAAAATAT
1 -AAAATTATAAAAGATTAT
*
53237069 AAAATTCGTAAAAGATTAT
1 AAAATT-ATAAAAGATTAT
53237088 AAAAATTATAAAA
1 -AAAATTATAAAA
53237101 TGTTTCTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 17
0.69 0.09 0.22
Matches are distributed among these distances:
17 4 0.08
18 15 0.28
19 24 0.45
20 10 0.19
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (18 bp):
AAAATTATAAAAGATTAT
Found at i:53251344 original size:12 final size:13
Alignment explanation
Indices: 53251321--53251384 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
53251311 AGTTTAATAT
53251321 TATTTTTGAAAAG
1 TATTTTTGAAAAG
*
53251334 TATTTTTAAAAAG
1 TATTTTTGAAAAG
**
53251347 TA-CATTGAAAA-
1 TATTTTTGAAAAG
*
53251358 AATTATTTCGAAAAG
1 TATT-TTT-GAAAAG
53251373 TATTTTTGAAAA
1 TATTTTTGAAAA
53251385 ATTTGATTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
11 1 0.03
12 6 0.15
13 21 0.54
14 8 0.21
15 3 0.08
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.41
Consensus pattern (13 bp):
TATTTTTGAAAAG
Found at i:53252262 original size:2 final size:2
Alignment explanation
Indices: 53252255--53252281 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53252245 ACTAATTCTC
53252255 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 A
53252282 AAAGGAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53252401 original size:17 final size:17
Alignment explanation
Indices: 53252381--53252413 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53252371 TAAAGAATTG
*
53252381 AGAAAGATGAAAAGTTA
1 AGAAAAATGAAAAGTTA
53252398 AGAAAAATGAAAAGTT
1 AGAAAAATGAAAAGTT
53252414 GAACATCCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18
Consensus pattern (17 bp):
AGAAAAATGAAAAGTTA
Found at i:53259003 original size:26 final size:24
Alignment explanation
Indices: 53258960--53259011 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
53258950 TAAAATATTC
53258960 AATAAATTAATATATATTTAAAATAA
1 AATAAATTAATATATA-TT-AAATAA
*
53258986 AATAAATTTAA-ATCTATTAAATAA
1 AATAAA-TTAATATATATTAAATAA
53259010 AA
1 AA
53259012 ATTATAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 8 0.33
25 2 0.08
26 10 0.42
27 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AATAAATTAATATATATTAAATAA
Found at i:53265734 original size:18 final size:18
Alignment explanation
Indices: 53265713--53265747 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
53265703 ATTAGTATTT
53265713 TTTTAA-TAATTTATTAAA
1 TTTTAATTAA-TTATTAAA
53265731 TTTTAATTAATTATTAA
1 TTTTAATTAATTATTAA
53265748 TATGATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAATTAATTATTAAA
Found at i:53265738 original size:33 final size:33
Alignment explanation
Indices: 53265676--53265739 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
53265666 AATTTTTATG
*
53265676 ATTTTTTTTAATTTTTTATAATTTATAATTAGT
1 ATTTTTTTTAATTTATTATAATTTATAATTAGT
53265709 ATTTTTTTAATAATTTATTA-AATTT-TAATTA
1 ATTTTTTT--TAATTTATTATAATTTATAATTA
53265740 ATTATTAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 14 0.50
34 5 0.18
35 9 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (33 bp):
ATTTTTTTTAATTTATTATAATTTATAATTAGT
Found at i:53266415 original size:34 final size:34
Alignment explanation
Indices: 53266344--53266408 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
53266334 CAAAAAACCT
*
53266344 TAAACCCTACTTTAAATAAACAAAACCCTAATAC
1 TAAACCCTAATTTAAATAAACAAAACCCTAATAC
* *
53266378 TAAATCCTAATTTAAATAAATAAAACCCTAA
1 TAAACCCTAATTTAAATAAACAAAACCCTAA
53266409 CTCTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (34 bp):
TAAACCCTAATTTAAATAAACAAAACCCTAATAC
Found at i:53267468 original size:60 final size:59
Alignment explanation
Indices: 53267380--53267505 Score: 243
Period size: 60 Copynumber: 2.1 Consensus size: 59
53267370 TTTTTAAATA
53267380 AAATTAACCTAAAAATATCAAATATGAACAAATCGAATCGGATCTGAATTTACTTTTTTT
1 AAATTAACCTAAAAATATCAAATATGAACAAATCGAATCGGATCTGAATTTA-TTTTTTT
53267440 AAATTAACCTAAAAATATCAAATATGAACAAATCGAATCGGATCTGAATTTATTTTTTT
1 AAATTAACCTAAAAATATCAAATATGAACAAATCGAATCGGATCTGAATTTATTTTTTT
53267499 AAATTAA
1 AAATTAA
53267506 GTAAAACTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
59 14 0.21
60 52 0.79
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (59 bp):
AAATTAACCTAAAAATATCAAATATGAACAAATCGAATCGGATCTGAATTTATTTTTTT
Found at i:53269144 original size:11 final size:11
Alignment explanation
Indices: 53269130--53269156 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
53269120 CCATTTTTTA
53269130 TTTTTTTTATT
1 TTTTTTTTATT
53269141 TTTTTTTTATT
1 TTTTTTTTATT
53269152 TTTTT
1 TTTTT
53269157 CAATGATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:53269156 original size:9 final size:9
Alignment explanation
Indices: 53269123--53269155 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
53269113 TTGGTAACCA
53269123 TTTTTTATT
1 TTTTTTATT
53269132 TTTTTTATT
1 TTTTTTATT
53269141 TTTTTT-TT
1 TTTTTTATT
53269149 ATTTTTT
1 -TTTTTT
53269156 TCAATGATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 2 0.09
9 21 0.91
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTATT
Found at i:53270694 original size:21 final size:21
Alignment explanation
Indices: 53270645--53270694 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
53270635 TACAAAAAAA
53270645 AATTATTTTAATTTTTTATTT
1 AATTATTTTAATTTTTTATTT
*
53270666 AATT-TTTTGCATTTTTTATTT
1 AATTATTTT-AATTTTTTATTT
*
53270687 -TTTATTTT
1 AATTATTTT
53270695 TGGTGAATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (21 bp):
AATTATTTTAATTTTTTATTT
Found at i:53273393 original size:34 final size:33
Alignment explanation
Indices: 53273330--53273394 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
53273320 TAAGTAACTA
*
53273330 AATTAAACAGTATTTATTATAAATAAATTATTT
1 AATTAAACAGTATTTATCATAAATAAATTATTT
* * *
53273363 AATTAAATTAGTATTTATCATTAATTAATTAT
1 AATTAAA-CAGTATTTATCATAAATAAATTAT
53273395 ACTTGATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 7 0.26
34 20 0.74
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (33 bp):
AATTAAACAGTATTTATCATAAATAAATTATTT
Found at i:53273403 original size:21 final size:22
Alignment explanation
Indices: 53273361--53273403 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
53273351 AATAAATTAT
*
53273361 TTAATTAAATTAGTATTTATCA
1 TTAATTAAATTAGTATTGATCA
53273383 TTAATT-AATTA-TACTTGATCA
1 TTAATTAAATTAGTA-TTGATCA
53273404 ATGATCATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 2 0.11
21 11 0.58
22 6 0.32
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.49
Consensus pattern (22 bp):
TTAATTAAATTAGTATTGATCA
Found at i:53273546 original size:22 final size:22
Alignment explanation
Indices: 53273520--53273564 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
53273510 CGAATATTCT
53273520 TTTTAAACTAGCATATTGCATA
1 TTTTAAACTAGCATATTGCATA
*
53273542 TTTTAGACTAGCATATTGCATA
1 TTTTAAACTAGCATATTGCATA
53273564 T
1 T
53273565 ATTGGTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (22 bp):
TTTTAAACTAGCATATTGCATA
Found at i:53277282 original size:59 final size:59
Alignment explanation
Indices: 53277169--53277283 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 59
53277159 TGAAAAAGTA
* * * * **
53277169 GAAGCCCAGAATTCAATACCCAGGTCGGTTCATATCTTAGGTATTCATGGGTAAAAATC
1 GAAGCCCAAAATTCAATACCCACGTCGGTTCATATCTCAGCTATTCATAAGTAAAAATC
*
53277228 GAAGCCCAAAATTCAATACCCACGTCGGTTTATATCTCAGCTATTCATAAGTAAAA
1 GAAGCCCAAAATTCAATACCCACGTCGGTTCATATCTCAGCTATTCATAAGTAAAA
53277284 TTTAAGCCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (59 bp):
GAAGCCCAAAATTCAATACCCACGTCGGTTCATATCTCAGCTATTCATAAGTAAAAATC
Found at i:53280895 original size:5 final size:5
Alignment explanation
Indices: 53280885--53280915 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
53280875 GGCAAATGCA
53280885 TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT T
1 TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT T
53280916 ATTACCTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TGTTT
Found at i:53282981 original size:4 final size:4
Alignment explanation
Indices: 53282972--53282999 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
53282962 GTTCCACTAT
53282972 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
53283000 TATATATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:53287210 original size:13 final size:14
Alignment explanation
Indices: 53287192--53287224 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
53287182 TATGTGGGTA
53287192 AAAAAATAAACTT-
1 AAAAAATAAACTTG
*
53287205 AAAAAATAGACTTG
1 AAAAAATAAACTTG
53287219 AAAAAA
1 AAAAAA
53287225 AAAAACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.18
Consensus pattern (14 bp):
AAAAAATAAACTTG
Found at i:53287374 original size:11 final size:11
Alignment explanation
Indices: 53287360--53287435 Score: 82
Period size: 11 Copynumber: 6.9 Consensus size: 11
53287350 ATTACGTTGC
*
53287360 TATTTTGTTAT
1 TATTTTATTAT
*
53287371 TATTTTGTTAT
1 TATTTTATTAT
*
53287382 CATTTTATTAT
1 TATTTTATTAT
*
53287393 TATATTATTAT
1 TATTTTATTAT
* *
53287404 TATTTAAATAT
1 TATTTTATTAT
53287415 TATTTTATTAT
1 TATTTTATTAT
53287426 T-TTATTATTA
1 TATT-TTATTA
53287436 ATTTTACTAC
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
10 2 0.04
11 53 0.96
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:53287910 original size:54 final size:55
Alignment explanation
Indices: 53287845--53287986 Score: 205
Period size: 54 Copynumber: 2.6 Consensus size: 55
53287835 ATTCCAAATA
* * * *
53287845 AGAATCGAATTCCAAATATCAAACAATCAAATTATATTCTAATTACCATATT-TG
1 AGAATCAAATTCCAAACATTAAAGAATCAAATTATATTCTAATTACCATATTCTG
* ** *
53287899 AGAATCAAATTCCAAACGTTAAAGAATCAAATCCTATTCTAATTATCATATTCTG
1 AGAATCAAATTCCAAACATTAAAGAATCAAATTATATTCTAATTACCATATTCTG
53287954 AGAATCAAATTCCAAACATTAAAGAATCAAATT
1 AGAATCAAATTCCAAACATTAAAGAATCAAATT
53287987 CCATTTTAAG
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
54 44 0.57
55 33 0.43
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (55 bp):
AGAATCAAATTCCAAACATTAAAGAATCAAATTATATTCTAATTACCATATTCTG
Found at i:53288122 original size:21 final size:18
Alignment explanation
Indices: 53288078--53288131 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 18
53288068 AATATTGTTA
*
53288078 ATTATTTTAAATATATTC
1 ATTATTTTAAATAAATTC
53288096 A-TATTTTATAATACAATTTC
1 ATTATTTTA-AATA-AA-TTC
*
53288116 ATTATTTTAAAAAAAT
1 ATTATTTTAAATAAAT
53288132 CAGTTCACCG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
17 7 0.23
18 6 0.20
19 3 0.10
20 7 0.23
21 7 0.23
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATTTTAAATAAATTC
Found at i:53290562 original size:28 final size:30
Alignment explanation
Indices: 53290516--53290578 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 30
53290506 AGAAATTAAC
* *
53290516 GATTGTTTTACCAC-TTTTTAACGTT-AGT
1 GATTGTTTTACCACATTTTCAAAGTTGAGT
**
53290544 GATTGTTTTGTCACATTTTCAAAGTTGAGT
1 GATTGTTTTACCACATTTTCAAAGTTGAGT
53290574 GATTG
1 GATTG
53290579 AAATGTAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 12 0.41
29 9 0.31
30 8 0.28
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.48
Consensus pattern (30 bp):
GATTGTTTTACCACATTTTCAAAGTTGAGT
Found at i:53290717 original size:16 final size:19
Alignment explanation
Indices: 53290660--53290724 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 19
53290650 TAATTTATAT
53290660 TTAATCATA-TAATAAATTA
1 TTAAT-ATATTAATAAATTA
53290679 TTAATATAATTAATATAATTTA
1 TTAATAT-ATTAATA-AA-TTA
53290701 TT-AT-T-TTAATAAATTA
1 TTAATATATTAATAAATTA
53290717 TTTAATAT
1 -TTAATAT
53290725 TTCAATTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.08
17 4 0.10
18 10 0.26
19 7 0.18
20 6 0.15
21 4 0.10
22 5 0.13
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAATATATTAATAAATTA
Found at i:53290760 original size:16 final size:14
Alignment explanation
Indices: 53290734--53290774 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
53290724 TTTCAATTTT
53290734 ATTTT-AATAATAA
1 ATTTTAAATAATAA
53290747 ATTTTTAAAATAAT-A
1 A-TTTT-AAATAATAA
53290762 ATTTTAAATAATA
1 ATTTTAAATAATA
53290775 CTCTTCATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 8 0.33
14 8 0.33
15 2 0.08
16 6 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTTTAAATAATAA
Found at i:53290825 original size:15 final size:15
Alignment explanation
Indices: 53290807--53290860 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 15
53290797 ATTCAATATT
53290807 AATATATTAATAATGA
1 AATATATTAATAAT-A
* *
53290823 ATATTTATTACAATTATA
1 A-ATATATT--AATAATA
53290841 AATATATTAATAATA
1 AATATATTAATAATA
53290856 AATAT
1 AATAT
53290861 TTTGTAGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 11 0.35
16 1 0.03
17 12 0.39
18 2 0.06
19 5 0.16
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:53293355 original size:13 final size:14
Alignment explanation
Indices: 53293326--53293355 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
53293316 GAGCTTTCAT
53293326 TTTGGTCACCACAA
1 TTTGGTCACCACAA
53293340 TTTGGTCACC-CAA
1 TTTGGTCACCACAA
53293353 TTT
1 TTT
53293356 TTAAGGCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (14 bp):
TTTGGTCACCACAA
Found at i:53299281 original size:30 final size:30
Alignment explanation
Indices: 53299247--53299310 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 30
53299237 ATCTAGCAAC
*
53299247 TTAATGACTTAAAT-AAAAATTTTCGAATAG
1 TTAATGACTTAAATGAAAAACTTTCG-ATAG
53299277 TTAATGACTTAAATGAAAAACTTTCGATAG
1 TTAATGACTTAAATGAAAAACTTTCGATAG
53299307 TTAA
1 TTAA
53299311 ATAACCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (30 bp):
TTAATGACTTAAATGAAAAACTTTCGATAG
Found at i:53301478 original size:35 final size:35
Alignment explanation
Indices: 53301439--53301527 Score: 144
Period size: 35 Copynumber: 2.5 Consensus size: 35
53301429 CCTAAATCCT
53301439 AAATCTTAAAT-TTCAAATCTTTAACCATAAACCCC
1 AAATCTTAAATCTT-AAATCTTTAACCATAAACCCC
*
53301474 AAATCTTGAATCTTAAATCTTTAACCATAAACCCC
1 AAATCTTAAATCTTAAATCTTTAACCATAAACCCC
*
53301509 AAATCTTAAATCATAAATC
1 AAATCTTAAATCTTAAATC
53301528 CAAATGCAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
35 48 0.96
36 2 0.04
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.31
Consensus pattern (35 bp):
AAATCTTAAATCTTAAATCTTTAACCATAAACCCC
Found at i:53309860 original size:14 final size:12
Alignment explanation
Indices: 53309836--53309869 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
53309826 CGTCACTGTT
*
53309836 GCCACGTCAGC-
1 GCCACATCAGCA
53309847 GCCACATCAGCA
1 GCCACATCAGCA
53309859 GCCACATCAGC
1 GCCACATCAGC
53309870 CACTGACTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.26, C:0.44, G:0.21, T:0.09
Consensus pattern (12 bp):
GCCACATCAGCA
Found at i:53313425 original size:21 final size:22
Alignment explanation
Indices: 53313387--53313431 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
53313377 ACATCTTTCA
* *
53313387 AATATTTGAATGAAATAATAAT
1 AATATTTGAATAAAATAAAAAT
53313409 AATATTT-AATAAAATAAAAAT
1 AATATTTGAATAAAATAAAAAT
53313430 AA
1 AA
53313432 AATGAGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
AATATTTGAATAAAATAAAAAT
Found at i:53314705 original size:26 final size:27
Alignment explanation
Indices: 53314669--53314729 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
53314659 ATCTTGACTT
* *
53314669 TTGAATTTTGAAATCCAAATTCGAA-C
1 TTGAATCTTGAAATCCAAACTCGAATC
* *
53314695 TTGAATCTTGAACTCCGAACTCGAATC
1 TTGAATCTTGAAATCCAAACTCGAATC
*
53314722 TTAAATCT
1 TTGAATCT
53314730 CGAACCCTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 21 0.72
27 8 0.28
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (27 bp):
TTGAATCTTGAAATCCAAACTCGAATC
Found at i:53314733 original size:20 final size:20
Alignment explanation
Indices: 53314685--53314734 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
53314675 TTTGAAATCC
*
53314685 AAAT-TCGAACTTGAATCTT
1 AAATCTCGAACTCGAATCTT
*
53314704 GAA-CTCCGAACTCGAATCTT
1 AAATCT-CGAACTCGAATCTT
53314724 AAATCTCGAAC
1 AAATCTCGAAC
53314735 CCTAAATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 3 0.12
20 20 0.80
21 2 0.08
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (20 bp):
AAATCTCGAACTCGAATCTT
Found at i:53314832 original size:20 final size:20
Alignment explanation
Indices: 53314807--53314850 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
53314797 AGAGTTCATG
53314807 ATTCGAGATTTAATTTTTGA
1 ATTCGAGATTTAATTTTTGA
53314827 ATTCGAGATTTAATTTTTGA
1 ATTCGAGATTTAATTTTTGA
53314847 ATTC
1 ATTC
53314851 AAAATTCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.50
Consensus pattern (20 bp):
ATTCGAGATTTAATTTTTGA
Found at i:53318155 original size:13 final size:13
Alignment explanation
Indices: 53318110--53318156 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
53318100 TTCCCCTGAA
53318110 ATTTCAAAATTAAT
1 ATTT-AAAATTAAT
* *
53318124 -TTTAAAAATATT
1 ATTTAAAATTAAT
53318136 ATCTTAAAATTAAT
1 AT-TTAAAATTAAT
53318150 ATTTAAA
1 ATTTAAA
53318157 CAAATAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
12 7 0.26
13 9 0.33
14 11 0.41
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTTAAAATTAAT
Done.