Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 134 of 168
Found at i:39134171 original size:21 final size:23
Alignment explanation
Indices: 39134115--39134172 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
39134105 TAGTATTCAT
* * *
39134115 TTTTTTTCGAATTATTGATAGTA
1 TTTTTTGCTAATTACTGATAGTA
*
39134138 TTTTTTTCTAATTACTGATAGTA
1 TTTTTTGCTAATTACTGATAGTA
39134161 -TTTTTGC-AATTA
1 TTTTTTGCTAATTA
39134173 ATGCATTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 5 0.16
22 6 0.19
23 21 0.66
ACGTcount: A:0.26, C:0.07, G:0.10, T:0.57
Consensus pattern (23 bp):
TTTTTTGCTAATTACTGATAGTA
Found at i:39137939 original size:17 final size:17
Alignment explanation
Indices: 39137917--39138014 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
39137907 AATTCAAGAC
39137917 TTATGTAATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
39137934 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
*
39137953 CTTATGTAATATTTTTAA
1 -TTATGTAATGTTTTTAA
* ***
39137971 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
39137990 TTTATGTAATGTTTTTAA
1 -TTATGTAATGTTTTTAA
39138008 TTATGTA
1 TTATGTA
39138015 GTGATTTAAT
Statistics
Matches: 57, Mismatches: 18, Indels: 12
0.66 0.21 0.14
Matches are distributed among these distances:
17 24 0.42
18 8 0.14
19 8 0.14
20 17 0.30
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:39137959 original size:20 final size:19
Alignment explanation
Indices: 39137933--39137997 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
39137923 AATGTTTTTA
39137933 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
* ***
39137952 ACTTATGTAAT-ATTTTTA-
1 A-TTATGTAGTGATTCAAAG
39137970 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
39137989 ATTTATGTA
1 A-TTATGTA
39137998 ATGTTTTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 6 0.18
20 15 0.44
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (19 bp):
ATTATGTAGTGATTCAAAG
Found at i:39137962 original size:37 final size:37
Alignment explanation
Indices: 39137908--39138020 Score: 201
Period size: 37 Copynumber: 3.1 Consensus size: 37
39137898 TTATGTGTTA
39137908 ATTC-AAGACTTATGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATGTTTTTAATTATGTAGTG
*
39137944 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATGTTTTTAATTATGTAGTG
*
39137981 ATTCAAAGATTTATGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATGTTTTTAATTATGTAGTG
39138018 ATT
1 ATT
39138021 TAATTTGGGT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 4 0.05
37 69 0.95
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATGTTTTTAATTATGTAGTG
Found at i:39138049 original size:9 final size:9
Alignment explanation
Indices: 39138021--39138074 Score: 63
Period size: 9 Copynumber: 5.7 Consensus size: 9
39138011 TGTAGTGATT
39138021 TAATTTGGG
1 TAATTTGGG
*
39138030 TAAATTCGGG
1 T-AATTTGGG
39138040 TAATTTGGG
1 TAATTTGGG
39138049 TAATTTTCGGG
1 TAA-TTT-GGG
*
39138060 TAATTCGGG
1 TAATTTGGG
39138069 TAATTT
1 TAATTT
39138075 TTAACCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 19 0.50
10 13 0.34
11 6 0.16
ACGTcount: A:0.24, C:0.06, G:0.28, T:0.43
Consensus pattern (9 bp):
TAATTTGGG
Found at i:39138059 original size:20 final size:20
Alignment explanation
Indices: 39138021--39138075 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
39138011 TGTAGTGATT
*
39138021 TAATTTGGGTAA-ATTCGGG
1 TAATTTGGGTAATTTTCGGG
39138040 TAATTTGGGTAATTTTCGGG
1 TAATTTGGGTAATTTTCGGG
*
39138060 TAATTCGGGTAATTTT
1 TAATTTGGGTAATTTT
39138076 TAACCAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 12 0.36
20 21 0.64
ACGTcount: A:0.24, C:0.05, G:0.27, T:0.44
Consensus pattern (20 bp):
TAATTTGGGTAATTTTCGGG
Found at i:39138181 original size:28 final size:27
Alignment explanation
Indices: 39138138--39138215 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 27
39138128 ATTAACCGAA
*
39138138 AAAAATTTCGGTTCGGTTAACGGTTA-
1 AAAAATTTCGGGTCGGTTAACGGTTAT
*
39138164 AAAAATTTGGGAGGTCGGTTAATTCGGTTAT
1 AAAAATTT-CG-GGTCGGTTAA--CGGTTAT
*
39138195 AATAATTTCGGGTCGGTTAAC
1 AAAAATTTCGGGTCGGTTAAC
39138216 CGGTCGATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
26 8 0.19
27 2 0.05
28 9 0.21
29 10 0.23
30 7 0.16
31 7 0.16
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.35
Consensus pattern (27 bp):
AAAAATTTCGGGTCGGTTAACGGTTAT
Found at i:39149567 original size:23 final size:23
Alignment explanation
Indices: 39149541--39149587 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
39149531 TATGAAGTCA
39149541 TGAAAATAAAATATGTACTTTGT
1 TGAAAATAAAATATGTACTTTGT
39149564 TGAAAATAAAATATGTACTTTGT
1 TGAAAATAAAATATGTACTTTGT
39149587 T
1 T
39149588 TTCTATTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.40
Consensus pattern (23 bp):
TGAAAATAAAATATGTACTTTGT
Found at i:39153893 original size:2 final size:2
Alignment explanation
Indices: 39153886--39153921 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
39153876 TCAATCAACT
39153886 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39153922 GCTTCAGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39157201 original size:44 final size:44
Alignment explanation
Indices: 39157128--39157221 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
39157118 CATTATTTAT
* * * *
39157128 CACTTAATTCACTTATGAACTATTCTTTTACTAACTCCACATGC
1 CACTTAATTCACTTATAAAATATTATTTTACTAACTCCACATAC
*
39157172 CACTTAA-TCTACTTATAAAATATTATTTTACTAACTCTACATAC
1 CACTTAATTC-ACTTATAAAATATTATTTTACTAACTCCACATAC
39157216 CACTTA
1 CACTTA
39157222 TCACATTCAC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 2 0.05
44 42 0.95
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.39
Consensus pattern (44 bp):
CACTTAATTCACTTATAAAATATTATTTTACTAACTCCACATAC
Found at i:39158180 original size:12 final size:12
Alignment explanation
Indices: 39158163--39158187 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39158153 GGTATTCATT
39158163 CGGTTAACCGAC
1 CGGTTAACCGAC
39158175 CGGTTAACCGAC
1 CGGTTAACCGAC
39158187 C
1 C
39158188 CGAAATAACA
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:39158362 original size:9 final size:9
Alignment explanation
Indices: 39158348--39158405 Score: 71
Period size: 9 Copynumber: 6.4 Consensus size: 9
39158338 TTTGGTTAAA
39158348 AATTAACCG
1 AATTAACCG
*
39158357 AATTAACTG
1 AATTAACCG
*
39158366 AATTACCCG
1 AATTAACCG
*
39158375 AATTACCCG
1 AATTAACCG
*
39158384 AATTAACCA
1 AATTAACCG
*
39158393 AATTAACCA
1 AATTAACCG
39158402 AATT
1 AATT
39158406 GAATCACTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 44 1.00
ACGTcount: A:0.45, C:0.22, G:0.07, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:39158544 original size:18 final size:18
Alignment explanation
Indices: 39158504--39158547 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
39158494 TAATTTTATG
**
39158504 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
39158522 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
39158540 CTTGGGTT
1 ATTGGGTT
39158548 TAGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:39163986 original size:21 final size:20
Alignment explanation
Indices: 39163960--39163999 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
39163950 TAAAATTATT
*
39163960 AAAATTATATATTTTAAATTA
1 AAAATTATA-ATATTAAATTA
39163981 AAAATTATAATATTAAATT
1 AAAATTATAATATTAAATT
39164000 TATATATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATTATAATATTAAATTA
Found at i:39164212 original size:12 final size:12
Alignment explanation
Indices: 39164195--39164220 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39164185 GTATCCATAC
39164195 TTTATAGGATAA
1 TTTATAGGATAA
39164207 TTTATAGGATAA
1 TTTATAGGATAA
39164219 TT
1 TT
39164221 GGTAGGATTA
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:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
TTTATAGGATAA
Found at i:39165314 original size:46 final size:46
Alignment explanation
Indices: 39165264--39165359 Score: 183
Period size: 46 Copynumber: 2.1 Consensus size: 46
39165254 ATTCATATAT
39165264 TAATTTTAACTATGTTCTCTATTTATATAGAACAAGTTTGTACATA
1 TAATTTTAACTATGTTCTCTATTTATATAGAACAAGTTTGTACATA
*
39165310 TAATTTTAACTATGTTCTCTATTTATATATAACAAGTTTGTACATA
1 TAATTTTAACTATGTTCTCTATTTATATAGAACAAGTTTGTACATA
39165356 TAAT
1 TAAT
39165360 GTGTTCAATG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (46 bp):
TAATTTTAACTATGTTCTCTATTTATATAGAACAAGTTTGTACATA
Found at i:39165342 original size:23 final size:23
Alignment explanation
Indices: 39165270--39165342 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
39165260 ATATTAATTT
39165270 TAACTATGTTCTCTATTTATATA
1 TAACTATGTTCTCTATTTATATA
* * * ** *
39165293 GAAC-AAGTT-TGTACATATAATTT
1 TAACTATGTTCTCTATTTAT-A-TA
39165316 TAACTATGTTCTCTATTTATATA
1 TAACTATGTTCTCTATTTATATA
39165339 TAAC
1 TAAC
39165343 AAGTTTGTAC
Statistics
Matches: 34, Mismatches: 12, Indels: 8
0.63 0.22 0.15
Matches are distributed among these distances:
21 6 0.18
22 5 0.15
23 12 0.35
24 5 0.15
25 6 0.18
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (23 bp):
TAACTATGTTCTCTATTTATATA
Found at i:39167131 original size:88 final size:88
Alignment explanation
Indices: 39166946--39167248 Score: 419
Period size: 89 Copynumber: 3.4 Consensus size: 88
39166936 TTAAGGATAC
* * * ** * * *
39166946 AAAAA-ACTCTCAAACTTTTTCAAAAAAAGTAATTAAGTCATTACTTTTTTTTGCACTCATTTAG
1 AAAAATACACTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTCCACTCAATTGG
* *
39167010 GTACTTAAACTTTCAAAATACATA
66 GTACTT-GACTTTCAAAATGCATA
*
39167034 AAAAATACACTCAAACTTTTTCGAAAAAAGCAATTAAGCCCCTACTTTTTTTTCCACTCAATTGG
1 AAAAATACACTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTCCACTCAATTGG
* *
39167099 GTACATGACTTTCAAAATGCATC
66 GTACTTGACTTTCAAAATGCATA
* * *
39167122 AAAAATACACTCAAACCTTTTCGAAAAAAGCAATTAAGCCCCTACTTTTTTTTCCATTCAATTGG
1 AAAAATACACTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTCCACTCAATTGG
39167187 GTACTTGAACTTTCAAAATGCATA
66 GTACTTG-ACTTTCAAAATGCATA
* *
39167211 AAAAAGACCCTCAAACTTTTTCAAAAAAAGCAATTAAG
1 AAAAATACACTCAAACTTTTTCAAAAAAAGCAATTAAG
39167249 TCCATTTTTT
Statistics
Matches: 192, Mismatches: 21, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
88 88 0.46
89 104 0.54
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (88 bp):
AAAAATACACTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTCCACTCAATTGG
GTACTTGACTTTCAAAATGCATA
Found at i:39167372 original size:28 final size:27
Alignment explanation
Indices: 39167341--39167429 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 27
39167331 TAAAAGTTAG
*
39167341 AAAAAATATAAAAATGGTAAAAAAATAT
1 AAAATATATAAAAAT-GTAAAAAAATAT
* *
39167369 AAAATTTTATAAAAATCGT-AAAAATTAT
1 AAAA-TATATAAAAAT-GTAAAAAAATAT
* *
39167397 AAAATATATAGAAATATAAAAAAATTAT
1 AAAATATATAAAAATGTAAAAAAA-TAT
39167425 AAAAT
1 AAAAT
39167430 TTTATAAAGC
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
26 1 0.02
27 14 0.28
28 24 0.48
29 11 0.22
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (27 bp):
AAAATATATAAAAATGTAAAAAAATAT
Found at i:39167382 original size:19 final size:19
Alignment explanation
Indices: 39167341--39167437 Score: 69
Period size: 19 Copynumber: 5.2 Consensus size: 19
39167331 TAAAAGTTAG
**
39167341 AAAAAATATAAAAATGGTA-
1 AAAAAATAT-AAAATTTTAT
39167360 AAAAAATATAAAATTTTAT
1 AAAAAATATAAAATTTTAT
* *
39167379 -AAAAATCGTAAAA-ATTAT
1 AAAAAAT-ATAAAATTTTAT
* *
39167397 AAAATATATAGAAA-TATA-
1 AAAAAATATA-AAATTTTAT
39167415 AAAAAATTATAAAATTTTAT
1 AAAAAA-TATAAAATTTTAT
39167435 AAA
1 AAA
39167438 GCCGTAAGAA
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
18 27 0.44
19 31 0.51
20 3 0.05
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (19 bp):
AAAAAATATAAAATTTTAT
Found at i:39167391 original size:56 final size:56
Alignment explanation
Indices: 39167331--39167437 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
39167321 TAAATTTTAT
* *
39167331 TAAAAGTTAGAAAAAATATAAAAATGGTAAAAAAA-TATAAAATTTTATAAAAATCG
1 TAAAAATTAGAAAAAATATAAAAAT-ATAAAAAAATTATAAAATTTTATAAAAATCG
* * *
39167387 TAAAAATTATAAAATATATAGAAATATAAAAAAATTATAAAATTTTATAAA
1 TAAAAATTAGAAAAAATATAAAAATATAAAAAAATTATAAAATTTTATAAA
39167438 GCCGTAAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 8 0.18
56 37 0.82
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.30
Consensus pattern (56 bp):
TAAAAATTAGAAAAAATATAAAAATATAAAAAAATTATAAAATTTTATAAAAATCG
Found at i:39167909 original size:88 final size:85
Alignment explanation
Indices: 39167805--39168057 Score: 337
Period size: 88 Copynumber: 2.9 Consensus size: 85
39167795 AACAAGAGCT
* *
39167805 TAATTGCTTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACTTAATT
1 TAATTGCTTTTTTGAAAAATTTTGAGGG-CTTTTTGATACATTTTGAAAGTTCAAGTACTCAATT
39167870 GAGTGAAAAAAAAACAGGGGCC
65 GAGTG-AAAAAAAACAGGGGCC
* * *
39167892 TAATTGCTTTTATTGAAAATTTTTGAGGGCCTTTTTGATACATTTTGAAAGTTTAAGTACCCAAT
1 TAATTGCTTTT-TTGAAAAATTTTGAGGG-CTTTTTGATACATTTTGAAAGTTCAAGTACTCAAT
* *
39167957 TGAGTGAAGAAAAATAGGGGCC
64 TGAGTGAAAAAAAACAGGGGCC
* * *
39167979 TAATTGCTTTTTTTGAAGAAA-TTTGAGGGCTTTTTGATACATTTTAAAAATTCAAGTGCTCAAT
1 TAATTGC-TTTTTTGAA-AAATTTTGAGGGCTTTTTGATACATTTTGAAAGTTCAAGTACTCAAT
*
39168043 TAAGTGCAAAAAAAA
64 TGAGTG-AAAAAAAA
39168058 GAAACATAAA
Statistics
Matches: 146, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
86 35 0.24
87 52 0.36
88 59 0.40
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.37
Consensus pattern (85 bp):
TAATTGCTTTTTTGAAAAATTTTGAGGGCTTTTTGATACATTTTGAAAGTTCAAGTACTCAATTG
AGTGAAAAAAAACAGGGGCC
Found at i:39168354 original size:22 final size:23
Alignment explanation
Indices: 39168335--39168401 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
39168325 TCCTTTTTTG
39168335 CATTTTATATATTCCATTTTTAA
1 CATTTTATATATTCCATTTTTAA
* **
39168358 CATTTTATAATTTTTAATTTTTAA
1 CATTTTAT-ATATTCCATTTTTAA
** *
39168382 TTTTTTGTA-ATTCCATTTTT
1 CATTTTATATATTCCATTTTT
39168402 TTTAAAAAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
22 8 0.24
23 9 0.26
24 17 0.50
ACGTcount: A:0.27, C:0.09, G:0.01, T:0.63
Consensus pattern (23 bp):
CATTTTATATATTCCATTTTTAA
Found at i:39187777 original size:22 final size:21
Alignment explanation
Indices: 39187739--39187782 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
39187729 AAGGAAATAG
39187739 AAGAGTGGAAAAGAAAAAGAAA
1 AAGAGTGGAAAAGAAAAA-AAA
*
39187761 AAGAGTTGGTAAA-AAAAAAAA
1 AAGAG-TGGAAAAGAAAAAAAA
39187782 A
1 A
39187783 GTAAAAGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 10 0.50
23 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.09
Consensus pattern (21 bp):
AAGAGTGGAAAAGAAAAAAAA
Found at i:39189987 original size:43 final size:43
Alignment explanation
Indices: 39189926--39190041 Score: 171
Period size: 43 Copynumber: 2.7 Consensus size: 43
39189916 ACGGGTACAG
* *
39189926 ACACGGGCTGGGACACGGCCGTGTGTCTCTATTTCGAATGCCC
1 ACACGGCCTGGGACACGGCCGTGTGTCCCTATTTCGAATGCCC
*
39189969 ACACGGCCTGGGACACGGCCGTGTGTCCCTATTTTGAATGCCC
1 ACACGGCCTGGGACACGGCCGTGTGTCCCTATTTCGAATGCCC
* *
39190012 ACACGGCCTGAGACACAGG-CGTTTGTCCCT
1 ACACGGCCTGGGACAC-GGCCGTGTGTCCCT
39190042 TGTACCTTTG
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
43 65 0.97
44 2 0.03
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.22
Consensus pattern (43 bp):
ACACGGCCTGGGACACGGCCGTGTGTCCCTATTTCGAATGCCC
Found at i:39192559 original size:4 final size:4
Alignment explanation
Indices: 39192544--39192573 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
39192534 TATGAAATGT
*
39192544 TTTA TCTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
39192574 ATTCCTTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:39194169 original size:24 final size:24
Alignment explanation
Indices: 39194153--39194205 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
39194143 TAATCAAAGT
39194153 TAAATATATTATGCTAATAAATGC
1 TAAATATATTATGCTAATAAATGC
* * *
39194177 TAAATATATTATACTCATAAATAC
1 TAAATATATTATGCTAATAAATGC
39194201 TAAAT
1 TAAAT
39194206 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (24 bp):
TAAATATATTATGCTAATAAATGC
Found at i:39214537 original size:31 final size:29
Alignment explanation
Indices: 39214491--39214564 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 29
39214481 GTTAATACAG
* * *
39214491 TAAACAAACCTTTAAATTACTATATTTTGTT
1 TAAATAAACCCTTAAATTA-TATATATTG-T
* *
39214522 TAAATAAACCCTTAAATTATTTCTATTGT
1 TAAATAAACCCTTAAATTATATATATTGT
39214551 TAAATAAACCCTTA
1 TAAATAAACCCTTA
39214565 TTTTATAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 15 0.39
30 6 0.16
31 17 0.45
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.42
Consensus pattern (29 bp):
TAAATAAACCCTTAAATTATATATATTGT
Found at i:39216580 original size:18 final size:19
Alignment explanation
Indices: 39216559--39216601 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
39216549 TGTTTGAAAC
39216559 ATTTTTAACATTAT-TTTT
1 ATTTTTAACATTATGTTTT
*
39216577 ATTTTTTACATTATGTTTT
1 ATTTTTAACATTATGTTTT
39216596 -TTTTTA
1 ATTTTTA
39216602 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (19 bp):
ATTTTTAACATTATGTTTT
Found at i:39218029 original size:14 final size:13
Alignment explanation
Indices: 39218000--39218028 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39217990 CAAATATATA
39218000 ATATTTTAAAAAT
1 ATATTTTAAAAAT
39218013 ATATTTTAAAAA-
1 ATATTTTAAAAAT
39218025 ATAT
1 ATAT
39218029 AAATTACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATTTTAAAAAT
Found at i:39219362 original size:17 final size:19
Alignment explanation
Indices: 39219329--39219363 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
39219319 ATTGTTTGGA
39219329 TATTGTATAACTTTTGTTT
1 TATTGTATAACTTTTGTTT
39219348 TATTGT-TAA-TTTTGTT
1 TATTGTATAACTTTTGTT
39219364 ACCATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (19 bp):
TATTGTATAACTTTTGTTT
Found at i:39226951 original size:2 final size:2
Alignment explanation
Indices: 39226944--39226975 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39226934 CACAACTCAC
39226944 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
39226976 AGAACCCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39232140 original size:17 final size:17
Alignment explanation
Indices: 39232118--39232152 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39232108 CATACAAATT
39232118 AATAAA-AATATTTTAAA
1 AATAAACAA-ATTTTAAA
39232135 AATAAACAAATTTTAAA
1 AATAAACAAATTTTAAA
39232152 A
1 A
39232153 TTTTCATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AATAAACAAATTTTAAA
Found at i:39234609 original size:100 final size:99
Alignment explanation
Indices: 39234329--39234628 Score: 464
Period size: 100 Copynumber: 3.0 Consensus size: 99
39234319 ACAATAAAAC
* * *
39234329 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATCCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
*
39234394 TTTAGAATCCTAAACTCGGAATATTTCCTT-T-A
66 TTTAGAATCCCAAACTCGGAATATTTCCTTATGA
*
39234426 CTTTAAAAGAACATCCACTTATCAAAGATTTAAGAAATCACA-CCAATACGTTAGGGCACAATTC
1 -TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTC
*
39234490 CTTTAGAATCTCAAACTCGGAATATTTCCTTCATGA
65 CTTTAGAATCCCAAACTCGGAATATTTCCTT-ATGA
*
39234526 TTTAAAAGAA-AGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTC
1 TTTAAAAGAACA-TCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTC
*
39234590 CTTTAAAATCCCAAACTCGGAATATTTCCTTTATGA
65 CTTTAGAATCCCAAACTCGGAATATTTCC-TTATGA
39234626 TTT
1 TTT
39234629 TTAAAAAATC
Statistics
Matches: 186, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
97 49 0.26
98 40 0.22
99 38 0.20
100 57 0.31
101 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (99 bp):
TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
TTTAGAATCCCAAACTCGGAATATTTCCTTATGA
Found at i:39235374 original size:26 final size:25
Alignment explanation
Indices: 39235331--39235380 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
39235321 ATATTAATTG
* *
39235331 AAAAATATAATATGTACATATATAT
1 AAAAAAATAATATATACATATATAT
39235356 AAAAAAATAATTATATACATATATA
1 AAAAAAATAA-TATATACATATATA
39235381 GATTATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (25 bp):
AAAAAAATAATATATACATATATAT
Found at i:39235583 original size:3 final size:3
Alignment explanation
Indices: 39235570--39235627 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
39235560 TTGTATGTAC
* *
39235570 ATA AAA ATA ATA ATT A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39235617 ATA ATA ATA AT
1 ATA ATA ATA AT
39235628 GATGAGGAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 1 0.02
3 49 0.98
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39237854 original size:15 final size:15
Alignment explanation
Indices: 39237834--39237864 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
39237824 AAACCTTTGC
39237834 GAACAATCACAACTT
1 GAACAATCACAACTT
39237849 GAACAATCACAACTT
1 GAACAATCACAACTT
39237864 G
1 G
39237865 TAGCCTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.26, G:0.10, T:0.19
Consensus pattern (15 bp):
GAACAATCACAACTT
Found at i:39239952 original size:21 final size:21
Alignment explanation
Indices: 39239914--39239954 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39239904 AATCTCGAAG
**
39239914 GCTAAATAGAATTACATAAGT
1 GCTAAATAGAAACACATAAGT
*
39239935 GCTAAATAGAAACCCATAAG
1 GCTAAATAGAAACACATAAG
39239955 GGTTGAACAG
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:0.49, C:0.15, G:0.15, T:0.22
Consensus pattern (21 bp):
GCTAAATAGAAACACATAAGT
Found at i:39241040 original size:3 final size:3
Alignment explanation
Indices: 39240981--39241021 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
39240971 AGATAAAAAA
*
39240981 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG GA- AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
39241022 GAAAACAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 3 0.09
3 31 0.91
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39241185 original size:2 final size:2
Alignment explanation
Indices: 39241178--39241205 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39241168 CTTTTTATCA
39241178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39241206 TAATTGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39242882 original size:20 final size:20
Alignment explanation
Indices: 39242843--39242882 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39242833 TTCAAATATC
* *
39242843 AAAAATAACATTTTAGAAGA
1 AAAAATAACATATTAAAAGA
*
39242863 AAAAATATCATATTAAAAGA
1 AAAAATAACATATTAAAAGA
39242883 TTTGATAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (20 bp):
AAAAATAACATATTAAAAGA
Found at i:39246289 original size:2 final size:2
Alignment explanation
Indices: 39246284--39246308 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39246274 GATGTGTGGG
39246284 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39246309 TATCTCCGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39246580 original size:327 final size:327
Alignment explanation
Indices: 39245986--39246633 Score: 1296
Period size: 327 Copynumber: 2.0 Consensus size: 327
39245976 TACATGGAGA
39245986 TCCGTGCTGCTGATGTACTAACAGATCTACCACCGGAACTGACAAGTGCAGTTTTTGGTCAGAAG
1 TCCGTGCTGCTGATGTACTAACAGATCTACCACCGGAACTGACAAGTGCAGTTTTTGGTCAGAAG
39246051 CACGGAGTTGTAATTGGTGAAGCACATCTTGAGGAATTATTTTCTCAAATTCCTTGATATGGTGG
66 CACGGAGTTGTAATTGGTGAAGCACATCTTGAGGAATTATTTTCTCAAATTCCTTGATATGGTGG
39246116 GTACTTTTAACTAAAATCTTAGAACTTGCATGTTTGATGCATGGTCTTGAGCACTTAAAACTGCT
131 GTACTTTTAACTAAAATCTTAGAACTTGCATGTTTGATGCATGGTCTTGAGCACTTAAAACTGCT
39246181 ACTGTACAAATATGTTTCCAATACTGTTATATATGTCGTGTGCCACAAGCCTGCAAAAATGAAGG
196 ACTGTACAAATATGTTTCCAATACTGTTATATATGTCGTGTGCCACAAGCCTGCAAAAATGAAGG
39246246 AAAACAACATACTTACAGCAATATTGTTGATGTGTGGGTATATATATATATATATATATATATTA
261 AAAACAACATACTTACAGCAATATTGTTGATGTGTGGGTATATATATATATATATATATATATTA
39246311 TC
326 TC
39246313 TCCGTGCTGCTGATGTACTAACAGATCTACCACCGGAACTGACAAGTGCAGTTTTTGGTCAGAAG
1 TCCGTGCTGCTGATGTACTAACAGATCTACCACCGGAACTGACAAGTGCAGTTTTTGGTCAGAAG
39246378 CACGGAGTTGTAATTGGTGAAGCACATCTTGAGGAATTATTTTCTCAAATTCCTTGATATGGTGG
66 CACGGAGTTGTAATTGGTGAAGCACATCTTGAGGAATTATTTTCTCAAATTCCTTGATATGGTGG
39246443 GTACTTTTAACTAAAATCTTAGAACTTGCATGTTTGATGCATGGTCTTGAGCACTTAAAACTGCT
131 GTACTTTTAACTAAAATCTTAGAACTTGCATGTTTGATGCATGGTCTTGAGCACTTAAAACTGCT
39246508 ACTGTACAAATATGTTTCCAATACTGTTATATATGTCGTGTGCCACAAGCCTGCAAAAATGAAGG
196 ACTGTACAAATATGTTTCCAATACTGTTATATATGTCGTGTGCCACAAGCCTGCAAAAATGAAGG
39246573 AAAACAACATACTTACAGCAATATTGTTGATGTGTGGGTATATATATATATATATATATAT
261 AAAACAACATACTTACAGCAATATTGTTGATGTGTGGGTATATATATATATATATATATAT
39246634 TATCTTTGAT
Statistics
Matches: 321, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
327 321 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (327 bp):
TCCGTGCTGCTGATGTACTAACAGATCTACCACCGGAACTGACAAGTGCAGTTTTTGGTCAGAAG
CACGGAGTTGTAATTGGTGAAGCACATCTTGAGGAATTATTTTCTCAAATTCCTTGATATGGTGG
GTACTTTTAACTAAAATCTTAGAACTTGCATGTTTGATGCATGGTCTTGAGCACTTAAAACTGCT
ACTGTACAAATATGTTTCCAATACTGTTATATATGTCGTGTGCCACAAGCCTGCAAAAATGAAGG
AAAACAACATACTTACAGCAATATTGTTGATGTGTGGGTATATATATATATATATATATATATTA
TC
Found at i:39269894 original size:8 final size:8
Alignment explanation
Indices: 39269881--39269905 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
39269871 TTTTAAATGA
39269881 TATTTTAT
1 TATTTTAT
39269889 TATTTTAT
1 TATTTTAT
39269897 TATTTTAT
1 TATTTTAT
39269905 T
1 T
39269906 TAGTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:39276750 original size:102 final size:102
Alignment explanation
Indices: 39276587--39277037 Score: 613
Period size: 102 Copynumber: 4.4 Consensus size: 102
39276577 AGTGAAAATG
* *
39276587 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATGGATAAATAATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
* *
39276652 AGTACTAAGTGAATGCTACAATATGTACCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAACATGTACCGAGAAGCT
*
39276689 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTTACATGTGT
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
* *
39276754 AGTACTAAGTGAAGGCTACAATATGTATCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAACATGTACCGAGAAGCT
* *
39276791 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
* * *
39276856 AGTACTAAGTGAAGGCTACTACGTGTACCGAAAAGCT
66 AGTACTAAGTGAAGGCTACAACATGTACCGAGAAGCT
* * * * * *
39276893 TTAGTCACGTATGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACGTGTG
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTG
* ** * * **
39276956 TAGTACTATGTGAAGGCTATTACGTGAACCGTA-AA-AA
65 TAGTACTAAGTGAAGGCTACAACATGTACCG-AGAAGCT
* *
39276993 TTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
39277038 ATGATAATAA
Statistics
Matches: 315, Mismatches: 31, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
100 39 0.12
101 44 0.14
102 232 0.74
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (102 bp):
TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
AGTACTAAGTGAAGGCTACAACATGTACCGAGAAGCT
Found at i:39276878 original size:51 final size:51
Alignment explanation
Indices: 39276582--39277031 Score: 457
Period size: 51 Copynumber: 8.9 Consensus size: 51
39276572 ATGAAAGTGA
* * **
39276582 AAATGTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATGGAT
1 AAATATTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAT
* * * * * ** * *
39276633 AAATAATGGTCACATGTGTAGTACTAAGTGAATGCTACAATATGTACCGAG
1 AAATATTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAT
* *
39276684 AAGCT-TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGAT
1 AA-ATATTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAT
* * * * * ** * * *
39276735 AAATAATGGTTACATGTGTAGTACTAAGTGAAGGCTACAATATGTATCGAG
1 AAATATTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAT
* **
39276786 AAGCT-TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATTGAT
1 AA-ATATTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAT
* * *
39276837 AAATGA-TGGTCACATGTGTAGTACTAAGTGAAGGCTACTACGTGTACCGA-
1 AAAT-ATTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAT
* *
39276887 AAAGCT-TTAGTCACGTATGTAGTACTATGTGAAGGCTACTACGTGAACCG-T
1 AAA--TATTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAT
* *
39276938 AAA-ACTTGATCACGTGTGTAGTACTATGTGAAGGCTATTACGTGAACCG-T
1 AAATA-TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAT
* *
39276988 AAAAATTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 AAATATTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
39277032 TATCGAATGA
Statistics
Matches: 326, Mismatches: 61, Indels: 25
0.79 0.15 0.06
Matches are distributed among these distances:
50 87 0.27
51 236 0.72
52 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (51 bp):
AAATATTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAT
Found at i:39277946 original size:5 final size:5
Alignment explanation
Indices: 39277936--39277998 Score: 81
Period size: 5 Copynumber: 12.6 Consensus size: 5
39277926 TGCTTGATGA
* * * *
39277936 AATGG AATGG AATGG AATGG TATGA AATGG AATAG TATGG AATGG AATGG
1 AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG
*
39277986 TATGG AATGG AAT
1 AATGG AATGG AAT
39277999 ATATATATAT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.40, C:0.00, G:0.35, T:0.25
Consensus pattern (5 bp):
AATGG
Found at i:39277964 original size:15 final size:15
Alignment explanation
Indices: 39277936--39277998 Score: 99
Period size: 15 Copynumber: 4.2 Consensus size: 15
39277926 TGCTTGATGA
*
39277936 AATGGAATGGAATGG
1 AATGGTATGGAATGG
*
39277951 AATGGTATGAAATGG
1 AATGGTATGGAATGG
*
39277966 AATAGTATGGAATGG
1 AATGGTATGGAATGG
39277981 AATGGTATGGAATGG
1 AATGGTATGGAATGG
39277996 AAT
1 AAT
39277999 ATATATATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.40, C:0.00, G:0.35, T:0.25
Consensus pattern (15 bp):
AATGGTATGGAATGG
Found at i:39280597 original size:20 final size:20
Alignment explanation
Indices: 39280572--39280611 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
39280562 AATATTTTCC
*
39280572 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
39280592 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
39280612 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:39282529 original size:21 final size:21
Alignment explanation
Indices: 39282505--39282546 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39282495 ATTTTTTCTT
*
39282505 AATTAACTATCTAAATATTAA
1 AATTAACTAACTAAATATTAA
* *
39282526 AATTACCTAACTAAATTTTAA
1 AATTAACTAACTAAATATTAA
39282547 TATGGCACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTAACTAACTAAATATTAA
Found at i:39283993 original size:17 final size:18
Alignment explanation
Indices: 39283971--39284007 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
39283961 CAATTAATTA
39283971 TAACATCAATAT-TATTT
1 TAACATCAATATATATTT
*
39283988 TAACATCAGTATATATTT
1 TAACATCAATATATATTT
39284006 TA
1 TA
39284008 TTGGTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.46
Consensus pattern (18 bp):
TAACATCAATATATATTT
Found at i:39284108 original size:20 final size:19
Alignment explanation
Indices: 39284075--39284123 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
39284065 AAAAAATATA
*
39284075 TAAATATTACGACTAAATTTG
1 TAAA-ATTAAGACTAAA-TTG
* *
39284096 TTAAATTAAGACTCAATTG
1 TAAAATTAAGACTAAATTG
39284115 TAAAATTAA
1 TAAAATTAA
39284124 TTCTCAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 11 0.46
20 10 0.42
21 3 0.12
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (19 bp):
TAAAATTAAGACTAAATTG
Found at i:39289793 original size:2 final size:2
Alignment explanation
Indices: 39289786--39289818 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39289776 ACTAGGCTGC
39289786 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39289819 TAAATTCTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39293596 original size:91 final size:91
Alignment explanation
Indices: 39293441--39293714 Score: 512
Period size: 91 Copynumber: 3.0 Consensus size: 91
39293431 TAATTTTTAA
39293441 AACAAAATCTTTGAGTTTTGAAGGATGCTAATGTTGTGGAAGTATAAAAGCCAATATCAATTCAT
1 AACAAAATCTTTGAGTTTTGAAGGATGCTAATGTTGTGGAAGTATAAAAGCCAATATCAATTCAT
39293506 TTGAAACAACTTATCTTGAAGATTAG
66 TTGAAACAACTTATCTTGAAGATTAG
* * *
39293532 AACAAAATCTTTAAGTTTTGAAGGATGCTAATGTTGTGAAAGTATTAAAGCCAATATCAATTCAT
1 AACAAAATCTTTGAGTTTTGAAGGATGCTAATGTTGTGGAAGTATAAAAGCCAATATCAATTCAT
39293597 TTGAAACAACTTATCTTGAAGATTAG
66 TTGAAACAACTTATCTTGAAGATTAG
39293623 AACAAAATCTTTGAGTTTTGAAGGATGCTAATGTTGTGGAAGTATAAAAGCCAATATCAATTCAT
1 AACAAAATCTTTGAGTTTTGAAGGATGCTAATGTTGTGGAAGTATAAAAGCCAATATCAATTCAT
*
39293688 TTTAAACAACTTATCTTGAAGATTAG
66 TTGAAACAACTTATCTTGAAGATTAG
39293714 A
1 A
39293715 TTAGATCGGC
Statistics
Matches: 176, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 176 1.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (91 bp):
AACAAAATCTTTGAGTTTTGAAGGATGCTAATGTTGTGGAAGTATAAAAGCCAATATCAATTCAT
TTGAAACAACTTATCTTGAAGATTAG
Found at i:39300218 original size:9 final size:9
Alignment explanation
Indices: 39300204--39300234 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39300194 GTTAAACGAA
39300204 TCGAGTTAT
1 TCGAGTTAT
*
39300213 TCGAGTTAA
1 TCGAGTTAT
39300222 TCGAGTTAT
1 TCGAGTTAT
39300231 TCGA
1 TCGA
39300235 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:39300304 original size:9 final size:9
Alignment explanation
Indices: 39300287--39300323 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
39300277 TGAGTTTTCG
39300287 AATTCGAAT
1 AATTCGAAT
*
39300296 AACTCGAAT
1 AATTCGAAT
39300305 AATTCGAAT
1 AATTCGAAT
39300314 AATTCGAAT
1 AATTCGAAT
39300323 A
1 A
39300324 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:39301361 original size:5 final size:5
Alignment explanation
Indices: 39301351--39301376 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39301341 CTCGAAAATT
39301351 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
39301377 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:39303581 original size:14 final size:13
Alignment explanation
Indices: 39303544--39303605 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 13
39303534 TAGCTCAAGG
39303544 ATTAAAATTTTAA
1 ATTAAAATTTTAA
39303557 AGGTGTAAAATTTTAA
1 A--T-TAAAATTTTAA
*
39303573 TATTAAAATATTAA
1 -ATTAAAATTTTAA
*
39303587 TATTTAAATATTTAA
1 -ATTAAAAT-TTTAA
39303602 ATTA
1 ATTA
39303606 TTTTTTTTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
13 1 0.03
14 21 0.52
15 6 0.15
16 11 0.28
17 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (13 bp):
ATTAAAATTTTAA
Found at i:39305601 original size:11 final size:13
Alignment explanation
Indices: 39305585--39305617 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
39305575 ATTTTACGGG
39305585 AAAATTTCG-T-A
1 AAAATTTCGTTCA
39305596 AAAATTTCGTTCA
1 AAAATTTCGTTCA
39305609 AAAATTTCG
1 AAAATTTCG
39305618 ACGTTTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 1 0.05
13 10 0.50
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (13 bp):
AAAATTTCGTTCA
Found at i:39306730 original size:33 final size:33
Alignment explanation
Indices: 39306680--39306895 Score: 150
Period size: 33 Copynumber: 6.6 Consensus size: 33
39306670 AATATGAAGG
* *
39306680 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATAGGT
* *
39306713 GGTTACTAAGTGCTGATTCCACCGTATCTTTAACTATAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A---TT--C-AT--AGGT
*
39306756 GGTTGTTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATAGGT
*
39306783 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATAGGT
*
39306816 GGTTGCTAAGTGCTAATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATAGGT
* * * * *
39306843 GATTGCTAAGTGCTGATTCCCTGAATGATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATAGGT
39306876 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
39306896 ACCATATCTT
Statistics
Matches: 145, Mismatches: 16, Indels: 44
0.71 0.08 0.21
Matches are distributed among these distances:
27 40 0.28
28 5 0.03
29 2 0.01
31 4 0.03
32 5 0.03
33 58 0.40
34 3 0.02
35 1 0.01
38 2 0.01
40 1 0.01
41 2 0.01
42 2 0.01
43 20 0.14
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATAGGT
Found at i:39306792 original size:27 final size:27
Alignment explanation
Indices: 39306754--39306863 Score: 130
Period size: 27 Copynumber: 3.9 Consensus size: 27
39306744 AACTATAAAG
*
39306754 GGGGTTGTTAAGTGCTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
*
39306781 GGGGTTGCTAAGTGCTGATTCCCCGATTCATT
1 GGGGTTGCTAAGTGCTGATTCCCC----CA-A
*
39306813 GGTGGTTGCTAAGTGCTAATTCCCCCAA
1 GG-GGTTGCTAAGTGCTGATTCCCCCAA
*
39306841 GGGATTGCTAAGTGCTGATTCCC
1 GGGGTTGCTAAGTGCTGATTCCC
39306864 TGAATGATTG
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
27 42 0.59
28 2 0.03
29 2 0.03
31 2 0.03
32 2 0.03
33 21 0.30
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:39306849 original size:60 final size:60
Alignment explanation
Indices: 39306756--39306895 Score: 226
Period size: 60 Copynumber: 2.3 Consensus size: 60
39306746 CTATAAAGGG
* * *
39306756 GGTTGTTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCCAAGGGATTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
39306816 GGTTGCTAAGTGCTAATTCCCCCAAGGGATTGCTAAGTGCTGATTCCCTGAATGATTGGT
1 GGTTGCTAAGTGCTGATTCCCCCAAGGGATTGCTAAGTGCTGATTCCCCGAATCATTGGT
39306876 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
39306896 ACCATATCTT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.33
Consensus pattern (60 bp):
GGTTGCTAAGTGCTGATTCCCCCAAGGGATTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:39313287 original size:23 final size:23
Alignment explanation
Indices: 39313261--39313335 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
39313251 ATAAGTGCCA
39313261 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
39313284 CACTGA-ATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
39313306 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
39313329 CACTGAT
1 CACTGAT
39313336 CAATAACACT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
22 21 0.44
23 27 0.56
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:39314448 original size:41 final size:41
Alignment explanation
Indices: 39314327--39314440 Score: 219
Period size: 41 Copynumber: 2.8 Consensus size: 41
39314317 GGTTTAAAGT
39314327 CTAATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGC
1 CTAATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGC
*
39314368 CTGATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGC
1 CTAATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGC
39314409 CTAATTCAGTTCACCGGCACTTAGCCTGCTAG
1 CTAATTCAGTTCACCGGCACTTAGCCTGCTAG
39314441 ACATATAGTC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.21, C:0.30, G:0.20, T:0.29
Consensus pattern (41 bp):
CTAATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGC
Found at i:39314463 original size:41 final size:41
Alignment explanation
Indices: 39314332--39314455 Score: 196
Period size: 41 Copynumber: 3.0 Consensus size: 41
39314322 AAAGTCTAAT
*
39314332 TCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGAT
1 TCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGAA
39314373 TCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCT-AA
1 TCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGAA
* * *
39314413 TTCAGTTCACCGGCACTTAGCCTGCTAGACATATAGTCTGAA
1 -TCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGAA
39314455 T
1 T
39314456 AATTTCACTG
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
40 1 0.01
41 74 0.96
42 2 0.03
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (41 bp):
TCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGAA
Found at i:39316251 original size:13 final size:13
Alignment explanation
Indices: 39316233--39316257 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39316223 ACCAACGATA
39316233 AAATTTTCACACG
1 AAATTTTCACACG
39316246 AAATTTTCACAC
1 AAATTTTCACAC
39316258 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:39318000 original size:11 final size:13
Alignment explanation
Indices: 39317984--39318017 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
39317974 AATTTTACGG
39317984 AAAAATTTCG-T-
1 AAAAATTTCGTTC
39317995 AAAAATTTCGTTC
1 AAAAATTTCGTTC
39318008 AAAAATTTCG
1 AAAAATTTCG
39318018 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:39319246 original size:33 final size:33
Alignment explanation
Indices: 39319199--39319539 Score: 166
Period size: 33 Copynumber: 9.8 Consensus size: 33
39319189 AATATGAAGG
39319199 GGTTGCTAAGTGCTGATTCCCCGATTTATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTTATTGGT
* *
39319232 GGTTACTAAGTGCTGATTCCACCGTATCTTTAAATATAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TTT--AT-T---GGT
* *
39319275 GGTTGTTAAGTGCTGATTCCCCCA---A--GG-
1 GGTTGCTAAGTGCTGATTCCCCGATTTATTGGT
*
39319302 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTTATTGGT
*
39319335 GGTTGCTAAGTGCTGATTCCACCGTATCTCTAAATGTGAAGCG
1 GGTTGCTAAGTGCTGATTCC-CCG-AT-T-T--AT-TG--G-T
* *
39319378 GGTTGCTAAGTGATGATTCCCCCA---A--GG-
1 GGTTGCTAAGTGCTGATTCCCCGATTTATTGGT
* *
39319405 GGTTGCTAAGTGCTGATTCCCCGAATGATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTTATTGGT
* *
39319438 GGTTGCTAAGTGCTGATTCCACCATATCTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CC-GA--TTT--AT-TG---GT
* * *
39319481 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTTATTGGT
* *
39319514 AGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
39319540 AACGGTTAAC
Statistics
Matches: 240, Mismatches: 25, Indels: 85
0.69 0.07 0.24
Matches are distributed among these distances:
27 44 0.18
28 2 0.01
29 1 0.00
30 2 0.01
31 1 0.00
32 4 0.02
33 78 0.32
34 14 0.06
35 4 0.02
36 3 0.01
37 5 0.02
39 7 0.03
40 5 0.02
41 3 0.01
42 7 0.03
43 60 0.25
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTTATTGGT
Found at i:39319381 original size:103 final size:102
Alignment explanation
Indices: 39319195--39319502 Score: 490
Period size: 103 Copynumber: 3.0 Consensus size: 102
39319185 ATTGAATATG
* *
39319195 AAGGGGTTGCTAAGTGCTGATTCCCCGATTTATTGGTGGTTACTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* * *
39319260 TTTAAATATAAAGGGGGTTGTTAAGTGCTGATTCCCCC
66 TTTAAATGTGAA-GGGGTTGCTAAGTGCTGATTCCCCC
39319298 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
39319363 TCTAAATGTGAAGCGGGTTGCTAAGTGATGATTCCCCC
66 TTTAAATGTGAAG-GGGTTGCTAAGTGCTGATTCCCCC
* * *
39319401 AAGGGGTTGCTAAGTGCTGATTCCCCGAATGATTGGTGGTTGCTAAGTGCTGATTCCACCATATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
39319466 TTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 TTTAAATGTG-AAGGGGTTGCTAAGTGCTGATTCCCC
39319503 GAATCACTGG
Statistics
Matches: 190, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
102 1 0.01
103 186 0.98
104 3 0.02
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.32
Consensus pattern (102 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTTAAATGTGAAGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:39320534 original size:2 final size:2
Alignment explanation
Indices: 39320527--39320554 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39320517 GCGTAAACTA
39320527 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39320555 GTTTCAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39325745 original size:14 final size:15
Alignment explanation
Indices: 39325713--39325743 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39325703 ATATTTTTTT
39325713 AATATTTAAACAAAA
1 AATATTTAAACAAAA
*
39325728 AATATTTAAAGAAAA
1 AATATTTAAACAAAA
39325743 A
1 A
39325744 TAAAATAGTA
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:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (15 bp):
AATATTTAAACAAAA
Found at i:39326987 original size:12 final size:12
Alignment explanation
Indices: 39326956--39326987 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
39326946 TTTATTTTTT
39326956 AAAA-AATTTAA
1 AAAATAATTTAA
39326967 AAAAT-ATTTAA
1 AAAATAATTTAA
39326978 AAAATAATTT
1 AAAATAATTT
39326988 TTTTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAAATAATTTAA
Found at i:39340706 original size:45 final size:44
Alignment explanation
Indices: 39340429--39340719 Score: 159
Period size: 44 Copynumber: 6.6 Consensus size: 44
39340419 TCTCGATCCA
* * * * * *
39340429 CTCCACTACAACGTCGGGGAGATAAGATTGGTATGTTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGCTTTGCTTAGTCTG
* * * *
39340473 -TCCCACAGTAATTTCAAGGG-GATAAGACTTGCTTT-CTTGAGTCTA
1 CT-CCACTGCAACTTC-AGGGAGATAAGA-TTGCTTTGCTT-AGTCTG
* ** ** * *
39340518 CTCTACTGCAACTTCAGGGAGATTAAGA-CCCGATG-TGA-TCTA
1 CTCCACTGCAACTTCAGGGAGA-TAAGATTGCTTTGCTTAGTCTG
* * * * * *
39340560 CTCTACTGCAACTTCAGAGAGATAAGA-T-CTGTGGTTATAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGCT-TTGCT-TAGTCTG
* * ** *
39340604 CTCCACTGCAACTTTAGGGAGATAGGATTG-TCGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGCTTTGC-TTAGTCTG
* *
39340648 TTCCGCTGCAACTTCAGGGAGATAAGATTTGCTTTGCTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-TTGCTTTGCTTAGTCTG
*
39340693 CTCCACTGCAACTTCAAGGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
39340720 CTAGATACGA
Statistics
Matches: 186, Mismatches: 44, Indels: 33
0.71 0.17 0.13
Matches are distributed among these distances:
40 1 0.01
41 6 0.03
42 26 0.14
43 3 0.02
44 80 0.43
45 61 0.33
46 9 0.05
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTGCTTTGCTTAGTCTG
Found at i:39340858 original size:45 final size:45
Alignment explanation
Indices: 39340794--39340912 Score: 136
Period size: 45 Copynumber: 2.6 Consensus size: 45
39340784 TTGGCTTTAA
* *
39340794 TCTGCTCCACCGCAACTTCAGGGAGATAAGATTTCCCAT-CTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTCCCATGCTT-AG
* * **
39340839 TCTGC-CTCACTGCAACTTCA-AGAGGATAAGACTTGCTTTGCTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTCCCATGCTTAG
39340884 TCTGCTCCACTGCAACTTCAGGGAGATAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAA
39340913 AACTAGATGC
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
44 3 0.05
45 53 0.85
46 6 0.10
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTCCCATGCTTAG
Found at i:39340934 original size:195 final size:196
Alignment explanation
Indices: 39340653--39341123 Score: 838
Period size: 196 Copynumber: 2.4 Consensus size: 196
39340643 ATCTGTTCCG
* * *
39340653 CTGCAACTTC-AGGGAGATAAGATTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAAGGAGATA
1 CTGCAACTTCAAGAG-GATAAGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATA
*
39340717 AGACTAGATACGATCTACTCTCTGCATCTTCAGA-AGATAAGATCTGAGGTTTTAATCCACTCCA
65 AGACTAGATGCGATCTACTCTCTGCATCTTCAGAGAGATAAGATCTGAGGTTTTAATCCACTCCA
*
39340781 CTGTTGGCTTTAATCTGCTCCACCGCAACTTCAGGGAGATAAGATTTCCCATCTTCAGTCTGCCT
130 CTGTTGGCTTTAATCTGCTCCACCGCAACTTCAGGGAGATAAGATTTCCCATCTTCAGCCTGCCT
39340846 CA
195 CA
39340848 CTGCAACTTCAAGAGGATAAGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAA
1 CTGCAACTTCAAGAGGATAAGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAA
*
39340913 AACTAGATGCGATCTACTCTCTGCATCTTCAGAGAGATAAGATCTGAGGTTTTAATCCACTCCAC
66 GACTAGATGCGATCTACTCTCTGCATCTTCAGAGAGATAAGATCTGAGGTTTTAATCCACTCCAC
*
39340978 TGTTGGCTTTAATCTGCTCCACCGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGCCTGCCTC
131 TGTTGGCTTTAATCTGCTCCACCGCAACTTCAGGGAGATAAGATTTCCCATCTTCAGCCTGCCTC
39341043 A
196 A
* *
39341044 CTGCAACTTCAGGAGGATAAGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGAGAGATAA
1 CTGCAACTTCAAGAGGATAAGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAA
39341109 GACTAGATGCGATCT
66 GACTAGATGCGATCT
39341124 GTTATCTTCA
Statistics
Matches: 264, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
195 89 0.34
196 175 0.66
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (196 bp):
CTGCAACTTCAAGAGGATAAGACTTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAA
GACTAGATGCGATCTACTCTCTGCATCTTCAGAGAGATAAGATCTGAGGTTTTAATCCACTCCAC
TGTTGGCTTTAATCTGCTCCACCGCAACTTCAGGGAGATAAGATTTCCCATCTTCAGCCTGCCTC
A
Found at i:39341065 original size:45 final size:46
Alignment explanation
Indices: 39340991--39341112 Score: 146
Period size: 45 Copynumber: 2.7 Consensus size: 46
39340981 TGGCTTTAAT
* *
39340991 CTGCTCCACCGCAACTTCAGG-GAGATAAGATTTGCCAT-CTTCAGC
1 CTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCCATGCTT-AGC
** *
39341036 CTGC-CTCACTGCAACTTCAGGAG-GATAAGACTTGCTTTGCTTAGT
1 CTGCTC-CACTGCAACTTCAGGAGAGATAAGACTTGCCATGCTTAGC
39341081 CTGCTCCACTGCAACTTCA-GAGAGATAAGACT
1 CTGCTCCACTGCAACTTCAGGAGAGATAAGACT
39341113 AGATGCGATC
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
44 4 0.06
45 58 0.87
46 5 0.07
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (46 bp):
CTGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCCATGCTTAGC
Found at i:39345920 original size:6 final size:6
Alignment explanation
Indices: 39345889--39345937 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
39345879 CCAAACACAC
* *
39345889 CAGTAAA CAGTAA TCAGTAA CGGTAA CAGTAA CAGTAA AAGTAA CAGTA
1 CAGT-AA CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
39345938 TTCAACACAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 27 0.73
7 10 0.27
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.18
Consensus pattern (6 bp):
CAGTAA
Found at i:39345968 original size:45 final size:46
Alignment explanation
Indices: 39345917--39346023 Score: 146
Period size: 46 Copynumber: 2.3 Consensus size: 46
39345907 AACGGTAACA
* **
39345917 GTAACAGTAAAAGTAACAGTA-TTCAACACACAAAGTGTTGAATCT-
1 GTAACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAAT-TG
* *
39345962 GTAACAGTAACGGTAACAGTATTTCGACACACAAAGTGCCGAATTG
1 GTAACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATTG
39346008 GTAACAGTAACAGTAA
1 GTAACAGTAACAGTAA
39346024 TCGGCACATA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
45 20 0.37
46 34 0.63
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (46 bp):
GTAACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATTG
Found at i:39348370 original size:16 final size:17
Alignment explanation
Indices: 39348321--39348370 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
39348311 ATTTATTCCA
*
39348321 TAATA-AAATAATACAAT
1 TAATATAAATAATA-ATT
* *
39348338 TAATATAAATTACAATT
1 TAATATAAATAATAATT
39348355 TAA-ATAAATAATAATT
1 TAATATAAATAATAATT
39348371 ATTATTATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 11 0.41
17 10 0.37
18 6 0.22
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
TAATATAAATAATAATT
Found at i:39351799 original size:12 final size:13
Alignment explanation
Indices: 39351782--39351810 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
39351772 AGTTGTAAAG
39351782 TTTTATTT-TTAT
1 TTTTATTTATTAT
39351794 TTTTATTTATTAT
1 TTTTATTTATTAT
39351807 TTTT
1 TTTT
39351811 TACTTAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTATTTATTAT
Found at i:39357357 original size:98 final size:98
Alignment explanation
Indices: 39357183--39357379 Score: 331
Period size: 98 Copynumber: 2.0 Consensus size: 98
39357173 GTACAATAAA
* * *
39357183 ACTTTAAAAGAATATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
* *
39357248 CCTCTAGAATCCTAAACTCAGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCAGAATATTTCCTTT
39357281 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
* *
39357346 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCAGAATATTTCCTTT
39357379 A
1 A
39357380 TAATTTTTAA
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
CCTCTAAAATCCCAAACTCAGAATATTTCCTTT
Found at i:39359579 original size:21 final size:21
Alignment explanation
Indices: 39359555--39359594 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39359545 ATAGACAGAA
39359555 AGGAAAATAAAAAGAAAAGGC
1 AGGAAAATAAAAAGAAAAGGC
* * *
39359576 AGGAGAGTGAAAAGAAAAG
1 AGGAAAATAAAAAGAAAAG
39359595 AAAAAGGAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.30, T:0.05
Consensus pattern (21 bp):
AGGAAAATAAAAAGAAAAGGC
Found at i:39360413 original size:5 final size:5
Alignment explanation
Indices: 39360405--39360446 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
39360395 AGATTTGATT
* * *
39360405 GTAGG GTAGG GTAGG GTAGG GTAGG GTTGG GTTGG GTTGG GT
1 GTAGG GTAGG GTAGG GTAGG GTAGG GTAGG GTAGG GTAGG GT
39360447 CTGAAATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.12, C:0.00, G:0.60, T:0.29
Consensus pattern (5 bp):
GTAGG
Found at i:39361645 original size:2 final size:2
Alignment explanation
Indices: 39361638--39361668 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39361628 TGACATTCTT
39361638 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39361669 GCAATTATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39377257 original size:19 final size:19
Alignment explanation
Indices: 39377233--39377285 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
39377223 GAAACTCTGT
*
39377233 TGTTTTGTTGTTTTTTCAC
1 TGTTTTGTTGTTATTTCAC
* * *
39377252 TGTTTTGCTATCATTTCAC
1 TGTTTTGTTGTTATTTCAC
*
39377271 TATTTTGTTGTTATT
1 TGTTTTGTTGTTATT
39377286 ATTTGGATAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.11, C:0.11, G:0.13, T:0.64
Consensus pattern (19 bp):
TGTTTTGTTGTTATTTCAC
Found at i:39378510 original size:46 final size:46
Alignment explanation
Indices: 39378443--39378532 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
39378433 CTTTCTTGGC
39378443 TTCATAGTCTGCTCACCTTTTCACCCTTCTTTACTCTCAATTATGT
1 TTCATAGTCTGCTCACCTTTTCACCCTTCTTTACTCTCAATTATGT
*
39378489 TTCATGGTCTGCTCACCTTTTCACCCTTCTTTACTCTCAATTAT
1 TTCATAGTCTGCTCACCTTTTCACCCTTCTTTACTCTCAATTAT
39378533 CTCTCTCTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.17, C:0.31, G:0.07, T:0.46
Consensus pattern (46 bp):
TTCATAGTCTGCTCACCTTTTCACCCTTCTTTACTCTCAATTATGT
Found at i:39383594 original size:23 final size:24
Alignment explanation
Indices: 39383554--39383614 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 24
39383544 TATATATAAA
* * *
39383554 CAAAAATAAAACACCAAT-ATATG
1 CAAAAAGAAAAAAACAATGATATG
* * *
39383577 CTAAAAGCAAAAAACAATGGTATG
1 CAAAAAGAAAAAAACAATGATATG
39383601 CAAAAAGAAAAAAA
1 CAAAAAGAAAAAAA
39383615 ATGTTATTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 13 0.45
24 16 0.55
ACGTcount: A:0.64, C:0.13, G:0.10, T:0.13
Consensus pattern (24 bp):
CAAAAAGAAAAAAACAATGATATG
Found at i:39383617 original size:22 final size:24
Alignment explanation
Indices: 39383573--39383617 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
39383563 AACACCAATA
*
39383573 TATGCTAAAAGCAAAAAACAATGG
1 TATGCAAAAAGCAAAAAACAATGG
39383597 TATGCAAAAAG-AAAAAA-AATG
1 TATGCAAAAAGCAAAAAACAATG
39383618 TTATTAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 6 0.30
24 10 0.50
ACGTcount: A:0.60, C:0.09, G:0.16, T:0.16
Consensus pattern (24 bp):
TATGCAAAAAGCAAAAAACAATGG
Found at i:39389091 original size:29 final size:30
Alignment explanation
Indices: 39389036--39389100 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 30
39389026 TGATCCTAGA
* *
39389036 TTAATATATAAGAGTGAGATTGCAACT-TG
1 TTAATGTATAAGAGTAAGATTGCAACTCTG
* * *
39389065 TTAATGTATAGGAGTAAGGTTGTAACTCTG
1 TTAATGTATAAGAGTAAGATTGCAACTCTG
*
39389095 TGAATG
1 TTAATG
39389101 GGTTAAACTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (30 bp):
TTAATGTATAAGAGTAAGATTGCAACTCTG
Found at i:39393463 original size:28 final size:29
Alignment explanation
Indices: 39393419--39393474 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
39393409 GGTTACTATC
39393419 ATTTTAAAAAATATAT-ATAAA-ATATAA
1 ATTTTAAAAAATATATAATAAATATATAA
*
39393446 ATTTATAAAAAGTATATAATAAATATATA
1 ATTT-TAAAAAATATATAATAAATATATA
39393475 TATATAAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 4 0.16
28 11 0.44
29 5 0.20
30 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (29 bp):
ATTTTAAAAAATATATAATAAATATATAA
Found at i:39393480 original size:28 final size:28
Alignment explanation
Indices: 39393423--39393481 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
39393413 ACTATCATTT
*
39393423 TAAAAAATATATATAAAATATAAATTTA
1 TAAAAAATATATATAAAATATAAATATA
* *
39393451 TAAAAAGTATATA-ATAAATATATATATA
1 TAAAAAATATATATA-AAATATAAATATA
39393479 TAA
1 TAA
39393482 GTTTACAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (28 bp):
TAAAAAATATATATAAAATATAAATATA
Found at i:39405940 original size:29 final size:30
Alignment explanation
Indices: 39405879--39405941 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
39405869 AATAAAGATA
* *
39405879 AAAAATGTATATGGGTATATATTTACAAAAT
1 AAAAATGTATA-GAGTATATATATACAAAAT
* *
39405910 AAAAATGTATA-AGTATATATATAGAATAT
1 AAAAATGTATAGAGTATATATATACAAAAT
39405939 AAA
1 AAA
39405942 GTATATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 17 0.61
31 11 0.39
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (30 bp):
AAAAATGTATAGAGTATATATATACAAAAT
Found at i:39409624 original size:22 final size:22
Alignment explanation
Indices: 39409581--39409625 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
39409571 AGCTGAAATG
* ***
39409581 ATACGATAAATTTATTTTAAAA
1 ATACAATAAATTTATAAAAAAA
39409603 ATACAATAAATTTATAAAAAAA
1 ATACAATAAATTTATAAAAAAA
39409625 A
1 A
39409626 ATACTTTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
ATACAATAAATTTATAAAAAAA
Found at i:39416760 original size:6 final size:6
Alignment explanation
Indices: 39416734--39416772 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
39416724 ACAGCACCTA
*
39416734 AACAGT AATCAGT AACGGT AACAGT AATCAGT AACAGT A
1 AACAGT AA-CAGT AACAGT AACAGT AA-CAGT AACAGT A
39416773 TTCAACACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 17 0.59
7 12 0.41
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (6 bp):
AACAGT
Found at i:39416767 original size:13 final size:12
Alignment explanation
Indices: 39416734--39416772 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
39416724 ACAGCACCTA
39416734 AACAGTAATCAGT
1 AACAGTAA-CAGT
*
39416747 AACGGTAACAGT
1 AACAGTAACAGT
39416759 AATCAGTAACAGT
1 AA-CAGTAACAGT
39416772 A
1 A
39416773 TTCAACACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (12 bp):
AACAGTAACAGT
Found at i:39416826 original size:45 final size:45
Alignment explanation
Indices: 39416751--39416852 Score: 143
Period size: 45 Copynumber: 2.2 Consensus size: 45
39416741 ATCAGTAACG
* *
39416751 GTAACAGTAATCAGTAACAGTATTCAACACACAAAGTG-CTGAATCT
1 GTAACAGTAA-CGGTAACAGTATTCAACACACAAAGTGTC-GAATCA
* *
39416797 GTAATAGTAACGGTAACAGTATTCGACACACAAAGTGTCGAATCA
1 GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGTCGAATCA
39416842 GTAACAGTAAC
1 GTAACAGTAAC
39416853 AATAGTCGAC
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
45 40 0.80
46 10 0.20
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.23
Consensus pattern (45 bp):
GTAACAGTAACGGTAACAGTATTCAACACACAAAGTGTCGAATCA
Found at i:39417116 original size:40 final size:40
Alignment explanation
Indices: 39417066--39417142 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
39417056 TTCATTAATC
* *
39417066 TCACAGTTCAATGCAGTACACATAACAATATTCAGTAACT
1 TCACAATTCAATGCAGTACACAAAACAATATTCAGTAACT
* *
39417106 TCACAATTCAATTCAGTACTCAAAACAATATTCAGTA
1 TCACAATTCAATGCAGTACACAAAACAATATTCAGTA
39417143 TTCCATAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.29
Consensus pattern (40 bp):
TCACAATTCAATGCAGTACACAAAACAATATTCAGTAACT
Found at i:39418287 original size:35 final size:35
Alignment explanation
Indices: 39418242--39418323 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 35
39418232 ATTTATTTAA
* *
39418242 TAATATAATAT-CATTATAATTTAATTATCATAAAT
1 TAATATAATATAAATTAT-ATTTAAATATCATAAAT
*
39418277 TAATATAATATAAATTATATTTAAATATCATTAAT
1 TAATATAATATAAATTATATTTAAATATCATAAAT
39418312 T-ATATAAT-TAAA
1 TAATATAATATAAA
39418324 ACAAATAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
33 4 0.09
34 7 0.16
35 27 0.63
36 5 0.12
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (35 bp):
TAATATAATATAAATTATATTTAAATATCATAAAT
Found at i:39422962 original size:32 final size:33
Alignment explanation
Indices: 39422904--39422971 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 33
39422894 TATAAAAAAT
*
39422904 ATTAATTTTTTTAAAAATATATAAAAATGCCAA
1 ATTAATTTTTTTAAAAATATATAAAAATGACAA
39422937 ATTATATTTTTTTAAAAATA-A-AAAAATGACAA
1 ATTA-ATTTTTTTAAAAATATATAAAAATGACAA
39422969 ATT
1 ATT
39422972 TGAGAACTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 5 0.15
34 15 0.45
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (33 bp):
ATTAATTTTTTTAAAAATATATAAAAATGACAA
Found at i:39428575 original size:107 final size:108
Alignment explanation
Indices: 39428389--39428796 Score: 540
Period size: 108 Copynumber: 3.8 Consensus size: 108
39428379 NNNNNNTCAA
* * *
39428389 ATATAAATATACGAAAAAATTTTAAAAAAATTTTGGGGTGCTGGCATGTCAATGGCCGGCACCTA
1 ATATAAATATACGAAAAAA-ATAAAAAAAATTTT-GGGTGCTGGCCTGTCAATGGCCGGCACCTA
*
39428454 GTACAAATTTAAAAAAAAATTC-TTTTTTTTCGTGTCAAAGTCAG
64 GTACAAATTTAAAAAAAAATTCTTTTTTTTTCGTGTCAGAGTCAG
39428498 ATATAAATATACGAAAAAAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACAC-AG
1 ATATAAATATACGAAAAAAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCAC-CTAG
* *
39428562 TACAAATTTAAAAAAAAAATCTTTTTTTTTTGTGTCAGAGTCAG
65 TACAAATTTAAAAAAAAATTCTTTTTTTTTCGTGTCAGAGTCAG
* ** **
39428606 ATATAAATATACGAAAAAAAT--TAAATTTTTTTTGTGCTGGCCTGTCAATGGCCGGCACCTAGT
1 ATATAAATATACGAAAAAAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCTAGT
* *
39428669 ACAAATTTAAAAAAAAA-TCTTTTTTTTTCATCTCAGAGTCAG
66 ACAAATTTAAAAAAAAATTCTTTTTTTTTCGTGTCAGAGTCAG
*** * *
39428711 ATATAAATATACGAAAAAAATTAGAAAATTTTTTTTTGGGTGCTGGCTTGTCAATGGCTGGCACC
1 ATATAAATATACGAAAAAAA-TA-AAAA--AAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACC
*
39428776 CAGTACAAA-TTAAAAAAAAAT
62 TAGTACAAATTTAAAAAAAAAT
39428797 AGGAATGAGG
Statistics
Matches: 268, Mismatches: 21, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
105 43 0.16
106 53 0.20
107 48 0.18
108 54 0.20
109 21 0.08
110 11 0.04
111 38 0.14
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (108 bp):
ATATAAATATACGAAAAAAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCTAGT
ACAAATTTAAAAAAAAATTCTTTTTTTTTCGTGTCAGAGTCAG
Found at i:39428660 original size:106 final size:106
Alignment explanation
Indices: 39428426--39428795 Score: 505
Period size: 105 Copynumber: 3.4 Consensus size: 106
39428416 AAATTTTGGG
* *
39428426 GTGCTGGCATGTCAATGGCCGGCACCTAGTACAAATTTAAAAAAAAATTC-TTTTTTTTCGTGTC
1 GTGCTGGCCTGTCAATGGCCGGCACCTAGTACAAATTTAAAAAAAAAATCTTTTTTTTTCGTGTC
* * ** **
39428490 AAAGTCAGATATAAATATACGAAAAAAATAAAAAAAATTTTGG
66 AGAGTCAGATATAAATATACGAAAAAAAT--TAAATTTTTTTT
*
39428533 GTGCTGGCCTGTCAATGGCCGGCACAC-AGTACAAATTTAAAAAAAAAATCTTTTTTTTTTGTGT
1 GTGCTGGCCTGTCAATGGCCGGCAC-CTAGTACAAATTTAAAAAAAAAATCTTTTTTTTTCGTGT
39428597 CAGAGTCAGATATAAATATACGAAAAAAATTAAATTTTTTTT
65 CAGAGTCAGATATAAATATACGAAAAAAATTAAATTTTTTTT
* *
39428639 GTGCTGGCCTGTCAATGGCCGGCACCTAGTACAAATTT-AAAAAAAAATCTTTTTTTTTCATCTC
1 GTGCTGGCCTGTCAATGGCCGGCACCTAGTACAAATTTAAAAAAAAAATCTTTTTTTTTCGTGTC
39428703 AGAGTCAGATATAAATATACGAAAAAAATTAGAAAATTTTTTTTT
66 AGAGTCAGATATAAATATACGAAAAAAATT---AAA-TTTTTTTT
* * *
39428748 GGGTGCTGGCTTGTCAATGGCTGGCACCCAGTACAAA-TTAAAAAAAAA
1 --GTGCTGGCCTGTCAATGGCCGGCACCTAGTACAAATTTAAAAAAAAA
39428796 TAGGAATGAG
Statistics
Matches: 238, Mismatches: 15, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
105 54 0.23
106 43 0.18
107 46 0.19
108 45 0.19
109 8 0.03
110 2 0.01
111 40 0.17
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (106 bp):
GTGCTGGCCTGTCAATGGCCGGCACCTAGTACAAATTTAAAAAAAAAATCTTTTTTTTTCGTGTC
AGAGTCAGATATAAATATACGAAAAAAATTAAATTTTTTTT
Found at i:39431453 original size:108 final size:107
Alignment explanation
Indices: 39431215--39431703 Score: 693
Period size: 108 Copynumber: 4.6 Consensus size: 107
39431205 AAATTTTTTG
* * * *
39431215 TATCTGACTCTGACACGAAAAAAAAGAATTTTTTTTTTAAATTTGTACTGGATGCCGGCCATTTA
1 TATCTGACTCTGACACGAAAAAAAAGAA-ATTTTTTTTAAAATTGTACTGGGTGCCGGCCATTGA
**** ** *
39431280 CAGGCCAGCACCAAAAAAAAATTTAAAATTTTTTCGTATATTTA
65 CAGGCCAGCACC-AAAATTTTTTTTTATTTTTTTCGTATATTTA
*
39431324 TATCTGACTCTGACACTAAAAAAAAAGAAATTTTTTTTAAAATTGTACTGGGTGCCGGCCATTGA
1 TATCTGACTCTGACAC-GAAAAAAAAGAAATTTTTTTTAAAATTGTACTGGGTGCCGGCCATTGA
*
39431389 CAGGCCAGCACCAAAATTTTTTTTTACTTTTTTCGTATATTTA
65 CAGGCCAGCACCAAAATTTTTTTTTATTTTTTTCGTATATTTA
* * *
39431432 TATCTGACTCTAACACGAAAAAAAAAGAAATTTTTTTAAAAATTGTACTGGGTGTCGGCCATTGA
1 TATCTGACTCTGACACG-AAAAAAAAGAAATTTTTTTTAAAATTGTACTGGGTGCCGGCCATTGA
*
39431497 CAGGCCAGCACCCAAAA--TTTTTTTATTTTTTTCGTATAATTA
65 CAGGCCAGCA-CCAAAATTTTTTTTTATTTTTTTCGTATATTTA
39431539 TATCT-ATCTCTGACACGAAAAAAAAGTAAA-TTTTTTT--AATTGTACTGGGTGCCGGCCATTG
1 TATCTGA-CTCTGACACGAAAAAAAAG-AAATTTTTTTTAAAATTGTACTGGGTGCCGGCCATTG
*
39431600 ACAGGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATATTTA
64 ACAGGCCAGCACCAAAATTTTTTTTTATTTTTTTCGTATATTTA
*
39431644 TATCTGACTCTGACACGAAAAAAAAGAAATTTTTTTTAAAATTTGTACTGGGTGCTGGCC
1 TATCTGACTCTGACACGAAAAAAAAGAAATTTTTTTTAAAA-TTGTACTGGGTGCCGGCC
39431704 TGTCATATCG
Statistics
Matches: 344, Mismatches: 24, Indels: 25
0.88 0.06 0.06
Matches are distributed among these distances:
103 5 0.01
104 37 0.11
105 55 0.16
106 17 0.05
107 42 0.12
108 111 0.32
109 66 0.19
110 11 0.03
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (107 bp):
TATCTGACTCTGACACGAAAAAAAAGAAATTTTTTTTAAAATTGTACTGGGTGCCGGCCATTGAC
AGGCCAGCACCAAAATTTTTTTTTATTTTTTTCGTATATTTA
Found at i:39431638 original size:212 final size:214
Alignment explanation
Indices: 39431215--39431703 Score: 718
Period size: 212 Copynumber: 2.3 Consensus size: 214
39431205 AAATTTTTTG
* * * *
39431215 TATCTGACTCTGACACGAAAAAAAAGAATTTTTTTTTTAAATTTGTACTGGATGCCGGCCATTTA
1 TATCTGACTCTGACACGAAAAAAAAGAA-ATTTTTTTAAAATTTGTACTGGGTGCCGGCCATTGA
*
39431280 CAGGCCAGCACCAAAAAAAAATTTAAAATTTTTTCGTATATTTATATCTGACTCTGACACTAAAA
65 CAGGCCAGCACC-AAAAAAAATTTAAAATTTTTTCGTATAATTATATCTGACTCTGACACTAAAA
39431345 AAAAAGAAATTTTTTTTAAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAAATTTTT
129 AAAAAGAAATTTTTTTT-AAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAAATTTTT
39431410 TTTTACTTTTTTCGTATATTTA
193 TTTTACTTTTTTCGTATATTTA
* * *
39431432 TATCTGACTCTAACACGAAAAAAAAAGAAATTTTTTTAAAAATTGTACTGGGTGTCGGCCATTGA
1 TATCTGACTCTGACACG-AAAAAAAAGAAATTTTTTTAAAATTTGTACTGGGTGCCGGCCATTGA
* ** ** * *
39431497 CAGGCCAGCACC-CAAAATTTTTTTATTTTTTTCGTATAATTATATCT-ATCTCTGACAC-GAAA
65 CAGGCCAGCACCAAAAAAAATTTAAAATTTTTTCGTATAATTATATCTGA-CTCTGACACTAAAA
*
39431559 AAAAAGTAAA-TTTTTTT-AATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTT
129 AAAAAG-AAATTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAAATTTTT
*
39431622 TTTTATTTTTTTCGTATATTTA
193 TTTTACTTTTTTCGTATATTTA
*
39431644 TATCTGACTCTGACACGAAAAAAAAGAAATTTTTTTTAAAATTTGTACTGGGTGCTGGCC
1 TATCTGACTCTGACACGAAAAAAAAGAAA-TTTTTTTAAAATTTGTACTGGGTGCCGGCC
39431704 TGTCATATCG
Statistics
Matches: 247, Mismatches: 21, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
211 12 0.05
212 109 0.44
214 17 0.07
215 40 0.16
217 58 0.23
218 11 0.04
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (214 bp):
TATCTGACTCTGACACGAAAAAAAAGAAATTTTTTTAAAATTTGTACTGGGTGCCGGCCATTGAC
AGGCCAGCACCAAAAAAAATTTAAAATTTTTTCGTATAATTATATCTGACTCTGACACTAAAAAA
AAAGAAATTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAAATTTTTTTT
TACTTTTTTCGTATATTTA
Found at i:39434476 original size:23 final size:23
Alignment explanation
Indices: 39434449--39434524 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
39434439 AGTGTTATTG
*
39434449 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
39434472 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
39434495 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
39434518 ATCAGTG
1 ATCAGTG
39434525 TTGCACTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:39441988 original size:78 final size:79
Alignment explanation
Indices: 39441900--39442059 Score: 236
Period size: 77 Copynumber: 2.0 Consensus size: 79
39441890 TTTCAGACCA
* * *
39441900 AATTATAATGAATAGTACTTTTTAAGTATTAATGTGAATAAATTAATAGAAC-T-GAAAGGG-AA
1 AATTATAATGAATAATAC-TTCTAAGTATTAAAGTGAATAAATTAATA-AACTTAGAAAGGGAAA
39441962 ATCATGAATTAAACTT
64 ATCATGAATTAAACTT
* *
39441978 AATTATAATGAATAATACTTCTAAGTATTAAAGTGAATAAATTACTATACTTAGAAAGGGAAAAT
1 AATTATAATGAATAATACTTCTAAGTATTAAAGTGAATAAATTAATAAACTTAGAAAGGGAAAAT
39442043 CATGAATTAAACTT
66 CATGAATTAAACTT
39442057 AAT
1 AAT
39442060 CAATTTTAGT
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
76 2 0.03
77 27 0.36
78 24 0.32
79 21 0.28
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (79 bp):
AATTATAATGAATAATACTTCTAAGTATTAAAGTGAATAAATTAATAAACTTAGAAAGGGAAAAT
CATGAATTAAACTT
Found at i:39446477 original size:19 final size:19
Alignment explanation
Indices: 39446453--39446493 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
39446443 CATGGTGAGT
39446453 TCACCTTTCTGCACATCGA
1 TCACCTTTCTGCACATCGA
*
39446472 TCACCTTTCTGCATATCGA
1 TCACCTTTCTGCACATCGA
39446491 TCA
1 TCA
39446494 ACGTCCTACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.22, C:0.34, G:0.10, T:0.34
Consensus pattern (19 bp):
TCACCTTTCTGCACATCGA
Found at i:39448696 original size:20 final size:19
Alignment explanation
Indices: 39448648--39448697 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
39448638 TAATAGAAAT
* *
39448648 TTATCCGTATCAATAGTAA
1 TTATCCATATCAACAGTAA
*
39448667 CTTATACATATCAACAGTAA
1 -TTATCCATATCAACAGTAA
39448687 TTCATCCATAT
1 TT-ATCCATAT
39448698 AATTACATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (19 bp):
TTATCCATATCAACAGTAA
Found at i:39452186 original size:4 final size:4
Alignment explanation
Indices: 39452177--39452213 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
39452167 TTCCTGACAG
39452177 AAGA AAGA AAG- AAGA AAG- AAGA AAGA AAG- AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
39452214 TGAAGTCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 9 0.30
4 21 0.70
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:39452191 original size:11 final size:11
Alignment explanation
Indices: 39452177--39452213 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
39452167 TTCCTGACAG
39452177 AAGAAAGAA-A
1 AAGAAAGAAGA
39452187 GAAGAAAGAAGA
1 -AAGAAAGAAGA
39452199 AAGAAAGAAGA
1 AAGAAAGAAGA
39452210 AAGA
1 AAGA
39452214 TGAAGTCGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 24 0.96
12 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAGA
Found at i:39452198 original size:18 final size:18
Alignment explanation
Indices: 39452175--39452213 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
39452165 GGTTCCTGAC
39452175 AGAAGAAAGAAAGAAGAA
1 AGAAGAAAGAAAGAAGAA
39452193 AGAAGAAAGAAAGAAGAA
1 AGAAGAAAGAAAGAAGAA
39452211 AGA
1 AGA
39452214 TGAAGTCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AGAAGAAAGAAAGAAGAA
Found at i:39452785 original size:30 final size:32
Alignment explanation
Indices: 39452746--39452806 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 32
39452736 ATTAATAATT
* *
39452746 AGATGTAAATTTTAAAATTAAAAAA-ATAAAG
1 AGATGTAAATTTCAAAAATAAAAAATATAAAG
39452777 AGAT-TAAATTTCAAAAATAAAAAATATAAA
1 AGATGTAAATTTCAAAAATAAAAAATATAAA
39452807 AACTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.28
Consensus pattern (32 bp):
AGATGTAAATTTCAAAAATAAAAAATATAAAG
Found at i:39452813 original size:29 final size:30
Alignment explanation
Indices: 39452751--39452815 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
39452741 TAATTAGATG
* * *
39452751 TAAATTTTAAAATTAAAAAAATAAAGAGAT
1 TAAATTTCAAAAATAAAAAAATAAAGAGAC
39452781 TAAATTTCAAAAATAAAAAATATAAA-A-AC
1 TAAATTTCAAAAATAAAAAA-ATAAAGAGAC
39452810 TAAATT
1 TAAATT
39452816 GGAAAATATC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 7 0.23
30 19 0.61
31 5 0.16
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (30 bp):
TAAATTTCAAAAATAAAAAAATAAAGAGAC
Found at i:39458663 original size:28 final size:30
Alignment explanation
Indices: 39458608--39458675 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
39458598 TTTAAAAATA
* *
39458608 CCTTATTTGAACACTTTCAAAAGGGTTTGG
1 CCTTATTTGAACACTTTCAAAAAGGTTTAG
**
39458638 CCTTATTTGTCCA-TTT-AAAAAGGTTTAG
1 CCTTATTTGAACACTTTCAAAAAGGTTTAG
*
39458666 CCTCATTTGA
1 CCTTATTTGA
39458676 GCATTTTTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 18 0.56
29 3 0.09
30 11 0.34
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (30 bp):
CCTTATTTGAACACTTTCAAAAAGGTTTAG
Found at i:39478306 original size:2 final size:2
Alignment explanation
Indices: 39478299--39478329 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39478289 TGATTTGCAT
39478299 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39478330 GTAACATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39479526 original size:34 final size:34
Alignment explanation
Indices: 39479478--39479542 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
39479468 AACACTATCA
*
39479478 ACACAATTGGCGCTTAGTTGTACAAGAGCCTCGG
1 ACACAATTGGCGCTTAGGTGTACAAGAGCCTCGG
* *
39479512 ACACTATTGGCGCTTAGGTGTGCAAGAGCCT
1 ACACAATTGGCGCTTAGGTGTACAAGAGCCT
39479543 TGAACACCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (34 bp):
ACACAATTGGCGCTTAGGTGTACAAGAGCCTCGG
Found at i:39488258 original size:13 final size:14
Alignment explanation
Indices: 39488233--39488261 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
39488223 TTAGGCTTCA
39488233 ATATTTATATTTTT
1 ATATTTATATTTTT
39488247 ATATTT-TATTTTT
1 ATATTTATATTTTT
39488260 AT
1 AT
39488262 TTATGACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
ATATTTATATTTTT
Found at i:39492275 original size:13 final size:13
Alignment explanation
Indices: 39492254--39492293 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
39492244 AGTTCTTCAT
39492254 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
39492267 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
39492280 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
39492293 T
1 T
39492294 TTGGTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:39498981 original size:15 final size:15
Alignment explanation
Indices: 39498961--39498990 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39498951 CTTTTTCGGC
39498961 CGATTTGCTCTCTGT
1 CGATTTGCTCTCTGT
39498976 CGATTTGCTCTCTGT
1 CGATTTGCTCTCTGT
39498991 TTTACCCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.27, G:0.20, T:0.47
Consensus pattern (15 bp):
CGATTTGCTCTCTGT
Found at i:39500044 original size:19 final size:19
Alignment explanation
Indices: 39500020--39500056 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39500010 GCATGACCTC
39500020 TATATGCACCTGAACGATG
1 TATATGCACCTGAACGATG
*
39500039 TATATGTACCTGAACGAT
1 TATATGCACCTGAACGAT
39500057 AATATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (19 bp):
TATATGCACCTGAACGATG
Found at i:39502304 original size:21 final size:21
Alignment explanation
Indices: 39502244--39502304 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 21
39502234 TAATTTGAAT
*
39502244 TTATATTAAATAAGTAATTGAAA
1 TTATATTTAATAA-TAATT-AAA
* * *
39502267 ATATATAT-AT-ATTATTAAA
1 TTATATTTAATAATAATTAAA
39502286 TTATATTTAATAATAATTA
1 TTATATTTAATAATAATTA
39502305 TGTTAAATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
19 9 0.31
20 6 0.21
21 7 0.24
22 2 0.07
23 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (21 bp):
TTATATTTAATAATAATTAAA
Done.