Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008245.1 Hibiscus syriacus cultivar Beakdansim tig00110895_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6601124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 33
Found at i:5225980 original size:25 final size:25
Alignment explanation
Indices: 5225952--5226001 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5225942 AATCAAATGC
* * *
5225952 TTTTAAATCTCTTTAAGAGTTCTAA
1 TTTTAAAGCTCTTCAAGAATTCTAA
*
5225977 TTTTGAAGCTCTTCAAGAATTCTAA
1 TTTTAAAGCTCTTCAAGAATTCTAA
5226002 CAATATTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (25 bp):
TTTTAAAGCTCTTCAAGAATTCTAA
Found at i:5227887 original size:5 final size:5
Alignment explanation
Indices: 5227877--5227910 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
5227867 AAATATATGT
5227877 ATATA ATATA ATATA ATATA ATATA ATATA ATAT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATAT
5227911 TTAATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:5228018 original size:42 final size:40
Alignment explanation
Indices: 5227945--5228024 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 40
5227935 TTAAAAAATA
**
5227945 TAAAATATATACATATAAAATATTAGGTAAAAAAATAAAG
1 TAAAATATATACATATAAAATATTAAATAAAAAAATAAAG
5227985 TAAAATATATACATATATAAACGTA-TAAATAAAAAAATAA
1 TAAAATATATACATATA-AAA--TATTAAATAAAAAAATAA
5228025 CTAAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 17 0.49
41 3 0.09
42 13 0.37
43 2 0.06
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.28
Consensus pattern (40 bp):
TAAAATATATACATATAAAATATTAAATAAAAAAATAAAG
Found at i:5228033 original size:4 final size:4
Alignment explanation
Indices: 5228009--5228084 Score: 68
Period size: 4 Copynumber: 19.2 Consensus size: 4
5227999 ATATAAACGT
* *
5228009 ATAA ATAA AAAA ATAA CTAA ATAA ATAA ATAA ATAA A-ACA A-AA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA
* * *
5228056 CTAA AAAA ATAA TACAA ATAA AT-A ATAA A
1 ATAA ATAA ATAA -ATAA ATAA ATAA ATAA A
5228085 AACCAAACAA
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
3 6 0.10
4 49 0.84
5 3 0.05
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (4 bp):
ATAA
Found at i:5228055 original size:31 final size:32
Alignment explanation
Indices: 5228017--5228077 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
5228007 GTATAAATAA
* *
5228017 AAAAATAACTAAATAAATAA-ATAAATAAAAC
1 AAAAATAACTAAAAAAATAATACAAATAAAAC
5228048 AAAAATAACTAAAAAAATAATACAAATAAA
1 AAAAATAACTAAAAAAATAATACAAATAAA
5228078 TAATAAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (32 bp):
AAAAATAACTAAAAAAATAATACAAATAAAAC
Found at i:5228096 original size:18 final size:18
Alignment explanation
Indices: 5228070--5228104 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5228060 AAAAATAATA
*
5228070 CAAATAAATAATAAAAAC
1 CAAACAAATAATAAAAAC
5228088 CAAACAAATAATAAAAA
1 CAAACAAATAATAAAAA
5228105 ATTGTAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.14
Consensus pattern (18 bp):
CAAACAAATAATAAAAAC
Found at i:5229420 original size:2 final size:2
Alignment explanation
Indices: 5229413--5229493 Score: 82
Period size: 2 Copynumber: 43.0 Consensus size: 2
5229403 ATGTATTATT
*
5229413 TA TA TA TA TA TA -A TA TA -A TA TA TA TA TA TA -A TA TG TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
5229451 TA T- TT TT TA AA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5229492 TA
1 TA
5229494 AAGACAAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
1 5 0.07
2 64 0.93
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5229691 original size:17 final size:17
Alignment explanation
Indices: 5229671--5229705 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5229661 CATTGCGAAG
5229671 TCGAATCCATCTTGAAA
1 TCGAATCCATCTTGAAA
*
5229688 TCGAGTCCATCTTGAAA
1 TCGAATCCATCTTGAAA
5229705 T
1 T
5229706 GATATGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (17 bp):
TCGAATCCATCTTGAAA
Found at i:5230944 original size:86 final size:86
Alignment explanation
Indices: 5230230--5231528 Score: 1612
Period size: 85 Copynumber: 15.2 Consensus size: 86
5230220 ATAGCCCCTA
* * * * * * *
5230230 TCGCCCTGAGCTATACTGTAAATATGACATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGT-A
1 TCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
5230294 TTTGTTGACAGATAACCCTTC
66 TTTGTTGACAGATAACCCTTC
* * * * * * * *
5230315 TCACATTGAGTTATGCTGTAAGTTTAATATACCTTTGAGTTGAGTATAATCGAACTCGAAGGTC-
1 TCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
* *
5230379 TTGGTGGACAGATAACCCTTC
66 TTTGTTGACAGATAACCCTTC
* * * * * *
5230400 TTGCCTTGAGCTATGCTATAAATTTGATATGCATTTGAG-TAGAATGTAATCAAACTCAAAGGTC
1 TCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCT-GAGTGTAATCGAACTCGAAGGTC
*
5230464 -TTTGTTGGA-AGATAGCCCTTC
65 TTTTGTT-GACAGATAACCCTTC
* * *
5230485 TCGCCTTGAGTTATGCTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACCCGAAGGTC-
1 TCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
* *
5230549 TTGGTTGAAAGATAACCCTTC
66 TTTGTTGACAGATAACCCTTC
* * *
5230570 TCGCCTTGAGTTATACTGTAAATTTGATATGCCTTTGAGCTGAGTATAATCGAACTCGAAGGTC-
1 TCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
* *
5230634 TTGGTGGACAGATAACCCTTC
66 TTTGTTGACAGATAACCCTTC
* * * *
5230655 TCGCCTTGAGCTATTCTGTAAATTTGATATGCCTTTTAGCTGAATGTAATCGAACTCGAAGG-CC
1 TCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
* *
5230719 TTTGTTGGCAGATAGCCCTTC
66 TTTGTTGACAGATAACCCTTC
** * *
5230740 TCGCCTTGAGCTATGCTACAAATTTGATATGCCTTTAAGCTGAGTGTAATCAAACTCGAAGGTC-
1 TCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
*
5230804 TTGGTTGACAGATAACCCTTC
66 TTTGTTGACAGATAACCCTTC
* * * * *
5230825 TTGCCTTGAGTTATGTTGTAAATTTGATATGCCTTTGAGATGAGTGTAATCAAACTCGAAGGTCT
1 TCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
*
5230890 TTTGTTGACAGATAGCCCTTC
66 TTTGTTGACAGATAACCCTTC
* * *
5230911 TCGCCTTGAGTTATGCTGTAAATTCGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
1 TCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
* * *
5230976 TTTATTAACAGATAGCCCTTC
66 TTTGTTGACAGATAACCCTTC
* * *
5230997 TCGCCTTGAGTTATGCTGTAAATTCGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
1 TCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
* * *
5231062 TTTGTTGATAGATAAGCCTTA
66 TTTGTTGACAGATAACCCTTC
* * * * *
5231083 TCGCCTTGAGTTATGCTGTAAGTTTGATATTCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTGT
1 TCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
* * *
5231148 TTTGTTAACAGATAATCTTTC
66 TTTGTTGACAGATAACCCTTC
* * * *
5231169 TCGCCTTGAGCGATGTTGTAAATTCGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-
1 TCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
*
5231233 TTGGTTGACAGATAACCCTTC
66 TTTGTTGACAGATAACCCTTC
* * **
5231254 TTGCCCTGATTTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
1 TCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
*
5231319 TTTGTTGACAGATAGCCCTTC
66 TTTGTTGACAGATAACCCTTC
* * * * * *
5231340 TCGCCATGAGCTATGTTATAAATTCGA-AGTGCCTTTGAGTTGAGTGTAATCGAACTCGAAGGTA
1 TCGCCTTGAGCTATGCTGTAAATTTGATA-TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
*
5231404 TTTTGTTGACAAATAACCCTTC
65 TTTTGTTGACAGATAACCCTTC
* * ** * * * *
5231426 TCTCTTTGAGCTATAATGTAAATTCGATGTGCCTATGAGCTGAGTGTTATCGAACTCGAAGGTCT
1 TCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
* *
5231491 TTTGTTGACATATAACCATTC
66 TTTGTTGACAGATAACCCTTC
5231512 TCGCCTTGAGCTATGCT
1 TCGCCTTGAGCTATGCT
5231529 TCCAATATTT
Statistics
Matches: 1051, Mismatches: 152, Indels: 21
0.86 0.12 0.02
Matches are distributed among these distances:
84 4 0.00
85 559 0.53
86 488 0.46
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (86 bp):
TCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
TTTGTTGACAGATAACCCTTC
Found at i:5237817 original size:22 final size:22
Alignment explanation
Indices: 5237792--5237833 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5237782 AAATGTCATG
5237792 AAATA-AAAAGAAATTAAATACA
1 AAATATAAAA-AAATTAAATACA
*
5237814 AAATATACAAAAATTAAATA
1 AAATATAAAAAAATTAAATA
5237834 AATTAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (22 bp):
AAATATAAAAAAATTAAATACA
Found at i:5237891 original size:10 final size:10
Alignment explanation
Indices: 5237878--5237902 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5237868 TAAAATAAAT
5237878 AAAAAGAAGA
1 AAAAAGAAGA
5237888 AAAAAGAAGA
1 AAAAAGAAGA
5237898 AAAAA
1 AAAAA
5237903 ACAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAGAAGA
Found at i:5237924 original size:20 final size:19
Alignment explanation
Indices: 5237899--5237936 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5237889 AAAAGAAGAA
*
5237899 AAAAACAATAAATAAAAAAC
1 AAAAACAA-AAAGAAAAAAC
5237919 AAAAACAAAAAGAAAAAA
1 AAAAACAAAAAGAAAAAA
5237937 TAATAATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.84, C:0.08, G:0.03, T:0.05
Consensus pattern (19 bp):
AAAAACAAAAAGAAAAAAC
Found at i:5238205 original size:40 final size:38
Alignment explanation
Indices: 5238133--5238234 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 38
5238123 ATTAAAAAAT
**
5238133 ATAAAATATATACATATAAAATATTAGGTAAAAA-AGA
1 ATAAAATATATACATATAAAATATTAAATAAAAATAGA
5238170 AGTAAAATATATACATATATAAACGTA-TAAATAAAAATTAGA
1 A-TAAAATATATACATATA-AAA--TATTAAATAAAAA-TAGA
* * *
5238212 ATAAAATAAATAAAAATAAAATA
1 ATAAAATATATACATATAAAATA
5238235 AAAAGAAATA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
37 1 0.02
38 19 0.35
39 3 0.06
40 11 0.20
41 16 0.30
42 4 0.07
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (38 bp):
ATAAAATATATACATATAAAATATTAAATAAAAATAGA
Found at i:5238234 original size:20 final size:21
Alignment explanation
Indices: 5238196--5238274 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
5238186 ATATAAACGT
*
5238196 ATAAATAAA-AATTAGAATAAA
1 ATAAATAAATAA-TAAAATAAA
5238217 ATAAATAAA-AATAAAATAAAA
1 ATAAATAAATAATAAAAT-AAA
* *
5238238 AGAAATAAATAAT-AAATAAT
1 ATAAATAAATAATAAAATAAA
*
5238258 ACAAATAAATAATAAAA
1 ATAAATAAATAATAAAA
5238275 ACCAAACAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
20 19 0.37
21 29 0.57
22 3 0.06
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.22
Consensus pattern (21 bp):
ATAAATAAATAATAAAATAAA
Found at i:5238306 original size:42 final size:42
Alignment explanation
Indices: 5238218--5238328 Score: 106
Period size: 42 Copynumber: 2.6 Consensus size: 42
5238208 TAGAATAAAA
*
5238218 TAAATAAA-AATAAAATAAAAAGAAATAAATAATAAATAATAC
1 TAAATAAATAATAAAA-AAAAACAAATAAATAATAAATAATAC
* *
5238260 -AAATAAATAATAAAAACCAAACAAAT-AATAA-AAATAATTC
1 TAAATAAATAATAAAAA-AAAACAAATAAATAATAAATAATAC
*
5238300 TTAAATAAAATAA-AAAAAAGAAAAAAATA
1 -TAAAT-AAATAATAAAAAA-AAACAAATA
5238329 TATGTACATA
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
40 8 0.14
41 13 0.23
42 30 0.53
43 6 0.11
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.20
Consensus pattern (42 bp):
TAAATAAATAATAAAAAAAAACAAATAAATAATAAATAATAC
Found at i:5239566 original size:2 final size:2
Alignment explanation
Indices: 5239561--5239598 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5239551 TAACATGTAT
5239561 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5239599 AAAAGACAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5239732 original size:12 final size:12
Alignment explanation
Indices: 5239715--5239741 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5239705 AATGACATTC
5239715 CCACCATTCAAA
1 CCACCATTCAAA
5239727 CCACCATTCAAA
1 CCACCATTCAAA
5239739 CCA
1 CCA
5239742 AAAAGTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (12 bp):
CCACCATTCAAA
Found at i:5241795 original size:2 final size:2
Alignment explanation
Indices: 5241790--5241815 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5241780 CATTGATAAC
5241790 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5241816 TGTAATAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5251000 original size:20 final size:20
Alignment explanation
Indices: 5250975--5251029 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
5250965 ACTGGTTACG
5250975 AATTTGACAAAACC-GATAGA
1 AATTTGACAAAACCAG-TAGA
* *
5250995 AATTTGACAATACCAGTTGA
1 AATTTGACAAAACCAGTAGA
*
5251015 AATTGGACAAAACCA
1 AATTTGACAAAACCA
5251030 TTATAGAGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (20 bp):
AATTTGACAAAACCAGTAGA
Found at i:5253201 original size:32 final size:31
Alignment explanation
Indices: 5253150--5253252 Score: 138
Period size: 32 Copynumber: 3.3 Consensus size: 31
5253140 TTTCCGAAAA
5253150 ACATAGGTAA-CTGTCCATATGTCCCAAAGG
1 ACATAGGTAACCTGTCCATATGTCCCAAAGG
*
5253180 ACATAGGTAATCCTGTCCATATGTCCCGAAGG
1 ACATAGGTAA-CCTGTCCATATGTCCCAAAGG
* * *
5253212 ACATAGGTAAACTATCCATATGTCTCGAAA-G
1 ACATAGGTAACCTGTCCATATGTC-CCAAAGG
5253243 ACATAGGTAA
1 ACATAGGTAA
5253253 TCCCTCGACT
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
30 10 0.15
31 23 0.35
32 32 0.49
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.24
Consensus pattern (31 bp):
ACATAGGTAACCTGTCCATATGTCCCAAAGG
Found at i:5263083 original size:20 final size:19
Alignment explanation
Indices: 5263058--5263101 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
5263048 GGCTAAAAAT
* *
5263058 CGGTTTGACTGGTTTTGAAC
1 CGGTTTGACCGGTTTCG-AC
5263078 CGGTTTGACCGGTTTCGAC
1 CGGTTTGACCGGTTTCGAC
5263097 CGGTT
1 CGGTT
5263102 CGAACCAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.11, C:0.20, G:0.32, T:0.36
Consensus pattern (19 bp):
CGGTTTGACCGGTTTCGAC
Found at i:5263084 original size:10 final size:9
Alignment explanation
Indices: 5263058--5263116 Score: 55
Period size: 10 Copynumber: 6.1 Consensus size: 9
5263048 GGCTAAAAAT
5263058 CGGTTTGAC
1 CGGTTTGAC
*
5263067 TGGTTTTGAAC
1 CGG-TTTG-AC
5263078 CGGTTTGAC
1 CGGTTTGAC
5263087 CGGTTTCGAC
1 CGGTTT-GAC
*
5263097 CGGTTCGAAC
1 CGGTTTG-AC
*
5263107 CAGTTTGAC
1 CGGTTTGAC
5263116 C
1 C
5263117 AGTCTGAATC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 14 0.34
10 23 0.56
11 4 0.10
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.32
Consensus pattern (9 bp):
CGGTTTGAC
Found at i:5263142 original size:5 final size:5
Alignment explanation
Indices: 5263132--5263197 Score: 55
Period size: 5 Copynumber: 12.8 Consensus size: 5
5263122 GAATCGGTCT
* * *
5263132 GACCC GACCC GA-CC GA-CT GACCC GACCC GACCGTT GACCC GACCGTT
1 GACCC GACCC GACCC GACCC GACCC GACCC GACC--C GACCC GACC--C
5263179 GACCC GACCC GACCC GACC
1 GACCC GACCC GACCC GACC
5263198 ATTGACCGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
4 7 0.14
5 35 0.70
7 8 0.16
ACGTcount: A:0.20, C:0.50, G:0.23, T:0.08
Consensus pattern (5 bp):
GACCC
Found at i:5263153 original size:18 final size:17
Alignment explanation
Indices: 5263130--5263197 Score: 77
Period size: 17 Copynumber: 3.9 Consensus size: 17
5263120 CTGAATCGGT
5263130 CTGACCCGACCCGACCG
1 CTGACCCGACCCGACCG
5263147 ACTGACCCGACCCGACCG
1 -CTGACCCGACCCGACCG
* *
5263165 TTGACCCGACCGTTGACC-
1 CTGACCCGACC--CGACCG
5263183 C-GACCCGACCCGACC
1 CTGACCCGACCCGACC
5263198 ATTGACCGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
15 4 0.09
17 19 0.43
18 17 0.39
19 4 0.09
ACGTcount: A:0.19, C:0.50, G:0.22, T:0.09
Consensus pattern (17 bp):
CTGACCCGACCCGACCG
Found at i:5263172 original size:12 final size:12
Alignment explanation
Indices: 5263155--5263204 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
5263145 CGACTGACCC
5263155 GACCCGACCGTT
1 GACCCGACCGTT
5263167 GACCCGACCGTT
1 GACCCGACCGTT
*
5263179 GACCCGACC--C
1 GACCCGACCGTT
*
5263189 GACCCGACCATT
1 GACCCGACCGTT
5263201 GACC
1 GACC
5263205 GTTGACCGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 9 0.26
12 25 0.74
ACGTcount: A:0.20, C:0.46, G:0.22, T:0.12
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:5270342 original size:10 final size:10
Alignment explanation
Indices: 5270314--5270355 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
5270304 TGAAAATCGG
5270314 TTTGACCGGT
1 TTTGACCGGT
*
5270324 TTTGAACCGAT
1 TTTG-ACCGGT
5270335 TTTGACCGGT
1 TTTGACCGGT
*
5270345 TTCGACCGGT
1 TTTGACCGGT
5270355 T
1 T
5270356 CGAACCAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.38
Consensus pattern (10 bp):
TTTGACCGGT
Found at i:5270432 original size:22 final size:22
Alignment explanation
Indices: 5270407--5270450 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5270397 ACCGACCAAT
*
5270407 CGACCCGACTCGACCGTTGACC
1 CGACCCGACCCGACCGTTGACC
*
5270429 CGACCCGACCCGACTGTTGACC
1 CGACCCGACCCGACCGTTGACC
5270451 ATTGACCGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (22 bp):
CGACCCGACCCGACCGTTGACC
Found at i:5272564 original size:2 final size:2
Alignment explanation
Indices: 5272557--5272587 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5272547 CACTTATTCT
5272557 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5272588 TCTCATATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5276944 original size:96 final size:95
Alignment explanation
Indices: 5276740--5276926 Score: 240
Period size: 96 Copynumber: 2.0 Consensus size: 95
5276730 TGATTTACTG
* * *
5276740 GTTTATGAACTATGGTTACTTGAAATATGTTCTCTGGTTACCTGTTTTCACAGTAAAATATGATC
1 GTTTATGAACTATGGTTACTTGAAATATGTTATATGGTTACCTATTTTCACAGTAAAATATGATC
* * *
5276805 GTTCCTGATTTATTGATCATGGAATCTACCA
66 ATTCCTGATTTACT-ATCATGAAATCTACCA
*
5276836 GTTTATGAACTATGGTTACCTT-AAATATGTTATATGGTTTA-TTATTTTCACTAG-AAAATATG
1 GTTTATGAACTATGGTTA-CTTGAAATATGTTATATGG-TTACCTATTTTCAC-AGTAAAATATG
5276898 ATCATTCCTGATTT-CT-TCATGAAATCTAC
63 ATCATTCCTGATTTACTATCATGAAATCTAC
5276927 TGTTACTATT
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
93 12 0.15
95 1 0.01
96 60 0.74
97 8 0.10
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.42
Consensus pattern (95 bp):
GTTTATGAACTATGGTTACTTGAAATATGTTATATGGTTACCTATTTTCACAGTAAAATATGATC
ATTCCTGATTTACTATCATGAAATCTACCA
Found at i:5277544 original size:16 final size:16
Alignment explanation
Indices: 5277523--5277555 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5277513 TATATATATA
5277523 TTATATAATGGATTAT
1 TTATATAATGGATTAT
*
5277539 TTATATTATGGATTAT
1 TTATATAATGGATTAT
5277555 T
1 T
5277556 AGATTTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (16 bp):
TTATATAATGGATTAT
Found at i:5284712 original size:145 final size:144
Alignment explanation
Indices: 5284429--5285414 Score: 917
Period size: 145 Copynumber: 7.0 Consensus size: 144
5284419 GTTTGCTCTA
* * **
5284429 TCAAACAATTTGCATG--AACGATATCGATACACATATATAAAGTATCG-TATATATAATTTTGA
1 TCAAACAATTTGCACGAAAATG-TATCGATACACATATATAAAGTATCGATATATATAATTTCAA
* * **
5284491 AACAATATATGCAATATCTGAAATGTCCAAG--TTGATATTTGTTATGCCCGTATCGATGCTTTT
65 AACAATATATGCAATATCTGAAATGTCCAAGTATTGATACTTGTTATGCCTGTATCGATAATTTT
5284554 ATTCCAGTATGCTTC
130 ATTCCAGTATGCTTC
**
5284569 TCAAACAATTTGCACGCAAAATGTATCGATACACATATATAAAGTATCGATATATATAATTTTGA
1 TCAAACAATTTGCACG-AAAATGTATCGATACACATATATAAAGTATCGATATATATAATTTCAA
5284634 AACAATATATGCAATATCTGAAATGTCCAAGTATTGATACTTGTTATGCCTGTATCGATAATTTT
65 AACAATATATGCAATATCTGAAATGTCCAAGTATTGATACTTGTTATGCCTGTATCGATAATTTT
*
5284699 ATTCCAATATGCTTC
130 ATTCCAGTATGCTTC
* * * * *
5284714 TTAAACAATTTGCACGCAAAATGTATCTATATATATATATATAAAGTATCGATATATATACTTTC
1 TCAAACAATTTGCACG-AAAATGTATC--GATACACATATATAAAGTATCGATATATATAATTTC
** * * **
5284779 AAAACAATATATGCAATATCTGAAATGTCCAAGTATCAATACTAGATAT--CAATA-C--T-A-T
63 AAAACAATATATGCAATATCTGAAATGTCCAAGTATTGATACTTGTTATGCCTGTATCGATAATT
*
5284837 TT-TTCCAGTATGCTCTA
128 TTATTCCAGTATGCT-TC
* ** * *
5284854 TCAAACAATTTGCATG-AACGGTATCGATA-AGCATATATAAAGTATCAATATATATACTTTCAA
1 TCAAACAATTTGCACGAAAATGTATCGATACA-CATATATAAAGTATCGATATATATAATTTCAA
* * * * *
5284917 AACAATATATACAATATCTGAAATGTCCAAGAATTGATACTTGTTATGCTTGTATCAATACTTTT
65 AACAATATATGCAATATCTGAAATGTCCAAGTATTGATACTTGTTATGCCTGTATCGATAATTTT
5284982 ATTCCAGTATGCTTC
130 ATTCCAGTATGCTTC
* * * *
5284997 TCAAACAATTTGCACGCAAAATGTATCAATACAAATATATAAAGTATCAATATATATACTTTCAA
1 TCAAACAATTTGCACG-AAAATGTATCGATACACATATATAAAGTATCGATATATATAATTTCAA
* * * * *
5285062 AATAATATATGTAATATCTGAAATGTCCAAGTATTGATATTTGTTATGCCCGTATCGATACTTTT
65 AACAATATATGCAATATCTGAAATGTCCAAGTATTGATACTTGTTATGCCTGTATCGATAATTTT
5285127 ATT-CA--A-----C
130 ATTCCAGTATGCTTC
* * * * *
5285134 T--AA-AATTTGCATGAAAATGTATCGATACACATATATAAAGTAGCTATATTTATAATTTCGAA
1 TCAAACAATTTGCACGAAAATGTATCGATACACATATATAAAGTATCGATATATATAATTTCAAA
* * * ** * * * ** * *
5285196 ACAAAAAATGGAAT-TCCTTCAACGTCGAAATATCAATATTTGTCAT-CACAT-TAT--ATAAAC
66 ACAATATATGCAATAT-CTGAAATGTCCAAGTATTGATACTTGTTATGC-C-TGTATCGAT-AA-
*
5285256 TTTT-TGTCCAGTATGCTTG
126 TTTTAT-TCCAGTATGCTTC
* * *
5285275 TCAAACAATTTGCATGAAAACGTATCGATACACATATATAAAGTATCGATATTTATAATTTCAAA
1 TCAAACAATTTGCACGAAAATGTATCGATACACATATATAAAGTATCGATATATATAATTTCAAA
* * ** * * * * * *
5285340 ACAAAACATGTGATATC-AAAATGTCAAAGTATCGATACTT-TATATGACTCTATCGATACTTGT
66 ACAATATATGCAATATCTGAAATGTCCAAGTATTGATACTTGT-TATGCCTGTATCGATAATT-T
*
5285403 T-TTCTAGTATGC
129 TATTCCAGTATGC
5285415 AAATATTGTT
Statistics
Matches: 707, Mismatches: 94, Indels: 87
0.80 0.11 0.10
Matches are distributed among these distances:
131 2 0.00
132 4 0.01
133 83 0.12
134 11 0.02
135 3 0.00
136 75 0.11
137 2 0.00
138 9 0.01
139 12 0.02
140 33 0.05
141 3 0.00
142 30 0.04
143 103 0.15
144 86 0.12
145 175 0.25
146 1 0.00
147 75 0.11
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (144 bp):
TCAAACAATTTGCACGAAAATGTATCGATACACATATATAAAGTATCGATATATATAATTTCAAA
ACAATATATGCAATATCTGAAATGTCCAAGTATTGATACTTGTTATGCCTGTATCGATAATTTTA
TTCCAGTATGCTTC
Found at i:5284940 original size:283 final size:283
Alignment explanation
Indices: 5284450--5285095 Score: 865
Period size: 283 Copynumber: 2.3 Consensus size: 283
5284440 GCATGAACGA
* * * **
5284450 TATCGATACACATATATAAAGTATCG-TATATATAATTTTGAAACAATATATGCAATATCTGAAA
1 TATCAATACAAATATATAAAGTATCGATATATATACTTTCAAAACAATATATGCAATATCTGAAA
* ** * * * *
5284514 TGTCCAAGTTGATATTTGTTATGCCCGTATCGATGCTTTTATTCCAGTATGCTTCTCAAACAATT
66 TGTCCAAG-T-ATATATACTATG--CATATCAATACTTTTATTCCAGTATGCTTATCAAACAATT
* * **
5284579 TGCACGCAAAATGTATCGATACACATATATAAAGTATCGATATATATAATTTTGAAACAATATAT
127 TGCACG-AAAAGGTATCGATACACATATATAAAGTATCAATATATATAATTTCAAAACAATATAT
* * *
5284644 GCAATATCTGAAATGTCCAAGTATTGATACTTGTTATGCCTGTATCGATAATTTTATTCCAATAT
191 ACAATATCTGAAATGTCCAAGAATTGATACTTGTTATGCCTGTATCAATAATTTTATTCCAATAT
*
5284709 GCTTCTTAAACAATTTGCACGCAAAATG
256 GCTTCTCAAACAATTTGCACGCAAAATG
* *
5284737 TATCTATATATATATATATAAAGTATCGATATATATACTTTCAAAACAATATATGCAATATCTGA
1 TATC-A-ATACAAATATATAAAGTATCGATATATATACTTTCAAAACAATATATGCAATATCTGA
5284802 AATGTCCAAGTATCA-ATACTA-G-ATATCAATACTATTT-TTCCAGTATGCTCTATCAAACAAT
64 AATGTCCAAGTAT-ATATACTATGCATATCAATACT-TTTATTCCAGTATGCT-TATCAAACAAT
* * *
5284863 TTGCATG-AACGGTATCGATA-AGCATATATAAAGTATCAATATATATACTTTCAAAACAATATA
126 TTGCACGAAAAGGTATCGATACA-CATATATAAAGTATCAATATATATAATTTCAAAACAATATA
* * *
5284926 TACAATATCTGAAATGTCCAAGAATTGATACTTGTTATGCTTGTATCAATACTTTTATTCCAGTA
190 TACAATATCTGAAATGTCCAAGAATTGATACTTGTTATGCCTGTATCAATAATTTTATTCCAATA
5284991 TGCTTCTCAAACAATTTGCACGCAAAATG
255 TGCTTCTCAAACAATTTGCACGCAAAATG
* * *
5285020 TATCAATACAAATATATAAAGTATCAATATATATACTTTCAAAATAATATATGTAATATCTGAAA
1 TATCAATACAAATATATAAAGTATCGATATATATACTTTCAAAACAATATATGCAATATCTGAAA
5285085 TGTCCAAGTAT
66 TGTCCAAGTAT
5285096 TGATATTTGT
Statistics
Matches: 320, Mismatches: 32, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
281 66 0.21
282 2 0.01
283 139 0.43
284 20 0.06
285 19 0.06
287 5 0.02
288 5 0.02
289 21 0.07
290 43 0.13
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.36
Consensus pattern (283 bp):
TATCAATACAAATATATAAAGTATCGATATATATACTTTCAAAACAATATATGCAATATCTGAAA
TGTCCAAGTATATATACTATGCATATCAATACTTTTATTCCAGTATGCTTATCAAACAATTTGCA
CGAAAAGGTATCGATACACATATATAAAGTATCAATATATATAATTTCAAAACAATATATACAAT
ATCTGAAATGTCCAAGAATTGATACTTGTTATGCCTGTATCAATAATTTTATTCCAATATGCTTC
TCAAACAATTTGCACGCAAAATG
Found at i:5285887 original size:231 final size:230
Alignment explanation
Indices: 5285520--5285982 Score: 567
Period size: 231 Copynumber: 2.0 Consensus size: 230
5285510 AACTTAATTT
* * * * * *
5285520 GTTAAAAAACAGTAGGTGCAACATGTTATGTTAAAGTTTCTATCGGTATAAGAATAATGTAAACA
1 GTTAAAAAACAATAAGCGCAACATGTTACGTTAAAGTATCTACCGGTATAAGAATAATGTAAACA
* * ** * *
5285585 GTTAAATATTTTCAACCTAACCAGTATAATCATAATGTAAACGGTATCATATTAACAACTTAACT
66 GATAAATATTTTCAACCTAACCAGTATAATCATAATGTAAACGATAAAATACTAACAACTTAACC
* ** * **
5285650 GGTTAAAATAATTTAGCTGCAACCTATTACTTTAAACTTCTTACCAGTTTGTTTATAGGTATATT
131 GGTTAAAACAATTTAGCAACAACCTATTACTTTAAACTTCATACCAAATT-TTTATAGGTATATT
* *
5285715 AATAATGT-ACACGTTAAAATACATACAACATAACCG
195 AATAAGGTCA-ACGGTAAAATACATACAACATAACCG
* * *
5285751 GTTAAAAAACAATAAGCGCAACCTGTTACGTTAAAGTATCTACCTGTATAATG-ATAATGTAGAC
1 GTTAAAAAACAATAAGCGCAACATGTTACGTTAAAGTATCTACCGGTATAA-GAATAATGTAAAC
* * *
5285815 -GATAATATTATTTT-AACCTAACCGGTATAATCATAATGTAAACGATAAAATACTGACGA-TCT
65 AGATAA-A-TATTTTCAACCTAACCAGTATAATCATAATGTAAACGATAAAATACTAACAACT-T
* * *
5285877 AACCGGTTAAAGCAATTTAGGAACAACCTATTACTTTAAACTTCATACTAAATTTTTATAGGTAT
127 AACCGGTTAAAACAATTTAGCAACAACCTATTACTTTAAACTTCATACCAAATTTTTATAGGTAT
*
5285942 ATTAATAAGGTCAACGGTAAAATACATACAACTTAACCG
192 ATTAATAAGGTCAACGGTAAAATACATACAACATAACCG
5285981 GT
1 GT
5285983 CGAAATATCA
Statistics
Matches: 197, Mismatches: 30, Indels: 11
0.83 0.13 0.05
Matches are distributed among these distances:
230 52 0.26
231 138 0.70
232 7 0.04
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (230 bp):
GTTAAAAAACAATAAGCGCAACATGTTACGTTAAAGTATCTACCGGTATAAGAATAATGTAAACA
GATAAATATTTTCAACCTAACCAGTATAATCATAATGTAAACGATAAAATACTAACAACTTAACC
GGTTAAAACAATTTAGCAACAACCTATTACTTTAAACTTCATACCAAATTTTTATAGGTATATTA
ATAAGGTCAACGGTAAAATACATACAACATAACCG
Found at i:5289819 original size:20 final size:20
Alignment explanation
Indices: 5289779--5289817 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
5289769 CATTGCAAGA
*
5289779 ATTTATGGCTTCAACAAAAG
1 ATTTATGGCCTCAACAAAAG
5289799 ATTTCATGGCCTCAACAAA
1 ATTT-ATGGCCTCAACAAA
5289818 GACCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:5293239 original size:10 final size:10
Alignment explanation
Indices: 5293224--5293250 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
5293214 TATGGGGAAT
5293224 AGACTTTATG
1 AGACTTTATG
5293234 AGACTTTATG
1 AGACTTTATG
5293244 AGACTTT
1 AGACTTT
5293251 TTCCCACTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (10 bp):
AGACTTTATG
Found at i:5305791 original size:46 final size:46
Alignment explanation
Indices: 5305741--5306088 Score: 389
Period size: 46 Copynumber: 7.6 Consensus size: 46
5305731 TGCTCTAAAT
* * *
5305741 GGTGCATTATCAGCATGAAAGGATGCCATAAATGATAATGCACAAT
1 GGTGCATTATCAGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* * *
5305787 GGTGCATTATCGGCATGAAAAGATGCCATAAATGAAAATGTATAAC
1 GGTGCATTATCAGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* * * *
5305833 GGTGCATTATCGGCATGAAATGATGTCATAAATTAAAATGCATAAC
1 GGTGCATTATCAGCATGAAAGGATGCCATAAATGAAAATGCATAAC
** * * * *
5305879 ATTGTATTATCGGCATGAAAGAATGCCATAAATGAAAATACATAAC
1 GGTGCATTATCAGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* * * ** *
5305925 GGTACATTATCATCATGAAACGATGCCATAAATGAAAACACATAAT
1 GGTGCATTATCAGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* *
5305971 AGTGCATTAT-AGGCATGAAAGGATGCCATAAATAAAAATGCATAATC
1 GGTGCATTATCA-GCATGAAAGGATGCCATAAATGAAAATGCATAA-C
* * *
5306018 -GTGCATTATC-GACATGAAATGAAGCCATAAATGAAAATGTATAAC
1 GGTGCATTATCAG-CATGAAAGGATGCCATAAATGAAAATGCATAAC
5306063 GGTGCATTATC-GACATGAAAGGATGC
1 GGTGCATTATCAG-CATGAAAGGATGC
5306089 TGTAACCCCT
Statistics
Matches: 255, Mismatches: 42, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
45 3 0.01
46 252 0.99
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (46 bp):
GGTGCATTATCAGCATGAAAGGATGCCATAAATGAAAATGCATAAC
Found at i:5305950 original size:138 final size:137
Alignment explanation
Indices: 5305742--5306088 Score: 428
Period size: 138 Copynumber: 2.5 Consensus size: 137
5305732 GCTCTAAATG
* * * * * *
5305742 GTGCATTATCAGCATGAAAGGATGCCATAAATGATAATGCACAATGGTGCATTATCGGCATGAAA
1 GTGCATTATCGGCATGAAAGAATGCCATAAATGAAAATGCATAACGGTGCATTATC-ACATGAAA
*** * * * * *
5305807 AGATGCCATAAATGAAAATGTATAACGGTGCATTATCGGCATGAAATGATGTCATAAATTAAAAT
65 AGATGCCATAAATGAAAACACATAACAGTGCATTATAGGCATGAAAGGATGCCATAAATAAAAAT
5305872 GCATAA-C
130 GCATAATC
* * * *
5305879 ATTGTATTATCGGCATGAAAGAATGCCATAAATGAAAATACATAACGGTACATTATCATCATGAA
1 -GTGCATTATCGGCATGAAAGAATGCCATAAATGAAAATGCATAACGGTGCATTATCA-CATGAA
* *
5305944 ACGATGCCATAAATGAAAACACATAATAGTGCATTATAGGCATGAAAGGATGCCATAAATAAAAA
64 AAGATGCCATAAATGAAAACACATAACAGTGCATTATAGGCATGAAAGGATGCCATAAATAAAAA
5306009 TGCATAATC
129 TGCATAATC
* *
5306018 GTGCATTATCGACATGAAATGAA-GCCATAAATGAAAATGTATAACGGTGCATTATCGACATGAA
1 GTGCATTATCGGCATGAAA-GAATGCCATAAATGAAAATGCATAACGGTGCATTATC-ACATGAA
*
5306082 AGGATGC
64 AAGATGC
5306089 TGTAACCCCT
Statistics
Matches: 178, Mismatches: 27, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
138 173 0.97
139 5 0.03
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (137 bp):
GTGCATTATCGGCATGAAAGAATGCCATAAATGAAAATGCATAACGGTGCATTATCACATGAAAA
GATGCCATAAATGAAAACACATAACAGTGCATTATAGGCATGAAAGGATGCCATAAATAAAAATG
CATAATC
Found at i:5307377 original size:17 final size:17
Alignment explanation
Indices: 5307357--5307408 Score: 104
Period size: 17 Copynumber: 3.1 Consensus size: 17
5307347 GGAGGTCAAC
5307357 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
5307374 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
5307391 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
5307408 G
1 G
5307409 TCGAGTCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.12, C:0.23, G:0.48, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:5314613 original size:17 final size:17
Alignment explanation
Indices: 5314593--5314630 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
5314583 GGTCAATGGA
*
5314593 GGTCAACGGTCGGTTCG
1 GGTCAACGGTCGGGTCG
5314610 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
5314627 GGTC
1 GGTC
5314631 GGGTCGGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.24, G:0.45, T:0.21
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:5314667 original size:10 final size:9
Alignment explanation
Indices: 5314637--5314694 Score: 62
Period size: 9 Copynumber: 6.0 Consensus size: 9
5314627 GGTCGGGTCG
*
5314637 GGTCAGACC
1 GGTCAAACC
*
5314646 GGTCAGACC
1 GGTCAAACC
5314655 GGTCGAAACC
1 GGTC-AAACC
5314665 GGTCAAAACC
1 GGTC-AAACC
5314675 AGGTCAAAACC
1 -GGTC-AAACC
5314686 GGTCAAACC
1 GGTCAAACC
5314695 AGTTTTCCAG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
9 18 0.40
10 17 0.38
11 10 0.22
ACGTcount: A:0.33, C:0.31, G:0.26, T:0.10
Consensus pattern (9 bp):
GGTCAAACC
Found at i:5314681 original size:11 final size:10
Alignment explanation
Indices: 5314643--5314692 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
5314633 GTCGGGTCAG
*
5314643 ACCGGTC-AG
1 ACCGGTCAAA
*
5314652 ACCGGTCGAA
1 ACCGGTCAAA
5314662 ACCGGTCAAA
1 ACCGGTCAAA
5314672 ACCAGGTCAAA
1 ACC-GGTCAAA
5314683 ACCGGTCAAA
1 ACCGGTCAAA
5314693 CCAGTTTTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
9 7 0.19
10 20 0.54
11 10 0.27
ACGTcount: A:0.36, C:0.30, G:0.24, T:0.10
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:5314684 original size:21 final size:20
Alignment explanation
Indices: 5314643--5314696 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
5314633 GTCGGGTCAG
* *
5314643 ACCGGTCAGACC-GGTCGAA
1 ACCGGTCAAACCAGGTCAAA
5314662 ACCGGTCAAAACCAGGTCAAA
1 ACCGGTC-AAACCAGGTCAAA
5314683 ACCGGTCAAACCAG
1 ACCGGTCAAACCAG
5314697 TTTTCCAGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 7 0.23
20 11 0.35
21 13 0.42
ACGTcount: A:0.35, C:0.31, G:0.24, T:0.09
Consensus pattern (20 bp):
ACCGGTCAAACCAGGTCAAA
Found at i:5315709 original size:21 final size:21
Alignment explanation
Indices: 5315683--5315737 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
5315673 ATTGGAAACA
5315683 AAGTATCGATACTGTCATACC
1 AAGTATCGATACTGTCATACC
*
5315704 AAGTATCGATACCGTCATACC
1 AAGTATCGATACTGTCATACC
5315725 AAGTATCGATACT
1 AAGTATCGATACT
5315738 TTGACGTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.27
Consensus pattern (21 bp):
AAGTATCGATACTGTCATACC
Found at i:5316065 original size:100 final size:99
Alignment explanation
Indices: 5315898--5316134 Score: 314
Period size: 100 Copynumber: 2.4 Consensus size: 99
5315888 AATTAACTGG
* * *
5315898 TTAGGTTGTAAATGTTTTACTGTTTACATTATTGTTAACCCTATAAACAAATCGGTAGCAATGTT
1 TTAGGTTGTAAATATTTTACT-TTTACATTATTATTAACCCTATAAACAAACCGGTAGCAATGTT
* * *
5315963 AAAGTAATATGTTACGCCTAAATTGTTTTAACAGA
65 AAAGAAATAGGCTACGCCTAAATTGTTTTAACAGA
*
5315998 TTAGGTTGTAAATATTTTACCTTTTACATTATTATTAACCCTATAAACAAACCGGTAGC-ATCTT
1 TTAGGTTGTAAATATTTTA-CTTTTACATTATTATTAACCCTATAAACAAACCGGTAGCAAT-GT
* * *
5316062 TAAAGAAATAGGCTGCGCCTAAATTGTTTTAACCGG
64 TAAAGAAATAGGCTACGCCTAAATTGTTTTAACAGA
** *
5316098 TTAGCATGTAAATATTTTATCATTTACATTATTATTA
1 TTAGGTTGTAAATATTTTA-CTTTTACATTATTATTA
5316135 GATCGGTATA
Statistics
Matches: 121, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
99 2 0.02
100 117 0.97
101 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.40
Consensus pattern (99 bp):
TTAGGTTGTAAATATTTTACTTTTACATTATTATTAACCCTATAAACAAACCGGTAGCAATGTTA
AAGAAATAGGCTACGCCTAAATTGTTTTAACAGA
Found at i:5326285 original size:17 final size:17
Alignment explanation
Indices: 5326263--5326311 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
5326253 ATTCGAATAA
5326263 TTGAATCGAATATAATT
1 TTGAATCGAATATAATT
*
5326280 TTGAATTGAATATAATT
1 TTGAATCGAATATAATT
*
5326297 TTGAATCAAATATAA
1 TTGAATCGAATATAA
5326312 AATCTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (17 bp):
TTGAATCGAATATAATT
Found at i:5327184 original size:21 final size:22
Alignment explanation
Indices: 5327160--5327202 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
5327150 TGTTTCATCA
* *
5327160 TTGCATGATGAATT-CTTCAAC
1 TTGCATAACGAATTCCTTCAAC
5327181 TTGCATAACGAATTCCTTCAAC
1 TTGCATAACGAATTCCTTCAAC
5327203 GAAATCATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (22 bp):
TTGCATAACGAATTCCTTCAAC
Found at i:5327330 original size:12 final size:12
Alignment explanation
Indices: 5327285--5327338 Score: 74
Period size: 12 Copynumber: 4.5 Consensus size: 12
5327275 TTATAAATGA
* *
5327285 GGTGGAGAATGA
1 GGTGGAGAAGGC
5327297 GGTGGAGAA-GC
1 GGTGGAGAAGGC
5327308 AGGTGGAGAAGGC
1 -GGTGGAGAAGGC
5327321 GGTGGAGAAGGC
1 GGTGGAGAAGGC
5327333 GGTGGA
1 GGTGGA
5327339 TAATCAAGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
11 1 0.03
12 36 0.92
13 2 0.05
ACGTcount: A:0.28, C:0.06, G:0.56, T:0.11
Consensus pattern (12 bp):
GGTGGAGAAGGC
Found at i:5327395 original size:21 final size:21
Alignment explanation
Indices: 5327351--5327395 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5327341 ATCAAGTACT
*
5327351 AAATGAAGAGGATGAAATTAC
1 AAATGAAGAGGATGAAAATAC
* * *
5327372 AAATGATGATGATGAAAATCC
1 AAATGAAGAGGATGAAAATAC
5327393 AAA
1 AAA
5327396 AAAATATATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (21 bp):
AAATGAAGAGGATGAAAATAC
Found at i:5328739 original size:222 final size:223
Alignment explanation
Indices: 5328468--5328914 Score: 887
Period size: 222 Copynumber: 2.0 Consensus size: 223
5328458 GAAAATTTAA
5328468 TTCGACCAAATGAAAAAAGAAGCCAATTAATTTAAATTACATATTTAATTAGAAAATATAAAGGA
1 TTCGACCAAATGAAAAAAGAAGCCAATTAATTTAAATTACATATTTAATTAGAAAATATAAAGGA
5328533 TGTTTAATTGTTTAAAAAGATCAAGACCAAATCTCTAATATAAATTAGACGAATTATCTCAACAA
66 TGTTTAATTGTTTAAAAAGATCAAGACCAAATCTCTAATATAAATTAGACGAATTATCTCAACAA
5328598 GTTTAAATAAAATAACATTTCCTTTTCCCTTTAATCTTGATTAATTTAAGCATACTAGATTTTTA
131 GTTTAAATAAAATAACATTTCCTTTTCCCTTTAATCTTGATTAATTTAAGCATACTAGATTTTTA
5328663 GGTTC-TTCAGTAGGGTATTTAATTATT
196 GGTTCTTTCAGTAGGGTATTTAATTATT
5328690 TTCGACCAAATGAAAAAAGAAGCCAATTAATTTAAATTACATATTTAATTAGAAAATATAAAGGA
1 TTCGACCAAATGAAAAAAGAAGCCAATTAATTTAAATTACATATTTAATTAGAAAATATAAAGGA
5328755 TGTTTAATTGTTTAAAAAGATCAAGACCAAATCTCTAATATAAATTAGACGAATTATCTCAACAA
66 TGTTTAATTGTTTAAAAAGATCAAGACCAAATCTCTAATATAAATTAGACGAATTATCTCAACAA
5328820 GTTTAAATAAAATAACATTTCCTTTTCCCTTTAATCTTGATTAATTTAAGCATACTAGATTTTTA
131 GTTTAAATAAAATAACATTTCCTTTTCCCTTTAATCTTGATTAATTTAAGCATACTAGATTTTTA
5328885 GGTTCTTTCAGTAGGGTATTTAATTATT
196 GGTTCTTTCAGTAGGGTATTTAATTATT
5328913 TT
1 TT
5328915 AAAATATCAA
Statistics
Matches: 224, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
222 200 0.89
223 24 0.11
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (223 bp):
TTCGACCAAATGAAAAAAGAAGCCAATTAATTTAAATTACATATTTAATTAGAAAATATAAAGGA
TGTTTAATTGTTTAAAAAGATCAAGACCAAATCTCTAATATAAATTAGACGAATTATCTCAACAA
GTTTAAATAAAATAACATTTCCTTTTCCCTTTAATCTTGATTAATTTAAGCATACTAGATTTTTA
GGTTCTTTCAGTAGGGTATTTAATTATT
Found at i:5331344 original size:41 final size:42
Alignment explanation
Indices: 5331294--5331374 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 42
5331284 AGGTCTTATG
* * * *
5331294 GATGGCCCGAAAGACTT-ATCATCTTGCTCGAAAGACTTACA
1 GATGACCCGAAAGACTTAAGCATCATACTCGAAAGACTTACA
* *
5331335 GATGACCCGAAGGATTTAAGCATCATACTCGAAAGACTTA
1 GATGACCCGAAAGACTTAAGCATCATACTCGAAAGACTTA
5331375 TTGATGGGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 14 0.42
42 19 0.58
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (42 bp):
GATGACCCGAAAGACTTAAGCATCATACTCGAAAGACTTACA
Found at i:5331531 original size:53 final size:53
Alignment explanation
Indices: 5331437--5331790 Score: 347
Period size: 53 Copynumber: 6.7 Consensus size: 53
5331427 TTTCTTAATT
* * ** * *
5331437 ATCAAGGAACCCATAAAAATTTGGCTTAACTCCTTTCAAATTCATTTAAAAAC
1 ATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAATTCATTTAAAAAC
* * * *
5331490 ATTAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTTAAATTCATTTGAAAAC
1 ATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAATTCATTTAAAAAC
* *
5331543 ATC-GGTAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAATTCATTTGAAAAC
1 ATCAAG-AAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAATTCATTTAAAAAC
* ** *
5331596 ATCAAGGAAA-CCCTAAAAATTAGGCTTAATTTCTTTCAAATTCATTTTAAAAC
1 ATCAA-GAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAATTCATTTAAAAAC
* * * *
5331649 ATTAAGAAACCCCTGAAAACCAGGCTTAG-TT-TTTCAAATTCATTTTAAAAC
1 ATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAATTCATTTAAAAAC
* * ** * * **
5331700 ATCAAGAAACCCCTAAAAATTAGGCTAAATTTCTTTGAAAGTTCTTTTAAACATT
1 ATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAA-TTCATTTAAA-AAC
** * * *
5331755 ATCAAGAAACTTCTGAAAATCAGACTTAGATTCTTT
1 ATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTT
5331791 AAAAACTAAT
Statistics
Matches: 250, Mismatches: 43, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
51 43 0.17
52 9 0.04
53 157 0.63
54 11 0.04
55 30 0.12
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (53 bp):
ATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTCAAATTCATTTAAAAAC
Found at i:5331759 original size:159 final size:161
Alignment explanation
Indices: 5331433--5331764 Score: 446
Period size: 159 Copynumber: 2.1 Consensus size: 161
5331423 TTAGTTTCTT
*
5331433 AATTATCAAGG-AACCCATAAAAATTTGGCTTAACTCCTTTCAAATTCATTTAAAAACATTAAGA
1 AATTATCAAGGAAACCCATAAAAATTAGGCTTAACTCCTTTCAAATTCATTTAAAAACATTAAGA
* * *
5331497 AACCCCTGAAAATCAGGCTTAGCTTCTTTTAAATTCATTTGAAAACATCGGTAAACCCCTAAAAA
66 AACCCCTGAAAACCAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAGTAAACCCCTAAAAA
* *
5331562 TCAGGCTTAGCTTCTTTCAAATTCATTTGAA
131 TCAGGCTAAACTTCTTTCAAATTCATTTGAA
* * * *
5331593 AA-CATCAAGGAAACCC-TAAAAATTAGGCTTAATTTCTTTCAAATTCATTTTAAAACATTAAGA
1 AATTATCAAGGAAACCCATAAAAATTAGGCTTAACTCCTTTCAAATTCATTTAAAAACATTAAGA
*
5331656 AACCCCTGAAAACCAGGCTTAG-TT-TTTCAAATTCATTTTAAAACATCAAG-AAACCCCTAAAA
66 AACCCCTGAAAACCAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATC-AGTAAACCCCTAAAA
* * * *
5331718 ATTAGGCTAAATTTCTTTGAAAGTTC-TTTTAA
130 ATCAGGCTAAACTTCTTTCAAA-TTCATTTGAA
5331750 ACATTATCAA-GAAAC
1 A-ATTATCAAGGAAAC
5331765 TTCTGAAAAT
Statistics
Matches: 151, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
157 56 0.37
158 12 0.08
159 76 0.50
160 7 0.05
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (161 bp):
AATTATCAAGGAAACCCATAAAAATTAGGCTTAACTCCTTTCAAATTCATTTAAAAACATTAAGA
AACCCCTGAAAACCAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCAGTAAACCCCTAAAAA
TCAGGCTAAACTTCTTTCAAATTCATTTGAA
Found at i:5331827 original size:54 final size:55
Alignment explanation
Indices: 5331755--5331947 Score: 216
Period size: 54 Copynumber: 3.5 Consensus size: 55
5331745 TTTAAACATT
5331755 ATCAAGAAACTTCTGAAAATCAGACTTAGATTCTTTAAAAACTAATTAAAAAATA
1 ATCAAGAAACTTCTGAAAATCAGACTTAGATTCTTTAAAAACTAATTAAAAAATA
* *** *
5331810 ATCAA-AAACTT-TCGAAAATCAGACTTAGTTTCTTT-AAAAC-ACATTTGGAAATC
1 ATCAAGAAACTTCT-GAAAATCAGACTTAGATTCTTTAAAAACTA-ATTAAAAAATA
5331863 ATCAAGAAACTTCTGAAAATCAGACTTA-ATTTCTTTAAAAAACTAATTAAAAAATA
1 ATCAAGAAACTTCTGAAAATCAGACTTAGA-TTCTTT-AAAAACTAATTAAAAAATA
* *
5331919 CCATGTCAAGAAACCTCTAAAAATCAGAC
1 --A--TCAAGAAACTTCTGAAAATCAGAC
5331948 GTAGTTCCTA
Statistics
Matches: 114, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
52 1 0.01
53 18 0.16
54 53 0.46
55 6 0.05
56 12 0.11
57 1 0.01
58 1 0.01
60 22 0.19
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (55 bp):
ATCAAGAAACTTCTGAAAATCAGACTTAGATTCTTTAAAAACTAATTAAAAAATA
Found at i:5340966 original size:147 final size:145
Alignment explanation
Indices: 5340676--5340966 Score: 530
Period size: 147 Copynumber: 2.0 Consensus size: 145
5340666 TCATCCATAA
5340676 GGATTATATAAGTCCTTATTATTTAAACCAAATTTCTTTCATACCATCATCGTAAACATTCTTAG
1 GGATTATATAAGTCCTTATTATTTAAACCAAATTTCTTTCATACCATCATCGTAAACATTCTTAG
5340741 TATGTCCAACATACTTTTCTTTTTGTACATTTTTCCCATTTTCTTTAGTTTCATTTTTATGCACC
66 TATGTCCAACATACTTTTCTTTTTGTACATTTTTCCCATTTTCTTTAGTTTCATTTTTATGCACC
5340806 ATTATGCTTCATTTATG
131 ATTATG--TCATTTATG
5340823 GGATTATATAAGTCCTTATTATTTAAACCAAATTTCTTTCATACCATCATCGTAAACATTCTTAG
1 GGATTATATAAGTCCTTATTATTTAAACCAAATTTCTTTCATACCATCATCGTAAACATTCTTAG
5340888 TATGTCCAACATACTTTTCTTTTTGTACATTATTTTCCCATTATTCTTTAGTTTCATTTTTATGC
66 TATGTCCAACATACTTTTCTTTTTGTACA-T-TTTTCCCATT-TTCTTTAGTTTCATTTTTATGC
5340953 ACCATTATG-CATTT
128 ACCATTATGTCATTT
5340967 CATTTATGGC
Statistics
Matches: 141, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
147 99 0.70
148 1 0.01
149 10 0.07
150 31 0.22
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.47
Consensus pattern (145 bp):
GGATTATATAAGTCCTTATTATTTAAACCAAATTTCTTTCATACCATCATCGTAAACATTCTTAG
TATGTCCAACATACTTTTCTTTTTGTACATTTTTCCCATTTTCTTTAGTTTCATTTTTATGCACC
ATTATGTCATTTATG
Found at i:5341396 original size:54 final size:54
Alignment explanation
Indices: 5341338--5341899 Score: 760
Period size: 54 Copynumber: 10.4 Consensus size: 54
5341328 CTATATGATC
* * * *
5341338 GTTCATCAACACATGATGAATTCTGTGAGATGCACACATAGTGCTTGTATGGTT
1 GTTCATCAACATATGATGAATTCCGTGAGTTGCACACATAGTGCTTGTACGGTT
*
5341392 GTTCATCAACATATGATGAATTCCGTGAGTTGCACACATAGTGCATGTACGGTT
1 GTTCATCAACATATGATGAATTCCGTGAGTTGCACACATAGTGCTTGTACGGTT
*
5341446 GTTCATCAACATATGATGAATTCCATGAGTTGCACACATAGTGCTTGTACGGTT
1 GTTCATCAACATATGATGAATTCCGTGAGTTGCACACATAGTGCTTGTACGGTT
5341500 G-T--TCAACATATGATGAATTCCGTGAGTTGCACACATAGTGCTTGTACGGTT
1 GTTCATCAACATATGATGAATTCCGTGAGTTGCACACATAGTGCTTGTACGGTT
* *
5341551 GTTCATCAACATATGATAAATTCCGTGAGTTGCACACATAGTGCATGTACGGTT
1 GTTCATCAACATATGATGAATTCCGTGAGTTGCACACATAGTGCTTGTACGGTT
* *
5341605 GTTCATCAACATATGATGAATTCCGAGGGTTGCACACATAGTGCTTGTACGGTT
1 GTTCATCAACATATGATGAATTCCGTGAGTTGCACACATAGTGCTTGTACGGTT
* * *
5341659 ATTCATCAATATATGATGAATTCCTTGAGTTGCACACATAGTG-TCTGTACGGTT
1 GTTCATCAACATATGATGAATTCCGTGAGTTGCACACATAGTGCT-TGTACGGTT
* * *
5341713 GTTCATCAACATATGATGAATTCCGTG-GTTTTGCACACATAGTGCCTATACGGTC
1 GTTCATCAACATATGATGAATTCCGTGAG--TTGCACACATAGTGCTTGTACGGTT
* * * *
5341768 GTTCATCAACATATGATGAATTTCGTG-GTTTTGCACACATAGTGCCTATACGGTC
1 GTTCATCAACATATGATGAATTCCGTGAG--TTGCACACATAGTGCTTGTACGGTT
* * * * * * *
5341823 CTTGATCAACATATGATGAATTTCGT-AGTTTTGCACACATAGTGCCTATACAGTC
1 GTTCATCAACATATGATGAATTCCGTGAG--TTGCACACATAGTGCTTGTACGGTT
*
5341878 ATTCATCAACATATGATGAATT
1 GTTCATCAACATATGATGAATT
5341900 ATGTGGTTTG
Statistics
Matches: 469, Mismatches: 31, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
51 49 0.10
52 1 0.00
53 3 0.01
54 270 0.58
55 146 0.31
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (54 bp):
GTTCATCAACATATGATGAATTCCGTGAGTTGCACACATAGTGCTTGTACGGTT
Found at i:5341637 original size:159 final size:159
Alignment explanation
Indices: 5341343--5341899 Score: 753
Period size: 159 Copynumber: 3.4 Consensus size: 159
5341333 TGATCGTTCA
* * * *
5341343 TCAACACATGATGAATTCTGTGAGATGCACACATAGTGCTTGTATGGTTGTTCATCAACATATGA
1 TCAACATATGATGAATTCCGTGAGTTGCACACATAGTGCTTGTACGGTTGTTCATCAACATATGA
5341408 TGAATTCCGTGAGTTGCACACATAGTGCATGTACGGTTGTTCATCAACATATGATGAATTCC-AT
66 TGAATTCCGTGAGTTGCACACATAGTGCATGTACGGTTGTTCATCAACATATGATGAATTCCGA-
*
5341472 GAGTTGCACACATAGTGCTTGTACGGTTGT
130 GGGTTGCACACATAGTGCTTGTACGGTTGT
5341502 TCAACATATGATGAATTCCGTGAGTTGCACACATAGTGCTTGTACGGTTGTTCATCAACATATGA
1 TCAACATATGATGAATTCCGTGAGTTGCACACATAGTGCTTGTACGGTTGTTCATCAACATATGA
*
5341567 TAAATTCCGTGAGTTGCACACATAGTGCATGTACGGTTGTTCATCAACATATGATGAATTCCGAG
66 TGAATTCCGTGAGTTGCACACATAGTGCATGTACGGTTGTTCATCAACATATGATGAATTCCGAG
*
5341632 GGTTGCACACATAGTGCTTGTACGGTTATT
131 GGTTGCACACATAGTGCTTGTACGGTT-GT
* *
5341662 CATCAATATATGATGAATTCCTTGAGTTGCACACATAGTG-TCTGTACGGTTGTTCATCAACATA
1 --TCAACATATGATGAATTCCGTGAGTTGCACACATAGTGCT-TGTACGGTTGTTCATCAACATA
* * *
5341726 TGATGAATTCCGTG-GTTTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATT
63 TGATGAATTCCGTGAG--TTGCACACATAGTGCATGTACGGTTGTTCATCAACATATGATGAATT
* * * * * *
5341790 TCGTGGTTTTGCACACATAGTGCCTATACGGTCCTTGA
126 CCGAGG-GTTGCACACATAGTGCTTGTACGG---TTGT
* * * * **
5341828 TCAACATATGATGAATTTCGT-AGTTTTGCACACATAGTGCCTATACAGTCATTCATCAACATAT
1 TCAACATATGATGAATTCCGTGAG--TTGCACACATAGTGCTTGTACGGTTGTTCATCAACATAT
5341892 GATGAATT
64 GATGAATT
5341900 ATGTGGTTTG
Statistics
Matches: 356, Mismatches: 28, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
159 149 0.42
160 2 0.01
161 2 0.01
162 71 0.20
163 50 0.14
164 39 0.11
165 41 0.12
167 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (159 bp):
TCAACATATGATGAATTCCGTGAGTTGCACACATAGTGCTTGTACGGTTGTTCATCAACATATGA
TGAATTCCGTGAGTTGCACACATAGTGCATGTACGGTTGTTCATCAACATATGATGAATTCCGAG
GGTTGCACACATAGTGCTTGTACGGTTGT
Found at i:5343529 original size:103 final size:98
Alignment explanation
Indices: 5343304--5343636 Score: 373
Period size: 100 Copynumber: 3.3 Consensus size: 98
5343294 ATCGATACCT
* * ** *
5343304 ATATTTACAACTTAATCGGTTAAAATAAAATAGACACTACTTATTACGTTAAAATAGTTA-CATG
1 ATATTTACAACTTAACCGGTTAAAATAAAATAGGCACTACCAATTACGTTAAACTA-TTATC-TG
* * *
5343368 TTTGTTTAAAGCAATAATATTAATGTAAACGGTCAA
64 TTTGTTTAAAGGAATAATATTAATGTAAA-AGTAAA
* * *
5343404 ATATTTTCAACTTAACCGGTTAAAGTAAAATAGGCACTACCAATTTCGTTAAACTATCTATCTGT
1 ATATTTACAACTTAACCGGTTAAAATAAAATAGGCACTACCAATTACGTTAAACTAT-TATCTGT
* *
5343469 TTGCTTAAAGGTATAATAATAATAATGTAAATAGTAAA
65 TTGTTTAAAGG---AATAATATTAATGTAAA-AGTAAA
* *** *
5343507 ATATTTACAACTTAACTGGTTAAAATAAAATAGGTGTTA-CATATTACGTTAAACTATTTATCGG
1 ATATTTACAACTTAACCGGTTAAAATAAAATAGGCACTACCA-ATTACGTTAAACTA-TTATCTG
*
5343571 TTTATTTAAAGGAATAATATTAATGTAAAATGTAAA
64 TTTGTTTAAAGGAATAATATTAATGTAAAA-GTAAA
*
5343607 ATATTTATAACTTAACCGGTTAAAATAAAA
1 ATATTTACAACTTAACCGGTTAAAATAAAA
5343637 CATGTTGAGT
Statistics
Matches: 198, Mismatches: 27, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
99 2 0.01
100 111 0.56
101 1 0.01
102 2 0.01
103 81 0.41
104 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (98 bp):
ATATTTACAACTTAACCGGTTAAAATAAAATAGGCACTACCAATTACGTTAAACTATTATCTGTT
TGTTTAAAGGAATAATATTAATGTAAAAGTAAA
Found at i:5349565 original size:21 final size:21
Alignment explanation
Indices: 5349539--5349578 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5349529 CCCCCTTTGA
*
5349539 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
5349560 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
5349579 CTGGGGTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:5353232 original size:6 final size:6
Alignment explanation
Indices: 5353218--5353252 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
5353208 CCAGTACTTA
* *
5353218 AATTTC AATTCC AATTTC AATTTT AATTTC AATTT
1 AATTTC AATTTC AATTTC AATTTC AATTTC AATTT
5353253 GAGCTTCGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (6 bp):
AATTTC
Found at i:5354471 original size:99 final size:99
Alignment explanation
Indices: 5354294--5354972 Score: 848
Period size: 100 Copynumber: 6.8 Consensus size: 99
5354284 TTAGTTAACA
* * *
5354294 TTAAAATAAAATAGGCGCTACCTATTACATTAAACTAGCTATTGGTTTGTTTAAAGG-ATAATAT
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTA-CGGTTTGTTTAAAGGTATAATAT
* *
5354358 TAAAGTAAACGGTAAAATATTTATAACTTAACCGG
65 TAATGTAAACGGTAAAATATTTACAACTTAACCGG
* * *
5354393 TTAAAATAATATAGGCGCTACCTAATACGTTAAACTACCTATCGGTTTGTTTAAATGTATAATAT
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTA-CGGTTTGTTTAAAGGTATAATAT
* * *
5354458 TAATGTAAA-GGTAAAATATTTGCAACTTAATCAG
65 TAATGTAAACGGTAAAATATTTACAACTTAACCGG
* * * * *
5354492 TTAAATTAAAATAGGCGCCACCTATTACGTTAAACAACCTACTGATTTGTTT-AAGATATAATAT
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTAC-GGTTTGTTTAAAGGTATAATAT
*
5354556 TAATGTAAAAGGTAAACA-ATTTACAACTTAACCGG
65 TAATGTAAACGGTAAA-ATATTTACAACTTAACCGG
* * * * *
5354591 TT-AAATAAAATAGGTGTTACCTATTACGTTAAACTACCTACATGCTTGCTTAAAGGTATAATAT
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTAC-GGTTTGTTTAAAGGTATAATAT
* * *
5354655 TAATGTAAATGGTCAAATATTTACAACTTAAACGG
65 TAATGTAAACGGTAAAATATTTACAACTTAACCGG
* * * * *
5354690 TTAAAATAAAATAGGCGTTACATAATATGTTAAACTACCTACCGATTTGTTTAAAGGTATAATAT
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTA-CGGTTTGTTTAAAGGTATAATAT
* *
5354755 TAAAGTAAACGGTCAAATATTTACAACTTAACCGG
65 TAATGTAAACGGTAAAATATTTACAACTTAACCGG
** * * * *
5354790 TTAAAATAAAATAGATGTTACCTATTACGTTAAACTACCTACCAGTTTGTTTAAAGGTCTAATAG
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTA-CGGTTTGTTTAAAGGTATAATAT
*
5354855 TATTGTAAACGGTAAAATATTTACAACTTAACCGG
65 TAATGTAAACGGTAAAATATTTACAACTTAACCGG
* * * *
5354890 TTAAAATAAAATAGACGCTACCTATTACGTTAAACTACCTACTAGTTTATTTAAAGGT-TAATAA
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTAC-GGTTTGTTTAAAGGTATAATAT
*
5354954 TAACGTAAACGGTAAAATA
65 TAATGTAAACGGTAAAATA
5354973 AAATATGCAC
Statistics
Matches: 506, Mismatches: 65, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
98 60 0.12
99 204 0.40
100 241 0.48
101 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (99 bp):
TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACGGTTTGTTTAAAGGTATAATATT
AATGTAAACGGTAAAATATTTACAACTTAACCGG
Found at i:5354675 original size:198 final size:197
Alignment explanation
Indices: 5354294--5354970 Score: 860
Period size: 198 Copynumber: 3.4 Consensus size: 197
5354284 TTAGTTAACA
* * * * *
5354294 TTAAAATAAAATAGGCGCTACCTATTACATTAAACTAGCTATTGGTTTGTTTAA-AGGATAATAT
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGATTTGTTTAAGA-TATAATAT
* * * * *
5354358 TAAAGTAAACGGTAAAATATTTATAACTTAACCGGTTAAAATAATATAGGCGCTACCTAATACGT
65 TAAAGTAAACGGTAAAA-ATTTACAACTTAACCGGTTAAAATAAAATAGGTGTTACCTATTACGT
* * * *
5354423 TAAACTACCTATCGGTTTGTTTAAATGTATAATATTAATGTAAAGGTAAAATATTTGCAACTTAA
129 TAAACTACCTACCAGTTTGTTTAAAGGTATAATATTAATGTAAAGGTAAAATATTTACAACTTAA
* *
5354488 TCAG
194 ACGG
* * *
5354492 TTAAATTAAAATAGGCGCCACCTATTACGTTAAACAACCTACTGATTTGTTTAAGATATAATATT
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGATTTGTTTAAGATATAATATT
* *
5354557 AATGTAAAAGGTAAACAATTTACAACTTAACCGGTT-AAATAAAATAGGTGTTACCTATTACGTT
66 AAAGTAAACGGTAAA-AATTTACAACTTAACCGGTTAAAATAAAATAGGTGTTACCTATTACGTT
* * *
5354621 AAACTACCTA-CATGCTTGCTTAAAGGTATAATATTAATGTAAATGGTCAAATATTTACAACTTA
130 AAACTACCTACCA-GTTTGTTTAAAGGTATAATATTAATGTAAA-GGTAAAATATTTACAACTTA
5354685 AACGG
193 AACGG
* * * * * *
5354690 TTAAAATAAAATAGGCGTTACATAATATGTTAAACTACCTACCGATTTGTTTAAAGGTATAATAT
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGATTTGTTT-AAGATATAATAT
* *
5354755 TAAAGTAAACGGTCAAATATTTACAACTTAACCGGTTAAAATAAAATAGATGTTACCTATTACGT
65 TAAAGTAAACGGT-AAAAATTTACAACTTAACCGGTTAAAATAAAATAGGTGTTACCTATTACGT
* * *
5354820 TAAACTACCTACCAGTTTGTTTAAAGGTCTAATAGTATTGTAAACGGTAAAATATTTACAACTTA
129 TAAACTACCTACCAGTTTGTTTAAAGGTATAATATTAATGTAAA-GGTAAAATATTTACAACTTA
*
5354885 ACCGG
193 AACGG
* * *
5354890 TTAAAATAAAATAGACGCTACCTATTACGTTAAACTACCTACT-AGTTTATTTAAAGGT-TAATA
1 TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGA-TTTGTTT-AAGATATAATA
* *
5354953 ATAACGTAAACGGTAAAA
64 TTAAAGTAAACGGTAAAA
5354971 TAAAATATGC
Statistics
Matches: 416, Mismatches: 54, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
196 1 0.00
197 61 0.15
198 154 0.37
199 61 0.15
200 137 0.33
201 2 0.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (197 bp):
TTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGATTTGTTTAAGATATAATATT
AAAGTAAACGGTAAAAATTTACAACTTAACCGGTTAAAATAAAATAGGTGTTACCTATTACGTTA
AACTACCTACCAGTTTGTTTAAAGGTATAATATTAATGTAAAGGTAAAATATTTACAACTTAAAC
GG
Found at i:5355089 original size:75 final size:75
Alignment explanation
Indices: 5354891--5355123 Score: 265
Period size: 75 Copynumber: 3.1 Consensus size: 75
5354881 CTTAACCGGT
* * * * * *
5354891 TAAAATAAAATAGACGCTACCTATTACGTTAAACTACCTACTAGTTTATTTAAAGGTTAATAATA
1 TAAAATAAAATTGGCACTACCTATTACGTTAAACTACCTACCAGTTTGTTTAAATGTTAATAATA
* *
5354956 ACGTAAACGG
66 ATGTAAACGA
* *
5354966 TAAAATAAAATAT-GCACTGCCTATTACGGTAAACTACCTACCAGTTTGTTTAAATGTTAATAAT
1 TAAAATAAAAT-TGGCACTACCTATTACGTTAAACTACCTACCAGTTTGTTTAAATGTTAATAAT
*
5355030 AATATAAACGA
65 AATGTAAACGA
* * * * *
5355041 TAAAATAAAATTGGCACTACCTATTACTTTAAACTACATATC-GATTTGTTAAAATATATAATAA
1 TAAAATAAAATTGGCACTACCTATTACGTTAAACTACCTACCAG-TTTGTTTAAATGT-TAATAA
5355105 TAATGTAAAC-A
64 TAATGTAAACGA
5355116 GTAAAATA
1 -TAAAATA
5355124 TTTACAATTT
Statistics
Matches: 134, Mismatches: 19, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
74 2 0.01
75 110 0.82
76 22 0.16
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (75 bp):
TAAAATAAAATTGGCACTACCTATTACGTTAAACTACCTACCAGTTTGTTTAAATGTTAATAATA
ATGTAAACGA
Found at i:5355859 original size:108 final size:108
Alignment explanation
Indices: 5355730--5356125 Score: 546
Period size: 108 Copynumber: 3.6 Consensus size: 108
5355720 TGTTAATATT
* * * * * *
5355730 TATTTATAACAAAAATAAGTAATTAACATATTCTGTTGTCG-TGAGATTTCGAATGCCCCATCAG
1 TATTAATAAC-AAAATAAGTAATTAACTTATTTTGTTATCGCTG-GATTTCTAAGGCCCCATCAG
*
5355794 CTTACACTTTAGTAATATTTTAGGCGCTACCTAATATGTTGATAA
64 CTTAAACTTTAGTAATATTTTAGGCGCTACCTAATATGTTGATAA
* * * *
5355839 TATTAATAACAAAATAAGTAATTAACTTATTTTGTTATCGTTGGATTTCTAAGACTCTATCAGCT
1 TATTAATAACAAAATAAGTAATTAACTTATTTTGTTATCGCTGGATTTCTAAGGCCCCATCAGCT
*
5355904 TAAACTTTGGTAATATTTTAGGCGCTACCTAATATGTTGATAA
66 TAAACTTTAGTAATATTTTAGGCGCTACCTAATATGTTGATAA
* * * *
5355947 TATCAATAACAAAATAAGTAATTAACCTATTTTGTTATCG-TCGGATTTCTAAGGTCTCATCAGC
1 TATTAATAACAAAATAAGTAATTAACTTATTTTGTTATCGCT-GGATTTCTAAGGCCCCATCAGC
* *
5356011 TTAAACTTTAGTAACATTTTAGGTGCTACCTAATATGTTGATAA
65 TTAAACTTTAGTAATATTTTAGGCGCTACCTAATATGTTGATAA
* *
5356055 TATTAATAAC-AAATGAAGTAATTAACTTATTTTGTCATCGCTGGATTTCTAAGGCCTCATCAGC
1 TATTAATAACAAAAT-AAGTAATTAACTTATTTTGTTATCGCTGGATTTCTAAGGCCCCATCAGC
5356119 TTTAAAC
65 -TTAAAC
5356126 AGACGCAACC
Statistics
Matches: 257, Mismatches: 25, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
107 5 0.02
108 234 0.91
109 18 0.07
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (108 bp):
TATTAATAACAAAATAAGTAATTAACTTATTTTGTTATCGCTGGATTTCTAAGGCCCCATCAGCT
TAAACTTTAGTAATATTTTAGGCGCTACCTAATATGTTGATAA
Found at i:5356032 original size:216 final size:218
Alignment explanation
Indices: 5355735--5356125 Score: 603
Period size: 216 Copynumber: 1.8 Consensus size: 218
5355725 ATATTTATTT
* * *
5355735 ATAACAAAAATAAGTAATTAACATATTCTGTTGTCGTGAGATTTCGAATGCCCCATCAGCTTACA
1 ATAACAAAAATAAGTAATTAACATATTCTGTTATCGTGAGATTTCGAAGGCCCCATCAGCTTAAA
*
5355800 CTTTAGTAATATTTTAGGCGCTACCTAATATGTTGATAATATTAATAACAAAAT-AAGTAATTAA
66 CTTTAGTAACATTTTAGGCGCTACCTAATATGTTGATAATATTAATAAC-AAATGAAGTAATTAA
* *
5355864 CTTATTTTGTTATCGTTGGATTTCTAAGA-CTCTATCAGC-TTAAACTTTGGTAATATTTTAGGC
130 CTTATTTTGTCATCGCTGGATTTCTAAGACCTC-ATCAGCTTTAAACTTTGGTAATATTTTAGGC
5355927 GCTACCTAATATGTTGATAATATCA
194 GCTACCTAATATGTTGATAATATCA
* * * * *
5355952 ATAAC-AAAATAAGTAATTAACCTATTTTGTTATCGTCG-GATTTCTAAGGTCTCATCAGCTTAA
1 ATAACAAAAATAAGTAATTAACATATTCTGTTATCGT-GAGATTTCGAAGGCCCCATCAGCTTAA
*
5356015 ACTTTAGTAACATTTTAGGTGCTACCTAATATGTTGATAATATTAATAACAAATGAAGTAATTAA
65 ACTTTAGTAACATTTTAGGCGCTACCTAATATGTTGATAATATTAATAACAAATGAAGTAATTAA
*
5356080 CTTATTTTGTCATCGCTGGATTTCTAAGGCCTCATCAGCTTTAAAC
130 CTTATTTTGTCATCGCTGGATTTCTAAGACCTCATCAGCTTTAAAC
5356126 AGACGCAACC
Statistics
Matches: 157, Mismatches: 13, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
215 4 0.03
216 138 0.88
217 15 0.10
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (218 bp):
ATAACAAAAATAAGTAATTAACATATTCTGTTATCGTGAGATTTCGAAGGCCCCATCAGCTTAAA
CTTTAGTAACATTTTAGGCGCTACCTAATATGTTGATAATATTAATAACAAATGAAGTAATTAAC
TTATTTTGTCATCGCTGGATTTCTAAGACCTCATCAGCTTTAAACTTTGGTAATATTTTAGGCGC
TACCTAATATGTTGATAATATCA
Found at i:5358886 original size:42 final size:42
Alignment explanation
Indices: 5358823--5358931 Score: 191
Period size: 42 Copynumber: 2.6 Consensus size: 42
5358813 TATGGTATAA
* *
5358823 AACCCTGCGGGCTAGGCATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
5358865 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
*
5358907 AACCTTGCGGGCTCGGAATGTAACC
1 AACCCTGCGGGCTCGGAATGTAACC
5358932 CTGCGGATAT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.22, C:0.25, G:0.34, T:0.19
Consensus pattern (42 bp):
AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
Found at i:5358936 original size:21 final size:21
Alignment explanation
Indices: 5358823--5358937 Score: 162
Period size: 21 Copynumber: 5.5 Consensus size: 21
5358813 TATGGTATAA
*
5358823 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
5358844 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
5358865 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
5358886 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* *
5358907 AACCTTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
5358928 AACCCTGCGG
1 AACCCTGCGG
5358938 ATATGGCATA
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
20 6 0.07
21 73 0.87
22 5 0.06
ACGTcount: A:0.21, C:0.25, G:0.35, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:5358987 original size:21 final size:21
Alignment explanation
Indices: 5358942--5358988 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5358932 CTGCGGATAT
* * *
5358942 GGCATATGAACTGGTGGGTTT
1 GGCATATGAACTGGAGGGCTG
*
5358963 GGCATATGAAGTGGAGGGCTG
1 GGCATATGAACTGGAGGGCTG
5358984 GGCAT
1 GGCAT
5358989 GTACCCCTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.11, G:0.43, T:0.26
Consensus pattern (21 bp):
GGCATATGAACTGGAGGGCTG
Found at i:5360533 original size:26 final size:27
Alignment explanation
Indices: 5360504--5360568 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
5360494 GTATCCTAAA
*
5360504 TAATATACATT-ATAAAAAATTAAAAT
1 TAATATAAATTCATAAAAAATTAAAAT
* * *
5360530 TAATATAAATTCATAATAACTTTAAAT
1 TAATATAAATTCATAAAAAATTAAAAT
*
5360557 TAAAAATAAATT
1 T-AATATAAATT
5360569 TAAATATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 10 0.31
27 13 0.41
28 9 0.28
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (27 bp):
TAATATAAATTCATAAAAAATTAAAAT
Found at i:5360557 original size:17 final size:17
Alignment explanation
Indices: 5360520--5360573 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
5360510 ACATTATAAA
* *
5360520 AAATT-AAAATTAATAT
1 AAATTAAAAATAAATTT
* * *
5360536 AAATTCATAATAACTTT
1 AAATTAAAAATAAATTT
5360553 AAATTAAAAATAAATTT
1 AAATTAAAAATAAATTT
5360570 AAAT
1 AAAT
5360574 ATTAACATTA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTAAAAATAAATTT
Found at i:5367890 original size:3 final size:3
Alignment explanation
Indices: 5367884--5367955 Score: 76
Period size: 3 Copynumber: 24.0 Consensus size: 3
5367874 ATTTTTGTTT
** * *
5367884 TTA TTA TTA TTA TTA TTA AAA TTA ATA TTA TTA TTA ATA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
5367932 TTA TTA -TA TATA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA
5367956 AAAAATAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
2 4 0.07
3 47 0.82
4 6 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:5369375 original size:2 final size:2
Alignment explanation
Indices: 5369357--5369391 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5369347 CTTTCATTAT
* *
5369357 TA TA TT TA TA TA AA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5369392 TTTGGTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5369670 original size:20 final size:19
Alignment explanation
Indices: 5369645--5369686 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
5369635 CTATTTTATA
5369645 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
5369665 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
5369684 AAT
1 AAT
5369687 ATCGAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:5370327 original size:28 final size:29
Alignment explanation
Indices: 5370274--5370338 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
5370264 TAATTCTTTC
* *
5370274 TTTTCAAAATTTTTATATATACTTATT-A
1 TTTTCATAATATTTATATATACTTATTAA
*
5370302 TTTTCATAATATTTATAT-TATTTTATTAA
1 TTTTCATAATATTTATATATA-CTTATTAA
5370331 TGTTTCAT
1 T-TTTCAT
5370339 TTTATTTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 2 0.06
28 21 0.68
29 2 0.06
30 6 0.19
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (29 bp):
TTTTCATAATATTTATATATACTTATTAA
Found at i:5370331 original size:20 final size:21
Alignment explanation
Indices: 5370297--5370346 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
5370287 TATATATACT
5370297 TATTATTTTCATAATATTT-A
1 TATTATTTTCATAATATTTCA
*
5370317 TATTATTTT-ATTAATGTTTCA
1 TATTATTTTCA-TAATATTTCA
*
5370338 TTTTATTTT
1 TATTATTTT
5370347 TCAAGTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.04
20 16 0.62
21 9 0.35
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (21 bp):
TATTATTTTCATAATATTTCA
Found at i:5375359 original size:15 final size:15
Alignment explanation
Indices: 5375320--5375379 Score: 77
Period size: 15 Copynumber: 3.9 Consensus size: 15
5375310 TTATGCTTGA
*
5375320 AAAAAAAGAAGAAAA-
1 AAAAAAGGAA-AAAAG
*
5375335 AAATAAGGAAAAAAG
1 AAAAAAGGAAAAAAG
5375350 AAAAAAGGAAAAAAAG
1 AAAAAAGG-AAAAAAG
5375366 AAAAAAGGAAAAAA
1 AAAAAAGGAAAAAA
5375380 ATTTGAACCA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
14 4 0.10
15 21 0.52
16 15 0.38
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (15 bp):
AAAAAAGGAAAAAAG
Found at i:5375360 original size:8 final size:8
Alignment explanation
Indices: 5375334--5375379 Score: 67
Period size: 8 Copynumber: 5.8 Consensus size: 8
5375324 AAAGAAGAAA
5375334 AAAATAAGG
1 AAAA-AAGG
5375343 AAAAAA-G
1 AAAAAAGG
5375350 AAAAAAGG
1 AAAAAAGG
*
5375358 AAAAAAAG
1 AAAAAAGG
5375366 AAAAAAGG
1 AAAAAAGG
5375374 AAAAAA
1 AAAAAA
5375380 ATTTGAACCA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
7 7 0.21
8 23 0.68
9 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (8 bp):
AAAAAAGG
Found at i:5375362 original size:16 final size:16
Alignment explanation
Indices: 5375320--5375380 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
5375310 TTATGCTTGA
* *
5375320 AAAAAAAGAAGAAAA-
1 AAAAAAGGAAAAAAAG
*
5375335 AAATAAGG-AAAAAAG
1 AAAAAAGGAAAAAAAG
5375350 AAAAAAGGAAAAAAAG
1 AAAAAAGGAAAAAAAG
5375366 AAAAAAGGAAAAAAA
1 AAAAAAGGAAAAAAA
5375381 TTTGAACCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
14 5 0.12
15 13 0.32
16 22 0.55
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (16 bp):
AAAAAAGGAAAAAAAG
Found at i:5380141 original size:22 final size:22
Alignment explanation
Indices: 5380093--5380150 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
5380083 CATCTACACT
*
5380093 TTTTTCAAAGATGATAGATTATC
1 TTTTT-AAAGATGATAGATTATA
*
5380116 TTTTTAAAGATGATAGATTCTA
1 TTTTTAAAGATGATAGATTATA
* *
5380138 TTTTCAAAAATGA
1 TTTTTAAAGATGA
5380151 AAACTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 26 0.84
23 5 0.16
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (22 bp):
TTTTTAAAGATGATAGATTATA
Found at i:5380891 original size:46 final size:46
Alignment explanation
Indices: 5380820--5381370 Score: 1014
Period size: 46 Copynumber: 12.0 Consensus size: 46
5380810 CTATTTCCCA
*
5380820 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
5380866 CATCTGTAAGTCCTTCAGTGAATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
5380912 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
5380958 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
5381004 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
5381050 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
5381096 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
5381142 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCATCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
5381188 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
5381234 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * *
5381280 CATCTGTAAGTTCTTCAGTGCATGATGTTTTC-AAAGCCTTAGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* *
5381325 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAA-CCTTCGGG
5381371 AGCTTTTTGA
Statistics
Matches: 490, Mismatches: 13, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
45 40 0.08
46 443 0.90
47 7 0.01
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (46 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
Found at i:5381587 original size:3 final size:3
Alignment explanation
Indices: 5381581--5381655 Score: 91
Period size: 3 Copynumber: 25.0 Consensus size: 3
5381571 TTTTTTCATT
** *
5381581 TTA TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA ATA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5381628 TATA TTA TTA -TA TATA TTA TTA TTA TTA
1 T-TA TTA TTA TTA T-TA TTA TTA TTA TTA
5381656 AAAAATAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
2 4 0.06
3 52 0.84
4 6 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:5383046 original size:2 final size:2
Alignment explanation
Indices: 5383030--5383067 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
5383020 CTTTCATTAT
*
5383030 TA TA TT TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5383068 TGGTTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:5383344 original size:20 final size:19
Alignment explanation
Indices: 5383319--5383360 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
5383309 CTATTTTATA
5383319 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
5383339 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
5383358 AAT
1 AAT
5383361 ATCGAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:5383448 original size:29 final size:29
Alignment explanation
Indices: 5383416--5383472 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
5383406 ATATTTCTAA
5383416 ATAAATAAATATTTTATTT-ATAAATATAT
1 ATAAATAAATATTTT-TTTCATAAATATAT
* *
5383445 ATAAATTAATATTTTTTTCATAATTATA
1 ATAAATAAATATTTTTTTCATAAATATA
5383473 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
ATAAATAAATATTTTTTTCATAAATATAT
Found at i:5383515 original size:39 final size:39
Alignment explanation
Indices: 5383472--5383587 Score: 103
Period size: 39 Copynumber: 3.3 Consensus size: 39
5383462 TCATAATTAT
5383472 AATTTTGAAATAATAGGATTATAAATTAAATATATTTTA
1 AATTTTGAAATAATAGGATTATAAATTAAATATATTTTA
* * * *
5383511 AATTTT----TAA-A--TTTCT-AA-T-CATA-ATTAT-
1 AATTTTGAAATAATAGGATTATAAATTAAATATATTTTA
5383538 AATTTTGAAATAATAGGATTATAAATTAAATATATTTTA
1 AATTTTGAAATAATAGGATTATAAATTAAATATATTTTA
*
5383577 AATTTTTAAAT
1 AATTTTGAAAT
5383588 TTCTAATAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 24
0.63 0.10 0.27
Matches are distributed among these distances:
27 6 0.11
28 4 0.07
29 3 0.05
30 1 0.02
31 5 0.09
32 4 0.07
34 4 0.07
35 5 0.09
36 1 0.02
37 3 0.05
38 4 0.07
39 16 0.29
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (39 bp):
AATTTTGAAATAATAGGATTATAAATTAAATATATTTTA
Found at i:5383536 original size:66 final size:66
Alignment explanation
Indices: 5383462--5383594 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
5383452 AATATTTTTT
5383462 TCATAATTATAATTTTGAAATAATAGGATTATAAATTAAATATATTTTAAATTTTTAAATTTCTA
1 TCATAATTATAATTTTGAAATAATAGGATTATAAATTAAATATATTTTAAATTTTTAAATTTCTA
5383527 A
66 A
5383528 TCATAATTATAATTTTGAAATAATAGGATTATAAATTAAATATATTTTAAATTTTTAAATTTCTA
1 TCATAATTATAATTTTGAAATAATAGGATTATAAATTAAATATATTTTAAATTTTTAAATTTCTA
5383593 A
66 A
5383594 T
1 T
5383595 AATAGAGGCA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (66 bp):
TCATAATTATAATTTTGAAATAATAGGATTATAAATTAAATATATTTTAAATTTTTAAATTTCTA
A
Found at i:5387045 original size:16 final size:16
Alignment explanation
Indices: 5387024--5387054 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5387014 AGTACGAGCA
5387024 GATGAATATCATTAAT
1 GATGAATATCATTAAT
5387040 GATGAATATCATTAA
1 GATGAATATCATTAA
5387055 ATTAGTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (16 bp):
GATGAATATCATTAAT
Found at i:5387119 original size:23 final size:23
Alignment explanation
Indices: 5387052--5387143 Score: 62
Period size: 22 Copynumber: 3.9 Consensus size: 23
5387042 TGAATATCAT
5387052 TAAATTAGTTTATAAAATATTAAATTA
1 TAAATTAG-TTA-AAAATA-T-AATTA
* * **
5387079 TAAAGTA-ATAAATGTATAATTA
1 TAAATTAGTTAAAAATATAATTA
* *
5387101 TAAATTAGTTAAAAATATAAATG
1 TAAATTAGTTAAAAATATAATTA
* *
5387124 TAATTTAATT-AAAATATAAT
1 TAAATTAGTTAAAAATATAAT
5387144 ATTTATAAAA
Statistics
Matches: 51, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
22 20 0.39
23 19 0.37
24 4 0.08
25 2 0.04
27 6 0.12
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.40
Consensus pattern (23 bp):
TAAATTAGTTAAAAATATAATTA
Found at i:5388188 original size:2 final size:2
Alignment explanation
Indices: 5388183--5388285 Score: 172
Period size: 2 Copynumber: 51.5 Consensus size: 2
5388173 TTTTTGTGTG
*
5388183 TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5388225 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5388266 TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA T-A TA T
5388286 TTTCGTATTA
Statistics
Matches: 95, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.01
2 92 0.97
3 2 0.02
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5388724 original size:20 final size:21
Alignment explanation
Indices: 5388694--5388734 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
5388684 ATATCATACA
*
5388694 CTATAGTAGTACTGATACTAC
1 CTATAGTAGTACCGATACTAC
5388715 CTAT-GTAGTACCGATACTAC
1 CTATAGTAGTACCGATACTAC
5388735 TCCTTTGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (21 bp):
CTATAGTAGTACCGATACTAC
Found at i:5391448 original size:44 final size:44
Alignment explanation
Indices: 5391395--5391479 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
5391385 GATACCTCTT
*
5391395 AAGGAGTATCGATACTACTATGTGTAGTACTATCGATACCGTCC
1 AAGGAGTATCGATACTACTATGTATAGTACTATCGATACCGTCC
*
5391439 AAGGAGTATCGATACTACTATGTATAGTAGTATCGATACCG
1 AAGGAGTATCGATACTACTATGTATAGTACTATCGATACCG
5391480 ATCATGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
AAGGAGTATCGATACTACTATGTATAGTACTATCGATACCGTCC
Found at i:5391472 original size:24 final size:24
Alignment explanation
Indices: 5391399--5391477 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 24
5391389 CCTCTTAAGG
*
5391399 AGTATCGATACTACTATGTGTAGT
1 AGTATCGATACTACTATGTATAGT
* * ** *
5391423 ACTATCGATAC--C-GTCCA-AGG
1 AGTATCGATACTACTATGTATAGT
5391443 AGTATCGATACTACTATGTATAGT
1 AGTATCGATACTACTATGTATAGT
5391467 AGTATCGATAC
1 AGTATCGATAC
5391478 CGATCATGGT
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
20 12 0.30
21 1 0.03
22 2 0.05
23 2 0.05
24 23 0.57
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (24 bp):
AGTATCGATACTACTATGTATAGT
Found at i:5392024 original size:2 final size:2
Alignment explanation
Indices: 5392017--5392057 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5392007 GCCAAAATTG
5392017 AT AT AT AT AT 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 AT AT AT AT AT A
5392058 GATCATGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5393389 original size:45 final size:44
Alignment explanation
Indices: 5393316--5393476 Score: 223
Period size: 45 Copynumber: 3.6 Consensus size: 44
5393306 ACGGCAACCA
* * *
5393316 TTCATGCCTTTTTATATACTATTATACATTTGATTTATGGCATCAT
1 TTCATGCC-TTTTATACACCATTATACATTTCATTTATGGCATC-T
* * *
5393362 TTCATGCCTTTTACACACCGTTATACATTTCATTTATGACATCT
1 TTCATGCCTTTTATACACCATTATACATTTCATTTATGGCATCT
*
5393406 TTCCATGCCTTTTATACACCATTATACATTTTATTTATGGCATCCT
1 TT-CATGCCTTTTATACACCATTATACATTTCATTTATGGCAT-CT
5393452 TTCATGCCTTTTATACACCATTATA
1 TTCATGCCTTTTATACACCATTATA
5393477 TATTGTTATA
Statistics
Matches: 103, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
44 3 0.03
45 88 0.85
46 12 0.12
ACGTcount: A:0.25, C:0.22, G:0.07, T:0.46
Consensus pattern (44 bp):
TTCATGCCTTTTATACACCATTATACATTTCATTTATGGCATCT
Found at i:5393613 original size:68 final size:68
Alignment explanation
Indices: 5393517--5393909 Score: 588
Period size: 68 Copynumber: 5.8 Consensus size: 68
5393507 GCATTTAACA
* * *
5393517 TTTCATCTAATTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCACTTA
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
5393582 GCC
66 GCC
* * *
5393585 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTTGGCCTAAAAGGTACTTA
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
5393650 GCC
66 GCC
* * * **
5393653 TTTTATCTAACTGTCATAATTGACACCTTTCTATCAAATGCACACCTAGGCCTCAAAGGCACTTA
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
5393718 GCC
66 GCC
* *
5393721 TTTCATCTAACTGGCATAATTGACACATTTCTTTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
5393786 GCC
66 GCC
* * * *
5393789 TTTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGTTAGTCCTCGAAGGCACTTT
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
*
5393854 GTC
66 GCC
** * *
5393857 TTTCATCTAACTGGCATAATTGACATATTTTTGTCAAATGCACAATTAGGCCT
1 TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCT
5393910 TTAATCTTTT
Statistics
Matches: 292, Mismatches: 33, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 292 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (68 bp):
TTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
GCC
Found at i:5395232 original size:18 final size:18
Alignment explanation
Indices: 5395204--5395249 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
5395194 CTAACAATTC
5395204 CTTAA-GCTTCTATCATG
1 CTTAAGGCTTCTATCATG
5395221 CTTAAGGCTTCTATCATG
1 CTTAAGGCTTCTATCATG
5395239 CTTAAGGCTTC
1 CTTAAGGCTTC
5395250 AATAACTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (18 bp):
CTTAAGGCTTCTATCATG
Found at i:5397188 original size:20 final size:20
Alignment explanation
Indices: 5397165--5397265 Score: 71
Period size: 22 Copynumber: 4.8 Consensus size: 20
5397155 TCAGTATTGC
*
5397165 ATGAGCAGTATCGATACTCG
1 ATGAGCAGTATCGATACTAG
5397185 ATGAGTGCAGTATCGATACTAG
1 ATGA--GCAGTATCGATACTAG
* * *
5397207 GTTAGTAGTATCGATACCTAG
1 ATGAGCAGTATCGATA-CTAG
*
5397228 CAAT-AGTAGTATCGATACTATG
1 --ATGAGCAGTATCGATACTA-G
* *
5397250 -TGAGTATTATCGATAC
1 ATGAGCAGTATCGATAC
5397266 CAAGTGCACA
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
19 1 0.01
20 28 0.41
21 7 0.10
22 31 0.46
23 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31
Consensus pattern (20 bp):
ATGAGCAGTATCGATACTAG
Found at i:5397217 original size:42 final size:40
Alignment explanation
Indices: 5397166--5397265 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 40
5397156 CAGTATTGCA
* *
5397166 TGAGCAGTATCGATACT-CGATGAGTGCAGTATCGATACTAGG
1 TGAGTAGTATCGATACTACAAT-AGT--AGTATCGATACTAGG
* *
5397208 TTAGTAGTATCGATACCTAGCAATAGTAGTATCGATACTATG
1 TGAGTAGTATCGATA-CTA-CAATAGTAGTATCGATACTAGG
*
5397250 TGAGTATTATCGATAC
1 TGAGTAGTATCGATAC
5397266 CAAGTGCACA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
41 1 0.02
42 40 0.82
43 2 0.04
44 3 0.06
45 3 0.06
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (40 bp):
TGAGTAGTATCGATACTACAATAGTAGTATCGATACTAGG
Found at i:5397237 original size:22 final size:21
Alignment explanation
Indices: 5397193--5397245 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
5397183 CGATGAGTGC
**
5397193 AGTATCGATA-CTAGGTTAGT
1 AGTATCGATACCTAGAATAGT
5397213 AGTATCGATACCTAGCAATAGT
1 AGTATCGATACCTAG-AATAGT
5397235 AGTATCGATAC
1 AGTATCGATAC
5397246 TATGTGAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 10 0.34
21 4 0.14
22 15 0.52
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (21 bp):
AGTATCGATACCTAGAATAGT
Found at i:5399079 original size:40 final size:40
Alignment explanation
Indices: 5399035--5399356 Score: 572
Period size: 40 Copynumber: 8.1 Consensus size: 40
5399025 ACCGTAGTGC
5399035 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
5399075 TACACATAAGGTCGTGCCCACCATATACATCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
5399115 TACACATAAGGTCGTGCCCACCATATATACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
5399155 TACACATAAGGTTGTGCCCACCATATACACCGAAGCGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
5399195 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
5399235 TACACATAAGGTCGTGCCCACAATATACACCGAAGTTTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
5399275 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
5399315 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
5399355 TA
1 TA
5399357 TAAACCTGTA
Statistics
Matches: 266, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 266 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:5403305 original size:21 final size:21
Alignment explanation
Indices: 5403281--5403327 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
5403271 GCCTTCTTCC
5403281 GAAACAACATGACCAAGAAAA
1 GAAACAACATGACCAAGAAAA
**
5403302 GAAACTTCATGACCAAGAAAA
1 GAAACAACATGACCAAGAAAA
5403323 GAAAC
1 GAAAC
5403328 TTCAGATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.57, C:0.19, G:0.15, T:0.09
Consensus pattern (21 bp):
GAAACAACATGACCAAGAAAA
Found at i:5403328 original size:21 final size:21
Alignment explanation
Indices: 5403288--5403331 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5403278 TCCGAAACAA
5403288 CATGACCAAGAAAAGAAACTT
1 CATGACCAAGAAAAGAAACTT
5403309 CATGACCAAGAAAAGAAACTT
1 CATGACCAAGAAAAGAAACTT
5403330 CA
1 CA
5403332 GATAACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.20, G:0.14, T:0.14
Consensus pattern (21 bp):
CATGACCAAGAAAAGAAACTT
Found at i:5408348 original size:20 final size:20
Alignment explanation
Indices: 5408323--5408369 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
5408313 TTCTTTACCA
5408323 AATTCCAAATTCAAAAATAT
1 AATTCCAAATTCAAAAATAT
5408343 AATTCCAAATTCAAAAATAT
1 AATTCCAAATTCAAAAATAT
5408363 AATTCCA
1 AATTCCA
5408370 TAAAACCCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (20 bp):
AATTCCAAATTCAAAAATAT
Found at i:5408797 original size:20 final size:20
Alignment explanation
Indices: 5408747--5408802 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
5408737 AATAGTAATT
* *
5408747 TACTATATGAATAGTACCGA
1 TACTGTATGAATAGTACCAA
* *
5408767 TATTGTATGAATAGTGCCAA
1 TACTGTATGAATAGTACCAA
* *
5408787 TACTGTGTGAACAGTA
1 TACTGTATGAATAGTA
5408803 GTATCGATAC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
TACTGTATGAATAGTACCAA
Found at i:5408919 original size:21 final size:21
Alignment explanation
Indices: 5408893--5408935 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5408883 ATACTGCTAT
5408893 AGTAGTATCGATACCATGAAC
1 AGTAGTATCGATACCATGAAC
*
5408914 AGTAGTATCGATACCGTGAAC
1 AGTAGTATCGATACCATGAAC
5408935 A
1 A
5408936 ATAATATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (21 bp):
AGTAGTATCGATACCATGAAC
Found at i:5408947 original size:21 final size:21
Alignment explanation
Indices: 5408898--5408948 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
5408888 GCTATAGTAG
* *
5408898 TATCGATACCATGAACAGTAG
1 TATCGATACCATGAACAATAA
*
5408919 TATCGATACCGTGAACAATAA
1 TATCGATACCATGAACAATAA
*
5408940 TATTGATAC
1 TATCGATAC
5408949 TATCAAGCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (21 bp):
TATCGATACCATGAACAATAA
Found at i:5411629 original size:20 final size:20
Alignment explanation
Indices: 5411604--5411654 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5411594 TAATATACTT
*
5411604 TATGAATAGTACCGATATTG
1 TATGAATAGTACCAATATTG
*
5411624 TATGAATAGTTCCAATATTG
1 TATGAATAGTACCAATATTG
* *
5411644 TGTGAACAGTA
1 TATGAATAGTA
5411655 GTATCGATAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (20 bp):
TATGAATAGTACCAATATTG
Found at i:5411748 original size:21 final size:21
Alignment explanation
Indices: 5411722--5411800 Score: 122
Period size: 21 Copynumber: 3.8 Consensus size: 21
5411712 CGATACTACT
*
5411722 ACAGTAGTATCGATACCATGA
1 ACAGTAGTATCGATACCGTGA
5411743 ACAGTAGTATCGATACCGTGA
1 ACAGTAGTATCGATACCGTGA
*
5411764 ACAGTATTATCGATACCGTGA
1 ACAGTAGTATCGATACCGTGA
**
5411785 ACAGTAAAATCGATAC
1 ACAGTAGTATCGATAC
5411801 TATCAAGCCC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (21 bp):
ACAGTAGTATCGATACCGTGA
Found at i:5415096 original size:15 final size:16
Alignment explanation
Indices: 5415078--5415110 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5415068 CTTTTGCAAA
5415078 TCAAAA-TTTTATTTT
1 TCAAAACTTTTATTTT
5415093 TCAAAATCTTTTATTTT
1 TCAAAA-CTTTTATTTT
5415110 T
1 T
5415111 TACTTGCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (16 bp):
TCAAAACTTTTATTTT
Found at i:5417830 original size:18 final size:19
Alignment explanation
Indices: 5417786--5417838 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
5417776 ACTGAATATT
*
5417786 TGTCCTGAAGGACCACTAC
1 TGTCCCGAAGGACCACTAC
* *
5417805 T-TCTCGAATGACCACTA-
1 TGTCCCGAAGGACCACTAC
5417822 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
5417839 GATAATCCCT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 1 0.04
18 26 0.93
19 1 0.04
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (19 bp):
TGTCCCGAAGGACCACTAC
Found at i:5420936 original size:2 final size:2
Alignment explanation
Indices: 5420931--5420994 Score: 119
Period size: 2 Copynumber: 31.5 Consensus size: 2
5420921 TGTGTGTGTG
5420931 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5420973 TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA T-A TA T
5420995 TTTCGTATTA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 59 0.97
3 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5422554 original size:21 final size:23
Alignment explanation
Indices: 5422528--5422572 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
5422518 TATAATTGTA
*
5422528 AACTCGG-ATGGT-GGTTGAGTT
1 AACTCGGCATGGTCAGTTGAGTT
5422549 AACTCGGCATGGTCAGTTGAGTT
1 AACTCGGCATGGTCAGTTGAGTT
5422572 A
1 A
5422573 TAACTGAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 5 0.24
23 9 0.43
ACGTcount: A:0.22, C:0.13, G:0.33, T:0.31
Consensus pattern (23 bp):
AACTCGGCATGGTCAGTTGAGTT
Found at i:5423245 original size:2 final size:2
Alignment explanation
Indices: 5423238--5423306 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
5423228 TTTAACCATA
5423238 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5423280 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5423307 ATTCACATTC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5426419 original size:18 final size:19
Alignment explanation
Indices: 5426384--5426421 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
5426374 CACGGAATGT
5426384 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
5426404 AAGATTACCA-GGGAATAA
1 AAGATTACCAGGGGAATAA
5426422 GATTACTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:5426434 original size:15 final size:16
Alignment explanation
Indices: 5426383--5426427 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 16
5426373 TCACGGAATG
5426383 TAAGATTACCAGTGGGAA
1 TAAGATTACCA--GGGAA
5426401 TAAAAGATTACCAGGGAA
1 T--AAGATTACCAGGGAA
5426419 TAAGATTAC
1 TAAGATTAC
5426428 TGGGAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 7 0.28
20 10 0.40
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (16 bp):
TAAGATTACCAGGGAA
Found at i:5430523 original size:3 final size:3
Alignment explanation
Indices: 5430515--5430548 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
5430505 CACGCAATAT
*
5430515 TTA TTA TTA TTA TTA TT- TTG TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5430549 TCACCTTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:5430835 original size:19 final size:20
Alignment explanation
Indices: 5430811--5430852 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
5430801 ATAAAAAAAT
*
5430811 TATATCCCATAATT-TAATA
1 TATATCCCAAAATTCTAATA
*
5430830 TATATCTCAAAATTCTAATA
1 TATATCCCAAAATTCTAATA
5430850 TAT
1 TAT
5430853 TCTAAAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (20 bp):
TATATCCCAAAATTCTAATA
Found at i:5437015 original size:18 final size:18
Alignment explanation
Indices: 5436981--5437015 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5436971 ATTATTTGTT
*
5436981 TTTTATTCAAGTAAACTC
1 TTTTATTCAAATAAACTC
*
5436999 TTTTATTCAAATGAACT
1 TTTTATTCAAATAAACT
5437016 TTAATTTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (18 bp):
TTTTATTCAAATAAACTC
Found at i:5437780 original size:23 final size:23
Alignment explanation
Indices: 5437753--5437805 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
5437743 CAATAATTAA
5437753 ATGTAAATTAATATA-TTTAATTT
1 ATGTAAATT-ATATAGTTTAATTT
5437776 ATGTAAATTATATAGTTTAATTT
1 ATGTAAATTATATAGTTTAATTT
5437799 ATGTAAA
1 ATGTAAA
5437806 GAAAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 5 0.17
23 24 0.83
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (23 bp):
ATGTAAATTATATAGTTTAATTT
Found at i:5441115 original size:7 final size:8
Alignment explanation
Indices: 5441098--5441122 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5441088 ATATTAAAAT
5441098 AAAAACAA
1 AAAAACAA
5441106 AAAAACAA
1 AAAAACAA
5441114 AAAAACAA
1 AAAAACAA
5441122 A
1 A
5441123 TATACCTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAACAA
Found at i:5441336 original size:25 final size:25
Alignment explanation
Indices: 5441300--5441351 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
5441290 GTTTAGATTT
* * *
5441300 GGGTTCTGGTTCTGGTTTGGGTTTA
1 GGGTTCTGGTTCAGGGTTGGGGTTA
5441325 GGGTTCAT-GTTCAGGGTTGGGGTTA
1 GGGTTC-TGGTTCAGGGTTGGGGTTA
5441350 GG
1 GG
5441352 TTACATAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.08, C:0.08, G:0.44, T:0.40
Consensus pattern (25 bp):
GGGTTCTGGTTCAGGGTTGGGGTTA
Done.