Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1220
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: 111372
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3336 original size:42 final size:42
Alignment explanation
Indices: 3277--3415 Score: 179
Period size: 42 Copynumber: 3.3 Consensus size: 42
3267 TCTACAAGCC
* * *
3277 ACACACCAGTCTGAACAGGTTGTGTGTCACACACGGCTTTAG
1 ACACACCCGTGTGAACAGGTCGTGTGTCACACACGGCTTTAG
*
3319 ACACACCCGTGTGAACAGGTCGTGTGTCACACGCGGCTTTAG
1 ACACACCCGTGTGAACAGGTCGTGTGTCACACACGGCTTTAG
* * * * *
3361 ACACACCCGTGTGAACAGGCCATATGTCACACATGACTTTAG
1 ACACACCCGTGTGAACAGGTCGTGTGTCACACACGGCTTTAG
* *
3403 ACACGCCTGTGTG
1 ACACACCCGTGTG
3416 TCTAGCCTGG
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 85 1.00
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.22
Consensus pattern (42 bp):
ACACACCCGTGTGAACAGGTCGTGTGTCACACACGGCTTTAG
Found at i:3853 original size:11 final size:10
Alignment explanation
Indices: 3832--3871 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
3822 TTCACCAACT
3832 AAATCATACC
1 AAATCATACC
3842 AAATCTATACC
1 AAATC-ATACC
3853 AAAATCATACC
1 -AAATCATACC
*
3864 AAAGCATA
1 AAATCATA
3872 TGTTTCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 12 0.44
11 10 0.37
12 5 0.19
ACGTcount: A:0.53, C:0.25, G:0.03, T:0.20
Consensus pattern (10 bp):
AAATCATACC
Found at i:4698 original size:43 final size:43
Alignment explanation
Indices: 4576--4699 Score: 112
Period size: 43 Copynumber: 2.9 Consensus size: 43
4566 AAAGCTCGTA
* * *
4576 CAATGCCAACATCCCAGACTTGGTCTTACATGT-AATCAAATAT
1 CAATG-CAACGTCCCAGACGTGGTCTTACACGTAAATCAAATAT
* * * *
4619 CGATGCCACTGTCCCAGACAG-GGTCTTACAC-AAAATCAAATCT
1 CAATGCAAC-GTCCCAGAC-GTGGTCTTACACGTAAATCAAATAT
*
4662 -AATGTCAACGTCCCAGACGTGGTTTTACACGTAAATCA
1 CAATG-CAACGTCCCAGACGTGGTCTTACACGTAAATCA
4700 TAAGTTGATG
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
41 1 0.02
42 24 0.38
43 39 0.61
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (43 bp):
CAATGCAACGTCCCAGACGTGGTCTTACACGTAAATCAAATAT
Found at i:9599 original size:15 final size:15
Alignment explanation
Indices: 9580--9619 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
9570 ACGAGTCTTC
*
9580 AAAAATAAATAGAAAT
1 AAAAATAAAGA-AAAT
*
9596 AAAAGTAAAGAAAAT
1 AAAAATAAAGAAAAT
9611 AAAAATAAA
1 AAAAATAAA
9620 ACGAGTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (15 bp):
AAAAATAAAGAAAAT
Found at i:22289 original size:43 final size:42
Alignment explanation
Indices: 22134--22292 Score: 119
Period size: 43 Copynumber: 3.7 Consensus size: 42
22124 TCATTTTTTT
* * *
22134 TGTAAGACCACGTCTGAGACGTTGGCATCGACTTCTGTTTTACA
1 TGTAAGACCACGTCTGAGACGTTGGCATTGA-TTATG-ATTACA
* * * * * ***
22178 TGTAAGACCATGTCTGGGACATCGGCA-TCATATATGATTTTG
1 TGTAAGACCACGTCTGAGACGTTGGCATTGAT-TATGATTACA
*
22220 TGTAAGACC-CTGTCTGAGACAG-TGGCATTGATGTTTGATTACA
1 TGTAAGACCAC-GTCTGAGAC-GTTGGCATTGAT-TATGATTACA
22263 TGTAAGACCACGTCT-AGGACGTTGGCATTG
1 TGTAAGACCACGTCTGA-GACGTTGGCATTG
22293 TATATGTTCT
Statistics
Matches: 87, Mismatches: 21, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
42 26 0.30
43 37 0.43
44 24 0.28
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (42 bp):
TGTAAGACCACGTCTGAGACGTTGGCATTGATTATGATTACA
Found at i:24613 original size:2 final size:2
Alignment explanation
Indices: 24608--24639 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
24598 TCAAACACCT
24608 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
24640 TATATATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:26143 original size:15 final size:15
Alignment explanation
Indices: 26120--26150 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
26110 TCAAAAATTC
26120 CAATACAAAACATAT
1 CAATACAAAACATAT
*
26135 CAATCCAAAACATAT
1 CAATACAAAACATAT
26150 C
1 C
26151 TTTCATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (15 bp):
CAATACAAAACATAT
Found at i:30215 original size:6 final size:6
Alignment explanation
Indices: 30206--30238 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
30196 AATAAAATTG
*
30206 AAATGA AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAA
30239 GATAGGAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:36350 original size:32 final size:32
Alignment explanation
Indices: 36309--36375 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
36299 AAAGAAGTTG
36309 AAATATCAGGGGCAAAAATATAATTCTGCCAT
1 AAATATCAGGGGCAAAAATATAATTCTGCCAT
*
36341 AAATATCAGGGGCAAAAATATAATTTTGCCAT
1 AAATATCAGGGGCAAAAATATAATTCTGCCAT
36373 AAA
1 AAA
36376 GTAATTTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.25
Consensus pattern (32 bp):
AAATATCAGGGGCAAAAATATAATTCTGCCAT
Found at i:36902 original size:28 final size:28
Alignment explanation
Indices: 36803--36900 Score: 160
Period size: 28 Copynumber: 3.5 Consensus size: 28
36793 GCAATCAAAT
*
36803 ATGGTACTTAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAGA
36831 ATGGCACTTAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAGA
* *
36859 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAGA
*
36887 ATGACACTTAGTGT
1 ATGGCACTTAGTGT
36901 GCAAAATACC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.31
Consensus pattern (28 bp):
ATGGCACTTAGTGTACGAAATATTGAGA
Found at i:38916 original size:28 final size:28
Alignment explanation
Indices: 38885--39038 Score: 175
Period size: 28 Copynumber: 5.5 Consensus size: 28
38875 GTGAACATAG
*
38885 GCACTGTGTGTGTGAGTTCCGTAATCGA
1 GCACTGTGTGTGCGAGTTCCGTAATCGA
*
38913 GCACTGTGTGTGCGAGTTTCGTAA-CTGA
1 GCACTGTGTGTGCGAGTTCCGTAATC-GA
* *
38941 GCACTGTGTATGCGAGTTCCGTAATTGA
1 GCACTGTGTGTGCGAGTTCCGTAATCGA
* * * ** *
38969 GCACTGTGTATGCGAGATCGGTTGTTGA
1 GCACTGTGTGTGCGAGTTCCGTAATCGA
* *
38997 GGCACTGTGTGTGCGAGTTCCGTAACCAA
1 -GCACTGTGTGTGCGAGTTCCGTAATCGA
39026 GCACTGTGTGTGC
1 GCACTGTGTGTGC
39039 AAGATCGGTT
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
27 1 0.01
28 85 0.80
29 20 0.19
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (28 bp):
GCACTGTGTGTGCGAGTTCCGTAATCGA
Found at i:38958 original size:56 final size:57
Alignment explanation
Indices: 38883--39047 Score: 208
Period size: 56 Copynumber: 2.9 Consensus size: 57
38873 AAGTGAACAT
* *
38883 AGGCACTGTGTGTGTGAGTTCCGTAATCGAGCACTGTGTGTGCGAGTTTC-GTAACTG
1 AGGCACTGTGTGTGCGAGTTCCGTAATCGAGCACTGTGTGTGCGAG-ATCGGTAACTG
* * * ***
38940 A-GCACTGTGTATGCGAGTTCCGTAATTGAGCACTGTGTATGCGAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAATCGAGCACTGTGTGTGCGAGATCGGTAACTG
* * *
38996 AGGCACTGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCAAGATCGGT
1 AGGCACTGTGTGTGCGAGTTCCGTAATCGAGCACTGTGTGTGCGAGATCGGT
39048 TGTTGAGGCA
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
55 2 0.02
56 45 0.49
57 45 0.49
ACGTcount: A:0.19, C:0.18, G:0.33, T:0.30
Consensus pattern (57 bp):
AGGCACTGTGTGTGCGAGTTCCGTAATCGAGCACTGTGTGTGCGAGATCGGTAACTG
Found at i:39011 original size:29 final size:29
Alignment explanation
Indices: 38883--39068 Score: 128
Period size: 28 Copynumber: 6.5 Consensus size: 29
38873 AAGTGAACAT
* * * *
38883 AGGCACTGTGTGTGTGAGTTCCGTAATCG
1 AGGCACTGTGTGTGCGAGATCCGTTATTG
* * * *
38912 A-GCACTGTGTGTGCGAGTTTCGTAACTG
1 AGGCACTGTGTGTGCGAGATCCGTTATTG
* * *
38940 A-GCACTGTGTATGCGAGTTCCGTAATTG
1 AGGCACTGTGTGTGCGAGATCCGTTATTG
* * *
38968 A-GCACTGTGTATGCGAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGATCCGTTATTG
* ***
38996 AGGCACTGTGTGTGCGAGTTCCG-TAACC
1 AGGCACTGTGTGTGCGAGATCCGTTATTG
* * * *
39024 AAGCACTGTGTGTGCAAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGATCCGTTATTG
39053 AGGCACTAAGTGTGTG
1 AGGCACT--GTGTGTG
39069 AAATGAGATC
Statistics
Matches: 126, Mismatches: 27, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
28 93 0.74
29 26 0.21
31 7 0.06
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.30
Consensus pattern (29 bp):
AGGCACTGTGTGTGCGAGATCCGTTATTG
Found at i:39021 original size:57 final size:57
Alignment explanation
Indices: 38883--39068 Score: 232
Period size: 57 Copynumber: 3.2 Consensus size: 57
38873 AAGTGAACAT
* * ***
38883 AGGCACTGTGTGTGTGAGTTCCGTAATCGAGCACTGTGTGTGCGAGTTTC-GTAACTG
1 AGGCACTGTGTGTGCGAGTTCCGTAATCGAGCACTGTGTGTGCGAG-ATCGGTTGTTG
* * *
38940 A-GCACTGTGTATGCGAGTTCCGTAATTGAGCACTGTGTATGCGAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAATCGAGCACTGTGTGTGCGAGATCGGTTGTTG
* * *
38996 AGGCACTGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCAAGATCGGTTGTTG
1 AGGCACTGTGTGTGCGAGTTCCGTAATCGAGCACTGTGTGTGCGAGATCGGTTGTTG
39053 AGGCACTAAGTGTGTG
1 AGGCACT--GTGTGTG
39069 AAATGAGATC
Statistics
Matches: 111, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
55 2 0.02
56 45 0.41
57 57 0.51
59 7 0.06
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.30
Consensus pattern (57 bp):
AGGCACTGTGTGTGCGAGTTCCGTAATCGAGCACTGTGTGTGCGAGATCGGTTGTTG
Found at i:44036 original size:28 final size:28
Alignment explanation
Indices: 44004--44105 Score: 159
Period size: 28 Copynumber: 3.6 Consensus size: 28
43994 CAAATATGGT
*
44004 ACTTAGTGTACGAAATATTGAGAATGGC
1 ACTTAGTGTACGAAATATTGAGAATGAC
44032 ACTTAGTGTACGAAATATTGAGAATGAC
1 ACTTAGTGTACGAAATATTGAGAATGAC
* *
44060 ACTTAGTGTGCGAGATATTGAGAATGAC
1 ACTTAGTGTACGAAATATTGAGAATGAC
* *
44088 ACTTAGTGTGCAAAATAT
1 ACTTAGTGTACGAAATAT
44106 CGAATGATTC
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 69 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (28 bp):
ACTTAGTGTACGAAATATTGAGAATGAC
Found at i:47453 original size:47 final size:47
Alignment explanation
Indices: 47259--47514 Score: 172
Period size: 47 Copynumber: 5.5 Consensus size: 47
47249 ATTGACGGTT
* *
47259 AAGGATACCATGTAAGAACATGTCA-AG-ACATGGCA-TTGGTAAGGC
1 AAGGATACCATGTAAGACCATGT-ATAGAACATGGCATTTGGTAAGAC
* * ** * * *
47304 AAGGATTCCGTGTAAGACCATGTCA-AG-ACATGGCA-TAAGCATTGATT
1 AAGGATACCATGTAAGACCATGT-ATAGAACATGGCATTTGGTA-AGA-C
** **
47351 AAGGACT-CCATGTAAGACCACATCA-AG-ATGTGGCA-TTGGCACTAAGAC
1 AAGGA-TACCATGTAAGACCATGT-ATAGAACATGGCATTTGG---TAAGAC
* *
47399 AAAGATACCATGTAAGACCATGTATGGAACATGGCATTTGGTAAGAC
1 AAGGATACCATGTAAGACCATGTATAGAACATGGCATTTGGTAAGAC
* * * *
47446 AAGGATACCATGTAAGACCATGTTTAGAATATGGCATTTGGTATGAT
1 AAGGATACCATGTAAGACCATGTATAGAACATGGCATTTGGTAAGAC
* *
47493 AAGGATATCATGCAAGACCATG
1 AAGGATACCATGTAAGACCATG
47515 CCAAGGCATG
Statistics
Matches: 168, Mismatches: 33, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
45 35 0.21
46 1 0.01
47 99 0.59
48 20 0.12
49 8 0.05
50 5 0.03
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (47 bp):
AAGGATACCATGTAAGACCATGTATAGAACATGGCATTTGGTAAGAC
Found at i:49384 original size:40 final size:40
Alignment explanation
Indices: 49289--49492 Score: 290
Period size: 40 Copynumber: 5.1 Consensus size: 40
49279 TGGATGATAA
*
49289 CCGGGCTAAGTCCCGAAGGCATTT-TGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG--AGTTACTA-TAT
* *
49330 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
49370 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
49410 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
49450 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
49489 CCGG
1 CCGG
49493 TTAAATCCTG
Statistics
Matches: 151, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
38 2 0.01
39 17 0.11
40 104 0.69
41 24 0.16
42 4 0.03
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:50919 original size:54 final size:55
Alignment explanation
Indices: 50856--50975 Score: 154
Period size: 55 Copynumber: 2.2 Consensus size: 55
50846 GGGGTGTTAC
* *
50856 ACATGGCATTGATAAGTT-CTATACGGC-AAGGAAATCATGTAAGACCATGCCAAG
1 ACATGGCATTGATAAGTTACTATAAGGCAAAGG-AACCATGTAAGACCATGCCAAG
* **
50910 ACATGGCATTGATGAGTTACTATAAGGCAAAGGTCCCATGTAAGACCATGCCAAG
1 ACATGGCATTGATAAGTTACTATAAGGCAAAGGAACCATGTAAGACCATGCCAAG
* *
50965 GCATAGCATTG
1 ACATGGCATTG
50976 GTGATGTAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
54 17 0.30
55 36 0.63
56 4 0.07
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (55 bp):
ACATGGCATTGATAAGTTACTATAAGGCAAAGGAACCATGTAAGACCATGCCAAG
Found at i:53578 original size:33 final size:35
Alignment explanation
Indices: 53540--53620 Score: 96
Period size: 33 Copynumber: 2.4 Consensus size: 35
53530 GCCTAAGCCC
*
53540 ATTCAGATAACAGTGATACTGGGCCAGAG-CCCTT
1 ATTCAGATAACAGTGAAACTGGGCCAGAGCCCCTT
* * **
53574 -TTCAGATTACA-TTAAACTGGGCCTTAGCCCCTT
1 ATTCAGATAACAGTGAAACTGGGCCAGAGCCCCTT
53607 ATTCAGATAACAGT
1 ATTCAGATAACAGT
53621 ATGGCCTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
32 12 0.32
33 15 0.39
34 10 0.26
35 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (35 bp):
ATTCAGATAACAGTGAAACTGGGCCAGAGCCCCTT
Found at i:53959 original size:26 final size:26
Alignment explanation
Indices: 53930--53982 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
53920 TCAAACATGC
53930 ATTTAGGTCAATTTA-CTCCTAGGGGT
1 ATTTAGGT-AATTTATCTCCTAGGGGT
* *
53956 ATTTCGGTACTTTATCTCCTAGGGGT
1 ATTTAGGTAATTTATCTCCTAGGGGT
53982 A
1 A
53983 AAACTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40
Consensus pattern (26 bp):
ATTTAGGTAATTTATCTCCTAGGGGT
Found at i:61456 original size:33 final size:35
Alignment explanation
Indices: 61418--61498 Score: 96
Period size: 33 Copynumber: 2.4 Consensus size: 35
61408 GCCTAAGCCC
*
61418 ATTCAGATAACAGTGATACTGGGCCAGAG-CCCTT
1 ATTCAGATAACAGTGAAACTGGGCCAGAGCCCCTT
* * **
61452 -TTCAGATTACA-TTAAACTGGGCCTTAGCCCCTT
1 ATTCAGATAACAGTGAAACTGGGCCAGAGCCCCTT
61485 ATTCAGATAACAGT
1 ATTCAGATAACAGT
61499 ACGGCCTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
32 12 0.32
33 15 0.39
34 10 0.26
35 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (35 bp):
ATTCAGATAACAGTGAAACTGGGCCAGAGCCCCTT
Found at i:61838 original size:26 final size:26
Alignment explanation
Indices: 61809--61861 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
61799 TTAAACATGC
*
61809 ATTTAGGTCAATTTA-CTCTTAGGGGT
1 ATTTAGGT-AATTTATCTCCTAGGGGT
* *
61835 ATTTTGGTACTTTATCTCCTAGGGGT
1 ATTTAGGTAATTTATCTCCTAGGGGT
61861 A
1 A
61862 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (26 bp):
ATTTAGGTAATTTATCTCCTAGGGGT
Found at i:63007 original size:17 final size:18
Alignment explanation
Indices: 62977--63010 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
62967 AAGAAAAAGT
62977 TGAAGAGAAAAGGAGAAA
1 TGAAGAGAAAAGGAGAAA
*
62995 TGAA-AGAAGAGGAGAA
1 TGAAGAGAAAAGGAGAA
63011 TGGTTAGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.59, C:0.00, G:0.35, T:0.06
Consensus pattern (18 bp):
TGAAGAGAAAAGGAGAAA
Found at i:63141 original size:24 final size:23
Alignment explanation
Indices: 63109--63214 Score: 131
Period size: 24 Copynumber: 4.4 Consensus size: 23
63099 GCCGGCCAAC
63109 TCCTACTCCTTGATCAGCTCCTAAA
1 TCCT-CTCCTT-ATCAGCTCCTAAA
* *
63134 TCTTCTCCTTTACCAGCTCCTAAA
1 TCCTCTCC-TTATCAGCTCCTAAA
*
63158 TCCTCTCCCTTATCACCTCCTAAA
1 TCCTCT-CCTTATCAGCTCCTAAA
63182 TCCTCTCCCTTATCAGCTCCTAAA
1 TCCTCT-CCTTATCAGCTCCTAAA
*
63206 TCTTCTCCT
1 TCCTCTCCT
63215 GACAGCCTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
23 3 0.04
24 62 0.86
25 7 0.10
ACGTcount: A:0.20, C:0.41, G:0.04, T:0.36
Consensus pattern (23 bp):
TCCTCTCCTTATCAGCTCCTAAA
Found at i:70152 original size:46 final size:46
Alignment explanation
Indices: 70102--70278 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
70092 ATGGTTGAGC
70102 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
* * *
70148 ATCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T
* *
70191 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAAC
1 ----ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
** * *
70241 GCCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
70279 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 12, Indels: 18
0.79 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 2 0.02
46 63 0.57
47 30 0.27
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
Found at i:70259 original size:93 final size:93
Alignment explanation
Indices: 70100--70271 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
70090 GGATGGTTGA
* *
70100 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATATCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
70165 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
70193 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
70258 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
70272 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:80141 original size:42 final size:43
Alignment explanation
Indices: 80062--80162 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
80052 TCCCTAACGT
* * ** *
80062 GGTCTTACATGTAATTCAATATCGATGCCTCTGTCCCAGATAG
1 GGTCTTACACGTAAATCAATATCGATGCCAATGTCCCAGACAG
*
80105 GGTCTTACACG-AAATCAGATA-CGATGCCAATGTCCCAGACAT
1 GGTCTTACACGTAAATCA-ATATCGATGCCAATGTCCCAGACAG
**
80147 GGTCTTGTACGTAAAT
1 GGTCTTACACGTAAAT
80163 ATCAATCGAG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
42 31 0.65
43 17 0.35
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
GGTCTTACACGTAAATCAATATCGATGCCAATGTCCCAGACAG
Found at i:87177 original size:40 final size:39
Alignment explanation
Indices: 87069--87203 Score: 193
Period size: 39 Copynumber: 3.4 Consensus size: 39
87059 AGATGATAAT
87069 CGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTC-CGAAGGCATTTGTGCGAGTTACTATATC
*
87109 CCGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATATC
* *
87148 CGGGCTAAGTCCCGAAGGCAGTTGAGCGAG-TAGCTATATC
1 CGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTA-CTATATC
*
87188 C-GGCTAAATCCGAAGG
1 CGGGCTAAGTCCGAAGG
87204 TACTTGGTTT
Statistics
Matches: 88, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
38 7 0.08
39 46 0.52
40 35 0.40
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (39 bp):
CGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:105559 original size:39 final size:40
Alignment explanation
Indices: 105505--105640 Score: 208
Period size: 39 Copynumber: 3.5 Consensus size: 40
105495 TCGATGATAA
105505 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
105544 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
105583 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
105623 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
105641 TACTTGGTTT
Statistics
Matches: 92, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
39 67 0.73
40 25 0.27
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Done.