Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015181.1 Kokia drynarioides strain JFW-HI SEQ_130225, 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: 642291
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 422 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:359418 original size:2 final size:2
Alignment explanation
Indices: 359405--359440 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
359395 TTAGATAGAT
* *
359405 AG AG AG AT AG AG AG AT AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
359441 GGGAAGTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.44, T:0.06
Consensus pattern (2 bp):
AG
Found at i:362097 original size:7 final size:7
Alignment explanation
Indices: 362085--362118 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
362075 GCATGGACGA
362085 AATAGCG
1 AATAGCG
362092 AATAGCG
1 AATAGCG
362099 AATAGCG
1 AATAGCG
* *
362106 AATGGAG
1 AATAGCG
362113 AATAGC
1 AATAGC
362119 AATGGATTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.44, C:0.12, G:0.29, T:0.15
Consensus pattern (7 bp):
AATAGCG
Found at i:362124 original size:13 final size:14
Alignment explanation
Indices: 362085--362124 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
362075 GCATGGACGA
* *
362085 AATAGCGAATAGCG
1 AATAGCGAATGGAG
362099 AATAGCGAATGGAG
1 AATAGCGAATGGAG
362113 AATAGC-AATGGA
1 AATAGCGAATGGA
362125 TTTGAGGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.45, C:0.10, G:0.30, T:0.15
Consensus pattern (14 bp):
AATAGCGAATGGAG
Found at i:363202 original size:2 final size:2
Alignment explanation
Indices: 363195--363225 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
363185 AATATAATTC
363195 AT AT 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 AT AT A
363226 ACTTTTGAAC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:366507 original size:19 final size:18
Alignment explanation
Indices: 366479--366532 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
366469 TAAATAGCAT
*
366479 TAATAATTATGAATAAAAA
1 TAATATTTAT-AATAAAAA
* *
366498 TATTATTTATAATAATAAT
1 TAATATTTATAATAA-AAA
366517 TAATATTTATAATAAA
1 TAATATTTATAATAAA
366533 TAAAAAATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 6 0.20
19 24 0.80
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TAATATTTATAATAAAAA
Found at i:367657 original size:31 final size:30
Alignment explanation
Indices: 367625--367809 Score: 79
Period size: 30 Copynumber: 6.3 Consensus size: 30
367615 AAAATTGCAT
367625 TTTTACCC-CCGAACTTCCTGAAAATTACCA
1 TTTTACCCTCCGAACTTCCT-AAAATTACCA
* *
367655 TTTTACCCTCTGAACTTTCTAAAATTTA--A
1 TTTTACCCTCCGAACTTCCTAAAA-TTACCA
* * *
367684 ATTTACCC-CCGACCTTTCC-AAAATTA-TA
1 TTTTACCCTCCGAAC-TTCCTAAAATTACCA
* * * *
367712 TTTTAACC-CC-AATTTCACCAAAAAATACCA
1 TTTTACCCTCCGAACTT--CCTAAAATTACCA
*
367742 TTTTACCCT-CGAAGTTTCC-AAAATT-CCA
1 TTTTACCCTCCGAA-CTTCCTAAAATTACCA
** ** *
367770 TTTTTGGCC-CCGATTTTACCAAAAATTACCA
1 -TTTTACCCTCCGAACTT-CCTAAAATTACCA
367801 TTTTACCCT
1 TTTTACCCT
367810 TAAAATTTCC
Statistics
Matches: 119, Mismatches: 19, Indels: 33
0.70 0.11 0.19
Matches are distributed among these distances:
26 2 0.02
27 4 0.03
28 25 0.21
29 33 0.28
30 35 0.29
31 17 0.14
32 3 0.03
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (30 bp):
TTTTACCCTCCGAACTTCCTAAAATTACCA
Found at i:367716 original size:28 final size:28
Alignment explanation
Indices: 367625--367766 Score: 85
Period size: 28 Copynumber: 4.9 Consensus size: 28
367615 AAAATTGCAT
*
367625 TTTTACCCCCGAAC-TTCCTGAAAATTACCA
1 TTTTACCCCCGAACTTTCC--AAAATTA-TA
* *
367655 TTTTACCCTCTGAACTTTCTAAAATT-TAA
1 TTTTACCC-CCGAACTTTCCAAAATTAT-A
* *
367684 ATTTACCCCCGACCTTTCCAAAATTATA
1 TTTTACCCCCGAACTTTCCAAAATTATA
* * *
367712 TTTTAACCCC-AA-TTTCACCAAAAAATACCA
1 TTTTACCCCCGAACTTT--CC-AAAATTA-TA
* *
367742 TTTTACCCTCGAAGTTTCCAAAATT
1 TTTTACCCCCGAACTTTCCAAAATT
367767 CCATTTTTGG
Statistics
Matches: 87, Mismatches: 15, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
26 3 0.03
27 1 0.01
28 25 0.29
29 20 0.23
30 25 0.29
31 7 0.08
32 6 0.07
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (28 bp):
TTTTACCCCCGAACTTTCCAAAATTATA
Found at i:367749 original size:29 final size:29
Alignment explanation
Indices: 367711--367868 Score: 73
Period size: 29 Copynumber: 5.4 Consensus size: 29
367701 CCAAAATTAT
*
367711 ATTTTAACCCCAATTTCACCAAAAAATACC
1 ATTTTGACCCCAATTT-ACCAAAAAATACC
*
367741 ATTTT-ACCCTCGAAGTTT-CC--AAAATTCC
1 ATTTTGACCC-C-AA-TTTACCAAAAAATACC
* * *
367769 ATTTTTGGCCCCGATTTTACCAAAAATTACC
1 A-TTTTGACCCC-AATTTACCAAAAAATACC
* *
367800 ATTTT-ACCCTTAAAATTT-CC--AAAATTCC
1 ATTTTGACCC---CAATTTACCAAAAAATACC
* *
367828 ATTTTTGACCCCGATTTCACCAAAAATTACC
1 A-TTTTGACCCCAATTT-ACCAAAAAATACC
367859 ATTTT-ACCCC
1 ATTTTGACCCC
367869 TGGATGTCTA
Statistics
Matches: 97, Mismatches: 14, Indels: 35
0.66 0.10 0.24
Matches are distributed among these distances:
27 4 0.04
28 18 0.19
29 27 0.28
30 25 0.26
31 20 0.21
32 3 0.03
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
ATTTTGACCCCAATTTACCAAAAAATACC
Found at i:367763 original size:30 final size:30
Alignment explanation
Indices: 367729--367823 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
367719 CCCAATTTCA
*
367729 CCAAAAAATACCATTTTACCCTCGAAGTTT
1 CCAAAAAATACCATTTTACCCTCGAAATTT
* * *
367759 CC--AAAATTCCATTTTTGGCCC-CG-ATTTT
1 CCAAAAAATACCA-TTTT-ACCCTCGAAATTT
* **
367787 ACCAAAAATTACCATTTTACCCTTAAAATTT
1 -CCAAAAAATACCATTTTACCCTCGAAATTT
367818 CCAAAA
1 CCAAAA
367824 TTCCATTTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
28 12 0.24
29 11 0.22
30 15 0.31
31 11 0.22
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (30 bp):
CCAAAAAATACCATTTTACCCTCGAAATTT
Found at i:367809 original size:59 final size:59
Alignment explanation
Indices: 367698--367867 Score: 245
Period size: 59 Copynumber: 2.9 Consensus size: 59
367688 ACCCCCGACC
* * * * *
367698 TTTCCAAAATT--ATATTTTAACCCCAATTTCACCAAAAAATACCATTTTACCCTCGAAG
1 TTTCCAAAATTCCAT-TTTTGACCCCGATTTCACCAAAAATTACCATTTTACCCTCAAAA
* * *
367756 TTTCCAAAATTCCATTTTTGGCCCCGATTTTACCAAAAATTACCATTTTACCCTTAAAA
1 TTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTACCCTCAAAA
367815 TTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTACCC
1 TTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTACCC
367868 CTGGATGTCT
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
58 11 0.11
59 87 0.87
60 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
TTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAAATTACCATTTTACCCTCAAAA
Found at i:373538 original size:13 final size:12
Alignment explanation
Indices: 373511--373544 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
373501 TTCAATGAAT
*
373511 AAAAGAAAAGGA
1 AAAAGAAAAGAA
373523 AAAAGACAAAGAA
1 AAAAGA-AAAGAA
373536 AAAAGAAAA
1 AAAAGAAAA
373545 AACGAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:374188 original size:106 final size:105
Alignment explanation
Indices: 374073--374327 Score: 402
Period size: 106 Copynumber: 2.4 Consensus size: 105
374063 GAACTAATGA
* *
374073 TTTTAATCTTTTCATTCATGCAAGTTTTGCCTTCAATAAAATTCATCCACCTAACTCTATTCTTT
1 TTTTAATCTTTTCATTCATG-AAGCTTTGCCTCCAATAAAATTCATCCACCTAACTCTATTCTTT
374138 GCTCACTTTATATTTGGCATCCTTTGACCAATATGGATCAC
65 GCTCACTTTATATTTGGCATCCTTTGACCAATATGGATCAC
* *
374179 TTTTGATCTTTTCATTCATGAGAGCTTTGCCTCCAGTAAAATTCATCCACCTAACTCTATTCTTT
1 TTTTAATCTTTTCATTCATGA-AGCTTTGCCTCCAATAAAATTCATCCACCTAACTCTATTCTTT
* *
374244 GCTCACTTTATATTTGGCATCCTTTTACCAATATGGGTCAC
65 GCTCACTTTATATTTGGCATCCTTTGACCAATATGGATCAC
* * *
374285 TTTTAATCTTTCCATTCATGTGAGCTTTACCTCCAATAAAATT
1 TTTTAATCTTTTCATTCATG-AAGCTTTGCCTCCAATAAAATT
374328 TCATTCGCCT
Statistics
Matches: 136, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
105 1 0.01
106 135 0.99
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.42
Consensus pattern (105 bp):
TTTTAATCTTTTCATTCATGAAGCTTTGCCTCCAATAAAATTCATCCACCTAACTCTATTCTTTG
CTCACTTTATATTTGGCATCCTTTGACCAATATGGATCAC
Found at i:375068 original size:100 final size:101
Alignment explanation
Indices: 374882--375068 Score: 241
Period size: 100 Copynumber: 1.9 Consensus size: 101
374872 TCAGTACCAT
* * *
374882 GAAGACATGAAGGGAAAGATTTAAGACCGCAACGGTGGATCCAGCGCCACAAAGATACAAAAGGG
1 GAAGACAAGAAGGGAAAGATTTAAGACCGCAACGGTGAATCCAGCACCACAAAGATACAAAAGGG
* * *
374947 AAAGGTCTATGTCGCAGTGGCGGACCATGTACCTCA
66 AAAGGTCTAAGTCACAATGGCGGACCATGTACCTCA
* ** *** *
374983 GAAGACAAGAAGGGAAAGATTTAAG-CCGCAACGGTGAATCCAGTACCATGAAGATTTGAAGGGG
1 GAAGACAAGAAGGGAAAGATTTAAGACCGCAACGGTGAATCCAGCACCACAAAGATACAAAAGGG
*
375047 AAAGGTTTAAGTCACAATGGCG
66 AAAGGTCTAAGTCACAATGGCG
375069 AACCCGATAC
Statistics
Matches: 72, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
100 48 0.67
101 24 0.33
ACGTcount: A:0.37, C:0.18, G:0.29, T:0.16
Consensus pattern (101 bp):
GAAGACAAGAAGGGAAAGATTTAAGACCGCAACGGTGAATCCAGCACCACAAAGATACAAAAGGG
AAAGGTCTAAGTCACAATGGCGGACCATGTACCTCA
Found at i:375474 original size:39 final size:39
Alignment explanation
Indices: 375420--375633 Score: 159
Period size: 39 Copynumber: 5.5 Consensus size: 39
375410 CTACATCGTT
* *
375420 AACCAAGCTCTTACCCCGAGCCTAGGGCAAATCATCATC
1 AACCAATCTCTTACCCCGAGCCTGGGGCAAATCATCATC
* * *
375459 AACCAATCTCTTACCCCAAGCCTGGGGTAAAT--TGA--
1 AACCAATCTCTTACCCCGAGCCTGGGGCAAATCATCATC
* * *
375494 AGCCATTTGATCTTTTACCCCGAGCCTGGGGCAGATCATCATC
1 AACCA----ATCTCTTACCCCGAGCCTGGGGCAAATCATCATC
* * * *
375537 AACCAATCTCTTACCCCGAGCCAGAGGCAGATTAT-AGTC
1 AACCAATCTCTTACCCCGAGCCTGGGGCAAATCATCA-TC
** * * * * *
375576 ATTCGATCTCTTACCCCGAGCTTGGGGTATATCATCGTC
1 AACCAATCTCTTACCCCGAGCCTGGGGCAAATCATCATC
* *
375615 AACCAAACTCCTACCCCGA
1 AACCAATCTCTTACCCCGA
375634 TCACGGGGCA
Statistics
Matches: 134, Mismatches: 31, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
35 4 0.03
37 2 0.01
38 1 0.01
39 121 0.90
41 2 0.01
43 4 0.03
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.23
Consensus pattern (39 bp):
AACCAATCTCTTACCCCGAGCCTGGGGCAAATCATCATC
Found at i:375644 original size:78 final size:78
Alignment explanation
Indices: 375427--375648 Score: 259
Period size: 78 Copynumber: 2.8 Consensus size: 78
375417 GTTAACCAAG
* * * * *
375427 CTCTTACCCCGAGCCTAGGGCAAATCATCATCAACCAATCTCTTACCCCAAGCCTGGGGTAAATT
1 CTCTTACCCCGAGCCTGGGGCAAATCATCATCAACCAATCTCTTACCCCGAGCCAGGGGCAGATT
*
375492 GAAGCCATTTGAT
66 GAAGCCATTCGAT
* * *
375505 CTTTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCAGAGGCAGATT
1 CTCTTACCCCGAGCCTGGGGCAAATCATCATCAACCAATCTCTTACCCCGAGCCAGGGGCAGATT
*
375570 -ATAGTCATTCGAT
66 GA-AGCCATTCGAT
* * * * * * *
375583 CTCTTACCCCGAGCTTGGGGTATATCATCGTCAACCAAACTCCTACCCCGA-TCACGGGGCAGAT
1 CTCTTACCCCGAGCCTGGGGCAAATCATCATCAACCAATCTCTTACCCCGAGCCA-GGGGCAGAT
375647 TG
65 TG
375649 TGATTATTCA
Statistics
Matches: 122, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
77 3 0.02
78 119 0.98
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.24
Consensus pattern (78 bp):
CTCTTACCCCGAGCCTGGGGCAAATCATCATCAACCAATCTCTTACCCCGAGCCAGGGGCAGATT
GAAGCCATTCGAT
Found at i:376256 original size:194 final size:193
Alignment explanation
Indices: 375673--376692 Score: 1130
Period size: 194 Copynumber: 5.2 Consensus size: 193
375663 CAATGTGGCA
* * *
375673 GTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAAGGTGAGCAAATCTTCGAA-CCCA
1 GTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTC-AATGCGAACAAATCTTCGAACCCCA
* * * *
375737 GCTTCCTGATGAGATACTAAGAAGCGAGTCGAAACAATAAAATGGTTAGCTTCTTGATGAGATAC
65 GCTTCCTGATGAGATACTGAGAAGAG-GTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATAC
* * * * * *
375802 TGAGAAGTGGACTAAATTCGTCTTCCTAATGAGATACAGAGAAGCGGATTGAAACAAACGACGTG
129 TGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGGATTGAAACAAGCGAGGCG
* * * * *
375867 GTCATCTTCCTGATGAGATACTGAGAA-TAAGACCAAATCAAACCCACACTCGAGGTAAGAAAAT
1 GTCATCTTCCTGATGAGATACAGAGAAGT-ATA-C----C-AACTCA-A-T-G-CG-AA-CAAAT
* * * * * *
375931 CTTCGAATCTCAGCTTCTTGATGAGATATTGAGAAGCGGGTCGAAGCAATAAAATGATTAGCTTC
53 CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAG-AGGTCGAAGCAATAAAATGGTTAGCTTC
*
375996 CTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAACGGATTGAA
117 CTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGGATTGAA
*
376061 ACAAGTGAGGCG
182 ACAAGCGAGGCG
* * *
376073 GTCATCTTCCTGATGAGATACAGAGAAGTATGCCAACTTAATGCGAACAAATCTTCGAACCCCAA
1 GTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAACCCCAG
* *
376138 CTTCCTGATGAGATACTGAGAAGTAGGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATACT
66 CTTCCTGATGAGATACTGAGAAG-AGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACT
* * *
376203 AAGAAGTGGACCAAATTCGTCTTCTTGATGAGGTACAGAGAAGCGGATTGAAACAAGTGAGGCG
130 GAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGGATTGAAACAAGCGAGGCG
*
376267 GTCATCTTCCTTATGAGATACAGAGAAGTATACCAACTCAAT-----C---T-TT-GAACCCCAG
1 GTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAACCCCAG
* * * * *
376322 TTTCCGGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGACACT
66 CTTCCTGATGAGATACTGAGAAG-AGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACT
* * * * *
376387 GAGAAGTGGACCAAATTCATCTTCCTGATGAGATATAGAGAAGCGGATTGAAACAAACGGGGCG
130 GAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGGATTGAAACAAGCGAGGCG
* * * * *
376451 ATTATCTTCCTAATGAGATACAGAGAAGTGTACCAACTCAAGGCTCGATGTGAGCAAATCTTCGA
1 GTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATG--CGA----A-CAAATCTTCGA
* * *
376516 ATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGAAATAAAATGGTTAGTTTCCTGATG
59 ACCCCAGCTTCCTGATGAGATACTGAGAAG-AGGTCGAAGCAATAAAATGGTTAGCTTCCTGATG
* ** * *
376581 AAATACTGAGAAGTAAACCAAATTCATCTTCTTGATGAGGTACAGAGAAGCGGATTGAAACAAGC
123 AGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGGATTGAAACAAGC
* **
376646 AATACG
188 GAGGCG
* * *
376652 GTCATCTTCCTGATAAGATACTA-AGAAGTAGACCAAATCAA
1 GTCATCTTCCTGATGAGATAC-AGAGAAGTATACCAACTCAA
376693 CGACACCAAA
Statistics
Matches: 700, Mismatches: 92, Indels: 61
0.82 0.11 0.07
Matches are distributed among these distances:
184 160 0.23
185 2 0.00
186 1 0.00
189 1 0.00
193 1 0.00
194 200 0.29
195 3 0.00
196 2 0.00
197 1 0.00
198 1 0.00
199 4 0.01
200 11 0.02
201 152 0.22
202 2 0.00
203 1 0.00
204 1 0.00
205 12 0.02
206 143 0.20
207 2 0.00
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (193 bp):
GTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAACCCCAG
CTTCCTGATGAGATACTGAGAAGAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTG
AGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGCGGATTGAAACAAGCGAGGCG
Found at i:376438 original size:184 final size:184
Alignment explanation
Indices: 376122--376692 Score: 667
Period size: 184 Copynumber: 3.0 Consensus size: 184
376112 AATGCGAACA
* * * *
376122 AATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGTAGGGCGAAGCAATAAAAAGGTTAGC
1 AATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGC
* *
376187 TTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCTTGATGAGGTACAGAGAAGCGGATT
66 TTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCTTGATGAGGTACAGAGAAGCGGATT
* *
376252 GAAACAAGTGAGGCGGTCATCTTCCTTATGAGATACAGAGAAGTATACCAACTC
131 GAAACAAGCGAGGCGGTCATCTTCCTAATGAGATACAGAGAAGTATACCAACTC
* * *
376306 AATCTTTGAACCCCAGTTTCCGGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAAAGGTTAGC
1 AATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGC
* * * *
376371 TTCCTGATGAGACACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATATAGAGAAGCGGATT
66 TTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCTTGATGAGGTACAGAGAAGCGGATT
* * * * *
376436 GAAACAAACGGGGCGATTATCTTCCTAATGAGATACAGAGAAGTGTACCAACTC
131 GAAACAAGCGAGGCGGTCATCTTCCTAATGAGATACAGAGAAGTATACCAACTC
*
376490 AAGGCTCGATGTGAGCAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAA
1 -A------A--T---C---T-TT-GAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAA
* * * * **
376555 GAAATAAAATGGTTAGTTTCCTGATGAAATACTGAGAAGTAAACCAAATTCATCTTCTTGATGAG
49 GCAATAAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCTTGATGAG
* ** * * *
376620 GTACAGAGAAGCGGATTGAAACAAGCAATACGGTCATCTTCCTGATAAGATACTA-AGAAGTAGA
114 GTACAGAGAAGCGGATTGAAACAAGCGAGGCGGTCATCTTCCTAATGAGATAC-AGAGAAGTATA
*
376684 CCAAATC
178 CCAACTC
376691 AA
1 AA
376693 CGACACCAAA
Statistics
Matches: 323, Mismatches: 46, Indels: 26
0.82 0.12 0.07
Matches are distributed among these distances:
184 164 0.51
185 1 0.00
191 1 0.00
193 1 0.00
194 1 0.00
196 1 0.00
199 1 0.00
200 3 0.01
201 149 0.46
202 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (184 bp):
AATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAGC
TTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCTTGATGAGGTACAGAGAAGCGGATT
GAAACAAGCGAGGCGGTCATCTTCCTAATGAGATACAGAGAAGTATACCAACTC
Found at i:384087 original size:28 final size:28
Alignment explanation
Indices: 384047--384100 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
384037 GATATCTGAT
384047 TTACTCCCTATTGACCCAAAGGTCATGC
1 TTACTCCCTATTGACCCAAAGGTCATGC
384075 TTACTCCCTATTGACCCAAAGGTCAT
1 TTACTCCCTATTGACCCAAAGGTCAT
384101 AATGCTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30
Consensus pattern (28 bp):
TTACTCCCTATTGACCCAAAGGTCATGC
Found at i:386790 original size:50 final size:50
Alignment explanation
Indices: 386641--387223 Score: 219
Period size: 50 Copynumber: 11.6 Consensus size: 50
386631 GAATTACGGT
* * * * * *
386641 AGCAAATCTT-TATTTCTCTGAAGTTATAGTAGAGAAAGAAGAGGCTACAAA
1 AGCAAATCTTATA-TCCT-TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAA
* * * * * ***
386692 ACCAAAACCTATACCCCTGAAGTTGTAGTGG-GTTGGAT-AGAGCTACAAA
1 AGCAAATCTTATATCCTTGAAGTTGTAGTGGAGCAAGATGA-AGCTACAAA
* * * *
386741 AGCAAATCTTATTTACTTGAAGTTGCAATGGAGCAAGATGAAGCTACAAA
1 AGCAAATCTTATATCCTTGAAGTTGTAGTGGAGCAAGATGAAGCTACAAA
* * * * *** *
386791 ATCAAAT-TCTATACCCCTGAAGTTGTAGTAG-GTTGGAT-AGATCTACAAA
1 AGCAAATCT-TATATCCTTGAAGTTGTAGTGGAGCAAGATGA-AGCTACAAA
*
386840 AGCAAATCTTTATCTCCTTGAAGTTGTAGTGGAGCAAGATGAAGCTACAAA
1 AGCAAATC-TTATATCCTTGAAGTTGTAGTGGAGCAAGATGAAGCTACAAA
* * * * * * *
386891 ATCAAAT-TCTATACCCCTGAAGTTGCAGTGG-GTCGAA-TTAAAGCTACGAA
1 AGCAAATCT-TATATCCTTGAAGTTGTAGTGGAG-C-AAGATGAAGCTACAAA
* * * * *
386941 AGAAAATCTTAT-CCCTCTGAAGTTGCAGTAGAG-ACATATGAAGCTACAAA
1 AGCAAATCTTATATCCT-TGAAGTTGTAGTGGAGCA-AGATGAAGCTACAAA
* * * * * * * *
386991 ATCAAATCCTATACCCTTAAAGTTGTAGTAGG-TC-GGATTGAAGCTATAGA
1 AGCAAATCTTATATCCTTGAAGTTGTAGT-GGAGCAAGA-TGAAGCTACAAA
* * * ** *
387041 AGCAAATCTTTATCTCCTTAAAGTTGCAGTGGAGCAAGATG-AGACTGTAAC
1 AGCAAATC-TTATATCCTTGAAGTTGTAGTGGAGCAAGATGAAG-CTACAAA
* * * * * * * * * *
387092 ACCAAATCCTATATCCCTGAAGTTGCAATGG-GTTGAA-TTGAAGTTATAGA
1 AGCAAATCTTATATCCTTGAAGTTGTAGTGGAG--CAAGATGAAGCTACAAA
* * * * * ** *
387142 AGCAAATTTTATCTCCTTGAAGATGCAGTGG-GTCAAGATGAAGTTATGAC
1 AGCAAATCTTATATCCTTGAAGTTGTAGTGGAG-CAAGATGAAGCTACAAA
* * *
387192 GGCAAGTTTTATATCCTTGAAGTTGTAGTGGA
1 AGCAAATCTTATATCCTTGAAGTTGTAGTGGA
387224 TTGGATTAAA
Statistics
Matches: 390, Mismatches: 111, Indels: 62
0.69 0.20 0.11
Matches are distributed among these distances:
48 3 0.01
49 63 0.16
50 247 0.63
51 72 0.18
52 5 0.01
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (50 bp):
AGCAAATCTTATATCCTTGAAGTTGTAGTGGAGCAAGATGAAGCTACAAA
Found at i:386907 original size:100 final size:100
Alignment explanation
Indices: 386641--387184 Score: 546
Period size: 100 Copynumber: 5.4 Consensus size: 100
386631 GAATTACGGT
* ** * * * * * *
386641 AGCAAATCTTTAT-TTCTCTGAAGTTATAGTAGAGAAAGAAGAGGCTACAAAACCAAAACCTATA
1 AGCAAATCTTTATCTCCT-TGAAGTTGCAGTGGAGCAAGATGAAGCTACAAAATCAAATCCTATA
386705 CCCCTGAAGTTGTAGTGGGTTGGATAGAGCTACAAA
65 CCCCTGAAGTTGTAGTGGGTTGGATAGAGCTACAAA
* * * *
386741 AGCAAATC-TTATTTACTTGAAGTTGCAATGGAGCAAGATGAAGCTACAAAATCAAATTCTATAC
1 AGCAAATCTTTATCTCCTTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAAATCAAATCCTATAC
* *
386805 CCCTGAAGTTGTAGTAGGTTGGATAGATCTACAAA
66 CCCTGAAGTTGTAGTGGGTTGGATAGAGCTACAAA
* *
386840 AGCAAATCTTTATCTCCTTGAAGTTGTAGTGGAGCAAGATGAAGCTACAAAATCAAATTCTATAC
1 AGCAAATCTTTATCTCCTTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAAATCAAATCCTATAC
* * * * *
386905 CCCTGAAGTTGCAGTGGGTCGAATTAAAGCTACGAA
66 CCCTGAAGTTGTAGTGGGTTGGA-TAGAGCTACAAA
* * *
386941 AGAAAATC-TTATC-CCTCTGAAGTTGCAGTAGAG-ACATATGAAGCTACAAAATCAAATCCTAT
1 AGCAAATCTTTATCTCCT-TGAAGTTGCAGTGGAGCA-AGATGAAGCTACAAAATCAAATCCTAT
* * * * * * *
387003 ACCCTTAAAGTTGTAGTAGGTCGGATTGAAGCTATAGA
64 ACCCCTGAAGTTGTAGTGGGTTGGATAG-AGCTACAAA
* ** * *
387041 AGCAAATCTTTATCTCCTTAAAGTTGCAGTGGAGCAAGATG-AGACTGTAACACCAAATCCTATA
1 AGCAAATCTTTATCTCCTTGAAGTTGCAGTGGAGCAAGATGAAG-CTACAAAATCAAATCCTATA
* * * * * * * *
387105 TCCCTGAAGTTGCAATGGGTTGAATTGAAGTTATAGA
65 CCCCTGAAGTTGTAGTGGGTTGGATAG-AGCTACAAA
*
387142 AGCAAAT-TTTATCTCCTTGAAGATGCAGTGG-GTCAAGATGAAG
1 AGCAAATCTTTATCTCCTTGAAGTTGCAGTGGAG-CAAGATGAAG
387185 TTATGACGGC
Statistics
Matches: 374, Mismatches: 58, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
99 88 0.24
100 190 0.51
101 92 0.25
102 4 0.01
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (100 bp):
AGCAAATCTTTATCTCCTTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAAATCAAATCCTATAC
CCCTGAAGTTGTAGTGGGTTGGATAGAGCTACAAA
Found at i:387220 original size:201 final size:200
Alignment explanation
Indices: 386684--387170 Score: 511
Period size: 201 Copynumber: 2.4 Consensus size: 200
386674 GAAAGAAGAG
* * * * * * *
386684 GCTACAAAACCAAAACCTATACCCCTGAAGTTGTAGTGGGTTGGA-TAGAGCTACA-AAAGCAAA
1 GCTACAAAACCAAATCCTATACCCCTGAAGTTGCAATGGGTCGAATTAAAGCTA-AGAAAGAAAA
** * * * * * *
386747 TCTTATTTACT-TGAAGTTGCAATGGAG-CAAGATGAAGCTACAAAATCAAATTCTATACCCCTG
65 TCTTA-TCCCTCTGAAGATGCAGTAGAGAC-AGATGAAGCTACAAAAGCAAATCCTATACCCTTG
* * * *
386810 AAGTTGTAGTAGGTTGGATAGATCTACAAAAGCAAATCTTTATCTCCTTGAAGTTGTAGTGGAGC
128 AAGTTGTAGTAGGTCGGATAGAGCTACAAAAGCAAATCTTTATCTCCTTAAAGTTGCAGTGGAGC
386875 AAGATGAA
193 AAGATGAA
* * * *
386883 GCTACAAAATCAAATTCTATACCCCTGAAGTTGCAGTGGGTCGAATTAAAGCTACGAAAGAAAAT
1 GCTACAAAACCAAATCCTATACCCCTGAAGTTGCAATGGGTCGAATTAAAGCTAAGAAAGAAAAT
* * * *
386948 CTTATCCCTCTGAAGTTGCAGTAGAGACATATGAAGCTACAAAATCAAATCCTATACCCTTAAAG
66 CTTATCCCTCTGAAGATGCAGTAGAGACAGATGAAGCTACAAAAGCAAATCCTATACCCTTGAAG
* * *
387013 TTGTAGTAGGTCGGATTGAAGCTATAGAAGCAAATCTTTATCTCCTTAAAGTTGCAGTGGAGCAA
131 TTGTAGTAGGTCGGATAG-AGCTACAAAAGCAAATCTTTATCTCCTTAAAGTTGCAGTGGAGCAA
387078 GATG-A
195 GATGAA
** * * * * * *
387083 GACTGTAACACCAAATCCTATATCCCTGAAGTTGCAATGGGTTGAATTGAAGTTATAG-AAGCAA
1 G-CTACAAAACCAAATCCTATACCCCTGAAGTTGCAATGGGTCGAATTAAAGCTA-AGAAAGAAA
*
387147 ATTTTATCTCCT-TGAAGATGCAGT
64 ATCTTATC-CCTCTGAAGATGCAGT
387171 GGGTCAAGAT
Statistics
Matches: 242, Mismatches: 38, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
199 42 0.17
200 84 0.35
201 112 0.46
202 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (200 bp):
GCTACAAAACCAAATCCTATACCCCTGAAGTTGCAATGGGTCGAATTAAAGCTAAGAAAGAAAAT
CTTATCCCTCTGAAGATGCAGTAGAGACAGATGAAGCTACAAAAGCAAATCCTATACCCTTGAAG
TTGTAGTAGGTCGGATAGAGCTACAAAAGCAAATCTTTATCTCCTTAAAGTTGCAGTGGAGCAAG
ATGAA
Found at i:388804 original size:20 final size:20
Alignment explanation
Indices: 388771--388814 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
388761 TCCTTCTGCC
388771 TTTTTGATCTTTTTAATTTAA
1 TTTTTGATCTTTTTAATTT-A
*
388792 TTTTTTATC-TTTTAATTTA
1 TTTTTGATCTTTTTAATTTA
388811 TTTT
1 TTTT
388815 AATTTTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 9 0.41
21 8 0.36
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTTGATCTTTTTAATTTA
Found at i:388835 original size:25 final size:26
Alignment explanation
Indices: 388781--388838 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
388771 TTTTTGATCT
* * * *
388781 TTTTAATTTAATTTTTTATCTTTTAA
1 TTTTATTTTAATTTTATATCCTTCAA
388807 -TTTATTTTAATTTTAT-TCCTTCAA
1 TTTTATTTTAATTTTATATCCTTCAA
388831 TTTTATTT
1 TTTTATTT
388839 GCTTTGTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 6 0.22
25 21 0.78
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (26 bp):
TTTTATTTTAATTTTATATCCTTCAA
Found at i:389075 original size:17 final size:16
Alignment explanation
Indices: 389030--389077 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
389020 ATTTACCATT
389030 TTTTATT-TTTATTTTA
1 TTTTATTATTTA-TTTA
*
389046 TTTTATTACTTATTTA
1 TTTTATTATTTATTTA
*
389062 TTTTGTTAATTTATTT
1 TTTTATT-ATTTATTT
389078 TTAGCATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTTATTATTTATTTA
Found at i:389205 original size:15 final size:16
Alignment explanation
Indices: 389187--389224 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
389177 TTTATTATTA
*
389187 TTATTTGTA-TTGCAT
1 TTATTTATATTTGCAT
389202 TTA-TTATATTTGCAT
1 TTATTTATATTTGCAT
389217 TTATTTAT
1 TTATTTAT
389225 TGTTATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 4 0.20
15 12 0.60
16 4 0.20
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.63
Consensus pattern (16 bp):
TTATTTATATTTGCAT
Found at i:389225 original size:14 final size:14
Alignment explanation
Indices: 389196--389238 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
389186 ATTATTTGTA
389196 TTGCATTTATTATAT
1 TTGCATTTATT-TAT
389211 TTGCATTTATTTA-
1 TTGCATTTATTTAT
*
389224 TTGTTATTTATTTAT
1 TTG-CATTTATTTAT
389239 CTTTTCTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 3 0.12
14 11 0.44
15 11 0.44
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (14 bp):
TTGCATTTATTTAT
Found at i:390839 original size:24 final size:24
Alignment explanation
Indices: 390807--390883 Score: 72
Period size: 24 Copynumber: 3.4 Consensus size: 24
390797 ATTCGCATAC
*
390807 AAGCTACCATGTAGGTTGTGGACG
1 AAGCCACCATGTAGGTTGTGGACG
** *
390831 AAGCCACCA---AATTTGTAGAC-
1 AAGCCACCATGTAGGTTGTGGACG
**
390851 AAGCTGCCATGTAGGTTGTGGACG
1 AAGCCACCATGTAGGTTGTGGACG
390875 AAGCCACCA
1 AAGCCACCA
390884 AATTTGCATT
Statistics
Matches: 38, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
20 7 0.18
21 8 0.21
23 8 0.21
24 15 0.39
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (24 bp):
AAGCCACCATGTAGGTTGTGGACG
Found at i:390903 original size:44 final size:44
Alignment explanation
Indices: 390783--390903 Score: 179
Period size: 44 Copynumber: 2.8 Consensus size: 44
390773 TATATATGTC
* * *
390783 GACGAAGTCACCAAATTCGCATACAAGCTACCATGTAGGTTGTG
1 GACGAAGCCACCAAATTTGCATACAAGCTGCCATGTAGGTTGTG
* *
390827 GACGAAGCCACCAAATTTGTAGACAAGCTGCCATGTAGGTTGTG
1 GACGAAGCCACCAAATTTGCATACAAGCTGCCATGTAGGTTGTG
* *
390871 GACGAAGCCACCAAATTTGCATTCAAGATGCCA
1 GACGAAGCCACCAAATTTGCATACAAGCTGCCA
390904 AATCTTCCTC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 68 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.21
Consensus pattern (44 bp):
GACGAAGCCACCAAATTTGCATACAAGCTGCCATGTAGGTTGTG
Found at i:401262 original size:37 final size:36
Alignment explanation
Indices: 401221--401329 Score: 159
Period size: 37 Copynumber: 3.0 Consensus size: 36
401211 TGCTATGGCA
*
401221 AAGATATATATATATAATAAGTATTAGAAATATATAT
1 AAGATATA-AAATATAATAAGTATTAGAAATATATAT
401258 AAGATA-AAAATATAATAAGTATTAGAAATATATAT
1 AAGATATAAAATATAATAAGTATTAGAAATATATAT
*
401293 AAAAGATA-AAAATATAATAAGTATTAAAAATATATAT
1 --AAGATATAAAATATAATAAGTATTAGAAATATATAT
401330 TGATGCTGGA
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
35 27 0.40
36 1 0.01
37 40 0.59
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (36 bp):
AAGATATAAAATATAATAAGTATTAGAAATATATAT
Found at i:401271 original size:35 final size:36
Alignment explanation
Indices: 401232--401329 Score: 171
Period size: 37 Copynumber: 2.7 Consensus size: 36
401222 AGATATATAT
401232 ATATAATAAGTATTAGAAATATATAT-AAGATAAAA
1 ATATAATAAGTATTAGAAATATATATAAAGATAAAA
401267 ATATAATAAGTATTAGAAATATATATAAAAGATAAAA
1 ATATAATAAGTATTAGAAATATATAT-AAAGATAAAA
*
401304 ATATAATAAGTATTAAAAATATATAT
1 ATATAATAAGTATTAGAAATATATAT
401330 TGATGCTGGA
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
35 26 0.43
37 34 0.57
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (36 bp):
ATATAATAAGTATTAGAAATATATATAAAGATAAAA
Found at i:404664 original size:25 final size:23
Alignment explanation
Indices: 404623--404668 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
404613 TCAATTAGGG
404623 AATTATTGTTTAGTTTTAATTCT
1 AATTATTGTTTAGTTTTAATTCT
*
404646 AATTATCTTTTTAGATTTTAATT
1 AATTAT-TGTTTAG-TTTTAATT
404669 TGGATCCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (23 bp):
AATTATTGTTTAGTTTTAATTCT
Found at i:410827 original size:17 final size:17
Alignment explanation
Indices: 410795--410828 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
410785 TTAGTGCCTT
* *
410795 GATTTTTCGTCTTTTAA
1 GATTTTTCCTCGTTTAA
410812 GATTTTTCCTCGTTTAA
1 GATTTTTCCTCGTTTAA
410829 TGTTGTTATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.15, G:0.12, T:0.56
Consensus pattern (17 bp):
GATTTTTCCTCGTTTAA
Found at i:414439 original size:319 final size:319
Alignment explanation
Indices: 413549--414503 Score: 1601
Period size: 318 Copynumber: 3.0 Consensus size: 319
413539 TCCAGTCTGA
*
413549 TATAACCAACTGGTATGGACAGAGACAGCATGATTCTTATGAAAGGACACCTGTACAATTTGGAA
1 TATAACCAACTGGTATGGACAGAGACAACATGATTCTTATGAAAGGACACCTGTACAATTTGGAA
*
413614 GAATATAAATATTCACAAGG-AA-AGAAAAAAAGGGAGTCTTTTTCGTGCATTATCTTCTTCAAC
66 GAATATAAATATTCACAAGGAAAGAGAAAAAAAGGGAGTCTTTTTCATGCATTATCTTCTTCAAC
** * * *
413677 TTATCCTTTGAAGCTTTTGTATATGGCGACTTAAGTCTCCTACGGCTGAACTGACGTGAAAGGGA
131 TTATCCTTTGAAGCTTTTGGCTATGGCGGCTTAAGTCTCCTACGGGTGAACCGACGTGAAAGGGA
* * * *
413742 TGCAGATCATCTCTTGATGAGGAGCCCTGAGTGCGACACAAGAGGGAATTAAGAGATCAAGTTGA
196 TGCAGATCAACTCTTGACGAGGAGCCTTGAGTGCGACACAAGAGGGAATTAAGAGATCAAGTCGA
* * * *
413807 GAGTGTCTAGGAATAGTATTCTCCACTTGTTTCATTTATATTTATTTTCTAAACGCTGG
261 GATTGTCTAGGAATAGTATTCTCCACTTGTTTCTTTTATATTTCTTTTCTAAACGTTGG
*
413866 TATAACCAACTAGTATGGACAGAGACAACATGATTCTTATGAAAGGACACCTGTACAATTTGGAA
1 TATAACCAACTGGTATGGACAGAGACAACATGATTCTTATGAAAGGACACCTGTACAATTTGGAA
*
413931 GAATATAAATATTCACAAGGAAAGAG-AAAAAAGGGAGTCTTTTTCATGCACTATCTTCTTCAAC
66 GAATATAAATATTCACAAGGAAAGAGAAAAAAAGGGAGTCTTTTTCATGCATTATCTTCTTCAAC
* * *
413995 TTATCCTGTGAAGCTTTTGGCTATGACGGCTTAAGTCTCCTACGGGTGAACCGACGTGAAAAGGA
131 TTATCCTTTGAAGCTTTTGGCTATGGCGGCTTAAGTCTCCTACGGGTGAACCGACGTGAAAGGGA
* *
414060 TGCAGATCAACTCTTGACGAGGAGCCTTGAGTGCGACACAAGAAGGAATTGAGAGATCAAGTCGA
196 TGCAGATCAACTCTTGACGAGGAGCCTTGAGTGCGACACAAGAGGGAATTAAGAGATCAAGTCGA
* * *
414125 GATTGTGTAGGAAGAGTATTCTCCACTTATTTCTTTTATATTTCTTTTCTAAACGTTGG
261 GATTGTCTAGGAATAGTATTCTCCACTTGTTTCTTTTATATTTCTTTTCTAAACGTTGG
* *
414184 TATAACCAACTGGTATGGACAGAGACAACATGATTCTTATGAAAGGACTCATGTACAATTTGGAA
1 TATAACCAACTGGTATGGACAGAGACAACATGATTCTTATGAAAGGACACCTGTACAATTTGGAA
414249 GAATATAAATATTCACAAGGAAAGAGAAAAAAAGGGAGTCTTTTTCATGCATTATCTTCTTCAAC
66 GAATATAAATATTCACAAGGAAAGAGAAAAAAAGGGAGTCTTTTTCATGCATTATCTTCTTCAAC
*
414314 TTATCCTTTGAAGCTTTTGGCTATGGCGGCTTAAGTCTCCTACGGGTGAACCGACATGAAAGGGA
131 TTATCCTTTGAAGCTTTTGGCTATGGCGGCTTAAGTCTCCTACGGGTGAACCGACGTGAAAGGGA
* * *
414379 TGCAGATCAGCTTTTGACGAGGAGCCTTGAGTGTGACACAAGAGGGAATTAAGAGATCAAGTCGA
196 TGCAGATCAACTCTTGACGAGGAGCCTTGAGTGCGACACAAGAGGGAATTAAGAGATCAAGTCGA
*
414444 GATTGTCTAGGAATAGTATTCTCCACTTGTTTCTTTTATATTTCTTTTCTAAAAGTTGG
261 GATTGTCTAGGAATAGTATTCTCCACTTGTTTCTTTTATATTTCTTTTCTAAACGTTGG
414503 T
1 T
414504 GATTACTTTC
Statistics
Matches: 593, Mismatches: 42, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
317 83 0.14
318 294 0.50
319 216 0.36
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (319 bp):
TATAACCAACTGGTATGGACAGAGACAACATGATTCTTATGAAAGGACACCTGTACAATTTGGAA
GAATATAAATATTCACAAGGAAAGAGAAAAAAAGGGAGTCTTTTTCATGCATTATCTTCTTCAAC
TTATCCTTTGAAGCTTTTGGCTATGGCGGCTTAAGTCTCCTACGGGTGAACCGACGTGAAAGGGA
TGCAGATCAACTCTTGACGAGGAGCCTTGAGTGCGACACAAGAGGGAATTAAGAGATCAAGTCGA
GATTGTCTAGGAATAGTATTCTCCACTTGTTTCTTTTATATTTCTTTTCTAAACGTTGG
Found at i:422550 original size:21 final size:21
Alignment explanation
Indices: 422512--422551 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
422502 ATCTGCTATT
**
422512 GAGGAGGAAGTTGATGTTGGA
1 GAGGAGGAAGTCCATGTTGGA
*
422533 GAGGAGGAAGTCCTTGTTG
1 GAGGAGGAAGTCCATGTTG
422552 AAGAAGTGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.05, G:0.45, T:0.25
Consensus pattern (21 bp):
GAGGAGGAAGTCCATGTTGGA
Found at i:432202 original size:17 final size:17
Alignment explanation
Indices: 432180--432213 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
432170 CTCGGTCTAG
432180 CCGCACAATGGCACAAC
1 CCGCACAATGGCACAAC
* *
432197 CCGCACATTGTCACAAC
1 CCGCACAATGGCACAAC
432214 TCACATATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.41, G:0.15, T:0.12
Consensus pattern (17 bp):
CCGCACAATGGCACAAC
Found at i:433905 original size:25 final size:25
Alignment explanation
Indices: 433835--433908 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
433825 ATCAGAGATA
* *
433835 GCCACAAAGGTGTCCTTTACAGATTT
1 GCCACAAAGGCGTCCTTTA-ACATTT
*
433861 GCCACAAAGGC-TCTTATTTAACATTT
1 GCCACAAAGGCGTC--CTTTAACATTT
*
433887 GCCACAAGGGCGTCCTTTAACA
1 GCCACAAAGGCGTCCTTTAACA
433909 GAGATAGCTA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
25 9 0.22
26 25 0.62
27 6 0.15
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (25 bp):
GCCACAAAGGCGTCCTTTAACATTT
Found at i:434073 original size:28 final size:29
Alignment explanation
Indices: 433982--434073 Score: 100
Period size: 28 Copynumber: 3.2 Consensus size: 29
433972 GCACACATGC
* * *
433982 TCACTTTTAATAAAATCAGCCACTAAGGCT
1 TCAC-TTTAATAGATTCAGCCACAAAGGCT
* * *
434012 TCA-TTTAATAGATTTAGCGATAAAGGCT
1 TCACTTTAATAGATTCAGCCACAAAGGCT
434040 TC-CTTTAATAGATTCAGCCACAAAGG-T
1 TCACTTTAATAGATTCAGCCACAAAGGCT
434067 TCACTTT
1 TCACTTT
434074 TCGTAAACTA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
27 3 0.06
28 45 0.88
30 3 0.06
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.34
Consensus pattern (29 bp):
TCACTTTAATAGATTCAGCCACAAAGGCT
Found at i:434735 original size:77 final size:77
Alignment explanation
Indices: 434608--434764 Score: 278
Period size: 77 Copynumber: 2.0 Consensus size: 77
434598 ATTCTTCACC
*
434608 AAATCAACATATTGCACTTGTATAACATACATTTTCATTTCACAAATTAGTCATTTAGTATAAAA
1 AAATCAACATATTGCACCTGTATAACATACATTTTCATTTCACAAATTAGTCATTTAGTATAAAA
*
434673 TAGTTTATAACA
66 GAGTTTATAACA
* *
434685 AAATCAACATATTGCACCTGTATAACTTACGTTTTCATTTCACAAATTAGTCATTTAGTATAAAA
1 AAATCAACATATTGCACCTGTATAACATACATTTTCATTTCACAAATTAGTCATTTAGTATAAAA
434750 GAGTTTATAACA
66 GAGTTTATAACA
434762 AAA
1 AAA
434765 GCATATTTCC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (77 bp):
AAATCAACATATTGCACCTGTATAACATACATTTTCATTTCACAAATTAGTCATTTAGTATAAAA
GAGTTTATAACA
Found at i:434747 original size:38 final size:38
Alignment explanation
Indices: 434627--434747 Score: 97
Period size: 38 Copynumber: 3.2 Consensus size: 38
434617 TATTGCACTT
*
434627 GTATAACATACATTTTCATTTCACAAATTAGTCATTTA
1 GTATAACATACGTTTTCATTTCACAAATTAGTCATTTA
* ** * **
434665 GTATAAAATA-GTTTATAACAAAATCAACATATT-G-CACCT-
1 GTATAACATACGTTT-T--C-ATTTC-ACAAATTAGTCATTTA
*
434704 GTATAACTTACGTTTTCATTTCACAAATTAGTCATTTA
1 GTATAACATACGTTTTCATTTCACAAATTAGTCATTTA
434742 GTATAA
1 GTATAA
434748 AAGAGTTTAT
Statistics
Matches: 60, Mismatches: 14, Indels: 18
0.65 0.15 0.20
Matches are distributed among these distances:
35 6 0.10
36 4 0.07
37 7 0.12
38 16 0.27
39 9 0.15
40 8 0.13
41 4 0.07
42 6 0.10
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (38 bp):
GTATAACATACGTTTTCATTTCACAAATTAGTCATTTA
Found at i:435948 original size:28 final size:28
Alignment explanation
Indices: 435905--436032 Score: 87
Period size: 28 Copynumber: 4.5 Consensus size: 28
435895 TTTTTATCAT
* * * *
435905 AGATAACCACAGAGGCGTCCTTGCACAA
1 AGATAGCCACAAAGGCATCCTTGAACAA
*
435933 AGATAGCCACAAAGGCATCATTGAACAA
1 AGATAGCCACAAAGGCATCCTTGAACAA
* * * * *
435961 CAGAAAGCCATAGAGGCATCCTTAAATAA
1 -AGATAGCCACAAAGGCATCCTTGAACAA
* * ** *
435990 AGATGGCCAGAAAGGTGTCCTT-AAGAAA
1 AGATAGCCACAAAGGCATCCTTGAA-CAA
*
436018 AGATAGCCATAAAGG
1 AGATAGCCACAAAGG
436033 AATTCCCGTC
Statistics
Matches: 78, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
27 2 0.03
28 54 0.69
29 22 0.28
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (28 bp):
AGATAGCCACAAAGGCATCCTTGAACAA
Found at i:436308 original size:56 final size:55
Alignment explanation
Indices: 436217--436365 Score: 190
Period size: 56 Copynumber: 2.7 Consensus size: 55
436207 CATACGATAT
* *
436217 CATACCCACCATGACTAGATCTTACACTATATGGTCTCCATTTCCCCATATGATGC
1 CATAGCCACCATGACTAG-TCTTACACTATATGGTCTCCATTTCCCCATATGAAGC
* * * *
436273 CATTGCCACCATGACTAAGTCTTACACTATATGGTCTTCGTTTCCCCATATGAAGT
1 CATAGCCACCATGACT-AGTCTTACACTATATGGTCTCCATTTCCCCATATGAAGC
* * *
436329 CATAGTCACCATGAATTGGTCTTACACTATATGGTCT
1 CATAGCCACCATG-ACTAGTCTTACACTATATGGTCT
436366 TGGATTGTCA
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
56 77 0.95
57 4 0.05
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (55 bp):
CATAGCCACCATGACTAGTCTTACACTATATGGTCTCCATTTCCCCATATGAAGC
Found at i:449293 original size:15 final size:16
Alignment explanation
Indices: 449261--449297 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
449251 AAAGATGGCC
*
449261 AGAAGAAGAAGAATGA
1 AGAAGAAGAAGAAGGA
449277 AGAAGAAG-AGAAGGA
1 AGAAGAAGAAGAAGGA
449292 AGAAGA
1 AGAAGA
449298 GAATGAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (16 bp):
AGAAGAAGAAGAAGGA
Found at i:449765 original size:17 final size:18
Alignment explanation
Indices: 449743--449784 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
449733 ATAGTTTGCA
449743 TGCATTTT-TATTGTCAC
1 TGCATTTTATATTGTCAC
* *
449760 TGCATTTTATTTTGTCAT
1 TGCATTTTATATTGTCAC
449778 TGCATTT
1 TGCATTT
449785 CTTTTGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.17, C:0.14, G:0.12, T:0.57
Consensus pattern (18 bp):
TGCATTTTATATTGTCAC
Found at i:449791 original size:17 final size:16
Alignment explanation
Indices: 449743--449791 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 16
449733 ATAGTTTGCA
449743 TGCATTTTTATTGTCAC
1 TGCATTTTT-TTGTCAC
*
449760 TGCATTTTATTTTGTCAT
1 TGCA-TTT-TTTTGTCAC
449778 TGCATTTCTTTTGT
1 TGCATTT-TTTTGT
449792 TAATTTAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 13 0.46
18 13 0.46
19 2 0.07
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.59
Consensus pattern (16 bp):
TGCATTTTTTTGTCAC
Found at i:456209 original size:27 final size:27
Alignment explanation
Indices: 456161--456214 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
456151 TGACTGAAAA
*
456161 AAAATGATTTACCACCATTGCTGCCAC
1 AAAATGATTTACCACCAGTGCTGCCAC
*
456188 AAAATGATATT-CCTCCAGTGCTGCCAC
1 AAAATGAT-TTACCACCAGTGCTGCCAC
456215 GAGCAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.26
Consensus pattern (27 bp):
AAAATGATTTACCACCAGTGCTGCCAC
Found at i:464053 original size:17 final size:18
Alignment explanation
Indices: 464003--464046 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
463993 GATATTTTCA
* *
464003 TGCATTTTTTTATTGTCCC
1 TGCATTTTATT-TTGTCAC
464022 TGCATTTTATTTTGTCAC
1 TGCATTTTATTTTGTCAC
464040 TGCATTT
1 TGCATTT
464047 CTTTTGTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.14, C:0.18, G:0.11, T:0.57
Consensus pattern (18 bp):
TGCATTTTATTTTGTCAC
Found at i:480858 original size:39 final size:38
Alignment explanation
Indices: 480740--480869 Score: 125
Period size: 39 Copynumber: 3.4 Consensus size: 38
480730 AGAGAAATAT
* * *
480740 TGATTTTACTGAATGCTTGCTCAAGTGAGCAAATCCAC
1 TGATTATACTGAATGCTTGCTCAAATGAGCATATCCAC
* * * * * *
480778 TGATTTTACTGAATGTTTGCTTAAATGAGAGATAACTAC
1 TGATTATACTGAATGCTTGCTCAAATGAG-CATATCCAC
* *
480817 TGATTATACTGAATGCTTACTCAAACGAGCATTATCCAC
1 TGATTATACTGAATGCTTGCTCAAATGAGCA-TATCCAC
* *
480856 TGAATATATTGAAT
1 TGATTATACTGAAT
480870 AAGATTTTTT
Statistics
Matches: 73, Mismatches: 17, Indels: 3
0.78 0.18 0.03
Matches are distributed among these distances:
38 27 0.37
39 46 0.63
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (38 bp):
TGATTATACTGAATGCTTGCTCAAATGAGCATATCCAC
Found at i:482427 original size:24 final size:24
Alignment explanation
Indices: 482400--482447 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
482390 TGATGCACCT
482400 CATGCTGCACCTCCTACCGTACCA
1 CATGCTGCACCTCCTACCGTACCA
* * *
482424 CATGTTGTACCTCCTACTGTACCA
1 CATGCTGCACCTCCTACCGTACCA
482448 TCTGTGGTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.40, G:0.12, T:0.27
Consensus pattern (24 bp):
CATGCTGCACCTCCTACCGTACCA
Found at i:482457 original size:24 final size:24
Alignment explanation
Indices: 482408--482461 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
482398 CTCATGCTGC
*
482408 ACCTCCTACCGTACCACATGTTGT
1 ACCTCCTACCGTACCACATGTGGT
*
482432 ACCTCCTACTGTACCATC-TGTGGT
1 ACCTCCTACCGTACCA-CATGTGGT
482456 ACCTCC
1 ACCTCC
482462 ATGATCGCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.19, C:0.39, G:0.13, T:0.30
Consensus pattern (24 bp):
ACCTCCTACCGTACCACATGTGGT
Found at i:493741 original size:3 final size:3
Alignment explanation
Indices: 493710--493756 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
493700 TTCATTTTCT
* * *
493710 TTA TTA TTC TTA GTA TTA -TA TTG TTA TTA TTA TTA TTA TTCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
493755 TT
1 TT
493757 TTGTGTGCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:496611 original size:17 final size:18
Alignment explanation
Indices: 496589--496622 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
496579 CTAAATTAAC
496589 AAAAT-AAATGCAATGAT
1 AAAATAAAATGCAATGAT
496606 AAAATAAAATGCAATGA
1 AAAATAAAATGCAATGA
496623 CAGTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (18 bp):
AAAATAAAATGCAATGAT
Found at i:497117 original size:19 final size:19
Alignment explanation
Indices: 497093--497129 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
497083 ACCAGGTATC
*
497093 AAAATTTTAGATCAAAAAT
1 AAAATTTCAGATCAAAAAT
*
497112 AAAATTTCAGTTCAAAAA
1 AAAATTTCAGATCAAAAA
497130 GTTTCAGACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAATTTCAGATCAAAAAT
Found at i:503118 original size:18 final size:17
Alignment explanation
Indices: 503095--503185 Score: 59
Period size: 18 Copynumber: 5.5 Consensus size: 17
503085 GGATTCAATG
503095 AAGAAAAATAAATAAAGA
1 AAGAAAAATAAA-AAAGA
503113 AAGAAAGAA-AAAAGAA-A
1 AAGAAA-AATAAAA-AAGA
503130 AAG-AAAATAAAAAAG-
1 AAGAAAAATAAAAAAGA
* *
503145 -AGAAAAAGAGAAAA-A
1 AAGAAAAATAAAAAAGA
* * *
503160 AAGGAAAAGAGAAAAACA
1 AAGAAAAATA-AAAAAGA
503178 AAGAAAAA
1 AAGAAAAA
503186 AAGGGAAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
14 2 0.03
15 13 0.22
16 14 0.24
17 9 0.15
18 19 0.32
19 2 0.03
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.03
Consensus pattern (17 bp):
AAGAAAAATAAAAAAGA
Found at i:503131 original size:8 final size:8
Alignment explanation
Indices: 503098--503200 Score: 73
Period size: 8 Copynumber: 12.2 Consensus size: 8
503088 TTCAATGAAG
*
503098 AAAAATAA
1 AAAAAGAA
*
503106 ATAAAGAA
1 AAAAAGAA
*
503114 AGAAAG-A
1 AAAAAGAA
503121 AAAAAGAA
1 AAAAAGAA
*
503129 AAAGAAAATA
1 AAA-AAGA-A
503139 AAAAAGAGA
1 AAAAAGA-A
503148 AAAAGAGAA
1 AAAA-AGAA
*
503157 AAAAAGGA
1 AAAAAGAA
*
503165 AAAGAGAAA
1 AAAAAG-AA
503174 AACAAAGAA
1 AA-AAAGAA
**
503183 AAAAAGGG
1 AAAAAGAA
503191 AAAAAGAA
1 AAAAAGAA
503199 AA
1 AA
503201 GGAGAGGTCG
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
7 6 0.08
8 35 0.47
9 23 0.31
10 10 0.14
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (8 bp):
AAAAAGAA
Found at i:503142 original size:12 final size:13
Alignment explanation
Indices: 503095--503200 Score: 63
Period size: 13 Copynumber: 7.5 Consensus size: 13
503085 GGATTCAATG
*
503095 AAGAAAAATAAATA
1 AAGAAAAAGAAA-A
503109 AAGAAAGAAAGAAAA
1 AAG-AA-AAAGAAAA
503124 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
503137 TAA-AAAAGAGAAAA
1 -AAGAAAA-AGAAAA
503151 AGAGAAAAAAAGGAAAA
1 A-AG--AAAAA-GAAAA
* *
503168 GAGAAAAACAAAGA
1 AAGAAAAAGAAA-A
* *
503182 AA-AAAAGGGAAA
1 AAGAAAAAGAAAA
503194 AAGAAAA
1 AAGAAAA
503201 GGAGAGGTCG
Statistics
Matches: 74, Mismatches: 7, Indels: 23
0.71 0.07 0.22
Matches are distributed among these distances:
12 3 0.04
13 26 0.35
14 21 0.28
15 6 0.08
16 9 0.12
17 9 0.12
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:503167 original size:26 final size:25
Alignment explanation
Indices: 503111--503200 Score: 92
Period size: 26 Copynumber: 3.5 Consensus size: 25
503101 AATAAATAAA
*
503111 GAAAGAAAGAAAAAAGA-AAAAGAAAA
1 GAAA-AAAGAAAAAAGAGAAAA-AAAG
*
503137 TAAAAAAGAGAAAAAGAGAAAAAAAG
1 GAAAAAAGA-AAAAAGAGAAAAAAAG
* *
503163 GAAAAGAGAAAAACAAAGAAAAAAAG
1 GAAAAAAGAAAAA-AGAGAAAAAAAG
*
503189 GGAAAAAGAAAA
1 GAAAAAAGAAAA
503201 GGAGAGGTCG
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
25 9 0.17
26 41 0.76
27 4 0.07
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.01
Consensus pattern (25 bp):
GAAAAAAGAAAAAAGAGAAAAAAAG
Found at i:503168 original size:36 final size:35
Alignment explanation
Indices: 503099--503200 Score: 104
Period size: 34 Copynumber: 2.9 Consensus size: 35
503089 TCAATGAAGA
*
503099 AAAATAAATAAAGAAAGAA-AG-AAAAAAGAAAAAG
1 AAAATAAA-AAAGAAAAAAGAGAAAAAAAGAAAAAG
*
503133 AAAATAAAAAAGAGAAAAAGAGAAAAAAAGGAAAAG
1 AAAATAAAAAAGA-AAAAAGAGAAAAAAAGAAAAAG
* **
503169 AGAAA-AACAAAGAAAAAA-AGGGAAAAAGAAAA
1 A-AAATAAAAAAGAAAAAAGAGAAAAAAAGAAAA
503201 GGAGAGGTCG
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
33 5 0.09
34 23 0.40
35 7 0.12
36 20 0.34
37 3 0.05
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (35 bp):
AAAATAAAAAAGAAAAAAGAGAAAAAAAGAAAAAG
Found at i:503173 original size:44 final size:43
Alignment explanation
Indices: 503110--503197 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 43
503100 AAATAAATAA
* *
503110 AGAAAGAAAGAAAAAAGAAAAAGAAA-ATAAAAAAGAGAAAAAG
1 AGAAAAAAAGAAAAAAGAAAAACAAAGA-AAAAAAGAGAAAAAG
* *
503153 AGAAAAAAAGGAAAAGAGAAAAACAAAGAAAAAAAGGGAAAAAG
1 AGAAAAAAA-GAAAAAAGAAAAACAAAGAAAAAAAGAGAAAAAG
503197 A
1 A
503198 AAAGGAGAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
43 8 0.21
44 30 0.77
45 1 0.03
ACGTcount: A:0.77, C:0.01, G:0.20, T:0.01
Consensus pattern (43 bp):
AGAAAAAAAGAAAAAAGAAAAACAAAGAAAAAAAGAGAAAAAG
Found at i:503180 original size:28 final size:26
Alignment explanation
Indices: 503149--503200 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
503139 AAAAAGAGAA
503149 AAAGAGAAAAAAAGGAAAAGAGAAAAAC
1 AAAGA-AAAAAAAGGAAAA-AGAAAAAC
*
503177 AAAGAAAAAAAGGGAAAAAGAAAA
1 AAAGAAAAAAAAGGAAAAAGAAAA
503201 GGAGAGGTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 6 0.26
27 12 0.52
28 5 0.22
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (26 bp):
AAAGAAAAAAAAGGAAAAAGAAAAAC
Found at i:504205 original size:50 final size:51
Alignment explanation
Indices: 504130--504867 Score: 431
Period size: 50 Copynumber: 14.9 Consensus size: 51
504120 TGAGACCGCG
* * *
504130 ACGGTGAATCCGATACCTTAA-AAGATGTGAAGGGAAAGGTTAAGG-CAGCA
1 ACGGTGAACCCGGTACC-TAAGAAGATGTGAAGGGAAAGGTTGAGGCCAGCA
** * * *
504180 ACGGCAAACCCAGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCA-TA
1 ACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCAGCA
** ** ** * * * *
504230 ACGACGAACCCAATACCTAAGAAGATGTGTTGAGAAAGGATGAGGTC-GTA
1 ACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCAGCA
* * * * *
504280 ACGATAAACCCGGTACC-ATGAAGATGTAAAGGGAAAGGTTGAGGTC-GCA
1 ACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCAGCA
* * *
504329 ATGGTGAACCCGGTACCTAAGAAGATGTGATGGCAAAGGTTGAGGCCA-CA
1 ACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCAGCA
* *
504379 ACGGTGAACCCGGTACC-ATGAAGA-GATGAAGGGAAAGATTGAGGCCATG-A
1 ACGGTGAACCCGGTACCTAAGAAGATG-TGAAGGGAAAGGTTGAGGCCA-GCA
* * * *
504429 TA--GTGAATCCAGTACCTTAA-AAGATGTGATGGGAAAGGTTGAGGCCA-TA
1 -ACGGTGAACCCGGTACC-TAAGAAGATGTGAAGGGAAAGGTTGAGGCCAGCA
* * ** ** *
504478 ACGGTGAACTCGGTACC-ACGAAGATACGAAACGAAAGGTTGAGGCC-GTA
1 ACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCAGCA
* * * *
504527 ATGGCGAACCCGGTACC-AGGAAGA-GATGAAGGG-AAGGATTGAGG-CAGCG
1 ACGGTGAACCCGGTACCTAAGAAGATG-TGAAGGGAAAGG-TTGAGGCCAGCA
* * * * *
504576 ACTGTGAATCTGGCACCTTAA-AAGATGTGATGGGAAAGGTTGAGGCC-GCA
1 ACGGTGAACCCGGTACC-TAAGAAGATGTGAAGGGAAAGGTTGAGGCCAGCA
* * * * * * *
504626 ACAGCGAACCCGATATC-ATGAAGATATGAAGGGAAAGGTTGAGGCCA-TA
1 ACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCAGCA
* * * * * *
504675 ATGGTGATCCCGGTACCTAAGAAGATGTGATGGGAAAGATTGAGGTC-GTA
1 ACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCAGCA
** * * * * **
504725 ACGACGAACCTGGTACC-ATGAAGA-GATGAAAGG-AAGCATTGAGG-CAGGG
1 ACGGTGAACCCGGTACCTAAGAAGATG-TGAAGGGAAAG-GTTGAGGCCAGCA
* * * * * * *
504774 ACGATGAATCTGATACCTTAGAAGATGTGACGGGAAAGGTTGAGG-CTGCA
1 ACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCAGCA
* * * * * *
504824 ACGGCGAACCCGATACC-ATGAAGTTATGAAGGGAAAGCTTGAGG
1 ACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTGAGG
504868 TCGCAACAGC
Statistics
Matches: 528, Mismatches: 125, Indels: 71
0.73 0.17 0.10
Matches are distributed among these distances:
48 14 0.03
49 234 0.44
50 264 0.50
51 16 0.03
ACGTcount: A:0.35, C:0.16, G:0.32, T:0.17
Consensus pattern (51 bp):
ACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCAGCA
Found at i:504536 original size:148 final size:148
Alignment explanation
Indices: 504363--504719 Score: 441
Period size: 148 Copynumber: 2.4 Consensus size: 148
504353 ATGTGATGGC
* * * *
504363 AAAGGTTGAGGCCACAACGGTGAACCCGGTACCATGAAGAGATGAAGGGAAAGATTGAGGCCA-T
1 AAAGGTTGAGGCCATAATGGTGAACCCGGTACCAAGAAGAGATGAAGGGAAAGATTGAGG-CAGC
* * * * * *
504427 GA-TAGTGAATCCAGTACCTTAAAAGATGTGATGGGAAAGGTTGAGGCCATAACGGTGAACTCGG
65 GACT-GTGAATCCAGCACCTTAAAAGATGTGATGGGAAAGGTTGAGGCCACAACAGCGAACCCGA
504491 TACCACGAAGATACGAAACG
129 TACCACGAAGATACGAAACG
* * * *
504511 AAAGGTTGAGGCCGTAATGGCGAACCCGGTACCAGGAAGAGATGAAGGGAAGGATTGAGGCAGCG
1 AAAGGTTGAGGCCATAATGGTGAACCCGGTACCAAGAAGAGATGAAGGGAAAGATTGAGGCAGCG
** *
504576 ACTGTGAATCTGGCACCTTAAAAGATGTGATGGGAAAGGTTGAGGCCGCAACAGCGAACCCGATA
66 ACTGTGAATCCAGCACCTTAAAAGATGTGATGGGAAAGGTTGAGGCCACAACAGCGAACCCGATA
* * * **
504641 TCATGAAGATATGAAGGG
131 CCACGAAGATACGAAACG
* *
504659 AAAGGTTGAGGCCATAATGGTGATCCCGGTACCTAAGAAGATG-TGATGGGAAAGATTGAGG
1 AAAGGTTGAGGCCATAATGGTGAACCCGGTACC-AAGAAGA-GATGAAGGGAAAGATTGAGG
504720 TCGTAACGAC
Statistics
Matches: 178, Mismatches: 27, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
147 2 0.01
148 152 0.85
149 23 0.13
150 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.33, T:0.17
Consensus pattern (148 bp):
AAAGGTTGAGGCCATAATGGTGAACCCGGTACCAAGAAGAGATGAAGGGAAAGATTGAGGCAGCG
ACTGTGAATCCAGCACCTTAAAAGATGTGATGGGAAAGGTTGAGGCCACAACAGCGAACCCGATA
CCACGAAGATACGAAACG
Found at i:504613 original size:198 final size:191
Alignment explanation
Indices: 504192--504819 Score: 532
Period size: 198 Copynumber: 3.2 Consensus size: 191
504182 GGCAAACCCA
* *
504192 GTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCATAACGACGAACCCAATACCTAAGAAGATG
1 GTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCATAA-G-CGAA-CCAGTACCTAA-AAGATG
* * * * * * * *
504257 TGTTGAGAAAGGATGAGGTCGTAACGATAAACCCGGTACCATGAAGATGTAAAGGGAAAGGTTGA
62 TGATGGGAAAGGTTGAGGCCATAACGGTGAACCCGGTACCAAGAAGATG-AAA-GGAAAGGTTGA
* * * * *
504322 GGTCGCAATGGTGAACCCGGTACCTAAGAAGATG-TGATGGCAAAGG-TTGAGGCCA-CAACGGT
125 GGTCGTAATGGCGAACCCGGTACC-AAGAAGA-GATGAAGG-GAAGGATTGAGG-CAGCGAC-GT
* *
504384 GAACCCG
185 GAATCTG
* * * *
504391 GTACCAT-GAAGA-GATGAAGGGAAAGATTGAGGCCATGATAGTGAATCCAGTACCTTAAAAGAT
1 GTACCTTAGAAGATG-TGATGGGAAAGGTTGAGGCCAT-A-AGCGAA-CCAGTACC-TAAAAGAT
* * *
504454 GTGATGGGAAAGGTTGAGGCCATAACGGTGAACTCGGTACCACGAAGATACGAAACGAAAGGTTG
61 GTGATGGGAAAGGTTGAGGCCATAACGGTGAACCCGGTACCAAGAAGAT--GAAAGGAAAGGTTG
* *
504519 AGGCCGTAATGGCGAACCCGGTACCAGGAAGAGATGAAGGGAAGGATTGAGGCAGCGACTGTGAA
124 AGGTCGTAATGGCGAACCCGGTACCAAGAAGAGATGAAGGGAAGGATTGAGGCAGCGAC-GTGAA
504584 TCTG
188 TCTG
* * * * *
504588 GCACCTTAAAAGATGTGATGGGAAAGGTTGAGGCCGCA-ACAGCGAACCCGATATC-ATGAAGAT
1 GTACCTTAGAAGATGTGATGGGAAAGGTTGAGG-C-CATA-AGCGAACCAG-TACCTA-AAAGAT
* * * * ** *
504651 ATGAAGGGAAAGGTTGAGGCCATAATGGTGATCCCGGTACCTAAGAAGATGTGATGGGAAAGATT
61 GTGATGGGAAAGGTTGAGGCCATAACGGTGAACCCGGTACC-AAGAAGA--TGAAAGGAAAGGTT
* * * * * * *
504716 GAGGTCGTAACGACGAACCTGGTACCATGAAGAGATGAAAGGAAGCATTGAGGCAGGGACGATGA
123 GAGGTCGTAATGGCGAACCCGGTACCAAGAAGAGATGAAGGGAAGGATTGAGGCAGCGACG-TGA
504781 ATCTG
187 ATCTG
* *
504786 ATACCTTAGAAGATGTGACGGGAAAGGTTGAGGC
1 GTACCTTAGAAGATGTGATGGGAAAGGTTGAGGC
504820 TGCAACGGCG
Statistics
Matches: 351, Mismatches: 59, Indels: 40
0.78 0.13 0.09
Matches are distributed among these distances:
196 8 0.02
197 79 0.23
198 244 0.70
199 15 0.04
200 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.32, T:0.18
Consensus pattern (191 bp):
GTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCATAAGCGAACCAGTACCTAAAAGATGTGAT
GGGAAAGGTTGAGGCCATAACGGTGAACCCGGTACCAAGAAGATGAAAGGAAAGGTTGAGGTCGT
AATGGCGAACCCGGTACCAAGAAGAGATGAAGGGAAGGATTGAGGCAGCGACGTGAATCTG
Found at i:504648 original size:247 final size:248
Alignment explanation
Indices: 504188--504734 Score: 635
Period size: 247 Copynumber: 2.2 Consensus size: 248
504178 CAACGGCAAA
504188 CCCAGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCATAACGACGAACCCAATACCTAAGAA
1 CCCAGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCATAACGACGAACCCAATACCTAAGAA
** ** * * *
504253 GATGTGTTGAGAAAGGATGAGGTCGTAACGATAAACCCGGTACCATGAAGATGTAAAGGGAAAGG
66 GATACGTAAAGAAAGGATGAGGCCGTAACGACAAACCCGGTACCAGGAAGATGTAAAGGGAAAGG
* *
504318 TTGAGGTCGCAATGGTGAACCCGGTACCTAAGAAGATGTGATGGCAAAGGTTGAGGCCACAACGG
131 TTGAGGTCGCAATGGTGAACCCGGCACCTAAGAAGATGTGATGGCAAAGGTTGAGGCCACAACAG
* * *
504383 TGAACCCGGTACCATGAAGAGATGAAGGGAAAGATTGAGGCCATGATAGTGAAT
196 CGAACCCGATACCATGAAGAGATGAAGGGAAAGATTGAGGCCATAATAGTG-AT
** * ** *
504437 -CCAGTACCTTAA-AAGATGTGATGGGAAAGGTTGAGGCCATAACGGTGAACTCGGTACC-ACGA
1 CCCAGTACC-TAAGAAGATGTGATGGGAAAGGTTGAGGCCATAACGACGAACCCAATACCTAAGA
* * * * *
504499 AGATACG-AAACGAAAGGTTGAGGCCGTAATGGCGAACCCGGTACCAGGAAGA-GATGAAGGG-A
65 AGATACGTAAA-GAAAGGATGAGGCCGTAACGACAAACCCGGTACCAGGAAGATG-TAAAGGGAA
* * * *
504561 AGGATTGAGG-CAGCGACT-GTGAATCTGGCACCTTAA-AAGATGTGATGGGAAAGGTTGAGGCC
128 AGG-TTGAGGTC-GC-AATGGTGAACCCGGCACC-TAAGAAGATGTGATGGCAAAGGTTGAGGCC
* * * * *
504623 GCAACAGCGAACCCGATATCATGAAGATATGAAGGGAAAGGTTGAGGCCATAATGGTGAT
189 ACAACAGCGAACCCGATACCATGAAGAGATGAAGGGAAAGATTGAGGCCATAATAGTGAT
* * * *
504683 CCCGGTACCTAAGAAGATGTGATGGGAAAGATTGAGGTCGTAACGACGAACC
1 CCCAGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCATAACGACGAACC
504735 TGGTACCATG
Statistics
Matches: 250, Mismatches: 39, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
246 12 0.05
247 181 0.72
248 54 0.22
249 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.18
Consensus pattern (248 bp):
CCCAGTACCTAAGAAGATGTGATGGGAAAGGTTGAGGCCATAACGACGAACCCAATACCTAAGAA
GATACGTAAAGAAAGGATGAGGCCGTAACGACAAACCCGGTACCAGGAAGATGTAAAGGGAAAGG
TTGAGGTCGCAATGGTGAACCCGGCACCTAAGAAGATGTGATGGCAAAGGTTGAGGCCACAACAG
CGAACCCGATACCATGAAGAGATGAAGGGAAAGATTGAGGCCATAATAGTGAT
Found at i:504733 original size:99 final size:99
Alignment explanation
Indices: 504151--504867 Score: 454
Period size: 99 Copynumber: 7.2 Consensus size: 99
504141 GATACCTTAA
* * * ** * *
504151 AAGATGTGAAGGGAAAGGTTAAGG-CAGCAACGGCAAACCCAGTACCTAAGAAGATGTGATGGGA
1 AAGATATGAAGGGAAAGGTTGAGGCCA-TAACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGA
* * *
504215 AAGGTTGAGGCCATAACGACGAACCCAATACCTAAG
65 AAGGTTGAGGCCGTAACGACGAACCCGATACC-ATG
* ** * * * * * * * *
504251 AAGATGTGTTGAGAAAGGATGAGGTCGTAACGATAAACCCGGTACC-ATGAAGATGTAAAGGGAA
1 AAGATATGAAGGGAAAGGTTGAGGCCATAACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGAA
* * * ** * *
504315 AGGTTGAGGTCGCAATGGTGAACCCGGTACCTAAG
66 AGGTTGAGGCCGTAACGACGAACCCGATACC-ATG
* * * * *
504350 AAGATGTGATGGCAAAGGTTGAGGCCACAACGGTGAACCCGGTACC-ATGAAGA-GATGAAGGGA
1 AAGATATGAAGGGAAAGGTTGAGGCCATAACGGTGAACCCGGTACCTAAGAAGATG-TGAAGGGA
* * * * * *
504413 AAGATTGAGGCCATGATA-G-TGAATCC-AGTACCTTAA
65 AAGGTTGAGGCCGT-A-ACGACGAACCCGA-TACCAT-G
* * * * ** **
504449 AAGATGTGATGGGAAAGGTTGAGGCCATAACGGTGAACTCGGTACC-ACGAAGATACGAAACGAA
1 AAGATATGAAGGGAAAGGTTGAGGCCATAACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGAA
* * * *
504513 AGGTTGAGGCCGTAATGGCGAACCCGGTACCAGG
66 AGGTTGAGGCCGTAACGACGAACCCGATACCATG
* ** * * * * *
504547 AAGAGATGAAGGG-AAGGATTGAGG-CAGCGACTGTGAATCTGGCACCTTAA-AAGATGTGATGG
1 AAGATATGAAGGGAAAGG-TTGAGGCCA-TAACGGTGAACCCGGTACC-TAAGAAGATGTGAAGG
* *
504609 GAAAGGTTGAGGCCGCAAC-AGCGAACCCGATATCATG
63 GAAAGGTTGAGGCCGTAACGA-CGAACCCGATACCATG
* * *
504646 AAGATATGAAGGGAAAGGTTGAGGCCATAATGGTGATCCCGGTACCTAAGAAGATGTGATGGGAA
1 AAGATATGAAGGGAAAGGTTGAGGCCATAACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGAA
* * * *
504711 AGATTGAGGTCGTAACGACGAACCTGGTACCATG
66 AGGTTGAGGCCGTAACGACGAACCCGATACCATG
* * * ** * * * * * *
504745 AAGAGATGAAAGG-AAGCATTGAGG-CAGGGACGATGAATCTGATACCTTAGAAGATGTGACGGG
1 AAGATATGAAGGGAAAG-GTTGAGGCCA-TAACGGTGAACCCGGTACCTAAGAAGATGTGAAGGG
* * *
504808 AAAGGTTGAGGCTGCAACGGCGAACCCGATACCATG
64 AAAGGTTGAGGCCGTAACGACGAACCCGATACCATG
* *
504844 AAGTTATGAAGGGAAAGCTTGAGG
1 AAGATATGAAGGGAAAGGTTGAGG
504868 TCGCAACAGC
Statistics
Matches: 478, Mismatches: 117, Indels: 45
0.75 0.18 0.07
Matches are distributed among these distances:
97 7 0.01
98 39 0.08
99 383 0.80
100 47 0.10
101 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.32, T:0.17
Consensus pattern (99 bp):
AAGATATGAAGGGAAAGGTTGAGGCCATAACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGAA
AGGTTGAGGCCGTAACGACGAACCCGATACCATG
Found at i:504833 original size:198 final size:197
Alignment explanation
Indices: 504449--504867 Score: 552
Period size: 198 Copynumber: 2.1 Consensus size: 197
504439 AGTACCTTAA
* * * *
504449 AAGATGTGATGGGAAAGGTTGAGGCCATAACGGTGAACTCGGTACCACGAAGATACGAAACGAAA
1 AAGATATGAAGGGAAAGGTTGAGGCCATAACGGTGAACCCGGTACCAAGAAGATACGAAACGAAA
* * * * *
504514 GGTTGAGGCCGTAATGGCGAACCCGGTACCAGGAAGAGATGAAGGGAAGGATTGAGGCAGCGACT
66 GATTGAGGCCGTAACGACGAACCCGGTACCAGGAAGAGATGAAAGGAAGCATTGAGGCAGCGACT
* * *
504579 GTGAATCTGGCACCTTAAAAGATGTGATGGGAAAGGTTGAGGCCGCAACAGCGAACCCGATATCA
131 GTGAATCTGACACCTTAAAAGATGTGACGGGAAAGGTTGAGGCCGCAACAGCGAACCCGATACCA
504644 TG
196 TG
* * ** ***
504646 AAGATATGAAGGGAAAGGTTGAGGCCATAATGGTGATCCCGGTACCTAAGAAGATGTGATGGGAA
1 AAGATATGAAGGGAAAGGTTGAGGCCATAACGGTGAACCCGGTACC-AAGAAGATACGAAACGAA
* * * *
504711 AGATTGAGGTCGTAACGACGAACCTGGTACCATGAAGAGATGAAAGGAAGCATTGAGGCAGGGAC
65 AGATTGAGGCCGTAACGACGAACCCGGTACCAGGAAGAGATGAAAGGAAGCATTGAGGCAGCGAC
* * * *
504776 -GATGAATCTGATACCTTAGAAGATGTGACGGGAAAGGTTGAGGCTGCAACGGCGAACCCGATAC
130 TG-TGAATCTGACACCTTAAAAGATGTGACGGGAAAGGTTGAGGCCGCAACAGCGAACCCGATAC
504840 CATG
194 CATG
* *
504844 AAGTTATGAAGGGAAAGCTTGAGG
1 AAGATATGAAGGGAAAGGTTGAGG
504868 TCGCAACAGC
Statistics
Matches: 191, Mismatches: 29, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
197 42 0.22
198 149 0.78
ACGTcount: A:0.34, C:0.16, G:0.33, T:0.17
Consensus pattern (197 bp):
AAGATATGAAGGGAAAGGTTGAGGCCATAACGGTGAACCCGGTACCAAGAAGATACGAAACGAAA
GATTGAGGCCGTAACGACGAACCCGGTACCAGGAAGAGATGAAAGGAAGCATTGAGGCAGCGACT
GTGAATCTGACACCTTAAAAGATGTGACGGGAAAGGTTGAGGCCGCAACAGCGAACCCGATACCA
TG
Found at i:504895 original size:99 final size:98
Alignment explanation
Indices: 504510--504909 Score: 324
Period size: 99 Copynumber: 4.1 Consensus size: 98
504500 GATACGAAAC
* * * * * *
504510 GAAAGGTTGAGGCCGTAATGGCGAACCCGGTACCAGGAAGAGATGAAGGGAAGGATTGAGGCAGC
1 GAAAGGTTGAGGCCGCAACGGCGAACCCGATACCATGAAGAGATGAAGGGAAAGCTTGAGGCAGC
* * * * *
504575 GACTGTGAATCTGGCACCTTAAAAGATGTGATGG
66 AAC-GTGAACCTGGCACCCTAGAAGATGTGACGG
* * * *
504609 GAAAGGTTGAGGCCGCAACAGCGAACCCGATATCATGAAGATATGAAGGGAAAGGTTGAGGCCA-
1 GAAAGGTTGAGGCCGCAACGGCGAACCCGATACCATGAAGAGATGAAGGGAAAGCTTGAGG-CAG
* * * * * *
504673 TAATGGTGATCCCGGTA-CCTAAGAAGATGTGATGG
65 CAA-CGTGAACCTGGCACCCT-AGAAGATGTGACGG
* * * * * * *
504708 GAAAGATTGAGGTCGTAACGACGAACCTGGTACCATGAAGAGATGAAAGG-AAGCATTGAGGCAG
1 GAAAGGTTGAGGCCGCAACGGCGAACCCGATACCATGAAGAGATGAAGGGAAAGC-TTGAGGCAG
** * ** *
504772 GGACGATGAATCTGATACCTTAGAAGATGTGACGG
65 CAACG-TGAACCTGGCACCCTAGAAGATGTGACGG
* **
504807 GAAAGGTTGAGGCTGCAACGGCGAACCCGATACCATGAAGTTATGAAGGGAAAGCTTGAGGTC-G
1 GAAAGGTTGAGGCCGCAACGGCGAACCCGATACCATGAAGAGATGAAGGGAAAGCTTGAGG-CAG
* * * *
504871 CAACAGCGAACCTAGCACCCTAGAA-ACGCGACGG
65 CAAC-GTGAACCTGGCACCCTAGAAGATGTGACGG
504905 GAAAG
1 GAAAG
504910 ATTAAAGCAC
Statistics
Matches: 233, Mismatches: 58, Indels: 21
0.75 0.19 0.07
Matches are distributed among these distances:
98 20 0.09
99 203 0.87
100 10 0.04
ACGTcount: A:0.34, C:0.17, G:0.33, T:0.17
Consensus pattern (98 bp):
GAAAGGTTGAGGCCGCAACGGCGAACCCGATACCATGAAGAGATGAAGGGAAAGCTTGAGGCAGC
AACGTGAACCTGGCACCCTAGAAGATGTGACGG
Found at i:505211 original size:39 final size:39
Alignment explanation
Indices: 505167--505653 Score: 116
Period size: 39 Copynumber: 12.5 Consensus size: 39
505157 GATTGAAGAT
*
505167 TCCGATCTCTTACCCCAATCATGGGACAGATCACAATCA
1 TCCGATCTCTTACCCCAAGCATGGGACAGATCACAATCA
* * * ** *
505206 TCCGATCTTTTACCCTAAGCTTGGGGTAGATCACCATCA
1 TCCGATCTCTTACCCCAAGCATGGGACAGATCACAATCA
* * * **
505245 GCCAATCTCTTACCCCGAGCCTAT-GG-CAGATTTCAATCA
1 TCCGATCTCTTACCCCAAG-C-ATGGGACAGATCACAATCA
* * ** * *
505284 TTCGATCTTTTACATCGAGCCTAGGG-CAGATCATC-ATCA
1 TCCGATCTCTTACCCCAAGCAT-GGGACAGATCA-CAATCA
* ** * * ** * ** *
505323 ACTAATCTCTTACCCCGAGCCTGGGGTAAATTGCAACCA
1 TCCGATCTCTTACCCCAAGCATGGGACAGATCACAATCA
* * *
505362 TCCGATCTTTTACCCCGAGCATGAGG-CAGATCACCATCA
1 TCCGATCTCTTACCCCAAGCATG-GGACAGATCACAATCA
* ** * * * * **
505401 GCTAATCTCTTACCCCGAGCCTGAGACAGATTACAGCCA
1 TCCGATCTCTTACCCCAAGCATGGGACAGATCACAATCA
* * * * * * **
505440 TTCGATCTTTTACCTCGAGCTTAGGTTAGATCATC-ATCA
1 TCCGATCTCTTACCCCAAGCATGGGACAGATCA-CAATCA
* * * * *
505479 GCCAATATCTTA-CCCAAGCCTAGGG-CAGATTACAGA-CA
1 TCCGATCTCTTACCCCAAGCAT-GGGACAGATCACA-ATCA
* * * * *
505517 TTCGATCTTTTACCCCGAGCTTAGGG-CAGATCACCATCA
1 TCCGATCTCTTACCCCAAGCAT-GGGACAGATCACAATCA
* * * * * * *
505556 GCCAATCTCTTACCCCGAGCCTGGGGCA-AACTACAGTCA
1 TCCGATCTCTTACCCCAAGCATGGGACAGATC-ACAATCA
* * * * * * *
505595 TTCGATCTTTTAACCCGAGCTTGGGGA-GGATCACCATCA
1 TCCGATCTCTTACCCCAAGCAT-GGGACAGATCACAATCA
* *
505634 GCCAATCTCTTACCCCAAGC
1 TCCGATCTCTTACCCCAAGC
505654 CTGTGGCAAA
Statistics
Matches: 311, Mismatches: 118, Indels: 38
0.67 0.25 0.08
Matches are distributed among these distances:
37 2 0.01
38 32 0.10
39 264 0.85
40 12 0.04
41 1 0.00
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (39 bp):
TCCGATCTCTTACCCCAAGCATGGGACAGATCACAATCA
Found at i:505275 original size:78 final size:78
Alignment explanation
Indices: 505171--505860 Score: 576
Period size: 78 Copynumber: 8.9 Consensus size: 78
505161 GAAGATTCCG
* * * * * * *
505171 ATCTCTTACCCCAATCAT-GGGACAGATCACAATCATCCGATCTTTTACCCTAAGCTTGGGGTAG
1 ATCTCTTACCCCGAGCCTAGGG-CAGATTACAACCATCCGATCTTTTACCCTGAGCTTGGGGCAG
505235 ATCACCATCAGCCA
65 ATCACCATCAGCCA
* * * * * * *
505249 ATCTCTTACCCCGAGCCTATGGCAGATTTCAATCATTCGATCTTTTA-CATCGAGCCTAGGGCAG
1 ATCTCTTACCCCGAGCCTAGGGCAGATTACAACCATCCGATCTTTTACCCT-GAGCTTGGGGCAG
* * *
505313 ATCATCATCAACTA
65 ATCACCATCAGCCA
* * * * * * *
505327 ATCTCTTACCCCGAGCCTGGGGTAAATTGCAACCATCCGATCTTTTACCCCGAGCATGAGGCAGA
1 ATCTCTTACCCCGAGCCTAGGGCAGATTACAACCATCCGATCTTTTACCCTGAGCTTGGGGCAGA
*
505392 TCACCATCAGCTA
66 TCACCATCAGCCA
* * * * **
505405 ATCTCTTACCCCGAGCCT-GAGACAGATTACAGCCATTCGATCTTTTA-CCTCGAGCTTAGGTTA
1 ATCTCTTACCCCGAGCCTAG-GGCAGATTACAACCATCCGATCTTTTACCCT-GAGCTTGGGGCA
*
505468 GATCATCATCAGCCA
64 GATCACCATCAGCCA
* * * * *
505483 ATATCTTA-CCCAAGCCTAGGGCAGATTACAGA-CATTCGATCTTTTACCCCGAGCTTAGGGCAG
1 ATCTCTTACCCCGAGCCTAGGGCAGATTACA-ACCATCCGATCTTTTACCCTGAGCTTGGGGCAG
505546 ATCACCATCAGCCA
65 ATCACCATCAGCCA
* * * ** *
505560 ATCTCTTACCCCGAGCCTGGGGCAAACTACAGTCATTCGATCTTTTAACCC-GAGCTTGGGG-AG
1 ATCTCTTACCCCGAGCCTAGGGCAGATTACAACCATCCGATCTTTT-ACCCTGAGCTTGGGGCA-
505623 GATCACCATCAGCCA
64 GATCACCATCAGCCA
* * * ** * *
505638 ATCTCTTACCCCAAGCCT-GTGGCAAATTGCAACCATCTAATCTTTTACCCTGAGCTTGGGACAA
1 ATCTCTTACCCCGAGCCTAG-GGCAGATTACAACCATCCGATCTTTTACCCTGAGCTTGGGGCAG
*
505702 ATCATCATCAGCCA
65 ATCACCATCAGCCA
* * * * * * * **
505716 ATCTCTTACCCCGAG-CTTGGAGCATATTGCAGCCACCCGATCTTTTACCCCGAGCCT-GGATAG
1 ATCTCTTACCCCGAGCCTAGG-GCAGATTACAACCATCCGATCTTTTACCCTGAGCTTGGGGCAG
*
505779 ATCACCATCAGTCA
65 ATCACCATCAGCCA
* * * * * * * * **
505793 ATCTCTTACCCCGAGCCT-TGGTATATTACAGCCACCCGATCTCTTACCCCGACCACGGGGCAGA
1 ATCTCTTACCCCGAGCCTAGGGCAGATTACAACCATCCGATCTTTTACCCTGAGCTTGGGGCAGA
505857 TCAC
66 TCAC
505861 AGCCATCTAA
Statistics
Matches: 503, Mismatches: 90, Indels: 39
0.80 0.14 0.06
Matches are distributed among these distances:
76 30 0.06
77 118 0.23
78 347 0.69
79 8 0.02
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTAGGGCAGATTACAACCATCCGATCTTTTACCCTGAGCTTGGGGCAGA
TCACCATCAGCCA
Found at i:505719 original size:39 final size:38
Alignment explanation
Indices: 505235--505813 Score: 158
Period size: 39 Copynumber: 14.9 Consensus size: 38
505225 CTTGGGGTAG
* *
505235 ATCACCATCAGCCAATCTCTTACCCCGAGCCTAT-GGCAG
1 ATCATCATCAGCCAATCTCTTACCCCGAG-CT-TGGGCAA
* ** * * ** * *
505274 AT-TTCAATCATTCGATCTTTTACATCGAGCCTAGGGCAG
1 ATCATC-ATCAGCCAATCTCTTACCCCGAG-CTTGGGCAA
* * * *
505313 ATCATCATCAACTAATCTCTTACCCCGAGCCTGGGGTAA
1 ATCATCATCAGCCAATCTCTTACCCCGAG-CTTGGGCAA
* * * * * *
505352 AT--TGCAACCATCCGATCTTTTACCCCGAGCATGAGGCAG
1 ATCAT-C-ATCAGCCAATCTCTTACCCCGAGCTTG-GGCAA
* * * * *
505391 ATCACCATCAGCTAATCTCTTACCCCGAGCCTGAGACAG
1 ATCATCATCAGCCAATCTCTTACCCCGAGCTTG-GGCAA
* * ** * * * ** *
505430 ATTA-CAGCCATTCGATCTTTTACCTCGAGCTTAGGTTAG
1 ATCATCA-TCAGCCAATCTCTTACCCCGAGCTT-GGGCAA
* * * *
505469 ATCATCATCAGCCAATATCTTA-CCCAAGCCTAGGGCAG
1 ATCATCATCAGCCAATCTCTTACCCCGAG-CTTGGGCAA
* * ** * * *
505507 ATTA-CAGACATTCGATCTTTTACCCCGAGCTTAGGGCAG
1 ATCATCA-TCAGCCAATCTCTTACCCCGAGCTT-GGGCAA
* *
505546 ATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAA
1 ATCATCATCAGCCAATCTCTTACCCCGAG-CTTGGGCAA
** * * * * *
505585 A-C-TACAGTCATTCGATCTTTTAACCCGAGCTTGGGGAGG
1 ATCAT-CA-TCAGCCAATCTCTTACCCCGAGCTTGGGCA-A
* * *
505624 ATCACCATCAGCCAATCTCTTACCCCAAGCCTGTGGCAA
1 ATCATCATCAGCCAATCTCTTACCCCGAGCTTG-GGCAA
* * * * *
505663 AT--TGCAACCATCTAATCTTTTACCCTGAGCTTGGGACAA
1 ATCAT-C-ATCAGCCAATCTCTTACCCCGAGCTTGGG-CAA
*
505702 ATCATCATCAGCCAATCTCTTACCCCGAGCTTGGAGCAT
1 ATCATCATCAGCCAATCTCTTACCCCGAGCTTGG-GCAA
* * * * * ** *
505741 AT--TGCAGCCACCCGATCTTTTACCCCGAGCCTGGATAG
1 ATCAT-CA-TCAGCCAATCTCTTACCCCGAGCTTGGGCAA
* *
505779 ATCACCATCAGTCAATCTCTTACCCCGAGCCTTGG
1 ATCATCATCAGCCAATCTCTTACCCCGAG-CTTGG
505814 TATATTACAG
Statistics
Matches: 381, Mismatches: 125, Indels: 68
0.66 0.22 0.12
Matches are distributed among these distances:
37 4 0.01
38 62 0.16
39 296 0.78
40 18 0.05
41 1 0.00
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (38 bp):
ATCATCATCAGCCAATCTCTTACCCCGAGCTTGGGCAA
Found at i:505835 original size:38 final size:38
Alignment explanation
Indices: 505716--505844 Score: 120
Period size: 38 Copynumber: 3.4 Consensus size: 38
505706 TCATCAGCCA
* *
505716 ATCTCTTACCCCGAG-CTTGGAGCATATTGCAGCCACCCG
1 ATCTCTTACCCCGAGCCTT-G-GTATATTACAGCCACCCG
* * * * ** *
505755 ATCTTTTACCCCGAGCC-TGGATAGATCACCA-TCAGTCA
1 ATCTCTTACCCCGAGCCTTGG-TATATTA-CAGCCACCCG
505793 ATCTCTTACCCCGAGCCTTGGTATATTACAGCCACCCG
1 ATCTCTTACCCCGAGCCTTGGTATATTACAGCCACCCG
505831 ATCTCTTACCCCGA
1 ATCTCTTACCCCGA
505845 CCACGGGGCA
Statistics
Matches: 69, Mismatches: 16, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
37 3 0.04
38 45 0.65
39 20 0.29
40 1 0.01
ACGTcount: A:0.22, C:0.36, G:0.16, T:0.26
Consensus pattern (38 bp):
ATCTCTTACCCCGAGCCTTGGTATATTACAGCCACCCG
Found at i:506634 original size:19 final size:19
Alignment explanation
Indices: 506610--506646 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
506600 ATTGGGTATC
506610 AAAATTTCAGATCAAAAAT
1 AAAATTTCAGATCAAAAAT
*
506629 AAAATTTCAGTTCAAAAA
1 AAAATTTCAGATCAAAAA
506647 GTTTCAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAATTTCAGATCAAAAAT
Found at i:522238 original size:21 final size:20
Alignment explanation
Indices: 522198--522239 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
522188 AGCTATTTTG
*
522198 ACTTGATTTAAATTATTTTA
1 ACTTGATTTAAATTAGTTTA
522218 ACTTGATTTTAAAATT-GTTTA
1 ACTTGA-TTT-AAATTAGTTTA
522239 A
1 A
522240 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (20 bp):
ACTTGATTTAAATTAGTTTA
Found at i:523165 original size:38 final size:38
Alignment explanation
Indices: 523079--523258 Score: 135
Period size: 38 Copynumber: 4.7 Consensus size: 38
523069 AAAGAGAAAT
* * * * * * *
523079 ATTGATTGTACTTAATGTTTGCTCAAATGAGAGATAACT
1 ATTGATTATACTAAATGCTTGCTCAAGTGAGTGA-ATCC
* * *
523118 ACTGATTATACTGAATGCTTGCTCAAGCGAGTGAATCC
1 ATTGATTATACTAAATGCTTGCTCAAGTGAGTGAATCC
* * **
523156 ATTGATTATACTGAATTCTTGCTCAAGTGAGCAAATCC
1 ATTGATTATACTAAATGCTTGCTCAAGTGAGTGAATCC
* * * * * * *
523194 ACTAATTTTACTAAATGTTTGCTCAAATGAGTGATAACT
1 ATTGATTATACTAAATGCTTGCTCAAGTGAGTGA-ATCC
* *
523233 ATTTATTATACTAAAAGCTTGCTCAA
1 ATTGATTATACTAAATGCTTGCTCAA
523259 ATAAGCATTA
Statistics
Matches: 110, Mismatches: 30, Indels: 2
0.77 0.21 0.01
Matches are distributed among these distances:
38 60 0.55
39 50 0.45
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (38 bp):
ATTGATTATACTAAATGCTTGCTCAAGTGAGTGAATCC
Found at i:532328 original size:4 final size:4
Alignment explanation
Indices: 532314--532358 Score: 54
Period size: 4 Copynumber: 10.5 Consensus size: 4
532304 TAACTAATTT
*
532314 TTAA TTAAA TTAA TTCAA TTAA TTAA TTAA TTAA TCAAA TTAA TT
1 TTAA TT-AA TTAA TT-AA TTAA TTAA TTAA TTAA T-TAA TTAA TT
532359 CGATTTCATC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 25 0.69
5 11 0.31
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (4 bp):
TTAA
Found at i:532328 original size:9 final size:9
Alignment explanation
Indices: 532314--532347 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
532304 TAACTAATTT
532314 TTAATTAAA
1 TTAATTAAA
*
532323 TTAATTCAA
1 TTAATTAAA
532332 TTAATT-AA
1 TTAATTAAA
532340 TTAATTAA
1 TTAATTAA
532348 TCAAATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (9 bp):
TTAATTAAA
Found at i:532333 original size:21 final size:21
Alignment explanation
Indices: 532314--532358 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
532304 TAACTAATTT
532314 TTAATTAAATTAATTCAATTAA
1 TTAATT-AATTAATTCAATTAA
532336 TTAATTAATTAA-TCAAATTAA
1 TTAATTAATTAATTC-AATTAA
532357 TT
1 TT
532359 CGATTTCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 2 0.09
21 14 0.64
22 6 0.27
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAATTAATTAATTCAATTAA
Found at i:537706 original size:131 final size:132
Alignment explanation
Indices: 537464--537858 Score: 693
Period size: 131 Copynumber: 3.0 Consensus size: 132
537454 TTATGTTGTT
* *
537464 TTCCTCTGTTGGTCTGCCATTAGAAGGTTAGGAATTTCTCACCAGCGGCAATTCCGTGCATTTCT
1 TTCCTCTGTTGGTCTGCTATTAGAAGGTTAGGAATTTCTCACCAGCGGCAATTCCATGCATTTCT
537529 CGCTTCAAAGTTTTACATGGTGCATTAATTTAACTCCAATGAAATCCATATATTGATTGTGGACA
66 CGCTTCAAAGTTTTACATGGTGCATTAATTTAACTCCAATGAAATCCATATATTGATTGTGGACA
537594 TA
131 TA
*
537596 TTCCTCT-TTGGTCTGCTATTAGAAGGTTAGGAATTTCTCACCAGCAGCAATTCCATGCATTTCT
1 TTCCTCTGTTGGTCTGCTATTAGAAGGTTAGGAATTTCTCACCAGCGGCAATTCCATGCATTTCT
*
537660 CGCTTCAAAGTTTTACATGGTGCATTAATTTAACTCCAATGAAATCCATTTATTGATTGTGGATG
66 CGCTTCAAAGTTTTACATGGTGCATTAATTTAACTCCAATGAAATCCATATATTGATTGT-G--G
537725 TACATA
128 -ACATA
*
537731 TTCCTCTGTTGGTCTGCTATTAGAAAGTTAGGAATTTCTCACCAGCGGCAATTCCATGCATTTCT
1 TTCCTCTGTTGGTCTGCTATTAGAAGGTTAGGAATTTCTCACCAGCGGCAATTCCATGCATTTCT
*
537796 CGCTTCAAAGTTTTATATGGTGCATTAATTTAACTCCAATGAAATCCATATATTGATTGTGGA
66 CGCTTCAAAGTTTTACATGGTGCATTAATTTAACTCCAATGAAATCCATATATTGATTGTGGA
537859 TGGACATAAT
Statistics
Matches: 250, Mismatches: 8, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
131 113 0.45
132 9 0.04
133 1 0.00
134 1 0.00
135 13 0.05
136 113 0.45
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.37
Consensus pattern (132 bp):
TTCCTCTGTTGGTCTGCTATTAGAAGGTTAGGAATTTCTCACCAGCGGCAATTCCATGCATTTCT
CGCTTCAAAGTTTTACATGGTGCATTAATTTAACTCCAATGAAATCCATATATTGATTGTGGACA
TA
Found at i:537816 original size:136 final size:135
Alignment explanation
Indices: 537464--537866 Score: 706
Period size: 136 Copynumber: 3.0 Consensus size: 135
537454 TTATGTTGTT
* *
537464 TTCCTCTGTTGGTCTGCCATTAGAAGGTTAGGAATTTCTCACCAGCGGCAATTCCGTGCATTTCT
1 TTCCTCTGTTGGTCTGCTATTAGAAGGTTAGGAATTTCTCACCAGCGGCAATTCCATGCATTTCT
537529 CGCTTCAAAGTTTTACATGGTGCATTAATTTAACTCCAATGAAATCCATATATTGATTGT-G--G
66 CGCTTCAAAGTTTTACATGGTGCATTAATTTAACTCCAATGAAATCCATATATTGATTGTGGATG
537591 ACATA
131 ACATA
*
537596 TTCCTCT-TTGGTCTGCTATTAGAAGGTTAGGAATTTCTCACCAGCAGCAATTCCATGCATTTCT
1 TTCCTCTGTTGGTCTGCTATTAGAAGGTTAGGAATTTCTCACCAGCGGCAATTCCATGCATTTCT
*
537660 CGCTTCAAAGTTTTACATGGTGCATTAATTTAACTCCAATGAAATCCATTTATTGATTGTGGATG
66 CGCTTCAAAGTTTTACATGGTGCATTAATTTAACTCCAATGAAATCCATATATTGATTGTGGATG
537725 TACATA
131 -ACATA
*
537731 TTCCTCTGTTGGTCTGCTATTAGAAAGTTAGGAATTTCTCACCAGCGGCAATTCCATGCATTTCT
1 TTCCTCTGTTGGTCTGCTATTAGAAGGTTAGGAATTTCTCACCAGCGGCAATTCCATGCATTTCT
*
537796 CGCTTCAAAGTTTTATATGGTGCATTAATTTAACTCCAATGAAATCCATATATTGATTGTGGATG
66 CGCTTCAAAGTTTTACATGGTGCATTAATTTAACTCCAATGAAATCCATATATTGATTGTGGAT-
537861 GACATA
130 GACATA
537867 ATTCACTTCT
Statistics
Matches: 257, Mismatches: 8, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
131 113 0.44
132 8 0.03
134 1 0.00
135 12 0.05
136 122 0.47
137 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (135 bp):
TTCCTCTGTTGGTCTGCTATTAGAAGGTTAGGAATTTCTCACCAGCGGCAATTCCATGCATTTCT
CGCTTCAAAGTTTTACATGGTGCATTAATTTAACTCCAATGAAATCCATATATTGATTGTGGATG
ACATA
Found at i:539838 original size:3 final size:3
Alignment explanation
Indices: 539783--539819 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
539773 GAACATTTCT
539783 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
539820 GACATCAGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:539994 original size:18 final size:18
Alignment explanation
Indices: 539954--539995 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
539944 TCTCCCTTGA
*
539954 CTTTTAATTTTCTATCTT
1 CTTTTAATTTTCTATATT
539972 C-TTTAATTTT-TCATATT
1 CTTTTAATTTTCT-ATATT
539989 CTTTTAA
1 CTTTTAA
539996 CTACTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 14 0.67
18 6 0.29
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (18 bp):
CTTTTAATTTTCTATATT
Found at i:545364 original size:17 final size:17
Alignment explanation
Indices: 545344--545385 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
545334 CTCCCTTGAC
*
545344 CTTTAACCTTTCATCTT
1 CTTTAACCTTTCATATT
545361 CTTTAACCTTTCATATT
1 CTTTAACCTTTCATATT
545378 CTTGTAAC
1 CTT-TAAC
545386 TATTTTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.50
Consensus pattern (17 bp):
CTTTAACCTTTCATATT
Found at i:545369 original size:24 final size:24
Alignment explanation
Indices: 545324--545371 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
545314 ATGAATGTTC
*
545324 AACCTTTCATCTCCCTTGACCTTT
1 AACCTTTCATCTCCCTTAACCTTT
* *
545348 AACCTTTCATCTTCTTTAACCTTT
1 AACCTTTCATCTCCCTTAACCTTT
545372 CATATTCTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.02, T:0.46
Consensus pattern (24 bp):
AACCTTTCATCTCCCTTAACCTTT
Found at i:549812 original size:23 final size:22
Alignment explanation
Indices: 549782--549827 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
549772 ATCTGCAAAA
*
549782 AGAGGAAACAGAGAGCCAAGAC
1 AGAGGAAACAGAGAACCAAGAC
*
549804 AGAGAGAAATAGAGAACCAAGAC
1 AGAG-GAAACAGAGAACCAAGAC
549827 A
1 A
549828 AAGACAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.54, C:0.15, G:0.28, T:0.02
Consensus pattern (22 bp):
AGAGGAAACAGAGAACCAAGAC
Found at i:561285 original size:11 final size:11
Alignment explanation
Indices: 561253--561279 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
561243 TAATAAATAT
561253 TATTTATTTAA
1 TATTTATTTAA
561264 TATTTATTTAA
1 TATTTATTTAA
561275 TATTT
1 TATTT
561280 CATTAAGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:563119 original size:24 final size:24
Alignment explanation
Indices: 563088--563168 Score: 108
Period size: 24 Copynumber: 3.4 Consensus size: 24
563078 AGTAATTCGT
* * *
563088 GAGCATAAATGTATACTGGCTGAT
1 GAGCATAAACGTATAGTGGCTGAC
* *
563112 GAGCATAAACGTATAGTGGTTGGC
1 GAGCATAAACGTATAGTGGCTGAC
*
563136 GAGCATAAACGTATAGTGGCTAAC
1 GAGCATAAACGTATAGTGGCTGAC
563160 GAGCATAAA
1 GAGCATAAA
563169 TGTACCTTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (24 bp):
GAGCATAAACGTATAGTGGCTGAC
Found at i:569901 original size:42 final size:41
Alignment explanation
Indices: 569854--570555 Score: 679
Period size: 42 Copynumber: 17.3 Consensus size: 41
569844 GCTACTATCT
* * * *
569854 AATCTCTTACCTCGATCAAGTGGCAGATTGAAGACCTCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGA-ATCATCC
* * * * *
569896 AATCTCTTACCCTGAACATGGGGCAAATTAAAGGCATCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAA-GAATCATCC
* *
569938 AATCTCTTACCCCGACCATGAGGCAGATTG-A-AA-CATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCATCC
* * *
569976 AATCTTTTACCCTGATCA-GAGGGCAAATTGAAGACA-CA-CC
1 AATCTCTTACCCCGATCATG-GGGCAGATTGAAGA-ATCATCC
* * * *
570016 AATCTCTTACCCCGACCATGGGGCAAATTGAAG--CCATTC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCATCC
* * *
570055 AATCTCTTACCCCAATCATGGGGTAGATTGAAGTCATCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAG-AATCATCC
*
570097 AATCTTTTACCCCGATCATGGGGCAGATTGAAGTAATCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAG-AATCATCC
* * * * *
570139 AAGCTCTTACCTCGACCATGGGACAGATTGAAG---CATTC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCATCC
* *** * *
570177 AATCTTTTACCGTAATCA-GAGGGTAGATTGAAG-A-CACGCC
1 AATCTCTTACCCCGATCATG-GGGCAGATTGAAGAATCA-TCC
* * *
570217 AATCTCTTACCTCGACCATTGGGCAGATTGAAG--TCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCATCC
* * ** *
570256 AATCTTTTATCCCGATTGTGGGGCAGATTGAAAATATCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGA-ATCATCC
*
570298 AATCTCTTACCCCGATCATGGGGTAGATTGAAGACATCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGA-ATCATCC
* ** * * * *
570340 AATCTTTTACCCTAACCATGAGGTAGATTGAAG--CCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCATCC
570379 AATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGA-ATCATCC
570421 AATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGA-ATCATCC
* *
570463 AATCTCTTACCCCGATCATAGGGCTGATTGAAGACATCATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGA-ATCATCC
*
570505 AATCTCTTACCCCGATCATGGGGAAGATTGAAG-A-CATCC
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCATCC
570544 AATCTCTTACCC
1 AATCTCTTACCC
570556 TAACTAGAGG
Statistics
Matches: 547, Mismatches: 91, Indels: 47
0.80 0.13 0.07
Matches are distributed among these distances:
37 2 0.00
38 57 0.10
39 110 0.20
40 60 0.11
41 5 0.01
42 312 0.57
43 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (41 bp):
AATCTCTTACCCCGATCATGGGGCAGATTGAAGAATCATCC
Found at i:570199 original size:201 final size:199
Alignment explanation
Indices: 569854--570555 Score: 872
Period size: 201 Copynumber: 3.5 Consensus size: 199
569844 GCTACTATCT
* * * * * *
569854 AATCTCTTACCTCGATCAAGTGGCAGATTGAAGACCTCATCCAATCTCTTACCCTGAACATGGGG
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
* * * *
569919 CAAATTAAAGGCATCATCCAATCTCTTACCCCGACCATGAGGCAGATTGAAACATCCAATCTTTT
66 CAGATTGAA-GAATCATCCAATCTCTTA-CCCGACCATGAGGCAGATTGAAGCATCCAATCTTTT
* *
569984 ACCCTGATCAGAGGGCAAATTGAAGACACACCAATCTCTTACCCCGACCATGGGGCAAATTGAAG
129 ACCCTGATCAGAGGGCAGATTGAAGACACACCAATCTCTTACCCCGACCATGGGGCAGATTGAAG
*
570049 CCATTC
194 CCATCC
* * * *
570055 AATCTCTTACCCCAATCATGGGGTAGATTGAAGTCATCATCCAATCTTTTACCCCGATCATGGGG
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
* *
570120 CAGATTGAAGTAATCATCCAAGCTCTTACCTCGACCATG-GGACAGATTGAAGCATTCAATCTTT
66 CAGATTGAAG-AATCATCCAATCTCTTACC-CGACCATGAGG-CAGATTGAAGCATCCAATCTTT
* * * * * *
570184 TACCGTAATCAGAGGGTAGATTGAAGACACGCCAATCTCTTACCTCGACCATTGGGCAGATTGAA
128 TACCCTGATCAGAGGGCAGATTGAAGACACACCAATCTCTTACCCCGACCATGGGGCAGATTGAA
*
570249 GTCATCC
193 GCCATCC
* * ** * *
570256 AATCTTTTATCCCGATTGTGGGGCAGATTGAAAATATCATCCAATCTCTTACCCCGATCATGGGG
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
* * * * *
570321 TAGATTGAAGACATCATCCAATCTTTTACCCTAACCATGAGGTAGATTGAAGCCATCCAATCTCT
66 CAGATTGAAGA-ATCATCCAATCTCTTACCC-GACCATGAGGCAGATTGAAG-CATCCAATCTTT
* *
570386 TACCCCGATCATG-GGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATT
128 TACCCTGATCA-GAGGGCAGATTGAAGACA-CA-CCAATCTCTTACCCCGACCATGGGGCAGATT
570450 GAAGACATCATCC
190 GAAG-C--CATCC
* *
570463 AATCTCTTACCCCGATCATAGGGCTGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
1 AATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
*
570528 AAGATTGAAG-A-CATCCAATCTCTTACCC
66 CAGATTGAAGAATCATCCAATCTCTTACCC
570556 TAACTAGAGG
Statistics
Matches: 426, Mismatches: 62, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
200 7 0.02
201 262 0.62
202 35 0.08
203 2 0.00
204 48 0.11
205 1 0.00
207 71 0.17
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (199 bp):
AATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
CAGATTGAAGAATCATCCAATCTCTTACCCGACCATGAGGCAGATTGAAGCATCCAATCTTTTAC
CCTGATCAGAGGGCAGATTGAAGACACACCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCC
ATCC
Found at i:570568 original size:123 final size:124
Alignment explanation
Indices: 569854--570585 Score: 699
Period size: 123 Copynumber: 6.0 Consensus size: 124
569844 GCTACTATCT
* * * *
569854 AATCTCTTACCTCGATCA-AGTGGCAGATTGAAGACCTCATCCAATCTCTTACCCTGAACATGGG
1 AATCTCTTACCCCGATCATAG-GGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGG
* * * *
569918 GCAA-ATTAAAGGCATCATCCAATCTCTTACCCCGACCATGAGGCAGATTG-A-A-A-CATCC
65 G-AAGATTGAA-G-ATCATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAGACATCATCC
* * * * *
569976 AATCTTTTACCCTGATCAGAGGGCAAATTGAAGACA-CA-CCAATCTCTTACCCCGACCATGGGG
1 AATCTCTTACCCCGATCATAGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
* * * *
570039 CAA-ATTGAAG-CCATTCAATCTCTTACCCCAATCATGGGGTAGATTGAAGTCATCATCC
66 -AAGATTGAAGATCATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAGACATCATCC
* * * * *
570097 AATCTTTTACCCCGATCATGGGGCAGATTGAAGTA-ATCATCCAAGCTCTTACCTCGACCAT-GG
1 AATCTCTTACCCCGATCATAGGGCAGATTGAAG-ACATCATCCAATCTCTTACCCCGATCATGGG
* * ** * *
570160 GACAGATTGAAG--CATTCAATCTTTTACCGTAATCA-GAGGGTAGATTGAAGACA-C-GCC
65 GA-AGATTGAAGATCATCCAATCTCTTACCCCAATCATG-GGGCAGATTGAAGACATCATCC
* * * * * **
570217 AATCTCTTACCTCGACCATTGGGCAGATTGAAG---TCATCCAATCTTTTATCCCGATTGTGGGG
1 AATCTCTTACCCCGATCATAGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
* * * *
570279 CAGATTGAAAATATCATCCAATCTCTTACCCCGATCATGGGGTAGATTGAAGACATCATCC
66 AAGATTG--AAGATCATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAGACATCATCC
* ** * *
570340 AATCTTTTACCCTAACCAT-GAGGTAGATTGAAG-C--CATCCAATCTCTTACCCCGATCATGGG
1 AATCTCTTACCCCGATCATAG-GGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGG
* *
570401 GCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCC
65 GAAGATTGAAG--ATCATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAGACATCATCC
*
570463 AATCTCTTACCCCGATCATAGGGCTGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
1 AATCTCTTACCCCGATCATAGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
* *
570528 AAGATTGAAGA-CATCCAATCTCTTACCCTAA-C-TAGAGGGCAGATTGAAGACAACATCC
66 AAGATTGAAGATCATCCAATCTCTTACCCCAATCAT-G-GGGCAGATTGAAGACATCATCC
570586 GAACTTTTTC
Statistics
Matches: 515, Mismatches: 66, Indels: 57
0.81 0.10 0.09
Matches are distributed among these distances:
117 54 0.10
118 4 0.01
119 3 0.01
120 63 0.12
121 77 0.15
122 75 0.15
123 199 0.39
124 3 0.01
126 37 0.07
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.25
Consensus pattern (124 bp):
AATCTCTTACCCCGATCATAGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
AAGATTGAAGATCATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAGACATCATCC
Found at i:571167 original size:23 final size:23
Alignment explanation
Indices: 571137--571186 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
571127 AACTACAAAA
* *
571137 AGAG-GAAATAGAGAGCCAAGAT
1 AGAGAGAAATAGAGAACCAAGAC
571159 AGAGAGAAATAGAGAACCAAGAC
1 AGAGAGAAATAGAGAACCAAGAC
571182 AGAGA
1 AGAGA
571187 CAATAGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.54, C:0.10, G:0.30, T:0.06
Consensus pattern (23 bp):
AGAGAGAAATAGAGAACCAAGAC
Found at i:580356 original size:150 final size:150
Alignment explanation
Indices: 580131--580400 Score: 382
Period size: 150 Copynumber: 1.8 Consensus size: 150
580121 AATAGGAGAG
* * * *
580131 TAAAATTTTGAAGGGAAAATATTTTAAAAAATTGAGGGGGAAATGGGTTTGAGGTAAATGGGGGG
1 TAAAATTTTGAAGGGAAAATATTTAAAAAAAATGAGAGGGAAATGAGTTTGAGGTAAATGGGGGG
* * * *
580196 TGAGATGAGAGAGGAGTAAAAGTTTTAGAGGGAAAGTAGGAGGGAGTAAAAGTTTTGAGAGTTTT
66 TGAAATGAGAG-GGAGTAAAAATTTT-GAGGGAAAGTAGGAAGGAGTAAAAATTTTGAGAGTTTT
580261 TAGGGAAAGTAAATGGGAAAAT
129 TAGGGAAAGTAAATGGGAAAAT
* * * *
580283 TAAAATTTTGGAGGGAAAATA-TTAAAAAAAATG-GAGGGAAATGAGTTTGGGGTAGATTGGGGG
1 TAAAATTTTGAAGGGAAAATATTTAAAAAAAATGAGAGGGAAATGAGTTTGAGGTAAATGGGGGG
* *
580346 TGAAATGAGAGGGGGTAAAAATTTTGAGGGAAAGTGGGAAGGAGTAAAAATTTTG
66 TGAAATGAGAGGGAGTAAAAATTTTGAGGGAAAGTAGGAAGGAGTAAAAATTTTG
580401 GGGGAAAAGT
Statistics
Matches: 104, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
148 27 0.26
149 12 0.12
150 35 0.34
151 10 0.10
152 20 0.19
ACGTcount: A:0.40, C:0.00, G:0.35, T:0.25
Consensus pattern (150 bp):
TAAAATTTTGAAGGGAAAATATTTAAAAAAAATGAGAGGGAAATGAGTTTGAGGTAAATGGGGGG
TGAAATGAGAGGGAGTAAAAATTTTGAGGGAAAGTAGGAAGGAGTAAAAATTTTGAGAGTTTTTA
GGGAAAGTAAATGGGAAAAT
Found at i:584263 original size:28 final size:28
Alignment explanation
Indices: 584202--584438 Score: 240
Period size: 28 Copynumber: 8.4 Consensus size: 28
584192 AACTAAAACT
* *
584202 ATTTTACAGTTTTACCACTGGTTTTCCAG
1 ATTTTACAGTTTTGCCACT-ATTTTCCAG
* *
584231 ATTTTACAGTTTTTCCACTATTTTCCAA
1 ATTTTACAGTTTTGCCACTATTTTCCAG
* *
584259 ATTTTACAGTTTTGCCACTGTTTTTCAG
1 ATTTTACAGTTTTGCCACTATTTTCCAG
* * *
584287 ATTTTACAGTTTTGCTAATGGTTTTCCAG
1 ATTTTACAGTTTTGCCACT-ATTTTCCAG
* * *
584316 ATTTTATAGTTTTGCCACTTTTTTACAG
1 ATTTTACAGTTTTGCCACTATTTTCCAG
*
584344 ATATTACAGTTTTGCCACTATTTTCCAG
1 ATTTTACAGTTTTGCCACTATTTTCCAG
* ** *
584372 ATTTTATAGTTTCACCACTATTTTCTAG
1 ATTTTACAGTTTTGCCACTATTTTCCAG
* * ** * *
584400 ATTTTATAATTTTGCTGCTATTTTCTAA
1 ATTTTACAGTTTTGCCACTATTTTCCAG
*
584428 ATTTTATAGTT
1 ATTTTACAGTT
584439 ACTATTTTTT
Statistics
Matches: 176, Mismatches: 31, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
28 134 0.76
29 42 0.24
ACGTcount: A:0.23, C:0.16, G:0.11, T:0.50
Consensus pattern (28 bp):
ATTTTACAGTTTTGCCACTATTTTCCAG
Found at i:584351 original size:85 final size:85
Alignment explanation
Indices: 584202--584423 Score: 257
Period size: 85 Copynumber: 2.6 Consensus size: 85
584192 AACTAAAACT
* * * *
584202 ATTTTACAGTTTTACCACTGGTTTTCCAGATTTTACAGTTTTTCCACTATTTTCCAAATTTTACA
1 ATTTTACAGTTTTACCAATGGTTTTCCAGATTTTACAGTTTTGCCACTATTTTACAAATATTACA
* *
584267 GTTTTGCCACTGTTTTTCAG
66 GTTTTGCCACTATTTTCCAG
* * * * *
584287 ATTTTACAGTTTTGCTAATGGTTTTCCAGATTTTATAGTTTTGCCACTTTTTTACAGATATTACA
1 ATTTTACAGTTTTACCAATGGTTTTCCAGATTTTACAGTTTTGCCACTATTTTACAAATATTACA
584352 GTTTTGCCACTATTTTCCAG
66 GTTTTGCCACTATTTTCCAG
* * * * * * * **
584372 ATTTTATAGTTTCACCACT-ATTTTCTAGATTTTATAATTTTGCTGCTATTTT
1 ATTTTACAGTTTTACCAATGGTTTTCCAGATTTTACAGTTTTGCCACTATTTT
584424 CTAAATTTTA
Statistics
Matches: 115, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
84 27 0.23
85 88 0.77
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.50
Consensus pattern (85 bp):
ATTTTACAGTTTTACCAATGGTTTTCCAGATTTTACAGTTTTGCCACTATTTTACAAATATTACA
GTTTTGCCACTATTTTCCAG
Found at i:584453 original size:113 final size:113
Alignment explanation
Indices: 584202--584438 Score: 262
Period size: 113 Copynumber: 2.1 Consensus size: 113
584192 AACTAAAACT
* * * * * *
584202 ATTTTACAGTTTTACCACTGGTTTTCCAGATTTTACAGTTTTTCCACTATTTTCCAAATTTTACA
1 ATTTTATAGTTCTACCACT-TTTTTACAGATATTACAGTTTTGCCACTATTTTCCAAATTTTACA
** * * * *
584267 GTTTTGCCACTGTTTTTCAGATTTTACAGTTTTGCTAATGGTTTTCCAG
65 GTTTCACCACTATTTTTCAGATTTTACAATTTTGCTAATGATTTTCCAA
* * * *
584316 ATTTTATAGTTTTGCCACTTTTTTACAGATATTACAGTTTTGCCACTATTTTCCAGATTTTATAG
1 ATTTTATAGTTCTACCACTTTTTTACAGATATTACAGTTTTGCCACTATTTTCCAAATTTTACAG
* ** *
584381 TTTCACCACTA-TTTTCTAGATTTTATAATTTTGCTGCT-ATTTTCTAA
66 TTTCACCACTATTTTTC-AGATTTTACAATTTTGCTAATGATTTTCCAA
584428 ATTTTATAGTT
1 ATTTTATAGTT
584439 ACTATTTTTT
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
112 22 0.21
113 65 0.62
114 17 0.16
ACGTcount: A:0.23, C:0.16, G:0.11, T:0.50
Consensus pattern (113 bp):
ATTTTATAGTTCTACCACTTTTTTACAGATATTACAGTTTTGCCACTATTTTCCAAATTTTACAG
TTTCACCACTATTTTTCAGATTTTACAATTTTGCTAATGATTTTCCAA
Found at i:588300 original size:25 final size:25
Alignment explanation
Indices: 588252--588302 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
588242 AACATGGGAC
*
588252 ATAAGAAATTAACATCATAATATAA
1 ATAAGAAATTAACATCAGAATATAA
* *
588277 ATAAGAAATTAACATTAGACTATAA
1 ATAAGAAATTAACATCAGAATATAA
588302 A
1 A
588303 ACAAGTTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (25 bp):
ATAAGAAATTAACATCAGAATATAA
Found at i:594925 original size:57 final size:59
Alignment explanation
Indices: 594837--594955 Score: 152
Period size: 57 Copynumber: 2.1 Consensus size: 59
594827 ATTTTTCAGG
* * * * * *
594837 TCATTTTCATTTTGGAGAAAACCACATTCATTTTCAAATGA-CT-CCATTTCTCTATTT
1 TCATTTTAATTTTGGAAAAAACCAAAATCATTTCCAAATGATCTCCCATTTCTCCATTT
* *
594894 TCATTTTAATTTTGGAAAAAATCAAAATCATTTCCAAATGATTTCCCATTTCTCCATTT
1 TCATTTTAATTTTGGAAAAAACCAAAATCATTTCCAAATGATCTCCCATTTCTCCATTT
594953 TCA
1 TCA
594956 CCATTTCTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 35 0.67
58 1 0.02
59 16 0.31
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (59 bp):
TCATTTTAATTTTGGAAAAAACCAAAATCATTTCCAAATGATCTCCCATTTCTCCATTT
Found at i:596813 original size:10 final size:10
Alignment explanation
Indices: 596786--596882 Score: 72
Period size: 10 Copynumber: 9.2 Consensus size: 10
596776 CATTTTTCAC
596786 ATCACATATTA
1 ATCACAT-TTA
596797 ATCACATTTA
1 ATCACATTTA
*
596807 GTCACATTTA
1 ATCACATTTA
596817 ATCACA-TTA
1 ATCACATTTA
* *
596826 GTCACATGAATA
1 ATCACAT--TTA
*
596838 TTTCAGCATTT-
1 -ATCA-CATTTA
596849 ATCACACATTTA
1 AT--CACATTTA
*
596861 GTCACATTTA
1 ATCACATTTA
596871 ATCACATTTA
1 ATCACATTTA
596881 AT
1 AT
596883 GATGGTTTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
9 8 0.12
10 37 0.54
11 12 0.17
12 6 0.09
13 3 0.04
14 3 0.04
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.38
Consensus pattern (10 bp):
ATCACATTTA
Found at i:596823 original size:68 final size:64
Alignment explanation
Indices: 596731--596882 Score: 214
Period size: 68 Copynumber: 2.3 Consensus size: 64
596721 TTAACAAAAT
* * *
596731 ACATATTAATCACATATAATCACATTAGTCACATGAATATTTTAGCATTTTTCACATCACATATT
1 ACAT-TTAATCACATTTAATCACATTAGTCACATGAATATTTCAGCATTTAT--CA-CACAT-TT
596796 AATC
61 AATC
* *
596800 ACATTTAGTCACATTTAATCACATTAGTCACATGAATATTTCAGCATTTATCACACATTTAGTC
1 ACATTTAATCACATTTAATCACATTAGTCACATGAATATTTCAGCATTTATCACACATTTAATC
596864 ACATTTAATCACATTTAAT
1 ACATTTAATCACATTTAAT
596883 GATGGTTTAT
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
64 23 0.30
65 5 0.06
66 2 0.03
68 43 0.56
69 4 0.05
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (64 bp):
ACATTTAATCACATTTAATCACATTAGTCACATGAATATTTCAGCATTTATCACACATTTAATC
Found at i:596828 original size:19 final size:21
Alignment explanation
Indices: 596787--596882 Score: 83
Period size: 21 Copynumber: 4.6 Consensus size: 21
596777 ATTTTTCACA
596787 TCACATATTAATCACATTTAG
1 TCACATATTAATCACATTTAG
596808 TCACAT-TTAATCACA-TTAG
1 TCACATATTAATCACATTTAG
* *
596827 TCACATGAATATTTCAGCATTTA-
1 TCACAT-ATTA-ATCA-CATTTAG
* * *
596850 TCACACATTTAGTCACATTTAA
1 TCACATA-TTAATCACATTTAG
596872 TCACAT-TTAAT
1 TCACATATTAAT
596883 GATGGTTTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 15
0.73 0.08 0.18
Matches are distributed among these distances:
19 10 0.16
20 13 0.21
21 14 0.23
22 12 0.20
23 9 0.15
24 3 0.05
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (21 bp):
TCACATATTAATCACATTTAG
Found at i:596853 original size:23 final size:23
Alignment explanation
Indices: 596750--596854 Score: 71
Period size: 23 Copynumber: 4.7 Consensus size: 23
596740 TCACATATAA
596750 TCACA-TTAGTCACATGAATATT
1 TCACATTTAGTCACATGAATATT
* * *
596772 TTAGCATTT-TTCACATCACATATT
1 TCA-CATTTAGTCACATGA-ATATT
* *
596796 AATCACATTTAGTCACAT--TTA-A
1 --TCACATTTAGTCACATGAATATT
596818 TCACA-TTAGTCACATGAATATT
1 TCACATTTAGTCACATGAATATT
596840 TCAGCATTTA-TCACA
1 TCA-CATTTAGTCACA
596855 CATTTAGTCA
Statistics
Matches: 63, Mismatches: 9, Indels: 21
0.68 0.10 0.23
Matches are distributed among these distances:
19 10 0.16
20 5 0.08
21 2 0.03
22 5 0.08
23 18 0.29
24 10 0.16
25 5 0.08
26 8 0.13
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (23 bp):
TCACATTTAGTCACATGAATATT
Found at i:597357 original size:36 final size:36
Alignment explanation
Indices: 597327--597465 Score: 158
Period size: 36 Copynumber: 3.9 Consensus size: 36
597317 ATATTTTCTG
* *
597327 TCTCATGGAATGAATAACATGCTCACATATTTATTG
1 TCTCATGGAATGAATAACATACTCACATATTTATTA
* * *
597363 TCACAT-GACATGAATAACATAC-CAATATATTTACTA
1 TCTCATGGA-ATGAATAACATACTC-ACATATTTATTA
*
597399 TC-CTATGGCATGAATAACATACTCACATATTTATTA
1 TCTC-ATGGAATGAATAACATACTCACATATTTATTA
* *
597435 TCTCATGGCATGAATAACATACCCACATATT
1 TCTCATGGAATGAATAACATACTCACATATT
597466 CACTTTTACA
Statistics
Matches: 88, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
35 4 0.05
36 81 0.92
37 3 0.03
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.33
Consensus pattern (36 bp):
TCTCATGGAATGAATAACATACTCACATATTTATTA
Found at i:597465 original size:72 final size:72
Alignment explanation
Indices: 597289--597465 Score: 230
Period size: 72 Copynumber: 2.5 Consensus size: 72
597279 ATATAATTAC
* * * * * *
597289 TATCACTTGACATGAAAAACAAACCCATATATTTTCTGTCTCATGGAATGAATAACATGCTCACA
1 TATCACATGACATGAATAACATACCCATATATTTACTATCTCATGGAATGAATAACATACTCACA
597354 TATTTAT
66 TATTTAT
* * *
597361 TGTCACATGACATGAATAACATACCAATATATTTACTATC-CTATGGCATGAATAACATACTCAC
1 TATCACATGACATGAATAACATACCCATATATTTACTATCTC-ATGGAATGAATAACATACTCAC
597425 ATATTTAT
65 ATATTTAT
* * *
597433 TATCTCATGGCATGAATAACATACCCACATATT
1 TATCACATGACATGAATAACATACCCATATATT
597466 CACTTTTACA
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
71 1 0.01
72 89 0.99
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (72 bp):
TATCACATGACATGAATAACATACCCATATATTTACTATCTCATGGAATGAATAACATACTCACA
TATTTAT
Found at i:599935 original size:22 final size:22
Alignment explanation
Indices: 599907--599959 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
599897 GGGAGTCTTA
599907 TCTCGAGACA-ATCGAGCA-AATG
1 TCTCGAGACATAT--AGCATAATG
*
599929 TCTCGAGACATATAGCATATTG
1 TCTCGAGACATATAGCATAATG
599951 TCTCGAGAC
1 TCTCGAGAC
599960 CTTAGGCTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 4 0.14
22 22 0.79
23 2 0.07
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (22 bp):
TCTCGAGACATATAGCATAATG
Found at i:602351 original size:18 final size:20
Alignment explanation
Indices: 602331--602370 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
602321 GAGTGAATCT
602331 TCAAAGAAAGTTGGAAATTCAC
1 TCAAAGAAAGTTGGAAATT--C
602353 TCAAAGAAAGTTGGAAAT
1 TCAAAGAAAGTTGGAAAT
602371 ATAAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (20 bp):
TCAAAGAAAGTTGGAAATTC
Found at i:605619 original size:21 final size:21
Alignment explanation
Indices: 605595--605651 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
605585 TGTTCTTGAA
* *
605595 TTTCAACAGCAATCTATAGAT
1 TTTCAAAAGCAAACTATAGAT
* *
605616 TTTCAAAAGCAAACTGTGGAT
1 TTTCAAAAGCAAACTATAGAT
*
605637 TTTCAAAAGAAAACT
1 TTTCAAAAGCAAACT
605652 GAGGCATCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (21 bp):
TTTCAAAAGCAAACTATAGAT
Found at i:605652 original size:21 final size:21
Alignment explanation
Indices: 605613--605652 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
605603 GCAATCTATA
*
605613 GATTTTCAAAAGCAAACTGTG
1 GATTTTCAAAAGAAAACTGTG
605634 GATTTTCAAAAGAAAACTG
1 GATTTTCAAAAGAAAACTG
605653 AGGCATCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (21 bp):
GATTTTCAAAAGAAAACTGTG
Found at i:609695 original size:4 final size:4
Alignment explanation
Indices: 609686--609737 Score: 54
Period size: 4 Copynumber: 12.8 Consensus size: 4
609676 TACTTTTATT
*
609686 TTTA TTTA TTT- TTT- TTTT TTCTA TCTTA TTTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TT-TA T-TTA -TTTA TTTA TTTA TTTA TTTA
609735 TTT
1 TTT
609738 TTGTCTAGGA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
3 6 0.14
4 28 0.65
5 7 0.16
6 2 0.05
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:612125 original size:15 final size:16
Alignment explanation
Indices: 612107--612136 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
612097 CTTTCCTATT
612107 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
612122 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
612137 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:612129 original size:22 final size:22
Alignment explanation
Indices: 612102--612162 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
612092 TTCGACTTTC
612102 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
612124 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
* *
612146 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTACTTTT
612163 TCTTAGATCG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:612163 original size:22 final size:22
Alignment explanation
Indices: 612116--612162 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
612106 TTTCTATTTC
*
612116 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
612138 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
612159 TTTT
1 TTTT
612163 TCTTAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTCTTTTAT
Found at i:613724 original size:24 final size:25
Alignment explanation
Indices: 613683--613760 Score: 81
Period size: 24 Copynumber: 3.2 Consensus size: 25
613673 GGGTTAGAGA
* *
613683 TGAAAGGTTTAAGAAAGATGGAAGG
1 TGAAAGGTTAAAGAAAGATGAAAGG
*
613708 TTAAAGGTTAAAG-AAGATGAAAGG
1 TGAAAGGTTAAAGAAAGATGAAAGG
* *
613732 TGAAAGGTCAAGAGAAA-A-GAAAAG
1 TGAAAGGTTAA-AGAAAGATGAAAGG
613756 TGAAA
1 TGAAA
613761 AGTTGAACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
24 29 0.64
25 14 0.31
26 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.31, T:0.17
Consensus pattern (25 bp):
TGAAAGGTTAAAGAAAGATGAAAGG
Found at i:621034 original size:99 final size:98
Alignment explanation
Indices: 620927--621184 Score: 372
Period size: 99 Copynumber: 2.6 Consensus size: 98
620917 AAGCCATAAG
* * * *
620927 CAGATCTCAATGTCCCTGAGGTTATAGTGGAATGGGGTAAAGCTTCAACATCAAATCCTATCTTC
1 CAGATCTCAATGTCCCTGAGGTTACAGTGGAATGGAGTGAAG-TACAACATCAAATCCTATCTTC
* *
620992 TTGAGGTTACAATGAAGTGGATTAAAATAAGTAA
65 TTGAGGTTACAATGAAGTGAATTAAAACAAGTAA
* **
621026 TAGATCTCAATGTCTTTGAGGTTACAGTGGAATGGAGTGAAGTCACAACATCAAATCCTATCTTC
1 CAGATCTCAATGTCCCTGAGGTTACAGTGGAATGGAGTGAAGT-ACAACATCAAATCCTATCTTC
* *
621091 TTGAGGTTATAGTGAAGTGAATTAAAACAAGTAA
65 TTGAGGTTACAATGAAGTGAATTAAAACAAGTAA
* * *
621125 CAGATCTCAATGTTCCTGAGGTTACAGTGGAATAGAGTGAAGTACAACACCAAATCCTAT
1 CAGATCTCAATGTCCCTGAGGTTACAGTGGAATGGAGTGAAGTACAACATCAAATCCTAT
621185 ACCCGTGAAG
Statistics
Matches: 141, Mismatches: 17, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
98 17 0.12
99 124 0.88
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.29
Consensus pattern (98 bp):
CAGATCTCAATGTCCCTGAGGTTACAGTGGAATGGAGTGAAGTACAACATCAAATCCTATCTTCT
TGAGGTTACAATGAAGTGAATTAAAACAAGTAA
Found at i:621354 original size:181 final size:182
Alignment explanation
Indices: 621044--621394 Score: 491
Period size: 181 Copynumber: 1.9 Consensus size: 182
621034 AATGTCTTTG
* * *
621044 AGGTTACAGTGGAATGGAGTGAAGTCACAACATCAAATCCTATCTTCTTGAGGTTATAGTGAAGT
1 AGGTTACAGTGGAATGGAGTGAACTCACAACATCAAATCCTATCTTCTTGAGGTTACAGTGAAGA
* *
621109 GAATTAAAACAAGTAACAGATCTCAATGTTCCTGAGGTTACAGTGGAATAGAGTGAAGTACAACA
66 GAATTAAAACAAGTAACAAATCTCAATGTTCCTGAGGTTACAGTGGAATAGAGTAAAGTACAACA
621174 CCAAATCCTATACCCGTGAAGTTGTAGT-GGTTCGGATTAAAACAACAAAAGA
131 CCAAATCCTATACCCGTGAAGTTGTAGTGGGTT-GGATTAAAACAACAAAAGA
* * *
621226 AGGTTACAGTGGAATGGAGTGAAACT-TCAACA-CAAGTCTTATCTT-TCTGAGGTTACAGTGAA
1 AGGTTACAGTGGAATGGAGTG-AACTCACAACATCAAATCCTATCTTCT-TGAGGTTACAGTGAA
* *
621288 GCAG-ATTAAAACAAGTAACAAATCTC-ATG-TCCTTGAGGTTACAGTGGAATGGAGTCAAATTA
64 G-AGAATTAAAACAAGTAACAAATCTCAATGTTCC-TGAGGTTACAGTGGAATAGAGT-AAAGTA
* *
621350 CAACACCAAATCCTATACCCTTGAAGTTGTCGTGGGTTGGATTAA
126 CAACACCAAATCCTATACCCGTGAAGTTGTAGTGGGTTGGATTAA
621395 TGTTACAGAA
Statistics
Matches: 151, Mismatches: 12, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
179 3 0.02
180 25 0.17
181 89 0.59
182 31 0.21
183 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (182 bp):
AGGTTACAGTGGAATGGAGTGAACTCACAACATCAAATCCTATCTTCTTGAGGTTACAGTGAAGA
GAATTAAAACAAGTAACAAATCTCAATGTTCCTGAGGTTACAGTGGAATAGAGTAAAGTACAACA
CCAAATCCTATACCCGTGAAGTTGTAGTGGGTTGGATTAAAACAACAAAAGA
Found at i:621816 original size:23 final size:24
Alignment explanation
Indices: 621772--621816 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
621762 ATTACATTTA
* *
621772 ACCCATAACAAACCTAACCCAAGT
1 ACCCATAACAAACCCAAACCAAGT
*
621796 ACCC-TAACTAACCCAAACCAA
1 ACCCATAACAAACCCAAACCAA
621817 CTAAACCCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.47, C:0.40, G:0.02, T:0.11
Consensus pattern (24 bp):
ACCCATAACAAACCCAAACCAAGT
Found at i:626697 original size:23 final size:23
Alignment explanation
Indices: 626671--626781 Score: 127
Period size: 23 Copynumber: 4.7 Consensus size: 23
626661 ACACTAGCGC
626671 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
626694 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
626717 GCTCTCTGTTTAGCAC-GTCTCAT
1 GCTCTCTGTTTAGCACTGTGT-GT
*
626740 GCTCTTTGTTATTAGCACT-TCGTGT
1 GCTCTCTG-T-TTAGCACTGT-GTGT
* *
626765 GCTCTCTGATTATCACT
1 GCTCTCTGTTTAGCACT
626782 TAGGTTGCTC
Statistics
Matches: 75, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
22 3 0.04
23 54 0.72
24 1 0.01
25 16 0.21
26 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:626743 original size:46 final size:48
Alignment explanation
Indices: 626671--626781 Score: 131
Period size: 48 Copynumber: 2.4 Consensus size: 48
626661 ACACTAGCGC
* *
626671 GCTCTCTGTTTAGCACTGTGTGTGCTCTCTG-T-TTAGCACTGT-GTGT
1 GCTCTCTGTTTAGCACTGTCTATGCTCTCTGTTATTAGCACT-TCGTGT
*
626717 GCTCTCTGTTTAGCAC-GTCTCATGCTCTTTGTTATTAGCACTTCGTGT
1 GCTCTCTGTTTAGCACTGTCT-ATGCTCTCTGTTATTAGCACTTCGTGT
* *
626765 GCTCTCTGATTATCACT
1 GCTCTCTGTTTAGCACT
626782 TAGGTTGCTC
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
45 3 0.05
46 24 0.44
47 2 0.04
48 26 0.47
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (48 bp):
GCTCTCTGTTTAGCACTGTCTATGCTCTCTGTTATTAGCACTTCGTGT
Found at i:628396 original size:25 final size:25
Alignment explanation
Indices: 628367--628421 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
628357 ATGACATAAC
628367 TAATTGAGATATTCCACTATATTCA
1 TAATTGAGATATTCCACTATATTCA
628392 TAATTGAGATATTCCACTATATTCA
1 TAATTGAGATATTCCACTATATTCA
628417 TAATT
1 TAATT
628422 TCAAGTACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (25 bp):
TAATTGAGATATTCCACTATATTCA
Found at i:630059 original size:21 final size:21
Alignment explanation
Indices: 630033--630083 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
630023 AAAAATATGA
630033 TTTTATGCATTATTATATAGT
1 TTTTATGCATTATTATATAGT
630054 TTTTATGCATTATTATATAGT
1 TTTTATGCATTATTATATAGT
630075 TTTTATGCA
1 TTTTATGCA
630084 CAAAATGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.57
Consensus pattern (21 bp):
TTTTATGCATTATTATATAGT
Found at i:631785 original size:4 final size:4
Alignment explanation
Indices: 631770--631809 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
631760 TGGTTTTCAT
*
631770 TTTA TTTAA TTTA TTTA TCTA TTTA TTTA TTT- TTTA TTTA
1 TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
631810 CTAACTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.09
4 25 0.78
5 4 0.12
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:637943 original size:41 final size:41
Alignment explanation
Indices: 637886--638013 Score: 143
Period size: 41 Copynumber: 3.1 Consensus size: 41
637876 AAATACCGCA
* *
637886 AAAGGT-AAAGTAATAGCGGCGCTTATGGAAAAGAGTCGCT
1 AAAGGTCAAAGCAATAGCGGCGCTTATGGGAAAGAGTCGCT
* *
637926 AAAGGTCAAAGCAATAGCAGCGCTTATGGGAAAGCACT-GCT
1 AAAGGTCAAAGCAATAGCGGCGCTTATGGGAAAG-AGTCGCT
* * * * * *
637967 AAAGATCAGAGCAATAGCGGTGCTTATGGGCAAGCGCCGCT
1 AAAGGTCAAAGCAATAGCGGCGCTTATGGGAAAGAGTCGCT
638008 AAAGGT
1 AAAGGT
638014 TTTGAAAAGC
Statistics
Matches: 72, Mismatches: 13, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
40 6 0.08
41 64 0.89
42 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.18
Consensus pattern (41 bp):
AAAGGTCAAAGCAATAGCGGCGCTTATGGGAAAGAGTCGCT
Found at i:638065 original size:63 final size:63
Alignment explanation
Indices: 637956--638076 Score: 179
Period size: 63 Copynumber: 1.9 Consensus size: 63
637946 CGCTTATGGG
* **
637956 AAAGCACTGCTAAAGATCAGAGCAATAGCGGTGCTTATGGGCAAGCGCCGCTAAAGGTTTTGA
1 AAAGCACTGCTAAAGATCAGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTTTTGA
* * * *
638019 AAAGCACTGCTAAAGGTTAGAGCAATAGCGGCGCTTTTTGAAAAGCGCCGCTAAAGGT
1 AAAGCACTGCTAAAGATCAGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGT
638077 CAAAGCAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (63 bp):
AAAGCACTGCTAAAGATCAGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTTTTGA
Done.