Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168464.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_674, 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: 14073
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19
Found at i:436 original size:27 final size:27
Alignment explanation
Indices: 406--475 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
396 AAGTTAATAC
*
406 AAAATAAATAAAAGAAAACAAGAAAAA
1 AAAAAAAATAAAAGAAAACAAGAAAAA
* *
433 AAAAGAAATGAGAA-AAAACAAGAAAAA
1 AAAAAAAAT-AAAAGAAAACAAGAAAAA
*
460 AATAAAAAATGAAAGA
1 AA-AAAAAATAAAAGA
476 CAAAAACATG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 25 0.71
28 10 0.29
ACGTcount: A:0.79, C:0.03, G:0.11, T:0.07
Consensus pattern (27 bp):
AAAAAAAATAAAAGAAAACAAGAAAAA
Found at i:780 original size:29 final size:29
Alignment explanation
Indices: 748--809 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
738 AAAAAGTAAG
748 AAAATGAAAA-AAAAAAAAAAAAACGAAT
1 AAAATGAAAACAAAAAAAAAAAAACGAAT
** *
776 CAAAA-GAAAACAATTAAAAAAAAATGAAT
1 -AAAATGAAAACAAAAAAAAAAAAACGAAT
805 AAAAT
1 AAAAT
810 TTTCAAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.77, C:0.05, G:0.06, T:0.11
Consensus pattern (29 bp):
AAAATGAAAACAAAAAAAAAAAAACGAAT
Found at i:799 original size:14 final size:15
Alignment explanation
Indices: 762--808 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
752 TGAAAAAAAA
762 AAAAAAAAACGAATC
1 AAAAAAAAACGAATC
* *
777 AAAAGAAAAC-AATT
1 AAAAAAAAACGAATC
*
791 AAAAAAAAATGAAT-
1 AAAAAAAAACGAATC
805 AAAA
1 AAAA
809 TTTTCAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (15 bp):
AAAAAAAAACGAATC
Found at i:1894 original size:17 final size:16
Alignment explanation
Indices: 1860--1914 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1850 AAGTGGAAAA
1860 AAAAAAAAGAAACAAG
1 AAAAAAAAGAAACAAG
**
1876 AAATAAAAAGAAATGAG
1 AAA-AAAAAGAAACAAG
* * *
1893 AAAAACAAGAAAAAAT
1 AAAAAAAAGAAACAAG
1909 AAAAAA
1 AAAAAA
1915 TGAAAGACAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.80, C:0.04, G:0.11, T:0.05
Consensus pattern (16 bp):
AAAAAAAAGAAACAAG
Found at i:1904 original size:26 final size:25
Alignment explanation
Indices: 1869--1951 Score: 78
Period size: 30 Copynumber: 3.1 Consensus size: 25
1859 AAAAAAAAAG
1869 AAACAAGAAATAAAAAGAAATGAGAA
1 AAACAAGAAATAAAAAGAAA-GAGAA
*
1895 AAACAAGAAAAAATAAAAAATGAAAGACAA
1 AAACAAG---AAAT-AAAAA-GAAAGAGAA
* *
1925 AAACATGAAAT-AAAACAAAGAGAA
1 AAACAAGAAATAAAAAGAAAGAGAA
1949 AAA
1 AAA
1952 AGTTTATAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
24 10 0.21
25 4 0.08
26 7 0.15
27 4 0.08
29 4 0.08
30 15 0.31
31 4 0.08
ACGTcount: A:0.75, C:0.06, G:0.12, T:0.07
Consensus pattern (25 bp):
AAACAAGAAATAAAAAGAAAGAGAA
Found at i:1919 original size:24 final size:23
Alignment explanation
Indices: 1855--1924 Score: 65
Period size: 26 Copynumber: 3.0 Consensus size: 23
1845 CAAGGAAGTG
1855 GAAAAAAAAAAAA-G--AAACAA
1 GAAAAAAAAAAAATGAAAAACAA
*
1875 GAAATAAAAAGAAATGAGAAAAACAA
1 GAAA-AAAAAAAAAT--GAAAAACAA
*
1901 GAAAAAATAAAAAATGAAAGACAA
1 GAAAAAA-AAAAAATGAAAAACAA
1925 AAACATGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
20 4 0.10
21 8 0.20
24 9 0.22
25 3 0.08
26 16 0.40
ACGTcount: A:0.77, C:0.04, G:0.13, T:0.06
Consensus pattern (23 bp):
GAAAAAAAAAAAATGAAAAACAA
Found at i:1926 original size:29 final size:26
Alignment explanation
Indices: 1869--1951 Score: 73
Period size: 26 Copynumber: 3.1 Consensus size: 26
1859 AAAAAAAAAG
*
1869 AAACAAGAAATAAAAAGAAATGAGAA
1 AAACAAGAAATAAAAAAAAATGAGAA
1895 AAACAAGAAA-AAATAAAAAATGAAAGACAA
1 AAACAAGAAATAAA-AAAAAATG--AG--AA
* *
1925 AAACATGAAAT-AAAACAAA-GAGAA
1 AAACAAGAAATAAAAAAAAATGAGAA
1949 AAA
1 AAA
1952 AGTTTATAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
24 5 0.10
25 3 0.06
26 19 0.40
28 3 0.06
29 5 0.10
30 13 0.27
ACGTcount: A:0.75, C:0.06, G:0.12, T:0.07
Consensus pattern (26 bp):
AAACAAGAAATAAAAAAAAATGAGAA
Found at i:2228 original size:28 final size:28
Alignment explanation
Indices: 2175--2256 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 28
2165 AAATAAACAA
* * *
2175 AAAACAAAATAGAAAAA-GTAAGAAAATG
1 AAAACAAAAAAAAAAAACG-AATAAAATG
2203 AAAA-AAAAAAAAAAAACGAATCAAAA-G
1 AAAACAAAAAAAAAAAACGAAT-AAAATG
** *
2230 AAAACAATTAAAAAAAATGAATAAAAT
1 AAAACAAAAAAAAAAAACGAATAAAAT
2257 TTTCAAAATG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
27 21 0.48
28 23 0.52
ACGTcount: A:0.76, C:0.05, G:0.09, T:0.11
Consensus pattern (28 bp):
AAAACAAAAAAAAAAAACGAATAAAATG
Found at i:2721 original size:16 final size:17
Alignment explanation
Indices: 2685--2725 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
2675 ATAAAGAATC
2685 TTAAAACAAAGAAAAAA
1 TTAAAACAAAGAAAAAA
*
2702 TTAAAACAAA-AAATAA
1 TTAAAACAAAGAAAAAA
2718 TTAAAACA
1 TTAAAACA
2726 TATGAACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.17
Consensus pattern (17 bp):
TTAAAACAAAGAAAAAA
Found at i:2917 original size:17 final size:17
Alignment explanation
Indices: 2897--2943 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
2887 AAAAGCAATT
2897 AAAAATAAACAAAA-ACA
1 AAAAATAAA-AAAAGACA
2914 AAAAATAAAAAAAGACA
1 AAAAATAAAAAAAGACA
**
2931 AAATTTAAAAAAA
1 AAAAATAAAAAAA
2944 TGAAAAGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.81, C:0.06, G:0.02, T:0.11
Consensus pattern (17 bp):
AAAAATAAAAAAAGACA
Found at i:3207 original size:35 final size:33
Alignment explanation
Indices: 3148--3224 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
3138 AGATATGAAA
* *
3148 TAAAACAAAGAGAAAAAACAAAATACATAAAATTT
1 TAAAACAAACAGAAAAAACAAAAT--AGAAAATTT
* *
3183 TACAACAAACA-AAAAAATAGAAATAGAAAATTT
1 TAAAACAAACAGAAAAAACA-AAATAGAAAATTT
3216 TAAAACAAA
1 TAAAACAAA
3225 AATAGTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 16 0.44
34 7 0.19
35 13 0.36
ACGTcount: A:0.69, C:0.09, G:0.05, T:0.17
Consensus pattern (33 bp):
TAAAACAAACAGAAAAAACAAAATAGAAAATTT
Found at i:3567 original size:16 final size:17
Alignment explanation
Indices: 3532--3570 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3522 AAATATTAAT
3532 ATAAAAGACAAAATAAA
1 ATAAAAGACAAAATAAA
* *
3549 ATAAAATACTAAA-AAA
1 ATAAAAGACAAAATAAA
3565 ATAAAA
1 ATAAAA
3571 AAGTATGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (17 bp):
ATAAAAGACAAAATAAA
Found at i:4257 original size:7 final size:7
Alignment explanation
Indices: 4247--4348 Score: 60
Period size: 7 Copynumber: 12.7 Consensus size: 7
4237 ATAAAATACA
4247 AAAAAAT
1 AAAAAAT
4254 AAAAAAT
1 AAAAAAT
4261 AGAACAAAT
1 A-AA-AAAT
4270 AATAAGAAAT
1 -A-AA-AAAT
4280 AAAGAAAT
1 AAA-AAAT
4288 AAAAAAT
1 AAAAAAT
* *
4295 CAAAGAT
1 AAAAAAT
4302 AAAAAATT
1 AAAAAA-T
*
4310 AAAAGAAG
1 AAAA-AAT
4318 AAAAAAGT
1 AAAAAA-T
4326 CAATACAAAAT
1 --A-A-AAAAT
4337 AAAAAAT
1 AAAAAAT
4344 AAAAA
1 AAAAA
4349 CAAAAGAAGG
Statistics
Matches: 77, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
7 33 0.43
8 22 0.29
9 8 0.10
10 8 0.10
11 2 0.03
12 4 0.05
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:4279 original size:19 final size:18
Alignment explanation
Indices: 4239--4293 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 18
4229 ATTAGTTTAT
4239 AAAATACAA-AAA-AATAA
1 AAAATA-AACAAATAATAA
4256 AAAATAGAACAAATAATAA
1 AAAATA-AACAAATAATAA
* *
4275 GAAATAAAGAAATAA-AA
1 AAAATAAACAAATAATAA
4292 AA
1 AA
4294 TCAAAGATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 11 0.34
18 11 0.34
19 10 0.31
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.13
Consensus pattern (18 bp):
AAAATAAACAAATAATAA
Found at i:4307 original size:16 final size:15
Alignment explanation
Indices: 4250--4308 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 15
4240 AAATACAAAA
*
4250 AAATAAAAAATAGAAC
1 AAATAAAAAATA-AAG
4266 AAATAATAAGAAATAAAG
1 AAAT-A-AA-AAATAAAG
4284 AAATAAAAAATCAAAG
1 AAATAAAAAAT-AAAG
4300 --ATAAAAAAT
1 AAATAAAAAAT
4309 TAAAAGAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 9 0.24
15 4 0.11
16 10 0.26
17 2 0.05
18 8 0.21
19 5 0.13
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (15 bp):
AAATAAAAAATAAAG
Found at i:5658 original size:19 final size:19
Alignment explanation
Indices: 5637--5672 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5627 TATTAACAAA
5637 AAAAGCAA-TAAAAATAAG
1 AAAAGCAATTAAAAATAAG
5655 AAAAGCAATTAAAAATAA
1 AAAAGCAATTAAAAATAA
5673 ACAAAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.14
Consensus pattern (19 bp):
AAAAGCAATTAAAAATAAG
Found at i:5770 original size:19 final size:18
Alignment explanation
Indices: 5724--5767 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
5714 ACGAATCAAC
*
5724 AAAATAATAAAAAAAGAC
1 AAAATAATAAAAAAAGAA
**
5742 AAAATGAATAAAAAATTAA
1 AAAAT-AATAAAAAAAGAA
5761 AAAATAA
1 AAAATAA
5768 ATAGGAATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAATAATAAAAAAAGAA
Found at i:6135 original size:15 final size:16
Alignment explanation
Indices: 6117--6146 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6107 AATAAAGTAC
6117 TAAAAAAAGA-AAAAG
1 TAAAAAAAGACAAAAG
6132 TAAAAAAAGACAAAA
1 TAAAAAAAGACAAAA
6147 ATGGAAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (16 bp):
TAAAAAAAGACAAAAG
Found at i:6664 original size:17 final size:16
Alignment explanation
Indices: 6630--6684 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
6620 AGTGGAAAAA
6630 AAAAAAAAGAAACAAG
1 AAAAAAAAGAAACAAG
**
6646 AAATAAAAAGAAATGAG
1 AAA-AAAAAGAAACAAG
* * *
6663 AAAAACAAGAAAAAAT
1 AAAAAAAAGAAACAAG
6679 AAAAAA
1 AAAAAA
6685 TGAAAGACAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.80, C:0.04, G:0.11, T:0.05
Consensus pattern (16 bp):
AAAAAAAAGAAACAAG
Found at i:6684 original size:30 final size:29
Alignment explanation
Indices: 6646--6704 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
6636 AAGAAACAAG
*
6646 AAATAAAAA-GAAATGAGAAAAACAAGAAA
1 AAATAAAAATGAAA-GACAAAAACAAGAAA
*
6675 AAATAAAAAATGAAAGACAAAAACATGAAA
1 AAAT-AAAAATGAAAGACAAAAACAAGAAA
6705 TAAAACAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 4 0.15
30 18 0.69
31 4 0.15
ACGTcount: A:0.75, C:0.05, G:0.12, T:0.08
Consensus pattern (29 bp):
AAATAAAAATGAAAGACAAAAACAAGAAA
Found at i:6696 original size:29 final size:26
Alignment explanation
Indices: 6639--6721 Score: 73
Period size: 26 Copynumber: 3.1 Consensus size: 26
6629 AAAAAAAAAG
*
6639 AAACAAGAAATAAAAAGAAATGAGAA
1 AAACAAGAAATAAAAAAAAATGAGAA
6665 AAACAAGAAA-AAATAAAAAATGAAAGACAA
1 AAACAAGAAATAAA-AAAAAATG--AG--AA
* *
6695 AAACATGAAAT-AAAACAAA-GAGAA
1 AAACAAGAAATAAAAAAAAATGAGAA
6719 AAA
1 AAA
6722 AGTTTATAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
24 5 0.10
25 3 0.06
26 19 0.40
28 3 0.06
29 5 0.10
30 13 0.27
ACGTcount: A:0.75, C:0.06, G:0.12, T:0.07
Consensus pattern (26 bp):
AAACAAGAAATAAAAAAAAATGAGAA
Found at i:6709 original size:26 final size:26
Alignment explanation
Indices: 6639--6709 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 26
6629 AAAAAAAAAG
*
6639 AAACAAGAAATAAAAAGAAATGAGAA
1 AAACAAGAAATAAAAAGAAATGACAA
6665 AAACAAGAAAAAATAAAAAATGAAA-GACAA
1 AAACAAG---AAAT-AAAAA-GAAATGACAA
*
6695 AAACATGAAATAAAA
1 AAACAAGAAATAAAA
6710 CAAAGAGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
26 11 0.29
27 4 0.11
29 4 0.11
30 15 0.39
31 4 0.11
ACGTcount: A:0.75, C:0.06, G:0.11, T:0.08
Consensus pattern (26 bp):
AAACAAGAAATAAAAAGAAATGACAA
Found at i:7440 original size:16 final size:16
Alignment explanation
Indices: 7419--7458 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
7409 ATAAAGAATC
7419 TTAAAACAAAGAAA-AA
1 TTAAAACAAA-AAATAA
7435 TTAAAACAAAAAATAA
1 TTAAAACAAAAAATAA
7451 TTAAAACA
1 TTAAAACA
7459 TATGAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 3 0.13
16 20 0.87
ACGTcount: A:0.72, C:0.07, G:0.03, T:0.17
Consensus pattern (16 bp):
TTAAAACAAAAAATAA
Found at i:7921 original size:35 final size:33
Alignment explanation
Indices: 7862--7938 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
7852 AGATATGAAA
* *
7862 TAAAACAAAGAGAAAAAACAAAATACATAAAATTT
1 TAAAACAAACAGAAAAAACAAAAT--AGAAAATTT
* *
7897 TACAACAAACA-AAAAAATAGAAATAGAAAATTT
1 TAAAACAAACAGAAAAAACA-AAATAGAAAATTT
7930 TAAAACAAA
1 TAAAACAAA
7939 AATAGTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 16 0.44
34 7 0.19
35 13 0.36
ACGTcount: A:0.69, C:0.09, G:0.05, T:0.17
Consensus pattern (33 bp):
TAAAACAAACAGAAAAAACAAAATAGAAAATTT
Found at i:8281 original size:16 final size:17
Alignment explanation
Indices: 8246--8284 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
8236 AAATATTAAT
8246 ATAAAAGACAAAATAAA
1 ATAAAAGACAAAATAAA
* *
8263 ATAAAATACTAAA-AAA
1 ATAAAAGACAAAATAAA
8279 ATAAAA
1 ATAAAA
8285 AAGTATGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (17 bp):
ATAAAAGACAAAATAAA
Found at i:8828 original size:8 final size:8
Alignment explanation
Indices: 8807--8883 Score: 52
Period size: 8 Copynumber: 9.4 Consensus size: 8
8797 AAATAAGTAC
8807 TAAAAAAGA
1 TAAAAAA-A
*
8816 GAAAAAAA
1 TAAAAAAA
8824 T-AAAAAA
1 TAAAAAAA
8831 TAAACAAAA
1 TAAA-AAAA
*
8840 -ACACAAAA
1 TA-AAAAAA
8848 TAAAAAAA
1 TAAAAAAA
8856 -AATAAAAA
1 TAA-AAAAA
**
8864 GTAAGGAAA
1 -TAAAAAAA
8873 TAAAAAAA
1 TAAAAAAA
8881 TAA
1 TAA
8884 CGAGTCAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 15
0.70 0.11 0.20
Matches are distributed among these distances:
7 9 0.17
8 27 0.51
9 15 0.28
10 2 0.04
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.10
Consensus pattern (8 bp):
TAAAAAAA
Found at i:8829 original size:17 final size:16
Alignment explanation
Indices: 8807--8863 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
8797 AAATAAGTAC
*
8807 TAAAAAAGAGAAAAAAA
1 TAAAAAATA-AAAAAAA
8824 TAAAAAATAAACAAAAA
1 TAAAAAATAAA-AAAAA
* *
8841 CACAAAATAAAAAAAAA
1 TAAAAAAT-AAAAAAAA
8858 TAAAAA
1 TAAAAA
8864 GTAAGGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 2 0.06
17 28 0.85
18 3 0.09
ACGTcount: A:0.82, C:0.05, G:0.04, T:0.09
Consensus pattern (16 bp):
TAAAAAATAAAAAAAA
Found at i:8991 original size:7 final size:7
Alignment explanation
Indices: 8939--9045 Score: 54
Period size: 7 Copynumber: 13.4 Consensus size: 7
8929 ATTAGTTTAT
8939 AAAATACA
1 AAAATA-A
8947 AAAA-AA
1 AAAATAA
8953 AAAATAGA
1 AAAATA-A
8961 ACAAATAATA
1 A-AAAT-A-A
8971 AGAAATAA
1 A-AAATAA
8979 AGAAATAA
1 A-AAATAA
*
8987 AAAATCA
1 AAAATAA
*
8994 AAGATAA
1 AAAATAA
9001 AAAATTAA
1 AAAA-TAA
*
9009 AAGAAGAA
1 AA-AATAA
9017 AAAAGTCAATA
1 AAAA-T--A-A
9028 CAAAATAA
1 -AAAATAA
9036 AAAATAA
1 AAAATAA
9043 AAA
1 AAA
9046 CAAAAGAAGG
Statistics
Matches: 80, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
6 5 0.06
7 27 0.34
8 26 0.32
9 8 0.10
10 8 0.10
11 2 0.03
12 4 0.05
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:8991 original size:15 final size:15
Alignment explanation
Indices: 8962--9025 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 15
8952 AAAAATAGAA
* *
8962 CAAATAATAAGAAAT
1 CAAAGAATAAAAAAT
8977 -AAAGAAATAAAAAAT
1 CAAAG-AATAAAAAAT
8992 CAAAG-ATAAAAAATT
1 CAAAGAATAAAAAA-T
* *
9007 AAAAGAAGAAAAAAGT
1 CAAAGAATAAAAAA-T
9023 CAA
1 CAA
9026 TACAAAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
14 11 0.28
15 14 0.36
16 14 0.36
ACGTcount: A:0.72, C:0.05, G:0.09, T:0.14
Consensus pattern (15 bp):
CAAAGAATAAAAAAT
Found at i:10196 original size:18 final size:18
Alignment explanation
Indices: 10173--10227 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
10163 GAAAAGTTAT
*
10173 TAAAAAATAAAAAAAAAAC
1 TAAAAAA-AAAAAAAAGAC
*
10192 TAAAAGAAAAGAAAAAAGAT
1 TAAAA-AAAA-AAAAAAGAC
10212 TAAAAAAATAAAAAAA
1 TAAAAAAA-AAAAAAA
10228 TCCAAAACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.82, C:0.02, G:0.05, T:0.11
Consensus pattern (18 bp):
TAAAAAAAAAAAAAAGAC
Found at i:10321 original size:19 final size:19
Alignment explanation
Indices: 10300--10335 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
10290 TATTAACAAA
10300 AAAAGCAA-TAAAAATAAG
1 AAAAGCAATTAAAAATAAG
10318 AAAAGCAATTAAAAATAA
1 AAAAGCAATTAAAAATAA
10336 ACAAAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.14
Consensus pattern (19 bp):
AAAAGCAATTAAAAATAAG
Found at i:10433 original size:19 final size:18
Alignment explanation
Indices: 10387--10430 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
10377 ACGAATCAAC
*
10387 AAAATAATAAAAAAAGAC
1 AAAATAATAAAAAAAGAA
**
10405 AAAATGAATAAAAAATTAA
1 AAAAT-AATAAAAAAAGAA
10424 AAAATAA
1 AAAATAA
10431 ATAGGAATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAATAATAAAAAAAGAA
Found at i:10801 original size:15 final size:16
Alignment explanation
Indices: 10783--10812 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10773 AATAAAGTAC
10783 TAAAAAAAGA-AAAAG
1 TAAAAAAAGACAAAAG
10798 TAAAAAAAGACAAAA
1 TAAAAAAAGACAAAA
10813 ATGGAAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.07
Consensus pattern (16 bp):
TAAAAAAAGACAAAAG
Found at i:11299 original size:16 final size:15
Alignment explanation
Indices: 11267--11324 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
11257 AAGTGGAAAA
11267 AAAAAAAGAAACAAG
1 AAAAAAAGAAACAAG
**
11282 AAATAAAAGAAATGAG
1 AAA-AAAAGAAACAAG
* *
11298 AAAAACAAGAAAAAAT
1 AAAAA-AAGAAACAAG
*
11314 AAAAAATGAAA
1 AAAAAAAGAAA
11325 GACAAAAACA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 10 0.29
16 25 0.71
ACGTcount: A:0.78, C:0.03, G:0.12, T:0.07
Consensus pattern (15 bp):
AAAAAAAGAAACAAG
Found at i:11629 original size:29 final size:29
Alignment explanation
Indices: 11597--11658 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
11587 AAAAAGTAAG
11597 AAAATGAAAA-AAAAAAAAAAAAACGAAT
1 AAAATGAAAACAAAAAAAAAAAAACGAAT
** *
11625 CAAAA-GAAAACAATTAAAAAAAAATGAAT
1 -AAAATGAAAACAAAAAAAAAAAAACGAAT
11654 AAAAT
1 AAAAT
11659 TTTCAAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.77, C:0.05, G:0.06, T:0.11
Consensus pattern (29 bp):
AAAATGAAAACAAAAAAAAAAAAACGAAT
Found at i:11648 original size:14 final size:15
Alignment explanation
Indices: 11611--11657 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
11601 TGAAAAAAAA
11611 AAAAAAAAACGAATC
1 AAAAAAAAACGAATC
* *
11626 AAAAGAAAAC-AATT
1 AAAAAAAAACGAATC
*
11640 AAAAAAAAATGAAT-
1 AAAAAAAAACGAATC
11654 AAAA
1 AAAA
11658 TTTTCAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (15 bp):
AAAAAAAAACGAATC
Found at i:12213 original size:18 final size:17
Alignment explanation
Indices: 12176--12240 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 17
12166 ATTTAAAATA
*
12176 AAAATAAATGAAAA-AAT
1 AAAATAAA-GAAAATATT
12193 AAAATAAGAGAAAATATT
1 AAAATAA-AGAAAATATT
* *
12211 AAAGTAAAATAAAATATT
1 AAAAT-AAAGAAAATATT
12229 AAAA-AAAGAAAA
1 AAAATAAAGAAAA
12241 AGCAATTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.17
17 12 0.30
18 19 0.47
19 2 0.05
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (17 bp):
AAAATAAAGAAAATATT
Found at i:12268 original size:17 final size:17
Alignment explanation
Indices: 12248--12294 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
12238 AAAAGCAATT
12248 AAAAATAAACAAAA-ACA
1 AAAAATAAA-AAAAGACA
12265 AAAAATAAAAAAAGACA
1 AAAAATAAAAAAAGACA
**
12282 AAATTTAAAAAAA
1 AAAAATAAAAAAA
12295 TGAAAAGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.81, C:0.06, G:0.02, T:0.11
Consensus pattern (17 bp):
AAAAATAAAAAAAGACA
Found at i:12556 original size:35 final size:33
Alignment explanation
Indices: 12497--12573 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
12487 AGATATGAAA
* *
12497 TAAAACAAAGAGAAAAAACAAAATACATAAAATTT
1 TAAAACAAACAGAAAAAACAAAAT--AGAAAATTT
* *
12532 TACAACAAACA-AAAAAATAGAAATAGAAAATTT
1 TAAAACAAACAGAAAAAACA-AAATAGAAAATTT
12565 TAAAACAAA
1 TAAAACAAA
12574 AATAGTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 16 0.44
34 7 0.19
35 13 0.36
ACGTcount: A:0.69, C:0.09, G:0.05, T:0.17
Consensus pattern (33 bp):
TAAAACAAACAGAAAAAACAAAATAGAAAATTT
Found at i:13582 original size:7 final size:7
Alignment explanation
Indices: 13572--13670 Score: 56
Period size: 7 Copynumber: 12.7 Consensus size: 7
13562 ATAAAATACA
13572 AAAAAAT
1 AAAAAAT
13579 AAAAAAT
1 AAAAAAT
13586 AGAACAAAT
1 A-AA-AAAT
13595 AATAAGAAAT
1 -A-AA-AAAT
13605 AAAGAAAT
1 AAA-AAAT
13613 -AAAAAT
1 AAAAAAT
* *
13619 CAAAGAT
1 AAAAAAT
*
13626 AAAAATT
1 AAAAAAT
*
13633 AAAAGAAG
1 AAAA-AAT
13641 AAAAAAGT
1 AAAAAA-T
13649 CAATACAAAT
1 -AA-A-AAAT
13659 AAAAAAT
1 AAAAAAT
13666 AAAAA
1 AAAAA
13671 CAAAAGAAGG
Statistics
Matches: 74, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
6 4 0.05
7 34 0.46
8 15 0.20
9 9 0.12
10 9 0.12
11 3 0.04
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:13604 original size:19 final size:18
Alignment explanation
Indices: 13564--13614 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
13554 ATTAGTTTAT
13564 AAAATACAA-AAA-AATAA
1 AAAATA-AACAAATAATAA
13581 AAAATAGAACAAATAATAA
1 AAAATA-AACAAATAATAA
* *
13600 GAAATAAAGAAATAA
1 AAAATAAACAAATAA
13615 AAATCAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 8 0.28
18 11 0.38
19 10 0.34
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (18 bp):
AAAATAAACAAATAATAA
Found at i:13642 original size:40 final size:39
Alignment explanation
Indices: 13573--13679 Score: 101
Period size: 40 Copynumber: 2.7 Consensus size: 39
13563 TAAAATACAA
* *
13573 AAAAATAAAAAATAGAACAA-ATAATAAGAAATAAAG-AAAT
1 AAAAATAAAAAATA-AA-AACAAAAGAAGAAA-AAAGTAAAT
* * * *
13613 AAAAATCAAAGATAAAAATTAAAAGAAGAAAAAAGTCAAT
1 AAAAATAAAAAATAAAAA-CAAAAGAAGAAAAAAGTAAAT
*
13653 ACAAATAAAAAATAAAAACAAAAGAAG
1 AAAAATAAAAAATAAAAACAAAAGAAG
13680 GAAGTGCGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
38 2 0.04
39 14 0.25
40 39 0.71
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (39 bp):
AAAAATAAAAAATAAAAACAAAAGAAGAAAAAAGTAAAT
Done.