Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 9 of 103
Found at i:3474437 original size:50 final size:48
Alignment explanation
Indices: 3474379--3474474 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
3474369 GGAAGGGGGG
*
3474379 GATCTTGGGTGAGAGAGCAAAAGGAGATCTTGGGTGAGAGAGCAAAAAGA
1 GATCTTGGGTGAGAGAGCAAAA-G-GATCTTGGGTGAGAAAGCAAAAAGA
3474429 GATCTTGGGTGAGAGAGCAAAAGGATCTTGGGTGAGAAAGCAAAAA
1 GATCTTGGGTGAGAGAGCAAAAGGATCTTGGGTGAGAAAGCAAAAA
3474475 AGAAACGGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 22 0.49
49 1 0.02
50 22 0.49
ACGTcount: A:0.39, C:0.08, G:0.36, T:0.17
Consensus pattern (48 bp):
GATCTTGGGTGAGAGAGCAAAAGGATCTTGGGTGAGAAAGCAAAAAGA
Found at i:3474455 original size:23 final size:24
Alignment explanation
Indices: 3474379--3474473 Score: 156
Period size: 25 Copynumber: 3.9 Consensus size: 24
3474369 GGAAGGGGGG
3474379 GATCTTGGGTGAGAGAGCAAAAGGA
1 GATCTTGGGTGAGAGAGCAAAA-GA
3474404 GATCTTGGGTGAGAGAGCAAAAAGA
1 GATCTTGGGTGAGAGAGC-AAAAGA
3474429 GATCTTGGGTGAGAGAGCAAAAG-
1 GATCTTGGGTGAGAGAGCAAAAGA
*
3474452 GATCTTGGGTGAGAAAGCAAAA
1 GATCTTGGGTGAGAGAGCAAAA
3474474 AAGAAACGGG
Statistics
Matches: 68, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
23 21 0.31
24 5 0.07
25 38 0.56
26 4 0.06
ACGTcount: A:0.38, C:0.08, G:0.37, T:0.17
Consensus pattern (24 bp):
GATCTTGGGTGAGAGAGCAAAAGA
Found at i:3477110 original size:20 final size:20
Alignment explanation
Indices: 3477052--3477113 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
3477042 GTTCCATTAT
3477052 CATGATGAACGTGTTCTTCC
1 CATGATGAACGTGTTCTTCC
* * *** *
3477072 CATAATTATTTTGTCCTTCC
1 CATGATGAACGTGTTCTTCC
3477092 CATGATGAACGTGTTCTTCC
1 CATGATGAACGTGTTCTTCC
3477112 CA
1 CA
3477114 ATCGTGCATT
Statistics
Matches: 30, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.39
Consensus pattern (20 bp):
CATGATGAACGTGTTCTTCC
Found at i:3478081 original size:20 final size:20
Alignment explanation
Indices: 3478034--3478081 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
3478024 GTATTAGGCT
* *
3478034 AACATGTTATTCCTATGATG
1 AACATGTTATTCCCATAATG
* *
3478054 AACGTGTTTTTCCCATAATG
1 AACATGTTATTCCCATAATG
*
3478074 GACATGTT
1 AACATGTT
3478082 CTTGTTGTGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (20 bp):
AACATGTTATTCCCATAATG
Found at i:3482675 original size:21 final size:21
Alignment explanation
Indices: 3482638--3482692 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
3482628 ACTTCTTAAT
* *
3482638 TTTTTATTATATATAT-ATATA
1 TTTTTATTATTTTTATAAT-TA
3482659 TTTTTATTATTTTTATAATTA
1 TTTTTATTATTTTTATAATTA
*
3482680 TTTTT-TAATTTTT
1 TTTTTATTATTTTT
3482693 TTTCGTACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.23
21 21 0.70
22 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTATTATTTTTATAATTA
Found at i:3482688 original size:11 final size:11
Alignment explanation
Indices: 3482659--3482695 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
3482649 TATATATATA
3482659 TTTTT-ATTAT
1 TTTTTAATTAT
3482669 TTTTATAATTAT
1 TTTT-TAATTAT
3482681 TTTTTAATT-T
1 TTTTTAATTAT
3482691 TTTTT
1 TTTTT
3482696 CGTACAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.40
11 6 0.24
12 9 0.36
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTAATTAT
Found at i:3491020 original size:112 final size:111
Alignment explanation
Indices: 3490864--3491089 Score: 427
Period size: 112 Copynumber: 2.0 Consensus size: 111
3490854 CATCTGCATG
3490864 CAAGCATGCTCACAAAAGTGAGCATTTTATGCATTGCCAAAAAATCTGAAGGCAACTTAAATATC
1 CAAGCATGCTCACAAAAGTGAGCATTTTATGCATTGCCAAAAAATCTGAAGGCAACTTAAATATC
3490929 ATCAGGCAATTTATA-TGCTCCAGGCAAGAACACTTATTCGAATTCA
66 ATCAGGCAATTTATACT-CTCCAGGCAAGAACACTTATTCGAATTCA
3490975 CAAGCATGCTCACAAAAAGTGAGCATTTTATGCATTGCCAAAAAATCTGAAGGCAACTTAAATAT
1 CAAGCATGCTCAC-AAAAGTGAGCATTTTATGCATTGCCAAAAAATCTGAAGGCAACTTAAATAT
3491040 CATCAGGCAATTTATACTCTCCAGGCAAGAACACTTATTCGAATTCA
65 CATCAGGCAATTTATACTCTCCAGGCAAGAACACTTATTCGAATTCA
3491087 CAA
1 CAA
3491090 TTATAAATGC
Statistics
Matches: 113, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
111 13 0.12
112 99 0.88
113 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (111 bp):
CAAGCATGCTCACAAAAGTGAGCATTTTATGCATTGCCAAAAAATCTGAAGGCAACTTAAATATC
ATCAGGCAATTTATACTCTCCAGGCAAGAACACTTATTCGAATTCA
Found at i:3492451 original size:9 final size:9
Alignment explanation
Indices: 3492437--3492485 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
3492427 AATAATACGT
3492437 TTAACACGA
1 TTAACACGA
* *
3492446 TTAACATGT
1 TTAACACGA
3492455 TTAACACGA
1 TTAACACGA
*
3492464 TTAACACGT
1 TTAACACGA
3492473 TTAACACGA
1 TTAACACGA
3492482 TTAA
1 TTAA
3492486 ATAAAAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (9 bp):
TTAACACGA
Found at i:3492458 original size:18 final size:18
Alignment explanation
Indices: 3492433--3492485 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
3492423 GATTAATAAT
3492433 ACGTTTAACACGATTAAC
1 ACGTTTAACACGATTAAC
*
3492451 ATGTTTAACACGATTAAC
1 ACGTTTAACACGATTAAC
3492469 ACGTTTAACACGATTAA
1 ACGTTTAACACGATTAA
3492486 ATAAAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (18 bp):
ACGTTTAACACGATTAAC
Found at i:3494050 original size:21 final size:21
Alignment explanation
Indices: 3494026--3494101 Score: 125
Period size: 21 Copynumber: 3.6 Consensus size: 21
3494016 TGTTGTAATG
3494026 CAGCTTCTCTCTTTTGCCATT
1 CAGCTTCTCTCTTTTGCCATT
*
3494047 CAGCTTCACTCTTTTGCCATT
1 CAGCTTCTCTCTTTTGCCATT
3494068 CAGCTTCTCTCTTTTGCCATT
1 CAGCTTCTCTCTTTTGCCATT
* *
3494089 CAGTTTCTTTCTT
1 CAGCTTCTCTCTT
3494102 ACTCAAAACA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.11, C:0.32, G:0.09, T:0.49
Consensus pattern (21 bp):
CAGCTTCTCTCTTTTGCCATT
Found at i:3497997 original size:17 final size:17
Alignment explanation
Indices: 3497971--3498003 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3497961 CGCCTTCTTG
3497971 CATAAAGTCA-TCTGTT
1 CATAAAGTCATTCTGTT
3497987 CATAGAAGTCATTCTGT
1 CATA-AAGTCATTCTGT
3498004 AATTGCTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (17 bp):
CATAAAGTCATTCTGTT
Found at i:3498919 original size:25 final size:26
Alignment explanation
Indices: 3498868--3498920 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
3498858 GTAAGAATTC
* *
3498868 ATGATATGTTTCATATAAAATAGTAA
1 ATGATATGTTTAATATAAAATAATAA
3498894 ATGATAT-TTTAAT-TAATAATAATAA
1 ATGATATGTTTAATATAA-AATAATAA
3498919 AT
1 AT
3498921 CAATCTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.12
25 14 0.58
26 7 0.29
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.42
Consensus pattern (26 bp):
ATGATATGTTTAATATAAAATAATAA
Found at i:3506606 original size:2 final size:2
Alignment explanation
Indices: 3506599--3506658 Score: 85
Period size: 2 Copynumber: 32.5 Consensus size: 2
3506589 TGACCCTTAG
3506599 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3506639 -A TA -A TA -A TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
3506659 TTTACTTTTC
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
1 5 0.09
2 48 0.91
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3507248 original size:2 final size:2
Alignment explanation
Indices: 3507235--3507272 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3507225 TCAATTCTCT
*
3507235 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3507273 AAACAAACTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3523104 original size:10 final size:12
Alignment explanation
Indices: 3523079--3523104 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3523069 ATGCACTAAG
3523079 ACACCTCATAAC
1 ACACCTCATAAC
3523091 ACACCTCATAAC
1 ACACCTCATAAC
3523103 AC
1 AC
3523105 TGCTGTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.15
Consensus pattern (12 bp):
ACACCTCATAAC
Found at i:3526935 original size:34 final size:34
Alignment explanation
Indices: 3526897--3526962 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
3526887 AAAATTTATG
* *
3526897 AGAAATGACAACACATGTATTTAATTATTAGACT
1 AGAAAGGACAACACATGCATTTAATTATTAGACT
* *
3526931 AGAAAGGACAGCACATGCATTTTATTATTAGA
1 AGAAAGGACAACACATGCATTTAATTATTAGA
3526963 TTAAATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (34 bp):
AGAAAGGACAACACATGCATTTAATTATTAGACT
Found at i:3537189 original size:13 final size:13
Alignment explanation
Indices: 3537151--3537193 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
3537141 AAGAGAGTCT
3537151 TTTTAATAATAAAAA
1 TTTTAA-AAT-AAAA
*
3537166 TTATAAAAATAAAA
1 TT-TTAAAATAAAA
3537180 TTTTAAAATAAAA
1 TTTTAAAATAAAA
3537193 T
1 T
3537194 AGATGATGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 11 0.44
14 6 0.24
15 5 0.20
16 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TTTTAAAATAAAA
Found at i:3537502 original size:15 final size:15
Alignment explanation
Indices: 3537482--3537510 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3537472 AAAAGTTAGT
3537482 TAGTTTCACTCCTGC
1 TAGTTTCACTCCTGC
3537497 TAGTTTCACTCCTG
1 TAGTTTCACTCCTG
3537511 TTAAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.31, G:0.14, T:0.41
Consensus pattern (15 bp):
TAGTTTCACTCCTGC
Found at i:3540514 original size:19 final size:19
Alignment explanation
Indices: 3540490--3540527 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3540480 TCTCTTTCTC
3540490 TCTCTTTTT-TTTTCTCTTT
1 TCTCTTTTTATTTT-TCTTT
3540509 TCTCTTTTTATTTTTCTTT
1 TCTCTTTTTATTTTTCTTT
3540528 GGTCTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (19 bp):
TCTCTTTTTATTTTTCTTT
Found at i:3540522 original size:21 final size:22
Alignment explanation
Indices: 3540480--3540525 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
3540470 TTTCTTTACG
3540480 TCTCTTTCTCTCTCTTTTTTTT
1 TCTCTTTCTCTCTCTTTTTTTT
3540502 TCTCTTT-TCTCT-TTTTATTTT
1 TCTCTTTCTCTCTCTTTT-TTTT
3540523 TCT
1 TCT
3540526 TTGGTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.17
21 12 0.52
22 7 0.30
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (22 bp):
TCTCTTTCTCTCTCTTTTTTTT
Found at i:3540533 original size:19 final size:19
Alignment explanation
Indices: 3540491--3540535 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3540481 CTCTTTCTCT
*
3540491 CTCTTTTTTTTTCTCTTTT
1 CTCTTTTTTTTTCTCTTTG
3540510 CTCTTTTTATTTT-TCTTTG
1 CTCTTTTT-TTTTCTCTTTG
*
3540529 GTCTTTT
1 CTCTTTT
3540536 CTCTATAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (19 bp):
CTCTTTTTTTTTCTCTTTG
Found at i:3554114 original size:3 final size:3
Alignment explanation
Indices: 3554101--3554148 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
3554091 AATATAGATT
*
3554101 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3554149 AGATTTTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3557322 original size:16 final size:16
Alignment explanation
Indices: 3557297--3557350 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
3557287 TTCAGGTAAT
*
3557297 TTATTGTTTATTATTA
1 TTATTTTTTATTATTA
3557313 TTATTTTTTATTA-TA
1 TTATTTTTTATTATTA
**
3557328 CCATTTTTTA-TATATA
1 TTATTTTTTATTAT-TA
3557344 TTATTTT
1 TTATTTT
3557351 AAACAACAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 2 0.06
15 10 0.32
16 19 0.61
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.69
Consensus pattern (16 bp):
TTATTTTTTATTATTA
Found at i:3571882 original size:71 final size:71
Alignment explanation
Indices: 3571774--3571934 Score: 277
Period size: 71 Copynumber: 2.3 Consensus size: 71
3571764 CTTCTCTTCC
* * * *
3571774 CGTCGACTTCTCTCTCTCTTCTCTCTCTCTCGGCGGATCTCTTCGCCTTCTGTCGGCCGATCCCT
1 CGTCGACCTCTCTCTCTCTTCTCTCTCCCCCGACGGATCTCTTCGCCTTCTGTCGGCCGATCCCT
3571839 CTCTTT
66 CTCTTT
3571845 CGTCGACCTCTCTCTCTCTTCTCTCTCCCCCGACGGATCTCTTCGCCTTCTGTCGGCCGATCCCT
1 CGTCGACCTCTCTCTCTCTTCTCTCTCCCCCGACGGATCTCTTCGCCTTCTGTCGGCCGATCCCT
3571910 CTCTTT
66 CTCTTT
*
3571916 CGTCGGCCTCTCTCTCTCT
1 CGTCGACCTCTCTCTCTCT
3571935 CTTCTCAGAT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 85 1.00
ACGTcount: A:0.04, C:0.43, G:0.15, T:0.37
Consensus pattern (71 bp):
CGTCGACCTCTCTCTCTCTTCTCTCTCCCCCGACGGATCTCTTCGCCTTCTGTCGGCCGATCCCT
CTCTTT
Found at i:3572881 original size:39 final size:39
Alignment explanation
Indices: 3572827--3572905 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
3572817 GCTGATTTTA
3572827 GAATCACGTAAGTCTTAAAAAGACAAAAAATTAGTAAAG
1 GAATCACGTAAGTCTTAAAAAGACAAAAAATTAGTAAAG
* * *
3572866 GAATCACGTAAGTCTTGAAAAGATAAAATATTAGTAAAG
1 GAATCACGTAAGTCTTAAAAAGACAAAAAATTAGTAAAG
3572905 G
1 G
3572906 GATAGGATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.51, C:0.09, G:0.18, T:0.23
Consensus pattern (39 bp):
GAATCACGTAAGTCTTAAAAAGACAAAAAATTAGTAAAG
Found at i:3573505 original size:212 final size:216
Alignment explanation
Indices: 3573189--3573576 Score: 563
Period size: 212 Copynumber: 1.8 Consensus size: 216
3573179 ATATATTGCT
* *
3573189 TTATTATATATGAAATTAATTACACAATTTATTAGTTATAATATTTTAATTTTTATATCACAATT
1 TTATTATATATGAAATTAATGACACAACTTATTAGTTATAATA--TTAATTTTTATATCACAATT
* * * *
3573254 TGTATAAATAATAACTAATTATAAACAATATATTATAAAAAATAAGGTGATACTTAATAAAATTA
64 TATATAAATAATAACTAATTATAAACAATATATTATAAAAAATAAGATAATAATTAATAAAATTA
* *
3573319 TTAAGTGTAATTATATAAATAAAGTTTATTATAAGTTACAGTAATATTTTTGTATAAATTAAATA
129 TTAAGTGTAATCATATAAATAAAATTTATTATAAGTTACAGTAATATTTTTGTATAAATTAAATA
3573384 TATGTATATATTATTTTATTTTA
194 TATGTATATATTATTTTATTTTA
*
3573407 TTATGTATATATGAAATTAATGACACAACTTATTTGTTAT-A-A-T-A-TTTTATATCA-AAGTT
1 TTAT-TATATATGAAATTAATGACACAACTTATTAGTTATAATATTAATTTTTATATCACAA-TT
* * * *
3573466 TATATAAATAATAACTAATTATAAATAATATGTTATAAAAACTAAGATAATAATTAATAAAGTTA
64 TATATAAATAATAACTAATTATAAACAATATATTATAAAAAATAAGATAATAATTAATAAAATTA
* *
3573531 TTGAGTGTAATCATATAAATAAAATTTATTATAAGTTATAGTAATA
129 TTAAGTGTAATCATATAAATAAAATTTATTATAAGTTACAGTAATA
3573577 CTTATACGAA
Statistics
Matches: 153, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
211 2 0.01
212 111 0.73
213 1 0.01
214 1 0.01
217 1 0.01
218 5 0.03
219 32 0.21
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (216 bp):
TTATTATATATGAAATTAATGACACAACTTATTAGTTATAATATTAATTTTTATATCACAATTTA
TATAAATAATAACTAATTATAAACAATATATTATAAAAAATAAGATAATAATTAATAAAATTATT
AAGTGTAATCATATAAATAAAATTTATTATAAGTTACAGTAATATTTTTGTATAAATTAAATATA
TGTATATATTATTTTATTTTA
Found at i:3582115 original size:7 final size:7
Alignment explanation
Indices: 3582100--3582137 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
3582090 TGAAGGGTTC
3582100 AATAATG
1 AATAATG
*
3582107 AATACTG
1 AATAATG
3582114 AATAATG
1 AATAATG
3582121 AATAATG
1 AATAATG
*
3582128 AATTATG
1 AATAATG
3582135 AAT
1 AAT
3582138 CTCTAGCGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.32
Consensus pattern (7 bp):
AATAATG
Found at i:3583879 original size:6 final size:6
Alignment explanation
Indices: 3583868--3583893 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3583858 TAGATTGGAT
3583868 AATTAG AATTAG AATTAG AATTAG AA
1 AATTAG AATTAG AATTAG AATTAG AA
3583894 AGTAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (6 bp):
AATTAG
Found at i:3588956 original size:14 final size:14
Alignment explanation
Indices: 3588918--3588956 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3588908 AGAATAAAAT
3588918 AATATT-TTATTAA
1 AATATTATTATTAA
* *
3588931 AATAATAATATTAA
1 AATATTATTATTAA
3588945 AATATTATTATT
1 AATATTATTATT
3588957 TTATTCAATG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AATATTATTATTAA
Found at i:3590393 original size:38 final size:40
Alignment explanation
Indices: 3590350--3590452 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 40
3590340 ATAGTGCTCG
*
3590350 TGTGCACGATGTGGGGGAATGTACACGAT-G-G-CA-CTGA
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGCCAGCT-A
* *
3590387 TTGTGCACGATGTGGGGGGATGCACATGATGGTGCCAGCTA
1 -TGTGCACGATGTGGGGGGATGTACACGATGGTGCCAGCTA
3590428 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
3590453 TGAGTTGGGT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
38 26 0.46
39 1 0.02
40 25 0.44
41 3 0.05
42 2 0.04
ACGTcount: A:0.21, C:0.16, G:0.40, T:0.23
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGTGCCAGCTA
Found at i:3590442 original size:40 final size:38
Alignment explanation
Indices: 3590350--3590455 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 38
3590340 ATAGTGCTCG
* *
3590350 TGTGCACGATGTGGGGGAATGTACACGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACTGAT
*
3590388 TGTGCACGATGTGGGGGGATGCACATGATGGTGCCAGCT-A-
1 TGTGCACGATGTGGGGGGATGTACATGAT-G-G-CA-CTGAT
3590428 TGTGCACGATGTGGGGGGATGTACATGA
1 TGTGCACGATGTGGGGGGATGTACATGA
3590456 GTTGGGTGTG
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
38 26 0.43
39 1 0.02
40 28 0.47
41 3 0.05
42 2 0.03
ACGTcount: A:0.22, C:0.15, G:0.40, T:0.24
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACATGATGGCACTGAT
Found at i:3599837 original size:19 final size:19
Alignment explanation
Indices: 3599800--3599838 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3599790 TTTTATTACT
* **
3599800 GAAAAACAGGAAAGGAAAA
1 GAAAAACAGAAAAAAAAAA
3599819 GAAAAACAGAAAAAAAAAA
1 GAAAAACAGAAAAAAAAAA
3599838 G
1 G
3599839 GCTACGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (19 bp):
GAAAAACAGAAAAAAAAAA
Found at i:3618485 original size:3 final size:3
Alignment explanation
Indices: 3618477--3618504 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3618467 TTATATTTGA
3618477 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3618505 TTGTTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3638142 original size:38 final size:38
Alignment explanation
Indices: 3638098--3638173 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
3638088 AAATGATTGG
*
3638098 GGTTTTTCTACTGCTTCTAATCTAGTTGATGTCCATTT
1 GGTTTTTCTACTACTTCTAATCTAGTTGATGTCCATTT
3638136 GGTTTTTCTACTACTTCTAATCTAGTTGATGTCCATTT
1 GGTTTTTCTACTACTTCTAATCTAGTTGATGTCCATTT
3638174 TCTATCTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.17, C:0.18, G:0.14, T:0.50
Consensus pattern (38 bp):
GGTTTTTCTACTACTTCTAATCTAGTTGATGTCCATTT
Found at i:3644654 original size:14 final size:15
Alignment explanation
Indices: 3644637--3644671 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
3644627 TTTTTTATAA
3644637 ATTAATTTTAATTT-
1 ATTAATTTTAATTTC
*
3644651 ATTAATTTTATTTTC
1 ATTAATTTTAATTTC
3644666 ATTAAT
1 ATTAAT
3644672 AATATGCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTAATTTTAATTTC
Found at i:3652995 original size:49 final size:49
Alignment explanation
Indices: 3652923--3653019 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
3652913 TTGATATAAA
3652923 ATCAGTGGACCCCCAATGTAGACCAATGGTCTAGGCAAACTCGAACTAG
1 ATCAGTGGACCCCCAATGTAGACCAATGGTCTAGGCAAACTCGAACTAG
*
3652972 ATCAGTGGACCTCCAATGTAGACCAATGGTCTAGGCAAACTCGAACTA
1 ATCAGTGGACCCCCAATGTAGACCAATGGTCTAGGCAAACTCGAACTA
3653020 ATGTAAAAGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.20
Consensus pattern (49 bp):
ATCAGTGGACCCCCAATGTAGACCAATGGTCTAGGCAAACTCGAACTAG
Found at i:3674889 original size:14 final size:14
Alignment explanation
Indices: 3674870--3674897 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3674860 CTTAAATAAA
3674870 ATATTGACAAGTCT
1 ATATTGACAAGTCT
3674884 ATATTGACAAGTCT
1 ATATTGACAAGTCT
3674898 TAATTCGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
ATATTGACAAGTCT
Found at i:3704244 original size:28 final size:28
Alignment explanation
Indices: 3704204--3704303 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
3704194 TCAAAATATT
3704204 GGGATTAAATTGACCAATATGGATTAAA
1 GGGATTAAATTGACCAATATGGATTAAA
** * **
3704232 GGGATTAAATTGATGAAAATCCCA-TAATA
1 GGGATTAAATTGACCAATAT-GGATTAA-A
3704261 TTGGGATTAAATTGACCAATATGGATTAAA
1 --GGGATTAAATTGACCAATATGGATTAAA
3704291 GGGATTAAATTGA
1 GGGATTAAATTGA
3704304 TGAAAATCCC
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
28 33 0.58
29 2 0.04
30 2 0.04
31 20 0.35
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (28 bp):
GGGATTAAATTGACCAATATGGATTAAA
Found at i:3704264 original size:59 final size:59
Alignment explanation
Indices: 3704188--3704319 Score: 246
Period size: 59 Copynumber: 2.2 Consensus size: 59
3704178 ATTTTTTAAC
* *
3704188 AAAATCTCAAAATATTGGGATTAAATTGACCAATATGGATTAAAGGGATTAAATTGATG
1 AAAATCCCATAATATTGGGATTAAATTGACCAATATGGATTAAAGGGATTAAATTGATG
3704247 AAAATCCCATAATATTGGGATTAAATTGACCAATATGGATTAAAGGGATTAAATTGATG
1 AAAATCCCATAATATTGGGATTAAATTGACCAATATGGATTAAAGGGATTAAATTGATG
3704306 AAAATCCCATAATA
1 AAAATCCCATAATA
3704320 CAGGGACTTA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 71 1.00
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (59 bp):
AAAATCCCATAATATTGGGATTAAATTGACCAATATGGATTAAAGGGATTAAATTGATG
Found at i:3704270 original size:31 final size:29
Alignment explanation
Indices: 3704231--3704319 Score: 92
Period size: 28 Copynumber: 3.0 Consensus size: 29
3704221 TATGGATTAA
3704231 AGGGATTAAATTGATGAAAATCCCATAAT
1 AGGGATTAAATTGATGAAAATCCCATAAT
** * **
3704260 ATTGGGATTAAATTGACCAATAT-GGATTAA-
1 A--GGGATTAAATTGATGAAAATCCCA-TAAT
3704290 AGGGATTAAATTGATGAAAATCCCATAAT
1 AGGGATTAAATTGATGAAAATCCCATAAT
3704319 A
1 A
3704320 CAGGGACTTA
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
28 20 0.44
29 3 0.07
30 2 0.04
31 20 0.44
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (29 bp):
AGGGATTAAATTGATGAAAATCCCATAAT
Found at i:3704444 original size:19 final size:18
Alignment explanation
Indices: 3704406--3704455 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
3704396 TTCAAATTTT
*
3704406 TAATCAAAAATTATAAATA
1 TAAT-AAAATTTATAAATA
* *
3704425 TCATAATATTTATCAAATA
1 TAATAAAATTTAT-AAATA
3704444 TAATAAAATTTA
1 TAATAAAATTTA
3704456 ATATCAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (18 bp):
TAATAAAATTTATAAATA
Found at i:3704464 original size:16 final size:17
Alignment explanation
Indices: 3704440--3704493 Score: 53
Period size: 16 Copynumber: 3.3 Consensus size: 17
3704430 ATATTTATCA
3704440 AATAT-AATAAAAT-TT
1 AATATCAATAAAATATT
*
3704455 AATATCAAT-AAATGTT
1 AATATCAATAAAATATT
3704471 AATCATC-ATAAAAGTATT
1 AAT-ATCAATAAAA-TATT
3704489 AATAT
1 AATAT
3704494 TTATATGGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 9 0.27
16 10 0.30
17 8 0.24
18 6 0.18
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (17 bp):
AATATCAATAAAATATT
Found at i:3705329 original size:35 final size:33
Alignment explanation
Indices: 3705286--3705491 Score: 115
Period size: 35 Copynumber: 6.1 Consensus size: 33
3705276 GAAAAGTTAG
*
3705286 TTGTT-AGGTTTTGGTTGATCTCGTGAAAAACCA
1 TTGTTGAGGTTTTGGTTGAGC-CGTGAAAAACCA
* * *
3705319 TTGTTGTAGGTTGTGGTTGAGCCTTTGAAAAATCA
1 TTGTTG-AGGTTTTGGTTGAGCC-GTGAAAAACCA
* *
3705354 CT-TTG-GGTTTTGGTTGAGCTTGTGAAAAACCA
1 TTGTTGAGGTTTTGGTTGAGC-CGTGAAAAACCA
* * *
3705386 TTG-TGAAAGGTTGTGGTTGAGCCTTTGAAAAACTA
1 TTGTTG--AGGTTTTGGTTGAGCC-GTGAAAAACCA
* *
3705421 CT-TTG-GGTTTTGGTTGATCCCG-GTAAAAACCA
1 TTGTTGAGGTTTTGGTTGA-GCCGTG-AAAAACCA
* *
3705453 TTG-TGAAAGGTTTTGGCTAAGCC-TGATAAAAGCCA
1 TTGTTG--AGGTTTTGGTTGAGCCGTGA-AAAA-CCA
3705488 TTGT
1 TTGT
3705492 AAAGCTTGGT
Statistics
Matches: 130, Mismatches: 23, Indels: 37
0.68 0.12 0.19
Matches are distributed among these distances:
31 1 0.01
32 46 0.35
33 8 0.06
34 11 0.08
35 64 0.49
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.36
Consensus pattern (33 bp):
TTGTTGAGGTTTTGGTTGAGCCGTGAAAAACCA
Found at i:3705369 original size:67 final size:68
Alignment explanation
Indices: 3705292--3705464 Score: 257
Period size: 67 Copynumber: 2.6 Consensus size: 68
3705282 TTAGTTGTTA
*
3705292 GGTTTTGGTTGATCTCGTGAAAAACCATTGTTG-TAGGTTGTGGTTGAGCCTTTGAAAAA-TCAC
1 GGTTTTGGTTGATCTCGTGAAAAACCATTGTTGAAAGGTTGTGGTTGAGCCTTTGAAAAACT-AC
3705355 TTTG
65 TTTG
* *
3705359 GGTTTTGGTTGAGCTTGTGAAAAACCATTG-TGAAAGGTTGTGGTTGAGCCTTTGAAAAACTACT
1 GGTTTTGGTTGATCTCGTGAAAAACCATTGTTGAAAGGTTGTGGTTGAGCCTTTGAAAAACTACT
3705423 TTG
66 TTG
*
3705426 GGTTTTGGTTGATCCCG-GTAAAAACCATTG-TGAAAGGTT
1 GGTTTTGGTTGATCTCGTG-AAAAACCATTGTTGAAAGGTT
3705465 TTGGCTAAGC
Statistics
Matches: 97, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
66 3 0.03
67 93 0.96
68 1 0.01
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (68 bp):
GGTTTTGGTTGATCTCGTGAAAAACCATTGTTGAAAGGTTGTGGTTGAGCCTTTGAAAAACTACT
TTG
Found at i:3705380 original size:32 final size:33
Alignment explanation
Indices: 3705291--3705437 Score: 133
Period size: 35 Copynumber: 4.4 Consensus size: 33
3705281 GTTAGTTGTT
* * *
3705291 AGGTTTTGGTTGA-TCTCGTGAAAAACCATTGTTG
1 AGGTTTTGGTTGAGCCT-TTGAAAAACCACT-TTG
* *
3705325 TAGGTTGTGGTTGAGCCTTTGAAAAATCACTTTG
1 -AGGTTTTGGTTGAGCCTTTGAAAAACCACTTTG
3705359 -GGTTTTGGTTGAG-CTTGTGAAAAACCA-TTGTG
1 AGGTTTTGGTTGAGCCTT-TGAAAAACCACTT-TG
* *
3705391 AAAGGTTGTGGTTGAGCCTTTGAAAAACTACTTTG
1 --AGGTTTTGGTTGAGCCTTTGAAAAACCACTTTG
3705426 -GGTTTTGGTTGA
1 AGGTTTTGGTTGA
3705438 TCCCGGTAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 19
0.76 0.08 0.15
Matches are distributed among these distances:
31 5 0.05
32 34 0.36
34 3 0.03
35 45 0.48
36 7 0.07
ACGTcount: A:0.23, C:0.10, G:0.29, T:0.38
Consensus pattern (33 bp):
AGGTTTTGGTTGAGCCTTTGAAAAACCACTTTG
Found at i:3714110 original size:16 final size:18
Alignment explanation
Indices: 3714089--3714131 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
3714079 CTTTCAACAT
3714089 ATTTTTTAAT-AATATA-
1 ATTTTTTAATAAATATAC
*
3714105 ATTTTTAAATAAAATATAC
1 ATTTTTTAAT-AAATATAC
3714124 ATTTTTTA
1 ATTTTTTA
3714132 TGTTAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 9 0.41
18 6 0.27
19 7 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTTTAATAAATATAC
Found at i:3717534 original size:38 final size:38
Alignment explanation
Indices: 3717491--3717564 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
3717481 TAATAATCAT
*
3717491 ATTATGTGACATAACTTTTAAGTTAAAATAACTTTTTC
1 ATTATGTGACATAACTTTTAAATTAAAATAACTTTTTC
*
3717529 ATTATGTGACATAACTTTTAAATTAAGATAACTTTT
1 ATTATGTGACATAACTTTTAAATTAAAATAACTTTT
3717565 CATATGAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (38 bp):
ATTATGTGACATAACTTTTAAATTAAAATAACTTTTTC
Found at i:3717553 original size:21 final size:21
Alignment explanation
Indices: 3717491--3717553 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
3717481 TAATAATCAT
3717491 ATTATGTGACATAACTTTTAA
1 ATTATGTGACATAACTTTTAA
* * **
3717512 GTTA----AAATAACTTTTTC
1 ATTATGTGACATAACTTTTAA
3717529 ATTATGTGACATAACTTTTAA
1 ATTATGTGACATAACTTTTAA
3717550 ATTA
1 ATTA
3717554 AGATAACTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
17 13 0.43
21 17 0.57
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (21 bp):
ATTATGTGACATAACTTTTAA
Found at i:3720683 original size:15 final size:16
Alignment explanation
Indices: 3720663--3720693 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3720653 ATTGCTATTT
3720663 AAATAATTAA-ATTAA
1 AAATAATTAATATTAA
3720678 AAATAATTAATATTAA
1 AAATAATTAATATTAA
3720694 TATATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATAATTAATATTAA
Found at i:3721357 original size:17 final size:17
Alignment explanation
Indices: 3721335--3721371 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3721325 ATACATTGAA
* *
3721335 ATACTTTTAATATATAT
1 ATACTTTGAATATAAAT
3721352 ATACTTTGAATATAAAT
1 ATACTTTGAATATAAAT
3721369 ATA
1 ATA
3721372 TTTACATTTT
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:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (17 bp):
ATACTTTGAATATAAAT
Found at i:3723682 original size:45 final size:45
Alignment explanation
Indices: 3723618--3723703 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
3723608 TGACAACTGG
*
3723618 CTTTTTCTATGAATCATCTTGCTTCCATGACGAATTAATTATTGC
1 CTTTTTCTATAAATCATCTTGCTTCCATGACGAATTAATTATTGC
* * *
3723663 CTTTTTCTTTAAATCATCTTGCTTCCATGGCTAATTAATTA
1 CTTTTTCTATAAATCATCTTGCTTCCATGACGAATTAATTA
3723704 GGAAATTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.47
Consensus pattern (45 bp):
CTTTTTCTATAAATCATCTTGCTTCCATGACGAATTAATTATTGC
Found at i:3724365 original size:16 final size:16
Alignment explanation
Indices: 3724342--3724398 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
3724332 CAATAATTAT
3724342 AAAA-AAAATTATAAC
1 AAAACAAAATTATAAC
* *
3724357 AAAACAAAATAATAAG
1 AAAACAAAATTATAAC
*
3724373 AATATC-AAA-TATAAC
1 AA-AACAAAATTATAAC
3724388 AAAACAAAATT
1 AAAACAAAATT
3724399 TAAAATTAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
14 2 0.06
15 13 0.41
16 15 0.47
17 2 0.06
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.19
Consensus pattern (16 bp):
AAAACAAAATTATAAC
Found at i:3724577 original size:18 final size:18
Alignment explanation
Indices: 3724554--3724617 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
3724544 GTATATACGT
3724554 TTAAACACGATAACACGA
1 TTAAACACGATAACACGA
* * * *
3724572 TTAAACACGTTTATACGT
1 TTAAACACGATAACACGA
* *
3724590 TTAAACATGATAACATGA
1 TTAAACACGATAACACGA
3724608 TT-AACACGAT
1 TTAAACACGAT
3724618 TAATTAAACG
Statistics
Matches: 35, Mismatches: 11, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
17 7 0.20
18 28 0.80
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (18 bp):
TTAAACACGATAACACGA
Found at i:3724587 original size:36 final size:35
Alignment explanation
Indices: 3724547--3724615 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 35
3724537 GTACCATGTA
3724547 TATACGTTTAAACACGATAACACGATTAAACACGTT
1 TATACGTTTAAACACGATAACACGATT-AACACGTT
* *
3724583 TATACGTTTAAACATGATAACATGATTAACACG
1 TATACGTTTAAACACGATAACACGATTAACACG
3724616 ATTAATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 6 0.19
36 25 0.81
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (35 bp):
TATACGTTTAAACACGATAACACGATTAACACGTT
Found at i:3725172 original size:43 final size:43
Alignment explanation
Indices: 3725107--3725237 Score: 219
Period size: 43 Copynumber: 3.0 Consensus size: 43
3725097 GCGTTTCATA
3725107 TGAGATGTTCCACATTTGAGATACTGGACATGTTCTTTTTGTG
1 TGAGATGTTCCACATTTGAGATACTGGACATGTTCTTTTTGTG
*
3725150 TGAGATGCTCCACAGTTT-AGATACTGGACATGTTCTTTTTGTG
1 TGAGATGTTCCACA-TTTGAGATACTGGACATGTTCTTTTTGTG
* *
3725193 TGAGATGTTCCACATTTGAGATATTGGACATCTTCTTTTTGTG
1 TGAGATGTTCCACATTTGAGATACTGGACATGTTCTTTTTGTG
3725236 TG
1 TG
3725238 TACTTTTTTT
Statistics
Matches: 82, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
42 3 0.04
43 76 0.93
44 3 0.04
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.42
Consensus pattern (43 bp):
TGAGATGTTCCACATTTGAGATACTGGACATGTTCTTTTTGTG
Found at i:3726174 original size:79 final size:77
Alignment explanation
Indices: 3726079--3726246 Score: 203
Period size: 79 Copynumber: 2.2 Consensus size: 77
3726069 TAATTAAATT
* * * *
3726079 TTATTTAATCAATTAAAC-AGCTTAATTAAGTTATTAATATATTAATTAATTTAATTATTTTTAA
1 TTATTTAATTAATTAAACTA-CTTAATTAAGTTATTAATACACTAATTAATTT-AGT-TTTTTAA
* ** *
3726143 ATTAAATGCTATTAC
63 ACTAAATAATACTAC
* * *
3726158 TTATTTTATTAATTAAACTATTTAATTAAGTTATTAGTACACTAATTAATTTAGTTTTTTAAACT
1 TTATTTAATTAATTAAACTACTTAATTAAGTTATTAATACACTAATTAATTTAGTTTTTTAAACT
3726223 AAATAATACTAC
66 AAATAATACTAC
3726235 TTATTTAATTAA
1 TTATTTAATTAA
3726247 ATTTTATTTA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
77 29 0.38
78 2 0.03
79 44 0.58
80 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.49
Consensus pattern (77 bp):
TTATTTAATTAATTAAACTACTTAATTAAGTTATTAATACACTAATTAATTTAGTTTTTTAAACT
AAATAATACTAC
Found at i:3726264 original size:92 final size:92
Alignment explanation
Indices: 3726158--3726500 Score: 253
Period size: 96 Copynumber: 3.6 Consensus size: 92
3726148 ATGCTATTAC
* * * *
3726158 TTATTTTATTAATTAAACTATTTAATTAAGTTATTAGTACACTA-ATTAATTTAGTTTTTTAAAC
1 TTATTTAATCAATTAAACTATTTAATTAAGTTATTAATACATTATATTAA-TTAGTTTTTTAAAC
*
3726222 TAAATAATACTACTTATTTAATTAAATT
65 TAAATAATATTACTTATTTAATTAAATT
* * *
3726250 TTATTTAATCAATTAAACTATTTAATTAATTTCTTAATACATTATTTGATTTAATTATTTTTTTA
1 TTATTTAATCAATTAAACTATTTAATTAAGTTATTAATACATTA--T-A-TTAATTAGTTTTTTA
* * * *
3726315 AATTAAATATTTTTACTTATTTAATTAATTGT
62 AACTAAATAATATTACTTATTTAATTAAAT-T
* * * * * * * *
3726347 TTA-CTAAT-ATATTATTTTAGTTTATTAATTAACTATTTAATTAAGTTATGAGTACATTAATTA
1 TTATTTAATCA-ATTA---AACTAT-TTAATT-A--AGTT-ATTAA--TA-CATTATATTAATTA
* * * *
3726410 TTTTTTTAAAACTAAATAATATTAGTTAATTATTTAAATT
54 GTTTTTT-AAACTAAATAATATTACTTATTTAATTAAATT
* *
3726450 TTATTGAATCAATTAAACTATTTAATTAAGTTATTAATACGTTA-ATTAATT
1 TTATTTAATCAATTAAACTATTTAATTAAGTTATTAATACATTATATTAATT
3726501 TCAGTTTATT
Statistics
Matches: 194, Mismatches: 36, Indels: 42
0.71 0.13 0.15
Matches are distributed among these distances:
92 45 0.23
93 2 0.01
94 2 0.01
95 1 0.01
96 49 0.25
97 11 0.06
99 4 0.02
100 12 0.06
101 4 0.02
103 22 0.11
104 36 0.19
105 1 0.01
106 2 0.01
107 3 0.02
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.52
Consensus pattern (92 bp):
TTATTTAATCAATTAAACTATTTAATTAAGTTATTAATACATTATATTAATTAGTTTTTTAAACT
AAATAATATTACTTATTTAATTAAATT
Found at i:3726304 original size:171 final size:174
Alignment explanation
Indices: 3726008--3726344 Score: 486
Period size: 171 Copynumber: 1.9 Consensus size: 174
3725998 TGTTGTTGTC
* * *
3726008 AATTAATTTATTAGTACATTAATTAATTTAATTTTTTTTAAACTAAATAATATCACTGATTTAAT
1 AATTAAGTTATTAGTACACTAATTAATTTAATGTTTTTTAAACTAAATAATATCACTGATTTAAT
*
3726073 TAAATTTTATTTAATCAATTAAACAGCTTAATTAAGTTATTAATATATTAATTAATTTAATTA-T
66 TAAATTTTATTTAATCAATTAAACAGCTTAATTAAGTTATTAATACATTAATTAATTTAATTATT
* *
3726137 TTTTAAATTAAATGCTATTACTTATTTTATTAATTAAACTATTT
131 TTTTAAATTAAATACTATTACTTATTTAATTAATTAAACTATTT
*
3726181 AATTAAGTTATTAGTACACTAATTAATTT-A-GTTTTTTAAACTAAATAATA-CTACTTATTTAA
1 AATTAAGTTATTAGTACACTAATTAATTTAATGTTTTTTAAACTAAATAATATC-ACTGATTTAA
* * * * *
3726243 TTAAATTTTATTTAATCAATTAAACTA-TTTAATTAATTTCTTAATACATTATTTGATTTAATTA
65 TTAAATTTTATTTAATCAATTAAAC-AGCTTAATTAAGTTATTAATACATTAATTAATTTAATTA
* *
3726307 TTTTTTTAAATTAAATATTTTTACTTATTTAATTAATT
129 -TTTTTTAAATTAAATACTATTACTTATTTAATTAATT
3726345 GTTTACTAAT
Statistics
Matches: 146, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
170 1 0.01
171 84 0.58
172 2 0.01
173 59 0.40
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (174 bp):
AATTAAGTTATTAGTACACTAATTAATTTAATGTTTTTTAAACTAAATAATATCACTGATTTAAT
TAAATTTTATTTAATCAATTAAACAGCTTAATTAAGTTATTAATACATTAATTAATTTAATTATT
TTTTAAATTAAATACTATTACTTATTTAATTAATTAAACTATTT
Found at i:3726424 original size:200 final size:203
Alignment explanation
Indices: 3726162--3726823 Score: 826
Period size: 200 Copynumber: 3.3 Consensus size: 203
3726152 TATTACTTAT
* *
3726162 TTTATTAATTAAACTATTTAATTAAGTTATTAGTACACTAATTAATTTAGTTTTTTAAACTAAAT
1 TTTATTAATTAAACTATTTAATTAAGTTATTAGTACATTAATTAATTTA-TTTTTAAAACTAAAT
* * *
3726227 AATACTACTTATTTAATTAAATTTTATTTAATCAATTAAACTATTTAATTAATTTCTTAATACAT
65 AATATTACTTATTTAATTAAATTTTATTTAATCAATTAAACTATTTAATTAAGTTATTAATACAT
* * * *
3726292 TATTTGATTTAATTATTTTTTTAAATTAAATATTTTTACTTATTTAATTAATTGTTTACTAATAT
130 TAATTAATTTAATTA-TTTTTTAAATTAAATATTATTACTTATTTAATTAATTGTTTACTAATAC
*
3726357 ATTATTTTAG
194 ATTATTTTAA
*
3726367 TTTATTAATT-AACTATTTAATTAAGTTATGAGTACATTAATT-A-TT-TTTTTAAAACTAAATA
1 TTTATTAATTAAACTATTTAATTAAGTTATTAGTACATTAATTAATTTATTTTTAAAACTAAATA
* * * * *
3726428 ATATTAGTTAATTATTTAAATTTTATTGAATCAATTAAACTATTTAATTAAGTTATTAATACGTT
66 ATATTACTTATTTAATTAAATTTTATTTAATCAATTAAACTATTTAATTAAGTTATTAATACATT
* * * * ** * *
3726493 AATTAATTTCAGTT-TATTTTCAAATTATATAATATTACCAATTT-TTTAATTTTTTACTAATAC
131 AATTAATTT-AATTAT-TTTTTAAATTAAATATTATTACTTATTTAATTAATTGTTTACTAATAC
3726556 ATTATTTTAA
194 ATTATTTTAA
* * *
3726566 TTTATTAATTAAAATATTTAATTAAGTTATTAGTACATTAATTAATTTAATTTTTACAATTAAAT
1 TTTATTAATTAAACTATTTAATTAAGTTATTAGTACATTAATTAATTT-ATTTTTAAAACTAAAT
* * * *
3726631 AATATTACATATTTAATTAAATTTTATTTCATAAATTAAA-TATTTAATTAAGTTATTAGA-ATA
65 AATATTACTTATTTAATTAAATTTTATTTAATCAATTAAACTATTTAATTAAGTTATTA-ATACA
* *
3726694 TTAATTAATGTAATTA--TTTTCAATTAAATATTATTACTTATTTAATTAATTGTTTACTAAT-C
129 TTAATTAATTTAATTATTTTTTAAATTAAATATTATTACTTATTTAATTAATTGTTTACTAATAC
*
3726756 ATTA-TTTAT
194 ATTATTTTAA
* * * * *
3726765 TTTAGTAATTAAATTATTTAGTTAAGTTATTTGTACATTAATTAATTAATTTTTTAAAA
1 TTTATTAATTAAACTATTTAATTAAGTTATTAGTACATTAATTAATTTA-TTTTTAAAA
3726824 ANNNNNNNNN
Statistics
Matches: 392, Mismatches: 54, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
198 1 0.00
199 91 0.23
200 157 0.40
201 19 0.05
202 7 0.02
203 30 0.08
204 77 0.20
205 10 0.03
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.52
Consensus pattern (203 bp):
TTTATTAATTAAACTATTTAATTAAGTTATTAGTACATTAATTAATTTATTTTTAAAACTAAATA
ATATTACTTATTTAATTAAATTTTATTTAATCAATTAAACTATTTAATTAAGTTATTAATACATT
AATTAATTTAATTATTTTTTAAATTAAATATTATTACTTATTTAATTAATTGTTTACTAATACAT
TATTTTAA
Found at i:3726668 original size:92 final size:92
Alignment explanation
Indices: 3726559--3726742 Score: 273
Period size: 91 Copynumber: 2.0 Consensus size: 92
3726549 CTAATACATT
* * *
3726559 ATTTTAATTTATTAATTAAAATATTTAATTAAGTTATTAGTACATTAATTAATTTAATT-TTTAC
1 ATTTTAATTTATAAATT-AAATATTTAATTAAGTTATTAGAACATTAATTAATGTAATTATTTAC
3726623 AATTAAATAATATTACATATTTAATTAA
65 AATTAAATAATATTACATATTTAATTAA
* *
3726651 ATTTT-ATTTCATAAATTAAATATTTAATTAAGTTATTAGAATATTAATTAATGTAATTATTTTC
1 ATTTTAATTT-ATAAATTAAATATTTAATTAAGTTATTAGAACATTAATTAATGTAATTATTTAC
* *
3726715 AATTAAATATTATTACTTATTTAATTAA
65 AATTAAATAATATTACATATTTAATTAA
3726743 TTGTTTACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
91 42 0.51
92 41 0.49
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (92 bp):
ATTTTAATTTATAAATTAAATATTTAATTAAGTTATTAGAACATTAATTAATGTAATTATTTACA
ATTAAATAATATTACATATTTAATTAA
Found at i:3726677 original size:112 final size:113
Alignment explanation
Indices: 3726460--3726701 Score: 252
Period size: 112 Copynumber: 2.2 Consensus size: 113
3726450 TTATTGAATC
* * * * *
3726460 AATTAAACTATTTAATTAAGTTATTAATACGTTAATTAATTTCAGTTTATTTTCAAATTATATAA
1 AATTAAAATATTTAATTAAGTTATTAATACATTAATTAATTTCAGATTATTTACAAATTAAATAA
* * *
3726525 TATTACCAATTTTTTAATTTTTTACTAATACATTATTTTAATTTA-TT
66 TATTACCAATTTTTAAATTTTTTACTAATACAATATTTTAATTAAGTT
*
3726572 AATTAAAATATTTAATTAAGTTATTAGTACATTAATTAATTT-A-ATT-TTTAC-AATTAAATAA
1 AATTAAAATATTTAATTAAGTTATTAATACATTAATTAATTTCAGATTATTTACAAATTAAATAA
*
3726633 TATTA-CATATTTAATTAAATTTTATTTCATAAATTA-AATA-TTTAATTAAGTT
66 TATTACCA-ATTT--TTAAATTTT-TTAC-T-AA-TACAATATTTTAATTAAGTT
*
3726685 -ATTAGAATA-TTAATTAA
1 AATTAAAATATTTAATTAA
3726702 TGTAATTATT
Statistics
Matches: 111, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
107 2 0.02
108 18 0.16
109 4 0.04
110 10 0.09
111 12 0.11
112 56 0.50
113 7 0.06
114 2 0.02
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (113 bp):
AATTAAAATATTTAATTAAGTTATTAATACATTAATTAATTTCAGATTATTTACAAATTAAATAA
TATTACCAATTTTTAAATTTTTTACTAATACAATATTTTAATTAAGTT
Found at i:3727321 original size:113 final size:116
Alignment explanation
Indices: 3727084--3727290 Score: 264
Period size: 113 Copynumber: 1.8 Consensus size: 116
3727074 TTAAACTATA
** * *
3727084 ATTAA-TACATTAATTTAATTATTTTTTGAAATTAAATATTATTACTTATTTAATTAATTGCTTA
1 ATTAATTA-ATTAATTTAATTATTTGATGAAATTAAATAATATTACTTATTCAATTAATTGCTTA
* *
3727148 GTAATGCATTATTTTATTTCATTAATTGAATTACTTAATTTAAGAGATTAAT
65 GTAATACATTATTTTATTTAATTAATTGAATTACTTAATTTAAGAGATTAAT
* * * *
3727200 ACT--TTAATTAATTTAATTATTTGAT-AAATTAAATAATATTTCTTCTTCAATTACTTGCTTAG
1 ATTAATTAATTAATTTAATTATTTGATGAAATTAAATAATATTACTTATTCAATTAATTGCTTAG
*
3727262 TAATATATTA-TTTATTTAATTAATT-AATT
66 TAATACATTATTTTATTTAATTAATTGAATT
3727291 TTTTATTAAG
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
111 4 0.05
112 14 0.18
113 40 0.51
114 17 0.22
115 2 0.03
116 2 0.03
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.52
Consensus pattern (116 bp):
ATTAATTAATTAATTTAATTATTTGATGAAATTAAATAATATTACTTATTCAATTAATTGCTTAG
TAATACATTATTTTATTTAATTAATTGAATTACTTAATTTAAGAGATTAAT
Found at i:3729795 original size:16 final size:16
Alignment explanation
Indices: 3729774--3729807 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3729764 ATTAAACTAT
*
3729774 TTAATTAAGTTATTTA
1 TTAATTAAGTTAATTA
*
3729790 TTAATTAATTTAATTA
1 TTAATTAAGTTAATTA
3729806 TT
1 TT
3729808 TTTTGAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTAATTAAGTTAATTA
Found at i:3733523 original size:15 final size:15
Alignment explanation
Indices: 3733503--3733534 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3733493 AAATGTAGAA
3733503 AACTGTTTATCCATT
1 AACTGTTTATCCATT
*
3733518 AACTGTTTCTCCATT
1 AACTGTTTATCCATT
3733533 AA
1 AA
3733535 TACAAAGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (15 bp):
AACTGTTTATCCATT
Found at i:3736164 original size:2 final size:2
Alignment explanation
Indices: 3736157--3736182 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3736147 AGATATCCCC
3736157 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
3736183 AATCGGCTTT
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:3736870 original size:17 final size:17
Alignment explanation
Indices: 3736845--3736883 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3736835 GATGAAAGGA
3736845 ATATATATAAATAATAT
1 ATATATATAAATAATAT
* *
3736862 ATATTTATAATTAATAT
1 ATATATATAAATAATAT
*
3736879 TTATA
1 ATATA
3736884 AAACTATTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATATAAATAATAT
Found at i:3739553 original size:17 final size:18
Alignment explanation
Indices: 3739519--3739554 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3739509 TATAACTATA
*
3739519 TTTGTTGTTTGAGATATT
1 TTTGTTGGTTGAGATATT
3739537 TTTGTTGGTTG-GATATT
1 TTTGTTGGTTGAGATATT
3739554 T
1 T
3739555 GCATCTCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.14, C:0.00, G:0.25, T:0.61
Consensus pattern (18 bp):
TTTGTTGGTTGAGATATT
Found at i:3747426 original size:12 final size:12
Alignment explanation
Indices: 3747409--3747447 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
3747399 TAATGCTATA
3747409 AAAATGCATTAC
1 AAAATGCATTAC
3747421 AAAATGC-TATA-
1 AAAATGCAT-TAC
3747432 AAAATGCATTAC
1 AAAATGCATTAC
3747444 AAAA
1 AAAA
3747448 AAGTTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.56, C:0.13, G:0.08, T:0.23
Consensus pattern (12 bp):
AAAATGCATTAC
Found at i:3747430 original size:23 final size:23
Alignment explanation
Indices: 3747400--3747447 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
3747390 AGAAGAAGAT
3747400 AATGCTATAAAAATGCATTACAA
1 AATGCTATAAAAATGCATTACAA
3747423 AATGCTATAAAAATGCATTACAA
1 AATGCTATAAAAATGCATTACAA
3747446 AA
1 AA
3747448 AAGTTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.25
Consensus pattern (23 bp):
AATGCTATAAAAATGCATTACAA
Found at i:3747437 original size:11 final size:11
Alignment explanation
Indices: 3747400--3747438 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
3747390 AGAAGAAGAT
3747400 AATGCTATAAA
1 AATGCTATAAA
3747411 AATGC-ATTACAA
1 AATGCTA-TA-AA
3747423 AATGCTATAAA
1 AATGCTATAAA
3747434 AATGC
1 AATGC
3747439 ATTACAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.04
11 14 0.56
12 9 0.36
13 1 0.04
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.26
Consensus pattern (11 bp):
AATGCTATAAA
Found at i:3748552 original size:7 final size:7
Alignment explanation
Indices: 3748540--3748567 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3748530 AGTTGAGATA
3748540 ATTTGCT
1 ATTTGCT
3748547 ATTTGCT
1 ATTTGCT
3748554 ATTTGCT
1 ATTTGCT
3748561 ATTTGCT
1 ATTTGCT
3748568 TCTGAAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (7 bp):
ATTTGCT
Found at i:3748717 original size:17 final size:16
Alignment explanation
Indices: 3748674--3748721 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
3748664 CATAGATTGA
3748674 TTATCTTATTTTAATTC
1 TTAT-TTATTTTAATTC
* *
3748691 GTATTATATTTTAATTAT
1 TTATT-TATTTTAATT-C
3748709 TTATTTATTTTAA
1 TTATTTATTTTAA
3748722 ATTAATTCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.04
17 21 0.81
18 4 0.15
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTATTTTAATTC
Found at i:3749167 original size:63 final size:63
Alignment explanation
Indices: 3749096--3749241 Score: 256
Period size: 63 Copynumber: 2.3 Consensus size: 63
3749086 AATAAACATG
* *
3749096 TAACACGATTAACACGTTTATTAAACGTGTCAATATATGACACGACACGATTAATAACACGTT
1 TAACACGATTAACACGTTTATTAAACGTATCAATATATGACACGACACAATTAATAACACGTT
*
3749159 TAACACGATTAACACGTTTATTAAACGTATTAATATATGACACGACACAATTAATAACACGTT
1 TAACACGATTAACACGTTTATTAAACGTATCAATATATGACACGACACAATTAATAACACGTT
*
3749222 TAATACGATTAACACGTTTA
1 TAACACGATTAACACGTTTA
3749242 ACACGATTAA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 79 1.00
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (63 bp):
TAACACGATTAACACGTTTATTAAACGTATCAATATATGACACGACACAATTAATAACACGTT
Found at i:3749236 original size:18 final size:18
Alignment explanation
Indices: 3749213--3749251 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3749203 ACACAATTAA
*
3749213 TAACACGTTTAATACGAT
1 TAACACGTTTAACACGAT
3749231 TAACACGTTTAACACGAT
1 TAACACGTTTAACACGAT
3749249 TAA
1 TAA
3749252 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (18 bp):
TAACACGTTTAACACGAT
Found at i:3749242 original size:9 final size:9
Alignment explanation
Indices: 3749213--3749251 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
3749203 ACACAATTAA
*
3749213 TAACACGTT
1 TAACACGAT
*
3749222 TAATACGAT
1 TAACACGAT
*
3749231 TAACACGTT
1 TAACACGAT
3749240 TAACACGAT
1 TAACACGAT
3749249 TAA
1 TAA
3749252 ATAAAAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (9 bp):
TAACACGAT
Found at i:3749408 original size:25 final size:24
Alignment explanation
Indices: 3749349--3749411 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
3749339 AATAACATCA
*
3749349 AATATAATAAAATTTAATATATAT
1 AATATAATAAAATTCAATATATAT
* *
3749373 AACATACATAAAATTCATTATAATAT
1 AATATA-ATAAAATTCAATAT-ATAT
*
3749399 AATATGATAAAAT
1 AATATAATAAAAT
3749412 ACATCATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 5 0.16
25 19 0.59
26 8 0.25
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (24 bp):
AATATAATAAAATTCAATATATAT
Found at i:3749950 original size:14 final size:14
Alignment explanation
Indices: 3749931--3749964 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3749921 ATTCAAAAAG
3749931 TAAAAAATAAATAA
1 TAAAAAATAAATAA
* *
3749945 TAAAAAATAAGTAG
1 TAAAAAATAAATAA
3749959 TAAAAA
1 TAAAAA
3749965 CATCAACCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (14 bp):
TAAAAAATAAATAA
Found at i:3751128 original size:16 final size:15
Alignment explanation
Indices: 3751089--3751131 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
3751079 TTATTCATTA
* *
3751089 TATTTTTAA-ATTAT
1 TATTTTAAATATTTT
3751103 TATTTTAAATATTTT
1 TATTTTAAATATTTT
3751118 TATTATTAAATATT
1 TATT-TTAAATATT
3751132 ATTAAAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 8 0.32
15 8 0.32
16 9 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTTTAAATATTTT
Found at i:3751199 original size:85 final size:82
Alignment explanation
Indices: 3751109--3751285 Score: 189
Period size: 82 Copynumber: 2.1 Consensus size: 82
3751099 TTATTATTTT
* * * *
3751109 AAATATTTTTATTATT-AAATATTATTAAAGTTTA-TCTGATTTGTAAATATAAAAAATTTTAAT
1 AAATATTTTT-TTATTAAAATATTAATAAAATTTATTC-AAATTGT-AA-AT-AAAAATTTTAAT
* * *
3751172 AATATTGAATGACTTTCATTAA
61 AACATTGAACGACTGTCATTAA
*
3751194 AAATA-TTTTTTATTCAAAATATTAATAAAATTTATTCAAATTGTAACTAAAAATTTTAATAACA
1 AAATATTTTTTTATT-AAAATATTAATAAAATTTATTCAAATTGTAAATAAAAATTTTAATAACA
*
3751258 TTTAACGACTGTCATTAA
65 TTGAACGACTGTCATTAA
*
3751276 AAATGTTTTT
1 AAATATTTTT
3751286 CCATAATTCT
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
82 34 0.44
83 10 0.13
84 6 0.08
85 26 0.33
86 2 0.03
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (82 bp):
AAATATTTTTTTATTAAAATATTAATAAAATTTATTCAAATTGTAAATAAAAATTTTAATAACAT
TGAACGACTGTCATTAA
Found at i:3757134 original size:32 final size:32
Alignment explanation
Indices: 3757098--3757165 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 32
3757088 CCAAAACAGA
3757098 CCAAA-CACGAAACGGTCTGAATCCAAAATGA-T
1 CCAAATCACGAAAC--TCTGAATCCAAAATGATT
* * *
3757130 CCAAATCCCTAAACTCTGAATCCAAAGTGATT
1 CCAAATCACGAAACTCTGAATCCAAAATGATT
3757162 CCAA
1 CCAA
3757166 CCTGAGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
31 15 0.48
32 10 0.32
33 6 0.19
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.19
Consensus pattern (32 bp):
CCAAATCACGAAACTCTGAATCCAAAATGATT
Found at i:3763064 original size:17 final size:17
Alignment explanation
Indices: 3763042--3763076 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3763032 TAAGTATGAC
3763042 ATGTGAAAACATTTTCT
1 ATGTGAAAACATTTTCT
3763059 ATGTGAAAACATTTTCT
1 ATGTGAAAACATTTTCT
3763076 A
1 A
3763077 GCAGTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40
Consensus pattern (17 bp):
ATGTGAAAACATTTTCT
Found at i:3769617 original size:19 final size:20
Alignment explanation
Indices: 3769593--3769638 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
3769583 AATCTTGACA
*
3769593 GAAATT-AGCCGGTGTAAAG
1 GAAATTAAGCCAGTGTAAAG
3769612 GAAATTCAAGCCAGTGTAAAG
1 GAAATT-AAGCCAGTGTAAAG
3769633 GAAATT
1 GAAATT
3769639 CAATAACCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
21 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.26, T:0.22
Consensus pattern (20 bp):
GAAATTAAGCCAGTGTAAAG
Found at i:3769628 original size:21 final size:21
Alignment explanation
Indices: 3769599--3769641 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3769589 GACAGAAATT
*
3769599 AGCCGGTGTAAAGGAAATTCA
1 AGCCAGTGTAAAGGAAATTCA
3769620 AGCCAGTGTAAAGGAAATTCA
1 AGCCAGTGTAAAGGAAATTCA
3769641 A
1 A
3769642 TAACCATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.14, G:0.26, T:0.19
Consensus pattern (21 bp):
AGCCAGTGTAAAGGAAATTCA
Found at i:3784522 original size:20 final size:20
Alignment explanation
Indices: 3784494--3784531 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3784484 ATGTTTTATG
*
3784494 ATATTTTAAAAAAATATTTA
1 ATATATTAAAAAAATATTTA
*
3784514 ATATATTAAAAAATTATT
1 ATATATTAAAAAAATATT
3784532 ATTTTATATA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATATTAAAAAAATATTTA
Found at i:3785913 original size:28 final size:26
Alignment explanation
Indices: 3785874--3785925 Score: 86
Period size: 28 Copynumber: 1.9 Consensus size: 26
3785864 CTGAGAAAGC
3785874 TCTCTTTTTATTTTCTATTTGCCTAT
1 TCTCTTTTTATTTTCTATTTGCCTAT
3785900 TCTCTTCTTCTATTTTCTATTTGCCT
1 TCTCTT-TT-TATTTTCTATTTGCCT
3785926 CTTCAATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 6 0.25
27 2 0.08
28 16 0.67
ACGTcount: A:0.10, C:0.23, G:0.04, T:0.63
Consensus pattern (26 bp):
TCTCTTTTTATTTTCTATTTGCCTAT
Found at i:3788412 original size:11 final size:12
Alignment explanation
Indices: 3788380--3788416 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
3788370 TTTTTGGTCA
3788380 TTTATTATTA-T
1 TTTATTATTATT
*
3788391 TTAATTATTATT
1 TTTATTATTATT
3788403 TTTATT-TTATT
1 TTTATTATTATT
3788414 TTT
1 TTT
3788417 TNNNNNNNNN
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 17 0.74
12 6 0.26
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTATTATT
Found at i:3804352 original size:34 final size:32
Alignment explanation
Indices: 3804277--3804482 Score: 160
Period size: 32 Copynumber: 6.5 Consensus size: 32
3804267 NNNNNNNNNN
3804277 CGCTCCTCTCTCTCTGGTGCCGCGCCAGCCGC
1 CGCTCCTCTCTCTCTGGTGCCGCGCCAGCCGC
3804309 CGCTCCTCTCTCTCTGGTGCCGCGCCAGCCGC
1 CGCTCCTCTCTCTCTGGTGCCGCGCCAGCCGC
* * *
3804341 CGCTCCTCTCTCTCT--T--C-CTCC-GTTCGA
1 CGCTCCTCTCTCTCTGGTGCCGCGCCAG-CCGC
* * * * **
3804368 TGCTCCT-TCT-TCTCGCGCCAGATCTTCACTA-TTGC
1 CGCTCCTCTCTCTCTGGTGCC-G--C-GC-C-AGCCGC
* * *
3804403 TGCTCCCTTTCTCTCTGGTGCCGCGCCAGCTGC
1 CGCT-CCTCTCTCTCTGGTGCCGCGCCAGCCGC
3804436 CGCTCCTCTCTCTCTGGTGCCGCGCCAGCCGC
1 CGCTCCTCTCTCTCTGGTGCCGCGCCAGCCGC
*
3804468 CGCTTCTCTCTCTCT
1 CGCTCCTCTCTCTCT
3804483 TTCTCCGTTC
Statistics
Matches: 142, Mismatches: 15, Indels: 34
0.74 0.08 0.18
Matches are distributed among these distances:
25 3 0.02
26 4 0.03
27 11 0.08
28 1 0.01
29 1 0.01
30 1 0.01
32 88 0.62
33 8 0.06
34 3 0.02
35 8 0.06
36 3 0.02
37 4 0.03
38 7 0.05
ACGTcount: A:0.04, C:0.46, G:0.20, T:0.30
Consensus pattern (32 bp):
CGCTCCTCTCTCTCTGGTGCCGCGCCAGCCGC
Found at i:3805137 original size:16 final size:15
Alignment explanation
Indices: 3805116--3805154 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3805106 TATAGATCCC
*
3805116 AAATAAAAATAATAAT
1 AAATAAAAACAA-AAT
3805132 AAATAACAAACAAAAT
1 AAATAA-AAACAAAAT
3805148 AAATAAA
1 AAATAAA
3805155 TCACTCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 15 0.71
17 5 0.24
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (15 bp):
AAATAAAAACAAAAT
Found at i:3807210 original size:22 final size:21
Alignment explanation
Indices: 3807179--3807234 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
3807169 TTGAATGTAC
*
3807179 AAAAATATATAATAAAATAAA
1 AAAAAAATATAATAAAATAAA
* * *
3807200 ATAAAAAATATAGTTAGATAAA
1 A-AAAAAATATAATAAAATAAA
3807222 AAAATAAATATAA
1 AAAA-AAATATAA
3807235 CATATTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 4 0.14
22 24 0.86
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (21 bp):
AAAAAAATATAATAAAATAAA
Found at i:3810224 original size:3 final size:3
Alignment explanation
Indices: 3810216--3810249 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3810206 GTAGGTTTTA
*
3810216 TTC TTC TTC TTC TTC TTC TTC TTC TCC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
3810250 CTTTTATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:3815787 original size:15 final size:15
Alignment explanation
Indices: 3815767--3815797 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3815757 ACTTTACAAT
*
3815767 GTAATGTGATTGTAA
1 GTAATGTAATTGTAA
3815782 GTAATGTAATTGTAA
1 GTAATGTAATTGTAA
3815797 G
1 G
3815798 CATAGTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (15 bp):
GTAATGTAATTGTAA
Found at i:3816066 original size:33 final size:34
Alignment explanation
Indices: 3816029--3816099 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
3816019 TTTAATGTTG
* * *
3816029 TATATTTTAATTTCATTTCTTATTATAA-TCTTA
1 TATATTCTAATTTCATTGCTTAATATAATTCTTA
*
3816062 TATATTCTATTTTCATTGCTTAATATAATTTCTTA
1 TATATTCTAATTTCATTGCTTAATATAA-TTCTTA
3816097 TAT
1 TAT
3816100 TATATATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.75
35 8 0.25
ACGTcount: A:0.30, C:0.10, G:0.01, T:0.59
Consensus pattern (34 bp):
TATATTCTAATTTCATTGCTTAATATAATTCTTA
Found at i:3816108 original size:35 final size:33
Alignment explanation
Indices: 3816029--3816109 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 33
3816019 TTTAATGTTG
* * * *
3816029 TATATTTTAATTTCATTTCTTATTATAATCTTA
1 TATATTATATTTTCATTGCTTAATATAATCTTA
*
3816062 TATATTCTATTTTCATTGCTTAATATAATTTCTTA
1 TATATTATATTTTCATTGCTTAATATAA--TCTTA
3816097 TAT-TATATATTTT
1 TATAT-TATATTTT
3816110 AATTTAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 24 0.60
34 1 0.03
35 15 0.38
ACGTcount: A:0.30, C:0.09, G:0.01, T:0.60
Consensus pattern (33 bp):
TATATTATATTTTCATTGCTTAATATAATCTTA
Found at i:3816948 original size:17 final size:17
Alignment explanation
Indices: 3816926--3816962 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3816916 AAGAGGAAAA
*
3816926 TATGGCTATATATAAAT
1 TATGGCAATATATAAAT
*
3816943 TATGGCAATATATTAAT
1 TATGGCAATATATAAAT
3816960 TAT
1 TAT
3816963 TGACCTGACA
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:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (17 bp):
TATGGCAATATATAAAT
Found at i:3820602 original size:14 final size:14
Alignment explanation
Indices: 3820574--3820607 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3820564 TTTACCCTCC
*
3820574 TACCTTGTTCTCGTA
1 TACC-TGTTCACGTA
3820589 TACCTGTTCACGTA
1 TACCTGTTCACGTA
3820603 TACCT
1 TACCT
3820608 TTTTCTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.18, C:0.29, G:0.12, T:0.41
Consensus pattern (14 bp):
TACCTGTTCACGTA
Found at i:3820642 original size:29 final size:29
Alignment explanation
Indices: 3820589--3820647 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3820579 TGTTCTCGTA
* * * *
3820589 TACCTGTTCACGTATACCTTTTTCTATTG
1 TACCCGTTCACGTACAACTTCTTCTATTG
*
3820618 TACCCGTTCACGTACAACTTCTTCTCTTG
1 TACCCGTTCACGTACAACTTCTTCTATTG
3820647 T
1 T
3820648 GCCTTTCCAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.17, C:0.29, G:0.10, T:0.44
Consensus pattern (29 bp):
TACCCGTTCACGTACAACTTCTTCTATTG
Found at i:3822858 original size:103 final size:102
Alignment explanation
Indices: 3822627--3822917 Score: 258
Period size: 103 Copynumber: 2.8 Consensus size: 102
3822617 AAAGAAATTC
* * * * * * * *
3822627 ATACTTTAGCTACTAGCTTTATCGCTTATACTTTGGTTATAATTATATTATACTATTGGTTGTAA
1 ATACTTCAGCTGCTAGCTTTATCGCTCATAATTTGGCTATAATAATATTATACTATTGGTCGCAA
* * * * *
3822692 GCTTTATCACTCATTCTTTGACCATAGCTCATCACTC
66 GCTTTATCGCTCATTTTTTAACCATAACTCATCACTA
* ** * * * * * * * *
3822729 TTACTTCAATTGCAAACCTTACCGCTCATATTTTAGCTATAATAATATTGTTTCTATTGGTCGCA
1 ATACTTCAGCTGCTAGCTTTATCGCTCATAATTTGGCTATAATAATATT-ATACTATTGGTCGCA
* *
3822794 AGCTTTATCGCTCATTTTTTAACCATAATTCATCATTA
65 AGCTTTATCGCTCATTTTTTAACCATAACTCATCACTA
* * * ** * *
3822832 ATATTTCAGCTGCTAGCTTTATCGCTCATAATTTGGCTGTAATGATGCTATGCTATTGGCCGCAA
1 ATACTTCAGCTGCTAGCTTTATCGCTCATAATTTGGCTATAATAATATTATACTATTGGTCGCAA
* *
3822897 GCTTTATTGCTCATTTCTTAA
66 GCTTTATCGCTCATTTTTTAA
3822918 TCCTAGCTTA
Statistics
Matches: 144, Mismatches: 44, Indels: 2
0.76 0.23 0.01
Matches are distributed among these distances:
102 67 0.47
103 77 0.53
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (102 bp):
ATACTTCAGCTGCTAGCTTTATCGCTCATAATTTGGCTATAATAATATTATACTATTGGTCGCAA
GCTTTATCGCTCATTTTTTAACCATAACTCATCACTA
Found at i:3824113 original size:18 final size:18
Alignment explanation
Indices: 3824071--3824114 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
3824061 AAAATATAAC
3824071 ATAAAAAATAAAAATGCA
1 ATAAAAAATAAAAATGCA
3824089 A-ATAAAAATAAAAAAT-CA
1 ATA-AAAAAT-AAAAATGCA
3824107 ATAAAAAA
1 ATAAAAAA
3824115 ATCACTAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.04
18 15 0.65
19 7 0.30
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (18 bp):
ATAAAAAATAAAAATGCA
Found at i:3824115 original size:19 final size:18
Alignment explanation
Indices: 3824073--3824116 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
3824063 AATATAACAT
3824073 AAAAAATAAAAATGCAAA
1 AAAAAATAAAAATGCAAA
*
3824091 TAAAAATAAAAAAT-CAATA
1 AAAAAAT-AAAAATGCAA-A
3824110 AAAAAAT
1 AAAAAAT
3824117 CACTAGCCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (18 bp):
AAAAAATAAAAATGCAAA
Found at i:3825377 original size:35 final size:35
Alignment explanation
Indices: 3825290--3825381 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 35
3825280 AAGTGAGACA
* *
3825290 CTATTTTATGCAGAACAACTAAAACAAGTGAAGTG
1 CTATTTTATGCAAAACAACTAGAACAAGTGAAGTG
* * * ** * *
3825325 TTACTTCACACATAACAACTAGAACAAGTGATGTG
1 CTATTTTATGCAAAACAACTAGAACAAGTGAAGTG
3825360 CTATTTTATGCAAAACAACTAG
1 CTATTTTATGCAAAACAACTAG
3825382 CATAAGTGGA
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.27
Consensus pattern (35 bp):
CTATTTTATGCAAAACAACTAGAACAAGTGAAGTG
Found at i:3825671 original size:29 final size:29
Alignment explanation
Indices: 3825639--3825698 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
3825629 ATAGTTGTTT
* *
3825639 ACATACACCTTCTTTTATTATACCTATTC
1 ACATACACATTCTTCTATTATACCTATTC
* * *
3825668 ACATACAGATTCTTCTCTTATACCTTTTC
1 ACATACACATTCTTCTATTATACCTATTC
3825697 AC
1 AC
3825699 GTATACCTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.27, C:0.28, G:0.02, T:0.43
Consensus pattern (29 bp):
ACATACACATTCTTCTATTATACCTATTC
Found at i:3828778 original size:20 final size:21
Alignment explanation
Indices: 3828753--3828806 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
3828743 ATCAGTTGGT
*
3828753 AGAAAGGAGAAAG-GAAAGAA
1 AGAAAGGAGAAAGAAAAAGAA
*
3828773 AGAAAGGAGAAAGAAAAAGAG
1 AGAAAGGAGAAAGAAAAAGAA
3828794 AGAAAGGAAGAAA
1 AGAAAGG-AGAAA
3828807 AAACTTGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 13 0.43
21 12 0.40
22 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (21 bp):
AGAAAGGAGAAAGAAAAAGAA
Found at i:3829981 original size:35 final size:35
Alignment explanation
Indices: 3829942--3830009 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
3829932 ATTGCGTGTG
* *
3829942 ATGATATTGAAATGTGCGTGTAGGGAGTGCACATA
1 ATGATATTGAAATATGCATGTAGGGAGTGCACATA
***
3829977 ATGATATTGCCTTATGCATGTAGGGAGTGCACA
1 ATGATATTGAAATATGCATGTAGGGAGTGCACA
3830010 AGAGCTAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (35 bp):
ATGATATTGAAATATGCATGTAGGGAGTGCACATA
Found at i:3831684 original size:16 final size:16
Alignment explanation
Indices: 3831655--3831689 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3831645 CACTCGTTAC
3831655 AAAACAAATATCATAT
1 AAAACAAATATCATAT
* *
3831671 AAAACCAATTTCATAT
1 AAAACAAATATCATAT
3831687 AAA
1 AAA
3831690 GATAGATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAACAAATATCATAT
Found at i:3837408 original size:124 final size:123
Alignment explanation
Indices: 3837251--3837497 Score: 458
Period size: 124 Copynumber: 2.0 Consensus size: 123
3837241 TGTTTGTGTA
*
3837251 CAACATTGAATAATTGCATGGTTTTAAACTTCTTATTCCACATTGAATCCTAATCACATTCTACT
1 CAACATTGAATAATTGCATGGTTTTAAACTTCTTATTCCACATCGAATCCTAATCACATTCTACT
3837316 TTGGACTTTTATACTATAAAAGTGGATTTCTAGGCTTTAGAATTGAAAGTAGTGCTTT
66 TTGGACTTTTATACTATAAAAGTGGATTTCTAGGCTTTAGAATTGAAAGTAGTGCTTT
* *
3837374 NCAACATTGAATAATTGCATGGTTTTAAACTTCTTATTCCACATCGAATCTTAATCACATTTTAC
1 -CAACATTGAATAATTGCATGGTTTTAAACTTCTTATTCCACATCGAATCCTAATCACATTCTAC
3837439 TTTGGACTTTTATACTATAAAAGTGGATTTCTAGGCTTTAGAATTGAAAGTAGTGCTTT
65 TTTGGACTTTTATACTATAAAAGTGGATTTCTAGGCTTTAGAATTGAAAGTAGTGCTTT
3837498 GAGAGCTCAA
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 120 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (123 bp):
CAACATTGAATAATTGCATGGTTTTAAACTTCTTATTCCACATCGAATCCTAATCACATTCTACT
TTGGACTTTTATACTATAAAAGTGGATTTCTAGGCTTTAGAATTGAAAGTAGTGCTTT
Found at i:3838151 original size:2 final size:2
Alignment explanation
Indices: 3838144--3838186 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
3838134 CATACATAAT
3838144 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3838185 TA
1 TA
3838187 CTGCTAATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3847138 original size:78 final size:78
Alignment explanation
Indices: 3847005--3847216 Score: 307
Period size: 78 Copynumber: 2.7 Consensus size: 78
3846995 GACATAAGGC
* * * *
3847005 GTGGGCATGTAACATTCCTATTATACGTTAAGGTATAATGATGTTAGTATCTAAATACCATCAAA
1 GTGGGCATGTAACATTCTTATTATACATTAAGGTATAATGATGTTAATATGTAAATACCATCAAA
3847070 GTCCATGTGATAG
66 GTCCATGTGATAG
* * *
3847083 GTGGGCATGTGACATTCTTATTATACATTAAGGTATAATGATGTCAATATGTAAATACCATCAAG
1 GTGGGCATGTAACATTCTTATTATACATTAAGGTATAATGATGTTAATATGTAAATACCATCAAA
3847148 GTCCATGTGATAG
66 GTCCATGTGATAG
* * * * * *
3847161 GTGCGCATGTCACATTCTTATTATACATGAAGATAAAATGGTGTTAATATGTAAAT
1 GTGGGCATGTAACATTCTTATTATACATTAAGGTATAATGATGTTAATATGTAAAT
3847217 TTAACATTTT
Statistics
Matches: 120, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 120 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (78 bp):
GTGGGCATGTAACATTCTTATTATACATTAAGGTATAATGATGTTAATATGTAAATACCATCAAA
GTCCATGTGATAG
Found at i:3853170 original size:20 final size:20
Alignment explanation
Indices: 3853145--3853250 Score: 212
Period size: 20 Copynumber: 5.3 Consensus size: 20
3853135 AGAAAGCCGG
3853145 TCCCCCCTTGCTGCAGGTTC
1 TCCCCCCTTGCTGCAGGTTC
3853165 TCCCCCCTTGCTGCAGGTTC
1 TCCCCCCTTGCTGCAGGTTC
3853185 TCCCCCCTTGCTGCAGGTTC
1 TCCCCCCTTGCTGCAGGTTC
3853205 TCCCCCCTTGCTGCAGGTTC
1 TCCCCCCTTGCTGCAGGTTC
3853225 TCCCCCCTTGCTGCAGGTTC
1 TCCCCCCTTGCTGCAGGTTC
3853245 TCCCCC
1 TCCCCC
3853251 TCCCATTTAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 86 1.00
ACGTcount: A:0.05, C:0.47, G:0.19, T:0.29
Consensus pattern (20 bp):
TCCCCCCTTGCTGCAGGTTC
Found at i:3853341 original size:16 final size:15
Alignment explanation
Indices: 3853320--3853352 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
3853310 ACCTCTCTCC
3853320 TTTTTTCATTCTTTCA
1 TTTTTTCATT-TTTCA
3853336 TTTTTTCATTTTTCA
1 TTTTTTCATTTTTCA
3853351 TT
1 TT
3853353 ATTAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTCATTTTTCA
Found at i:3857893 original size:35 final size:35
Alignment explanation
Indices: 3857847--3858116 Score: 258
Period size: 35 Copynumber: 7.7 Consensus size: 35
3857837 TCCTTAAGAA
*** *
3857847 GCCCAATTAACTTAATTGTTTAATTTAATCAATTAG
1 GCCCAA-TAACTTAATTAAATAATTTAATTAATTAG
* *
3857883 GCCCAATAACTTAATTAAACAATTTAATTAATTAA
1 GCCCAATAACTTAATTAAATAATTTAATTAATTAG
* * * *
3857918 GCCCAACAATTTAATTAAACAATTTTAATTAACTAG
1 GCCCAATAACTTAATTAAATAA-TTTAATTAATTAG
** * * *
3857954 GCATAATGACTTAATTAAACAAATTTAATCAATTAG
1 GCCCAATAACTTAATTAAA-TAATTTAATTAATTAG
*** *
3857990 GCCCAATAACTTAATTGTTTAATTTAATTAATTAA
1 GCCCAATAACTTAATTAAATAATTTAATTAATTAG
*
3858025 GCCCAATAACTTAATTAAATAATTTAATTTATTAG
1 GCCCAATAACTTAATTAAATAATTTAATTAATTAG
* * * *
3858060 GCCCAATGATTTAATTAAACAATTTAGTTAATTAG
1 GCCCAATAACTTAATTAAATAATTTAATTAATTAG
* *
3858095 G--C-ACAACTTAATTAAACAATTT
1 GCCCAATAACTTAATTAAATAATTT
3858117 TAATCAAGTG
Statistics
Matches: 192, Mismatches: 40, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
32 17 0.09
33 1 0.01
35 117 0.61
36 55 0.29
37 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (35 bp):
GCCCAATAACTTAATTAAATAATTTAATTAATTAG
Found at i:3857990 original size:107 final size:105
Alignment explanation
Indices: 3857868--3858116 Score: 324
Period size: 107 Copynumber: 2.4 Consensus size: 105
3857858 TTAATTGTTT
*
3857868 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAATTTAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAAT
*
3857933 TAAACAATTTTAATTAACTAGGCATAATGACTTAATTAAAC
66 TAAACAA-TTTAATTAACTAGGCACAATGACTTAATTAAAC
**** *
3857974 AAATTTAATCAATTAGGCCCAATAACTTAATTGTTTAATTTAATTAATTAAGCCCAATAACTTAA
1 -AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAA
* * * * *
3858039 TTAAATAATTTAATTTATTAGGCCCAATGATTTAATTAAAC
65 TTAAACAATTTAATTAACTAGGCACAATGACTTAATTAAAC
* * *
3858080 AATTTAGTTAATTAGG--C-ACAACTTAATTAAACAATTT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTT
3858117 TAATCAAGTG
Statistics
Matches: 123, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
102 15 0.12
103 1 0.01
105 14 0.11
106 28 0.23
107 65 0.53
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (105 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAAT
TAAACAATTTAATTAACTAGGCACAATGACTTAATTAAAC
Found at i:3858008 original size:142 final size:139
Alignment explanation
Indices: 3857847--3858123 Score: 412
Period size: 142 Copynumber: 2.0 Consensus size: 139
3857837 TCCTTAAGAA
*
3857847 GCCCAATTAACTTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATT
1 GCCCAATTAACTTAATTGTTTAATTTAATCAATTAAGCCCAATAACTTAATTAAACAATTTAATT
3857912 AATTAAGCCCAACAATTTAATTAAACAATTTTAATTAACTAGGCATAATGACTTAATTAAACAAA
66 AATTAAGCCCAACAATTTAATTAAACAA-TTTAATTAACTAGGCA-AA--ACTTAATTAAACAAA
3857977 TTTAATCAATTAG
127 TTTAATCAATTAG
* *
3857990 GCCCAA-TAACTTAATTGTTTAATTTAATTAATTAAGCCCAATAACTTAATTAAATAATTTAATT
1 GCCCAATTAACTTAATTGTTTAATTTAATCAATTAAGCCCAATAACTTAATTAAACAATTTAATT
* * ** * * * *
3858054 TATTAGGCCCAATGATTTAATTAAACAATTTAGTTAATTAGGCACAACTTAATTAAACAATTTTA
66 AATTAAGCCCAACAATTTAATTAAACAATTTAATTAACTAGGCAAAACTTAATTAAACAAATTTA
3858119 ATCAA
131 ATCAA
3858124 GTGCTTGAGA
Statistics
Matches: 123, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
138 23 0.19
140 1 0.01
141 14 0.11
142 79 0.64
143 6 0.05
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.37
Consensus pattern (139 bp):
GCCCAATTAACTTAATTGTTTAATTTAATCAATTAAGCCCAATAACTTAATTAAACAATTTAATT
AATTAAGCCCAACAATTTAATTAAACAATTTAATTAACTAGGCAAAACTTAATTAAACAAATTTA
ATCAATTAG
Found at i:3875883 original size:43 final size:43
Alignment explanation
Indices: 3875815--3875987 Score: 211
Period size: 43 Copynumber: 4.0 Consensus size: 43
3875805 GGGTCGTGAC
* * * *
3875815 AAAGACATCACAAGGTGCACAGTAAAAAACATATTCTCTGCCA
1 AAAGACATCACGAGGCGCACAGTAAAAAACAGATTCCCTGCCA
** * *
3875858 AAAGACATCACGAGGTACACCGTAAAAAGCAACAGATTCCCTACCA
1 AAAGACATCACGAGGCGCACAGT-AAAA--AACAGATTCCCTGCCA
* *
3875904 AAAGACATCACGAGGCGCACAGTAAAAAGCAGATTCCCTTCCA
1 AAAGACATCACGAGGCGCACAGTAAAAAACAGATTCCCTGCCA
* *
3875947 AAAGACATCACGAGGCGCACAGTAAAAAACAAATTCTCTGC
1 AAAGACATCACGAGGCGCACAGTAAAAAACAGATTCCCTGC
3875988 AAATAAATGT
Statistics
Matches: 112, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
43 71 0.63
44 4 0.04
45 4 0.04
46 33 0.29
ACGTcount: A:0.43, C:0.26, G:0.16, T:0.15
Consensus pattern (43 bp):
AAAGACATCACGAGGCGCACAGTAAAAAACAGATTCCCTGCCA
Found at i:3876024 original size:23 final size:23
Alignment explanation
Indices: 3875988--3876031 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
3875978 AATTCTCTGC
3875988 AAATAAATGTAAAATTCAAATTG
1 AAATAAATGTAAAATTCAAATTG
3876011 AAATGAAATG-AAAATTCAAAT
1 AAAT-AAATGTAAAATTCAAAT
3876032 GTAAGATCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.09, T:0.27
Consensus pattern (23 bp):
AAATAAATGTAAAATTCAAATTG
Found at i:3885791 original size:20 final size:21
Alignment explanation
Indices: 3885763--3885804 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
3885753 TGGAGAAAAA
*
3885763 AAAAGGAAAAAGGAAAAAATT
1 AAAAGGAAAAAAGAAAAAATT
3885784 AAAA-GAAAAAAGAAAAAATT
1 AAAAGGAAAAAAGAAAAAATT
3885804 A
1 A
3885805 TTTATAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (21 bp):
AAAAGGAAAAAAGAAAAAATT
Found at i:3885793 original size:21 final size:20
Alignment explanation
Indices: 3885756--3885804 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3885746 CGGTCTGTGG
*
3885756 AGAAAAAA--AAAGGAAAAA
1 AGAAAAAATTAAAAGAAAAA
*
3885774 GGAAAAAATTAAAAGAAAAA
1 AGAAAAAATTAAAAGAAAAA
3885794 AGAAAAAATTA
1 AGAAAAAATTA
3885805 TTTATAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 7 0.27
20 19 0.73
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (20 bp):
AGAAAAAATTAAAAGAAAAA
Found at i:3885861 original size:23 final size:19
Alignment explanation
Indices: 3885825--3885882 Score: 53
Period size: 23 Copynumber: 2.8 Consensus size: 19
3885815 TTACAATATT
*
3885825 AATATTTTATATATAATTTAA
1 AATATTATA-ATATAA-TTAA
*
3885846 ACATTATTAATAATATGATTAA
1 A-A-TATT-ATAATATAATTAA
3885868 AATATTATAATATAA
1 AATATTATAATATAA
3885883 ATATTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 8 0.26
20 4 0.13
21 2 0.06
22 6 0.19
23 9 0.29
24 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
AATATTATAATATAATTAA
Found at i:3890370 original size:23 final size:23
Alignment explanation
Indices: 3890340--3890393 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
3890330 GGGTCTAACT
*
3890340 TTGCGTGATTGATTGATAGGTCA
1 TTGCGTGACTGATTGATAGGTCA
* ** *
3890363 TTGCGTGACTGGTTTCTAGGTTA
1 TTGCGTGACTGATTGATAGGTCA
3890386 TTGCGTGA
1 TTGCGTGA
3890394 ATATTGTTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.17, C:0.11, G:0.31, T:0.41
Consensus pattern (23 bp):
TTGCGTGACTGATTGATAGGTCA
Found at i:3892217 original size:24 final size:24
Alignment explanation
Indices: 3892163--3892218 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
3892153 CCTCATTCTC
* * *
3892163 CTCCTGCAGCTTTTCATGGTGCTT
1 CTCCTGCTGCTTATCATGCTGCTT
*
3892187 CTGCTGCTGCTTATCATGCTG-TT
1 CTCCTGCTGCTTATCATGCTGCTT
3892210 ACTCCTGCT
1 -CTCCTGCT
3892219 ACTCCTCCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.09, C:0.30, G:0.20, T:0.41
Consensus pattern (24 bp):
CTCCTGCTGCTTATCATGCTGCTT
Found at i:3896216 original size:15 final size:15
Alignment explanation
Indices: 3896196--3896226 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3896186 CGATATTAAG
*
3896196 AACAACTAGCATAAA
1 AACAACTACCATAAA
3896211 AACAACTACCATAAA
1 AACAACTACCATAAA
3896226 A
1 A
3896227 CCCTAAACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.23, G:0.03, T:0.13
Consensus pattern (15 bp):
AACAACTACCATAAA
Done.