Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 103 of 126
Found at i:20207854 original size:6 final size:6
Alignment explanation
Indices: 20207843--20207877 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
20207833 GGGTTTGGAG
*
20207843 TTAGGT TTAGGT TTAGGGT TTAGGA TTAGGT TTAG
1 TTAGGT TTAGGT TTA-GGT TTAGGT TTAGGT TTAG
20207878 TAAGGTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (6 bp):
TTAGGT
Found at i:20207862 original size:13 final size:12
Alignment explanation
Indices: 20207834--20207877 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
20207824 GCTTGACTAG
20207834 GGTTT-GGAGTTA
1 GGTTTAGGA-TTA
*
20207846 GGTTTAGGTTTA
1 GGTTTAGGATTA
20207858 GGGTTTAGGATTA
1 -GGTTTAGGATTA
20207871 GGTTTAG
1 GGTTTAG
20207878 TAAGGTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 15 0.54
13 13 0.46
ACGTcount: A:0.18, C:0.00, G:0.39, T:0.43
Consensus pattern (12 bp):
GGTTTAGGATTA
Found at i:20208047 original size:21 final size:20
Alignment explanation
Indices: 20207910--20208059 Score: 85
Period size: 20 Copynumber: 7.2 Consensus size: 20
20207900 ACTTTATCAT
* *
20207910 TTTAAAGTTTAACTTTAGGG
1 TTTAGAGTTTGACTTTAGGG
* *
20207930 TTTAAAGTTTGACTTTAGGT
1 TTTAGAGTTTGACTTTAGGG
* *
20207950 TTTAAGGTATATTTTGAAGTTTAGGG
1 TTT-A-G---AGTTTG-ACTTTAGGG
20207976 -TTA-AGTTTGGACTTTAGGG
1 TTTAGAGTTT-GACTTTAGGG
*
20207995 TTTA-AGGGTTGA-TTTGAGGG
1 TTTAGA-GTTTGACTTT-AGGG
20208015 TTTTAG-GTTTGACTTTAGGG
1 -TTTAGAGTTTGACTTTAGGG
* *
20208035 TTATAGAGTTTGATTTTGGGG
1 TT-TAGAGTTTGACTTTAGGG
20208056 TTTA
1 TTTA
20208060 AAGGTTAGGT
Statistics
Matches: 103, Mismatches: 12, Indels: 30
0.71 0.08 0.21
Matches are distributed among these distances:
19 17 0.17
20 46 0.45
21 25 0.24
24 1 0.01
25 7 0.07
26 7 0.07
ACGTcount: A:0.23, C:0.03, G:0.28, T:0.47
Consensus pattern (20 bp):
TTTAGAGTTTGACTTTAGGG
Found at i:20208048 original size:41 final size:41
Alignment explanation
Indices: 20207980--20208058 Score: 101
Period size: 41 Copynumber: 1.9 Consensus size: 41
20207970 TTAGGGTTAA
20207980 GTTTGGACTTTAGGGTTTAAGGGTTGA-TTTGAGGGTTTTAG
1 GTTTGGACTTTAGGGTTTAAGGGTTGATTTTG-GGGTTTTAG
*
20208021 GTTT-GACTTTAGGG-TTATAGAGTTTGATTTTGGGGTTT
1 GTTTGGACTTTAGGGTTTA-AG-GGTTGATTTTGGGGTTT
20208059 AAAGGTTAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
39 3 0.09
40 12 0.35
41 15 0.44
42 4 0.12
ACGTcount: A:0.16, C:0.03, G:0.34, T:0.47
Consensus pattern (41 bp):
GTTTGGACTTTAGGGTTTAAGGGTTGATTTTGGGGTTTTAG
Found at i:20208085 original size:20 final size:20
Alignment explanation
Indices: 20208060--20208098 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
20208050 TTGGGGTTTA
20208060 AAGGTTA-GGTTTAGACTTTT
1 AAGGTTATGGTTT-GACTTTT
20208080 AAGGTTATGGTTTGACTTT
1 AAGGTTATGGTTTGACTTT
20208099 GAGATTCGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.23, C:0.05, G:0.26, T:0.46
Consensus pattern (20 bp):
AAGGTTATGGTTTGACTTTT
Found at i:20211501 original size:30 final size:31
Alignment explanation
Indices: 20211429--20211504 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
20211419 AATATAGATA
**
20211429 TTTAAAGATTTAATT-GCATGAAAATAAATG
1 TTTAAAGGCTTAATTAGCATGAAAATAAATG
*
20211459 TTTAAATGCTTAATTAG-ATGAAAATAAATG
1 TTTAAAGGCTTAATTAGCATGAAAATAAATG
*
20211489 TTT-GAGGACTTAATTA
1 TTTAAAGG-CTTAATTA
20211505 ATTATAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 2 0.05
30 36 0.92
31 1 0.03
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.38
Consensus pattern (31 bp):
TTTAAAGGCTTAATTAGCATGAAAATAAATG
Found at i:20214833 original size:8 final size:8
Alignment explanation
Indices: 20214815--20214850 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
20214805 TCGGTTGAGT
*
20214815 TTTTAGGG
1 TTTTAGAG
*
20214823 TTTTGGAG
1 TTTTAGAG
20214831 TTTTAGAG
1 TTTTAGAG
20214839 TTTTAGAG
1 TTTTAGAG
20214847 TTTT
1 TTTT
20214851 GAAGATTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.56
Consensus pattern (8 bp):
TTTTAGAG
Found at i:20215253 original size:62 final size:62
Alignment explanation
Indices: 20215181--20215331 Score: 203
Period size: 62 Copynumber: 2.4 Consensus size: 62
20215171 GTTATAAACT
* * * * * * *
20215181 AATTACGACATTTTGATATTAAGAAACACCGTAGTATTTTATTTAAATTTTCATTCTATATC
1 AATTATGACATTTTCATATTAAAAAACAACATAGAATTTGATTTAAATTTTCATTCTATATC
**
20215243 AATTATGACATTTTCATATTAAAAAACAACATAGAATTTGATTTAAATTTTTGTTCTATATC
1 AATTATGACATTTTCATATTAAAAAACAACATAGAATTTGATTTAAATTTTCATTCTATATC
* *
20215305 AATTATGACGTTTTTATATTAAAAAAC
1 AATTATGACATTTTCATATTAAAAAAC
20215332 GTATGATTTG
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 78 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (62 bp):
AATTATGACATTTTCATATTAAAAAACAACATAGAATTTGATTTAAATTTTCATTCTATATC
Found at i:20219458 original size:21 final size:21
Alignment explanation
Indices: 20219428--20219479 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
20219418 AAAAACTTAT
20219428 TTTTTTGTTTCCTTTTGTATA
1 TTTTTTGTTTCCTTTTGTATA
*
20219449 TTTTTGGTTTCCTTTTGTATA
1 TTTTTTGTTTCCTTTTGTATA
20219470 TTTTTTGTTT
1 TTTTTTGTTT
20219480 AAGTGAGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.08, C:0.08, G:0.12, T:0.73
Consensus pattern (21 bp):
TTTTTTGTTTCCTTTTGTATA
Found at i:20224147 original size:13 final size:14
Alignment explanation
Indices: 20224120--20224154 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
20224110 AACTTCTTTT
20224120 TTTTTTGTTTCTTGA
1 TTTTTT-TTTCTTGA
20224135 TTTTTTTTT-TTGA
1 TTTTTTTTTCTTGA
20224148 TTTTTTT
1 TTTTTTT
20224155 CTTCGAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.55
14 3 0.15
15 6 0.30
ACGTcount: A:0.06, C:0.03, G:0.09, T:0.83
Consensus pattern (14 bp):
TTTTTTTTTCTTGA
Found at i:20228250 original size:5 final size:5
Alignment explanation
Indices: 20228222--20228264 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
20228212 CCAAGCACAT
20228222 TTTTA -TTTA -TTTA -TTTA TTTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA
20228265 CATAAAATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 12 0.33
5 20 0.56
6 4 0.11
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:20230789 original size:28 final size:28
Alignment explanation
Indices: 20230741--20230795 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
20230731 CATTTATGCT
* *
20230741 TTTAGATATATAATATTTTTAATATTTA
1 TTTAAATATATAAAATTTTTAATATTTA
*
20230769 TTTAAATA-ATAAAATTATTTATTATTT
1 TTTAAATATATAAAATT-TTTAATATTT
20230796 TACCCATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTAAATATATAAAATTTTTAATATTTA
Found at i:20231363 original size:19 final size:20
Alignment explanation
Indices: 20231328--20231366 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
20231318 AATTTTGCTT
20231328 TTAAACATATTAAAAATAAA
1 TTAAACATATTAAAAATAAA
20231348 TTAAA-ATA-TAATAAATAAA
1 TTAAACATATTAA-AAATAAA
20231367 AAAATCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 10 0.56
20 5 0.28
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
TTAAACATATTAAAAATAAA
Found at i:20231839 original size:5 final size:5
Alignment explanation
Indices: 20231829--20231868 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
20231819 ATGCAACACC
*
20231829 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTG TTTTA CTTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTT
20231869 CAGGCCAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:20233891 original size:29 final size:30
Alignment explanation
Indices: 20233832--20233891 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
20233822 GTTACATAGT
* ***
20233832 ATTGTTTGCATATTTACTAGTTTATTTTTA
1 ATTGGTTGCATATTTACTAGTTTACAATTA
*
20233862 ATTGGTTG-ATATTTAGTAGTTTACAATTA
1 ATTGGTTGCATATTTACTAGTTTACAATTA
20233891 A
1 A
20233892 AGTTTAGTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.28, C:0.05, G:0.13, T:0.53
Consensus pattern (30 bp):
ATTGGTTGCATATTTACTAGTTTACAATTA
Found at i:20234563 original size:19 final size:19
Alignment explanation
Indices: 20234539--20234576 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20234529 TATTATATAA
20234539 ATTAGTTTACATATATTTT
1 ATTAGTTTACATATATTTT
20234558 ATTAGTTTACATATATTTT
1 ATTAGTTTACATATATTTT
20234577 TTCTTAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (19 bp):
ATTAGTTTACATATATTTT
Found at i:20234669 original size:19 final size:19
Alignment explanation
Indices: 20234645--20234681 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
20234635 AGAAAAAGTA
20234645 AATAAAATAAAGGAATAGT
1 AATAAAATAAAGGAATAGT
20234664 AATAAAATAAAGGAATAG
1 AATAAAATAAAGGAATAG
20234682 GAATGGTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (19 bp):
AATAAAATAAAGGAATAGT
Found at i:20237849 original size:8 final size:8
Alignment explanation
Indices: 20237836--20237878 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
20237826 TCCAAATACA
20237836 TTATTTTT
1 TTATTTTT
20237844 TTATTTTATT
1 TTA-TTT-TT
20237854 TTATTTTT
1 TTATTTTT
*
20237862 ATATTTTT
1 TTATTTTT
20237870 TTATATTTT
1 TTAT-TTTT
20237879 ACATGTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 15 0.50
9 10 0.33
10 5 0.17
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (8 bp):
TTATTTTT
Found at i:20237859 original size:18 final size:17
Alignment explanation
Indices: 20237836--20237878 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
20237826 TCCAAATACA
*
20237836 TTATTTTTTTATTTTATT
1 TTATTTTTATATTTT-TT
20237854 TTATTTTTATATTTTTT
1 TTATTTTTATATTTTTT
20237871 TATATTTT
1 T-TATTTT
20237879 ACATGTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (17 bp):
TTATTTTTATATTTTTT
Found at i:20239499 original size:16 final size:17
Alignment explanation
Indices: 20239467--20239499 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20239457 TGGCATTGTC
20239467 CTCCATACCCCCAGTAT
1 CTCCATACCCCCAGTAT
*
20239484 CTCCAT-CCCCCGGTAT
1 CTCCATACCCCCAGTAT
20239500 ATACTGAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.18, C:0.48, G:0.09, T:0.24
Consensus pattern (17 bp):
CTCCATACCCCCAGTAT
Found at i:20240782 original size:19 final size:20
Alignment explanation
Indices: 20240747--20240785 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
20240737 ATTTTTGCTT
20240747 TTAAATATATTAAAAATAAA
1 TTAAATATATTAAAAATAAA
20240767 TTAAA-ATA-TAATAAATAAA
1 TTAAATATATTAA-AAATAAA
20240786 AAAATCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 10 0.56
20 5 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAATATATTAAAAATAAA
Found at i:20242915 original size:25 final size:23
Alignment explanation
Indices: 20242887--20242932 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
20242877 AGGGCATGTA
*
20242887 TATTTATATTTAAAAAATAAAAAAT
1 TATTT-TACTTAAAAAA-AAAAAAT
*
20242912 TATTTTCCTTAAAAAAAAAAA
1 TATTTTACTTAAAAAAAAAAA
20242933 CCAATGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 9 0.47
25 5 0.26
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (23 bp):
TATTTTACTTAAAAAAAAAAAAT
Found at i:20245068 original size:2 final size:2
Alignment explanation
Indices: 20245061--20245085 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20245051 TCAATCTAGT
20245061 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
20245086 CATTCGGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20248331 original size:17 final size:17
Alignment explanation
Indices: 20248309--20248342 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
20248299 ATCATGAAAT
20248309 TTATGAGAAACTCAAGC
1 TTATGAGAAACTCAAGC
20248326 TTATGAGAAACTCAAGC
1 TTATGAGAAACTCAAGC
20248343 CCTTACGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (17 bp):
TTATGAGAAACTCAAGC
Found at i:20249858 original size:20 final size:20
Alignment explanation
Indices: 20249817--20249865 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
20249807 TTGATATTCG
**
20249817 AAAAAAA-AATCATTAAAAA
1 AAAAAAAGAATCAAGAAAAA
*
20249836 AAAAAAAGAATCAAGAAAGA
1 AAAAAAAGAATCAAGAAAAA
*
20249856 AAAGAAAGAA
1 AAAAAAAGAA
20249866 GTCTTGAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.78, C:0.04, G:0.10, T:0.08
Consensus pattern (20 bp):
AAAAAAAGAATCAAGAAAAA
Found at i:20250328 original size:25 final size:24
Alignment explanation
Indices: 20250300--20250363 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
20250290 TATCTTCATC
*
20250300 AATTTTGAGGTAATTTATTCGCTTG
1 AATTTT-AGATAATTTATTCGCTTG
* *
20250325 AATTTTATATAATTTTTTCGCTTG
1 AATTTTAGATAATTTATTCGCTTG
*
20250349 AATTTTATATAATTT
1 AATTTTAGATAATTT
20250364 TTTCTTGTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
24 30 0.83
25 6 0.17
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.55
Consensus pattern (24 bp):
AATTTTAGATAATTTATTCGCTTG
Found at i:20250377 original size:24 final size:24
Alignment explanation
Indices: 20250310--20250367 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
20250300 AATTTTGAGG
*
20250310 TAATTTATTCGCTTGAATTTTATA
1 TAATTTTTTCGCTTGAATTTTATA
20250334 TAATTTTTTCGCTTGAATTTTATA
1 TAATTTTTTCGCTTGAATTTTATA
20250358 TAATTTTTTC
1 TAATTTTTTC
20250368 TTGTTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.26, C:0.09, G:0.07, T:0.59
Consensus pattern (24 bp):
TAATTTTTTCGCTTGAATTTTATA
Found at i:20253616 original size:34 final size:34
Alignment explanation
Indices: 20253569--20253635 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
20253559 TGCATTTTAA
*
20253569 GTCAAATCCTTAAACTTTCTGTTTAATTTGTTGG
1 GTCAAATCCTTAAACTTTCTGTCTAATTTGTTGG
** * *
20253603 GTCAAATTTTTAAACTTTTTGTCTGATTTGTTG
1 GTCAAATCCTTAAACTTTCTGTCTAATTTGTTG
20253636 TGTTTTTGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.51
Consensus pattern (34 bp):
GTCAAATCCTTAAACTTTCTGTCTAATTTGTTGG
Found at i:20254133 original size:21 final size:21
Alignment explanation
Indices: 20254107--20254151 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
20254097 TGTCGCCGTT
*
20254107 CAAGCTCCATTTCAACATTGG
1 CAAGCTCCATTTCAACATTAG
20254128 CAAGCTCCATTTCAACATTAG
1 CAAGCTCCATTTCAACATTAG
20254149 CAA
1 CAA
20254152 TTTTTAGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.29, G:0.11, T:0.27
Consensus pattern (21 bp):
CAAGCTCCATTTCAACATTAG
Found at i:20254441 original size:453 final size:453
Alignment explanation
Indices: 20253593--20254503 Score: 1599
Period size: 453 Copynumber: 2.0 Consensus size: 453
20253583 CTTTCTGTTT
** *
20253593 AATTTGTTGGGTCAAATTTTTAAACTTTTTGTCTGATTTGTTGTGTTTTTGTCACCTTTCAAGCT
1 AATTTGTTGCATCAAATTTTTAAACTTTTTGTCTGATTTGTTGTGTTTTTGTCACCGTTCAAGCT
*
20253658 CCATTTCAACATTGGCAACCTCCATTTCAACATTAACAATTTTCAGTGTTTGACTATTCTTTTTT
66 CCATTTCAACATTGGCAACCTCCATTTCAACATTAACAATTTTCAGTGTTTGACCATTC-TTTTT
20253723 TTTTTTACCAATTTATTTCGTTATTGCAATTTTGAGTTTAGTTTTATTTGGTTGATGAGAAAAAT
130 TTTTTTACCAATTTATTTCGTTATTGCAATTTTGAGTTTAGTTTTATTTGGTTGATGAGAAAAAT
*
20253788 TCAAGATAAAACAGAAAGTAAAAGAAATAGAGTTTTTCTCTGAAAAATTTGAAATTAAATGTTGA
195 TCAAGATAAAACAGAAAGTAAAAGAAATAGAGTTTTTCTCTGAAAAACTTGAAATTAAATGTTGA
*
20253853 ATTTAGTTACAAACACAAATAAAATTTTAGATTTAGTTTTTTTTTCAACAAAATATTTTTGAAAT
260 ATTCAGTTACAAACACAAATAAAATTTTAGATTTAGTTTTTTTTTCAACAAAATATTTTTGAAAT
* *
20253918 TACTAAAAACTTGTTACTTGTTAACATGAATTTGTTGATTCATTCAAAATATTATTGGGAAACCA
325 TACTAAAAAATTGTTACTTATTAACATGAATTTGTTGATTCATTCAAAATATTATTGGGAAACCA
* *
20253983 TTCTGAAATAATCTATTATGTTTTTTTCTCATCTCATCTTGGCATATGTTTTATTTTTTTTTTCA
390 TTCTGAAATAATCTATTAT-ATTTTTTATCATCTCATCTTGGCATATGTTTTATTTTTTTTTTCA
*
20254048 AATTTGTTGCATCAAATTTTTAAACTTTTTGTCTGATTTGTTGTGTTTTTGTCGCCGTTCAAGCT
1 AATTTGTTGCATCAAATTTTTAAACTTTTTGTCTGATTTGTTGTGTTTTTGTCACCGTTCAAGCT
* * *
20254113 CCATTTCAACATTGGCAAGCTCCATTTCAACATTAGCAATTTTTAGTGTTTGACCATTC-TTTTT
66 CCATTTCAACATTGGCAACCTCCATTTCAACATTAACAATTTTCAGTGTTTGACCATTCTTTTTT
20254177 TTTTTACCAATTTATTTCGTTATTGCAATTTTGAGTTTAGTTTTATTTGGTTGATGAGAAAAATT
131 TTTTTACCAATTTATTTCGTTATTGCAATTTTGAGTTTAGTTTTATTTGGTTGATGAGAAAAATT
* *
20254242 CAAGATAGAACAGAAAGTAAAAGAAATAGGGTTTTTCTCTGAAAAACTTGAAATTAAATGTTGAA
196 CAAGATAAAACAGAAAGTAAAAGAAATAGAGTTTTTCTCTGAAAAACTTGAAATTAAATGTTGAA
* *
20254307 TTCAGTTACAAACACAAATGAAATTTTAGGTTTAGTTTTTTTTTCAACAAAATATTTTTGAAATT
261 TTCAGTTACAAACACAAATAAAATTTTAGATTTAGTTTTTTTTTCAACAAAATATTTTTGAAATT
* *
20254372 ACTAAAAAATTGTTACTTATTAACATGAATTTGTTGATTCATTCAAGATATTCTTGGGAAACCAT
326 ACTAAAAAATTGTTACTTATTAACATGAATTTGTTGATTCATTCAAAATATTATTGGGAAACCAT
* *
20254437 TCTGAAATAATCTATTATATTTTTTATCATCTTATCTTGGCATTTGTTTTATTTTTTTTTTCA
391 TCTGAAATAATCTATTATATTTTTTATCATCTCATCTTGGCATATGTTTTATTTTTTTTTTCA
20254500 AATT
1 AATT
20254504 ATGGTGTTTG
Statistics
Matches: 434, Mismatches: 22, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
452 45 0.10
453 273 0.63
455 116 0.27
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (453 bp):
AATTTGTTGCATCAAATTTTTAAACTTTTTGTCTGATTTGTTGTGTTTTTGTCACCGTTCAAGCT
CCATTTCAACATTGGCAACCTCCATTTCAACATTAACAATTTTCAGTGTTTGACCATTCTTTTTT
TTTTTACCAATTTATTTCGTTATTGCAATTTTGAGTTTAGTTTTATTTGGTTGATGAGAAAAATT
CAAGATAAAACAGAAAGTAAAAGAAATAGAGTTTTTCTCTGAAAAACTTGAAATTAAATGTTGAA
TTCAGTTACAAACACAAATAAAATTTTAGATTTAGTTTTTTTTTCAACAAAATATTTTTGAAATT
ACTAAAAAATTGTTACTTATTAACATGAATTTGTTGATTCATTCAAAATATTATTGGGAAACCAT
TCTGAAATAATCTATTATATTTTTTATCATCTCATCTTGGCATATGTTTTATTTTTTTTTTCA
Found at i:20255417 original size:34 final size:34
Alignment explanation
Indices: 20255331--20255418 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 34
20255321 AAACACCATT
* * * **
20255331 AAATTTAGTGGTGTTTTACACAATAAATGTTGTT
1 AAATTTAGTAGTGTTTTATACAATAAACGTTGCA
* *
20255365 AAATTTAGTAGCGTTTTATACTATAAACGTTGCA
1 AAATTTAGTAGTGTTTTATACAATAAACGTTGCA
*
20255399 AAATTTAGTAGTATTTTATA
1 AAATTTAGTAGTGTTTTATA
20255419 ATAAAAATGC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (34 bp):
AAATTTAGTAGTGTTTTATACAATAAACGTTGCA
Found at i:20258548 original size:36 final size:36
Alignment explanation
Indices: 20258507--20258582 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
20258497 GGTGCTCAGA
20258507 AAGTATGAAGCCAGTAAACCAATGGAGGAAAGAAAT
1 AAGTATGAAGCCAGTAAACCAATGGAGGAAAGAAAT
20258543 AAGTATGAAGCCAGTAAACCAATGGAGGAAAGAAAT
1 AAGTATGAAGCCAGTAAACCAATGGAGGAAAGAAAT
20258579 AAGT
1 AAGT
20258583 TGCCGCCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.50, C:0.11, G:0.25, T:0.14
Consensus pattern (36 bp):
AAGTATGAAGCCAGTAAACCAATGGAGGAAAGAAAT
Found at i:20264400 original size:2 final size:2
Alignment explanation
Indices: 20264376--20264414 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
20264366 TCACTACCCC
* * *
20264376 AT AT AA AT AT AA AT AT TT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20264415 GATACCCAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:20267322 original size:2 final size:2
Alignment explanation
Indices: 20267315--20267350 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
20267305 AAACCAATCT
*
20267315 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20267351 GACACACACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20267443 original size:8 final size:8
Alignment explanation
Indices: 20267427--20267486 Score: 79
Period size: 8 Copynumber: 7.8 Consensus size: 8
20267417 CATCATCCCT
*
20267427 CATAAATA
1 CATATATA
20267435 CATATATA
1 CATATATA
20267443 CATATATA
1 CATATATA
*
20267451 CATACATA
1 CATATATA
20267459 CATATAT-
1 CATATATA
20267466 -ATATATA
1 CATATATA
*
20267473 TATATATA
1 CATATATA
20267481 CATATA
1 CATATA
20267487 AGAGGAGATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
6 6 0.13
8 40 0.87
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.37
Consensus pattern (8 bp):
CATATATA
Found at i:20267467 original size:4 final size:4
Alignment explanation
Indices: 20267436--20267486 Score: 57
Period size: 4 Copynumber: 12.8 Consensus size: 4
20267426 TCATAAATAC
* * * * *
20267436 ATAT ATAC ATAT ATAC ATAC ATAC ATAT ATAT ATAT ATAT ATAT ACAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
20267484 ATA
1 ATA
20267487 AGAGGAGATA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (4 bp):
ATAT
Found at i:20270056 original size:42 final size:42
Alignment explanation
Indices: 20270010--20270089 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
20270000 TACTTAATAA
20270010 TTAAACTAATTACTAATTATTTTCATATAACTTGTAAGATAG
1 TTAAACTAATTACTAATTATTTTCATATAACTTGTAAGATAG
20270052 TTAAACTAATTACTAATTATTTTCATATAACTTGTAAG
1 TTAAACTAATTACTAATTATTTTCATATAACTTGTAAG
20270090 GCCTTGATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (42 bp):
TTAAACTAATTACTAATTATTTTCATATAACTTGTAAGATAG
Found at i:20270545 original size:2 final size:2
Alignment explanation
Indices: 20270538--20270570 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20270528 AAGTCTTAGA
20270538 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20270571 GTATCACAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20271298 original size:22 final size:20
Alignment explanation
Indices: 20271263--20271307 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
20271253 ATAAAAAATT
*
20271263 ATTTTTTAATTATTTATTTA
1 ATTTTTTAATTATTTATGTA
20271283 ATTTTTTAAATATATTTATGTA
1 ATTTTTT-AAT-TATTTATGTA
20271305 ATT
1 ATT
20271308 ATATATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.32
21 3 0.14
22 12 0.55
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTTTTTAATTATTTATGTA
Found at i:20271340 original size:20 final size:20
Alignment explanation
Indices: 20271315--20271363 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
20271305 ATTATATATT
20271315 TAATATTTAT-GTTTAAACAA
1 TAATATTTATAGTTTAAA-AA
*
20271335 TAATATTTTATATTTTAAAAA
1 TAATA-TTTATAGTTTAAAAA
20271356 TAATATTT
1 TAATATTT
20271364 TATTAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
21 12 0.46
22 6 0.23
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TAATATTTATAGTTTAAAAA
Found at i:20271357 original size:21 final size:22
Alignment explanation
Indices: 20271326--20271366 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
20271316 AATATTTATG
20271326 TTTAAACAATAATATTTTATAT
1 TTTAAACAATAATATTTTATAT
20271348 TTTAAA-AATAATATTTTAT
1 TTTAAACAATAATATTTTAT
20271367 TAATTTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAAACAATAATATTTTATAT
Found at i:20271412 original size:5 final size:5
Alignment explanation
Indices: 20271404--20271436 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
20271394 AAAAAAATAT
20271404 TTAGG TTAGG TTAGG TTAGG TTAGG TTCAGG TT
1 TTAGG TTAGG TTAGG TTAGG TTAGG TT-AGG TT
20271437 TGATGAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.18, C:0.03, G:0.36, T:0.42
Consensus pattern (5 bp):
TTAGG
Found at i:20272642 original size:18 final size:19
Alignment explanation
Indices: 20272619--20272654 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20272609 TAATATATCC
*
20272619 TTATTA-ATTTATTTTTTA
1 TTATTATATATATTTTTTA
20272637 TTATTATATATATTTTTT
1 TTATTATATATATTTTTT
20272655 TGTAATTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATTATATATATTTTTTA
Found at i:20279806 original size:14 final size:15
Alignment explanation
Indices: 20279781--20279809 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20279771 TCACTTAAAA
20279781 ATTTTTTAGAAATTT
1 ATTTTTTAGAAATTT
20279796 ATTTTTT-GAAATTT
1 ATTTTTTAGAAATTT
20279810 TTAAGAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
ATTTTTTAGAAATTT
Found at i:20280026 original size:8 final size:8
Alignment explanation
Indices: 20280015--20280044 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
20280005 TAATTCCAAA
20280015 ATTTTTAT
1 ATTTTTAT
20280023 ATTTTTAT
1 ATTTTTAT
20280031 ATTTTTAT
1 ATTTTTAT
20280039 ATTTTT
1 ATTTTT
20280045 TTTTATTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
ATTTTTAT
Found at i:20285773 original size:9 final size:9
Alignment explanation
Indices: 20285759--20285783 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
20285749 TCTTAATCCT
20285759 AAAATTTTA
1 AAAATTTTA
20285768 AAAATTTTA
1 AAAATTTTA
20285777 AAAATTT
1 AAAATTT
20285784 CTTAATCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAATTTTA
Found at i:20316472 original size:20 final size:20
Alignment explanation
Indices: 20316447--20316493 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
20316437 ATTAAATTTT
*
20316447 TTTTTTTTAAATTCACAAAA
1 TTTTTTTAAAATTCACAAAA
***
20316467 TTTTTTTAAAATTTTTAAAA
1 TTTTTTTAAAATTCACAAAA
20316487 TTTTTTT
1 TTTTTTT
20316494 GAGTAATCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTTTAAAATTCACAAAA
Found at i:20316603 original size:20 final size:20
Alignment explanation
Indices: 20316578--20316621 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
20316568 AGGAAACAAA
*
20316578 AAAATTTTAAAAAAAATCTC
1 AAAATTTTAAAAAAAATCAC
*
20316598 AAAATTTTAATAAAAATCAC
1 AAAATTTTAAAAAAAATCAC
20316618 AAAA
1 AAAA
20316622 AATTCAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAATTTTAAAAAAAATCAC
Found at i:20316671 original size:19 final size:20
Alignment explanation
Indices: 20316649--20316693 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
20316639 GAAAATTCAA
20316649 AAAAAATTGCAAA-ATTTTT
1 AAAAAATTGCAAATATTTTT
* *
20316668 AAAAAATTGTAAATTTTTTT
1 AAAAAATTGCAAATATTTTT
20316688 AAAAAA
1 AAAAAA
20316694 ACTATGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (20 bp):
AAAAAATTGCAAATATTTTT
Found at i:20316687 original size:21 final size:21
Alignment explanation
Indices: 20316663--20316709 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
20316653 AATTGCAAAA
* *
20316663 TTTTT-AAAAAATTGTAAATT
1 TTTTTAAAAAAACTATAAATT
*
20316683 TTTTTAAAAAAACTATGAATT
1 TTTTTAAAAAAACTATAAATT
20316704 TTTTTA
1 TTTTTA
20316710 TTTTTAATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTTTAAAAAAACTATAAATT
Found at i:20316769 original size:26 final size:25
Alignment explanation
Indices: 20316721--20316783 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
20316711 TTTTAATCTG
20316721 AAATTTTTAATTTTTATATATTTTATA
1 AAATTTTT-ATTTTTATATATTTT-TA
* *
20316748 AAATTTTTATTTTTTTGA-ATTTTTT
1 AAATTTTTATTTTTAT-ATATTTTTA
*
20316773 AGATTTTTATT
1 AAATTTTTATT
20316784 AAAATTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 11 0.34
26 12 0.38
27 9 0.28
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (25 bp):
AAATTTTTATTTTTATATATTTTTA
Found at i:20318002 original size:24 final size:23
Alignment explanation
Indices: 20317959--20318024 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
20317949 TCGACTCAAT
** *
20317959 TTTAATTAAATTTTTTTATTTAA
1 TTTAATTAAATTTTAATATTAAA
20317982 TTTGAATTAAATTTTAATATTAAA
1 TTT-AATTAAATTTTAATATTAAA
* *
20318006 TATATATTAAATTTAAATA
1 TTTA-ATTAAATTTTAATA
20318025 AAATATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 4 0.11
24 32 0.89
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTAATTAAATTTTAATATTAAA
Found at i:20318087 original size:20 final size:21
Alignment explanation
Indices: 20318062--20318101 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
20318052 AATCTAATTT
*
20318062 ATATATTTATATT-AATTTTC
1 ATATATATATATTAAATTTTC
*
20318082 ATATATATATTTTAAATTTT
1 ATATATATATATTAAATTTT
20318102 TATAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATATATATTAAATTTTC
Found at i:20323979 original size:20 final size:20
Alignment explanation
Indices: 20323954--20323994 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20323944 CCGCCTCCTC
20323954 AAGGCTTTAAGAAAATTGAG
1 AAGGCTTTAAGAAAATTGAG
20323974 AAGGCTTTAAGAAAATTGAG
1 AAGGCTTTAAGAAAATTGAG
20323994 A
1 A
20323995 CTAAGACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (20 bp):
AAGGCTTTAAGAAAATTGAG
Found at i:20329798 original size:124 final size:125
Alignment explanation
Indices: 20329656--20329904 Score: 405
Period size: 124 Copynumber: 2.0 Consensus size: 125
20329646 GAAAAAAGTT
*
20329656 GTTGTAACTTTTTTTTAATGAATGAAAATTGGCAGTGAAATATTGATCATAATTGATTAAAAACT
1 GTTGTAACTTTTTTTTAATGAATAAAAATTGGCAGTGAAATATTGATCATAATTGATTAAAAACT
* *
20329721 GTTTCTTTCCCTTGCTT-GAAAGGATGGAAAA-ATGGTTTTTGTAGGGAAATAGAGGGATGG
66 GTTTCTTTCCCTTGCTTCG-AAGGATGGAAAATATGG-CTTTGTAGGGAAACAGAGGGATGG
* * *
20329781 GTTGTAAC-TTTTTTTAATGAATAAAAATTGGCAGTGAAATCTTGATCATAATTGATTAGAAAGT
1 GTTGTAACTTTTTTTTAATGAATAAAAATTGGCAGTGAAATATTGATCATAATTGATTAAAAACT
20329845 GTTTCTTTCCCTTGCTTCGAAGGATGGAAAATATGGCTTTGTAGGGAAACAGAGGGATGG
66 GTTTCTTTCCCTTGCTTCGAAGGATGGAAAATATGGCTTTGTAGGGAAACAGAGGGATGG
20329905 CTGTTTCACT
Statistics
Matches: 116, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
124 103 0.89
125 13 0.11
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (125 bp):
GTTGTAACTTTTTTTTAATGAATAAAAATTGGCAGTGAAATATTGATCATAATTGATTAAAAACT
GTTTCTTTCCCTTGCTTCGAAGGATGGAAAATATGGCTTTGTAGGGAAACAGAGGGATGG
Found at i:20330238 original size:7 final size:8
Alignment explanation
Indices: 20330208--20330237 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
20330198 TTGGTGTAGT
20330208 TTTTTTTC
1 TTTTTTTC
20330216 TTTTTTTC
1 TTTTTTTC
20330224 TTTTTTTC
1 TTTTTTTC
20330232 TTTTTT
1 TTTTTT
20330238 CAAAGGAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTC
Found at i:20341325 original size:14 final size:13
Alignment explanation
Indices: 20341287--20341327 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
20341277 TAAAAATCCG
*
20341287 TTTAAAAATATAA
1 TTTAAAAATTTAA
20341300 -TTAAAAATTTAA
1 TTTAAAAATTTAA
20341312 TTTAAAATATTTAA
1 TTTAAAA-ATTTAA
20341326 TT
1 TT
20341328 ATTTAGTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 11 0.44
13 6 0.24
14 8 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTAAAAATTTAA
Found at i:20343072 original size:30 final size:30
Alignment explanation
Indices: 20343038--20343148 Score: 125
Period size: 30 Copynumber: 3.7 Consensus size: 30
20343028 TTGATTTATT
*
20343038 TTAAAGCTTTATTTAAATATAAATTAAAAA
1 TTAAAGATTTATTTAAATATAAATTAAAAA
** *
20343068 TTAAAGATTTATTTAAATGCAAATAAAAAA
1 TTAAAGATTTATTTAAATATAAATTAAAAA
*
20343098 GTTAATA-ATTTATTTAGATATAAATTAAAAA
1 -TTAA-AGATTTATTTAAATATAAATTAAAAA
* * *
20343129 TTAAAAAATTATTTTAATAT
1 TTAAAGATTTATTTAAATAT
20343149 GATAAAAGTA
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
29 1 0.01
30 41 0.61
31 24 0.36
32 1 0.01
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (30 bp):
TTAAAGATTTATTTAAATATAAATTAAAAA
Found at i:20359081 original size:70 final size:70
Alignment explanation
Indices: 20358968--20359108 Score: 264
Period size: 70 Copynumber: 2.0 Consensus size: 70
20358958 GTTTGGTTTT
20358968 ACTTCGTGCTTGATGGTCAATTGCATATATCGACACATACTTATATACTGGTTTGCAGCAAAAGA
1 ACTTCGTGCTTGATGGTCAATTGCATATATCGACACATACTTATATACTGGTTTGCAGCAAAAGA
20359033 AGACA
66 AGACA
* *
20359038 ACTTCGTGCTTGATGGTCAGTTGCATATATCGACACATACTTATATACTGGTTTGCAGCATAAGA
1 ACTTCGTGCTTGATGGTCAATTGCATATATCGACACATACTTATATACTGGTTTGCAGCAAAAGA
20359103 AGACA
66 AGACA
20359108 A
1 A
20359109 AGCTGGTTGG
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (70 bp):
ACTTCGTGCTTGATGGTCAATTGCATATATCGACACATACTTATATACTGGTTTGCAGCAAAAGA
AGACA
Found at i:20359160 original size:29 final size:29
Alignment explanation
Indices: 20359074--20359161 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
20359064 ATATCGACAC
20359074 ATACTTATATACTGGTTTGCAGCATAAGA
1 ATACTTATATACTGGTTTGCAGCATAAGA
* * * * *
20359103 AGAC--A-A-AGCTGGTTGGTA-CAATTATA
1 ATACTTATATA-CTGGTTTGCAGC-ATAAGA
20359129 ATACTTATATACTGGTTTGCAGCATAAGA
1 ATACTTATATACTGGTTTGCAGCATAAGA
20359158 ATAC
1 ATAC
20359162 AAAACCGGAT
Statistics
Matches: 42, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 2 0.05
26 16 0.38
27 1 0.02
28 1 0.02
29 20 0.48
30 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (29 bp):
ATACTTATATACTGGTTTGCAGCATAAGA
Found at i:20359175 original size:55 final size:55
Alignment explanation
Indices: 20359074--20359177 Score: 172
Period size: 55 Copynumber: 1.9 Consensus size: 55
20359064 ATATCGACAC
* * *
20359074 ATACTTATATACTGGTTTGCAGCATAAGAAGACAAAGCTGGTTGGTACAATTATA
1 ATACTTATATACTGGTTTGCAGCATAAGAAGACAAAACCGGATGGTACAATTATA
*
20359129 ATACTTATATACTGGTTTGCAGCATAAGAATACAAAACCGGATGGTACA
1 ATACTTATATACTGGTTTGCAGCATAAGAAGACAAAACCGGATGGTACA
20359178 CCTAAAAGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (55 bp):
ATACTTATATACTGGTTTGCAGCATAAGAAGACAAAACCGGATGGTACAATTATA
Found at i:20361238 original size:142 final size:142
Alignment explanation
Indices: 20360978--20361239 Score: 425
Period size: 142 Copynumber: 1.8 Consensus size: 142
20360968 TAATTGATTT
*
20360978 ATATAATAATTTTAAAAATATATATTTAATAAATTTAAAATTCAAATTTTAATAATTACAACCCT
1 ATATAATAATTTTAAAAAAATATATTTAATAAATTTAAAATTCAAATTTTAATAATTACAACCCT
* * *
20361043 TTCTCTTATTTACAGGTTACAATCCTTTTACACACACATATACATATACATATATTCTCTTCGAA
66 TACTCTTATTTACAGATTACAATCCTTTTACACACACATACACATATACATATATTCTCTTCGAA
20361108 GAATTAAAATTC
131 GAATTAAAATTC
**
20361120 ATATAATAATTTTAAAAAAATATATTTAATAAATTTAAAATTCAAATTTTAATAATTGTAACCCT
1 ATATAATAATTTTAAAAAAATATATTTAATAAATTTAAAATTCAAATTTTAATAATTACAACCCT
* *** *
20361185 TACTCTTATTTACAGATTACAATCGTTTTACACACGTGTACACATATATATATAT
66 TACTCTTATTTACAGATTACAATCCTTTTACACACACATACACATATACATATAT
20361240 ATATGTATAT
Statistics
Matches: 109, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
142 109 1.00
ACGTcount: A:0.43, C:0.13, G:0.03, T:0.40
Consensus pattern (142 bp):
ATATAATAATTTTAAAAAAATATATTTAATAAATTTAAAATTCAAATTTTAATAATTACAACCCT
TACTCTTATTTACAGATTACAATCCTTTTACACACACATACACATATACATATATTCTCTTCGAA
GAATTAAAATTC
Found at i:20363509 original size:22 final size:23
Alignment explanation
Indices: 20363465--20363509 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
20363455 TCTGTATATT
20363465 TATTTGTATCTCTAGAAATTAAG
1 TATTTGTATCTCTAGAAATTAAG
20363488 TATTTGTATC-CTTAG-AATTAAG
1 TATTTGTATCTC-TAGAAATTAAG
20363510 GACAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (23 bp):
TATTTGTATCTCTAGAAATTAAG
Found at i:20363681 original size:23 final size:24
Alignment explanation
Indices: 20363655--20363700 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20363645 ATACATTCAA
20363655 TTTTA-TTCTTAGTTTTTACACAG
1 TTTTATTTCTTAGTTTTTACACAG
* *
20363678 TTTTATTTTTTAGTTTTTCCACA
1 TTTTATTTCTTAGTTTTTACACA
20363701 TGGTATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.61
Consensus pattern (24 bp):
TTTTATTTCTTAGTTTTTACACAG
Found at i:20363798 original size:25 final size:25
Alignment explanation
Indices: 20363768--20363830 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
20363758 TGACTTCTAT
*
20363768 TTTAGGCCTTCATTGCCGAACCCTG
1 TTTAGGCCTTCATTGCCGAACCCTA
* **
20363793 TTTAGGTCTTCATTGTTGAACCCTA
1 TTTAGGCCTTCATTGCCGAACCCTA
*
20363818 TTAAGGCCTTCAT
1 TTTAGGCCTTCAT
20363831 AGCCATTCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.38
Consensus pattern (25 bp):
TTTAGGCCTTCATTGCCGAACCCTA
Found at i:20374010 original size:13 final size:12
Alignment explanation
Indices: 20373985--20374019 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
20373975 ATATATATAT
20373985 AAATGTTTTTTA
1 AAATGTTTTTTA
*
20373997 ATATGTTCTTTTA
1 AAATGTT-TTTTA
20374010 AAATGTTTTT
1 AAATGTTTTT
20374020 ATTTATGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.60
Consensus pattern (12 bp):
AAATGTTTTTTA
Found at i:20374235 original size:33 final size:32
Alignment explanation
Indices: 20374192--20374267 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
20374182 ATCATATAAA
20374192 ATATAATATAAA-TATATAAATTATTAATATTTT
1 ATATAATATAAATTAT-TAAATTATTAA-ATTTT
*
20374225 ATATGATATAAATTATTAAATTATTAAA-TTT
1 ATATAATATAAATTATTAAATTATTAAATTTT
*
20374256 AAATAA-ATAAAT
1 ATATAATATAAAT
20374268 AAAATATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
30 6 0.15
31 7 0.18
32 1 0.03
33 22 0.56
34 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (32 bp):
ATATAATATAAATTATTAAATTATTAAATTTT
Found at i:20376018 original size:23 final size:23
Alignment explanation
Indices: 20375985--20376042 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
20375975 TAGACAAATA
*
20375985 AAAATAAACAGTTAAGTCTATAC
1 AAAATAGACAGTTAAGTCTATAC
* *
20376008 AAAATAGACAGATAAGTCTATTC
1 AAAATAGACAGTTAAGTCTATAC
20376031 -AAATAGACAGTT
1 AAAATAGACAGTT
20376043 TTAATTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 11 0.35
23 20 0.65
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (23 bp):
AAAATAGACAGTTAAGTCTATAC
Found at i:20381119 original size:23 final size:23
Alignment explanation
Indices: 20381070--20381122 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
20381060 TCTAATTAAT
* * * *
20381070 TTAGTTTATTTAAAACAAATAGT
1 TTAGTCTATATAAAACAAAAAGA
*
20381093 TTAGTCTATATAAAATAAAAAGA
1 TTAGTCTATATAAAACAAAAAGA
20381116 TTAGTCT
1 TTAGTCT
20381123 GTTCAAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (23 bp):
TTAGTCTATATAAAACAAAAAGA
Found at i:20382942 original size:18 final size:17
Alignment explanation
Indices: 20382919--20382957 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
20382909 ATATAATTTT
20382919 TATTAAAATTTTAAATTA
1 TATT-AAATTTTAAATTA
*
20382937 TATT-AATTTTATATTA
1 TATTAAATTTTAAATTA
20382953 TATTA
1 TATTA
20382958 TCGTATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 15 0.79
18 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTAAATTTTAAATTA
Found at i:20382944 original size:16 final size:16
Alignment explanation
Indices: 20382925--20382957 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20382915 TTTTTATTAA
20382925 AATTTTAAATTATATT
1 AATTTTAAATTATATT
*
20382941 AATTTTATATTATATT
1 AATTTTAAATTATATT
20382957 A
1 A
20382958 TCGTATCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTTTAAATTATATT
Found at i:20384396 original size:50 final size:50
Alignment explanation
Indices: 20384328--20384427 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
20384318 TATTTGTTTC
20384328 AACCTTGAGAAACCGTTCGTTTGTTTAACGAATCGATTATAGGTATTTTA
1 AACCTTGAGAAACCGTTCGTTTGTTTAACGAATCGATTATAGGTATTTTA
20384378 AACCTTGAGAAACCGTTCGTTTGTTTAACGAATCGATTATAGGTATTTTA
1 AACCTTGAGAAACCGTTCGTTTGTTTAACGAATCGATTATAGGTATTTTA
20384428 GTCTGAACCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (50 bp):
AACCTTGAGAAACCGTTCGTTTGTTTAACGAATCGATTATAGGTATTTTA
Found at i:20388547 original size:33 final size:34
Alignment explanation
Indices: 20388510--20388577 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
20388500 TCCAAACAAA
20388510 GGAAAAAGTGGGAAG-AAAATGATAAAAAAACTT
1 GGAAAAAGTGGGAAGAAAAATGATAAAAAAACTT
*
20388543 GGAAAAAGTGGGAAGAAAAATGATCAAAAAACTT
1 GGAAAAAGTGGGAAGAAAAATGATAAAAAAACTT
20388577 G
1 G
20388578 ATGAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 15 0.45
34 18 0.55
ACGTcount: A:0.56, C:0.04, G:0.25, T:0.15
Consensus pattern (34 bp):
GGAAAAAGTGGGAAGAAAAATGATAAAAAAACTT
Found at i:20394062 original size:45 final size:44
Alignment explanation
Indices: 20393999--20394107 Score: 139
Period size: 45 Copynumber: 2.5 Consensus size: 44
20393989 TGTTTCATTA
* *
20393999 TTATGATTTTTCATGTGTATTAACTTATTTGTTTATTTTATAGT
1 TTATGATTTTTCATGTGTACTAACTTATTTGTTTATTGTATAGT
* *
20394043 TTATGATTTTTTTATGTGTACTAATTTATTTGTTTATTGTATAGAT
1 TTATGA-TTTTTCATGTGTACTAACTTATTTGTTTATTGTATAG-T
* *
20394089 TT-TGACTTTTCATATGTAC
1 TTATGATTTTTCATGTGTAC
20394108 CAATTTGTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
44 17 0.30
45 36 0.64
46 3 0.05
ACGTcount: A:0.23, C:0.06, G:0.12, T:0.60
Consensus pattern (44 bp):
TTATGATTTTTCATGTGTACTAACTTATTTGTTTATTGTATAGT
Found at i:20395209 original size:137 final size:138
Alignment explanation
Indices: 20394767--20395291 Score: 623
Period size: 138 Copynumber: 3.8 Consensus size: 138
20394757 TTTCTTCAGT
* *
20394767 TTTGTACACAGTTGTGAATATAAATTCTTATTGTTACTATGTATTGCATACATGTATTTGCATAT
1 TTTGTACATAGTTGTGAATATGAATTCTTATTGTTACTATGTATTGCATACATGTATTTGCATAT
* * *
20394832 ACATTTTTATCTATGTAAATATTTTTGTAT-TACATTATTTCATTTATTTGGAGGCAATCATTCT
66 ATATTTTTATCTATGTAAATATTTTTGTATGTACATTATTTCATTTATTTGGA-GAAATCATTTT
*
20394896 -CTTTTTATT
130 CCTTTTTA-G
* * * *
20394905 TTTGTACATAATTGTGAATATGAATTCTTATTGTTATTATGTATTGCATATATATATTTGCATAT
1 TTTGTACATAGTTGTGAATATGAATTCTTATTGTTACTATGTATTGCATACATGTATTTGCATAT
* * *
20394970 ATATTTTTAT-TGATGAAAATATTTTTGTATGTACATTATTTCATTTATTTGGGGGTAAT-ATTT
66 ATATTTTTATCT-ATGTAAATATTTTTGTATGTACATTATTTCATTTATTT-GGAGAAATCATTT
*
20395033 GCCTTTTTAG
129 TCCTTTTTAG
* * * * * * * *
20395043 TTTGTATATAGTTTTGAGTGTGAATTCTTGTT-TCTACTATGCATTACATACATGTATTTACATA
1 TTTGTACATAGTTGTGAATATGAATTCTTATTGT-TACTATGTATTGCATACATGTATTTGCATA
* * * * * *
20395107 TATATTTTTGTCTATCTAAATATCTTTGTATGTACATTA-TTCATTTGTTTGGAAAAATCTTTTT
65 TATATTTTTATCTATGTAAATATTTTTGTATGTACATTATTTCATTTATTTGGAGAAATCATTTT
20395171 CCTTTTTAG
130 CCTTTTTAG
* * * *
20395180 TTTGTATATAGTTTTGAATATGAATTCTTGTTTTTACTATGTATTGCATACATGTATTTGCATAT
1 TTTGTACATAGTTGTGAATATGAATTCTTATTGTTACTATGTATTGCATACATGTATTTGCATAT
* * *
20395245 GCAT-TTTTTATCCATGTAAACATTTTTGTATGTATATTATTTCATTT
66 --ATATTTTTATCTATGTAAATATTTTTGTATGTACATTATTTCATTT
20395292 GTTTAGGGTG
Statistics
Matches: 330, Mismatches: 46, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
136 5 0.02
137 82 0.25
138 201 0.61
139 40 0.12
140 2 0.01
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.52
Consensus pattern (138 bp):
TTTGTACATAGTTGTGAATATGAATTCTTATTGTTACTATGTATTGCATACATGTATTTGCATAT
ATATTTTTATCTATGTAAATATTTTTGTATGTACATTATTTCATTTATTTGGAGAAATCATTTTC
CTTTTTAG
Found at i:20396944 original size:16 final size:16
Alignment explanation
Indices: 20396925--20396955 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20396915 AAAATATTAA
*
20396925 TAATATTTATTTATTT
1 TAATATTTAATTATTT
20396941 TAATATTTAATTATT
1 TAATATTTAATTATT
20396956 AAATTTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATATTTAATTATTT
Found at i:20398691 original size:18 final size:20
Alignment explanation
Indices: 20398655--20398696 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
20398645 TAACTCTTAA
20398655 AAAAATCAAATTAATAAAAG
1 AAAAATCAAATTAATAAAAG
*
20398675 AAAAAT-AATTTAA-AAAAG
1 AAAAATCAAATTAATAAAAG
20398693 AAAA
1 AAAA
20398697 GTATTTTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (20 bp):
AAAAATCAAATTAATAAAAG
Found at i:20400732 original size:18 final size:18
Alignment explanation
Indices: 20400688--20400740 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
20400678 CGTATCATAT
*
20400688 TTATGTTTAAAATTTAAA
1 TTATGTTTATAATTTAAA
**
20400706 TATAT-TTTATAATTTATG
1 T-TATGTTTATAATTTAAA
*
20400724 TTATGTTTATATTTTAA
1 TTATGTTTATAATTTAA
20400741 TAATTTGTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 3 0.11
18 22 0.79
19 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (18 bp):
TTATGTTTATAATTTAAA
Found at i:20401432 original size:18 final size:18
Alignment explanation
Indices: 20401411--20401449 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
20401401 AATAATGATA
20401411 AAAAAAAAAAAAACAAAG
1 AAAAAAAAAAAAACAAAG
* * *
20401429 AAAAAGAAAGAAAGAAAG
1 AAAAAAAAAAAAACAAAG
20401447 AAA
1 AAA
20401450 GAGAAGGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.85, C:0.03, G:0.13, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAACAAAG
Found at i:20413529 original size:14 final size:15
Alignment explanation
Indices: 20413496--20413547 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
20413486 AAGTAAAATC
20413496 TTTACAAATATATATT
1 TTTA-AAATATATATT
*
20413512 TTTAAAATA-ATTTT
1 TTTAAAATATATATT
*
20413526 TTTAAAA-ATTTATT
1 TTTAAAATATATATT
20413540 ATTTAAAA
1 -TTTAAAA
20413548 AAAAAAGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 1 0.03
14 14 0.45
15 12 0.39
16 4 0.13
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTAAAATATATATT
Found at i:20417155 original size:33 final size:33
Alignment explanation
Indices: 20417100--20417163 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
20417090 AATGTTAGAT
* *
20417100 GAATAGTTCGTGCACATATTCGATTTTTATTAC
1 GAATAGTTCGTGAACATATTCGATTTCTATTAC
* *
20417133 GAATAGTTTGTGAACATGTTCGATTTCTATT
1 GAATAGTTCGTGAACATATTCGATTTCTATT
20417164 TATTTATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (33 bp):
GAATAGTTCGTGAACATATTCGATTTCTATTAC
Found at i:20418609 original size:179 final size:178
Alignment explanation
Indices: 20418289--20418629 Score: 556
Period size: 179 Copynumber: 1.9 Consensus size: 178
20418279 AAATCGTCAG
* *
20418289 TAATCCGTTGCTAAAAGTTTTACCAACAAATTTTTTCAGTCAGTAAAAAATTCAGTTTAAAAAAT
1 TAATCCATTGCTAAAAATTTTACCAACAAATTTTTTCAGTCAGTAAAAAATTCAGTTTAAAAAAT
* *
20418354 ATATGTTTTTGGGAATTAAATTGGGAGAAAAAAATTTTAATTAGCGACGGATTCCATTGATAATC
66 ATATGTTTTTCGGAATTAAATTGGGAGAAAAAAATTTTAATTAGCGACAGATTCCATTGATAATC
* *
20418419 CATCACTAAAAGTTAGAAATACCAATGGATTTTTCTGGCTATCATCAA
131 CATCACTAAAAGTAAAAAATACCAATGGATTTTTCTGGCTATCATCAA
* * *
20418467 TAATCCATTGTTAAAAATTTTACCAACGAATTTTTTCAGTCTGTAAAAAATTCAGTTTAAAAATA
1 TAATCCATTGCTAAAAATTTTACCAACAAATTTTTTCAGTCAGTAAAAAATTCAGTTTAAAAA-A
* *
20418532 TATATGTTTTTCGGAATTAAATTGGGAGGAAAAATTTTTAATTAGCGACAGATTCCATTGATAAT
65 TATATGTTTTTCGGAATTAAATTGGGAGAAAAAAATTTTAATTAGCGACAGATTCCATTGATAAT
* *
20418597 TCATCGCTAAAAGTAAAAAATACCAATGGATTT
130 CCATCACTAAAAGTAAAAAATACCAATGGATTT
20418630 CATCGATAAT
Statistics
Matches: 149, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
178 58 0.39
179 91 0.61
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (178 bp):
TAATCCATTGCTAAAAATTTTACCAACAAATTTTTTCAGTCAGTAAAAAATTCAGTTTAAAAAAT
ATATGTTTTTCGGAATTAAATTGGGAGAAAAAAATTTTAATTAGCGACAGATTCCATTGATAATC
CATCACTAAAAGTAAAAAATACCAATGGATTTTTCTGGCTATCATCAA
Found at i:20421265 original size:7 final size:7
Alignment explanation
Indices: 20421238--20421309 Score: 58
Period size: 7 Copynumber: 10.4 Consensus size: 7
20421228 TGGGCTCCAA
*
20421238 TTTAAGG
1 TTTAGGG
*
20421245 TTTGGGG
1 TTTAGGG
20421252 TTT--GG
1 TTTAGGG
20421257 TTTAGGG
1 TTTAGGG
* *
20421264 TTTATGA
1 TTTAGGG
*
20421271 TTTATGG
1 TTTAGGG
*
20421278 TTTAAGG
1 TTTAGGG
20421285 TTTATGGG
1 TTTA-GGG
*
20421293 TTTAGGA
1 TTTAGGG
20421300 TTTAGGG
1 TTTAGGG
20421307 TTT
1 TTT
20421310 CATGGAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
5 5 0.09
7 42 0.79
8 6 0.11
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (7 bp):
TTTAGGG
Found at i:20421280 original size:21 final size:22
Alignment explanation
Indices: 20421254--20421326 Score: 78
Period size: 21 Copynumber: 3.3 Consensus size: 22
20421244 GTTTGGGGTT
20421254 TGGTTTAGGGTTTAT-GATTTA
1 TGGTTTAGGGTTTATGGATTTA
* *
20421275 TGGTTTAAGGTTTATGGGTTTA
1 TGGTTTAGGGTTTATGGATTTA
20421297 -GGATTTAGGGTTTCATGGAATTTA
1 TGG-TTTAGGGTTT-ATGG-ATTTA
*
20421321 GGGTTT
1 TGGTTT
20421327 TATGGGATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
21 16 0.37
22 14 0.33
23 4 0.09
24 7 0.16
25 2 0.05
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.48
Consensus pattern (22 bp):
TGGTTTAGGGTTTATGGATTTA
Found at i:20421342 original size:16 final size:17
Alignment explanation
Indices: 20421297--20421345 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
20421287 TATGGGTTTA
20421297 GGATTTAGGGTTTCATG
1 GGATTTAGGGTTTCATG
* *
20421314 GAATTTAGGGTTTTATG
1 GGATTTAGGGTTTCATG
20421331 GGATTT-GGGTTTCAT
1 GGATTTAGGGTTTCAT
20421346 AAGATTATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 8 0.29
17 20 0.71
ACGTcount: A:0.18, C:0.04, G:0.33, T:0.45
Consensus pattern (17 bp):
GGATTTAGGGTTTCATG
Found at i:20421849 original size:20 final size:20
Alignment explanation
Indices: 20421826--20421885 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 20
20421816 AACTTATGAT
20421826 ATGAACCAAAATAACATGTA
1 ATGAACCAAAATAACATGTA
*
20421846 ATGAACCATAATAACAAACATGTA
1 ATGAACC--AA-AA-TAACATGTA
*
20421870 ATAAACCAAAATAACA
1 ATGAACCAAAATAACA
20421886 AGAAAATTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
20 11 0.33
21 2 0.06
22 4 0.12
23 2 0.06
24 14 0.42
ACGTcount: A:0.58, C:0.17, G:0.07, T:0.18
Consensus pattern (20 bp):
ATGAACCAAAATAACATGTA
Found at i:20421865 original size:24 final size:24
Alignment explanation
Indices: 20421838--20421886 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
20421828 GAACCAAAAT
* *
20421838 AACATGTAATGAACCATAATAACA
1 AACATGTAATAAACCAAAATAACA
20421862 AACATGTAATAAACCAAAATAACA
1 AACATGTAATAAACCAAAATAACA
20421886 A
1 A
20421887 GAAAATTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.59, C:0.16, G:0.06, T:0.18
Consensus pattern (24 bp):
AACATGTAATAAACCAAAATAACA
Found at i:20421968 original size:22 final size:20
Alignment explanation
Indices: 20421943--20421986 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
20421933 AATTATGCAA
20421943 AAACATGATAAACATATCAATT
1 AAACATGATAAACA-A-CAATT
*
20421965 AAACATTATAAACAACAATT
1 AAACATGATAAACAACAATT
20421985 AA
1 AA
20421987 TAGCAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 1 0.05
22 13 0.62
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (20 bp):
AAACATGATAAACAACAATT
Found at i:20428962 original size:21 final size:21
Alignment explanation
Indices: 20428938--20428983 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
20428928 TGTTGAGGAC
*
20428938 TTTTGTGGATGTTATTG-ATAT
1 TTTTATGGATGTTA-TGAATAT
20428959 TTTTATGGATGTTATGAATAT
1 TTTTATGGATGTTATGAATAT
20428980 TTTT
1 TTTT
20428984 TAGTATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.22, C:0.00, G:0.20, T:0.59
Consensus pattern (21 bp):
TTTTATGGATGTTATGAATAT
Found at i:20429317 original size:13 final size:13
Alignment explanation
Indices: 20429296--20429339 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
20429286 TATCAACGGA
* *
20429296 TTACTAATGGATT
1 TTACCAATGGAAT
*
20429309 TTACCAATGAAAT
1 TTACCAATGGAAT
*
20429322 TTAGCAATGGAAT
1 TTACCAATGGAAT
20429335 TTACC
1 TTACC
20429340 GATAAAAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (13 bp):
TTACCAATGGAAT
Found at i:20431262 original size:13 final size:13
Alignment explanation
Indices: 20431244--20431270 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20431234 GTAAAAGACC
20431244 AATATATATATAT
1 AATATATATATAT
20431257 AATATATATATAT
1 AATATATATATAT
20431270 A
1 A
20431271 TCTTCAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATATATATATAT
Found at i:20444383 original size:26 final size:28
Alignment explanation
Indices: 20444326--20444385 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
20444316 ATAAAAATTT
* *
20444326 AAAAAATATTAAAAATAAAATTAATTAT
1 AAAAAATATTAAAAATAAAATGAATTAC
* *
20444354 AAAAAATATT-AAATTAAAA-GCATTAC
1 AAAAAATATTAAAAATAAAATGAATTAC
20444380 AAAAAA
1 AAAAAA
20444386 ACTTATGACG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 10 0.36
27 8 0.29
28 10 0.36
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (28 bp):
AAAAAATATTAAAAATAAAATGAATTAC
Found at i:20451056 original size:10 final size:10
Alignment explanation
Indices: 20451043--20451067 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20451033 ATAATTATTT
20451043 ATAATAAAAA
1 ATAATAAAAA
20451053 ATAATAAAAA
1 ATAATAAAAA
20451063 ATAAT
1 ATAAT
20451068 TATTTAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
ATAATAAAAA
Found at i:20451624 original size:21 final size:21
Alignment explanation
Indices: 20451567--20451617 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
20451557 ATGAAATGGT
20451567 TTTTTTTTTAAGAAAAAGTGA
1 TTTTTTTTTAAGAAAAAGTGA
20451588 TTTTTTTTTAAGAAAAAGTGA
1 TTTTTTTTTAAGAAAAAGTGA
20451609 TTTTTTTTT
1 TTTTTTTTT
20451618 TCTAAAAGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (21 bp):
TTTTTTTTTAAGAAAAAGTGA
Found at i:20456775 original size:3 final size:3
Alignment explanation
Indices: 20456769--20456815 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
20456759 ATAAATTTAA
20456769 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20456816 GAAATTGGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20463755 original size:19 final size:18
Alignment explanation
Indices: 20463733--20463787 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
20463723 TTTTTGTAAG
20463733 TTAAATTTATTATATATTT
1 TTAAATTTATTATAT-TTT
20463752 TTAAA--TA-TATATTTT
1 TTAAATTTATTATATTTT
* *
20463767 TTCACACTTATTATATTTT
1 TT-AAATTTATTATATTTT
20463786 TT
1 TT
20463788 TATATTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
15 5 0.16
16 7 0.23
17 2 0.06
18 2 0.06
19 15 0.48
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAAATTTATTATATTTT
Found at i:20463909 original size:21 final size:20
Alignment explanation
Indices: 20463880--20463919 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
20463870 TTTTAAATGT
*
20463880 ATTTATTAATTCAACAATTA
1 ATTTATTAATCCAACAATTA
*
20463900 ATTTAATTAATCCAATAATT
1 ATTT-ATTAATCCAACAATT
20463920 GAACCAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTATTAATCCAACAATTA
Found at i:20469174 original size:216 final size:215
Alignment explanation
Indices: 20468746--20469139 Score: 610
Period size: 216 Copynumber: 1.8 Consensus size: 215
20468736 GTAAAAGAGG
* *
20468746 AAAGAAGGAAAGAATGAAGTTGGAGGAAGAAAGGGACTCAATTCTCCTTGGTTGCTTTCCTTTAT
1 AAAGAAGGAAAGAATGAAGTTAGAGGAAGAAAGGGACTCAATTCTCCTTGGTTGCTTCCCTTTAT
* * * * *
20468811 TATGTGCCCACTTGCTCTTCTTTATGCCTTTTACCCTTTACTATCTAAGACCTTAATAAATAAAG
66 TACGTGCCCACCTGCTCTCCTTTATGCCTTTTACCCTTCACTATCTAAGACCTTAATAAATAAAA
*
20468876 AAAGGCAAAAAATTATTAAAATAGATCAAATTATGATAATGGTCTTGAAGTTTATAGTAAAAGAG
131 AAAGGCAAAAAATTATTAAAATAGATCAAATTATGATAATGATCTTGAAG-TTATAG-AAAAGAG
20468941 GAAAGATCTTACTTTTTAGAAT
194 GAAAGATCTTACTTTTTAGAAT
* * * *
20468963 AAAGGAGGAAAGAATGAAGTTAGAGGAAGAAAGGGA-TCGATTCTCCTTGTTTGCTTCCCTTTGT
1 AAAGAAGGAAAGAATGAAGTTAGAGGAAGAAAGGGACTCAATTCTCCTTGGTTGCTTCCCTTTAT
* *
20469027 TACGTGCCCACCTGCTCTCCTTTATGCCTTTTACCCTTCACTATTTGAGACCTTAATAAATAAAA
66 TACGTGCCCACCTGCTCTCCTTTATGCCTTTTACCCTTCACTATCTAAGACCTTAATAAAT-AAA
*
20469092 AAAATGCAAAAAAATTATTAAAATAGATCAAATTATGATAATGATCTT
130 AAAAGGC-AAAAAATTATTAAAATAGATCAAATTATGATAATGATCTT
20469140 TATATTATAA
Statistics
Matches: 160, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
216 79 0.49
217 42 0.26
218 39 0.24
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (215 bp):
AAAGAAGGAAAGAATGAAGTTAGAGGAAGAAAGGGACTCAATTCTCCTTGGTTGCTTCCCTTTAT
TACGTGCCCACCTGCTCTCCTTTATGCCTTTTACCCTTCACTATCTAAGACCTTAATAAATAAAA
AAAGGCAAAAAATTATTAAAATAGATCAAATTATGATAATGATCTTGAAGTTATAGAAAAGAGGA
AAGATCTTACTTTTTAGAAT
Found at i:20471891 original size:2 final size:2
Alignment explanation
Indices: 20471884--20471916 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20471874 TTTTGCCATG
20471884 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20471917 TTCAAAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20481972 original size:32 final size:32
Alignment explanation
Indices: 20481936--20482000 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
20481926 TAAATATGTG
20481936 TAACTCCTTCACTAGG-AAGGCATTCAATCCTA
1 TAACTCCTTCACTAGGAAAGG-ATTCAATCCTA
* *
20481968 TAACTCCTTTATTAGGAAAGGATTCAATCCTA
1 TAACTCCTTCACTAGGAAAGGATTCAATCCTA
20482000 T
1 T
20482001 CTTCCTCCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 26 0.87
33 4 0.13
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (32 bp):
TAACTCCTTCACTAGGAAAGGATTCAATCCTA
Found at i:20483697 original size:2 final size:2
Alignment explanation
Indices: 20483690--20483719 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20483680 TGCTCTGTTT
20483690 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20483720 ATTTTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20484515 original size:2 final size:2
Alignment explanation
Indices: 20484508--20484540 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
20484498 ATTTCACGTG
*
20484508 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20484541 GCTATGGACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20485521 original size:2 final size:2
Alignment explanation
Indices: 20485514--20485542 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20485504 TTGAGTTTAT
20485514 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
20485543 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:20486363 original size:39 final size:39
Alignment explanation
Indices: 20486309--20486464 Score: 267
Period size: 39 Copynumber: 4.0 Consensus size: 39
20486299 GACCTAACAG
20486309 ACCTAGAATAATCATCCCTCTTCCGATCATCTTTCTCCC
1 ACCTAGAATAATCATCCCTCTTCCGATCATCTTTCTCCC
*
20486348 ACCTAGAATAATCATCCCTCTTCTGATCATCTTTCTCCC
1 ACCTAGAATAATCATCCCTCTTCCGATCATCTTTCTCCC
* * *
20486387 ACCTAGAATAATCAACCCTCTTCCTATCATCTGTCTCCC
1 ACCTAGAATAATCATCCCTCTTCCGATCATCTTTCTCCC
*
20486426 ACCTAGAATAATCTTCCCTCTTCCGATCATCTTTCTCCC
1 ACCTAGAATAATCATCCCTCTTCCGATCATCTTTCTCCC
20486465 TATTAGCTCT
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 108 1.00
ACGTcount: A:0.23, C:0.38, G:0.05, T:0.34
Consensus pattern (39 bp):
ACCTAGAATAATCATCCCTCTTCCGATCATCTTTCTCCC
Found at i:20487414 original size:192 final size:192
Alignment explanation
Indices: 20487080--20487455 Score: 531
Period size: 192 Copynumber: 2.0 Consensus size: 192
20487070 CTATCACGTC
* *
20487080 CTTTCTTTACTGTTTCCTTTTTAAGATGTCTTGTAATGTCTGCATCAGAATCAGATTCACTACCC
1 CTTTCTTAACTGTTTCCTTTTTAAGATCTCTTGTAATGTCTGCATCAGAATCAGATTCACTACCC
* * * * * *
20487145 ATGTTGTCCCTCCCTGTCCTCCGGCTCCCAGTTAGCTCAATCTTTCGTCTTTGAACTTCACCTCT
66 AAGTTGTACCTCCCTCTCCTCCGACTCCCAGTCAGCTCAATCTTTCGACTTTGAACTTCACCTCT
* *
20487210 ATTCTTTTCCCTCCCATCATCAGTGTCAGATTCCTCCTCACTGGACTCATGCCTACGACTAA
131 ATTCTCTTCCCTCCCATCATCAGTGTCAGAGTCCTCCTCACTGGACTCATGCCTACGACTAA
* * * *
20487272 CTTTCTTAACTGTTTCCTTTTTACGGTCTCTTGCT-CTGTCTGCATCAGAATCGGATTCACTACC
1 CTTTCTTAACTGTTTCCTTTTTAAGATCTCTTG-TAATGTCTGCATCAGAATCAGATTCACTACC
** * * *
20487336 CAAGTTGTACCT-CCTCCTCCTCTTACTCTCAGTCAGCTCAATCTTTTGACTTTGAGCTTCACCT
65 CAAGTTGTACCTCCCT-CTCCTCCGACTCCCAGTCAGCTCAATCTTTCGACTTTGAACTTCACCT
* *
20487400 CTATTCTCTTCCCTCCCATCATCAGTGTCAGAGTCGTCCTCACTGGAGTCATGCCT
129 CTATTCTCTTCCCTCCCATCATCAGTGTCAGAGTCCTCCTCACTGGACTCATGCCT
20487456 CCTACGAGAT
Statistics
Matches: 161, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
191 3 0.02
192 157 0.98
193 1 0.01
ACGTcount: A:0.17, C:0.32, G:0.13, T:0.38
Consensus pattern (192 bp):
CTTTCTTAACTGTTTCCTTTTTAAGATCTCTTGTAATGTCTGCATCAGAATCAGATTCACTACCC
AAGTTGTACCTCCCTCTCCTCCGACTCCCAGTCAGCTCAATCTTTCGACTTTGAACTTCACCTCT
ATTCTCTTCCCTCCCATCATCAGTGTCAGAGTCCTCCTCACTGGACTCATGCCTACGACTAA
Found at i:20491094 original size:40 final size:41
Alignment explanation
Indices: 20491038--20491148 Score: 131
Period size: 40 Copynumber: 2.8 Consensus size: 41
20491028 GCAAACCTGA
* * * *
20491038 ACTTTTTTATAATGAAACAAATTTAG-AAAAATAAACTAAT
1 ACTTTTTTATAGTGAAACAAATTGAGCAAAAAAAAACAAAT
*
20491078 ACTTTTTTATAGTGAAACATATTGAGCAAAAAAAAACAAAT
1 ACTTTTTTATAGTGAAACAAATTGAGCAAAAAAAAACAAAT
* *
20491119 A--TTTTT-TAGTGAAACAAATTAAACAAAAAA
1 ACTTTTTTATAGTGAAACAAATTGAGCAAAAAA
20491149 GACTTTTTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
38 21 0.34
39 5 0.08
40 23 0.37
41 13 0.21
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.32
Consensus pattern (41 bp):
ACTTTTTTATAGTGAAACAAATTGAGCAAAAAAAAACAAAT
Found at i:20491146 original size:38 final size:39
Alignment explanation
Indices: 20491041--20491148 Score: 112
Period size: 38 Copynumber: 2.7 Consensus size: 39
20491031 AACCTGAACT
* * * * *
20491041 TTTTTATAATGAAACAAATTTAGAAAAATAAACTAATAC
1 TTTTTATAGTGAAACAAATTAACAAAAAAAAACAAATAC
* *
20491080 TTTTTTATAGTGAAACATATTGAGCAAAAAAAAACAAATA-
1 -TTTTTATAGTGAAACAAATT-AACAAAAAAAAACAAATAC
20491120 TTTTT-TAGTGAAACAAATTAAACAAAAAA
1 TTTTTATAGTGAAACAAATT-AACAAAAAA
20491149 GACTTTTTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
38 21 0.37
39 5 0.09
40 18 0.32
41 13 0.23
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.31
Consensus pattern (39 bp):
TTTTTATAGTGAAACAAATTAACAAAAAAAAACAAATAC
Found at i:20491185 original size:38 final size:38
Alignment explanation
Indices: 20491040--20491185 Score: 118
Period size: 40 Copynumber: 3.8 Consensus size: 38
20491030 AAACCTGAAC
* * * *
20491040 TTTTTTATAATGAAACAAATTTAG-AAAAATAAACTAATA
1 TTTTTTTTAGTGAAACAAATTGAGCAAAAAAAAAC-AA-A
* *
20491079 CTTTTTTATAGTGAAACATATTGAGCAAAAAAAAACAAA
1 -TTTTTTTTAGTGAAACAAATTGAGCAAAAAAAAACAAA
* * * * **
20491118 TATTTTTTAGTGAAACAAATTAAAC-AAAAAAGAC-TT
1 TTTTTTTTAGTGAAACAAATTGAGCAAAAAAAAACAAA
* *
20491154 TTTTTTTTAATGAAACAGATTGAGCAAAAAAA
1 TTTTTTTTAGTGAAACAAATTGAGCAAAAAAA
20491186 GCAAAGTCCA
Statistics
Matches: 87, Mismatches: 17, Indels: 7
0.78 0.15 0.06
Matches are distributed among these distances:
36 20 0.23
37 14 0.16
38 20 0.23
39 1 0.01
40 23 0.26
41 9 0.10
ACGTcount: A:0.51, C:0.08, G:0.09, T:0.33
Consensus pattern (38 bp):
TTTTTTTTAGTGAAACAAATTGAGCAAAAAAAAACAAA
Found at i:20493114 original size:141 final size:145
Alignment explanation
Indices: 20492927--20493206 Score: 338
Period size: 149 Copynumber: 1.9 Consensus size: 145
20492917 TATGAAAGAA
* *
20492927 TTATTAAAGACGTTTATGGCCAAAAACACCTTAAATAATTCCTAAACCTTAAA-T-C-CTAAACT
1 TTATTAAAGACGTTTATAGCCAAAAACACCTTAAATAATTCCTAAACCCTAAATTACTCTAAACT
* * *
20492989 CAT-AAAATTTAAAGGGATTATTCAAGGTATTTTTGCCTAAAAACTGCTTTAAATAATC-TCTTA
66 CATAAAAATTTAAAGAGATTATTCAAGGCATTTTTGCCTAAAAAATGCTTTAAATAATCAT-TTA
20493052 CAAAAATTGAATAGGG
130 CAAAAATTGAATAGGG
* * * * * *
20493068 TTATTGAAA-ACGTTTCTAGCCAAATACTCCTTGAATAATTCTTAAACCCTAAACTTTAAACTTT
1 TTATT-AAAGACGTTTATAGCCAAAAACACCTTAAATAATTCCTAAACCCTAAA--TT--ACTCT
* * *
20493132 AAACTCATAAAAATTTAAAGAGATTATTCAATGCATTTTTGTCTAAAAAATGCTTTCAATAATCA
61 AAACTCATAAAAATTTAAAGAGATTATTCAAGGCATTTTTGCCTAAAAAATGCTTTAAATAATCA
20493197 TTTACAAAAA
126 TTTACAAAAA
20493207 ATTAAATGGG
Statistics
Matches: 115, Mismatches: 14, Indels: 12
0.82 0.10 0.09
Matches are distributed among these distances:
141 42 0.37
142 3 0.03
144 1 0.01
147 1 0.01
148 9 0.08
149 58 0.50
150 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (145 bp):
TTATTAAAGACGTTTATAGCCAAAAACACCTTAAATAATTCCTAAACCCTAAATTACTCTAAACT
CATAAAAATTTAAAGAGATTATTCAAGGCATTTTTGCCTAAAAAATGCTTTAAATAATCATTTAC
AAAAATTGAATAGGG
Found at i:20493733 original size:62 final size:61
Alignment explanation
Indices: 20493468--20493733 Score: 154
Period size: 62 Copynumber: 4.3 Consensus size: 61
20493458 TTTAATGGGG
* * ** *
20493468 TTATTCAAAGAGTTTCTAGCCAAAAACACTTTCG-ATAATTC-ACTTAAATTTTTATGAAGTGA
1 TTATTCAAAGAGTTTTTAGCTAAAAACACTTT-GAATAACCCTA-TTAAATTTTT-TGAAGAGA
* * * * * * * *
20493530 TTATTCAAGGCGTTTTTAGTTAGAAACGA-TTTCAATAACCCCATTAAATTTTTTGTAAAAAA
1 TTATTCAAAGAGTTTTTAGCTAAAAAC-ACTTTGAATAACCCTATTAAATTTTTTG-AAGAGA
* * * * * *
20493592 TTATTCAAGATATTTTTTGGGC-AAAAACACCTTAAATAATTACCTCA-TAAA--TTTTGAAGTA
1 TTATTCAA-AGAGTTTTT-AGCTAAAAACACTTTGAATAA--CCCT-ATTAAATTTTTTGAAG-A
20493653 GA
60 GA
*
20493655 TTATT-AAATGTA-TTTTTAGCTAAAAACACATTGAATAACCCTATTAAATTTTTTGTAAGAGA
1 TTATTCAAA-G-AGTTTTTAGCTAAAAACACTTTGAATAACCCTATTAAATTTTTTG-AAGAGA
*
20493717 TTATTCAAAGCGTTTTT
1 TTATTCAAAGAGTTTTT
20493734 GACCAAACAA
Statistics
Matches: 153, Mismatches: 31, Indels: 40
0.68 0.14 0.18
Matches are distributed among these distances:
59 1 0.01
60 7 0.05
61 5 0.03
62 94 0.61
63 38 0.25
64 1 0.01
65 6 0.04
66 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (61 bp):
TTATTCAAAGAGTTTTTAGCTAAAAACACTTTGAATAACCCTATTAAATTTTTTGAAGAGA
Found at i:20496824 original size:13 final size:13
Alignment explanation
Indices: 20496785--20496833 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
20496775 TATCTAAAAC
*
20496785 TATTTAAAT-ATA
1 TATTAAAATAATA
**
20496797 TATTAAAATTTTA
1 TATTAAAATAATA
20496810 TATTAAAATAATA
1 TATTAAAATAATA
*
20496823 TATAAAAATAA
1 TATTAAAATAA
20496834 AAAATAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
12 8 0.26
13 23 0.74
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TATTAAAATAATA
Found at i:20500552 original size:13 final size:13
Alignment explanation
Indices: 20500534--20500558 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20500524 TACAAAACAT
20500534 ATTATGTCAATTA
1 ATTATGTCAATTA
20500547 ATTATGTCAATT
1 ATTATGTCAATT
20500559 GAAATTGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (13 bp):
ATTATGTCAATTA
Found at i:20513260 original size:22 final size:21
Alignment explanation
Indices: 20513235--20513284 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
20513225 AAATAAAAAT
*
20513235 AAAATAATTTA-AAATTTTAATA
1 AAAATAATATATAAA-TTT-ATA
*
20513257 AAAATTATATATAAATTTATA
1 AAAATAATATATAAATTTATA
20513278 AAAATAA
1 AAAATAA
20513285 AAAAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 9 0.38
22 12 0.50
23 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATAATATATAAATTTATA
Found at i:20517530 original size:7 final size:7
Alignment explanation
Indices: 20517518--20517542 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20517508 ATTCATTGGT
20517518 TTTTAAA
1 TTTTAAA
20517525 TTTTAAA
1 TTTTAAA
20517532 TTTTAAA
1 TTTTAAA
20517539 TTTT
1 TTTT
20517543 TATATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:20517576 original size:21 final size:23
Alignment explanation
Indices: 20517540--20517592 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
20517530 AATTTTAAAT
*
20517540 TTTTATATATTATTTTGATAGAA
1 TTTTATATATTATTTTAATAGAA
20517563 TTTTA-ATA-TATTTTAATAG-A
1 TTTTATATATTATTTTAATAGAA
20517583 TTTATATATA
1 TTT-TATATA
20517593 AATAATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.15
21 12 0.44
22 6 0.22
23 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (23 bp):
TTTTATATATTATTTTAATAGAA
Found at i:20521498 original size:2 final size:2
Alignment explanation
Indices: 20521491--20521517 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20521481 AGAAATGAAC
20521491 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
20521518 TGAAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20521994 original size:152 final size:152
Alignment explanation
Indices: 20521718--20522022 Score: 601
Period size: 152 Copynumber: 2.0 Consensus size: 152
20521708 CATTAGAGTC
20521718 GATAATGTGAATATGGATGCAAATTCAACTTTTTTAAAGATTTATTTTATTTATTTATTTATTTG
1 GATAATGTGAATATGGATGCAAATTCAACTTTTTTAAAGATTTATTTTATTTATTTATTTATTTG
20521783 TATGTTTGCAAGATTTGTACTTTAGTTCTAAGCCGAGCCTGGAGACTGTCTTATGTTAACAACCA
66 TATGTTTGCAAGATTTGTACTTTAGTTCTAAGCCGAGCCTGGAGACTGTCTTATGTTAACAACCA
*
20521848 TGGTAATGCTCAAATGGGAGGA
131 CGGTAATGCTCAAATGGGAGGA
20521870 GATAATGTGAATATGGATGCAAATTCAACTTTTTTAAAGATTTATTTTATTTATTTATTTATTTG
1 GATAATGTGAATATGGATGCAAATTCAACTTTTTTAAAGATTTATTTTATTTATTTATTTATTTG
20521935 TATGTTTGCAAGATTTGTACTTTAGTTCTAAGCCGAGCCTGGAGACTGTCTTATGTTAACAACCA
66 TATGTTTGCAAGATTTGTACTTTAGTTCTAAGCCGAGCCTGGAGACTGTCTTATGTTAACAACCA
20522000 CGGTAATGCTCAAATGGGAGGA
131 CGGTAATGCTCAAATGGGAGGA
20522022 G
1 G
20522023 CATCAGGATG
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 152 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (152 bp):
GATAATGTGAATATGGATGCAAATTCAACTTTTTTAAAGATTTATTTTATTTATTTATTTATTTG
TATGTTTGCAAGATTTGTACTTTAGTTCTAAGCCGAGCCTGGAGACTGTCTTATGTTAACAACCA
CGGTAATGCTCAAATGGGAGGA
Found at i:20526673 original size:22 final size:22
Alignment explanation
Indices: 20526648--20526690 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
20526638 TGTATATTTA
*
20526648 TATTTACATCTCTAGAATTAAG
1 TATTTACATCCCTAGAATTAAG
**
20526670 TATTTGTATCCCTAGAATTAA
1 TATTTACATCCCTAGAATTAA
20526691 TGACAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (22 bp):
TATTTACATCCCTAGAATTAAG
Found at i:20530613 original size:22 final size:22
Alignment explanation
Indices: 20530587--20530632 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
20530577 TGTATATTTA
*
20530587 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
20530609 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
20530631 TA
1 TA
20530633 CAAAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:20545372 original size:34 final size:34
Alignment explanation
Indices: 20545289--20545373 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 34
20545279 TTCAGTAGGT
* * * * *
20545289 TATCAAAAATAAATTTTTGAAAACTTTTTGATTG
1 TATCAAAAATATATTTTCGAAAACTTCTTAATTA
20545323 TATCAAAAATATATTTTCGAAAACTTCTTAATTA
1 TATCAAAAATATATTTTCGAAAACTTCTTAATTA
* *
20545357 TATCAAAATTTTATTTT
1 TATCAAAAATATATTTT
20545374 TGCAATTATC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (34 bp):
TATCAAAAATATATTTTCGAAAACTTCTTAATTA
Done.