Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 99 of 203
Found at i:31322284 original size:38 final size:38
Alignment explanation
Indices: 31322233--31322310 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
31322223 AGATTGAATC
31322233 TTTCAACATCTTGAAGATGAAGTTGTAAGAGAGAAAGT
1 TTTCAACATCTTGAAGATGAAGTTGTAAGAGAGAAAGT
31322271 TTTCAACATCTTGAAGATGAAGTTGTAAGAGAGAAAGT
1 TTTCAACATCTTGAAGATGAAGTTGTAAGAGAGAAAGT
31322309 TT
1 TT
31322311 AAGGTGAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (38 bp):
TTTCAACATCTTGAAGATGAAGTTGTAAGAGAGAAAGT
Found at i:31326879 original size:4 final size:4
Alignment explanation
Indices: 31325541--31326870 Score: 1777
Period size: 4 Copynumber: 332.8 Consensus size: 4
31325531 GAATATCATG
*
31325541 CATA CATG CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
31325589 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATC CCTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
31325637 CATA CATA CATA CATA CATC CCTA CATA CATA CATC CCTA CATA CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
31325685 CATA CATA TATG CATC CATA CATG CATA CATA CATA CATG CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
31325733 CATG GATC CATA CATA CATA CATA CATA CATA CATC CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
31325781 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
** * *
31325829 CATA TTTG CATA CATA CATA CATA CATA CATA CATA CATA CATA CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
31325877 CATG CATA CCTA CATA CATA CATG CATA CATA CATA CATA CAT- CTATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C-ATA
*
31325925 CATA CATA CATA CATA CATA CATA CGTA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
31325973 CATG CATG CATA CATG CATA CATG CATA CATA CATA CATA CATG TATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
31326021 CATA CATA CATA CATA CATA CATA CATG CATG CATG CATA CATA CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
31326069 CATG CATG CATA CATA CATA CATG CATA CATA CATA CACA CATA CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
31326117 CATA CATA CATA C--A CACA CACA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
31326163 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
31326211 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
31326259 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
31326307 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
31326355 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
31326403 CATA CATG CATA CATA TATG CATA CATA TATA CATA CATA CATA CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
31326451 CATG CATA CATA CATG CATA CATA TATG CATA CATA TATG CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
31326499 TATA CATA CATA CATG CATA CATA CATA CATG CATG CATA TATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
31326547 CATG CATG CATA CATA CATG CATA CATA CATA CATA CATG CATG TATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
31326595 CATA CATA CATA CATA CATA TATA CATA CATG CATG CATA CATG CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
31326643 CATA CATA CATG CATG CATA CATG CATG CATA CATA CATG CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
31326691 CATG CATA CATA CATG CATG CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
31326739 TATA CATA CATA CATA CATA CATA CATA TATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
31326787 CATA CATG CATG CATA CATG CATA CATA TATG CATA CATA CATA CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
31326835 CATA CATGA -ATA CATG CATG CATG CATA TCATA CAT
1 CATA CAT-A CATA CATA CATA CATA CATA -CATA CAT
31326871 GCATGCATGT
Statistics
Matches: 1178, Mismatches: 141, Indels: 14
0.88 0.11 0.01
Matches are distributed among these distances:
2 2 0.00
3 2 0.00
4 1168 0.99
5 6 0.01
ACGTcount: A:0.44, C:0.25, G:0.05, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:31327404 original size:21 final size:21
Alignment explanation
Indices: 31327378--31327420 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
31327368 CGTATGAAGG
*
31327378 GGTTACACGGTCGTGTGGCTA
1 GGTTACACGATCGTGTGGCTA
31327399 GGTTACACGATCGTGTGGCTA
1 GGTTACACGATCGTGTGGCTA
31327420 G
1 G
31327421 CCAATATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.19, G:0.37, T:0.28
Consensus pattern (21 bp):
GGTTACACGATCGTGTGGCTA
Found at i:31331667 original size:15 final size:15
Alignment explanation
Indices: 31331647--31331678 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31331637 CATTTCACTA
*
31331647 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
31331662 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
31331677 TT
1 TT
31331679 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:31338580 original size:23 final size:23
Alignment explanation
Indices: 31338550--31338604 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
31338540 GGATTTGCCG
31338550 ATCAGGCACTATATGTGTCGTAT
1 ATCAGGCACTATATGTGTCGTAT
* *
31338573 ATCAGGCATTTTATGTGTCGTAT
1 ATCAGGCACTATATGTGTCGTAT
*
31338596 TTCAGGCAC
1 ATCAGGCAC
31338605 CTCGTGGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (23 bp):
ATCAGGCACTATATGTGTCGTAT
Found at i:31338646 original size:21 final size:21
Alignment explanation
Indices: 31338594--31338646 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
31338584 TATGTGTCGT
*
31338594 ATTTCAGGCACCTCGTGGGTC
1 ATTTCAGGCACCTCGTGGATC
* * *
31338615 GTATCAGGCACCTCGTGTATC
1 ATTTCAGGCACCTCGTGGATC
*
31338636 ATTTCAAGCAC
1 ATTTCAGGCAC
31338647 TTATGTGTCG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (21 bp):
ATTTCAGGCACCTCGTGGATC
Found at i:31339801 original size:18 final size:18
Alignment explanation
Indices: 31339778--31339831 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
31339768 ATTCCAAAAA
*
31339778 TAATATTATTTTAATAGT
1 TAATATTATATTAATAGT
* *
31339796 TAATATTAAATTAA-ATT
1 TAATATTATATTAATAGT
*
31339813 TAATACTTATCTTAATAGT
1 TAATA-TTATATTAATAGT
31339832 ATTTTATTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 7 0.25
18 19 0.68
19 2 0.07
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (18 bp):
TAATATTATATTAATAGT
Found at i:31339852 original size:11 final size:11
Alignment explanation
Indices: 31339778--31339852 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
31339768 ATTCCAAAAA
*
31339778 TAATATTATTT
1 TAATATTAATT
31339789 TAATAGTTAATAT
1 TAATA-TTAAT-T
31339802 TAA-ATTAAATT
1 TAATATT-AATT
31339813 TAATACTT-ATCT
1 TAATA-TTAAT-T
*
31339825 TAATAGT-ATT
1 TAATATTAATT
31339835 T--TATTAATT
1 TAATATTAATT
31339844 TAATATTAA
1 TAATATTAA
31339853 AGTGATTATC
Statistics
Matches: 52, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 2 0.04
11 22 0.42
12 15 0.29
13 6 0.12
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.52
Consensus pattern (11 bp):
TAATATTAATT
Found at i:31340073 original size:18 final size:18
Alignment explanation
Indices: 31340050--31340103 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
31340040 ATTCCAAAAA
*
31340050 TAATATTATTTTAATAGT
1 TAATATTATATTAATAGT
* *
31340068 TAATATTAAATTAA-ATT
1 TAATATTATATTAATAGT
*
31340085 TAATACTTATCTTAATAGT
1 TAATA-TTATATTAATAGT
31340104 ATTTTATTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 7 0.25
18 19 0.68
19 2 0.07
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (18 bp):
TAATATTATATTAATAGT
Found at i:31340124 original size:11 final size:11
Alignment explanation
Indices: 31340050--31340124 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
31340040 ATTCCAAAAA
*
31340050 TAATATTATTT
1 TAATATTAATT
31340061 TAATAGTTAATAT
1 TAATA-TTAAT-T
31340074 TAA-ATTAAATT
1 TAATATT-AATT
31340085 TAATACTT-ATCT
1 TAATA-TTAAT-T
*
31340097 TAATAGT-ATT
1 TAATATTAATT
31340107 T--TATTAATT
1 TAATATTAATT
31340116 TAATATTAA
1 TAATATTAA
31340125 AGTGATTATC
Statistics
Matches: 52, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 2 0.04
11 22 0.42
12 15 0.29
13 6 0.12
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.52
Consensus pattern (11 bp):
TAATATTAATT
Found at i:31340155 original size:272 final size:272
Alignment explanation
Indices: 31339669--31340212 Score: 1088
Period size: 272 Copynumber: 2.0 Consensus size: 272
31339659 GTAAATTGAC
31339669 CGATATGTTCTGTAATGCCTCATAGCCCTGTTTCGGTGACGGTTTGGGGTTAGGGGGTGTTACAG
1 CGATATGTTCTGTAATGCCTCATAGCCCTGTTTCGGTGACGGTTTGGGGTTAGGGGGTGTTACAG
31339734 GGACTCTACTAGAGAATTTGATTTCAGATTAATTATTCCAAAAATAATATTATTTTAATAGTTAA
66 GGACTCTACTAGAGAATTTGATTTCAGATTAATTATTCCAAAAATAATATTATTTTAATAGTTAA
31339799 TATTAAATTAAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATATTAAAGTGATTATCT
131 TATTAAATTAAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATATTAAAGTGATTATCT
31339864 TAATATTTAATTTAATTTTTATTTTATAGATAAATATTCTATTATTTTAATAAGATTTAATATTA
196 TAATATTTAATTTAATTTTTATTTTATAGATAAATATTCTATTATTTTAATAAGATTTAATATTA
31339929 AATTTAATCTAA
261 AATTTAATCTAA
31339941 CGATATGTTCTGTAATGCCTCATAGCCCTGTTTCGGTGACGGTTTGGGGTTAGGGGGTGTTACAG
1 CGATATGTTCTGTAATGCCTCATAGCCCTGTTTCGGTGACGGTTTGGGGTTAGGGGGTGTTACAG
31340006 GGACTCTACTAGAGAATTTGATTTCAGATTAATTATTCCAAAAATAATATTATTTTAATAGTTAA
66 GGACTCTACTAGAGAATTTGATTTCAGATTAATTATTCCAAAAATAATATTATTTTAATAGTTAA
31340071 TATTAAATTAAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATATTAAAGTGATTATCT
131 TATTAAATTAAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATATTAAAGTGATTATCT
31340136 TAATATTTAATTTAATTTTTATTTTATAGATAAATATTCTATTATTTTAATAAGATTTAATATTA
196 TAATATTTAATTTAATTTTTATTTTATAGATAAATATTCTATTATTTTAATAAGATTTAATATTA
31340201 AATTTAATCTAA
261 AATTTAATCTAA
31340213 TATTTATCTT
Statistics
Matches: 272, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
272 272 1.00
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (272 bp):
CGATATGTTCTGTAATGCCTCATAGCCCTGTTTCGGTGACGGTTTGGGGTTAGGGGGTGTTACAG
GGACTCTACTAGAGAATTTGATTTCAGATTAATTATTCCAAAAATAATATTATTTTAATAGTTAA
TATTAAATTAAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATATTAAAGTGATTATCT
TAATATTTAATTTAATTTTTATTTTATAGATAAATATTCTATTATTTTAATAAGATTTAATATTA
AATTTAATCTAA
Found at i:31341951 original size:35 final size:35
Alignment explanation
Indices: 31341905--31342025 Score: 145
Period size: 35 Copynumber: 3.5 Consensus size: 35
31341895 TTTCAAGGTT
* *
31341905 TCGCCCTGAAGGACCTAATAATCGTTTCTAAGATG
1 TCGCCCCGAAGGACCTAATAATCGTTTCCAAGATG
* * *
31341940 TCGCCCCGAAGGACCTAATAATCATTTCCACGGTG
1 TCGCCCCGAAGGACCTAATAATCGTTTCCAAGATG
* * *
31341975 TCGCCCCGAATGACCTAATAATTGTTTCCACA-ATT
1 TCGCCCCGAAGGACCTAATAATCGTTTCCA-AGATG
*
31342010 TCGCCCCAAAGGACCT
1 TCGCCCCGAAGGACCT
31342026 TATCGCCATC
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
35 72 1.00
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (35 bp):
TCGCCCCGAAGGACCTAATAATCGTTTCCAAGATG
Found at i:31348228 original size:8 final size:8
Alignment explanation
Indices: 31348215--31348252 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
31348205 AACTTATGCT
31348215 TATATTGA
1 TATATTGA
31348223 TATATTGA
1 TATATTGA
31348231 TATATTGA
1 TATATTGA
31348239 TATATTGA
1 TATATTGA
31348247 TATATT
1 TATATT
31348253 ATAGATTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (8 bp):
TATATTGA
Found at i:31348268 original size:24 final size:24
Alignment explanation
Indices: 31348215--31348259 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
31348205 AACTTATGCT
*
31348215 TATATTGATATATTGATATATTGA
1 TATATTGATATATTGATAGATTGA
31348239 TATATTGATATATT-ATAGATT
1 TATATTGATATATTGATAGATT
31348260 ATAGATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (24 bp):
TATATTGATATATTGATAGATTGA
Found at i:31349713 original size:45 final size:45
Alignment explanation
Indices: 31349616--31349725 Score: 123
Period size: 45 Copynumber: 2.5 Consensus size: 45
31349606 GTTGTCGTTG
** * *
31349616 GGTTGTGGATGCACAACAAAAATGTTGCAGATGGAATCTATCTTT
1 GGTTGTGGATGCACAACAAAAACATTGCAGATGGAATCTACCTAT
* * * * *
31349661 GGCTGTGGGTTCACAGCAAAAACATTGCAGATGGGATCTACCTAT
1 GGTTGTGGATGCACAACAAAAACATTGCAGATGGAATCTACCTAT
*
31349706 GGTTGTGG-TACACAACAAAA
1 GGTTGTGGATGCACAACAAAA
31349726 TTATGTTGAT
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
44 10 0.19
45 43 0.81
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (45 bp):
GGTTGTGGATGCACAACAAAAACATTGCAGATGGAATCTACCTAT
Found at i:31352960 original size:28 final size:28
Alignment explanation
Indices: 31352920--31353055 Score: 100
Period size: 28 Copynumber: 4.9 Consensus size: 28
31352910 GTATCCCCTG
31352920 TTTTTCAAATTTTACAATTTTGCCCATA
1 TTTTTCAAATTTTACAATTTTGCCCATA
* * * **
31352948 TTTTTCAAATTTTATAGTTTTACCTTTA
1 TTTTTCAAATTTTACAATTTTGCCCATA
* * * *
31352976 TTTTTTTAGATTTTAC-ATTTTTCCCTTA
1 -TTTTTCAAATTTTACAATTTTGCCCATA
* * *
31353004 TTTTTCATATTTTATAGTTTT--CCAT-
1 TTTTTCAAATTTTACAATTTTGCCCATA
31353029 TTGCTTTACAAATTTTACAATTTTGCC
1 TT--TTT-CAAATTTTACAATTTTGCC
31353056 TTGAATTTTA
Statistics
Matches: 82, Mismatches: 19, Indels: 12
0.73 0.17 0.11
Matches are distributed among these distances:
25 2 0.02
26 3 0.04
27 15 0.18
28 49 0.60
29 12 0.15
30 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.04, T:0.57
Consensus pattern (28 bp):
TTTTTCAAATTTTACAATTTTGCCCATA
Found at i:31353052 original size:56 final size:57
Alignment explanation
Indices: 31352925--31353055 Score: 160
Period size: 56 Copynumber: 2.3 Consensus size: 57
31352915 CCCTGTTTTT
** *
31352925 CAAATTTTACAATTTTGCCCATATTTTTCAAATTTTATAGTTTTACCTTTATTTTTT
1 CAAATTTTACAATTTTGCCCATATTTTTCAAATTTTATAGTTTTACCTTTAGCTTTA
* * * * *
31352982 TAGATTTTAC-ATTTTTCCCTTATTTTTCATATTTTATAGTTTT-CCATTT-GCTTTA
1 CAAATTTTACAATTTTGCCCATATTTTTCAAATTTTATAGTTTTACC-TTTAGCTTTA
31353037 CAAATTTTACAATTTTGCC
1 CAAATTTTACAATTTTGCC
31353056 TTGAATTTTA
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
55 13 0.21
56 40 0.66
57 8 0.13
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (57 bp):
CAAATTTTACAATTTTGCCCATATTTTTCAAATTTTATAGTTTTACCTTTAGCTTTA
Found at i:31354479 original size:2 final size:2
Alignment explanation
Indices: 31354472--31354500 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31354462 GAGAATTTAC
31354472 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
31354501 AAATAATGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31354672 original size:17 final size:17
Alignment explanation
Indices: 31354650--31354682 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
31354640 TCCCAAATTT
*
31354650 TGATACTCATATCTTTC
1 TGATACCCATATCTTTC
31354667 TGATACCCATATCTTT
1 TGATACCCATATCTTT
31354683 GACTTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:31357290 original size:79 final size:79
Alignment explanation
Indices: 31357159--31357310 Score: 270
Period size: 79 Copynumber: 1.9 Consensus size: 79
31357149 ATTGCCACAT
*
31357159 ACCAAAATTATTGGTACCATCAAATTTCTCTACTTCAAATTTCGCATTGGTCACAGTAGTCTTTG
1 ACCAAAATTATTGGTACCATCAAATTTCTCTACTTCAAATTTCACATTGGTCACAGTAGTCTTTG
31357224 AC-GATGACTTTTCC
66 -CTGATGACTTTTCC
*
31357238 ACCAAAATTATTGGTACCATCAAATTTCTCTACTTCAAATTTTACATTGGTCACAGTAGTCTTTG
1 ACCAAAATTATTGGTACCATCAAATTTCTCTACTTCAAATTTCACATTGGTCACAGTAGTCTTTG
31357303 CTGATGAC
66 CTGATGAC
31357311 GATGCCTTTT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
78 1 0.01
79 69 0.99
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (79 bp):
ACCAAAATTATTGGTACCATCAAATTTCTCTACTTCAAATTTCACATTGGTCACAGTAGTCTTTG
CTGATGACTTTTCC
Found at i:31357896 original size:17 final size:17
Alignment explanation
Indices: 31357874--31357906 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31357864 TCCCAGATTT
31357874 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
31357891 TGATACCCATATCTTT
1 TGATACCCATATCTTT
31357907 GACTTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.42
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:31358781 original size:8 final size:8
Alignment explanation
Indices: 31358770--31358823 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
31358760 TTTAAAACAA
31358770 ATTTTTAT
1 ATTTTTAT
*
31358778 ATTTTTTT
1 ATTTTTAT
*
31358786 AGTTTTAT
1 ATTTTTAT
31358794 A--TTTAT
1 ATTTTTAT
31358800 A-TTTTAT
1 ATTTTTAT
31358807 AGTTTTTAT
1 A-TTTTTAT
*
31358816 AATTTTAT
1 ATTTTTAT
31358824 TTTATTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 6 0.15
7 6 0.15
8 20 0.51
9 7 0.18
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (8 bp):
ATTTTTAT
Found at i:31358804 original size:29 final size:29
Alignment explanation
Indices: 31358772--31358828 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
31358762 TAAAACAAAT
* *
31358772 TTTTATA-TTTTTTTAGTTTTATATTTATA
1 TTTTATAGTTTTTATAATTTTAT-TTTATA
31358801 TTTTATAGTTTTTATAATTTTATTTTAT
1 TTTTATAGTTTTTATAATTTTATTTTAT
31358829 TTAATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.72
Consensus pattern (29 bp):
TTTTATAGTTTTTATAATTTTATTTTATA
Found at i:31359120 original size:12 final size:13
Alignment explanation
Indices: 31359098--31359129 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
31359088 ACAATTAAAA
31359098 TATTATTATTTAT
1 TATTATTATTTAT
31359111 TATT-TTATTTAT
1 TATTATTATTTAT
31359123 T-TTATTA
1 TATTATTA
31359130 AAATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 12 0.67
13 4 0.22
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTATTATTTAT
Found at i:31365516 original size:31 final size:31
Alignment explanation
Indices: 31365481--31365544 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
31365471 TTGAGTGACT
*
31365481 AAAATAAAAGCACCCTAAAATTTA-AGTGATC
1 AAAATAAAAGCACCCTAAAAGTTAGA-TGATC
* **
31365512 AAAATGAAAGTGCCCTAAAAGTTAGATGATC
1 AAAATAAAAGCACCCTAAAAGTTAGATGATC
31365543 AA
1 AA
31365545 CTATGTTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.22
Consensus pattern (31 bp):
AAAATAAAAGCACCCTAAAAGTTAGATGATC
Found at i:31376069 original size:5 final size:5
Alignment explanation
Indices: 31376061--31376138 Score: 65
Period size: 5 Copynumber: 15.6 Consensus size: 5
31376051 ATTTAAAATA
*
31376061 TATAT TATAT TATAT T-TACT TA-AT TA-AT AAGTAT GT-TAT TATAT
1 TATAT TATAT TATAT TATA-T TATAT TATAT TA-TAT -TATAT TATAT
* *
31376105 TATAT TATTAT AATAT TATAT AATAT TATAT TAT
1 TATAT TA-TAT TATAT TATAT TATAT TATAT TAT
31376139 TATATATATA
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
4 9 0.15
5 45 0.75
6 6 0.10
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:31376113 original size:8 final size:8
Alignment explanation
Indices: 31376102--31376143 Score: 57
Period size: 8 Copynumber: 5.0 Consensus size: 8
31376092 TATGTTATTA
31376102 TATTATAT
1 TATTATAT
*
31376110 TATTATAA
1 TATTATAT
31376118 TATTATAT
1 TATTATAT
31376126 AATATTATAT
1 --TATTATAT
31376136 TATTATAT
1 TATTATAT
31376144 ATATAAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 22 0.73
10 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TATTATAT
Found at i:31376131 original size:18 final size:17
Alignment explanation
Indices: 31376096--31376147 Score: 70
Period size: 18 Copynumber: 3.1 Consensus size: 17
31376086 AATAAGTATG
*
31376096 TTATTATATTATAT-TA
1 TTATAATATTATATATA
31376112 TTATAATATTATATAATA
1 TTATAATATTATAT-ATA
*
31376130 TTATATTATTATATATA
1 TTATAATATTATATATA
31376147 T
1 T
31376148 AAAACAACAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
16 13 0.41
17 4 0.12
18 15 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATAATATTATATATA
Found at i:31379428 original size:30 final size:30
Alignment explanation
Indices: 31379396--31379555 Score: 216
Period size: 30 Copynumber: 5.3 Consensus size: 30
31379386 CTTAGCTTTT
*
31379396 TCCACCACCAACTCCACTAGCCACACCTTT
1 TCCACCACCAACTCCACTAGCCACACCTTC
* *
31379426 TCCACCACCAACTCCACTAGCCACTCCTTT
1 TCCACCACCAACTCCACTAGCCACACCTTC
31379456 TCCACCACCAACTCCACTAGCCACACCTTC
1 TCCACCACCAACTCCACTAGCCACACCTTC
*
31379486 TCCACCACCAAATCCACTAGCCACA-CTTGC
1 TCCACCACCAACTCCACTAGCCACACCTT-C
** * *
31379516 TCCATTACCTACTCCACTAACCACA-CTTGC
1 TCCACCACCAACTCCACTAGCCACACCTT-C
31379546 TCCACCACCA
1 TCCACCACCA
31379556 CTTGTACCTA
Statistics
Matches: 117, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
29 3 0.03
30 114 0.97
ACGTcount: A:0.27, C:0.49, G:0.04, T:0.20
Consensus pattern (30 bp):
TCCACCACCAACTCCACTAGCCACACCTTC
Found at i:31380141 original size:25 final size:25
Alignment explanation
Indices: 31380113--31380171 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
31380103 ATATTACGTA
* *
31380113 TATATATATTTTATACTATTTTATT
1 TATATATATTTAATACTATATTATT
* *
31380138 TATATATCTTTAATATTATATTATT
1 TATATATATTTAATACTATATTATT
31380163 TATATATAT
1 TATATATAT
31380172 ATATATTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (25 bp):
TATATATATTTAATACTATATTATT
Found at i:31380141 original size:27 final size:26
Alignment explanation
Indices: 31380102--31380173 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 26
31380092 TTTTAAATTT
* *
31380102 TATATTACGTATATATATATTTTATAC
1 TATATTA-TTATATATATATTTAATAC
* * *
31380129 TATTTTATT-TATATATCTTTAATAT
1 TATATTATTATATATATATTTAATAC
31380154 TATATTATTTATATATATAT
1 TATATTA-TTATATATATAT
31380174 ATATTTTTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
25 19 0.53
26 3 0.08
27 14 0.39
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (26 bp):
TATATTATTATATATATATTTAATAC
Found at i:31380156 original size:16 final size:17
Alignment explanation
Indices: 31380115--31380179 Score: 68
Period size: 16 Copynumber: 4.1 Consensus size: 17
31380105 ATTACGTATA
*
31380115 TATATATTTTATACTATT
1 TATATATTATATA-TATT
*
31380133 T-TAT-TTATATATCTT
1 TATATATTATATATATT
31380148 TA-ATATTATAT-TATT
1 TATATATTATATATATT
31380163 TATATA-TATATATATT
1 TATATATTATATATATT
31380179 T
1 T
31380180 TTTCTACATG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
15 16 0.40
16 20 0.50
17 3 0.08
18 1 0.03
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATATTATATATATT
Found at i:31380243 original size:25 final size:25
Alignment explanation
Indices: 31380195--31380280 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 25
31380185 ACATGTTATC
*
31380195 TTATGTATATA-TCTT-A-ACTATA
1 TTATGTATATATTTTTAACACTATA
*
31380217 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATATTTTTAACACTATA
* *
31380242 TTATGTACATATTTTTAATA-T-TA
1 TTATGTATATATTTTTAACACTATA
* *
31380265 TCATGTATTTATTTTT
1 TTATGTATATATTTTT
31380281 TATATATGTA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
22 10 0.19
23 18 0.34
24 2 0.04
25 23 0.43
ACGTcount: A:0.31, C:0.07, G:0.06, T:0.56
Consensus pattern (25 bp):
TTATGTATATATTTTTAACACTATA
Found at i:31380277 original size:23 final size:24
Alignment explanation
Indices: 31380197--31380287 Score: 73
Period size: 23 Copynumber: 3.9 Consensus size: 24
31380187 ATGTTATCTT
*
31380197 ATGTATATA-TCTTAACTATAT-T-
1 ATGTATATATTTTTAA-TATATATC
* * *
31380219 ATGTATGTATTTTTAACACTATATT
1 ATGTATATATTTTTAATA-TATATC
*
31380244 ATGTACATATTTTTAATAT-TATC
1 ATGTATATATTTTTAATATATATC
* *
31380267 ATGTATTTATTTTTTATATAT
1 ATGTATATATTTTTAATATAT
31380288 GTACATATTG
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
22 9 0.17
23 27 0.50
24 3 0.06
25 15 0.28
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (24 bp):
ATGTATATATTTTTAATATATATC
Found at i:31380437 original size:16 final size:15
Alignment explanation
Indices: 31380413--31380460 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
31380403 TAATTATTAT
* *
31380413 TATTCTAATATTTTGG
1 TATTTTAATATTTT-A
31380429 TATTTTAATATTTTA
1 TATTTTAATATTTTA
31380444 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
31380460 T
1 T
31380461 TATTCACATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 7 0.24
16 22 0.76
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:31380440 original size:8 final size:8
Alignment explanation
Indices: 31380413--31380464 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
31380403 TAATTATTAT
*
31380413 TATTCTAA
1 TATTTTAA
**
31380421 TATTTTGG
1 TATTTTAA
31380429 TATTTTAA
1 TATTTTAA
31380437 TATTTT-A
1 TATTTTAA
31380444 TATTTTATA
1 TATTTTA-A
*
31380453 TATTTTAT
1 TATTTTAA
31380461 TATT
1 TATT
31380465 CACATCATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 7 0.19
8 21 0.58
9 8 0.22
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:31382314 original size:73 final size:71
Alignment explanation
Indices: 31382135--31382508 Score: 302
Period size: 73 Copynumber: 5.0 Consensus size: 71
31382125 ATTTTCGTTT
* * *
31382135 TTTTAATTTATGTTTCAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACGCT
1 TTTTAATTTATG-TTCATAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAACACGCT
31382200 GAGGTAA
65 GAGGTAA
* * ** *
31382207 TTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
1 TTTTAATTTATGTTCATAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA--ACACGC
**
31382272 TGAGGTGG
64 TGAGGTAA
* * *
31382280 TTTTAATTTATGTTCATAAAAAATTAGCTCATATTGCAAGAGGTGAGTTGAGCTTTGGCTC-ACA
1 TTTTAATTTATGTTCATAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC-----CTCAACA
*
31382344 CACTGAGGT-A
61 CGCTGAGGTAA
* **
31382354 TTTTCAATTTCTGGTTTTTAATTTCTATTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
1 TTTT-AATTTAT-G--------TTC-A--TAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
31382419 CCTCAGGACACGCTGAGGTAA
53 CCTCA--ACACGCTGAGGTAA
* * ** * * * *
31382440 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTA
1 TTTTAATTTATGTTCATAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAACACGCTG
31382505 AGGT
66 AGGT
31382509 GTTTTCCATT
Statistics
Matches: 243, Mismatches: 35, Indels: 49
0.74 0.11 0.15
Matches are distributed among these distances:
71 50 0.21
72 10 0.04
73 94 0.39
74 4 0.02
75 17 0.07
76 3 0.01
78 3 0.01
82 3 0.01
84 4 0.02
85 19 0.08
86 4 0.02
87 32 0.13
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (71 bp):
TTTTAATTTATGTTCATAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAACACGCTG
AGGTAA
Found at i:31382392 original size:160 final size:158
Alignment explanation
Indices: 31382208--31383775 Score: 2205
Period size: 160 Copynumber: 9.8 Consensus size: 158
31382198 CTGAGGTAAT
* * *
31382208 TTCAATTTTTGTTTGTCAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
1 TTCAATTTCTGTTT-TTAAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGC
** * * ** * * * * *
31382272 TGAGGTGGTTTTAATTTATGTTCATAAAAAATTAGCTCATATTGCAAGAGGTGAGTTGAGCTTTG
65 TGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAAC----
* * * * * *
31382337 GCTC-ACACACTGAGGTATTTTCAATTTCTGGTT-
126 -CTCAAGACGCTAAGGTGTTTTCCATTT-TTGTTC
* * *
31382370 TTTAATTTCTATTTTT-AAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
1 TTCAATTTCTGTTTTTAAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCT
31382433 GAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAA
66 GAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAA
31382498 GACGCTAAGGTGTTTTCCATTTTTGTTC
131 GACGCTAAGGTGTTTTCCATTTTTGTTC
31382526 TTCAATTTCTGTTTTTCAAAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
1 TTCAATTTCTGTTTTT--AAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
31382591 CTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
64 CTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
31382656 AAGACGCTAAGGTGTTTTCCATTTTTGTTC
129 AAGACGCTAAGGTGTTTTCCATTTTTGTTC
31382686 TTCAATTTCTGTTTTTCAAAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
1 TTCAATTTCTGTTTTT--AAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
31382751 CTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
64 CTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
31382816 AAGACGCTAAGGTGTTTTCCATTTTTGTTC
129 AAGACGCTAAGGTGTTTTCCATTTTTGTTC
31382846 TTCAATTTCTGTTTTTCAAAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
1 TTCAATTTCTGTTTTT--AAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
31382911 CTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
64 CTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
31382976 AAGACGCTAAGGTGTTTTCCATTTTTGTTC
129 AAGACGCTAAGGTGTTTTCCATTTTTGTTC
31383006 TTCAATTTCTGTTTTTCAAAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
1 TTCAATTTCTGTTTTT--AAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
31383071 CTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
64 CTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
31383136 AAGACGCTAAGGTGTTTTCCATTTTTGTTC
129 AAGACGCTAAGGTGTTTTCCATTTTTGTTC
31383166 TTCAATTTCTGTTTTTCAAAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
1 TTCAATTTCTGTTTTT--AAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
31383231 CTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
64 CTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
31383296 AAGACGCTAAGGTGTTTTCCATTTTTGTTC
129 AAGACGCTAAGGTGTTTTCCATTTTTGTTC
* * * * *
31383326 TTCAATTTCTGTTTTTCAAAAACATCAACTCATATTGCGAGAGATAAGTTGAGCCTCAAGACACA
1 TTCAATTTCTGTTTTT--AAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
* * *
31383391 TTGAGGTATTTTCAATTTCTGTCTT-TCAAAAACATCAGCTCATATTGCGAGAGGTGAGTTGAAC
64 CTGAGGTAATTTCAATTTCTGT-TTGTC-AAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAAC
31383455 CTCAAGACGCTAAGGTGTTTTCCATTTTTGTTC
126 CTCAAGACGCTAAGGTGTTTTCCATTTTTGTTC
*
31383488 TTCAATTTCTGTTTTTCAAAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACG
1 TTCAATTTCTGTTTTT--AAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
* * * * * *
31383553 CTGAGGTATTTTCAAATTCCATTTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAG
64 CTGAGGTAATTTC-AATTTC-TGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAA
* * * * **
31383618 CCTCGGGACACGCTGAGGTATTTT-CA----AATTC
125 CCTC--AAGACGCTAAGGTGTTTTCCATTTTTGTTC
* ** * * * *
31383649 --C-ATTT-T-TATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCT
1 TTCAATTTCTGTTTTTAAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCT
* * * * * *
31383709 GAGGTATTTTCAAATTCCATTTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCC
66 GAGGTAATTTC-AATTTC-TGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACC
31383774 TC
127 TC
31383776 GGGACACGCT
Statistics
Matches: 1335, Mismatches: 56, Indels: 38
0.93 0.04 0.03
Matches are distributed among these distances:
154 113 0.08
155 7 0.01
156 34 0.03
157 1 0.00
158 4 0.00
159 4 0.00
160 954 0.71
161 10 0.01
162 145 0.11
163 7 0.01
164 35 0.03
165 7 0.01
166 14 0.01
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (158 bp):
TTCAATTTCTGTTTTTAAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCT
GAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAA
GACGCTAAGGTGTTTTCCATTTTTGTTC
Found at i:31383592 original size:77 final size:77
Alignment explanation
Indices: 31383499--31383881 Score: 687
Period size: 77 Copynumber: 5.0 Consensus size: 77
31383489 TCAATTTCTG
* * *
31383499 TTTT-TCAAAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATT
1 TTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATT
31383563 TTCAAATTCCAT
66 TTCAAATTCCAT
31383575 TTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATT
1 TTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATT
31383640 TTCAAATTCCAT
66 TTCAAATTCCAT
31383652 TTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATT
1 TTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATT
31383717 TTCAAATTCCAT
66 TTCAAATTCCAT
31383729 TTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATT
1 TTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATT
31383794 TTCAAATTCCAT
66 TTCAAATTCCAT
* * *
31383806 TTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGTCTCGGGCCACACACTGAGGTC
1 TTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGG--ACACGCTGAGGTA
31383871 TTTTCAAATTC
64 TTTTCAAATTC
31383882 TGTTTTTAAT
Statistics
Matches: 298, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
76 4 0.01
77 272 0.91
79 22 0.07
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (77 bp):
TTTTATCAAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATT
TTCAAATTCCAT
Found at i:31384117 original size:14 final size:14
Alignment explanation
Indices: 31384094--31384128 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
31384084 CGCTGAGGTG
* *
31384094 TTTTCCATTTCTGT
1 TTTTCAATTTCTGC
31384108 TTTTCAATTTCTGC
1 TTTTCAATTTCTGC
31384122 TTTTCAA
1 TTTTCAA
31384129 AAATCAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.14, C:0.20, G:0.06, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGC
Found at i:31384146 original size:85 final size:87
Alignment explanation
Indices: 31384023--31384216 Score: 250
Period size: 85 Copynumber: 2.2 Consensus size: 87
31384013 GAGTTGAGCC
* * *
31384023 TTTTAATTTCTGTTTTTCAAAAAAAAAACTCATATTGCGAGAGGTGAGTTGA-AC-C-TCAAGAC
1 TTTTAATTTCTGCTTTTC-AAAAAAAAACTCATATTGCGAGAGGTGAGTTGAGACTCGGCAACAC
* * *
31384085 GCTGAGGTGTTTTCCATTTCTGT
65 GCTGAGGTCTTTTCAAATTCTGT
** * *
31384108 TTTTCAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGGCTACA
1 TTTT-AATTTCTGCTTTTCAAAAAAAAACTCATATTGCGAGAGGTGAGTTGAGACTC-GGCAACA
31384173 CGCTGAGGTCTTTTCAAATTCTGT
64 CGCTGAGGTCTTTTCAAATTCTGT
31384197 TTTTAATTTCTGCTTTTCAA
1 TTTTAATTTCTGCTTTTCAA
31384217 TTTCTGTTTT
Statistics
Matches: 94, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
85 35 0.37
86 14 0.15
87 1 0.01
88 16 0.17
89 28 0.30
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (87 bp):
TTTTAATTTCTGCTTTTCAAAAAAAAACTCATATTGCGAGAGGTGAGTTGAGACTCGGCAACACG
CTGAGGTCTTTTCAAATTCTGT
Found at i:31384228 original size:14 final size:14
Alignment explanation
Indices: 31384183--31384245 Score: 74
Period size: 14 Copynumber: 4.5 Consensus size: 14
31384173 CGCTGAGGTC
*
31384183 TTTTCAAATTCTGT
1 TTTTCAATTTCTGT
*
31384197 TTTT-AATTTCTGC
1 TTTTCAATTTCTGT
31384210 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
* *
31384224 TTTTCCAATTTATAT
1 TTTT-CAATTTCTGT
31384239 TTTTCAA
1 TTTTCAA
31384246 AAATCAACTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.26
14 19 0.45
15 12 0.29
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:31384332 original size:117 final size:115
Alignment explanation
Indices: 31384095--31384333 Score: 284
Period size: 117 Copynumber: 2.1 Consensus size: 115
31384085 GCTGAGGTGT
* * * *
31384095 TTTCCATTTCTGTTTTTCAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1 TTTCAATTTCTGTTTTTCAATTTATACTTTTCAAAAATCAACTCATATCGCGAGAGGTGAGTTGA
* * * * **
31384160 GTCTCGGGCTACACGCTGAGGTCTTTTCAAATTCTGTTTTTAATTTCTGC
66 GCCTCGGGCTACACGCTGAGGTATTTTCAAAATCTGTTTTTAAATTAAGC
* *
31384210 TTTTCAATTTCTGTTTTTCCAATTTATATTTTTCAAAAATCAACTCATATCGCGAGATGTGAGTT
1 -TTTCAATTTCTGTTTTT-CAATTTATACTTTTCAAAAATCAACTCATATCGCGAGAGGTGAGTT
* * *
31384275 GAGCCTTGGGTTCACATG-TCGAGGTATTTTCAAAATCTGTTTTTCAAATTAAG-
64 GAGCCTCGGGCT-ACACGCT-GAGGTATTTTCAAAATCTGTTTTT-AAATTAAGC
31384328 TTTCAA
1 TTTCAA
31384334 AAAAACCAAC
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
116 16 0.15
117 57 0.55
118 26 0.25
119 5 0.05
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (115 bp):
TTTCAATTTCTGTTTTTCAATTTATACTTTTCAAAAATCAACTCATATCGCGAGAGGTGAGTTGA
GCCTCGGGCTACACGCTGAGGTATTTTCAAAATCTGTTTTTAAATTAAGC
Found at i:31385580 original size:16 final size:15
Alignment explanation
Indices: 31385556--31385603 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
31385546 TAATTATTAT
*
31385556 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
31385572 TATTTTAATATTTTA
1 TATTTTAATATTTTA
31385587 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
31385603 T
1 T
31385604 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:31385591 original size:7 final size:8
Alignment explanation
Indices: 31385556--31385607 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
31385546 TAATTATTAT
*
31385556 TATTCTAA
1 TATTTTAA
*
31385564 TATTTTGA
1 TATTTTAA
31385572 TATTTTAA
1 TATTTTAA
31385580 TATTTT-A
1 TATTTTAA
31385587 TATTTTATA
1 TATTTTA-A
*
31385596 TATTTTAT
1 TATTTTAA
31385604 TATT
1 TATT
31385608 CACATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:31387235 original size:15 final size:15
Alignment explanation
Indices: 31387215--31387245 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31387205 TAATTTATAC
31387215 TTCCATATAGCCAAA
1 TTCCATATAGCCAAA
31387230 TTCCATATAGCCAAA
1 TTCCATATAGCCAAA
31387245 T
1 T
31387246 GAGCACATTT
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:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (15 bp):
TTCCATATAGCCAAA
Found at i:31387628 original size:43 final size:43
Alignment explanation
Indices: 31387575--31387692 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
31387565 ATGTAATCTT
*
31387575 TATCGATGCCAATAGCCCAGCCATGGTCTTACACGAAATCACA
1 TATCGATGCCAATAGCCCAGACATGGTCTTACACGAAATCACA
* * *
31387618 TATCGATGCCAAT-GTCCCAGACATGATCTTACACGAAGTCTCA
1 TATCGATGCCAATAG-CCCAGACATGGTCTTACACGAAATCACA
* * *
31387661 TATCAATGCC-ATATCCCAGATATGGTCTTACA
1 TATCGATGCCAATAGCCCAGACATGGTCTTACA
31387693 TGTAATCTCG
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
42 19 0.29
43 46 0.71
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.25
Consensus pattern (43 bp):
TATCGATGCCAATAGCCCAGACATGGTCTTACACGAAATCACA
Found at i:31387691 original size:42 final size:42
Alignment explanation
Indices: 31387544--31387701 Score: 149
Period size: 42 Copynumber: 3.7 Consensus size: 42
31387534 TAACAATGTC
* * * * *
31387544 ATATCCCATATATGGTCTTACATGTAATCT-TTATCGATGCCA
1 ATATCCCAGACATGGTCTTACACG-AATCTCATATCAATGCCA
* * * *
31387586 ATAGCCCAGCCATGGTCTTACACGAAATCACATATCGATGCCA
1 ATATCCCAGACATGGTCTTACACG-AATCTCATATCAATGCCA
* *
31387629 ATGTCCCAGACATGATCTTACACGAAGTCTCATATCAATGCC-
1 ATATCCCAGACATGGTCTTACACGAA-TCTCATATCAATGCCA
* *
31387671 ATATCCCAGATATGGTCTTACATGTAATCTC
1 ATATCCCAGACATGGTCTTACACG-AATCTC
31387702 GGTAACCCTA
Statistics
Matches: 95, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
42 49 0.52
43 46 0.48
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (42 bp):
ATATCCCAGACATGGTCTTACACGAATCTCATATCAATGCCA
Found at i:31390017 original size:3 final size:3
Alignment explanation
Indices: 31390009--31390047 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
31389999 TCATGAAATT
31390009 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
31390048 ATAAGGAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:31390549 original size:15 final size:16
Alignment explanation
Indices: 31390529--31390571 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
31390519 TTTTTACTTT
*
31390529 TTTTTATAATTTT-CA
1 TTTTTAAAATTTTACA
*
31390544 TTTTTAAAATTTTATA
1 TTTTTAAAATTTTACA
31390560 TTTTTAAAATTT
1 TTTTTAAAATTT
31390572 ATTTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTAAAATTTTACA
Found at i:31390562 original size:16 final size:16
Alignment explanation
Indices: 31390529--31390585 Score: 64
Period size: 15 Copynumber: 3.6 Consensus size: 16
31390519 TTTTTACTTT
* *
31390529 TTTTTATAATTTT-CA
1 TTTTTAAAATTTTATA
31390544 TTTTTAAAATTTTATA
1 TTTTTAAAATTTTATA
*
31390560 TTTTTAAAA-TTTATT
1 TTTTTAAAATTTTATA
31390575 TTTTTATAAAT
1 TTTTTA-AAAT
31390586 AATTCAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 23 0.64
16 13 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTAAAATTTTATA
Found at i:31390665 original size:17 final size:18
Alignment explanation
Indices: 31390643--31390680 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
31390633 GTCAACAAAA
31390643 TTATAT-TTTTAATTTTT
1 TTATATGTTTTAATTTTT
*
31390660 TTATATGTTTTATTTTTT
1 TTATATGTTTTAATTTTT
31390678 TTA
1 TTA
31390681 AATTATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (18 bp):
TTATATGTTTTAATTTTT
Found at i:31390949 original size:19 final size:17
Alignment explanation
Indices: 31390914--31391012 Score: 63
Period size: 19 Copynumber: 5.4 Consensus size: 17
31390904 ATTAGGGGTG
*
31390914 AATTTTGTAATTTTTAAT
1 AATTTT-TAAATTTTAAT
*
31390932 AATTATTTACAATTTTAAC
1 AATT-TTTA-AATTTTAAT
* *
31390951 AATTTTTAATTTTTATT
1 AATTTTTAAATTTTAAT
*
31390968 ATTTTTTATAATTTTAAAT
1 AATTTTTA-AATTTT-AAT
* *
31390987 CAACTTTAAAATTTTTAAAT
1 -AATTTTTAAA-TTTT-AAT
31391007 AATTTT
1 AATTTT
31391013 AATCTATTTA
Statistics
Matches: 63, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
17 13 0.21
18 15 0.24
19 22 0.35
20 13 0.21
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (17 bp):
AATTTTTAAATTTTAAT
Found at i:31390995 original size:36 final size:36
Alignment explanation
Indices: 31390921--31391010 Score: 85
Period size: 35 Copynumber: 2.4 Consensus size: 36
31390911 GTGAATTTTG
*
31390921 TAATTTTTAATAATTATTTACAATTTTAACAATTTT
1 TAATTTTTAATAATTATTTACAATTTTAACAATCTT
* * *
31390957 TAATTTTT-ATTATTTTTTATAATTTTAAATCAA-CTT
1 TAATTTTTAATAATTATTTACAATTTT-AA-CAATCTT
31390993 TAAAATTTTTAAATAATT
1 T--AATTTTT-AATAATT
31391011 TTAATCTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
35 15 0.35
36 13 0.30
37 3 0.07
38 7 0.16
40 5 0.12
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (36 bp):
TAATTTTTAATAATTATTTACAATTTTAACAATCTT
Found at i:31391053 original size:21 final size:19
Alignment explanation
Indices: 31391007--31391075 Score: 77
Period size: 21 Copynumber: 3.5 Consensus size: 19
31390997 ATTTTTAAAT
*
31391007 AATTTTAAT-CTATTTACA
1 AATTTTAATAATATTTACA
31391025 AATTTTAATAAATATTTACA
1 AATTTTAAT-AATATTTACA
*
31391045 ATTTTTTAATAATCATTTACA
1 A-ATTTTAATAAT-ATTTACA
31391066 AACTTTTAAT
1 AA-TTTTAAT
31391076 GATTTTTTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
18 9 0.21
20 12 0.28
21 22 0.51
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTTTAATAATATTTACA
Found at i:31391115 original size:25 final size:25
Alignment explanation
Indices: 31391082--31391129 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
31391072 TAATGATTTT
31391082 TTGAATTTTTTATTATTTAAAATAA
1 TTGAATTTTTTATTATTTAAAATAA
*
31391107 TTGAATTTTTTATTATTTTAAAT
1 TTGAATTTTTTATTATTTAAAAT
31391130 CATTTTTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (25 bp):
TTGAATTTTTTATTATTTAAAATAA
Found at i:31395626 original size:18 final size:18
Alignment explanation
Indices: 31395585--31395628 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
31395575 ACAATTATTT
* *
31395585 TTTAAAAATTAGAAATTA
1 TTTAAAAAGTAGAAATAA
31395603 TTTAAAAAGTAGAAA-AA
1 TTTAAAAAGTAGAAATAA
31395620 TTATAAAAA
1 TT-TAAAAA
31395629 TATTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (18 bp):
TTTAAAAAGTAGAAATAA
Found at i:31395658 original size:21 final size:21
Alignment explanation
Indices: 31395615--31395658 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
31395605 TAAAAAGTAG
*
31395615 AAAAATTATAAAAATATTTTT
1 AAAAATTATAAAAATATTATT
*
31395636 AAAAATTTTAAAAA-ATTAATT
1 AAAAATTATAAAAATATT-ATT
31395657 AA
1 AA
31395659 TTGTTGATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAATTATAAAAATATTATT
Found at i:31396081 original size:16 final size:17
Alignment explanation
Indices: 31396060--31396094 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
31396050 AAACCTTTTC
31396060 TTATAAAGATTAT-TTA
1 TTATAAAGATTATATTA
*
31396076 TTATAAAGTTTATATTA
1 TTATAAAGATTATATTA
31396093 TT
1 TT
31396095 TTTGTTACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TTATAAAGATTATATTA
Found at i:31407808 original size:4 final size:5
Alignment explanation
Indices: 31407779--31407813 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
31407769 TGTTCTAGTA
31407779 TAAAT TAAAT TAAAT TAAAT TAAA- TAAA- TAAAT TA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TA
31407814 TTATAGTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
TAAAT
Found at i:31437849 original size:23 final size:23
Alignment explanation
Indices: 31437819--31437868 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
31437809 AGTATTATAC
31437819 TGGTGGGTATACTGCTTTTGTTT
1 TGGTGGGTATACTGCTTTTGTTT
31437842 TGGTGGGTATACTGCTTTTGTTT
1 TGGTGGGTATACTGCTTTTGTTT
31437865 TGGT
1 TGGT
31437869 ACTAGTACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.08, C:0.08, G:0.32, T:0.52
Consensus pattern (23 bp):
TGGTGGGTATACTGCTTTTGTTT
Found at i:31441086 original size:76 final size:78
Alignment explanation
Indices: 31440906--31441079 Score: 280
Period size: 78 Copynumber: 2.3 Consensus size: 78
31440896 TGAAATAGCG
* * * *
31440906 AAAAAGTCATTACATAAATACAAAGTTTATTATTTAAATTGTAAAAAACAAACCATAAAATTGAT
1 AAAAAGTCATTACATAAATAAAAAGTTGACTATTTAAATTGCAAAAAACAAACCATAAAATTGAT
*
31440971 AAATAAAATGACA
66 AAATAAAATGAAA
31440984 AAAAAGTCATTACATAAATAAAAAGTTGACTATTTAAATTGCAAAAAA-AAA-CATAAAATTGAT
1 AAAAAGTCATTACATAAATAAAAAGTTGACTATTTAAATTGCAAAAAACAAACCATAAAATTGAT
31441047 AAATAAAATGAAA
66 AAATAAAATGAAA
*
31441060 AAAAATTCATTACATAAATA
1 AAAAAGTCATTACATAAATA
31441080 TGAAGTTATT
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
76 43 0.48
77 3 0.03
78 44 0.49
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (78 bp):
AAAAAGTCATTACATAAATAAAAAGTTGACTATTTAAATTGCAAAAAACAAACCATAAAATTGAT
AAATAAAATGAAA
Found at i:31441839 original size:9 final size:9
Alignment explanation
Indices: 31441825--31441918 Score: 125
Period size: 9 Copynumber: 10.4 Consensus size: 9
31441815 TTTGGTTAAA
31441825 AATTAACCG
1 AATTAACCG
*
31441834 AATTAACCA
1 AATTAACCG
31441843 AATTAACCG
1 AATTAACCG
**
31441852 AATTGCCCG
1 AATTAACCG
31441861 AATTAACCG
1 AATTAACCG
*
31441870 AATTACCCG
1 AATTAACCG
31441879 AATTAACCG
1 AATTAACCG
31441888 AATTAACCG
1 AATTAACCG
* *
31441897 AATTACCCA
1 AATTAACCG
*
31441906 AATTAACCT
1 AATTAACCG
31441915 AATT
1 AATT
31441919 GAATCATACA
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 73 1.00
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:31444100 original size:16 final size:16
Alignment explanation
Indices: 31444060--31444100 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
31444050 TAAAGAAAAA
*
31444060 TAAAATAAAATTACAT
1 TAAAAAAAAATTACAT
* *
31444076 TATATAAAAATTACAT
1 TAAAAAAAAATTACAT
31444092 TAAAAAAAA
1 TAAAAAAAA
31444101 TCACAAAATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAAAAAAATTACAT
Found at i:31444202 original size:103 final size:103
Alignment explanation
Indices: 31444095--31444739 Score: 939
Period size: 103 Copynumber: 6.2 Consensus size: 103
31444085 ATTACATTAA
*
31444095 AAAAAATCACAAAATAC-TAAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
1 AAAAAATCACAAAACACAT-AACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
31444159 AAAATAACTATAAAATTATATTTTTTAAAATACATTGCT
65 AAAATAACTATAAAATTATATTTTTTAAAATACATTGCT
31444198 AAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACA
1 AAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACA
** * *
31444263 AAATAACTATAAAA-T-TATTTTAAAAAAAACATTACAT
66 AAATAACTATAAAATTATATTTTTTAAAATACATTGC-T
* * * *
31444300 CACAAAAAAATAAAAAAAC-CCTATACTAAACACTAACAA-TT-TGTAACCTAATCCCATAAATT
1 ----AAAAAATCACAAAACACATA-ACTAAACACTAACAATTTATATAACCTAAT--CATAAATT
* *
31444362 ATTAACAAAATAAATAACTATAACAA--AAATTTTTTAAAATACATTGCT
59 ACTAAC---A-AAATAACTATAA-AATTATATTTTTTAAAATACATTGCT
31444410 AAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACA
1 AAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACA
31444475 AAATAACTATAAAATTATATTTTTTAAAATACATTGCT
66 AAATAACTATAAAATTATATTTTTTAAAATACATTGCT
31444513 AAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACA
1 AAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACA
31444578 AAATAACTATAAAATTATATTTTTTAAAATACATTGCT
66 AAATAACTATAAAATTATATTTTTTAAAATACATTGCT
31444616 AAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACA
1 AAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACA
* *
31444681 AAATAACTATAAAATTAT-TTTTTAAAAAAATTTACATTACT
66 AAATAACTATAAAATTATATTTTT--TAAAA--TACATTGCT
*
31444722 AAAAACTCACAAAACACA
1 AAAAAATCACAAAACACA
31444740 ACAATTTATA
Statistics
Matches: 494, Mismatches: 24, Indels: 45
0.88 0.04 0.08
Matches are distributed among these distances:
101 18 0.04
102 19 0.04
103 284 0.57
104 15 0.03
105 5 0.01
106 107 0.22
107 5 0.01
108 10 0.02
109 1 0.00
110 13 0.03
111 17 0.03
ACGTcount: A:0.55, C:0.16, G:0.01, T:0.29
Consensus pattern (103 bp):
AAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACA
AAATAACTATAAAATTATATTTTTTAAAATACATTGCT
Found at i:31444908 original size:52 final size:53
Alignment explanation
Indices: 31444815--31444921 Score: 189
Period size: 52 Copynumber: 2.0 Consensus size: 53
31444805 TACTAAACTA
*
31444815 AACACAACAACTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAAT
1 AACACAACAACTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAAT
*
31444868 AACACAACAATTTATAACAT-ATCCTAAATTACTAACAAATTAATTTTAAAAT
1 AACACAACAACTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAAT
31444920 AA
1 AA
31444922 TTATAAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
52 33 0.63
53 19 0.37
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (53 bp):
AACACAACAACTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAAT
Found at i:31445104 original size:8 final size:7
Alignment explanation
Indices: 31445086--31445141 Score: 64
Period size: 6 Copynumber: 8.1 Consensus size: 7
31445076 TAATACATTA
*
31445086 TCTTTTT
1 TCTTTCT
31445093 TCTTTCTT
1 TCTTTC-T
31445101 TCTTTCT
1 TCTTTCT
31445108 TC-TTCT
1 TCTTTCT
31445114 TC-TTCT
1 TCTTTCT
31445120 TC-TTCT
1 TCTTTCT
31445126 TCTCTTCT
1 TCT-TTCT
31445134 TCTTTCT
1 TCTTTCT
31445141 T
1 T
31445142 TCCTTTCTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
6 18 0.40
7 13 0.29
8 14 0.31
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (7 bp):
TCTTTCT
Found at i:31445108 original size:12 final size:11
Alignment explanation
Indices: 31445086--31445160 Score: 65
Period size: 9 Copynumber: 7.2 Consensus size: 11
31445076 TAATACATTA
*
31445086 TCTTTTTTCTT
1 TCTTTCTTCTT
31445097 TCTTTCTT-TCT
1 TCTTTCTTCT-T
31445108 TC-TTCTTC-T
1 TCTTTCTTCTT
31445117 TC-TTCTTC-T
1 TCTTTCTTCTT
31445126 TCTCTTCTTCTT
1 TCT-TTCTTCTT
31445138 TCTTTC--CTT
1 TCTTTCTTCTT
31445147 TCTTTCTCTCTT
1 TCTTTCT-TCTT
31445159 TC
1 TC
31445161 GGTGCTTGAA
Statistics
Matches: 55, Mismatches: 1, Indels: 15
0.77 0.01 0.21
Matches are distributed among these distances:
9 21 0.38
10 6 0.11
11 19 0.35
12 9 0.16
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (11 bp):
TCTTTCTTCTT
Found at i:31445112 original size:3 final size:3
Alignment explanation
Indices: 31445104--31445137 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
31445094 CTTTCTTTCT
31445104 TTC TTC TTC TTC TTC TTC TTC TTC -TC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
31445138 TCTTTCCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:31445147 original size:5 final size:4
Alignment explanation
Indices: 31445086--31445160 Score: 60
Period size: 4 Copynumber: 20.5 Consensus size: 4
31445076 TAATACATTA
31445086 TCTT T-TT TCTT TCTT TCTT TC-T TC-T TC-T TC-T TC-T TC-T TC-T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
*
31445126 TCTCT TC-T TCTT TCTT TCCTT TCTT TCTC TCTT TC
1 TCT-T TCTT TCTT TCTT T-CTT TCTT TCTT TCTT TC
31445161 GGTGCTTGAA
Statistics
Matches: 64, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
3 27 0.42
4 30 0.47
5 7 0.11
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TCTT
Found at i:31450516 original size:21 final size:23
Alignment explanation
Indices: 31450472--31450521 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 23
31450462 CCAATTAGCC
31450472 CATAAATCAAGGAAAATAATATA
1 CATAAATCAAGGAAAATAATATA
*
31450495 CATAAAT-AAGGAAAA-GATATA
1 CATAAATCAAGGAAAATAATATA
31450516 CATAAA
1 CATAAA
31450522 ATATTCATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 11 0.42
22 8 0.31
23 7 0.27
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.20
Consensus pattern (23 bp):
CATAAATCAAGGAAAATAATATA
Found at i:31460039 original size:14 final size:14
Alignment explanation
Indices: 31460020--31460076 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
31460010 ACCTCCTTGC
* *
31460020 ATGTGAGCCCATGT
1 ATGTGAGCCCCTAT
*
31460034 ATGTGAACCCCTAT
1 ATGTGAGCCCCTAT
*
31460048 AAGTGAGCCCCTAT
1 ATGTGAGCCCCTAT
*
31460062 ATGTGAACCCCTAT
1 ATGTGAGCCCCTAT
31460076 A
1 A
31460077 GGCGAGCGCC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (14 bp):
ATGTGAGCCCCTAT
Found at i:31460064 original size:28 final size:28
Alignment explanation
Indices: 31460022--31460125 Score: 127
Period size: 28 Copynumber: 3.7 Consensus size: 28
31460012 CTCCTTGCAT
*
31460022 GTGAGCCCATGTATGTGAACCCCTATAA
1 GTGAGCCCCTGTATGTGAACCCCTATAA
* *
31460050 GTGAGCCCCTATATGTGAACCCCTATAG
1 GTGAGCCCCTGTATGTGAACCCCTATAA
* * **
31460078 GCGAGCGCCTGTATACGAACCCCTATAA
1 GTGAGCCCCTGTATGTGAACCCCTATAA
* *
31460106 GTGAACCTCTGTATGTGAAC
1 GTGAGCCCCTGTATGTGAAC
31460126 TTGGAATGTA
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 61 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (28 bp):
GTGAGCCCCTGTATGTGAACCCCTATAA
Found at i:31460367 original size:27 final size:28
Alignment explanation
Indices: 31460330--31460402 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 28
31460320 TGTATATGCA
*
31460330 AACCCTATATGTGCGAACCTCTAGGTGC-
1 AACCC-ATATGTGCGAACCACTAGGTGCG
**
31460358 AACCCATATGTAAGAACCACTAGGTGCG
1 AACCCATATGTGCGAACCACTAGGTGCG
*
31460386 AA-CCATATGTGCTAACC
1 AACCCATATGTGCGAACC
31460403 CTGTGTGTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 31 0.82
28 7 0.18
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (28 bp):
AACCCATATGTGCGAACCACTAGGTGCG
Found at i:31477127 original size:40 final size:40
Alignment explanation
Indices: 31477090--31477314 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
31477080 GCTACTCGTT
* *
31477090 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
31477130 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
31477170 CAAATGCCTTCGGGCCTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
31477210 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
31477249 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
31477290 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
31477315 CATCATTCAA
Statistics
Matches: 166, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
38 2 0.01
39 33 0.20
40 118 0.71
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:31477274 original size:119 final size:120
Alignment explanation
Indices: 31477090--31477314 Score: 296
Period size: 119 Copynumber: 1.9 Consensus size: 120
31477080 GCTACTCGTT
*
31477090 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* * *
31477155 ATTTAGTAAC-TCGCACAAATGCCTTCGGGCCTTAACCCGGATTTAGTAACTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * **
31477210 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
31477272 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
31477315 CATCATTCAA
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
118 4 0.04
119 65 0.71
120 22 0.24
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:31485147 original size:40 final size:40
Alignment explanation
Indices: 31485103--31485195 Score: 143
Period size: 40 Copynumber: 2.3 Consensus size: 40
31485093 GCTCCTCGTT
* *
31485103 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAGTAACTCGCA
*
31485143 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
31485183 CAAATGCCTTCGG
1 CAAATGCCTTCGG
31485196 ATTTTAGTCC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
40 47 0.96
41 2 0.04
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:31485248 original size:40 final size:39
Alignment explanation
Indices: 31485103--31485248 Score: 123
Period size: 40 Copynumber: 3.6 Consensus size: 39
31485093 GCTCCTCGTT
* * * * *
31485103 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTC-GGACTTAGCCCAGATATAGTAACTAGCA
* * * *
31485143 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCAGATATAGTAACTAGCA
* * * *
31485183 CAAATGCCTTCGGATTTTAGTCCAGATATGGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCAGATATAGTAAC-TAGCA
31485224 CAAA-GCCTTCGAGACTTAGCCCAGA
1 CAAATGCCTTCG-GACTTAGCCCAGA
31485249 CATCATTCGA
Statistics
Matches: 88, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
39 3 0.03
40 75 0.85
41 10 0.11
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCAGATATAGTAACTAGCA
Found at i:31486667 original size:49 final size:49
Alignment explanation
Indices: 31486540--31487036 Score: 801
Period size: 49 Copynumber: 10.3 Consensus size: 49
31486530 CCCTTCGGGA
* * * * *
31486540 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
31486587 CCTGTCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
31486634 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
31486683 CTTATCAC--ACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACT-TTCACATTCATCACATCGGCCATTAGGC
31486730 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31486779 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31486828 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31486877 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31486926 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31486975 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31487024 CTTATCACATATA
1 CTTATCACATATA
31487037 CTATCATGTA
Statistics
Matches: 429, Mismatches: 13, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
46 2 0.00
47 88 0.21
49 338 0.79
50 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:31490606 original size:30 final size:31
Alignment explanation
Indices: 31490559--31490618 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
31490549 GGAGGTCGGA
*
31490559 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGAGAATAAAAGTTTTAAGGGAAAAG
*
31490590 TGGGAAGA-AGTAAAAGTTTTAAGGGAAAA
1 TGGGAAGAGAATAAAAGTTTTAAGGGAAAA
31490619 ATAAAAAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.20
Consensus pattern (31 bp):
TGGGAAGAGAATAAAAGTTTTAAGGGAAAAG
Found at i:31490683 original size:9 final size:9
Alignment explanation
Indices: 31490669--31490705 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
31490659 TATAGTTTGA
31490669 TATTCGAAT
1 TATTCGAAT
31490678 TATTCGAAT
1 TATTCGAAT
*
31490687 TATTCGAGT
1 TATTCGAAT
31490696 TATTCGAAT
1 TATTCGAAT
31490705 T
1 T
31490706 CGAAAACTCA
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:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:31490774 original size:9 final size:9
Alignment explanation
Indices: 31490757--31490787 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
31490747 TCAAGTTGAT
31490757 TCGAATAAC
1 TCGAATAAC
*
31490766 TCGATTAAC
1 TCGAATAAC
31490775 TCGAATAAC
1 TCGAATAAC
31490784 TCGA
1 TCGA
31490788 TTCGTTTAAC
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:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:31495407 original size:161 final size:161
Alignment explanation
Indices: 31495142--31495463 Score: 635
Period size: 161 Copynumber: 2.0 Consensus size: 161
31495132 ACCATAGTTT
31495142 TTAATGAAGGGCATTTTGGTCATTTGGTTAATAAAAGAAATAAGAAAAGGGAAATAAGGCCAAAA
1 TTAATGAAGGGCATTTTGGTCATTTGGTTAATAAAAGAAATAAGAAAAGGGAAATAAGGCCAAAA
31495207 TTGTGTCCATCTTCTCCATGCTTGGCTGAATTTTTCTAAGTCTCCATAGCTAGGGTTTTTCAAGC
66 TTGTGTCCATCTTCTCCATGCTTGGCTGAATTTTTCTAAGTCTCCATAGCTAGGGTTTTTCAAGC
31495272 TTCCAAGCTTAATAGTAAGTGCATCCTAGCC
131 TTCCAAGCTTAATAGTAAGTGCATCCTAGCC
31495303 TTAATGAAGGGCATTTTGGTCATTTGGTTAATAAAAGAAATAAGAAAAGGGAAATAAGGCCAAAA
1 TTAATGAAGGGCATTTTGGTCATTTGGTTAATAAAAGAAATAAGAAAAGGGAAATAAGGCCAAAA
*
31495368 TTGTGTCCATCTTCTCTATGCTTGGCTGAATTTTTCTAAGTCTCCATAGCTAGGGTTTTTCAAGC
66 TTGTGTCCATCTTCTCCATGCTTGGCTGAATTTTTCTAAGTCTCCATAGCTAGGGTTTTTCAAGC
31495433 TTCCAAGCTTAATAGTAAGTGCATCCTAGCC
131 TTCCAAGCTTAATAGTAAGTGCATCCTAGCC
31495464 CCGTTTTTAA
Statistics
Matches: 160, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 160 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (161 bp):
TTAATGAAGGGCATTTTGGTCATTTGGTTAATAAAAGAAATAAGAAAAGGGAAATAAGGCCAAAA
TTGTGTCCATCTTCTCCATGCTTGGCTGAATTTTTCTAAGTCTCCATAGCTAGGGTTTTTCAAGC
TTCCAAGCTTAATAGTAAGTGCATCCTAGCC
Found at i:31496289 original size:51 final size:51
Alignment explanation
Indices: 31496213--31496397 Score: 219
Period size: 51 Copynumber: 3.6 Consensus size: 51
31496203 CATGAGAACT
* * * * * ***
31496213 CATGTGTAGTACTATGCGTATGCTACTATGAGTATAAGATAGTTATGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAGTTATGGTCA
*
31496264 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAGTTTTGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAGTTATGGTCA
* * * *
31496315 CGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-GGTATTGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAGTTA-TGGTCA
* *
31496366 CATGTGCAGTACTAAGTGTAGGCTACTATGTG
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTG
31496398 CGGAACCACC
Statistics
Matches: 114, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
50 2 0.02
51 112 0.98
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (51 bp):
CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAGTTATGGTCA
Found at i:31528865 original size:9 final size:9
Alignment explanation
Indices: 31528807--31528864 Score: 89
Period size: 9 Copynumber: 6.4 Consensus size: 9
31528797 GTAGTGATTC
*
31528807 AATTTGGTT
1 AATTCGGTT
31528816 AATTCGGTT
1 AATTCGGTT
*
31528825 AATTCGGGT
1 AATTCGGTT
31528834 AATTCGGTT
1 AATTCGGTT
31528843 AATTCGGTT
1 AATTCGGTT
*
31528852 AATTTGGTT
1 AATTCGGTT
31528861 AATT
1 AATT
31528865 TTTAACCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.47
Consensus pattern (9 bp):
AATTCGGTT
Found at i:31532902 original size:71 final size:71
Alignment explanation
Indices: 31532817--31532959 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
31532807 ATAGAAAAGC
31532817 AAGTAAATTGTACCTAAGTCAGAAAGGGTACATTGAGAAAGTTCTTTGCAGGTTTAATATGCAGA
1 AAGTAAATTGTACCTAAGTCAGAAAGGGTACATTGAGAAAGTTCTTTGCAGGTTTAATATGCAGA
31532882 GTGCTA
66 GTGCTA
*
31532888 AAGTAATTTGTACCTAAGTCAGAAAGGGTACATTGAGAAAGTTCTTTGCAGGTTTAATATGCAGA
1 AAGTAAATTGTACCTAAGTCAGAAAGGGTACATTGAGAAAGTTCTTTGCAGGTTTAATATGCAGA
31532953 GTGCTA
66 GTGCTA
31532959 A
1 A
31532960 TCCTGTTCGT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (71 bp):
AAGTAAATTGTACCTAAGTCAGAAAGGGTACATTGAGAAAGTTCTTTGCAGGTTTAATATGCAGA
GTGCTA
Found at i:31533892 original size:24 final size:24
Alignment explanation
Indices: 31533858--31533909 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
31533848 TTTCTAGAAG
* **
31533858 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
31533882 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
31533906 ATTT
1 ATTT
31533910 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:31537968 original size:14 final size:14
Alignment explanation
Indices: 31537949--31537976 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31537939 TCTTGAATAA
31537949 TGATTTAGATTAGG
1 TGATTTAGATTAGG
31537963 TGATTTAGATTAGG
1 TGATTTAGATTAGG
31537977 AGTCAATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (14 bp):
TGATTTAGATTAGG
Found at i:31544655 original size:35 final size:34
Alignment explanation
Indices: 31544563--31544656 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 34
31544553 ACCCTAAATC
31544563 CTAAATCCCAAACTCCAAACC-T-AAACCTTAAACT
1 CTAAAT-CCAAAC-CCAAACCTTGAAACCTTAAACT
* * *
31544597 CTAAACCCAGAACCAAAAACTTGAAACCTTAAACT
1 CTAAATCCA-AACCCAAACCTTGAAACCTTAAACT
31544632 CTAAATCCAAACCCTAAACCTTGAA
1 CTAAATCCAAACCC-AAACCTTGAA
31544657 TCTTGAATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
33 8 0.16
34 13 0.26
35 29 0.58
ACGTcount: A:0.46, C:0.32, G:0.03, T:0.19
Consensus pattern (34 bp):
CTAAATCCAAACCCAAACCTTGAAACCTTAAACT
Found at i:31547761 original size:20 final size:19
Alignment explanation
Indices: 31547733--31547777 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
31547723 AATAAATTTT
*
31547733 TAAAATTTTTAATTAAATAC
1 TAAAATTTTTAACT-AATAC
*
31547753 TAAATTTTTTAACTAATAC
1 TAAAATTTTTAACTAATAC
31547772 TAAAAT
1 TAAAAT
31547778 CTATAATGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAATTTTTAACTAATAC
Found at i:31548487 original size:19 final size:19
Alignment explanation
Indices: 31548463--31548521 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
31548453 AAATTGTACC
31548463 AAAATTTCTAATGGATACA
1 AAAATTTCTAATGGATACA
** *** *
31548482 AAAATTGGTAACAAAATACT
1 AAAATTTCTAA-TGGATACA
31548502 AAAATTTCTAATGGATACA
1 AAAATTTCTAATGGATACA
31548521 A
1 A
31548522 GAACTTCAAA
Statistics
Matches: 27, Mismatches: 12, Indels: 2
0.66 0.29 0.05
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (19 bp):
AAAATTTCTAATGGATACA
Found at i:31548956 original size:19 final size:19
Alignment explanation
Indices: 31548896--31548957 Score: 88
Period size: 19 Copynumber: 3.2 Consensus size: 19
31548886 TAGGAATGTA
31548896 GGTATCCATTAGAGATTTT
1 GGTATCCATTAGAGATTTT
* * *
31548915 GGCATTCATTAGGAAATTTT
1 GGTATCCATTA-GAGATTTT
31548935 GGTATCCATTAGAGATTTT
1 GGTATCCATTAGAGATTTT
31548954 GGTA
1 GGTA
31548958 ACGTGTTAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (19 bp):
GGTATCCATTAGAGATTTT
Found at i:31548970 original size:39 final size:39
Alignment explanation
Indices: 31548896--31548977 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
31548886 TAGGAATGTA
* *
31548896 GGTATCCATTAGAGATTTTGGCATTCATTAGGAAATTTT
1 GGTATCCATTAGAGATTTTGGAAGTCATTAGGAAATTTT
*
31548935 GGTATCCATTAGAGATTTTGGTAACGT-GTTA-GAAATTTT
1 GGTATCCATTAGAGATTTTGG-AA-GTCATTAGGAAATTTT
31548974 GGTA
1 GGTA
31548978 CCCCTTTAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 33 0.87
40 4 0.11
41 1 0.03
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (39 bp):
GGTATCCATTAGAGATTTTGGAAGTCATTAGGAAATTTT
Found at i:31549038 original size:20 final size:20
Alignment explanation
Indices: 31548927--31549038 Score: 102
Period size: 20 Copynumber: 5.7 Consensus size: 20
31548917 CATTCATTAG
*
31548927 GAAATTTTGGTAT-CCATTA
1 GAAATTTTGGTATACCTTTA
* *
31548946 GAGATTTTGGTA-ACGTGTTA
1 GAAATTTTGGTATACCT-TTA
**
31548966 GAAATTTTGGTACCCCTTTA
1 GAAATTTTGGTATACCTTTA
* ** *
31548986 GAAATTTTGATATTTCTTCA
1 GAAATTTTGGTATACCTTTA
*
31549006 GATATTTTGGTATACCTTTA
1 GAAATTTTGGTATACCTTTA
*
31549026 GAAATTTTAGTAT
1 GAAATTTTGGTAT
31549039 GTTGCATAAG
Statistics
Matches: 72, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 12 0.17
20 58 0.81
21 2 0.03
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.45
Consensus pattern (20 bp):
GAAATTTTGGTATACCTTTA
Found at i:31551644 original size:41 final size:41
Alignment explanation
Indices: 31551527--31551657 Score: 137
Period size: 41 Copynumber: 3.3 Consensus size: 41
31551517 CACCAGTTTG
* * *
31551527 AGTGCCTCATC-AAATAATTCGAAGTAATAAATTGACTCCC
1 AGTGCCTCATCGAAATAATCCGAAGTAGTAAATTGACACCC
* * * * *
31551567 AGTGTCTCATCG-ACTAAACCG-A--CGTAAATTGGCACCC
1 AGTGCCTCATCGAAATAATCCGAAGTAGTAAATTGACACCC
*
31551604 AGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGACACCC
1 AGTGCCTCATCGAAATAATCCGAAGTAGTAAATTGACACCC
*
31551645 AGTGTCTCATCGA
1 AGTGCCTCATCGA
31551658 CTCGAAATCG
Statistics
Matches: 72, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
37 22 0.31
38 7 0.10
39 2 0.03
40 16 0.22
41 25 0.35
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (41 bp):
AGTGCCTCATCGAAATAATCCGAAGTAGTAAATTGACACCC
Found at i:31556112 original size:132 final size:132
Alignment explanation
Indices: 31555947--31556207 Score: 450
Period size: 132 Copynumber: 2.0 Consensus size: 132
31555937 AATGAATTCT
*
31555947 TTGACGCCTCTTTTTTGAATTTCTCAAATAGGATCAACCTTATGGGGAGTCATAGTAGGCACAAG
1 TTGACACCTCTTTTTTGAATTTCTCAAATAGGATCAACCTTATGGGGAGTCATAGTAGGCACAAG
* * *
31556012 TGAAGCAGGTTGAGTCGGGCGAACCACTTCAGGTTGTGGTTGAAAAGGGTGTTGCAGTTATTGTT
66 TGAAGCAAGTTGAGTCGGACGAACCACTTCAGGTTGTGGTTGAAAAGAGTGTTGCAGTTATTGTT
31556077 CC
131 CC
* * *
31556079 TTGACACCTCTTTTTTGAATTTCTCGAATAGGATCAACCTTATGGGGAGTCGTAGTAGGCACAGG
1 TTGACACCTCTTTTTTGAATTTCTCAAATAGGATCAACCTTATGGGGAGTCATAGTAGGCACAAG
*
31556144 TGAAGCAAGTTGAGTCGGACGAACCATTTCAGGTTGTGGTTGAAAAGAGTGTTGCAGTTATTGT
66 TGAAGCAAGTTGAGTCGGACGAACCACTTCAGGTTGTGGTTGAAAAGAGTGTTGCAGTTATTGT
31556208 GGCTATTATT
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 121 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (132 bp):
TTGACACCTCTTTTTTGAATTTCTCAAATAGGATCAACCTTATGGGGAGTCATAGTAGGCACAAG
TGAAGCAAGTTGAGTCGGACGAACCACTTCAGGTTGTGGTTGAAAAGAGTGTTGCAGTTATTGTT
CC
Found at i:31557485 original size:39 final size:38
Alignment explanation
Indices: 31557431--31557518 Score: 131
Period size: 39 Copynumber: 2.3 Consensus size: 38
31557421 AACGACAAGC
*
31557431 ATCCATTACTTTTGCACAAATATTTTATATTCGCCAAAT
1 ATCCA-TACTTTTGCACAAATATTTTATATTCACCAAAT
*
31557470 ATCCATCACTTTTGCACAAATATTTTATATTCACCGAAT
1 ATCCAT-ACTTTTGCACAAATATTTTATATTCACCAAAT
*
31557509 ATGCATACTT
1 ATCCATACTT
31557519 ACCTTAAACG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 5 0.11
39 40 0.89
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.40
Consensus pattern (38 bp):
ATCCATACTTTTGCACAAATATTTTATATTCACCAAAT
Found at i:31563646 original size:18 final size:18
Alignment explanation
Indices: 31563616--31563650 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31563606 TCGTTTGTTT
31563616 TTTTTCATTATTTATTTA
1 TTTTTCATTATTTATTTA
31563634 TTTTT-ATTAATTTATTT
1 TTTTTCATT-ATTTATTT
31563651 CTATCCCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTCATTATTTATTTA
Found at i:31565536 original size:20 final size:21
Alignment explanation
Indices: 31565501--31565548 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
31565491 ATCTAATAAT
31565501 ATATATTATATCTATAAGCACA
1 ATATATTATA-CTATAAGCACA
**
31565523 ATATATTATA-TATAAGTGCA
1 ATATATTATACTATAAGCACA
31565543 ATATAT
1 ATATAT
31565549 ATAACCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 14 0.58
22 10 0.42
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (21 bp):
ATATATTATACTATAAGCACA
Found at i:31565548 original size:22 final size:21
Alignment explanation
Indices: 31565498--31565550 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 21
31565488 AAAATCTAAT
31565498 AATATATATTATATCTATAAGC
1 AATATATATTATA-CTATAAGC
31565520 ACA-ATATATTATA-TATAAGTGC
1 A-ATATATATTATACTATAA--GC
31565542 AATATATAT
1 AATATATAT
31565551 AACCAATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
20 5 0.19
21 1 0.04
22 20 0.74
23 1 0.04
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (21 bp):
AATATATATTATACTATAAGC
Found at i:31567129 original size:31 final size:31
Alignment explanation
Indices: 31567072--31567130 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
31567062 GTGTAATTCA
*
31567072 TATTTGAGTTAAACCGAAAAATTTAATTTTT
1 TATTTGAGTTAAACCGAAAAACTTAATTTTT
* *
31567103 TATTTGAGTTGATCC-AAATAACTTAATT
1 TATTTGAGTTAAACCGAAA-AACTTAATT
31567131 AACTCAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 21 0.88
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.44
Consensus pattern (31 bp):
TATTTGAGTTAAACCGAAAAACTTAATTTTT
Found at i:31571567 original size:21 final size:23
Alignment explanation
Indices: 31571533--31571580 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
31571523 TATTTTCTTT
31571533 TTATATTTACTTAT-TCATTACCA
1 TTATATTTACTTATATCA-TACCA
*
31571556 TTATA-TTA-TTATATTATACCA
1 TTATATTTACTTATATCATACCA
31571577 TTAT
1 TTAT
31571581 CTTTGTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 13 0.57
22 5 0.22
23 5 0.22
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.54
Consensus pattern (23 bp):
TTATATTTACTTATATCATACCA
Found at i:31571600 original size:3 final size:3
Alignment explanation
Indices: 31571586--31571636 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
31571576 ATTATCTTTG
* * *
31571586 TAT TAT TGT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
31571634 TAT
1 TAT
31571637 ATTTACTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:31571606 original size:15 final size:15
Alignment explanation
Indices: 31571595--31571636 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
31571585 GTATTATTGT
31571595 TATTATTATTATTAC
1 TATTATTATTATTAC
31571610 TATTATTATTATTAC
1 TATTATTATTATTAC
31571625 TATTATTATTAT
1 TATTATTATTAT
31571637 ATTTACTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:31573091 original size:4 final size:4
Alignment explanation
Indices: 31573082--31573108 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
31573072 AACAATGGAT
31573082 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
31573109 ATGATGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:31574221 original size:13 final size:13
Alignment explanation
Indices: 31574203--31574227 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31574193 AAAAGGAAAA
31574203 TAAAATAAAAATC
1 TAAAATAAAAATC
31574216 TAAAATAAAAAT
1 TAAAATAAAAAT
31574228 ACAATATGTT
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:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAATAAAAATC
Found at i:31574450 original size:25 final size:26
Alignment explanation
Indices: 31574421--31574492 Score: 103
Period size: 26 Copynumber: 2.8 Consensus size: 26
31574411 TTTAGGCCAG
31574421 TTGGGCTAGGTT-ATTGGGCTTAG-GT
1 TTGGGCTAGGTTAATTGGG-TTAGAGT
* *
31574446 TTGGGCTTGGTTAATTGGGTTAGATT
1 TTGGGCTAGGTTAATTGGGTTAGAGT
31574472 TTGGGCTAGGTTAATTGGGTT
1 TTGGGCTAGGTTAATTGGGTT
31574493 TGTAAAAGCT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 15 0.36
26 27 0.64
ACGTcount: A:0.14, C:0.06, G:0.38, T:0.43
Consensus pattern (26 bp):
TTGGGCTAGGTTAATTGGGTTAGAGT
Found at i:31574927 original size:100 final size:100
Alignment explanation
Indices: 31574790--31575574 Score: 1097
Period size: 100 Copynumber: 7.8 Consensus size: 100
31574780 TAACTCGTAA
* ** * ** * * *
31574790 CTTTAATCTGTTTAACTGTGATGTCGAGGAAGCAAGATTCGCTGTTGTAGCTTCAATTTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCATTGTGGCTTTAATCTGTTCCA
* * *
31574855 CTACACCGCCTGGGAAGTAAGATTCGCTGTTGTAG
66 CTGCACCGCTTGGGGAGTAAGATTCGCTGTTGTAG
* * * * * *
31574890 CTTTAATCTTTCTAACTGCAATATTGGGGAAGTAAGATTCACCATTGTGGCGTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCATTGTGGCTTTAATCTGTTCCA
** *
31574955 CTGCACCGCTTAAGAAGTAAGATTCGCTGTTGTAG
66 CTGCACCGCTTGGGGAGTAAGATTCGCTGTTGTAG
* *
31574990 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGGTTCGCCATTGTGGCTTTAATTTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCATTGTGGCTTTAATCTGTTCCA
*
31575055 CTGCACTGCTTGGGGAGTAAGATTCGCTGTTGTAG
66 CTGCACCGCTTGGGGAGTAAGATTCGCTGTTGTAG
* *
31575090 CTTTAATCTTTTTAACTACAATGTCGGGGAAGCAAGATTCGCCATTGTGGCTTTAATCTATTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCATTGTGGCTTTAATCTGTTCCA
31575155 CTGCACCGCTTGGGGAGTAAGATTCGCTGTTGTAG
66 CTGCACCGCTTGGGGAGTAAGATTCGCTGTTGTAG
31575190 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCATTGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCATTGTGGCTTTAATCTGTTCCA
* * * *
31575255 TTGCACCGCTTGGGGAGTAACATTTGCTATTGTAG
66 CTGCACCGCTTGGGGAGTAAGATTCGCTGTTGTAG
31575290 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCATTGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCATTGTGGCTTTAATCTGTTCCA
* * * *
31575355 TTGCACCGCTTGGGGAGTAACATTTGCTATTGTAG
66 CTGCACCGCTTGGGGAGTAAGATTCGCTGTTGTAG
* *
31575390 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGA-TGTGGCTTTAATCTATTCC
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCC-ATTGTGGCTTTAATCTGTTCC
* ** * * *
31575454 ATTGCATTGCCTAGGGAGTAAGATTCACTGTTGTAG
65 ACTGCACCGCTTGGGGAGTAAGATTCGCTGTTGTAG
* * *
31575490 CTTTAATCTTTTTAACTACAATGTCGGGGAGGCAAGATTCACCGA-TGTGGCTTTAATCTGTTCC
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCC-ATTGTGGCTTTAATCTGTTCC
* * * *
31575554 ATTGCATCGCCTGGGAAGTAA
65 ACTGCACCGCTTGGGGAGTAA
31575575 AACTGGTATT
Statistics
Matches: 626, Mismatches: 58, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
100 625 1.00
101 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (100 bp):
CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCATTGTGGCTTTAATCTGTTCCA
CTGCACCGCTTGGGGAGTAAGATTCGCTGTTGTAG
Found at i:31575527 original size:50 final size:49
Alignment explanation
Indices: 31574873--31575548 Score: 458
Period size: 50 Copynumber: 13.5 Consensus size: 49
31574863 CCTGGGAAGT
** * * * *
31574873 AAGATTCGCTGTTGTAGCTTTAATCTTTCTAACTGCAATATTGGGGAAGT
1 AAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGG-AGC
* * * * ** ** *** * *
31574923 AAGATTCACCATTGTGGCGTTAATCTGTTCCACTGCACCGCTTAAGAAGT
1 AAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATG-TCGGGGAGC
**
31574973 AAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
1 AAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGG-AGC
* * ** * * *
31575023 AAGGTTCGCCATTGTGGCTTTAAT-TTGTTCCACTGCACTGCTTGGGGAGT
1 AAGATTCGCCATTGTAGCTTTAATCTT-TTTAACTGCAATG-TCGGGGAGC
** *
31575073 AAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTACAATGTCGGGGAAGC
1 AAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGG-AGC
* * ** ** * *
31575123 AAGATTCGCCATTGTGGCTTTAATCTATTCCACTGCACCGCTTGGGGAGT
1 AAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATG-TCGGGGAGC
**
31575173 AAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
1 AAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGG-AGC
* * ** * ** * *
31575223 AAGATTCGCCATTGTGGCTTTAATCTGTTCCATTGCACCGCTTGGGGAGT
1 AAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATG-TCGGGGAGC
* * *
31575273 AACATTTGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
1 AAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGG-AGC
* * ** * ** * *
31575323 AAGATTCGCCATTGTGGCTTTAATCTGTTCCATTGCACCGCTTGGGGAGT
1 AAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATG-TCGGGGAGC
* * *
31575373 AACATTTGCTATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
1 AAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGG-AGC
* * * ** * * * * *
31575423 AAGATTCACCGA-TGTGGCTTTAATCTATTCCATTGCATTGCCTAGGGAGT
1 AAGATTCGCC-ATTGTAGCTTTAATCTTTTTAACTGCAATGTC-GGGGAGC
* ** *
31575473 AAGATTCACTGTTGTAGCTTTAATCTTTTTAACTACAATGTCGGGGAGGC
1 AAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGA-GC
* *
31575523 AAGATTCACCGA-TGTGGCTTTAATCT
1 AAGATTCGCC-ATTGTAGCTTTAATCT
31575549 GTTCCATTGC
Statistics
Matches: 464, Mismatches: 145, Indels: 34
0.72 0.23 0.05
Matches are distributed among these distances:
49 28 0.06
50 407 0.88
51 29 0.06
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (49 bp):
AAGATTCGCCATTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAGC
Found at i:31576880 original size:7 final size:7
Alignment explanation
Indices: 31576861--31576911 Score: 70
Period size: 7 Copynumber: 7.3 Consensus size: 7
31576851 TTGGCCTCTC
31576861 CATTTTT
1 CATTTTT
31576868 GC-TTTTT
1 -CATTTTT
31576875 CATTTTT
1 CATTTTT
31576882 CATTTTT
1 CATTTTT
31576889 CATTTTT
1 CATTTTT
31576896 -ATTTTTT
1 CA-TTTTT
31576903 CATTTTT
1 CATTTTT
31576910 CA
1 CA
31576912 CAATTTTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
6 2 0.05
7 36 0.90
8 2 0.05
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.71
Consensus pattern (7 bp):
CATTTTT
Found at i:31587556 original size:16 final size:16
Alignment explanation
Indices: 31587535--31587566 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31587525 GCAAAGGTCA
31587535 GTGTAGTCAATCCCTG
1 GTGTAGTCAATCCCTG
*
31587551 GTGTAGTCGATCCCTG
1 GTGTAGTCAATCCCTG
31587567 TAACATGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.25, G:0.28, T:0.31
Consensus pattern (16 bp):
GTGTAGTCAATCCCTG
Found at i:31595983 original size:16 final size:16
Alignment explanation
Indices: 31595962--31595996 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
31595952 TTGTGTTTTG
*
31595962 TTTTGATTGCATGGCA
1 TTTTGACTGCATGGCA
31595978 TTTTGACTGCATGGCA
1 TTTTGACTGCATGGCA
31595994 TTT
1 TTT
31595997 CATTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.14, G:0.23, T:0.46
Consensus pattern (16 bp):
TTTTGACTGCATGGCA
Found at i:31596869 original size:16 final size:16
Alignment explanation
Indices: 31596848--31596882 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
31596838 TTGTGTTTTG
*
31596848 TTTTGATTGCATGGCA
1 TTTTGACTGCATGGCA
31596864 TTTTGACTGCATGGCA
1 TTTTGACTGCATGGCA
31596880 TTT
1 TTT
31596883 CATTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.14, G:0.23, T:0.46
Consensus pattern (16 bp):
TTTTGACTGCATGGCA
Found at i:31596917 original size:886 final size:886
Alignment explanation
Indices: 31595205--31596976 Score: 3544
Period size: 886 Copynumber: 2.0 Consensus size: 886
31595195 TACGTAATCG
31595205 ATTCCCGAACCCATTTTTCTAAAGCTTGTAGAACAAAATTGTGATTTTAATAAATAACCACTTTT
1 ATTCCCGAACCCATTTTTCTAAAGCTTGTAGAACAAAATTGTGATTTTAATAAATAACCACTTTT
31595270 CGAGGTGACCCAATCACAGCTCATTAAAAATGATTGGTGGCGACTCCTATGTTCGTTTTCATTTT
66 CGAGGTGACCCAATCACAGCTCATTAAAAATGATTGGTGGCGACTCCTATGTTCGTTTTCATTTT
31595335 CAAAATCCAAGTCGACCCCGTTTTATAAAAAAATGGTTTCGACAGCTTGGCAACTCCACTGGGGA
131 CAAAATCCAAGTCGACCCCGTTTTATAAAAAAATGGTTTCGACAGCTTGGCAACTCCACTGGGGA
31595400 CGTAAAAAAGAGAGTCAAGCCACGTGTTGATTACTTTTTGTCTTTTTGTTGAAAATTGAAAACTT
196 CGTAAAAAAGAGAGTCAAGCCACGTGTTGATTACTTTTTGTCTTTTTGTTGAAAATTGAAAACTT
31595465 GGTTTATATTTACGATAATTTTGATGCATTTTATTCGTTTTTTTATGATCTTCATCAGTTGGTTT
261 GGTTTATATTTACGATAATTTTGATGCATTTTATTCGTTTTTTTATGATCTTCATCAGTTGGTTT
31595530 ATAATCGCTTTCCTAGTTTGAATTTTTGATATGTTTCTACACATTGCATTACATGACCACTCGAT
326 ATAATCGCTTTCCTAGTTTGAATTTTTGATATGTTTCTACACATTGCATTACATGACCACTCGAT
31595595 TATACCCTTTGAAGTGGGAGTGAGAAACTATTATTTCGTGAGGTCTTCACCTTCATGCAGGATAG
391 TATACCCTTTGAAGTGGGAGTGAGAAACTATTATTTCGTGAGGTCTTCACCTTCATGCAGGATAG
31595660 GGAATCACTTTCAGGATACATCCGTACCTATGTCTTCGTGAGATTTTCATCTCCGTGCAGCCATA
456 GGAATCACTTTCAGGATACATCCGTACCTATGTCTTCGTGAGATTTTCATCTCCGTGCAGCCATA
31595725 GGGAAATGTATTCCCCTGAACTGAACTCAGTCCATATGAGCCTATAATGGGTGAGGATTGAAGAA
521 GGGAAATGTATTCCCCTGAACTGAACTCAGTCCATATGAGCCTATAATGGGTGAGGATTGAAGAA
31595790 TCTGCTGGTTCAGGTACCTTTACTTTAGAACCAAACCACATATAGTGAACCTTAGGAACTTGCCC
586 TCTGCTGGTTCAGGTACCTTTACTTTAGAACCAAACCACATATAGTGAACCTTAGGAACTTGCCC
31595855 TAGGTAGAACTACGCCAAACCCTAGTAGATACCCAAATTGGTGCTTTATTATTTCTTATTTGTAT
651 TAGGTAGAACTACGCCAAACCCTAGTAGATACCCAAATTGGTGCTTTATTATTTCTTATTTGTAT
31595920 TAAATTTTATTTTTATACATGATACTGACTTGTTGTGTTTTGTTTTGATTGCATGGCATTTTGAC
716 TAAATTTTATTTTTATACATGATACTGACTTGTTGTGTTTTGTTTTGATTGCATGGCATTTTGAC
31595985 TGCATGGCATTTCATTATAAAAGGCGTTCATTCAGATTCGGTTACTAGATAGAAAGCTTATCATG
781 TGCATGGCATTTCATTATAAAAGGCGTTCATTCAGATTCGGTTACTAGATAGAAAGCTTATCATG
31596050 GAAAAAGGGTTTCTTGATAAGGTGAAGGGTAATACGGCTGT
846 GAAAAAGGGTTTCTTGATAAGGTGAAGGGTAATACGGCTGT
31596091 ATTCCCGAACCCATTTTTCTAAAGCTTGTAGAACAAAATTGTGATTTTAATAAATAACCACTTTT
1 ATTCCCGAACCCATTTTTCTAAAGCTTGTAGAACAAAATTGTGATTTTAATAAATAACCACTTTT
31596156 CGAGGTGACCCAATCACAGCTCATTAAAAATGATTGGTGGCGACTCCTATGTTCGTTTTCATTTT
66 CGAGGTGACCCAATCACAGCTCATTAAAAATGATTGGTGGCGACTCCTATGTTCGTTTTCATTTT
31596221 CAAAATCCAAGTCGACCCCGTTTTATAAAAAAATGGTTTCGACAGCTTGGCAACTCCACTGGGGA
131 CAAAATCCAAGTCGACCCCGTTTTATAAAAAAATGGTTTCGACAGCTTGGCAACTCCACTGGGGA
31596286 CGTAAAAAAGAGAGTCAAGCCACGTGTTGATTACTTTTTGTCTTTTTGTTGAAAATTGAAAACTT
196 CGTAAAAAAGAGAGTCAAGCCACGTGTTGATTACTTTTTGTCTTTTTGTTGAAAATTGAAAACTT
31596351 GGTTTATATTTACGATAATTTTGATGCATTTTATTCGTTTTTTTATGATCTTCATCAGTTGGTTT
261 GGTTTATATTTACGATAATTTTGATGCATTTTATTCGTTTTTTTATGATCTTCATCAGTTGGTTT
31596416 ATAATCGCTTTCCTAGTTTGAATTTTTGATATGTTTCTACACATTGCATTACATGACCACTCGAT
326 ATAATCGCTTTCCTAGTTTGAATTTTTGATATGTTTCTACACATTGCATTACATGACCACTCGAT
31596481 TATACCCTTTGAAGTGGGAGTGAGAAACTATTATTTCGTGAGGTCTTCACCTTCATGCAGGATAG
391 TATACCCTTTGAAGTGGGAGTGAGAAACTATTATTTCGTGAGGTCTTCACCTTCATGCAGGATAG
31596546 GGAATCACTTTCAGGATACATCCGTACCTATGTCTTCGTGAGATTTTCATCTCCGTGCAGCCATA
456 GGAATCACTTTCAGGATACATCCGTACCTATGTCTTCGTGAGATTTTCATCTCCGTGCAGCCATA
31596611 GGGAAATGTATTCCCCTGAACTGAACTCAGTCCATATGAGCCTATAATGGGTGAGGATTGAAGAA
521 GGGAAATGTATTCCCCTGAACTGAACTCAGTCCATATGAGCCTATAATGGGTGAGGATTGAAGAA
31596676 TCTGCTGGTTCAGGTACCTTTACTTTAGAACCAAACCACATATAGTGAACCTTAGGAACTTGCCC
586 TCTGCTGGTTCAGGTACCTTTACTTTAGAACCAAACCACATATAGTGAACCTTAGGAACTTGCCC
31596741 TAGGTAGAACTACGCCAAACCCTAGTAGATACCCAAATTGGTGCTTTATTATTTCTTATTTGTAT
651 TAGGTAGAACTACGCCAAACCCTAGTAGATACCCAAATTGGTGCTTTATTATTTCTTATTTGTAT
31596806 TAAATTTTATTTTTATACATGATACTGACTTGTTGTGTTTTGTTTTGATTGCATGGCATTTTGAC
716 TAAATTTTATTTTTATACATGATACTGACTTGTTGTGTTTTGTTTTGATTGCATGGCATTTTGAC
31596871 TGCATGGCATTTCATTATAAAAGGCGTTCATTCAGATTCGGTTACTAGATAGAAAGCTTATCATG
781 TGCATGGCATTTCATTATAAAAGGCGTTCATTCAGATTCGGTTACTAGATAGAAAGCTTATCATG
31596936 GAAAAAGGGTTTCTTGATAAGGTGAAGGGTAATACGGCTGT
846 GAAAAAGGGTTTCTTGATAAGGTGAAGGGTAATACGGCTGT
31596977 CTAAACCTAG
Statistics
Matches: 886, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
886 886 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (886 bp):
ATTCCCGAACCCATTTTTCTAAAGCTTGTAGAACAAAATTGTGATTTTAATAAATAACCACTTTT
CGAGGTGACCCAATCACAGCTCATTAAAAATGATTGGTGGCGACTCCTATGTTCGTTTTCATTTT
CAAAATCCAAGTCGACCCCGTTTTATAAAAAAATGGTTTCGACAGCTTGGCAACTCCACTGGGGA
CGTAAAAAAGAGAGTCAAGCCACGTGTTGATTACTTTTTGTCTTTTTGTTGAAAATTGAAAACTT
GGTTTATATTTACGATAATTTTGATGCATTTTATTCGTTTTTTTATGATCTTCATCAGTTGGTTT
ATAATCGCTTTCCTAGTTTGAATTTTTGATATGTTTCTACACATTGCATTACATGACCACTCGAT
TATACCCTTTGAAGTGGGAGTGAGAAACTATTATTTCGTGAGGTCTTCACCTTCATGCAGGATAG
GGAATCACTTTCAGGATACATCCGTACCTATGTCTTCGTGAGATTTTCATCTCCGTGCAGCCATA
GGGAAATGTATTCCCCTGAACTGAACTCAGTCCATATGAGCCTATAATGGGTGAGGATTGAAGAA
TCTGCTGGTTCAGGTACCTTTACTTTAGAACCAAACCACATATAGTGAACCTTAGGAACTTGCCC
TAGGTAGAACTACGCCAAACCCTAGTAGATACCCAAATTGGTGCTTTATTATTTCTTATTTGTAT
TAAATTTTATTTTTATACATGATACTGACTTGTTGTGTTTTGTTTTGATTGCATGGCATTTTGAC
TGCATGGCATTTCATTATAAAAGGCGTTCATTCAGATTCGGTTACTAGATAGAAAGCTTATCATG
GAAAAAGGGTTTCTTGATAAGGTGAAGGGTAATACGGCTGT
Found at i:31600357 original size:11 final size:11
Alignment explanation
Indices: 31600343--31600381 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
31600333 AAATGATGAA
31600343 AAAAAGAAAAG
1 AAAAAGAAAAG
*
31600354 AAAAAGAGAAG
1 AAAAAGAAAAG
*
31600365 AAAAGGAAAAGG
1 AAAAAGAAAA-G
31600377 AAAAA
1 AAAAA
31600382 AATAGGAGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:31600368 original size:22 final size:22
Alignment explanation
Indices: 31600322--31600381 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
31600312 AAAATATTTC
* *
31600322 AAAAA-AAATGAAAATGATGAA
1 AAAAAGAAAAGAAAAAGATGAA
31600343 AAAAAGAAAAGAAAAAGA-GAA
1 AAAAAGAAAAGAAAAAGATGAA
*
31600364 GAAAAGGAAAAGGAAAAA
1 -AAAAAGAAAA-GAAAAA
31600382 AATAGGAGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 8 0.24
22 19 0.58
23 6 0.18
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (22 bp):
AAAAAGAAAAGAAAAAGATGAA
Found at i:31601363 original size:44 final size:46
Alignment explanation
Indices: 31601283--31601394 Score: 156
Period size: 44 Copynumber: 2.5 Consensus size: 46
31601273 AAAGAGAAGG
* ** * *
31601283 GACCAAGGCGAAAACTTGCAAAGGGCGCTTTGAGTTC-T-AAAAAA
1 GACCAAGGTGAAAACCCGCAAAGGGCGCCTTAAGTTCTTAAAAAAA
*
31601327 GACTAAGGTGAAAACCCGCAAAGGGCGCCTTAAGTTCTTAAAAAAA
1 GACCAAGGTGAAAACCCGCAAAGGGCGCCTTAAGTTCTTAAAAAAA
31601373 GACCAAGGTGAAAACCCGCAAA
1 GACCAAGGTGAAAACCCGCAAA
31601395 AGGGTGCTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 31 0.53
45 1 0.02
46 27 0.46
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (46 bp):
GACCAAGGTGAAAACCCGCAAAGGGCGCCTTAAGTTCTTAAAAAAA
Found at i:31601415 original size:46 final size:45
Alignment explanation
Indices: 31601283--31601417 Score: 166
Period size: 46 Copynumber: 3.0 Consensus size: 45
31601273 AAAGAGAAGG
* **
31601283 GACCAAGGCGAAAACTTGCAAAGGGCGCTTTGAGTTCT-AAAAAA
1 GACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAGTTCTAAAAAAA
* * *
31601327 GACTAAGGTGAAAACCCGCAAAGGGCGCCTTAAGTTCTTAAAAAAA
1 GACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAGTTC-TAAAAAAA
*
31601373 GACCAAGGTGAAAACCCGCAAAAGGGTGCTTTGAG-TCATAAAAAA
1 GACCAAGGTGAAAACCCGC-AAAGGGCGCTTTGAGTTC-TAAAAAA
31601418 TAATATAAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
44 31 0.40
45 1 0.01
46 33 0.43
47 12 0.16
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.17
Consensus pattern (45 bp):
GACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAGTTCTAAAAAAA
Found at i:31602971 original size:51 final size:51
Alignment explanation
Indices: 31602898--31603059 Score: 191
Period size: 51 Copynumber: 3.2 Consensus size: 51
31602888 AGTGGAGATA
* * * * *
31602898 ATTAAAGCTGAAGGCAGCGAATCCTATCTCCTTAGCGTTACAGTGGAACAG
1 ATTAAAGCTAAAGGTAGCGAATCATATTTCCTTAGCGTTGCAGTGGAACAG
* * * *
31602949 ATTAAAGCTAAAGGTAGAGAATCTTGTTTCTCTGA-CGTTGCAGTGGAACAG
1 ATTAAAGCTAAAGGTAGCGAATCATATTTC-CTTAGCGTTGCAGTGGAACAG
* * * *
31603000 ATTAAAGCTAAAGGTAGCGAATCATATTTCCCTGGCGTTGCACTGGAATAG
1 ATTAAAGCTAAAGGTAGCGAATCATATTTCCTTAGCGTTGCAGTGGAACAG
31603051 ATTAAAGCT
1 ATTAAAGCT
31603060 GAAGTGGAGT
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
50 1 0.01
51 89 0.96
52 3 0.03
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (51 bp):
ATTAAAGCTAAAGGTAGCGAATCATATTTCCTTAGCGTTGCAGTGGAACAG
Found at i:31603083 original size:174 final size:174
Alignment explanation
Indices: 31602793--31603233 Score: 591
Period size: 174 Copynumber: 2.5 Consensus size: 174
31602783 TGTAGGCAGC
* * * *
31602793 GAATCTTTTTTCTCTGGCATTGCCA-TGGAACAGATTAAAGCTAAAGATAGCGAATCTTATTTCC
1 GAATCTTGTTTCTCTGGCGTTG-CAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCATATTTCC
* * *
31602857 CTAGCGTTGCACTAGAATAGATGAAAGCTGAAGTGGAGATAATTAAAGCTGAAGGCAGCGAATCC
65 CTGGCGTTGCACTGGAATAGATTAAAGCTGAAGTGGAGATAATTAAAGCTGAAGGCAGCGAATCC
*
31602922 TATCTCCTTAGCGTTACAGTGGAACAGATTAAAGCTAAAGGTAGA
130 TATCTCCTTAGCCTTACAGTGGAACAGATTAAAGCTAAAGGTAGA
*
31602967 GAATCTTGTTTCTCTGACGTTGCAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCATATTTCCC
1 GAATCTTGTTTCTCTGGCGTTGCAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCATATTTCCC
*
31603032 TGGCGTTGCACTGGAATAGATTAAAGCTGAAGTGGAG-TGGATTAAAGCTGAAGGCAGCGAATCC
66 TGGCGTTGCACTGGAATAGATTAAAGCTGAAGTGGAGAT-AATTAAAGCTGAAGGCAGCGAATCC
* * *
31603096 TATCTCCTTGGCCTTATAGTGGAATAGATTAAAGCTAAAGGTAGA
130 TATCTCCTTAGCCTTACAGTGGAACAGATTAAAGCTAAAGGTAGA
* * ** ** * * *
31603141 GAATCTTGTTTCCCTGGTGTTATAGCAGAGCAGATTAAAGCTAAAGGCAGCGAATCCTATCTT-C
1 GAATCTTGTTTCTCTGGCGTTGCAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCATAT-TTCC
* * * * *
31603205 TTGGCATTACAGTGGAACAGATTAAAGCT
65 CTGGCGTTGCACTGGAATAGATTAAAGCT
31603234 AAAGGTAGAG
Statistics
Matches: 236, Mismatches: 28, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
173 3 0.01
174 231 0.98
175 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (174 bp):
GAATCTTGTTTCTCTGGCGTTGCAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCATATTTCCC
TGGCGTTGCACTGGAATAGATTAAAGCTGAAGTGGAGATAATTAAAGCTGAAGGCAGCGAATCCT
ATCTCCTTAGCCTTACAGTGGAACAGATTAAAGCTAAAGGTAGA
Done.