Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015298.1 Kokia drynarioides strain JFW-HI SEQ_130343, whole genome shotgun sequence
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: 570056
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 343 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:12952 original size:38 final size:39
Alignment explanation
Indices: 12888--12961 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 39
12878 ATTCACAAAC
* * *
12888 TGAAATGAATCACCAATGATTAATGAT-CGATGATACCA
1 TGAAATGAATCACCAACGATCAATGATACCATGATACCA
* *
12926 TGAAATGAATCACCTACGATCCATGATACCATGATA
1 TGAAATGAATCACCAACGATCAATGATACCATGATA
12962 GCGTGTTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 23 0.77
39 7 0.23
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (39 bp):
TGAAATGAATCACCAACGATCAATGATACCATGATACCA
Found at i:19017 original size:16 final size:16
Alignment explanation
Indices: 18986--19015 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18976 CAACTTCTCT
18986 TTTTTCCCTCCTTTTC
1 TTTTTCCCTCCTTTTC
19002 TTTTT-CCTCCTTTT
1 TTTTTCCCTCCTTTT
19016 TCGCTGCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTCCCTCCTTTTC
Found at i:23611 original size:57 final size:58
Alignment explanation
Indices: 23550--23664 Score: 187
Period size: 57 Copynumber: 2.0 Consensus size: 58
23540 ATCAACAAAT
23550 TAAACCCAAATATTTTTAAACCCAAATATAATTTTATTATTAAA-AACACTCATAAAC
1 TAAACCCAAATATTTTTAAACCCAAATATAATTTTATTATTAAATAACACTCATAAAC
* * * *
23607 TAAACCTAATTATTTTTAAACTCAAATATAATTTTATTCTTAAATAACACTCATAAAC
1 TAAACCCAAATATTTTTAAACCCAAATATAATTTTATTATTAAATAACACTCATAAAC
23665 AACTCCTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
57 40 0.75
58 13 0.25
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (58 bp):
TAAACCCAAATATTTTTAAACCCAAATATAATTTTATTATTAAATAACACTCATAAAC
Found at i:30916 original size:29 final size:29
Alignment explanation
Indices: 30884--31141 Score: 215
Period size: 30 Copynumber: 8.8 Consensus size: 29
30874 TTTTAAGAGT
30884 TTCGAGGTTGAAAATGGGATTTTTGGAA-G
1 TTCGAGGTT-AAAATGGGATTTTTGGAAGG
* * *
30913 TTCGGAGG-TAGAATGGTAATTTTGGAAGG
1 TTC-GAGGTTAAAATGGGATTTTTGGAAGG
* * *
30942 TTCGGGGTCAAAAAAGGGATTTTTGGAA-G
1 TTCGAGGT-TAAAATGGGATTTTTGGAAGG
* *
30971 TTCG-GGGTAAAATGGTAATTTTTGGAAGG
1 TTCGAGGTTAAAATGG-GATTTTTGGAAGG
* * *
31000 TTCGGGGTTAAAATGAGATTTTTGG-AGT
1 TTCGAGGTTAAAATGGGATTTTTGGAAGG
* * *
31028 TTCGAGGGTAAAATGGTAACTTTTGGAAGG
1 TTCGAGGTTAAAATGG-GATTTTTGGAAGG
*
31058 TTTTG-GGTTAAAAATGGGATTTTTGGAA-G
1 -TTCGAGGTT-AAAATGGGATTTTTGGAAGG
* *
31087 CTCGAAGGGTAAAATGGTGATTTTTGGAAGG
1 TTCG-AGGTTAAAATGG-GATTTTTGGAAGG
*
31118 TTCAAGGTTAAAAATGGGATTTTT
1 TTCGAGGTT-AAAATGGGATTTTT
31142 TGAGAGGATT
Statistics
Matches: 180, Mismatches: 33, Indels: 31
0.74 0.14 0.13
Matches are distributed among these distances:
27 6 0.03
28 47 0.26
29 41 0.23
30 66 0.37
31 20 0.11
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.34
Consensus pattern (29 bp):
TTCGAGGTTAAAATGGGATTTTTGGAAGG
Found at i:30963 original size:58 final size:60
Alignment explanation
Indices: 30884--31141 Score: 323
Period size: 58 Copynumber: 4.4 Consensus size: 60
30874 TTTTAAGAGT
* * *
30884 TTCGAGGTTGAAAATGGGATTTTTGGAAGTTCGGA-GGTAGAATGGTAA-TTTTGGAAGG
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGAGGGTAAAATGGTAACTTTTGGAAGG
* * *
30942 TTCGGGGTCAAAAAAGGGATTTTTGGAAGTTC-G-GGGTAAAATGGTAATTTTTGGAAGG
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGAGGGTAAAATGGTAACTTTTGGAAGG
*
31000 TTCGGGGTT-AAAATGAGATTTTTGG-AGTTTC-GAGGGTAAAATGGTAACTTTTGGAAGG
1 TTCGGGGTTAAAAATGGGATTTTTGGAAG-TTCGGAGGGTAAAATGGTAACTTTTGGAAGG
** * * * *
31058 TTTTGGGTTAAAAATGGGATTTTTGGAAGCTCGAAGGGTAAAATGGTGATTTTTGGAAGG
1 TTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGAGGGTAAAATGGTAACTTTTGGAAGG
**
31118 TTCAAGGTTAAAAATGGGATTTTT
1 TTCGGGGTTAAAAATGGGATTTTT
31142 TGAGAGGATT
Statistics
Matches: 174, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
56 2 0.01
57 31 0.18
58 77 0.44
59 17 0.10
60 47 0.27
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.34
Consensus pattern (60 bp):
TTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGAGGGTAAAATGGTAACTTTTGGAAGG
Found at i:31745 original size:31 final size:30
Alignment explanation
Indices: 31693--31803 Score: 127
Period size: 31 Copynumber: 3.7 Consensus size: 30
31683 GAGGTCCCTA
*
31693 AACCTTCCAAAAATCCCATTTTTAACCTCG
1 AACCTTCCAAAAATCCCATTTTTAACCACG
* *
31723 AACCTTCCAAAAATCCCCATTTTAAACCACA
1 AACCTTCCAAAAAT-CCCATTTTTAACCACG
* * *
31754 AACCTTCCAAAAATTACCA-TTTTACCCCCG
1 AACCTTCCAAAAA-TCCCATTTTTAACCACG
*
31784 AA-CTTCTAAAAATCCCATTT
1 AACCTTCCAAAAATCCCATTT
31804 CCAAAAATCA
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
28 4 0.06
29 11 0.16
30 23 0.34
31 29 0.43
32 1 0.01
ACGTcount: A:0.37, C:0.33, G:0.02, T:0.28
Consensus pattern (30 bp):
AACCTTCCAAAAATCCCATTTTTAACCACG
Found at i:31821 original size:44 final size:45
Alignment explanation
Indices: 31758--31848 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 45
31748 ACCACAAACC
* *
31758 TTCCAAAAATTACCATTTTACCC-CCGAACTTCTAAAAATCCCAT
1 TTCCAAAAATCACCATTTTACCCTCCGAACTTCCAAAAATCCCAT
* * *
31802 TTCCAAAAATCACCATTTTACCCTCCGAGCTTCCAGAAATCTCAT
1 TTCCAAAAATCACCATTTTACCCTCCGAACTTCCAAAAATCCCAT
31847 TT
1 TT
31849 TTAACCCCGA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 22 0.54
45 19 0.46
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (45 bp):
TTCCAAAAATCACCATTTTACCCTCCGAACTTCCAAAAATCCCAT
Found at i:31842 original size:30 final size:29
Alignment explanation
Indices: 31802--32203 Score: 304
Period size: 30 Copynumber: 13.6 Consensus size: 29
31792 AAAATCCCAT
*
31802 TTCCAAAAATCACCATTTTACCCTCCGAGC
1 TTCCAAAAATC-CCATTTTACCCTCCGACC
* * *
31832 TTCCAGAAATCTCATTTTTAACC-CCGAACC
1 TTCCAAAAATCCCA-TTTTACCCTCCG-ACC
* ** *
31862 TTCCAAAAATTACCATTTTACCCTCAAAAC
1 TTCCAAAAA-TCCCATTTTACCCTCCGACC
*
31892 -TCCAAAAATCCCATTTTGAACC-CCGAACC
1 TTCCAAAAATCCCATTTT-ACCCTCCG-ACC
* *
31921 TTCCAAAAATTACCATTTTACCC-CCGAAC
1 TTCCAAAAA-TCCCATTTTACCCTCCGACC
*
31950 TTCCAAAAATCCCATTTTTAACCT-CGAACC
1 TTCCAAAAATCCCA-TTTTACCCTCCG-ACC
*
31980 TTCCAAAAATCACCATTTTACCCTCCGAGC
1 TTCCAAAAATC-CCATTTTACCCTCCGACC
*
32010 TTCCAAAAATCCCATTTTTAACC-CCGAACC
1 TTCCAAAAATCCCA-TTTTACCCTCCG-ACC
* * ** *
32040 TTCCAAAAGTTACCATTTTACCCTCAAAAC
1 TTCCAAAA-ATCCCATTTTACCCTCCGACC
**
32070 -TCCAAAAATCCCATTTTAACCC-CAAACC
1 TTCCAAAAATCCCATTTT-ACCCTCCGACC
* * *
32098 TTCCAAAAATTACCATTCTA-CCTCCGAAC
1 TTCCAAAAA-TCCCATTTTACCCTCCGACC
*
32127 TTCCAAAAATCCCATTTTTAACC-CCGAACC
1 TTCCAAAAATCCCA-TTTTACCCTCCG-ACC
* * * *
32157 TTCCAAAAATTACCATTCTA-CCTCCAAAC
1 TTCCAAAAA-TCCCATTTTACCCTCCGACC
32186 TTCCAAAAATCCCATTTT
1 TTCCAAAAATCCCATTTT
32204 CGACCTCGAA
Statistics
Matches: 297, Mismatches: 49, Indels: 54
0.74 0.12 0.14
Matches are distributed among these distances:
28 39 0.13
29 96 0.32
30 136 0.46
31 26 0.09
ACGTcount: A:0.34, C:0.35, G:0.03, T:0.28
Consensus pattern (29 bp):
TTCCAAAAATCCCATTTTACCCTCCGACC
Found at i:31884 original size:104 final size:105
Alignment explanation
Indices: 31697--31907 Score: 277
Period size: 104 Copynumber: 2.0 Consensus size: 105
31687 TCCCTAAACC
31697 TTCCAAAAATCCCATTTTTAACCTCGAACCTTCCAAAAATCCCCATTTTAAACCACAAACCTTCC
1 TTCCAAAAATCCCATTTTTAACCTCGAACCTTCCAAAAATCCCCATTTTAAACCACAAACCTTCC
** *
31762 AAAAATTACCATTTTACCC-CCGAACTTCTAAAAATCCCAT
66 AAAAATTACCATTTTACCCTCAAAAC-TCCAAAAATCCCAT
* * * * * * *
31802 TTCCAAAAATCACCA-TTTTACCCTCCG-AGCTTCCAGAAAT-CTCATTTTTAACCCCGAACCTT
1 TTCCAAAAATC-CCATTTTTAACCT-CGAACCTTCCAAAAATCCCCATTTTAAACCACAAACCTT
31864 CCAAAAATTACCATTTTACCCTCAAAACTCCAAAAATCCCAT
64 CCAAAAATTACCATTTTACCCTCAAAACTCCAAAAATCCCAT
31906 TT
1 TT
31908 TGAACCCCGA
Statistics
Matches: 93, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
104 54 0.58
105 34 0.37
106 5 0.05
ACGTcount: A:0.36, C:0.33, G:0.03, T:0.28
Consensus pattern (105 bp):
TTCCAAAAATCCCATTTTTAACCTCGAACCTTCCAAAAATCCCCATTTTAAACCACAAACCTTCC
AAAAATTACCATTTTACCCTCAAAACTCCAAAAATCCCAT
Found at i:31938 original size:135 final size:135
Alignment explanation
Indices: 31696--31938 Score: 330
Period size: 135 Copynumber: 1.8 Consensus size: 135
31686 GTCCCTAAAC
* * *
31696 CTTCCAAAAATCCCATTTTTAACCTCGAACCTTCCAAAAATCCCCATTTTAAACCACAAACCTTC
1 CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATCACCATTTTAAACCACAAAACTTC
* * *
31761 CAAAAATTACCATTTTACCCCCGAACTTCTAAAAATCCCATTTCCAAAAATCACCATTTTACCCT
66 CAAAAATTACCATTTTAACCCCGAACTTCCAAAAATACCATTTCCAAAAATCACCATTTTACCCT
31826 CCGAG
131 CCGAG
* * * * *
31831 CTTCCAGAAATCTCATTTTTAACCCCGAACCTTCCAAAAATTACCATTTT-ACCCTCAAAAC-TC
1 CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATCACCATTTTAAACCACAAAACTTC
*
31894 CAAAAA-TCCCATTTTGAACCCCGAACCTTCCAAAAATTACCATTT
66 CAAAAATTACCATTTT-AACCCCGAA-CTTCCAAAAA-TACCATTT
31939 TACCCCCGAA
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
132 8 0.09
133 16 0.17
134 17 0.18
135 52 0.56
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.28
Consensus pattern (135 bp):
CTTCCAAAAATCCCATTTTTAACCCCGAACCTTCCAAAAATCACCATTTTAAACCACAAAACTTC
CAAAAATTACCATTTTAACCCCGAACTTCCAAAAATACCATTTCCAAAAATCACCATTTTACCCT
CCGAG
Found at i:32223 original size:59 final size:60
Alignment explanation
Indices: 31802--32203 Score: 609
Period size: 59 Copynumber: 6.8 Consensus size: 60
31792 AAAATCCCAT
* * * *
31802 TTCCAAAAATCACCATTTTACCCTCCGAGCTTCCAGAAATCTCATTTTTAACCCCGAACC
1 TTCCAAAAATTACCATTTTACCCTCCGAACTTCCAAAAATCCCATTTTTAACCCCGAACC
** *
31862 TTCCAAAAATTACCATTTTACCCTCAAAAC-TCCAAAAATCCCATTTTGAACCCCGAACC
1 TTCCAAAAATTACCATTTTACCCTCCGAACTTCCAAAAATCCCATTTTTAACCCCGAACC
*
31921 TTCCAAAAATTACCATTTTACCC-CCGAACTTCCAAAAATCCCATTTTTAACCTCGAACC
1 TTCCAAAAATTACCATTTTACCCTCCGAACTTCCAAAAATCCCATTTTTAACCCCGAACC
* *
31980 TTCCAAAAATCACCATTTTACCCTCCGAGCTTCCAAAAATCCCATTTTTAACCCCGAACC
1 TTCCAAAAATTACCATTTTACCCTCCGAACTTCCAAAAATCCCATTTTTAACCCCGAACC
* ** *
32040 TTCCAAAAGTTACCATTTTACCCTCAAAAC-TCCAAAAATCCCA-TTTTAACCCCAAACC
1 TTCCAAAAATTACCATTTTACCCTCCGAACTTCCAAAAATCCCATTTTTAACCCCGAACC
*
32098 TTCCAAAAATTACCATTCTA-CCTCCGAACTTCCAAAAATCCCATTTTTAACCCCGAACC
1 TTCCAAAAATTACCATTTTACCCTCCGAACTTCCAAAAATCCCATTTTTAACCCCGAACC
* *
32157 TTCCAAAAATTACCATTCTA-CCTCCAAACTTCCAAAAATCCCATTTT
1 TTCCAAAAATTACCATTTTACCCTCCGAACTTCCAAAAATCCCATTTT
32204 CGACCTCGAA
Statistics
Matches: 312, Mismatches: 26, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
57 7 0.02
58 49 0.16
59 171 0.55
60 85 0.27
ACGTcount: A:0.34, C:0.35, G:0.03, T:0.28
Consensus pattern (60 bp):
TTCCAAAAATTACCATTTTACCCTCCGAACTTCCAAAAATCCCATTTTTAACCCCGAACC
Found at i:38693 original size:15 final size:14
Alignment explanation
Indices: 38673--38702 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
38663 AGAGGTCGCA
38673 TTCTTTTTTCCTTTT
1 TTCTTTTTT-CTTTT
38688 TTCTTTTTTCTTTT
1 TTCTTTTTTCTTTT
38702 T
1 T
38703 CATCGGTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTTTTTCTTTT
Found at i:38703 original size:6 final size:7
Alignment explanation
Indices: 38673--38702 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
38663 AGAGGTCGCA
38673 TTCTTTT
1 TTCTTTT
38680 TTCCTTTT
1 TT-CTTTT
38688 TTCTTTT
1 TTCTTTT
38695 TTCTTTT
1 TTCTTTT
38702 T
1 T
38703 CATCGGTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTCTTTT
Found at i:45725 original size:16 final size:16
Alignment explanation
Indices: 45700--45742 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
45690 TAACATTACT
*
45700 AATTTAAAATTATATA
1 AATTAAAAATTATATA
* * *
45716 AATTATAAATGATCTA
1 AATTAAAAATTATATA
45732 AATTAAAAATT
1 AATTAAAAATT
45743 TATCATTTTA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
AATTAAAAATTATATA
Found at i:61893 original size:192 final size:192
Alignment explanation
Indices: 61566--61937 Score: 654
Period size: 192 Copynumber: 1.9 Consensus size: 192
61556 TGCCACAAGT
*
61566 GGATGATCAGGGTAGTCTGGATCAAATTTTGGTTAAACACAAATCAAAATCAGAGAAAGAGAAGA
1 GGATGATCAGGGTAGTCTGGACCAAATTTTGGTTAAACACAAATCAAAATCAGAGAAAGAGAAGA
* *
61631 TGGCAAGTGCTGAGCAAGCAAGTGAGCAGATTAGATTATCTGTATCTCGTAGAGAAGCAAGGGAG
66 TGGCAACTGCTGAGCAACCAAGTGAGCAGATTAGATTATCTGTATCTCGTAGAGAAGCAAGGGAG
* *
61696 AGAGAGTTTCAAGAAGCATGGGGTGGCTTAAGCTTAGGAAACTCCATTAAACAACAGGTGGC
131 AGAGAGTTGCAAGAAGCATGGGGAGGCTTAAGCTTAGGAAACTCCATTAAACAACAGGTGGC
*
61758 GGATGATCAGGGTAGTCTGGACCAAATTTTGGTTAAACACAAATCAAAATTAGAGAAAGAGAAGA
1 GGATGATCAGGGTAGTCTGGACCAAATTTTGGTTAAACACAAATCAAAATCAGAGAAAGAGAAGA
* * *
61823 TGGCTACTTCTGAGCAACCAAGTGAGCAGATTAGATTCTCTGTATCTCGTAGAGAAGCAAGGGAG
66 TGGCAACTGCTGAGCAACCAAGTGAGCAGATTAGATTATCTGTATCTCGTAGAGAAGCAAGGGAG
*
61888 AGAGAGTTGCAAGAAGCATGGGGAGGCTTAGGCTTAGGAAACTCCATTAA
131 AGAGAGTTGCAAGAAGCATGGGGAGGCTTAAGCTTAGGAAACTCCATTAA
61938 GCCACATTTA
Statistics
Matches: 170, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
192 170 1.00
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (192 bp):
GGATGATCAGGGTAGTCTGGACCAAATTTTGGTTAAACACAAATCAAAATCAGAGAAAGAGAAGA
TGGCAACTGCTGAGCAACCAAGTGAGCAGATTAGATTATCTGTATCTCGTAGAGAAGCAAGGGAG
AGAGAGTTGCAAGAAGCATGGGGAGGCTTAAGCTTAGGAAACTCCATTAAACAACAGGTGGC
Found at i:62122 original size:34 final size:35
Alignment explanation
Indices: 62064--62133 Score: 115
Period size: 34 Copynumber: 2.0 Consensus size: 35
62054 TCAGGCTGCC
62064 TGGAGAAAAGCTGAAGAGGAGGAAAGGATGCTAGCCA
1 TGGAGAAAAGCT--AGAGGAGGAAAGGATGCTAGCCA
62101 TGGAGAAAAGCT-GAGGAGGAAAGGATGCTAGCC
1 TGGAGAAAAGCTAGAGGAGGAAAGGATGCTAGCC
62134 TGGCCGTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
34 21 0.64
37 12 0.36
ACGTcount: A:0.39, C:0.11, G:0.39, T:0.11
Consensus pattern (35 bp):
TGGAGAAAAGCTAGAGGAGGAAAGGATGCTAGCCA
Found at i:62228 original size:41 final size:41
Alignment explanation
Indices: 62181--62261 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
62171 TTTGTACAAG
*
62181 AAACATTGAGTTGAAATGTTTATCCTTAATTTATTTGTATA
1 AAACATTGAGTTGAAATGATTATCCTTAATTTATTTGTATA
62222 AAACATTGAGTTGAAATGATTATCCTTAATTTATTTGTAT
1 AAACATTGAGTTGAAATGATTATCCTTAATTTATTTGTAT
62262 GATCCCATCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (41 bp):
AAACATTGAGTTGAAATGATTATCCTTAATTTATTTGTATA
Found at i:66457 original size:13 final size:16
Alignment explanation
Indices: 66429--66465 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
66419 CAATTGAGTC
66429 ATTTTCATTTATAATT
1 ATTTTCATTTATAATT
66445 -TTTTC-TTTA-AATT
1 ATTTTCATTTATAATT
66458 ATTTTCAT
1 ATTTTCAT
66466 AATTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
13 4 0.21
14 9 0.47
15 6 0.32
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTTCATTTATAATT
Found at i:66705 original size:6 final size:6
Alignment explanation
Indices: 66688--66718 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
66678 TTGCTTGCTT
*
66688 AACATC AGCATC AACATC AACATC AACATC A
1 AACATC AACATC AACATC AACATC AACATC A
66719 TCTTCTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.32, G:0.03, T:0.16
Consensus pattern (6 bp):
AACATC
Found at i:87804 original size:24 final size:21
Alignment explanation
Indices: 87764--87812 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
87754 AGACAATTTT
87764 ATTTTTTTTAAAATTAAATAA
1 ATTTTTTTTAAAATTAAATAA
*
87785 ATTTGTTTTTAAAATT--TTAA
1 ATTT-TTTTTAAAATTAAATAA
87805 ATTTTTTT
1 ATTTTTTT
87813 ATATAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 4 0.15
20 7 0.27
21 4 0.15
22 11 0.42
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTTTTTTAAAATTAAATAA
Found at i:92364 original size:22 final size:22
Alignment explanation
Indices: 92322--92364 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
92312 ATATTCAAAA
* *
92322 ATATATTTTCAATTGATATTTT
1 ATATATTTACAATTGAAATTTT
92344 ATATACTTTACAATT-AAATTT
1 ATATA-TTTACAATTGAAATTT
92365 AAAAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (22 bp):
ATATATTTACAATTGAAATTTT
Found at i:98133 original size:19 final size:19
Alignment explanation
Indices: 98095--98133 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
98085 AGAGTAAATT
*
98095 TCCAGAAATCAAATGTAAA
1 TCCAGAAATCAAATGGAAA
*
98114 TCCAGAAATCAAGTGGAAA
1 TCCAGAAATCAAATGGAAA
98133 T
1 T
98134 AATAGACATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (19 bp):
TCCAGAAATCAAATGGAAA
Found at i:101616 original size:28 final size:28
Alignment explanation
Indices: 101563--101616 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
101553 TTATCTTTTA
* **
101563 TTTAATAAAGATAATTTTTTTTTATAAT
1 TTTAATAAAGATAATTTTGTAGTATAAT
*
101591 TTTAATAAGGATAATTTTGTAGTATA
1 TTTAATAAAGATAATTTTGTAGTATA
101617 TAATTACATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (28 bp):
TTTAATAAAGATAATTTTGTAGTATAAT
Found at i:106436 original size:10 final size:9
Alignment explanation
Indices: 106386--106492 Score: 61
Period size: 9 Copynumber: 11.1 Consensus size: 9
106376 TAAAAATTAT
106386 TTTTAAAAA
1 TTTTAAAAA
**
106395 AATTAAAAA
1 TTTTAAAAA
* *
106404 CTATAAAAGA
1 TTTTAAAA-A
*
106414 TCTTGTAAGAA
1 T-TT-TAAAAA
106425 TTTTAAAAAA
1 TTTT-AAAAA
106435 TTATTAAAAA
1 TT-TTAAAAA
*
106445 TTATAAAAA
1 TTTTAAAAA
* *
106454 TATTAAAGA
1 TTTTAAAAA
*
106463 TATTAAAAA
1 TTTTAAAAA
*
106472 GTTTTAAAAT
1 -TTTTAAAAA
106482 TTATTAAAAA
1 TT-TTAAAAA
106492 T
1 T
106493 ATAAAATAAA
Statistics
Matches: 74, Mismatches: 17, Indels: 13
0.71 0.16 0.12
Matches are distributed among these distances:
9 35 0.47
10 30 0.41
11 5 0.07
12 4 0.05
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:106451 original size:20 final size:20
Alignment explanation
Indices: 106396--106492 Score: 60
Period size: 19 Copynumber: 5.0 Consensus size: 20
106386 TTTTAAAAAA
* *
106396 ATTAAAAACTATAAAAGATCT
1 ATTAAAAATTATAAAAAAT-T
* *
106417 -TGTAAGAATTTTAAAAAATT
1 AT-TAAAAATTATAAAAAATT
106437 ATTAAAAATTAT-AAAAA-T
1 ATTAAAAATTATAAAAAATT
* *
106455 ATTAAAGA-TATTAAAAAGTT
1 ATTAAAAATTA-TAAAAAATT
* *
106475 -TTAAAATTTATTAAAAAT
1 ATTAAAAATTATAAAAAAT
106493 ATAAAATAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
17 2 0.03
18 9 0.16
19 20 0.34
20 13 0.22
21 14 0.24
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (20 bp):
ATTAAAAATTATAAAAAATT
Found at i:106469 original size:38 final size:40
Alignment explanation
Indices: 106388--106494 Score: 107
Period size: 38 Copynumber: 2.8 Consensus size: 40
106378 AAAATTATTT
* * * *
106388 TTAAAAAA--ATTAAAAACTATAAAAGATCTTGTAAGAATT
1 TTAAAAAATTATTAAAAATTATAAAA-ATATTGAAAGAATA
106427 TTAAAAAATTATTAAAAATTATAAAAATATT-AAAG-ATA
1 TTAAAAAATTATTAAAAATTATAAAAATATTGAAAGAATA
* *
106465 TTAAAAAGTT-TTAAAATTTATTAAAAATAT
1 TTAAAAAATTATTAAAAATTA-TAAAAATAT
106495 AAAATAAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
37 9 0.15
38 20 0.34
39 11 0.19
40 4 0.07
41 15 0.25
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (40 bp):
TTAAAAAATTATTAAAAATTATAAAAATATTGAAAGAATA
Found at i:106499 original size:18 final size:18
Alignment explanation
Indices: 106439--106499 Score: 52
Period size: 20 Copynumber: 3.3 Consensus size: 18
106429 AAAAAATTAT
*
106439 TAAAAATTA-TAAAAATA
1 TAAAATTTATTAAAAATA
* ** *
106456 TTAAAGATATTAAAAAGTTT
1 TAAAATTTATTAAAAA--TA
106476 TAAAATTTATTAAAAATA
1 TAAAATTTATTAAAAATA
106494 TAAAAT
1 TAAAAT
106500 AAAATAAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
17 6 0.18
18 13 0.39
20 14 0.42
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TAAAATTTATTAAAAATA
Found at i:108602 original size:27 final size:26
Alignment explanation
Indices: 108555--108640 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 26
108545 AATCTCTTTG
108555 TTATAATAATTTTTACA-ATTTGTCATTT
1 TTATAA-AA-TTTTA-ATATTTGTCATTT
108583 TTATAAAATTTTAATTATTT-TCATACTT
1 TTATAAAATTTTAA-TATTTGTCAT--TT
*
108611 TT-TAAAGTTTTAATATTTGTTACATTT
1 TTATAAAATTTTAATATTTG-T-CATTT
108638 TTA
1 TTA
108641 AAATAAAAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 16
0.74 0.02 0.24
Matches are distributed among these distances:
25 1 0.02
26 14 0.29
27 20 0.41
28 11 0.22
29 3 0.06
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (26 bp):
TTATAAAATTTTAATATTTGTCATTT
Found at i:108606 original size:26 final size:26
Alignment explanation
Indices: 108572--108644 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
108562 AATTTTTACA
108572 ATTTGTCAT-TTTTATAAAATTTTAATT
1 ATTTGTCATATTTT-TAAAATTTTAA-T
*
108599 ATTT-TCATACTTTTTAAAGTTTTAAT
1 ATTTGTCATA-TTTTTAAAATTTTAAT
* *
108625 ATTTGTTACATTTTTAAAAT
1 ATTTGTCATATTTTTAAAAT
108645 AAAAATTACA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 18 0.46
27 17 0.44
28 4 0.10
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (26 bp):
ATTTGTCATATTTTTAAAATTTTAAT
Found at i:109892 original size:103 final size:103
Alignment explanation
Indices: 109713--110029 Score: 589
Period size: 103 Copynumber: 3.1 Consensus size: 103
109703 GCTAGACTGG
* * * *
109713 TTGTTTATCGACTGTTTCATTTCTTTATTTTCAGAGAGTAATGGATTCCTGGTATGTGGCTAGCT
1 TTGTTTATCGACTGTTTCATTTCTTTATTTTCAGAGAGTTATCGATTCCAGGTATGAGGCTAGCT
109778 TGCGCATGTGCAAAGACAGTACATTCTGCCTAATTTAT
66 TGCGCATGTGCAAAGACAGTACATTCTGCCTAATTTAT
109816 TTGTTTATCGACTGTTTCATTTCTTTATTTTCAGAGAGTTATCGATTCCAGGTATGAGGCTAGCT
1 TTGTTTATCGACTGTTTCATTTCTTTATTTTCAGAGAGTTATCGATTCCAGGTATGAGGCTAGCT
*
109881 TGCGCATGTGCAAAGACAGTACATTCTGCCTAATTTAA
66 TGCGCATGTGCAAAGACAGTACATTCTGCCTAATTTAT
109919 TTGTTTATCGACTGTTTCATTTCTTTATTTTCAGAGAGTTATCGATTCCAGGTATGAGGCTAGCT
1 TTGTTTATCGACTGTTTCATTTCTTTATTTTCAGAGAGTTATCGATTCCAGGTATGAGGCTAGCT
109984 TGCGCATGTGCAAAGACAGTACATTCTGCCTAATTTAT
66 TGCGCATGTGCAAAGACAGTACATTCTGCCTAATTTAT
110022 TTGTTTAT
1 TTGTTTAT
110030 AATATAAATG
Statistics
Matches: 208, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 208 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.41
Consensus pattern (103 bp):
TTGTTTATCGACTGTTTCATTTCTTTATTTTCAGAGAGTTATCGATTCCAGGTATGAGGCTAGCT
TGCGCATGTGCAAAGACAGTACATTCTGCCTAATTTAT
Found at i:114221 original size:15 final size:15
Alignment explanation
Indices: 114203--114285 Score: 76
Period size: 15 Copynumber: 5.5 Consensus size: 15
114193 AGCATATTGA
*
114203 GGAGGATATCCCTGC
1 GGAGGATATCCCTGT
*
114218 GGAGGGTATCCCTGT
1 GGAGGATATCCCTGT
* * *
114233 TGAGCATATCCTTGT
1 GGAGGATATCCCTGT
*
114248 GGAGGATATCCTTGT
1 GGAGGATATCCCTGT
* * *
114263 GGGGGATACCCCGGT
1 GGAGGATATCCCTGT
*
114278 GGTGGATA
1 GGAGGATA
114286 AGCATCCTTT
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 55 1.00
ACGTcount: A:0.18, C:0.19, G:0.36, T:0.27
Consensus pattern (15 bp):
GGAGGATATCCCTGT
Found at i:128406 original size:15 final size:16
Alignment explanation
Indices: 128373--128406 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
128363 AATAACTATG
*
128373 TTTAGAACAACTTGTA
1 TTTAGAACAACTCGTA
128389 TTTAGAACAA-TCGTA
1 TTTAGAACAACTCGTA
128404 TTT
1 TTT
128407 CTCTAGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (16 bp):
TTTAGAACAACTCGTA
Found at i:129375 original size:19 final size:19
Alignment explanation
Indices: 129313--129378 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
129303 CTCTCACAAC
* *
129313 AAAAATTACAAAATAATATT
1 AAAAATT-CAAAATCATTTT
* *
129333 CAAAATTCAACATCATTTT
1 AAAAATTCAAAATCATTTT
*
129352 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATCATTT-T
129371 AAAAATTC
1 AAAAATTC
129379 CACAATTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 4 0.11
19 28 0.74
20 6 0.16
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTCAAAATCATTTT
Found at i:129424 original size:11 final size:10
Alignment explanation
Indices: 129393--129427 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
129383 ATTTATATTT
129393 TAAAAAATTA
1 TAAAAAATTA
129403 TAAAAAA-TA
1 TAAAAAATTA
129412 TAAAGAAATTA
1 TAAA-AAATTA
129423 TAAAA
1 TAAAA
129428 TTCATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 6 0.26
10 11 0.48
11 6 0.26
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:131446 original size:2 final size:2
Alignment explanation
Indices: 131439--131465 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
131429 CTGCAATTAG
131439 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
131466 AAATATGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:134209 original size:24 final size:25
Alignment explanation
Indices: 134176--134229 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
134166 TTGGAAATTA
*
134176 TTTAATTATT-ATTT-GATTTTTTAT
1 TTTAAGTATTAATTTAGATTTTTT-T
134200 TTTAAGTATTAAATTTAGATTTTTTT
1 TTTAAGTATT-AATTTAGATTTTTTT
134226 TTTA
1 TTTA
134230 TCACGAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 9 0.35
26 9 0.35
27 8 0.31
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (25 bp):
TTTAAGTATTAATTTAGATTTTTTT
Found at i:136001 original size:2 final size:2
Alignment explanation
Indices: 135994--136029 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
135984 TTTGATTAGC
135994 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
136030 TGAATGTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:140697 original size:22 final size:22
Alignment explanation
Indices: 140669--140729 Score: 59
Period size: 26 Copynumber: 2.6 Consensus size: 22
140659 AATTATATAT
*
140669 TTTTTAAAAATAAATACATTTA
1 TTTTTAAAAATAAATACAATTA
*
140691 TTTTTAATATTAGATAAATATAATTA
1 TTTTTAA-A--A-ATAAATACAATTA
*
140717 TTTATAAAAATAA
1 TTTTTAAAAATAA
140730 GGTTACGTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
22 11 0.34
23 2 0.06
25 2 0.06
26 17 0.53
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
TTTTTAAAAATAAATACAATTA
Found at i:141628 original size:9 final size:9
Alignment explanation
Indices: 141616--141665 Score: 50
Period size: 8 Copynumber: 5.6 Consensus size: 9
141606 AAAATATTAG
141616 AAATTATTAA
1 AAATTA-TAA
141626 AATATTATAA
1 AA-ATTATAA
141636 AAATTATAA
1 AAATTATAA
**
141645 AAA-TAGGA
1 AAATTATAA
141653 AAA-TATAA
1 AAATTATAA
141661 AAATT
1 AAATT
141666 CATACAAGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
8 12 0.35
9 11 0.32
10 7 0.21
11 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (9 bp):
AAATTATAA
Found at i:141648 original size:29 final size:29
Alignment explanation
Indices: 141590--141648 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
141580 AATAATAATT
* * *
141590 TTATTAAATTTTTAAAAAAATATTAGAAA
1 TTATTAAAATATTAAAAAAATATTAAAAA
*
141619 TTATTAAAATATTATAAAAAT-TATAAAAA
1 TTATTAAAATATTAAAAAAATAT-TAAAAA
141648 T
1 T
141649 AGGAAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (29 bp):
TTATTAAAATATTAAAAAAATATTAAAAA
Found at i:143546 original size:193 final size:193
Alignment explanation
Indices: 143217--143608 Score: 766
Period size: 193 Copynumber: 2.0 Consensus size: 193
143207 CTTACTAATA
143217 ATTGAATAATCAAATTGCAAATTTACTCATCCCTACATCTAACTTCTGTTAGCAACTTAATCGTC
1 ATTGAATAATCAAATTGCAAATTTACTCATCCCTACATCTAACTTCTGTTAGCAACTTAATCGTC
143282 CAATCACTTAAAAAATACATTTCAAATAATTTAATTACTAATTTATGACTTTTTTTTTATAAATT
66 CAATCACTTAAAAAATACATTTCAAATAATTTAATTACTAATTTATGACTTTTTTTTTATAAATT
*
143347 ATACTTTGTATTATTTTTCAAACATTTATGGCAAGATTAAATTGAATAACCAAAAAGAAATCT
131 ATACTTTGTATTATTTTTCAAACATTTATGGCAAGATTAAATTAAATAACCAAAAAGAAATCT
*
143410 ATTGAATAATCAAATTGTAAATTTACTCATCCCTACATCTAACTTCTGTTAGCAACTTAATCGTC
1 ATTGAATAATCAAATTGCAAATTTACTCATCCCTACATCTAACTTCTGTTAGCAACTTAATCGTC
143475 CAATCACTTAAAAAATACATTTCAAATAATTTAATTACTAATTTATGACTTTTTTTTTATAAATT
66 CAATCACTTAAAAAATACATTTCAAATAATTTAATTACTAATTTATGACTTTTTTTTTATAAATT
143540 ATACTTTGTATTATTTTTCAAACATTTATGGCAAGATTAAATTAAATAACCAAAAAGAAATCT
131 ATACTTTGTATTATTTTTCAAACATTTATGGCAAGATTAAATTAAATAACCAAAAAGAAATCT
143603 ATTGAA
1 ATTGAA
143609 AGACAAAAAC
Statistics
Matches: 197, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
193 197 1.00
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (193 bp):
ATTGAATAATCAAATTGCAAATTTACTCATCCCTACATCTAACTTCTGTTAGCAACTTAATCGTC
CAATCACTTAAAAAATACATTTCAAATAATTTAATTACTAATTTATGACTTTTTTTTTATAAATT
ATACTTTGTATTATTTTTCAAACATTTATGGCAAGATTAAATTAAATAACCAAAAAGAAATCT
Found at i:146279 original size:15 final size:15
Alignment explanation
Indices: 146259--146292 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
146249 TACACAAAAA
146259 GAAAAAAAAAAGTGT
1 GAAAAAAAAAAGTGT
*
146274 GAAAAAAGAAAGTGT
1 GAAAAAAAAAAGTGT
146289 -AAAA
1 GAAAA
146293 TTAATCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.12
Consensus pattern (15 bp):
GAAAAAAAAAAGTGT
Found at i:149565 original size:31 final size:29
Alignment explanation
Indices: 149530--149598 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
149520 GATATTAAAA
149530 TTATATATGGATTTTGATTTAATATATAATG
1 TTATATATGGATTTTGATTT--TATATAATG
* * * *
149561 TTATACATAGATTTTGATTTTATGTAATT
1 TTATATATGGATTTTGATTTTATATAATG
149590 TTATATATG
1 TTATATATG
149599 AAATTCTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 14 0.44
31 18 0.56
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (29 bp):
TTATATATGGATTTTGATTTTATATAATG
Found at i:188370 original size:18 final size:18
Alignment explanation
Indices: 188347--188385 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
188337 AGTGTTCATG
188347 AAAGTGCAAAACAAAGTA
1 AAAGTGCAAAACAAAGTA
188365 AAAGTGCAAAACAAAGTA
1 AAAGTGCAAAACAAAGTA
188383 AAA
1 AAA
188386 CTTGGAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.64, C:0.10, G:0.15, T:0.10
Consensus pattern (18 bp):
AAAGTGCAAAACAAAGTA
Found at i:188872 original size:60 final size:60
Alignment explanation
Indices: 188804--188922 Score: 238
Period size: 60 Copynumber: 2.0 Consensus size: 60
188794 ATGTTACCCC
188804 ATCATTTTTTAGTTCTTTTCTCATAATCCAGCAATTCAATATTTAAGAAAAGACAAGCAT
1 ATCATTTTTTAGTTCTTTTCTCATAATCCAGCAATTCAATATTTAAGAAAAGACAAGCAT
188864 ATCATTTTTTAGTTCTTTTCTCATAATCCAGCAATTCAATATTTAAGAAAAGACAAGCA
1 ATCATTTTTTAGTTCTTTTCTCATAATCCAGCAATTCAATATTTAAGAAAAGACAAGCA
188923 ACCATCAAGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (60 bp):
ATCATTTTTTAGTTCTTTTCTCATAATCCAGCAATTCAATATTTAAGAAAAGACAAGCAT
Found at i:194022 original size:19 final size:21
Alignment explanation
Indices: 193987--194025 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
193977 ATATTAAAAT
193987 TAATTTTGAATAAAATTAAAG
1 TAATTTTGAATAAAATTAAAG
194008 TAATTTT-AA-AAAATTAAA
1 TAATTTTGAATAAAATTAAA
194026 AAAATTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
TAATTTTGAATAAAATTAAAG
Found at i:194031 original size:19 final size:21
Alignment explanation
Indices: 193979--194031 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 21
193969 AATATATGAT
*
193979 ATTAAAATTAATTTTGAATAAA
1 ATTAAAA-AAATTTTGAATAAA
**
194001 ATTAAAGTAATTTT-AA-AAA
1 ATTAAAAAAATTTTGAATAAA
194020 ATTAAAAAAATT
1 ATTAAAAAAATT
194032 ATAACACGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 13 0.46
20 2 0.07
21 7 0.25
22 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
ATTAAAAAAATTTTGAATAAA
Found at i:197103 original size:29 final size:29
Alignment explanation
Indices: 197071--197146 Score: 71
Period size: 31 Copynumber: 2.5 Consensus size: 29
197061 CAATTTGATT
**
197071 CATGAACTTTAATTTGATGCAGTTATATA
1 CATGAACTTTAATTTGATGCAAATATATA
* ** *
197100 CATGAAGCTTTGATTGTGATTTAAATGTATA
1 CATGAA-CTTTAATT-TGATGCAAATATATA
197131 CATGAAACTTTAATTT
1 CATG-AACTTTAATTT
197147 TGATTCAATC
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
29 6 0.16
30 8 0.22
31 21 0.57
32 2 0.05
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.42
Consensus pattern (29 bp):
CATGAACTTTAATTTGATGCAAATATATA
Found at i:197576 original size:15 final size:15
Alignment explanation
Indices: 197556--197584 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
197546 TCTGTTTGTA
197556 TGTAAAATATTTTTT
1 TGTAAAATATTTTTT
197571 TGTAAAATATTTTT
1 TGTAAAATATTTTT
197585 ATTGGTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (15 bp):
TGTAAAATATTTTTT
Found at i:197829 original size:18 final size:18
Alignment explanation
Indices: 197792--197830 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
197782 ATGTTTTTTT
**
197792 AAAAATATTTTTGAGTAA
1 AAAAATATTTTTGAAAAA
197810 AAAAATATTTTTGAAAAA
1 AAAAATATTTTTGAAAAA
197828 AAA
1 AAA
197831 GTTAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (18 bp):
AAAAATATTTTTGAAAAA
Found at i:197958 original size:18 final size:18
Alignment explanation
Indices: 197935--197977 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
197925 TATTTAATAA
197935 TATTTTTTATCTCAAAAG
1 TATTTTTTATCTCAAAAG
197953 TATTTTTTATCTCAAAAG
1 TATTTTTTATCTCAAAAG
*
197971 TACTTTT
1 TATTTTT
197978 GAGAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (18 bp):
TATTTTTTATCTCAAAAG
Found at i:201938 original size:60 final size:59
Alignment explanation
Indices: 201863--202025 Score: 193
Period size: 60 Copynumber: 2.7 Consensus size: 59
201853 ATTTAGTACT
201863 TAAACTTGACACTTTTTCCTAATTTAGTACCTAAACTTTTTTTTGACCCAATTTGATACC
1 TAAACTTGACACTTTTTCCTAATTT-GTACCTAAACTTTTTTTTGACCCAATTTGATACC
* * * * * *
201923 TAAACTTGACGCTTTTTTCTAATTTGATACCTAAACTTTTTTTGGACCTAATTTGGTACT
1 TAAACTTGACACTTTTTCCTAATTTG-TACCTAAACTTTTTTTTGACCCAATTTGATACC
* * * * *
201983 TGAACTTGATA-TTTTTCTTAATTTGGTATCTAAACTTTCTTTT
1 TAAACTTGACACTTTTTCCTAATTT-GTACCTAAACTTTTTTTT
202026 AAGATTCAAT
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
59 26 0.30
60 61 0.70
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (59 bp):
TAAACTTGACACTTTTTCCTAATTTGTACCTAAACTTTTTTTTGACCCAATTTGATACC
Found at i:210309 original size:23 final size:24
Alignment explanation
Indices: 210265--210314 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
210255 TTAATATTCG
* *
210265 TGAACATGTTCGATTAAGTTAA-A
1 TGAACATGTTCGATGAAATTAACA
210288 TGAACATGTTCG-TGAATATTAACA
1 TGAACATGTTCGATGAA-ATTAACA
210312 TGA
1 TGA
210315 GCACACATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.13
23 16 0.70
24 4 0.17
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (24 bp):
TGAACATGTTCGATGAAATTAACA
Found at i:214533 original size:21 final size:20
Alignment explanation
Indices: 214509--214551 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
214499 ATGAAAAGCC
*
214509 TTTTTAGTTACTTATTTAATT
1 TTTTTAGTTACTT-TTAAATT
* *
214530 TTTTTCGTTTCTTTTAAATT
1 TTTTTAGTTACTTTTAAATT
214550 TT
1 TT
214552 AAATCTACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTTAGTTACTTTTAAATT
Found at i:216771 original size:33 final size:33
Alignment explanation
Indices: 216724--216793 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
216714 AAAATTTAAA
216724 TTGAATTCTGTTGTTAAAATAAGATTCGTCAAC
1 TTGAATTCTGTTGTTAAAATAAGATTCGTCAAC
*
216757 TTGACTTCTGTTGTTAAAATAAGATTCGTCAAC
1 TTGAATTCTGTTGTTAAAATAAGATTCGTCAAC
216790 TTGA
1 TTGA
216794 TTAACTTGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (33 bp):
TTGAATTCTGTTGTTAAAATAAGATTCGTCAAC
Found at i:216869 original size:23 final size:23
Alignment explanation
Indices: 216839--216886 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
216829 TTGATCGAAT
*
216839 ACTAACCCCTAGATTAAAGCCTA
1 ACTAACCCCTAAATTAAAGCCTA
216862 ACTAACCCCTAAATTAAAGCCTA
1 ACTAACCCCTAAATTAAAGCCTA
216885 AC
1 AC
216887 ATGTGTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.31, G:0.06, T:0.21
Consensus pattern (23 bp):
ACTAACCCCTAAATTAAAGCCTA
Found at i:229497 original size:25 final size:24
Alignment explanation
Indices: 229467--229515 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
229457 CATGTTTATA
* *
229467 ATATAAAAATTTACAATTTAAATTT
1 ATATAAAAAATTA-AAATTAAATTT
229492 ATATAAAAAATTAAAATTAAATTT
1 ATATAAAAAATTAAAATTAAATTT
229516 TTGTGTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
ATATAAAAAATTAAAATTAAATTT
Found at i:233920 original size:129 final size:131
Alignment explanation
Indices: 233751--234011 Score: 402
Period size: 129 Copynumber: 2.0 Consensus size: 131
233741 ATATTCTATT
* *
233751 AATTTAATCTTAATCTTAAAAAAATAATTTAACCCTCATTTACA-CTTACTGTCAATTAATTTTT
1 AATTTAATCTTAATCTTAAAAAAATAATTTAAACCTCATTTACATC-TACTGGCAATTAATTTTT
*
233815 ACTTTTAAAATTTTAAAAATAA-ATTTTTAATAATATTTCGACTAAATTTATTAAAAATTAAAAT
65 ACTTTTAAAATTTTAAAAATAATATTTTTAATAATATGTCGACTAAATTTATTAAAAATTAAAAT
233879 AG
130 AG
*
233881 AATTTAGTCTTAATCTT-AAAAAATAATTTAAACCTCATTTACATCTACTGGCAATTAATTTTTA
1 AATTTAATCTTAATCTTAAAAAAATAATTTAAACCTCATTTACATCTACTGGCAATTAATTTTTA
* * * *
233945 CTTTTAAAATTTTAAAAATAATTTTTTTTTAATAATATGTCGGCTGAATTTATTAGAAATTAAAA
66 CTTTTAAAATTTTAAAAATAA--TATTTTTAATAATATGTCGACTAAATTTATTAAAAATTAAAA
234010 TA
129 TA
234012 AAGAAATATG
Statistics
Matches: 119, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
129 64 0.54
130 17 0.14
132 38 0.32
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.44
Consensus pattern (131 bp):
AATTTAATCTTAATCTTAAAAAAATAATTTAAACCTCATTTACATCTACTGGCAATTAATTTTTA
CTTTTAAAATTTTAAAAATAATATTTTTAATAATATGTCGACTAAATTTATTAAAAATTAAAATA
G
Found at i:235627 original size:14 final size:15
Alignment explanation
Indices: 235610--235638 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
235600 TTTAAAAAGC
235610 ACTACTAAA-AAAAT
1 ACTACTAAACAAAAT
235624 ACTACTAAACAAAAT
1 ACTACTAAACAAAAT
235639 CTTCAAGCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (15 bp):
ACTACTAAACAAAAT
Found at i:239993 original size:7 final size:7
Alignment explanation
Indices: 239979--240010 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
239969 AATAAATAAA
239979 AAATATT
1 AAATATT
*
239986 AAACATT
1 AAATATT
239993 AAATATT
1 AAATATT
240000 AAATATT
1 AAATATT
240007 AAAT
1 AAAT
240011 TAAAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (7 bp):
AAATATT
Found at i:250366 original size:25 final size:24
Alignment explanation
Indices: 250338--250384 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
250328 GAAAAAAAAG
250338 AATGAAAAGTTTTTTTTTAAAAACA
1 AATG-AAAGTTTTTTTTTAAAAACA
***
250363 AATGATTTTTTTTTTTTAAAAA
1 AATGAAAGTTTTTTTTTAAAAA
250385 TTCACTTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (24 bp):
AATGAAAGTTTTTTTTTAAAAACA
Found at i:250753 original size:30 final size:30
Alignment explanation
Indices: 250717--250905 Score: 155
Period size: 30 Copynumber: 6.3 Consensus size: 30
250707 TTTAAATTTT
* *
250717 TTTGACCCCCAAACTATCCAAAAATTCAAA
1 TTTGACCCCCAAATTTTCCAAAAATTCAAA
*** *
250747 TTTGACCCTTGAATTTTCCAAAACTTCAAA
1 TTTGACCCCCAAATTTTCCAAAAATTCAAA
* *
250777 TTTTGACTCCCAAATTTTCCAAAAAATT-GAA
1 -TTTGACCCCCAAATTTTCC-AAAAATTCAAA
** *
250808 TTTGATACCCAAATTTTCCAAAAATTCCAA
1 TTTGACCCCCAAATTTTCCAAAAATTCAAA
* * ***
250838 TTTGATCCCTAAATTTTCCAAAAATTTTGA
1 TTTGACCCCCAAATTTTCCAAAAATTCAAA
*** ** *
250868 TTTGACCCTTGAAGCTTCCAAAAATTCAAT
1 TTTGACCCCCAAATTTTCCAAAAATTCAAA
250898 TTTGACCC
1 TTTGACCC
250906 GGTTTTAATG
Statistics
Matches: 127, Mismatches: 29, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
29 7 0.06
30 97 0.76
31 17 0.13
32 6 0.05
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.34
Consensus pattern (30 bp):
TTTGACCCCCAAATTTTCCAAAAATTCAAA
Found at i:250887 original size:60 final size:60
Alignment explanation
Indices: 250717--250899 Score: 180
Period size: 61 Copynumber: 3.0 Consensus size: 60
250707 TTTAAATTTT
* * * * * *
250717 TTTGACCCCCAAACTATCC-AAAAATTCAAATTTGACCCTTGAATTTTCCAAAACTTCAAA
1 TTTGACTCCCAAATTTTCCAAAAAATT-GAATTTGACCCTTGAATTTTCCAAAAATTCCAA
*
250777 TTTTGACTCCCAAATTTTCCAAAAAATTGAATTTGATACCC--AAATTTTCCAAAAATTCCAA
1 -TTTGACTCCCAAATTTTCCAAAAAATTGAATTTG--ACCCTTGAATTTTCCAAAAATTCCAA
* **
250838 TTTGA-TCCCTAAATTTTCCAAAAATTTTG-ATTTGACCCTTGAAGCTTCCAAAAATT-CAA
1 TTTGACTCCC-AAATTTTCCAAAAA-ATTGAATTTGACCCTTGAATTTTCCAAAAATTCCAA
250897 TTT
1 TTT
250900 TGACCCGGTT
Statistics
Matches: 104, Mismatches: 11, Indels: 16
0.79 0.08 0.12
Matches are distributed among these distances:
58 4 0.04
59 10 0.10
60 37 0.36
61 42 0.40
62 7 0.07
63 4 0.04
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (60 bp):
TTTGACTCCCAAATTTTCCAAAAAATTGAATTTGACCCTTGAATTTTCCAAAAATTCCAA
Found at i:250902 original size:60 final size:60
Alignment explanation
Indices: 250716--250903 Score: 190
Period size: 60 Copynumber: 3.1 Consensus size: 60
250706 TTTTAAATTT
* * * * *
250716 TTTTGACCCCCAAACTATCC-AAAAATTCAAATTTGACCCTTGAATTTTCCAAAACTTCAAA
1 TTTTGACTCCCAAATTTTCCAAAAAATT-GAATTTGACCCTTGAATTTTCCAAAAATTC-AA
*
250777 TTTTGACTCCCAAATTTTCCAAAAAATTGAATTTGATACCC--AAATTTTCCAAAAATTCCAA
1 TTTTGACTCCCAAATTTTCCAAAAAATTGAATTTG--ACCCTTGAATTTTCCAAAAATT-CAA
* **
250838 -TTTGA-TCCCTAAATTTTCCAAAAATTTTG-ATTTGACCCTTGAAGCTTCCAAAAATTCAA
1 TTTTGACTCCC-AAATTTTCCAAAAA-ATTGAATTTGACCCTTGAATTTTCCAAAAATTCAA
250897 TTTTGAC
1 TTTTGAC
250904 CCGGTTTTAA
Statistics
Matches: 107, Mismatches: 10, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
58 4 0.04
59 7 0.07
60 42 0.39
61 42 0.39
62 8 0.07
63 4 0.04
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.35
Consensus pattern (60 bp):
TTTTGACTCCCAAATTTTCCAAAAAATTGAATTTGACCCTTGAATTTTCCAAAAATTCAA
Found at i:250969 original size:26 final size:24
Alignment explanation
Indices: 250921--250979 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 24
250911 TAATGTTTAT
250921 TTATTTAT-TTATTTTATCT-TATA
1 TTATTTATATTATTTTAT-TGTATA
250944 TGTATATTATATTATTTTATTGTATA
1 T-TAT-TTATATTATTTTATTGTATA
*
250970 TTATGTATAT
1 TTATTTATAT
250980 ATTGTTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 1 0.03
24 8 0.26
25 8 0.26
26 14 0.45
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (24 bp):
TTATTTATATTATTTTATTGTATA
Found at i:250981 original size:31 final size:29
Alignment explanation
Indices: 250913--250982 Score: 70
Period size: 31 Copynumber: 2.4 Consensus size: 29
250903 CCCGGTTTTA
* * *
250913 ATGTTTAT-TTATTTATTTATTTTATCTT
1 ATGTATATATTATTTATTTATTGTATATT
* *
250941 ATATGTATATTATATTATTTTATTGTATATT
1 ATGTATATATTAT-TTA-TTTATTGTATATT
250972 ATGTATATATT
1 ATGTATATATT
250983 GTTTTTATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 6 0.18
29 4 0.12
30 3 0.09
31 20 0.61
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.64
Consensus pattern (29 bp):
ATGTATATATTATTTATTTATTGTATATT
Found at i:250984 original size:18 final size:19
Alignment explanation
Indices: 250950--250998 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
250940 TATATGTATA
250950 TTATATTAT-T-T-TATTG
1 TTATATTATGTATATATTG
250966 -TATATTATGTATATATTG
1 TTATATTATGTATATATTG
*
250984 TTTTTATTATGTATA
1 -TTATATTATGTATA
250999 CTTGTAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 8 0.30
16 1 0.04
17 1 0.04
18 5 0.19
20 12 0.44
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (19 bp):
TTATATTATGTATATATTG
Found at i:255235 original size:2 final size:2
Alignment explanation
Indices: 255228--255252 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
255218 GATTCAGCAT
255228 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 T
255253 GAATGTATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:257085 original size:21 final size:21
Alignment explanation
Indices: 257060--257133 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
257050 TTCATCCGCA
*
257060 TACCCTCCTCCACCTTCGGCT
1 TACCCTCCACCACCTTCGGCT
*
257081 TACCCTCCGCCACCTTCGGCT
1 TACCCTCCACCACCTTCGGCT
** *
257102 TACCCTCCACCACCTTCCACA
1 TACCCTCCACCACCTTCGGCT
257123 TACCCTCCACC
1 TACCCTCCACC
257134 TCCACCACCT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.15, C:0.55, G:0.07, T:0.23
Consensus pattern (21 bp):
TACCCTCCACCACCTTCGGCT
Found at i:264027 original size:6 final size:6
Alignment explanation
Indices: 264003--264057 Score: 74
Period size: 6 Copynumber: 8.7 Consensus size: 6
263993 GCTAAACTCT
*
264003 CTTCTC CTTCCTC CTTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTCCTC
1 CTTCCC CTTCC-C C-TTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTCC-C
264054 CTTC
1 CTTC
264058 GTTCCGATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
6 32 0.71
7 9 0.20
8 4 0.09
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (6 bp):
CTTCCC
Found at i:266973 original size:33 final size:33
Alignment explanation
Indices: 266931--267003 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
266921 TAAGCACCAA
266931 AAAATATTTTACACAAATTCATCCAAACATCAG
1 AAAATATTTTACACAAATTCATCCAAACATCAG
* * **
266964 AAAATATTTTATACAGATTTGTCCAAACATCAG
1 AAAATATTTTACACAAATTCATCCAAACATCAG
266997 AAAATAT
1 AAAATAT
267004 AAACTTTTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.30
Consensus pattern (33 bp):
AAAATATTTTACACAAATTCATCCAAACATCAG
Found at i:269405 original size:16 final size:16
Alignment explanation
Indices: 269374--269403 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
269364 ACATGTATCT
269374 TTTTTTTAAATATTTA
1 TTTTTTTAAATATTTA
269390 TTTTTTT-AATATTT
1 TTTTTTTAAATATTT
269404 TACTATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTAAATATTTA
Found at i:271913 original size:71 final size:71
Alignment explanation
Indices: 271829--272042 Score: 428
Period size: 71 Copynumber: 3.0 Consensus size: 71
271819 AAAATAATCC
271829 ATCAAAACCCAAAATCAAAATAAGTAAAATTTTCTTAGTTATAATTCAAAATCATGAAAAACCCA
1 ATCAAAACCCAAAATCAAAATAAGTAAAATTTTCTTAGTTATAATTCAAAATCATGAAAAACCCA
271894 CAAAAT
66 CAAAAT
271900 ATCAAAACCCAAAATCAAAATAAGTAAAATTTTCTTAGTTATAATTCAAAATCATGAAAAACCCA
1 ATCAAAACCCAAAATCAAAATAAGTAAAATTTTCTTAGTTATAATTCAAAATCATGAAAAACCCA
271965 CAAAAT
66 CAAAAT
271971 ATCAAAACCCAAAATCAAAATAAGTAAAATTTTCTTAGTTATAATTCAAAATCATGAAAAACCCA
1 ATCAAAACCCAAAATCAAAATAAGTAAAATTTTCTTAGTTATAATTCAAAATCATGAAAAACCCA
272036 CAAAAT
66 CAAAAT
272042 A
1 A
272043 CTCTTACTTT
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 143 1.00
ACGTcount: A:0.54, C:0.17, G:0.04, T:0.25
Consensus pattern (71 bp):
ATCAAAACCCAAAATCAAAATAAGTAAAATTTTCTTAGTTATAATTCAAAATCATGAAAAACCCA
CAAAAT
Found at i:272199 original size:16 final size:17
Alignment explanation
Indices: 272168--272200 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
272158 TGTAAAACAA
272168 CATTCATCCCTTCATCT
1 CATTCATCCCTTCATCT
*
272185 CATTC-TCCGTTCATCT
1 CATTCATCCCTTCATCT
272201 TTAAGCTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.15, C:0.39, G:0.03, T:0.42
Consensus pattern (17 bp):
CATTCATCCCTTCATCT
Found at i:274121 original size:21 final size:21
Alignment explanation
Indices: 274069--274119 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
274059 ATCCACGTGT
*
274069 ATTCAAAATATATGAAAATAA
1 ATTCAAAAAATATGAAAATAA
274090 ATTCAAAAAATAT-AAAA-AA
1 ATTCAAAAAATATGAAAATAA
274109 ATTCCAAAAAA
1 ATT-CAAAAAA
274120 ATTAGCATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 5 0.18
20 11 0.39
21 12 0.43
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.24
Consensus pattern (21 bp):
ATTCAAAAAATATGAAAATAA
Found at i:281960 original size:189 final size:186
Alignment explanation
Indices: 281534--282191 Score: 601
Period size: 190 Copynumber: 3.5 Consensus size: 186
281524 GCAAGCACCA
** * * * * ** *
281534 AATATGGCAAACATAATAAAATCCAGTGGACCAAATCGAAGCTAAAATGTCAACATCGACTTGAG
1 AATATGGCAAACATAATAAAGGCCA-TGGA-CAAATTGAAGCTAAAAGGTCAACATCAAATCAAA
** * * *
281599 GAAGCAAATGGAACAGCAACAACAACGATGGCAATGACAACATAATGAAGCCTTGGGATTTAGGT
64 GAAGCAAAAAGAACAACAACAACAACGA---CAACGACAACATAATGAAGCCTTGGGATTTGGGT
** * * * * * *
281664 GGTTTTCAGAGA-TTACCTTGTTTTCGGGTTCAAG-AAAGCACCATAACCAAAAGATGGGAATA
126 -ACTTT-A-AGATTTACCTGGTTTTCGGATTCAAGCAAAGCACCATAGCCAAAACAAGGGAATG
* * * * *
281726 AATATGGCAAACATAATCAAGTCCAATGGACCAAATTGAAGCTAAAAGCTCAATATTAAAATCAA
1 AATATGGCAAACATAATAAAGGCC-ATGGA-CAAATTGAAGCTAAAAGGTCAACA-TCAAATCAA
**
281791 AGAAG-AAAAAGGAACAACAACAACAACGACCGCGACAACATAATGAAGCCTTGGGATTTGGGTA
63 AGAAGCAAAAA-GAACAACAACAACAACGACAACGACAACATAATGAAGCCTTGGGATTTGGGTA
* * * *
281855 CTTTAAGATTTACCCGGTTTTAGGATTCAAGCAAAGCACCATAGCCAGAACAAGGGAAGG
127 CTTTAAGATTTACCTGGTTTTCGGATTCAAGCAAAGCACCATAGCCAAAACAAGGGAATG
* * *
281915 AATATGGAAAACATAATAAAGGCCAGTGGACAAATTCGAAGCTAAAAGGTTAACATCAAACCAAA
1 AATATGGCAAACATAATAAAGGCCA-TGGACAAATT-GAAGCTAAAAGGTCAACATCAAATCAAA
* * * * * * * * * *
281980 GAAGCAAACACAA-AATAAAAATGGCGATGACAACTACGATATAATGAAGCCTTGGGATTTGAGT
64 GAAGCAAAAAGAACAACAACAA---CAACGACAACGACAACATAATGAAGCCTTGGGATTTGGGT
** * * * *
282044 ACTTTCGGATTTACCTGGGTTTCGGAATCAAGCAGAGCACCATAGCCAAAACAAGGAAATG
126 ACTTTAAGATTTACCTGGTTTTCGGATTCAAGCAAAGCACCATAGCCAAAACAAGGGAATG
* *
282105 AATATGGCAAACATAATAAATG-C--GGACAAATTTGAAGCTACAAGGTCAACATCAAATCAAAG
1 AATATGGCAAACATAATAAAGGCCATGGACAAA-TTGAAGCTAAAAGGTCAACATCAAATCAAAG
* *
282167 AAGCAAATAGAACAACAACGACAAC
65 AAGCAAAAAGAACAACAACAACAAC
282192 TATGACTTAA
Statistics
Matches: 380, Mismatches: 73, Indels: 34
0.78 0.15 0.07
Matches are distributed among these distances:
184 2 0.01
186 43 0.11
187 16 0.04
188 40 0.11
189 70 0.18
190 133 0.35
192 50 0.13
193 26 0.07
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (186 bp):
AATATGGCAAACATAATAAAGGCCATGGACAAATTGAAGCTAAAAGGTCAACATCAAATCAAAGA
AGCAAAAAGAACAACAACAACAACGACAACGACAACATAATGAAGCCTTGGGATTTGGGTACTTT
AAGATTTACCTGGTTTTCGGATTCAAGCAAAGCACCATAGCCAAAACAAGGGAATG
Found at i:287338 original size:25 final size:25
Alignment explanation
Indices: 287291--287339 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
287281 TTATATGTTT
**
287291 TAAAATTATTTTATTTTTTATAAAG
1 TAAAATTATTTTATTTTAAATAAAG
287316 TAAAA-TATTTTATTTTAAAATAAA
1 TAAAATTATTTTATTTT-AAATAAA
287340 CGATAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TAAAATTATTTTATTTTAAATAAAG
Found at i:287430 original size:30 final size:30
Alignment explanation
Indices: 287368--287431 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
287358 TGGATGTAAG
* * *
287368 AAAATCTGGTTTTGATTAAAGATATATAAT
1 AAAATCTGATTTTGATGAAAAATATATAAT
*
287398 AAAATCTGATTTTGATGAAATAATTTAT-AT
1 AAAATCTGATTTTGATGAAA-AATATATAAT
287428 AAAA
1 AAAA
287432 ATTATTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (30 bp):
AAAATCTGATTTTGATGAAAAATATATAAT
Found at i:292758 original size:17 final size:17
Alignment explanation
Indices: 292738--292771 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
292728 TATCTTGGAT
292738 TTTTTTGTATATTTTCA
1 TTTTTTGTATATTTTCA
292755 TTTTTTGTATATTTTCA
1 TTTTTTGTATATTTTCA
292772 ATCGAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTTTTGTATATTTTCA
Found at i:296719 original size:13 final size:13
Alignment explanation
Indices: 296701--296734 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
296691 ATATAAATTC
296701 AAACAAATAAGAA
1 AAACAAATAAGAA
*
296714 AAACAAATAGGAA
1 AAACAAATAAGAA
*
296727 CAACAAAT
1 AAACAAAT
296735 TAAAAAAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.71, C:0.12, G:0.09, T:0.09
Consensus pattern (13 bp):
AAACAAATAAGAA
Found at i:297622 original size:86 final size:86
Alignment explanation
Indices: 297493--297671 Score: 205
Period size: 86 Copynumber: 2.1 Consensus size: 86
297483 GAGCTACTCG
* * * * *
297493 AGCTCAAGCTCGATTAAGCTCATTTATCAATTTTTGTACTCAAGTTTGAACTTCAGCTCAATTAA
1 AGCTCGAGCTCGATTAAGCTCATTTATCAAATTTTATACTCAAGCTTGAACTTCAGCTCAATAAA
* * *
297558 GCTCATATGTATTAAAGCTCA
66 GCTCACACGCATTAAAGCTCA
* * * * * * *
297579 AGCTCGAGCTTGATTCAGCTTATTTATCAAATTTTATATTCAAGCTTGAATTTTAGCTCGATAAA
1 AGCTCGAGCTCGATTAAGCTCATTTATCAAATTTTATACTCAAGCTTGAACTTCAGCTCAATAAA
* *
297644 GCTCGCACGCATTAAAGCTTA
66 GCTCACACGCATTAAAGCTCA
297665 AGCTCGA
1 AGCTCGA
297672 ACTCAGCTTG
Statistics
Matches: 76, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
86 76 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (86 bp):
AGCTCGAGCTCGATTAAGCTCATTTATCAAATTTTATACTCAAGCTTGAACTTCAGCTCAATAAA
GCTCACACGCATTAAAGCTCA
Found at i:314393 original size:31 final size:31
Alignment explanation
Indices: 314355--314421 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
314345 CAAAAATATC
*
314355 ATTGAACTATTAGAAAATTTTTATTTAAGTT
1 ATTGAACTATTAGAAAATTTTCATTTAAGTT
* *
314386 ATTGAACTATTAGAGAGTTTTCATTTAAGTT
1 ATTGAACTATTAGAAAATTTTCATTTAAGTT
314417 ATTGA
1 ATTGA
314422 GCTGTTAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.46
Consensus pattern (31 bp):
ATTGAACTATTAGAAAATTTTCATTTAAGTT
Found at i:326159 original size:20 final size:19
Alignment explanation
Indices: 326113--326160 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 19
326103 TTAAACCAGA
326113 TTTTTAATATTTTTAAAAT
1 TTTTTAATATTTTTAAAAT
326132 TTTATTAATA-TTTTAATAAT
1 TTT-TTAATATTTTTAA-AAT
326152 TTATTTAAT
1 TT-TTTAAT
326161 TCAATCAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.35
20 16 0.62
21 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTAATATTTTTAAAAT
Found at i:327256 original size:7 final size:7
Alignment explanation
Indices: 327244--327284 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
327234 GGAGAGAAGG
327244 AGAGAGT
1 AGAGAGT
327251 AGAGAGT
1 AGAGAGT
327258 AGAGAGT
1 AGAGAGT
327265 AGAGAGT
1 AGAGAGT
327272 -GAGAGT
1 AGAGAGT
327278 AGAGAGT
1 AGAGAGT
327285 GTGTCTTGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.18
7 27 0.82
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.15
Consensus pattern (7 bp):
AGAGAGT
Found at i:334220 original size:39 final size:40
Alignment explanation
Indices: 334166--334246 Score: 155
Period size: 39 Copynumber: 2.0 Consensus size: 40
334156 TGATCCAACC
334166 CCAATAATATAGGGGTCTCTTAGATATTTTAAT-CTTTTT
1 CCAATAATATAGGGGTCTCTTAGATATTTTAATCCTTTTT
334205 CCAATAATATAGGGGTCTCTTAGATATTTTAATCCTTTTT
1 CCAATAATATAGGGGTCTCTTAGATATTTTAATCCTTTTT
334245 CC
1 CC
334247 TTTATAATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 33 0.80
40 8 0.20
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.44
Consensus pattern (40 bp):
CCAATAATATAGGGGTCTCTTAGATATTTTAATCCTTTTT
Found at i:335864 original size:23 final size:23
Alignment explanation
Indices: 335838--335907 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
335828 TAGATTATCT
335838 TTTTGGTTTACAAGGACTTAAAA
1 TTTTGGTTTACAAGGACTTAAAA
** ***
335861 TTTT-GTTT-TTA-GA-TTATCT
1 TTTTGGTTTACAAGGACTTAAAA
335880 TTTTGGTTTACAAGGACTTAAAA
1 TTTTGGTTTACAAGGACTTAAAA
335903 TTTTG
1 TTTTG
335908 TTTTTGTTTG
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
19 7 0.21
20 6 0.18
21 2 0.06
22 6 0.18
23 12 0.36
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.50
Consensus pattern (23 bp):
TTTTGGTTTACAAGGACTTAAAA
Found at i:335871 original size:24 final size:24
Alignment explanation
Indices: 335844--335912 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 24
335834 ATCTTTTTGG
335844 TTTACAAGGACTTAAAATTTTGTT
1 TTTACAAGGACTTAAAATTTTGTT
*** *
335868 TTT---A-GA-TTATCTTTTTG-G
1 TTTACAAGGACTTAAAATTTTGTT
335886 TTTACAAGGACTTAAAATTTTGTT
1 TTTACAAGGACTTAAAATTTTGTT
335910 TTT
1 TTT
335913 GTTTGTTTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 12
0.61 0.16 0.24
Matches are distributed among these distances:
18 3 0.10
19 8 0.26
20 2 0.06
21 2 0.06
22 2 0.06
23 8 0.26
24 6 0.19
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (24 bp):
TTTACAAGGACTTAAAATTTTGTT
Found at i:335878 original size:42 final size:42
Alignment explanation
Indices: 335822--335912 Score: 182
Period size: 42 Copynumber: 2.2 Consensus size: 42
335812 TTGGGTTTTG
335822 TGTTTTTAGATTATCTTTTTGGTTTACAAGGACTTAAAATTT
1 TGTTTTTAGATTATCTTTTTGGTTTACAAGGACTTAAAATTT
335864 TGTTTTTAGATTATCTTTTTGGTTTACAAGGACTTAAAATTT
1 TGTTTTTAGATTATCTTTTTGGTTTACAAGGACTTAAAATTT
335906 TGTTTTT
1 TGTTTTT
335913 GTTTGTTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (42 bp):
TGTTTTTAGATTATCTTTTTGGTTTACAAGGACTTAAAATTT
Found at i:337918 original size:11 final size:11
Alignment explanation
Indices: 337892--337935 Score: 56
Period size: 10 Copynumber: 4.1 Consensus size: 11
337882 TTTTAAAAGA
337892 TATATATTTCTT
1 TATATATTT-TT
337904 TATATATTTTT
1 TATATATTTTT
*
337915 TATAT-TTTAT
1 TATATATTTTT
337925 TA-ATATTTTT
1 TATATATTTTT
337935 T
1 T
337936 TAAAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 2 0.07
10 11 0.38
11 7 0.24
12 9 0.31
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (11 bp):
TATATATTTTT
Found at i:337938 original size:11 final size:10
Alignment explanation
Indices: 337894--337937 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
337884 TTAAAAGATA
*
337894 TATATTTCTT
1 TATATTTTTT
337904 TATATATTTTT
1 TATAT-TTTTT
337915 TATATTTTATT
1 TATATTTT-TT
*
337926 AATATTTTTT
1 TATATTTTTT
337936 TA
1 TA
337938 AAATTTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 11 0.38
11 18 0.62
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (10 bp):
TATATTTTTT
Found at i:339366 original size:3 final size:3
Alignment explanation
Indices: 339358--339394 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
339348 TGACTACACG
339358 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
339395 CCTTTTTGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:342704 original size:133 final size:132
Alignment explanation
Indices: 342432--342811 Score: 466
Period size: 132 Copynumber: 2.9 Consensus size: 132
342422 AACTGCTTTC
* * *
342432 CCTGTATGTCACGAATTTGGGTTTTATGTG-TTCTTTTACCTGACTGCTAACTTGTATCATTTTG
1 CCTGTATGTCACGAATCTGGG-TTTATGTGTTTCTTTTACCTGACTGATAACTAGTATCATTTTG
* *
342496 CTCATCCCATCTCGTATCAAGAATCATAGACCACGGATGTCTTTGTACTGCTTATATCGGTTAAT
65 CTCATCCCATCTCGTATCAAGAATCATAGACCACAGATGTCTTTGTACTGCTCATATCGGTTAAT
342561 ATA
130 ATA
342564 CCTGTATGTCAC-AATCTGGGTTTGATGTGTTTCTTTTACCTGACTGATAACTAGTATCATTTTG
1 CCTGTATGTCACGAATCTGGGTTT-ATGTGTTTCTTTTACCTGACTGATAACTAGTATCATTTTG
* * * * **
342628 CTCATGCCACTCTTGTATCAAGATTCATGGACTGCAGATGTCTTTGTACTGCTCATATCGGTTAA
65 CTCATCCCA-TCTCGTATCAAGAATCATAGACCACAGATGTCTTTGTACTGCTCATATCGGTTAA
342693 TATA
129 TATA
* * * *
342697 CCTGTATGTCACGAATCTTGGTTT-TATGTTTATTTTACCTGACTGGTAACTCA-TATCATTTTA
1 CCTGTATGTCACGAATCTGGGTTTATGTGTTTCTTTTACCTGACTGATAACT-AGTATCATTTT-
** * ** *
342760 G-TTGT-CCAGTTTCGTATTGAGAATCATAGACCGCAGATGTCTTTTGTACTGC
64 GCTCATCCCA-TCTCGTATCAAGAATCATAGACCACAGATGTC-TTTGTACTGC
342812 ATATATCTGT
Statistics
Matches: 216, Mismatches: 25, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
130 3 0.01
131 40 0.19
132 97 0.45
133 66 0.31
134 10 0.05
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (132 bp):
CCTGTATGTCACGAATCTGGGTTTATGTGTTTCTTTTACCTGACTGATAACTAGTATCATTTTGC
TCATCCCATCTCGTATCAAGAATCATAGACCACAGATGTCTTTGTACTGCTCATATCGGTTAATA
TA
Found at i:350040 original size:313 final size:313
Alignment explanation
Indices: 349469--350393 Score: 1284
Period size: 313 Copynumber: 2.9 Consensus size: 313
349459 ATCCGGAGGT
* *
349469 AACTATAAGCCATTACTACAAAATGCTTAGATCACCAGCATTTTGAAACTCATTTTTATTATCAT
1 AACTATAAGCCATTACTACGAAATTCTTAGATCACCAGCATTTTGAAACTCATTTTTATTATCAT
* *
349534 ACATCTG-TTTAAGAACCAACCAAACTCAAATC-ATACACTCTAAATCAATGTTCACTCGGACTC
66 ACATCTGTTTTAAGAACCAACCAAAC-CCAA-CGA-ACACTCTAAATCTATGTTCACTCGGACT-
* * * * *
349597 GGGCAAGAGTTTCAAATAAAGCCAAGTGTTTGACACAGATATATTCACATTTTTTCAAGTACCTA
127 TGGTAAGAGTTTCAAATAAAGGCATGTGTTTGACACAGATATATTCACATTTTTTCATGTACCTA
* * *
349662 GAGGATCTTTGAAAAGACATATCGCCACAAACATGTTAAGATATTAGTCTAAAACAGGTACTTCA
192 GAGGATCTTTGAAAAGACATATCACCGCAAACATGTTCAGATATTAGTCTAAAACAGGTACTTCA
349727 AGCAAAACTGAGAGTCAGAGAAACTTAGCTCTAAACCACTTTATCCAATCCAGAGAA
257 AGCAAAACTGAGAGTCAGAGAAACTTAGCTCTAAACCACTTTATCCAATCCAGAGAA
*
349784 AACTATAAGCCATTACTACGAAATTCTTAGATCACCAGCATTTCGAAACTCATTTTTATTATCAT
1 AACTATAAGCCATTACTACGAAATTCTTAGATCACCAGCATTTTGAAACTCATTTTTATTATCAT
* * *
349849 ACATCTGTTTTGACAACCAACCAAACCCAACGCACACTCTAAATCTATGTTCACTCGGACTTGGT
66 ACATCTGTTTTAAGAACCAACCAAACCCAACGAACACTCTAAATCTATGTTCACTCGGACTTGG-
*
349914 TAAGAGTTTCAAATAAAGGCATGTGTTTGACACAGATATATTCACA-TTTTTCATGTACCTAGGG
130 TAAGAGTTTCAAATAAAGGCATGTGTTTGACACAGATATATTCACATTTTTTCATGTACCTAGAG
*
349978 GATCTTTGAAAAGACATATCACCGCAAACATGTTCAGATATTAGTCTAAAACGGGTACTTCAAGC
195 GATCTTTGAAAAGACATATCACCGCAAACATGTTCAGATATTAGTCTAAAACAGGTACTTCAAGC
*
350043 AAAACTGAGAGTCAGAGAAACTTAGCTCTAAACCACTTTATCCAATCCGGAGAA
260 AAAACTGAGAGTCAGAGAAACTTAGCTCTAAACCACTTTATCCAATCCAGAGAA
* * * *
350097 AACTATAAGCCATTACTACGAAATTCTTAGATAAATAACCAGCATTTTGAAATTCTTTTTTAATA
1 AACTATAAGCCATTACTACGAAATTCTTAG----ATCACCAGCATTTTGAAACTCATTTTTATTA
* * * *
350162 TCATACATCTGTTTTCAGAACCAACCAAACTCAGCGAACACTCTAAATATATGTTCACTCGGACT
62 TCATACATCTGTTTTAAGAACCAACCAAACCCAACGAACACTCTAAATCTATGTTCACTCGGACT
* * * **
350227 ATGGTATGAGTTTCAAATACAGGTATGTGTTTGACATGGATATATTCA-ATTTTTTTTCATGTAC
127 -TGGTAAGAGTTTCAAATAAAGGCATGTGTTTGACACAGATATATTCACA--TTTTTTCATGTAC
* *** * ***
350291 CTAGAAGGATCTTTGAAAA-CCATATCACCGTGCACATGTTCGGATATTGAGTCTAAAACCCATA
189 CTAG-AGGATCTTTGAAAAGACATATCACCGCAAACATGTTCAGATATT-AGTCTAAAACAGGTA
* ** * *
350355 CTTAAAGCAAAACCAAAAATCAGAGAAACTTAGCTCTAA
252 CTTCAAGCAAAACTGAGAGTCAGAGAAACTTAGCTCTAA
350394 TTTTGCAGAC
Statistics
Matches: 548, Mismatches: 49, Indels: 21
0.89 0.08 0.03
Matches are distributed among these distances:
313 162 0.30
314 71 0.13
315 72 0.13
316 17 0.03
317 124 0.23
318 3 0.01
319 40 0.07
320 59 0.11
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.29
Consensus pattern (313 bp):
AACTATAAGCCATTACTACGAAATTCTTAGATCACCAGCATTTTGAAACTCATTTTTATTATCAT
ACATCTGTTTTAAGAACCAACCAAACCCAACGAACACTCTAAATCTATGTTCACTCGGACTTGGT
AAGAGTTTCAAATAAAGGCATGTGTTTGACACAGATATATTCACATTTTTTCATGTACCTAGAGG
ATCTTTGAAAAGACATATCACCGCAAACATGTTCAGATATTAGTCTAAAACAGGTACTTCAAGCA
AAACTGAGAGTCAGAGAAACTTAGCTCTAAACCACTTTATCCAATCCAGAGAA
Found at i:367782 original size:25 final size:25
Alignment explanation
Indices: 367754--367802 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
367744 TAAATATGCA
367754 TTTTAAATAATATTCAAATTAGTTT
1 TTTTAAATAATATTCAAATTAGTTT
*
367779 TTTTAAATAATGTTCAAATTAGTT
1 TTTTAAATAATATTCAAATTAGTT
367803 AATATTATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (25 bp):
TTTTAAATAATATTCAAATTAGTTT
Found at i:367956 original size:33 final size:33
Alignment explanation
Indices: 367877--367957 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 33
367867 TATATGAAAT
367877 ATTA-ATTTTAAATATTT--TTAGTAAATAATA
1 ATTATATTTTAAATATTTAATTAGTAAATAATA
*
367907 ATTAT-TTATAAA-ATTTAATTAG--AATATATAA
1 ATTATATTTTAAATATTTAATTAGTAAATA-AT-A
367938 ATTATATTTTAAATATTTAA
1 ATTATATTTTAAATATTTAA
367958 ATATAATCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
29 8 0.19
30 12 0.29
31 10 0.24
32 6 0.14
33 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (33 bp):
ATTATATTTTAAATATTTAATTAGTAAATAATA
Found at i:368959 original size:33 final size:34
Alignment explanation
Indices: 368861--368961 Score: 141
Period size: 34 Copynumber: 3.0 Consensus size: 34
368851 ACAACTCATT
* * *
368861 TTGTAAGTTTTCAAGCTCAAGAAATCAATATGTA
1 TTGTAAGTTTTCAAACTCAAGAAATTAGTATGTA
368895 TTGTAAGTTTTCAAACTCAAGAAATTAGTATGTA
1 TTGTAAGTTTTCAAACTCAAGAAATTAGTATGTA
* **
368929 TTTTAAGTTTTCAAACTGGAG-AATTAGTATGTA
1 TTGTAAGTTTTCAAACTCAAGAAATTAGTATGTA
368962 AAAATGACAC
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 12 0.20
34 49 0.80
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (34 bp):
TTGTAAGTTTTCAAACTCAAGAAATTAGTATGTA
Found at i:380950 original size:121 final size:120
Alignment explanation
Indices: 380649--381008 Score: 474
Period size: 121 Copynumber: 3.0 Consensus size: 120
380639 TGTAACCAAA
* * * *
380649 GTTGCTAGAATAAGATAGTATCTGTTCTCATGATTGTTCAAAGGTTGTGCATTAGTCCTCTTAAT
1 GTTGGTAGAATAAGATAGTATATGTTCTCATGATTGTTCAAAGGCTGTGCATTAATCCTCTTAAT
*
380714 CCGAACAGAGGGATTGCAGGGAGGCATTGTAATTTGTAACCCGAAGTTGCATTTTTTCCGTT
66 CCGAGCAGAGGGATTGCAGGGAGGC------A-TTGTAACCCGAAGTTGCATTTTTTCCGTT
* *
380776 GTTGGTAGAATAAGATAGTATATGTTCTCATGATTGTTCAAAGGCTGTACATTACTCCTCTTAAT
1 GTTGGTAGAATAAGATAGTATATGTTCTCATGATTGTTCAAAGGCTGTGCATTAATCCTCTTAAT
*
380841 CTGAGCAGAGGGATTGCAGGGAGGCATTGTAACCCGAAGTTGCATTCTTTTCCGTT
66 CCGAGCAGAGGGATTGCAGGGAGGCATTGTAACCCGAAGTTGCATT-TTTTCCGTT
* ** * *
380897 GTTGGTAGAATAAGATAGTATTTGTTCTTGTGATTGTTCAAAGGCTGTGCATTAATCTTCCTAAT
1 GTTGGTAGAATAAGATAGTATATGTTCTCATGATTGTTCAAAGGCTGTGCATTAATCCTCTTAAT
* * *
380962 CCGAGCAGAGAGATTGCGGTGGA-G-A-CGTAACCCGAAGTTGCATTTTT
66 CCGAGCAGAGGGATTGCAG-GGAGGCATTGTAACCCGAAGTTGCATTTTT
381009 GTTGTACATT
Statistics
Matches: 213, Mismatches: 18, Indels: 13
0.87 0.07 0.05
Matches are distributed among these distances:
118 3 0.01
119 18 0.08
120 21 0.10
121 85 0.40
122 3 0.01
127 83 0.39
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (120 bp):
GTTGGTAGAATAAGATAGTATATGTTCTCATGATTGTTCAAAGGCTGTGCATTAATCCTCTTAAT
CCGAGCAGAGGGATTGCAGGGAGGCATTGTAACCCGAAGTTGCATTTTTTCCGTT
Found at i:382621 original size:31 final size:31
Alignment explanation
Indices: 382578--382636 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
382568 GATGCAATTA
* *
382578 TATATATGAAATTTTGATTGTGGTTTAAATC
1 TATATATAAAATTTTGATTGTAGTTTAAATC
*
382609 TATATATAAAATTTTGGTTGTAGTTTAA
1 TATATATAAAATTTTGATTGTAGTTTAA
382637 TCATACACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (31 bp):
TATATATAAAATTTTGATTGTAGTTTAAATC
Found at i:407718 original size:15 final size:18
Alignment explanation
Indices: 407684--407721 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
407674 AATGTAACTA
407684 TAAAATAATAAATGTGGT
1 TAAAATAATAAATGTGGT
407702 TAAAATAA-AAA-GT-GT
1 TAAAATAATAAATGTGGT
407717 TAAAA
1 TAAAA
407722 ATTATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
16 2 0.10
17 3 0.15
18 8 0.40
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (18 bp):
TAAAATAATAAATGTGGT
Found at i:417508 original size:28 final size:29
Alignment explanation
Indices: 417467--417525 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
417457 TTATACTATT
*
417467 ATCAATTTATTTAT-ATTC-CTTTAAAAAA
1 ATCAATTTAGTTATCATTCTC-TTAAAAAA
* *
417495 ATCAATTTGGTTATCATTTTCTTAAAAAA
1 ATCAATTTAGTTATCATTCTCTTAAAAAA
417524 AT
1 AT
417526 GTTGAATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 12 0.46
29 13 0.50
30 1 0.04
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (29 bp):
ATCAATTTAGTTATCATTCTCTTAAAAAA
Found at i:420287 original size:7 final size:8
Alignment explanation
Indices: 420227--420295 Score: 50
Period size: 8 Copynumber: 8.1 Consensus size: 8
420217 AATAATTTTA
420227 AAAAATAT
1 AAAAATAT
*
420235 AAAAAAAT
1 AAAAATAT
*
420243 AAAATATTT
1 AAAA-ATAT
*
420252 AAAATTCA-
1 AAAAAT-AT
420260 AAATAATTAT
1 AAA-AA-TAT
420270 AAAAATAT
1 AAAAATAT
*
420278 AAAAATTAA
1 AAAAA-TAT
420287 AAAAATAT
1 AAAAATAT
420295 A
1 A
420296 TTAAATACAT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
8 26 0.55
9 17 0.36
10 4 0.09
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (8 bp):
AAAAATAT
Found at i:420775 original size:14 final size:13
Alignment explanation
Indices: 420746--420788 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
420736 ATCCTTTGAA
420746 ATTTTATTTATT-T
1 ATTTTATTT-TTAT
420759 ATTTTAATTTTTAT
1 ATTTT-ATTTTTAT
420773 ATTGTTATTTTTAT
1 ATT-TTATTTTTAT
420787 AT
1 AT
420789 AAATGGGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.26
14 18 0.67
15 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
ATTTTATTTTTAT
Found at i:425280 original size:23 final size:22
Alignment explanation
Indices: 425254--425310 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
425244 ATTTGTTCGG
425254 TTTATTAATTTTTAAAATTA-ATT
1 TTTATTAATTTTTAAAA--AGATT
* *
425277 TTTATTTATTATTAAAAAGATT
1 TTTATTAATTTTTAAAAAGATT
425299 TTTCATTAATTT
1 TTT-ATTAATTT
425311 AAATAGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 1 0.04
22 6 0.21
23 21 0.75
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTATTAATTTTTAAAAAGATT
Found at i:436610 original size:65 final size:65
Alignment explanation
Indices: 436528--436658 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 65
436518 TCACTAAGCT
436528 TGTTTTAGTGGATATCTTAGAAAAAAAAGAGAAGTCCTATCACGTGTGGAAACCAAATATGTGTG
1 TGTTTTAGTGGATATCTTAGAAAAAAAAGAGAAGTCCTATCACGTGTGGAAACCAAATATGTGTG
*
436593 TGTTTTATTGGATATCTTAGAAAAAAAAGAGAAGTCCTATCACGTGTGGAAACCAAATATGTGTG
1 TGTTTTAGTGGATATCTTAGAAAAAAAAGAGAAGTCCTATCACGTGTGGAAACCAAATATGTGTG
436658 T
1 T
436659 TTAAAATTAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.31
Consensus pattern (65 bp):
TGTTTTAGTGGATATCTTAGAAAAAAAAGAGAAGTCCTATCACGTGTGGAAACCAAATATGTGTG
Found at i:447142 original size:3 final size:3
Alignment explanation
Indices: 447136--447169 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
447126 TTATTTTGGC
*
447136 ACT ACT ACT ACT ACT ACT ACT ACT ACT ATT ACT A
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT A
447170 TTACGAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (3 bp):
ACT
Found at i:449932 original size:3 final size:3
Alignment explanation
Indices: 449912--449946 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
449902 AACACAGCAT
* *
449912 CTC CTT CTC CTT CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
449947 ACTACTACGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (3 bp):
CTC
Found at i:450107 original size:78 final size:78
Alignment explanation
Indices: 449973--450207 Score: 344
Period size: 78 Copynumber: 3.0 Consensus size: 78
449963 GTCGGGCAGA
* * *
449973 GCCAACTAGTGTGACTCAGAAAACCAATTCGACTCTTCCTAATGAAGCTACTGAGTCTGAGGGAC
1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCATCCTAATGAAGCTACTGAGTCAGAGGGAC
*
450038 CAGCTTTCTGGAC
66 CGGCTTTCTGGAC
* * *
450051 GCCAACTAGTGTAACTCAGAAAACAAATTCAACTCATCCTAATGAAGCTACAGAGTCAGAGGGAC
1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCATCCTAATGAAGCTACTGAGTCAGAGGGAC
*
450116 GGGCTTTCTGGAC
66 CGGCTTTCTGGAC
* * * * * *
450129 GCCAATTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATCAAACCACTGAGTCAGAAGGAC
1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCATCCTAATGAAGCTACTGAGTCAGAGGGAC
450194 CGGCTTTCTGGAC
66 CGGCTTTCTGGAC
450207 G
1 G
450208 GCATGTCCAT
Statistics
Matches: 139, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 139 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (78 bp):
GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCATCCTAATGAAGCTACTGAGTCAGAGGGAC
CGGCTTTCTGGAC
Found at i:451339 original size:193 final size:190
Alignment explanation
Indices: 450999--451352 Score: 559
Period size: 194 Copynumber: 1.8 Consensus size: 190
450989 GTTAGGATTA
* *
450999 TTGTTAGCAAGGGTTTTACTTCAGGTTTTTATATTCACTGATATTCTGTCGATTTTGGGCCGGTA
1 TTGTTAGCAAGGGTTTTACTTCAGGTTTTTATATTCACTGATATTCTGTCGATTTCGAGCCGGTA
* ** *
451064 TTGCGATTTGAATTGCTATTTTTGCTTGCTTCGTGGTTTTATTATTCGGGGTTGTGCCGTAGTTT
66 TTGCGATTTGAATTGCTACTTTTGCTTGCTTCGTGGTTTTATTATTC-GGGTCATGCAGTAGTTT
451129 ATTTCCATACCATAGTAAAGAGCTTCTTTATTGTAGCAATTCAAAAGATATTATGGTTATTG
130 ATTTCCATACCATAGTAAA-AGCTTCTTTATTGTAGCAATTCAAAAGATATTATGGTTATTG
* *
451191 TTGTATAGCAAGGGTTTTACTTCAGGTTTTTATATTCACTGATTATTCTGTCGATTTCGATCTGG
1 TTGT-TAGCAAGGGTTTTACTTCAGGTTTTTATATTCACTGA-TATTCTGTCGATTTCGAGCCGG
*
451256 TATTGC-ATTTTGAATTGCTACTTTTGCTTGTTTCGTGGTTTTATTATTC-GGTCATGCAGTAGT
64 TATTGCGA-TTTGAATTGCTACTTTTGCTTGCTTCGTGGTTTTATTATTCGGGTCATGCAGTAGT
451319 TTATTTTCCATACCATAGTAAAAGCTTCTTTATT
128 TTA-TTTCCATACCATAGTAAAAGCTTCTTTATT
451353 ATATATAATC
Statistics
Matches: 149, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
192 30 0.20
193 56 0.38
194 63 0.42
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (190 bp):
TTGTTAGCAAGGGTTTTACTTCAGGTTTTTATATTCACTGATATTCTGTCGATTTCGAGCCGGTA
TTGCGATTTGAATTGCTACTTTTGCTTGCTTCGTGGTTTTATTATTCGGGTCATGCAGTAGTTTA
TTTCCATACCATAGTAAAAGCTTCTTTATTGTAGCAATTCAAAAGATATTATGGTTATTG
Found at i:452701 original size:15 final size:14
Alignment explanation
Indices: 452683--452713 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
452673 TTGAAAATAG
*
452683 TTTTCGGAAAATGA
1 TTTTTGGAAAATGA
452697 TTTTTGGAAAATGA
1 TTTTTGGAAAATGA
452711 TTT
1 TTT
452714 ATTTTTTTGG
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:0.32, C:0.03, G:0.19, T:0.45
Consensus pattern (14 bp):
TTTTTGGAAAATGA
Found at i:452738 original size:19 final size:19
Alignment explanation
Indices: 452697--452742 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
452687 CGGAAAATGA
*
452697 TTTTTGGAAAATGATTTATT
1 TTTTTGGAAAA-GATTAATT
452717 TTTTTGGAAAA-ATTAATAT
1 TTTTTGGAAAAGATTAAT-T
452736 TTTTTGG
1 TTTTTGG
452743 TGTTTGAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 8 0.33
20 11 0.46
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.54
Consensus pattern (19 bp):
TTTTTGGAAAAGATTAATT
Found at i:461027 original size:18 final size:18
Alignment explanation
Indices: 461004--461044 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
460994 AAAAATTTTA
461004 AAAAATATAT-AA-AAATCT
1 AAAAAT-TATGAAGAAAT-T
461022 AAAAATTATGAAGAAATT
1 AAAAATTATGAAGAAATT
461040 AAAAA
1 AAAAA
461045 GTTTTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.14
18 14 0.67
19 4 0.19
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.24
Consensus pattern (18 bp):
AAAAATTATGAAGAAATT
Found at i:462758 original size:122 final size:122
Alignment explanation
Indices: 462598--462825 Score: 354
Period size: 122 Copynumber: 1.9 Consensus size: 122
462588 TTTGCCTCAT
* *
462598 CTGGATTGTTGATGAAATTCGGGTTCGAAACTAAAAGCTTATTCGAGTTAGTAAGT-GAAAGGTT
1 CTGGATTGTTGACGAAATTCGGGTTCGAAACTAAAAGCTCATTCGAGTTAGTAA-TCGAAAGGTT
* *
462662 CGAGTCC-TTTCCATTCGTGTTTTAGCTTTGTTCATCTTGTTTCGCCTTGTATGGATTG
65 CAAGTCCTTTTCCATT-GTGTTGTAGCTTTGTTCATCTTGTTTCGCCTTGTATGGATTG
462720 CTGGATTGTTGACGAAATTCGGGCTT-GAAACTAAAAGCTCATTCGAGTTAGTAATCGAAAGGTT
1 CTGGATTGTTGACGAAATTCGGG-TTCGAAACTAAAAGCTCATTCGAGTTAGTAATCGAAAGGTT
* *
462784 CAAGTCCTTTTCGATTGTGTTGTAGTTTTGTTCATCTTGTTT
65 CAAGTCCTTTTCCATTGTGTTGTAGCTTTGTTCATCTTGTTT
462826 AGATTGTTGT
Statistics
Matches: 97, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
121 1 0.01
122 87 0.90
123 9 0.09
ACGTcount: A:0.22, C:0.14, G:0.23, T:0.40
Consensus pattern (122 bp):
CTGGATTGTTGACGAAATTCGGGTTCGAAACTAAAAGCTCATTCGAGTTAGTAATCGAAAGGTTC
AAGTCCTTTTCCATTGTGTTGTAGCTTTGTTCATCTTGTTTCGCCTTGTATGGATTG
Found at i:464606 original size:60 final size:62
Alignment explanation
Indices: 464507--464627 Score: 185
Period size: 60 Copynumber: 2.0 Consensus size: 62
464497 ACGTTCACCT
*
464507 CAGGATCCGAGCCACATAAGCAGACACACAAATCCCAAAAAATAGATAAGCGGAAAAAAAAAAC
1 CAGGATCCGAGCCAC--AAGCAGACACACAAATCCCAAAAAATAGATAACCGGAAAAAAAAAAC
464571 CAGGATCCGAGCCAC-A-CAGACACACTAAA-CCCAAAAAATAGATAACCGGAAAAAAAA
1 CAGGATCCGAGCCACAAGCAGACACAC-AAATCCCAAAAAATAGATAACCGGAAAAAAAA
464628 CCACGAATCT
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
60 36 0.65
61 4 0.07
64 15 0.27
ACGTcount: A:0.53, C:0.25, G:0.15, T:0.07
Consensus pattern (62 bp):
CAGGATCCGAGCCACAAGCAGACACACAAATCCCAAAAAATAGATAACCGGAAAAAAAAAAC
Found at i:466624 original size:6 final size:6
Alignment explanation
Indices: 466609--466638 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
466599 CCTTAGTATG
*
466609 AGGAGT AGGAGC AGGAGC AGGAGC AGGAGC
1 AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC
466639 TGCTGAGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.50, T:0.03
Consensus pattern (6 bp):
AGGAGC
Found at i:467210 original size:174 final size:175
Alignment explanation
Indices: 466919--467278 Score: 605
Period size: 174 Copynumber: 2.0 Consensus size: 175
466909 TCTAGGGCTT
* * *
466919 CTCACAAACAGTGATTGCGTAACTTGCGCTTGGGTTTCTTTCAACGGCGTTTGCATGAATAGTGT
1 CTCACAAACAGTGATTGCGTAACTTGCGCTTGCGTTTCTTTCAACGGCGTTTGCATAAATAGCGT
* * *
466984 TTGGGTTTCTTTCGGCGGTGGTGGTTGCTGCATAAACA-GCGTCTGTGTCTGCGGTTGCGGTTGC
66 TTGCGTTTCTTTCGGCGGTGGTGGTTGCTGCAAAAACACGCGTCTGCGTCTGCGGTTGCGGTTGC
467048 TGAACTTGTGGCTGTTCTTGTTGATAATGTTGCTGACCGAGTTGA
131 TGAACTTGTGGCTGTTCTTGTTGATAATGTTGCTGACCGAGTTGA
467093 CTCACAAACAGTGATTGCGTAACTTGCGCTTGCGTTTCTTTCAACGGCGTTTGCATAAATAGCGT
1 CTCACAAACAGTGATTGCGTAACTTGCGCTTGCGTTTCTTTCAACGGCGTTTGCATAAATAGCGT
467158 TTGCGTTTCTTTCGGCGGTGGTGGTTGCTGCAAAAACAGCGTCTGCGTCTGCGTCTGCGGTTGCG
66 TTGCGTTTCTTTCGGCGGTGGTGGTTGCTGCAAAAACA----C-GCGTCTGCGTCTGCGGTTGCG
*
467223 GTTGCTGAATTTGTGGCTGTTCTTGTTGATAATGTTGCTGACCGAGTTGA
126 GTTGCTGAACTTGTGGCTGTTCTTGTTGATAATGTTGCTGACCGAGTTGA
467273 CTCACA
1 CTCACA
467279 TGACCAAACT
Statistics
Matches: 173, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
174 98 0.57
180 75 0.43
ACGTcount: A:0.16, C:0.19, G:0.29, T:0.35
Consensus pattern (175 bp):
CTCACAAACAGTGATTGCGTAACTTGCGCTTGCGTTTCTTTCAACGGCGTTTGCATAAATAGCGT
TTGCGTTTCTTTCGGCGGTGGTGGTTGCTGCAAAAACACGCGTCTGCGTCTGCGGTTGCGGTTGC
TGAACTTGTGGCTGTTCTTGTTGATAATGTTGCTGACCGAGTTGA
Found at i:472997 original size:25 final size:25
Alignment explanation
Indices: 472950--472999 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
472940 TATTAAAAAA
*
472950 AAATACTATTTTTATATAATTTTTT
1 AAATACTATTTTTACATAATTTTTT
*
472975 AAATA-TATTTTTACCTAACTTTTTT
1 AAATACTATTTTTACATAA-TTTTTT
473000 CCACGTGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (25 bp):
AAATACTATTTTTACATAATTTTTT
Found at i:489156 original size:21 final size:22
Alignment explanation
Indices: 489132--489175 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
489122 TTAGCAAAAA
489132 TAATAAATTAAAAA-AATAATT
1 TAATAAATTAAAAATAATAATT
* * *
489153 TAATTATTTAAAAATAATTATT
1 TAATAAATTAAAAATAATAATT
489175 T
1 T
489176 TGTTAACCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATAAATTAAAAATAATAATT
Found at i:490259 original size:12 final size:12
Alignment explanation
Indices: 490237--490269 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
490227 TTTTGATTTT
490237 TTCTT-TTGTTC
1 TTCTTCTTGTTC
*
490248 TTGTTCTTGTTC
1 TTCTTCTTGTTC
490260 TTCTTCTTGT
1 TTCTTCTTGT
490270 GTCTGTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.00, C:0.18, G:0.12, T:0.70
Consensus pattern (12 bp):
TTCTTCTTGTTC
Found at i:492445 original size:6 final size:6
Alignment explanation
Indices: 492434--492465 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
492424 TTCCCGGAAG
492434 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AA
492466 CTCGACTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:498113 original size:30 final size:30
Alignment explanation
Indices: 498008--498115 Score: 87
Period size: 30 Copynumber: 3.5 Consensus size: 30
497998 ATTTAATCAC
* * *
498008 TATATTTAAATATTTAAAATATAGTTTATATAA
1 TATATTAAAATATTTAAAAT-TA--ATATTTAA
*
498041 TATATT-AAATTTTTAAATAATTAATA-TTAA
1 TATATTAAAATATTT-AA-AATTAATATTTAA
*
498071 T-TACTTAGAAATATTTAAAATTAATATTTCA
1 TATA-TTA-AAATATTTAAAATTAATATTTAA
498102 TATATTAAAATATT
1 TATATTAAAATATT
498116 AACAATAAGT
Statistics
Matches: 63, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
29 2 0.03
30 21 0.33
31 11 0.17
32 16 0.25
33 10 0.16
34 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (30 bp):
TATATTAAAATATTTAAAATTAATATTTAA
Done.