Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
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 92 of 182
Found at i:29673355 original size:18 final size:18
Alignment explanation
Indices: 29673324--29673358 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29673314 TATGCTCTAT
29673324 ATTTTATTATTTTTATAC
1 ATTTTATTATTTTTATAC
29673342 ATTTT-TTATATTTTATA
1 ATTTTATTAT-TTTTATA
29673359 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTATTATTTTTATAC
Found at i:29674707 original size:20 final size:20
Alignment explanation
Indices: 29674684--29674722 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29674674 ATTTTGACAA
*
29674684 GTTAAAAGAATTTTTACTTT
1 GTTAAAAGAATTTTAACTTT
*
29674704 GTTAAAAGTATTTTAACTT
1 GTTAAAAGAATTTTAACTT
29674723 ATTTTAAAGT
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:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (20 bp):
GTTAAAAGAATTTTAACTTT
Found at i:29676849 original size:19 final size:19
Alignment explanation
Indices: 29676821--29676860 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
29676811 ATTGGTCAAA
29676821 AAAGTCAACGATCAAAGTC
1 AAAGTCAACGATCAAAGTC
*
29676840 AAAGTTAACGATCAAAGTC
1 AAAGTCAACGATCAAAGTC
29676859 AA
1 AA
29676861 CATGTTTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.17
Consensus pattern (19 bp):
AAAGTCAACGATCAAAGTC
Found at i:29678965 original size:3 final size:3
Alignment explanation
Indices: 29678957--29678987 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
29678947 AACCCACAAG
29678957 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
29678988 ATTTTTTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:29683007 original size:13 final size:13
Alignment explanation
Indices: 29682991--29683017 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29682981 TCAACATGTT
29682991 TGGTCAAAGTCAA
1 TGGTCAAAGTCAA
29683004 TGGTCAAAGTCAA
1 TGGTCAAAGTCAA
29683017 T
1 T
29683018 AGGTTGGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (13 bp):
TGGTCAAAGTCAA
Found at i:29683131 original size:15 final size:15
Alignment explanation
Indices: 29683072--29683145 Score: 55
Period size: 15 Copynumber: 5.0 Consensus size: 15
29683062 GGGTCTAGGG
* *
29683072 TTTGGGTGATTTGGT
1 TTTGGGTTATTGGGT
*
29683087 TTTAGGTTATTGGG-
1 TTTGGGTTATTGGGT
29683101 TTTGGGCTTCA-T-GGT
1 TTTGGG-TT-ATTGGGT
*
29683116 TTTGGGTTATAGGGT
1 TTTGGGTTATTGGGT
**
29683131 TAAGGGTTATTGGGT
1 TTTGGGTTATTGGGT
29683146 CTCTTTTTCG
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
13 1 0.02
14 9 0.20
15 35 0.76
16 1 0.02
ACGTcount: A:0.12, C:0.03, G:0.38, T:0.47
Consensus pattern (15 bp):
TTTGGGTTATTGGGT
Found at i:29685443 original size:21 final size:22
Alignment explanation
Indices: 29685405--29685448 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29685395 AGAGGTATTG
*
29685405 ATATTTTTTAATGAGTATCGAT
1 ATATTTTTAAATGAGTATCGAT
*
29685427 ATATTTTTAAATG-GTATTGAT
1 ATATTTTTAAATGAGTATCGAT
29685448 A
1 A
29685449 CCAAAATGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.50
Consensus pattern (22 bp):
ATATTTTTAAATGAGTATCGAT
Found at i:29688741 original size:29 final size:29
Alignment explanation
Indices: 29688684--29688756 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
29688674 TCCCTTTGCC
* * * **
29688684 ATAGATAACAATAAAGGTGTCCTTGAACA
1 ATAGATAGCAACAAAGGCGTCCTCAAACA
29688713 ATAGATAGCAACAAAGGCGTCCTCAAACA
1 ATAGATAGCAACAAAGGCGTCCTCAAACA
* *
29688742 TTAGATAGCCACAAA
1 ATAGATAGCAACAAA
29688757 TATTTCCTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (29 bp):
ATAGATAGCAACAAAGGCGTCCTCAAACA
Found at i:29692956 original size:21 final size:21
Alignment explanation
Indices: 29692932--29692972 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29692922 CTATTATTTC
*
29692932 AAATTATATTTGA-ATTTAAAG
1 AAATTA-AATTGATATTTAAAG
29692953 AAATTAAATTGATATTTAAA
1 AAATTAAATTGATATTTAAA
29692973 TACTGTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (21 bp):
AAATTAAATTGATATTTAAAG
Found at i:29693671 original size:37 final size:37
Alignment explanation
Indices: 29693624--29693712 Score: 133
Period size: 37 Copynumber: 2.4 Consensus size: 37
29693614 ATTTGATTGT
* *
29693624 ATGTTAAACATGCCCTACATGATATTATTCAATTTGC
1 ATGTTAAACATGCCCTACATAATATTATCCAATTTGC
* *
29693661 ATGTTGAACATGCCCTACATAATATTATCCGATTTGC
1 ATGTTAAACATGCCCTACATAATATTATCCAATTTGC
*
29693698 ATGTTTAACATGCCC
1 ATGTTAAACATGCCC
29693713 AATGTGACAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (37 bp):
ATGTTAAACATGCCCTACATAATATTATCCAATTTGC
Found at i:29694666 original size:28 final size:28
Alignment explanation
Indices: 29694623--29694693 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
29694613 GGTGTTACAG
*
29694623 TCACTTCAACAAATTCAACCAACAAGAC
1 TCACTTTAACAAATTCAACCAACAAGAC
* * * *
29694651 TCACTTTAACAGATTCAGCTATCAAGAC
1 TCACTTTAACAAATTCAACCAACAAGAC
29694679 TCACTTTAACAAATT
1 TCACTTTAACAAATT
29694694 AAGCTACAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.41, C:0.27, G:0.06, T:0.27
Consensus pattern (28 bp):
TCACTTTAACAAATTCAACCAACAAGAC
Found at i:29694891 original size:53 final size:54
Alignment explanation
Indices: 29694828--29695061 Score: 215
Period size: 53 Copynumber: 4.4 Consensus size: 54
29694818 CACATGACGT
* * *
29694828 CATAGCCACCAGACTAGGTCTTACACTATGTGAT-TTCTTTCCCCATATGATGC
1 CATAGCCACCAGACTACGTCTTACACTATATGATCTTCTATCCCCATATGATGC
* * * * * * *
29694881 CATAGCCACCAAACTAGGTCATACATTATAT-CTCTTCTTTCCTCATATGATGC
1 CATAGCCACCAGACTACGTCTTACACTATATGATCTTCTATCCCCATATGATGC
* * * * ** * * *
29694934 CAAAGCTACCAAATTAAATCTTACACTATATGTTCTTCGATCCCTATATGATGC
1 CATAGCCACCAGACTACGTCTTACACTATATGATCTTCTATCCCCATATGATGC
** * *
29694988 CATAGCCAATAGACTACGTCTTACACTATATGGTCTT-TGATCCCCATATGGTG-
1 CATAGCCACCAGACTACGTCTTACACTATATGATCTTCT-ATCCCCATATGATGC
*
29695041 TATAGCCACCAGACTACGTCT
1 CATAGCCACCAGACTACGTCT
29695062 GGTCATCAAT
Statistics
Matches: 145, Mismatches: 33, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
52 1 0.01
53 87 0.60
54 57 0.39
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (54 bp):
CATAGCCACCAGACTACGTCTTACACTATATGATCTTCTATCCCCATATGATGC
Found at i:29697197 original size:26 final size:26
Alignment explanation
Indices: 29697168--29697226 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
29697158 GGAACTTGTT
*
29697168 CAGAATTATCGCTCCATGAATATGTC
1 CAGAATTATCGCTCCATGAATAGGTC
* * * *
29697194 CAGAGTTTTCGCTGCATGAGTAGGTC
1 CAGAATTATCGCTCCATGAATAGGTC
*
29697220 CAAAATT
1 CAGAATT
29697227 GCGCCCAGGA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (26 bp):
CAGAATTATCGCTCCATGAATAGGTC
Found at i:29706375 original size:31 final size:32
Alignment explanation
Indices: 29706340--29706410 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
29706330 AGTTTTCCTG
*
29706340 AAATATTTT-CAGAAATT-TGCCAAACAACAGA
1 AAATATTTTACACAAATTAT-CCAAACAACAGA
* *
29706371 AAATATTTTACACATATTCATCCAAACACCAGA
1 AAATATTTTACACAAATT-ATCCAAACAACAGA
29706404 AAATATT
1 AAATATT
29706411 AACTTTTCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 9 0.26
32 6 0.18
33 18 0.53
34 1 0.03
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.28
Consensus pattern (32 bp):
AAATATTTTACACAAATTATCCAAACAACAGA
Found at i:29722930 original size:29 final size:29
Alignment explanation
Indices: 29722871--29722976 Score: 97
Period size: 29 Copynumber: 3.7 Consensus size: 29
29722861 CAACATTGAT
*** * *
29722871 CAATAGATAGCCATAAAGGTGTCCACTAA
1 CAATAGATAGCCATAAAGACATCCTCAAA
*
29722900 CATTAGATAGCCA-AAACGACATCCTCAAA
1 CAATAGATAGCCATAAA-GACATCCTCAAA
* * *
29722929 CAATAGAAATCCATAAAGGCATCCTCAAA
1 CAATAGATAGCCATAAAGACATCCTCAAA
* *
29722958 CAATATATAGCCACAAAGA
1 CAATAGATAGCCATAAAGA
29722977 TGTTCATTCA
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
28 3 0.05
29 54 0.90
30 3 0.05
ACGTcount: A:0.46, C:0.24, G:0.12, T:0.18
Consensus pattern (29 bp):
CAATAGATAGCCATAAAGACATCCTCAAA
Found at i:29727256 original size:54 final size:54
Alignment explanation
Indices: 29727193--29727446 Score: 330
Period size: 54 Copynumber: 4.7 Consensus size: 54
29727183 CACATGACGC
* * *
29727193 CATAGCCACTAGACTAGGTCTTACACTATGTGGTATTCTTTCCCCATATGATGT
1 CATAGCCACCAGACTAGGTCTTACACTATATGGTCTTCTTTCCCCATATGATGT
* * * * * *
29727247 CATAGCCACTAGACTAGGTCTAACACTATGTGCTCTTCTTTCCCAATATGATGG
1 CATAGCCACCAGACTAGGTCTTACACTATATGGTCTTCTTTCCCCATATGATGT
* * *
29727301 CATATCCACCAGACTAGGTTTTACACTTTATGGTCTTCTTTCCCCATATGAT-T
1 CATAGCCACCAGACTAGGTCTTACACTATATGGTCTTCTTTCCCCATATGATGT
** * *
29727354 CCATAGTAACCAGACTAGGTCTTACACTTTATGGTCTTCTTTCCCCATATGATTT
1 -CATAGCCACCAGACTAGGTCTTACACTATATGGTCTTCTTTCCCCATATGATGT
* *
29727409 CATAGTCACCAAACTAGGTCTTACACTATATGGTCTTC
1 CATAGCCACCAGACTAGGTCTTACACTATATGGTCTTC
29727447 GATTGTCGTG
Statistics
Matches: 177, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
54 176 0.99
55 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (54 bp):
CATAGCCACCAGACTAGGTCTTACACTATATGGTCTTCTTTCCCCATATGATGT
Found at i:29732632 original size:43 final size:43
Alignment explanation
Indices: 29732584--29732705 Score: 138
Period size: 43 Copynumber: 2.8 Consensus size: 43
29732574 GACATTGAGA
* * * **
29732584 GGAACATTGTTTCCTAAAATTGGAAGTATGTGATTGATTGTGT
1 GGAACACTGTTTCCTAATATTGGAAGTATGTGATTGAATGAAT
* * **
29732627 GGAACACTGTTTCCTATTATTGAAAGTATGTGAACGAATGAAT
1 GGAACACTGTTTCCTAATATTGGAAGTATGTGATTGAATGAAT
*
29732670 AGAACACTGTTTCCTAATATT-GATAGTATGTGATTG
1 GGAACACTGTTTCCTAATATTGGA-AGTATGTGATTG
29732706 GTTGAGAGCA
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 1 0.02
43 63 0.98
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (43 bp):
GGAACACTGTTTCCTAATATTGGAAGTATGTGATTGAATGAAT
Found at i:29733351 original size:3 final size:3
Alignment explanation
Indices: 29733337--29733366 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
29733327 CATTTGGATT
29733337 TTA TTAA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TT
29733367 CAGTTTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29737039 original size:30 final size:30
Alignment explanation
Indices: 29736987--29737054 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
29736977 GAGGATGTTT
* * *
29736987 AGGAACTTGAGAAGACCTGATATCTCGTTC
1 AGGAGCTTGAGAAGACCTGATATCGCATTC
* *
29737017 AGGAGCTTGGGAAGA-CTCGATATCGCATTT
1 AGGAGCTTGAGAAGACCT-GATATCGCATTC
29737047 AGGAGCTT
1 AGGAGCTT
29737055 TAGATTGAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 2 0.06
30 30 0.94
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (30 bp):
AGGAGCTTGAGAAGACCTGATATCGCATTC
Found at i:29739088 original size:37 final size:37
Alignment explanation
Indices: 29739047--29739117 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
29739037 CTATATACTC
*
29739047 ATTTTGGAGAAACTGAAGATATTACAAGGTCCATTTT
1 ATTTTCGAGAAACTGAAGATATTACAAGGTCCATTTT
29739084 ATTTTCGAGAAACTGAAGATATTACAAGGTCCAT
1 ATTTTCGAGAAACTGAAGATATTACAAGGTCCAT
29739118 ATTTTGTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (37 bp):
ATTTTCGAGAAACTGAAGATATTACAAGGTCCATTTT
Found at i:29747614 original size:20 final size:20
Alignment explanation
Indices: 29747589--29747627 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
29747579 ATCGCTTAAT
29747589 ACAATTTTAGTTTCTTTTTC
1 ACAATTTTAGTTTCTTTTTC
29747609 ACAATTTTAGTTTCTTTTT
1 ACAATTTTAGTTTCTTTTT
29747628 AATTCTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.62
Consensus pattern (20 bp):
ACAATTTTAGTTTCTTTTTC
Found at i:29751331 original size:20 final size:21
Alignment explanation
Indices: 29751294--29751332 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29751284 AAACTGAGCA
29751294 TCACTAAGTAAGAAAATGCAG
1 TCACTAAGTAAGAAAATGCAG
*
29751315 TCACTAAGTTA-AAAATGC
1 TCACTAAGTAAGAAAATGC
29751333 TAAAAATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (21 bp):
TCACTAAGTAAGAAAATGCAG
Found at i:29770399 original size:10 final size:10
Alignment explanation
Indices: 29770378--29770411 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
29770368 TTCTGAATTT
29770378 GAAAAATCATA
1 GAAAAAT-ATA
29770389 GAAAAATATA
1 GAAAAATATA
29770399 GAAAAATTATA
1 GAAAAA-TATA
29770410 GA
1 GA
29770412 GACTTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.21
Consensus pattern (10 bp):
GAAAAATATA
Found at i:29770926 original size:6 final size:6
Alignment explanation
Indices: 29770915--29770972 Score: 62
Period size: 6 Copynumber: 9.5 Consensus size: 6
29770905 TGATCAAAAT
* * * * *
29770915 TGAAAG TGAAAG TGAAAG TGAAAT TGGAATG TGAAAG TGAAAT TGGAAT
1 TGAAAG TGAAAG TGAAAG TGAAAG T-GAAAG TGAAAG TGAAAG TGAAAG
29770964 TGAAAG TGA
1 TGAAAG TGA
29770973 TATGAATTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
6 39 0.91
7 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (6 bp):
TGAAAG
Found at i:29770950 original size:13 final size:12
Alignment explanation
Indices: 29770911--29770972 Score: 70
Period size: 12 Copynumber: 5.1 Consensus size: 12
29770901 TTTGTGATCA
29770911 AAATTGAAAGTG
1 AAATTGAAAGTG
*
29770923 AAAGTGAAAGTG
1 AAATTGAAAGTG
*
29770935 AAATTGGAATGTG
1 AAATT-GAAAGTG
* *
29770948 AAAGTGAAATTG
1 AAATTGAAAGTG
*
29770960 GAATTGAAAGTG
1 AAATTGAAAGTG
29770972 A
1 A
29770973 TATGAATTGT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
12 29 0.74
13 10 0.26
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (12 bp):
AAATTGAAAGTG
Found at i:29770950 original size:19 final size:19
Alignment explanation
Indices: 29770926--29770972 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
29770916 GAAAGTGAAA
29770926 GTGAAAGTGAAATTGGAAT
1 GTGAAAGTGAAATTGGAAT
29770945 GTGAAAGTGAAATTGGAAT
1 GTGAAAGTGAAATTGGAAT
29770964 -TGAAAGTGA
1 GTGAAAGTGA
29770973 TATGAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.26
Consensus pattern (19 bp):
GTGAAAGTGAAATTGGAAT
Found at i:29770950 original size:25 final size:25
Alignment explanation
Indices: 29770911--29770972 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
29770901 TTTGTGATCA
29770911 AAATT-GAAAGTGAAAGTGAAAGTG
1 AAATTGGAAAGTGAAAGTGAAAGTG
* *
29770935 AAATTGGAATGTGAAAGTGAAATTG
1 AAATTGGAAAGTGAAAGTGAAAGTG
*
29770960 GAATT-GAAAGTGA
1 AAATTGGAAAGTGA
29770973 TATGAATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 12 0.36
25 21 0.64
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (25 bp):
AAATTGGAAAGTGAAAGTGAAAGTG
Found at i:29772684 original size:20 final size:21
Alignment explanation
Indices: 29772645--29772685 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29772635 TTAAACCGAG
*
29772645 AATCACTGAGTTAGAAAATGC
1 AATCACTAAGTTAGAAAATGC
29772666 AATCACTAAGTTA-AAAATGC
1 AATCACTAAGTTAGAAAATGC
29772686 TAAAAATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (21 bp):
AATCACTAAGTTAGAAAATGC
Found at i:29800442 original size:43 final size:43
Alignment explanation
Indices: 29800394--29800477 Score: 150
Period size: 43 Copynumber: 2.0 Consensus size: 43
29800384 AAAAAGAAGG
* *
29800394 ATTCAACATTCAATCACATTCATCCAATTCATGGATCAACAGT
1 ATTCAACATTCAATCACATTCATCCAATTCACGCATCAACAGT
29800437 ATTCAACATTCAATCACATTCATCCAATTCACGCATCAACA
1 ATTCAACATTCAATCACATTCATCCAATTCACGCATCAACA
29800478 TTCCAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.38, C:0.29, G:0.05, T:0.29
Consensus pattern (43 bp):
ATTCAACATTCAATCACATTCATCCAATTCACGCATCAACAGT
Found at i:29801191 original size:15 final size:14
Alignment explanation
Indices: 29801152--29801193 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
29801142 GGTAAATTTT
*
29801152 TCTTCTTCTTCCTTC
1 TCTTCTTC-TCTTTC
29801167 TCTTCTTCTCTTTC
1 TCTTCTTCTCTTTC
29801181 TCCTTCTTCTCTT
1 T-CTTCTTCTCTT
29801194 GCTTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (14 bp):
TCTTCTTCTCTTTC
Found at i:29809180 original size:25 final size:23
Alignment explanation
Indices: 29809139--29809184 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
29809129 CCAATTAAGG
29809139 AATTATTATTTAGATTTAATTCT
1 AATTATTATTTAGATTTAATTCT
*
29809162 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
29809185 TAGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCT
Found at i:29810197 original size:16 final size:17
Alignment explanation
Indices: 29810166--29810199 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
29810156 AGTTAGTTTC
29810166 GACTGCATCAAGTTTTG
1 GACTGCATCAAGTTTTG
29810183 GACTGCA-CAAGTTTTG
1 GACTGCATCAAGTTTTG
29810199 G
1 G
29810200 CGTCATTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (17 bp):
GACTGCATCAAGTTTTG
Found at i:29810299 original size:15 final size:16
Alignment explanation
Indices: 29810281--29810315 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29810271 AATATTTACA
29810281 TTTT-TAATTTAATTT
1 TTTTATAATTTAATTT
*
29810296 TTTTATATTTTAATTT
1 TTTTATAATTTAATTT
29810312 TTTT
1 TTTT
29810316 CTCTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATAATTTAATTT
Found at i:29815861 original size:6 final size:6
Alignment explanation
Indices: 29815850--29815943 Score: 68
Period size: 6 Copynumber: 15.5 Consensus size: 6
29815840 AATTAGTACA
* * * *
29815850 TTTATT TTTATT TTCATT TTCATT TTCATT TTTAGT TTTA-- TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* * *
29815896 TTTATTT TTTATT TTT-TT TATTATGC ATTATT TTTATT CTTATGT TTT
1 TTTA-TT TTTATT TTTATT T-TTAT-T TTTATT TTTATT TTTAT-T TTT
29815944 TTTAGTTGTT
Statistics
Matches: 72, Mismatches: 9, Indels: 13
0.77 0.10 0.14
Matches are distributed among these distances:
4 4 0.06
5 3 0.04
6 51 0.71
7 14 0.19
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.74
Consensus pattern (6 bp):
TTTATT
Found at i:29815898 original size:16 final size:17
Alignment explanation
Indices: 29815877--29815916 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
29815867 TTTCATTTTC
29815877 ATTTTTA-GTTTTATTT
1 ATTTTTATGTTTTATTT
*
29815893 ATTTTTATTTTTTATTT
1 ATTTTTATGTTTTATTT
29815910 -TTTTTAT
1 ATTTTTAT
29815917 TATGCATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (17 bp):
ATTTTTATGTTTTATTT
Found at i:29815917 original size:16 final size:17
Alignment explanation
Indices: 29815885--29815917 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
29815875 TCATTTTTAG
29815885 TTTTATTTATTTTTATT
1 TTTTATTTATTTTTATT
29815902 TTTTATTT-TTTTTATT
1 TTTTATTTATTTTTATT
29815918 ATGCATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTATTTATTTTTATT
Found at i:29815929 original size:16 final size:16
Alignment explanation
Indices: 29815891--29815933 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
29815881 TTAGTTTTAT
* **
29815891 TTATTTTTATTTTTTA
1 TTATTTTTATTATGCA
*
29815907 TTTTTTTTATTATGCA
1 TTATTTTTATTATGCA
29815923 TTATTTTTATT
1 TTATTTTTATT
29815934 CTTATGTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (16 bp):
TTATTTTTATTATGCA
Found at i:29819056 original size:6 final size:6
Alignment explanation
Indices: 29819045--29819073 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
29819035 CATCCTTCTC
29819045 TCCCCT TCCCCT T-CCCT TCCCCT TCCCCT
1 TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT
29819074 CCCTTCTCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
TCCCCT
Found at i:29819063 original size:11 final size:11
Alignment explanation
Indices: 29819047--29819094 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
29819037 TCCTTCTCTC
29819047 CCCTTCCCCTT
1 CCCTTCCCCTT
29819058 CCCTTCCCCTT
1 CCCTTCCCCTT
*
29819069 CCCCT-CCCTT
1 CCCTTCCCCTT
* *
29819079 CTCGTCTCCCTT
1 CCCTTC-CCCTT
29819091 CCCT
1 CCCT
29819095 ACCATCGCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
10 8 0.27
11 15 0.50
12 7 0.23
ACGTcount: A:0.00, C:0.62, G:0.02, T:0.35
Consensus pattern (11 bp):
CCCTTCCCCTT
Found at i:29819067 original size:17 final size:16
Alignment explanation
Indices: 29819045--29819079 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
29819035 CATCCTTCTC
29819045 TCCCCTTCCCCTTCCCT
1 TCCCCTTCCCC-TCCCT
29819062 TCCCCTTCCCCTCCCT
1 TCCCCTTCCCCTCCCT
29819078 TC
1 TC
29819080 TCGTCTCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (16 bp):
TCCCCTTCCCCTCCCT
Found at i:29820121 original size:22 final size:24
Alignment explanation
Indices: 29820096--29820148 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 24
29820086 GTGGGTTAGC
29820096 AGAGGGAAAGGGAT-G-GTAGGGG
1 AGAGGGAAAGGGATGGAGTAGGGG
*
29820118 AGAGGGAAAGGGTTGGAGTAGGGG
1 AGAGGGAAAGGGATGGAGTAGGGG
*
29820142 GGAGGGA
1 AGAGGGA
29820149 TGGTGGGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 13 0.48
23 1 0.04
24 13 0.48
ACGTcount: A:0.30, C:0.00, G:0.60, T:0.09
Consensus pattern (24 bp):
AGAGGGAAAGGGATGGAGTAGGGG
Found at i:29820177 original size:40 final size:39
Alignment explanation
Indices: 29820104--29820206 Score: 100
Period size: 40 Copynumber: 2.6 Consensus size: 39
29820094 GCAGAGGGAA
* * ** ** *
29820104 AGGGATGGTAGGGGAGAGGGAAAGGGTTGGAGTAGGGGGG
1 AGGGATGGTGGGGGAGAGGGAGAGAATCAGAGTA-CGGGG
29820144 AGGGATGGTGGGGGAGAGGGAGAGAATCAGAGTACGGGG
1 AGGGATGGTGGGGGAGAGGGAGAGAATCAGAGTACGGGG
* *
29820183 A-AGACTGGTGGGGAAGAGGGAGAG
1 AGGGA-TGGTGGGGGAGAGGGAGAG
29820207 GGATGGGAGA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
38 2 0.04
39 23 0.43
40 28 0.53
ACGTcount: A:0.28, C:0.03, G:0.58, T:0.11
Consensus pattern (39 bp):
AGGGATGGTGGGGGAGAGGGAGAGAATCAGAGTACGGGG
Found at i:29826718 original size:62 final size:59
Alignment explanation
Indices: 29826622--29826740 Score: 175
Period size: 62 Copynumber: 2.0 Consensus size: 59
29826612 TTACTCTAAT
* *
29826622 ATTAAATTAATATAATACTTATTAAGATAAACATTAGATTCAATTTAATATTAAATTTG
1 ATTAAATTAATAGAATACTTATTAAGATAAACATTAAATTCAATTTAATATTAAATTTG
* *
29826681 ATTAAATTAATAGAATATTTATCTACAAGATAAACATTAAATTTAATTTAATATTAAATT
1 ATTAAATTAATAGAATACTTAT-T--AAGATAAACATTAAATTCAATTTAATATTAAATT
29826741 AATGAAATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 20 0.38
60 1 0.02
62 32 0.60
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (59 bp):
ATTAAATTAATAGAATACTTATTAAGATAAACATTAAATTCAATTTAATATTAAATTTG
Found at i:29837555 original size:16 final size:16
Alignment explanation
Indices: 29837534--29837564 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29837524 CAATTAATCA
*
29837534 AATTAACCTAAAAATT
1 AATTAAACTAAAAATT
29837550 AATTAAACTAAAAAT
1 AATTAAACTAAAAAT
29837565 CAACCAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (16 bp):
AATTAAACTAAAAATT
Found at i:29839418 original size:174 final size:174
Alignment explanation
Indices: 29839123--29839477 Score: 701
Period size: 174 Copynumber: 2.0 Consensus size: 174
29839113 ATAAATCATA
*
29839123 TCACTTAGGTCACATAGGTCTTTTTAGCTTTTAACGTTCTGAGGCTTAGGTTGGTTTGGAATCAA
1 TCACCTAGGTCACATAGGTCTTTTTAGCTTTTAACGTTCTGAGGCTTAGGTTGGTTTGGAATCAA
29839188 TGAATAGACACGCAAAATGATTAAAACACAAAATTATTTTCGCATATTATATTGACCCCAATACT
66 TGAATAGACACGCAAAATGATTAAAACACAAAATTATTTTCGCATATTATATTGACCCCAATACT
29839253 TCCCCGATTAGACCCTTTAGCTCACCACCTTATATCCCCTTCTC
131 TCCCCGATTAGACCCTTTAGCTCACCACCTTATATCCCCTTCTC
29839297 TCACCTAGGTCACATAGGTCTTTTTAGCTTTTAACGTTCTGAGGCTTAGGTTGGTTTGGAATCAA
1 TCACCTAGGTCACATAGGTCTTTTTAGCTTTTAACGTTCTGAGGCTTAGGTTGGTTTGGAATCAA
29839362 TGAATAGACACGCAAAATGATTAAAACACAAAATTATTTTCGCATATTATATTGACCCCAATACT
66 TGAATAGACACGCAAAATGATTAAAACACAAAATTATTTTCGCATATTATATTGACCCCAATACT
29839427 TCCCCGATTAGACCCTTTAGCTCACCACCTTATATCCCCTTCTC
131 TCCCCGATTAGACCCTTTAGCTCACCACCTTATATCCCCTTCTC
29839471 TCACCTA
1 TCACCTA
29839478 CTTTTTCTCT
Statistics
Matches: 180, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 180 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (174 bp):
TCACCTAGGTCACATAGGTCTTTTTAGCTTTTAACGTTCTGAGGCTTAGGTTGGTTTGGAATCAA
TGAATAGACACGCAAAATGATTAAAACACAAAATTATTTTCGCATATTATATTGACCCCAATACT
TCCCCGATTAGACCCTTTAGCTCACCACCTTATATCCCCTTCTC
Found at i:29839585 original size:17 final size:17
Alignment explanation
Indices: 29839563--29839610 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
29839553 ACGAGGAGTT
29839563 TTTTTCATTTTCTTTTC
1 TTTTTCATTTTCTTTTC
* **
29839580 TTTTTCACTCACTTTTC
1 TTTTTCATTTTCTTTTC
29839597 -TTTTCTATTTTCTT
1 TTTTTC-ATTTTCTT
29839611 GAGAATTTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTCATTTTCTTTTC
Found at i:29845389 original size:17 final size:17
Alignment explanation
Indices: 29845367--29845399 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29845357 TCAAAAAGTT
*
29845367 AGGAATAGGTTCGATGA
1 AGGAATAGGCTCGATGA
29845384 AGGAATAGGCTCGATG
1 AGGAATAGGCTCGATG
29845400 TAGCCAACTG
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:0.33, C:0.09, G:0.36, T:0.21
Consensus pattern (17 bp):
AGGAATAGGCTCGATGA
Found at i:29849120 original size:16 final size:16
Alignment explanation
Indices: 29849099--29849130 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29849089 ACAAAGCCTA
29849099 GGTTATAAAATCCCTT
1 GGTTATAAAATCCCTT
29849115 GGTTATAAAATCCCTT
1 GGTTATAAAATCCCTT
29849131 CCTCTGCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (16 bp):
GGTTATAAAATCCCTT
Found at i:29851115 original size:27 final size:24
Alignment explanation
Indices: 29851064--29851109 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
29851054 GGCTCGACGA
* *
29851064 ATAAAAAGAGGAAGAGGCACAAAG
1 ATAAAAAGAAGAAGAAGCACAAAG
29851088 ATAAAAAGAAGAAGAAGCACAA
1 ATAAAAAGAAGAAGAAGCACAA
29851110 GGAAGAGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.63, C:0.09, G:0.24, T:0.04
Consensus pattern (24 bp):
ATAAAAAGAAGAAGAAGCACAAAG
Found at i:29861424 original size:17 final size:18
Alignment explanation
Indices: 29861382--29861431 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
29861372 ATCACTTTCC
29861382 CATTATCATTACATTTTA
1 CATTATCATTACATTTTA
*
29861400 -ATTATCATTGCA-TTTA
1 CATTATCATTACATTTTA
* *
29861416 CATTGTCATTATATTT
1 CATTATCATTACATTT
29861432 CCATTTGTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 4 0.15
17 20 0.77
18 2 0.08
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.52
Consensus pattern (18 bp):
CATTATCATTACATTTTA
Found at i:29865663 original size:162 final size:162
Alignment explanation
Indices: 29865396--29865715 Score: 595
Period size: 162 Copynumber: 2.0 Consensus size: 162
29865386 GAAAGAACTG
* *
29865396 CGCAAAATGATTATCAGTACCCGATTTCTTGTTCTGCTCAGGTGAAAACAAATCTTGGAGATATT
1 CGCAAAATGATTATCAGTACCCGATTTCTTGTTCTGCTCAAGCGAAAACAAATCTTGGAGATATT
*
29865461 GAGTTAGATGTCATTTCATCCCTAAGTGTACAAGTATCCTCTTTGGCAAACATGATTATAAACAT
66 GAGTTAGATGTCATTTCATCCCTAAGTGCACAAGTATCCTCTTTGGCAAACATGATTATAAACAT
*
29865526 GAAGGGGATGAGTGATGTTGCCCCTATTACTA
131 GAAGGGGACGAGTGATGTTGCCCCTATTACTA
*
29865558 CGCAAAATGATTATCAGTACCCGATTTCTTGTTCTGGTCAAGCGAAAACAAATCTTGGAGATATT
1 CGCAAAATGATTATCAGTACCCGATTTCTTGTTCTGCTCAAGCGAAAACAAATCTTGGAGATATT
29865623 GAGTTAGATGTCATTTCATCCCTAAGTGCACAAGTATCCTCTTTGGCAAACATGATTATAAACAT
66 GAGTTAGATGTCATTTCATCCCTAAGTGCACAAGTATCCTCTTTGGCAAACATGATTATAAACAT
29865688 GAAGGGGACGAGTGATGTTGCCCCTATT
131 GAAGGGGACGAGTGATGTTGCCCCTATT
29865716 CAAGTAGCCT
Statistics
Matches: 153, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
162 153 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (162 bp):
CGCAAAATGATTATCAGTACCCGATTTCTTGTTCTGCTCAAGCGAAAACAAATCTTGGAGATATT
GAGTTAGATGTCATTTCATCCCTAAGTGCACAAGTATCCTCTTTGGCAAACATGATTATAAACAT
GAAGGGGACGAGTGATGTTGCCCCTATTACTA
Found at i:29872113 original size:9 final size:9
Alignment explanation
Indices: 29872096--29872155 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 9
29872086 TGCGGGTATT
*
29872096 AAAGCAGAA
1 AAAGAAGAA
29872105 AAAGAAG--
1 AAAGAAGAA
29872112 AAAGAA-AA
1 AAAGAAGAA
*
29872120 GAAGAAGAA
1 AAAGAAGAA
29872129 AAAGAA-AA
1 AAAGAAGAA
*
29872137 GAAGGAAGAA
1 -AAAGAAGAA
29872147 AAAGAAGAA
1 AAAGAAGAA
29872156 GATATTACCC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
7 6 0.15
8 7 0.17
9 26 0.63
10 2 0.05
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (9 bp):
AAAGAAGAA
Found at i:29872121 original size:12 final size:11
Alignment explanation
Indices: 29872106--29872157 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
29872096 AAAGCAGAAA
29872106 AAGAAG-AAAG
1 AAGAAGAAAAG
29872116 AA-AAGAAGAAG
1 AAGAAGAA-AAG
*
29872127 AAAAAGAAAAG
1 AAGAAGAAAAG
29872138 AAGGAAGAAAAAG
1 AA-GAAG-AAAAG
29872151 AAGAAGA
1 AAGAAGA
29872158 TATTACCCCG
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
9 3 0.08
10 3 0.08
11 11 0.31
12 12 0.33
13 7 0.19
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (11 bp):
AAGAAGAAAAG
Found at i:29872125 original size:21 final size:21
Alignment explanation
Indices: 29872096--29872155 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
29872086 TGCGGGTATT
*
29872096 AAAGCAGAAAAAGAAG-AAAG
1 AAAGAAGAAAAAGAAGAAAAG
29872116 AAAAGAAGAAGAAA-AAGAAAAG
1 -AAAGAAGAA-AAAGAAGAAAAG
*
29872138 AAGGAAGAAAAAGAAGAA
1 AAAGAAGAAAAAGAAGAA
29872156 GATATTACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 3 0.09
21 24 0.71
22 7 0.21
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (21 bp):
AAAGAAGAAAAAGAAGAAAAG
Found at i:29893307 original size:3 final size:3
Alignment explanation
Indices: 29893292--29893366 Score: 66
Period size: 3 Copynumber: 25.0 Consensus size: 3
29893282 AGGTAATATG
* * *
29893292 TTC TTC TTT TTC TTC TT- TCTC TTC TTA TTC TTC TTC TTC TTT TTC
1 TTC TTC TTC TTC TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC
*
29893337 TT- TTC TTTC TTC TTC ATT- TCC TTC TTC TTC
1 TTC TTC -TTC TTC TTC -TTC TTC TTC TTC TTC
29893367 CTCTACCTCA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
2 4 0.07
3 48 0.83
4 6 0.10
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:29897893 original size:13 final size:13
Alignment explanation
Indices: 29897875--29897912 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
29897865 TAGCAATATT
29897875 TCTTTTTCTTTTC
1 TCTTTTTCTTTTC
*
29897888 TCTTTTTCTTTTTT
1 TCTTTTTC-TTTTC
29897902 TCTTTTT-TTTT
1 TCTTTTTCTTTT
29897913 ATTCATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 4 0.17
13 8 0.35
14 11 0.48
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TCTTTTTCTTTTC
Found at i:29898547 original size:16 final size:17
Alignment explanation
Indices: 29898512--29898550 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
29898502 TTATCAAAAG
29898512 AAATGTAATGACAAAATA
1 AAATGTAATGAC-AAATA
*
29898530 AAATGTAGTGAC-AATA
1 AAATGTAATGACAAATA
29898546 AAATG
1 AAATG
29898551 CATGCAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
18 11 0.55
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.23
Consensus pattern (17 bp):
AAATGTAATGACAAATA
Found at i:29906910 original size:15 final size:15
Alignment explanation
Indices: 29906890--29906919 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29906880 AATGCTGGAT
29906890 GAGTTAACAAGGTAC
1 GAGTTAACAAGGTAC
29906905 GAGTTAACAAGGTAC
1 GAGTTAACAAGGTAC
29906920 TGTATAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (15 bp):
GAGTTAACAAGGTAC
Found at i:29914784 original size:16 final size:16
Alignment explanation
Indices: 29914760--29914811 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
29914750 TTTGTCATTT
*
29914760 TTCATGATTTTTCTCA
1 TTCAAGATTTTTCTCA
*
29914776 TTCAAGATTATTT-TCT
1 TTCAAGATT-TTTCTCA
**
29914792 TTCAATTTTTTTCTCA
1 TTCAAGATTTTTCTCA
29914808 TTCA
1 TTCA
29914812 TTTCTACTCG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 3 0.10
16 23 0.79
17 3 0.10
ACGTcount: A:0.21, C:0.17, G:0.04, T:0.58
Consensus pattern (16 bp):
TTCAAGATTTTTCTCA
Found at i:29915461 original size:6 final size:6
Alignment explanation
Indices: 29915450--29915514 Score: 58
Period size: 6 Copynumber: 10.2 Consensus size: 6
29915440 CAAGTACATG
* * * *
29915450 ACAAAA ATAAAA GACAAAA ACAAAA GCAAAA ATAAAA ATAAAAA ACAAAA
1 ACAAAA ACAAAA -ACAAAA ACAAAA ACAAAA ACAAAA A-CAAAA ACAAAA
29915500 ACAAATA AGCAAAA A
1 ACAAA-A A-CAAAA A
29915515 TTTCTATGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
6 30 0.62
7 14 0.29
8 4 0.08
ACGTcount: A:0.78, C:0.11, G:0.05, T:0.06
Consensus pattern (6 bp):
ACAAAA
Found at i:29915487 original size:13 final size:13
Alignment explanation
Indices: 29915449--29915486 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
29915439 ACAAGTACAT
29915449 GACAAAAATAAAA
1 GACAAAAATAAAA
*
29915462 GACAAAAACAAAA
1 GACAAAAATAAAA
29915475 G-CAAAAATAAAA
1 GACAAAAATAAAA
29915487 ATAAAAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.76, C:0.11, G:0.08, T:0.05
Consensus pattern (13 bp):
GACAAAAATAAAA
Found at i:29915490 original size:31 final size:33
Alignment explanation
Indices: 29915452--29915515 Score: 105
Period size: 31 Copynumber: 2.0 Consensus size: 33
29915442 AGTACATGAC
*
29915452 AAAAATAAAAGACAAAAAC-AA-AAGCAAAAAT
1 AAAAATAAAAAACAAAAACAAATAAGCAAAAAT
29915483 AAAAATAAAAAACAAAAACAAATAAGCAAAAAT
1 AAAAATAAAAAACAAAAACAAATAAGCAAAAAT
29915516 TTCTATGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 18 0.60
32 2 0.07
33 10 0.33
ACGTcount: A:0.78, C:0.09, G:0.05, T:0.08
Consensus pattern (33 bp):
AAAAATAAAAAACAAAAACAAATAAGCAAAAAT
Found at i:29915492 original size:12 final size:12
Alignment explanation
Indices: 29915450--29915504 Score: 56
Period size: 13 Copynumber: 4.4 Consensus size: 12
29915440 CAAGTACATG
29915450 ACAAAAATAAAA
1 ACAAAAATAAAA
*
29915462 GACAAAAACAAAA
1 -ACAAAAATAAAA
*
29915475 GCAAAAATAAAA
1 ACAAAAATAAAA
* *
29915487 ATAAAAAACAAAA
1 A-CAAAAATAAAA
29915500 ACAAA
1 ACAAA
29915505 TAAGCAAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
12 13 0.38
13 21 0.62
ACGTcount: A:0.80, C:0.11, G:0.04, T:0.05
Consensus pattern (12 bp):
ACAAAAATAAAA
Found at i:29917303 original size:18 final size:18
Alignment explanation
Indices: 29917272--29917315 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
29917262 ATCCTCAAGT
*
29917272 AAACAAAACAAGAAAAGC
1 AAACAAAGCAAGAAAAGC
*
29917290 AAAGAAAGCAAGAAAAGC
1 AAACAAAGCAAGAAAAGC
29917308 AAACAAAG
1 AAACAAAG
29917316 AGCTTGAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.70, C:0.14, G:0.16, T:0.00
Consensus pattern (18 bp):
AAACAAAGCAAGAAAAGC
Found at i:29926667 original size:13 final size:13
Alignment explanation
Indices: 29926649--29926679 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
29926639 AAATTAGAAG
29926649 AAAGTAAAAATAA
1 AAAGTAAAAATAA
29926662 AAAGTAAAAATAA
1 AAAGTAAAAATAA
29926675 AAAGT
1 AAAGT
29926680 TAAGTAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (13 bp):
AAAGTAAAAATAA
Found at i:29945258 original size:12 final size:12
Alignment explanation
Indices: 29945241--29945265 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29945231 TTTGTCTCGA
29945241 CATCTTTTTCTT
1 CATCTTTTTCTT
29945253 CATCTTTTTCTT
1 CATCTTTTTCTT
29945265 C
1 C
29945266 CTCCACATGA
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:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (12 bp):
CATCTTTTTCTT
Found at i:29954054 original size:21 final size:21
Alignment explanation
Indices: 29954030--29954079 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
29954020 AGTGCAGACC
29954030 TCTACCGATACAAGTGAC-AGT
1 TCTACCGATACAAGTGACTA-T
29954051 TCTACCGATACAAGTGACTAT
1 TCTACCGATACAAGTGACTAT
29954072 TCTACCGA
1 TCTACCGA
29954080 AACTAGTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (21 bp):
TCTACCGATACAAGTGACTAT
Found at i:29954922 original size:53 final size:53
Alignment explanation
Indices: 29954749--29955204 Score: 600
Period size: 53 Copynumber: 8.7 Consensus size: 53
29954739 TTCGCATTTG
* * * * *
29954749 ATAACTCACAATGACACAGAGTCATTGGACCTTTAATCCATGAT-GGATTCGT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* * * * * * *
29954801 GTATCTCACGATGACACAAAGTCATCAGACCCTTAATTCGTAATA-GATTCTT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
*
29954853 ATAACTCACGATGACACATAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* * * *
29954906 TTAACTCACGATGACAC--AGTCATCGGACCTTTAATTCATAATAAGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* * *
29954957 ATAACTCATGATGACAC--AGTCATCGGACCTTCAATCCGTGATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* *
29955008 ATAACTCACGATGACACAGAGTCATCGGACCTTCAATCCGTGATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* * * *
29955061 ATAAATGACGATGACACAGAGTCATCAGACCTTTAATCTGTAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* *
29955114 ATAACTCACGATGACACAGAGTCATCAGACCTTTAATCTGTAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* *
29955167 ATAACTCACGATGACATAGAGTCATCAGACCTTTAATC
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATC
29955205 TATGGCACAA
Statistics
Matches: 361, Mismatches: 39, Indels: 7
0.89 0.10 0.02
Matches are distributed among these distances:
51 91 0.25
52 79 0.22
53 191 0.53
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (53 bp):
ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
Found at i:29959047 original size:15 final size:16
Alignment explanation
Indices: 29959005--29959048 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
29958995 AGCAATATCT
*
29959005 TTTTTCTTTTTTTCTC
1 TTTTTCTTTTCTTCTC
* *
29959021 TTTTCCTCTTCTTC-C
1 TTTTTCTTTTCTTCTC
29959036 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
29959049 TTTTTTTAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTCTTTTCTTCTC
Found at i:29959612 original size:17 final size:18
Alignment explanation
Indices: 29959590--29959631 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
29959580 AATGGAATGC
29959590 AAATGCACTAACAAAT-A
1 AAATGCACTAACAAATAA
* *
29959607 AAATGCAGTGACAAATAA
1 AAATGCACTAACAAATAA
29959625 AAATGCA
1 AAATGCA
29959632 ATGACAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.57, C:0.14, G:0.12, T:0.17
Consensus pattern (18 bp):
AAATGCACTAACAAATAA
Found at i:29959629 original size:18 final size:18
Alignment explanation
Indices: 29959590--29959643 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
29959580 AATGGAATGC
* *
29959590 AAATGCACTAACAAAT-A
1 AAATGCAATGACAAATAA
*
29959607 AAATGCAGTGACAAATAA
1 AAATGCAATGACAAATAA
*
29959625 AAATGCAATGACAACTAA
1 AAATGCAATGACAAATAA
29959643 A
1 A
29959644 TAAAATGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 14 0.44
18 18 0.56
ACGTcount: A:0.57, C:0.15, G:0.11, T:0.17
Consensus pattern (18 bp):
AAATGCAATGACAAATAA
Found at i:29962454 original size:22 final size:24
Alignment explanation
Indices: 29962416--29962460 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
29962406 AGTGAAAAGA
29962416 AAAAAACGAAAATGAGT-AGAAAT
1 AAAAAACGAAAATGAGTAAGAAAT
*
29962439 AAAAAATGAAAA-GAGTAAGAAA
1 AAAAAACGAAAATGAGTAAGAAA
29962461 AAGTGTGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.69, C:0.02, G:0.18, T:0.11
Consensus pattern (24 bp):
AAAAAACGAAAATGAGTAAGAAAT
Found at i:29976247 original size:17 final size:17
Alignment explanation
Indices: 29976225--29976257 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29976215 GGTTTCGGCC
29976225 TTCTTTATTT-GTATTTT
1 TTCTTT-TTTGGTATTTT
29976242 TTCTTTTTTGGTATTT
1 TTCTTTTTTGGTATTT
29976258 GGCAATAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTGGTATTTT
Found at i:29978361 original size:19 final size:19
Alignment explanation
Indices: 29978339--29978394 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
29978329 TTTTATCAAC
29978339 TTTTTATAAATATTTTTTA
1 TTTTTATAAATATTTTTTA
29978358 -TTTT-TAAATATTTTTATAA
1 TTTTTATAAATATTTTT-T-A
*
29978377 TTTTTA-AATTATTTTTTA
1 TTTTTATAAATATTTTTTA
29978395 ACGTGACATA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
17 11 0.34
18 6 0.19
19 2 0.06
20 13 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTATAAATATTTTTTA
Found at i:29978372 original size:11 final size:10
Alignment explanation
Indices: 29978340--29978392 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
29978330 TTTATCAACT
29978340 TTTTATAAATA
1 TTTT-TAAATA
29978351 TTTTT---TA
1 TTTTTAAATA
29978358 TTTTTAAATA
1 TTTTTAAATA
*
29978368 TTTTTATA-A
1 TTTTTAAATA
29978377 TTTTTAAATTA
1 TTTTTAAA-TA
29978388 TTTTT
1 TTTTT
29978393 TAACGTGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
7 7 0.20
9 8 0.23
10 10 0.29
11 10 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:29982393 original size:30 final size:30
Alignment explanation
Indices: 29982355--29982460 Score: 158
Period size: 30 Copynumber: 3.5 Consensus size: 30
29982345 ATAGGTTCTA
*
29982355 CCAAAAAGGCTTCCACATATCAGAGAATAG
1 CCAAAAAGGCTTCCACATATCAGAGAACAG
* *
29982385 CTAAAAAGGCTTCCACATATCAGAGAACAA
1 CCAAAAAGGCTTCCACATATCAGAGAACAG
* *
29982415 CCACAAGGGCTTCCACATATCAGAGAACAG
1 CCAAAAAGGCTTCCACATATCAGAGAACAG
*
29982445 CCATAAAGGCTTCCAC
1 CCAAAAAGGCTTCCAC
29982461 TTTTTGGTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (30 bp):
CCAAAAAGGCTTCCACATATCAGAGAACAG
Found at i:29986992 original size:24 final size:24
Alignment explanation
Indices: 29986936--29986992 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
29986926 TTAAACTCTG
29986936 TCTGGGCTCGTAAGAGCTAATCAT
1 TCTGGGCTCGTAAGAGCTAATCAT
* **
29986960 TTTAAGCTCGTAAGAGCTAATCAT
1 TCTGGGCTCGTAAGAGCTAATCAT
29986984 TCTGGGCTC
1 TCTGGGCTC
29986993 ATGTTGGCTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (24 bp):
TCTGGGCTCGTAAGAGCTAATCAT
Found at i:30006899 original size:22 final size:23
Alignment explanation
Indices: 30006858--30006900 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
30006848 ATCGATTAAT
*
30006858 AATAGGATTTATTAAGGTTAAAA
1 AATAGGATTAATTAAGGTTAAAA
*
30006881 AATATGATTAATTAA-GTTAA
1 AATAGGATTAATTAAGGTTAA
30006901 TAATGAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (23 bp):
AATAGGATTAATTAAGGTTAAAA
Found at i:30007877 original size:50 final size:51
Alignment explanation
Indices: 30007768--30007955 Score: 234
Period size: 50 Copynumber: 3.7 Consensus size: 51
30007758 AAGGTTCGAC
* * * * * *
30007768 GACTAAGTTTCATTGTGAGTAAATGAATCCTTTATGGATTTAAGATCTAAT
1 GACTAAGTGTCATCGTGAGTAAATGAATCCTATACGGATTTAAGGTCTGAT
* *
30007819 GACTAAGTGTCATCGTGAGTAAATGTATCCTATACAGA-TTAAGGTCTGAT
1 GACTAAGTGTCATCGTGAGTAAATGAATCCTATACGGATTTAAGGTCTGAT
* * * *
30007869 GACTAAGTGTTATCGTGAGTAAATGAATCCTTTACGGATTGTGAGGTCCGAT
1 GACTAAGTGTCATCGTGAGTAAATGAATCCTATACGGATT-TAAGGTCTGAT
*
30007921 GACTAAGTGTCATCGTGAGTACATGAATTCCTATA
1 GACTAAGTGTCATCGTGAGTAAATGAA-TCCTATA
30007956 TGGAACAAGA
Statistics
Matches: 117, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
50 44 0.38
51 33 0.28
52 34 0.29
53 6 0.05
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (51 bp):
GACTAAGTGTCATCGTGAGTAAATGAATCCTATACGGATTTAAGGTCTGAT
Found at i:30013807 original size:22 final size:21
Alignment explanation
Indices: 30013782--30013833 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 21
30013772 CAAATATTGA
30013782 TTAATAATAGGATTT-ATTAAGG
1 TTAATAATAGG-TTTAATTAA-G
* *
30013804 TTAAAAAATATGTTTAATTAAG
1 TT-AATAATAGGTTTAATTAAG
30013826 TTAATAAT
1 TTAATAAT
30013834 GGAAGTCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 5 0.20
22 8 0.32
23 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (21 bp):
TTAATAATAGGTTTAATTAAG
Found at i:30014759 original size:51 final size:51
Alignment explanation
Indices: 30014676--30014914 Score: 255
Period size: 51 Copynumber: 4.6 Consensus size: 51
30014666 CCGTAAACAA
* * * *
30014676 AAAGGTCCGATGACTAAGTGTTATCATAAGTAAATGAATCCTTTATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
30014727 TAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTCTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * **
30014778 AAAGGTTCGATGACTAAGTGTTATCGTGAGCAAATGAATCCTTTAAAGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
** * * * * **
30014829 GTGAGGTCCGATGAGTAAGTGTCGTCGTGAGTACATGAATTCCTATACGGAACA
1 -AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGG-ATT
*
30014883 AAAGGTCCGATGAC-AATATGTCATCGTGAGTA
1 AAAGGTCCGATGACTAA-GTGTCATCGTGAGTA
30014915 TTAAATGAAA
Statistics
Matches: 153, Mismatches: 31, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
51 89 0.58
52 32 0.21
53 31 0.20
54 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:30035069 original size:16 final size:16
Alignment explanation
Indices: 30035048--30035080 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
30035038 TGTATACCTT
30035048 CAACAAGTTATCCAAA
1 CAACAAGTTATCCAAA
30035064 CAACAAGTTATCCAAA
1 CAACAAGTTATCCAAA
30035080 C
1 C
30035081 TGTTAGCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.27, G:0.06, T:0.18
Consensus pattern (16 bp):
CAACAAGTTATCCAAA
Found at i:30063876 original size:20 final size:21
Alignment explanation
Indices: 30063839--30063877 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30063829 TAAACGAGCA
*
30063839 TCACTGAGTTAGAAAATGCAG
1 TCACTAAGTTAGAAAATGCAG
30063860 TCACTAAGTTA-AAAATGC
1 TCACTAAGTTAGAAAATGC
30063878 TAAAAATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (21 bp):
TCACTAAGTTAGAAAATGCAG
Found at i:30063892 original size:13 final size:13
Alignment explanation
Indices: 30063874--30063898 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30063864 TAAGTTAAAA
30063874 ATGCTAAAAATGC
1 ATGCTAAAAATGC
30063887 ATGCTAAAAATG
1 ATGCTAAAAATG
30063899 ATAAAATGGG
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:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGCTAAAAATGC
Found at i:30067334 original size:13 final size:13
Alignment explanation
Indices: 30067316--30067340 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30067306 TAAGTATGAA
30067316 ATGCTAAAAATGT
1 ATGCTAAAAATGT
30067329 ATGCTAAAAATG
1 ATGCTAAAAATG
30067341 ATACAAAAGG
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:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (13 bp):
ATGCTAAAAATGT
Found at i:30074992 original size:18 final size:19
Alignment explanation
Indices: 30074951--30074992 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
30074941 TGTCCTTACA
*
30074951 TATGTGGCTGCATTCTTGC
1 TATGTGGCTGCATTCTAGC
*
30074970 T-TGTGGTTGCA-TCTAGC
1 TATGTGGCTGCATTCTAGC
30074987 TATGTG
1 TATGTG
30074993 CCTGTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 6 0.30
18 13 0.65
19 1 0.05
ACGTcount: A:0.12, C:0.17, G:0.29, T:0.43
Consensus pattern (19 bp):
TATGTGGCTGCATTCTAGC
Found at i:30080780 original size:21 final size:21
Alignment explanation
Indices: 30080754--30080802 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
30080744 GGTCAAACGG
30080754 CCGTGTGGCTCTT-CCACATGC
1 CCGTGTGGC-CTTCCCACATGC
30080775 CCGTGTGGCCTTCCCACATGC
1 CCGTGTGGCCTTCCCACATGC
*
30080796 CCATGTG
1 CCGTGTG
30080803 CTCAATCGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.10, C:0.39, G:0.24, T:0.27
Consensus pattern (21 bp):
CCGTGTGGCCTTCCCACATGC
Found at i:30081999 original size:33 final size:33
Alignment explanation
Indices: 30081962--30082088 Score: 146
Period size: 33 Copynumber: 3.8 Consensus size: 33
30081952 ATGACAAGTA
* ** *
30081962 AGTACACAGTATGCTTATAAGAGCTAATCAATC
1 AGTACACTGTATGCTCGTAAGAGCTAACCAATC
**
30081995 AGTACTTTGTATGCTCGTAAGAGCTAACCAATC
1 AGTACACTGTATGCTCGTAAGAGCTAACCAATC
*
30082028 AGTACACTGTATGCTCGTAAGAGCTAACCAATT
1 AGTACACTGTATGCTCGTAAGAGCTAACCAATC
* * * * *
30082061 ACTACACTATATTCTCATAAGAGTTAAC
1 AGTACACTGTATGCTCGTAAGAGCTAAC
30082089 TAGCGAACAC
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (33 bp):
AGTACACTGTATGCTCGTAAGAGCTAACCAATC
Found at i:30088763 original size:12 final size:12
Alignment explanation
Indices: 30088746--30088781 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
30088736 TTTTGAGAGC
30088746 ATAAAATAAAAG
1 ATAAAATAAAAG
*
30088758 ATAAAATAAAAT
1 ATAAAATAAAAG
*
30088770 AGAAAATAAAAG
1 ATAAAATAAAAG
30088782 CGAAAGTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:30088768 original size:17 final size:17
Alignment explanation
Indices: 30088746--30088780 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30088736 TTTTGAGAGC
30088746 ATAAAATA-AAAGATAAA
1 ATAAAATAGAAA-ATAAA
30088763 ATAAAATAGAAAATAAA
1 ATAAAATAGAAAATAAA
30088780 A
1 A
30088781 GCGAAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (17 bp):
ATAAAATAGAAAATAAA
Found at i:30088786 original size:12 final size:12
Alignment explanation
Indices: 30088748--30088786 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
30088738 TTGAGAGCAT
*
30088748 AAAATAAAAGAT
1 AAAATAAAAGAG
*
30088760 AAAATAAAATAG
1 AAAATAAAAGAG
*
30088772 AAAATAAAAGCG
1 AAAATAAAAGAG
30088784 AAA
1 AAA
30088787 GTTTGAGATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (12 bp):
AAAATAAAAGAG
Found at i:30093739 original size:6 final size:6
Alignment explanation
Indices: 30093728--30093770 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
30093718 TATAGCAATA
30093728 TTTCTT TTTCTT TTCTCTT TTTCTCT TTT-TCT TTTCTT TTTCT
1 TTTCTT TTTCTT TT-TCTT TTTCT-T TTTCT-T TTTCTT TTTCT
30093771 CATTTAACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 23 0.68
7 11 0.32
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTCTT
Found at i:30093748 original size:13 final size:13
Alignment explanation
Indices: 30093730--30093767 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
30093720 TAGCAATATT
30093730 TCTTTTTCTTTTC
1 TCTTTTTCTTTTC
*
30093743 TCTTTTTCTCTTTT
1 TCTTTTTCT-TTTC
30093757 TC-TTTTCTTTT
1 TCTTTTTCTTTT
30093768 TCTCATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 3 0.13
13 15 0.65
14 5 0.22
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TCTTTTTCTTTTC
Found at i:30093755 original size:21 final size:20
Alignment explanation
Indices: 30093730--30093768 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
30093720 TAGCAATATT
30093730 TCTTTTTCTTTTCTCTTTTTC
1 TCTTTTTCTTTTCT-TTTTTC
30093751 TCTTTTTCTTTTCTTTTT
1 TCTTTTTCTTTTCTTTTT
30093769 CTCATTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TCTTTTTCTTTTCTTTTTTC
Found at i:30095636 original size:261 final size:261
Alignment explanation
Indices: 30095169--30095684 Score: 798
Period size: 261 Copynumber: 2.0 Consensus size: 261
30095159 ATTTTGTAGC
* * * * *
30095169 CTACCATTAGGAGTAGGCTGGTCGGAGGATGATGCCATTGGGCGAAAAATAGAGGGAAAGTTTGG
1 CTACCATCAAGAGTAGGCTGGTCGAAGGATGATACAATTGGGCGAAAAATAGAGGGAAAGTTTGG
* * * * *
30095234 GAAATCAGGCAGCGGATTTGGGCTTATGCTGCCCAATACAGCGATAATTACCTCATTCCATGCTT
66 GAAATAAGGCAGCGCATTTAGGCTTATGCTGCCCAATACAGCAACAATTACCTCATTCCATGCTT
* * *
30095299 TTGTATACGCATAGAACATATGTTGTCTGTAGTCCATATCCTCTAATACGCCGACAGTACGAATA
131 TTGTATACGCATAGAACATATCTTGTCTGTAGTCCATATCCTATAATACGCCGACAATACGAATA
* *
30095364 GTGCGCATGTCGATATGATCAATATTTGCTTCCATAGCAGCCAACCTCTTTCCCAACAGATTTGG
196 GTGCACATGTCGATATGATCAATATTTACTTCCATAGCAGCCAACCTCTTTCCCAACAGATTTGG
30095429 G
261 G
* *
30095430 CTACCATCAAGAGTCGGCTGGTCGAAGGATGATACAATTGGGCGGAAAATAGAGGGAAAGTTTGG
1 CTACCATCAAGAGTAGGCTGGTCGAAGGATGATACAATTGGGCGAAAAATAGAGGGAAAGTTTGG
* * * * *
30095495 GAAATAAGGCAGCGCATTTAGGTTTATGCTGCGCAATACGGTAACAATTGCCTCATTCCATGCTT
66 GAAATAAGGCAGCGCATTTAGGCTTATGCTGCCCAATACAGCAACAATTACCTCATTCCATGCTT
* * *
30095560 TTGTATACGTATAGAAGATATCTTGTCTGTAGTCCATATCCTATAATATGCCGACAATACGAATA
131 TTGTATACGCATAGAACATATCTTGTCTGTAGTCCATATCCTATAATACGCCGACAATACGAATA
*
30095625 GTGCACATGTCGATGTGATCAATATTTACTTCCATAGCAGCCAACCTCTTTCCCAACAGA
196 GTGCACATGTCGATATGATCAATATTTACTTCCATAGCAGCCAACCTCTTTCCCAACAGA
30095685 GGATCTGTGG
Statistics
Matches: 229, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
261 229 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (261 bp):
CTACCATCAAGAGTAGGCTGGTCGAAGGATGATACAATTGGGCGAAAAATAGAGGGAAAGTTTGG
GAAATAAGGCAGCGCATTTAGGCTTATGCTGCCCAATACAGCAACAATTACCTCATTCCATGCTT
TTGTATACGCATAGAACATATCTTGTCTGTAGTCCATATCCTATAATACGCCGACAATACGAATA
GTGCACATGTCGATATGATCAATATTTACTTCCATAGCAGCCAACCTCTTTCCCAACAGATTTGG
G
Found at i:30114293 original size:23 final size:25
Alignment explanation
Indices: 30114247--30114294 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
30114237 TCAGTCACAT
*
30114247 AAAAAGGAAAATGAGATAAAAAAAG
1 AAAAAGGAAAATGAGAGAAAAAAAG
30114272 AAAAA-GAAAA-GAGAGAAGAAAAA
1 AAAAAGGAAAATGAGAGAA-AAAAA
30114295 TAAGAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 10 0.48
25 5 0.24
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (25 bp):
AAAAAGGAAAATGAGAGAAAAAAAG
Found at i:30114807 original size:14 final size:14
Alignment explanation
Indices: 30114788--30114852 Score: 67
Period size: 14 Copynumber: 4.4 Consensus size: 14
30114778 AACTCATCTC
30114788 AGAAGATCAATACT
1 AGAAGATCAATACT
** *
30114802 AGAAGAAGAATGCAGCC
1 AGAAGATCAAT--A-CT
*
30114819 ACAAGATCAATACT
1 AGAAGATCAATACT
30114833 AGAAGATCAATACT
1 AGAAGATCAATACT
30114847 AGAAGA
1 AGAAGA
30114853 AGAATGCAGC
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
14 29 0.73
15 1 0.03
16 1 0.03
17 9 0.22
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.15
Consensus pattern (14 bp):
AGAAGATCAATACT
Found at i:30127566 original size:12 final size:12
Alignment explanation
Indices: 30127549--30127584 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
30127539 TTTTGAGAGC
30127549 ATAAAATAAAAG
1 ATAAAATAAAAG
*
30127561 ATAAAATAAAAT
1 ATAAAATAAAAG
*
30127573 AGAAAATAAAAG
1 ATAAAATAAAAG
30127585 GAAATGTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:30127571 original size:17 final size:17
Alignment explanation
Indices: 30127549--30127583 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30127539 TTTTGAGAGC
30127549 ATAAAATA-AAAGATAAA
1 ATAAAATAGAAA-ATAAA
30127566 ATAAAATAGAAAATAAA
1 ATAAAATAGAAAATAAA
30127583 A
1 A
30127584 GGAAATGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (17 bp):
ATAAAATAGAAAATAAA
Found at i:30133555 original size:6 final size:6
Alignment explanation
Indices: 30133546--30133578 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
30133536 AACATTGGCA
30133546 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTT
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTT
30133579 CCATTTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTCC
Found at i:30135324 original size:18 final size:19
Alignment explanation
Indices: 30135281--30135326 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
30135271 TATCATTAAT
*
30135281 AATTCAATTTTAATATAAA
1 AATTCAATATTAATATAAA
* *
30135300 TATTCAATATTATTA-AAA
1 AATTCAATATTAATATAAA
30135318 AATTCAATA
1 AATTCAATA
30135327 ATATAAATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCAATATTAATATAAA
Found at i:30138456 original size:21 final size:21
Alignment explanation
Indices: 30138423--30138462 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
30138413 TTTTTTTCAC
* * *
30138423 TGTTGTTTGTTGTTATTTTAT
1 TGTTATTTATTGTCATTTTAT
30138444 TGTTATTTATTGTCATTTT
1 TGTTATTTATTGTCATTTT
30138463 GATGTTGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.03, G:0.15, T:0.70
Consensus pattern (21 bp):
TGTTATTTATTGTCATTTTAT
Found at i:30138904 original size:28 final size:28
Alignment explanation
Indices: 30138873--30138965 Score: 73
Period size: 28 Copynumber: 3.3 Consensus size: 28
30138863 AATATAAAGC
30138873 TTATAAATTTAATATACATTATAAAAAA
1 TTATAAATTTAATATACATTATAAAAAA
* * * *
30138901 TTAT-AATTATATTATAAATTTTTAAAAA
1 TTATAAATT-TAATATACATTATAAAAAA
* * * *
30138929 -TATATATTAAAAATACATATTATAAAAAT
1 TTATAAATTTAATATAC--ATTATAAAAAA
30138958 TTATAAAT
1 TTATAAAT
30138966 ATATATTATA
Statistics
Matches: 47, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
27 11 0.23
28 22 0.47
29 8 0.17
30 6 0.13
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
TTATAAATTTAATATACATTATAAAAAA
Found at i:30138914 original size:21 final size:21
Alignment explanation
Indices: 30138877--30138918 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
30138867 TAAAGCTTAT
30138877 AAATTTAATATACATTATAAA
1 AAATTTAATATACATTATAAA
*
30138898 AAATTATAAT-TATATTATAAA
1 AAATT-TAATATACATTATAAA
30138919 TTTTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTTAATATACATTATAAA
Found at i:30138957 original size:15 final size:13
Alignment explanation
Indices: 30138922--30138955 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
30138912 TTATAAATTT
*
30138922 TTAAAAATATATA
1 TTAAAAATACATA
30138935 TTAAAAATACATA
1 TTAAAAATACATA
30138948 TTATAAAA
1 TTA-AAAA
30138956 ATTTATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (13 bp):
TTAAAAATACATA
Found at i:30138982 original size:15 final size:15
Alignment explanation
Indices: 30138956--30139008 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
30138946 TATTATAAAA
30138956 ATTTAT-AAATATAT
1 ATTTATAAAATATAT
*
30138970 A-TTATAGAAATATGT
1 ATTTATA-AAATATAT
30138985 ATTTATAAAATATAT
1 ATTTATAAAATATAT
30139000 -TTTAATAAA
1 ATTT-ATAAA
30139009 TTTATAAAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 4 0.12
14 4 0.12
15 20 0.61
16 5 0.15
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (15 bp):
ATTTATAAAATATAT
Found at i:30144496 original size:32 final size:32
Alignment explanation
Indices: 30144460--30144526 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
30144450 TTGCATTCAT
*
30144460 ATTCCTTATTGTATATAATTAGATTCAAATGG
1 ATTCCTTATTGTATACAATTAGATTCAAATGG
*
30144492 ATTCCTTATTGTATACAATTAGATTCCAATGG
1 ATTCCTTATTGTATACAATTAGATTCAAATGG
30144524 ATT
1 ATT
30144527 TTGCCACGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (32 bp):
ATTCCTTATTGTATACAATTAGATTCAAATGG
Found at i:30144679 original size:18 final size:18
Alignment explanation
Indices: 30144631--30144681 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
30144621 TTTCGGATAA
*
30144631 AATCGAATTAATTCGGTT
1 AATCGAATTAATTCGATT
*
30144649 -ATCCG-ATCAAATTCGATT
1 AAT-CGAAT-TAATTCGATT
30144667 AATCGAATTAATTCG
1 AATCGAATTAATTCG
30144682 GTCAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 8
0.70 0.08 0.22
Matches are distributed among these distances:
17 4 0.15
18 18 0.69
19 4 0.15
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (18 bp):
AATCGAATTAATTCGATT
Found at i:30144858 original size:9 final size:9
Alignment explanation
Indices: 30144844--30144870 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
30144834 AAAATTAATC
30144844 AATTAATTT
1 AATTAATTT
30144853 AATTAATTT
1 AATTAATTT
30144862 AATTAATTT
1 AATTAATTT
30144871 TTTATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTAATTT
Found at i:30150043 original size:16 final size:14
Alignment explanation
Indices: 30150011--30150041 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
30150001 TTAAAAAATA
30150011 ATAATTTTTTACAT
1 ATAATTTTTTACAT
*
30150025 ATAATTTTTTACTT
1 ATAATTTTTTACAT
30150039 ATA
1 ATA
30150042 TATTGAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (14 bp):
ATAATTTTTTACAT
Found at i:30150206 original size:15 final size:15
Alignment explanation
Indices: 30150181--30150216 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
30150171 TTATTTGAGT
30150181 TAATC-AAGTTATTC
1 TAATCAAAGTTATTC
30150195 TAATCAAAGTTATTC
1 TAATCAAAGTTATTC
30150210 TAATCAA
1 TAATCAA
30150217 CTCGAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.39
Consensus pattern (15 bp):
TAATCAAAGTTATTC
Found at i:30150363 original size:21 final size:21
Alignment explanation
Indices: 30150339--30150378 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
30150329 ACATTTTCTA
30150339 AAGTTAAAA-GTCAAAACTATT
1 AAGTTAAAAGGT-AAAACTATT
30150360 AAGTTAAAAGGTAAAACTA
1 AAGTTAAAAGGTAAAACTA
30150379 CGTTGTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.25
Consensus pattern (21 bp):
AAGTTAAAAGGTAAAACTATT
Found at i:30151095 original size:22 final size:22
Alignment explanation
Indices: 30151070--30151128 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 22
30151060 TCTCTTCAGA
30151070 GTTAAGGTTTTCATTTTTTAAG
1 GTTAAGGTTTTCATTTTTTAAG
* * * *
30151092 GTTAGGGTTAATGATTTTTTAGG
1 GTTAAGGTT-TTCATTTTTTAAG
*
30151115 GTTTAGGATTTTCA
1 GTTAAGG-TTTTCA
30151129 ACTGAAATGG
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
22 8 0.30
23 17 0.63
24 2 0.07
ACGTcount: A:0.22, C:0.03, G:0.24, T:0.51
Consensus pattern (22 bp):
GTTAAGGTTTTCATTTTTTAAG
Found at i:30151124 original size:17 final size:17
Alignment explanation
Indices: 30151093--30151126 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30151083 TTTTTTAAGG
*
30151093 TTAGGGTTAATGATTTT
1 TTAGGGTTAAGGATTTT
*
30151110 TTAGGGTTTAGGATTTT
1 TTAGGGTTAAGGATTTT
30151127 CAACTGAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (17 bp):
TTAGGGTTAAGGATTTT
Found at i:30151850 original size:44 final size:43
Alignment explanation
Indices: 30151801--30151963 Score: 200
Period size: 43 Copynumber: 3.7 Consensus size: 43
30151791 CCGACATATA
*
30151801 TGTGGATGAAGCCACCAAATTCGCAAACAAGCTGTCATGTAGAT
1 TGTGGAT-AAGCCACCAAATTCGCAAACAAGCTGTCATGTAGGT
* * * * **
30151845 TGTGGATAAACCACCAAATTCGCATACAAGTTGCCATACAGGT
1 TGTGGATAAGCCACCAAATTCGCAAACAAGCTGTCATGTAGGT
* *
30151888 TGTGGATAAGCCACCAAATTTGCAAACAAGCTGTCGTGTAGGT
1 TGTGGATAAGCCACCAAATTCGCAAACAAGCTGTCATGTAGGT
* * *
30151931 TGTGGACAAAGCCACCAAATTTGCAGACAAGCT
1 TGTGGA-TAAGCCACCAAATTCGCAAACAAGCT
30151964 TCCAAATCTT
Statistics
Matches: 101, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 70 0.69
44 31 0.31
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (43 bp):
TGTGGATAAGCCACCAAATTCGCAAACAAGCTGTCATGTAGGT
Found at i:30156689 original size:17 final size:17
Alignment explanation
Indices: 30156650--30156698 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
30156640 ATATATATGG
**
30156650 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* *
30156667 AGATGCAGTGACAATAA
1 AAATGCAATGACAATAA
*
30156684 AAATGCAAGGACAAT
1 AAATGCAATGACAAT
30156699 TATACTACAG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.18
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:30167374 original size:20 final size:20
Alignment explanation
Indices: 30167349--30167392 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
30167339 GCAAACATTT
30167349 TTTTCTTCTTT-TC-TTTTCTC
1 TTTTCTT-TTTCTCATTTTC-C
30167369 TTTTCTTTTTCTCATTTTCC
1 TTTTCTTTTTCTCATTTTCC
30167389 TTTT
1 TTTT
30167393 TCAAGTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.14
20 14 0.64
21 5 0.23
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTCTTTTTCTCATTTTCC
Found at i:30167393 original size:15 final size:13
Alignment explanation
Indices: 30167348--30167394 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
30167338 AGCAAACATT
30167348 TTTTTCTTCTTTTC
1 TTTTTC-TCTTTTC
30167362 -TTTTCTCTTTTC
1 TTTTTCTCTTTTC
30167374 TTTTTCTCATTTTCC
1 TTTTTCTC-TTTT-C
30167389 TTTTTC
1 TTTTTC
30167395 AAGTGATTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.23
13 12 0.40
14 4 0.13
15 7 0.23
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTCTCTTTTC
Found at i:30194806 original size:28 final size:28
Alignment explanation
Indices: 30194760--30194813 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
30194750 GCTATTTTAA
*
30194760 AATATTTGCAGAAAAGACAACTAATTTC
1 AATATTTACAGAAAAGACAACTAATTTC
*
30194788 AATATTTACA-AAAATGACATCTAATT
1 AATATTTACAGAAAA-GACAACTAATT
30194814 ATTAAAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (28 bp):
AATATTTACAGAAAAGACAACTAATTTC
Found at i:30202527 original size:20 final size:20
Alignment explanation
Indices: 30202502--30202541 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
30202492 ATATTCCTTA
*
30202502 ACACTAAGCACTCTCAAATC
1 ACACTAAACACTCTCAAATC
*
30202522 ACACTAAACTCTCTCAAATC
1 ACACTAAACACTCTCAAATC
30202542 CCTTCGTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.35, G:0.03, T:0.23
Consensus pattern (20 bp):
ACACTAAACACTCTCAAATC
Done.