Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014745.1 Kokia drynarioides strain JFW-HI SEQ_129784, 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: 532331
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 76 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:5323 original size:30 final size:30
Alignment explanation
Indices: 5272--5345 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
5262 AGAAAATAGA
* *
5272 TTAAGTACCACTTT-TGAAAAAAAAAAAAAT
1 TTAAGTACCA-TTTAAGAAAAATAAAAAAAT
* *
5302 TTAAGTACCGATTTAAGAAAAATAATATAAT
1 TTAAGTACC-ATTTAAGAAAAATAAAAAAAT
*
5333 TTAGGTACCATTT
1 TTAAGTACCATTT
5346 TATTATTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 16 0.43
31 21 0.57
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.32
Consensus pattern (30 bp):
TTAAGTACCATTTAAGAAAAATAAAAAAAT
Found at i:5616 original size:6 final size:6
Alignment explanation
Indices: 5606--5642 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
5596 ATGGATGTCC
*
5606 ATCAAC ATCAAG ATCAAG ATCAAG ATCAAG A-CAAG AT
1 ATCAAG ATCAAG ATCAAG ATCAAG ATCAAG ATCAAG AT
5643 TTGGTATACC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (6 bp):
ATCAAG
Found at i:14405 original size:17 final size:17
Alignment explanation
Indices: 14383--14419 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
14373 TATTAAATTA
14383 ATTTTTTATAA-ATGTTT
1 ATTTTTTA-AATATGTTT
14400 ATTTTTTAAATATGTTT
1 ATTTTTTAAATATGTTT
14417 ATT
1 ATT
14420 ATATTATGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (17 bp):
ATTTTTTAAATATGTTT
Found at i:15283 original size:22 final size:21
Alignment explanation
Indices: 15258--15298 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
15248 GAAATCAAGT
*
15258 ATTTTCGCTTATGTTTTTATGG
1 ATTTTAGCTTA-GTTTTTATGG
*
15280 ATTTTAGTTTAGTTTTTAT
1 ATTTTAGCTTAGTTTTTAT
15299 CTTTCGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.17, C:0.05, G:0.15, T:0.63
Consensus pattern (21 bp):
ATTTTAGCTTAGTTTTTATGG
Found at i:18431 original size:3 final size:3
Alignment explanation
Indices: 18423--18456 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
18413 GCTATTTTTG
18423 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA C
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA C
18457 CCGTCGAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CTA
Found at i:19493 original size:14 final size:13
Alignment explanation
Indices: 19474--19520 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
19464 TATTATTTTA
19474 ATTATTTTTTATCT
1 ATTATTTTTTAT-T
*
19488 ATTATTTATTTGTT
1 ATTATTT-TTTATT
*
19502 ACTATTTTTTA-T
1 ATTATTTTTTATT
19514 ATTATTT
1 ATTATTT
19521 ACATTTATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 7 0.25
13 3 0.11
14 14 0.50
15 4 0.14
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70
Consensus pattern (13 bp):
ATTATTTTTTATT
Found at i:19570 original size:20 final size:19
Alignment explanation
Indices: 19534--19596 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
19524 TTTATGCCTT
19534 ATTTAATTTTATTTATTTA
1 ATTTAATTTTATTTATTTA
* *
19553 ATTTAATGTTTTTTTATTTC
1 ATTTAAT-TTTATTTATTTA
*
19573 A-TT--TTTTATTTAATTA
1 ATTTAATTTTATTTATTTA
*
19589 AATTAATT
1 ATTTAATT
19597 AGATTATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 10 0.29
17 3 0.09
19 11 0.31
20 11 0.31
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTAATTTTATTTATTTA
Found at i:19672 original size:14 final size:14
Alignment explanation
Indices: 19653--19695 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
19643 TTTATTTTCA
19653 TTATTACTATGATT
1 TTATTACTATGATT
**
19667 TTATTACTATTTTTT
1 TTATTACTA-TGATT
*
19682 TTATTACCATGATT
1 TTATTACTATGATT
19696 ATGTTATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.26, C:0.09, G:0.05, T:0.60
Consensus pattern (14 bp):
TTATTACTATGATT
Found at i:19710 original size:29 final size:31
Alignment explanation
Indices: 19643--19713 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 31
19633 TTAATTGATA
* *
19643 TTTATTTTCATTATTACTATGATTTTATTACT
1 TTTATTTT-ATTATTACCATGATTATATTACT
* *
19675 ATT-TTTT-TTATTACCATGATTATGTTA-T
1 TTTATTTTATTATTACCATGATTATATTACT
19703 TTTATTTTATT
1 TTTATTTTATT
19714 GTGTTATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
28 3 0.09
29 21 0.66
30 2 0.06
31 4 0.12
32 2 0.06
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (31 bp):
TTTATTTTATTATTACCATGATTATATTACT
Found at i:30808 original size:49 final size:49
Alignment explanation
Indices: 30742--31444 Score: 433
Period size: 49 Copynumber: 14.3 Consensus size: 49
30732 ATCCTAAAGT
* * * * *
30742 TGAAGAGGGACAAATTAAAGACATAACGGCGAATCTTACACCTTAAAAT
1 TGAAGAGGGACAGATTAAAGTCGTAACGGTGAATCTTACACCTTAAAAC
* * * * * * *
30791 TGAAGAGGGATAGATTAAAGCCGCAATGATAAATCTTACACCCTAAAAC
1 TGAAGAGGGACAGATTAAAGTCGTAACGGTGAATCTTACACCTTAAAAC
* ***
30840 TGAAGAGGGACAGATTAAAGTCGCAAC-AACAAGTCTTACACCTTAAAAC
1 TGAAGAGGGACAGATTAAAGTCGTAACGGTGAA-TCTTACACCTTAAAAC
** * * *
30889 CAAAGAGGGATAGATTAAAG-CTGTAATGGTGAATCTTACACCTCAAAA-
1 TGAAGAGGGACAGATTAAAGTC-GTAACGGTGAATCTTACACCTTAAAAC
* ** * *
30937 T-AAAATAGACATATTAAAG-C-TACAACGGTGAATCTTACATCC-CAAAAC
1 TGAAGAGGGACAGATTAAAGTCGT--AACGGTGAATCTTACA-CCTTAAAAC
** * * ** *
30985 CAAAGAGGGACAGATTAAAG-CTGCAATGGTGAATCTTACACCCCAAAAAT
1 TGAAGAGGGACAGATTAAAGTC-GTAACGGTGAATCTTACA-CCTTAAAAC
** * **
31035 TGAAGAGGGACAGATTAAAGTCGTAACGAAGAATCTTACATCGCAAAAC
1 TGAAGAGGGACAGATTAAAGTCGTAACGGTGAATCTTACACCTTAAAAC
* * ** **
31084 TGAAGAGTGACAGATTAAAGTCGCAACAATGAATCTTACACCCAAAAAC
1 TGAAGAGGGACAGATTAAAGTCGTAACGGTGAATCTTACACCTTAAAAC
* * * * * *
31133 TAAAAAGGGATAGATTAAAGTCATAA-TGTCAAATCTTACACCTTAAAA-
1 TGAAGAGGGACAGATTAAAGTCGTAACGGT-GAATCTTACACCTTAAAAC
* * * * * * *
31181 TCGAAGAGAGATAGATTAAAGTCGTAACAGTGTATCTTATACCGTAAAAA
1 T-GAAGAGGGACAGATTAAAGTCGTAACGGTGAATCTTACACCTTAAAAC
* **
31231 TGAAGAGGGACAGATTAAAG-CTGCAACGACGAATCTTACATCC-TAAAA-
1 TGAAGAGGGACAGATTAAAGTC-GTAACGGTGAATCTTACA-CCTTAAAAC
* * ** ** *
31279 TCGAAGAAGGACAGATTATAGTCACAACAATGAATCTTACACCCCTAAAAC
1 T-GAAGAGGGACAGATTAAAGTCGTAACGGTGAATCTTACA-CCTTAAAAC
** * * * *
31330 TGAAGAGAAACAGATTAAAGTTGTAACGGCGAATCTTACACCCTTATACC
1 TGAAGAGGGACAGATTAAAGTCGTAACGGTGAATCTTACA-CCTTAAAAC
* * * ** * ** *
31380 CGAAGAGAGACAAATTAAAGTCACAAAGGCAAATCGTACACCTTAAAAC
1 TGAAGAGGGACAGATTAAAGTCGTAACGGTGAATCTTACACCTTAAAAC
* *
31429 TGTAGAGGGATAGATT
1 TGAAGAGGGACAGATT
31445 GAAGCTGCAA
Statistics
Matches: 509, Mismatches: 123, Indels: 44
0.75 0.18 0.07
Matches are distributed among these distances:
45 1 0.00
47 34 0.07
48 10 0.02
49 346 0.68
50 116 0.23
51 2 0.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (49 bp):
TGAAGAGGGACAGATTAAAGTCGTAACGGTGAATCTTACACCTTAAAAC
Found at i:31315 original size:147 final size:146
Alignment explanation
Indices: 30734--31371 Score: 490
Period size: 147 Copynumber: 4.3 Consensus size: 146
30724 CACACCAAAT
* * * * * * * * *
30734 CCTAAAGTTGAAGAGGGACAAATTAAAGACATAACGGCGAATCTTACACCTTAAAATTGAAGAGG
1 CCTAAAATCGAAGAGAGACAGATTAAAGTCGTAAC-GTGAATCTTACACCGTAAAAATGAAGAGG
* * * * * *
30799 GATAGATTAAAGCCGCAATGATAAATCTTACA-CCCTAAAACTGAAGAGGGACAGATTAAAGTCG
65 GACAGATTAAAGCTGCAACGATGAATCTTACATCCC-AAAAC-GAAGAAGGACAGATTAAAGTCA
*
30863 CAACAA-CAAGTCTTACA-C
128 CAACAATGAA-TCTTACACC
* * * * * * * * *
30881 CTTAAAACCAAAGAGGGATAGATTAAAG-CTGTAATGGTGAATCTTACACC-TCAAAAT-AAAAT
1 CCTAAAATCGAAGAGAGACAGATTAAAGTC-GTAA-CGTGAATCTTACACCGTAAAAATGAAGAG
* * * * * *
30943 AGACATATTAAAGCTACAACGGTGAATCTTACATCCCAAAACCAAAGAGGGACAGATTAAAG-CT
64 GGACAGATTAAAGCTGCAACGATGAATCTTACATCCCAAAA-CGAAGAAGGACAGATTAAAGTC-
* ***
31007 GCAATGGTGAATCTTACACC
127 ACAACAATGAATCTTACACC
* * * * * * * *
31027 CCAAAAATTGAAGAGGGACAGATTAAAGTCGTAACGAAGAATCTTACATCGCAAAACTGAAGAGT
1 CCTAAAATCGAAGAGAGACAGATTAAAGTCGTAACG-TGAATCTTACACCGTAAAAATGAAGAGG
* * * *
31092 GACAGATTAAAG-TCGCAACAATGAATCTTACA-CCCAAAAACTAAAAAGGGATAGATTAAAGTC
65 GACAGATTAAAGCT-GCAACGATGAATCTTACATCCC-AAAACGAAGAA-GGACAGATTAAAGTC
* ** *
31155 ATAA-TGTCAAATCTTACA-C
127 ACAACAAT-GAATCTTACACC
* * * *
31174 CTTAAAATCGAAGAGAGATAGATTAAAGTCGTAACAGTGTATCTTATACCGTAAAAATGAAGAGG
1 CCTAAAATCGAAGAGAGACAGATTAAAGTCGTAAC-GTGAATCTTACACCGTAAAAATGAAGAGG
* * *
31239 GACAGATTAAAGCTGCAACGACGAATCTTACATCCTAAAATCGAAGAAGGACAGATTATAGTCAC
65 GACAGATTAAAGCTGCAACGATGAATCTTACATCCCAAAA-CGAAGAAGGACAGATTAAAGTCAC
31304 AACAATGAATCTTACACC
129 AACAATGAATCTTACACC
* * *
31322 CCTAAAA-CTGAAGAGAAACAGATTAAAGTTGTAACGGCGAATCTTACACC
1 CCTAAAATC-GAAGAGAGACAGATTAAAGTCGTAAC-GTGAATCTTACACC
31372 CTTATACCCG
Statistics
Matches: 383, Mismatches: 85, Indels: 45
0.75 0.17 0.09
Matches are distributed among these distances:
144 1 0.00
145 62 0.16
146 50 0.13
147 162 0.42
148 107 0.28
149 1 0.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (146 bp):
CCTAAAATCGAAGAGAGACAGATTAAAGTCGTAACGTGAATCTTACACCGTAAAAATGAAGAGGG
ACAGATTAAAGCTGCAACGATGAATCTTACATCCCAAAACGAAGAAGGACAGATTAAAGTCACAA
CAATGAATCTTACACC
Found at i:31780 original size:3 final size:3
Alignment explanation
Indices: 31774--31819 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
31764 CTACTACTAC
31774 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
31820 TATTTTTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:31828 original size:7 final size:7
Alignment explanation
Indices: 31776--31828 Score: 55
Period size: 6 Copynumber: 8.4 Consensus size: 7
31766 ACTACTACTA
31776 TTATTA-
1 TTATTAT
31782 TTATTA-
1 TTATTAT
31788 TTATTA-
1 TTATTAT
31794 TTATTA-
1 TTATTAT
31800 TTATTA-
1 TTATTAT
31806 TTATTA-
1 TTATTAT
31812 TTATTAT
1 TTATTAT
*
31819 TTATTTT
1 TTATTAT
31826 TTA
1 TTA
31829 AACCCAAAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
6 36 0.80
7 9 0.20
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTATTAT
Found at i:32494 original size:25 final size:25
Alignment explanation
Indices: 32460--32510 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
32450 TGAGGAAAAA
32460 GTTGGAGAGTGCGAAAAGGTAAATG
1 GTTGGAGAGTGCGAAAAGGTAAATG
32485 GTTGGAGAGTGCGAAAAGGTAAATG
1 GTTGGAGAGTGCGAAAAGGTAAATG
32510 G
1 G
32511 GAGGTTTTTG
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:0.35, C:0.04, G:0.41, T:0.20
Consensus pattern (25 bp):
GTTGGAGAGTGCGAAAAGGTAAATG
Found at i:36396 original size:69 final size:69
Alignment explanation
Indices: 36285--36422 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
36275 TCATAAAAAT
36285 TAAGAAAGCGAAGGGATGAATATTCAAAGACATTAAAGAAACTTACAACTAATTTCGAGGAAAAC
1 TAAGAAAGCGAAGGGATGAATATTCAAAGACATTAAAGAAACTTACAACTAATTTCGAGGAAAAC
36350 GAAA
66 GAAA
36354 TAAGAAAGCGAAGGGATGAATATTCAAAGACATTAAAGAAACTTACAACTAATTTCGAGGAAAAC
1 TAAGAAAGCGAAGGGATGAATATTCAAAGACATTAAAGAAACTTACAACTAATTTCGAGGAAAAC
36419 GAAA
66 GAAA
36423 CGCCCCTCTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.51, C:0.12, G:0.19, T:0.19
Consensus pattern (69 bp):
TAAGAAAGCGAAGGGATGAATATTCAAAGACATTAAAGAAACTTACAACTAATTTCGAGGAAAAC
GAAA
Found at i:52236 original size:23 final size:23
Alignment explanation
Indices: 52192--52236 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
52182 TATTTATGCT
*
52192 TTAATTAACTTAATTAACCATTA
1 TTAATTAACTTAATTAAACATTA
52215 TTAATTAAC-TAATTAATACATT
1 TTAATTAACTTAATTAA-ACATT
52237 TTATGTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (23 bp):
TTAATTAACTTAATTAAACATTA
Found at i:53308 original size:21 final size:21
Alignment explanation
Indices: 53282--53324 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
53272 TATGAAAAAG
53282 AAAGTACAAAACAAAAAAGGT
1 AAAGTACAAAACAAAAAAGGT
53303 AAAGTACAAAACAAAAAAGGT
1 AAAGTACAAAACAAAAAAGGT
53324 A
1 A
53325 TACCCGCACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.67, C:0.09, G:0.14, T:0.09
Consensus pattern (21 bp):
AAAGTACAAAACAAAAAAGGT
Found at i:59596 original size:121 final size:121
Alignment explanation
Indices: 59382--59619 Score: 449
Period size: 121 Copynumber: 2.0 Consensus size: 121
59372 CAATCTGGTC
*
59382 AAAGAAGTTAGGAAAGAAAATGGTTATGGTTGGTCAACTAGCTAAATGTACAACTTAACATCCTA
1 AAAGAAGTTAGGAAAGAAAATGGTTATGGTTGGTCAACTAGCTAAATGGACAACTTAACATCCTA
*
59447 TACAAAAGTCTCACTTATCAATAAATTACTAGACATATGAGACAATGTTTCAGGTT
66 TACAAAAATCTCACTTATCAATAAATTACTAGACATATGAGACAATGTTTCAGGTT
59503 AAAGAAGTTAGGAAAGAAAATGGTTATGGTTGGTCAACTAGCTAAATGGACAACTTAACATCCTA
1 AAAGAAGTTAGGAAAGAAAATGGTTATGGTTGGTCAACTAGCTAAATGGACAACTTAACATCCTA
*
59568 TACAAAAATCTCACTTATCAATCAATTACTAGACATATGAGACAATGTTTCA
66 TACAAAAATCTCACTTATCAATAAATTACTAGACATATGAGACAATGTTTCA
59620 CCATAAGGTT
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 114 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (121 bp):
AAAGAAGTTAGGAAAGAAAATGGTTATGGTTGGTCAACTAGCTAAATGGACAACTTAACATCCTA
TACAAAAATCTCACTTATCAATAAATTACTAGACATATGAGACAATGTTTCAGGTT
Found at i:61233 original size:23 final size:23
Alignment explanation
Indices: 61203--61248 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
61193 TTTTTTTTTT
61203 AAGTTCAAACATTAAAATGTAAA
1 AAGTTCAAACATTAAAATGTAAA
61226 AAGTTCAAACATTAAAATGTAAA
1 AAGTTCAAACATTAAAATGTAAA
61249 TAAATATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.26
Consensus pattern (23 bp):
AAGTTCAAACATTAAAATGTAAA
Found at i:64527 original size:19 final size:20
Alignment explanation
Indices: 64500--64538 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
64490 AGGCCTAAAC
*
64500 ATGGACAACTTCACA-ATGG
1 ATGGACAACCTCACACATGG
*
64519 ATGGTCAACCTCACACATGG
1 ATGGACAACCTCACACATGG
64539 GGTTAGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.21
Consensus pattern (20 bp):
ATGGACAACCTCACACATGG
Found at i:68158 original size:30 final size:30
Alignment explanation
Indices: 68122--68181 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
68112 GGCACCACTG
68122 GCTACTTTTTCCTTGATAAAATGACGATCT
1 GCTACTTTTTCCTTGATAAAATGACGATCT
68152 GCTACTTTTTCCTTGATAAAATGACGATCT
1 GCTACTTTTTCCTTGATAAAATGACGATCT
68182 ATTTCGATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (30 bp):
GCTACTTTTTCCTTGATAAAATGACGATCT
Found at i:75701 original size:4 final size:4
Alignment explanation
Indices: 75692--75766 Score: 63
Period size: 4 Copynumber: 19.2 Consensus size: 4
75682 AAATTTAATG
*
75692 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ACAA GAT-A AT-A AT-A AT-A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA -ATAA ATAA ATAA ATAA
75737 ATAA ATGTAA ATTAA ATAA A-AA AT-A ATAA A
1 ATAA A--TAA A-TAA ATAA ATAA ATAA ATAA A
75767 AGAGATAACA
Statistics
Matches: 62, Mismatches: 3, Indels: 12
0.81 0.04 0.16
Matches are distributed among these distances:
3 17 0.27
4 36 0.58
5 5 0.08
6 4 0.06
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:98834 original size:38 final size:38
Alignment explanation
Indices: 98783--98855 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
98773 ATGGCTTCAG
*
98783 ACCTCTTCGATCATTACCCTGTAAGTAAATTCATTTAC
1 ACCTCTTCAATCATTACCCTGTAAGTAAATTCATTTAC
*
98821 ACCTCTTCAATCATTATCCTGTAAGTAAATTCATT
1 ACCTCTTCAATCATTACCCTGTAAGTAAATTCATT
98856 CGGCTTCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (38 bp):
ACCTCTTCAATCATTACCCTGTAAGTAAATTCATTTAC
Found at i:99474 original size:210 final size:206
Alignment explanation
Indices: 98982--99487 Score: 561
Period size: 207 Copynumber: 2.4 Consensus size: 206
98972 CTTCAGCAAC
* * * * *
98982 CATCTTACTAAGCAAGCTTGCTGCTTCTCCACATTGT-CCTGAATTGCATAATCCATGTATTAAA
1 CATCCTACTAAACAAGCTTG-TGCTTCTGCACATT-TACCTGAATTGCACAATCCAAGTATTAAA
** * * * * * *
99046 CAACTGTAGGAAACGATGTCTGGTTTCAGATCTCTCTGTATCATTAATTTATACAAGGTAATGGC
64 CAACTGTAGGTGACAATGTCAGGTTTCACATCTCTCTGAATCATTAATTCATACAAGCTAATGGC
* * * *
99111 TTCTTCAATCTTTTTTTCTTTGCTCAAAGCATTGATTAAAGAGCTTAAGGTTTCCACATCAGGCT
129 TTCTTCAATCTTGTTTTCCTTGCACAAAGCATTGATTAAAGAGCTTAAAGTTTCCACATCAGGCT
99176 GGACTCCATTCAA
194 GGACTCCATTCAA
* * * * * * * *
99189 CATCCTACTAAATAAGCTAGTCACTTCTGCACAATTACCTAAACTCCACAATCCAATTATTAAA-
1 CATCCTACTAAACAAGCTTGT-GCTTCTGCACATTTACCTGAATTGCACAATCCAAGTATTAAAC
* * * * *
99253 AAGCAGTAGGTGACAATGTCAGGTTTTACATTTCTCT-AACTCATTAGTTCCA-ACATGCTAATG
65 AA-CTGTAGGTGACAATGTCAGGTTTCACATCTCTCTGAA-TCATTAATT-CATACAAGCTAATG
** * *
99316 GCTTCTTCGTTCTTGTTTTCCTTGCACAAAGCATTGATTAAATAGCTTAAAGTTTCCATATCAGG
127 GCTTCTTCAATCTTGTTTTCCTTGCACAAAGCATTGATTAAAGAGCTTAAAGTTTCCACATCAGG
99381 CTGGACACCTCCATTCAA
192 CTGG--A-CTCCATTCAA
* *
99399 CATCCTACTAAACAAGCTTGTGGCTTCTGCACATTTATCTGAATTGCACAATCCACGTATTAAAC
1 CATCCTACTAAACAAGCTTGT-GCTTCTGCACATTTACCTGAATTGCACAATCCAAGTATTAAAC
*
99464 AATTGTAGGTGACAATGTCAGGTT
65 AACTGTAGGTGACAATGTCAGGTT
99488 GCTTCTGTCC
Statistics
Matches: 243, Mismatches: 47, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
206 5 0.02
207 151 0.62
208 1 0.00
209 1 0.00
210 83 0.34
211 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (206 bp):
CATCCTACTAAACAAGCTTGTGCTTCTGCACATTTACCTGAATTGCACAATCCAAGTATTAAACA
ACTGTAGGTGACAATGTCAGGTTTCACATCTCTCTGAATCATTAATTCATACAAGCTAATGGCTT
CTTCAATCTTGTTTTCCTTGCACAAAGCATTGATTAAAGAGCTTAAAGTTTCCACATCAGGCTGG
ACTCCATTCAA
Found at i:101554 original size:19 final size:19
Alignment explanation
Indices: 101530--101569 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
101520 CGGAAAAAAA
*
101530 CAGAAATGTGTGAGCTGTC
1 CAGAAATGAGTGAGCTGTC
*
101549 CAGAAATGAGTGAGTTGTC
1 CAGAAATGAGTGAGCTGTC
101568 CA
1 CA
101570 ATCTGGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (19 bp):
CAGAAATGAGTGAGCTGTC
Found at i:102316 original size:16 final size:16
Alignment explanation
Indices: 102295--102326 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
102285 TTGGGATCCC
102295 ATTTTATTATTATTTT
1 ATTTTATTATTATTTT
*
102311 ATTTTATTTTTATTTT
1 ATTTTATTATTATTTT
102327 CAAGTTATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
ATTTTATTATTATTTT
Found at i:110510 original size:16 final size:17
Alignment explanation
Indices: 110472--110510 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
110462 ACATTGTTGT
*
110472 TGCATTTTAATTGTCAT
1 TGCATTTTAATTGTCAG
*
110489 TGCATTTTAA-TGTTAG
1 TGCATTTTAATTGTCAG
110505 TGCATT
1 TGCATT
110511 GGGGACAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.51
Consensus pattern (17 bp):
TGCATTTTAATTGTCAG
Found at i:128375 original size:19 final size:19
Alignment explanation
Indices: 128351--128389 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
128341 GAGAAAGAGT
128351 TACTACAGTAGGTTTTGCA
1 TACTACAGTAGGTTTTGCA
128370 TACTACAGTAGGTTTTGCA
1 TACTACAGTAGGTTTTGCA
128389 T
1 T
128390 TTGACAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (19 bp):
TACTACAGTAGGTTTTGCA
Found at i:131724 original size:3 final size:3
Alignment explanation
Indices: 131718--131759 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
131708 GGAAGAGGAG
* *
131718 GAA GAA G-A GAA GAGA GAA GAA GAA AAA GAA AAA GAA GAA GAA
1 GAA GAA GAA GAA GA-A GAA GAA GAA GAA GAA GAA GAA GAA GAA
131760 TTTGTAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:139717 original size:24 final size:24
Alignment explanation
Indices: 139669--139729 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
139659 TTCCTAACAC
* *
139669 GGAGAAATAAGGAAGGTGAGAGAA
1 GGAGAAATAAAGAAGGAGAGAGAA
139693 GGAGAAATAAAG-AGGAGAGATGAA
1 GGAGAAATAAAGAAGGAGAGA-GAA
*
139717 GTGAGACATAAAG
1 G-GAGAAATAAAG
139730 GGGGAGAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.22
24 15 0.47
25 10 0.31
ACGTcount: A:0.51, C:0.02, G:0.38, T:0.10
Consensus pattern (24 bp):
GGAGAAATAAAGAAGGAGAGAGAA
Found at i:140614 original size:24 final size:24
Alignment explanation
Indices: 140566--140612 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
140556 AAGAGTTAAT
*
140566 TTGTCAATGCAAATATAAAATAAA
1 TTGTCAAAGCAAATATAAAATAAA
*
140590 TTGTCAAAGCAAAT-TAAGATAAA
1 TTGTCAAAGCAAATATAAAATAAA
140613 ATGAGTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.28
Consensus pattern (24 bp):
TTGTCAAAGCAAATATAAAATAAA
Found at i:147452 original size:13 final size:13
Alignment explanation
Indices: 147434--147461 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
147424 ATAGTAATAG
147434 GCTTTACCAGCCA
1 GCTTTACCAGCCA
147447 GCTTTACCAGCCA
1 GCTTTACCAGCCA
147460 GC
1 GC
147462 CTATCCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.39, G:0.18, T:0.21
Consensus pattern (13 bp):
GCTTTACCAGCCA
Found at i:157067 original size:55 final size:51
Alignment explanation
Indices: 156881--157121 Score: 304
Period size: 51 Copynumber: 4.6 Consensus size: 51
156871 TTTCATTTAA
* * * *
156881 TACTCATGATGACA-TATTGTCATCGGACCATTTAATTCGTCATGGATTCATT
1 TACTCATGATGACACT-TAGTCATCGGACC-TTTAATCCGTAAAGGATTCATT
* * *
156933 TACTCACGATGACACTTAGTCATCGGACCTTTCATCTGTAAAGGATTCATT
1 TACTCATGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * *
156984 TACTCATGATGACACTCAGCCATTGGACCTTTAATCCGTAAAGGATTCATTTTTT
1 TACTCATGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCA----TT
*
157039 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCATGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
157090 TACTCATGATGACACTTAGTCACCAGACCTTT
1 TACTCATGATGACACTTAGTCATCGGACCTTT
157122 CATTTATAGC
Statistics
Matches: 164, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
51 91 0.55
52 25 0.15
53 1 0.01
55 47 0.29
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (51 bp):
TACTCATGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:157119 original size:106 final size:106
Alignment explanation
Indices: 156931--157121 Score: 319
Period size: 106 Copynumber: 1.8 Consensus size: 106
156921 CATGGATTCA
* *
156931 TTTACTCACGATGACACTTAGTCATCGGACCTTTCATCTGTAAAGGATTCATTTACTCATGATGA
1 TTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCATGATGA
***
156996 CACTCAGCCATTGGACCTTTAATCCGTAAAGGATTCATTTT
66 CACTCAGCCACCAGACCTTTAATCCGTAAAGGATTCATTTT
157037 TTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCATGATGA
1 TTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCATGATGA
* *
157102 CACTTAGTCACCAGACCTTT
66 CACTCAGCCACCAGACCTTT
157122 CATTTATAGC
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 78 1.00
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.34
Consensus pattern (106 bp):
TTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCATGATGA
CACTCAGCCACCAGACCTTTAATCCGTAAAGGATTCATTTT
Found at i:172791 original size:21 final size:22
Alignment explanation
Indices: 172760--172801 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
172750 TATCACTAAT
172760 TGTGCATTTGCTTTA-GTGGTTA
1 TGTGCATTTGC-TTACGTGGTTA
172782 TGTGC-TTTGCTTACGTGGTT
1 TGTGCATTTGCTTACGTGGTT
172802 GAGATTAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 11 0.58
22 5 0.26
ACGTcount: A:0.10, C:0.12, G:0.29, T:0.50
Consensus pattern (22 bp):
TGTGCATTTGCTTACGTGGTTA
Found at i:173083 original size:26 final size:26
Alignment explanation
Indices: 173050--173109 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
173040 TCTTTCCCTC
173050 TTTTCTTTTTCATGTTCATTGTTTTT
1 TTTTCTTTTTCATGTTCATTGTTTTT
173076 TTTTCTTTTTCATGTTCATTGTTTTT
1 TTTTCTTTTTCATGTTCATTGTTTTT
173102 TTTT-TTTT
1 TTTTCTTTT
173110 CCTGTAGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.12
26 30 0.88
ACGTcount: A:0.07, C:0.10, G:0.07, T:0.77
Consensus pattern (26 bp):
TTTTCTTTTTCATGTTCATTGTTTTT
Found at i:175543 original size:3 final size:3
Alignment explanation
Indices: 175535--175604 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
175525 TAAAAAATAT
175535 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
175583 TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
175605 CACACTTATA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:181142 original size:22 final size:22
Alignment explanation
Indices: 181117--181169 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
181107 ACCGATGTTA
*
181117 CGACGAAGAACCCCTAATGTCG
1 CGACAAAGAACCCCTAATGTCG
**
181139 CGACAAAGAGTCCCTAATGTCG
1 CGACAAAGAACCCCTAATGTCG
181161 CGACAAAGA
1 CGACAAAGA
181170 GTATAGATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.28, G:0.23, T:0.13
Consensus pattern (22 bp):
CGACAAAGAACCCCTAATGTCG
Found at i:181170 original size:22 final size:22
Alignment explanation
Indices: 181128--181171 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
181118 GACGAAGAAC
181128 CCCTAATGTCGCGACAAAGAGT
1 CCCTAATGTCGCGACAAAGAGT
181150 CCCTAATGTCGCGACAAAGAGT
1 CCCTAATGTCGCGACAAAGAGT
181172 ATAGATTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.18
Consensus pattern (22 bp):
CCCTAATGTCGCGACAAAGAGT
Found at i:187707 original size:21 final size:20
Alignment explanation
Indices: 187683--187729 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
187673 ACACAAAAAA
187683 TAAAATGAAATAAAATTAAAT
1 TAAAATGAAATAAAA-TAAAT
* *
187704 TAAAATGCAGTAAAATAAAT
1 TAAAATGAAATAAAATAAAT
187724 TGAAAA
1 T-AAAA
187730 ACTTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.26
Consensus pattern (20 bp):
TAAAATGAAATAAAATAAAT
Found at i:192964 original size:23 final size:23
Alignment explanation
Indices: 192935--193317 Score: 561
Period size: 23 Copynumber: 16.6 Consensus size: 23
192925 CTTATATCTA
192935 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
*
192958 TGTTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
192981 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
*
193004 TG-TTCAAATATTAATGTGATTTG
1 TGCTT-AAATATTAATATGATTTG
193027 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* * *
193050 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATATGATTTG
*
193073 TGCTTAAATCTTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
*
193096 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
193119 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* * *
193142 TGCTCAAATATTAATGTGATATG
1 TGCTTAAATATTAATATGATTTG
193165 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* *
193188 TGCTCAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
193211 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* * *
193234 TGCTCAAATATTAATGTGACTTG
1 TGCTTAAATATTAATATGATTTG
**
193257 TGCTTAAATATTAATATGATTAA
1 TGCTTAAATATTAATATGATTTG
* *
193280 TGGTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
*
193303 TGCTCAAATAATTAA
1 TGCTTAAAT-ATTAA
193318 GATGTGATAT
Statistics
Matches: 319, Mismatches: 38, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
22 2 0.01
23 310 0.97
24 7 0.02
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (23 bp):
TGCTTAAATATTAATATGATTTG
Found at i:193002 original size:46 final size:46
Alignment explanation
Indices: 192935--193317 Score: 631
Period size: 46 Copynumber: 8.3 Consensus size: 46
192925 CTTATATCTA
* * *
192935 TGCTTAAATATTAATATGATTTGTGTTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTG
*
192981 TGCTTAAATATTAATATGATTTGTGTTCAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTG
*
193027 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTG
* *
193073 TGCTTAAATCTTAATATGATTTGTGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTG
*
193119 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATATG
1 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTG
193165 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTG
*
193211 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGACTTG
1 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTG
** * *
193257 TGCTTAAATATTAATATGATTAATGGTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTG
*
193303 TGCTCAAATAATTAA
1 TGCTTAAAT-ATTAA
193318 GATGTGATAT
Statistics
Matches: 318, Mismatches: 18, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
46 313 0.98
47 5 0.02
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (46 bp):
TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTG
Found at i:193487 original size:3 final size:3
Alignment explanation
Indices: 193479--193503 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
193469 GAATACGTAG
193479 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
193504 GTGGATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:195984 original size:30 final size:31
Alignment explanation
Indices: 195950--196012 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
195940 AGTTTATATC
* *
195950 TTTATAATTTTTAAAAGATTAAATTA-AATT
1 TTTATAATTTTTAAAAGATCAAAGTATAATT
* *
195980 TTTATCATTTTTATAAGATCAAAGTATAATT
1 TTTATAATTTTTAAAAGATCAAAGTATAATT
196011 TT
1 TT
196013 ACATTTACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (31 bp):
TTTATAATTTTTAAAAGATCAAAGTATAATT
Found at i:205921 original size:6 final size:6
Alignment explanation
Indices: 205910--205934 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
205900 AAAAATACAA
205910 TGAGAT TGAGAT TGAGAT TGAGAT T
1 TGAGAT TGAGAT TGAGAT TGAGAT T
205935 AATTGTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TGAGAT
Found at i:207908 original size:23 final size:25
Alignment explanation
Indices: 207853--207927 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 25
207843 ATGAGTTTGA
207853 AAATAAAACCAAAAGTCCAACAGAAATCC
1 AAAT-AAA-CAAAAGT-CAACA-AAATCC
*
207882 AAATACACAAAAG-CAACAAAAT-C
1 AAATAAACAAAAGTCAACAAAATCC
*
207905 AAATAAACAAAAGTAAACAAAAT
1 AAATAAACAAAAGTCAACAAAAT
207928 GCCCAAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 13 0.31
24 12 0.29
25 5 0.12
27 6 0.14
28 2 0.05
29 4 0.10
ACGTcount: A:0.65, C:0.19, G:0.05, T:0.11
Consensus pattern (25 bp):
AAATAAACAAAAGTCAACAAAATCC
Found at i:208792 original size:9 final size:9
Alignment explanation
Indices: 208768--208810 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
208758 TGGTTAATCG
208768 ATCAATTAA
1 ATCAATTAA
* *
208777 CTGAATTAA
1 ATCAATTAA
*
208786 ATCAATTCA
1 ATCAATTAA
*
208795 ATCGATTAA
1 ATCAATTAA
208804 ATCAATT
1 ATCAATT
208811 TTAATCAAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.35
Consensus pattern (9 bp):
ATCAATTAA
Found at i:235083 original size:21 final size:21
Alignment explanation
Indices: 235059--235107 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
235049 TACCCTTTAT
235059 CGATACTCAACAAGCTTCTAC
1 CGATACTCAACAAGCTTCTAC
** *
235080 CGATACTCGGCATGCTTCTAC
1 CGATACTCAACAAGCTTCTAC
235101 CGATACT
1 CGATACT
235108 AAAAACTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.27
Consensus pattern (21 bp):
CGATACTCAACAAGCTTCTAC
Found at i:235797 original size:17 final size:17
Alignment explanation
Indices: 235741--235830 Score: 90
Period size: 17 Copynumber: 5.1 Consensus size: 17
235731 CTCTTGCAAT
235741 CCAGTAATGCTCAAACGAG
1 CCAGT-ATGCTC-AACGAG
*
235760 CCACTATGCTCAAACGAG
1 CCAGTATGCTC-AACGAG
*
235778 CCAGTATGCTCAATGAG
1 CCAGTATGCTCAACGAG
* *
235795 CCAGCATGCTCAACAAG
1 CCAGTATGCTCAACGAG
* * *
235812 CCAATACGCTCAAAGAG
1 CCAGTATGCTCAACGAG
235829 CC
1 CC
235831 CCATTATCAA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
17 33 0.55
18 23 0.38
19 4 0.07
ACGTcount: A:0.34, C:0.31, G:0.19, T:0.16
Consensus pattern (17 bp):
CCAGTATGCTCAACGAG
Found at i:237584 original size:34 final size:34
Alignment explanation
Indices: 237541--237608 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
237531 AGCTAAGAAT
237541 GCCTCGTAGCCCTTACAAACCAGTTTCTGTGCAG
1 GCCTCGTAGCCCTTACAAACCAGTTTCTGTGCAG
237575 GCCTCGTAGCCCTTACAAACCAGTTTCTGTGCAG
1 GCCTCGTAGCCCTTACAAACCAGTTTCTGTGCAG
237609 AAATGGCTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.26
Consensus pattern (34 bp):
GCCTCGTAGCCCTTACAAACCAGTTTCTGTGCAG
Found at i:240607 original size:17 final size:17
Alignment explanation
Indices: 240585--240620 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
240575 AATATACTCA
240585 AACGAGCCAGTATGCTC
1 AACGAGCCAGTATGCTC
*
240602 AACGAGCTAGTATGCTC
1 AACGAGCCAGTATGCTC
240619 AA
1 AA
240621 ACGACTGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.19
Consensus pattern (17 bp):
AACGAGCCAGTATGCTC
Found at i:247012 original size:17 final size:17
Alignment explanation
Indices: 246990--247028 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
246980 AGGTGGAGAA
*
246990 CTTGTTCGCT-GAGAGTT
1 CTTGTTCG-TAGAGAATT
247007 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
247024 CTTGT
1 CTTGT
247029 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:258905 original size:38 final size:39
Alignment explanation
Indices: 258858--258932 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 39
258848 CGAAAAATAA
* *
258858 TAGATGATTTTCCTCAA-CAAAAAATATTTTGCAACAGT
1 TAGAGGATTTTCCTCAATCAAAAAATATTTTACAACAGT
* *
258896 TAGAGGATTTTCCTCAATCGAAAACTATTTTACAACA
1 TAGAGGATTTTCCTCAATCAAAAAATATTTTACAACA
258933 AAAAATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 16 0.50
39 16 0.50
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (39 bp):
TAGAGGATTTTCCTCAATCAAAAAATATTTTACAACAGT
Found at i:273914 original size:54 final size:54
Alignment explanation
Indices: 273851--273961 Score: 159
Period size: 54 Copynumber: 2.1 Consensus size: 54
273841 GAAAACCTTA
** * * *
273851 TTCCAGAAAACACCATTGTTCAAGGGGAAGCTACTGTTTAGGGGGAGACTATTG
1 TTCCAGAAAACACCATTGTTCAAAAGGAAGCTACTGCTCAGGGGGAGACTACTG
**
273905 TTCCAGAAAACACCATTGTTCAAAAGGAAGCTTTTGCTCAGGGGGAGACTACTG
1 TTCCAGAAAACACCATTGTTCAAAAGGAAGCTACTGCTCAGGGGGAGACTACTG
273959 TTC
1 TTC
273962 AAAAGGAGAT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (54 bp):
TTCCAGAAAACACCATTGTTCAAAAGGAAGCTACTGCTCAGGGGGAGACTACTG
Found at i:284110 original size:15 final size:16
Alignment explanation
Indices: 284086--284118 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
284076 ATACATACAT
*
284086 ATTTTTTTATTTC-AC
1 ATTTTGTTATTTCGAC
284101 ATTTTGTTATTTCGAC
1 ATTTTGTTATTTCGAC
284117 AT
1 AT
284119 ATAGTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.61
Consensus pattern (16 bp):
ATTTTGTTATTTCGAC
Found at i:284428 original size:6 final size:6
Alignment explanation
Indices: 284417--284444 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
284407 TCTACGTTTG
284417 AAATAA AAATAA AAATAA AAATAA AAAT
1 AAATAA AAATAA AAATAA AAATAA AAAT
284445 TAGGTCTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:284847 original size:102 final size:102
Alignment explanation
Indices: 284671--284876 Score: 394
Period size: 102 Copynumber: 2.0 Consensus size: 102
284661 TAGAACCTAG
*
284671 AACGACGTCATATCCCTGCGTGTTTTTGAAAAGGGGCAAATTGCCTATTTGGTCATTTAGTATTT
1 AACGACGTCATATCCCCGCGTGTTTTTGAAAAGGGGCAAATTGCCTATTTGGTCATTTAGTATTT
284736 TTTATTTGTTTCAATTTAGTCCTTTTATGCTACTTTT
66 TTTATTTGTTTCAATTTAGTCCTTTTATGCTACTTTT
*
284773 AACGACGTCATATCCCCGCGTGTTTTTGAAAAGGGGCAAATTGCCTATTTGGTCATTTCGTATTT
1 AACGACGTCATATCCCCGCGTGTTTTTGAAAAGGGGCAAATTGCCTATTTGGTCATTTAGTATTT
284838 TTTATTTGTTTCAATTTAGTCCTTTTATGCTACTTTT
66 TTTATTTGTTTCAATTTAGTCCTTTTATGCTACTTTT
284875 AA
1 AA
284877 TTTATTTCAA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.45
Consensus pattern (102 bp):
AACGACGTCATATCCCCGCGTGTTTTTGAAAAGGGGCAAATTGCCTATTTGGTCATTTAGTATTT
TTTATTTGTTTCAATTTAGTCCTTTTATGCTACTTTT
Found at i:285085 original size:60 final size:60
Alignment explanation
Indices: 285008--285181 Score: 176
Period size: 60 Copynumber: 2.9 Consensus size: 60
284998 GTTTTAACCA
*
285008 TCAAACTTTCAAGAAATTTGAATTTGACCTCCAAACTTTCTAAAAATTTAAATTTGAC-CC
1 TCAAACTTTCTAGAAATTTGAATTTGACC-CCAAACTTTCTAAAAATTTAAATTTGACTCC
* ** * * * *
285068 TCAAGCTTTCTAGAAATTCAAATTTGACCCCTTAACTTTTTGAAAATTTGAATTTGACTCC
1 TCAAACTTTCTAGAAATTTGAATTTGACCCC-AAACTTTCTAAAAATTTAAATTTGACTCC
* * * *
285129 T-AAACTTT-TCA-AAAATTGAATTTAACCCTTAAACTTTCTAAAAATTCAAATTT
1 TCAAACTTTCT-AGAAATTTGAATTTGACCC-CAAACTTTCTAAAAATTTAAATTT
285182 AGCCCCAAAC
Statistics
Matches: 91, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
59 34 0.37
60 54 0.59
61 3 0.03
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.38
Consensus pattern (60 bp):
TCAAACTTTCTAGAAATTTGAATTTGACCCCAAACTTTCTAAAAATTTAAATTTGACTCC
Found at i:285147 original size:29 final size:28
Alignment explanation
Indices: 285010--285200 Score: 136
Period size: 30 Copynumber: 6.5 Consensus size: 28
285000 TTTAACCATC
*
285010 AAACTTTC-AAGAAATTTGAATTTGACCTCC
1 AAACTTTCTAA-AAA-TTGAATTTGACC-CT
*
285040 AAACTTTCTAAAAATTTAAATTTGACCCT
1 AAACTTTCTAAAAA-TTGAATTTGACCCT
* * *
285069 CAAGCTTTCTAGAAATTCAAATTTGACCCCT
1 -AAACTTTCTAAAAATT-GAATTTGA-CCCT
* * *
285100 TAACTTTTTGAAAATTTGAATTTGACTCCT
1 AAACTTTCT-AAAAATTGAATTTGAC-CCT
*
285130 AAACTTT-TCAAAAATTGAATTTAACCCTT
1 AAACTTTCT-AAAAATTGAATTTGACCC-T
* *
285159 AAACTTTCTAAAAATTCAAATTT-AGCCCC
1 AAACTTTCTAAAAATT-GAATTTGA-CCCT
*
285188 AAACTTTCCAAAA
1 AAACTTTCTAAAA
285201 TTTTGTTTTT
Statistics
Matches: 134, Mismatches: 17, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 47 0.35
30 74 0.55
31 11 0.08
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (28 bp):
AAACTTTCTAAAAATTGAATTTGACCCT
Found at i:286693 original size:29 final size:30
Alignment explanation
Indices: 286660--286724 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
286650 TTAATTTTGA
* *
286660 GATTAAATT-GAGAATTTGGTG-ATTTTAAG
1 GATTAAATTGGA-AATTTAGTGAAATTTAAG
286689 GATTAAATTGGAAATTTAGTGAAATTTAAG
1 GATTAAATTGGAAATTTAGTGAAATTTAAG
*
286719 GTTTAA
1 GATTAA
286725 CTAATAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 17 0.55
30 14 0.45
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.40
Consensus pattern (30 bp):
GATTAAATTGGAAATTTAGTGAAATTTAAG
Found at i:291504 original size:70 final size:70
Alignment explanation
Indices: 291422--291775 Score: 286
Period size: 70 Copynumber: 5.1 Consensus size: 70
291412 TATAGTCTTG
* * *
291422 GCTGATATTACAAAGGCTTGTCGATTTATGATTGTCAGCCTCCAACACAGGTAACAAACCTACGT
1 GCTGATATTACAAAGGCTTGTCGATTTATGATCGTCAGCCTCCAACACAGCTAACGAACCTACGT
291487 TCCCA
66 TCCCA
** * *** * * * * * *
291492 ATTGATAGTACAAAGGCTCAACGATTTGTGATCGCCAGTCTCCAACACAACTAGCGAACCTACGC
1 GCTGATATTACAAAGGCTTGTCGATTTATGATCGTCAGCCTCCAACACAGCTAACGAACCTACGT
*
291557 TCCTA
66 TCCCA
* * * * * * * *
291562 GCTGATATTACAAAGGCTTGTCGATTTATGATCATCAACCTTCAACATAGTTAATGGACCTACCT
1 GCTGATATTACAAAGGCTTGTCGATTTATGATCGTCAGCCTCCAACACAGCTAACGAACCTACGT
291627 TCCCA
66 TCCCA
* * * * * * *
291632 GCTGAAATTACAAAGGCTTG-CTGGTTTATGATTGTC-GCCTCCAACACATCTATCAAACCTATG
1 GCTGATATTACAAAGGCTTGTC-GATTTATGATCGTCAGCCTCCAACACAGCTAACGAACCTACG
291695 TTCCCAA
65 TTCCC-A
* * * * * * *
291702 G-T-ACTATTATAAAGGTTTGTTGGTTTATGATCG-CAACCTCCAACACAGTTAACGAACCTATG
1 GCTGA-TATTACAAAGGCTTGTCGATTTATGATCGTCAGCCTCCAACACAGCTAACGAACCTACG
*
291764 CTCCCA
65 TTCCCA
*
291770 GTTGAT
1 GCTGAT
291776 GCTAAGGTCT
Statistics
Matches: 214, Mismatches: 63, Indels: 15
0.73 0.22 0.05
Matches are distributed among these distances:
68 4 0.02
69 74 0.35
70 136 0.64
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (70 bp):
GCTGATATTACAAAGGCTTGTCGATTTATGATCGTCAGCCTCCAACACAGCTAACGAACCTACGT
TCCCA
Found at i:291760 original size:69 final size:69
Alignment explanation
Indices: 291638--291769 Score: 160
Period size: 69 Copynumber: 1.9 Consensus size: 69
291628 CCCAGCTGAA
* * * *
291638 ATTACAAAGGCTTGCTGGTTTATGATTGTCGCCTCCAACACATCTATCAAACCTATGTTCCCAAG
1 ATTACAAAGGCTTGCTGGTTTATGATCGTCACCTCCAACACATCTAACAAACCTATGCTCCCAAG
291703 TACT
66 TACT
* * * *
291707 ATTATAAAGGTTTGTTGGTTTATGATCG-CAACCTCCAACACAGT-TAACGAACCTATGCTCCCA
1 ATTACAAAGGCTTGCTGGTTTATGATCGTC-ACCTCCAACACA-TCTAACAAACCTATGCTCCCA
291770 GTTGATGCTA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
68 1 0.02
69 51 0.96
70 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (69 bp):
ATTACAAAGGCTTGCTGGTTTATGATCGTCACCTCCAACACATCTAACAAACCTATGCTCCCAAG
TACT
Found at i:300310 original size:37 final size:37
Alignment explanation
Indices: 300260--300334 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
300250 TTTTTAAATG
*
300260 TATGTTTGTTTCATTTAAAACTGTTTTCCTGAAATAT
1 TATGTTTGTTTCATTTAAAACCGTTTTCCTGAAATAT
300297 TATGTTTGTTTCATTTAAAACCGTTTTCCTGAAATAT
1 TATGTTTGTTTCATTTAAAACCGTTTTCCTGAAATAT
300334 T
1 T
300335 TTCAGGAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.51
Consensus pattern (37 bp):
TATGTTTGTTTCATTTAAAACCGTTTTCCTGAAATAT
Found at i:303090 original size:18 final size:17
Alignment explanation
Indices: 303065--303098 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
303055 TATTCCTTTT
303065 CTAACTTTTATTGATTA
1 CTAACTTTTATTGATTA
*
303082 CTAATCTTTTGTTGATT
1 CTAA-CTTTTATTGATT
303099 TTCTTTTAAA
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:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (17 bp):
CTAACTTTTATTGATTA
Found at i:314488 original size:15 final size:16
Alignment explanation
Indices: 314463--314492 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
314453 TTTTATTCTC
314463 TTTATAATTTTTATAA
1 TTTATAATTTTTATAA
314479 TTTA-AATTTTTATA
1 TTTATAATTTTTATA
314493 TTTTGGGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTATAATTTTTATAA
Found at i:316151 original size:22 final size:22
Alignment explanation
Indices: 316109--316155 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
316099 CTTTATTGAC
316109 CATATAATCGCAGCTCTTATGGA
1 CATATAATCGCAGCTCTTAT-GA
*
316132 CATA-AATTGCAGCATC-TATGA
1 CATATAATCGCAGC-TCTTATGA
316153 CAT
1 CAT
316156 TTATGAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 5 0.23
22 11 0.50
23 6 0.27
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (22 bp):
CATATAATCGCAGCTCTTATGA
Found at i:331189 original size:165 final size:165
Alignment explanation
Indices: 330917--331244 Score: 647
Period size: 165 Copynumber: 2.0 Consensus size: 165
330907 CAGGGAACTA
330917 TCCCCAAAATGTACCAGAAATATATCATAGTGAAAGCATTGCCCCAAGGCCTTTAAGAAAAACAA
1 TCCCCAAAATGTACCAGAAATATATCATAGTGAAAGCATTGCCCCAAGGCCTTTAAGAAAAACAA
330982 AGAATGCTCTCTTTTTGTCTTACATAGGCATGCTATCTAAATTACTAAGTGATTTCCTCATCACA
66 AGAATGCTCTCTTTTTGTCTTACATAGGCATGCTATCTAAATTACTAAGTGATTTCCTCATCACA
331047 CATTGCTGTAAGGTGAACCACTTAATACAAAGAGT
131 CATTGCTGTAAGGTGAACCACTTAATACAAAGAGT
331082 TCCCCAAAATGTACCAGAAATATATCATAGTGAAAGCATTGCCCCAAGGCCTTTAAGAAAAACAA
1 TCCCCAAAATGTACCAGAAATATATCATAGTGAAAGCATTGCCCCAAGGCCTTTAAGAAAAACAA
331147 AGAATGCTCTCTTTTTGTCTTACATAGGCATGCTATCTAAATTACTAAGTGATTTCCTCATCACA
66 AGAATGCTCTCTTTTTGTCTTACATAGGCATGCTATCTAAATTACTAAGTGATTTCCTCATCACA
*
331212 CATTGCTGTAAGGTGAACCACTTAATATAAAGA
131 CATTGCTGTAAGGTGAACCACTTAATACAAAGA
331245 TAGAGATGCC
Statistics
Matches: 162, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
165 162 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (165 bp):
TCCCCAAAATGTACCAGAAATATATCATAGTGAAAGCATTGCCCCAAGGCCTTTAAGAAAAACAA
AGAATGCTCTCTTTTTGTCTTACATAGGCATGCTATCTAAATTACTAAGTGATTTCCTCATCACA
CATTGCTGTAAGGTGAACCACTTAATACAAAGAGT
Found at i:335306 original size:21 final size:21
Alignment explanation
Indices: 335266--335306 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
335256 GCGGAGGAGG
* *
335266 TGGAGGTGGTGATGGTGATGT
1 TGGAGGTGGGGATGGGGATGT
*
335287 TGGAGGTGGGGGTGGGGATG
1 TGGAGGTGGGGATGGGGATG
335307 GAGAGGGTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.61, T:0.27
Consensus pattern (21 bp):
TGGAGGTGGGGATGGGGATGT
Found at i:341153 original size:13 final size:14
Alignment explanation
Indices: 341135--341166 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
341125 GTTTCATCCC
341135 AAAAATTAAAAA-A
1 AAAAATTAAAAATA
341148 AAAAATTAAAAATA
1 AAAAATTAAAAATA
341162 AAAAA
1 AAAAA
341167 CTTGCATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAAATTAAAAATA
Found at i:345433 original size:37 final size:37
Alignment explanation
Indices: 345392--345616 Score: 274
Period size: 37 Copynumber: 6.1 Consensus size: 37
345382 ACATGGTTCA
*
345392 AATACACCGACATGAAGCCTACT-GGTCACACAGCCTG
1 AATACACCGACACGAAGCCTACTAGG-CACACAGCCTG
* * *
345429 AATACATC-AGCACGAAGCTTACTAGGCACACAGCTTG
1 AATACACCGA-CACGAAGCCTACTAGGCACACAGCCTG
*
345466 AATACACCAACACGAAGCCTACTAGGCACACAGCCTG
1 AATACACCGACACGAAGCCTACTAGGCACACAGCCTG
* * *
345503 AATACACCGGCATGAAGCTTACTAGGCACACAGCCTG
1 AATACACCGACACGAAGCCTACTAGGCACACAGCCTG
* * * **
345540 AATGCACCGGCACGAAGCCTACTAGGCACACAACAAG
1 AATACACCGACACGAAGCCTACTAGGCACACAGCCTG
* * *
345577 AATACACCGGCACAAAGCCTACTAGGCACATAGCCTG
1 AATACACCGACACGAAGCCTACTAGGCACACAGCCTG
345614 AAT
1 AAT
345617 TTCTTAAATG
Statistics
Matches: 162, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
36 1 0.01
37 158 0.98
38 3 0.02
ACGTcount: A:0.36, C:0.31, G:0.19, T:0.14
Consensus pattern (37 bp):
AATACACCGACACGAAGCCTACTAGGCACACAGCCTG
Found at i:345483 original size:74 final size:74
Alignment explanation
Indices: 345392--345616 Score: 308
Period size: 74 Copynumber: 3.0 Consensus size: 74
345382 ACATGGTTCA
* * *
345392 AATACACCGACATGAAGCCTACT-GGTCACACAGCCTGAATACATCAGCACGAAGCTTACTAGGC
1 AATACACCGACACGAAGCCTACTAGG-CACACAGCCTGAATACACCGGCACGAAGCTTACTAGGC
*
345456 ACACAGCTTG
65 ACACAGCCTG
* *
345466 AATACACCAACACGAAGCCTACTAGGCACACAGCCTGAATACACCGGCATGAAGCTTACTAGGCA
1 AATACACCGACACGAAGCCTACTAGGCACACAGCCTGAATACACCGGCACGAAGCTTACTAGGCA
345531 CACAGCCTG
66 CACAGCCTG
* * * ** * *
345540 AATGCACCGGCACGAAGCCTACTAGGCACACAACAAGAATACACCGGCACAAAGCCTACTAGGCA
1 AATACACCGACACGAAGCCTACTAGGCACACAGCCTGAATACACCGGCACGAAGCTTACTAGGCA
*
345605 CATAGCCTG
66 CACAGCCTG
345614 AAT
1 AAT
345617 TTCTTAAATG
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
74 132 0.99
75 2 0.01
ACGTcount: A:0.36, C:0.31, G:0.19, T:0.14
Consensus pattern (74 bp):
AATACACCGACACGAAGCCTACTAGGCACACAGCCTGAATACACCGGCACGAAGCTTACTAGGCA
CACAGCCTG
Found at i:345553 original size:111 final size:111
Alignment explanation
Indices: 345392--345616 Score: 317
Period size: 111 Copynumber: 2.0 Consensus size: 111
345382 ACATGGTTCA
* *
345392 AATACACCGACATGAAGCCTACTGGTCACACAGCCTGAATACATCAGCACGAAGCTTACTAGGCA
1 AATACACCGACATGAAGCCTACTGGTCACACAGCCTGAATACACCAGCACGAAGCCTACTAGGCA
* ** *
345457 CACAGCTTGAATACACCAACACGAAGCCTACTAGGCACACAGCCTG
66 CACAACAAGAATACACCAACACAAAGCCTACTAGGCACACAGCCTG
* * * *
345503 AATACACCGGCATGAAGCTTACTAGG-CACACAGCCTGAATGCACCGGCACGAAGCCTACTAGGC
1 AATACACCGACATGAAGCCTACT-GGTCACACAGCCTGAATACACCAGCACGAAGCCTACTAGGC
** *
345567 ACACAACAAGAATACACCGGCACAAAGCCTACTAGGCACATAGCCTG
65 ACACAACAAGAATACACCAACACAAAGCCTACTAGGCACACAGCCTG
345614 AAT
1 AAT
345617 TTCTTAAATG
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
111 98 0.98
112 2 0.02
ACGTcount: A:0.36, C:0.31, G:0.19, T:0.14
Consensus pattern (111 bp):
AATACACCGACATGAAGCCTACTGGTCACACAGCCTGAATACACCAGCACGAAGCCTACTAGGCA
CACAACAAGAATACACCAACACAAAGCCTACTAGGCACACAGCCTG
Found at i:346071 original size:20 final size:19
Alignment explanation
Indices: 346029--346075 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
346019 CACTTAAATG
* *
346029 CATTATTATTCATTTAGTC
1 CATTATTATTCATTTACTA
*
346048 CATTATTATTTCATTTCCTA
1 CATTATTA-TTCATTTACTA
346068 CATTATTA
1 CATTATTA
346076 GCTAACAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.28, C:0.17, G:0.02, T:0.53
Consensus pattern (19 bp):
CATTATTATTCATTTACTA
Found at i:348276 original size:55 final size:55
Alignment explanation
Indices: 348209--348349 Score: 203
Period size: 55 Copynumber: 2.6 Consensus size: 55
348199 GGCAAACCAG
* *
348209 AGCTTTACCCGAGCTATAATAACATTACTCTCTAATTGAGACGTAAGCATGTTAAA
1 AGCTCTACCCGAGCTATAATAGCATTACTCTCTAATTGAGACGTAAGCATG-TAAA
* * **
348265 AGCTCTA-CCGAGCTATAATAGCATTACACTCTAATTGAGATGTAAGCATGTCCA
1 AGCTCTACCCGAGCTATAATAGCATTACTCTCTAATTGAGACGTAAGCATGTAAA
*
348319 AGCTCTACCCAAGCTATAATAGCATTACTCT
1 AGCTCTACCCGAGCTATAATAGCATTACTCT
348350 AAATAAGATG
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
54 9 0.12
55 61 0.80
56 6 0.08
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (55 bp):
AGCTCTACCCGAGCTATAATAGCATTACTCTCTAATTGAGACGTAAGCATGTAAA
Found at i:348376 original size:53 final size:54
Alignment explanation
Indices: 348209--348391 Score: 174
Period size: 55 Copynumber: 3.4 Consensus size: 54
348199 GGCAAACCAG
* * * * * * * **
348209 AGCTTTACCCGAGCTATAATAACATTACTCTCTAATTGAGACGTAAGCATGTTAAA
1 AGCTCTACCCAAGCTATAATAGCATTA-ACTCTAAATAAGATGTAAGCATG-TCCA
* * *
348265 AGCTCTA-CCGAGCTATAATAGCATTACACTCTAATTGAGATGTAAGCATGTCCA
1 AGCTCTACCCAAGCTATAATAGCATTA-ACTCTAAATAAGATGTAAGCATGTCCA
**
348319 AGCTCTACCCAAGCTATAATAGCATT-ACTCTAAATAAGATGTAAGCA-GATCGG
1 AGCTCTACCCAAGCTATAATAGCATTAACTCTAAATAAGATGTAAGCATG-TCCA
*
348372 AGCTCTACCTAAGCTATAAT
1 AGCTCTACCCAAGCTATAAT
348392 GAATCAAAGC
Statistics
Matches: 113, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
52 1 0.01
53 40 0.35
54 9 0.08
55 57 0.50
56 6 0.05
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (54 bp):
AGCTCTACCCAAGCTATAATAGCATTAACTCTAAATAAGATGTAAGCATGTCCA
Found at i:352814 original size:21 final size:22
Alignment explanation
Indices: 352771--352814 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
352761 TATCGGTAAT
352771 TTTGTGTCTTGATGTACCAGTAG
1 TTTGTGTCTTGATGTA-CAGTAG
352794 TTTGTGTACTTG-TGT-CAGTAG
1 TTTGTGT-CTTGATGTACAGTAG
352815 AAGTTACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.30
23 10 0.50
24 4 0.20
ACGTcount: A:0.16, C:0.11, G:0.27, T:0.45
Consensus pattern (22 bp):
TTTGTGTCTTGATGTACAGTAG
Found at i:358411 original size:27 final size:27
Alignment explanation
Indices: 358388--358444 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
358378 CTCTACCAGA
358388 ACCATTACTACCCCTACCTATACCATG
1 ACCATTACTACCCCTACCTATACCATG
** *
358415 ACCATTACTACCTTTACCTATACCACG
1 ACCATTACTACCCCTACCTATACCATG
358442 ACC
1 ACC
358445 CCTAGGTGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.40, G:0.04, T:0.26
Consensus pattern (27 bp):
ACCATTACTACCCCTACCTATACCATG
Found at i:359777 original size:39 final size:39
Alignment explanation
Indices: 359697--359779 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
359687 TGGGCTGGGT
* * *
359697 CGTGTGTGACCTGCAGCAAACACGCCTAAGTCTCACGCC
1 CGTGTGTGACCTGCAGCAAACACGCCTAAATCCCACACC
* * *
359736 CGTGTGTGCCCTGTAGCAAGCAC-CCTCAAATCCCACACC
1 CGTGTGTGACCTGCAGCAAACACGCCT-AAATCCCACACC
359775 CGTGT
1 CGTGT
359780 AAGACTAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
38 3 0.08
39 34 0.92
ACGTcount: A:0.22, C:0.37, G:0.22, T:0.19
Consensus pattern (39 bp):
CGTGTGTGACCTGCAGCAAACACGCCTAAATCCCACACC
Found at i:360510 original size:28 final size:27
Alignment explanation
Indices: 360478--360666 Score: 110
Period size: 28 Copynumber: 7.2 Consensus size: 27
360468 TTTTCATATA
*
360478 CATTTACGCTCGCCAACTTATACTTATG
1 CATTTACGCTCGCCAGCTTATAC-TATG
**
360506 CATTTACGCTCGCCAGCTTGCAC-A--
1 CATTTACGCTCGCCAGCTTATACTATG
* *
360530 CATTTACGCTCGTCAGCTTATTCATATG
1 CATTTACGCTCGCCAGCTTATAC-TATG
* **
360558 CGTTTACGCTCGCCAGCTTGCAC-A--
1 CATTTACGCTCGCCAGCTTATACTATG
* * *
360582 CGTTTATGCTCGTCAGCTTATTTA-TATG
1 CATTTACGCTCGCCAGCTTA--TACTATG
** * *
360610 TGTTTACGCTCACCAGCTTACAC-A--
1 CATTTACGCTCGCCAGCTTATACTATG
* *
360634 CGTTTACGCTCGTCAGCTTATACTTATG
1 CATTTACGCTCGCCAGCTTATAC-TATG
360662 CATTT
1 CATTT
360667 TATGCTATTC
Statistics
Matches: 121, Mismatches: 26, Indels: 28
0.69 0.15 0.16
Matches are distributed among these distances:
24 55 0.45
26 8 0.07
28 58 0.48
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (27 bp):
CATTTACGCTCGCCAGCTTATACTATG
Found at i:360539 original size:52 final size:52
Alignment explanation
Indices: 360477--360666 Score: 247
Period size: 52 Copynumber: 3.7 Consensus size: 52
360467 CTTTTCATAT
* *
360477 ACATTTACGCTCGCCAACTTATACTTATGCATTTACGCTCGCCAGCTTGCAC
1 ACATTTACGCTCGTCAGCTTATACTTATGCATTTACGCTCGCCAGCTTGCAC
* * *
360529 ACATTTACGCTCGTCAGCTTATTCATATGCGTTTACGCTCGCCAGCTTGCAC
1 ACATTTACGCTCGTCAGCTTATACTTATGCATTTACGCTCGCCAGCTTGCAC
* * * ** * *
360581 ACGTTTATGCTCGTCAGCTTAT-TTATATGTGTTTACGCTCACCAGCTTACAC
1 ACATTTACGCTCGTCAGCTTATACT-TATGCATTTACGCTCGCCAGCTTGCAC
*
360633 ACGTTTACGCTCGTCAGCTTATACTTATGCATTT
1 ACATTTACGCTCGTCAGCTTATACTTATGCATTT
360667 TATGCTATTC
Statistics
Matches: 120, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
52 119 0.99
53 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.35
Consensus pattern (52 bp):
ACATTTACGCTCGTCAGCTTATACTTATGCATTTACGCTCGCCAGCTTGCAC
Found at i:360643 original size:24 final size:24
Alignment explanation
Indices: 360508--360653 Score: 112
Period size: 24 Copynumber: 5.8 Consensus size: 24
360498 TACTTATGCA
* *
360508 TTTACGCTCGCCAGCTTGCACACA
1 TTTACGCTCGCCAGCTTACACACG
* *
360532 TTTACGCTCGTCAGCTTATTCATATGCG
1 TTTACGCTCGCCAGCTTA--CACA--CG
*
360560 TTTACGCTCGCCAGCTTGCACACG
1 TTTACGCTCGCCAGCTTACACACG
* * * * *
360584 TTTATGCTCGTCAGCTTATTTATATGTG
1 TTTACGCTCGCCAGCTTA--CACA--CG
*
360612 TTTACGCTCACCAGCTTACACACG
1 TTTACGCTCGCCAGCTTACACACG
*
360636 TTTACGCTCGTCAGCTTA
1 TTTACGCTCGCCAGCTTA
360654 TACTTATGCA
Statistics
Matches: 93, Mismatches: 21, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
24 50 0.54
26 10 0.11
28 33 0.35
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.34
Consensus pattern (24 bp):
TTTACGCTCGCCAGCTTACACACG
Found at i:366559 original size:26 final size:26
Alignment explanation
Indices: 366485--366591 Score: 128
Period size: 26 Copynumber: 4.2 Consensus size: 26
366475 TTGGCGAGTG
*
366485 TAAACACATATATAAGATGATGAGCA
1 TAAACACATATATAAGCTGATGAGCA
* *
366511 T-AA-ATATCTATAAGCTGATGAGCA
1 TAAACACATATATAAGCTGATGAGCA
* * *
366535 TAAACGCATATATAAGCTGACGAGCG
1 TAAACACATATATAAGCTGATGAGCA
* *
366561 TAAACACATATATAAGCTGATAAGCG
1 TAAACACATATATAAGCTGATGAGCA
366587 TAAAC
1 TAAAC
366592 GTGTGAAAGA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
24 19 0.28
25 4 0.06
26 45 0.66
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (26 bp):
TAAACACATATATAAGCTGATGAGCA
Found at i:366637 original size:50 final size:50
Alignment explanation
Indices: 366555--366668 Score: 147
Period size: 50 Copynumber: 2.3 Consensus size: 50
366545 TATAAGCTGA
* * * *
366555 CGAGCGTAAACACATATATAAGCTGATAAGCGTAAACGTGTGAAAGATGG
1 CGAGAGTAAACGCAGATATAAGCAGATAAGCGTAAACGTGTGAAAGATGG
* * * * *
366605 TGAGTGTAAACGCAGATATAAGCAGATGAGCGTAAACGTGTGCAAGCTGG
1 CGAGAGTAAACGCAGATATAAGCAGATAAGCGTAAACGTGTGAAAGATGG
366655 CGAGAGTAAACGCA
1 CGAGAGTAAACGCA
366669 AACGTGTGCA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.38, C:0.15, G:0.29, T:0.18
Consensus pattern (50 bp):
CGAGAGTAAACGCAGATATAAGCAGATAAGCGTAAACGTGTGAAAGATGG
Found at i:366639 original size:26 final size:26
Alignment explanation
Indices: 366519--366642 Score: 119
Period size: 26 Copynumber: 4.8 Consensus size: 26
366509 CATAAATATC
* *
366519 TATAAGCTGATGAGCATAAACGCATA
1 TATAAGCTGATGAGCGTAAACGCAGA
* * *
366545 TATAAGCTGACGAGCGTAAACACATA
1 TATAAGCTGATGAGCGTAAACGCAGA
* *
366571 TATAAGCTGATAAGCGTAAACG-TG-
1 TATAAGCTGATGAGCGTAAACGCAGA
* * *
366595 TGA-AAGATGGTGAGTGTAAACGCAGA
1 T-ATAAGCTGATGAGCGTAAACGCAGA
*
366621 TATAAGCAGATGAGCGTAAACG
1 TATAAGCTGATGAGCGTAAACG
366643 TGTGCAAGCT
Statistics
Matches: 77, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
24 16 0.21
25 3 0.04
26 58 0.75
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (26 bp):
TATAAGCTGATGAGCGTAAACGCAGA
Found at i:366674 original size:30 final size:30
Alignment explanation
Indices: 366638--366698 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
366628 AGATGAGCGT
*
366638 AAACGTGTGCAAGCTGGCGAGAGTAAACGC
1 AAACGTGTGCAAGCTAGCGAGAGTAAACGC
* *
366668 AAACGTGTGCAAGCTAGTGAGCGTAAACGC
1 AAACGTGTGCAAGCTAGCGAGAGTAAACGC
366698 A
1 A
366699 TATGTATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.20, G:0.31, T:0.15
Consensus pattern (30 bp):
AAACGTGTGCAAGCTAGCGAGAGTAAACGC
Found at i:366694 original size:80 final size:81
Alignment explanation
Indices: 366588--366748 Score: 198
Period size: 82 Copynumber: 2.0 Consensus size: 81
366578 TGATAAGCGT
* * * * *
366588 AAACGTGTGAAAGATGGTGAGTGTAAACGCAGA-TATAAGCAGATGAGCGTAAACGTGTGCAAGC
1 AAACGTGTGAAAGATAGTGAGCGTAAACGCAGAGTATAAACAGACGAGCGTAAACATGTGCAAGC
366652 TGGCGAGAGTAAACGC
66 TGGCGAGAGTAAACGC
* * * * *
366668 AAACGTGTGCAAGCTAGTGAGCGTAAACGCATATGTATAAACTGACGAGTGTAAACATGTGCAAG
1 AAACGTGTGAAAGATAGTGAGCGTAAACGCAGA-GTATAAACAGACGAGCGTAAACATGTGCAAG
* *
366733 TTGGCGAGCGTAAACG
65 CTGGCGAGAGTAAACG
366749 TATATAAATA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
80 28 0.42
82 39 0.58
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.19
Consensus pattern (81 bp):
AAACGTGTGAAAGATAGTGAGCGTAAACGCAGAGTATAAACAGACGAGCGTAAACATGTGCAAGC
TGGCGAGAGTAAACGC
Found at i:366769 original size:52 final size:52
Alignment explanation
Indices: 366668--366775 Score: 126
Period size: 52 Copynumber: 2.1 Consensus size: 52
366658 GAGTAAACGC
* * **
366668 AAACGTGTGCAAGCTAGTGAGCGTAAACGCATATGTATAAACTGACGAGTGT
1 AAACATGTGCAAGCTAGCGAGCGTAAACGCATATAAATAAACTGACGAGTGT
* * * ** *
366720 AAACATGTGCAAGTTGGCGAGCGTAAACGTATATAAATAAGTTGGCGAGTGT
1 AAACATGTGCAAGCTAGCGAGCGTAAACGCATATAAATAAACTGACGAGTGT
366772 AAAC
1 AAAC
366776 GCATATATAG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (52 bp):
AAACATGTGCAAGCTAGCGAGCGTAAACGCATATAAATAAACTGACGAGTGT
Found at i:366802 original size:53 final size:50
Alignment explanation
Indices: 366739--366851 Score: 156
Period size: 49 Copynumber: 2.2 Consensus size: 50
366729 CAAGTTGGCG
366739 AGCGTAAACGTATATAAATAAGTTGGCGAGTGTAAACGCATATATAGCTAACA
1 AGCGTAAACGT-TATAAA-AA-TTGGCGAGTGTAAACGCATATATAGCTAACA
* ** *
366792 AGCGTAAACG-TGTGCAAATTGGTGAGTGTAAACGCATATATAGCTAACA
1 AGCGTAAACGTTATAAAAATTGGCGAGTGTAAACGCATATATAGCTAACA
366841 AGCGTAAACGT
1 AGCGTAAACGT
366852 GTGCAAGCTA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
49 40 0.73
50 2 0.04
51 3 0.05
53 10 0.18
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (50 bp):
AGCGTAAACGTTATAAAAATTGGCGAGTGTAAACGCATATATAGCTAACA
Found at i:366825 original size:49 final size:49
Alignment explanation
Indices: 366761--366857 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
366751 TATAAATAAG
366761 TTGGCGAGTGTAAACGCATATATAGCTAACAAGCGTAAACGTGTGCAAA
1 TTGGCGAGTGTAAACGCATATATAGCTAACAAGCGTAAACGTGTGCAAA
*
366810 TTGGTGAGTGTAAACGCATATATAGCTAACAAGCGTAAACGTGTGCAA
1 TTGGCGAGTGTAAACGCATATATAGCTAACAAGCGTAAACGTGTGCAA
366858 GCTAACGAGC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (49 bp):
TTGGCGAGTGTAAACGCATATATAGCTAACAAGCGTAAACGTGTGCAAA
Found at i:366872 original size:49 final size:49
Alignment explanation
Indices: 366765--366872 Score: 162
Period size: 49 Copynumber: 2.2 Consensus size: 49
366755 AATAAGTTGG
* **
366765 CGAGTGTAAACGCATATATAGCTAACAAGCGTAAACGTGTGCAAATTGG
1 CGAGTGTAAACGCATATATAGCTAACAAGCGTAAACGTGTGCAAACTAA
* *
366814 TGAGTGTAAACGCATATATAGCTAACAAGCGTAAACGTGTGCAAGCTAA
1 CGAGTGTAAACGCATATATAGCTAACAAGCGTAAACGTGTGCAAACTAA
*
366863 CGAGCGTAAA
1 CGAGTGTAAA
366873 TGTATGAAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (49 bp):
CGAGTGTAAACGCATATATAGCTAACAAGCGTAAACGTGTGCAAACTAA
Found at i:366883 original size:24 final size:24
Alignment explanation
Indices: 366833--366896 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
366823 ACGCATATAT
* * *
366833 AGCTAACAAGCGTAAACGTGTGCA
1 AGCTAACGAGCGTAAACGTATGAA
*
366857 AGCTAACGAGCGTAAATGTATGAA
1 AGCTAACGAGCGTAAACGTATGAA
**
366881 AGCTGGCGAGCGTAAA
1 AGCTAACGAGCGTAAA
366897 ATGCAATGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (24 bp):
AGCTAACGAGCGTAAACGTATGAA
Found at i:369930 original size:12 final size:12
Alignment explanation
Indices: 369913--369983 Score: 58
Period size: 12 Copynumber: 6.1 Consensus size: 12
369903 ATAACATTCA
369913 AACAACCAAAAT
1 AACAACCAAAAT
*
369925 AACAACCAAAAC
1 AACAACCAAAAT
*
369937 AACAGA-AAAAAT
1 AACA-ACCAAAAT
*
369949 AGCAA-CAAAAT
1 AACAACCAAAAT
** *
369960 AACAATAAAAAC
1 AACAACCAAAAT
369972 AAC-ACCAAAAT
1 AACAACCAAAAT
369983 A
1 A
369984 GTAAAAAAAA
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
11 16 0.35
12 29 0.63
13 1 0.02
ACGTcount: A:0.69, C:0.21, G:0.03, T:0.07
Consensus pattern (12 bp):
AACAACCAAAAT
Found at i:369957 original size:23 final size:22
Alignment explanation
Indices: 369920--370094 Score: 124
Period size: 23 Copynumber: 7.9 Consensus size: 22
369910 TCAAACAACC
*
369920 AAAATAACAACCAAAACAACAGAA
1 AAAATAGC-ACCAAAACAACA-AA
* *
369944 AAAATAGCAACAAAATAACAATA
1 AAAATAGCACCAAAACAACAA-A
* * *
369967 AAAACAACACCAAAATAGTA-AAA
1 AAAATAGCACCAAAACA--ACAAA
* **
369990 AAAATAGCACCAAAATAGTAAA
1 AAAATAGCACCAAAACAACAAA
* *
370012 AAAA-AGCATCAAAACAATAAA
1 AAAATAGCACCAAAACAACAAA
* * * *
370033 AACACAACACCAAAACAGC-AA
1 AAAATAGCACCAAAACAACAAA
*
370054 AAAATAGCAACCAAAACAGCAAA
1 AAAATAGC-ACCAAAACAACAAA
370077 AAAA-AGCACCAAAACAAC
1 AAAATAGCACCAAAACAAC
370095 GATATTTTTA
Statistics
Matches: 123, Mismatches: 21, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
21 34 0.28
22 32 0.26
23 47 0.38
24 9 0.07
25 1 0.01
ACGTcount: A:0.67, C:0.20, G:0.06, T:0.07
Consensus pattern (22 bp):
AAAATAGCACCAAAACAACAAA
Found at i:369994 original size:35 final size:35
Alignment explanation
Indices: 369920--370004 Score: 82
Period size: 35 Copynumber: 2.4 Consensus size: 35
369910 TCAAACAACC
* * *
369920 AAAATAACAACCAAAACAACAGAAAAAATAGCAAC
1 AAAATAACAACAAAAACAACAGAAAAAATAGAAAA
* **
369955 AAAATAACAATAAAAACAACA-CCAAAATAGTAAAA
1 AAAATAACAACAAAAACAACAGAAAAAATAG-AAAA
* *
369990 AAAATAGCACCAAAA
1 AAAATAACAACAAAA
370005 TAGTAAAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
34 7 0.17
35 33 0.82
ACGTcount: A:0.69, C:0.18, G:0.05, T:0.08
Consensus pattern (35 bp):
AAAATAACAACAAAAACAACAGAAAAAATAGAAAA
Found at i:370034 original size:43 final size:43
Alignment explanation
Indices: 369929--370090 Score: 139
Period size: 43 Copynumber: 3.7 Consensus size: 43
369919 CAAAATAACA
* * *
369929 ACCAAAACAACAGAAAAAATAGCAACAAAATAACAATAAAAACAAC
1 ACCAAAACAACA-AAAAAATAGCACCAAAATAGCAA-AAAAA-AGC
* *
369975 ACCAAAATAGTA-AAAAAAATAGCACCAAAATAGTAAAAAAAAGC
1 ACCAAAACA--ACAAAAAAATAGCACCAAAATAGCAAAAAAAAGC
* * * * * * *
370019 ATCAAAACAATAAAAACACAACACCAAAACAGCAAAAAATAGC
1 ACCAAAACAACAAAAAAATAGCACCAAAATAGCAAAAAAAAGC
*
370062 AACCAAAACAGCAAAAAAA-AGCACCAAAA
1 -ACCAAAACAACAAAAAAATAGCACCAAAA
370091 CAACGATATT
Statistics
Matches: 94, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
42 1 0.01
43 35 0.37
44 23 0.24
45 5 0.05
46 28 0.30
47 1 0.01
48 1 0.01
ACGTcount: A:0.67, C:0.20, G:0.06, T:0.07
Consensus pattern (43 bp):
ACCAAAACAACAAAAAAATAGCACCAAAATAGCAAAAAAAAGC
Found at i:370064 original size:24 final size:23
Alignment explanation
Indices: 369928--370092 Score: 77
Period size: 22 Copynumber: 7.4 Consensus size: 23
369918 CCAAAATAAC
*
369928 AACCAAAACAACAGAAAAAATAGC-
1 AACCAAAACAGCA-AAAAAA-AGCA
* * *
369952 AA-CAAAATAACAATAAAAA-CA
1 AACCAAAACAGCAAAAAAAAGCA
* *
369973 ACACCAAAATAGTAAAAAAAATAGC-
1 A-ACCAAAACAG-CAAAAAAA-AGCA
* *
369998 -ACCAAAATAGTAAAAAAAAGC-
1 AACCAAAACAGCAAAAAAAAGCA
* *
370019 -ATCAAAACA--ATAAAAACA-CA
1 AACCAAAACAGCA-AAAAAAAGCA
*
370039 ACACCAAAACAGCAAAAAATAGC-
1 A-ACCAAAACAGCAAAAAAAAGCA
370062 AACCAAAACAGCAAAAAAAAGC-
1 AACCAAAACAGCAAAAAAAAGCA
370084 -ACCAAAACA
1 AACCAAAACA
370093 ACGATATTTT
Statistics
Matches: 116, Mismatches: 12, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
19 2 0.02
20 7 0.06
21 21 0.18
22 41 0.35
23 33 0.28
24 10 0.09
25 1 0.01
26 1 0.01
ACGTcount: A:0.67, C:0.20, G:0.06, T:0.07
Consensus pattern (23 bp):
AACCAAAACAGCAAAAAAAAGCA
Found at i:370661 original size:52 final size:53
Alignment explanation
Indices: 370579--370971 Score: 233
Period size: 52 Copynumber: 7.6 Consensus size: 53
370569 TCTAATTATC
* * *
370579 TTAACTTAAAGTT-CTAGTTATCTTAACTAAAATCTAAATTATTATCTAATCTA
1 TTAATTTAAA-TTCCTAATTATCTTATCTAAAATCTAAATTATTATCTAATCTA
* * * **
370632 TTAA-TTAAATTCCTAATTTTATTATCTAAATTAAAAATTTAATTATCCTAA--T-
1 TTAATTTAAATTCCTAATTATCTTATCTAAAATCTAAA-TT-ATTAT-CTAATCTA
* * * *
370684 TCAATTTAAAGTCCT-A--A--TTATCT-AAATCTAAATTATTACCTAATATA
1 TTAATTTAAATTCCTAATTATCTTATCTAAAATCTAAATTATTATCTAATCTA
** * **
370731 TTAATTTAAATTATTAATCATCTTAAAT-AAAT-TAGAACTCTAATTATTCTAA--T-
1 TTAATTTAAATTCCTAATTATCTTATCTAAAATCTA-AA-T-T-ATTA-TCTAATCTA
* * *
370784 TTAATTTAAACTCCTAATTA-CGTTAACTAAAATCTAAATTATTATCTAACCTA
1 TTAATTTAAATTCCTAATTATC-TTATCTAAAATCTAAATTATTATCTAATCTA
* *
370837 TTAA-TTAAAATCCTAATTATCTTAT-TTAAAT-TAAAATT-TTAAT-T-ATCCTAA
1 TTAATTTAAATTCCTAATTATCTTATCTAAAATCT-AAATTATT-ATCTAAT-CT-A
* * *
370888 TTTAATTTAAACT-CTAATTATCTTAAT-TAATATCTAAATTATTATCTAACCTA
1 -TTAATTTAAATTCCTAATTATCTT-ATCTAAAATCTAAATTATTATCTAATCTA
*
370941 TTAATTTAAATTCCTAATTATCTTAACTAAA
1 TTAATTTAAATTCCTAATTATCTTATCTAAA
370972 TCAAATCTCT
Statistics
Matches: 265, Mismatches: 37, Indels: 76
0.70 0.10 0.20
Matches are distributed among these distances:
44 4 0.02
45 4 0.02
46 3 0.01
47 17 0.06
48 7 0.03
49 1 0.00
50 12 0.05
51 21 0.08
52 84 0.32
53 78 0.29
54 19 0.07
55 11 0.04
56 4 0.02
ACGTcount: A:0.42, C:0.12, G:0.01, T:0.45
Consensus pattern (53 bp):
TTAATTTAAATTCCTAATTATCTTATCTAAAATCTAAATTATTATCTAATCTA
Found at i:370854 original size:205 final size:203
Alignment explanation
Indices: 370507--371019 Score: 633
Period size: 205 Copynumber: 2.5 Consensus size: 203
370497 ATCTTAACAA
* ** * *
370507 AAATCTAAATTGTTATCTAATCTATTAACATAAATTATTAATTATTTTAAATTAATTAGAACTCT
1 AAATCTAAATTATTATCTAATCTATTAATTTAAATTATTAATTATCTTAAATAAATTAGAACTCT
* * * * *
370572 AATTATC----TTAACTTAAAGTTCTAGTTATCTTAACTAAAATCTAAATTATTATCTAATCTAT
66 AATTATCTAATTTAATTTAAACTCCTAATTA-CTTAACTAAAATCTAAATTATTATCTAACCTAT
* * *
370633 TAATTAAATTCCTAATTTTATTATCTAAATTAAAAATTTAATTATCCTAATTCAATTTAAAGTCC
130 TAATTAAAATCCTAATTATATTATCTAAATTAAAAATTTAATTATCCTAATTCAATTTAAACT-C
370698 TAATTATC-T
194 TAATTATCTT
* * *
370707 AAATCTAAATTATTACCTAATATATTAATTTAAATTATTAATCATCTTAAATAAATTAGAACTCT
1 AAATCTAAATTATTATCTAATCTATTAATTTAAATTATTAATTATCTTAAATAAATTAGAACTCT
370772 AATTATTCTAATTTAATTTAAACTCCTAATTACGTTAACTAAAATCTAAATTATTATCTAACCTA
66 AATTA-TCTAATTTAATTTAAACTCCTAATTAC-TTAACTAAAATCTAAATTATTATCTAACCTA
* * * *
370837 TTAATTAAAATCCTAATTATCTTATTTAAATTAAAATTTTAATTATCCTAATTTAATTTAAACTC
129 TTAATTAAAATCCTAATTATATTATCTAAATTAAAAATTTAATTATCCTAATTCAATTTAAACTC
370902 TAATTATCTTAATT
194 TAATTATC----TT
* ** * *
370916 AATATCTAAATTATTATCTAACCTATTAATTTAAATTCCTAATTATCTTAACTAAATCA-AATCT
1 AA-ATCTAAATTATTATCTAATCTATTAATTTAAATTATTAATTATCTTAAATAAATTAGAA-CT
* *
370980 CTAATTATCGTAATATATTTTAAACTCCTAATTACCTTAA
64 CTAATTATC-TAATTTAATTTAAACTCCTAATTA-CTTAA
371020 TCTACAAAAA
Statistics
Matches: 268, Mismatches: 30, Indels: 20
0.84 0.09 0.06
Matches are distributed among these distances:
200 62 0.23
201 2 0.01
204 10 0.04
205 103 0.38
209 7 0.03
210 83 0.31
211 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.02, T:0.44
Consensus pattern (203 bp):
AAATCTAAATTATTATCTAATCTATTAATTTAAATTATTAATTATCTTAAATAAATTAGAACTCT
AATTATCTAATTTAATTTAAACTCCTAATTACTTAACTAAAATCTAAATTATTATCTAACCTATT
AATTAAAATCCTAATTATATTATCTAAATTAAAAATTTAATTATCCTAATTCAATTTAAACTCTA
ATTATCTT
Found at i:370872 original size:26 final size:25
Alignment explanation
Indices: 370839--370917 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 25
370829 CTAACCTATT
370839 AATTAAAATCCTAATTATCTTATTTA
1 AATTAAAAT-CTAATTATCTTATTTA
* *
370865 AATTAAAATTTTAATTATCCTAATTTA
1 AATTAAAA-TCTAATTAT-CTTATTTA
* * *
370892 ATTTAAACTCTAATTATCTTAATTA
1 AATTAAAATCTAATTATCTTATTTA
370917 A
1 A
370918 TATCTAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
25 7 0.16
26 23 0.52
27 14 0.32
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (25 bp):
AATTAAAATCTAATTATCTTATTTA
Found at i:370880 original size:105 final size:105
Alignment explanation
Indices: 370484--371019 Score: 508
Period size: 105 Copynumber: 5.2 Consensus size: 105
370474 CGAGAAACAC
* * * * * ** **
370484 TAAACTTCAAATTATCTTAACAAAAATCTAAATTGTTATCTAATCTATTAACATAAATTATTAAT
1 TAAACTCCTAATTA-CTTAACTAAAATCTAAATTATTATCTAACCTATTAATTTAAATTCCTAAT
* * * * * *
370549 TATTTTAAATTAATTAGAACTCTAATTAT-C----TTAACT
65 TATCTTAACTAAATTAAAATTCTAATTATCCTAATTTAATT
* * * *
370585 TAAAGTTCTAGTTATCTTAACTAAAATCTAAATTATTATCTAATCTATTAA-TTAAATTCCTAAT
1 TAAACTCCTAATTA-CTTAACTAAAATCTAAATTATTATCTAACCTATTAATTTAAATTCCTAAT
* * * *
370649 TTTATTATCTAAATTAAAAATT-TAATTATCCTAATTCAATT
65 TATCTTAACTAAATT-AAAATTCTAATTATCCTAATTTAATT
* * ** ** *
370690 TAAAGTCCTAATTA--T--CT-AAATCTAAATTATTACCTAATATATTAATTTAAATTATTAATC
1 TAAACTCCTAATTACTTAACTAAAATCTAAATTATTATCTAACCTATTAATTTAAATTCCTAATT
* * * *
370750 ATCTTAAATAAATTAGAACTCTAATTATTCTAATTTAATT
66 ATCTTAACTAAATTAAAATTCTAATTATCCTAATTTAATT
*
370790 TAAACTCCTAATTACGTTAACTAAAATCTAAATTATTATCTAACCTATTAA-TTAAAATCCTAAT
1 TAAACTCCTAATTAC-TTAACTAAAATCTAAATTATTATCTAACCTATTAATTTAAATTCCTAAT
** *
370854 TATCTTATTTAAATTAAAATTTTAATTATCCTAATTTAATT
65 TATCTTAACTAAATTAAAATTCTAATTATCCTAATTTAATT
* *
370895 TAAACT-CTAATTATCTTAATTAATATCTAAATTATTATCTAACCTATTAATTTAAATTCCTAAT
1 TAAACTCCTAATTA-CTTAACTAAAATCTAAATTATTATCTAACCTATTAATTTAAATTCCTAAT
* * * *
370959 TATCTTAACTAAA-TCAAATCTCTAATTATCGTAATATATTT
65 TATCTTAACTAAATTAAAAT-TCTAATTATCCTAATTTAATT
371000 TAAACTCCTAATTACCTTAA
1 TAAACTCCTAATTA-CTTAA
371020 TCTACAAAAA
Statistics
Matches: 360, Mismatches: 57, Indels: 31
0.80 0.13 0.07
Matches are distributed among these distances:
99 30 0.08
100 80 0.22
101 51 0.14
102 1 0.00
103 1 0.00
104 45 0.12
105 115 0.32
106 37 0.10
ACGTcount: A:0.42, C:0.13, G:0.01, T:0.44
Consensus pattern (105 bp):
TAAACTCCTAATTACTTAACTAAAATCTAAATTATTATCTAACCTATTAATTTAAATTCCTAATT
ATCTTAACTAAATTAAAATTCTAATTATCCTAATTTAATT
Found at i:371002 original size:53 final size:49
Alignment explanation
Indices: 370596--371019 Score: 210
Period size: 53 Copynumber: 8.2 Consensus size: 49
370586 AAAGTTCTAG
*
370596 TTATCTTAACTAAAATCTAAATT-ATTATCTAATCTATTAA-TTAAATTCCTAA
1 TTATCTTAACT-AAATC-AAATTAATTATCTAA--TA-TAATTTAAACTCCTAA
* * * * *
370648 TTTTATTATCTAAATTAAAAATTTAATTATCCTAAT-TCAATTTAAAGTCCTAA
1 TTATCTTAACTAAA-T-CAAA-TTAATTAT-CTAATAT-AATTTAAACTCCTAA
* * **
370701 TTA---T--CTAAATCTAAATT-ATTACCTAATATATTAATTTAAATTATTAA
1 TTATCTTAACTAAATC-AAATTAATTATCT-A-ATA-TAATTTAAACTCCTAA
* * * *
370748 TCATCTTAAATAAATTAGAACTCTAATTATTCTAATTTAATTTAAACTCCTAA
1 TTATCTTAACTAAATCA-AA-T-TAATTA-TCTAATATAATTTAAACTCCTAA
*
370801 TTA-CGTTAACTAAAATCTAAATT-ATTATCTAACCTATTAA-TTAAAATCCTAA
1 TTATC-TTAACT-AAATC-AAATTAATTATCTAA--TA-TAATTTAAACTCCTAA
** * *
370853 TTATCTTATTTAAATTAAAATTTTAATTATCCTAATTTAATTTAAACT-CTAA
1 TTATCTTAACTAAA-TCAAA--TTAATTAT-CTAATATAATTTAAACTCCTAA
* *
370905 TTATCTTAATTAATATCTAAATT-ATTATCTAACCTATTAATTTAAATTCCTAA
1 TTATCTTAACTAA-ATC-AAATTAATTATCTAA--TA-TAATTTAAACTCCTAA
*
370958 TTATCTTAACTAAATCAAATCTCTAATTATCGTAATATATTTTAAACTCCTAA
1 TTATCTTAACTAAATCAAA--T-TAATTATC-TAATATAATTTAAACTCCTAA
*
371011 TTACCTTAA
1 TTATCTTAA
371020 TCTACAAAAA
Statistics
Matches: 289, Mismatches: 37, Indels: 91
0.69 0.09 0.22
Matches are distributed among these distances:
44 2 0.01
45 5 0.02
46 4 0.01
47 18 0.06
48 6 0.02
49 4 0.01
50 12 0.04
51 21 0.07
52 76 0.26
53 94 0.33
54 22 0.08
55 20 0.07
56 5 0.02
ACGTcount: A:0.42, C:0.13, G:0.01, T:0.44
Consensus pattern (49 bp):
TTATCTTAACTAAATCAAATTAATTATCTAATATAATTTAAACTCCTAA
Found at i:371980 original size:30 final size:30
Alignment explanation
Indices: 371887--371981 Score: 163
Period size: 30 Copynumber: 3.2 Consensus size: 30
371877 ACTTATTTTA
**
371887 TTGTTAATTTTGTTGTTATTTTAGAGGCAT
1 TTGTTAATTTTGTTACTATTTTAGAGGCAT
*
371917 TTGATAATTTTGTTACTATTTTAGAGGCAT
1 TTGTTAATTTTGTTACTATTTTAGAGGCAT
371947 TTGTTAATTTTGTTACTATTTTAGAGGCAT
1 TTGTTAATTTTGTTACTATTTTAGAGGCAT
371977 TTGTT
1 TTGTT
371982 TATTAAGTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.22, C:0.05, G:0.18, T:0.55
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAGAGGCAT
Found at i:375480 original size:22 final size:22
Alignment explanation
Indices: 375455--375507 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
375445 TAGAAGTATA
*
375455 AGAGCCCTTTATGGGACGTT-TG
1 AGAGCCCTTCATGGGAC-TTATG
*
375477 AGAGCCCCTCATGGGACTTATG
1 AGAGCCCTTCATGGGACTTATG
375499 AGAGCCCTT
1 AGAGCCCTT
375508 AGTAGGAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (22 bp):
AGAGCCCTTCATGGGACTTATG
Found at i:375605 original size:26 final size:27
Alignment explanation
Indices: 375538--375612 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 27
375528 ATGGCCATGT
*
375538 CATTATCCTAAATGTGGGAAGTTCGCAAG
1 CATTAT-CT-AATGTGGGAAGTTCACAAG
* * * *
375567 GACTATTTTATGT-GGAAGTTCACAAG
1 CATTATCTAATGTGGGAAGTTCACAAG
375593 CATTATCTAATGTGGGAAGT
1 CATTATCTAATGTGGGAAGT
375613 CCGCTTGGAC
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
26 21 0.58
27 10 0.28
28 1 0.03
29 4 0.11
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (27 bp):
CATTATCTAATGTGGGAAGTTCACAAG
Found at i:378910 original size:51 final size:51
Alignment explanation
Indices: 378815--379037 Score: 272
Period size: 51 Copynumber: 4.3 Consensus size: 51
378805 TGATAACATA
* *
378815 TAGTCATCGGACCTCTT-GTTC-TATATAGGAATTCATATACTCACGATGACACT
1 TAGTCATCGGACCT-TTAATTCGTA-A-AGG-ATTCATTTACTCACGATGACACT
* * * * *
378868 GAGTCATCGGACCCTTAATTCATCATGGATTCATTTACTCACGATGACACT
1 TAGTCATCGGACCTTTAATTCGTAAAGGATTCATTTACTCACGATGACACT
* *
378919 TAGTCATCGGACCTTTAA-TCTGTAAAGGATTCATTTACTCATGATGACTCT
1 TAGTCATCGGACCTTTAATTC-GTAAAGGATTCATTTACTCACGATGACACT
*
378970 TAGTCATCGGACCTTTAATTCGTAAAGGACTCATTTACTCACGATGACACT
1 TAGTCATCGGACCTTTAATTCGTAAAGGATTCATTTACTCACGATGACACT
*
379021 TAGTCATCAGACTCTTT
1 TAGTCATCGGAC-CTTT
379038 CGTTTATAGC
Statistics
Matches: 148, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
50 2 0.01
51 119 0.80
52 10 0.07
53 16 0.11
54 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (51 bp):
TAGTCATCGGACCTTTAATTCGTAAAGGATTCATTTACTCACGATGACACT
Found at i:384923 original size:29 final size:28
Alignment explanation
Indices: 384891--385110 Score: 190
Period size: 30 Copynumber: 7.4 Consensus size: 28
384881 ATATTTCTAC
*
384891 CCCCAAACTTCTTAAAAATTCATATTTGA
1 CCCCAAACTTTTTAAAAATTCAT-TTTGA
* * * *
384920 CCCCTTAACTTTCTAAAAAATACATTTTGG
1 CCCC-AAACTTT-TTAAAAATTCATTTTGA
* *
384950 CCCCTTAAACTTCTTAAAAATT-ATAATTTAA
1 CCCC--AAACTTTTTAAAAATTCAT--TTTGA
*
384981 CCCTTAAACTTTTTAAAAATTTCATTTTGA
1 CCC-CAAACTTTTTAAAAA-TTCATTTTGA
*
385011 CCCTCAAACTTTTTAAAAATTTTATTTTGA
1 CCC-CAAACTTTTTAAAAA-TTCATTTTGA
385041 TCCCCAAACTTTTTAAAAATTCATTTTGA
1 -CCCCAAACTTTTTAAAAATTCATTTTGA
* *
385070 TACCCAAACTTTTTGAAAATTGCATTTTGA
1 -CCCCAAACTTTTTAAAAATT-CATTTTGA
* *
385100 ACCCATACTTT
1 CCCCAAACTTT
385111 CCAAAATTTT
Statistics
Matches: 161, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
29 44 0.27
30 88 0.55
31 27 0.17
32 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.40
Consensus pattern (28 bp):
CCCCAAACTTTTTAAAAATTCATTTTGA
Found at i:384964 original size:61 final size:60
Alignment explanation
Indices: 384889--385031 Score: 173
Period size: 61 Copynumber: 2.4 Consensus size: 60
384879 TTATATTTCT
* *
384889 ACCCCCAAACTTCTTAAAAATTCAT-ATTTGACCCCTT-AACTTTCTAAAAAATACATTTTGG
1 ACCCTCAAACTTCTTAAAAATT-ATAATTT-AACCCTTAAACTTTCTAAAAAATACATTTT-G
* * * * *
384950 CCCCTTAAACTTCTTAAAAATTATAATTTAACCCTTAAACTTTTTAAAAATTTCATTTTG
1 ACCCTCAAACTTCTTAAAAATTATAATTTAACCCTTAAACTTTCTAAAAAATACATTTTG
*
385010 ACCCTCAAACTTTTTAAAAATT
1 ACCCTCAAACTTCTTAAAAATT
385032 TTATTTTGAT
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
60 28 0.40
61 42 0.60
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (60 bp):
ACCCTCAAACTTCTTAAAAATTATAATTTAACCCTTAAACTTTCTAAAAAATACATTTTG
Found at i:385089 original size:59 final size:60
Alignment explanation
Indices: 384894--385099 Score: 170
Period size: 61 Copynumber: 3.4 Consensus size: 60
384884 TTTCTACCCC
* * * * * **
384894 CAAACTTCTTAAAAATT-CATATTTGA-CCCCTTAACTTTCTAAAAAATACATTTTGGCCCCT
1 CAAACTTTTTAAAAATTGCAT-TTTGATCCCC-AAACTTTTTAAAAATTTCATTTT-GAACCT
* * ** * * * *
384955 TAAACTTCTTAAAAATTATAATTT-AACCCTTAAACTTTTTAAAAATTTCATTTTGACCCT
1 CAAACTTTTTAAAAATTGCATTTTGATCCC-CAAACTTTTTAAAAATTTCATTTTGAACCT
**
385015 CAAACTTTTTAAAAATTTTATTTTGATCCCCAAACTTTTTAAAAA-TTCATTTTGATACC-
1 CAAACTTTTTAAAAATTGCATTTTGATCCCCAAACTTTTTAAAAATTTCATTTTGA-ACCT
*
385074 CAAACTTTTTGAAAATTGCATTTTGA
1 CAAACTTTTTAAAAATTGCATTTTGA
385100 ACCCATACTT
Statistics
Matches: 121, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
59 33 0.27
60 42 0.35
61 45 0.37
62 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.41
Consensus pattern (60 bp):
CAAACTTTTTAAAAATTGCATTTTGATCCCCAAACTTTTTAAAAATTTCATTTTGAACCT
Found at i:388200 original size:2 final size:2
Alignment explanation
Indices: 388193--388223 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
388183 TTATAAATTC
388193 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
388224 CAATTTTTCT
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:407052 original size:12 final size:12
Alignment explanation
Indices: 407035--407063 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
407025 GTGGAGATCT
407035 GCTTCAAAGATG
1 GCTTCAAAGATG
407047 GCTTCAAAGATG
1 GCTTCAAAGATG
407059 GCTTC
1 GCTTC
407064 TATGGTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (12 bp):
GCTTCAAAGATG
Found at i:407238 original size:25 final size:23
Alignment explanation
Indices: 407209--407254 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
407199 GTTGGATCCA
407209 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
407234 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
407255 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:408287 original size:12 final size:11
Alignment explanation
Indices: 408252--408304 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
408242 CACAAACATA
408252 TTTTTCTC-TT
1 TTTTTCTCATT
*
408262 TTTCTTCTCTTT
1 TTT-TTCTCATT
408274 TTTTTCTCAATT
1 TTTTTCTC-ATT
*
408286 TTTTTTTCAATT
1 TTTTTCTC-ATT
408298 TTTTTCT
1 TTTTTCT
408305 TTTTTTCAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 3 0.08
11 10 0.27
12 24 0.65
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTTCTCATT
Found at i:408288 original size:14 final size:12
Alignment explanation
Indices: 408271--408302 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
408261 TTTTCTTCTC
408271 TTTTTTTTCTCAA
1 TTTTTTTT-TCAA
408284 TTTTTTTTTCAA
1 TTTTTTTTTCAA
408296 TTTTTTT
1 TTTTTTT
408303 CTTTTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:408299 original size:10 final size:10
Alignment explanation
Indices: 408286--408317 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
408276 TTTCTCAATT
408286 TTTTTTTCAA
1 TTTTTTTCAA
408296 TTTTTTTC--
1 TTTTTTTCAA
408304 TTTTTTTCAA
1 TTTTTTTCAA
408314 TTTT
1 TTTT
408318 CTTCGACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.40
10 12 0.60
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:410859 original size:14 final size:13
Alignment explanation
Indices: 410827--410869 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
410817 AAGAACCTAT
*
410827 AAAA-TAAAATAA
1 AAAATTAAATTAA
410839 AATAATTAAATGTAA
1 AA-AATTAAAT-TAA
410854 AAAATTAAATTAA
1 AAAATTAAATTAA
410867 AAA
1 AAA
410870 CAAAAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 2 0.07
13 8 0.30
14 12 0.44
15 5 0.19
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (13 bp):
AAAATTAAATTAA
Found at i:410877 original size:22 final size:22
Alignment explanation
Indices: 410852--410897 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
410842 AATTAAATGT
* *
410852 AAAAAATTAAATTAAAAACAAA
1 AAAAAATGAAAATAAAAACAAA
* *
410874 AAAATATGAAAATAAAAATAAA
1 AAAAAATGAAAATAAAAACAAA
410896 AA
1 AA
410898 TGGCTAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (22 bp):
AAAAAATGAAAATAAAAACAAA
Found at i:411987 original size:25 final size:23
Alignment explanation
Indices: 411959--412004 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
411949 GTTGGATCCA
411959 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
411984 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
412005 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:413933 original size:21 final size:22
Alignment explanation
Indices: 413887--413937 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
413877 ATAGTGCAGA
*
413887 CTTCTACCGATACCTATGACAG
1 CTTCTACCGATACCAATGACAG
413909 -TTCTACCGATA-CAAGTGA-AG
1 CTTCTACCGATACCAA-TGACAG
413929 CTTCTACCG
1 CTTCTACCG
413938 GTACTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.27
Consensus pattern (22 bp):
CTTCTACCGATACCAATGACAG
Found at i:414745 original size:106 final size:107
Alignment explanation
Indices: 414619--414816 Score: 274
Period size: 106 Copynumber: 1.9 Consensus size: 107
414609 ATCCGTAAAA
* * *
414619 GATTCATATAGTCACGATGACACATAATCATTAGACCTCATAATCCGTAA-AGGATTCATAT-AC
1 GATTCATATACTCACGATGACACATAATCATCAGACCTCATAATCCATAATAGGATTCATATAAC
* *
414682 TCACGATGACACATAGTCATCAGACCTCATAAGTCATAATAG
66 TCACGATGACACAGAGTCATCAAACCTCATAAGTCATAATAG
* * *
414724 GATTCATATAACTCACGATGACACGTAGTCATCGGACCTCATAATCCATAATAGGATTCATATAA
1 GATTCATAT-ACTCACGATGACACATAATCATCAGACCTCATAATCCATAATAGGATTCATATAA
* * *
414789 CTCATGATGATATAGAGTCATCAAACCT
65 CTCACGATGACACAGAGTCATCAAACCT
414817 TTTGCATTTA
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
105 9 0.11
106 35 0.44
107 11 0.14
108 24 0.30
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (107 bp):
GATTCATATACTCACGATGACACATAATCATCAGACCTCATAATCCATAATAGGATTCATATAAC
TCACGATGACACAGAGTCATCAAACCTCATAAGTCATAATAG
Found at i:414753 original size:54 final size:53
Alignment explanation
Indices: 414576--414816 Score: 267
Period size: 54 Copynumber: 4.6 Consensus size: 53
414566 TTCTCATTTA
* ** * * *
414576 ATACTCATGATGACAC--AGTCATGGGACCTTATAATCCGTAA-AAGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCATAATAGGATTCAT
* * * *
414626 ATAGTCACGATGACACATAATCATTAGACCTCATAATCCGTAA-AGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCATAATAGGATTCAT
414678 ATACTCACGATGACACATAGTCATCAGACCTCATAAGT-CATAATAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAA-TCCATAATAGGATTCAT
* *
414731 ATAACTCACGATGACACGTAGTCATCGGACCTCATAATCCATAATAGGATTCAT
1 AT-ACTCACGATGACACATAGTCATCAGACCTCATAATCCATAATAGGATTCAT
* * * * *
414785 ATAACTCATGATGATATAGAGTCATCAAACCT
1 AT-ACTCACGATGACACATAGTCATCAGACCT
414817 TTTGCATTTA
Statistics
Matches: 165, Mismatches: 20, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
50 14 0.08
52 66 0.40
53 13 0.08
54 72 0.44
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (53 bp):
ATACTCACGATGACACATAGTCATCAGACCTCATAATCCATAATAGGATTCAT
Done.