Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 22 of 27
Found at i:3796205 original size:2 final size:2
Alignment explanation
Indices: 3796192--3796227 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3796182 TTACTATTAC
*
3796192 TA TA TT 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 TA TA TA
3796228 ATGACATAAT
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:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3797651 original size:17 final size:18
Alignment explanation
Indices: 3797616--3797654 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3797606 TACACTTTTT
*
3797616 TATATATAAATTATTAAA
1 TATATAAAAATTATTAAA
3797634 TATATAAAAATT-TTAAA
1 TATATAAAAATTATTAAA
3797651 TATA
1 TATA
3797655 ATCATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATATAAAAATTATTAAA
Found at i:3797680 original size:14 final size:13
Alignment explanation
Indices: 3797653--3797694 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
3797643 ATTTTAAATA
*
3797653 TAATCATATTTAT
1 TAATTATATTTAT
3797666 TAAGTT-TATTTTAT
1 TAA-TTATA-TTTAT
3797680 TAATTATATTTAT
1 TAATTATATTTAT
3797693 TA
1 TA
3797695 TATTTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (13 bp):
TAATTATATTTAT
Found at i:3797699 original size:9 final size:9
Alignment explanation
Indices: 3797658--3797700 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
3797648 AAATATAATC
3797658 ATATTTATT
1 ATATTTATT
3797667 A-AGTTTATT
1 ATA-TTTATT
* *
3797676 TTATTAATT
1 ATATTTATT
3797685 ATATTTATT
1 ATATTTATT
3797694 ATATTTA
1 ATATTTA
3797701 AAAAATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 1 0.04
9 26 0.93
10 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
ATATTTATT
Found at i:3797740 original size:17 final size:19
Alignment explanation
Indices: 3797690--3797741 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
3797680 TAATTATATT
*
3797690 TATTATATTTAAAAAATAA
1 TATTATTTTTAAAAAATAA
* *
3797709 TATTA-TGTTGAAAAA-AA
1 TATTATTTTTAAAAAATAA
3797726 TATTTATTTTTAAAAA
1 TA-TTATTTTTAAAAA
3797742 TTTTATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 4 0.15
18 10 0.38
19 12 0.46
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (19 bp):
TATTATTTTTAAAAAATAA
Found at i:3798570 original size:14 final size:15
Alignment explanation
Indices: 3798537--3798574 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
3798527 TTTTAATTCA
*
3798537 TATATTATTAAATTTT
1 TATATT-TTAAATATT
3798553 TATATTTT-AATATT
1 TATATTTTAAATATT
3798567 TATATTTT
1 TATATTTT
3798575 TAAAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 2 0.10
16 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATATTTTAAATATT
Found at i:3798583 original size:14 final size:14
Alignment explanation
Indices: 3798537--3798584 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
3798527 TTTTAATTCA
*
3798537 TATATTATTAAATT
1 TATATTTTTAAATT
*
3798551 TTTATATTTTAATATT
1 TATAT-TTTTAA-ATT
*
3798567 TATATTTTTAAAAT
1 TATATTTTTAAATT
3798581 TATA
1 TATA
3798585 ATAAAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 10 0.36
15 11 0.39
16 7 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATATTTTTAAATT
Found at i:3798870 original size:29 final size:31
Alignment explanation
Indices: 3798811--3798869 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
3798801 TTCTATTATT
*
3798811 TATTATAATTTCAAAAATATATGAATTAAAA
1 TATTATAATTTCAAAAATATATAAATTAAAA
*
3798842 TATTA-AATTT-AATAATATA-AAATTAAAA
1 TATTATAATTTCAAAAATATATAAATTAAAA
3798870 AAATTCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 8 0.31
29 8 0.31
30 5 0.19
31 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (31 bp):
TATTATAATTTCAAAAATATATAAATTAAAA
Found at i:3799519 original size:2 final size:2
Alignment explanation
Indices: 3799512--3799546 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3799502 TATGGTAGGA
3799512 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 A
3799547 ACTTGTTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3799912 original size:15 final size:16
Alignment explanation
Indices: 3799886--3799918 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3799876 ATAGTTTATT
*
3799886 TTATTATTTATTGATA
1 TTATTATTTATTAATA
3799902 TTATT-TTTATTAATA
1 TTATTATTTATTAATA
3799917 TT
1 TT
3799919 TATATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TTATTATTTATTAATA
Found at i:3799918 original size:21 final size:21
Alignment explanation
Indices: 3799884--3799940 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
3799874 TGATAGTTTA
*
3799884 TTTTATTATTTATTGATATTAT
1 TTTTATTATATATTGATA-TAT
*
3799906 TTTTATTA-ATATTTATATAT
1 TTTTATTATATATTGATATAT
*
3799926 TTTTATAATTATATT
1 TTTTATTA-TATATT
3799941 TTAAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 10 0.33
21 7 0.23
22 13 0.43
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTATTATATATTGATATAT
Found at i:3805640 original size:4 final size:4
Alignment explanation
Indices: 3805631--3805655 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3805621 CTCTTTAGTC
3805631 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
3805656 GTTTTAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:3808411 original size:17 final size:17
Alignment explanation
Indices: 3808389--3808422 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3808379 TTTAAACATC
*
3808389 ATTTTATTTATAGTATA
1 ATTTTATTTATAATATA
3808406 ATTTTATTTATAATATA
1 ATTTTATTTATAATATA
3808423 TTATATGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
ATTTTATTTATAATATA
Found at i:3808535 original size:12 final size:12
Alignment explanation
Indices: 3808513--3808568 Score: 62
Period size: 11 Copynumber: 4.7 Consensus size: 12
3808503 TTTGGAAAAC
3808513 TTTTA-TTATAA
1 TTTTATTTATAA
3808524 TTTTATTTATAA
1 TTTTATTTATAA
*
3808536 -TATATTTATATA
1 TTTTATTTATA-A
3808548 TTTATATTTATAA
1 TTT-TATTTATAA
*
3808561 TTATATTT
1 TTTTATTT
3808569 TTTGTTTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
11 14 0.37
12 12 0.32
13 4 0.11
14 8 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTTATTTATAA
Found at i:3808579 original size:25 final size:25
Alignment explanation
Indices: 3808518--3808568 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
3808508 AAAACTTTTA
3808518 TTATA-ATTT-TATTTATAATATAT
1 TTATATATTTATATTTATAATATAT
3808541 TTATATATTTATATTTATAATTATAT
1 TTATATATTTATATTTATAA-TATAT
3808567 TT
1 TT
3808569 TTTGTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 5 0.20
24 4 0.16
25 9 0.36
26 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TTATATATTTATATTTATAATATAT
Found at i:3808583 original size:20 final size:21
Alignment explanation
Indices: 3808527--3808595 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 21
3808517 ATTATAATTT
*
3808527 TATTTATA-ATATAT-TTATA
1 TATTTATATTTATATATTATA
3808546 TATTTATATTTATA-ATTATA
1 TATTTATATTTATATATTATA
* * *
3808566 T-TTTTTGTTTATATATTATT
1 TATTTATATTTATATATTATA
3808586 TATTT-TATTT
1 TATTTATATTT
3808596 GTACTATAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
19 18 0.44
20 20 0.49
21 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (21 bp):
TATTTATATTTATATATTATA
Found at i:3808596 original size:24 final size:24
Alignment explanation
Indices: 3808527--3808597 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
3808517 ATTATAATTT
* * *
3808527 TATTTATAATATATTTATATATTTA
1 TATTTATATTATATTT-TTTGTTTA
3808552 TATTTATAATTATATTTTTTGTTTA
1 TATTTAT-ATTATATTTTTTGTTTA
3808577 TATATTAT-TTAT-TTTATTTGT
1 TAT-TTATATTATATTT-TTTGT
3808598 ACTATAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 3 0.08
24 9 0.22
25 16 0.40
26 12 0.30
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (24 bp):
TATTTATATTATATTTTTTGTTTA
Found at i:3809194 original size:16 final size:16
Alignment explanation
Indices: 3809146--3809202 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
3809136 TCTGATTTTT
* *
3809146 TTATTTGAATTTTATA
1 TTATTTTAATTTTAAA
* * *
3809162 TTATTTTGAGTTCAAA
1 TTATTTTAATTTTAAA
3809178 TTATTTTAATTTTAAA
1 TTATTTTAATTTTAAA
*
3809194 TCATTTTAA
1 TTATTTTAA
3809203 ATTCATATAA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (16 bp):
TTATTTTAATTTTAAA
Found at i:3809300 original size:15 final size:15
Alignment explanation
Indices: 3809266--3809346 Score: 53
Period size: 16 Copynumber: 5.1 Consensus size: 15
3809256 TTAATCAAAT
3809266 TTAATATTT-AATTCAA
1 TTAAT-TTTAAATT-AA
*
3809282 TTAATTTTAAATTAT
1 TTAATTTTAAATTAA
3809297 TTAAATTTATCAAATATAA
1 TT-AATTT-T-AAAT-TAA
3809316 TT-ATTTTAAATTTAAA
1 TTAATTTTAAA-TT-AA
3809332 TT-ATTTTAAA-TAA
1 TTAATTTTAAATTAA
3809345 TT
1 TT
3809347 TTTTTAAGCA
Statistics
Matches: 56, Mismatches: 2, Indels: 17
0.75 0.03 0.23
Matches are distributed among these distances:
13 4 0.07
14 1 0.02
15 10 0.18
16 28 0.50
17 5 0.09
18 4 0.07
19 4 0.07
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATTTTAAATTAA
Found at i:3809694 original size:54 final size:55
Alignment explanation
Indices: 3809593--3809705 Score: 156
Period size: 54 Copynumber: 2.1 Consensus size: 55
3809583 AAAATTAAAA
* *
3809593 AAAAAAAATTGAAATGATCGACAAATGAATAACCTTGCAAGCCAAGAAAACTTCC
1 AAAAAAAATTAAAATGATCGACAAATGAATAACCTAGCAAGCCAAGAAAACTTCC
* ** * *
3809648 AAAAAAAATTAAAATGGTCGACACGTGGAT-ACCTAGCAAGCTAAGAAAACTTCC
1 AAAAAAAATTAAAATGATCGACAAATGAATAACCTAGCAAGCCAAGAAAACTTCC
3809702 AAAA
1 AAAA
3809706 TTTATATATA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
54 26 0.51
55 25 0.49
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (55 bp):
AAAAAAAATTAAAATGATCGACAAATGAATAACCTAGCAAGCCAAGAAAACTTCC
Found at i:3815944 original size:2 final size:2
Alignment explanation
Indices: 3815937--3815971 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3815927 AATTAGAGTC
3815937 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 T
3815972 CAGGCAAACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3819419 original size:2 final size:2
Alignment explanation
Indices: 3819412--3819441 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3819402 TGAAAGAGCA
*
3819412 AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3819442 CAATCTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3821253 original size:15 final size:15
Alignment explanation
Indices: 3821230--3821297 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 15
3821220 AATTAATACT
*
3821230 AAATGATATTAATTA
1 AAATAATATTAATTA
*
3821245 AAATAATATT--TTT
1 AAATAATATTAATTA
* *
3821258 AAATTA-ATTAATATT
1 AAATAATATTAAT-TA
*
3821273 TAATAATATTAATTA
1 AAATAATATTAATTA
3821288 AAATAATATT
1 AAATAATATT
3821298 TTAAATAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
12 3 0.07
13 7 0.17
14 1 0.02
15 25 0.60
16 6 0.14
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (15 bp):
AAATAATATTAATTA
Found at i:3821264 original size:43 final size:42
Alignment explanation
Indices: 3821217--3821303 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 42
3821207 ATATAAAAAT
*
3821217 ATTAATTAATACTAAATGATATTAATTAAAATAATATTTTTAA
1 ATTAATTAATACTAAATAATATTAATTAAAATAATA-TTTTAA
* *
3821260 ATTAATTAATATTTAATAATATTAATTAAAATAATATTTTAA
1 ATTAATTAATACTAAATAATATTAATTAAAATAATATTTTAA
3821302 AT
1 AT
3821304 AAAATACAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 8 0.20
43 33 0.80
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (42 bp):
ATTAATTAATACTAAATAATATTAATTAAAATAATATTTTAA
Found at i:3821285 original size:20 final size:21
Alignment explanation
Indices: 3821194--3821288 Score: 72
Period size: 20 Copynumber: 4.6 Consensus size: 21
3821184 TTACACCTTA
* *
3821194 AATATTAATT-ATAATATAAA
1 AATATTAATTAATAATTTAAT
* *
3821214 AATATTAATTAAT-ACTAAAT
1 AATATTAATTAATAATTTAAT
* **
3821234 GATATTAATTAAAATAATATTTTT
1 AATATTAATT--AATAAT-TTAAT
3821258 AA-ATTAATTAAT-ATTTAAT
1 AATATTAATTAATAATTTAAT
3821277 AATATTAATTAA
1 AATATTAATTAA
3821289 AATAATATTT
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
19 5 0.09
20 33 0.58
21 5 0.09
22 3 0.05
23 8 0.14
24 3 0.05
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (21 bp):
AATATTAATTAATAATTTAAT
Found at i:3821639 original size:29 final size:29
Alignment explanation
Indices: 3821607--3821748 Score: 74
Period size: 27 Copynumber: 5.2 Consensus size: 29
3821597 TTATGTGGTG
3821607 TTTATATATTTTTATATATTATAATTATA
1 TTTATATATTTTTATATATTATAATTATA
* * * *
3821636 TTTA-A-ATTATTATATATAATAA-AATT
1 TTTATATATTTTTATATATTATAATTATA
* *
3821662 TTTA-ATATATTAATA-ATT-TATATTATA
1 TTTATATATTTTTATATATTATA-ATTATA
* * * *
3821689 TTT-T-TAATATT-TATATTATATTTTTA
1 TTTATATATTTTTATATATTATAATTATA
* *
3821715 TATATCATA-TTTTATAT-TT-TAATTATT
1 TTTAT-ATATTTTTATATATTATAATTATA
3821742 TTTATAT
1 TTTATAT
3821749 TACAACCTTT
Statistics
Matches: 81, Mismatches: 22, Indels: 23
0.64 0.17 0.18
Matches are distributed among these distances:
25 4 0.05
26 24 0.30
27 38 0.47
28 6 0.07
29 9 0.11
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTATATATTTTTATATATTATAATTATA
Found at i:3821679 original size:18 final size:17
Alignment explanation
Indices: 3821625--3821690 Score: 53
Period size: 18 Copynumber: 3.7 Consensus size: 17
3821615 TTTTTATATA
*
3821625 TTATAATTATATTTAAA-
1 TTATAA-TATATTAAAAT
*
3821642 TTATTATATATAATAAAAT
1 TTA-TA-ATATATTAAAAT
*
3821661 TTTTAATATATTAATAAT
1 TTATAATATATTAA-AAT
*
3821679 TTATATTATATT
1 TTATAATATATT
3821691 TTTAATATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
17 11 0.28
18 25 0.64
19 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATAATATATTAAAAT
Found at i:3821689 original size:20 final size:19
Alignment explanation
Indices: 3821666--3821732 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
3821656 AAAATTTTTA
3821666 ATATATTAATAATTTATATT
1 ATATATTAAT-ATTTATATT
*
3821686 ATATTTTTAATATTTATATT
1 ATA-TATTAATATTTATATT
* * *
3821706 ATATTTTTATATATCATATT
1 ATATATTAATAT-TTATATT
*
3821726 TTATATT
1 ATATATT
3821733 TTAATTATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 8 0.20
20 26 0.65
21 6 0.15
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATATTAATATTTATATT
Found at i:3821715 original size:33 final size:32
Alignment explanation
Indices: 3821678--3821750 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
3821668 ATATTAATAA
*
3821678 TTTATATTAT-AT-TTTTAATATTTATATTATATT
1 TTTATATTATCATATTTT-ATATTT-TAAT-TATT
3821711 TTTATA-TATCATATTTTATATTTTAATTATT
1 TTTATATTATCATATTTTATATTTTAATTATT
3821742 TTTATATTA
1 TTTATATTA
3821751 CAACCTTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
31 10 0.28
32 8 0.22
33 14 0.39
34 4 0.11
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (32 bp):
TTTATATTATCATATTTTATATTTTAATTATT
Found at i:3821732 original size:22 final size:20
Alignment explanation
Indices: 3821680--3821734 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
3821670 ATTAATAATT
*
3821680 TATATTATATTTTTAATATT
1 TATATTATATTTTTAATATA
3821700 TATATTATATTTTTATATATCA
1 TATATTATATTTTTA-ATAT-A
*
3821722 TATTTTATATTTT
1 TATATTATATTTT
3821735 AATTATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 15 0.48
21 4 0.13
22 12 0.39
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TATATTATATTTTTAATATA
Found at i:3822486 original size:22 final size:22
Alignment explanation
Indices: 3822458--3822503 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3822448 TTCTTCTTCT
*
3822458 TTTGTTGATGATAATTGTATGA
1 TTTGTTGATGATAAATGTATGA
*
3822480 TTTGTTGATGATAAATGTCTGA
1 TTTGTTGATGATAAATGTATGA
3822502 TT
1 TT
3822504 CGTTCTCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.02, G:0.22, T:0.50
Consensus pattern (22 bp):
TTTGTTGATGATAAATGTATGA
Found at i:3825713 original size:16 final size:16
Alignment explanation
Indices: 3825691--3825782 Score: 78
Period size: 16 Copynumber: 5.8 Consensus size: 16
3825681 AGTCATTTTT
3825691 GAATTCGGATCATTTC
1 GAATTCGGATCATTTC
* * * *
3825707 AAATTCGAATTATTTT
1 GAATTCGGATCATTTC
* *
3825723 GGATTCAGATCATTTC
1 GAATTCGGATCATTTC
* *
3825739 GAGTTCGGGTCATTT-
1 GAATTCGGATCATTTC
* *
3825754 TAAGTTCGGGTCATTTC
1 GAA-TTCGGATCATTTC
3825771 GAATTCGGATCA
1 GAATTCGGATCA
3825783 ATTAAGTTTA
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
15 1 0.02
16 53 0.95
17 2 0.04
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (16 bp):
GAATTCGGATCATTTC
Found at i:3825754 original size:32 final size:32
Alignment explanation
Indices: 3825680--3825777 Score: 81
Period size: 32 Copynumber: 3.0 Consensus size: 32
3825670 TAAAATTTTT
*
3825680 GAGTCATTTTTGAATTCGGATCATTTCAAATTC
1 GAGTCA-TTTTGAATTCAGATCATTTCAAATTC
* * * * *
3825713 GAATTATTTTGGATTCAGATCATTTCGAGTTC
1 GAGTCATTTTGAATTCAGATCATTTCAAATTC
* * * *
3825745 GGGTCATTTT-AAGTTCGGGTCATTTCGAATTC
1 GAGTCATTTTGAA-TTCAGATCATTTCAAATTC
3825777 G
1 G
3825778 GATCAATTAA
Statistics
Matches: 51, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
31 1 0.02
32 46 0.90
33 4 0.08
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.42
Consensus pattern (32 bp):
GAGTCATTTTGAATTCAGATCATTTCAAATTC
Found at i:3826325 original size:16 final size:16
Alignment explanation
Indices: 3826304--3826334 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3826294 AATAACAATT
*
3826304 TAAAAATTTAAAATAA
1 TAAAAATTAAAAATAA
3826320 TAAAAATTAAAAATA
1 TAAAAATTAAAAATA
3826335 GTTATAATAG
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAAATTAAAAATAA
Found at i:3826549 original size:19 final size:20
Alignment explanation
Indices: 3826508--3826561 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
3826498 ATAACTTATA
* **
3826508 AATATTATTTTTATTAACTT
1 AATATTATTTTTAATAAAAT
3826528 AATATT-TTTTTAATAAAAT
1 AATATTATTTTTAATAAAAT
*
3826547 AATACTTAATTTTAA
1 AATA-TTATTTTTAA
3826562 GTTCGGGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 14 0.50
20 8 0.29
21 6 0.21
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATTATTTTTAATAAAAT
Found at i:3826621 original size:16 final size:16
Alignment explanation
Indices: 3826592--3826679 Score: 56
Period size: 16 Copynumber: 5.5 Consensus size: 16
3826582 ATTGTCAAGG
* *
3826592 TCATTTTGGGTTCGGA
1 TCATTTCGGATTCGGA
3826608 TCATTTCGGATTC-GA
1 TCATTTCGGATTCGGA
* *
3826623 GTCATTTCGAATTCAGGC
1 -TCATTTCGGATTC-GGA
** *
3826641 T-ATTTTAGATTCTGA
1 TCATTTCGGATTCGGA
3826656 TCATTTC-GAGTTCGGA
1 TCATTTCGGA-TTCGGA
*
3826672 TTATTTCG
1 TCATTTCG
3826680 AGTTTCGAGT
Statistics
Matches: 54, Mismatches: 12, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
15 6 0.11
16 46 0.85
17 1 0.02
18 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (16 bp):
TCATTTCGGATTCGGA
Found at i:3827926 original size:26 final size:30
Alignment explanation
Indices: 3827890--3827957 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 30
3827880 TTATAATTAT
* *
3827890 ATTTTAAAATATTATATATT-TAT-ATA-AA
1 ATTTTAATATAATATA-ATTATATCATATAA
3827918 ATTTTAATATAATATAATTAATATCATATAA
1 ATTTTAATATAATATAATT-ATATCATATAA
3827949 ATTTTAATA
1 ATTTTAATA
3827958 AATTTTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 3 0.09
28 14 0.41
29 3 0.09
30 3 0.09
31 11 0.32
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTTTAATATAATATAATTATATCATATAA
Found at i:3827932 original size:31 final size:30
Alignment explanation
Indices: 3827872--3827985 Score: 89
Period size: 31 Copynumber: 3.9 Consensus size: 30
3827862 ATAATTTATT
*
3827872 TATT-TATATTATA-ATTATATTTT-A-AAA
1 TATTATATATTATATA-TAAATTTTAATAAA
3827899 TATTATATATT-TATATAAAATTTTAATATAA
1 TATTATATATTATATAT-AAATTTTAATA-AA
* *
3827930 TATAAT-TAATATCATATAAATTTTAATAAA
1 TATTATATATTAT-ATATAAATTTTAATAAA
* * *
3827960 T-TTTTATATTATATTTATATTTTAAT
1 TATTATATATTATATATAAATTTTAAT
3827986 TATTTTTTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
27 7 0.10
28 13 0.19
29 15 0.21
30 12 0.17
31 19 0.27
32 4 0.06
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (30 bp):
TATTATATATTATATATAAATTTTAATAAA
Found at i:3827982 original size:29 final size:29
Alignment explanation
Indices: 3827949--3828009 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
3827939 TATCATATAA
* *
3827949 ATTTTAATAAATTTTTATATTATATTTAT
1 ATTTTAATAAATTTTTATATCATATTGAT
* *
3827978 ATTTTAATTATTTTTTATATCATATTGAT
1 ATTTTAATAAATTTTTATATCATATTGAT
3828007 ATT
1 ATT
3828010 ATCATATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (29 bp):
ATTTTAATAAATTTTTATATCATATTGAT
Found at i:3828122 original size:16 final size:17
Alignment explanation
Indices: 3828101--3828133 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3828091 AACTAAGACA
3828101 AACTTTAA-TCACTACT
1 AACTTTAATTCACTACT
3828117 AACTTTAATTCACTACT
1 AACTTTAATTCACTACT
3828134 GCCACTACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.39
Consensus pattern (17 bp):
AACTTTAATTCACTACT
Found at i:3829946 original size:17 final size:18
Alignment explanation
Indices: 3829900--3829948 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3829890 GTATTTTAAT
* *
3829900 TTTATATTAAATAAATTT
1 TTTATATTATATAAATTG
*
3829918 TTTTTAATTATATAAA-TG
1 TTTAT-ATTATATAAATTG
3829936 TTTATATTATATA
1 TTTATATTATATA
3829949 TTTTATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 8 0.31
18 9 0.35
19 9 0.35
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTATATTATATAAATTG
Found at i:3830438 original size:32 final size:31
Alignment explanation
Indices: 3830365--3830457 Score: 88
Period size: 32 Copynumber: 3.0 Consensus size: 31
3830355 TTTGGGTTTA
*
3830365 TAATAATA-TTTAA-AATATTATATATTTAT-T
1 TAATTATATTTTAATAATATTAT-T-TTTATAT
*
3830395 TATTTATATTTTAATAATATTATTTTTATAT
1 TAATTATATTTTAATAATATTATTTTTATAT
3830426 TAAATTATATTTTAATTAAT-TT-TTTATTATAT
1 T-AATTATATTTTAA-TAATATTATTT-TTATAT
3830458 ATTTGTACAA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
30 11 0.20
31 11 0.20
32 28 0.52
33 4 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
TAATTATATTTTAATAATATTATTTTTATAT
Found at i:3830443 original size:16 final size:17
Alignment explanation
Indices: 3830378--3830445 Score: 74
Period size: 16 Copynumber: 4.2 Consensus size: 17
3830368 TAATATTTAA
3830378 AATATTATATATTT-ATT
1 AATATTATAT-TTTAATT
*
3830395 TAT-TTATATTTTAA-T
1 AATATTATATTTTAATT
3830410 AATATTAT-TTTTATATT
1 AATATTATATTTTA-ATT
3830427 AA-ATTATATTTTAATT
1 AATATTATATTTTAATT
3830443 AAT
1 AAT
3830446 TTTTTATTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
15 11 0.26
16 22 0.51
17 10 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AATATTATATTTTAATT
Found at i:3830943 original size:13 final size:13
Alignment explanation
Indices: 3830925--3830950 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3830915 TTTTTTAAAA
3830925 AATATTTATTTTT
1 AATATTTATTTTT
3830938 AATATTTATTTTT
1 AATATTTATTTTT
3830951 TTATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
AATATTTATTTTT
Found at i:3830956 original size:14 final size:14
Alignment explanation
Indices: 3830925--3830962 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3830915 TTTTTTAAAA
3830925 AATATTTA-TTTTT
1 AATATTTATTTTTT
3830938 AATATTTATTTTTT
1 AATATTTATTTTTT
* *
3830952 TATATATATTT
1 AATATTTATTT
3830963 AAATATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
AATATTTATTTTTT
Found at i:3831059 original size:18 final size:16
Alignment explanation
Indices: 3831014--3831061 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
3831004 TTAAAAAATT
*
3831014 AAATATATCATATTAA
1 AAATATATTATATTAA
*
3831030 ATATATACTTATATTAAA
1 AAATATA-TTATATT-AA
3831048 AAATATATTTATAT
1 AAATATA-TTATAT
3831062 CAATATTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 6 0.23
17 6 0.23
18 14 0.54
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATATTATATTAA
Found at i:3831284 original size:15 final size:15
Alignment explanation
Indices: 3831264--3831302 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
3831254 TAAAAGCACC
3831264 AAAAAGCAAAAAAAA-
1 AAAAAG-AAAAAAAAG
3831279 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
3831294 AAAAA-AAAA
1 AAAAAGAAAA
3831303 GAAGGAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.90, C:0.03, G:0.08, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:3831302 original size:10 final size:10
Alignment explanation
Indices: 3831271--3831305 Score: 56
Period size: 9 Copynumber: 3.7 Consensus size: 10
3831261 ACCAAAAAGC
3831271 AAAA-AAAAA
1 AAAAGAAAAA
3831280 AAAAG-AAAA
1 AAAAGAAAAA
3831289 AAAAGAAAAA
1 AAAAGAAAAA
3831299 AAAAGAA
1 AAAAGAA
3831306 GGAATGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 13 0.54
10 11 0.46
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:3832805 original size:4 final size:4
Alignment explanation
Indices: 3832796--3832845 Score: 75
Period size: 4 Copynumber: 12.8 Consensus size: 4
3832786 ACTTTATTAT
* *
3832796 TGTA TGTA TGTA TGTA TGTA TGTA TG-A TGTA TTTA TGTA TTTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
3832843 TGT
1 TGT
3832846 GATTTTCTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 3 0.07
4 38 0.93
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (4 bp):
TGTA
Found at i:3832827 original size:23 final size:23
Alignment explanation
Indices: 3832799--3832844 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3832789 TTATTATTGT
3832799 ATGTATGTATGTATGTATGTATG
1 ATGTATGTATGTATGTATGTATG
* *
3832822 ATGTATTTATGTATTTATGTATG
1 ATGTATGTATGTATGTATGTATG
3832845 TGATTTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (23 bp):
ATGTATGTATGTATGTATGTATG
Found at i:3836196 original size:20 final size:18
Alignment explanation
Indices: 3836164--3836201 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
3836154 ATATATATAT
3836164 ATATGAATATGAATAATA
1 ATATGAATATGAATAATA
3836182 ATATGAATAATTGAATAATA
1 ATATGAAT-A-TGAATAATA
3836202 TGTATATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 1 0.06
20 9 0.50
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (18 bp):
ATATGAATATGAATAATA
Found at i:3836625 original size:18 final size:18
Alignment explanation
Indices: 3836602--3836638 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3836592 TTTTAAAGTT
3836602 ATTTAAAAATATTTTTAA
1 ATTTAAAAATATTTTTAA
*
3836620 ATTTAAAATTATTTTTAA
1 ATTTAAAAATATTTTTAA
3836638 A
1 A
3836639 ATATAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTAAAAATATTTTTAA
Found at i:3836649 original size:19 final size:18
Alignment explanation
Indices: 3836605--3836649 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3836595 TAAAGTTATT
* *
3836605 TAAAAATATTTTTAAATT
1 TAAAATTATTTTTAAATA
3836623 TAAAATTATTTTTAAAATA
1 TAAAATTATTTTT-AAATA
*
3836642 TAACATTA
1 TAAAATTA
3836650 AATAAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAAATTATTTTTAAATA
Found at i:3836661 original size:16 final size:17
Alignment explanation
Indices: 3836637--3836669 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3836627 ATTATTTTTA
3836637 AAATATAACA-TTAAAT
1 AAATATAACATTTAAAT
*
3836653 AAATTTAACATTTAAAT
1 AAATATAACATTTAAAT
3836670 TTTACGGTTG
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:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATAACATTTAAAT
Found at i:3839084 original size:2 final size:2
Alignment explanation
Indices: 3839079--3839110 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3839069 AATTTTTTAG
3839079 AT AT AT 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
3839111 CCAATAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3842903 original size:52 final size:52
Alignment explanation
Indices: 3842841--3842947 Score: 205
Period size: 52 Copynumber: 2.1 Consensus size: 52
3842831 GTCAATAAAG
*
3842841 AAGACAACACTCTTATCAATTTCCACAATGAATTTTATTCCTAATAAACTGC
1 AAGACAACACTATTATCAATTTCCACAATGAATTTTATTCCTAATAAACTGC
3842893 AAGACAACACTATTATCAATTTCCACAATGAATTTTATTCCTAATAAACTGC
1 AAGACAACACTATTATCAATTTCCACAATGAATTTTATTCCTAATAAACTGC
3842945 AAG
1 AAG
3842948 CGATGCTGGC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.32
Consensus pattern (52 bp):
AAGACAACACTATTATCAATTTCCACAATGAATTTTATTCCTAATAAACTGC
Found at i:3844609 original size:7 final size:7
Alignment explanation
Indices: 3844597--3844621 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3844587 AAATATAAAT
3844597 TTATTTA
1 TTATTTA
3844604 TTATTTA
1 TTATTTA
3844611 TTATTTA
1 TTATTTA
3844618 TTAT
1 TTAT
3844622 AAAAACAATA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTATTTA
Found at i:3844950 original size:26 final size:25
Alignment explanation
Indices: 3844909--3844967 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
3844899 AATTTATTCT
3844909 TTAAATTTTTAAAAATTTTAAAAAA
1 TTAAATTTTTAAAAATTTTAAAAAA
* * *
3844934 TTAAATATTTTATAAATTTTTAAATA
1 TTAAAT-TTTTAAAAATTTTAAAAAA
3844960 TTAAATTT
1 TTAAATTT
3844968 ATTTTAATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 8 0.27
26 22 0.73
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTAAATTTTTAAAAATTTTAAAAAA
Found at i:3844971 original size:19 final size:19
Alignment explanation
Indices: 3844949--3844989 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
3844939 TATTTTATAA
*
3844949 ATTTTTAA-ATATTAAATT
1 ATTTTTAATAGATTAAATT
3844967 -TATTTTAATAGATTAAATT
1 AT-TTTTAATAGATTAAATT
3844986 ATTT
1 ATTT
3844990 GATGTAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 5
0.76 0.04 0.20
Matches are distributed among these distances:
17 1 0.05
18 6 0.32
19 11 0.58
20 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTTTAATAGATTAAATT
Found at i:3845798 original size:43 final size:44
Alignment explanation
Indices: 3845717--3845811 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
3845707 TTTTATATAT
*
3845717 AAATTATAATAATAAAATTTAAATATTTGTATTCAAGA-TAAAA
1 AAATTATAATAATAAAATTTAAATATTTATATTCAAGATTAAAA
* *
3845760 AAATTATAAATAATAAAGTTTAAATATTTATGTT-AAGATTAAAA
1 AAATTAT-AATAATAAAATTTAAATATTTATATTCAAGATTAAAA
3845804 ATAATTAT
1 A-AATTAT
3845812 TGAGTTAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
43 11 0.24
44 29 0.63
45 6 0.13
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (44 bp):
AAATTATAATAATAAAATTTAAATATTTATATTCAAGATTAAAA
Found at i:3845837 original size:18 final size:17
Alignment explanation
Indices: 3845796--3845838 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
3845786 TTTATGTTAA
3845796 GATTAAAAATAATTATT
1 GATTAAAAATAATTATT
*
3845813 GAGTTAAAATATAATTTTT
1 GA-TTAAAA-ATAATTATT
*
3845832 TATTAAA
1 GATTAAA
3845839 TATTATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 11 0.50
19 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (17 bp):
GATTAAAAATAATTATT
Found at i:3846035 original size:22 final size:21
Alignment explanation
Indices: 3846010--3846076 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
3846000 TATAATTAAA
3846010 ATAAAAATAATTAAAATATTAT
1 ATAAAAATAA-TAAAATATTAT
*
3846032 ATAAAAGATGATAAAATGTATTAT
1 ATAAAA-ATAATAAAA--TATTAT
3846056 A-ATAAAATAAATAAAATATTA
1 ATA-AAAAT-AATAAAATATTA
3846077 AATATATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
22 16 0.42
23 6 0.16
24 16 0.42
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (21 bp):
ATAAAAATAATAAAATATTAT
Found at i:3846100 original size:20 final size:21
Alignment explanation
Indices: 3846070--3846122 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 21
3846060 AAATAAATAA
3846070 AATATTAAATATATTAAAATTT
1 AATA-TAAATATATTAAAATTT
*
3846092 -ATAT-AA-ATATTATAATTT
1 AATATAAATATATTAAAATTT
3846110 AAATATAAATATA
1 -AATATAAATATA
3846123 AAACATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
18 11 0.42
19 2 0.08
20 5 0.19
21 5 0.19
22 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATATAAATATATTAAAATTT
Found at i:3846103 original size:18 final size:19
Alignment explanation
Indices: 3846080--3846125 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
3846070 AATATTAAAT
3846080 ATATTAAAATTT-ATATAA
1 ATATTAAAATTTAATATAA
*
3846098 ATATTATAATTTAAATATAA
1 ATATTAAAATTT-AATATAA
3846118 ATA-TAAAA
1 ATATTAAAA
3846126 CATAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.46
19 4 0.17
20 9 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATTAAAATTTAATATAA
Found at i:3848959 original size:30 final size:32
Alignment explanation
Indices: 3848919--3848998 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
3848909 TATAAATAAA
3848919 AAAATTTAAATATAATATAAT-GTAATA-ATT
1 AAAATTTAAATATAATATAATAGTAATATATT
* *
3848949 -AAATTTTAA-ATAATATAAATATTAATATATT
1 AAAATTTAAATATAATAT-AATAGTAATATATT
*
3848980 AAAATTTATATA-AATATAA
1 AAAATTTAAATATAATATAA
3848999 AATATTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
28 7 0.17
29 11 0.27
30 5 0.12
31 5 0.12
32 12 0.29
33 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (32 bp):
AAAATTTAAATATAATATAATAGTAATATATT
Found at i:3848960 original size:15 final size:15
Alignment explanation
Indices: 3848942--3848992 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3848932 AATATAATGT
3848942 AATAATTAAATTTTA
1 AATAATTAAATTTTA
*
3848957 AATAATATAAATATT-
1 AATAAT-TAAATTTTA
*
3848972 AATATATTAAAATTTA
1 AATA-ATTAAATTTTA
*
3848988 TATAA
1 AATAA
3848993 ATATAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAATTAAATTTTA
Found at i:3849009 original size:35 final size:33
Alignment explanation
Indices: 3848925--3849033 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 33
3848915 TAAAAAAATT
* * *
3848925 TAAATATAATATAATGTAATAATTAAATTTTAAA
1 TAAATATAAAAT-ATTTAATAATTAAAATTTAAA
*
3848959 T-AATAT-AAATA-TTAATATATTAAAATTTATA
1 TAAATATAAAATATTTAATA-ATTAAAATTTAAA
*
3848990 TAAATATAAAATATTT--TAATTATAA-TTATAA
1 TAAATATAAAATATTTAATAATTAAAATTTA-AA
*
3849021 TATA-ATAAAATAT
1 TAAATATAAAATAT
3849034 GAAAATTATA
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
30 17 0.27
31 23 0.37
32 10 0.16
33 10 0.16
34 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (33 bp):
TAAATATAAAATATTTAATAATTAAAATTTAAA
Found at i:3850958 original size:18 final size:18
Alignment explanation
Indices: 3850935--3850973 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
3850925 TGAATTTGCG
3850935 CTTTGCCAAAAGATTGAT
1 CTTTGCCAAAAGATTGAT
3850953 CTTTGCCAAAAGATTGAT
1 CTTTGCCAAAAGATTGAT
3850971 CTT
1 CTT
3850974 GGTAATAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (18 bp):
CTTTGCCAAAAGATTGAT
Found at i:3854527 original size:18 final size:18
Alignment explanation
Indices: 3854484--3854555 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
3854474 GGATTATATA
*
3854484 TATATATATATTTAAAAAT
1 TATAT-TATAATTAAAAAT
3854503 TATTATTATAATTAAAAAT
1 TA-TATTATAATTAAAAAT
* * *
3854522 TATATTTTTATAAAAAAT
1 TATATTATAATTAAAAAT
*
3854540 TAAATT-TAATATAAAA
1 TATATTATAAT-TAAAA
3854556 TTAAAATAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
17 3 0.07
18 22 0.50
19 16 0.36
20 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TATATTATAATTAAAAAT
Found at i:3854893 original size:13 final size:14
Alignment explanation
Indices: 3854869--3854897 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3854859 TTAAATAACA
3854869 ATAATCAAATTTTT
1 ATAATCAAATTTTT
3854883 ATAAT-AAATTTTT
1 ATAATCAAATTTTT
3854896 AT
1 AT
3854898 TTATTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAATCAAATTTTT
Found at i:3855866 original size:28 final size:27
Alignment explanation
Indices: 3855779--3855868 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 27
3855769 TTTTAATTAA
3855779 ATAAAATTATAATTAAT--AAAATTTAT
1 ATAAAATT-TAATTAATAAAAAATTTAT
* * * *
3855805 TTAAAA-ATATTTAATAAATAAATTTAA
1 ATAAAATTTAATTAATAAA-AAATTTAT
3855832 AGTTAAAATTTAATTATATAAAAAATTTAT
1 A--TAAAATTTAATTA-ATAAAAAATTTAT
3855862 ATAAAAT
1 ATAAAAT
3855869 ATAAGATAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
24 7 0.14
26 6 0.12
27 7 0.14
28 6 0.12
29 5 0.10
30 13 0.27
31 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
ATAAAATTTAATTAATAAAAAATTTAT
Found at i:3856238 original size:23 final size:23
Alignment explanation
Indices: 3856186--3856247 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
3856176 GAAACACGAA
*
3856186 ATGAACACAACATAAAAAATAAT
1 ATGAATACAACATAAAAAATAAT
* *
3856209 -TAAAATACAGCATAAAAAATAAT
1 AT-GAATACAACATAAAAAATAAT
* *
3856232 ATGAATATAATATAAA
1 ATGAATACAACATAAA
3856248 TAAGCAAATG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
22 1 0.03
23 28 0.93
24 1 0.03
ACGTcount: A:0.65, C:0.08, G:0.05, T:0.23
Consensus pattern (23 bp):
ATGAATACAACATAAAAAATAAT
Found at i:3857093 original size:58 final size:59
Alignment explanation
Indices: 3857014--3857126 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
3857004 TAATTTTTTT
* * *
3857014 AATTAAATCATTATAACAAATTATG-AAAAAATGTCACGAATTGAGATATGATACATTA
1 AATTAAATCATTATAAAAAATTATGTAAAAAATGTCACGAATGGAGATACGATACATTA
* * *
3857072 AATTAAATTATTA-AGAAAAATTATGTAAAATATGTCATGAATGGAGATACGATAC
1 AATTAAATCATTATA-AAAAATTATGTAAAAAATGTCACGAATGGAGATACGATAC
3857127 GAATATGATA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 1 0.02
58 21 0.45
59 25 0.53
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (59 bp):
AATTAAATCATTATAAAAAATTATGTAAAAAATGTCACGAATGGAGATACGATACATTA
Found at i:3858159 original size:31 final size:31
Alignment explanation
Indices: 3858117--3858207 Score: 146
Period size: 31 Copynumber: 2.9 Consensus size: 31
3858107 AAACGAATTA
*
3858117 TTTATATATAAAAAATACAAAAATATAATAT
1 TTTACATATAAAAAATACAAAAATATAATAT
*
3858148 TTTACATATAAAAAATAAAAAAATATAATAT
1 TTTACATATAAAAAATACAAAAATATAATAT
*
3858179 TTTACATATAAAAAATAACATAAATATAA
1 TTTACATATAAAAAAT-ACAAAAATATAA
3858208 ATACAAATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
31 45 0.82
32 10 0.18
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (31 bp):
TTTACATATAAAAAATACAAAAATATAATAT
Found at i:3858253 original size:4 final size:4
Alignment explanation
Indices: 3858219--3858282 Score: 50
Period size: 4 Copynumber: 17.2 Consensus size: 4
3858209 TACAAATATT
* * *
3858219 TTTC -TTC TTT- TTT- TTTC TTT- TTTC CTCC TTTC TTTTT TTTC TTT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC
3858263 TTT- TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC T
3858283 CTCCTGCCGA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
3 18 0.37
4 28 0.57
5 3 0.06
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:3858266 original size:27 final size:27
Alignment explanation
Indices: 3858219--3858280 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
3858209 TACAAATATT
3858219 TTTCTTCTTTTTTTTTCTTTTTTCCTCC
1 TTTCTT-TTTTTTTTTCTTTTTTCCTCC
* *
3858247 TTTCTTTTTTTTCTTT-TTTTTTCTTTC
1 TTTCTTTTTTTT-TTTCTTTTTTCCTCC
3858274 TTTCTTT
1 TTTCTTT
3858281 CTCTCCTGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 22 0.71
28 9 0.29
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (27 bp):
TTTCTTTTTTTTTTTCTTTTTTCCTCC
Found at i:3858281 original size:8 final size:8
Alignment explanation
Indices: 3858219--3858282 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 8
3858209 TACAAATATT
3858219 TTTC-TTC
1 TTTCTTTC
3858226 TTT-TTT-
1 TTTCTTTC
3858232 TTTCTTT-
1 TTTCTTTC
* *
3858239 TTTCCTCC
1 TTTCTTTC
*
3858247 TTTCTTTTT
1 TTTC-TTTC
3858256 TTTCTTT-
1 TTTCTTTC
3858263 TTT-TTTC
1 TTTCTTTC
3858270 TTTCTTTC
1 TTTCTTTC
3858278 TTTCT
1 TTTCT
3858283 CTCCTGCCGA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
6 6 0.13
7 19 0.41
8 16 0.35
9 5 0.11
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTCTTTC
Found at i:3859049 original size:17 final size:19
Alignment explanation
Indices: 3859018--3859054 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3859008 ATATTATTTA
*
3859018 TCTTTTCAAATTAAA-ACG
1 TCTTTTCAAACTAAACACG
3859036 TCTTTT-AAACTAAACACG
1 TCTTTTCAAACTAAACACG
3859054 T
1 T
3859055 ACTAATAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (19 bp):
TCTTTTCAAACTAAACACG
Found at i:3866380 original size:2 final size:2
Alignment explanation
Indices: 3866373--3866406 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3866363 TATGGCAGAA
3866373 AT AT AT AT 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 AT
3866407 TCAAACATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3873398 original size:13 final size:13
Alignment explanation
Indices: 3873380--3873408 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3873370 TTCGAATACA
3873380 AATATATAATTAT
1 AATATATAATTAT
3873393 AATATATAATTAT
1 AATATATAATTAT
3873406 AAT
1 AAT
3873409 CCTAATGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATATATAATTAT
Found at i:3877575 original size:2 final size:2
Alignment explanation
Indices: 3877568--3877600 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3877558 GTTCCTGGTG
3877568 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
3877601 GGGATTTATA
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:3886468 original size:26 final size:26
Alignment explanation
Indices: 3886433--3886483 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
3886423 AGGAATATAT
3886433 TTATAAAAATTTAA-TTAAATTAATAA
1 TTATAAAAATTTAAGTTAAA-TAATAA
*
3886459 TTATACAAATTTAAGTTAAATAATA
1 TTATAAAAATTTAAGTTAAATAATA
3886484 TTAAATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
TTATAAAAATTTAAGTTAAATAATAA
Found at i:3886529 original size:17 final size:17
Alignment explanation
Indices: 3886503--3886538 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3886493 TATTATTTAT
* *
3886503 TTTAATATTTTTTATAA
1 TTTAAAATTTTATATAA
3886520 TTTAAAATTTTATATAA
1 TTTAAAATTTTATATAA
3886537 TT
1 TT
3886539 AAATTTGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAAAATTTTATATAA
Found at i:3886542 original size:15 final size:16
Alignment explanation
Indices: 3886503--3886544 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
3886493 TATTATTTAT
*
3886503 TTTAATATTTTTTATAA
1 TTTAA-ATTTTATATAA
3886520 TTTAAAATTTTATATAA
1 TTT-AAATTTTATATAA
3886537 -TTAAATTT
1 TTTAAATTT
3886545 GAAGTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 6 0.26
16 2 0.09
17 13 0.57
18 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAAATTTTATATAA
Found at i:3886706 original size:32 final size:33
Alignment explanation
Indices: 3886652--3886723 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
3886642 TACAAAAATA
* * * *
3886652 ATATAACATAAATATATAAACATGTCAAAATTT
1 ATATAAAAAAAATATATAAACATATAAAAATTT
*
3886685 ATATAAAAAAAAT-TATGAACATATAAAAATTT
1 ATATAAAAAAAATATATAAACATATAAAAATTT
3886717 ATATAAA
1 ATATAAA
3886724 TTTATAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 23 0.68
33 11 0.32
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.32
Consensus pattern (33 bp):
ATATAAAAAAAATATATAAACATATAAAAATTT
Found at i:3887692 original size:20 final size:21
Alignment explanation
Indices: 3887654--3887692 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
3887644 TAAATATGAT
*
3887654 ATAAAAATTAATTAAAACACA
1 ATAAAAATTAAATAAAACACA
*
3887675 ATAAAAA-TAAATATAACA
1 ATAAAAATTAAATAAAACA
3887693 TAAATATAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (21 bp):
ATAAAAATTAAATAAAACACA
Found at i:3887832 original size:16 final size:15
Alignment explanation
Indices: 3887803--3887831 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3887793 ATTTCCTTTC
3887803 TTTTCTTTTTTTTTA
1 TTTTCTTTTTTTTTA
3887818 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
3887832 TTGGCCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTCTTTTTTTTTA
Found at i:3888833 original size:60 final size:60
Alignment explanation
Indices: 3888765--3888881 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
3888755 TCTCATATTT
* * *
3888765 TGGCCCATATTTTGATGTGGTTGCTGTCGTGGATATCGGAACTGGGGCTCTGACCTACTC
1 TGGCCCATATTTTGAGGTGGTTCCTGTCGTGGATATCGGAACTGAGGCTCTGACCTACTC
* *
3888825 TGGCCCATATTTTGAGGTGGTTCCTGTCGTTGATATGGGAACTGAGGCTCTGACCTA
1 TGGCCCATATTTTGAGGTGGTTCCTGTCGTGGATATCGGAACTGAGGCTCTGACCTA
3888882 ACTGAGACTC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.16, C:0.21, G:0.30, T:0.33
Consensus pattern (60 bp):
TGGCCCATATTTTGAGGTGGTTCCTGTCGTGGATATCGGAACTGAGGCTCTGACCTACTC
Found at i:3894833 original size:20 final size:21
Alignment explanation
Indices: 3894810--3894867 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
3894800 TTATTTTTAT
3894810 ATATTTAAAATTAAATAAA-A
1 ATATTTAAAATTAAATAAATA
** *
3894830 ATATTTTTAATTAATTAAATA
1 ATATTTAAAATTAAATAAATA
3894851 ATAATTTAAAA-TAAATA
1 AT-ATTTAAAATTAAATA
3894868 TTAATCCGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 16 0.53
21 8 0.27
22 6 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATTTAAAATTAAATAAATA
Found at i:3894833 original size:22 final size:23
Alignment explanation
Indices: 3894808--3894867 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 23
3894798 TATTATTTTT
3894808 ATATATTTAAAATTAAATAAA-A
1 ATATATTTAAAATTAAATAAATA
* *
3894830 ATAT-TTT-TAATTAATTAAATA
1 ATATATTTAAAATTAAATAAATA
3894851 ATA-ATTTAAAA-TAAATA
1 ATATATTTAAAATTAAATA
3894868 TTAATCCGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
20 10 0.32
21 15 0.48
22 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATATATTTAAAATTAAATAAATA
Found at i:3895394 original size:6 final size:6
Alignment explanation
Indices: 3895379--3895408 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3895369 TAGATTTCTT
*
3895379 AAAAAA AAAAAG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
3895409 GTGTTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3895796 original size:17 final size:16
Alignment explanation
Indices: 3895757--3895796 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3895747 TTATTATATA
3895757 ATAAATTTTTTTTAAT
1 ATAAATTTTTTTTAAT
* *
3895773 ATTAATTTTTTTTATTT
1 ATAAATTTTTTTTA-AT
3895790 ATAAATT
1 ATAAATT
3895797 CAAATGTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATAAATTTTTTTTAAT
Found at i:3896456 original size:21 final size:21
Alignment explanation
Indices: 3896432--3896471 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3896422 TTTGATATAA
3896432 AAATTATAAATAT-TTAAATTT
1 AAATT-TAAATATATTAAATTT
*
3896453 AAATTTAAATTTATTAAAT
1 AAATTTAAATATATTAAAT
3896472 ATTATTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATTTAAATATATTAAATTT
Found at i:3896663 original size:37 final size:35
Alignment explanation
Indices: 3896622--3896719 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
3896612 ATGATTCTAT
3896622 TTTAATTATTGTTTAAATAATTAA-A-AAATATTTTATA
1 TTTAATTATT-TTTAAATAATTAATATAAA-A-TTTA-A
* *
3896659 TTTAAATTTAATTATAAAT-ATTAATATAAAATTTAA
1 TTT-AA-TTATTTTTAAATAATTAATATAAAATTTAA
3896695 TTTAATT-TTTTTAAATAATT-ATATA
1 TTTAATTATTTTTAAATAATTAATATA
3896720 GATTTATAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
33 12 0.23
34 5 0.10
35 2 0.04
36 4 0.08
37 12 0.23
38 10 0.19
39 7 0.13
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (35 bp):
TTTAATTATTTTTAAATAATTAATATAAAATTTAA
Found at i:3899723 original size:23 final size:23
Alignment explanation
Indices: 3899692--3899741 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3899682 TAATAAATAA
* *
3899692 TAAAAT-AAAATTTTAAATTAATT
1 TAAAATAAAAAATTTAAA-AAATT
*
3899715 TAAACTAAAAAATTTAAAAAATT
1 TAAAATAAAAAATTTAAAAAATT
3899738 TAAA
1 TAAA
3899742 TTATAATCGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAAATAAAAAATTTAAAAAATT
Found at i:3900398 original size:3 final size:3
Alignment explanation
Indices: 3900390--3900416 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3900380 CATTTCATTT
3900390 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
3900417 AATTATCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3903066 original size:18 final size:18
Alignment explanation
Indices: 3903045--3903102 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
3903035 GGAAAGGAAG
3903045 TGATTGATGGTTATCCAT
1 TGATTGATGGTTATCCAT
* ** *** *
3903063 TGATTTATGGAAAGGAAG
1 TGATTGATGGTTATCCAT
3903081 TGATTGATGGTTATCCAT
1 TGATTGATGGTTATCCAT
3903099 TGAT
1 TGAT
3903103 ATGGCATGTA
Statistics
Matches: 26, Mismatches: 14, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.28, C:0.07, G:0.26, T:0.40
Consensus pattern (18 bp):
TGATTGATGGTTATCCAT
Found at i:3903080 original size:36 final size:36
Alignment explanation
Indices: 3903033--3903102 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
3903023 CGTGGATCTC
3903033 ATGGAAAGGAAGTGATTGATGGTTATCCATTGATTT
1 ATGGAAAGGAAGTGATTGATGGTTATCCATTGATTT
3903069 ATGGAAAGGAAGTGATTGATGGTTATCCATTGAT
1 ATGGAAAGGAAGTGATTGATGGTTATCCATTGAT
3903103 ATGGCATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.34
Consensus pattern (36 bp):
ATGGAAAGGAAGTGATTGATGGTTATCCATTGATTT
Found at i:3907603 original size:26 final size:26
Alignment explanation
Indices: 3907567--3907619 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
3907557 CCAGTGGACA
*
3907567 TTGGGTATATGTCTGTTTCAAAAATC
1 TTGGGTATATGTCTGCTTCAAAAATC
3907593 TTGGGTATATGTCTGCTTCAAAAATC
1 TTGGGTATATGTCTGCTTCAAAAATC
3907619 T
1 T
3907620 GTGCTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (26 bp):
TTGGGTATATGTCTGCTTCAAAAATC
Found at i:3913974 original size:1 final size:1
Alignment explanation
Indices: 3913968--3913992 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3913958 TAACAGAGTT
3913968 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
3913993 GAAGCTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:3922240 original size:2 final size:2
Alignment explanation
Indices: 3922235--3922266 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3922225 TGTATGTGTG
3922235 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3922267 TCAAATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3927001 original size:2 final size:2
Alignment explanation
Indices: 3926994--3927018 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3926984 CAAATGCAAA
3926994 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 A
3927019 TATTTACTTA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3935553 original size:2 final size:2
Alignment explanation
Indices: 3935548--3935578 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3935538 TTCCTATAAA
*
3935548 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3935579 AAGAATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3936387 original size:21 final size:19
Alignment explanation
Indices: 3936360--3936410 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
3936350 CCACTGCTTC
3936360 TTTTTTATAAATAAAAATAA
1 TTTTTTATAAA-AAAAATAA
*
3936380 TATTTTTATTCAAAAAAAATTA
1 T-TTTTTA-T-AAAAAAAATAA
3936402 TTTTTTATA
1 TTTTTTATA
3936411 CATCTATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 1 0.04
20 2 0.07
21 12 0.44
22 9 0.33
23 3 0.11
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTTTATAAAAAAAATAA
Found at i:3936672 original size:14 final size:15
Alignment explanation
Indices: 3936634--3936691 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
3936624 ATATATATTT
* *
3936634 ATATTATTTTTATATT
1 ATATTATATTTATA-A
3936650 ATAATTATATTTA-AA
1 AT-ATTATATTTATAA
*
3936665 ATATTATATATATAA
1 ATATTATATTTATAA
3936680 AT-TTATATTTAT
1 ATATTATATTTAT
3936692 TTAATGTATC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 18 0.50
15 6 0.17
16 3 0.08
17 9 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATTATATTTATAA
Found at i:3936683 original size:22 final size:20
Alignment explanation
Indices: 3936645--3936684 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3936635 TATTATTTTT
*
3936645 ATATTATAATTATATTTAAA
1 ATATTATAATTAAATTTAAA
3936665 ATATTATATATATAAATTTA
1 ATATTATA-AT-TAAATTTA
3936685 TATTTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAATTAAATTTAAA
Found at i:3936857 original size:15 final size:15
Alignment explanation
Indices: 3936830--3936884 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
3936820 TTAATAACGT
*
3936830 ATATAAATTTATATA
1 ATATAAATATATATA
* *
3936845 ATATTAATATATAAA
1 ATATAAATATATATA
*
3936860 ATATAAATATTATATTT
1 ATATAAATA-TATA-TA
3936877 ATATAAAT
1 ATATAAAT
3936885 TTAATATGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 20 0.62
16 4 0.12
17 8 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATAAATATATATA
Found at i:3936891 original size:17 final size:16
Alignment explanation
Indices: 3936862--3936930 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
3936852 TATATAAAAT
3936862 ATAAATATT-ATATTTA
1 ATAAAT-TTAATATTTA
3936878 TATAAATTTAATATGTTA
1 -ATAAATTTAATAT-TTA
*
3936896 AT-AAGTTAATA-TTA
1 ATAAATTTAATATTTA
*
3936910 ATAAATTTAAAATTTA
1 ATAAATTTAATATTTA
3936926 A-AAAT
1 ATAAAT
3936931 AAATCATTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 5 0.11
15 11 0.24
16 14 0.31
17 12 0.27
18 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
ATAAATTTAATATTTA
Found at i:3937576 original size:20 final size:21
Alignment explanation
Indices: 3937548--3937590 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
3937538 TTACATAAAT
* * *
3937548 AAATAAATTTATATATAATTA
1 AAATAAATTAACATAAAATTA
3937569 AAAT-AATTAACATAAAATTA
1 AAATAAATTAACATAAAATTA
3937589 AA
1 AA
3937591 TCAAATTCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATAAATTAACATAAAATTA
Found at i:3937672 original size:2 final size:2
Alignment explanation
Indices: 3937665--3937695 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3937655 TCTCGTTAAT
3937665 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 T
3937696 GTATGCAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3940621 original size:26 final size:27
Alignment explanation
Indices: 3940592--3940646 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
3940582 TGAGTGTATT
3940592 AATTTTAAATT-TATATATATATTTAA
1 AATTTTAAATTATATATATATATTTAA
* *
3940618 AATTTTATATTAATATATTTATATTTAA
1 AATTTTAAATT-ATATATATATATTTAA
3940646 A
1 A
3940647 TATCTGATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.40
28 15 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
AATTTTAAATTATATATATATATTTAA
Found at i:3940628 original size:14 final size:15
Alignment explanation
Indices: 3940604--3940646 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
3940594 TTTTAAATTT
*
3940604 ATATATATATTTAAA
1 ATATTTATATTTAAA
*
3940619 AT-TTTATA-TTAAT
1 ATATTTATATTTAAA
3940632 ATATTTATATTTAAA
1 ATATTTATATTTAAA
3940647 TATCTGATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 6 0.26
14 11 0.48
15 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTATATTTAAA
Found at i:3940649 original size:14 final size:14
Alignment explanation
Indices: 3940604--3940649 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
3940594 TTTTAAATTT
*
3940604 ATATATATATTTAA
1 ATATTTATATTTAA
3940618 A-ATTT-TATATTAA
1 ATATTTATAT-TTAA
3940631 TATATTTATATTTAA
1 -ATATTTATATTTAA
3940646 ATAT
1 ATAT
3940650 CTGATGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
12 3 0.11
13 7 0.26
14 6 0.22
15 8 0.30
16 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATATTTATATTTAA
Found at i:3943787 original size:3 final size:3
Alignment explanation
Indices: 3943767--3943816 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
3943757 GTCAAAACAC
* *
3943767 ATT ATT ACT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3943815 AT
1 AT
3943817 CAGGGGAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:3945567 original size:33 final size:33
Alignment explanation
Indices: 3945473--3945554 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
3945463 TTTTATCCTC
* ***
3945473 ATCATCATCAATGTCACTGTAAACATCATCATA
1 ATCATCATCACTGTCACCACAAACATCATCATA
3945506 ATCATCATCACTGTCACCACAAACATCATCATA
1 ATCATCATCACTGTCACCACAAACATCATCATA
3945539 ATCATCATCACTGTCA
1 ATCATCATCACTGTCA
3945555 TCTGCCTCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.38, C:0.29, G:0.05, T:0.28
Consensus pattern (33 bp):
ATCATCATCACTGTCACCACAAACATCATCATA
Found at i:3945632 original size:3 final size:3
Alignment explanation
Indices: 3945626--3945655 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3945616 AAAAATTATA
3945626 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
3945656 CACCTCGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:3949676 original size:23 final size:25
Alignment explanation
Indices: 3949644--3949700 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
3949634 TCATATATAT
* *
3949644 ATATATATATATATT-AAAAATATA
1 ATATAAATATATATTAAAAAATAAA
* *
3949668 ATA-AAATATTTTTTAAAAAATAAA
1 ATATAAATATATATTAAAAAATAAA
3949692 ATATAAATA
1 ATATAAATA
3949701 AAATCTATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 8 0.30
24 14 0.52
25 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATATAAATATATATTAAAAAATAAA
Found at i:3949845 original size:12 final size:12
Alignment explanation
Indices: 3949828--3949866 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3949818 AAATTTTATG
3949828 TATTTATATTTT
1 TATTTATATTTT
*
3949840 TATTTATATTAT
1 TATTTATATTTT
*
3949852 TATTTTTATTATT
1 TATTTATATT-TT
3949865 TA
1 TA
3949867 AAGTATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 20 0.87
13 3 0.13
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTTATATTTT
Found at i:3949852 original size:21 final size:22
Alignment explanation
Indices: 3949820--3949982 Score: 62
Period size: 21 Copynumber: 7.4 Consensus size: 22
3949810 AAAAGAAAAA
3949820 ATTT-TATGTATTTATATTT-TT
1 ATTTATAT-TATTTATATTTATT
*
3949841 ATTTATATTA-TTATTTTTATT
1 ATTTATATTATTTATATTTATT
* *
3949862 ATTTAAAGTATTATATATTTATAT
1 ATTTATATTATT-TATATTTAT-T
*
3949886 AAATTTATA-TATTT-TATGT-TT
1 --ATTTATATTATTTATATTTATT
* *
3949907 -TTTAT-TCGTA-TCATGTTTATT
1 ATTTATAT--TATTTATATTTATT
* *
3949928 -TTTATATTATATTTTAATTATT
1 ATTTATATTAT-TTATATTTATT
3949950 -TTTATATCATATTTATA-TTATTT
1 ATTTATAT--TATTTATATTTA-TT
3949973 ATTGTATATT
1 ATT-TATATT
3949983 TAAAATATTA
Statistics
Matches: 108, Mismatches: 14, Indels: 38
0.68 0.09 0.24
Matches are distributed among these distances:
18 5 0.05
19 1 0.01
20 14 0.13
21 24 0.22
22 23 0.21
23 19 0.18
24 7 0.06
25 9 0.08
26 6 0.06
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (22 bp):
ATTTATATTATTTATATTTATT
Found at i:3949855 original size:18 final size:16
Alignment explanation
Indices: 3949821--3949885 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
3949811 AAAGAAAAAA
*
3949821 TTTTATGTATTTATAT
1 TTTTATTTATTTATAT
3949837 TTTTATTTATATTATTAT
1 TTTTATTTAT-TTA-TAT
* *
3949855 TTTTA-TTATTTAAAG
1 TTTTATTTATTTATAT
* *
3949870 TATTATATATTTATAT
1 TTTTATTTATTTATAT
3949886 AAATTTATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
15 5 0.13
16 19 0.49
17 7 0.18
18 8 0.21
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
TTTTATTTATTTATAT
Done.