Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168046.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_298, whole genome shotgun sequence
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: 37270
ACGTcount: A:0.65, C:0.05, G:0.12, T:0.18
Found at i:2215 original size:23 final size:23
Alignment explanation
Indices: 2180--2231 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
2170 AAAAAGTTAT
**
2180 TAAAAATTTACAAAGTAAAAAAA
1 TAAAAATAAACAAAGTAAAAAAA
*
2203 TAAAAATAAACAAAGTAAGAAAA
1 TAAAAATAAACAAAGTAAAAAAA
2226 TAAAAA
1 TAAAAA
2232 ATTAGGGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (23 bp):
TAAAAATAAACAAAGTAAAAAAA
Found at i:2451 original size:19 final size:20
Alignment explanation
Indices: 2418--2457 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2408 ATATTTGAGA
*
2418 AAAAAAATGAGAAAAAGAAG
1 AAAAAAATGAAAAAAAGAAG
*
2438 AAAAAAAT-AAAAAATGAAG
1 AAAAAAATGAAAAAAAGAAG
2457 A
1 A
2458 GGCAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (20 bp):
AAAAAAATGAAAAAAAGAAG
Found at i:3182 original size:22 final size:21
Alignment explanation
Indices: 3157--3197 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3147 AGATTTAAGA
3157 AAAAAATAAAAAATGAAAATGC
1 AAAAAATAAAAAAT-AAAATGC
* *
3179 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
3198 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATGC
Found at i:3261 original size:56 final size:55
Alignment explanation
Indices: 3157--3263 Score: 135
Period size: 55 Copynumber: 1.9 Consensus size: 55
3147 AGATTTAAGA
* * ***
3157 AAAAAATAAAAAATGAAAATGCAAAATATATAAAATAAAATTTGAGAAAAAGAAG
1 AAAAAATAAAAAATGAAAAGGCAAAATATATAAAAAAAAATAAAAGAAAAAGAAG
*
3212 AAAAAATAAAAAATGAAGAGGCAAAA-ATATGAAAAAAAAATAAAAAGAAAAA
1 AAAAAATAAAAAATGAAAAGGCAAAATATAT-AAAAAAAAAT-AAAAGAAAAA
3264 AATTTATAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
54 4 0.09
55 33 0.75
56 7 0.16
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.14
Consensus pattern (55 bp):
AAAAAATAAAAAATGAAAAGGCAAAATATATAAAAAAAAATAAAAGAAAAAGAAG
Found at i:3748 original size:18 final size:18
Alignment explanation
Indices: 3721--3755 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3711 AGGAAATTTA
3721 TGGAAAAAAAAAAAGAAT
1 TGGAAAAAAAAAAAGAAT
* *
3739 TGGAATAAAAAATAGAA
1 TGGAAAAAAAAAAAGAA
3756 AAATAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (18 bp):
TGGAAAAAAAAAAAGAAT
Found at i:3830 original size:22 final size:20
Alignment explanation
Indices: 3790--3830 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
3780 AAATTAAAAT
*
3790 AAGAAAAAAAATTAAAGCAA
1 AAGAAAAAAAAATAAAGCAA
3810 AAGAAAAAGATAAATAAAGCA
1 AAGAAAAA-A-AAATAAAGCA
3831 TGAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.73, C:0.05, G:0.12, T:0.10
Consensus pattern (20 bp):
AAGAAAAAAAAATAAAGCAA
Found at i:5276 original size:28 final size:27
Alignment explanation
Indices: 5221--5276 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
5211 AGGAAATTTG
*
5221 TGGAAAAAAAAGAAAAGACAAAAGATT
1 TGGAAAAAAAAGAAAAAACAAAAGATT
*
5248 TGGAATAAAAAAGAGAAAAATAAAA-ATT
1 TGGAA-AAAAAAGA-AAAAACAAAAGATT
5276 T
1 T
5277 TTAAAACAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 12 0.48
29 8 0.32
ACGTcount: A:0.66, C:0.02, G:0.16, T:0.16
Consensus pattern (27 bp):
TGGAAAAAAAAGAAAAAACAAAAGATT
Found at i:5700 original size:22 final size:21
Alignment explanation
Indices: 5675--5715 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5665 AAGATTTAAG
5675 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
5697 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
5716 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:6459 original size:23 final size:23
Alignment explanation
Indices: 6424--6476 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
6414 GAAAAGTTAT
**
6424 TAAAAATTTACAAAGTAAAAAAA
1 TAAAAATAAACAAAGTAAAAAAA
*
6447 TAAAAATAAACAAAGTAAGAAAA
1 TAAAAATAAACAAAGTAAAAAAA
6470 TAAAAAT
1 TAAAAAT
6477 TAGGGAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.19
Consensus pattern (23 bp):
TAAAAATAAACAAAGTAAAAAAA
Found at i:6677 original size:20 final size:19
Alignment explanation
Indices: 6652--6693 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
6642 AAAATATTTG
6652 AGAAAAAAATGAGAAAAA-GA
1 AGAAAAAAAT-A-AAAAATGA
6672 AGAAAAAAATAAAAAATGA
1 AGAAAAAAATAAAAAATGA
6691 AGA
1 AGA
6694 GGCAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 6 0.29
20 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (19 bp):
AGAAAAAAATAAAAAATGA
Found at i:6687 original size:19 final size:20
Alignment explanation
Indices: 6652--6693 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
6642 AAAATATTTG
*
6652 AGAAAAAAATGAGAAAAAGA
1 AGAAAAAAATGAAAAAAAGA
*
6672 AGAAAAAAAT-AAAAAATGA
1 AGAAAAAAATGAAAAAAAGA
6691 AGA
1 AGA
6694 GGCAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (20 bp):
AGAAAAAAATGAAAAAAAGA
Found at i:7418 original size:22 final size:21
Alignment explanation
Indices: 7384--7424 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
7374 AAGATTTAAG
7384 AAAAAATAAAAAATGAAAATGC
1 AAAAAATAAAAAAT-AAAATGC
* *
7406 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
7425 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATGC
Found at i:7458 original size:22 final size:24
Alignment explanation
Indices: 7433--7476 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
7423 ATTTGAGAAA
7433 AAGAAG-AAAAAAAT-AAAAAATG
1 AAGAAGCAAAAAAATGAAAAAATG
* *
7455 AAGAGGCAAAAATATGAAAAAA
1 AAGAAGCAAAAAAATGAAAAAA
7477 AAATAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 7 0.39
24 6 0.33
ACGTcount: A:0.73, C:0.02, G:0.16, T:0.09
Consensus pattern (24 bp):
AAGAAGCAAAAAAATGAAAAAATG
Found at i:7489 original size:57 final size:56
Alignment explanation
Indices: 7384--7491 Score: 137
Period size: 56 Copynumber: 1.9 Consensus size: 56
7374 AAGATTTAAG
* * ***
7384 AAAAAATAAAAAATGAAAATGCAAAATATATAAAATAAAATTTGAGAAAAAGAAGA
1 AAAAAATAAAAAATGAAAAGGCAAAATATATAAAAAAAAATAAAAGAAAAAGAAGA
*
7440 AAAAAATAAAAAATGAAGAGGCAAAA-ATATGAAAAAAAAATAAAAAGAAAAA
1 AAAAAATAAAAAATGAAAAGGCAAAATATAT-AAAAAAAAAT-AAAAGAAAAA
7492 AATTTATAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
55 4 0.09
56 33 0.75
57 7 0.16
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.14
Consensus pattern (56 bp):
AAAAAATAAAAAATGAAAAGGCAAAATATATAAAAAAAAATAAAAGAAAAAGAAGA
Found at i:7745 original size:23 final size:22
Alignment explanation
Indices: 7710--7756 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
7700 ATAAATAAAG
7710 AAAGAAAATTAAAGCAAAAGAAA
1 AAAGAAAATTAAAGCAAAA-AAA
*
7733 AAAGATAAA-TAAAGCACAAAAA
1 AAAGA-AAATTAAAGCAAAAAAA
7755 AA
1 AA
7757 CAAAAATACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 14 0.64
24 3 0.14
ACGTcount: A:0.74, C:0.06, G:0.11, T:0.09
Consensus pattern (22 bp):
AAAGAAAATTAAAGCAAAAAAA
Found at i:8082 original size:25 final size:23
Alignment explanation
Indices: 8028--8083 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
8018 AAATAAGAAA
* *
8028 AAAAATTAAAGCAAAAGAAAAAAG
1 AAAAA-TAAAGCAAAAAAAAAAAC
*
8052 ATAAATAAAGCATGAAAAAAAAAAC
1 AAAAATAAAGCA--AAAAAAAAAAC
8077 AAAAATA
1 AAAAATA
8084 CAAAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 7 0.27
24 4 0.15
25 15 0.58
ACGTcount: A:0.75, C:0.05, G:0.09, T:0.11
Consensus pattern (23 bp):
AAAAATAAAGCAAAAAAAAAAAC
Found at i:9931 original size:22 final size:21
Alignment explanation
Indices: 9906--9946 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
9896 AGATTTAAGA
9906 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
9928 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
9947 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:10051 original size:13 final size:14
Alignment explanation
Indices: 10026--10054 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
10016 AAAATTTTAA
10026 AACAAAGAAAAATG
1 AACAAAGAAAAATG
10040 AACAAA-AAAAATG
1 AACAAAGAAAAATG
10053 AA
1 AA
10055 AGCACATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.76, C:0.07, G:0.10, T:0.07
Consensus pattern (14 bp):
AACAAAGAAAAATG
Found at i:10251 original size:19 final size:18
Alignment explanation
Indices: 10211--10257 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
10201 ATAAAGAAAG
10211 AAAATAAAAATACTACAA
1 AAAATAAAAATACTACAA
*
10229 AAAACAAAAATACTACAAA
1 AAAATAAAAATACTAC-AA
10248 AAAATAAAAA
1 AAAATAAAAA
10258 GTAAGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.77, C:0.11, G:0.00, T:0.13
Consensus pattern (18 bp):
AAAATAAAAATACTACAA
Found at i:11950 original size:28 final size:27
Alignment explanation
Indices: 11895--11950 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
11885 AGGAAATTTG
*
11895 TGGAAAAAAAAGAAAAGACAAAAGATT
1 TGGAAAAAAAAGAAAAAACAAAAGATT
*
11922 TGGAATAAAAAAGAGAAAAATAAAA-ATT
1 TGGAA-AAAAAAGA-AAAAACAAAAGATT
11950 T
1 T
11951 TTAAAACAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 12 0.48
29 8 0.32
ACGTcount: A:0.66, C:0.02, G:0.16, T:0.16
Consensus pattern (27 bp):
TGGAAAAAAAAGAAAAAACAAAAGATT
Found at i:13000 original size:28 final size:27
Alignment explanation
Indices: 12945--13000 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
12935 AGGAAATTTG
*
12945 TGGAAAAAAAAGAAAAGACAAAAGATT
1 TGGAAAAAAAAGAAAAAACAAAAGATT
*
12972 TGGAATAAAAAAGAGAAAAATAAAA-ATT
1 TGGAA-AAAAAAGA-AAAAACAAAAGATT
13000 T
1 T
13001 TTAAAACAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 12 0.48
29 8 0.32
ACGTcount: A:0.66, C:0.02, G:0.16, T:0.16
Consensus pattern (27 bp):
TGGAAAAAAAAGAAAAAACAAAAGATT
Found at i:13368 original size:20 final size:19
Alignment explanation
Indices: 13343--13384 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
13333 AAAATATTTG
13343 AGAAAAAAATGAGAAAAA-GA
1 AGAAAAAAAT-A-AAAAATGA
13363 AGAAAAAAATAAAAAATGA
1 AGAAAAAAATAAAAAATGA
13382 AGA
1 AGA
13385 GGCAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 6 0.29
20 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (19 bp):
AGAAAAAAATAAAAAATGA
Found at i:13378 original size:19 final size:20
Alignment explanation
Indices: 13343--13384 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
13333 AAAATATTTG
*
13343 AGAAAAAAATGAGAAAAAGA
1 AGAAAAAAATGAAAAAAAGA
*
13363 AGAAAAAAAT-AAAAAATGA
1 AGAAAAAAATGAAAAAAAGA
13382 AGA
1 AGA
13385 GGCAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (20 bp):
AGAAAAAAATGAAAAAAAGA
Found at i:14096 original size:22 final size:21
Alignment explanation
Indices: 14071--14111 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
14061 AAGATTTAAG
14071 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
14093 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
14112 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:14155 original size:19 final size:19
Alignment explanation
Indices: 14102--14156 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 19
14092 CAAAATATAT
**
14102 AAAATAAAATTTG-AGAAA
1 AAAATAAAAAATGAAGAAA
*
14120 AAAATGAGAACAA-GAAGAAA
1 AAAAT-A-AAAAATGAAGAAA
14140 AAAATAAAAAATGAAGA
1 AAAATAAAAAATGAAGA
14157 GGCAAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
18 9 0.31
19 8 0.28
20 12 0.41
ACGTcount: A:0.71, C:0.02, G:0.15, T:0.13
Consensus pattern (19 bp):
AAAATAAAAAATGAAGAAA
Found at i:14693 original size:17 final size:18
Alignment explanation
Indices: 14667--14700 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
14657 AGGAAATTTA
14667 TGGAAAAAAAAA-AGAAT
1 TGGAAAAAAAAATAGAAT
*
14684 TGGAATAAAAAATAGAA
1 TGGAAAAAAAAATAGAA
14701 AAATAAAATT
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:0.68, C:0.00, G:0.18, T:0.15
Consensus pattern (18 bp):
TGGAAAAAAAAATAGAAT
Found at i:14695 original size:18 final size:17
Alignment explanation
Indices: 14667--14700 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
14657 AGGAAATTTA
14667 TGGAAAAAAAAAAGAAT
1 TGGAAAAAAAAAAGAAT
*
14684 TGGAATAAAAAATAGAA
1 TGGAA-AAAAAAAAGAA
14701 AAATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.15
Consensus pattern (17 bp):
TGGAAAAAAAAAAGAAT
Found at i:16224 original size:28 final size:27
Alignment explanation
Indices: 16169--16224 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
16159 AGGAAATTTG
*
16169 TGGAAAAAAAAGAAAAGACAAAAGATT
1 TGGAAAAAAAAGAAAAAACAAAAGATT
*
16196 TGGAATAAAAAAGAGAAAAATAAAA-ATT
1 TGGAA-AAAAAAGA-AAAAACAAAAGATT
16224 T
1 T
16225 TTAAAACAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 12 0.48
29 8 0.32
ACGTcount: A:0.66, C:0.02, G:0.16, T:0.16
Consensus pattern (27 bp):
TGGAAAAAAAAGAAAAAACAAAAGATT
Found at i:16649 original size:22 final size:21
Alignment explanation
Indices: 16624--16664 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
16614 AGATTTAAGA
16624 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
16646 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
16665 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:17715 original size:22 final size:21
Alignment explanation
Indices: 17690--17730 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
17680 AGATTTAAGA
17690 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
17712 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
17731 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:18015 original size:18 final size:19
Alignment explanation
Indices: 17971--18049 Score: 51
Period size: 17 Copynumber: 4.2 Consensus size: 19
17961 AAAATTTATG
*
17971 AAATTATAAATAAAGAAAGA
1 AAATTA-AAATAAAGAAAAA
*
17991 AAA-TAAAAT-ACGAAAAA
1 AAATTAAAATAAAGAAAAA
18008 AAATTAAAGCA-AAAGAAAAA
1 AAATTAAA--ATAAAGAAAAA
*
18028 AGA-T-AAATAAAGCACAAAA
1 AAATTAAAATAAAG-A-AAAA
18047 AAA
1 AAA
18050 CAAAAATACT
Statistics
Matches: 47, Mismatches: 5, Indels: 15
0.70 0.07 0.22
Matches are distributed among these distances:
16 1 0.02
17 13 0.28
18 11 0.23
19 9 0.19
20 13 0.28
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.13
Consensus pattern (19 bp):
AAATTAAAATAAAGAAAAA
Found at i:18272 original size:17 final size:18
Alignment explanation
Indices: 18246--18279 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18236 AGGAAATTTA
18246 TGGAAAAAAAAA-AGAAT
1 TGGAAAAAAAAATAGAAT
*
18263 TGGAATAAAAAATAGAA
1 TGGAAAAAAAAATAGAA
18280 AAATAAAATT
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:0.68, C:0.00, G:0.18, T:0.15
Consensus pattern (18 bp):
TGGAAAAAAAAATAGAAT
Found at i:18274 original size:18 final size:17
Alignment explanation
Indices: 18246--18279 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
18236 AGGAAATTTA
18246 TGGAAAAAAAAAAGAAT
1 TGGAAAAAAAAAAGAAT
*
18263 TGGAATAAAAAATAGAA
1 TGGAA-AAAAAAAAGAA
18280 AAATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.15
Consensus pattern (17 bp):
TGGAAAAAAAAAAGAAT
Found at i:18872 original size:22 final size:22
Alignment explanation
Indices: 18819--18872 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
18809 GAGAAAAATT
18819 AAATAAAATACCAAAAAAGGAAA
1 AAATAAAATA-CAAAAAAGGAAA
* *
18842 AAATAAAAATA-AACAAAGTAAGA
1 AAAT-AAAATACAAAAAAGGAA-A
18865 AAATAAAA
1 AAATAAAA
18873 AATTAGCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 12 0.44
23 9 0.33
24 6 0.22
ACGTcount: A:0.76, C:0.06, G:0.07, T:0.11
Consensus pattern (22 bp):
AAATAAAATACAAAAAAGGAAA
Found at i:19797 original size:28 final size:27
Alignment explanation
Indices: 19742--19797 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
19732 AGGAAATTTG
*
19742 TGGAAAAAAAAGAAAAGACAAAAGATT
1 TGGAAAAAAAAGAAAAAACAAAAGATT
*
19769 TGGAATAAAAAAGAGAAAAATAAAA-ATT
1 TGGAA-AAAAAAGA-AAAAACAAAAGATT
19797 T
1 T
19798 TTAAAACAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 12 0.48
29 8 0.32
ACGTcount: A:0.66, C:0.02, G:0.16, T:0.16
Consensus pattern (27 bp):
TGGAAAAAAAAGAAAAAACAAAAGATT
Found at i:20824 original size:28 final size:27
Alignment explanation
Indices: 20769--20824 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
20759 AGGAAATTTG
*
20769 TGGAAAAAAAAGAAAAGACAAAAGATT
1 TGGAAAAAAAAGAAAAAACAAAAGATT
*
20796 TGGAATAAAAAAGAGAAAAATAAAA-ATT
1 TGGAA-AAAAAAGA-AAAAACAAAAGATT
20824 T
1 T
20825 TTAAAACAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 12 0.48
29 8 0.32
ACGTcount: A:0.66, C:0.02, G:0.16, T:0.16
Consensus pattern (27 bp):
TGGAAAAAAAAGAAAAAACAAAAGATT
Found at i:21248 original size:22 final size:21
Alignment explanation
Indices: 21223--21263 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
21213 AGATTTAAGA
21223 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
21245 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
21264 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:22060 original size:23 final size:21
Alignment explanation
Indices: 22014--22062 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
22004 TTAGGGAATC
*
22014 AAAAATATAAAAGGAAAAAAT
1 AAAAATAAAAAAGGAAAAAAT
*
22035 AAAAATAAACAAAGTAAGAAAAT
1 AAAAATAAA-AAAGGAA-AAAAT
22058 AAAAA
1 AAAAA
22063 ATTAGGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.33
22 6 0.25
23 10 0.42
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.12
Consensus pattern (21 bp):
AAAAATAAAAAAGGAAAAAAT
Found at i:22271 original size:20 final size:19
Alignment explanation
Indices: 22246--22287 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
22236 AAAATATTTG
22246 AGAAAAAAATGAGAAAAA-GA
1 AGAAAAAAAT-A-AAAAATGA
22266 AGAAAAAAATAAAAAATGA
1 AGAAAAAAATAAAAAATGA
22285 AGA
1 AGA
22288 GGCAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 6 0.29
20 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (19 bp):
AGAAAAAAATAAAAAATGA
Found at i:22281 original size:19 final size:20
Alignment explanation
Indices: 22246--22287 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
22236 AAAATATTTG
*
22246 AGAAAAAAATGAGAAAAAGA
1 AGAAAAAAATGAAAAAAAGA
*
22266 AGAAAAAAAT-AAAAAATGA
1 AGAAAAAAATGAAAAAAAGA
22285 AGA
1 AGA
22288 GGCAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (20 bp):
AGAAAAAAATGAAAAAAAGA
Found at i:22987 original size:22 final size:21
Alignment explanation
Indices: 22962--23002 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
22952 AGATTTAAGA
22962 AAAAAATAAAAAATGAAAATGC
1 AAAAAATAAAAAAT-AAAATGC
* *
22984 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
23003 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATGC
Found at i:23110 original size:16 final size:16
Alignment explanation
Indices: 23089--23127 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
23079 AAAATTTTAA
*
23089 AACAAAGAAAAAAGTG
1 AACAAAAAAAAAAGTG
23105 AACAAAAAAAAAAGT-
1 AACAAAAAAAAAAGTG
23120 AA-AAAAAA
1 AACAAAAAA
23128 GAAGAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.27
15 2 0.09
16 14 0.64
ACGTcount: A:0.79, C:0.05, G:0.10, T:0.05
Consensus pattern (16 bp):
AACAAAAAAAAAAGTG
Found at i:23298 original size:18 final size:19
Alignment explanation
Indices: 23254--23332 Score: 51
Period size: 17 Copynumber: 4.2 Consensus size: 19
23244 AAAATTTATG
*
23254 AAATTATAAATAAAGAAAGA
1 AAATTA-AAATAAAGAAAAA
*
23274 AAA-TAAAAT-ACGAAAAA
1 AAATTAAAATAAAGAAAAA
23291 AAATTAAAGCA-AAAGAAAAA
1 AAATTAAA--ATAAAGAAAAA
*
23311 AGA-T-AAATAAAGCACAAAA
1 AAATTAAAATAAAG-A-AAAA
23330 AAA
1 AAA
23333 CAAAAATACT
Statistics
Matches: 47, Mismatches: 5, Indels: 15
0.70 0.07 0.22
Matches are distributed among these distances:
16 1 0.02
17 13 0.28
18 11 0.23
19 9 0.19
20 13 0.28
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.13
Consensus pattern (19 bp):
AAATTAAAATAAAGAAAAA
Found at i:23656 original size:25 final size:23
Alignment explanation
Indices: 23602--23667 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 23
23592 AAATAAGAAA
* *
23602 AAAAATTAAAGCAAAAGAAAAAAG
1 AAAAA-TAAAGCAAAAAAAAAAAC
*
23626 ATAAATAAAGCATGAAAAAAAAAAC
1 AAAAATAAAGCA--AAAAAAAAAAC
23651 AAAAATACAA-CAAAAAA
1 AAAAATA-AAGCAAAAAA
23668 TTATAAAAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
23 12 0.34
24 4 0.11
25 17 0.49
26 2 0.06
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.09
Consensus pattern (23 bp):
AAAAATAAAGCAAAAAAAAAAAC
Found at i:24098 original size:24 final size:24
Alignment explanation
Indices: 24068--24129 Score: 76
Period size: 23 Copynumber: 2.6 Consensus size: 24
24058 GTAGAAAAAA
*
24068 AAGAAAATAAAAAATAAATTAAGAG-
1 AAGAAAATAAAAAATAAA-CAA-AGT
24093 AA-AAAAT-AAAAATAAACAAAGT
1 AAGAAAATAAAAAATAAACAAAGT
24115 AAGAAAATAAAAAAT
1 AAGAAAATAAAAAAT
24130 TAGCGAATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 2 0.06
22 4 0.12
23 14 0.42
24 11 0.33
25 2 0.06
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.15
Consensus pattern (24 bp):
AAGAAAATAAAAAATAAACAAAGT
Found at i:25476 original size:22 final size:21
Alignment explanation
Indices: 25451--25491 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
25441 AGATTTAAGA
25451 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
25473 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
25492 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:26118 original size:28 final size:27
Alignment explanation
Indices: 26063--26118 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
26053 AGGAAATTTG
*
26063 TGGAAAAAAAAGAAAAGACAAAAGATT
1 TGGAAAAAAAAGAAAAAACAAAAGATT
*
26090 TGGAATAAAAAAGAGAAAAATAAAA-ATT
1 TGGAA-AAAAAAGA-AAAAACAAAAGATT
26118 T
1 T
26119 TTAAAACAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 12 0.48
29 8 0.32
ACGTcount: A:0.66, C:0.02, G:0.16, T:0.16
Consensus pattern (27 bp):
TGGAAAAAAAAGAAAAAACAAAAGATT
Found at i:26287 original size:23 final size:21
Alignment explanation
Indices: 26245--26293 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
26235 TAGGGAATCA
*
26245 AAAAATATAAAAGGAAAAAAT
1 AAAAATAAAAAAGGAAAAAAT
*
26266 AAAAATAAACAAAGTAAGAAAAT
1 AAAAATAAA-AAAGGAA-AAAAT
26289 AAAAA
1 AAAAA
26294 ATTAGGAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.33
22 6 0.25
23 10 0.42
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.12
Consensus pattern (21 bp):
AAAAATAAAAAAGGAAAAAAT
Found at i:26509 original size:19 final size:19
Alignment explanation
Indices: 26475--26515 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
26465 AAAATATTTG
**
26475 AGAAAAAAATGGAAAAAGA
1 AGAAAAAAATAAAAAAAGA
*
26494 AGAAAAAAATAAAAAATGA
1 AGAAAAAAATAAAAAAAGA
26513 AGA
1 AGA
26516 GGCAAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (19 bp):
AGAAAAAAATAAAAAAAGA
Found at i:26645 original size:19 final size:20
Alignment explanation
Indices: 26603--26646 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
26593 ATGGAATGAC
* * *
26603 AAAATGAAAAAAAATAGTTT
1 AAAAAGAAAAAAAATAATTG
26623 AAAAAGAAAAAAAA-AATTG
1 AAAAAGAAAAAAAATAATTG
26642 AAAAA
1 AAAAA
26647 CATTAAGTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (20 bp):
AAAAAGAAAAAAAATAATTG
Found at i:26940 original size:18 final size:17
Alignment explanation
Indices: 26919--26952 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
26909 CAAAGTTGAA
26919 AAAAAAATAAATTAAGAG
1 AAAAAAATAAA-TAAGAG
*
26937 AAAAAATTAAATAAGA
1 AAAAAAATAAATAAGA
26953 ATACCCAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (17 bp):
AAAAAAATAAATAAGAG
Found at i:27271 original size:22 final size:21
Alignment explanation
Indices: 27246--27286 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
27236 AGATTTAAGA
27246 AAAAAATAAAAAATGAAAATGC
1 AAAAAATAAAAAAT-AAAATGC
* *
27268 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
27287 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATGC
Found at i:27320 original size:22 final size:24
Alignment explanation
Indices: 27295--27338 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
27285 ATTTGAGAAA
27295 AAGAAG-AAAAAAAT-AAAAAATG
1 AAGAAGCAAAAAAATGAAAAAATG
* *
27317 AAGAGGCAAAAATATGAAAAAA
1 AAGAAGCAAAAAAATGAAAAAA
27339 AAATAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 7 0.39
24 6 0.33
ACGTcount: A:0.73, C:0.02, G:0.16, T:0.09
Consensus pattern (24 bp):
AAGAAGCAAAAAAATGAAAAAATG
Found at i:27351 original size:57 final size:56
Alignment explanation
Indices: 27242--27353 Score: 145
Period size: 56 Copynumber: 2.0 Consensus size: 56
27232 AAAAAGATTT
* * ***
27242 AAGAAAAAAATAAAAAATGAAAATGCAAAATATATAAAATAAAATTTGAGAAAAAG
1 AAGAAAAAAATAAAAAATGAAAAGGCAAAATATATAAAAAAAAATAAAAGAAAAAG
*
27298 AAGAAAAAAATAAAAAATGAAGAGGCAAAA-ATATGAAAAAAAAATAAAAAGAAAAA
1 AAGAAAAAAATAAAAAATGAAAAGGCAAAATATAT-AAAAAAAAAT-AAAAGAAAAA
27354 AATTTATAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
55 4 0.08
56 37 0.77
57 7 0.15
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.13
Consensus pattern (56 bp):
AAGAAAAAAATAAAAAATGAAAAGGCAAAATATATAAAAAAAAATAAAAGAAAAAG
Found at i:27601 original size:18 final size:19
Alignment explanation
Indices: 27557--27635 Score: 51
Period size: 17 Copynumber: 4.2 Consensus size: 19
27547 AAAATTTATG
*
27557 AAATTATAAATAAAGAAAGA
1 AAATTA-AAATAAAGAAAAA
*
27577 AAA-TAAAAT-ACGAAAAA
1 AAATTAAAATAAAGAAAAA
27594 AAATTAAAGCA-AAAGAAAAA
1 AAATTAAA--ATAAAGAAAAA
*
27614 AGA-T-AAATAAAGCACAAAA
1 AAATTAAAATAAAG-A-AAAA
27633 AAA
1 AAA
27636 CAAAAATACT
Statistics
Matches: 47, Mismatches: 5, Indels: 15
0.70 0.07 0.22
Matches are distributed among these distances:
16 1 0.02
17 13 0.28
18 11 0.23
19 9 0.19
20 13 0.28
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.13
Consensus pattern (19 bp):
AAATTAAAATAAAGAAAAA
Found at i:27960 original size:25 final size:23
Alignment explanation
Indices: 27906--27971 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 23
27896 AAATAAGAAA
* *
27906 AAAAATTAAAGCAAAAGAAAAAAG
1 AAAAA-TAAAGCAAAAAAAAAAAC
*
27930 ATAAATAAAGCATGAAAAAAAAAAC
1 AAAAATAAAGCA--AAAAAAAAAAC
27955 AAAAATACAA-CAAAAAA
1 AAAAATA-AAGCAAAAAA
27972 TTATAAAAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
23 12 0.34
24 4 0.11
25 17 0.49
26 2 0.06
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.09
Consensus pattern (23 bp):
AAAAATAAAGCAAAAAAAAAAAC
Found at i:28456 original size:22 final size:22
Alignment explanation
Indices: 28403--28456 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
28393 AGAAAAAATT
28403 AAATAAAATACCAAAAAAGGAAA
1 AAATAAAATA-CAAAAAAGGAAA
* *
28426 AAATAAAAATA-AACAAAGTAAGA
1 AAAT-AAAATACAAAAAAGGAA-A
28449 AAATAAAA
1 AAATAAAA
28457 AATTAGCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 12 0.44
23 9 0.33
24 6 0.22
ACGTcount: A:0.76, C:0.06, G:0.07, T:0.11
Consensus pattern (22 bp):
AAATAAAATACAAAAAAGGAAA
Found at i:29037 original size:17 final size:18
Alignment explanation
Indices: 29001--29033 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28991 TGAAATTATG
29001 AAATAAAGAAAGAAAATA
1 AAATAAAGAAAGAAAATA
29019 AAAT-AAGAAA-AAAAT
1 AAATAAAGAAAGAAAAT
29034 TAAAGCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (18 bp):
AAATAAAGAAAGAAAATA
Found at i:29745 original size:22 final size:21
Alignment explanation
Indices: 29720--29760 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
29710 AGATTTAAGA
29720 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
29742 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
29761 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:30551 original size:23 final size:24
Alignment explanation
Indices: 30525--30577 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
30515 TTAGGGAATC
*
30525 AAAAAATATA-AAAGGAAAAAAAT
1 AAAAAATAAACAAAGGAAAAAAAT
* *
30548 -AAAAATAAACAAAGTAAGAAAAT
1 AAAAAATAAACAAAGGAAAAAAAT
30571 AAAAAAT
1 AAAAAAT
30578 TAGGGAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 8 0.32
23 11 0.44
24 6 0.24
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.13
Consensus pattern (24 bp):
AAAAAATAAACAAAGGAAAAAAAT
Found at i:30791 original size:19 final size:19
Alignment explanation
Indices: 30759--30797 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
30749 AAATATTTGA
**
30759 AAAAAAATGGAAAAAGAAG
1 AAAAAAATAAAAAAAGAAG
*
30778 AAAAAAATAAAAAATGAAG
1 AAAAAAATAAAAAAAGAAG
30797 A
1 A
30798 GGCAAAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (19 bp):
AAAAAAATAAAAAAAGAAG
Found at i:31540 original size:22 final size:21
Alignment explanation
Indices: 31515--31555 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
31505 AAGATTTAAG
31515 AAAAAATAAAAAATGAAAATGC
1 AAAAAATAAAAAAT-AAAATGC
* *
31537 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
31556 TTGAAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATGC
Found at i:31582 original size:54 final size:51
Alignment explanation
Indices: 31515--31623 Score: 139
Period size: 54 Copynumber: 2.1 Consensus size: 51
31505 AAGATTTAAG
* **
31515 AAAAAATAAAAAATGAAAATGCAAAATATAT-AAAATAAAATTTGAAAAAGAAGA
1 AAAAAATAAAAAATGAAAAGGCAAAA-ATATGAAAA-AAAAAAT-AAAAAGAA-A
*
31569 AAAAAATAAAAAATGAAGAGGCAAAAATATGAAAAAAAAAATAAAAAGAAA
1 AAAAAATAAAAAATGAAAAGGCAAAAATATGAAAAAAAAAATAAAAAGAAA
31620 AAAA
1 AAAA
31624 TTTATAGAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
51 5 0.10
52 8 0.16
53 9 0.18
54 28 0.56
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.14
Consensus pattern (51 bp):
AAAAAATAAAAAATGAAAAGGCAAAAATATGAAAAAAAAAATAAAAAGAAA
Found at i:31587 original size:22 final size:24
Alignment explanation
Indices: 31562--31605 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
31552 AAATTTGAAA
31562 AAGAAG-AAAAAAAT-AAAAAATG
1 AAGAAGCAAAAAAATGAAAAAATG
* *
31584 AAGAGGCAAAAATATGAAAAAA
1 AAGAAGCAAAAAAATGAAAAAA
31606 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 7 0.39
24 6 0.33
ACGTcount: A:0.73, C:0.02, G:0.16, T:0.09
Consensus pattern (24 bp):
AAGAAGCAAAAAAATGAAAAAATG
Found at i:31867 original size:18 final size:19
Alignment explanation
Indices: 31823--31880 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 19
31813 AAAATTTATG
*
31823 AAATTATAAATAAAGAAAGA
1 AAATTA-AAATAAAGAAAAA
*
31843 AAA-TAAAAT-ACGAAAAA
1 AAATTAAAATAAAGAAAAA
31860 AAATTAAAGCA-AAAGAAAAA
1 AAATTAAA--ATAAAGAAAAA
31880 A
1 A
31881 GATAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 9 0.29
18 8 0.26
19 2 0.06
20 12 0.39
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (19 bp):
AAATTAAAATAAAGAAAAA
Found at i:32125 original size:18 final size:18
Alignment explanation
Indices: 32098--32132 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
32088 AGGAAATTTA
32098 TGGAAAAAAAAAAAGAAT
1 TGGAAAAAAAAAAAGAAT
* *
32116 TGGAATAAAAAATAGAA
1 TGGAAAAAAAAAAAGAA
32133 AAATAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (18 bp):
TGGAAAAAAAAAAAGAAT
Found at i:32191 original size:19 final size:17
Alignment explanation
Indices: 32155--32194 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
32145 TAAAACGACG
*
32155 AAAAATTAAAATAAGAA
1 AAAAATTAAAAAAAGAA
32172 AAAAATTAAAGCAAAAGAA
1 AAAAATTAAA--AAAAGAA
32191 AAAA
1 AAAA
32195 GATAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
19 10 0.50
ACGTcount: A:0.78, C:0.03, G:0.07, T:0.12
Consensus pattern (17 bp):
AAAAATTAAAAAAAGAA
Found at i:32226 original size:25 final size:23
Alignment explanation
Indices: 32172--32227 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
32162 AAAATAAGAA
* *
32172 AAAAATTAAAGCAAAAGAAAAAAG
1 AAAAA-TAAAGCAAAAAAAAAAAC
*
32196 ATAAATAAAGCATGAAAAAAAAAAC
1 AAAAATAAAGCA--AAAAAAAAAAC
32221 AAAAATA
1 AAAAATA
32228 CAAAAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 7 0.27
24 4 0.15
25 15 0.58
ACGTcount: A:0.75, C:0.05, G:0.09, T:0.11
Consensus pattern (23 bp):
AAAAATAAAGCAAAAAAAAAAAC
Found at i:32717 original size:22 final size:22
Alignment explanation
Indices: 32664--32717 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
32654 AGAAAAAATT
32664 AAATAAAATACCAAAAAAGGAAA
1 AAATAAAATA-CAAAAAAGGAAA
* *
32687 AAATAAAAATA-AACAAAGTAAGA
1 AAAT-AAAATACAAAAAAGGAA-A
32710 AAATAAAA
1 AAATAAAA
32718 AATTAGCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 12 0.44
23 9 0.33
24 6 0.22
ACGTcount: A:0.76, C:0.06, G:0.07, T:0.11
Consensus pattern (22 bp):
AAATAAAATACAAAAAAGGAAA
Found at i:34029 original size:22 final size:21
Alignment explanation
Indices: 34004--34044 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
33994 AGATTTAAGA
34004 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
34026 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
34045 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:34844 original size:23 final size:21
Alignment explanation
Indices: 34802--34851 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
34792 TAGGGAATCA
*
34802 AAAAATATAAAAGGAAAAAAT
1 AAAAATAAAAAAGGAAAAAAT
*
34823 AAAAATAAACAAAGTAAGAAAAT
1 AAAAATAAA-AAAGGAA-AAAAT
34846 AAAAAT
1 AAAAAT
34852 TAGGGAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.32
22 6 0.24
23 11 0.44
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (21 bp):
AAAAATAAAAAAGGAAAAAAT
Found at i:35066 original size:17 final size:18
Alignment explanation
Indices: 35033--35073 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
35023 AAAATATTTG
*
35033 AGAA-AAAAAATGGAAAA
1 AGAAGAAAAAATGAAAAA
35050 AGAAGAAAAAAT-AAAAA
1 AGAAGAAAAAATGAAAAA
35067 ATGAAGA
1 A-GAAGA
35074 GGCAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (18 bp):
AGAAGAAAAAATGAAAAA
Found at i:35819 original size:22 final size:21
Alignment explanation
Indices: 35794--35834 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
35784 AGATTTAAGA
35794 AAAAAATAAAAAATGAAAATGC
1 AAAAAATAAAAAAT-AAAATGC
* *
35816 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
35835 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATGC
Found at i:35898 original size:56 final size:55
Alignment explanation
Indices: 35794--35900 Score: 135
Period size: 55 Copynumber: 1.9 Consensus size: 55
35784 AGATTTAAGA
* * ***
35794 AAAAAATAAAAAATGAAAATGCAAAATATATAAAATAAAATTTGAGAAAAAGAAG
1 AAAAAATAAAAAATGAAAAGGCAAAATATATAAAAAAAAATAAAAGAAAAAGAAG
*
35849 AAAAAATAAAAAATGAAGAGGCAAAA-ATATGAAAAAAAAATAAAAAGAAAAA
1 AAAAAATAAAAAATGAAAAGGCAAAATATAT-AAAAAAAAAT-AAAAGAAAAA
35901 AATTTATAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
54 4 0.09
55 33 0.75
56 7 0.16
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.14
Consensus pattern (55 bp):
AAAAAATAAAAAATGAAAAGGCAAAATATATAAAAAAAAATAAAAGAAAAAGAAG
Found at i:36147 original size:18 final size:19
Alignment explanation
Indices: 36103--36160 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 19
36093 AAAATTTATG
*
36103 AAATTATAAATAAAGAAAGA
1 AAATTA-AAATAAAGAAAAA
*
36123 AAA-TAAAAT-ACGAAAAA
1 AAATTAAAATAAAGAAAAA
36140 AAATTAAAGCA-AAAGAAAAA
1 AAATTAAA--ATAAAGAAAAA
36160 A
1 A
36161 GATAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 9 0.29
18 8 0.26
19 2 0.06
20 12 0.39
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (19 bp):
AAATTAAAATAAAGAAAAA
Found at i:37122 original size:23 final size:24
Alignment explanation
Indices: 37079--37131 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
37069 AAGAAAATAA
37079 AAAAAATATAACAAGAGGAAAAAT
1 AAAAAATATAACAAGAGGAAAAAT
* * *
37103 ATAAAATATGA-AAGATGAAAAAT
1 AAAAAATATAACAAGAGGAAAAAT
37126 AAAAAA
1 AAAAAA
37132 AGAAAGTGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (24 bp):
AAAAAATATAACAAGAGGAAAAAT
Found at i:37136 original size:21 final size:23
Alignment explanation
Indices: 37091--37137 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
37081 AAAATATAAC
*
37091 AAGAGGAAAAATATAAAATATGA
1 AAGAGGAAAAATATAAAATAAGA
*
37114 AAGATGAAAAATA-AAAA-AAGA
1 AAGAGGAAAAATATAAAATAAGA
37135 AAG
1 AAG
37138 TGCACAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 4 0.18
23 12 0.55
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (23 bp):
AAGAGGAAAAATATAAAATAAGA
Done.