Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397263.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_86.0, 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: 8461613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 85630 characters in sequence are not A, C, G, or T
File 1 of 18
Found at i:1456 original size:16 final size:16
Alignment explanation
Indices: 1435--1465 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1425 NNNNNNNNNN
1435 GGAACCCGGAACCCTT
1 GGAACCCGGAACCCTT
*
1451 GGAACCCTGAACCCT
1 GGAACCCGGAACCCT
1466 GAACCTTACA
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:0.26, C:0.39, G:0.23, T:0.13
Consensus pattern (16 bp):
GGAACCCGGAACCCTT
Found at i:6497 original size:32 final size:32
Alignment explanation
Indices: 6456--6535 Score: 160
Period size: 32 Copynumber: 2.5 Consensus size: 32
6446 GATCACGAGT
6456 TATAGTGCTTCCCATTTTCTTTTTGAAAAATA
1 TATAGTGCTTCCCATTTTCTTTTTGAAAAATA
6488 TATAGTGCTTCCCATTTTCTTTTTGAAAAATA
1 TATAGTGCTTCCCATTTTCTTTTTGAAAAATA
6520 TATAGTGCTTCCCATT
1 TATAGTGCTTCCCATT
6536 GATGGAAATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.46
Consensus pattern (32 bp):
TATAGTGCTTCCCATTTTCTTTTTGAAAAATA
Found at i:15213 original size:81 final size:81
Alignment explanation
Indices: 15078--15241 Score: 310
Period size: 81 Copynumber: 2.0 Consensus size: 81
15068 TTCCCTCTTT
*
15078 ATAGTATTAGCAAAGAATTACAAGGATGTAGAGTTCAAGTGATGCATGCATGCATGTGTGAGTAT
1 ATAGTATTAGCAAAGAATTACAAGGATGTAGAGTTCAAGTGATGCATGCATGCATGTGTGAGTAA
15143 TGGGAAAAGCCAAGTA
66 TGGGAAAAGCCAAGTA
*
15159 ATAGTATTAGCGAAGAATTACAAGGATGTAGAGTTCAAGTGATGCATGCATGCATGTGTGAGTAA
1 ATAGTATTAGCAAAGAATTACAAGGATGTAGAGTTCAAGTGATGCATGCATGCATGTGTGAGTAA
15224 TGGGAAAAGCCAAGTA
66 TGGGAAAAGCCAAGTA
15240 AT
1 AT
15242 CATTTTACAA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.26
Consensus pattern (81 bp):
ATAGTATTAGCAAAGAATTACAAGGATGTAGAGTTCAAGTGATGCATGCATGCATGTGTGAGTAA
TGGGAAAAGCCAAGTA
Found at i:21676 original size:19 final size:19
Alignment explanation
Indices: 21645--21690 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
21635 TTGTCTATAA
*
21645 TTTCTTCTCTCTCTAAGTAC
1 TTTCTT-TCTCTCTAAATAC
21665 TTTCTTTCTCTCTAAATAC
1 TTTCTTTCTCTCTAAATAC
21684 TTTCTTT
1 TTTCTTT
21691 TTTAGTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.15, C:0.26, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTCTTTCTCTCTAAATAC
Found at i:24171 original size:51 final size:51
Alignment explanation
Indices: 24089--24186 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
24079 AAAGGAAAAG
* * * *
24089 AAGAAAAAAGAGGCACTATTCATATATCTACTCTGATATTCATTAATTCAA
1 AAGAAAAAAGAAGCACTAGTCACATACCTACTCTGATATTCATTAATTCAA
*
24140 AAGAAAAAAGAAGCAGTAGTCACATACCTACTCTGATATTCATTAAT
1 AAGAAAAAAGAAGCACTAGTCACATACCTACTCTGATATTCATTAAT
24187 ACCAAAATGA
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:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (51 bp):
AAGAAAAAAGAAGCACTAGTCACATACCTACTCTGATATTCATTAATTCAA
Found at i:26098 original size:2 final size:2
Alignment explanation
Indices: 26091--26119 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
26081 AATAGAAAGC
26091 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
26120 CTCTTACTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27247 original size:51 final size:49
Alignment explanation
Indices: 27133--27257 Score: 133
Period size: 51 Copynumber: 2.5 Consensus size: 49
27123 CGCACATCAT
* *
27133 AGGCCCTTGGGCGAGCCAGCCCGACGGATGCCAGGAGGGCAAACGGCAC
1 AGGCCCATGGGCGAGCCAGCCCGACGGATGCCAGAAGGGCAAACGGCAC
* * * ** *
27182 AGGCCCCTGGGCGAGCTAGCCCGACAGGATGCTAGCAAGGGCGCACGGCTC
1 AGGCCCATGGGCGAGCCAGCCCGAC-GGATGCCAG-AAGGGCAAACGGCAC
* * *
27233 GGGCCCATGAGCGAGCCGGCCCGAC
1 AGGCCCATGGGCGAGCCAGCCCGAC
27258 CAAGGCTAGC
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
49 23 0.37
50 8 0.13
51 31 0.50
ACGTcount: A:0.20, C:0.34, G:0.38, T:0.07
Consensus pattern (49 bp):
AGGCCCATGGGCGAGCCAGCCCGACGGATGCCAGAAGGGCAAACGGCAC
Found at i:57862 original size:3 final size:3
Alignment explanation
Indices: 57854--57900 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
57844 CTCTACGCCT
* *
57854 CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG CAA CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
57901 AAGTCNNNNN
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.38, C:0.34, G:0.28, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:59614 original size:12 final size:12
Alignment explanation
Indices: 59597--59621 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59587 TGTTTTATGT
59597 ACCGAAATCACC
1 ACCGAAATCACC
59609 ACCGAAATCACC
1 ACCGAAATCACC
59621 A
1 A
59622 GTTAAAGAAG
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:0.44, C:0.40, G:0.08, T:0.08
Consensus pattern (12 bp):
ACCGAAATCACC
Found at i:65415 original size:2 final size:2
Alignment explanation
Indices: 65408--65441 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
65398 ATTTGGTTTA
65408 AT AT AT 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 AT AT AT
65442 GTAGAGAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65449 original size:2 final size:2
Alignment explanation
Indices: 65444--65476 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
65434 ATATATATGT
65444 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
65477 AACAACAGGC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:75605 original size:4 final size:4
Alignment explanation
Indices: 75596--75621 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
75586 ACTTTGTAAC
75596 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
75622 GCTGTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:107793 original size:16 final size:16
Alignment explanation
Indices: 107772--107805 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
107762 TTAATATATT
*
107772 TTAAATATATTATTAA
1 TTAAATATATTATCAA
*
107788 TTAAATTTATTATCAA
1 TTAAATATATTATCAA
107804 TT
1 TT
107806 CTTCTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATATATTATCAA
Found at i:125501 original size:2 final size:2
Alignment explanation
Indices: 125485--125524 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
125475 AAAGAGAGGG
* *
125485 TA TA CA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
125525 GCTTTTGGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:126270 original size:2 final size:2
Alignment explanation
Indices: 126265--126295 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
126255 TGTGCATGCA
*
126265 AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
126296 ATGTGACAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:140876 original size:2 final size:2
Alignment explanation
Indices: 140869--140895 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
140859 AAGATTGACC
140869 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
140896 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:142359 original size:29 final size:29
Alignment explanation
Indices: 142326--142427 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 29
142316 CTAAATTCTA
142326 ACAATCATAATTATTCGTTCAATTTAATT
1 ACAATCATAATTATTCGTTCAATTTAATT
** *
142355 ACAAT-ATAATTATT-GGAC-ATTTATTTCT
1 ACAATCATAATTATTCGTTCAATTTA-AT-T
*
142383 AGCAATCATAATTATTCATT-ATATTTAATT
1 A-CAATCATAATTATTCGTTCA-ATTTAATT
*
142413 GCAATCATAATTATT
1 ACAATCATAATTATT
142428 GCCTATATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
26 5 0.09
27 3 0.05
28 11 0.19
29 23 0.40
30 10 0.17
31 1 0.02
32 5 0.09
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (29 bp):
ACAATCATAATTATTCGTTCAATTTAATT
Found at i:142434 original size:29 final size:29
Alignment explanation
Indices: 142327--142441 Score: 94
Period size: 29 Copynumber: 4.0 Consensus size: 29
142317 TAAATTCTAA
** *
142327 CAATCATAATTATTCGTTCA-ATTTAATTA
1 CAATCATAATTATTCACT-ATATTTAATTG
* * * *
142356 CAAT-ATAATTATTGGACATTTATTT-CTAG
1 CAATCATAATTATT-CAC-TATATTTAATTG
*
142385 CAATCATAATTATTCATTATATTTAATTG
1 CAATCATAATTATTCACTATATTTAATTG
142414 CAATCATAATTATTGC-CTATATTTAATT
1 CAATCATAATTATT-CACTATATTTAATT
142442 AGTGTCTCAG
Statistics
Matches: 67, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
28 15 0.22
29 37 0.55
30 15 0.22
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (29 bp):
CAATCATAATTATTCACTATATTTAATTG
Found at i:144534 original size:5 final size:5
Alignment explanation
Indices: 144524--144550 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
144514 TGCCTTATTC
144524 TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT
144551 TTATCTCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:148463 original size:22 final size:22
Alignment explanation
Indices: 148435--148476 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
148425 GTTATAGGCG
* *
148435 TTACGTGATTTATTTTTAAGTA
1 TTACGTGACTAATTTTTAAGTA
148457 TTACGTGACTAATTTTTAAG
1 TTACGTGACTAATTTTTAAG
148477 CAATGCCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (22 bp):
TTACGTGACTAATTTTTAAGTA
Found at i:148563 original size:21 final size:21
Alignment explanation
Indices: 148539--148601 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
148529 ATCAGTCATG
148539 CAATGCCCAAAATCAATCACA
1 CAATGCCCAAAATCAATCACA
* * * *
148560 CAATACCTAAAAATTAGTCACA
1 CAATGCC-CAAAATCAATCACA
** *
148582 CAATGTTCAAAGTCAATCAC
1 CAATGCCCAAAATCAATCAC
148602 GTAATATTTA
Statistics
Matches: 30, Mismatches: 11, Indels: 2
0.70 0.26 0.05
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.46, C:0.27, G:0.06, T:0.21
Consensus pattern (21 bp):
CAATGCCCAAAATCAATCACA
Found at i:152927 original size:2 final size:2
Alignment explanation
Indices: 152922--152959 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
152912 GTCTGTGTGT
* *
152922 GA GA GA GT GA GT GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
152960 ATAGAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.50, T:0.05
Consensus pattern (2 bp):
GA
Found at i:157777 original size:6 final size:6
Alignment explanation
Indices: 157766--157804 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
157756 GTTCACGGAG
* *
157766 TAGAGC TAGAGC TAGAGC TAGAGA TACAGC TTAGAGC TA
1 TAGAGC TAGAGC TAGAGC TAGAGC TAGAGC -TAGAGC TA
157805 CACCTACACC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (6 bp):
TAGAGC
Found at i:159945 original size:22 final size:22
Alignment explanation
Indices: 159920--159961 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
159910 ATCCATATTA
*
159920 ATCAATTCAAATCGATTGAAAT
1 ATCAATACAAATCGATTGAAAT
* *
159942 ATCAATAGAAATTGATTGAA
1 ATCAATACAAATCGATTGAA
159962 TTTGATTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.31
Consensus pattern (22 bp):
ATCAATACAAATCGATTGAAAT
Found at i:167544 original size:2 final size:2
Alignment explanation
Indices: 167537--167575 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
167527 GGTTTCTATT
*
167537 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
167576 TTTGAGTGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:194323 original size:28 final size:28
Alignment explanation
Indices: 194278--194346 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
194268 TAAATAATAA
* *
194278 AAACATATAACAAATAAATAAATTACACC
1 AAACATA-AATAAGTAAATAAATTACACC
* * *
194307 AAATATAAATAAGTAAATACATTACATC
1 AAACATAAATAAGTAAATAAATTACACC
194335 AAACATAAATAA
1 AAACATAAATAA
194347 AATTTTAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 28 0.82
29 6 0.18
ACGTcount: A:0.62, C:0.13, G:0.01, T:0.23
Consensus pattern (28 bp):
AAACATAAATAAGTAAATAAATTACACC
Found at i:204463 original size:33 final size:33
Alignment explanation
Indices: 204408--204475 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
204398 TTTTGGATGA
* *
204408 ACTTGAACAAAATATGAGCTGACCCCCTCATCG
1 ACTTAAACAAAATATGAACTGACCCCCTCATCG
*
204441 ACTTAAACAGAATATGAACTGACCCCCTCATCG
1 ACTTAAACAAAATATGAACTGACCCCCTCATCG
204474 AC
1 AC
204476 GACTTATATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.31, G:0.13, T:0.21
Consensus pattern (33 bp):
ACTTAAACAAAATATGAACTGACCCCCTCATCG
Found at i:229431 original size:47 final size:45
Alignment explanation
Indices: 229383--229475 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
229373 AAAAAATATT
**
229383 AAGAGCTACCAATAAACAATTTCATGGGGAAGCAATTTCTTAAAATTA
1 AAGA-CTACCAATAAACAA-TT-AACGGGAAGCAATTTCTTAAAATTA
* *
229431 AAGACTACCAATAAATAATTAACGGGAAGTAATTTCTTAAAATTA
1 AAGACTACCAATAAACAATTAACGGGAAGCAATTTCTTAAAATTA
229476 TCATAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
45 22 0.54
46 2 0.05
47 13 0.32
48 4 0.10
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (45 bp):
AAGACTACCAATAAACAATTAACGGGAAGCAATTTCTTAAAATTA
Found at i:244456 original size:21 final size:21
Alignment explanation
Indices: 244432--244484 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
244422 AATTTTTAAG
244432 CATTGCGTAACAGACTTTAGA
1 CATTGCGTAACAGACTTTAGA
* * * * *
244453 CATTACTTGACTGACTTTGGA
1 CATTGCGTAACAGACTTTAGA
*
244474 CATTGTGTAAC
1 CATTGCGTAAC
244485 TAATTTTTAA
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (21 bp):
CATTGCGTAACAGACTTTAGA
Found at i:244508 original size:22 final size:22
Alignment explanation
Indices: 244483--244548 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
244473 ACATTGTGTA
*
244483 ACTAATTTTTAAGTATTGCGTG
1 ACTAATTTTTAAGTATTACGTG
** *
244505 ACTAA-TTTTAAACATTACGTA
1 ACTAATTTTTAAGTATTACGTG
*
244526 ACTAGTTTTTAAGTATTACGTG
1 ACTAATTTTTAAGTATTACGTG
244548 A
1 A
244549 TTAGTTGATA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 16 0.46
22 19 0.54
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (22 bp):
ACTAATTTTTAAGTATTACGTG
Found at i:269486 original size:39 final size:39
Alignment explanation
Indices: 269432--269511 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
269422 GATAGGAAAG
* *
269432 CTAACACAGATGCAATTAAACTTATTTGGTGCTCTTTTC
1 CTAACACAGATGCAATTAAACATATTTAGTGCTCTTTTC
269471 CTAACACAGATGCAATTAAACATATTTAGTGCTCTTTTC
1 CTAACACAGATGCAATTAAACATATTTAGTGCTCTTTTC
269510 CT
1 CT
269512 TGATGAAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (39 bp):
CTAACACAGATGCAATTAAACATATTTAGTGCTCTTTTC
Found at i:274003 original size:21 final size:20
Alignment explanation
Indices: 273956--274004 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
273946 TTATATTACA
**
273956 ATTTGAAATTTATGATTTAG
1 ATTTGAAATTTAAAATTTAG
*
273976 AGATTGAAATTTAAAATTTATG
1 A-TTTGAAATTTAAAATTTA-G
273998 ATTTGAA
1 ATTTGAA
274005 TATTCGAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 20 0.87
22 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (20 bp):
ATTTGAAATTTAAAATTTAG
Found at i:293776 original size:36 final size:36
Alignment explanation
Indices: 293736--293808 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
293726 GACAACTTAC
*
293736 CAACTCTCTGTTTATTCTATCCTAACTCTGTTCCTT
1 CAACTCTCTGTTTATTCTATCCTAACCCTGTTCCTT
*
293772 CAACTCTCTGTTTATTCTGTCCTAACCCTGTTCCTT
1 CAACTCTCTGTTTATTCTATCCTAACCCTGTTCCTT
293808 C
1 C
293809 CAGTATTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.15, C:0.33, G:0.07, T:0.45
Consensus pattern (36 bp):
CAACTCTCTGTTTATTCTATCCTAACCCTGTTCCTT
Found at i:297746 original size:147 final size:147
Alignment explanation
Indices: 297486--297800 Score: 488
Period size: 147 Copynumber: 2.1 Consensus size: 147
297476 CAATGATACC
* ** * *
297486 CCCTCCACCACCACCACCACCCTCTGTTTTCTCTGCTTTGGTTTCTTCACCAACCTTCCCCATTT
1 CCCTCCTCCACCACCACCACCCTCTGTTTTCTCTGCTTTACTTTCTTCACCAACCTTCACCACTT
* * * *
297551 CTTCCTTCTTGTTTTCATCAGGACTCTCTCTTACTTCACTTTCGGAGTGGTGAAAGAGGTTGGAT
66 CTTCCTTCTTGTTTTCATCAGGACTCCCTCTTACTTCACCTTCAGAGTGGTGAAAGAGGTTGGAC
*
297616 ACGATGTTGTTGATAAG
131 ACGATATTGTTGATAAG
* *
297633 CCCTCCTCCACCACCACTC-TCCTCTGTTTTCTCTGCTTTACTTTCTTCACCAACCTTGACCACT
1 CCCTCCTCCACCACCAC-CACCCTCTGTTTTCTCTGCTTTACTTTCTTCACCAACCTTCACCACT
* *
297697 TCTTCCTTTTTGTTTTCATCAGTACTCCCTCTTACTTCACCTTCAGAGTGGTGAAAGAGGTTGGA
65 TCTTCCTTCTTGTTTTCATCAGGACTCCCTCTTACTTCACCTTCAGAGTGGTGAAAGAGGTTGGA
297762 CACGATATTGTTGATAAG
130 CACGATATTGTTGATAAG
297780 CCCTCCTCCACCACCACCACC
1 CCCTCCTCCACCACCACCACC
297801 ACCCACTTCT
Statistics
Matches: 151, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
146 1 0.01
147 149 0.99
148 1 0.01
ACGTcount: A:0.18, C:0.34, G:0.13, T:0.35
Consensus pattern (147 bp):
CCCTCCTCCACCACCACCACCCTCTGTTTTCTCTGCTTTACTTTCTTCACCAACCTTCACCACTT
CTTCCTTCTTGTTTTCATCAGGACTCCCTCTTACTTCACCTTCAGAGTGGTGAAAGAGGTTGGAC
ACGATATTGTTGATAAG
Found at i:302078 original size:16 final size:18
Alignment explanation
Indices: 302046--302079 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
302036 TAGATCCGTC
302046 ATCACATAACAATAAATA
1 ATCACATAACAATAAATA
302064 ATCAC-TAAC-ATAAATA
1 ATCACATAACAATAAATA
302080 CAAAAATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.24
Consensus pattern (18 bp):
ATCACATAACAATAAATA
Found at i:311411 original size:2 final size:2
Alignment explanation
Indices: 311404--311428 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
311394 AAGTCTCAAT
311404 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
311429 TTTCGTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:313328 original size:25 final size:24
Alignment explanation
Indices: 313288--313337 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
313278 ATCGATATGT
313288 TTATTACATCTATTACATGACAAG
1 TTATTACATCTATTACATGACAAG
*
313312 TTATTATCATCTGTTACATGACAAG
1 TTATTA-CATCTATTACATGACAAG
313337 T
1 T
313338 CACTGATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (24 bp):
TTATTACATCTATTACATGACAAG
Found at i:316195 original size:48 final size:49
Alignment explanation
Indices: 316120--316221 Score: 172
Period size: 48 Copynumber: 2.1 Consensus size: 49
316110 TCTTTGTTTT
316120 ATTTATTTCAGACGAAAACTTTTTAATTACAATGG-AGAATTCTTGTATTC
1 ATTTATTTCAGAC-AAAACTTTTTAATTACAA-GGAAGAATTCTTGTATTC
316170 ATTTATTTCAGAC-AAACTTTTTAATTACAAGGAAGAATTCTTGTATTC
1 ATTTATTTCAGACAAAACTTTTTAATTACAAGGAAGAATTCTTGTATTC
316218 ATTT
1 ATTT
316222 GTTTTATTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
47 2 0.04
48 36 0.71
50 13 0.25
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (49 bp):
ATTTATTTCAGACAAAACTTTTTAATTACAAGGAAGAATTCTTGTATTC
Found at i:322846 original size:2 final size:2
Alignment explanation
Indices: 322839--322870 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
322829 ATCAGGAATG
322839 AT AT 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 AT AT
322871 TTCTGTTGAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:323453 original size:19 final size:19
Alignment explanation
Indices: 323429--323466 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
323419 CAAGGCAAGG
323429 TCCATGATTAAGCTCGAAA
1 TCCATGATTAAGCTCGAAA
323448 TCCATGATTAAGCTCGAAA
1 TCCATGATTAAGCTCGAAA
323467 ATTAAGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (19 bp):
TCCATGATTAAGCTCGAAA
Found at i:331673 original size:39 final size:39
Alignment explanation
Indices: 331619--331697 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
331609 GATGATGAAC
*
331619 GCTCGACTGATTGTCAGAGCATTTTTGAGACAAATGCAA
1 GCTCGACTGATTGTCAGAGCACTTTTGAGACAAATGCAA
331658 GCTCGACTGATTGTCAGAGCACTTTTGAGACAAATGCAA
1 GCTCGACTGATTGTCAGAGCACTTTTGAGACAAATGCAA
331697 G
1 G
331698 AATCTTGGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (39 bp):
GCTCGACTGATTGTCAGAGCACTTTTGAGACAAATGCAA
Found at i:336747 original size:21 final size:21
Alignment explanation
Indices: 336693--336747 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 21
336683 AATTTTAGTT
* * *
336693 ATATTTTAAAAATATTAATAC
1 ATATTTTAAAAAAATAAAAAC
* *
336714 -TA-TTTATACAAATAAAAAC
1 ATATTTTAAAAAAATAAAAAC
336733 ATATTTTAAAAAAAT
1 ATATTTTAAAAAAAT
336748 TATTCAATAT
Statistics
Matches: 25, Mismatches: 7, Indels: 4
0.69 0.19 0.11
Matches are distributed among these distances:
19 12 0.48
20 4 0.16
21 9 0.36
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATTTTAAAAAAATAAAAAC
Found at i:342327 original size:22 final size:22
Alignment explanation
Indices: 342267--342327 Score: 52
Period size: 22 Copynumber: 2.8 Consensus size: 22
342257 TTATAAAAGA
*
342267 TTAAAAAAAAAATATTTTTTAC
1 TTAAAAAATAAATATTTTTTAC
** * **
342289 TT-AAATTTTAATAATTTTTTTT
1 TTAAAAAATAAAT-ATTTTTTAC
342311 TTAAAAAATAAATATTT
1 TTAAAAAATAAATATTT
342328 AAAGAAAAAG
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
21 6 0.21
22 15 0.54
23 7 0.25
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAAAAAATAAATATTTTTTAC
Found at i:344305 original size:7 final size:7
Alignment explanation
Indices: 344288--344317 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
344278 AACAAGACGA
344288 AGGCTTTC
1 AGGC-TTC
344296 AGGCTTC
1 AGGCTTC
344303 AGGCTTC
1 AGGCTTC
344310 AGGCTTC
1 AGGCTTC
344317 A
1 A
344318 AGGTTCAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.30
Consensus pattern (7 bp):
AGGCTTC
Found at i:351724 original size:36 final size:36
Alignment explanation
Indices: 351677--351748 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
351667 TTTTTTATAT
* *
351677 GATAATTTCGAATTCACGTTCCTTCTTCTTTTCTTA
1 GATAACTTCGAATTCACATTCCTTCTTCTTTTCTTA
351713 GATAACTTCGAATTCACATTCCTTCTTCTTTTCTTA
1 GATAACTTCGAATTCACATTCCTTCTTCTTTTCTTA
351749 TTACTTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.21, C:0.24, G:0.07, T:0.49
Consensus pattern (36 bp):
GATAACTTCGAATTCACATTCCTTCTTCTTTTCTTA
Found at i:352978 original size:21 final size:21
Alignment explanation
Indices: 352952--352991 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
352942 AATAAGTCTC
352952 ACTATT-TAATAACTTTTTTTT
1 ACTATTCTAATAA-TTTTTTTT
*
352973 ACTATTCTAATTATTTTTT
1 ACTATTCTAATAATTTTTT
352992 GTTTTAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (21 bp):
ACTATTCTAATAATTTTTTTT
Found at i:370535 original size:21 final size:22
Alignment explanation
Indices: 370506--370547 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
370496 GATACAATAA
370506 AATTATTAAAAT-AAAATAAAT
1 AATTATTAAAATCAAAATAAAT
* *
370527 AATTTTTAAAGTCAAAATAAA
1 AATTATTAAAATCAAAATAAA
370548 ATGAATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AATTATTAAAATCAAAATAAAT
Found at i:379247 original size:80 final size:80
Alignment explanation
Indices: 379110--379269 Score: 250
Period size: 80 Copynumber: 2.0 Consensus size: 80
379100 TTTTCATATG
* * *
379110 AAGAGATAAGGTTTTGAAAATACACCAATAATTACAAATTTGGTTGAATGTTTATCTTTCTTTGG
1 AAGAGATAAGGTTTTGAAAATACACCAATAATTACAAATTTGATTGAAAGTTGATCTTTCTTTGG
379175 ATAATGAAGTTTGGT
66 ATAATGAAGTTTGGT
* *
379190 AAGAGATAA-GTTTATGAAAATACACCAATAATTGCAAGTTTGATTGAAAGTTGATCTTTCTTTG
1 AAGAGATAAGGTTT-TGAAAATACACCAATAATTACAAATTTGATTGAAAGTTGATCTTTCTTTG
*
379254 GATAATTAAGTTTGGT
65 GATAATGAAGTTTGGT
379270 TAAATGCCCA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
79 4 0.05
80 69 0.95
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (80 bp):
AAGAGATAAGGTTTTGAAAATACACCAATAATTACAAATTTGATTGAAAGTTGATCTTTCTTTGG
ATAATGAAGTTTGGT
Found at i:380235 original size:22 final size:22
Alignment explanation
Indices: 380210--380252 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
380200 GCTATTTTGC
*
380210 TTTTTGAAAGTGAGGAAAATGG
1 TTTTTAAAAGTGAGGAAAATGG
380232 TTTTTAAAAGTGAGGAAAATG
1 TTTTTAAAAGTGAGGAAAATG
380253 TTGAAAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.33
Consensus pattern (22 bp):
TTTTTAAAAGTGAGGAAAATGG
Found at i:380638 original size:2 final size:2
Alignment explanation
Indices: 380631--380657 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
380621 AGTACGATTC
380631 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 T
380658 TGAAAAGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:385527 original size:21 final size:22
Alignment explanation
Indices: 385486--385529 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
385476 ATATTTTTCA
*
385486 AAAAAATCTATAAATTATTTTT
1 AAAAAATCTATAAATAATTTTT
385508 AAAAAAT-T-TAAATAAGTTTTT
1 AAAAAATCTATAAATAA-TTTTT
385529 A
1 A
385530 TACTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 7 0.35
22 7 0.35
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAAAATCTATAAATAATTTTT
Found at i:385592 original size:24 final size:25
Alignment explanation
Indices: 385546--385594 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
385536 AATTAAGTTT
*
385546 AACCAAATTTTTATATTTTTATTTTA
1 AACCAAA-TTTTATATTTATATTTTA
*
385572 AACCAAA-TTTATCTTTATATTTT
1 AACCAAATTTTATATTTATATTTT
385595 TATTTTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
26 7 0.33
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (25 bp):
AACCAAATTTTATATTTATATTTTA
Found at i:385619 original size:30 final size:30
Alignment explanation
Indices: 385550--385619 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
385540 AAGTTTAACC
385550 AAATTTTTATATTTTTATTTTAAACCAAAT
1 AAATTTTTATATTTTTATTTTAAACCAAAT
** * * *
385580 TTATCTTTATATTTTTATTTTGAATCAAAT
1 AAATTTTTATATTTTTATTTTAAACCAAAT
385610 AAATTTTTAT
1 AAATTTTTAT
385620 GATTAATTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (30 bp):
AAATTTTTATATTTTTATTTTAAACCAAAT
Found at i:390494 original size:2 final size:2
Alignment explanation
Indices: 390487--390511 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
390477 CGTAAAATTC
390487 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
390512 ATTCTTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:409717 original size:173 final size:174
Alignment explanation
Indices: 409418--409730 Score: 450
Period size: 173 Copynumber: 1.8 Consensus size: 174
409408 AAAAGAAGTG
*
409418 AAAAAGATACCAACAAGCTACCTAAAACAGAAACAAAACTGATCAAAGACTTGAAATAAATTGAA
1 AAAAAGATACCAAAAAGCTACCTAAAACAGAAACAAAACTGATCAAAGACTTGAAATAAATTGAA
* * ** * * *
409483 AGAGAGAAATACTTACCGGGAATCAGACCGTTTCATTATTGAATTTGGAGAAAGAGAAAAAGATT
66 AGAGAGAAAGACTTACCAGGAATCAGACCACTCCATTATTGAATTTAGAGAAAGAGAAAAAGACT
*
409548 TAATATCCAATAATCTGAAAAAAATAAGAAATGAACCATGAATA
131 TAAGATCCAATAATCTGAAAAAAATAAGAAATGAACCATGAATA
* * *
409592 AAAAAGAATACCAAAAAGCTACCTAAACCA-AAA-TAAACTGATCAAAGACTTGAAATGAATTGA
1 AAAAAG-ATACCAAAAAGCTACCTAAAACAGAAACAAAACTGATCAAAGACTTGAAATAAATTGA
* * * * *
409655 AAGAGAGAAAGACTTACCAGGAATCTGATCACTCCCTTGTTGAATTTAGAGAAAGGGAAAAAGAC
65 AAGAGAGAAAGACTTACCAGGAATCAGACCACTCCATTATTGAATTTAGAGAAAGAGAAAAAGAC
409720 TTAAGATCCAA
130 TTAAGATCCAA
409731 AAAAAATTTT
Statistics
Matches: 121, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
173 91 0.75
174 9 0.07
175 21 0.17
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (174 bp):
AAAAAGATACCAAAAAGCTACCTAAAACAGAAACAAAACTGATCAAAGACTTGAAATAAATTGAA
AGAGAGAAAGACTTACCAGGAATCAGACCACTCCATTATTGAATTTAGAGAAAGAGAAAAAGACT
TAAGATCCAATAATCTGAAAAAAATAAGAAATGAACCATGAATA
Found at i:410174 original size:26 final size:27
Alignment explanation
Indices: 410145--410196 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
410135 CATTTTTCCC
*
410145 TTTTAATGAATAAAA-AGAATGTATTT
1 TTTTAATGAATAAAACAGAATATATTT
**
410171 TTTTGTTGAATAAAACAGAATATATT
1 TTTTAATGAATAAAACAGAATATATT
410197 ACCCCTCCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (27 bp):
TTTTAATGAATAAAACAGAATATATTT
Found at i:411172 original size:14 final size:15
Alignment explanation
Indices: 411145--411173 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
411135 TATTTGAAGC
411145 AAGATAATTAAAAAA
1 AAGATAATTAAAAAA
411160 AAGATAA-TAAAAAA
1 AAGATAATTAAAAAA
411174 TAATCAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AAGATAATTAAAAAA
Found at i:413693 original size:177 final size:176
Alignment explanation
Indices: 413429--413747 Score: 433
Period size: 177 Copynumber: 1.8 Consensus size: 176
413419 GAAACAAAAC
* ** ***
413429 TGATCAAAGACTTGAAATAAATTGAAAGAAAGAAATACTTACTGGGAATCAGACGGTTTCATTGT
1 TGATCAAAGACTTGAAATAAATTGAAAGAAAGAAAGACTTACCAGGAATCAGACCACTTCATTGT
* * * ** * *
413494 TGAATTTGGAGAAAGAGAAAAAGATTTAATATCCAATGATCT-GAAAAGAAAAAAAAGAAATGAA
66 TGAATTTAGAGAAAGAGAAAAAGACTTAAGATCCAAAAAT-TAAAAAAAAAAAAAAAG-AATGAA
413558 CCATGAATGAAAAAGAATACGAAAGAGCTATCTAAAGCCAAAATAAAT
129 CCATGAATGAAAAAGAATACGAAAGAGCTATCTAAAGCCAAAATAAAT
* * * *
413606 TGATCAAAGACTTGAAATGAATTGAAAGAGAGAAAGACTTACCAGGAATCTGACCACTTCCTTGT
1 TGATCAAAGACTTGAAATAAATTGAAAGAAAGAAAGACTTACCAGGAATCAGACCACTTCATTGT
* *
413671 TGAATTTAGAGAAAGGGAAAAAGACTTAAGATCCAAAAATTAAAAAAAAAAAAAAAGAATGAATC
66 TGAATTTAGAGAAAGAGAAAAAGACTTAAGATCCAAAAATTAAAAAAAAAAAAAAAGAATGAACC
*
413736 ATGAATGGAAAA
131 ATGAATGAAAAA
413748 CAAATACAAA
Statistics
Matches: 121, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
176 19 0.16
177 102 0.84
ACGTcount: A:0.50, C:0.10, G:0.18, T:0.21
Consensus pattern (176 bp):
TGATCAAAGACTTGAAATAAATTGAAAGAAAGAAAGACTTACCAGGAATCAGACCACTTCATTGT
TGAATTTAGAGAAAGAGAAAAAGACTTAAGATCCAAAAATTAAAAAAAAAAAAAAAGAATGAACC
ATGAATGAAAAAGAATACGAAAGAGCTATCTAAAGCCAAAATAAAT
Found at i:414168 original size:27 final size:27
Alignment explanation
Indices: 414121--414173 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
414111 CCATTTCCCC
* *
414121 TTTTATTTTAATAAAAAGAATGTATTT
1 TTTTATTTGAATAAAAAGAATATATTT
*
414148 TTTTA-TTGAATAAAACGGAATATATT
1 TTTTATTTGAATAAAA-AGAATATATT
414174 ACCCCTCCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (27 bp):
TTTTATTTGAATAAAAAGAATATATTT
Found at i:414763 original size:43 final size:43
Alignment explanation
Indices: 414715--414801 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
414705 GTTTAAATAT
414715 CAAATTAATTAGAATCTTATGATGTAGCCCAAATGATTATGAG
1 CAAATTAATTAGAATCTTATGATGTAGCCCAAATGATTATGAG
414758 CAAATTAATTAGAATCTTATGATGTAGCCCAAATGATTATGAG
1 CAAATTAATTAGAATCTTATGATGTAGCCCAAATGATTATGAG
414801 C
1 C
414802 TTGAACGGGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (43 bp):
CAAATTAATTAGAATCTTATGATGTAGCCCAAATGATTATGAG
Found at i:425571 original size:21 final size:20
Alignment explanation
Indices: 425537--425578 Score: 50
Period size: 19 Copynumber: 2.0 Consensus size: 20
425527 AAATAAGTTG
*
425537 ATTAGAAAATATATCTTTTATA
1 ATTAGAAAA-A-ATATTTTATA
425559 ATTA-AAAAAATATTTTATA
1 ATTAGAAAAAATATTTTATA
425578 A
1 A
425579 AAAATACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 10 0.53
20 1 0.05
21 4 0.21
22 4 0.21
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTAGAAAAAATATTTTATA
Found at i:425711 original size:18 final size:20
Alignment explanation
Indices: 425688--425735 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
425678 TGAAAATATT
425688 TAAATATTATTTAA-TAT-A
1 TAAATATTATTTAACTATAA
* *
425706 TTAATATTAGTTAACTATAA
1 TAAATATTATTTAACTATAA
425726 TAAATATTAT
1 TAAATATTAT
425736 AAACAATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 12 0.50
19 3 0.12
20 9 0.38
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
TAAATATTATTTAACTATAA
Found at i:425752 original size:9 final size:9
Alignment explanation
Indices: 425690--425758 Score: 50
Period size: 9 Copynumber: 7.1 Consensus size: 9
425680 AAAATATTTA
425690 AATATTATTT
1 AATATTA-TT
425700 AATA-TATT
1 AATATTATT
425708 AATATTAGTT
1 AATATTA-TT
* *
425718 AACTATAATA
1 AA-TATTATT
*
425728 AATATTATAAAC
1 AATATTAT---T
425740 AATATTATT
1 AATATTATT
425749 AATATTATT
1 AATATTATT
425758 A
1 A
425759 TTTGAATATA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
8 6 0.12
9 19 0.40
10 11 0.23
11 4 0.08
12 8 0.17
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (9 bp):
AATATTATT
Found at i:429446 original size:20 final size:19
Alignment explanation
Indices: 429412--429450 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
429402 ATTCCTGATT
429412 AAGTGTATGGTAATGGTAAA
1 AAGTGTATGGTAAT-GTAAA
429432 AAGTGTATTGG-AATGTAAA
1 AAGTGTA-TGGTAATGTAAA
429451 GAATATAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 10 0.56
21 3 0.17
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (19 bp):
AAGTGTATGGTAATGTAAA
Found at i:439254 original size:2 final size:2
Alignment explanation
Indices: 439247--439280 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
439237 TTTTCTTCAT
439247 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
439281 GACATATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:454988 original size:79 final size:80
Alignment explanation
Indices: 454855--455082 Score: 297
Period size: 80 Copynumber: 2.9 Consensus size: 80
454845 TCCTTAGGTG
* * * *
454855 TTTTCTGTGCTTGGAA-ACCCCTA-GATGCTTCT-TACTTGGAATGCCTCTGAGTGCTTCTGCGT
1 TTTT-TGTGCTTGGAACACCCTTATG-TGCTTCTGTACTTGGAATGCCCCTGGGTGCTTCTGCGC
454917 TTGGAACACCCT-AGACA
64 TTGGAACACCCTAAG-CA
*
454934 TTTTTGTGCTTGGAACACCCTTATGTGCTTTTGTACTT-GAATGCCCCTGGGTGCTTCTGCGCTT
1 TTTTTGTGCTTGGAACACCCTTATGTGCTTCTGTACTTGGAATGCCCCTGGGTGCTTCTGCGCTT
454998 GGAACACCCTAAGCA
66 GGAACACCCTAAGCA
* * * *
455013 TTTATGTTGCTTGGAACACCCTTATGTGCTTCTGTACTTGGAACGCCCCT-GGTGCTTTTGCACT
1 TTTTTG-TGCTTGGAACACCCTTATGTGCTTCTGTACTTGGAATGCCCCTGGGTGCTTCTGCGCT
455077 TGGAAC
65 TGGAAC
455083 GCTACTGGGC
Statistics
Matches: 133, Mismatches: 10, Indels: 11
0.86 0.06 0.07
Matches are distributed among these distances:
78 11 0.08
79 56 0.42
80 57 0.43
81 9 0.07
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (80 bp):
TTTTTGTGCTTGGAACACCCTTATGTGCTTCTGTACTTGGAATGCCCCTGGGTGCTTCTGCGCTT
GGAACACCCTAAGCA
Found at i:455052 original size:27 final size:27
Alignment explanation
Indices: 454832--455082 Score: 93
Period size: 26 Copynumber: 9.4 Consensus size: 27
454822 TGGACGTTTA
** * *
454832 TGTACTTGGAACGTCCTTAGGTGTTTTC
1 TGTACTTGGAACACCCCTAGGTG-CTTC
* *
454860 TGTGCTTGGAA-ACCCCTAGATGCTTC
1 TGTACTTGGAACACCCCTAGGTGCTTC
** *
454886 T-TACTTGGAATGCCTCT-GAGTGCTTC
1 TGTACTTGGAACACCCCTAG-GTGCTTC
*** **** *
454912 TGCGTTTGGAACA-CCCTAGACATTTT
1 TGTACTTGGAACACCCCTAGGTGCTTC
* * * *
454938 TGTGCTTGGAACACCCTTATGTGCTTT
1 TGTACTTGGAACACCCCTAGGTGCTTC
** *
454965 TGTACTT-GAATGCCCCTGGGTGCTTC
1 TGTACTTGGAACACCCCTAGGTGCTTC
** * *** *
454991 TGCGCTTGGAACA-CCCTAAGCATTTA
1 TGTACTTGGAACACCCCTAGGTGCTTC
* * *
455017 TGTTGCTTGGAACACCCTTATGTGCTTC
1 TG-TACTTGGAACACCCCTAGGTGCTTC
* *
455045 TGTACTTGGAACGCCCCT-GGTGCTTT
1 TGTACTTGGAACACCCCTAGGTGCTTC
*
455071 TGCACTTGGAAC
1 TGTACTTGGAAC
455083 GCTACTGGGC
Statistics
Matches: 156, Mismatches: 59, Indels: 18
0.67 0.25 0.08
Matches are distributed among these distances:
25 9 0.06
26 75 0.48
27 53 0.34
28 19 0.12
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.35
Consensus pattern (27 bp):
TGTACTTGGAACACCCCTAGGTGCTTC
Found at i:455090 original size:26 final size:26
Alignment explanation
Indices: 455038--455090 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
455028 ACACCCTTAT
* *
455038 GTGCTTCTGTACTTGGAACGCCCCTG
1 GTGCTTCTGCACTTGGAACGCCACTG
* *
455064 GTGCTTTTGCACTTGGAACGCTACTG
1 GTGCTTCTGCACTTGGAACGCCACTG
455090 G
1 G
455091 GCACTTCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.13, C:0.26, G:0.28, T:0.32
Consensus pattern (26 bp):
GTGCTTCTGCACTTGGAACGCCACTG
Found at i:455237 original size:25 final size:25
Alignment explanation
Indices: 455209--455261 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
455199 TTTTGTCTTG
* * *
455209 GAACGCCTTTGGTGCTTCTGCGCTT
1 GAACGCCCTAGGTGCTTCAGCGCTT
* *
455234 GAACTCCCTAGGTGCTTCAGCGTTT
1 GAACGCCCTAGGTGCTTCAGCGCTT
455259 GAA
1 GAA
455262 ACACTTCGGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.15, C:0.26, G:0.26, T:0.32
Consensus pattern (25 bp):
GAACGCCCTAGGTGCTTCAGCGCTT
Found at i:460025 original size:21 final size:23
Alignment explanation
Indices: 459986--460028 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
459976 TGTTGATATG
459986 TATACATCAAATACATATACGTA
1 TATACATCAAATACATATACGTA
*
460009 TATACAT-AAATA-TTATACGT
1 TATACATCAAATACATATACGT
460029 TTGACAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.35
Consensus pattern (23 bp):
TATACATCAAATACATATACGTA
Found at i:463276 original size:23 final size:24
Alignment explanation
Indices: 463250--463297 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
463240 TTAGATATTT
**
463250 TAAAA-TATTTTTTTTATTTTTTA
1 TAAAATTATTTTTCGTATTTTTTA
463273 TAAAATTATTTTTCGTATTTTTTA
1 TAAAATTATTTTTCGTATTTTTTA
463297 T
1 T
463298 TTTAAAAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (24 bp):
TAAAATTATTTTTCGTATTTTTTA
Found at i:464075 original size:17 final size:17
Alignment explanation
Indices: 464036--464084 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
464026 TTTTTAAAAT
* *
464036 TAAATTAAATATATTTTA
1 TAAAATAAAT-TATTTGA
464054 T-AAATAAATTATTTGA
1 TAAAATAAATTATTTGA
*
464070 TAAAATAATTTATTT
1 TAAAATAAATTATTT
464085 AAATTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 7 0.26
17 19 0.70
18 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TAAAATAAATTATTTGA
Found at i:464429 original size:15 final size:15
Alignment explanation
Indices: 464409--464437 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
464399 ATTTTTTATT
464409 TTATTTTTTAAAAAA
1 TTATTTTTTAAAAAA
464424 TTATTTTTTAAAAA
1 TTATTTTTTAAAAA
464438 TATTTGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATTTTTTAAAAAA
Found at i:479951 original size:2 final size:2
Alignment explanation
Indices: 479939--479970 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
479929 GTTAAAGCAA
479939 TC TC TC ATC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC -TC TC TC TC TC TC TC TC TC TC TC TC T
479971 TTTGACTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:489778 original size:2 final size:2
Alignment explanation
Indices: 489771--489800 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
489761 GCAACTTCTT
489771 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
489801 CCCTTGATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:492419 original size:2 final size:2
Alignment explanation
Indices: 492412--492436 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
492402 GCACCTCAAA
492412 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
492437 TTTGAAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:503559 original size:64 final size:64
Alignment explanation
Indices: 503486--503615 Score: 242
Period size: 64 Copynumber: 2.0 Consensus size: 64
503476 ATTGCCAAGC
*
503486 AAAAGTTGGTAAAGCAGCTGCAGAAATTTTCTCCATTAAAGCACAAGCTATCATTTTTATGGTG
1 AAAAGTTGGTAAAGCAGCTGCAGAAATTTTCTCCATCAAAGCACAAGCTATCATTTTTATGGTG
*
503550 AAAAGTTGGTACAGCAGCTGCAGAAATTTTCTCCATCAAAGCACAAGCTATCATTTTTATGGTG
1 AAAAGTTGGTAAAGCAGCTGCAGAAATTTTCTCCATCAAAGCACAAGCTATCATTTTTATGGTG
503614 AA
1 AA
503616 TGTGTTAGCT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (64 bp):
AAAAGTTGGTAAAGCAGCTGCAGAAATTTTCTCCATCAAAGCACAAGCTATCATTTTTATGGTG
Found at i:515697 original size:13 final size:13
Alignment explanation
Indices: 515679--515705 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
515669 ATCATTATCA
515679 TTCTTTAGTATTC
1 TTCTTTAGTATTC
515692 TTCTTTAGTATTC
1 TTCTTTAGTATTC
515705 T
1 T
515706 ATTGATGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (13 bp):
TTCTTTAGTATTC
Found at i:521896 original size:20 final size:20
Alignment explanation
Indices: 521871--521908 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
521861 TAACCAATCA
521871 TTTTTACTATTTAATCAAAT
1 TTTTTACTATTTAATCAAAT
*
521891 TTTTTACTGTTTAATCAA
1 TTTTTACTATTTAATCAA
521909 TCATTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTTACTATTTAATCAAAT
Found at i:521915 original size:20 final size:20
Alignment explanation
Indices: 521865--521916 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
521855 ATCTTATAAC
521865 CAATCATTTTTACTATTTAAT
1 CAATCA-TTTTACTATTTAAT
* *
521886 CAAAT-TTTTTACTGTTTAAT
1 C-AATCATTTTACTATTTAAT
521906 CAATCATTTTA
1 CAATCATTTTA
521917 TAATTGATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 3 0.12
20 19 0.73
21 1 0.04
22 3 0.12
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.52
Consensus pattern (20 bp):
CAATCATTTTACTATTTAAT
Found at i:525393 original size:38 final size:39
Alignment explanation
Indices: 525331--525409 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 39
525321 TTTCAAACGG
*
525331 GATGGTAAATATGAGGATGTAAATGGATAGTTGTTATTT
1 GATGGTAAATATGAGGATGTAAATGGATAGTTATTATTT
525370 GATGGTAAATAT-AGGATGTAAATGGATAGTTATTATTT
1 GATGGTAAATATGAGGATGTAAATGGATAGTTATTATTT
525408 GA
1 GA
525410 GTATTCACGA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 27 0.69
39 12 0.31
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (39 bp):
GATGGTAAATATGAGGATGTAAATGGATAGTTATTATTT
Found at i:525724 original size:2 final size:2
Alignment explanation
Indices: 525717--525741 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
525707 TAACTACTAT
525717 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
525742 TGCAAAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:526262 original size:20 final size:20
Alignment explanation
Indices: 526234--526271 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
526224 TTCTATGAAA
526234 TTATAAAAATTTTATATAAT
1 TTATAAAAATTTTATATAAT
* *
526254 TTATGAAAATTTTCTATA
1 TTATAAAAATTTTATATA
526272 TATAATTAAT
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:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
TTATAAAAATTTTATATAAT
Found at i:527039 original size:21 final size:21
Alignment explanation
Indices: 527013--527052 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
527003 TGAATACAGT
*
527013 TGGTTGGGTTGTCTTTATTAA
1 TGGTTGGGATGTCTTTATTAA
527034 TGGTTGGGATGTCTTTATT
1 TGGTTGGGATGTCTTTATT
527053 GCAGAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.05, G:0.30, T:0.53
Consensus pattern (21 bp):
TGGTTGGGATGTCTTTATTAA
Found at i:528873 original size:74 final size:75
Alignment explanation
Indices: 528769--528999 Score: 290
Period size: 74 Copynumber: 3.1 Consensus size: 75
528759 ACGTATTAAT
* * *
528769 TAGATTTGGAATATAAAAACGTA-CTTGATTCTTTATTCATAATTTGATACAAATCATCATAAAA
1 TAGATTTAGAATATAAAAACGTATCTAGATTCTTTATTCATAATTTGACACAAATCATCATAAAA
*
528833 ACATACAAAC
66 ACATACTAAC
* *
528843 TAGATTTAAAATATAAAAACGTATC-AGATTCTTTATTCATAATTTGACACAAATCATCTTAAAA
1 TAGATTTAGAATATAAAAACGTATCTAGATTCTTTATTCATAATTTGACACAAATCATCATAAAA
* *
528907 CCATACTAAG
66 ACATACTAAC
* * * *
528917 TAGATTTAGAATATAAAAACACTTTCTA-ATTTTTTTATTCATAATTTGACACAAAATCATAATA
1 TAGATTTAGAATATAAAAAC-GTATCTAGA-TTCTTTATTCATAATTTGACAC-AAATCATCATA
*
528981 CAAACATACTAAC
63 AAAACATACTAAC
528994 TA-ATTT
1 TAGATTT
529000 GTTTATTCAT
Statistics
Matches: 135, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
74 83 0.61
75 5 0.04
76 26 0.19
77 21 0.16
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (75 bp):
TAGATTTAGAATATAAAAACGTATCTAGATTCTTTATTCATAATTTGACACAAATCATCATAAAA
ACATACTAAC
Found at i:529027 original size:51 final size:51
Alignment explanation
Indices: 528942--529047 Score: 140
Period size: 51 Copynumber: 2.1 Consensus size: 51
528932 AAAACACTTT
* *
528942 CTAATTTTTTTATTCATAATTTGACACAAAATCATAATACAAACATACTAA
1 CTAATTTGTTTATTCATAATTTGACACAAAATCATAATAAAAACATACTAA
* * * * **
528993 CTAATTTGTTTATTCATAATTTGATAGAACATCATCATAAAAATGTACTAA
1 CTAATTTGTTTATTCATAATTTGACACAAAATCATAATAAAAACATACTAA
529044 CTAA
1 CTAA
529048 ATTTAAAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (51 bp):
CTAATTTGTTTATTCATAATTTGACACAAAATCATAATAAAAACATACTAA
Found at i:529864 original size:32 final size:32
Alignment explanation
Indices: 529823--529887 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
529813 CATAATACTT
529823 AGTTTTTCTTGTACTATCTTCTTCAAAAGTCA
1 AGTTTTTCTTGTACTATCTTCTTCAAAAGTCA
*
529855 AGTTTTTCTTGTACTATCTTGTTCAAAAGTCA
1 AGTTTTTCTTGTACTATCTTCTTCAAAAGTCA
529887 A
1 A
529888 AACCCTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (32 bp):
AGTTTTTCTTGTACTATCTTCTTCAAAAGTCA
Found at i:529977 original size:15 final size:15
Alignment explanation
Indices: 529957--530007 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
529947 ATCACATTCT
529957 CAAGAAATAGAAATG
1 CAAGAAATAGAAATG
* *
529972 CAAGAAATTGAAACG
1 CAAGAAATAGAAATG
*
529987 -AA-AGATAGAAATG
1 CAAGAAATAGAAATG
530000 CAGAGAAA
1 CA-AGAAA
530008 AAACCCAAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
13 8 0.30
14 3 0.11
15 14 0.52
16 2 0.07
ACGTcount: A:0.59, C:0.08, G:0.22, T:0.12
Consensus pattern (15 bp):
CAAGAAATAGAAATG
Found at i:532245 original size:165 final size:165
Alignment explanation
Indices: 531966--532293 Score: 446
Period size: 165 Copynumber: 2.0 Consensus size: 165
531956 CATTCAATTT
* *** * *
531966 TACGCCATGGCCTTCTTTATTAGAATCACCGGGAGAGTTAGCTCCTTCCTCGTTGAGAATCTCCT
1 TACGCCATGGCCTTCTTCATTAGAATCACCAACAGAGTTAGCCCCTTCCTCATTGAGAATCTCCT
* * ** *
532031 TGTTCTTGTTGCTCATCCTTAACTTGGTGATCAAGACGCACTTTCTTTCTGCGGTATCTGAGAC-
66 TGTTCATGTTGCTCATCCTTAACTTGGTGATCAAGACGCACTGTCTTTCTGCCATATATGAG-CT
* *
532095 CAGCACACAGAAAAGGAATTACGATAAACACAACCA
130 CACCACACAGAAAAGGAATAACGATAAACACAACCA
* *
532131 TACGTCATGGCCTTCTTCATTAGAATCACCAACAG-GATTTGCCCCTTCCTCATTGAGAATCTCC
1 TACGCCATGGCCTTCTTCATTAGAATCACCAACAGAG-TTAGCCCCTTCCTCATTGAGAATCTCC
* *
532195 TTGTTCATGTTGCTCAT-CTTCAATTTGGTGATCAAGACTCACTGTCTTTCTGCCATATATGAGC
65 TTGTTCATGTTGCTCATCCTT-AACTTGGTGATCAAGACGCACTGTCTTTCTGCCATATATGAGC
*
532259 TCACCATACAGAAAAGGAATAACGATAAACACAAC
129 TCACCACACAGAAAAGGAATAACGATAAACACAAC
532294 TATAGAAGAA
Statistics
Matches: 142, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
164 5 0.04
165 137 0.96
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (165 bp):
TACGCCATGGCCTTCTTCATTAGAATCACCAACAGAGTTAGCCCCTTCCTCATTGAGAATCTCCT
TGTTCATGTTGCTCATCCTTAACTTGGTGATCAAGACGCACTGTCTTTCTGCCATATATGAGCTC
ACCACACAGAAAAGGAATAACGATAAACACAACCA
Found at i:532370 original size:45 final size:45
Alignment explanation
Indices: 532306--532395 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
532296 TAGAAGAAAG
* *
532306 GATTAACAAGTTCAAAGACGGTTACATTTTTACTTTTTGTGCAAT
1 GATTAACAAGTTCAAAGACGGTTACATCTTTACTTTTTGTACAAT
*
532351 GATTAACAAGTTCAGAGACGGTTACATCTTTACTTTTTGTACAAT
1 GATTAACAAGTTCAAAGACGGTTACATCTTTACTTTTTGTACAAT
532396 TGGCTTGGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (45 bp):
GATTAACAAGTTCAAAGACGGTTACATCTTTACTTTTTGTACAAT
Found at i:534342 original size:21 final size:20
Alignment explanation
Indices: 534312--534355 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
534302 TGTGTTTTTG
534312 TTTTTATTTATTTATTTTATAA
1 TTTTTATTTATTT-TTTT-TAA
534334 TTTTT-TTTATTTTTTTTAA
1 TTTTTATTTATTTTTTTTAA
534353 TTT
1 TTT
534356 AAAAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.27
20 4 0.18
21 7 0.32
22 5 0.23
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTATTTATTTTTTTTAA
Found at i:534556 original size:15 final size:16
Alignment explanation
Indices: 534538--534567 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
534528 TTTTGATTCG
534538 GGTTTTTTT-TTTGTA
1 GGTTTTTTTCTTTGTA
534553 GGTTTTTTTCTTTGT
1 GGTTTTTTTCTTTGT
534568 TTCTTACAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.03, C:0.03, G:0.20, T:0.73
Consensus pattern (16 bp):
GGTTTTTTTCTTTGTA
Found at i:549609 original size:8 final size:8
Alignment explanation
Indices: 549596--549620 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
549586 TTAATTTAAT
549596 TTTTAAAA
1 TTTTAAAA
549604 TTTTAAAA
1 TTTTAAAA
549612 TTTTAAAA
1 TTTTAAAA
549620 T
1 T
549621 CGAACCGACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTTAAAA
Found at i:567889 original size:51 final size:51
Alignment explanation
Indices: 567823--568008 Score: 194
Period size: 51 Copynumber: 3.6 Consensus size: 51
567813 GTTTGATGGT
* * *
567823 AAATTATCTATCCACTTCTAATAGTAAAATTATTCTTAGGTTTTGATGATA
1 AAATTATCCATCCACTTCTAATAGTAAAATTATTCTTAGATTCTGATGATA
* * * *
567874 AAATGATCCATCCACTTC-AAGTGGTAAAATTATCCTTAGATTCTGATGGTA
1 AAATTATCCATCCACTTCTAA-TAGTAAAATTATTCTTAGATTCTGATGATA
** ** * * * *
567925 AAATTATCCATTTACTTCTTGTGGTAAAATTATTCTTAAATTCAGATAATA
1 AAATTATCCATCCACTTCTAATAGTAAAATTATTCTTAGATTCTGATGATA
* **
567976 AAATTATTCATCCACTTCTGGTAGTAAAATTAT
1 AAATTATCCATCCACTTCTAATAGTAAAATTAT
568009 AATTGAAATA
Statistics
Matches: 111, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
50 2 0.02
51 109 0.98
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (51 bp):
AAATTATCCATCCACTTCTAATAGTAAAATTATTCTTAGATTCTGATGATA
Found at i:567908 original size:26 final size:25
Alignment explanation
Indices: 567872--567957 Score: 75
Period size: 26 Copynumber: 3.4 Consensus size: 25
567862 GTTTTGATGA
* * *
567872 TAAAATGATCCATCCACTTCAAGTGG
1 TAAAATTATCCATACACTTC-TGTGG
* *
567898 TAAAATTATCCTTAGA-TTCTGATGG
1 TAAAATTATCCATACACTTCTG-TGG
**
567923 TAAAATTATCCATTTACTTCTTGTGG
1 TAAAATTATCCATACACTTC-TGTGG
567949 TAAAATTAT
1 TAAAATTAT
567958 TCTTAAATTC
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
24 1 0.02
25 19 0.39
26 27 0.55
27 2 0.04
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (25 bp):
TAAAATTATCCATACACTTCTGTGG
Found at i:567929 original size:25 final size:24
Alignment explanation
Indices: 567895--567982 Score: 79
Period size: 25 Copynumber: 3.5 Consensus size: 24
567885 CCACTTCAAG
567895 TGGTAAAATTATCCTTAGATTCTGA
1 TGGTAAAATTATCCTTA-ATTCTGA
*
567920 TGGTAAAATTATCCATTTACTTCTTG-
1 TGGTAAAATTATCC--TTAATTC-TGA
* *
567946 TGGTAAAATTATTCTTAAATTCAGA
1 TGGTAAAATTATCCTT-AATTCTGA
**
567971 TAATAAAATTAT
1 TGGTAAAATTAT
567983 TCATCCACTT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
24 3 0.06
25 28 0.54
26 16 0.31
27 5 0.10
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.42
Consensus pattern (24 bp):
TGGTAAAATTATCCTTAATTCTGA
Found at i:578948 original size:2 final size:2
Alignment explanation
Indices: 578941--578966 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
578931 AATAAGTGTT
578941 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
578967 ATGCTAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:591551 original size:17 final size:17
Alignment explanation
Indices: 591531--591564 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
591521 AACATTACGA
* *
591531 GTTCAAAGTCATTTCAG
1 GTTCAAACTAATTTCAG
591548 GTTCAAACTAATTTCAG
1 GTTCAAACTAATTTCAG
591565 ATCAGATTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (17 bp):
GTTCAAACTAATTTCAG
Found at i:610312 original size:29 final size:27
Alignment explanation
Indices: 610279--610354 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 27
610269 TTAAAAAAAT
*
610279 TTTAAATAAAATTGTATTGT-TTTATTATG
1 TTTAAATAAAATT-T-TTATATTT-TTATG
*
610308 TTT-AATAAAATTTTTATATTTTTATT
1 TTTAAATAAAATTTTTATATTTTTATG
610334 TTTAAATAAAAATTTATTATA
1 TTTAAAT-AAAATTT-TTATA
610355 ATTAATAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 10 0.24
27 7 0.17
28 16 0.39
29 8 0.20
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (27 bp):
TTTAAATAAAATTTTTATATTTTTATG
Found at i:611379 original size:171 final size:169
Alignment explanation
Indices: 611064--611390 Score: 451
Period size: 171 Copynumber: 1.9 Consensus size: 169
611054 TCTTTCTTTC
* * * * * * *
611064 TTTTTTTTAGATTTTTGGATATTAAGTCTTTTTCTCTTTCTCCAAATTCAACAATGGAGCGGTTT
1 TTTTTTTTAGATTATTGAATATTAAATCATTTTCTCTTTCCCCAAATTCAACAATGGAGCGATCT
* * * *
611129 GATTCTCGGTAAGTCTTTCTCTCTTTCAATTCATTTCAAGTCTTTGATCAGTTTATTTCGATTTT
66 GATTCTCAGTAAGTATTCCTCTCTTTCAATTCATTTCAAGTCCTTGATCAGTTTATTTCGATTTT
*
611194 AGGTAGCTTTTTTGGTTTTCTTTTTCATTCAGGGTTCATT
131 AGGTAGCTTTTTTGGTATT-TTTTTCATTCAGGGTTCATT
611234 TTTTTTTTCAGATTATTGAATATTAAATCATTTTCTCTTTCCCCAAATTCAACAATGGAGCGATC
1 TTTTTTTT-AGATTATTGAATATTAAATCATTTTCTCTTTCCCCAAATTCAACAATGGAGCGATC
* * ** *
611299 TGGTTCTCAGTAAGTATTCCTCTCTTTCAATTTATTTCAAGTCCTTGATTGGTTATATTTTTG-T
65 TGATTCTCAGTAAGTATTCCTCTCTTTCAATTCATTTCAAGTCCTTGATCAGTT-TA-TTTCGAT
611363 TTTAGGTAGC-TTTTTGGTATTTTTTTCA
128 TTTAGGTAGCTTTTTTGGTATTTTTTTCA
611391 CTTCTTTTCT
Statistics
Matches: 137, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
170 15 0.11
171 105 0.77
172 13 0.09
173 4 0.03
ACGTcount: A:0.20, C:0.15, G:0.14, T:0.51
Consensus pattern (169 bp):
TTTTTTTTAGATTATTGAATATTAAATCATTTTCTCTTTCCCCAAATTCAACAATGGAGCGATCT
GATTCTCAGTAAGTATTCCTCTCTTTCAATTCATTTCAAGTCCTTGATCAGTTTATTTCGATTTT
AGGTAGCTTTTTTGGTATTTTTTTCATTCAGGGTTCATT
Found at i:619969 original size:3 final size:3
Alignment explanation
Indices: 619961--619985 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
619951 TTCTTATTTG
619961 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
619986 CATTATTATT
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:634641 original size:34 final size:34
Alignment explanation
Indices: 634598--634672 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
634588 ACTTTGGATC
634598 ACATTCCAAGTGTTGGTATTTAAGTCCACAATTT
1 ACATTCCAAGTGTTGGTATTTAAGTCCACAATTT
634632 ACATTCCAAGTGTTGGTATTTAAGTCCACAATTT
1 ACATTCCAAGTGTTGGTATTTAAGTCCACAATTT
634666 ACTATTC
1 AC-ATTC
634673 ACTATCAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 36 0.90
35 4 0.10
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (34 bp):
ACATTCCAAGTGTTGGTATTTAAGTCCACAATTT
Found at i:652016 original size:28 final size:29
Alignment explanation
Indices: 651943--652022 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 29
651933 TATTTAAAAA
*
651943 ATTTTAAATAAATTTT-TA-ATATTTTGTT
1 ATTTT-AATAAATTTTATATATATATTGTT
*
651971 ATATTTAATTAAATTTTTATATTTATATT-TT
1 AT-TTTAA-TAAA-TTTTATATATATATTGTT
652002 ATTTTAATAAATTTTATATAT
1 ATTTTAATAAATTTTATATAT
652023 TTTTTTATAC
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
28 13 0.30
29 11 0.25
30 9 0.20
31 6 0.14
32 5 0.11
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (29 bp):
ATTTTAATAAATTTTATATATATATTGTT
Found at i:652022 original size:30 final size:28
Alignment explanation
Indices: 651943--652031 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 28
651933 TATTTAAAAA
*
651943 ATTTTAAATAAATTTTTAATATTTTGTTAT
1 ATTTT-AATAAATTTTT-ATATTTTATTAT
*
651973 A-TTTAATTAAATTTTTATATTTATATTTT
1 ATTTTAA-TAAATTTTTATATTT-TATTAT
*
652002 ATTTTAATAAATTTTATATATTTTTTTAT
1 ATTTTAATAAATTTT-TATATTTTATTAT
652031 A
1 A
652032 CAACGATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
28 8 0.16
29 30 0.59
30 13 0.25
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (28 bp):
ATTTTAATAAATTTTTATATTTTATTAT
Found at i:652140 original size:24 final size:24
Alignment explanation
Indices: 652109--652158 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
652099 ATTGATTAAT
*
652109 TATATATATTTGATATAAAATA-AA
1 TATATATATTTAAT-TAAAATATAA
652133 TATATATATTTAATTAAAATATAA
1 TATATATATTTAATTAAAATATAA
652157 TA
1 TA
652159 AAAATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TATATATATTTAATTAAAATATAA
Found at i:652167 original size:23 final size:23
Alignment explanation
Indices: 652114--652168 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
652104 TTAATTATAT
* * *
652114 ATATTTGATATAAAATAAATATAT
1 ATATTTAAT-TAAAATAAATAAAA
652138 ATATTTAATTAAAATATAATAAAA
1 ATATTTAATTAAAATA-AATAAAA
652162 AT-TTTAA
1 ATATTTAA
652169 AAATTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
ATATTTAATTAAAATAAATAAAA
Found at i:666070 original size:30 final size:30
Alignment explanation
Indices: 665949--666072 Score: 117
Period size: 30 Copynumber: 4.1 Consensus size: 30
665939 ACTGGTCGAT
* * *
665949 CATCTTCAGTAACGAGATCAGCTCCCACAA
1 CATCTTCAGTAACAAAATCAGCTCCCACTA
* *
665979 CTTCTTCAGTACCAAAATCAGCTCCC-CTTA
1 CATCTTCAGTAACAAAATCAGCTCCCAC-TA
* * ** *
666009 CTTCTTCAGTTATGAAATCAGC-CGCCGCTA
1 CATCTTCAGTAACAAAATCAGCTC-CCACTA
*
666039 CATCTTCTGTAACAAAATCAGCTCCCACTA
1 CATCTTCAGTAACAAAATCAGCTCCCACTA
666069 CATC
1 CATC
666073 GAAAAATTCA
Statistics
Matches: 75, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
29 2 0.03
30 71 0.95
31 2 0.03
ACGTcount: A:0.29, C:0.34, G:0.10, T:0.27
Consensus pattern (30 bp):
CATCTTCAGTAACAAAATCAGCTCCCACTA
Found at i:671765 original size:2 final size:2
Alignment explanation
Indices: 671760--671792 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
671750 TGTGTGTGTA
671760 AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
671793 CAGATTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:675630 original size:303 final size:310
Alignment explanation
Indices: 675068--675639 Score: 820
Period size: 303 Copynumber: 1.9 Consensus size: 310
675058 AATGTAAACA
* * *
675068 GCTATGACCATGAGCACTGCACTACTCCTTTTCTTTCAGAGTAAAGCTGAAACAGCAATTGAGCA
1 GCTATGACCATGAACACTGCACTACACCTTTCCTTTCAGAGTAAAGCTGAAACAGCAATTGAGCA
* **
675133 TATCATTTAATTTGGTGCCAGGAAGTCAACTACTATGACAATGCATGTTCACATAATATTATACT
66 TATCATTTAATTTGGTACCAAAAAGTCAACTACTATGACAATGCATGTTCACATAATA-TATACT
* * *
675198 ATGACAAGTCAACTACCAAGAAGAATGGATTTCACAATAAGCTGCAACACTTAGTCAATGCTAAA
130 ATGACAAGACAACTACCAAGAAGAATGGATTTCACAATAACCTGCAACACTCAGTCAATGCTAAA
* * *
675263 GCAAATTCACCAACTCCACGAAGGATAATGAAACACATCATAAATTCATGTCAACTTCAAGGTAA
195 GCAAATTCAACAACTCCACGAAGGATAACGAAACACATAATAAATTCATGTCAACTTCAAGGTAA
* *
675328 TATTCACACTCTTCATCCCATGACCTTCAGAATTAGCTCCAGCCCACATAG
260 CATACACACTCTTCATCCCATGACCTTCAGAATTAGCTCCAGCCCACATAG
* * *
675379 GCTATGACCATGAACACTGCACTGCACCTTTCCTTTCAGAGTAGAGCTG-AACAGCAATTGCA-T
1 GCTATGACCATGAACACTGCACTACACCTTTCCTTTCAGAGTAAAGCTGAAACAGCAATTG-AGC
*
675442 ATATCATTT-ATTTGGTACCAAAAAGTCAACTATTATGACAATGCATGTTCACATAATA-A-ACT
65 ATATCATTTAATTTGGTACCAAAAAGTCAACTACTATGACAATGCATGTTCACATAATATATACT
*
675504 ATGACAAGACAACTACCAAGAAGAA-GGAATTTCACAA-CACCTGC-A-ACTCAGTCAATGCTAA
130 ATGACAAGACAACTACCAAGAAGAATGG-ATTTCACAATAACCTGCAACACTCAGTCAATGCTAA
* *** * * *
675565 AGCAATTTCAACAACTCTGTGTAGGATAACGAAACGCATAATAAATTCATGTCAACTTTAAGGTA
194 AGCAAATTCAACAACTCCACGAAGGATAACGAAACACATAATAAATTCATGTCAACTTCAAGGTA
675630 ACATACACAC
259 ACATACACAC
675640 ACTAGTCACA
Statistics
Matches: 233, Mismatches: 26, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
303 78 0.33
304 1 0.00
305 7 0.03
306 36 0.15
307 1 0.00
309 45 0.19
310 20 0.09
311 45 0.19
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (310 bp):
GCTATGACCATGAACACTGCACTACACCTTTCCTTTCAGAGTAAAGCTGAAACAGCAATTGAGCA
TATCATTTAATTTGGTACCAAAAAGTCAACTACTATGACAATGCATGTTCACATAATATATACTA
TGACAAGACAACTACCAAGAAGAATGGATTTCACAATAACCTGCAACACTCAGTCAATGCTAAAG
CAAATTCAACAACTCCACGAAGGATAACGAAACACATAATAAATTCATGTCAACTTCAAGGTAAC
ATACACACTCTTCATCCCATGACCTTCAGAATTAGCTCCAGCCCACATAG
Found at i:691590 original size:30 final size:30
Alignment explanation
Indices: 691554--691616 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
691544 TTATCAAGCT
691554 GTTCCTCCTCATCCTTGGACACTGCAGTAG
1 GTTCCTCCTCATCCTTGGACACTGCAGTAG
*
691584 GTTCCTCCTCATCCTTGGACACTGCAGTTG
1 GTTCCTCCTCATCCTTGGACACTGCAGTAG
691614 GTT
1 GTT
691617 TTTCTTCCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.14, C:0.32, G:0.21, T:0.33
Consensus pattern (30 bp):
GTTCCTCCTCATCCTTGGACACTGCAGTAG
Found at i:698185 original size:2 final size:2
Alignment explanation
Indices: 698178--698208 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
698168 TAATTGGAAC
698178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
698209 GTTTAATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:720202 original size:18 final size:18
Alignment explanation
Indices: 720176--720211 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
720166 ATTACCAATC
720176 TTCTCTACCATATCATTG
1 TTCTCTACCATATCATTG
* *
720194 TTCTTTACCATCTCATTG
1 TTCTCTACCATATCATTG
720212 GCTGCTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.28, G:0.06, T:0.47
Consensus pattern (18 bp):
TTCTCTACCATATCATTG
Found at i:727662 original size:3 final size:3
Alignment explanation
Indices: 727654--727678 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
727644 CAAGGAGAAC
727654 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
727679 TGTCAGGTTT
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:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:729415 original size:18 final size:18
Alignment explanation
Indices: 729380--729422 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
729370 ATTTAAGAAA
* *
729380 TACTGCGACTGCTACTGC
1 TACTGCTACTGCCACTGC
*
729398 TACTGCTACTGCCGCTGC
1 TACTGCTACTGCCACTGC
*
729416 TTCTGCT
1 TACTGCT
729423 GCAGCTGCAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.35, G:0.21, T:0.33
Consensus pattern (18 bp):
TACTGCTACTGCCACTGC
Found at i:729422 original size:6 final size:6
Alignment explanation
Indices: 729380--729409 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
729370 ATTTAAGAAA
*
729380 TACTGC GACTGC TACTGC TACTGC TACTGC
1 TACTGC TACTGC TACTGC TACTGC TACTGC
729410 CGCTGCTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.33, G:0.20, T:0.30
Consensus pattern (6 bp):
TACTGC
Found at i:733752 original size:78 final size:78
Alignment explanation
Indices: 733591--733737 Score: 186
Period size: 78 Copynumber: 1.9 Consensus size: 78
733581 ACCATACACG
* * ** * * * ** *
733591 TTATCTAAATAGAACAAACATTATTTTGTATAAATATTGTAACTATATGGTGATTGATCTCTAAT
1 TTATTTAAACAGAACATGCATTATTTTGTATAAATATTATAACTATACGATGATCAATCCCTAAT
733656 TAACCTTTTAACA
66 TAACCTTTTAACA
* *
733669 TTATTTAAACAGAACATGCATTATTTTTTATAAATATTATAATTATACGATGATCAATCCCTAAT
1 TTATTTAAACAGAACATGCATTATTTTGTATAAATATTATAACTATACGATGATCAATCCCTAAT
733734 TAAC
66 TAAC
733738 TTTCTAATTA
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
78 57 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (78 bp):
TTATTTAAACAGAACATGCATTATTTTGTATAAATATTATAACTATACGATGATCAATCCCTAAT
TAACCTTTTAACA
Found at i:735380 original size:18 final size:18
Alignment explanation
Indices: 735357--735391 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
735347 ACAATCGAAT
735357 CGTAATCTCAATCATAAA
1 CGTAATCTCAATCATAAA
735375 CGTAATCTCAATCATAA
1 CGTAATCTCAATCATAA
735392 TCGTGTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.29
Consensus pattern (18 bp):
CGTAATCTCAATCATAAA
Found at i:735562 original size:2 final size:2
Alignment explanation
Indices: 735555--735580 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
735545 TAGACAACTA
735555 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
735581 TGGGAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:737405 original size:3 final size:3
Alignment explanation
Indices: 737391--737428 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
737381 TGGAAATAGA
*
737391 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
737429 CGGTGGCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:754894 original size:18 final size:20
Alignment explanation
Indices: 754850--754888 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
754840 ATATCACTCA
754850 ATAT-ATATATATATATATT
1 ATATAATATATATATATATT
754869 ATATAATAT-TATA-ATATT
1 ATATAATATATATATATATT
754887 AT
1 AT
754889 TAAATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 8 0.42
20 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATAATATATATATATATT
Done.