Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold65
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: 3097370
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.31
Warning! 315397 characters in sequence are not A, C, G, or T
File 15 of 17
Found at i:2710381 original size:1 final size:1
Alignment explanation
Indices: 2710297--2710374 Score: 66
Period size: 1 Copynumber: 78.0 Consensus size: 1
2710287 AAATCTTCAC
* * ** * * * **
2710297 TTTTTTTTTTTGTTTTTTTTTTGTTTTTCCTTTTTTTTGTTTTGTTTTTTTCTTTTTCCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
2710362 TTGTTTTTTTTTT
1 TTTTTTTTTTTTT
2710375 CCTTTTTCCA
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.87
Consensus pattern (1 bp):
T
Found at i:2715110 original size:4 final size:4
Alignment explanation
Indices: 2715101--2715133 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
2715091 GAATTGTCAC
2715101 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
2715134 CTGTGAGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:2715339 original size:2 final size:2
Alignment explanation
Indices: 2715332--2715368 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2715322 CTTCATACAA
2715332 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2715369 AGGGAGATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2715822 original size:2 final size:2
Alignment explanation
Indices: 2715815--2715860 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2715805 TAATGGTAAT
2715815 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2715857 TC TC
1 TC TC
2715861 ACATCAATCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2715998 original size:2 final size:2
Alignment explanation
Indices: 2715991--2716034 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2715981 TCAGTTCAGC
2715991 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
2716033 AT
1 AT
2716035 TTGGATCAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2725911 original size:35 final size:35
Alignment explanation
Indices: 2725870--2725939 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
2725860 AAAAAGTTGA
2725870 ACACAATTTAAATTCTAGAAATACCCTGCACTTAT
1 ACACAATTTAAATTCTAGAAATACCCTGCACTTAT
* * *
2725905 ACACAATTTAACTTCTAGAAATCCCCTGTACTTAT
1 ACACAATTTAAATTCTAGAAATACCCTGCACTTAT
2725940 CTAAAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (35 bp):
ACACAATTTAAATTCTAGAAATACCCTGCACTTAT
Found at i:2727418 original size:19 final size:19
Alignment explanation
Indices: 2727387--2727423 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
2727377 CGCGTGACCT
2727387 ACGACCTCCCCTC-CTTCC
1 ACGACCTCCCCTCGCTTCC
2727405 ACGACCTCCCCCTCGCTTC
1 ACGACCT-CCCCTCGCTTC
2727424 TCTCCCAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 6 0.35
20 4 0.24
ACGTcount: A:0.11, C:0.59, G:0.08, T:0.22
Consensus pattern (19 bp):
ACGACCTCCCCTCGCTTCC
Found at i:2727805 original size:16 final size:16
Alignment explanation
Indices: 2727786--2727841 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
2727776 TATAAAAAAT
2727786 AAATAATTTAAAATTA
1 AAATAATTTAAAATTA
* * *
2727802 AAATTATTTATATTTA
1 AAATAATTTAAAATTA
2727818 AAATAA-TTAAAATTTA
1 AAATAATTTAAAA-TTA
2727834 AAACTAAT
1 AAA-TAAT
2727842 ATGAAATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 4 0.13
16 24 0.77
17 3 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATAATTTAAAATTA
Found at i:2729006 original size:18 final size:18
Alignment explanation
Indices: 2728973--2729015 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2728963 GAGATTAATG
*
2728973 TTTTAAATTTTGTTTT-T
1 TTTTATATTTTGTTTTAT
*
2728990 TTGTTATATTTTTTTTTAT
1 TT-TTATATTTTGTTTTAT
2729009 TTTTATA
1 TTTTATA
2729016 CCAATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 17 0.77
19 3 0.14
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTTATATTTTGTTTTAT
Found at i:2730206 original size:2 final size:2
Alignment explanation
Indices: 2730199--2730224 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2730189 TTTATGTTCA
2730199 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
2730225 TAAATTTTCT
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:2731140 original size:3 final size:3
Alignment explanation
Indices: 2731132--2731173 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
2731122 TTTCATAAAT
2731132 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2731174 AATTGCTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2737700 original size:1 final size:1
Alignment explanation
Indices: 2737694--2737730 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
2737684 CAGGTGAGCC
* *
2737694 TTTTTTTTCTTTTTCTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2737731 GCATCTATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:2741585 original size:21 final size:23
Alignment explanation
Indices: 2741559--2741603 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
2741549 ATTAAACTAA
2741559 TTTTTACCT-ATTTTATAT-AAT
1 TTTTTACCTAATTTTATATCAAT
*
2741580 TTTTTACCTAATTTTTTATCAAT
1 TTTTTACCTAATTTTATATCAAT
2741603 T
1 T
2741604 AAAATCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 8 0.38
23 4 0.19
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTTACCTAATTTTATATCAAT
Found at i:2742586 original size:13 final size:13
Alignment explanation
Indices: 2742568--2742593 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2742558 AATCATGGGG
2742568 AGAGAGAAAGAAA
1 AGAGAGAAAGAAA
2742581 AGAGAGAAAGAAA
1 AGAGAGAAAGAAA
2742594 GAAAAAACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AGAGAGAAAGAAA
Found at i:2742609 original size:17 final size:17
Alignment explanation
Indices: 2742568--2742615 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
2742558 AATCATGGGG
* *
2742568 AGAGAGAAAGAAAAGAG
1 AGAGAGAAAGAAAAAAC
*
2742585 AGAAAGAAAGAAAAAAC
1 AGAGAGAAAGAAAAAAC
*
2742602 AGAGAGAAATAAAA
1 AGAGAGAAAGAAAA
2742616 GTAAAATGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.71, C:0.02, G:0.25, T:0.02
Consensus pattern (17 bp):
AGAGAGAAAGAAAAAAC
Found at i:2742804 original size:11 final size:12
Alignment explanation
Indices: 2742757--2742815 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 12
2742747 TATATACTCG
2742757 TATTATA-TTTA
1 TATTATATTTTA
* *
2742768 TGTTATTTTTTATA
1 TATTA-TATTT-TA
2742782 TCATTATATTTTA
1 T-ATTATATTTTA
*
2742795 -ATTATTTTTTA
1 TATTATATTTTA
2742806 TATTATATTT
1 TATTATATTT
2742816 GTGTTATACT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
11 14 0.38
12 9 0.24
13 4 0.11
14 7 0.19
15 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (12 bp):
TATTATATTTTA
Found at i:2742822 original size:23 final size:23
Alignment explanation
Indices: 2742757--2742822 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 23
2742747 TATATACTCG
2742757 TATTATATTTATGTTATTTTTTATA
1 TATTATATTT-TGTTA-TTTTTATA
*
2742782 TCATTATATTTTAATTATTTTT-TA
1 T-ATTATATTTT-GTTATTTTTATA
2742806 TATTATATTTGTGTTAT
1 TATTATATTT-TGTTAT
2742823 ACTTTAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
23 13 0.36
24 4 0.11
25 7 0.19
26 12 0.33
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (23 bp):
TATTATATTTTGTTATTTTTATA
Found at i:2743120 original size:12 final size:13
Alignment explanation
Indices: 2743096--2743124 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2743086 GGCTGGGCAT
2743096 GGGAGAGAGGGAG
1 GGGAGAGAGGGAG
2743109 GGGAGA-AGGGAG
1 GGGAGAGAGGGAG
2743121 GGGA
1 GGGA
2743125 AGGGAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (13 bp):
GGGAGAGAGGGAG
Found at i:2743250 original size:8 final size:8
Alignment explanation
Indices: 2743239--2743385 Score: 56
Period size: 8 Copynumber: 17.6 Consensus size: 8
2743229 AAATAAAAAA
2743239 TTATATTT
1 TTATATTT
*
2743247 TTATGTTT
1 TTATATTT
2743255 ATGT-TATTT
1 -T-TATATTT
2743264 TT-TATGTGT
1 TTATAT-T-T
2743273 TTATAAATTT
1 TTAT--ATTT
2743283 TTATATTT
1 TTATATTT
** *
2743291 AAATA-AT
1 TTATATTT
2743298 TTAT-TTT
1 TTATATTT
*
2743305 ATA-ATTTT
1 TTATAT-TT
2743313 TTATATATT
1 TTATAT-TT
2743322 TATATATTT
1 T-TATATTT
2743331 TTATATATT
1 TTATAT-TT
*
2743340 TAAATATTT
1 T-TATATTT
*
2743349 TTATAATAT
1 TTAT-ATTT
2743358 TTAT-TTT
1 TTATATTT
*
2743365 ATTTTATTT
1 -TTATATTT
2743374 TT-TATTT
1 TTATATTT
2743381 TTATA
1 TTATA
2743386 CATTAAATAT
Statistics
Matches: 105, Mismatches: 16, Indels: 36
0.67 0.10 0.23
Matches are distributed among these distances:
7 20 0.19
8 34 0.32
9 32 0.30
10 16 0.15
11 1 0.01
12 2 0.02
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (8 bp):
TTATATTT
Found at i:2743325 original size:18 final size:19
Alignment explanation
Indices: 2743302--2743361 Score: 90
Period size: 18 Copynumber: 3.3 Consensus size: 19
2743292 AATAATTTAT
2743302 TTTATAAT-TTTTTATATA
1 TTTATAATATTTTTATATA
2743320 TTTAT-ATATTTTTATATA
1 TTTATAATATTTTTATATA
2743338 TTTA-AATATTTTTATAATA
1 TTTATAATATTTTTAT-ATA
2743357 TTTAT
1 TTTAT
2743362 TTTATTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.05
18 29 0.76
19 7 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATAATATTTTTATATA
Found at i:2743343 original size:50 final size:49
Alignment explanation
Indices: 2743260--2743405 Score: 140
Period size: 50 Copynumber: 3.0 Consensus size: 49
2743250 TGTTTATGTT
* * *
2743260 ATTTTTTATGTGTTTATA-AATTTT-TATATTTAAATAATTTATTTTATA
1 ATTTTTTATATATTTATATATTTTTATATATTTAAAT-ATTTATTTTATA
*
2743308 ATTTTTTATATATTTATATATTTTTATATATTTAAATATTT-TTATAATA
1 ATTTTTTATATATTTATATATTTTTATATATTTAAATATTTATT-TTATA
* * * * *
2743357 TTTATTTTATTTTATTT-TTTATTTTTATACA-TTAAATATTAATTTTATA
1 ATT-TTTTA-TATATTTATATATTTTTATATATTTAAATATTTATTTTATA
2743406 TCGATATTAT
Statistics
Matches: 82, Mismatches: 10, Indels: 11
0.80 0.10 0.11
Matches are distributed among these distances:
48 18 0.22
49 28 0.34
50 30 0.37
51 6 0.07
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (49 bp):
ATTTTTTATATATTTATATATTTTTATATATTTAAATATTTATTTTATA
Found at i:2743635 original size:17 final size:15
Alignment explanation
Indices: 2743603--2743632 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2743593 TGATAAAATG
2743603 TAAAAAATTATTTTA
1 TAAAAAATTATTTTA
2743618 TAAAATAATTATTTT
1 TAAAA-AATTATTTT
2743633 TATTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAAAAATTATTTTA
Found at i:2743961 original size:16 final size:18
Alignment explanation
Indices: 2743921--2743962 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
2743911 ATTAAAAAAA
2743921 TTAAATAAGTAATTATATT
1 TTAAATAAG-AATTATATT
2743940 TT-AATAA-AATT-TATT
1 TTAAATAAGAATTATATT
2743955 TTAAATAA
1 TTAAATAA
2743963 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.27
16 9 0.41
18 5 0.23
19 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TTAAATAAGAATTATATT
Found at i:2744436 original size:22 final size:19
Alignment explanation
Indices: 2744402--2744445 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 19
2744392 CTTTTTTATT
*
2744402 AAAAAAGATAAAAGTAAATAA
1 AAAAAAGAAAAAAG-AAA-AA
2744423 AAAACAAGAAAAAAGAAAAA
1 AAAA-AAGAAAAAAGAAAAA
2744443 AAA
1 AAA
2744446 TGAAGAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 7 0.33
22 9 0.43
ACGTcount: A:0.82, C:0.02, G:0.09, T:0.07
Consensus pattern (19 bp):
AAAAAAGAAAAAAGAAAAA
Found at i:2746637 original size:4 final size:4
Alignment explanation
Indices: 2746624--2746664 Score: 57
Period size: 4 Copynumber: 10.0 Consensus size: 4
2746614 AGATAGACAG
2746624 TAAA -AAA TAAA TAAA TAAA TAAA CTTAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA --TAAA TAAA TAAA TAAA
2746665 CTTTGCGGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.09
4 27 0.79
6 4 0.12
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:2746654 original size:14 final size:12
Alignment explanation
Indices: 2746624--2746664 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 12
2746614 AGATAGACAG
2746624 TAAA-AAATAAA
1 TAAATAAATAAA
2746635 TAAATAAATAAA
1 TAAATAAATAAA
2746647 CTTAAATAAATAAA
1 --TAAATAAATAAA
2746661 TAAA
1 TAAA
2746665 CTTTGCGGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 4 0.15
12 11 0.41
14 12 0.44
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAATAAATAAA
Found at i:2746654 original size:18 final size:18
Alignment explanation
Indices: 2746631--2746667 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2746621 CAGTAAAAAA
2746631 TAAATAAATAAATAAACT
1 TAAATAAATAAATAAACT
2746649 TAAATAAATAAATAAACT
1 TAAATAAATAAATAAACT
2746667 T
1 T
2746668 TGCGGCTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAATAAATAAATAAACT
Found at i:2751454 original size:15 final size:15
Alignment explanation
Indices: 2751436--2751486 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
2751426 TAAAATAAAT
2751436 ATATATAAATTATTA
1 ATATATAAATTATTA
2751451 ATATATAAATT-TT-
1 ATATATAAATTATTA
*
2751464 -TTTATAAATTA-TA
1 ATATATAAATTATTA
2751477 ATA-ATAAATT
1 ATATATAAATT
2751487 TTTATAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 10 0.32
13 7 0.23
14 3 0.10
15 11 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATAAATTATTA
Found at i:2751498 original size:25 final size:26
Alignment explanation
Indices: 2751440--2751506 Score: 84
Period size: 25 Copynumber: 2.6 Consensus size: 26
2751430 ATAAATATAT
*
2751440 ATAAATTATTAATATATAAATTTTTTT
1 ATAAATTA-TAATATATAAATTTTTTA
2751467 ATAAATTATAATA-ATAAATTTTTATA
1 ATAAATTATAATATATAAATTTTT-TA
*
2751493 AT-AATTAAAATATA
1 ATAAATTATAATATA
2751507 CAAAAAGGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 19 0.53
26 9 0.25
27 8 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
ATAAATTATAATATATAAATTTTTTA
Found at i:2752121 original size:194 final size:191
Alignment explanation
Indices: 2751884--2752245 Score: 476
Period size: 194 Copynumber: 1.9 Consensus size: 191
2751874 AAAGTTTCTT
* **
2751884 AAATGTCTCATTTTTATTTTAAATTATTTTTTATTATATTTAAAAAGTAAGTATCATCCGTTATT
1 AAATATCTCATTTTTATTTTAAATTATTTTTTATTATATTTAAAAAGTAAGTATCATCCGTTAAC
* * *
2751949 ACTACTTATGAAGTTTAAAAATT-TTATGGATAATATATAAAATAAATTTTTTAAAATAAATAGT
66 ACTACTTATGAAATTTAAAAATTCTAAT-GATAACATATAAAATAAATTTTTTAAAATAAATAGT
*
2752013 TTTTTACTTTTGAAAGAAGATGAT-TTTTTAAAAATTAAATAGATTTTTGAAGAAAAAATTTATC
130 TTTTTA-TTTT-AAAAAAGATGATATTTTTAAAAA-TAAATAGATTTTTGAAGAAAAAATTTATC
* * *
2752077 AAATATCTTATTTTTATTTTTAATTAATTTTTTATTATATTTAAAAAGTATGTATCATCCGTTAA
1 AAATATCTCATTTTTATTTTAAATT-ATTTTTTATTATATTTAAAAAGTAAGTATCATCCGTTAA
* * ** * * * * * *
2752142 CACTGCTTGTGAAATTTAAAAATTCTAATGATGGCGTATAGAATAATTTTTTTATAGTAAATGGT
65 CACTACTTATGAAATTTAAAAATTCTAATGATAACATATAAAATAAATTTTTTAAAATAAATAGT
*
2752207 TTTTTATTTTAAAAAAGATGATATTTTTAGAAATAAATA
130 TTTTTATTTTAAAAAAGATGATATTTTTAAAAATAAATA
2752246 AAATTTTAAA
Statistics
Matches: 145, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
192 17 0.12
193 35 0.24
194 90 0.62
195 3 0.02
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (191 bp):
AAATATCTCATTTTTATTTTAAATTATTTTTTATTATATTTAAAAAGTAAGTATCATCCGTTAAC
ACTACTTATGAAATTTAAAAATTCTAATGATAACATATAAAATAAATTTTTTAAAATAAATAGTT
TTTTATTTTAAAAAAGATGATATTTTTAAAAATAAATAGATTTTTGAAGAAAAAATTTATC
Found at i:2752328 original size:17 final size:14
Alignment explanation
Indices: 2752291--2752340 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
2752281 AAAAATATTA
2752291 ATATTAATATTTTT
1 ATATTAATATTTTT
*
2752305 ATTTTAATATTATAATT
1 ATATTAATATT-T--TT
*
2752322 ATATTAATTTTTTT
1 ATATTAATATTTTT
2752336 ATATT
1 ATATT
2752341 TTTACTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 17 0.57
15 1 0.03
16 1 0.03
17 11 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATATTAATATTTTT
Found at i:2752953 original size:21 final size:21
Alignment explanation
Indices: 2752929--2752987 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
2752919 AATCTTAAAG
*
2752929 ATTTTTATTTAGATTTAATTA
1 ATTTTTATTTATATTTAATTA
** *
2752950 ATTTTTAAATATTTTTAAATTA
1 ATTTTTATTTATATTT-AATTA
2752972 A-TTTTATTTATATTTA
1 ATTTTTATTTATATTTA
2752988 TTTTATATAA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.03
21 23 0.77
22 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTTTTATTTATATTTAATTA
Found at i:2754204 original size:22 final size:20
Alignment explanation
Indices: 2754179--2754235 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
2754169 TAGTAAAAAA
*
2754179 ATTTACATAATTTTAAATATT
1 ATTTA-ATAATTTTAAACATT
* *
2754200 CATTTATTAATTTTTAACATT
1 -ATTTAATAATTTTAAACATT
*
2754221 AATTAAATAATTTTA
1 -ATTTAATAATTTTA
2754236 TATTTTTAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTAATAATTTTAAACATT
Found at i:2755763 original size:34 final size:33
Alignment explanation
Indices: 2755710--2755931 Score: 264
Period size: 34 Copynumber: 6.5 Consensus size: 33
2755700 TTTGAATAAT
2755710 ATTGTCTGATTAAATGGTGATTTGGTAGTTTACC
1 ATTGT-TGATTAAATGGTGATTTGGTAGTTTACC
*
2755744 ATTGTTGATTAAATAGGTGATTTGGTAGTTTGCC
1 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
* * * * *
2755778 ATTATTGACTAAATGAGAGATTTGGTAGCTTATC
1 ATTGTTGATTAAATG-GTGATTTGGTAGTTTACC
** *
2755812 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATG-GTGATTTGGTAGTTTACC
* *
2755846 ATTATTGATTAAATGAGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATG-GTGATTTGGTAGTTTACC
* * *
2755880 ATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGT-GATTTGGTAGTTTACC
2755914 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
2755932 GTTTTTACCA
Statistics
Matches: 163, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
33 13 0.08
34 150 0.92
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (33 bp):
ATTGTTGATTAAATGGTGATTTGGTAGTTTACC
Found at i:2755888 original size:102 final size:101
Alignment explanation
Indices: 2755710--2755929 Score: 300
Period size: 102 Copynumber: 2.2 Consensus size: 101
2755700 TTTGAATAAT
** * *
2755710 ATTGTCTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATAGGTGATTTGGTAGTTT
1 ATTGT-TGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTAGTTT
* *
2755775 GCCATTATTGACTAAATGAG-AGATTTGGTAGCTTATC
65 ACCATTATTGACTAAATG-GTAGATTTGGTAGCTTACC
*
2755812 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAAT-GAGTGATTTGGTGGTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATAG-GTGATTTGGTAGTT
* * *
2755876 TACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
64 TACCATTATTGACTAAATGGTAGATTTGGTAGCTTACC
2755914 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2755930 TGGTTTTTAC
Statistics
Matches: 105, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
101 13 0.12
102 92 0.88
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTAGTTTA
CCATTATTGACTAAATGGTAGATTTGGTAGCTTACC
Found at i:2760406 original size:34 final size:34
Alignment explanation
Indices: 2760337--2760555 Score: 271
Period size: 34 Copynumber: 6.5 Consensus size: 34
2760327 AAGTGGGAGA
*
2760337 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
2760370 ATTGTTGATTAAATGGGTGATTTGATGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2760404 ATTATTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
2760438 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2760472 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2760506 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
2760540 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2760556 TGGTTTTTAC
Statistics
Matches: 158, Mismatches: 25, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
33 17 0.11
34 140 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:2760472 original size:102 final size:101
Alignment explanation
Indices: 2760337--2760555 Score: 330
Period size: 102 Copynumber: 2.2 Consensus size: 101
2760327 AAGTGGGAGA
** * * * *
2760337 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGATGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGATGGCTTA
2760402 CCATTATTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTATTGACTAAATGGGAGATTTGGTAGCTTACC
*
2760438 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGATGGCTT
* * * *
2760503 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTATTGACTAAATGGGAGATTTGGTAGCTTACC
2760540 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2760556 TGGTTTTTAC
Statistics
Matches: 106, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 16 0.15
102 90 0.85
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGATGGCTTA
CCATTATTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:2761073 original size:20 final size:21
Alignment explanation
Indices: 2761048--2761089 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
2761038 TTATTTTTCA
*
2761048 TATTTAATTTTAAA-TTAAAT
1 TATTTAAATTTAAATTTAAAT
2761068 TATTTAAATTTAAATTTAAAT
1 TATTTAAATTTAAATTTAAAT
2761089 T
1 T
2761090 TATATTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTAAATTTAAATTTAAAT
Found at i:2761078 original size:6 final size:6
Alignment explanation
Indices: 2761049--2761108 Score: 57
Period size: 6 Copynumber: 9.7 Consensus size: 6
2761039 TATTTTTCAT
* * * *
2761049 ATTTAA TTTTAA ATTAAA TTATTTAA ATTTAA ATTTAA ATTTAT ATTTGA
1 ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
2761099 ATTAAA ATTT
1 ATTTAA ATTT
2761109 TTTTAATATT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
6 37 0.88
8 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:2761096 original size:18 final size:18
Alignment explanation
Indices: 2761049--2761108 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
2761039 TATTTTTCAT
*
2761049 ATTTAATTTTAAATTAAA
1 ATTTAAATTTAAATTAAA
*
2761067 TTATTTAAATTTAAATTTAA
1 --ATTTAAATTTAAATTAAA
* *
2761087 ATTTATATTTGAATTAAA
1 ATTTAAATTTAAATTAAA
2761105 ATTT
1 ATTT
2761109 TTTTAATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 19 0.54
20 16 0.46
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTTAAATTTAAATTAAA
Found at i:2766165 original size:30 final size:30
Alignment explanation
Indices: 2766131--2766190 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
2766121 TAGAAAAATG
2766131 GTAAATGGGTTGAGAGTGGGGTTGGTATGC
1 GTAAATGGGTTGAGAGTGGGGTTGGTATGC
2766161 GTAAATGGGTTGAGAGTGGGGTTGGTATGC
1 GTAAATGGGTTGAGAGTGGGGTTGGTATGC
2766191 TTTAGGTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.03, G:0.47, T:0.30
Consensus pattern (30 bp):
GTAAATGGGTTGAGAGTGGGGTTGGTATGC
Found at i:2772889 original size:27 final size:27
Alignment explanation
Indices: 2772857--2772912 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
2772847 ACTCTCACCA
2772857 AGTTCAAGTAACATAAATTCCTGATCC
1 AGTTCAAGTAACATAAATTCCTGATCC
2772884 AGTTCAAGTAACATAAATTCCTGATCC
1 AGTTCAAGTAACATAAATTCCTGATCC
2772911 AG
1 AG
2772913 GTCTTCATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (27 bp):
AGTTCAAGTAACATAAATTCCTGATCC
Found at i:2778105 original size:15 final size:15
Alignment explanation
Indices: 2778053--2778106 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
2778043 CAAATATAAC
2778053 ATTAATTAATTTTTT
1 ATTAATTAATTTTTT
*
2778068 AATAATTAATATTTTT
1 ATTAATTAAT-TTTTT
2778084 ATT-ATT-ATTTTTT
1 ATTAATTAATTTTTT
2778097 ATCTAATTAA
1 AT-TAATTAA
2778107 GATAAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 7 0.21
14 3 0.09
15 15 0.45
16 8 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTAATTAATTTTTT
Found at i:2790755 original size:168 final size:165
Alignment explanation
Indices: 2790462--2790781 Score: 482
Period size: 168 Copynumber: 1.9 Consensus size: 165
2790452 TCCTAAAACA
2790462 AGGAGCAAATTTAATATTATTTATTTATTTTTGAAAAAAAAATCATTTCGTACCTTAATGGATAC
1 AGGAGCAAATTTAATATTATTTATTTATTTTTGAAAAAAAAATCATTTCGTACCTTAATGGATAC
*
2790527 CCGAAAAGATACAAAAATTTTTTGAAATCTTTTATACCTCTACAGAAACTCATAGGAATATAAAA
66 CCGAAAAGATACAAAAATTTTTTGAAATCTTTTATACCTCTACAGAAACCCATAGGAATATAAAA
2790592 AATTTAAAAATGATCAATATTTGATGTAATTAACG
131 AATTTAAAAATGATCAATATTTGATGTAATTAACG
* *** *
2790627 AGGAGTAAATTTAATATTATTTATTTATTTATTTTTGAAAAAAATTATTTCGTA-CTATAATGGA
1 AGGAGCAAATTTAATATTATTTATTTA-TT-TTTGAAAAAAAAATCATTTCGTACCT-TAATGGA
* * *
2790691 TACCCGAAAAGATATAAAAAGTTTTTTGAAATCTTTTATA-CTCCTACGGATACCCATAGGAATA
63 TACCCGAAAAGATACAAAAA-TTTTTTGAAATCTTTTATACCT-CTACAGAAACCCATAGGAATA
* *
2790755 TAAAAGATTTAAAAATGATTAATATTT
126 TAAAAAATTTAAAAATGATCAATATTT
2790782 ATAATATATA
Statistics
Matches: 139, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
165 26 0.19
166 4 0.03
167 47 0.34
168 62 0.45
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (165 bp):
AGGAGCAAATTTAATATTATTTATTTATTTTTGAAAAAAAAATCATTTCGTACCTTAATGGATAC
CCGAAAAGATACAAAAATTTTTTGAAATCTTTTATACCTCTACAGAAACCCATAGGAATATAAAA
AATTTAAAAATGATCAATATTTGATGTAATTAACG
Found at i:2791615 original size:14 final size:14
Alignment explanation
Indices: 2791598--2791636 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2791588 TCTATTTTAC
2791598 TTTCTCTTTTCTTT
1 TTTCTCTTTTCTTT
* *
2791612 TTTCTTTTTTTTTT
1 TTTCTCTTTTCTTT
2791626 TTTGCTCTTTT
1 TTT-CTCTTTT
2791637 TAGCTGAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (14 bp):
TTTCTCTTTTCTTT
Found at i:2792703 original size:163 final size:165
Alignment explanation
Indices: 2792213--2792747 Score: 724
Period size: 167 Copynumber: 3.2 Consensus size: 165
2792203 TTTATATCTG
* * * * * *
2792213 GAAAAAT-TCTCTTGAAAAAATTTACGGAGTAAAAAAC-TCGATTTTTCG-GAGAAAGAAGATTT
1 GAAAAATCTC-CTCGAAAAAATTTACGGAGTAGAAAACAT-TATATTTCGAAAAAAAG-AGATTT
* *
2792275 TAAGGTAAAAAATCCAAAACTTATGAAAATGAATTTATTTTTTAAAACTGAATTAATATGAAATA
63 CAAGG-AAAAAATCCAAAACTCATGAAAATGAATTTATTTTTTAAAACTGAATTAATATGAAATA
2792340 AATAATGACT-TTTGATGAATTTTAAAAATTAAAAATTAA
127 AATAATGA-TATTTGATGAATTTTAAAAATTAAAAATTAA
* * * **
2792379 GAAAAATTTCCTCGAAAAAATTTACGGAGTAGAAAATACTATATTTTTAAAAAAAGAGAAATTTC
1 GAAAAATCTCCTCGAAAAAATTTACGGAGTAGAAAACATTATATTTCGAAAAAAAGAG--ATTTC
*
2792444 AAAGAAAAAATCCAAAACTCATGAAAATGAATTTATTTTTTAAAACTGAATTAATATGAAATAAA
64 AAGGAAAAAATCCAAAACTCATGAAAATGAATTTATTTTTTAAAACTGAATTAATATGAAATAAA
*
2792509 TAATGATATTTGATGAATTTTAAAGATTAAAAATTAA
129 TAATGATATTTGATGAATTTTAAAAATTAAAAATTAA
* * * * *
2792546 GAAAAATCCCCTCGAAAAAA-TTACGAAGCAGAAAACATTGTA-TTCGAAAAAAAG-GATTTGAA
1 GAAAAATCTCCTCGAAAAAATTTACGGAGTAGAAAACATTATATTTCGAAAAAAAGAGATTTCAA
* * *
2792608 GGAAAAAATCCAAAACTCATGAAAATAAATTTATTTTTTTAAAACTGAATTGATATTAAATAAAT
66 GGAAAAAATCCAAAACTCATGAAAATGAATTTA-TTTTTTAAAACTGAATTAATATGAAATAAAT
* *
2792673 AATGATATTTGATGAACTTTAAAAATTAAAAATTTA
130 AATGATATTTGATGAATTTTAAAAATTAAAAATTAA
2792709 GAAAAATCTCCTCGAAAAAATTTACGGAGTAGAAAACAT
1 GAAAAATCTCCTCGAAAAAATTTACGGAGTAGAAAACAT
2792748 CTTGTAATAC
Statistics
Matches: 327, Mismatches: 34, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
162 37 0.11
163 81 0.25
164 17 0.05
165 10 0.03
166 56 0.17
167 119 0.36
168 7 0.02
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (165 bp):
GAAAAATCTCCTCGAAAAAATTTACGGAGTAGAAAACATTATATTTCGAAAAAAAGAGATTTCAA
GGAAAAAATCCAAAACTCATGAAAATGAATTTATTTTTTAAAACTGAATTAATATGAAATAAATA
ATGATATTTGATGAATTTTAAAAATTAAAAATTAA
Found at i:2794003 original size:10 final size:10
Alignment explanation
Indices: 2793988--2794050 Score: 58
Period size: 10 Copynumber: 6.0 Consensus size: 10
2793978 AAATATTTTA
2793988 TAATTTAAAT
1 TAATTTAAAT
2793998 TAATTTAAAT
1 TAATTTAAAT
2794008 TATTATTTAAA-
1 TA--ATTTAAAT
*
2794019 TAATAATAAAT
1 TAAT-TTAAAT
2794030 T-ATTTAAATT
1 TAATTTAAA-T
2794040 TAATTATAAAT
1 TAATT-TAAAT
2794051 ATTAATATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
9 6 0.14
10 20 0.45
11 7 0.16
12 11 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TAATTTAAAT
Found at i:2794015 original size:22 final size:22
Alignment explanation
Indices: 2793961--2794033 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
2793951 TGATTTATAT
*
2793961 TAAATTA-TATTTAGATAA-AA
1 TAAATTATTATTTAAATAATAA
** * *
2793981 TATTTTATAATTTAAATTAAT-T
1 TAAATTATTATTTAAA-TAATAA
2794003 TAAATTATTATTTAAATAATAA
1 TAAATTATTATTTAAATAATAA
2794025 TAAATTATT
1 TAAATTATT
2794034 TAAATTTAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
20 5 0.12
21 10 0.25
22 25 0.62
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (22 bp):
TAAATTATTATTTAAATAATAA
Found at i:2794050 original size:31 final size:32
Alignment explanation
Indices: 2793993--2794057 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
2793983 TTTTATAATT
*
2793993 TAAATTAATTTAAATTATTATTTAAATAATAA
1 TAAATTAATTTAAATTATAATTTAAATAATAA
*
2794025 TAAATT-ATTTAAATT-TAATTATAAATATTAA
1 TAAATTAATTTAAATTATAATT-TAAATAATAA
2794056 TA
1 TA
2794058 TAAAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 4 0.13
31 20 0.67
32 6 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
TAAATTAATTTAAATTATAATTTAAATAATAA
Found at i:2796587 original size:30 final size:31
Alignment explanation
Indices: 2796553--2796612 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2796543 TTAAATTTTG
*
2796553 ATTT-ATTTTTAAATTAAA-CTATGAGAGTTA
1 ATTTAATTTATAAA-TAAATCTATGAGAGTTA
2796583 ATTTAATTTATAAATAAATCTATGAGAGTT
1 ATTTAATTTATAAATAAATCTATGAGAGTT
2796613 GAGCGGTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (31 bp):
ATTTAATTTATAAATAAATCTATGAGAGTTA
Found at i:2797962 original size:12 final size:12
Alignment explanation
Indices: 2797945--2797982 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2797935 TCACATTTAA
2797945 ATATATATAACT
1 ATATATATAACT
*
2797957 ATATATATAAAT
1 ATATATATAACT
2797969 ATA-ATATAAC-
1 ATATATATAACT
2797979 ATAT
1 ATAT
2797983 TACATGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 3 0.13
11 6 0.26
12 14 0.61
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATATATAACT
Found at i:2798191 original size:18 final size:18
Alignment explanation
Indices: 2798170--2798216 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
2798160 CGTAAATTTA
2798170 AATTATA-TTATATTAAAT
1 AATTATATTTAT-TTAAAT
2798188 AATTATAATTTATTTAAAT
1 AATTAT-ATTTATTTAAAT
2798207 AATT-TATTTA
1 AATTATATTTA
2798217 ATTTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.19
18 7 0.26
19 11 0.41
20 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTATATTTATTTAAAT
Found at i:2798208 original size:13 final size:13
Alignment explanation
Indices: 2798192--2798217 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2798182 TTAAATAATT
2798192 ATAATTTATTTAA
1 ATAATTTATTTAA
2798205 ATAATTTATTTAA
1 ATAATTTATTTAA
2798218 TTTTTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATAATTTATTTAA
Found at i:2798950 original size:12 final size:12
Alignment explanation
Indices: 2798873--2798961 Score: 53
Period size: 12 Copynumber: 7.6 Consensus size: 12
2798863 TTCAAACACG
*
2798873 ATATAAATATA-
1 ATATAAAAATAT
2798884 ATATAAAAA-AT
1 ATATAAAAATAT
*
2798895 A-ATTAAAATAT
1 ATATAAAAATAT
* *
2798906 AATTTAATAAA-AA
1 -ATATAA-AAATAT
* *
2798919 ATACATAAATAT
1 ATATAAAAATAT
2798931 ATCA-AAAAATAT
1 AT-ATAAAAATAT
*
2798943 ATATAAAAATTT
1 ATATAAAAATAT
2798955 ATATAAA
1 ATATAAA
2798962 TTTATAATAT
Statistics
Matches: 59, Mismatches: 11, Indels: 15
0.69 0.13 0.18
Matches are distributed among these distances:
10 7 0.12
11 15 0.25
12 30 0.51
13 4 0.07
14 3 0.05
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATAAAAATAT
Found at i:2799070 original size:20 final size:20
Alignment explanation
Indices: 2799016--2799105 Score: 60
Period size: 20 Copynumber: 4.3 Consensus size: 20
2799006 TTTTTTTTCC
* *
2799016 TCTTTCCTTTTT-TTCCCCT
1 TCTTTCCTTTTTCTTCTCTT
2799035 TCTTTTCCGTTCTTTTCTTCTCTT
1 TC-TTTCC--T-TTTTCTTCTCTT
2799059 TCTTTCCTTTTTCATT-TCTT
1 TCTTTCCTTTTTC-TTCTCTT
* *
2799079 CCTTTCTCCTTTTCTTCT-TT
1 TCTTTC-CTTTTTCTTCTCTT
2799099 CTCTTTC
1 -TCTTTC
2799106 TCGCATGCTG
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
19 2 0.04
20 23 0.40
21 15 0.26
22 1 0.02
23 9 0.16
24 7 0.12
ACGTcount: A:0.01, C:0.32, G:0.01, T:0.66
Consensus pattern (20 bp):
TCTTTCCTTTTTCTTCTCTT
Found at i:2799718 original size:20 final size:17
Alignment explanation
Indices: 2799693--2799739 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 17
2799683 TCTTTTTCTC
2799693 TTAATTTTTTTAAATTTTT
1 TTAATTTTTTT--ATTTTT
*
2799712 ATTAATTATTTTATTTTT
1 -TTAATTTTTTTATTTTT
2799730 TTAATTTTTT
1 TTAATTTTTT
2799740 ATTCATCGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 9 0.36
18 6 0.24
20 10 0.40
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTAATTTTTTTATTTTT
Found at i:2806807 original size:41 final size:41
Alignment explanation
Indices: 2806756--2806839 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
2806746 ACAAAATTGC
*
2806756 AAATAATGAACAACACCTATACCTCAATAATTTTTAAATTT
1 AAATAATGAACAACACCTATACCTCAATAATTTTTAAAATT
* * *
2806797 AAATAATGAACAACACTTCTACCTTAATAATTTTTAAAATT
1 AAATAATGAACAACACCTATACCTCAATAATTTTTAAAATT
2806838 AA
1 AA
2806840 CTATTTTATC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (41 bp):
AAATAATGAACAACACCTATACCTCAATAATTTTTAAAATT
Found at i:2818006 original size:16 final size:16
Alignment explanation
Indices: 2817954--2818007 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
2817944 TATATATATT
2817954 TATATAAATTTTAATA
1 TATATAAATTTTAATA
* * *
2817970 AAT-TAATAATTTAATTT
1 TATATAA-ATTTTAA-TA
2817987 TATATAAATTTTAATA
1 TATATAAATTTTAATA
2818003 TATAT
1 TATAT
2818008 TTATAATACT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
15 3 0.10
16 14 0.48
17 9 0.31
18 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATAAATTTTAATA
Found at i:2818009 original size:23 final size:22
Alignment explanation
Indices: 2817955--2818015 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 22
2817945 ATATATATTT
2817955 ATATAAATTTTAATAAATTAATA
1 ATAT-AATTTTAATAAATTAATA
* *
2817978 ATTTAATTTTATATAAATT-TTA
1 ATATAATTTTA-ATAAATTAATA
2818000 ATATATATTTATAATA
1 ATATA-ATTT-TAATA
2818016 CTTATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 13 0.41
23 17 0.53
24 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATAATTTTAATAAATTAATA
Found at i:2818026 original size:12 final size:12
Alignment explanation
Indices: 2817937--2818033 Score: 64
Period size: 12 Copynumber: 8.2 Consensus size: 12
2817927 TATAATTATG
2817937 TTTTAAATATATA
1 TTTT-AATATATA
*
2817950 TATTT-ATATAAA
1 T-TTTAATATATA
2817962 TTTTAATA-A-A
1 TTTTAATATATA
* *
2817972 TTAATAATTTA-A
1 TT-TTAATATATA
*
2817984 TTTT-ATATAAA
1 TTTTAATATATA
2817995 TTTTAATATATA
1 TTTTAATATATA
2818007 TTTATAATACT-TA
1 TTT-TAATA-TATA
2818020 TTTTAAT-TATA
1 TTTTAATATATA
2818031 TTT
1 TTT
2818034 AATTTTTTAT
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
10 8 0.12
11 19 0.28
12 27 0.39
13 11 0.16
14 4 0.06
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTTAATATATA
Found at i:2818041 original size:18 final size:18
Alignment explanation
Indices: 2818020--2818072 Score: 72
Period size: 19 Copynumber: 2.9 Consensus size: 18
2818010 ATAATACTTA
2818020 TTTTAATTATATTTAATT
1 TTTTAATTATATTTAATT
*
2818038 TTTTATATTATATTTATTT
1 TTTTA-ATTATATTTAATT
2818057 TTTATAATTAT-TTTAA
1 TTT-TAATTATATTTAA
2818073 AATCATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 9 0.29
19 20 0.65
20 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTAATTATATTTAATT
Found at i:2818049 original size:19 final size:19
Alignment explanation
Indices: 2818020--2818072 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 19
2818010 ATAATACTTA
2818020 TTTTA-ATTATATTTAATT
1 TTTTATATTATATTTAATT
2818038 TTTTATATTATATTT-ATT
1 TTTTATATTATATTTAATT
2818056 TTTTATAATTAT-TTTAA
1 TTTTAT-ATTATATTTAA
2818073 AATCATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 17 0.53
19 15 0.47
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTATATTATATTTAATT
Found at i:2818655 original size:25 final size:26
Alignment explanation
Indices: 2818604--2818676 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 26
2818594 AACTTTACTG
2818604 TTATATTTAAATAAATTTTTATGTTTTTA
1 TTATATTTAAATAAA---TTATGTTTTTA
2818633 TTATATTTAAATAAA-TAT-TTTTTA
1 TTATATTTAAATAAATTATGTTTTTA
* * *
2818657 TTTAAATCTAAATAAGTTAT
1 -TTATATTTAAATAAATTAT
2818677 TATTTTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 6 0.15
25 15 0.38
26 3 0.08
29 15 0.38
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (26 bp):
TTATATTTAAATAAATTATGTTTTTA
Found at i:2818689 original size:21 final size:20
Alignment explanation
Indices: 2818630--2818689 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
2818620 TTTTATGTTT
*
2818630 TTATTATATTTAAATAAATAT
1 TTATTAT-TTTAAATAAATAG
*
2818651 TTTTTA-TTTAAATCTAAATAAG
1 TTATTATTTTAAA--TAAAT-AG
2818673 TTATTATTTTAAATAAA
1 TTATTATTTTAAATAAA
2818690 ATATTAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 6 0.19
21 14 0.44
22 6 0.19
23 6 0.19
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
TTATTATTTTAAATAAATAG
Found at i:2818908 original size:30 final size:30
Alignment explanation
Indices: 2818848--2818909 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
2818838 AATATATAAA
* *
2818848 TATTAATTTAAAAATAAATATTTTATTTTT
1 TATTAATTTAAAAATAAATATTTAAATTTT
* *
2818878 TATTAATTTATAAAT-AGTAATTTAAATTTT
1 TATTAATTTAAAAATAAAT-ATTTAAATTTT
2818908 TA
1 TA
2818910 AACTTAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
TATTAATTTAAAAATAAATATTTAAATTTT
Found at i:2820840 original size:25 final size:23
Alignment explanation
Indices: 2820795--2820841 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2820785 TAATTCTTCT
* *
2820795 ATCTTATTTTTTTTTGGAATTTA
1 ATCTTATTTTTTATTGAAATTTA
2820818 ATCTATATTTTTTAATTGAAATTT
1 ATCT-TATTTTTT-ATTGAAATTT
2820842 GATTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 8 0.40
25 8 0.40
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (23 bp):
ATCTTATTTTTTATTGAAATTTA
Found at i:2821609 original size:15 final size:15
Alignment explanation
Indices: 2821585--2821618 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2821575 ATTAATATAA
2821585 TTAT-TTTTACAAAT
1 TTATATTTTACAAAT
*
2821599 TTATATTTTACATAT
1 TTATATTTTACAAAT
2821614 TTATA
1 TTATA
2821619 ATTCGAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATTTTACAAAT
Found at i:2824031 original size:19 final size:20
Alignment explanation
Indices: 2823994--2824031 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2823984 TTCTACTTTT
* *
2823994 AAAAAAAATTTAAAGCAAAA
1 AAAAAAAAATCAAAGCAAAA
2824014 AAAAAAAAATCAAA-CAAA
1 AAAAAAAAATCAAAGCAAA
2824032 TACTAAACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.79, C:0.08, G:0.03, T:0.11
Consensus pattern (20 bp):
AAAAAAAAATCAAAGCAAAA
Found at i:2824809 original size:21 final size:21
Alignment explanation
Indices: 2824784--2824826 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2824774 TAATGTTATT
* *
2824784 TAAATTTAATTATAAAAAATA
1 TAAATATAAATATAAAAAATA
*
2824805 TAAATATAAATATAAAACATA
1 TAAATATAAATATAAAAAATA
2824826 T
1 T
2824827 TTTTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATATAAATATAAAAAATA
Found at i:2831637 original size:23 final size:22
Alignment explanation
Indices: 2831609--2831674 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 22
2831599 ACATAAATAT
2831609 TATAAACATTATAATATATTTAA
1 TATAAA-ATTATAATATATTTAA
2831632 TAT-AAA-TAT--TATATTTACA
1 TATAAAATTATAATATATTTA-A
* *
2831651 TTTAAAATTTTAATATATTTAA
1 TATAAAATTATAATATATTTAA
2831673 TA
1 TA
2831675 ATTTTTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
18 8 0.23
19 3 0.09
20 6 0.17
21 3 0.09
22 4 0.11
23 11 0.31
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (22 bp):
TATAAAATTATAATATATTTAA
Found at i:2831663 original size:32 final size:31
Alignment explanation
Indices: 2831591--2831667 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
2831581 ACATAATATG
*
2831591 AAAA-TTTAACATAAATATTATAAACATTAT
1 AAAATTTTAATATAAATATTATAAACATTAT
* *
2831621 AATATATTTAATATAAATATTATATTTACATT-T
1 AAAAT-TTTAATATAAATATTATA--AACATTAT
2831654 AAAATTTTAATATA
1 AAAATTTTAATATA
2831668 TTTAATAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 3 0.08
32 26 0.67
33 5 0.13
34 5 0.13
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (31 bp):
AAAATTTTAATATAAATATTATAAACATTAT
Found at i:2831689 original size:19 final size:18
Alignment explanation
Indices: 2831643--2831690 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
2831633 ATAAATATTA
2831643 TATTTACATTTAAAATTTT
1 TATTT-CATTTAAAATTTT
* *
2831662 AATAT-ATTTAATAATTTT
1 TATTTCATTTAA-AATTTT
2831680 TATTTCATTTA
1 TATTTCATTTA
2831691 TATTTACACA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
17 6 0.26
18 9 0.39
19 8 0.35
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTCATTTAAAATTTT
Found at i:2832479 original size:36 final size:35
Alignment explanation
Indices: 2832406--2832479 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 35
2832396 TTTATATTCA
* *
2832406 TTATTTATTATTTAATAAAATATTAAAAATTATTT
1 TTATTTAATATTTAATAAAATATTAAAAATTAATT
2832441 TTATATTAATATTTATATAAAAT-TT-AAAATTAAATT
1 TTAT-TTAATATTTA-ATAAAATATTAAAAATT-AATT
2832477 TTA
1 TTA
2832480 AAAAATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 10 0.29
36 17 0.50
37 7 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (35 bp):
TTATTTAATATTTAATAAAATATTAAAAATTAATT
Found at i:2833280 original size:6 final size:6
Alignment explanation
Indices: 2833271--2833298 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2833261 AAGATAGGTT
2833271 AGGGAG AGGGAG AGGGAG AGGGAG AGGG
1 AGGGAG AGGGAG AGGGAG AGGGAG AGGG
2833299 GTAGGATTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
AGGGAG
Found at i:2839383 original size:15 final size:15
Alignment explanation
Indices: 2839361--2839398 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
2839351 ATAGTTCTGT
2839361 TTTTATTATAATA-A
1 TTTTATTATAATATA
2839375 TTTTAATTA-AATATA
1 TTTT-ATTATAATATA
2839390 TTTTATTAT
1 TTTTATTAT
2839399 TTATTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTATTATAATATA
Found at i:2839424 original size:22 final size:21
Alignment explanation
Indices: 2839375--2839424 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2839365 ATTATAATAA
* *
2839375 TTTTAATTAAATATATTTTAT
1 TTTTATTTAAATATATTTAAT
*
2839396 TATTTATTTATATATTATTTAAT
1 T-TTTATTTAAATA-TATTTAAT
2839419 TTTTAT
1 TTTTAT
2839425 AGGATATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.62
23 8 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTATTTAAATATATTTAAT
Found at i:2839909 original size:61 final size:60
Alignment explanation
Indices: 2839778--2839915 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 60
2839768 TCCATATTGA
* * * * *
2839778 TAATTATATATATATATATATTGAAATTATCATGTGTTGTTTAAATTATATATTGTAAAGT
1 TAATTATAT-TATATATAAATTGAAATTATCACGTATTGTTGAAATTATATATTGTAAAAT
* *
2839839 TAATGATATTATATATAAATTGAAATTATCACGTTATTGTTGATATTATATATTGTAAAAT
1 TAATTATATTATATATAAATTGAAATTATCACG-TATTGTTGAAATTATATATTGTAAAAT
*
2839900 TAGTTATATTATATAT
1 TAATTATATTATATAT
2839916 TGTAAAATGA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
60 22 0.33
61 45 0.67
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (60 bp):
TAATTATATTATATATAAATTGAAATTATCACGTATTGTTGAAATTATATATTGTAAAAT
Found at i:2840058 original size:62 final size:62
Alignment explanation
Indices: 2839953--2840070 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 62
2839943 TATTTAAATT
* *
2839953 GTTATAATTTTAGATTAACTCTCACTTAATTATTGTTACAATTATATA-TCAATTAAACTAGA
1 GTTATAATTTTAGATTAACTCTCACTTAATTAGTATTACAATTATATACT-AATTAAACTAGA
* * ** *
2840015 GTTATAATTTTAGATTAATTTTTTCTTAATTAGTATTAGAATTATATACTAATTAA
1 GTTATAATTTTAGATTAACTCTCACTTAATTAGTATTACAATTATATACTAATTAA
2840071 GCTAATAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
62 47 0.98
63 1 0.02
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.47
Consensus pattern (62 bp):
GTTATAATTTTAGATTAACTCTCACTTAATTAGTATTACAATTATATACTAATTAAACTAGA
Found at i:2842087 original size:471 final size:458
Alignment explanation
Indices: 2841210--2842100 Score: 1014
Period size: 471 Copynumber: 1.9 Consensus size: 458
2841200 TAAAAATTAG
* * **
2841210 TATATATGAAAGCATGAAAGTGAAAAATCTTTTAAATTGACAAAAATAATTTTAGGTATTAATTA
1 TATATATAAAAGCATGAAAGCGAAAAATCTTTTAAATTGACAAAAATAATCATAGGTATTAATTA
*
2841275 TATTTTTAAATTGCTATTACAAATATACTTATTATTAATAATATTTATCTAATTTATAAGTAAAA
66 TATTTTTAAATTGCTATTACAAATATACTTATTATTAATAAGATTTATCTAATTTATAAGTAAAA
* * * *
2841340 ATTTTGATTTCATTAAAAAATTTTCATTAAATATATTTAGTTAAATATAATGTTAAATTTACATT
131 ATTTTAATTTCATTAAAAAATTTTCATTAAATATATTTAATTAAATAAAATGTTAAATTTAAATT
** * * *
2841405 AAATTACTTTATTTTCGTATTTTTAATTTTTTATCAACCTTAAAATATAAATGAATTTATTTGAT
196 AAATTACTTTATTTTCAAAGTTTTAATTTTTCATCAACCTTAAAATATAAACGAATTTATTTGAT
* *
2841470 AAAAATAAAAGAGTTAAATTTGATTTTTTTATTTTCATAAATTTTACTTTATATTAAAATTAAAA
261 AAAAATAAAAGAG-AAAATTTAATTTTTTTATTTTCATAAATTTTACTTTATATTAAAATTAAAA
* ** ** * * * *
2841535 ATAATAAATTTATATTTTTGAAACTTGAAAAAACTTTTACATTTTTATGCATTAATTTTACTTAT
325 ATAACAAATTTATA-TAATGAAACTTG-AAAAACTTCAACAATTTTATACATTAA-TTAAATTAT
*
2841600 TATAAAATATATAACTACATATATTTTTAAAACAATGAGTATTTACATATGTCATACGTGAAAAT
387 TATAAAATAAATAACT--ATATATTTTTAAAACAATGAGTATTTACATATGTCATACGTGAAAAT
2841665 AAATACTAC
450 AAATACTAC
* * * *
2841674 TATATATAAAAGCATGAATA-CGAAAAAT-TTTTGAGA-TGACAAAAATAGTCATATGTATTTAT
1 TATATATAAAAGCATGAA-AGCGAAAAATCTTTT-AAATTGACAAAAATAATCATAGGTATTAAT
* * ** *
2841736 TGTATTTTTAAATT-ATCATTGTAAATAT-TTTATTATTAATAAGATTTATCTAATTTATAAGTA
64 TATATTTTTAAATTGCT-ATTACAAATATACTTATTATTAATAAGATTTATCTAATTTATAAGTA
* **
2841799 AAAATTTTAATTTTATTAAAAGTTTTTCATTAAATAAATATATTTAATAATAAATAAAAAATGTT
128 AAAATTTTAATTTCATTAAAAAATTTTCA-T---TAAATATATTTAAT--TAAAT--AAAATGTT
* * * *
2841864 AAATTTTAAATTAAATTACTTTATTTTTAAAGTTTTAATTTTTCGTTAACCTTAAAATCTAAACG
185 AAA-TTTAAATTAAATTACTTTATTTTCAAAGTTTTAATTTTTCATCAACCTTAAAATATAAACG
* *
2841929 ACTTTATTTGATAAAAATAAAAGTA-AAAATTTATACAATTTTTTTATTTTCA-AAAGTTTTAAT
249 AATTTATTTGATAAAAATAAAAG-AGAAAA-TT-T--AATTTTTTTATTTTCATAAA-TTTT-AC
* *
2841992 TTTATATTAAAATTAAACATAACAAATTTATA-AATGAGAACATTG-AACA-TTCAACAAATTTT
307 TTTATATTAAAATTAAAAATAACAAATTTATATAATGA-AAC-TTGAAAAACTTCAAC-AATTTT
*
2842054 ATATATTAA-TAAATT-TTATAAAAATAAATAACTATATATTTTTAAAA
369 ATACATTAATTAAATTATTAT-AAAATAAATAACTATATATTTTTAAAA
2842101 TAAATAAAAT
Statistics
Matches: 357, Mismatches: 47, Indels: 41
0.80 0.11 0.09
Matches are distributed among these distances:
462 59 0.17
463 48 0.13
464 26 0.07
465 1 0.00
466 13 0.04
468 5 0.01
469 14 0.04
470 17 0.05
471 91 0.25
472 6 0.02
473 21 0.06
474 22 0.06
475 34 0.10
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (458 bp):
TATATATAAAAGCATGAAAGCGAAAAATCTTTTAAATTGACAAAAATAATCATAGGTATTAATTA
TATTTTTAAATTGCTATTACAAATATACTTATTATTAATAAGATTTATCTAATTTATAAGTAAAA
ATTTTAATTTCATTAAAAAATTTTCATTAAATATATTTAATTAAATAAAATGTTAAATTTAAATT
AAATTACTTTATTTTCAAAGTTTTAATTTTTCATCAACCTTAAAATATAAACGAATTTATTTGAT
AAAAATAAAAGAGAAAATTTAATTTTTTTATTTTCATAAATTTTACTTTATATTAAAATTAAAAA
TAACAAATTTATATAATGAAACTTGAAAAACTTCAACAATTTTATACATTAATTAAATTATTATA
AAATAAATAACTATATATTTTTAAAACAATGAGTATTTACATATGTCATACGTGAAAATAAATAC
TAC
Found at i:2843961 original size:17 final size:18
Alignment explanation
Indices: 2843935--2843968 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2843925 TCCCCATGAC
*
2843935 TTGCATTTGCAT-TGCTG
1 TTGCACTTGCATGTGCTG
2843952 TTGCACTTGCATGTGCT
1 TTGCACTTGCATGTGCT
2843969 CTACCTCAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.44
Consensus pattern (18 bp):
TTGCACTTGCATGTGCTG
Found at i:2847977 original size:20 final size:21
Alignment explanation
Indices: 2847946--2847986 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2847936 AATTTAATAT
*
2847946 TTATATATTTTTATTTTAAAA
1 TTATATATTTTTATTGTAAAA
2847967 TTATA-ATTTTTATTGTAAAA
1 TTATATATTTTTATTGTAAAA
2847987 AAATTGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTATATATTTTTATTGTAAAA
Found at i:2847987 original size:21 final size:21
Alignment explanation
Indices: 2847937--2847987 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2847927 TATTTGATAA
* *
2847937 ATTTAATATTTATATATTTTT
1 ATTTAAAAATTATATATTTTT
*
2847958 ATTTTAAAATTATA-ATTTTT
1 ATTTAAAAATTATATATTTTT
2847978 ATTGTAAAAA
1 ATT-TAAAAA
2847988 AATTGATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTTAAAAATTATATATTTTT
Found at i:2848587 original size:3 final size:3
Alignment explanation
Indices: 2848579--2848606 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2848569 ATTAATATTT
2848579 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2848607 GATACCATTA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2851185 original size:21 final size:21
Alignment explanation
Indices: 2851150--2851201 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
2851140 AGTAGAAATA
2851150 AAAATATTAATTTTTAAATTTAT
1 AAAATATTAATTTTT-AATTT-T
2851173 AAAA-ATT-ATTTTTAATTTT
1 AAAATATTAATTTTTAATTTT
*
2851192 AAAATTTTAA
1 AAAATATTAA
2851202 CTATAATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 5 0.19
20 7 0.27
21 7 0.27
22 3 0.12
23 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAAATATTAATTTTTAATTTT
Found at i:2851398 original size:17 final size:17
Alignment explanation
Indices: 2851372--2851422 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
2851362 TATATTATAT
*
2851372 AATTATATTTAAATAAA
1 AATTAAATTTAAATAAA
2851389 AATTAAATTTAAAT-AA
1 AATTAAATTTAAATAAA
2851405 AA-T-AATTTAAATTAAA
1 AATTAAATTTAAA-TAAA
2851421 AA
1 AA
2851423 AATATAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 8 0.26
15 2 0.06
16 8 0.26
17 13 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATTAAATTTAAATAAA
Found at i:2851430 original size:15 final size:15
Alignment explanation
Indices: 2851378--2851432 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
2851368 ATATAATTAT
*
2851378 ATTTAAATAAAAATTAA
1 ATTTAAATTAAAA--AA
*
2851395 ATTTAAA-TAAAATA
1 ATTTAAATTAAAAAA
2851409 ATTTAAATTAAAAAA
1 ATTTAAATTAAAAAA
*
2851424 ATATAAATT
1 ATTTAAATT
2851433 TTAATTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.24
15 14 0.42
16 4 0.12
17 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATTTAAATTAAAAAA
Found at i:2852454 original size:27 final size:27
Alignment explanation
Indices: 2852377--2852446 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
2852367 TATAAAATTT
* **
2852377 ATATAATTATATAAAATCTTAAATATAG
1 ATATAA-TATAAAAAATAATAAATATAG
*
2852405 TTATAATATAAAAAATAATAAATATA-
1 ATATAATATAAAAAATAATAAATATAG
2852431 ATATAA-ATACAAAAAT
1 ATATAATATA-AAAAAT
2852447 TATCAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 3 0.08
26 11 0.31
27 17 0.47
28 5 0.14
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.34
Consensus pattern (27 bp):
ATATAATATAAAAAATAATAAATATAG
Found at i:2853173 original size:17 final size:17
Alignment explanation
Indices: 2853151--2853185 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2853141 GAAGATAAAC
2853151 AAAAAATAAAATAAAAT
1 AAAAAATAAAATAAAAT
* *
2853168 AAAAAATGAAATTAAAT
1 AAAAAATAAAATAAAAT
2853185 A
1 A
2853186 TTTGGGTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (17 bp):
AAAAAATAAAATAAAAT
Found at i:2853418 original size:22 final size:23
Alignment explanation
Indices: 2853393--2853454 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 23
2853383 AATACAATAC
2853393 AAATTATTTAATATATT-TATTA
1 AAATTATTTAATATATTATATTA
* *
2853415 AAA-TATTTTAT-TAATTATATTT
1 AAATTATTTAATAT-ATTATATTA
2853437 AAATATATTATAATATAT
1 AAAT-TATT-TAATATAT
2853455 ATTAAATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
20 1 0.03
21 10 0.32
22 10 0.32
24 4 0.13
25 5 0.16
26 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AAATTATTTAATATATTATATTA
Found at i:2853419 original size:14 final size:13
Alignment explanation
Indices: 2853396--2853437 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2853386 ACAATACAAA
*
2853396 TTATTTAATATAT
1 TTATTAAATATAT
2853409 TTATTAAA-ATATT
1 TTATTAAATATA-T
*
2853422 TTATTAATTATAT
1 TTATTAAATATAT
2853435 TTA
1 TTA
2853438 AATATATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 3 0.12
13 19 0.76
14 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATTAAATATAT
Found at i:2853421 original size:21 final size:21
Alignment explanation
Indices: 2853397--2853472 Score: 56
Period size: 21 Copynumber: 3.7 Consensus size: 21
2853387 CAATACAAAT
2853397 TATTTAATATATTTATTAAAA
1 TATTTAATATATTTATTAAAA
*
2853418 TATTTTAT-TAATTATATTTAAATA
1 TATTTAATAT-ATT-TA-TTAAA-A
2853442 TATTATAATATA--TATT-AAA
1 TATT-TAATATATTTATTAAAA
2853461 TA--TAATATATTT
1 TATTTAATATATTT
2853473 TTTTATATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 19
0.68 0.03 0.29
Matches are distributed among these distances:
16 7 0.16
18 1 0.02
19 3 0.07
20 3 0.07
21 12 0.27
22 4 0.09
23 5 0.11
24 5 0.11
25 4 0.09
26 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTTAATATATTTATTAAAA
Found at i:2853455 original size:22 final size:22
Alignment explanation
Indices: 2853393--2853469 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 22
2853383 AATACAATAC
*
2853393 AAAT-TATT-TAATATATTTATTA
1 AAATATATTATAATATA--TATTT
*
2853415 AAATATTTTATTAAT-TATATTT
1 AAATATATTA-TAATATATATTT
2853437 AAATATATTATAATATATA-TT
1 AAATATATTATAATATATATTT
*
2853458 AAATATAATATA
1 AAATATATTATA
2853470 TTTTTTTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
21 17 0.36
22 21 0.45
23 3 0.06
24 2 0.04
25 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATATATTATAATATATATTT
Found at i:2853468 original size:12 final size:12
Alignment explanation
Indices: 2853397--2853464 Score: 58
Period size: 12 Copynumber: 6.0 Consensus size: 12
2853387 CAATACAAAT
2853397 TATT-TAATATA
1 TATTATAATATA
*
2853408 T-TTATTAAAATA
1 TATTA-TAATATA
*
2853420 TTTTATTAAT-TA
1 TATTA-TAATATA
2853432 TATT-TAA-ATA
1 TATTATAATATA
2853442 TATTATAATATA
1 TATTATAATATA
2853454 TATTA-AATATA
1 TATTATAATATA
2853465 ATATATTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
10 11 0.23
11 10 0.21
12 20 0.42
13 7 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TATTATAATATA
Found at i:2854082 original size:6 final size:6
Alignment explanation
Indices: 2854073--2854118 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
2854063 ATTATATGAC
* *
2854073 ATAAAT ATAACAT A-AAAA ATAAAT ATAAAT AT-GAT ATAAAT ATAAA
1 ATAAAT ATAA-AT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAA
2854119 AATATGTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 6 0.18
6 24 0.73
7 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (6 bp):
ATAAAT
Found at i:2854187 original size:16 final size:15
Alignment explanation
Indices: 2854166--2854227 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 15
2854156 ATCAATATGT
2854166 ATTTAAATATATGATA
1 ATTTAAATATAT-ATA
2854182 ATTTAAATATAGTAATA
1 ATTTAAATATA-T-ATA
**
2854199 ATAAAAATATATA-A
1 ATTTAAATATATATA
2854213 ATTTAAATACTATAT
1 ATTTAAATA-TATAT
2854228 GAAAATATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 8 0.21
15 5 0.13
16 12 0.32
17 13 0.34
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (15 bp):
ATTTAAATATATATA
Found at i:2854509 original size:22 final size:22
Alignment explanation
Indices: 2854483--2854526 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2854473 AAAATTTTTA
*
2854483 AAAAAATACAATTGACAAAAATC
1 AAAATATA-AATTGACAAAAATC
* *
2854506 AAAATTTAAATTTACAAAAAT
1 AAAATATAAATTGACAAAAAT
2854527 TCACTTCCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAATATAAATTGACAAAAATC
Found at i:2854890 original size:2 final size:2
Alignment explanation
Indices: 2854847--2854871 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2854837 TGACAAAATA
2854847 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 A
2854872 AAGTAGTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2855545 original size:15 final size:16
Alignment explanation
Indices: 2855517--2855546 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2855507 ATTTTTTAGT
2855517 ATTTTTTAACAAAATA
1 ATTTTTTAACAAAATA
2855533 ATTTTTTAA-AAAAT
1 ATTTTTTAACAAAAT
2855547 CACTTGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTTTTAACAAAATA
Found at i:2856033 original size:17 final size:17
Alignment explanation
Indices: 2856011--2856046 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2856001 TAGTTAAAAA
* *
2856011 TTTTTAAATTAATTTAT
1 TTTTTAAAATAATATAT
2856028 TTTTTAAAATAATATAT
1 TTTTTAAAATAATATAT
2856045 TT
1 TT
2856047 AAAATAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTTAAAATAATATAT
Found at i:2856750 original size:2 final size:2
Alignment explanation
Indices: 2856743--2856782 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
2856733 AGAACCTATG
* *
2856743 AT AT AT AT AT AT AT AT AT AT AT AT AT TT GT AT AT -T 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
2856783 CTAGGACAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2857321 original size:6 final size:6
Alignment explanation
Indices: 2857302--2857440 Score: 156
Period size: 6 Copynumber: 22.8 Consensus size: 6
2857292 TGCTACTCAT
*
2857302 ATATAC ATAT-- ATATAC ATATAC ATATAC ATATATAC ATACAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC --ATATAC ATATAC ATATAC
* * *
2857350 ATATAC ATATAC ATATAC ATATAT ATATAT ATATAC ATATATAC ATATAT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC --ATATAC ATATAC
* * * *
2857400 ACATAT ATATAC ATATAC ATATAC ATATAT ATATAT ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
2857441 TACATAGGAG
Statistics
Matches: 118, Mismatches: 9, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
4 4 0.03
6 102 0.86
8 12 0.10
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.37
Consensus pattern (6 bp):
ATATAC
Found at i:2857352 original size:26 final size:26
Alignment explanation
Indices: 2857302--2857446 Score: 136
Period size: 26 Copynumber: 5.7 Consensus size: 26
2857292 TGCTACTCAT
2857302 ATATACATATAT--AT--ACATATAC
1 ATATACATATATACATACACATATAC
2857324 ATATACATATATACATACACATATAC
1 ATATACATATATACATACACATATAC
* * * *
2857350 ATATACATATACATATACATATATAT
1 ATATACATATATACATACACATATAC
* * * *
2857376 ATATATATACATATATACATATATAC
1 ATATACATATATACATACACATATAC
* * *
2857402 ATATATATACATATACATATACATATAT
1 ATATACAT--ATATACATACACATATAC
*
2857430 ATATATATATATACATA
1 ATATACATATATACATA
2857447 GGAGATCAAA
Statistics
Matches: 104, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
22 12 0.12
24 2 0.02
26 69 0.66
28 21 0.20
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.37
Consensus pattern (26 bp):
ATATACATATATACATACACATATAC
Found at i:2859031 original size:18 final size:18
Alignment explanation
Indices: 2858979--2859031 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
2858969 TAAATGAATG
2858979 TATCAAAATTTATATAAA
1 TATCAAAATTTATATAAA
2858997 -AT--AAA-TTAT-TAACA
1 TATCAAAATTTATATAA-A
2859011 TATCAAAATTTATATAAA
1 TATCAAAATTTATATAAA
2859029 TAT
1 TAT
2859032 ATAATACGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
13 3 0.10
14 5 0.17
15 5 0.17
17 5 0.17
18 8 0.28
19 3 0.10
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
TATCAAAATTTATATAAA
Found at i:2859266 original size:69 final size:66
Alignment explanation
Indices: 2859182--2859312 Score: 174
Period size: 69 Copynumber: 1.9 Consensus size: 66
2859172 AGCATAATAC
* *
2859182 AAAAAATGAAAAATGATACAAAT-ACATTAACATAAAAAATAATTTATATATATATATTAAAATT
1 AAAAAATGAAAAATGAAACAAATAAAATTAACAT--AAAATAATTTAT-TA-ATATATTAAAATT
2859246 AACAT
62 AACAT
**
2859251 AAAAAATGAAAAATGAAACATGTCAAAATTAACATAAAATAATTTATTAATATATTAAAATT
1 AAAAAATGAAAAATGAAACAAAT-AAAATTAACATAAAATAATTTATTAATATATTAAAATT
2859313 TATATAAATA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
67 13 0.23
68 2 0.04
69 32 0.57
71 9 0.16
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (66 bp):
AAAAAATGAAAAATGAAACAAATAAAATTAACATAAAATAATTTATTAATATATTAAAATTAACA
T
Found at i:2859312 original size:18 final size:20
Alignment explanation
Indices: 2859291--2859327 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2859281 AACATAAAAT
2859291 AATTTAT-T-AATATATTAA
1 AATTTATATAAATATATTAA
2859309 AATTTATATAAATATATTA
1 AATTTATATAAATATATTA
2859328 TATATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTATATAAATATATTAA
Found at i:2859976 original size:34 final size:29
Alignment explanation
Indices: 2859948--2860011 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
2859938 ATTAACATTT
2859948 TATATACAACATAATACATATCATATTAATTA
1 TATATA-AACAT-AT-CATATCATATTAATTA
* *
2859980 TATTTAAACATATCATATCATATTTATTA
1 TATATAAACATATCATATCATATTAATTA
2860009 TAT
1 TAT
2860012 TATTTTTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 18 0.60
30 2 0.07
31 5 0.17
32 5 0.17
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (29 bp):
TATATAAACATATCATATCATATTAATTA
Found at i:2860869 original size:15 final size:13
Alignment explanation
Indices: 2860847--2860886 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 13
2860837 TTTAATATTT
2860847 AATAATAATAAATA
1 AATAATAA-AAATA
2860861 AATTAATAAAATATA
1 AA-TAATAAAA-ATA
2860876 AATAATAAAAA
1 AATAATAAAAA
2860887 ATTAACTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.04
14 12 0.50
15 11 0.46
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:2861237 original size:18 final size:17
Alignment explanation
Indices: 2861212--2861245 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2861202 TAATTTTTAA
2861212 TATTTTGTAAATTAATT
1 TATTTTGTAAATTAATT
*
2861229 TATTGTTGTTAATTAAT
1 TATT-TTGTAAATTAAT
2861246 AAAATAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (17 bp):
TATTTTGTAAATTAATT
Found at i:2862201 original size:22 final size:22
Alignment explanation
Indices: 2862166--2862242 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 22
2862156 TAAAATTATT
2862166 TTAAAATATTTAAATTTTATTTA
1 TTAAAA-ATTTAAATTTTATTTA
2862189 TTAAAAATTTAAAATTTT-TTTA
1 TTAAAAATTT-AAATTTTATTTA
2862211 TATAATTAAA-TTAAATTATTATTATAA
1 T-TAA--AAATTTAAATT-TTATT-T-A
2862238 TTAAA
1 TTAAA
2862243 TTATTTTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
22 9 0.20
23 21 0.46
24 5 0.11
25 5 0.11
26 4 0.09
27 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAAAAATTTAAATTTTATTTA
Found at i:2862241 original size:17 final size:17
Alignment explanation
Indices: 2862215--2862254 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2862205 TTTTTATATA
2862215 ATTA-AATTAAATTATT
1 ATTATAATTAAATTATT
2862231 ATTATAATTAAATTATT
1 ATTATAATTAAATTATT
*
2862248 TTTATAA
1 ATTATAA
2862255 AATAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATAATTAAATTATT
Found at i:2866464 original size:3 final size:3
Alignment explanation
Indices: 2866456--2866486 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2866446 GAAAATACAA
2866456 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
2866487 GGAGGAGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2871643 original size:3 final size:3
Alignment explanation
Indices: 2871635--2871659 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2871625 GGAAGCAGGG
2871635 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
2871660 GGGAAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2872230 original size:3 final size:3
Alignment explanation
Indices: 2872217--2872260 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
2872207 TTACTGTCCA
2872217 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2872261 TATTACATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2872468 original size:20 final size:20
Alignment explanation
Indices: 2872432--2872469 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2872422 TATTTTTATT
*
2872432 TAAATTTAATTATAAATATA
1 TAAATTTAATTAAAAATATA
2872452 TAAATATTAA-TAAAAATA
1 TAAAT-TTAATTAAAAATA
2872470 ATTTTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAATTTAATTAAAAATATA
Found at i:2874425 original size:21 final size:19
Alignment explanation
Indices: 2874383--2874426 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
2874373 AAAAGTTTAT
2874383 AATTTTTAAAAATTAAAAG
1 AATTTTTAAAAATTAAAAG
* *
2874402 AATTGTTTCAAAATTCAAAGG
1 AATT-TTTAAAAATT-AAAAG
2874423 AATT
1 AATT
2874427 ATTCTTGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 9 0.43
21 8 0.38
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (19 bp):
AATTTTTAAAAATTAAAAG
Found at i:2882318 original size:30 final size:30
Alignment explanation
Indices: 2882277--2882336 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2882267 ATTATTTAGA
*
2882277 TTTATTTTAATTTAAATTATAATTTTTAAAT
1 TTTATTTTAATTTAAATTAT-ATTTATAAAT
* *
2882308 TTTA-TTTAATTTTATTTATATTTATAAAT
1 TTTATTTTAATTTAAATTATATTTATAAAT
2882337 AAATAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 9 0.35
30 13 0.50
31 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTATTTTAATTTAAATTATATTTATAAAT
Found at i:2882398 original size:18 final size:18
Alignment explanation
Indices: 2882377--2882436 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
2882367 ATTTAATTTG
2882377 ATTTTTATTAATTTAATA
1 ATTTTTATTAATTTAATA
2882395 ATTTTTATTAAAATTT-A-A
1 ATTTTTATT--AATTTAATA
* *
2882413 ATTTTAAATAATTTAATA
1 ATTTTTATTAATTTAATA
2882431 ATTTTT
1 ATTTTT
2882437 TAATATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
16 5 0.14
17 1 0.03
18 23 0.66
19 1 0.03
20 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTTATTAATTTAATA
Found at i:2883504 original size:20 final size:20
Alignment explanation
Indices: 2883366--2883542 Score: 75
Period size: 20 Copynumber: 9.0 Consensus size: 20
2883356 ATTTTAAAAT
* * *
2883366 TTTAAAATTAATTTAAATTT
1 TTTAAATTTAATATAAATTA
*
2883386 TATTAAGATATAAT-TAAATTA
1 T-TTAA-ATTTAATATAAATTA
* *
2883407 TTTAAA-TTATTATTAATTTA
1 TTTAAATTTAATA-TAAATTA
* *
2883427 TTATTAA-TAAATAT-AATTA
1 TT-TAAATTTAATATAAATTA
* **
2883446 TTT-AATTTTATATTTTATT-
1 TTTAAATTTAATA-TAAATTA
*
2883465 TTTAAATTT-A-A-AATTTA
1 TTTAAATTTAATATAAATTA
2883482 TTTAAATTTAATATAAATTA
1 TTTAAATTTAATATAAATTA
** * *
2883502 TTTAAATAAAAAATTAAAATA
1 TTTAAATTTAATA-TAAATTA
* *
2883523 TTTAAATTCAATTTAAATTA
1 TTTAAATTTAATATAAATTA
2883543 AAATTAAATT
Statistics
Matches: 117, Mismatches: 26, Indels: 28
0.68 0.15 0.16
Matches are distributed among these distances:
16 2 0.02
17 11 0.09
18 10 0.09
19 13 0.11
20 43 0.37
21 33 0.28
22 5 0.04
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (20 bp):
TTTAAATTTAATATAAATTA
Found at i:2883564 original size:37 final size:38
Alignment explanation
Indices: 2883466--2883564 Score: 101
Period size: 41 Copynumber: 2.5 Consensus size: 38
2883456 TATTTTATTT
*
2883466 TTAAATTTAAAATTTATTTAAATTTAATATAAATTATTTAAA
1 TTAAATTTAAAA-TT-TTTAAATTCAATATAAATTA--TAAA
* * * *
2883508 TAAAAAATTAAAATATTTAAATTCAATTTAAATTA-AAA
1 T-TAAATTTAAAATTTTTAAATTCAATATAAATTATAAA
2883546 TTAAATTTAAAATTTTTAA
1 TTAAATTTAAAATTTTTAA
2883565 TAACATTACC
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
37 15 0.31
38 4 0.08
41 18 0.38
42 2 0.04
43 9 0.19
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (38 bp):
TTAAATTTAAAATTTTTAAATTCAATATAAATTATAAA
Found at i:2885709 original size:47 final size:48
Alignment explanation
Indices: 2885630--2885731 Score: 179
Period size: 47 Copynumber: 2.1 Consensus size: 48
2885620 TGTTATAAGC
*
2885630 AGGGTTAACATTTGGCAATCCCTCTTTTTTTCTTTGTATCTGTGGCAG
1 AGGGTTAACATTTGGCAATCCCTCTTTTTTTCTTTGTATCTGGGGCAG
*
2885678 AGGGTTAACATTTGGCAATCCCTC-TTTTTTCTTTGTGTCTGGGGCAG
1 AGGGTTAACATTTGGCAATCCCTCTTTTTTTCTTTGTATCTGGGGCAG
2885725 AGGGTTA
1 AGGGTTA
2885732 TGTTTCTCCC
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
47 28 0.54
48 24 0.46
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.41
Consensus pattern (48 bp):
AGGGTTAACATTTGGCAATCCCTCTTTTTTTCTTTGTATCTGGGGCAG
Done.