Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014826.1 Kokia drynarioides strain JFW-HI SEQ_129868, 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: 591985
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 238 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:6445 original size:6 final size:6
Alignment explanation
Indices: 6436--6479 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
6426 GATACAGTCC
6436 CTGCCT CTGCCT CTGCCT CTGCCT CTGCCT CTGCCT CTGCCT CT
1 CTGCCT CTGCCT CTGCCT CTGCCT CTGCCT CTGCCT CTGCCT CT
6480 TCACTGTCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.16, T:0.34
Consensus pattern (6 bp):
CTGCCT
Found at i:8383 original size:29 final size:31
Alignment explanation
Indices: 8304--8384 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 31
8294 AATAAAAATT
* *
8304 AAAGTTTCAAGTATACATTTGAACCATAACT
1 AAAGTTTCAAGTATACAATTGAACCATAACA
* * * *
8335 AAAGTTTCACGTGTATAATTGTACCA-AACA
1 AAAGTTTCAAGTATACAATTGAACCATAACA
*
8365 AAAG-TTCATGTATACAATTG
1 AAAGTTTCAAGTATACAATTG
8385 CACATTAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 13 0.32
30 7 0.17
31 21 0.51
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (31 bp):
AAAGTTTCAAGTATACAATTGAACCATAACA
Found at i:16315 original size:23 final size:22
Alignment explanation
Indices: 16280--16361 Score: 101
Period size: 23 Copynumber: 3.6 Consensus size: 22
16270 CATTAAGGAA
* *
16280 CACTAGTGCGCTCTCTGATTAG
1 CACTTGTGTGCTCTCTGATTAG
16302 CACTGTGTGTGCTCTCTGATTAG
1 CACT-TGTGTGCTCTCTGATTAG
*
16325 CACTTCGTGTGCTCTCTGGTTAG
1 CACTT-GTGTGCTCTCTGATTAG
*
16348 CACTTTGTATGCTC
1 CAC-TTGTGTGCTC
16362 AGTACTTTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
22 5 0.09
23 46 0.87
24 2 0.04
ACGTcount: A:0.13, C:0.26, G:0.23, T:0.38
Consensus pattern (22 bp):
CACTTGTGTGCTCTCTGATTAG
Found at i:16390 original size:39 final size:39
Alignment explanation
Indices: 16326--16400 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
16316 TCTGATTAGC
*
16326 ACTTCGTGTGCTCTCTGGTTAGCACTTTGTATGCTCAGT
1 ACTTCGTGTACTCTCTGGTTAGCACTTTGTATGCTCAGT
* * *
16365 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGGTTAGCACTTTGTATGCTC
16401 TCTATTGTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGGTTAGCACTTTGTATGCTCAGT
Found at i:16395 original size:23 final size:23
Alignment explanation
Indices: 16365--16454 Score: 69
Period size: 22 Copynumber: 3.9 Consensus size: 23
16355 TATGCTCAGT
16365 ACTTTGTGTACTCTCTGTTTAGC
1 ACTTTGTGTACTCTCTGTTTAGC
* *
16388 ACTTTGTGTGCTCTCTATTGTCTAGC
1 ACTTTGTGTACTCTC---TGTTTAGC
* * *
16414 ACTTATGTG--CTCTATGTTCAGT
1 ACTT-TGTGTACTCTCTGTTTAGC
*
16436 ACTTTG-GTACTCTCCGTTT
1 ACTTTGTGTACTCTCTGTTT
16455 GTTCCGTTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
20 1 0.02
21 2 0.04
22 16 0.31
23 14 0.27
25 4 0.08
26 11 0.21
27 4 0.08
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (23 bp):
ACTTTGTGTACTCTCTGTTTAGC
Found at i:16403 original size:25 final size:25
Alignment explanation
Indices: 16375--16426 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
16365 ACTTTGTGTA
* *
16375 CTCT-CTGTTTAGCACTTTGTGTGCT
1 CTCTACTGTCTAGCAC-TTATGTGCT
*
16400 CTCTATTGTCTAGCACTTATGTGCT
1 CTCTACTGTCTAGCACTTATGTGCT
16425 CT
1 CT
16427 ATGTTCAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (25 bp):
CTCTACTGTCTAGCACTTATGTGCT
Found at i:18242 original size:11 final size:12
Alignment explanation
Indices: 18221--18254 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
18211 AAAACATAAG
18221 AAAATGATTAATT
1 AAAA-GATTAATT
18234 AAAAG-TTAATT
1 AAAAGATTAATT
18245 AAAAGATTAA
1 AAAAGATTAA
18255 CTAATACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
12 5 0.25
13 4 0.20
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (12 bp):
AAAAGATTAATT
Found at i:18265 original size:23 final size:24
Alignment explanation
Indices: 18221--18266 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
18211 AAAACATAAG
* *
18221 AAAATGATTAATTAAAAGTTAATT
1 AAAATGATTAACTAAAACTTAATT
*
18245 AAAA-GATTAACTAATACTTAAT
1 AAAATGATTAACTAAAACTTAAT
18267 CATAGTATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (24 bp):
AAAATGATTAACTAAAACTTAATT
Found at i:23432 original size:92 final size:93
Alignment explanation
Indices: 23245--23432 Score: 306
Period size: 92 Copynumber: 2.0 Consensus size: 93
23235 TGACAAAGAT
* *
23245 GAGGATTAGATAATTCTCTATATACTGGCTGTGTTGCATAATGGAAAAAAAAGGGGAAAAAAGAA
1 GAGGATTAGATAATTCTCTATATACTGGCTGTGCTGCATAATGG-AAAAAAAGAGGAAAAAAGAA
* *
23310 CACCCAAATCTAGATTTTATCTTCCAGGA
65 CAACCAAATCTAGATTGTATCTTCCAGGA
* *
23339 GAGGATTAGATAATTCTTTATATACTGGCTGTGCTGCATATTGG-AAAAAAGAGGAAAAAAGAAC
1 GAGGATTAGATAATTCTCTATATACTGGCTGTGCTGCATAATGGAAAAAAAGAGGAAAAAAGAAC
23403 AACCAAATCTAGATTGTATCTTCCAGGA
66 AACCAAATCTAGATTGTATCTTCCAGGA
23431 GA
1 GA
23433 AGTGGTATAC
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
92 47 0.53
94 41 0.47
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (93 bp):
GAGGATTAGATAATTCTCTATATACTGGCTGTGCTGCATAATGGAAAAAAAGAGGAAAAAAGAAC
AACCAAATCTAGATTGTATCTTCCAGGA
Found at i:26636 original size:29 final size:29
Alignment explanation
Indices: 26604--26661 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
26594 AGAATGATAA
* *
26604 TTTTTTTAGTTTAGTTGGTAGAATTTAAAT
1 TTTTTTTA-TTTAGTTGGAAGAATATAAAT
*
26634 TTTTTTTATTTGGTTGGAAGAATATAAA
1 TTTTTTTATTTAGTTGGAAGAATATAAA
26662 ATAAGTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.53
Consensus pattern (29 bp):
TTTTTTTATTTAGTTGGAAGAATATAAAT
Found at i:30567 original size:12 final size:12
Alignment explanation
Indices: 30550--30588 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
30540 TTTAAAATTT
30550 AAAATTATAAAA
1 AAAATTATAAAA
*
30562 AAAATTATTAAA
1 AAAATTATAAAA
*
30574 AATATATATAAAA
1 AAAAT-TATAAAA
30587 AA
1 AA
30589 TTAAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 15 0.65
13 8 0.35
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAATTATAAAA
Found at i:32871 original size:21 final size:21
Alignment explanation
Indices: 32833--32887 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
32823 CAGTGCAAAT
* ** *
32833 TTCTACCGGTACCTGTATTAG
1 TTCTACCGATACAAGTATAAG
*
32854 TTCTACCGATACAAGTATAAT
1 TTCTACCGATACAAGTATAAG
*
32875 TTCTACCAATACA
1 TTCTACCGATACA
32888 TATCATGCAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.35
Consensus pattern (21 bp):
TTCTACCGATACAAGTATAAG
Found at i:33013 original size:21 final size:24
Alignment explanation
Indices: 32965--33021 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 24
32955 TAAGCATGCA
32965 AACTACCGATACTACTATACATAC
1 AACTACCGATACTACTATACATAC
**
32989 AACTACCGATACT-C-ATA-ATTT
1 AACTACCGATACTACTATACATAC
33010 AACTACCGATAC
1 AACTACCGATAC
33022 AACTCAAGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 14 0.45
22 3 0.10
23 1 0.03
24 13 0.42
ACGTcount: A:0.40, C:0.28, G:0.05, T:0.26
Consensus pattern (24 bp):
AACTACCGATACTACTATACATAC
Found at i:33793 original size:52 final size:51
Alignment explanation
Indices: 33602--33810 Score: 276
Period size: 51 Copynumber: 4.0 Consensus size: 51
33592 TTTCATTTAA
** * *
33602 TACTCACGATGACA-TATAGTCATCGGACCTCTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATT
* * * * *
33655 TACTCACGATGACTCTAAGTCATCGAACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
33706 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
33757 TACTCACGATCAACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
1 TACTCACGAT-GACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
33809 TA
1 TA
33811 ACCTTTTAGT
Statistics
Matches: 137, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
51 61 0.45
52 50 0.36
53 25 0.18
54 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:33806 original size:103 final size:104
Alignment explanation
Indices: 33602--33810 Score: 280
Period size: 103 Copynumber: 2.0 Consensus size: 104
33592 TTTCATTTAA
** * *
33602 TACTCACGATGACATATAGTCATCGGACCTCTTGTTCCATATAGGAATTCATATACTCACGATGA
1 TACTCACGATGACATATAGTCATCGGACCTCTTAATCCATAAAGGAATTCATATACTCACGATAA
* * *
33667 CTCTAAGTCATCGAACCTTTAATCCATCATGGATTCATT
66 CACTAAGTCATCGAACCTTTAATCCATAAAGGATTCATT
* *
33706 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCGTAAAGG-ATTCATTTACTCACGATC
1 TACTCACGATGACA-TATAGTCATCGGACCTCTTAATCCATAAAGGAATTCATATACTCACGAT-
* *
33768 AACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
64 AACACTAAGTCATCGAACCTTTAATCCATAAAGGATTCATT
33809 TA
1 TA
33811 ACCTTTTAGT
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
102 16 0.17
103 47 0.51
104 28 0.30
105 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (104 bp):
TACTCACGATGACATATAGTCATCGGACCTCTTAATCCATAAAGGAATTCATATACTCACGATAA
CACTAAGTCATCGAACCTTTAATCCATAAAGGATTCATT
Found at i:37262 original size:21 final size:20
Alignment explanation
Indices: 37209--37260 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
37199 TTTTTATAAA
*
37209 TATTTT-AAATTTTAAAAGT
1 TATTTTGAATTTTTAAAAGT
37228 TATTTTGAATTTTTGAAAA-T
1 TATTTTGAATTTTT-AAAAGT
37248 TATTTTG-ATTTTT
1 TATTTTGAATTTTT
37261 TTTGGTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 12 0.40
20 14 0.47
21 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (20 bp):
TATTTTGAATTTTTAAAAGT
Found at i:42257 original size:28 final size:28
Alignment explanation
Indices: 42186--42276 Score: 91
Period size: 28 Copynumber: 3.3 Consensus size: 28
42176 TGAAACGTGG
* *
42186 AAATTAAATTATATATT-TTTAAAATAATA
1 AAATTAAATTAT-TATTATTT-TAAGAATA
* *
42215 AAAATATAATT-TTATTATTTTAAGAATT
1 AAATTA-AATTATTATTATTTTAAGAATA
42243 AAATTAAATTATTATTATTTTAA-AA-A
1 AAATTAAATTATTATTATTTTAAGAATA
42269 AAATTAAA
1 AAATTAAA
42277 ATATAATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
26 8 0.15
27 6 0.11
28 26 0.49
29 9 0.17
30 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (28 bp):
AAATTAAATTATTATTATTTTAAGAATA
Found at i:42288 original size:28 final size:29
Alignment explanation
Indices: 42192--42288 Score: 85
Period size: 28 Copynumber: 3.3 Consensus size: 29
42182 GTGGAAATTA
* * *
42192 AATTATATATTTTTAAAATAATAAAAATAT
1 AATTAT-TATTTTAAAAAAAATTAAAATAT
*
42222 AATTTTATTATTTTAAGAATTAAATT-AAAT-T
1 AA--TTATTATTTTAA-AA-AAAATTAAAATAT
42253 -ATTATTATTTTAAAAAAAATTAAAATAT
1 AATTATTATTTTAAAAAAAATTAAAATAT
42281 AATT-TTAT
1 AATTATTAT
42289 CATTATAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
26 5 0.09
27 6 0.11
28 17 0.31
29 3 0.05
30 3 0.05
31 8 0.15
32 10 0.18
33 3 0.05
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
AATTATTATTTTAAAAAAAATTAAAATAT
Found at i:43279 original size:2 final size:2
Alignment explanation
Indices: 43272--43303 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
43262 GACATGATGT
43272 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
43304 GCAGGGGCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:43731 original size:24 final size:24
Alignment explanation
Indices: 43704--43780 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
43694 ATATTTAATG
43704 AAATAGATTGATTGATATGTCATA
1 AAATAGATTGATTGATATGTCATA
* ** * * * * **
43728 AAATATATTTTTTTAAATTTAAGG
1 AAATAGATTGATTGATATGTCATA
43752 AAATAGATTGATTGATATGTCATA
1 AAATAGATTGATTGATATGTCATA
43776 AAATA
1 AAATA
43781 TATTTTTTTA
Statistics
Matches: 35, Mismatches: 18, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.40
Consensus pattern (24 bp):
AAATAGATTGATTGATATGTCATA
Found at i:43757 original size:48 final size:48
Alignment explanation
Indices: 43686--43794 Score: 191
Period size: 48 Copynumber: 2.2 Consensus size: 48
43676 CGATTTAGAT
* *
43686 TTTTTTTCATATTTAATGAAATAGATTGATTGATATGTCATAAAATATA
1 TTTTTTT-AAATTTAAGGAAATAGATTGATTGATATGTCATAAAATATA
43735 TTTTTTTAAATTTAAGGAAATAGATTGATTGATATGTCATAAAATATA
1 TTTTTTTAAATTTAAGGAAATAGATTGATTGATATGTCATAAAATATA
43783 TTTTTTTAAATT
1 TTTTTTTAAATT
43795 ATTTGACATA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
48 51 0.88
49 7 0.12
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.49
Consensus pattern (48 bp):
TTTTTTTAAATTTAAGGAAATAGATTGATTGATATGTCATAAAATATA
Found at i:53374 original size:17 final size:17
Alignment explanation
Indices: 53352--53408 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
53342 TTGGAAATTG
*
53352 AATTTATTTTAAAATTA
1 AATTTATTTTAAATTTA
*
53369 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
53386 AATTTATTATAAATTTA
1 AATTTATTTTAAATTTA
53403 AATTTA
1 AATTTA
53409 AAATGTCCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:53385 original size:23 final size:24
Alignment explanation
Indices: 53359--53412 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
53349 TTGAATTTAT
*
53359 TTTAAAATTAAGTT-T-ATTTTAAA
1 TTTAAAATTAA-TTATAAATTTAAA
*
53382 TTT-AAATTTATTATAAATTTAAA
1 TTTAAAATTAATTATAAATTTAAA
53405 TTTAAAAT
1 TTTAAAAT
53413 GTCCAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 2 0.08
22 7 0.27
23 13 0.50
24 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTAAAATTAATTATAAATTTAAA
Found at i:53499 original size:15 final size:14
Alignment explanation
Indices: 53446--53501 Score: 58
Period size: 15 Copynumber: 3.8 Consensus size: 14
53436 GTACAAATCT
*
53446 AAATGACCCAAATAC
1 AAATGGCCC-AATAC
53461 AAATGGCCCAATTAC
1 AAATGGCCCAA-TAC
**
53476 AAACAGCCCAATCAC
1 AAATGGCCCAAT-AC
53491 AAATGGCCCAA
1 AAATGGCCCAA
53502 GATTCCAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
14 3 0.09
15 31 0.91
ACGTcount: A:0.46, C:0.30, G:0.11, T:0.12
Consensus pattern (14 bp):
AAATGGCCCAATAC
Found at i:54037 original size:3 final size:3
Alignment explanation
Indices: 54029--54056 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54019 AGGCATAAGT
54029 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
54057 GTGACAACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:55297 original size:59 final size:57
Alignment explanation
Indices: 55184--55598 Score: 327
Period size: 59 Copynumber: 7.0 Consensus size: 57
55174 AAAAAATCTG
* * * *
55184 TTTTTACCCCCTAACATCCAAAATACCCATTTTTAACCCCCAAAACTTCTAAAAATTCCA
1 TTTTTA-CCCCGAACTTCAAAAAT-CCCATTTTTAA-CCCCAAAACTTCCAAAAATTCCA
* * * * *
55244 TTTTTACCCCGAACTTCAAAAAATCCCATTTTTTACCTCGAAACTTCAAAAAAATCCCA
1 TTTTTACCCCGAACTTC-AAAAATCCCATTTTTAACCCCAAAACTTC-CAAAAATTCCA
* * * *
55303 TTTTTACCCTCGAACTTCCAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTTCA
1 TTTTTACCC-CGAACTTCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCA
* * * *
55361 TTTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACACCGAAACTTCCAAAAATTCCA
1 TTTTTA-CCCCGAACTT-CAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCA
* * *
55420 TTCTTACCCCTAAAACTTCCAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTACCA
1 TTTTTACCCC--GAACTTCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATT-CCA
* * * ** * *
55480 -TTTTACCCTCGAA-TGTCGAAAAGCTCTATTTTCGACCTCGAAAC-TCTC-AAAATTACC-
1 TTTTTACCC-CGAACT-TCAAAAATC-CCATTTTTAACCCCAAAACTTC-CAAAAATT-CCA
* * * ** *
55537 TTTTTACCCTCGAATATTTAAAAATTCCATTTTTAACCCCAAATTTTCCCAAAATTACCA
1 TTTTTACCC-CGAA-CTTCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATT-CCA
55597 TT
1 TT
55599 CTCCCCCGGG
Statistics
Matches: 290, Mismatches: 47, Indels: 36
0.78 0.13 0.10
Matches are distributed among these distances:
57 1 0.00
58 81 0.28
59 177 0.61
60 31 0.11
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (57 bp):
TTTTTACCCCGAACTTCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCA
Found at i:55392 original size:118 final size:118
Alignment explanation
Indices: 55184--55598 Score: 418
Period size: 118 Copynumber: 3.5 Consensus size: 118
55174 AAAAAATCTG
* * * *
55184 TTTTTACCCCCTAACATCCAAAATACCCATTTTTAACCCCCAAAACTTCTAAAAATTCCATTTTT
1 TTTTTACCCTCAAACTTCCAAAAT-CCCATTTTTAA-CCCCAAAACTTCCAAAAATTCCATTTTT
* * *
55249 A-CCCCGAACTTCAAAAAATCCCATTTTTTACCTCGAAACTTCAAAAAAATCCCA
64 ACCCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAAACTTCAAAAAAATCCCA
* * * *
55303 TTTTTACCCTCGAACTTCCAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTTCATTTTTAC
1 TTTTTACCCTCAAACTTCCAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAC
* *
55368 CCCCGAACTTCCAAAAATCTCATTTTTGACAC-CGAAACTTC-CAAAAATTCCA
66 CCCCGAACTTCCAAAAATCTCATTTTTGAC-CTCGAAACTTCAAAAAAATCCCA
* *
55420 TTCTTACCCCTAAAACTTCCAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTACCA-TTTT
1 TTTTTA-CCCTCAAACTTCCAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATT-CCATTTTT
* * * * * *
55484 ACCCTCGAA-TGT-CGAAAAGCTCTATTTTCGACCTCGAAACTCTC--AAAATTACC-
64 ACCCCCGAACT-TCCAAAAATCTC-ATTTTTGACCTCGAAACT-TCAAAAAAATCCCA
** * ** *
55537 TTTTTACCCTCGAATA-TTTAAAAATTCCATTTTTAACCCCAAATTTTCCCAAAATTACCATT
1 TTTTTACCCTC-AA-ACTTCCAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATT-CCATT
55599 CTCCCCCGGG
Statistics
Matches: 253, Mismatches: 32, Indels: 23
0.82 0.10 0.07
Matches are distributed among these distances:
116 4 0.02
117 95 0.38
118 128 0.51
119 26 0.10
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (118 bp):
TTTTTACCCTCAAACTTCCAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTAC
CCCCGAACTTCCAAAAATCTCATTTTTGACCTCGAAACTTCAAAAAAATCCCA
Found at i:55487 original size:29 final size:29
Alignment explanation
Indices: 55184--55487 Score: 253
Period size: 29 Copynumber: 10.3 Consensus size: 29
55174 AAAAAATCTG
** * *
55184 TTTTTACCCCCTAACATCC-AAAATACCCA
1 TTTTTACCCCAAAACTTCCAAAAAT-TCCA
*
55213 TTTTTAACCCCCAAAACTTCTAAAAATTCCA
1 TTTTT-A-CCCCAAAACTTCCAAAAATTCCA
* * *
55244 TTTTTACCCC-GAACTTCAAAAAATCCCA
1 TTTTTACCCCAAAACTTCCAAAAATTCCA
* * * *
55272 TTTTTTACCTCGAAACTTCAAAAAAATCCCA
1 -TTTTTACCCCAAAACTTC-CAAAAATTCCA
* *
55303 TTTTTACCCTC-GAACTTCC-AAAATCCCA
1 TTTTTACCC-CAAAACTTCCAAAAATTCCA
* *
55331 TTTTTGACCTCAAAACTTCCAAAAATTTCA
1 TTTTT-ACCCCAAAACTTCCAAAAATTCCA
**
55361 TTTTTACCCCCGAACTTCCAAAAA-TCTCA
1 TTTTTACCCCAAAACTTCCAAAAATTC-CA
* *
55390 TTTTTGACACCGAAACTTCCAAAAATTCCA
1 TTTTT-ACCCCAAAACTTCCAAAAATTCCA
* *
55420 TTCTTACCCCTAAAACTTCC-AAAATCCCA
1 TTTTTACCCC-AAAACTTCCAAAAATTCCA
55449 TTTTTAACCCCAAAACTTCCAAAAATTACCA
1 TTTTT-ACCCCAAAACTTCCAAAAATT-CCA
55480 -TTTTACCC
1 TTTTTACCC
55488 TCGAATGTCG
Statistics
Matches: 228, Mismatches: 30, Indels: 34
0.78 0.10 0.12
Matches are distributed among these distances:
28 31 0.14
29 80 0.35
30 78 0.34
31 34 0.15
32 5 0.02
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.31
Consensus pattern (29 bp):
TTTTTACCCCAAAACTTCCAAAAATTCCA
Found at i:67457 original size:206 final size:207
Alignment explanation
Indices: 67089--67560 Score: 702
Period size: 206 Copynumber: 2.3 Consensus size: 207
67079 CAATATTCAT
* * *
67089 AAACGACTCGGTCATCTTTCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCAAGG
1 AAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCAAAG
* * *
67154 CATTCAAAATCTTTGAATCCCAGCCTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAAAAAACG
66 CATGCAAAATCTTTGAATCCCAGCCTCCTGATGAAACACCGAGAAGCAAGTCGAAGCAAAAAACG
67219 GTTAGCTTCCTCATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAG
131 GTTAGCTTCCTCATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAG
*
67284 C-AAATTGAAAC
196 CGAAATTAAAAC
* * *
67295 AAGCGATGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAATCCACGCTCAAAG
1 AAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCAAAG
*
67360 CGA-GCAAAATCTTTGAA-CCGCAGCCTCCTGATGAAACACCGAGAAGCAAGTCGAAGCAATAAA
66 C-ATGCAAAATCTTTGAATCC-CAGCCTCCTGATGAAACACCGAGAAGCAAGTCGAAGCAAAAAA
* *
67423 CGGTTAGCTT-CT-AGTGGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGA
129 CGGTTAGCTTCCTCA-T-GAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAA
* *
67486 GAAGCGGATTTAAAAC
192 GAAGCGAAATTAAAAC
* * * *
67502 AAACGACGTGGTCATCTTCTTGATGAGATACTGAGGAGAAGACCAAATCAAACCCACGC
1 AAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGC
67561 GTGATGAATG
Statistics
Matches: 239, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
204 1 0.00
205 5 0.02
206 173 0.72
207 60 0.25
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (207 bp):
AAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCAAAG
CATGCAAAATCTTTGAATCCCAGCCTCCTGATGAAACACCGAGAAGCAAGTCGAAGCAAAAAACG
GTTAGCTTCCTCATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAG
CGAAATTAAAAC
Found at i:67914 original size:17 final size:17
Alignment explanation
Indices: 67892--67948 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
67882 TTGGAAATTG
*
67892 AATTTATTTTAAAATTA
1 AATTTATTTTAAATTTA
*
67909 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
67926 AATTTATTATAAATTTA
1 AATTTATTTTAAATTTA
67943 AATTTA
1 AATTTA
67949 AAATGTCCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:67925 original size:23 final size:24
Alignment explanation
Indices: 67899--67952 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
67889 TTGAATTTAT
*
67899 TTTAAAATTAAGTT-T-ATTTTAAA
1 TTTAAAATTAA-TTATAAATTTAAA
*
67922 TTT-AAATTTATTATAAATTTAAA
1 TTTAAAATTAATTATAAATTTAAA
67945 TTTAAAAT
1 TTTAAAAT
67953 GTCCAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 2 0.08
22 7 0.27
23 13 0.50
24 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTAAAATTAATTATAAATTTAAA
Found at i:68571 original size:3 final size:3
Alignment explanation
Indices: 68563--68587 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
68553 AGGCATAAGT
68563 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
68588 GTGACATCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:69721 original size:30 final size:29
Alignment explanation
Indices: 69674--70104 Score: 435
Period size: 30 Copynumber: 14.5 Consensus size: 29
69664 CAAAAATTTT
* *
69674 ATTTTTACCCCCGAACTTCAAAAAATCCC
1 ATTTTTACCCTCGAACTTCCAAAAATCCC
*
69703 ATTTTTGACCCTCGAACTTCAAAAAATCCC
1 ATTTTT-ACCCTCGAACTTCCAAAAATCCC
*
69733 ATTTTTTACCC-CGAAACTTCAAAAAATCCC
1 A-TTTTTACCCTCG-AACTTCCAAAAATCCC
69763 ATTTTTGACCC-CGAAACTTCCAAAAATCCC
1 ATTTTT-ACCCTCG-AACTTCCAAAAATCCC
**
69793 ATTTTTACCCTCGAACAATTTTAAAAATCCC
1 ATTTTTACCCTCGAAC--TTCCAAAAATCCC
** *
69824 ATTTTTAATCTCAAAACTTCCAAAAATCCC
1 ATTTTTACCCTC-GAACTTCCAAAAATCCC
69854 ATTTTTAGCCCTCCGAACTTCCAAAAATCCC
1 ATTTTTA-CCCT-CGAACTTCCAAAAATCCC
* *
69885 ATTTTTAACCC-CGAAACTTTCAAAAATTCC
1 ATTTTT-ACCCTCG-AACTTCCAAAAATCCC
69915 ATTTTTACCCTCGAACTTCCAAAAATCCC
1 ATTTTTACCCTCGAACTTCCAAAAATCCC
*
69944 ATTTTTGA-CCTTGAACTTCCAAAAATCCC
1 ATTTTT-ACCCTCGAACTTCCAAAAATCCC
* *
69973 ATTTTGA-CCTCGAACTTCCAAATATCCC
1 ATTTTTACCCTCGAACTTCCAAAAATCCC
* * *
70001 ATTTTGACCC-CAAAACTTCCAAAAATTCC
1 ATTTTTACCCTC-GAACTTCCAAAAATCCC
* * *
70030 ATTCTTACCCCCGAAACTTCTAAAAATCCC
1 ATTTTTACCCTCG-AACTTCCAAAAATCCC
*** *
70060 ATTTTTGACCCAAAAACTTCCAAAAATTACC
1 ATTTTT-ACCCTCGAACTTCCAAAAA-TCCC
*
70091 A-TTTTACCCCCGAA
1 ATTTTTACCCTCGAA
70105 TGTCTAAAAA
Statistics
Matches: 345, Mismatches: 37, Indels: 40
0.82 0.09 0.09
Matches are distributed among these distances:
28 28 0.08
29 101 0.29
30 150 0.43
31 61 0.18
32 5 0.01
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.30
Consensus pattern (29 bp):
ATTTTTACCCTCGAACTTCCAAAAATCCC
Found at i:69755 original size:60 final size:57
Alignment explanation
Indices: 69674--70100 Score: 453
Period size: 61 Copynumber: 7.2 Consensus size: 57
69664 CAAAAATTTT
* *
69674 ATTTTTACCCCCGAACTTCAAAAAATCCCATTTTTGACCCTCGAACTTCAAAAAATCCC
1 ATTTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCC-CGAACTTCCAAAAATCCC
*
69733 ATTTTTTACCCCGAAACTTCAAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATCCC
1 A-TTTTTACCCCG-AACTTCCAAAAATCCCATTTTTGACCCCG-AACTTCCAAAAATCCC
** * * **
69793 ATTTTTACCCTCGAACAATTTTAAAAATCCCATTTTTAATCTCAAAACTTCCAAAAATCCC
1 ATTTTTACCC-CGAAC--TTCCAAAAATCCCATTTTTGA-CCCCGAACTTCCAAAAATCCC
* * *
69854 ATTTTTAGCCCTCCGAACTTCCAAAAATCCCATTTTTAACCCCGAAACTTTCAAAAATTCC
1 ATTTTTA--CC-CCGAACTTCCAAAAATCCCATTTTTGACCCCG-AACTTCCAAAAATCCC
**
69915 ATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTTGAACTTCCAAAAATCCC
1 ATTTTTACCC-CGAACTTCCAAAAATCCCATTTTTGACCCCGAACTTCCAAAAATCCC
* * * * *
69973 ATTTTGACCTCGAACTTCCAAATATCCCA-TTTTGACCCCAAAACTTCCAAAAATTCC
1 ATTTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCCC-GAACTTCCAAAAATCCC
* * ** *
70030 ATTCTTACCCCCGAAACTTCTAAAAATCCCATTTTTGACCCAAAAACTTCCAAAAATTACC
1 ATTTTTA-CCCCG-AACTTCCAAAAATCCCATTTTTGACCC-CGAACTTCCAAAAA-TCCC
70091 A-TTTTACCCC
1 ATTTTTACCCC
70101 CGAATGTCTA
Statistics
Matches: 316, Mismatches: 34, Indels: 36
0.82 0.09 0.09
Matches are distributed among these distances:
56 8 0.03
57 38 0.12
58 27 0.09
59 69 0.22
60 79 0.25
61 85 0.27
62 2 0.01
63 7 0.02
64 1 0.00
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (57 bp):
ATTTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACTTCCAAAAATCCC
Found at i:70113 original size:29 final size:28
Alignment explanation
Indices: 70021--70181 Score: 112
Period size: 29 Copynumber: 5.5 Consensus size: 28
70011 CAAAACTTCC
70021 AAAAATTCCATTCTTACCCCCGAAACT-TCT
1 AAAAATTCCATT-TTACCCCCG-AA-TGTCT
* *** *
70051 AAAAATCCCATTTTTGACCCAAAAACT-TCC
1 AAAAATTCCA-TTTT-ACCCCCGAA-TGTCT
70081 AAAAATTACCATTTTACCCCCGAATGTCT
1 AAAAATT-CCATTTTACCCCCGAATGTCT
* * **
70110 AAAAAATCCATTTT-CGACCTCGAAACTCT
1 AAAAATTCCATTTTAC--CCCCGAATGTCT
* *
70139 CAAAATTACCCTTTTACCCCCGAATGTCT
1 AAAAATT-CCATTTTACCCCCGAATGTCT
70168 AAAAATTCCATTTT
1 AAAAATTCCATTTT
70182 TAACCCTGAA
Statistics
Matches: 101, Mismatches: 22, Indels: 18
0.72 0.16 0.13
Matches are distributed among these distances:
27 1 0.01
28 14 0.14
29 43 0.43
30 33 0.33
31 10 0.10
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.30
Consensus pattern (28 bp):
AAAAATTCCATTTTACCCCCGAATGTCT
Found at i:70192 original size:29 final size:30
Alignment explanation
Indices: 70081--70210 Score: 97
Period size: 29 Copynumber: 4.4 Consensus size: 30
70071 AAAAACTTCC
*
70081 AAAAATTACCA-TTTTACCCCCGAATGTCT
1 AAAAATTACCATTTTTAACCCCGAATGTCT
* ** * **
70110 AAAAAAT-CCATTTTCGACCTCGAAACTCT
1 AAAAATTACCATTTTTAACCCCGAATGTCT
* * *
70139 CAAAATTACC-CTTTTACCCCCGAATGTCT
1 AAAAATTACCATTTTTAACCCCGAATGTCT
* * *
70168 AAAAATT-CCATTTTTAACCCTGAATTTTCC
1 AAAAATTACCATTTTTAACCCCGAA-TGTCT
*
70198 CAAAATTACCATT
1 AAAAATTACCATT
70211 CCTCGTAGGT
Statistics
Matches: 73, Mismatches: 23, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
28 5 0.07
29 52 0.71
30 11 0.15
31 5 0.07
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (30 bp):
AAAAATTACCATTTTTAACCCCGAATGTCT
Found at i:72954 original size:20 final size:20
Alignment explanation
Indices: 72921--72973 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
72911 ATTGTTTCTT
* *
72921 TATTTCTTTATTATT-TTGAA
1 TATTTATTTTTTATTCTT-AA
72941 TATTTATTTTTTATTCTTAA
1 TATTTATTTTTTATTCTTAA
72961 -ATTTATTATTTTA
1 TATTTATT-TTTTA
72974 GTTATTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 7 0.24
20 20 0.69
21 2 0.07
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (20 bp):
TATTTATTTTTTATTCTTAA
Found at i:72980 original size:35 final size:36
Alignment explanation
Indices: 72927--72995 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 36
72917 TCTTTATTTC
72927 TTTATTATTTTGAATATTTATTTT-TTATTCTTAAA
1 TTTATTATTTTGAATATTTATTTTGTTATTCTTAAA
* * *
72962 TTTATTATTTT-AGTTATTTTTTTTGTTTTTCTTA
1 TTTATTATTTTGA-ATATTTATTTTGTTATTCTTA
72996 TTTTCTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 1 0.03
35 20 0.69
36 8 0.28
ACGTcount: A:0.22, C:0.03, G:0.04, T:0.71
Consensus pattern (36 bp):
TTTATTATTTTGAATATTTATTTTGTTATTCTTAAA
Found at i:75474 original size:18 final size:18
Alignment explanation
Indices: 75444--75480 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
75434 ATACTTATTT
75444 ACAATTAATATAAAATTA
1 ACAATTAATATAAAATTA
75462 ACAA-TAATAATAAAATTA
1 ACAATTAAT-ATAAAATTA
75480 A
1 A
75481 ATATTCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (18 bp):
ACAATTAATATAAAATTA
Found at i:89996 original size:43 final size:43
Alignment explanation
Indices: 89932--90015 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
89922 GATTTTCCAA
89932 TAGGTTTCTCAATTGTAATTTTATTTCAGTAGATTGCTTTCTT
1 TAGGTTTCTCAATTGTAATTTTATTTCAGTAGATTGCTTTCTT
* * *
89975 TAGGTTTCTCGATTG-AGATTTTATTTCAGTTGATTTCTTTC
1 TAGGTTTCTCAATTGTA-ATTTTATTTCAGTAGATTGCTTTC
90016 CTTTCTACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 36 0.97
ACGTcount: A:0.19, C:0.12, G:0.15, T:0.54
Consensus pattern (43 bp):
TAGGTTTCTCAATTGTAATTTTATTTCAGTAGATTGCTTTCTT
Found at i:92338 original size:22 final size:21
Alignment explanation
Indices: 92314--92373 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 21
92304 TCATTCAACT
*
92314 CTCTCAATTCTTTTATTCT-AA
1 CTCTCAATT-TTTAATTCTCAA
92335 -TCTCAATTTTTAATTCTCAA
1 CTCTCAATTTTTAATTCTCAA
92355 CCTCTCAATATTCTTAATT
1 -CTCTCAAT-TT-TTAATT
92374 TTTTATTCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 8 0.24
20 10 0.30
22 7 0.21
23 2 0.06
24 6 0.18
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (21 bp):
CTCTCAATTTTTAATTCTCAA
Found at i:94140 original size:20 final size:20
Alignment explanation
Indices: 94117--94164 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
94107 GATAAGCCCT
*
94117 TTGATTGTTAGATTTAATGG
1 TTGATTGTTAGATTTAACGG
*** *
94137 TTGACCATTGGATTTAACGG
1 TTGATTGTTAGATTTAACGG
94157 TTGATTGT
1 TTGATTGT
94165 AAAGTCCCCG
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.06, G:0.25, T:0.46
Consensus pattern (20 bp):
TTGATTGTTAGATTTAACGG
Found at i:95337 original size:21 final size:21
Alignment explanation
Indices: 95313--95366 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
95303 CTTGGAAAAG
* *
95313 TTCTACCGATACAAGT-GTAAC
1 TTCTACCGATACAAATCAT-AC
*
95334 TTCTACCGAAACAAATCATAC
1 TTCTACCGATACAAATCATAC
95355 TTCTACCGATAC
1 TTCTACCGATAC
95367 TAAAAACTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.35, C:0.28, G:0.09, T:0.28
Consensus pattern (21 bp):
TTCTACCGATACAAATCATAC
Found at i:98070 original size:112 final size:113
Alignment explanation
Indices: 97947--98150 Score: 306
Period size: 114 Copynumber: 1.8 Consensus size: 113
97937 TTATAATTAT
* *
97947 TTTTTATTGATTTATTATAT-AAAAAGATAAAAATA-TTCTCATAAAAATATAACTTAATTTATA
1 TTTTTATTGATTTATTACATAAAAAAGA-AAAAAAACTTCTCATAAAAATATAACTTAATTTATA
*
98010 TAT-AAAAATGTATTTTAACAATTTCAATTTCAAATCTCTTGAGATAAAA
65 TATGAAAAA-ATATTTTAACAATTTCAATTTCAAATCTCTTGAGATAAAA
* *
98059 TTTTTATTGATTTATTACATAAAAAAGAAAAAAAACGTTCTTATAAAAATATAACTTAATTTATG
1 TTTTTATTGATTTATTACATAAAAAAGAAAAAAAAC-TTCTCATAAAAATATAACTTAATTTATA
*
98124 TATGAAAAAATATTTTAATAATTTCAA
65 TATGAAAAAATATTTTAACAATTTCAA
98151 AATTGAATTA
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
112 25 0.30
113 7 0.09
114 45 0.55
115 5 0.06
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (113 bp):
TTTTTATTGATTTATTACATAAAAAAGAAAAAAAACTTCTCATAAAAATATAACTTAATTTATAT
ATGAAAAAATATTTTAACAATTTCAATTTCAAATCTCTTGAGATAAAA
Found at i:100377 original size:61 final size:60
Alignment explanation
Indices: 100216--100414 Score: 231
Period size: 61 Copynumber: 3.2 Consensus size: 60
100206 CATTGAATGG
** * *
100216 TGATTTGT-TTTCTATTTTTTTAATTAGATTCAGCTGCTCA-TTGAAACTCTGATTACTGTTT
1 TGATTTGTATTTCT-TTTGATTAATTAGATTCAGCTGCT-ATTTGAAAC-CTGAATACTGATT
* *
100277 TGGTTTGTGTTTCTTTTTGATTAATTAGATTCAGCTGCTATTTGAAATCCTGAATACTGATT
1 TGATTTGTATTTC-TTTTGATTAATTAGATTCAGCTGCTATTTGAAA-CCTGAATACTGATT
** * *
100339 TGATTTGTATTTCTTTTGATTAATTAGATTCAGCTGCTATTCAAAACCCTGAATATTGAGT
1 TGATTTGTATTTCTTTTGATTAATTAGATTCAGCTGCTATTTGAAA-CCTGAATACTGATT
*
100400 TGATCTGTATTTCTT
1 TGATTTGTATTTCTT
100415 CCTAAATGCT
Statistics
Matches: 121, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
61 65 0.54
62 54 0.45
63 2 0.02
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.49
Consensus pattern (60 bp):
TGATTTGTATTTCTTTTGATTAATTAGATTCAGCTGCTATTTGAAACCTGAATACTGATT
Found at i:108230 original size:2 final size:2
Alignment explanation
Indices: 108223--108250 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
108213 GAGAAACAGC
108223 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
108251 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:108943 original size:25 final size:25
Alignment explanation
Indices: 108915--108963 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
108905 CATAAAAGCG
*
108915 ACTGATCTATCAGAAGACAAGAAAA
1 ACTGATCTAGCAGAAGACAAGAAAA
* * *
108940 ACTGGTCTAGGAGAAGACGAGAAA
1 ACTGATCTAGCAGAAGACAAGAAA
108964 GAAAAGCTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.47, C:0.14, G:0.24, T:0.14
Consensus pattern (25 bp):
ACTGATCTAGCAGAAGACAAGAAAA
Found at i:118039 original size:2 final size:2
Alignment explanation
Indices: 118032--118064 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
118022 TATTCAACTT
118032 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
118065 TGAATACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:133400 original size:51 final size:51
Alignment explanation
Indices: 133324--133421 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
133314 AAAGAGAGCT
* *
133324 TGACACGATTCATTCTGATTCTATATAGTTGACAAGCTTAAACGTTCTGTC
1 TGACACGATTCATTCTGATTCTATATAGCTAACAAGCTTAAACGTTCTGTC
* * *
133375 TGACATGATTTATTCTGATTCTATATAGCTAACGAGCTTAAACGTTC
1 TGACACGATTCATTCTGATTCTATATAGCTAACAAGCTTAAACGTTC
133422 AGTAATTATG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (51 bp):
TGACACGATTCATTCTGATTCTATATAGCTAACAAGCTTAAACGTTCTGTC
Found at i:135254 original size:66 final size:66
Alignment explanation
Indices: 135133--135257 Score: 160
Period size: 66 Copynumber: 1.9 Consensus size: 66
135123 AACTCAAGAA
* * * * *
135133 CAAGATGAAATGAATCCTAAATAGAAAATGTACACATATAAACAAAGCACCAATGTTGCTCAATA
1 CAAGATGAAAAGAATCCTAAACAAAAAATGCACACATATAAACAAAACACCAATGTTGCTCAATA
135198 G
66 G
* * * * *
135199 CAAGATGAAAAGAATCTTGAACAAAAAATGCACACATCTAAACAAAATACTAATGTTGC
1 CAAGATGAAAAGAATCCTAAACAAAAAATGCACACATATAAACAAAACACCAATGTTGC
135258 ATCCAAATAA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 49 1.00
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.21
Consensus pattern (66 bp):
CAAGATGAAAAGAATCCTAAACAAAAAATGCACACATATAAACAAAACACCAATGTTGCTCAATA
G
Found at i:142339 original size:14 final size:14
Alignment explanation
Indices: 142310--142345 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
142300 GAACTTTATT
142310 TATTAAAATAATAA
1 TATTAAAATAATAA
142324 TATTATAAATAA-AA
1 TATTA-AAATAATAA
142338 TATTAAAA
1 TATTAAAA
142346 AAACTCACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 12 0.57
15 6 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TATTAAAATAATAA
Found at i:148422 original size:23 final size:23
Alignment explanation
Indices: 148396--148441 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
148386 TCACAGTAAG
148396 ATAGTTTAATTTCCCAACTATCA
1 ATAGTTTAATTTCCCAACTATCA
148419 ATAGTTTAATTTCCCAACTATCA
1 ATAGTTTAATTTCCCAACTATCA
148442 TCTGATATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (23 bp):
ATAGTTTAATTTCCCAACTATCA
Found at i:155188 original size:163 final size:163
Alignment explanation
Indices: 155014--155310 Score: 416
Period size: 163 Copynumber: 1.8 Consensus size: 163
155004 CTCTAACGTT
* * * * *
155014 TAGCGGCGCTTTCCTATAAGCGTCGCTATTGCTTTGACCTTTAACGGCACT-TGCCTAAAAGCGT
1 TAGCGGCGCTTTCCTATAAGCGCCGCTATTGCTCTAACCTTTAACGGCACTAT-CCCAAAAGCGC
* * * * * **
155078 CGCTATTTCTCTGACCTTTAACGGCTCTTGCCTATAAGCGTCGCTATTTCTCTGACCTTTAGCGA
65 CGCTATTGCTCTAACCTTTAACGGCGCTTGCCCATAACCGTCGCTATTGATCTGACCTTTAGCGA
155143 CGCTTGCCCATAGTACACCTATTGCTTTGACCTC
130 CGCTTGCCCATAGTACACCTATTGCTTTGACCTC
* * *
155177 TAGCGGCGCTTTCCTATAAGCGCCGCTATTGCTCTAACCTTTAGCGGCGCTATCCCATAAGCGCC
1 TAGCGGCGCTTTCCTATAAGCGCCGCTATTGCTCTAACCTTTAACGGCACTATCCCAAAAGCGCC
* * *
155242 GTTATTGCTCTAACCTTTAGCGGCGCTTTCCCATAACCGTCGCTATTGATCTGACCTTTAGCGAC
66 GCTATTGCTCTAACCTTTAACGGCGCTTGCCCATAACCGTCGCTATTGATCTGACCTTTAGCGAC
155307 GCTT
131 GCTT
155311 TCCAATAAGC
Statistics
Matches: 115, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
163 114 0.99
164 1 0.01
ACGTcount: A:0.18, C:0.30, G:0.19, T:0.32
Consensus pattern (163 bp):
TAGCGGCGCTTTCCTATAAGCGCCGCTATTGCTCTAACCTTTAACGGCACTATCCCAAAAGCGCC
GCTATTGCTCTAACCTTTAACGGCGCTTGCCCATAACCGTCGCTATTGATCTGACCTTTAGCGAC
GCTTGCCCATAGTACACCTATTGCTTTGACCTC
Found at i:155329 original size:41 final size:41
Alignment explanation
Indices: 154906--155342 Score: 405
Period size: 41 Copynumber: 10.7 Consensus size: 41
154896 TATACTTACC
* ** *
154906 ATAAGCGTCGCTATTGCTCTGATATTTAGCTGCGCTTTCAC-
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTC-CT
* * * * * *
154947 ATAAGTGACGATAATGCTCTAACTTTTAGCGGCG-TTTGCCT
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTT-CCT
* * *
154988 ATAAGCGCTGCTATTGCTCTAACGTTTAGCGGCGCTTTCCT
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCT
* * * * *
155029 ATAAGCGTCGCTATTGCTTTGACCTTTAACGGCACTTGCCT
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCT
* * * * * *
155070 AAAAGCGTCGCTATTTCTCTGACCTTTAACGGCTCTTGCCT
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCT
* * * * *
155111 ATAAGCGTCGCTATTTCTCTGACCTTTAGCGACGCTTGCCC
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCT
** * *
155152 AT-AGTACAC-CTATTGCTTTGACCTCTAGCGGCGCTTTCCT
1 ATAAGCGC-CGCTATTGCTCTGACCTTTAGCGGCGCTTTCCT
* * *
155192 ATAAGCGCCGCTATTGCTCTAACCTTTAGCGGCGCTATCCC
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCT
* * *
155233 ATAAGCGCCGTTATTGCTCTAACCTTTAGCGGCGCTTTCCC
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCT
* * * * *
155274 ATAACCGTCGCTATTGATCTGACCTTTAGCGACGCTTTCCA
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCT
* *
155315 ATAAGCGCCACTATTGCTCTTACCTTTA
1 ATAAGCGCCGCTATTGCTCTGACCTTTA
155343 TCGGGGCCTA
Statistics
Matches: 329, Mismatches: 61, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
40 34 0.10
41 292 0.89
42 3 0.01
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (41 bp):
ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCT
Found at i:155342 original size:204 final size:204
Alignment explanation
Indices: 154973--155342 Score: 499
Period size: 204 Copynumber: 1.8 Consensus size: 204
154963 CTCTAACTTT
* * * * *
154973 TAGCGGCGTTTGCCTATAAGCGCTGCTATTGCTCTAACGTTTAGCGGCGCTTTCCTATAAGCGTC
1 TAGCGGCGTTTGCCTATAAGCGCCGCTATTGCTCTAACCTTTAGCGGCGCTATCCCATAAGCGCC
* * * * ** *
155038 GCTATTGCTTTGACCTTTAACGGCACTTGCCTAAAAGCGTCGCTATTTCTCTGACCTTTAACGGC
66 GCTATTGCTCTAACCTTTAACGGCACTTGCCCAAAACCGTCGCTATTGATCTGACCTTTAACGAC
* * * * *
155103 TCTTGCCTATAAGCGTCGCTATTTCTCTGACCTTTAGCGACGCTTGCCCATAGTACACCTATTGC
131 GCTTGCCAATAAGCGCCACTATTGCTCTGACCTTTAGCGACGCTTGCCCATAGTACACCTATTGC
155168 TTTGACCTC
196 TTTGACCTC
155177 TAGCGGCGCTTT-CCTATAAGCGCCGCTATTGCTCTAACCTTTAGCGGCGCTATCCCATAAGCGC
1 TAGCGGCG-TTTGCCTATAAGCGCCGCTATTGCTCTAACCTTTAGCGGCGCTATCCCATAAGCGC
* * * * * *
155241 CGTTATTGCTCTAACCTTTAGCGGCGCTTTCCCATAACCGTCGCTATTGATCTGACCTTTAGCGA
65 CGCTATTGCTCTAACCTTTAACGGCACTTGCCCAAAACCGTCGCTATTGATCTGACCTTTAACGA
* *
155306 CGCTTTCCAATAAGCGCCACTATTGCTCTTACCTTTA
130 CGCTTGCCAATAAGCGCCACTATTGCTCTGACCTTTA
155343 TCGGGGCCTA
Statistics
Matches: 140, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
204 137 0.98
205 3 0.02
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.33
Consensus pattern (204 bp):
TAGCGGCGTTTGCCTATAAGCGCCGCTATTGCTCTAACCTTTAGCGGCGCTATCCCATAAGCGCC
GCTATTGCTCTAACCTTTAACGGCACTTGCCCAAAACCGTCGCTATTGATCTGACCTTTAACGAC
GCTTGCCAATAAGCGCCACTATTGCTCTGACCTTTAGCGACGCTTGCCCATAGTACACCTATTGC
TTTGACCTC
Found at i:156240 original size:13 final size:13
Alignment explanation
Indices: 156224--156248 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
156214 TTTTCCTTTT
156224 AAAAAAAATGTTA
1 AAAAAAAATGTTA
156237 AAAAAAAATGTT
1 AAAAAAAATGTT
156249 TCCTTTTATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
AAAAAAAATGTTA
Found at i:159587 original size:35 final size:35
Alignment explanation
Indices: 159547--159627 Score: 87
Period size: 35 Copynumber: 2.3 Consensus size: 35
159537 ATAAAAATGA
*
159547 ATTAAAAAATATAATACATCAAATAAATT-AAAA-AC
1 ATTAAAAAATATAATAC-TC-AACAAATTGAAAATAC
* *
159582 ATTAAAATAA-ATATTTCTCAACAAATTGAAAATAC
1 ATTAAAA-AATATAATACTCAACAAATTGAAAATAC
159617 ATTAAAAAATA
1 ATTAAAAAATA
159628 ATTATATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
33 7 0.18
34 8 0.21
35 22 0.56
36 2 0.05
ACGTcount: A:0.62, C:0.09, G:0.01, T:0.28
Consensus pattern (35 bp):
ATTAAAAAATATAATACTCAACAAATTGAAAATAC
Found at i:165879 original size:21 final size:20
Alignment explanation
Indices: 165853--165904 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
165843 TGTGCCTAGT
165853 AGGCTTCGTGCCGGTGTTTTC
1 AGGCTT-GTGCCGGTGTTTTC
*
165874 AGGCTT-TGTCGGTGTTTTC
1 AGGCTTGTGCCGGTGTTTTC
*
165893 AAGCTTTGTGCC
1 AGGC-TTGTGCC
165905 TGTAGGCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 15 0.58
20 2 0.08
21 9 0.35
ACGTcount: A:0.08, C:0.21, G:0.31, T:0.40
Consensus pattern (20 bp):
AGGCTTGTGCCGGTGTTTTC
Found at i:165888 original size:19 final size:19
Alignment explanation
Indices: 165864--165901 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
165854 GGCTTCGTGC
*
165864 CGGTGTTTTCAGGCTTTGT
1 CGGTGTTTTCAAGCTTTGT
165883 CGGTGTTTTCAAGCTTTGT
1 CGGTGTTTTCAAGCTTTGT
165902 GCCTGTAGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.08, C:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
CGGTGTTTTCAAGCTTTGT
Found at i:168518 original size:20 final size:21
Alignment explanation
Indices: 168493--168532 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
168483 GATATATTTA
*
168493 AATGTAATATTTTTA-AAATT
1 AATGTAATATATTTATAAATT
*
168513 AATGTATTATATTTATAAAT
1 AATGTAATATATTTATAAAT
168533 ATTTATGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
AATGTAATATATTTATAAATT
Found at i:174420 original size:113 final size:114
Alignment explanation
Indices: 174304--174542 Score: 281
Period size: 114 Copynumber: 2.1 Consensus size: 114
174294 TTACACTAAA
* * * * * *
174304 AAAAATATTTTTT-GTTATTTGCCTAGTCATGGTCGACACTTAAAAA-ATACTG-AT-AAAAATT
1 AAAAATATTTTTTGGGTATTTGACAAGTAATGATCGACAC-TAAAAATATA-TGAATAAAAAAAT
* * *
174365 TATTTTTTGAGTATTTG-CTACTCAATGGTTTACATCACCTTTTTCAAATTT
64 AATTTTTTGAGTATTTGAC-ACTCAATGGTTGACACCACCTTTTTCAAATTT
*
174416 AAAAATATTTTTTGGGTATTTGACAAGTAATGATCGATACTAAAAATATATGAATAAAAAAATAA
1 AAAAATATTTTTTGGGTATTTGACAAGTAATGATCGACACTAAAAATATATGAATAAAAAAATAA
* * * * *
174481 TTTTTTGGGTGTTTGACACTTAATGGTTGACACCACTTTTTTCAGATTT
66 TTTTTTGAGTATTTGACACTCAATGGTTGACACCACCTTTTTCAAATTT
174530 AAAAATATTTTTT
1 AAAAATATTTTTT
174543 TTGGGTGTTG
Statistics
Matches: 107, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
112 21 0.20
113 25 0.23
114 60 0.56
115 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (114 bp):
AAAAATATTTTTTGGGTATTTGACAAGTAATGATCGACACTAAAAATATATGAATAAAAAAATAA
TTTTTTGAGTATTTGACACTCAATGGTTGACACCACCTTTTTCAAATTT
Found at i:175151 original size:113 final size:111
Alignment explanation
Indices: 174945--175252 Score: 289
Period size: 115 Copynumber: 2.7 Consensus size: 111
174935 ATTGGGTGCC
* * * * *
174945 AAACACCCAAAAAACATTTTTTTTTATTCGTATTTTTTGGGTGTCAACCAAT-GCTTGCCAAACA
1 AAACACCCAAAAAATATTTTTTTTTCTT-AT-TTTTTTGGGTGTCGACC-ATGGCTTGACAAACA
* * ** * *
175009 CTTAAAAAATATTTTTAAATTTGGGAAAGGTGGTGTAGGCCATTGA-ATGAG-
63 C-CAAAAAA-ATTTTTAAACTTGAAAAAGGTGGTATAGACCA-TGACATG-GT
175060 AAACACCCAAAAAATATTTTTTTTTCTTATTTTTTTGGGTGTCGACCATGGCTTGACAAACACCA
1 AAACACCCAAAAAATATTTTTTTTTCTTATTTTTTTGGGTGTCGACCATGGCTTGACAAACACCA
* * *
175125 AAAAAATTTTTGAAGACTTGAAAAAGGTGGTATCGATCATGACTTGGT
66 AAAAAATTTTT-AA-ACTTGAAAAAGGTGGTATAGACCATGACATGGT
* * ** * * *
175173 AGACACCCAAAAAAATATTTTTTTATTCGTATTTTTTTGGGTGTCGGTCATGGGTTGGCCAACAT
1 AAACACCC-AAAAAATATTTTTTT-TTCTTATTTTTTTGGGTGTCGACCATGGCTTGACAAACA-
175238 CCAAAAAAATATTTT
63 CCAAAAAAAT-TTTT
175253 TTTAATGTAA
Statistics
Matches: 163, Mismatches: 21, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
111 6 0.04
112 14 0.09
113 54 0.33
114 16 0.10
115 59 0.36
116 10 0.06
117 4 0.02
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (111 bp):
AAACACCCAAAAAATATTTTTTTTTCTTATTTTTTTGGGTGTCGACCATGGCTTGACAAACACCA
AAAAAATTTTTAAACTTGAAAAAGGTGGTATAGACCATGACATGGT
Found at i:175641 original size:1 final size:1
Alignment explanation
Indices: 175631--175668 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
175621 CACAAGGTTG
* *
175631 TTTTTGTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
175669 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.05, T:0.95
Consensus pattern (1 bp):
T
Found at i:175647 original size:14 final size:13
Alignment explanation
Indices: 175628--175668 Score: 66
Period size: 12 Copynumber: 3.2 Consensus size: 13
175618 TTACACAAGG
175628 TTGTTTTTGTTTTT
1 TTGTTTTT-TTTTT
175642 TTGTTTTTTTTTT
1 TTGTTTTTTTTTT
175655 TT-TTTTTTTTTT
1 TTGTTTTTTTTTT
175667 TT
1 TT
175669 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.44
13 7 0.26
14 8 0.30
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (13 bp):
TTGTTTTTTTTTT
Found at i:175729 original size:1 final size:1
Alignment explanation
Indices: 175679--175715 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
175669 NNNNNNNNNN
175679 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
175716 AGATGCTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:177993 original size:23 final size:24
Alignment explanation
Indices: 177967--178013 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
177957 TAGAATTATC
*
177967 AAATATT-AAATTAAAAATAATGT
1 AAATATTAAAATTAAAAAAAATGT
177990 AAATATTAAAAATTAAAAAAAATG
1 AAATATT-AAAATTAAAAAAAATG
178014 GATAAACCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
25 14 0.67
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (24 bp):
AAATATTAAAATTAAAAAAAATGT
Found at i:185350 original size:18 final size:17
Alignment explanation
Indices: 185329--185385 Score: 53
Period size: 16 Copynumber: 3.3 Consensus size: 17
185319 CAACAAAAAT
185329 TAAAATTCAAAATATTTA
1 TAAAATTCAAAA-ATTTA
*
185347 TAAAAATTGAAAAATTTA
1 T-AAAATTCAAAAATTTA
** *
185365 T-ATTTTTAAAAATTTA
1 TAAAATTCAAAAATTTA
185381 TAAAA
1 TAAAA
185386 ACTTTAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
16 13 0.42
17 1 0.03
18 7 0.23
19 10 0.32
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAAATTCAAAAATTTA
Found at i:185352 original size:19 final size:18
Alignment explanation
Indices: 185330--185366 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
185320 AACAAAAATT
185330 AAAATTCAAAATATTTATA
1 AAAATTCAAAA-ATTTATA
*
185349 AAAATTGAAAAATTTATA
1 AAAATTCAAAAATTTATA
185367 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (18 bp):
AAAATTCAAAAATTTATA
Found at i:191210 original size:18 final size:17
Alignment explanation
Indices: 191163--191221 Score: 54
Period size: 18 Copynumber: 3.6 Consensus size: 17
191153 CTCTTCCAAC
191163 AAAAA-TTATAAAAA--
1 AAAAATTTATAAAAATT
* *
191177 AATAATTT-TCAAAATT
1 AAAAATTTATAAAAATT
*
191193 TAAAATATTATAAAAATT
1 AAAAAT-TTATAAAAATT
191211 AAAAATTTATA
1 AAAAATTTATA
191222 TTTTTAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
14 9 0.26
15 2 0.06
16 4 0.12
17 7 0.21
18 12 0.35
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAAATTTATAAAAATT
Found at i:194062 original size:25 final size:25
Alignment explanation
Indices: 194025--194072 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
194015 TCATTTTTCG
194025 TTCTTTCAATTTATTATTGTTCTCA
1 TTCTTTCAATTTATTATTGTTCTCA
* *
194050 TTCTTTCACTTTATTCTTGTTCT
1 TTCTTTCAATTTATTATTGTTCT
194073 TTGAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.15, C:0.19, G:0.04, T:0.62
Consensus pattern (25 bp):
TTCTTTCAATTTATTATTGTTCTCA
Found at i:194523 original size:18 final size:18
Alignment explanation
Indices: 194500--194537 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
194490 TTCTTTCTTT
194500 CACATGTTAACTGTATCA
1 CACATGTTAACTGTATCA
194518 CACATGTTAACTGTATCA
1 CACATGTTAACTGTATCA
194536 CA
1 CA
194538 ACGGGAAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (18 bp):
CACATGTTAACTGTATCA
Found at i:194587 original size:77 final size:77
Alignment explanation
Indices: 194443--194743 Score: 312
Period size: 80 Copynumber: 4.0 Consensus size: 77
194433 TTTGCTGTTT
*
194443 ACGGGAAACGGGAAACGGGAAATGGG--ACGGGTTCG-TTTTTGATTAGTTTCTTTCTTTCACAT
1 ACGGGAAACGGGAAAC--G-AACGGGAAACGGGTTCGTTTTTTGATTAGTTTCTTTCTTTCACAT
194505 GTTAACTGTATCAC-
63 GTTAACTGTATCACA
* ** * * *
194519 ACATGTTAACTGTATCAC-AACGGGAAACGGGTTCGTTTTTTGATTAGTTTCTTTCTTTCACATG
1 AC-GGGAAACGGGA-AACGAACGGGAAACGGGTTCGTTTTTTGATTAGTTTCTTTCTTTCACATG
194583 TTAACTGTATCACA
64 TTAACTGTATCACA
*
194597 ACGGGAAACGGGAAACGGGAAACGGGAAACGGGTTTGTTTTTTGATTAGTTTCTTTCTTTCACAT
1 ACGGGAAACGGGAAAC--G-AACGGGAAACGGGTTCGTTTTTTGATTAGTTTCTTTCTTTCACAT
194662 GTTAACTGTATCACA
63 GTTAACTGTATCACA
* *
194677 AC--G----GGG-AACG---GGG-AACGGGTTTGTTCTTTGATT-GATTTCTTTCTTTCACATGT
1 ACGGGAAACGGGAAACGAACGGGAAACGGGTTCGTTTTTTGATTAG-TTTCTTTCTTTCACATGT
194730 TAACTGTATCACA
65 TAACTGTATCACA
194743 A
1 A
194744 AGTCTGTTTA
Statistics
Matches: 199, Mismatches: 15, Indels: 32
0.81 0.06 0.13
Matches are distributed among these distances:
65 1 0.01
66 51 0.26
67 3 0.02
71 1 0.01
73 3 0.02
74 8 0.04
76 13 0.07
77 53 0.27
78 5 0.03
80 61 0.31
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (77 bp):
ACGGGAAACGGGAAACGAACGGGAAACGGGTTCGTTTTTTGATTAGTTTCTTTCTTTCACATGTT
AACTGTATCACA
Found at i:194608 original size:7 final size:7
Alignment explanation
Indices: 194596--194629 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
194586 ACTGTATCAC
194596 AACGGGA
1 AACGGGA
194603 AACGGGA
1 AACGGGA
194610 AACGGGA
1 AACGGGA
194617 AACGGGA
1 AACGGGA
194624 AACGGG
1 AACGGG
194630 TTTGTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.44, T:0.00
Consensus pattern (7 bp):
AACGGGA
Found at i:194659 original size:80 final size:80
Alignment explanation
Indices: 194443--194695 Score: 342
Period size: 80 Copynumber: 3.2 Consensus size: 80
194433 TTTGCTGTTT
*
194443 ACGGGAAACGGGAAACGGGAAATGGG--ACGGGTTCG-TTTTTGATTAGTTTCTTTCTTTCACAT
1 ACGGGAAACGGGAAACGGGAAACGGGAAACGGGTTCGTTTTTTGATTAGTTTCTTTCTTTCACAT
194505 GTTAACTGTATCAC-
66 GTTAACTGTATCACA
* ** * * *
194519 ACATGTTAAC-TGTATC---ACAACGGGAAACGGGTTCGTTTTTTGATTAGTTTCTTTCTTTCAC
1 AC-GGGAAACGGGAAACGGGA-AACGGGAAACGGGTTCGTTTTTTGATTAGTTTCTTTCTTTCAC
194580 ATGTTAACTGTATCACA
64 ATGTTAACTGTATCACA
*
194597 ACGGGAAACGGGAAACGGGAAACGGGAAACGGGTTTGTTTTTTGATTAGTTTCTTTCTTTCACAT
1 ACGGGAAACGGGAAACGGGAAACGGGAAACGGGTTCGTTTTTTGATTAGTTTCTTTCTTTCACAT
194662 GTTAACTGTATCACA
66 GTTAACTGTATCACA
* *
194677 ACGGGGAACGGGGAACGGG
1 ACGGGAAACGGGAAACGGG
194696 TTTGTTCTTT
Statistics
Matches: 151, Mismatches: 16, Indels: 16
0.83 0.09 0.09
Matches are distributed among these distances:
73 1 0.01
74 5 0.03
76 14 0.09
77 49 0.32
78 5 0.03
80 76 0.50
81 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.32
Consensus pattern (80 bp):
ACGGGAAACGGGAAACGGGAAACGGGAAACGGGTTCGTTTTTTGATTAGTTTCTTTCTTTCACAT
GTTAACTGTATCACA
Found at i:194680 original size:73 final size:66
Alignment explanation
Indices: 194610--194743 Score: 225
Period size: 66 Copynumber: 2.0 Consensus size: 66
194600 GGAAACGGGA
* *
194610 AACGGGAAACGGGAAACGGGTTTGTTTTTTGATT-AGTTTCTTTCTTTCACATGTTAACTGTATC
1 AACGGGGAACGGGAAACGGGTTTGTTCTTTGATTGA-TTTCTTTCTTTCACATGTTAACTGTATC
194674 AC
65 AC
*
194676 AACGGGGAACGGGGAACGGGTTTGTTCTTTGATTGATTTCTTTCTTTCACATGTTAACTGTATCA
1 AACGGGGAACGGGAAACGGGTTTGTTCTTTGATTGATTTCTTTCTTTCACATGTTAACTGTATCA
194741 C
66 C
194742 AA
1 AA
194744 AGTCTGTTTA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 63 0.98
67 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (66 bp):
AACGGGGAACGGGAAACGGGTTTGTTCTTTGATTGATTTCTTTCTTTCACATGTTAACTGTATCA
C
Found at i:200156 original size:3 final size:3
Alignment explanation
Indices: 200133--200175 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
200123 TATTATTAAC
* * *
200133 ATA ATG ATA ATA GTG ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
200176 ATTACTTACA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:202611 original size:16 final size:15
Alignment explanation
Indices: 202590--202619 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
202580 TTTATTGTTG
202590 TTTATTATATTAATAT
1 TTTATTAT-TTAATAT
202606 TTTATTATTTAATA
1 TTTATTATTTAATA
202620 AAATAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATTATTTAATAT
Found at i:203564 original size:9 final size:9
Alignment explanation
Indices: 203550--203574 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
203540 ACAAAACATT
203550 TTAAAATTA
1 TTAAAATTA
203559 TTAAAATTA
1 TTAAAATTA
203568 TTAAAAT
1 TTAAAAT
203575 AATATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTAAAATTA
Found at i:204421 original size:12 final size:12
Alignment explanation
Indices: 204404--204428 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
204394 CATTTACTTC
204404 CGGAAAATGGAG
1 CGGAAAATGGAG
204416 CGGAAAATGGAG
1 CGGAAAATGGAG
204428 C
1 C
204429 ATTATCAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.12, G:0.40, T:0.08
Consensus pattern (12 bp):
CGGAAAATGGAG
Found at i:210802 original size:21 final size:21
Alignment explanation
Indices: 210764--210803 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
210754 ATCATTGCTT
**
210764 TAAATTTTTTTAACTTTTTCA
1 TAAATTTTTAGAACTTTTTCA
*
210785 TAAATTTTTAGAATTTTTT
1 TAAATTTTTAGAACTTTTT
210804 TAGAATTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (21 bp):
TAAATTTTTAGAACTTTTTCA
Found at i:210834 original size:16 final size:16
Alignment explanation
Indices: 210800--210846 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 16
210790 TTTTAGAATT
210800 TTTTTAGAAT-TAT-TA
1 TTTTTA-AATATATATA
210815 TTTTT-AATATATATA
1 TTTTTAAATATATATA
210830 TTTTTAAATATATATA
1 TTTTTAAATATATATA
210846 T
1 T
210847 ATATAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.10
14 3 0.10
15 12 0.41
16 11 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTTAAATATATATA
Found at i:210853 original size:16 final size:16
Alignment explanation
Indices: 210820--210854 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
210810 TATTATTTTT
* *
210820 AATATATATATTTTTA
1 AATATATATATATATA
210836 AATATATATATATATA
1 AATATATATATATATA
210852 AAT
1 AAT
210855 TTTGGAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATATATATATATATA
Found at i:210869 original size:24 final size:24
Alignment explanation
Indices: 210814--210874 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 24
210804 TAGAATTATT
* *
210814 ATTTTTA-ATATATATATTTTTAA
1 ATTTTTATATATATAAATTTTGAA
* * *
210837 ATATATATATATATAAATTTTGGA
1 ATTTTTATATATATAAATTTTGAA
*
210861 ATTTTTATAAATAT
1 ATTTTTATATATAT
210875 TTGGATTTTT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (24 bp):
ATTTTTATATATATAAATTTTGAA
Found at i:210871 original size:18 final size:18
Alignment explanation
Indices: 210848--210885 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
210838 TATATATATA
210848 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGG-ATTTT
210866 TATAAATATTTGGATTTT
1 TATAAATATTTGGATTTT
210884 TA
1 TA
210886 AAAACTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (18 bp):
TATAAATATTTGGATTTT
Found at i:216141 original size:6 final size:6
Alignment explanation
Indices: 216130--216180 Score: 84
Period size: 6 Copynumber: 8.3 Consensus size: 6
216120 ATTAAAACTT
*
216130 TAAAGA TAAAGAA AAAAGA TAAAGA TAAAGA TAAAGA TAAAGA TAAAGA
1 TAAAGA TAAAG-A TAAAGA TAAAGA TAAAGA TAAAGA TAAAGA TAAAGA
216179 TA
1 TA
216181 TTTTCAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 37 0.88
7 5 0.12
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
TAAAGA
Found at i:216423 original size:6 final size:6
Alignment explanation
Indices: 216412--216440 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
216402 AAAGCACTTG
216412 ATATAA ATATAA ATATAA ATATAA ATATA
1 ATATAA ATATAA ATATAA ATATAA ATATA
216441 TGATTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:218961 original size:16 final size:16
Alignment explanation
Indices: 218940--218970 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
218930 AAAAATTCAT
*
218940 AAAAATGTTAAAAATA
1 AAAAATATTAAAAATA
218956 AAAAATATTAAAAAT
1 AAAAATATTAAAAAT
218971 GTTCAACTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAAATATTAAAAATA
Found at i:221365 original size:29 final size:29
Alignment explanation
Indices: 221330--221389 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
221320 GTTGATTAAG
* *
221330 TCTTAATTTTATTGATATGAGTATTGTTA
1 TCTTAATTTTATTGACATGAGTATTATTA
221359 TCTTAATTTTATTGACATGAGTATTATTA
1 TCTTAATTTTATTGACATGAGTATTATTA
221388 TC
1 TC
221390 AATATAAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.53
Consensus pattern (29 bp):
TCTTAATTTTATTGACATGAGTATTATTA
Found at i:226868 original size:22 final size:22
Alignment explanation
Indices: 226840--226884 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
226830 TTCCATACAA
226840 AACCCTAAGACGCTAATTATTC
1 AACCCTAAGACGCTAATTATTC
* *
226862 AACCCTAATATGCTAATTATTC
1 AACCCTAAGACGCTAATTATTC
226884 A
1 A
226885 TTTTTAAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (22 bp):
AACCCTAAGACGCTAATTATTC
Found at i:233702 original size:14 final size:14
Alignment explanation
Indices: 233685--233732 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
233675 TCCGAATGAA
233685 TATATTGAAAAGGT
1 TATATTGAAAAGGT
** *
233699 TATATCCAAAAGGA
1 TATATTGAAAAGGT
*
233713 TATATTGAAAATGT
1 TATATTGAAAAGGT
233727 TATATT
1 TATATT
233733 CAATGATATA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.38
Consensus pattern (14 bp):
TATATTGAAAAGGT
Found at i:233715 original size:28 final size:28
Alignment explanation
Indices: 233665--233731 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
233655 AATATTTTTA
* *
233665 AAAAGG-TATATCCGAATGAATATATTG
1 AAAAGGTTATATCCAAAAGAATATATTG
*
233692 AAAAGGTTATATCCAAAAGGATATATTG
1 AAAAGGTTATATCCAAAAGAATATATTG
*
233720 AAAATGTTATAT
1 AAAAGGTTATAT
233732 TCAATGATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
27 6 0.17
28 29 0.83
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.31
Consensus pattern (28 bp):
AAAAGGTTATATCCAAAAGAATATATTG
Found at i:233743 original size:28 final size:27
Alignment explanation
Indices: 233665--233743 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 27
233655 AATATTTTTA
233665 AAAAGG-TATATCCGAATGAATATATTG
1 AAAAGGTTATATCC-AATGAATATATTG
* *
233692 AAAAGGTTATATCCAAAAGGATATATTG
1 AAAAGGTTATATCC-AATGAATATATTG
* *
233720 AAAATGTTATATTCAATG-ATATAT
1 AAAAGGTTATATCCAATGAATATAT
233744 CCGAGAGTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 6 0.13
27 9 0.20
28 30 0.67
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (27 bp):
AAAAGGTTATATCCAATGAATATATTG
Found at i:233837 original size:28 final size:28
Alignment explanation
Indices: 233799--234019 Score: 248
Period size: 28 Copynumber: 7.8 Consensus size: 28
233789 ATATAACCAT
*
233799 GATATTTTTGAAAAGGTTATATCCGTAAG
1 GATA-TTTTGAAAAGGTTATATCCGAAAG
*
233828 GATATATTGAAAAGGTTATATCCGTAAA-
1 GATATTTTGAAAAGGTTATATCCG-AAAG
* *
233856 GATATATTGAAAATGTTATATCCGAAAG
1 GATATTTTGAAAAGGTTATATCCGAAAG
* * * *
233884 AATATTTTGAAAATGTTATATCTGAAAA
1 GATATTTTGAAAAGGTTATATCCGAAAG
* **
233912 GATATTTTAAAAAGGTTATATCTAAAAG
1 GATATTTTGAAAAGGTTATATCCGAAAG
*
233940 GATATTTTTGAAAAGGTTATATCTGAAAG
1 GATA-TTTTGAAAAGGTTATATCCGAAAG
* *
233969 GATATTTTGAAAAGG-TATATCCAAAAA
1 GATATTTTGAAAAGGTTATATCCGAAAG
*
233996 GATATTATTGAAAAAGGTTGTATC
1 GATATT-TTG-AAAAGGTTATATC
234020 TAAAACGAGC
Statistics
Matches: 168, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
27 18 0.11
28 107 0.64
29 38 0.23
30 5 0.03
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.35
Consensus pattern (28 bp):
GATATTTTGAAAAGGTTATATCCGAAAG
Found at i:233875 original size:14 final size:14
Alignment explanation
Indices: 233807--233989 Score: 65
Period size: 14 Copynumber: 13.0 Consensus size: 14
233797 ATGATATTTT
233807 TGAAAAGGTTATATC
1 TGAAAA-GTTATATC
* * * *
233822 CGTAAGGATATAT-
1 TGAAAAGTTATATC
233835 TGAAAAGGTTATATC
1 TGAAAA-GTTATATC
* * *
233850 CGTAAAGATATAT-
1 TGAAAAGTTATATC
233863 TGAAAATGTTATATC
1 TGAAAA-GTTATATC
* * *
233878 CG-AAAG-AATATTT
1 TGAAAAGTTATA-TC
233891 TGAAAATGTTATATC
1 TGAAAA-GTTATATC
* *
233906 TGAAAAGATAT-TT
1 TGAAAAGTTATATC
*
233919 TAAAAAGGTTATATC
1 TGAAAA-GTTATATC
* * *
233934 T-AAAAGGATATTTT
1 TGAAAA-GTTATATC
233948 TGAAAAGGTTATATC
1 TGAAAA-GTTATATC
* * *
233963 TGAAAGGATAT-TT
1 TGAAAAGTTATATC
*
233976 TGAAAAGGTATATC
1 TGAAAAGTTATATC
233990 CAAAAAGATA
Statistics
Matches: 119, Mismatches: 37, Indels: 25
0.66 0.20 0.14
Matches are distributed among these distances:
12 3 0.03
13 26 0.22
14 54 0.45
15 33 0.28
16 3 0.03
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.35
Consensus pattern (14 bp):
TGAAAAGTTATATC
Found at i:234822 original size:10 final size:11
Alignment explanation
Indices: 234805--234830 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
234795 AGAAGAGAAT
234805 GAAAAAAAAAA
1 GAAAAAAAAAA
234816 GAAAAAAAAAA
1 GAAAAAAAAAA
234827 GAAA
1 GAAA
234831 GTTAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:237963 original size:50 final size:52
Alignment explanation
Indices: 237897--238017 Score: 156
Period size: 50 Copynumber: 2.4 Consensus size: 52
237887 TTTAAATTAT
* * **
237897 TTTCAAATCTAATGTTTTAAATAAATATAAATATTT-TTTTAATTTGTTTTG
1 TTTCAGATCTAGTGTTTTAAATAAATATAAATATTTATTTTAATTAATTTTG
* *
237948 TTT-AGATCTAGTGTTTTACATCAATATAAATATTTATTTTAATTAATTTTG
1 TTTCAGATCTAGTGTTTTAAATAAATATAAATATTTATTTTAATTAATTTTG
* *
237999 TTTCAGATCTTGTATTTTA
1 TTTCAGATCTAGTGTTTTA
238018 TATTTATATT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
50 28 0.47
51 19 0.32
52 13 0.22
ACGTcount: A:0.32, C:0.06, G:0.07, T:0.55
Consensus pattern (52 bp):
TTTCAGATCTAGTGTTTTAAATAAATATAAATATTTATTTTAATTAATTTTG
Found at i:239861 original size:21 final size:22
Alignment explanation
Indices: 239828--239871 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
239818 CTTTTACGTT
*
239828 AAAAAAGATGGAGAAG-AGAAG
1 AAAAAAGAGGGAGAAGCAGAAG
*
239849 AAAATAGAGGGAGAAGCAGAAG
1 AAAAAAGAGGGAGAAGCAGAAG
239871 A
1 A
239872 GAATGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.59, C:0.02, G:0.34, T:0.05
Consensus pattern (22 bp):
AAAAAAGAGGGAGAAGCAGAAG
Found at i:246847 original size:15 final size:16
Alignment explanation
Indices: 246827--246856 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
246817 AATGGTCATC
246827 CCTCTTG-TTTTCTTT
1 CCTCTTGCTTTTCTTT
246842 CCTCTTGCTTTTCTT
1 CCTCTTGCTTTTCTT
246857 CCCAACCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.30, G:0.07, T:0.63
Consensus pattern (16 bp):
CCTCTTGCTTTTCTTT
Found at i:248612 original size:24 final size:25
Alignment explanation
Indices: 248580--248627 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
248570 TTTGTTTGAT
*
248580 AGAGTAAAAA-AAAAAAAAAAAAAG
1 AGAGGAAAAATAAAAAAAAAAAAAG
* *
248604 AGAGGAAAAATTAAAAGAAAAAAA
1 AGAGGAAAAATAAAAAAAAAAAAA
248628 TTATTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (25 bp):
AGAGGAAAAATAAAAAAAAAAAAAG
Found at i:249157 original size:16 final size:17
Alignment explanation
Indices: 249136--249171 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
249126 CATACGTTTG
249136 TTTACTGAG-AAATTTT
1 TTTACTGAGTAAATTTT
*
249152 TTTACTGAGTTAATTTT
1 TTTACTGAGTAAATTTT
249169 TTT
1 TTT
249172 TAAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.25, C:0.06, G:0.11, T:0.58
Consensus pattern (17 bp):
TTTACTGAGTAAATTTT
Found at i:249404 original size:19 final size:19
Alignment explanation
Indices: 249367--249405 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
249357 TAAATATGTT
*
249367 AAAAAAAAAAAACAGATTG
1 AAAAAAAAAAAACAAATTG
* *
249386 AAAAAAAAAACATAAATTG
1 AAAAAAAAAAAACAAATTG
249405 A
1 A
249406 TGACAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (19 bp):
AAAAAAAAAAAACAAATTG
Found at i:256869 original size:57 final size:57
Alignment explanation
Indices: 256808--256928 Score: 179
Period size: 57 Copynumber: 2.1 Consensus size: 57
256798 TAAATGTCAC
* * *
256808 GACTTTGCTGCTGTTTGAGATCAACTTCCATCTTCAGGCTATTGGCTTGAATGTTGT
1 GACTTTGCTGCTGTTTGAGATCAACTTCCATCTTCAAGCTACTAGCTTGAATGTTGT
* * * *
256865 GACTTTGCTGTTGTTTGTGATCAACTTTCATCTTCAAGCTACTAGTTTGAATGTTGT
1 GACTTTGCTGCTGTTTGAGATCAACTTCCATCTTCAAGCTACTAGCTTGAATGTTGT
256922 GACTTTG
1 GACTTTG
256929 AGGATCAGTG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.43
Consensus pattern (57 bp):
GACTTTGCTGCTGTTTGAGATCAACTTCCATCTTCAAGCTACTAGCTTGAATGTTGT
Found at i:259251 original size:11 final size:11
Alignment explanation
Indices: 259237--259325 Score: 52
Period size: 11 Copynumber: 7.7 Consensus size: 11
259227 CAAATACTTC
259237 TAAAATAATAG
1 TAAAATAATAG
*
259248 TAAAATTAATAA
1 TAAAA-TAATAG
*
259260 TAAAATAAGAG
1 TAAAATAATAG
* * *
259271 TTATATAATAT
1 TAAAATAATAG
* *
259282 TCAAATAATAACAA
1 T--AA-AATAATAG
* *
259296 TAAATTAGTAG
1 TAAAATAATAG
*
259307 TAATATAATAG
1 TAAAATAATAG
259318 TAAAATAA
1 TAAAATAA
259326 CAACAAAACA
Statistics
Matches: 55, Mismatches: 19, Indels: 8
0.67 0.23 0.10
Matches are distributed among these distances:
11 36 0.65
12 12 0.22
13 1 0.02
14 6 0.11
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (11 bp):
TAAAATAATAG
Found at i:269516 original size:9 final size:9
Alignment explanation
Indices: 269502--269527 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
269492 CGATTTTCGA
269502 ATTCGAATT
1 ATTCGAATT
269511 ATTCGAATT
1 ATTCGAATT
269520 ATTCGAAT
1 ATTCGAAT
269528 AAACCAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (9 bp):
ATTCGAATT
Found at i:269750 original size:57 final size:57
Alignment explanation
Indices: 269675--269795 Score: 179
Period size: 57 Copynumber: 2.1 Consensus size: 57
269665 ACCCATCAAC
*
269675 AAACTAAACCCAAATATTTTTAAACCTAAATATAATTTCATTATTAAAAAACACTCAT
1 AAAC-AAACCCAAATATTTTTAAACCTAAATATAATTTCATTACTAAAAAACACTCAT
* * * * *
269733 AAACAAACTCAAATATTTTTAATCCTAAATATAATTTTATTCCTAAATAACACTCAT
1 AAACAAACCCAAATATTTTTAAACCTAAATATAATTTCATTACTAAAAAACACTCAT
269790 AAACAA
1 AAACAA
269796 CTCCTTTTCG
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 53 0.93
58 4 0.07
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (57 bp):
AAACAAACCCAAATATTTTTAAACCTAAATATAATTTCATTACTAAAAAACACTCAT
Found at i:269764 original size:16 final size:17
Alignment explanation
Indices: 269743--269781 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
269733 AAACAAACTC
269743 AAATAT-TTTTAATCCT
1 AAATATATTTTAATCCT
*
269759 AAATATAATTTTATTCCT
1 AAATAT-ATTTTAATCCT
269777 AAATA
1 AAATA
269782 ACACTCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
18 14 0.70
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATATATTTTAATCCT
Found at i:282264 original size:22 final size:23
Alignment explanation
Indices: 282223--282267 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
282213 GCTACATTAT
*
282223 TTATTTGTATCTCTTTTTTAATA
1 TTATTTGTATATCTTTTTTAATA
282246 TTATTTGTATAT-TTTTTTAATA
1 TTATTTGTATATCTTTTTTAATA
282268 GTTTAATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (23 bp):
TTATTTGTATATCTTTTTTAATA
Found at i:284565 original size:14 final size:15
Alignment explanation
Indices: 284546--284574 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
284536 CTCCCCCCTA
284546 CAACTC-CAAAAACC
1 CAACTCGCAAAAACC
284560 CAACTCGCAAAAACC
1 CAACTCGCAAAAACC
284575 TGATCCTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.41, G:0.03, T:0.07
Consensus pattern (15 bp):
CAACTCGCAAAAACC
Found at i:286352 original size:3 final size:3
Alignment explanation
Indices: 286335--286373 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
286325 AAGAAACCCA
* *
286335 AAG AAG -AG AAC AAG AAG AAG AAG AAG AAG AAG GAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
286374 GCGACAGAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.64, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:286637 original size:15 final size:15
Alignment explanation
Indices: 286617--286646 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
286607 AGGAAGCGAA
*
286617 AGGAAGAAGTAGAAG
1 AGGAAGAAGAAGAAG
286632 AGGAAGAAGAAGAAG
1 AGGAAGAAGAAGAAG
286647 CAAAGGTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (15 bp):
AGGAAGAAGAAGAAG
Found at i:299795 original size:21 final size:21
Alignment explanation
Indices: 299761--299803 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
299751 AAAATACTCG
* *
299761 AAAATAAATTTATTATTTTATA
1 AAAATAAATATATT-TTTAATA
299783 AAAAT-AATATATTTTTAATA
1 AAAATAAATATATTTTTAATA
299803 A
1 A
299804 TTCACAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 7 0.37
22 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAATAAATATATTTTTAATA
Found at i:299872 original size:16 final size:16
Alignment explanation
Indices: 299826--299874 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
299816 TAAATCTAGC
299826 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
299842 T-A-TAATATA--AAAA
1 TAATTAAT-TACCAAAA
299855 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
299871 TAAT
1 TAAT
299875 ATCCCCATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 5 0.18
14 7 0.25
15 7 0.25
16 9 0.32
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:299941 original size:30 final size:30
Alignment explanation
Indices: 299907--300007 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 30
299897 AAATGGTACA
*
299907 AAATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATTTATTTGGTACCATTTTAGT
** * * *
299937 AAAT-AAT-GGTGTGTGGATACCATTTTGGT
1 AAATAAATATTTATTTGG-TACCATTTTAGT
* *
299966 ATATAAATATATATTTGGTACCATTTTAGT
1 AAATAAATATTTATTTGGTACCATTTTAGT
*
299996 AAATAACTATTT
1 AAATAAATATTT
300008 TGGTATTTAA
Statistics
Matches: 53, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
28 4 0.08
29 17 0.32
30 27 0.51
31 5 0.09
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.45
Consensus pattern (30 bp):
AAATAAATATTTATTTGGTACCATTTTAGT
Found at i:301235 original size:43 final size:43
Alignment explanation
Indices: 301153--301237 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
301143 ATTAACATGT
* *
301153 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
301196 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
301238 TTAATTGTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:301872 original size:45 final size:46
Alignment explanation
Indices: 301807--301986 Score: 222
Period size: 45 Copynumber: 4.0 Consensus size: 46
301797 ATAGCTCATC
* * * * *
301807 AAGCCAAGGATATCAGCCTCAATTTGACGAGTCACCGTAATGCTCA
1 AAGCCAAGGATATTAGCCTCAGTTTGACGAGCCACCGCAATACTCA
* *
301853 AAG-CAAGTATATTAGCCTCAGTTTGACAAGCCACCGCAATACTC-
1 AAGCCAAGGATATTAGCCTCAGTTTGACGAGCCACCGCAATACTCA
*
301897 AAGCCAAGGATATTAGCCTTAGTTTGACGAGCCACCGCAATACTC-
1 AAGCCAAGGATATTAGCCTCAGTTTGACGAGCCACCGCAATACTCA
* * * * *
301942 AAGCCAAGCATATCAGGCTGAGTTTGACGGGCCACCGCAATACTC
1 AAGCCAAGGATATTAGCCTCAGTTTGACGAGCCACCGCAATACTC
301987 TACTCCTCTC
Statistics
Matches: 118, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
44 3 0.03
45 112 0.95
46 3 0.03
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (46 bp):
AAGCCAAGGATATTAGCCTCAGTTTGACGAGCCACCGCAATACTCA
Found at i:302004 original size:21 final size:20
Alignment explanation
Indices: 301978--302019 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 20
301968 ACGGGCCACC
301978 GCAATACTCTACTCCTCTCGG
1 GCAATACTCTACTCCT-TCGG
301999 GCAATACTCTACTCCTTCGG
1 GCAATACTCTACTCCTTCGG
302019 G
1 G
302020 GTAAATGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.19, C:0.36, G:0.17, T:0.29
Consensus pattern (20 bp):
GCAATACTCTACTCCTTCGG
Found at i:302141 original size:37 final size:37
Alignment explanation
Indices: 302096--302207 Score: 206
Period size: 37 Copynumber: 3.0 Consensus size: 37
302086 CTTCTCCCAC
302096 AACGTCTAAAAATTTTTACACTAATCCTTGCTTTCAT
1 AACGTCTAAAAATTTTTACACTAATCCTTGCTTTCAT
*
302133 AATGTCTAAAAATTTTTACACTAATCCTTGCTTTCAT
1 AACGTCTAAAAATTTTTACACTAATCCTTGCTTTCAT
*
302170 AACGTCTAAAAATTTTTACACTAATCCTTGTTTTCAT
1 AACGTCTAAAAATTTTTACACTAATCCTTGCTTTCAT
302207 A
1 A
302208 TAATCAATCG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (37 bp):
AACGTCTAAAAATTTTTACACTAATCCTTGCTTTCAT
Found at i:302453 original size:4 final size:4
Alignment explanation
Indices: 302434--302476 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
302424 ACACATTACA
* * *
302434 TTTC TTTC CTTC -TTC TTTC TTTC CTTC TTTC CTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
302477 CCGTTTATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTC
Found at i:302454 original size:15 final size:16
Alignment explanation
Indices: 302434--302472 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
302424 ACACATTACA
302434 TTTCTTTCCTTC-TTC
1 TTTCTTTCCTTCTTTC
302449 TTTCTTTCCTTCTTTC
1 TTTCTTTCCTTCTTTC
*
302465 CTTCTTTC
1 TTTCTTTC
302473 TTTCCCGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTCTTTCCTTCTTTC
Found at i:302461 original size:8 final size:8
Alignment explanation
Indices: 302435--302472 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
302425 CACATTACAT
302435 TTCTTTCC
1 TTCTTTCC
*
302443 TTC-TTCT
1 TTCTTTCC
302450 TTCTTTCC
1 TTCTTTCC
302458 TTCTTTCC
1 TTCTTTCC
302466 TTCTTTC
1 TTCTTTC
302473 TTTCCCGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (8 bp):
TTCTTTCC
Done.