Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1094.1
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: 579465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 7165 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:18101 original size:31 final size:31
Alignment explanation
Indices: 18062--18189 Score: 184
Period size: 31 Copynumber: 4.1 Consensus size: 31
18052 CTTAGATAAT
* * *
18062 TTGAAAGAGTTTTATTAGCATTCAATTTCTT
1 TTGAAAGAGTTTTATTAGGATTCAATTACTC
* * * *
18093 TTTAAAGAGTTTTTATTATGATTAAATTCCTC
1 TTGAAAGAG-TTTTATTAGGATTCAATTACTC
18125 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTGAAAGAGTTTTATTAGGATTCAATTACTC
18156 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTGAAAGAGTTTTATTAGGATTCAATTACTC
18187 TTG
1 TTG
18190 TAATTTGCCT
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 61 0.71
32 25 0.29
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTGAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:18134 original size:63 final size:62
Alignment explanation
Indices: 18062--18189 Score: 184
Period size: 63 Copynumber: 2.0 Consensus size: 62
18052 CTTAGATAAT
* * * * *
18062 TTGAAAGAGTTTTATTAGCATTCAATTTCTTTTTAAAGAGTTTTTATTATGATTAAATTCCTC
1 TTGAAAGAGTTTTATTAGCATTCAATTACTCTTGAAAGAG-TTTTATTAGGATTAAATTACTC
* *
18125 TTGAAAGAGTTTTATTAGGATTCAATTACTCTTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTGAAAGAGTTTTATTAGCATTCAATTACTCTTGAAAGAGTTTTATTAGGATTAAATTACTC
18187 TTG
1 TTG
18190 TAATTTGCCT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
62 22 0.38
63 36 0.62
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.46
Consensus pattern (62 bp):
TTGAAAGAGTTTTATTAGCATTCAATTACTCTTGAAAGAGTTTTATTAGGATTAAATTACTC
Found at i:21398 original size:21 final size:24
Alignment explanation
Indices: 21354--21401 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 24
21344 CGAATTACTT
*
21354 ATTCGAATTGACTCAAATAATTCA
1 ATTCGAATTAACTCAAATAATTCA
21378 ATTCG-ATTAACT-AAA-AATTCA
1 ATTCGAATTAACTCAAATAATTCA
21399 ATT
1 ATT
21402 TAATTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 3 0.13
23 6 0.26
24 5 0.22
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (24 bp):
ATTCGAATTAACTCAAATAATTCA
Found at i:27539 original size:96 final size:96
Alignment explanation
Indices: 27375--27570 Score: 383
Period size: 96 Copynumber: 2.0 Consensus size: 96
27365 ATCCCAAAAA
*
27375 TTTTAAGGACGAGTATTATCCTCAAACTTATCAAAACAGGATTAAAGTTCAATGTATGTGGGATA
1 TTTTAAGGACGAGTATTATCCTCAAACTCATCAAAACAGGATTAAAGTTCAATGTATGTGGGATA
27440 GCAAATGAGGATAGTGCAAGTTGTCTAGGTG
66 GCAAATGAGGATAGTGCAAGTTGTCTAGGTG
27471 TTTTAAGGACGAGTATTATCCTCAAACTCATCAAAACAGGATTAAAGTTCAATGTATGTGGGATA
1 TTTTAAGGACGAGTATTATCCTCAAACTCATCAAAACAGGATTAAAGTTCAATGTATGTGGGATA
27536 GCAAATGAGGATAGTGCAAGTTGTCTAGGTG
66 GCAAATGAGGATAGTGCAAGTTGTCTAGGTG
27567 TTTT
1 TTTT
27571 GAGAGATATG
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 99 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (96 bp):
TTTTAAGGACGAGTATTATCCTCAAACTCATCAAAACAGGATTAAAGTTCAATGTATGTGGGATA
GCAAATGAGGATAGTGCAAGTTGTCTAGGTG
Found at i:31280 original size:24 final size:24
Alignment explanation
Indices: 31248--31295 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31238 AAATTAAGTA
31248 AAAAAATTTCAAATTAATCGAGTT
1 AAAAAATTTCAAATTAATCGAGTT
* * * *
31272 AAAAGATTTTAAGTTAATTGAGTT
1 AAAAAATTTCAAATTAATCGAGTT
31296 GACGAGTCCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (24 bp):
AAAAAATTTCAAATTAATCGAGTT
Found at i:35125 original size:18 final size:20
Alignment explanation
Indices: 35091--35134 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
35081 TGCCAGGATT
35091 TATACTTTGCAATATATATA
1 TATACTTTGCAATATATATA
35111 TATACTTTGCAATATATATA
1 TATACTTTGCAATATATATA
35131 TATA
1 TATA
35135 GTTTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (20 bp):
TATACTTTGCAATATATATA
Found at i:45140 original size:16 final size:16
Alignment explanation
Indices: 45118--45186 Score: 111
Period size: 16 Copynumber: 4.2 Consensus size: 16
45108 TTTGGTTCGC
45118 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
45134 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
45150 TGTATTGGGATTAAAGG
1 TGTATT-GGATTAGAGG
45167 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
45183 TGTA
1 TGTA
45187 ATAGCTAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
16 33 0.69
17 15 0.31
ACGTcount: A:0.26, C:0.01, G:0.36, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:45172 original size:33 final size:32
Alignment explanation
Indices: 45118--45186 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
45108 TTTGGTTCGC
*
45118 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAAAGGCGTATTGGATTAGAGG
*
45150 TGTATTGGGATTAAAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAAAGGCGTATTGGATTAGAGG
45183 TGTA
1 TGTA
45187 ATAGCTAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.26, C:0.01, G:0.36, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAAAGGCGTATTGGATTAGAGG
Found at i:45251 original size:44 final size:45
Alignment explanation
Indices: 45167--45257 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
45157 GGATTAAAGG
* * *
45167 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
45212 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
45256 TG
1 TG
45258 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:45443 original size:18 final size:17
Alignment explanation
Indices: 45422--45456 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
45412 TTATTATTAA
*
45422 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
45440 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
45457 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:47940 original size:13 final size:13
Alignment explanation
Indices: 47896--47954 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
47886 GATGTTGGTG
47896 ATATTTTTAATTA
1 ATATTTTTAATTA
* *
47909 AT-TAATTTAGATAA
1 ATAT-TTTTA-ATTA
47923 ATATTTTTAATTA
1 ATATTTTTAATTA
47936 ATA-TTTT-ATTA
1 ATATTTTTAATTA
*
47947 AGATTTTT
1 ATATTTTT
47955 CGTATTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
11 6 0.16
12 9 0.24
13 12 0.32
14 9 0.24
15 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
ATATTTTTAATTA
Found at i:53218 original size:33 final size:27
Alignment explanation
Indices: 53145--53198 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
53135 AACATAAAAG
*
53145 GGGGTTGCTAAGTGCTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCAAA
53172 GGGGTTGCTAAGTGCTGATTCCCCAAA
1 GGGGTTGCTAAGTGCTGATTCCCCAAA
53199 TTATCGGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGATTCCCCAAA
Found at i:53296 original size:33 final size:33
Alignment explanation
Indices: 53254--53380 Score: 121
Period size: 33 Copynumber: 3.6 Consensus size: 33
53244 GCAAAAGGGG
* *
53254 GGTTGCTAAGTGTTGATTCCCCAAATCATCGGT
1 GGTTGCTAAGTGCTGATTCCCCAAATCATAGGT
*
53287 GGTTGCTAAGTGCTGATTCCACCGTAACGGATTGTATAAGG-
1 GGTTGCTAAGTGCTGATTCC-CC--AA---A-T-CAT-AGGT
* *
53328 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCAAATCATAGGT
53361 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
53381 ACCATATTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
32 2 0.03
33 41 0.53
34 3 0.04
35 1 0.01
36 2 0.03
38 1 0.01
39 1 0.01
40 3 0.04
41 22 0.28
42 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCAAATCATAGGT
Found at i:53305 original size:80 final size:80
Alignment explanation
Indices: 53172--53429 Score: 366
Period size: 80 Copynumber: 3.3 Consensus size: 80
53162 ATTCCCCCAA
* *
53172 GGGGTTGCTAAGTGCTGATTCCCCAAATTATCGGTGGTTGCTAAGTGTTGATTCCACCATATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCATATTTT
53237 TGAATGTGCAAAAGG
66 TGAATGTGCAAAAGG
* * *
53252 GGGGTTGCTAAGTGTTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCGTA---A
1 GGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCATATTTT
* * * *
53314 CGGAT-TGTATAA--
66 TGAATGTGCAAAAGG
* *
53326 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCATATTTT
*
53391 TTAATGTGCAAAAGG
66 TGAATGTGCAAAAGG
53406 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
53430 CAAGGGGTTG
Statistics
Matches: 153, Mismatches: 19, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
74 57 0.37
76 5 0.03
77 5 0.03
78 5 0.03
80 81 0.53
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (80 bp):
GGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCATATTTT
TGAATGTGCAAAAGG
Found at i:53439 original size:74 final size:77
Alignment explanation
Indices: 53172--53454 Score: 314
Period size: 74 Copynumber: 3.7 Consensus size: 77
53162 ATTCCCCCAA
* *
53172 GGGGTTGCTAAGTGCTGATTCCCCAAATTATCGGTGGTTGCTAAGTGTTGATTCCACCATATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCACA-TA--GGTGGTTGCTAAGTGCTGATTCCACCATATTTT
53237 TGAATGTGCAAAAGG
63 TGAATGTGCAAAAGG
* * * *
53252 GGGGTTGCTAAGTGTTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCGTA---A
1 GGGGTTGCTAAGTGCTGATTCCCC--A-CATAGGTGGTTGCTAAGTGCTGATTCCACCATATTTT
* * * *
53314 CGGAT-TGTATAA--
63 TGAATGTGCAAAAGG
*
53326 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATTTT
1 GGGGTTGCTAAGTGCTGATTCCCC--A-CATAGGTGGTTGCTAAGTGCTGATTCCACCATATTTT
*
53391 TTAATGTGCAAAAGG
63 TGAATGTGCAAAAGG
53406 GGGGTTGCTAAGTGCTGATTCCCC-CA-AGG-GGTTGCTAAGTGCTGATTCC
1 GGGGTTGCTAAGTGCTGATTCCCCACATAGGTGGTTGCTAAGTGCTGATTCC
53455 CCCAAATAAC
Statistics
Matches: 173, Mismatches: 21, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
74 77 0.45
75 2 0.01
76 7 0.04
77 5 0.03
78 5 0.03
80 74 0.43
82 2 0.01
83 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (77 bp):
GGGGTTGCTAAGTGCTGATTCCCCACATAGGTGGTTGCTAAGTGCTGATTCCACCATATTTTTGA
ATGTGCAAAAGG
Found at i:53442 original size:27 final size:27
Alignment explanation
Indices: 53406--53459 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
53396 GTGCAAAAGG
53406 GGGGTTGCTAAGTGCTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
53433 GGGGTTGCTAAGTGCTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
53460 ATAACNTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:53479 original size:29 final size:29
Alignment explanation
Indices: 53409--53494 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
53399 CAAAAGGGGG
***
53409 GTTGCTAAGTGCTGATTCCCCC-AA-GGG
1 GTTGCTAAGTGCTGATTCCCCCAAATAAC
53436 GTTGCTAAGTGCTGATTCCCCCAAATAAC
1 GTTGCTAAGTGCTGATTCCCCCAAATAAC
* * *
53465 NTTGCTAAGTGCTGAATCCACCAAATAAC
1 GTTGCTAAGTGCTGATTCCCCCAAATAAC
53494 G
1 G
53495 GTTAATATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 22 0.44
28 2 0.04
29 26 0.52
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (29 bp):
GTTGCTAAGTGCTGATTCCCCCAAATAAC
Found at i:63268 original size:49 final size:49
Alignment explanation
Indices: 63196--63294 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
63186 TAGTCAAATG
63196 GGAAAGAGCCGTAGGCAGTCTAAGAAGAGGTGTACAAAACCGACTCAGA
1 GGAAAGAGCCGTAGGCAGTCTAAGAAGAGGTGTACAAAACCGACTCAGA
*
63245 GGAAAGAGTCGTAGGCAGTCTAAGAAGAGGTGTACAAAACCGACTCAGA
1 GGAAAGAGCCGTAGGCAGTCTAAGAAGAGGTGTACAAAACCGACTCAGA
63294 G
1 G
63295 TTTCATTAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.38, C:0.17, G:0.31, T:0.13
Consensus pattern (49 bp):
GGAAAGAGCCGTAGGCAGTCTAAGAAGAGGTGTACAAAACCGACTCAGA
Found at i:63581 original size:13 final size:13
Alignment explanation
Indices: 63565--63594 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
63555 ATTGTCATGT
63565 AATTGTTTTTCTG
1 AATTGTTTTTCTG
63578 AATTGTTTTTCTG
1 AATTGTTTTTCTG
63591 AATT
1 AATT
63595 TAGCTGATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (13 bp):
AATTGTTTTTCTG
Found at i:64562 original size:82 final size:81
Alignment explanation
Indices: 64471--64720 Score: 186
Period size: 82 Copynumber: 3.1 Consensus size: 81
64461 CATATAAGAA
*
64471 TATTAATTATTAAGAATTTTATTAAATTATATATTTTAAGTATAATATATTTAATAATAATTATG
1 TATTTATTATTAAGAATTTTATTAAATTATATATTTTAA-TATAATATATTTAATAATAATTATG
64536 TTTAAATATGATTAAAT
65 TTTAAATATGATTAAAT
* * * * * * * *
64553 TATTTATTATT---CATATTAATAATCTTATCAAAATTTAA-ATAACA-A--TAACAATAA-TA-
1 TATTTATTATTAAGAATTTTATTAA-ATTAT-ATATTTTAATATAATATATTTAATAATAATTAT
* *
64609 ATTTACCAA-A--A-CAAAT
64 GTTTA--AATATGATTAAAT
* *
64625 T-TCTGGTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATGTTTAATAATAAT
1 TAT-T--T-ATTATTAAGAATTTTATTAAATTATATATTTTAA-TATAATATATTTAATAATAAT
*
64689 TATGTTTAAATATGATTAAAA
61 TATGTTTAAATATGATTAAAT
64710 TATTTATTATT
1 TATTTATTATT
64721 GATAATAATA
Statistics
Matches: 121, Mismatches: 24, Indels: 46
0.63 0.13 0.24
Matches are distributed among these distances:
71 1 0.01
72 6 0.05
73 1 0.01
74 5 0.04
75 9 0.07
76 17 0.14
77 4 0.03
78 13 0.11
79 13 0.11
80 4 0.03
81 17 0.14
82 19 0.16
83 5 0.04
84 1 0.01
85 5 0.04
86 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (81 bp):
TATTTATTATTAAGAATTTTATTAAATTATATATTTTAATATAATATATTTAATAATAATTATGT
TTAAATATGATTAAAT
Found at i:64821 original size:157 final size:153
Alignment explanation
Indices: 64485--64929 Score: 371
Period size: 157 Copynumber: 2.8 Consensus size: 153
64475 AATTATTAAG
* *
64485 AATTTTATTAAATTATATATTTTAAGTATAATATATTTAATAATAATTATGTTTAAATATGATTA
1 AATTTTATTAAATTATAAATTTTAA-TAAAATAT-TTTAATAATAATTATGTTTAAATATGATTA
* * * * * *
64550 AATTATTTATTATTCATATTAATAATCTTATCAAAAT-T-TAA-ATAACAATAA--CAATAATAA
64 AAATATTTATTATT-ATAATAATAATCTTATTAAAATATATAATTTAATAA-AATTC-TTAATAA
64610 TTTACCAAAACAAATTTCTGGTAATTATT
126 -TTACCAAAACAAATTTCTGGTAATTATT
*
64639 AAGAATTTTATTAAATTATATATTTTAATTAAAATATGTTTAATAATAATTATGTTTAAATATGA
1 ---AATTTTATTAAATTATAAATTTTAA-TAAAATAT-TTTAATAATAATTATGTTTAAATATGA
64704 TTAAAATATTTATTATTGATAATAATAATCTTATTAAAATATATAATTTAATAAAATTCTTAATA
61 TTAAAATATTTATTATT-ATAATAATAATCTTATTAAAATATATAATTTAATAAAATTCTTAATA
* ** *
64769 ATTACCAGAA-ATTTGTTTTGGTAAATTATT
125 ATTACCAAAACAAAT-TTCTGGT-AATTATT
** * * * *
64799 -ATTGTTATTGTTATT-TAAATTTTGATAAGATTATTAATATGAATAATAAATA-ATTT-AATCA
1 AATT-TTATT-AAATTATAAATTTTAATAA-AATATT--T-T-AATAATAATTATGTTTAAAT-A
*
64860 T-ATTTAAACATAATTATTATTA-AAT-AT-AT-TATACTTAAAATATATAATTTAATAAAATTC
58 TGA-TTAAA-ATATTTATTATTATAATAATAATCT-TA-TTAAAATATATAATTTAATAAAATTC
64920 TTAATAATTA
119 TTAATAATTA
64930 ATATTCTTAT
Statistics
Matches: 247, Mismatches: 22, Indels: 38
0.80 0.07 0.12
Matches are distributed among these distances:
155 1 0.00
156 11 0.04
157 150 0.61
158 14 0.06
159 31 0.13
160 39 0.16
161 1 0.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (153 bp):
AATTTTATTAAATTATAAATTTTAATAAAATATTTTAATAATAATTATGTTTAAATATGATTAAA
ATATTTATTATTATAATAATAATCTTATTAAAATATATAATTTAATAAAATTCTTAATAATTACC
AAAACAAATTTCTGGTAATTATT
Found at i:66394 original size:23 final size:23
Alignment explanation
Indices: 66358--66409 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
66348 ATTAAATTGT
*
66358 AATTTTTACGATAATAAAAGTATA
1 AATTTTTACAATAATAAAAGTA-A
* *
66382 AATTTTTA-AATAATTAAATTAA
1 AATTTTTACAATAATAAAAGTAA
66404 AATTTT
1 AATTTT
66410 ATCATTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.28
23 10 0.40
24 8 0.32
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (23 bp):
AATTTTTACAATAATAAAAGTAA
Found at i:73560 original size:21 final size:21
Alignment explanation
Indices: 73536--73583 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
73526 GTAATATTAA
*
73536 ATTTTAATTCATAGATA-AATT
1 ATTTTAATTCA-AAATATAATT
*
73557 A-TTTAATTTAAAATATAATT
1 ATTTTAATTCAAAATATAATT
73577 ATTTTAA
1 ATTTTAA
73584 AAGAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 4 0.17
20 13 0.57
21 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTTTAATTCAAAATATAATT
Found at i:76173 original size:20 final size:20
Alignment explanation
Indices: 76121--76173 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
76111 TCTTACATAA
* **
76121 AAAATTTAGGTAAAATTTTT
1 AAAATTTAGTTAACCTTTTT
*
76141 AAAATTTATTTAACCTTTTT
1 AAAATTTAGTTAACCTTTTT
76161 -AAATCTTAGTTAA
1 AAAAT-TTAGTTAA
76174 AATCTTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (20 bp):
AAAATTTAGTTAACCTTTTT
Found at i:86183 original size:32 final size:32
Alignment explanation
Indices: 86142--86204 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
86132 ATTATTTAAA
86142 ATGATGATTTAGGTTGTGACATAAACATACAT
1 ATGATGATTTAGGTTGTGACATAAACATACAT
86174 ATGATGATTTAGGTTGTGACATAAACATACA
1 ATGATGATTTAGGTTGTGACATAAACATACA
86205 AACAAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (32 bp):
ATGATGATTTAGGTTGTGACATAAACATACAT
Found at i:94477 original size:21 final size:21
Alignment explanation
Indices: 94453--94515 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
94443 AAATGGGGTA
94453 ATAAATTGGCCAAAAGGTGTG
1 ATAAATTGGCCAAAAGGTGTG
* * *
94474 AT-AA-T---AAAAATGGGGTA
1 ATAAATTGGCCAAAA-GGTGTG
94491 ATAAATTGGCCAAAAGGTGTG
1 ATAAATTGGCCAAAAGGTGTG
94512 ATAA
1 ATAA
94516 TTTGTAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
16 4 0.13
17 6 0.20
18 2 0.07
19 2 0.07
20 2 0.07
21 10 0.33
22 4 0.13
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.24
Consensus pattern (21 bp):
ATAAATTGGCCAAAAGGTGTG
Found at i:94482 original size:38 final size:38
Alignment explanation
Indices: 94440--94516 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
94430 TCAAAACAAG
94440 TAAAAATGGGGTAATAAATTGGCCAAAAGGTGTGATAA
1 TAAAAATGGGGTAATAAATTGGCCAAAAGGTGTGATAA
94478 TAAAAATGGGGTAATAAATTGGCCAAAAGGTGTGATAA
1 TAAAAATGGGGTAATAAATTGGCCAAAAGGTGTGATAA
94516 T
1 T
94517 TTGTAAATAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.25
Consensus pattern (38 bp):
TAAAAATGGGGTAATAAATTGGCCAAAAGGTGTGATAA
Found at i:100169 original size:14 final size:15
Alignment explanation
Indices: 100150--100178 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
100140 TCTTAAGCTT
100150 CAAGGCAAAC-ACCA
1 CAAGGCAAACTACCA
100164 CAAGGCAAACTACCA
1 CAAGGCAAACTACCA
100179 TAACAGTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.34, G:0.14, T:0.03
Consensus pattern (15 bp):
CAAGGCAAACTACCA
Found at i:100983 original size:29 final size:29
Alignment explanation
Indices: 100934--100990 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
100924 ATTCTTAAAA
*
100934 ATAAAAATACAAAAATTAAATTTTAAATTT
1 ATAAAAATACAAAAA-TAAATTATAAATTT
100964 ATAAAAACTACAAAAA-AAATTATAAAT
1 ATAAAAA-TACAAAAATAAATTATAAAT
100991 ATTTTAACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 10 0.40
30 7 0.28
31 8 0.32
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (29 bp):
ATAAAAATACAAAAATAAATTATAAATTT
Found at i:101816 original size:18 final size:19
Alignment explanation
Indices: 101792--101831 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
101782 AGTATATTAT
*
101792 AATTTTTTACATTTTTTAA
1 AATTTTATACATTTTTTAA
*
101811 AATTTTATACTTTTTTTAA
1 AATTTTATACATTTTTTAA
101830 AA
1 AA
101832 AGTTATAATA
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:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTATACATTTTTTAA
Found at i:101917 original size:22 final size:22
Alignment explanation
Indices: 101888--101936 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
101878 TGTTTTTAGT
101888 AATT-TTTTTATAA-TTTTTAAA
1 AATTCTTTTT-TAATTTTTTAAA
*
101909 AATTCTTTTTTAATTTTTTCAA
1 AATTCTTTTTTAATTTTTTAAA
101931 AATTCT
1 AATTCT
101937 AATTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (22 bp):
AATTCTTTTTTAATTTTTTAAA
Found at i:101947 original size:22 final size:21
Alignment explanation
Indices: 101872--101949 Score: 61
Period size: 22 Copynumber: 3.7 Consensus size: 21
101862 AATTTTCTAA
**
101872 TTTTTATGTTTTTAGTAATT-T
1 TTTTTAT-TTTTTAAAAATTCT
*
101893 TTTTATAATTTTTAAAAATTCT
1 TTTT-TATTTTTTAAAAATTCT
*
101915 TTTTTAATTTTTTCAAAATTCT
1 TTTTT-ATTTTTTAAAAATTCT
**
101937 AATTT-TTTTTTAA
1 TTTTTATTTTTTAA
101950 TTTTAAAGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
20 7 0.15
21 15 0.33
22 24 0.52
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTTTATTTTTTAAAAATTCT
Found at i:106131 original size:22 final size:23
Alignment explanation
Indices: 106106--106157 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
106096 GTAACACGTG
*
106106 AAATTAACAACA-TAAATACATT
1 AAATTAACAACACTAAATACACT
*
106128 AAATTAACAATACTAAATACACT
1 AAATTAACAACACTAAATACACT
106151 ACAATTA
1 A-AATTA
106158 TTTATTATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 11 0.42
23 10 0.38
24 5 0.19
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (23 bp):
AAATTAACAACACTAAATACACT
Found at i:106588 original size:30 final size:30
Alignment explanation
Indices: 106554--106613 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
106544 ACTTAACAAG
106554 CAAATGCCTCTAAAAT-AATAACAAAATTAA
1 CAAATGCCTCTAAAATAAAT-ACAAAATTAA
*
106584 CAAATGCCTTTAAAATAAATACAAAATTAA
1 CAAATGCCTCTAAAATAAATACAAAATTAA
106614 TAATAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.57, C:0.15, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAAATACAAAATTAA
Found at i:110622 original size:21 final size:21
Alignment explanation
Indices: 110598--110637 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
110588 TTAACCAACA
110598 ATAA-ATTTTTTTAGAATTTGC
1 ATAATATTTTTTTA-AATTTGC
*
110619 ATAATGTTTTTTTAAATTT
1 ATAATATTTTTTTAAATTT
110638 AAATGTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (21 bp):
ATAATATTTTTTTAAATTTGC
Found at i:117385 original size:89 final size:89
Alignment explanation
Indices: 117207--117385 Score: 270
Period size: 89 Copynumber: 2.0 Consensus size: 89
117197 CTTGAGAAAG
*
117207 GAAATACAATGTCATACTATATTCAATCCGCTAATAAGGTCAACATCCAATAAGAATTAACTTTA
1 GAAATACAATGTCATACTATATTCAATCCGCTAATAAGGTCAACATCCAATAAGAATTAACTGTA
*
117272 ATAGTTTACATGTAACCGAGAAAT
66 ATAGTTTACATGTAACCGACAAAT
* * * * *
117296 GAAATACAATGTCATAGTATATTCAATCTGCTAATAAGGT-TACATCCGATAATAATTAACTGTA
1 GAAATACAATGTCATACTATATTCAATCCGCTAATAAGGTCAACATCCAATAAGAATTAACTGTA
*
117360 ATATTTTACATGTAACCAGACAAAT
66 ATAGTTTACATGTAACC-GACAAAT
117385 G
1 G
117386 CATGAAGCTT
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
88 36 0.44
89 45 0.56
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.31
Consensus pattern (89 bp):
GAAATACAATGTCATACTATATTCAATCCGCTAATAAGGTCAACATCCAATAAGAATTAACTGTA
ATAGTTTACATGTAACCGACAAAT
Found at i:122456 original size:12 final size:12
Alignment explanation
Indices: 122439--122463 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
122429 TAGGTTACAC
122439 TATTTGTAATTG
1 TATTTGTAATTG
122451 TATTTGTAATTG
1 TATTTGTAATTG
122463 T
1 T
122464 GAAGACTAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (12 bp):
TATTTGTAATTG
Found at i:124623 original size:46 final size:46
Alignment explanation
Indices: 124551--124690 Score: 235
Period size: 46 Copynumber: 3.0 Consensus size: 46
124541 ACAATGCTAT
* * *
124551 AACTCAGTATGGTTTCCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
124597 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
* *
124643 AATTCAATATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
124689 AA
1 AA
124691 TTTGCCATGG
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 89 1.00
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
Found at i:130809 original size:23 final size:24
Alignment explanation
Indices: 130749--130811 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
130739 TGCTAGGATG
* *
130749 AAATTACATAATTATCATTTTTAA
1 AAATTACATAATTATCAGTTTAAA
* **
130773 AAA-TATATTTTTAT-AGTTTAAA
1 AAATTACATAATTATCAGTTTAAA
130795 AAATTACATAATTATCA
1 AAATTACATAATTATCA
130812 TTTTCTGTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
22 9 0.31
23 16 0.55
24 4 0.14
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (24 bp):
AAATTACATAATTATCAGTTTAAA
Found at i:131835 original size:17 final size:17
Alignment explanation
Indices: 131784--131841 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
131774 TATTTTCTCT
*
131784 TTTTTCTAACATAAAAT-
1 TTTTTATAA-ATAAAATA
*
131801 TTATTTATTAAA-ACAATA
1 TT-TTTA-TAAATAAAATA
131819 TTTTTATAAATAAAATA
1 TTTTTATAAATAAAATA
131836 TTTTTA
1 TTTTTA
131842 AAAAAACCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 4 0.12
17 21 0.62
18 6 0.18
19 3 0.09
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTTATAAATAAAATA
Found at i:133280 original size:23 final size:23
Alignment explanation
Indices: 133253--133297 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
133243 AGATTTTTCC
*
133253 TAAATATTATTACTAAATAATTT
1 TAAATATTATCACTAAATAATTT
133276 TAAATATTATCACTAAATAATT
1 TAAATATTATCACTAAATAATT
133298 CAAAATTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAATATTATCACTAAATAATTT
Found at i:133303 original size:23 final size:23
Alignment explanation
Indices: 133254--133303 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
133244 GATTTTTCCT
* **
133254 AAATATTATTACTAAATAATTTT
1 AAATATTATCACTAAATAATTCA
133277 AAATATTATCACTAAATAATTCA
1 AAATATTATCACTAAATAATTCA
133300 AAAT
1 AAAT
133304 TCAAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATATTATCACTAAATAATTCA
Found at i:141402 original size:13 final size:13
Alignment explanation
Indices: 141384--141408 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
141374 CACCCCATAC
141384 ATATATACAGAAT
1 ATATATACAGAAT
141397 ATATATACAGAA
1 ATATATACAGAA
141409 ATAACAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (13 bp):
ATATATACAGAAT
Found at i:143265 original size:13 final size:13
Alignment explanation
Indices: 143247--143289 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
143237 TAGATTTTTC
143247 CTAAATATTATCA
1 CTAAATATTATCA
*
143260 CTAAATAAT-TCA
1 CTAAATATTATCA
143272 --AAATATTATCA
1 CTAAATATTATCA
143283 CTAAATA
1 CTAAATA
143290 ATTCAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.24
11 3 0.12
12 3 0.12
13 13 0.52
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:143279 original size:23 final size:23
Alignment explanation
Indices: 143249--143298 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
143239 GATTTTTCCT
143249 AAATATTATCACTAAATAATTCA
1 AAATATTATCACTAAATAATTCA
143272 AAATATTATCACTAAATAATTCA
1 AAATATTATCACTAAATAATTCA
143295 AAAT
1 AAAT
143299 TTAAAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATATTATCACTAAATAATTCA
Found at i:143311 original size:23 final size:23
Alignment explanation
Indices: 143249--143304 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
143239 GATTTTTCCT
**
143249 AAATATTATCACTAAATAATTCA
1 AAATATTAAAACTAAATAATTCA
**
143272 AAATATTATCACTAAATAATTCA
1 AAATATTAAAACTAAATAATTCA
143295 AAAT-TTAAAA
1 AAATATTAAAA
143305 ATTAAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 4 0.13
23 27 0.87
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATATTAAAACTAAATAATTCA
Found at i:149411 original size:26 final size:25
Alignment explanation
Indices: 149353--149422 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 25
149343 ATTTAATTAC
*
149353 AATACTGTAATTTCTAAAATAATTT
1 AATACTGTAATTTCTAAAAAAATTT
149378 --TA-T-T-ATTTCTAAATAAAATTT
1 AATACTGTAATTTCTAAA-AAAATTT
149399 AATACTGTAATTTCTTAAGAAAAA
1 AATACTGTAATTTC-TAA-AAAAA
149423 AATGAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
20 9 0.25
21 7 0.19
22 1 0.03
23 4 0.11
24 1 0.03
25 1 0.03
26 5 0.14
27 7 0.19
28 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (25 bp):
AATACTGTAATTTCTAAAAAAATTT
Found at i:155674 original size:22 final size:22
Alignment explanation
Indices: 155639--155684 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
155629 CTGCACAACT
155639 TACAACCAACTAACTGATAAGC
1 TACAACCAACTAACTGATAAGC
* *
155661 TACAACTAATTAACTGATAAGC
1 TACAACCAACTAACTGATAAGC
155683 TA
1 TA
155685 ACAGTTAACA
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:0.46, C:0.22, G:0.09, T:0.24
Consensus pattern (22 bp):
TACAACCAACTAACTGATAAGC
Found at i:158809 original size:22 final size:22
Alignment explanation
Indices: 158774--158815 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
158764 CTGCACAACT
158774 TACAACCAACTAACTGATAAAG
1 TACAACCAACTAACTGATAAAG
* *
158796 TACAACTAATTAACTGATAA
1 TACAACCAACTAACTGATAA
158816 GCTAACAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.19, G:0.07, T:0.24
Consensus pattern (22 bp):
TACAACCAACTAACTGATAAAG
Found at i:159593 original size:19 final size:19
Alignment explanation
Indices: 159549--159594 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
159539 AACATGAGTG
*
159549 TTTTATATTGAAAAAACAT
1 TTTTATTTTGAAAAAACAT
*
159568 TTTTATTTTGAAAATA-AT
1 TTTTATTTTGAAAAAACAT
159586 TTTCTATTT
1 TTT-TATTT
159595 AATAACACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (19 bp):
TTTTATTTTGAAAAAACAT
Found at i:162879 original size:20 final size:20
Alignment explanation
Indices: 162833--162892 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
162823 ACAACACACT
*
162833 CAAAAACCCAATATCCAAA-A
1 CAAAAACCCAA-ACCCAAATA
162853 C-AAAACCCAAACCCAAATA
1 CAAAAACCCAAACCCAAATA
*
162872 CAAAAACCCTAAGCCCAAATA
1 CAAAAACCC-AAACCCAAATA
162893 AGCTAGCCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 6 0.17
19 11 0.31
20 8 0.23
21 10 0.29
ACGTcount: A:0.57, C:0.33, G:0.02, T:0.08
Consensus pattern (20 bp):
CAAAAACCCAAACCCAAATA
Found at i:165711 original size:30 final size:30
Alignment explanation
Indices: 165643--165718 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
165633 CAATTAAATA
*
165643 AATTTTTAAAAAATTATTTTTATAATTTTT
1 AATTTTTAAAAAATTATTTATATAATTTTT
* * **
165673 AATATTTAAATAA-TATTTATATTTTTTTT
1 AATTTTTAAAAAATTATTTATATAATTTTT
*
165702 GAATTTTTAAAATATTA
1 -AATTTTTAAAAAATTA
165719 AAATATTATT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 13 0.36
30 21 0.58
31 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (30 bp):
AATTTTTAAAAAATTATTTATATAATTTTT
Found at i:166269 original size:21 final size:21
Alignment explanation
Indices: 166245--166287 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
166235 TCAGCTCTCT
166245 GGCCATCTTCCAT-CAAACATG
1 GGCC-TCTTCCATCCAAACATG
* *
166266 GGCCTTTTCCTTCCAAACATG
1 GGCCTCTTCCATCCAAACATG
166287 G
1 G
166288 AGATTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.28
Consensus pattern (21 bp):
GGCCTCTTCCATCCAAACATG
Found at i:170938 original size:21 final size:20
Alignment explanation
Indices: 170904--170945 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
170894 AGTGGCGTTT
*
170904 TAAAAAAAATGCCGCAAAAG
1 TAAAAAAAACGCCGCAAAAG
*
170924 TAAAAAAAAGCGCCGCACAAG
1 TAAAAAAAA-CGCCGCAAAAG
170945 T
1 T
170946 GTTAAGCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.55, C:0.19, G:0.17, T:0.10
Consensus pattern (20 bp):
TAAAAAAAACGCCGCAAAAG
Found at i:171012 original size:94 final size:96
Alignment explanation
Indices: 170834--171093 Score: 228
Period size: 94 Copynumber: 2.7 Consensus size: 96
170824 GCGATTTCCC
* * * * * *
170834 AAAAGCGCCGC-AAAGAGTTAGGCAAACG--GTACCGTTTTCTTGTTGAGCTTCAAAGACATTAG
1 AAAAGCGCCGCAAAAGTGTTAAGCAAACGACGT--CGTTTTCCTGTTGAGCTTTAGACACATTAG
* * ** *
170896 TGGCG-TTTTAAAAAAAATGCCGCAAAAG-TAAAA
64 TGGCGCTTAT-CAGGAAACGCCGCAAAAGAT-AAA
* * * *
170929 AAAAGCGCCGCACAAGTGTTAAGCAGACGATGTCGTTTTCCT-TT-AGCTTTAGAGACATTAGTG
1 AAAAGCGCCGCAAAAGTGTTAAGCAAACGACGTCGTTTTCCTGTTGAGCTTTAGACACATTAGTG
* *
170992 GCGCTTATCAGGAAACGCCGCAAAAGATCAT
66 GCGCTTATCAGGAAACGCCGCAAAAGATAAA
* * * * *
171023 GAAAGCGTCGCAAAAGTTTTTAGCAAACGACGTCGTTTTCTTGTTGAGCTTTAGACACATTAGTG
1 AAAAGCGCCGCAAAAGTGTTAAGCAAACGACGTCGTTTTCCTGTTGAGCTTTAGACACATTAGTG
*
171088 GTGCTT
66 GCGCTT
171094 TTTGAAAAAC
Statistics
Matches: 134, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
94 69 0.51
95 19 0.14
96 44 0.33
98 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (96 bp):
AAAAGCGCCGCAAAAGTGTTAAGCAAACGACGTCGTTTTCCTGTTGAGCTTTAGACACATTAGTG
GCGCTTATCAGGAAACGCCGCAAAAGATAAA
Found at i:171026 original size:20 final size:21
Alignment explanation
Indices: 170998--171038 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
170988 AGTGGCGCTT
170998 ATCAGGAAA-CGCCGCAAAAG
1 ATCAGGAAAGCGCCGCAAAAG
* *
171018 ATCATGAAAGCGTCGCAAAAG
1 ATCAGGAAAGCGCCGCAAAAG
171039 TTTTTAGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (21 bp):
ATCAGGAAAGCGCCGCAAAAG
Found at i:171333 original size:113 final size:113
Alignment explanation
Indices: 171024--171461 Score: 565
Period size: 113 Copynumber: 3.8 Consensus size: 113
171014 AAAGATCATG
* * * * * *
171024 AAAGCGTCGCAAAAGTTTTTAGCAAACGACGTCGTTTTCTTGTTGAGCTTTAGACACATTAGTGG
1 AAAGCGCCACAAAAGTTTTAAGCAAACAACGTCGTTTTTTTGTTGAGCTTTAGAGACATTAGTGG
* ** * * * * **
171089 TGCTTTTTGAAAAACGCCGC-AGATGTCAATCATTAGCGGCCCTTTCTGG
66 CGC-TTTACAAAAACGTCGCAAAAT-TCAAGCATTAGCGGCGCTTTCTCA
*
171138 TAAGCGCCACAAAAAGTTTTAAGCAAACAACGTCGTTTTTTTTTGTTGAGCTTTAGAGACATTAG
1 AAAGCGCCAC-AAAAGTTTTAAGCAAACAACGTCG--TTTTTTTGTTGAGCTTTAGAGACATTAG
171203 TGGCGCTTTACAAAAACGTCGCAAAATTCAAGCATTAGCGGCGCTTTCTCA
63 TGGCGCTTTACAAAAACGTCGCAAAATTCAAGCATTAGCGGCGCTTTCTCA
*
171254 AAAGCGCCACAAAAGTTTTAAGCAAACAGCGTCGTTTTTTTGTTGAGCTTTAGAGACATTAGTGG
1 AAAGCGCCACAAAAGTTTTAAGCAAACAACGTCGTTTTTTTGTTGAGCTTTAGAGACATTAGTGG
* *
171319 CGCTTTACAGAAACGTCACAAAATTCAAGCATTAGCGGCGCTTTCTCA
66 CGCTTTACAAAAACGTCGCAAAATTCAAGCATTAGCGGCGCTTTCTCA
* * * *
171367 AAAGCGCCACAAAAGTTTTAAGCAAACAACATCATTTTCTTT-TTCAGCTTTAAAGACATTAGTG
1 AAAGCGCCACAAAAGTTTTAAGCAAACAACGTCGTTTT-TTTGTTGAGCTTTAGAGACATTAGTG
* * *
171431 GCGCTTTACTAAAAACGCCACAAAAGTCAAG
65 GCGCTTTAC-AAAAACGTCGCAAAATTCAAG
171462 ATTTAACGGT
Statistics
Matches: 290, Mismatches: 28, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
113 141 0.49
114 28 0.10
115 45 0.16
116 42 0.14
117 34 0.12
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (113 bp):
AAAGCGCCACAAAAGTTTTAAGCAAACAACGTCGTTTTTTTGTTGAGCTTTAGAGACATTAGTGG
CGCTTTACAAAAACGTCGCAAAATTCAAGCATTAGCGGCGCTTTCTCA
Found at i:171700 original size:114 final size:114
Alignment explanation
Indices: 171493--171740 Score: 261
Period size: 114 Copynumber: 2.2 Consensus size: 114
171483 AACGACAACA
* * * * *
171493 TTTTATTGTTAAGGTTTAG-GCACATTAGTGGCGCTTTTATAAAAACGCTGCAGAAGTCAAGCAT
1 TTTTTTTGTTAAGCTTTAGAG-ACATTAGTGGCGCTTTTAAAAAAACGCCGCAAAAGTCAAGCAT
* * * * * * *
171557 TAGCGGCTCTTTCTCAGAAGCGCCACAAAAAATTTAAG-TAAACGACGTTG
65 TAGCGGCGCTTTCTCAGAAACGCCACAAAAAAGTTAAGCAAAACAAC-CTC
* *
171607 TTTTTTTGTTGAGCTTTAGAGACATTAGTGGCGC-TTTACAAAAAATGCCGCAAAAGTCAAGCAT
1 TTTTTTTGTTAAGCTTTAGAGACATTAGTGGCGCTTTTA-AAAAAACGCCGCAAAAGTCAAGCAT
* ** * *
171671 TCGCGGCGCTTT-TTTGAAAACGTCGCAAAAAAGTTAAGCAAAACAACCTC
65 TAGCGGCGCTTTCTCAG-AAACGCCACAAAAAAGTTAAGCAAAACAACCTC
171721 TTTTTTTGTTAAGCTTTAGA
1 TTTTTTTGTTAAGCTTTAGA
171741 CGCATTGGCG
Statistics
Matches: 110, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
113 6 0.05
114 97 0.88
115 7 0.06
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (114 bp):
TTTTTTTGTTAAGCTTTAGAGACATTAGTGGCGCTTTTAAAAAAACGCCGCAAAAGTCAAGCATT
AGCGGCGCTTTCTCAGAAACGCCACAAAAAAGTTAAGCAAAACAACCTC
Found at i:171772 original size:15 final size:14
Alignment explanation
Indices: 171750--171784 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
171740 ACGCATTGGC
171750 GGTTTAGGGATTAT
1 GGTTTAGGGATTAT
171764 GGATTTAGGGATTAT
1 GG-TTTAGGGATTAT
171779 GGTTTA
1 GGTTTA
171785 TTGTTTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.43
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:171855 original size:39 final size:39
Alignment explanation
Indices: 171807--171893 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
171797 TAAGGGTTGA
171807 GGTTTAAGGTTTATAGTTTATATATGTTCTATGATTCAG
1 GGTTTAAGGTTTATAGTTTATATATGTTCTATGATTCAG
* *
171846 GGTTTAAGGTTTATAGTTTATATATGTTTTATGATTTAG
1 GGTTTAAGGTTTATAGTTTATATATGTTCTATGATTCAG
171885 GGTTTAAGG
1 GGTTTAAGG
171894 AATATGGGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.25, C:0.02, G:0.23, T:0.49
Consensus pattern (39 bp):
GGTTTAAGGTTTATAGTTTATATATGTTCTATGATTCAG
Found at i:171931 original size:22 final size:22
Alignment explanation
Indices: 171883--171932 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
171873 TTTATGATTT
171883 AGGGTTTAAGGAATATGGGTTA
1 AGGGTTTAAGGAATATGGGTTA
* * *
171905 GGGGTTTAGGGATTAT-GGTGTA
1 AGGGTTTAAGGAATATGGGT-TA
171927 AGGGTT
1 AGGGTT
171933 GGGATTTCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.34
Consensus pattern (22 bp):
AGGGTTTAAGGAATATGGGTTA
Found at i:172162 original size:7 final size:7
Alignment explanation
Indices: 172142--172222 Score: 58
Period size: 7 Copynumber: 11.1 Consensus size: 7
172132 TAGGGATAAA
172142 AGGGTTT
1 AGGGTTT
**
172149 AAAGTTT
1 AGGGTTT
172156 AGGGTTT
1 AGGGTTT
172163 AGGGTTT
1 AGGGTTT
172170 ATGGG-TT
1 A-GGGTTT
**
172177 ATTGTTT
1 AGGGTTT
172184 -GGAGTTT
1 AGG-GTTT
172191 ATGGGTTT
1 A-GGGTTT
*
172199 AAGGTTT
1 AGGGTTT
172206 AAGGGTTT
1 -AGGGTTT
172214 AAGGGTTT
1 -AGGGTTT
172222 A
1 A
172223 AGGTCTATGA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
6 1 0.02
7 33 0.57
8 22 0.38
9 2 0.03
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.44
Consensus pattern (7 bp):
AGGGTTT
Found at i:172205 original size:15 final size:16
Alignment explanation
Indices: 172187--172225 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
172177 ATTGTTTGGA
*
172187 GTTTATGGGTTTAA-G
1 GTTTAAGGGTTTAAGG
172202 GTTTAAGGGTTTAAGG
1 GTTTAAGGGTTTAAGG
172218 GTTTAAGG
1 GTTTAAGG
172226 TCTATGATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.23, C:0.00, G:0.36, T:0.41
Consensus pattern (16 bp):
GTTTAAGGGTTTAAGG
Found at i:172212 original size:8 final size:8
Alignment explanation
Indices: 172187--172225 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
172177 ATTGTTTGGA
*
172187 GTTTATGG
1 GTTTAAGG
172195 GTTTAA-G
1 GTTTAAGG
172202 GTTTAAGG
1 GTTTAAGG
172210 GTTTAAGG
1 GTTTAAGG
172218 GTTTAAGG
1 GTTTAAGG
172226 TCTATGATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.23, C:0.00, G:0.36, T:0.41
Consensus pattern (8 bp):
GTTTAAGG
Found at i:172271 original size:14 final size:14
Alignment explanation
Indices: 172252--172284 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
172242 TAAGGTATAG
172252 GGTTTACGGTTTTT
1 GGTTTACGGTTTTT
172266 GGTTTACGGTTTTT
1 GGTTTACGGTTTTT
172280 GGTTT
1 GGTTT
172285 TCAAGATAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.06, G:0.30, T:0.58
Consensus pattern (14 bp):
GGTTTACGGTTTTT
Found at i:174508 original size:31 final size:31
Alignment explanation
Indices: 174470--174549 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
174460 AAGGATTTTA
*
174470 ATTGGTTTTTGCAGCTAAGATGGTACCTTAT
1 ATTGGTTTTTGCTGCTAAGATGGTACCTTAT
* *
174501 ATTGGTTTTTGCTGCCAAGATGGTACCTTCT
1 ATTGGTTTTTGCTGCTAAGATGGTACCTTAT
*
174532 ATTGTTTTTTGCTGCTAA
1 ATTGGTTTTTGCTGCTAA
174550 ATCAACCATG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.45
Consensus pattern (31 bp):
ATTGGTTTTTGCTGCTAAGATGGTACCTTAT
Found at i:174610 original size:34 final size:34
Alignment explanation
Indices: 174567--174637 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
174557 ATGTATGGAG
174567 ACCGAATTTAGACTTCGCTTAAATCACAAATTGT
1 ACCGAATTTAGACTTCGCTTAAATCACAAATTGT
174601 ACCGAATTTAGACTTCGCTTAAATCACAAATTGT
1 ACCGAATTTAGACTTCGCTTAAATCACAAATTGT
174635 ACC
1 ACC
174638 TCATGTGTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (34 bp):
ACCGAATTTAGACTTCGCTTAAATCACAAATTGT
Found at i:175857 original size:20 final size:20
Alignment explanation
Indices: 175832--175875 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
175822 TATTTACTTA
175832 GAATAAATTCAATTGTTTGG
1 GAATAAATTCAATTGTTTGG
175852 GAATAAATTCAATTGTTTGG
1 GAATAAATTCAATTGTTTGG
175872 GAAT
1 GAAT
175876 TACGATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (20 bp):
GAATAAATTCAATTGTTTGG
Found at i:177028 original size:28 final size:29
Alignment explanation
Indices: 176979--177039 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
176969 TAACTTCTGT
* *
176979 CAGACTCTTGTTTGGTAGATAGTCATT-G
1 CAGACTCTTGTTTGATAAATAGTCATTGG
*
177007 CAGACTCTTGATTT-ATAAATAGTCTTTGG
1 CAGACTCTTG-TTTGATAAATAGTCATTGG
177036 CAGA
1 CAGA
177040 TTCCTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (29 bp):
CAGACTCTTGTTTGATAAATAGTCATTGG
Found at i:179373 original size:22 final size:22
Alignment explanation
Indices: 179337--179378 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
179327 TATACAAGTA
179337 ATATTACTTGAATAATTATGAG
1 ATATTACTTGAATAATTATGAG
* *
179359 ATATTAGTTGCATAATTATG
1 ATATTACTTGAATAATTATG
179379 TCTATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATTACTTGAATAATTATGAG
Found at i:183144 original size:15 final size:15
Alignment explanation
Indices: 183124--183153 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
183114 GCTGTTATGA
*
183124 TTTAAATTTAAAATT
1 TTTAAATTGAAAATT
183139 TTTAAATTGAAAATT
1 TTTAAATTGAAAATT
183154 CTTGATTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TTTAAATTGAAAATT
Found at i:183436 original size:44 final size:43
Alignment explanation
Indices: 183387--183918 Score: 265
Period size: 44 Copynumber: 12.2 Consensus size: 43
183377 TATATTCATA
183387 GAGATAAGATCTAAAGTTTTAATCTGCTCCACTGCAACTTCAGG
1 GAGATAAGATCT-AAGTTTTAATCTGCTCCACTGCAACTTCAGG
* * ** * *
183431 GAGATAGGATTGTTGGCTTTAATCTGCTCCACTACAACTTCAGG
1 GAGATAAGA-TCTAAGTTTTAATCTGCTCCACTGCAACTTCAGG
* * *
183475 GAGATAAGAT-T-TGTCATCTTCAGTCTGCCCCACTGCAACTTCA-G
1 GAGATAAGATCTAAGT--T-TT-AATCTGCTCCACTGCAACTTCAGG
* *
183519 GAGGATAAGA-CT-TGCTTACTTAGTCTGCTCCACTGCAACTTCAGG
1 GA-GATAAGATCTAAG-TT--TTAATCTGCTCCACTGCAACTTCAGG
* *** * **
183564 GAGATAAGA-CT-AGATGCGATGTGCT-CTTTGCAACTTC-GG
1 GAGATAAGATCTAAGTTTTAATCTGCTCCACTGCAACTTCAGG
* * *
183603 AGAGATAAGATCTAAGGTTTTAATCCGCTCCAATGTAACTTCAGG
1 -GAGATAAGATCTAA-GTTTTAATCTGCTCCACTGCAACTTCAGG
* * * * *
183648 GAGATAGGAT-TATCGGCTCTAATCTGCTGCACTGCAACTTCAGG
1 GAGATAAGATCTA--AGTTTTAATCTGCTCCACTGCAACTTCAGG
* * * *
183692 AAGATAAGATTTGCCA-TCTTTAGTCTGC-CTCACTGCAACTTCA-G
1 GAGATAAGATCT--AAGT-TTTAATCTGCTC-CACTGCAACTTCAGG
* *
183736 GAGGATAAGA-CT-TGCTTATTTATTCTGCTCCACTGCAACTTCAGG
1 GA-GATAAGATCTAAG--T-TTTAATCTGCTCCACTGCAACTTCAGG
* * *** * *
183781 GAGATGAGA-CT-AGATGCGATCTGCT-CTCTGCAACTTCAGA
1 GAGATAAGATCTAAGTTTTAATCTGCTCCACTGCAACTTCAGG
* * * *
183821 GAGATAAGATCTGAGGTTTTAATCCGCTCTACTGCAACTTCTGG
1 GAGATAAGATCT-AAGTTTTAATCTGCTCCACTGCAACTTCAGG
* * * * * *
183865 TAGATAGGAT-TATCGACTTTAATCTACTTCACTGCAACTTCAGG
1 GAGATAAGATCTA-AG-TTTTAATCTGCTCCACTGCAACTTCAGG
183909 GAGATAAGAT
1 GAGATAAGAT
183919 TTGCCATCTT
Statistics
Matches: 370, Mismatches: 83, Indels: 70
0.71 0.16 0.13
Matches are distributed among these distances:
39 2 0.01
40 40 0.11
41 17 0.05
42 3 0.01
43 22 0.06
44 213 0.58
45 72 0.19
46 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (43 bp):
GAGATAAGATCTAAGTTTTAATCTGCTCCACTGCAACTTCAGG
Found at i:183546 original size:89 final size:89
Alignment explanation
Indices: 183409--183572 Score: 235
Period size: 89 Copynumber: 1.8 Consensus size: 89
183399 AAAGTTTTAA
* * *
183409 TCTGCTCCACTGCAACTTCAGGGAGATAGGATTGTTGGCTTTAATCTGCTCCACTACAACTTCAG
1 TCTGCCCCACTGCAACTTCAGGGAGATAAGATTGTTGACTTTAATCTGCTCCACTACAACTTCAG
183474 GGAGATAAGATTTGTCATCTTCAG
66 GGAGATAAGATTTGTCATCTTCAG
* *
183498 TCTGCCCCACTGCAACTTCA-GGAGGATAAGACTTGCTT-AC-TTAGTCTGCTCCACTGCAACTT
1 TCTGCCCCACTGCAACTTCAGGGA-GATAAGA-TTG-TTGACTTTAATCTGCTCCACTACAACTT
183560 CAGGGAGATAAGA
63 CAGGGAGATAAGA
183573 CTAGATGCGA
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
88 3 0.04
89 58 0.87
90 4 0.06
91 2 0.03
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (89 bp):
TCTGCCCCACTGCAACTTCAGGGAGATAAGATTGTTGACTTTAATCTGCTCCACTACAACTTCAG
GGAGATAAGATTTGTCATCTTCAG
Found at i:183765 original size:217 final size:217
Alignment explanation
Indices: 183381--183930 Score: 857
Period size: 217 Copynumber: 2.5 Consensus size: 217
183371 ATACTTTATA
* * * * *
183381 TTCATAGAGATAAGATCTAAAGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGTTG
1 TTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCG
* *
183446 GCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGTCATCTTCAGTCTGCCCCACTGC
66 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCCCACTGC
183511 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
131 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
* *
183576 GATGCGATGTGCTCTTTGCAAC
196 GATGCGATCTGCTCTCTGCAAC
* * *
183598 TTCGGAGAGATAAGATCTAAGGTTTTAATCCGCTCCAATGTAACTTCAGGGAGATAGGATTATCG
1 TTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCG
* * * * *
183663 GCTCTAATCTGCTGCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTTAGTCTGCCTCACTGC
66 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCCCACTGC
* * *
183728 AACTTCAGGAGGATAAGACTTGCTTATTTATTCTGCTCCACTGCAACTTCAGGGAGATGAGACTA
131 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
183793 GATGCGATCTGCTCTCTGCAAC
196 GATGCGATCTGCTCTCTGCAAC
* * * *
183815 TTCAGAGAGATAAGATCTGAGGTTTTAATCCGCTCTACTGCAACTTCTGGTAGATAGGATTATCG
1 TTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCG
* * *
183880 ACTTTAATCTACTTCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCA
66 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCA
183931 CTGATCTGTT
Statistics
Matches: 300, Mismatches: 33, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
217 300 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (217 bp):
TTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCG
GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCCCACTGC
AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
GATGCGATCTGCTCTCTGCAAC
Found at i:198815 original size:17 final size:17
Alignment explanation
Indices: 198790--198830 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
198780 GCATGGTATT
*
198790 AGCGGCGCTTTTTGATA
1 AGCGCCGCTTTTTGATA
198807 AGCGCCGCTTTTTGATA
1 AGCGCCGCTTTTTGATA
198824 AGCGCCG
1 AGCGCCG
198831 GAAAATGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (17 bp):
AGCGCCGCTTTTTGATA
Found at i:198913 original size:93 final size:93
Alignment explanation
Indices: 198797--198982 Score: 372
Period size: 93 Copynumber: 2.0 Consensus size: 93
198787 ATTAGCGGCG
198797 CTTTTTGATAAGCGCCGCTTTTTGATAAGCGCCGGAAAATGTATTAACCAATTATATAATGTAGG
1 CTTTTTGATAAGCGCCGCTTTTTGATAAGCGCCGGAAAATGTATTAACCAATTATATAATGTAGG
198862 TTATTATATATGTTTTTGATAAGCGCCA
66 TTATTATATATGTTTTTGATAAGCGCCA
198890 CTTTTTGATAAGCGCCGCTTTTTGATAAGCGCCGGAAAATGTATTAACCAATTATATAATGTAGG
1 CTTTTTGATAAGCGCCGCTTTTTGATAAGCGCCGGAAAATGTATTAACCAATTATATAATGTAGG
198955 TTATTATATATGTTTTTGATAAGCGCCA
66 TTATTATATATGTTTTTGATAAGCGCCA
198983 TACATAAATT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (93 bp):
CTTTTTGATAAGCGCCGCTTTTTGATAAGCGCCGGAAAATGTATTAACCAATTATATAATGTAGG
TTATTATATATGTTTTTGATAAGCGCCA
Found at i:198923 original size:17 final size:17
Alignment explanation
Indices: 198874--198923 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
198864 ATTATATATG
*
198874 TTTTTGATAAGCGCCAC
1 TTTTTGATAAGCGCCGC
198891 TTTTTGATAAGCGCCGC
1 TTTTTGATAAGCGCCGC
198908 TTTTTGATAAGCGCCG
1 TTTTTGATAAGCGCCG
198924 GAAAATGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (17 bp):
TTTTTGATAAGCGCCGC
Found at i:199189 original size:117 final size:117
Alignment explanation
Indices: 198983--202684 Score: 7377
Period size: 117 Copynumber: 31.6 Consensus size: 117
198973 ATAAGCGCCA
198983 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
199048 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
199100 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
199165 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
199217 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
199282 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
199334 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
199399 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
199451 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
199516 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
199568 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
199633 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
199685 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
199750 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
199802 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
199867 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
199919 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
199984 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
200036 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
200101 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
200153 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
200218 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
200270 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
200335 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
200387 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
200452 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
200504 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
200569 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
200621 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
200686 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
200738 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
200803 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
200855 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
200920 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
200972 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
201037 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
201089 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
201154 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
201206 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
201271 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
201323 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
201388 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
201440 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
201505 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
201557 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
201622 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
201674 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
201739 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
201791 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
201856 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
201908 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
201973 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
202025 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
202090 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
202142 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
202207 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
202259 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
202324 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
202376 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
202441 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
202493 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
202558 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
66 CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
* *
202610 TACATAAATTAAATATCTTACATAACTTATATAAATTAAGTAAATTAAATAACTTACATAACTTA
1 TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
*
202675 CATAAATTAA
66 CATGAATTAA
202685 GCTTTTTGAT
Statistics
Matches: 3582, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 3582 1.00
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.38
Consensus pattern (117 bp):
TACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAATTAAATAACTTGCATAACTTA
CATGAATTAAATATCTTACATAATTTACATAAATTAAATATCTTACATAATT
Found at i:202705 original size:17 final size:17
Alignment explanation
Indices: 202685--202719 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
202675 CATAAATTAA
202685 GCTTTTTGATAAGCGCC
1 GCTTTTTGATAAGCGCC
202702 GCTTTTTGATAAGCGCC
1 GCTTTTTGATAAGCGCC
202719 G
1 G
202720 GAAAATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (17 bp):
GCTTTTTGATAAGCGCC
Found at i:202775 original size:21 final size:20
Alignment explanation
Indices: 202751--202789 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
202741 TTTGGTCTAT
*
202751 GGTTTATGGTTTAAAGGTTGG
1 GGTTTAAGGTTT-AAGGTTGG
202772 GGTTTAAGGTTTAAGGTT
1 GGTTTAAGGTTTAAGGTT
202790 AATATGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.44
Consensus pattern (20 bp):
GGTTTAAGGTTTAAGGTTGG
Found at i:205951 original size:18 final size:18
Alignment explanation
Indices: 205911--205965 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
205901 ATGTCTGTTC
205911 TAAATTTATAATTTATAT
1 TAAATTTATAATTTATAT
* *
205929 AAAATTTAT-ATTTCCTAT
1 TAAATTTATAATTT-ATAT
*
205947 TAAA-TTATTAATTTTTAT
1 TAAATTTA-TAATTTATAT
205965 T
1 T
205966 TCATACAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
17 7 0.23
18 19 0.63
19 4 0.13
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (18 bp):
TAAATTTATAATTTATAT
Found at i:206161 original size:9 final size:9
Alignment explanation
Indices: 206125--206491 Score: 221
Period size: 9 Copynumber: 40.9 Consensus size: 9
206115 ATTTGGCTAA
206125 TTACATAAC
1 TTACATAAC
* *
206134 TTACAAAAA
1 TTACATAAC
*
206143 TTAAATAAC
1 TTACATAAC
206152 TTACATAAC
1 TTACATAAC
*
206161 TTACATAAA
1 TTACATAAC
*
206170 TTA-AGTAAT
1 TTACA-TAAC
206179 TTACATAAC
1 TTACATAAC
*
206188 TTACATAAA
1 TTACATAAC
* *
206197 TTAAATATC
1 TTACATAAC
* *
206206 TTGCACAAC
1 TTACATAAC
*
206215 TTACATAAA
1 TTACATAAC
206224 TTA-AGTTAA-
1 TTACA--TAAC
*
206233 TTAAATAAC
1 TTACATAAC
*
206242 TTACATAAA
1 TTACATAAC
*
206251 TTA-AGTAAA
1 TTACA-TAAC
*
206260 TTAAATAAC
1 TTACATAAC
*
206269 TTATATAAC
1 TTACATAAC
*
206278 TTACATAAA
1 TTACATAAC
* *
206287 TTAAATATC
1 TTACATAAC
206296 TTACATAAC
1 TTACATAAC
*
206305 TTACATAAA
1 TTACATAAC
* *
206314 TTAAATATC
1 TTACATAAC
*
206323 TTACACAAC
1 TTACATAAC
*
206332 TTACATAAA
1 TTACATAAC
*
206341 TTA-AGTAAA
1 TTACA-TAAC
*
206350 TTAAATAAC
1 TTACATAAC
*
206359 TTGCATAAC
1 TTACATAAC
*
206368 TTTACATAAA
1 -TTACATAAC
* *
206378 TTAAATATC
1 TTACATAAC
206387 TTACATAAC
1 TTACATAAC
*
206396 TTACATAAA
1 TTACATAAC
* *
206405 TTAAATATC
1 TTACATAAC
*
206414 TTACATTAC
1 TTACATAAC
* **
206423 TTGCATAGT
1 TTACATAAC
*
206432 TTACATTAC
1 TTACATAAC
**
206441 TTACATGGGGC
1 TTACAT--AAC
*
206452 ATACATAA-
1 TTACATAAC
206460 -TACATAA-
1 TTACATAAC
*
206467 -TACAGAAC
1 TTACATAAC
206475 TTACATAAC
1 TTACATAAC
206484 TTACATAA
1 TTACATAA
206492 TACATAAAAA
Statistics
Matches: 271, Mismatches: 72, Indels: 30
0.73 0.19 0.08
Matches are distributed among these distances:
7 13 0.05
8 7 0.03
9 231 0.85
10 14 0.05
11 6 0.02
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (9 bp):
TTACATAAC
Found at i:206163 original size:27 final size:27
Alignment explanation
Indices: 206125--206419 Score: 259
Period size: 27 Copynumber: 10.6 Consensus size: 27
206115 ATTTGGCTAA
*
206125 TTACATAACTTACAAAAATTAAATAAC
1 TTACATAACTTACATAAATTAAATAAC
* *
206152 TTACATAACTTACATAAATTAAGTAAT
1 TTACATAACTTACATAAATTAAATAAC
*
206179 TTACATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
* *
206206 TTGCACAACTTACATAAATTAAGTTAATTAAATAAC
1 TTACATAACTTAC----A-T-A---AATTAAATAAC
*
206242 TTACATAAATTA-AGTAAATTAAATAAC
1 TTACATAACTTACA-TAAATTAAATAAC
* *
206269 TTATATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
*
206296 TTACATAACTTACATAAATTAAATATC
1 TTACATAACTTACATAAATTAAATAAC
* * *
206323 TTACACAACTTACATAAATTAAGTAAA
1 TTACATAACTTACATAAATTAAATAAC
* * * * *
206350 TTAAATAACTTGCATAACTTTACATAAA
1 TTACATAACTTACATAA-ATTAAATAAC
* * * * *
206378 TTAAATATCTTACATAACTTACATAAA
1 TTACATAACTTACATAAATTAAATAAC
* *
206405 TTAAATATCTTACAT
1 TTACATAACTTACAT
206420 TACTTGCATA
Statistics
Matches: 227, Mismatches: 30, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
27 179 0.79
28 23 0.10
30 1 0.00
31 3 0.01
32 1 0.00
33 1 0.00
36 19 0.08
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (27 bp):
TTACATAACTTACATAAATTAAATAAC
Found at i:206198 original size:54 final size:54
Alignment explanation
Indices: 206125--206408 Score: 293
Period size: 54 Copynumber: 4.9 Consensus size: 54
206115 ATTTGGCTAA
* *
206125 TTACATAACTTACAAAAATTAAATAACTTACATAACTTACATAAATTAAGTAAT
1 TTACATAACTTACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAT
* *
206179 TTACATAACTTACATAAATTAAATATCTTGCACAACTTACATAAATTAAGTTAA-
1 TTACATAACTTACATAAATTAAATATCTTACATAACTTACATAAATTAAG-TAAT
* * *
206233 TTAAATAACTTACATAAATTAAGTAAATTAAATAACTTATATAACTTACATAAATTAAAT-AT
1 TTACATAACTTACATAAA-T---TAAA-T--AT--CTTACATAACTTACATAAATTAAGTAAT
*
206295 CTTACATAACTTACATAAATTAAATATCTTACACAACTTACATAAATTAAGTAAAT
1 -TTACATAACTTACATAAATTAAATATCTTACATAACTTACATAAATTAAGT-AAT
206351 TAAATAACTTGCATAACTTTACATAAATTAAATATCTTACATAACTTACATAAATTAA
1 T---T-A----CATAAC-TTACATAAATTAAATATCTTACATAACTTACATAAATTAA
206409 ATATCTTACA
Statistics
Matches: 193, Mismatches: 14, Indels: 36
0.79 0.06 0.15
Matches are distributed among these distances:
54 85 0.44
55 5 0.03
56 4 0.02
58 6 0.03
59 6 0.03
61 3 0.02
62 2 0.01
63 43 0.22
64 39 0.20
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (54 bp):
TTACATAACTTACATAAATTAAATATCTTACATAACTTACATAAATTAAGTAAT
Found at i:212024 original size:21 final size:20
Alignment explanation
Indices: 211999--212088 Score: 99
Period size: 21 Copynumber: 4.3 Consensus size: 20
211989 CAGCAACTTA
*
211999 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGC-GCAGCGAGAG
* * *
212020 AAGCAGTGGCTACAACGAGAG
1 AAGCAGAGGC-GCAGCGAGAG
212041 AAGCAGAGGCCGCAGCGAGAG
1 AAGCAGAGG-CGCAGCGAGAG
*
212062 AAGCAGAGATCGCAGCGAGAG
1 AAGCAGAG-GCGCAGCGAGAG
212083 AAGCAG
1 AAGCAG
212089 CAATAGAAGC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
21 57 0.98
22 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.41, T:0.03
Consensus pattern (20 bp):
AAGCAGAGGCGCAGCGAGAG
Found at i:212570 original size:42 final size:42
Alignment explanation
Indices: 212519--212788 Score: 255
Period size: 42 Copynumber: 6.4 Consensus size: 42
212509 GCGTTTGTGA
212519 AATAAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTTT
1 AATAAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTTT
* * * *
212561 AATAAGCGCCGCTATAGAACATTA-CTTTTAGAGGCGCTTTCTTC
1 AATAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCG-TTT-TTT
* *
212605 CA-AAGCGCCGCTAAAGAACATGATCTTTAGCGACGTTTTTT
1 AATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
* * * *
212646 --CAAGCGCAGCTAAAGAACATGATCTTTAGGGGTGTTTTTT
1 AATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
* * *
212686 TATCAGCGCCGCTAAAGAGCATGATCTTTAGCGGCGTTTTTT
1 AATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
** * * *
212728 TCTAAGTGCCACAAAAGAACATGATCTTTAGCGGCGTTTTTTT
1 AATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTT
* *
212771 ATGTAAGCGCCGCAAAAG
1 A-ATAAGCGCCGCTAAAG
212789 TTAGTGACGT
Statistics
Matches: 190, Mismatches: 29, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
40 35 0.18
41 3 0.02
42 99 0.52
43 36 0.19
44 17 0.09
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (42 bp):
AATAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
Found at i:212694 original size:125 final size:124
Alignment explanation
Indices: 212522--212769 Score: 295
Period size: 125 Copynumber: 2.0 Consensus size: 124
212512 TTTGTGAAAT
* * *
212522 AAGCGCCGCTAAAGAACACTACTTTTAGCGGCGTTTTTTAATAAGCGCCGCTATAGAACATTA-C
1 AAGCGCAGCTAAAGAACACTACTTTTAGCGGCGTTTTTTAATAAGCGCCGCTAAAGAACATGATC
* *
212586 TTTTAGAGGCGCTTTCTTCCAAAGCGCCGCTAAAGAACATGATCTTTAGCGACGTTTTTTC
66 -TTTAGAGGCG-TTTCTTCCAAAGCGCCACAAAAGAACATGATCTTTAGCGACGTTTTTTC
* * * * *
212647 AAGCGCAGCTAAAGAACA-TGA-TCTTTAGGGGTGTTTTTTTATCAGCGCCGCTAAAGAGCATGA
1 AAGCGCAGCTAAAGAACACT-ACT-TTTAGCGGCGTTTTTTAATAAGCGCCGCTAAAGAACATGA
* * * * * *
212710 TCTTTAGCGGCGTTTTTTTCTAAGTGCCACAAAAGAACATGATCTTTAGCGGCGTTTTTT
64 TCTTTAGAGGCGTTTCTTCCAAAGCGCCACAAAAGAACATGATCTTTAGCGACGTTTTTT
212770 TATGTAAGCG
Statistics
Matches: 104, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
124 43 0.41
125 60 0.58
126 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (124 bp):
AAGCGCAGCTAAAGAACACTACTTTTAGCGGCGTTTTTTAATAAGCGCCGCTAAAGAACATGATC
TTTAGAGGCGTTTCTTCCAAAGCGCCACAAAAGAACATGATCTTTAGCGACGTTTTTTC
Found at i:212891 original size:22 final size:22
Alignment explanation
Indices: 212860--212903 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
212850 TAGTGGCGTT
* *
212860 AAAAAGCGCCGCTAAAGACCTA
1 AAAAAACGCCGCTAAAAACCTA
212882 AAAAAACGCCGCTAAAAACCTA
1 AAAAAACGCCGCTAAAAACCTA
212904 TTCTGCTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.27, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:214235 original size:52 final size:52
Alignment explanation
Indices: 214178--214283 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
214168 GCTACAAATA
214178 CTTAAATTGTAATAAAATAAATATAATGTCCATCAACAATTATGCATGAGAT
1 CTTAAATTGTAATAAAATAAATATAATGTCCATCAACAATTATGCATGAGAT
* *
214230 CTTAAATTGTAATAACATAAATATAATGTGCATCAACAATTATGCATGAGAT
1 CTTAAATTGTAATAAAATAAATATAATGTCCATCAACAATTATGCATGAGAT
214282 CT
1 CT
214284 ATTTCTTTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.33
Consensus pattern (52 bp):
CTTAAATTGTAATAAAATAAATATAATGTCCATCAACAATTATGCATGAGAT
Found at i:217764 original size:25 final size:25
Alignment explanation
Indices: 217718--217775 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
217708 TATTAATTGG
* *
217718 GAAGCTCATACGAGCTATATATCAA
1 GAAGCTCATACGAGCCAAATATCAA
* * **
217743 GAAGCTCTTGCGAGCCAAATATCGG
1 GAAGCTCATACGAGCCAAATATCAA
217768 GAAGCTCA
1 GAAGCTCA
217776 AGAGAGACGT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (25 bp):
GAAGCTCATACGAGCCAAATATCAA
Found at i:220054 original size:8 final size:9
Alignment explanation
Indices: 220010--220052 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
220000 TTAATTGAGA
*
220010 AATTTATTT
1 AATTAATTT
*
220019 ATTTAATTT
1 AATTAATTT
*
220028 AATGAATTT
1 AATTAATTT
220037 AATTAA-TT
1 AATTAATTT
220045 AATTAATT
1 AATTAATT
220053 AAAATTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
8 8 0.29
9 20 0.71
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (9 bp):
AATTAATTT
Found at i:220440 original size:20 final size:20
Alignment explanation
Indices: 220415--220458 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
220405 TATTTACTTA
220415 GAATAAATTCAATTGTTTGG
1 GAATAAATTCAATTGTTTGG
220435 GAATAAATTCAATTGTTTGG
1 GAATAAATTCAATTGTTTGG
220455 GAAT
1 GAAT
220459 TACGATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (20 bp):
GAATAAATTCAATTGTTTGG
Found at i:225837 original size:21 final size:21
Alignment explanation
Indices: 225811--225851 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
225801 ATCTGCTCAA
* *
225811 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
225832 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
225852 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:229278 original size:22 final size:22
Alignment explanation
Indices: 229242--229283 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
229232 TATACAAGTA
229242 ATATTACTTGAATAATTATGAG
1 ATATTACTTGAATAATTATGAG
* *
229264 ATATTAGTTGCATAATTATG
1 ATATTACTTGAATAATTATG
229284 TCTCTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATTACTTGAATAATTATGAG
Found at i:230466 original size:11 final size:11
Alignment explanation
Indices: 230452--230488 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
230442 TTTAAATATA
230452 ATTTTCTTTTT
1 ATTTTCTTTTT
230463 ATTTTC-TTTT
1 ATTTTCTTTTT
*
230473 CTTTTCTTTTT
1 ATTTTCTTTTT
230484 -TTTTC
1 ATTTTC
230489 CCTAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (11 bp):
ATTTTCTTTTT
Found at i:234043 original size:26 final size:25
Alignment explanation
Indices: 233985--234054 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 25
233975 ATTTAATTAC
*
233985 AATACTGTAATTTCTAAAATAATTT
1 AATACTGTAATTTCTAAAAAAATTT
234010 --TA-T-T-ATTTCTAAATAAAATTT
1 AATACTGTAATTTCTAAA-AAAATTT
234031 AATACTGTAATTTCTTAAGAAAAA
1 AATACTGTAATTTC-TAA-AAAAA
234055 AATGAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
20 9 0.25
21 7 0.19
22 1 0.03
23 4 0.11
24 1 0.03
25 1 0.03
26 5 0.14
27 7 0.19
28 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (25 bp):
AATACTGTAATTTCTAAAAAAATTT
Found at i:236260 original size:21 final size:21
Alignment explanation
Indices: 236236--236278 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
236226 TCAGCTCTCT
236236 GGCCATCTTCCAT-CAAACATG
1 GGCC-TCTTCCATCCAAACATG
* *
236257 GGCCTTTTCCTTCCAAACATG
1 GGCCTCTTCCATCCAAACATG
236278 G
1 G
236279 AGGAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.28
Consensus pattern (21 bp):
GGCCTCTTCCATCCAAACATG
Found at i:241449 original size:23 final size:19
Alignment explanation
Indices: 241405--241444 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
241395 TTACATATTC
241405 TAAAAAATTTAATAATTTT
1 TAAAAAATTTAATAATTTT
241424 TAAAATAATTTAATAATTTT
1 TAAAA-AATTTAATAATTTT
241444 T
1 T
241445 TTTAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAAAAATTTAATAATTTT
Found at i:242297 original size:212 final size:212
Alignment explanation
Indices: 241930--242354 Score: 850
Period size: 212 Copynumber: 2.0 Consensus size: 212
241920 TATATTTTTT
241930 ATTTTCAACAATTTATAAATTTTCTTTTATGTTCTTCTAACTTTTTTTTTCCATTCTCTTATGCT
1 ATTTTCAACAATTTATAAATTTTCTTTTATGTTCTTCTAACTTTTTTTTTCCATTCTCTTATGCT
241995 TCTCCCTCTATTTTCCTCATTCTTCATTTCTTTTAACATAGTTTTTCTATGCTTTCCATTTGTAA
66 TCTCCCTCTATTTTCCTCATTCTTCATTTCTTTTAACATAGTTTTTCTATGCTTTCCATTTGTAA
242060 CTAGTCCACAAGCTCGCCTCACTCGGGAAAATTAAATTGTTCAAAAAAATAAAACATAGAAAAAC
131 CTAGTCCACAAGCTCGCCTCACTCGGGAAAATTAAATTGTTCAAAAAAATAAAACATAGAAAAAC
242125 TACGTTGAAAGAAATGG
196 TACGTTGAAAGAAATGG
242142 ATTTTCAACAATTTATAAATTTTCTTTTATGTTCTTCTAACTTTTTTTTTCCATTCTCTTATGCT
1 ATTTTCAACAATTTATAAATTTTCTTTTATGTTCTTCTAACTTTTTTTTTCCATTCTCTTATGCT
242207 TCTCCCTCTATTTTCCTCATTCTTCATTTCTTTTAACATAGTTTTTCTATGCTTTCCATTTGTAA
66 TCTCCCTCTATTTTCCTCATTCTTCATTTCTTTTAACATAGTTTTTCTATGCTTTCCATTTGTAA
242272 CTAGTCCACAAGCTCGCCTCACTCGGGAAAATTAAATTGTTCAAAAAAATAAAACATAGAAAAAC
131 CTAGTCCACAAGCTCGCCTCACTCGGGAAAATTAAATTGTTCAAAAAAATAAAACATAGAAAAAC
242337 TACGTTGAAAGAAATGG
196 TACGTTGAAAGAAATGG
242354 A
1 A
242355 GAAGGGAGGA
Statistics
Matches: 213, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
212 213 1.00
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.42
Consensus pattern (212 bp):
ATTTTCAACAATTTATAAATTTTCTTTTATGTTCTTCTAACTTTTTTTTTCCATTCTCTTATGCT
TCTCCCTCTATTTTCCTCATTCTTCATTTCTTTTAACATAGTTTTTCTATGCTTTCCATTTGTAA
CTAGTCCACAAGCTCGCCTCACTCGGGAAAATTAAATTGTTCAAAAAAATAAAACATAGAAAAAC
TACGTTGAAAGAAATGG
Found at i:247108 original size:23 final size:25
Alignment explanation
Indices: 247047--247111 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 25
247037 TGCTAGGATG
* *
247047 AAATTACATAATTATCATTTTTTAA
1 AAATTACATAATTATCATGTTTAAA
* **
247072 AAA-TATATTTTTAT-A-GTTTAAA
1 AAATTACATAATTATCATGTTTAAA
247094 AAATTACATAATTATCAT
1 AAATTACATAATTATCAT
247112 TTTCTGTAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
22 8 0.28
23 9 0.31
24 9 0.31
25 3 0.10
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (25 bp):
AAATTACATAATTATCATGTTTAAA
Found at i:248826 original size:17 final size:17
Alignment explanation
Indices: 248775--248829 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
248765 CATTTTCTCT
*
248775 TTTTTCTAACATAAAAT-
1 TTTTTATAA-ATAAAATA
*
248792 TTATTTATTAAA-ATAATA
1 TT-TTTA-TAAATAAAATA
248810 TTTTTATAAATAAAATA
1 TTTTTATAAATAAAATA
248827 TTT
1 TTT
248830 AAAAAAACCT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 4 0.13
17 18 0.58
18 6 0.19
19 3 0.10
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTTATAAATAAAATA
Found at i:250828 original size:16 final size:16
Alignment explanation
Indices: 250807--250837 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
250797 CCTGTTATGA
*
250807 TTTAAATTTAAAATTT
1 TTTAAATTGAAAATTT
250823 TTTAAATTGAAAATT
1 TTTAAATTGAAAATT
250838 CTTGATCTCT
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:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
TTTAAATTGAAAATTT
Found at i:251378 original size:19 final size:19
Alignment explanation
Indices: 251352--251397 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
251342 AATTAATTAT
*
251352 ATATTTTTAAAA-ATTTTA
1 ATATTTTTAAAATAATTTA
251370 ATAATTTTTAAAATAATTTA
1 AT-ATTTTTAAAATAATTTA
251390 ATATTTTT
1 ATATTTTT
251398 TGAATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 2 0.08
19 16 0.64
20 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTTTTAAAATAATTTA
Found at i:251398 original size:20 final size:19
Alignment explanation
Indices: 251350--251398 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
251340 GCAATTAATT
*
251350 ATATATTTTTAAAAATTTTA
1 ATAT-TTTTTAAAAAATTTA
*
251370 ATAATTTTTAAAATAATTTA
1 ATATTTTTTAAAA-AATTTA
251390 ATATTTTTT
1 ATATTTTTT
251399 GAATTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTTTTTAAAAAATTTA
Found at i:254948 original size:21 final size:21
Alignment explanation
Indices: 254924--254966 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
254914 TCAGCTCTCT
254924 GGCCATCTTCCAT-CAAACATG
1 GGCC-TCTTCCATCCAAACATG
* *
254945 GGCCTTTTCCTTCCAAACATG
1 GGCCTCTTCCATCCAAACATG
254966 G
1 G
254967 AGCAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.28
Consensus pattern (21 bp):
GGCCTCTTCCATCCAAACATG
Found at i:260334 original size:16 final size:16
Alignment explanation
Indices: 260313--260343 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
260303 GTTTCACTTT
260313 GACTGCATGGCATTTA
1 GACTGCATGGCATTTA
260329 GACTGCATGGCATTT
1 GACTGCATGGCATTT
260344 CATTATAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (16 bp):
GACTGCATGGCATTTA
Found at i:263645 original size:6 final size:7
Alignment explanation
Indices: 263630--263669 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
263620 AATTGACGAG
263630 ATGAAAA
1 ATGAAAA
263637 ATG-AAA
1 ATGAAAA
263643 ATGAAAA
1 ATGAAAA
263650 ATGAAAA
1 ATGAAAA
263657 ATGAAAA
1 ATGAAAA
263664 AT-AAAA
1 ATGAAAA
263670 TAGAGAGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 10 0.31
7 22 0.69
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.15
Consensus pattern (7 bp):
ATGAAAA
Found at i:265107 original size:43 final size:43
Alignment explanation
Indices: 265058--265250 Score: 115
Period size: 44 Copynumber: 4.4 Consensus size: 43
265048 TCCGTGGTTA
* *
265058 CAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGTAG
1 CAGTGGAGTAGATTGAAGCCAGTAATTCTACTTCCCTGGGCAG
* * * **
265101 CAGTGGAATAGATTGAAGATTTCAG-ATATTGT-C-TCCCTAAGCAG
1 CAGTGGAGTAGATTGAAG---CCAGTA-ATTCTACTTCCCTGGGCAG
* * ** **** * * *
265145 TAGTGGAGCAGATCAAAAATGGTGAATTTTACCTCCCTGTGGTTA-
1 CAGTGGAGTAGATTGAAGCCAGT-AATTCTACTTCCCTG-GG-CAG
*
265190 CAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAG
1 CAGTGGAGTAGATTGAAGCCAGTAATTCTACTTCCCTGGGCAG
*
265233 CAGTGGAATAGATTGAAG
1 CAGTGGAGTAGATTGAAG
265251 ATTTCAGATC
Statistics
Matches: 105, Mismatches: 34, Indels: 22
0.65 0.21 0.14
Matches are distributed among these distances:
41 1 0.01
42 5 0.05
43 36 0.34
44 38 0.36
45 17 0.16
46 8 0.08
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (43 bp):
CAGTGGAGTAGATTGAAGCCAGTAATTCTACTTCCCTGGGCAG
Found at i:265174 original size:132 final size:132
Alignment explanation
Indices: 264981--265667 Score: 1126
Period size: 132 Copynumber: 5.2 Consensus size: 132
264971 GTAGAGCAGG
*
264981 TTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTATC
1 TTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACC
*
265046 TCTCC-GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGTAGCAGTGGAAT
66 TC-CCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAAT
265110 AGA
130 AGA
*
265113 TTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAAATGGTGAATTTTACC
1 TTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACC
265178 TCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATA
66 TCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATA
265243 GA
131 GA
* * * *
265245 TTGAAGATTTCAGATCTTATCTCCCCAAGCAGTAGTGAAGCAGATCAAAGATGGTGAATTTTACC
1 TTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACC
* * *
265310 TCCCTGTAGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGGCAACAGTGGAATA
66 TCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATA
265375 GA
131 GA
* * * *
265377 TTGAAGATTTCAGATCTTGTCCCCCTAAGCAGTAGTGGAGCAGATCAAAAATGGTGAATTGTACC
1 TTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACC
265442 TCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATA
66 TCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATA
265507 GA
131 GA
* *
265509 TTGAAGATTTCAGATCTTGTCCCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACC
1 TTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACC
* * * *
265574 TCCCTGTGATTACAGTGGAGTATATTGAAACCAATAATTCTA-TCTCCCTGGGCAGCAGTGGAAT
66 TCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGTGGAAT
265638 AGA
130 AGA
* ** *
265641 TTAAAGATAACAGATATTGTCTTCCTA
1 TTGAAGATTTCAGATATTGTCTCCCTA
265668 TATTGGTAGC
Statistics
Matches: 521, Mismatches: 32, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
131 3 0.01
132 518 0.99
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (132 bp):
TTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACC
TCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATA
GA
Found at i:265879 original size:132 final size:133
Alignment explanation
Indices: 265637--266090 Score: 540
Period size: 133 Copynumber: 3.4 Consensus size: 133
265627 AGCAGTGGAA
* * * * *
265637 TAGATTAAAGATAACAGATATTGTCTTCCTATATTGGTAGCGAAGTGGATCAAAGAAAGCAGATC
1 TAGATCAAAGATAACAGATATTGTCTTCCTATACTGGTGGTGAAGTAGATCAAAGAAAGCAGATC
* *
265702 TTCTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAAATCTTGTCTTCATGTACT-GACGT
66 TTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTAG-CGT
265766 GAAG
130 GAAG
* * * * *
265770 TAGATCAAAGACAACAGATCTTGTC-TCCCATACTGGTGGTGGAGTAGATCGAAGAAAGCAGATC
1 TAGATCAAAGATAACAGATATTGTCTTCCTATACTGGTGGTGAAGTAGATCAAAGAAAGCAGATC
* * *
265834 TTGTCTTCATGTACTGGCGTGAAGAAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTAGCGTG
66 TTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTAGCGTG
265899 AAG
131 AAG
* * *
265902 TAGATCAAAAATAGCAGATATTGTCTTCCTATACTGGCGGTGAAGTAGATCAAAGATAA-CAGAT
1 TAGATCAAAGATAACAGATATTGTCTTCCTATACTGGTGGTGAAGTAGATCAAAGA-AAGCAGAT
* * * *** * *
265966 CTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGAAAACAGATCTTGTTTTCCCATACTGGTGG
65 CTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTAG-CG
*
266031 CGAAG
129 TGAAG
* * * * * *
266036 AAGATCGAAGA-AAGCAGATATTGTCTTCATGTACTGG-CGTGAAGTAGATCGAAGA
1 TAGATCAAAGATAA-CAGATATTGTCTTCCTATACTGGTGGTGAAGTAGATCAAAGA
266091 TTACAGATCT
Statistics
Matches: 273, Mismatches: 43, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
132 114 0.42
133 123 0.45
134 36 0.13
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (133 bp):
TAGATCAAAGATAACAGATATTGTCTTCCTATACTGGTGGTGAAGTAGATCAAAGAAAGCAGATC
TTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTAGCGTG
AAG
Found at i:266098 original size:44 final size:44
Alignment explanation
Indices: 265678--266090 Score: 476
Period size: 44 Copynumber: 9.3 Consensus size: 44
265668 TATTGGTAGC
* * *
265678 GAAGTGGATCAAAGAAAGCAGATCTTCTCTTCATGTATTGGCGT
1 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGT
* *
265722 GAAGTAGATCAAAGAAAGCAAATCTTGTCTTCATGTACTGACGT
1 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGT
* *
265766 GAAGTAGATCAAAGACAA-CAGATCTTGTCTCCCA--TACTGGTGGT
1 GAAGTAGATCAAAGA-AAGCAGATCTTGTCT-TCATGTACTGG-CGT
* *
265810 GGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGCGT
1 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGT
* * *
265854 GAAGAAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTAGCGT
1 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGT
* * *
265898 GAAGTAGATCAAA-AATAGCAGATATTGTCTTCCTATACTGGCGGT
1 GAAGTAGATCAAAGAA-AGCAGATCTTGTCTTCATGTACTGGC-GT
* *
265943 GAAGTAGATCAAAGATAA-CAGATCTTGTCTTCATGTATTGGCAT
1 GAAGTAGATCAAAGA-AAGCAGATCTTGTCTTCATGTACTGGCGT
* * *** * *
265987 GAAGTAGATCAAAGAAAACAGATCTTGTTTTCCCATACTGGTGGC
1 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGG-CGT
* * *
266032 GAAGAAGATCGAAGAAAGCAGATATTGTCTTCATGTACTGGCGT
1 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGT
*
266076 GAAGTAGATCGAAGA
1 GAAGTAGATCAAAGA
266091 TTACAGATCT
Statistics
Matches: 311, Mismatches: 46, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
43 13 0.04
44 217 0.70
45 78 0.25
46 2 0.01
47 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (44 bp):
GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGT
Found at i:266101 original size:89 final size:89
Alignment explanation
Indices: 265637--266090 Score: 485
Period size: 89 Copynumber: 5.1 Consensus size: 89
265627 AGCAGTGGAA
* * * * * *
265637 TAGATTAAAGATAA-CAGATATTGTCTTCCTATATTGGTAGCGAAGTGGATCAAAGAAAGCAGAT
1 TAGATCAAAGA-AAGCAGATCTTGTCTTCCTATACTGGTCGTGAAGTAGATCAAAGAAAGCAGAT
* *
265701 CTTCTCTTCATGTATTGGCGTGAAG
65 CTTGTCTTCATGTACTGGCGTGAAG
* * * *
265726 TAGATCAAAGAAAGCAAATCTTGTCTTCATGTACT-GACGTGAAGTAGATCAAAGACAA-CAGAT
1 TAGATCAAAGAAAGCAGATCTTGTCTTCCTATACTGGTCGTGAAGTAGATCAAAGA-AAGCAGAT
* * *
265789 CTTGTCTCCCA--TACTGGTGGTGGAG
65 CTTGTCT-TCATGTACTGG-CGTGAAG
* * * * *
265814 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGAAGAAGATCGAAGAAAGCAGATC
1 TAGATCAAAGAAAGCAGATCTTGTCTTCCTATACTGGTCGTGAAGTAGATCAAAGAAAGCAGATC
*
265878 TTGTCTTCATGTACTAGCGTGAAG
66 TTGTCTTCATGTACTGGCGTGAAG
*
265902 TAGATCAAA-AATAGCAGATATTGTCTTCCTATACTGG-CGGTGAAGTAGATCAAAGATAA-CAG
1 TAGATCAAAGAA-AGCAGATCTTGTCTTCCTATACTGGTC-GTGAAGTAGATCAAAGA-AAGCAG
* *
265964 ATCTTGTCTTCATGTATTGGCATGAAG
63 ATCTTGTCTTCATGTACTGGCGTGAAG
* * * * * * * *
265991 TAGATCAAAGAAAACAGATCTTGTTTTCCCATACTGGTGGCGAAGAAGATCGAAGAAAGCAGATA
1 TAGATCAAAGAAAGCAGATCTTGTCTTCCTATACTGGTCGTGAAGTAGATCAAAGAAAGCAGATC
266056 TTGTCTTCATGTACTGGCGTGAAG
66 TTGTCTTCATGTACTGGCGTGAAG
*
266080 TAGATCGAAGA
1 TAGATCAAAGA
266091 TTACAGATCT
Statistics
Matches: 307, Mismatches: 44, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
87 11 0.04
88 133 0.43
89 159 0.52
90 4 0.01
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (89 bp):
TAGATCAAAGAAAGCAGATCTTGTCTTCCTATACTGGTCGTGAAGTAGATCAAAGAAAGCAGATC
TTGTCTTCATGTACTGGCGTGAAG
Found at i:266560 original size:263 final size:263
Alignment explanation
Indices: 266080--266590 Score: 907
Period size: 263 Copynumber: 1.9 Consensus size: 263
266070 TGGCGTGAAG
* **
266080 TAGATCGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAAATGGTGGATTT
1 TAGATCGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAAATGACGGATTT
*
266145 TACCTCCCTAATGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
66 TACCTCCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
266210 AATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAATATGGTGGAT
131 AATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAATATGGTGGAT
*
266275 TTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATT-CTATCTCCCTGGGAATAGT
196 TTTACCTCCCTGAGGATACAGTGGAGTACATTGAAGCCAGT-ATTCCTATCTCCCTGGGAATAGT
266339 GGAA
260 GGAA
* * *
266343 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACGGATTT
1 TAGATCGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAAATGACGGATTT
*
266408 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
66 TACCTCCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
* *
266473 AATAGATTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAGATCAAATATGGTGGAT
131 AATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAATATGGTGGAT
266538 TTTACCTCCCTGAGGATACAGTGGAGTACATTGAAGCCAGTATTCCTATCTCC
196 TTTACCTCCCTGAGGATACAGTGGAGTACATTGAAGCCAGTATTCCTATCTCC
266591 TTGAAGTTGT
Statistics
Matches: 236, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
262 3 0.01
263 233 0.99
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (263 bp):
TAGATCGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAAATGACGGATTT
TACCTCCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
AATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAATATGGTGGAT
TTTACCTCCCTGAGGATACAGTGGAGTACATTGAAGCCAGTATTCCTATCTCCCTGGGAATAGTG
GAA
Found at i:266633 original size:132 final size:132
Alignment explanation
Indices: 266080--266590 Score: 882
Period size: 132 Copynumber: 3.9 Consensus size: 132
266070 TGGCGTGAAG
* * *
266080 TAGATCGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAAATGGTGGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAATATGGTGGATTT
* *
266145 TACCTCCCTAATGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
266210 AA
131 AA
*
266212 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAATATGGTGGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAATATGGTGGATTT
*
266277 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGG-AATAGTGG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
266341 AA
131 AA
* * **
266343 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACGGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAATATGGTGGATTT
266408 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
266473 AA
131 AA
*
266475 TAGATTGAAGATTACAGATCTTATCTCCTTAAGCAGTAGTGGAGCAGATCAAATATGGTGGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAATATGGTGGATTT
*
266540 TACCTCCCTGAGGATACAGTGGAGTACATTGAAGCCAGT-ATTCCTATCTCC
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATT-CTATCTCC
266591 TTGAAGTTGT
Statistics
Matches: 358, Mismatches: 19, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
131 128 0.36
132 230 0.64
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (132 bp):
TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAATATGGTGGATTT
TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
AA
Found at i:269402 original size:22 final size:20
Alignment explanation
Indices: 269371--269411 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
269361 ACCCGCATGA
*
269371 ATGAAGATGAATGAGAAAAGGG
1 ATGAAAATGAA-G-GAAAAGGG
269393 ATGAAAATGAAGGAAAAGG
1 ATGAAAATGAAGGAAAAGG
269412 AAAGGAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.54, C:0.00, G:0.34, T:0.12
Consensus pattern (20 bp):
ATGAAAATGAAGGAAAAGGG
Found at i:269934 original size:27 final size:27
Alignment explanation
Indices: 269898--269951 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
269888 TTCAACTTAA
*
269898 TTTTTTTCTAATTTGGTACTT-AATTT
1 TTTTTTTCTAAATTGGTACTTGAATTT
269924 TTTTTTGTCTAAATTGGTACTTGAATTT
1 TTTTTT-TCTAAATTGGTACTTGAATTT
269952 ATCACTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 6 0.24
27 14 0.56
28 5 0.20
ACGTcount: A:0.20, C:0.07, G:0.11, T:0.61
Consensus pattern (27 bp):
TTTTTTTCTAAATTGGTACTTGAATTT
Found at i:300925 original size:24 final size:23
Alignment explanation
Indices: 300880--300966 Score: 70
Period size: 24 Copynumber: 3.6 Consensus size: 23
300870 ATTCAACTTA
300880 AAAAAATA-AAAAGAAATTTAAAATCT
1 AAAAAATATAAAA-AAA--TAAAAT-T
*
300906 -AAAAATATATAACAAATAAAATT
1 AAAAAATATA-AAAAAATAAAATT
300929 AAAAAATATAAAAAAATAAATATT
1 AAAAAATATAAAAAAATAAA-ATT
* * *
300953 CAAAATTTTAAAAA
1 AAAAAATATAAAAA
300967 TATTATAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
23 10 0.19
24 29 0.56
25 7 0.13
26 4 0.08
27 2 0.04
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.25
Consensus pattern (23 bp):
AAAAAATATAAAAAAATAAAATT
Found at i:301182 original size:22 final size:23
Alignment explanation
Indices: 301150--301193 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
301140 GATTTATTTA
301150 TTTTGAATTTTAAAC-AATTTTT
1 TTTTGAATTTTAAACTAATTTTT
* *
301172 TTTTGACTTTTTAACTAATTTT
1 TTTTGAATTTTAAACTAATTTT
301194 GTTATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTTGAATTTTAAACTAATTTTT
Found at i:301241 original size:31 final size:31
Alignment explanation
Indices: 301190--301249 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
301180 TTTTAACTAA
*
301190 TTTTGTTATTTTATTTTCAATTTATATATTC
1 TTTTGTTATTTTAATTTCAATTTATATATTC
301221 TTTT-TTATTTTCAATTTCAATTTATATAT
1 TTTTGTTATTTT-AATTTCAATTTATATAT
301250 ATTTGAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.67
Consensus pattern (31 bp):
TTTTGTTATTTTAATTTCAATTTATATATTC
Found at i:305460 original size:27 final size:25
Alignment explanation
Indices: 305413--305470 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 25
305403 AATTTCTTCC
*
305413 AATTTAATTTTAATATATATTT-TAA
1 AATTTTATTTTAATATATATTTGT-A
*
305438 AATTTTATTTTATTATAACTATTTGTA
1 AATTTTATTTTAATAT-A-TATTTGTA
305465 AATTTT
1 AATTTT
305471 GAGACAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 14 0.50
26 1 0.04
27 12 0.43
28 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
AATTTTATTTTAATATATATTTGTA
Done.