Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 11 of 325
Found at i:3879719 original size:11 final size:11
Alignment explanation
Indices: 3879666--3879735 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
3879656 ATAGTTTAAG
*
3879666 AAAATTAATAT
1 AAAATTAAAAT
3879677 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
3879689 AATAA-T-AATT
1 AA-AATTAAAAT
3879699 AAAA--AAAAT
1 AAAATTAAAAT
3879708 AAAATTAAAAT
1 AAAATTAAAAT
*
3879719 AAACTTAAAAT
1 AAAATTAAAAT
*
3879730 AGAATT
1 AAAATT
3879736 TCTTATTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
9 9 0.19
10 5 0.10
11 25 0.52
12 7 0.15
13 2 0.04
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:3883424 original size:23 final size:23
Alignment explanation
Indices: 3883342--3883428 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
3883332 CCTGATCAGT
*
3883342 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
3883364 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
3883384 ATACGACACACGATGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
3883407 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
3883429 TCGATAAAGC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.02
21 33 0.61
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:3890116 original size:39 final size:37
Alignment explanation
Indices: 3890049--3890141 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
3890039 ACCAGAATGG
* *
3890049 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
3890088 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
3890125 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
3890142 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:3891267 original size:17 final size:16
Alignment explanation
Indices: 3891235--3891268 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3891225 TTGGCTATTC
*
3891235 TGTTTCTTTCTTCTTT
1 TGTTTCTTTATTCTTT
3891251 TGTTTCTTTTATTCTTT
1 TGTTTC-TTTATTCTTT
3891268 T
1 T
3891269 ATTTTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTATTCTTT
Found at i:3891316 original size:14 final size:14
Alignment explanation
Indices: 3891257--3891307 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
3891247 CTTTTGTTTC
*
3891257 TTTTA-TTCTTTTA
1 TTTTATTTCCTTTA
* *
3891270 TTTTAACTTACTTTA
1 TTTT-ATTTCCTTTA
*
3891285 CTTTATTTCCTTTA
1 TTTTATTTCCTTTA
3891299 TTTTATTTC
1 TTTTATTTC
3891308 TTTTGTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 4 0.13
14 17 0.57
15 9 0.30
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTCCTTTA
Found at i:3901369 original size:46 final size:46
Alignment explanation
Indices: 3901319--3901494 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
3901309 TGGTTGAGCA
3901319 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
3901365 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
3901410 CATCCGAACTCGTTGATTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
3901458 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3901495 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:3901475 original size:93 final size:93
Alignment explanation
Indices: 3901316--3901487 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
3901306 GGATGGTTGA
* *
3901316 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3901381 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
3901409 GCATCCGAACTCGTTGATTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
3901474 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
3901488 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:3903327 original size:46 final size:44
Alignment explanation
Indices: 3903223--3903330 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
3903213 TGTCTTTGAC
** * * *
3903223 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
3903267 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
3903313 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
3903331 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:3909534 original size:20 final size:20
Alignment explanation
Indices: 3909492--3909534 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
3909482 ATATATATTC
* ** *
3909492 TAAATTTTTTTTTCAGGATT
1 TAAATTTTTTTTCCAAAAAT
3909512 TAAATTTTTTTTCCAAAAAT
1 TAAATTTTTTTTCCAAAAAT
3909532 TAA
1 TAA
3909535 TAAAATTATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (20 bp):
TAAATTTTTTTTCCAAAAAT
Found at i:3920575 original size:82 final size:83
Alignment explanation
Indices: 3920423--3920575 Score: 211
Period size: 82 Copynumber: 1.9 Consensus size: 83
3920413 TAAAAAATTC
* * * *
3920423 AATTTAATCCTCTTATAAATAGAAAATTTATAAATATATATATAGTGAAATTGCACTTTAACCTC
1 AATTTAATCCTCTTATAAATAGAAAAATTATAAATATATATATAGTAAAATTACACTTTAACCCC
*
3920488 TTAAAATAATTTTTTTTT
66 CTAAAATAATTTTTTTTT
* * *
3920506 AATTTAGTCTTCTTATAAATA-AAAAATTATAAAT-TAATATATAGTAAAATTACACTTTAGCCC
1 AATTTAATCCTCTTATAAATAGAAAAATTATAAATAT-ATATATAGTAAAATTACACTTTAACCC
3920569 CCTAAAA
65 CCTAAAA
3920576 ATAAAAATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
81 1 0.02
82 41 0.67
83 19 0.31
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.41
Consensus pattern (83 bp):
AATTTAATCCTCTTATAAATAGAAAAATTATAAATATATATATAGTAAAATTACACTTTAACCCC
CTAAAATAATTTTTTTTT
Found at i:3936098 original size:47 final size:47
Alignment explanation
Indices: 3935963--3936169 Score: 175
Period size: 47 Copynumber: 4.3 Consensus size: 47
3935953 ATAGTAAAAT
** * *
3935963 TATGGTCTTGCACA-TAGTCACATATCACATACCGAGGCCATAGCCCAGC
1 TATGGTCTTATACAGTAG-CACATATCAC--ACCGATGCCATAGCCCAGA
* * * * * *
3936012 CATGGTCTTATAC-GGATCACATATCACACTGATGTCATATCCCAGA
1 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
* *
3936058 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATATCCCGGA
1 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
* * * * *
3936105 TATGGTCTTATACGGAAGCACAAATCACATTTCTCTGAAGCCATAGCCCAGC
1 TATGGTCTTATACAGTAGCACATATCACA---C-C-GATGCCATAGCCCAGA
3936157 TATGGTCTTATAC
1 TATGGTCTTATAC
3936170 GGAAATCACA
Statistics
Matches: 128, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
46 26 0.20
47 54 0.42
48 10 0.08
49 11 0.09
50 1 0.01
51 1 0.01
52 25 0.20
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (47 bp):
TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
Found at i:3941749 original size:13 final size:13
Alignment explanation
Indices: 3941731--3941757 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3941721 AAAATGAACT
3941731 ATTATCAATGGAC
1 ATTATCAATGGAC
3941744 ATTATCAATGGAC
1 ATTATCAATGGAC
3941757 A
1 A
3941758 GCCTTGTGTA
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATTATCAATGGAC
Found at i:3950982 original size:44 final size:44
Alignment explanation
Indices: 3950934--3951017 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
3950924 GTAGTAATCA
3950934 TTTTATCCTTGTGTGGTTTAGATCTAAGAACGGTCCATCTAATT
1 TTTTATCCTTGTGTGGTTTAGATCTAAGAACGGTCCATCTAATT
3950978 TTTTATCCTTGTGTGGTTTAGATCTAAGAACGGTCCATCT
1 TTTTATCCTTGTGTGGTTTAGATCTAAGAACGGTCCATCT
3951018 GGTTTTGCTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (44 bp):
TTTTATCCTTGTGTGGTTTAGATCTAAGAACGGTCCATCTAATT
Found at i:3955259 original size:16 final size:17
Alignment explanation
Indices: 3955238--3955273 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
3955228 TTGAGATTAA
3955238 TTTAAAATTTTAAT-TT
1 TTTAAAATTTTAATATT
3955254 TTTAAAATTTTAATATT
1 TTTAAAATTTTAATATT
3955271 TTT
1 TTT
3955274 GCTTCAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTAAAATTTTAATATT
Found at i:3956899 original size:17 final size:17
Alignment explanation
Indices: 3956873--3956906 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3956863 CTCTTTCTGA
3956873 TTGTTTCTTTTT-TTTT
1 TTGTTTCTTTTTATTTT
3956889 TTGTATTCTTTTTATTTT
1 TTGT-TTCTTTTTATTTT
3956907 AATGGTTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 8 0.50
18 4 0.25
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.82
Consensus pattern (17 bp):
TTGTTTCTTTTTATTTT
Found at i:3963990 original size:30 final size:30
Alignment explanation
Indices: 3963955--3964015 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
3963945 ACGCACCATC
*
3963955 TATCCAAACTCACCTAAGTAAACTTCAATA
1 TATCCAAACTAACCTAAGTAAACTTCAATA
3963985 TATCCAAACTAACCTAAGTAAACTTCAATA
1 TATCCAAACTAACCTAAGTAAACTTCAATA
3964015 T
1 T
3964016 TATTCAAAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.44, C:0.25, G:0.03, T:0.28
Consensus pattern (30 bp):
TATCCAAACTAACCTAAGTAAACTTCAATA
Found at i:3969849 original size:18 final size:18
Alignment explanation
Indices: 3969826--3969866 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3969816 AAATAATTTT
**
3969826 TAATTTTTTTAAAAAATA
1 TAATTTTTAAAAAAAATA
3969844 TAATTTTTAAAAAAAATA
1 TAATTTTTAAAAAAAATA
3969862 -AATTT
1 TAATTT
3969867 AAAATGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATTTTTAAAAAAAATA
Found at i:3969866 original size:17 final size:16
Alignment explanation
Indices: 3969831--3969862 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3969821 ATTTTTAATT
*
3969831 TTTTTAAAAAATATAA
1 TTTTTAAAAAAAATAA
3969847 TTTTTAAAAAAAATAA
1 TTTTTAAAAAAAATAA
3969863 ATTTAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTTTAAAAAAAATAA
Found at i:3969867 original size:15 final size:16
Alignment explanation
Indices: 3969833--3969870 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3969823 TTTTAATTTT
* *
3969833 TTTAAAAAATATAATT
1 TTTAAAAAAAATAATA
3969849 TTTAAAAAAAATAA-A
1 TTTAAAAAAAATAATA
3969864 TTTAAAA
1 TTTAAAA
3969871 TGTTAATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TTTAAAAAAAATAATA
Found at i:3970016 original size:3 final size:3
Alignment explanation
Indices: 3970008--3970032 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3969998 GCTAAAATGT
3970008 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
3970033 AACCGATCAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3979361 original size:46 final size:46
Alignment explanation
Indices: 3979297--3979446 Score: 158
Period size: 46 Copynumber: 3.1 Consensus size: 46
3979287 ACACACTGTA
*
3979297 GCCATAGCCCAGCCATGGTCTTACACGAATCACATATCACATTGAT
1 GCCATAGCCCAGCTATGGTCTTACACGAATCACATATCACATTGAT
* * * * *
3979343 GCCATATCCCAGATATGGTCTTATACGGAAGCACGTAATCACATATCTCTGAT
1 GCCATAGCCCAGCTATGGTCTTACAC-GAATCACAT-ATCAC--A--T-TGAT
*
3979396 GCCATAGCCCAGCTACGGTCTTACAC-AGATCACATATCACATTGAT
1 GCCATAGCCCAGCTATGGTCTTACACGA-ATCACATATCACATTGAT
3979442 GCCAT
1 GCCAT
3979447 GGTCCAACCA
Statistics
Matches: 84, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
46 31 0.37
47 8 0.10
48 5 0.06
49 1 0.01
50 1 0.01
51 6 0.07
52 6 0.07
53 26 0.31
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (46 bp):
GCCATAGCCCAGCTATGGTCTTACACGAATCACATATCACATTGAT
Found at i:3980631 original size:23 final size:22
Alignment explanation
Indices: 3980529--3980635 Score: 123
Period size: 21 Copynumber: 5.0 Consensus size: 22
3980519 CCTGATCAGT
*
3980529 ATACGACACATAA-GTGCCTGA
1 ATACGACACACAAGGTGCCTGA
* *
3980550 A-ACGACACACGAGGTACCTGA
1 ATACGACACACAAGGTGCCTGA
*
3980571 A-ACGACACACGAGGTGCCTG-
1 ATACGACACACAAGGTGCCTGA
3980591 ATACGACACACAAGGTGCCTGAA
1 ATACGACACACAAGGTGCCTG-A
* *
3980614 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAGGTGCCTGA
3980636 TCAGTATAGC
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.13
21 45 0.60
22 1 0.01
23 19 0.25
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.14
Consensus pattern (22 bp):
ATACGACACACAAGGTGCCTGA
Found at i:3980872 original size:28 final size:29
Alignment explanation
Indices: 3980840--3980951 Score: 176
Period size: 28 Copynumber: 4.0 Consensus size: 29
3980830 AACACACCAG
* *
3980840 TATAATCC-TCCAAAACACACCAGTATCA
1 TATAATCCATCCAAAACACACCAGAATAA
*
3980868 TATAATCC-TCCCAAACACACCAGAATAA
1 TATAATCCATCCAAAACACACCAGAATAA
3980896 TATAATCCATCCAAAACACACCAGAATAA
1 TATAATCCATCCAAAACACACCAGAATAA
3980925 TATAATCCATCCAAAACAC-CCAGAATA
1 TATAATCCATCCAAAACACACCAGAATA
3980952 GCACAAAGTG
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 41 0.52
29 38 0.48
ACGTcount: A:0.47, C:0.30, G:0.04, T:0.19
Consensus pattern (29 bp):
TATAATCCATCCAAAACACACCAGAATAA
Found at i:3980912 original size:57 final size:56
Alignment explanation
Indices: 3980840--3980951 Score: 172
Period size: 57 Copynumber: 2.0 Consensus size: 56
3980830 AACACACCAG
* * *
3980840 TATAATCCTCCAAAACACACCAGTATCATATAATCC-TCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAATATAATCCATCCAAAACAC-CCAGAATAA
3980896 TATAATCCATCCAAAACACACCAGAATAATATAATCCATCCAAAACACCCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATAATATAATCCATCCAAAACACCCAGAATA
3980952 GCACAAAGTG
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
56 8 0.16
57 34 0.67
58 9 0.18
ACGTcount: A:0.47, C:0.30, G:0.04, T:0.19
Consensus pattern (56 bp):
TATAATCCTCCAAAACACACCAGAATAATATAATCCATCCAAAACACCCAGAATAA
Found at i:3986676 original size:46 final size:46
Alignment explanation
Indices: 3986611--3986716 Score: 133
Period size: 46 Copynumber: 2.3 Consensus size: 46
3986601 TTATCTTTGA
* * * * * *
3986611 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
3986657 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
3986703 CAGGTTGCCATGGT
1 CATGTTGCCATGGT
3986717 GTAATAGCCC
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
45 4 0.08
46 48 0.92
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:3988805 original size:52 final size:49
Alignment explanation
Indices: 3988720--3989086 Score: 440
Period size: 46 Copynumber: 7.6 Consensus size: 49
3988710 TTTGAGTACT
* **
3988720 TCTGATCAAGTG---ATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
3988766 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
3988818 TCTGATCAAGTG---ATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
3988864 TCTGATCAAGTGAC---AAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
3988910 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
3988962 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* **
3989014 TCTGATCAAGAGAC---AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
3989060 TCTGATCAAGAGAC---AAAGTGATAAGTG
1 TCTGATCAAGTGACAATAAAGTGATAAGTG
3989087 GCTACACTTA
Statistics
Matches: 292, Mismatches: 15, Indels: 28
0.87 0.04 0.08
Matches are distributed among these distances:
46 155 0.53
48 1 0.00
49 2 0.01
50 1 0.00
52 133 0.46
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (49 bp):
TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:3988840 original size:98 final size:97
Alignment explanation
Indices: 3988720--3989086 Score: 501
Period size: 98 Copynumber: 3.7 Consensus size: 97
3988710 TTTGAGTACT
* *
3988720 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
*
3988785 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
* *
3988818 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
3988878 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
3988910 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
3988975 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * * *
3989014 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGT
3989079 GATAAGTG
65 GA-AAGTG
3989087 GCTACACTTA
Statistics
Matches: 240, Mismatches: 15, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
92 41 0.17
95 1 0.00
96 1 0.00
98 145 0.60
99 10 0.04
101 1 0.00
104 41 0.17
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (97 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:3989068 original size:196 final size:196
Alignment explanation
Indices: 3988734--3989086 Score: 607
Period size: 196 Copynumber: 1.8 Consensus size: 196
3988724 ATCAAGTGAT
* * *
3988734 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
* * * *
3988799 ATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
3988864 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
3988929 G
196 G
* *
3988930 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
*
3988995 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
3989060 TCTGATCAAGAGACAAAGTGATAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTG
3989087 GCTACACTTA
Statistics
Matches: 146, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
196 146 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (196 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
G
Found at i:3989094 original size:37 final size:37
Alignment explanation
Indices: 3989050--3989195 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
3989040 GATAGCTTTA
*
3989050 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
3989087 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
* *
3989124 GCTACACTTATGTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
3989161 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
3989196 ATCATACGTA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 87 0.85
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:3989123 original size:150 final size:149
Alignment explanation
Indices: 3988720--3989075 Score: 467
Period size: 150 Copynumber: 2.4 Consensus size: 149
3988710 TTTGAGTACT
* * * * *
3988720 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
* * * *
3988785 GAAAGTGATAAGTAATAGCTTC-G---GCTATACTTATC---TGATCAAGTGATAAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGCAAACTAAACTGATCAAGTGA-CAAGTGATAAAGTGATAAG
3988843 TGATAGCTTCGGCTATACTTA
129 TGATAGCTTCGGCTATACTTA
* *
3988864 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
* * * * *
3988929 GAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA-AAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGC-AAACTAAACTGATCAAGTGACAAGTGATAAAGTGATAAG
3988993 TGATAGCTTCGGCTATACTTA
129 TGATAGCTTCGGCTATACTTA
*
3989014 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAA
3989076 AGTGATAAGT
Statistics
Matches: 192, Mismatches: 12, Indels: 10
0.90 0.06 0.05
Matches are distributed among these distances:
144 83 0.43
145 1 0.01
149 7 0.04
150 91 0.47
151 7 0.04
152 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (149 bp):
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
GAAAGTGATAACTATAGCTTCAGCAAACTAAACTGATCAAGTGACAAGTGATAAAGTGATAAGTG
ATAGCTTCGGCTATACTTA
Found at i:3989139 original size:150 final size:143
Alignment explanation
Indices: 3988720--3989091 Score: 382
Period size: 144 Copynumber: 2.6 Consensus size: 143
3988710 TTTGAGTACT
* * * * *
3988720 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC-----
* * * * * * *
3988785 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTG---A-T--AAAGTGATAAGT
61 GAAAGTGATAAGT--GAGCTACGACTACACTGATCAGAACAAGTGACAAGTGAAAAGTGATAAGT
3988844 GATAGCTTCGGCTATACTTA
124 GATAGCTTCGGCTATACTTA
* *
3988864 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC-----
* * * * *
3988929 GAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGT
61 GAAAGTGATAAGTG--AGCTACGACTACACTGATCAGAACAAGTGACAAGTGAAAAGTGATAAGT
3988994 GATAGCTTCGGCTATACTTA
124 GATAGCTTCGGCTATACTTA
*
3989014 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC-AAAG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACGAAAG
3989078 TGATAAGTG-GCTAC
66 TGATAAGTGAGCTAC
3989092 ACTTATCTGA
Statistics
Matches: 211, Mismatches: 9, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
141 4 0.02
144 116 0.55
147 1 0.00
148 1 0.00
150 89 0.42
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (143 bp):
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACGAAAG
TGATAAGTGAGCTACGACTACACTGATCAGAACAAGTGACAAGTGAAAAGTGATAAGTGATAGCT
TCGGCTATACTTA
Found at i:3989864 original size:46 final size:46
Alignment explanation
Indices: 3989797--3989970 Score: 312
Period size: 46 Copynumber: 3.8 Consensus size: 46
3989787 GGGTGTTACA
* * *
3989797 CATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCATGTTGC
1 CATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGC
*
3989843 CATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGC
1 CATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGC
3989889 CATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGC
1 CATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGC
3989935 CATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGGTATCTTTCAACCATGGTCTTACACATTTCAT
3989971 TTCAAAGAGC
Statistics
Matches: 125, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 125 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (46 bp):
CATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGC
Found at i:3992440 original size:30 final size:30
Alignment explanation
Indices: 3992373--3992440 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
3992363 CACCCTTAAA
* * *
3992373 ATATTTGCACTATTAGTCCTTCAACTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
*
3992403 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAAATTTTC
3992432 AGTATTTAC
1 A-TATTTAC
3992441 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:3995198 original size:46 final size:46
Alignment explanation
Indices: 3995138--3995498 Score: 596
Period size: 46 Copynumber: 7.8 Consensus size: 46
3995128 TTTGACATGA
* * * * ** * * *
3995138 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*
3995184 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
* * *
3995230 TGTCATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
3995276 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*
3995322 TGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
3995368 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
3995414 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
3995460 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
3995499 TTCAAAGAGC
Statistics
Matches: 300, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 300 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
Found at i:3997650 original size:39 final size:38
Alignment explanation
Indices: 3997607--3997696 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 38
3997597 ATATGGCACT
*
3997607 CAGTGCCTCATCGG-ATAGTTCGAAGTAATAGTTGACACC
1 CAGTGCCTCATCGGCATAG-CCGAAGTAA-AGTTGACACC
* * **
3997646 CAGTGTCTCATCGGCCTAGCCGAAGTAAAGTTGGTACC
1 CAGTGCCTCATCGGCATAGCCGAAGTAAAGTTGACACC
*
3997684 CAGTACCTCATCG
1 CAGTGCCTCATCG
3997697 AATCTATCCG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
38 19 0.44
39 21 0.49
40 3 0.07
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (38 bp):
CAGTGCCTCATCGGCATAGCCGAAGTAAAGTTGACACC
Found at i:3999647 original size:21 final size:20
Alignment explanation
Indices: 3999621--3999680 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
3999611 TTAAGTAATC
3999621 ATAATAATTTAATATAAAACT
1 ATAATAATTTAATATAAAA-T
* * *
3999642 ATAATAATAATCATTATAATAT
1 ATAATAAT--TTAATATAAAAT
3999664 ATATATAATTTAATATA
1 ATA-ATAATTTAATATA
3999681 TAAAACCTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 14 0.45
22 4 0.13
23 13 0.42
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAATAATTTAATATAAAAT
Found at i:4003587 original size:46 final size:46
Alignment explanation
Indices: 4003511--4003824 Score: 443
Period size: 46 Copynumber: 6.8 Consensus size: 46
4003501 TGATGTCATA
* * * * *
4003511 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATATCAGGTTGCCATG
* *** *
4003557 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGTTGCCATG
*
4003604 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
4003650 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
*
4003696 TTATCTTTCAACCATGGTCTTA-TACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACT-CATTTCATATCAGGTTGCCATG
*
4003742 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
*
4003788 GTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAG
4003825 AGAGCACACT
Statistics
Matches: 248, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
45 1 0.00
46 208 0.84
47 39 0.16
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
Found at i:4013817 original size:15 final size:17
Alignment explanation
Indices: 4013787--4013819 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
4013777 AATGATTTGT
4013787 TAATCAACTCATCATCA
1 TAATCAACTCATCATCA
4013804 TAATCAA-T-ATCATCA
1 TAATCAACTCATCATCA
4013819 T
1 T
4013820 CCTCAATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.33
Consensus pattern (17 bp):
TAATCAACTCATCATCA
Found at i:4020119 original size:5 final size:5
Alignment explanation
Indices: 4020109--4020146 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
4020099 ACAATATCTC
* *
4020109 TTTCT TTTCT TTTCT TTTCT TTTCC TTTCC TTT-T TTTC
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
4020147 GCTCTTCGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 27 0.90
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTCT
Found at i:4026240 original size:13 final size:13
Alignment explanation
Indices: 4026224--4026251 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4026214 AAATTAATAC
4026224 AAATTATAATCTA
1 AAATTATAATCTA
4026237 AAATTATAATCTA
1 AAATTATAATCTA
4026250 AA
1 AA
4026252 TTAAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATTATAATCTA
Found at i:4031662 original size:16 final size:17
Alignment explanation
Indices: 4031634--4031665 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4031624 ATTTATATTT
4031634 TTTAAATAAAATTAATA
1 TTTAAATAAAATTAATA
4031651 TTTAAA-AAAATTAAT
1 TTTAAATAAAATTAAT
4031666 GATATTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTAAATAAAATTAATA
Found at i:4050476 original size:270 final size:269
Alignment explanation
Indices: 4049996--4050538 Score: 1016
Period size: 270 Copynumber: 2.0 Consensus size: 269
4049986 TATCACCTAG
4049996 AGGCAGAGTAGATAAACTTCCTGTCTGTTCTTGTGTGATATCCTGATGTTCTCATCAGTTTGGGA
1 AGGCAGAGTAGATAAACTTCCTGTCTGTTCTTGTGTGATATCCTGATGTTCTCATCAGTTTGGGA
4050061 TTTAAAAAAAAAAAGTTTTCAGTTCAATTTGCTTTATAAAGAAGATACCAGATTTTGTTTCCAAT
66 TTTAAAAAAAAAAAGTTTTCAGTTCAATTTGCTTTATAAAGAAGATACCAGATTTTGTTTCCAAT
4050126 TGACGAGAACAAAGTAATACATTGTTAGATGTAGGCTACATAGCTACATTTTTGCATGTGAAATG
131 TGACGAGAACAAAGTAATACATTGTTAGATGTAGGCTACATAGCTACATTTTTGCATGTGAAATG
*
4050191 ATTAACCAAGTGCAAAGTATATCATCAAGTTGAGCTAGTGCTATATCTGGCAATATAGTTGCTTT
196 ATTAACCAAGTGCAAAGTATATCATCAAGTTGAGCTAGTGCTATATCTGGCAAAATAGTTGCTTT
4050256 GAGTCAAAA
261 GAGTCAAAA
4050265 AGGCAGAGTAGATAAACTTCCTAG-CTGTTCTTGTGTGATATCCTGATGTTCTCATCAGTTTGGG
1 AGGCAGAGTAGATAAACTTCCT-GTCTGTTCTTGTGTGATATCCTGATGTTCTCATCAGTTTGGG
*
4050329 ATTTTAAAAAGAAAAAGTTTTCAGTTCAATTTGCTTTATAAAGAAGATACCAGATTTTGTTTCCA
65 A-TTTAAAAAAAAAAAGTTTTCAGTTCAATTTGCTTTATAAAGAAGATACCAGATTTTGTTTCCA
* *
4050394 ATTGACGAGAACAAAGTAATACATTGTTAGATGTAGGCTATATTGCTACATTTTTGCATGTGAAA
129 ATTGACGAGAACAAAGTAATACATTGTTAGATGTAGGCTACATAGCTACATTTTTGCATGTGAAA
4050459 TGATTAACCAAGTGCAAAGTATATCATCAAGTTGAGCTAGTGCTATATCTGGCAAAATAGTTGCT
194 TGATTAACCAAGTGCAAAGTATATCATCAAGTTGAGCTAGTGCTATATCTGGCAAAATAGTTGCT
*
4050524 TTGAGTCCAAA
259 TTGAGTCAAAA
4050535 AGGC
1 AGGC
4050539 TAAAAAAAGG
Statistics
Matches: 267, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
269 63 0.24
270 204 0.76
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (269 bp):
AGGCAGAGTAGATAAACTTCCTGTCTGTTCTTGTGTGATATCCTGATGTTCTCATCAGTTTGGGA
TTTAAAAAAAAAAAGTTTTCAGTTCAATTTGCTTTATAAAGAAGATACCAGATTTTGTTTCCAAT
TGACGAGAACAAAGTAATACATTGTTAGATGTAGGCTACATAGCTACATTTTTGCATGTGAAATG
ATTAACCAAGTGCAAAGTATATCATCAAGTTGAGCTAGTGCTATATCTGGCAAAATAGTTGCTTT
GAGTCAAAA
Found at i:4052856 original size:13 final size:14
Alignment explanation
Indices: 4052829--4052858 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4052819 AACAAGGTTC
4052829 TTTTGTTCAATTTT
1 TTTTGTTCAATTTT
*
4052843 TTTTGTTCCATTTT
1 TTTTGTTCAATTTT
4052857 TT
1 TT
4052859 GCATGTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.10, G:0.07, T:0.73
Consensus pattern (14 bp):
TTTTGTTCAATTTT
Found at i:4054689 original size:14 final size:15
Alignment explanation
Indices: 4054661--4054691 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4054651 TTAAAATATT
4054661 TTTTAATATTTAAAC
1 TTTTAATATTTAAAC
4054676 TTTTAATA-TTAAAC
1 TTTTAATATTTAAAC
4054690 TT
1 TT
4054692 ATAACATACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTAATATTTAAAC
Found at i:4054983 original size:24 final size:23
Alignment explanation
Indices: 4054940--4054998 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
4054930 TGCGACCCAT
4054940 TTTTTTAATAATATAATTTATTA
1 TTTTTTAATAATATAATTTATTA
*
4054963 TTTTTTAA-AATATTATTTTTATTA
1 TTTTTTAATAATA-TA-ATTTATTA
*
4054987 TATTTTAATAAT
1 TTTTTTAATAAT
4054999 TTTTAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 4 0.13
23 10 0.32
24 14 0.45
25 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTTTTAATAATATAATTTATTA
Found at i:4055080 original size:27 final size:27
Alignment explanation
Indices: 4055050--4055113 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
4055040 GCCAGACCCG
4055050 GAGGCGCGACCAGTCGCTCCTGCTGCA
1 GAGGCGCGACCAGTCGCTCCTGCTGCA
*
4055077 GAGGCGTGACCAGTCGCTCCTGCTGCA
1 GAGGCGCGACCAGTCGCTCCTGCTGCA
4055104 GAGGCGCGAC
1 GAGGCGCGAC
4055114 TCCCCTGCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.16, C:0.34, G:0.36, T:0.14
Consensus pattern (27 bp):
GAGGCGCGACCAGTCGCTCCTGCTGCA
Found at i:4057365 original size:3 final size:3
Alignment explanation
Indices: 4057359--4057430 Score: 74
Period size: 3 Copynumber: 23.7 Consensus size: 3
4057349 ACTAACATTT
* * * * *
4057359 TTC TTC TTTC TCC TCC TTC TCC TTT TTC TTC TTC TTC TTT TTC TTC
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
4057405 TTC TTC TTC TTC TTC TT- TTC TCTC TT
1 TTC TTC TTC TTC TTC TTC TTC T-TC TT
4057431 TGCTGCTGCA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.03
3 50 0.86
4 6 0.10
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:4057695 original size:16 final size:16
Alignment explanation
Indices: 4057666--4057705 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
4057656 TAAAATATAA
*
4057666 TAAAATAATAATATTTT
1 TAAAA-AATAATATTAT
*
4057683 TAAAAAATTATATTAT
1 TAAAAAATAATATTAT
4057699 TAAAAAA
1 TAAAAAA
4057706 ATGGGTCGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAAAAATAATATTAT
Found at i:4060608 original size:26 final size:25
Alignment explanation
Indices: 4060574--4060625 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
4060564 CTTTTTACTT
* *
4060574 AAAAAAAAGTTTAAAAATATTCATA
1 AAAAAAAAGTATAAAAACATTCATA
*
4060599 AAAAATAAAGTATAAAAACATTTATA
1 AAAAA-AAAGTATAAAAACATTCATA
4060625 A
1 A
4060626 TTTAAATCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (25 bp):
AAAAAAAAGTATAAAAACATTCATA
Found at i:4069137 original size:21 final size:21
Alignment explanation
Indices: 4069113--4069163 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
4069103 CATATTTTAG
4069113 ATATAAAATAATTA-AATATAA
1 ATAT-AAATAATTATAATATAA
* *
4069134 ATATTAATAATTATATTATAA
1 ATATAAATAATTATAATATAA
*
4069155 ATATTAATA
1 ATATAAATA
4069164 TTAATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATAAATAATTATAATATAA
Found at i:4069170 original size:21 final size:21
Alignment explanation
Indices: 4069119--4069173 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
4069109 TTAGATATAA
*
4069119 AATAATTA-AATATAAATATT
1 AATAATTATATTATAAATATT
4069139 AATAATTATATTATAAATATT
1 AATAATTATATTATAAATATT
4069160 AAT-ATTAATATTAT
1 AATAATT-ATATTAT
4069174 TAATTAACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAATTATATTATAAATATT
Found at i:4069189 original size:27 final size:27
Alignment explanation
Indices: 4069120--4069190 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
4069110 TAGATATAAA
4069120 ATAATTAAATATA-AATATTAATAATT
1 ATAATTAAATATATAATATTAATAATT
*
4069146 ATATTATAAATAT-TAATATTAAT-ATT
1 ATAAT-TAAATATATAATATTAATAATT
*
4069172 ATTAATTAACTATATAATA
1 A-TAATTAAATATATAATA
4069191 ATCCAACAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
26 14 0.37
27 24 0.63
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (27 bp):
ATAATTAAATATATAATATTAATAATT
Found at i:4069358 original size:18 final size:18
Alignment explanation
Indices: 4069328--4069371 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 18
4069318 AATTATACTA
4069328 AAAAAAGAAAAAAAAACCAG
1 AAAAAAGAAAAAAAAA--AG
4069348 AAAAAAGAAAAAAAAAAG
1 AAAAAAGAAAAAAAAAAG
4069366 AAAAAA
1 AAAAAA
4069372 CCTACCAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.33
20 16 0.67
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAAAAAAG
Found at i:4080989 original size:4 final size:4
Alignment explanation
Indices: 4080982--4081024 Score: 59
Period size: 4 Copynumber: 10.0 Consensus size: 4
4080972 GACTGACTTA
4080982 AATT AATT AATT AATT AATT GAATT AAATT AATT AATTT AATT
1 AATT AATT AATT AATT AATT -AATT -AATT AATT AA-TT AATT
4081025 TTAATCGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
4 24 0.67
5 12 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (4 bp):
AATT
Found at i:4081013 original size:18 final size:16
Alignment explanation
Indices: 4080982--4081024 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 16
4080972 GACTGACTTA
4080982 AATTAATTAATTAATT
1 AATTAATTAATTAATT
4080998 AATTGAATTAAATTAATT
1 AATT-AATT-AATTAATT
4081016 AATTTAATT
1 AA-TTAATT
4081025 TTAATCGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.17
17 4 0.17
18 14 0.58
19 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
AATTAATTAATTAATT
Found at i:4083816 original size:15 final size:16
Alignment explanation
Indices: 4083786--4083824 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
4083776 TAGTAAAAAT
4083786 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
4083803 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
4083818 ATAATTT
1 ATAATTT
4083825 TTAAAGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:4087981 original size:19 final size:18
Alignment explanation
Indices: 4087957--4088000 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
4087947 TAACAACGAG
*
4087957 ATTCTTTTCTCCTTCTCTT
1 ATTCTTTTC-CCTTCACTT
4087976 ATTC-TTTCCCTTCACTT
1 ATTCTTTTCCCTTCACTT
4087993 ATT-TTTTC
1 ATTCTTTTC
4088001 AAAAAATCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 15 0.65
18 4 0.17
19 4 0.17
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTCTTTTCCCTTCACTT
Found at i:4095210 original size:73 final size:73
Alignment explanation
Indices: 4095128--4095386 Score: 473
Period size: 73 Copynumber: 3.5 Consensus size: 73
4095118 ACAACTTGAC
4095128 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
4095193 CACTAACA
66 CACTAACA
* *
4095201 AACTTAGTTGGAATACAACTAAGTTTTATCATTACATCCACTTAAAATAAATCACCACCTATTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
4095266 CACTAACA
66 CACTAACA
* *
4095274 AACTTAGTTGGAATACAACTAAGTTTTATCATTACATCCACTTAAAATAAATCACCACCAACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
4095339 CACTAACA
66 CACTAACA
*
4095347 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
4095387 AATAATAATA
Statistics
Matches: 180, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 180 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:4097061 original size:30 final size:30
Alignment explanation
Indices: 4097013--4097072 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
4097003 AAGATTTAAG
*
4097013 AAAAAAGAGAGCTTAGATTAGAAACATACT
1 AAAAAAAAGAGCTTAGATTAGAAACATACT
*
4097043 AAAAAAAAGA-CTTCAGATTAGTAACATACT
1 AAAAAAAAGAGCTT-AGATTAGAAACATACT
4097073 TATTTTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 3 0.11
30 24 0.89
ACGTcount: A:0.53, C:0.12, G:0.13, T:0.22
Consensus pattern (30 bp):
AAAAAAAAGAGCTTAGATTAGAAACATACT
Found at i:4104482 original size:2 final size:2
Alignment explanation
Indices: 4104475--4104500 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4104465 CACATTCAAA
4104475 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
4104501 GAGAGATTCA
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:4107183 original size:53 final size:53
Alignment explanation
Indices: 4107027--4107192 Score: 221
Period size: 53 Copynumber: 3.1 Consensus size: 53
4107017 GACGAAAAAT
* **
4107027 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
4107079 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
4107132 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
4107186 TATGTGA
1 -ATGTGA
4107193 ACCGTGTAAG
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 81 0.79
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:4114702 original size:53 final size:53
Alignment explanation
Indices: 4114546--4114711 Score: 221
Period size: 53 Copynumber: 3.1 Consensus size: 53
4114536 GACGAAAAAT
* **
4114546 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
4114598 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
4114651 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
4114705 TATGTGA
1 -ATGTGA
4114712 ACCGTGTAAG
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 81 0.79
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:4123466 original size:19 final size:19
Alignment explanation
Indices: 4123442--4123483 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
4123432 TTCTCCTTGG
4123442 AATCCATGCTGCGAATTCA
1 AATCCATGCTGCGAATTCA
4123461 AATCCATGCTGCGAATTCA
1 AATCCATGCTGCGAATTCA
4123480 AATC
1 AATC
4123484 ATTCAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (19 bp):
AATCCATGCTGCGAATTCA
Found at i:4135027 original size:9 final size:9
Alignment explanation
Indices: 4135013--4135044 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
4135003 AAAGTTTGCC
4135013 AAAAAGGGA
1 AAAAAGGGA
4135022 AAAAAGGGA
1 AAAAAGGGA
4135031 AAAAAGGGA
1 AAAAAGGGA
4135040 AAAAA
1 AAAAA
4135045 TAATGGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (9 bp):
AAAAAGGGA
Found at i:4141109 original size:28 final size:29
Alignment explanation
Indices: 4141076--4141139 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
4141066 CATGCTCATC
4141076 AAAATATA-ATTTAATTTAATTT-ATAAAT
1 AAAATATATATTTAA-TTAATTTAATAAAT
* *
4141104 AAAATA-ATATTTTATTAATTTAATAATT
1 AAAATATATATTTAATTAATTTAATAAAT
*
4141132 AAATTATA
1 AAAATATA
4141140 GTTAAGTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 8 0.27
28 21 0.70
29 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
AAAATATATATTTAATTAATTTAATAAAT
Found at i:4147738 original size:55 final size:53
Alignment explanation
Indices: 4147619--4147740 Score: 122
Period size: 55 Copynumber: 2.3 Consensus size: 53
4147609 TATAGTAGTA
* *
4147619 GTCACTCAATTATTAGTATTTTTTTATCACCTAACTATGAAAATTTATAAAAT
1 GTCAATCAATTATTAATATTTTTTTATCACCTAACTATGAAAATTTATAAAAT
* * * * * *
4147672 ATCATTTAATTATTAATAATTTTTTTTGTCA-CTGAATTATGAAATTTTA-AAAAT
1 GTCAATCAATTATTAAT-A-TTTTTTTATCACCT-AACTATGAAAATTTATAAAAT
4147726 GGTCAATCAATTATT
1 -GTCAATCAATTATT
4147741 CAATTTCATC
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
53 13 0.24
54 8 0.15
55 34 0.62
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (53 bp):
GTCAATCAATTATTAATATTTTTTTATCACCTAACTATGAAAATTTATAAAAT
Found at i:4149060 original size:29 final size:28
Alignment explanation
Indices: 4149028--4149083 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
4149018 TTTTTCTTAT
*
4149028 TTTTAATGACTTTTTGGTAACAAATATTG
1 TTTTAATGA-ATTTTGGTAACAAATATTG
** *
4149057 TTTTCTTGAATTTTGGTAACAATTATT
1 TTTTAATGAATTTTGGTAACAAATATT
4149084 ATTAAACAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (28 bp):
TTTTAATGAATTTTGGTAACAAATATTG
Found at i:4151707 original size:46 final size:46
Alignment explanation
Indices: 4151654--4151829 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 46
4151644 TTGTTGAGCA
*
4151654 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*** * * ** *
4151700 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-AAACG
* *
4151747 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
4151793 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4151830 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
46 69 0.66
47 36 0.34
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:4151810 original size:93 final size:93
Alignment explanation
Indices: 4151651--4151822 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
4151641 GGATTGTTGA
* * *
4151651 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACGCCCGAACTCGTTGAGT
4151716 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
4151744 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACGCCCGAACTCGTTGAGT
4151809 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
4151823 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:4154815 original size:15 final size:15
Alignment explanation
Indices: 4154776--4154854 Score: 90
Period size: 15 Copynumber: 5.4 Consensus size: 15
4154766 GTATCTTGGG
*
4154776 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
4154791 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
4154806 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
4154821 TTTCTCTATT-TGGA
1 TTTCTTTATTCTGGA
*
4154835 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
4154849 TTTCTT
1 TTTCTT
4154855 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.10, C:0.18, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:4157265 original size:46 final size:46
Alignment explanation
Indices: 4157212--4157387 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
4157202 TTGTTGAGCA
4157212 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
4157258 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
4157303 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
4157351 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4157388 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 65 0.58
47 28 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:4157368 original size:93 final size:93
Alignment explanation
Indices: 4157209--4157379 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
4157199 GGATTGTTGA
* *
4157209 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
4157274 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
4157302 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
4157367 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
4157380 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:4166934 original size:94 final size:94
Alignment explanation
Indices: 4166773--4166960 Score: 367
Period size: 94 Copynumber: 2.0 Consensus size: 94
4166763 TAATAACATC
4166773 GAACATGGGGTGTCAACTGAATAAACATAAGATGAATATGCATATTTCAAAAGATATTACCAGTA
1 GAACATGGGGTGTCAACTGAATAAACATAAGATGAATATGCATATTTCAAAAGATATTACCAGTA
4166838 GTAGCATTAGAAAATCTAGCAAGTATCTT
66 GTAGCATTAGAAAATCTAGCAAGTATCTT
*
4166867 GAACATGGGGTGTCAACTGAATAAACATAAGATGAATATGCATATTTCACAAGATATTACCAGTA
1 GAACATGGGGTGTCAACTGAATAAACATAAGATGAATATGCATATTTCAAAAGATATTACCAGTA
4166932 GTAGCATTAGAAAATCTAGCAAGTATCTT
66 GTAGCATTAGAAAATCTAGCAAGTATCTT
4166961 TGCATCTTGT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (94 bp):
GAACATGGGGTGTCAACTGAATAAACATAAGATGAATATGCATATTTCAAAAGATATTACCAGTA
GTAGCATTAGAAAATCTAGCAAGTATCTT
Found at i:4172798 original size:29 final size:29
Alignment explanation
Indices: 4172745--4172800 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
4172735 TTATTTAACA
*
4172745 AATAAAATCTTTAATATTAATATTTAATT
1 AATAAAATCTTTAATATTAAAATTTAATT
*
4172774 AATAAATATCTTTAA-CTTAAAATTTAA
1 AATAAA-ATCTTTAATATTAAAATTTAA
4172801 GTAAATACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (29 bp):
AATAAAATCTTTAATATTAAAATTTAATT
Found at i:4176420 original size:21 final size:21
Alignment explanation
Indices: 4176395--4176462 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 21
4176385 TATATTATTT
4176395 ATTATATA-AAGTATTAAATTA
1 ATTATATAGAA-TATTAAATTA
*
4176416 ATTATAAAGGATATTTATTAAATTA
1 ATTATATA-GA-A--TATTAAATTA
* *
4176441 ATTATATATAATATTATATTA
1 ATTATATAGAATATTAAATTA
4176462 A
1 A
4176463 GAAATAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
21 17 0.45
23 2 0.05
24 2 0.05
25 17 0.45
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (21 bp):
ATTATATAGAATATTAAATTA
Found at i:4176454 original size:25 final size:26
Alignment explanation
Indices: 4176406--4176462 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
4176396 TTATATAAAG
*
4176406 TATTAAATTAATTATAAAGGATATT-
1 TATTAAATTAATTATAAAGAATATTA
* *
4176431 TATTAAATTAATTATATATAATATTA
1 TATTAAATTAATTATAAAGAATATTA
4176457 TATTAA
1 TATTAA
4176463 GAAATAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 22 0.79
26 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (26 bp):
TATTAAATTAATTATAAAGAATATTA
Found at i:4177631 original size:24 final size:25
Alignment explanation
Indices: 4177586--4177645 Score: 61
Period size: 27 Copynumber: 2.4 Consensus size: 25
4177576 TTGTGAATAT
*
4177586 ATTG-ATTGAAGGTGGGAAAAA-TG
1 ATTGAATTGAAAGTGGGAAAAATTG
* *
4177609 ATTGAATTGAAAGTGTGAGAAATTGTG
1 ATTGAATTGAAAGTGGGA-AAAAT-TG
4177636 ATTGAATTGA
1 ATTGAATTGA
4177646 GATATATGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.13
24 11 0.37
25 3 0.10
27 12 0.40
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.32
Consensus pattern (25 bp):
ATTGAATTGAAAGTGGGAAAAATTG
Found at i:4178043 original size:13 final size:14
Alignment explanation
Indices: 4178018--4178058 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
4178008 TAGAAAAACG
4178018 TTGAAATTGTGAAA
1 TTGAAATTGTGAAA
4178032 TTGAAA-TGTGAAA
1 TTGAAATTGTGAAA
* *
4178045 -TGAGATTGAGAAA
1 TTGAAATTGTGAAA
4178058 T
1 T
4178059 GAACCTAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.17
13 13 0.57
14 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (14 bp):
TTGAAATTGTGAAA
Found at i:4179231 original size:17 final size:16
Alignment explanation
Indices: 4179209--4179240 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
4179199 CAACCTTTAT
4179209 TATAATAATGCTAATAA
1 TATAATAAT-CTAATAA
4179226 TATAATAATCTAATA
1 TATAATAATCTAATA
4179241 TGAAACCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
TATAATAATCTAATAA
Found at i:4183909 original size:23 final size:23
Alignment explanation
Indices: 4183824--4183915 Score: 102
Period size: 23 Copynumber: 4.1 Consensus size: 23
4183814 GTGTATGGTC
* *
4183824 GTGGTAGCTGCGG-TACATTTCA
1 GTGGTAGCTTCGGCTACATATCA
* * *
4183846 TTGCGTAGCTTTGGCTACAT-CCA
1 GTG-GTAGCTTCGGCTACATATCA
4183869 GT-GTAGCTTC-GCTACATATCA
1 GTGGTAGCTTCGGCTACATATCA
4183890 GTGGTAGCTTCGGCTACATATCA
1 GTGGTAGCTTCGGCTACATATCA
4183913 GTG
1 GTG
4183916 TTTGCACTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
20 7 0.12
21 11 0.19
22 10 0.17
23 25 0.43
24 5 0.09
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.33
Consensus pattern (23 bp):
GTGGTAGCTTCGGCTACATATCA
Found at i:4201678 original size:92 final size:91
Alignment explanation
Indices: 4201522--4201705 Score: 279
Period size: 92 Copynumber: 2.0 Consensus size: 91
4201512 TAATAACATC
4201522 GAACATGGGGTGTCAACTGAATAACATAAGATGAAATGCATATTTCAAAGATATTTACCAGTAGT
1 GAACATGGGGTGTCAACTGAATAACATAAGATGAAATGCATATTTCAAAGATATTTACCAGTAGT
4201587 AGCATTAGAAAATCTAGCAAGTA-CTT
66 AGCATTAG-AAATCTAGCAAGTATCTT
4201613 GAACAT-GGGTGTCAAACTGAATAAACATAAGATGAAATGTGCA-ATTTCACAA-ATA-TTACCA
1 GAACATGGGGTGTC-AACTGAAT-AACATAAGATGAAA--TGCATATTTCA-AAGATATTTACCA
4201674 GTAGTAGCATTAGAAATCTAGCAAGTATCTT
61 GTAGTAGCATTAGAAATCTAGCAAGTATCTT
4201705 G
1 G
4201706 CATCTTGTAC
Statistics
Matches: 87, Mismatches: 0, Indels: 11
0.89 0.00 0.11
Matches are distributed among these distances:
90 7 0.08
91 28 0.32
92 37 0.43
93 9 0.10
94 6 0.07
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (91 bp):
GAACATGGGGTGTCAACTGAATAACATAAGATGAAATGCATATTTCAAAGATATTTACCAGTAGT
AGCATTAGAAATCTAGCAAGTATCTT
Found at i:4207239 original size:14 final size:15
Alignment explanation
Indices: 4207215--4207244 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
4207205 CTAGTTTTTC
4207215 CTTTCCTTTTTCTTT
1 CTTTCCTTTTTCTTT
4207230 CTTT-CTTTTTCTTT
1 CTTTCCTTTTTCTTT
4207244 C
1 C
4207245 CCTATTTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
CTTTCCTTTTTCTTT
Found at i:4207340 original size:18 final size:17
Alignment explanation
Indices: 4207305--4207337 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4207295 CTTTTTATTC
4207305 TTTTATTATTTCATTTA
1 TTTTATTATTTCATTTA
4207322 TTTTACTTATTT-ATTT
1 TTTTA-TTATTTCATTT
4207338 TATCATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTCATTTA
Found at i:4211204 original size:14 final size:17
Alignment explanation
Indices: 4211173--4211209 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
4211163 ATTATAAAGG
4211173 ATATTATTAAATTAATT
1 ATATTATTAAATTAATT
4211190 ATATTA-TAAA-T-ATT
1 ATATTATTAAATTAATT
4211204 ATATTA
1 ATATTA
4211210 AGAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 1 0.05
16 4 0.20
17 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATTAAATTAATT
Found at i:4211385 original size:14 final size:14
Alignment explanation
Indices: 4211359--4211409 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
4211349 GAAAACAAAA
4211359 GAAATAAAATAAAG
1 GAAATAAAATAAAG
*
4211373 GAAATAAAGTAAAG
1 GAAATAAAATAAAG
* * *
4211387 TAAGTTAAAATAAAA
1 GAA-ATAAAATAAAG
4211402 G-AATAAAA
1 GAAATAAAA
4211410 GAAACAAAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
13 5 0.17
14 16 0.55
15 8 0.28
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.18
Consensus pattern (14 bp):
GAAATAAAATAAAG
Found at i:4211420 original size:17 final size:16
Alignment explanation
Indices: 4211398--4211431 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4211388 AAGTTAAAAT
4211398 AAAAGAATAAAAGAAAC
1 AAAAGAA-AAAAGAAAC
*
4211415 AAAAGAAGAAAGAAAC
1 AAAAGAAAAAAGAAAC
4211431 A
1 A
4211432 GAATAGCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAGAAAC
Found at i:4212585 original size:37 final size:39
Alignment explanation
Indices: 4212526--4212621 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
4212516 CGGATAGATT
* * * *
4212526 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
4212563 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
4212602 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
4212622 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:4213653 original size:14 final size:14
Alignment explanation
Indices: 4213631--4213665 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
4213621 AATTAGCATA
*
4213631 TATTATAAAATATC
1 TATTTTAAAATATC
4213645 TATTTT-AAATATC
1 TATTTTAAAATATC
4213658 TATTTTAA
1 TATTTTAA
4213666 CATCATTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTTTAAAATATC
Found at i:4213656 original size:13 final size:13
Alignment explanation
Indices: 4213638--4213665 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4213628 ATATATTATA
4213638 AAATATCTATTTT
1 AAATATCTATTTT
4213651 AAATATCTATTTT
1 AAATATCTATTTT
4213664 AA
1 AA
4213666 CATCATTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATATCTATTTT
Found at i:4213927 original size:15 final size:14
Alignment explanation
Indices: 4213909--4213939 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4213899 TTAATTTATT
4213909 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
4213924 TAATAATAATCTAA
1 TAATAATAATCTAA
4213938 TA
1 TA
4213940 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:4213950 original size:21 final size:20
Alignment explanation
Indices: 4213926--4213994 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
4213916 AATGCTAATA
4213926 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
4213947 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
4213966 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
4213987 ATAATAAT
1 ATAATAAT
4213995 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:4218071 original size:18 final size:17
Alignment explanation
Indices: 4218038--4218076 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
4218028 TTGTATAAAT
4218038 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
4218056 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
4218073 TGTG
1 TGTG
4218077 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:4218328 original size:23 final size:23
Alignment explanation
Indices: 4218301--4218398 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
4218291 AGTGTTATTG
4218301 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
4218324 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
4218347 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
4218369 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
4218392 ATCAGTG
1 ATCAGTG
4218399 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:4218367 original size:45 final size:45
Alignment explanation
Indices: 4218303--4218391 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
4218293 TGTTATTGAT
* *
4218303 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
4218348 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
4218392 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:4223138 original size:8 final size:8
Alignment explanation
Indices: 4223125--4223156 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
4223115 TTATTAAGTA
4223125 AATTTTGC
1 AATTTTGC
4223133 AATTTTGC
1 AATTTTGC
*
4223141 AATTTTCC
1 AATTTTGC
4223149 AATTTTGC
1 AATTTTGC
4223157 CCTTATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.50
Consensus pattern (8 bp):
AATTTTGC
Found at i:4238857 original size:19 final size:19
Alignment explanation
Indices: 4238835--4238879 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4238825 CTTTTTTGAG
*
4238835 TTTTTTTCACATTTT-AAT
1 TTTTTTTTACATTTTAAAT
*
4238853 TTTTTATATACATTTTAAAT
1 TTTTT-TTTACATTTTAAAT
4238873 TTTTTTT
1 TTTTTTT
4238880 ATAATTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 5 0.23
19 9 0.41
20 8 0.36
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTTTACATTTTAAAT
Found at i:4238888 original size:20 final size:20
Alignment explanation
Indices: 4238843--4238887 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
4238833 AGTTTTTTTC
4238843 ACATTTT-AATTTTTTATAT
1 ACATTTTAAATTTTTTATAT
*
4238862 ACATTTTAAATTTTTTTTAT
1 ACATTTTAAATTTTTTATAT
4238882 A-ATTTT
1 ACATTTT
4238888 TGAAGTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (20 bp):
ACATTTTAAATTTTTTATAT
Found at i:4244913 original size:6 final size:6
Alignment explanation
Indices: 4244904--4244938 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
4244894 AATCAGAATT
4244904 GGAAGC GGAAGC GGAAGC GGAAGC GGAAGC GGAAG
1 GGAAGC GGAAGC GGAAGC GGAAGC GGAAGC GGAAG
4244939 AGGAGAGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.51, T:0.00
Consensus pattern (6 bp):
GGAAGC
Found at i:4254890 original size:58 final size:59
Alignment explanation
Indices: 4254793--4254911 Score: 213
Period size: 58 Copynumber: 2.0 Consensus size: 59
4254783 ACATACAAGT
*
4254793 ACTTTCTTGATTAATAAAAAAATATAGAAGTAATATGTGTAACTATTACCAAAAATATA
1 ACTTTCTTGATTAATAAAAAAATATAGAAGTAATATGTGTAACTACTACCAAAAATATA
*
4254852 ACTTTCTTGATTAAT-AAAAAATATAGAAGTAATGTGTGTAACTACTACCAAAAATATA
1 ACTTTCTTGATTAATAAAAAAATATAGAAGTAATATGTGTAACTACTACCAAAAATATA
4254910 AC
1 AC
4254912 GTATTAGTTA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
58 43 0.74
59 15 0.26
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (59 bp):
ACTTTCTTGATTAATAAAAAAATATAGAAGTAATATGTGTAACTACTACCAAAAATATA
Found at i:4262364 original size:21 final size:21
Alignment explanation
Indices: 4262332--4262372 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4262322 GAACATTTGG
4262332 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
4262353 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
4262373 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:4280406 original size:96 final size:97
Alignment explanation
Indices: 4280287--4280506 Score: 278
Period size: 96 Copynumber: 2.3 Consensus size: 97
4280277 AATTTTAGGG
* * ** *
4280287 TTTTAAGGAAAAAAATTAAATAAATTAGGGTTTAGTGTTTGTTAATTAAATTAATTACT-AATTT
1 TTTTAAGGAAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTAAGTAAATTAATTA-TAAATTT
*
4280351 TAAAAAATTAGATTATGGTTTAGTGTTTACGCT
65 TAAAAAAATAGATTATGGTTTAGTGTTTACGCT
4280384 TTTTAAGG-AAAAAATCAAATAAATTAGGGTTTAGGGTTACTTAAGTAAATTAATTATAAATTTT
1 TTTTAAGGAAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTAAGTAAATTAATTATAAATTTT
*
4280448 AAAAAAATAGATTA-GG---A-T-TTTAAAG-T
66 AAAAAAATAGATTATGGTTTAGTGTTT-ACGCT
* *
4280474 ATTTAAGAAAAAAAATCAAATAAATTAGGGTTT
1 TTTTAAGGAAAAAAATCAAATAAATTAGGGTTT
4280507 GGAGTTTAGA
Statistics
Matches: 111, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
90 10 0.09
91 27 0.24
92 1 0.01
95 3 0.03
96 62 0.56
97 8 0.07
ACGTcount: A:0.45, C:0.03, G:0.14, T:0.39
Consensus pattern (97 bp):
TTTTAAGGAAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTAAGTAAATTAATTATAAATTTT
AAAAAAATAGATTATGGTTTAGTGTTTACGCT
Found at i:4280774 original size:126 final size:126
Alignment explanation
Indices: 4280557--4281094 Score: 819
Period size: 126 Copynumber: 4.3 Consensus size: 126
4280547 AAAAGCTTCT
* * * *
4280557 ACGTGGACGTTCTTTTGCTACAGTAATCTCTGAAAAAATAAATTTGAGAAGATGTGTCTGCGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCGCAA
*
4280622 ACAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAACAAAAGTACTGAAAGAAGCTCCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAACAAAAGTACTGAAAGAAGCTCCC
* * *
4280683 ACGTGGACACTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTGTCTGTGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCGCAA
* * *
4280748 ATAGTGTAAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTTCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAACAAAAGTACTGAAAGAAGCTCCC
4280809 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTG-AAAAATAATTTTGAGAAGACGTGTCTGCGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCGCAA
* * * * *
4280873 ATAGTGGT-AAAAACGCTTCAAGAAGGATGCATTTTCAGCAAAATTACTGGAAGAAGCTCCC
66 ATAGT-GTCAAAAACGCTTCAAGCAGGATGCATTGTCAACAAAAGTACTGAAAGAAGCTCCC
* * * **
4280934 ACGTGGATGCTCTTTTGCTACAGTGGTCTCTGAAAAAATAATTTTGAGAAGATGTGTCTGCATAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCGCAA
* *
4280999 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTTTCAACAAAAGTACTGAAAGAAGTTCCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAACAAAAGTACTGAAAGAAGCTCCC
* * *
4281060 ACGTGGACGCTCCTTTGCTACAGTGGTTTCTGAAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAA
4281095 TAACTTGGGC
Statistics
Matches: 377, Mismatches: 32, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
125 116 0.31
126 261 0.69
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (126 bp):
ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCGCAA
ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAACAAAAGTACTGAAAGAAGCTCCC
Found at i:4280993 original size:251 final size:251
Alignment explanation
Indices: 4280549--4281094 Score: 826
Period size: 251 Copynumber: 2.2 Consensus size: 251
4280539 TAATCTAAAA
* * * *
4280549 AAGCTTCTACGTGGACGTTCTTTTGCTACAGTAATCTCTGAAAAAATAAATTTGAGAAGATGTGT
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTG-AAAAATAAATTTGAGAAGACGTGT
*
4280614 CTGCGCAAACAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAACAAAAGTACTGAAAGAAGC
65 CTGCGCAAACAGTGTCAAAAACGCTTCAAGAAGGATGCATTGTCAACAAAAGTACTGAAAGAAGC
*
4280679 TCCCACGTGGACACTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTGTCTGT
130 TCCCACGTGGACACTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTGTCTGC
* *
4280744 GCAAATAGTGTAAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
195 ACAAATAGTGTAAAAAACGCTTCAAGCAGGATGCATTGTCAACAAAAGTACTGAAAG
*
4280801 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAATAATTTTGAGAAGACGTGTC
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAATAAATTTGAGAAGACGTGTC
* * * * *
4280866 TGCGCAAATAGTGGT-AAAAACGCTTCAAGAAGGATGCATTTTCAGCAAAATTACTGGAAGAAGC
66 TGCGCAAACAGT-GTCAAAAACGCTTCAAGAAGGATGCATTGTCAACAAAAGTACTGAAAGAAGC
** * * *
4280930 TCCCACGTGGATGCTCTTTTGCTACAGTGGTCTCTGAAAAAATAATTTTGAGAAGATGTGTCTGC
130 TCCCACGTGGACACTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTGTCTGC
* * *
4280995 ATAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTTTCAACAAAAGTACTGAAAG
195 ACAAATAGTGTAAAAAACGCTTCAAGCAGGATGCATTGTCAACAAAAGTACTGAAAG
* * *
4281052 AAG-TTCCCACGTGGACGCTCCTTTGCTACAGTGGTTTCTGAAA
1 AAGCTT-CCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAA
4281095 TAACTTGGGC
Statistics
Matches: 267, Mismatches: 25, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
250 2 0.01
251 226 0.85
252 39 0.15
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (251 bp):
AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAATAAATTTGAGAAGACGTGTC
TGCGCAAACAGTGTCAAAAACGCTTCAAGAAGGATGCATTGTCAACAAAAGTACTGAAAGAAGCT
CCCACGTGGACACTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTGTCTGCA
CAAATAGTGTAAAAAACGCTTCAAGCAGGATGCATTGTCAACAAAAGTACTGAAAG
Found at i:4283423 original size:11 final size:11
Alignment explanation
Indices: 4283384--4283435 Score: 63
Period size: 11 Copynumber: 4.9 Consensus size: 11
4283374 TAACGAGAGT
*
4283384 TTTGAGAGGAA
1 TTTGAGAGAAA
* *
4283395 TTTAAGATAAA
1 TTTGAGAGAAA
4283406 TTTGAGAG--A
1 TTTGAGAGAAA
4283415 TTTGAGAGAAA
1 TTTGAGAGAAA
4283426 TTTGAGAGAA
1 TTTGAGAGAA
4283436 TATTGAAAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 9 0.26
11 25 0.74
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (11 bp):
TTTGAGAGAAA
Found at i:4283426 original size:20 final size:20
Alignment explanation
Indices: 4283384--4283434 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
4283374 TAACGAGAGT
*
4283384 TTTGAGAGGAATTTAAGATAAA
1 TTTGAGA-G-ATTTAAGAGAAA
*
4283406 TTTGAGAGATTTGAGAGAAA
1 TTTGAGAGATTTAAGAGAAA
4283426 TTTGAGAGA
1 TTTGAGAGA
4283435 ATATTGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 19 0.70
21 1 0.04
22 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.31
Consensus pattern (20 bp):
TTTGAGAGATTTAAGAGAAA
Found at i:4283447 original size:31 final size:31
Alignment explanation
Indices: 4283384--4283447 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
4283374 TAACGAGAGT
* * *
4283384 TTTGAGAGGAATTTAAGATAAATTTGAGAGA
1 TTTGAGAGAAATTTAAGAGAAATTTGAAAGA
*
4283415 TTTGAGAGAAATTTGAGAG-AATATTGAAAGA
1 TTTGAGAGAAATTTAAGAGAAAT-TTGAAAGA
4283446 TT
1 TT
4283448 GAAGATTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.11
31 25 0.89
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (31 bp):
TTTGAGAGAAATTTAAGAGAAATTTGAAAGA
Found at i:4284969 original size:2 final size:2
Alignment explanation
Indices: 4284962--4284991 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
4284952 AAGGCTTAAA
4284962 AC AC AC AC AC AC AC AC AC AC AC AC ATC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A-C AC A
4284992 TTCACAAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:4290856 original size:15 final size:15
Alignment explanation
Indices: 4290828--4290862 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
4290818 TAAATATTTG
4290828 TTAATAATAAAAATA
1 TTAATAATAAAAATA
4290843 TTAA-AATAATAAATA
1 TTAATAATAA-AAATA
4290858 TTAAT
1 TTAAT
4290863 TTTATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAATAATAAAAATA
Found at i:4324224 original size:111 final size:111
Alignment explanation
Indices: 4323934--4324395 Score: 620
Period size: 111 Copynumber: 4.1 Consensus size: 111
4323924 GTAAGTGGGC
* * *
4323934 CTGCTGCTGCCGAACCAGCTGGCCATTCCAGGCAGGACCTGTGCCTTGAGCACATGACTGCTCAT
1 CTGCTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATATGACTGCTCAT
* * * *
4323999 ATCGAGGCGAGCCCATGTTTGATACACTTCCATTTC-CATAAAAGTTATT
66 ATCGAGGTGATCCCATGTTTGATACAGTTCCA-TTCGCATGAAA---ATT
* * * *
4324048 CTGATGATGCTGCTGAACCAGCTGACCATTCCAGGCAGGACCTGTGCCTTGAGCATATGTCTGCT
1 C---TGCTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATATGACTGCT
* * *
4324113 CATATCGAGGTGATCCCATGTTCGATACAGTTCCGTTCACATGAAAATT
63 CATATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
* * *
4324162 CTGCTGCTGCTGAACCATCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATACGAATGCTCAT
1 CTGCTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATATGACTGCTCAT
*
4324227 ATCGAGGTGATCCCATGTTTGGTACAGTTCCATTCGCATGAAAATT
66 ATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
* * * ** *
4324273 CTGCTGCTGCTGAGCCATCTGGCCATTCCAGGCATGACCCATCCCTTGAACATATGACTGCTCAT
1 CTGCTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATATGACTGCTCAT
* *
4324338 ATCGAGGTGATCCCATGTTAGATACAGTTCCATTCGCATGAAACTT
66 ATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
4324384 CTGCTGCTGCTG
1 CTGCTGCTGCTG
4324396 CTGAATTTGA
Statistics
Matches: 312, Mismatches: 32, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
111 212 0.68
114 5 0.02
116 3 0.01
117 92 0.29
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (111 bp):
CTGCTGCTGCTGAACCAGCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATATGACTGCTCAT
ATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
Found at i:4325642 original size:6 final size:6
Alignment explanation
Indices: 4325631--4325667 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
4325621 ATTATAAGTG
4325631 AAAACA AAAAC- AAAA-A AAAACA AAAACA AAAA-A AAAA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAA
4325668 AACAGTCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
5 13 0.45
6 16 0.55
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:4325652 original size:16 final size:16
Alignment explanation
Indices: 4325631--4325666 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
4325621 ATTATAAGTG
4325631 AAAACAAAAACAAAAA
1 AAAACAAAAACAAAAA
4325647 AAAACAAAAACAAAAA
1 AAAACAAAAACAAAAA
4325663 AAAA
1 AAAA
4325667 AAACAGTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAACAAAAACAAAAA
Found at i:4330311 original size:31 final size:29
Alignment explanation
Indices: 4330276--4330335 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
4330266 GTTATTGGGG
* * *
4330276 AATGAATAACAAACACGAATATAAATTATTT
1 AATGAAAAAAAAACAC-AA-ATAAAATATTT
4330307 AATGAAAAAAAAACACAAATAAAATATTT
1 AATGAAAAAAAAACACAAATAAAATATTT
4330336 CCACCCGCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 10 0.38
30 2 0.08
31 14 0.54
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (29 bp):
AATGAAAAAAAAACACAAATAAAATATTT
Found at i:4339157 original size:29 final size:29
Alignment explanation
Indices: 4339125--4339182 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
4339115 ACAAATTCCG
4339125 ATTATCAGGAACCGTGAACAAGAAGTTTA
1 ATTATCAGGAACCGTGAACAAGAAGTTTA
4339154 ATTATCAGGAACCGTGAACAAGAAGTTTA
1 ATTATCAGGAACCGTGAACAAGAAGTTTA
4339183 GGTGTTCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (29 bp):
ATTATCAGGAACCGTGAACAAGAAGTTTA
Found at i:4345626 original size:114 final size:114
Alignment explanation
Indices: 4345482--4345716 Score: 407
Period size: 114 Copynumber: 2.1 Consensus size: 114
4345472 AGTAAACTCC
* *
4345482 AATATTCTCTCTCAGCATCACCTAAACATATTACCCGGCACTTTATCAGTTGCTCATCTAATATA
1 AATATTCTCTCTCAGCATCAACTAAACATATTACCCAGCACTTTATCAGTTGCTCATCTAATATA
4345547 TCACGTTCATATCATTGACCTAAAGTCATTAGTTCCTCTTGTATTACAT
66 TCACGTTCATATCATTGACCTAAAGTCATTAGTTCCTCTTGTATTACAT
*
4345596 AATATTCTCTCTCGGCATCAACTAAACATATTACCCAGCACTTTATCAGTTGCTCATCTAATATA
1 AATATTCTCTCTCAGCATCAACTAAACATATTACCCAGCACTTTATCAGTTGCTCATCTAATATA
* * *
4345661 TCAGGTTCATATTATTGACCTAAAGTCATTAGTTTCTCTTGTATTACAT
66 TCACGTTCATATCATTGACCTAAAGTCATTAGTTCCTCTTGTATTACAT
*
4345710 ATTATTC
1 AATATTC
4345717 CTTATGCAAG
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 114 1.00
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.38
Consensus pattern (114 bp):
AATATTCTCTCTCAGCATCAACTAAACATATTACCCAGCACTTTATCAGTTGCTCATCTAATATA
TCACGTTCATATCATTGACCTAAAGTCATTAGTTCCTCTTGTATTACAT
Found at i:4348404 original size:17 final size:17
Alignment explanation
Indices: 4348382--4348418 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4348372 GATTGAAAAT
* *
4348382 TTTATTGTAATCATATC
1 TTTATTGAAATCACATC
4348399 TTTATTGAAATCACATC
1 TTTATTGAAATCACATC
4348416 TTT
1 TTT
4348419 GAAGTAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.51
Consensus pattern (17 bp):
TTTATTGAAATCACATC
Found at i:4352203 original size:14 final size:14
Alignment explanation
Indices: 4352184--4352213 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4352174 TTAAATCTAG
4352184 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
4352198 ACCAATCCAATTCA
1 ACCAATCCAAATCA
4352212 AC
1 AC
4352214 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:4355047 original size:31 final size:31
Alignment explanation
Indices: 4354988--4355063 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
4354978 ACACACATAT
*
4354988 ATATACTAAATAAAATAATAAAATAATAATAA
1 ATAT-CTAATTAAAATAATAAAATAATAATAA
* *
4355020 ATATCTTATTAAAAT-ATTAAATAAATAATAA
1 ATATCTAATTAAAATAATAAAAT-AATAATAA
*
4355051 TTATCTAATTAAA
1 ATATCTAATTAAA
4355064 TAACTATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 6 0.16
31 28 0.74
32 4 0.11
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (31 bp):
ATATCTAATTAAAATAATAAAATAATAATAA
Found at i:4355053 original size:23 final size:23
Alignment explanation
Indices: 4354994--4355053 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
4354984 ATATATATAC
4354994 TAAAT-AA-AATAA-TAAAATAA
1 TAAATAAATAATAATTAAAATAA
* * *
4355014 T-AATAAATATCTTATTAAAATAT
1 TAAATAAATA-ATAATTAAAATAA
4355037 TAAATAAATAATAATTA
1 TAAATAAATAATAATTA
4355054 TCTAATTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.10
20 3 0.10
21 1 0.03
22 2 0.07
23 13 0.43
24 8 0.27
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAATAAATAATAATTAAAATAA
Found at i:4359271 original size:44 final size:44
Alignment explanation
Indices: 4359208--4359368 Score: 214
Period size: 44 Copynumber: 3.5 Consensus size: 44
4359198 TTTGAGTACT
4359208 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
4359252 TCTGATTAGTGACAAGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAA--G-----TGATAAGTGGTAGCTTTAGCTACACTTA
* * *
4359303 TCTAATCAATGACAAGTGATAAGTGGTAGTTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
4359347 TCTGATCAGTAACAAGTGATAA
1 TCTGATCAGTGACAAGTGATAA
4359369 ATGTGATCAG
Statistics
Matches: 102, Mismatches: 8, Indels: 14
0.82 0.06 0.11
Matches are distributed among these distances:
44 60 0.59
46 1 0.01
49 1 0.01
51 40 0.39
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:4359291 original size:51 final size:49
Alignment explanation
Indices: 4359215--4359371 Score: 198
Period size: 51 Copynumber: 3.2 Consensus size: 49
4359205 ACTTCTGATC
*
4359215 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATTAGTGACA
1 AGTGACAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGA-TAGT-ACA
*
4359266 AGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCT-A-A-T-CA
1 AGTGACAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATAGTACA
* *
4359311 A-TGACAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTAACA
1 AGTGACAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGAT-AGT-ACA
*
4359361 AGTGATAAATG
1 AGTGACAAATG
4359372 TGATCAGTGT
Statistics
Matches: 92, Mismatches: 7, Indels: 14
0.81 0.06 0.12
Matches are distributed among these distances:
44 35 0.38
45 4 0.04
47 2 0.02
48 2 0.02
50 4 0.04
51 45 0.49
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (49 bp):
AGTGACAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATAGTACA
Done.