Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 78 of 182
Found at i:23620280 original size:20 final size:19
Alignment explanation
Indices: 23620257--23620312 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
23620247 TGATTTAGGG
23620257 TTTTTTTATATTTTTTAAGT
1 TTTTTTTATATTTTTTAA-T
* *
23620277 TTTTTATATATTCTTTAAT
1 TTTTTTTATATTTTTTAAT
23620296 TTTTTTTATAATTTTTT
1 TTTTTTTAT-ATTTTTT
23620313 GAGATGTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.29
20 22 0.71
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTTTTATATTTTTTAAT
Found at i:23625809 original size:5 final size:5
Alignment explanation
Indices: 23625784--23625880 Score: 51
Period size: 5 Copynumber: 19.4 Consensus size: 5
23625774 TTTTTCATTA
* * * * * *
23625784 TTCTT TTCTT CTCTT AT-TT TTCTT TT-TC TT-TT TTATT TTC-C CTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
*
23625830 ATTCTTT TTCATT ATTCTT TTCTT TTCTT TTCTT AT-TT TTCTTT TTCTT
1 -TTC-TT TTC-TT -TTCTT TTCTT TTCTT TTCTT TTCTT TTC-TT TTCTT
23625879 TT
1 TT
23625881 TTCTGAGCGT
Statistics
Matches: 71, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
4 14 0.20
5 38 0.54
6 14 0.20
7 5 0.07
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (5 bp):
TTCTT
Found at i:23625811 original size:6 final size:6
Alignment explanation
Indices: 23625800--23625881 Score: 53
Period size: 6 Copynumber: 12.8 Consensus size: 6
23625790 TCTTCTCTTA
*
23625800 TTTTTC TTTTTC TTTTT- TATTTTCCC TCTTATTC TTTTTC ATTATTC
1 TTTTTC TTTTTC TTTTTC T-TTTT--C T-TT-TTC TTTTTC -TTTTTC
*
23625847 -TTTTC -TTTTC TTTTCTTA TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC -TTT-TTC TTTTTC TTTTTC TTTTT
23625882 TCTGAGCGTG
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
5 10 0.16
6 31 0.50
7 12 0.19
8 4 0.06
9 3 0.05
10 2 0.03
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:23625816 original size:13 final size:13
Alignment explanation
Indices: 23625800--23625884 Score: 61
Period size: 13 Copynumber: 6.5 Consensus size: 13
23625790 TCTTCTCTTA
23625800 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
* *
23625813 TTTTTATTTTCCCT
1 TTTTTCTTTT-TCT
* *
23625827 CTTATTCTTTTTCA
1 -TTTTTCTTTTTCT
*
23625841 TTATTC-TTTTC-
1 TTTTTCTTTTTCT
23625852 -TTTTC-TTTTCTT
1 TTTTTCTTTTTC-T
23625864 ATTTTTCTTTTTCT
1 -TTTTTCTTTTTCT
23625878 TTTTTCT
1 TTTTTCT
23625885 GAGCGTGCCT
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
10 9 0.16
12 5 0.09
13 22 0.38
14 9 0.16
15 13 0.22
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:23625850 original size:28 final size:30
Alignment explanation
Indices: 23625774--23625852 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 30
23625764 TGGAATCTTA
*
23625774 TTTTTCATTATTCTTTTCTTCTCTTATTTTTC
1 TTTTTCATTATTCTTTTCTCCTCTTA--TTTC
* * *
23625806 TTTTTCTTTTTTATTTTC-CCTCTTA-TTC
1 TTTTTCATTATTCTTTTCTCCTCTTATTTC
23625834 TTTTTCATTATTCTTTTCT
1 TTTTTCATTATTCTTTTCT
23625853 TTTCTTTTCT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 18 0.46
31 6 0.15
32 15 0.38
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (30 bp):
TTTTTCATTATTCTTTTCTCCTCTTATTTC
Found at i:23625862 original size:28 final size:28
Alignment explanation
Indices: 23625774--23625863 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
23625764 TGGAATCTTA
*
23625774 TTTTTCATTATTCTTTTCTTCTCTTATTTTTC
1 TTTTTCATTATTCTTTTC-T-T-TT-CTTTTC
* * * **
23625806 TTTTTCTTTTTTATTTTC-CCTCTTATTC
1 TTTTTCATTATTCTTTTCTTTTCTT-TTC
23625834 TTTTTCATTATTCTTTTCTTTTCTTTTC
1 TTTTTCATTATTCTTTTCTTTTCTTTTC
23625862 TT
1 TT
23625864 ATTTTTCTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
27 2 0.04
28 24 0.53
29 4 0.09
32 15 0.33
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (28 bp):
TTTTTCATTATTCTTTTCTTTTCTTTTC
Found at i:23626709 original size:12 final size:12
Alignment explanation
Indices: 23626692--23626716 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23626682 ACGATGAAAG
23626692 ATAAGAAAAGAA
1 ATAAGAAAAGAA
23626704 ATAAGAAAAGAA
1 ATAAGAAAAGAA
23626716 A
1 A
23626717 AAAAAGCTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
ATAAGAAAAGAA
Found at i:23627715 original size:5 final size:5
Alignment explanation
Indices: 23627705--23627730 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
23627695 CAAGAAATAT
23627705 TTAAA TTAAA TTAAA TTAAA TTAAA T
1 TTAAA TTAAA TTAAA TTAAA TTAAA T
23627731 AGTATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TTAAA
Found at i:23627921 original size:22 final size:23
Alignment explanation
Indices: 23627896--23627940 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
23627886 AAAAAAGAGT
*
23627896 TGAGAGAGGAATAA-AAATTGAG
1 TGAGAAAGGAATAAGAAATTGAG
**
23627918 TGAGAAATTAATAAGAAATTGAG
1 TGAGAAAGGAATAAGAAATTGAG
23627941 AGAAATTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (23 bp):
TGAGAAAGGAATAAGAAATTGAG
Found at i:23627945 original size:21 final size:21
Alignment explanation
Indices: 23627905--23627947 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
23627895 TTGAGAGAGG
23627905 AATAAAAATTGAGTGAGAAATT
1 AATAAAAATTGAG-GAGAAATT
23627927 AATAAGAAATTGA-GAGAAATT
1 AATAA-AAATTGAGGAGAAATT
23627948 TGAAAGAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 5 0.25
23 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.26
Consensus pattern (21 bp):
AATAAAAATTGAGGAGAAATT
Found at i:23628037 original size:12 final size:12
Alignment explanation
Indices: 23628020--23628055 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
23628010 AATTGGGGTT
23628020 GATATATATATA
1 GATATATATATA
*
23628032 GATATAGATATA
1 GATATATATATA
23628044 GATATATATATA
1 GATATATATATA
23628056 TATTAGGCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (12 bp):
GATATATATATA
Found at i:23628058 original size:6 final size:6
Alignment explanation
Indices: 23628020--23628055 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
23628010 AATTGGGGTT
* *
23628020 GATATA TATATA GATATA GATATA GATATA TATATA
1 GATATA GATATA GATATA GATATA GATATA GATATA
23628056 TATTAGGCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (6 bp):
GATATA
Found at i:23629303 original size:9 final size:9
Alignment explanation
Indices: 23629286--23629464 Score: 62
Period size: 9 Copynumber: 19.0 Consensus size: 9
23629276 TGACGTAAAC
*
23629286 TTATTAAAA
1 TTATAAAAA
23629295 TTATAAAAAAA
1 TTAT--AAAAA
*
23629306 TTACAAAAA
1 TTATAAAAA
* *
23629315 CATATAAATA
1 -TTATAAAAA
23629325 TTATAAAAA
1 TTATAAAAA
*
23629334 TCTA-ATAAA
1 T-TATAAAAA
23629343 TTAT-AAAA
1 TTATAAAAA
*
23629351 TTAATAAAAC
1 TT-ATAAAAA
23629361 TTAATTAAAATA
1 TT-A-TAAAA-A
23629373 TT-T-AAAA
1 TTATAAAAA
23629380 TT-TAAAAA
1 TTATAAAAA
* *
23629388 TTATTAGAA
1 TTATAAAAA
* *
23629397 TTCTTAAAA
1 TTATAAAAA
23629406 TTATAAAAAA
1 TTAT-AAAAA
* *
23629416 ATATTAAAA
1 TTATAAAAA
* *
23629425 TTGGTATAAAC
1 TT-ATA-AAAA
23629436 TTATAAAAA
1 TTATAAAAA
*
23629445 TAAGTAAAAAA
1 TTA-T-AAAAA
*
23629456 TCATAAAAA
1 TTATAAAAA
23629465 CTTGAATTGG
Statistics
Matches: 127, Mismatches: 27, Indels: 32
0.68 0.15 0.17
Matches are distributed among these distances:
7 4 0.03
8 16 0.13
9 54 0.43
10 27 0.21
11 24 0.19
12 2 0.02
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:23629355 original size:16 final size:18
Alignment explanation
Indices: 23629324--23629358 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
23629314 ACATATAAAT
23629324 ATTATAAAAATCTAATAA
1 ATTATAAAAATCTAATAA
23629342 ATTAT-AAAAT-TAATAA
1 ATTATAAAAATCTAATAA
23629358 A
1 A
23629359 ACTTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 5 0.29
18 5 0.29
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTATAAAAATCTAATAA
Found at i:23629405 original size:46 final size:44
Alignment explanation
Indices: 23629320--23629453 Score: 101
Period size: 46 Copynumber: 2.9 Consensus size: 44
23629310 AAAAACATAT
* *
23629320 AAATATTATAAAAATCTAATAAATTATAAAATTAATAAAACTTAATTA
1 AAATATT-T-AAAATTTAATAAATTATAAAATTAATAAAA-TT-ATAA
* **
23629368 AAATATTTAAAATTTAA-AAATTATTAGAATTCTTAAAATTATAA
1 AAATATTTAAAATTTAATAAATTA-TAAAATTAATAAAATTATAA
* *
23629412 AAAAATATTAAAATTGGT-ATAAACTTATAAAAATAAGTAAAA
1 AAATAT-TTAAAATT--TAATAAA-TTATAAAATTAA-TAAAA
23629454 AATCATAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
44 8 0.12
45 16 0.23
46 20 0.29
47 10 0.14
48 15 0.22
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (44 bp):
AAATATTTAAAATTTAATAAATTATAAAATTAATAAAATTATAA
Found at i:23629422 original size:54 final size:55
Alignment explanation
Indices: 23629289--23629425 Score: 129
Period size: 56 Copynumber: 2.5 Consensus size: 55
23629279 CGTAAACTTA
** *
23629289 TTAAAATTATAAAAAAATTACAAAAACATATAAATATTATAAAAATCTAATAAATT
1 TTAAAATTATAAAAAAA-TATTAAAATATATAAATATTATAAAAATCTAATAAATT
* ** * *
23629345 ATAAAATTA-ATAAAACTTAATTAAAATATTTAAA-ATT-TAAAAAT-TATTAGAATT
1 TTAAAATTATA-AAAAAAT-ATTAAAATATATAAATATTATAAAAATCTAATA-AATT
23629399 CTTAAAATTATAAAAAAATATTAAAAT
1 -TTAAAATTATAAAAAAATATTAAAAT
23629426 TGGTATAAAC
Statistics
Matches: 65, Mismatches: 11, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
53 4 0.06
54 19 0.29
55 18 0.28
56 24 0.37
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.35
Consensus pattern (55 bp):
TTAAAATTATAAAAAAATATTAAAATATATAAATATTATAAAAATCTAATAAATT
Found at i:23630035 original size:12 final size:10
Alignment explanation
Indices: 23630012--23630096 Score: 63
Period size: 10 Copynumber: 8.5 Consensus size: 10
23630002 GTTTATACCA
*
23630012 ATTTTCATAT
1 ATTTTTATAT
23630022 ATTTTTAAATAT
1 ATTTTT--ATAT
23630034 ATTTTTATAT
1 ATTTTTATAT
*
23630044 ATTTTGATA-
1 ATTTTTATAT
*
23630053 ATGTTTT-TCT
1 AT-TTTTATAT
23630063 GATTTTT-TAT
1 -ATTTTTATAT
23630073 ATTTTT-TAT
1 ATTTTTATAT
23630082 GATTTTTA-AT
1 -ATTTTTATAT
23630092 ATTTT
1 ATTTT
23630097 ATAGGAAAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
9 17 0.27
10 34 0.54
11 2 0.03
12 10 0.16
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:23630084 original size:19 final size:19
Alignment explanation
Indices: 23630022--23630096 Score: 71
Period size: 19 Copynumber: 3.7 Consensus size: 19
23630012 ATTTTCATAT
23630022 ATTTTTAAATATATTTTTAT-
1 ATTTTT-AATAT-TTTTTATG
* *
23630042 ATATTTTGATAATGTTTTTCTG
1 AT-TTTTAAT-AT-TTTTTATG
*
23630064 ATTTTTTATATTTTTTATG
1 ATTTTTAATATTTTTTATG
23630083 ATTTTTAATATTTT
1 ATTTTTAATATTTT
23630097 ATAGGAAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
19 20 0.43
20 6 0.13
21 18 0.39
22 2 0.04
ACGTcount: A:0.27, C:0.01, G:0.05, T:0.67
Consensus pattern (19 bp):
ATTTTTAATATTTTTTATG
Found at i:23630953 original size:21 final size:20
Alignment explanation
Indices: 23630912--23630955 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
23630902 ATTAGGTTAT
**
23630912 TTAAAAATAAAAATATTAAA
1 TTAAAAATAAAAATAAAAAA
*
23630932 TTAAAATTAAAAAATAAAAAA
1 TTAAAAAT-AAAAATAAAAAA
23630953 TTA
1 TTA
23630956 TAATATCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TTAAAAATAAAAATAAAAAA
Found at i:23632051 original size:141 final size:140
Alignment explanation
Indices: 23631773--23632054 Score: 555
Period size: 141 Copynumber: 2.0 Consensus size: 140
23631763 TCACTGCTAA
23631773 TCTCACCGCCCAACCAAAGTCAAATTTGATTTTTATATCAATTTGTATAAATTTGTTAAATAAAT
1 TCTCACCGCCCAACCAAAGTCAAATTTGATTTTTATATCAATTTGTATAAATTTGTTAAATAAAT
23631838 ATTTTTTAACCCACATCTTGAGTGTAACATTATGTAATAATAATAAAATAGTTAATGGTAAACTA
66 ATTTTTTAACCCACATCTTGAGTGTAACATTATGTAATAATAATAAAATAGTTAATGGTAAACTA
23631903 AATCATTAGT
131 AATCATTAGT
23631913 TCTCACCGCCCAACCAAAGTCAAATTTGATTTTTATATCAATTTGTATAAATTTGTTAAATAAAT
1 TCTCACCGCCCAACCAAAGTCAAATTTGATTTTTATATCAATTTGTATAAATTTGTTAAATAAAT
23631978 ATTTTTTTAACCCACATCTTGAGTGTAACATTATGTAATAATAATAAAATAGTTAATGGTAAACT
66 A-TTTTTTAACCCACATCTTGAGTGTAACATTATGTAATAATAATAAAATAGTTAATGGTAAACT
23632043 AAATCATTAGT
130 AAATCATTAGT
23632054 T
1 T
23632055 ACTCTAAAAT
Statistics
Matches: 141, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
140 66 0.47
141 75 0.53
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.38
Consensus pattern (140 bp):
TCTCACCGCCCAACCAAAGTCAAATTTGATTTTTATATCAATTTGTATAAATTTGTTAAATAAAT
ATTTTTTAACCCACATCTTGAGTGTAACATTATGTAATAATAATAAAATAGTTAATGGTAAACTA
AATCATTAGT
Found at i:23634948 original size:6 final size:7
Alignment explanation
Indices: 23634930--23634955 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
23634920 CTGGGAAATT
23634930 TAAAAAA
1 TAAAAAA
23634937 TAAAAAA
1 TAAAAAA
23634944 TAAAAAA
1 TAAAAAA
23634951 TAAAA
1 TAAAA
23634956 TTATGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:23635843 original size:7 final size:7
Alignment explanation
Indices: 23635831--23635860 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
23635821 AATAAAATAA
23635831 TTAAATT
1 TTAAATT
23635838 TTAAATT
1 TTAAATT
23635845 TTAAATT
1 TTAAATT
23635852 TTAAATT
1 TTAAATT
23635859 TT
1 TT
23635861 CAAAGACTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTAAATT
Found at i:23637508 original size:9 final size:9
Alignment explanation
Indices: 23637494--23637531 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
23637484 TTTGGTTAAA
*
23637494 AATTACTCG
1 AATTACCCG
23637503 AATTACCCG
1 AATTACCCG
23637512 AATTACCCG
1 AATTACCCG
*
23637521 AATTACTCG
1 AATTACCCG
23637530 AA
1 AA
23637532 AATCTTAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (9 bp):
AATTACCCG
Found at i:23639880 original size:38 final size:38
Alignment explanation
Indices: 23639829--23639973 Score: 200
Period size: 38 Copynumber: 3.8 Consensus size: 38
23639819 CAGTGAATTC
* * * *
23639829 TTTTGCTCAATTGAGCGACATTCAGTATATTCAATAAA
1 TTTTGCTCGATTGAGCAACATTCAGTATATTCAGTAGA
* **
23639867 TTTTGCTCGATTGAGAAATGTTCAGTATATTCAGTAGA
1 TTTTGCTCGATTGAGCAACATTCAGTATATTCAGTAGA
* * *
23639905 TTTTGCTCGACTGAGCAGCATTCAGTATATACAGTAGA
1 TTTTGCTCGATTGAGCAACATTCAGTATATTCAGTAGA
23639943 TTTTGCTCGATTGAGCAACATTCAGTATATT
1 TTTTGCTCGATTGAGCAACATTCAGTATATT
23639974 TGGTATTTCA
Statistics
Matches: 91, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 91 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (38 bp):
TTTTGCTCGATTGAGCAACATTCAGTATATTCAGTAGA
Found at i:23641915 original size:17 final size:17
Alignment explanation
Indices: 23641895--23642027 Score: 135
Period size: 17 Copynumber: 7.9 Consensus size: 17
23641885 ACAATTCACT
*
23641895 TATAAACACAGCTCGTA
1 TATAAACACAGCTCGCA
* *
23641912 TATAAATACAAC-CTGCA
1 TATAAACACAGCTC-GCA
*
23641929 TAT-AACGCAGCTCGCA
1 TATAAACACAGCTCGCA
* *
23641945 TACAAACACAACTCGCA
1 TATAAACACAGCTCGCA
* *
23641962 TATAAACATAGCTCACA
1 TATAAACACAGCTCGCA
23641979 TATAAACACAGCTCGCA
1 TATAAACACAGCTCGCA
* * **
23641996 TATAAGCACAACTAACA
1 TATAAACACAGCTCGCA
23642013 TATAAACACAGCTCG
1 TATAAACACAGCTCG
23642028 TACATTGTCA
Statistics
Matches: 90, Mismatches: 23, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
16 11 0.12
17 79 0.88
ACGTcount: A:0.44, C:0.27, G:0.10, T:0.20
Consensus pattern (17 bp):
TATAAACACAGCTCGCA
Found at i:23642908 original size:25 final size:25
Alignment explanation
Indices: 23642875--23642926 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
23642865 TTTGTATTAA
*
23642875 TCCAATCATTTATATCCATTTCTAT
1 TCCAATCATTTATAGCCATTTCTAT
23642900 TCCAATCATTTATAGCCATTTCTAT
1 TCCAATCATTTATAGCCATTTCTAT
23642925 TC
1 TC
23642927 ACCACACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.02, T:0.46
Consensus pattern (25 bp):
TCCAATCATTTATAGCCATTTCTAT
Found at i:23650257 original size:19 final size:19
Alignment explanation
Indices: 23650230--23650277 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
23650220 GGACATACGA
23650230 TTCCACTAATCACACACAG
1 TTCCACTAATCACACACAG
* *
23650249 TTTCACTAATCAGACACAG
1 TTCCACTAATCACACACAG
23650268 TTCCACTAAT
1 TTCCACTAAT
23650278 AAAACACCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.35, C:0.31, G:0.06, T:0.27
Consensus pattern (19 bp):
TTCCACTAATCACACACAG
Found at i:23650284 original size:19 final size:19
Alignment explanation
Indices: 23650230--23650284 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
23650220 GGACATACGA
*
23650230 TTCCACTAATCACACACAG
1 TTCCACTAATCAAACACAG
* *
23650249 TTTCACTAATCAGACACAG
1 TTCCACTAATCAAACACAG
*
23650268 TTCCACTAATAAAACAC
1 TTCCACTAATCAAACAC
23650285 CATTAACGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.40, C:0.31, G:0.05, T:0.24
Consensus pattern (19 bp):
TTCCACTAATCAAACACAG
Found at i:23652253 original size:31 final size:31
Alignment explanation
Indices: 23652218--23652284 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
23652208 AAAAAAACTT
23652218 AATAGCCTAGTGACTTAAATAAAAACTTTTA
1 AATAGCCTAGTGACTTAAATAAAAACTTTTA
** * *
23652249 AATAGTTTAGTGACTTAAATGAAAATTTTTA
1 AATAGCCTAGTGACTTAAATAAAAACTTTTA
23652280 AATAG
1 AATAG
23652285 TTTAGTGGCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (31 bp):
AATAGCCTAGTGACTTAAATAAAAACTTTTA
Found at i:23652285 original size:31 final size:31
Alignment explanation
Indices: 23652225--23652291 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
23652215 CTTAATAGCC
23652225 TAGTGACTTAAATAAAAACTTTTAAATAGTT
1 TAGTGACTTAAATAAAAACTTTTAAATAGTT
* *
23652256 TAGTGACTTAAATGAAAATTTTTAAATAGTT
1 TAGTGACTTAAATAAAAACTTTTAAATAGTT
23652287 TAGTG
1 TAGTG
23652292 GCCAAATTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.40
Consensus pattern (31 bp):
TAGTGACTTAAATAAAAACTTTTAAATAGTT
Found at i:23653467 original size:16 final size:16
Alignment explanation
Indices: 23653448--23653496 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
23653438 TTCGCTGTAT
*
23653448 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
*
23653464 TGGAATAGAGACGTAA
1 TGGAATAGAGGCGTAA
23653480 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
23653496 T
1 T
23653497 AGCAAATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.39, C:0.04, G:0.35, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:23653618 original size:44 final size:45
Alignment explanation
Indices: 23653539--23653624 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 45
23653529 GAGGTGTATT
* *
23653539 TGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAATGTAA
1 TGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAATGTAA
***
23653584 TGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAATG
1 TGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAATG
23653625 GAATAGAGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 19 0.53
45 17 0.47
ACGTcount: A:0.28, C:0.07, G:0.29, T:0.36
Consensus pattern (45 bp):
TGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAATGTAA
Found at i:23663856 original size:98 final size:98
Alignment explanation
Indices: 23663682--23663878 Score: 367
Period size: 98 Copynumber: 2.0 Consensus size: 98
23663672 GTACAATAAA
*
23663682 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* *
23663747 CCTTTAGAATCCCAAACTTGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
23663780 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
23663845 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
23663878 A
1 A
23663879 TTATTTTTAA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:23664170 original size:15 final size:15
Alignment explanation
Indices: 23664152--23664184 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
23664142 CAAATGCTAT
23664152 AATAATAAATACAAC
1 AATAATAAATACAAC
*
23664167 AATAATAAATACATC
1 AATAATAAATACAAC
23664182 AAT
1 AAT
23664185 GACATATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:23665841 original size:25 final size:25
Alignment explanation
Indices: 23665807--23665856 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
23665797 GTTCAAGTAG
23665807 ATGTCTTTAATGGTAATTTTATCTT
1 ATGTCTTTAATGGTAATTTTATCTT
23665832 ATGTCTTTAATGGTAATTTTATCTT
1 ATGTCTTTAATGGTAATTTTATCTT
23665857 TTTTTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.56
Consensus pattern (25 bp):
ATGTCTTTAATGGTAATTTTATCTT
Found at i:23667047 original size:9 final size:9
Alignment explanation
Indices: 23666996--23667095 Score: 94
Period size: 9 Copynumber: 11.1 Consensus size: 9
23666986 ACCATTTCCT
*
23666996 CAAATTCCA
1 CAAATCCCA
*
23667005 GAAATCCCA
1 CAAATCCCA
*
23667014 -AGAATTCCA
1 CA-AATCCCA
* *
23667023 CAGATCCCC
1 CAAATCCCA
*
23667032 CAGATCCCA
1 CAAATCCCA
23667041 CAAATCCCA
1 CAAATCCCA
*
23667050 CAAATTCCA
1 CAAATCCCA
*
23667059 CTAATCCCA
1 CAAATCCCA
*
23667068 CAGATCCCA
1 CAAATCCCA
*
23667077 CAAGTCCCA
1 CAAATCCCA
23667086 CAAATCCCA
1 CAAATCCCA
23667095 C
1 C
23667096 TAATGCCAGG
Statistics
Matches: 73, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
8 1 0.01
9 71 0.97
10 1 0.01
ACGTcount: A:0.38, C:0.41, G:0.06, T:0.15
Consensus pattern (9 bp):
CAAATCCCA
Found at i:23667056 original size:36 final size:36
Alignment explanation
Indices: 23667006--23667099 Score: 129
Period size: 36 Copynumber: 2.6 Consensus size: 36
23666996 CAAATTCCAG
*
23667006 AAATCCCA-AGAATTCCAC-AGATCCCCCAGATCCCAC
1 AAATCCCACA-AATTCCACTA-ATCCCACAGATCCCAC
23667042 AAATCCCACAAATTCCACTAATCCCACAGATCCCAC
1 AAATCCCACAAATTCCACTAATCCCACAGATCCCAC
* *
23667078 AAGTCCCACAAATCCCACTAAT
1 AAATCCCACAAATTCCACTAAT
23667100 GCCAGGACAG
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
36 51 0.96
37 2 0.04
ACGTcount: A:0.38, C:0.40, G:0.05, T:0.16
Consensus pattern (36 bp):
AAATCCCACAAATTCCACTAATCCCACAGATCCCAC
Found at i:23668884 original size:14 final size:15
Alignment explanation
Indices: 23668850--23668891 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
23668840 TTTCTAATAT
*
23668850 AAATTTAACACTTATA
1 AAATTTAACA-GTATA
23668866 AAATTTAACAGTA-A
1 AAATTTAACAGTATA
*
23668880 AAATTTAGCAGT
1 AAATTTAACAGT
23668892 TTATTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 2 0.08
16 10 0.42
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (15 bp):
AAATTTAACAGTATA
Found at i:23669229 original size:15 final size:15
Alignment explanation
Indices: 23669206--23669236 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
23669196 TTATCTAAGT
*
23669206 AATTTTTTTAAAATA
1 AATTATTTTAAAATA
23669221 AATTATTTTAAAATA
1 AATTATTTTAAAATA
23669236 A
1 A
23669237 TAATCAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTATTTTAAAATA
Found at i:23670323 original size:24 final size:23
Alignment explanation
Indices: 23670291--23670339 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
23670281 TTATTATTTT
*
23670291 TATTTTTTATTTACA-TATATACAA
1 TATTATTTATTT-CATTATATA-AA
23670315 TATTATTTATTTCATTATATAAA
1 TATTATTTATTTCATTATATAAA
23670338 TA
1 TA
23670340 CCTTCAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTATTTATTTCATTATATAAA
Found at i:23677114 original size:22 final size:22
Alignment explanation
Indices: 23677089--23677135 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
23677079 GATTTACCTA
23677089 ACATGTGAGGTGTTGAACTAAG
1 ACATGTGAGGTGTTGAACTAAG
*
23677111 ACATGTGAGGTGTTGAGCTAAG
1 ACATGTGAGGTGTTGAACTAAG
23677133 ACA
1 ACA
23677136 CGTACCATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.26
Consensus pattern (22 bp):
ACATGTGAGGTGTTGAACTAAG
Found at i:23682206 original size:17 final size:17
Alignment explanation
Indices: 23682184--23682217 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
23682174 AATAATATAA
*
23682184 GATAATTTTTTATTATT
1 GATAATTTATTATTATT
23682201 GATAATTTATTATTATT
1 GATAATTTATTATTATT
23682218 AAATAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
GATAATTTATTATTATT
Found at i:23694622 original size:21 final size:21
Alignment explanation
Indices: 23694583--23694623 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
23694573 ATCTGCTCAA
* * *
23694583 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTAGAGTAC
23694604 ACTCCACCTGCTGTAGAGTA
1 ACTCCACCTGCTGTAGAGTA
23694624 TTGCTCGTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTAGAGTAC
Found at i:23707178 original size:25 final size:24
Alignment explanation
Indices: 23707133--23707180 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
23707123 AAATAAAAAT
* * *
23707133 TAAATTTAGTTTTATTTGAAATAA
1 TAAAATTAGTTGTATTAGAAATAA
23707157 TAAAATTAGTTGTATATAGAAATA
1 TAAAATTAGTTGTAT-TAGAAATA
23707181 TAACAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (24 bp):
TAAAATTAGTTGTATTAGAAATAA
Found at i:23707183 original size:24 final size:23
Alignment explanation
Indices: 23707129--23707183 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
23707119 GTTCAAATAA
* * *
23707129 AAAT-TAAATTTAGTTTTATTTG
1 AAATATAAAATTAGTTGTATTAG
23707151 AAATAATAAAATTAGTTGTATATAG
1 AAAT-ATAAAATTAGTTGTAT-TAG
23707176 AAATATAA
1 AAATATAA
23707184 CAAATAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
24 17 0.63
25 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (23 bp):
AAATATAAAATTAGTTGTATTAG
Found at i:23714825 original size:15 final size:15
Alignment explanation
Indices: 23714800--23714834 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
23714790 GACTCTATTT
*
23714800 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
23714814 TAATTAATATTAAGA
1 TAATTAATATTAAGA
23714829 TAATTA
1 TAATTA
23714835 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:23721303 original size:20 final size:20
Alignment explanation
Indices: 23721278--23721350 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
23721268 GTAAGCCAAT
*
23721278 TTTTATTATTTATTTATTTA
1 TTTTATTACTTATTTATTTA
*
23721298 TTTTATT--TTCTTTACTTTA
1 TTTTATTACTTATTTA-TTTA
23721317 -TTTATTACTT-TTT-TTTA
1 TTTTATTACTTATTTATTTA
23721334 TTATTTATTACTTATTT
1 -T-TTTATTACTTATTT
23721351 GGATATTAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
17 4 0.09
18 12 0.27
19 7 0.16
20 19 0.42
21 3 0.07
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATTACTTATTTATTTA
Found at i:23722378 original size:17 final size:17
Alignment explanation
Indices: 23722351--23722391 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
23722341 TTCCTAAAGT
23722351 ATAAA-AAATATAAATA
1 ATAAATAAATATAAATA
*
23722367 ATAAATAAATATAAATC
1 ATAAATAAATATAAATA
23722384 A-AAATAAA
1 ATAAATAAA
23722392 GAAAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAAATAAATATAAATA
Found at i:23726457 original size:22 final size:22
Alignment explanation
Indices: 23726395--23726466 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 22
23726385 GTAGGGGTTT
23726395 AGCACTTCTGTGCTCTCTATTC
1 AGCACTTCTGTGCTCTCTATTC
* * * *
23726417 AGTACTTCGGTACTCTCTAATC
1 AGCACTTCTGTGCTCTCTATTC
* * *
23726439 AGCACTTTTGTGCTATCTATTT
1 AGCACTTCTGTGCTCTCTATTC
23726461 AGCACT
1 AGCACT
23726467 ACGATGCTCT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.19, C:0.26, G:0.14, T:0.40
Consensus pattern (22 bp):
AGCACTTCTGTGCTCTCTATTC
Found at i:23732637 original size:20 final size:21
Alignment explanation
Indices: 23732597--23732637 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
23732587 ATAAAGATAT
* *
23732597 TTATAAATATTAATTAATTAA
1 TTATAAATATAAATAAATTAA
23732618 TTATAAA-ATAAATAAATTAA
1 TTATAAATATAAATAAATTAA
23732638 ATGGTGCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTATAAATATAAATAAATTAA
Found at i:23732746 original size:19 final size:19
Alignment explanation
Indices: 23732706--23732760 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
23732696 CTTATGTTAT
* * *
23732706 AATTAAAAGA-TATTTATT
1 AATTAAATGATTATTAATA
23732724 AATTAAATGATTATTAATA
1 AATTAAATGATTATTAATA
* *
23732743 AATTATATTATTA-TAATA
1 AATTAAATGATTATTAATA
23732761 TAAAGTAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (19 bp):
AATTAAATGATTATTAATA
Found at i:23742617 original size:37 final size:37
Alignment explanation
Indices: 23742576--23742657 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
23742566 AAATATTTAT
* * *
23742576 TAATCAATGTTCAAACTTTGAACATGCTTTATTAAAC
1 TAATCAATGCTAAAACTTTGAACATGCTTTAATAAAC
*
23742613 TAATCAATGCTAAAACTTTGAACATGCTTTAATGAAC
1 TAATCAATGCTAAAACTTTGAACATGCTTTAATAAAC
23742650 TAATCAAT
1 TAATCAAT
23742658 ATATTTATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (37 bp):
TAATCAATGCTAAAACTTTGAACATGCTTTAATAAAC
Found at i:23742737 original size:33 final size:33
Alignment explanation
Indices: 23742700--23742775 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
23742690 TTAAAACTTG
*
23742700 AATTATACATATACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
23742733 AATTATACATACACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
23742766 AATTATACAT
1 AATTATACAT
23742776 GCTTTATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (33 bp):
AATTATACATACACCAACAATTAATTTTAGGTC
Found at i:23747405 original size:18 final size:17
Alignment explanation
Indices: 23747377--23747411 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
23747367 ATTATTAAGA
*
23747377 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
23747394 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
23747412 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:23747641 original size:44 final size:45
Alignment explanation
Indices: 23747576--23747666 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
23747566 ACCTCTATTC
* * *
23747576 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
23747620 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
23747665 CA
1 CA
23747667 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:23747668 original size:16 final size:16
Alignment explanation
Indices: 23747647--23747715 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
23747637 GATTAGCTAT
23747647 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
23747663 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
23747680 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
23747696 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
23747712 TACA
1 TACA
23747716 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:23747689 original size:33 final size:32
Alignment explanation
Indices: 23747647--23747715 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
23747637 GATTAGCTAT
23747647 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
23747680 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
23747712 TACA
1 TACA
23747716 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:23752189 original size:9 final size:9
Alignment explanation
Indices: 23752172--23752208 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
23752162 TGAGTTTTCA
23752172 AATTCGAAT
1 AATTCGAAT
23752181 -ATCTCGAAT
1 AAT-TCGAAT
23752190 AATTCGAAT
1 AATTCGAAT
23752199 AATTCGAAT
1 AATTCGAAT
23752208 A
1 A
23752209 TCAAACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:23752301 original size:58 final size:58
Alignment explanation
Indices: 23752221--23752336 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
23752211 AAACTATAAT
*
23752221 ATTTTACAGTTTTACCCCAAACTCTCAAACTTTTTTACTTTTCCCTCAAAACTTTTAC
1 ATTTTACAGTTTTACCCCAAACTCTCAAACATTTTTACTTTTCCCTCAAAACTTTTAC
* * * * *
23752279 ATTTTACATTTTTACCCTAAACTCTTAAACATTTTTACTTTTTCTTCAAAACTTTTAC
1 ATTTTACAGTTTTACCCCAAACTCTCAAACATTTTTACTTTTCCCTCAAAACTTTTAC
23752337 TCTTTCCCAC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.28, C:0.24, G:0.01, T:0.47
Consensus pattern (58 bp):
ATTTTACAGTTTTACCCCAAACTCTCAAACATTTTTACTTTTCCCTCAAAACTTTTAC
Found at i:23752313 original size:30 final size:29
Alignment explanation
Indices: 23752221--23752321 Score: 75
Period size: 30 Copynumber: 3.4 Consensus size: 29
23752211 AAACTATAAT
* * *
23752221 ATTTTACAGTTTTACCCCAAACTCTCAAAC
1 ATTTTAC-TTTTTACCCTAAACTCTTAAAC
* *
23752251 TTTTTTAC-TTTT-CCCTCAAAACT-TT-TAC
1 -ATTTTACTTTTTACCCT--AAACTCTTAAAC
23752279 ATTTTACATTTTTACCCTAAACTCTTAAAC
1 ATTTTAC-TTTTTACCCTAAACTCTTAAAC
23752309 ATTTTTACTTTTT
1 A-TTTTACTTTTT
23752322 CTTCAAAACT
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
27 6 0.11
28 10 0.18
29 11 0.20
30 17 0.30
31 12 0.21
ACGTcount: A:0.28, C:0.24, G:0.01, T:0.48
Consensus pattern (29 bp):
ATTTTACTTTTTACCCTAAACTCTTAAAC
Found at i:23752331 original size:30 final size:29
Alignment explanation
Indices: 23752239--23752331 Score: 75
Period size: 30 Copynumber: 3.2 Consensus size: 29
23752229 GTTTTACCCC
* * *
23752239 AAACTCTCAAACTTTTTTACTTTTCCCTCA
1 AAACTCTTAAACATTTTTACTTTT-TCTCA
* * *
23752269 AAACT-TT-TACA-TTTTACATTTTTACCCT
1 AAACTCTTAAACATTTTTAC-TTTTT-CTCA
23752297 AAACTCTTAAACATTTTTACTTTTTCTTCA
1 AAACTCTTAAACATTTTTACTTTTTC-TCA
23752327 AAACT
1 AAACT
23752332 TTTACTCTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
27 6 0.12
28 13 0.27
29 4 0.08
30 19 0.40
31 6 0.12
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (29 bp):
AAACTCTTAAACATTTTTACTTTTTCTCA
Found at i:23752651 original size:16 final size:17
Alignment explanation
Indices: 23752630--23752661 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
23752620 ACTTTTCCTC
23752630 AAAC-TTTTATTTTCCA
1 AAACTTTTTATTTTCCA
23752646 AAACTTTTTATTTTCC
1 AAACTTTTTATTTTCC
23752662 CAATTTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (17 bp):
AAACTTTTTATTTTCCA
Found at i:23752667 original size:62 final size:63
Alignment explanation
Indices: 23752601--23752725 Score: 189
Period size: 63 Copynumber: 2.0 Consensus size: 63
23752591 TTCCCTCCAA
* * **
23752601 AATTTTACT-CCTCCTATTTACTTTTCCTCAAACTTTTATTTTCCAAAACTTTTTATTTTCCC
1 AATTTTACTCCCCCCTATTTACTTTCCCTCAAACTTTTATTCCCCAAAACTTTTTATTTTCCC
* *
23752663 AATTTTACTCCCCCCTCTTTACTTTCCCTCAAATTTTTATTCCCCAAAACTTTTTATTTTCCC
1 AATTTTACTCCCCCCTATTTACTTTCCCTCAAACTTTTATTCCCCAAAACTTTTTATTTTCCC
23752726 CCTAAACTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
62 9 0.16
63 47 0.84
ACGTcount: A:0.22, C:0.30, G:0.00, T:0.49
Consensus pattern (63 bp):
AATTTTACTCCCCCCTATTTACTTTCCCTCAAACTTTTATTCCCCAAAACTTTTTATTTTCCC
Found at i:23753365 original size:5 final size:5
Alignment explanation
Indices: 23753355--23753380 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
23753345 CTCAAAAATT
23753355 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
23753381 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:23755400 original size:96 final size:96
Alignment explanation
Indices: 23755236--23755487 Score: 468
Period size: 96 Copynumber: 2.6 Consensus size: 96
23755226 TTATTTGTAG
*
23755236 TAAAAGAATCCAATTTTTCTTATTAAAATAATTCTCTAATTTCTCCTCTATACTAGTATTATTGG
1 TAAAAAAATCCAATTTTTCTTATTAAAATAATTCTCTAATTTCTCCTCTATACTAGTATTATTGG
23755301 TATAGGGTCGGAAGCAGTTCCTGTCCTAATC
66 TATAGGGTCGGAAGCAGTTCCTGTCCTAATC
23755332 TAAAAAAATCCAATTTTTCTTATTAAAATAATTCTCTAATTTCTCCTCTATACTAGTATTATTGG
1 TAAAAAAATCCAATTTTTCTTATTAAAATAATTCTCTAATTTCTCCTCTATACTAGTATTATTGG
23755397 TATAGGGTCGGAAGCAGTTCCTGTCCTAATC
66 TATAGGGTCGGAAGCAGTTCCTGTCCTAATC
* * *
23755428 TAAAAAAATCCAATTTTTCTTATTAAAATAATTCTCTAATTGCTGCTCTGTACTAGTATT
1 TAAAAAAATCCAATTTTTCTTATTAAAATAATTCTCTAATTTCTCCTCTATACTAGTATT
23755488 GTTGAAGTTA
Statistics
Matches: 152, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 152 1.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (96 bp):
TAAAAAAATCCAATTTTTCTTATTAAAATAATTCTCTAATTTCTCCTCTATACTAGTATTATTGG
TATAGGGTCGGAAGCAGTTCCTGTCCTAATC
Found at i:23755539 original size:13 final size:12
Alignment explanation
Indices: 23755509--23755541 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
23755499 TTATTCGCTA
23755509 TATTT-AATATT
1 TATTTAAATATT
23755520 TATTTAAATATT
1 TATTTAAATATT
23755532 TGATTTAAAT
1 T-ATTTAAAT
23755542 GAATCAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 7 0.35
13 8 0.40
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (12 bp):
TATTTAAATATT
Found at i:23756282 original size:22 final size:21
Alignment explanation
Indices: 23756257--23756300 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
23756247 AAGCATATGA
*
23756257 AAATGATTTGGTTATATTCAAT
1 AAATGATTTGGTTA-ATACAAT
23756279 AAATGATTTGGTTAATACAAT
1 AAATGATTTGGTTAATACAAT
23756300 A
1 A
23756301 CTTATATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (21 bp):
AAATGATTTGGTTAATACAAT
Found at i:23757874 original size:15 final size:15
Alignment explanation
Indices: 23757854--23757885 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
23757844 AGAGTGCATG
23757854 AACATAAAAAAGAAC
1 AACATAAAAAAGAAC
23757869 AACATAAAAAAGAAC
1 AACATAAAAAAGAAC
23757884 AA
1 AA
23757886 TATAGCAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.75, C:0.12, G:0.06, T:0.06
Consensus pattern (15 bp):
AACATAAAAAAGAAC
Found at i:23763015 original size:22 final size:22
Alignment explanation
Indices: 23762980--23763038 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
23762970 TCGTAATGGT
*
23762980 TCAGATA-AGATGCATAACAAA
1 TCAGATACAGATGCAGAACAAA
*
23763001 TCAGATACAGATGCAGAACAGA
1 TCAGATACAGATGCAGAACAAA
*
23763023 TTAGA-ACCAGATGCAG
1 TCAGATA-CAGATGCAG
23763039 TTTCCTACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.24
22 25 0.76
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (22 bp):
TCAGATACAGATGCAGAACAAA
Found at i:23764426 original size:21 final size:21
Alignment explanation
Indices: 23764379--23764426 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
23764369 ATCAAGCGAA
**
23764379 AGAAGAAAACGGGAAAAAAAG
1 AGAAGAAAAAAGGAAAAAAAG
* *
23764400 AAAAGAAAAAAGGAAAAAAGG
1 AGAAGAAAAAAGGAAAAAAAG
23764421 AGAAGA
1 AGAAGA
23764427 GAGCGTCAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (21 bp):
AGAAGAAAAAAGGAAAAAAAG
Found at i:23764461 original size:17 final size:16
Alignment explanation
Indices: 23764441--23764473 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
23764431 GTCAAATTTT
23764441 AACTAAATAAAAATAAA
1 AACTAAAT-AAAATAAA
23764458 AACTAAATAAAATAAA
1 AACTAAATAAAATAAA
23764474 TAAATAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (16 bp):
AACTAAATAAAATAAA
Found at i:23764481 original size:17 final size:17
Alignment explanation
Indices: 23764444--23764492 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
23764434 AAATTTTAAC
*
23764444 TAAATAAAAATAAA-AAC
1 TAAAT-AAAATAAATAAA
23764461 TAAATAAAATAAATAAA
1 TAAATAAAATAAATAAA
*
23764478 TAAAGAAAACTAAAT
1 TAAATAAAA-TAAAT
23764493 GATTTACTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 8 0.29
17 15 0.54
18 5 0.18
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (17 bp):
TAAATAAAATAAATAAA
Found at i:23767910 original size:64 final size:64
Alignment explanation
Indices: 23767823--23767952 Score: 161
Period size: 64 Copynumber: 2.0 Consensus size: 64
23767813 CACGAAGAGA
* * * ** * * * *
23767823 CATATATCGGGACGCTCATAAAGAGCTGTGGTATGTCCGCAATAAATGCAGGATCAATACCGAT
1 CATATAACAGGACGCTCACAAAGAGCTGCAGTATATCCACAACAAAGGCAGGATCAATACCGAT
* *
23767887 CATATAACAGGACGCTCACAAAGAGCTGCAGTATATCCACAACACAGGCAGGATCAATACTGAT
1 CATATAACAGGACGCTCACAAAGAGCTGCAGTATATCCACAACAAAGGCAGGATCAATACCGAT
23767951 CA
1 CA
23767953 GGATGCTCGC
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (64 bp):
CATATAACAGGACGCTCACAAAGAGCTGCAGTATATCCACAACAAAGGCAGGATCAATACCGAT
Found at i:23771375 original size:43 final size:42
Alignment explanation
Indices: 23771327--23771491 Score: 138
Period size: 43 Copynumber: 3.9 Consensus size: 42
23771317 AGCTTGTGCA
* * *
23771327 ATGCCAATGTCCCAGACGTAGTCTTACATGTATTCAAATAACG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGAAATCAAAT-ACG
* *
23771370 ATGCCACTGTCCCAGACAG-GGTCTTACATGAAATCATATACG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACATGAAATCAAATACG
* * * *
23771412 ATGCAAATGTCCCAGACATGGTCTTACACGTAAATTTTAAAT--G
1 ATGCCAATGTCCCAGACGTGGTCTTACATG-AAA--TCAAATACG
* * * *
23771455 AATGCCAACGTCCCAGATGTGGTCTTATATGATATCA
1 -ATGCCAATGTCCCAGACGTGGTCTTACATGAAATCA
23771492 CGTATTGGAA
Statistics
Matches: 97, Mismatches: 19, Indels: 14
0.75 0.15 0.11
Matches are distributed among these distances:
41 2 0.02
42 28 0.29
43 38 0.39
44 25 0.26
45 4 0.04
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACATGAAATCAAATACG
Found at i:23771426 original size:42 final size:43
Alignment explanation
Indices: 23771327--23771439 Score: 140
Period size: 43 Copynumber: 2.7 Consensus size: 43
23771317 AGCTTGTGCA
* * *
23771327 ATGCCAATGTCCCAGAC-GTAGTCTTACATGTATTCAAATAACG
1 ATGCCAATGTCCCAGACAG-GGTCTTACATGAAATCAAATAACG
* *
23771370 ATGCCACTGTCCCAGACAGGGTCTTACATGAAATCATAT-ACG
1 ATGCCAATGTCCCAGACAGGGTCTTACATGAAATCAAATAACG
* *
23771412 ATGCAAATGTCCCAGACATGGTCTTACA
1 ATGCCAATGTCCCAGACAGGGTCTTACA
23771440 CGTAAATTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
42 28 0.46
43 32 0.52
44 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACATGAAATCAAATAACG
Found at i:23774866 original size:210 final size:209
Alignment explanation
Indices: 23774533--23774954 Score: 799
Period size: 210 Copynumber: 2.0 Consensus size: 209
23774523 AAATACAGAT
23774533 ATCTGGGGAAGCAAAATACATTACTAGTAATTATAGCTACCGGGATAAATTTAGAACAAGAAGAG
1 ATCTGGGGAAGCAAAATACATTACTAGTAATTATAGCTACCGGGATAAATTTAGAACAAGAAGAG
*
23774598 GTTTGAGTCAGTGTTTTAAAAACAAACAAAAACGTCATAGGATGGATAATTGCTGATATTAAGGG
66 GTTTGAGTCAGTGTTTTAAAAACAAACAAAAACGTCATAGGATGGATAATTACTGATATTAAGGG
23774663 AATCAATCTTGTGCTATGTGAACATAAGATTAGATTAGAAGAAGGAAAAAAACCTGTAGTGGATG
131 AATCAATCTTGTGCTATGTGAACATAAGATTAGATTAGAAGAAGG-AAAAAACCTGTAGTGGATG
23774728 CACAACGCCGGCTTA
195 CACAACGCCGGCTTA
23774743 ATCTGGGGAAGCAAAATACATTACTAGTAATTATAGCTACCGGGATAAATTTAGAACAAGAAGAG
1 ATCTGGGGAAGCAAAATACATTACTAGTAATTATAGCTACCGGGATAAATTTAGAACAAGAAGAG
* *
23774808 GTTTGATTCAGTGTTTTAAAAACACACAAAAACGTCATAGGATGGATAATTACTGATATTAAGGG
66 GTTTGAGTCAGTGTTTTAAAAACAAACAAAAACGTCATAGGATGGATAATTACTGATATTAAGGG
23774873 AATCAATCTTGTGCTATGTGAACATAAGATTAGATTAGAAGAAGGAAAAAACCTGTAGTGGATGC
131 AATCAATCTTGTGCTATGTGAACATAAGATTAGATTAGAAGAAGGAAAAAACCTGTAGTGGATGC
*
23774938 ACATCGCCGGCTTA
196 ACAACGCCGGCTTA
23774952 ATC
1 ATC
23774955 CAACTATGAA
Statistics
Matches: 208, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
209 36 0.17
210 172 0.83
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.26
Consensus pattern (209 bp):
ATCTGGGGAAGCAAAATACATTACTAGTAATTATAGCTACCGGGATAAATTTAGAACAAGAAGAG
GTTTGAGTCAGTGTTTTAAAAACAAACAAAAACGTCATAGGATGGATAATTACTGATATTAAGGG
AATCAATCTTGTGCTATGTGAACATAAGATTAGATTAGAAGAAGGAAAAAACCTGTAGTGGATGC
ACAACGCCGGCTTA
Found at i:23798052 original size:35 final size:35
Alignment explanation
Indices: 23798013--23798082 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
23798003 AAAATTTTTA
23798013 AAACTCTGATTTTTCTTTAAATTTATTTTCCACTG
1 AAACTCTGATTTTTCTTTAAATTTATTTTCCACTG
23798048 AAACTCTGATTTTTCTTTAAATTTATTTTCCACTG
1 AAACTCTGATTTTTCTTTAAATTTATTTTCCACTG
23798083 CGTTTTTCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (35 bp):
AAACTCTGATTTTTCTTTAAATTTATTTTCCACTG
Found at i:23799784 original size:5 final size:5
Alignment explanation
Indices: 23799774--23799798 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
23799764 GAGCATTCGG
23799774 TCGAA TCGAA TCGAA TCGAA TCGAA
1 TCGAA TCGAA TCGAA TCGAA TCGAA
23799799 AATTTTCGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (5 bp):
TCGAA
Found at i:23803120 original size:237 final size:237
Alignment explanation
Indices: 23802703--23803401 Score: 1337
Period size: 237 Copynumber: 2.9 Consensus size: 237
23802693 AAACTTAATA
** *
23802703 AATCGATTAAATTAAAAATTAAATAATATACAACAACATAAATTAAACAAAAAATATA-TATGTT
1 AATCGATTAAATTAAAAATTAAATAATATACAGTAGCATAAATTAAACAAAAAA-A-AGTATGTT
23802767 AAACTACATTTATAAAAAATGGTTGAATTGTTTTATTTTTATAATTATAAGTTTTTGAATATATA
64 AAACTACATTTAT-AAAAATGGTTGAATTGTTTTATTTTTATAATTATAAGTTTTTGAATATATA
23802832 AAATAATAACTAAATTAGAAAGAACAACAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTG
128 AAATAATAACTAAATTAGAAAGAACAACAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTG
23802897 ATGATGATTGGTGCATACAAAAATAATTGACATTATTTTCTCCTC
193 ATGATGATTGGTGCATACAAAAATAATTGACATTATTTTCTCCTC
23802942 AATCGATTAAATTAAAAATTAAATAATATACAGTAGCATAAATTAAACAAAAAAAAGTATGTTAA
1 AATCGATTAAATTAAAAATTAAATAATATACAGTAGCATAAATTAAACAAAAAAAAGTATGTTAA
23803007 ACTACATTTATAAAAATGGTTGAATTGTTTTATTTTTATAATTATAAGTTTTTGAATATATAAAA
66 ACTACATTTATAAAAATGGTTGAATTGTTTTATTTTTATAATTATAAGTTTTTGAATATATAAAA
23803072 TAATAACTAAATTAGAAAGAACAACAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTGATG
131 TAATAACTAAATTAGAAAGAACAACAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTGATG
23803137 ATGATTGGTGCATACAAAAATAATTGACATTATTTTCTCCTC
196 ATGATTGGTGCATACAAAAATAATTGACATTATTTTCTCCTC
23803179 AATCGATTAAATTAAAAATTAAATAATATACAGTAGCATAAATTAAACAAAAAAAAGTATGTTAA
1 AATCGATTAAATTAAAAATTAAATAATATACAGTAGCATAAATTAAACAAAAAAAAGTATGTTAA
23803244 ACTACATTTATAAAAATGGTTGAATTGTTTTATTTTTATAATTATAAGTTTTTGAATATATAAAA
66 ACTACATTTATAAAAATGGTTGAATTGTTTTATTTTTATAATTATAAGTTTTTGAATATATAAAA
23803309 TAATAACTAAATTAGAAAGAACAACAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTGATG
131 TAATAACTAAATTAGAAAGAACAACAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTGATG
23803374 ATGATTGGTGCATACAAAAATAATTGAC
196 ATGATTGGTGCATACAAAAATAATTGAC
23803402 TGCATATTCC
Statistics
Matches: 456, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
237 385 0.84
238 20 0.04
239 51 0.11
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.35
Consensus pattern (237 bp):
AATCGATTAAATTAAAAATTAAATAATATACAGTAGCATAAATTAAACAAAAAAAAGTATGTTAA
ACTACATTTATAAAAATGGTTGAATTGTTTTATTTTTATAATTATAAGTTTTTGAATATATAAAA
TAATAACTAAATTAGAAAGAACAACAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTGATG
ATGATTGGTGCATACAAAAATAATTGACATTATTTTCTCCTC
Found at i:23805089 original size:28 final size:29
Alignment explanation
Indices: 23805037--23805091 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
23805027 GTTTTAAATA
*
23805037 TAGTGTATTTTAAAAATAAAAAATATATG
1 TAGTATATTTTAAAAATAAAAAATATATG
23805066 TAGTATATTTTAAAAAT-AAAAATATA
1 TAGTATATTTTAAAAATAAAAAATATA
23805092 GTTTTTATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (29 bp):
TAGTATATTTTAAAAATAAAAAATATATG
Found at i:23805110 original size:9 final size:9
Alignment explanation
Indices: 23805096--23805134 Score: 69
Period size: 9 Copynumber: 4.3 Consensus size: 9
23805086 AATATAGTTT
23805096 TTATTCGAA
1 TTATTCGAA
23805105 TTATTCGAA
1 TTATTCGAA
*
23805114 TTATTCGAG
1 TTATTCGAA
23805123 TTATTCGAA
1 TTATTCGAA
23805132 TTA
1 TTA
23805135 GAAAATTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (9 bp):
TTATTCGAA
Found at i:23805189 original size:9 final size:9
Alignment explanation
Indices: 23805175--23805219 Score: 81
Period size: 9 Copynumber: 5.0 Consensus size: 9
23805165 CGAAAGAAAA
23805175 AATTCGATT
1 AATTCGATT
23805184 AATTCGATT
1 AATTCGATT
23805193 AATTCGATT
1 AATTCGATT
23805202 AATTCGATT
1 AATTCGATT
*
23805211 AACTCGATT
1 AATTCGATT
23805220 CGAATAATTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (9 bp):
AATTCGATT
Found at i:23813567 original size:39 final size:39
Alignment explanation
Indices: 23813499--23813573 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
23813489 CTAAAGGTCG
*
23813499 AGCATTAACGGCGATTGTTGAAAAACGCCGCTAAAATTA
1 AGCATTAACGGCGATTGTTGAAAAACGCCGCAAAAATTA
* * * * *
23813538 AGCATTAGCGGCGTTTTTTGGAAAGCGCCGCAAAAA
1 AGCATTAACGGCGATTGTTGAAAAACGCCGCAAAAA
23813574 GCCTAAACCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.23
Consensus pattern (39 bp):
AGCATTAACGGCGATTGTTGAAAAACGCCGCAAAAATTA
Found at i:23813975 original size:114 final size:113
Alignment explanation
Indices: 23813542--23814179 Score: 1069
Period size: 113 Copynumber: 5.6 Consensus size: 113
23813532 AAATTAAGCA
* ** *
23813542 TTAGCGGCGTTTTTTGGAAAGCGCCGCAAAAAGCCTAAACCCAACGACACCGTTTTCTGAGTTTT
1 TTAGCAGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTT
23813607 TGGGGTCTTTAGCGGCGTTTCTGTAATGCGCCGCTAATTCTCAGGTCT
66 TGGGGTCTTTAGCGGCGTTTCTGTAATGCGCCGCTAATTCTCAGGTCT
23813655 TTAGCAGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTT
1 TTAGCAGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTT
23813720 TGGGGTCTTTAGCGGCGTTTCTGTAATGCGCCGCTAATTCTCAGGTCT
66 TGGGGTCTTTAGCGGCGTTTCTGTAATGCGCCGCTAATTCTCAGGTCT
23813768 TTAGCAGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTT
1 TTAGCAGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTT
*
23813833 TGGGGTCTTTAGCGGCGTTTCTGTAATGCGTCGCTAATTCTCAGGTCT
66 TGGGGTCTTTAGCGGCGTTTCTGTAATGCGCCGCTAATTCTCAGGTCT
* * * *
23813881 TTAGCGGCGTTTTTTTAAAAGCGCTGCAAAAAAGCCTAAGCCCAACGGCACCGTTTTATGAGTTT
1 TTAGCAGCGTTTTTTTAAAAGCGCCGC-AAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTT
*
23813946 TTGGGGTCTTTAGCGGCGTTTCTGTAATGCGTCGCTAATTCTCAGGTCT
65 TTGGGGTCTTTAGCGGCGTTTCTGTAATGCGCCGCTAATTCTCAGGTCT
* * * *
23813995 TTAGCGGCGTTTTTTTAAAAGCGCTGCAAAAAAGCCTAAGCCCAACGGCACCGTTTTATGAGTTT
1 TTAGCAGCGTTTTTTTAAAAGCGCCGC-AAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTT
* * *
23814060 TTGGGGTCTTTAGCGGCGTTTCTGTAAAGCGCCGCTAATGCTCAGGTGT
65 TTGGGGTCTTTAGCGGCGTTTCTGTAATGCGCCGCTAATTCTCAGGTCT
** * *
23814109 TTAGCAGCGTTTTTTTAAAAGCATCGCAAAAAGCCTAAGCCCAACGACACCGTTTTCTGAGTTTT
1 TTAGCAGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTT
23814174 TGGGGT
66 TGGGGT
23814180 TTTTGGGGTT
Statistics
Matches: 505, Mismatches: 19, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
113 288 0.57
114 217 0.43
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (113 bp):
TTAGCAGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTT
TGGGGTCTTTAGCGGCGTTTCTGTAATGCGCCGCTAATTCTCAGGTCT
Found at i:23814142 original size:227 final size:225
Alignment explanation
Indices: 23813542--23814179 Score: 1069
Period size: 227 Copynumber: 2.8 Consensus size: 225
23813532 AAATTAAGCA
** *
23813542 TTAGCGGCGTTTTTTGGAAAGCGCCGCAAAAAGCCTAAACCCAACGACACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTT
23813607 TGGGGTCTTTAGCGGCGTTTCTGTAATGCGCCGCTAATTCTCAGGTCTTTAGCAGCGTTTTTTTA
66 TGGGGTCTTTAGCGGCGTTTCTGTAATGCGCCGCTAATTCTCAGGTCTTTAGCAGCGTTTTTTTA
*
23813672 AAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTTTGGGGTCTTTAGCGGCG
131 AAAGC-CCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTTTGGGGTCTTTAGCGGCG
23813737 TTTCTGTAATGCGCCGCTAATTCTCAGGTCT
195 TTTCTGTAATGCGCCGCTAATTCTCAGGTCT
*
23813768 TTAGCAGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTT
* *
23813833 TGGGGTCTTTAGCGGCGTTTCTGTAATGCGTCGCTAATTCTCAGGTCTTTAGCGGCGTTTTTTTA
66 TGGGGTCTTTAGCGGCGTTTCTGTAATGCGCCGCTAATTCTCAGGTCTTTAGCAGCGTTTTTTTA
* *
23813898 AAAGCGCTGCAAAAAAGCCTAAGCCCAACGGCACCGTTTTATGAGTTTTTGGGGTCTTTAGCGGC
131 AAAGC-CCGC-AAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTTTGGGGTCTTTAGCGGC
*
23813963 GTTTCTGTAATGCGTCGCTAATTCTCAGGTCT
194 GTTTCTGTAATGCGCCGCTAATTCTCAGGTCT
* * *
23813995 TTAGCGGCGTTTTTTTAAAAGCGCTGCAAAAAAGCCTAAGCCCAACGGCACCGTTTTATGAGTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGC-AAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTT
* * *
23814060 TTGGGGTCTTTAGCGGCGTTTCTGTAAAGCGCCGCTAATGCTCAGGTGTTTAGCAGCGTTTTTTT
65 TTGGGGTCTTTAGCGGCGTTTCTGTAATGCGCCGCTAATTCTCAGGTCTTTAGCAGCGTTTTTTT
* *
23814125 AAAAGCATCGCAAAAAGCCTAAGCCCAACGACACCGTTTTCTGAGTTTTTGGGGT
130 AAAAGC-CCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTTTGGGGT
23814180 TTTTGGGGTT
Statistics
Matches: 386, Mismatches: 24, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
226 133 0.34
227 150 0.39
228 103 0.27
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (225 bp):
TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTT
TGGGGTCTTTAGCGGCGTTTCTGTAATGCGCCGCTAATTCTCAGGTCTTTAGCAGCGTTTTTTTA
AAAGCCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTTTGGGGTCTTTAGCGGCGT
TTCTGTAATGCGCCGCTAATTCTCAGGTCT
Found at i:23814191 original size:8 final size:9
Alignment explanation
Indices: 23814169--23814194 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
23814159 CGTTTTCTGA
23814169 GTTTTTGGG
1 GTTTTTGGG
23814178 GTTTTTGGG
1 GTTTTTGGG
23814187 GTTTTTGG
1 GTTTTTGG
23814195 CGGTGTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.42, T:0.58
Consensus pattern (9 bp):
GTTTTTGGG
Found at i:23814638 original size:7 final size:7
Alignment explanation
Indices: 23814626--23814651 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
23814616 GGGTTTATTA
23814626 GTTAGGG
1 GTTAGGG
23814633 GTTAGGG
1 GTTAGGG
23814640 GTTAGGG
1 GTTAGGG
23814647 GTTAG
1 GTTAG
23814652 ATGTTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.54, T:0.31
Consensus pattern (7 bp):
GTTAGGG
Found at i:23814785 original size:87 final size:82
Alignment explanation
Indices: 23814701--23814946 Score: 208
Period size: 87 Copynumber: 3.0 Consensus size: 82
23814691 TATGGATTCG
*
23814701 GTGTTAGGTTAGAGTTTAGGGTTTAGACTAAGTAATATATATTTTAAATTATATAATATTAAATA
1 GTGTTAGGTTAGAGTTTAGGGTTTAGATTAAGTAAT-TAT-TTTTAAATTATAT-ATATTAAATA
23814766 ATGTTTAGGGGTTAGGGA--
63 ATGTTTAGGGGTTAGGGATT
* * * * *
23814784 -T-TTAGGGTTAGGGTTTA-GGATT-GATTAATTAGTGT-TTTTTAATTTATATATATTAAATAA
1 GTGTTA-GGTTAGAGTTTAGGGTTTAGATTAAGTAAT-TATTTTTAAATTATATATATTAAATAA
23814844 TGTTTAGGGGTTTAGGG-TT
64 TGTTTAGGGG-TTAGGGATT
* * *
23814863 AGTGATTCGGGTT-GAG-TTAGGGTTTAGGATTCAGATAATTAGTGTTTTTTAATT-TATATATT
1 -GTG-TT-AGGTTAGAGTTTAGGGTTTA-GATTAAG-TAATTA---TTTTTAAATTATATATATT
23814925 AAATAATGTTTAGGGGTTAGGG
58 AAATAATGTTTAGGGGTTAGGG
23814947 GTTAGTGATT
Statistics
Matches: 131, Mismatches: 15, Indels: 31
0.74 0.08 0.18
Matches are distributed among these distances:
77 21 0.16
78 18 0.14
79 1 0.01
80 9 0.07
81 11 0.08
82 18 0.14
83 6 0.05
84 6 0.05
85 3 0.02
86 6 0.05
87 24 0.18
88 8 0.06
ACGTcount: A:0.30, C:0.01, G:0.25, T:0.44
Consensus pattern (82 bp):
GTGTTAGGTTAGAGTTTAGGGTTTAGATTAAGTAATTATTTTTAAATTATATATATTAAATAATG
TTTAGGGGTTAGGGATT
Found at i:23814793 original size:14 final size:13
Alignment explanation
Indices: 23814768--23814802 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
23814758 ATTAAATAAT
23814768 GTTTAGGGGTTAGG
1 GTTTA-GGGTTAGG
23814782 GATTTAGGGTTAGG
1 G-TTTAGGGTTAGG
23814796 GTTTAGG
1 GTTTAGG
23814803 ATTGATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.30
14 10 0.50
15 4 0.20
ACGTcount: A:0.17, C:0.00, G:0.46, T:0.37
Consensus pattern (13 bp):
GTTTAGGGTTAGG
Found at i:23814949 original size:87 final size:89
Alignment explanation
Indices: 23814790--23814986 Score: 305
Period size: 88 Copynumber: 2.2 Consensus size: 89
23814780 GGGATTTAGG
23814790 GTTAGGGTTTAGGATT-GATTAATTAGTGTTTTTTAATTTATATATATTAAATAATGTTTAGGGG
1 GTTAGGGTTTAGGATTAGA-TAATTAGTGTTTTTTAATTTATATATATTAAATAATGTTTAGGGG
*
23814854 TTTAGGGTTAGTGATTC-GGGTTGA
65 TTTAGGGTTAGTGATTCGGGGTCGA
23814878 GTTAGGGTTTAGGATTCAGATAATTAGTGTTTTTTAA-TT-TATATATTAAATAATGTTTAGGGG
1 GTTAGGGTTTAGGATT-AGATAATTAGTGTTTTTTAATTTATATATATTAAATAATGTTTAGGGG
23814941 -TTAGGGGTTAGTGATTCGGGGTCGA
65 TTTA-GGGTTAGTGATTCGGGGTCGA
*
23814966 GTTAGGGTTTATGATTTAGAT
1 GTTAGGGTTTAGGA-TTAGAT
23814987 TATATAATAT
Statistics
Matches: 102, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
86 3 0.03
87 37 0.36
88 41 0.40
89 19 0.19
90 2 0.02
ACGTcount: A:0.26, C:0.02, G:0.27, T:0.45
Consensus pattern (89 bp):
GTTAGGGTTTAGGATTAGATAATTAGTGTTTTTTAATTTATATATATTAAATAATGTTTAGGGGT
TTAGGGTTAGTGATTCGGGGTCGA
Found at i:23815010 original size:237 final size:237
Alignment explanation
Indices: 23814743--23815186 Score: 838
Period size: 237 Copynumber: 1.9 Consensus size: 237
23814733 TAATATATAT
23814743 TTTAAATTATATAATATTAAATAATGTTTAGGGGTTAGGGATTTAGGGTTAGGGTTTAGGA-TT-
1 TTTAAATTATATAATATTAAATAATGTTTAGGGGTTAGGGATTTAGGGTTAGGGTTTAGGATTTA
23814806 GATTAATTAGTGTTTTTTAATTTATATATATTAAATAATGTTTAGGGGTTTAGGGTTAGTGATTC
66 GATTAATTAGTGTTTTTTAA-TT-TATATATTAAATAATGTTTAGGGGTTTAGGGTTAGTGATTC
23814871 GGGTTGAGTTAGGGTTTAGGATTCAGATAATTAGTGTTTTTTAATTTATATATTAAATAATGTTT
129 GGGTTGAGTTAGGGTTTAGGATTCAGATAATTAGTGTTTTTTAATTTATATATTAAATAATGTTT
23814936 AGGGGTTAGGGGTTAGTGATTCGGGGTCGAGTTAGGGTTTATGA
194 AGGGGTTAGGGGTTAGTGATTCGGGGTCGAGTTAGGGTTTATGA
*
23814980 TTTAGATTATATAATATTAAATAATGTTTAGGGGTTAGGGATTTAGGGTTAGGGTTTAGGATTTA
1 TTTAAATTATATAATATTAAATAATGTTTAGGGGTTAGGGATTTAGGGTTAGGGTTTAGGATTTA
23815045 GATTAATTAGTGTTTTTTAATTTATATATTAAATAATGTTTAGGGGTTTAGGGTTAGTGATTCGG
66 GATTAATTAGTGTTTTTTAATTTATATATTAAATAATGTTTAGGGGTTTAGGGTTAGTGATTCGG
23815110 GTTGAGTTAGGGTTTAGGATTCAGATAATTAGTGTTTTTTAATTTATATATTAAATAATGTTTAG
131 GTTGAGTTAGGGTTTAGGATTCAGATAATTAGTGTTTTTTAATTTATATATTAAATAATGTTTAG
*
23815175 GGTTTAGGGGTT
196 GGGTTAGGGGTT
23815187 TGAGGTTTGA
Statistics
Matches: 203, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
237 179 0.88
238 4 0.02
239 20 0.10
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (237 bp):
TTTAAATTATATAATATTAAATAATGTTTAGGGGTTAGGGATTTAGGGTTAGGGTTTAGGATTTA
GATTAATTAGTGTTTTTTAATTTATATATTAAATAATGTTTAGGGGTTTAGGGTTAGTGATTCGG
GTTGAGTTAGGGTTTAGGATTCAGATAATTAGTGTTTTTTAATTTATATATTAAATAATGTTTAG
GGGTTAGGGGTTAGTGATTCGGGGTCGAGTTAGGGTTTATGA
Found at i:23815041 original size:20 final size:21
Alignment explanation
Indices: 23815007--23815045 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
23814997 TAAATAATGT
23815007 TTAGGGGTTAGGGATTTAGGG
1 TTAGGGGTTAGGGATTTAGGG
*
23815028 TTAGGGTTTA-GGATTTAG
1 TTAGGGGTTAGGGATTTAG
23815046 ATTAATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.21, C:0.00, G:0.41, T:0.38
Consensus pattern (21 bp):
TTAGGGGTTAGGGATTTAGGG
Found at i:23815045 original size:14 final size:14
Alignment explanation
Indices: 23815006--23815039 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
23814996 TTAAATAATG
23815006 TTTAGGGGTTAGGGA
1 TTTA-GGGTTAGGGA
23815021 TTTAGGGTTAGGG-
1 TTTAGGGTTAGGGA
23815034 TTTAGG
1 TTTAGG
23815040 ATTTAGATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 9 0.47
15 4 0.21
ACGTcount: A:0.18, C:0.00, G:0.44, T:0.38
Consensus pattern (14 bp):
TTTAGGGTTAGGGA
Found at i:23815081 original size:87 final size:84
Alignment explanation
Indices: 23815005--23815183 Score: 236
Period size: 87 Copynumber: 2.1 Consensus size: 84
23814995 ATTAAATAAT
* *
23815005 GTTTAGGGGTTAGGGATT-TAGGGTTAGGGTTTAGGATTTAGATTAATTAGTGTTTTTTAATTTA
1 GTTTA-GGGTTAGGGATTGTAGAGTTAGGGTTTAGGATTCAGA-TAATTAGTGTTTTTTAATTTA
* *
23815069 TATATTAAATAATGTTTAGGG
64 TATATTAAATAATATTTAGAG
* *
23815090 GTTTAGGGTTAGTGATTCGGGTTGAGTTAGGGTTTAGGATTCAGATAATTAGTGTTTTTTAATTT
1 GTTTAGGGTTAGGGATT---GTAGAGTTAGGGTTTAGGATTCAGATAATTAGTGTTTTTTAATTT
*
23815155 ATATATTAAATAATGTTTAG-G
63 ATATATTAAATAATATTTAGAG
23815176 GTTTAGGG
1 GTTTAGGG
23815184 GTTTGAGGTT
Statistics
Matches: 86, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
84 11 0.13
85 5 0.06
86 9 0.10
87 40 0.47
88 21 0.24
ACGTcount: A:0.26, C:0.01, G:0.27, T:0.45
Consensus pattern (84 bp):
GTTTAGGGTTAGGGATTGTAGAGTTAGGGTTTAGGATTCAGATAATTAGTGTTTTTTAATTTATA
TATTAAATAATATTTAGAG
Found at i:23815243 original size:17 final size:18
Alignment explanation
Indices: 23815221--23815259 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
23815211 AGTTAGTGAT
23815221 TTAAGGTTT-AGATCAGA
1 TTAAGGTTTAAGATCAGA
*
23815238 TTAAGGTTTAAGCTCAGA
1 TTAAGGTTTAAGATCAGA
23815256 TTAA
1 TTAA
23815260 TTAGTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (18 bp):
TTAAGGTTTAAGATCAGA
Found at i:23815607 original size:21 final size:20
Alignment explanation
Indices: 23815568--23815612 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
23815558 AATTTGGACC
23815568 AAAATATAAGAAAAAATAAA
1 AAAATATAAGAAAAAATAAA
23815588 AAAATATAA-AAAGGAAATAAA
1 AAAATATAAGAAA--AAATAAA
23815609 AAAA
1 AAAA
23815613 CTAATAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.13
20 9 0.39
21 11 0.48
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (20 bp):
AAAATATAAGAAAAAATAAA
Found at i:23817340 original size:56 final size:56
Alignment explanation
Indices: 23817291--23817404 Score: 142
Period size: 56 Copynumber: 2.0 Consensus size: 56
23817281 CATAAGTTAG
23817291 TTAATTAAAATACATAAATTACATAA-CTAATTACACTT-ATATTATACATAACTTACA
1 TTAA-TAAAATACATAAATTACATAAGCTAATTA-A-TTAATATTATACATAACTTACA
** * * *
23817348 TTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACA
1 TTAATAAAATACATAAATTACATAAGCTAATTAATTAATATTATACATAACTTACA
23817404 T
1 T
23817405 CACTTACAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
55 2 0.04
56 39 0.78
57 9 0.18
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.40
Consensus pattern (56 bp):
TTAATAAAATACATAAATTACATAAGCTAATTAATTAATATTATACATAACTTACA
Found at i:23817354 original size:22 final size:21
Alignment explanation
Indices: 23817319--23817370 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
23817309 TTACATAACT
23817319 AATTACACTTATATTATACATA
1 AATTACA-TTATATTATACATA
* *
23817341 ACTTACATTAATATTATACTTA
1 AATTACATT-ATATTATACATA
23817363 AATTACAT
1 AATTACAT
23817371 AAGTTAGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTACATTATATTATACATA
Found at i:23817409 original size:9 final size:9
Alignment explanation
Indices: 23817391--23817672 Score: 67
Period size: 9 Copynumber: 31.6 Consensus size: 9
23817381 ATTAATATTA
23817391 TACATAACT
1 TACATAACT
*
23817400 TACATCACT
1 TACATAACT
23817409 TAC--AACT
1 TACATAACT
*
23817416 TATATAACT
1 TACATAACT
*
23817425 TACATTAATATT
1 TACA-T-A-ACT
* *
23817437 ATACTTAAAT
1 -TACATAACT
*
23817447 TACATAAGT
1 TACATAACT
**
23817456 TAGTTAA-T
1 TACATAACT
*
23817464 TA-AT-ATT
1 TACATAACT
23817471 ATACATAACT
1 -TACATAACT
*
23817481 TACATCACT
1 TACATAACT
23817490 TAC--AACT
1 TACATAACT
*
23817497 TATATAACT
1 TACATAACT
*
23817506 TACATTAATATT
1 TACA-T-A-ACT
* *
23817518 ATACTTAAAT
1 -TACATAACT
*
23817528 TACATAAGT
1 TACATAACT
**
23817537 TAGTTAA-T
1 TACATAACT
*
23817545 TA-AT-ATT
1 TACATAACT
23817552 ATACATAACT
1 -TACATAACT
*
23817562 TACATCACT
1 TACATAACT
23817571 TAC--AACT
1 TACATAACT
*
23817578 TATATAACT
1 TACATAACT
*
23817587 TACATTAATATT
1 TACA-T-A-ACT
* *
23817599 ATACTTAAAT
1 -TACATAACT
*
23817609 TACATAAGT
1 TACATAACT
**
23817618 TAGTTAA-T
1 TACATAACT
*
23817626 TA-AT-ATT
1 TACATAACT
23817633 ATACATAACT
1 -TACATAACT
23817643 TACATAACT
1 TACATAACT
23817652 TAC--AACT
1 TACATAACT
23817659 TACATAACT
1 TACATAACT
23817668 TACAT
1 TACAT
23817673 TTTTTTTAAT
Statistics
Matches: 202, Mismatches: 39, Indels: 64
0.66 0.13 0.21
Matches are distributed among these distances:
6 3 0.01
7 28 0.14
8 15 0.07
9 117 0.58
10 15 0.07
11 6 0.03
12 9 0.04
13 9 0.04
ACGTcount: A:0.43, C:0.15, G:0.02, T:0.40
Consensus pattern (9 bp):
TACATAACT
Found at i:23817435 original size:81 final size:81
Alignment explanation
Indices: 23817338--23817673 Score: 654
Period size: 81 Copynumber: 4.1 Consensus size: 81
23817328 TATATTATAC
23817338 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTAC
1 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTAC
23817403 ATCACTTACAACTTAT
66 ATCACTTACAACTTAT
23817419 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTAC
1 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTAC
23817484 ATCACTTACAACTTAT
66 ATCACTTACAACTTAT
23817500 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTAC
1 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTAC
23817565 ATCACTTACAACTTAT
66 ATCACTTACAACTTAT
23817581 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTAC
1 ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTAC
* *
23817646 ATAACTTACAACTTAC
66 ATCACTTACAACTTAT
23817662 ATAACTTACATT
1 ATAACTTACATT
23817674 TTTTTTAATT
Statistics
Matches: 253, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 253 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.40
Consensus pattern (81 bp):
ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTAC
ATCACTTACAACTTAT
Found at i:23817545 original size:162 final size:162
Alignment explanation
Indices: 23817272--23817673 Score: 657
Period size: 162 Copynumber: 2.4 Consensus size: 162
23817262 TAAAATAATT
* * *
23817272 CTTAAATTACATAAGTTAGTTAATTAA-A--ATACATAAATTACATAACTAATTACACTTATATT
1 CTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACAT--C-ACTTACA---A-CTT
23817334 ATACATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAAC
59 AT--ATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAAC
23817399 TTACATCACTTACAACTTATATAACTTACATTAATATTATA
122 TTACATCACTTACAACTTATATAACTTACATTAATATTATA
23817440 CTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACATCACTTACAACTTATATAAC
1 CTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACATCACTTACAACTTATATAAC
23817505 TTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACATCAC
66 TTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACATCAC
23817570 TTACAACTTATATAACTTACATTAATATTATA
131 TTACAACTTATATAACTTACATTAATATTATA
* *
23817602 CTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACATAACTTACAACTTACATAAC
1 CTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACATCACTTACAACTTATATAAC
23817667 TTACATT
66 TTACATT
23817674 TTTTTTAATT
Statistics
Matches: 226, Mismatches: 5, Indels: 12
0.93 0.02 0.05
Matches are distributed among these distances:
162 172 0.76
164 4 0.02
165 1 0.00
168 33 0.15
169 2 0.01
171 14 0.06
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.40
Consensus pattern (162 bp):
CTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACATCACTTACAACTTATATAAC
TTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACATCAC
TTACAACTTATATAACTTACATTAATATTATA
Found at i:23817660 original size:16 final size:16
Alignment explanation
Indices: 23817639--23817671 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
23817629 TATTATACAT
23817639 AACTTACATAACTTAC
1 AACTTACATAACTTAC
23817655 AACTTACATAACTTAC
1 AACTTACATAACTTAC
23817671 A
1 A
23817672 TTTTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:23817734 original size:9 final size:9
Alignment explanation
Indices: 23817693--23817776 Score: 50
Period size: 9 Copynumber: 9.8 Consensus size: 9
23817683 TATTCGTAAA
23817693 TTACATAAC
1 TTACATAAC
* *
23817702 TTACTTAAT
1 TTACATAAC
*
23817711 TTTCATAA-
1 TTACATAAC
*
23817719 -TAAATAAC
1 TTACATAAC
*
23817727 TTACATAAA
1 TTACATAAC
* *
23817736 TAAC-T-TC
1 TTACATAAC
23817743 TTACATAAC
1 TTACATAAC
** *
23817752 TTATGTGAC
1 TTACATAAC
23817761 TTACATAAC
1 TTACATAAC
23817770 TTACATA
1 TTACATA
23817777 GCATAATTTT
Statistics
Matches: 52, Mismatches: 19, Indels: 8
0.66 0.24 0.10
Matches are distributed among these distances:
7 8 0.15
8 2 0.04
9 42 0.81
ACGTcount: A:0.42, C:0.17, G:0.02, T:0.39
Consensus pattern (9 bp):
TTACATAAC
Found at i:23817776 original size:162 final size:160
Alignment explanation
Indices: 23817274--23817776 Score: 471
Period size: 162 Copynumber: 3.1 Consensus size: 160
23817264 AAATAATTCT
* *
23817274 TAAATTACATAAGTTAGTTAATTAA-A--ATACATAAATTACATAACTAATTACACTTATATTAT
1 TAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACATAAC---TT--AC--A-ACT-T
* * * * *
23817336 ACATAACTTACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTT
57 ACATAACTTACATTAATATTATACGTAAATTACATAACTTACTTAATTAATATAATAAATAACTT
* * * * * * *
23817401 ACATCACTTACAACTTATATAACTTACATTAATATTATACT
122 ACATAAATAACAACTTACATAACTTA-ATT-AGACTATACA
* *
23817442 TAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACATCACTTACAACTTATATAACTT
1 TAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACATAACTTACAACTTACATAACTT
* * * * * * * *
23817507 ACATTAATATTATACTTAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACATCACTT
66 ACATTAATATTATACGTAAATTACATAACTTACTTAATTAATATAATAAATAACTTACATAAATA
* * * *
23817572 ACAACTTATATAACTTACATTAATATTATACT
131 ACAACTTACATAACTTA-ATT-AGACTATACA
23817604 TAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACATAACTTACAACTTACATAACTT
1 TAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACATAACTTACAACTTACATAACTT
** * *
23817669 ACATTTTTTTTAATTATTCGTAAATTACATAACTTACTTAATT-TTCATAATAAATAACTTACAT
66 ACA---TTAAT-ATTATACGTAAATTACATAACTTACTTAATTAAT-ATAATAAATAACTTACAT
**
23817733 AAATAACTTCTTACATAACTT-ATGT-GACT-TACA
126 AAATAACAACTTACATAACTTAAT-TAGACTATACA
*
23817766 TAACTTACATA
1 TAAATTACATA
23817777 GCATAATTTT
Statistics
Matches: 301, Mismatches: 25, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
162 185 0.61
163 4 0.01
164 3 0.01
165 5 0.02
166 60 0.20
168 27 0.09
169 1 0.00
171 16 0.05
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.41
Consensus pattern (160 bp):
TAAATTACATAAGTTAGTTAATTAATATTATACATAACTTACATAACTTACAACTTACATAACTT
ACATTAATATTATACGTAAATTACATAACTTACTTAATTAATATAATAAATAACTTACATAAATA
ACAACTTACATAACTTAATTAGACTATACA
Found at i:23817807 original size:25 final size:25
Alignment explanation
Indices: 23817778--23817834 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
23817768 ACTTACATAG
* *
23817778 CATAATTTTCATAATACACAACTTA
1 CATAATTTGCATAATAAACAACTTA
** *
23817803 CATAATTTGGGTAATAAATAACTTA
1 CATAATTTGCATAATAAACAACTTA
23817828 CATAATT
1 CATAATT
23817835 AGGAAATACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (25 bp):
CATAATTTGCATAATAAACAACTTA
Found at i:23823382 original size:66 final size:65
Alignment explanation
Indices: 23823275--23823425 Score: 205
Period size: 66 Copynumber: 2.3 Consensus size: 65
23823265 GAGCAAATTA
* * *
23823275 CACAACTTAAAGCGGAGGCAACATCGAGAGAAACTGAGGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAACAGCGAGAGAAACTGAGGTTCAACAAAAG-TATGAAGAACTCCA
23823339 G
65 G
* * *
23823340 CTACAACTGAAAGCAGATGCAACAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAACAGCGAGAGAAACTGAGGTTCAACAAAAGTATGAAGAACTCCA
23823405 G
65 G
*
23823406 CAGCAGCTTAAAGCAGATGC
1 CA-CAACTTAAAGCAGATGC
23823426 GGCAACAAGA
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
65 2 0.03
66 69 0.92
67 4 0.05
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.14
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAACAGCGAGAGAAACTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:23823437 original size:66 final size:66
Alignment explanation
Indices: 23823276--23823445 Score: 182
Period size: 66 Copynumber: 2.6 Consensus size: 66
23823266 AGCAAATTAC
* * * * * *
23823276 ACAACTTAAAGCGGAGGCAACATCGAGAGAAACTGAGGTTCAAAAAAGATATGAAGAACTCCAGC
1 ACAACTGAAAGCAGATGCAACAACAAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGC
23823341 T
66 T
* * *
23823342 ACAACTGAAAGCAGATGCAACAGCGAGAGAAGCTGAGGTTCAACGAAAG-TATGAAGAACTCCAG
1 ACAACTGAAAGCAGATGCAACAACAAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAG
23823406 C-
65 CT
* * ** *
23823407 AGCAGCTTAAAGCAGATGCGGCAACAAGAGAAGCAGAGG
1 A-CAACTGAAAGCAGATGCAACAACAAGAGAAGCTGAGG
23823446 CGGCAGCGTG
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 1 0.01
66 84 0.94
67 4 0.04
ACGTcount: A:0.42, C:0.19, G:0.26, T:0.12
Consensus pattern (66 bp):
ACAACTGAAAGCAGATGCAACAACAAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGC
T
Found at i:23823458 original size:21 final size:21
Alignment explanation
Indices: 23823416--23823528 Score: 91
Period size: 21 Copynumber: 5.4 Consensus size: 21
23823406 CAGCAGCTTA
* * *
23823416 AAGCAGATGCGGCAACAAGAG
1 AAGCAGAGGCGGCAGCGAGAG
*
23823437 AAGCAGAGGCGGCAGCGTGAG
1 AAGCAGAGGCGGCAGCGAGAG
* * * *
23823458 AAGTACAGGCTGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
*** *
23823479 AAGCAGAGGCTAAAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
* * *
23823500 AAGCAGAGACTGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
23823521 AAGCAGAG
1 AAGCAGAG
23823529 CAGCGTCAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.35, C:0.18, G:0.42, T:0.05
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:23823482 original size:42 final size:42
Alignment explanation
Indices: 23823436--23823528 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
23823426 GGCAACAAGA
** * * *
23823436 GAAGCAGAGGCGGCAGCGTGAGAAGTACAGGCTGCAGCGAGG
1 GAAGCAGAGGCGAAAGCGAGAGAAGCACAGACTGCAGCGAGG
* * *
23823478 GAAGCAGAGGCTAAAGCGAGGGAAGCAGAGACTGCAGCGAGG
1 GAAGCAGAGGCGAAAGCGAGAGAAGCACAGACTGCAGCGAGG
23823520 GAAGCAGAG
1 GAAGCAGAG
23823529 CAGCGTCAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.17, G:0.44, T:0.05
Consensus pattern (42 bp):
GAAGCAGAGGCGAAAGCGAGAGAAGCACAGACTGCAGCGAGG
Found at i:23823926 original size:43 final size:43
Alignment explanation
Indices: 23823879--23824039 Score: 196
Period size: 43 Copynumber: 3.7 Consensus size: 43
23823869 AGGCGTTGGC
* *
23823879 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATAAGGGT
** * * *
23823922 CTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATAAGGGT
** * * *
23823965 CTTTAGCGGCGTTTGTGGGGAAAACGCCGCTAAAGATTAGGTT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATAAGGGT
* *
23824008 CTTTAGTGGCGTTTGTGGTCGAAGCGCCGCTA
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTA
23824040 TATGATTTAT
Statistics
Matches: 99, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 99 1.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATAAGGGT
Found at i:23826198 original size:73 final size:73
Alignment explanation
Indices: 23826112--23826257 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
23826102 TTTTCAAAAC
23826112 TCAAATTAGACTCTTTTTTTTTTTACAAATTTTAGAGTGTCGGGGCACTTGTCCACAATAGAACT
1 TCAAATTAGACTCTTTTTTTTTTTACAAATTTTAGAGTGTCGGGGCACTTGTCCACAATAGAACT
23826177 TAGGTAAA
66 TAGGTAAA
*
23826185 TCAAATTAGACTCTTTTTTTTTTTACAAATTTTAGAGTGTCGGGTCACTTGTCCACAATAGAACT
1 TCAAATTAGACTCTTTTTTTTTTTACAAATTTTAGAGTGTCGGGGCACTTGTCCACAATAGAACT
23826250 TAGGTAAA
66 TAGGTAAA
23826258 GAAATATCGA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (73 bp):
TCAAATTAGACTCTTTTTTTTTTTACAAATTTTAGAGTGTCGGGGCACTTGTCCACAATAGAACT
TAGGTAAA
Found at i:23833949 original size:44 final size:43
Alignment explanation
Indices: 23833900--23833988 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 43
23833890 CAATTGTAAC
* * *
23833900 TTAAATTTTAATTATTTTTAAATGTGTAATTATCACAACTTCTA
1 TTAAATTATAATTATTTCTAAATGTATAATTATCA-AACTTCTA
*
23833944 TTAAATTATAATTATTTCTAAATGTATAATTATCAATCTTCTA
1 TTAAATTATAATTATTTCTAAATGTATAATTATCAAACTTCTA
23833987 TT
1 TT
23833989 TTATTTCAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 9 0.22
44 32 0.78
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (43 bp):
TTAAATTATAATTATTTCTAAATGTATAATTATCAAACTTCTA
Found at i:23842288 original size:15 final size:15
Alignment explanation
Indices: 23842240--23842300 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 15
23842230 TGATGAACTA
**
23842240 AAAAATTAAGTGCTG
1 AAAAATTAAGTATTG
* * *
23842255 AAAAAATAAGCATTA
1 AAAAATTAAGTATTG
23842270 AAAAATTAAGTATTG
1 AAAAATTAAGTATTG
* *
23842285 AAAATTTAAATATTG
1 AAAAATTAAGTATTG
23842300 A
1 A
23842301 GTTTAAGTTA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.30
Consensus pattern (15 bp):
AAAAATTAAGTATTG
Found at i:23844225 original size:14 final size:15
Alignment explanation
Indices: 23844193--23844231 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
23844183 GGGAAGAGAG
23844193 AAAAATAAAAAAATA
1 AAAAATAAAAAAATA
* *
23844208 AAAAATAATAAGAT-
1 AAAAATAAAAAAATA
23844222 AAAAATAAAA
1 AAAAATAAAA
23844232 TTGATTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (15 bp):
AAAAATAAAAAAATA
Found at i:23845993 original size:3 final size:3
Alignment explanation
Indices: 23845985--23846014 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
23845975 CAACTTATCT
23845985 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
23846015 GCAAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:23850652 original size:17 final size:17
Alignment explanation
Indices: 23850614--23850653 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
23850604 CTCACCTATT
23850614 ATCCT-TCACTTTTTTC
1 ATCCTATCACTTTTTTC
23850630 -TCCTATCA-TTTTGTTC
1 ATCCTATCACTTTT-TTC
23850646 ATCCTATC
1 ATCCTATC
23850654 TTTCCTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.38
16 6 0.29
17 7 0.33
ACGTcount: A:0.15, C:0.30, G:0.03, T:0.53
Consensus pattern (17 bp):
ATCCTATCACTTTTTTC
Found at i:23851335 original size:13 final size:13
Alignment explanation
Indices: 23851317--23851342 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23851307 ATGACGCCAA
23851317 AAAATTTTATATT
1 AAAATTTTATATT
23851330 AAAATTTTATATT
1 AAAATTTTATATT
23851343 GGTATCAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAATTTTATATT
Found at i:23853874 original size:27 final size:27
Alignment explanation
Indices: 23853792--23853874 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 27
23853782 TCTCGGCGGG
* * *
23853792 CTACCCCGCATTTAATGTCCCAACAAA
1 CTACCCAGCATTTAATGTCTCGACAAA
* * *
23853819 ATACCTAGCATTTAATGTCTCGACGAA
1 CTACCCAGCATTTAATGTCTCGACAAA
*
23853846 CTACCCAGCGTTTAATGTCAT-GACAAA
1 CTACCCAGCATTTAATGTC-TCGACAAA
23853873 CT
1 CT
23853875 CTCTATGTTG
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
27 44 0.98
28 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.27
Consensus pattern (27 bp):
CTACCCAGCATTTAATGTCTCGACAAA
Found at i:23854008 original size:67 final size:67
Alignment explanation
Indices: 23853855--23854254 Score: 414
Period size: 67 Copynumber: 6.0 Consensus size: 67
23853845 ACTACCCAGC
* ** * * * *
23853855 GTTTAATGTCATGACAAACTCTCTATGTTGTCATAGCCGAGCCAAGGTCTTACACA-CATACCCC
1 GTTTAATGTCCTGACGGACTCTCTATGTTGCCATAGCCGAGCTATGGTCTTACACATTATACCCC
23853919 AT
66 AT
* * * * *
23853921 GTTTAATTTCCT-AGCAGACTCT-TCAGGTTGCCATAGCCGAGCTATAGTCTTACACGTTATACC
1 GTTTAATGTCCTGA-CGGACTCTCT-ATGTTGCCATAGCCGAGCTATGGTCTTACACATTATACC
23853984 CCAT
64 CCAT
* **
23853988 GTTTAATGTCCTGACGGACTCTTTATGTTGCCATAGTTGCA-CTATGGTCTTACACATTATACCC
1 GTTTAATGTCCTGACGGACTCTCTATGTTGCCATAGCCG-AGCTATGGTCTTACACATTATACCC
23854052 CAT
65 CAT
** * ** ** *
23854055 GTTTAATGTCCTGGTGTACTCTCTATGTTTTCATAGTTGAGCTATGGTCTTACACATTATACCAC
1 GTTTAATGTCCTGACGGACTCTCTATGTTGCCATAGCCGAGCTATGGTCTTACACATTATACCCC
23854120 AT
66 AT
* * * * * *
23854122 GCTTAATGTCCTGACGAACTCTCTATGTTGCCATAGTCAAGTTATGGTCTTAAACATTATA-CCC
1 GTTTAATGTCCTGACGGACTCTCTATGTTGCCATAGCCGAGCTATGGTCTTACACATTATACCCC
23854186 AT
66 AT
* ** * * * *
23854188 GCTTAATGTTTTGGCGGACTCTCTATGTTTCCATAGCCGAGCTATGGTTTTACAAATTATACCCC
1 GTTTAATGTCCTGACGGACTCTCTATGTTGCCATAGCCGAGCTATGGTCTTACACATTATACCCC
23854253 AT
66 AT
23854255 TATAGTCCAT
Statistics
Matches: 280, Mismatches: 46, Indels: 15
0.82 0.13 0.04
Matches are distributed among these distances:
65 2 0.01
66 98 0.35
67 177 0.63
68 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (67 bp):
GTTTAATGTCCTGACGGACTCTCTATGTTGCCATAGCCGAGCTATGGTCTTACACATTATACCCC
AT
Found at i:23854208 original size:200 final size:200
Alignment explanation
Indices: 23853872--23854254 Score: 452
Period size: 200 Copynumber: 1.9 Consensus size: 200
23853862 GTCATGACAA
* * *
23853872 ACTCTCTATGTTGTCATAGCCGAGCCAAGGTCTTACACACATACCCCATGTTTAATTTCCTAGCA
1 ACTCTCTATGTTGTCATAGCCGAGCCAAGGTCTTACACACATACCACATGCTTAATGTCCTAGCA
* * * *
23853937 GACTCTTCAGGTTGCCATAGCCGAGCTATAGTCTTACACGTTATACCCCATGTTTAATGTCCTGA
66 GACTCTTCAGGTTGCCATAGCCAAGCTATAGTCTTAAACATTATACCCCATGCTTAATGTCCTGA
* ** *
23854002 CGGACTCTTTATGTTGCCATAGTTGCA-CTATGGTCTTACACATTATACCCCATGTTTAATGTCC
131 CGGACTCTCTATGTTGCCATAGCCG-AGCTATGGTCTTACAAATTATACCCCATGTTTAATGTCC
23854066 TGGTGT
195 TGGTGT
* ** * * *
23854072 ACTCTCTATGTTTTCATAGTTGAGCTATGGTCTTACACATTATACCACATGCTTAATGTCCT-G-
1 ACTCTCTATGTTGTCATAGCCGAGCCAAGGTCTTACACA-CATACCACATGCTTAATGTCCTAGC
* * * * *
23854135 ACGAACTC-TCTATGTTGCCATAGTCAAGTTATGGTCTTAAACATTATA-CCCATGCTTAATGTT
65 A-G-ACTCTTC-AGGTTGCCATAGCCAAGCTATAGTCTTAAACATTATACCCCATGCTTAATGTC
* * * *
23854198 TTGGCGGACTCTCTATGTTTCCATAGCCGAGCTATGGTTTTACAAATTATACCCCAT
127 CTGACGGACTCTCTATGTTGCCATAGCCGAGCTATGGTCTTACAAATTATACCCCAT
23854255 TATAGTCCAT
Statistics
Matches: 152, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
199 2 0.01
200 98 0.64
201 52 0.34
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (200 bp):
ACTCTCTATGTTGTCATAGCCGAGCCAAGGTCTTACACACATACCACATGCTTAATGTCCTAGCA
GACTCTTCAGGTTGCCATAGCCAAGCTATAGTCTTAAACATTATACCCCATGCTTAATGTCCTGA
CGGACTCTCTATGTTGCCATAGCCGAGCTATGGTCTTACAAATTATACCCCATGTTTAATGTCCT
GGTGT
Done.