Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168449.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_660, 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: 20401
ACGTcount: A:0.65, C:0.05, G:0.13, T:0.17
Found at i:1078 original size:22 final size:21
Alignment explanation
Indices: 1053--1093 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1043 AGATTTAAGA
1053 AAAAAATAAAAAATGAAAATGC
1 AAAAAATAAAAAAT-AAAATGC
* *
1075 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
1094 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:2266 original size:22 final size:22
Alignment explanation
Indices: 2213--2266 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
2203 AGAAAAAATT
2213 AAATAAAATACCAAAAAAGGAAA
1 AAATAAAATA-CAAAAAAGGAAA
* *
2236 AAATAAAAATA-AACAAAGTAAGA
1 AAAT-AAAATACAAAAAAGGAA-A
2259 AAATAAAA
1 AAATAAAA
2267 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:2824 original size:13 final size:13
Alignment explanation
Indices: 2806--2865 Score: 63
Period size: 13 Copynumber: 4.6 Consensus size: 13
2796 ATGAAATTAT
2806 AAATAAAGAAAGA
1 AAATAAAGAAAGA
2819 AAATAAA-AAAGA
1 AAATAAAGAAAGA
2831 AAA-AAAGTAAAGCA
1 AAATAAAG-AAAG-A
*
2845 AAAGAAA-AAAGA
1 AAATAAAGAAAGA
2857 TAAATAAAG
1 -AAATAAAG
2866 CACAAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
11 3 0.08
12 9 0.22
13 21 0.52
14 4 0.10
15 3 0.08
ACGTcount: A:0.77, C:0.02, G:0.13, T:0.08
Consensus pattern (13 bp):
AAATAAAGAAAGA
Found at i:3948 original size:18 final size:17
Alignment explanation
Indices: 3927--3969 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3917 AAAAATTTAT
*
3927 GAAATTATAATAAAGAAA
1 GAAATTAAAAT-AAGAAA
*
3945 GAAAATAAAATAAGAAA
1 GAAATTAAAATAAGAAA
3962 -AAATTAAA
1 GAAATTAAA
3970 GCAAAAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 7 0.32
17 6 0.27
18 9 0.41
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (17 bp):
GAAATTAAAATAAGAAA
Found at i:4447 original size:60 final size:56
Alignment explanation
Indices: 4399--4513 Score: 144
Period size: 59 Copynumber: 2.0 Consensus size: 56
4389 AAAAAGTTAT
**
4399 TAAAAATTTACAAAGT-AAA-AAAAATTAGGGAATCAAAAAATATAAAAGGAAAAAA
1 TAAAAATAAACAAAGTAAAATAAAAATTAGGGAATC-AAAAATATAAAAGGAAAAAA
* *
4454 TAAAAATAAACAAAGTAAGAAAATAAAAATTAGGGAATCAAAAATATAAAAAGACAAAA
1 TAAAAATAAACAAAGT---AAAATAAAAATTAGGGAATCAAAAATATAAAAGGAAAAAA
4513 T
1 T
4514 GAATAAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
55 14 0.27
59 22 0.43
60 15 0.29
ACGTcount: A:0.68, C:0.04, G:0.10, T:0.17
Consensus pattern (56 bp):
TAAAAATAAACAAAGTAAAATAAAAATTAGGGAATCAAAAATATAAAAGGAAAAAA
Found at i:4476 original size:23 final size:21
Alignment explanation
Indices: 4434--4483 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
4424 TAGGGAATCA
*
4434 AAAAATATAAAAGGAAAAAAT
1 AAAAATAAAAAAGGAAAAAAT
*
4455 AAAAATAAACAAAGTAAGAAAAT
1 AAAAATAAA-AAAGGAA-AAAAT
4478 AAAAAT
1 AAAAAT
4484 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:5464 original size:22 final size:21
Alignment explanation
Indices: 5439--5479 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5429 AGATTTAAGA
5439 AAAAAATAAAAAATGAAAATGC
1 AAAAAATAAAAAAT-AAAATGC
* *
5461 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
5480 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:5513 original size:22 final size:24
Alignment explanation
Indices: 5488--5531 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
5478 ATTTGAGAAA
5488 AAGAAG-AAAAAAAT-AAAAAATG
1 AAGAAGCAAAAAAATGAAAAAATG
* *
5510 AAGAGGCAAAAATATGAAAAAA
1 AAGAAGCAAAAAAATGAAAAAA
5532 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:5544 original size:57 final size:56
Alignment explanation
Indices: 5435--5546 Score: 145
Period size: 56 Copynumber: 2.0 Consensus size: 56
5425 AAAAAGATTT
* * ***
5435 AAGAAAAAAATAAAAAATGAAAATGCAAAATATATAAAATAAAATTTGAGAAAAAG
1 AAGAAAAAAATAAAAAATGAAAAGGCAAAATATATAAAAAAAAATAAAAGAAAAAG
*
5491 AAGAAAAAAATAAAAAATGAAGAGGCAAAA-ATATGAAAAAAAAATAAAAAGAAAAA
1 AAGAAAAAAATAAAAAATGAAAAGGCAAAATATAT-AAAAAAAAAT-AAAAGAAAAA
5547 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:6970 original size:21 final size:22
Alignment explanation
Indices: 6946--7003 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 22
6936 ATTTGAGAAA
6946 AAGAAGAAAAAAT-AAA-AAATG
1 AAGAAGAAAAAATGAAATAAA-G
*
6967 AAGAGGCAAAAATATGAAATAAAG
1 AAGAAG-AAAAA-ATGAAATAAAG
*
6991 AAAAAGAAAAAAT
1 AAGAAGAAAAAAT
7004 TTATAGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
21 5 0.17
22 7 0.23
23 7 0.23
24 8 0.27
25 3 0.10
ACGTcount: A:0.72, C:0.02, G:0.16, T:0.10
Consensus pattern (22 bp):
AAGAAGAAAAAATGAAATAAAG
Found at i:7582 original size:29 final size:28
Alignment explanation
Indices: 7530--7586 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
7520 GAAATTTGTG
7530 GGAAAAAAAAAAGAAAAGACAAAAGATTT
1 GGAAAAAAAAAAGAAAAGACAAAA-ATTT
* *
7559 GGAATAAAAAACAGAAAA-ATAAAAATTT
1 GGAA-AAAAAAAAGAAAAGACAAAAATTT
7587 TAAAACAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.16
29 9 0.36
30 12 0.48
ACGTcount: A:0.68, C:0.04, G:0.14, T:0.14
Consensus pattern (28 bp):
GGAAAAAAAAAAGAAAAGACAAAAATTT
Found at i:7724 original size:18 final size:16
Alignment explanation
Indices: 7692--7749 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 16
7682 TACAAAGTAG
7692 AAAAAAATAAGAAAATA
1 AAAAAAATAA-AAAATA
7709 AAAAAAATAAATAAAATA
1 AAAAAAAT-AA-AAAATA
**
7727 CCAAAAAAGGAAAAAATA
1 --AAAAAAATAAAAAATA
7745 AAAAA
1 AAAAA
7750 TTAGCGAATC
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 5 0.14
17 8 0.23
18 14 0.40
19 2 0.06
20 6 0.17
ACGTcount: A:0.81, C:0.03, G:0.05, T:0.10
Consensus pattern (16 bp):
AAAAAAATAAAAAATA
Found at i:8004 original size:22 final size:21
Alignment explanation
Indices: 7979--8019 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
7969 AGATTTAAGA
7979 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
8001 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
8020 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:9067 original size:20 final size:19
Alignment explanation
Indices: 9042--9083 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
9032 AAAATATTTG
9042 AGAAAAAAATGAGAAAAA-GA
1 AGAAAAAAAT-A-AAAAATGA
9062 AGAAAAAAATAAAAAATGA
1 AGAAAAAAATAAAAAATGA
9081 AGA
1 AGA
9084 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:9077 original size:19 final size:20
Alignment explanation
Indices: 9042--9083 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
9032 AAAATATTTG
*
9042 AGAAAAAAATGAGAAAAAGA
1 AGAAAAAAATGAAAAAAAGA
*
9062 AGAAAAAAAT-AAAAAATGA
1 AGAAAAAAATGAAAAAAAGA
9081 AGA
1 AGA
9084 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:9849 original size:22 final size:21
Alignment explanation
Indices: 9824--9864 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
9814 AGATTTAAGA
9824 AAAAAATAAAAAATGAAAATGC
1 AAAAAATAAAAAAT-AAAATGC
* *
9846 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
9865 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:9928 original size:56 final size:55
Alignment explanation
Indices: 9824--9930 Score: 135
Period size: 55 Copynumber: 1.9 Consensus size: 55
9814 AGATTTAAGA
* * ***
9824 AAAAAATAAAAAATGAAAATGCAAAATATATAAAATAAAATTTGAGAAAAAGAAG
1 AAAAAATAAAAAATGAAAAGGCAAAATATATAAAAAAAAATAAAAGAAAAAGAAG
*
9879 AAAAAATAAAAAATGAAGAGGCAAAA-ATATGAAAAAAAAATAAAAAGAAAAA
1 AAAAAATAAAAAATGAAAAGGCAAAATATAT-AAAAAAAAAT-AAAAGAAAAA
9931 ATTTATAGAA
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:10180 original size:23 final size:24
Alignment explanation
Indices: 10145--10194 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
10135 ATAAATAAAG
*
10145 AAAGAAAATTAAAGCA-AAAGAAA
1 AAAGAAAATTAAAGCACAAAAAAA
10168 AAAGATAAA-TAAAGCACAAAAAAA
1 AAAGA-AAATTAAAGCACAAAAAAA
10192 AAA
1 AAA
10195 ACAAAAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.76, C:0.06, G:0.10, T:0.08
Consensus pattern (24 bp):
AAAGAAAATTAAAGCACAAAAAAA
Found at i:11027 original size:22 final size:22
Alignment explanation
Indices: 10974--11027 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
10964 AGAAAAAATT
10974 AAATAAAATACCAAAAAAGGAAA
1 AAATAAAATA-CAAAAAAGGAAA
* *
10997 AAATAAAAATA-AACAAAGTAAGA
1 AAAT-AAAATACAAAAAAGGAA-A
11020 AAATAAAA
1 AAATAAAA
11028 ATTAGCGAAT
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:11602 original size:24 final size:23
Alignment explanation
Indices: 11574--11622 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
11564 ATGAAATTAT
11574 AAATAAAGA-AAGAAAATAAAAATA
1 AAATAAA-ATAAGAAAA-AAAAATA
*
11598 AAATAAAATAAGAAAAAAAAGTA
1 AAATAAAATAAGAAAAAAAAATA
11621 AA
1 AA
11623 GCAAAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (23 bp):
AAATAAAATAAGAAAAAAAAATA
Found at i:11954 original size:29 final size:28
Alignment explanation
Indices: 11901--11958 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 28
11891 AGGAAATTTG
11901 TGGAAAAAAAAAAGAAAAGACAAAAGATT
1 TGGAAAAAAAAAAGAAAAGACAAAA-ATT
* *
11930 TGGAATAAAAAACAGAAAA-ATAAAAATT
1 TGGAA-AAAAAAAAGAAAAGACAAAAATT
11958 T
1 T
11959 TTAAAACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 4 0.15
29 10 0.38
30 12 0.46
ACGTcount: A:0.67, C:0.03, G:0.14, T:0.16
Consensus pattern (28 bp):
TGGAAAAAAAAAAGAAAAGACAAAAATT
Found at i:12104 original size:20 final size:20
Alignment explanation
Indices: 12072--12111 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12062 TAGAAAAAAA
12072 TAAGAAAATAAAAAATAAAT
1 TAAGAAAATAAAAAATAAAT
*
12092 TAAGAGAAA-AAAAATTAAAT
1 TAAGA-AAATAAAAAATAAAT
12112 AAAATACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.20
Consensus pattern (20 bp):
TAAGAAAATAAAAAATAAAT
Found at i:12669 original size:13 final size:12
Alignment explanation
Indices: 12651--12710 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 12
12641 ATGAAATTAT
12651 AAATAAAGAAAGA
1 AAATAAA-AAAGA
12664 AAATAAAATAAGA
1 AAATAAAA-AAGA
12677 AAA-AAATTAAAGCA
1 AAATAAA--AAAG-A
*
12691 AAAGAAAAAAGA
1 AAATAAAAAAGA
12703 TAAATAAA
1 -AAATAAA
12711 GCACGAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
12 5 0.12
13 27 0.68
14 5 0.12
15 3 0.08
ACGTcount: A:0.77, C:0.02, G:0.10, T:0.12
Consensus pattern (12 bp):
AAATAAAAAAGA
Found at i:12676 original size:17 final size:17
Alignment explanation
Indices: 12651--12711 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
12641 ATGAAATTAT
12651 AAATAAAGAAAGAAAATA
1 AAATAAAGAAA-AAAATA
12669 AAAT-AAGAAAAAAATTA
1 AAATAAAGAAAAAAA-TA
12686 AAGCA-AAAGAAAAAAGAT-
1 AA--ATAAAGAAAAAA-ATA
12704 AAATAAAG
1 AAATAAAG
12712 CACGAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
16 5 0.14
17 14 0.38
18 6 0.16
19 11 0.30
20 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.11, T:0.11
Consensus pattern (17 bp):
AAATAAAGAAAAAAATA
Found at i:13181 original size:61 final size:59
Alignment explanation
Indices: 13132--13259 Score: 161
Period size: 61 Copynumber: 2.1 Consensus size: 59
13122 AAAAAGTTAT
** *
13132 TAAAAATTTACAAAGT-AAAA-AAAAGTTAGGGAATCAAAAAATATAAAAGGAAAAAAA
1 TAAAAATAAACAAAGTAAAAATAAAAATTAGGGAATCAAAAAATATAAAAGGAAAAAAA
*
13189 TAAAAATAAACAAAGTAAGAAAATAAAAATTAGGGAATCAAAAAATATAAAAAGACAAAATGAA
1 TAAAAATAAACAAAGT-A-AAAATAAAAATTAGGGAATCAAAAAATATAAAAGGA-AAAA--AA
13253 TAAAAAT
1 TAAAAAT
13260 TTCAAATATA
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
57 14 0.23
60 4 0.07
61 29 0.48
62 4 0.07
64 9 0.15
ACGTcount: A:0.68, C:0.04, G:0.11, T:0.17
Consensus pattern (59 bp):
TAAAAATAAACAAAGTAAAAATAAAAATTAGGGAATCAAAAAATATAAAAGGAAAAAAA
Found at i:13218 original size:23 final size:22
Alignment explanation
Indices: 13168--13218 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
13158 TAGGGAATCA
*
13168 AAAAATATAAAAGGAAAAAAAT
1 AAAAATAAAAAAGGAAAAAAAT
* *
13190 AAAAATAAACAAAGTAAGAAAAT
1 AAAAATAAA-AAAGGAAAAAAAT
13213 AAAAAT
1 AAAAAT
13219 TAGGGAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (22 bp):
AAAAATAAAAAAGGAAAAAAAT
Found at i:13421 original size:20 final size:19
Alignment explanation
Indices: 13396--13437 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
13386 AAAATATTTG
13396 AGAAAAAAATGAGAAAAA-GA
1 AGAAAAAAAT-A-AAAAATGA
13416 AGAAAAAAATAAAAAATGA
1 AGAAAAAAATAAAAAATGA
13435 AGA
1 AGA
13438 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:13431 original size:19 final size:20
Alignment explanation
Indices: 13396--13437 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
13386 AAAATATTTG
*
13396 AGAAAAAAATGAGAAAAAGA
1 AGAAAAAAATGAAAAAAAGA
*
13416 AGAAAAAAAT-AAAAAATGA
1 AGAAAAAAATGAAAAAAAGA
13435 AGA
1 AGA
13438 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:13468 original size:24 final size:25
Alignment explanation
Indices: 13441--13495 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
13431 ATGAAGAGGC
* *
13441 AAAAATATGAAA-TAAAACAAAAGA
1 AAAAATAAGAAATTAAAACAAAAAA
* *
13465 AAAATTAAGAAATTTTAAACAAAAAA
1 AAAAATAAGAAA-TTAAAACAAAAAA
13491 AAAAA
1 AAAAA
13496 GGACAAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 10 0.42
26 14 0.58
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (25 bp):
AAAAATAAGAAATTAAAACAAAAAA
Found at i:14183 original size:721 final size:703
Alignment explanation
Indices: 12771--14129 Score: 1621
Period size: 721 Copynumber: 1.9 Consensus size: 703
12761 TAAGAAAATG
*
12771 AAAAAGGACAAAAATTGAATAAAAATTTCAAAAATGAAATGGAATGACAAAATGAAAAAAAAAAT
1 AAAAAGGACAAAAATTGAATAAAAATTTCAAAAATGAAATGGAACGACAAAATGAAAAAAAAAAT
* * *
12836 TAGTTTAAAAAATACAAAAATTAAAAAACATATAAGACCAAACAATCTAAAAAGTCTGACAAAAA
66 TAGTTTAAAAAAGACAAAAATTAAAAAACATATAAGACCAAACAATATAAAAAGTCAGACAAAAA
*
12901 ATTAAAAAAGAGAAAAGTTAATGCAAAATTAAAAAAAAAAGTATGAGAATTTAAAAACGCAAATA
131 ATTAAAAAAGAGAAAAGTTAATGC-AAA-TAAAAAAAAAAGTATGAGAATTTAAAAACACAAATA
*
12966 AGAAATGAAAGGAAATTTGTGGAAAAAAAAGAAAAGACAAAAGATTTGGAATAAAAAGAGAAAAA
194 AGAAATGAAAGGAAATGTGTGGAAAAAAAAGAAAAGACAAAAGATTTGGAATAAAAAGAGAAAAA
13031 TAAAAATTTTTAAAACAACGAAAAAATCAAAAAAAGTAAAAATGAAAACATATGAAAAAAAAAAA
259 TAAAAATTTTTAAAACAACGAAAAAATCAAAAAAAGTAAAAATGAAAACATATG--AAAAAAAAA
* * *
13096 GCAAAAAGAAGGAAAATTGCAAAGGGAAAAAGTTATTAAAAATTTACAAAGTAAAAAAAAGTTAG
322 GCAAAAAGAAGGAAAATTGCAAAGGAAAAAAGTTATTAAAAAATTACAAAGTAAAAAAAAATTAG
* * * * *
13161 GGAATCAAAAAATATAAAAGGAAAAAAATAAAAATAAACAAAGTAAGAAAATAAAAATTAGGGAA
387 CGAATAAAAAAATAAAAAAGAAAAAAAATAAAAATAAACAAAGTAAGAAAATAAAAATTAGCGAA
*
13226 TCAAAAAATATAAAAAGACAAAATGAATAAAAATTTCAAATATAAAAAGAAAGTGCACAAAAAAA
452 GCAAAAAATATAAAAAGACAAAATGAATAAAAATTTCAAATAT---AAGAAAGTG----AAAAAA
* * * * * **
13291 GAAGTTTGAGGTTTTAAATTACAAAGAAGAATAAAAAAAGGTGTGAACAAAAAGATTTAAGAAAA
510 GAACTTTGAGGTTTTAAATTACAAAGAAAAACAAAAAAA-----GAAAAAAAAAATAGAAGAAAA
* * *
13356 AAATAACAAATGAAAATACAAAATATATAAAAAATATTTGAGAAAAAAATGAGAAAAAGAAGAAA
570 AAATAACAAATGAAAATACAAAATAAATAAAAAATATGTGACAAAAAAATGAGAAAAAGAAGAAA
**
13421 AAAATAAAAAATGAAGAGGCAAAAATATGAAATAAAACAAAAGAAAAATTAAGAAATTTTAAACA
635 AAAATAAAAAATGAAGAAACAAAAATA-GAAATAAAACAAAAGAAAAATTAAGAAATTTTAAACA
13486 AAAAA
699 AAAAA
13491 AAAAAGGACAAAAATTGAAATAAAAATTTCAAAAATGAAATGGAACGACAAAATG-AAAAAAAAA
1 AAAAAGGACAAAAATTG-AATAAAAATTTCAAAAATGAAATGGAACGACAAAATGAAAAAAAAAA
* * * *
13555 -TAGTTTAAAAAAGACAAAAAAAATT-GAAAACGTATAAGTCCTAACAATATAAAAAGTCAGACA
65 TTAGTTTAAAAAAGAC---AAAAATTAAAAAACATATAAGACCAAACAATATAAAAAGTCAGACA
*
13618 AAAAATTTAAAAAAGAGAAAAGTTAATGC-AA-AAAAAAAAAAGTATGAGAATTTAAAAATACAA
127 AAAAA-TTAAAAAAGAGAAAAGTTAATGCAAATAAAAAAAAAAGTATGAGAATTTAAAAACACAA
13681 ATAAGAAATGAAAAGGAAATGTGTGGAAAAAAAAAGAGAAGCAAGAAAAGACAAAAGATTTGGAA
191 ATAAGAAATG-AAAGGAAATGTGTGG------AAA-A-AA--AAGAAAAGACAAAAGATTTGGAA
* * ** *
13746 TAAAAAATAGAAAAATTAAAAA-TTTT-AAACAACGAAAAAAT-TAAACCAGTAAAAATGAAAGC
245 T-AAAAAGAGAAAAA-TAAAAATTTTTAAAACAACGAAAAAATCAAAAAAAGTAAAAATGAAAAC
**
13808 ATATG-AAAAAAAAGCAAAAAGAAGGAAAATTGTGAAGGAAAAAAGTTATTAAAAAATTACAAAG
308 ATATGAAAAAAAAAGCAAAAAGAAGGAAAATTGCAAAGGAAAAAAGTTATTAAAAAATTACAAAG
13872 TTGAAAAAAAATAAATTAAGCGAA-AAAATTAAATAAAATACCCAGAAAGGAAAAATAAAAATAA
373 -T---AAAAAA-AAATT-AGCGAATAAAA--AAATAAAA-A---AGAAA--AAAAATAAAAATAA
13936 ACAAAGTAAGAAAATAAAAAATTAGCGAAGCAAAAAAATATAAAAAGAC-AAATGAATAAAAATT
424 ACAAAGTAAGAAAAT-AAAAATTAGCGAAGC-AAAAAATATAAAAAGACAAAATGAATAAAAATT
* * *
14000 TCAAATAT-A-AAA-TG-GAAAA-AACTTTTA-G-TTTAGAATGTAGAAAGAAAAACAAAAAAA-
487 TCAAATATAAGAAAGTGAAAAAAGAACTTTGAGGTTTTA-AAT-TACAAAGAAAAACAAAAAAAG
*
14057 AAAAAAAAAATAGAGGAAAAAGATATAA-AATATGAAAGATGA-AAAATAAAATAAAAGAA-A-G
550 AAAAAAAAAATAGAAGAAAAA-A-ATAACAA-ATGAAA-AT-ACAAAAT-AAATAAAA-AATATG
14118 TGCACAAAAAAA
608 TG-ACAAAAAAA
14130 GAAGTTTGAG
Statistics
Matches: 554, Mismatches: 41, Indels: 83
0.82 0.06 0.12
Matches are distributed among these distances:
718 40 0.07
719 28 0.05
720 28 0.05
721 89 0.16
722 33 0.06
723 10 0.02
724 9 0.02
725 79 0.14
726 8 0.01
727 25 0.05
728 26 0.05
729 45 0.08
730 23 0.04
731 11 0.02
732 7 0.01
733 3 0.01
734 3 0.01
735 1 0.00
736 4 0.01
738 29 0.05
739 36 0.06
740 17 0.03
ACGTcount: A:0.65, C:0.05, G:0.13, T:0.17
Consensus pattern (703 bp):
AAAAAGGACAAAAATTGAATAAAAATTTCAAAAATGAAATGGAACGACAAAATGAAAAAAAAAAT
TAGTTTAAAAAAGACAAAAATTAAAAAACATATAAGACCAAACAATATAAAAAGTCAGACAAAAA
ATTAAAAAAGAGAAAAGTTAATGCAAATAAAAAAAAAAGTATGAGAATTTAAAAACACAAATAAG
AAATGAAAGGAAATGTGTGGAAAAAAAAGAAAAGACAAAAGATTTGGAATAAAAAGAGAAAAATA
AAAATTTTTAAAACAACGAAAAAATCAAAAAAAGTAAAAATGAAAACATATGAAAAAAAAAGCAA
AAAGAAGGAAAATTGCAAAGGAAAAAAGTTATTAAAAAATTACAAAGTAAAAAAAAATTAGCGAA
TAAAAAAATAAAAAAGAAAAAAAATAAAAATAAACAAAGTAAGAAAATAAAAATTAGCGAAGCAA
AAAATATAAAAAGACAAAATGAATAAAAATTTCAAATATAAGAAAGTGAAAAAAGAACTTTGAGG
TTTTAAATTACAAAGAAAAACAAAAAAAGAAAAAAAAAATAGAAGAAAAAAATAACAAATGAAAA
TACAAAATAAATAAAAAATATGTGACAAAAAAATGAGAAAAAGAAGAAAAAAATAAAAAATGAAG
AAACAAAAATAGAAATAAAACAAAAGAAAAATTAAGAAATTTTAAACAAAAAA
Found at i:14219 original size:22 final size:21
Alignment explanation
Indices: 14194--14234 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
14184 AGATTTAAGA
14194 AAAAAATAAAAAATGAAAATGC
1 AAAAAATAAAAAAT-AAAATGC
* *
14216 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
14235 TGAGAAAAAG
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:14810 original size:26 final size:26
Alignment explanation
Indices: 14781--14833 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
14771 AGGAAATTTA
14781 TGGAA-AAAAAAAAGAAAAGACAAAAT
1 TGGAATAAAAAAAAGAAAA-ACAAAAT
* *
14807 TGGAATAAAAAATAGAAAAATAAAAT
1 TGGAATAAAAAAAAGAAAAACAAAAT
14833 T
1 T
14834 TTTAAAACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.70, C:0.02, G:0.13, T:0.15
Consensus pattern (26 bp):
TGGAATAAAAAAAAGAAAAACAAAAT
Found at i:15397 original size:22 final size:22
Alignment explanation
Indices: 15344--15397 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
15334 GAGAAAAATT
15344 AAATAAAATACCAAAAAAGGAAA
1 AAATAAAATA-CAAAAAAGGAAA
* *
15367 AAATAAAAATA-AACAAAGTAAGA
1 AAAT-AAAATACAAAAAAGGAA-A
15390 AAATAAAA
1 AAATAAAA
15398 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:15981 original size:27 final size:27
Alignment explanation
Indices: 15930--15999 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
15920 TGGAAATTAT
* *
15930 AAATAAGAAAGAAAA-TAAAATAAAATA
1 AAATAAGAAA-AAAAGTAAAACAAAAGA
*
15957 AAATAAGAAAAAAAGTAAAGCAAAAGA
1 AAATAAGAAAAAAAGTAAAACAAAAGA
15984 AAA-AAGATAAATAAAG
1 AAATAAGA-AAA-AAAG
16000 CACAAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 8 0.22
27 25 0.68
28 4 0.11
ACGTcount: A:0.76, C:0.01, G:0.11, T:0.11
Consensus pattern (27 bp):
AAATAAGAAAAAAAGTAAAACAAAAGA
Found at i:16445 original size:17 final size:18
Alignment explanation
Indices: 16401--16447 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
16391 AAGAAATTAC
16401 AAAGTAGAAAAAAATAAGA
1 AAAG-AGAAAAAAATAAGA
*
16420 AAATA-AAAAAAATAA-A
1 AAAGAGAAAAAAATAAGA
*
16436 TAAGAGAAAAAA
1 AAAGAGAAAAAA
16448 TTAGCGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 1 0.04
19 3 0.12
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAGAGAAAAAAATAAGA
Found at i:16704 original size:22 final size:21
Alignment explanation
Indices: 16679--16719 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
16669 AGATTGAACA
16679 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
16701 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
16720 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:17389 original size:17 final size:17
Alignment explanation
Indices: 17367--17417 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
17357 ATAAAAATTT
*
17367 TTAAAACAACGAAAAAA
1 TTAAAACAAAGAAAAAA
*
17384 TTAAAA-AAAGTAAAAA
1 TTAAAACAAAGAAAAAA
* *
17400 TGAAAACATATGAAAAAA
1 TTAAAACA-AAGAAAAAA
17418 AAAAGCAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 13 0.48
17 7 0.26
18 7 0.26
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.16
Consensus pattern (17 bp):
TTAAAACAAAGAAAAAA
Found at i:17514 original size:735 final size:731
Alignment explanation
Indices: 16980--18350 Score: 1720
Period size: 740 Copynumber: 1.8 Consensus size: 731
16970 TGAAATTATG
* * *
16980 AATAAAGAAAGAAAAT-A-AAATAAGAA-AAAAAATTAAAGCAA-AAGA-AAAAAGAT-AGATAA
1 AATAAAGAAA-AAAATGAGAAA-AAGAAGAAAAAAATAAA-AAAGAAGAGAAAAAGATGAAATAA
17039 AGCACGAAAAAAGAAAAAAAA-ACAAA-AATACAACAAAAAATTATAAAAAGTAAGAAAATGAAA
63 A--AC--AAAAAGAAAAAAAATACAAATAATA-AACAAAAAA--A-AAAAA-T---AAAA--AAA
17102 AAGGACAAAAATTGAATAAAAATTTCAAAAATGAAATGGAATGACAAAATGAAAAAAAAATTAGT
114 AAGGACAAAAATTGAATAAAAATTTCAAAAATGAAATGGAATGACAAAATGAAAAAAAAA--AGT
* *
17167 TTAAAAA-AACAAAAAATTAAAAAACATATAAGACCAAACAATCTAAAAAGTCTGAC-AAAAATT
177 TTAAAAACAA-AAAAAATTAAAAAACATATAAGACCAAACAATATAAAAAGTCAGACAAAAAATT
*
17230 AAAAAA-AGAAAAGTTAATGCAAAATAAAAAAAAAAAGTATGAGAATTTAAAAACGCAAATAAGA
241 AAAAAAGAAAAAAGTTAATGCAAAAT---AAAAAAAAGTATGAGAATTTAAAAACGCAAATAAGA
*
17294 AATGAAAGGAAATTTGTGG-AAAA-A-AA-AAGAAAAGACAAAAGATTTGGAATAAAAAAGAGAA
303 AATGAAAGGAAATGTGTGGAAAAAGAGAACAAGAAAAGACAAAAGATTTGGAATAAAAAAGAGAA
17355 AAATAAAAATTTTTAAAACAACGAAAAAATTAAAAAAAGTAAAAATGAAAACATATGAAAAAAAA
368 AAATAAAAATTTTTAAAACAACGAAAAAATTAAAAAAAGTAAAAATGAAAACATATG--AAAAAA
*
17420 AAGCAAAAAGAAGGAAAATTGCAAAGGGAAAAAGTTATTAAAAATTTACAAAG-TAAAAAAAAAT
431 AAGCAAAAAGAAGGAAAATTGCAAAGGGAAAAAGTTATTAAAAAATTACAAAGTTAAAAAAAAAT
* * * *
17484 TAGGGAATCAAAAAATATAAAAGGAAAAAAATAAAAATAAACAAAGTAAGAAAATAAAAAATTAG
496 TAGGGAATCAAAAAATATAAAAAGAAAAAAATAAAAATAAACAAAGTAAGAAAACAAAAAATAAC
* *
17549 GGAATCAAAAAATATAAAAAGACAAAATGAATAAAAATTTCAAATATAAAAAGAAAGTGCACAAA
561 GGAATCAAAAAATATAAAAAGACAAAATGAATAAAAATGTCAAATATAAAAAGAAAATGCACAAA
** * * * ** **
17614 AAAAGAAGTTTGAGGTTTTAAAATTACAAAGAAGAAATAAAAAAAGGTGTGAACAAAAAGATTTA
626 AAAAGAAGTTTGAAATTATAAAAATACAAAGAAGAAATAAAAAAAGATAAGAACAAAAAGATAGA
*
17679 AGAAAAAAATAACAAATGAAAATACAAAATATATAAAAAAAT
691 AAAAAAAAATAACAAA-GAAAATACAAAATATATAAAAAAAT
* ** *
17721 ATTTGAGAAAAAAATGAGAAAAAGAAGAAAAAAATAAAAAATGAAGAGGCAAAAATATGAAATAA
1 AATAAAGAAAAAAATGAGAAAAAGAAGAAAAAAATAAAAAA-GAAGA-G-AAAAAGATGAAATAA
* ** * *
17786 AACAAAAAGAAAAAAAATAGAAATTTTAAACAAAGAAAAAAAATACAAAAAAAGGACAAAAATTG
63 AACAAAAAGAAAAAAAATACAAATAATAAACAAAAAAAAAAAATAAAAAAAAAGGACAAAAATTG
17851 AATAAAAATTTCAAAAATGAAATGGAATGACAAAATGAAAAAAAAAAGTTTAAAAACAAAAAAAA
128 AATAAAAATTTCAAAAATGAAATGGAATGACAAAATGAAAAAAAAAAGTTTAAAAACAAAAAAAA
* * *
17916 TTGAAAAACATATAAGTCCTAACAATATAAAAAGTCAGACAAAAAATTAAAAAAGAAAAAAGTTA
193 TTAAAAAACATATAAGACCAAACAATATAAAAAGTCAGACAAAAAATTAAAAAAGAAAAAAGTTA
*
17981 ATGCAAAATAAAAAAAAGTATGAGAATTTAAAAATGCAAATAAGAAATGAAAGGAAATGTGTGGA
258 ATGCAAAATAAAAAAAAGTATGAGAATTTAAAAACGCAAATAAGAAATGAAAGGAAATGTGTGG-
*
18046 AAAAAAAGAGAAGCAAGAAAAGACAAAAGATTTGGAATAAAAAATAGAAAAATAAAAATTTTTAA
322 --AAAAAGAGAA-CAAGAAAAGACAAAAGATTTGGAATAAAAAAGAGAAAAATAAAAATTTTTAA
** *
18111 AACAACGAAAAAATTAAAACCAGTAAAAATGAAAGCATATGAAAAAAAAGCAAAAAGAAGGAAAA
384 AACAACGAAAAAATTAAAAAAAGTAAAAATGAAAACATATGAAAAAAAAGCAAAAAGAAGGAAAA
** * *
18176 TTGTGAAGGGAAAAAGTTATTAAAAAATTACAAAGTTGAAAAAAAATAAATTAAGCGAA-AAAAT
449 TTGCAAAGGGAAAAAGTTATTAAAAAATTACAAAGTT---AAAAAA-AAATT-AGGGAATCAAA-
* *
18240 TAAATA-AAATACCCAGAAAGGAAAAATAAAAATAAACAAAGTAAGAAAATAAAAAATTA-GCGA
508 -AAATATAAA-A---AG-AA--AAAAATAAAAATAAACAAAGTAAGAAAACAAAAAATAACG-GA
* *
18303 AGCAAAAAAATATAAAAAGAC-AAATGAATAAAAATTTCAAATATAAAA
564 ATC-AAAAAATATAAAAAGACAAAATGAATAAAAATGTCAAATATAAAA
18351 TGGAAAAAAC
Statistics
Matches: 560, Mismatches: 31, Indels: 68
0.85 0.05 0.10
Matches are distributed among these distances:
732 53 0.09
733 51 0.09
734 15 0.03
735 81 0.14
736 4 0.01
737 4 0.01
738 58 0.10
739 1 0.00
740 94 0.17
741 20 0.04
742 20 0.04
743 26 0.05
744 20 0.04
745 10 0.02
746 7 0.01
747 6 0.01
748 1 0.00
749 2 0.00
750 1 0.00
751 69 0.12
752 17 0.03
ACGTcount: A:0.66, C:0.05, G:0.12, T:0.17
Consensus pattern (731 bp):
AATAAAGAAAAAAATGAGAAAAAGAAGAAAAAAATAAAAAAGAAGAGAAAAAGATGAAATAAAAC
AAAAAGAAAAAAAATACAAATAATAAACAAAAAAAAAAAATAAAAAAAAAGGACAAAAATTGAAT
AAAAATTTCAAAAATGAAATGGAATGACAAAATGAAAAAAAAAAGTTTAAAAACAAAAAAAATTA
AAAAACATATAAGACCAAACAATATAAAAAGTCAGACAAAAAATTAAAAAAGAAAAAAGTTAATG
CAAAATAAAAAAAAGTATGAGAATTTAAAAACGCAAATAAGAAATGAAAGGAAATGTGTGGAAAA
AGAGAACAAGAAAAGACAAAAGATTTGGAATAAAAAAGAGAAAAATAAAAATTTTTAAAACAACG
AAAAAATTAAAAAAAGTAAAAATGAAAACATATGAAAAAAAAGCAAAAAGAAGGAAAATTGCAAA
GGGAAAAAGTTATTAAAAAATTACAAAGTTAAAAAAAAATTAGGGAATCAAAAAATATAAAAAGA
AAAAAATAAAAATAAACAAAGTAAGAAAACAAAAAATAACGGAATCAAAAAATATAAAAAGACAA
AATGAATAAAAATGTCAAATATAAAAAGAAAATGCACAAAAAAAGAAGTTTGAAATTATAAAAAT
ACAAAGAAGAAATAAAAAAAGATAAGAACAAAAAGATAGAAAAAAAAAATAACAAAGAAAATACA
AAATATATAAAAAAAT
Found at i:17519 original size:23 final size:24
Alignment explanation
Indices: 17493--17545 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
17483 TTAGGGAATC
*
17493 AAAAAATATA-AAAGGAAAAAAAT
1 AAAAAATAAACAAAGGAAAAAAAT
* *
17516 -AAAAATAAACAAAGTAAGAAAAT
1 AAAAAATAAACAAAGGAAAAAAAT
17539 AAAAAAT
1 AAAAAAT
17546 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:17751 original size:20 final size:19
Alignment explanation
Indices: 17726--17767 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
17716 AAAATATTTG
17726 AGAAAAAAATGAGAAAAA-GA
1 AGAAAAAAAT-A-AAAAATGA
17746 AGAAAAAAATAAAAAATGA
1 AGAAAAAAATAAAAAATGA
17765 AGA
1 AGA
17768 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:17761 original size:19 final size:20
Alignment explanation
Indices: 17726--17767 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
17716 AAAATATTTG
*
17726 AGAAAAAAATGAGAAAAAGA
1 AGAAAAAAATGAAAAAAAGA
*
17746 AGAAAAAAAT-AAAAAATGA
1 AGAAAAAAATGAAAAAAAGA
17765 AGA
1 AGA
17768 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:17801 original size:27 final size:25
Alignment explanation
Indices: 17771--17830 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
17761 ATGAAGAGGC
17771 AAAAATATGAAA-TAAAACAAAAAGAAA
1 AAAAATA-GAAATTAAAAC--AAAGAAA
*
17798 AAAAATAGAAATTTTAAACAAAGAAA
1 AAAAATAGAAA-TTAAAACAAAGAAA
17824 AAAAATA
1 AAAAATA
17831 CAAAAAAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 18 0.60
27 7 0.23
28 5 0.17
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (25 bp):
AAAAATAGAAATTAAAACAAAGAAA
Found at i:17913 original size:18 final size:17
Alignment explanation
Indices: 17890--17925 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17880 ACAAAATGAA
*
17890 AAAAAAAAGTTTAAAAAC
1 AAAAAAAA-TTGAAAAAC
17908 AAAAAAAATTGAAAAAC
1 AAAAAAAATTGAAAAAC
17925 A
1 A
17926 TATAAGTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAAAAAATTGAAAAAC
Found at i:18556 original size:22 final size:21
Alignment explanation
Indices: 18531--18571 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
18521 AGATTTAAGA
18531 AAAAAATAAAAAATGAAAATGC
1 AAAAAATAAAAAAT-AAAATGC
* *
18553 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
18572 TGAGAAAAAG
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:20318 original size:16 final size:17
Alignment explanation
Indices: 20295--20334 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
20285 TATAATAAAG
20295 AAAG-AAAATAA-AAATA
1 AAAGTAAAATAAGAAA-A
20311 AAA-TAAAATAAGAAAA
1 AAAGTAAAATAAGAAAA
20327 AAAGTAAA
1 AAAGTAAA
20335 GCAAAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (17 bp):
AAAGTAAAATAAGAAAA
Found at i:20358 original size:21 final size:19
Alignment explanation
Indices: 20332--20396 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 19
20322 GAAAAAAAGT
20332 AAAGCAAAAGAAAAAGATAAA
1 AAAGCAAAA-AAAAA-ATAAA
*
20353 AAAGCACAAAAAAAAACAAA
1 AAAGCA-AAAAAAAAATAAA
*
20373 AAA-AAAAACAAAAAATATAA
1 AAAGCAAAA-AAAAAATA-AA
20393 AAAG
1 AAAG
20397 TAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 3 0.08
19 8 0.22
20 12 0.32
21 11 0.30
22 3 0.08
ACGTcount: A:0.80, C:0.08, G:0.08, T:0.05
Consensus pattern (19 bp):
AAAGCAAAAAAAAAATAAA
Found at i:20379 original size:12 final size:12
Alignment explanation
Indices: 20350--20387 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
20340 AGAAAAAGAT
* *
20350 AAAAAAGCACAA
1 AAAAAAACAAAA
20362 AAAAAAACAAAA
1 AAAAAAACAAAA
20374 AAAAAAACAAAA
1 AAAAAAACAAAA
20386 AA
1 AA
20388 TATAAAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAA
Done.