Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 83 of 190
Found at i:24172400 original size:25 final size:26
Alignment explanation
Indices: 24172363--24172418 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
24172353 GCAAAAGAAA
24172363 AAAATCGAAAAAGTGA-GAGAAAAAG
1 AAAATCGAAAAAGTGACGAGAAAAAG
*
24172388 AAAAT-GAAGAAAGTGAGCGAGAACAAG
1 AAAATCGAA-AAAGTGA-CGAGAAAAAG
24172415 AAAA
1 AAAA
24172419 GGAGAACGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 3 0.11
25 12 0.44
27 12 0.44
ACGTcount: A:0.62, C:0.05, G:0.25, T:0.07
Consensus pattern (26 bp):
AAAATCGAAAAAGTGACGAGAAAAAG
Found at i:24174408 original size:21 final size:21
Alignment explanation
Indices: 24174382--24174444 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
24174372 TTGGTATTTG
24174382 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
24174403 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
24174424 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
24174445 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:24176523 original size:20 final size:19
Alignment explanation
Indices: 24176500--24176564 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
24176490 AAGCTCAAAC
24176500 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
24176520 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
24176540 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
24176560 GAGCT
1 GAGCT
24176565 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:24177162 original size:12 final size:12
Alignment explanation
Indices: 24177145--24177199 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
24177135 AGTTGTAAAG
*
24177145 TTTTATTTTTAT
1 TTTTATATTTAT
24177157 TTTTATTTATTTAT
1 TTTTA--TATTTAT
24177171 TTATT-TATTTAT
1 TT-TTATATTTAT
24177183 TTATT-TATTTAT
1 TT-TTATATTTAT
24177195 TTTTA
1 TTTTA
24177200 CTTAGTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 2 0.05
12 26 0.68
14 8 0.21
15 2 0.05
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTATATTTAT
Found at i:24177167 original size:4 final size:4
Alignment explanation
Indices: 24177158--24177196 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
24177148 TATTTTTATT
24177158 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
24177197 TTACTTAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:24177167 original size:16 final size:18
Alignment explanation
Indices: 24177152--24177199 Score: 78
Period size: 20 Copynumber: 2.6 Consensus size: 18
24177142 AAGTTTTATT
24177152 TTTATTTTTATTTATTTA
1 TTTATTTTTATTTATTTA
24177170 TTTATTTATTTATTTATTTA
1 TTTA-TT-TTTATTTATTTA
24177190 TTTATTTTTA
1 TTTATTTTTA
24177200 CTTAGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.29
19 4 0.14
20 16 0.57
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATTTTTATTTATTTA
Found at i:24192060 original size:20 final size:20
Alignment explanation
Indices: 24192008--24192063 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
24191998 TACTTCAAGT
* ** *
24192008 TCATTCAGCTCAACCATAGT
1 TCATTCAGCTCATCTTTAGC
*
24192028 TCATTGAGCTCATCTTTAGC
1 TCATTCAGCTCATCTTTAGC
24192048 TCATTCAGCTCATCTT
1 TCATTCAGCTCATCTT
24192064 CATTTTTTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.23, C:0.29, G:0.11, T:0.38
Consensus pattern (20 bp):
TCATTCAGCTCATCTTTAGC
Found at i:24193909 original size:29 final size:29
Alignment explanation
Indices: 24193872--24193944 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
24193862 ATGTATTAGT
* * *
24193872 TTAGAACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
*
24193901 TTAGGACATAATTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
24193930 TTAGGACATATTTAA
1 TTAGGACATATTTAA
24193945 TAATATCTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:24195951 original size:12 final size:12
Alignment explanation
Indices: 24195934--24195958 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24195924 AAAATTTGAT
24195934 TTCAATGTGTAA
1 TTCAATGTGTAA
24195946 TTCAATGTGTAA
1 TTCAATGTGTAA
24195958 T
1 T
24195959 GTGTATAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTCAATGTGTAA
Found at i:24205386 original size:20 final size:20
Alignment explanation
Indices: 24205361--24205407 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
24205351 AGCTCGTTTC
24205361 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* * * *
24205381 CAGCTCATTCGAGTTGAATT
1 CAGCTCACTCGAGCTCAAGT
24205401 CAGCTCA
1 CAGCTCA
24205408 ACCTCAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:24213399 original size:19 final size:18
Alignment explanation
Indices: 24213363--24213402 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
24213353 TTTCCACTCG
*
24213363 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
24213381 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
24213400 TTT
1 TTT
24213403 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:24213511 original size:17 final size:18
Alignment explanation
Indices: 24213486--24213539 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 18
24213476 TTTCTTTCTC
24213486 CAATCTTTT-TCTCTTTTT
1 CAAT-TTTTCTCTCTTTTT
* *
24213504 CAATTTTTGTTTCTTTTT
1 CAATTTTTCTCTCTTTTT
24213522 C--TTTTGTCTCTCTTTTT
1 CAATTTT-TCTCTCTTTTT
24213539 C
1 C
24213540 TTCTCTCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 4 0.13
17 14 0.45
18 13 0.42
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.69
Consensus pattern (18 bp):
CAATTTTTCTCTCTTTTT
Found at i:24214469 original size:14 final size:13
Alignment explanation
Indices: 24214450--24214487 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
24214440 TAGCTCTCTC
24214450 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
24214463 TTTTTTTTTTCAA
1 TTTTTTTTTTCAA
24214476 TTTTTTTTTTCA
1 TTTTTTTTTTCA
24214488 CAACTTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTTCAA
Found at i:24214545 original size:12 final size:12
Alignment explanation
Indices: 24214528--24214574 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
24214518 TGGAAACTAG
24214528 ATTTTTTTTTGA
1 ATTTTTTTTTGA
24214540 A-TTTTTTTTGA
1 ATTTTTTTTTGA
*
24214551 ATTTTTTTTCGA
1 ATTTTTTTTTGA
*
24214563 GTTTTTTTTTGA
1 ATTTTTTTTTGA
24214575 GAAACTACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.15, C:0.02, G:0.11, T:0.72
Consensus pattern (12 bp):
ATTTTTTTTTGA
Found at i:24214546 original size:11 final size:11
Alignment explanation
Indices: 24214530--24214571 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
24214520 GAAACTAGAT
24214530 TTTTTTTTGAA
1 TTTTTTTTGAA
24214541 TTTTTTTTGAA
1 TTTTTTTTGAA
*
24214552 TTTTTTTTCGAG
1 TTTTTTTT-GAA
24214564 TTTTTTTT
1 TTTTTTTT
24214572 TGAGAAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:24233900 original size:30 final size:30
Alignment explanation
Indices: 24233866--24233937 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
24233856 ACTAGCATCC
* *
24233866 CCATTCAGCTCCCTAAATACATGCATGCCT
1 CCATTCAGCTCCCTAAACACATGCATGCAT
* *
24233896 CCATTCAGCTCCTTAAACACATTCATGCAT
1 CCATTCAGCTCCCTAAACACATGCATGCAT
**
24233926 TAATTCAGCTCC
1 CCATTCAGCTCC
24233938 ATATGCACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.28, C:0.35, G:0.08, T:0.29
Consensus pattern (30 bp):
CCATTCAGCTCCCTAAACACATGCATGCAT
Found at i:24236209 original size:52 final size:52
Alignment explanation
Indices: 24236126--24236226 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
24236116 TAAGGAAACG
* *
24236126 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
24236178 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
24236227 TATGTGCATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:24271995 original size:9 final size:9
Alignment explanation
Indices: 24271981--24272017 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
24271971 TATAGTTTGA
24271981 TATTCGAAT
1 TATTCGAAT
24271990 TATTCGAAT
1 TATTCGAAT
24271999 TATTC-AAGT
1 TATTCGAA-T
24272008 TATTCGAAT
1 TATTCGAAT
24272017 T
1 T
24272018 CGAAAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:24272089 original size:9 final size:9
Alignment explanation
Indices: 24272072--24272103 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
24272062 TCGAGTTGAT
24272072 TCGAATAAC
1 TCGAATAAC
*
24272081 TCGATTAAC
1 TCGAATAAC
24272090 TCGAATAAC
1 TCGAATAAC
24272099 TCGAA
1 TCGAA
24272104 ATTCAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (9 bp):
TCGAATAAC
Found at i:24272814 original size:24 final size:24
Alignment explanation
Indices: 24272757--24272831 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
24272747 GTGATCATCG
*
24272757 TCTTCATCTTCACCTCGACCC-CA
1 TCTTCATCTTCATCTCGACCCTCA
*
24272780 TATTCATCTTCATCTCGACCCTCA
1 TCTTCATCTTCATCTCGACCCTCA
*
24272804 TCTTCATCTTCATCTCCACCCTCA
1 TCTTCATCTTCATCTCGACCCTCA
24272828 TCTT
1 TCTT
24272832 TGTCTTCGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
23 19 0.40
24 28 0.60
ACGTcount: A:0.17, C:0.43, G:0.03, T:0.37
Consensus pattern (24 bp):
TCTTCATCTTCATCTCGACCCTCA
Found at i:24280885 original size:2 final size:2
Alignment explanation
Indices: 24280878--24280904 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24280868 TACAAAGTTT
24280878 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
24280905 TTTCAGTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:24282404 original size:5 final size:5
Alignment explanation
Indices: 24282394--24282437 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 5
24282384 TTGGTGTCCT
24282394 TTTTC TTTTC TTTTC -TTTC -TTTC -TTTC -TTTC TTTTC TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
24282438 TTGTTTTGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
4 20 0.53
5 18 0.47
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:24282449 original size:21 final size:20
Alignment explanation
Indices: 24282393--24282461 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
24282383 TTTGGTGTCC
*
24282393 TTTTTCTTTTCTTTTCTTTCT
1 TTTTTTTTTTCTTTTCTTT-T
* *
24282414 TTCTTTCTTTCTTTTCTTTT
1 TTTTTTTTTTCTTTTCTTTT
*
24282434 TTTTTTGTTTTGTTTTGCTTTAT
1 TTTTTT-TTTTCTTTT-CTTT-T
24282457 TTTTT
1 TTTTT
24282462 CCTTAAACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.15
21 23 0.59
22 4 0.10
23 6 0.15
ACGTcount: A:0.01, C:0.13, G:0.04, T:0.81
Consensus pattern (20 bp):
TTTTTTTTTTCTTTTCTTTT
Found at i:24288904 original size:27 final size:27
Alignment explanation
Indices: 24288868--24288943 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
24288858 AATTATGACT
*
24288868 GCCAGCAGGTTTGGCAAGCTAGAGTTC
1 GCCAGAAGGTTTGGCAAGCTAGAGTTC
* * * *
24288895 GCCAGTAGGTTTGGCGAGTTAAAGTTC
1 GCCAGAAGGTTTGGCAAGCTAGAGTTC
* *
24288922 ACCAGAAGGCTTGGCAAGCTAG
1 GCCAGAAGGTTTGGCAAGCTAG
24288944 TATTCACCCA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.22
Consensus pattern (27 bp):
GCCAGAAGGTTTGGCAAGCTAGAGTTC
Found at i:24289449 original size:24 final size:24
Alignment explanation
Indices: 24289404--24289449 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
24289394 TCGTAGTAGT
* *
24289404 TTGAGTAGGTGTCTTGATAGCAGG
1 TTGAGTAGGTGTCTTAACAGCAGG
24289428 TTGAGTAGGT-TCTTCAACAGCA
1 TTGAGTAGGTGTCTT-AACAGCA
24289450 ACTTGAGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.24, C:0.13, G:0.30, T:0.33
Consensus pattern (24 bp):
TTGAGTAGGTGTCTTAACAGCAGG
Found at i:24296165 original size:27 final size:22
Alignment explanation
Indices: 24296112--24296155 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
24296102 GCTAAATTAC
24296112 ATGTCTGATTGGATTGCTTAAT
1 ATGTCTGATTGGATTGCTTAAT
24296134 ATGTCTGATTGGATTGCTTAAT
1 ATGTCTGATTGGATTGCTTAAT
24296156 TAATTTTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (22 bp):
ATGTCTGATTGGATTGCTTAAT
Found at i:24297746 original size:11 final size:11
Alignment explanation
Indices: 24297730--24297760 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
24297720 ATAGGTTTGT
24297730 AAAAAAATTGA
1 AAAAAAATTGA
24297741 AAAAAAATTGA
1 AAAAAAATTGA
24297752 AAAAAAATT
1 AAAAAAATT
24297761 TTGTGAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:24305494 original size:10 final size:10
Alignment explanation
Indices: 24305479--24305528 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
24305469 ATTGGGTTAA
24305479 AATTGAGCTG
1 AATTGAGCTG
*
24305489 AATTGATCTCG
1 AATTGAGCT-G
24305500 AA-TGAGCTG
1 AATTGAGCTG
*
24305509 AATTGAGCTC
1 AATTGAGCTG
*
24305519 AAGTGAGCTG
1 AATTGAGCTG
24305529 GAAACGAGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 27 0.82
11 3 0.09
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (10 bp):
AATTGAGCTG
Found at i:24305505 original size:20 final size:20
Alignment explanation
Indices: 24305482--24305528 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
24305472 GGGTTAAAAT
*
24305482 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
24305502 TGAGCTGAATTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
24305522 TGAGCTG
1 TGAGCTG
24305529 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:24307463 original size:21 final size:22
Alignment explanation
Indices: 24307439--24307498 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 22
24307429 TTTTCCACTC
*
24307439 TTTCTTTTTC-TTCTCTTTTAA
1 TTTCTTTTTCAATCTCTTTTAA
24307460 TTTCTTTTTCAATCTC-TTT--
1 TTTCTTTTTCAATCTCTTTTAA
*
24307479 TTTC-TTTTCACTCTCTTTTA
1 TTTCTTTTTCAATCTCTTTTA
24307499 TTTTTGAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 10 0.29
19 7 0.21
21 13 0.38
22 4 0.12
ACGTcount: A:0.10, C:0.22, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTCTTTTTCAATCTCTTTTAA
Found at i:24307488 original size:18 final size:19
Alignment explanation
Indices: 24307460--24307497 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
24307450 TCTCTTTTAA
24307460 TTTCTTTTTCAATCTCTTT
1 TTTCTTTTTCAATCTCTTT
*
24307479 TTTC-TTTTCACTCTCTTT
1 TTTCTTTTTCAATCTCTTT
24307497 T
1 T
24307498 ATTTTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTCTTTTTCAATCTCTTT
Found at i:24307533 original size:15 final size:15
Alignment explanation
Indices: 24307510--24307551 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
24307500 TTTTGAAATC
24307510 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
24307525 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
24307540 TCATTTTCATTT
1 TCATTTTCATTT
24307552 TCCTTATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 2 0.08
15 22 0.92
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:24307551 original size:28 final size:29
Alignment explanation
Indices: 24307510--24307566 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
24307500 TTTTGAAATC
* *
24307510 TCATTTTCATATTTTTCTTTTTCATTTCTT
1 TCATTTTCA-ATTTTCCTTATTCATTTCTT
*
24307540 TCATTTTC-ATTTTCCTTATTCTTTTCT
1 TCATTTTCAATTTTCCTTATTCATTTCT
24307567 CGCTCAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 16 0.67
30 8 0.33
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.68
Consensus pattern (29 bp):
TCATTTTCAATTTTCCTTATTCATTTCTT
Found at i:24308623 original size:13 final size:13
Alignment explanation
Indices: 24308593--24308635 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
24308583 CTCGCAAGAC
*
24308593 TTTTCACTTCTTT
1 TTTTTACTTCTTT
24308606 TTTTT-CTTCTTT
1 TTTTTACTTCTTT
24308618 TCTTTTAC-TCTTT
1 T-TTTTACTTCTTT
24308631 TTTTT
1 TTTTT
24308636 TTGCTCACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 12 0.44
13 14 0.52
14 1 0.04
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTACTTCTTT
Found at i:24308636 original size:13 final size:13
Alignment explanation
Indices: 24308599--24308665 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 13
24308589 AGACTTTTCA
24308599 CTTC-TTTTTTTT
1 CTTCTTTTTTTTT
24308611 CTTCTTTTCTTTTACT
1 CTTCTTTT-TTTT--T
*
24308627 CTT-TTTTTTTTG
1 CTTCTTTTTTTTT
*
24308639 CTCACTTCTTTTTTT
1 CT-TCTT-TTTTTTT
24308654 CTT-TTTTTTTTT
1 CTTCTTTTTTTTT
24308666 GAATTTTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
12 13 0.30
13 5 0.11
14 10 0.23
15 12 0.27
16 4 0.09
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (13 bp):
CTTCTTTTTTTTT
Found at i:24310206 original size:10 final size:10
Alignment explanation
Indices: 24310191--24310240 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
24310181 ATTGGGTTAA
24310191 AATTGAGCTG
1 AATTGAGCTG
*
24310201 AATTGATCTCG
1 AATTGAGCT-G
24310212 AA-TGAGCTG
1 AATTGAGCTG
*
24310221 AATTGAGCTC
1 AATTGAGCTG
*
24310231 AAGTGAGCTG
1 AATTGAGCTG
24310241 CAAACGAGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 27 0.82
11 3 0.09
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (10 bp):
AATTGAGCTG
Found at i:24310217 original size:20 final size:20
Alignment explanation
Indices: 24310194--24310240 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
24310184 GGGTTAAAAT
*
24310194 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
24310214 TGAGCTGAATTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
24310234 TGAGCTG
1 TGAGCTG
24310241 CAAACGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:24312885 original size:20 final size:20
Alignment explanation
Indices: 24312862--24312915 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
24312852 AGTTTTTCCC
*
24312862 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
24312882 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
24312902 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
24312916 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:24312897 original size:30 final size:30
Alignment explanation
Indices: 24312862--24312935 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
24312852 AGTTTTTCCC
24312862 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
24312892 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
24312922 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
24312936 TGGATTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:24312925 original size:20 final size:20
Alignment explanation
Indices: 24312862--24312926 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
24312852 AGTTTTTCCC
* * * *
24312862 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
24312882 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
24312901 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
24312922 AGCTC
1 AGCTC
24312927 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:24319092 original size:10 final size:10
Alignment explanation
Indices: 24319079--24319135 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
24319069 AGCTCCGACT
*
24319079 AGCTCAATTG
1 AGCTCAATTC
*
24319089 AGCTCATTTC
1 AGCTCAATTC
24319099 AGCTCAA-TC
1 AGCTCAATTC
*
24319108 GAGCTCAATTT
1 -AGCTCAATTC
24319119 AGCTACAATTC
1 AGCT-CAATTC
24319130 AGCTCA
1 AGCTCA
24319136 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:24319102 original size:20 final size:19
Alignment explanation
Indices: 24319078--24319139 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 19
24319068 CAGCTCCGAC
24319078 TAGCTCAATTGAGCTCATT
1 TAGCTCAATTGAGCTCATT
*
24319097 TCAGCTCAATCGAGCTCAATT
1 T-AGCTCAATTGAGCTC-ATT
*
24319118 TAGCTACAATTCAGCTCATT
1 TAGCT-CAATTGAGCTCATT
24319138 TA
1 TA
24319140 TTTTATTGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.03
20 23 0.62
21 13 0.35
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (19 bp):
TAGCTCAATTGAGCTCATT
Found at i:24320400 original size:16 final size:17
Alignment explanation
Indices: 24320379--24320419 Score: 75
Period size: 16 Copynumber: 2.5 Consensus size: 17
24320369 TCGTGAATTG
24320379 AAAAAAAATTCGTGCA-
1 AAAAAAAATTCGTGCAT
24320395 AAAAAAAATTCGTGCAT
1 AAAAAAAATTCGTGCAT
24320412 AAAAAAAA
1 AAAAAAAA
24320420 GAGGTTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.63, C:0.10, G:0.10, T:0.17
Consensus pattern (17 bp):
AAAAAAAATTCGTGCAT
Found at i:24323932 original size:10 final size:10
Alignment explanation
Indices: 24323918--24323975 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
24323908 CAGCTCCGAC
24323918 CAGCTCAATT
1 CAGCTCAATT
* *
24323928 GAGCTCATTT
1 CAGCTCAATT
24323938 CAGCTCAA-T
1 CAGCTCAATT
24323947 CGAGCTCAATT
1 C-AGCTCAATT
*
24323958 TAGCTACAATT
1 CAGCT-CAATT
24323969 CAGCTCA
1 CAGCTCA
24323976 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:24323941 original size:20 final size:20
Alignment explanation
Indices: 24323918--24323978 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
24323908 CAGCTCCGAC
24323918 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
24323938 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
24323959 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
24323979 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:24333883 original size:13 final size:14
Alignment explanation
Indices: 24333861--24333914 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 14
24333851 AAATTGTAGT
24333861 TTCGAAAAAAAAAA
1 TTCGAAAAAAAAAA
24333875 TTC--AAAAAAAAA
1 TTCGAAAAAAAAAA
24333887 TTCGAAAAGAAAAAAAA
1 TTCG--AA-AAAAAAAA
24333904 TT-GAAAAAAAA
1 TTCGAAAAAAAA
24333915 TTGTATACGG
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
12 12 0.34
13 6 0.17
14 5 0.14
16 2 0.06
17 10 0.29
ACGTcount: A:0.72, C:0.06, G:0.07, T:0.15
Consensus pattern (14 bp):
TTCGAAAAAAAAAA
Found at i:24333886 original size:16 final size:17
Alignment explanation
Indices: 24333878--24333914 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
24333868 AAAAAAATTC
24333878 AAAAAAAAATTCGAAAA
1 AAAAAAAAATTCGAAAA
*
24333895 GAAAAAAAATT-GAAAA
1 AAAAAAAAATTCGAAAA
24333911 AAAA
1 AAAA
24333915 TTGTATACGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.11
Consensus pattern (17 bp):
AAAAAAAAATTCGAAAA
Found at i:24341731 original size:20 final size:20
Alignment explanation
Indices: 24341706--24341752 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
24341696 AGCTCGTTTC
*
24341706 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
24341726 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
24341746 CAGCTCA
1 CAGCTCA
24341753 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:24343359 original size:20 final size:20
Alignment explanation
Indices: 24343334--24343378 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
24343324 TAAATACACA
24343334 TAATTAAAACT-AGACACAAT
1 TAATT-AAACTAAGACACAAT
**
24343354 TAATTAAGTTAAGACACAAT
1 TAATTAAACTAAGACACAAT
24343374 TAATT
1 TAATT
24343379 CGGTTGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (20 bp):
TAATTAAACTAAGACACAAT
Found at i:24346024 original size:16 final size:16
Alignment explanation
Indices: 24346005--24346037 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
24345995 TTGCTGTTGC
24346005 TGTTTAATGCTGCTGT
1 TGTTTAATGCTGCTGT
*
24346021 TGTTTAATGCTGTTGT
1 TGTTTAATGCTGCTGT
24346037 T
1 T
24346038 TAAATGCAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.24, T:0.55
Consensus pattern (16 bp):
TGTTTAATGCTGCTGT
Found at i:24348359 original size:22 final size:22
Alignment explanation
Indices: 24348331--24348374 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
24348321 TTTTGAACCA
24348331 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
24348353 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
24348375 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:24350261 original size:12 final size:11
Alignment explanation
Indices: 24350244--24350378 Score: 57
Period size: 12 Copynumber: 11.8 Consensus size: 11
24350234 GAAAGTAAAT
24350244 AAAAAGAAAACG
1 AAAAAGAAAA-G
24350256 AAAAAGAAAAAG
1 AAAAAG-AAAAG
**
24350268 AAATTGCAAAAG
1 AAAAAG-AAAAG
24350280 AAAAAGAAATCA-
1 AAAAAGAAA--AG
* *
24350292 AAAAAGTGAGAG
1 AAAAAG-AAAAG
24350304 AAAAAGAAAATG
1 AAAAAGAAAA-G
24350316 ---AAGAAAAG
1 AAAAAGAAAAG
*
24350324 AAAATTGAAAAAG
1 AAAA-AG-AAAAG
**
24350337 AAAAAGAGATTG
1 AAAAAGA-AAAG
*
24350349 AAAAAGAAATTG
1 AAAAAGAAA-AG
24350361 AAAAAG--AAG
1 AAAAAGAAAAG
24350370 AAAAAGAAA
1 AAAAAGAAA
24350379 GAGTGGAAAT
Statistics
Matches: 93, Mismatches: 15, Indels: 31
0.67 0.11 0.22
Matches are distributed among these distances:
8 1 0.01
9 14 0.15
10 1 0.01
11 10 0.11
12 52 0.56
13 15 0.16
ACGTcount: A:0.71, C:0.02, G:0.19, T:0.08
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:24350267 original size:18 final size:18
Alignment explanation
Indices: 24350244--24350357 Score: 86
Period size: 18 Copynumber: 6.2 Consensus size: 18
24350234 GAAAGTAAAT
*
24350244 AAAAAGAAAACGAAAAAG
1 AAAAAGAAAATGAAAAAG
* *
24350262 AAAAAGAAATTGCAAAAG
1 AAAAAGAAAATGAAAAAG
*
24350280 AAAAAG-AAATCAAAAAAG
1 AAAAAGAAAAT-GAAAAAG
** * * *
24350298 TGAGAGAAAAAGAAAATG
1 AAAAAGAAAATGAAAAAG
24350316 AAGAAAAGAAAATTGAAAAAG
1 -A-AAAAGAAAA-TGAAAAAG
* *
24350337 AAAAAGAGATTGAAAAAG
1 AAAAAGAAAATGAAAAAG
24350355 AAA
1 AAA
24350358 TTGAAAAAGA
Statistics
Matches: 72, Mismatches: 19, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
17 3 0.04
18 45 0.62
19 10 0.14
20 8 0.11
21 6 0.08
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.08
Consensus pattern (18 bp):
AAAAAGAAAATGAAAAAG
Found at i:24350296 original size:30 final size:30
Alignment explanation
Indices: 24350244--24350368 Score: 96
Period size: 30 Copynumber: 4.3 Consensus size: 30
24350234 GAAAGTAAAT
*
24350244 AAAAAGAAAACGAAA-AAGAAAAAGAAATTG
1 AAAAAGAAAAAGAAATAA-AAAAAGAAATTG
* * ** **
24350274 CAAAAGAAAAAGAAATCAAAAAAGTGAGAG
1 AAAAAGAAAAAGAAATAAAAAAAGAAATTG
* * *
24350304 AAAAAGAAAATG-AA-GAAAAGA-AAATTG
1 AAAAAGAAAAAGAAATAAAAAAAGAAATTG
* **
24350331 AAAAAGAAAAAGAGATTGAAAAAGAAATTG
1 AAAAAGAAAAAGAAATAAAAAAAGAAATTG
24350361 AAAAAGAA
1 AAAAAGAA
24350369 GAAAAAGAAA
Statistics
Matches: 71, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
27 13 0.18
28 6 0.08
29 6 0.08
30 45 0.63
31 1 0.01
ACGTcount: A:0.70, C:0.02, G:0.18, T:0.09
Consensus pattern (30 bp):
AAAAAGAAAAAGAAATAAAAAAAGAAATTG
Found at i:24350377 original size:57 final size:57
Alignment explanation
Indices: 24350255--24350378 Score: 135
Period size: 57 Copynumber: 2.2 Consensus size: 57
24350245 AAAAGAAAAC
* **
24350255 GAAAAAGAAAAAGAAATTGCAAAAGAAAAAGAAATCAAAAAAGTGAGAGAAAAAGAA
1 GAAAAAGAAAAAGAAATTGAAAAAGAAAAAGAAATCAAAAAAGAAAGAGAAAAAGAA
* * ** **
24350312 -AATGAAG-AAAAGAAAATTGAAAAAGAAAAAGAGATTGAAAAAGAAATTGAAAAAGAA
1 GAA-AAAGAAAAAG-AAATTGAAAAAGAAAAAGAAATCAAAAAAGAAAGAGAAAAAGAA
24350369 GAAAAAGAAA
1 GAAAAAGAAA
24350379 GAGTGGAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
56 7 0.13
57 42 0.79
58 4 0.08
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (57 bp):
GAAAAAGAAAAAGAAATTGAAAAAGAAAAAGAAATCAAAAAAGAAAGAGAAAAAGAA
Found at i:24352709 original size:16 final size:16
Alignment explanation
Indices: 24352670--24352709 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
24352660 ATGTGTTTTG
* *
24352670 CTGTTGCTGTTTAATG
1 CTGTTGTTGTTTAATA
*
24352686 CTGCTGTTGTTTAATA
1 CTGTTGTTGTTTAATA
24352702 CTGTTGTT
1 CTGTTGTT
24352710 TAAATGCAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.12, C:0.12, G:0.23, T:0.53
Consensus pattern (16 bp):
CTGTTGTTGTTTAATA
Found at i:24356728 original size:822 final size:820
Alignment explanation
Indices: 24355131--24357249 Score: 2848
Period size: 822 Copynumber: 2.6 Consensus size: 820
24355121 ACTCGTAGCA
* *
24355131 CTTTCCTTTAATTTGCAGGTT-GATTCTTGTCTGCTTGTTTCTAATATTTTATTTCTTTACTTCC
1 CTTTCCTTTAATTTGTA-GTTCGATTCTTGTCTGTTTGTTTCTAATA-TTTATTTCTTTACTTCC
* *
24355195 ATATCAGGAATCAACAAGAAAAGACATTCTCCCTCATTAATACACCAAGAACCATTGAAAACAAA
64 ATATCAGGAATCAACAAGAAAAGACGTTCTCCCTCCTTAATACACCAAGAACCATTGAAAACAAA
* * * *
24355260 GAAGTCTCTTCTTTTCTTATTGAGGCGATTGCTTTTATCACAAAACAATTTTATTATGGCTTAAA
129 GAAGCCCCTTCTTTTCTTATTGTGCCGATTGCTTTTATCACAAAA-AATTTTATTATGGCTTAAA
* * * *
24355325 AATCTATTCTGACAATCTGTTTACTTCTTTTGATTCCAGATATAGTTTGAGGCC-TCTTTTGGTT
193 AATCCATTCTGACAATCTGTTTTCTTCTTTCGATTCCAGATCTAGTTTGAGGCCTTCTTTTGGTT
* *
24355389 TAAGAATGGTTCTTTCTCATTCAAGAAACCCGTATCCCACTTGTTCTTGCACTCCTCTTTGCCCA
258 CAAGAATGGTTCTTTCTCATTCAAGAAACCCGTATCCCACTCGTTCTTGCA-----C-TT-CCCA
* * * *
24355454 CCTCTCTCCTCCCATGTTGTTTGGTTTACTTTTTCATTCTTTTAACAAT-AAATCTAAATTGTTT
316 CCTCTCTCATTCCATGCTGTTTGGTTTACTTTTTCATTCTTTT-AC--TGAAATCTAATTTGTTT
*
24355518 TATTT-TTTTGTTTAGATCTCGATTTGACATCATCTTTTCATCCAAGAATGGTTCAAATCATCTT
378 TATTTCTTTTGTTTAGATCTCGATTCGACATCATCTTTTCATCCAAGAATGGTTCAAATCATCTT
* * * * *
24355582 AATATAGTTGATTCTTCATGTTTTTTATTGGTCAGGCATTCCTTTAATCTTTCTTGTGATTTCAT
443 AATATACTTGATTCTTCAAGTTCTTTACTGGTCAGGCATTCCTTTAATCTATCTTGTGATTTCAT
* * * ** *
24355647 TAGATTTTGCTTTTTATTCTTCAGGTCTGCCAACCATTTGTTTTCACTTAATTTGCAACTTTGAC
508 TAGATTTTGATCTTTATTCTACAAATCTGCCAACCATTTGTTTTCACTTAATTTGCAACCTTGAC
* * *
24355712 CCCTTTGGATTTCATATAGAATAGTGCTTCCCTAACCTACTTGGTGTCCTCCAAGAACCTTAATT
573 CCCTTTGGATTTCATACAGAATAGTGCTTCCCTAACCTACTTGGTCTCCTCCAAGAACCCTAATT
*
24355777 TGGATTTAGTTTCCTTATTTTTTAATGACTTGATTTGTGTTGTTACCCTTTTAATCCTAACATGG
638 TCGATTTAGTTTCCTTATTTTTTAATGACTTGATTTGTGTTGTTACCCTTTTAATCCTAACATGG
* * *
24355842 ATTTTTTGAGGTTTGGGTGGGTTCAAAATCCATGATTCCTTAATCTTGAGAATGCAATAATCTAA
703 ATTGTTTGAGGTTTGGGTGGGGTCAAAATCCATGATTCCTTAATCTTGAGAATGCAACAATCTAA
* *
24355907 TGCTCCTTAAGACATCTTCA-CCCGACTTTAGTCTTTTCCCAACTAT-CTTTTCT
768 TGCTCCTTAAGACAGCTTCATCCC-ACTTTAGTCTTTTCCCAACT-TCCTTCTCT
* * * * *
24355960 TTTTCCTTTAATTTGTAGTTCGATTCTTTTTTGTTTGTTTCTAGTATTTATTTCTTTACTTTCAT
1 CTTTCCTTTAATTTGTAGTTCGATTCTTGTCTGTTTGTTTCTAATATTTATTTCTTTACTTCCAT
* * *
24356025 ATTAGGAATCAACAAGAAAAGACGTTCTCCCTCCTTAATGCACCAAGAACCATTGAAAACAAGGA
66 ATCAGGAATCAACAAGAAAAGACGTTCTCCCTCCTTAATACACCAAGAACCATTGAAAACAAAGA
*
24356090 AGCCCCTTCTTTTCTTATTGTGTCGATTGCTTTTATCACAAAATAATTTTATTATGGCTTAAAAA
131 AGCCCCTTCTTTTCTTATTGTGCCGATTGCTTTTATCACAAAA-AATTTTATTATGGCTTAAAAA
*
24356155 TCCATTCTGACAATCTGTTTTCTTCTTTCAATTCCAGATCTAGTTTGAGGCCTTCTTTTGGTTCA
195 TCCATTCTGACAATCTGTTTTCTTCTTTCGATTCCAGATCTAGTTTGAGGCCTTCTTTTGGTTCA
* *
24356220 AGAATGGTTCTTTCTTATTCAAGAAACCCGTATCTCACTCGTTCTTGCAC-TCCCACCTCTCTCA
260 AGAATGGTTCTTTCTCATTCAAGAAACCCGTATCCCACTCGTTCTTGCACTTCCCACCTCTCTCA
* *
24356284 TTCCATGCTATTTGGTTTACTTTTTCATTCTTTTGACTGAACATCTAATTTCTTTTATTTCTTTT
325 TTCCATGCTGTTTGGTTTACTTTTTCATTCTTTT-ACTGAA-ATCTAATTTGTTTTATTTCTTTT
*
24356349 GTTTAGATCTCGATTCGACATAATCTTTTCATCCAAGAATGGTTCAAATCATCTTAATATACTTG
388 GTTTAGATCTCGATTCGACATCATCTTTTCATCCAAGAATGGTTCAAATCATCTTAATATACTTG
24356414 ATTCTTCAAGTTCTTTACTGGTCAGGCATTCCTTTAATCTATCTTGTGATCTT-ATTCA-ATTTT
453 ATTCTTCAAGTTCTTTACTGGTCAGGCATTCCTTTAATCTATCTTGTGAT-TTCATT-AGATTTT
** * *
24356477 GATCTTTATTCTACAAATCTGTCCAACTGTTTGTTTTCACTTAATTTGCAGCCTTG-CCCTTTTG
516 GATCTTTATTCTACAAATCTG-CCAACCATTTGTTTTCACTTAATTTGCAACCTTGACCCCTTTG
* *
24356541 GATTTCATACAGAATAGTGCTTCCTTAACCTACTTGGTCTCTTCCAAGAACCCTAATTTCGATTT
580 GATTTCATACAGAATAGTGCTTCCCTAACCTACTTGGTCTCCTCCAAGAACCCTAATTTCGATTT
* * * *
24356606 AGTTTCCTTATTCTTTT-ATGACTTGATTTGTGTTGTTTCCTTTTTAATTCTAACTTGGATTGTT
645 AGTTTCCTTATT-TTTTAATGACTTGATTTGTGTTGTTACCCTTTTAATCCTAACATGGATTGTT
* * * * *
24356670 TGAGTTTTGGGTGGGGTCGAACTCTATGATTCCTTAATCTTGAGAATGCAACAATCTAATGCTGC
709 TGAGGTTTGGGTGGGGTCAAAATCCATGATTCCTTAATCTTGAGAATGCAACAATCTAATGCTCC
* *
24356735 TTAGGACAGCTTCATGCCACTTTAGTCTTTTCCCAACTTCCTTCTCT
774 TTAAGACAGCTTCATCCCACTTTAGTCTTTTCCCAACTTCCTTCTCT
* * *
24356782 CTTTCCTTTAATTTGTAGTTCGATTCTTGTCTATTTATTTCTAATCTTTTATTTCTTTACTTCCA
1 CTTTCCTTTAATTTGTAGTTCGATTCTTGTCTGTTTGTTTCTAAT-ATTTATTTCTTTACTTCCA
* *
24356847 TATGAGGAATCAACAAGAAAAGACGTTC-CCCATTCTTAATACACCAAGAACCATTGAAAACAAA
65 TATCAGGAATCAACAAGAAAAGACGTTCTCCC-TCCTTAATACACCAAGAACCATTGAAAACAAA
* * * * * *
24356911 TAAGTCTCTTTTTTTTCTTATTGTGCCGATTGCTTTTATCACAAAAAATTTTTGTTATTGCTTAA
129 GAAG-CCCCTTCTTTTCTTATTGTGCCGATTGCTTTTATCACAAAAAA-TTTTATTATGGCTTAA
** * * * * * *
24356976 AAATCCATTAC-GATTATCTTTTTTCTTCTTTCGATTTCAAAACTAGTTGGAGTCCTTCTTTTGG
192 AAATCCATT-CTGACAATCTGTTTTCTTCTTTCGATTCCAGATCTAGTTTGAGGCCTTCTTTTGG
* * * * * * *
24357040 TTCAAGAGTGGTTCATTCTCATCCATGAAA-CCATATCCCACTCATTCTTAGACTCCTCTTTTCG
256 TTCAAGAATGGTTCTTTCTCATTCAAGAAACCCGTATCCCACTCGTTCTT-G----CAC--TTC-
* * * * *** *
24357104 CCATCTCTCTCTTTCCTTGCTGTTTGGTTTTCTTTTTCATTCTTTTAGAAAAAT-TAATTGGTTT
313 CCACCTCTCTCATTCCATGCTGTTTGGTTTACTTTTTCATTCTTTTACTGAAATCTAATTTGTTT
* *
24357168 TA-TTCTTTTGTTTAGATCTCGACTCGACATCATCTTTTCATCTAAGAATGGTTCAAATCATCTT
378 TATTTCTTTTGTTTAGATCTCGATTCGACATCATCTTTTCATCCAAGAATGGTTCAAATCATCTT
24357232 AATATACTTGATTCTTCA
443 AATATACTTGATTCTTCA
24357250 TCTAGAGCCC
Statistics
Matches: 1143, Mismatches: 122, Indels: 51
0.87 0.09 0.04
Matches are distributed among these distances:
819 1 0.00
820 2 0.00
821 62 0.05
822 395 0.35
823 133 0.12
824 131 0.11
825 1 0.00
828 267 0.23
829 103 0.09
830 2 0.00
831 5 0.00
832 41 0.04
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (820 bp):
CTTTCCTTTAATTTGTAGTTCGATTCTTGTCTGTTTGTTTCTAATATTTATTTCTTTACTTCCAT
ATCAGGAATCAACAAGAAAAGACGTTCTCCCTCCTTAATACACCAAGAACCATTGAAAACAAAGA
AGCCCCTTCTTTTCTTATTGTGCCGATTGCTTTTATCACAAAAAATTTTATTATGGCTTAAAAAT
CCATTCTGACAATCTGTTTTCTTCTTTCGATTCCAGATCTAGTTTGAGGCCTTCTTTTGGTTCAA
GAATGGTTCTTTCTCATTCAAGAAACCCGTATCCCACTCGTTCTTGCACTTCCCACCTCTCTCAT
TCCATGCTGTTTGGTTTACTTTTTCATTCTTTTACTGAAATCTAATTTGTTTTATTTCTTTTGTT
TAGATCTCGATTCGACATCATCTTTTCATCCAAGAATGGTTCAAATCATCTTAATATACTTGATT
CTTCAAGTTCTTTACTGGTCAGGCATTCCTTTAATCTATCTTGTGATTTCATTAGATTTTGATCT
TTATTCTACAAATCTGCCAACCATTTGTTTTCACTTAATTTGCAACCTTGACCCCTTTGGATTTC
ATACAGAATAGTGCTTCCCTAACCTACTTGGTCTCCTCCAAGAACCCTAATTTCGATTTAGTTTC
CTTATTTTTTAATGACTTGATTTGTGTTGTTACCCTTTTAATCCTAACATGGATTGTTTGAGGTT
TGGGTGGGGTCAAAATCCATGATTCCTTAATCTTGAGAATGCAACAATCTAATGCTCCTTAAGAC
AGCTTCATCCCACTTTAGTCTTTTCCCAACTTCCTTCTCT
Found at i:24362576 original size:22 final size:22
Alignment explanation
Indices: 24362548--24362655 Score: 144
Period size: 22 Copynumber: 4.9 Consensus size: 22
24362538 TTTATTGTTC
*
24362548 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
24362570 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
24362592 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
24362614 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
24362636 AAACATGAGAGCTTAGTACG
1 AAACATGAGAGCTTAGTACG
24362656 GTCAAAATGG
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 75 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:24363090 original size:39 final size:39
Alignment explanation
Indices: 24363058--24363174 Score: 162
Period size: 39 Copynumber: 3.0 Consensus size: 39
24363048 TAAAAACATG
* * * *
24363058 TATTAAAGATGTCCAAACTATGACATAATTAAAAACTCT
1 TATTAATGATGTTCAAATTATGACATAATTAAAAACTCA
* *
24363097 TATTAATGATGTTCAGATTATGACATATTTAAAAACTCA
1 TATTAATGATGTTCAAATTATGACATAATTAAAAACTCA
* *
24363136 TATTAATGATGTTGAAATTATGACATAATTAAAGACTCA
1 TATTAATGATGTTCAAATTATGACATAATTAAAAACTCA
24363175 AACAAAATTA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 68 1.00
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (39 bp):
TATTAATGATGTTCAAATTATGACATAATTAAAAACTCA
Found at i:24366742 original size:45 final size:45
Alignment explanation
Indices: 24366649--24366823 Score: 221
Period size: 45 Copynumber: 3.9 Consensus size: 45
24366639 AACCGTTACA
* * *
24366649 TGGTGG-ATCAGCACATAGC-ACCACCCTTATAATCAATTATATTC
1 TGGTGGAATCAACACATAGCAACCACCTTTATAATCAATGAT-TTC
* **
24366693 -GGTGGAATCAGCACATAGCAACCACCTTTATTTTCAATGATTTC
1 TGGTGGAATCAACACATAGCAACCACCTTTATAATCAATGATTTC
* * **
24366737 TGGTGGAGTCAACACATAGCAACCACCTTTATAATCAATGGTACC
1 TGGTGGAATCAACACATAGCAACCACCTTTATAATCAATGATTTC
*
24366782 CGGTGGAATCAACACATAGCAACCACCTTTATAATCAATGAT
1 TGGTGGAATCAACACATAGCAACCACCTTTATAATCAATGAT
24366824 ACTCAGTAGA
Statistics
Matches: 114, Mismatches: 14, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
43 5 0.04
44 16 0.14
45 93 0.82
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27
Consensus pattern (45 bp):
TGGTGGAATCAACACATAGCAACCACCTTTATAATCAATGATTTC
Found at i:24366821 original size:90 final size:88
Alignment explanation
Indices: 24366649--24366823 Score: 251
Period size: 90 Copynumber: 2.0 Consensus size: 88
24366639 AACCGTTACA
* * ** *
24366649 TGGTGGATCAGCACATAGCACCACCCTTATAATCAATTATATTCGGTGGAATCAGCACATAGCAA
1 TGGTGGATCAACACATAGCACCACCCTTATAATCAATGATACCCGGTGGAATCAACACATAGCAA
**
24366714 CCACCTTTATTTTCAATGATTTC
66 CCACCTTTATAATCAATGATTTC
* *
24366737 TGGTGGAGTCAACACATAGCAACCACCTTTATAATCAATGGTACCCGGTGGAATCAACACATAGC
1 TGGTGGA-TCAACACATAGC-ACCACCCTTATAATCAATGATACCCGGTGGAATCAACACATAGC
24366802 AACCACCTTTATAATCAATGAT
64 AACCACCTTTATAATCAATGAT
24366824 ACTCAGTAGA
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
88 7 0.09
89 11 0.14
90 58 0.76
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27
Consensus pattern (88 bp):
TGGTGGATCAACACATAGCACCACCCTTATAATCAATGATACCCGGTGGAATCAACACATAGCAA
CCACCTTTATAATCAATGATTTC
Found at i:24372033 original size:45 final size:45
Alignment explanation
Indices: 24371960--24372117 Score: 172
Period size: 45 Copynumber: 3.5 Consensus size: 45
24371950 AGCACATAAT
* * * ** * *
24371960 ACCACCCTTATAATAAATTATATTCGGTGGAATCAACACATAGCA
1 ACCACCTTTATAATCAATGATACCCGGTGGAATTAGCACATAGCA
** ** * *
24372005 ACCACCTTTATTTTCAATGATTTCCGGTGGAGTTGGCACATAGCA
1 ACCACCTTTATAATCAATGATACCCGGTGGAATTAGCACATAGCA
* *
24372050 ACCCCCTTTATAATCAATGGTACCCGGTGGAATTAGCACATAGCA
1 ACCACCTTTATAATCAATGATACCCGGTGGAATTAGCACATAGCA
*
24372095 ACCACCTTTATAATTAATGATAC
1 ACCACCTTTATAATCAATGATAC
24372118 TCAGTACACA
Statistics
Matches: 91, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 91 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (45 bp):
ACCACCTTTATAATCAATGATACCCGGTGGAATTAGCACATAGCA
Found at i:24373552 original size:15 final size:17
Alignment explanation
Indices: 24373534--24373574 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
24373524 TGGTTGTGTT
24373534 TATATA-ATGTGTG-AA
1 TATATATATGTGTGTAA
24373549 TATATATATGTGTGTAA
1 TATATATATGTGTGTAA
24373566 TATATATAT
1 TATATATAT
24373575 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 6 0.25
16 7 0.29
17 11 0.46
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (17 bp):
TATATATATGTGTGTAA
Found at i:24373863 original size:41 final size:41
Alignment explanation
Indices: 24373808--24373894 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
24373798 ATTGGTGAAT
*
24373808 TGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATC
1 TGAATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATC
*
24373849 TGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATC
1 TGAATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATC
*
24373890 CGAAT
1 TGAAT
24373895 ATGATGAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.23
Consensus pattern (41 bp):
TGAATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATC
Found at i:24374133 original size:33 final size:35
Alignment explanation
Indices: 24374095--24374181 Score: 106
Period size: 37 Copynumber: 2.5 Consensus size: 35
24374085 GCATATTTAG
*
24374095 GCATTCGGCATAGGTGGATAT-A-TATATTTGTAT
1 GCATTCGGCATAGGTGGATATAAGTATATATGTAT
* * *
24374128 GCATTCGACATAGATAGATATAAGTGTATATATGTAT
1 GCATTCGGCATAGGTGGATATAA--GTATATATGTAT
24374165 GCATTCGGCATAGGTGG
1 GCATTCGGCATAGGTGG
24374182 GTAATAGTGA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
33 18 0.42
34 1 0.02
37 24 0.56
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.34
Consensus pattern (35 bp):
GCATTCGGCATAGGTGGATATAAGTATATATGTAT
Found at i:24386055 original size:10 final size:10
Alignment explanation
Indices: 24386040--24386089 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
24386030 ATTGGGTTAA
24386040 AATTGAGCTG
1 AATTGAGCTG
*
24386050 AATTGATCTCG
1 AATTGAGCT-G
24386061 AA-TGAGCTG
1 AATTGAGCTG
*
24386070 AATTGAGCTC
1 AATTGAGCTG
*
24386080 AAGTGAGCTG
1 AATTGAGCTG
24386090 GAAACGAGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 27 0.82
11 3 0.09
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (10 bp):
AATTGAGCTG
Found at i:24386066 original size:20 final size:20
Alignment explanation
Indices: 24386043--24386089 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
24386033 GGGTTAAAAT
*
24386043 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
24386063 TGAGCTGAATTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
24386083 TGAGCTG
1 TGAGCTG
24386090 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:24390527 original size:25 final size:25
Alignment explanation
Indices: 24390499--24390546 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
24390489 ATATGCTGTC
*
24390499 ACGAGCTGTA-AATTGGTAAGCTCAT
1 ACGAGCTG-AGAATCGGTAAGCTCAT
24390524 ACGAGCTGAGAATCGGTAAGCTC
1 ACGAGCTGAGAATCGGTAAGCTC
24390547 TCATGAGCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (25 bp):
ACGAGCTGAGAATCGGTAAGCTCAT
Found at i:24394762 original size:10 final size:10
Alignment explanation
Indices: 24394740--24394787 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
24394730 AGCTAATAAC
24394740 GAGCTGAATT
1 GAGCTGAATT
24394750 GAGCTCGAA-T
1 GAGCT-GAATT
*
24394760 GAGCTGACTT
1 GAGCTGAATT
* *
24394770 GAGCTCAAGT
1 GAGCTGAATT
24394780 GAGCTGAA
1 GAGCTGAA
24394788 CCACATCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 26 0.84
11 3 0.10
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (10 bp):
GAGCTGAATT
Found at i:24394765 original size:20 final size:20
Alignment explanation
Indices: 24394740--24394787 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
24394730 AGCTAATAAC
24394740 GAGCTGAATTGAGCTCGAA-T
1 GAGCTGAATTGAGCTC-AAGT
*
24394760 GAGCTGACTTGAGCTCAAGT
1 GAGCTGAATTGAGCTCAAGT
24394780 GAGCTGAA
1 GAGCTGAA
24394788 CCACATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (20 bp):
GAGCTGAATTGAGCTCAAGT
Found at i:24395534 original size:32 final size:32
Alignment explanation
Indices: 24395498--24395597 Score: 86
Period size: 32 Copynumber: 3.2 Consensus size: 32
24395488 AACTTTGAAA
24395498 GTCACACGGTATGGGGTGTTCCACACAGCCTG
1 GTCACACGGTATGGGGTGTTCCACACAGCCTG
* * * *
24395530 GTCACA-TG-ATCGTGTG-TCC-CA-A-CTTTG
1 GTCACACGGTATGGGGTGTTCCACACAGC-CTG
24395557 AAAGTCACACGGTATGGGGTGTTCCACACAGCCTG
1 ---GTCACACGGTATGGGGTGTTCCACACAGCCTG
24395592 GTCACA
1 GTCACA
24395598 TGATCGTGTG
Statistics
Matches: 50, Mismatches: 8, Indels: 20
0.64 0.10 0.26
Matches are distributed among these distances:
26 1 0.02
27 3 0.06
28 2 0.04
29 3 0.06
30 12 0.24
31 2 0.04
32 18 0.36
33 3 0.06
34 2 0.04
35 3 0.06
36 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (32 bp):
GTCACACGGTATGGGGTGTTCCACACAGCCTG
Found at i:24395553 original size:62 final size:62
Alignment explanation
Indices: 24395477--24395611 Score: 261
Period size: 62 Copynumber: 2.2 Consensus size: 62
24395467 TGGGACACTG
*
24395477 TCGTGGGTCCCAACTTTGAAAGTCACACGGTATGGGGTGTTCCACACAGCCTGGTCACATGA
1 TCGTGTGTCCCAACTTTGAAAGTCACACGGTATGGGGTGTTCCACACAGCCTGGTCACATGA
24395539 TCGTGTGTCCCAACTTTGAAAGTCACACGGTATGGGGTGTTCCACACAGCCTGGTCACATGA
1 TCGTGTGTCCCAACTTTGAAAGTCACACGGTATGGGGTGTTCCACACAGCCTGGTCACATGA
24395601 TCGTGTGTCCC
1 TCGTGTGTCCC
24395612 TTATTTTTGA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 72 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.26
Consensus pattern (62 bp):
TCGTGTGTCCCAACTTTGAAAGTCACACGGTATGGGGTGTTCCACACAGCCTGGTCACATGA
Found at i:24398551 original size:24 final size:26
Alignment explanation
Indices: 24398502--24398553 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
24398492 AAAAAGGGCT
*
24398502 GAAATTGGCTAAGTGAAATGATGATG
1 GAAATTGGCTAAGTGAAATGAGGATG
*
24398528 GAAA-TGGCTAGGTG-AATGAGGATG
1 GAAATTGGCTAAGTGAAATGAGGATG
24398552 GA
1 GA
24398554 GATTTGCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 11 0.46
25 9 0.38
26 4 0.17
ACGTcount: A:0.37, C:0.04, G:0.37, T:0.23
Consensus pattern (26 bp):
GAAATTGGCTAAGTGAAATGAGGATG
Found at i:24401898 original size:18 final size:19
Alignment explanation
Indices: 24401872--24401912 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
24401862 TCCAAGTTAG
24401872 ATAAAACAATTAAAATA-A
1 ATAAAACAATTAAAATAGA
*
24401890 ATAAGACAATTAAAATAGA
1 ATAAAACAATTAAAATAGA
24401909 ATAA
1 ATAA
24401913 TAAATCTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (19 bp):
ATAAAACAATTAAAATAGA
Found at i:24402175 original size:27 final size:25
Alignment explanation
Indices: 24402123--24402175 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
24402113 AAACTTTTCT
*
24402123 AAAAGAAACTCAAGAGAAATTCTTA
1 AAAAGAAACTCAAGAGAAATTATTA
*
24402148 AAAAGAAAACTCAAAGAGAATTTATTA
1 AAAAG-AAACTC-AAGAGAAATTATTA
24402175 A
1 A
24402176 CTAAAAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 6 0.25
27 13 0.54
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (25 bp):
AAAAGAAACTCAAGAGAAATTATTA
Found at i:24412753 original size:12 final size:12
Alignment explanation
Indices: 24412738--24412784 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
24412728 TTTTTTTTTG
24412738 TTTTTCACAATTT
1 TTTTTCACAA-TT
24412751 TTTTTCA-AATT
1 TTTTTCACAATT
**
24412762 TTTTTTTCAATT
1 TTTTTCACAATT
24412774 TCTTTTCACAA
1 T-TTTTCACAA
24412785 CTTGATATCC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 7 0.25
12 7 0.25
13 14 0.50
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTTCACAATT
Found at i:24412763 original size:11 final size:13
Alignment explanation
Indices: 24412738--24412784 Score: 62
Period size: 12 Copynumber: 3.8 Consensus size: 13
24412728 TTTTTTTTTG
24412738 TTTTTCACAATTT
1 TTTTTCACAATTT
24412751 TTTTTCA-AATTT
1 TTTTTCACAATTT
*
24412763 TTTTT-TCAATTT
1 TTTTTCACAATTT
*
24412775 CTTTTCACAA
1 TTTTTCACAA
24412785 CTTGATATCC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTCACAATTT
Found at i:24412856 original size:11 final size:12
Alignment explanation
Indices: 24412823--24412853 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
24412813 GGAAACTAGT
24412823 TTTTTTTTCGAA
1 TTTTTTTTCGAA
24412835 TTTTTTTTCGAA
1 TTTTTTTTCGAA
24412847 TTTTTTT
1 TTTTTTT
24412854 CGAGAAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:24417331 original size:17 final size:17
Alignment explanation
Indices: 24417306--24417342 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
24417296 TTGAAGTAGG
* *
24417306 TTCGTATTAAAAAAAGT
1 TTCGAATTAAAAAAAAT
24417323 TTCGAATTAAAAAAAAT
1 TTCGAATTAAAAAAAAT
24417340 TTC
1 TTC
24417343 AAGTTGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (17 bp):
TTCGAATTAAAAAAAAT
Found at i:24440064 original size:43 final size:43
Alignment explanation
Indices: 24439968--24440174 Score: 219
Period size: 43 Copynumber: 4.9 Consensus size: 43
24439958 ATCCGTTACT
* **
24439968 CGGTGGATTCAACACTTAGCAACCACC-TTA-AATTCAGTGATA
1 CGGTGGAATCAACACTTAGCAACCACCTTTACAA-TCAAAGATA
*
24440010 CGG-GGAATCAACACATAGCAACC-CCTTTCACAATCAAAGATA
1 CGGTGGAATCAACACTTAGCAACCACCTTT-ACAATCAAAGATA
* * * * *
24440052 CGGTGGAATCAACACTTAACAACCACCTTTATATTCAATGGTA
1 CGGTGGAATCAACACTTAGCAACCACCTTTACAATCAAAGATA
* * *
24440095 CGG-GGAATCAGCACATAGCAACC-CCTTTCACAATCAAATATA
1 CGGTGGAATCAACACTTAGCAACCACCTTT-ACAATCAAAGATA
* *
24440137 CGGTGGAATCAGCACTTAGCAACCACCTTTAGAATCAA
1 CGGTGGAATCAACACTTAGCAACCACCTTTACAATCAA
24440175 TATTCGGGAA
Statistics
Matches: 137, Mismatches: 20, Indels: 15
0.80 0.12 0.09
Matches are distributed among these distances:
40 2 0.01
41 25 0.18
42 42 0.31
43 58 0.42
44 10 0.07
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.22
Consensus pattern (43 bp):
CGGTGGAATCAACACTTAGCAACCACCTTTACAATCAAAGATA
Found at i:24440115 original size:85 final size:85
Alignment explanation
Indices: 24439968--24440203 Score: 336
Period size: 85 Copynumber: 2.8 Consensus size: 85
24439958 ATCCGTTACT
* * *
24439968 CGGTGGATTCAACACTTAGCAACCACC-TTAAATTCAGTGATACGGGGAATCAACACATAGCAAC
1 CGGTGGAATCAACACTTAGCAACCACCTTTAAATTCAATGATACGGGGAATCAGCACATAGCAAC
24440032 CCCTTTCACAATCAAAGATA
66 CCCTTTCACAATCAAAGATA
* * *
24440052 CGGTGGAATCAACACTTAACAACCACCTTTATATTCAATGGTACGGGGAATCAGCACATAGCAAC
1 CGGTGGAATCAACACTTAGCAACCACCTTTAAATTCAATGATACGGGGAATCAGCACATAGCAAC
*
24440117 CCCTTTCACAATCAAATATA
66 CCCTTTCACAATCAAAGATA
* * * *
24440137 CGGTGGAATCAGCACTTAGCAACCACCTTTAGAA-TCAAT-ATTC-GGGAATCAGCACTTAGCGA
1 CGGTGGAATCAACACTTAGCAACCACCTTTA-AATTCAATGATACGGGGAATCAGCACATAGCAA
24440199 CCCCT
65 CCCCT
24440204 CGGGGAATTT
Statistics
Matches: 136, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
83 22 0.16
84 27 0.20
85 86 0.63
86 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (85 bp):
CGGTGGAATCAACACTTAGCAACCACCTTTAAATTCAATGATACGGGGAATCAGCACATAGCAAC
CCCTTTCACAATCAAAGATA
Found at i:24440210 original size:26 final size:26
Alignment explanation
Indices: 24440180--24440229 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
24440170 ATCAATATTC
24440180 GGGAATCAGCACTTAGCGACCCCTCG
1 GGGAATCAGCACTTAGCGACCCCTCG
**
24440206 GGGAATTTGCACTTAGCGACCCCT
1 GGGAATCAGCACTTAGCGACCCCT
24440230 TTTTATCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.22, C:0.32, G:0.26, T:0.20
Consensus pattern (26 bp):
GGGAATCAGCACTTAGCGACCCCTCG
Found at i:24444134 original size:27 final size:26
Alignment explanation
Indices: 24444103--24444164 Score: 99
Period size: 25 Copynumber: 2.4 Consensus size: 26
24444093 ATGTGACAAG
*
24444103 TATATCTTCAAATGAGCAAAATGTATA
1 TATATGTTC-AATGAGCAAAATGTATA
24444130 TATATGTTC-ATGAGCAAAATGTATA
1 TATATGTTCAATGAGCAAAATGTATA
24444155 TATATGTTCA
1 TATATGTTCA
24444165 TTATGACCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 25 0.76
27 8 0.24
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (26 bp):
TATATGTTCAATGAGCAAAATGTATA
Found at i:24444142 original size:25 final size:25
Alignment explanation
Indices: 24444114--24444165 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
24444104 ATATCTTCAA
24444114 ATGAGCAAAATGTATATATATGTTC
1 ATGAGCAAAATGTATATATATGTTC
24444139 ATGAGCAAAATGTATATATATGTTC
1 ATGAGCAAAATGTATATATATGTTC
24444164 AT
1 AT
24444166 TATGACCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (25 bp):
ATGAGCAAAATGTATATATATGTTC
Found at i:24446273 original size:20 final size:20
Alignment explanation
Indices: 24446250--24446306 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
24446240 CACATACGTG
24446250 CCCCTATTTGTACTTCGGTA
1 CCCCTATTTGTACTTCGGTA
* * *
24446270 CCCCTATTTGCACGTAC-GTG
1 CCCCTATTTGTAC-TTCGGTA
*
24446290 CCCCTGTTTGTACTTCG
1 CCCCTATTTGTACTTCG
24446307 ATACTCCTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.12, C:0.33, G:0.18, T:0.37
Consensus pattern (20 bp):
CCCCTATTTGTACTTCGGTA
Found at i:24447777 original size:15 final size:13
Alignment explanation
Indices: 24447746--24447771 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24447736 CTACAAATGA
24447746 CACATGGTCGTGT
1 CACATGGTCGTGT
24447759 CACATGGTCGTGT
1 CACATGGTCGTGT
24447772 GTCACACACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (13 bp):
CACATGGTCGTGT
Found at i:24455782 original size:14 final size:14
Alignment explanation
Indices: 24455763--24455790 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
24455753 CCAATTTACT
24455763 AATGAATTATTAAA
1 AATGAATTATTAAA
24455777 AATGAATTATTAAA
1 AATGAATTATTAAA
24455791 TATAGCTTTA
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:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:24464155 original size:7 final size:8
Alignment explanation
Indices: 24464126--24464154 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
24464116 ATAGTTTCGA
24464126 CTTTTTGG
1 CTTTTTGG
24464134 CTTTTTGG
1 CTTTTTGG
24464142 CTTTTTGG
1 CTTTTTGG
24464150 CTTTT
1 CTTTT
24464155 GCCGATTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.21, T:0.66
Consensus pattern (8 bp):
CTTTTTGG
Found at i:24469655 original size:40 final size:41
Alignment explanation
Indices: 24469611--24469689 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 41
24469601 GGTATATAAC
*
24469611 ATGTTTATATTAGTGAATGAAATATTATTTTAAT-TTTTAT
1 ATGTTTATATTAGTGAATGAAATATTATTTAAATGTTTTAT
24469651 ATGTTTATATTAGTGAATGAAATATTATTTAAATGTTTT
1 ATGTTTATATTAGTGAATGAAATATTATTTAAATGTTTT
24469690 CGATTGTACG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 33 0.89
41 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.53
Consensus pattern (41 bp):
ATGTTTATATTAGTGAATGAAATATTATTTAAATGTTTTAT
Found at i:24472885 original size:56 final size:50
Alignment explanation
Indices: 24472781--24472904 Score: 140
Period size: 50 Copynumber: 2.4 Consensus size: 50
24472771 TCGGTGCATG
*
24472781 TCCCAAACATGGTCTTACGAGGGACCTCTCATCTTAGTGCCAACGCCATA
1 TCCCAAACATGGTCTTACGAGGGACCTCTCATCTTAATGCCAACGCCATA
* * * *
24472831 TCCCAAACATGGTCTTACGTGGGACCTTTCATAACCTCAATAATGCCAATGCCATG
1 TCCCAAACATGGTCTTACGAGGGACCTCTCAT---CT---TAATGCCAACGCCATA
*
24472887 TCCCAGACATGGTCTTAC
1 TCCCAAACATGGTCTTAC
24472905 ATGGTATCTC
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
50 30 0.48
53 2 0.03
56 30 0.48
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.26
Consensus pattern (50 bp):
TCCCAAACATGGTCTTACGAGGGACCTCTCATCTTAATGCCAACGCCATA
Found at i:24473061 original size:22 final size:21
Alignment explanation
Indices: 24473017--24473066 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
24473007 TCAACATTAA
* **
24473017 ATAATTTCTTGAAATAAGTAC
1 ATAATTTCTGGAAATAACAAC
24473038 ATAATTTCTGGAAAATAACAAC
1 ATAATTTCTGG-AAATAACAAC
24473060 ATTAATT
1 A-TAATT
24473067 ATAATTATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.42
22 9 0.38
23 5 0.21
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (21 bp):
ATAATTTCTGGAAATAACAAC
Found at i:24476732 original size:50 final size:50
Alignment explanation
Indices: 24476659--24476895 Score: 215
Period size: 50 Copynumber: 4.6 Consensus size: 50
24476649 TCTTGTACTA
* * * * ** *
24476659 CCAATGCCATATCCCAAATATGGTCTTACATGAGAGTTCTCATATAGGTG
1 CCAATGCCATGTCCTAGACATGGTCTTACATGAGACCTCTCATATCGGTG
* ** * *
24476709 CCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCTAGACATGGTCTTACATGAGACCTCTCATATCGGTG
* * * *
24476759 TCAATGCCAT-TCCCAGACATGGTCTTACATGAGGCCTCTCATCTCGGTG
1 CCAATGCCATGTCCTAGACATGGTCTTACATGAGACCTCTCATATCGGTG
* * * *
24476808 CCAACGTCATGTCCTAGACATTGTCTTACATGAGACCTCTCATAATCTCAATGATG
1 CCAATGCCATGTCCTAGACATGGTCTTACATGAGACCTCTCAT-A--TC---GGTG
* *
24476864 CCAATGCCATGTCCCAGACATGGTTTTACATG
1 CCAATGCCATGTCCTAGACATGGTCTTACATG
24476896 GGATCTCTTT
Statistics
Matches: 148, Mismatches: 32, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
49 41 0.28
50 75 0.51
53 2 0.01
56 30 0.20
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (50 bp):
CCAATGCCATGTCCTAGACATGGTCTTACATGAGACCTCTCATATCGGTG
Found at i:24476773 original size:99 final size:100
Alignment explanation
Indices: 24476660--24476850 Score: 251
Period size: 99 Copynumber: 1.9 Consensus size: 100
24476650 CTTGTACTAC
* * * *
24476660 CAATGCCATATCCCAAATATGGTCTTACATGAGAG-TTCTCATATAGGTGCCCATGCCATGTCCT
1 CAATGCCATATCCCAAACATGGTCTTACATGAG-GCCTCTCATATAGGTGCCAACGCCATGTCCT
* *
24476724 AGACATGGTCTTACGGGGGACCTCTCATCTCGGTGT
65 AGACATGGTCTTACAGGAGACCTCTCATCTCGGTGT
* * * *
24476760 CAATGCCAT-TCCCAGACATGGTCTTACATGAGGCCTCTCATCTCGGTGCCAACGTCATGTCCTA
1 CAATGCCATATCCCAAACATGGTCTTACATGAGGCCTCTCATATAGGTGCCAACGCCATGTCCTA
* *
24476824 GACATTGTCTTACATGAGACCTCTCAT
66 GACATGGTCTTACAGGAGACCTCTCAT
24476851 AATCTCAATG
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
98 1 0.01
99 68 0.87
100 9 0.12
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (100 bp):
CAATGCCATATCCCAAACATGGTCTTACATGAGGCCTCTCATATAGGTGCCAACGCCATGTCCTA
GACATGGTCTTACAGGAGACCTCTCATCTCGGTGT
Found at i:24491392 original size:50 final size:50
Alignment explanation
Indices: 24491301--24491435 Score: 159
Period size: 50 Copynumber: 2.7 Consensus size: 50
24491291 TCTTGTACAT
* * * *
24491301 CCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCAT-ATAGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACGTGGGAGTTCTCATCAT-GGTG
*
24491351 TCC-ATGCCATGTCCCAGACATGGTCTTACGGGGGACG-TCTCATCATGGTG
1 -CCAATGCCATGTCCCAGACATGGTCTTACGTGGGA-GTTCTCATCATGGTG
**
24491401 CCAAAACCATGTCCCAGACATGGTCTTACGTGGGA
1 CCAATGCCATGTCCCAGACATGGTCTTACGTGGGA
24491436 TCTCTTTACC
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
49 2 0.03
50 66 0.90
51 5 0.07
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACGTGGGAGTTCTCATCATGGTG
Found at i:24493496 original size:22 final size:22
Alignment explanation
Indices: 24493471--24493512 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
24493461 ACATTAATAT
24493471 TCAATTATATTGGCACAATAAA
1 TCAATTATATTGGCACAATAAA
*
24493493 TCAATTATATTGGCATAATA
1 TCAATTATATTGGCACAATA
24493513 CGTCCATGGT
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:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (22 bp):
TCAATTATATTGGCACAATAAA
Found at i:24496439 original size:40 final size:41
Alignment explanation
Indices: 24496384--24496568 Score: 286
Period size: 40 Copynumber: 4.5 Consensus size: 41
24496374 AAATATATTT
* * *
24496384 ATTTTTTAAAATTTTAAAATATTTTTTACATAC-TTTTTTA
1 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTA
24496424 ATTTTTTTAAATTTTAAAATATTTTTAAAATAC-TTTTTTA
1 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTA
24496464 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTA
24496505 ATTTTTTT-AATTTTAAAATATTTTTAAAATACTTTTTTTTTA
1 ATTTTTTTAAATTTTAAAATATTTTTAAAATAC--TTTTTTTA
*
24496547 ATTTTTTAAAATTTTTAAAATA
1 ATTTTTTTAAA-TTTTAAAATA
24496569 AAAATGGGCC
Statistics
Matches: 136, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
40 94 0.69
41 15 0.11
42 15 0.11
43 2 0.01
44 10 0.07
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (41 bp):
ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:24496449 original size:11 final size:11
Alignment explanation
Indices: 24496435--24496541 Score: 72
Period size: 11 Copynumber: 10.4 Consensus size: 11
24496425 TTTTTTTAAA
24496435 TTTTAAAATAT
1 TTTTAAAATAT
24496446 TTTTAAAATACT
1 TTTTAAAATA-T
*
24496458 TTTT-TAAT-T
1 TTTTAAAATAT
*
24496467 TTTT-TAA-A-
1 TTTTAAAATAT
24496475 TTTTAAAATAT
1 TTTTAAAATAT
24496486 TTTTAAAATACT
1 TTTTAAAATA-T
**
24496498 TTTTTTAAT-T
1 TTTTAAAATAT
*
24496508 TTTT----TAA
1 TTTTAAAATAT
24496515 TTTTAAAATAT
1 TTTTAAAATAT
24496526 TTTTAAAATACT
1 TTTTAAAATA-T
24496538 TTTT
1 TTTT
24496542 TTTTAATTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 23
0.73 0.06 0.21
Matches are distributed among these distances:
6 1 0.01
7 4 0.05
8 4 0.05
9 10 0.13
10 6 0.08
11 35 0.45
12 18 0.23
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:24496548 original size:33 final size:33
Alignment explanation
Indices: 24496506--24496568 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
24496496 CTTTTTTTAA
24496506 TTTTTTTAA-TTTTAAAATATTTTTAAAATACTT
1 TTTTTTTAATTTTTAAAA-ATTTTTAAAATACTT
*
24496539 TTTTTTTAATTTTTTAAAATTTTTAAAATA
1 TTTTTTTAATTTTTAAAAATTTTTAAAATA
24496569 AAAATGGGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (33 bp):
TTTTTTTAATTTTTAAAAATTTTTAAAATACTT
Found at i:24502619 original size:10 final size:10
Alignment explanation
Indices: 24502604--24502665 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
24502594 TTTGAACCAT
*
24502604 TACCAATTCG
1 TACCAATTCA
*
24502614 TACCAAATACCA
1 TACC-AAT-TCA
*
24502626 TACCATTTCA
1 TACCAATTCA
24502636 TACCAATTCCA
1 TACCAATT-CA
* *
24502647 TACCATTTCG
1 TACCAATTCA
24502657 TACCAATTC
1 TACCAATTC
24502666 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:24502649 original size:21 final size:21
Alignment explanation
Indices: 24502604--24502666 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
24502594 TTTGAACCAT
* *
24502604 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
24502626 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
24502647 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
24502667 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:24502985 original size:15 final size:14
Alignment explanation
Indices: 24502965--24503046 Score: 53
Period size: 14 Copynumber: 5.7 Consensus size: 14
24502955 ATAGGTACGT
*
24502965 AAAAAAAGTTCGAA
1 AAAAAAAATTCGAA
*
24502979 AAAAAAAATTTGAA
1 AAAAAAAATTCGAA
**
24502993 AAAAAACAA--AAACA
1 AAAAAA-AATTCGA-A
*
24503007 AAAAAAAATTCAAAA
1 AAAAAAAATTC-GAA
24503022 GAAAAAAAATT-GAA
1 -AAAAAAAATTCGAA
24503036 AGAAAAAAATT
1 A-AAAAAAATT
24503047 GTATACGGTT
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
13 4 0.07
14 36 0.65
15 3 0.05
16 12 0.22
ACGTcount: A:0.74, C:0.05, G:0.07, T:0.13
Consensus pattern (14 bp):
AAAAAAAATTCGAA
Found at i:24503026 original size:28 final size:27
Alignment explanation
Indices: 24502978--24503030 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
24502968 AAAAGTTCGA
*
24502978 AAAAAAAAATTTGAAAAAAAACAAAAAC
1 AAAAAAAAATTTCAAAAAAAA-AAAAAC
*
24503006 AAAAAAAAA-TTCAAAAGAAAAAAAA
1 AAAAAAAAATTTCAAAAAAAAAAAAA
24503031 TTGAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 9 0.39
28 9 0.39
ACGTcount: A:0.81, C:0.06, G:0.04, T:0.09
Consensus pattern (27 bp):
AAAAAAAAATTTCAAAAAAAAAAAAAC
Found at i:24503047 original size:14 final size:15
Alignment explanation
Indices: 24503007--24503044 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
24502997 AACAAAAACA
*
24503007 AAAAAAAATTCAAAAG
1 AAAAAAAATT-GAAAG
24503023 AAAAAAAATTGAAAG
1 AAAAAAAATTGAAAG
24503038 AAAAAAA
1 AAAAAAA
24503045 TTGTATACGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.11
Consensus pattern (15 bp):
AAAAAAAATTGAAAG
Found at i:24503466 original size:13 final size:13
Alignment explanation
Indices: 24503448--24503472 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24503438 CGAGAGATTC
24503448 GTGAGGTTTTTTT
1 GTGAGGTTTTTTT
24503461 GTGAGGTTTTTT
1 GTGAGGTTTTTT
24503473 ATTTTCATGT
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:0.08, C:0.00, G:0.32, T:0.60
Consensus pattern (13 bp):
GTGAGGTTTTTTT
Found at i:24505247 original size:20 final size:20
Alignment explanation
Indices: 24505218--24505273 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
24505208 TCGAAAATAC
*
24505218 AAAAGAAAAGAAAAATGAAAA
1 AAAAG-AAAGAAAAATCAAAA
*
24505239 AAAAGAAAGAAAATTCAAAA
1 AAAAGAAAGAAAAATCAAAA
*
24505259 AAAGAGAATGAAAAA
1 AAA-AGAAAGAAAAA
24505274 AAAATGAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (20 bp):
AAAAGAAAGAAAAATCAAAA
Found at i:24505251 original size:37 final size:34
Alignment explanation
Indices: 24505198--24505276 Score: 95
Period size: 37 Copynumber: 2.2 Consensus size: 34
24505188 AATGAGAGAA
**
24505198 AAAAAAAAGATCGAAAATACAAAAGAAAAGAAAAATG
1 AAAAAAAAGAAAGAAAATAC-AAA-AAAAG-AAAATG
* *
24505235 AAAAAAAAGAAAGAAAATTCAAAAAAAGAGAATG
1 AAAAAAAAGAAAGAAAATACAAAAAAAGAAAATG
24505269 AAAAAAAA
1 AAAAAAAA
24505277 ATGAGAAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 13 0.34
35 5 0.13
36 3 0.08
37 17 0.45
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.08
Consensus pattern (34 bp):
AAAAAAAAGAAAGAAAATACAAAAAAAGAAAATG
Found at i:24512373 original size:20 final size:22
Alignment explanation
Indices: 24512348--24512391 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
24512338 TTATGATTCA
24512348 TTGAATTGGT-TGTTT-TATGC
1 TTGAATTGGTATGTTTATATGC
24512368 TTGAATTGGTATGTTTATATGC
1 TTGAATTGGTATGTTTATATGC
24512390 TT
1 TT
24512392 TGGTTAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 10 0.45
21 5 0.23
22 7 0.32
ACGTcount: A:0.18, C:0.05, G:0.23, T:0.55
Consensus pattern (22 bp):
TTGAATTGGTATGTTTATATGC
Found at i:24517041 original size:10 final size:10
Alignment explanation
Indices: 24517026--24517052 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
24517016 AATTTAAAAA
24517026 TTAAAAAATT
1 TTAAAAAATT
24517036 TTAAAAAATT
1 TTAAAAAATT
24517046 TTAAAAA
1 TTAAAAA
24517053 TTAGCTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TTAAAAAATT
Found at i:24520241 original size:51 final size:49
Alignment explanation
Indices: 24520161--24520348 Score: 225
Period size: 51 Copynumber: 3.7 Consensus size: 49
24520151 TGCCTATAGA
* * * * *
24520161 CACGTGTGTAGTACTAAGTGCAGGTTACTACATGTATC-GATAGATAATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-AG-T-TTGGT
* *
24520212 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGAAGGTTTTGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAA-G-TTTGGT
* *
24520263 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCAGAAAGTTTGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAG-AAGTTTGGT
*
24520313 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA
24520349 TTGAATGATA
Statistics
Matches: 120, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
50 39 0.32
51 75 0.62
52 6 0.05
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (49 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAGTTTGGT
Found at i:24520348 original size:101 final size:102
Alignment explanation
Indices: 24520161--24520348 Score: 254
Period size: 101 Copynumber: 1.9 Consensus size: 102
24520151 TGCCTATAGA
* * * * *
24520161 CACGTGTGTAGTACTAAGTGCAGGTTACTACATGTATCGATAGATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACATGAACCGAAAGATAATGATCACATGTGTAGTAC
* *
24520226 TATGTGCAGGCTACTATGTGTACCAGAAGGTTTTGGT
66 TATGTGAAGGCTACTACGTGTACCAGAAGGTTTTGGT
* * * *
24520263 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCAGAAAG-T-TTGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACATGAACC-GAAAGATAATGATCACATGTGTAGTA
24520326 CTATGTGAAGGCTACTACGTGTA
65 CTATGTGAAGGCTACTACGTGTA
24520349 TTGAATGATA
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
101 36 0.49
102 34 0.46
103 4 0.05
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (102 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACATGAACCGAAAGATAATGATCACATGTGTAGTAC
TATGTGAAGGCTACTACGTGTACCAGAAGGTTTTGGT
Found at i:24525943 original size:82 final size:82
Alignment explanation
Indices: 24525790--24525952 Score: 238
Period size: 82 Copynumber: 2.0 Consensus size: 82
24525780 TTGTGTTTGC
* * * *
24525790 AGGTCATTGAATTCGGCTACTTAATGGCTAAGGAGACATGCATTTAAGGTGCTGTTAACATGCAA
1 AGGTCATTGAATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCAA
24525855 GGAACGGCATTTAAAGA
66 GGAACGGCATTTAAAGA
**
24525872 AGGTCATTGAAATTCGGCTACTTAATGGCAAAGGAAACATGCA-TTAAGGAGATGTTCCCATGCA
1 AGGTCATTG-AATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCA
* *
24525936 TGGAACGGTATTTAAAG
65 AGGAACGGCATTTAAAG
24525953 GGAAGTAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
82 41 0.57
83 31 0.43
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (82 bp):
AGGTCATTGAATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCAA
GGAACGGCATTTAAAGA
Found at i:24526024 original size:32 final size:32
Alignment explanation
Indices: 24525988--24526074 Score: 147
Period size: 32 Copynumber: 2.7 Consensus size: 32
24525978 GGTGTTCCCA
* * *
24525988 TGCATGGACGGCATTAATTAGTTGCTGTAGCT
1 TGCATGCATGGCATTAATTAGTTGCTGGAGCT
24526020 TGCATGCATGGCATTAATTAGTTGCTGGAGCT
1 TGCATGCATGGCATTAATTAGTTGCTGGAGCT
24526052 TGCATGCATGGCATTAATTAGTT
1 TGCATGCATGGCATTAATTAGTT
24526075 AATTTTTCAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (32 bp):
TGCATGCATGGCATTAATTAGTTGCTGGAGCT
Found at i:24529862 original size:115 final size:115
Alignment explanation
Indices: 24529733--24529963 Score: 453
Period size: 115 Copynumber: 2.0 Consensus size: 115
24529723 AGGGGGATAA
*
24529733 TAAAGGAAGGAGGAGAAACATAAGGGAGGAAAGAATCTCTTACACAAGGTAAGAATTTTGGGCGA
1 TAAAGGAAGGAGGAGAAACATAAGAGAGGAAAGAATCTCTTACACAAGGTAAGAATTTTGGGCGA
24529798 CAAAAAGGTTGACTAAAGGGGCTATTGAATTTAAAAGTAAATTGCAAAAG
66 CAAAAAGGTTGACTAAAGGGGCTATTGAATTTAAAAGTAAATTGCAAAAG
24529848 TAAAGGAAGGAGGAGAAACATAAGAGAGGAAAGAATCTCTTACACAAGGTAAGAATTTTGGGCGA
1 TAAAGGAAGGAGGAGAAACATAAGAGAGGAAAGAATCTCTTACACAAGGTAAGAATTTTGGGCGA
24529913 CAAAAAGGTTGACTAAAGGGGCTATTGAATTTAAAAGTAAATTGCAAAAG
66 CAAAAAGGTTGACTAAAGGGGCTATTGAATTTAAAAGTAAATTGCAAAAG
24529963 T
1 T
24529964 GAGGACTTGA
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 115 1.00
ACGTcount: A:0.45, C:0.09, G:0.26, T:0.20
Consensus pattern (115 bp):
TAAAGGAAGGAGGAGAAACATAAGAGAGGAAAGAATCTCTTACACAAGGTAAGAATTTTGGGCGA
CAAAAAGGTTGACTAAAGGGGCTATTGAATTTAAAAGTAAATTGCAAAAG
Found at i:24532725 original size:29 final size:28
Alignment explanation
Indices: 24532692--24532776 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 28
24532682 TCAAATGATA
*
24532692 CCCTTGTGGCTAGTTTTATTAAAAGGATG
1 CCCTTGTGGCTA-TTTTGTTAAAAGGATG
24532721 CCCTTGTGGCTATTTCTGTTAAAAGGATG
1 CCCTTGTGGCTATTT-TGTTAAAAGGATG
*
24532750 CCCTTATGG-TAATCTTTGTTAAAAGGA
1 CCCTTGTGGCT-AT-TTTGTTAAAAGGA
24532777 AGCATTTCTA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.08
29 45 0.88
30 2 0.04
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (28 bp):
CCCTTGTGGCTATTTTGTTAAAAGGATG
Found at i:24532828 original size:29 final size:29
Alignment explanation
Indices: 24532710--24532980 Score: 195
Period size: 29 Copynumber: 9.3 Consensus size: 29
24532700 GCTAGTTTTA
** * * *
24532710 TTAAAAGGATGCCCTTGTGGCTATTTCTG
1 TTAAAAGGAAACCTTTGTGGCAATCTCTG
** * * * *
24532739 TTAAAAGGATGCCCTTATGGTAATCTTTG
1 TTAAAAGGAAACCTTTGTGGCAATCTCTG
* * * * *
24532768 TTAAAAGGAAGCATTTCTAGCAATCTCCG
1 TTAAAAGGAAACCTTTGTGGCAATCTCTG
* ** *
24532797 TTAAAAGGAAACCTTTATGGTGATATCTG
1 TTAAAAGGAAACCTTTGTGGCAATCTCTG
* *
24532826 TTAAAA-GAAAGCATTTGTGCCAATCTTTCTG
1 TTAAAAGGAAA-CCTTTGTGGCAATC--TCTG
* * ** *
24532857 TTAAAAAGAAGCCTTTGTGGTGATTTCTG
1 TTAAAAGGAAACCTTTGTGGCAATCTCTG
* *
24532886 TTAAAAGTATACCTTTGTGGCAATCTCTG
1 TTAAAAGGAAACCTTTGTGGCAATCTCTG
*
24532915 TTAAAA-GAAAGCCTTTGTGGCAATCTTTG
1 TTAAAAGGAAA-CCTTTGTGGCAATCTCTG
* **
24532944 TTAAAAGAAAACCTTTGTGGTGATCTCTG
1 TTAAAAGGAAACCTTTGTGGCAATCTCTG
24532973 TTAAAAGG
1 TTAAAAGG
24532981 TTTTCTTTAT
Statistics
Matches: 188, Mismatches: 48, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
28 6 0.03
29 157 0.84
30 3 0.02
31 19 0.10
32 3 0.02
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.35
Consensus pattern (29 bp):
TTAAAAGGAAACCTTTGTGGCAATCTCTG
Found at i:24532850 original size:58 final size:58
Alignment explanation
Indices: 24532724--24532980 Score: 221
Period size: 58 Copynumber: 4.4 Consensus size: 58
24532714 AAGGATGCCC
* * ** * * *
24532724 TTGTGGCTATTTCTGTTAAAAGGATGCCCTTATGGTAATCTTTGTTAAAAGGAAGCAT
1 TTGTGGCAATCTCTGTTAAAAGGAAACCTTTATGGTAATCTCTGTTAAAAGAAAGCAT
* * * * *
24532782 TTCTAGCAATCTCCGTTAAAAGGAAACCTTTATGGTGATATCTGTTAAAAGAAAGCAT
1 TTGTGGCAATCTCTGTTAAAAGGAAACCTTTATGGTAATCTCTGTTAAAAGAAAGCAT
* * * * * * * *
24532840 TTGTGCCAATCTTTCTGTTAAAAAGAAGCCTTTGTGGTGATTTCTGTTAAAAGTATA-CCT
1 TTGTGGCAATC--TCTGTTAAAAGGAAACCTTTATGGTAATCTCTGTTAAAAG-AAAGCAT
* * * * *
24532900 TTGTGGCAATCTCTGTTAAAA-GAAAGCCTTTGTGGCAATCTTTGTTAAAAGAAAACCT
1 TTGTGGCAATCTCTGTTAAAAGGAAA-CCTTTATGGTAATCTCTGTTAAAAGAAAGCAT
**
24532958 TTGTGGTGATCTCTGTTAAAAGG
1 TTGTGGCAATCTCTGTTAAAAGG
24532981 TTTTCTTTAT
Statistics
Matches: 162, Mismatches: 31, Indels: 11
0.79 0.15 0.05
Matches are distributed among these distances:
57 5 0.03
58 107 0.66
59 1 0.01
60 47 0.29
61 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (58 bp):
TTGTGGCAATCTCTGTTAAAAGGAAACCTTTATGGTAATCTCTGTTAAAAGAAAGCAT
Found at i:24532892 original size:89 final size:87
Alignment explanation
Indices: 24532790--24532980 Score: 249
Period size: 89 Copynumber: 2.2 Consensus size: 87
24532780 ATTTCTAGCA
* **
24532790 ATCTCCGTTAAAAGGAAACCTTTATGGTGATATCTGTTAAAAGAAAGCATTTGTGCCAATCTTTC
1 ATCTCTGTTAAAAGGAAACCTTTATGGCAATATCTGTTAAAAGAAAGCATTTGTGCCAATC-TT-
*
24532855 TGTTAAAA-AGAAGCCTTTGTGGTG
64 TGTTAAAAGA-AAACCTTTGTGGTG
* * * * * * *
24532879 ATTTCTGTTAAAAGTATACCTTTGTGGCAATCTCTGTTAAAAGAAAGCCTTTGTGGCAATCTTTG
1 ATCTCTGTTAAAAGGAAACCTTTATGGCAATATCTGTTAAAAGAAAGCATTTGTGCCAATCTTTG
24532944 TTAAAAGAAAACCTTTGTGGTG
66 TTAAAAGAAAACCTTTGTGGTG
24532966 ATCTCTGTTAAAAGG
1 ATCTCTGTTAAAAGG
24532981 TTTTCTTTAT
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
87 34 0.39
88 3 0.03
89 51 0.58
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (87 bp):
ATCTCTGTTAAAAGGAAACCTTTATGGCAATATCTGTTAAAAGAAAGCATTTGTGCCAATCTTTG
TTAAAAGAAAACCTTTGTGGTG
Found at i:24532938 original size:147 final size:147
Alignment explanation
Indices: 24532710--24532979 Score: 362
Period size: 147 Copynumber: 1.8 Consensus size: 147
24532700 GCTAGTTTTA
* * * * *
24532710 TTAAAAGGATGCCCTTGTGGCTATTTCTGTTAAAAGGATGCCCTTATGGTAATCTTTGTTAAAAG
1 TTAAAAAGAAGCCCTTGTGGCTATTTCTGTTAAAAGGATACCCTTATGGCAATCTCTGTTAAAAG
* *
24532775 GAAGCATTTCTAGCAATCTCCGTTAAAAGGAAACCTTTATGGTGATATCTGTTAAAAGAAAGCAT
66 AAAGCATTTCTAGCAATCTCCGTTAAAAGAAAACCTTTATGGTGATATCTGTTAAAAGAAAGCAT
24532840 TTGTGCCAATCTTTCTG
131 TTGTGCCAATCTTTCTG
* * * *
24532857 TTAAAAAGAAGCCTTTGTGG-TGATTTCTGTTAAAAGTATACCTTTGTGGCAATCTCTGTTAAAA
1 TTAAAAAGAAGCCCTTGTGGCT-ATTTCTGTTAAAAGGATACCCTTATGGCAATCTCTGTTAAAA
* * * ** * *
24532921 GAAAGCCTTTGTGGCAATCTTTGTTAAAAGAAAACCTTTGTGGTGATCTCTGTTAAAAG
65 GAAAGCATTTCTAGCAATCTCCGTTAAAAGAAAACCTTTATGGTGATATCTGTTAAAAG
24532980 GTTTTCTTTA
Statistics
Matches: 104, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
146 1 0.01
147 103 0.99
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.35
Consensus pattern (147 bp):
TTAAAAAGAAGCCCTTGTGGCTATTTCTGTTAAAAGGATACCCTTATGGCAATCTCTGTTAAAAG
AAAGCATTTCTAGCAATCTCCGTTAAAAGAAAACCTTTATGGTGATATCTGTTAAAAGAAAGCAT
TTGTGCCAATCTTTCTG
Found at i:24537058 original size:20 final size:20
Alignment explanation
Indices: 24537035--24537137 Score: 66
Period size: 20 Copynumber: 5.2 Consensus size: 20
24537025 CACTTACGTG
24537035 CCCCTATTTGTACTTCGGTA
1 CCCCTATTTGTACTTCGGTA
* * ** *
24537055 CCCCTGA-CTGCACTTATGTG
1 CCCCT-ATTTGTACTTCGGTA
* * *
24537075 CCCCTGTTCGTACTTCAGTA
1 CCCCTATTTGTACTTCGGTA
* * *
24537095 CCCCTAATTGCACTTAC-GTG
1 CCCCTATTTGTACTT-CGGTA
*
24537115 CCCCTATTTGTACTTTGGTA
1 CCCCTATTTGTACTTCGGTA
24537135 CCC
1 CCC
24537138 TTGATTGCAC
Statistics
Matches: 58, Mismatches: 21, Indels: 8
0.67 0.24 0.09
Matches are distributed among these distances:
20 56 0.97
21 2 0.03
ACGTcount: A:0.16, C:0.34, G:0.16, T:0.35
Consensus pattern (20 bp):
CCCCTATTTGTACTTCGGTA
Found at i:24537070 original size:40 final size:40
Alignment explanation
Indices: 24537024--24537227 Score: 246
Period size: 40 Copynumber: 5.1 Consensus size: 40
24537014 ATACCCTGAC
*
24537024 GCACTTACGTGCCCCTATTTGTACTTCGGTACCCCTGACT
1 GCACTTACGTGCCCCTATTTGTACTTCGGTACCCCTGATT
* * * * *
24537064 GCACTTATGTGCCCCTGTTCGTACTTCAGTACCCCTAATT
1 GCACTTACGTGCCCCTATTTGTACTTCGGTACCCCTGATT
* *
24537104 GCACTTACGTGCCCCTATTTGTACTTTGGTACCCTTGATT
1 GCACTTACGTGCCCCTATTTGTACTTCGGTACCCCTGATT
** * *
24537144 GCACTTACGTGCCATTTTTTGTACTTCGGTACCCTTGATT
1 GCACTTACGTGCCCCTATTTGTACTTCGGTACCCCTGATT
* * * * * *
24537184 ACACTTACGTTCCCTTGTTTGTACTTCGATACCCCTAATT
1 GCACTTACGTGCCCCTATTTGTACTTCGGTACCCCTGATT
24537224 GCAC
1 GCAC
24537228 GTACTTCGAT
Statistics
Matches: 139, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 139 1.00
ACGTcount: A:0.17, C:0.30, G:0.16, T:0.37
Consensus pattern (40 bp):
GCACTTACGTGCCCCTATTTGTACTTCGGTACCCCTGATT
Done.