Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 10 of 199
Found at i:3272649 original size:19 final size:19
Alignment explanation
Indices: 3272625--3272686 Score: 74
Period size: 18 Copynumber: 3.3 Consensus size: 19
3272615 TATTTTAGAA
*
3272625 TTTTTAATATATATTTAAT
1 TTTTTAAAATATATTTAAT
*
3272644 TTTTTAAAATAT-TTTGAT
1 TTTTTAAAATATATTTAAT
3272662 TTTTTAAAAT-TATTTTGAAT
1 TTTTTAAAATATA-TTT-AAT
3272682 TTTTT
1 TTTTT
3272687 CTGAAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.03
18 15 0.41
19 14 0.38
20 7 0.19
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTTAAAATATATTTAAT
Found at i:3276670 original size:25 final size:25
Alignment explanation
Indices: 3276620--3276668 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3276610 AGTTTTCATC
* *
3276620 AAATATATTTATTTATTTTTTAAAT
1 AAATATAATTATTTATTTTGTAAAT
*
3276645 AAATATAATTATTTGTATTTGTAA
1 AAATATAATTATTTAT-TTTGTAA
3276669 TATGTAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (25 bp):
AAATATAATTATTTATTTTGTAAAT
Found at i:3280313 original size:17 final size:18
Alignment explanation
Indices: 3280281--3280314 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3280271 AATTTTCAAG
*
3280281 AATTTAAAATATTTATAA
1 AATTCAAAATATTTATAA
3280299 AATTCAAAA-ATTTATA
1 AATTCAAAATATTTATA
3280315 TTTTTTTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTCAAAATATTTATAA
Found at i:3284171 original size:21 final size:21
Alignment explanation
Indices: 3284121--3284175 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
3284111 ACCATTGTTT
* *
3284121 CTAATCTCACTGCTACAATAT
1 CTAATCTCACCGCTACAATAA
* * *
3284142 CCAAACTCACCGCTACAGTAA
1 CTAATCTCACCGCTACAATAA
3284163 CTAATCTCACCGC
1 CTAATCTCACCGC
3284176 CACCGCTATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.36, G:0.07, T:0.24
Consensus pattern (21 bp):
CTAATCTCACCGCTACAATAA
Found at i:3289689 original size:33 final size:32
Alignment explanation
Indices: 3289620--3289689 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
3289610 ATATTTGAAA
*
3289620 TGTT-ACATTTTAGTCACTTACGTTAACGTGT
1 TGTTAACATTTTAGTCACTAACGTTAACGTGT
*
3289651 T-TTAACATTTTAGTCACTAAGCCGTTAA-TTGT
1 TGTTAACATTTTAGTCACTAA--CGTTAACGTGT
3289683 TGTTAAC
1 TGTTAAC
3289690 GGTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
30 2 0.06
31 16 0.48
32 4 0.12
33 11 0.33
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (32 bp):
TGTTAACATTTTAGTCACTAACGTTAACGTGT
Found at i:3291870 original size:29 final size:29
Alignment explanation
Indices: 3291812--3291874 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
3291802 ACCAAAAATT
***
3291812 TATTTTAAAAATAAAAAAGTATTTAAAAA
1 TATTTTAAAAATAAAAAAGTAAAAAAAAA
*
3291841 TATTTTAAAATTAAAAAA-TAAAAAACAAA
1 TATTTTAAAAATAAAAAAGTAAAAAA-AAA
3291870 TATTT
1 TATTT
3291875 ATTATATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (29 bp):
TATTTTAAAAATAAAAAAGTAAAAAAAAA
Found at i:3292672 original size:20 final size:19
Alignment explanation
Indices: 3292623--3292672 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
3292613 TTTTTTTAAT
*
3292623 TCAAATAAATTTATTCGAC
1 TCAACTAAATTTATTCGAC
* *
3292642 TCAACTCAATTTCATTCTAC
1 TCAACTAAATTT-ATTCGAC
*
3292662 TCTACTAAATT
1 TCAACTAAATT
3292673 AGAAAAAACC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.40
Consensus pattern (19 bp):
TCAACTAAATTTATTCGAC
Found at i:3307025 original size:29 final size:29
Alignment explanation
Indices: 3306993--3307052 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
3306983 AAATATCTAA
3306993 AATTAAACTAAAA-TCAAAATTATATATTT
1 AATTAAACTAAAAGT-AAAATTATATATTT
* * * *
3307022 AATTTAATTAAAAGTAAGATTTTATATTT
1 AATTAAACTAAAAGTAAAATTATATATTT
3307051 AA
1 AA
3307053 CAAATACACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (29 bp):
AATTAAACTAAAAGTAAAATTATATATTT
Found at i:3307652 original size:21 final size:20
Alignment explanation
Indices: 3307628--3307674 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
3307618 AAATTAAATT
3307628 TTAAAATTTGAAATATAAAAA
1 TTAAAATTTGAAA-ATAAAAA
*
3307649 TTAAAAATTTTAAAATAAAAA
1 TT-AAAATTTGAAAATAAAAA
3307670 -TAAAA
1 TTAAAA
3307675 AAAAGGGGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.17
20 1 0.04
21 9 0.38
22 10 0.42
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
TTAAAATTTGAAAATAAAAA
Found at i:3307675 original size:21 final size:22
Alignment explanation
Indices: 3307630--3307676 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
3307620 ATTAAATTTT
*
3307630 AAAATTTGAAATATAAAAATTA
1 AAAATTTGAAATATAAAAATAA
*
3307652 AAAATTTTAAA-ATAAAAATAA
1 AAAATTTGAAATATAAAAATAA
3307673 AAAA
1 AAAA
3307677 AAGGGGGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAATTTGAAATATAAAAATAA
Found at i:3316515 original size:22 final size:20
Alignment explanation
Indices: 3316477--3316521 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
3316467 ACTTATCCCT
*
3316477 AAATTTTAAGTTTAAATTAA
1 AAATTTTAAGTTCAAATTAA
3316497 AAATTTTAAAAGTTCAAATTAA
1 AAATTTT--AAGTTCAAATTAA
3316519 AAA
1 AAA
3316522 AAAAAACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.32
22 15 0.68
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (20 bp):
AAATTTTAAGTTCAAATTAA
Found at i:3319793 original size:31 final size:29
Alignment explanation
Indices: 3319758--3319834 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
3319748 TTAATAGCTC
*
3319758 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* * ***
3319789 AGTGACAAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
3319818 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
3319835 CTAAGGTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 21 0.55
30 1 0.03
31 16 0.42
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:3321698 original size:16 final size:16
Alignment explanation
Indices: 3321677--3321710 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3321667 AGATAAGAAA
*
3321677 AATAGGGTAGGACGTT
1 AATAGGGTAGGAAGTT
*
3321693 AATAGGGTTGGAAGTT
1 AATAGGGTAGGAAGTT
3321709 AA
1 AA
3321711 AAAGAGGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.35, T:0.26
Consensus pattern (16 bp):
AATAGGGTAGGAAGTT
Found at i:3332069 original size:2 final size:2
Alignment explanation
Indices: 3332062--3332087 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3332052 AACCAAACAC
3332062 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
3332088 TTACCAAGGG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3339683 original size:30 final size:29
Alignment explanation
Indices: 3339626--3339684 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
3339616 ATTTTAAAAA
*
3339626 TTCAAAAAATATAAAAATACATAAATATT
1 TTCAAAAAATATAAAAATAAATAAATATT
* *
3339655 TTCAAAAATATATAATAATAAATTAATATT
1 TTCAAAAA-ATATAAAAATAAATAAATATT
3339685 AAATAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (29 bp):
TTCAAAAAATATAAAAATAAATAAATATT
Found at i:3339704 original size:25 final size:24
Alignment explanation
Indices: 3339668--3339718 Score: 84
Period size: 25 Copynumber: 2.1 Consensus size: 24
3339658 AAAAATATAT
3339668 AATAATAAATTAATATTAAATAAA
1 AATAATAAATTAATATTAAATAAA
*
3339692 AATAATTATATTAATATTAAATAAA
1 AATAA-TAAATTAATATTAAATAAA
3339717 AA
1 AA
3339719 AACCCTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AATAATAAATTAATATTAAATAAA
Found at i:3339932 original size:19 final size:20
Alignment explanation
Indices: 3339908--3339955 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
3339898 CAATGGTTTC
3339908 TTTTTAAAATTTTAAT-ATT
1 TTTTTAAAATTTTAATGATT
* *
3339927 TTTTTAGAATTTTGATGATT
1 TTTTTAAAATTTTAATGATT
3339947 TTTTATAAA
1 TTTT-TAAA
3339956 TTCAGAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 14 0.58
20 7 0.29
21 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (20 bp):
TTTTTAAAATTTTAATGATT
Found at i:3339957 original size:20 final size:19
Alignment explanation
Indices: 3339908--3339957 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
3339898 CAATGGTTTC
3339908 TTTTTA-AAATTTTAATAT
1 TTTTTATAAATTTTAATAT
*
3339926 TTTTT-TAGAATTTTGATGAT
1 TTTTTATA-AATTTTAAT-AT
3339946 TTTTTATAAATT
1 TTTTTATAAATT
3339958 CAGAATGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 6 0.22
19 8 0.30
20 11 0.41
21 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (19 bp):
TTTTTATAAATTTTAATAT
Found at i:3346494 original size:45 final size:45
Alignment explanation
Indices: 3346430--3346524 Score: 190
Period size: 45 Copynumber: 2.1 Consensus size: 45
3346420 GAGAAAAGTG
3346430 ATTACTTTTAAGAGTTAAATCATACATTAAGCATTTAAGATATTT
1 ATTACTTTTAAGAGTTAAATCATACATTAAGCATTTAAGATATTT
3346475 ATTACTTTTAAGAGTTAAATCATACATTAAGCATTTAAGATATTT
1 ATTACTTTTAAGAGTTAAATCATACATTAAGCATTTAAGATATTT
3346520 ATTAC
1 ATTAC
3346525 AAATTTATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.42
Consensus pattern (45 bp):
ATTACTTTTAAGAGTTAAATCATACATTAAGCATTTAAGATATTT
Found at i:3348284 original size:27 final size:28
Alignment explanation
Indices: 3348254--3348316 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 28
3348244 AAAAATAATT
* *
3348254 AAAATATTAT-AACTTTTTTTATTTATC
1 AAAATATTATAAAATTTTTTTATTTACC
3348281 AAAATATTATAAAAATTTTTTTATTTACC
1 AAAATATTAT-AAAATTTTTTTATTTACC
3348310 AAAATAT
1 AAAATAT
3348317 ACAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 10 0.31
29 22 0.69
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.49
Consensus pattern (28 bp):
AAAATATTATAAAATTTTTTTATTTACC
Found at i:3348322 original size:28 final size:29
Alignment explanation
Indices: 3348267--3348323 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
3348257 ATATTATAAC
* *
3348267 TTTTTTTATTTATCAAAATATTATAAAAA
1 TTTTTTTATTTACCAAAATATTACAAAAA
3348296 TTTTTTTATTTACCAAAATA-TACAAAAA
1 TTTTTTTATTTACCAAAATATTACAAAAA
3348324 AAAACAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTTTTTATTTACCAAAATATTACAAAAA
Found at i:3348591 original size:19 final size:18
Alignment explanation
Indices: 3348553--3348662 Score: 98
Period size: 19 Copynumber: 5.8 Consensus size: 18
3348543 TCCTTATTTA
3348553 TTATTTTAATTAAATAATAAC
1 TTATTTTAATT---TAATAAC
3348574 TTTATTTTAATTTAATAAAC
1 -TTATTTTAATTTAAT-AAC
* *
3348594 -TATTCTCATTTAATAAC
1 TTATTTTAATTTAATAAC
3348611 TCTATTTTAATTTAATAAAC
1 T-TATTTTAATTTAAT-AAC
* *
3348631 -TATTCTCATTTAATAAC
1 TTATTTTAATTTAATAAC
3348648 TCTATTTTAATTTAA
1 T-TATTTTAATTTAA
3348663 AAAATTAAGT
Statistics
Matches: 74, Mismatches: 8, Indels: 15
0.76 0.08 0.15
Matches are distributed among these distances:
17 6 0.08
18 24 0.32
19 27 0.36
20 6 0.08
22 11 0.15
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTTTAATTTAATAAC
Found at i:3348597 original size:18 final size:19
Alignment explanation
Indices: 3348576--3348662 Score: 106
Period size: 18 Copynumber: 4.7 Consensus size: 19
3348566 ATAATAACTT
3348576 TATTTTAATTTAATAA-AC
1 TATTTTAATTTAATAACAC
* * *
3348594 TATTCTCATTTAATAACTC
1 TATTTTAATTTAATAACAC
3348613 TATTTTAATTTAATAA-AC
1 TATTTTAATTTAATAACAC
* * *
3348631 TATTCTCATTTAATAACTC
1 TATTTTAATTTAATAACAC
3348650 TATTTTAATTTAA
1 TATTTTAATTTAA
3348663 AAAATTAAGT
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
18 29 0.52
19 27 0.48
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTTAATTTAATAACAC
Found at i:3348608 original size:37 final size:37
Alignment explanation
Indices: 3348567--3348662 Score: 183
Period size: 37 Copynumber: 2.6 Consensus size: 37
3348557 TTTAATTAAA
*
3348567 TAATAACTTTATTTTAATTTAATAAACTATTCTCATT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
3348604 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
1 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
3348641 TAATAACTCTATTTTAATTTAA
1 TAATAACTCTATTTTAATTTAA
3348663 AAAATTAAGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (37 bp):
TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
Found at i:3348757 original size:18 final size:19
Alignment explanation
Indices: 3348694--3348752 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
3348684 ATTTAATTTT
3348694 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
3348713 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
3348731 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
3348750 TTA
1 TTA
3348753 CTTAATTAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:3349337 original size:27 final size:27
Alignment explanation
Indices: 3349300--3349382 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
3349290 GTTACATTTT
3349300 AATC-CTTTGGCACCATTGGTGCCACC
1 AATCTCTTTGGCACCATTGGTGCCACC
*
3349326 AATCTCTTTGGCACCATTGGTGCCGCC
1 AATCTCTTTGGCACCATTGGTGCCACC
* *
3349353 AATCTCATTT-GCACCTTTGGTGCCTCC
1 AATCTC-TTTGGCACCATTGGTGCCACC
3349380 AAT
1 AAT
3349383 GTGATTGGCC
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
26 4 0.08
27 45 0.87
28 3 0.06
ACGTcount: A:0.18, C:0.33, G:0.18, T:0.31
Consensus pattern (27 bp):
AATCTCTTTGGCACCATTGGTGCCACC
Found at i:3349707 original size:30 final size:30
Alignment explanation
Indices: 3349639--3349707 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
3349629 TTTAAGATAA
* *
3349639 GTTAAAAAATTATAATTTAATTATTAAATT
1 GTTAAAAAATTATAATTTAATAATTAAATC
* *
3349669 ATTCAAAAAATT-TTATTTAAGTAATTAAATC
1 GTT-AAAAAATTATAATTTAA-TAATTAAATC
3349700 GTTAAAAA
1 GTTAAAAA
3349708 TGTTATGTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
30 14 0.44
31 18 0.56
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (30 bp):
GTTAAAAAATTATAATTTAATAATTAAATC
Found at i:3352860 original size:60 final size:61
Alignment explanation
Indices: 3352768--3352898 Score: 194
Period size: 60 Copynumber: 2.2 Consensus size: 61
3352758 ATGGACTTCA
**
3352768 CGTTAC-ACTTATTCAGACAACATCATCAATATTATTATGGCTGTTATTGAAAAT-AAAAT
1 CGTTACGACTTATTCAGACAACATCATCAATATTATTATGAATGTTATTGAAAATAAAAAT
* * * *
3352827 CGTTACGATTTATTCTGACAACATCATTAATATTGTTATGAATGTTATTGAAAATAAAAAT
1 CGTTACGACTTATTCAGACAACATCATCAATATTATTATGAATGTTATTGAAAATAAAAAT
3352888 CGTTACGACTT
1 CGTTACGACTT
3352899 TCAACATAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
59 6 0.10
60 42 0.67
61 15 0.24
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (61 bp):
CGTTACGACTTATTCAGACAACATCATCAATATTATTATGAATGTTATTGAAAATAAAAAT
Found at i:3358284 original size:9 final size:9
Alignment explanation
Indices: 3358267--3358303 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
3358257 TTTTTTCTCC
3358267 AAAACCCTA
1 AAAACCCTA
*
3358276 AAAATCCTA
1 AAAACCCTA
3358285 AAAACCCT-
1 AAAACCCTA
3358293 -AAACCCTA
1 AAAACCCTA
3358301 AAA
1 AAA
3358304 TCCAAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
7 7 0.29
9 17 0.71
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAACCCTA
Found at i:3361176 original size:21 final size:20
Alignment explanation
Indices: 3361144--3361185 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
3361134 TTGAAAACTA
3361144 ATTTCCAATAATATAATATTT
1 ATTTCCAATAATATAAT-TTT
*
3361165 ATTT-CAATTAATTTAATTTT
1 ATTTCCAA-TAATATAATTTT
3361185 A
1 A
3361186 CTTGATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTCCAATAATATAATTTT
Found at i:3363735 original size:41 final size:41
Alignment explanation
Indices: 3363690--3363958 Score: 351
Period size: 41 Copynumber: 6.6 Consensus size: 41
3363680 GGTTTTAAAA
*
3363690 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAA
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
3363731 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
* * *
3363772 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
* ** **
3363813 CCTAGCAGGCTAAGTGCCGGTGAACTGGATCAGACTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
* * ** * *
3363854 CCTAGCAGGCTAAGTGTCGGTGAGCTGGATTAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
*
3363895 CCTAGCAGGCTAAGTGCCGGTAATCTAAATCAGGCTT-TAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGG-TTATAAG
* * *
3363936 CCTAACAAGCTAAGTGCCAGTGA
1 CCTAGCAGGCTAAGTGCCGGTGA
3363959 ATCTGTTTAA
Statistics
Matches: 206, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
41 205 1.00
42 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
Found at i:3365922 original size:20 final size:20
Alignment explanation
Indices: 3365876--3365915 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3365866 ACAAAAACAC
3365876 AAAAAATATAATAGTGAAAT
1 AAAAAATATAATAGTGAAAT
3365896 AAAAAATATAATAGTGAAAT
1 AAAAAATATAATAGTGAAAT
3365916 GTGAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (20 bp):
AAAAAATATAATAGTGAAAT
Found at i:3367801 original size:83 final size:83
Alignment explanation
Indices: 3367662--3367827 Score: 332
Period size: 83 Copynumber: 2.0 Consensus size: 83
3367652 CCAAAACCAA
3367662 TGCTTACAATAATCATGTATTAAAATTATAAAGTTTAGTAGATTAAGTTTTAGCTTAATTGATAT
1 TGCTTACAATAATCATGTATTAAAATTATAAAGTTTAGTAGATTAAGTTTTAGCTTAATTGATAT
3367727 GGTTTTCGTCGTCAATGT
66 GGTTTTCGTCGTCAATGT
3367745 TGCTTACAATAATCATGTATTAAAATTATAAAGTTTAGTAGATTAAGTTTTAGCTTAATTGATAT
1 TGCTTACAATAATCATGTATTAAAATTATAAAGTTTAGTAGATTAAGTTTTAGCTTAATTGATAT
3367810 GGTTTTCGTCGTCAATGT
66 GGTTTTCGTCGTCAATGT
3367828 ATGAGGATAT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (83 bp):
TGCTTACAATAATCATGTATTAAAATTATAAAGTTTAGTAGATTAAGTTTTAGCTTAATTGATAT
GGTTTTCGTCGTCAATGT
Found at i:3373787 original size:44 final size:44
Alignment explanation
Indices: 3373341--3374212 Score: 232
Period size: 44 Copynumber: 19.8 Consensus size: 44
3373331 CTACAACCTC
* ** * *
3373341 AGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCAATACTGCTT
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * * ** **
3373385 AGGGAGATAAGATCTG-TAATCTTCAATCTATTCCACTGTTGCCC
1 AGGGAGGTAAAATCTGCT-ATCTTCAATCTACTCCACTACTGCTT
* ** * * ** * * *
3373429 AGGAAAATAGAAT-TACTGGCTTCAATGTACTCCACTGTAAT-CTC
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCAC--TACTGCTT
* * ** *
3373473 AGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTT
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * ** * * * **
3373517 AGGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCC
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * * ** * **
3373561 AGGGAAGTAGAAT-TACTGGCTTCAATGTACTCCACTACAACTT
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * * * *
3373604 CAAGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTT
1 -AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * * ** * * * *
3373649 AAGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCT
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * * ** * * **
3373693 AGGGAAGTAGAAT-TACTGGCTTCAATGTACTCCACTGCAACTT
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * *
3373736 CAGGGAGGTAAAATCCGCTATCTTCGATCTGCTCCACTACTGCTT
1 -AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * ** * * * **
3373781 AGGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCC
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * * * ** * **
3373825 AAGGAAGTAGAAT-TACTGGCTTCAATGTACTCCACTACAACTTT
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGC-TT
* * * *
3373869 AGGGAGGTAAAATCCG-TCATCTTCGATCTGCTCCACTACTACTT
1 AGGGAGGTAAAATCTGCT-ATCTTCAATCTACTCCACTACTGCTT
** * * ** * * * *
3373913 AGGGAGACAAGATTTGAAATCTTCAATCTATTTCGCTACTGCTC
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * * * **
3373957 AGGGAAGTAAAAT-TACT-GCTTCAATGTACTCCACTGTAAC--CAC
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCAC--T-ACTGCTT
* * * *
3374000 AGGGAGGTAAAATCCG-TCATCTTCGATCTGCTCTACTACTGCTT
1 AGGGAGGTAAAATCTGCT-ATCTTCAATCTACTCCACTACTGCTT
* * *** * * * **
3374044 AGGGAGATAAGATCTAAAATCTTCAGTCTATTCCACTGCTGCCA
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
* * * ** * **
3374088 AGGGAAGTAGAAT-TACTGGCTTCAATGTACTCCACTGTAAC--CAC
1 AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCAC--T-ACTGCTT
* * * *
3374132 AGGGAGGTAAAATCTG-TCATCTTCGATCTGCCCCACTACTGCTC
1 AGGGAGGTAAAATCTGCT-ATCTTCAATCTACTCCACTACTGCTT
* * *
3374176 AAGG-GG-ACAAGATCTGCTATCTTCAACCTGCTCCACT
1 AGGGAGGTA-AA-ATCTGCTATCTTCAATCTACTCCACT
3374213 GTCTCCGAGG
Statistics
Matches: 556, Mismatches: 239, Indels: 66
0.65 0.28 0.08
Matches are distributed among these distances:
42 17 0.03
43 108 0.19
44 328 0.59
45 102 0.18
46 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
AGGGAGGTAAAATCTGCTATCTTCAATCTACTCCACTACTGCTT
Found at i:3374224 original size:132 final size:132
Alignment explanation
Indices: 3373257--3374201 Score: 1293
Period size: 132 Copynumber: 7.2 Consensus size: 132
3373247 CAATACATGA
*** * * **
3373257 AGACAAGATCTGTTTTCTTCGATCGATTCCACTGCTGACCGGGGGAA-TAGAATTACTGGCTTCA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTG-CCCAGGGAAGTAGAATTACTGGCTTCA
* * * * * *
3373321 ATATACTCCGCTACAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCAATACTGCTTA
65 ATGTACTCCACTGCAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTA
3373386 GGG
130 GGG
* * * * *
3373389 AGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGAAAATAGAATTACTGGCTTCAA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAA
* * *
3373454 TGTACTCCACTGTAATCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAG
66 TGTACTCCACTGCAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAG
3373519 GG
131 GG
* *
3373521 AGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAA
* * * *
3373586 TGTACTCCACTACAACTTCAAGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAA
66 TGTACTCCACTGCAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAG
3373651 GG
131 GG
* * *
3373653 AGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCTAGGGAAGTAGAATTACTGGCTTCAA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAA
* *
3373718 TGTACTCCACTGCAACTTCAGGGAGGTAAAATCCGCTATCTTCGATCTGCTCCACTACTGCTTAG
66 TGTACTCCACTGCAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAG
3373783 GG
131 GG
* * *
3373785 AGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAAGGAAGTAGAATTACTGGCTTCAA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAA
* * * * *
3373850 TGTACTCCACTACAACTTTAGGGAGGTAAAATCCGTCATCTTCGATCTGCTCCACTACTACTTAG
66 TGTACTCCACTGCAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAG
3373915 GG
131 GG
* * * * * *
3373917 AGACAAGATTTGAAATCTTCAATCTATTTCGCTACTGCTCAGGGAAGTAAAATTACT-GCTTCAA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAA
* * * *
3373981 TGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCATCTTCGATCTGCTCTACTACTGCTTAG
66 TGTACTCCACTGCAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAG
3374046 GG
131 GG
* * * *
3374048 AGATAAGATCTAAAATCTTCAGTCTATTCCACTGCTGCCAAGGGAAGTAGAATTACTGGCTTCAA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAA
* * * * * *
3374113 TGTACTCCACTGTAACCACAGGGAGGTAAAATCTGTCATCTTCGATCTGCCCCACTACTGCTCAA
66 TGTACTCCACTGCAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCT-TA
3374178 GGG
130 GGG
**
3374181 -GACAAGATCTGCTATCTTCAA
1 AGACAAGATCTGAAATCTTCAA
3374202 CCTGCTCCAC
Statistics
Matches: 735, Mismatches: 75, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
131 120 0.16
132 611 0.83
133 4 0.01
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (132 bp):
AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAA
TGTACTCCACTGCAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAG
GG
Found at i:3380415 original size:10 final size:11
Alignment explanation
Indices: 3380403--3380432 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
3380393 ATTTTATACG
3380403 AAATAAAACGA
1 AAATAAAACGA
3380414 AAATAAAA-GA
1 AAATAAAACGA
3380424 AAATAAAAC
1 AAATAAAAC
3380433 ATATGTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.10
Consensus pattern (11 bp):
AAATAAAACGA
Found at i:3380861 original size:18 final size:17
Alignment explanation
Indices: 3380825--3380868 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3380815 AAATTAGTTG
*
3380825 TTGGGCCTGTTAATGGT
1 TTGGGCCCGTTAATGGT
*
3380842 TTGGGCCCGTTTATTGGT
1 TTGGGCCCG-TTAATGGT
*
3380860 TTAGGCCCG
1 TTGGGCCCG
3380869 GGCATTATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.09, C:0.18, G:0.34, T:0.39
Consensus pattern (17 bp):
TTGGGCCCGTTAATGGT
Found at i:3405363 original size:9 final size:10
Alignment explanation
Indices: 3405350--3405380 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3405340 AATTTTTATT
*
3405350 TTTTTATAAA
1 TTTTTAGAAA
3405360 TTTTTAGAAA
1 TTTTTAGAAA
3405370 TTTTTAGAAA
1 TTTTTAGAAA
3405380 T
1 T
3405381 ATAATGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (10 bp):
TTTTTAGAAA
Found at i:3412617 original size:15 final size:16
Alignment explanation
Indices: 3412593--3412624 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3412583 AGTATATATA
3412593 AAAAAGTAAAAAAAAC
1 AAAAAGTAAAAAAAAC
3412609 AAAAA-TAAAAAAAAC
1 AAAAAGTAAAAAAAAC
3412624 A
1 A
3412625 TACATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.84, C:0.06, G:0.03, T:0.06
Consensus pattern (16 bp):
AAAAAGTAAAAAAAAC
Found at i:3412722 original size:162 final size:162
Alignment explanation
Indices: 3412546--3412883 Score: 660
Period size: 162 Copynumber: 2.1 Consensus size: 162
3412536 TACATGTGTA
3412546 TATATTTACAAAAAAAAAGTATATATATAAAATATAAAGTATATATAAAAAAGTAAAAAAAACAA
1 TATATTTACAAAAAAAAAGTATATATATAAAATATAAAGTATATATAAAAAAGTAAAAAAAACAA
3412611 AAATAAAAAAAACATACATATAAAATATATGCATGTATTTATAAAAGCTTAAAAATATATATATA
66 AAATAAAAAAAACATACATATAAAATATATGCATGTATTTATAAAAGCTTAAAAATATATATATA
3412676 CCTATATATATAAAAAATGCCCATATGTATAT
131 CCTATATATATAAAAAATGCCCATATGTATAT
3412708 TATATTTACAAAAAAAAAGTATATATATAAAATATAAAGTATATATAAAAAAGTAAAAAAAACAA
1 TATATTTACAAAAAAAAAGTATATATATAAAATATAAAGTATATATAAAAAAGTAAAAAAAACAA
3412773 AAATAAAAAAAACATACATATAAAATATATGCATGTATTTATAAAAGCTTAAAAATATATATATA
66 AAATAAAAAAAACATACATATAAAATATATGCATGTATTTATAAAAGCTTAAAAATATATATATA
3412838 CCTATATATATAAAAAATGCCCATATGTATAT
131 CCTATATATATAAAAAATGCCCATATGTATAT
*
3412870 TATATATA-AAAAAA
1 TATATTTACAAAAAA
3412884 CTATGCGTAT
Statistics
Matches: 175, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
161 6 0.03
162 169 0.97
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (162 bp):
TATATTTACAAAAAAAAAGTATATATATAAAATATAAAGTATATATAAAAAAGTAAAAAAAACAA
AAATAAAAAAAACATACATATAAAATATATGCATGTATTTATAAAAGCTTAAAAATATATATATA
CCTATATATATAAAAAATGCCCATATGTATAT
Found at i:3412779 original size:15 final size:16
Alignment explanation
Indices: 3412755--3412786 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3412745 AGTATATATA
3412755 AAAAAGTAAAAAAAAC
1 AAAAAGTAAAAAAAAC
3412771 AAAAA-TAAAAAAAAC
1 AAAAAGTAAAAAAAAC
3412786 A
1 A
3412787 TACATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.84, C:0.06, G:0.03, T:0.06
Consensus pattern (16 bp):
AAAAAGTAAAAAAAAC
Found at i:3412901 original size:32 final size:30
Alignment explanation
Indices: 3412828--3412901 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
3412818 AGCTTAAAAA
* *
3412828 TATATATATACCTATATATATAAAAAATGCC
1 TATATATATA-TTATATATAAAAAAAATGCC
* * *
3412859 CATATGTATATTATATATAAAAAAACTATGCG
1 TATATATATATTATATATAAAAAAA--ATGCC
3412891 TATATATATAT
1 TATATATATAT
3412902 ATAGAAAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
30 13 0.38
31 8 0.24
32 13 0.38
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.38
Consensus pattern (30 bp):
TATATATATATTATATATAAAAAAAATGCC
Found at i:3412955 original size:27 final size:27
Alignment explanation
Indices: 3412900--3412978 Score: 65
Period size: 27 Copynumber: 2.9 Consensus size: 27
3412890 GTATATATAT
* *
3412900 ATATAGAA-AATATGATAATAATTAATA
1 ATATA-AATAATATAATAATAAATAATA
3412927 ATATAAATAATATAATAA-AAATAATTA
1 ATATAAATAATATAATAATAAATAA-TA
* * *
3412954 ATTTTAATAATA-ACATAATTAATAA
1 ATATAAATAATATA-ATAATAAATAA
3412979 CAAGGGACCC
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
26 8 0.19
27 30 0.70
28 5 0.12
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (27 bp):
ATATAAATAATATAATAATAAATAATA
Found at i:3414439 original size:59 final size:60
Alignment explanation
Indices: 3414357--3414507 Score: 191
Period size: 59 Copynumber: 2.5 Consensus size: 60
3414347 TAAGGCTTGG
* * * ** *
3414357 GTGACTAAAATGAAAGCACCCTAAACTTTGGGTGACTAAATTG-AAAGGATTTAATTTTGA
1 GTGACAAAAATAAAAGCGCCCTAAAAGTTGGGTGACTAAATTGCAAA-AATTTAATTTTGA
* *
3414417 -TGACAAAAATAAAAGCGTCCTAAAAGTTGGGTGATTAAATTGCAAAAATTTAATTTTGA
1 GTGACAAAAATAAAAGCGCCCTAAAAGTTGGGTGACTAAATTGCAAAAATTTAATTTTGA
*
3414476 GTGACCAAAATAAAA-CGCCCTAAAAGTTGGGT
1 GTGACAAAAATAAAAGCGCCCTAAAAGTTGGGT
3414508 AACCAACTAG
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
59 63 0.80
60 16 0.20
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (60 bp):
GTGACAAAAATAAAAGCGCCCTAAAAGTTGGGTGACTAAATTGCAAAAATTTAATTTTGA
Found at i:3414981 original size:20 final size:19
Alignment explanation
Indices: 3414946--3414988 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
3414936 AATATTAAAA
3414946 AAATATTTTTATAATTTTT
1 AAATATTTTTATAATTTTT
3414965 AAATAATTTTCTA-AATTTTT
1 AAAT-ATTTT-TATAATTTTT
3414985 AAAT
1 AAAT
3414989 TAAAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.18
20 16 0.73
21 2 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATATTTTTATAATTTTT
Found at i:3431479 original size:9 final size:9
Alignment explanation
Indices: 3431465--3431490 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3431455 TTTCTTCTCC
3431465 TCTCTCCCA
1 TCTCTCCCA
3431474 TCTCTCCCA
1 TCTCTCCCA
3431483 TCTCTCCC
1 TCTCTCCC
3431491 CGCTGCCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.58, G:0.00, T:0.35
Consensus pattern (9 bp):
TCTCTCCCA
Found at i:3438306 original size:28 final size:28
Alignment explanation
Indices: 3438266--3438326 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
3438256 ATTCTTAGAG
*
3438266 CTTTAAACATACTCTAATACATTTTCAT
1 CTTTAAACATACTCTAACACATTTTCAT
**
3438294 CTTTAAACATACTCTAACATGTTTTCAT
1 CTTTAAACATACTCTAACACATTTTCAT
3438322 CTTTA
1 CTTTA
3438327 TTCTTCAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (28 bp):
CTTTAAACATACTCTAACACATTTTCAT
Found at i:3440095 original size:50 final size:50
Alignment explanation
Indices: 3439990--3440110 Score: 127
Period size: 50 Copynumber: 2.4 Consensus size: 50
3439980 CAGACACACC
*
3439990 ATGGCTCTCACGAGCTTCCCGTTATTTAGCTCATATGAGTACCCTGATAT
1 ATGGCTCTCACGAGCTTCCCGATATTTAGCTCATATGAGTACCCTGATAT
* * * * * * *
3440040 TTGGCTCTCATGAGTTTCCCGATATTTGGCTCGTATGAGCTTCCC-GTTAT
1 ATGGCTCTCACGAGCTTCCCGATATTTAGCTCATATGAG-TACCCTGATAT
** *
3440090 ATGGCTCGGAAGAGCTTCCCG
1 ATGGCTCTCACGAGCTTCCCG
3440111 TTAACATGCT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
50 53 0.93
51 4 0.07
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (50 bp):
ATGGCTCTCACGAGCTTCCCGATATTTAGCTCATATGAGTACCCTGATAT
Found at i:3440097 original size:25 final size:25
Alignment explanation
Indices: 3440001--3440113 Score: 113
Period size: 25 Copynumber: 4.5 Consensus size: 25
3439991 TGGCTCTCAC
* *
3440001 GAGCTTCCCGTTATTTAGCTCATAT
1 GAGCTTCCCGTTATTTGGCTCGTAT
* *
3440026 GAG-TACCCTGATATTTGGCTC-TCAT
1 GAGCTTCCC-GTTATTTGGCTCGT-AT
* *
3440051 GAGTTTCCCGATATTTGGCTCGTAT
1 GAGCTTCCCGTTATTTGGCTCGTAT
* * *
3440076 GAGCTTCCCGTTATATGGCTCGGAA
1 GAGCTTCCCGTTATTTGGCTCGTAT
3440101 GAGCTTCCCGTTA
1 GAGCTTCCCGTTA
3440114 ACATGCTCGT
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
24 5 0.07
25 65 0.87
26 5 0.07
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (25 bp):
GAGCTTCCCGTTATTTGGCTCGTAT
Found at i:3440129 original size:25 final size:25
Alignment explanation
Indices: 3440066--3440129 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
3440056 TCCCGATATT
*
3440066 TGGCTCGTATGAGCTTCCCGTTATA
1 TGGCTCGTATGAGCTTCCCGTTACA
* *
3440091 TGGCTCGGAAGAGCTTCCCGTTAACA
1 TGGCTCGTATGAGCTTCCCGTT-ACA
3440117 T-GCTCGTATGAGC
1 TGGCTCGTATGAGC
3440130 ACATATGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
25 30 0.91
26 3 0.09
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.30
Consensus pattern (25 bp):
TGGCTCGTATGAGCTTCCCGTTACA
Found at i:3440599 original size:29 final size:30
Alignment explanation
Indices: 3440564--3440621 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
3440554 ACAACAAGAC
*
3440564 CCAACCCAAACTCAAA-CCAACCAAAACCA
1 CCAACCCAAACCCAAACCCAACCAAAACCA
*
3440593 CCAACCCAAACCCAAACCCAACCTAAACC
1 CCAACCCAAACCCAAACCCAACCAAAACC
3440622 TAACCCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.48, C:0.48, G:0.00, T:0.03
Consensus pattern (30 bp):
CCAACCCAAACCCAAACCCAACCAAAACCA
Found at i:3440604 original size:6 final size:6
Alignment explanation
Indices: 3440546--3440613 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
3440536 CCGAGGCCCA
* * *
3440546 AAACCC AAACAAC AAGACCC -AACCC AAACTC AAA-CC -AACCA AAACCAC
1 AAACCC AAAC-CC AA-ACCC AAACCC AAACCC AAACCC AAACCC AAACC-C
*
3440594 CAACCC AAACCC AAACCC AA
1 AAACCC AAACCC AAACCC AA
3440614 CCTAAACCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
4 2 0.04
5 6 0.12
6 30 0.62
7 8 0.17
8 2 0.04
ACGTcount: A:0.53, C:0.44, G:0.01, T:0.01
Consensus pattern (6 bp):
AAACCC
Found at i:3441909 original size:28 final size:28
Alignment explanation
Indices: 3441842--3441910 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
3441832 TCGAATATGC
*
3441842 TATTCATTTATTTATTTTAAATCCTTTTCT
1 TATT-ATTTA-TTATTTTAAATCCTTTTAT
* **
3441872 CA-TATATTATTATTTTAAATTGTTTTAT
1 TATTAT-TTATTATTTTAAATCCTTTTAT
3441900 TATTATTTATT
1 TATTATTTATT
3441911 TCAAGTTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
28 24 0.75
29 7 0.22
30 1 0.03
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (28 bp):
TATTATTTATTATTTTAAATCCTTTTAT
Found at i:3442065 original size:26 final size:27
Alignment explanation
Indices: 3442031--3442098 Score: 86
Period size: 26 Copynumber: 2.5 Consensus size: 27
3442021 TACACATCAT
3442031 TTATTTATTTTAAACTAT-TTTGT-ATA
1 TTATTTATTTTAAACT-TCTTTGTAATA
* *
3442057 TTATTTATTTGAAACTTCTTTTTACATA
1 TTATTTATTTTAAACTTCTTTGTA-ATA
3442085 TTATTTATTTTAAA
1 TTATTTATTTTAAA
3442099 TTTTTTACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 1 0.03
26 19 0.53
28 16 0.44
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (27 bp):
TTATTTATTTTAAACTTCTTTGTAATA
Found at i:3442112 original size:28 final size:27
Alignment explanation
Indices: 3442031--3442114 Score: 82
Period size: 28 Copynumber: 3.1 Consensus size: 27
3442021 TACACATCAT
* **
3442031 TTATTTATTTTAAACTATTTT-GTATA
1 TTATTTATTTTAAACTTTTTTCACATA
* *
3442057 TTATTTATTTGAAACTTCTTTTTACATA
1 TTATTTATTTTAAACTT-TTTTCACATA
3442085 TTATTTATTTTAAA-TTTTTTACATCATA
1 TTATTTATTTTAAACTTTTTT-CA-CATA
3442113 TT
1 TT
3442115 TTAAATTGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
26 19 0.40
27 7 0.15
28 22 0.46
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (27 bp):
TTATTTATTTTAAACTTTTTTCACATA
Found at i:3442219 original size:27 final size:26
Alignment explanation
Indices: 3442162--3442233 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
3442152 TGTAGTTTGT
* *
3442162 ATATTATTTATTTTAATTTGTTTTAC
1 ATATTATTTACTTTAAATTGTTTTAC
*
3442188 ATATTATTTGCTTTAAATTGTTTT--
1 ATATTATTTACTTTAAATTGTTTTAC
* **
3442212 ATACTATTTACTCCAAATTGTT
1 ATATTATTTACTTTAAATTGTT
3442234 CTATATTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 18 0.46
26 21 0.54
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (26 bp):
ATATTATTTACTTTAAATTGTTTTAC
Found at i:3445582 original size:22 final size:22
Alignment explanation
Indices: 3445554--3445597 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3445544 TAGGGGGACA
3445554 AAGGGTCCCATGTCTCACTCCT
1 AAGGGTCCCATGTCTCACTCCT
3445576 AAGGGTCCCATGTCTCACTCCT
1 AAGGGTCCCATGTCTCACTCCT
3445598 TTTTCTCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.36, G:0.18, T:0.27
Consensus pattern (22 bp):
AAGGGTCCCATGTCTCACTCCT
Found at i:3461193 original size:29 final size:29
Alignment explanation
Indices: 3461142--3461218 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
3461132 TTAACCTTTA
*
3461142 TCAAAGTGCTCAAATGAATGTCAAAC-ATT
1 TCAAAGTGCTCAAAT-AAAGTCAAACTATT
* *
3461171 TCAAAGTGCTTAAATAAGAGTCAAACTTTT
1 TCAAAGTGCTCAAATAA-AGTCAAACTATT
*
3461201 TGAAAGTGCTCAAATAAA
1 TCAAAGTGCTCAAATAAA
3461219 TTACGTCTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 2 0.05
29 22 0.54
30 17 0.41
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (29 bp):
TCAAAGTGCTCAAATAAAGTCAAACTATT
Found at i:3464553 original size:40 final size:40
Alignment explanation
Indices: 3464498--3464580 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
3464488 ATTTATAGAG
3464498 TTACACATGTAATTTCTATCTAAAGGAAAATAGATATTAA
1 TTACACATGTAATTTCTATCTAAAGGAAAATAGATATTAA
3464538 TTACACATGTAATTTCTATCTAAAGGAAAATAGATATTAA
1 TTACACATGTAATTTCTATCTAAAGGAAAATAGATATTAA
3464578 TTA
1 TTA
3464581 TGAATAAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.36
Consensus pattern (40 bp):
TTACACATGTAATTTCTATCTAAAGGAAAATAGATATTAA
Found at i:3467948 original size:15 final size:17
Alignment explanation
Indices: 3467911--3467954 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
3467901 CTAATATCCT
3467911 AATCCAAAAATTATCAG
1 AATCCAAAAATTATCAG
*
3467928 AATCCAAAAGTTA-CA-
1 AATCCAAAAATTATCAG
3467943 AATCCAACAAAT
1 AATCCAA-AAAT
3467955 GATGTTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 5 0.21
17 12 0.50
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (17 bp):
AATCCAAAAATTATCAG
Found at i:3479392 original size:19 final size:18
Alignment explanation
Indices: 3479352--3479392 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
3479342 TTTATAATAT
3479352 TTTATTTTATTATTTCAG
1 TTTATTTTATTATTTCAG
3479370 TTTATTTTATAGTATTT-AG
1 TTTATTTTAT--TATTTCAG
3479389 TTTA
1 TTTA
3479393 AGTATTGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.48
19 6 0.29
20 5 0.24
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.66
Consensus pattern (18 bp):
TTTATTTTATTATTTCAG
Found at i:3486479 original size:15 final size:16
Alignment explanation
Indices: 3486455--3486487 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3486445 GCAATAAAAA
*
3486455 TTCAGTACTTA-ATTT
1 TTCAGCACTTAGATTT
3486470 TTCAGCACTTAGATTT
1 TTCAGCACTTAGATTT
3486486 TT
1 TT
3486488 AGTTTATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (16 bp):
TTCAGCACTTAGATTT
Found at i:3488170 original size:50 final size:50
Alignment explanation
Indices: 3488116--3488213 Score: 146
Period size: 49 Copynumber: 2.0 Consensus size: 50
3488106 AAAAGATAAT
*
3488116 ATTAATATATTTAA-ATATTTTCAATAATTTTTATTATTA-CAAATATTTTA
1 ATTAA-ATATTTAATA-ATTTTCAATAATCTTTATTATTATCAAATATTTTA
*
3488166 ATTAAGTATTTAATAATTTTCAATAATCTTTATTATTATCAAATATTT
1 ATTAAATATTTAATAATTTTCAATAATCTTTATTATTATCAAATATTT
3488214 GAACTAACCA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
49 29 0.66
50 15 0.34
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (50 bp):
ATTAAATATTTAATAATTTTCAATAATCTTTATTATTATCAAATATTTTA
Found at i:3488234 original size:49 final size:48
Alignment explanation
Indices: 3488129--3488234 Score: 124
Period size: 49 Copynumber: 2.2 Consensus size: 48
3488119 AATATATTTA
* * * ** *
3488129 AATATTTTCAATAATTTTTATTATTACAAATATTTTAATTAAGTATTT
1 AATATTTTCAATAATCTTTATTATTACAAATATTTGAACTAACAATAT
3488177 AATAATTTTCAATAATCTTTATTATTATCAAATATTTGAACTAACCAATAT
1 AAT-ATTTTCAATAATCTTTATTATTA-CAAATATTTGAACTAA-CAATAT
3488228 -ATATTTT
1 AATATTTT
3488235 ATCCACAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
48 3 0.06
49 27 0.55
50 16 0.33
51 3 0.06
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.50
Consensus pattern (48 bp):
AATATTTTCAATAATCTTTATTATTACAAATATTTGAACTAACAATAT
Found at i:3492500 original size:41 final size:41
Alignment explanation
Indices: 3492443--3492532 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
3492433 ACAAATTTGA
3492443 GGAAAATGTCTTACGCTTTTAAACTCGGTAAGACATTTTCC
1 GGAAAATGTCTTACGCTTTTAAACTCGGTAAGACATTTTCC
3492484 GGAAAATGTCTTACGCTTTTAAACTCGGTAAGACATTTTCC
1 GGAAAATGTCTTACGCTTTTAAACTCGGTAAGACATTTTCC
3492525 GGAAAATG
1 GGAAAATG
3492533 ACGCCTTCTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (41 bp):
GGAAAATGTCTTACGCTTTTAAACTCGGTAAGACATTTTCC
Found at i:3492581 original size:18 final size:17
Alignment explanation
Indices: 3492554--3492587 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3492544 TCCCCTTTAA
3492554 CCTTTCCCTTCCCCTTC
1 CCTTTCCCTTCCCCTTC
3492571 CCTTCTCCCTTCCCCTT
1 CCTT-TCCCTTCCCCTT
3492588 GTGTTGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (17 bp):
CCTTTCCCTTCCCCTTC
Found at i:3492709 original size:25 final size:27
Alignment explanation
Indices: 3492647--3492709 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 27
3492637 CAGGTAAGGC
3492647 TCCTTCTTCTTCTTCTTCCATTCTTCAT
1 TCCTTC-TCTTCTTCTTCCATTCTTCAT
**
3492675 TCCTT-T-TTCTTCTTCTGTTCTTCA-
1 TCCTTCTCTTCTTCTTCCATTCTTCAT
3492699 T-CTTCTCTTCT
1 TCCTTCTCTTCT
3492710 CAGCATATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
23 3 0.10
24 2 0.06
25 20 0.65
26 1 0.03
28 5 0.16
ACGTcount: A:0.05, C:0.33, G:0.02, T:0.60
Consensus pattern (27 bp):
TCCTTCTCTTCTTCTTCCATTCTTCAT
Found at i:3495520 original size:14 final size:15
Alignment explanation
Indices: 3495498--3495574 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
3495488 CAATCAAACA
3495498 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
3495512 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
3495527 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
3495547 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
3495561 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
3495575 ACTACCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:3495539 original size:20 final size:20
Alignment explanation
Indices: 3495514--3495553 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3495504 AATATTTTCC
*
3495514 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
3495534 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
3495554 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:3495559 original size:34 final size:35
Alignment explanation
Indices: 3495502--3495568 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3495492 CAAACACCAG
*
3495502 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
3495537 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
3495569 CATTTTACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:3495575 original size:14 final size:14
Alignment explanation
Indices: 3495537--3495576 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3495527 ACAGAAAAGT
*
3495537 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
3495551 AAATCATTTTACGG
1 AAAACATTTTACAG
3495565 AAAACATTTTAC
1 AAAACATTTTAC
3495577 TACCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:3498022 original size:20 final size:20
Alignment explanation
Indices: 3498001--3498053 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
3497991 TACTTAATAT
3498001 TTTAT-TTAATTATTTAAAA
1 TTTATATTAATTATTTAAAA
**
3498020 TTTATATTAATT-TATTAATT
1 TTTATATTAATTAT-TTAAAA
3498040 TTTATATTATATTA
1 TTTATATTA-ATTA
3498054 AAAAGAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 6 0.21
20 19 0.68
21 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATATTAATTATTTAAAA
Found at i:3504472 original size:3 final size:3
Alignment explanation
Indices: 3504464--3504491 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3504454 AAATGTTTTT
3504464 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3504492 GGAACAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3506503 original size:33 final size:32
Alignment explanation
Indices: 3506431--3506506 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 32
3506421 ATGTTTAAAT
* * * *
3506431 GTAAGACCATAGCTAGGCTATGGCATTTTAAT
1 GTAAGACCATAACTAGGCTATGACATTTGAAC
* *
3506463 GAAAAGACCATAACTAGGTTATGACACTTTGAAC
1 G-TAAGACCATAACTAGGCTATGACA-TTTGAAC
3506497 GTAAGACCAT
1 GTAAGACCAT
3506507 GGTTAGATCA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
32 1 0.03
33 28 0.80
34 6 0.17
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (32 bp):
GTAAGACCATAACTAGGCTATGACATTTGAAC
Found at i:3512322 original size:45 final size:45
Alignment explanation
Indices: 3512224--3512429 Score: 344
Period size: 45 Copynumber: 4.6 Consensus size: 45
3512214 TTTGAGTGCT
*
3512224 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
*
3512270 TCTGATCAAGTGACAAAGTGATAAATGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
3512315 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
*
3512360 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAACTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
* *
3512405 TCTGATC-AGGGA-TAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
3512430 ATCATACGTA
Statistics
Matches: 154, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
43 12 0.08
44 4 0.03
45 107 0.69
46 31 0.20
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
Found at i:3519681 original size:13 final size:13
Alignment explanation
Indices: 3519663--3519687 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3519653 CCTCTCTCAC
3519663 TTCTTTTTTTCTT
1 TTCTTTTTTTCTT
3519676 TTCTTTTTTTCT
1 TTCTTTTTTTCT
3519688 AATGGAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTCTTTTTTTCTT
Found at i:3524712 original size:23 final size:24
Alignment explanation
Indices: 3524668--3524712 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
3524658 ATTTACCCAT
*
3524668 GGGAGAAGCCAGAATAATTTTTTA
1 GGGAGAAGCCAGAATAAATTTTTA
3524692 GGGAG-AGCC-GAATGAAATTTT
1 GGGAGAAGCCAGAAT-AAATTTT
3524713 AATTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 10 0.53
24 5 0.26
ACGTcount: A:0.36, C:0.09, G:0.29, T:0.27
Consensus pattern (24 bp):
GGGAGAAGCCAGAATAAATTTTTA
Found at i:3526130 original size:15 final size:16
Alignment explanation
Indices: 3526110--3526142 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3526100 ATTAGTTAAA
3526110 ATTAACTACAA-ATAT
1 ATTAACTACAATATAT
*
3526125 ATTAACTATAATATAT
1 ATTAACTACAATATAT
3526141 AT
1 AT
3526143 ATATACACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAACTACAATATAT
Found at i:3526716 original size:4 final size:4
Alignment explanation
Indices: 3526707--3526731 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3526697 TTTTCTTACA
3526707 TGTT TGTT TGTT TGTT TGTT TGTT T
1 TGTT TGTT TGTT TGTT TGTT TGTT T
3526732 ATGTCCAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
TGTT
Found at i:3535383 original size:3 final size:3
Alignment explanation
Indices: 3535375--3535405 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3535365 TTTGGCTCCT
3535375 AAC AAC AAC AAC AAC AAC AAC AAC AA- AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
3535406 TTAAAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.29, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:3539655 original size:20 final size:20
Alignment explanation
Indices: 3539630--3539672 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
3539620 TGTAGCTTTG
3539630 GTTTCTTTTAAAGCAGTTTA
1 GTTTCTTTTAAAGCAGTTTA
3539650 GTTTCTTTTAAAGCAGTTTA
1 GTTTCTTTTAAAGCAGTTTA
3539670 GTT
1 GTT
3539673 AATCATTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.16, T:0.51
Consensus pattern (20 bp):
GTTTCTTTTAAAGCAGTTTA
Found at i:3549502 original size:44 final size:43
Alignment explanation
Indices: 3549453--3549581 Score: 102
Period size: 47 Copynumber: 2.9 Consensus size: 43
3549443 AATAATAATT
3549453 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGA
1 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTAT-AAGA
* * * **
3549497 ATTTTATGAAATTATATATCATT-AT-TAA-ATTATATTTAATAATAATT
1 A-TTT-T-AAATTATATA-AATTCATATAAGA--AAATTT-ATTATAAGA
* *
3549544 ATTTAAAATTATACAAATTCATATAAGAAAATTTATTA
1 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTA
3549582 GTTATAATTA
Statistics
Matches: 65, Mismatches: 10, Indels: 21
0.68 0.10 0.22
Matches are distributed among these distances:
43 6 0.09
44 17 0.26
45 7 0.11
46 8 0.12
47 20 0.31
48 7 0.11
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (43 bp):
ATTTTAAATTATATAAATTCATATAAGAAAATTTATTATAAGA
Found at i:3549746 original size:18 final size:17
Alignment explanation
Indices: 3549718--3549752 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3549708 ATTATTAAGA
*
3549718 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3549735 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3549753 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3550009 original size:16 final size:16
Alignment explanation
Indices: 3549988--3550039 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
3549978 GATTTGCTAT
* *
3549988 TACACCTCTATTCTAA
1 TACACCTCTAATCCAA
*
3550004 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
3550020 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3550036 TACA
1 TACA
3550040 GCGAACCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:3552608 original size:37 final size:37
Alignment explanation
Indices: 3552564--3552729 Score: 305
Period size: 37 Copynumber: 4.5 Consensus size: 37
3552554 CACTTGTCCC
*
3552564 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
*
3552601 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTAT
1 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
3552638 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
*
3552675 TGATCAGATAAGTGTAGCCACTTATCACTTTGTCTCT
1 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
3552712 TGATCAGATAAGTGTAGC
1 TGATCAGATAAGTGTAGC
3552730 TAAAGCTATC
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 125 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (37 bp):
TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
Found at i:3552746 original size:46 final size:46
Alignment explanation
Indices: 3552693--3552961 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
3552683 TAAGTGTAGC
* **
3552693 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
3552739 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
3552785 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
3552837 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
3552883 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
3552935 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
3552962 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:3552812 original size:52 final size:52
Alignment explanation
Indices: 3552736--3552955 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
3552726 TAGCTAAAGC
* *
3552736 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
3552789 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
3552841 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
3552887 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
3552939 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
3552956 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:3552858 original size:98 final size:98
Alignment explanation
Indices: 3552693--3552961 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
3552683 TAAGTGTAGC
* * *
3552693 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
3552758 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
3552792 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
3552857 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
3552890 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
3552955 GATCAGA
66 GATCAGA
3552962 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:3556029 original size:15 final size:15
Alignment explanation
Indices: 3556009--3556037 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3555999 GAACTATTAG
3556009 TTTTTTCTATTAATC
1 TTTTTTCTATTAATC
3556024 TTTTTTCTATTAAT
1 TTTTTTCTATTAAT
3556038 TCCTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTTCTATTAATC
Found at i:3559506 original size:27 final size:27
Alignment explanation
Indices: 3559467--3559566 Score: 146
Period size: 27 Copynumber: 3.7 Consensus size: 27
3559457 GTCGGGTGGC
* *
3559467 GCCTCATAGGGAGGCACCATTAAAAGT
1 GCCTCATAAGGAGGCGCCATTAAAAGT
*
3559494 GCCTCATAAGGAGGTGCCATTAAAAGT
1 GCCTCATAAGGAGGCGCCATTAAAAGT
*
3559521 GCCTCATAAGGAGGTGCCATTAAAAGT
1 GCCTCATAAGGAGGCGCCATTAAAAGT
* *
3559548 GTCTCATAGGGAGGCGCCA
1 GCCTCATAAGGAGGCGCCA
3559567 ATGGGTAATT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.20
Consensus pattern (27 bp):
GCCTCATAAGGAGGCGCCATTAAAAGT
Found at i:3559702 original size:22 final size:22
Alignment explanation
Indices: 3559676--3559721 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
3559666 TGGATTAGTA
3559676 TTTTGTATGAATAGTGTAATTT
1 TTTTGTATGAATAGTGTAATTT
*
3559698 TTTTGTATGAATATTGTAATTT
1 TTTTGTATGAATAGTGTAATTT
3559720 TT
1 TT
3559722 ATGAATATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (22 bp):
TTTTGTATGAATAGTGTAATTT
Found at i:3559726 original size:18 final size:19
Alignment explanation
Indices: 3559571--3560107 Score: 137
Period size: 19 Copynumber: 26.3 Consensus size: 19
3559561 GCGCCAATGG
*
3559571 GTAATTTTGTATGTATATT
1 GTAATTTTGTATGAATATT
3559590 GTAACTTTTTGTATGAATATT
1 GTAA--TTTTGTATGAATATT
*
3559611 ATAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
* * *
3559630 GTAATTACTTTATAATTAATTTT
1 GTAA-T--TTTGT-ATGAATATT
* * *
3559653 GT-ATTTATAGTTTTGGAT-TA
1 GTAATTT-T-G-TATGAATATT
*
3559673 GT-ATTTTGTATGAATAGT
1 GTAATTTTGTATGAATATT
3559691 GTAATTTTTTTGTATGAATATT
1 GTAA---TTTTGTATGAATATT
3559713 GTAATTTT-TATGAATATT
1 GTAATTTTGTATGAATATT
*
3559731 GTAATTATTTTAT-AATTAATTTT
1 GTAATT-TTGTATGAA-T-A--TT
* * * *
3559754 GT-ATTTACAGTTTTTAAT-TA
1 GTAATTT--TG-TATGAATATT
3559774 GT-ATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
3559792 GTAATTTTG--T-AATTTT
1 GTAATTTTGTATGAATATT
* *
3559808 GTATGAATATTG-A--AATTTT
1 G--T-AATTTTGTATGAATATT
3559827 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
3559846 GTAATTATTTTAT-AATTAATTAT
1 GTAATT-TTGTATGAA-T-A-T-T
***
3559869 GT-ATTTATAGT-TTTTTATT
1 GTAATTT-T-GTATGAATATT
3559888 AGT-ATTTTGTATGAATATT
1 -GTAATTTTGTATGAATATT
* *
3559907 ATAATGTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
3559926 GTAATTATTTTAT-AATTAATTTT
1 GTAATT-TTGTATGAA-T-A--TT
* * *
3559949 GT-ATTTATAGTTTTGGAT-TA
1 GTAATTT-T-G-TATGAATATT
3559969 GT-ATTTTGTATGAATATTGTAATTTT
1 GTAATTTTGTATG-A-A---T-A--TT
3559995 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
3560014 GTAATATTGTTTGTATGAATATT
1 GT-A-A-T-TTTGTATGAATATT
*
3560037 GTAATTTTGTATGGATATT
1 GTAATTTTGTATGAATATT
3560056 GTAGTATTGTTTGTATGAATATT
1 GTA--A-T-TTTGTATGAATATT
3560079 GTAATATTGTTTGTATGAATATT
1 GT-A-A-T-TTTGTATGAATATT
3560102 GTAATT
1 GTAATT
3560108 ATTTTATAAT
Statistics
Matches: 397, Mismatches: 49, Indels: 144
0.67 0.08 0.24
Matches are distributed among these distances:
16 12 0.03
17 16 0.04
18 28 0.07
19 117 0.29
20 49 0.12
21 33 0.08
22 44 0.11
23 73 0.18
24 7 0.02
25 4 0.01
26 4 0.01
27 10 0.03
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (19 bp):
GTAATTTTGTATGAATATT
Found at i:3559790 original size:61 final size:59
Alignment explanation
Indices: 3559716--3559911 Score: 196
Period size: 61 Copynumber: 3.4 Consensus size: 59
3559706 GAATATTGTA
3559716 ATTTT-TATGAATATTGTAATTATTTTATAATTAATTTTGTATTTACAGTTTTTAATTAGT
1 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTA-AGTTTTT-ATTAGT
* * * *
3559776 ATTTTGTATGAATATTGT-A--ATTTTGTAATT--TTGTATGAATATTGAA-ATTTT-GTA--
1 ATTTTGTATGAATATTGTAATTATTTTATAATTAATT-T-TG--TATTTAAGTTTTTATTAGT
*
3559830 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTATGTATTTATAGTTTTTTATTAGT
1 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTA-AG-TTTTTATTAGT
*
3559891 ATTTTGTATGAATATTATAAT
1 ATTTTGTATGAATATTGTAAT
3559912 GTTGTATGAA
Statistics
Matches: 110, Mismatches: 10, Indels: 31
0.73 0.07 0.21
Matches are distributed among these distances:
54 18 0.16
55 6 0.05
56 5 0.05
57 13 0.12
58 20 0.18
59 5 0.05
60 11 0.10
61 32 0.29
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.57
Consensus pattern (59 bp):
ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTAAGTTTTTATTAGT
Found at i:3559803 original size:8 final size:8
Alignment explanation
Indices: 3559790--3559837 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
3559780 TGTATGAATA
3559790 TTGTAATT
1 TTGTAATT
3559798 TTGTAATT
1 TTGTAATT
*
3559806 TTGTATGAATA
1 TTG--T-AATT
*
3559817 TTGAAATT
1 TTGTAATT
3559825 TTGTAATT
1 TTGTAATT
3559833 TTGTA
1 TTGTA
3559838 TGAATATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 26 0.79
10 1 0.03
11 6 0.18
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (8 bp):
TTGTAATT
Found at i:3559806 original size:27 final size:27
Alignment explanation
Indices: 3559776--3560047 Score: 156
Period size: 27 Copynumber: 10.0 Consensus size: 27
3559766 TTTAATTAGT
3559776 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
3559803 ATTTTGTATGAATATTGAAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
3559830 ATTTTGTATGAATATTGTAATTATTTTATA
1 ATTTTGTATGAATATTGT-A--ATTTTGTA
** *
3559860 ATTAATTATGTATTTATAGTT-T-TTTATTAGT-
1 A-T--TT-TGTATGAATA-TTGTAATT-TT-GTA
* *
3559891 ATTTTGTATGAATATTATAATGTTGTATGA
1 ATTTTGTATGAATATTGTAAT-TT-TGT-A
* * * **
3559921 ATATTGTA--ATTATT-TTATAAT-TA
1 ATTTTGTATGAATATTGTAATTTTGTA
** * * *
3559944 ATTTTGTATTTATAGTTTTGGA-TTAGT-
1 ATTTTGTATGAATA-TTGT-AATTTTGTA
3559971 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
3559998 ATTTTGTATGAATATTGTAATATTG--
1 ATTTTGTATGAATATTGTAATTTTGTA
3560023 --TTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
3560048 TGGATATTGT
Statistics
Matches: 189, Mismatches: 30, Indels: 54
0.69 0.11 0.20
Matches are distributed among these distances:
23 30 0.16
24 1 0.01
25 4 0.02
26 11 0.06
27 92 0.49
28 13 0.07
29 2 0.01
30 18 0.10
31 4 0.02
32 1 0.01
33 2 0.01
34 9 0.05
35 2 0.01
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.56
Consensus pattern (27 bp):
ATTTTGTATGAATATTGTAATTTTGTA
Found at i:3559850 original size:115 final size:114
Alignment explanation
Indices: 3559711--3559917 Score: 360
Period size: 115 Copynumber: 1.8 Consensus size: 114
3559701 TGTATGAATA
*
3559711 TTGTAATTTTTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTACAGTTTTTAATTAGT
1 TTGTAATTTTTATGAATATTGTAATTATTTTATAATTAATTATGTATTTACAGTTTTTAATTAGT
* *
3559776 ATTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTGAAATT
66 ATTTTGTATGAATATTATAATGTTGTAATTTTGTATGAATATTGAAATT
* *
3559825 TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTATGTATTTATAGTTTTTTATTAG
1 TTGTAATTTT-TATGAATATTGTAATTATTTTATAATTAATTATGTATTTACAGTTTTTAATTAG
3559890 TATTTTGTATGAATATTATAATGTTGTA
65 TATTTTGTATGAATATTATAATGTTGTA
3559918 TGAATATTGT
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
114 10 0.11
115 77 0.89
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (114 bp):
TTGTAATTTTTATGAATATTGTAATTATTTTATAATTAATTATGTATTTACAGTTTTTAATTAGT
ATTTTGTATGAATATTATAATGTTGTAATTTTGTATGAATATTGAAATT
Found at i:3559929 original size:80 final size:80
Alignment explanation
Indices: 3559828--3559997 Score: 295
Period size: 80 Copynumber: 2.1 Consensus size: 80
3559818 TGAAATTTTG
**
3559828 TAATTTTGTATGAATATTGTAATTATTTTATAATTAATTATGTATTTATAGTTTTTTATTAGTAT
1 TAATTTTGTATGAATATTGTAATTATTTTATAATTAATTATGTATTTATAGTTTTGGATTAGTAT
3559893 TTTGTATGAATATTA
66 TTTGTATGAATATTA
* *
3559908 TAATGTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTAT
1 TAATTTTGTATGAATATTGTAATTATTTTATAATTAATTATGTATTTATAGTTTTGGATTAGTAT
*
3559973 TTTGTATGAATATTG
66 TTTGTATGAATATTA
3559988 TAATTTTGTA
1 TAATTTTGTA
3559998 ATTTTGTATG
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 84 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (80 bp):
TAATTTTGTATGAATATTGTAATTATTTTATAATTAATTATGTATTTATAGTTTTGGATTAGTAT
TTTGTATGAATATTA
Found at i:3560030 original size:23 final size:23
Alignment explanation
Indices: 3559973--3560106 Score: 177
Period size: 23 Copynumber: 5.8 Consensus size: 23
3559963 GGATTAGTAT
*
3559973 TTTGTATGAATATTGTAATTTTG
1 TTTGTATGAATATTGTAATATTG
3559996 TAATTTTGTATGAATATTGTAATATTG
1 ----TTTGTATGAATATTGTAATATTG
3560023 TTTGTATGAATATTGT-A-A-T-
1 TTTGTATGAATATTGTAATATTG
* *
3560042 TTTGTATGGATATTGTAGTATTG
1 TTTGTATGAATATTGTAATATTG
3560065 TTTGTATGAATATTGTAATATTG
1 TTTGTATGAATATTGTAATATTG
3560088 TTTGTATGAATATTGTAAT
1 TTTGTATGAATATTGTAAT
3560107 TATTTTATAA
Statistics
Matches: 98, Mismatches: 5, Indels: 12
0.85 0.04 0.10
Matches are distributed among these distances:
19 15 0.15
20 1 0.01
21 2 0.02
22 2 0.02
23 56 0.57
27 22 0.22
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (23 bp):
TTTGTATGAATATTGTAATATTG
Found at i:3560039 original size:42 final size:42
Alignment explanation
Indices: 3559993--3560106 Score: 174
Period size: 42 Copynumber: 2.6 Consensus size: 42
3559983 TATTGTAATT
3559993 TTGTAATTTTGTATGAATATTGTAATATTGTTTGTATGAATA
1 TTGTAATTTTGTATGAATATTGTAATATTGTTTGTATGAATA
* *
3560035 TTGTAATTTTGTATGGATATTGTAGTATTGTTTGTATGAATA
1 TTGTAATTTTGTATGAATATTGTAATATTGTTTGTATGAATA
3560077 TTGTAATATTGTTTGTATGAATATTGTAAT
1 TTGT-A-A-T-TTTGTATGAATATTGTAAT
3560107 TATTTTATAA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
42 44 0.69
43 1 0.02
44 1 0.02
45 1 0.02
46 17 0.27
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (42 bp):
TTGTAATTTTGTATGAATATTGTAATATTGTTTGTATGAATA
Found at i:3560094 original size:195 final size:190
Alignment explanation
Indices: 3559672--3560107 Score: 576
Period size: 195 Copynumber: 2.3 Consensus size: 190
3559662 GTTTTGGATT
* * *
3559672 AGTAT-TTTGTATGAATAGTGTAATTTTTTTGTATGAATATTGTAATTTTTATGAATATTGTAAT
1 AGTATGTTTGTATGAATATTGTAATATTTTTGTATGAATATTGTAATTTGTATGAATATTGTAAT
*
3559736 TATTTTATAATTAATTTTGTATTTACAGTTTTTAATTAGTATTTTGTATGAATATTGTAATTTTG
66 TATTTTATAATTAATTTTGTATTTACAGTTTTGAATTAGTATTTTGTATGAATATTGTAATTTTG
* *
3559801 TAATTTTGTATGAATATTGAAATTTTGTAATTTTGTATGAATATTGTAATTATTTTATAATTA
131 TAATTTTGTATGAATATTGAAATATTG--A-TTTGTATGAATATTGTAATTATTGTATAATTA
* * * * * *
3559864 ATTATGTATT-TAT-AGTTTTTTATTAGTATTTTGTATGAATATTATAATGTTGTATGAATATTG
1 AGTATGT-TTGTATGAATATTGTAATA-T-TTTTGTATGAATATTGTAAT-TTGTATGAATATTG
* *
3559927 TAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTAAT
62 TAATTATTTTATAATTAATTTTGTATTTACAGTTTTGAATTAGTATTTTGTATGAATATTGTAAT
*
3559992 TTTGTAATTTTGTATGAATATTGTAATATTG-TTTGTATGAATATTGTAATT-TTGTATGGATAT
127 TTTGTAATTTTGTATGAATATTGAAATATTGATTTGTATGAATATTGTAATTATTGTAT--A-AT
*
3560055 TGT
189 T-A
3560058 AGTATTGTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATT
1 AGTA-TGTTTGTATGAATATTGTAATATT-TTTGTATGAATATTGTAATT
3560108 ATTTTATAAT
Statistics
Matches: 209, Mismatches: 22, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
190 5 0.02
191 20 0.10
192 11 0.05
193 8 0.04
194 28 0.13
195 129 0.62
196 8 0.04
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (190 bp):
AGTATGTTTGTATGAATATTGTAATATTTTTGTATGAATATTGTAATTTGTATGAATATTGTAAT
TATTTTATAATTAATTTTGTATTTACAGTTTTGAATTAGTATTTTGTATGAATATTGTAATTTTG
TAATTTTGTATGAATATTGAAATATTGATTTGTATGAATATTGTAATTATTGTATAATTA
Found at i:3560157 original size:88 final size:88
Alignment explanation
Indices: 3559804--3560240 Score: 221
Period size: 88 Copynumber: 5.1 Consensus size: 88
3559794 AATTTTGTAA
* *
3559804 TTTTGTATGAATATTGAAATTTTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAA-TTA
1 TTTTGTATGAATATTGTAATATTG----TTTGTATGAATATTGTAATTATTTTATAATTAATTTA
* * * *
3559868 -T-GT-ATTTA-TAGTT-TTTTATTAGT
62 TTAGTAATTTAGGA-TTATGTTATAAAT
*
3559891 ATTTTGTATGAATA-T-T-ATAATG-TTGTATGAATATTGTAATTATTTTATAATTAA-TT-TT-
1 -TTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATTATTTTATAATTAATTTATTA
* * * * *
3559949 GT-ATTTA-TAGTTTTG-GATTAGT
65 GTAATTTAGGA-TTATGTTATAAAT
* * *
3559971 ATTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTGTAA-TATTGTT-TGTATGAA-
1 -TTTTGTATGAATATTGTAATATTG----TTTGTATGAATATTGTAATTATT-TTAT-AATTAAT
* * * * * *
3560033 -TATT-GTAATTTTGTATGGATATTGTAGTAT
59 TTATTAGTAATTTAGGAT-TATGTTATA-AAT
*
3560063 TGTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATTATTTTATAATTAATTTGTTA
1 T-TTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATTATTTTATAATTAATTTATTA
3560128 GTAATTTAGGATTATGTTATAAAT
65 GTAATTTAGGATTATGTTATAAAT
* * * * *
3560152 TTTTGTAGGATTA-TGTTATAAATT-TTTG--TG--T-TTGTAATTA-TTTAAAATTTAATTTAC
1 TTTTGTATGAATATTG-TA-ATATTGTTTGTATGAATATTGTAATTATTTTATAA-TTAATTTAT
* *
3560209 TAGTAATTTAGGATTAAGCTATAAAT
63 TAGTAATTTAGGATTATGTTATAAAT
*
3560235 TGTTGT
1 TTTTGT
3560241 GTTTAGTTTA
Statistics
Matches: 285, Mismatches: 37, Indels: 59
0.75 0.10 0.15
Matches are distributed among these distances:
80 67 0.24
81 2 0.01
82 7 0.02
83 49 0.17
84 1 0.00
85 4 0.01
86 2 0.01
87 9 0.03
88 80 0.28
89 17 0.06
90 12 0.04
91 12 0.04
92 23 0.08
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.54
Consensus pattern (88 bp):
TTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATTATTTTATAATTAATTTATTAG
TAATTTAGGATTATGTTATAAAT
Found at i:3560160 original size:23 final size:23
Alignment explanation
Indices: 3560134--3560180 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3560124 GTTAGTAATT
3560134 TAGGATTATGTTATAAATTTTTG
1 TAGGATTATGTTATAAATTTTTG
3560157 TAGGATTATGTTATAAATTTTTG
1 TAGGATTATGTTATAAATTTTTG
3560180 T
1 T
3560181 GTTTGTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (23 bp):
TAGGATTATGTTATAAATTTTTG
Found at i:3560398 original size:15 final size:16
Alignment explanation
Indices: 3560362--3560398 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3560352 CTCATTTAAT
3560362 TTTTATATAATGTAAC
1 TTTTATATAATGTAAC
*
3560378 TTTTATATTATGTAA-
1 TTTTATATAATGTAAC
3560393 TTTTAT
1 TTTTAT
3560399 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTTATATAATGTAAC
Found at i:3564023 original size:18 final size:20
Alignment explanation
Indices: 3563975--3564028 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 20
3563965 AAATGAGTAC
3563975 ATTATAAAAAAAATTATAAA
1 ATTATAAAAAAAATTATAAA
* *
3563995 ATT-TCATAAAAATTA-AAA
1 ATTATAAAAAAAATTATAAA
3564013 ATTAT-AAAAAAATTAT
1 ATTATAAAAAAAATTAT
3564029 TTTAAGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 15 0.52
19 11 0.38
20 3 0.10
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTATAAAAAAAATTATAAA
Found at i:3565604 original size:9 final size:9
Alignment explanation
Indices: 3565586--3565626 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
3565576 TGGCTGAAGC
3565586 TCTTCCTCT
1 TCTTCCTCT
*
3565595 TCTTCATCT
1 TCTTCCTCT
*
3565604 TCTTCCTCC
1 TCTTCCTCT
3565613 TCTTCCTCT
1 TCTTCCTCT
3565622 TCTTC
1 TCTTC
3565627 TTCACCTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.54
Consensus pattern (9 bp):
TCTTCCTCT
Found at i:3565793 original size:21 final size:21
Alignment explanation
Indices: 3565769--3565808 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3565759 ATCTTCCTCC
3565769 TCACCTGCAT-CTTCATCTTGA
1 TCACCTGC-TGCTTCATCTTGA
3565790 TCACCTGCTGCTTCATCTT
1 TCACCTGCTGCTTCATCTT
3565809 CCTCATCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.15, C:0.35, G:0.10, T:0.40
Consensus pattern (21 bp):
TCACCTGCTGCTTCATCTTGA
Found at i:3565816 original size:24 final size:24
Alignment explanation
Indices: 3565758--3565816 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 24
3565748 TCACCTGATC
*
3565758 CATCTTCCTCCTCACCTGCATCTT
1 CATCTTCCTCATCACCTGCATCTT
*
3565782 CATC-T--TGATCACCTGC-TGCTT
1 CATCTTCCTCATCACCTGCAT-CTT
3565803 CATCTTCCTCATCA
1 CATCTTCCTCATCA
3565817 TCATTGTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
20 1 0.04
21 16 0.57
22 1 0.04
23 1 0.04
24 9 0.32
ACGTcount: A:0.15, C:0.41, G:0.07, T:0.37
Consensus pattern (24 bp):
CATCTTCCTCATCACCTGCATCTT
Found at i:3568061 original size:11 final size:11
Alignment explanation
Indices: 3568045--3568074 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
3568035 TATTAAGAAT
3568045 TGGACCTTAGA
1 TGGACCTTAGA
3568056 TGGACCTTAGA
1 TGGACCTTAGA
3568067 TGGACCTT
1 TGGACCTT
3568075 CGAAGCCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (11 bp):
TGGACCTTAGA
Found at i:3569588 original size:100 final size:101
Alignment explanation
Indices: 3569401--3569638 Score: 370
Period size: 100 Copynumber: 2.4 Consensus size: 101
3569391 AATTCATCAT
* *
3569401 TTACATTCATAATGTCATAACCCAGTTATGGTCTTATCATCAGAACGCCATAGCCCAACTATGGT
1 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATCAGAACGCCATAGCCCAACTATGGT
* ** * *
3569466 CTTACATATAAACATTGTCATGGTCCAAATATGGTC
66 CTTACATATAAACACTACCATGGTCCAAACATGATC
* * *
3569502 TTACGTTCATAGTGCCATAACCCAGTT-TGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGT
1 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATCAGAACGCCATAGCCCAACTATGGT
*
3569566 CTTACATATAAACACTACCATGGTCCAACCATGATC
66 CTTACATATAAACACTACCATGGTCCAAACATGATC
3569602 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTAT
1 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTAT
3569639 TCGTCAATTC
Statistics
Matches: 124, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
100 91 0.73
101 33 0.27
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (101 bp):
TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATCAGAACGCCATAGCCCAACTATGGT
CTTACATATAAACACTACCATGGTCCAAACATGATC
Found at i:3575950 original size:18 final size:17
Alignment explanation
Indices: 3575906--3575950 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
3575896 TGTATATACT
3575906 AAATAAAATAATAATAA
1 AAATAAAATAATAATAA
*
3575923 ATAATAAAATAATATTTAA
1 A-AATAAAATAATA-ATAA
*
3575942 AAATTAAAT
1 AAATAAAAT
3575951 TAAAATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 19 0.79
19 4 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATAAAATAATAATAA
Found at i:3578672 original size:11 final size:12
Alignment explanation
Indices: 3578643--3578669 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3578633 TAATTTTAAT
3578643 TTTTATAAAATA
1 TTTTATAAAATA
3578655 TTTTATAAAATA
1 TTTTATAAAATA
3578667 TTT
1 TTT
3578670 ATATTAGATA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTTATAAAATA
Found at i:3594296 original size:24 final size:23
Alignment explanation
Indices: 3594263--3594314 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 23
3594253 GGCCCGGCCT
3594263 ATTTTTTTAATAAA-TACAAAAA-A
1 ATTTTTTTAA-AAATTA-AAAAAGA
3594286 ATTTATTTTAAAAATTAAAAAAGA
1 ATTT-TTTTAAAAATTAAAAAAGA
3594310 ATTTT
1 ATTTT
3594315 AAATATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTTTTTTAAAAATTAAAAAAGA
Found at i:3594322 original size:29 final size:26
Alignment explanation
Indices: 3594289--3594343 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 26
3594279 CAAAAAAATT
3594289 TATTTTAAAAATTAAAAAAGAATTTTAAA
1 TATTTT-AAAATT-AAAAA-AATTTTAAA
3594318 TATTTTAAAATTAAAAAAATTTTAAA
1 TATTTTAAAATTAAAAAAATTTTAAA
3594344 AAAGAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 9 0.35
27 5 0.19
28 6 0.23
29 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (26 bp):
TATTTTAAAATTAAAAAAATTTTAAA
Found at i:3594328 original size:41 final size:40
Alignment explanation
Indices: 3594295--3594379 Score: 122
Period size: 39 Copynumber: 2.1 Consensus size: 40
3594285 AATTTATTTT
3594295 AAAAA-TTAAAAAAGAATTTT-AAATATTTTAAAA-TTAA
1 AAAAATTTAAAAAAGAATTTTAAAATATTTTAAAATTTAA
*
3594332 AAAAATTTTAAAAAAGAATTTTAAAAATATTTTAAAATTAAA
1 AAAAA-TTTAAAAAAGAATTTT-AAAATATTTTAAAATTTAA
3594374 AAAAAT
1 AAAAAT
3594380 ATTTTAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
37 5 0.12
39 15 0.36
41 14 0.33
42 8 0.19
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (40 bp):
AAAAATTTAAAAAAGAATTTTAAAATATTTTAAAATTTAA
Found at i:3594344 original size:11 final size:11
Alignment explanation
Indices: 3594328--3594368 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
3594318 TATTTTAAAA
3594328 TTAAAAAAATT
1 TTAAAAAAATT
3594339 TTAAAAAAGAATT
1 TT-AAAAA-AATT
*
3594352 TTAAAAATATT
1 TTAAAAAAATT
3594363 TTAAAA
1 TTAAAA
3594369 TTAAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 11 0.41
12 10 0.37
13 6 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
TTAAAAAAATT
Found at i:3594350 original size:39 final size:40
Alignment explanation
Indices: 3594300--3594377 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 40
3594290 ATTTTAAAAA
3594300 TTAAAAAAGAATTTT-AAATATTTTAAAATTAAAAAAATT
1 TTAAAAAAGAATTTTAAAATATTTTAAAATTAAAAAAATT
3594339 TTAAAAAAGAATTTTAAAAATATTTTAAAATTAAAAAAA
1 TTAAAAAAGAATTTT-AAAATATTTTAAAATTAAAAAAA
3594378 ATATTTTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 15 0.41
41 22 0.59
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (40 bp):
TTAAAAAAGAATTTTAAAATATTTTAAAATTAAAAAAATT
Found at i:3594351 original size:13 final size:12
Alignment explanation
Indices: 3594330--3594368 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3594320 TTTTAAAATT
3594330 AAAAAAATTTTA
1 AAAAAAATTTTA
3594342 AAAAAGAATTTT-
1 AAAAA-AATTTTA
*
3594354 AAAAATATTTTA
1 AAAAAAATTTTA
3594366 AAA
1 AAA
3594369 TTAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 5 0.21
12 13 0.54
13 6 0.25
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (12 bp):
AAAAAAATTTTA
Found at i:3594393 original size:21 final size:20
Alignment explanation
Indices: 3594315--3594397 Score: 80
Period size: 20 Copynumber: 4.0 Consensus size: 20
3594305 AAAGAATTTT
3594315 AAATATTTTAAAATT-AAAA
1 AAATATTTTAAAATTAAAAA
* ** *
3594334 AAAT-TTTAAAAAAGAATTTTAA
1 AAATATTTTAAAATTAA---AAA
3594356 AAATATTTTAAAATTAAAAA
1 AAATATTTTAAAATTAAAAA
3594376 AAATATTTTAAAATTTAAAAA
1 AAATATTTTAAAA-TTAAAAA
3594397 A
1 A
3594398 TAAATATATT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
18 7 0.14
19 5 0.10
20 15 0.30
21 8 0.16
22 6 0.12
23 9 0.18
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (20 bp):
AAATATTTTAAAATTAAAAA
Found at i:3597528 original size:75 final size:74
Alignment explanation
Indices: 3597316--3597613 Score: 306
Period size: 75 Copynumber: 4.0 Consensus size: 74
3597306 TGGGTATGAT
* * * * *
3597316 GTATGAATATGGA-G-GT-GAACACTGAATTGCTACCATATCTTATAGAAGATTCTACAAGTGCT
1 GTAT-AATATGGAGGAGTGGAACATTGAATTGATATCAAAGCTTATAGAAGATTCTACAAGTGCT
3597378 AAAGAGATGG
65 AAAGAGATGG
* * * *
3597388 GTA-AGACTATGGA-GA-T-GAACATTGAATAGTTACCAAAGCCTTATAGAAGATTCTACAAGTC
1 GTATA-A-TATGGAGGAGTGGAACATTGAATTGATATCAAAG-CTTATAGAAGATTCTACAAGTG
3597449 CTAAAGAGATGG
63 CTAAAGAGATGG
* * *
3597461 GTCATAATATGGAGGAGTGGAGCATCGAATTGATATCAAAGCTTATAGAAGATTCTCCAAGTGCT
1 GT-ATAATATGGAGGAGTGGAACATTGAATTGATATCAAAGCTTATAGAAGATTCTACAAGTGCT
*
3597526 AAAGAGATAG
65 AAAGAGATGG
* * * * * *
3597536 ATATGAATATTGAGGAG-GAGAACGTTGAATTGATGTCAAAGCTTATAGAAGATTCTTCAAATGC
1 GTAT-AATATGGAGGAGTG-GAACATTGAATTGATATCAAAGCTTATAGAAGATTCTACAAGTGC
3597600 TAAAGAGATGG
64 TAAAGAGATGG
3597611 GTA
1 GTA
3597614 AGGATGTGGC
Statistics
Matches: 191, Mismatches: 24, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
70 1 0.01
71 1 0.01
72 28 0.15
73 41 0.21
74 7 0.04
75 96 0.50
76 17 0.09
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (74 bp):
GTATAATATGGAGGAGTGGAACATTGAATTGATATCAAAGCTTATAGAAGATTCTACAAGTGCTA
AAGAGATGG
Found at i:3601948 original size:19 final size:19
Alignment explanation
Indices: 3601924--3601973 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
3601914 TTGTTTGATA
3601924 AAATTAATCTTATTTTATT
1 AAATTAATCTTATTTTATT
*
3601943 AAATTAA--TTA-TTTCTT
1 AAATTAATCTTATTTTATT
3601959 AAATCTAATCTTATT
1 AAAT-TAATCTTATT
3601974 AATATTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 9 0.35
17 6 0.23
19 10 0.38
20 1 0.04
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (19 bp):
AAATTAATCTTATTTTATT
Done.