Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007298.1 Hibiscus syriacus cultivar Beakdansim tig00019423_pilon, whole genome shotgun sequence
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: 730416
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 3
Found at i:182373 original size:2 final size:2
Alignment explanation
Indices: 182366--182403 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
182356 AAGTATTTTA
*
182366 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
182404 TCTAAACTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:182505 original size:21 final size:20
Alignment explanation
Indices: 182476--182514 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
182466 AATATAAATA
* *
182476 TAAATTGAATTAAGAATATTT
1 TAAACTGAAATAA-AATATTT
182497 TAAACTGAAATAAAATAT
1 TAAACTGAAATAAAATAT
182515 ATTATAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (20 bp):
TAAACTGAAATAAAATATTT
Found at i:188067 original size:86 final size:86
Alignment explanation
Indices: 187966--188133 Score: 248
Period size: 86 Copynumber: 2.0 Consensus size: 86
187956 TACCTAAACA
* * **
187966 TCCATTCCCAAAGAAATAACACTCTAAAAATAAATGACTTCCACTCTCATCAACACCTT-GACAT
1 TCCATTCCCAAAGAAAGAACACTCAAAAAATAAATGACTGACACTCTCATCAACA-CTTCGACAT
*
188030 AGTATGCAAGTCTACACCGATC
65 AGTATGCAAATCTACACCGATC
* * *
188052 TCCATTCCCAGAGAAAGAACACTCAAAAAATAAATGACTGATACTCTCATCAACACTTCTACATA
1 TCCATTCCCAAAGAAAGAACACTCAAAAAATAAATGACTGACACTCTCATCAACACTTCGACATA
188117 GTATGCAAATCTACACC
66 GTATGCAAATCTACACC
188134 CAGTCCCATT
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
85 3 0.04
86 70 0.96
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (86 bp):
TCCATTCCCAAAGAAAGAACACTCAAAAAATAAATGACTGACACTCTCATCAACACTTCGACATA
GTATGCAAATCTACACCGATC
Found at i:189999 original size:63 final size:63
Alignment explanation
Indices: 189900--190027 Score: 220
Period size: 63 Copynumber: 2.0 Consensus size: 63
189890 TACCAAGTCT
* *
189900 CAAATTCCCATTATCATGTCCATTGTTTACATTCCTTTGCTATGAAACGGATGCAAATGGAAG
1 CAAATTCCCATTATCATGTCCACTGTCTACATTCCTTTGCTATGAAACGGATGCAAATGGAAG
* *
189963 CAAATTCCCATTATCATGTCCACTGTCTACATTCCTTTGCTATGACACGGATGCAGATGGAAG
1 CAAATTCCCATTATCATGTCCACTGTCTACATTCCTTTGCTATGAAACGGATGCAAATGGAAG
190026 CA
1 CA
190028 CATACTTTGC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (63 bp):
CAAATTCCCATTATCATGTCCACTGTCTACATTCCTTTGCTATGAAACGGATGCAAATGGAAG
Found at i:190810 original size:35 final size:35
Alignment explanation
Indices: 190771--190850 Score: 115
Period size: 35 Copynumber: 2.3 Consensus size: 35
190761 TTACATTATT
* *
190771 GTGTTTGGTTTGTTTTAAATGAATATATGATTACA
1 GTGTTTGGTTTGTTTGAAAGGAATATATGATTACA
* * *
190806 GTGTTTGATTTGTTTGATAGGAATGTATGATTACA
1 GTGTTTGGTTTGTTTGAAAGGAATATATGATTACA
190841 GTGTTTGGTT
1 GTGTTTGGTT
190851 AAAGGAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.24, C:0.03, G:0.25, T:0.49
Consensus pattern (35 bp):
GTGTTTGGTTTGTTTGAAAGGAATATATGATTACA
Found at i:195557 original size:42 final size:41
Alignment explanation
Indices: 195484--195578 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 41
195474 AGCCAAACAA
* * * * *
195484 GATGGCTCACCTTCGCGGTTTAAGTTGGTCTTGATTATTTG
1 GATGACTCCCCTTCGAGGTTTAAATCGGTCTTGATTATTTG
* *
195525 GGTGACTCCCCTTCGAGGTTCTAAATCGGTCTTGATTCTTTG
1 GATGACTCCCCTTCGAGGTT-TAAATCGGTCTTGATTATTTG
195567 GATGACTCCCCT
1 GATGACTCCCCT
195579 CACAGGTCTA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 16 0.36
42 29 0.64
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (41 bp):
GATGACTCCCCTTCGAGGTTTAAATCGGTCTTGATTATTTG
Found at i:195859 original size:70 final size:71
Alignment explanation
Indices: 195769--196070 Score: 300
Period size: 73 Copynumber: 4.3 Consensus size: 71
195759 GGACAAAATT
** *
195769 TTTTCAAGAGAAAATATCTCAAGTTAGATGAAATTTTGGTTTCGAG-GAAAACTGTCTCGAGTGA
1 TTTTCAAGAG-AAATATCTCAAGGGAGATGAAATTTT-GTTTCAAGAG-AAACTGTCTCGAGTGA
*
195833 GACGAAAAT
63 GACGAAAAA
* *
195842 TTTTCAAG-G-AATATCTCAAGTGAGATTG-AATTTTCG-TTCTAAGAGGAA-TGTCTCGAGTGA
1 TTTTCAAGAGAAATATCTCAAGGGAGA-TGAAATTTT-GTTTC-AAGAGAAACTGTCTCGAGTGA
*
195902 GA-TAAAAA
63 GACGAAAAA
* * * * *
195910 ATTTCAAGAAAAATATCTCAAGGGAGATGAAA--TT-TTTCAAGAGAAACTGTCACGTGTAAGAC
1 TTTTCAAGAGAAATATCTCAAGGGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGAC
* *
195972 GGAAAG
66 GAAAAA
*
195978 TTTTCAAGAGAAAATATCTCAAGGGAGATGAAATTTTAGTTTCAAGAGAAATTGTCTCGAGTGAG
1 TTTTCAAGAG-AAATATCTCAAGGGAGATGAAATTTT-GTTTCAAGAGAAACTGTCTCGAGTGAG
*
196043 ACAAAAAA
64 ACGAAAAA
*
196051 ATTTCAAGAGAAACTATCTC
1 TTTTCAAGAGAAA-TATCTC
196071 TAGTGAAACG
Statistics
Matches: 188, Mismatches: 26, Indels: 30
0.77 0.11 0.12
Matches are distributed among these distances:
66 7 0.04
67 14 0.07
68 24 0.13
69 41 0.22
70 43 0.23
71 5 0.03
72 4 0.02
73 50 0.27
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.28
Consensus pattern (71 bp):
TTTTCAAGAGAAATATCTCAAGGGAGATGAAATTTTGTTTCAAGAGAAACTGTCTCGAGTGAGAC
GAAAAA
Found at i:196184 original size:37 final size:38
Alignment explanation
Indices: 196142--196225 Score: 100
Period size: 37 Copynumber: 2.2 Consensus size: 38
196132 GACTATTTCA
** *
196142 AGTGAGACGAAATTTGTT-TTTGAGGA-AAGCTATCTCG
1 AGTGAGAAAAAATTT-TTGTTTGAAGAGAAGCTATCTCG
*
196179 AGTGAGAAAAAATTTTTGTTTGAAGAGAAGCTGTCTCG
1 AGTGAGAAAAAATTTTTGTTTGAAGAGAAGCTATCTCG
*
196217 AATGAGAAA
1 AGTGAGAAA
196226 TTTTTTTGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
36 2 0.05
37 20 0.50
38 18 0.45
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (38 bp):
AGTGAGAAAAAATTTTTGTTTGAAGAGAAGCTATCTCG
Found at i:196233 original size:37 final size:37
Alignment explanation
Indices: 196151--196225 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
196141 AAGTGAGACG
* *
196151 AAATTTGTT-TTTGAGGAAAGCTATCTCGAGTGAGAAA
1 AAATTT-TTGTTTGAAGAAAGCTATCTCGAATGAGAAA
*
196188 AAATTTTTGTTTGAAGAGAAGCTGTCTCGAATGAGAAA
1 AAATTTTTGTTTGAAGA-AAGCTATCTCGAATGAGAAA
196226 TTTTTTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 2 0.06
37 13 0.39
38 18 0.55
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (37 bp):
AAATTTTTGTTTGAAGAAAGCTATCTCGAATGAGAAA
Found at i:199753 original size:3 final size:3
Alignment explanation
Indices: 199739--199850 Score: 57
Period size: 3 Copynumber: 35.3 Consensus size: 3
199729 GTTATAAGAT
* * * * *
199739 TAA TACA TAA TAA TAC TAG TAAA TAT TAA CAA TAC TAA TAA TAA CTAA
1 TAA TA-A TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA -TAA
** * *
199787 TAA TAA TAA TGAA CTGT TAA TAA TAA TAA -AA CTAA TAA TAGG TAA TAT
1 TAA TAA TAA T-AA -TAA TAA TAA TAA TAA TAA -TAA TAA TA-A TAA TAA
199835 TAA TAAA TAA T-A TAA T
1 TAA T-AA TAA TAA TAA T
199851 GACATATAGT
Statistics
Matches: 82, Mismatches: 17, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
2 4 0.05
3 60 0.73
4 17 0.21
5 1 0.01
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:199754 original size:10 final size:9
Alignment explanation
Indices: 199739--199850 Score: 57
Period size: 10 Copynumber: 11.8 Consensus size: 9
199729 GTTATAAGAT
199739 TAATACATAA
1 TAATA-ATAA
* *
199749 TAATACTAG
1 TAATAATAA
*
199758 TAAATATTAA
1 T-AATAATAA
* *
199768 CAATACTAA
1 TAATAATAA
199777 TAATAACTAA
1 TAATAA-TAA
199787 TAATAATAA
1 TAATAATAA
**
199796 TGAACTGTTAA
1 T-AA-TAATAA
199807 TAATAATAA
1 TAATAATAA
199816 -AACTAATAA
1 TAA-TAATAA
* *
199825 TAGGTAATAT
1 TA-ATAATAA
199835 TAATAAATAA
1 TAAT-AATAA
199845 T-ATAAT
1 TAATAAT
199851 GACATATAGT
Statistics
Matches: 78, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
8 5 0.06
9 31 0.40
10 37 0.47
11 5 0.06
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.33
Consensus pattern (9 bp):
TAATAATAA
Found at i:199807 original size:17 final size:16
Alignment explanation
Indices: 199739--199826 Score: 69
Period size: 15 Copynumber: 5.5 Consensus size: 16
199729 GTTATAAGAT
199739 TAATACATAATAAT-AC
1 TAATA-ATAATAATAAC
* *
199755 TAGT-A-AATATTAAC
1 TAATAATAATAATAAC
*
199769 -AATACTAATAATAAC
1 TAATAATAATAATAAC
199784 TAATAATAATAATGAAC
1 TAATAATAATAAT-AAC
199801 TGTTAATAATAATAA-AAC
1 ---TAATAATAATAATAAC
199819 TAATAATA
1 TAATAATA
199827 GGTAATATTA
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
13 7 0.12
14 3 0.05
15 16 0.28
16 14 0.24
17 3 0.05
18 3 0.05
20 12 0.21
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (16 bp):
TAATAATAATAATAAC
Found at i:200703 original size:30 final size:31
Alignment explanation
Indices: 200669--200734 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
200659 GCCGTAGATT
200669 CCAAAATAAT-TT-TTTGTGTGCCCTATTAAG
1 CCAAAATAATCTTATTTG-GTGCCCTATTAAG
* **
200699 CC-AAATAATCTTATTTGGTGCGCTATTGGG
1 CCAAAATAATCTTATTTGGTGCCCTATTAAG
200729 CCAAAA
1 CCAAAA
200735 ACACCTGGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 7 0.23
30 16 0.53
31 7 0.23
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (31 bp):
CCAAAATAATCTTATTTGGTGCCCTATTAAG
Found at i:202845 original size:40 final size:40
Alignment explanation
Indices: 202767--202845 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
202757 ATGAAAAATG
* * *
202767 CAAGCAACCCAACATTTAATACTTGGAAACTTGAAATTTT
1 CAAGCAACCCAACATTAAATACCTGGAAACTTAAAATTTT
202807 CAAGCAACCCAAC-TTGAAATACCTGGAAA-TTAATAATTT
1 CAAGCAACCCAACATT-AAATACCTGGAAACTTAA-AATTT
202846 GTGTTGGAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 5 0.15
40 29 0.85
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (40 bp):
CAAGCAACCCAACATTAAATACCTGGAAACTTAAAATTTT
Found at i:217060 original size:26 final size:25
Alignment explanation
Indices: 217038--217091 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
217028 TATTTTTTAT
*
217038 AATAATAAATTTTTTATAATTTTAAA
1 AATAATAAATTTTATAT-ATTTTAAA
*
217064 AATTATAAATTTTATATATTTTGAAA
1 AATAATAAATTTTATATATTTT-AAA
217090 AA
1 AA
217092 ATTATTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
AATAATAAATTTTATATATTTTAAA
Found at i:224270 original size:31 final size:31
Alignment explanation
Indices: 224232--224305 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
224222 ATTTGTACAC
* * *
224232 TTTTGGTCATTTATGTTATCGTTTTATTATG
1 TTTTGGTCACTTACGTTATCGTTTTATTAAG
224263 TTTTGGTCACTTACGTTATCGTTTTATTAAG
1 TTTTGGTCACTTACGTTATCGTTTTATTAAG
224294 TTTTGGTCACTT
1 TTTTGGTCACTT
224306 GGACGTTGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.57
Consensus pattern (31 bp):
TTTTGGTCACTTACGTTATCGTTTTATTAAG
Found at i:225067 original size:31 final size:31
Alignment explanation
Indices: 225029--225097 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
225019 TTTTCGAGTG
* *
225029 ACCAAAACTTAACAAAACGATAACGTAAGTA
1 ACCAAAACTTAACAAAACGATAAAGTAAATA
* *
225060 ACCAAAACTTAATAAAACGATAAAGTAAATG
1 ACCAAAACTTAACAAAACGATAAAGTAAATA
225091 ACCAAAA
1 ACCAAAA
225098 GTGTACAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.58, C:0.17, G:0.09, T:0.16
Consensus pattern (31 bp):
ACCAAAACTTAACAAAACGATAAAGTAAATA
Found at i:232353 original size:15 final size:16
Alignment explanation
Indices: 232335--232368 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
232325 TATGAACATC
*
232335 AAATAAATTAACAA-A
1 AAATAAAATAACAATA
232350 AAATAAAATAACAATA
1 AAATAAAATAACAATA
232366 AAA
1 AAA
232369 ATAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (16 bp):
AAATAAAATAACAATA
Found at i:232947 original size:28 final size:28
Alignment explanation
Indices: 232831--232947 Score: 76
Period size: 29 Copynumber: 4.1 Consensus size: 28
232821 CTAAAACGGT
* * *
232831 AAAAACAGAATCTTCAAGGGCTAAACAGC
1 AAAAACAGAATC-TAAAGGACTAAACACC
* ** * *
232860 AAAAACAGGAATTTAAAATACCAAA-ATC
1 AAAAACA-GAATCTAAAGGACTAAACACC
* * *
232888 AATAACAGAAAAT-TAAAGGACCAAAACGCC
1 AAAAACAG--AATCTAAAGGA-CTAAACACC
232918 AAAAACAGAATCTAAAGGACTAAACACC
1 AAAAACAGAATCTAAAGGACTAAACACC
232946 AA
1 AA
232948 TTACAAAACA
Statistics
Matches: 66, Mismatches: 16, Indels: 13
0.69 0.17 0.14
Matches are distributed among these distances:
27 1 0.02
28 25 0.38
29 28 0.42
30 12 0.18
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.13
Consensus pattern (28 bp):
AAAAACAGAATCTAAAGGACTAAACACC
Found at i:234342 original size:25 final size:25
Alignment explanation
Indices: 234311--234430 Score: 213
Period size: 25 Copynumber: 4.8 Consensus size: 25
234301 CAGTTGGGGA
234311 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
234336 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
234361 TTAGGGTTTGAAACCCTAATCTGATT
1 TTAGGGTTTGAAACCCTAAACTGA-T
*
234387 TTAGGGTTTGAAGCCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
234412 TTAGGGTTTGAAACCCTAA
1 TTAGGGTTTGAAACCCTAA
234431 TCTGGTGGGT
Statistics
Matches: 90, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
25 67 0.74
26 23 0.26
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:234411 original size:51 final size:50
Alignment explanation
Indices: 234311--234434 Score: 221
Period size: 51 Copynumber: 2.5 Consensus size: 50
234301 CAGTTGGGGA
*
234311 TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAATCTGATTTAGGGTTTGAAACCCTAAACTGAT
*
234361 TTAGGGTTTGAAACCCTAATCTGATTTTAGGGTTTGAAGCCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAATCTGA-TTTAGGGTTTGAAACCCTAAACTGAT
234412 TTAGGGTTTGAAACCCTAATCTG
1 TTAGGGTTTGAAACCCTAATCTG
234435 GTGGGTTGTT
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
50 23 0.32
51 48 0.68
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (50 bp):
TTAGGGTTTGAAACCCTAATCTGATTTAGGGTTTGAAACCCTAAACTGAT
Found at i:234530 original size:3 final size:3
Alignment explanation
Indices: 234516--234574 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
234506 TAATATGTAA
*
234516 AAT AATT AAT AAT AAT AATT AAT AAT -AT AAT GAT AAT AAT AAT AAT
1 AAT AA-T AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
234562 AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AA
234575 CGGAAAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
2 4 0.08
3 40 0.80
4 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:234932 original size:90 final size:89
Alignment explanation
Indices: 234817--234986 Score: 288
Period size: 90 Copynumber: 1.9 Consensus size: 89
234807 TTTTAGGAAG
* *
234817 GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAAT-GTTGACACGGCTCTTAC
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTAT-CT-ATGGTTGACACGGCTCATAC
234881 ATGATGAAGAGATCTGGCCATCTAAA
64 ATGATGAAGAGATCTGGCCATCTAAA
*
234907 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGT
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACAT
234972 GATGAAGAGATCTGG
66 GATGAAGAGATCTGG
234987 TCTGGGGATG
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
88 2 0.03
89 34 0.45
90 40 0.53
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (89 bp):
GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACAT
GATGAAGAGATCTGGCCATCTAAA
Found at i:234950 original size:46 final size:46
Alignment explanation
Indices: 234817--234950 Score: 132
Period size: 46 Copynumber: 3.0 Consensus size: 46
234807 TTTTAGGAAG
*
234817 GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCT-AA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTAT-CTAAA
* * * * * * * **
234863 --TGTTGACACGGCTCTTACATGATGAAGA-GATCTGGCCATCTAAA
1 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAAA
234907 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
234951 TGGTTGACAC
Statistics
Matches: 64, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
43 3 0.05
44 29 0.45
46 31 0.48
47 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (46 bp):
GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAA
Found at i:234971 original size:43 final size:44
Alignment explanation
Indices: 234834--234976 Score: 139
Period size: 46 Copynumber: 3.2 Consensus size: 44
234824 ACTCGGTTCC
*
234834 TACGTGATGAGGACGGCTGGTTATCCTAAT-GTTGACACGGCTCT
1 TACGTGATGAGGACGGCTGGTTAT-CTAATGGTTGACACGGCTCA
* * * ** * * * *
234878 TACATGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAGGACG-GCTGGTTATCTAATGGT--TGACACGGCTCA
234924 TACGTGATGAGGACGGCTGGTTATCT-ATGGTTGACACGGCTCA
1 TACGTGATGAGGACGGCTGGTTATCTAATGGTTGACACGGCTCA
234967 TACGTGATGA
1 TACGTGATGA
234977 AGAGATCTGG
Statistics
Matches: 76, Mismatches: 18, Indels: 11
0.72 0.17 0.10
Matches are distributed among these distances:
43 24 0.32
44 19 0.25
45 4 0.05
46 28 0.37
47 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (44 bp):
TACGTGATGAGGACGGCTGGTTATCTAATGGTTGACACGGCTCA
Found at i:234987 original size:43 final size:44
Alignment explanation
Indices: 234850--234987 Score: 129
Period size: 43 Copynumber: 3.1 Consensus size: 44
234840 ATGAGGACGG
* *
234850 CTGGTTATCCTAAT-GTTGACACGGCTCTTACATGATGAAGAGAT
1 CTGGTTAT-CTAATGGTTGACACGGCTCATACGTGATGAAGAGAT
** * * * * * *
234894 CTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-G
1 CTGGTTATCTAATGGT--TGACACGGCTCATACGTGATGAAGA-GAT
234940 CTGGTTATCT-ATGGTTGACACGGCTCATACGTGATGAAGAGAT
1 CTGGTTATCTAATGGTTGACACGGCTCATACGTGATGAAGAGAT
234983 CTGGT
1 CTGGT
234988 CTGGGGATGA
Statistics
Matches: 72, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
42 1 0.01
43 30 0.42
44 8 0.11
45 4 0.06
46 28 0.39
47 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (44 bp):
CTGGTTATCTAATGGTTGACACGGCTCATACGTGATGAAGAGAT
Found at i:236073 original size:15 final size:15
Alignment explanation
Indices: 236053--236104 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
236043 TTGAACCCTC
236053 CTTTTTTATTTTCTT
1 CTTTTTTATTTTCTT
*
236068 CTTTTTCATTTTC-T
1 CTTTTTTATTTTCTT
*
236082 CATTTTTT-TTTTTTT
1 C-TTTTTTATTTTCTT
*
236097 TTTTTTTA
1 CTTTTTTA
236105 GGTGTAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (15 bp):
CTTTTTTATTTTCTT
Found at i:248343 original size:28 final size:28
Alignment explanation
Indices: 248228--248343 Score: 67
Period size: 29 Copynumber: 4.1 Consensus size: 28
248218 CTAAAACGGT
* * *
248228 AAAAACAGAATCTTCAAGGGCTAAACAGC
1 AAAAACAGAATC-TAAAGGACTAAACACC
* ** * *
248257 AAAAACAGGAATTTAAAATAC-CAA-ATC
1 AAAAACA-GAATCTAAAGGACTAAACACC
* * *
248284 AATAACAGAAAAT-TAAAGGACCAAAACGCC
1 AAAAACAG--AATCTAAAGGA-CTAAACACC
248314 AAAAACAGAATCTAAAGGACTAAACACC
1 AAAAACAGAATCTAAAGGACTAAACACC
248342 AA
1 AA
248344 TTACAAACAA
Statistics
Matches: 64, Mismatches: 16, Indels: 15
0.67 0.17 0.16
Matches are distributed among these distances:
26 1 0.02
27 13 0.20
28 18 0.28
29 20 0.31
30 12 0.19
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.13
Consensus pattern (28 bp):
AAAAACAGAATCTAAAGGACTAAACACC
Found at i:249740 original size:25 final size:25
Alignment explanation
Indices: 249709--249828 Score: 222
Period size: 25 Copynumber: 4.8 Consensus size: 25
249699 CAGTTGGGGA
249709 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
249734 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
249759 TTAGGGTTTGAAACCCTAATCTGATT
1 TTAGGGTTTGAAACCCTAAACTGA-T
249785 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
249810 TTAGGGTTTGAAACCCTAA
1 TTAGGGTTTGAAACCCTAA
249829 TCTGGTGGGT
Statistics
Matches: 92, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
25 68 0.74
26 24 0.26
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:249809 original size:51 final size:50
Alignment explanation
Indices: 249709--249832 Score: 230
Period size: 51 Copynumber: 2.5 Consensus size: 50
249699 CAGTTGGGGA
*
249709 TTAGGGTTTGAAACCCTAAACTGATTTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAATCTGATTTAGGGTTTGAAACCCTAAACTGAT
249759 TTAGGGTTTGAAACCCTAATCTGATTTTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAATCTGA-TTTAGGGTTTGAAACCCTAAACTGAT
249810 TTAGGGTTTGAAACCCTAATCTG
1 TTAGGGTTTGAAACCCTAATCTG
249833 GTGGGTTGTT
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
50 23 0.32
51 49 0.68
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (50 bp):
TTAGGGTTTGAAACCCTAATCTGATTTAGGGTTTGAAACCCTAAACTGAT
Found at i:249927 original size:3 final size:3
Alignment explanation
Indices: 249913--249971 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
249903 TAATATGTAA
*
249913 AAT AATT AAT AAT AAT AATT AAT AAT -AT AAT GAT AAT AAT AAT AAT
1 AAT AA-T AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
249959 AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AA
249972 CGGAAAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
2 4 0.08
3 40 0.80
4 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:252386 original size:29 final size:29
Alignment explanation
Indices: 252306--252392 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 29
252296 TCTGAGTATC
* *
252306 GATATAAAATATTTTGAAGTTTAGGGACT
1 GATATAAAATATTTTGAAGTTTAAGGAAT
* * *
252335 AATCTATAATAGAGATTAT--AGTTTAAGGAAT
1 GA--TATAA-A-ATATTTTGAAGTTTAAGGAAT
252366 GATATAAAATATTTTGAAGTTTAAGGA
1 GATATAAAATATTTTGAAGTTTAAGGA
252393 TCAATTTGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
27 5 0.11
28 1 0.02
29 16 0.36
31 16 0.36
32 1 0.02
33 5 0.11
ACGTcount: A:0.43, C:0.02, G:0.18, T:0.37
Consensus pattern (29 bp):
GATATAAAATATTTTGAAGTTTAAGGAAT
Found at i:252406 original size:60 final size:60
Alignment explanation
Indices: 252306--252418 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
252296 TCTGAGTATC
* *
252306 GATATAAAATATTTTGAAGTTTAGGGACTAATCTATAATAGAGATTATAGTTTAAGGAAT
1 GATATAAAATATTTTGAAGTTTAAGGACTAATCTATAATAGAGATCATAGTTTAAGGAAT
* *
252366 GATATAAAATATTTTGAAGTTTAAGGA-TCAATTTGA-AATAGGGATCATAGTTT
1 GATATAAAATATTTTGAAGTTTAAGGACT-AATCT-ATAATAGAGATCATAGTTT
252419 GGGGATATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
59 1 0.02
60 45 0.96
61 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.37
Consensus pattern (60 bp):
GATATAAAATATTTTGAAGTTTAAGGACTAATCTATAATAGAGATCATAGTTTAAGGAAT
Found at i:256228 original size:16 final size:16
Alignment explanation
Indices: 256207--256239 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
256197 TACTATTTAC
*
256207 GTGAATAGTGAATTTT
1 GTGAATAGTGAAATTT
256223 GTGAATAGTGAAATTT
1 GTGAATAGTGAAATTT
256239 G
1 G
256240 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.39
Consensus pattern (16 bp):
GTGAATAGTGAAATTT
Found at i:264476 original size:16 final size:16
Alignment explanation
Indices: 264457--264496 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
264447 GAGCCGAGTC
*
264457 GAGCTCGAGTATTGTT
1 GAGCTCGAGTATTGCT
*
264473 GAGCTTGAGTATTGCT
1 GAGCTCGAGTATTGCT
264489 GAGCTCGA
1 GAGCTCGA
264497 CTCGACTCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.33, T:0.33
Consensus pattern (16 bp):
GAGCTCGAGTATTGCT
Found at i:266240 original size:2 final size:2
Alignment explanation
Indices: 266235--266262 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
266225 TTTTTTAATT
266235 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
266263 ATTTTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:268236 original size:24 final size:23
Alignment explanation
Indices: 268203--268253 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
268193 GTTGAGAGGA
* *
268203 AAATTTAATTATTATTGTTATTT
1 AAATTTAATTATAATTATTATTT
268226 AAATTATAATTATAATTATTATTT
1 AAATT-TAATTATAATTATTATTT
268250 AAAT
1 AAAT
268254 AATTATTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
AAATTTAATTATAATTATTATTT
Found at i:268270 original size:24 final size:24
Alignment explanation
Indices: 268220--268270 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
268210 ATTATTATTG
* *
268220 TTATTTAAATTATAATTATAATTA
1 TTATTTAAATAATAATTATAATCA
* * *
268244 TTATTTAAATAATTATTGTTATCA
1 TTATTTAAATAATAATTATAATCA
268268 TTA
1 TTA
268271 GTAATTTTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TTATTTAAATAATAATTATAATCA
Found at i:275206 original size:11 final size:11
Alignment explanation
Indices: 275190--275215 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
275180 AAATTCACGT
275190 GAATTTAGAAC
1 GAATTTAGAAC
275201 GAATTTAGAAC
1 GAATTTAGAAC
275212 GAAT
1 GAAT
275216 ACGGTGCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (11 bp):
GAATTTAGAAC
Found at i:275969 original size:59 final size:60
Alignment explanation
Indices: 275836--275972 Score: 170
Period size: 59 Copynumber: 2.3 Consensus size: 60
275826 AACATAATGA
* * * **
275836 ATAGTTGGGTGACCATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAGCAATATTTT
1 ATAGTCGGGTGACCATTTTATAACTTTTAATAGTCAAAAGACTCAACAAAGCAATACCTT
* * * *
275896 ATAGTCAGAG-GACCATTTTATAAC-TTTAATAGTCAAAAGACTTAATAAAGTAATACCTT
1 ATAGTC-GGGTGACCATTTTATAACTTTTAATAGTCAAAAGACTCAACAAAGCAATACCTT
275955 ATAGTCGGGTGACCATTT
1 ATAGTCGGGTGACCATTT
275973 GTGTACATTA
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
58 2 0.03
59 42 0.65
60 19 0.29
61 2 0.03
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (60 bp):
ATAGTCGGGTGACCATTTTATAACTTTTAATAGTCAAAAGACTCAACAAAGCAATACCTT
Found at i:283061 original size:60 final size:61
Alignment explanation
Indices: 282932--283065 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 61
282922 AAAATTGGGG
* * * * *
282932 ACCAATATAGAATGAGGGTCATAGTTTGGGGGATGACATTATAATGTTCAAAAGTTTAGGA
1 ACCAATTTAGAATGAGAGTCATAGTTTGGAGAATGACATTAGAATGTTCAAAAGTTTAGGA
** *
282993 ACTGATTTAGAATGAGAGTCATAGTTT-GAGAATGTA-ATTGGAATGTTCAAAAGTTTA-GA
1 ACCAATTTAGAATGAGAGTCATAGTTTGGAGAATG-ACATTAGAATGTTCAAAAGTTTAGGA
283052 ATCCAATTTAGAAT
1 A-CCAATTTAGAAT
283066 AAAGGTCATA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
59 3 0.05
60 34 0.56
61 24 0.39
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.32
Consensus pattern (61 bp):
ACCAATTTAGAATGAGAGTCATAGTTTGGAGAATGACATTAGAATGTTCAAAAGTTTAGGA
Found at i:286959 original size:38 final size:38
Alignment explanation
Indices: 286897--286973 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
286887 AGTGACGGTG
* *
286897 AGGGTGTCTCTGAAAAATCTCGAGTTCATAATCTATTC
1 AGGGTGTCTCAGAAAAATCCCGAGTTCATAATCTATTC
* **
286935 AGGGTGTCTCAGAAGAATCCCGAGTTCATTGTCTATTC
1 AGGGTGTCTCAGAAAAATCCCGAGTTCATAATCTATTC
286973 A
1 A
286974 TTGATTTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (38 bp):
AGGGTGTCTCAGAAAAATCCCGAGTTCATAATCTATTC
Found at i:296577 original size:15 final size:15
Alignment explanation
Indices: 296559--296624 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
296549 CTCCATAATT
*
296559 ACCACCACCATATCC
1 ACCACCACCATAGCC
*
296574 ACCACCA-TATCCA-CC
1 ACCACCACCAT--AGCC
296589 ACCACCACCATAGCC
1 ACCACCACCATAGCC
*
296604 ACCACCGCCATAGCC
1 ACCACCACCATAGCC
296619 ACCACC
1 ACCACC
296625 TCCAAAGTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
14 3 0.07
15 38 0.86
16 3 0.07
ACGTcount: A:0.32, C:0.55, G:0.05, T:0.09
Consensus pattern (15 bp):
ACCACCACCATAGCC
Found at i:296609 original size:12 final size:12
Alignment explanation
Indices: 296560--296592 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
296550 TCCATAATTA
296560 CCACCACCATAT
1 CCACCACCATAT
296572 CCACCACCATAT
1 CCACCACCATAT
296584 CCACCACCA
1 CCACCACCA
296593 CCACCATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.55, G:0.00, T:0.12
Consensus pattern (12 bp):
CCACCACCATAT
Found at i:296624 original size:18 final size:18
Alignment explanation
Indices: 296572--296609 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
296562 ACCACCATAT
*
296572 CCACCACCATATCCACCA
1 CCACCACCATAGCCACCA
296590 CCACCACCATAGCCACCA
1 CCACCACCATAGCCACCA
296608 CC
1 CC
296610 GCCATAGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.58, G:0.03, T:0.08
Consensus pattern (18 bp):
CCACCACCATAGCCACCA
Found at i:300951 original size:18 final size:19
Alignment explanation
Indices: 300914--300952 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
300904 GTTTGTCATA
*
300914 ATTATATGTGATTATATGT
1 ATTATATGTAATTATATGT
*
300933 ATTATAT-TAATTGTATGT
1 ATTATATGTAATTATATGT
300951 AT
1 AT
300953 GCATGACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (19 bp):
ATTATATGTAATTATATGT
Found at i:301569 original size:30 final size:29
Alignment explanation
Indices: 301530--301588 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
301520 GAGAATTAAC
* *
301530 ATGAACTACGTGATTACATGTATATGTGA
1 ATGAACTACGAGATTACATGAATATGTGA
* *
301559 ATGAAGCTACGAGTTTATATGAATATGTGA
1 ATGAA-CTACGAGATTACATGAATATGTGA
301589 TATGTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGAACTACGAGATTACATGAATATGTGA
Found at i:301852 original size:23 final size:23
Alignment explanation
Indices: 301819--301885 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
301809 ATCTTATATG
301819 GCACTTTGGTGCATTTCTACGCA
1 GCACTTTGGTGCATTTCTACGCA
* * **
301842 GCACTTAGGTGCAATTCTACGTG
1 GCACTTTGGTGCATTTCTACGCA
*
301865 GCACTTTGGTGCATTTATACG
1 GCACTTTGGTGCATTTCTACG
301886 AGTTGTGGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.34
Consensus pattern (23 bp):
GCACTTTGGTGCATTTCTACGCA
Found at i:321655 original size:11 final size:11
Alignment explanation
Indices: 321639--321664 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
321629 ATACACACTC
321639 AAAATAAAAAT
1 AAAATAAAAAT
321650 AAAATAAAAAT
1 AAAATAAAAAT
321661 AAAA
1 AAAA
321665 AGGTTAGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:324784 original size:3 final size:3
Alignment explanation
Indices: 324776--324819 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
324766 TAAAATTAAA
* *
324776 AAT AAT AAT AAT AAT AAT AGTT AAT AAT AAT AA- AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AA
324820 ATATAAACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:324799 original size:25 final size:24
Alignment explanation
Indices: 324771--324818 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
324761 ATATGTAAAA
*
324771 TTAAAAATAATAATAATAATAATAG
1 TTAAAAATAATAA-AATAAAAATAG
*
324796 TTAATAATAATAAAATAAAAATA
1 TTAAAAATAATAAAATAAAAATA
324819 AATATAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (24 bp):
TTAAAAATAATAAAATAAAAATAG
Found at i:328704 original size:3 final size:3
Alignment explanation
Indices: 328696--328733 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
328686 TAAAATTAAA
*
328696 AAT AAT AAT AAT AAT AAT AGTT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AA
328734 AAAATAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:331172 original size:2 final size:2
Alignment explanation
Indices: 331165--331198 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
331155 CTATTAACCA
* *
331165 AT AT AT AT AT AT AT AT AT AT AT CT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
331199 TTCCTAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:335326 original size:432 final size:432
Alignment explanation
Indices: 334521--335380 Score: 1326
Period size: 432 Copynumber: 2.0 Consensus size: 432
334511 GCTTCTTGAA
* * * * * *
334521 AATTCTCATAACTGACAGGTTTAGGTGATTCCAGCTTGTTTTCTAACAAGTGTGTTTCAAATAAA
1 AATTCTCATAACCGAAAGGATTAGGCGATTCCAGCTTATTTTCTAACAAATGTGTTTCAAATAAA
* *
334586 GAGGCCGGGATGCCTCTTGATCTATCAGACTTAACCATGAGATACTCATTAGATTGATTATCTTG
66 GAGGCCGGGATGCCTCTAGATCTAGCAGACTTAACCATGAGATACTCATTAGATTGATTATCTTG
* *
334651 AAAATGAACACCTACATCACCAAAATCTTCTCTTTTCTCAGAACTCTGTCTGATCTCTTCACGAG
131 AAAATGAACACCTACATCACCAAAATCTTCTCTTTTCTCAGAACTCTGCCTGATCTCTTCACAAG
* *
334716 CATTATTAGTCCTAGAAGCATGAGGCAACTCCAGATGCTGCTGTTTGCTCCTTTGCCACCTCGAT
196 CATTATTAGTCCTAGAAGCATGAGGCAACTCCAGATACTGCTGTTTGCTCCTTTCCCACCTCGAT
* * *
334781 TCATAGCTCTTTCCGGAATAATGGTGCAGATAACGACAAGACACTCCACGGTAGCACTTGCCTCG
261 TCATAACTCTTGCCGGAATAATGGTGCAAATAACGACAAGACACTCCACGGTAGCACTTGCCTCG
* **
334846 ACTGAAGTCAAAACAGAATGGCATCTGTCCCTTCACCTGTCCCTTATTTTCACCACTGAATTCAT
326 ACGGAAGTCAAAACAGAATGGCATCTGTCCCTTCACCAATCCCTTATTTTCACCACTGAATTCAT
334911 CTGTACACTTAAAACT-AGGACATCTGCCCCTGCTTCTCAGAC
391 CTGTACACTTAAAA-TGAGGACATCTGCCCCTGCTTCTCAGAC
* *
334953 AATTCTCATAACCGAAAGGATTAGGCGTTTCCTGCTTATTTTCTAACAAATGTGTTTCAAATAAA
1 AATTCTCATAACCGAAAGGATTAGGCGATTCCAGCTTATTTTCTAACAAATGTGTTTCAAATAAA
* * * * *
335018 GAGGTCGGGGTGTCTCTAGATCTAGCAGACTTAACCATGTGATACTCATTCGATTGATTATCTTG
66 GAGGCCGGGATGCCTCTAGATCTAGCAGACTTAACCATGAGATACTCATTAGATTGATTATCTTG
** *
335083 AAAATGGGCACCTACATCACCAGAATCTTCTCTTTTCTCAGAACTCTGCCTGATCTCTTCACAAG
131 AAAATGAACACCTACATCACCAAAATCTTCTCTTTTCTCAGAACTCTGCCTGATCTCTTCACAAG
* * *
335148 CATTGTTAGTCCTAGAAGTATGAGGCAACTCCAGATACTGCTGTTTGCTCCTTTCCCACCTTGAT
196 CATTATTAGTCCTAGAAGCATGAGGCAACTCCAGATACTGCTGTTTGCTCCTTTCCCACCTCGAT
* * * *
335213 TCGTAACTCTTGCCTGAATCATGGTGCAAATAACGACAAGACATTCCACGGTAGCACTTGCCTCG
261 TCATAACTCTTGCCGGAATAATGGTGCAAATAACGACAAGACACTCCACGGTAGCACTTGCCTCG
* *
335278 ACGGAAGTGAAAACAGAATGGCATCTGTCCCTTCACCAATCTCTTATTTTCACCACTGAATTCAT
326 ACGGAAGTCAAAACAGAATGGCATCTGTCCCTTCACCAATCCCTTATTTTCACCACTGAATTCAT
** * * *
335343 CTGTATGCTTAAAATGGGGAGATCTGCTCCTGCTTCTC
391 CTGTACACTTAAAATGAGGACATCTGCCCCTGCTTCTC
335381 CGATTTCTGG
Statistics
Matches: 385, Mismatches: 42, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
431 1 0.00
432 384 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (432 bp):
AATTCTCATAACCGAAAGGATTAGGCGATTCCAGCTTATTTTCTAACAAATGTGTTTCAAATAAA
GAGGCCGGGATGCCTCTAGATCTAGCAGACTTAACCATGAGATACTCATTAGATTGATTATCTTG
AAAATGAACACCTACATCACCAAAATCTTCTCTTTTCTCAGAACTCTGCCTGATCTCTTCACAAG
CATTATTAGTCCTAGAAGCATGAGGCAACTCCAGATACTGCTGTTTGCTCCTTTCCCACCTCGAT
TCATAACTCTTGCCGGAATAATGGTGCAAATAACGACAAGACACTCCACGGTAGCACTTGCCTCG
ACGGAAGTCAAAACAGAATGGCATCTGTCCCTTCACCAATCCCTTATTTTCACCACTGAATTCAT
CTGTACACTTAAAATGAGGACATCTGCCCCTGCTTCTCAGAC
Found at i:335400 original size:30 final size:30
Alignment explanation
Indices: 335359--335726 Score: 414
Period size: 30 Copynumber: 12.3 Consensus size: 30
335349 GCTTAAAATG
* *
335359 GGGAGATCTGCTCCTGCTTCTCCGATTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* * **
335389 GGGAGACCTGCTCCTGCTCCTCAGACTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* * * **
335419 GGGAGACCTGCTCTTGCTCCTCAGACTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* * *
335449 GGGAGACCTGCTCCTGCTTCTCTGATTTCC
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* *
335479 GGGAGACCTGCTCCTGCTACTCCGGTTTCC
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* *
335509 GGGAAACCTGCTCCTGCTTCTTCGGTTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* * * *
335539 GGGAGACCTGCTCCTGCTACTCTGTTTTCC
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* * *
335569 GGGAGACCTGCTCCTGCTACTCTGGTTTCC
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* * *
335599 AGGAGACCTGCTCCTG-TTACTCTGGTTTCC
1 GGGAGACCTGCTCCTGCTT-CTCCGGTTTCT
* *
335629 GGGAGATCTGCTCCTGCTTCTTCGGTTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* *
335659 GGGAGACCAGCTCCTGCTTCTTCGGTTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* *
335689 GGGAGACCTGCTCCTGCTTCTCTGATTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
335719 GGGAGACC
1 GGGAGACC
335727 AACTAAAACA
Statistics
Matches: 299, Mismatches: 37, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
29 1 0.00
30 296 0.99
31 2 0.01
ACGTcount: A:0.11, C:0.32, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
Found at i:339889 original size:6 final size:6
Alignment explanation
Indices: 339878--339904 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
339868 TTTCTTTTCT
339878 CCCTAA CCCTAA CCCTAA CCCTAA CCC
1 CCCTAA CCCTAA CCCTAA CCCTAA CCC
339905 CTAATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.56, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCTAA
Found at i:341849 original size:13 final size:13
Alignment explanation
Indices: 341833--341868 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
341823 GCCCCGATTA
*
341833 CCCGATTACCCTC
1 CCCGATTACCCGC
341846 CCCGATTACCCGC
1 CCCGATTACCCGC
341859 CCCGA-TACCC
1 CCCGATTACCC
341869 AACCCGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.17, C:0.56, G:0.11, T:0.17
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:341950 original size:31 final size:31
Alignment explanation
Indices: 341910--341980 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
341900 ATATATATAT
341910 ATATAATATTAATAAATTTAATTTAAATAAAA
1 ATAT-ATATTAATAAATTTAATTTAAATAAAA
* * * *
341942 ATATATATTTATATATTTAATTTAAATATAT
1 ATATATATTAATAAATTTAATTTAAATAAAA
341973 ATATATAT
1 ATATATAT
341981 ATACCCGGCC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
ATATATATTAATAAATTTAATTTAAATAAAA
Found at i:343252 original size:15 final size:14
Alignment explanation
Indices: 343218--343252 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
343208 ATGTCACGTT
343218 TATATTTTTAAAAA
1 TATATTTTTAAAAA
343232 TGATATTTTTAAAAAA
1 T-ATATTTTT-AAAAA
343248 TATAT
1 TATAT
343253 AATAGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.05
15 12 0.63
16 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
TATATTTTTAAAAA
Found at i:343261 original size:21 final size:21
Alignment explanation
Indices: 343237--343276 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
343227 AAAAATGATA
343237 TTTTTAAAAAATATATAATAG
1 TTTTTAAAAAATATATAATAG
343258 TTTTTAAAAAATATATAAT
1 TTTTTAAAAAATATATAAT
343277 TTTCATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
TTTTTAAAAAATATATAATAG
Found at i:344068 original size:18 final size:19
Alignment explanation
Indices: 344024--344073 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
344014 AAATATTTTT
344024 ATTTTATTATAATTAATCA
1 ATTTTATTATAATTAATCA
* *
344043 ATAATTTATTAT-TTTATTCA
1 AT--TTTATTATAATTAATCA
344063 ATTTTATTATA
1 ATTTTATTATA
344074 CTAATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 8 0.31
19 2 0.08
20 8 0.31
21 8 0.31
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTATTATAATTAATCA
Found at i:345886 original size:20 final size:21
Alignment explanation
Indices: 345856--345895 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
345846 AGCCATTGGG
*
345856 GCCTGATGGTATTGATACTAT
1 GCCTGATGGTATCGATACTAT
345877 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
345896 CTATACAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:347469 original size:19 final size:20
Alignment explanation
Indices: 347441--347478 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
347431 CAAAATTTCA
347441 TTTTGACTTTCAAAATCAAT
1 TTTTGACTTTCAAAATCAAT
347461 TTTTG-CTTTCAAAATCAA
1 TTTTGACTTTCAAAATCAA
347479 ATCGTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTTGACTTTCAAAATCAAT
Found at i:347983 original size:15 final size:15
Alignment explanation
Indices: 347963--348022 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
347953 GCCTACCTTT
347963 TTCTTCTTTTCTTCA
1 TTCTTCTTTTCTTCA
* *
347978 TTCTTC-ATTCTTCT
1 TTCTTCTTTTCTTCA
347992 TGTCATTCTTTTCTTCA
1 T-TC-TTCTTTTCTTCA
*
348009 -TCATCTTTCTCTTC
1 TTCTTCTTT-TCTTC
348023 TTTCAATATC
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
14 12 0.33
15 15 0.42
16 3 0.08
17 6 0.17
ACGTcount: A:0.08, C:0.28, G:0.02, T:0.62
Consensus pattern (15 bp):
TTCTTCTTTTCTTCA
Found at i:349179 original size:31 final size:31
Alignment explanation
Indices: 349141--349202 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
349131 TAAAATTCTT
*
349141 CTCTTGTGTTTGATTTATTGGATATGTGTTC
1 CTCTTGTGTTTGATTTATTGGATAGGTGTTC
349172 CTCTTGTGTTTGATTTATTGGATAGGTGTTC
1 CTCTTGTGTTTGATTTATTGGATAGGTGTTC
349203 TAACCCTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.13, C:0.10, G:0.24, T:0.53
Consensus pattern (31 bp):
CTCTTGTGTTTGATTTATTGGATAGGTGTTC
Found at i:349360 original size:21 final size:21
Alignment explanation
Indices: 349336--349386 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
349326 AGTACAGAGG
*
349336 GTATTAGTACTCCTAAAGGGA
1 GTATCAGTACTCCTAAAGGGA
*
349357 GTATCAATACTCCTAAAGGGA
1 GTATCAGTACTCCTAAAGGGA
349378 GTATCAGTA
1 GTATCAGTA
349387 TTACGTTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (21 bp):
GTATCAGTACTCCTAAAGGGA
Found at i:354754 original size:14 final size:14
Alignment explanation
Indices: 354732--354763 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
354722 TTCGGTAATC
*
354732 CGTTTGTTTATGTT
1 CGTTCGTTTATGTT
354746 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
354760 CGTT
1 CGTT
354764 TATATTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.22, T:0.59
Consensus pattern (14 bp):
CGTTCGTTTATGTT
Found at i:355009 original size:14 final size:14
Alignment explanation
Indices: 354992--355023 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
354982 AATCCGTTTG
354992 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
*
355006 TTTATGTTCGTTCG
1 TTTATGTTCGTTCA
355020 TTTA
1 TTTA
355024 CTTTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.59
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:360307 original size:2 final size:2
Alignment explanation
Indices: 360300--360329 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
360290 TTAATGCATT
360300 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
360330 AACATATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:360461 original size:63 final size:64
Alignment explanation
Indices: 360365--360489 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 64
360355 GTTTATTATA
* * * **
360365 CATGCATGCATGGCACAAACCGATATGTGACTTGTA-CTAAGTGTAATCTGGTGATGTAATATG
1 CATGCATCCATAGCACAAACCGATATGCGACTTGTATCTAAGTGTAATCTGAAGATGTAATATG
* * *
360428 CATGCATCCATAGCGCAAACCGATATGCGACTTGTATTTATGTGTAATCTGAAGATGTAATA
1 CATGCATCCATAGCACAAACCGATATGCGACTTGTATCTAAGTGTAATCTGAAGATGTAATA
360490 AACATACATG
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
63 32 0.60
64 21 0.40
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (64 bp):
CATGCATCCATAGCACAAACCGATATGCGACTTGTATCTAAGTGTAATCTGAAGATGTAATATG
Found at i:362806 original size:23 final size:23
Alignment explanation
Indices: 362775--362818 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
362765 AGGGTTTTGT
362775 TGTTGTATTGTAATTAAATTATG
1 TGTTGTATTGTAATTAAATTATG
* * *
362798 TGTTTTATTTTATTTAAATTA
1 TGTTGTATTGTAATTAAATTA
362819 ATTCATAGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (23 bp):
TGTTGTATTGTAATTAAATTATG
Found at i:363091 original size:15 final size:15
Alignment explanation
Indices: 363071--363100 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
363061 TTTATATTTT
363071 AATCTAAAATCTTAA
1 AATCTAAAATCTTAA
*
363086 AATCTAAAATTTTAA
1 AATCTAAAATCTTAA
363101 CTCTAATTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (15 bp):
AATCTAAAATCTTAA
Found at i:364601 original size:17 final size:19
Alignment explanation
Indices: 364579--364618 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
364569 CAAGGAAAAT
*
364579 TTTAAA-ATTTTGTTTA-A
1 TTTAAATATTTTCTTTATA
364596 TTTAAATATTTTCTTTATA
1 TTTAAATATTTTCTTTATA
364615 TTTA
1 TTTA
364619 TTTTTGACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 9 0.45
19 5 0.25
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTAAATATTTTCTTTATA
Found at i:365527 original size:2 final size:2
Alignment explanation
Indices: 365520--365558 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
365510 AAGTGAAAAT
365520 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
365559 TGACATAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:367848 original size:13 final size:14
Alignment explanation
Indices: 367819--367852 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
367809 CTAAAACAAC
367819 GGAAGACCGAGGAGT
1 GGAAG-CCGAGGAGT
367834 GGAAGCCGA-GAGT
1 GGAAGCCGAGGAGT
367847 GGAAGC
1 GGAAGC
367853 ACCATTCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 4 0.21
15 5 0.26
ACGTcount: A:0.32, C:0.15, G:0.47, T:0.06
Consensus pattern (14 bp):
GGAAGCCGAGGAGT
Found at i:370287 original size:23 final size:24
Alignment explanation
Indices: 370256--370301 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
370246 TTATGTCGAT
370256 TGAAATTATAAAATTTT-AGAGAG
1 TGAAATTATAAAATTTTAAGAGAG
*
370279 TGAATTTATAAAATTTTAAGAGA
1 TGAAATTATAAAATTTTAAGAGA
370302 CGAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (24 bp):
TGAAATTATAAAATTTTAAGAGAG
Found at i:370311 original size:23 final size:23
Alignment explanation
Indices: 370257--370311 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
370247 TATGTCGATT
*
370257 GAAATTATAAAATTTTAGAGAGT
1 GAAATTATAAAATTTTAGAGAGC
*
370280 GAATTTATAAAATTTTA-AGAGAC
1 GAAATTATAAAATTTTAGAGAG-C
*
370303 GAAAATATA
1 GAAATTATA
370312 TTATTAATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.33
Consensus pattern (23 bp):
GAAATTATAAAATTTTAGAGAGC
Found at i:370893 original size:2 final size:2
Alignment explanation
Indices: 370886--370916 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
370876 TTCAATAATA
370886 AG 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 AG A
370917 ACTAACATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:372495 original size:72 final size:70
Alignment explanation
Indices: 372412--372549 Score: 204
Period size: 72 Copynumber: 1.9 Consensus size: 70
372402 TACTACAAAT
* ** *
372412 TTATTTATTTATTTTCAATACATTTTTCATATTACTTTGAAATACTCATTTCGTTAATAATATAT
1 TTATTTATTTATTTTCAATACA-TTTTCATATTACTTCGAAATA-AAATTTCGTTAATAATACAT
372477 TTTGAAG
64 TTTGAAG
* *
372484 TTATTTATTTATTTTTAATACATTTTCATTTTACTTCGAAATAAAATTTCGTTAATAATACATTT
1 TTATTTATTTATTTTCAATACATTTTCATATTACTTCGAAATAAAATTTCGTTAATAATACATTT
372549 T
66 T
372550 AAAATTTTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 20 0.33
71 19 0.32
72 21 0.35
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (70 bp):
TTATTTATTTATTTTCAATACATTTTCATATTACTTCGAAATAAAATTTCGTTAATAATACATTT
TGAAG
Found at i:373339 original size:22 final size:21
Alignment explanation
Indices: 373311--373357 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
373301 CCATAAATGT
*
373311 TAAAAAACATTAATGTTTTAGA
1 TAAAAAA-AATAATGTTTTAGA
*
373333 TAAAAAAAATAATGTTTTAGG
1 TAAAAAAAATAATGTTTTAGA
373354 TAAA
1 TAAA
373358 TTTTTTACCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.34
Consensus pattern (21 bp):
TAAAAAAAATAATGTTTTAGA
Found at i:373949 original size:36 final size:36
Alignment explanation
Indices: 373907--373980 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
373897 TTTATATACG
* *
373907 TAGTGTATTTTTGTTTTATAAGGAAAGTGGTTCGAA
1 TAGTGTATTTTTATTTTAGAAGGAAAGTGGTTCGAA
*
373943 TAGTGTATTTTTATTTTAGAAGGAATGTGGTTCGAA
1 TAGTGTATTTTTATTTTAGAAGGAAAGTGGTTCGAA
373979 TA
1 TA
373981 TAATTTTGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.28, C:0.03, G:0.24, T:0.45
Consensus pattern (36 bp):
TAGTGTATTTTTATTTTAGAAGGAAAGTGGTTCGAA
Found at i:374934 original size:22 final size:22
Alignment explanation
Indices: 374892--374935 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
374882 AATAATACGA
*
374892 AAAAATAGTTTAAAAATGAAAAG
1 AAAAATAG-TTAAAAAGGAAAAG
374915 AAAAATA-TTAAAATAGGAAAA
1 AAAAATAGTTAAAA-AGGAAAA
374936 CCAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.20
Consensus pattern (22 bp):
AAAAATAGTTAAAAAGGAAAAG
Found at i:376913 original size:164 final size:163
Alignment explanation
Indices: 376665--378093 Score: 1202
Period size: 164 Copynumber: 8.5 Consensus size: 163
376655 GCTATGTTGT
* * * * * * *
376665 AAATGATGTTCCTTGGAGCTGAGAGAAGTCGAACTCGAAGGTCTTTGGCAGATAGCTCTTCTAGC
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGA
* * * * * * * * * *
376730 CTTGAGCTATACCGCAAATGATGTGTCGTT-GAGCTGAGCGTAATCGAACTCAAATGTCTGTGTT
66 CTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTT
* *
376794 GGCAGATAACCCTTCT-AACCTTGAGTTATACTGC
130 GGCAGATAACCCTTCTCGA-CTTAAGTTATACTGC
* * * * * * * *
376828 AAATGATGTGCCCTCGAAGCTGAGTGTAGTCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAG
*
376893 ACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGT
65 ACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GT
* *
376958 TGGCAGATAACCCTTCTCGATTTAAGTTATGCTGC
129 TGGCAGATAACCCTTCTCGACTTAAGTTATACTGC
* * * *
376993 AAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTATTTGGTGACATATAACTCTTCT
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-G-G-CAGATAACCCTTCT
* * * * * * * * * *
377058 AGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGTTGAGCGTAGTCAAACTCGAAGG--TAT
63 AGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
* * *
377121 -TTGGCAGATAGCCCTTCTTGACTTAAGCTATGA-TGC
127 GTTGGCAGATAACCCTTCTCGACTTAAGTTAT-ACTGC
*
377157 AAATGATATGCCTTGGAGCTGAGCGTAGTCGACCTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC--T--TTGGCAGATAACCCTTC
* * *
377222 TCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTAAGCGTAGTCGAACTCGAAGGTCTTT
62 TAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
* * * * * * * ** *
377287 GGTGACAAATAACTCTTCTAGCCTTGAGTTATGTTGT
127 GTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGC
* * * * **
377324 AAATGATGTGCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCTA
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGA
* *
377389 CTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTGGTT
66 CTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTT
* **
377454 GGCAGATAACCCTTCTCGATTTAAGTTATGTTGC
130 GGCAGATAACCCTTCTCGACTTAAGTTATACTGC
*
377488 AAATGATATGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-G-G-CAGATAACCCTTCT
* * * * * * * * *
377553 AGCCTTGAGTTATGCTGTAAATGATGTGCCTTCGAAGCTGAGTGTAATTGAACTCGAGGGTC--T
63 AGACTTAAGTTATGCTGCAAATGATATGCCTT-GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
* * *
377616 -TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTAC
127 GTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGC
* *
377652 AAATGATGTGCCTTGGAGCTAAGCGTTTGGAGCTAAGCGTAGTCGAACTCAAAGGTCTTTGGTTG
1 AAATGATATGCCTT-G-G---AGC---T---G---AGCGTAGTCGAACTCGAAGGTC--T--TTG
* * * * * * * *
377717 GCAGATAACCCTTCTCGATTTAATTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
48 GCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCG
** * * * * * *
377782 AACTCGGTGGTCTTTTGGATGGTAGATAGCCCTTCTCGATTTAAGCTATACTAC
112 AACTCGAAGGTC-TTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGC
* * * *
377836 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTTTTTGGTTGGCAGATAACACTTC
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG--TCT--TTGGCAGATAACCCTTC
* * * *** * * ** *
377901 TCGACTTAAGTTATGTTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTATT
62 TAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT-CT
* * *
377966 TTGGATGGCAGATAGCCCTTCTCGACTTAAGCTATACTGC
125 TT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGC
** *
378006 AAATGATGCGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCT
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC--T-TTGGCAGATAACCCTTCT
* * * *
378071 AGCCCTGAGTTATGCTGTAAATG
63 AGACTTAAGTTATGCTGCAAATG
378094 TTGTAAAAAA
Statistics
Matches: 1052, Mismatches: 163, Indels: 96
0.80 0.12 0.07
Matches are distributed among these distances:
163 88 0.08
164 330 0.31
165 77 0.07
166 11 0.01
167 135 0.13
168 52 0.05
169 38 0.04
170 173 0.16
172 2 0.00
173 1 0.00
175 1 0.00
176 1 0.00
178 20 0.02
179 65 0.06
180 5 0.00
181 1 0.00
182 4 0.00
183 1 0.00
184 47 0.04
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (163 bp):
AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGA
CTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTG
GCAGATAACCCTTCTCGACTTAAGTTATACTGC
Found at i:377084 original size:248 final size:248
Alignment explanation
Indices: 376633--378093 Score: 1667
Period size: 248 Copynumber: 5.8 Consensus size: 248
376623 AATTTATTGA
* * * * * * * * *
376633 CAGATAGCCCTTCTTGCCTTGAGCTATGTTGTAAATGATGTTCCTTGGAGCTGAGAGAAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAGTCGAA
* * * ** * * * * * *
376698 CTCGAAGGTC--T--TTGGCAGATAGCTCTTCTAGCCTTGAGCTATACCGCAAATGATGTGTCGT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATG-CCT
* * * * * * *
376759 T-GAGCTGAGCGTAATCGAACTCAAATGTCTGTGTTGGCAGATAACCCTTCTAACCTTGAGTTAT
130 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTAT
* * * *
376823 ACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAGTCGAACTTGAGGGTCTTTGG
195 GCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGG
*
376877 CAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAGTCGAA
376942 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTT
* * * *
377007 GGAGCTGAGCATAGTCGAACTCGAAGGTATTTGGTGACATATAACTCTTCTAGCCTTGAGTTATG
131 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * * *
377072 TTGTAAATGATGTGCCCTCGAAGTTGAGCGTAGTCAAACTCGAAGGTATTTGG
196 CTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGG
* * * *
377125 CAGATAGCCCTTCTTGACTTAAGCTATGATGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAC
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAGTCGAA
377190 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTT
* * *
377255 GGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAAATAACTCTTCTAGCCTTGAGTTATG
131 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* *
377320 TTGTAAATGATGTG-CCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
196 CTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGG
* *
377372 CAGATAGCCCTTCTCTACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAGTCGAA
* *
377437 CTTGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGTTGCAAATGATATGCCTT
66 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTT
*
377502 GGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
131 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * *
377567 CTGTAAATGATGTGCCTTCGAAGCTGAGTGTAATTGAACTCGAGGGTCTTTGG
196 CTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGG
* * *
377620 CAGATAGCCCTTCTCGACTTAAGCTATACTACAAATGATGTGCCTTGGAGCTAAGCGTTTGGAGC
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTT-G-G---AGC---T-GAG-
* *
377685 TAAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAATTTATGCTGC
56 T----GTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGC
* * * * * ** ** *
377750 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGTGGTCTTTTGGATGGTAGATAGCCCT
117 AAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG-TGACAGATAACCCT
* ** * * * ** * * * *
377815 TCTCGATTTAAGCTATACTACAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTT
179 TCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTC-GAGG-G
*
377879 TTTGGTTGG
242 TCT--TTGG
* * * * * *** *
377888 CAGATAACACTTCTCGACTTAAGTTATGTTGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATG-CCTTGGAGCTGAGTGTAGTCGA
** * * * * * * **
377953 ACTCGGGGGTATTTTGGATGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGCGCC
65 ACTCGAAGGT-CTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCC
* * * *
378018 TTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCCTGAGTTA
129 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTA
378083 TGCTGTAAATG
194 TGCTGTAAATG
378094 TTGTAAAAAA
Statistics
Matches: 1044, Mismatches: 144, Indels: 49
0.84 0.12 0.04
Matches are distributed among these distances:
244 65 0.06
246 1 0.00
247 236 0.23
248 408 0.39
249 1 0.00
250 1 0.00
253 32 0.03
254 4 0.00
255 40 0.04
256 45 0.04
257 3 0.00
259 1 0.00
260 3 0.00
261 1 0.00
262 65 0.06
263 28 0.03
264 28 0.03
265 37 0.04
266 2 0.00
268 40 0.04
269 3 0.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (248 bp):
CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAGTCGAA
CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTT
GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
CTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGG
Found at i:377683 original size:14 final size:14
Alignment explanation
Indices: 377664--377691 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
377654 ATGATGTGCC
377664 TTGGAGCTAAGCGT
1 TTGGAGCTAAGCGT
377678 TTGGAGCTAAGCGT
1 TTGGAGCTAAGCGT
377692 AGTCGAACTC
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:0.21, C:0.14, G:0.36, T:0.29
Consensus pattern (14 bp):
TTGGAGCTAAGCGT
Found at i:377839 original size:86 final size:86
Alignment explanation
Indices: 377682--378070 Score: 421
Period size: 85 Copynumber: 4.6 Consensus size: 86
377672 AAGCGTTTGG
* * * * * ** *
377682 AGCTAAGCGTAGTCGAACTCAAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGATTTAATTTATG
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGATGGCAGATAACCCTTCTCGACTTAAGCTATA
377746 CTGCAAATGATGTGCCCTCGA
66 CTGCAAATGATGTGCCCTCGA
* ** * * *
377767 AGCTGAGTGTAATCGAACTCGGTGGTCTTTTGGATGGTAGATAGCCCTTCTCGATTTAAGCTATA
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGATGGCAGATAACCCTTCTCGACTTAAGCTATA
* * *
377832 CTACAAATGATGTG-CCTTGG
66 CTGCAAATGATGTGCCCTCGA
* * * * * *
377852 AGCTGAGCGTAGTCGAACTCAAAGGT-TTTTGGTTGGCAGATAACACTTCTCGACTTAAGTTATG
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGATGGCAGATAACCCTTCTCGACTTAAGCTATA
* *
377916 TTGCAAATGATGTGCCCTCAA
66 CTGCAAATGATGTGCCCTCGA
* ** * *
377937 AGCTGAGTGTAATCGAACTCGGGGGTATTTTGGATGGCAGATAGCCCTTCTCGACTTAAGCTATA
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGATGGCAGATAACCCTTCTCGACTTAAGCTATA
* * *
378002 CTGCAAATGATGCGCCTTAG-
66 CTGCAAATGATGTGCCCTCGA
* *
378022 AGCTGAGCGTAGTCGAACTCGAAGGTC-TTT-GTTGGCAGATAACCCTTCT
1 AGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGATGGCAGATAACCCTTCT
378071 AGCCCTGAGT
Statistics
Matches: 247, Mismatches: 54, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
83 17 0.07
84 46 0.19
85 92 0.37
86 92 0.37
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (86 bp):
AGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGATGGCAGATAACCCTTCTCGACTTAAGCTATA
CTGCAAATGATGTGCCCTCGA
Found at i:384353 original size:21 final size:21
Alignment explanation
Indices: 384327--384366 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
384317 CAGAACCCCA
*
384327 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
384348 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
384367 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:388060 original size:20 final size:20
Alignment explanation
Indices: 388023--388061 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
388013 AGAGATTTAA
** *
388023 GATCATCATTTTCTTTTGAT
1 GATCATCATTGACCTTTGAT
388043 GATCATCATTGACCTTTGA
1 GATCATCATTGACCTTTGA
388062 AAGTAAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (20 bp):
GATCATCATTGACCTTTGAT
Found at i:393142 original size:22 final size:22
Alignment explanation
Indices: 393100--393143 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
393090 AATAATACGA
*
393100 AAAAATAGTTTAAAAATGAAAAG
1 AAAAATAG-TTAAAAAGGAAAAG
393123 AAAAATA-TTAAAATAGGAAAA
1 AAAAATAGTTAAAA-AGGAAAA
393144 CCAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.20
Consensus pattern (22 bp):
AAAAATAGTTAAAAAGGAAAAG
Found at i:395328 original size:38 final size:38
Alignment explanation
Indices: 395237--395340 Score: 165
Period size: 37 Copynumber: 2.8 Consensus size: 38
395227 AGAATTTAGT
*
395237 GTTAGAACATAGGGTAATACTTATGTTACTCAAATAGA
1 GTTAGAACATAGGGCAATACTTATGTTACTCAAATAGA
395275 G-TAGAACATAGGGCAATACTTATGTTACTCAAATAGA
1 GTTAGAACATAGGGCAATACTTATGTTACTCAAATAGA
* * *
395312 GTTAGAACATAAGGCAATACCTACGTTAC
1 GTTAGAACATAGGGCAATACTTATGTTAC
395341 CCATACTCGT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
37 36 0.59
38 25 0.41
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (38 bp):
GTTAGAACATAGGGCAATACTTATGTTACTCAAATAGA
Found at i:395674 original size:34 final size:34
Alignment explanation
Indices: 395560--395896 Score: 162
Period size: 34 Copynumber: 9.5 Consensus size: 34
395550 TTTTATATAC
*
395560 ATATAT-ATAATATAGTTTTGAAAACATATTTGAAACA
1 ATATATAAT-ATATAGTTTTTAAAACAT-TTT-AAA-A
* * *
395597 TTTATATATTATATAGTTTTTAAAACACTTTGAAAA
1 -ATATATAATATATAGTTTTTAAAACA-TTTTAAAA
* *
395633 TAAATATAATATATAGTTTTTAAAACGTTTTAAAA
1 -ATATATAATATATAGTTTTTAAAACATTTTAAAA
* *
395668 ATATAT-ATATTATACGGTTTTAAAAAACATTTT-TAA
1 ATATATAATA-TATA--GTTTT-TAAAACATTTTAAAA
395704 A-ATA-AATATA-A-TTTTTAAAAAGAAACATTTTGAAAA
1 ATATATAATATATAGTTTTT----A-AAACATTTT-AAAA
* *
395740 CATATATATATTATATAGTTTTGAAATCATTTTAAAA
1 -ATATATA-A-TATATAGTTTTTAAAACATTTTAAAA
*
395777 ACT-TATAATATATAGTTTTAAAAACATTTTTGAAAA
1 A-TATATAATATATAGTTTTTAAAACA-TTTT-AAAA
* * * *
395813 CTATATAATTTTGAAAGTGTTTTTAAA-A----AAAA
1 ATATATAA-TAT-ATAGT-TTTTAAAACATTTTAAAA
* * *
395845 ATATATAATATATA-ATTTTAAAATACTTTTGAAA
1 ATATATAATATATAGTTTTTAAAACA-TTTTAAAA
*
395879 ATATATATTATATAGTTT
1 ATATATAATATATAGTTT
395897 GTAGAAAATA
Statistics
Matches: 232, Mismatches: 32, Indels: 73
0.69 0.09 0.22
Matches are distributed among these distances:
28 7 0.03
29 1 0.00
30 6 0.03
31 2 0.01
32 11 0.05
33 5 0.02
34 52 0.22
35 21 0.09
36 48 0.21
37 20 0.09
38 39 0.17
39 10 0.04
40 1 0.00
41 4 0.02
42 1 0.00
43 4 0.02
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (34 bp):
ATATATAATATATAGTTTTTAAAACATTTTAAAA
Found at i:395808 original size:73 final size:71
Alignment explanation
Indices: 395560--395819 Score: 230
Period size: 72 Copynumber: 3.6 Consensus size: 71
395550 TTTTATATAC
* * * *
395560 ATATATATAATATAGTTTTGAAAACATATTTG-AAACATTTATATATTATATAGTTTTTAAAACA
1 ATATA-AT-ATATAGTTTTAAAAACATTTTTGAAAACATATATATATTATATAGTTTTAAAAACA
*
395624 CTTTGAAAATAA
64 -TTT--TAA-AA
* * **
395636 ATATAATATATAGTTTTTAAAAC-GTTTT-AAAA-ATATATATATTATACGGTTTTAAAAAACAT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAACATATATATATTATATAGTTTT-AAAAACAT
*
395698 TTTTAAA
65 TTTAAAA
* * *
395705 ATA-AATATA-ATTTTTAAAAAGAAACA-TTTTGAAAACATATATATATTATATAGTTTTGAAAT
1 ATATAATATATAGTTTT---AA-AAACATTTTTGAAAACATATATATATTATATAGTTTTAAAAA
395767 CATTTTAAAA
62 CATTTTAAAA
395777 ACTTATAATATATAGTTTTAAAAACATTTTTGAAAAC-TATATA
1 A--TATAATATATAGTTTTAAAAACATTTTTGAAAACATATATA
395820 ATTTTGAAAG
Statistics
Matches: 153, Mismatches: 17, Indels: 32
0.76 0.08 0.16
Matches are distributed among these distances:
67 5 0.03
68 6 0.04
69 5 0.03
70 2 0.01
71 8 0.05
72 49 0.32
73 43 0.28
74 17 0.11
75 8 0.05
76 10 0.07
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (71 bp):
ATATAATATATAGTTTTAAAAACATTTTTGAAAACATATATATATTATATAGTTTTAAAAACATT
TTAAAA
Found at i:395821 original size:36 final size:35
Alignment explanation
Indices: 395560--395821 Score: 173
Period size: 36 Copynumber: 7.2 Consensus size: 35
395550 TTTTATATAC
* *
395560 ATATATATAATATAGTTTTGAAAACATATTTGAAACATTT
1 ATATA-AT-ATATAGTTTTAAAAACAT-TTTGAAA-A-CT
* * *
395600 ATATATTATATAGTTTTTAAAACACTTTGAAAA-T
1 ATATAATATATAGTTTTAAAAACATTTTGAAAACT
* * *
395634 AAATATAATATATAGTTTTTAAAACGTTTT-AAAAAT
1 --ATATAATATATAGTTTTAAAAACATTTTGAAAACT
*
395670 ATAT-ATATTATACGGTTTTAAAAAACATTTT-TAAA--
1 ATATAATA-TATA--GTTTT-AAAAACATTTTGAAAACT
*
395705 ATA-AATATA-ATTTTTAAAAAGAAACATTTTGAAAACAT
1 ATATAATATATAGTTTT---AA-AAACATTTTGAAAAC-T
* * *
395743 ATATATATTATATAGTTTTGAAATCATTTTAAAAACT
1 ATATA-A-TATATAGTTTTAAAAACATTTTGAAAACT
395780 -TATAATATATAGTTTTAAAAACATTTTTGAAAACT
1 ATATAATATATAGTTTTAAAAACA-TTTTGAAAACT
395815 ATATAAT
1 ATATAAT
395822 TTTGAAAGTG
Statistics
Matches: 183, Mismatches: 18, Indels: 46
0.74 0.07 0.19
Matches are distributed among these distances:
31 4 0.02
33 7 0.04
34 36 0.20
35 24 0.13
36 42 0.23
37 20 0.11
38 32 0.17
39 3 0.02
40 6 0.03
41 4 0.02
42 5 0.03
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (35 bp):
ATATAATATATAGTTTTAAAAACATTTTGAAAACT
Found at i:395858 original size:145 final size:143
Alignment explanation
Indices: 395581--395867 Score: 316
Period size: 145 Copynumber: 2.0 Consensus size: 143
395571 ATAGTTTTGA
* *
395581 AAACATATTTGAAACATTTATATATTATATAGTTTTTAAAACACTTTGAAAATAAATATAATATA
1 AAACATATTTGAAACATATATATATTATATAGTTTTGAAAACACTTTGAAAATAAATATAATATA
* * ** *
395646 TAGTTTTTAAAACGTTTTAAAAATATATATATTATACGGTTTTAAAAAACATTTTTAAAATAAAT
66 TAGTTTTAAAAACGTTTTAAAAATATATATATTATAAGGTTTTAAAAAACAAATATAAAAT-AAT
395711 ATAATTTTTAAAAAG
130 ATAA-TTTTAAAAAG
* * **
395726 AAACAT-TTTGAAAACATATATATATTATATAGTTTTGAAATCA-TTTTAAAA-ACTTATAATAT
1 AAACATATTTG-AAACATATATATATTATATAGTTTTGAAAACACTTTGAAAATAAATATAATAT
* * * *
395788 ATAGTTTTAAAAACATTTTTGAAAACTATATA-ATTTTGAAAGTGTTTTTAAAAAA-AAATATAT
65 ATAGTTTTAAAAAC-GTTTT-AAAAATATATATATTAT--AAG-G-TTTTAAAAAACAAATATAA
395851 AAT-ATATAATTTTAAAA
124 AATAATATAATTTTAAAA
395868 TACTTTTGAA
Statistics
Matches: 120, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
143 22 0.18
144 27 0.22
145 51 0.43
146 2 0.02
147 8 0.07
148 10 0.08
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (143 bp):
AAACATATTTGAAACATATATATATTATATAGTTTTGAAAACACTTTGAAAATAAATATAATATA
TAGTTTTAAAAACGTTTTAAAAATATATATATTATAAGGTTTTAAAAAACAAATATAAAATAATA
TAATTTTAAAAAG
Found at i:395951 original size:14 final size:14
Alignment explanation
Indices: 395932--395976 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
395922 ATTATCGTTG
395932 TTATTTATTTTTAT
1 TTATTTATTTTTAT
395946 TTATTTATTTTTAT
1 TTATTTATTTTTAT
* *
395960 TAATTTTATTTTCAT
1 TTA-TTTATTTTTAT
395975 TT
1 TT
395977 TAATTGTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTTATTTTTAT
Found at i:396656 original size:20 final size:21
Alignment explanation
Indices: 396621--396664 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
396611 CAACCAGAAC
* *
396621 GCAAAATAAACCAAAACAACA
1 GCAAAATAAACAAAAACAAAA
396642 GCAAAA-AAACAAAAACAAAA
1 GCAAAATAAACAAAAACAAAA
396662 GCA
1 GCA
396665 GACAGCCCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.70, C:0.20, G:0.07, T:0.02
Consensus pattern (21 bp):
GCAAAATAAACAAAAACAAAA
Found at i:397476 original size:25 final size:25
Alignment explanation
Indices: 397405--397476 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
397395 TATCTATCAT
* *
397405 ATTTTTCTTTCCTCTTTGACTTATTT
1 ATTTTTATTTCCT-TTTGACTTATTA
* * *
397431 CTGTTTATTT-CTTTGTCACTTATTA
1 ATTTTTATTTCCTTT-TGACTTATTA
*
397456 ATTTTTTTTTCCTTTTGACTT
1 ATTTTTATTTCCTTTTGACTT
397477 GTTATTATTA
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
24 2 0.06
25 22 0.63
26 11 0.31
ACGTcount: A:0.12, C:0.17, G:0.06, T:0.65
Consensus pattern (25 bp):
ATTTTTATTTCCTTTTGACTTATTA
Found at i:403215 original size:22 final size:23
Alignment explanation
Indices: 403180--403230 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
403170 CATAATTATT
*
403180 TAAAAA-ATTAAAT-AAAAATAC
1 TAAAAATATTAAATAAAAAATAA
*
403201 TAAAAATATTTAATAAAAAATAA
1 TAAAAATATTAAATAAAAAATAA
403224 TAAAAAT
1 TAAAAAT
403231 TAGGTTGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 6 0.23
22 6 0.23
23 14 0.54
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAAAATATTAAATAAAAAATAA
Found at i:415841 original size:2 final size:2
Alignment explanation
Indices: 415803--415829 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
415793 GTCACTGTGA
415803 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
415830 AGGTTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:416401 original size:2 final size:2
Alignment explanation
Indices: 416390--416419 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
416380 TTATAATAGC
416390 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
416420 CTCACAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:416876 original size:28 final size:28
Alignment explanation
Indices: 416844--416899 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
416834 ATTTGATGAC
416844 GTGACACTTAAAGAACGTTATTTTAGAA
1 GTGACACTTAAAGAACGTTATTTTAGAA
416872 GTGACACTTAAAGAACGTTATTTTAGAA
1 GTGACACTTAAAGAACGTTATTTTAGAA
416900 TTAACCTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (28 bp):
GTGACACTTAAAGAACGTTATTTTAGAA
Found at i:421488 original size:14 final size:14
Alignment explanation
Indices: 421469--421498 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
421459 CGTGGCAGTT
421469 AGTCAGCAGCGTCC
1 AGTCAGCAGCGTCC
*
421483 AGTCAGCAGCTTCC
1 AGTCAGCAGCGTCC
421497 AG
1 AG
421499 AAGGTGGACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.33, G:0.27, T:0.17
Consensus pattern (14 bp):
AGTCAGCAGCGTCC
Found at i:428010 original size:14 final size:14
Alignment explanation
Indices: 427975--428010 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
427965 AATTTATTTC
*
427975 AATTTTTCGTTTTT
1 AATTTTTGGTTTTT
427989 AATTTTTGGTTTTT
1 AATTTTTGGTTTTT
*
428003 GATTTTTG
1 AATTTTTG
428011 TAGGTACCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.03, G:0.14, T:0.69
Consensus pattern (14 bp):
AATTTTTGGTTTTT
Found at i:428766 original size:25 final size:26
Alignment explanation
Indices: 428728--428777 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
428718 TAAACTATAC
*
428728 ATTTAGTACTTAAA-TTATTTTTTCT
1 ATTTAGTACCTAAACTTATTTTTTCT
*
428753 ATTTGGTACCTAAACTTTATTTTTT
1 ATTTAGTACCTAAAC-TTATTTTTT
428778 TAAAATCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
27 9 0.43
ACGTcount: A:0.26, C:0.10, G:0.06, T:0.58
Consensus pattern (26 bp):
ATTTAGTACCTAAACTTATTTTTTCT
Found at i:435456 original size:20 final size:19
Alignment explanation
Indices: 435420--435458 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
435410 TGTCAAAATT
*
435420 AAACCCCAAATCTCATAGA
1 AAACCCCAAATCGCATAGA
*
435439 AAACCCCTAAATGGCATAGA
1 AAACCCC-AAATCGCATAGA
435459 TCTAAAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.28, G:0.10, T:0.15
Consensus pattern (19 bp):
AAACCCCAAATCGCATAGA
Found at i:438519 original size:33 final size:32
Alignment explanation
Indices: 438470--438548 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 32
438460 ATTTAAATTT
*
438470 GAAAAATTTAAATGATAGTTTAATCAAAATAA
1 GAAAAATTTAAATGATAGTGTAATCAAAATAA
* *
438502 GAAAAATATTTAATGATAGTGTAGTCAAAATAA
1 GAAAAAT-TTAAATGATAGTGTAATCAAAATAA
438535 GAAAAATTTGAAAT
1 GAAAAATTT-AAAT
438549 TTAACGATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
32 9 0.22
33 32 0.78
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.30
Consensus pattern (32 bp):
GAAAAATTTAAATGATAGTGTAATCAAAATAA
Found at i:438857 original size:163 final size:165
Alignment explanation
Indices: 438579--438910 Score: 562
Period size: 163 Copynumber: 2.0 Consensus size: 165
438569 TAAATTTAAG
*
438579 TAAATAAAATAAGAGTGAGAAAGGAGTGAAGAAATTTGTAATTTACCTAAAAATAAAATAGGATC
1 TAAATAAAATAAGAGTGAGAAACGAGTGAAGAAATTTGTAATTTACCTAAAAATAAAATAGGATC
* *
438644 TATATTTGGTACCTAAACTTTTAGTCATTGACAATGGTGGAAATAGTATGATGAACTAGTATTAC
66 TATATTTGGTACCTAAACGTTTAGTCATTGACAATGGTGGAAAGAGTATGATGAACTAGTATTAC
* *
438709 TCAATAACTAATTCTTAATCGTAGTGGGTCGGTCT
131 TCAATAACTAATTCTTAATCGTAGTGGGTCAGTCA
*
438744 TAAATAAAATAAGATTGAGAAACGAGTGAAGAAATTTGTAATTTACCT-AAAA-AAAATAGGAT-
1 TAAATAAAATAAGAGTGAGAAACGAGTGAAGAAATTTGTAATTTACCTAAAAATAAAATAGGATC
* *
438806 TCGTATTTGGTACTTAAACGTTTAGTCATTGACAATGGTGGAAAGAGTATGATGAACTAGTATTA
66 T-ATATTTGGTACCTAAACGTTTAGTCATTGACAATGGTGGAAAGAGTATGATGAACTAGTATTA
438871 CTCAATAACTAATTCTTAATCGTAGTGGGTCAGTCA
130 CTCAATAACTAATTCTTAATCGTAGTGGGTCAGTCA
438907 TAAA
1 TAAA
438911 GACCACTGAA
Statistics
Matches: 158, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
162 1 0.01
163 107 0.68
164 4 0.03
165 46 0.29
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (165 bp):
TAAATAAAATAAGAGTGAGAAACGAGTGAAGAAATTTGTAATTTACCTAAAAATAAAATAGGATC
TATATTTGGTACCTAAACGTTTAGTCATTGACAATGGTGGAAAGAGTATGATGAACTAGTATTAC
TCAATAACTAATTCTTAATCGTAGTGGGTCAGTCA
Found at i:457792 original size:21 final size:21
Alignment explanation
Indices: 457768--457835 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
457758 AAAACCAAAT
457768 ATATAATAATTTATAATTTAA
1 ATATAATAATTTATAATTTAA
*
457789 ATAT--TAATATTATGATTT-A
1 ATATAATAAT-TTATAATTTAA
*
457808 ATA-AATTATATATATAATTTAA
1 ATATAA-TA-ATTTATAATTTAA
457830 AT-TAAT
1 ATATAAT
457836 TTAAGAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 14
0.69 0.06 0.26
Matches are distributed among these distances:
19 8 0.22
20 8 0.22
21 14 0.38
22 7 0.19
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
ATATAATAATTTATAATTTAA
Found at i:457983 original size:21 final size:23
Alignment explanation
Indices: 457959--458002 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
457949 AATTGTCTAA
*
457959 ATTAATTTAA-TTTA-AGAATAT
1 ATTAATATAATTTTATAGAATAT
457980 ATTAATATAATTTTATAGAATAT
1 ATTAATATAATTTTATAGAATAT
458003 GATTGGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 4 0.20
23 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
ATTAATATAATTTTATAGAATAT
Found at i:459178 original size:26 final size:26
Alignment explanation
Indices: 459117--459206 Score: 89
Period size: 26 Copynumber: 3.5 Consensus size: 26
459107 GAGAATAAAT
*
459117 TAATTTAATTTAAGAATAAATT-ATA
1 TAATTTAATTTAAGAATATATTAATA
* *
459142 TAA-TAATATTTTA-AATAATATTAGA-A
1 TAATTTA-ATTTAAGAAT-ATATTA-ATA
459168 TAATTTAATTTAAGAATATATTAATA
1 TAATTTAATTTAAGAATATATTAATA
*
459194 TAATTTAAATTAA
1 TAATTTAATTTAA
459207 TATATTCTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
24 5 0.10
25 13 0.25
26 28 0.54
27 6 0.12
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (26 bp):
TAATTTAATTTAAGAATATATTAATA
Found at i:460027 original size:23 final size:23
Alignment explanation
Indices: 459984--460027 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
459974 CACCTTTGAG
*
459984 TTCACAACAGGAGCAATTTATTT
1 TTCACAACAGGAGCAACTTATTT
*
460007 TTCACAACAGGAGCACCTTAT
1 TTCACAACAGGAGCAACTTAT
460028 CATTTTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (23 bp):
TTCACAACAGGAGCAACTTATTT
Found at i:462575 original size:13 final size:13
Alignment explanation
Indices: 462557--462581 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
462547 AATATATTAA
462557 TATAATTTAAATT
1 TATAATTTAAATT
462570 TATAATTTAAAT
1 TATAATTTAAAT
462582 ATTAATATTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATAATTTAAATT
Found at i:463238 original size:395 final size:394
Alignment explanation
Indices: 462508--463282 Score: 1237
Period size: 395 Copynumber: 2.0 Consensus size: 394
462498 TGATAATCCA
*
462508 AAGAATTGATTAATAGAGTCAAGGGGTACATTTCTTAAGAATATATTAATATAATTTAAATTTAT
1 AAGAATTGATTAATAGAGTCAAGGGGTACATTTCTTAAAAATATATTAATATAATTTAAATTTAT
** * *
462573 AATTTAAATATTAATATTATTACATGGGGTTGGACCAATTACACTGTGTAAAACCCTTTTAGTTT
66 AATTTAAATATTAATATTATTACATGGGGCAGGACCAATTACACTGTGTAAAACCCTTCTACTTT
* *
462638 TACAATCATTTTACGATCATTGGATGAGAGAAATTAAAGACTGAGATTAACCGTGGAAAATGAAC
131 TACAATCATTTTACGACCATTGGATGAGAGAAATTAAAGACTGAGATTAACAGTGGAAAATGAAC
* * * * *
462703 AGATATTCAATAAAAAACGAGTTGATCTCAACATTTGATTTCTCTCAATTCAATGGCAATAAAAA
196 AGATATTCAATAAAAAACAAGTTGATCTCAACATTCGATTTCTCCCAATCCAATGGAAATAAAAA
* * * *
462768 GGTGTAAAACTAAAAGTGTTTTACACAGTACAAGTAGATCCAACTCCTTATTATATTTATAAATT
261 AGTGTAAAACTAAAAGAGTTTTACACAGTA-AAGTAGAACCAACTCCATATTATATTTATAAATT
462833 ATAGAAATAAATTAAATTAATTTAAGAATAAATTATATAAAAATATATAATTATTATTTTTATAG
325 ATAGAAATAAATTAAATTAATTTAAGAATAAATTATATAAAAATATATAATTATTATTTTTATAG
462898 AAACT
390 AAACT
462903 AAGAATTGATTAATAGAGTCAAGGGGTACATTTCTTAAAAATATATTAATATAATTTAAATTTAT
1 AAGAATTGATTAATAGAGTCAAGGGGTACATTTCTTAAAAATATATTAATATAATTTAAATTTAT
* *
462968 AATTTTAATATTAATATTATTACATGGGGCAGGACCAATTACACTGTGTAAAACTCTTCTACTTT
66 AATTTAAATATTAATATTATTACATGGGGCAGGACCAATTACACTGTGTAAAACCCTTCTACTTT
* * * *
463033 TACAATTATTTTAGGACCATTGGATGAGATATATTAAAGACTGAGATTAACAGTGGAAAATGAAC
131 TACAATCATTTTACGACCATTGGATGAGAGAAATTAAAGACTGAGATTAACAGTGGAAAATGAAC
* * *
463098 AGATATTCACTAAAAAAACAAGTTGATCTCGACCTTCGATTTCTCCCAATCCAATGGAAATAAAA
196 AGATATTCAAT-AAAAAACAAGTTGATCTCAACATTCGATTTCTCCCAATCCAATGGAAATAAAA
* * *
463163 AAGTGTAAAACTAAATGAGTTTTACACAGGT-AAGTAGAACCTACTCCATATTATATTTATTAAT
260 AAGTGTAAAACTAAAAGAGTTTTACACA-GTAAAGTAGAACCAACTCCATATTATATTTATAAAT
* * *
463227 TATATAAATAAATTAAATTGATTTAAGAATAAATTATATAAAAATATTTAATTATT
324 TATAGAAATAAATTAAATTAATTTAAGAATAAATTATATAAAAATATATAATTATT
463283 GAACATGTAA
Statistics
Matches: 347, Mismatches: 31, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
395 274 0.79
396 71 0.20
397 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (394 bp):
AAGAATTGATTAATAGAGTCAAGGGGTACATTTCTTAAAAATATATTAATATAATTTAAATTTAT
AATTTAAATATTAATATTATTACATGGGGCAGGACCAATTACACTGTGTAAAACCCTTCTACTTT
TACAATCATTTTACGACCATTGGATGAGAGAAATTAAAGACTGAGATTAACAGTGGAAAATGAAC
AGATATTCAATAAAAAACAAGTTGATCTCAACATTCGATTTCTCCCAATCCAATGGAAATAAAAA
AGTGTAAAACTAAAAGAGTTTTACACAGTAAAGTAGAACCAACTCCATATTATATTTATAAATTA
TAGAAATAAATTAAATTAATTTAAGAATAAATTATATAAAAATATATAATTATTATTTTTATAGA
AACT
Found at i:464965 original size:10 final size:10
Alignment explanation
Indices: 464943--464972 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
464933 TGGGATTTCA
464943 AATAATATTAT
1 AATAAT-TTAT
464954 AATAATTTAT
1 AATAATTTAT
464964 AATAATTTA
1 AATAATTTA
464973 AATTAAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AATAATTTAT
Found at i:464985 original size:21 final size:20
Alignment explanation
Indices: 464961--465014 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
464951 TATAATAATT
464961 TATAATAATTTAAATTAAGAA
1 TATAATAATTTAAATTAA-AA
* * *
464982 TATATTAATATAATTTAAAA
1 TATAATAATTTAAATTAAAA
465002 T-T-ATAATTTAAAT
1 TATAATAATTTAAAT
465015 ATTAGTATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 8 0.30
19 1 0.04
20 3 0.11
21 15 0.56
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TATAATAATTTAAATTAAAA
Found at i:465008 original size:13 final size:14
Alignment explanation
Indices: 464990--465018 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
464980 AATATATTAA
464990 TATAATTTAAA-AT
1 TATAATTTAAATAT
465003 TATAATTTAAATAT
1 TATAATTTAAATAT
465017 TA
1 TA
465019 GTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAATTTAAATAT
Found at i:468092 original size:14 final size:16
Alignment explanation
Indices: 468062--468100 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
468052 TATTTATAAA
468062 TAAAATCTGATATTTT
1 TAAAATCTGATATTTT
* *
468078 TAAAATCTAATTTTTT
1 TAAAATCTGATATTTT
468094 TAAAATC
1 TAAAATC
468101 AACTATCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (16 bp):
TAAAATCTGATATTTT
Found at i:476052 original size:32 final size:32
Alignment explanation
Indices: 476011--476245 Score: 303
Period size: 32 Copynumber: 7.3 Consensus size: 32
476001 AGAGTCAAGT
* *
476011 ATTACCTATGTCTTTCAGGACATATAGACAGA
1 ATTACCTATGTCTTTCGGGACATATGGACAGA
476043 ATTACCTATGTCTTTCGGGACATATGGACA-A
1 ATTACCTATGTCTTTCGGGACATATGGACAGA
*
476074 TATTACCTATGTCTTTCGGGACATATGGA-TGAA
1 -ATTACCTATGTCTTTCGGGACATATGGACAG-A
* * * *
476107 ATTACATACGTCTTTCGGGACATATGGATAGT
1 ATTACCTATGTCTTTCGGGACATATGGACAGA
* * *
476139 ATTACCTATGTCTTTTGAGACATATGGACAAA
1 ATTACCTATGTCTTTCGGGACATATGGACAGA
* * * *
476171 ATTACCTATGTCTTTTGGGACATATTGACGGT
1 ATTACCTATGTCTTTCGGGACATATGGACAGA
*
476203 ATTACCTATGTCTTTCGGGACATATGAACAGA
1 ATTACCTATGTCTTTCGGGACATATGGACAGA
476235 ATTACCTATGT
1 ATTACCTATGT
476246 GAGTAACGTG
Statistics
Matches: 175, Mismatches: 24, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
31 1 0.01
32 172 0.98
33 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (32 bp):
ATTACCTATGTCTTTCGGGACATATGGACAGA
Found at i:476089 original size:64 final size:64
Alignment explanation
Indices: 476008--476245 Score: 334
Period size: 64 Copynumber: 3.7 Consensus size: 64
475998 CCAAGAGTCA
* *
476008 AGTATTACCTATGTCTTTCAGGACATATAGACAGAATTACCTATGTCTTTCGGGACATATGGAC
1 AGTATTACCTATGTCTTTCGGGACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
* * * * *
476072 AATATTACCTATGTCTTTCGGGACATATGGA-TGAAATTACATACGTCTTTCGGGACATATGGAT
1 AGTATTACCTATGTCTTTCGGGACATATGGACAG-AATTACCTATGTCTTTCGGGACATATGGAC
* * * * *
476136 AGTATTACCTATGTCTTTTGAGACATATGGACAAAATTACCTATGTCTTTTGGGACATATTGAC
1 AGTATTACCTATGTCTTTCGGGACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
* *
476200 GGTATTACCTATGTCTTTCGGGACATATGAACAGAATTACCTATGT
1 AGTATTACCTATGTCTTTCGGGACATATGGACAGAATTACCTATGT
476246 GAGTAACGTG
Statistics
Matches: 150, Mismatches: 22, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
63 1 0.01
64 149 0.99
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (64 bp):
AGTATTACCTATGTCTTTCGGGACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
Found at i:476175 original size:96 final size:96
Alignment explanation
Indices: 476011--476245 Score: 335
Period size: 96 Copynumber: 2.4 Consensus size: 96
476001 AGAGTCAAGT
* * * *
476011 ATTACCTATGTCTTTCAGGACATATAGACAGAATTACCTATGTCTTTCGGGACATATGGACAATA
1 ATTACCTATGTCTTTCGGGACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACAAAA
*
476076 TTACCTATGTCTTTCGGGACATATGGATGAA
66 TTACCTATGTCTTTCGGGACATATGGACGAA
* * * * *
476107 ATTACATACGTCTTTCGGGACATATGGATAGTATTACCTATGTCTTTTGAGACATATGGACAAAA
1 ATTACCTATGTCTTTCGGGACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACAAAA
* * **
476172 TTACCTATGTCTTTTGGGACATATTGACGGT
66 TTACCTATGTCTTTCGGGACATATGGACGAA
*
476203 ATTACCTATGTCTTTCGGGACATATGAACAGAATTACCTATGT
1 ATTACCTATGTCTTTCGGGACATATGGACAGAATTACCTATGT
476246 GAGTAACGTG
Statistics
Matches: 120, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
96 120 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (96 bp):
ATTACCTATGTCTTTCGGGACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACAAAA
TTACCTATGTCTTTCGGGACATATGGACGAA
Done.