Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168142.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_384, 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: 29638
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Found at i:369 original size:44 final size:45
Alignment explanation
Indices: 285--369 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
275 TTCTAACTTA
285 ACCCTTATTTAAAACTCTTTATATTAGGACAGATTGCAAACCCAT
1 ACCCTTATTTAAAACTCTTTATATTAGGACAGATTGCAAACCCAT
*
330 ACCCTTATTTAAAACTC-TTATAATTAGGACGGA-TGCAAAC
1 ACCCTTATTTAAAACTCTTTAT-ATTAGGACAGATTGCAAAC
370 TCATCGATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
44 11 0.29
45 27 0.71
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (45 bp):
ACCCTTATTTAAAACTCTTTATATTAGGACAGATTGCAAACCCAT
Found at i:1659 original size:21 final size:21
Alignment explanation
Indices: 1569--1659 Score: 96
Period size: 21 Copynumber: 4.4 Consensus size: 21
1559 TTGATTGAAT
*
1569 TAATTTTGGTAACCCTTAATA
1 TAATTTTGGTAACCTTTAATA
* * *
1590 CACTTTTGGTAACCTTTGATA
1 TAATTTTGGTAACCTTTAATA
* *
1611 AAATTATGGTAA-CTTT-ATA
1 TAATTTTGGTAACCTTTAATA
*
1630 TAATTTTTGGCAACCTTTAATA
1 TAA-TTTTGGTAACCTTTAATA
1652 TAATTTTG
1 TAATTTTG
1660 ATTTCGATAA
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 5 0.09
20 11 0.19
21 35 0.61
22 6 0.11
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (21 bp):
TAATTTTGGTAACCTTTAATA
Found at i:7669 original size:23 final size:25
Alignment explanation
Indices: 7633--7679 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
7623 ATTTAATATT
7633 TGACTTTTTAATAT-C-TATTTTTC
1 TGACTTTTTAATATACATATTTTTC
7656 TGACTATTTT-ATATACATATTTTT
1 TGACT-TTTTAATATACATATTTTT
7680 TTTAAATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 9 0.43
24 5 0.24
25 7 0.33
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.60
Consensus pattern (25 bp):
TGACTTTTTAATATACATATTTTTC
Found at i:7681 original size:66 final size:68
Alignment explanation
Indices: 7563--7697 Score: 177
Period size: 66 Copynumber: 2.0 Consensus size: 68
7553 GGAATTGCCG
* * ** *
7563 TTTGACTTGTTTTAATATTTATTTTTTCTGACGATTTTATGTATTTATTTTTTTATAGTGATTTA
1 TTTGACTTGTTTTAATATCTATTTTTTCTGACGATTTTATATACATATTTTTTTAAAGTGATTTA
7628 ATA
66 ATA
* *
7631 TTTGAC-T-TTTTAATATCTA-TTTTTCTGACTATTTTATATACATATTTTTTTTAAATTGATTT
1 TTTGACTTGTTTTAATATCTATTTTTTCTGACGATTTTATATACATA-TTTTTTTAAAGTGATTT
7693 AATA
65 AATA
7697 T
1 T
7698 ATTTAAATTT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 21 0.36
66 31 0.53
67 1 0.02
68 6 0.10
ACGTcount: A:0.26, C:0.06, G:0.07, T:0.61
Consensus pattern (68 bp):
TTTGACTTGTTTTAATATCTATTTTTTCTGACGATTTTATATACATATTTTTTTAAAGTGATTTA
ATA
Found at i:7885 original size:17 final size:16
Alignment explanation
Indices: 7863--7902 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
7853 GATCTAATTC
7863 TATAATTAAATCAGTTT
1 TATAATTAAATCA-TTT
*
7880 TATAATTAAATTATTT
1 TATAATTAAATCATTT
7896 TA-AATTA
1 TATAATTA
7903 TTATGAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.23
16 5 0.23
17 12 0.55
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (16 bp):
TATAATTAAATCATTT
Found at i:8285 original size:15 final size:16
Alignment explanation
Indices: 8267--8299 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
8257 CTATAATTAA
8267 AATAAT-TATAAAATT
1 AATAATATATAAAATT
8282 AATAATATATAAAATT
1 AATAATATATAAAATT
8298 AA
1 AA
8300 CAAAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATAATATATAAAATT
Found at i:8571 original size:21 final size:21
Alignment explanation
Indices: 8517--8571 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
8507 AAAATTAATT
* *
8517 ATTTTATATTAATAAATAATA
1 ATTTTATATTAATAAAAAAAA
* *
8538 ATTATATTTTAATAAAAAAAA
1 ATTTTATATTAATAAAAAAAA
*
8559 ATTTTATAATAAT
1 ATTTTATATTAAT
8572 TTATTAGTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTTATATTAATAAAAAAAA
Found at i:9388 original size:11 final size:11
Alignment explanation
Indices: 9372--9413 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
9362 AATCCCATAA
9372 GAGATTTGTTT
1 GAGATTTGTTT
*
9383 GAGATTTGTTA
1 GAGATTTGTTT
*
9394 GAAATTTGTTT
1 GAGATTTGTTT
9405 GAGATTTGT
1 GAGATTTGT
9414 CAAATATTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:9507 original size:52 final size:53
Alignment explanation
Indices: 9448--9594 Score: 140
Period size: 52 Copynumber: 2.8 Consensus size: 53
9438 TACTTGCAAA
* * *
9448 AGAAGAATTTC-AAGAAAAAA-AGGATTTTTAATAGGTAAGTTTGACTTACAGG
1 AGAAGAATTTCTAAGAAAAAAGA-GATTCTTAATAGGCAAGTTTGACTCACAGG
** * *
9500 AGAAGAA-TTCTAAGAGGAGAGAGATTCTTAATGGGCAAGTTTGACTCACAGG
1 AGAAGAATTTCTAAGAAAAAAGAGATTCTTAATAGGCAAGTTTGACTCACAGG
** * * * *
9552 AGAAGAA-TTCTAAGAGGAGAGGGATTCTTAATGGGTAAGTTTG
1 AGAAGAATTTCTAAGAAAAAAGAGATTCTTAATAGGCAAGTTTG
9595 TATGGTTACA
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 3 0.04
52 80 0.95
53 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.27, T:0.27
Consensus pattern (53 bp):
AGAAGAATTTCTAAGAAAAAAGAGATTCTTAATAGGCAAGTTTGACTCACAGG
Found at i:10613 original size:52 final size:52
Alignment explanation
Indices: 10546--10700 Score: 152
Period size: 52 Copynumber: 3.0 Consensus size: 52
10536 GGATAAGAAG
* * *
10546 ACTTGCAAAAGAAGAATT-T-CAAGAGAAAGAAGATTCTTAATAGGTAAGTTTA
1 ACTTGCAAAAAAAGAATTCTAAAAG-GAAAG-AGATTCTTAATAGGCAAGTTTA
* *
10598 ACTTGCAAAAAAAGAATTCTAAAAGGAAAGAGATTTTTAATAGGCAAGTTTG
1 ACTTGCAAAAAAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTTA
** ** * * * * *
10650 ACTTATAGGAGAAGAATTCTAAGAGGAGAGGGATTCTTAATGGGCAAGTTT
1 ACTTGCAAAAAAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
10701 GTATGGTTAT
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
52 77 0.90
53 6 0.07
54 3 0.03
ACGTcount: A:0.43, C:0.08, G:0.23, T:0.27
Consensus pattern (52 bp):
ACTTGCAAAAAAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTTA
Found at i:11284 original size:25 final size:25
Alignment explanation
Indices: 11264--11340 Score: 79
Period size: 24 Copynumber: 3.1 Consensus size: 25
11254 AGAAGAGTTG
11264 AAGATTCAAGATGTGGAAAGAGCTA
1 AAGATTCAAGATGTGGAAAGAGCTA
* * *
11289 AAGGTTCGAGATGT-GAAAAAGCTGA
1 AAGATTCAAGATGTGGAAAGAGCT-A
*
11314 AAG-TTCGAGATGT-GAGAAGAGCTA
1 AAGATTCAAGATGTGGA-AAGAGCTA
11338 AAG
1 AAG
11341 GTTTGGGAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
24 24 0.52
25 22 0.48
ACGTcount: A:0.42, C:0.08, G:0.31, T:0.19
Consensus pattern (25 bp):
AAGATTCAAGATGTGGAAAGAGCTA
Found at i:11311 original size:24 final size:24
Alignment explanation
Indices: 11272--11343 Score: 101
Period size: 24 Copynumber: 2.9 Consensus size: 24
11262 TGAAGATTCA
11272 AGATGTGGAAAGAGCTAAAGGTTCG
1 AGATGT-GAAAGAGCTAAAGGTTCG
*
11297 AGATGTGAAAAAGCTGAAA-GTTCG
1 AGATGTGAAAGAGCT-AAAGGTTCG
11321 AGATGTGAGAAGAGCTAAAGGTT
1 AGATGTGA-AAGAGCTAAAGGTT
11344 TGGGAAGTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
24 24 0.57
25 18 0.43
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.21
Consensus pattern (24 bp):
AGATGTGAAAGAGCTAAAGGTTCG
Found at i:11709 original size:52 final size:52
Alignment explanation
Indices: 11647--11803 Score: 176
Period size: 52 Copynumber: 3.0 Consensus size: 52
11637 TGGACAAAAA
* *
11647 GACTTGCAAAAAAAGAATT-T-CAAGAGAAAGAAGATTCTTAATAGGTAAGTTT
1 GACTTGCAAAAAAAGAATTCTAAAAG-GAAAG-AGATTCTTAATAGGCAAGTTT
*
11699 GACTTGCAAAAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
1 GACTTGCAAAAAAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
* * * * * * *
11751 GACTTACAGGAGAAA-AATTCTAAGAGGAGAGGGATTCTTAATGGGCAAGTTT
1 GACTTGCA-AAAAAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
11803 G
1 G
11804 TATGGTTATA
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
52 79 0.87
53 9 0.10
54 3 0.03
ACGTcount: A:0.42, C:0.09, G:0.24, T:0.25
Consensus pattern (52 bp):
GACTTGCAAAAAAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTT
Found at i:12442 original size:24 final size:24
Alignment explanation
Indices: 12374--12442 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 24
12364 TGAAGATTCA
*
12374 AGATGTGGAAAGAGCCAAAGGTTCG
1 AGATGTGGAAAGAGCTAAA-GTTCG
12399 AG-TCGT-GAAAGAGCTGAAAGTTCG
1 AGAT-GTGGAAAGAGCT-AAAGTTCG
*
12423 AGATGTGGGAAGAGCTAAAG
1 AGATGTGGAAAGAGCTAAAG
12443 GTTTGAGAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
24 22 0.58
25 16 0.42
ACGTcount: A:0.36, C:0.10, G:0.36, T:0.17
Consensus pattern (24 bp):
AGATGTGGAAAGAGCTAAAGTTCG
Found at i:12450 original size:25 final size:25
Alignment explanation
Indices: 12374--12450 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 25
12364 TGAAGATTCA
*
12374 AGATGTGGAAAGAGCCAAAGGTTCG
1 AGATGTGGAAAGAGCTAAAGGTTCG
12399 AG-TCGT-GAAAGAGCTGAAA-GTTCG
1 AGAT-GTGGAAAGAGCT-AAAGGTTCG
* *
12423 AGATGTGGGAAGAGCTAAAGGTTTG
1 AGATGTGGAAAGAGCTAAAGGTTCG
12448 AGA
1 AGA
12451 AGTGCATGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
24 21 0.48
25 23 0.52
ACGTcount: A:0.35, C:0.09, G:0.36, T:0.19
Consensus pattern (25 bp):
AGATGTGGAAAGAGCTAAAGGTTCG
Found at i:12709 original size:11 final size:11
Alignment explanation
Indices: 12693--12734 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
12683 AATCTCATAA
12693 GAGATTTGTTT
1 GAGATTTGTTT
*
12704 GAGATTTGTTA
1 GAGATTTGTTT
12715 GAGATTTGTTT
1 GAGATTTGTTT
12726 GAGATTTGT
1 GAGATTTGT
12735 CAGATATTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:12720 original size:22 final size:22
Alignment explanation
Indices: 12692--12734 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
12682 AAATCTCATA
12692 AGAGATTTGTTTGAGATTTGTT
1 AGAGATTTGTTTGAGATTTGTT
12714 AGAGATTTGTTTGAGATTTGT
1 AGAGATTTGTTTGAGATTTGT
12735 CAGATATTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (22 bp):
AGAGATTTGTTTGAGATTTGTT
Found at i:12848 original size:52 final size:51
Alignment explanation
Indices: 12759--12912 Score: 150
Period size: 51 Copynumber: 3.0 Consensus size: 51
12749 TGGACAAGAA
* * *
12759 GACTTGCAAAAGAAGAATTTCAAGAA--AAAGAAGATTCTTAATAAGTAAGTTT
1 GACTTGCAAGAGAAGAATTTTAA-AAGGAAAGAA-ATTCTTAATAAGCAAG-TT
*
12811 GACTTGCAAGAGAAGAATTTTAAAAGGAAAGAAATTCTTAATAGGCAAGTT
1 GACTTGCAAGAGAAGAATTTTAAAAGGAAAGAAATTCTTAATAAGCAAGTT
* * * * * ** **
12862 GACTTACAGGAGAAGAATTCTAAGAGGAGAGTGATTCTTAATGGGCAAGTT
1 GACTTGCAAGAGAAGAATTTTAAAAGGAAAGAAATTCTTAATAAGCAAGTT
12913 TGTATGGTTA
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
51 47 0.53
52 35 0.40
53 6 0.07
ACGTcount: A:0.43, C:0.08, G:0.23, T:0.26
Consensus pattern (51 bp):
GACTTGCAAGAGAAGAATTTTAAAAGGAAAGAAATTCTTAATAAGCAAGTT
Found at i:17571 original size:62 final size:63
Alignment explanation
Indices: 17441--17584 Score: 163
Period size: 62 Copynumber: 2.3 Consensus size: 63
17431 AATAATCCAC
* * * *
17441 GAATTATTGAAGACATTTTTGCCTAAAAATGCATTTAATAATCCTATCTAAAAAATTAGAAGT
1 GAATTATTGAAGGCATTTTTACCTAAAAATGCATTCAATAATCCCATCTAAAAAATTAGAAGT
*
17504 G-ATTATTGAAGGCAATTTTTACC-AAAAATGCCTTCAATAATCCCATC-ATAAAAATT-GAAG-
1 GAATTATTGAAGGC-ATTTTTACCTAAAAATGCATTCAATAATCCCATCTA-AAAAATTAGAAGT
* *
17564 GAAATTATTCAAGGCGTTTTT
1 G-AATTATTGAAGGCATTTTT
17585 TGCCATAAAC
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
60 1 0.01
61 10 0.14
62 50 0.71
63 9 0.13
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (63 bp):
GAATTATTGAAGGCATTTTTACCTAAAAATGCATTCAATAATCCCATCTAAAAAATTAGAAGT
Found at i:17675 original size:124 final size:123
Alignment explanation
Indices: 17527--17921 Score: 389
Period size: 124 Copynumber: 3.2 Consensus size: 123
17517 AATTTTTACC
* * *
17527 AAAAATGCCTTCAATAATCCCATCATAAAAATTGAAGGAAATTATTCAAGGCGTTTTTTGCCATA
1 AAAAACGCCTTCAATAATCTCATCATAAAAATTAAAGGAAATTATTCAAGGCGTTTTTTGCCATA
* ** * * *
17592 AACAG-CTTGACTAACTCTTTTCGATTTTTTTTAAGGGATTATGCAAGGTGTTATTTGCT
66 AA-TGCCTTGACTAACTCCATTCAATTTTTTCTAAAGGATTATGCAAGGTGTT-TTTGCT
* * * * * *
17651 AAAAACGCCTTTAATAATCTCATCATAAAAGTTAAAGGCAATTATTCAATGTGTTTTTTGTCATA
1 AAAAACGCCTTCAATAATCTCATCATAAAAATTAAAGGAAATTATTCAAGGCGTTTTTTGCCATA
** * * * ** *
17716 AATGTATTGACTAACCCCATTCAATTTTTTCTAAAGGATAATGTAAGGCATTTTCTGGT
66 AATGCCTTGACTAACTCCATTCAATTTTTTCTAAAGGATTATGCAAGGTGTTTT-TGCT
* * * * ** * *
17775 TAAAACACATTCAATAATCTCGTCATAAAAATTAAAAAAGGGGATTATTCAAGGCATTTTTAGCC
1 AAAAACGCCTTCAATAATCTCATCATAAAAATT---AAAGGAAATTATTCAAGGCGTTTTTTGCC
*
17840 ATAAATGCCTTGACTAA-TCCCATTCAATTTTTTCTAAAGGATTATGCAAGGTGTTTTTTGGCA
63 ATAAATGCCTTGACTAACT-CCATTCAATTTTTTCTAAAGGATTATGCAAGGTG-TTTTT-GCT
**
17903 AAAAATACCTTCAATAATC
1 AAAAACGCCTTCAATAATC
17922 CAAAAAAAAA
Statistics
Matches: 216, Mismatches: 47, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
123 3 0.01
124 124 0.57
127 68 0.31
128 21 0.10
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Consensus pattern (123 bp):
AAAAACGCCTTCAATAATCTCATCATAAAAATTAAAGGAAATTATTCAAGGCGTTTTTTGCCATA
AATGCCTTGACTAACTCCATTCAATTTTTTCTAAAGGATTATGCAAGGTGTTTTTGCT
Found at i:19949 original size:21 final size:21
Alignment explanation
Indices: 19920--19975 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
19910 TAAAGTTATG
19920 AGTCATTGCTGTTGATCATTCA
1 AGTCATTGCTGTTGATCA-TCA
* *
19942 AG-CATTGCTCTTGGTCATCA
1 AGTCATTGCTGTTGATCATCA
*
19962 AGTCTTTGCTGTTG
1 AGTCATTGCTGTTG
19976 TTACTCAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 5 0.17
21 22 0.76
22 2 0.07
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (21 bp):
AGTCATTGCTGTTGATCATCA
Found at i:21857 original size:8 final size:8
Alignment explanation
Indices: 21844--21875 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
21834 TTTTATTAAT
21844 AAAAAATA
1 AAAAAATA
21852 AAAAAATA
1 AAAAAATA
21860 AAAAAATA
1 AAAAAATA
21868 AAAAAATA
1 AAAAAATA
21876 GGTGTTGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAATA
Found at i:26434 original size:14 final size:13
Alignment explanation
Indices: 26410--26453 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 13
26400 TCTCAAAGAT
26410 AAAAAGCAAAAAA
1 AAAAAGCAAAAAA
*
26423 AGAAAAGTAAAAAA
1 A-AAAAGCAAAAAA
26437 AAAAAGCAAGAAAA
1 AAAAAGCAA-AAAA
26451 AAA
1 AAA
26454 GAAAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 8 0.30
14 19 0.70
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02
Consensus pattern (13 bp):
AAAAAGCAAAAAA
Found at i:26812 original size:12 final size:12
Alignment explanation
Indices: 26795--26851 Score: 55
Period size: 12 Copynumber: 4.9 Consensus size: 12
26785 TGATGGATGG
26795 AAAAAATGAAAA
1 AAAAAATGAAAA
*
26807 AAAAAAGGAAAA
1 AAAAAATGAAAA
**
26819 AAGGAA--AAAA
1 AAAAAATGAAAA
**
26829 ATGAAATGAAAA
1 AAAAAATGAAAA
26841 AAAAAATGAAA
1 AAAAAATGAAA
26852 GAATGGGAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
10 8 0.22
12 28 0.78
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAAAATGAAAA
Found at i:26836 original size:34 final size:34
Alignment explanation
Indices: 26798--26881 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 34
26788 TGGATGGAAA
26798 AAATGAAAAAAAAAAGGAAA-AAAGGAAAAAAATG-
1 AAATGAAAAAAAAAAGGAAAGAAAGG--AAAAATGT
* * *
26832 AAATGAAAAAAAAAATGAAAGAATGGGAAAATGT
1 AAATGAAAAAAAAAAGGAAAGAAAGGAAAAATGT
26866 AAATGAGAAAAAAAAA
1 AAATGA-AAAAAAAAA
26882 AGACTCAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
33 6 0.14
34 25 0.57
35 13 0.30
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.10
Consensus pattern (34 bp):
AAATGAAAAAAAAAAGGAAAGAAAGGAAAAATGT
Found at i:26843 original size:17 final size:17
Alignment explanation
Indices: 26798--26851 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
26788 TGGATGGAAA
*
26798 AAATGAAAAAAAAAAGG
1 AAATGAAAAAAAAAATG
26815 AAA--AAAGGAAAAAAATG
1 AAATGAAA--AAAAAAATG
26832 AAATGAAAAAAAAAATG
1 AAATGAAAAAAAAAATG
26849 AAA
1 AAA
26852 GAATGGGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
15 3 0.09
17 26 0.81
19 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (17 bp):
AAATGAAAAAAAAAATG
Found at i:28066 original size:21 final size:21
Alignment explanation
Indices: 28040--28548 Score: 212
Period size: 21 Copynumber: 22.8 Consensus size: 21
28030 AAAAATTCTC
28040 AAATGAGAATCTTTGAGTCTT
1 AAATGAGAATCTTTGAGTCTT
* * *
28061 AAATGAAAATCATTAAGAAATCCTT
1 AAATGAGAATC-TT-TG-AGT-CTT
28086 AAATGAGAATCTTTGAGTTCTT
1 AAATGAGAATCTTTGAG-TCTT
* * *
28108 AAATGAAAATCTTTAAGAAATCCTC
1 AAATGAGAATCTTT--G-AGT-CTT
* *
28133 AAGTAAGAATCTTTGAGTTCTT
1 AAATGAGAATCTTTGAG-TCTT
* **
28155 AAATGAGAATCTTTAAGGAATT
1 AAATGAGAATCTTTGA-GTCTT
* * *
28177 --CTCGAGAATCTTTAAGGAATTCTC
1 AAAT-GAGAATCTTT---G-AGTCTT
28201 AAATGAGAATCTTTGAGTCTT
1 AAATGAGAATCTTTGAGTCTT
28222 AAATGAGAAATC--T---TC--
1 AAATGAG-AATCTTTGAGTCTT
*
28237 AAATGAGAATCTTTAAGTCTT
1 AAATGAGAATCTTTGAGTCTT
* *
28258 AAATGAGAATCTTTAAGAAATCCTC
1 AAATGAGAATCTTT--G-AGT-CTT
* * *
28283 AAATGAGAATCTGTAAGTTTT
1 AAATGAGAATCTTTGAGTCTT
*
28304 AAATGAGAATCTTTAAGAAATCTT
1 AAATGAGAATCTTT--G-AGTCTT
*
28328 CAAATGAGAATCTTTAAGTCTT
1 -AAATGAGAATCTTTGAGTCTT
* * *
28350 AAATAAGAATCTTTAAGAAATTTT
1 AAATGAGAATCTTT--G-AGTCTT
* * * *
28374 CAAATGAGATTCTTTAAAAAATCCTC
1 -AAATGAGAATCTTT---GAGT-CTT
*
28400 AAATAAGAATCTTTGAGTCTT
1 AAATGAGAATCTTTGAGTCTT
* *
28421 AAATGAGAATTTTTAAGTCTT
1 AAATGAGAATCTTTGAGTCTT
* *
28442 AAATGAGAATCTTTAAAAAATCTT
1 AAATGAGAATCTTT---GAGTCTT
** *
28466 CAAATGAGAATAATTAAGT-TT
1 -AAATGAGAATCTTTGAGTCTT
*
28487 CAAATGAGAATCTTTGAGTATT
1 -AAATGAGAATCTTTGAGTCTT
* *
28509 CAAATAAGAAAT-TTTGAGTTTT
1 -AAATGAG-AATCTTTGAGTCTT
28531 CAAATGAGAATCTTTGAG
1 -AAATGAGAATCTTTGAG
28549 ATGAGAAACC
Statistics
Matches: 371, Mismatches: 70, Indels: 93
0.69 0.13 0.17
Matches are distributed among these distances:
14 4 0.01
15 7 0.02
16 1 0.00
17 2 0.01
19 2 0.01
20 2 0.01
21 126 0.34
22 85 0.23
23 9 0.02
24 23 0.06
25 106 0.29
26 4 0.01
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (21 bp):
AAATGAGAATCTTTGAGTCTT
Found at i:28086 original size:25 final size:24
Alignment explanation
Indices: 28008--28476 Score: 138
Period size: 25 Copynumber: 19.7 Consensus size: 24
27998 TAAAATCATG
*
28008 AATCCTTAAATGAGAATCATTAAAA
1 AATCCTTAAATGAGAATC-TTAAGA
* * *
28033 AATTCTCAAATGAGAATCTT-TG-
1 AATCCTTAAATGAGAATCTTAAGA
* *
28055 AGT-CTTAAATGAAAATCATTAAGA
1 AATCCTTAAATGAGAATC-TTAAGA
*
28079 AATCCTTAAATGAGAATCTT-TG-
1 AATCCTTAAATGAGAATCTTAAGA
* * *
28101 AGTTCTTAAATGAAAATCTTTAAGA
1 AATCCTTAAATGAGAATC-TTAAGA
* * * *
28126 AATCCTCAAGTAAGAATCTT-TG-
1 AATCCTTAAATGAGAATCTTAAGA
* * *
28148 AGTTCTTAAATGAGAATCTTTAAGG
1 AATCCTTAAATGAGAATC-TTAAGA
* * *
28173 AATTC-T---CGAGAATCTTTAAGG
1 AATCCTTAAATGAGAATC-TTAAGA
* * *
28194 AATTCTCAAATGAGAATCTT-TG-
1 AATCCTTAAATGAGAATCTTAAGA
*
28216 AGT-CTTAAATGAGAAATCTTCAAATGA
1 AATCCTTAAATGAG-AATCTT--AA-GA
28243 GAATCTTTAAGTCTTAAATGAGAATCTTTAAGA
1 -AATC-------CTTAAATGAGAATC-TTAAGA
*
28276 AATCCTCAAATGAGAATCTGTAAG-
1 AATCCTTAAATGAGAATCT-TAAGA
*
28300 --T-TTTAAATGAGAATCTTTAAGA
1 AATCCTTAAATGAGAATC-TTAAGA
28322 AAT-CTTCAAATGAGAATCTTTAAG-
1 AATCCTT-AAATGAGAATC-TTAAGA
*
28346 --T-CTTAAATAAGAATCTTTAAGA
1 AATCCTTAAATGAGAATC-TTAAGA
* * *
28368 AAT-TTTCAAATGAGATTCTTTAAAA
1 AATCCTT-AAATGAGAATC-TTAAGA
* * *
28393 AATCCTCAAATAAGAATCTT-TG-
1 AATCCTTAAATGAGAATCTTAAGA
* *
28415 AGT-CTTAAATGAGAATTTTTAAG-
1 AATCCTTAAATGAGAA-TCTTAAGA
*
28438 --T-CTTAAATGAGAATCTTTAAAA
1 AATCCTTAAATGAGAATC-TTAAGA
28460 AAT-CTTCAAATGAGAAT
1 AATCCTT-AAATGAGAAT
28477 AATTAAGTTT
Statistics
Matches: 337, Mismatches: 59, Indels: 96
0.68 0.12 0.20
Matches are distributed among these distances:
20 1 0.00
21 99 0.29
22 51 0.15
23 9 0.03
24 26 0.08
25 123 0.36
26 2 0.01
28 2 0.01
32 4 0.01
33 2 0.01
34 2 0.01
35 4 0.01
36 12 0.04
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (24 bp):
AATCCTTAAATGAGAATCTTAAGA
Found at i:28124 original size:47 final size:47
Alignment explanation
Indices: 28012--28171 Score: 232
Period size: 47 Copynumber: 3.4 Consensus size: 47
28002 ATCATGAATC
* * *
28012 CTTAAATGAGAATCATTAAAAAATTCTCAAATGAGAATCTTTGAG-T
1 CTTAAATGAAAATCATTAAGAAATCCTCAAATGAGAATCTTTGAGTT
*
28058 CTTAAATGAAAATCATTAAGAAATCCTTAAATGAGAATCTTTGAGTT
1 CTTAAATGAAAATCATTAAGAAATCCTCAAATGAGAATCTTTGAGTT
* * *
28105 CTTAAATGAAAATCTTTAAGAAATCCTCAAGTAAGAATCTTTGAGTT
1 CTTAAATGAAAATCATTAAGAAATCCTCAAATGAGAATCTTTGAGTT
* *
28152 CTTAAATGAGAATCTTTAAG
1 CTTAAATGAAAATCATTAAG
28172 GAATTCTCGA
Statistics
Matches: 104, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
46 41 0.39
47 63 0.61
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (47 bp):
CTTAAATGAAAATCATTAAGAAATCCTCAAATGAGAATCTTTGAGTT
Found at i:28230 original size:46 final size:45
Alignment explanation
Indices: 28038--28545 Score: 196
Period size: 46 Copynumber: 11.4 Consensus size: 45
28028 TAAAAAATTC
* * * *
28038 TCAAATGAGAATCTTTGAG-TCTTAAATGAAAATCATTAAGAAATCCT
1 TCAAATGAGAATCTTTAAGTTCTCAAATGAGAATC-TTTAG-AAT-CT
* * * *
28085 T-AAATGAGAATCTTTGAGTTCTTAAATGAAAATCTTTAAGAAATCC
1 TCAAATGAGAATCTTTAAGTTCTCAAATGAGAATCTTT-AG-AATCT
* * * *
28131 TCAAGTAAGAATCTTTGAGTTCTTAAATGAGAATCTTTAAGGAA--T
1 TCAAATGAGAATCTTTAAGTTCTCAAATGAGAATCTTT-A-GAATCT
*
28176 TC---TCGAGAATCTTTAAGGAATTCTCAAATGAGAATCTTT-GAGTCT
1 TCAAAT-GAGAATCTTTAA-G--TTCTCAAATGAGAATCTTTAGAATCT
*
28221 T-AAATGAG-A-----AA--TCTTCAAATGAGAATCTTTA-AGTCT
1 TCAAATGAGAATCTTTAAGTTC-TCAAATGAGAATCTTTAGAATCT
* * *
28257 T-AAATGAGAATCTTTAAGAAATCCTCAAATGAGAATCTGTA-AGT-T
1 TCAAATGAGAATCTTTAAG---TTCTCAAATGAGAATCTTTAGAATCT
* * *
28302 TTAAATGAGAATCTTTAAGAAATCTTCAAATGAGAATCTTTA-AGTCT
1 TCAAATGAGAATCTTTAAG--TTC-TCAAATGAGAATCTTTAGAATCT
* * * * *
28349 T-AAATAAGAATCTTTAAGAAATTTTCAAATGAGATTCTTTAAAAAATCC
1 TCAAATGAGAATCTTTAAG---TTCTCAAATGAGAATCTTT--AGAATCT
* * * * *
28398 TCAAATAAGAATCTTTGAG-TCTTAAATGAGAATTTTTA-AGTCT
1 TCAAATGAGAATCTTTAAGTTCTCAAATGAGAATCTTTAGAATCT
** ** *
28441 T-AAATGAGAATCTTTAAAAAATCTTCAAATGAGAATAATTA-AGT-T
1 TCAAATGAGAATCTTT--AAGTTC-TCAAATGAGAATCTTTAGAATCT
* * * *
28486 TCAAATGAGAATCTTTGAGTAT-TCAAATAAGAAAT-TTT-GAGTTT
1 TCAAATGAGAATCTTTAAGT-TCTCAAATGAG-AATCTTTAGAATCT
28530 TCAAATGAGAATCTTT
1 TCAAATGAGAATCTTT
28546 GAGATGAGAA
Statistics
Matches: 379, Mismatches: 39, Indels: 89
0.75 0.08 0.18
Matches are distributed among these distances:
35 2 0.01
36 29 0.08
37 1 0.00
40 2 0.01
42 16 0.04
43 29 0.08
44 24 0.06
45 15 0.04
46 173 0.46
47 66 0.17
48 2 0.01
49 4 0.01
50 16 0.04
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (45 bp):
TCAAATGAGAATCTTTAAGTTCTCAAATGAGAATCTTTAGAATCT
Found at i:28246 original size:36 final size:35
Alignment explanation
Indices: 28199--28270 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 35
28189 TAAGGAATTC
*
28199 TCAAATGAGAATCTTTGAGTCTTAAATGAGAAATCT
1 TCAAATGAGAATCTTTAAGTCTTAAATGAG-AATCT
28235 TCAAATGAGAATCTTTAAGTCTTAAATGAGAATCT
1 TCAAATGAGAATCTTTAAGTCTTAAATGAGAATCT
28270 T
1 T
28271 TAAGAAATCC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 6 0.17
36 29 0.83
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (35 bp):
TCAAATGAGAATCTTTAAGTCTTAAATGAGAATCT
Found at i:28341 original size:14 final size:13
Alignment explanation
Indices: 28218--28341 Score: 53
Period size: 14 Copynumber: 10.3 Consensus size: 13
28208 AATCTTTGAG
28218 TCTTAAATGAGAAA
1 TCTTAAATGAG-AA
28232 TCTTCAAATGAGAA
1 TCTT-AAATGAGAA
*
28246 TCTT---T-A-AG
1 TCTTAAATGAGAA
28254 TCTTAAATGAGAA
1 TCTTAAATGAGAA
*
28267 TCTTTAA-GA-AA
1 TCTTAAATGAGAA
*
28278 TCCTCAAATGAGAA
1 T-CTTAAATGAGAA
28292 TCTGT--A--AG--
1 TCT-TAAATGAGAA
*
28300 TTTTAAATGAGAA
1 TCTTAAATGAGAA
*
28313 TCTTTAA-GA-AA
1 TCTTAAATGAGAA
28324 TCTTCAAATGAGAA
1 TCTT-AAATGAGAA
28338 TCTT
1 TCTT
28342 TAAGTCTTAA
Statistics
Matches: 81, Mismatches: 10, Indels: 38
0.63 0.08 0.29
Matches are distributed among these distances:
7 1 0.01
8 7 0.09
9 2 0.02
10 3 0.04
11 12 0.15
12 12 0.15
13 18 0.22
14 19 0.23
15 7 0.09
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (13 bp):
TCTTAAATGAGAA
Found at i:28425 original size:92 final size:91
Alignment explanation
Indices: 28227--28545 Score: 328
Period size: 92 Copynumber: 3.5 Consensus size: 91
28217 GTCTTAAATG
*
28227 AGAAATCTTCAAATGAGAATCTTTAAGTCTTAAATGAGAATCTTTAAGAAATCCTCAAATGAGAA
1 AGAAATCTTCAAATGAGAATCTTTAAGTCTTAAATGAGAATCTTTAAGAAATCTTCAAATGAGAA
* * * *
28292 TCTGTAAGTTTTAAATGAGAATCTTT
66 TCTGTAAATCTCAAATAAGAATCTTT
* *
28318 AAGAAATCTTCAAATGAGAATCTTTAAGTCTTAAATAAGAATCTTTAAGAAATTTTCAAATGAGA
1 -AGAAATCTTCAAATGAGAATCTTTAAGTCTTAAATGAGAATCTTTAAGAAATCTTCAAATGAGA
* *
28383 TTCTTTAAAAAATCCTCAAATAAGAATCTTT
65 ATCTGT---AAAT-CTCAAATAAGAATCTTT
* * *
28414 -G-AGTCTT-AAATGAGAATTTTTAAGTCTTAAATGAGAATCTTTAAAAAATCTTCAAATGAGAA
1 AGAAATCTTCAAATGAGAATCTTTAAGTCTTAAATGAGAATCTTTAAGAAATCTTCAAATGAGAA
* * * *
28476 TAAT-TAAGTTTCAAATGAGAATCTTT
66 T-CTGTAAATCTCAAATAAGAATCTTT
* * * * *
28502 -G-AGTATTCAAATAAGAAAT-TTTGAGTTTTCAAATGAGAATCTTT
1 AGAAATCTTCAAATGAG-AATCTTTAAGTCTT-AAATGAGAATCTTT
28546 GAGATGAGAA
Statistics
Matches: 196, Mismatches: 23, Indels: 18
0.83 0.10 0.08
Matches are distributed among these distances:
88 21 0.11
89 17 0.09
90 17 0.09
92 117 0.60
93 6 0.03
94 1 0.01
95 3 0.02
96 14 0.07
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (91 bp):
AGAAATCTTCAAATGAGAATCTTTAAGTCTTAAATGAGAATCTTTAAGAAATCTTCAAATGAGAA
TCTGTAAATCTCAAATAAGAATCTTT
Found at i:28834 original size:20 final size:20
Alignment explanation
Indices: 28801--28839 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28791 AAGATTTATT
*
28801 GAATGTGAACCTTTGAACTC
1 GAATGAGAACCTTTGAACTC
*
28821 GAATGAGAAGCTTTGAACT
1 GAATGAGAACCTTTGAACT
28840 TTTGGATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (20 bp):
GAATGAGAACCTTTGAACTC
Found at i:28851 original size:42 final size:42
Alignment explanation
Indices: 28803--28897 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
28793 GATTTATTGA
** * *
28803 ATGTGAACCTT-TGAACTCGAATGAGAAGCTTTGAACTTTTGG
1 ATGTGAACCTTCAAAACTCGAATGAGAAGCTTT-AAATGTTGG
* * *
28845 ATGTGAATCTTCAAAATTCGAATGAGAATCTTTAAATGTTGG
1 ATGTGAACCTTCAAAACTCGAATGAGAAGCTTTAAATGTTGG
28887 ATGTGAACCTT
1 ATGTGAACCTT
28898 GCAATTTGCA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 27 0.61
43 17 0.39
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.35
Consensus pattern (42 bp):
ATGTGAACCTTCAAAACTCGAATGAGAAGCTTTAAATGTTGG
Found at i:28983 original size:16 final size:16
Alignment explanation
Indices: 28954--28996 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
28944 CACAAATGCC
28954 AATATTGAAATCTTGCA
1 AATA-TGAAATCTTGCA
*
28971 AATATGAATTCTTGCA
1 AATATGAAATCTTGCA
*
28987 TATATGAAAT
1 AATATGAAAT
28997 TTTGTGAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (16 bp):
AATATGAAATCTTGCA
Found at i:29299 original size:42 final size:42
Alignment explanation
Indices: 29182--29307 Score: 132
Period size: 42 Copynumber: 3.0 Consensus size: 42
29172 TGAGCCTTAT
* *
29182 TTTATTTTTCAAAAGTTGTTGAGCCTCTGATTGTAG-GAGCCTT
1 TTTATTTTTTAAAAGTTGTTGAGCCTCTG-TT-TAGAGAGCCTC
* * * *
29225 TTTATTTTTT-AAAGTTGTTAAGCTTTTATTTAGAAGAGCC-C
1 TTTATTTTTTAAAAGTTGTTGAGCCTCTGTTTAG-AGAGCCTC
*
29266 TTTATTTTTTAAAAGTTGTTGTGCCTCTGTTTAGAGGAGCCT
1 TTTATTTTTTAAAAGTTGTTGAGCCTCTGTTTAGA-GAGCCT
29308 TCCAGTGACT
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
40 3 0.04
41 13 0.19
42 42 0.63
43 9 0.13
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (42 bp):
TTTATTTTTTAAAAGTTGTTGAGCCTCTGTTTAGAGAGCCTC
Done.