Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 132 of 143
Found at i:38824083 original size:17 final size:17
Alignment explanation
Indices: 38824063--38824104 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
38824053 TGCATAATTA
38824063 AAAATAAAAAATAAAAT
1 AAAATAAAAAATAAAAT
* *
38824080 AAAATTAAAATTAAAAT
1 AAAATAAAAAATAAAAT
*
38824097 TAAATAAA
1 AAAATAAA
38824105 TAAACTAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATAAAAAATAAAAT
Found at i:38824128 original size:18 final size:19
Alignment explanation
Indices: 38824105--38824142 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
38824095 ATTAAATAAA
38824105 TAAACTAAT-AATTTTTTT
1 TAAACTAATCAATTTTTTT
**
38824123 TAAACTTTTCAATTTTTTT
1 TAAACTAATCAATTTTTTT
38824142 T
1 T
38824143 TACTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (19 bp):
TAAACTAATCAATTTTTTT
Found at i:38829719 original size:10 final size:10
Alignment explanation
Indices: 38829697--38829726 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
38829687 TAAAAATGCA
38829697 AATAATAAAAT
1 AATAAT-AAAT
38829708 AATAATAAAT
1 AATAATAAAT
38829718 AATAATAAA
1 AATAATAAA
38829727 ATGGCTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AATAATAAAT
Found at i:38834221 original size:17 final size:17
Alignment explanation
Indices: 38834199--38834231 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38834189 ATCTATAAAT
*
38834199 ATAAATTCAATACAATC
1 ATAAATTAAATACAATC
38834216 ATAAATTAAATACAAT
1 ATAAATTAAATACAAT
38834232 ATAGTTATGT
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:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAAATTAAATACAATC
Found at i:38834231 original size:22 final size:24
Alignment explanation
Indices: 38834188--38834232 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
38834178 AAATTTTTAG
*
38834188 AATCTATAAATATAAATTCAATAC
1 AATCTATAAATATAAATACAATAC
38834212 AATC-ATAAAT-TAAATACAATA
1 AATCTATAAATATAAATACAATA
38834233 TAGTTATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 6 0.30
24 4 0.20
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (24 bp):
AATCTATAAATATAAATACAATAC
Found at i:38836320 original size:25 final size:25
Alignment explanation
Indices: 38836292--38836339 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
38836282 ATATGTTTCG
*
38836292 TATA-TCTAGATTTATTTTTTCATAT
1 TATACTCTAG-TTTATTTATTCATAT
*
38836317 TATACTCTTGTTTATTTATTCAT
1 TATACTCTAGTTTATTTATTCAT
38836340 TTAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.25, C:0.10, G:0.04, T:0.60
Consensus pattern (25 bp):
TATACTCTAGTTTATTTATTCATAT
Found at i:38846223 original size:22 final size:23
Alignment explanation
Indices: 38846180--38846223 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
38846170 TTAATCCTTT
* * *
38846180 AAAATTATATTTTTATTATCGTA
1 AAAATTACAATTTAATTATCGTA
38846203 AAAATTACAATTTAATT-TCGT
1 AAAATTACAATTTAATTATCGT
38846224 CTGTTAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (23 bp):
AAAATTACAATTTAATTATCGTA
Found at i:38853637 original size:7 final size:7
Alignment explanation
Indices: 38853627--38853653 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
38853617 TGAATTTAAA
38853627 GTTTGAG
1 GTTTGAG
38853634 GTTTGAG
1 GTTTGAG
38853641 GTTTGAG
1 GTTTGAG
38853648 GTTTGA
1 GTTTGA
38853654 AATTTAAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (7 bp):
GTTTGAG
Found at i:38854143 original size:14 final size:15
Alignment explanation
Indices: 38854126--38854155 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
38854116 TTTAATTTTT
38854126 TATTTATTT-TAAAA
1 TATTTATTTATAAAA
38854140 TATTTATTTATAAAA
1 TATTTATTTATAAAA
38854155 T
1 T
38854156 TTAAATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTATTTATAAAA
Found at i:38854184 original size:24 final size:22
Alignment explanation
Indices: 38854135--38854185 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
38854125 TTATTTATTT
*
38854135 TAAAATATTTATTTATAAAATT
1 TAAAATATTTATTTATAAAATA
* *
38854157 TAAATTATTTATTGATATAACATA
1 TAAAATATTTATT--TATAAAATA
38854181 TAAAA
1 TAAAA
38854186 CAAATAGTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 12 0.52
24 11 0.48
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
TAAAATATTTATTTATAAAATA
Found at i:38861352 original size:3 final size:3
Alignment explanation
Indices: 38861346--38861379 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
38861336 ATCTATTTAT
38861346 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38861380 ATAAGGCAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:38872889 original size:29 final size:25
Alignment explanation
Indices: 38872847--38872909 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 25
38872837 CAAAATTGTG
38872847 TTTTTTTATTTTTAAGGGGCTCCAAAAA
1 TTTTTTTATTTTTAA-GGGCT-C-AAAA
*
38872875 TTTTTTTAGTTTTTAAGGGCTCAAAT
1 TTTTTTTA-TTTTTAAGGGCTCAAAA
38872901 TTTTTTTAT
1 TTTTTTTAT
38872910 CAACTTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 1 0.03
26 11 0.33
27 1 0.03
28 13 0.39
29 7 0.21
ACGTcount: A:0.24, C:0.08, G:0.13, T:0.56
Consensus pattern (25 bp):
TTTTTTTATTTTTAAGGGCTCAAAA
Found at i:38872947 original size:29 final size:29
Alignment explanation
Indices: 38872897--38872958 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
38872887 TTAAGGGCTC
* *
38872897 AAATTTTTTTTATCAACTTTTAAGAGATCT
1 AAATTTTTTTTATCAAC-TTTAAAAAATCT
38872927 AAATTTTTTTTATCCAA-TTTAAAAAATCT
1 AAATTTTTTTTAT-CAACTTTAAAAAATCT
38872956 AAA
1 AAA
38872959 ATCCCATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 13 0.45
30 13 0.45
31 3 0.10
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (29 bp):
AAATTTTTTTTATCAACTTTAAAAAATCT
Found at i:38884696 original size:36 final size:36
Alignment explanation
Indices: 38884656--38884724 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
38884646 CCATGGAAAC
38884656 AGACGTAAAAGCTTTGTGTGATCTAATGATACAAAT
1 AGACGTAAAAGCTTTGTGTGATCTAATGATACAAAT
*
38884692 AGACGTAAAAGTTTTGTGTGATCTAATGATACA
1 AGACGTAAAAGCTTTGTGTGATCTAATGATACA
38884725 CTGACACACC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (36 bp):
AGACGTAAAAGCTTTGTGTGATCTAATGATACAAAT
Found at i:38900373 original size:20 final size:20
Alignment explanation
Indices: 38900344--38900382 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38900334 AAATTTGCAT
* *
38900344 ATTTTGAATTTATTTCAATA
1 ATTTTCAATTTAGTTCAATA
38900364 ATTTTCAATTTAGTTCAAT
1 ATTTTCAATTTAGTTCAAT
38900383 CTTTGTCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAATTTAGTTCAATA
Found at i:38902786 original size:29 final size:30
Alignment explanation
Indices: 38902729--38902807 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
38902719 ATCTCAAAAT
* *
38902729 TATACATGAACTTTGATTTAATGTGCAATTA
1 TATACATGAACTTTAATTT-ATGTACAATTA
38902760 TATACATGAACTTTAATTT-TGTACAATTA
1 TATACATGAACTTTAATTTATGTACAATTA
* *
38902789 TATACGTGAAACTCTAATT
1 TATACATG-AACTTTAATT
38902808 GTAGTTCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 16 0.37
30 9 0.21
31 18 0.42
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (30 bp):
TATACATGAACTTTAATTTATGTACAATTA
Found at i:38906948 original size:8 final size:8
Alignment explanation
Indices: 38906911--38906947 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
38906901 TAACTAAGAT
38906911 AAATAATA
1 AAATAATA
38906919 AAATAATA
1 AAATAATA
*
38906927 AAATAACA
1 AAATAATA
*
38906935 AAATAGTA
1 AAATAATA
38906943 AAATA
1 AAATA
38906948 GCATGATTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (8 bp):
AAATAATA
Found at i:38913342 original size:14 final size:14
Alignment explanation
Indices: 38913323--38913350 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38913313 GAGAGATGAT
38913323 GATTTTTCATCCTA
1 GATTTTTCATCCTA
38913337 GATTTTTCATCCTA
1 GATTTTTCATCCTA
38913351 ATGCATTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
GATTTTTCATCCTA
Found at i:38914756 original size:21 final size:23
Alignment explanation
Indices: 38914713--38914758 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
38914703 AATAAGAAAT
*
38914713 TATAATTAAAACATTTCAAAAAA
1 TATAATTAAAACATTTAAAAAAA
38914736 TATAATTAAAA-A-TTAAAAAAA
1 TATAATTAAAACATTTAAAAAAA
38914757 TA
1 TA
38914759 GCTAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.45
22 1 0.05
23 11 0.50
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (23 bp):
TATAATTAAAACATTTAAAAAAA
Found at i:38920190 original size:35 final size:35
Alignment explanation
Indices: 38920120--38920191 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
38920110 TAATAGATTG
*
38920120 ATAATTATAATTTAATTTATAATTATTAATTAAAA
1 ATAATTATAATTTAATTTATAATTATTAATAAAAA
38920155 ATAATTATAATTTAATTT-TGACATTATT-ATAAAAA
1 ATAATTATAATTTAATTTAT-A-ATTATTAATAAAAA
38920190 AT
1 AT
38920192 TATTTTTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
34 1 0.03
35 27 0.79
36 6 0.18
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (35 bp):
ATAATTATAATTTAATTTATAATTATTAATAAAAA
Found at i:38922617 original size:21 final size:21
Alignment explanation
Indices: 38922572--38922618 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
38922562 AAGTTTTATG
* *
38922572 TTTTTTGGAATTTTATATATC
1 TTTTTTGAAATTTTATATATA
* *
38922593 TTTTTTGAAATTTTATTTTTA
1 TTTTTTGAAATTTTATATATA
38922614 TTTTT
1 TTTTT
38922619 CATTCAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.70
Consensus pattern (21 bp):
TTTTTTGAAATTTTATATATA
Found at i:38922995 original size:16 final size:15
Alignment explanation
Indices: 38922974--38923003 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
38922964 GAATATTCTT
38922974 ATATTATTTATTTTTA
1 ATATTA-TTATTTTTA
38922990 ATATTATTATTTTT
1 ATATTATTATTTTT
38923004 CTTTTATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATATTATTATTTTTA
Found at i:38923015 original size:20 final size:19
Alignment explanation
Indices: 38922975--38923021 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
38922965 AATATTCTTA
*
38922975 TATTATTTATTTTTAATAT
1 TATTATTTTTTTTTAATAT
38922994 TATTATTTTTCTTTT-ATA-
1 TATTATTTTT-TTTTAATAT
38923012 -ATTATTTTTT
1 TATTATTTTTT
38923022 AATTTGTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 9 0.35
19 12 0.46
20 4 0.15
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTATTTTTTTTTAATAT
Found at i:38925975 original size:16 final size:16
Alignment explanation
Indices: 38925933--38925984 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
38925923 AAAAATTATG
*
38925933 TTTTCCATCCTTCTAA
1 TTTTTCATCCTTCTAA
*
38925949 -TTTTC-TACCTTTTAA
1 TTTTTCAT-CCTTCTAA
*
38925964 TTTTTCATCCTTCAAA
1 TTTTTCATCCTTCTAA
38925980 TTTTT
1 TTTTT
38925985 TTTCTACTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 11 0.38
16 16 0.55
17 1 0.03
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTTCATCCTTCTAA
Found at i:38929451 original size:26 final size:26
Alignment explanation
Indices: 38929416--38929493 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 26
38929406 TTAAGATAAC
38929416 TATATAAAAAATTTCAATAAATAAAAA
1 TATATAAAAAATTT-AATAAATAAAAA
*
38929443 TATAT--AAAA-TTATTAAATATTAAAA
1 TATATAAAAAATTTAATAAATA--AAAA
*
38929468 TAATATAAAAAATTTAAAAAATAAAA
1 T-ATATAAAAAATTTAATAAATAAAA
38929494 TGGGCGAGCC
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
23 7 0.17
24 2 0.05
25 9 0.21
26 4 0.10
27 8 0.19
28 4 0.10
29 8 0.19
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (26 bp):
TATATAAAAAATTTAATAAATAAAAA
Found at i:38929494 original size:26 final size:26
Alignment explanation
Indices: 38929417--38929494 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
38929407 TAAGATAACT
*
38929417 ATATAAAAAATTTCAATAAAT-AAA-A
1 ATATAAAAAATTT-AAAAAATAAAATA
* * *
38929442 ATATATAAAATTATTAAATATTAAAATA
1 ATATA-AAAAAT-TTAAAAAATAAAATA
38929470 ATATAAAAAATTTAAAAAATAAAAT
1 ATATAAAAAATTTAAAAAATAAAAT
38929495 GGGCGAGCCT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
25 5 0.12
26 21 0.50
27 10 0.24
28 6 0.14
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (26 bp):
ATATAAAAAATTTAAAAAATAAAATA
Found at i:38929696 original size:21 final size:21
Alignment explanation
Indices: 38929672--38929715 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
38929662 TACTTTTAAC
38929672 TTATCATGTT-GAAATATT-TTT
1 TTAT-ATGTTAGAAA-ATTGTTT
38929693 TTATATGTTAGAAAATTGTTT
1 TTATATGTTAGAAAATTGTTT
38929714 TT
1 TT
38929716 TTTTTAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (21 bp):
TTATATGTTAGAAAATTGTTT
Found at i:38929714 original size:20 final size:21
Alignment explanation
Indices: 38929672--38929714 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
38929662 TACTTTTAAC
*
38929672 TTATCATGTTGAAATATTTTT
1 TTATCATGTTGAAATATTGTT
38929693 TTAT-ATGTTAGAAA-ATTGTT
1 TTATCATGTT-GAAATATTGTT
38929713 TT
1 TT
38929715 TTTTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (21 bp):
TTATCATGTTGAAATATTGTT
Found at i:38931142 original size:2 final size:2
Alignment explanation
Indices: 38931135--38931174 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
38931125 TATTATTCAA
*
38931135 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38931175 CTTTTACTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38931907 original size:59 final size:60
Alignment explanation
Indices: 38931792--38931912 Score: 158
Period size: 59 Copynumber: 2.0 Consensus size: 60
38931782 AGCCACCCAT
* *
38931792 CTATTAGTAAATTTATTTTTTAATCACTTAACTATGAACAGTTACAAAATAGTCACTTAA
1 CTATTAGTAAATTTATTTTTTAATCACTTAACTATGAAAAGTTACAAAATAGTCACTCAA
** *
38931852 CTATTAGTAAATTTA-TTTTTGGTCA-TCTAATTATGAAAAGTTACAAAAT-GATCACTCAA
1 CTATTAGTAAATTTATTTTTTAATCACT-TAACTATGAAAAGTTACAAAATAG-TCACTCAA
38931911 CT
1 CT
38931913 GTTTAATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
58 2 0.04
59 37 0.69
60 15 0.28
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (60 bp):
CTATTAGTAAATTTATTTTTTAATCACTTAACTATGAAAAGTTACAAAATAGTCACTCAA
Found at i:38933856 original size:6 final size:6
Alignment explanation
Indices: 38933845--38933883 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
38933835 TGATCAAAAT
*
38933845 TGAAAG TGAAAG TGAAAG TG-AAG TTGAAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG -TGAAAG TGAAAG TGA
38933884 TATGAATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 3 0.10
6 24 0.83
7 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:38938297 original size:6 final size:6
Alignment explanation
Indices: 38938288--38938313 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
38938278 GGAACTTGAA
38938288 CTGGAT CTGGAT CTGGAT CTGGAT CT
1 CTGGAT CTGGAT CTGGAT CTGGAT CT
38938314 CTCACTCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.19, G:0.31, T:0.35
Consensus pattern (6 bp):
CTGGAT
Found at i:38953160 original size:24 final size:23
Alignment explanation
Indices: 38953117--38953161 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
38953107 TTCAATGTTT
*
38953117 TATATCTTCATGCTTTTTTTATA
1 TATATCTTCATGCTTATTTTATA
38953140 TATATACTTCATG-TCTATTTTA
1 TATAT-CTTCATGCT-TATTTTA
38953162 CGGTTCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.24, C:0.13, G:0.04, T:0.58
Consensus pattern (23 bp):
TATATCTTCATGCTTATTTTATA
Found at i:38954677 original size:12 final size:12
Alignment explanation
Indices: 38954662--38954687 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
38954652 AATTTTTATA
38954662 AATTATTAATAT
1 AATTATTAATAT
38954674 AATTATTAATAT
1 AATTATTAATAT
38954686 AA
1 AA
38954688 CATCATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AATTATTAATAT
Found at i:38969951 original size:22 final size:22
Alignment explanation
Indices: 38969926--38969979 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
38969916 GTAACAATGT
*
38969926 AATAGTAAAATGGTAGCAAAAC
1 AATAGTAAAATGATAGCAAAAC
*
38969948 AATA-TCGAAATGATAGCAAAAC
1 AATAGT-AAAATGATAGCAAAAC
* *
38969970 AGTAGCAAAA
1 AATAGTAAAA
38969980 AAAAAAAGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.56, C:0.11, G:0.17, T:0.17
Consensus pattern (22 bp):
AATAGTAAAATGATAGCAAAAC
Found at i:38972369 original size:29 final size:29
Alignment explanation
Indices: 38972328--38972394 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
38972318 AATTTGTGAG
* *
38972328 AATTGTATCAAATAAAAAATT-ATGAATAA
1 AATTGCATAAAAT-AAAAATTCATGAATAA
* * *
38972357 AATTGCATAAAATTAAAGTTCATGTATAA
1 AATTGCATAAAATAAAAATTCATGAATAA
38972386 AATTGCATA
1 AATTGCATA
38972395 TTAAGCCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 5 0.16
29 27 0.84
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (29 bp):
AATTGCATAAAATAAAAATTCATGAATAA
Found at i:38972816 original size:25 final size:25
Alignment explanation
Indices: 38972779--38972826 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
38972769 TGGAATTTCT
38972779 AGTCATAGATAATTTTTTTTGTGAA
1 AGTCATAGATAATTTTTTTTGTGAA
*
38972804 AGTCATAGGTAATTTTTTTTGTG
1 AGTCATAGATAATTTTTTTTGTG
38972827 TGTGCGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.04, G:0.19, T:0.50
Consensus pattern (25 bp):
AGTCATAGATAATTTTTTTTGTGAA
Found at i:38974499 original size:15 final size:16
Alignment explanation
Indices: 38974479--38974514 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
38974469 TTCCACCCTG
*
38974479 AAAAAGAAGGAAAA-A
1 AAAAAGAAAGAAAAGA
38974494 AAAAAGAAAGAAAAGA
1 AAAAAGAAAGAAAAGA
38974510 AAAAA
1 AAAAA
38974515 AAGCTGCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAGAAAAGA
Found at i:38991558 original size:4 final size:4
Alignment explanation
Indices: 38991544--38991578 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
38991534 TTTCTTTGAT
* *
38991544 ATAC TTAC ATAC ATAC ATAC ATAC ATGC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
38991579 TAAAATCTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:38999539 original size:11 final size:12
Alignment explanation
Indices: 38999512--38999539 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
38999502 TAACATCAAA
38999512 TTTTTTGTTTTC
1 TTTTTTGTTTTC
38999524 TTTTTTGTTTTC
1 TTTTTTGTTTTC
38999536 TTTT
1 TTTT
38999540 CCAATAGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (12 bp):
TTTTTTGTTTTC
Found at i:39007145 original size:14 final size:13
Alignment explanation
Indices: 39007111--39007143 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
39007101 TAATCAAAAA
39007111 ATTTTTTAAACTC
1 ATTTTTTAAACTC
39007124 ATTTTTTAAAC-C
1 ATTTTTTAAACTC
39007136 TATTTTTT
1 -ATTTTTT
39007144 TACCTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 1 0.05
13 18 0.95
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTTTTTAAACTC
Found at i:39008099 original size:31 final size:30
Alignment explanation
Indices: 39008020--39008110 Score: 94
Period size: 31 Copynumber: 3.0 Consensus size: 30
39008010 AAAGTACAAT
*
39008020 AACTAAATTTGACCAATTTAAAAAGTATAGG
1 AACTAAAATTGACCAATTT-AAAAGTATAGG
** *
39008051 GGCTAAAATCGACCAATTTGAAAAGTATAGG
1 AACTAAAATTGACCAATTT-AAAAGTATAGG
* * *
39008082 AATTAAGATTGATCAATTTAAAA-TATAGG
1 AACTAAAATTGACCAATTTAAAAGTATAGG
39008111 GACCAATTTC
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
29 6 0.12
30 4 0.08
31 39 0.80
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.29
Consensus pattern (30 bp):
AACTAAAATTGACCAATTTAAAAGTATAGG
Found at i:39008354 original size:17 final size:17
Alignment explanation
Indices: 39008332--39008375 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 17
39008322 TACTTTTATT
39008332 TATAAGTTGGGAGGGGC
1 TATAAGTTGGGAGGGGC
39008349 TATAAGTAATTGGGAGGGGC
1 TATAAG---TTGGGAGGGGC
39008369 TATAAGT
1 TATAAGT
39008376 AATTTTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 7 0.29
20 17 0.71
ACGTcount: A:0.30, C:0.05, G:0.39, T:0.27
Consensus pattern (17 bp):
TATAAGTTGGGAGGGGC
Found at i:39008363 original size:20 final size:20
Alignment explanation
Indices: 39008338--39008379 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
39008328 TATTTATAAG
39008338 TTGGGAGGGGCTATAAGTAA
1 TTGGGAGGGGCTATAAGTAA
39008358 TTGGGAGGGGCTATAAGTAA
1 TTGGGAGGGGCTATAAGTAA
39008378 TT
1 TT
39008380 TTATGATAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.05, G:0.38, T:0.29
Consensus pattern (20 bp):
TTGGGAGGGGCTATAAGTAA
Found at i:39014494 original size:15 final size:16
Alignment explanation
Indices: 39014464--39014502 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
39014454 TAATAAAAAT
39014464 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
39014481 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
39014496 ATAATTT
1 ATAATTT
39014503 TTAAAAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:39016719 original size:3 final size:3
Alignment explanation
Indices: 39016706--39016767 Score: 106
Period size: 3 Copynumber: 20.3 Consensus size: 3
39016696 AGAGGAGAGT
*
39016706 AGA ACGA AGA AGA AGC AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
39016752 AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA A
39016768 ATGGACGCAC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.65, C:0.03, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:39017063 original size:23 final size:24
Alignment explanation
Indices: 39017037--39017084 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
39017027 ATTTTCCTTT
*
39017037 AATTAATTTA-GAAAATTCAATTA
1 AATTAATTTATGAAAAATCAATTA
* *
39017060 AATTTATTTATTAAAAATCAATTA
1 AATTAATTTATGAAAAATCAATTA
39017084 A
1 A
39017085 TTTACTTGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (24 bp):
AATTAATTTATGAAAAATCAATTA
Found at i:39017086 original size:23 final size:22
Alignment explanation
Indices: 39017035--39017088 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
39017025 ATATTTTCCT
* *
39017035 TTAATTAATTTAGAAAATTCAA
1 TTAATTTATTTAGAAAAATCAA
*
39017057 TTAAATTTATTTATTAAAAATCAA
1 TT-AATTTATTTA-GAAAAATCAA
39017081 TTAATTTA
1 TTAATTTA
39017089 CTTGGTTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.07
23 15 0.56
24 10 0.37
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (22 bp):
TTAATTTATTTAGAAAAATCAA
Found at i:39018961 original size:59 final size:57
Alignment explanation
Indices: 39018827--39018952 Score: 171
Period size: 57 Copynumber: 2.2 Consensus size: 57
39018817 TTGGTACCTA
* * *
39018827 AACTGGGCTTCAAGGTTCAATTTGGTACTAAGGTTTTTTTGGTCCAATTAAGTACTG
1 AACTTGGCTTTAAGGTTCAATTTGGTACTAAAGTTTTTTTGGTCCAATTAAGTACTG
* * *
39018884 AACTTGGCTTTAAGGTTCAGTTTGGTACTAAAGTTTATTTTTGTCCAATTAGGTACCTG
1 AACTTGGCTTTAAGGTTCAATTTGGTACTAAAGTTT-TTTTGGTCCAATTAAGTA-CTG
*
39018943 AATTTGGCTT
1 AACTTGGCTT
39018953 CTTAGTTCAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 32 0.53
58 16 0.27
59 12 0.20
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.41
Consensus pattern (57 bp):
AACTTGGCTTTAAGGTTCAATTTGGTACTAAAGTTTTTTTGGTCCAATTAAGTACTG
Found at i:39018969 original size:59 final size:57
Alignment explanation
Indices: 39018827--39018969 Score: 144
Period size: 57 Copynumber: 2.5 Consensus size: 57
39018817 TTGGTACCTA
* * ** *
39018827 AACTGGGCTTCAAGGTTCAATTTGGTACTAAGGTTTTTTTGGTCCAATTAAGTACTG
1 AACTTGGCTTTAAGGTTCAAACTGGTACTAAAGTTTTTTTGGTCCAATTAAGTACTG
*** * *
39018884 AACTTGGCTTTAAGGTTCAGTTTGGTACTAAAGTTTATTTTTGTCCAATTAGGTACCTG
1 AACTTGGCTTTAAGGTTCAAACTGGTACTAAAGTTT-TTTTGGTCCAATTAAGTA-CTG
* *
39018943 AATTTGGCTTCTTA-GTTCAAACTGGTA
1 AACTTGGCTT-TAAGGTTCAAACTGGTA
39018970 GCTGAACTTG
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
57 32 0.44
58 16 0.22
59 22 0.31
60 2 0.03
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (57 bp):
AACTTGGCTTTAAGGTTCAAACTGGTACTAAAGTTTTTTTGGTCCAATTAAGTACTG
Found at i:39021500 original size:21 final size:21
Alignment explanation
Indices: 39021476--39021521 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
39021466 TCTCCTGCTA
* *
39021476 TTTTTTCATGTTTTGCTGTTG
1 TTTTCTCATGTTTTGCTATTG
* *
39021497 TTTTCTCATTTTTTGTTATTG
1 TTTTCTCATGTTTTGCTATTG
39021518 TTTT
1 TTTT
39021522 GTTATCATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.07, C:0.09, G:0.13, T:0.72
Consensus pattern (21 bp):
TTTTCTCATGTTTTGCTATTG
Found at i:39030286 original size:14 final size:15
Alignment explanation
Indices: 39030260--39030288 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39030250 TTGAGGTGAG
39030260 AATGAAGAACAGCTC
1 AATGAAGAACAGCTC
39030275 AATGAA-AACAGCTC
1 AATGAAGAACAGCTC
39030289 CAAATGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.14
Consensus pattern (15 bp):
AATGAAGAACAGCTC
Found at i:39039742 original size:25 final size:24
Alignment explanation
Indices: 39039714--39039769 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
39039704 ATATAATTGA
39039714 TAAATATAAAATATTTTAAATTTAT
1 TAAATATAAAATATTTTAAATTT-T
* **
39039739 TAAATTTAATTTATTTTAAATTTT
1 TAAATATAAAATATTTTAAATTTT
39039763 TAAATAT
1 TAAATAT
39039770 TTTTATATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TAAATATAAAATATTTTAAATTTT
Found at i:39040121 original size:24 final size:24
Alignment explanation
Indices: 39040089--39040135 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
39040079 TGTATTCAAG
*
39040089 TTAAAATAAATAT-TAAATTATAT
1 TTAAAATAAATATCAAAATTATAT
39040112 TTAAAGATAAATATCAAAATTATA
1 TTAAA-ATAAATATCAAAATTATA
39040136 CATAAGCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 8 0.38
25 8 0.38
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
TTAAAATAAATATCAAAATTATAT
Found at i:39051769 original size:28 final size:26
Alignment explanation
Indices: 39051736--39051789 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 26
39051726 TAATTATTTT
39051736 TATTTAAAAAATTCAAAAATTA-TAAAAA
1 TATTT-AAAAATT--AAAATTATTAAAAA
39051764 TATTTAAAAATTAAAATTATTAAAAA
1 TATTTAAAAATTAAAATTATTAAAAA
39051790 ATATAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 7 0.28
26 6 0.24
27 7 0.28
28 5 0.20
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
TATTTAAAAATTAAAATTATTAAAAA
Found at i:39051772 original size:19 final size:18
Alignment explanation
Indices: 39051740--39051776 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
39051730 TATTTTTATT
39051740 TAAAAAATTCAAAAATTA
1 TAAAAAATTCAAAAATTA
*
39051758 TAAAAATATTTAAAAATTA
1 TAAAAA-ATTCAAAAATTA
39051777 AAATTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAAATTCAAAAATTA
Found at i:39051778 original size:17 final size:17
Alignment explanation
Indices: 39051739--39051791 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
39051729 TTATTTTTAT
*
39051739 TTAAAAA-ATTCAAAAAT
1 TTAAAAATATT-AAAAAA
*
39051756 TATAAAAATATTTAAAAA
1 T-TAAAAATATTAAAAAA
*
39051774 TTAAAATTATTAAAAAA
1 TTAAAAATATTAAAAAA
39051791 T
1 T
39051792 ATAATTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 16 0.53
18 11 0.37
19 3 0.10
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
TTAAAAATATTAAAAAA
Found at i:39051790 original size:28 final size:28
Alignment explanation
Indices: 39051736--39051790 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
39051726 TAATTATTTT
*
39051736 TATTTAAAAAATTCAAAAATTATAAAAA
1 TATTTAAAAAATTCAAAAATTAAAAAAA
39051764 TATTT-AAAAATT-AAAATTATTAAAAAA
1 TATTTAAAAAATTCAAAA--ATTAAAAAA
39051791 TATAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.17
27 7 0.29
28 13 0.54
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (28 bp):
TATTTAAAAAATTCAAAAATTAAAAAAA
Found at i:39053165 original size:11 final size:11
Alignment explanation
Indices: 39053149--39053202 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 11
39053139 CTTCATGATG
39053149 TTTTTTTTGAA
1 TTTTTTTTGAA
*
39053160 TTTTTTATGAA
1 TTTTTTTTGAA
39053171 CTTTTTATTTTTGTAA
1 ---TTT-TTTTTG-AA
39053187 TTTTTTTTGAA
1 TTTTTTTTGAA
39053198 TTTTT
1 TTTTT
39053203 ATGAGGCACG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
11 17 0.47
12 6 0.17
13 3 0.08
14 3 0.08
15 5 0.14
16 2 0.06
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.72
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:39053188 original size:27 final size:25
Alignment explanation
Indices: 39053152--39053204 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 25
39053142 CATGATGTTT
39053152 TTTTTGAATTTTTTATGAACTTTTTA
1 TTTTTGAATTTTTTATGAA-TTTTTA
*
39053178 TTTTTGTAATTTTTTTTGAATTTTTA
1 TTTTTG-AATTTTTTATGAATTTTTA
39053204 T
1 T
39053205 GAGGCACGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.70
Consensus pattern (25 bp):
TTTTTGAATTTTTTATGAATTTTTA
Found at i:39056510 original size:22 final size:22
Alignment explanation
Indices: 39056479--39056520 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
39056469 AAACACCATA
*
39056479 TGAAAGTTA-TTATTTATTTACT
1 TGAAAATTATTTATTT-TTTACT
39056501 TGAAAATTATTTATTTTTTA
1 TGAAAATTATTTATTTTTTA
39056521 GAAAGATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (22 bp):
TGAAAATTATTTATTTTTTACT
Found at i:39057002 original size:9 final size:8
Alignment explanation
Indices: 39056967--39056999 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
39056957 TTTTATAACT
39056967 TTTTAAATA
1 TTTTAAA-A
39056976 TTTTAAAA
1 TTTTAAAA
39056984 TTTTAAAA
1 TTTTAAAA
39056992 TTTTAAAA
1 TTTTAAAA
39057000 ATTAACCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTTAAAA
Found at i:39060932 original size:2 final size:2
Alignment explanation
Indices: 39060925--39060954 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39060915 ATAAATCTTC
39060925 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
39060955 TTTTCCCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:39063869 original size:83 final size:83
Alignment explanation
Indices: 39063730--39063896 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
39063720 TTAGCCCTAC
39063730 TCCAACACCGGTATGTGCTTTGCACATTTAGTTCCTTTTGTAGAAGAACTATTTGGTAGTAATGA
1 TCCAACACCGGTATGTGCTTTGCACATTTAGTTCCTTTTGTAGAAGAACTATTTGGTAGTAATGA
39063795 TTCCATGTGTTTAATTTT
66 TTCCATGTGTTTAATTTT
39063813 TCCAACACCGGTATGTGCTTTGCACATTTAGTTCCTTTTGTAGAAGAACTATTTGGTAGTAATGA
1 TCCAACACCGGTATGTGCTTTGCACATTTAGTTCCTTTTGTAGAAGAACTATTTGGTAGTAATGA
39063878 TTCCATGTGTTTAATTTT
66 TTCCATGTGTTTAATTTT
39063896 T
1 T
39063897 TATTTTCTTC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.43
Consensus pattern (83 bp):
TCCAACACCGGTATGTGCTTTGCACATTTAGTTCCTTTTGTAGAAGAACTATTTGGTAGTAATGA
TTCCATGTGTTTAATTTT
Found at i:39066899 original size:12 final size:12
Alignment explanation
Indices: 39066882--39066985 Score: 64
Period size: 12 Copynumber: 8.1 Consensus size: 12
39066872 ATAACATCCA
39066882 AACAACAAAAAT
1 AACAACAAAAAT
*
39066894 AACAACTAAAAT
1 AACAACAAAAAT
** *
39066906 TGCAGCAAAAATGAT
1 AACAAC-AAAA--AT
*
39066921 AACAAACAACATTAAA
1 AAC-AACAA-A--AAT
39066937 AACAACAAAAAT
1 AACAACAAAAAT
* *
39066949 AGCAACAAAAAC
1 AACAACAAAAAT
*
39066961 AGCAACAAAAAT
1 AACAACAAAAAT
*
39066973 AACAACCAAAAT
1 AACAACAAAAAT
39066985 A
1 A
39066986 GTAAAAAAAG
Statistics
Matches: 70, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
12 48 0.69
13 3 0.04
14 1 0.01
15 10 0.14
16 7 0.10
18 1 0.01
ACGTcount: A:0.66, C:0.18, G:0.05, T:0.11
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:39066994 original size:24 final size:24
Alignment explanation
Indices: 39066943--39066994 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
39066933 TAAAAACAAC
* *
39066943 AAAAATAGCAACAAAAACAGCAAC
1 AAAAATAACAACAAAAACAGCAAA
* * *
39066967 AAAAATAACAACCAAAATAGTAAA
1 AAAAATAACAACAAAAACAGCAAA
39066991 AAAA
1 AAAA
39066995 GTACCAAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.71, C:0.15, G:0.06, T:0.08
Consensus pattern (24 bp):
AAAAATAACAACAAAAACAGCAAA
Found at i:39073550 original size:30 final size:30
Alignment explanation
Indices: 39073516--39073575 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
39073506 TCTTATGTAC
*
39073516 TTGCAATAACTATTTTAGTCTTCTAGTCAT
1 TTGCAATAACTATTTTAGTCTTCTACTCAT
39073546 TTGCAATAACTATTTTAGTCTTCTACTCAT
1 TTGCAATAACTATTTTAGTCTTCTACTCAT
39073576 CTAAATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (30 bp):
TTGCAATAACTATTTTAGTCTTCTACTCAT
Found at i:39087583 original size:22 final size:22
Alignment explanation
Indices: 39087545--39087599 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
39087535 CTTTTTAGTG
* * *
39087545 TTTAATTTATATTTTATGATTGA
1 TTTAA-TTAAATTTTATAATTAA
39087568 TTTAATTAAATTTTATAATTAA
1 TTTAATTAAATTTTATAATTAA
39087590 TTTATATTAA
1 TTTA-ATTAA
39087600 CAATTAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
TTTAATTAAATTTTATAATTAA
Found at i:39092748 original size:37 final size:36
Alignment explanation
Indices: 39092707--39092777 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
39092697 TTAATATTTT
39092707 AGTGTATTTAGTGTATT-ATTTTTTTATATTAAAAAAA
1 AGTGTA-TTAGTGTATTAATTTTTTTATA-TAAAAAAA
* * *
39092744 AGTGTATTATTTTTTTAATTTTTTTATATAAAAA
1 AGTGTATTAGTGTATTAATTTTTTTATATAAAAA
39092778 TTAAAAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 13 0.43
37 17 0.57
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (36 bp):
AGTGTATTAGTGTATTAATTTTTTTATATAAAAAAA
Found at i:39096145 original size:2 final size:2
Alignment explanation
Indices: 39096138--39096183 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
39096128 TGCCATGCTA
39096138 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
39096180 AT AT
1 AT AT
39096184 GTTTTATCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39098115 original size:28 final size:28
Alignment explanation
Indices: 39098074--39098130 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
39098064 AATTTTATTT
* *
39098074 TTTTATTTAATATATAAT-TAATTTTTA
1 TTTTATTTAATATAAAATAAAATTTTTA
*
39098101 TTTTATTATGATATAAAATAAAATTTTTA
1 TTTTATT-TAATATAAAATAAAATTTTTA
39098130 T
1 T
39098131 ATTAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.28
28 9 0.36
29 9 0.36
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTTATTTAATATAAAATAAAATTTTTA
Found at i:39099894 original size:69 final size:70
Alignment explanation
Indices: 39099762--39099901 Score: 237
Period size: 69 Copynumber: 2.0 Consensus size: 70
39099752 TTTGTATTCA
* *
39099762 TCCCATTGTACTTCACTTCTTCTTGAGTTAAAAGAATATTATATTTGAGAGCATTTACTCAAACA
1 TCCCATTATACTTCACTTATTCTTGAGTTAAAAGAATATTATATTTGAGAGCATTTACTCAAACA
39099827 CATTG
66 CATTG
*
39099832 TCCCATTATACTTCACTTATTCTTGAGTT-AAATAATATTATATTTGAGAGCATTTACTCAAACA
1 TCCCATTATACTTCACTTATTCTTGAGTTAAAAGAATATTATATTTGAGAGCATTTACTCAAACA
*
39099896 TATTG
66 CATTG
39099901 T
1 T
39099902 GTGCATTGCC
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 39 0.59
70 27 0.41
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (70 bp):
TCCCATTATACTTCACTTATTCTTGAGTTAAAAGAATATTATATTTGAGAGCATTTACTCAAACA
CATTG
Found at i:39102377 original size:16 final size:15
Alignment explanation
Indices: 39102342--39102385 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
39102332 TAACATATTC
39102342 AATTAAAAATTATTAGAA
1 AATTAAAAA--ATTA-AA
*
39102360 ATTTAAAAAATTAAA
1 AATTAAAAAATTAAA
39102375 AATTAAAAAAT
1 AATTAAAAAAT
39102386 CTAGGTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 12 0.50
16 4 0.17
18 8 0.33
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (15 bp):
AATTAAAAAATTAAA
Found at i:39108874 original size:9 final size:9
Alignment explanation
Indices: 39108860--39108884 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
39108850 ATTGTATTTG
39108860 AGTTTTAAT
1 AGTTTTAAT
39108869 AGTTTTAAT
1 AGTTTTAAT
39108878 AGTTTTA
1 AGTTTTA
39108885 GTTACTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (9 bp):
AGTTTTAAT
Found at i:39117307 original size:21 final size:18
Alignment explanation
Indices: 39117286--39117322 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
39117276 AAAACTTATT
39117286 TTTAAAAAATAATAATAAA
1 TTTAAAAAATAAT-ATAAA
*
39117305 TTTAAAAAATTATATAAA
1 TTTAAAAAATAATATAAA
39117323 ATTATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTAAAAAATAATATAAA
Found at i:39120543 original size:31 final size:31
Alignment explanation
Indices: 39120503--39120566 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
39120493 AAATGATCAT
*
39120503 TGAATTATTCAAAAATTTCCATTTAAGTCAC
1 TGAACTATTCAAAAATTTCCATTTAAGTCAC
* **
39120534 TGAACTATTCAAAAGTTTTTATTTAAGTCAC
1 TGAACTATTCAAAAATTTCCATTTAAGTCAC
39120565 TG
1 TG
39120567 GGTTGCTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (31 bp):
TGAACTATTCAAAAATTTCCATTTAAGTCAC
Found at i:39131983 original size:19 final size:19
Alignment explanation
Indices: 39131918--39131975 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
39131908 GAATTTTATG
*
39131918 AAAAGATAAAA-TAATATATT
1 AAAA-ATAAAATTAA-ATTTT
*
39131938 AATAATAAAATTAAATTTT
1 AAAAATAAAATTAAATTTT
*
39131957 AAAAATAAGATT-AATTTT
1 AAAAATAAAATTAAATTTT
39131975 A
1 A
39131976 TCAAATAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 7 0.21
19 20 0.61
20 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
AAAAATAAAATTAAATTTT
Found at i:39132924 original size:2 final size:2
Alignment explanation
Indices: 39132919--39132949 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39132909 CTTCTCTCCG
39132919 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
39132950 ATCCCTTAAA
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:39134574 original size:12 final size:12
Alignment explanation
Indices: 39134557--39134583 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39134547 AGCGTGTCAG
39134557 ACATGAACTCAA
1 ACATGAACTCAA
39134569 ACATGAACTCAA
1 ACATGAACTCAA
39134581 ACA
1 ACA
39134584 GGTAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.07, T:0.15
Consensus pattern (12 bp):
ACATGAACTCAA
Found at i:39150025 original size:9 final size:9
Alignment explanation
Indices: 39150008--39150050 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
39149998 TGGCACTGGA
39150008 GACGAGGAT
1 GACGAGGAT
*
39150017 GATGAGGAT
1 GACGAGGAT
*
39150026 GACGATGAT
1 GACGAGGAT
*
39150035 GACGACGAT
1 GACGAGGAT
*
39150044 GATGAGG
1 GACGAGG
39150051 GTGAGGAAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.33, C:0.09, G:0.42, T:0.16
Consensus pattern (9 bp):
GACGAGGAT
Found at i:39150073 original size:15 final size:15
Alignment explanation
Indices: 39150053--39150094 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
39150043 TGATGAGGGT
*
39150053 GAGGAAGAGGAAGAG
1 GAGGAAGAAGAAGAG
*
39150068 GAGGAAGAAGATGAG
1 GAGGAAGAAGAAGAG
39150083 GAGGAAGAAGAA
1 GAGGAAGAAGAA
39150095 CTTCAGCCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (15 bp):
GAGGAAGAAGAAGAG
Found at i:39150077 original size:18 final size:18
Alignment explanation
Indices: 39150056--39150094 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
39150046 TGAGGGTGAG
*
39150056 GAAGAGGAAGAGGAGGAA
1 GAAGAGGAAGAGGAAGAA
* *
39150074 GAAGATGAGGAGGAAGAA
1 GAAGAGGAAGAGGAAGAA
39150092 GAA
1 GAA
39150095 CTTCAGCCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.03
Consensus pattern (18 bp):
GAAGAGGAAGAGGAAGAA
Found at i:39158721 original size:23 final size:23
Alignment explanation
Indices: 39158695--39158756 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
39158685 AGTTAATAAA
* *
39158695 ATATTTTTATTAATGTTAAATTT
1 ATATTTTTATTAATATTAAATAT
*
39158718 ATATTTTAATTAATATTAAATAT
1 ATATTTTTATTAATATTAAATAT
39158741 ATATTTTTAATTAATA
1 ATATTTTT-ATTAATA
39158757 ATTCATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 27 0.79
24 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATATTTTTATTAATATTAAATAT
Found at i:39159341 original size:45 final size:45
Alignment explanation
Indices: 39159277--39159366 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
39159267 AAATTTAAAC
39159277 ATATTAGAAGGACCAAATTTGAAAATTAATCATTTTACATAAAAT
1 ATATTAGAAGGACCAAATTTGAAAATTAATCATTTTACATAAAAT
39159322 ATATTAGAAGGACCAAATTTGAAAATTAATCATTTTACATAAAAT
1 ATATTAGAAGGACCAAATTTGAAAATTAATCATTTTACATAAAAT
39159367 GAAAAAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (45 bp):
ATATTAGAAGGACCAAATTTGAAAATTAATCATTTTACATAAAAT
Found at i:39159582 original size:14 final size:14
Alignment explanation
Indices: 39159563--39159595 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
39159553 AACTTTTGGA
39159563 TTTAAAAATTTAAG
1 TTTAAAAATTTAAG
39159577 TTTAAAAATTTAAG
1 TTTAAAAATTTAAG
39159591 TTTAA
1 TTTAA
39159596 TTGTTGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (14 bp):
TTTAAAAATTTAAG
Found at i:39164470 original size:4 final size:4
Alignment explanation
Indices: 39164461--39164500 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
39164451 CCCATTTGGA
* * *
39164461 CATG CATG CATG CATG CATA CATA CATC CATG CATG CATG
1 CATG CATG CATG CATG CATG CATG CATG CATG CATG CATG
39164501 TAGCAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (4 bp):
CATG
Found at i:39167516 original size:18 final size:19
Alignment explanation
Indices: 39167476--39167525 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
39167466 ATTTTGAGTA
*
39167476 AAATTAATTTAA-TCGATT
1 AAATTAAATTAATTCGATT
39167494 AAATTAAATTAATTCGATT
1 AAATTAAATTAATTCGATT
*
39167513 -AATTGAATTAATT
1 AAATTAAATTAATT
39167526 TAATCAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 23 0.79
19 6 0.21
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (19 bp):
AAATTAAATTAATTCGATT
Found at i:39174862 original size:32 final size:31
Alignment explanation
Indices: 39174821--39174887 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
39174811 TCTAGTGATC
* * * *
39174821 ATAACTTATGGATTCATGTCTTTCTATATTG
1 ATAACTTATGAATTCATGTCCTCCTACATTG
39174852 ATAACTTTATGAATTCATGTCCTCCTACATTG
1 ATAAC-TTATGAATTCATGTCCTCCTACATTG
39174884 ATAA
1 ATAA
39174888 TAATGTCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 5 0.16
32 26 0.84
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.43
Consensus pattern (31 bp):
ATAACTTATGAATTCATGTCCTCCTACATTG
Found at i:39178200 original size:35 final size:35
Alignment explanation
Indices: 39178154--39178225 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
39178144 AACTAGAGCC
39178154 AATTGTGGTGGAGCATTAAGTATGGCAATGGTTTT
1 AATTGTGGTGGAGCATTAAGTATGGCAATGGTTTT
39178189 AATTGTGGTGGAGCATTAAGTATGGCAATGGTTTT
1 AATTGTGGTGGAGCATTAAGTATGGCAATGGTTTT
39178224 AA
1 AA
39178226 GTGGACGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.06, G:0.31, T:0.36
Consensus pattern (35 bp):
AATTGTGGTGGAGCATTAAGTATGGCAATGGTTTT
Found at i:39183584 original size:6 final size:6
Alignment explanation
Indices: 39183575--39183599 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39183565 AAAGAAAGAG
39183575 AAAGGA AAAGGA AAAGGA AAAGGA A
1 AAAGGA AAAGGA AAAGGA AAAGGA A
39183600 TGAAAGATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:39184189 original size:17 final size:16
Alignment explanation
Indices: 39184165--39184203 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
39184155 ATTCAAATTT
*
39184165 ATTCAAACCTTAAATA
1 ATTCAAACCTAAAATA
39184181 ATTCTAAACCTAAAAT-
1 ATTC-AAACCTAAAATA
39184197 ATTCAAA
1 ATTCAAA
39184204 TTTGAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 8 0.38
17 10 0.48
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTCAAACCTAAAATA
Found at i:39186527 original size:112 final size:108
Alignment explanation
Indices: 39186359--39186592 Score: 351
Period size: 112 Copynumber: 2.1 Consensus size: 108
39186349 TACGTTGGCA
* * * *
39186359 TCAAAGTTTAAGGGACTAATTTAACAAAAAAAGAAGTCTAAGGGACTAATCATTCAATGACTAAT
1 TCAAAGTCTAAGGGACTAATTTAAAAAAAAAAAAAGTCTAAGAGACTAATCATTCAATGACTAAT
39186424 AAGCCGCCAGTTTAATCATAAAAACACACACTATAAATTTGGT
66 AAGCCGCCAGTTTAATCATAAAAACACACACTATAAATTTGGT
39186467 TCAAAGTCTAAGGGACTAATTTATAAAAAAAAAAAAAAAGTCTAAGAGACTAATCATTCAATGAC
1 TCAAAGTCTAAGGGACTAA-TT-T--AAAAAAAAAAAAAGTCTAAGAGACTAATCATTCAATGAC
* * * *
39186532 TAATAAGCCGCCAGTTTAATCATAATAAGACATACTATAATTTTGGT
62 TAATAAGCCGCCAGTTTAATCATAAAAACACACACTATAAATTTGGT
*
39186579 TCAAAGTCCAAGGG
1 TCAAAGTCTAAGGG
39186593 GCAATTCGAT
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
108 18 0.16
109 2 0.02
110 1 0.01
112 92 0.81
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (108 bp):
TCAAAGTCTAAGGGACTAATTTAAAAAAAAAAAAAGTCTAAGAGACTAATCATTCAATGACTAAT
AAGCCGCCAGTTTAATCATAAAAACACACACTATAAATTTGGT
Found at i:39196517 original size:2 final size:2
Alignment explanation
Indices: 39196506--39196557 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
39196496 ATTATGATTC
39196506 AT AT -T AT 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 AT AT AT AT
39196547 AT AT AT A- AT AT
1 AT AT AT AT AT AT
39196558 TAAATTTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39199992 original size:4 final size:4
Alignment explanation
Indices: 39199983--39200029 Score: 76
Period size: 4 Copynumber: 11.8 Consensus size: 4
39199973 GTATTTTGTT
* *
39199983 TTTA TTTA TTTA TTTA TTTA TTTG TTTG TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
39200030 GTCTCTTCTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:39208960 original size:30 final size:29
Alignment explanation
Indices: 39208926--39208989 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
39208916 AATTTACAAG
*
39208926 AATTGAATC-AAATCAAAATTTCATGTATAC
1 AATTGAA-CAAAATC-AAAGTTCATGTATAC
*
39208956 AATTGCACAAAATCAAAGTTCATGTATAC
1 AATTGAACAAAATCAAAGTTCATGTATAC
39208985 AATTG
1 AATTG
39208990 CACATTAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.31
Consensus pattern (29 bp):
AATTGAACAAAATCAAAGTTCATGTATAC
Found at i:39208978 original size:29 final size:30
Alignment explanation
Indices: 39208935--39208993 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
39208925 GAATTGAATC
*
39208935 AAATCAAAATTTCATGTATACAATTGCACA
1 AAATCAAAAGTTCATGTATACAATTGCACA
39208965 AAATC-AAAGTTCATGTATACAATTGCACA
1 AAATCAAAAGTTCATGTATACAATTGCACA
39208994 TTAAACTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATACAATTGCACA
Found at i:39209650 original size:21 final size:22
Alignment explanation
Indices: 39209616--39209660 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
39209606 AAATATCTCT
39209616 AAAATAATCAAAATTTAATTGAA
1 AAAATAATCAAAATTTAATT-AA
39209639 AAAATAA-C-AAATTTAATTAA
1 AAAATAATCAAAATTTAATTAA
39209659 AA
1 AA
39209661 GAAAAATACG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.18
21 10 0.45
22 1 0.05
23 7 0.32
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATAATCAAAATTTAATTAA
Found at i:39213109 original size:3 final size:3
Alignment explanation
Indices: 39213101--39213151 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
39213091 TATATATTCT
39213101 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
39213149 ATG
1 ATG
39213152 GTGGTGGTGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:39215833 original size:3 final size:3
Alignment explanation
Indices: 39215827--39215851 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39215817 AATTGATATC
39215827 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
39215852 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:39217744 original size:2 final size:2
Alignment explanation
Indices: 39217737--39217763 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39217727 GTATTTAAAT
39217737 TA 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 T
39217764 TGTTATATGC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39219793 original size:17 final size:17
Alignment explanation
Indices: 39219757--39219795 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
39219747 AAATCATTAA
*
39219757 AATTATTTAAAAAGTAT
1 AATTATTTAAAAAATAT
* *
39219774 AATTTTTTAAAAAATTT
1 AATTATTTAAAAAATAT
39219791 AATTA
1 AATTA
39219796 AATGCTGATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
AATTATTTAAAAAATAT
Found at i:39222092 original size:3 final size:3
Alignment explanation
Indices: 39222084--39222111 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
39222074 CTCCCACATC
39222084 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
39222112 AGTAGCGCTT
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:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:39236366 original size:29 final size:30
Alignment explanation
Indices: 39236333--39236389 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39236323 TTAATAAAAG
*
39236333 TAAAA-TTCACTTTAATCCGTTAAAAATAA
1 TAAAATTTCAATTTAATCCGTTAAAAATAA
* *
39236362 TAAAATTTTAATTTAATCCTTTAAAAAT
1 TAAAATTTCAATTTAATCCGTTAAAAAT
39236390 TATATTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (30 bp):
TAAAATTTCAATTTAATCCGTTAAAAATAA
Found at i:39246373 original size:11 final size:11
Alignment explanation
Indices: 39246318--39246376 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
39246308 ATTTTTCCAC
*
39246318 TTTTGTCATTA
1 TTTTGTTATTA
* *
39246329 TTTTGTTGTCA
1 TTTTGTTATTA
*
39246340 TTTTATTATTA
1 TTTTGTTATTA
* *
39246351 TATTGCTATTA
1 TTTTGTTATTA
*
39246362 TTTTGTTGTTA
1 TTTTGTTATTA
39246373 TTTT
1 TTTT
39246377 TTGGATATAA
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.17, C:0.05, G:0.10, T:0.68
Consensus pattern (11 bp):
TTTTGTTATTA
Found at i:39254144 original size:18 final size:18
Alignment explanation
Indices: 39254121--39254163 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
39254111 GAATAGGTTT
39254121 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
39254139 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
39254157 TTAATTA
1 TTAATTA
39254164 CACTTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:39255291 original size:15 final size:17
Alignment explanation
Indices: 39255262--39255294 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
39255252 TATTTTAAAA
39255262 TTTTAACTAATTTTATT
1 TTTTAACTAATTTTATT
39255279 TTTTAA-TAA-TTTATT
1 TTTTAACTAATTTTATT
39255294 T
1 T
39255295 AACTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTAACTAATTTTATT
Found at i:39255639 original size:15 final size:16
Alignment explanation
Indices: 39255610--39255641 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
39255600 TATATGATAA
39255610 AATTTTATGTTTTATT
1 AATTTTATGTTTTATT
39255626 AATTTTAT-TTTTATT
1 AATTTTATGTTTTATT
39255641 A
1 A
39255642 TATATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
AATTTTATGTTTTATT
Found at i:39257546 original size:6 final size:6
Alignment explanation
Indices: 39257535--39257559 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39257525 AGGTATATAC
39257535 ATACAT ATACAT ATACAT ATACAT A
1 ATACAT ATACAT ATACAT ATACAT A
39257560 CAACAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ATACAT
Found at i:39265602 original size:45 final size:45
Alignment explanation
Indices: 39265553--39265665 Score: 158
Period size: 45 Copynumber: 2.5 Consensus size: 45
39265543 GCAAACCCAG
* **
39265553 CAGCACCCCCACCCCCACCACCAC-CCCCCACTACTGGTTCATCAT
1 CAGCACCCCCACCCCCACCACC-CTCACCCAAAACTGGTTCATCAT
*
39265598 CAGCACCCCCACCCCCACCACCCTCACTCAAAACTGGTTCATCAT
1 CAGCACCCCCACCCCCACCACCCTCACCCAAAACTGGTTCATCAT
*
39265643 CAGCACCCCCACCGCCACC-CCCT
1 CAGCACCCCCACCCCCACCACCCT
39265666 GCTCCTTTTG
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
44 5 0.08
45 57 0.92
ACGTcount: A:0.23, C:0.58, G:0.07, T:0.12
Consensus pattern (45 bp):
CAGCACCCCCACCCCCACCACCCTCACCCAAAACTGGTTCATCAT
Found at i:39279107 original size:16 final size:15
Alignment explanation
Indices: 39279054--39279118 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 15
39279044 AGTTTCAATC
*
39279054 CATTTAAATTTAGAT
1 CATTTAAATTTAAAT
39279069 CATATTAAA-TTAAAT
1 CAT-TTAAATTTAAAT
*
39279084 AATTTTTAAATTTAAAT
1 CA--TTTAAATTTAAAT
* *
39279101 CGATTTAAGTTTTAAT
1 C-ATTTAAATTTAAAT
39279117 CA
1 CA
39279119 ATTCGAACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
15 10 0.25
16 22 0.55
17 7 0.17
18 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (15 bp):
CATTTAAATTTAAAT
Found at i:39280269 original size:30 final size:30
Alignment explanation
Indices: 39280233--39280292 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
39280223 GACTATGTAC
39280233 AATCATATGATTTATATAAAATATAGTTTT
1 AATCATATGATTTATATAAAATATAGTTTT
39280263 AATCATATGATTTATATAAAATATAGTTTT
1 AATCATATGATTTATATAAAATATAGTTTT
39280293 TCGTTTCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (30 bp):
AATCATATGATTTATATAAAATATAGTTTT
Found at i:39282059 original size:14 final size:14
Alignment explanation
Indices: 39282040--39282074 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
39282030 AAAGTTATAC
39282040 AATAATAATAACAA
1 AATAATAATAACAA
*
39282054 AATAATAATAACAT
1 AATAATAATAACAA
39282068 AATAATA
1 AATAATA
39282075 GAATTGTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAATAATAACAA
Found at i:39286443 original size:18 final size:18
Alignment explanation
Indices: 39286416--39286457 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
39286406 TAGAGCTATT
39286416 ATTTTTA-T-TTTTA-AC
1 ATTTTTATTATTTTAGAC
*
39286431 ATTTTTATTATTTTAGAT
1 ATTTTTATTATTTTAGAC
39286449 ATTTTTATT
1 ATTTTTATT
39286458 TTCTTTTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 1 0.04
17 5 0.22
18 10 0.43
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
ATTTTTATTATTTTAGAC
Found at i:39289620 original size:16 final size:18
Alignment explanation
Indices: 39289601--39289640 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
39289591 TAATCGCATT
*
39289601 TTATAACAA-T-ATTTTA
1 TTATAACAATTAAATTTA
39289617 TTATAACAATTAAATTTA
1 TTATAACAATTAAATTTA
39289635 TTATAA
1 TTATAA
39289641 AATCGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 1 0.05
18 11 0.52
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TTATAACAATTAAATTTA
Found at i:39290203 original size:20 final size:19
Alignment explanation
Indices: 39290180--39290243 Score: 65
Period size: 24 Copynumber: 3.1 Consensus size: 19
39290170 AAAACACATT
39290180 AAAAATAACATCCAAACAAC
1 AAAAATAACA-CCAAACAAC
39290200 AAAAATAACAACCAAAACAGTAAC
1 AAAAATAAC-ACC-AAAC---AAC
*
39290224 AAAAATAACAGCAAACAAC
1 AAAAATAACACCAAACAAC
39290243 A
1 A
39290244 TTAAAAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
19 4 0.11
20 11 0.29
21 5 0.13
22 4 0.11
23 2 0.05
24 12 0.32
ACGTcount: A:0.67, C:0.22, G:0.03, T:0.08
Consensus pattern (19 bp):
AAAAATAACACCAAACAAC
Found at i:39290225 original size:15 final size:12
Alignment explanation
Indices: 39290194--39290318 Score: 55
Period size: 12 Copynumber: 10.8 Consensus size: 12
39290184 ATAACATCCA
39290194 AACAACAAAAAT
1 AACAACAAAAAT
* *
39290206 AACAACCAAAAC
1 AACAACAAAAAT
**
39290218 AGTAACAAAAAT
1 AACAACAAAAAT
* *
39290230 AACAGC--AAAC
1 AACAACAAAAAT
**
39290240 AACATTAAAAAT
1 AACAACAAAAAT
39290252 ---AACAAAAAT
1 AACAACAAAAAT
* *
39290261 AGCAACAAAAAC
1 AACAACAAAAAT
**
39290273 AGTAACAAAAAT
1 AACAACAAAAAT
**
39290285 AACAGTAAAAAT
1 AACAACAAAAAT
* *
39290297 AGC-ACGAAAAT
1 AACAACAAAAAT
39290308 AACAACCAAAA
1 AACAA-CAAAA
39290319 CAGTAAAAAA
Statistics
Matches: 78, Mismatches: 28, Indels: 13
0.66 0.24 0.11
Matches are distributed among these distances:
9 7 0.09
10 7 0.09
11 7 0.09
12 53 0.68
13 4 0.05
ACGTcount: A:0.67, C:0.18, G:0.06, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:39290256 original size:55 final size:53
Alignment explanation
Indices: 39290197--39290382 Score: 174
Period size: 55 Copynumber: 3.6 Consensus size: 53
39290187 ACATCCAAAC
*
39290197 AACAAAAATAACAACCAAAACAGTAACAAAAATAACAGCAAACAACATTAAAAAT
1 AACAAAAATAACAACCAAAACAGTAACAAAAATAACAGCAAA-AACA-TAAAAAA
* * * *
39290252 AACAAAAATAGCAACAAAAACAGTAACAAAAATAACAG-TAAAA-AT----AG
1 AACAAAAATAACAACCAAAACAGTAACAAAAATAACAGCAAAAACATAAAAAA
* * * *
39290299 CACGAAAATAACAACCAAAACAGTAA-AAAAA-AGCA-CCAAAACAGTAAAAAA
1 AACAAAAATAACAACCAAAACAGTAACAAAAATAACAGCAAAAACA-TAAAAAA
* *
39290350 ACACAAAAATAGCAACCAAAACAGTAACCAAAA
1 A-ACAAAAATAACAACCAAAACAGTAACAAAAA
39290383 CAGCACCAAA
Statistics
Matches: 107, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
45 7 0.07
46 6 0.06
47 24 0.22
51 2 0.02
52 24 0.22
53 6 0.06
54 2 0.02
55 36 0.34
ACGTcount: A:0.67, C:0.18, G:0.06, T:0.09
Consensus pattern (53 bp):
AACAAAAATAACAACCAAAACAGTAACAAAAATAACAGCAAAAACATAAAAAA
Found at i:39290266 original size:24 final size:24
Alignment explanation
Indices: 39290251--39290350 Score: 84
Period size: 23 Copynumber: 4.4 Consensus size: 24
39290241 ACATTAAAAA
39290251 TAACAAAAATAGCAACAAAAACAG
1 TAACAAAAATAGCAACAAAAACAG
* ** *
39290275 TAACAAAAATAACAGTAAAAATAG
1 TAACAAAAATAGCAACAAAAACAG
* * * *
39290299 -CACGAAAATAACAACCAAAACAG
1 TAACAAAAATAGCAACAAAAACAG
*
39290322 TAA-AAAAA-AGC-ACCAAAACAG
1 TAACAAAAATAGCAACAAAAACAG
39290343 TAA-AAAAA
1 TAACAAAAA
39290351 CACAAAAATA
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
21 18 0.29
22 2 0.03
23 21 0.34
24 21 0.34
ACGTcount: A:0.67, C:0.16, G:0.08, T:0.09
Consensus pattern (24 bp):
TAACAAAAATAGCAACAAAAACAG
Found at i:39290319 original size:47 final size:45
Alignment explanation
Indices: 39290240--39290330 Score: 119
Period size: 47 Copynumber: 2.0 Consensus size: 45
39290230 AACAGCAAAC
* * *
39290240 AACATTAAAAATAACAAAAATAGCAACAAAAACAGTAACAAAAAT
1 AACAGTAAAAATAACAAAAATAACAACAAAAACAGTAAAAAAAAT
* *
39290285 AACAGTAAAAATAGCACGAAAATAACAACCAAAACAGTAAAAAAAA
1 AACAGTAAAAATA--ACAAAAATAACAACAAAAACAGTAAAAAAAA
39290331 GCACCAAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 12 0.31
47 27 0.69
ACGTcount: A:0.68, C:0.14, G:0.07, T:0.11
Consensus pattern (45 bp):
AACAGTAAAAATAACAAAAATAACAACAAAAACAGTAAAAAAAAT
Found at i:39290358 original size:99 final size:102
Alignment explanation
Indices: 39290201--39290382 Score: 273
Period size: 99 Copynumber: 1.8 Consensus size: 102
39290191 CCAAACAACA
* *
39290201 AAAATAACAACCAAAACAGTAACAAAAATAACAGCAAACAACATTAAAAATAACAAAAATAGCAA
1 AAAATAACAACCAAAACAGTAACAAAAATAACAGCAAACAACAGTAAAAAAAACAAAAATAGCAA
39290266 CAAAAACAGTAACAAAAATAACAGTAAAAATAGCACG
66 CAAAAACAGTAACAAAAATAACAGTAAAAATAGCACG
* *
39290303 AAAATAACAACCAAAACAGTAA-AAAAA-AGCA-CCAA-AACAGTAAAAAAACACAAAAATAGCA
1 AAAATAACAACCAAAACAGTAACAAAAATAACAGCAAACAACAGTAAAAAAA-ACAAAAATAGCA
* *
39290364 ACCAAAACAGTAACCAAAA
65 ACAAAAACAGTAACAAAAA
39290383 CAGCACCAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
98 11 0.15
99 32 0.44
100 3 0.04
101 5 0.07
102 22 0.30
ACGTcount: A:0.66, C:0.18, G:0.07, T:0.09
Consensus pattern (102 bp):
AAAATAACAACCAAAACAGTAACAAAAATAACAGCAAACAACAGTAAAAAAAACAAAAATAGCAA
CAAAAACAGTAACAAAAATAACAGTAAAAATAGCACG
Done.