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 112 of 143
Found at i:34179200 original size:117 final size:116
Alignment explanation
Indices: 34178993--34179279 Score: 373
Period size: 117 Copynumber: 2.4 Consensus size: 116
34178983 TCCAGCAGCA
* * * *
34178993 GCAGCAGCCATGAGGAGGGACTGTTGATGCGCTAGCAAAGCTAGTTGTTGTTGTTGAGTTGGTAG
1 GCAGCAGCCATGAGAAGGGACTGTTGCTGAGCTAGC-AAGCTAGTTGTTGTTGTTGAGTGGGTAG
*** * * *
34179058 GCTTGTGGTGGTTGATGGAGGCTGTTGA-CTGTTTCCAGGAGCAGCTTTAGCT
65 GCTTGTGGCCATTGATGGAGACTGTTGAGC-ATTTCCAGGAGCAGATTTAGCT
* * *
34179110 GCAGCAGCCATAAGAAGGGACTGTTGCTGTGCTAACATAGCTAGTTGTTGTTGTTGAGTGGGTA-
1 GCAGCAGCCATGAGAAGGGACTGTTGCTGAGCTAGCA-AGCTAGTTGTTGTTGTTGAGTGGGTAG
*
34179174 TCATTGT-GCCATTGGATGGAGACTGTTGAGCATTTCCAGGAGCAGATTTAGCT
65 GC-TTGTGGCCATT-GATGGAGACTGTTGAGCATTTCCAGGAGCAGATTTAGCT
34179227 GCAGCAGCCATGAGAAGGGACTGTTGCTGAGCTAGCGAAGCTAGTTGTTGTTG
1 GCAGCAGCCATGAGAAGGGACTGTTGCTGAGCTAGC-AAGCTAGTTGTTGTTG
34179280 ATGCATTGCA
Statistics
Matches: 149, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
116 5 0.03
117 142 0.95
118 2 0.01
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.30
Consensus pattern (116 bp):
GCAGCAGCCATGAGAAGGGACTGTTGCTGAGCTAGCAAGCTAGTTGTTGTTGTTGAGTGGGTAGG
CTTGTGGCCATTGATGGAGACTGTTGAGCATTTCCAGGAGCAGATTTAGCT
Found at i:34181821 original size:18 final size:18
Alignment explanation
Indices: 34181798--34181832 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
34181788 TGTATATAAT
34181798 ATATGCATATACATACAC
1 ATATGCATATACATACAC
34181816 ATATGCATATACATACA
1 ATATGCATATACATACA
34181833 AAGAATGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.29
Consensus pattern (18 bp):
ATATGCATATACATACAC
Found at i:34182517 original size:4 final size:4
Alignment explanation
Indices: 34182508--34182532 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
34182498 TATGGCGCGG
34182508 GCGT GCGT GCGT GCGT GCGT GCGT G
1 GCGT GCGT GCGT GCGT GCGT GCGT G
34182533 AGAGAGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.52, T:0.24
Consensus pattern (4 bp):
GCGT
Found at i:34184446 original size:16 final size:16
Alignment explanation
Indices: 34184427--34184457 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34184417 TTAAAAAATA
34184427 ATATAAAATTTATAAT
1 ATATAAAATTTATAAT
*
34184443 ATATAACATTTATAA
1 ATATAAAATTTATAA
34184458 ATTGTTCAAA
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:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAAAATTTATAAT
Found at i:34185205 original size:24 final size:25
Alignment explanation
Indices: 34185161--34185207 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
34185151 GAATGATAAT
34185161 TTTTAAAAAGAGTTCCCTAAATTCG
1 TTTTAAAAAGAGTTCCCTAAATTCG
*
34185186 TTTTGAAAAGA-TTCCCTAAATT
1 TTTTAAAAAGAGTTCCCTAAATT
34185208 TAAATGATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (25 bp):
TTTTAAAAAGAGTTCCCTAAATTCG
Found at i:34198186 original size:16 final size:15
Alignment explanation
Indices: 34198167--34198244 Score: 70
Period size: 15 Copynumber: 5.1 Consensus size: 15
34198157 TTAAAAATTT
34198167 AAAATTAAAAAATACA
1 AAAATTAAAAAATA-A
*
34198183 AAAACT-AAAAATAA
1 AAAATTAAAAAATAA
34198197 CAAAATTAAAAAAATACA
1 -AAAATT-AAAAAATA-A
*
34198215 AAAACT-AAAAATAA
1 AAAATTAAAAAATAA
* *
34198229 TAAATTAAAATATAA
1 AAAATTAAAAAATAA
34198244 A
1 A
34198245 GACTAAATCC
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
14 6 0.12
15 26 0.52
16 5 0.10
17 12 0.24
18 1 0.02
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATTAAAAAATAA
Found at i:34198209 original size:17 final size:18
Alignment explanation
Indices: 34198173--34198231 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 18
34198163 ATTTAAAATT
34198173 AAAAAAT-ACAAAAACT-
1 AAAAAATAACAAAAACTA
*
34198189 -AAAAATAAC-AAAATTA
1 AAAAAATAACAAAAACTA
34198205 AAAAAAT-ACAAAAACTA
1 AAAAAATAACAAAAACTA
34198222 AAAATAATAA
1 AAAA-AATAA
34198232 ATTAAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 11 0.31
16 4 0.11
17 16 0.46
18 3 0.09
19 1 0.03
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAAATAACAAAAACTA
Found at i:34198214 original size:32 final size:31
Alignment explanation
Indices: 34198158--34198238 Score: 119
Period size: 32 Copynumber: 2.6 Consensus size: 31
34198148 TGGTGAAGAT
**
34198158 TAAAAATTTAAAATT-AAAAAATACAAAAAC
1 TAAAAATAAAAAATTAAAAAAATACAAAAAC
34198188 TAAAAATAACAAAATTAAAAAAATACAAAAAC
1 TAAAAATAA-AAAATTAAAAAAATACAAAAAC
*
34198220 TAAAAATAATAAATTAAAA
1 TAAAAATAAAAAATTAAAA
34198239 TATAAAGACT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 7 0.15
31 15 0.33
32 24 0.52
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (31 bp):
TAAAAATAAAAAATTAAAAAAATACAAAAAC
Found at i:34203751 original size:23 final size:23
Alignment explanation
Indices: 34203721--34203782 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
34203711 TTTATCTAAA
34203721 GAACGGAACGGAACGGGTTCACT
1 GAACGGAACGGAACGGGTTCACT
*
34203744 GAACGGAACGGAACGGGTTCAGT
1 GAACGGAACGGAACGGGTTCACT
*
34203767 GAATGGAACGGAACGG
1 GAACGGAACGGAACGG
34203783 AACGGAACGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.18, G:0.39, T:0.11
Consensus pattern (23 bp):
GAACGGAACGGAACGGGTTCACT
Found at i:34203775 original size:28 final size:28
Alignment explanation
Indices: 34203721--34204106 Score: 189
Period size: 28 Copynumber: 13.2 Consensus size: 28
34203711 TTTATCTAAA
*
34203721 GAACGGAACGGAACGGGTTCACTGAACG
1 GAACGGAACGGAACGGGTTCAGTGAACG
** * * *
34203749 GAACGGAACGGGTTC-AG-TGAATGGAACG
1 GAACGGAAC-GGAACGGGTTCAGT-GAACG
34203777 GAACGGAACGGAACGGGTTCAGTGAACG
1 GAACGGAACGGAACGGGTTCAGTGAACG
* * **
34203805 GAACGGAACGGGTTCAC-TGAAC-G-GAACG
1 GAACGGAAC-GG--AACGGGTTCAGTGAACG
*
34203833 GAACGGAACGGAACGGGTTCACTGAACG
1 GAACGGAACGGAACGGGTTCAGTGAACG
*
34203861 GAACGGAACGGAACGGGTTCACTGAACG
1 GAACGGAACGGAACGGGTTCAGTGAACG
* * ** * ** *
34203889 GAACGGGTTCACTGAACTGAACGGAACGGGTTCACT
1 GAAC-GG--AACGGAAC-G---GGTTC-AGTGAACG
* *
34203925 GAACTGAACGGAACGGAACGGGTTCACTGAACG
1 GAACGGAAC-G---G-AACGGGTTCAGTGAACG
*
34203958 GAACGGGTTCACTGAACGGAACGGGTTCACTGAACG
1 GAAC--G------GAACGGAACGGGTTCAGTGAACG
*
34203994 GAACGGAACGGAACGGGTTCACTGAACG
1 GAACGGAACGGAACGGGTTCAGTGAACG
*
34204022 GAACGGAACGGAACGGGTTC-----ACT
1 GAACGGAACGGAACGGGTTCAGTGAACG
* * * *
34204045 GAACTGAACGGAATGGGTTCACTGAACT
1 GAACGGAACGGAACGGGTTCAGTGAACG
* *
34204073 GAACGGAACGGAACGGGTTAACTGAACG
1 GAACGGAACGGAACGGGTTCAGTGAACG
34204101 GAACGG
1 GAACGG
34204107 GTTCACTGAA
Statistics
Matches: 276, Mismatches: 46, Indels: 72
0.70 0.12 0.18
Matches are distributed among these distances:
23 20 0.07
25 2 0.01
26 2 0.01
27 8 0.03
28 166 0.60
29 11 0.04
30 2 0.01
31 8 0.03
32 1 0.00
33 9 0.03
34 4 0.01
35 4 0.01
36 28 0.10
37 3 0.01
38 3 0.01
40 1 0.00
41 4 0.01
ACGTcount: A:0.32, C:0.20, G:0.35, T:0.13
Consensus pattern (28 bp):
GAACGGAACGGAACGGGTTCAGTGAACG
Found at i:34203781 original size:33 final size:33
Alignment explanation
Indices: 34203744--34203815 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
34203734 CGGGTTCACT
*
34203744 GAACGGAACGGAACGGGTTCAGTGAATGGAACG
1 GAACGGAACGGAACGGGTTCAGTGAACGGAACG
34203777 GAACGGAACGGAACGGGTTCAGTGAACGGAACG
1 GAACGGAACGGAACGGGTTCAGTGAACGGAACG
34203810 GAACGG
1 GAACGG
34203816 GTTCACTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.33, C:0.17, G:0.40, T:0.10
Consensus pattern (33 bp):
GAACGGAACGGAACGGGTTCAGTGAACGGAACG
Found at i:34203803 original size:23 final size:23
Alignment explanation
Indices: 34203777--34204157 Score: 205
Period size: 23 Copynumber: 16.7 Consensus size: 23
34203767 GAATGGAACG
*
34203777 GAACGGAACGGAACGGGTTCAGT
1 GAACGGAACGGAACGGGTTCACT
34203800 GAACGGAACGGAACGGGTTCACT
1 GAACGGAACGGAACGGGTTCACT
* *
34203823 GAACGGAACGGAAC-GG--AACG
1 GAACGGAACGGAACGGGTTCACT
* * * *
34203843 GAACGGGTTCACTGAAC-GG--AACG
1 GAAC-GG--AACGGAACGGGTTCACT
34203866 GAAC-G---G-AACGGGTTCACT
1 GAACGGAACGGAACGGGTTCACT
34203884 G-A----ACGGAACGGGTTCACT
1 GAACGGAACGGAACGGGTTCACT
*
34203902 GAACTGAACGGAACGGGTTCACTGAACT
1 GAACGGAACGGAACGGGTT--C---ACT
34203930 GAACGGAACGGAACGGGTTCACT
1 GAACGGAACGGAACGGGTTCACT
34203953 -----GAACGGAACGGGTTCACT
1 GAACGGAACGGAACGGGTTCACT
** ** ** *
34203971 GAACGGAACGGGTTC-ACTGAACG
1 GAACGGAAC-GGAACGGGTTCACT
34203994 GAACGGAACGGAACGGGTTCACT
1 GAACGGAACGGAACGGGTTCACT
34204017 GAACGGAACGGAACGGAACGGGTTCACT
1 -----GAACGGAACGGAACGGGTTCACT
* *
34204045 GAACTGAACGGAATGGGTTCACT
1 GAACGGAACGGAACGGGTTCACT
* ** **
34204068 GAACTGAACGGAAC-GGAACGGGT
1 GAACGGAACGGAACGGGTTC-ACT
* *
34204091 TAACTGAACGGAACGGGTTCACT
1 GAACGGAACGGAACGGGTTCACT
34204114 GAACGGAACGGAACGGAACGGGTTCACT
1 -----GAACGGAACGGAACGGGTTCACT
34204142 GAACGGAACGGAACGG
1 GAACGGAACGGAACGG
34204158 AACGGGTTCA
Statistics
Matches: 283, Mismatches: 37, Indels: 76
0.71 0.09 0.19
Matches are distributed among these distances:
15 3 0.01
16 2 0.01
17 2 0.01
18 34 0.12
19 1 0.00
20 6 0.02
21 3 0.01
22 8 0.03
23 151 0.53
24 6 0.02
25 1 0.00
26 1 0.00
28 65 0.23
ACGTcount: A:0.31, C:0.21, G:0.35, T:0.13
Consensus pattern (23 bp):
GAACGGAACGGAACGGGTTCACT
Found at i:34203827 original size:46 final size:46
Alignment explanation
Indices: 34203777--34204157 Score: 173
Period size: 51 Copynumber: 8.3 Consensus size: 46
34203767 GAATGGAACG
34203777 GAACGGAACGGAACGGGTTCAGTGAACGGAACGGAACGGGTTCACT
1 GAACGGAACGGAACGGGTTCAGTGAACGGAACGGAACGGGTTCACT
** * * * *
34203823 GAACGGAACGGAAC-GGAAC-G-GAACGGGTTCACTGAAC-GG--AACG
1 GAACGGAACGGAACGGGTTCAGTGAAC-GG--AACGGAACGGGTTCACT
*
34203866 GAACGG-A---A-CGGGTTC-----ACTGAACGGAACGGGTTCACT
1 GAACGGAACGGAACGGGTTCAGTGAACGGAACGGAACGGGTTCACT
*
34203902 GAACTGAACGGAACGGGTTCACTGAACTGAACGGAACGGAACGGGTTCACT
1 GAACGGAACGGAACGGGTTCA--G---TGAACGGAACGGAACGGGTTCACT
* ** ** ** *
34203953 -----GAACGGAACGGGTTCACTGAACGGAACGGGTTC-ACTGAACG
1 GAACGGAACGGAACGGGTTCAGTGAACGGAAC-GGAACGGGTTCACT
*
34203994 GAACGGAACGGAACGGGTTCACTGAACGGAACGGAACGGAACGGGTTCACT
1 GAACGGAACGGAACGGGTTCA--G---TGAACGGAACGGAACGGGTTCACT
* * *
34204045 GAACTGAACGGAATGGGTTCACTGAACTGAACGGAACGGAACGGGTTAACT
1 GAACGGAACGGAACGGGTTCA--G---TGAACGGAACGGAACGGGTTCACT
* * **
34204096 GAACGGAACGGGTTCAC-TGAAC-G-GAACGGAACGGAACGGGTTCACT
1 GAACGGAAC-GG--AACGGGTTCAGTGAACGGAACGGAACGGGTTCACT
34204142 GAACGGAACGGAACGG
1 GAACGGAACGGAACGG
34204158 AACGGGTTCA
Statistics
Matches: 252, Mismatches: 45, Indels: 78
0.67 0.12 0.21
Matches are distributed among these distances:
33 6 0.02
34 2 0.01
35 1 0.00
36 9 0.04
37 1 0.00
38 1 0.00
39 4 0.02
40 1 0.00
41 20 0.08
42 4 0.02
43 14 0.06
44 3 0.01
45 7 0.03
46 83 0.33
50 4 0.02
51 87 0.35
52 2 0.01
53 2 0.01
54 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.35, T:0.13
Consensus pattern (46 bp):
GAACGGAACGGAACGGGTTCAGTGAACGGAACGGAACGGGTTCACT
Found at i:34203894 original size:5 final size:5
Alignment explanation
Indices: 34203721--34203876 Score: 78
Period size: 5 Copynumber: 28.2 Consensus size: 5
34203711 TTTATCTAAA
* * ** *
34203721 GAACG GAACG GAACGG GTTCACT GAACG GAACG GAACGG GTTCAG TGAATG
1 GAACG GAACG GAAC-G G--AACG GAACG GAACG GAAC-G GAAC-G -GAACG
** * *
34203772 GAACG GAACG GAACG GAACGG GTTCAG TGAACG GAACG GAACGG GTTCACT
1 GAACG GAACG GAACG GAAC-G GAAC-G -GAACG GAACG GAAC-G G--AACG
* *
34203823 GAACG GAACG GAACG GAACG GAACGG GTTCACT GAACG GAACG GAACG
1 GAACG GAACG GAACG GAACG GAAC-G G--AACG GAACG GAACG GAACG
34203871 GAACG G
1 GAACG G
34203877 GTTCACTGAA
Statistics
Matches: 114, Mismatches: 24, Indels: 26
0.70 0.15 0.16
Matches are distributed among these distances:
5 86 0.75
6 16 0.14
7 6 0.05
8 6 0.05
ACGTcount: A:0.33, C:0.19, G:0.38, T:0.10
Consensus pattern (5 bp):
GAACG
Found at i:34203997 original size:5 final size:5
Alignment explanation
Indices: 34203989--34204162 Score: 60
Period size: 5 Copynumber: 31.2 Consensus size: 5
34203979 CGGGTTCACT
* *
34203989 GAACG GAACG GAACG GAACGG GTTCACT GAACG GAACG GAACG GAACGG
1 GAACG GAACG GAACG GAAC-G G--AACG GAACG GAACG GAACG GAAC-G
* * * * * * *
34204038 GTTCACT GAACT GAACG GAATGG GTTCACT GAACT GAACG GAACG GAACGG
1 G--AACG GAACG GAACG GAA-CG G--AACG GAACG GAACG GAACG GAAC-G
* * * * *
34204089 GTTAACT GAACG GAACGG GTTCACT GAACG GAACG GAACG GAACGG GTTCACT
1 G--AACG GAACG GAAC-G G--AACG GAACG GAACG GAACG GAAC-G G--AACG
34204142 GAACG GAACG GAACG GAACG G
1 GAACG GAACG GAACG GAACG G
34204163 GTTCACTGCA
Statistics
Matches: 127, Mismatches: 24, Indels: 36
0.68 0.13 0.19
Matches are distributed among these distances:
5 97 0.76
6 12 0.09
7 6 0.05
8 12 0.09
ACGTcount: A:0.33, C:0.20, G:0.35, T:0.12
Consensus pattern (5 bp):
GAACG
Found at i:34204127 original size:28 final size:28
Alignment explanation
Indices: 34204096--34204170 Score: 150
Period size: 28 Copynumber: 2.7 Consensus size: 28
34204086 CGGGTTAACT
34204096 GAACGGAACGGGTTCACTGAACGGAACG
1 GAACGGAACGGGTTCACTGAACGGAACG
34204124 GAACGGAACGGGTTCACTGAACGGAACG
1 GAACGGAACGGGTTCACTGAACGGAACG
34204152 GAACGGAACGGGTTCACTG
1 GAACGGAACGGGTTCACTG
34204171 CACATCCTCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.31, C:0.21, G:0.36, T:0.12
Consensus pattern (28 bp):
GAACGGAACGGGTTCACTGAACGGAACG
Found at i:34204602 original size:16 final size:17
Alignment explanation
Indices: 34204581--34204614 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
34204571 GGGTATATTC
*
34204581 AATTTTCTTTCC-TCAA
1 AATTTTCATTCCTTCAA
34204597 AATTTTCATTCCTTCAA
1 AATTTTCATTCCTTCAA
34204614 A
1 A
34204615 GATCATATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTTCATTCCTTCAA
Found at i:34208555 original size:18 final size:18
Alignment explanation
Indices: 34208525--34208566 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
34208515 AATAAACGAA
34208525 TAAAAATGATATA-ATAT
1 TAAAAATGATATAGATAT
* *
34208542 TAAAAATGGTTATAGCTAT
1 TAAAAAT-GATATAGATAT
34208561 TAAAAA
1 TAAAAA
34208567 ATTTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 7 0.33
18 5 0.24
19 9 0.43
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (18 bp):
TAAAAATGATATAGATAT
Found at i:34208583 original size:18 final size:18
Alignment explanation
Indices: 34208561--34208602 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
34208551 TTATAGCTAT
34208561 TAAAAAATTTT-AAATTA
1 TAAAAAATTTTAAAATTA
*
34208578 T-AAAAATTTTCAAAATTT
1 TAAAAAATTTT-AAAATTA
34208596 TAAAAAA
1 TAAAAAA
34208603 ATATGAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.43
17 1 0.05
18 6 0.29
19 5 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAAATTTTAAAATTA
Found at i:34213806 original size:2 final size:2
Alignment explanation
Indices: 34213799--34213829 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
34213789 GTGACATTTC
*
34213799 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34213830 AACGATAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:34214909 original size:2 final size:2
Alignment explanation
Indices: 34214902--34214971 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
34214892 TTTATATTAA
34214902 AT AT AT 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
34214944 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
34214972 TATTTTTTGT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34217547 original size:18 final size:21
Alignment explanation
Indices: 34217524--34217567 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 21
34217514 AGAATTATGA
*
34217524 AAAAAAT-TATTTAAA-AT-T
1 AAAAAATAAATTTAAATATAT
34217542 AAAAAATAAATTTAAATATAT
1 AAAAAATAAATTTAAATATAT
34217563 AAAAA
1 AAAAA
34217568 TTTCAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 2 0.09
21 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAAATAAATTTAAATATAT
Found at i:34217567 original size:22 final size:22
Alignment explanation
Indices: 34217494--34217567 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
34217484 CATAAAAACT
** *
34217494 ATATATATTAAAATAAATCTAGA
1 ATATATAAAAAAATAAATTTA-A
*
34217517 AT-TATGAAAAAAAT-TATTTAA
1 ATATAT-AAAAAAATAAATTTAA
34217538 A-AT-T-AAAAAATAAATTTAA
1 ATATATAAAAAAATAAATTTAA
34217557 ATATATAAAAA
1 ATATATAAAAA
34217568 TTTCAAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 13
0.69 0.09 0.22
Matches are distributed among these distances:
18 7 0.17
19 7 0.17
20 3 0.08
21 4 0.10
22 11 0.28
23 8 0.20
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (22 bp):
ATATATAAAAAAATAAATTTAA
Found at i:34217944 original size:5 final size:6
Alignment explanation
Indices: 34217928--34217953 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
34217918 AATAAATTAT
34217928 TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA
34217954 CTAAAAAACT
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:34221276 original size:18 final size:18
Alignment explanation
Indices: 34221255--34221297 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
34221245 TCTGGTGAGA
34221255 ATGATGAGGAGTTATCAG
1 ATGATGAGGAGTTATCAG
** * *
34221273 ATGATGCTGAGTTTTCGG
1 ATGATGAGGAGTTATCAG
34221291 ATGATGA
1 ATGATGA
34221298 AAAGGAGGCC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.07, G:0.33, T:0.33
Consensus pattern (18 bp):
ATGATGAGGAGTTATCAG
Found at i:34227338 original size:28 final size:28
Alignment explanation
Indices: 34227295--34227355 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
34227285 CTTGAACAAT
* *
34227295 AGATAGCCACAAAGGCGTCTATAAGCAA
1 AGATAGCCACAAAGGCGTCCATAAGAAA
* * *
34227323 AGATGGCCACATAGGCTTCCATAAGAAA
1 AGATAGCCACAAAGGCGTCCATAAGAAA
34227351 AGATA
1 AGATA
34227356 ATCATACAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (28 bp):
AGATAGCCACAAAGGCGTCCATAAGAAA
Found at i:34229277 original size:23 final size:23
Alignment explanation
Indices: 34229250--34229415 Score: 134
Period size: 23 Copynumber: 7.5 Consensus size: 23
34229240 AGGAACACTA
34229250 GTGTGCTCTCTGATTAGCACTGT
1 GTGTGCTCTCTGATTAGCACTGT
* *
34229273 GTGTGCTCTCCGTTTAGCAC-GT
1 GTGTGCTCTCTGATTAGCACTGT
* * *
34229295 CTCGTGCTCTCCGTTTAGCACT-T
1 GT-GTGCTCTCTGATTAGCACTGT
* *
34229318 CGCGTGCTCTCTGATTAGCACTTT
1 -GTGTGCTCTCTGATTAGCACTGT
*
34229342 GTGTGCTCTTTGATTAGCACT-T
1 GTGTGCTCTCTGATTAGCACTGT
* * *
34229364 -TGTG-----TGCTTAGTACTTT
1 GTGTGCTCTCTGATTAGCACTGT
* *
34229381 GTGTACTCTCTGTTTAGCACTGT
1 GTGTGCTCTCTGATTAGCACTGT
34229404 GTGTGCTCTCTG
1 GTGTGCTCTCTG
34229416 TTGCCCAACA
Statistics
Matches: 116, Mismatches: 16, Indels: 22
0.75 0.10 0.14
Matches are distributed among these distances:
16 9 0.08
17 1 0.01
18 3 0.03
21 4 0.03
22 4 0.03
23 94 0.81
24 1 0.01
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.42
Consensus pattern (23 bp):
GTGTGCTCTCTGATTAGCACTGT
Found at i:34229398 original size:39 final size:39
Alignment explanation
Indices: 34229332--34229410 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
34229322 TGCTCTCTGA
* * *
34229332 TTAGCACTTTGTGTGCTCTTTGATTAGCACTTTGTGTGC
1 TTAGCACTTTGTGTACTCTCTGATTAGCACTGTGTGTGC
* *
34229371 TTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGC
1 TTAGCACTTTGTGTACTCTCTGATTAGCACTGTGTGTGC
34229410 T
1 T
34229411 CTCTGTTGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.13, C:0.18, G:0.23, T:0.47
Consensus pattern (39 bp):
TTAGCACTTTGTGTACTCTCTGATTAGCACTGTGTGTGC
Found at i:34230654 original size:29 final size:29
Alignment explanation
Indices: 34230615--34230717 Score: 111
Period size: 29 Copynumber: 3.6 Consensus size: 29
34230605 ACACTCTCAC
*
34230615 ATAACAAAATCAACCACAAAAGCTTACAT
1 ATAACAGAATCAACCACAAAAGCTTACAT
*
34230644 ATAACAGAATCAACCACAAAGGCTCT-CAT
1 ATAACAGAATCAACCACAAAAGCT-TACAT
* * *
34230673 ATAATAGAATCATCCACAAACA-CTCACAT
1 ATAACAGAATCAACCACAAA-AGCTTACAT
* *
34230702 ATAATAGATTCAACCA
1 ATAACAGAATCAACCA
34230718 TAAAGGCGCT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
29 62 0.98
30 1 0.02
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (29 bp):
ATAACAGAATCAACCACAAAAGCTTACAT
Found at i:34230702 original size:58 final size:58
Alignment explanation
Indices: 34230608--34230783 Score: 160
Period size: 58 Copynumber: 3.0 Consensus size: 58
34230598 GGGTGTTACA
* *
34230608 CTCTCACATAACAAAATCAACCACAAAAGCTTACATATAACAGAATCAACCACAAAGG
1 CTCTCAAATAACAAAATCAACCACAAAAGCTCACATATAACAGAATCAACCACAAAGG
* * * * * * *
34230666 CTCTCATATAATAGAATCATCCACAAACA-CTCACATATAATAGATTCAACCATAAAGG
1 CTCTCAAATAACAAAATCAACCACAAA-AGCTCACATATAACAGAATCAACCACAAAGG
* * ** * * *
34230724 CGCTCAAATAACAAATTCAGTCACAAAGTATCTCAC--ATAACAAAATCAGCCACAAAGG
1 CTCTCAAATAACAAAATCAACCACAAA--AGCTCACATATAACAGAATCAACCACAAAGG
34230782 CT
1 CT
34230784 TTACTTTTAG
Statistics
Matches: 93, Mismatches: 22, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
58 86 0.92
59 2 0.02
60 5 0.05
ACGTcount: A:0.47, C:0.26, G:0.08, T:0.19
Consensus pattern (58 bp):
CTCTCAAATAACAAAATCAACCACAAAAGCTCACATATAACAGAATCAACCACAAAGG
Found at i:34230734 original size:29 final size:29
Alignment explanation
Indices: 34230622--34230734 Score: 88
Period size: 29 Copynumber: 3.9 Consensus size: 29
34230612 CACATAACAA
* * * *
34230622 AATCAACCACAAAAGC-TTACATATAACAG
1 AATCAACCACAAAGGCACT-CAAATAATAG
* *
34230651 AATCAACCACAAAGGCTCTCATATAATAG
1 AATCAACCACAAAGGCACTCAAATAATAG
*
34230680 AATCATCCACAAA--CACTCACATATAATAG
1 AATCAACCACAAAGGCACTCA-A-ATAATAG
* * *
34230709 ATTCAACCATAAAGGCGCTCAAATAA
1 AATCAACCACAAAGGCACTCAAATAA
34230735 CAAATTCAGT
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
27 5 0.07
29 57 0.83
30 2 0.03
31 5 0.07
ACGTcount: A:0.48, C:0.25, G:0.08, T:0.19
Consensus pattern (29 bp):
AATCAACCACAAAGGCACTCAAATAATAG
Found at i:34230751 original size:29 final size:29
Alignment explanation
Indices: 34230610--34230782 Score: 82
Period size: 29 Copynumber: 6.0 Consensus size: 29
34230600 GTGTTACACT
* * *
34230610 CTCACATAACAAAATCAACCACAAAAGC-
1 CTCAAATAACAAAATCAGCCACAAAGGCG
* * * * *
34230638 TTACATATAACAGAATCAACCACAAAGGCT
1 CT-CAAATAACAAAATCAGCCACAAAGGCG
* * * * *
34230668 CTCATATAATAGAATCATCCACAAA--CA
1 CTCAAATAACAAAATCAGCCACAAAGGCG
* * * * *
34230695 CTCACATATAATAGATTCAACCATAAAGGCG
1 CTCA-A-ATAACAAAATCAGCCACAAAGGCG
* * ***
34230726 CTCAAATAACAAATTCAGTCACAAAGTAT
1 CTCAAATAACAAAATCAGCCACAAAGGCG
*
34230755 CTCACATAACAAAATCAGCCACAAAGGC
1 CTCAAATAACAAAATCAGCCACAAAGGC
34230783 TTTACTTTTA
Statistics
Matches: 113, Mismatches: 26, Indels: 11
0.75 0.17 0.07
Matches are distributed among these distances:
27 5 0.04
28 1 0.01
29 100 0.88
30 2 0.02
31 5 0.04
ACGTcount: A:0.47, C:0.26, G:0.08, T:0.18
Consensus pattern (29 bp):
CTCAAATAACAAAATCAGCCACAAAGGCG
Found at i:34235063 original size:58 final size:57
Alignment explanation
Indices: 34234969--34235092 Score: 133
Period size: 58 Copynumber: 2.2 Consensus size: 57
34234959 TAGGGCCTAG
* * * * * *
34234969 ACTTTTTTTTTCAAGTTAGTCCTTAAATTTAGCAATTATTTTCACATTAGGACATGA
1 ACTTTTTTTATCAAGTTACTCCTTAAACTTAACAATTATTCTCACATTAGGACATAA
* * **
34235026 ACTTTTTTTATCTAAGTTACT-CTCTAAACTTAACAATTGTTCTCACATTGGGATTTAA
1 ACTTTTTTTATC-AAGTTACTCCT-TAAACTTAACAATTATTCTCACATTAGGACATAA
34235084 ACTTTTTTT
1 ACTTTTTTT
34235093 TGGGTTCAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
57 13 0.24
58 42 0.76
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (57 bp):
ACTTTTTTTATCAAGTTACTCCTTAAACTTAACAATTATTCTCACATTAGGACATAA
Found at i:34236440 original size:59 final size:59
Alignment explanation
Indices: 34236377--34236806 Score: 414
Period size: 59 Copynumber: 7.4 Consensus size: 59
34236367 TGGATGCCAG
* * ** *
34236377 GGGGTGAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAATTAAATTTTAGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTA
* * * *
34236436 GGGGTAAAATGATAA-TTTTGGTGAAATCGAGGTTAAAAACTAG-ATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAA-TGGAATTTTGGAAAGTTTA
* *
34236494 AGGGTAAAATGGTAATTTTTGGTGAAATC-AGGGT--AAAATGGGATTTTGGAAAGTTT-
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGA-GGTCAAAAATGGAATTTTGGAAAGTTTA
* * * * * * **
34236550 GAGGGTAAAACGGTAATTTTGGGTGAAGTCGGGGTCAAAAATGGGATTTTGAAAAGTTCG
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTA
* * * *
34236610 GGGGTAAAATAGTAA-TTTTGGATGAAGTCGAGGTCAAAAATGGAATTTTGGGAAGTTCA
1 GGGGTAAAATGGTAATTTTTGG-TGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTA
* * ** * * *
34236669 AGGGTAAAATAGTAA-TTTTGGAAAAAT-TAGGGTTAAAAATGGAATTTTAGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGA-GGTCAAAAATGGAATTTTGGAAAGTTTA
** * *
34236727 GGGGTAAAATGGTAATTTTTGGAAAAATAGGGGTCAAAAATGGAATTTTGGAAAGTTT-
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTA
34236785 GGGGTCAAAATGG-AAGTTTTTG
1 GGGGT-AAAATGGTAA-TTTTTG
34236807 AAGCTTTAAG
Statistics
Matches: 314, Mismatches: 42, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
56 2 0.01
57 46 0.15
58 101 0.32
59 164 0.52
60 1 0.00
ACGTcount: A:0.37, C:0.03, G:0.29, T:0.31
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTA
Found at i:34236584 original size:29 final size:28
Alignment explanation
Indices: 34236436--34236689 Score: 119
Period size: 29 Copynumber: 8.8 Consensus size: 28
34236426 AGAAAGTTTA
* *
34236436 GGGGTAAAATGATAATTTTGGTGAAATC
1 GGGGTAAAATGGTAATTTTGGTGAAGTC
* ** *
34236464 GAGGTTAAAA-ACTAGATTTTGG-AAAGTTC
1 G-GGGTAAAATGGTA-ATTTTGGTGAAG-TC
* *
34236493 AAGGGTAAAATGGTAATTTTTGGTGAAATC
1 -GGGGTAAAATGGTAA-TTTTGGTGAAGTC
* * * *
34236523 AGGGTAAAATGG-GATTTTGG-AAAGTTT
1 GGGGTAAAATGGTAATTTTGGTGAAG-TC
*
34236550 GAGGGTAAAACGGTAATTTTGGGTGAAGTC
1 G-GGGTAAAATGGTAATTTT-GGTGAAGTC
* **
34236580 GGGGTCAAAAATGG-GATTTT-GAAAAGTTC
1 GGGGT--AAAATGGTAATTTTGGTGAAG-TC
*
34236609 GGGGGTAAAATAGTAATTTTGGATGAAGTC
1 -GGGGTAAAATGGTAATTTTGG-TGAAGTC
*
34236639 GAGGTCAAAAATGG-AATTTTGG-GAAGTTC
1 GGGGT--AAAATGGTAATTTTGGTGAAG-TC
* *
34236668 AAGGGTAAAATAGTAATTTTGG
1 -GGGGTAAAATGGTAATTTTGG
34236690 AAAAATTAGG
Statistics
Matches: 169, Mismatches: 33, Indels: 47
0.68 0.13 0.19
Matches are distributed among these distances:
26 2 0.01
27 7 0.04
28 36 0.21
29 66 0.39
30 38 0.22
31 20 0.12
ACGTcount: A:0.35, C:0.04, G:0.30, T:0.30
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTGGTGAAGTC
Found at i:34236600 original size:30 final size:30
Alignment explanation
Indices: 34236564--34236661 Score: 87
Period size: 30 Copynumber: 3.3 Consensus size: 30
34236554 GTAAAACGGT
34236564 AATTTTGGGTGAAGTCGGGGTCAAAAATGG
1 AATTTTGGGTGAAGTCGGGGTCAAAAATGG
* ** *
34236594 GATTTT--GAAAAGTTCGGGGGT--AAAATAGT
1 AATTTTGGGTGAAG-TC-GGGGTCAAAAAT-GG
* *
34236623 AATTTTGGATGAAGTCGAGGTCAAAAATGG
1 AATTTTGGGTGAAGTCGGGGTCAAAAATGG
34236653 AATTTTGGG
1 AATTTTGGG
34236662 AAGTTCAAGG
Statistics
Matches: 50, Mismatches: 11, Indels: 14
0.67 0.15 0.19
Matches are distributed among these distances:
28 9 0.18
29 12 0.24
30 21 0.42
31 8 0.16
ACGTcount: A:0.33, C:0.05, G:0.33, T:0.30
Consensus pattern (30 bp):
AATTTTGGGTGAAGTCGGGGTCAAAAATGG
Found at i:34236788 original size:29 final size:27
Alignment explanation
Indices: 34236524--34236804 Score: 152
Period size: 29 Copynumber: 9.6 Consensus size: 27
34236514 GGTGAAATCA
*
34236524 GGGTAAAATGGGATTTTGGAAAGTTTG
1 GGGTAAAATGGAATTTTGGAAAGTTTG
* * *
34236551 AGGGTAAAACGGTAATTTTGGGTGAAG-TCG
1 -GGGTAAAATGG-AATTTT-GG-AAAGTTTG
* * *
34236581 GGGTCAAAAATGGGATTTTGAAAAGTTCGG
1 GGGT--AAAATGGAATTTTGGAAAGTT-TG
* *
34236611 GGGTAAAATAGTAATTTTGGATGAAG-TCG
1 GGGTAAAAT-GGAATTTTGGA--AAGTTTG
* * **
34236640 AGGTCAAAAATGGAATTTTGGGAAGTTCAA
1 GGGT--AAAATGGAATTTTGGAAAGTT-TG
* * *
34236670 GGGTAAAATAGTAATTTTGGAAAAATTAG
1 GGGTAAAAT-GGAATTTTGG-AAAGTTTG
* *
34236699 GGTTAAAAATGGAATTTTAGAAAGTTTAG
1 GGGT-AAAATGGAATTTTGGAAAGTTT-G
** *
34236728 GGGTAAAATGGTAATTTTTGGAAAAATAG
1 GGGTAAAATGG-AA-TTTTGGAAAGTTTG
34236757 GGGTCAAAAATGGAATTTTGGAAAGTTTG
1 GGGT--AAAATGGAATTTTGGAAAGTTTG
34236786 GGGTCAAAATGGAAGTTTT
1 GGGT-AAAATGGAA-TTTT
34236805 TGAAGCTTTA
Statistics
Matches: 193, Mismatches: 37, Indels: 45
0.70 0.13 0.16
Matches are distributed among these distances:
28 47 0.24
29 75 0.39
30 47 0.24
31 24 0.12
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.30
Consensus pattern (27 bp):
GGGTAAAATGGAATTTTGGAAAGTTTG
Found at i:34238604 original size:11 final size:11
Alignment explanation
Indices: 34238590--34238634 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
34238580 TAAATGTATT
34238590 TAAATTTAAAA
1 TAAATTTAAAA
34238601 TAAATTTAAAA
1 TAAATTTAAAA
* * *
34238612 TTAATTCAAAT
1 TAAATTTAAAA
*
34238623 TTAATTTAAAA
1 TAAATTTAAAA
34238634 T
1 T
34238635 TCAAGTTGGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:34238607 original size:17 final size:18
Alignment explanation
Indices: 34238587--34238634 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
34238577 TTTTAAATGT
34238587 ATTTAAATTTAAAAT-AA
1 ATTTAAATTTAAAATCAA
* *
34238604 ATTTAAAATT-AATTCAA
1 ATTTAAATTTAAAATCAA
34238621 ATTT-AATTTAAAAT
1 ATTTAAATTTAAAAT
34238635 TCAAGTTGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTAAATTTAAAATCAA
Found at i:34241347 original size:16 final size:17
Alignment explanation
Indices: 34241326--34241358 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
34241316 TTAGTTTTAT
34241326 TATATTTTTAAA-AAAA
1 TATATTTTTAAATAAAA
34241342 TATATTTTTAAATAAAA
1 TATATTTTTAAATAAAA
34241359 AATAATCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATATTTTTAAATAAAA
Found at i:34243473 original size:178 final size:176
Alignment explanation
Indices: 34243150--34243611 Score: 782
Period size: 178 Copynumber: 2.6 Consensus size: 176
34243140 TATGGATACC
* *
34243150 CGGGGGCAAAATGGTAATTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
* * *
34243215 AAAATGGTAATTTTTGGCGAAATCGGGGTTAAAAACGGAATTTTAAAAGATTCGGGGGTAAAATG
66 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGAGGGTAAAATG
* **
34243280 GTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
131 GTAATTTTCGGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATT
*
34243326 CGGGGGGTAAAATAGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGG
1 C-GGGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGG
34243391 GTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGAGGGTAAAA
64 GTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGAGGGTAAAA
34243456 TGGTAATTTTCGGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATT
129 TGGTAATTTTCGGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATT
**
34243504 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATTCGGGGG
1 CGGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGG
*
34243569 TAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGTAATTT
65 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTT
34243612 GGGAAAAGTT
Statistics
Matches: 270, Mismatches: 13, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
176 12 0.04
177 105 0.39
178 153 0.57
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (176 bp):
CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGAGGGTAAAATG
GTAATTTTCGGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATT
Found at i:34243628 original size:59 final size:59
Alignment explanation
Indices: 34243150--34243611 Score: 784
Period size: 59 Copynumber: 7.8 Consensus size: 59
34243140 TATGGATACC
* *
34243150 CGGGGGCAAAATGGTAA-TTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
34243208 CGGGGGTAAAATGGTAATTTTTGGCGAAATCGGGGTTAAAAACGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
34243267 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* *
34243326 CGGGGGGTAAAATAGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 C-GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
34243386 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
* * **
34243445 CGAGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
**
34243504 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAACAGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
*
34243563 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGTAATTT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTT
34243612 GGGAAAAGTT
Statistics
Matches: 383, Mismatches: 19, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
58 25 0.07
59 301 0.79
60 57 0.15
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATT
Found at i:34244060 original size:161 final size:162
Alignment explanation
Indices: 34243756--34244062 Score: 456
Period size: 161 Copynumber: 1.9 Consensus size: 162
34243746 AAATTTTGGA
*
34243756 CCAATTTTGTAATTAAATAAAAGTCGATTTAAGGATTAAATTAAAACAAATTAAAAATAAAAAGG
1 CCAATTTCGTAATTAAATAAAAGTCGATTTAAGGATTAAATTAAAACAAATTAAAAATAAAAAGG
**
34243821 ACTAAATGCAGAAATAACCCAAAAAATGACACGTGGCAACCTCTGGTGCAGTCAAAAAGTCAAAA
66 ACTAAATGCAGAAATAACCCAAAAAATGACACGTGGCAACCTCTGGCACAGTCAAAAAGTCAAAA
**
34243886 GACCAGTTTATAAACCTCGAAAAATTATGGGG
131 GACCAAATTATAAACCTCGAAAAATTATGGGG
* * *
34243918 CCAATTTCGTAATTAAA-ACAAAGTTGATTT-GGGATTAAATTAAAACAAATTAAAAATGAAAAG
1 CCAATTTCGTAATTAAATA-AAAGTCGATTTAAGGATTAAATTAAAACAAATTAAAAATAAAAAG
* * * * *
34243981 GACTAAATGCATAAATAATCCAATACATGACACGTGGCAACCTCTGGCACAGTCAAACAGTCAAA
65 GACTAAATGCAGAAATAACCCAAAAAATGACACGTGGCAACCTCTGGCACAGTCAAAAAGTCAAA
* *
34244046 GGACTAAATTATAAACC
130 AGACCAAATTATAAACC
34244063 AATTAAAATT
Statistics
Matches: 129, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
161 103 0.80
162 26 0.20
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (162 bp):
CCAATTTCGTAATTAAATAAAAGTCGATTTAAGGATTAAATTAAAACAAATTAAAAATAAAAAGG
ACTAAATGCAGAAATAACCCAAAAAATGACACGTGGCAACCTCTGGCACAGTCAAAAAGTCAAAA
GACCAAATTATAAACCTCGAAAAATTATGGGG
Found at i:34244135 original size:161 final size:161
Alignment explanation
Indices: 34243784--34244136 Score: 399
Period size: 161 Copynumber: 2.2 Consensus size: 161
34243774 AAAAGTCGAT
*
34243784 TTAAGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAACCCAAAAAATG
1 TTAAGGATTAAATTAAAACAAATTAAAAATGAAAAGGACTAAATGCAGAAATAACCCAAAAAATG
** ** ** *
34243849 ACACGTGGCAACCTCTGGTGCAGTCAAAAAGTCAAAAGACCAGTTTATAAACCTCGAAAAATTAT
66 ACACGTGGCAACCTCTGGCACAGTCAAAAAGTCAAAAGACCAAATTATAAACCAAGAAAAATTAC
* * * * *
34243914 GGGGCCAATTTCGTAATTAAAACAAAGTTGA
131 AGGGCAAATTTCGCAAATAAAACAAAGATGA
** * * * *
34243945 TTTGGGATTAAATTAAAACAAATTAAAAATGAAAAGGACTAAATGCATAAATAATCCAATACATG
1 TTAAGGATTAAATTAAAACAAATTAAAAATGAAAAGGACTAAATGCAGAAATAACCCAAAAAATG
* * * **
34244010 ACACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTATAAACCAATTAAAATTAC
66 ACACGTGGCAACCTCTGGCACAGTCAAAAAGTCAAAAGACCAAATTATAAACCAAGAAAAATTAC
34244075 AGGGCAAATTT-GCAAATAATTAA-AAAGATGCCA
131 AGGGCAAATTTCGCAAATAA--AACAAAGATG--A
* * *
34244108 -TAAGGACTAAATTGAAGCAAA-TAAAAATG
1 TTAAGGATTAAATTAAAACAAATTAAAAATG
34244137 CGGAAGGACT
Statistics
Matches: 159, Mismatches: 29, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
160 6 0.04
161 134 0.84
162 18 0.11
163 1 0.01
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.22
Consensus pattern (161 bp):
TTAAGGATTAAATTAAAACAAATTAAAAATGAAAAGGACTAAATGCAGAAATAACCCAAAAAATG
ACACGTGGCAACCTCTGGCACAGTCAAAAAGTCAAAAGACCAAATTATAAACCAAGAAAAATTAC
AGGGCAAATTTCGCAAATAAAACAAAGATGA
Found at i:34244498 original size:12 final size:12
Alignment explanation
Indices: 34244478--34244522 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
34244468 GGTGCGCTCC
*
34244478 TTTCCTCCTTTT
1 TTTCTTCCTTTT
34244490 TTTCTTCC-TTT
1 TTTCTTCCTTTT
*
34244501 TTTCTTCCCTTT
1 TTTCTTCCTTTT
34244513 TTTCTTCCTT
1 TTTCTTCCTT
34244523 AATCTCCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 11 0.37
12 19 0.63
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTCTTCCTTTT
Found at i:34244503 original size:11 final size:11
Alignment explanation
Indices: 34244487--34244522 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
34244477 CTTTCCTCCT
34244487 TTTTTTCTTCC
1 TTTTTTCTTCC
34244498 TTTTTTCTTCCC
1 TTTTTTCTT-CC
34244510 TTTTTTCTTCC
1 TTTTTTCTTCC
34244521 TT
1 TT
34244523 AATCTCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTTTCTTCC
Found at i:34244513 original size:23 final size:23
Alignment explanation
Indices: 34244478--34244522 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
34244468 GGTGCGCTCC
*
34244478 TTTCCTCCTTTTTTTCTTCCTTT
1 TTTCCTCCCTTTTTTCTTCCTTT
*
34244501 TTTCTTCCCTTTTTTCTTCCTT
1 TTTCCTCCCTTTTTTCTTCCTT
34244523 AATCTCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTCCTCCCTTTTTTCTTCCTTT
Found at i:34244830 original size:2 final size:2
Alignment explanation
Indices: 34244823--34244855 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34244813 TTTAAGAAAT
34244823 TA TA TA 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 TA TA TA T
34244856 TCTGAGAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34245575 original size:6 final size:6
Alignment explanation
Indices: 34245564--34245630 Score: 75
Period size: 6 Copynumber: 11.2 Consensus size: 6
34245554 TTTAATCTTT
*
34245564 ATTTAA ATTTAA ATTTAA A-TTAA ATTTAA ATATCTAA TTTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-T-TAA ATTTAA ATTTAA
* *
34245613 A-ATAA ATCTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA A
34245631 CAAATTTAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
5 9 0.17
6 37 0.71
7 2 0.04
8 4 0.08
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:34245635 original size:27 final size:25
Alignment explanation
Indices: 34245605--34245654 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 25
34245595 ATCTAATTTT
34245605 AAATTTA-AAATAAATCTAAATTTAAAC
1 AAATTTAGAAA-AAATC--AATTTAAAC
34245632 AAATTTAGAAAAAATCAATTTAA
1 AAATTTAGAAAAAATCAATTTAA
34245655 CTCAAAAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 7 0.32
27 12 0.55
28 3 0.14
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (25 bp):
AAATTTAGAAAAAATCAATTTAAAC
Found at i:34246687 original size:14 final size:14
Alignment explanation
Indices: 34246668--34246700 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
34246658 TTTTTTCAAC
34246668 TTTAAATATTTAAA
1 TTTAAATATTTAAA
*
34246682 TTTAAATATTTTAA
1 TTTAAATATTTAAA
34246696 TTTAA
1 TTTAA
34246701 TCATAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAAATATTTAAA
Found at i:34247858 original size:3 final size:3
Alignment explanation
Indices: 34247852--34247876 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
34247842 TATTAAGTTG
34247852 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
34247877 AAATGAGGGT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:34248110 original size:19 final size:19
Alignment explanation
Indices: 34248086--34248125 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
34248076 GCGAGATATT
34248086 TGGGGTTGTCAAATATTGA
1 TGGGGTTGTCAAATATTGA
34248105 TGGGGTTGTCAAATATTGA
1 TGGGGTTGTCAAATATTGA
34248124 TG
1 TG
34248126 CCATATATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.05, G:0.33, T:0.38
Consensus pattern (19 bp):
TGGGGTTGTCAAATATTGA
Found at i:34255500 original size:20 final size:20
Alignment explanation
Indices: 34255468--34255517 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
34255458 TTTTATTGGT
*
34255468 TATATTTTA-ATATTTAAAA
1 TATAATTTATATATTTAAAA
* *
34255487 TATAATTTATATATTTGAAC
1 TATAATTTATATATTTAAAA
*
34255507 TAAAATTTATA
1 TATAATTTATA
34255518 AATAATTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
TATAATTTATATATTTAAAA
Found at i:34257534 original size:20 final size:20
Alignment explanation
Indices: 34257506--34257543 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34257496 TAAAAAATTT
*
34257506 AAAATTTAAAAATTAAAACA
1 AAAAATTAAAAATTAAAACA
*
34257526 AAAAATTAATAATTAAAA
1 AAAAATTAAAAATTAAAA
34257544 AACCTAGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAATTAAAAATTAAAACA
Found at i:34257545 original size:15 final size:14
Alignment explanation
Indices: 34257495--34257545 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
34257485 ATATTTAATT
34257495 TTAAAAAATTTAAAA
1 TTAAAAAA-TTAAAA
*
34257510 TTTAAAAATTAAAA
1 TTAAAAAATTAAAA
*
34257524 -CAAAAAATTAATAA
1 TTAAAAAATTAA-AA
34257538 TTAAAAAA
1 TTAAAAAA
34257546 CCTAGATACA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 9 0.30
14 8 0.27
15 13 0.43
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (14 bp):
TTAAAAAATTAAAA
Found at i:34265010 original size:22 final size:21
Alignment explanation
Indices: 34264978--34265028 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
34264968 AACTTAGCTC
*
34264978 AAAT-TTAAATTAAATAATTA
1 AAATATTAAATTAAATAATAA
* *
34264998 AAATATTATAATTTAATTATAA
1 AAATATTA-AATTAAATAATAA
34265020 AAATATTAA
1 AAATATTAA
34265029 CATAAAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 4 0.15
22 18 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATATTAAATTAAATAATAA
Found at i:34267016 original size:30 final size:29
Alignment explanation
Indices: 34266950--34267022 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
34266940 TTATAAATTA
* *
34266950 AAAATTTAGTTTCTATATTTTTTATTTTT
1 AAAATTTAGTTTCTATATTTTTCAATTTT
*
34266979 AAGAATTTAGTCTT-TTTATTTTTCAGATTTT
1 AA-AATTTAGT-TTCTATATTTTTCA-ATTTT
34267010 AAAATTTAAGTTT
1 AAAATTT-AGTTT
34267023 AGTTGTTAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
29 2 0.05
30 24 0.65
31 11 0.30
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (29 bp):
AAAATTTAGTTTCTATATTTTTCAATTTT
Found at i:34267207 original size:29 final size:28
Alignment explanation
Indices: 34267175--34267258 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 28
34267165 CAATTGAACT
34267175 TAAATTTTGAAATATAAAAATAAAATAAC
1 TAAATTTT-AAATATAAAAATAAAATAAC
*
34267204 TAAAATTTTAAAAATAAAAATACAAA-AAC
1 T-AAATTTTAAATATAAAAATA-AAATAAC
* *
34267233 TAAATTCTAAATTTAAAAA-AAAATAA
1 TAAATTTTAAATATAAAAATAAAATAA
34267259 AACAACTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
26 3 0.06
27 3 0.06
28 15 0.31
29 17 0.35
30 10 0.21
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.29
Consensus pattern (28 bp):
TAAATTTTAAATATAAAAATAAAATAAC
Found at i:34267381 original size:15 final size:15
Alignment explanation
Indices: 34267361--34267401 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
34267351 CAAGAAAGAA
34267361 TAAACTCATCCGTCT
1 TAAACTCATCCGTCT
34267376 TAAACTCATCCGTCT
1 TAAACTCATCCGTCT
34267391 TAAACTCATCC
1 TAAACTCATCC
34267402 ATTCCTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (15 bp):
TAAACTCATCCGTCT
Found at i:34271383 original size:13 final size:12
Alignment explanation
Indices: 34271353--34271388 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
34271343 TTTGAATTAA
*
34271353 TTTTAAATTCAT
1 TTTTAAATTTAT
34271365 TTTTAAATTTAT
1 TTTTAAATTTAT
34271377 CTTTTAAATTTA
1 -TTTTAAATTTA
34271389 AACTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTTAAATTTAT
Found at i:34271483 original size:28 final size:27
Alignment explanation
Indices: 34271440--34271502 Score: 108
Period size: 28 Copynumber: 2.3 Consensus size: 27
34271430 CAATGTCCAT
34271440 TTACAAAAGCCCAAATCAAAGGCCCGA
1 TTACAAAAGCCCAAATCAAAGGCCCGA
*
34271467 TTACAAGAAGCCCAAATTAAAGGCCCGA
1 TTACAA-AAGCCCAAATCAAAGGCCCGA
34271495 TTACAAAA
1 TTACAAAA
34271503 AGCTCAATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 8 0.24
28 26 0.76
ACGTcount: A:0.46, C:0.25, G:0.14, T:0.14
Consensus pattern (27 bp):
TTACAAAAGCCCAAATCAAAGGCCCGA
Found at i:34272959 original size:161 final size:162
Alignment explanation
Indices: 34272693--34273002 Score: 437
Period size: 161 Copynumber: 1.9 Consensus size: 162
34272683 TTCAATTTAA
* * * *
34272693 TCCTTTGACTGTTTTACTGTACCAGAGGCTGCCACGTGTCATGTTTTGGCTTATTTCTGCATATA
1 TCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATGTTTTGGCCTATTTATGCATATA
*
34272758 GTCCCTGACATTATTAATTTGTCTTAATTTAATCCTTAAATCAACTTTTATTTAATTACAAAATT
66 GTCCCTGACATTATTAATTTATCTTAATTTAATCCTTAAATCAACTTTTATTTAATTACAAAATT
*
34272823 GG-CCCAACAATTTTTCAAGGTTTATAAAGAAG
131 GGTCCCAA-AATTTTCCAAGGTTTATAAAGAAG
* * *
34272855 TCCTTTGACTGTTTGACTGCACTAGAGGCTGCCACGTGTC-TTTTTTGGCCTATTTATGCATTTA
1 TCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATGTTTTGGCCTATTTATGCATATA
** * * * *
34272919 GT-CCTTTCTATTTTTAATTTATTTTAATTTAGTCCTTAAATTAACTTTTATTTAATTACAAAAT
66 GTCCCTGAC-ATTATTAATTTATCTTAATTTAATCCTTAAATCAACTTTTATTTAATTACAAAAT
*
34272983 TGGTCCGAAAATTTTCCAAG
130 TGGTCCCAAAATTTTCCAAG
34273003 ATTTTCAAAT
Statistics
Matches: 130, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
160 4 0.03
161 85 0.65
162 41 0.32
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (162 bp):
TCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATGTTTTGGCCTATTTATGCATATA
GTCCCTGACATTATTAATTTATCTTAATTTAATCCTTAAATCAACTTTTATTTAATTACAAAATT
GGTCCCAAAATTTTCCAAGGTTTATAAAGAAG
Found at i:34273415 original size:30 final size:29
Alignment explanation
Indices: 34273099--34273415 Score: 303
Period size: 30 Copynumber: 10.7 Consensus size: 29
34273089 AAATTGTCCA
* * *
34273099 AAAATTACATTTCAACCCTAAAACTTTCTA
1 AAAATTACATTTTAACCCCAAAACTTTC-C
* * *
34273129 AAAATTATATTTTAACCTCGAAACTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTCC
* *
34273158 AAAATTACATTTTAACCCTTAAAATTTTCC
1 AAAATTACATTTTAACCC-CAAAACTTTCC
*
34273188 AAAATTATATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAAC-TTTCC
* *
34273218 AAAATTACATTTCAACCCCAAAACTTTCTA
1 AAAATTACATTTTAACCCCAAAACTTTC-C
** * * * *
34273248 AAAATTATTTTTTGACCCTAAAACCTTCT
1 AAAATTACATTTTAACCCCAAAACTTTCC
*
34273277 AGAAATTACATTTTGACCCCAAAACTTTTCC
1 A-AAATTACATTTTAACCCCAAAAC-TTTCC
* *
34273308 AAAATTACATTTTGACTCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAAC-TTTCC
* * * *
34273338 AAAATTATACTTTAACCCTAAAACTTTCA
1 AAAATTACATTTTAACCCCAAAACTTTCC
*
34273367 AAAATTACCATTTT-ACCCCTAAACTTTCC
1 AAAATTA-CATTTTAACCCCAAAACTTTCC
* *
34273396 TAAATTCCATTTTTAACCCC
1 AAAATTACA-TTTTAACCCC
34273416 GATTTCACCA
Statistics
Matches: 236, Mismatches: 43, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
28 2 0.01
29 57 0.24
30 173 0.73
31 4 0.02
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTAACCCCAAAACTTTCC
Found at i:34273428 original size:59 final size:57
Alignment explanation
Indices: 34273365--34273560 Score: 216
Period size: 59 Copynumber: 3.4 Consensus size: 57
34273355 CTAAAACTTT
34273365 CAAAAATTACCATTTTACCCCTAAACTTTCCTAAATTCCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCC-AAACTTTCC-AAATTCCATTTTTAACCCCGATTTCAC
* * * * * * ** * **
34273424 CAAAACTTACCGTTTTGCCTCCGAACTTTCCAAAATTTCATTTTTGACCTTGTTTTTGC
1 CAAAAATTACCATTTTACC-CCAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCAC
*
34273483 CAAAATTTACCATTTTATTCCCCAAACTTTCCAAATTCCA-TTTTAACCCCGATTTCA-
1 CAAAAATTACCATTTTA--CCCCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCAC
34273540 CAAAAATTACCATTTTACCCC
1 CAAAAATTACCATTTTACCCC
34273561 TAAAAACCTA
Statistics
Matches: 110, Mismatches: 24, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
55 4 0.04
57 16 0.15
58 11 0.10
59 65 0.59
60 12 0.11
61 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.04, T:0.37
Consensus pattern (57 bp):
CAAAAATTACCATTTTACCCCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCAC
Found at i:34276154 original size:12 final size:13
Alignment explanation
Indices: 34276137--34276168 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
34276127 ATTTAGTAAT
34276137 TTTTTAAAAA-TA
1 TTTTTAAAAAGTA
34276149 TTTTTAAAAAGTA
1 TTTTTAAAAAGTA
34276162 TTTTTAA
1 TTTTTAA
34276169 TGAAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
TTTTTAAAAAGTA
Found at i:34276547 original size:29 final size:32
Alignment explanation
Indices: 34276480--34276557 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 32
34276470 GTATATATTT
*
34276480 ATTATTAAG-ATATTGATATAAATATTTTTAAA
1 ATTATTAAGAATATTAATATAAATA-TTTTAAA
**
34276512 AAAATTAAGAATATTAAT-TAAA-A-TTTAAA
1 ATTATTAAGAATATTAATATAAATATTTTAAA
34276541 ATTATTATA-AATATTAA
1 ATTATTA-AGAATATTAA
34276558 AATTTATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
29 19 0.49
30 1 0.03
31 1 0.03
32 11 0.28
33 7 0.18
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (32 bp):
ATTATTAAGAATATTAATATAAATATTTTAAA
Found at i:34276557 original size:18 final size:18
Alignment explanation
Indices: 34276528--34276579 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
34276518 AAGAATATTA
34276528 ATTA-AAAT-TTAAAATT
1 ATTATAAATATTAAAATT
34276544 ATTATAAATATTAAAATTT
1 ATTATAAATATTAAAA-TT
*
34276563 ATTATTAA-ATTAAAATT
1 ATTATAAATATTAAAATT
34276580 GTAAAATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 4 0.12
17 6 0.19
18 13 0.41
19 9 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTATAAATATTAAAATT
Found at i:34276612 original size:17 final size:19
Alignment explanation
Indices: 34276581--34276624 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
34276571 ATTAAAATTG
*
34276581 TAAAATTAAATAATT-TAT
1 TAAAATTAAAAAATTGTAT
34276599 TAAAA-TAAAAAATTGTAT
1 TAAAATTAAAAAATTGTAT
34276617 TAATAATT
1 TAA-AATT
34276625 TGTTATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 8 0.36
18 11 0.50
19 2 0.09
20 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
TAAAATTAAAAAATTGTAT
Found at i:34280653 original size:21 final size:21
Alignment explanation
Indices: 34280627--34280667 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
34280617 ATCCCACAAA
*
34280627 TCAGCATTGGGACTGTAAAAC
1 TCAGCATTAGGACTGTAAAAC
34280648 TCAGCATTAGGACTGTAAAA
1 TCAGCATTAGGACTGTAAAA
34280668 TATTGCTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (21 bp):
TCAGCATTAGGACTGTAAAAC
Found at i:34282036 original size:15 final size:15
Alignment explanation
Indices: 34281982--34282037 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
34281972 TTTATACTAC
34281982 AAAATATTTATTATT
1 AAAATATTTATTATT
* *
34281997 AATATATTATAATT-GT
1 AAAATATT-T-ATTATT
34282013 AGTAAATATTTATTATT
1 A--AAATATTTATTATT
34282030 AAAATATT
1 AAAATATT
34282038 AATATTCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 14 0.44
16 6 0.19
17 6 0.19
18 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:34282102 original size:16 final size:16
Alignment explanation
Indices: 34282065--34282104 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
34282055 ATAATATATG
34282065 AAATA-TATTATTTAA
1 AAATATTATTATTTAA
34282080 AAATATTATT-TTT-A
1 AAATATTATTATTTAA
34282094 AAAT-TTATTAT
1 AAATATTATTAT
34282105 CAAAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.22
14 6 0.26
15 8 0.35
16 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATATTATTATTTAA
Found at i:34282726 original size:104 final size:104
Alignment explanation
Indices: 34282546--34282751 Score: 403
Period size: 104 Copynumber: 2.0 Consensus size: 104
34282536 TTATCAATAT
34282546 TTGGTACTTAGCAAATTTGTGATTGTCCTTTTATGGTTATTGACCAATAATTCCCCACTTTTGCT
1 TTGGTACTTAGCAAATTTGTGATTGTCCTTTTATGGTTATTGACCAATAATTCCCCACTTTTGCT
34282611 ATAGATTTTGTTTCTGTTTTCTGCTGCTGCTGCTGTTAA
66 ATAGATTTTGTTTCTGTTTTCTGCTGCTGCTGCTGTTAA
34282650 TTGGTACTTAGCAAATTTGTGATTGTCCTTTTATGGTTATTGACCAATAATTCCCCACTTTTGCT
1 TTGGTACTTAGCAAATTTGTGATTGTCCTTTTATGGTTATTGACCAATAATTCCCCACTTTTGCT
*
34282715 ATAGATTTTGTTTCTGTTTTCTGCTGCTGCTGTTGTT
66 ATAGATTTTGTTTCTGTTTTCTGCTGCTGCTGCTGTT
34282752 GTTGTTGTTG
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (104 bp):
TTGGTACTTAGCAAATTTGTGATTGTCCTTTTATGGTTATTGACCAATAATTCCCCACTTTTGCT
ATAGATTTTGTTTCTGTTTTCTGCTGCTGCTGCTGTTAA
Found at i:34286097 original size:18 final size:20
Alignment explanation
Indices: 34286068--34286122 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 20
34286058 TATTATTTTT
34286068 TAAATATGAGTTTT-TA-CAA
1 TAAAT-TGAGTTTTATAGCAA
34286087 TAAATTGAGTTATTCATAGCAA
1 TAAATTGAGTT-TT-ATAGCAA
34286109 TGAAATTGAGTTTT
1 T-AAATTGAGTTTT
34286123 GTTTTCCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 6 0.19
19 7 0.23
21 2 0.06
22 6 0.19
23 10 0.32
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (20 bp):
TAAATTGAGTTTTATAGCAA
Found at i:34291338 original size:30 final size:29
Alignment explanation
Indices: 34291319--34291682 Score: 103
Period size: 30 Copynumber: 12.1 Consensus size: 29
34291309 GAAAATGAAG
* *
34291319 TTTTGAAGAATTTTAGGGTCAAAATATAA
1 TTTTGAAAAAGTTTAGGGTCAAAATATAA
* *
34291348 TTTTGAAAAAGTTTAGGGCTAAAAAAATCTAA
1 TTTTGAAAAAGTTTAGGG-T--CAAAATATAA
** * * ** * *
34291380 -TTACAGGAAAGTTTGGGGGTTTAAATGTGA
1 TTTTGA-AAAAGTTT-AGGGTCAAAATATAA
** * *
34291410 TTTTGGGGAAA-TTT-GGGATTAAAATGTAA
1 TTTT-GAAAAAGTTTAGGG-TCAAAATATAA
* * * * * *
34291439 TTTTGGAAAGGTTAAGGGGTCGAAATGTGA
1 TTTTGAAAAAGTTTA-GGGTCAAAATATAA
** * **
34291469 TTTTGGGAAAGTTTAGAGGTTAAAATGCAA
1 TTTTGAAAAAGTTTAG-GGTCAAAATATAA
* * * *
34291499 TTTT-AGGAAAGTTTAGGGGTTAAAATGTGA
1 TTTTGA-AAAAGTTTA-GGGTCAAAATATAA
*
34291529 TTTTGAAAAA-TTTAGGAGTCAAAATGTAA
1 TTTTGAAAAAGTTTAGG-GTCAAAATATAA
* * * *
34291558 TTTTGGAAAAGTTTAGGGGTTAAAAATGTAC
1 TTTTGAAAAAGTTTA-GGG-TCAAAATATAA
* ** *
34291589 TTTTGGAAAAGTATGGGGGTTAAAATATAA
1 TTTTGAAAAAGT-TTAGGGTCAAAATATAA
* * *
34291619 TTTTGGAAAAGTTTAGGGGTTAAAATGTAA
1 TTTTGAAAAAGTTTA-GGGTCAAAATATAA
* *
34291649 TTTT-AAGAAA-TTTAGAGGGTTAAAATATGA
1 TTTTGAA-AAAGTTT--AGGGTCAAAATATAA
34291679 TTTT
1 TTTT
34291683 TGGAAAGTTC
Statistics
Matches: 261, Mismatches: 50, Indels: 47
0.73 0.14 0.13
Matches are distributed among these distances:
28 9 0.03
29 60 0.23
30 131 0.50
31 41 0.16
32 17 0.07
33 3 0.01
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
TTTTGAAAAAGTTTAGGGTCAAAATATAA
Found at i:34291343 original size:29 final size:30
Alignment explanation
Indices: 34291304--34291365 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
34291294 GAAACAAGCG
* * *
34291304 GGGTCGAAAATGA-AGTTTTGAAGAATTTTA
1 GGGTCGAAAAT-ATAATTTTGAAAAAGTTTA
34291334 GGGTC-AAAATATAATTTTGAAAAAGTTTA
1 GGGTCGAAAATATAATTTTGAAAAAGTTTA
34291363 GGG
1 GGG
34291366 CTAAAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.04
29 22 0.79
30 5 0.18
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (30 bp):
GGGTCGAAAATATAATTTTGAAAAAGTTTA
Found at i:34291458 original size:59 final size:59
Alignment explanation
Indices: 34291387--34291652 Score: 281
Period size: 59 Copynumber: 4.5 Consensus size: 59
34291377 TAATTACAGG
* * *
34291387 AAAGTTTGGGGGTTTAAATGTGATTTTGGGGAAA-TTTGGGATTAAAATGTAATTTTGGA
1 AAAGTTTAGGGGTTAAAATGTGATTTT-GGAAAAGTTTGGGATTAAAATGTAATTTTGGA
* * ** * *
34291446 AAGGTTAAGGGGTCGAAATGTGATTTTGGGAAAGTTTAGAGG-TTAAAATGCAATTTTAGG-
1 AAAGTTTAGGGGTTAAAATGTGATTTTGGAAAAGTTT-G-GGATTAAAATGTAATTTT-GGA
* * *
34291506 AAAGTTTAGGGGTTAAAATGTGATTTT-GAAAAATTTAGGAGTCAAAATGTAATTTTGGA
1 AAAGTTTAGGGGTTAAAATGTGATTTTGGAAAAGTTTGGGA-TTAAAATGTAATTTTGGA
* * *
34291565 AAAGTTTAGGGGTTAAAAATGT-ACTTTTGGAAAAGTATGGGGGTTAAAATATAATTTTGGA
1 AAAGTTTAGGGGTT-AAAATGTGA-TTTTGGAAAAGT-TTGGGATTAAAATGTAATTTTGGA
*
34291626 AAAGTTTAGGGGTTAAAATGTAATTTT
1 AAAGTTTAGGGGTTAAAATGTGATTTT
34291653 AAGAAATTTA
Statistics
Matches: 174, Mismatches: 21, Indels: 23
0.80 0.10 0.11
Matches are distributed among these distances:
57 2 0.01
58 8 0.05
59 60 0.34
60 60 0.34
61 41 0.24
62 3 0.02
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (59 bp):
AAAGTTTAGGGGTTAAAATGTGATTTTGGAAAAGTTTGGGATTAAAATGTAATTTTGGA
Found at i:34291517 original size:60 final size:57
Alignment explanation
Indices: 34291385--34291696 Score: 295
Period size: 60 Copynumber: 5.2 Consensus size: 57
34291375 TCTAATTACA
* *
34291385 GGAAAGTTTGGGGGTTTAAATGTGATTTTGGGGAAATTT-GGGATTAAAATGTAATTTT
1 GGAAAGTTTAGGGGTTAAAATGTGATTTT-GGGAAATTTAGGG-TTAAAATGTAATTTT
* ** *
34291443 GGAAAGGTTAAGGGGTCGAAATGTGATTTTGGGAAAGTTTAGAGGTTAAAATGCAATTTT
1 GGAAA-GTTTAGGGGTTAAAATGTGATTTTGGGAAA-TTTAG-GGTTAAAATGTAATTTT
** *
34291503 AGGAAAGTTTAGGGGTTAAAATGTGATTTTGAAAAATTTAGGAGTCAAAATGTAATTTT
1 -GGAAAGTTTAGGGGTTAAAATGTGATTTTGGGAAATTTAGG-GTTAAAATGTAATTTT
* ** *
34291562 GGAAAAGTTTAGGGGTTAAAAATGT-ACTTTTGGAAAAGTATGGGGGTTAAAATATAATTTT
1 GG-AAAGTTTAGGGGTT-AAAATGTGA-TTTTGGGAAA-T-TTAGGGTTAAAATGTAATTTT
* ** * *
34291623 GGAAAAGTTTAGGGGTTAAAATGTAATTTTAAGAAATTTAGAGGGTTAAAATATGATTTTT
1 GG-AAAGTTTAGGGGTTAAAATGTGATTTTGGGAAATTT--AGGGTTAAAATGT-AATTTT
*
34291684 GGAAAGTTCAGGG
1 GGAAAGTTTAGGG
34291697 ACCTACTGAG
Statistics
Matches: 215, Mismatches: 24, Indels: 28
0.81 0.09 0.10
Matches are distributed among these distances:
58 15 0.07
59 58 0.27
60 92 0.43
61 47 0.22
62 3 0.01
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.35
Consensus pattern (57 bp):
GGAAAGTTTAGGGGTTAAAATGTGATTTTGGGAAATTTAGGGTTAAAATGTAATTTT
Found at i:34291525 original size:119 final size:120
Alignment explanation
Indices: 34291384--34291663 Score: 336
Period size: 120 Copynumber: 2.3 Consensus size: 120
34291374 ATCTAATTAC
* * ** * *
34291384 AGGAAAGTTTGGGGGTTTAAATGTGATTTTGGGGAAATTTGGGA-TTAAAATGTAATTTTGGAAA
1 AGGAAAGTTTAGGGGTTAAAATGTGATTTT-GAAAAATTTAGGAGTCAAAATGTAATTTTGGAAA
* ** * * *
34291448 GGTTAAGGGG-TCGAAATGTGA-TTTTGGGAAAGTTTAGAGGTTAAAATGCAATTTT
65 AGTTAAGGGGTTAAAAATGT-ACTTTTGGAAAAGTATAGAGGTTAAAATACAATTTT
34291503 AGGAAAGTTTAGGGGTTAAAATGTGATTTTGAAAAATTTAGGAGTCAAAATGTAATTTTGGAAAA
1 AGGAAAGTTTAGGGGTTAAAATGTGATTTTGAAAAATTTAGGAGTCAAAATGTAATTTTGGAAAA
* * * *
34291568 GTTTAGGGGTTAAAAATGTACTTTTGGAAAAGTATGGGGGTTAAAATATAATTTT
66 GTTAAGGGGTTAAAAATGTACTTTTGGAAAAGTATAGAGGTTAAAATACAATTTT
*
34291623 -GGAAAAGTTTAGGGGTTAAAATGTAATTTT-AAGAAATTTAG
1 AGG-AAAGTTTAGGGGTTAAAATGTGATTTTGAA-AAATTTAG
34291664 AGGGTTAAAA
Statistics
Matches: 139, Mismatches: 17, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
118 10 0.07
119 60 0.43
120 69 0.50
ACGTcount: A:0.36, C:0.01, G:0.28, T:0.35
Consensus pattern (120 bp):
AGGAAAGTTTAGGGGTTAAAATGTGATTTTGAAAAATTTAGGAGTCAAAATGTAATTTTGGAAAA
GTTAAGGGGTTAAAAATGTACTTTTGGAAAAGTATAGAGGTTAAAATACAATTTT
Found at i:34293129 original size:48 final size:48
Alignment explanation
Indices: 34293075--34293168 Score: 116
Period size: 48 Copynumber: 2.0 Consensus size: 48
34293065 TATTGAGCTT
** ** * *
34293075 CGCTTCATTAAATTGGTCTTCTTCTCTGTATCTCATTAGGAAGATGAC
1 CGCTTCATTAAATTAATCCACTTCTCAGTATCTCATCAGGAAGATGAC
* *
34293123 CGCTTCATTGATTTAATCCACTTCTCAGTATCTCATCAGGAAGATG
1 CGCTTCATTAAATTAATCCACTTCTCAGTATCTCATCAGGAAGATG
34293169 GGGTTCAAAG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (48 bp):
CGCTTCATTAAATTAATCCACTTCTCAGTATCTCATCAGGAAGATGAC
Found at i:34293447 original size:209 final size:208
Alignment explanation
Indices: 34293087--34293708 Score: 879
Period size: 209 Copynumber: 3.0 Consensus size: 208
34293077 CTTCATTAAA
* * * * *
34293087 TTGGTCTTCTTCTCTGTATCTCATTAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCAGT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTAACCCACTTCTCAGT
* * ** * * * * * *
34293152 ATCTCATCAGGAAGATGGGGTTCAAAGTTTCGCTTACATTGAGCTTCGCTTCATCGATTTGGTAT
66 ATCTCATAAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCATTGAATTGGTCT
**
34293217 ACTTCTCTGTATCTCATCAGGAAGATGAGTGCATCACTTGTTTTAATCCACTTCTCTGTATCTCA
131 ACTTCTCTGTA-CTCATCAGGAAGATGAACGCATCACTTGTTTTAATCCACTTCTCTGTATCTCA
*
34293282 TCAAGAAGACAGAT
195 TCAGGAAGACAGAT
* * *
34293296 TTGGTCTACTTTTATGTATCTCATCAGGAAGATGACCGGTTTATTGCTTTAACCCACTTCTCAGT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTAACCCACTTCTCAGT
* * *
34293361 ATCTCATAAAGAAGATGGGGTTTGAAGTTTCACTCAAATTAAGCTTCACTTCATTGAATTAGTCT
66 ATCTCATAAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCATTGAATTGGTCT
* *
34293426 ACTTCTCTGTACATCATCAGGAAGATGACCACATCACTTGTTTTAATCCACTTCTCTGTATCTCA
131 ACTTCTCTGTAC-TCATCAGGAAGATGAACGCATCACTTGTTTTAATCCACTTCTCTGTATCTCA
* *
34293491 TCAGGAACACGGAT
195 TCAGGAAGACAGAT
* * *
34293505 TTGGT-TCACTTCTCTATATCTCATCAGGAAGATGACCTCTTTATTGCTTTGACCCACTTCTCAG
1 TTGGTCT-ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTAACCCACTTCTCAG
*
34293569 TATCTCA-ATAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGTTTCACTTCATTGAATTGGT
65 TATCTCATA-AAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCATTGAATTGGT
* *
34293633 CTACTTCTCTCTACCTTATCAGGAAGATGAACGCATCACTTGTTTTAATCCACTTCTCTGTATCT
129 CTACTTCTCTGTA-CTCATCAGGAAGATGAACGCATCACTTGTTTTAATCCACTTCTCTGTATCT
34293698 CATCAGGAAGA
193 CATCAGGAAGA
34293709 TGACCTCTTT
Statistics
Matches: 367, Mismatches: 42, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
208 3 0.01
209 363 0.99
210 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (208 bp):
TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTAACCCACTTCTCAGT
ATCTCATAAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCATTGAATTGGTCT
ACTTCTCTGTACTCATCAGGAAGATGAACGCATCACTTGTTTTAATCCACTTCTCTGTATCTCAT
CAGGAAGACAGAT
Found at i:34293808 original size:172 final size:171
Alignment explanation
Indices: 34293510--34293879 Score: 607
Period size: 172 Copynumber: 2.2 Consensus size: 171
34293500 CGGATTTGGT
* *
34293510 TCACTTCTCTATATCTCATCAGGAAGATGACCTCTTTATTGCTTTGACCCACTTCTCAGTATCTC
1 TCACTTCTCTGTATCTCATCAGGAAGATGACCTCTTTATTGCTTTAACCCACTTCTCAGTATCTC
* *
34293575 AATAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGTTTCACTTCATTGAATTGGTCTACTTC
66 AATAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCATTGAATCGGTCTACTTC
* *
34293640 TCTCTACCTTATCAGGAAGATGAACGCATCACTTGTTTTAA
131 TATCTACCTCATCAGGAAGATGAACGCATCACTTGTTTTAA
34293681 TCCACTTCTCTGTATCTCATCAGGAAGATGACCTCTTTATTGCTTTAACCCACTTCTCAGTATCT
1 T-CACTTCTCTGTATCTCATCAGGAAGATGACCTCTTTATTGCTTTAACCCACTTCTCAGTATCT
* * *
34293746 -TATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCGTTGAATCGGTCTACT
65 CAAT-AAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCATTGAATCGGTCTACT
* *
34293810 TCTATGTACCTCATCAGGAAGATGACCGCATCACTTGTTTTAA
129 TCTATCTACCTCATCAGGAAGATGAACGCATCACTTGTTTTAA
*
34293853 TCACTTCTCTGTATCTCATCAAGAAGA
1 TCACTTCTCTGTATCTCATCAGGAAGA
34293880 CGGATTTGGT
Statistics
Matches: 185, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
171 28 0.15
172 157 0.85
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (171 bp):
TCACTTCTCTGTATCTCATCAGGAAGATGACCTCTTTATTGCTTTAACCCACTTCTCAGTATCTC
AATAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCATTGAATCGGTCTACTTC
TATCTACCTCATCAGGAAGATGAACGCATCACTTGTTTTAA
Found at i:34293952 original size:85 final size:85
Alignment explanation
Indices: 34293807--34293964 Score: 221
Period size: 85 Copynumber: 1.9 Consensus size: 85
34293797 GAATCGGTCT
* *
34293807 ACTTCTATGTACCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCACTTCTCTGTATCTCAT
1 ACTTCTATGTACCTCATCAGGAAGATGACCGCATCACTTGCTTTAATCACTTCTCAGTATCTCAT
34293872 CAAGAAGACGGATTTGGTTC
66 CAAGAAGACGGATTTGGTTC
* * * * *
34293892 ACTTCTCTGTATCTCATCAGGAATATGACC-TATTTA-TTGCTTTAATCTACTTCTCAGTATCTC
1 ACTTCTATGTACCTCATCAGGAAGATGACCGCA-TCACTTGCTTTAATC-ACTTCTCAGTATCTC
34293955 ATCAAGAAGA
64 ATCAAGAAGA
34293965 TCAGGTTTGA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
84 11 0.17
85 53 0.83
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (85 bp):
ACTTCTATGTACCTCATCAGGAAGATGACCGCATCACTTGCTTTAATCACTTCTCAGTATCTCAT
CAAGAAGACGGATTTGGTTC
Found at i:34303551 original size:30 final size:29
Alignment explanation
Indices: 34303476--34303553 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
34303466 AGTTTAGGAG
* **
34303476 AATTTTAGGGTCAAAATGTAATTTTAGAA
1 AATTTTAGGGTAAAAATGTAATTCGAGAA
* *
34303505 AAGTTTAAGGTAAAAATGTAATTACGAGAA
1 AATTTTAGGGTAAAAATGTAATT-CGAGAA
* *
34303535 AATTTTGGGGTTAAAATGT
1 AATTTTAGGGTAAAAATGT
34303554 GATTTTGGGA
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 20 0.51
30 19 0.49
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.35
Consensus pattern (29 bp):
AATTTTAGGGTAAAAATGTAATTCGAGAA
Found at i:34303640 original size:30 final size:30
Alignment explanation
Indices: 34303479--34303789 Score: 276
Period size: 30 Copynumber: 10.5 Consensus size: 30
34303469 TTAGGAGAAT
* * *
34303479 TTTA-GGGTCAAAATGTAATTTTAGAAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGGAAAG
* * ** * *
34303508 TTTA-AGGTAAAAATGTAATTACGAGAAAA
1 TTTAGGGGTTAAAATGTAATTTTGGGAAAG
* *
34303537 TTTTGGGGTTAAAATGTGATTTTGGGAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGGAAAG
* *
34303567 TTTA-GGATTAAAATGTAATTTT-AGAAAGG
1 TTTAGGGGTTAAAATGTAATTTTGGGAAA-G
* * *
34303596 TTAAGGGG-TCAAATATAATTTTGGGAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGGAAAG
* *
34303625 TTTAGGGGTTAAAATATGATTTTGGGAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGGAAAG
** **
34303655 TTTAACGGTTAAAATGTAATTTTGAAAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGGAAAG
* * *
34303685 TTTAGAGGTCAAAATGTAATTTTGGAAAAG
1 TTTAGGGGTTAAAATGTAATTTTGGGAAAG
* * *
34303715 TATGGGGGTTAAAATGT-ATTTTTGGATAAG
1 TTTAGGGGTTAAAATGTAATTTTGGGA-AAG
* *
34303745 TTTATGGGTTAAAATGTAATTTTAGG-AAG
1 TTTAGGGGTTAAAATGTAATTTTGGGAAAG
34303774 TTTAGGGGGTTAAAAT
1 TTTA-GGGGTTAAAAT
34303790 ATGATTTTTG
Statistics
Matches: 225, Mismatches: 49, Indels: 15
0.78 0.17 0.05
Matches are distributed among these distances:
28 4 0.02
29 78 0.35
30 136 0.60
31 7 0.03
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.36
Consensus pattern (30 bp):
TTTAGGGGTTAAAATGTAATTTTGGGAAAG
Found at i:34306177 original size:4 final size:4
Alignment explanation
Indices: 34306168--34306192 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
34306158 TTAAGGGTCA
34306168 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
34306193 GTTGACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:34306393 original size:48 final size:48
Alignment explanation
Indices: 34306339--34306444 Score: 144
Period size: 48 Copynumber: 2.2 Consensus size: 48
34306329 ATTATACCAA
* *
34306339 ATTTTATTTTAT-AAGATAATAAATATTATTTTAA-GAGTAGTATTATTT
1 ATTTTATTTTATAAAG-TAATAAATATTATTTGAAGGA-TAATATTATTT
*
34306387 TTTTTATTTTATAAAGTAATAAATATTATTTGAAGGATAATATTATTT
1 ATTTTATTTTATAAAGTAATAAATATTATTTGAAGGATAATATTATTT
*
34306435 ATTATATTTT
1 ATTTTATTTT
34306445 TATATAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
48 46 0.90
49 5 0.10
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.54
Consensus pattern (48 bp):
ATTTTATTTTATAAAGTAATAAATATTATTTGAAGGATAATATTATTT
Found at i:34317235 original size:14 final size:15
Alignment explanation
Indices: 34317211--34317240 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
34317201 ATTAATAGTA
34317211 TAACATATAGAAAGT
1 TAACATATAGAAAGT
34317226 TAAC-TATAGAAAGT
1 TAACATATAGAAAGT
34317240 T
1 T
34317241 GTTAATACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (15 bp):
TAACATATAGAAAGT
Found at i:34321295 original size:3 final size:3
Alignment explanation
Indices: 34321287--34321317 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
34321277 GAAGTAAACC
*
34321287 AAG AAG AAG AAG AAG AAG AAG AAG ATG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
34321318 GTACTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:34326930 original size:23 final size:23
Alignment explanation
Indices: 34326876--34326930 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
34326866 AAATGAAGAT
*
34326876 TTAAATT-TTTATATTTATATAA
1 TTAAATTATTCATATTTATATAA
* *
34326898 TTAAAATATTCATATTT-TATAC
1 TTAAATTATTCATATTTATATAA
34326920 TATAAATTATT
1 T-TAAATTATT
34326931 AATTATCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAAATTATTCATATTTATATAA
Found at i:34340534 original size:9 final size:9
Alignment explanation
Indices: 34340509--34340621 Score: 102
Period size: 9 Copynumber: 12.6 Consensus size: 9
34340499 CTGTCCTGGC
*
34340509 ATTTGTGGT
1 ATTTGTGGG
*
34340518 ATTAGTGGG
1 ATTTGTGGG
34340527 ATTTGTGGG
1 ATTTGTGGG
**
34340536 ACCTGTGGG
1 ATTTGTGGG
**
34340545 ATCAGTGGG
1 ATTTGTGGG
34340554 ATTTGTGGG
1 ATTTGTGGG
*
34340563 ATCTGTGGG
1 ATTTGTGGG
34340572 ATTTGTGGG
1 ATTTGTGGG
* *
34340581 ATTTCTGGA
1 ATTTGTGGG
34340590 ATTCT-TGGG
1 ATT-TGTGGG
*
34340599 ATTTCTGGG
1 ATTTGTGGG
* *
34340608 ATTTCTGGA
1 ATTTGTGGG
34340617 ATTTG
1 ATTTG
34340622 AGGAAATGGT
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
8 1 0.01
9 84 0.98
10 1 0.01
ACGTcount: A:0.15, C:0.07, G:0.37, T:0.41
Consensus pattern (9 bp):
ATTTGTGGG
Found at i:34342086 original size:13 final size:15
Alignment explanation
Indices: 34342058--34342095 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
34342048 GTAATTATTT
34342058 ACTTTTATATTATAA
1 ACTTTTATATTATAA
34342073 A-TTTTATA-TATAA
1 ACTTTTATATTATAA
34342086 ACTTTT-TATT
1 ACTTTTATATT
34342096 TTTTTGCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 8 0.38
14 12 0.57
15 1 0.05
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (15 bp):
ACTTTTATATTATAA
Found at i:34344332 original size:94 final size:94
Alignment explanation
Indices: 34344171--34344359 Score: 378
Period size: 94 Copynumber: 2.0 Consensus size: 94
34344161 ATCCACCAAT
34344171 AAATCGAGTTGTAGAGCTACGTCATTGAGAGTAATTGTACACTCACCGTATGGAAGATGGAATGT
1 AAATCGAGTTGTAGAGCTACGTCATTGAGAGTAATTGTACACTCACCGTATGGAAGATGGAATGT
34344236 GTGTGACTCAGGTCTCCATCTTTTCACCA
66 GTGTGACTCAGGTCTCCATCTTTTCACCA
34344265 AAATCGAGTTGTAGAGCTACGTCATTGAGAGTAATTGTACACTCACCGTATGGAAGATGGAATGT
1 AAATCGAGTTGTAGAGCTACGTCATTGAGAGTAATTGTACACTCACCGTATGGAAGATGGAATGT
34344330 GTGTGACTCAGGTCTCCATCTTTTCACCA
66 GTGTGACTCAGGTCTCCATCTTTTCACCA
34344359 A
1 A
34344360 CGCGCTGATG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (94 bp):
AAATCGAGTTGTAGAGCTACGTCATTGAGAGTAATTGTACACTCACCGTATGGAAGATGGAATGT
GTGTGACTCAGGTCTCCATCTTTTCACCA
Found at i:34345379 original size:7 final size:7
Alignment explanation
Indices: 34345367--34345409 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
34345357 GTATTTTCTG
34345367 AAAATTT
1 AAAATTT
34345374 AAAATTT
1 AAAATTT
34345381 AAAATTT
1 AAAATTT
**
34345388 AATTTTT
1 AAAATTT
* *
34345395 ATATTTT
1 AAAATTT
34345402 AAAATTT
1 AAAATTT
34345409 A
1 A
34345410 GATTTAACTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (7 bp):
AAAATTT
Found at i:34345423 original size:28 final size:28
Alignment explanation
Indices: 34345371--34345430 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
34345361 TTTCTGAAAA
*
34345371 TTTAAAATTTAAAATTTAATTTTTATAT
1 TTTAAAATTTAAAATTTAATGTTTATAT
* *
34345399 TTTAAAATTT-AGATTTAACTGTTTATTT
1 TTTAAAATTTAAAATTTAA-TGTTTATAT
34345427 TTTA
1 TTTA
34345431 TTAAATTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (28 bp):
TTTAAAATTTAAAATTTAATGTTTATAT
Found at i:34345865 original size:26 final size:26
Alignment explanation
Indices: 34345818--34345867 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
34345808 TTCGAATTAA
*
34345818 ATATTTTCTTATAAAATCTTTAATTC
1 ATATTTTATTATAAAATCTTTAATTC
* * *
34345844 ATATTTTATTCTAATATTTTTAAT
1 ATATTTTATTATAAAATCTTTAAT
34345868 AAATTAATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (26 bp):
ATATTTTATTATAAAATCTTTAATTC
Found at i:34349574 original size:24 final size:24
Alignment explanation
Indices: 34349546--34349604 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
34349536 TAGACTAATA
*
34349546 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* * *
34349570 AGAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAC
34349594 AGAGTTTAACT
1 AGAGTTTAACT
34349605 AAAAGATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:34353952 original size:21 final size:21
Alignment explanation
Indices: 34353914--34353954 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
34353904 GGCGAGTTTG
* *
34353914 ACGACGACGATGAGGATGATA
1 ACGACGACGAGGACGATGATA
*
34353935 ACGACGAGGAGGACGATGAT
1 ACGACGACGAGGACGATGAT
34353955 GGTGGCAAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.15, G:0.37, T:0.12
Consensus pattern (21 bp):
ACGACGACGAGGACGATGATA
Found at i:34376538 original size:2 final size:2
Alignment explanation
Indices: 34376531--34376574 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
34376521 AGAAAGAATG
34376531 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
34376573 TC
1 TC
34376575 AGTCTTTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:34378528 original size:16 final size:17
Alignment explanation
Indices: 34378503--34378536 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
34378493 AGTTTTTTAA
34378503 TAAATGTTATA-TATTT
1 TAAATGTTATATTATTT
*
34378519 TAAATTTTATATTATTT
1 TAAATGTTATATTATTT
34378536 T
1 T
34378537 TAACTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TAAATGTTATATTATTT
Found at i:34379274 original size:30 final size:28
Alignment explanation
Indices: 34379238--34379304 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 28
34379228 ATAGTTGGAT
*
34379238 CTAAATTTTGAAATATAAAAAG-TAAAGGAA
1 CTAAATTTTGAAA-ATAAAAGGAT-AAGG-A
*
34379268 CTAAATTACTGAAAATAAAAGGATAAGGA
1 CTAAATT-TTGAAAATAAAAGGATAAGGA
34379297 CTAAATTT
1 CTAAATTT
34379305 CAAACTTGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
29 8 0.25
30 18 0.56
31 6 0.19
ACGTcount: A:0.54, C:0.06, G:0.13, T:0.27
Consensus pattern (28 bp):
CTAAATTTTGAAAATAAAAGGATAAGGA
Found at i:34382419 original size:85 final size:85
Alignment explanation
Indices: 34382276--34382446 Score: 324
Period size: 85 Copynumber: 2.0 Consensus size: 85
34382266 GCACTCAACA
*
34382276 TTTATTTGTAATTTATTCTTATAAGACCTTAATTATTATTTGTCTGCCCAAGAAAATTATTAATA
1 TTTATTTGTAATTTATTCTTATAAGACCTTAATTATTATTTGTCTGCCCAAGAAAATTAATAATA
34382341 ATATTATTTTCAATAGTACT
66 ATATTATTTTCAATAGTACT
34382361 TTTATTTGTAATTTATTCTTATAAGACCTTAATTATTATTTGTCTGCCCAAGAAAATTAATAATA
1 TTTATTTGTAATTTATTCTTATAAGACCTTAATTATTATTTGTCTGCCCAAGAAAATTAATAATA
*
34382426 ATATTATTTTCAATATTACT
66 ATATTATTTTCAATAGTACT
34382446 T
1 T
34382447 GGTATGTATA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.49
Consensus pattern (85 bp):
TTTATTTGTAATTTATTCTTATAAGACCTTAATTATTATTTGTCTGCCCAAGAAAATTAATAATA
ATATTATTTTCAATAGTACT
Found at i:34383430 original size:18 final size:19
Alignment explanation
Indices: 34383389--34383431 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
34383379 ACTTTGATTA
*
34383389 AAAATTCAAAATGATTTTT
1 AAAATTCAAAATGATTTAT
* *
34383408 GAAATTCAAAGT-ATTTAT
1 AAAATTCAAAATGATTTAT
34383426 AAAATT
1 AAAATT
34383432 TTCAAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (19 bp):
AAAATTCAAAATGATTTAT
Found at i:34383467 original size:9 final size:9
Alignment explanation
Indices: 34383435--34383478 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
34383425 TAAAATTTTC
34383435 AAAAAAATCT
1 AAAAAAAT-T
34383445 AAAAAATATAT
1 AAAAAA-AT-T
*
34383456 AAAAAAGTT
1 AAAAAAATT
34383465 AAAAAAATT
1 AAAAAAATT
34383474 AAAAA
1 AAAAA
34383479 TTGTATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
9 14 0.47
10 7 0.23
11 9 0.30
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (9 bp):
AAAAAAATT
Found at i:34387821 original size:3 final size:3
Alignment explanation
Indices: 34387813--34387860 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
34387803 TACATCCCAA
34387813 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
34387860 A
1 A
34387861 GAATAGAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:34390439 original size:23 final size:23
Alignment explanation
Indices: 34390395--34390482 Score: 70
Period size: 23 Copynumber: 3.8 Consensus size: 23
34390385 TTAATGTTCA
**
34390395 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-CGAACATTAAT
* *
34390418 CAAACATGTTCACGAACATTAAA
1 CGAACATGTTCACGAACATTAAT
* *
34390441 CGAGCATGTTCATGAACATATAAT
1 CGAACATGTTCACGAACAT-TAAT
* * *
34390465 TGCACATGTTCACAAACA
1 CGAACATGTTCACGAACA
34390483 ATGTTAATGA
Statistics
Matches: 50, Mismatches: 13, Indels: 3
0.76 0.20 0.05
Matches are distributed among these distances:
22 3 0.06
23 31 0.62
24 16 0.32
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.28
Consensus pattern (23 bp):
CGAACATGTTCACGAACATTAAT
Found at i:34390508 original size:4 final size:4
Alignment explanation
Indices: 34390499--34390523 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
34390489 ATGAATAATT
34390499 AACA AACA AACA AACA AACA AACA A
1 AACA AACA AACA AACA AACA AACA A
34390524 TAAATACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
AACA
Found at i:34391895 original size:15 final size:17
Alignment explanation
Indices: 34391877--34391909 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
34391867 TTCGTGATAA
34391877 TTTT-TATTTT-TATTT
1 TTTTATATTTTATATTT
34391892 TTTTATATTTTATATTT
1 TTTTATATTTTATATTT
34391909 T
1 T
34391910 ATCAAAGCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 6 0.38
17 6 0.38
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTATATTTTATATTT
Found at i:34391896 original size:14 final size:16
Alignment explanation
Indices: 34391877--34391909 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
34391867 TTCGTGATAA
34391877 TTTTTAT-TTTTAT-T
1 TTTTTATATTTTATAT
34391891 TTTTTATATTTTATAT
1 TTTTTATATTTTATAT
34391907 TTT
1 TTT
34391910 ATCAAAGCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 6 0.35
16 4 0.24
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTATATTTTATAT
Found at i:34392354 original size:2 final size:2
Alignment explanation
Indices: 34392347--34392371 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34392337 AAATACCTCC
34392347 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
34392372 GATTAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34393434 original size:17 final size:15
Alignment explanation
Indices: 34393414--34393457 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
34393404 TTTATTTTGT
34393414 ATTTAAATTTGTATACA
1 ATTTAAATTT-TATA-A
34393431 ATTTAAATCTATTATAA
1 ATTTAAAT-T-TTATAA
34393448 ATTTAAATTT
1 ATTTAAATTT
34393458 AAGATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.04
16 1 0.04
17 17 0.68
18 5 0.20
19 1 0.04
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTTAAATTTTATAA
Found at i:34395358 original size:58 final size:58
Alignment explanation
Indices: 34395288--34395596 Score: 299
Period size: 58 Copynumber: 5.3 Consensus size: 58
34395278 GAACTGTCCA
* **
34395288 AAAATTAGCATTTTACCCTTAAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACC
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACC
* * * * * *
34395346 AAAATTACCATTTTACCCCCGAACTTTTCAAAATCCCA-TTATGACCCCGATTTCATC
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACC
* * *
34395403 AAAATTACCATTTTACCCCAAAATCTTT-CAAAATCCCATTTTTGACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCAAA-CTTTCCAAAATCCCATTTTTAACCCTGATTTCACC
* * * * *
34395461 AAAATTACCATTTTAACCTCAAACTCTCCAAAA-CCTCA-TTTTAA-CCTCGATTTTACTA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATCC-CATTTTTAACCCT-GATTTCAC-C
* * * * * *
34395519 AAAATTATCATTTTACCCCCGAACCTTCTAAAATCCCATCTTTAACCCTAAATTTTC-CC
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCT-GA-TTTCACC
34395578 AAAATTA-CATTTTTACCCC
1 AAAATTACCA-TTTTACCCC
34395597 TCGAAAGTCA
Statistics
Matches: 207, Mismatches: 33, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
56 2 0.01
57 63 0.30
58 111 0.54
59 23 0.11
60 5 0.02
61 3 0.01
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACC
Found at i:34395360 original size:29 final size:29
Alignment explanation
Indices: 34395327--34395478 Score: 116
Period size: 29 Copynumber: 5.3 Consensus size: 29
34395317 AAAATCCCAT
* *
34395327 TTTTAACCCTGATTTCACCAAAATTACCA
1 TTTTAACCCCGATTTCATCAAAATTACCA
* *
34395356 TTTTACCCCCGAACTTT--TCAAAA-TCCCA
1 TTTTAACCCCG-A-TTTCATCAAAATTACCA
* *
34395384 TTATGACCCCGATTTCATCAAAATTACCA
1 TTTTAACCCCGATTTCATCAAAATTACCA
* ** * *
34395413 TTTT-ACCCCAAAATCTTTCAAAA-TCCCA
1 TTTTAACCCCGATTTC-ATCAAAATTACCA
* *
34395441 TTTTTGACCCCGATTTCACCAAAATTACCA
1 -TTTTAACCCCGATTTCATCAAAATTACCA
34395471 TTTTAACC
1 TTTTAACC
34395479 TCAAACTCTC
Statistics
Matches: 93, Mismatches: 21, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
26 3 0.03
27 1 0.01
28 30 0.32
29 43 0.46
30 13 0.14
31 3 0.03
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (29 bp):
TTTTAACCCCGATTTCATCAAAATTACCA
Found at i:34395385 original size:28 final size:26
Alignment explanation
Indices: 34395353--34395453 Score: 78
Period size: 28 Copynumber: 3.5 Consensus size: 26
34395343 ACCAAAATTA
34395353 CCATTTTACCCCCGAACTTTTCAAAATC
1 CCATTTTA-CCCCGAA-TTTTCAAAATC
* *
34395381 CCATTATGACCCCG-ATTTCATCAAAATTA
1 CCATT-TTACCCCGAATTT--TCAAAA-TC
*
34395410 CCATTTTACCCCAAAATCTTTCAAAATC
1 CCATTTTACCCC-GAAT-TTTCAAAATC
34395438 CCATTTTTGACCCCGA
1 CCA-TTTT-ACCCCGA
34395454 TTTCACCAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
26 3 0.05
27 1 0.02
28 26 0.45
29 19 0.33
30 7 0.12
31 2 0.03
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.32
Consensus pattern (26 bp):
CCATTTTACCCCGAATTTTCAAAATC
Found at i:34395493 original size:115 final size:116
Alignment explanation
Indices: 34395287--34395596 Score: 333
Period size: 115 Copynumber: 2.7 Consensus size: 116
34395277 TGAACTGTCC
* ** *
34395287 AAAAATTAGCATTTTACCCTTAAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACCAAAATT
1 AAAAATTACCATTTTACCCCAAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAATT
* * * * *
34395352 ACCATTTTACCCCCGAACTTTTCAAAATCC-CATTATGACCCCGATTTCA-T
66 ACCATTTTAACCCCAAACTCTCCAAAA-CCTCATTATAACCCCGATTTCACT
* *
34395402 CAAAATTACCATTTTACCCCAAAATCTTT-CAAAATCCCATTTTTGACCCCGATTTCACCAAAAT
1 AAAAATTACCATTTTACCCCAAAA-CTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAT
* * * *
34395466 TACCATTTTAACCTCAAACTCTCCAAAACCTCATTTTAACCTCGATTTTACT
65 TACCATTTTAACCCCAAACTCTCCAAAACCTCATTATAACCCCGATTTCACT
* ** * * * **
34395518 AAAAATTATCATTTTACCCCCGAACCTTCTAAAATCCCATCTTTAACCCTAAATTTTC-CCAAAA
1 AAAAATTACCATTTTACCCCAAAACTTTCCAAAATCCCATTTTTAACCC-CGA-TTTCACCAAAA
*
34395582 TTA-CATTTTTACCCC
64 TTACCATTTTAACCCC
34395597 TCGAAAGTCA
Statistics
Matches: 162, Mismatches: 27, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
114 2 0.01
115 94 0.58
116 52 0.32
117 10 0.06
118 4 0.02
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.34
Consensus pattern (116 bp):
AAAAATTACCATTTTACCCCAAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAATT
ACCATTTTAACCCCAAACTCTCCAAAACCTCATTATAACCCCGATTTCACT
Found at i:34397847 original size:18 final size:19
Alignment explanation
Indices: 34397815--34397858 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
34397805 TTTCTATGTG
* * *
34397815 ATACAAATCACATAATAT-
1 ATACAAATAAAATAAAATA
34397833 ATACAAATAAAATAAAATA
1 ATACAAATAAAATAAAATA
34397852 ATACAAA
1 ATACAAA
34397859 ATCCTAAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (19 bp):
ATACAAATAAAATAAAATA
Found at i:34404573 original size:11 final size:11
Alignment explanation
Indices: 34404533--34404573 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
34404523 AAAAGCAGCC
*
34404533 AAAGCAGCT-A
1 AAAGAAGCTGA
34404543 AAAG-AGCTGA
1 AAAGAAGCTGA
34404553 AAAGGAAGCTGA
1 AAA-GAAGCTGA
34404565 AAAGAAGCT
1 AAAGAAGCT
34404574 CAAGGAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.14
10 8 0.29
11 7 0.25
12 9 0.32
ACGTcount: A:0.51, C:0.12, G:0.27, T:0.10
Consensus pattern (11 bp):
AAAGAAGCTGA
Found at i:34407974 original size:15 final size:15
Alignment explanation
Indices: 34407945--34407973 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
34407935 TCAACAAGCA
34407945 AGAGAAAGTTTTTTT
1 AGAGAAAGTTTTTTT
34407960 AGAGAAA-TTTTTTT
1 AGAGAAAGTTTTTTT
34407974 TGGAGGTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (15 bp):
AGAGAAAGTTTTTTT
Found at i:34408037 original size:12 final size:12
Alignment explanation
Indices: 34408020--34408044 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34408010 GTAAAAATGT
34408020 AATTTTTAAAGG
1 AATTTTTAAAGG
34408032 AATTTTTAAAGG
1 AATTTTTAAAGG
34408044 A
1 A
34408045 TTAAATCAAA
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:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (12 bp):
AATTTTTAAAGG
Found at i:34417633 original size:20 final size:20
Alignment explanation
Indices: 34417608--34417648 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
34417598 CTAAATATTA
*
34417608 GAAAATATCCTTTTTTTGGG
1 GAAAATATCCTTTTTTCGGG
34417628 GAAAATATCCTTTTTTCGGG
1 GAAAATATCCTTTTTTCGGG
34417648 G
1 G
34417649 GTGGGGGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.41
Consensus pattern (20 bp):
GAAAATATCCTTTTTTCGGG
Done.