Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003346.1 Hibiscus syriacus cultivar Beakdansim tig00007045_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: 173681
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2012 original size:23 final size:23
Alignment explanation
Indices: 1958--2013 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
1948 ATTTTATATA
* **
1958 AAATTTT-AAAAAATAAAATTAT
1 AAATTTTAAAAAAAGAAAAACAT
* *
1980 ATATTATAAAAAAAGAAAAACAT
1 AAATTTTAAAAAAAGAAAAACAT
2003 AAATTTTAAAA
1 AAATTTTAAAA
2014 TAACCCCTAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATTTTAAAAAAAGAAAAACAT
Found at i:5865 original size:2 final size:2
Alignment explanation
Indices: 5858--5892 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5848 CATCATCATC
5858 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5893 GTATGTATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:7564 original size:15 final size:15
Alignment explanation
Indices: 7544--7578 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
7534 GTAAAAAGCG
*
7544 TTGCTTTTGGACAGT
1 TTGCTTTTGGACAAT
7559 TTGC-TTTGGACAAT
1 TTGCTTTTGGACAAT
7573 TTGCTT
1 TTGCTT
7579 GTAATTGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (15 bp):
TTGCTTTTGGACAAT
Found at i:10961 original size:13 final size:13
Alignment explanation
Indices: 10943--10968 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10933 GTTGAGTGGT
10943 GGTTTAAAAGTTG
1 GGTTTAAAAGTTG
10956 GGTTTAAAAGTTG
1 GGTTTAAAAGTTG
10969 AGGGACAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (13 bp):
GGTTTAAAAGTTG
Found at i:11780 original size:21 final size:21
Alignment explanation
Indices: 11754--11808 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
11744 AAGTTGAAAG
*
11754 GGAGTATTGATACGCTCAAGA
1 GGAGTATCGATACGCTCAAGA
11775 GGAGTATCGATACGCTCAAGA
1 GGAGTATCGATACGCTCAAGA
11796 GGAGTATCGATAC
1 GGAGTATCGATAC
11809 TTCAGGGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (21 bp):
GGAGTATCGATACGCTCAAGA
Found at i:19871 original size:30 final size:30
Alignment explanation
Indices: 19835--19894 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
19825 ACAATTTAAG
19835 GCAAAATGTTTTTGGACTGGAATTAAATTT
1 GCAAAATGTTTTTGGACTGGAATTAAATTT
* * *
19865 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTGGAATTAAATTT
19895 ATTCAAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTGGAATTAAATTT
Found at i:20002 original size:21 final size:21
Alignment explanation
Indices: 19976--20033 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
19966 AGGGTGTCAA
19976 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
19997 AGTGCATCCATGTATCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
20018 AGCGCATCCATGCATC
1 AGTGCATCCATGCATC
20034 TGCACTAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:20122 original size:21 final size:21
Alignment explanation
Indices: 20096--20171 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
20086 ATGCAATTAG
20096 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
20117 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
20138 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
*
20158 TGCATCCATGCATC
1 TGCATCGATGCATC
20172 AAGGCTGCAA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 18 0.33
21 36 0.67
ACGTcount: A:0.20, C:0.34, G:0.18, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:21386 original size:19 final size:20
Alignment explanation
Indices: 21362--21409 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
21352 AATGATTTTC
*
21362 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
21381 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
21401 TTTTGAAAA
1 TTTTGAAAA
21410 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:22809 original size:34 final size:32
Alignment explanation
Indices: 22770--22839 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
22760 TTTTGTAAAG
* *
22770 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
22804 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
22836 GGGA
1 GGGA
22840 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:28335 original size:21 final size:21
Alignment explanation
Indices: 28287--28349 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
28277 CCCCCCATGA
28287 GGGAACCGATTCCCCCCTTTGAAG
1 GGGAACCGATTCCCCCC--T-AAG
28311 GGGAACCGATTCCCCCC-ACAG
1 GGGAACCGATTCCCCCCTA-AG
* *
28332 GGGAATCGATACCCCCCT
1 GGGAACCGATTCCCCCCT
28350 GGGGTTCTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 17 0.49
24 17 0.49
ACGTcount: A:0.22, C:0.38, G:0.24, T:0.16
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCTAAG
Found at i:31128 original size:20 final size:20
Alignment explanation
Indices: 31103--31153 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
31093 CACTTAGGGA
*
31103 ACCGATTCCCCATAGGGGGT
1 ACCGATTCCCCAAAGGGGGT
31123 ACCGATTCCCCAAAGGGGGT
1 ACCGATTCCCCAAAGGGGGT
31143 ACCGATTCCCC
1 ACCGATTCCCC
31154 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.18
Consensus pattern (20 bp):
ACCGATTCCCCAAAGGGGGT
Found at i:32522 original size:57 final size:57
Alignment explanation
Indices: 32434--32545 Score: 161
Period size: 57 Copynumber: 2.0 Consensus size: 57
32424 GAACCACCAG
* * * *
32434 CACCTCTGCAGCAAAACCTAGAATATGATCCTAGTCCAAGATCTTGTGAAGATCCAA
1 CACCTCTGCAGAAAAAACAAGAATATGATCCTAGTCCAAGATCTTATGAAGATCCAA
* * *
32491 CACCTCTGCAGAAAAAACAAGAATTTGATCCTGGTCCAAGATGTTATGAAGATCC
1 CACCTCTGCAGAAAAAACAAGAATATGATCCTAGTCCAAGATCTTATGAAGATCC
32546 TTCAGGTAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (57 bp):
CACCTCTGCAGAAAAAACAAGAATATGATCCTAGTCCAAGATCTTATGAAGATCCAA
Found at i:37849 original size:28 final size:29
Alignment explanation
Indices: 37818--37872 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
37808 TTTTTAGGTC
* *
37818 ATAAACTTG-ACTTTTAAAATTCTAGGAA
1 ATAAAATTGAACTTATAAAATTCTAGGAA
*
37846 ATAAAATTGAACTTATAAAATTTTAGG
1 ATAAAATTGAACTTATAAAATTCTAGG
37873 GTGAAAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.36
Consensus pattern (29 bp):
ATAAAATTGAACTTATAAAATTCTAGGAA
Found at i:37872 original size:29 final size:28
Alignment explanation
Indices: 37809--37872 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
37799 ACTGAGGATT
** * *
37809 TTTTAGGTCATAAACTTGACTTTTAAAA
1 TTTTAGGAAATAAAATTGACTTATAAAA
*
37837 TTCTAGGAAATAAAATTGAACTTATAAAA
1 TTTTAGGAAATAAAATTG-ACTTATAAAA
37866 TTTTAGG
1 TTTTAGG
37873 GTGAAAACAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (28 bp):
TTTTAGGAAATAAAATTGACTTATAAAA
Found at i:38589 original size:157 final size:157
Alignment explanation
Indices: 38298--38614 Score: 562
Period size: 157 Copynumber: 2.0 Consensus size: 157
38288 ATGAATCTAA
* **
38298 ACCCTGACCGAAATAGACCAGCACTCAATGTAGCAGGACGAACAAAACACAGCAACACATAATAA
1 ACCCAGACCGAAATAGACCAGCACTCAATACAGCAGGACGAACAAAACACAGCAACACATAATAA
*
38363 CATCTAACTAAGATGTAAATCTAGAAAAACAACAATCGCATTCTTCAAAACTGGACCCTGGCCAA
66 CATCCAACTAAGATGTAAATCTAGAAAAACAACAATCGCATTCTTCAAAACTGGACCCTGGCCAA
38428 AGGGAGCAAGCGAGGCCACACCTTTAC
131 AGGGAGCAAGCGAGGCCACACCTTTAC
* *
38455 ACCCAGACCGAAATAGACCAGCACTCAATACAGCAGGACGAACAAATCCCAGCAACACATAATAA
1 ACCCAGACCGAAATAGACCAGCACTCAATACAGCAGGACGAACAAAACACAGCAACACATAATAA
* *
38520 CATCCGACTAAGATGTAAATCTAGAAAAACAACAATCGCATTCTTCGAAACTGGACCCTGGCCAA
66 CATCCAACTAAGATGTAAATCTAGAAAAACAACAATCGCATTCTTCAAAACTGGACCCTGGCCAA
38585 AGGGAGCAAGCGAGGCCACACCTTTAC
131 AGGGAGCAAGCGAGGCCACACCTTTAC
38612 ACC
1 ACC
38615 TTTACTACCA
Statistics
Matches: 152, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 152 1.00
ACGTcount: A:0.41, C:0.28, G:0.17, T:0.15
Consensus pattern (157 bp):
ACCCAGACCGAAATAGACCAGCACTCAATACAGCAGGACGAACAAAACACAGCAACACATAATAA
CATCCAACTAAGATGTAAATCTAGAAAAACAACAATCGCATTCTTCAAAACTGGACCCTGGCCAA
AGGGAGCAAGCGAGGCCACACCTTTAC
Found at i:40484 original size:13 final size:13
Alignment explanation
Indices: 40439--40486 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
40429 ATACAAACGA
40439 TTAATCAAATCAG
1 TTAATCAAATCAG
** *
40452 TTTCTCAAATCAA
1 TTAATCAAATCAG
*
40465 CTAATCAAATCAG
1 TTAATCAAATCAG
*
40478 TTGATCAAA
1 TTAATCAAA
40487 CCAGCTACTG
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (13 bp):
TTAATCAAATCAG
Found at i:40504 original size:13 final size:13
Alignment explanation
Indices: 40488--40520 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
40478 TTGATCAAAC
40488 CAGCTACTGGAAT
1 CAGCTACTGGAAT
40501 CAGCTACTGGAAT
1 CAGCTACTGGAAT
40514 CAGCTAC
1 CAGCTAC
40521 CATCTATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.21
Consensus pattern (13 bp):
CAGCTACTGGAAT
Found at i:48218 original size:16 final size:17
Alignment explanation
Indices: 48187--48220 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
48177 AACTATTATT
*
48187 TTATTATTTATTTTAAA
1 TTATTATTTATATTAAA
48204 TTATT-TTTATATTAAA
1 TTATTATTTATATTAAA
48220 T
1 T
48221 AATACAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTATATTAAA
Found at i:48516 original size:14 final size:14
Alignment explanation
Indices: 48497--48525 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
48487 TTCTATTATA
48497 TTTTTTGACTTTTT
1 TTTTTTGACTTTTT
48511 TTTTTTGACTTTTT
1 TTTTTTGACTTTTT
48525 T
1 T
48526 GAATTGTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTTTTGACTTTTT
Found at i:48965 original size:60 final size:60
Alignment explanation
Indices: 48884--49015 Score: 156
Period size: 60 Copynumber: 2.2 Consensus size: 60
48874 AGTTATGATT
* * * * * *
48884 TTATTTTAAATTAGTCTTTAAACTTTCAAACACTCCAATTTCATCCCAAAATTATGACCC
1 TTATTCTAAATTAATCCTTAAACTTTCAAACACTCCAATTTCATCCCAAAACTATGAACA
** * * * *
48944 TTATTCTAAATTAATCCTTAAACTTTTGAATATTCCAATTTCATCCCCAAACTATGAATA
1 TTATTCTAAATTAATCCTTAAACTTTCAAACACTCCAATTTCATCCCAAAACTATGAACA
49004 TTATTCTAAATT
1 TTATTCTAAATT
49016 GGTCCCTAAC
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.41
Consensus pattern (60 bp):
TTATTCTAAATTAATCCTTAAACTTTCAAACACTCCAATTTCATCCCAAAACTATGAACA
Found at i:56536 original size:27 final size:29
Alignment explanation
Indices: 56497--56553 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
56487 TTATGCATAT
* *
56497 TATTTATCCAAATTATTTCCAAA-TTATA
1 TATTTATCAAAATGATTTCCAAACTTATA
*
56525 TATTT-TCAAAATGCTTTCCAAACTTATA
1 TATTTATCAAAATGATTTCCAAACTTATA
56553 T
1 T
56554 TATATAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.37, C:0.16, G:0.02, T:0.46
Consensus pattern (29 bp):
TATTTATCAAAATGATTTCCAAACTTATA
Found at i:57471 original size:20 final size:20
Alignment explanation
Indices: 57411--57472 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
57401 AAGGCTTACA
*
57411 GATGACCCGAAGGATTTAAT
1 GATGACCTGAAGGATTTAAT
* * * * *
57431 TATAAGGCTTGAAAGACTTAAT
1 GAT--GACCTGAAGGATTTAAT
57453 GATGACCTGAAGGATTTAAT
1 GATGACCTGAAGGATTTAAT
57473 CATCTTGGAA
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
20 15 0.52
22 14 0.48
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (20 bp):
GATGACCTGAAGGATTTAAT
Found at i:62341 original size:19 final size:19
Alignment explanation
Indices: 62317--62368 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
62307 GAATGCAATT
*
62317 AGTGCATTGATGCATAAGG
1 AGTGCATCGATGCATAAGG
62336 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
62355 AGTGCATCGATGCA
1 AGTGCATCGATGCA
62369 CCCCCTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:62412 original size:83 final size:83
Alignment explanation
Indices: 62258--62432 Score: 196
Period size: 83 Copynumber: 2.1 Consensus size: 83
62248 TGTTCAGAGT
* *
62258 ATCGATGCACAGGAAGTGCATCGATGCACCCATTAAAAATAGAAACATCGAATGCAATTAGTGCA
1 ATCGATGCAAAGGAAGTGCATCGATGCACCCATTAAAAATAGAAACATCGAAGGCAATTAGTGCA
*
62323 TTGATGCATAAGG-AGTGC
66 TCGATGCAT-AGGTAGTGC
* * ** *
62341 ATCGATGCATAAGG-AGTGCATCGATGCACCCCCTT-AAAAT-GAAAACATTGAAGGTGATTTGT
1 ATCGATGCA-AAGGAAGTGCATCGATGCA-CCCATTAAAAATAG-AAACATCGAAGGCAATTAGT
* *
62403 GTATCGATGCATGGGTAGTGC
63 GCATCGATGCATAGGTAGTGC
62424 ATCGATGCA
1 ATCGATGCA
62433 CTTCAAGGGA
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
82 3 0.04
83 67 0.86
84 8 0.10
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.24
Consensus pattern (83 bp):
ATCGATGCAAAGGAAGTGCATCGATGCACCCATTAAAAATAGAAACATCGAAGGCAATTAGTGCA
TCGATGCATAGGTAGTGC
Found at i:63030 original size:21 final size:21
Alignment explanation
Indices: 63006--63048 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
62996 ATATAAATTA
63006 TGCATCGATGCACTGCTACAG
1 TGCATCGATGCACTGCTACAG
63027 TGCATCGATGCACTGCTACAG
1 TGCATCGATGCACTGCTACAG
63048 T
1 T
63049 ACTACTATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (21 bp):
TGCATCGATGCACTGCTACAG
Found at i:63084 original size:16 final size:16
Alignment explanation
Indices: 63063--63093 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
63053 CTATAGTAAC
63063 TTCATAAAAATATAAA
1 TTCATAAAAATATAAA
63079 TTCATAAAAATATAA
1 TTCATAAAAATATAA
63094 CCTTTTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (16 bp):
TTCATAAAAATATAAA
Found at i:63816 original size:23 final size:23
Alignment explanation
Indices: 63759--63835 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
63749 TGTGCACTGT
63759 AGTGCCACGTAGAATTTGTC-CCGA
1 AGTGCCACGTAGAA-TTG-CACCGA
* *
63783 AG-GACCGCGTAGAAATGCACCGA
1 AGTG-CCACGTAGAATTGCACCGA
* *
63806 AGTGCCACGTAGAATTGCACTGT
1 AGTGCCACGTAGAATTGCACCGA
63829 AGTGCCA
1 AGTGCCA
63836 TATAAGATTG
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
22 1 0.02
23 31 0.70
24 12 0.27
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.19
Consensus pattern (23 bp):
AGTGCCACGTAGAATTGCACCGA
Found at i:64087 original size:16 final size:17
Alignment explanation
Indices: 64063--64095 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
64053 ATCTTTTATA
*
64063 ATTATCACATA-TTCAC
1 ATTAGCACATAGTTCAC
64079 ATTAGCACATAGTTCAC
1 ATTAGCACATAGTTCAC
64096 TTACACGTAG
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:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (17 bp):
ATTAGCACATAGTTCAC
Found at i:66140 original size:23 final size:23
Alignment explanation
Indices: 66106--66175 Score: 104
Period size: 24 Copynumber: 3.0 Consensus size: 23
66096 TAACTTTATA
66106 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* *
66129 TGGCACTACGGTGCAAATTCTACG
1 TGGCACTTCGGTGC-ATTTCTACG
*
66153 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
66176 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
23 20 0.49
24 21 0.51
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:73413 original size:27 final size:28
Alignment explanation
Indices: 73354--73413 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
73344 CAAAACTTAT
73354 ATTATACATTTCTCAAAATGGTTTTCAA
1 ATTATACATTTCTCAAAATGGTTTTCAA
*
73382 A-TATACTATTT-TCAAAA-GGTTTTTAA
1 ATTATAC-ATTTCTCAAAATGGTTTTCAA
73408 ATTATA
1 ATTATA
73414 TAATATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 9 0.31
27 15 0.52
28 5 0.17
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (28 bp):
ATTATACATTTCTCAAAATGGTTTTCAA
Found at i:73446 original size:34 final size:34
Alignment explanation
Indices: 73381--73447 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
73371 ATGGTTTTCA
* ** * *
73381 AATATACTATTTTCAAAAGGTTTTTAAATTATAT
1 AATATAATATTTTCAAAAAATATATAAATTATAT
*
73415 AATATAATATTTTCAAAAAATATATATATTATA
1 AATATAATATTTTCAAAAAATATATAAATTATA
73448 CTTTATTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (34 bp):
AATATAATATTTTCAAAAAATATATAAATTATAT
Found at i:80042 original size:16 final size:16
Alignment explanation
Indices: 80021--80054 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
80011 GGATAGAATC
80021 AATGGAGCTATAGAAG
1 AATGGAGCTATAGAAG
80037 AATGGAGCTATAGAAG
1 AATGGAGCTATAGAAG
80053 AA
1 AA
80055 CTCAAAGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.29, T:0.18
Consensus pattern (16 bp):
AATGGAGCTATAGAAG
Found at i:85702 original size:31 final size:28
Alignment explanation
Indices: 85650--85706 Score: 78
Period size: 31 Copynumber: 1.9 Consensus size: 28
85640 GGTATAATTT
*
85650 AAAAAAAATAAAGTTTGGGTACTAAAAC
1 AAAAAAAATAAAGTTTAGGTACTAAAAC
85678 AAAACAAAAGTAATAGTTTAGGTACTAAA
1 AAAA-AAAA-TAA-AGTTTAGGTACTAAA
85707 CATATAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 4 0.16
30 3 0.12
31 14 0.56
ACGTcount: A:0.56, C:0.07, G:0.14, T:0.23
Consensus pattern (28 bp):
AAAAAAAATAAAGTTTAGGTACTAAAAC
Found at i:86089 original size:42 final size:40
Alignment explanation
Indices: 86032--86117 Score: 109
Period size: 42 Copynumber: 2.1 Consensus size: 40
86022 ACTATGACCC
* * *
86032 TCATTTCAAATTAGTCCTTAGACTTTTAAACATTCCAATA
1 TCATTTCAAATTAGTCCATAAACTTTTAAACATTCAAATA
* *
86072 TCATTCTCTAAATTAGTCCATAAACTTTTAAATATTCAAATT
1 TCATT-TC-AAATTAGTCCATAAACTTTTAAACATTCAAATA
86114 TCAT
1 TCAT
86118 CCTCAAACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 5 0.13
41 2 0.05
42 32 0.82
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (40 bp):
TCATTTCAAATTAGTCCATAAACTTTTAAACATTCAAATA
Found at i:86555 original size:14 final size:15
Alignment explanation
Indices: 86520--86556 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
86510 CTCTTATAAG
86520 TTTTATT-TTAATAT
1 TTTTATTATTAATAT
*
86534 TTTAATTATTAAT-T
1 TTTTATTATTAATAT
86548 TTTTATTAT
1 TTTTATTAT
86557 AAAAAAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTATTATTAATAT
Found at i:104254 original size:129 final size:129
Alignment explanation
Indices: 104049--104312 Score: 465
Period size: 129 Copynumber: 2.0 Consensus size: 129
104039 TATTAAAGGC
* *
104049 AAAGATTCACATCCTTGTGTACTGGAATCACTATTAGTTGGAGCTGTTGGAACTTGTTCATCCAA
1 AAAGATTCACATACTTGTGTACTGGAATCACTATTAGTTGGAACTGTTGGAACTTGTTCATCCAA
* *
104114 AACCTTATTCAAGTTGTCACCTATCACACGAGAATTATCATGAGCAGCAACCTCATTTCCAGGT
66 AACCTCATTCAAGTTGTCACCTATCACACGAGAATTATCATAAGCAGCAACCTCATTTCCAGGT
*
104178 AAAGATTCACATACTTGTGTACTGGAATCACTATTAGTTGGAACTGTTGGACCTTGTTCATCCAA
1 AAAGATTCACATACTTGTGTACTGGAATCACTATTAGTTGGAACTGTTGGAACTTGTTCATCCAA
* *
104243 AACCTCATTCAAGTTGTCACCTATCACACGAGCATTATCATAAGCAGCAACCTCATTTTCAGGT
66 AACCTCATTCAAGTTGTCACCTATCACACGAGAATTATCATAAGCAGCAACCTCATTTCCAGGT
104307 AAAGAT
1 AAAGAT
104313 CCTGACACGA
Statistics
Matches: 128, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 128 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (129 bp):
AAAGATTCACATACTTGTGTACTGGAATCACTATTAGTTGGAACTGTTGGAACTTGTTCATCCAA
AACCTCATTCAAGTTGTCACCTATCACACGAGAATTATCATAAGCAGCAACCTCATTTCCAGGT
Found at i:115322 original size:19 final size:19
Alignment explanation
Indices: 115275--115312 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
115265 TTTGCGAATT
* *
115275 TATGCGGTTTCTATGTTGC
1 TATGTGGTTTCTATGCTGC
115294 TATGTGGTTTCTATGCTGC
1 TATGTGGTTTCTATGCTGC
115313 CTTTTGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.16, G:0.26, T:0.47
Consensus pattern (19 bp):
TATGTGGTTTCTATGCTGC
Found at i:117854 original size:20 final size:20
Alignment explanation
Indices: 117818--117855 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
117808 ATCATATTCC
**
117818 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
117838 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
117856 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:124230 original size:2 final size:2
Alignment explanation
Indices: 124212--124272 Score: 104
Period size: 2 Copynumber: 30.0 Consensus size: 2
124202 ATATCAACTC
*
124212 TA TA TGA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
124255 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
124273 GAAAATCATT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 54 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:125197 original size:88 final size:83
Alignment explanation
Indices: 125014--125296 Score: 284
Period size: 88 Copynumber: 3.3 Consensus size: 83
125004 TGAAATTGTC
*
125014 AAAAATTAGAGGCATTAATTATAAAGGTAGAAATTGAGATTAAAAAAA-T-AGGGCCTCAATTAT
1 AAAAATTAGGGGC-TTAATTATAAAGGTAGAAATTGAGATTAAAAAAATTAAGGGCCTCAATTAT
* * *
125077 AAAGGT-ATAGTTGAGATCGA
65 AAAGTTAAAAG-TGAGAT-TA
** * * *
125097 AAATTCTTAGGGGCTTCAATTAGAAAGTTAGAAAGTGAGATTAAAAAAAATTTAAGGGCCTCAAT
1 AAA-AATTAGGGGCTT-AATTATAAAGGTAGAAATTGAGATT-AAAAAAA-TTAAGGGCCTCAAT
125162 TATAAAGTTAAAAAAGTGAGATTA
62 TATAAAGTT--AAAAGTGAGATTA
* * ** *
125186 AAAAATTAGGGGCCGTAATTATAAAGGTAGAAATTGAGATTGAAAAAACTTAAAAGCCTCAAATA
1 AAAAATTAGGGG-CTTAATTATAAAGGTAGAAATTGAGATT-AAAAAAATTAAGGGCCTCAATTA
125251 TAAAGTTAAAAGTGAGATTA
64 TAAAGTTAAAAGTGAGATTA
* * *
125271 CAAAATTAGGGACCTCAATTATAAAG
1 AAAAATTAGGG-GCTTAATTATAAAG
125297 TTAAAAAAGG
Statistics
Matches: 165, Mismatches: 24, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
83 5 0.03
84 29 0.18
85 41 0.25
87 21 0.13
88 54 0.33
89 6 0.04
90 6 0.04
91 3 0.02
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.26
Consensus pattern (83 bp):
AAAAATTAGGGGCTTAATTATAAAGGTAGAAATTGAGATTAAAAAAATTAAGGGCCTCAATTATA
AAGTTAAAAGTGAGATTA
Found at i:125305 original size:43 final size:42
Alignment explanation
Indices: 125030--125425 Score: 236
Period size: 43 Copynumber: 9.2 Consensus size: 42
125020 TAGAGGCATT
* * * *
125030 AATTATAAAGGTAGAAATTGAGATTAAAAAAATAGGG-CCTC
1 AATTATAAAGTTAAAAAGTGAGATTAAAAAATTAGGGACCTC
* * * ** * *
125071 AATTATAAAGGT--ATAGTTGAGATCGAAAATTCTTAGGGGCTTC
1 AATTATAAAGTTAAAAAG-TGAGAT-TAAAA-AATTAGGGACCTC
* *
125114 AATTAGAAAGTTAGAAAGTGAGATTAAAAAAAATTTAAGGG-CCTC
1 AATTATAAAGTTAAAAAGTGAGATT--AAAAAA-TT-AGGGACCTC
*
125159 AATTATAAAGTTAAAAAAGTGAGATTAAAAAATTAGGGGCCGT-
1 AATTATAAAGTT-AAAAAGTGAGATTAAAAAATTAGGGACC-TC
* * * **
125202 AATTATAAAGGTAGAAATTGAGATTGAAAAAACTTA-AAAGCCTC
1 AATTATAAAGTTAAAAAGTGAGATT-AAAAAA-TTAGGGA-CCTC
* *
125246 AAATATAAAGTT-AAAAGTGAGATTACAAAATTAGGGACCTC
1 AATTATAAAGTTAAAAAGTGAGATTAAAAAATTAGGGACCTC
* ** * **
125287 AATTATAAAGTTAAAAAAGGGATTGAAAAAAAAATTAGAGATTTC
1 AATTATAAAGTT-AAAAAGTGA--GATTAAAAAATTAGGGACCTC
* * * * *
125332 AATTATAAAGATAAAAAGTTATATTGAATAATATTA-GAACCTC
1 AATTATAAAGTTAAAAAGTGAGATT-AA-AAAATTAGGGACCTC
* * * *
125375 AATTATAAAGGTGAAAAA-TAAGATTTAAAAATTAAGGACCT-
1 AATTATAAA-GTTAAAAAGTGAGATTAAAAAATTAGGGACCTC
125416 AATTATAAAG
1 AATTATAAAG
125426 ATGAAAAAAT
Statistics
Matches: 274, Mismatches: 55, Indels: 53
0.72 0.14 0.14
Matches are distributed among these distances:
39 2 0.01
40 7 0.03
41 49 0.18
42 33 0.12
43 71 0.26
44 47 0.17
45 49 0.18
46 16 0.06
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (42 bp):
AATTATAAAGTTAAAAAGTGAGATTAAAAAATTAGGGACCTC
Found at i:125317 original size:85 final size:86
Alignment explanation
Indices: 125103--125318 Score: 233
Period size: 85 Copynumber: 2.5 Consensus size: 86
125093 TCGAAAATTC
* * * * * ** *
125103 TTAGGGGCTTCAATTAGAAAGTT-AGAAAGTGAGATTAAAAAAAATTTAAGGGCCTCAATTATAA
1 TTAGGGGCCTCAATTATAAAGTTAAAAAAG-G-GATTGAAAAAAACTTAAAAGCCTCAAATATAA
125167 AGTTAAAAAAGTGAGATTAAAAAA
64 AGTT-AAAAAGTGAGATTAAAAAA
* ** *
125191 TTAGGGGCCGT-AATTATAAAGGTAGAAATTGAGATTG-AAAAAACTTAAAAGCCTCAAATATAA
1 TTAGGGGCC-TCAATTATAAAGTTA-AAAAAGGGATTGAAAAAAACTTAAAAGCCTCAAATATAA
*
125254 AGTT-AAAAGTGAGATTACAAAA
64 AGTTAAAAAGTGAGATTAAAAAA
*
125276 TTAGGGACCTCAATTATAAAGTTAAAAAAGGGATTGAAAAAAA
1 TTAGGGGCCTCAATTATAAAGTTAAAAAAGGGATTGAAAAAAA
125319 AATTAGAGAT
Statistics
Matches: 105, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
84 10 0.10
85 43 0.41
87 26 0.25
88 22 0.21
89 1 0.01
90 3 0.03
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (86 bp):
TTAGGGGCCTCAATTATAAAGTTAAAAAAGGGATTGAAAAAAACTTAAAAGCCTCAAATATAAAG
TTAAAAAGTGAGATTAAAAAA
Found at i:125433 original size:29 final size:29
Alignment explanation
Indices: 125401--125464 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
125391 AATAAGATTT
* * *
125401 AAAAATTAAGGACCTAATTATAAAGATGA
1 AAAAATGAAGGACCCAATTATAAAGATAA
* * *
125430 AAAAATGGAGGGCCCAATTATAAGGATAA
1 AAAAATGAAGGACCCAATTATAAAGATAA
125459 AAAAAT
1 AAAAAT
125465 ATGGGGGCCC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.55, C:0.08, G:0.17, T:0.20
Consensus pattern (29 bp):
AAAAATGAAGGACCCAATTATAAAGATAA
Found at i:129164 original size:19 final size:19
Alignment explanation
Indices: 129140--129179 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
129130 TGATATAGAT
*
129140 ATTTAAAT-TTTTTTATATA
1 ATTTAAATATATTTTAT-TA
129159 ATTTAAATATATTTTATTA
1 ATTTAAATATATTTTATTA
129178 AT
1 AT
129180 ATTTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTAAATATATTTTATTA
Found at i:129227 original size:24 final size:24
Alignment explanation
Indices: 129195--129244 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
129185 TTTTTACTTC
*
129195 TTTTAAAATCTAATAAATTTATCT
1 TTTTAAAATCTAATAAATTTAGCT
* * *
129219 TTTTTAAATTTTATAAATTTAGCT
1 TTTTAAAATCTAATAAATTTAGCT
129243 TT
1 TT
129245 GACGTAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTAAAATCTAATAAATTTAGCT
Found at i:130175 original size:19 final size:19
Alignment explanation
Indices: 130120--130180 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 19
130110 GTTACAAGCC
*
130120 TAACTAACAACCTAACTAAT
1 TAAC-AACAGCCTAACTAAT
* *
130140 TAATAACTGCAATCTAACTAAT
1 TAACAACAGC---CTAACTAAT
130162 TAACAACAGCCTAACTAAT
1 TAACAACAGCCTAACTAAT
130181 CAAATAACAG
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
19 13 0.39
20 3 0.09
22 17 0.52
ACGTcount: A:0.48, C:0.23, G:0.03, T:0.26
Consensus pattern (19 bp):
TAACAACAGCCTAACTAAT
Found at i:134519 original size:13 final size:13
Alignment explanation
Indices: 134501--134538 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
134491 TGGCTGCTGC
134501 GGAGAAGAGAAAA
1 GGAGAAGAGAAAA
134514 GGAGAAGAGAAAA
1 GGAGAAGAGAAAA
134527 GGAGAAGAGAAA
1 GGAGAAGAGAAA
134539 TCCCTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (13 bp):
GGAGAAGAGAAAA
Found at i:138066 original size:9 final size:9
Alignment explanation
Indices: 138052--138079 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
138042 ATCCTTGTCT
138052 AGTGAGAGA
1 AGTGAGAGA
138061 AGTGAGAGA
1 AGTGAGAGA
138070 AGTGAGAGA
1 AGTGAGAGA
138079 A
1 A
138080 AGCTCCAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.43, T:0.11
Consensus pattern (9 bp):
AGTGAGAGA
Found at i:145027 original size:17 final size:18
Alignment explanation
Indices: 145007--145042 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
144997 TTTATAAAAA
145007 TATAAAAAAT-ATATATT
1 TATAAAAAATAATATATT
*
145024 TATAAAAATTAATATATT
1 TATAAAAAATAATATATT
145042 T
1 T
145043 TCTTGGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAAAAATAATATATT
Found at i:146445 original size:36 final size:36
Alignment explanation
Indices: 146398--146466 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
146388 GGGAGCTATG
* *
146398 TACACAAAGATCCTGTTATATCGATACCAAAAGTAT
1 TACACAAAGATCCTGTTAGATCAATACCAAAAGTAT
*
146434 TACACAAAGATCCTGTTAGATTAATACCAAAAG
1 TACACAAAGATCCTGTTAGATCAATACCAAAAG
146467 CATTCTACGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (36 bp):
TACACAAAGATCCTGTTAGATCAATACCAAAAGTAT
Found at i:146998 original size:43 final size:44
Alignment explanation
Indices: 146937--147023 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 44
146927 TGGCTTTAGA
*
146937 GAAGTTAGGAGAGAAAGTTATCCCCTATATGT-AAAGTTTTGTT
1 GAAGTTAGGAGAGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
*
146980 GAAGTTAGGA-ATGAAAGTTGTCCCCTACATGTAAAAGTTTTGTT
1 GAAGTTAGGAGA-GAAAGTTATCCCCTACATGTAAAAGTTTTGTT
147024 TGATGCACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
42 1 0.03
43 28 0.70
44 11 0.28
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.34
Consensus pattern (44 bp):
GAAGTTAGGAGAGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
Found at i:147113 original size:21 final size:21
Alignment explanation
Indices: 147088--147134 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
147078 GAGCAACACC
147088 TTTTCATAC-ATGCATTTGCAT
1 TTTTCAT-CTATGCATTTGCAT
* *
147109 TTTTCATCTTTGCATTTTCAT
1 TTTTCATCTATGCATTTGCAT
147130 TTTTC
1 TTTTC
147135 CATTTGAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.17, C:0.19, G:0.06, T:0.57
Consensus pattern (21 bp):
TTTTCATCTATGCATTTGCAT
Found at i:147211 original size:22 final size:20
Alignment explanation
Indices: 147184--147228 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 20
147174 CATTCTTATT
147184 TTTGCATTTCTACATCTTTTTA
1 TTTGCA-TT-TACATCTTTTTA
*
147206 TTTGCATTTGCATCTTTTTA
1 TTTGCATTTACATCTTTTTA
147226 TTT
1 TTT
147229 TTACATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 2 0.09
22 6 0.27
ACGTcount: A:0.16, C:0.16, G:0.07, T:0.62
Consensus pattern (20 bp):
TTTGCATTTACATCTTTTTA
Found at i:147234 original size:36 final size:35
Alignment explanation
Indices: 147189--147258 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 35
147179 TTATTTTTGC
*
147189 ATTTCTACATCTTT-TTATTTGCATTTGCATCTTTTT
1 ATTTCTACAT-TTTATT-GTTGCATTTGCATCTTTTT
*
147225 ATTTTTACATTTTCATTGTTGCATTTGCATCTTT
1 ATTTCTACATTTT-ATTGTTGCATTTGCATCTTT
147259 GCATAATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 3 0.10
36 25 0.83
37 2 0.07
ACGTcount: A:0.17, C:0.16, G:0.07, T:0.60
Consensus pattern (35 bp):
ATTTCTACATTTTATTGTTGCATTTGCATCTTTTT
Found at i:149139 original size:21 final size:20
Alignment explanation
Indices: 149101--149156 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
149091 CTCATTCATC
* *
149101 AAAAAAAGAAGAAGAAGAAT-
1 AAAAAAAGAAAAAAAAG-ATG
149121 AAAAAAAGAAAAAAAAAGATG
1 AAAAAAAG-AAAAAAAAGATG
149142 AAAAAAAGGAAAAAA
1 AAAAAAA-GAAAAAA
149157 TTGAATCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 10 0.32
21 20 0.65
22 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (20 bp):
AAAAAAAGAAAAAAAAGATG
Found at i:149149 original size:11 final size:10
Alignment explanation
Indices: 149101--149156 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
149091 CTCATTCATC
149101 AAAAAAAG-A
1 AAAAAAAGAA
* *
149110 AGAAGAAGAA
1 AAAAAAAGAA
149120 TAAAAAAAGAA
1 -AAAAAAAGAA
149131 AAAAAAAGATGA
1 AAAAAAAGA--A
*
149143 AAAAAAGGAA
1 AAAAAAAGAA
149153 AAAA
1 AAAA
149157 TTGAATCAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
9 6 0.16
10 15 0.39
11 8 0.21
12 9 0.24
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:152761 original size:54 final size:54
Alignment explanation
Indices: 152640--152795 Score: 208
Period size: 54 Copynumber: 2.9 Consensus size: 54
152630 CTGACCAGAA
* * *
152640 ATCTGTGCAGAAACCATAGAAAAGGATGAACGT-TTGTCAAATGTTTTACGAAC
1 ATCTGTGCAGAAGCCATAGAAAAGGATGAATGTGTTGTCAAATGTTTTACAAAC
* * *
152693 ATCTGTGCAAAAGCCACAGAAAAGGATGAATGTGTTATCAAATGTTTTACAAAC
1 ATCTGTGCAGAAGCCATAGAAAAGGATGAATGTGTTGTCAAATGTTTTACAAAC
* **
152747 ATCTAG-GCAGAAGCCATAGGAAATAATGAATGTGTTGTCAAATGTTTTA
1 ATCT-GTGCAGAAGCCATAGAAAAGGATGAATGTGTTGTCAAATGTTTTA
152796 TGAACCAATG
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
53 29 0.33
54 59 0.66
55 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (54 bp):
ATCTGTGCAGAAGCCATAGAAAAGGATGAATGTGTTGTCAAATGTTTTACAAAC
Found at i:153193 original size:22 final size:22
Alignment explanation
Indices: 153165--153309 Score: 254
Period size: 22 Copynumber: 6.6 Consensus size: 22
153155 ACATCTACGT
153165 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
153187 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
153209 TCTTTAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAGATTCTC
153231 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
153253 TCTTTAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
153275 TCTTCAAATATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
153297 TCTTCAAAGATGA
1 TCTTCAAAGATGA
153310 AAGCTTTATT
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 115 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:154360 original size:123 final size:123
Alignment explanation
Indices: 154153--154458 Score: 524
Period size: 123 Copynumber: 2.5 Consensus size: 123
154143 TTCCAAAAAG
*
154153 AGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATAATAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
*
154217 AACCTTTTGCTCGATTCTATCCCAAAAGGAGATAGATCAACACCAACATTTCCAGAGGA
65 AACCTTTTGCTCGATTCTATCCCAAAAGGAGATAGATCAACACCAACATTTCCAGAGAA
* *
154276 AGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCA
* * *
154341 ACCTTTTGCTCGATTCTATCCCAAAAGGAGATAGATCAGCACTAACATTTTCAGAGAA
66 ACCTTTTGCTCGATTCTATCCCAAAAGGAGATAGATCAACACCAACATTTCCAGAGAA
*
154399 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTT
154459 ATCTGAAGAG
Statistics
Matches: 172, Mismatches: 10, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
122 3 0.02
123 169 0.98
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (123 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCA
ACCTTTTGCTCGATTCTATCCCAAAAGGAGATAGATCAACACCAACATTTCCAGAGAA
Found at i:154437 original size:22 final size:22
Alignment explanation
Indices: 154410--154477 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
154400 GTTCATAATG
154410 AGAAGAACTTATCTGAAGAGGA
1 AGAAGAACTTATCTGAAGAGGA
* *
154432 AGAAGAA-GT-TC--ATA-A-TA
1 AGAAGAACTTATCTGA-AGAGGA
154449 AGAAGAACTTATCTGAAGAGGA
1 AGAAGAACTTATCTGAAGAGGA
154471 AGAAGAA
1 AGAAGAA
154478 GTTCATAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
17 8 0.23
18 3 0.09
19 3 0.09
20 3 0.09
21 3 0.09
22 15 0.43
ACGTcount: A:0.50, C:0.07, G:0.25, T:0.18
Consensus pattern (22 bp):
AGAAGAACTTATCTGAAGAGGA
Found at i:154450 original size:162 final size:162
Alignment explanation
Indices: 154274--154619 Score: 516
Period size: 162 Copynumber: 2.1 Consensus size: 162
154264 ATTTCCAGAG
154274 GAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * *
154339 CAACCTTTTGCTCGATTCTATCCCAAAAGGAGATAGATCAGCA-CTAACATTTTCAG-AGAAAGT
66 CAACCTTTTGCTCGACTCTATCACAAAAGAAGATAGATCAGCATC-AACATTTCCAGAAG-AAGT
* *
154402 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAA
129 TCATAATAAGAAGAACTTATCAGAAGAGGAAGAA
*
154436 GAAGTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * * *
154501 CAACCTTTTGCTTGACTCTATCACAGAAGAATATAGATCAGCATCAATATTTCCAGAAGGATTTC
66 CAACCTTTTGCTCGACTCTATCACAAAAGAAGATAGATCAGCATCAACATTTCCAGAAGAAGTTC
*
154566 GTAATAAGAAGAACTTATCAGAAGAGGAAGAA
131 ATAATAAGAAGAACTTATCAGAAGAGGAAGAA
* *
154598 GAAGTTCATAATGAGAATAACT
1 GAAGTTCATAATAAGAAGAACT
154620 TGTTCGACCT
Statistics
Matches: 166, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
162 163 0.98
163 3 0.02
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (162 bp):
GAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTTTGCTCGACTCTATCACAAAAGAAGATAGATCAGCATCAACATTTCCAGAAGAAGTTC
ATAATAAGAAGAACTTATCAGAAGAGGAAGAA
Found at i:154453 original size:39 final size:39
Alignment explanation
Indices: 154398--154497 Score: 191
Period size: 39 Copynumber: 2.6 Consensus size: 39
154388 TTTTCAGAGA
154398 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
*
154437 AAGTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
154476 AAGTTCATAATGAGAAGAACTT
1 AAGTTCATAATGAGAAGAACTT
154498 GTTCAACCTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.47, C:0.08, G:0.23, T:0.22
Consensus pattern (39 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
Found at i:154870 original size:137 final size:137
Alignment explanation
Indices: 154567--155040 Score: 655
Period size: 137 Copynumber: 3.4 Consensus size: 137
154557 AAGGATTTCG
* * * * *
154567 TAATAAGAAGAACTTATCAGAAGAGGAAGAAGAAGTTCATAATGAGAATAACTTGTTCGACCTTA
1 TAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
* * * * * * * * *
154632 GCTTGATTCATCACCTATGGAGTTGAATGAAAGAAGAACCTCTATTGAGGATCAATATTTTCAGA
66 CCTTAATTCATCACATATGAAGTTGAATCAACG-A-CACCTCTTTTGAGGATCAGTATTTTCAGA
154697 GAAAGTTCA
129 GAAAGTTCA
* *
154706 TAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTA
1 TAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
*
154771 CCTTAATTCATCACATATGAAGTTGAATCAACGACACCTCTTTTGAGGATCAGCATTTTCAGAGA
66 CCTTAATTCATCACATATGAAGTTGAATCAACGACACCTCTTTTGAGGATCAGTATTTTCAGAGA
154836 AAGTTCA
131 AAGTTCA
* * *
154843 TAATGTGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTG
1 TAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
* * *
154908 CCTTAATTAATCACATATGAAGTTGAATCAACGACACCTCTTTTGAGGATAAGTATTTCCA-A-A
66 CCTTAATTCATCACATATGAAGTTGAATCAACGACACCTCTTTTGAGGATCAGTATTTTCAGAGA
154971 AGGAGTTCA
131 A--AGTTCA
** * *
154980 CGATGAGAAGAACTCATCTGAAGATGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAAC
1 TAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
155041 TTTTTGATAG
Statistics
Matches: 301, Mismatches: 32, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
135 2 0.01
136 1 0.00
137 212 0.70
138 1 0.00
139 85 0.28
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (137 bp):
TAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTA
CCTTAATTCATCACATATGAAGTTGAATCAACGACACCTCTTTTGAGGATCAGTATTTTCAGAGA
AAGTTCA
Found at i:156492 original size:16 final size:17
Alignment explanation
Indices: 156449--156492 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
156439 AATTTCTATT
156449 TTATTTTATTTTAGTCA
1 TTATTTTATTTTAGTCA
* * *
156466 TTAGTTAATTTT-GTTA
1 TTATTTTATTTTAGTCA
156482 TTATTTTATTT
1 TTATTTTATTT
156493 ATGAATATGA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (17 bp):
TTATTTTATTTTAGTCA
Found at i:157105 original size:145 final size:147
Alignment explanation
Indices: 156837--157105 Score: 339
Period size: 145 Copynumber: 1.8 Consensus size: 147
156827 TTTATTTATT
* *
156837 TATTTATTTATTTTTAATATTAAGAAAAGGGTTGTCTTAAAGCAACTAGAAGTCATTTTCTGATA
1 TATTTATTAATTTTTAATATTAAGAAAAGGGCTGTCTTAAAGCAACTAGAAGTCATTTTCTGATA
* ** * * ** ***
156902 TTTTTAAATAAATAAATATCCTACTTTTATAAATTATATATAATTTATTTTTTTAATTATTTTTA
66 TTTCTAAATAAATAAATATCCTACTTTTATAAAAAATAAAAAAAATATTTTAAAAATTATTTTTA
156967 GAAAAATGTTTTATTAA
131 GAAAAATGTTTTATTAA
* *
156984 TATTTATTAATTTTT-ATATTAA-AAATGGGCTGTCTTAAAGTAACTAGAAGTCATTTTCTGATA
1 TATTTATTAATTTTTAATATTAAGAAAAGGGCTGTCTTAAAGCAACTAGAAGTCATTTTCTGATA
* **
157047 TTTCTAAGTAAATAAATATTTTA--TTTATAAAAAAATAAAAAAAATATTTATAAAAATTA
66 TTTCTAAATAAATAAATATCCTACTTTTAT-AAAAAATAAAAAAAATATTT-TAAAAATTA
157106 ATATATTTTC
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
143 5 0.05
144 14 0.14
145 63 0.61
146 7 0.07
147 14 0.14
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (147 bp):
TATTTATTAATTTTTAATATTAAGAAAAGGGCTGTCTTAAAGCAACTAGAAGTCATTTTCTGATA
TTTCTAAATAAATAAATATCCTACTTTTATAAAAAATAAAAAAAATATTTTAAAAATTATTTTTA
GAAAAATGTTTTATTAA
Found at i:163745 original size:42 final size:40
Alignment explanation
Indices: 163694--163784 Score: 101
Period size: 42 Copynumber: 2.2 Consensus size: 40
163684 ATTGAAAAAT
* **
163694 AAATAAATATTAAAATAAAAATAATTTATGACTATATAATAAA
1 AAAT-AATATTAAAATAAAAATAAATTAAAAC-ATA-AATAAA
* *
163737 AAATAATATTTAAATATAAATAAATTAAAACATAAATAAA
1 AAATAATATTAAAATAAAAATAAATTAAAACATAAATAAA
*
163777 CAATAATA
1 AAATAATA
163785 AAAATACGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
40 13 0.31
41 3 0.07
42 22 0.52
43 4 0.10
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (40 bp):
AAATAATATTAAAATAAAAATAAATTAAAACATAAATAAA
Found at i:163773 original size:16 final size:16
Alignment explanation
Indices: 163737--163776 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
163727 ATATAATAAA
* *
163737 AAATAATATTTAAATAT
1 AAATAA-ATTAAAACAT
163754 AAATAAATTAAAACAT
1 AAATAAATTAAAACAT
163770 AAATAAA
1 AAATAAA
163777 CAATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAATTAAAACAT
Found at i:163860 original size:28 final size:26
Alignment explanation
Indices: 163828--163882 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
163818 TGAAAATATT
*
163828 TAAAATTAATTACTAAATTATAATCTAA
1 TAAAATTAAATACTAAATT-TAAT-TAA
*
163856 TAAAATTAAATACTTAATTTAATTAA
1 TAAAATTAAATACTAAATTTAATTAA
163882 T
1 T
163883 TATTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.16
27 4 0.16
28 17 0.68
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAAATTAAATACTAAATTTAATTAA
Found at i:165153 original size:10 final size:10
Alignment explanation
Indices: 165124--165162 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
165114 CTTGTAATTA
165124 TTATTATATTT
1 TTATT-TATTT
165135 TTATATTATTT
1 TTAT-TTATTT
165146 TTATTTATTT
1 TTATTTATTT
*
165156 TTTTTTA
1 TTATTTA
165163 ATAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 12 0.46
11 13 0.50
12 1 0.04
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTATTTATTT
Found at i:167355 original size:44 final size:43
Alignment explanation
Indices: 167258--167357 Score: 132
Period size: 44 Copynumber: 2.3 Consensus size: 43
167248 TTTAATTTGA
* *
167258 TGTATTTGTGGA-TGTTACTCTAGTTTTAATATGTTAGTTTGG
1 TGTATTTGTGGATTGTTACTCTAGTTTTAATATGCTAGTTTAG
* *
167300 TGAATTTGTGGATTGTTACGT-TAGTTTTAATGCTGCTAGTTTAG
1 TGTATTTGTGGATTGTTAC-TCTAGTTTTAAT-ATGCTAGTTTAG
167344 TGTATTTGTGGATT
1 TGTATTTGTGGATT
167358 CTTAATTTAG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
42 11 0.22
43 16 0.32
44 23 0.46
ACGTcount: A:0.19, C:0.05, G:0.25, T:0.51
Consensus pattern (43 bp):
TGTATTTGTGGATTGTTACTCTAGTTTTAATATGCTAGTTTAG
Done.