Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002283.1 Hibiscus syriacus cultivar Beakdansim tig00004647_pilon, 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: 151295
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:9480 original size:16 final size:17
Alignment explanation
Indices: 9449--9481 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9439 ACTGATTCGA
*
9449 GAATTGATGCGTTGGTG
1 GAATTGAAGCGTTGGTG
9466 GAATTGAAG-GTTGGTG
1 GAATTGAAGCGTTGGTG
9482 ACAACTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.21, C:0.03, G:0.42, T:0.33
Consensus pattern (17 bp):
GAATTGAAGCGTTGGTG
Found at i:14346 original size:41 final size:41
Alignment explanation
Indices: 14298--14376 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
14288 TTGGAAGACG
*
14298 GGGATTTTCCGCAACAGGTGCTGGATAGTTCTTGTTGTTTA
1 GGGATTTTCCGCAACAGGTGCTGGATAATTCTTGTTGTTTA
14339 GGGATTTTCCGCAACAGGTGCTGGATAATTCTTGTTGT
1 GGGATTTTCCGCAACAGGTGCTGGATAATTCTTGTTGT
14377 ATAGCTTACT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.18, C:0.15, G:0.29, T:0.38
Consensus pattern (41 bp):
GGGATTTTCCGCAACAGGTGCTGGATAATTCTTGTTGTTTA
Found at i:18735 original size:31 final size:32
Alignment explanation
Indices: 18700--18765 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 32
18690 GTAACTATTG
18700 GGGGACCATATTGAAAACGGACTAAAAGTT-A
1 GGGGACCATATTGAAAACGGACTAAAAGTTGA
* *
18731 GGGGACCATATTGCAAATGGACTAAAAGTTGA
1 GGGGACCATATTGAAAACGGACTAAAAGTTGA
18763 GGG
1 GGG
18766 ACTGTATTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (32 bp):
GGGGACCATATTGAAAACGGACTAAAAGTTGA
Found at i:21131 original size:2 final size:2
Alignment explanation
Indices: 21124--21149 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21114 TTATAAGATA
21124 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
21150 TCGAATCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29675 original size:50 final size:50
Alignment explanation
Indices: 29619--29720 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
29609 TACCATAAAT
* * * *
29619 ATGAAATTAAAATTCTGGTCCAACTTGCCAAACACAATAATTCATAATGA
1 ATGAAATTAAAACTCTGGTCCAACTTGCCAAACACAAGAATCCAGAATGA
*
29669 ATGAAATTAAAACTCTGGTCCAGCTTGCCAAACACAAGAATCCAGAATGA
1 ATGAAATTAAAACTCTGGTCCAACTTGCCAAACACAAGAATCCAGAATGA
29719 AT
1 AT
29721 TAGTTTCAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.25
Consensus pattern (50 bp):
ATGAAATTAAAACTCTGGTCCAACTTGCCAAACACAAGAATCCAGAATGA
Found at i:31778 original size:24 final size:25
Alignment explanation
Indices: 31729--31785 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
31719 AGAGATAATG
* *
31729 GAAAACAAATAGACGAAGCAAGACA
1 GAAAGCAAATAGACGAAGCAAAACA
31754 GAAAGCAAA-AGACGAA-CACAAACA
1 GAAAGCAAATAGACGAAGCA-AAACA
*
31778 GACAGCAA
1 GAAAGCAA
31786 CCACCCACAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 2 0.07
24 18 0.64
25 8 0.29
ACGTcount: A:0.60, C:0.19, G:0.19, T:0.02
Consensus pattern (25 bp):
GAAAGCAAATAGACGAAGCAAAACA
Found at i:33237 original size:11 final size:13
Alignment explanation
Indices: 33200--33239 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
33190 TGTTTAATAA
33200 AATATA-TATATT
1 AATATATTATATT
*
33212 AATATATTATCTT
1 AATATATTATATT
33225 AA-A-ATTATATT
1 AATATATTATATT
33236 AATA
1 AATA
33240 AACTTAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:35224 original size:43 final size:44
Alignment explanation
Indices: 35157--35243 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 44
35147 TGGCTTTAGA
* *
35157 GAAGTTATGAGGGAAAGTTATCCCCTATATGT-AAAGTTTTGTT
1 GAAGTTATGAGGGAAAGCTATCCCCTACATGTAAAAGTTTTGTT
** * *
35200 GAAGTTATGATTGAAAGCTGTCCCCTGCATGTAAAAGTTTTGTT
1 GAAGTTATGAGGGAAAGCTATCCCCTACATGTAAAAGTTTTGTT
35244 TGATGCACGG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 26 0.70
44 11 0.30
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (44 bp):
GAAGTTATGAGGGAAAGCTATCCCCTACATGTAAAAGTTTTGTT
Found at i:43118 original size:112 final size:112
Alignment explanation
Indices: 42861--43400 Score: 786
Period size: 112 Copynumber: 4.8 Consensus size: 112
42851 TGACAGGAAT
*
42861 TTCAACCTTTTGCCTGAATTCATCACTTGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGA
1 TTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAACTTTTCCAGA-GAAGTTCATAATGAGA
* *
42926 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
65 AGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
* *
42974 TTTAACCTTTTG-CTCGAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAG
1 TTCAACCTTTTGCCT-GAATTCATCACTTGATGGATCAACTTTTCCAGAG-AAGTTCATAATGAG
*
43038 AAGAACTTATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTG
64 AAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
* *
43086 TTCAACCTTTTGCCTGAATTCATTACTTGATGGATTAACTTTTCCAGAGGAAGTTCATAATGAGA
1 TTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAACTTTTCCAGA-GAAGTTCATAATGAGA
* *
43151 AGAACTCATTTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAATTTG
65 AGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
* * ** *
43198 TTTAACTTTTTGTTTGAATTCATCA-TTCGATGGATCAACTTTTCCAGAGAAGCTCATAATGAGA
1 TTCAACCTTTTGCCTGAATTCATCACTT-GATGGATCAACTTTTCCAGAGAAGTTCATAATGAGA
*
43262 AGAACTCATCTGAAGAAGGAAGAAAAAATTCATAATGAGAAGAATTTG
65 AGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
* ** * *
43310 TCCAAACCTTTTGTTTGAACTCATCA-TTCGATGGATCAACTTTTCCAGAGAGGTTCATAATGAG
1 TTC-AACCTTTTGCCTGAATTCATCACTT-GATGGATCAACTTTTCCAGAGAAGTTCATAATGAG
43374 AAGAACTCATCTGAAGAAGG-AGAAGAA
64 AAGAACTCATCTGAAGAAGGAAGAAGAA
43401 TTTGTTCAAC
Statistics
Matches: 389, Mismatches: 30, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
111 35 0.09
112 201 0.52
113 153 0.39
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (112 bp):
TTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAACTTTTCCAGAGAAGTTCATAATGAGAA
GAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTG
Found at i:43695 original size:3 final size:3
Alignment explanation
Indices: 43687--43740 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
43677 CATTTGCTTA
*
43687 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TGT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
43733 TAT TAT TA
1 TAT TAT TA
43741 AATAATAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
2 3 0.06
3 44 0.94
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:45764 original size:11 final size:13
Alignment explanation
Indices: 45727--45766 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
45717 TGTTTAATAA
45727 AATATA-TATATT
1 AATATATTATATT
*
45739 AATATATTATCTT
1 AATATATTATATT
45752 AA-A-ATTATATT
1 AATATATTATATT
45763 AATA
1 AATA
45767 AACTTAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:46051 original size:77 final size:77
Alignment explanation
Indices: 45958--46108 Score: 284
Period size: 77 Copynumber: 2.0 Consensus size: 77
45948 CCAGTTTATC
45958 TTTTAACTGATGTTTTTCTAAAAACTCTTTTAAAAGATAATTTTTAGGTATTCGACCTACCTAAT
1 TTTTAACTGATGTTTTTCTAAAAACTCTTTTAAAAGATAATTTTTAGGTATTCGACCTACCTAAT
46023 CCAAAAGGTTGA
66 CCAAAAGGTTGA
* *
46035 TTTTAACTGATGTTTTTCTAAAAACTCTTTTAAAAGATAATTTTTAGGTATTCTACCTACCTGAT
1 TTTTAACTGATGTTTTTCTAAAAACTCTTTTAAAAGATAATTTTTAGGTATTCGACCTACCTAAT
46100 CCAAAAGGT
66 CCAAAAGGT
46109 CGATGGCGAC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 72 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (77 bp):
TTTTAACTGATGTTTTTCTAAAAACTCTTTTAAAAGATAATTTTTAGGTATTCGACCTACCTAAT
CCAAAAGGTTGA
Found at i:49045 original size:33 final size:33
Alignment explanation
Indices: 49008--49106 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 33
48998 ATTTGGCAAG
49008 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
** * * *
49041 TTGGAAGTTTTATCTTGGTTGGTGGTCAATTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
* *
49074 TTAGAAAATTCATCTTTGGTAGGTGGCCAACTT
1 TTGGAAAATTCATC-TTGGTTGGTGGCCAACTT
49107 TGCACATGGG
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
33 38 0.72
34 15 0.28
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.40
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:49517 original size:11 final size:11
Alignment explanation
Indices: 49503--49569 Score: 80
Period size: 11 Copynumber: 5.9 Consensus size: 11
49493 AACTCAAGAC
49503 TCAAGCTCGAT
1 TCAAGCTCGAT
49514 TCAAGCTCGATT
1 TCAAGCTCGA-T
**
49526 TTGAGCTCGAT
1 TCAAGCTCGAT
49537 TCAAGCTCGATT
1 TCAAGCTCGA-T
**
49549 TTGAGCTCGAT
1 TCAAGCTCGAT
49560 TCAAGCTCGA
1 TCAAGCTCGA
49570 CTTTGAGCTC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
11 28 0.61
12 18 0.39
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (11 bp):
TCAAGCTCGAT
Found at i:49533 original size:23 final size:23
Alignment explanation
Indices: 49506--49603 Score: 146
Period size: 23 Copynumber: 4.3 Consensus size: 23
49496 TCAAGACTCA
49506 AGCTCGATTCAAGCTCGATTTTG
1 AGCTCGATTCAAGCTCGATTTTG
49529 AGCTCGATTCAAGCTCGATTTTG
1 AGCTCGATTCAAGCTCGATTTTG
*
49552 AGCTCGATTCAAGCTCGACTTTG
1 AGCTCGATTCAAGCTCGATTTTG
* *
49575 AGCTCAATTTAAGCTC--TTTTG
1 AGCTCGATTCAAGCTCGATTTTG
49596 AAGCTCGA
1 -AGCTCGA
49604 AACGGATTAG
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
21 4 0.06
22 6 0.09
23 59 0.86
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.34
Consensus pattern (23 bp):
AGCTCGATTCAAGCTCGATTTTG
Found at i:49534 original size:12 final size:12
Alignment explanation
Indices: 49517--49584 Score: 68
Period size: 12 Copynumber: 5.8 Consensus size: 12
49507 GCTCGATTCA
49517 AGCTCGATTTTG
1 AGCTCGATTTTG
**
49529 AGCTCGA-TTCA
1 AGCTCGATTTTG
49540 AGCTCGATTTTG
1 AGCTCGATTTTG
**
49552 AGCTCGA-TTCA
1 AGCTCGATTTTG
*
49563 AGCTCGACTTTG
1 AGCTCGATTTTG
*
49575 AGCTCAATTT
1 AGCTCGATTT
49585 AAGCTCTTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
11 18 0.41
12 26 0.59
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (12 bp):
AGCTCGATTTTG
Found at i:51223 original size:21 final size:21
Alignment explanation
Indices: 51194--51247 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
51184 CAGATTTAGA
51194 TTTAGGGTTTATAGTATATAG
1 TTTAGGGTTTATAGTATATAG
* * *
51215 TTTATGGTTTATGGTTTATAG
1 TTTAGGGTTTATAGTATATAG
51236 TTTAGGGTTTAT
1 TTTAGGGTTTAT
51248 TACAAAGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.54
Consensus pattern (21 bp):
TTTAGGGTTTATAGTATATAG
Found at i:51224 original size:7 final size:7
Alignment explanation
Indices: 51194--51247 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
51184 CAGATTTAGA
*
51194 TTTAGGG
1 TTTATGG
*
51201 TTTATAG
1 TTTATGG
* *
51208 TATATAG
1 TTTATGG
51215 TTTATGG
1 TTTATGG
51222 TTTATGG
1 TTTATGG
*
51229 TTTATAG
1 TTTATGG
*
51236 TTTAGGG
1 TTTATGG
51243 TTTAT
1 TTTAT
51248 TACAAAGATA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.54
Consensus pattern (7 bp):
TTTATGG
Found at i:51238 original size:14 final size:14
Alignment explanation
Indices: 51194--51247 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
51184 CAGATTTAGA
51194 TTTAGGGTTTATAG
1 TTTAGGGTTTATAG
* ** *
51208 TATATAGTTTATGG
1 TTTAGGGTTTATAG
*
51222 TTTATGGTTTATAG
1 TTTAGGGTTTATAG
51236 TTTAGGGTTTAT
1 TTTAGGGTTTAT
51248 TACAAAGATA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.54
Consensus pattern (14 bp):
TTTAGGGTTTATAG
Found at i:51470 original size:11 final size:11
Alignment explanation
Indices: 51456--51497 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
51446 TCGTTAAGAA
51456 CTCGAGTCGAG
1 CTCGAGTCGAG
51467 CTCGAGTCGAG
1 CTCGAGTCGAG
*
51478 CTCGTGTCGAG
1 CTCGAGTCGAG
*
51489 -TCGATTCGA
1 CTCGAGTCGA
51498 TTCGAGTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 7 0.25
11 21 0.75
ACGTcount: A:0.17, C:0.26, G:0.33, T:0.24
Consensus pattern (11 bp):
CTCGAGTCGAG
Found at i:51476 original size:5 final size:5
Alignment explanation
Indices: 51457--51504 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
51447 CGTTAAGAAC
* * *
51457 TCGAG TCGAG CTCGAG TCGAG CTCGTG TCGAG TCGAT TCGAT TCGAG T
1 TCGAG TCGAG -TCGAG TCGAG -TCGAG TCGAG TCGAG TCGAG TCGAG T
51505 ATTTATCGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 28 0.76
6 9 0.24
ACGTcount: A:0.17, C:0.23, G:0.33, T:0.27
Consensus pattern (5 bp):
TCGAG
Found at i:54379 original size:14 final size:14
Alignment explanation
Indices: 54360--54389 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
54350 TGGATGAAGA
54360 AATGCAATCTCTTC
1 AATGCAATCTCTTC
54374 AATGCAATCTCTTC
1 AATGCAATCTCTTC
54388 AA
1 AA
54390 AAGAACAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (14 bp):
AATGCAATCTCTTC
Found at i:56032 original size:34 final size:33
Alignment explanation
Indices: 55947--56042 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 33
55937 ATTTGGCAAG
55947 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
55980 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
* *
56013 TTGGAAAATTCAGCTTTGGTAGGTGGCCAA
1 TTGGAAAATTCATC-TTGGTTGGTGGCCAA
56043 TTTGCATATG
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:68115 original size:30 final size:31
Alignment explanation
Indices: 68081--68149 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
68071 CTAAAAATTT
* * * *
68081 AATTAAGTCCTTAAACTT-TCCAAAAGAATC
1 AATTAAGCCCTCAAACTTAACCAAAAAAATC
* *
68111 AATTAGGCCCTCAAACTTAACTAAAAAAATC
1 AATTAAGCCCTCAAACTTAACCAAAAAAATC
68142 AATTAAGC
1 AATTAAGC
68150 TCATCCACCT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.26
Consensus pattern (31 bp):
AATTAAGCCCTCAAACTTAACCAAAAAAATC
Found at i:68595 original size:27 final size:25
Alignment explanation
Indices: 68543--68595 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
68533 TAAATTTATG
*
68543 TAATAAATTTTTAATGACTATATTT
1 TAATAAATTTTTAATAACTATATTT
* *
68568 TAATATAATTATTTAATAATTATTTTT
1 TAATA-AATT-TTTAATAACTATATTT
68595 T
1 T
68596 CATCTCTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 4 0.17
27 14 0.61
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
TAATAAATTTTTAATAACTATATTT
Found at i:70238 original size:38 final size:38
Alignment explanation
Indices: 70162--70238 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
70152 CTCATGTCTG
* * *
70162 TGAGTTGTCACTAACATTAAGCGCACCTAAATCTAGTC
1 TGAGTTGTCACTAAAATTAAGCGCACCTAAAGCCAGTC
*
70200 TGAGTTGTCCCTAAAATTAAGCGCACCTAAAGCCAGTC
1 TGAGTTGTCACTAAAATTAAGCGCACCTAAAGCCAGTC
70238 T
1 T
70239 TCCACACCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (38 bp):
TGAGTTGTCACTAAAATTAAGCGCACCTAAAGCCAGTC
Found at i:71602 original size:23 final size:21
Alignment explanation
Indices: 71576--71618 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
71566 TATAAAAAAT
71576 TATTTTCTATTAAATATTTTTAG
1 TATTTT-TATTAAAT-TTTTTAG
*
71599 TATTTTTATTTAATTTTTTA
1 TATTTTTATTAAATTTTTTA
71619 AATAATTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 7 0.37
23 6 0.32
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTAG
Found at i:75531 original size:41 final size:42
Alignment explanation
Indices: 75473--75578 Score: 108
Period size: 42 Copynumber: 2.5 Consensus size: 42
75463 CATCCTACCC
* * ** * *
75473 AAAGGTCTTACGGATGACCTGAAGGATTT-ATCATCTTGCTCT
1 AAAGG-CTTACAGATGACCCGAAAAATTTAATCATCATGCTCG
75515 AAAGGCTTACAGATGACCCGAAAAATTTAATCATCATGCTCG
1 AAAGGCTTACAGATGACCCGAAAAATTTAATCATCATGCTCG
* *
75557 AAAGACTTA-ATGATGGCCCGAA
1 AAAGGCTTACA-GATGACCCGAA
75579 GGACTTATAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 20 0.37
42 34 0.63
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (42 bp):
AAAGGCTTACAGATGACCCGAAAAATTTAATCATCATGCTCG
Found at i:75749 original size:41 final size:41
Alignment explanation
Indices: 75699--75800 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
75689 ATGTCTTATG
* * *
75699 GATGGCCCGAATGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGAATGACTTATCATCATGCTCGAAAGACTTACA
* * * *
75740 GATGACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAATGACTT-ATCATCATGCTCGAAAGACTTACA
*
75782 GATGGCCCGAATGCCTTAT
1 GATGGCCCGAATGACTTAT
75801 AAATTGTGAA
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (41 bp):
GATGGCCCGAATGACTTATCATCATGCTCGAAAGACTTACA
Found at i:75778 original size:214 final size:215
Alignment explanation
Indices: 75307--76002 Score: 1056
Period size: 214 Copynumber: 3.2 Consensus size: 215
75297 GCTCGGAAGA
* * *
75307 CTTACAAATGACCCGAATGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCGGAAGGACTT
1 CTTACAGATGACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* * *
75372 ATAAATTGTGAAATTTTGAAAATCGTATTCTTTGTTTTCAAAAAATTCATCTTTTTAAAACATCA
66 ATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAAATTCATCTTCTTAAAACATCA
* * * * * * *
75437 TTTTC--ATTTTCAAATTCATTTGAACACATCCTACCCAAAGGTCTTACGGATGACCTGAAGGAT
131 TTTTCTTATTTTCAAATTCATATGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGAC
75500 TTATCATCTTGCTCTAAAGG
196 TTATCATCTTGCTCTAAAGG
** * *
75520 CTTACAGATGACCCGAAAAATTTAATCATCATGCTCGAAAGACTTAATGATGGCCCGAAGGACTT
1 CTTACAGATGACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* * * *
75585 ATAAATTGTGAAATTTTGAAACTCGCATTCTTCATTTTTAAAAAATTCATCATCTTAAAACATCA
66 ATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAAATTCATCTTCTTAAAACATCA
* *
75650 TTTTCTTATTTTCAAATTCA-ATGAAAACATCCTACCCGAATGTCTTATGGATGGCCCGAATGAC
131 TTTTCTTATTTTCAAATTCATATGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGAC
75714 TTATCATCTTGCTCTAAAGG
196 TTATCATCTTGCTCTAAAGG
* *
75734 CTTACAGATGACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAATGCCTT
1 CTTACAGATGACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
*
75799 ATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCA
66 ATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAAATTCATCTTCTTAAAACATCA
* * * *
75864 TTTTTTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATTGCCCGAAGGA
131 TTTTCTT-ATTTTCAAATTCATATGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGA
75929 CTTATCATCTTGCTCTAAAGG
195 CTTATCATCTTGCTCTAAAGG
* * * *
75950 CTTATAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG
1 CTTACAGATGACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
76003 AGTTACTTCA
Statistics
Matches: 435, Mismatches: 44, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
213 121 0.28
214 180 0.41
215 26 0.06
216 108 0.25
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Consensus pattern (215 bp):
CTTACAGATGACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
ATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAAATTCATCTTCTTAAAACATCA
TTTTCTTATTTTCAAATTCATATGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGAC
TTATCATCTTGCTCTAAAGG
Found at i:76315 original size:36 final size:35
Alignment explanation
Indices: 76121--76403 Score: 356
Period size: 36 Copynumber: 7.9 Consensus size: 35
76111 GCTGATGGAT
*
76121 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGAG
1 TTGCTTCACTACTCTCCGGTGAAGGCTTAAGA-TG-G
* * *
76158 TTGCTTCACTATTCTCCGGTGGAGGCTTAGGATGG
1 TTGCTTCACTACTCTCCGGTGAAGGCTTAAGATGG
*
76193 -TGCTTCACTACTC-CTCTGTGAAGGCTTAAGATGG
1 TTGCTTCACTACTCTC-CGGTGAAGGCTTAAGATGG
* *
76227 -TGCTTCACTACTCTTCTGTGAAGGCTTAAGATTGAG
1 TTGCTTCACTACTCTCCGGTGAAGGCTTAAGA-TG-G
* *
76263 TTGCTTCACTATTCTCCGGTAAAGGCTTAAGATGG
1 TTGCTTCACTACTCTCCGGTGAAGGCTTAAGATGG
* *
76298 TTTGCTTCACTACTCTCCAGTGAAGGCTTCAGATGG
1 -TTGCTTCACTACTCTCCGGTGAAGGCTTAAGATGG
*
76334 TTTGCTTCACTATTCTCCGGTGAAGGCTTAAGATGG
1 -TTGCTTCACTACTCTCCGGTGAAGGCTTAAGATGG
*
76370 TTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
1 -TTGCTTCACTACTCTCCGGTGAAGGCTTAAGAT
76404 TGACTTGCCC
Statistics
Matches: 218, Mismatches: 22, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
33 1 0.00
34 57 0.26
35 4 0.02
36 101 0.46
37 55 0.25
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (35 bp):
TTGCTTCACTACTCTCCGGTGAAGGCTTAAGATGG
Found at i:81397 original size:21 final size:21
Alignment explanation
Indices: 81371--81477 Score: 146
Period size: 21 Copynumber: 5.1 Consensus size: 21
81361 CGCAAAAATA
*
81371 GTCTTCAT-GTCTTTGTGAATG
1 GTCTTC-TCGTCTTTATGAATG
*
81392 GTCTTCTCATCTTTATGAATG
1 GTCTTCTCGTCTTTATGAATG
81413 GTCTTCTCGTCTTTATGAATG
1 GTCTTCTCGTCTTTATGAATG
* *
81434 GTCTTCTCGTCCTTGTGAATG
1 GTCTTCTCGTCTTTATGAATG
81455 GTCTTCTCGTCCTTT-TGAATG
1 GTCTTCTCGT-CTTTATGAATG
81476 GT
1 GT
81478 TATATATATC
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
20 1 0.01
21 74 0.95
22 3 0.04
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.47
Consensus pattern (21 bp):
GTCTTCTCGTCTTTATGAATG
Found at i:91728 original size:13 final size:13
Alignment explanation
Indices: 91710--91737 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
91700 TCCTTAAATG
91710 TGCTTTAGAGTTT
1 TGCTTTAGAGTTT
91723 TGCTTTAGAGTTT
1 TGCTTTAGAGTTT
91736 TG
1 TG
91738 TTTTGTTTTG
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:0.14, C:0.07, G:0.25, T:0.54
Consensus pattern (13 bp):
TGCTTTAGAGTTT
Found at i:95376 original size:3 final size:3
Alignment explanation
Indices: 95368--95436 Score: 67
Period size: 3 Copynumber: 24.0 Consensus size: 3
95358 ATTAATTATT
*
95368 TAA TAA TAA TAA TAA T-A TATA TAA T-A TAA TAA TAA TAT TAA -AA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
95411 CAA -AA TAA TAA TAA TAAA TAA -AA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA
95437 ATGAAATAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
2 10 0.18
3 41 0.72
4 6 0.11
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:95921 original size:6 final size:6
Alignment explanation
Indices: 95910--95948 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
95900 GAGAGAGTTT
* *
95910 TGATGG TGATGG TGATGG TGATGG TGAGGG TGAGGG TGA
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGA
95949 GGAAAGTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.18, C:0.00, G:0.54, T:0.28
Consensus pattern (6 bp):
TGATGG
Found at i:96489 original size:15 final size:15
Alignment explanation
Indices: 96469--96498 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
96459 TGTCAAAATG
96469 GTTTGACCTTTCATT
1 GTTTGACCTTTCATT
96484 GTTTGACCTTTCATT
1 GTTTGACCTTTCATT
96499 TGTTCGTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.13, T:0.53
Consensus pattern (15 bp):
GTTTGACCTTTCATT
Found at i:102301 original size:14 final size:16
Alignment explanation
Indices: 102270--102306 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
102260 AATCCTTAAA
102270 TTAATTTTTTAATAAT
1 TTAATTTTTTAATAAT
*
102286 TTCATTTTTT-AT-AT
1 TTAATTTTTTAATAAT
102300 TTAATTT
1 TTAATTT
102307 ATTGAATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 8 0.42
15 2 0.11
16 9 0.47
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTAATTTTTTAATAAT
Found at i:104902 original size:17 final size:17
Alignment explanation
Indices: 104880--104917 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
104870 CAACGGTCAC
104880 GGTCAACGGTC-GTGTCG
1 GGTCAACGGTCGGT-TCG
*
104897 GGTCAATGGTCGGTTCG
1 GGTCAACGGTCGGTTCG
104914 GGTC
1 GGTC
104918 GGTCGGGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.11, C:0.21, G:0.42, T:0.26
Consensus pattern (17 bp):
GGTCAACGGTCGGTTCG
Found at i:112093 original size:17 final size:17
Alignment explanation
Indices: 112067--112106 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
112057 CAACGGTCAC
* * *
112067 GGTCAACGGTTGGGTCG
1 GGTCAGCGGTCGGATCG
112084 GGTCAGCGGTCGGATCG
1 GGTCAGCGGTCGGATCG
112101 GGTCAG
1 GGTCAG
112107 ACCGGTCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.12, C:0.20, G:0.47, T:0.20
Consensus pattern (17 bp):
GGTCAGCGGTCGGATCG
Found at i:112152 original size:10 final size:9
Alignment explanation
Indices: 112101--112180 Score: 70
Period size: 10 Copynumber: 8.3 Consensus size: 9
112091 GGTCGGATCG
*
112101 GGTCAGACC
1 GGTCAAACC
112110 GGTCAAACC
1 GGTCAAACC
*
112119 GGTTCAGACC
1 GG-TCAAACC
*
112129 GGTTCGAACC
1 GG-TCAAACC
112139 GGTCGAAACC
1 GGTC-AAACC
112149 GGTCAAACC
1 GGTCAAACC
* *
112158 GATTCAAAATC
1 G-GTC-AAACC
112169 GGTCAAACC
1 GGTCAAACC
112178 GGT
1 GGT
112181 TTTCCAGCTG
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
9 25 0.43
10 28 0.48
11 5 0.09
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:126661 original size:20 final size:21
Alignment explanation
Indices: 126635--126682 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
126625 TACTCAGGGG
126635 AGTATCGAAACCATAGA-AAA
1 AGTATCGAAACCATAGATAAA
* * *
126655 TGTATCGATACCCTAGATAAA
1 AGTATCGAAACCATAGATAAA
126676 AGTATCG
1 AGTATCG
126683 GTACTTACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.23
Consensus pattern (21 bp):
AGTATCGAAACCATAGATAAA
Found at i:131013 original size:22 final size:23
Alignment explanation
Indices: 130988--131049 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 23
130978 TAATATGAAT
130988 ATTTATTTTTTTAATAA-TTTAA
1 ATTTATTTTTTTAATAAGTTTAA
*
131010 ATTT-TTATTTTTAATAAGTTTTAT
1 ATTTATT-TTTTTAATAAG-TTTAA
131034 ATTTATTTTTTTAATA
1 ATTTATTTTTTTAATA
131050 CTTAGATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
21 2 0.06
22 14 0.40
24 17 0.49
25 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
ATTTATTTTTTTAATAAGTTTAA
Found at i:131016 original size:24 final size:24
Alignment explanation
Indices: 130985--131049 Score: 91
Period size: 22 Copynumber: 2.8 Consensus size: 24
130975 TTTTAATATG
130985 AATATTTATTTTTTTAATAA-TTT
1 AATATTTATTTTTTTAATAAGTTT
131008 AA-ATTT-TTATTTTTAATAAGTTT
1 AATATTTATT-TTTTTAATAAGTTT
*
131031 TATATTTATTTTTTTAATA
1 AATATTTATTTTTTTAATA
131050 CTTAGATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 2 0.05
22 14 0.38
23 6 0.16
24 13 0.35
25 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
AATATTTATTTTTTTAATAAGTTT
Found at i:131061 original size:24 final size:22
Alignment explanation
Indices: 130973--131049 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
130963 ATTTTTAGTA
*
130973 TTTTTTAATATGA-ATATTTAT
1 TTTTTTAATATTATATATTTAT
*
130994 TTTTTTAATAATT-TAAATTT-T
1 TTTTTTAAT-ATTATATATTTAT
*
131015 TATTTTTAATAAGTTTTATATTTAT
1 T-TTTTTAAT-A-TTATATATTTAT
131040 TTTTTTAATA
1 TTTTTTAATA
131050 CTTAGATAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
21 11 0.23
22 17 0.36
23 3 0.06
24 14 0.30
25 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (22 bp):
TTTTTTAATATTATATATTTAT
Found at i:131626 original size:17 final size:17
Alignment explanation
Indices: 131604--131637 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
131594 ATGGATCTAT
131604 TCTATCGAGTTATTTGA
1 TCTATCGAGTTATTTGA
*
131621 TCTATCGGGTTATTTGA
1 TCTATCGAGTTATTTGA
131638 AGATGCAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (17 bp):
TCTATCGAGTTATTTGA
Found at i:131708 original size:17 final size:17
Alignment explanation
Indices: 131675--131719 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
131665 GTTTATTTGT
*
131675 GTTAT-TTATAATATTC
1 GTTATATTATTATATTC
*
131691 GTTATATTATTATTTTC
1 GTTATATTATTATATTC
*
131708 GTAATATTATTA
1 GTTATATTATTA
131720 ATGATATTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (17 bp):
GTTATATTATTATATTC
Found at i:131777 original size:19 final size:19
Alignment explanation
Indices: 131750--131788 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
131740 TTATTATATA
*
131750 TTATTCTATAGAATTCTAT
1 TTATCCTATAGAATTCTAT
131769 TTATCCTATAGAATTCTAT
1 TTATCCTATAGAATTCTAT
131788 T
1 T
131789 CTAATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (19 bp):
TTATCCTATAGAATTCTAT
Found at i:136950 original size:42 final size:42
Alignment explanation
Indices: 136903--137023 Score: 185
Period size: 39 Copynumber: 3.0 Consensus size: 42
136893 TGAACTAAAG
136903 ATCAGTAATACATCTTACAGTCTTGGCCAAAGTATAGCAAAA
1 ATCAGTAATACATCTTACAGTCTTGGCCAAAGTATAGCAAAA
* * *
136945 ATCAGTAATGCATCTAACAGTC-T-GCCAAAGTACAG-AAAA
1 ATCAGTAATACATCTTACAGTCTTGGCCAAAGTATAGCAAAA
*
136984 ATCAGTAATACATCTTACAGTCTTGGCCAAATTATAGCAA
1 ATCAGTAATACATCTTACAGTCTTGGCCAAAGTATAGCAA
137024 CGATATACAA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
39 24 0.35
40 12 0.17
41 11 0.16
42 22 0.32
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (42 bp):
ATCAGTAATACATCTTACAGTCTTGGCCAAAGTATAGCAAAA
Found at i:143474 original size:31 final size:31
Alignment explanation
Indices: 143397--143463 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
143387 CAGTTACATA
*
143397 GGGGACCATATTGCAGACAGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
*
143428 GGGGACCATATTGCAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
143459 GGGGA
1 GGGGA
143464 TTGTATTGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.31, C:0.15, G:0.33, T:0.21
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:145159 original size:5 final size:5
Alignment explanation
Indices: 145149--145175 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
145139 TAACCTTAAG
145149 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
145176 GAAATTTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:148835 original size:13 final size:13
Alignment explanation
Indices: 148817--148862 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
148807 TTTTTATTTG
148817 TATATTATTAAAA
1 TATATTATTAAAA
**
148830 TATATTATTTTAA
1 TATATTATTAAAA
148843 T-TATT-TTAAAA
1 TATATTATTAAAA
148854 TATTATTAT
1 TA-TATTAT
148863 ATTTGGATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
11 5 0.19
12 4 0.15
13 16 0.62
14 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TATATTATTAAAA
Found at i:148847 original size:22 final size:26
Alignment explanation
Indices: 148810--148862 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
148800 TTATGAATTT
148810 TTATTTGTATATTA-TTAAAATA-TA
1 TTATTTGTATATTATTTAAAATATTA
148834 TTATTT-TA-ATTATTTTAAAATATTA
1 TTATTTGTATATTA-TTTAAAATATTA
148859 TTAT
1 TTAT
148863 ATTTGGATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.15
23 2 0.08
24 14 0.54
25 6 0.23
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
TTATTTGTATATTATTTAAAATATTA
Done.