Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 68 of 97
Found at i:27374223 original size:111 final size:111
Alignment explanation
Indices: 27373883--27374690 Score: 981
Period size: 111 Copynumber: 7.1 Consensus size: 111
27373873 AACAAGAGGC
* **
27373883 GAATTGCACAAGTCACGCGCCACCGCTCTCGCAATATATAACAACAGGTCAA-ATAATATATAAA
1 GAATTGCACAAGTCACGCGCCACCACTCTCGC------T-ACAACAGGT-AACGCAATATATAAA
* * *
27373947 AACTAGTAACGCAATCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACAT
58 AACCAGTCACGCAAGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACAT
* * *
27374001 GAATTGCACAAGTCACGTGCCACCACTCTTGCAATACATAACAATAGGTCACGCAATATATAAAA
1 GAATTGCACAAGTCACGCGCCACCACTCTCGC--TAC--AAC---AGGTAACGCAATATATAAAA
* * **
27374066 ATCAGTCACGCAAGCCTAAAAAACTACTGAATAAAAGCCTTTAAACAACACAT
59 ACCAGTCACGCAAGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACAT
* * * *
27374119 GAATTGCACAAGTCACACGCCACCACTCACGCTACAACAGGTAATGCAATATATAAAAATCAGTC
1 GAATTGCACAAGTCACGCGCCACCACTCTCGCTACAACAGGTAACGCAATATATAAAAACCAGTC
* * * *
27374184 ACGCAAGTCTCAAAAACTACTAAACAAAAACCTCAAAACAACACAT
66 ACGCAAGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACAT
* * * * *
27374230 GAATTACACAAGTCATGCACCACCACTCTCGCTACAACAAGTAACGCAATATATAAAAACCAATC
1 GAATTGCACAAGTCACGCGCCACCACTCTCGCTACAACAGGTAACGCAATATATAAAAACCAGTC
*
27374295 ACGCAAGCCTAAAAAACTACTGAACAAAAACCTCAAAACAACACAT
66 ACGCAAGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACAT
* *
27374341 GAATTGCACAAGTCACGCGCCACCACTCACGCTACAACAAGTAACGCAATATATAAAAACCAGTC
1 GAATTGCACAAGTCACGCGCCACCACTCTCGCTACAACAGGTAACGCAATATATAAAAACCAGTC
* * * * *
27374406 ATGCAAGCCTAAAAAACTATTAAATAAAAGCCTCACAACAACACAT
66 ACGCAAGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACAT
* * * *
27374452 GAATTGCACAAGTCACGCGCCACCGCTCTTGCTATAATAGGTAACGCAATATATAAAAACCAGTC
1 GAATTGCACAAGTCACGCGCCACCACTCTCGCTACAACAGGTAACGCAATATATAAAAACCAGTC
* * *
27374517 ATGCATTGCCTAAAAAACTACTGAACAAAAGCCTCAAAATAACACAT
66 ACGCA-AGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACAT
* * * ** * *
27374564 GAATTGCACAAGTCATGTGCCACCACTTTCGCTACAACAGGTAACATAATATATAAAAACTAGCC
1 GAATTGCACAAGTCACGCGCCACCACTCTCGCTACAACAGGTAACGCAATATATAAAAACCAGTC
* * *
27374629 ACGCACTA-CATAAAAAATTACTGAACAAAAACCTCAAAACAACACAT
66 ACGCA--AGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACAT
27374676 GAATTGCACAAGTCA
1 GAATTGCACAAGTCA
27374691 GTCACGCACC
Statistics
Matches: 603, Mismatches: 79, Indels: 22
0.86 0.11 0.03
Matches are distributed among these distances:
111 327 0.54
112 143 0.24
113 3 0.00
114 5 0.01
115 3 0.00
116 3 0.00
117 1 0.00
118 118 0.20
ACGTcount: A:0.45, C:0.26, G:0.11, T:0.18
Consensus pattern (111 bp):
GAATTGCACAAGTCACGCGCCACCACTCTCGCTACAACAGGTAACGCAATATATAAAAACCAGTC
ACGCAAGCCTAAAAAACTACTGAACAAAAGCCTCAAAACAACACAT
Found at i:27375369 original size:30 final size:30
Alignment explanation
Indices: 27375333--27375422 Score: 162
Period size: 30 Copynumber: 3.0 Consensus size: 30
27375323 CTCCTACTGG
*
27375333 AATATGTGTAACTGGTCCCTCACACTCAAA
1 AATATGTGCAACTGGTCCCTCACACTCAAA
27375363 AATATGTGCAACTGGTCCCTCACACTCAAA
1 AATATGTGCAACTGGTCCCTCACACTCAAA
*
27375393 AATATGTGCAACTGGTCCCTCAAACTCAAA
1 AATATGTGCAACTGGTCCCTCACACTCAAA
27375423 GGCACCTCTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.24
Consensus pattern (30 bp):
AATATGTGCAACTGGTCCCTCACACTCAAA
Found at i:27376200 original size:103 final size:102
Alignment explanation
Indices: 27376022--27376220 Score: 326
Period size: 103 Copynumber: 1.9 Consensus size: 102
27376012 ATGCTCAACA
* * * *
27376022 AATATTCAGTCACGTAACGCCTGTCATGCAACGCTAACAAATATTCAGTCACGTAATGCCTTTAA
1 AATATTCAGTCACGTAACACCTGTCACGCAACACTAACAAATATTCAGTCACGTAATGCCTATAA
27376087 AGAACTCACGCAATGCTCAACAAATATTCAGTCAAGT
66 AGAACTCACGCAATGCTCAACAAATATTCAGTCAAGT
** *
27376124 AATATTCAGTCACGTATTACCTGTCACGCAACACTCAACATATATTCAGTCACGTAATGCCTATA
1 AATATTCAGTCACGTAACACCTGTCACGCAACACT-AACAAATATTCAGTCACGTAATGCCTATA
27376189 AAGAACTCACGCAATGCTCAACAAATATTCAG
65 AAGAACTCACGCAATGCTCAACAAATATTCAG
27376221 GCACCTAATG
Statistics
Matches: 89, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
102 30 0.34
103 59 0.66
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.26
Consensus pattern (102 bp):
AATATTCAGTCACGTAACACCTGTCACGCAACACTAACAAATATTCAGTCACGTAATGCCTATAA
AGAACTCACGCAATGCTCAACAAATATTCAGTCAAGT
Found at i:27388046 original size:11 final size:10
Alignment explanation
Indices: 27388032--27388075 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
27388022 ACCCATGGAG
27388032 AAAAAGAAAA
1 AAAAAGAAAA
27388042 GAAAAAGGAAAA
1 -AAAAA-GAAAA
*
27388054 AAATAGAAAA
1 AAAAAGAAAA
*
27388064 AAAGAGAAAA
1 AAAAAGAAAA
27388074 AA
1 AA
27388076 TTATTTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
10 16 0.53
11 9 0.30
12 5 0.17
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:27388061 original size:17 final size:18
Alignment explanation
Indices: 27388031--27388064 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
27388021 AACCCATGGA
27388031 GAAAAAGAAAAGAAAAAG
1 GAAAAAGAAAAGAAAAAG
*
27388049 GAAAAA-AATAGAAAAA
1 GAAAAAGAAAAGAAAAA
27388065 AAGAGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (18 bp):
GAAAAAGAAAAGAAAAAG
Found at i:27388105 original size:8 final size:8
Alignment explanation
Indices: 27388094--27388174 Score: 58
Period size: 8 Copynumber: 9.9 Consensus size: 8
27388084 AAATTATAAA
27388094 ATATTAAT
1 ATATTAAT
*
27388102 ATATTNATT
1 ATATT-AAT
27388111 AATATTAAT
1 -ATATTAAT
*
27388120 ATGATTAAA
1 AT-ATTAAT
*
27388129 ATATTAAA
1 ATATTAAT
27388137 ATATTAAT
1 ATATTAAT
* *
27388145 GT-TTTAT
1 ATATTAAT
*
27388152 TTATTAA-
1 ATATTAAT
27388159 ATTATTAAT
1 A-TATTAAT
27388168 ATATTAA
1 ATATTAA
27388175 ATTTTTAATG
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
7 5 0.09
8 36 0.62
9 12 0.21
10 5 0.09
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.49
Consensus pattern (8 bp):
ATATTAAT
Found at i:27388174 original size:16 final size:16
Alignment explanation
Indices: 27388090--27388183 Score: 68
Period size: 16 Copynumber: 5.8 Consensus size: 16
27388080 TTATAAATTA
*
27388090 TAAAATATTAATATAT
1 TAAATTATTAATATAT
27388106 TNATTAA-TATTAATATGAT
1 T-A--AATTATTAATAT-AT
* *
27388125 TAAAATATTAAAATAT
1 TAAATTATTAATATAT
* *
27388141 T-AATGT-TTTATTTAT
1 TAAAT-TATTAATATAT
27388156 TAAATTATTAATATAT
1 TAAATTATTAATATAT
*
27388172 TAAATTTTTAAT
1 TAAATTATTAAT
27388184 GAGTCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
15 10 0.16
16 28 0.45
17 9 0.15
18 10 0.16
19 5 0.08
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TAAATTATTAATATAT
Found at i:27388256 original size:8 final size:8
Alignment explanation
Indices: 27388245--27388272 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
27388235 CTAATATTTT
27388245 AATTATAA
1 AATTATAA
27388253 AATTATAA
1 AATTATAA
27388261 AATTATAA
1 AATTATAA
27388269 AATT
1 AATT
27388273 TTAATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AATTATAA
Found at i:27388524 original size:25 final size:25
Alignment explanation
Indices: 27388479--27388542 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 25
27388469 TTAATCATAA
27388479 TAATATTAAATTATAAATAAAATAT
1 TAATATTAAATTATAAATAAAATAT
*
27388504 TAATAATTAAATTAT-ACTAAAATAT
1 TAAT-ATTAAATTATAAATAAAATAT
27388529 TAATATTATAATTA
1 TAATATTA-AATTA
27388543 AATTATTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
24 4 0.11
25 22 0.61
26 10 0.28
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
TAATATTAAATTATAAATAAAATAT
Found at i:27388550 original size:45 final size:42
Alignment explanation
Indices: 27388449--27388552 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 42
27388439 ATTTGGAAAT
* * *
27388449 TAATTAAAATTATTAATATTTTAATCATAATAATATTAAATTA
1 TAATT-AAATTATTAATAATTAAATCATAAAAATATTAAATTA
* * *
27388492 TAAATAAAATATTAATAATTAAATTATACTAAAATATTAATATTA
1 TAATTAAATTATTAATAATTAAATCATA--AAAATATTAA-ATTA
27388537 TAATTAAATTATTAAT
1 TAATTAAATTATTAAT
27388553 TTTTAATTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
42 19 0.38
43 4 0.08
44 9 0.18
45 18 0.36
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (42 bp):
TAATTAAATTATTAATAATTAAATCATAAAAATATTAAATTA
Found at i:27388766 original size:16 final size:16
Alignment explanation
Indices: 27388745--27388775 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27388735 TAATTATTGT
27388745 ATTCTATTCTCACGTC
1 ATTCTATTCTCACGTC
*
27388761 ATTCTATTTTCACGT
1 ATTCTATTCTCACGT
27388776 AATAATTATT
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:0.19, C:0.26, G:0.06, T:0.48
Consensus pattern (16 bp):
ATTCTATTCTCACGTC
Found at i:27391480 original size:47 final size:47
Alignment explanation
Indices: 27391409--27391501 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 47
27391399 CTCCGGTGGC
*
27391409 ATAGTAATTCTAGCTAGTGATAGCAAAGTTCTATACAATTACAAAAG
1 ATAGTAATTCTACCTAGTGATAGCAAAGTTCTATACAATTACAAAAG
*
27391456 ATAGTAATTCTACCTAGTGGTAGCAAAGTTCTATACAATTACAAAA
1 ATAGTAATTCTACCTAGTGATAGCAAAGTTCTATACAATTACAAAA
27391502 ATTTTCCGCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (47 bp):
ATAGTAATTCTACCTAGTGATAGCAAAGTTCTATACAATTACAAAAG
Found at i:27394727 original size:25 final size:25
Alignment explanation
Indices: 27394680--27394728 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
27394670 TGGAAATTCT
*
27394680 ATTTCCAACGGAAAAATCGGTTGGC
1 ATTTCCAACGGAAAAATCCGTTGGC
*
27394705 ATTTCCAAC-GAAAATTTCCGTTGG
1 ATTTCCAACGGAAAA-ATCCGTTGG
27394729 AAATATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (25 bp):
ATTTCCAACGGAAAAATCCGTTGGC
Found at i:27395238 original size:35 final size:36
Alignment explanation
Indices: 27395174--27395254 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 36
27395164 ATTTTCTTTC
* * * *
27395174 ACAAAAATATTAAAATTTAAATTTTAATAA-TCAAAA
1 ACAAAAATCTTAAAACTTAAAATTAAATAACT-AAAA
27395210 ACAAAAATCTT-AAACTTAAAATTAAATAACTAAAA
1 ACAAAAATCTTAAAACTTAAAATTAAATAACTAAAA
*
27395245 ACAAATATCT
1 ACAAAAATCT
27395255 GGGGAACCAG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 28 0.72
36 11 0.28
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (36 bp):
ACAAAAATCTTAAAACTTAAAATTAAATAACTAAAA
Found at i:27396545 original size:89 final size:89
Alignment explanation
Indices: 27396436--27396636 Score: 339
Period size: 89 Copynumber: 2.2 Consensus size: 89
27396426 GCCGCCGATG
27396436 AAAGGAAGAAGTGAGAGAGAGAAGATCTGGGTTCCTGTGCCGTCGGTTCTAGAGAGAGTTGGGGC
1 AAAGGAAGAAGTGAGAGAGAGAAGATCTGGGTTCCTGTGCCGTCGGTTCTAGAGAGAGTTGGGGC
*
27396501 TTCAGGCTTGTGTCGTTGGCTAAA
66 TTCAGGCTTGTGTCGTCGGCTAAA
* *
27396525 AAAGGAAGAAGCGAGAGAGAGAAGATCTGGGTTCCTGTGTCGTCGGTTCTAGAGAGAGTTGGGGC
1 AAAGGAAGAAGTGAGAGAGAGAAGATCTGGGTTCCTGTGCCGTCGGTTCTAGAGAGAGTTGGGGC
* *
27396590 TTCGGGCTTGTGTCGTCGGCTGAA
66 TTCAGGCTTGTGTCGTCGGCTAAA
*
27396614 AAAGGAAGGAGTTGAGAGAGAGA
1 AAAGGAAGAAG-TGAGAGAGAGA
27396637 GCTGCGAGTT
Statistics
Matches: 104, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 94 0.90
90 10 0.10
ACGTcount: A:0.26, C:0.12, G:0.39, T:0.22
Consensus pattern (89 bp):
AAAGGAAGAAGTGAGAGAGAGAAGATCTGGGTTCCTGTGCCGTCGGTTCTAGAGAGAGTTGGGGC
TTCAGGCTTGTGTCGTCGGCTAAA
Found at i:27399244 original size:11 final size:11
Alignment explanation
Indices: 27399230--27399266 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
27399220 ACTCCGTGGT
27399230 AAATCCGTTGC
1 AAATCCGTTGC
*
27399241 AAATCTGTTGC
1 AAATCCGTTGC
*
27399252 AAATCCGTTGG
1 AAATCCGTTGC
27399263 AAAT
1 AAAT
27399267 ACAATGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (11 bp):
AAATCCGTTGC
Found at i:27402317 original size:59 final size:59
Alignment explanation
Indices: 27402225--27402385 Score: 277
Period size: 59 Copynumber: 2.7 Consensus size: 59
27402215 NNNNNNNNNN
*
27402225 ACTTAATTTAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTGAAATTCCTAG
1 ACTTAATATAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTGAAATTCCTAG
* * * *
27402284 ACTTAATCTAGGCTCGACCTATCTCACCACAGGTTCAATTTAAAAATTGAAATTTCTAG
1 ACTTAATATAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTGAAATTCCTAG
27402343 ACTTAATATAGGCTCGACCTATCTCACAACAGGTTCGATTTAA
1 ACTTAATATAGGCTCGACCTATCTCACAACAGGTTCGATTTAA
27402386 TTCTTTAATG
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 95 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.32
Consensus pattern (59 bp):
ACTTAATATAGGCTCGACCTATCTCACAACAGGTTCGATTTAAAAATTGAAATTCCTAG
Found at i:27415639 original size:5 final size:5
Alignment explanation
Indices: 27415629--27415702 Score: 53
Period size: 5 Copynumber: 14.2 Consensus size: 5
27415619 TTCCCTCTTT
* * *
27415629 TTTTA TTTTA TTTTA CTTTATA TTTTA TTTTA TTATAA TTTAA TTTTT
1 TTTTA TTTTA TTTTA -TTT-TA TTTTA TTTTA TT-TTA TTTTA TTTTA
*
27415677 TATTTA -TTTA -TTTA TTATTT TTTTA T
1 T-TTTA TTTTA TTTTA TT-TTA TTTTA T
27415703 GTGTCTACAA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
4 8 0.14
5 30 0.53
6 17 0.30
7 2 0.04
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:27415654 original size:22 final size:21
Alignment explanation
Indices: 27415629--27415697 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
27415619 TTCCCTCTTT
27415629 TTTTATTTTATTTTACTTTATA
1 TTTTATTTTATTTTA-TTTATA
*
27415651 TTTTATTTTATTATAATTTA-A
1 TTTTATTTTATT-TTATTTATA
*
27415672 TTTTTTATTTA-TTTATTTATTA
1 TTTTAT-TTTATTTTATTTA-TA
27415694 TTTT
1 TTTT
27415698 TTTATGTGTC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 6 0.15
21 7 0.17
22 25 0.62
23 2 0.05
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTATTTTATTTTATTTATA
Found at i:27415664 original size:15 final size:15
Alignment explanation
Indices: 27415632--27415698 Score: 59
Period size: 15 Copynumber: 4.4 Consensus size: 15
27415622 CCTCTTTTTT
27415632 TATTTTATTTTACTTTA
1 TATTTTATTTTA--TTA
27415649 TATTTTATTTTATTA
1 TATTTTATTTTATTA
*
27415664 TAATTTAATTTT-TTA
1 T-ATTTTATTTTATTA
*
27415679 TTTATTTA-TTTATTA
1 TAT-TTTATTTTATTA
27415694 T-TTTT
1 TATTTT
27415699 TTATGTGTCT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
13 3 0.07
14 5 0.11
15 15 0.34
16 9 0.20
17 12 0.27
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTTTATTTTATTA
Found at i:27422620 original size:23 final size:23
Alignment explanation
Indices: 27422569--27422621 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
27422559 GTTTAGAGTT
* * *
27422569 TGTGAAACGGCATGTTGGGAATG
1 TGTGACACGACATGATGGGAATG
27422592 TGTGACACGACATGATGGGAATG
1 TGTGACACGACATGATGGGAATG
27422615 TGTGACA
1 TGTGACA
27422622 TGGTTGTGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.11, G:0.36, T:0.25
Consensus pattern (23 bp):
TGTGACACGACATGATGGGAATG
Found at i:27422721 original size:58 final size:58
Alignment explanation
Indices: 27422592--27422786 Score: 266
Period size: 58 Copynumber: 3.4 Consensus size: 58
27422582 GTTGGGAATG
* *
27422592 TGTGACACGACATGATGGGAATGTGTGACATGGTTGTGACA-GGCAGGGTTTAGAGTT
1 TGTGACACGACATGGTGGGAATGTGTGACATGGTTGTGACATGACAGGGTTTAGAGTT
* *
27422649 TGTGACACGACATGGTTGGAATGTGTGACATGGTTGTGACATGATAGGGTTTAGAGTT
1 TGTGACACGACATGGTGGGAATGTGTGACATGGTTGTGACATGACAGGGTTTAGAGTT
* * * ** *
27422707 TGTGACACGCCATGGTGGGAATGTGTGACACGGTTGTGACATGCCAACGTTCAGAGTT
1 TGTGACACGACATGGTGGGAATGTGTGACATGGTTGTGACATGACAGGGTTTAGAGTT
* * *
27422765 TGTAACACGTCATGGAGGGAAT
1 TGTGACACGACATGGTGGGAAT
27422787 CTATGACACG
Statistics
Matches: 122, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
57 39 0.32
58 83 0.68
ACGTcount: A:0.25, C:0.13, G:0.34, T:0.28
Consensus pattern (58 bp):
TGTGACACGACATGGTGGGAATGTGTGACATGGTTGTGACATGACAGGGTTTAGAGTT
Found at i:27422817 original size:47 final size:47
Alignment explanation
Indices: 27422755--27422937 Score: 215
Period size: 47 Copynumber: 3.9 Consensus size: 47
27422745 ACATGCCAAC
* *
27422755 GTTCAGAGTTTGTAACACGTCATGGAGGGAATCTATGACACGTCAGA
1 GTTCAGAGTTTGTAACACGCCATGGAGGGAATCTATGACACGCCAGA
* * *
27422802 GTTCAGAGTTGGTAACACGCCATGGAGGGAATCTGTGACACGCCAGC
1 GTTCAGAGTTTGTAACACGCCATGGAGGGAATCTATGACACGCCAGA
* * * * *
27422849 GTTCAAAGTTCGTGACACACCATGGAGGGAATCTATGACACACCAGCA
1 GTTCAGAGTTTGTAACACGCCATGGAGGGAATCTATGACACGCCAG-A
* * ** *
27422897 -TTCATAGTTTGTGACATTCCATGGAGGGAATCTGTGACACG
1 GTTCAGAGTTTGTAACACGCCATGGAGGGAATCTATGACACG
27422938 ACAACATTCA
Statistics
Matches: 117, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
47 117 1.00
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.23
Consensus pattern (47 bp):
GTTCAGAGTTTGTAACACGCCATGGAGGGAATCTATGACACGCCAGA
Found at i:27422919 original size:94 final size:94
Alignment explanation
Indices: 27422741--27422952 Score: 255
Period size: 94 Copynumber: 2.3 Consensus size: 94
27422731 GTGACACGGT
* * * ** **
27422741 TGTGACATGCCAACGTTCAGAGTTTGTAACACGTCATGGAGGGAATCTATGACACGTCAGAGTTC
1 TGTGACACGCCAACGTTCAAAGTTCGTAACACACCATGGAGGGAATCTATGACACACCAGAGTTC
27422806 AGAGTTGGTAACACGCCATGGAGGGAATC
66 AGAGTTGGTAACACGCCATGGAGGGAATC
* *
27422835 TGTGACACGCCAGCGTTCAAAGTTCGTGACACACCATGGAGGGAATCTATGACACACCAGCA-TT
1 TGTGACACGCCAACGTTCAAAGTTCGTAACACACCATGGAGGGAATCTATGACACACCAG-AGTT
* * * **
27422899 CATAGTTTGTGACATTCCATGGAGGGAATC
65 CAGAGTTGGTAACACGCCATGGAGGGAATC
* * *
27422929 TGTGACACGACAACATTCATAGTT
1 TGTGACACGCCAACGTTCAAAGTT
27422953 TATCAGACTC
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
94 98 0.99
95 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.24
Consensus pattern (94 bp):
TGTGACACGCCAACGTTCAAAGTTCGTAACACACCATGGAGGGAATCTATGACACACCAGAGTTC
AGAGTTGGTAACACGCCATGGAGGGAATC
Found at i:27422965 original size:47 final size:47
Alignment explanation
Indices: 27422756--27422969 Score: 209
Period size: 47 Copynumber: 4.6 Consensus size: 47
27422746 CATGCCAACG
* * * *
27422756 TTCAGAGTTTGTAACACGT-CATGGAGGGAATCTATGACACGTCAG-A
1 TTCATAGTTTGTGACAC-TCCATGGAGGGAATCTGTGACACGACAGCA
* * * * * *
27422802 GTTCAGAGTTGGTAACACGCCATGGAGGGAATCTGTGACACGCCAGCG
1 -TTCATAGTTTGTGACACTCCATGGAGGGAATCTGTGACACGACAGCA
* * * *
27422850 TTCAAAGTTCGTGACACACCATGGAGGGAATCTATGACAC-ACCAGCA
1 TTCATAGTTTGTGACACTCCATGGAGGGAATCTGTGACACGA-CAGCA
* *
27422897 TTCATAGTTTGTGACATTCCATGGAGGGAATCTGTGACACGACAACA
1 TTCATAGTTTGTGACACTCCATGGAGGGAATCTGTGACACGACAGCA
* * *
27422944 TTCATAGTTTATCAGACTCCATGGAG
1 TTCATAGTTTGTGACACTCCATGGAG
27422970 ATCCGTGACA
Statistics
Matches: 141, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
47 140 0.99
48 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.24
Consensus pattern (47 bp):
TTCATAGTTTGTGACACTCCATGGAGGGAATCTGTGACACGACAGCA
Found at i:27423672 original size:31 final size:31
Alignment explanation
Indices: 27423634--27423830 Score: 245
Period size: 31 Copynumber: 6.4 Consensus size: 31
27423624 AGCGTTAGCG
* *
27423634 TGTTACAACATTTGAC-TTGATACGCATGGCA
1 TGTTACAACATTTTACATT-ATATGCATGGCA
*
27423665 TGTTACAACATTTTACATTATATGCATGGCG
1 TGTTACAACATTTTACATTATATGCATGGCA
* * *
27423696 TGTTACGACATTTTACGTTATACGCATGGCA
1 TGTTACAACATTTTACATTATATGCATGGCA
* *
27423727 TGTTACCACATTTTACATTATATGCATGACA
1 TGTTACAACATTTTACATTATATGCATGGCA
* * *
27423758 TGTTACAATATTTTACGTTATATGCATGGCG
1 TGTTACAACATTTTACATTATATGCATGGCA
* *
27423789 TGTTACCACATTTTAC-GTATATGCATGGCA
1 TGTTACAACATTTTACATTATATGCATGGCA
*
27423819 TGTTACCACATT
1 TGTTACAACATT
27423831 ATGGGTTAAC
Statistics
Matches: 145, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
30 24 0.17
31 119 0.82
32 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (31 bp):
TGTTACAACATTTTACATTATATGCATGGCA
Found at i:27423708 original size:62 final size:62
Alignment explanation
Indices: 27423634--27423830 Score: 281
Period size: 62 Copynumber: 3.2 Consensus size: 62
27423624 AGCGTTAGCG
* * *
27423634 TGTTACAACATTTGAC-TTGATACGCATGGCATGTTACAACATTTTACATTATATGCATGGCG
1 TGTTACAACATTTTACGTT-ATACGCATGGCATGTTACCACATTTTACATTATATGCATGGCA
* *
27423696 TGTTACGACATTTTACGTTATACGCATGGCATGTTACCACATTTTACATTATATGCATGACA
1 TGTTACAACATTTTACGTTATACGCATGGCATGTTACCACATTTTACATTATATGCATGGCA
* * * *
27423758 TGTTACAATATTTTACGTTATATGCATGGCGTGTTACCACATTTTAC-GTATATGCATGGCA
1 TGTTACAACATTTTACGTTATACGCATGGCATGTTACCACATTTTACATTATATGCATGGCA
*
27423819 TGTTACCACATT
1 TGTTACAACATT
27423831 ATGGGTTAAC
Statistics
Matches: 121, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
61 22 0.18
62 97 0.80
63 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (62 bp):
TGTTACAACATTTTACGTTATACGCATGGCATGTTACCACATTTTACATTATATGCATGGCA
Found at i:27423793 original size:93 final size:92
Alignment explanation
Indices: 27423634--27423830 Score: 297
Period size: 93 Copynumber: 2.1 Consensus size: 92
27423624 AGCGTTAGCG
* *
27423634 TGTTACAACATTTGACTTGATACGCATGGCATGTTACAACATTTTACATTATATGCATGGCGTGT
1 TGTTACCACATTTGACTTGATACGCATGACATGTTACAACATTTTACATTATATGCATGGCGTGT
*
27423699 TACGACATTTTACGTTATACGCATGGCA
66 TACCACATTTTACG-TATACGCATGGCA
* * * *
27423727 TGTTACCACATTTTACATT-ATATGCATGACATGTTACAATATTTTACGTTATATGCATGGCGTG
1 TGTTACCACATTTGAC-TTGATACGCATGACATGTTACAACATTTTACATTATATGCATGGCGTG
*
27423791 TTACCACATTTTACGTATATGCATGGCA
65 TTACCACATTTTACGTATACGCATGGCA
27423819 TGTTACCACATT
1 TGTTACCACATT
27423831 ATGGGTTAAC
Statistics
Matches: 95, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
92 24 0.25
93 69 0.73
94 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (92 bp):
TGTTACCACATTTGACTTGATACGCATGACATGTTACAACATTTTACATTATATGCATGGCGTGT
TACCACATTTTACGTATACGCATGGCA
Found at i:27427644 original size:118 final size:118
Alignment explanation
Indices: 27427457--27427906 Score: 536
Period size: 118 Copynumber: 3.9 Consensus size: 118
27427447 AAGTATCTGG
* * **
27427457 TTCCACTCAGCGTGTCACCACAA-TTGGGGCATGCCGTGTCACCCCACAATACAACAAGAAGTCA
1 TTCCACTCAGCGTGTCACCACAAGATGGGGCGTGCCGTGTCACCCCACAATACTGCAAGAAGTCA
* * *
27427521 GCGTGTCACCACAGAAATATGCATGAACACAGCGTGTTACGCCAACTATCGAC
66 GCGTGTCACCACAGAAATCTGCATGCACTCAGCGTGTTACGCCAACTATCGAC
* *
27427574 TTCCACTCAGCATGTCACCACAAGATGGGGCGTGCCGTGTCACCCCACAATACTGCAAGAAGTTA
1 TTCCACTCAGCGTGTCACCACAAGATGGGGCGTGCCGTGTCACCCCACAATACTGCAAGAAGTCA
* * * * *
27427639 GCGTGTCACCATAAAAATCTGCATGCACTCATCGTGTTACGCCAACTATCTAG
66 GCGTGTCACCACAGAAATCTGCATGCACTCAGCGTGTTACGCCAACTATCGAC
* * * * *
27427692 TTCCACTCAGCGTGCCACCATAAAATGTGGCGTGCCGTGTCACCCAACAATACTGCAAGAAGTCA
1 TTCCACTCAGCGTGTCACCACAAGATGGGGCGTGCCGTGTCACCCCACAATACTGCAAGAAGTCA
* * * *
27427757 GCGTGTCACCACAGAAATCTACATGCACTTAGCGTGTGACGCCAACTATATG-C
66 GCGTGTCACCACAGAAATCTGCATGCACTCAGCGTGTTACGCCAACTAT-CGAC
* * * * * *
27427810 TTCCACTTAGTGTGTCACCACAAGATGGGGTGTGTCATGTCACCCCACAATAATGC----A-TCA
1 TTCCACTCAGCGTGTCACCACAAGATGGGGCGTGCCGTGTCACCCCACAATACTGCAAGAAGTCA
* * * * *
27427870 ACATGTCACCACAAAAATCTGCATACACTCAACGTGT
66 GCGTGTCACCACAGAAATCTGCATGCACTCAGCGTGT
27427907 CAACTTAGCA
Statistics
Matches: 283, Mismatches: 48, Indels: 8
0.83 0.14 0.02
Matches are distributed among these distances:
113 33 0.12
114 1 0.00
117 22 0.08
118 227 0.80
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (118 bp):
TTCCACTCAGCGTGTCACCACAAGATGGGGCGTGCCGTGTCACCCCACAATACTGCAAGAAGTCA
GCGTGTCACCACAGAAATCTGCATGCACTCAGCGTGTTACGCCAACTATCGAC
Found at i:27431441 original size:22 final size:21
Alignment explanation
Indices: 27431387--27431426 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
27431377 CCCTAGAGAG
27431387 GAAAATTCAAGAGAAATTTGT
1 GAAAATTCAAGAGAAATTTGT
27431408 GAAAATTCAAGAGAAATTT
1 GAAAATTCAAGAGAAATTT
27431427 TTTGAATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.28
Consensus pattern (21 bp):
GAAAATTCAAGAGAAATTTGT
Found at i:27432518 original size:2 final size:2
Alignment explanation
Indices: 27432513--27432539 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27432503 TTGTGTTATC
27432513 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
27432540 GGTTTGAATT
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:27434818 original size:31 final size:31
Alignment explanation
Indices: 27434780--27434953 Score: 260
Period size: 31 Copynumber: 5.6 Consensus size: 31
27434770 CTAGAATACA
27434780 TAAAATGTGGTAACACGCCATGCATATAACG
1 TAAAATGTGGTAACACGCCATGCATATAACG
*
27434811 TAAAATGTTGTAACACGCCATGCATATAACG
1 TAAAATGTGGTAACACGCCATGCATATAACG
*
27434842 TAAAATGTGGTAACATGCCATGCATATAACG
1 TAAAATGTGGTAACACGCCATGCATATAACG
* * *
27434873 TAAAATGTTGTAACACGACATGCATATAACA
1 TAAAATGTGGTAACACGCCATGCATATAACG
* *
27434904 TAAAATCTGGTAA-ACACCATGCATATAACG
1 TAAAATGTGGTAACACGCCATGCATATAACG
* *
27434934 TAAGATGTTGTAACACGCCA
1 TAAAATGTGGTAACACGCCA
27434954 ATCACCACAA
Statistics
Matches: 126, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
30 24 0.19
31 102 0.81
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (31 bp):
TAAAATGTGGTAACACGCCATGCATATAACG
Found at i:27436998 original size:2 final size:2
Alignment explanation
Indices: 27436991--27437036 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
27436981 TTAATGAAAG
*
27436991 AT AT AT AT AT AT TT 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 AT AT AT AT
27437033 AT AT
1 AT AT
27437037 TGTCTCTAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:27440721 original size:25 final size:24
Alignment explanation
Indices: 27440670--27440729 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
27440660 ATGTGTGAAG
* *
27440670 ATATTTACTATGTATAGTGTATTA
1 ATATTTACTATATATAGTGTATAA
27440694 ATATATTACTATATATAGT-TAATAA
1 ATAT-TTACTATATATAGTGT-ATAA
*
27440719 ATACTTA-TATA
1 ATATTTACTATA
27440730 AAATATAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 4 0.13
24 8 0.26
25 19 0.61
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (24 bp):
ATATTTACTATATATAGTGTATAA
Found at i:27440797 original size:18 final size:18
Alignment explanation
Indices: 27440759--27440797 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
27440749 AGTCATAATA
*
27440759 TATATAATAGTATATTAT
1 TATATAATAGTAAATTAT
*
27440777 TATATAATAGTAAATTGT
1 TATATAATAGTAAATTAT
27440795 TAT
1 TAT
27440798 TGACTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (18 bp):
TATATAATAGTAAATTAT
Found at i:27440924 original size:18 final size:19
Alignment explanation
Indices: 27440901--27440946 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
27440891 TTTTAATAAT
27440901 TTAATATAACT-TACTATA
1 TTAATATAACTATACTATA
*
27440919 TTAATATAAATTATACTATA
1 TTAATAT-AACTATACTATA
*
27440939 TTACTATA
1 TTAATATA
27440947 GTTTATTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.29
19 4 0.17
20 13 0.54
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAATATAACTATACTATA
Found at i:27441054 original size:16 final size:17
Alignment explanation
Indices: 27441015--27441047 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27441005 CTATTTATTG
27441015 TATATTAATA-AATATAC
1 TATA-TAATATAATATAC
27441032 TATATAATATAATATA
1 TATATAATATAATATA
27441048 TTAATAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TATATAATATAATATAC
Found at i:27441060 original size:16 final size:16
Alignment explanation
Indices: 27441050--27441080 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27441040 ATAATATATT
27441050 AATAACTTAATATAAA
1 AATAACTTAATATAAA
*
27441066 AATAAGTTAATATAA
1 AATAACTTAATATAA
27441081 TAAGTTATAT
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:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (16 bp):
AATAACTTAATATAAA
Found at i:27446947 original size:37 final size:37
Alignment explanation
Indices: 27446906--27446987 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
27446896 CAACGAAGAG
* *
27446906 TCAAATCACCCGCAGTGTTGAAACAACTAGCAGAGGT
1 TCAAATCACCCGCAGTGTAGAAACAACTAGCAAAGGT
** **
27446943 TCAAATCATGCTTAGTGTAGAAACAACTAGCAAAGGT
1 TCAAATCACCCGCAGTGTAGAAACAACTAGCAAAGGT
27446980 TCAAATCA
1 TCAAATCA
27446988 AGCTCAATGC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (37 bp):
TCAAATCACCCGCAGTGTAGAAACAACTAGCAAAGGT
Found at i:27447010 original size:37 final size:37
Alignment explanation
Indices: 27446925--27446997 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
27446915 CCGCAGTGTT
* * * * *
27446925 GAAACAACTAGCAGAGGTTCAAATCATGCTTAGTGTA
1 GAAACAACTAGCAAAGGTTCAAATCAAGCTCAATGCA
27446962 GAAACAACTAGCAAAGGTTCAAATCAAGCTCAATGC
1 GAAACAACTAGCAAAGGTTCAAATCAAGCTCAATGC
27446998 CGAAGTAACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (37 bp):
GAAACAACTAGCAAAGGTTCAAATCAAGCTCAATGCA
Found at i:27448001 original size:20 final size:20
Alignment explanation
Indices: 27447976--27448013 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27447966 TTTATTACGC
27447976 GCATCTATCGATAAATTAAT
1 GCATCTATCGATAAATTAAT
* *
27447996 GCATCTATTGATAGATTA
1 GCATCTATCGATAAATTA
27448014 CCTTGAATTC
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:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (20 bp):
GCATCTATCGATAAATTAAT
Found at i:27451085 original size:2 final size:2
Alignment explanation
Indices: 27451073--27451137 Score: 112
Period size: 2 Copynumber: 31.5 Consensus size: 2
27451063 AAGACTTTAC
27451073 AT AT AT CAT 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 AT AT AT AT
27451116 AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT A-T AT A
27451138 CACAAACAAC
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 57 0.93
3 4 0.07
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27464459 original size:6 final size:6
Alignment explanation
Indices: 27464448--27464493 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
27464438 CATGCGCGCA
* *
27464448 CACATG CACATG CACATG CACATG CACACG CACACG CACATG CACA
1 CACATG CACATG CACATG CACATG CACATG CACATG CACATG CACA
27464494 CACACACACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.35, C:0.39, G:0.15, T:0.11
Consensus pattern (6 bp):
CACATG
Found at i:27464469 original size:18 final size:18
Alignment explanation
Indices: 27464448--27464505 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
27464438 CATGCGCGCA
* *
27464448 CACATGCACATGCACATG
1 CACATGCACACGCACACG
27464466 CACATGCACACGCACACG
1 CACATGCACACGCACACG
* *
27464484 CACATGCACACACACACA
1 CACATGCACACGCACACG
27464502 CACA
1 CACA
27464506 CTCACACACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.38, C:0.41, G:0.12, T:0.09
Consensus pattern (18 bp):
CACATGCACACGCACACG
Found at i:27464494 original size:12 final size:12
Alignment explanation
Indices: 27464448--27464499 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
27464438 CATGCGCGCA
*
27464448 CACATGCACATG
1 CACATGCACACG
*
27464460 CACATGCACATG
1 CACATGCACACG
*
27464472 CACACGCACACG
1 CACATGCACACG
*
27464484 CACATGCACACA
1 CACATGCACACG
27464496 CACA
1 CACA
27464500 CACACACTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.37, C:0.40, G:0.13, T:0.10
Consensus pattern (12 bp):
CACATGCACACG
Found at i:27465487 original size:36 final size:36
Alignment explanation
Indices: 27465416--27465565 Score: 140
Period size: 39 Copynumber: 4.0 Consensus size: 36
27465406 CTCAACTCAG
* * *
27465416 CTCATGTGCACTCCCACACCGCATATCGC-TAATATC
1 CTCATGTGCACTCCCACACCACACATGGCAT-ATATC
*
27465452 CTCATGTGCACTCCCACACTACACATGGCATATATC
1 CTCATGTGCACTCCCACACCACACATGGCATATATC
* * **
27465488 ATCATCATGTGCTCTCCCATACTGCACATGGCACATATCATC
1 --C-TCATGTGCACTCCCACACCACACATGG--CATAT-ATC
* *
27465530 ATCATGTGCTCTCCCACACCACACATGGCATATATC
1 CTCATGTGCACTCCCACACCACACATGGCATATATC
27465566 ATCGGCATGC
Statistics
Matches: 96, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
36 33 0.34
37 6 0.06
38 1 0.01
39 48 0.50
41 5 0.05
42 3 0.03
ACGTcount: A:0.27, C:0.36, G:0.11, T:0.26
Consensus pattern (36 bp):
CTCATGTGCACTCCCACACCACACATGGCATATATC
Found at i:27465506 original size:39 final size:39
Alignment explanation
Indices: 27465453--27465593 Score: 201
Period size: 39 Copynumber: 3.6 Consensus size: 39
27465443 GCTAATATCC
*
27465453 TCATGTGCACTCCCACACTACACATGGCATATATCATCA
1 TCATGTGCTCTCCCACACTACACATGGCATATATCATCA
* * *
27465492 TCATGTGCTCTCCCATACTGCACATGGCACATATCATCA
1 TCATGTGCTCTCCCACACTACACATGGCATATATCATCA
* *
27465531 TCATGTGCTCTCCCACACCACACATGGCATATATCATCG
1 TCATGTGCTCTCCCACACTACACATGGCATATATCATCA
* * *
27465570 GCATGCGCTCTCCCACACTGCACA
1 TCATGTGCTCTCCCACACTACACA
27465594 CTACTGGCAC
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.26, C:0.36, G:0.13, T:0.25
Consensus pattern (39 bp):
TCATGTGCTCTCCCACACTACACATGGCATATATCATCA
Found at i:27466508 original size:19 final size:19
Alignment explanation
Indices: 27466472--27466523 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
27466462 AAGGCAGGAG
* *
27466472 AAGGAAGAAGTAAGAAAAGA
1 AAGGAA-AAGAAAAAAAAGA
* *
27466492 AAGGAAAGGAAAAAAAAGG
1 AAGGAAAAGAAAAAAAAGA
27466511 AAGGAAAAGAAAA
1 AAGGAAAAGAAAA
27466524 TGAAAATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (19 bp):
AAGGAAAAGAAAAAAAAGA
Found at i:27466509 original size:15 final size:15
Alignment explanation
Indices: 27466485--27466528 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
27466475 GAAGAAGTAA
*
27466485 GAAAAGAAAGGAAAG
1 GAAAAAAAAGGAAAG
27466500 GAAAAAAAAGG-AAG
1 GAAAAAAAAGGAAAG
*
27466514 GAAAAGAAAATGAAA
1 GAAAA-AAAAGGAAA
27466529 ATTTTGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 8 0.32
15 15 0.60
16 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.02
Consensus pattern (15 bp):
GAAAAAAAAGGAAAG
Found at i:27475069 original size:16 final size:15
Alignment explanation
Indices: 27475040--27475078 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
27475030 GTTTCGTTTC
27475040 AAAAAGAATAAAAAATT
1 AAAAA-AATAAAAAA-T
*
27475057 AAAAAAATCAAAAAT
1 AAAAAAATAAAAAAT
27475072 AAAAAAA
1 AAAAAAA
27475079 AAGAGTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 8 0.38
17 5 0.24
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.13
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:27475079 original size:16 final size:16
Alignment explanation
Indices: 27475040--27475079 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
27475030 GTTTCGTTTC
*
27475040 AAAAAGAATAAAAAAT
1 AAAAAAAATAAAAAAT
* *
27475056 TAAAAAAATCAAAAAT
1 AAAAAAAATAAAAAAT
27475072 AAAAAAAA
1 AAAAAAAA
27475080 AGAGTTAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (16 bp):
AAAAAAAATAAAAAAT
Found at i:27477331 original size:36 final size:33
Alignment explanation
Indices: 27477257--27477333 Score: 84
Period size: 35 Copynumber: 2.3 Consensus size: 33
27477247 AGTTTTTTCG
*
27477257 CATTTATTTAGTTTATGCTTTTCATTATGTTAA
1 CATTTATTTAGTTTATGCTTTTAATTATGTTAA
* * *
27477290 C-TTTATTTAGTTTTATTGGCTTTTAATTGTTTTTA
1 CATTTATTTAG-TTTA-T-GCTTTTAATTATGTTAA
27477325 CATTTATTT
1 CATTTATTT
27477334 GAAGTTATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 9 0.25
33 5 0.14
34 1 0.03
35 14 0.39
36 7 0.19
ACGTcount: A:0.21, C:0.08, G:0.09, T:0.62
Consensus pattern (33 bp):
CATTTATTTAGTTTATGCTTTTAATTATGTTAA
Found at i:27478621 original size:16 final size:16
Alignment explanation
Indices: 27478608--27478650 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
27478598 TTAATTATTT
27478608 TTAGTTTTTTTTATAG
1 TTAGTTTTTTTTATAG
*
27478624 TTAGTTTTTTTTAAAG
1 TTAGTTTTTTTTATAG
*
27478640 TGAGTTATTTT
1 TTAGTT-TTTT
27478651 AATTTTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.65
Consensus pattern (16 bp):
TTAGTTTTTTTTATAG
Found at i:27478685 original size:21 final size:21
Alignment explanation
Indices: 27478648--27478688 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27478638 AGTGAGTTAT
*
27478648 TTTAATTTTATGTTTATTTAC
1 TTTAATTTGATGTTTATTTAC
27478669 TTTAATTTGAT-TATTATTTA
1 TTTAATTTGATGT-TTATTTA
27478689 TTAGTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (21 bp):
TTTAATTTGATGTTTATTTAC
Found at i:27480846 original size:2 final size:2
Alignment explanation
Indices: 27480839--27480866 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27480829 TTGTTATTGA
27480839 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
27480867 TATTTCTTGG
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:27495006 original size:43 final size:44
Alignment explanation
Indices: 27494891--27495058 Score: 191
Period size: 43 Copynumber: 3.9 Consensus size: 44
27494881 TTGTGTGATA
* *
27494891 ATGATGACCCAGCTATGTGCGATGTA-AGAGTGCACATGAGTTG
1 ATGATGACCCAGCTATGTGCGATGTAGGGAGTGCACATGAGCTG
*
27494934 ATGATGACCCAGCTATGTGCGATGT-GGGAGTGAACATGAGCTG
1 ATGATGACCCAGCTATGTGCGATGTAGGGAGTGCACATGAGCTG
** * * * *
27494977 ATGATGACCTGGCTATGTGTGA-GTAGGGAGTGCGCATAAGCCG
1 ATGATGACCCAGCTATGTGCGATGTAGGGAGTGCACATGAGCTG
* * * *
27495020 ATGATGATCCGGTTATGTGCGA-ATAGGGAGTGCACATGA
1 ATGATGACCCAGCTATGTGCGATGTAGGGAGTGCACATGA
27495059 TGATGAATGA
Statistics
Matches: 106, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
42 2 0.02
43 104 0.98
ACGTcount: A:0.26, C:0.15, G:0.34, T:0.24
Consensus pattern (44 bp):
ATGATGACCCAGCTATGTGCGATGTAGGGAGTGCACATGAGCTG
Found at i:27500874 original size:2 final size:2
Alignment explanation
Indices: 27500867--27500912 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
27500857 TTGCATAAAC
* *
27500867 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT -T AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27500908 AT AT A
1 AT AT A
27500913 AACACTAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:27502592 original size:39 final size:40
Alignment explanation
Indices: 27502532--27502611 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
27502522 TATTGTAAAG
* *
27502532 ACACCAATCATGGCTAGGTT-AAAAACCCCACTAAGGTGA
1 ACACCAATCATGGCAAGGTTAAAAAACCCCACTAAAGTGA
* *
27502571 ACACCAATCTTGGCAATGTTAAAAAACCCCACTAAAGTGA
1 ACACCAATCATGGCAAGGTTAAAAAACCCCACTAAAGTGA
27502611 A
1 A
27502612 TTATGGCCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 17 0.47
40 19 0.53
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.19
Consensus pattern (40 bp):
ACACCAATCATGGCAAGGTTAAAAAACCCCACTAAAGTGA
Found at i:27504591 original size:21 final size:21
Alignment explanation
Indices: 27504567--27504607 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
27504557 CATACTAATG
*
27504567 TAACATGATAACATGACCATA
1 TAACATGATAACATAACCATA
27504588 TAACATGATAACATAACCAT
1 TAACATGATAACATAACCAT
27504608 GTGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.24
Consensus pattern (21 bp):
TAACATGATAACATAACCATA
Found at i:27505512 original size:2 final size:2
Alignment explanation
Indices: 27505500--27505533 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
27505490 AGGTAAAATC
27505500 TA TA T- 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 TA T
27505534 TTTGAGACCC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:27506231 original size:2 final size:2
Alignment explanation
Indices: 27506218--27506267 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
27506208 ATAAGACTTA
*
27506218 AT AT AT AA 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 AT AT AT AT
27506260 AT AT AT AT
1 AT AT AT AT
27506268 TCTTTTCCCC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27517214 original size:24 final size:25
Alignment explanation
Indices: 27517186--27517241 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
27517176 GTCGCAACTG
27517186 CGTATATCA-CCCGTGGCCTAGCCA
1 CGTATATCATCCCGTGGCCTAGCCA
* *
27517210 TGTATATCATCCCGTGGCCTTGCCA
1 CGTATATCATCCCGTGGCCTAGCCA
27517235 CGTATAT
1 CGTATAT
27517242 ATCACAAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.20, C:0.32, G:0.20, T:0.29
Consensus pattern (25 bp):
CGTATATCATCCCGTGGCCTAGCCA
Found at i:27518569 original size:14 final size:13
Alignment explanation
Indices: 27518528--27518587 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 13
27518518 CATGCCGAAC
*
27518528 CTTCCTTCTTTTCT
1 CTTCTTTCTTTT-T
27518542 CTGT-TTT-TTTTT
1 CT-TCTTTCTTTTT
27518554 CTTCTTTCTTTCTT
1 CTTCTTTCTTT-TT
*
27518568 CTCCTTTCTTTTGT
1 CTTCTTTCTTTT-T
27518582 CTTCTT
1 CTTCTT
27518588 GGTTATGGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
11 1 0.03
12 6 0.16
13 8 0.21
14 22 0.58
15 1 0.03
ACGTcount: A:0.00, C:0.27, G:0.03, T:0.70
Consensus pattern (13 bp):
CTTCTTTCTTTTT
Found at i:27526394 original size:16 final size:16
Alignment explanation
Indices: 27526354--27526395 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
27526344 GACAAATATT
*
27526354 ACAAAAAATTACAATA
1 ACAAAAAATTAAAATA
* *
27526370 ATAAGAAATTAAAATA
1 ACAAAAAATTAAAATA
27526386 ACAAAAAATT
1 ACAAAAAATT
27526396 TTGAATATAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.21
Consensus pattern (16 bp):
ACAAAAAATTAAAATA
Found at i:27530207 original size:1 final size:1
Alignment explanation
Indices: 27530201--27530252 Score: 104
Period size: 1 Copynumber: 52.0 Consensus size: 1
27530191 TAAGGGAAAG
27530201 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27530253 AGTATAAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:27537101 original size:24 final size:23
Alignment explanation
Indices: 27537074--27537151 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 23
27537064 AATAACATGG
27537074 TAATACAAATTAAAAATATAAAAA
1 TAATA-AAATTAAAAATATAAAAA
* * *
27537098 TAATAATAAATAAAAAAATCAAAA
1 TAATAA-AATTAAAAATATAAAAA
* *
27537122 TCATTAAAATAAAAAATATATAAAA
1 T-AATAAAATTAAAAATATA-AAAA
*
27537147 AAATA
1 TAATA
27537152 GGTAAATAAC
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
23 1 0.02
24 32 0.78
25 8 0.20
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (23 bp):
TAATAAAATTAAAAATATAAAAA
Found at i:27537114 original size:18 final size:17
Alignment explanation
Indices: 27537087--27537151 Score: 60
Period size: 18 Copynumber: 3.8 Consensus size: 17
27537077 TACAAATTAA
*
27537087 AAATATAAAAATAATAAT
1 AAATAAAAAAATAA-AAT
27537105 AAATAAAAAAATCAAAAT
1 AAATAAAAAAAT-AAAAT
* * *
27537123 CATTAAAATAA-AAAAT
1 AAATAAAAAAATAAAAT
*
27537139 ATATAAAAAAATA
1 AAATAAAAAAATA
27537152 GGTAAATAAC
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
16 12 0.32
17 1 0.03
18 22 0.59
19 2 0.05
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATAAAAAAATAAAAT
Found at i:27537145 original size:34 final size:32
Alignment explanation
Indices: 27537086--27537150 Score: 85
Period size: 34 Copynumber: 2.0 Consensus size: 32
27537076 ATACAAATTA
*
27537086 AAAATATAAAAATAATAATAAATAAAAAAATC
1 AAAATATAAAAATAAAAATAAATAAAAAAATC
* *
27537118 AAAATCATTAAAATAAAAAATATATAAAAAAAT
1 AAAAT-ATAAAAAT-AAAAATAAATAAAAAAAT
27537151 AGGTAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 5 0.18
33 7 0.25
34 16 0.57
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (32 bp):
AAAATATAAAAATAAAAATAAATAAAAAAATC
Found at i:27537180 original size:50 final size:47
Alignment explanation
Indices: 27537074--27537192 Score: 116
Period size: 49 Copynumber: 2.4 Consensus size: 47
27537064 AATAACATGG
* *
27537074 TAATACAAATTAAAAATATAAAAATAATAATAAATAAAAAAATCAAAA
1 TAATA-AAATAAAAAATATAAAAAAAATAATAAATAAAAAAATCAAAA
* * *
27537122 TCATTAAAATAAAAAATATATAAAAAAATAGGTAAATAACAAAAA-CAATGA
1 T-AATAAAATAAAAAATATA-AAAAAAATA-ATAAATAA-AAAAATCAA-AA
*
27537173 TAATAAAAT-AATAATATAAA
1 TAATAAAATAAAAAATATAAA
27537193 CGAATGAAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
48 16 0.27
49 19 0.32
50 17 0.29
51 7 0.12
ACGTcount: A:0.70, C:0.04, G:0.03, T:0.24
Consensus pattern (47 bp):
TAATAAAATAAAAAATATAAAAAAAATAATAAATAAAAAAATCAAAA
Found at i:27537540 original size:27 final size:27
Alignment explanation
Indices: 27537510--27537562 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
27537500 AAAAATTACT
27537510 TGAT-AAAAATAATAAATAAATAATAAA
1 TGATAAAAAATAATAAA-AAATAATAAA
*
27537537 TGATAAAAAATGATAAAAAATAATAA
1 TGATAAAAAATAATAAAAAATAATAA
27537563 CAATTCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.25
Consensus pattern (27 bp):
TGATAAAAAATAATAAAAAATAATAAA
Found at i:27537547 original size:10 final size:10
Alignment explanation
Indices: 27537529--27537562 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
27537519 TAATAAATAA
*
27537529 ATAATAAATG
1 ATAAAAAATG
27537539 ATAAAAAATG
1 ATAAAAAATG
*
27537549 ATAAAAAATA
1 ATAAAAAATG
27537559 ATAA
1 ATAA
27537563 CAATTCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (10 bp):
ATAAAAAATG
Found at i:27537547 original size:17 final size:18
Alignment explanation
Indices: 27537512--27537559 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
27537502 AAATTACTTG
27537512 ATAA-AAATAATAAATAA
1 ATAATAAATAATAAATAA
*
27537529 ATAATAAATGATAAA-AA
1 ATAATAAATAATAAATAA
* *
27537546 ATGATAAAAAATAA
1 ATAATAAATAATAA
27537560 TAACAATTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (18 bp):
ATAATAAATAATAAATAA
Found at i:27537795 original size:15 final size:13
Alignment explanation
Indices: 27537775--27537836 Score: 65
Period size: 13 Copynumber: 4.7 Consensus size: 13
27537765 ATCGCTTATG
27537775 AAAAATATAATAA
1 AAAAATATAATAA
27537788 TAATAAATAT-ATAA
1 -AA-AAATATAATAA
*
27537802 AAATATATAA-AA
1 AAAAATATAATAA
*
27537814 AAATAGTATAATAA
1 AAA-AATATAATAA
27537828 AAAAATATA
1 AAAAATATA
27537837 TAATTTTTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
12 10 0.25
13 13 0.32
14 11 0.28
15 6 0.15
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (13 bp):
AAAAATATAATAA
Found at i:27537805 original size:10 final size:10
Alignment explanation
Indices: 27537783--27537839 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
27537773 TGAAAAATAT
27537783 AATA-ATAATA
1 AATATATAA-A
27537793 AATATATAAA
1 AATATATAAA
27537803 AATATATAAA
1 AATATATAAA
* *
27537813 AAAATAGT-AT
1 AATATA-TAAA
27537823 AATA-A-AAA
1 AATATATAAA
27537831 AATATATAA
1 AATATATAA
27537840 TTTTTGTTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
8 5 0.13
9 2 0.05
10 26 0.68
11 5 0.13
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (10 bp):
AATATATAAA
Found at i:27537818 original size:26 final size:28
Alignment explanation
Indices: 27537775--27537839 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
27537765 ATCGCTTATG
* * *
27537775 AAAAATATA-ATAATAATA-AAT-ATAT
1 AAAAATATATAAAAAAATAGAATAATAA
*
27537800 AAAAATATATAAAAAAATAGTATAATAA
1 AAAAATATATAAAAAAATAGAATAATAA
27537828 AAAAATATATAA
1 AAAAATATATAA
27537840 TTTTTGTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 9 0.27
26 7 0.21
27 2 0.06
28 15 0.45
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.28
Consensus pattern (28 bp):
AAAAATATATAAAAAAATAGAATAATAA
Found at i:27537829 original size:25 final size:25
Alignment explanation
Indices: 27537775--27537824 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
27537765 ATCGCTTATG
27537775 AAAAATATAATAATAATAAATATAT
1 AAAAATATAATAATAATAAATATAT
27537800 AAAAATAT-ATAA-AA-AAATAGTAT
1 AAAAATATAATAATAATAAATA-TAT
27537823 AA
1 AA
27537825 TAAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.21
23 7 0.29
24 4 0.17
25 8 0.33
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (25 bp):
AAAAATATAATAATAATAAATATAT
Found at i:27537838 original size:15 final size:15
Alignment explanation
Indices: 27537800--27537840 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
27537790 ATAAATATAT
27537800 AAAA-ATAT-ATAAA
1 AAAATATATAATAAA
27537813 AAAATAGTATAATAAA
1 AAAATA-TATAATAAA
27537829 AAAATATATAAT
1 AAAATATATAAT
27537841 TTTTGTTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.16
14 1 0.04
15 9 0.36
16 11 0.44
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (15 bp):
AAAATATATAATAAA
Found at i:27539702 original size:84 final size:84
Alignment explanation
Indices: 27539556--27539722 Score: 226
Period size: 84 Copynumber: 2.0 Consensus size: 84
27539546 CACCTCTTTT
* * * * *
27539556 AATCGATTTTGATTATAATAGTATAATAGAGCTTACACATATTTAAGCCTTGTTTCCTATTCTTT
1 AATCAATTTTGATGATAATAGTATAATAGAGCTTACACATATTCAAACCTTGTCTCCTATTCTTT
27539621 GATTATATTTCTAAATTGC
66 GATTATATTTCTAAATTGC
* * * ** * *
27539640 AATCAATTTTGATGATAATGGTATAATGGGGCTTATGCATATTCAAACTTTGTCTCTTATTCTTT
1 AATCAATTTTGATGATAATAGTATAATAGAGCTTACACATATTCAAACCTTGTCTCCTATTCTTT
27539705 GATTATATTTCTAAATTG
66 GATTATATTTCTAAATTG
27539723 TAAACAGTAT
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 71 1.00
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.46
Consensus pattern (84 bp):
AATCAATTTTGATGATAATAGTATAATAGAGCTTACACATATTCAAACCTTGTCTCCTATTCTTT
GATTATATTTCTAAATTGC
Found at i:27542722 original size:207 final size:207
Alignment explanation
Indices: 27542366--27542749 Score: 561
Period size: 207 Copynumber: 1.9 Consensus size: 207
27542356 GTTAAGTTAA
* * *
27542366 GACACCCACAAAATGTTTGATCTTTTAACTTTAAATCAAATAGTATTTTTTTTTGTTTTAAACAT
1 GACACCCACAAAATGTTTGATCTTTTAACTTTAAATCAAATAGTACTTTCTTTTGTCTTAAACAT
* * *
27542431 TCAAGTATGAAATTTAATGATGACGTTTTCTTGGTCTTATACTATTAATTCATGGTTACTGCTGA
66 TAAAGTATAAAATTTAATGATGACGTTTTCTTGGTCTTACACTATTAATTCATGGTTACTGCTGA
* ** * * *
27542496 TTGGTTTTAGGTTTTTTATGATGTTCAGAATAAAGTAAATTGGCTAGATTAGAGTTTGGTTGGGT
131 ATGGTTTTAGGGGTTTTATGATATTCAGAAGAAAGCAAATTGGCTAGATTAGAGTTTGGTTGGGT
27542561 CTACTGAGTGAT
196 CTACTGAGTGAT
* * *
27542573 GACACCCACCAAATGTTTGATCTTTTAACTTTAAATCAAATGGTACTTTCTTTTGTCTTAAATAT
1 GACACCCACAAAATGTTTGATCTTTTAACTTTAAATCAAATAGTACTTTCTTTTGTCTTAAACAT
* * * ** *
27542638 TAAAGTATAAAATTTCATGATGACGTTTTTTTGGTGTTACACTATTAATTTGTGGTTACTGTTGA
66 TAAAGTATAAAATTTAATGATGACGTTTTCTTGGTCTTACACTATTAATTCATGGTTACTGCTGA
* *
27542703 ATGGTTTTAGGGGTTTTATGATATTGAGAAGAAAGCAGATTGGCTAG
131 ATGGTTTTAGGGGTTTTATGATATTCAGAAGAAAGCAAATTGGCTAG
27542750 GTTTTAATGA
Statistics
Matches: 154, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
207 154 1.00
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.42
Consensus pattern (207 bp):
GACACCCACAAAATGTTTGATCTTTTAACTTTAAATCAAATAGTACTTTCTTTTGTCTTAAACAT
TAAAGTATAAAATTTAATGATGACGTTTTCTTGGTCTTACACTATTAATTCATGGTTACTGCTGA
ATGGTTTTAGGGGTTTTATGATATTCAGAAGAAAGCAAATTGGCTAGATTAGAGTTTGGTTGGGT
CTACTGAGTGAT
Found at i:27544286 original size:2 final size:2
Alignment explanation
Indices: 27544279--27544384 Score: 103
Period size: 2 Copynumber: 54.5 Consensus size: 2
27544269 CTTGCATCAA
*
27544279 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * **
27544320 AT CAT AN AT A- AC CT AC AT -T TT GC AT A- 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 AT AT AT AT
27544360 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
27544385 ACAATGAATT
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
1 4 0.05
2 81 0.93
3 2 0.02
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.44
Consensus pattern (2 bp):
AT
Found at i:27544974 original size:22 final size:22
Alignment explanation
Indices: 27544946--27544989 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
27544936 ATAAAGAAAC
27544946 ATCCTTTACCATTGAGATAATA
1 ATCCTTTACCATTGAGATAATA
27544968 ATCCTTTACCATTGAGATAATA
1 ATCCTTTACCATTGAGATAATA
27544990 GGGAAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
ATCCTTTACCATTGAGATAATA
Found at i:27547340 original size:47 final size:47
Alignment explanation
Indices: 27547271--27547366 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
27547261 AGTCTCTCTC
27547271 TTTCTCTCTCAGTTTCGTAACACATTTTTCTTCCCACATCCCACAAT
1 TTTCTCTCTCAGTTTCGTAACACATTTTTCTTCCCACATCCCACAAT
27547318 TTTCTCTCTCAGTTTCGTAACACATTTTTCTTCCCACATCCCACAAT
1 TTTCTCTCTCAGTTTCGTAACACATTTTTCTTCCCACATCCCACAAT
27547365 TT
1 TT
27547367 AAACCCCTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.21, C:0.33, G:0.04, T:0.42
Consensus pattern (47 bp):
TTTCTCTCTCAGTTTCGTAACACATTTTTCTTCCCACATCCCACAAT
Found at i:27547348 original size:26 final size:26
Alignment explanation
Indices: 27547271--27547348 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
27547261 AGTCTCTCTC
27547271 TTTCTCTCTCAGTTTCGTAACACATT
1 TTTCTCTCTCAGTTTCGTAACACATT
* * ** *
27547297 TTTCT-TCCCA----CATCCCACAAT
1 TTTCTCTCTCAGTTTCGTAACACATT
27547318 TTTCTCTCTCAGTTTCGTAACACATT
1 TTTCTCTCTCAGTTTCGTAACACATT
27547344 TTTCT
1 TTTCT
27547349 TCCCACATCC
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
21 12 0.32
22 4 0.11
25 4 0.11
26 17 0.46
ACGTcount: A:0.19, C:0.31, G:0.05, T:0.45
Consensus pattern (26 bp):
TTTCTCTCTCAGTTTCGTAACACATT
Found at i:27554406 original size:45 final size:45
Alignment explanation
Indices: 27554341--27554430 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
27554331 TATCATACCG
* *
27554341 TCTCACAATCCCCCTTTAAAGGCCA-GAGAAGAGAAGAGAAACTGT
1 TCTCACAATCCCCCTCTAAA-GACAGGAGAAGAGAAGAGAAACTGT
* *
27554386 TCTCACATTCTCCCTCTAAAGACAGGAGAAGAGAAGAGAAACTGT
1 TCTCACAATCCCCCTCTAAAGACAGGAGAAGAGAAGAGAAACTGT
27554431 GTTTCTCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 3 0.08
45 37 0.93
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (45 bp):
TCTCACAATCCCCCTCTAAAGACAGGAGAAGAGAAGAGAAACTGT
Found at i:27556994 original size:3 final size:3
Alignment explanation
Indices: 27556986--27557015 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
27556976 TCAACTCCAA
27556986 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27557016 AAAACATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:27562755 original size:67 final size:67
Alignment explanation
Indices: 27562681--27562808 Score: 220
Period size: 67 Copynumber: 1.9 Consensus size: 67
27562671 TAATATAACT
* * *
27562681 CTTTTGGAAGCAAGGTACTTGAATTGTTTTTTGAGATATGCATCTCTTGATATATAATTTTTAAT
1 CTTTTGGAAGCAAAGTACTTGAATTGTTTTTTGAGATACGCATATCTTGATATATAATTTTTAAT
27562746 CC
66 CC
*
27562748 CTTTTGGAAGCAAAGTACTTGAATTGTTTTTTGAGATACGCATATCTTGATCTATAATTTT
1 CTTTTGGAAGCAAAGTACTTGAATTGTTTTTTGAGATACGCATATCTTGATATATAATTTT
27562809 CTTGTGGTAG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (67 bp):
CTTTTGGAAGCAAAGTACTTGAATTGTTTTTTGAGATACGCATATCTTGATATATAATTTTTAAT
CC
Found at i:27563855 original size:13 final size:14
Alignment explanation
Indices: 27563832--27563863 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
27563822 AGTAACATGA
27563832 AGAAA-AAAAAAAG
1 AGAAACAAAAAAAG
27563845 A-AAACAAAAAAAG
1 AGAAACAAAAAAAG
27563858 AGAAAC
1 AGAAAC
27563864 CAAACTAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 10 0.59
14 4 0.24
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.00
Consensus pattern (14 bp):
AGAAACAAAAAAAG
Found at i:27564186 original size:28 final size:28
Alignment explanation
Indices: 27564146--27564205 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
27564136 TGTTTAAAGA
*
27564146 TTATGCTTCATCTTTGAAAAAGCAATAG
1 TTATGATTCATCTTTGAAAAAGCAATAG
* * *
27564174 TTATGATTGATCTTTGAAAAGGCAGTAG
1 TTATGATTCATCTTTGAAAAAGCAATAG
27564202 TTAT
1 TTAT
27564206 ACTTAATCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (28 bp):
TTATGATTCATCTTTGAAAAAGCAATAG
Found at i:27574889 original size:15 final size:15
Alignment explanation
Indices: 27574865--27574899 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
27574855 AAACTAAATG
27574865 TCAATAATCACATTT
1 TCAATAATCACATTT
*
27574880 TCAATTATCACATTT
1 TCAATAATCACATTT
*
27574895 CCAAT
1 TCAAT
27574900 CAATTACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (15 bp):
TCAATAATCACATTT
Found at i:27576308 original size:29 final size:30
Alignment explanation
Indices: 27576266--27576322 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
27576256 AGCGTAACCA
27576266 TATCATTTCGTAATAG-TTTCTAGTCTTGT
1 TATCATTTCGTAATAGTTTTCTAGTCTTGT
27576295 TATCA-TTCAGTAATAGTTTTCTAGTCTT
1 TATCATTTC-GTAATAGTTTTCTAGTCTT
27576323 CTTCTGGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 3 0.12
29 12 0.46
30 11 0.42
ACGTcount: A:0.23, C:0.14, G:0.12, T:0.51
Consensus pattern (30 bp):
TATCATTTCGTAATAGTTTTCTAGTCTTGT
Found at i:27578229 original size:40 final size:35
Alignment explanation
Indices: 27578141--27578235 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 35
27578131 TTTTAATATC
* *
27578141 ATATATTTTATTTTCATTTCTTATTATGATCTTAT
1 ATATATTTTATTTTCATTTCTTAATATAATCTTAT
27578176 ATATA-TTT-TTTTCATTTCTTAATATAATTTCCTATATT
1 ATATATTTTATTTTCATTTCTTAATATAA--T-CT-TA-T
*
27578214 TTATATTTTATTTTCATTTCTT
1 ATATATTTTATTTTCATTTCTT
27578236 TTTCCTTTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
33 17 0.34
34 3 0.06
35 6 0.12
36 2 0.04
37 2 0.04
38 5 0.10
39 3 0.06
40 12 0.24
ACGTcount: A:0.25, C:0.09, G:0.01, T:0.64
Consensus pattern (35 bp):
ATATATTTTATTTTCATTTCTTAATATAATCTTAT
Found at i:27587936 original size:24 final size:24
Alignment explanation
Indices: 27587884--27587947 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 24
27587874 ATGCTAATGC
27587884 AATTATCTATTTTTTTTATCATTT
1 AATTATCTATTTTTTTTATCATTT
27587908 AATTAT-TATTTTTGTTT-T-ATTT
1 AATTATCTATTTTT-TTTATCATTT
27587930 CATATTATCATATTTTTT
1 -A-ATTATC-TATTTTTT
27587948 ACTTTTTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
22 4 0.11
23 9 0.26
24 14 0.40
25 1 0.03
26 7 0.20
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (24 bp):
AATTATCTATTTTTTTTATCATTT
Found at i:27588291 original size:14 final size:13
Alignment explanation
Indices: 27588249--27588300 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 13
27588239 CGAATTATTA
27588249 TTATTATTTTTAT
1 TTATTATTTTTAT
*
27588262 CT-TT-TTTTTAT
1 TTATTATTTTTAT
* *
27588273 CTATTGTTATTTAT
1 TTATTATT-TTTAT
27588287 TTATTATTTTTAT
1 TTATTATTTTTAT
27588300 T
1 T
27588301 GAGTAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 9 0.27
12 4 0.12
13 9 0.27
14 11 0.33
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (13 bp):
TTATTATTTTTAT
Found at i:27588293 original size:21 final size:20
Alignment explanation
Indices: 27588246--27588294 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
27588236 ATTCGAATTA
*
27588246 TTATTATTATTTTTATCTTT
1 TTATTATTATTGTTATCTTT
*
27588266 TTTTTATCTATTGTTAT-TTAT
1 TTATTAT-TATTGTTATCTT-T
27588287 TTATTATT
1 TTATTATT
27588295 TTTATTGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (20 bp):
TTATTATTATTGTTATCTTT
Found at i:27588604 original size:8 final size:8
Alignment explanation
Indices: 27588593--27588620 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
27588583 TATTTTCTAT
27588593 TTTTATTA
1 TTTTATTA
27588601 TTTTATTA
1 TTTTATTA
27588609 TTTTATTA
1 TTTTATTA
27588617 TTTT
1 TTTT
27588621 TTCAAATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTATTA
Found at i:27589960 original size:14 final size:14
Alignment explanation
Indices: 27589943--27589969 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27589933 CTCTCTCTTT
27589943 TTTTTATATTTTTA
1 TTTTTATATTTTTA
27589957 TTTTTATATTTTT
1 TTTTTATATTTTT
27589970 TTGGTGTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTATATTTTTA
Found at i:27590188 original size:37 final size:37
Alignment explanation
Indices: 27590142--27590349 Score: 137
Period size: 37 Copynumber: 5.5 Consensus size: 37
27590132 TTTTTAAATG
* * *
27590142 AACTTCTCAAGATTGAGGTAATAACACTTTAAGAATA
1 AACTCCTCAAAATTGAGGTAATAAAACTTTAAGAATA
* * *
27590179 GACTCCTCAAAATTGAGGCAATAAAACTTTAAGAGTA
1 AACTCCTCAAAATTGAGGTAATAAAACTTTAAGAATA
* * ** * * *
27590216 AACTCTTCAAAATTAAGGTAACGAAACTTAAAAAAATG
1 AACTCCTCAAAATTGAGGTAATAAAACTT-TAAGAATA
* * * * *
27590254 AACTCCTCAAAGTTGAGGTAACGAAACTTCTTTAAAAATG
1 AACTCCTCAAAATTGAGGTAA-TAAA--ACTTTAAGAATA
* * * * * * *
27590294 AACTCCTCAAAACTGAGGCAGTGAGACTTTTAAAAATG
1 AACTCCTCAAAATTGAGGTAATAAAAC-TTTAAGAATA
*
27590332 AACTCCTCAAAACTGAGG
1 AACTCCTCAAAATTGAGG
27590350 CAACGAAACC
Statistics
Matches: 135, Mismatches: 31, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
37 55 0.41
38 50 0.37
39 3 0.02
40 24 0.18
41 3 0.02
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (37 bp):
AACTCCTCAAAATTGAGGTAATAAAACTTTAAGAATA
Found at i:27590273 original size:38 final size:38
Alignment explanation
Indices: 27590180--27590358 Score: 171
Period size: 38 Copynumber: 4.7 Consensus size: 38
27590170 TTAAGAATAG
* ** * * *
27590180 ACTCCTCAAAATTGAGGCAATAAAAC-TTTAAGAGTAA
1 ACTCCTCAAAACTGAGGCAACGAAACTTTTAAAAATGA
* * * * **
27590217 ACTCTTCAAAATTAAGGTAACGAAACTTAAAAAAATGA
1 ACTCCTCAAAACTGAGGCAACGAAACTTTTAAAAATGA
** *
27590255 ACTCCTCAAAGTTGAGGTAACGAAACTTCTTTAAAAATGA
1 ACTCCTCAAAACTGAGGCAACGAAAC-T-TTTAAAAATGA
** *
27590295 ACTCCTCAAAACTGAGGCAGTGAGACTTTTAAAAATGA
1 ACTCCTCAAAACTGAGGCAACGAAACTTTTAAAAATGA
27590333 ACTCCTCAAAACTGAGGCAACGAAAC
1 ACTCCTCAAAACTGAGGCAACGAAAC
27590359 CTTTGTTCTT
Statistics
Matches: 115, Mismatches: 24, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
37 21 0.18
38 63 0.55
39 2 0.02
40 29 0.25
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (38 bp):
ACTCCTCAAAACTGAGGCAACGAAACTTTTAAAAATGA
Found at i:27630844 original size:22 final size:22
Alignment explanation
Indices: 27630819--27630890 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
27630809 TGTATGACTA
27630819 GTTTTTAGGCATTACGTGATTG
1 GTTTTTAGGCATTACGTGATTG
* *
27630841 G-TTTTAGGCATTACGTGACTA
1 GTTTTTAGGCATTACGTGATTG
* *
27630862 GTTTTTAGACATTACATGATTG
1 GTTTTTAGGCATTACGTGATTG
*
27630884 ATTTTTA
1 GTTTTTA
27630891 AGCAATGCCT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.45
22 23 0.55
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.46
Consensus pattern (22 bp):
GTTTTTAGGCATTACGTGATTG
Found at i:27630847 original size:21 final size:21
Alignment explanation
Indices: 27630821--27630888 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
27630811 TATGACTAGT
*
27630821 TTTTAGGCATTACGTGATTGG
1 TTTTAGGCATTACGTGATTGA
* *
27630842 TTTTAGGCATTACGTGACTAGT
1 TTTTAGGCATTACGTGA-TTGA
* *
27630864 TTTTAGACATTACATGATTGA
1 TTTTAGGCATTACGTGATTGA
27630885 TTTT
1 TTTT
27630889 TAAGCAATGC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
21 23 0.57
22 17 0.43
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.46
Consensus pattern (21 bp):
TTTTAGGCATTACGTGATTGA
Found at i:27631066 original size:26 final size:26
Alignment explanation
Indices: 27630969--27631275 Score: 276
Period size: 26 Copynumber: 12.6 Consensus size: 26
27630959 ACCTATCAAT
* *
27630969 TAGTCACGCAAGGCCTTATCAGAAAC
1 TAGTCACGCAATGCCTTATCAAAAAC
* * * *
27630995 TAGTTACGTAATACCTTA-C--TAAC
1 TAGTCACGCAATGCCTTATCAAAAAC
* *
27631018 AAGTCACGCAATGCC-TAT---TAAC
1 TAGTCACGCAATGCCTTATCAAAAAC
* *
27631040 TAGTTACGCAATGCCTTATTAAAAAC
1 TAGTCACGCAATGCCTTATCAAAAAC
*
27631066 TAGTCATGCAATGCCTTATCAAAAAC
1 TAGTCACGCAATGCCTTATCAAAAAC
* **
27631092 TAATCACGCAATGCC----C-AAAGT
1 TAGTCACGCAATGCCTTATCAAAAAC
27631113 TAGTCACGCAATGCC-TATC---AAC
1 TAGTCACGCAATGCCTTATCAAAAAC
* *
27631135 TAATCACGCAATGCCTTATCAGAAAC
1 TAGTCACGCAATGCCTTATCAAAAAC
*
27631161 TAGTCACGCAATACCTTATCAAAAAC
1 TAGTCACGCAATGCCTTATCAAAAAC
27631187 TAGTCACGCAATGCC-TATC---AAC
1 TAGTCACGCAATGCCTTATCAAAAAC
*
27631209 TAGTCACGCAATGCCTTATCAGAAAC
1 TAGTCACGCAATGCCTTATCAAAAAC
* ** *
27631235 TAATCACGCAATAACTTATCAAAAAT
1 TAGTCACGCAATGCCTTATCAAAAAC
27631261 TAGTCACGCAATGCC
1 TAGTCACGCAATGCC
27631276 CAAAGTCAGT
Statistics
Matches: 230, Mismatches: 35, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
21 17 0.07
22 53 0.23
23 25 0.11
24 1 0.00
25 5 0.02
26 129 0.56
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.24
Consensus pattern (26 bp):
TAGTCACGCAATGCCTTATCAAAAAC
Found at i:27631083 original size:71 final size:70
Alignment explanation
Indices: 27630909--27631226 Score: 210
Period size: 71 Copynumber: 4.5 Consensus size: 70
27630899 CTAAGTCATA
* * *
27630909 CAATGCCTTATT--AACTAGTCACT-CAATGTCTTATTAACAAGTCACGCAATACCTATCAATTA
1 CAATGCCTTATTAAAACTAGTCA-TGCAATGCCTTACTAACAAGTCACGCAATACCTATCAACTA
27630971 GTCACG
65 GTCACG
* * * * * * * *
27630977 CAAGGCCTTATCAGAAACTAGTTACGTAATACCTTACTAACAAGTCACGCAATGCCTATTAACTA
1 CAATGCCTTATTA-AAACTAGTCATGCAATGCCTTACTAACAAGTCACGCAATACCTATCAACTA
*
27631042 GTTACG
65 GTCACG
* * *
27631048 CAATGCCTTATTAAAAACTAGTCATGCAATGCCTTATCAAAAACTAA-TCACGCAATGCCCA--A
1 CAATGCCTTATT-AAAACTAGTCATGCAATGCCTTA-C--TAAC-AAGTCACGCAATACCTATCA
*
27631110 AGTTAGTCACG
61 A-CTAGTCACG
* * * * *
27631121 CAATGCC-TA-T-CAACTAATCACGCAATGCCTTATCAGAAACTAGTCACGCAATACCTTATCAA
1 CAATGCCTTATTAAAACTAGTCATGCAATGCCTTA-C--TAACAAGTCACGCAATACC-TATC--
27631183 AAACTAGTCACG
60 -AACTAGTCACG
* *
27631195 CAATGCC-TA-T-CAACTAGTCACGCAATGCCTTA
1 CAATGCCTTATTAAAACTAGTCATGCAATGCCTTA
27631227 TCAGAAACTA
Statistics
Matches: 202, Mismatches: 31, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
68 11 0.05
69 37 0.18
70 1 0.00
71 74 0.37
72 6 0.03
73 14 0.07
74 55 0.27
75 4 0.02
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (70 bp):
CAATGCCTTATTAAAACTAGTCATGCAATGCCTTACTAACAAGTCACGCAATACCTATCAACTAG
TCACG
Found at i:27631210 original size:48 final size:47
Alignment explanation
Indices: 27630909--27631246 Score: 257
Period size: 48 Copynumber: 7.1 Consensus size: 47
27630899 CTAAGTCATA
* * * * *
27630909 CAATGCCTTATTAACTAGTCACTCAATGTCTTAT--TAACAAGTCACG
1 CAATGCC-TATCAACTAGTCACGCAATGCCTTATCAAAACTAGTCACG
* * * *
27630955 CAATACCTATCAATTAGTCACGCAAGGCCTTATCAGAAACTAGTTACG
1 CAATGCCTATCAACTAGTCACGCAATGCCTTATCA-AAACTAGTCACG
* * * * *
27631003 TAATACCT-TACTAACAAGTCACGCAATGCC-TAT--TAACTAGTTACG
1 CAATGCCTAT-C-AACTAGTCACGCAATGCCTTATCAAAACTAGTCACG
* * *
27631048 CAATGCCTTATTAAAAACTAGTCATGCAATGCCTTATCAAAAACTAATCACG
1 CAATGCC-TA-T--CAACTAGTCACGCAATGCCTTATC-AAAACTAGTCACG
* * *
27631100 CAATGCCCA--AAGTTAGTCACGCAATGCC-TATC--AACTAATCACG
1 CAATGCCTATCAA-CTAGTCACGCAATGCCTTATCAAAACTAGTCACG
*
27631143 CAATGCCTTATCAGAAACTAGTCACGCAATACCTTATCAAAAACTAGTCACG
1 CAATGCC-TATC---AACTAGTCACGCAATGCCTTATC-AAAACTAGTCACG
*
27631195 CAATGCCTATCAACTAGTCACGCAATGCCTTATCAGAAACTAATCACG
1 CAATGCCTATCAACTAGTCACGCAATGCCTTATCA-AAACTAGTCACG
27631243 CAAT
1 CAAT
27631247 AACTTATCAA
Statistics
Matches: 236, Mismatches: 31, Indels: 48
0.75 0.10 0.15
Matches are distributed among these distances:
43 18 0.08
44 1 0.00
45 37 0.16
46 13 0.06
47 16 0.07
48 88 0.37
49 25 0.11
51 5 0.02
52 33 0.14
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (47 bp):
CAATGCCTATCAACTAGTCACGCAATGCCTTATCAAAACTAGTCACG
Found at i:27631216 original size:74 final size:74
Alignment explanation
Indices: 27631063--27631275 Score: 319
Period size: 74 Copynumber: 2.9 Consensus size: 74
27631053 CCTTATTAAA
* * * *
27631063 AACTAGTCATGCAATGCCTTATCAAAAACTAATCACGCAATGCC----C-AAAGTTAGTCACGCA
1 AACTAGTCACGCAATGCCTTATCAGAAACTAATCACGCAATACCTTATCAAAAATTAGTCACGCA
27631123 ATGCCTATC
66 ATGCCTATC
* * *
27631132 AACTAATCACGCAATGCCTTATCAGAAACTAGTCACGCAATACCTTATCAAAAACTAGTCACGCA
1 AACTAGTCACGCAATGCCTTATCAGAAACTAATCACGCAATACCTTATCAAAAATTAGTCACGCA
27631197 ATGCCTATC
66 ATGCCTATC
*
27631206 AACTAGTCACGCAATGCCTTATCAGAAACTAATCACGCAATAACTTATCAAAAATTAGTCACGCA
1 AACTAGTCACGCAATGCCTTATCAGAAACTAATCACGCAATACCTTATCAAAAATTAGTCACGCA
27631271 ATGCC
66 ATGCC
27631276 CAAAGTCAGT
Statistics
Matches: 128, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
69 39 0.30
73 1 0.01
74 88 0.69
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.23
Consensus pattern (74 bp):
AACTAGTCACGCAATGCCTTATCAGAAACTAATCACGCAATACCTTATCAAAAATTAGTCACGCA
ATGCCTATC
Found at i:27631270 original size:169 final size:166
Alignment explanation
Indices: 27630948--27631296 Score: 500
Period size: 169 Copynumber: 2.1 Consensus size: 166
27630938 CTTATTAACA
* * * *
27630948 AGTCACGCAATACCTATCAATTAGTCACGCAAGGCCTTATCAGAAACTAGTTACGTAATACCTTA
1 AGTCACGCAATACCTATCAACTAATCACGCAAGGCCTTATCAGAAACTAGTCACGCAATACCTTA
* * * * * *
27631013 CTAACAAGTCACGCAATGCCTATTAACTAGTTACGCAATGCCTTATTAAAAACTAGTCATGCAAT
66 CAAACAAGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATCAAAAACTAATCACGCAAT
** *
27631078 GCCTTATCAAAAACTAATCACGCAATGCCCAAAGTT
131 AACTTATCAAAAACTAATCACGCAATGCCCAAAGTC
* *
27631114 AGTCACGCAATGCCTATCAACTAATCACGCAATGCCTTATCAGAAACTAGTCACGCAATACCTTA
1 AGTCACGCAATACCTATCAACTAATCACGCAAGGCCTTATCAGAAACTAGTCACGCAATACCTTA
* *
27631179 TCAAAAACTAGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATCAGAAACTAATCACGC
66 -C--AAACAAGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATCAAAAACTAATCACGC
* *
27631244 AATAACTTATCAAAAATTAGTCACGCAATGCCCAAAGTC
128 AATAACTTATCAAAAACTAATCACGCAATGCCCAAAGTC
27631283 AGTCACGCAATACC
1 AGTCACGCAATACC
27631297 CAAAGTTAGT
Statistics
Matches: 160, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
166 59 0.37
167 1 0.01
169 100 0.62
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (166 bp):
AGTCACGCAATACCTATCAACTAATCACGCAAGGCCTTATCAGAAACTAGTCACGCAATACCTTA
CAAACAAGTCACGCAATGCCTATCAACTAGTCACGCAATGCCTTATCAAAAACTAATCACGCAAT
AACTTATCAAAAACTAATCACGCAATGCCCAAAGTC
Found at i:27631286 original size:21 final size:21
Alignment explanation
Indices: 27631262--27631317 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
27631252 ATCAAAAATT
27631262 AGTCACGCAATGCCCAAAGTC
1 AGTCACGCAATGCCCAAAGTC
* *
27631283 AGTCACGCAATACCCAAAGTT
1 AGTCACGCAATGCCCAAAGTC
27631304 AGTCACGCAATGCC
1 AGTCACGCAATGCC
27631318 TAAAAACTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.32, G:0.18, T:0.16
Consensus pattern (21 bp):
AGTCACGCAATGCCCAAAGTC
Found at i:27635823 original size:31 final size:32
Alignment explanation
Indices: 27635776--27635837 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
27635766 CTTTATTTTT
*
27635776 TTATGAAATGCCACATGGCTG-ACAACAAAGCA
1 TTATGAAACGCCACATGGCTGCA-AACAAAGCA
27635808 TTAT-AAACGCCACATGGCTGCAAACAAAGC
1 TTATGAAACGCCACATGGCTGCAAACAAAGC
27635838 GTAACCAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (32 bp):
TTATGAAACGCCACATGGCTGCAAACAAAGCA
Found at i:27646645 original size:18 final size:18
Alignment explanation
Indices: 27646624--27646664 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
27646614 ACTAATACAA
* *
27646624 ATAGAACAACTACTTTGC
1 ATAGAACAACCACTTTAC
*
27646642 ATAGAATAACCACTTTAC
1 ATAGAACAACCACTTTAC
27646660 ATAGA
1 ATAGA
27646665 TAACAGTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (18 bp):
ATAGAACAACCACTTTAC
Found at i:27646839 original size:14 final size:14
Alignment explanation
Indices: 27646820--27646869 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
27646810 TCTCGTTTAC
*
27646820 CTTGTTCTCTTATA
1 CTTGTTCTCCTATA
*
27646834 CTTGTTCACCTATA
1 CTTGTTCTCCTATA
*
27646848 GCTTATTCTCCTATA
1 -CTTGTTCTCCTATA
27646863 CTTGTTC
1 CTTGTTC
27646870 AATATAACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.16, C:0.26, G:0.08, T:0.50
Consensus pattern (14 bp):
CTTGTTCTCCTATA
Found at i:27647749 original size:2 final size:2
Alignment explanation
Indices: 27647742--27647773 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
27647732 ATGATGAGAC
27647742 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
27647774 GCTATGGTAA
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:27647850 original size:26 final size:26
Alignment explanation
Indices: 27647796--27647850 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
27647786 CGATTATCTA
* *
27647796 TTTTATTATTATCATTTTTTGTCATT
1 TTTTATTATTAACATTATTTGTCATT
27647822 TTTTATTATTTAACTATTATTT-TCATT
1 TTTTATTA-TTAAC-ATTATTTGTCATT
27647849 TT
1 TT
27647851 ATTTCATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.32
27 11 0.44
28 6 0.24
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (26 bp):
TTTTATTATTAACATTATTTGTCATT
Found at i:27650156 original size:445 final size:442
Alignment explanation
Indices: 27649390--27650206 Score: 1176
Period size: 445 Copynumber: 1.8 Consensus size: 442
27649380 TAGGAAAAAT
*
27649390 TAGGAGTCACCACCAATCTTTTTTTACTAGGTGCGATTGGCCACCTATTGACTCGATTCTAATCG
1 TAGGAGTCACCACCAATCTTTTTTTACTAGGTGCGATTGGCCACCTAATGACTCGATTCTAATCG
* *
27649455 ATGAAGCTTTAAATTAATTTTAAGCCCACCGAAAAAAACCTTAAACTGGTTTATGTTTTTCTAGA
66 ATGAAACTTTAAATTAATTTTAAGCCCACCGAAAAAAACCTTAAACCGGTTTATGTTTTTCTAGA
* * *
27649520 TCTAAGTTCGGGAGTACGGTTACGCTCGGAGAAGGATTAGCACCCCCGGGACGCCTATTCCATGA
131 TCTAAGTTCGGGAGTACGGTTACGCCCGGAGAAAGATTAGCACCCCCGGGACGCCCATTCCATGA
* * * * *
27649585 ATGGTATCATTTTTAGATTATCCTATTAGGCTTTAATTTTTAATTTCGCTATATTTTCTTAGTTA
196 ACGGTACCATTTTTAGATTATCCTATTAGGCTTTAATTTTTAATTTCACTATATTTCCTTAATTA
*
27649650 TTATTCTCTTATTTTATCTCCTATTTAACCTAAAATAAAATACAAATATTAGGCAAGATGAAATG
261 TTATTCTCTTATTTTATCTCCTATTTAACCTAAAATAAAATACAAATAGTAGGCAAGATGAAATG
* * * *
27649715 CATGGCGTGGGATAAAAATATGTCAGACGATTAACCTTTTATCGAGGATGTCGTAACGTGCGGGT
326 CATGACGTGAGAT-AAAA-ATGCCAGACGAATAACCTTTTATCGAGGATGTCGTAACGTGCGGGT
27649780 CCGGGAACCCGACCGCCAGACACTAACGTGAAAAAACTCACTAAAAAATTAAAC
389 CCGGGAACCCGACCGCCAGACACTAACGTGAAAAAACTCACTAAAAAATTAAAC
* * * *
27649834 TAGGAGTCGCCACCAATC-TTTTTTACTGGGTGTGGTTGGCCACCTAATGACTCGATTCTAATCG
1 TAGGAGTCACCACCAATCTTTTTTTACTAGGTGCGATTGGCCACCTAATGACTCGATTCTAATCG
* * *
27649898 ATGAAAAC-TTAAATTAATTTTAAGTCCACCGAAAAGAACCTTAAACCGGTCTGTGAT-TTTTTT
66 ATG-AAACTTTAAATTAATTTTAAGCCCACCGAAAAAAACCTTAAACCGGT-T-T-ATGTTTTTC
* * * *
27649961 TAGCTCTAGGTTCGGGAGTACGGTTACGCCCAGG-GAAAGATTAGCACCCCTGGGACGCCCGTTC
127 TAGATCTAAGTTCGGGAGTACGGTTACGCCC-GGAGAAAGATTAGCACCCCCGGGACGCCCATTC
* * *
27650025 TATGAACGGTACCATTTTTAGATTATCCTATTGGGTTTTAATTTTTAATTTCACTATATTTCCTT
191 CATGAACGGTACCATTTTTAGATTATCCTATTAGGCTTTAATTTTTAATTTCACTATATTTCCTT
* * ** * * *
27650090 AATTATTATTCTTTTATTTTATCTCCTATTTAACTTAAAATGGAATGCAAATGGGT-GGCGAGAT
256 AATTATTATTCTCTTATTTTATCTCCTATTTAACCTAAAATAAAATACAAAT-AGTAGGCAAGAT
* *
27650154 GAAGTGCATGACGTGAGATAAAAATGCCGGACGAATAACCTTTTATCGAGGAT
320 GAAATGCATGACGTGAGATAAAAATGCCAGACGAATAACCTTTTATCGAGGAT
27650207 ATTTTTCCAA
Statistics
Matches: 328, Mismatches: 39, Indels: 13
0.86 0.10 0.03
Matches are distributed among these distances:
443 111 0.34
444 25 0.08
445 187 0.57
446 5 0.02
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (442 bp):
TAGGAGTCACCACCAATCTTTTTTTACTAGGTGCGATTGGCCACCTAATGACTCGATTCTAATCG
ATGAAACTTTAAATTAATTTTAAGCCCACCGAAAAAAACCTTAAACCGGTTTATGTTTTTCTAGA
TCTAAGTTCGGGAGTACGGTTACGCCCGGAGAAAGATTAGCACCCCCGGGACGCCCATTCCATGA
ACGGTACCATTTTTAGATTATCCTATTAGGCTTTAATTTTTAATTTCACTATATTTCCTTAATTA
TTATTCTCTTATTTTATCTCCTATTTAACCTAAAATAAAATACAAATAGTAGGCAAGATGAAATG
CATGACGTGAGATAAAAATGCCAGACGAATAACCTTTTATCGAGGATGTCGTAACGTGCGGGTCC
GGGAACCCGACCGCCAGACACTAACGTGAAAAAACTCACTAAAAAATTAAAC
Found at i:27650632 original size:18 final size:19
Alignment explanation
Indices: 27650583--27650634 Score: 52
Period size: 22 Copynumber: 2.6 Consensus size: 19
27650573 TGCTAATGCA
* *
27650583 ATTATCTATTTTTTTTGTT
1 ATTATATATTTTTATTGTT
27650602 ATTATTAATTATTTTTATT-TT
1 ATTA-T-A-TATTTTTATTGTT
27650623 ATTATATATTTT
1 ATTATATATTTT
27650635 ATTATCATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.21
19 5 0.18
20 2 0.07
21 6 0.21
22 9 0.32
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
ATTATATATTTTTATTGTT
Found at i:27650634 original size:12 final size:13
Alignment explanation
Indices: 27650617--27650647 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
27650607 TAATTATTTT
27650617 TATTTTATTAT-A
1 TATTTTATTATCA
27650629 TATTTTATTATCA
1 TATTTTATTATCA
27650642 TATTTT
1 TATTTT
27650648 CTATTCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTTATTATCA
Found at i:27650658 original size:13 final size:14
Alignment explanation
Indices: 27650621--27650677 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 14
27650611 TATTTTTATT
*
27650621 TTATTATATATTTTA
1 TTATTAT-TATTTTC
*
27650636 TTATCA-TATTTTC
1 TTATTATTATTTTC
*
27650649 -TATTCTTA-TTTC
1 TTATTATTATTTTC
27650661 TTATTATTATTTT-
1 TTATTATTATTTTC
27650674 TTAT
1 TTAT
27650678 ACTTTACATT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
12 7 0.21
13 19 0.56
14 3 0.09
15 5 0.15
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTATTATTTTC
Found at i:27661681 original size:2 final size:2
Alignment explanation
Indices: 27661674--27661699 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27661664 ATGTTTTTGT
27661674 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
27661700 NATGCTGAAA
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):
TA
Found at i:27661728 original size:51 final size:50
Alignment explanation
Indices: 27661650--27661750 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 50
27661640 AATATGAATT
27661650 ATGCTGAAATGATGATGTTTTTGTTATATATATATATATATATATATATA
1 ATGCTGAAATGATGATGTTTTTGTTATATATATATATATATATATATATA
27661700 NATGCTGAAATGATGATG-TTTTGTTTATATATATATATATATATATATATA
1 -ATGCTGAAATGATGATGTTTTTG-TTATATATATATATATATATATATATA
27661751 TAGTGCATGA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 5 0.10
51 44 0.90
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (50 bp):
ATGCTGAAATGATGATGTTTTTGTTATATATATATATATATATATATATA
Found at i:27661732 original size:2 final size:2
Alignment explanation
Indices: 27661725--27661752 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27661715 ATGTTTTGTT
27661725 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
27661753 GTGCATGATA
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):
TA
Found at i:27668576 original size:438 final size:438
Alignment explanation
Indices: 27667761--27668634 Score: 1471
Period size: 438 Copynumber: 2.0 Consensus size: 438
27667751 AAGTACTTAG
*
27667761 ATTTGGAGATGTCTAGGTATATTAATGTAGACTAATTCCTTCATACGATGTTGTCCAAAGATATA
1 ATTTGGAGATGTCTAGGTATATTAATGTAGACTAATTCCCTCATACGATGTTGTCCAAAGATATA
*
27667826 CAGCTTATATATGAACTTGCTATCCACCACTTACTACACCCAAGAATGCTATCCAAATTAAGCAT
66 CAGCTTATATATGAACTTGCTATACACCACTTACTACACCCAAGAATGCTATCCAAATTAAGCAT
* * *
27667891 TACATTCGGATCTCTAACCATGTTAACCCAAGCCATAGTTTTCAAGTTATGACATATGCTGTCTG
131 TACATTCGGATCTCTAACCATGTTAACCCAAGCCATAGTTTTCAAGTTACGACATATGCTATCCG
** *
27667956 AATCTAATTACAATTGAAACTCTACATTTAAAGTCTTAGATTCCAAAAAGCTGAAGGCTTGCGAT
196 AATCTAATTACAATCAAAACTCTACATTTAAAGTCTCAGATTCCAAAAAGCTGAAGGCTTGCGAT
* *
27668021 GGTAGATCCTTATTTTAACGATAACAACTCAAACCTATCCAAATTCATTTTTGAATTAAGGACAA
261 GGTAGAGCCCTATTTTAACGATAACAACTCAAACCTATCCAAATTCATTTTTGAATTAAGGACAA
* * *
27668086 GTCTGAGCTATCTATAATTTTGTGAACCCCATGACCCCTATATTTGTGTCCACTATCCCTCTATC
326 GTCTGAGCTATCTATAATTTTGTGAACCCCATCACCCCCATATTTATGTCCACTATCCCTCTATC
27668151 ATATTTAAACTCCT-CTTAATTCATGTCAAATTATATGGCAATCATATT
391 ATATTTAAACT-CTACTTAATTCATGTCAAATTATATGGCAATCATATT
* * *
27668199 ATTTGGAGATGTCTAGGTCTATTAATGTAGGCTAATTCCCTCATATGATGTTGTCCAAAGATATA
1 ATTTGGAGATGTCTAGGTATATTAATGTAGACTAATTCCCTCATACGATGTTGTCCAAAGATATA
* * * ** *
27668264 TAGCTTATATATGAACTTGCTATACTCCACTTACTACACCCGAGAATGCTATCTGAATTAGGCAT
66 CAGCTTATATATGAACTTGCTATACACCACTTACTACACCCAAGAATGCTATCCAAATTAAGCAT
* *
27668329 TACATTCGGATCTTTAACCATGTTAACCCAAGCCGTAGTTTTCAAGTTACGACATATGCTATCCG
131 TACATTCGGATCTCTAACCATGTTAACCCAAGCCATAGTTTTCAAGTTACGACATATGCTATCCG
27668394 AATCTAATTACAATCAAAACTCTACATTTAAAGTCTCAGATTCCAAAAAGCTGAAGGCTTGCGAT
196 AATCTAATTACAATCAAAACTCTACATTTAAAGTCTCAGATTCCAAAAAGCTGAAGGCTTGCGAT
*
27668459 GGTAGAGCCCTATTTTAACTATAACAACTCAAACCTATCCAAATTCATTTTTGAATTAAGGACAA
261 GGTAGAGCCCTATTTTAACGATAACAACTCAAACCTATCCAAATTCATTTTTGAATTAAGGACAA
* *
27668524 GTCTGAGCTATCTATACTTTTGTGAACCCCATCACCCCCATGTTTATGTCCACTATCCCTCTATC
326 GTCTGAGCTATCTATAATTTTGTGAACCCCATCACCCCCATATTTATGTCCACTATCCCTCTATC
* *
27668589 ATATTTAAACTCTATTTAATTCATGTCAAATTATATGGCAGTCATA
391 ATATTTAAACTCTACTTAATTCATGTCAAATTATATGGCAATCATA
27668635 ATATGCGCTT
Statistics
Matches: 406, Mismatches: 29, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
437 2 0.00
438 404 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (438 bp):
ATTTGGAGATGTCTAGGTATATTAATGTAGACTAATTCCCTCATACGATGTTGTCCAAAGATATA
CAGCTTATATATGAACTTGCTATACACCACTTACTACACCCAAGAATGCTATCCAAATTAAGCAT
TACATTCGGATCTCTAACCATGTTAACCCAAGCCATAGTTTTCAAGTTACGACATATGCTATCCG
AATCTAATTACAATCAAAACTCTACATTTAAAGTCTCAGATTCCAAAAAGCTGAAGGCTTGCGAT
GGTAGAGCCCTATTTTAACGATAACAACTCAAACCTATCCAAATTCATTTTTGAATTAAGGACAA
GTCTGAGCTATCTATAATTTTGTGAACCCCATCACCCCCATATTTATGTCCACTATCCCTCTATC
ATATTTAAACTCTACTTAATTCATGTCAAATTATATGGCAATCATATT
Found at i:27671037 original size:43 final size:43
Alignment explanation
Indices: 27670989--27671197 Score: 255
Period size: 43 Copynumber: 4.9 Consensus size: 43
27670979 ATTATGTGAT
* *
27670989 GATGATGACCCGGCTATGTGCGAGTAGGGAGTGCACATGAACC
1 GATGATGACCTGGCTATGTGCGAGTAGGGAGTGCACATGAGCC
**
27671032 GATGATGACCTTACTATGTGCGAGTAGGGAGTGCACATGAGCC
1 GATGATGACCTGGCTATGTGCGAGTAGGGAGTGCACATGAGCC
* *
27671075 GATGATGACCCGGATATGTGCGAGTTA-GGAGTGCACATGAGCC
1 GATGATGACCTGGCTATGTGCGAG-TAGGGAGTGCACATGAGCC
* * * * *
27671118 GATGATGACCTGGCTATGTACAAATAGAGAGTGCACATGAGCT
1 GATGATGACCTGGCTATGTGCGAGTAGGGAGTGCACATGAGCC
* **
27671161 GATGATG---TTGAAATGTGCGAGTAGGGAGTGCACATGA
1 GATGATGACCTGGCTATGTGCGAGTAGGGAGTGCACATGA
27671198 TGATGAATGA
Statistics
Matches: 142, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
40 23 0.16
42 2 0.01
43 115 0.81
44 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22
Consensus pattern (43 bp):
GATGATGACCTGGCTATGTGCGAGTAGGGAGTGCACATGAGCC
Done.