Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold629
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: 42132
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:312 original size:30 final size:30
Alignment explanation
Indices: 278--361 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
268 TAAACTAAAA
*
278 TGAGCTAAGCTTTAGCTCTTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCTTGAGCTAAAGT
* * * ** *
308 TGAGCTGAGATTAAACTCTCAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCTTGAGCTAAAGT
* *
338 T-AGCTAAGGTTTAGCTCGTGAGCT
1 TGAGCTAAGATTTAGCTCTTGAGCT
362 GAATCATGAC
Statistics
Matches: 40, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
29 16 0.40
30 24 0.60
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCTTGAGCTAAAGT
Found at i:650 original size:17 final size:16
Alignment explanation
Indices: 620--654 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
610 CTTTCCTCTC
*
620 TTTTCTTTTGATCTTT
1 TTTTCTTTTCATCTTT
636 TTTTGCTTTTCATCTTT
1 TTTT-CTTTTCATCTTT
653 TT
1 TT
655 CTTTTCTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTCTTTTCATCTTT
Found at i:1655 original size:8 final size:9
Alignment explanation
Indices: 1643--1667 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1633 ATTTTTTCAT
1643 TTTTTTTTA
1 TTTTTTTTA
1652 TTTTTTTTA
1 TTTTTTTTA
1661 TTTTTTT
1 TTTTTTT
1668 CACTTTACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:4085 original size:26 final size:26
Alignment explanation
Indices: 4029--4085 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
4019 GGCTTGAATA
* *
4029 CAAGAGAGCTACTGATTTAGTTCTTC
1 CAAGTGAGCTACTGATTTAGTTCTCC
* *
4055 AAAGTGAGCTATTGATTTAGTTCTCC
1 CAAGTGAGCTACTGATTTAGTTCTCC
4081 CAAGT
1 CAAGT
4086 ACCCTTCGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (26 bp):
CAAGTGAGCTACTGATTTAGTTCTCC
Found at i:4635 original size:30 final size:30
Alignment explanation
Indices: 4601--4697 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
4591 AGCTCACTCC
4601 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
4631 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
4661 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
4691 TAGCTCA
1 TAGCTCA
4698 TTTTTAGTTT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:5804 original size:20 final size:20
Alignment explanation
Indices: 5758--5804 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
5748 AGCTCGTTTC
*
5758 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
5778 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
5798 CAGCTCA
1 CAGCTCA
5805 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:7892 original size:13 final size:13
Alignment explanation
Indices: 7874--7921 Score: 69
Period size: 13 Copynumber: 3.6 Consensus size: 13
7864 TATACAAGTC
7874 AAAAAAAATTTCG
1 AAAAAAAATTTCG
* *
7887 AAAAAAAAATTCA
1 AAAAAAAATTTCG
7900 AAAAAAAATTTCG
1 AAAAAAAATTTCG
7913 AAAAGAAAA
1 AAAA-AAAA
7922 AAAAATCTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
13 26 0.87
14 4 0.13
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (13 bp):
AAAAAAAATTTCG
Found at i:7935 original size:19 final size:19
Alignment explanation
Indices: 7899--7934 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
7889 AAAAAAATTC
*
7899 AAAAAAAAATTTCGAAAAG
1 AAAAAAAAATCTCGAAAAG
7918 AAAAAAAAATCT-GAAAA
1 AAAAAAAAATCTCGAAAA
7935 AAAGTGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.14
Consensus pattern (19 bp):
AAAAAAAAATCTCGAAAAG
Found at i:8879 original size:21 final size:20
Alignment explanation
Indices: 8845--8912 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
8835 ACATTCTCGT
8845 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
8866 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
8887 AAAGAAAACGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
8908 AAAGA
1 AAAGA
8913 GAGGCAAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:8880 original size:6 final size:5
Alignment explanation
Indices: 8856--8912 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
8846 AAGAGAAAAC
*
8856 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
8903 AAAGA AAAGA
1 AAAGA AAAGA
8913 GAGGCAAAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:8887 original size:15 final size:14
Alignment explanation
Indices: 8856--8912 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
8846 AAGAGAAAAC
8856 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
8872 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
8887 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
8903 AAAGAAAAGA
1 AAAGAAAAGA
8913 GAGGCAAAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:8988 original size:12 final size:12
Alignment explanation
Indices: 8980--9004 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8970 TTTGAAAAGC
8980 AAAAAGAAAATG
1 AAAAAGAAAATG
8992 AAAAAGAAAATG
1 AAAAAGAAAATG
9004 A
1 A
9005 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:9001 original size:18 final size:18
Alignment explanation
Indices: 8974--9029 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
8964 AAAGCCTTTG
8974 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
8993 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
9011 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
9028 AA
1 AA
9030 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:9014 original size:30 final size:31
Alignment explanation
Indices: 8980--9061 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
8970 TTTGAAAAGC
*
8980 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
9010 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
9040 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
9062 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:11197 original size:30 final size:30
Alignment explanation
Indices: 11163--11259 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
11153 AGCTCACTCC
11163 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
11193 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
11223 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
11253 TAGCTCA
1 TAGCTCA
11260 TTTTTAGTTT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:14395 original size:20 final size:20
Alignment explanation
Indices: 14372--14425 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
14362 AGTTTTTCCC
*
14372 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
14392 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
14412 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
14426 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:14407 original size:30 final size:30
Alignment explanation
Indices: 14372--14445 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
14362 AGTTTTTCCC
14372 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
14402 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
14432 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
14446 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:14435 original size:20 final size:20
Alignment explanation
Indices: 14372--14436 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
14362 AGTTTTTCCC
* * * *
14372 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
14392 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
14411 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
14432 AGCTC
1 AGCTC
14437 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:16042 original size:10 final size:11
Alignment explanation
Indices: 16027--16070 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 11
16017 ATTGGAGTAA
16027 CAAAAAAAA-T
1 CAAAAAAAATT
16037 CAAAAAAAATT
1 CAAAAAAAATT
16048 CGAAAAAAAAAATT
1 C---AAAAAAAATT
16062 CAAAAAAAA
1 CAAAAAAAA
16071 AGTGAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.30
11 10 0.33
14 11 0.37
ACGTcount: A:0.77, C:0.09, G:0.02, T:0.11
Consensus pattern (11 bp):
CAAAAAAAATT
Found at i:16045 original size:12 final size:12
Alignment explanation
Indices: 16028--16082 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 12
16018 TTGGAGTAAC
16028 AAAAAAAATC-A
1 AAAAAAAATCAA
*
16039 AAAAAAATTCGAA
1 AAAAAAAATC-AA
16052 AAAAAAAATTCAA
1 AAAAAAAA-TCAA
* *
16065 AAAAAAAGTGAA
1 AAAAAAAATCAA
16077 AAAAAA
1 AAAAAA
16083 TCGAGCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 9 0.24
12 9 0.24
13 17 0.46
14 2 0.05
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.11
Consensus pattern (12 bp):
AAAAAAAATCAA
Found at i:16055 original size:14 final size:13
Alignment explanation
Indices: 16038--16071 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
16028 AAAAAAAATC
16038 AAAAAAAATTCGAA
1 AAAAAAAATTC-AA
16052 AAAAAAAATTCAA
1 AAAAAAAATTCAA
16065 AAAAAAA
1 AAAAAAA
16072 GTGAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:16077 original size:25 final size:24
Alignment explanation
Indices: 16028--16082 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
16018 TTGGAGTAAC
*
16028 AAAAAAAATCAAAAAAAATTCGAA
1 AAAAAAAATCAAAAAAAAGTCGAA
16052 AAAAAAAATTCAAAAAAAAAGT-GAA
1 AAAAAAAA-TC-AAAAAAAAGTCGAA
16077 AAAAAA
1 AAAAAA
16083 TCGAGCAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 8 0.29
25 11 0.39
26 9 0.32
ACGTcount: A:0.78, C:0.05, G:0.05, T:0.11
Consensus pattern (24 bp):
AAAAAAAATCAAAAAAAAGTCGAA
Found at i:17181 original size:12 final size:12
Alignment explanation
Indices: 17166--17276 Score: 64
Period size: 12 Copynumber: 8.8 Consensus size: 12
17156 TTGAAAGAAA
17166 AAAAAGAAAACG
1 AAAAAGAAAACG
*
17178 AAAAAGAAAAAG
1 AAAAAGAAAACG
**
17190 AAATTGCAAAA-G
1 AAAAAG-AAAACG
*
17202 AAAAAGAAATCG
1 AAAAAGAAAACG
* *
17214 AAAAAGTGAGA-G
1 AAAAAG-AAAACG
*
17226 AAAAAGAAAATG
1 AAAAAGAAAACG
*
17238 AAGAAAAGAAAATTG
1 -A-AAAAGAAAA-CG
17253 AAAAAGAAAAAGCG
1 AAAAAG-AAAA-CG
17267 AAAAAAGAAA
1 -AAAAAGAAA
17277 TTGAAAGAGA
Statistics
Matches: 77, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
11 5 0.06
12 35 0.45
13 11 0.14
14 18 0.23
15 8 0.10
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (12 bp):
AAAAAGAAAACG
Found at i:17182 original size:7 final size:6
Alignment explanation
Indices: 17166--17264 Score: 72
Period size: 6 Copynumber: 16.0 Consensus size: 6
17156 TTGAAAGAAA
* ** * **
17166 AAAAAG AAAACG AAAAAG AAAAAG AAATTG CAAAAG AAAAAG AAATCG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
** * * *
17214 AAAAAG TGAGAG AAAAAG AAAATG AAGAAAAG AAAATTG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG -A-AAAAG AAAA-AG AAAAAG AAAAAG
17265 CGAAAAAAGA
Statistics
Matches: 68, Mismatches: 22, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
6 57 0.84
7 7 0.10
8 4 0.06
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAAAG
Found at i:17207 original size:18 final size:18
Alignment explanation
Indices: 17147--17264 Score: 94
Period size: 18 Copynumber: 6.4 Consensus size: 18
17137 GAAAGAGATT
17147 GAAAAA-AAATTGAAAGAA
1 GAAAAAGAAATTGAAA-AA
* **
17165 AAAAAAGAAAACGAAAAA
1 GAAAAAGAAATTGAAAAA
*
17183 GAAAAAGAAATTGCAAAA
1 GAAAAAGAAATTGAAAAA
*
17201 GAAAAAGAAATCGAAAAA
1 GAAAAAGAAATTGAAAAA
** * ** *
17219 GTGAGAGAAAAAGAAAAT
1 GAAAAAGAAATTGAAAAA
17237 GAAGAAAAGAAAATTGAAAAA
1 G-A-AAAAG-AAATTGAAAAA
17258 GAAAAAG
1 GAAAAAG
17265 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 21, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
18 50 0.67
19 12 0.16
20 4 0.05
21 9 0.12
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.08
Consensus pattern (18 bp):
GAAAAAGAAATTGAAAAA
Found at i:17246 original size:14 final size:13
Alignment explanation
Indices: 17225--17262 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
17215 AAAAGTGAGA
17225 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
17237 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
17252 GAAAAAGAAAA
1 GAAAAAGAAAA
17263 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:17276 original size:21 final size:21
Alignment explanation
Indices: 17159--17276 Score: 55
Period size: 21 Copynumber: 5.3 Consensus size: 21
17149 AAAAAAATTG
*
17159 AAAGAAAAAAAAGAAAACG-AA
1 AAAGAAAAAGAAGAAAA-GAAA
17180 AAAGAAAAAGAAATTGCAAAAG-AA
1 AAAGAAAAAG-AA--G-AAAAGAAA
**
17204 AAAGAAATCGAA-AAAGTGAGAGAA
1 AAAGAAAAAGAAGAAA---AGA-AA
*
17228 AAAGAAAATGAAGAAAAGAAA
1 AAAGAAAAAGAAGAAAAGAAA
** *
17249 ATTGAAAAAGAA-AAAGCGAAA
1 AAAGAAAAAGAAGAAA-AGAAA
17270 AAAGAAA
1 AAAGAAA
17277 TTGAAAGAGA
Statistics
Matches: 75, Mismatches: 11, Indels: 22
0.69 0.10 0.20
Matches are distributed among these distances:
19 3 0.04
20 3 0.04
21 29 0.39
22 7 0.09
23 2 0.03
24 24 0.32
25 7 0.09
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.06
Consensus pattern (21 bp):
AAAGAAAAAGAAGAAAAGAAA
Found at i:17316 original size:33 final size:33
Alignment explanation
Indices: 17279--17341 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
17269 AAAAGAAATT
17279 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
17312 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
17342 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:19141 original size:20 final size:20
Alignment explanation
Indices: 19118--19171 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
19108 AGTTTTTCCC
*
19118 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
19138 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
19158 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
19172 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:19153 original size:30 final size:30
Alignment explanation
Indices: 19118--19191 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
19108 AGTTTTTCCC
19118 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
19148 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
19178 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
19192 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:19181 original size:20 final size:20
Alignment explanation
Indices: 19118--19182 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
19108 AGTTTTTCCC
* * * *
19118 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
19138 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
19157 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
19178 AGCTC
1 AGCTC
19183 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:23356 original size:14 final size:14
Alignment explanation
Indices: 23337--23380 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
23327 AAACTTTATA
23337 TCCATAAACCCATC
1 TCCATAAACCCATC
* *
23351 TCCATAAACTTCATA
1 TCCATAAAC-CCATC
*
23366 TCCATAAACCTATC
1 TCCATAAACCCATC
23380 T
1 T
23381 TTGAATCCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.36, C:0.34, G:0.00, T:0.30
Consensus pattern (14 bp):
TCCATAAACCCATC
Found at i:23371 original size:15 final size:15
Alignment explanation
Indices: 23327--23374 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
23317 AAACCTACAA
*
23327 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* *
23342 AAAC-CCATCTCCAT
1 AAACTTCATATCCAT
23356 AAACTTCATATCCAT
1 AAACTTCATATCCAT
23371 AAAC
1 AAAC
23375 CTATCTTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:23627 original size:11 final size:12
Alignment explanation
Indices: 23596--23648 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 12
23586 AGTAAGTTTC
23596 AAAAAAAATCGA
1 AAAAAAAATCGA
23608 AAAAAAAATC-A
1 AAAAAAAATCGA
*
23619 AAAAAAAATTTGGA
1 AAAAAAAA--TCGA
23633 AAAAAAAATCTGA
1 AAAAAAAATC-GA
23646 AAA
1 AAA
23649 TTTGAACATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
11 9 0.26
12 11 0.31
13 6 0.17
14 9 0.26
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.13
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:24712 original size:18 final size:19
Alignment explanation
Indices: 24669--24714 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
24659 TGAGATAAGC
*
24669 GAAAAAG-AGAAAGAATGT
1 GAAAAAGAAAAAAGAATGT
* *
24687 GAACAAGAAAAAAGAGTG-
1 GAAAAAGAAAAAAGAATGT
24705 GAAAAAGAAA
1 GAAAAAGAAA
24715 TTGAGATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.65, C:0.02, G:0.26, T:0.07
Consensus pattern (19 bp):
GAAAAAGAAAAAAGAATGT
Found at i:25612 original size:29 final size:29
Alignment explanation
Indices: 25579--25638 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
25569 ATAACCAAAC
* *
25579 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCACATCCATAAACCCAT
*
25608 CTACATAAACTTCACATCCATAAACCCAT
1 CTACAAAAACTTCACATCCATAAACCCAT
25637 CT
1 CT
25639 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.27
Consensus pattern (29 bp):
CTACAAAAACTTCACATCCATAAACCCAT
Found at i:26108 original size:10 final size:10
Alignment explanation
Indices: 26095--26140 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
26085 AGCTCACTTG
26095 AGCTCGTTTT
1 AGCTCGTTTT
*
26105 AGCTCGTTTG
1 AGCTCGTTTT
*
26115 AGCTCGAATTT
1 AGCTCG-TTTT
*
26126 AGCTCGTTTC
1 AGCTCGTTTT
26136 AGCTC
1 AGCTC
26141 ATTCCTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:26128 original size:21 final size:20
Alignment explanation
Indices: 26092--26140 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
26082 ATCAGCTCAC
*
26092 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
26112 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
26133 TTCAGCTC
1 TTGAGCTC
26141 ATTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:26286 original size:13 final size:13
Alignment explanation
Indices: 26268--26294 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
26258 CAATGTTTGG
26268 AGGACATACATTC
1 AGGACATACATTC
26281 AGGACATACATTC
1 AGGACATACATTC
26294 A
1 A
26295 TGTATGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (13 bp):
AGGACATACATTC
Found at i:30476 original size:23 final size:22
Alignment explanation
Indices: 30425--30476 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
30415 CCTCGTCTTT
*
30425 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
30447 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
30470 TTCTTTT
1 TTCTTTT
30477 TCAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:30485 original size:12 final size:12
Alignment explanation
Indices: 30434--30488 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
30424 TTTCTTTTGT
30434 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
30447 -TCATTTTC-TC
1 TTCTTTTTCAAC
30457 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
30470 TTCTTTTTCAAT
1 TTCTTTTTCAAC
30482 TTCTTTT
1 TTCTTTT
30489 CTGTTTCACA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 1 0.03
11 4 0.12
12 22 0.65
13 7 0.21
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:30495 original size:17 final size:18
Alignment explanation
Indices: 30470--30507 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
30460 TTTCTTCAAC
* *
30470 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
30487 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
30505 TTC
1 TTC
30508 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Done.