Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2638
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: 30082
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:4367 original size:17 final size:18
Alignment explanation
Indices: 4345--4385 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
4335 CGTTTCTTTT
4345 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
4362 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
4380 T-TTTTG
1 TCTTTTG
4386 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:4369 original size:24 final size:25
Alignment explanation
Indices: 4316--4369 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
4306 AACAAATTCT
* *
4316 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
4341 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
4364 TTTTTT
1 TTTTTT
4370 ATCACTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:6642 original size:15 final size:14
Alignment explanation
Indices: 6617--6656 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
6607 CTAGACCGTA
6617 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
6631 TGCAATTTTTTTTT
1 TGCAATTTTTTTTT
6645 T-C--TTTTTTTTT
1 TGCAATTTTTTTTT
6656 T
1 T
6657 CGAAGCTACG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.38
13 1 0.04
14 15 0.58
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (14 bp):
TGCAATTTTTTTTT
Found at i:8464 original size:22 final size:22
Alignment explanation
Indices: 8437--8484 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
8427 CAATCTTTGG
*
8437 AGAATTTGAAAGA-ACTGAAAA
1 AGAAATTGAAAGAGACTGAAAA
* *
8458 AGAAATTGAGAGAGAGTGAAAA
1 AGAAATTGAAAGAGACTGAAAA
8480 AGAAA
1 AGAAA
8485 AGAAAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (22 bp):
AGAAATTGAAAGAGACTGAAAA
Found at i:8533 original size:20 final size:20
Alignment explanation
Indices: 8508--8550 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
8498 AAAAGAAAAG
8508 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
8528 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
8548 AAA
1 AAA
8551 ACAAGAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:12343 original size:22 final size:22
Alignment explanation
Indices: 12315--12358 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
12305 TTTTGAACCA
12315 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
12337 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
12359 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:13048 original size:21 final size:24
Alignment explanation
Indices: 12986--13040 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
12976 GTTAGGACAT
*
12986 ATTAAATTCGTCCACCAGCAGCTC
1 ATTAAATTCGTCAACCAGCAGCTC
13010 ATTAAATTCGTCAACCAGCAGCTC
1 ATTAAATTCGTCAACCAGCAGCTC
13034 ATTAAAT
1 ATTAAAT
13041 CTATCCAGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.27
Consensus pattern (24 bp):
ATTAAATTCGTCAACCAGCAGCTC
Found at i:13134 original size:17 final size:18
Alignment explanation
Indices: 13114--13148 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
13104 TGTACACACA
13114 AATTAATTCA-ACACATT
1 AATTAATTCAGACACATT
*
13131 AATTAATTTAGACACATT
1 AATTAATTCAGACACATT
13149 TAAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (18 bp):
AATTAATTCAGACACATT
Found at i:13417 original size:9 final size:9
Alignment explanation
Indices: 13403--13427 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
13393 TAATTGTTAA
13403 AACTAATTT
1 AACTAATTT
13412 AACTAATTT
1 AACTAATTT
13421 AACTAAT
1 AACTAAT
13428 CAGCAAATCA
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:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (9 bp):
AACTAATTT
Found at i:17170 original size:21 final size:21
Alignment explanation
Indices: 17125--17187 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
17115 TTTGAACCAT
* *
17125 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
17147 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
17168 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
17188 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:17525 original size:14 final size:14
Alignment explanation
Indices: 17487--17537 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
17477 TAGGTACATA
* *
17487 AAAAAAAAGAGTTCG
1 AAAAAAAA-ATTTTG
17502 AAAAAAAAATTTTG
1 AAAAAAAAATTTTG
17516 AAAAAAAAATTATT-
1 AAAAAAAAATT-TTG
17530 AAAAAAAA
1 AAAAAAAA
17538 TTGCATACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 23 0.70
15 10 0.30
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.20
Consensus pattern (14 bp):
AAAAAAAAATTTTG
Found at i:19154 original size:20 final size:20
Alignment explanation
Indices: 19131--19176 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
19121 CCAGCTCGAA
*
19131 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
19151 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
19171 TTAGCT
1 TTAGCT
19177 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:19158 original size:30 final size:30
Alignment explanation
Indices: 19123--19196 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
19113 AGTTTTTCCC
19123 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
19153 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
19183 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
19197 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:20795 original size:11 final size:11
Alignment explanation
Indices: 20779--20808 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
20769 TTGGAGTAAC
20779 AAAAAAATCAA
1 AAAAAAATCAA
*
20790 AAAAAATTCAA
1 AAAAAAATCAA
20801 AAAAAAAT
1 AAAAAAAT
20809 TTGATTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:21911 original size:12 final size:12
Alignment explanation
Indices: 21899--22016 Score: 50
Period size: 12 Copynumber: 9.8 Consensus size: 12
21889 GAAAGAGATT
*
21899 GAAAAAGAAATT
1 GAAAAAGAAATA
21911 G--AAAGAAA-A
1 GAAAAAGAAATA
*
21920 CAAAAAGAAA-A
1 GAAAAAGAAATA
*
21931 CGAAAAAGAAAAA
1 -GAAAAAGAAATA
**
21944 GAAATTGCAAA-A
1 GAAAAAG-AAATA
*
21956 GAAAAAGAAATC
1 GAAAAAGAAATA
** *
21968 GAAAAAGTGAGA
1 GAAAAAGAAATA
21980 GAAAAAGAAA-A
1 GAAAAAGAAATA
*
21991 TGAAGAAAAGAAAATT
1 -G-A-AAAAG-AAATA
22007 GAAAAAGAAA
1 GAAAAAGAAA
22017 AAGCGAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
10 7 0.09
11 12 0.15
12 41 0.51
13 10 0.12
14 6 0.08
15 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
GAAAAAGAAATA
Found at i:21942 original size:18 final size:18
Alignment explanation
Indices: 21916--22019 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
21906 AAATTGAAAG
*
21916 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
21934 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
21952 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
21970 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
21988 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
22009 AAAAGAAAAAG
1 AAAAGAAAAAG
22020 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:21944 original size:6 final size:6
Alignment explanation
Indices: 21912--22019 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
21902 AAAGAAATTG
* * ** *
21912 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
21959 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
22010 AAAGAA AAAG
1 AAAGAA AAAG
22020 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.81
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:22001 original size:14 final size:13
Alignment explanation
Indices: 21980--22017 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
21970 AAAAGTGAGA
21980 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
21992 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
22007 GAAAAAGAAAA
1 GAAAAAGAAAA
22018 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:22031 original size:21 final size:21
Alignment explanation
Indices: 21981--22031 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
21971 AAAGTGAGAG
*
21981 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
22002 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
22023 AAAAAGAAA
1 AAAAAGAAA
22032 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:22071 original size:33 final size:33
Alignment explanation
Indices: 22034--22096 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
22024 AAAAGAAATT
22034 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
22067 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
22097 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:23893 original size:20 final size:20
Alignment explanation
Indices: 23870--23923 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
23860 AGTTTTTCCC
*
23870 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
23890 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
23910 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
23924 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:23905 original size:30 final size:30
Alignment explanation
Indices: 23870--23943 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
23860 AGTTTTTCCC
23870 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
23900 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
23930 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
23944 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:23933 original size:20 final size:20
Alignment explanation
Indices: 23870--23934 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
23860 AGTTTTTCCC
* * * *
23870 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
23890 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
23909 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
23930 AGCTC
1 AGCTC
23935 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:25545 original size:12 final size:13
Alignment explanation
Indices: 25528--25560 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
25518 TTGGAGTAAC
25528 AAAAAAATC-AAA
1 AAAAAAATCGAAA
*
25540 AAAAAATTCGAAA
1 AAAAAAATCGAAA
25553 AAAAAAAT
1 AAAAAAAT
25561 TTGATTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAAAAATCGAAA
Found at i:25599 original size:28 final size:28
Alignment explanation
Indices: 25568--25648 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
25558 AATTTGATTG
25568 AAAAAAAAAGTGAAAAAAAA-TCGAGCAA
1 AAAAAAAAAGTGAAAAAAAAGT-GAGCAA
*
25596 AAAAAAGAAA-AGAAAAAAAAGTGAGCAA
1 AAAAAA-AAAGTGAAAAAAAAGTGAGCAA
** *
25624 AAAAATCAAGTTAAAAAAAAAGTGA
1 AAAAAAAAAG-TGAAAAAAAAGTGA
25649 AAAGTCTTGC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
27 2 0.05
28 26 0.59
29 16 0.36
ACGTcount: A:0.72, C:0.05, G:0.15, T:0.09
Consensus pattern (28 bp):
AAAAAAAAAGTGAAAAAAAAGTGAGCAA
Found at i:26673 original size:11 final size:12
Alignment explanation
Indices: 26657--26772 Score: 73
Period size: 12 Copynumber: 9.6 Consensus size: 12
26647 AAAGAAATTG
26657 AAAGAAAAC-AA
1 AAAGAAAACGAA
26668 AAAGAAAACGAA
1 AAAGAAAACGAA
*
26680 AAAGAAAAAGAA
1 AAAGAAAACGAA
**
26692 ATTGCAAAA-GAA
1 AAAG-AAAACGAA
*
26704 AAAGAAATCGAA
1 AAAGAAAACGAA
26716 AAAG---A-GAA
1 AAAGAAAACGAA
*
26724 AAAGAAAATGAAGA
1 AAAGAAAACG-A-A
*
26738 AAAGAAAATTGAA
1 AAAGAAAA-CGAA
26751 AAAGAAAAAGCGAAA
1 AAAG-AAAA-CG-AA
26766 AAAGAAA
1 AAAGAAA
26773 TTGAAAGAGA
Statistics
Matches: 84, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
8 7 0.08
11 13 0.15
12 28 0.33
13 10 0.12
14 18 0.21
15 8 0.10
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.05
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:26687 original size:18 final size:18
Alignment explanation
Indices: 26661--26760 Score: 83
Period size: 18 Copynumber: 5.3 Consensus size: 18
26651 AAATTGAAAG
*
26661 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
26679 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
26697 AAAAGAAAAAGAAATCGAA
1 AAAAGAAAAAGAAAACG-A
*
26716 AAAGAGAAAAAGAAAATGAA
1 AAA-AGAAAAAGAAAACG-A
* *
26736 GAAAAGAAAATTGAAAAAGA
1 -AAAAGAAAA-AGAAAACGA
26756 AAAAG
1 AAAAG
26761 CGAAAAAAGA
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
18 30 0.44
19 8 0.12
20 21 0.31
21 9 0.13
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.06
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:26689 original size:6 final size:6
Alignment explanation
Indices: 26657--26760 Score: 75
Period size: 6 Copynumber: 16.7 Consensus size: 6
26647 AAAGAAATTG
* * ** *
26657 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** * *
26704 AAAGAA ATCGAAA AAGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA AAAGAA
1 AAAGAA AAAG-AA AA-AGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA
26757 AAAG
1 AAAG
26761 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 18, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
5 3 0.04
6 53 0.71
7 14 0.19
8 5 0.07
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:26730 original size:14 final size:14
Alignment explanation
Indices: 26713--26772 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
26703 AAAAGAAATC
26713 GAAAAAGAGAAAAA
1 GAAAAAGAGAAAAA
*
26727 GAAAATGA-AGAAAA
1 GAAAAAGAGA-AAAA
**
26741 G-AAAATTGAAAAA
1 GAAAAAGAGAAAAA
*
26754 GAAAAAGCGAAAAAA
1 GAAAAAGAG-AAAAA
26769 GAAA
1 GAAA
26773 TTGAAAGAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
13 9 0.25
14 18 0.50
15 9 0.25
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (14 bp):
GAAAAAGAGAAAAA
Found at i:26812 original size:33 final size:33
Alignment explanation
Indices: 26775--26837 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
26765 AAAAGAAATT
26775 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
26808 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
26838 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:28636 original size:20 final size:20
Alignment explanation
Indices: 28611--28656 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
28601 CCCAGCTCGA
*
28611 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
28631 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
28651 TTAGCT
1 TTAGCT
28657 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:28648 original size:30 final size:30
Alignment explanation
Indices: 28604--28676 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
28594 TATTTTTCCC
*
28604 AGCTCGATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCGTTTGAGCTCA-ATTGAGCTTAATTT
* *
28633 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
28663 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
28677 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 9 0.23
30 30 0.77
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Done.