Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3434
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: 39111
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:4071 original size:30 final size:30
Alignment explanation
Indices: 4037--4096 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
4027 ATTTAATACG
*
4037 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* *
4067 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
4097 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:11620 original size:30 final size:30
Alignment explanation
Indices: 11575--11634 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
11565 CATTTAATAC
11575 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACATTTTTGCCCCTA
* *
11605 AACTTTTGCATAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACATTTTTGCCCCTA
11635 GGCTTGGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.40
Consensus pattern (30 bp):
AACTTTGGCAAAATTACATTTTTGCCCCTA
Found at i:14007 original size:56 final size:56
Alignment explanation
Indices: 13916--14345 Score: 693
Period size: 56 Copynumber: 7.7 Consensus size: 56
13906 CCTTACATGT
** *** *
13916 AATCACATATCGATGCCATTGTCCCAAACCG-GGTCTTACTCGCACACATATATCGG
1 AATCACATATCGATGCCAACGTATTAAA-CGTGGTCTTACTCGCACACATATATCAG
* * *
13972 AGTGACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCGG
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
14028 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
** * ** *
14084 AATCACATATCGATGCCAACGTATTAAGTGTGGCCTTACT-TTACACATATATCGG
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
14139 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
14195 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
*
14251 AATCACATATCGATGCCAACGTATTGAACGTGGTCTTACTCGCACACATATATCAG
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
14307 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTAC
1 AATCACATATCGATGCCAACGTATTAAACGTGGTCTTAC
14346 ACATCATCAA
Statistics
Matches: 348, Mismatches: 24, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
55 51 0.15
56 297 0.85
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (56 bp):
AATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAG
Found at i:14149 original size:167 final size:168
Alignment explanation
Indices: 13950--14345 Score: 697
Period size: 167 Copynumber: 2.4 Consensus size: 168
13940 CAAACCGGGT
* *
13950 CTTACTCGCACACATATATCGGAGTGACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGC
1 CTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGC
*
14015 ACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATA
66 ACACATATATCAGAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATA
*
14080 TCAGAATCACATATCGATGCCAACGTATT-AAGTGTGGC
131 TCAGAATCACATATCGATGCCAACGTATTGAA-CGTGGC
**
14118 CTTACT-TTACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGC
1 CTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGC
14182 ACACATATATCAGAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATA
66 ACACATATATCAGAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATA
*
14247 TCAGAATCACATATCGATGCCAACGTATTGAACGTGGT
131 TCAGAATCACATATCGATGCCAACGTATTGAACGTGGC
*
14285 CTTACTCGCACACATATATCAGAATCACATATCGATGCCAACGTATTAAACGTGGTCTTAC
1 CTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGTGGTCTTAC
14346 ACATCATCAA
Statistics
Matches: 216, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
167 157 0.73
168 59 0.27
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (168 bp):
CTTACTCGCACACATATATCGGAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGC
ACACATATATCAGAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATA
TCAGAATCACATATCGATGCCAACGTATTGAACGTGGC
Found at i:14304 original size:223 final size:223
Alignment explanation
Indices: 13916--14333 Score: 730
Period size: 223 Copynumber: 1.9 Consensus size: 223
13906 CCTTACATGT
** * * * *
13916 AATCACATATCGATGCCATTGTCCCAAACCGGGTCTTACTCGCACACATATATCGGAGTGACATA
1 AATCACATATCGATGCCAACGTACCAAACCGGGTCTTACTCGCACACATATATCAGAATCACATA
*
13981 TCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCGGAATCACATATCGATGCCA
66 TCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCA
14046 ACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACGTATTAA
131 ACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACGTATTAA
14111 GTGTGGCCTTACTTTACACATATATCGG
196 GTGTGGCCTTACTTTACACATATATCGG
**
14139 AATCACATATCGATGCCAACGTATTAAA-CGTGGTCTTACTCGCACACATATATCAGAATCACAT
1 AATCACATATCGATGCCAACGTACCAAACCG-GGTCTTACTCGCACACATATATCAGAATCACAT
14203 ATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCACATATCGATGCC
65 ATCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCACATATCGATGCC
*
14268 AACGTATTGAACGTGGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACGTATTA
130 AACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACGTATTA
14333 A
195 A
14334 ACGTGGTCTT
Statistics
Matches: 184, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
222 2 0.01
223 182 0.99
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.27
Consensus pattern (223 bp):
AATCACATATCGATGCCAACGTACCAAACCGGGTCTTACTCGCACACATATATCAGAATCACATA
TCGATGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCA
ACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACGTATTAA
GTGTGGCCTTACTTTACACATATATCGG
Found at i:17049 original size:37 final size:36
Alignment explanation
Indices: 16991--17067 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 36
16981 AATAATTCAA
*
16991 ATGATACAACATTTGTTCAGTTTGATGGTTTGCAGG
1 ATGATACAACATTTGTTCAGTTTGATGATTTGCAGG
17027 ATGATACAACAGTTTGTTCAGTTTGATGATTTGCAGG
1 ATGATACAACA-TTTGTTCAGTTTGATGATTTGCAGG
17064 ATGA
1 ATGA
17068 GGATCCAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 11 0.28
37 28 0.72
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (36 bp):
ATGATACAACATTTGTTCAGTTTGATGATTTGCAGG
Found at i:19800 original size:13 final size:13
Alignment explanation
Indices: 19784--19813 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19774 GACATTGCCA
19784 TGTGACACGGCCC
1 TGTGACACGGCCC
*
19797 TGTGACACGGCCG
1 TGTGACACGGCCC
19810 TGTG
1 TGTG
19814 CACTAACACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.30, G:0.37, T:0.20
Consensus pattern (13 bp):
TGTGACACGGCCC
Found at i:25129 original size:93 final size:93
Alignment explanation
Indices: 25017--25187 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
25007 CGCCCATAAG
* * *
25017 CGAACTCGGACTCAACTCAACGAGCTTAGG-CGTTCGCATCCATAAGTGAACTCGGACTCGACTC
1 CGAACTCGGACTCAACTCAACGAG-TTAGGACATTCGCATCCATAAGTGAACTCGAACTCAACTC
25081 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
25110 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTAGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
25175 ACGAGTTCGGATG
66 ACGAGTTCGGATG
25188 GTCAATCATC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 4 0.05
93 69 0.95
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGTTAGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:25182 original size:46 final size:46
Alignment explanation
Indices: 25010--25185 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
25000 TGTAACCCGC
* *
25010 CCATAAGCGAACTCGGACTCAACTCAACGAGCTTAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCAT
* * *
25056 CCATAAGTGAACTCGGACTCGACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
25106 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
25149 CCATAAGTGAACTCGAACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
25186 TGGTCAATCA
Statistics
Matches: 108, Mismatches: 12, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 6 0.06
46 57 0.53
47 28 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:29309 original size:85 final size:85
Alignment explanation
Indices: 29166--29344 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
29156 GGCCGGCCAT
29166 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
29231 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
29251 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
29316 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
29336 GGGCATGGG
1 GAGCATGGG
29345 CAATAAAATT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:30700 original size:71 final size:71
Alignment explanation
Indices: 30624--30762 Score: 269
Period size: 71 Copynumber: 2.0 Consensus size: 71
30614 GTGAAAGTGT
*
30624 ATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 ATATATGTGATAAGGCCTAATAACCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
30689 AATAGC
66 AATAGC
30695 ATATATGTGATAAGGCCTAATAACCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 ATATATGTGATAAGGCCTAATAACCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
30760 AAT
66 AAT
30763 GGCCGATGTG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.30
Consensus pattern (71 bp):
ATATATGTGATAAGGCCTAATAACCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
AATAGC
Found at i:30701 original size:24 final size:24
Alignment explanation
Indices: 30671--30716 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
30661 GTGAAAGTGT
30671 ATATATGTGATAAGGCCTAATAGC
1 ATATATGTGATAAGGCCTAATAGC
30695 ATATATGTGATAAGGCCTAATA
1 ATATATGTGATAAGGCCTAATA
30717 ACCGATGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (24 bp):
ATATATGTGATAAGGCCTAATAGC
Found at i:30727 original size:22 final size:23
Alignment explanation
Indices: 30675--30727 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
30665 AAGTGTATAT
* *
30675 ATGTGATAAGGCCTAATAGCATAT
1 ATGTGATAAGGCCTAATA-CACAG
*
30699 ATGTGATAAGGCCTAATA-ACCG
1 ATGTGATAAGGCCTAATACACAG
30721 ATGTGAT
1 ATGTGAT
30728 GAATGTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 8 0.31
24 18 0.69
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (23 bp):
ATGTGATAAGGCCTAATACACAG
Found at i:30748 original size:47 final size:47
Alignment explanation
Indices: 30695--31133 Score: 598
Period size: 47 Copynumber: 9.3 Consensus size: 47
30685 GCCTAATAGC
* ** *
30695 ATATATGTGATAAGGCCTAATAACCGATGTGATGAATGTGAA-AGTGT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGT
* *
30742 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA-AGTGTAT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG--T
*
30791 ATATATGTGAGAAGGCCGAATGGCCAATGTGATGAATGTGAACATGT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGT
* * *
30838 GTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGT
*
30885 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGT
* *
30932 GTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGT
* * *
30979 GTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGT
* * *
31026 ATATATGAGATAAGGCCGAGTGACCAATGTGATGAATGTGAA-AGTGT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGT
* *
31073 ATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGGAA-GTGT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGT-GAACATGT
*
31120 ATAAATGTGATAAG
1 ATATATGTGATAAG
31134 TCCCGAAGGG
Statistics
Matches: 358, Mismatches: 29, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
46 1 0.00
47 311 0.87
48 3 0.01
49 42 0.12
50 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (47 bp):
ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGT
Found at i:30821 original size:118 final size:118
Alignment explanation
Indices: 30611--30823 Score: 349
Period size: 118 Copynumber: 1.8 Consensus size: 118
30601 TATTTGAATA
30611 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
* * *
30676 TGTGATAAGGCCTAATAGCATATATGTGATAAGGCCTAATAACCGATGTGATG
66 TGTGAGAAGGCCGAATAGCACATATGTGATAAGGCCTAATAACCGATGTGATG
*
30729 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG--TATA
*
30794 TATGTGAGAAGGCCGAATGGC-CA-ATGTGAT
64 TATGTGAGAAGGCCGAATAGCACATATGTGAT
30824 GAATGTGAAC
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
118 65 0.74
119 1 0.01
120 22 0.25
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (118 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
TGTGAGAAGGCCGAATAGCACATATGTGATAAGGCCTAATAACCGATGTGATG
Found at i:33625 original size:38 final size:38
Alignment explanation
Indices: 33561--33635 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
33551 AATCCGAGTT
*
33561 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
33599 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
33636 ATTAAAATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:33744 original size:40 final size:40
Alignment explanation
Indices: 33692--34008 Score: 438
Period size: 40 Copynumber: 7.9 Consensus size: 40
33682 CTCGACGGTG
*
33692 ATCCGGGATAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
33732 ATCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* **
33771 ATCCGGGCTAAGTTCCGAAGAGCATTTGTGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
*
33811 ATCCGGGCTAAGTCCCGAAGAGAATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
*
33851 ATCCGGGCTAAGTCCCAAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
** * *
33891 ATCCGGGCTAAGTTTCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* ** * * * *
33931 ATCCGTGCTAAACCCCGAAGAGCATTTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCA-TTCATGCTAGTGATGT
* * *
33972 ATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
34009 CGTGTATTCG
Statistics
Matches: 247, Mismatches: 28, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
39 39 0.16
40 174 0.70
41 34 0.14
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
Found at i:35366 original size:84 final size:84
Alignment explanation
Indices: 35264--35440 Score: 320
Period size: 84 Copynumber: 2.1 Consensus size: 84
35254 GGCCGGCCAT
35264 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTT-GGGTAGTGCATTTA
1 GAGCAT-GGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCA-TTA
35328 TGTAAGGATTAATAAAATAAA
64 TGTAAGGATTAATAAAATAAA
35349 GAGCATGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTATG
1 GAGCATGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTATG
35414 TAAGGATTAATAAAATAAA
66 TAAGGATTAATAAAATAAA
*
35433 GGGCATGG
1 GAGCATGG
35441 GCAATAAAAT
Statistics
Matches: 90, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
84 74 0.82
85 16 0.18
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.27
Consensus pattern (84 bp):
GAGCATGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTATG
TAAGGATTAATAAAATAAA
Found at i:36793 original size:71 final size:72
Alignment explanation
Indices: 36714--36853 Score: 255
Period size: 71 Copynumber: 1.9 Consensus size: 72
36704 TGTGAAAGTG
36714 TATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCT
1 TATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCT
36778 AATAGCA
66 AATAGCA
*
36785 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCC
36850 TAAT
65 TAAT
36854 GGCCATGTGA
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
71 44 0.67
73 22 0.33
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31
Consensus pattern (72 bp):
TATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCT
AATAGCA
Found at i:36927 original size:47 final size:48
Alignment explanation
Indices: 36784--37269 Score: 717
Period size: 47 Copynumber: 10.3 Consensus size: 48
36774 GCCTAATAGC
* *
36784 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA-AGTGTAT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTG--T
*
36833 ATATATGTGATAAGGCCTAATGGCC-ATGTGATGAATGTGAA-AGTGT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTGT
36879 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTGTAT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTG--T
36928 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTGT
* * *
36975 GTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTGT
*
37022 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTG-
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTGT
*
37069 -TATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTGT
* * *
37115 GTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTGT
*
37162 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTGT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTGT
* *
37209 ATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGGA-AGTGT
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTGT
*
37256 ATAAATGTGATAAG
1 ATATATGTGATAAG
37270 TCCCGAAGGG
Statistics
Matches: 411, Mismatches: 18, Indels: 18
0.92 0.04 0.04
Matches are distributed among these distances:
45 2 0.00
46 67 0.16
47 249 0.61
48 22 0.05
49 70 0.17
50 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (48 bp):
ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAGTGT
Found at i:37129 original size:140 final size:140
Alignment explanation
Indices: 36784--37248 Score: 740
Period size: 140 Copynumber: 3.3 Consensus size: 140
36774 GCCTAATAGC
* * * *
36784 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA-AGTGTATATATATGTGATAAGG
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG--TGTATGTGTGATAAGG
* * *
36848 CCTAATGGCC-ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGA
63 CCGAATGGCCAATGTGATGAATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGA
36911 TGAATGTGAAAGTG
127 TGAATGTGAAAGTG
36925 TATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGG
1 ---ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGG
36990 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGAT
63 CCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGAT
37055 GAATGTGAACAGTG
128 GAATGTGAA-AGTG
*
37069 -TATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCG
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCG
37133 AATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAA
66 AATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAA
37198 TGTGAAAGTG
131 TGTGAAAGTG
*
37208 TATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTG
1 -ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
37249 GAAGTGTATA
Statistics
Matches: 305, Mismatches: 10, Indels: 15
0.92 0.03 0.05
Matches are distributed among these distances:
139 4 0.01
140 134 0.44
141 37 0.12
142 23 0.08
143 59 0.19
144 47 0.15
145 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (140 bp):
ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCG
AATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAA
TGTGAAAGTG
Found at i:37147 original size:22 final size:22
Alignment explanation
Indices: 37120--37241 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
37110 CATGTGTATG
37120 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
37142 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
37167 TGAGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * ***
37189 TGTGATGAATG-TGAAAGTGTATATA
1 TGTGAT-AAGGCCG-AA-TGGCCA-A
37214 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
37236 TGTGAT
1 TGTGAT
37242 GGATGTGGAA
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 21 0.30
23 17 0.24
24 17 0.24
25 15 0.21
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:37189 original size:187 final size:187
Alignment explanation
Indices: 36782--37269 Score: 732
Period size: 187 Copynumber: 2.6 Consensus size: 187
36772 AGGCCTAATA
* *
36782 GCATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
1 GCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG--TATATATGTGATAAG
*
36847 GCCTAATGGCC-ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGA
64 GCCGAATGGCCAATGTGATGAATGTGAAAGTG--TATATGTGATAAGGCCGAATGGCCAATGTGA
36911 TGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAT
127 TGAATGTGAAAGTG-ATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAT
** * * *
36973 GTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGCATATATGAGATAAGG
1 GCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTGTATATATGTGATAAGG
*
37037 CCGAATGGCCAATGTGATGAATGTGAACAGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
65 CCGAATGGCCAATGTGATGAATGTGAA-AGTGTATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
37102 AATGTGAACA-TG-TGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAT
129 AATGTGAA-AGTGATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAT
*
37160 GCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
1 GCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
* *
37225 CGAATGGCCAATGTGATGGATGTGGAAGTGTATAAATGTGATAAG
66 CGAATGGCCAATGTGATGAATGTGAAAGTGTAT--ATGTGATAAG
37270 TCCCGAAGGG
Statistics
Matches: 270, Mismatches: 20, Indels: 17
0.88 0.07 0.06
Matches are distributed among these distances:
186 8 0.03
187 125 0.46
188 9 0.03
189 65 0.24
190 17 0.06
191 45 0.17
192 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (187 bp):
GCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGC
CGAATGGCCAATGTGATGAATGTGAAAGTGTATATGTGATAAGGCCGAATGGCCAATGTGATGAA
TGTGAAAGTGATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACAT
Done.