Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397259.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_147.0, 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: 10737078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 75620 characters in sequence are not A, C, G, or T
File 17 of 22
Found at i:7233154 original size:5 final size:5
Alignment explanation
Indices: 7233140--7233168 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
7233130 GCTAGTATTT
7233140 AAAA- AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
7233169 GACTGGTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:7238455 original size:17 final size:19
Alignment explanation
Indices: 7238433--7238467 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
7238423 CAGAACCCTA
7238433 AGAGAGA-GA-CAGAGAAG
1 AGAGAGAGGAGCAGAGAAG
7238450 AGAGAGAGGAGCAGAGAA
1 AGAGAGAGGAGCAGAGAA
7238468 ACAGAGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.51, C:0.06, G:0.43, T:0.00
Consensus pattern (19 bp):
AGAGAGAGGAGCAGAGAAG
Found at i:7240311 original size:28 final size:24
Alignment explanation
Indices: 7240253--7240305 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
7240243 AAAATTATTT
*
7240253 TATAAACAAATAAATTACATTAAA
1 TATAAATAAATAAATTACATTAAA
7240277 TATAAATAAATAAATTACA-TAAA
1 TATAAATAAATAAATTACATTAAA
7240300 TA-AAAT
1 TATAAAT
7240306 TTAAATCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 4 0.14
23 6 0.21
24 18 0.64
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
TATAAATAAATAAATTACATTAAA
Found at i:7252465 original size:15 final size:15
Alignment explanation
Indices: 7252447--7252484 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
7252437 TTATAGGTAG
*
7252447 TGTGATTGCA-AGTAA
1 TGTGATTGCAGA-CAA
7252462 TGTGATTGCAGACAA
1 TGTGATTGCAGACAA
7252477 TGTGATTG
1 TGTGATTG
7252485 TAAGAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 20 0.95
16 1 0.05
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.34
Consensus pattern (15 bp):
TGTGATTGCAGACAA
Found at i:7252746 original size:32 final size:34
Alignment explanation
Indices: 7252706--7252787 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 34
7252696 AAAGTCATAC
*
7252706 ATTTTATTTTCATTTA-TTATTATAATCTTATAT
1 ATTTTATTTTCATTTATTTAATATAATCTTATAT
* * *
7252739 -TTTTATTTTTATTTATTTAATATAATTTTTTAT
1 ATTTTATTTTCATTTATTTAATATAATCTTATAT
*
7252772 ATTATATATTTCATTT
1 ATTTTAT-TTTCATTT
7252788 TAATTTCTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 14 0.35
33 14 0.35
34 5 0.12
35 7 0.17
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (34 bp):
ATTTTATTTTCATTTATTTAATATAATCTTATAT
Found at i:7252830 original size:19 final size:19
Alignment explanation
Indices: 7252806--7252843 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
7252796 TTTACCTATA
7252806 TTATA-TAAATTTTAATTTT
1 TTATATTAAATTTT-ATTTT
*
7252825 TTATATTATATTTTATTTT
1 TTATATTAAATTTTATTTT
7252844 AAATTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATATTAAATTTTATTTT
Found at i:7252863 original size:31 final size:33
Alignment explanation
Indices: 7252811--7252883 Score: 105
Period size: 32 Copynumber: 2.2 Consensus size: 33
7252801 CTATATTATA
*
7252811 TAAATTTTAATTTTTTATATTA-TATTTTATTT
1 TAAATTTTAATTTCTTATATTATTATTTTATTT
*
7252843 TAAATTTTGA-TTCTTATATTATTATTTTATTT
1 TAAATTTTAATTTCTTATATTATTATTTTATTT
7252875 TAATATTTT
1 TAA-ATTTT
7252884 TTATTTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 10 0.27
32 22 0.59
33 5 0.14
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (33 bp):
TAAATTTTAATTTCTTATATTATTATTTTATTT
Found at i:7252896 original size:32 final size:31
Alignment explanation
Indices: 7252823--7252896 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 31
7252813 AATTTTAATT
7252823 TTTTATATTA-TATTTTATTTTAAATTTTGA
1 TTTTATATTATTATTTTATTTTAAATTTTGA
*
7252853 TTCTTATATTATTATTTTATTTTAATATTTTTTA
1 TT-TTATATTATTATTTTATTTTAA-A-TTTTGA
7252887 TTTTA-ATTAT
1 TTTTATATTAT
7252897 AACATTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
30 2 0.05
31 8 0.21
32 18 0.46
33 4 0.10
34 7 0.18
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (31 bp):
TTTTATATTATTATTTTATTTTAAATTTTGA
Found at i:7252998 original size:11 final size:11
Alignment explanation
Indices: 7252982--7253011 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
7252972 TGTAATATAA
7252982 TTGAATTGGTT
1 TTGAATTGGTT
7252993 TTGAATTGGTT
1 TTGAATTGGTT
7253004 TTGAATTG
1 TTGAATTG
7253012 CAATCACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (11 bp):
TTGAATTGGTT
Found at i:7260819 original size:47 final size:48
Alignment explanation
Indices: 7260748--7260838 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
7260738 AATCAACTCT
* *
7260748 ATTAATTCAATTTGTATGAATTTCATGACGTTGAAGATA-ATAAAAAG
1 ATTAACTCAATTTGTATGAATTTCATGACATTGAAGATATATAAAAAG
* *
7260795 ATTAACTCAATTTGTATGAGTTTCATGGCATTGAAGATATATAA
1 ATTAACTCAATTTGTATGAATTTCATGACATTGAAGATATATAA
7260839 CAAAAAGAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 35 0.90
48 4 0.10
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (48 bp):
ATTAACTCAATTTGTATGAATTTCATGACATTGAAGATATATAAAAAG
Found at i:7263242 original size:6 final size:6
Alignment explanation
Indices: 7263231--7263257 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
7263221 TGTAGAATTT
7263231 GGATTA GGATTA GGATTA GGATTA GGA
1 GGATTA GGATTA GGATTA GGATTA GGA
7263258 GTGTTAGCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (6 bp):
GGATTA
Found at i:7270615 original size:25 final size:25
Alignment explanation
Indices: 7270568--7270614 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
7270558 ATCATTGATA
7270568 TAATTTTTATAAATTTATATTTTAT
1 TAATTTTTATAAATTTATATTTTAT
7270593 TAATTATTTA-AAATTT-TATTTT
1 TAATT-TTTATAAATTTATATTTT
7270615 TTTATGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.29
25 11 0.52
26 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
TAATTTTTATAAATTTATATTTTAT
Found at i:7272773 original size:16 final size:17
Alignment explanation
Indices: 7272742--7272773 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
7272732 ATAAACTTAA
7272742 TATTCTTAATTCTTTTT
1 TATTCTTAATTCTTTTT
7272759 TATTC-TAATT-TTTTT
1 TATTCTTAATTCTTTTT
7272774 CATGATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTCTTAATTCTTTTT
Found at i:7272896 original size:95 final size:95
Alignment explanation
Indices: 7272706--7272880 Score: 280
Period size: 95 Copynumber: 1.8 Consensus size: 95
7272696 TTTTTAAATG
* * *
7272706 TTCCAAATTCTTATTTTTCCTTTTTCATAAACTTAATATTCTTAATTCTTTTTTATTCTAATTTT
1 TTCCAAATTCTTATTTTTCCTTTTTCAAAAACTTAATATTCTTAATTCATTTTTATTCCAATTTT
*
7272771 TTTCATGATTTTTTTCCTATGTAATTTTTT
66 GTTCATGATTTTTTTCCTATGTAATTTTTT
* *
7272801 TTCCAAATTGTTATTTTT-CTTGTTTCAAAAATTTAATATTCTTAATTCATTTTTATTCCAATTT
1 TTCCAAATTCTTATTTTTCCTT-TTTCAAAAACTTAATATTCTTAATTCATTTTTATTCCAATTT
7272865 TGTTCATGATTTTTTT
65 TGTTCATGATTTTTTT
7272881 TCTTATTTGA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
94 3 0.04
95 70 0.96
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.61
Consensus pattern (95 bp):
TTCCAAATTCTTATTTTTCCTTTTTCAAAAACTTAATATTCTTAATTCATTTTTATTCCAATTTT
GTTCATGATTTTTTTCCTATGTAATTTTTT
Found at i:7277470 original size:29 final size:28
Alignment explanation
Indices: 7277432--7277590 Score: 117
Period size: 28 Copynumber: 5.7 Consensus size: 28
7277422 GGCGCTTGAT
* * * *
7277432 TATTAGAAAATTTTAATTATTATATATTA
1 TATTA-AAAAATTTAATTATTACACATCA
*
7277461 TATTAAAAAATTTAATTATTACACGTCA
1 TATTAAAAAATTTAATTATTACACATCA
** * ** *
7277489 GGTTAAAAAAATATAATTATTACATGTTA
1 TATT-AAAAAATTTAATTATTACACATCA
* *
7277518 TATT-AAAATTTTAATTATTATACATCA
1 TATTAAAAAATTTAATTATTACACATCA
* *
7277545 TGTTAAAAAATTTAATTTTTACA-AGTCA
1 TATTAAAAAATTTAATTATTACACA-TCA
* *
7277573 TAATAAAAAAATT-ATTAT
1 TATTAAAAAATTTAATTAT
7277591 ATGTTATGCT
Statistics
Matches: 101, Mismatches: 26, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
27 25 0.25
28 48 0.48
29 28 0.28
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (28 bp):
TATTAAAAAATTTAATTATTACACATCA
Found at i:7277554 original size:57 final size:57
Alignment explanation
Indices: 7277445--7277567 Score: 160
Period size: 56 Copynumber: 2.2 Consensus size: 57
7277435 TAGAAAATTT
* *
7277445 TAATTATTATATATTATATTAAAAAATTTAATTATTACACGTCAGGTTAAAAAAATA
1 TAATTATTACATATTATATTAAAAAATTTAATTATTACACATCAGGTTAAAAAAATA
* * * * *
7277502 TAATTATTACATGTTATATT-AAAATTTTAATTATTATACATCATGTT-AAAAAATT
1 TAATTATTACATATTATATTAAAAAATTTAATTATTACACATCAGGTTAAAAAAATA
*
7277557 TAATTTTTACA
1 TAATTATTACA
7277568 AGTCATAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
55 17 0.29
56 23 0.40
57 18 0.31
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (57 bp):
TAATTATTACATATTATATTAAAAAATTTAATTATTACACATCAGGTTAAAAAAATA
Found at i:7277580 original size:55 final size:56
Alignment explanation
Indices: 7277466--7277581 Score: 144
Period size: 55 Copynumber: 2.1 Consensus size: 56
7277456 TATTATATTA
* * * *
7277466 AAAAATTTAATTATTACACGTCAGGTTAAAAAAATATAATTATTACATGTTATATT
1 AAAAATTTAATTATTACACATCAGGTTAAAAAAATATAATTATTACAAGTCATAAT
* * * * *
7277522 AAAATTTTAATTATTATACATCATGTT-AAAAAATTTAATTTTTACAAGTCATAAT
1 AAAAATTTAATTATTACACATCAGGTTAAAAAAATATAATTATTACAAGTCATAAT
7277577 AAAAA
1 AAAAA
7277582 AATTATTATA
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
55 27 0.54
56 23 0.46
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (56 bp):
AAAAATTTAATTATTACACATCAGGTTAAAAAAATATAATTATTACAAGTCATAAT
Found at i:7281240 original size:31 final size:29
Alignment explanation
Indices: 7281181--7281243 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
7281171 AAATAAAAAT
*
7281181 AAAAAAGATAAGATAAAAATAAATTAACA
1 AAAAAAGATAAAATAAAAATAAATTAACA
*
7281210 AAAAAAGATGAATAATAAAAAGTGAA-TAACA
1 AAAAAAGAT-AA-AATAAAAA-TAAATTAACA
7281241 AAA
1 AAA
7281244 GTATCAACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 9 0.31
30 2 0.07
31 15 0.52
32 3 0.10
ACGTcount: A:0.71, C:0.03, G:0.10, T:0.16
Consensus pattern (29 bp):
AAAAAAGATAAAATAAAAATAAATTAACA
Found at i:7287613 original size:20 final size:20
Alignment explanation
Indices: 7287567--7287615 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
7287557 AATAACTACA
*
7287567 GTTGAAAATCCAATATATAT
1 GTTGAATATCCAATATATAT
7287587 GTTGAATATCCAATATATAT
1 GTTGAATATCCAATATATAT
7287607 GTTGAATAT
1 GTTGAATAT
7287616 GTAGTTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (20 bp):
GTTGAATATCCAATATATAT
Found at i:7300230 original size:21 final size:21
Alignment explanation
Indices: 7300184--7300239 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
7300174 ATATCACAAG
*
7300184 AAATATA-ATTACTATT-ATAT
1 AAATATATA-TACTTTTAATAT
* *
7300204 ATATATCTATACTTTTAATAT
1 AAATATATATACTTTTAATAT
*
7300225 AAATATATTTACTTT
1 AAATATATATACTTT
7300240 CTATTTTGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATATATATACTTTTAATAT
Found at i:7304575 original size:2 final size:2
Alignment explanation
Indices: 7304564--7304594 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
7304554 AGCTGGGATG
7304564 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7304595 TTATTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:7305557 original size:25 final size:26
Alignment explanation
Indices: 7305529--7305579 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
7305519 TAAATTAAAA
*
7305529 TATTTACAA-TTAAAA-AAAATAATAT
1 TATTTA-AATTTAAAATAAAAAAATAT
7305554 TATTTAAATTTAAAATAAAAAAATAT
1 TATTTAAATTTAAAATAAAAAAATAT
7305580 AAAAATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 2 0.09
25 12 0.52
26 9 0.39
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TATTTAAATTTAAAATAAAAAAATAT
Found at i:7305909 original size:21 final size:21
Alignment explanation
Indices: 7305885--7305924 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
7305875 GAAACAATGC
*
7305885 AATAATGGGTGAAATTAGTTG
1 AATAATGGATGAAATTAGTTG
*
7305906 AATAATTGATGAAATTAGT
1 AATAATGGATGAAATTAGT
7305925 GAGAAAGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (21 bp):
AATAATGGATGAAATTAGTTG
Found at i:7307921 original size:2 final size:2
Alignment explanation
Indices: 7307902--7307956 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
7307892 CTCCTCCTCC
* *
7307902 CT CT CG CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
7307944 CT CT CT CT CT CT C
1 CT CT CT CT CT CT C
7307957 CTAAGTTCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.53, G:0.02, T:0.45
Consensus pattern (2 bp):
CT
Found at i:7308875 original size:46 final size:46
Alignment explanation
Indices: 7308822--7308915 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
7308812 GTAATTGATA
* *
7308822 GATTACTTATTAGATTTCATAATTTTTTTAAATATAGATTTTGTTG
1 GATTACTTATTAGATTTCATAATTTTTTTAAAAATAGATTTTATTG
7308868 GATTACTTATTAGATTTCATAATTTTTTTAAAAATAGATTTTATTG
1 GATTACTTATTAGATTTCATAATTTTTTTAAAAATAGATTTTATTG
7308914 GA
1 GA
7308916 ATGCATTGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.52
Consensus pattern (46 bp):
GATTACTTATTAGATTTCATAATTTTTTTAAAAATAGATTTTATTG
Found at i:7309309 original size:12 final size:12
Alignment explanation
Indices: 7309294--7309360 Score: 80
Period size: 12 Copynumber: 5.5 Consensus size: 12
7309284 TTTTTTAAAT
7309294 TTTTTATTTATA
1 TTTTTATTTATA
7309306 TTTTTATTTATA
1 TTTTTATTTATA
* *
7309318 TTATTATTTATT
1 TTTTTATTTATA
*
7309330 TTTTTAATTATA
1 TTTTTATTTATA
* *
7309342 TTCTTACTTATA
1 TTTTTATTTATA
7309354 TGTTTTA
1 T-TTTTA
7309361 AATTTTTATA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
12 42 0.91
13 4 0.09
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.70
Consensus pattern (12 bp):
TTTTTATTTATA
Found at i:7310919 original size:26 final size:26
Alignment explanation
Indices: 7310876--7310927 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
7310866 TACAAAAGAA
*
7310876 AATTATTAATCTTGTATGTCA-TATTT
1 AATTATTAATATTGTATG-CATTATTT
* *
7310902 AATTATTTATATTTTATGCATTATTT
1 AATTATTAATATTGTATGCATTATTT
7310928 CTCTCCTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (26 bp):
AATTATTAATATTGTATGCATTATTT
Found at i:7310981 original size:2 final size:2
Alignment explanation
Indices: 7310974--7311012 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
7310964 TCTATCCCTC
7310974 TA TA TA 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 TA TA TA T
7311013 TCTCAGCGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7317549 original size:36 final size:36
Alignment explanation
Indices: 7317509--7317591 Score: 132
Period size: 36 Copynumber: 2.3 Consensus size: 36
7317499 TTTAAAAATT
* *
7317509 ATGAAAGCTTTTTAATTTTAATGTTAAACCATTAAA
1 ATGAAAACTTTTTAATTTTAATGTAAAACCATTAAA
*
7317545 ATGAAAACTTTTTTATTTTAATGTAAAACCATTAAA
1 ATGAAAACTTTTTAATTTTAATGTAAAACCATTAAA
7317581 ATGAAAA-TTTT
1 ATGAAAACTTTT
7317592 CCTAATCCAC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 4 0.09
36 40 0.91
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.42
Consensus pattern (36 bp):
ATGAAAACTTTTTAATTTTAATGTAAAACCATTAAA
Found at i:7318864 original size:2 final size:2
Alignment explanation
Indices: 7318853--7318892 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
7318843 ACTTTGAATG
7318853 AT AT -T AT 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 AT AT AT AT A
7318893 ATTTCAAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7322173 original size:28 final size:27
Alignment explanation
Indices: 7322132--7322186 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
7322122 CTCCTTTGGG
*
7322132 ATCTTTCCTTGGCTCTCACATCGACAT
1 ATCTTTCCTTGGCTCACACATCGACAT
7322159 ATCTTTCCCTTGGCTCACACATCGACAT
1 ATCTTT-CCTTGGCTCACACATCGACAT
7322187 CCTCCCTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.20, C:0.35, G:0.11, T:0.35
Consensus pattern (27 bp):
ATCTTTCCTTGGCTCACACATCGACAT
Found at i:7322198 original size:25 final size:27
Alignment explanation
Indices: 7322138--7322199 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
7322128 TGGGATCTTT
* *
7322138 CCTTGGCTCTCACATCGACATATCTTTC
1 CCTTGGCTCACACATCGACA-ATCTCTC
7322166 CCTTGGCTCACACATCGAC-ATC-CTC
1 CCTTGGCTCACACATCGACAATCTCTC
7322191 CCTTGGCTC
1 CCTTGGCTC
7322200 CTTTGTTCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 11 0.34
26 3 0.09
28 18 0.56
ACGTcount: A:0.16, C:0.40, G:0.13, T:0.31
Consensus pattern (27 bp):
CCTTGGCTCACACATCGACAATCTCTC
Found at i:7322648 original size:17 final size:17
Alignment explanation
Indices: 7322626--7322660 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
7322616 CCATGATATC
7322626 CAATAGGACTCGACTCT
1 CAATAGGACTCGACTCT
7322643 CAATAGGACTCGACTCT
1 CAATAGGACTCGACTCT
7322660 C
1 C
7322661 GTTGAAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (17 bp):
CAATAGGACTCGACTCT
Found at i:7336263 original size:12 final size:12
Alignment explanation
Indices: 7336232--7336265 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
7336222 CCTTGCCCAA
7336232 CTCTCTCTC--T
1 CTCTCTCTCGAT
7336242 CTCTCTCTCGAT
1 CTCTCTCTCGAT
7336254 CTCTCTCTCGAT
1 CTCTCTCTCGAT
7336266 TGGCATATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.06, C:0.44, G:0.06, T:0.44
Consensus pattern (12 bp):
CTCTCTCTCGAT
Found at i:7336353 original size:93 final size:94
Alignment explanation
Indices: 7336232--7336512 Score: 241
Period size: 93 Copynumber: 3.1 Consensus size: 94
7336222 CCTTGCCCAA
* * * *
7336232 CTCTCTCTCTCTCTCTCTCGATC-TCTCTCTCGATTGGCATATCTTT-TTCTCCATA-ATCGATG
1 CTCTCTCTCTCTCTCTCTCTATCGCCTCTCTCGATT-GC-TATCTTTCTTCT--ATACATAGATC
*
7336294 ACAATTGCA-CCCCTT-CCCCAAC-CTCTCTCT
62 ACAATTGCACCCCCTTCCCCCAACTCTCTATCT
* * *
7336324 CTTCTTTCTCTCCCTCTCTCTTTCGCTCTCTCTCGATTGCTATCTTTCTTCTATACATAGATCAC
1 C-TCTCTCTCTCTCTCTCTCTATCGC-CTCTCTCGATTGCTATCTTTCTTCTATACATAGATCAC
*
7336389 AATTGCACCCCCTTCCCCCAACTCTTTATCT
64 AATTGCACCCCCTTCCCCCAACTCTCTATCT
* ** ** *
7336420 CTCTCTCTCTCTCTCTCTC--TGGATTGAC-CGA-T-CT-T-TTTCTTCTATACATCGATCACAA
1 CTCTCTCTCTCTCTCTCTCTATCGCCTCTCTCGATTGCTATCTTTCTTCTATACATAGATCACAA
* * *
7336478 TTGCACCCCC-T-ACCCATCTCTCTCTCT
66 TTGCACCCCCTTCCCCCAACTCTCTATCT
7336505 CTCTCTCT
1 CTCTCTCT
7336513 TCCAATTGAT
Statistics
Matches: 160, Mismatches: 21, Indels: 23
0.78 0.10 0.11
Matches are distributed among these distances:
85 20 0.12
86 1 0.01
87 32 0.20
88 1 0.01
89 2 0.01
90 1 0.01
91 3 0.02
92 6 0.04
93 41 0.26
94 12 0.08
95 34 0.21
96 7 0.04
ACGTcount: A:0.15, C:0.39, G:0.06, T:0.40
Consensus pattern (94 bp):
CTCTCTCTCTCTCTCTCTCTATCGCCTCTCTCGATTGCTATCTTTCTTCTATACATAGATCACAA
TTGCACCCCCTTCCCCCAACTCTCTATCT
Found at i:7337846 original size:94 final size:90
Alignment explanation
Indices: 7337678--7337861 Score: 305
Period size: 94 Copynumber: 2.0 Consensus size: 90
7337668 TAGTCAAGAA
7337678 GTAACTGTGACTGCCTCTCTAATGGCAGCAAATAATGCAGGCCTTAAGGTTAGAGTTTCAGTAAT
1 GTAACTGTGACTGCCTCTCTAATGGCAGCAAATAATGCAGGCCTTAAGGTTAGAGTTTCAGTAAT
7337743 TTGCTGTGTTTGAGTTAAAGGGTAG
66 TTGCTGTGTTTGAGTTAAAGGGTAG
*
7337768 GTAACTGTGACTGCCTCTCTAATGGCAGCAAATAATGGGGGCAGGTCTTAAGGTTAGAGTTTCAG
1 GTAACTGTGACTGCCTCTCTAATGGCAGCAAATAAT----GCAGGCCTTAAGGTTAGAGTTTCAG
* *
7337833 TAATTTGTTGTGTTTGAGTTGAAGGGTAG
62 TAATTTGCTGTGTTTGAGTTAAAGGGTAG
7337862 TTACTGGTTA
Statistics
Matches: 87, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
90 36 0.41
94 51 0.59
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (90 bp):
GTAACTGTGACTGCCTCTCTAATGGCAGCAAATAATGCAGGCCTTAAGGTTAGAGTTTCAGTAAT
TTGCTGTGTTTGAGTTAAAGGGTAG
Found at i:7355040 original size:20 final size:20
Alignment explanation
Indices: 7354994--7355044 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
7354984 TATCAAATGG
* *
7354994 ATATAAAATGATAATATAAT
1 ATATTAAATAATAATATAAT
*
7355014 ATTTTAAATAATAATAATAAT
1 ATATTAAATAATAAT-ATAAT
7355035 A-ATT-AATAAT
1 ATATTAAATAAT
7355045 TAATTATCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 6 0.23
20 14 0.54
21 6 0.23
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
ATATTAAATAATAATATAAT
Found at i:7355800 original size:13 final size:14
Alignment explanation
Indices: 7355776--7355809 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
7355766 GTTGTCTGTT
7355776 TAATTATATTAAAA
1 TAATTATATTAAAA
*
7355790 TAATT-TATTAAAT
1 TAATTATATTAAAA
7355803 TAATTAT
1 TAATTAT
7355810 CAATTATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTATATTAAAA
Found at i:7360222 original size:21 final size:22
Alignment explanation
Indices: 7360161--7360222 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 22
7360151 TTTATTTTAA
*
7360161 TTAATTATTAATTATAAAAATTTAT
1 TTAATT-TTAA-T-TAAAAATATAT
* *
7360186 TTAATTTAAAAT-AAAATAT-T
1 TTAATTTTAATTAAAAATATAT
7360206 TTAATTTTAATTAAAAA
1 TTAATTTTAATTAAAAA
7360223 ATAAAGAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 11 0.35
21 10 0.32
22 1 0.03
24 3 0.10
25 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAATTTTAATTAAAAATATAT
Found at i:7365358 original size:18 final size:18
Alignment explanation
Indices: 7365332--7365384 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
7365322 AATATGATAT
*
7365332 ATTAAAATATTATAATTA
1 ATTATAATATTATAATTA
*
7365350 ATTATAATATAATATATTA
1 ATTATAATATTATA-ATTA
*
7365369 A-TATATTATTGATAAT
1 ATTATAATATT-ATAAT
7365385 GACATGATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 21 0.72
19 8 0.28
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTATAATATTATAATTA
Found at i:7365608 original size:11 final size:11
Alignment explanation
Indices: 7365563--7365608 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
7365553 TAATAATAAT
7365563 TTATTTAAATA
1 TTATTTAAATA
7365574 TT-TTTAAATA
1 TTATTTAAATA
*
7365584 AT-TTTAAA-A
1 TTATTTAAATA
7365593 TTTATTTAAATA
1 -TTATTTAAATA
7365605 TTAT
1 TTAT
7365609 GTCTATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 1 0.03
10 16 0.53
11 12 0.40
12 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTATTTAAATA
Found at i:7376670 original size:2 final size:2
Alignment explanation
Indices: 7376663--7376697 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
7376653 CCAGTCCACC
*
7376663 AT AT AT AT AG AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7376698 TAATCCAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:7394603 original size:31 final size:30
Alignment explanation
Indices: 7394564--7394628 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
7394554 TTAATTAAGT
7394564 ATTTATTAAAT-TAAAAATAAAAATATAAAA
1 ATTTATTAAATATAAAAA-AAAAATATAAAA
* * *
7394594 ATTTGATTAAATATAATAAAAAAATTTTAAA
1 ATTT-ATTAAATATAAAAAAAAAATATAAAA
7394625 ATTT
1 ATTT
7394629 TTGTAAAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 4 0.13
31 21 0.70
32 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (30 bp):
ATTTATTAAATATAAAAAAAAAATATAAAA
Found at i:7399532 original size:24 final size:22
Alignment explanation
Indices: 7399496--7399540 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
7399486 ATTAAATTAA
*
7399496 TAAAATTACATAAATAATAAAATT
1 TAAAATTAAAT-AATAA-AAAATT
*
7399520 TAAATTTAAATAATAAAAAAT
1 TAAAATTAAATAATAAAAAAT
7399541 AAATATCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 5 0.26
24 9 0.47
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATTAAATAATAAAAAATT
Found at i:7399543 original size:20 final size:20
Alignment explanation
Indices: 7399506--7399544 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7399496 TAAAATTACA
**
7399506 TAAATAATAAAATTTAAATT
1 TAAATAATAAAAAATAAATT
7399526 TAAATAATAAAAAATAAAT
1 TAAATAATAAAAAATAAAT
7399545 ATCTCAAATA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAATAATAAAAAATAAATT
Found at i:7406137 original size:20 final size:20
Alignment explanation
Indices: 7406109--7406148 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
7406099 TTCGAGAGTG
7406109 GAATAAAGC-TCTCTTGCTTT
1 GAATAAAGCTTCT-TTGCTTT
*
7406129 GAATCAAGCTTCTTTGCTTT
1 GAATAAAGCTTCTTTGCTTT
7406149 TCTACACCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (20 bp):
GAATAAAGCTTCTTTGCTTT
Found at i:7415255 original size:20 final size:21
Alignment explanation
Indices: 7415214--7415255 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
7415204 GGAGTTTTAT
*
7415214 ATCAATTTCTGTAACTATATTA
1 ATCAATTTCCGTAAC-ATATTA
7415236 ATCAATTTCCGTAA-ATATTA
1 ATCAATTTCCGTAACATATTA
7415256 CAAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
22 13 0.68
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (21 bp):
ATCAATTTCCGTAACATATTA
Found at i:7415286 original size:19 final size:19
Alignment explanation
Indices: 7415247--7415296 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
7415237 TCAATTTCCG
*
7415247 TAAATATTACAAA-AAAAT
1 TAAATATTAAAAATAAAAT
7415265 TAAATA-TAAAAATAAAAT
1 TAAATATTAAAAATAAAAT
*
7415283 TTAATATTAAAAAT
1 TAAATATTAAAAAT
7415297 TATTATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 5 0.18
18 16 0.57
19 7 0.25
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAATATTAAAAATAAAAT
Found at i:7424716 original size:20 final size:20
Alignment explanation
Indices: 7424691--7424731 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
7424681 CCACAGCGAT
7424691 ACATACAACA-ACAAAAATAA
1 ACATACAA-ATACAAAAATAA
*
7424711 ACATACAAATGCAAAAATAA
1 ACATACAAATACAAAAATAA
7424731 A
1 A
7424732 AAAAAGGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.68, C:0.17, G:0.02, T:0.12
Consensus pattern (20 bp):
ACATACAAATACAAAAATAA
Found at i:7429204 original size:2 final size:2
Alignment explanation
Indices: 7429199--7429223 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7429189 AAAAAAAAGA
7429199 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
7429224 CCAAGACCAC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7442170 original size:21 final size:21
Alignment explanation
Indices: 7442128--7442175 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
7442118 TTTAAGAGGT
* *
7442128 AAAATTATAAAATTTATTAAA
1 AAAATTATAAAATGTATAAAA
*
7442149 AAAATTATAAATATGTAAAAAA
1 AAAATTATAAA-ATGTATAAAA
7442171 AAAAT
1 AAAAT
7442176 ATTATAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAATTATAAAATGTATAAAA
Found at i:7455406 original size:416 final size:412
Alignment explanation
Indices: 7454588--7455373 Score: 1085
Period size: 416 Copynumber: 1.9 Consensus size: 412
7454578 TATAATGATT
7454588 AAAAAAACCAAAAATCAATATATGTTGAAACATAAACATCTGATTTTAATTAATTTGATTCAATT
1 AAAAAAACCAAAAATCAATATATGTTGAAACATAAACATCTGATTTTAATTAATTTGATTCAATT
** * * *
7454653 GTAGTAAAAAGAGAAAGTCCGTTCTATTGCTTTATCAATTTCAAAGAAAAAACAAACTAAAAACT
66 ACAATAAAAACAGAAAGTCCGTTCTATTGCTTTATCAATTTCAAAGAAAAAACAAAATAAAAACT
* * ** **
7454718 TTTCTATAATTTATTAGAGTCAGTCATCAAATTGTTAGTGTTGCTGTAAGTCAAACCAAAACAGT
131 TTTCTATAATTTATTAGAGTCAGTCAACAAATTGTTACTGTTGCTAAAAGTCAAACCAAAACAAC
* * * *
7454783 CAGATAAAAAAGAATAAATCACATGTTTATATATGAATGCTAAATAGTACATGACTTTCCCTTAA
196 CACATAAAAAAGAATAAATCACATGTCTATATATGAATGATAAATAGTACATGACTTTCCCATAA
** *
7454848 TTGTGGGTAATCAAAATGTCGGCCAAACCTTTTTCAGTCGACAACAGTGATACCATTCCTACGTT
261 CGGTGGGTAATCAAAATATCGGCCAAACCTTTTTCAGTCGACAACAGTGATACCATTCCTACGTT
*
7454913 TTATCTCAGTCAAAATCTTCAAATTAAAATTTTATGTTCTATTAACTTTAGAAAAAAAAATTTAT
326 TTATCTCAGTCAAAATCTTCAAATTAAAATTTTATGTTATATTAACTTTAGAAAAAAAAATTTAT
*
7454978 GTTCTAATATTATGCATTAGGA
391 GTTCAAATATTATGCATTAGGA
* *
7455000 AAAAAAACTCGAAAAATCAATATATGTTGAAACATAAACGTCTGATTTTAATTAATTTGATTCCA
1 AAAAAAAC-C-AAAAATCAATATATGTTGAAACATAAACATCTGATTTTAATTAATTTGATTCAA
* * * **
7455065 TTACAATAAAAACAGTACAGTCGGTTCTATTGCTTTATCAATTTCTAAGAAAAAGTAAAATAAAA
64 TTACAATAAAAACAG-AAAGTCCGTTCTATTGCTTTATCAATTTCAAAGAAAAAACAAAATAAAA
** ** * *
7455130 TTTTTTCTATGAA-TTATTAGAGTTTGTCAACAAATTGTTACTGTTTCTAAAAGTCAAACCGAAA
128 ACTTTTCTAT-AATTTATTAGAGTCAGTCAACAAATTGTTACTGTTGCTAAAAGTCAAACCAAAA
* *
7455194 CAACCACATAAAAAAAGAATGAATCACGTGTCTATATATGAATGATAAATAGTACATGAC-TTCT
192 CAACCACAT-AAAAAAGAATAAATCACATGTCTATATATGAATGATAAATAGTACATGACTTTC-
* * *
7455258 CCATGACGGTGGG-AATTCAAAATATCGGCCAACCCTTTTTCAGTCGACAACAGTGATATCATTC
255 CCATAACGGTGGGTAA-TCAAAATATCGGCCAAACCTTTTTCAGTCGACAACAGTGATACCATTC
* ** *
7455322 CTATGTTTTATC-CAAGTGGAAATCTTCAAATTAAAATTTTATTTTAATATTA
319 CTACGTTTTATCTC-AGTCAAAATCTTCAAATTAAAATTTTATGTT-ATATTA
7455374 CTATTTTTGA
Statistics
Matches: 324, Mismatches: 41, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
412 8 0.02
413 1 0.00
414 63 0.19
415 106 0.33
416 141 0.44
417 5 0.02
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (412 bp):
AAAAAAACCAAAAATCAATATATGTTGAAACATAAACATCTGATTTTAATTAATTTGATTCAATT
ACAATAAAAACAGAAAGTCCGTTCTATTGCTTTATCAATTTCAAAGAAAAAACAAAATAAAAACT
TTTCTATAATTTATTAGAGTCAGTCAACAAATTGTTACTGTTGCTAAAAGTCAAACCAAAACAAC
CACATAAAAAAGAATAAATCACATGTCTATATATGAATGATAAATAGTACATGACTTTCCCATAA
CGGTGGGTAATCAAAATATCGGCCAAACCTTTTTCAGTCGACAACAGTGATACCATTCCTACGTT
TTATCTCAGTCAAAATCTTCAAATTAAAATTTTATGTTATATTAACTTTAGAAAAAAAAATTTAT
GTTCAAATATTATGCATTAGGA
Found at i:7455487 original size:19 final size:19
Alignment explanation
Indices: 7455465--7455503 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
7455455 GAATAAATGT
*
7455465 TTTTTTTATGTTTA-AATTA
1 TTTTTATAT-TTTATAATTA
7455484 TTTTTATATTTTATAATTA
1 TTTTTATATTTTATAATTA
7455503 T
1 T
7455504 GAATAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTTATATTTTATAATTA
Found at i:7457293 original size:28 final size:28
Alignment explanation
Indices: 7457212--7457359 Score: 113
Period size: 29 Copynumber: 5.2 Consensus size: 28
7457202 TGACAACTTT
* *
7457212 AATAAGTTTATCTTAATTTAAACAAGAAA
1 AATATGTTTATCTTAATTTAGACAA-AAA
* * * *
7457241 ACATAT-TATGTTTTAATTTAGACAAAGA
1 A-ATATGTTTATCTTAATTTAGACAAAAA
*
7457269 AATATGTTTATCTTAATTTATACAAGAAA
1 AATATGTTTATCTTAATTTAGACAA-AAA
* **
7457298 TCATAT-TTGGTCTTAATTTAGACAAAAA
1 -AATATGTTTATCTTAATTTAGACAAAAA
* *
7457326 AATATGTTTGA-CTTAATTTAAGATAGAAA
1 AATATGTTT-ATCTTAATTT-AGACAAAAA
7457355 AATAT
1 AATAT
7457360 TTTTTATCAC
Statistics
Matches: 92, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
27 8 0.09
28 31 0.34
29 46 0.50
30 7 0.08
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (28 bp):
AATATGTTTATCTTAATTTAGACAAAAA
Found at i:7457314 original size:57 final size:57
Alignment explanation
Indices: 7457212--7457346 Score: 193
Period size: 57 Copynumber: 2.4 Consensus size: 57
7457202 TGACAACTTT
* * *
7457212 AATAAGTTTATCTTAATTTAAACAAGAAAACATATTATGTTTTAATTTAGACAAAGA
1 AATATGTTTATCTTAATTTAAACAAGAAAACATATTATGTCTTAATTTAGACAAAAA
* *
7457269 AATATGTTTATCTTAATTTATACAAGAAATCATATT-TGGTCTTAATTTAGACAAAAA
1 AATATGTTTATCTTAATTTAAACAAGAAAACATATTAT-GTCTTAATTTAGACAAAAA
7457326 AATATGTTTGA-CTTAATTTAA
1 AATATGTTT-ATCTTAATTTAA
7457347 GATAGAAAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
56 1 0.01
57 68 0.97
58 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (57 bp):
AATATGTTTATCTTAATTTAAACAAGAAAACATATTATGTCTTAATTTAGACAAAAA
Found at i:7458847 original size:131 final size:131
Alignment explanation
Indices: 7458611--7458874 Score: 307
Period size: 131 Copynumber: 2.0 Consensus size: 131
7458601 AGAACTCGTA
* *
7458611 AATCTCTCAACTACTCTTGAAGGAATTTTAAAATATAGTAGAATAGACTTTTTGTAAACACATAA
1 AATCTCTCAACTACTCTTAAAAGAATTTTAAAATATAGTAGAATAGACTTTTTGTAAACACATAA
** * * *
7458676 TGCTTAGAATGATCTGTTGAGAAAAAGGAGATTAAGAGAATTTTTGAAGCCAGGATACATGAGAT
66 AACTTAAAATGATCTGTTGAGAAAAAGGAGATTAAGAGAATTTCTGAAGCCAGGATACAGGAGAT
7458741 G
131 G
* * ** * * * *
7458742 AATCTCTCGACTGCTCTTAAAAGAATTTTAGTATGTTGTAGAATAGAGTTTTTGTAAACATGA-A
1 AATCTCTCAACTACTCTTAAAAGAATTTTAAAATATAGTAGAATAGACTTTTTGTAAACA-CATA
* * * * **
7458806 AAACTTAAAATGATTTTTTGAGAAAGAGTAGATT-AGAAGAATTTCTGAAGTTAGGATACAGGAG
65 AAACTTAAAATGATCTGTTGAGAAAAAGGAGATTAAG-AGAATTTCTGAAGCCAGGATACAGGAG
7458870 ATG
129 ATG
7458873 AA
1 AA
7458875 AAGTGCTTTT
Statistics
Matches: 110, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
130 2 0.02
131 107 0.97
132 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (131 bp):
AATCTCTCAACTACTCTTAAAAGAATTTTAAAATATAGTAGAATAGACTTTTTGTAAACACATAA
AACTTAAAATGATCTGTTGAGAAAAAGGAGATTAAGAGAATTTCTGAAGCCAGGATACAGGAGAT
G
Found at i:7461828 original size:45 final size:45
Alignment explanation
Indices: 7461770--7461865 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 45
7461760 AATAATTTTA
* * *
7461770 TTACACGTTATGTATAAAAACATGTTACACATCATGGTTAAATTG
1 TTACACGTCATGTACAAAAACATGTGACACATCATGGTTAAATTG
* * * **
7461815 TTACATGTCATGTACAAAAACATGTGATATATCATGGTTAGGTTG
1 TTACACGTCATGTACAAAAACATGTGACACATCATGGTTAAATTG
7461860 TTACAC
1 TTACAC
7461866 TCCATGTTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (45 bp):
TTACACGTCATGTACAAAAACATGTGACACATCATGGTTAAATTG
Found at i:7475702 original size:2 final size:2
Alignment explanation
Indices: 7475695--7475721 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7475685 TCTTTAGTTC
7475695 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 A
7475722 ATAAATCTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7490999 original size:26 final size:26
Alignment explanation
Indices: 7490944--7491006 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
7490934 TGCTATTCAC
*
7490944 AAAAACATGTTACACATCATAGTTAA
1 AAAAACATATTACACATCATAGTTAA
* * *
7490970 AAAAAGATATTACACGTCAT-GTTGA
1 AAAAACATATTACACATCATAGTTAA
*
7490995 TAAAACAATATT
1 AAAAAC-ATATT
7491007 GTTATTACAC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 8 0.27
26 22 0.73
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.29
Consensus pattern (26 bp):
AAAAACATATTACACATCATAGTTAA
Found at i:7504239 original size:14 final size:14
Alignment explanation
Indices: 7504220--7504247 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
7504210 AGAAAGAATG
7504220 AGTCACTTCTGGTA
1 AGTCACTTCTGGTA
7504234 AGTCACTTCTGGTA
1 AGTCACTTCTGGTA
7504248 TATCTGCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
AGTCACTTCTGGTA
Found at i:7508772 original size:28 final size:28
Alignment explanation
Indices: 7508720--7508773 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
7508710 GAATTTAAAT
**
7508720 ATATTTATAATAAATATAATCAAACATA
1 ATATTTATAATAAATATAAGAAAACATA
**
7508748 ATATTTATAATTCATATAAGAAAACA
1 ATATTTATAATAAATATAAGAAAACA
7508774 GACAAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (28 bp):
ATATTTATAATAAATATAAGAAAACATA
Found at i:7512252 original size:21 final size:19
Alignment explanation
Indices: 7512228--7512267 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 19
7512218 AAATGTACAA
7512228 TATTTGAAAAAATTCTTAAAT
1 TATTT-AAAAAATT-TTAAAT
7512249 TATTTAAAAAATTTTAAAT
1 TATTTAAAAAATTTTAAAT
7512268 AAATTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 8 0.42
21 5 0.26
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (19 bp):
TATTTAAAAAATTTTAAAT
Found at i:7512281 original size:28 final size:28
Alignment explanation
Indices: 7512249--7512310 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
7512239 ATTCTTAAAT
7512249 TATTTAAAAAATTTTAAATAAATTTTTA
1 TATTTAAAAAATTTTAAATAAATTTTTA
* ** * *
7512277 TATTTTTAGTATTTTTAATTAAATTTTTA
1 TA-TTTAAAAAATTTTAAATAAATTTTTA
7512306 TATTT
1 TATTT
7512311 TTATTTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (28 bp):
TATTTAAAAAATTTTAAATAAATTTTTA
Found at i:7512304 original size:21 final size:21
Alignment explanation
Indices: 7512278--7512322 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
7512268 AAATTTTTAT
7512278 ATTTTTAGTATTTTTA-ATTAA
1 ATTTTTA-TATTTTTATATTAA
*
7512299 ATTTTTATATTTTTATTTTAA
1 ATTTTTATATTTTTATATTAA
7512320 ATT
1 ATT
7512323 AAATAAGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTTTATATTTTTATATTAA
Found at i:7513145 original size:28 final size:28
Alignment explanation
Indices: 7513114--7513174 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
7513104 AAAATATGTT
*
7513114 ATAAATAGATAAATTACA-CGAAATACAA
1 ATAAATAAATAAATTACATC-AAATACAA
* *
7513142 ATAAGTAAATAAATTACATCAAATATAA
1 ATAAATAAATAAATTACATCAAATACAA
7513170 ATAAA
1 ATAAA
7513175 ATTTTAATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (28 bp):
ATAAATAAATAAATTACATCAAATACAA
Found at i:7513729 original size:16 final size:14
Alignment explanation
Indices: 7513704--7513738 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
7513694 AATTTTTTTA
7513704 TTATATATATAAAAT
1 TTATATATAT-AAAT
7513719 TTATGATATATAAAT
1 TTAT-ATATATAAAT
7513734 TTATA
1 TTATA
7513739 ATTTTATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.05
15 12 0.63
16 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
TTATATATATAAAT
Found at i:7515466 original size:23 final size:22
Alignment explanation
Indices: 7515381--7515459 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 22
7515371 TTAAAATTTT
* * *
7515381 ATAATATTATAATTAAA-TAAA
1 ATAATATAAAAATAAAATTAAA
* * *
7515402 AAAATATTAAAATAAAA-T-AT
1 ATAATATAAAAATAAAATTAAA
7515422 ATAATATAAAAATAAAATTAAA
1 ATAATATAAAAATAAAATTAAA
7515444 ATAA-ATAAAAATAAAA
1 ATAATATAAAAATAAAA
7515460 AATTAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
20 16 0.33
21 28 0.57
22 5 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
ATAATATAAAAATAAAATTAAA
Found at i:7515569 original size:33 final size:34
Alignment explanation
Indices: 7515494--7515578 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 34
7515484 AAATAAATTA
* * *
7515494 AAATAAATATATAATATA-AAAATTATATTAAAG
1 AAATAAAAATAAAATATATAAAATTATAATAAAG
* * *
7515527 AAATGAAAATAAAATATATAAGATTATAAT-AAT
1 AAATAAAAATAAAATATATAAAATTATAATAAAG
7515560 AAATAAAAATAAAATATAT
1 AAATAAAAATAAAATATAT
7515579 GACATTAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 35 0.80
34 9 0.20
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.31
Consensus pattern (34 bp):
AAATAAAAATAAAATATATAAAATTATAATAAAG
Found at i:7515569 original size:82 final size:83
Alignment explanation
Indices: 7515380--7515572 Score: 222
Period size: 82 Copynumber: 2.3 Consensus size: 83
7515370 ATTAAAATTT
7515380 TATAATATTATAAT--TAAATAAAAA-AATATTAAAATAAAATATATAATATAAAAATAAAATTA
1 TATAA-ATTATAATAATAAATAAAAATAA-ATTAAAATAAAATATATAATATAAAAATAAAATTA
*
7515442 AAATAAATAAAAATAAAAAA
64 AAAGAAATAAAAATAAAAAA
* * *
7515462 T-TAAATT-TATATAATATAGGT-AAAATAAATTAAAAT-AAATATATAATATAAAAATTATATT
1 TATAAATTATA-ATAATA-A-ATAAAAATAAATTAAAATAAAATATATAATATAAAAATAAAATT
* *
7515523 -AAAGAAATGAAAATAAAATA
63 AAAAGAAATAAAAATAAAAAA
7515543 TATAAGATTATAATAATAAATAAAAATAAA
1 TATAA-ATTATAATAATAAATAAAAATAAA
7515573 ATATATGACA
Statistics
Matches: 94, Mismatches: 7, Indels: 20
0.78 0.06 0.17
Matches are distributed among these distances:
79 2 0.02
80 5 0.05
81 22 0.23
82 38 0.40
83 22 0.23
84 5 0.05
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (83 bp):
TATAAATTATAATAATAAATAAAAATAAATTAAAATAAAATATATAATATAAAAATAAAATTAAA
AGAAATAAAAATAAAAAA
Found at i:7515575 original size:15 final size:15
Alignment explanation
Indices: 7515395--7515459 Score: 53
Period size: 15 Copynumber: 4.2 Consensus size: 15
7515385 TATTATAATT
7515395 AAATAAA-AAAATATTA
1 AAATAAATAAAA-A-TA
*
7515411 AAATAAAATATATAATA
1 AAAT-AAATA-AAAATA
* *
7515428 TAA-AAATAAAATTA
1 AAATAAATAAAAATA
7515442 AAATAAATAAAAATA
1 AAATAAATAAAAATA
7515457 AAA
1 AAA
7515460 AATTAAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
14 6 0.15
15 18 0.46
16 4 0.10
17 7 0.18
18 2 0.05
19 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAATAAATAAAAATA
Found at i:7515810 original size:15 final size:15
Alignment explanation
Indices: 7515790--7515833 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
7515780 TGTTATTTTC
*
7515790 CTTGTAATGACATTG
1 CTTGTAATCACATTG
*
7515805 CTTGTAATCACATTA
1 CTTGTAATCACATTG
* *
7515820 CCTGCAATCACATT
1 CTTGTAATCACATT
7515834 ACCTATAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (15 bp):
CTTGTAATCACATTG
Found at i:7515843 original size:15 final size:15
Alignment explanation
Indices: 7515809--7515844 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
7515799 ACATTGCTTG
*
7515809 TAATCACATTACCTG
1 TAATCACATTACCTA
*
7515824 CAATCACATTACCTA
1 TAATCACATTACCTA
7515839 TAATCA
1 TAATCA
7515845 TTTTATATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.28, G:0.03, T:0.31
Consensus pattern (15 bp):
TAATCACATTACCTA
Found at i:7516960 original size:8 final size:8
Alignment explanation
Indices: 7516949--7516987 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
7516939 AATATATAAG
7516949 ATTATATT
1 ATTATATT
7516957 ATTATATT
1 ATTATATT
*
7516965 ATTTTAATAT
1 ATTAT-AT-T
7516975 ATTATATT
1 ATTATATT
7516983 ATTAT
1 ATTAT
7516988 TAATTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 18 0.67
9 4 0.15
10 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTATATT
Found at i:7516975 original size:13 final size:13
Alignment explanation
Indices: 7516949--7516983 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
7516939 AATATATAAG
*
7516949 ATTATATTATTAT
1 ATTATATTAATAT
*
7516962 ATTATTTTAATAT
1 ATTATATTAATAT
7516975 ATTATATTA
1 ATTATATTA
7516984 TTATTAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTATATTAATAT
Found at i:7516977 original size:18 final size:19
Alignment explanation
Indices: 7516956--7516991 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
7516946 AAGATTATAT
7516956 TATTATATTATT-TTAATA
1 TATTATATTATTATTAATA
7516974 TATTATATTATTATTAAT
1 TATTATATTATTATTAAT
7516992 TATAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTATATTATTATTAATA
Found at i:7518277 original size:7 final size:7
Alignment explanation
Indices: 7518265--7518296 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
7518255 AGTCTGTCAA
7518265 TTGCATG
1 TTGCATG
7518272 TTGCATG
1 TTGCATG
7518279 TTGCATG
1 TTGCATG
7518286 TTGCATG
1 TTGCATG
7518293 TTGC
1 TTGC
7518297 TTGGTTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.16, G:0.28, T:0.44
Consensus pattern (7 bp):
TTGCATG
Found at i:7525461 original size:2 final size:2
Alignment explanation
Indices: 7525454--7525490 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
7525444 GGGCACAACA
7525454 AT AT 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 AT AT A
7525491 AATCTTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7525571 original size:18 final size:18
Alignment explanation
Indices: 7525548--7525582 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
7525538 ATATGTTTGG
7525548 GGAG-AACAAAGGCAAAAA
1 GGAGAAACAAAGG-AAAAA
7525566 GGAGAAACAAAGGAAAA
1 GGAGAAACAAAGGAAAA
7525583 GAGAACAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.63, C:0.09, G:0.29, T:0.00
Consensus pattern (18 bp):
GGAGAAACAAAGGAAAAA
Found at i:7532142 original size:26 final size:29
Alignment explanation
Indices: 7532094--7532150 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 29
7532084 TTTAAATAAA
* *
7532094 ATTTTTATTAAATATTATGAATTAAATTT
1 ATTTTTATTAAATATTATCAATTAAACTT
7532123 ATTTTT-TTAAAT-TTA-CAATTAAACTT
1 ATTTTTATTAAATATTATCAATTAAACTT
7532149 AT
1 AT
7532151 ATATAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 11 0.42
27 3 0.12
28 6 0.23
29 6 0.23
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (29 bp):
ATTTTTATTAAATATTATCAATTAAACTT
Found at i:7532197 original size:34 final size:35
Alignment explanation
Indices: 7532146--7532221 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 35
7532136 TACAATTAAA
* *
7532146 CTTATATATAATTTAAATT-TTTAATTTT-TTTTATT
1 CTTA-ATAAAATTTAAATTATTT-ATTTTAATTTATT
*
7532181 TTTAATAAAATTTAAATTATTTATTTTAATTTATT
1 CTTAATAAAATTTAAATTATTTATTTTAATTTATT
7532216 CTTAAT
1 CTTAAT
7532222 GCTTTATCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
34 18 0.51
35 17 0.49
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (35 bp):
CTTAATAAAATTTAAATTATTTATTTTAATTTATT
Found at i:7532635 original size:20 final size:20
Alignment explanation
Indices: 7532585--7532627 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
7532575 AAAAAAAATC
7532585 ATAACCAAAAAGAAACCAAAA
1 ATAA-CAAAAAGAAACCAAAA
*
7532606 ATATCAAAAAGAAAACCAAAA
1 ATAACAAAAAG-AAACCAAAA
7532627 A
1 A
7532628 AAGAAAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.72, C:0.16, G:0.05, T:0.07
Consensus pattern (20 bp):
ATAACAAAAAGAAACCAAAA
Found at i:7532635 original size:21 final size:20
Alignment explanation
Indices: 7532591--7532635 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
7532581 AATCATAACC
* **
7532591 AAAAAGAAACCAAAAATATC
1 AAAAAGAAACCAAAAAAAGA
7532611 AAAAAGAAAACCAAAAAAAGA
1 AAAAAG-AAACCAAAAAAAGA
7532632 AAAA
1 AAAA
7532636 CAAATCTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.78, C:0.11, G:0.07, T:0.04
Consensus pattern (20 bp):
AAAAAGAAACCAAAAAAAGA
Found at i:7548038 original size:2 final size:2
Alignment explanation
Indices: 7548031--7548057 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7548021 TATTTTAATT
7548031 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
7548058 TCTCAACCAA
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:7548322 original size:25 final size:25
Alignment explanation
Indices: 7548293--7548381 Score: 83
Period size: 25 Copynumber: 3.4 Consensus size: 25
7548283 TACAACATAT
*
7548293 ATATAATTCTTAATTTTATTAATAA
1 ATATAATTTTTAATTTTATTAATAA
* *
7548318 ATATAATTTTTTAATATTTTATGTCATAT
1 ATATAA-TTTTT-A-ATTTTAT-TAATAA
*
7548347 ATA-AATTTTTAATCTTT-TTAATTA
1 ATATAATTTTTAAT-TTTATTAATAA
7548371 ATATAATTTTT
1 ATATAATTTTT
7548382 TTTTGTTTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
24 6 0.12
25 16 0.31
26 8 0.15
27 6 0.12
28 9 0.17
29 7 0.13
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (25 bp):
ATATAATTTTTAATTTTATTAATAA
Found at i:7548374 original size:28 final size:27
Alignment explanation
Indices: 7548289--7548375 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
7548279 CTTTTACAAC
*
7548289 ATATATATAATTCTTAATTTTATTAA-TA
1 ATATATA-AATTTTTAATTTT-TTAATTA
* * *
7548317 A-ATATAATTTTTTAATATTTT-ATGTC
1 ATATATAAATTTTTAATTTTTTAAT-TA
7548343 ATATATAAATTTTTAATCTTTTTAATTA
1 ATATATAAATTTTTAAT-TTTTTAATTA
7548371 ATATA
1 ATATA
7548376 ATTTTTTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
24 1 0.02
25 2 0.04
26 12 0.26
27 19 0.40
28 11 0.23
29 2 0.04
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.55
Consensus pattern (27 bp):
ATATATAAATTTTTAATTTTTTAATTA
Found at i:7548383 original size:27 final size:25
Alignment explanation
Indices: 7548293--7548382 Score: 85
Period size: 26 Copynumber: 3.5 Consensus size: 25
7548283 TACAACATAT
* *
7548293 ATATAA-TTCTTAATTTTATTAATAA
1 ATATAATTTTTTAATTTT-TTAATTA
*
7548318 ATATAATTTTTTAATATTTT-ATGTCA
1 ATATAATTTTTTAATTTTTTAAT-T-A
*
7548344 TATATAAATTTTTAATCTTTTTAATTA
1 -ATATAATTTTTTAAT-TTTTTAATTA
7548371 ATATAATTTTTT
1 ATATAATTTTTT
7548383 TTTGTTTTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
24 2 0.04
25 8 0.15
26 21 0.40
27 15 0.28
28 5 0.09
29 2 0.04
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (25 bp):
ATATAATTTTTTAATTTTTTAATTA
Found at i:7548470 original size:67 final size:66
Alignment explanation
Indices: 7548410--7548537 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 66
7548400 TTTTTAGCAC
**
7548410 CTATTTTATGACATATATATAATTCTCAATTTTGTTAATAAATAGAATTTTTTATTTTTTTTAAA
1 CTATTTTATGACATATATATAA-TCTCAATTTCATTAATAAATAGAATTTTTTATTTTTTTTAAA
7548475 CG
65 CG
* * * * *
7548477 TCTCTTTTATGGCATATATATAATCTTAGTTTCATTAATAAATATAATTTTTTATTTTTTT
1 -CTATTTTATGACATATATATAATCTCAATTTCATTAATAAATAGAATTTTTTATTTTTTT
7548538 ACCATATATT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
67 33 0.62
68 20 0.38
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (66 bp):
CTATTTTATGACATATATATAATCTCAATTTCATTAATAAATAGAATTTTTTATTTTTTTTAAAC
G
Found at i:7554582 original size:16 final size:14
Alignment explanation
Indices: 7554542--7554592 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
7554532 ATTTTTTTAA
7554542 TTAATTTATTT-TT
1 TTAATTTATTTATT
* *
7554555 ATTGAGTTATTTAATT
1 -TTAATTTATTT-ATT
7554571 TTATATTTATTTATT
1 TTA-ATTTATTTATT
7554586 TTAATTT
1 TTAATTT
7554593 GACTATTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 13 0.43
15 8 0.27
16 9 0.30
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (14 bp):
TTAATTTATTTATT
Found at i:7554590 original size:21 final size:21
Alignment explanation
Indices: 7554564--7554606 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
7554554 TATTGAGTTA
*
7554564 TTTAATTTTA-TATTTATTTAT
1 TTTAATTTGACTA-TTATTTAT
7554585 TTTAATTTGACTATTATTTAT
1 TTTAATTTGACTATTATTTAT
7554606 T
1 T
7554607 AGCTTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTAATTTGACTATTATTTAT
Found at i:7558325 original size:2 final size:2
Alignment explanation
Indices: 7558320--7558350 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7558310 TCAGAAACAA
7558320 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 A
7558351 AAAGATTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7616122 original size:30 final size:31
Alignment explanation
Indices: 7616088--7616174 Score: 92
Period size: 29 Copynumber: 2.9 Consensus size: 31
7616078 ATTACCTTAT
** *
7616088 TAAAAATATTTTATAATATTATAAT-TAA-AA
1 TAAAAATATTAAATAA-AATATAATATAAGAA
7616118 TAAAAATATTAAATAAAATATAATATAAGAA
1 TAAAAATATTAAATAAAATATAATATAAGAA
* *
7616149 T-AAAAT-TAAAATAAAATAAAATATAA
1 TAAAAATATTAAATAAAATATAATATAA
7616175 AAAATTAACA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
29 25 0.50
30 22 0.44
31 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (31 bp):
TAAAAATATTAAATAAAATATAATATAAGAA
Found at i:7616136 original size:5 final size:5
Alignment explanation
Indices: 7616113--7616171 Score: 55
Period size: 5 Copynumber: 10.4 Consensus size: 5
7616103 ATATTATAAT
7616113 TAAAA TAAAAA TATTAAA TAAAA TATAATA TAAGAA TAAAA TTAAAA TAAAA
1 TAAAA T-AAAA TA--AAA TAAAA TA-AA-A TAA-AA TAAAA -TAAAA TAAAA
7616165 TAAAA TA
1 TAAAA TA
7616172 TAAAAAATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
5 21 0.45
6 17 0.36
7 9 0.19
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (5 bp):
TAAAA
Found at i:7616161 original size:11 final size:11
Alignment explanation
Indices: 7616113--7616171 Score: 50
Period size: 12 Copynumber: 5.2 Consensus size: 11
7616103 ATATTATAAT
*
7616113 TAAAATAAAAA
1 TAAAATTAAAA
7616124 TATTAAA-TAAAA
1 TA--AAATTAAAA
*
7616136 TATAATATAAGAA
1 TAAAAT-TAA-AA
7616149 TAAAATTAAAA
1 TAAAATTAAAA
7616160 TAAAA-TAAAA
1 TAAAATTAAAA
7616170 TA
1 TA
7616172 TAAAAAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
10 9 0.22
11 9 0.22
12 12 0.30
13 10 0.25
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (11 bp):
TAAAATTAAAA
Found at i:7616166 original size:34 final size:36
Alignment explanation
Indices: 7616099--7616174 Score: 102
Period size: 34 Copynumber: 2.1 Consensus size: 36
7616089 AAAAATATTT
* *
7616099 TATAATATTATAATTAAAATAAAAATATTAAATAAAA
1 TATAATATAAGAATTAAAATAAAAATA-TAAATAAAA
*
7616136 TATAATATAAGAA-TAAAATTAAAATA-AAATAAAA
1 TATAATATAAGAATTAAAATAAAAATATAAATAAAA
7616170 TATAA
1 TATAA
7616175 AAAATTAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
34 13 0.36
36 12 0.33
37 11 0.31
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (36 bp):
TATAATATAAGAATTAAAATAAAAATATAAATAAAA
Found at i:7616297 original size:33 final size:34
Alignment explanation
Indices: 7616212--7616406 Score: 132
Period size: 33 Copynumber: 5.6 Consensus size: 34
7616202 AAACAAATTA
* * * *
7616212 AAATAAAATATATAATATA-AAAAATATATTAAAG
1 AAATAAAATATAAAATATATAAAATTATAAT-AAT
*
7616246 AAATGAAA-ATAAAATATATAAAATTATAATAAT
1 AAATAAAATATAAAATATATAAAATTATAATAAT
* * *
7616279 AAATAAAA-ATAAAATATATGACATTAAAAT-AT
1 AAATAAAATATAAAATATATAAAATTATAATAAT
** * *
7616311 ATTTAAAATATGATATTATATAAAATTAATAAT-AT
1 AAATAAAATAT-AAAATATATAAAATT-ATAATAAT
*
7616346 AAATATAAATATATTAAAATAAAATATAAATATTATAATAGT
1 -AA-ATAAA-ATA-TAAAAT---ATATAAA-ATTATAATAAT
7616388 AAATAAAA-ATAAAATATAT
1 AAATAAAATATAAAATATAT
7616407 GACATTAAAA
Statistics
Matches: 127, Mismatches: 21, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
32 8 0.06
33 39 0.31
34 31 0.24
35 6 0.05
36 1 0.01
37 10 0.08
38 7 0.06
39 2 0.02
40 5 0.04
41 14 0.11
42 4 0.03
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.33
Consensus pattern (34 bp):
AAATAAAATATAAAATATATAAAATTATAATAAT
Found at i:7616352 original size:6 final size:6
Alignment explanation
Indices: 7616341--7616405 Score: 57
Period size: 6 Copynumber: 11.0 Consensus size: 6
7616331 TAAAATTAAT
*
7616341 AATATA AATATA AATAT- ATTA-A AATA-A AATATA AATATTA TAATAGTA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATA-TA -AATA-TA
*
7616389 AATAAA AATA-A AATATA
1 AATATA AATATA AATATA
7616406 TGACATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
5 16 0.32
6 22 0.44
7 6 0.12
8 6 0.12
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:7616371 original size:110 final size:110
Alignment explanation
Indices: 7616251--7616582 Score: 525
Period size: 110 Copynumber: 3.0 Consensus size: 110
7616241 TAAAGAAATG
*
7616251 AAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAATATATTTA
1 AAAATAAAATATATAAAATTATAATAGTAAATAAAAATAAAATATATGACATTAAAATATATTTA
7616316 A-AATATGATATTATAT-AAAATTAATAATATAAATATAAATATATT
66 AGAA-ATGATATTATATAAAAATTAATAATA-AAATATAAATATATT
*
7616361 AAAATAAAATATA-AATATTATAATAGTAAATAAAAATAAAATATATGACATTAAAA-ATATATT
1 AAAATAAAATATATAAAATTATAATAGTAAATAAAAATAAAATATATGACATTAAAATATAT-TT
*
7616424 AAGAAATGATATTATATAAAAATTAATAACAAAAATATAAATATATT
65 AAGAAATGATATTATATAAAAATTAATAA-TAAAATATAAATATATT
*
7616471 AAAA-ATAAA-ATATAAAATTATAATAGTAAAT-AAAATAAAATATATGATATTAAAAATATATT
1 AAAATA-AAATATATAAAATTATAATAGTAAATAAAAATAAAATATATGACATT-AAAATATATT
7616533 TAAGAAATGATATTATATAAAAATTAATAATAAAATATAAATATATT
64 TAAGAAATGATATTATATAAAAATTAATAATAAAATATAAATATATT
7616580 AAA
1 AAA
7616583 CTTATATTTT
Statistics
Matches: 208, Mismatches: 6, Indels: 17
0.90 0.03 0.07
Matches are distributed among these distances:
108 4 0.02
109 99 0.48
110 100 0.48
111 5 0.02
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (110 bp):
AAAATAAAATATATAAAATTATAATAGTAAATAAAAATAAAATATATGACATTAAAATATATTTA
AGAAATGATATTATATAAAAATTAATAATAAAATATAAATATATT
Found at i:7616406 original size:109 final size:108
Alignment explanation
Indices: 7616251--7616582 Score: 528
Period size: 109 Copynumber: 3.0 Consensus size: 108
7616241 TAAAGAAATG
*
7616251 AAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAATATATTTA
1 AAAAT-AAA-ATATAAAATTATAATAGTAAATAAAAATAAAATATATGACATTAAAATATATTTA
7616316 A-AATATGATATTATAT-AAAATTAATAATATAAATATAAATATATT
64 AGAA-ATGATATTATATAAAAATTAATAATA-AAATATAAATATATT
7616361 AAAATAAAATATAAATATTATAATAGTAAATAAAAATAAAATATATGACATTAAAA-ATATATTA
1 AAAATAAAATATAAA-ATTATAATAGTAAATAAAAATAAAATATATGACATTAAAATATAT-TTA
*
7616425 AGAAATGATATTATATAAAAATTAATAACAAAAATATAAATATATT
64 AGAAATGATATTATATAAAAATTAATAA-TAAAATATAAATATATT
*
7616471 AAAAATAAAATATAAAATTATAATAGTAAAT-AAAATAAAATATATGATATTAAAAATATATTTA
1 -AAAATAAAATATAAAATTATAATAGTAAATAAAAATAAAATATATGACATT-AAAATATATTTA
7616535 AGAAATGATATTATATAAAAATTAATAATAAAATATAAATATATT
64 AGAAATGATATTATATAAAAATTAATAATAAAATATAAATATATT
7616580 AAA
1 AAA
7616583 CTTATATTTT
Statistics
Matches: 210, Mismatches: 4, Indels: 18
0.91 0.02 0.08
Matches are distributed among these distances:
108 14 0.07
109 93 0.44
110 83 0.40
111 20 0.10
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (108 bp):
AAAATAAAATATAAAATTATAATAGTAAATAAAAATAAAATATATGACATTAAAATATATTTAAG
AAATGATATTATATAAAAATTAATAATAAAATATAAATATATT
Found at i:7616493 original size:30 final size:31
Alignment explanation
Indices: 7616454--7616532 Score: 74
Period size: 30 Copynumber: 2.5 Consensus size: 31
7616444 AATTAATAAC
*
7616454 AAAAATATAAATATATTA-AAAATAAAATAT
1 AAAATTATAAATATATTATAAAATAAAATAT
*
7616484 AAAATTAT-AATAGTA-AATAAAATAAAATAT
1 AAAATTATAAATA-TATTATAAAATAAAATAT
* *
7616514 ATGATATTAAAAATATATT
1 A--AAATTATAAATATATT
7616533 TAAGAAATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
29 5 0.13
30 22 0.58
32 7 0.18
33 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (31 bp):
AAAATTATAAATATATTATAAAATAAAATAT
Found at i:7616751 original size:15 final size:15
Alignment explanation
Indices: 7616731--7616771 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
7616721 TTTTCTCTGT
7616731 AATCACATTGCTTGC
1 AATCACATTGCTTGC
* *
7616746 AATCACATTACTTGT
1 AATCACATTGCTTGC
7616761 AATCACATTGC
1 AATCACATTGC
7616772 ATTGTAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (15 bp):
AATCACATTGCTTGC
Found at i:7623615 original size:18 final size:17
Alignment explanation
Indices: 7623588--7623621 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
7623578 TTTGATAAAT
7623588 TTATTAAACAAAATTAG
1 TTATTAAACAAAATTAG
*
7623605 TTATATAAACAATATTA
1 TTAT-TAAACAAAATTA
7623622 ATAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (17 bp):
TTATTAAACAAAATTAG
Found at i:7646502 original size:21 final size:20
Alignment explanation
Indices: 7646461--7646516 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
7646451 TTAGTCTATG
*
7646461 AAATTGAATTAGTTAATTTA
1 AAATTGAATTAATTAATTTA
*
7646481 AAATTGAATATAATTTATTT-
1 AAATTGAAT-TAATTAATTTA
7646501 AAATT-AATTAATTAAT
1 AAATTGAATTAATTAAT
7646517 CAAATTATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 7 0.22
19 3 0.09
20 14 0.44
21 8 0.25
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
AAATTGAATTAATTAATTTA
Found at i:7684405 original size:2 final size:2
Alignment explanation
Indices: 7684398--7684435 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
7684388 TAATTGGGGC
* *
7684398 AT AT AT AT AT AT AT AT AT AT AT AT TT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7684436 CCTATCTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:7689580 original size:2 final size:2
Alignment explanation
Indices: 7689573--7689599 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7689563 TTATCAATAC
7689573 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 A
7689600 CACACACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7690588 original size:20 final size:20
Alignment explanation
Indices: 7690559--7690601 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
7690549 TATGTTGATT
7690559 TAATTAAAAATTATTA-TTTA
1 TAATTAAAAATT-TTACTTTA
*
7690579 TAATTGAAAATTTTACTTTA
1 TAATTAAAAATTTTACTTTA
7690599 TAA
1 TAA
7690602 CCTCATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TAATTAAAAATTTTACTTTA
Found at i:7700473 original size:28 final size:28
Alignment explanation
Indices: 7700441--7700499 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
7700431 CAAACCAAAC
* *
7700441 AAAGACTTAAAATATATATATATAAAAA
1 AAAGACTTAAAACATATATAAATAAAAA
* * *
7700469 AAAGATTTTAAACATTTATAAATAAAAA
1 AAAGACTTAAAACATATATAAATAAAAA
7700497 AAA
1 AAA
7700500 ATACTATACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (28 bp):
AAAGACTTAAAACATATATAAATAAAAA
Found at i:7713570 original size:29 final size:30
Alignment explanation
Indices: 7713523--7713584 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
7713513 TTTCTTTTAC
7713523 ATTTCTTCAGGTTAAGTTTGTCGATCCTCT
1 ATTTCTTCAGGTTAAGTTTGTCGATCCTCT
* *
7713553 ATTT-TTCAGGTTAAGTTTGTTGATCCTTT
1 ATTTCTTCAGGTTAAGTTTGTCGATCCTCT
7713582 ATT
1 ATT
7713585 GCGGTCACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.18, C:0.15, G:0.16, T:0.52
Consensus pattern (30 bp):
ATTTCTTCAGGTTAAGTTTGTCGATCCTCT
Found at i:7723921 original size:25 final size:25
Alignment explanation
Indices: 7723893--7723943 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
7723883 TACGCTGCTG
7723893 CTTTAAGCTCATTTCTTTCTTTGTT
1 CTTTAAGCTCATTTCTTTCTTTGTT
7723918 CTTTAAGCTCATTTCTTTCTTTGTT
1 CTTTAAGCTCATTTCTTTCTTTGTT
7723943 C
1 C
7723944 ATGTATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.12, C:0.22, G:0.08, T:0.59
Consensus pattern (25 bp):
CTTTAAGCTCATTTCTTTCTTTGTT
Found at i:7729467 original size:32 final size:35
Alignment explanation
Indices: 7729431--7729502 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 35
7729421 CCCTTTCTAA
7729431 CATTTTAATTCTTC-A-A-ATATGTCTAAGAAAAT
1 CATTTTAATTCTTCAATATATATGTCTAAGAAAAT
7729463 CATTTTAATTCTTCAAATATATATGTCTAAGAAAAT
1 CATTTTAATTCTTC-AATATATATGTCTAAGAAAAT
7729499 CATT
1 CATT
7729503 CTCTTTGGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
32 14 0.39
34 1 0.03
35 1 0.03
36 20 0.56
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (35 bp):
CATTTTAATTCTTCAATATATATGTCTAAGAAAAT
Found at i:7743020 original size:14 final size:15
Alignment explanation
Indices: 7742990--7743023 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
7742980 CTTCAATGTA
*
7742990 TTTCTTCTGTTTGTT
1 TTTCTTCTGTTTATT
7743005 TTTCTT-TGTTTATT
1 TTTCTTCTGTTTATT
7743019 TTTCT
1 TTTCT
7743024 CCACTGCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.03, C:0.12, G:0.09, T:0.76
Consensus pattern (15 bp):
TTTCTTCTGTTTATT
Found at i:7772195 original size:2 final size:2
Alignment explanation
Indices: 7772188--7772220 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7772178 ATGAATATGA
7772188 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
7772221 ATGGTTGCCT
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:7781813 original size:16 final size:17
Alignment explanation
Indices: 7781792--7781826 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
7781782 ATCCTCCAAC
7781792 AAAAATG-AAAAGTTAA
1 AAAAATGCAAAAGTTAA
*
7781808 AAAAATGCCAAAGTTAA
1 AAAAATGCAAAAGTTAA
7781825 AA
1 AA
7781827 CTTCAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.66, C:0.06, G:0.11, T:0.17
Consensus pattern (17 bp):
AAAAATGCAAAAGTTAA
Found at i:7797374 original size:17 final size:17
Alignment explanation
Indices: 7797332--7797389 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
7797322 TCTCATTTTA
*
7797332 AAATTTTATTAAATTTT
1 AAATTTTATTAAATATT
* *
7797349 AAGTTTTTTTTCAAATATT
1 AA-ATTTTATT-AAATATT
7797368 AAATTTTATTAAATATT
1 AAATTTTATTAAATATT
7797385 AAATT
1 AAATT
7797390 AAATTTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 14 0.41
18 12 0.35
19 8 0.24
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
AAATTTTATTAAATATT
Found at i:7797377 original size:10 final size:10
Alignment explanation
Indices: 7797364--7797406 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
7797354 TTTTTTCAAA
7797364 TATTAAATTT
1 TATTAAATTT
7797374 TATTAAATATT
1 TATTAAAT-TT
*
7797385 AAATTAAATTT
1 -TATTAAATTT
*
7797396 TATTAAGTTT
1 TATTAAATTT
7797406 T
1 T
7797407 GAAAAGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 17 0.61
11 4 0.14
12 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
TATTAAATTT
Found at i:7804283 original size:19 final size:19
Alignment explanation
Indices: 7804259--7804318 Score: 120
Period size: 19 Copynumber: 3.2 Consensus size: 19
7804249 TTATGTAAAT
7804259 TTTCTTGAATAGCCTGCTG
1 TTTCTTGAATAGCCTGCTG
7804278 TTTCTTGAATAGCCTGCTG
1 TTTCTTGAATAGCCTGCTG
7804297 TTTCTTGAATAGCCTGCTG
1 TTTCTTGAATAGCCTGCTG
7804316 TTT
1 TTT
7804319 ATGTAAATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45
Consensus pattern (19 bp):
TTTCTTGAATAGCCTGCTG
Found at i:7817515 original size:21 final size:22
Alignment explanation
Indices: 7817480--7817523 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
7817470 AACTTAATTT
* *
7817480 ATTATATCAAAATAATAAAAAA
1 ATTATAACAAAATAACAAAAAA
7817502 ATTATAAC-AAATAACAAAAAA
1 ATTATAACAAAATAACAAAAAA
7817523 A
1 A
7817524 ACTGTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (22 bp):
ATTATAACAAAATAACAAAAAA
Found at i:7820575 original size:21 final size:22
Alignment explanation
Indices: 7820522--7820641 Score: 122
Period size: 21 Copynumber: 5.3 Consensus size: 22
7820512 TATTATATGT
7820522 TTTAT-TTAGATGTTAGATGTTA
1 TTTATATT-GATGTTAGATGTTA
7820544 TTTGTATATATTG-TGTTAGATGTTA
1 --T-T-TATATTGATGTTAGATGTTA
*
7820569 TTTATA-TGTTGTTAGATGTTA
1 TTTATATTGATGTTAGATGTTA
*
7820590 TTTATATTG-TGTTCGATGTTA
1 TTTATATTGATGTTAGATGTTA
7820611 TTTATATGTTAGATGTTAGATGTTA
1 TTTATA--TT-GATGTTAGATGTTA
7820636 TTTATA
1 TTTATA
7820642 ATTTCGATGT
Statistics
Matches: 85, Mismatches: 2, Indels: 17
0.82 0.02 0.16
Matches are distributed among these distances:
20 2 0.02
21 39 0.46
22 3 0.04
23 3 0.04
24 2 0.02
25 30 0.35
26 4 0.05
27 2 0.02
ACGTcount: A:0.25, C:0.01, G:0.18, T:0.56
Consensus pattern (22 bp):
TTTATATTGATGTTAGATGTTA
Found at i:7820589 original size:46 final size:46
Alignment explanation
Indices: 7820531--7820638 Score: 143
Period size: 42 Copynumber: 2.3 Consensus size: 46
7820521 TTTTATTTAG
7820531 ATGTTAGATGTTATTTGTATATATTGTGTTAGATGTTATTTATATG-T
1 ATGTTAGATGTTATTT-T-TATATTGTGTTAGATGTTATTTATATGTT
*
7820578 -TGTTAGATGTTA--TTTATATTGTGTTCGATGTTATTTATATGTT
1 ATGTTAGATGTTATTTTTATATTGTGTTAGATGTTATTTATATGTT
7820621 AGATGTTAGATGTTATTT
1 --ATGTTAGATGTTATTT
7820639 ATAATTTCGA
Statistics
Matches: 54, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
42 26 0.48
43 2 0.04
44 1 0.02
46 24 0.44
48 1 0.02
ACGTcount: A:0.24, C:0.01, G:0.19, T:0.56
Consensus pattern (46 bp):
ATGTTAGATGTTATTTTTATATTGTGTTAGATGTTATTTATATGTT
Found at i:7820650 original size:25 final size:23
Alignment explanation
Indices: 7820524--7820652 Score: 133
Period size: 25 Copynumber: 5.5 Consensus size: 23
7820514 TTATATGTTT
7820524 TATTTAGATGTTAGATGTTATTTGTA
1 TATTT-GATGTTAGATGTTA-TT-TA
7820550 TATATTG-TGTTAGATGTTATTTA
1 TAT-TTGATGTTAGATGTTATTTA
*
7820573 TA--TGTTGTTAGATGTTATTTA
1 TATTTGATGTTAGATGTTATTTA
*
7820594 TA-TTG-TGTTCGATGTTATTTA
1 TATTTGATGTTAGATGTTATTTA
7820615 TATGTTAGATGTTAGATGTTATTTA
1 TAT-TT-GATGTTAGATGTTATTTA
7820640 TAATTTCGATGTT
1 T-ATTT-GATGTT
7820653 TCAATTTTAT
Statistics
Matches: 92, Mismatches: 3, Indels: 17
0.82 0.03 0.15
Matches are distributed among these distances:
20 2 0.02
21 35 0.38
22 2 0.02
23 6 0.07
24 3 0.03
25 36 0.39
26 6 0.07
27 2 0.02
ACGTcount: A:0.25, C:0.02, G:0.19, T:0.55
Consensus pattern (23 bp):
TATTTGATGTTAGATGTTATTTA
Found at i:7828725 original size:42 final size:42
Alignment explanation
Indices: 7828661--7828746 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
7828651 TTGCTTTGAT
** *
7828661 ACCACTTGATGTAGCCGGAAGGTTTAGGGCAATTAGAACTCA
1 ACCACTTGATGTAGCCAAAAGGTTTAGGGCAATTAAAACTCA
7828703 ACCACTTGATGTAGCCAAAAGGTTTAGGGCAATTAAAACTCA
1 ACCACTTGATGTAGCCAAAAGGTTTAGGGCAATTAAAACTCA
7828745 AC
1 AC
7828747 AAGTAGGACT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (42 bp):
ACCACTTGATGTAGCCAAAAGGTTTAGGGCAATTAAAACTCA
Done.