Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1140
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: 141413
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:32791 original size:14 final size:14
Alignment explanation
Indices: 32772--32799 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
32762 ATATGTTAAA
32772 GTAGATGATACAGT
1 GTAGATGATACAGT
32786 GTAGATGATACAGT
1 GTAGATGATACAGT
32800 TTTTGGGGCG
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:0.07, G:0.29, T:0.29
Consensus pattern (14 bp):
GTAGATGATACAGT
Found at i:35804 original size:29 final size:29
Alignment explanation
Indices: 35741--35861 Score: 111
Period size: 29 Copynumber: 4.2 Consensus size: 29
35731 TTCACATACC
* * *
35741 TTTATCTGGCCCATTAAGCCC-AATCATA
1 TTTATATGGCCCATTAGGCCCAAATCACA
* *
35769 TTCATATGGCCCATTAGGCCCAAATCACC
1 TTTATATGGCCCATTAGGCCCAAATCACA
* * * *
35798 TGTATATGGCCTATTAGGCCTAAATCAGA
1 TTTATATGGCCCATTAGGCCCAAATCACA
* * *
35827 TTTATATGGCTCGTTAGGCCC-AGTCACA
1 TTTATATGGCCCATTAGGCCCAAATCACA
*
35855 TTCATAT
1 TTTATAT
35862 TCATGCTCAC
Statistics
Matches: 73, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
28 29 0.40
29 44 0.60
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (29 bp):
TTTATATGGCCCATTAGGCCCAAATCACA
Found at i:36093 original size:16 final size:15
Alignment explanation
Indices: 36071--36107 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
36061 CGTAGCCAAA
*
36071 CTTTTGGCTTTTCGG
1 CTTTTGGCATTTCGG
36086 CATTTTGGCATTTCGG
1 C-TTTTGGCATTTCGG
36102 CTTTTG
1 CTTTTG
36108 CCGATTCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.05, C:0.19, G:0.24, T:0.51
Consensus pattern (15 bp):
CTTTTGGCATTTCGG
Found at i:42419 original size:47 final size:46
Alignment explanation
Indices: 42306--42429 Score: 139
Period size: 47 Copynumber: 2.7 Consensus size: 46
42296 AGCATATCTG
* *
42306 TGCCGATGCCATGTCCCAGACATGGTCTTATACTAACACAACTCGTA
1 TGCCGATGCCATGTCCCAGACAT-GTCTTACACCAACACAACTCGTA
* *
42353 -GCCGATG-CATGTCCCAGACATGTCTTACACCAGCAC-TCGTC-TCAA
1 TGCCGATGCCATGTCCCAGACATGTCTTACACCAACACAAC-TCGT--A
*
42398 TGCCGATGCCATGTCCCAGACATGTCCTACAC
1 TGCCGATGCCATGTCCCAGACATGTCTTACAC
42430 TACCTCACGC
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
43 2 0.03
44 14 0.21
45 15 0.22
46 14 0.21
47 22 0.33
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (46 bp):
TGCCGATGCCATGTCCCAGACATGTCTTACACCAACACAACTCGTA
Found at i:45861 original size:10 final size:9
Alignment explanation
Indices: 45838--45863 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
45828 TTTGGTGTTG
45838 GTTTTTGAT
1 GTTTTTGAT
45847 GTTTTTGAT
1 GTTTTTGAT
45856 GTTTTTGA
1 GTTTTTGA
45864 GATCCTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.23, T:0.65
Consensus pattern (9 bp):
GTTTTTGAT
Found at i:46890 original size:46 final size:46
Alignment explanation
Indices: 46737--46907 Score: 186
Period size: 46 Copynumber: 3.7 Consensus size: 46
46727 ATTGTGGGCT
* * * *
46737 AGTGCAAGACATGTTTGGGACATGCATCGGCCA-C-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CATCGA-GACGAGAGCC
* *
46783 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGACGAGAGCC
* * * *
46831 AGTGTAAGACATGTCTAGGACATGCATTGGCCTCGAGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACG-AGAGCC
46877 AGTGTAAGACATGTCTGGGACATGCATCGGC
1 AGTGTAAGACATGTCTGGGACATGCATCGGC
46908 TGTGTCAGTG
Statistics
Matches: 106, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
46 53 0.50
47 29 0.27
48 23 0.22
49 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAGAGCC
Found at i:52341 original size:10 final size:9
Alignment explanation
Indices: 52318--52342 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52308 TTTGGTGTTG
52318 GTTTTTGAT
1 GTTTTTGAT
52327 GTTTTTGAT
1 GTTTTTGAT
52336 GTTTTTG
1 GTTTTTG
52343 GGATCCTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (9 bp):
GTTTTTGAT
Found at i:53289 original size:46 final size:47
Alignment explanation
Indices: 53237--53364 Score: 122
Period size: 48 Copynumber: 2.7 Consensus size: 47
53227 ATTGTGGGCT
* *
53237 AGTGTAAGATATGTCTGGTACATGCATCGGCTACATT-ATA-AAAGCC
1 AGTGTAAGACATGTCTGG-ACATGCATCGGCTACATTGAGACAAAGCC
* * *
53283 AGTGTAAGACCATGTCTTGGACACGGCATCGG---CATTGAGACGAGAGCT
1 AGTGTAAGA-CATGTC-TGGACA-TGCATCGGCTACATTGAGAC-AAAGCC
53331 AGTGTAAGACATGTCTGGGACATGCATCGGCTAC
1 AGTGTAAGACATGTCT-GGACATGCATCGGCTAC
53365 GAGATGTGTC
Statistics
Matches: 66, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
45 4 0.06
46 19 0.29
47 19 0.29
48 23 0.35
49 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGACATGCATCGGCTACATTGAGACAAAGCC
Found at i:55603 original size:29 final size:29
Alignment explanation
Indices: 55561--55678 Score: 116
Period size: 29 Copynumber: 4.1 Consensus size: 29
55551 GTGAGCATGA
*
55561 ATAT-AAGGTGATTTGGGCCTAACGGGCC
1 ATATAAAGGTGATTTGGGCCTAATGGGCC
*
55589 ATATAAAGGTGATTTGGGCGTAATGGGCC
1 ATATAAAGGTGATTTGGGCCTAATGGGCC
* ** * * *
55618 ATATGAATATGAATAGGGCCTGATGGGCC
1 ATATAAAGGTGATTTGGGCCTAATGGGCC
* *
55647 ATATAAATGAGA-TTGGG-CTAAGTGGGCC
1 ATATAAAGGTGATTTGGGCCTAA-TGGGCC
55675 ATAT
1 ATAT
55679 GCATGTATGT
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
27 3 0.04
28 18 0.24
29 53 0.72
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.26
Consensus pattern (29 bp):
ATATAAAGGTGATTTGGGCCTAATGGGCC
Found at i:59900 original size:20 final size:21
Alignment explanation
Indices: 59875--59914 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
59865 TTAAAATTAA
59875 TTTTTCAAAAATATT-TTTAT
1 TTTTTCAAAAATATTATTTAT
* *
59895 TTTTTCCAAATTATTATTTA
1 TTTTTCAAAAATATTATTTA
59915 ATCTATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTCAAAAATATTATTTAT
Found at i:61854 original size:27 final size:27
Alignment explanation
Indices: 61779--61891 Score: 122
Period size: 27 Copynumber: 4.2 Consensus size: 27
61769 GGAGGAAGCG
* *
61779 TTCTGGTGGCTCTACAAAAATATCTG-
1 TTCTGGTGGCTCTACCACAATATCTGT
* *
61805 ATCTGGTGGCTCTGCCACAAATATCTGT
1 TTCTGGTGGCTCTACCAC-AATATCTGT
*
61833 TTCTAGTGGCTCTACCACAATATCTGT
1 TTCTGGTGGCTCTACCACAATATCTGT
* * **
61860 ATCTGGTGACTCTGTCACAATATCTG-
1 TTCTGGTGGCTCTACCACAATATCTGT
61886 TTCTGG
1 TTCTGG
61892 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
26 19 0.26
27 38 0.53
28 15 0.21
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.35
Consensus pattern (27 bp):
TTCTGGTGGCTCTACCACAATATCTGT
Found at i:61882 original size:54 final size:54
Alignment explanation
Indices: 61779--61887 Score: 157
Period size: 54 Copynumber: 2.0 Consensus size: 54
61769 GGAGGAAGCG
* *
61779 TTCTGGTGGCTCTACAAAAATATCTGATCTGGTGGCTCTGCCACAAATATCTGT
1 TTCTAGTGGCTCTACAAAAATATCTGATCTGGTGACTCTGCCACAAATATCTGT
* * *
61833 TTCTAGTGGCTCTACCACAATATCTGTATCTGGTGACTCTGTCAC-AATATCTGT
1 TTCTAGTGGCTCTACAAAAATATCTG-ATCTGGTGACTCTGCCACAAATATCTGT
61887 T
1 T
61888 CTGGCAGCCA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
54 33 0.67
55 16 0.33
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (54 bp):
TTCTAGTGGCTCTACAAAAATATCTGATCTGGTGACTCTGCCACAAATATCTGT
Found at i:74811 original size:20 final size:21
Alignment explanation
Indices: 74774--74813 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
74764 TAAAATAGAT
74774 TAAATAATAATTTGGAAAAAA
1 TAAATAATAATTTGGAAAAAA
* *
74795 TAAA-AATATTTTTGAAAAA
1 TAAATAATAATTTGGAAAAA
74814 TTAATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (21 bp):
TAAATAATAATTTGGAAAAAA
Found at i:79103 original size:29 final size:29
Alignment explanation
Indices: 78998--79114 Score: 118
Period size: 29 Copynumber: 4.1 Consensus size: 29
78988 TACAACATGC
78998 ATATGGCCCACTTA-GCCC-AATCTA--TTT
1 ATATGGCCCA-TTAGGCCCAAATC-ACCTTT
* * ** *
79025 ATATGGCCCATTAGGCCCTATTCATATTC
1 ATATGGCCCATTAGGCCCAAATCACCTTT
*
79054 ATATGGCCCATTACGCCCAAATCACCTTT
1 ATATGGCCCATTAGGCCCAAATCACCTTT
*
79083 ATATGGCCCGTTAGGCCCAAATCACC-TT
1 ATATGGCCCATTAGGCCCAAATCACCTTT
79111 ATAT
1 ATAT
79115 TCATGCTCAC
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
26 3 0.04
27 15 0.20
28 9 0.12
29 49 0.64
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACCTTT
Found at i:81376 original size:47 final size:45
Alignment explanation
Indices: 81268--81398 Score: 127
Period size: 47 Copynumber: 2.8 Consensus size: 45
81258 GACACATCTC
* *
81268 GTAGCCGATGCATGTCCCAGACATGTCTTACACTATCTCTCATCT
1 GTAGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAT
** * * * * *
81313 CAATGCCGATACCATGTCCCAGACATGGTCTTTCATTGGCTCTTATAAT
1 GTA-GCCGAT-GCATGTCCCAGACAT-GTCTTACACTAGCTCTCAT-AT
* *
81362 GTAGCCGATGCATGTACCAGACATATCTTACACTAGC
1 GTAGCCGATGCATGTCCCAGACATGTCTTACACTAGC
81399 CCACAATAAC
Statistics
Matches: 65, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
45 1 0.02
46 15 0.23
47 27 0.42
48 20 0.31
49 2 0.03
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (45 bp):
GTAGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAT
Found at i:87772 original size:46 final size:46
Alignment explanation
Indices: 87720--87887 Score: 187
Period size: 46 Copynumber: 3.6 Consensus size: 46
87710 TGACACAGGT
87720 GATGCATGTCCCAGACATGTCTTACACTGGCT-TACATCTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATCTCGAGGCC
* * * * * *
87766 AATGCATGTCCTAGACATGTCTTACACTAGCTCTCGTCTCAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAGGCC
* * *
87812 GATGCCATGTCCCAGACATGGTCTTACACCGGCTCTCATAAT-GTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTCGAGGCC
* *
87860 GATGCATGTCCCAAACATGTCTTGCACT
1 GATGCATGTCCCAGACATGTCTTACACT
87888 AGCCCACAAT
Statistics
Matches: 100, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
46 49 0.49
47 27 0.27
48 23 0.23
49 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGAGGCC
Found at i:87866 original size:94 final size:92
Alignment explanation
Indices: 87720--87890 Score: 229
Period size: 94 Copynumber: 1.8 Consensus size: 92
87710 TGACACAGGT
* * * *
87720 GATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCAATGCATGTCCTAGACATG
1 GATGCATGTCCCAGACATGTCTTACACCGGCTTACATATCGAGGCCAATGCATGTCCCAAACATG
87785 TCTTACACTAGCTCTCGTCTCAATGCC
66 TCTTACACTAGCTCTCGTCTCAATGCC
* *
87812 GATGCCATGTCCCAGACATGGTCTTACACCGGCTCT-CATAAT-GTGGCCGATGCATGTCCCAAA
1 GATG-CATGTCCCAGACAT-GTCTTACACCGGCT-TACAT-ATCGAGGCCAATGCATGTCCCAAA
*
87875 CATGTCTTGCACTAGC
62 CATGTCTTACACTAGC
87891 CCACAATAGC
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
92 4 0.06
93 14 0.21
94 48 0.71
95 2 0.03
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (92 bp):
GATGCATGTCCCAGACATGTCTTACACCGGCTTACATATCGAGGCCAATGCATGTCCCAAACATG
TCTTACACTAGCTCTCGTCTCAATGCC
Found at i:93471 original size:39 final size:40
Alignment explanation
Indices: 93346--93527 Score: 210
Period size: 40 Copynumber: 4.6 Consensus size: 40
93336 GCTACTCGTT
*
93346 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
93386 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
93426 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
93465 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
93506 CAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
93528 AGACATCATT
Statistics
Matches: 120, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
38 2 0.02
39 31 0.26
40 74 0.62
41 13 0.11
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:93490 original size:79 final size:80
Alignment explanation
Indices: 93348--93527 Score: 215
Period size: 79 Copynumber: 2.3 Consensus size: 80
93338 TACTCGTTCA
* *
93348 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
*
93413 TTAGTAACTCA-CACC
66 ATAGTAACTCAGCA-C
* **
93428 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
93490 ATATGGTCACTTAGCAC
64 ATATAGTAACTCAGCAC
*
93507 AAAGCCTTCGGGACTTAGCCC
1 AATGCCTTCGGGACTTAGCCC
93528 AGACATCATT
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
78 4 0.05
79 60 0.70
80 22 0.26
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTCAGCAC
Found at i:94744 original size:56 final size:56
Alignment explanation
Indices: 94658--94777 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
94648 TATTAGTTTA
94658 TTGCCCATGCTTCTTATCTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATCTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
* *
94714 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATCTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
94770 TTGCCCAT
1 TTGCCCAT
94778 CATCCCTTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.44
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATCTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:102526 original size:40 final size:40
Alignment explanation
Indices: 102313--102518 Score: 283
Period size: 40 Copynumber: 5.2 Consensus size: 40
102303 AACCCAAGTA
* *
102313 CCTTCGGGAATTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
** *
102352 CCTTCGGGTTTTAGCCCGAATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
102392 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
102432 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
** *
102472 CCTTCGGGACTTAGTTCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
102512 CCTTCGG
1 CCTTCGG
102519 ATCTTAGTCT
Statistics
Matches: 152, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 13 0.09
40 138 0.91
41 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:106292 original size:22 final size:22
Alignment explanation
Indices: 106264--106435 Score: 79
Period size: 22 Copynumber: 7.4 Consensus size: 22
106254 ACATGTACAT
*
106264 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCTGAATGGCCA
* *
106286 ATGTGATGAATG-TGAACAT-GCATA
1 ATGTGAT-AAGGCTG-A-ATGGC-CA
*
106310 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCTGAATGGCCA
*
106333 ATGTGATGAATG-TGAACAT-G-CA
1 ATGTGAT-AAGGCTG-A-ATGGCCA
*
106355 TATGTGTGATAAGGCCGAATGGCCA
1 -A--TGTGATAAGGCTGAATGGCCA
*
106380 ATGTGATGAATG-TGAACAT-GCACA
1 ATGTGAT-AAGGCTG-A-ATGGC-CA
*
106404 TATGTGATAAGGCTGAATGACCA
1 -ATGTGATAAGGCTGAATGGCCA
106427 ATGTGATAA
1 ATGTGATAA
106436 ATGTGAACAT
Statistics
Matches: 113, Mismatches: 14, Indels: 46
0.65 0.08 0.27
Matches are distributed among these distances:
22 34 0.30
23 27 0.24
24 26 0.23
25 26 0.23
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCTGAATGGCCA
Found at i:106513 original size:141 final size:141
Alignment explanation
Indices: 106238--106517 Score: 427
Period size: 141 Copynumber: 2.0 Consensus size: 141
106228 TTTAGGATTT
* * *
106238 AATGTGATGAATGTGAACATGTACATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
1 AATGTGATGAATGTGAACATGCACATATGTGATAAGGCCGAATGACCAATGTGATAAATGTGAAC
** * * * *
106303 ATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAG
66 ATGCATATATGTGATAAGGCAAAATGGCCAATGTGATGAACGTGAACATGCATATATGTGAGAAA
106368 GCCGAATGGCC
131 GCCGAATGGCC
*
106379 AATGTGATGAATGTGAACATGCACATATGTGATAAGGCTGAATGACCAATGTGATAAATGTGAAC
1 AATGTGATGAATGTGAACATGCACATATGTGATAAGGCCGAATGACCAATGTGATAAATGTGAAC
* * *
106444 ATGCATATATGTGATAAGGCAAAATGGCCAATGTGATGAACGTGGAA-GTGTATATATGTGGGAA
66 ATGCATATATGTGATAAGGCAAAATGGCCAATGTGATGAACGT-GAACATGCATATATGTGAGAA
106508 AGCCGAATGG
130 AGCCGAATGG
106518 TTAATGCGAA
Statistics
Matches: 125, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
141 122 0.98
142 3 0.02
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.25
Consensus pattern (141 bp):
AATGTGATGAATGTGAACATGCACATATGTGATAAGGCCGAATGACCAATGTGATAAATGTGAAC
ATGCATATATGTGATAAGGCAAAATGGCCAATGTGATGAACGTGAACATGCATATATGTGAGAAA
GCCGAATGGCC
Found at i:106517 original size:47 final size:47
Alignment explanation
Indices: 106238--106483 Score: 411
Period size: 47 Copynumber: 5.2 Consensus size: 47
106228 TTTAGGATTT
* *
106238 AATGTGATGAATGTGAACATGTACATATGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
106285 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
*
106332 AATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* * *
106379 AATGTGATGAATGTGAACATGCACATATGTGATAAGGCTGAATGACC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* **
106426 AATGTGATAAATGTGAACATGCATATATGTGATAAGGCAAAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
106473 AATGTGATGAA
1 AATGTGATGAA
106484 CGTGGAAGTG
Statistics
Matches: 186, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 186 1.00
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.26
Consensus pattern (47 bp):
AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
Found at i:106550 original size:46 final size:46
Alignment explanation
Indices: 106497--106587 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
106487 GGAAGTGTAT
* * *
106497 ATATGTGGGAAAGCCGAATGGTTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
* * *
106543 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATG
106588 TGTATATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.34, C:0.07, G:0.32, T:0.27
Consensus pattern (46 bp):
ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
Found at i:108082 original size:40 final size:40
Alignment explanation
Indices: 108027--108360 Score: 553
Period size: 40 Copynumber: 8.3 Consensus size: 40
108017 TTCAGTATGT
* * *
108027 TATATCCAGACTAAGTCCTGAAGAGCATTCGTGCTAGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
* *
108067 TATATCCGGGCTAAGTTCCGAAGAGCATTAGTGCTAGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
*
108107 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
108147 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
*
108187 -AGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
1 TA-TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
108227 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
* * *
108267 TGTATCCAGGCTAAGTCCCGAAAAGCATTCGTGCTAGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
*
108307 TATATCCGGGCTAAGTCCCAAAGAGCATTCGTGCTAGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
108347 TATATCCGGGCTAA
1 TATATCCGGGCTAA
108361 ACCTCGAAGG
Statistics
Matches: 274, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
39 1 0.00
40 272 0.99
41 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA
Found at i:108530 original size:29 final size:28
Alignment explanation
Indices: 108392--108548 Score: 113
Period size: 28 Copynumber: 5.5 Consensus size: 28
108382 GAATCATGAG
* * * *
108392 GCACTGTGTGTGCAAGTTCGTCAACCGA
1 GCACTATGTGTGCGAGTTCGTTAATCGA
* * * *
108420 GCACTATGTGTGCCAGATCAG-TAGTTGA
1 GCACTATGTGTGCGAGTTC-GTTAATCGA
108448 GGCACTATGTGTGCGAGTTC-TTCAATCGA
1 -GCACTATGTGTGCGAGTTCGTT-AATCGA
* * * *
108477 GAACTATGTGGGCGAGATT-GATAATTGA
1 GCACTATGTGTGCGAG-TTCGTTAATCGA
*
108505 GGCACTATGTGTGCGAGTTCTTTAATCGA
1 -GCACTATGTGTGCGAGTTCGTTAATCGA
* *
108534 GCGCTATGCGTGCGA
1 GCACTATGTGTGCGA
108549 AATCAGTCAG
Statistics
Matches: 99, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
28 54 0.55
29 45 0.45
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
GCACTATGTGTGCGAGTTCGTTAATCGA
Found at i:108541 original size:57 final size:57
Alignment explanation
Indices: 108388--108541 Score: 193
Period size: 57 Copynumber: 2.7 Consensus size: 57
108378 GCCGGAATCA
* * * * * *
108388 TGAGGCACTGTGTGTGCAAGTTCGTCAACCGAGCACTATGTGTGCCAGATCAGTAGT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGGGCCAGATCAGTAAT
* * *
108445 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGAACTATGTGGGCGAGAT-TGATAAT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGGGCCAGATCAG-TAAT
* *
108502 TGAGGCACTATGTGTGCGAGTTCTTTAATCGAGCGCTATG
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATG
108542 CGTGCGAAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
56 1 0.01
57 83 0.99
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (57 bp):
TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGGGCCAGATCAGTAAT
Found at i:110084 original size:13 final size:13
Alignment explanation
Indices: 110066--110091 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
110056 ATATTATAAT
110066 TATTTTATGTTAA
1 TATTTTATGTTAA
110079 TATTTTATGTTAA
1 TATTTTATGTTAA
110092 AAATAAAAAT
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTTATGTTAA
Found at i:115928 original size:45 final size:44
Alignment explanation
Indices: 115777--115938 Score: 175
Period size: 45 Copynumber: 3.6 Consensus size: 44
115767 TTGTGTGAGG
* * * *
115777 TAGTGTAGGACATGTCTGGGACATGGCATCGACATTGAGACG-AGTGC
1 TAGTGTAAGACATGTCTGGGACAT-GCATCGGC-TCGAGATGTA--GC
115824 TAGTGTAAGACATGTCTGGGACATGCATCGGCTCGAGATGTAAGC
1 TAGTGTAAGACATGTCTGGGACATGCATCGGCTCGAGATGT-AGC
* * *
115869 CAGTGTAAGACATGTTTGGGACATGCATCGGCTACGAGATGT-GT
1 TAGTGTAAGACATGTCTGGGACATGCATCGGCT-CGAGATGTAGC
*
115913 TAGTATAAGACCATGTCTGGGACATG
1 TAGTGTAAGA-CATGTCTGGGACATG
115939 GTATCGACAC
Statistics
Matches: 101, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
44 9 0.09
45 53 0.52
46 15 0.15
47 24 0.24
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (44 bp):
TAGTGTAAGACATGTCTGGGACATGCATCGGCTCGAGATGTAGC
Found at i:122273 original size:24 final size:21
Alignment explanation
Indices: 122239--122290 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 21
122229 TATGAATCGG
*
122239 CAAAAGCCGAAATGCCAAAATGC
1 CAAAAGTCGAAATG-CAAAA-GC
122262 CGAAAAGTCGAAATGCAAAAGC
1 C-AAAAGTCGAAATGCAAAAGC
122284 CAAAAGT
1 CAAAAGT
122291 TTGGCTACGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 6 0.22
22 3 0.11
23 6 0.22
24 12 0.44
ACGTcount: A:0.50, C:0.21, G:0.19, T:0.10
Consensus pattern (21 bp):
CAAAAGTCGAAATGCAAAAGC
Found at i:122551 original size:29 final size:28
Alignment explanation
Indices: 122495--122607 Score: 113
Period size: 29 Copynumber: 4.0 Consensus size: 28
122485 GTGAGCATGA
* * * *
122495 ATATGAATGTGA-CTGGCCTAACGAGCC
1 ATATAAATGTGATTTGGCCTAATGGGCC
122522 ATATAAATGTGATTTAGGCCTAATGGGCC
1 ATATAAATGTGATTT-GGCCTAATGGGCC
* *
122551 ATATACAGGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGATTT-GGCCTAATGGGCC
* * *
122580 ATATGAATATGA-TTGGCTTAATGGGCC
1 ATATAAATGTGATTTGGCCTAATGGGCC
122607 A
1 A
122608 GATACAGGTA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
27 24 0.33
28 3 0.04
29 45 0.62
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (28 bp):
ATATAAATGTGATTTGGCCTAATGGGCC
Found at i:122581 original size:58 final size:56
Alignment explanation
Indices: 122509--122616 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
122499 GAATGTGACT
* *
122509 GGCCTAACGAGCCATATAAATGTGATTTAGGCCTAATGGGCCATATACAGGTGATTTG
1 GGCCTAACGAGCCATATAAATATGA-TT-GGCCTAATGGGCCAGATACAGGTGATTTG
* * * *
122567 GGCCTAATGGGCCATATGAATATGATTGGCTTAATGGGCCAGATACAGGT
1 GGCCTAACGAGCCATATAAATATGATTGGCCTAATGGGCCAGATACAGGT
122617 ATGTGAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
56 21 0.48
57 2 0.05
58 21 0.48
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.27
Consensus pattern (56 bp):
GGCCTAACGAGCCATATAAATATGATTGGCCTAATGGGCCAGATACAGGTGATTTG
Found at i:122619 original size:29 final size:31
Alignment explanation
Indices: 122531--122619 Score: 93
Period size: 29 Copynumber: 3.1 Consensus size: 31
122521 CATATAAATG
*
122531 TGATTTAGGCCTAATGGGCCATATACAGG--
1 TGATTTGGGCCTAATGGGCCATATACAGGTA
122560 TGATTTGGGCCTAATGGGCCATATGA-A--TA
1 TGATTTGGGCCTAATGGGCCATAT-ACAGGTA
* *
122589 TGA-TT-GGCTTAATGGGCCAGATACAGGTA
1 TGATTTGGGCCTAATGGGCCATATACAGGTA
122618 TG
1 TG
122620 TGAAATTGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
26 1 0.02
27 16 0.31
28 2 0.04
29 31 0.61
30 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (31 bp):
TGATTTGGGCCTAATGGGCCATATACAGGTA
Found at i:125505 original size:14 final size:14
Alignment explanation
Indices: 125486--125513 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
125476 CGCCCCAAAA
125486 ACTGTATCATCTAC
1 ACTGTATCATCTAC
125500 ACTGTATCATCTAC
1 ACTGTATCATCTAC
125514 TCTAACATAT
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:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (14 bp):
ACTGTATCATCTAC
Done.