Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 98 of 182
Found at i:29628727 original size:62 final size:62
Alignment explanation
Indices: 29628593--29629146 Score: 660
Period size: 62 Copynumber: 9.3 Consensus size: 62
29628583 AAAAACTTTA
* * * * *
29628593 GGTTAGTTTTGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTA-
1 GGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTA-GATTAGGGTTTTTAGTTAATTTAGGTTAG
29628655 ---TA--TTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAG
1 GGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAG
* * *
29628712 GGTTAGGTTAGGGTTTTTAATTAATTTAGGTTAGATTA-GGTTTTAAATTAATTTAGGTTA-
1 GGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAG
*
29628772 -G--A--TTAGGGTTTTTAGGTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAATTTAGGT
1 GGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTA--G--A--TTAGGGTTTTTAGTTAATTTAGGT
29628832 TA-
60 TAG
* * * *
29628834 ---TA--TTA-GGTTTTAAATTAATTTAGGTTAGATTAGGGTTTTTAGGTAATTTAAGTTAG
1 GGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAG
**
29628890 GGTTA-GTTAGGGTTTTTAGTTAATTTAGGTTAGATTA-GG-TTTTA---AA-TTACTTTA-
1 GGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAG
* *
29628944 GGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGATTATGGTTTTTAGTTAATTTAGGTTAG
1 GGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAG
*
29629006 GGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTAGATTATGGTTTTTAGTTAATTTAGGTTAG
1 GGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAG
* *
29629068 GGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGTTTTTTAATTAATTTAGGTTAG
1 GGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAG
*
29629130 TGTTAGGTTAGGGTTTT
1 GGTTAGGTTAGGGTTTT
29629147 CAATTAAATT
Statistics
Matches: 436, Mismatches: 28, Indels: 56
0.84 0.05 0.11
Matches are distributed among these distances:
54 5 0.01
55 85 0.19
56 30 0.07
57 32 0.07
59 12 0.03
60 9 0.02
61 73 0.17
62 190 0.44
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (62 bp):
GGTTAGGTTAGGGTTTTTAGTTAATTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAG
Found at i:29628779 original size:89 final size:88
Alignment explanation
Indices: 29628589--29629129 Score: 749
Period size: 89 Copynumber: 6.1 Consensus size: 88
29628579 GCCAAAAAAC
* * * *
29628589 TTTAGGTTAGTTTTGGGTTTTTAATTAATTTAGGTTA-GG-T--TTAGGGTTTTTAATTAATTTA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGTTAGGGTTTTTAGTTAATTTA
* * *
29628650 GGTTATATTAGGGTTTTTAGTTAA
66 GGTTAGATTA-GGTTTTAAATTAA
*
29628674 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAATTAATTT
1 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTA-GTTAGGGTTTTTAGTTAATTT
29628739 AGGTTAGATTAGGTTTTAAATTAA
65 AGGTTAGATTAGGTTTTAAATTAA
*
29628763 TTTAGGTTAGATTAGGGTTTTTAGGTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAATTT
1 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTA-GTTAGGGTTTTTAGTTAATTT
*
29628828 AGGTTATATTAGGTTTTAAATTAA
65 AGGTTAGATTAGGTTTTAAATTAA
* *
29628852 TTTAGGTTAGATTAGGGTTTTTAGGTAATTTAAGTTAGGGTTAGTTAGGGTTTTTAGTTAATTTA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGTTAGGGTTTTTAGTTAATTTA
*
29628917 GGTTAGATTAGGTTTTAAATTAC
66 GGTTAGATTAGGTTTTAAATTAA
*
29628940 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTA--G--A-TTATGGTTTTTAGTTAATTTA
1 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGTTAGGGTTTTTAGTTAATTTA
* *
29629000 GGTTAGGGTTAGGTTAGGGTTTTTAGTTAA
66 GGTTA--G--A--TTA-GGTTTTAAATTAA
*
29629030 TTTAGGTTAGATTATGGTTTTTAGTTAATTTAGGTTAGGGTTAGGTTAGGGTTTTTAGTTAATTT
1 TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTA-GTTAGGGTTTTTAGTTAATTT
*
29629095 AGGTTAGATTAGGTTTTTTAATTAA
65 AGGTTAGATTAGG-TTTTAAATTAA
29629120 TTTAGGTTAG
1 TTTAGGTTAG
29629130 TGTTAGGTTA
Statistics
Matches: 416, Mismatches: 21, Indels: 33
0.89 0.04 0.07
Matches are distributed among these distances:
83 25 0.06
84 1 0.00
85 35 0.08
86 3 0.01
87 2 0.00
88 78 0.19
89 144 0.35
90 99 0.24
92 2 0.00
94 2 0.00
96 25 0.06
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (88 bp):
TTTAGGTTAGATTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGTTAGGGTTTTTAGTTAATTTA
GGTTAGATTAGGTTTTAAATTAA
Found at i:29629238 original size:26 final size:25
Alignment explanation
Indices: 29629207--29629255 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
29629197 CTTAAAAAAT
29629207 TTCTATGCGTATTACATCAAATAAAC
1 TTCTAT-CGTATTACATCAAATAAAC
**
29629233 TTCTATTTTATTACATCAAATAA
1 TTCTATCGTATTACATCAAATAA
29629256 TAAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (25 bp):
TTCTATCGTATTACATCAAATAAAC
Found at i:29629404 original size:24 final size:24
Alignment explanation
Indices: 29629370--29629421 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
29629360 GCGGCTGTTA
*
29629370 TTCCTCTGGTGGTGATTGTGGTCC
1 TTCCTCCGGTGGTGATTGTGGTCC
* *
29629394 TTCCTCCGGTGGTGGTTGTGGTTC
1 TTCCTCCGGTGGTGATTGTGGTCC
29629418 TTCC
1 TTCC
29629422 GGTTCCGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.02, C:0.23, G:0.33, T:0.42
Consensus pattern (24 bp):
TTCCTCCGGTGGTGATTGTGGTCC
Found at i:29629720 original size:18 final size:18
Alignment explanation
Indices: 29629676--29629721 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
29629666 TATTCGGAAA
* *
29629676 AGGATACATGTAAGGGTT
1 AGGATACATATAAGGGCT
*
29629694 AGGGTACATATAAGGGCT
1 AGGATACATATAAGGGCT
*
29629712 AGGAAACATA
1 AGGATACATA
29629722 CCTGGCATCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.22
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:29630376 original size:7 final size:7
Alignment explanation
Indices: 29630366--29630395 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
29630356 TTATATACAT
29630366 AATACTA
1 AATACTA
29630373 AATACTA
1 AATACTA
29630380 AATACTA
1 AATACTA
29630387 AATA-TA
1 AATACTA
29630393 AAT
1 AAT
29630396 TGACTAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (7 bp):
AATACTA
Found at i:29631462 original size:30 final size:31
Alignment explanation
Indices: 29631409--29631472 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
29631399 GCCATTGATG
29631409 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
* *
29631440 AAAATATAAAAAAA-TTATAATTATTTTTAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
29631470 AAA
1 AAA
29631473 TGGATTTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (31 bp):
AAAATATAAAAAAATTTAAAATTATTTTAAA
Found at i:29631510 original size:40 final size:40
Alignment explanation
Indices: 29631466--29631541 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
29631456 ATAATTATTT
29631466 TTAAAAATG-GATTTGAGAGAATATTGGAAGGAAATTAAAA
1 TTAAAAATGAG-TTTGAGAGAATATTGGAAGGAAATTAAAA
* *
29631506 TTAAATATGAGTTTGAGAGAATTTTGGAAGGAAATT
1 TTAAAAATGAGTTTGAGAGAATATTGGAAGGAAATT
29631542 GAGAGGATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.32
Consensus pattern (40 bp):
TTAAAAATGAGTTTGAGAGAATATTGGAAGGAAATTAAAA
Found at i:29633128 original size:11 final size:11
Alignment explanation
Indices: 29633112--29633138 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
29633102 AACTTGAACA
29633112 AAAATAAAAAT
1 AAAATAAAAAT
29633123 AAAATAAAAAT
1 AAAATAAAAAT
29633134 AAAAT
1 AAAAT
29633139 TACATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:29649628 original size:15 final size:16
Alignment explanation
Indices: 29649608--29649642 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
29649598 AAATTGTTAT
29649608 TTATTATCATTATC-A
1 TTATTATCATTATCTA
*
29649623 TTATTATTATTATCTA
1 TTATTATCATTATCTA
29649639 TTAT
1 TTAT
29649643 CTTTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATTATCATTATCTA
Found at i:29650341 original size:13 final size:14
Alignment explanation
Indices: 29650307--29650344 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
29650297 TGCTTTTATA
29650307 TATATTCATTTCGTT
1 TATATT-ATTTCGTT
29650322 TAT-TTATTT-GTT
1 TATATTATTTCGTT
29650334 TATATTATTTC
1 TATATTATTTC
29650345 TATGCCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 2 0.10
15 3 0.14
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.66
Consensus pattern (14 bp):
TATATTATTTCGTT
Found at i:29652409 original size:20 final size:20
Alignment explanation
Indices: 29652386--29652436 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
29652376 CACAAACTTT
29652386 TCTTTGTTCATGTATAGCAG
1 TCTTTGTTCATGTATAGCAG
*
29652406 TCTTTGTTCATGTATAGTAG
1 TCTTTGTTCATGTATAGCAG
* *
29652426 CCTTTTTTCAT
1 TCTTTGTTCAT
29652437 TTAAAATCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.51
Consensus pattern (20 bp):
TCTTTGTTCATGTATAGCAG
Found at i:29654216 original size:62 final size:62
Alignment explanation
Indices: 29654106--29654228 Score: 210
Period size: 62 Copynumber: 2.0 Consensus size: 62
29654096 TGTAAGTGTG
*
29654106 ATTTTGTCCTATTTTTAATGATTTTTATGTTTTTGAAGTCACAACTTAATCTACCTAGCCCA
1 ATTTCGTCCTATTTTTAATGATTTTTATGTTTTTGAAGTCACAACTTAATCTACCTAGCCCA
* * *
29654168 ATTTCGTCCTGTTTTTAATGATTTTTATGTTTTTGAAGTCGCAGCTTAATCTACCTAGCCC
1 ATTTCGTCCTATTTTTAATGATTTTTATGTTTTTGAAGTCACAACTTAATCTACCTAGCCC
29654229 GAGGACTAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (62 bp):
ATTTCGTCCTATTTTTAATGATTTTTATGTTTTTGAAGTCACAACTTAATCTACCTAGCCCA
Found at i:29668785 original size:21 final size:21
Alignment explanation
Indices: 29668759--29668808 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
29668749 AAGGTGGAAG
* *
29668759 TTATGTGGCAGCTATCTACGA
1 TTATGTGGCAGCTATCGACAA
* *
29668780 TTATGTGGCTGTTATCGACAA
1 TTATGTGGCAGCTATCGACAA
29668801 TTATGTGG
1 TTATGTGG
29668809 TGGCTTGTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (21 bp):
TTATGTGGCAGCTATCGACAA
Found at i:29671011 original size:21 final size:21
Alignment explanation
Indices: 29670969--29671011 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
29670959 TACAAATAGG
**
29670969 ACATTAAAACATACATTTCAT
1 ACATTAAAACATACATAACAT
* *
29670990 ACATTAATATATACATAACAT
1 ACATTAAAACATACATAACAT
29671011 A
1 A
29671012 AATCATTCAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (21 bp):
ACATTAAAACATACATAACAT
Found at i:29678253 original size:43 final size:43
Alignment explanation
Indices: 29678200--29678342 Score: 155
Period size: 43 Copynumber: 3.3 Consensus size: 43
29678190 TTTGGGATTG
* * * *
29678200 CGCCACTAAAGACCATGACCTTTAGCTGCACTTTT-TTGACAAA
1 CGCCGCTAAAGACCCTGACCTTTAGCGGCACTTTTCCT-ACAAA
** *
29678243 CGCCGCTAAAGACCCTGATATTTAGCGGCACTTTTCCTACAAT
1 CGCCGCTAAAGACCCTGACCTTTAGCGGCACTTTTCCTACAAA
* * *
29678286 CGCCGCTAAAGACCCTGACCTTTAGCGGCGCTCTTTCC-ACGAG
1 CGCCGCTAAAGACCCTGACCTTTAGCGGCACT-TTTCCTACAAA
*
29678329 TGCCGCTAAAGACC
1 CGCCGCTAAAGACC
29678343 ACGACAAAGC
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
43 79 0.93
44 6 0.07
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.24
Consensus pattern (43 bp):
CGCCGCTAAAGACCCTGACCTTTAGCGGCACTTTTCCTACAAA
Found at i:29678424 original size:43 final size:43
Alignment explanation
Indices: 29678371--29678576 Score: 205
Period size: 44 Copynumber: 4.7 Consensus size: 43
29678361 AGACCCTAAT
* *
29678371 CTTTCGCGGCGCTTTTTTCACAAATGCCGTTAATGACCAGGAC
1 CTTTAGCGGCGCTTTTTTCACAAATGCCGCTAATGACCAGGAC
** *
29678414 CTTTAGCGGCGCTTTTGCCACAAATGCCGCTAATGACTAGGAC
1 CTTTAGCGGCGCTTTTTTCACAAATGCCGCTAATGACCAGGAC
* ** * * **
29678457 CTTTAGCAGCGGCTTTTGCCACAAACGCCGCTAAAGACCCTGAC
1 CTTTAGCGGC-GCTTTTTTCACAAATGCCGCTAATGACCAGGAC
* * * * *
29678501 CGTTAGCGGCGATTTTTTCCACAAACGCCGCTAATGACAACGAC
1 CTTTAGCGGCGCTTTTTT-CACAAATGCCGCTAATGACCAGGAC
* * * *
29678545 CTTTAGTGGTGCTTTTTTTAAAAATGCCGCTA
1 CTTTAGCGGCGCTTTTTTCACAAATGCCGCTA
29678577 GTTTTGGCAG
Statistics
Matches: 134, Mismatches: 27, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
43 63 0.47
44 71 0.53
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTTTCACAAATGCCGCTAATGACCAGGAC
Found at i:29678783 original size:19 final size:19
Alignment explanation
Indices: 29678759--29678795 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
29678749 ACAAAAATGA
*
29678759 TAAAAGTTAAAATGATAAT
1 TAAAAGTCAAAATGATAAT
29678778 TAAAAGTCAAAATGATAA
1 TAAAAGTCAAAATGATAA
29678796 AAATATTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.11, T:0.27
Consensus pattern (19 bp):
TAAAAGTCAAAATGATAAT
Found at i:29683101 original size:46 final size:46
Alignment explanation
Indices: 29683034--29683128 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
29683024 AGTTCTCCTT
*
29683034 TCTCAACACATCGTATGTCTCGACACTAGCCCATAATTGTTTTAAC
1 TCTCAACACATCGTATGTCTCGACACCAGCCCATAATTGTTTTAAC
*
29683080 TCTCAGCACATCGTATGTCTCGACACCAGCCCATAATTGTTTTAAC
1 TCTCAACACATCGTATGTCTCGACACCAGCCCATAATTGTTTTAAC
29683126 TCT
1 TCT
29683129 TCAATAACTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (46 bp):
TCTCAACACATCGTATGTCTCGACACCAGCCCATAATTGTTTTAAC
Found at i:29684504 original size:9 final size:9
Alignment explanation
Indices: 29684492--29684533 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
29684482 ATTAAGTCAA
29684492 TTATGTAAG
1 TTATGTAAG
*
29684501 TTATGTACG
1 TTATGTAAG
29684510 TGTA--TAAG
1 T-TATGTAAG
29684518 TTATGTAAG
1 TTATGTAAG
29684527 TTATGTA
1 TTATGTA
29684534 TTAAGTAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
7 2 0.07
8 4 0.14
9 20 0.71
10 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:29684584 original size:23 final size:23
Alignment explanation
Indices: 29684558--29684604 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
29684548 AAATTATATT
*
29684558 AAAAATATATATTAAATTTTAAA
1 AAAAATATAAATTAAATTTTAAA
29684581 AAAAATATAAATTAAATTTTAAA
1 AAAAATATAAATTAAATTTTAAA
29684604 A
1 A
29684605 GTATATGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAAATATAAATTAAATTTTAAA
Found at i:29684903 original size:22 final size:22
Alignment explanation
Indices: 29684878--29684919 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
29684868 TAATTAAGTT
29684878 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
*
29684900 ATGTAAGTTATGTATTATAT
1 ATGTAAGTTATGTATAATAT
29684920 AATAACAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:29685839 original size:12 final size:12
Alignment explanation
Indices: 29685819--29685858 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
29685809 CAAACAGTTT
*
29685819 CAAACTTATGAA
1 CAAAATTATGAA
*
29685831 CAAAATTATTAA
1 CAAAATTATGAA
*
29685843 CAAAATTATGAG
1 CAAAATTATGAA
29685855 CAAA
1 CAAA
29685859 CAGTATTACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.25
Consensus pattern (12 bp):
CAAAATTATGAA
Found at i:29685869 original size:24 final size:24
Alignment explanation
Indices: 29685808--29685869 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
29685798 ATCCTGTAAT
*
29685808 ACAAACAGT-TT-CAAACTTATGA
1 ACAAACAGTATTACAAAATTATGA
*
29685830 ACAAA-ATTATTAACAAAATTATGA
1 ACAAACAGTATT-ACAAAATTATGA
*
29685854 GCAAACAGTATTACAA
1 ACAAACAGTATTACAA
29685870 GCCTGCAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 2 0.06
22 7 0.22
24 18 0.56
25 5 0.16
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.26
Consensus pattern (24 bp):
ACAAACAGTATTACAAAATTATGA
Found at i:29685924 original size:12 final size:12
Alignment explanation
Indices: 29685907--29685932 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29685897 ACAGGATAGT
29685907 CAAAATTATGAA
1 CAAAATTATGAA
29685919 CAAAATTATGAA
1 CAAAATTATGAA
29685931 CA
1 CA
29685933 GTTTCAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.12, G:0.08, T:0.23
Consensus pattern (12 bp):
CAAAATTATGAA
Found at i:29686595 original size:16 final size:16
Alignment explanation
Indices: 29686550--29686605 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
29686540 TAAATCTCAC
*
29686550 ATCTTTTATTTATT-T
1 ATCTTTTATTAATTGT
* *
29686565 ATTTATTTCTTAATTGT
1 ATCT-TTTATTAATTGT
29686582 ATCTTTTATTAATTGT
1 ATCTTTTATTAATTGT
29686598 ATCTTTTA
1 ATCTTTTA
29686606 ATTACTAAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 3 0.09
16 27 0.79
17 4 0.12
ACGTcount: A:0.23, C:0.07, G:0.04, T:0.66
Consensus pattern (16 bp):
ATCTTTTATTAATTGT
Found at i:29687325 original size:22 final size:22
Alignment explanation
Indices: 29687284--29687326 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
29687274 CCCAAAGCAC
* * *
29687284 TAAATCCCTAACTCCTAACCCT
1 TAAATCCCAAACCCCAAACCCT
29687306 TAAATCCCAAACCCCAAACCC
1 TAAATCCCAAACCCCAAACCC
29687327 CTAACCCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.44, G:0.00, T:0.19
Consensus pattern (22 bp):
TAAATCCCAAACCCCAAACCCT
Found at i:29687411 original size:14 final size:14
Alignment explanation
Indices: 29687394--29687420 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29687384 CCTAACTAAT
29687394 AACCCTTAAATCAC
1 AACCCTTAAATCAC
29687408 AACCCTTAAATCA
1 AACCCTTAAATCA
29687421 AAATCCCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (14 bp):
AACCCTTAAATCAC
Found at i:29687439 original size:14 final size:15
Alignment explanation
Indices: 29687422--29687454 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
29687412 CTTAAATCAA
29687422 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
29687436 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
29687451 AATC
1 AATC
29687455 TATAAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:29687890 original size:41 final size:41
Alignment explanation
Indices: 29687833--29688152 Score: 338
Period size: 41 Copynumber: 7.8 Consensus size: 41
29687823 AAATGTTTTT
* *
29687833 GCGGCGCTTCTACAAAAACGCCGCTAAAGGCCCGAGCATTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* * *
29687874 GCGGCACTTATTCAAAAACGCCGCTAAAGGCCCGACCACTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* *
29687915 GCGGCGCTTATTCAAAAACGTCGCTAAAGGCCCGACCATTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* * *
29687956 GCGGTGCTTCA-TCAAAAACGTCGCTAATGGCCCGAGCATTA
1 GCGGCGCTT-ATTCAAAAACGCCGCTAAAGGCCCGAGCATTA
*
29687997 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* * * * * * *
29688038 GTGGCG-TTTTTGGATAAGCTCCGCTAAAGGCCAGAGCATTA
1 GCGGCGCTTATT-CAAAAACGCCGCTAAAGGCCCGAGCATTA
* ** * * *
29688079 GCGGCGATGCTTAAAAAACACAGCTAAAGGCCCGAGCATTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* * * * * *
29688120 GCGGTGCTTCTTAAAAAATGCCACTACAGGCCC
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGGCCC
29688153 CAAAAACTCA
Statistics
Matches: 236, Mismatches: 39, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
40 4 0.02
41 228 0.97
42 4 0.02
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.19
Consensus pattern (41 bp):
GCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGAGCATTA
Found at i:29693685 original size:27 final size:27
Alignment explanation
Indices: 29693655--29693706 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
29693645 ATCTTCTAAG
29693655 GGTATAATAGTCATTTTACCCTATGAA
1 GGTATAATAGTCATTTTACCCTATGAA
** *
29693682 GGTATTTTGGTCATTTTACCCTATG
1 GGTATAATAGTCATTTTACCCTATG
29693707 GGGGTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (27 bp):
GGTATAATAGTCATTTTACCCTATGAA
Found at i:29693712 original size:27 final size:27
Alignment explanation
Indices: 29693664--29694253 Score: 600
Period size: 27 Copynumber: 22.4 Consensus size: 27
29693654 GGGTATAATA
**
29693664 GTCATTTTACCCTATGAAGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
29693691 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
29693718 GTCATTCTAACCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * **
29693745 ATCATTTTACCGTATGGGGGTATTTAA
1 GTCATTTTACCCTATGGGGGTATTTTG
*
29693772 ATCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
29693799 GTCATTCTAACCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * **
29693826 ATCATTTTACCGTATGGGGGTATTTAA
1 GTCATTTTACCCTATGGGGGTATTTTG
*
29693853 ATCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
29693880 GTCATTCTAACCTATGGGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGGTATTTTG
* * **
29693908 ATCATTTTACCGTATGGGGGTATTTAA
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
29693935 ATTATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
29693962 GTCATTTTACCATATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * **
29693989 GTCATTTTACTCTATGAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
29694016 GTCATTTTACCATATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
*
29694043 GTCATTTTA-CC-A------TATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
29694062 ATCATTCTACCCTATTGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
29694089 GTTATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
29694116 GTCATTTTACCATATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
*
29694143 GTCATTTTA-CC-A------TATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
29694162 GTCATTCTACCCAATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
29694189 GTTATTCTACCCTATTGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
29694216 GTCATTTTACCCTTTGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
29694243 GTCATTTTACC
1 GTCATTTTACC
29694254 TATTTTAAGG
Statistics
Matches: 465, Mismatches: 81, Indels: 34
0.80 0.14 0.06
Matches are distributed among these distances:
19 27 0.06
20 4 0.01
21 2 0.00
25 2 0.00
26 2 0.00
27 406 0.87
28 22 0.05
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTTG
Found at i:29694067 original size:46 final size:46
Alignment explanation
Indices: 29694009--29694204 Score: 180
Period size: 46 Copynumber: 4.1 Consensus size: 46
29693999 TCTATGAGGG
*
29694009 TATTTC-AGTCATTTTACCATATAGGGGTATTTTGGTCATTTTACCA
1 TATTTCGA-TCATTCTACCATATAGGGGTATTTTGGTCATTTTACCA
* * *
29694055 TATTTCGATCATTCTACCCTATTGGGGTATTTTGGTTATTTTACCCTATGA
1 TATTTCGATCATTCTACCATATAGGGGTATTTTGGTCATTTTA-CC----A
* *
29694106 GGGTATTTCGGTCATTTTACCATATAGGGGTATTTTGGTCATTTTACCA
1 ---TATTTCGATCATTCTACCATATAGGGGTATTTTGGTCATTTTACCA
* * * * * *
29694155 TATTTCGGTCATTCTACCCA-ATGGGGGTATTTCGGTTATTCTACCC
1 TATTTCGATCATTCTA-CCATATAGGGGTATTTTGGTCATTTTACCA
29694201 TATT
1 TATT
29694205 GGGGTATTTT
Statistics
Matches: 125, Mismatches: 15, Indels: 20
0.78 0.09 0.12
Matches are distributed among these distances:
46 77 0.62
47 6 0.05
49 1 0.01
51 1 0.01
53 2 0.02
54 38 0.30
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.44
Consensus pattern (46 bp):
TATTTCGATCATTCTACCATATAGGGGTATTTTGGTCATTTTACCA
Found at i:29694128 original size:100 final size:100
Alignment explanation
Indices: 29693979--29694258 Score: 420
Period size: 100 Copynumber: 2.8 Consensus size: 100
29693969 TACCATATGA
* * *
29693979 GGGTATTTTGGTCATTTTACTCTATGAGGGTATTTCAGTCATTTTACCATATAGGGGTATTTTGG
1 GGGTATTTTGGTTATTTTACCCTATGAGGGTATTTCGGTCATTTTACCATATAGGGGTATTTTGG
* *
29694044 TCATTTTACCATATTTCGATCATTCTACCCTATTG
66 TCATTTTACCATATTTCGATCATTCTACCCAATGG
29694079 GGGTATTTTGGTTATTTTACCCTATGAGGGTATTTCGGTCATTTTACCATATAGGGGTATTTTGG
1 GGGTATTTTGGTTATTTTACCCTATGAGGGTATTTCGGTCATTTTACCATATAGGGGTATTTTGG
*
29694144 TCATTTTACCATATTTCGGTCATTCTACCCAATGG
66 TCATTTTACCATATTTCGATCATTCTACCCAATGG
* * * * * * *
29694179 GGGTATTTCGGTTATTCTACCCTATTG-GGGTATTTTGGTCATTTTACCCTTTGGGGGTATTTCG
1 GGGTATTTTGGTTATTTTACCCTA-TGAGGGTATTTCGGTCATTTTACCATATAGGGGTATTTTG
29694243 GTCATTTTACC-TATTT
65 GTCATTTTACCATATTT
29694259 TAAGGTCTTG
Statistics
Matches: 166, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
99 5 0.03
100 159 0.96
101 2 0.01
ACGTcount: A:0.19, C:0.16, G:0.20, T:0.45
Consensus pattern (100 bp):
GGGTATTTTGGTTATTTTACCCTATGAGGGTATTTCGGTCATTTTACCATATAGGGGTATTTTGG
TCATTTTACCATATTTCGATCATTCTACCCAATGG
Found at i:29694159 original size:73 final size:73
Alignment explanation
Indices: 29694082--29694226 Score: 209
Period size: 73 Copynumber: 2.0 Consensus size: 73
29694072 CCTATTGGGG
* * * * *
29694082 TATTTTGGTTATTTTACCCTATGAGGGTATTTCGGTCATTTTACCATATAGGGGTATTTTGGTCA
1 TATTTCGGTCATTCTACCCAATGAGGGTATTTCGGTCATTCTACCATATAGGGGTATTTTGGTCA
29694147 TTTTACCA
66 TTTTACCA
* * * *
29694155 TATTTCGGTCATTCTACCCAATGGGGGTATTTCGGTTATTCTACCCTATTGGGGTATTTTGGTCA
1 TATTTCGGTCATTCTACCCAATGAGGGTATTTCGGTCATTCTACCATATAGGGGTATTTTGGTCA
29694220 TTTTACC
66 TTTTACC
29694227 CTTTGGGGGT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.45
Consensus pattern (73 bp):
TATTTCGGTCATTCTACCCAATGAGGGTATTTCGGTCATTCTACCATATAGGGGTATTTTGGTCA
TTTTACCA
Found at i:29694164 original size:19 final size:19
Alignment explanation
Indices: 29694136--29694172 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29694126 CATATAGGGG
* *
29694136 TATTTTGGTCATTTTACCA
1 TATTTCGGTCATTCTACCA
29694155 TATTTCGGTCATTCTACC
1 TATTTCGGTCATTCTACC
29694173 CAATGGGGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (19 bp):
TATTTCGGTCATTCTACCA
Found at i:29698020 original size:6 final size:6
Alignment explanation
Indices: 29698011--29698055 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
29698001 AAAAGAAAAA
*
29698011 AAATAT AAATAT AAATAT AAAATAT AAAAAT AAATA- AAATAT AAA
1 AAATAT AAATAT AAATAT -AAATAT AAATAT AAATAT AAATAT AAA
29698056 ACTAAATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 5 0.14
6 24 0.69
7 6 0.17
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (6 bp):
AAATAT
Found at i:29698049 original size:17 final size:17
Alignment explanation
Indices: 29698010--29698067 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
29698000 CAAAAGAAAA
*
29698010 AAAATATAAATATAAATAT
1 AAAATATAAAAAT-AA-AT
29698029 AAAATATAAAAATAAAT
1 AAAATATAAAAATAAAT
*
29698046 AAAATATAAAACTAAAT
1 AAAATATAAAAATAAAT
*
29698063 GAAAT
1 AAAAT
29698068 CACTTTAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 22 0.61
18 2 0.06
19 12 0.33
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
AAAATATAAAAATAAAT
Found at i:29699456 original size:19 final size:19
Alignment explanation
Indices: 29699432--29699544 Score: 145
Period size: 19 Copynumber: 5.8 Consensus size: 19
29699422 AATTTTTGAG
*
29699432 GATATGCAATCTTATATAT
1 GATATGCAATCTTAGATAT
* *
29699451 GATATGCAATCCTAGAGAT
1 GATATGCAATCTTAGATAT
29699470 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29699489 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
* ** *
29699510 GATGTATAATTTTAGATAT
1 GATATGCAATCTTAGATAT
29699529 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
29699545 ATATATGATT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 60 0.76
21 19 0.24
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29699531 original size:59 final size:59
Alignment explanation
Indices: 29699433--29699544 Score: 161
Period size: 59 Copynumber: 1.9 Consensus size: 59
29699423 ATTTTTGAGG
* *
29699433 ATATGCAATCTTATATATGATATGCAATCCTAGAGATGATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATACAATCCTAGAGATGATATGCAATCTTAGATATGAT
* * ** *
29699492 ATATGCAATCTTAGATATGATGTATAATTTTAGATATGATATGCAATCTTAGA
1 ATATGCAATCTTAGATATGATATACAATCCTAGAGATGATATGCAATCTTAGA
29699545 ATATATGATT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (59 bp):
ATATGCAATCTTAGATATGATATACAATCCTAGAGATGATATGCAATCTTAGATATGAT
Found at i:29700852 original size:98 final size:98
Alignment explanation
Indices: 29700733--29700929 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
29700723 TAAAAAATCA
* * * *
29700733 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTATAATTTC
*
29700798 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCCTTTAAAG
*
29700831 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATCGTGCCCTAACGTATTGGGTATAATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTATAATTTC
29700896 TTAAATCTTGGATAAGTGGATGTTCCTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCCTTTAAAG
29700929 T
1 T
29700930 TTTATTGTAT
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTATAATTTC
TTAAATCTTGGATAAGTGGATGTTCCTTTAAAG
Found at i:29702618 original size:32 final size:32
Alignment explanation
Indices: 29702582--29702672 Score: 164
Period size: 32 Copynumber: 2.8 Consensus size: 32
29702572 TAAATTATGT
29702582 TAATATCTCTTTCGAGAGTAAGAGCAAAATGC
1 TAATATCTCTTTCGAGAGTAAGAGCAAAATGC
*
29702614 TAATATCTCTTTCGAGAGTAAGAGCAAAATGT
1 TAATATCTCTTTCGAGAGTAAGAGCAAAATGC
*
29702646 TAATATCTCTTTCGAAAGTAAGAGCAA
1 TAATATCTCTTTCGAGAGTAAGAGCAA
29702673 CTAACTCTAG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (32 bp):
TAATATCTCTTTCGAGAGTAAGAGCAAAATGC
Found at i:29711195 original size:27 final size:26
Alignment explanation
Indices: 29711165--29711333 Score: 160
Period size: 27 Copynumber: 6.3 Consensus size: 26
29711155 GATTTATAGG
**
29711165 AAAATGACCAAAATACCACCGGAGGGT
1 AAAATGACCAAAATACC-CCAAAGGGT
*
29711192 AAAATGACCAAAATATCCTC-AAGCGGT
1 AAAATGACCAAAATA-CCCCAAAG-GGT
*
29711219 AAAATGACCGAAATACCCCCAAAGGGT
1 AAAATGACCAAAATA-CCCCAAAGGGT
* * * *
29711246 AAAATGATCGAAATACCCTAGAGGGT
1 AAAATGACCAAAATACCCCAAAGGGT
* *
29711272 AAAATGACTAAAATACCCCCAAAAGGT
1 AAAATGACCAAAATA-CCCCAAAGGGT
** *
29711299 AAAATGACTGAAATACCCTCATAGGGT
1 AAAATGACCAAAATACCC-CAAAGGGT
29711326 AAAATGAC
1 AAAATGAC
29711334 TGTTATATCT
Statistics
Matches: 120, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
26 26 0.22
27 89 0.74
28 5 0.04
ACGTcount: A:0.46, C:0.21, G:0.18, T:0.16
Consensus pattern (26 bp):
AAAATGACCAAAATACCCCAAAGGGT
Found at i:29711233 original size:54 final size:54
Alignment explanation
Indices: 29711165--29711333 Score: 216
Period size: 54 Copynumber: 3.1 Consensus size: 54
29711155 GATTTATAGG
* ** * *
29711165 AAAATGACCAAAATACCACCGGAGGGTAAAATGACCAAAATATCCTCA-AGCGGT
1 AAAATGACCAAAATACCCCCAAAGGGTAAAATGACCGAAATACCCTCAGAG-GGT
* *
29711219 AAAATGACCGAAATACCCCCAAAGGGTAAAATGATCGAAATACCCT-AGAGGGT
1 AAAATGACCAAAATACCCCCAAAGGGTAAAATGACCGAAATACCCTCAGAGGGT
* * * *
29711272 AAAATGACTAAAATACCCCCAAAAGGTAAAATGACTGAAATACCCTCATAGGGT
1 AAAATGACCAAAATACCCCCAAAGGGTAAAATGACCGAAATACCCTCAGAGGGT
29711326 AAAATGAC
1 AAAATGAC
29711334 TGTTATATCT
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
53 45 0.45
54 55 0.55
ACGTcount: A:0.46, C:0.21, G:0.18, T:0.16
Consensus pattern (54 bp):
AAAATGACCAAAATACCCCCAAAGGGTAAAATGACCGAAATACCCTCAGAGGGT
Found at i:29711334 original size:27 final size:27
Alignment explanation
Indices: 29711187--29711335 Score: 169
Period size: 27 Copynumber: 5.6 Consensus size: 27
29711177 ATACCACCGG
** *
29711187 AGGGTAAAATGACCAAAATATCCTC-A
1 AGGGTAAAATGACTGAAATACCCTCAA
* *
29711213 AGCGGTAAAATGACCGAAATACCCCCAA
1 AG-GGTAAAATGACTGAAATACCCTCAA
*
29711241 AGGGTAAAATGA-TCGAAATACCCT-AG
1 AGGGTAAAATGACT-GAAATACCCTCAA
* *
29711267 AGGGTAAAATGACTAAAATACCCCCAA
1 AGGGTAAAATGACTGAAATACCCTCAA
* *
29711294 AAGGTAAAATGACTGAAATACCCTCAT
1 AGGGTAAAATGACTGAAATACCCTCAA
29711321 AGGGTAAAATGACTG
1 AGGGTAAAATGACTG
29711336 TTATATCTCT
Statistics
Matches: 104, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
26 23 0.22
27 78 0.75
28 3 0.03
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.17
Consensus pattern (27 bp):
AGGGTAAAATGACTGAAATACCCTCAA
Found at i:29714465 original size:13 final size:13
Alignment explanation
Indices: 29714447--29714471 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29714437 TTAAAACTAA
29714447 AATTAACTAAATT
1 AATTAACTAAATT
29714460 AATTAACTAAAT
1 AATTAACTAAAT
29714472 AACACAACAA
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAACTAAATT
Found at i:29717493 original size:33 final size:33
Alignment explanation
Indices: 29717456--29717720 Score: 284
Period size: 33 Copynumber: 8.0 Consensus size: 33
29717446 TCAACATAAG
* * * *
29717456 TGATTGGAACATCTATCAAGGAAGCTTCATAAA
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* *
29717489 TGATTGGAACATCTATCATGGCAGTTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* ** * *
29717522 TGATTGGAACATCTATCAGGGCAACTTTGTTAA
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* *
29717555 TGATTGAAACATCTATCGGGGCAGCTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
*
29717588 TTATTGGAACATCTATC-GAGGCAGCTTCATCAT
1 TGATTGGAACATCTATCAG-GGCAGCTTCATCAT
* * * * * *
29717621 TGTTTGGAAAATTTATCAGGGTAGGC-TCGTCAA
1 TGATTGGAACATCTATCAGGGCA-GCTTCATCAT
29717654 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* *
29717687 TGATTGGATCATCTA-CTGGGGCAGCTTCATCAT
1 TGATTGGAACATCTATC-AGGGCAGCTTCATCAT
29717720 T
1 T
29717721 TTGTTTGATT
Statistics
Matches: 191, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
32 4 0.02
33 184 0.96
34 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (33 bp):
TGATTGGAACATCTATCAGGGCAGCTTCATCAT
Found at i:29717628 original size:99 final size:99
Alignment explanation
Indices: 29717456--29717720 Score: 329
Period size: 99 Copynumber: 2.7 Consensus size: 99
29717446 TCAACATAAG
* * * * *
29717456 TGATTGGAACATCTATCAAGGAAGCTTCATAAATGATTGGAACATCTATC-ATGGCAGTTTCATC
1 TGATTGGAACATCTATCAGGGCAGCTTCATCATTGATTGGAACATCTATCGA-GGCAGCTTCATC
* * *
29717520 ATTGATTGGAACATCTATCAGGGCA-ACTTTGTTAA
65 ATTGATTGGAAAATCTATCAGGGCAGAC-TCGTCAA
* * *
29717555 TGATTGAAACATCTATCGGGGCAGCTTCATCATTTATTGGAACATCTATCGAGGCAGCTTCATCA
1 TGATTGGAACATCTATCAGGGCAGCTTCATCATTGATTGGAACATCTATCGAGGCAGCTTCATCA
* * * *
29717620 TTGTTTGGAAAATTTATCAGGGTAGGCTCGTCAA
66 TTGATTGGAAAATCTATCAGGGCAGACTCGTCAA
* *
29717654 TGATTGGAACATCTATCAGGGCAGCTTCATCATTGATTGGATCATCTA-CTGGGGCAGCTTCATC
1 TGATTGGAACATCTATCAGGGCAGCTTCATCATTGATTGGAACATCTATC-GAGGCAGCTTCATC
29717718 ATT
65 ATT
29717721 TTGTTTGATT
Statistics
Matches: 143, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
98 1 0.01
99 140 0.98
100 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (99 bp):
TGATTGGAACATCTATCAGGGCAGCTTCATCATTGATTGGAACATCTATCGAGGCAGCTTCATCA
TTGATTGGAAAATCTATCAGGGCAGACTCGTCAA
Found at i:29720833 original size:17 final size:17
Alignment explanation
Indices: 29720813--29720848 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
29720803 TATTATCTCC
29720813 TTAGTTGAAGCATCTGG
1 TTAGTTGAAGCATCTGG
29720830 TTAGTTGAAGCATCTGG
1 TTAGTTGAAGCATCTGG
29720847 TT
1 TT
29720849 CAATATTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.11, G:0.28, T:0.39
Consensus pattern (17 bp):
TTAGTTGAAGCATCTGG
Found at i:29721617 original size:29 final size:29
Alignment explanation
Indices: 29721575--29721631 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
29721565 AATAATATTG
*
29721575 TACTCTTCTATCTACCAGCAATTGTGCTT
1 TACTCTTCTATCTACCAACAATTGTGCTT
29721604 TACTCTTCTATCTACCAACAATTGTGCT
1 TACTCTTCTATCTACCAACAATTGTGCT
29721632 AACTTATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (29 bp):
TACTCTTCTATCTACCAACAATTGTGCTT
Found at i:29723376 original size:5 final size:5
Alignment explanation
Indices: 29723366--29723399 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
29723356 TATCGTACTT
*
29723366 ACCTC ACCTC ACCTC ACCTT ACCTC ACCTC ACCT
1 ACCTC ACCTC ACCTC ACCTC ACCTC ACCTC ACCT
29723400 TGTGGCTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.21, C:0.56, G:0.00, T:0.24
Consensus pattern (5 bp):
ACCTC
Found at i:29725984 original size:26 final size:26
Alignment explanation
Indices: 29725855--29725996 Score: 151
Period size: 27 Copynumber: 5.3 Consensus size: 26
29725845 CAGAAAGGTT
* * *
29725855 GGTAAAATGACTGAACTACCCTCGAAG
1 GGTAAAAT-ACTGAAATACCCCCGATG
* * *
29725882 GGTAAAATGACCGAATTACCCCCGAAG
1 GGTAAAAT-ACTGAAATACCCCCGATG
*
29725909 GGTAAAATTA-TCGAAATACCCTCGATG
1 GGTAAAA-TACT-GAAATACCCCCGATG
*
29725936 GGTAAAATTACTGAAATAACCCCGATG
1 GGTAAAA-TACTGAAATACCCCCGATG
*
29725963 GGTAAAATACTGAAATACCCCCAATG
1 GGTAAAATACTGAAATACCCCCGATG
29725989 GGTAAAAT
1 GGTAAAAT
29725997 TGACTATTAT
Statistics
Matches: 101, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
26 25 0.25
27 74 0.73
28 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (26 bp):
GGTAAAATACTGAAATACCCCCGATG
Found at i:29732338 original size:27 final size:27
Alignment explanation
Indices: 29732300--29732736 Score: 366
Period size: 27 Copynumber: 16.2 Consensus size: 27
29732290 ATTCGTGGGC
*
29732300 AAATGACCGAAATACCCTCGAAAGGTA
1 AAATGATCGAAATACCCTCGAAAGGTA
*
29732327 AAATGATCGAAATACCCT-TAAAGGATA
1 AAATGATCGAAATACCCTCGAAAGG-TA
* *
29732354 AAATGACCGAAATACCC-CTAAAGGTTA
1 AAATGATCGAAATACCCTCGAAAGG-TA
*
29732381 AAATGA-CAGAAATA-CCTCTGAAGGGTA
1 AAATGATC-GAAATACCCTC-GAAAGGTA
* *
29732408 AAATGA-CTGAAATACCCTTGAAGGGTA
1 AAATGATC-GAAATACCCTCGAAAGGTA
*
29732435 AAATGATCGAAATACCC-CTAAAAGGTA
1 AAATGATCGAAATACCCTC-GAAAGGTA
29732462 AAATGATCGAAATACCCTC-AAAGGGTA
1 AAATGATCGAAATACCCTCGAAA-GGTA
* * * *
29732489 AAATGACCAAAACACCCTC-AAAGGGGA
1 AAATGATCGAAATACCCTCGAAA-GGTA
* * *
29732516 CAATGACCAAAATACCCTC-AAAGGGTA
1 AAATGATCGAAATACCCTCGAAA-GGTA
* * *
29732543 AAATGACCGAAATACCTTCGAAGGGTA
1 AAATGATCGAAATACCCTCGAAAGGTA
* *
29732570 AAATGATTGAAATAACCC-CGAATGGTA
1 AAATGATCGAAAT-ACCCTCGAAAGGTA
*
29732597 AAATGATTGAAATATCCCT-GAAAGGTA
1 AAATGATCGAAATA-CCCTCGAAAGGTA
* **
29732624 AAATGA-CTAAAATACCCTCGATGGGTA
1 AAATGATC-GAAATACCCTCGAAAGGTA
* * *
29732651 AAATAACCGAAATATCCC-CAAAAGGTA
1 AAATGATCGAAATA-CCCTCGAAAGGTA
*
29732678 AAATGATC-AAA-AACCTCCGAAAGGTA
1 AAATGATCGAAATACCCT-CGAAAGGTA
*
29732704 AAATGATCGAAATACCCTC-ATAGGGTA
1 AAATGATCGAAATACCCTCGA-AAGGTA
29732731 AAATGA
1 AAATGA
29732737 CTGATATACC
Statistics
Matches: 345, Mismatches: 42, Indels: 46
0.80 0.10 0.11
Matches are distributed among these distances:
24 2 0.01
25 1 0.00
26 36 0.10
27 284 0.82
28 22 0.06
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.19
Consensus pattern (27 bp):
AAATGATCGAAATACCCTCGAAAGGTA
Found at i:29732437 original size:81 final size:80
Alignment explanation
Indices: 29732300--29732748 Score: 439
Period size: 81 Copynumber: 5.5 Consensus size: 80
29732290 ATTCGTGGGC
* * * *
29732300 AAATGACCGAAATACCCTCGAAAGGTAAAATGA-TCGAAATACCCTTAAAGGATAAAATGACCGA
1 AAATGA-CGAAATACCCTCGAAGGGTAAAATGACT-GAAATACCCTCAAAGGGTAAAATGATCGA
29732364 AATACCCCT-AAAGGTTA
64 AATACCCCTAAAAGG-TA
**
29732381 AAATGACAGAAATA-CCTCTGAAGGGTAAAATGACTGAAATACCCTTGAAGGGTAAAATGATCGA
1 AAATGAC-GAAATACCCTC-GAAGGGTAAAATGACTGAAATACCCTCAAAGGGTAAAATGATCGA
29732445 AATACCCCTAAAAGGTA
64 AATACCCCTAAAAGGTA
* ** * * * * *
29732462 AAATGATCGAAATACCCTCAAAGGGTAAAATGACCAAAACACCCTCAAAGGGGACAATGACCAAA
1 AAATGA-CGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCTCAAAGGGTAAAATGATCGAA
*
29732527 ATA-CCCTCAAAGGGTA
65 ATACCCCT-AAAAGGTA
* * * * *
29732543 AAATGACCGAAATACCTTCGAAGGGTAAAATGATTGAAATAACCC-CGAATGGTAAAATGATTGA
1 AAATGA-CGAAATACCCTCGAAGGGTAAAATGACTGAAAT-ACCCTCAAAGGGTAAAATGATCGA
* *
29732607 AATATCCCTGAAAGGTA
64 AATACCCCTAAAAGGTA
* * * * *
29732624 AAATGACTAAAATACCCTCGATGGGTAAAATAACCGAAATATCCC-CAAAAGGTAAAATGATC-A
1 AAATGAC-GAAATACCCTCGAAGGGTAAAATGACTGAAATA-CCCTCAAAGGGTAAAATGATCGA
* *
29732687 AAAACCTCC-GAAAGGTA
64 AATACC-CCTAAAAGGTA
*
29732704 AAATGATCGAAATACCCTC-ATAGGGTAAAATGACTGATATACCCT
1 AAATGA-CGAAATACCCTCGA-AGGGTAAAATGACTGAAATACCCT
29732749 TAGGAGTTGA
Statistics
Matches: 306, Mismatches: 47, Indels: 31
0.80 0.12 0.08
Matches are distributed among these distances:
79 4 0.01
80 56 0.18
81 227 0.74
82 19 0.06
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (80 bp):
AAATGACGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCTCAAAGGGTAAAATGATCGAAA
TACCCCTAAAAGGTA
Found at i:29733012 original size:26 final size:27
Alignment explanation
Indices: 29732948--29733023 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 27
29732938 ACTGTAGACC
** *
29732948 TACTGGTGGCTTTGCCACATATACTGT
1 TACTGGTGGCTTTGCTGCATATACTAT
** *
29732975 TACTGGCAGCTTTGCTGCA-ATTCTAT
1 TACTGGTGGCTTTGCTGCATATACTAT
*
29733001 TACTGGTGGCTTTCCTGCGATAT
1 TACTGGTGGCTTTGCTGC-ATAT
29733024 TGGTGTATTG
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
26 20 0.53
27 16 0.42
28 2 0.05
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (27 bp):
TACTGGTGGCTTTGCTGCATATACTAT
Found at i:29737882 original size:20 final size:20
Alignment explanation
Indices: 29737837--29737890 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
29737827 TGAACCCTTC
* *
29737837 CATTTACTTTCTTTTCGTAT
1 CATTTACTTACTTTTCATAT
*
29737857 CATTTACTTACTTTTCATTT
1 CATTTACTTACTTTTCATAT
*
29737877 CGTTTACTTACTTT
1 CATTTACTTACTTT
29737891 AGCTTAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.20, G:0.04, T:0.59
Consensus pattern (20 bp):
CATTTACTTACTTTTCATAT
Found at i:29738872 original size:138 final size:137
Alignment explanation
Indices: 29738620--29738888 Score: 337
Period size: 138 Copynumber: 2.0 Consensus size: 137
29738610 TAAATGGGTC
* * *
29738620 TGCTCACACAAGTTGACAAACGGAATATAGCTACACAATGTCGCTTACACAAGCTTACGAGTATC
1 TGCTCACACAAGTTGACAAACGGAATATAGCTACACAATGTCCCTTACACAAGCTGACGAATATC
* ** * * *
29738685 CATAACAAATGTCAGAACTTAGCCATCAGTAGAACATTCAGGACTAGCACCCTG-AACATAGTAA
66 CACAACAAATGTCAGAACACAGCCATCACTAGAACATTCAAGACCAGCACCC-GAAACATAGTAA
29738749 CCTACATT
130 CCTACATT
** *
29738757 TGCTCACACAAGTTGACAGTCGGAATGTAAGCTACACAATG-CCCTTCACACAAGCTGACGAATA
1 TGCTCACACAAGTTGACAAACGGAATAT-AGCTACACAATGTCCCTT-ACACAAGCTGACGAATA
* ** *
29738821 TCTACAACAAATGTC-GAACCACAGCCATCACTAGGGCATTCAAGACCAGCACCCGAAACATGGT
64 TCCACAACAAATGTCAGAA-CACAGCCATCACTAGAACATTCAAGACCAGCACCCGAAACATAGT
29738885 AACC
128 AACC
29738889 CTAATGACAT
Statistics
Matches: 112, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
137 33 0.29
138 79 0.71
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.20
Consensus pattern (137 bp):
TGCTCACACAAGTTGACAAACGGAATATAGCTACACAATGTCCCTTACACAAGCTGACGAATATC
CACAACAAATGTCAGAACACAGCCATCACTAGAACATTCAAGACCAGCACCCGAAACATAGTAAC
CTACATT
Found at i:29739278 original size:17 final size:19
Alignment explanation
Indices: 29739256--29739295 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
29739246 CATTTTTACA
29739256 AAATT-ACC-TTTTATTGC
1 AAATTAACCATTTTATTGC
29739273 AAATTAACCATTTTTATTGC
1 AAATTAACCA-TTTTATTGC
29739293 AAA
1 AAA
29739296 CCCATGCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 3 0.15
20 12 0.60
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (19 bp):
AAATTAACCATTTTATTGC
Found at i:29741546 original size:30 final size:31
Alignment explanation
Indices: 29741478--29741536 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
29741468 GACCCTTAAA
** *
29741478 ATATTTACACTATTGGTCCTTCAAATTTTTC
1 ATATTTACACTATTAATCCCTCAAATTTTTC
29741509 ATATTTACACT-TTAATCCCTCAAATTTT
1 ATATTTACACTATTAATCCCTCAAATTTT
29741537 GAGTATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.29, C:0.20, G:0.03, T:0.47
Consensus pattern (31 bp):
ATATTTACACTATTAATCCCTCAAATTTTTC
Found at i:29742069 original size:5 final size:5
Alignment explanation
Indices: 29742059--29742087 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
29742049 GATAATAAAT
29742059 TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
29742088 TCAAATTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:29744088 original size:26 final size:27
Alignment explanation
Indices: 29744029--29744088 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
29744019 CTAATAGATG
29744029 AAAATGACCGTAATGCCCATGTAAGGT
1 AAAATGACCGTAATGCCCATGTAAGGT
* * *
29744056 AAAATGATCGTGATGCCCTTGT-AGGT
1 AAAATGACCGTAATGCCCATGTAAGGT
29744082 AAAATGA
1 AAAATGA
29744089 ATGTAATACC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 11 0.37
27 19 0.63
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (27 bp):
AAAATGACCGTAATGCCCATGTAAGGT
Found at i:29744197 original size:24 final size:24
Alignment explanation
Indices: 29744161--29744222 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
29744151 CCCCTCGAGG
** *
29744161 TTAAATGTTTGATTTGTCTGTGAT
1 TTAAATGACTGATTTGCCTGTGAT
29744185 TTAAATGACTGATTTGCCTGTGAT
1 TTAAATGACTGATTTGCCTGTGAT
**
29744209 TTGTATGACTGATT
1 TTAAATGACTGATT
29744223 CTGAGCATGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.23, C:0.08, G:0.21, T:0.48
Consensus pattern (24 bp):
TTAAATGACTGATTTGCCTGTGAT
Found at i:29744392 original size:26 final size:26
Alignment explanation
Indices: 29744356--29744458 Score: 118
Period size: 26 Copynumber: 4.0 Consensus size: 26
29744346 CTTGCCACGT
29744356 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
* * *
29744382 ATACTGTTACTGGCAGTTTTGTTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
* * *
29744408 TTACTGTTACTGGCAGCTTTACTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
* *
29744434 -TCATTATCACTGGCAGCTTTGCTGC
1 AT-ACTATTACTGGCAGCTTTGCTGC
29744459 AATATTGGTG
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
25 1 0.02
26 64 0.98
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTGCG
Found at i:29750613 original size:67 final size:67
Alignment explanation
Indices: 29750494--29750631 Score: 213
Period size: 67 Copynumber: 2.1 Consensus size: 67
29750484 GAGGTAGGGA
* * * *
29750494 CACACGGCCGTGTCCCAGCCCGTGTCCGTGCCTATGTAACTCACTGACTTGGGTCACACAGACAA
1 CACAAGGCCGTGTCCCAGCCCATGTCCGTGCCTATGTAACTCACTAAATTGGGTCACACAGACAA
29750559 GC
66 GC
* * *
29750561 CACAAGGCCGTGTCCCAGCCCATGTCCGTGCCTGTGTAACTCACTAAATTGGGTCACACGGCCAA
1 CACAAGGCCGTGTCCCAGCCCATGTCCGTGCCTATGTAACTCACTAAATTGGGTCACACAGACAA
29750626 GC
66 GC
29750628 CACA
1 CACA
29750632 CACCCGTGTG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.22, C:0.36, G:0.23, T:0.19
Consensus pattern (67 bp):
CACAAGGCCGTGTCCCAGCCCATGTCCGTGCCTATGTAACTCACTAAATTGGGTCACACAGACAA
GC
Found at i:29750639 original size:67 final size:67
Alignment explanation
Indices: 29750501--29750650 Score: 203
Period size: 67 Copynumber: 2.2 Consensus size: 67
29750491 GGACACACGG
* * *
29750501 CCGTGTCCCAGCCCGTGTCCGTGCCTATGTAACTCACTGACTTGGGTCACACAGACAAGCCACAA
1 CCGTGTCCCAGCCCATGTCCGTGCCTATGTAACTCACTAAATTGGGTCACACAGACAAGCCACAA
*
29750566 GG
66 GC
* * *
29750568 CCGTGTCCCAGCCCATGTCCGTGCCTGTGTAACTCACTAAATTGGGTCACACGGCCAAGCCACAC
1 CCGTGTCCCAGCCCATGTCCGTGCCTATGTAACTCACTAAATTGGGTCACACAGACAAGCCACA-
29750633 A-C
65 AGC
* *
29750635 CCGTGTGCCAGGCCAT
1 CCGTGTCCCAGCCCAT
29750651 ATGCCCGTGT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
67 72 0.99
68 1 0.01
ACGTcount: A:0.21, C:0.36, G:0.23, T:0.19
Consensus pattern (67 bp):
CCGTGTCCCAGCCCATGTCCGTGCCTATGTAACTCACTAAATTGGGTCACACAGACAAGCCACAA
GC
Found at i:29752252 original size:21 final size:20
Alignment explanation
Indices: 29752201--29752252 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
29752191 TAAATAATAA
* *
29752201 TAATTTATTTAACCTAAAAT
1 TAATTTATTAAAACTAAAAT
* *
29752221 AAATTGGATTAAAACTAAAAT
1 TAATT-TATTAAAACTAAAAT
29752242 TAATTATATTA
1 TAATT-TATTA
29752253 TGAATTAATA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (20 bp):
TAATTTATTAAAACTAAAAT
Found at i:29753822 original size:20 final size:19
Alignment explanation
Indices: 29753795--29753836 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
29753785 CTTTCCAAAT
29753795 TTTCTTACTTT-CATTTGCA
1 TTTCTTACTTTCCA-TTGCA
29753814 TTTCATTACTTTCCATTGCA
1 TTTC-TTACTTTCCATTGCA
29753834 TTT
1 TTT
29753837 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 15 0.71
21 2 0.10
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTCTTACTTTCCATTGCA
Found at i:29755377 original size:20 final size:19
Alignment explanation
Indices: 29755350--29755391 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
29755340 CTTTCCAAAT
29755350 TTTCTTACTTT-CATTTGCA
1 TTTCTTACTTTCCA-TTGCA
29755369 TTTCATTACTTTCCATTGCA
1 TTTC-TTACTTTCCATTGCA
29755389 TTT
1 TTT
29755392 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 15 0.71
21 2 0.10
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTCTTACTTTCCATTGCA
Found at i:29757517 original size:79 final size:82
Alignment explanation
Indices: 29757406--29757590 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
29757396 GCTACTCGTT
* * *
29757406 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
29757469 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
29757486 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
29757549 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
29757566 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29757591 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:29757590 original size:40 final size:40
Alignment explanation
Indices: 29757387--29757590 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
29757377 CGGAATTTAA
** *
29757387 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
29757427 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
29757467 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
29757506 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
29757546 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
29757586 CCGGA
1 CCGGA
29757591 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:29759503 original size:2 final size:2
Alignment explanation
Indices: 29759496--29759520 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29759486 ATACTAACAC
29759496 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
29759521 GATTTAATAA
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:29760144 original size:20 final size:20
Alignment explanation
Indices: 29760121--29760158 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29760111 CCAAATTTTT
*
29760121 TTACTTTCATTTGCATTTCA
1 TTACTTTCAGTTGCATTTCA
*
29760141 TTACTTTCCGTTGCATTT
1 TTACTTTCAGTTGCATTT
29760159 ACTTTCTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.21, G:0.08, T:0.55
Consensus pattern (20 bp):
TTACTTTCAGTTGCATTTCA
Found at i:29761817 original size:27 final size:25
Alignment explanation
Indices: 29761777--29761954 Score: 131
Period size: 27 Copynumber: 6.6 Consensus size: 25
29761767 TTAAACTGCT
*
29761777 ATGACCGAAATACCCTCATAGGGTAGA
1 ATGACC-AAATACCC-CATAGGGTAAA
*
29761804 ATGACCAAACTACCCCCATAGGGAAAA
1 ATGACCAAA-TA-CCCCATAGGGTAAA
*
29761831 ATGATCGAAATACCCCTATAGGGTAAA
1 ATGA-CCAAATACCCC-ATAGGGTAAA
* * *
29761858 ATGACTGAAATACCCCCATATGATAAA
1 ATGAC-CAAATA-CCCCATAGGGTAAA
* * * *
29761885 ATGACTGAAATTCCCCCATATGATAAA
1 ATGAC-CAAA-TACCCCATAGGGTAAA
*
29761912 ATGACTGAAATACCCCAATAGGGTAAA
1 ATGAC-CAAATACCCC-ATAGGGTAAA
*
29761939 ATGAACGAAATACCCC
1 ATG-ACCAAATACCCC
29761955 CATCGAAATA
Statistics
Matches: 132, Mismatches: 10, Indels: 18
0.82 0.06 0.11
Matches are distributed among these distances:
26 13 0.10
27 105 0.80
28 14 0.11
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (25 bp):
ATGACCAAATACCCCATAGGGTAAA
Found at i:29761955 original size:54 final size:54
Alignment explanation
Indices: 29761777--29762276 Score: 223
Period size: 54 Copynumber: 9.1 Consensus size: 54
29761767 TTAAACTGCT
* * * * *
29761777 ATGACCGAAATACCCTCATAGGGTAGAATGAC-CAAACTACCCCCATAGGGAAAA
1 ATGAACGAAATACCCCCATAGGGTAAAATGACTGAAA-TACCCCCATAGGGTAAA
* * * *
29761831 ATGATCGAAATACCCCTATAGGGTAAAATGACTGAAATACCCCCATATGATAAA
1 ATGAACGAAATACCCCCATAGGGTAAAATGACTGAAATACCCCCATAGGGTAAA
* * * *
29761885 ATG-ACTGAAATTCCCCCATATGATAAAATGACTGAAATACCCCAATAGGGTAAA
1 ATGAAC-GAAATACCCCCATAGGGTAAAATGACTGAAATACCCCCATAGGGTAAA
* ** * * * ** * * *
29761939 ATGAACGAAATACCCCCATCGAAATACCCCCATAAGGTAGAATGACCGAAATGCCC-CATAGGTT
1 ATGAACGAAATACCCCCATAG-GGTA-----A-AA--T-GACTGA--AATACCCCCATA-GGGTA
29762003 AA
53 AA
*** ** * * * * *
29762005 AATGACCGAA-ATACCCCCATAAGGTAAAATGACTGAAATACCTCCACAAGG-AAA
1 ATGAACGAAATA-CCCCC-ATAGGGTAAAATGACTGAAATACCCCCATAGGGTAAA
* * * * *
29762059 ATGACCGAAATATCCCCATAGGGTAAAAT-AATCGAAATACCCCTATAAGGTAAA
1 ATGAACGAAATACCCCCATAGGGTAAAATGACT-GAAATACCCCCATAGGGTAAA
** * * *
29762113 ATGATTGAAATACCCCTATAAGGTAAAATGA-TCGAAATACCCCCGTAGGGTAAA
1 ATGAACGAAATACCCCCATAGGGTAAAATGACT-GAAATACCCCCATAGGGTAAA
* ** *
29762167 ATG-ACTGAAATATCCTAATAGGGTAAAATGA-TCGAAA-A-ACCCATAGGGTAAA
1 ATGAAC-GAAATACCCCCATAGGGTAAAATGACT-GAAATACCCCCATAGGGTAAA
* * ** * * *
29762219 ATGACCAAAATACCCTTACAAGGTAGAATGA-TCGAAATACCCCCATAGGGTAAA
1 ATGAACGAAATACCCCCATAGGGTAAAATGACT-GAAATACCCCCATAGGGTAAA
29762273 ATGA
1 ATGA
29762277 TTGTTATATC
Statistics
Matches: 337, Mismatches: 82, Indels: 54
0.71 0.17 0.11
Matches are distributed among these distances:
52 42 0.12
53 29 0.09
54 205 0.61
55 17 0.05
56 2 0.01
57 5 0.01
58 1 0.00
60 3 0.01
61 3 0.01
63 1 0.00
64 5 0.01
65 2 0.01
66 20 0.06
67 2 0.01
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (54 bp):
ATGAACGAAATACCCCCATAGGGTAAAATGACTGAAATACCCCCATAGGGTAAA
Found at i:29761963 original size:14 final size:14
Alignment explanation
Indices: 29761944--29761971 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29761934 GTAAAATGAA
29761944 CGAAATACCCCCAT
1 CGAAATACCCCCAT
29761958 CGAAATACCCCCAT
1 CGAAATACCCCCAT
29761972 AAGGTAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.43, G:0.07, T:0.14
Consensus pattern (14 bp):
CGAAATACCCCCAT
Found at i:29761983 original size:41 final size:41
Alignment explanation
Indices: 29761918--29761995 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
29761908 TAAAATGACT
*
29761918 GAAATACCCCAATAGGGTAAAATGAACGAAATACCCCCATC
1 GAAATACCCCAATAAGGTAAAATGAACGAAATACCCCCATC
* * * *
29761959 GAAATACCCCCATAAGGTAGAATGACCGAAATGCCCC
1 GAAATACCCCAATAAGGTAAAATGAACGAAATACCCC
29761996 ATAGGTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.41, C:0.28, G:0.17, T:0.14
Consensus pattern (41 bp):
GAAATACCCCAATAAGGTAAAATGAACGAAATACCCCCATC
Found at i:29762031 original size:94 final size:95
Alignment explanation
Indices: 29761864--29762046 Score: 253
Period size: 94 Copynumber: 1.9 Consensus size: 95
29761854 TAAAATGACT
* * * *
29761864 GAAATACCCCCATATGATAAAATGACTGAAATTCCCCCATATGATAAAATGACTGAAATACCCCA
1 GAAATACCCCCATAAGATAAAATGACCGAAATTCCCCCATAGGATAAAATGACCGAAATACCCCA
*
29761929 ATAGGGTAAAATGAAC-GAAATACCCCCATC
66 ATAAGGTAAAATG-ACTGAAATACCCCCATC
* * * * *
29761959 GAAATACCCCCATAAGGTAGAATGACCGAAA-TGCCCCATAGGTTAAAATGACCGAAATACCCCC
1 GAAATACCCCCATAAGATAAAATGACCGAAATTCCCCCATAGGATAAAATGACCGAAATACCCCA
29762023 ATAAGGTAAAATGACTGAAATACC
66 ATAAGGTAAAATGACTGAAATACC
29762047 TCCACAAGGA
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
93 2 0.03
94 48 0.62
95 27 0.35
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.19
Consensus pattern (95 bp):
GAAATACCCCCATAAGATAAAATGACCGAAATTCCCCCATAGGATAAAATGACCGAAATACCCCA
ATAAGGTAAAATGACTGAAATACCCCCATC
Found at i:29762277 original size:27 final size:27
Alignment explanation
Indices: 29761956--29762277 Score: 316
Period size: 27 Copynumber: 12.1 Consensus size: 27
29761946 AAATACCCCC
*
29761956 ATCGAAATACCCCCATAAGGTAGAATG
1 ATCGAAATACCCCCATAAGGTAAAATG
* *
29761983 ACCGAAAT-GCCCCAT-AGGTTAAAATG
1 ATCGAAATACCCCCATAAGG-TAAAATG
*
29762009 ACCGAAATACCCCCATAAGGTAAAATG
1 ATCGAAATACCCCCATAAGGTAAAATG
* *
29762036 A-CTGAAATACCTCCACAAGG-AAAATG
1 ATC-GAAATACCCCCATAAGGTAAAATG
* * * *
29762062 ACCGAAATATCCCCATAGGGTAAAATA
1 ATCGAAATACCCCCATAAGGTAAAATG
*
29762089 ATCGAAATACCCCTATAAGGTAAAATG
1 ATCGAAATACCCCCATAAGGTAAAATG
* *
29762116 ATTGAAATACCCCTATAAGGTAAAATG
1 ATCGAAATACCCCCATAAGGTAAAATG
* *
29762143 ATCGAAATACCCCCGTAGGGTAAAATG
1 ATCGAAATACCCCCATAAGGTAAAATG
* ** *
29762170 A-CTGAAATATCCTAATAGGGTAAAATG
1 ATC-GAAATACCCCCATAAGGTAAAATG
* *
29762197 ATCGAAA-A-ACCCATAGGGTAAAATG
1 ATCGAAATACCCCCATAAGGTAAAATG
* * ** * *
29762222 ACCAAAATACCCTTACAAGGTAGAATG
1 ATCGAAATACCCCCATAAGGTAAAATG
*
29762249 ATCGAAATACCCCCATAGGGTAAAATG
1 ATCGAAATACCCCCATAAGGTAAAATG
29762276 AT
1 AT
29762278 TGTTATATCC
Statistics
Matches: 242, Mismatches: 43, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
25 22 0.09
26 44 0.18
27 172 0.71
28 4 0.02
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (27 bp):
ATCGAAATACCCCCATAAGGTAAAATG
Found at i:29762287 original size:106 final size:107
Alignment explanation
Indices: 29761993--29762276 Score: 367
Period size: 106 Copynumber: 2.7 Consensus size: 107
29761983 ACCGAAATGC
* * * * *
29761993 CCCATAGGTTAAAATGACCGAAATACCCCCATAAGGTAAAATGA-CTGAAATACCTCCACAAGG-
1 CCCATAGGGTAAAATGACCGAAATACCCCTATAAGGTAAAATGATC-GAAATACCCCCATAGGGT
* * *
29762056 AAAATGACCGAAATATCCCCATAGGGTAAAATAATCGAAATAC
65 AAAATGACTGAAATATCCCAATAGGGTAAAATAATCGAAATAA
* ** *
29762099 CCCTATAAGGTAAAATGATTGAAATACCCCTATAAGGTAAAATGATCGAAATACCCCCGTAGGGT
1 CCC-ATAGGGTAAAATGACCGAAATACCCCTATAAGGTAAAATGATCGAAATACCCCCATAGGGT
* *
29762164 AAAATGACTGAAATATCCTAATAGGGTAAAATGATCGAAA-AA
65 AAAATGACTGAAATATCCCAATAGGGTAAAATAATCGAAATAA
* * * *
29762206 CCCATAGGGTAAAATGACCAAAATACCCTTACAAGGTAGAATGATCGAAATACCCCCATAGGGTA
1 CCCATAGGGTAAAATGACCGAAATACCCCTATAAGGTAAAATGATCGAAATACCCCCATAGGGTA
29762271 AAATGA
66 AAATGA
29762277 TTGTTATATC
Statistics
Matches: 153, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
106 63 0.41
107 53 0.35
108 37 0.24
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.20
Consensus pattern (107 bp):
CCCATAGGGTAAAATGACCGAAATACCCCTATAAGGTAAAATGATCGAAATACCCCCATAGGGTA
AAATGACTGAAATATCCCAATAGGGTAAAATAATCGAAATAA
Found at i:29764510 original size:12 final size:12
Alignment explanation
Indices: 29764472--29764513 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
29764462 ATTTGTCATA
29764472 GAGAGATTTGAG
1 GAGAGATTTGAG
* *
29764484 GAGGGATATT-TG
1 GAGAGAT-TTGAG
29764496 GAGAGATTTGAG
1 GAGAGATTTGAG
29764508 GAGAGA
1 GAGAGA
29764514 ATATTGGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24
Consensus pattern (12 bp):
GAGAGATTTGAG
Found at i:29764520 original size:24 final size:24
Alignment explanation
Indices: 29764472--29764518 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
29764462 ATTTGTCATA
*
29764472 GAGAGATTTGAGGAGGGATATTTG
1 GAGAGATTTGAGGAGGAATATTTG
29764496 GAGAGATTTGAGGAGAGAATATT
1 GAGAGATTTGAGGAG-GAATATT
29764519 GGGATTTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28
Consensus pattern (24 bp):
GAGAGATTTGAGGAGGAATATTTG
Found at i:29765169 original size:27 final size:27
Alignment explanation
Indices: 29765123--29765585 Score: 403
Period size: 27 Copynumber: 17.2 Consensus size: 27
29765113 TTACACTATT
* *
29765123 ATGACCGAAATACCCTCATAGAGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * **
29765150 ATAATCGAAATACCCCCATAGAATAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
29765177 ATGTA-CAAAATACCCTCATAAGGTAAA
1 ATG-ACCGAAATACCCCCATAGGGTAAA
* *
29765204 ATGACCAAAATACCCCCATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
29765231 ATGACCGAAATACCCTCATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
29765258 ATGACCAAAATA-CCCCATAAGATAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
***
29765284 ATGACCGAAATACCAATATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
29765311 ATGACCGAAATACCCTCC-CAGGGAAAA
1 ATGACCGAAATACCC-CCATAGGGTAAA
* * * *
29765338 ATGATCAAAATGCCCCAATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
29765365 ATAACCGAAATACCCCTATAGGTTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* ** *
29765392 ACGACTAAAATACCCCCATATGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
29765419 ATGATCGAAATATCCCCATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
29765446 ATGACCGAAATACCCTCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
** * * *
29765473 ATGACTAAAATACCCTCACAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * * *
29765500 ATTA-CTAACATACCCCTATAGGGTAGA
1 ATGACCGAA-ATACCCCCATAGGGTAAA
* ** * *
29765527 ATGACTGAAATACCCTTATAAGCTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
29765554 ATGACCGAAATACTCCAATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
29765581 ATGAC
1 ATGAC
29765586 TGTTATATCC
Statistics
Matches: 345, Mismatches: 84, Indels: 14
0.78 0.19 0.03
Matches are distributed among these distances:
26 25 0.07
27 317 0.92
28 3 0.01
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.19
Consensus pattern (27 bp):
ATGACCGAAATACCCCCATAGGGTAAA
Found at i:29765267 original size:81 final size:80
Alignment explanation
Indices: 29765123--29765585 Score: 448
Period size: 81 Copynumber: 5.7 Consensus size: 80
29765113 TTACACTATT
* * * * **
29765123 ATGACCGAAATACCCTCATAGAGTAAAATAATCGAAATACCCCCATAGAATAAAATGTA-CAAAA
1 ATGACCGAAATACCCTCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATG-ACCAAAA
*
29765187 TACCCTCATAAGGTAAA
65 TACCC-CATAGGGTAAA
* * * *
29765204 ATGACCAAAATACCCCCATAGGGTAGAATGACCGAAATACCCTCATAGGGTAGAATGACCAAAAT
1 ATGACCGAAATACCCTCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGACCAAAAT
* *
29765269 ACCCCATAAGATAAA
66 ACCCCATAGGGTAAA
* ** * *
29765284 ATGACCGAAATACCAAT-ATAGGGTAAAATGACCGAAATACCCTCCCAGGGAAAAATGATCAAAA
1 ATGACCGAAATACC-CTCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGACCAAAA
*
29765348 TGCCCCAATAGGGTAAA
65 TACCCC-ATAGGGTAAA
* * * ** * * * *
29765365 ATAACCGAAATACCC-CTATAGGTTAAAACGACTAAAATACCCCCATATGGTAAAATGATCGAAA
1 ATGACCGAAATACCCTC-ATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGACCAAAA
*
29765429 TATCCCCATAGGGTAGA
65 TA-CCCCATAGGGTAAA
** * * * * *
29765446 ATGACCGAAATACCCTCATAGGGTAAAATGACTAAAATACCCTCACAGGGTAGAATTACTAACAT
1 ATGACCGAAATACCCTCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGACCAAAAT
*
29765511 ACCCCTATAGGGTAGA
66 ACCCC-ATAGGGTAAA
* * * * *
29765527 ATGACTGAAATACCCTTATAAGCTAAAATGACCGAAATACTCC-AATAGGGTAAAATGAC
1 ATGACCGAAATACCCTCATAGGGTAAAATGACCGAAATAC-CCTCATAGGGTAAAATGAC
29765586 TGTTATATCC
Statistics
Matches: 314, Mismatches: 59, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
80 74 0.24
81 233 0.74
82 7 0.02
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.19
Consensus pattern (80 bp):
ATGACCGAAATACCCTCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAAATGACCAAAAT
ACCCCATAGGGTAAA
Found at i:29771801 original size:20 final size:19
Alignment explanation
Indices: 29771774--29771815 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
29771764 TTTTCCAAAT
29771774 TTTCTTACTTT-CATTTGCA
1 TTTCTTACTTTCCA-TTGCA
29771793 TTTCATTACTTTCCATTGCA
1 TTTC-TTACTTTCCATTGCA
29771813 TTT
1 TTT
29771816 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 15 0.71
21 2 0.10
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTCTTACTTTCCATTGCA
Found at i:29777491 original size:16 final size:16
Alignment explanation
Indices: 29777466--29777549 Score: 80
Period size: 16 Copynumber: 5.2 Consensus size: 16
29777456 TTTAGATTTG
29777466 AAACTATAGACTGTGA
1 AAACTATAGACTGTGA
* *
29777482 AAACTGTAGACTATGAA
1 AAACTATAGACTGTG-A
* * *
29777499 AAACAATAGATTGAGA
1 AAACTATAGACTGTGA
*
29777515 CAACTATAGACTGTGA
1 AAACTATAGACTGTGA
*
29777531 AAACTCTAGA-TAGTGA
1 AAACTATAGACT-GTGA
29777547 AAA
1 AAA
29777550 TGATAGATAA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
15 1 0.02
16 41 0.77
17 11 0.21
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.23
Consensus pattern (16 bp):
AAACTATAGACTGTGA
Found at i:29777508 original size:33 final size:33
Alignment explanation
Indices: 29777466--29777533 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 33
29777456 TTTAGATTTG
* * *
29777466 AAACTATAGACTGTGAAAACTGTAGACTATGAA
1 AAACAATAGACTGAGAAAACTATAGACTATGAA
* * *
29777499 AAACAATAGATTGAGACAACTATAGACTGTGAA
1 AAACAATAGACTGAGAAAACTATAGACTATGAA
29777532 AA
1 AA
29777534 CTCTAGATAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.22
Consensus pattern (33 bp):
AAACAATAGACTGAGAAAACTATAGACTATGAA
Found at i:29779472 original size:14 final size:15
Alignment explanation
Indices: 29779453--29779481 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29779443 CTCTTTGTTA
29779453 TTTCTTT-TCATTTT
1 TTTCTTTATCATTTT
29779467 TTTCTTTATCATTTT
1 TTTCTTTATCATTTT
29779482 ATTATGCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTCTTTATCATTTT
Found at i:29782563 original size:20 final size:19
Alignment explanation
Indices: 29782538--29782586 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 19
29782528 GCAAAAGTTG
29782538 AGTTGGTGGACAGTTGGTTA
1 AGTTGGTGGACA-TTGGTTA
29782558 AG-T--TGGACCATTGGTTA
1 AGTTGGTGGA-CATTGGTTA
29782575 AGTTGGTGGACA
1 AGTTGGTGGACA
29782587 AAAATGGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
17 13 0.52
18 3 0.12
19 3 0.12
20 6 0.24
ACGTcount: A:0.22, C:0.08, G:0.37, T:0.33
Consensus pattern (19 bp):
AGTTGGTGGACATTGGTTA
Found at i:29793742 original size:37 final size:37
Alignment explanation
Indices: 29793683--29793765 Score: 130
Period size: 37 Copynumber: 2.2 Consensus size: 37
29793673 AGCTCAGACG
* *
29793683 AAATCTCCACATGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
*
29793720 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
*
29793757 TAATCTCCA
1 AAATCTCCA
29793766 AGTTTCATGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
Found at i:29793902 original size:37 final size:37
Alignment explanation
Indices: 29793832--29793970 Score: 257
Period size: 37 Copynumber: 3.8 Consensus size: 37
29793822 AATTCATTTG
29793832 CTCCACACGTAGTCATCGGG---TACCCGGACATAAT
1 CTCCACACGTAGTCATCGGGTCTTACCCGGACATAAT
29793866 CTCCACACGTAGTCATCGGGTCTTACCCGGACATAAT
1 CTCCACACGTAGTCATCGGGTCTTACCCGGACATAAT
29793903 CTCCACACGTAGTCATCGGGTCTTACCCGGACATAAT
1 CTCCACACGTAGTCATCGGGTCTTACCCGGACATAAT
29793940 CTCCACACGTAGTCATCGGGTCTTACCCGGA
1 CTCCACACGTAGTCATCGGGTCTTACCCGGA
29793971 ATATATTTCC
Statistics
Matches: 102, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
34 20 0.20
37 82 0.80
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (37 bp):
CTCCACACGTAGTCATCGGGTCTTACCCGGACATAAT
Found at i:29794243 original size:47 final size:47
Alignment explanation
Indices: 29794181--29794753 Score: 744
Period size: 47 Copynumber: 12.1 Consensus size: 47
29794171 ACACGTTTCG
* * * **
29794181 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * *
29794228 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
29794275 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
** *
29794322 CATTGGCCATTCGGCCTTATCACACATATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACAC------ATACGCATGTTCACATTCATCA
*
29794375 CATTGGCCATTTGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * * *
29794422 CATTGGCCATTCGGCCTTATCACACATA--TATATACGGGCATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTC--ACATTCATCA
*
29794469 CATTGGCCATTCGGCCTTATCACGCATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * * *
29794516 CATTGGCCATTCGGCCTTATCACACATA--TATATACGGGCATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTC--ACATTCATCA
* * * ***
29794563 CATTGGCCATTCGGCCTTATCACACATA--TATATACGGGTTCACATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATT--CATCA
29794610 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
29794657 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
29794704 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
29794751 CAT
1 CAT
29794754 AAAATCCTAA
Statistics
Matches: 472, Mismatches: 38, Indels: 32
0.87 0.07 0.06
Matches are distributed among these distances:
45 11 0.02
47 408 0.86
49 10 0.02
53 43 0.09
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Found at i:29794445 original size:22 final size:22
Alignment explanation
Indices: 29794418--29794491 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
29794408 GTTCACATTC
29794418 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* **** * *
29794440 ATCACACATATATATACGGGCATT
1 ATCACA-TTGGCCATTC-GGCCTT
29794464 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
29794487 ATCAC
1 ATCAC
29794492 GCATACGCAT
Statistics
Matches: 35, Mismatches: 14, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
22 11 0.31
23 9 0.26
24 9 0.26
25 6 0.17
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.30
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:29797883 original size:18 final size:18
Alignment explanation
Indices: 29797849--29797906 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
29797839 CAATAAGTGC
*
29797849 CGTTTTGAAAATTAATAA
1 CGTTTTGAAAATGAATAA
29797867 CGTTTTGAAAGA-GAATAA
1 CGTTTTGAAA-ATGAATAA
* * *
29797885 C-TTTTGAATACGAATCA
1 CGTTTTGAAAATGAATAA
29797902 CGTTT
1 CGTTT
29797907 AAATTGATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 1 0.03
17 13 0.38
18 19 0.56
19 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (18 bp):
CGTTTTGAAAATGAATAA
Found at i:29803456 original size:34 final size:34
Alignment explanation
Indices: 29803417--29803484 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
29803407 CCTAAACCAA
29803417 ATTTTAGTATAAATTCAATCAATTTACCATTAAT
1 ATTTTAGTATAAATTCAATCAATTTACCATTAAT
29803451 ATTTTAGTATAAATTCAATCAATTTACCATTAAT
1 ATTTTAGTATAAATTCAATCAATTTACCATTAAT
29803485 CCAGCCCCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (34 bp):
ATTTTAGTATAAATTCAATCAATTTACCATTAAT
Found at i:29808181 original size:6 final size:6
Alignment explanation
Indices: 29808155--29808217 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
29808145 AGAGCAGAAT
* * *
29808155 AAAAT- AAAATAA AACAATA AAAATA AAAATA AAAACA AAAGTA AAAGTA
1 AAAATA AAAAT-A AA-AATA AAAATA AAAATA AAAATA AAAATA AAAATA
* *
29808204 AAAGTA AAAGTA AA
1 AAAATA AAAATA AA
29808218 CAAAATTAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
5 5 0.10
6 39 0.75
7 5 0.10
8 3 0.06
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:29808212 original size:18 final size:18
Alignment explanation
Indices: 29808152--29808217 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
29808142 TACAGAGCAG
29808152 AATAAAA-T-AAAATAAAA
1 AATAAAAGTAAAAAT-AAA
*
29808169 CAATAAAAATAAAAATAAA
1 -AATAAAAGTAAAAATAAA
* *
29808188 AACAAAAGTAAAAGTAAA
1 AATAAAAGTAAAAATAAA
*
29808206 AGTAAAAGTAAA
1 AATAAAAGTAAA
29808218 CAAAATTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 32 0.78
19 4 0.10
20 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (18 bp):
AATAAAAGTAAAAATAAA
Found at i:29811165 original size:14 final size:14
Alignment explanation
Indices: 29811146--29811174 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29811136 TAAAAATTAA
29811146 ATTAAAATAAAAAT
1 ATTAAAATAAAAAT
29811160 ATTAAAATAAAAAT
1 ATTAAAATAAAAAT
29811174 A
1 A
29811175 GGTAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATTAAAATAAAAAT
Found at i:29814128 original size:17 final size:17
Alignment explanation
Indices: 29814106--29814139 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29814096 GCACTAACAC
*
29814106 TAAAATGTAATGACAAT
1 TAAAATGCAATGACAAT
29814123 TAAAATGCAATGACAAT
1 TAAAATGCAATGACAAT
29814140 GTATACTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (17 bp):
TAAAATGCAATGACAAT
Found at i:29814457 original size:17 final size:18
Alignment explanation
Indices: 29814420--29814466 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
29814410 TCATTTTTAG
*
29814420 CAAC-TCTTCTTCAGCAT
1 CAACTTCTTCTTCAGCAA
29814437 CAACTTCTTCTTC-GCAA
1 CAACTTCTTCTTCAGCAA
*
29814454 CAACTTCTACTTC
1 CAACTTCTTCTTC
29814467 TGCAGCATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.23, C:0.36, G:0.04, T:0.36
Consensus pattern (18 bp):
CAACTTCTTCTTCAGCAA
Found at i:29824844 original size:79 final size:81
Alignment explanation
Indices: 29824746--29824930 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 81
29824736 GCTCCTCGTT
** *
29824746 CAAATGCCTAAGGGACTTAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAACC
* *
29824808 CGGATTTAGTAAC-TCGCA
63 CGGATATAGTAACTTAGCA
**
29824826 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
29824890 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
29824906 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29824931 CAACATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
78 5 0.05
79 54 0.59
80 32 0.35
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:29824930 original size:40 final size:40
Alignment explanation
Indices: 29824746--29824930 Score: 202
Period size: 40 Copynumber: 4.7 Consensus size: 40
29824736 GCTCCTCGTT
** * *
29824746 CAAATGCCTAAGGGACTTAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCA
* *
29824786 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ACTTCGCA
29824826 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTA-TCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTACT-TCGCA
* * *
29824865 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGT-ACTTCGCA
29824906 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29824931 CAACATTCAA
Statistics
Matches: 123, Mismatches: 12, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
38 3 0.02
39 30 0.24
40 75 0.61
41 14 0.11
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCA
Found at i:29837128 original size:40 final size:40
Alignment explanation
Indices: 29837084--29837345 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
29837074 GCTCCTCGTT
* *
29837084 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
29837124 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
29837164 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
29837203 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
29837242 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
29837281 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
29837322 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29837346 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:29840405 original size:12 final size:12
Alignment explanation
Indices: 29840370--29840413 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
29840360 ACCATCTCTT
29840370 CTTTAACTATAA
1 CTTTAACTATAA
**
29840382 CTTGGA-TATAA
1 CTTTAACTATAA
29840393 CTTTAACTATAA
1 CTTTAACTATAA
29840405 CTTTAACTA
1 CTTTAACTA
29840414 ACATAGTTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.41
Consensus pattern (12 bp):
CTTTAACTATAA
Found at i:29840571 original size:25 final size:25
Alignment explanation
Indices: 29840524--29840571 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
29840514 CCTCATATTC
*
29840524 TTTTCCAAATTAAACTCTGTTATCT
1 TTTTCCAAATTAAACTCTATTATCT
*
29840549 TTTTCC-AGTTAAACTCTAATTAT
1 TTTTCCAAATTAAACTCT-ATTAT
29840572 TCCAGGGACG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.29, C:0.19, G:0.04, T:0.48
Consensus pattern (25 bp):
TTTTCCAAATTAAACTCTATTATCT
Found at i:29841382 original size:14 final size:15
Alignment explanation
Indices: 29841363--29841392 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
29841353 TTCCAAGTTC
29841363 AAATTTTTTT-CTTT
1 AAATTTTTTTCCTTT
29841377 AAATTTTTTTCCTTT
1 AAATTTTTTTCCTTT
29841392 A
1 A
29841393 CTAAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (15 bp):
AAATTTTTTTCCTTT
Found at i:29844264 original size:54 final size:53
Alignment explanation
Indices: 29844202--29844470 Score: 140
Period size: 54 Copynumber: 5.0 Consensus size: 53
29844192 AAGGTCATAA
* *
29844202 CAGTCATTTCATCTCCTA-GATGTATAACAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTCA-C-CCTAGGAGGTATAACAGTCATTCTACCCTATGGGGGTATTT
* * **
29844256 CAGTCATTTTACCCTATGGGGGTATTTCAGTCATTCTACCCTATGGGGGTATTT
1 CAGTCATTTCACCCTA-GGAGGTATAACAGTCATTCTACCCTATGGGGGTATTT
* ** * * *
29844310 C-GATCATTTTACCCAATAGG-GGTATTTC-GATCATTTTACCCCATAGGGGTATTT
1 CAG-TCATTTCACCC--TAGGAGGTATAACAG-TCATTCTACCCTATGGGGGTATTT
* * ** * *
29844364 -TGATCATTTTACCCTATAGG-GGTATTTCGGTCATTCTATCCTATGGGGGTATTT
1 CAG-TCATTTCACCC--TAGGAGGTATAACAGTCATTCTACCCTATGGGGGTATTT
* * ** ** *
29844418 C-GATCATTTTACCTTATAAGGGTATTTC-GATCATTTTACCCTATGGGGGTATT
1 CAG-TCATTTCACCCTAGGA-GGTATAACAG-TCATTCTACCCTATGGGGGTATT
29844471 CTTGTTATTT
Statistics
Matches: 184, Mismatches: 19, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
52 6 0.03
53 4 0.02
54 169 0.92
55 3 0.02
56 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.40
Consensus pattern (53 bp):
CAGTCATTTCACCCTAGGAGGTATAACAGTCATTCTACCCTATGGGGGTATTT
Found at i:29844482 original size:27 final size:27
Alignment explanation
Indices: 29844232--29844470 Score: 329
Period size: 27 Copynumber: 8.9 Consensus size: 27
29844222 TGTATAACAG
29844232 TCATTTTACCCTATGGGGGTATTTC-A
1 TCATTTTACCCTATGGGGGTATTTCGA
29844258 GTCATTTTACCCTATGGGGGTATTTC-A
1 -TCATTTTACCCTATGGGGGTATTTCGA
*
29844285 GTCATTCTACCCTATGGGGGTATTTCGA
1 -TCATTTTACCCTATGGGGGTATTTCGA
* *
29844313 TCATTTTACCCAATAGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* * *
29844340 TCATTTTACCCCATAGGGGTATTTTGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
29844367 TCATTTTACCCTATAGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGA
* *
29844394 TCATTCTATCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* **
29844421 TCATTTTACCTTATAAGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
29844448 TCATTTTACCCTATGGGGGTATT
1 TCATTTTACCCTATGGGGGTATT
29844471 CTTGTTATTT
Statistics
Matches: 190, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
27 189 0.99
28 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGA
Found at i:29851862 original size:389 final size:389
Alignment explanation
Indices: 29851134--29851901 Score: 1207
Period size: 389 Copynumber: 2.0 Consensus size: 389
29851124 TGAATTTTTG
* *
29851134 TTTTGAGTCATAAACTATCTGTTTTATGTTTTTGTGTAATTCGATCCTCGATCAAGCCTCGGTAA
1 TTTTGAGTCATAAACTATCTATTTTATGTTTTTGTGTAATTCGACCCTCGATCAAGCCTCGGTAA
*
29851199 GTGTGTTTGGGACTCGATTTAGCTTGGTTCGTGTATATATGTGGGATTATGGGCTTTAATCTATT
66 GTGTGTTTGGGACTCGACTTAGCTTGGTTCGTGTATATATGTGGGATTATGGGCTTTAATCTATT
*
29851264 TAGTCATTTATGTGATGAATAAGTATGAGTGTTTTATTATTGTCATAACTGAATATTAGAATACA
131 TACTCATTTATGTGATGAATAAGTATGAGTGTTTTATTATTGTCATAACTGAATATTAGAATACA
* * ** *
29851329 AGTGTAATCAAATCTGAATTTGTTTTACTAGAAGTGTTAATGTCCGTTTCTGTATGTTGCCTGCA
196 AGTGTAATCAAATCTAAATCTGTTCAACTAGAAGTGTTAATGTCCGTTTCTGTAAGTTGCCTGCA
* *
29851394 TAATGTGTACATTGTTACACAGCATGAAAATTTTGGGATCTGGATATGAAGAGAAGGAAGACAGA
261 TAATGTGTACATTGTTACACAGCATGAAAATTTTGGGATCTAGATATGAAGAGAAGGAAGACAAA
* * * * * *
29851459 CTTAGTAGTTTTAACTGCGATACTTTTGTATAGCGGTTTATCACACTATCCTATTTTGCAAATT
326 CTTAGCAATTTTAACCGAGATACTTTTGTATAGCGATTTACCACACTATCCTATTTTGCAAATT
* * * *
29851523 TTTTTAGTCATAAAGTATCTATTTTATGTTTTTGTGTAATTCGACCCTCGGTCAATCCTCGGTAA
1 TTTTGAGTCATAAACTATCTATTTTATGTTTTTGTGTAATTCGACCCTCGATCAAGCCTCGGTAA
* * * * *
29851588 GTGTGTTTTGGACTCGACTTAGTTTGGTTTGTGTATGTATGTGTGATTATGGGCTTTAATCTATT
66 GTGTGTTTGGGACTCGACTTAGCTTGGTTCGTGTATATATGTGGGATTATGGGCTTTAATCTATT
* * *
29851653 TACTCGTTTATGTGATGAATAAGTATGAGT-TTATTATTGTTGTCGTAACTGAATATTAGAATAC
131 TACTCATTTATGTGATGAATAAGTATGAGTGTT-TTATTATTGTCATAACTGAATATTAGAATAC
29851717 AAGTGTAATCAAATCTAAATCTGTTCAACTCA-AAGTGTTAATGTCCGTTTCTGTAAGTTGCCTG
195 AAGTGTAATCAAATCTAAATCTGTTCAACT-AGAAGTGTTAATGTCCGTTTCTGTAAGTTGCCTG
* * *
29851781 CATAATGTGTGCATTGTTGCATAGCATGAAAATTTTGGGATCTAGATATGAAGAGAAGGAAGACA
259 CATAATGTGTACATTGTTACACAGCATGAAAATTTTGGGATCTAGATATGAAGAGAAGGAAGACA
*
29851846 AACTTAGCAATTTTAACCGAGATACTTTTGTATAGCGATTTACCGCACTATCCTAT
324 AACTTAGCAATTTTAACCGAGATACTTTTGTATAGCGATTTACCACACTATCCTAT
29851902 ACGTATATCA
Statistics
Matches: 344, Mismatches: 33, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
388 2 0.01
389 341 0.99
390 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (389 bp):
TTTTGAGTCATAAACTATCTATTTTATGTTTTTGTGTAATTCGACCCTCGATCAAGCCTCGGTAA
GTGTGTTTGGGACTCGACTTAGCTTGGTTCGTGTATATATGTGGGATTATGGGCTTTAATCTATT
TACTCATTTATGTGATGAATAAGTATGAGTGTTTTATTATTGTCATAACTGAATATTAGAATACA
AGTGTAATCAAATCTAAATCTGTTCAACTAGAAGTGTTAATGTCCGTTTCTGTAAGTTGCCTGCA
TAATGTGTACATTGTTACACAGCATGAAAATTTTGGGATCTAGATATGAAGAGAAGGAAGACAAA
CTTAGCAATTTTAACCGAGATACTTTTGTATAGCGATTTACCACACTATCCTATTTTGCAAATT
Found at i:29852146 original size:21 final size:20
Alignment explanation
Indices: 29852113--29852151 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
29852103 AATATACGCT
29852113 TGTTTGTCAGAACATTTTGTC
1 TGTTTGTCAGAAC-TTTTGTC
**
29852134 TGTTTGTGTGAACTTTTG
1 TGTTTGTCAGAACTTTTG
29852152 GTTATTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.15, C:0.10, G:0.23, T:0.51
Consensus pattern (20 bp):
TGTTTGTCAGAACTTTTGTC
Found at i:29852327 original size:10 final size:10
Alignment explanation
Indices: 29852312--29852337 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
29852302 TTGTGTCACT
29852312 CCATCTTTTG
1 CCATCTTTTG
29852322 CCATCTTTTG
1 CCATCTTTTG
29852332 CCATCT
1 CCATCT
29852338 GTTCATCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.35, G:0.08, T:0.46
Consensus pattern (10 bp):
CCATCTTTTG
Found at i:29852932 original size:70 final size:70
Alignment explanation
Indices: 29852848--29852988 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
29852838 ATTGTTTTTA
29852848 TGTTCTGATGATAAATAATTTCAGAGTCCATTGCCAATAGTCTAAAAAATCACTTGCATGTCACT
1 TGTTCTGATGATAAATAATTTCAGAGTCCATTGCCAATAGTCTAAAAAATCACTTGCATGTCACT
29852913 TTAAC
66 TTAAC
29852918 TGTTCTGATGATAAATAATTTCAGAGTCCATTGCCAATAGTCTAAAAAATCACTTGCATGTCACT
1 TGTTCTGATGATAAATAATTTCAGAGTCCATTGCCAATAGTCTAAAAAATCACTTGCATGTCACT
29852983 TTAAC
66 TTAAC
29852988 T
1 T
29852989 CAAATAGTTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (70 bp):
TGTTCTGATGATAAATAATTTCAGAGTCCATTGCCAATAGTCTAAAAAATCACTTGCATGTCACT
TTAAC
Found at i:29854713 original size:25 final size:24
Alignment explanation
Indices: 29854627--29854714 Score: 88
Period size: 25 Copynumber: 3.5 Consensus size: 24
29854617 ATGCATGTAT
* *
29854627 GCTCATACGAGCATATAAACGAGAA
1 GCTCATGCGAGCATAT-AACGGGAA
*
29854652 GCTC-TTCTGAGCCATATAACGGGAA
1 GCTCATGC-GAG-CATATAACGGGAA
* *
29854677 GCTTATGTGAGCTATATAACGGGAA
1 GCTCATGCGAGC-ATATAACGGGAA
29854702 GCTCATGCGAGCA
1 GCTCATGCGAGCA
29854715 AAATATTGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
24 4 0.08
25 42 0.81
26 6 0.12
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (24 bp):
GCTCATGCGAGCATATAACGGGAA
Found at i:29859218 original size:33 final size:33
Alignment explanation
Indices: 29859179--29859288 Score: 159
Period size: 33 Copynumber: 3.3 Consensus size: 33
29859169 ATTATAAAGC
29859179 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* *
29859212 ATGTATAATTGACCTAAAATTAATTCTTGGTTT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* * *
29859245 AT-TTTTATTTACCCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGA-CCTAAAATTAATTGTTGGTGT
29859278 ATGTATAATTG
1 ATGTATAATTG
29859289 TTGGTGTATG
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
32 6 0.09
33 54 0.83
34 5 0.08
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTGT
Found at i:29859288 original size:18 final size:18
Alignment explanation
Indices: 29859265--29859306 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
29859255 ACCCTAAAAT
29859265 TAATTGTTGGTGTATGTA
1 TAATTGTTGGTGTATGTA
29859283 TAATTGTTGGTGTATGTA
1 TAATTGTTGGTGTATGTA
29859301 TAATTG
1 TAATTG
29859307 ACCTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (18 bp):
TAATTGTTGGTGTATGTA
Found at i:29860691 original size:28 final size:28
Alignment explanation
Indices: 29860658--29860770 Score: 75
Period size: 28 Copynumber: 3.6 Consensus size: 28
29860648 TTTTTATTAT
29860658 AATATTTTATTATTTCAGTTTATTTCAC
1 AATATTTTATTATTTCAGTTTATTTCAC
* * *
29860686 AATATTTATTTTAAGTATT-AGATATATTATACATT
1 AATATTT-TATT-A-T-TTCAG-TTTATT-T-CA-C
*
29860721 AATATTTATTTTATTATTTCAGTTCATTTCAC
1 AATA--T--TTTATTATTTCAGTTTATTTCAC
29860753 AATATTTTATTATTTCAG
1 AATATTTTATTATTTCAG
29860771 CTTTTATTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 26
0.66 0.07 0.27
Matches are distributed among these distances:
28 20 0.31
29 3 0.05
30 2 0.03
31 3 0.05
32 11 0.17
33 3 0.05
34 3 0.05
35 10 0.15
36 3 0.05
37 2 0.03
38 3 0.05
39 2 0.03
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.55
Consensus pattern (28 bp):
AATATTTTATTATTTCAGTTTATTTCAC
Found at i:29860696 original size:32 final size:32
Alignment explanation
Indices: 29860660--29860759 Score: 105
Period size: 32 Copynumber: 3.0 Consensus size: 32
29860650 TTTATTATAA
29860660 TATTTTATTATTTCAGTTTATTTCACAATATT
1 TATTTTATTATTTCAGTTTATTTCACAATATT
* * *
29860692 TATTTTAAGTA-TT-AGATATATTATACATTAATATT
1 TATTTT-ATTATTTCAG-TTTATT-T-CA-CAATATT
*
29860727 TATTTTATTATTTCAGTTCATTTCACAATATT
1 TATTTTATTATTTCAGTTTATTTCACAATATT
29860759 T
1 T
29860760 TATTATTTCA
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
31 2 0.04
32 20 0.37
33 6 0.11
34 6 0.11
35 18 0.33
36 2 0.04
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (32 bp):
TATTTTATTATTTCAGTTTATTTCACAATATT
Found at i:29860777 original size:15 final size:15
Alignment explanation
Indices: 29860757--29860785 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29860747 TTTCACAATA
29860757 TTTTATTATTTCAGC
1 TTTTATTATTTCAGC
29860772 TTTTATTATTTCAG
1 TTTTATTATTTCAG
29860786 TTTATTTCAC
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:0.07, T:0.62
Consensus pattern (15 bp):
TTTTATTATTTCAGC
Found at i:29865540 original size:44 final size:44
Alignment explanation
Indices: 29865438--29866111 Score: 234
Period size: 44 Copynumber: 15.7 Consensus size: 44
29865428 GCTATCTTAG
* * * * *
29865438 TCTGCTCCACTACAATCTTCAGGGAAATAAGA-CT-AGA-TGCGA
1 TCTGCTCCACTGCAA-CTTCAGGGAGATAAGATCTGTGATTTCAA
* * *
29865480 TCTGCT-CTCTACAACTTCAGAGAGATAAGATCTGTGATTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTCAA
* * * *
29865523 TCCGCTCCACTGCAACTTCAGGAAGATAGGATTACTG-GCTTT-AA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-T-CTGTGATTTCAA
* ** *
29865567 TCTGCT---C--C-ACTTCAGGGAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGAT-TTCAA
* * * *
29865606 TCTGC-CTTACTGCAACTTCA-GGAGGATAAGA-CT-TGCTTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGATCTGTGATT--TCAA
* * ** * *
29865650 TCCGCTCCACTACAACTTCAGGGAGATAAGA-CT-AAATGT-GA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTCAA
* * * * * * ** * *
29865691 CCTGCT-CTCTACAATTTCAGAGAAATAAGATCTAAGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTCAA
* * * **
29865734 TCCGC-CCACTGCAACTTCAGCGAGATAGGAT-TACCGACTTT-AA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-GTGA-TTTCAA
* * ** *
29865777 TCTGCTCCATTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGAT-TTCAA
* * *
29865822 TCTGC-CTCACTGCAACTTCA-AGAGGATAAGA-CT-TGCTTACTCAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGATCTGTGATT--TCAA
* * * *
29865866 TCCGCTCCACTGCAACTTCAGGGAGATAAGA-CT-AGA-TGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTCAA
* * * * * *
29865907 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATATGAGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTCAA
** * * *
29865950 TCCAC-CCACTGCAACTTCAGCGAGATAGGAT-TGTCGCTTT-AA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGT-GATTTCAA
* * *** *
29865992 TCTGCTCCACTGCAACTTCAGGGAGATGAGATTTGCCCTCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGAT-TTCAA
* * * * *
29866037 TCTGC-CTCGCTGCAACTTCA-GGAGAATAAGACTTTCTTATTT-AG
1 TCTGCTC-CACTGCAACTTCAGGGAG-ATAAGA-TCTGTGATTTCAA
29866081 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
29866112 CTCGGTATGT
Statistics
Matches: 475, Mismatches: 106, Indels: 100
0.70 0.16 0.15
Matches are distributed among these distances:
36 2 0.00
37 2 0.00
38 17 0.04
39 7 0.01
40 56 0.12
41 23 0.05
42 25 0.05
43 98 0.21
44 157 0.33
45 81 0.17
46 7 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGATTTCAA
Found at i:29866100 original size:215 final size:215
Alignment explanation
Indices: 29865433--29866113 Score: 989
Period size: 216 Copynumber: 3.2 Consensus size: 215
29865423 AATTTGCTAT
* *
29865433 CTTAGTCTGCTCCACTACAATCTTCAGGGAAATAAGACTAGATGCGATCTGCTCTCTACAACTTC
1 CTTAGTCCGCTCCACTACAA-CTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTACAACTTC
* * * *
29865498 AGAGAGATAAGATCTGTGATTTCAATCCGCTCCACTGCAACTTCAG-GAAGATAGGATTACTGGC
65 AGAGAGATAAGATCTGAGGTTTTAATCCGC-CCACTGCAACTTCAGCG-AGATAGGATTA-TCGC
*
29865562 TTTAATCTGCT---C--C-ACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTTACTGCAA
127 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAA
29865621 CTTCAGGAGGATAAGACTTGCTTA
192 CTTCAGGAGGATAAGACTTGCTTA
* * * *
29865645 CTTAGTCCGCTCCACTACAACTTCAGGGAGATAAGACTAAATGTGACCTGCTCTCTACAATTTCA
1 CTTAGTCCGCTCCACTACAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTACAACTTCA
* * *
29865710 GAGAAATAAGATCTAAGGTTTTAATCCGCCCACTGCAACTTCAGCGAGATAGGATTACCGACTTT
66 GAGAGATAAGATCTGAGGTTTTAATCCGCCCACTGCAACTTCAGCGAGATAGGATTATCG-CTTT
* *
29865775 AATCTGCTCCATTGCAACTTCAGGGAGATAAGATTTGCCATCTTCATTCTGCCTCACTGCAACTT
130 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
*
29865840 CAAGAGGATAAGACTTGCTTA
195 CAGGAGGATAAGACTTGCTTA
* * *
29865861 CTCAGTCCGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCA
1 CTTAGTCCGCTCCACTACAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTACAACTTCA
* * *
29865926 GAGAGATAAGATATGAGGTTTTAATCCACCCACTGCAACTTCAGCGAGATAGGATTGTCGCTTTA
66 GAGAGATAAGATCTGAGGTTTTAATCCGCCCACTGCAACTTCAGCGAGATAGGATTATCGCTTTA
* * *
29865991 ATCTGCTCCACTGCAACTTCAGGGAGATGAGATTTGCCCTCTTCAGTCTGCCTCGCTGCAACTTC
131 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
* *
29866056 AGGAGAATAAGACTTTCTTA
196 AGGAGGATAAGACTTGCTTA
* * *
29866076 TTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 CTTAGTCCGCTCCACTACAACTTCAGGGAGATAAGACT
29866114 CGGTATGTTA
Statistics
Matches: 420, Mismatches: 41, Indels: 13
0.89 0.09 0.03
Matches are distributed among these distances:
209 1 0.00
210 38 0.09
211 65 0.15
212 19 0.05
215 118 0.28
216 179 0.43
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (215 bp):
CTTAGTCCGCTCCACTACAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTACAACTTCA
GAGAGATAAGATCTGAGGTTTTAATCCGCCCACTGCAACTTCAGCGAGATAGGATTATCGCTTTA
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
AGGAGGATAAGACTTGCTTA
Found at i:29878204 original size:67 final size:67
Alignment explanation
Indices: 29878094--29878227 Score: 241
Period size: 67 Copynumber: 2.0 Consensus size: 67
29878084 GTTAGGACAC
**
29878094 AACGTGTTAAATTCCCAATAATGAGCTCTTATTTTTTTGATTAAAGAGAAATGCTTGATTGTTGG
1 AACGTGTTAAATTCCCAATAATGAGCTCTTATTTTTTTGATTAAAGAGAAATGCTCAATTGTTGG
29878159 AT
66 AT
*
29878161 AACGTGTTAAATTCCCAATAATGAGCTCTTATTTTTTTTATTAAAGAGAAATGCTCAATTGTTGG
1 AACGTGTTAAATTCCCAATAATGAGCTCTTATTTTTTTGATTAAAGAGAAATGCTCAATTGTTGG
29878226 AT
66 AT
29878228 TTAACGAAGA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (67 bp):
AACGTGTTAAATTCCCAATAATGAGCTCTTATTTTTTTGATTAAAGAGAAATGCTCAATTGTTGG
AT
Done.