Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002197.1 Kokia drynarioides strain JFW-HI SEQ_114177, 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: 46434
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:204 original size:4 final size:4
Alignment explanation
Indices: 187--253 Score: 71
Period size: 4 Copynumber: 16.2 Consensus size: 4
177 AACACATTAC
* * * * *
187 CTTT CTTT CCTT CTTT CTTT CCTCT CCTT CTTC CTTC CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT CTTT
236 CTTTT CTTT CTTT CTTT C
1 C-TTT CTTT CTTT CTTT C
254 CCGTTTATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
4 46 0.87
5 7 0.13
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
CTTT
Found at i:243 original size:13 final size:13
Alignment explanation
Indices: 225--252 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
215 TCTTCCTTCC
225 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
238 TTTCTTTCTTTCT
1 TTTCTTTCTTTCT
251 TT
1 TT
253 CCCGTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTTCTTTCT
Found at i:8941 original size:34 final size:34
Alignment explanation
Indices: 8901--8992 Score: 141
Period size: 34 Copynumber: 2.7 Consensus size: 34
8891 TTGAGCCCAA
*
8901 ATTTTAAATTTTAAA-TTATTTTAAGTTTGAATTT
1 ATTTTAAA-TTTAAACTTATTTTAAATTTGAATTT
8935 ATTTTAAATTTAAACTTATTTTAAATTTGAATTT
1 ATTTTAAATTTAAACTTATTTTAAATTTGAATTT
* *
8969 TTTTTAAATTTAAATTTATTTTAA
1 ATTTTAAATTTAAACTTATTTTAA
8993 CTTAAAATTA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 6 0.11
34 48 0.89
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (34 bp):
ATTTTAAATTTAAACTTATTTTAAATTTGAATTT
Found at i:9001 original size:17 final size:17
Alignment explanation
Indices: 8901--8992 Score: 123
Period size: 17 Copynumber: 5.4 Consensus size: 17
8891 TTGAGCCCAA
8901 ATTTTAAATTTTAAA-TT
1 ATTTTAAA-TTTAAATTT
* *
8918 ATTTTAAGTTTGAATTT
1 ATTTTAAATTTAAATTT
*
8935 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
*
8952 ATTTTAAATTTGAATTT
1 ATTTTAAATTTAAATTT
*
8969 TTTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
8986 ATTTTAA
1 ATTTTAA
8993 CTTAAAATTA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
16 5 0.08
17 59 0.92
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:10691 original size:30 final size:30
Alignment explanation
Indices: 10657--10713 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
10647 TAAGCTCTTC
* *
10657 AAAAATCATATTTTTAACCCTAAACTTTCT
1 AAAAATCACATGTTTAACCCTAAACTTTCT
* *
10687 AAAAATTACATGTTTACCCCTAAACTT
1 AAAAATCACATGTTTAACCCTAAACTT
10714 ATCAAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAAATCACATGTTTAACCCTAAACTTTCT
Found at i:10721 original size:29 final size:28
Alignment explanation
Indices: 10668--10778 Score: 104
Period size: 29 Copynumber: 3.9 Consensus size: 28
10658 AAAATCATAT
*
10668 TTTTAACCCTAAACTT-TCTAAAAATTACA
1 TTTTACCCCTAAACTTATC--AAAATTACA
10697 TGTTTACCCCTAAACTTATCAAAATTACAA
1 T-TTTACCCCTAAACTTATCAAAATTAC-A
*
10727 TTTTACCCTTAAAC--ATCAAAATTATCA
1 TTTTACCCCTAAACTTATCAAAATTA-CA
*
10754 TTTTAACCCC-AAACTTTTCCAAAAT
1 TTTT-ACCCCTAAACTTAT-CAAAAT
10779 CATACTTTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
27 19 0.27
28 5 0.07
29 22 0.31
30 22 0.31
31 2 0.03
ACGTcount: A:0.40, C:0.23, G:0.01, T:0.36
Consensus pattern (28 bp):
TTTTACCCCTAAACTTATCAAAATTACA
Found at i:10863 original size:29 final size:28
Alignment explanation
Indices: 10829--10903 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 28
10819 CCTCAAACTT
* *
10829 TCCAAAAATTACTATTTTACCCCCGAACA
1 TCCAAAAATTAC-ATTTTACCACCAAACA
*
10858 TCCAAAAATTACCATTTTACCACCAAATA
1 TCCAAAAATTA-CATTTTACCACCAAACA
*
10887 TCCAAAAATCACATTTT
1 TCCAAAAATTACATTTT
10904 TGACTATGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
28 6 0.15
29 34 0.83
30 1 0.02
ACGTcount: A:0.41, C:0.28, G:0.01, T:0.29
Consensus pattern (28 bp):
TCCAAAAATTACATTTTACCACCAAACA
Found at i:10951 original size:29 final size:29
Alignment explanation
Indices: 10919--11055 Score: 150
Period size: 29 Copynumber: 4.7 Consensus size: 29
10909 ATGAACTTTT
* * *
10919 CAAAAATTACCATTTTACTCTCGGGTATC
1 CAAAAATTACCATTTTACCCTCAGGTGTC
* * * *
10948 CAAAAATTATCGTTTTACTCTAAGGTGTC
1 CAAAAATTACCATTTTACCCTCAGGTGTC
* **
10977 CAAAAATTACCATTTTACCCTTAGACGTC
1 CAAAAATTACCATTTTACCCTCAGGTGTC
11006 CAAAAATTACCATTTTACCCTC-GAGTGTC
1 CAAAAATTACCATTTTACCCTCAG-GTGTC
**
11035 CAAAAATTACTGTTTTACCCT
1 CAAAAATTACCATTTTACCCT
11056 TCGAACGTTT
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
28 1 0.01
29 90 0.99
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.34
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCTCAGGTGTC
Found at i:11008 original size:58 final size:58
Alignment explanation
Indices: 10919--11113 Score: 153
Period size: 58 Copynumber: 3.4 Consensus size: 58
10909 ATGAACTTTT
* ** ** * * *
10919 CAAAAATTACCATTTTACTCTCGGGTATCCAAAAATTATCGTTTTACTCTA-AGGTGTC
1 CAAAAATTACCATTTTACCCTTAGACATCCAAAAATTACCATTTTACCCTAGA-GTGTC
* *
10977 CAAAAATTACCATTTTACCCTTAGACGTCCAAAAATTACCATTTTACCCTCGAGTGTC
1 CAAAAATTACCATTTTACCCTTAGACATCCAAAAATTACCATTTTACCCTAGAGTGTC
** * * ** * * *
11035 CAAAAATTACTGTTTTACCCTTCGAACGTTTAATAAATTACCATTTT-GCCGA-AATGTC
1 CAAAAATTACCATTTTACCCTTAG-ACATCCAA-AAATTACCATTTTACCCTAGAGTGTC
* *
11093 CAAAAATTATCGTTTTACCCT
1 CAAAAATTACCATTTTACCCT
11114 CGAACATCTG
Statistics
Matches: 113, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
58 91 0.81
59 9 0.08
60 13 0.12
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCTTAGACATCCAAAAATTACCATTTTACCCTAGAGTGTC
Found at i:11221 original size:29 final size:30
Alignment explanation
Indices: 10829--11221 Score: 95
Period size: 29 Copynumber: 13.6 Consensus size: 30
10819 CCTCAAACTT
*
10829 TCCAAAAATTA-C-TATTTTACCCCCGAACA
1 TCCAAAAATTATCAT-TTTTACCCTCGAACA
* * *
10858 TCCAAAAATTACCA-TTTTACCAC-CAAATA
1 TCCAAAAATTATCATTTTTACC-CTCGAACA
* ** *
10887 TCCAAAAATCA-CATTTTTGACTAT-GAACTT
1 TCCAAAAATTATCATTTTT-ACCCTCGAAC-A
* * * ***
10917 TTCAAAAATTACCA-TTTTACTCTCGGGTA
1 TCCAAAAATTATCATTTTTACCCTCGAACA
* * **
10946 TCCAAAAATTATC-GTTTTA--CTCTAAGGTG
1 TCCAAAAATTATCATTTTTACCCTCGAA--CA
* * *
10975 TCCAAAAATTACCA-TTTTACCCT-TAGACG
1 TCCAAAAATTATCATTTTTACCCTCGA-ACA
* ***
11004 TCCAAAAATTACCA-TTTTACCCTCGAGTG
1 TCCAAAAATTATCATTTTTACCCTCGAACA
*
11033 TCCAAAAATTA-C-TGTTTTACCCTTCGAACG
1 TCCAAAAATTATCAT-TTTTACCC-TCGAACA
** * *
11063 TTTAATAAATTACCA-TTTT--GC-CGAA-A
1 TCCAA-AAATTATCATTTTTACCCTCGAACA
*
11089 TGTCCAAAAATTATC-GTTTTACCCTCGAACA
1 --TCCAAAAATTATCATTTTTACCCTCGAACA
** * * * *
11120 TCTGAAAATTATC-CTTTTGCCATCGAGCA
1 TCCAAAAATTATCATTTTTACCCTCGAACA
* * * *
11149 T-CTAAAA-TAACATTTTTATCC-CGAACT
1 TCCAAAAATTATCATTTTTACCCTCGAACA
* *
11176 TCC-AAAATTACCA-TTTTACCCTCGAGCA
1 TCCAAAAATTATCATTTTTACCCTCGAACA
11204 TCCAAAAATTA-CATTTTT
1 TCCAAAAATTATCATTTTT
11222 GACTCCGTTT
Statistics
Matches: 273, Mismatches: 55, Indels: 72
0.68 0.14 0.18
Matches are distributed among these distances:
27 37 0.14
28 29 0.11
29 157 0.58
30 33 0.12
31 16 0.06
32 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (30 bp):
TCCAAAAATTATCATTTTTACCCTCGAACA
Found at i:16441 original size:10 final size:10
Alignment explanation
Indices: 16422--16475 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
16412 GGATTCAATG
16422 AAGAAAAAAA
1 AAGAAAAAAA
*
16432 AAGAAGAAAA
1 AAGAAAAAAA
16442 AAGAAAATAAA
1 AAGAAAA-AAA
*
16453 AATAAAATATAA
1 AAGAAAA-A-AA
*
16465 AATAAAAAAA
1 AAGAAAAAAA
16475 A
1 A
16476 GGGGAAAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
10 18 0.46
11 12 0.31
12 9 0.23
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.09
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:16459 original size:18 final size:18
Alignment explanation
Indices: 16438--16472 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16428 AAAAAAGAAG
16438 AAAAAAGAAAATAAAAAT
1 AAAAAAGAAAATAAAAAT
* *
16456 AAAATATAAAATAAAAA
1 AAAAAAGAAAATAAAAA
16473 AAAGGGGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (18 bp):
AAAAAAGAAAATAAAAAT
Found at i:17575 original size:50 final size:50
Alignment explanation
Indices: 17426--17776 Score: 397
Period size: 50 Copynumber: 7.0 Consensus size: 50
17416 GCGAATTTGG
* * * *
17426 TACCTTAAGAAGATGTGAAAGGAAAGGTTGAGGTCGCAATGGCAAACCCGA
1 TACC-TAAGAAGATGTGAAGGGAAAGGTTGAGGCCACAATGGCGAACCCGA
* ** *
17477 TACCTTATA-AAGATGTAAAGGGAAAGGTTGAGATCACAATGGCAAACCCGA
1 TACC-TA-AGAAGATGTGAAGGGAAAGGTTGAGGCCACAATGGCGAACCCGA
* *
17528 TACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGA
1 TACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCACAATGGCGAACCCGA
* *
17578 TACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCATAATGGCGAACCC-A
1 TACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCACAATGGCGAACCCGA
* * ** *
17627 GTACC-ATGAAGA-GATGATAGGG-GAGGATTGAGGCCGTAATGGCGAACCCGG
1 -TACCTAAGAAGATG-TGA-AGGGAAAGG-TTGAGGCCACAATGGCGAACCCGA
* * *
17678 TACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCACAACGACGAACTCGA
1 TACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCACAATGGCGAACCCGA
* * *
17728 TACCTATGAAGATGTGAACGGAAAGGTTGAGGTCACAATGGCGAACCCG
1 TACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCACAATGGCGAACCCG
17777 GTTCTTAAGA
Statistics
Matches: 257, Mismatches: 33, Indels: 21
0.83 0.11 0.07
Matches are distributed among these distances:
48 1 0.00
49 14 0.05
50 179 0.70
51 61 0.24
52 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.31, T:0.17
Consensus pattern (50 bp):
TACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCACAATGGCGAACCCGA
Found at i:18578 original size:37 final size:38
Alignment explanation
Indices: 18497--18580 Score: 118
Period size: 37 Copynumber: 2.2 Consensus size: 38
18487 TTACCTCTAG
*
18497 GATGAGATATAGAGAAGTTGAACCAGATTCCTCTTCCT
1 GATGAGATATAGAGAAGTTGAACCAGAATCCTCTTCCT
* *
18535 GATGAGATATAGAGAAG-TGGACCA-AATCCGTCTTCTT
1 GATGAGATATAGAGAAGTTGAACCAGAATCC-TCTTCCT
18572 GATGAGATA
1 GATGAGATA
18581 CAGATAAGCG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 4 0.10
37 21 0.50
38 17 0.40
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.27
Consensus pattern (38 bp):
GATGAGATATAGAGAAGTTGAACCAGAATCCTCTTCCT
Found at i:18889 original size:209 final size:208
Alignment explanation
Indices: 18529--19841 Score: 1404
Period size: 209 Copynumber: 6.3 Consensus size: 208
18519 CCAGATTCCT
* * * * *
18529 CTTCCTGATGAGATA-TAGAGAAGTGGACCAAATCCGTCTTCTTGATGAGATACAGATAAGCGAA
1 CTTCCTGATGAGATACT-GAGAAGTGAACCAAATCCATCTTCCTGATGAGATACAGAGAAGCGGA
** ** * * *
18593 TTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACAAAATCAATGAAACG
65 TCAAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAAC-
* * *
18658 AAGCTCAATGTGAGTGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
129 AAGCTCAATATGAGCGAAACTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
**
18723 CAATAAAATGGTCAG
194 CAATAAAGCGGTCAG
* * * * *
18738 CTTCCTGATGAGATACTGAGAAGTGGACCAAATCTATCTTCTTGATGAGATACAAAGAAGTGGAT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATCCATCTTCCTGATGAGATACAGAGAAGCGGAT
* * * * * * *
18803 TAAAACAGGTGATACGGTCATCTTCTTGATGAGATACAGGGAAGTATACCGAATCAATGAAACAA
66 CAAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAA
*
18868 GGCTCAATATGAGCGAAACTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGTAGGTCGAAGC
131 -GCTCAATATGAGCGAAACTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
* *
18933 AATAAAGCGGTTAC
195 AATAAAGCGGTCAG
* * * **
18947 CTTCCTGATGAGATA-TAGAGAAGTAAACCAGATCCATCTTCCTGATGAGACACAGAGAATTGGA
1 CTTCCTGATGAGATACT-GAGAAGTGAACCAAATCCATCTTCCTGATGAGATACAGAGAAGCGGA
* * * *
19011 TCAAAACAAGTGATATGGTCATCTTCTTGATGAGATTCTGAGAAGTAGACCAAGTCAATGAAACT
65 TCAAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAAC-
* * *
19076 AGGCTCAA-AGTGAGC-AAATCTTCGAACTCCAACTTCCTGATGAGATACTGAGAAGCGGGTCGA
129 AAGCTCAATA-TGAGCGAAA-CTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGA
* * * *
19139 AGTAATAAAGCAGTTAC
192 AGCAATAAAGCGGTCAG
* * * * * *
19156 CTTCCTGATGAGATA-TAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGTGAAGTGAA
1 CTTCCTGATGAGATACT-GAGAAGTGAACCAAATCCATCTTCCTGATGAGATACAGAGAAGCGGA
* * * * *
19220 TCAAAACAAGAGATGCGGTCATCTTCTTGATGAGATACTTAGAAGTAGACCAAATTAATGAAACA
65 TCAAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAAC-
* * * * * * * * * *
19285 AAACTCGATGTGAGTGAAACTTTGAACACCAGCTTCTTGATGAGATACTAAGAAGCGGGTCGAAG
129 AAGCTCAATATGAGCGAAACTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
*
19350 CAATAAAGCGATC-G
194 CAATAAAGCGGTCAG
* ** * * *
19364 TCTTCTTGATGAGATACAAAGAAGTGGACCAAATCCGTCTTCCGGATGAGATACAGAGAAGCGGA
1 -CTTCCTGATGAGATACTGAGAAGTGAACCAAATCCATCTTCCTGATGAGATACAGAGAAGCGGA
* * * * *
19429 TCAAAACATGTGATGCGATCATATTCCTGATGAGATACTGAGAAGTAGACCAAATCAATAAAACC
65 TCAAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAA-C
* * * * *
19494 AAGCTCAA-AGTGAG-AAAATCTTTGAACCCCAACTTCCTAATGAGATACTAAGAAGCAGGTCAA
129 AAGCTCAATA-TGAGCGAAA-CTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGA
* * * *
19557 AGTAATAAAGTGGTTAT
192 AGCAATAAAGCGGTCAG
* * * * * * * **
19574 CTTCCTAATGAGATACAGAGAAGTGCACCAAATTCATCTTCCTGATAATATACAAAGAAGCATAT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATCCATCTTCCTGATGAGATACAGAGAAGCGGAT
* ** *
19639 TAAAACAAGAAATACGGTCATTTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA
66 CAAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAA-CA
* * * *
19704 AGCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCTTGATGAGGTACTGAGAAGCAGGTCGAAGC
130 AGCTCAATATGAGCGAAACTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
19769 AATAAAAG-GGTC-G
195 AAT-AAAGCGGTCAG
** * * *
19782 TCTTCCTGATGAGATACAAAGAAGTGAATCAAATCCTTCTTCTTGATGAGATACAGAGAA
1 -CTTCCTGATGAGATACTGAGAAGTGAACCAAATCCATCTTCCTGATGAGATACAGAGAA
19842 ACAAGTCGAA
Statistics
Matches: 938, Mismatches: 148, Indels: 36
0.84 0.13 0.03
Matches are distributed among these distances:
208 10 0.01
209 915 0.98
210 13 0.01
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (208 bp):
CTTCCTGATGAGATACTGAGAAGTGAACCAAATCCATCTTCCTGATGAGATACAGAGAAGCGGAT
CAAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAA
GCTCAATATGAGCGAAACTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
ATAAAGCGGTCAG
Found at i:19131 original size:418 final size:417
Alignment explanation
Indices: 18528--19841 Score: 1630
Period size: 418 Copynumber: 3.1 Consensus size: 417
18518 ACCAGATTCC
* * * * * *
18528 TCTTCCTGATGAGATATAGAGAAGTGGACCAAATCCGTCTTCTTGATGAGATACAGATAAGCGAA
1 TCTTCCTGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGGA
** * * * * *
18593 TTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACAAAATCAATGAAACG
66 TCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACC
* * *
18658 AAGCTCAATGTGAGTGAAA-CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAA
131 AAGCTCAAAGTGAG-AAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAA
* * * * * *
18722 GCAATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATCTATCTTCTTGATGAG
195 GTAATAAAGTGGTTACCTTCCTGATGAGATACTGAGAAGTGAACCAAATCTATCTTCCTGATGAG
* * * * * *
18787 ATACAAAGAAGTGGATTAAAACAGGTGATACGGTCATCTTCTTGATGAGATACAGGGAAGTATAC
260 ATACAAAGAAGTGAATTAAAACAAGAGATACGGTCATCTTCTTGATGAGATACTGAGAAGTAGAC
* * * *
18852 CGAATCAATGAAACAAGGCTCAATATGAGCGAAACTTCGAACCCCAACTTCCTGATGAGATACTG
325 CAAATCAATGAAACAA-GCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCTTGATGAGATACTG
* **
18917 AGAAGTAGGTCGAAGCAATAAAGCGGTTA
389 AGAAGCAGGTCGAAGCAATAAAGCGGTCG
* * * * * * * **
18946 CCTTCCTGATGAGATATAGAGAAGTAAACCAGATCCATCTTCCTGATGAGACACAGAGAATTGGA
1 TCTTCCTGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGGA
** * * * *
19011 TCAAAACAAGTGATATGGTCATCTTCTTGATGAGATTCTGAGAAGTAGACCAAGTCAATGAAACT
66 TCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACC
* * * *
19076 AGGCTCAAAGTGAGCAAATCTTCGAACTCCAACTTCCTGATGAGATACTGAGAAGCGGGTCGAAG
131 AAGCTCAAAGTGAGAAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
** * **
19141 TAATAAAGCAGTTACCTTCCTGATGAGATA-TAGAGAAGTGAACCAGATCCGTCTTCCTGATGAG
196 TAATAAAGTGGTTACCTTCCTGATGAGATACT-GAGAAGTGAACCAAATCTATCTTCCTGATGAG
* ** * * *
19205 ACACAGTGAAGTGAATCAAAACAAGAGATGCGGTCATCTTCTTGATGAGATACTTAGAAGTAGAC
260 ATACAAAGAAGTGAATTAAAACAAGAGATACGGTCATCTTCTTGATGAGATACTGAGAAGTAGAC
* * * * * * *
19270 CAAATTAATGAAACAAAACTCGATGTGAGTGAAACTTTGAACACCAGCTTCTTGATGAGATACTA
325 CAAATCAATGAAAC-AAGCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCTTGATGAGATACTG
* *
19335 AGAAGCGGGTCGAAGCAATAAAGCGATCG
389 AGAAGCAGGTCGAAGCAATAAAGCGGTCG
* * *
19364 TCTTCTTGATGAGATACAAAGAAGTGGACCAAATCCGTCTTCCGGATGAGATACAGAGAAGCGGA
1 TCTTCCTGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGGA
* * * *
19429 TCAAAACATGTGATGCGATCATATTCCTGATGAGATACTGAGAAGTAGACCAAATCAATAAAACC
66 TCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACC
* * * *
19494 AAGCTCAAAGTGAGAAAATCTTTGAACCCCAACTTCCTAATGAGATACTAAGAAGCAGGTCAAAG
131 AAGCTCAAAGTGAGAAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
* * * * * *
19559 TAATAAAGTGGTTATCTTCCTAATGAGATACAGAGAAGTGCACCAAAT-TCATCTTCCTGATAAT
196 TAATAAAGTGGTTACCTTCCTGATGAGATACTGAGAAGTGAACCAAATCT-ATCTTCCTGATGAG
* * * *
19623 ATACAAAGAAG-CATATTAAAACAAGAAATACGGTCATTTTCCTGATGAGATACTGAGAAGTAGA
260 ATACAAAGAAGTGA-ATTAAAACAAGAGATACGGTCATCTTCTTGATGAGATACTGAGAAGTAGA
*
19687 CCAAATCAATGAAACCAAGCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCTTGATGAGGTACT
324 CCAAATCAATGAAA-CAAGCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCTTGATGAGATACT
19752 GAGAAGCAGGTCGAAGCAATAAAAG-GGTCG
388 GAGAAGCAGGTCGAAGCAAT-AAAGCGGTCG
* * *
19782 TCTTCCTGATGAGATACAAAGAAGTGAATCAAATCCTTCTTCTTGATGAGATACAGAGAA
1 TCTTCCTGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAGAGAA
19842 ACAAGTCGAA
Statistics
Matches: 753, Mismatches: 135, Indels: 16
0.83 0.15 0.02
Matches are distributed among these distances:
417 5 0.01
418 741 0.98
419 7 0.01
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (417 bp):
TCTTCCTGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGGA
TCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACC
AAGCTCAAAGTGAGAAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
TAATAAAGTGGTTACCTTCCTGATGAGATACTGAGAAGTGAACCAAATCTATCTTCCTGATGAGA
TACAAAGAAGTGAATTAAAACAAGAGATACGGTCATCTTCTTGATGAGATACTGAGAAGTAGACC
AAATCAATGAAACAAGCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCTTGATGAGATACTGAG
AAGCAGGTCGAAGCAATAAAGCGGTCG
Found at i:19412 original size:37 final size:37
Alignment explanation
Indices: 19362--19433 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
19352 ATAAAGCGAT
** *
19362 CGTCTTCTTGATGAGATACAAAGAAGTGGACCAAATC
1 CGTCTTCCGGATGAGATACAAAGAAGCGGACCAAATC
* *
19399 CGTCTTCCGGATGAGATACAGAGAAGCGGATCAAA
1 CGTCTTCCGGATGAGATACAAAGAAGCGGACCAAA
19434 ACATGTGATG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (37 bp):
CGTCTTCCGGATGAGATACAAAGAAGCGGACCAAATC
Found at i:19728 original size:627 final size:627
Alignment explanation
Indices: 18529--19891 Score: 1664
Period size: 627 Copynumber: 2.2 Consensus size: 627
18519 CCAGATTCCT
*
18529 CTTCCTGATGAGATATAGAGAAGTGGACCAAATCCGTCTTCTTGATGAGATACAGATAAGCGAAT
1 CTTCCTGATGAGATATAGAGAAGTGAACCAAATCCGTCTTCTTGATGAGATACAGATAAGCGAAT
** * * *
18594 TGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACAAAATCAATGAAACGA
66 CAAAACAAGAGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACAAAATCAATGAAACAA
* * *
18659 AGCTCAATGTGAGTGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
131 AACTCAATGTGAGTGAAACTTCGAACACCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGC
* * ** * **
18724 AATAAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATCTATCTTCTTGATGAGAT
196 AATAAAACGATCAGCTTCCTGATGAGATACAAAGAAGTGGACCAAATCCATCTTCCGGATGAGAT
* * * * * * * *
18789 ACAAAGAAGTGGATTAAAACAGGTGATACGGTCATCTTCTTGATGAGATACAGGGAAGTATACCG
261 ACAAAGAAGCGGATCAAAACAGGTGATACGATCATATTCCTGATGAGATACAGAGAAGTAGACCA
* * * *
18854 AATCAATGAAACAAGGCTCAATATGAGCGAAACTTCGAACCCCAACTTCCTGATGAGATACTGAG
326 AATCAATAAAACAAGGCTCAATATGAGCAAAACTTCGAACCCCAACTTCCTAATGAGATACTAAG
* * * * *
18919 AAGTAGGTCGAAGCAATAAAGCGGTTACCTTCCTGATGAGATATAGAGAAGTAAACCAGATCCAT
391 AAGCAGGTCAAAGCAATAAAGCGGTTACCTTCCTAATGAGATACAGAGAAGTAAACCAAATCCAT
* * *** ** * * *
18984 CTTCCTGATGAGACACAGAGAATTGGATCAAAACAAGTGATATGGTCATCTTCTTGATGAGATTC
456 CTTCCTGATAAGACACAAAGAAGCAGATCAAAACAAGAAATACGGTCATCTTCCTGATGAGATAC
* * * *
19049 TGAGAAGTAGACCAAGTCAATGAAACTAGGCTCAAAGTGAGCAAATCTTCGAACTCCAACTTCCT
521 TGAGAAGTAGACCAAATCAATGAAACCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAACTTCCT
* * *
19114 GATGAGATACTGAGAAGCGGGTCGAAGTAAT-AAAGCAGTTAC
586 GATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAG-AGTCAC
* * * *
19156 CTTCCTGATGAGATATAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAG-TGAAGTGAA
1 CTTCCTGATGAGATATAGAGAAGTGAACCAAATCCGTCTTCTTGATGAGATACAGAT-AAGCGAA
* * ** * *
19220 TCAAAACAAGAGATGCGGTCATCTTCTTGATGAGATACTTAGAAGTAGACCAAATTAATGAAACA
65 TCAAAACAAGAGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACAAAATCAATGAAACA
* * * *
19285 AAACTCGATGTGAGTGAAACTTTGAACACCAGCTTCTTGATGAGATACTAAGAAGCGGGTCGAAG
130 AAACTCAATGTGAGTGAAACTTCGAACACCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAG
* * *
19350 CAATAAAGCGATC-GTCTTCTTGATGAGATACAAAGAAGTGGACCAAATCCGTCTTCCGGATGAG
195 CAATAAAACGATCAG-CTTCCTGATGAGATACAAAGAAGTGGACCAAATCCATCTTCCGGATGAG
* * * *
19414 ATACAGAGAAGCGGATCAAAACATGTGATGCGATCATATTCCTGATGAGATACTGAGAAGTAGAC
259 ATACAAAGAAGCGGATCAAAACAGGTGATACGATCATATTCCTGATGAGATACAGAGAAGTAGAC
*
19479 CAAATCAATAAAACCAA-GCTCAA-AGTGAG-AAAATCTTTGAACCCCAACTTCCTAATGAGATA
324 CAAATCAATAAAA-CAAGGCTCAATA-TGAGCAAAA-CTTCGAACCCCAACTTCCTAATGAGATA
* * * **
19541 CTAAGAAGCAGGTCAAAGTAATAAAGTGGTTATCTTCCTAATGAGATACAGAGAAGTGCACCAAA
386 CTAAGAAGCAGGTCAAAGCAATAAAGCGGTTACCTTCCTAATGAGATACAGAGAAGTAAACCAAA
* * * * * *
19606 TTCATCTTCCTGATAATATACAAAGAAGCATATTAAAACAAGAAATACGGTCATTTTCCTGATGA
451 TCCATCTTCCTGATAAGACACAAAGAAGCAGATCAAAACAAGAAATACGGTCATCTTCCTGATGA
* *
19671 GATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAATGTGAGCGAAA-CTTCGAACCCCAG
516 GATACTGAGAAGTAGACCAAATCAATGAAACCAAGCTCAAAGTGAGC-AAATCTTCGAACCCCAA
* * * **
19735 CTTCTTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAAGGGTCGT
580 CTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGAGTCAC
* * * * * *
19783 CTTCCTGATGAGATACAAAGAAGTGAATCAAATCCTTCTTCTTGATGAGATACAGAGAAAC-AAG
1 CTTCCTGATGAGATATAGAGAAGTGAACCAAATCCGTCTTCTTGATGAGATACAGATAAGCGAA-
* * * * * * *
19847 TCGAAGCAATAAAAG-GGTCGTCTTCCTGATGAGATACAAAGAAGT
65 TCAAAACAAGAGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGT
19892 GGATTAAATC
Statistics
Matches: 618, Mismatches: 109, Indels: 19
0.83 0.15 0.03
Matches are distributed among these distances:
626 34 0.06
627 574 0.93
628 10 0.02
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (627 bp):
CTTCCTGATGAGATATAGAGAAGTGAACCAAATCCGTCTTCTTGATGAGATACAGATAAGCGAAT
CAAAACAAGAGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACAAAATCAATGAAACAA
AACTCAATGTGAGTGAAACTTCGAACACCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGC
AATAAAACGATCAGCTTCCTGATGAGATACAAAGAAGTGGACCAAATCCATCTTCCGGATGAGAT
ACAAAGAAGCGGATCAAAACAGGTGATACGATCATATTCCTGATGAGATACAGAGAAGTAGACCA
AATCAATAAAACAAGGCTCAATATGAGCAAAACTTCGAACCCCAACTTCCTAATGAGATACTAAG
AAGCAGGTCAAAGCAATAAAGCGGTTACCTTCCTAATGAGATACAGAGAAGTAAACCAAATCCAT
CTTCCTGATAAGACACAAAGAAGCAGATCAAAACAAGAAATACGGTCATCTTCCTGATGAGATAC
TGAGAAGTAGACCAAATCAATGAAACCAAGCTCAAAGTGAGCAAATCTTCGAACCCCAACTTCCT
GATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGAGTCAC
Found at i:19878 original size:85 final size:85
Alignment explanation
Indices: 19735--19918 Score: 296
Period size: 85 Copynumber: 2.2 Consensus size: 85
19725 CGAACCCCAG
* * * *
19735 CTTCTTGATGAGGTACTGAGAAGCAGGTCGAAGCAATAAAAGGGTCGTCTTCCTGATGAGATACA
1 CTTCTTGATGAGATACAGAGAAACAAGTCGAAGCAATAAAAGGGTCGTCTTCCTGATGAGATACA
*
19800 AAGAAGTGAATCAAATCCTT
66 AAGAAGTGAATCAAATCCGT
19820 CTTCTTGATGAGATACAGAGAAACAAGTCGAAGCAATAAAAGGGTCGTCTTCCTGATGAGATACA
1 CTTCTTGATGAGATACAGAGAAACAAGTCGAAGCAATAAAAGGGTCGTCTTCCTGATGAGATACA
* *
19885 AAGAAGTGGATTAAATCCGT
66 AAGAAGTGAATCAAATCCGT
*
19905 CTTCCTGATGAGAT
1 CTTCTTGATGAGAT
19919 GTAGAGAAGC
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 91 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (85 bp):
CTTCTTGATGAGATACAGAGAAACAAGTCGAAGCAATAAAAGGGTCGTCTTCCTGATGAGATACA
AAGAAGTGAATCAAATCCGT
Found at i:19915 original size:37 final size:37
Alignment explanation
Indices: 19865--19936 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
19855 ATAAAAGGGT
*
19865 CGTCTTCCTGATGAGATACAAAGAAGTGGATTAAATC
1 CGTCTTCCTGATGAGATACAAAGAAGCGGATTAAATC
** *
19902 CGTCTTCCTGATGAGATGTAGAGAAGCGGATTAAA
1 CGTCTTCCTGATGAGATACAAAGAAGCGGATTAAA
19937 ACAAGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.26
Consensus pattern (37 bp):
CGTCTTCCTGATGAGATACAAAGAAGCGGATTAAATC
Found at i:20499 original size:34 final size:34
Alignment explanation
Indices: 20460--20551 Score: 132
Period size: 34 Copynumber: 2.7 Consensus size: 34
20450 TTGAGCCTAA
20460 ATTTTAAATTTTAAA-TTATTTTAAGTTTGAATTT
1 ATTTTAAA-TTTAAACTTATTTTAAGTTTGAATTT
*
20494 ATTTTAAATTTAAACTTATTTCAAGTTTGAATTT
1 ATTTTAAATTTAAACTTATTTTAAGTTTGAATTT
* * *
20528 ACTTTAAACTTAAATTTATTTTAA
1 ATTTTAAATTTAAACTTATTTTAA
20552 ATTAAAATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
33 6 0.12
34 46 0.88
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (34 bp):
ATTTTAAATTTAAACTTATTTTAAGTTTGAATTT
Found at i:20559 original size:17 final size:17
Alignment explanation
Indices: 20460--20560 Score: 105
Period size: 17 Copynumber: 5.9 Consensus size: 17
20450 TTGAGCCTAA
20460 ATTTTAAATTTTAAA-TT
1 ATTTTAAA-TTTAAATTT
* *
20477 ATTTTAAGTTTGAATTT
1 ATTTTAAATTTAAATTT
*
20494 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* * *
20511 ATTTCAAGTTTGAATTT
1 ATTTTAAATTTAAATTT
* *
20528 ACTTTAAACTTAAATTT
1 ATTTTAAATTTAAATTT
*
20545 ATTTTAAATTAAAATT
1 ATTTTAAATTTAAATT
20561 AATTAAGGAA
Statistics
Matches: 66, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
16 5 0.08
17 61 0.92
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:22271 original size:29 final size:30
Alignment explanation
Indices: 22205--22408 Score: 127
Period size: 30 Copynumber: 7.0 Consensus size: 30
22195 CCCAAAATGT
* * * *
22205 CCCTAAACTCTCCAAAAATCAT-ATTTTTGA
1 CCCTAAACTTTTCAAAAATTATCA-TTTTAA
22235 CCCTAAACTTTTCAAAAATTA-CA-TTTAA
1 CCCTAAACTTTTCAAAAATTATCATTTTAA
*
22263 CCCTTAAACTTCTCAAAAATTATCATTTTAA
1 CCC-TAAACTTTTCAAAAATTATCATTTTAA
* * **
22294 CCCTAAACTTTTCTAAAATCAT-ATTTTTG
1 CCCTAAACTTTTCAAAAATTATCATTTTAA
* * * **
22323 CCCTCGAAC-TTTC-AAATTTACCATTTTGG
1 CCCT-AAACTTTTCAAAAATTATCATTTTAA
* * * * *
22352 CCCCAAACTTTCCAAAAATTACCATTTCAC
1 CCCTAAACTTTTCAAAAATTATCATTTTAA
* * *
22382 CCCTGAAC-ATT-AAAAATTACCATTTTA
1 CCCTAAACTTTTCAAAAATTATCATTTTA
22409 CCACTAGACA
Statistics
Matches: 139, Mismatches: 27, Indels: 18
0.76 0.15 0.10
Matches are distributed among these distances:
28 30 0.22
29 43 0.31
30 58 0.42
31 8 0.06
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (30 bp):
CCCTAAACTTTTCAAAAATTATCATTTTAA
Found at i:22419 original size:28 final size:30
Alignment explanation
Indices: 22362--22494 Score: 114
Period size: 29 Copynumber: 4.6 Consensus size: 30
22352 CCCCAAACTT
* *
22362 TCCAAAAATTACCATTTCACCCCT-GAACA
1 TCCAAAAATTACCATTTTACCACTAGAACA
*
22391 T-TAAAAATTACCATTTTACCACTAG-ACA
1 TCCAAAAATTACCATTTTACCACTAGAACA
* ***
22419 TCCAAGAATTACCATTTTACCACTAG-GTG
1 TCCAAAAATTACCATTTTACCACTAGAACA
* ** *
22448 TCCAAAAATTACCGTTTTACC-CCCGAACG
1 TCCAAAAATTACCATTTTACCACTAGAACA
* *
22477 TCCCAAAATTACCCTTTT
1 TCCAAAAATTACCATTTT
22495 TCCCTCGAGC
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
28 25 0.29
29 60 0.71
ACGTcount: A:0.35, C:0.29, G:0.07, T:0.29
Consensus pattern (30 bp):
TCCAAAAATTACCATTTTACCACTAGAACA
Found at i:22434 original size:29 final size:29
Alignment explanation
Indices: 22362--22468 Score: 119
Period size: 29 Copynumber: 3.7 Consensus size: 29
22352 CCCCAAACTT
* *
22362 TCCAAAAATTACCATTTCACCCCT-GAACA
1 TCCAAAAATTACCATTTTACCACTAG-ACA
*
22391 T-TAAAAATTACCATTTTACCACTAGACA
1 TCCAAAAATTACCATTTTACCACTAGACA
* ***
22419 TCCAAGAATTACCATTTTACCACTAGGTG
1 TCCAAAAATTACCATTTTACCACTAGACA
*
22448 TCCAAAAATTACCGTTTTACC
1 TCCAAAAATTACCATTTTACC
22469 CCCGAACGTC
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
28 23 0.35
29 43 0.65
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCACTAGACA
Found at i:22479 original size:29 final size:29
Alignment explanation
Indices: 22362--22570 Score: 108
Period size: 29 Copynumber: 7.3 Consensus size: 29
22352 CCCCAAACTT
* * *
22362 TCCAAAAATTACCATTTCACCCCTGAACA
1 TCCAAAAATTACCATTTTACCCCCGAACG
* * * *
22391 T-TAAAAATTACCATTTTA-CCACTAGACA
1 TCCAAAAATTACCATTTTACCCCCGA-ACG
* * * **
22419 TCCAAGAATTACCATTTTA-CCACTAGGTG
1 TCCAAAAATTACCATTTTACCCCCGA-ACG
*
22448 TCCAAAAATTACCGTTTTACCCCCGAACG
1 TCCAAAAATTACCATTTTACCCCCGAACG
* * * * * *
22477 TCCCAAAATTACCCTTTTTCCCTCGAGCA
1 TCCAAAAATTACCATTTTACCCCCGAACG
* * * *
22506 TCTAAAAATT-GCATTTTTA-CGCCGAACT
1 TCCAAAAATTACCA-TTTTACCCCCGAACG
* * *
22534 TTC-AAAATTACCATTTTACCCTCG-ACC
1 TCCAAAAATTACCATTTTACCCCCGAACG
22561 TCCAAAAATT
1 TCCAAAAATT
22571 GCATTTTTAA
Statistics
Matches: 135, Mismatches: 38, Indels: 15
0.72 0.20 0.08
Matches are distributed among these distances:
27 18 0.13
28 37 0.27
29 76 0.56
30 4 0.03
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.30
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCCCGAACG
Found at i:22540 original size:28 final size:28
Alignment explanation
Indices: 22491--22579 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 28
22481 AAAATTACCC
* *
22491 TTTTT-CCCTCGAGCATCTAAAAATTGCA
1 TTTTTACCCTCGA-CCTCCAAAAATTGCA
* * * *
22519 TTTTTACGC-CGAACTTTC-AAAATTACCA
1 TTTTTACCCTCG-ACCTCCAAAAATT-GCA
22547 -TTTTACCCTCGACCTCCAAAAATTGCA
1 TTTTTACCCTCGACCTCCAAAAATTGCA
22574 TTTTTA
1 TTTTTA
22580 ACTCCGTTTG
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
27 19 0.41
28 24 0.52
29 3 0.07
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (28 bp):
TTTTTACCCTCGACCTCCAAAAATTGCA
Found at i:23961 original size:29 final size:30
Alignment explanation
Indices: 23906--23966 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
23896 TTTTAAAATA
* *
23906 TTTTAATATTTAATATTATAGTTTTTTATT
1 TTTTAAAATTTAATATTATAATTTTTTATT
23936 TTTTAAAATTTAA-ATT-TAATGTTTTTATT
1 TTTTAAAATTTAATATTATAAT-TTTTTATT
23965 TT
1 TT
23967 AATTGCCACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 3 0.11
29 13 0.46
30 12 0.43
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (30 bp):
TTTTAAAATTTAATATTATAATTTTTTATT
Found at i:26028 original size:55 final size:55
Alignment explanation
Indices: 25938--26041 Score: 156
Period size: 55 Copynumber: 1.9 Consensus size: 55
25928 TCGTCTTAAT
* * * *
25938 TGTTGGAATATTGCTCTTTTGAATTGATTTTTTTATATGTTTAAATCGATTGTCG
1 TGTTGAAATACTGCTCTTTTGAATCGATTTGTTTATATGTTTAAATCGATTGTCG
25993 TGTTGAAATACTGCTTCTTTTGAATCGA-TTGTTTATATGTTTAAATCGA
1 TGTTGAAATACTGC-TCTTTTGAATCGATTTGTTTATATGTTTAAATCGA
26042 CCGTTACATA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
55 32 0.73
56 12 0.27
ACGTcount: A:0.24, C:0.09, G:0.17, T:0.50
Consensus pattern (55 bp):
TGTTGAAATACTGCTCTTTTGAATCGATTTGTTTATATGTTTAAATCGATTGTCG
Found at i:29671 original size:2 final size:2
Alignment explanation
Indices: 29664--29688 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29654 TTTTATTTTA
29664 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
29689 GTGTTAAGCA
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:30940 original size:4 final size:4
Alignment explanation
Indices: 30931--30955 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
30921 NNNNNNNNNA
30931 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
30956 GAGTGAGACA
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:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:38002 original size:17 final size:17
Alignment explanation
Indices: 37978--38037 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
37968 ACAGAATTTG
37978 AATTTATTTTAAAATTA
1 AATTTATTTTAAAATTA
* *
37995 AGTTTATTTTAAATTTA
1 AATTTATTTTAAAATTA
*
38012 AATTTA-TTGAAAATTTA
1 AATTTATTTTAAAA-TTA
*
38029 AAGTTATTT
1 AATTTATTT
38038 AAATAATGCC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
16 5 0.14
17 28 0.80
18 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAAATTA
Found at i:38753 original size:3 final size:3
Alignment explanation
Indices: 38745--38778 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
38735 AATATCTTTG
*
38745 ATA ATA ATA ATA ATA ATA TTA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38779 AATGAAATGT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:45342 original size:49 final size:49
Alignment explanation
Indices: 45270--45816 Score: 411
Period size: 49 Copynumber: 11.2 Consensus size: 49
45260 CTACAAGTCT
* * * *
45270 CAGTACCATGAAGATAGGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
1 CAGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATC
* * * * *
45319 CAGTACCACGAAGACACGAAGGGAAAGGTTTAAGTCGCAACGGTGAA-C
1 CAGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATC
* * * * *
45367 CTTGTACCTAAGAAG-CGTGAAGGGAAAGATTTAAGCTGCAACGGCGAATC
1 C-AGTACC-ACGAAGACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATC
* * * * * *
45417 CAGTATCACGAACACACGAAGGGAAAGGTTTAAGTCGCAATGGTGAA-C
1 CAGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATC
* * * * * *
45465 CTTA-TACCTCAAAGACATGAAGGGAAAGATTTAAGCCACAACGGCAAATG
1 C--AGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATC
* * * *
45515 CAGTACCACAAAGACATAAAGGGAAAGATTTAAGTCGGAATGGCGAA-C
1 CAGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATC
* *
45563 CTTA-TACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCAATGGCAAATC
1 C--AGTACCAC-GAAGACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATC
* * * * *
45613 CAGTACCACAAAGACACGAAGGGAAAGGTTTAAGTCGCAATGGC-AAAC
1 CAGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATC
* *
45661 CTTA-TACCTC-AGAGACATGAAGGGAAAGATTTAAACCGCAATGGCGAATC
1 C--AGTACCACGA-AGACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATC
* ** * * * *
45711 CAGTACCACGAAGATACAAAAGGAAAGGTTTAAGTCGCAATGACGAA-C
1 CAGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATC
* * * *
45759 CTTA-TACCTTA-GAAG-CATGAAAGGAAAAATTTAAGCCGCAACGGCGAATT
1 C--AGTACC--ACGAAGACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATC
*
45809 TAGTACCA
1 CAGTACCA
45817 TGCAGATTAA
Statistics
Matches: 390, Mismatches: 82, Indels: 54
0.74 0.16 0.10
Matches are distributed among these distances:
47 1 0.00
48 23 0.06
49 339 0.87
50 26 0.07
51 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.17
Consensus pattern (49 bp):
CAGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAATGGCGAATC
Found at i:45441 original size:98 final size:98
Alignment explanation
Indices: 45287--45816 Score: 740
Period size: 98 Copynumber: 5.4 Consensus size: 98
45277 ATGAAGATAG
45287 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGGGAAAGGTTTAA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGGGAAAGGTTTAA
* * * * *
45352 GTCGCAACGGTGAACCTTGTACCTAAGAAGCGT
66 GTCGCAATGGCGAACCTTATACCTCAGAAGCAT
* * *
45385 GAAGGGAAAGATTTAAGCTGCAACGGCGAATCCAGTATCACGAACACACGAAGGGAAAGGTTTAA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGGGAAAGGTTTAA
*
45450 GTCGCAATGGTGAACCTTATACCTCA-AAGACAT
66 GTCGCAATGGCGAACCTTATACCTCAGAAG-CAT
* * * * ** *
45483 GAAGGGAAAGATTTAAGCCACAACGGCAAATGCAGTACCACAAAGACATAAAGGGAAAGATTTAA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGGGAAAGGTTTAA
*
45548 GTCGGAATGGCGAACCTTATACCTCAGAAGCAT
66 GTCGCAATGGCGAACCTTATACCTCAGAAGCAT
* * *
45581 GAAGGGAAAGATTTAAGCCGCAATGGCAAATCCAGTACCACAAAGACACGAAGGGAAAGGTTTAA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGGGAAAGGTTTAA
*
45646 GTCGCAATGGCAAACCTTATACCTCAG-AGACAT
66 GTCGCAATGGCGAACCTTATACCTCAGAAG-CAT
* * * * *
45679 GAAGGGAAAGATTTAAACCGCAATGGCGAATCCAGTACCACGAAGATACAAAAGGAAAGGTTTAA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGGGAAAGGTTTAA
* *
45744 GTCGCAATGACGAACCTTATACCTTAGAAGCAT
66 GTCGCAATGGCGAACCTTATACCTCAGAAGCAT
* * **
45777 GAAAGGAAAAATTTAAGCCGCAACGGCGAATTTAGTACCA
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCA
45817 TGCAGATTAA
Statistics
Matches: 386, Mismatches: 42, Indels: 8
0.89 0.10 0.02
Matches are distributed among these distances:
97 5 0.01
98 376 0.97
99 5 0.01
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.17
Consensus pattern (98 bp):
GAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAAGGGAAAGGTTTAA
GTCGCAATGGCGAACCTTATACCTCAGAAGCAT
Found at i:46252 original size:17 final size:17
Alignment explanation
Indices: 46228--46301 Score: 76
Period size: 17 Copynumber: 4.4 Consensus size: 17
46218 ACAGAATTTG
46228 AATTTATTTTAAAATTA
1 AATTTATTTTAAAATTA
* *
46245 AGTTTATTTTAAATTTA
1 AATTTATTTTAAAATTA
** *
46262 AATTTATTAGAAATTTA
1 AATTTATTTTAAAATTA
** *
46279 AATTTATCATAAATTTA
1 AATTTATTTTAAAATTA
46296 AATTTA
1 AATTTA
46302 AATTTATTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 50 1.00
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
AATTTATTTTAAAATTA
Found at i:46260 original size:34 final size:34
Alignment explanation
Indices: 46222--46301 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 34
46212 GGCCCAACAG
* ** * **
46222 AATTTGAATTTATTTTAAAATTAAGTTTATTTTA
1 AATTTAAATTTATTAGAAAATTAAATTTATCATA
*
46256 AATTTAAATTTATTAGAAATTTAAATTTATCATA
1 AATTTAAATTTATTAGAAAATTAAATTTATCATA
46290 AATTTAAATTTA
1 AATTTAAATTTA
46302 AATTTATTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (34 bp):
AATTTAAATTTATTAGAAAATTAAATTTATCATA
Done.