Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 87 of 141
Found at i:28321299 original size:21 final size:23
Alignment explanation
Indices: 28321250--28321300 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 23
28321240 CAGCATTAAA
*
28321250 AAAGATTGATCACAAAGTTGATC
1 AAAGATTGATCACAAAGGTGATC
*
28321273 -AA-ATTGA-CACCAAGGTG-TC
1 AAAGATTGATCACAAAGGTGATC
28321292 AAAGATTGA
1 AAAGATTGA
28321301 AAAGTCGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
19 2 0.08
20 10 0.42
21 10 0.42
22 2 0.08
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.24
Consensus pattern (23 bp):
AAAGATTGATCACAAAGGTGATC
Found at i:28330712 original size:24 final size:24
Alignment explanation
Indices: 28330662--28330712 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
28330652 CAAAATTAAT
* *
28330662 AAAATAACATATAATTATATTTCA
1 AAAATAAAATATAATTATATATCA
*
28330686 AAAATAAAATATTATTATTATAT-A
1 AAAATAAAATATAATTA-TATATCA
28330710 AAA
1 AAA
28330713 CTGATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATAAAATATAATTATATATCA
Found at i:28346607 original size:21 final size:20
Alignment explanation
Indices: 28346581--28346642 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 20
28346571 TTTTGGTGGA
28346581 TCAGCTCTTACGAGCTTCTGT
1 TCAGCT-TTACGAGCTTCTGT
*
28346602 TCAGCTTTTACGGGCTTCTGT
1 TCAGC-TTTACGAGCTTCTGT
*
28346623 TAAGCTTT-CGAGCTTCTGT
1 TCAGCTTTACGAGCTTCTGT
28346642 T
1 T
28346643 GGCGTATTCG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 11 0.30
20 3 0.08
21 22 0.59
22 1 0.03
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (20 bp):
TCAGCTTTACGAGCTTCTGT
Found at i:28352087 original size:19 final size:20
Alignment explanation
Indices: 28352060--28352107 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
28352050 GTTGGTAAAT
*
28352060 ACATGTGTA-ATAATAATAA
1 ACATATGTATATAATAATAA
*
28352079 ACATATGTATTTAATAATAA
1 ACATATGTATATAATAATAA
28352099 A-ATATGTAT
1 ACATATGTAT
28352108 TGCTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (20 bp):
ACATATGTATATAATAATAA
Found at i:28352108 original size:19 final size:20
Alignment explanation
Indices: 28352070--28352108 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
28352060 ACATGTGTAA
28352070 TAATAATAAACATATGTATT
1 TAATAATAAACATATGTATT
28352090 TAATAATAAA-ATATGTATT
1 TAATAATAAACATATGTATT
28352109 GCTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TAATAATAAACATATGTATT
Found at i:28352245 original size:15 final size:15
Alignment explanation
Indices: 28352221--28352251 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28352211 AAACAGGGGG
*
28352221 AAAAAGAAAGAAAGA
1 AAAAAAAAAGAAAGA
28352236 AAAAAAAAAGAAAGA
1 AAAAAAAAAGAAAGA
28352251 A
1 A
28352252 GGAGAAACGT
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGAAAGA
Found at i:28355372 original size:67 final size:67
Alignment explanation
Indices: 28355264--28355392 Score: 213
Period size: 67 Copynumber: 1.9 Consensus size: 67
28355254 TTTCCAATTC
* * *
28355264 AGAGAGCACACTGCCGCAAACCTCATTTCTTACAGCGGGATTACCAGTCCAGTCTAAATCCCTTG
1 AGAGAGCACACTCCCGCAAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCTTG
28355329 CA
66 CA
* *
28355331 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCAGGATTACCGGTCCAGGCTAAATCCC
1 AGAGAGCACACTCCCGCAAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCC
28355393 CTGTAATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.21
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCAAACCTCATTTCTTACAGCAGGATTACCAGTCCAGGCTAAATCCCTTG
CA
Found at i:28358587 original size:40 final size:40
Alignment explanation
Indices: 28358466--28358605 Score: 121
Period size: 40 Copynumber: 3.5 Consensus size: 40
28358456 GACTTTGAGT
* *
28358466 CGATGAGACACTGGGTGTC-AATTCATTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAAATT-ATTACTTCGAATT-ATC
* * *
28358507 CGATGAAGA-ACTGGGTG-CCAA-T-TTACTTC-AGTTTAGC
1 CGATG-AGACACTGGGTGTCAAATTATTACTTCGA-ATTATC
*
28358544 CGATGAGACACTAGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
* * *
28358584 CGATAAGGCACTGGGTGCCAAA
1 CGATGAGACACTGGGTGTCAAA
28358606 CTGTTGTGTT
Statistics
Matches: 79, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
36 3 0.04
37 13 0.16
38 12 0.15
39 1 0.01
40 31 0.39
41 16 0.20
42 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
Found at i:28358844 original size:57 final size:57
Alignment explanation
Indices: 28358776--28358892 Score: 216
Period size: 57 Copynumber: 2.1 Consensus size: 57
28358766 CATAGAATAC
* *
28358776 ATGAGTTAAATACTCATGAATTGAATATGGAATGGATAGTGCCATTGTTTAAATGAT
1 ATGAGTTAAATACTCATGAACTAAATATGGAATGGATAGTGCCATTGTTTAAATGAT
28358833 ATGAGTTAAATACTCATGAACTAAATATGGAATGGATAGTGCCATTGTTTAAATGAT
1 ATGAGTTAAATACTCATGAACTAAATATGGAATGGATAGTGCCATTGTTTAAATGAT
28358890 ATG
1 ATG
28358893 TGAACCAATT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.34
Consensus pattern (57 bp):
ATGAGTTAAATACTCATGAACTAAATATGGAATGGATAGTGCCATTGTTTAAATGAT
Found at i:28361233 original size:9 final size:10
Alignment explanation
Indices: 28361210--28361279 Score: 56
Period size: 10 Copynumber: 6.9 Consensus size: 10
28361200 TGGTTAATTT
28361210 TATTTTTTAA
1 TATTTTTTAA
28361220 TATTTTTTAA
1 TATTTTTTAA
*
28361230 -ATTTTTTATT
1 TATTTTTTA-A
28361240 TCATTTTTATAA
1 T-ATTTTT-TAA
**
28361252 T-TTAGTTAA
1 TATTTTTTAA
28361261 TATTTTTT-A
1 TATTTTTTAA
28361270 TATTATTTTA
1 TATT-TTTTA
28361280 TAATAGCCGG
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
9 17 0.36
10 21 0.45
12 7 0.15
13 2 0.04
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (10 bp):
TATTTTTTAA
Found at i:28362068 original size:18 final size:18
Alignment explanation
Indices: 28362047--28362088 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
28362037 TTAAAATAAA
*
28362047 ATTTTATGCTAAAATTTT
1 ATTTAATGCTAAAATTTT
28362065 ATTTAATGCTAAAATTTT
1 ATTTAATGCTAAAATTTT
28362083 ATTTAA
1 ATTTAA
28362089 ATAGGTGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (18 bp):
ATTTAATGCTAAAATTTT
Found at i:28365133 original size:9 final size:9
Alignment explanation
Indices: 28365116--28365152 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
28365106 TGAGTTTTCG
28365116 AATTCGAAT
1 AATTCGAAT
*
28365125 AACTCGAAT
1 AATTCGAAT
*
28365134 ATTTCGAAT
1 AATTCGAAT
28365143 AATTCGAAT
1 AATTCGAAT
28365152 A
1 A
28365153 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28365141 original size:18 final size:18
Alignment explanation
Indices: 28365118--28365153 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
28365108 AGTTTTCGAA
28365118 TTCGAATAACTCGAATAT
1 TTCGAATAACTCGAATAT
*
28365136 TTCGAATAATTCGAATAT
1 TTCGAATAACTCGAATAT
28365154 CAAACTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (18 bp):
TTCGAATAACTCGAATAT
Found at i:28365235 original size:30 final size:31
Alignment explanation
Indices: 28365201--28365261 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
28365191 AAACTTTTTT
* *
28365201 ACTTTTCCCTCAAAACTTTTACT-CCTTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCCTTCCC
28365231 ACTTTCCCCCCAAAACTTTTACTCCCTTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCCTTCCC
28365262 CTCCCCTCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.36
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACTCCCTTCCC
Found at i:28365273 original size:30 final size:30
Alignment explanation
Indices: 28365211--28365273 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
28365201 ACTTTTCCCT
*
28365211 CAAAACTTTTACTCCTTCCCACTTTCCCCC
1 CAAAACTTTTACTCCTTCCCACTTCCCCCC
28365241 CAAAACTTTTACTCCCTTCCC-C-TCCCCTCC
1 CAAAACTTTTACT-CCTTCCCACTTCCCC-CC
28365271 CAA
1 CAA
28365274 CCCCCCAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 4 0.13
30 19 0.63
31 7 0.23
ACGTcount: A:0.21, C:0.49, G:0.00, T:0.30
Consensus pattern (30 bp):
CAAAACTTTTACTCCTTCCCACTTCCCCCC
Found at i:28366537 original size:170 final size:170
Alignment explanation
Indices: 28366255--28366585 Score: 572
Period size: 170 Copynumber: 1.9 Consensus size: 170
28366245 TAAAGGTGTT
* * * *
28366255 CCAGAATGGGAAAAGGGCAATGGTAGAAGAAATTTCAACACTCATCAAGAATGACATGTGAGAGC
1 CCAGAATGGGAAAAAGGCAATGGTAGAAGAAATTTCAACACTCAACAAGAATGACACGTGAAAGC
28366320 TTGTACCAAAATCATTGGATGCTGATTTTGTTACCTGTAAATGGGTTTACAAATTAAAAAAATGA
66 TTGTACCAAAATCATTGGATGCTGATTTTGTTACCTGTAAATGGGTTTACAAATTAAAAAAATGA
* * *
28366385 GTTGATGGTACAATCGAGAGGTCCAAATCTCGATTTTGTA
131 GTTGACGGTACAATCGAGAGATACAAATCTCGATTTTGTA
*
28366425 CCAGAATGGGAAAAATGCAATGGTAGAAGAAATTTCAACACTCAACAAGAATGACACGTGAAAGC
1 CCAGAATGGGAAAAAGGCAATGGTAGAAGAAATTTCAACACTCAACAAGAATGACACGTGAAAGC
* *
28366490 TTGTACCAAAATCATTGGATGTTGATTTTGTTACTTGTAAATGGGTTTACAAATTAAAAAAATGA
66 TTGTACCAAAATCATTGGATGCTGATTTTGTTACCTGTAAATGGGTTTACAAATTAAAAAAATGA
28366555 GTTGACGGTACAATCGAGAGATACAAATCTC
131 GTTGACGGTACAATCGAGAGATACAAATCTC
28366586 TCCTTGTTGC
Statistics
Matches: 151, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
170 151 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (170 bp):
CCAGAATGGGAAAAAGGCAATGGTAGAAGAAATTTCAACACTCAACAAGAATGACACGTGAAAGC
TTGTACCAAAATCATTGGATGCTGATTTTGTTACCTGTAAATGGGTTTACAAATTAAAAAAATGA
GTTGACGGTACAATCGAGAGATACAAATCTCGATTTTGTA
Found at i:28371017 original size:89 final size:90
Alignment explanation
Indices: 28370901--28371086 Score: 356
Period size: 89 Copynumber: 2.1 Consensus size: 90
28370891 TAAAAATATT
28370901 AAAATAAATGTTTCTCAACAAATTAAAAATAAATTTAAAAAATTATGTATACTTAAATAACACTA
1 AAAATAAATGTTTCTCAACAAATTAAAAATAAATTTAAAAAATTATGTATACTTAAATAACACTA
28370966 AGTACAACTTAACAAGTAACTATGA
66 AGTACAACTTAACAAGTAACTATGA
28370991 AAAATAAATG-TTCTCAACAAATTAAAAATAAATTTAAAAAATTATGTATACTTAAATAACACTA
1 AAAATAAATGTTTCTCAACAAATTAAAAATAAATTTAAAAAATTATGTATACTTAAATAACACTA
28371055 AGTACAACTTAACAAGTAACTATGA
66 AGTACAACTTAACAAGTAACTATGA
*
28371080 AATATAA
1 AAAATAA
28371087 TAAAAAATTC
Statistics
Matches: 95, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
89 85 0.89
90 10 0.11
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (90 bp):
AAAATAAATGTTTCTCAACAAATTAAAAATAAATTTAAAAAATTATGTATACTTAAATAACACTA
AGTACAACTTAACAAGTAACTATGA
Found at i:28371238 original size:35 final size:36
Alignment explanation
Indices: 28371171--28371238 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 36
28371161 AAATGATAAC
* **
28371171 AAAATAGTAAAAAAAGTAACAAGAATTTTTTTTAAG
1 AAAATAGTAAAAAAAGTAACAAAAATAGTTTTTAAG
28371207 AAAA-AGTAAAAAACAGTAA-AAAAATAGTTTTT
1 AAAATAGTAAAAAA-AGTAACAAAAATAGTTTTT
28371239 TTTTTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
35 19 0.68
36 9 0.32
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.28
Consensus pattern (36 bp):
AAAATAGTAAAAAAAGTAACAAAAATAGTTTTTAAG
Found at i:28371238 original size:36 final size:36
Alignment explanation
Indices: 28371171--28371239 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
28371161 AAATGATAAC
* *
28371171 AAAATAGTAAAAAAAGTAACAAGAATTTTTTTTAAG
1 AAAATAGTAAAAAAAGTAACAAAAATGTTTTTTAAG
28371207 AAAA-AGTAAAAAACAGTAA-AAAAATAGTTTTTT
1 AAAATAGTAAAAAA-AGTAACAAAAAT-GTTTTTT
28371240 TTTTATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 14 0.48
36 15 0.52
ACGTcount: A:0.58, C:0.03, G:0.10, T:0.29
Consensus pattern (36 bp):
AAAATAGTAAAAAAAGTAACAAAAATGTTTTTTAAG
Found at i:28371619 original size:16 final size:17
Alignment explanation
Indices: 28371580--28371620 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
28371570 ATATTAAAAA
*
28371580 TATAATATTATTATTTT
1 TATAATTTTATTATTTT
*
28371597 AAT-ATTTTA-TATTTT
1 TATAATTTTATTATTTT
28371612 TATAATTTT
1 TATAATTTT
28371621 TAAAAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 8 0.40
16 10 0.50
17 2 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATAATTTTATTATTTT
Found at i:28373052 original size:4 final size:4
Alignment explanation
Indices: 28373043--28373074 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
28373033 AACAGAAGGG
28373043 AGAA AGAA AGAA A-AA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
28373075 AGGATCAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:28373316 original size:15 final size:15
Alignment explanation
Indices: 28373296--28373345 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
28373286 TGATAAATTT
28373296 ATTGAATTTATATTG
1 ATTGAATTTATATTG
28373311 ATTGAATTTGTATATAT-
1 ATTGAA-TT-TATAT-TG
*
28373328 ATTGAATATATATTG
1 ATTGAATTTATATTG
28373343 ATT
1 ATT
28373346 ATTTGAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 1 0.03
15 14 0.47
16 3 0.10
17 11 0.37
18 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:28376006 original size:42 final size:42
Alignment explanation
Indices: 28375891--28376010 Score: 177
Period size: 42 Copynumber: 2.9 Consensus size: 42
28375881 TGATTCAGTA
* * * * **
28375891 CACCGGCTTTAAGCTTGCTAGACTTATAGTCCAAATTTATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTTATTT
*
28375933 CACCGGCATTAAGCCTACTAGACGTAAAGTCTGAATTTATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTTATTT
28375975 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAT
28376011 GGTTTCATTG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (42 bp):
CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTTATTT
Found at i:28376030 original size:41 final size:42
Alignment explanation
Indices: 28375924--28376036 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
28375914 TTATAGTCCA
* **
28375924 AATTTATTTCACCGGCATTAAGCCTACTAGACGTAAAGTCTG
1 AATTGATTTCACCGGCAACAAGCCTACTAGACGTAAAGTCTG
* ** *
28375966 AATTTATTTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTG
1 AATTGATTTCACCGGCAACAAGCCTACTAGACGTAAAGTCTG
* **
28376008 AA-TGGTTTCATTGGCAACAAGCCTACTAG
1 AATTGATTTCACCGGCAACAAGCCTACTAG
28376037 GTGCTAAGCC
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 20 0.32
42 43 0.68
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (42 bp):
AATTGATTTCACCGGCAACAAGCCTACTAGACGTAAAGTCTG
Found at i:28381690 original size:21 final size:21
Alignment explanation
Indices: 28381650--28381709 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
28381640 CGAATATGCC
*
28381650 AACAGAAGCTC-GAA-AGCTG
1 AACAGAAGCTCATAAGAGCTG
28381669 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
28381690 AACAGAAGCTCATAAGAGCT
1 AACAGAAGCTCATAAGAGCT
28381710 TATCCATCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 11 0.29
20 2 0.05
21 25 0.66
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:28386456 original size:17 final size:19
Alignment explanation
Indices: 28386434--28386469 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
28386424 ATTATAAGTT
28386434 AAATAA-TAAAG-TAAAAA
1 AAATAAGTAAAGTTAAAAA
28386451 AAATAAGTAAAGTTAAAAA
1 AAATAAGTAAAGTTAAAAA
28386470 TAAGAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 5 0.29
19 6 0.35
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (19 bp):
AAATAAGTAAAGTTAAAAA
Found at i:28400613 original size:147 final size:147
Alignment explanation
Indices: 28400346--28400614 Score: 502
Period size: 147 Copynumber: 1.8 Consensus size: 147
28400336 GACACACGAG
28400346 ATGGTAAGTATGCAAATGGATTGACTCATGATCCTATAAAAATGTTGGTGTGTTAAATGATGTTT
1 ATGGTAAGTATGCAAATGGATTGACTCATGATCCTATAAAAATGTTGGTGTGTTAAATGATGTTT
*
28400411 ATATATATAGAATTCTACTTATCTTATAGTTAAATTCATTTGTATCATGAACAAGTAAGAAAAGG
66 ATATAAATAGAATTCTACTTATCTTATAGTTAAATTCATTTGTATCATGAACAAGTAAGAAAAGG
28400476 AAATGAAATGAAATGAA
131 AAATGAAATGAAATGAA
* *
28400493 ATGGTAAGTATGCAAATGGATTGACTCATGATCTTATTAAAATGTTGGTGTGTTAAATGATGTTT
1 ATGGTAAGTATGCAAATGGATTGACTCATGATCCTATAAAAATGTTGGTGTGTTAAATGATGTTT
*
28400558 ATATAAATAGAATTCTACTTATCTTATAGTTAAATTCGTTTGTATCATGAACAAGTA
66 ATATAAATAGAATTCTACTTATCTTATAGTTAAATTCATTTGTATCATGAACAAGTA
28400615 TATTAACTTG
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 118 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (147 bp):
ATGGTAAGTATGCAAATGGATTGACTCATGATCCTATAAAAATGTTGGTGTGTTAAATGATGTTT
ATATAAATAGAATTCTACTTATCTTATAGTTAAATTCATTTGTATCATGAACAAGTAAGAAAAGG
AAATGAAATGAAATGAA
Found at i:28409911 original size:31 final size:31
Alignment explanation
Indices: 28409863--28410032 Score: 127
Period size: 31 Copynumber: 5.5 Consensus size: 31
28409853 TAAGTTGCCG
* * *
28409863 AAATGATTCGTATATGGTTGA-ACATTGCTGA
1 AAATAATTTGTATATGGTT-ATACATTGTTGA
* *
28409894 AAATAATTTTTATATGGTTATTCATTGTTGA
1 AAATAATTTGTATATGGTTATACATTGTTGA
* *
28409925 AATTGAA-TTGTATAT-GTATATA-AGTTGCTG-
1 AAAT-AATTTGTATATGGT-TATACA-TTGTTGA
* * *
28409955 AAATGATTCGTATATGGTTGA-ACATTATTGA
1 AAATAATTTGTATATGGTT-ATACATTGTTGA
*
28409986 AAATAATTTTTATATGGTTATACATTGTTGA
1 AAATAATTTGTATATGGTTATACATTGTTGA
* * *
28410017 AATTAAATTGTTTATG
1 AAATAATTTGTATATG
28410033 AATATAGGAT
Statistics
Matches: 107, Mismatches: 22, Indels: 20
0.72 0.15 0.13
Matches are distributed among these distances:
29 1 0.01
30 21 0.20
31 83 0.78
32 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (31 bp):
AAATAATTTGTATATGGTTATACATTGTTGA
Found at i:28409973 original size:92 final size:92
Alignment explanation
Indices: 28409817--28410106 Score: 361
Period size: 92 Copynumber: 3.2 Consensus size: 92
28409807 GAATTGTTTT
* * *
28409817 TGGTTATACATTGCTGATATTGAATTGTATAT-TACATAAGTTGCCGAAATGATTCGTATATGGT
1 TGGTTATACATTGTTGAAATTGAATTGTATATGTATATAAGTTGCCGAAATGATTCGTATATGGT
28409881 TGAACATTGCTGAAAATAATTTTTATA
66 TGAACATTGCTGAAAATAATTTTTATA
* *
28409908 TGGTTATTCATTGTTGAAATTGAATTGTATATGTATATAAGTTGCTGAAATGATTCGTATATGGT
1 TGGTTATACATTGTTGAAATTGAATTGTATATGTATATAAGTTGCCGAAATGATTCGTATATGGT
**
28409973 TGAACATTATTGAAAATAATTTTTATA
66 TGAACATTGCTGAAAATAATTTTTATA
* * * * * * * *
28410000 TGGTTATACATTGTTGAAATTAAATTGTTTATGAATATAGGATGCCGAATTTGATTTGTATATGA
1 TGGTTATACATTGTTGAAATTGAATTGTATATGTATATAAGTTGCCGAA-ATGATTCGTATATGG
* * *
28410065 TT-ATACATTGC-CAAATTAGATTCTTATA
65 TTGA-ACATTGCTGAAAATA-ATTTTTATA
*
28410093 TGGTTATATATTGT
1 TGGTTATACATTGT
28410107 CGAATTGCTT
Statistics
Matches: 172, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
91 29 0.17
92 103 0.60
93 40 0.23
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (92 bp):
TGGTTATACATTGTTGAAATTGAATTGTATATGTATATAAGTTGCCGAAATGATTCGTATATGGT
TGAACATTGCTGAAAATAATTTTTATA
Found at i:28410135 original size:61 final size:63
Alignment explanation
Indices: 28410050--28410181 Score: 146
Period size: 61 Copynumber: 2.1 Consensus size: 63
28410040 GATGCCGAAT
* * *
28410050 TTGATTTGTATATGATTATACATTGCCAAATTAGATTCTTATATG-GT-TATATATTG-TCGAA
1 TTGATTGGTATATGATTATACATTGCCAAATTAGATTCGTATATGAATATATATATTGCT-GAA
* * * * *
28410111 TTGCTTGGTATATCGA-TATTCATTGTCGAATTTGATTCGTATATGAATATATATATTGCTGAA
1 TTGATTGGTATAT-GATTATACATTGCCAAATTAGATTCGTATATGAATATATATATTGCTGAA
28410174 TTGATTGG
1 TTGATTGG
28410182 AGCATTAGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
61 35 0.60
62 3 0.05
63 19 0.33
64 1 0.02
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.45
Consensus pattern (63 bp):
TTGATTGGTATATGATTATACATTGCCAAATTAGATTCGTATATGAATATATATATTGCTGAA
Found at i:28417014 original size:13 final size:13
Alignment explanation
Indices: 28416996--28417021 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28416986 AAATTTAAGC
28416996 CCCTAACTATTTT
1 CCCTAACTATTTT
28417009 CCCTAACTATTTT
1 CCCTAACTATTTT
28417022 TCTCCAATTT
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:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (13 bp):
CCCTAACTATTTT
Found at i:28424389 original size:28 final size:28
Alignment explanation
Indices: 28424354--28424419 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
28424344 ATAAAAAATA
**
28424354 ACCAAAATATTATAATTTTTTTTTATTT
1 ACCAAAATATTATAAAATTTTTTTATTT
28424382 ACCAAAATATTATAAAATTTTTTTATTT
1 ACCAAAATATTATAAAATTTTTTTATTT
*
28424410 ACTAAAATAT
1 ACCAAAATAT
28424420 ACCAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (28 bp):
ACCAAAATATTATAAAATTTTTTTATTT
Found at i:28427400 original size:27 final size:28
Alignment explanation
Indices: 28427370--28427431 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
28427360 TTTTTTTGGT
*
28427370 ATATTTTGGTAAAT-AAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
28427397 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
28427425 ATATTTT
1 ATATTTT
28427432 AGTTATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 14 0.42
28 19 0.58
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:28429010 original size:14 final size:14
Alignment explanation
Indices: 28428993--28429042 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
28428983 TGGATTAAAG
28428993 CTTAATTAAATTAA
1 CTTAATTAAATTAA
*
28429007 CTTAATTAACATAAA
1 CTTAATTAA-ATTAA
* *
28429022 CATAATTTAATTAA
1 CTTAATTAAATTAA
28429036 CTTAATT
1 CTTAATT
28429043 CAACATTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (14 bp):
CTTAATTAAATTAA
Found at i:28432341 original size:28 final size:28
Alignment explanation
Indices: 28432301--28432358 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
28432291 ATCAATGGTG
*
28432301 ACAACTTTTATGGTGACTTTCTCTAGAT
1 ACAACTTTTATGGCGACTTTCTCTAGAT
*
28432329 ACAATTTTTATGGCGACTTTCTCTAGAT
1 ACAACTTTTATGGCGACTTTCTCTAGAT
28432357 AC
1 AC
28432359 CAGGTTCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (28 bp):
ACAACTTTTATGGCGACTTTCTCTAGAT
Found at i:28442256 original size:2 final size:2
Alignment explanation
Indices: 28442249--28442451 Score: 406
Period size: 2 Copynumber: 101.5 Consensus size: 2
28442239 TCTACTGTTT
28442249 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28442291 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28442333 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28442375 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28442417 TA 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 TA T
28442452 TCTCTCTTCA
Statistics
Matches: 201, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 201 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28447057 original size:46 final size:46
Alignment explanation
Indices: 28446968--28447057 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 46
28446958 GAACCTTAAA
* *
28446968 TTGAAGCCTTCGTTAATTTATCATATATTCATTTTTATTCCCACCG
1 TTGAAGCCTTCGTTAATTTATCATAAATTCATTTTTATCCCCACCG
* * * *
28447014 TTGAAGCTTTCGTTAATTTCTCATAAATTTATTTTTGTCCCCAC
1 TTGAAGCCTTCGTTAATTTATCATAAATTCATTTTTATCCCCAC
28447058 ACCAACAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (46 bp):
TTGAAGCCTTCGTTAATTTATCATAAATTCATTTTTATCCCCACCG
Found at i:28448978 original size:22 final size:22
Alignment explanation
Indices: 28448952--28448998 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
28448942 ACACAAATAA
28448952 ATATAAAGTTTCACCATGTGAT
1 ATATAAAGTTTCACCATGTGAT
28448974 ATATAAAGTTTCACCATGTGAT
1 ATATAAAGTTTCACCATGTGAT
28448996 ATA
1 ATA
28448999 GATAATTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (22 bp):
ATATAAAGTTTCACCATGTGAT
Found at i:28450526 original size:30 final size:30
Alignment explanation
Indices: 28450482--28450538 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
28450472 CACGGGCTGG
* *
28450482 CACATGGGCATGTGTCCATCCCATGTGTAT
1 CACATGAGCATGTGTCCAGCCCATGTGTAT
* *
28450512 CACATGAGCGTGTGTCTAGCCCATGTG
1 CACATGAGCATGTGTCCAGCCCATGTG
28450539 GCTCTTGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (30 bp):
CACATGAGCATGTGTCCAGCCCATGTGTAT
Found at i:28452353 original size:6 final size:6
Alignment explanation
Indices: 28452342--28452407 Score: 60
Period size: 6 Copynumber: 10.5 Consensus size: 6
28452332 CAAGTCTAAG
* * *
28452342 AAAATA AAAATAA AACAACTA AAAATA AAAATA AACATA AACATA AAAAGA
1 AAAATA AAAAT-A AA-AA-TA AAAATA AAAATA AAAATA AAAATA AAAATA
* *
28452393 AAAAGA GAAATA AAA
1 AAAATA AAAATA AAA
28452408 CAAATAAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
6 40 0.78
7 5 0.10
8 5 0.10
9 1 0.02
ACGTcount: A:0.77, C:0.06, G:0.05, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:28452366 original size:21 final size:23
Alignment explanation
Indices: 28452315--28452376 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 23
28452305 AATATAGTTC
* *
28452315 AAAAGATAAAAAAAAAACAAGTCT
1 AAAAAATAAAAATAAAACAAG-CT
28452339 AAGAAAATAAAAATAAAACAA-CT
1 AA-AAAATAAAAATAAAACAAGCT
28452362 -AAAAATAAAAATAAA
1 AAAAAATAAAAATAAA
28452377 CATAAACATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 14 0.40
22 1 0.03
23 2 0.06
24 2 0.06
25 16 0.46
ACGTcount: A:0.76, C:0.06, G:0.05, T:0.13
Consensus pattern (23 bp):
AAAAAATAAAAATAAAACAAGCT
Found at i:28453354 original size:16 final size:16
Alignment explanation
Indices: 28453333--28453364 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28453323 AAAACTCTAA
28453333 GGTCAGCTCCAAATAG
1 GGTCAGCTCCAAATAG
28453349 GGTCAGCTCCAAATAG
1 GGTCAGCTCCAAATAG
28453365 CTGGGCTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (16 bp):
GGTCAGCTCCAAATAG
Found at i:28457946 original size:6 final size:6
Alignment explanation
Indices: 28457937--28457973 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
28457927 AATTATAATG
28457937 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TATAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA-AAAA
28457974 AATGGCTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 26 0.87
7 4 0.13
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:28467220 original size:26 final size:26
Alignment explanation
Indices: 28467184--28467236 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
28467174 TGGAGGACCC
28467184 TATCTCGATGTTCTACTCTTAATGTT
1 TATCTCGATGTTCTACTCTTAATGTT
*
28467210 TATCTCGATGTTTTACTCTTAATGTT
1 TATCTCGATGTTCTACTCTTAATGTT
28467236 T
1 T
28467237 GTTATTTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (26 bp):
TATCTCGATGTTCTACTCTTAATGTT
Found at i:28467236 original size:14 final size:14
Alignment explanation
Indices: 28467191--28467236 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
28467181 CCCTATCTCG
*
28467191 ATGTTCTACTCTTA
1 ATGTTTTACTCTTA
**
28467205 ATG-TTTA-TCTCG
1 ATGTTTTACTCTTA
28467217 ATGTTTTACTCTTA
1 ATGTTTTACTCTTA
28467231 ATGTTT
1 ATGTTT
28467237 GTTATTTTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
12 6 0.24
13 7 0.28
14 12 0.48
ACGTcount: A:0.20, C:0.15, G:0.11, T:0.54
Consensus pattern (14 bp):
ATGTTTTACTCTTA
Found at i:28470532 original size:111 final size:112
Alignment explanation
Indices: 28470327--28470550 Score: 441
Period size: 111 Copynumber: 2.0 Consensus size: 112
28470317 AGAATAGTCC
28470327 ACTATGCACTGAGCAATGTATAACAAGAAGCTCAATTTCTACAAAGGATTTCTGCAGTAATACTT
1 ACTATGCACTGAGCAATGTATAACAAGAAGCTCAATTTCTACAAAGGATTTCTGCAGTAATACTT
28470392 TATAGAATAATCTAATAATATTAGAAAATGAAATAAGGAAAGAAAGA
66 TATAGAATAATCTAATAATATTAGAAAATGAAATAAGGAAAGAAAGA
28470439 ACTATGCACT-AGCAATGTATAACAAGAAGCTCAATTTCTACAAAGGATTTCTGCAGTAATACTT
1 ACTATGCACTGAGCAATGTATAACAAGAAGCTCAATTTCTACAAAGGATTTCTGCAGTAATACTT
28470503 TATAGAATAATCTAATAATATTAGAAAATGAAATAAGGAAAGAAAGA
66 TATAGAATAATCTAATAATATTAGAAAATGAAATAAGGAAAGAAAGA
28470550 A
1 A
28470551 TATTATAACT
Statistics
Matches: 112, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
111 102 0.91
112 10 0.09
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.27
Consensus pattern (112 bp):
ACTATGCACTGAGCAATGTATAACAAGAAGCTCAATTTCTACAAAGGATTTCTGCAGTAATACTT
TATAGAATAATCTAATAATATTAGAAAATGAAATAAGGAAAGAAAGA
Found at i:28470740 original size:34 final size:33
Alignment explanation
Indices: 28470678--28470745 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 33
28470668 AAATAAACAC
28470678 ATAATTATTCATTTAATATTATAACTA-TTCAA
1 ATAATTATTCATTTAATATTATAACTATTTCAA
28470710 ATAA-TATT-ATTTAAATAGTTATAATTCTATTTCAA
1 ATAATTATTCATTT-AATA-TTATAA--CTATTTCAA
28470745 A
1 A
28470746 AAATCAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
30 4 0.13
31 8 0.26
32 10 0.32
34 3 0.10
35 6 0.19
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.47
Consensus pattern (33 bp):
ATAATTATTCATTTAATATTATAACTATTTCAA
Found at i:28475907 original size:146 final size:146
Alignment explanation
Indices: 28475635--28475926 Score: 566
Period size: 146 Copynumber: 2.0 Consensus size: 146
28475625 GCCCCACCTA
28475635 ACTTCGGTGTGCAAATGAGTTCCAAGCAAATTAACCTCGATGATACAATGAAGCCAATGACTATT
1 ACTTCGGTGTGCAAATGAGTTCCAAGCAAATTAACCTCGATGATACAATGAAGCCAATGACTATT
28475700 TGCGTTTTGCACTGACGAGAATAGTCCACTATGCACTGAACAATGTATAACAAAAAACTCAATTT
66 TGCGTTTTGCACTGACGAGAATAGTCCACTATGCACTGAACAATGTATAACAAAAAACTCAATTT
28475765 CTACAAAGGATTTCTG
131 CTACAAAGGATTTCTG
28475781 ACTTCGGTGTGCAAATGAGTTCCAAGCAAATTAACCTCGATGATACAATGAAGCCAATGACTATT
1 ACTTCGGTGTGCAAATGAGTTCCAAGCAAATTAACCTCGATGATACAATGAAGCCAATGACTATT
* *
28475846 TGCGTTTTGCACTGACGAGAATAGTCCACTATGCACTGAACAATGTATAACAAGAAGCTCAATTT
66 TGCGTTTTGCACTGACGAGAATAGTCCACTATGCACTGAACAATGTATAACAAAAAACTCAATTT
28475911 CTACAAAGGATTTCTG
131 CTACAAAGGATTTCTG
28475927 CAGTAATACT
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
146 144 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (146 bp):
ACTTCGGTGTGCAAATGAGTTCCAAGCAAATTAACCTCGATGATACAATGAAGCCAATGACTATT
TGCGTTTTGCACTGACGAGAATAGTCCACTATGCACTGAACAATGTATAACAAAAAACTCAATTT
CTACAAAGGATTTCTG
Found at i:28478430 original size:4 final size:4
Alignment explanation
Indices: 28478421--28478448 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
28478411 AAAAATATAT
28478421 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
28478449 ATCTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:28479314 original size:26 final size:25
Alignment explanation
Indices: 28479266--28479323 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
28479256 ATCGCTCCAA
*
28479266 GAAAGAGAAAATTCTTGAAAGAAATC
1 GAAAGAGAAAATTCTTG-AAGAAAAC
28479292 GAAAGAGAAATATTCTCTG-AGAAAAC
1 GAAAGAGAAA-ATTCT-TGAAGAAAAC
28479318 GAAAGA
1 GAAAGA
28479324 AGAAGAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 22 0.76
27 5 0.17
28 2 0.07
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.17
Consensus pattern (25 bp):
GAAAGAGAAAATTCTTGAAGAAAAC
Found at i:28480027 original size:3 final size:3
Alignment explanation
Indices: 28480019--28480045 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
28480009 GAGCAGAGCA
28480019 GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG
28480046 ACGGTTTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:28482701 original size:18 final size:18
Alignment explanation
Indices: 28482674--28482708 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28482664 CTGTAATTAG
*
28482674 TTTAAATTTTAATTTTAA
1 TTTAAATTTTAAATTTAA
*
28482692 TTTAATTTTTAAATTTA
1 TTTAAATTTTAAATTTA
28482709 GAATTATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTAAATTTTAAATTTAA
Found at i:28482817 original size:12 final size:12
Alignment explanation
Indices: 28482800--28482824 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28482790 GGTGTTCATT
28482800 CGGTTAACCGAC
1 CGGTTAACCGAC
28482812 CGGTTAACCGAC
1 CGGTTAACCGAC
28482824 C
1 C
28482825 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:28482914 original size:67 final size:67
Alignment explanation
Indices: 28482834--28483320 Score: 974
Period size: 67 Copynumber: 7.3 Consensus size: 67
28482824 CCGAAATAAC
28482834 ATTAACCGAATTAACCGACTTTTCAAAATCTTTAACCGTTAACCGAATCGAATTTTTTTTCAAAA
1 ATTAACCGAATTAACCGACTTTTCAAAATCTTTAACCGTTAACCGAATCGAATTTTTTTTCAAAA
28482899 AA
66 AA
28482901 ATTAACCGAATTAACCGACTTTTCAAAATCTTTAACCGTTAACCGAATCGAATTTTTTTTCAAAA
1 ATTAACCGAATTAACCGACTTTTCAAAATCTTTAACCGTTAACCGAATCGAATTTTTTTTCAAAA
28482966 AA
66 AA
28482968 ATTAACCGAATTAACCGACTTTTCAAAATCTTTAACCGTTAACCGAATCGAATTTTTTTTCAAAA
1 ATTAACCGAATTAACCGACTTTTCAAAATCTTTAACCGTTAACCGAATCGAATTTTTTTTCAAAA
28483033 AA
66 AA
28483035 ATTAACCGAATTAACCGACTTTTCAAAATCTTTAACCGTTAACCGAATCGAATTTTTTTTCAAAA
1 ATTAACCGAATTAACCGACTTTTCAAAATCTTTAACCGTTAACCGAATCGAATTTTTTTTCAAAA
28483100 AA
66 AA
28483102 ATTAACCGAATTAACCGACTTTTCAAAATCTTTAACCGTTAACCGAATCGAATTTTTTTTCAAAA
1 ATTAACCGAATTAACCGACTTTTCAAAATCTTTAACCGTTAACCGAATCGAATTTTTTTTCAAAA
28483167 AA
66 AA
28483169 ATTAACCGAATTAACCGACTTTTCAAAATCTTTAACCGTTAACCGAATCGAATTTTTTTTCAAAA
1 ATTAACCGAATTAACCGACTTTTCAAAATCTTTAACCGTTAACCGAATCGAATTTTTTTTCAAAA
28483234 AA
66 AA
28483236 ATTAACCGAATTAACCGACTTTTCAAAATCTTTAACCGTTAACCGAATCGAATTTTTTTTCAAAA
1 ATTAACCGAATTAACCGACTTTTCAAAATCTTTAACCGTTAACCGAATCGAATTTTTTTTCAAAA
28483301 AA
66 AA
28483303 ATTAACCGAATTAACCGA
1 ATTAACCGAATTAACCGA
28483321 AAAAATTCGG
Statistics
Matches: 420, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 420 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.34
Consensus pattern (67 bp):
ATTAACCGAATTAACCGACTTTTCAAAATCTTTAACCGTTAACCGAATCGAATTTTTTTTCAAAA
AA
Found at i:28484226 original size:17 final size:17
Alignment explanation
Indices: 28484192--28484231 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
28484182 GCTTAAAAAA
*
28484192 TATTTTATTTATCCATT
1 TATTTTATTTATCAATT
* *
28484209 TATTTTATTTTTTAATT
1 TATTTTATTTATCAATT
28484226 TATTTT
1 TATTTT
28484232 TGCATTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTTTATTTATCAATT
Found at i:28486363 original size:17 final size:17
Alignment explanation
Indices: 28486341--28486373 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28486331 TGAATGATAC
28486341 ATTTTTTGA-ATTTTTAT
1 ATTTTTT-ATATTTTTAT
28486358 ATTTTTTATATTTTTA
1 ATTTTTTATATTTTTA
28486374 AAATTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
ATTTTTTATATTTTTAT
Found at i:28486781 original size:20 final size:18
Alignment explanation
Indices: 28486738--28486786 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
28486728 TAATATTACT
28486738 ATATTATTAATAAAATTTA
1 ATATT-TTAATAAAATTTA
*
28486757 TTATTTTAATAAATGATTTA
1 ATATTTTAATAAA--ATTTA
*
28486777 ATATTGTAAT
1 ATATTTTAAT
28486787 TTTATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 8 0.32
19 4 0.16
20 13 0.52
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
ATATTTTAATAAAATTTA
Found at i:28489105 original size:19 final size:19
Alignment explanation
Indices: 28489081--28489156 Score: 125
Period size: 19 Copynumber: 4.0 Consensus size: 19
28489071 AATCTTCAGG
28489081 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28489100 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
28489119 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28489138 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28489157 NNNNNNNNNN
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:28496172 original size:19 final size:19
Alignment explanation
Indices: 28496148--28496258 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
28496138 AATCTTCAGG
28496148 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28496167 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
28496186 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28496205 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
28496224 GGTATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28496243 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
28496259 AGATATGATT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 80 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:28496198 original size:38 final size:38
Alignment explanation
Indices: 28496155--28496258 Score: 190
Period size: 38 Copynumber: 2.7 Consensus size: 38
28496145 AGGGATATGC
28496155 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
**
28496193 AATCTTAGATATGATATGCAATCTTAGATATGGTATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
28496231 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
28496259 AGATATGATT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.38
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:28496284 original size:22 final size:21
Alignment explanation
Indices: 28496148--28496284 Score: 105
Period size: 19 Copynumber: 6.9 Consensus size: 21
28496138 AATCTTCAGG
*
28496148 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
28496167 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* *
28496186 AATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
28496205 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* *
28496224 GGTATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
28496243 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
28496265 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
28496285 TTAATTTGTA
Statistics
Matches: 100, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
19 77 0.77
22 12 0.12
23 11 0.11
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:28499111 original size:143 final size:143
Alignment explanation
Indices: 28498943--28499230 Score: 576
Period size: 143 Copynumber: 2.0 Consensus size: 143
28498933 CTTAAAAACA
28498943 GGCCGAACCAAGTTGGGCTTAGACCTTAAATGTTTAAGCTTAACTTCTACCCGTATTTTAAACAA
1 GGCCGAACCAAGTTGGGCTTAGACCTTAAATGTTTAAGCTTAACTTCTACCCGTATTTTAAACAA
28499008 GCTTAATTTTTTTGCCCAAACCCTTTTTCCGGGCATAATATTTTTATCAAAACTCTCCAAAATTT
66 GCTTAATTTTTTTGCCCAAACCCTTTTTCCGGGCATAATATTTTTATCAAAACTCTCCAAAATTT
28499073 TAAGCAAAAAGGT
131 TAAGCAAAAAGGT
28499086 GGCCGAACCAAGTTGGGCTTAGACCTTAAATGTTTAAGCTTAACTTCTACCCGTATTTTAAACAA
1 GGCCGAACCAAGTTGGGCTTAGACCTTAAATGTTTAAGCTTAACTTCTACCCGTATTTTAAACAA
28499151 GCTTAATTTTTTTGCCCAAACCCTTTTTCCGGGCATAATATTTTTATCAAAACTCTCCAAAATTT
66 GCTTAATTTTTTTGCCCAAACCCTTTTTCCGGGCATAATATTTTTATCAAAACTCTCCAAAATTT
28499216 TAAGCAAAAAGGT
131 TAAGCAAAAAGGT
28499229 GG
1 GG
28499231 GTAACCCAGC
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
143 145 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (143 bp):
GGCCGAACCAAGTTGGGCTTAGACCTTAAATGTTTAAGCTTAACTTCTACCCGTATTTTAAACAA
GCTTAATTTTTTTGCCCAAACCCTTTTTCCGGGCATAATATTTTTATCAAAACTCTCCAAAATTT
TAAGCAAAAAGGT
Found at i:28503476 original size:14 final size:14
Alignment explanation
Indices: 28503443--28503476 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28503433 TAATCCTGAA
*
28503443 CCCAAACTTTAAAC
1 CCCAAACCTTAAAC
*
28503457 CTCAAACCTTAAAC
1 CCCAAACCTTAAAC
28503471 CCCAAA
1 CCCAAA
28503477 TGCAAAACTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (14 bp):
CCCAAACCTTAAAC
Found at i:28504635 original size:20 final size:19
Alignment explanation
Indices: 28504621--28504660 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
28504611 ATTATTTTGC
28504621 TTATATATTTTTTATTTTA
1 TTATATATTTTTTATTTTA
*
28504640 TTTTATATTTTTATATTTTA
1 TTATATATTTTT-TATTTTA
28504660 T
1 T
28504661 ATTTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (19 bp):
TTATATATTTTTTATTTTA
Found at i:28504653 original size:8 final size:8
Alignment explanation
Indices: 28504640--28504668 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
28504630 TTTTATTTTA
28504640 TTTTATAT
1 TTTTATAT
28504648 TTTTATA-
1 TTTTATAT
28504655 TTTTATAT
1 TTTTATAT
28504663 TTTTAT
1 TTTTAT
28504669 TTATCCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTATAT
Found at i:28504658 original size:15 final size:15
Alignment explanation
Indices: 28504638--28504668 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28504628 TTTTTTATTT
28504638 TATTTTATATTTTTA
1 TATTTTATATTTTTA
28504653 TATTTTATATTTTTA
1 TATTTTATATTTTTA
28504668 T
1 T
28504669 TTATCCATTT
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTTATATTTTTA
Found at i:28504775 original size:19 final size:18
Alignment explanation
Indices: 28504747--28504788 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
28504737 TTTATATATA
*
28504747 TATTTTTATATTTTCATT
1 TATTTCTATATTTTCATT
*
28504765 TCATTTCTATATTTTTATT
1 T-ATTTCTATATTTTCATT
28504784 TATTT
1 TATTT
28504789 TATTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTTCTATATTTTCATT
Found at i:28509206 original size:3 final size:3
Alignment explanation
Indices: 28509198--28509242 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
28509188 AACGATACTT
* *
28509198 ATA ATA ATA ATA ATA AAA ATA ATA ATA ATA GTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28509243 GAAAAAAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:28509218 original size:15 final size:15
Alignment explanation
Indices: 28509200--28509247 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
28509190 CGATACTTAT
28509200 AATAATAATAATAAA
1 AATAATAATAATAAA
**
28509215 AATAATAATAATAGT
1 AATAATAATAATAAA
28509230 AATAATAATAATAGAA
1 AATAATAATAATA-AA
28509246 AA
1 AA
28509248 AAAGATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 26 0.93
16 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (15 bp):
AATAATAATAATAAA
Found at i:28511610 original size:14 final size:14
Alignment explanation
Indices: 28511591--28511627 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
28511581 TACAATATCC
28511591 AAATAGTAACAACA
1 AAATAGTAACAACA
*
28511605 AAATAGTAGCAACA
1 AAATAGTAACAACA
*
28511619 TAATAGTAA
1 AAATAGTAA
28511628 AATAGTAGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:28511642 original size:11 final size:11
Alignment explanation
Indices: 28511603--28511643 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
28511593 ATAGTAACAA
28511603 CAAAATAGTAG
1 CAAAATAGTAG
* *
28511614 CAACATAATAG
1 CAAAATAGTAG
*
28511625 TAAAATAGTAG
1 CAAAATAGTAG
28511636 CAAAATAG
1 CAAAATAG
28511644 AAAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:28511651 original size:22 final size:22
Alignment explanation
Indices: 28511604--28511653 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
28511594 TAGTAACAAC
* *
28511604 AAAATAGTAGCAACATAATAGT
1 AAAATAGTAGCAAAATAAAAGT
28511626 AAAATAGTAGCAAAATAGAAAG-
1 AAAATAGTAGCAAAATA-AAAGT
28511648 AAAATA
1 AAAATA
28511654 ATAAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.62, C:0.06, G:0.14, T:0.18
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAAAGT
Found at i:28514763 original size:3 final size:3
Alignment explanation
Indices: 28514755--28514789 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
28514745 AATCCAGAAT
28514755 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
28514790 TTAATTGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:28516885 original size:16 final size:16
Alignment explanation
Indices: 28516864--28516897 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
28516854 TTAGATTCTT
28516864 TTTTTCTACTT-TTATA
1 TTTTTCTA-TTATTATA
28516880 TTTTTCTATTATTATA
1 TTTTTCTATTATTATA
28516896 TT
1 TT
28516898 AATTTAAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTCTATTATTATA
Found at i:28517166 original size:20 final size:20
Alignment explanation
Indices: 28517141--28517203 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
28517131 AATTTTAATA
*
28517141 AAAAATTAGAAAAAAATTAT
1 AAAAATTAGTAAAAAATTAT
* **
28517161 AAAAATTTGTAAAACTTTAT
1 AAAAATTAGTAAAAAATTAT
*
28517181 AAAAATCA-TAAAAAATTAT
1 AAAAATTAGTAAAAAATTAT
28517200 AAAA
1 AAAA
28517204 TACATAAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAAATTAGTAAAAAATTAT
Found at i:28517173 original size:10 final size:10
Alignment explanation
Indices: 28517111--28517203 Score: 55
Period size: 10 Copynumber: 9.3 Consensus size: 10
28517101 AAAAATCAAT
*
28517111 AAAAGTTATA
1 AAAATTTATA
* *
28517121 CAAA-TTATT
1 AAAATTTATA
*
28517130 AAATTTTAATA
1 AAAATTT-ATA
* *
28517141 AAAAATTAGAA
1 AAAATTTA-TA
*
28517152 AAAAATTATA
1 AAAATTTATA
*
28517162 AAAATTTGTA
1 AAAATTTATA
*
28517172 AAACTTTATA
1 AAAATTTATA
*
28517182 AAAA-TCATA
1 AAAATTTATA
*
28517191 AAAAATTATA
1 AAAATTTATA
28517201 AAA
1 AAA
28517204 TACATAAAAA
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
9 14 0.22
10 33 0.52
11 16 0.25
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (10 bp):
AAAATTTATA
Found at i:28517192 original size:19 final size:19
Alignment explanation
Indices: 28517177--28517214 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
28517167 TTGTAAAACT
28517177 TTATAAAA-ATCATAAAAAA
1 TTATAAAATA-CATAAAAAA
28517196 TTATAAAATACATAAAAAA
1 TTATAAAATACATAAAAAA
28517215 AATCCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
TTATAAAATACATAAAAAA
Found at i:28517343 original size:10 final size:9
Alignment explanation
Indices: 28517316--28517357 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 9
28517306 ACATGTGGTG
28517316 AAAAATAAT
1 AAAAATAAT
28517325 AAAAA-AAT
1 AAAAATAAT
28517333 AAAAATCAAT
1 AAAAAT-AAT
28517343 AAAAATAAT
1 AAAAATAAT
28517352 AGAAAA
1 A-AAAA
28517358 ATTATAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.27
9 9 0.30
10 13 0.43
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (9 bp):
AAAAATAAT
Found at i:28517405 original size:13 final size:13
Alignment explanation
Indices: 28517387--28517415 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
28517377 AGTACCATAA
28517387 TTTTTATATATTT
1 TTTTTATATATTT
28517400 TTTTTATATATTT
1 TTTTTATATATTT
28517413 TTT
1 TTT
28517416 CTGATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTATATATTT
Found at i:28517454 original size:29 final size:28
Alignment explanation
Indices: 28517401--28517499 Score: 74
Period size: 28 Copynumber: 3.5 Consensus size: 28
28517391 TATATATTTT
* * **
28517401 TTTTATATATTTTTTCTGATTTTTAATA
1 TTTTATATATTTTTTATTAAATTTAATA
*
28517429 TTTTATATATTTTTTATTAAAATTTATTCA
1 TTTTATATATTTTTTATT-AAATTTAAT-A
** * * *
28517459 TTTT-TATAACTTTTATTGATTTTTATA
1 TTTTATATATTTTTTATTAAATTTAATA
28517486 TTTTATCATATTTT
1 TTTTAT-ATATTTT
28517500 AGCCACATAT
Statistics
Matches: 54, Mismatches: 13, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
27 5 0.09
28 22 0.41
29 22 0.41
30 5 0.09
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (28 bp):
TTTTATATATTTTTTATTAAATTTAATA
Found at i:28518268 original size:31 final size:32
Alignment explanation
Indices: 28518233--28518299 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
28518223 TTACAATTTG
*
28518233 GTCAC-TGAACTATTCGAAAGTTTTCATTTAA
1 GTCACTTGAACTATTCAAAAGTTTTCATTTAA
* *
28518264 GTCACTTTAACTATTCAAAAGTTTTTATTTAA
1 GTCACTTGAACTATTCAAAAGTTTTCATTTAA
28518296 GTCA
1 GTCA
28518300 TTAGATTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 5 0.16
32 27 0.84
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (32 bp):
GTCACTTGAACTATTCAAAAGTTTTCATTTAA
Found at i:28526395 original size:101 final size:102
Alignment explanation
Indices: 28526278--28526462 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
28526268 AAAGTGATGG
28526278 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATGATAATGGTCGCATGTGTAGT
* *
28526341 ACTATGTGCAGGCTACTATGCGTACTGGATAGTTTCGA
65 ACTATGTGCAAGATACTATGCGTACTGGATAGTTTCGA
* *
28526379 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCTGATGGTAATGGTCGCATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGATAATGGTCGCATGTGTAGTA
28526444 CTATGTGCAAGATACTATG
66 CTATGTGCAAGATACTATG
28526463 TGAACCAAAC
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
100 4 0.05
101 41 0.53
102 33 0.42
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGATAATGGTCGCATGTGTAGTA
CTATGTGCAAGATACTATGCGTACTGGATAGTTTCGA
Found at i:28526460 original size:51 final size:50
Alignment explanation
Indices: 28526274--28526452 Score: 209
Period size: 51 Copynumber: 3.5 Consensus size: 50
28526264 AGTGAAAGTG
* * *
28526274 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCTG-ATGGT
* * * *
28526325 A-GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTA-CTGGATAGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCT-GATGGT
* * *
28526374 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCTGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCTGATGGT
*
28526425 AATGGTCGCATGTGTAGTACTATGTGCA
1 -ATGGTCACATGTGTAGTACTATGTGCA
28526453 AGATACTATG
Statistics
Matches: 105, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
49 4 0.04
50 36 0.34
51 62 0.59
52 3 0.03
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.32
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCTGATGGT
Found at i:28526535 original size:45 final size:45
Alignment explanation
Indices: 28526471--28526557 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
28526461 TGTGAACCAA
*
28526471 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGATTCCACTGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACTGG
28526516 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCAC
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCAC
28526558 CGAGTATCTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACTGG
Found at i:28532957 original size:21 final size:22
Alignment explanation
Indices: 28532931--28532975 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
28532921 CCGAAATTAT
28532931 TAAAAAAAAAA-CAATCAAGTC
1 TAAAAAAAAAACCAATCAAGTC
28532952 TAAAAAAAAAACCAATCAAGTC
1 TAAAAAAAAAACCAATCAAGTC
28532974 TA
1 TA
28532976 TATCTTTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (22 bp):
TAAAAAAAAAACCAATCAAGTC
Found at i:28538159 original size:22 final size:22
Alignment explanation
Indices: 28538112--28538159 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
28538102 ATCGTAATTC
*
28538112 GAAGTGGGTATCGTGAAACCGC
1 GAAGTGGGTATCGTGAAACCGA
* * *
28538134 GAAGTGGGTATTGTGATATCGA
1 GAAGTGGGTATCGTGAAACCGA
28538156 GAAG
1 GAAG
28538160 CCAAGACCCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.38, T:0.23
Consensus pattern (22 bp):
GAAGTGGGTATCGTGAAACCGA
Found at i:28539765 original size:12 final size:12
Alignment explanation
Indices: 28539748--28539772 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28539738 TGTGTATTTC
28539748 ATTAATTTTATA
1 ATTAATTTTATA
28539760 ATTAATTTTATA
1 ATTAATTTTATA
28539772 A
1 A
28539773 ATTATAAATA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTAATTTTATA
Found at i:28539817 original size:16 final size:16
Alignment explanation
Indices: 28539798--28539830 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28539788 TTTTATTTTT
28539798 TTGAA-TTTTTATATAC
1 TTGAACTTTTTA-ATAC
28539814 TTGAACTTTTTAATAC
1 TTGAACTTTTTAATAC
28539830 T
1 T
28539831 ATTTTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (16 bp):
TTGAACTTTTTAATAC
Found at i:28543775 original size:52 final size:53
Alignment explanation
Indices: 28543703--28543807 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 53
28543693 TTACTTCTCG
28543703 TCGAGCATTGTATTCACGTCATTGGTACGACGACTCTTCCTCGTCATGATGTT
1 TCGAGCATTGTATTCACGTCATTGGTACGACGACTCTTCCTCGTCATGATGTT
28543756 TCGAGCATTG-ATTCACGTCATTGGTACGACGACTCTTCCTCGTCATGATGTT
1 TCGAGCATTGTATTCACGTCATTGGTACGACGACTCTTCCTCGTCATGATGTT
28543808 ATCTCTGTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 42 0.81
53 10 0.19
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (53 bp):
TCGAGCATTGTATTCACGTCATTGGTACGACGACTCTTCCTCGTCATGATGTT
Found at i:28543801 original size:25 final size:25
Alignment explanation
Indices: 28543719--28543801 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 25
28543709 ATTGTATTCA
28543719 CGTCATTGGTACGACGACTCTTCCT
1 CGTCATTGGTACGACGACTCTTCCT
* * * * *
28543744 CGTCATGATGTTTCGA-GCATTGATT-CA
1 CGTCAT--TGGTACGACG-ACT-CTTCCT
28543771 CGTCATTGGTACGACGACTCTTCCT
1 CGTCATTGGTACGACGACTCTTCCT
28543796 CGTCAT
1 CGTCAT
28543802 GATGTTATCT
Statistics
Matches: 42, Mismatches: 10, Indels: 12
0.66 0.16 0.19
Matches are distributed among these distances:
24 2 0.05
25 21 0.50
26 2 0.05
27 15 0.36
28 2 0.05
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (25 bp):
CGTCATTGGTACGACGACTCTTCCT
Found at i:28545406 original size:22 final size:22
Alignment explanation
Indices: 28545353--28545397 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
28545343 AAAATAAATC
* * *
28545353 AAAATTTATCAAAATTAATTAT
1 AAAATTAATTAAAATTAAATAT
28545375 AAAATTAATTAAAATTAAATAT
1 AAAATTAATTAAAATTAAATAT
28545397 A
1 A
28545398 TTAATAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAATTAATTAAAATTAAATAT
Found at i:28553966 original size:30 final size:31
Alignment explanation
Indices: 28553930--28553989 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
28553920 AGTTAATACT
* **
28553930 AAAAAATTGAGGGGTTAA-AGTGTAAATATG
1 AAAAAATTGAAGGACTAATAGTGTAAATATG
28553960 AAAAAATTGAAGGACTAATAGTGTAAATAT
1 AAAAAATTGAAGGACTAATAGTGTAAATAT
28553990 TTTAAGGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.50, C:0.02, G:0.22, T:0.27
Consensus pattern (31 bp):
AAAAAATTGAAGGACTAATAGTGTAAATATG
Found at i:28555920 original size:43 final size:44
Alignment explanation
Indices: 28555853--28556094 Score: 312
Period size: 43 Copynumber: 5.4 Consensus size: 44
28555843 TTTCAGTACT
*
28555853 TCTGATCAGTGACAAGT-GATAAGTGTAGCTTCAGCTACACTTA
1 TCTGATCAGTGACAAGTGGCTAAGTGTAGCTTCAGCTACACTTA
* *
28555896 TCTGATCAGTGACAAGTGGCAAGTGATAAGTGATAGCTTCAGTTACCCTTA
1 TCTGATCAGTGACAAGTGGC------TAAGTG-TAGCTTCAGCTACACTTA
28555947 TCTGATCAGTGACAAGT-GCTAAGTGTAGCTTCAGCTACACTTA
1 TCTGATCAGTGACAAGTGGCTAAGTGTAGCTTCAGCTACACTTA
* * * *
28555990 TCTGATCAGGGACAAGT-GATAAGTGATAGCTTCAGTTACCCTTA
1 TCTGATCAGTGACAAGTGGCTAAGTG-TAGCTTCAGCTACACTTA
28556034 TCTGATCAGTGACAAGT-GCTAAGTGTAGCTTCAGCTACACTTA
1 TCTGATCAGTGACAAGTGGCTAAGTGTAGCTTCAGCTACACTTA
*
28556077 TCTGATCAGGGACAAGTG
1 TCTGATCAGTGACAAGTG
28556095 ATAAGTGATC
Statistics
Matches: 175, Mismatches: 14, Indels: 19
0.84 0.07 0.09
Matches are distributed among these distances:
43 88 0.50
44 46 0.26
50 8 0.05
51 33 0.19
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGGCTAAGTGTAGCTTCAGCTACACTTA
Found at i:28556014 original size:94 final size:92
Alignment explanation
Indices: 28555853--28556095 Score: 415
Period size: 87 Copynumber: 2.7 Consensus size: 92
28555843 TTTCAGTACT
* *
28555853 TCTGATCAGTGACAAGTGATAAGTGTAGCTTCAGCTACACTTATCTGATCAGTGACAAGTGGCAA
1 TCTGATCAGTGACAAGTGCTAAGTGTAGCTTCAGCTACACTTATCTGATCAGGGACAAGT-G-AA
28555918 GTGATAAGTGATAGCTTCAGTTACCCTTA
64 GTGATAAGTGATAGCTTCAGTTACCCTTA
28555947 TCTGATCAGTGACAAGTGCTAAGTGTAGCTTCAGCTACACTTATCTGATCAGGGAC-----AAGT
1 TCTGATCAGTGACAAGTGCTAAGTGTAGCTTCAGCTACACTTATCTGATCAGGGACAAGTGAAGT
28556007 GATAAGTGATAGCTTCAGTTACCCTTA
66 GATAAGTGATAGCTTCAGTTACCCTTA
28556034 TCTGATCAGTGACAAGTGCTAAGTGTAGCTTCAGCTACACTTATCTGATCAGGGACAAGTGA
1 TCTGATCAGTGACAAGTGCTAAGTGTAGCTTCAGCTACACTTATCTGATCAGGGACAAGTGA
28556096 TAAGTGATCA
Statistics
Matches: 142, Mismatches: 2, Indels: 12
0.91 0.01 0.08
Matches are distributed among these distances:
87 87 0.61
92 1 0.01
94 54 0.38
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (92 bp):
TCTGATCAGTGACAAGTGCTAAGTGTAGCTTCAGCTACACTTATCTGATCAGGGACAAGTGAAGT
GATAAGTGATAGCTTCAGTTACCCTTA
Found at i:28556138 original size:87 final size:86
Alignment explanation
Indices: 28555915--28556119 Score: 288
Period size: 87 Copynumber: 2.4 Consensus size: 86
28555905 TGACAAGTGG
* * * *
28555915 CAAGTGATAAGTGATAGCTTCAGTTACCCTTATCTGATCAGTGACAAGTGCTAAGTGTAGCTTCA
1 CAAGTGATAAGTGATA-CTACAGTAAACCATATCTGATCAGTGACAAGTGCTAAGTGTAGCTTCA
28555980 GCTACACTTATCTGATCAGGGA
65 GCTACACTTATCTGATCAGGGA
* * * *
28556002 CAAGTGATAAGTGATAGCTTCAGTTACCCTTATCTGATCAGTGACAAGTGCTAAGTGTAGCTTCA
1 CAAGTGATAAGTGATA-CTACAGTAAACCATATCTGATCAGTGACAAGTGCTAAGTGTAGCTTCA
28556067 GCTACACTTATCTGATCAGGGA
65 GCTACACTTATCTGATCAGGGA
28556089 CAAGTGATAAGTGAT-CATAC-GTAAGACCATA
1 CAAGTGATAAGTGATAC-TACAGTAA-ACCATA
28556120 GTTATACTAT
Statistics
Matches: 112, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
85 4 0.04
86 6 0.05
87 102 0.91
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (86 bp):
CAAGTGATAAGTGATACTACAGTAAACCATATCTGATCAGTGACAAGTGCTAAGTGTAGCTTCAG
CTACACTTATCTGATCAGGGA
Found at i:28559311 original size:59 final size:61
Alignment explanation
Indices: 28559232--28559349 Score: 161
Period size: 62 Copynumber: 2.0 Consensus size: 61
28559222 AATTACTTTA
* * *
28559232 ATATTAAATTAATATGATATTTA-T-CAAGATAAATATTAGATTAAATTTAATATTAAATT
1 ATATTAAATTAAGATGATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAATT
*
28559291 ATATTAAATTAAGA-GAATATTTATCTACAAGATAAACATTAAATTTAATTTAATATTAA
1 ATATTAAATTAAGATG-ATATTTA-CTACAAGATAAACATTAAATTAAATTTAATATTAA
28559350 GATAATAACT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
58 1 0.02
59 20 0.39
61 1 0.02
62 29 0.57
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (61 bp):
ATATTAAATTAAGATGATATTTACTACAAGATAAACATTAAATTAAATTTAATATTAAATT
Found at i:28559375 original size:20 final size:19
Alignment explanation
Indices: 28559328--28559377 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
28559318 CAAGATAAAC
28559328 ATTAAATT--TAATTTAAT
1 ATTAAATTAATAATTTAAT
28559345 ATTAAGA-TAATAACTTTAAT
1 ATTAA-ATTAATAA-TTTAAT
28559365 ATTAAATTAATAA
1 ATTAAATTAATAA
28559378 AATATTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.21
18 1 0.04
19 4 0.14
20 17 0.61
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
ATTAAATTAATAATTTAAT
Found at i:28559381 original size:25 final size:25
Alignment explanation
Indices: 28559334--28559381 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
28559324 AAACATTAAA
*
28559334 TTTAATTTAATATTAAGATAATAAC
1 TTTAATTTAATATTAAGAAAATAAC
*
28559359 TTTAATATTAA-ATTAATAAAATA
1 TTTAAT-TTAATATTAAGAAAATA
28559382 TTATTAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATAAC
Found at i:28559434 original size:68 final size:71
Alignment explanation
Indices: 28559291--28559440 Score: 164
Period size: 68 Copynumber: 2.1 Consensus size: 71
28559281 ATATTAAATT
*
28559291 ATATTAAATTAAGAGAATATTTATCTACAAGATAAACATTAAATTTAATTTAATATTAAGATAAT
1 ATATTAAATTAAGAAAATATTTATCTA-AAGATAAACATTAAATTTAATTTAATATTAAGATAAT
****
28559356 AACTTTA
65 AAAAACA
* ** *
28559363 ATATTAAATTAATAAAATA-TTAT-T-AAGATAAGTATTAAATTTAATTTAATATTTAA-ATATT
1 ATATTAAATTAAGAAAATATTTATCTAAAGATAAACATTAAATTTAATTTAATA-TTAAGATAAT
28559424 AAAAACA
65 AAAAACA
28559431 ATATTGAAAT
1 ATATT-AAAT
28559441 AGTTAATCTG
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
68 37 0.55
69 8 0.12
70 1 0.01
71 4 0.06
72 17 0.25
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (71 bp):
ATATTAAATTAAGAAAATATTTATCTAAAGATAAACATTAAATTTAATTTAATATTAAGATAATA
AAAACA
Found at i:28561950 original size:45 final size:44
Alignment explanation
Indices: 28561846--28561983 Score: 179
Period size: 45 Copynumber: 3.1 Consensus size: 44
28561836 TCCAAACACT
* * * *
28561846 CCAA-ATTTGCAGACAAGCTGTCATGTAGGTTGTGGATAAACCA
1 CCAATATTCGCAGACAAGCTGCCATGTAGGTTGTGGAGAAGCCA
*
28561889 CCAAAATTCGCAGACAAGCTGCCATGTAGGTTGTGGACGAAGCCA
1 CCAATATTCGCAGACAAGCTGCCATGTAGGTTGTGGA-GAAGCCA
* * *
28561934 CCAATATTCGCAGACAAGCTACCATGTAGGTTGTAGATGAAGGCA
1 CCAATATTCGCAGACAAGCTGCCATGTAGGTTGTGGA-GAAGCCA
28561979 CCAAT
1 CCAAT
28561984 TCTTTCTCCT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
43 4 0.05
44 30 0.36
45 50 0.60
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (44 bp):
CCAATATTCGCAGACAAGCTGCCATGTAGGTTGTGGAGAAGCCA
Found at i:28565963 original size:3 final size:3
Alignment explanation
Indices: 28565955--28565980 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28565945 TAATTAAATC
28565955 ACA ACA ACA ACA ACA ACA ACA ACA AC
1 ACA ACA ACA ACA ACA ACA ACA ACA AC
28565981 TAATTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:28575736 original size:25 final size:25
Alignment explanation
Indices: 28575704--28575847 Score: 82
Period size: 25 Copynumber: 5.9 Consensus size: 25
28575694 AGCCCTCTCT
28575704 CGAGCCATATAACGGGAAGCTCATA
1 CGAGCCATATAACGGGAAGCTCATA
* * * * * *
28575729 TGAGCCATGTGACGGAAAGCTTATC
1 CGAGCCATATAACGGGAAGCTCATA
* * * ** *
28575754 CGGGCTATCTAACGAAAAGCTCAAA
1 CGAGCCATATAACGGGAAGCTCATA
* * *
28575779 AGAGCCATA-ATCGGGAAGCTCATG
1 CGAGCCATATAACGGGAAGCTCATA
*
28575803 CGAGCCA-ATAACGGGTAGCTTCGA-A
1 CGAGCCATATAACGGGAAGC-TC-ATA
*
28575828 -GAGCTAT-TAACGGGAAGCTC
1 CGAGCCATATAACGGGAAGCTC
28575848 CTGATAGCCA
Statistics
Matches: 85, Mismatches: 30, Indels: 10
0.68 0.24 0.08
Matches are distributed among these distances:
23 3 0.04
24 39 0.46
25 42 0.49
26 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.18
Consensus pattern (25 bp):
CGAGCCATATAACGGGAAGCTCATA
Found at i:28575947 original size:26 final size:26
Alignment explanation
Indices: 28575877--28575951 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
28575867 AAGTTCAAGC
28575877 GAGCCATAT--CGGGAAGCTCACAAA
1 GAGCCATATAACGGGAAGCTCACAAA
* *
28575901 GAGCC-TTTAACCAGGAAGCTCA-AGAA
1 GAGCCATATAA-CGGGAAGCTCACA-AA
*
28575927 GAGCCATATAACGGGATGCTCACAA
1 GAGCCATATAACGGGAAGCTCACAA
28575952 GTGCTGCGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
23 2 0.05
24 5 0.12
25 1 0.03
26 27 0.68
27 5 0.12
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (26 bp):
GAGCCATATAACGGGAAGCTCACAAA
Found at i:28581339 original size:15 final size:15
Alignment explanation
Indices: 28581321--28581351 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28581311 TGACATCAGT
28581321 GATCACGTCATCGAG
1 GATCACGTCATCGAG
28581336 GATCACGTCATCGAG
1 GATCACGTCATCGAG
28581351 G
1 G
28581352 CAACACTTCT
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:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (15 bp):
GATCACGTCATCGAG
Found at i:28593745 original size:17 final size:16
Alignment explanation
Indices: 28593725--28593756 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
28593715 TATGGAGTAA
28593725 TTTCTTTTTCTTTTTTT
1 TTTCTTTTT-TTTTTTT
28593742 TTTCTTTTTTTTTTT
1 TTTCTTTTTTTTTTT
28593757 GTTTAGGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (16 bp):
TTTCTTTTTTTTTTTT
Found at i:28593756 original size:12 final size:11
Alignment explanation
Indices: 28593729--28593755 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
28593719 GAGTAATTTC
28593729 TTTTTCTTTTT
1 TTTTTCTTTTT
28593740 TTTTTCTTTTT
1 TTTTTCTTTTT
28593751 TTTTT
1 TTTTT
28593756 TGTTTAGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:28595256 original size:18 final size:19
Alignment explanation
Indices: 28595214--28595256 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
28595204 TCTGCTTCAA
*
28595214 TTTAATTTTTACTAATTATT
1 TTTAATTTTTA-TAAATATT
*
28595234 ATTAATTTTT-TAAATATT
1 TTTAATTTTTATAAATATT
28595252 TTTAA
1 TTTAA
28595257 AGTTAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 11 0.55
20 9 0.45
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTAATTTTTATAAATATT
Found at i:28595947 original size:21 final size:21
Alignment explanation
Indices: 28595922--28595992 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
28595912 GTTTTTAAGG
28595922 TTAGGGTTTTGTTAAAATAAT
1 TTAGGGTTTTGTTAAAATAAT
** *** ***
28595943 TTAGGGTTAAGTTTGTAGGGT
1 TTAGGGTTTTGTTAAAATAAT
28595964 TTAGGGTTTTGTTAAAATAAT
1 TTAGGGTTTTGTTAAAATAAT
*
28595985 TTAAGGTT
1 TTAGGGTT
28595993 CAAGGTTTTA
Statistics
Matches: 33, Mismatches: 17, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.46
Consensus pattern (21 bp):
TTAGGGTTTTGTTAAAATAAT
Found at i:28596087 original size:34 final size:34
Alignment explanation
Indices: 28596042--28596133 Score: 116
Period size: 34 Copynumber: 2.7 Consensus size: 34
28596032 GTTCCTTTTT
28596042 AAAAATTAATTAAATTAGGGTTTAG-GGGTTTAA
1 AAAAATTAATTAAATTAGGGTTTAGTGGGTTTAA
* **
28596075 AATAAATTAATTAAATTTGGGTTTAGTGTTTTTAA
1 AA-AAATTAATTAAATTAGGGTTTAGTGGGTTTAA
*
28596110 GAAAATTAATTAAATTTA-GGTTTA
1 AAAAATTAATTAAA-TTAGGGTTTA
28596134 TTTTTAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 2 0.04
34 40 0.78
35 9 0.18
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.42
Consensus pattern (34 bp):
AAAAATTAATTAAATTAGGGTTTAGTGGGTTTAA
Found at i:28596481 original size:126 final size:126
Alignment explanation
Indices: 28596207--28596662 Score: 672
Period size: 126 Copynumber: 3.6 Consensus size: 126
28596197 GGATTTTGGT
* * *
28596207 TTTTTCTACAATAGTTCCT-AAAAAATAATTTTGAGAATACGGTTCTGAACAAATAGTGTC-AAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTCAAAA
* ** * * *
28596270 ACGCTTCAAACAGGATGCACGGTCAGC-AAATT-ACT-AGAAAAAGCTCTCACGTG-GTCGCTC
66 ACGCTTCAAGCAGGATGCACTATCAGCAAAATTGA-TGA-AAAAAGCTCCCACGTGAAT-GTTC
* *
28596330 TTTTTCTATAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTCAAAA
28596395 ACGCTTCAAGCAGGATGCACTATCAGCAAAATTGATGAAAAAAGCTCCCACGTGAATGTTC
66 ACGCTTCAAGCAGGATGCACTATCAGCAAAATTGATGAAAAAAGCTCCCACGTGAATGTTC
* * *
28596456 TTTTTCTACAGTAGTTACTGAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTCAAAA
* *
28596521 ACACTTCAAGCAGGATGCACTATCAGCAAAATTGATGAAAAAAGCTCCCACGTGAACGTTC
66 ACGCTTCAAGCAGGATGCACTATCAGCAAAATTGATGAAAAAAGCTCCCACGTGAATGTTC
* *
28596582 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAAACGTTTCTAAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTCAAAA
*
28596647 ACGTTTCAAGCAGGAT
66 ACGCTTCAAGCAGGAT
28596663 TTACGTGGAC
Statistics
Matches: 305, Mismatches: 22, Indels: 9
0.91 0.07 0.03
Matches are distributed among these distances:
123 17 0.06
124 39 0.13
125 27 0.09
126 219 0.72
127 3 0.01
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.28
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTATCAGCAAAATTGATGAAAAAAGCTCCCACGTGAATGTTC
Found at i:28598259 original size:18 final size:17
Alignment explanation
Indices: 28598222--28598273 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
28598212 CTAAAGGACG
* *
28598222 ACAAATAATCGATAAAT
1 ACAAATAAGCAATAAAT
28598239 ACAAATAAGCAATACAAT
1 ACAAATAAGCAATA-AAT
*
28598257 ACACATGAGAGCAATAA
1 ACAAAT-A-AGCAATAA
28598274 TCTCACATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 12 0.41
18 8 0.28
19 2 0.07
20 7 0.24
ACGTcount: A:0.58, C:0.15, G:0.10, T:0.17
Consensus pattern (17 bp):
ACAAATAAGCAATAAAT
Found at i:28599042 original size:3 final size:3
Alignment explanation
Indices: 28599026--28599082 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
28599016 ACTAATATAG
* * * *
28599026 TAA TAA T-A TCAA TAA TAA TAA TAT TAG TAA TAA TAA TGA TAA TGA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28599071 TAA TAA TAA TAA
1 TAA TAA TAA TAA
28599083 ATTAATTGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.91
4 2 0.04
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:28599092 original size:21 final size:20
Alignment explanation
Indices: 28599036--28599105 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 20
28599026 TAATAATATC
28599036 AATAATAATAATATT-A-G-T
1 AATAATAATAA-ATTAATGAT
*
28599054 AATAATAAT-GA-TAATGAT
1 AATAATAATAAATTAATGAT
28599072 AATAATAATAAATTAATTGAT
1 AATAATAATAAATTAA-TGAT
28599093 AA-AATAAATAAAT
1 AATAAT-AATAAAT
28599106 AACAAAAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
15 1 0.02
16 2 0.05
17 1 0.02
18 19 0.44
19 1 0.02
20 6 0.14
21 13 0.30
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (20 bp):
AATAATAATAAATTAATGAT
Found at i:28599157 original size:12 final size:12
Alignment explanation
Indices: 28599140--28599164 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28599130 AAACTTAATT
28599140 AACAGGAAACAA
1 AACAGGAAACAA
28599152 AACAGGAAACAA
1 AACAGGAAACAA
28599164 A
1 A
28599165 CGAAATTAAA
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:0.68, C:0.16, G:0.16, T:0.00
Consensus pattern (12 bp):
AACAGGAAACAA
Found at i:28603059 original size:26 final size:27
Alignment explanation
Indices: 28603030--28603102 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 27
28603020 TATTCAAAAG
28603030 AAATTTTATTTTATTAAAAAATATAAA
1 AAATTTTATTTTATTAAAAAATATAAA
* * * *
28603057 AATAATTTA--CTATTAAAATATTTAAA
1 AA-ATTTTATTTTATTAAAAAATATAAA
28603083 ACAACTTTTATTTTATTAAA
1 A-AA-TTTTATTTTATTAAA
28603103 TGAAACAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
26 16 0.46
27 7 0.20
28 5 0.14
29 7 0.20
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (27 bp):
AAATTTTATTTTATTAAAAAATATAAA
Found at i:28603190 original size:21 final size:21
Alignment explanation
Indices: 28603164--28603208 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
28603154 TAGTTCAGCT
*
28603164 TCCGGTGAGGGTTGTGGTTGC
1 TCCGGTGAGGGTTGTGGTTCC
28603185 TCCGGTGAGGGTTGTGGTTCC
1 TCCGGTGAGGGTTGTGGTTCC
28603206 TCC
1 TCC
28603209 TGTTGTGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.04, C:0.20, G:0.42, T:0.33
Consensus pattern (21 bp):
TCCGGTGAGGGTTGTGGTTCC
Found at i:28605495 original size:18 final size:18
Alignment explanation
Indices: 28605472--28605507 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
28605462 GGAAAAGCAA
*
28605472 ACATATAAGGGTTAGGAT
1 ACATATAAGGGCTAGGAT
28605490 ACATATAAGGGCTAGGAT
1 ACATATAAGGGCTAGGAT
28605508 GCGTACCTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25
Consensus pattern (18 bp):
ACATATAAGGGCTAGGAT
Found at i:28607205 original size:30 final size:30
Alignment explanation
Indices: 28607171--28607229 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
28607161 AATTAAAGAG
28607171 AGCTTTGAGAAATTGAAAGAAAAATTTGAA
1 AGCTTTGAGAAATTGAAAGAAAAATTTGAA
* * *
28607201 AGCTTTGAGAAATTTAGAGAGAAATTTGA
1 AGCTTTGAGAAATTGAAAGAAAAATTTGA
28607230 GAGTTTTGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.46, C:0.03, G:0.22, T:0.29
Consensus pattern (30 bp):
AGCTTTGAGAAATTGAAAGAAAAATTTGAA
Found at i:28607244 original size:30 final size:29
Alignment explanation
Indices: 28607171--28607256 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 29
28607161 AATTAAAGAG
*
28607171 AGCTTTGAGAAATTGA-AAGAAAAATTTGAA
1 AGCTTTGAGAAATTTAGAAG--AAATTTGAA
*
28607201 AGCTTTGAGAAATTTAGAGAGAAATTTGAG
1 AGCTTTGAGAAATTTAGA-AGAAATTTGAA
* ** *
28607231 AGTTTTGCTAAATTTTGAAGAAATTT
1 AGCTTTGAGAAATTTAGAAGAAATTT
28607257 TGTGTACAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
29 8 0.17
30 37 0.77
31 1 0.02
32 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (29 bp):
AGCTTTGAGAAATTTAGAAGAAATTTGAA
Found at i:28607882 original size:19 final size:17
Alignment explanation
Indices: 28607858--28607907 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
28607848 TTTTCTTTTT
28607858 TTCTCATTTATTTCTCAC
1 TTCTCATTTATTT-TCAC
* *
28607876 TTACTCATGTATTTTTAC
1 TT-CTCATTTATTTTCAC
*
28607894 TTTTCATTTATTTT
1 TTCTCATTTATTTT
28607908 ATTTTTTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 10 0.37
18 7 0.26
19 10 0.37
ACGTcount: A:0.18, C:0.18, G:0.02, T:0.62
Consensus pattern (17 bp):
TTCTCATTTATTTTCAC
Done.