Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1596
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: 47206
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:1503 original size:19 final size:20
Alignment explanation
Indices: 1479--1533 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
1469 GTATCGATAT
*
1479 ATTGTATTGATACATGC-TC
1 ATTGTATTGATACATGCTTA
*** *
1498 ATTGTAACAATACATACTTA
1 ATTGTATTGATACATGCTTA
1518 ATTGTATTGATACATG
1 ATTGTATTGATACATG
1534 AAACTAGTAG
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
ATTGTATTGATACATGCTTA
Found at i:1589 original size:20 final size:20
Alignment explanation
Indices: 1564--1614 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1554 AAGTGAAATC
*
1564 TATCGATACATG-GGACACTG
1 TATCGATACATGAAGA-ACTG
*
1584 TATCGATACATGAAGAATTG
1 TATCGATACATGAAGAACTG
1604 TATCGATACAT
1 TATCGATACAT
1615 TATGCCCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (20 bp):
TATCGATACATGAAGAACTG
Found at i:3649 original size:13 final size:13
Alignment explanation
Indices: 3631--3656 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3621 ATTTTTTTTG
3631 TGTATCGATACAT
1 TGTATCGATACAT
3644 TGTATCGATACAT
1 TGTATCGATACAT
3657 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6036 original size:21 final size:21
Alignment explanation
Indices: 6012--6058 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
6002 TTTGATGCTG
6012 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
6032 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
6053 ATTTTG
1 ATTTTG
6059 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:6197 original size:13 final size:13
Alignment explanation
Indices: 6179--6204 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6169 ATAATCACCC
6179 TGTATCGATACAA
1 TGTATCGATACAA
6192 TGTATCGATACAA
1 TGTATCGATACAA
6205 AGAAAAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:8305 original size:15 final size:15
Alignment explanation
Indices: 8285--8315 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
8275 ATTTCGTTTG
*
8285 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
8300 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
8315 G
1 G
8316 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:12982 original size:52 final size:52
Alignment explanation
Indices: 12912--13032 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
12902 GAAAATTTAT
*
12912 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
12964 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
13016 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
13033 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:13045 original size:52 final size:51
Alignment explanation
Indices: 12912--13052 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
12902 GAAAATTTAT
12912 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
12964 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
13016 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
13053 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:13059 original size:13 final size:13
Alignment explanation
Indices: 13041--13065 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13031 CAAAGATCAG
13041 TGTATCGATACAA
1 TGTATCGATACAA
13054 TGTATCGATACA
1 TGTATCGATACA
13066 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:13149 original size:13 final size:13
Alignment explanation
Indices: 13131--13155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13121 CAAAAAAATA
13131 TGTATCGATACAT
1 TGTATCGATACAT
13144 TGTATCGATACA
1 TGTATCGATACA
13156 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:13151 original size:33 final size:33
Alignment explanation
Indices: 13109--13175 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
13099 AGTAGCTTAA
13109 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
13142 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
13175 A
1 A
13176 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:14166 original size:52 final size:47
Alignment explanation
Indices: 14102--14233 Score: 155
Period size: 43 Copynumber: 2.8 Consensus size: 47
14092 GATGTCAACG
* *
14102 TGCTGATTCAAGGCCAGTTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG-----GTGCCAATA
* *
14154 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--GGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGGTGCCAATA
14197 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
14234 AAGATGAGAA
Statistics
Matches: 71, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
43 37 0.52
44 2 0.03
45 1 0.01
48 1 0.01
50 1 0.01
51 2 0.03
52 27 0.38
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (47 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGGTGCCAATA
Found at i:14335 original size:56 final size:52
Alignment explanation
Indices: 14251--14451 Score: 186
Period size: 43 Copynumber: 4.0 Consensus size: 52
14241 GAAAAGTGAT
* * * * * *
14251 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGATGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG--G-A
* * * *
14306 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
*
14359 AAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* *
14402 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG
14452 AAGATGAGAA
Statistics
Matches: 120, Mismatches: 18, Indels: 21
0.75 0.11 0.13
Matches are distributed among these distances:
43 38 0.32
44 1 0.01
46 1 0.01
49 1 0.01
51 1 0.01
52 31 0.26
53 6 0.05
54 1 0.01
55 4 0.03
56 36 0.30
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
Found at i:14412 original size:218 final size:218
Alignment explanation
Indices: 13968--14666 Score: 1310
Period size: 218 Copynumber: 3.2 Consensus size: 218
13958 AGAGATGATG
* * *
13968 AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAGTGA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGAGAAAAGTGA
* *
14033 TAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGA-GAAAAAGGATGT
66 TAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGATGAAAAAGGATGT
* * * *
14097 CAACGTGCTGATTCAAGGCCAGTTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATT
131 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATT
14162 CAAGGCCAGCTATATTGGACTTA
196 CAAGGCCAGCTATATTGGACTTA
14185 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGAGAAAAGTGA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGAGAAAAGTGA
14250 TAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGATGAAAAAGGATGT
66 TAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGATGAAAAAGGATGT
14315 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATT
131 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATT
14380 CAAGGCCAGCTATATTGGACTTA
196 CAAGGCCAGCTATATTGGACTTA
14403 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGAGAAAAGTGA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGAGAAAAGTGA
14468 TAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGATGAAAAAGGATGT
66 TAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGATGAAAAAGGATGT
14533 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATT
131 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATT
14598 CAAGGCCAGCTATATTGGACTTA
196 CAAGGCCAGCTATATTGGACTTA
14621 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
14667 GTGAGGTGCC
Statistics
Matches: 472, Mismatches: 9, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
217 112 0.24
218 360 0.76
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (218 bp):
AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGAGAAAAGTGA
TAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGATGAAAAAGGATGT
CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATT
CAAGGCCAGCTATATTGGACTTA
Found at i:14553 original size:56 final size:52
Alignment explanation
Indices: 14469--14860 Score: 374
Period size: 48 Copynumber: 7.8 Consensus size: 52
14459 GAAAAGTGAT
* * * * * *
14469 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGATGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG--G-A
* * * *
14524 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
*
14577 AAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * *
14620 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* **
14670 --AGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * * *
14718 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGGCTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * * *
14767 --AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
*
14817 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
14861 GAGGGGTTGC
Statistics
Matches: 295, Mismatches: 29, Indels: 29
0.84 0.08 0.08
Matches are distributed among these distances:
43 38 0.13
44 1 0.00
46 1 0.00
48 92 0.31
49 46 0.16
51 1 0.00
52 69 0.23
53 6 0.02
54 1 0.00
55 4 0.01
56 36 0.12
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
Found at i:14693 original size:48 final size:49
Alignment explanation
Indices: 14533--14860 Score: 438
Period size: 48 Copynumber: 6.7 Consensus size: 49
14523 AAAAGGATGT
*
14533 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * *
14585 CGATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
14628 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
14676 CAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
14725 CAATGTGCTGAGTCAAGGCCAGCTACATTGGGCTTAAAGATG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
14773 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG---AAGGTGC
* * *
14825 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
14861 GAGGGGTTGC
Statistics
Matches: 247, Mismatches: 18, Indels: 22
0.86 0.06 0.08
Matches are distributed among these distances:
43 39 0.16
48 94 0.38
49 45 0.18
52 69 0.28
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:14761 original size:97 final size:97
Alignment explanation
Indices: 14533--14860 Score: 443
Period size: 97 Copynumber: 3.4 Consensus size: 97
14523 AAAAGGATGT
* * *
14533 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G---AGGTGCCAATGTGCTGATT
*
14598 CAAGGCCAGCTATATTGGACTT----A--AAGGTGC
62 CAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
14628 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAGGTGCCAATGTGCTGATTCAAG
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAGGTGCCAATGTGCTGATTCAAG
*
14693 GCCAGCTACGTTGGACTTAAAGATGAAGGTGC
66 GCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
14725 CAATGTGCTGAGTCAAGGCCAGCTACATTGGGCTTAAAGATGAGGTGCCAATGTGCTGAGTCAAG
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAGGTGCCAATGTGCTGATTCAAG
14790 GCCAGCTACATTGGACTTAAAGATGAAAAAGGTGC
66 GCCAGCTACATTGGACTTAAAGATG---AAGGTGC
* * *
14825 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
14861 GAGGGGTTGC
Statistics
Matches: 210, Mismatches: 14, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
91 37 0.18
94 1 0.00
95 40 0.19
97 92 0.44
100 40 0.19
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (97 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAGGTGCCAATGTGCTGATTCAAG
GCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:14961 original size:32 final size:33
Alignment explanation
Indices: 14865--14957 Score: 163
Period size: 33 Copynumber: 2.8 Consensus size: 33
14855 GGCTTAGAGG
14865 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
14898 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG-A
1 GGTTGCCACCGACTTGTGTGGGCTTT-GGAAGAA
14931 -GTTGCCACCGACTTGTGTGGGCTTTGG
1 GGTTGCCACCGACTTGTGTGGGCTTTGG
14958 GAAGGAAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
31 2 0.03
32 25 0.42
33 27 0.46
34 5 0.08
ACGTcount: A:0.15, C:0.19, G:0.37, T:0.29
Consensus pattern (33 bp):
GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
Found at i:15010 original size:35 final size:35
Alignment explanation
Indices: 14959--15891 Score: 905
Period size: 33 Copynumber: 27.3 Consensus size: 35
14949 GGGCTTTGGG
*
14959 AAGGAAAAA-AGATGCCACGGAGTTGTGGAC-TTAA
1 AAGGAAAAAGAG-TGCCACGGAGTTGTGGGCTTTAA
14993 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
15029 AA-GAAAAA-AGTGCCACGGAGTTGTGGGCTTT-G
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
15061 AAGG-AAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
15095 ACGGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
* **
15130 AAGGGAAAGAGAGTGCCACAAAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
15166 AA-GAAGAAG-GTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
* * *
15200 AA-GAAGAAG-GTTGCCACCGACTTGTGTGGGCTTT--
1 AAGGAAAAAGAG-TGCCACGGA-GT-TGTGGGCTTTAA
* *
15234 -AGG---AAGAGTTGCCACCGACTTGTGTGGGCTTTAGA
1 AAGGAAAAAGAG-TGCCACGGA-GT-TGTGGGCTTTA-A
** * *
15269 AAGGGTGAAAGA-TGCCACGAAGTTGTGGAC-TTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* * * *
15303 AAAGAACAAG-GTGCCGCAGAGTTGTGGGCTTTAAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
*
15338 AAGGAAAAAAAAGAGTGCCACGGAGTTGTGGGC-TTAG
1 AAGG---AAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
15375 AAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAG
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
15409 AAGG-AAAAGAGTGCCACGGAGTTGTGGGCTTT-A
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* *
15442 AAGG-AAAAGAGTGCCACGGAGTCGTGGAC-TTAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
15475 AA-G-----G-GTGCCACGGAGTTGTGGGC-TTAG
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
15502 AAGG-AAAAGAAGGTGCCACGGAGTTGTGGGCTTTAAA
1 AAGGAAAAAG-A-GTGCCACGGAGTTGTGGGCTTT-AA
15539 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
15575 AAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
*
15610 AAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* * * *
15646 AAAGAAAAAGTGTGCCACAGAGTTATGGGCTTTAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
15681 AA-GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
*
15715 AAGGAAAAAATAGTGCCACGGAGTTGTGGGCTTTAA
1 AAGG-AAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* * *
15751 AAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* * * *
15786 AAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTT-G
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* * *
15820 AA-GAAAAA-A-TGCCACTGAGTCGTGGGCTTT-G
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* * *
15851 AA-GAAAAAGA-TGCCACTGAGTCGTGGAC-TTAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
15883 AAAGAAAAA
1 AAGGAAAAA
15892 TGTTCAACTA
Statistics
Matches: 787, Mismatches: 57, Indels: 111
0.82 0.06 0.12
Matches are distributed among these distances:
27 22 0.03
28 2 0.00
31 33 0.04
32 55 0.07
33 173 0.22
34 127 0.16
35 172 0.22
36 54 0.07
37 106 0.13
38 17 0.02
39 22 0.03
40 4 0.01
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.20
Consensus pattern (35 bp):
AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
Found at i:15250 original size:32 final size:31
Alignment explanation
Indices: 15205--15272 Score: 118
Period size: 32 Copynumber: 2.2 Consensus size: 31
15195 TTGAAAAGAA
15205 GAAGGTTGCCACCGACTTGTGTGGGCTTTAG
1 GAAGGTTGCCACCGACTTGTGTGGGCTTTAG
15236 GAAGAGTTGCCACCGACTTGTGTGGGCTTTAG
1 GAAG-GTTGCCACCGACTTGTGTGGGCTTTAG
*
15268 AAAGG
1 GAAGG
15273 GTGAAAGATG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 5 0.14
32 30 0.86
ACGTcount: A:0.21, C:0.18, G:0.35, T:0.26
Consensus pattern (31 bp):
GAAGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:15484 original size:27 final size:27
Alignment explanation
Indices: 15446--15505 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
15436 GCTTTAAAGG
*
15446 AAAAGAGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
* *
15473 AAAAGGGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
*
15500 AGAAGG
1 AAAAGG
15506 AAAAGAAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.38, T:0.18
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTCGTGGACTT
Found at i:15612 original size:71 final size:68
Alignment explanation
Indices: 15473--15891 Score: 483
Period size: 71 Copynumber: 6.1 Consensus size: 68
15463 TCGTGGACTT
* * *
15473 AAAAGGGTGCCACGGAGTTGTGGGC-TTAGAAGGAAAAGAAGGTGCCACGGAGTTGTGGGCTTTA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG-AAA-AAGGTGCCACGGAGTTGTGGGCTTT-
15537 AAAAGGGA
63 AAAA--GA
15545 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AA
15610 AAGGGA
65 AA--GA
* * *
15616 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTATGGGCTTTAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAA
15681 AAGA
65 AAGA
* *
15685 AAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAATAGTGCCACGGAGTTGTGGGCTTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAAG-AAAAA-GGTGCCACGGAGTTGTGGGCTTT
15749 AAAAAGA
63 -AAAAGA
* * * *
15756 AAAAGTGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTT-G
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAA
15820 AAGA
65 AAGA
* * * * * * * *
15824 AAAA-A-TGCCACTGAGTCGTGGGCTTT--GAAGAAAAAGATGCCACTGAGTCGTGGACTTAAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
15885 AGA
66 AGA
15888 AAAA
1 AAAA
15892 TGTTCAACTA
Statistics
Matches: 311, Mismatches: 27, Indels: 26
0.85 0.07 0.07
Matches are distributed among these distances:
63 17 0.05
64 17 0.05
66 19 0.06
68 29 0.09
69 12 0.04
70 51 0.16
71 92 0.30
72 68 0.22
73 6 0.02
ACGTcount: A:0.36, C:0.12, G:0.32, T:0.21
Consensus pattern (68 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
AGA
Found at i:15828 original size:105 final size:103
Alignment explanation
Indices: 15473--15891 Score: 523
Period size: 105 Copynumber: 4.0 Consensus size: 103
15463 TCGTGGACTT
* * * *
15473 AAAAGGGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAGAAGGTGCCACGGAGTTGTGGGCTTTAA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAA-GAAAAAAAAGTGCCACGGAGTTGTGGGCTTTAA
* *
15538 AAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG
65 AAA--GAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAAAAG
*
15579 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAA-AAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAGAA---AAAAA-AGTGCCACGGAGTTGTGGGCTT
*
15643 TAAAAAGAAAAAGTGTGCCACAGAGTTATGGGCTTT-AAAAG
62 TAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAAAAG
*
15684 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAATAGTGCCACGGAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTG--AA-GAAAAAAAAGTGCCACGGAGTTGTGGGCTTT
15749 AAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAAAAG
63 AAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAAAAG
* * *
15790 AAAAAGTGTGCCACAGAGTTGTGGGCTTTGAAG--AAAAAA-TGCCACTGAGTCGTGGGCTTT--
1 AAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAGAAAAAAAAGTGCCACGGAGTTGTGGGCTTTAA
* * * * *
15850 GAAGAAAAAG-ATGCCACTGAGTCGTGGAC-TTAAAAAG
65 AAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAAAAG
15887 AAAAA
1 AAAAA
15892 TGTTCAACTA
Statistics
Matches: 283, Mismatches: 20, Indels: 29
0.85 0.06 0.09
Matches are distributed among these distances:
97 13 0.05
98 15 0.05
99 9 0.03
101 19 0.07
102 5 0.02
104 3 0.01
105 92 0.33
106 71 0.25
107 28 0.10
108 26 0.09
109 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.32, T:0.21
Consensus pattern (103 bp):
AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAGAAAAAAAAGTGCCACGGAGTTGTGGGCTTTAAA
AAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAAAAG
Found at i:15887 original size:27 final size:29
Alignment explanation
Indices: 15798--15885 Score: 79
Period size: 32 Copynumber: 2.9 Consensus size: 29
15788 AGAAAAAGTG
* * * *
15798 TGCCACAGAGTTGTGGGCTTTGAAGAAAAAA
1 TGCCACTGAGTCGTGGACTTT-AA-AAAAGA
*
15829 TGCCACTGAGTCGTGGGCTTTGAAGAAAAAGA
1 TGCCACTGAGTCGTGGACTTT--A-AAAAAGA
15861 TGCCACTGAGTCGTGGAC-TTAAAAA
1 TGCCACTGAGTCGTGGACTTTAAAAA
15886 GAAAAATGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
28 4 0.08
29 1 0.02
31 21 0.42
32 23 0.46
33 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (29 bp):
TGCCACTGAGTCGTGGACTTTAAAAAAGA
Found at i:16807 original size:1 final size:1
Alignment explanation
Indices: 16801--16833 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
16791 TGAAAAGGGG
16801 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16834 GGTGAAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:24170 original size:52 final size:52
Alignment explanation
Indices: 24100--24220 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
24090 GAAAATTTAT
*
24100 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
24152 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
24204 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
24221 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:24233 original size:52 final size:51
Alignment explanation
Indices: 24100--24240 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
24090 GAAAATTTAT
24100 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
24152 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
24204 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
24241 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:24247 original size:13 final size:13
Alignment explanation
Indices: 24229--24253 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24219 CAAAGATCAG
24229 TGTATCGATACAA
1 TGTATCGATACAA
24242 TGTATCGATACA
1 TGTATCGATACA
24254 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:24337 original size:13 final size:13
Alignment explanation
Indices: 24319--24343 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24309 CAAAAAAATA
24319 TGTATCGATACAT
1 TGTATCGATACAT
24332 TGTATCGATACA
1 TGTATCGATACA
24344 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:24339 original size:33 final size:33
Alignment explanation
Indices: 24297--24363 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
24287 AGTAGCTTAA
24297 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
24330 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
24363 A
1 A
24364 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:24982 original size:21 final size:21
Alignment explanation
Indices: 24953--24997 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
24943 AAGTTTTCAT
*
24953 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
24973 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
24995 TTT
1 TTT
24998 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:27237 original size:13 final size:13
Alignment explanation
Indices: 27219--27244 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27209 ATTTTTTTTG
27219 TGTATCGATACAT
1 TGTATCGATACAT
27232 TGTATCGATACAT
1 TGTATCGATACAT
27245 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:29623 original size:21 final size:21
Alignment explanation
Indices: 29599--29645 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
29589 TTTGATGCTG
29599 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
29619 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
29640 ATTTTG
1 ATTTTG
29646 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:29784 original size:13 final size:13
Alignment explanation
Indices: 29766--29791 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29756 ATAATCACCC
29766 TGTATCGATACAA
1 TGTATCGATACAA
29779 TGTATCGATACAA
1 TGTATCGATACAA
29792 AGAAAAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:31891 original size:15 final size:15
Alignment explanation
Indices: 31871--31901 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31861 ATTTCGTTTG
*
31871 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
31886 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
31901 G
1 G
31902 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:33733 original size:21 final size:21
Alignment explanation
Indices: 33704--33748 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
33694 AAGTTTTCAT
*
33704 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
33724 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
33746 TTT
1 TTT
33749 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:35985 original size:13 final size:13
Alignment explanation
Indices: 35967--35992 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35957 AATTTTTTTG
35967 TGTATCGATACAT
1 TGTATCGATACAT
35980 TGTATCGATACAT
1 TGTATCGATACAT
35993 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:42597 original size:21 final size:21
Alignment explanation
Indices: 42573--42618 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
42563 TGCAGTTTTC
42573 ATTTTC-TTAGCTAACTCCATT
1 ATTTTCATTAGC-AACTCCATT
* *
42594 ATTTTCATTAGCAACTTCTTT
1 ATTTTCATTAGCAACTCCATT
42615 ATTT
1 ATTT
42619 CAACTTGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.52
Consensus pattern (21 bp):
ATTTTCATTAGCAACTCCATT
Done.