Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013793.1 Kokia drynarioides strain JFW-HI SEQ_128821, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 80064
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:690 original size:15 final size:15
Alignment explanation
Indices: 664--716 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
654 GGGCACTTTA
*
664 TAATTGGACCATTTG
1 TAATTGGGCCATTTG
* *
679 TATTTGGGCCATCTG
1 TAATTGGGCCATTTG
* *
694 TAACTGGGTCATTTG
1 TAATTGGGCCATTTG
709 TAATTGGG
1 TAATTGGG
717 ACTTTTGTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.40
Consensus pattern (15 bp):
TAATTGGGCCATTTG
Found at i:813 original size:17 final size:17
Alignment explanation
Indices: 753--815 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
743 TGGACTTTTC
* *
753 TAAATTTAATTTTATAA
1 TAAATTTAAATTTAAAA
*
770 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
787 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
804 TAAACTTAAATT
1 TAAATTTAAATT
816 CAATTTCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:2832 original size:17 final size:18
Alignment explanation
Indices: 2797--2833 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2787 CCTTTTCGTA
2797 TATATAATTTTAAACATT
1 TATATAATTTTAAACATT
*
2815 TATATATTTTTAAA-ATT
1 TATATAATTTTAAACATT
2832 TA
1 TA
2834 AATTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TATATAATTTTAAACATT
Found at i:2857 original size:23 final size:24
Alignment explanation
Indices: 2813--2867 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
2803 ATTTTAAACA
2813 TTTATATATTTTTAAAATTTAAAT
1 TTTATATATTTTTAAAATTTAAAT
* *
2837 TTTATTATATTTTT-TAATTAAAAT
1 TTTA-TATATTTTTAAAATTTAAAT
*
2861 TTGATAT
1 TTTATAT
2868 TAATCTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 3 0.11
24 15 0.56
25 9 0.33
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTATATATTTTTAAAATTTAAAT
Found at i:2868 original size:26 final size:24
Alignment explanation
Indices: 2813--2879 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 24
2803 ATTTTAAACA
* *
2813 TTTA-TATATTTTTAAAATTTAAAT
1 TTTATTATATTTTT-TAATTAAAAT
2837 TTTATTATATTTTTTAATTAAAAT
1 TTTATTATATTTTTTAATTAAAAT
2861 TTGATATTA-ATCTTTTTAA
1 TT--TATTATAT-TTTTTAA
2880 GAGAATTAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
24 14 0.38
25 11 0.30
26 12 0.32
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (24 bp):
TTTATTATATTTTTTAATTAAAAT
Found at i:3664 original size:28 final size:26
Alignment explanation
Indices: 3617--3671 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 26
3607 ACTTTTATTT
3617 TATTTAAGTTACATTTTAGTCACTTA
1 TATTTAAGTTACATTTTAGTCACTTA
*
3643 TATTTGAATGTTACGTTTTAGTCACTTA
1 TATTT-AA-GTTACATTTTAGTCACTTA
3671 T
1 T
3672 GTTAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 5 0.19
27 2 0.08
28 19 0.73
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (26 bp):
TATTTAAGTTACATTTTAGTCACTTA
Found at i:8413 original size:21 final size:20
Alignment explanation
Indices: 8387--8431 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 20
8377 AGAAAGTTGT
8387 TGGATAAA-GAATGATGCATGG
1 TGGATAAATGAA-GATG-ATGG
8408 TGGATAAATTGAAGATGATGG
1 TGGATAAA-TGAAGATGATGG
8429 TGG
1 TGG
8432 GATTTTGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 15 0.68
22 4 0.18
23 3 0.14
ACGTcount: A:0.36, C:0.02, G:0.36, T:0.27
Consensus pattern (20 bp):
TGGATAAATGAAGATGATGG
Found at i:10928 original size:28 final size:28
Alignment explanation
Indices: 10888--10941 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
10878 TGAGACTTAG
10888 TAAAACTTATATTTGTCAATGATCAACC
1 TAAAACTTATATTTGTCAATGATCAACC
10916 TAAAACTTATATTTGTCAATGATCAA
1 TAAAACTTATATTTGTCAATGATCAA
10942 ACTTACCTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (28 bp):
TAAAACTTATATTTGTCAATGATCAACC
Found at i:12454 original size:20 final size:21
Alignment explanation
Indices: 12412--12455 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
12402 TAACTACAAA
*
12412 ATTAAATACACAATACATTTT
1 ATTAAATACACAATACATATT
* *
12433 ATTAAA-ACACATTCCATATT
1 ATTAAATACACAATACATATT
12453 ATT
1 ATT
12456 CTAACTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTAAATACACAATACATATT
Found at i:17021 original size:38 final size:38
Alignment explanation
Indices: 16962--17035 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
16952 CCCTACTGAG
*
16962 TACATGTTAAGCATGTTTACTGCTAGTGTTGAATTGAA
1 TACATGTTAAGCATGTCTACTGCTAGTGTTGAATTGAA
*
17000 TACATGTTAAGTATGTCTACTGCTAGTGTTGAATTG
1 TACATGTTAAGCATGTCTACTGCTAGTGTTGAATTG
17036 TTCTATTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.41
Consensus pattern (38 bp):
TACATGTTAAGCATGTCTACTGCTAGTGTTGAATTGAA
Found at i:17882 original size:19 final size:20
Alignment explanation
Indices: 17841--17883 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
17831 AATTTGCATG
17841 AAATCTAGTTTTCACTAAAA
1 AAATCTAGTTTTCACTAAAA
17861 AAATCTAGTTTTCACTAAAA
1 AAATCTAGTTTTCACTAAAA
17881 AAA
1 AAA
17884 CTATGTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.33
Consensus pattern (20 bp):
AAATCTAGTTTTCACTAAAA
Found at i:26251 original size:10 final size:9
Alignment explanation
Indices: 26221--26263 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
26211 AAAAAAATTC
*
26221 AAAATTTAA
1 AAAATTTTA
* *
26230 AAAATATAA
1 AAAATTTTA
26239 AAAATCTTTA
1 AAAAT-TTTA
26249 AAAATTTTA
1 AAAATTTTA
26258 AAAATT
1 AAAATT
26264 AAAGTGGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 23 0.77
10 7 0.23
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAATTTTA
Found at i:28386 original size:20 final size:20
Alignment explanation
Indices: 28350--28394 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
28340 AACTTTTTGT
*
28350 GTTTATTTAATAAAAAAT-A
1 GTTTATTTAACAAAAAATAA
*
28369 GTTTATTTTAACATAAAATAA
1 GTTTA-TTTAACAAAAAATAA
28390 GTTTA
1 GTTTA
28395 AGAGTTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 11 0.50
21 6 0.27
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (20 bp):
GTTTATTTAACAAAAAATAA
Found at i:33230 original size:23 final size:23
Alignment explanation
Indices: 33200--33264 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
33190 TAACTAGACT
33200 TTCTGGAAGTTGCTGACTGCATC
1 TTCTGGAAGTTGCTGACTGCATC
33223 TTCTGGAAGTTGCTGACTGCATC
1 TTCTGGAAGTTGCTGACTGCATC
* *
33246 TTCTAGAAGCTGCTGACTG
1 TTCTGGAAGTTGCTGACTG
33265 GATGCCACGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (23 bp):
TTCTGGAAGTTGCTGACTGCATC
Found at i:44387 original size:24 final size:24
Alignment explanation
Indices: 44356--44414 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
44346 TAAAAGTTCT
*
44356 CAAACTACTGATACTT-CTATGAA
1 CAAACTACCGATACTTACTATGAA
44379 CAAATCTACCGATACTTACTATG--
1 CAAA-CTACCGATACTTACTATGAA
44402 C-AACTACCGATAC
1 CAAACTACCGATAC
44415 AACTCAAGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 10 0.30
22 2 0.06
23 5 0.15
24 11 0.33
25 5 0.15
ACGTcount: A:0.37, C:0.27, G:0.08, T:0.27
Consensus pattern (24 bp):
CAAACTACCGATACTTACTATGAA
Found at i:45285 original size:10 final size:10
Alignment explanation
Indices: 45270--45313 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
45260 TACTAACACC
*
45270 TATACATAAA
1 TATACATATA
*
45280 TATACACATA
1 TATACATATA
*
45290 TATATATATA
1 TATACATATA
*
45300 TATATATATA
1 TATACATATA
45310 TATA
1 TATA
45314 TATTTATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
TATACATATA
Found at i:45294 original size:2 final size:2
Alignment explanation
Indices: 45287--45316 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
45277 AAATATACAC
45287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45317 TTATTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45321 original size:4 final size:4
Alignment explanation
Indices: 45314--45338 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
45304 TATATATATA
45314 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
45339 TTTTCTTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:50052 original size:8 final size:7
Alignment explanation
Indices: 50034--50060 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
50024 AAAGAAAAGA
50034 AAAAAAC
1 AAAAAAC
50041 AAAAAAC
1 AAAAAAC
50048 AAAAAAC
1 AAAAAAC
50055 AAAAAA
1 AAAAAA
50061 GGAGAGGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:51053 original size:50 final size:49
Alignment explanation
Indices: 50990--51486 Score: 378
Period size: 49 Copynumber: 10.1 Consensus size: 49
50980 AATGAGCCGT
** * **
50990 GGTACCATGAAGATTTGAAGGGAAAGGTTGAGATTGCAATGATGAACCC
1 GGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCC
* * *
51039 GGTACCTTAGAAGA--TGCAATGGGAAAGGTTGAGGTTGCAACGGTGAACCC
1 GGTACCAT-GAAGATTTG-AA-GGGAAAGGTTGAGGCTGCAACGGCGAACCC
*
51089 GGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCT
1 GGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCC
* * * * * * *
51138 GGTACCTTAAAAGATGTGATGAGAAAGGTTGAGGCTGCAACGGCTAATCC
1 GGTACCAT-GAAGATTTGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCC
* *
51188 GAG-ACCATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGACGAACCC
1 G-GTACCATGAAGATTTGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCC
* * * * * *
51237 TGTACCATGAAGATATGAAGGAAAAGGTTGA-GCCGTAATGGCGAACCC
1 GGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCC
* * * * * *
51285 GTTACCATGAAGATTTAAAGGGAAAGGTTAAGACTGAAATGGCGAACCC
1 GGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCC
* * * ** * ** *
51334 AGTACCTTAGAAGATGTGGTGGG-AAGGATTGAGG-TCGTAACAACGAATCC
1 GGTACCAT-GAAGATTTGAAGGGAAAGG-TTGAGGCT-GCAACGGCGAACCC
* * * * * * *** **
51384 GGTACCATGAA-ATGTGATGAGAAAGGTTGATGCCGTAACAATGAACTT
1 GGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCC
* * * * *
51432 GGTGCCATGAAGATTTAAAGGGAAAGGTTGAGGCCGCAACGGTGAACCT
1 GGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCC
51481 GGTACC
1 GGTACC
51487 TTAGGAACAT
Statistics
Matches: 358, Mismatches: 75, Indels: 30
0.77 0.16 0.06
Matches are distributed among these distances:
48 75 0.21
49 171 0.48
50 109 0.30
51 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.20
Consensus pattern (49 bp):
GGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCC
Found at i:51164 original size:99 final size:98
Alignment explanation
Indices: 50990--51413 Score: 415
Period size: 99 Copynumber: 4.3 Consensus size: 98
50980 AATGAGCCGT
* * *
50990 GGTACCATGAAGATTTGAAGGGAAAGGTTGAGATTGCAATGATGAACCCGGTACCTTAGAAGATG
1 GGTACCATGAAGATTTGAAGGGAAAGGTTGAGACTGCAACGACGAACCCGGTACCTTAGAAGATG
** ** *
51055 CAATGGGAAAGGTTGAGGTTGCAACGGTGAACCC
66 TGAT-GGAAAGGTTGAGGCCGCAACGGCGAACCC
* * * *
51089 GGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCTGCAACGGCGAACCTGGTACCTTAAAAGATG
1 GGTACCATGAAGATTTGAAGGGAAAGGTTGAGACTGCAACGACGAACCCGGTACCTTAGAAGATG
* * *
51154 TGATGAGAAAGGTTGAGGCTGCAACGGCTAATCC
66 TGATG-GAAAGGTTGAGGCCGCAACGGCGAACCC
* * * *
51188 GAG-ACCATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCTGTACCAT-GAAGAT
1 G-GTACCATGAAGATTTGAAGGGAAAGGTTGAGACTGCAACGACGAACCCGGTACCTTAGAAGAT
* * * *
51251 ATGAAGGAAAAGGTTGA-GCCGTAATGGCGAACCC
65 GTGATGG-AAAGGTTGAGGCCGCAACGGCGAACCC
* * * * * * *
51285 GTTACCATGAAGATTTAAAGGGAAAGGTTAAGACTGAAATGGCGAACCCAGTACCTTAGAAGATG
1 GGTACCATGAAGATTTGAAGGGAAAGGTTGAGACTGCAACGACGAACCCGGTACCTTAGAAGATG
* * * * ** *
51350 TGGTGGGAAGGATTGAGGTCGTAACAACGAATCC
66 TGATGGAAAGG-TTGAGGCCGCAACGGCGAACCC
* * *
51384 GGTACCATGAA-ATGTGATGAGAAAGGTTGA
1 GGTACCATGAAGATTTGAAGGGAAAGGTTGA
51414 TGCCGTAACA
Statistics
Matches: 267, Mismatches: 51, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
97 63 0.24
98 47 0.18
99 156 0.58
100 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.20
Consensus pattern (98 bp):
GGTACCATGAAGATTTGAAGGGAAAGGTTGAGACTGCAACGACGAACCCGGTACCTTAGAAGATG
TGATGGAAAGGTTGAGGCCGCAACGGCGAACCC
Found at i:51380 original size:147 final size:148
Alignment explanation
Indices: 50989--51490 Score: 458
Period size: 147 Copynumber: 3.4 Consensus size: 148
50979 AAATGAGCCG
* * ** *
50989 TGGTACCATGAAGATTTGAAGGGAAAGGTTGAGATTGCAATGATGAACCCGGTACCTTAGAAGAT
1 TGGTACCATGAAGATTTAAAGGGAAAGGTTGAGACTGCAATGGCGAACCCAGTACCTTAGAAGAT
** * ** * *
51054 GCAATGGGAAAGGTTGAGGTTGCAACGGTGAACCCGGTACCATGAAGATTTGAAGGGAAAGGTTG
66 GTGATGGGAAAGGTTGAGGTCGCAACGACGAACCCGGTACCATGAAGATATGAAGGAAAAGGTTG
* *
51119 AGGCTGCAACGGCGAACC
131 AGGCCGTAACGGCGAACC
* * * * * * * * * * *
51137 TGGTACCTTAAAAGATGTGATGAGAAAGGTTGAGGCTGCAACGGCTAATCCGAG-ACCAT-GAAG
1 TGGTACCAT-GAAGATTTAAAGGGAAAGGTTGAGACTGCAATGGCGAA-CCCAGTACCTTAGAAG
* * * *
51200 ATTTGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCTGTACCATGAAGATATGAAGGAAAAGGT
64 ATGTGATGGGAAAGGTTGAGGTCGCAACGACGAACCCGGTACCATGAAGATATGAAGGAAAAGGT
*
51265 TGA-GCCGTAATGGCGAACC
129 TGAGGCCGTAACGGCGAACC
* * * *
51284 CGTTACCATGAAGATTTAAAGGGAAAGGTTAAGACTGAAATGGCGAACCCAGTACCTTAGAAGAT
1 TGGTACCATGAAGATTTAAAGGGAAAGGTTGAGACTGCAATGGCGAACCCAGTACCTTAGAAGAT
* * * * * *
51349 GTGGTGGG-AAGGATTGAGGTCGTAACAACGAATCCGGTACCATGAA-ATGTG-ATGAGAAAGGT
66 GTGATGGGAAAGG-TTGAGGTCGCAACGACGAACCCGGTACCATGAAGATATGAAGGA-AAAGGT
* *** *
51411 TGATGCCGTAACAATGAACT
129 TGAGGCCGTAACGGCGAACC
* * * * * **
51431 TGGTGCCATGAAGATTTAAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTGGTACCTTAG
1 TGGTACCATGAAGATTTAAAGGGAAAGGTTGAGACTGCAATGGCGAACCCAGTACCTTAG
51491 GAACATGACG
Statistics
Matches: 278, Mismatches: 69, Indels: 15
0.77 0.19 0.04
Matches are distributed among these distances:
145 7 0.03
146 49 0.18
147 118 0.42
148 69 0.25
149 32 0.12
150 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.20
Consensus pattern (148 bp):
TGGTACCATGAAGATTTAAAGGGAAAGGTTGAGACTGCAATGGCGAACCCAGTACCTTAGAAGAT
GTGATGGGAAAGGTTGAGGTCGCAACGACGAACCCGGTACCATGAAGATATGAAGGAAAAGGTTG
AGGCCGTAACGGCGAACC
Found at i:51838 original size:42 final size:42
Alignment explanation
Indices: 51723--52136 Score: 434
Period size: 42 Copynumber: 10.1 Consensus size: 42
51713 GCAATTACAT
** * *
51723 CATCATCCAATCTCTTACCCCGATTGTGGGGCATAAT---GC
1 CATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
*
51762 CATCATCCAATCTCTTA-CTCGATCATGGGGCAGATTGCAGC
1 CATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* * * *
51803 CATAATCCAATCTCTTACCTCGATCATGGGGCAGATTACA-T
1 CATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* * * * * *
51844 CATCATTCAATCTCTTACCCTGATCATGGGGTAAATTACA-T
1 CATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* * *
51885 CATCATCCAATCTCTTACCCTGATCTTGAGGCAGATTGCAGC
1 CATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* * * *
51927 CATCATCCAATCTCTTACCTCGATCATGGTGTAGATTGTAGC
1 CATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* * *
51969 CATCATCCAATCTCTTACCCCGATCATAGGGTAGATTGTAG-
1 CATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* * * *
52010 C--CATCCGATCTCTTACCCCGATTATAGGGCA-ATTGCAGT
1 CATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* **
52049 CATCATCCAATTTCTTACCCCGATCATAAGGCAGATTGCAGC
1 CATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
* * * *
52091 CATTATCCAATCTCTTACCCCGACCATGGGGCAGATTACAGT
1 CATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
52133 CATC
1 CATC
52137 CGAAGCAATA
Statistics
Matches: 318, Mismatches: 48, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
38 20 0.06
39 45 0.14
41 114 0.36
42 139 0.44
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (42 bp):
CATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGC
Found at i:52083 original size:164 final size:165
Alignment explanation
Indices: 51715--52127 Score: 496
Period size: 164 Copynumber: 2.5 Consensus size: 165
51705 AATCAAGTGC
** ** * *
51715 AATTACATCATCATCCAATCTCTTACCCCGATTGTGGGGCATAAT---GCCATCATCCAATCTCT
1 AATTACATCATCATCCAATCTCTTACCCCGATCATAAGGCAGATTGCAGCCATCATCCAATCTCT
* *
51777 TA-CTCGATCATGGGGCAGATTGCAGCCATAATCCAATCTCTTACCTCGATCATGGGGCAGATTA
66 TACCTCGATCATGGGGCAGATTGCAGCCATAATCCAATCTCTTACCCCGATCATAGGGCAGATTA
* * * *
51841 CATCATCATTCAATCTCTTACCCTGATCATGGGGTA
131 CAGCA-CATCCAATCTCTTACCCCGATCATAGGGTA
* * *
51877 AATTACATCATCATCCAATCTCTTACCCTGATCTTGAGGCAGATTGCAGCCATCATCCAATCTCT
1 AATTACATCATCATCCAATCTCTTACCCCGATCATAAGGCAGATTGCAGCCATCATCCAATCTCT
* * * * * *
51942 TACCTCGATCATGGTGTAGATTGTAGCCATCATCCAATCTCTTACCCCGATCATAGGGTAGATTG
66 TACCTCGATCATGGGGCAGATTGCAGCCATAATCCAATCTCTTACCCCGATCATAGGGCAGATTA
* * * *
52007 TAGC-CATCCGATCTCTTACCCCGATTATAGGG-C
131 CAGCACATCCAATCTCTTACCCCGATCATAGGGTA
* * *
52040 AATTGCAGTCATCATCCAATTTCTTACCCCGATCATAAGGCAGATTGCAGCCATTATCCAATCTC
1 AATTACA-TCATCATCCAATCTCTTACCCCGATCATAAGGCAGATTGCAGCCATCATCCAATCTC
* *
52105 TTACCCCGACCATGGGGCAGATT
65 TTACCTCGATCATGGGGCAGATT
52128 ACAGTCATCC
Statistics
Matches: 214, Mismatches: 32, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
162 39 0.18
163 6 0.03
164 94 0.44
165 19 0.09
166 56 0.26
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (165 bp):
AATTACATCATCATCCAATCTCTTACCCCGATCATAAGGCAGATTGCAGCCATCATCCAATCTCT
TACCTCGATCATGGGGCAGATTGCAGCCATAATCCAATCTCTTACCCCGATCATAGGGCAGATTA
CAGCACATCCAATCTCTTACCCCGATCATAGGGTA
Found at i:52472 original size:85 final size:85
Alignment explanation
Indices: 52324--52484 Score: 225
Period size: 85 Copynumber: 1.9 Consensus size: 85
52314 CATCTTTCTA
* * * *
52324 ATGAGATACAGTGAAGTGGGTCAATGCAATAAAGTGATCATATTCTTGATGAGATACAGAGAAGT
1 ATGAGATACAGAGAAGTGGGTAAATGCAATAAAGTGATCATATTCCTGATGAGATACAAAGAAGT
52389 AGACCAAATCCGCCTTCGTG
66 AGACCAAATCCGCCTTCGTG
* * * * *
52409 ATGAGATATAGAGAAGTGGATTAAAT-CAATGAAGTGGTCATCTTCCTGATGAGATACAAAGAAG
1 ATGAGATACAGAGAAGTGG-GTAAATGCAATAAAGTGATCATATTCCTGATGAGATACAAAGAAG
52473 TAGACCAAATCC
65 TAGACCAAATCC
52485 ATGAAACGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
85 62 0.94
86 4 0.06
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (85 bp):
ATGAGATACAGAGAAGTGGGTAAATGCAATAAAGTGATCATATTCCTGATGAGATACAAAGAAGT
AGACCAAATCCGCCTTCGTG
Found at i:52505 original size:208 final size:208
Alignment explanation
Indices: 52139--53235 Score: 1405
Period size: 208 Copynumber: 5.2 Consensus size: 208
52129 CAGTCATCCG
* * * *
52139 AAGCAATAAAATGATCACCTTCCTGATGAGATACAGAGAAGT-GAACCAAATTCGTCTTCCTGAT
1 AAGCAATAAAGTGATCATCTTCCTGATGAGATACAGAGAAGTAG-ACCAAATCCGCCTTCCTGAT
* * ** *
52203 AAGATACAGAGAAGTGGATTAAATGAATGAAGTGACCATCTTCCTGATAAGATACAGAGAAGTAG
65 GAGATACAGAGAAGTGGATTAAATCAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAG
* * *
52268 ACCAAATCAATGAAGCAAAGCTTAATACGAATGAGACTTCAAACCCCATCTTTCTAATGAGATAC
130 ACCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTAATGAGATAC
*
52333 AGTGAAGTGGGTCA
195 AGAGAAGTGGGTCA
* * * *
52347 ATGCAATAAAGTGATCATATTCTTGATGAGATACAGAGAAGTAGACCAAATCCGCCTTCGTGATG
1 AAGCAATAAAGTGATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCGCCTTCCTGATG
* *
52412 AGATATAGAGAAGTGGATTAAATCAATGAAGTGGTCATCTTCCTGATGAGATACAAAGAAGTAGA
66 AGATACAGAGAAGTGGATTAAATCAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGA
* * * * * * *
52477 CCAAATCCATGAAACGAAGCTCAATACGAAAGAGACTTCAAATCCCATGTTCTTAACGAGATAC-
131 CCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTAATGAGATACA
52541 GAAGAAGTGGGTCA
196 G-AGAAGTGGGTCA
* * * * **
52555 AAGCAATAAAGCGGTTATCTTTCTGATGAGATACAGAGAAGTAGACCAAATTTGCCTTCCTGATG
1 AAGCAATAAAGTGATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCGCCTTCCTGATG
* * *
52620 AGATACAGAGAAGCGGATTAAAT-AATTGAAGCGGTAAGTGGTCATCTTCTTGATGAGATAAAGA
66 AGATACAGAGAAGTGGATTAAATCAA-T------G-AAGTGGTCATCTTCCTGATGAGATACAGA
* * * *
52684 GAAGTAGACCAAATCAATGAAGCAAAACTCAAAACGAATGAGACTTCAAGCACCCATCTTCCTAA
123 GAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAAC-CCCATCTTCCTAA
52749 TGAGATACAGAGAAGTGGGTCA
187 TGAGATACAGAGAAGTGGGTCA
* * * *
52771 AATCAATAAAGTGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAATCCACCTTCCTGATG
1 AAGCAATAAAGTGATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCGCCTTCCTGATG
* * * * * *
52836 ATATACAAAGAAGTGAATTAAATCAATGAAGCGATCATCTTCCTGATGAGATACAGAGAAGTAAA
66 AGATACAGAGAAGTGGATTAAATCAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGA
* ** * *
52901 CCAAAGCAATGAAGCGAAGCTCAATAAAAATAAGACTTCAAACCCCATCTTCCTAATGAGATATA
131 CCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTAATGAGATACA
52966 GAGAAGTGGGTCA
196 GAGAAGTGGGTCA
* *
52979 AAGCAAAAAATTGATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCGCCTTCCTGATG
1 AAGCAATAAAGTGATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCGCCTTCCTGATG
* * * * * *
53044 AGATACAAAGAAGTGAATTCAATCAAT-AAG-GCGATCATCTTTCTAATAAGATACAGAGAAGTA
66 AGATACAGAGAAGTGGATTAAATCAATGAAGTG-G-TCATCTTCCTGATGAGATACAGAGAAGTA
* * * *
53107 GACCAAATTAATGAAGCGAAACTCAATATGAATGAGACTTCAAACCCCATCTTCCTGATGAGATA
129 GACCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTAATGAGATA
53172 CAGAGAAGTGGGTCA
194 CAGAGAAGTGGGTCA
* * *
53187 AACCAATAAAAT-AGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAA
1 AAGCAATAAAGTGA-TCATCTTCCTGATGAGATACAGAGAAGTAGACCAA
53236 GAGATGAAGC
Statistics
Matches: 770, Mismatches: 103, Indels: 32
0.85 0.11 0.04
Matches are distributed among these distances:
206 1 0.00
207 7 0.01
208 513 0.67
209 68 0.09
210 1 0.00
214 1 0.00
215 69 0.09
216 107 0.14
217 3 0.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (208 bp):
AAGCAATAAAGTGATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCGCCTTCCTGATG
AGATACAGAGAAGTGGATTAAATCAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGA
CCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTAATGAGATACA
GAGAAGTGGGTCA
Found at i:52884 original size:85 final size:85
Alignment explanation
Indices: 52741--52905 Score: 231
Period size: 85 Copynumber: 1.9 Consensus size: 85
52731 AAGCACCCAT
* ** * * *
52741 CTTCCTAATGAGATACAGAGAAGTGGGTCAAATCAATAAAGTGGTCATCTTCTTGATGAGATACA
1 CTTCCTAATGAGATACAAAGAAGTGAATCAAATCAATAAAGCGATCATCTTCCTGATGAGATACA
*
52806 GAGAAGTAGACCAAATCCAC
66 GAGAAGTAAACCAAATCCAC
* * * *
52826 CTTCCTGATGATATACAAAGAAGTGAATTAAATCAATGAAGCGATCATCTTCCTGATGAGATACA
1 CTTCCTAATGAGATACAAAGAAGTGAATCAAATCAATAAAGCGATCATCTTCCTGATGAGATACA
52891 GAGAAGTAAACCAAA
66 GAGAAGTAAACCAAA
52906 GCAATGAAGC
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 69 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (85 bp):
CTTCCTAATGAGATACAAAGAAGTGAATCAAATCAATAAAGCGATCATCTTCCTGATGAGATACA
GAGAAGTAAACCAAATCCAC
Found at i:52897 original size:48 final size:48
Alignment explanation
Indices: 52826--52917 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
52816 CCAAATCCAC
* * ** *
52826 CTTCCTGATGATATACAAAGAAGTGAATTAAATCAATGAAGCGATCAT
1 CTTCCTGATGAGATACAAAGAAGTAAACCAAAGCAATGAAGCGATCAT
*
52874 CTTCCTGATGAGATACAGAGAAGTAAACCAAAGCAATGAAGCGA
1 CTTCCTGATGAGATACAAAGAAGTAAACCAAAGCAATGAAGCGA
52918 AGCTCAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (48 bp):
CTTCCTGATGAGATACAAAGAAGTAAACCAAAGCAATGAAGCGATCAT
Found at i:52921 original size:424 final size:418
Alignment explanation
Indices: 52151--53235 Score: 1431
Period size: 424 Copynumber: 2.6 Consensus size: 418
52141 GCAATAAAAT
* * *
52151 GATCACCTTCCTGATGAGATACAGAGAAGT-GAACCAAATTCGTCTTCCTGATAAGATACAGAGA
1 GATCATCTTCCTGATGAGATACAGAGAAGTAG-ACCAAATTCGCCTTCCTGATGAGATACAGAGA
* * *
52215 AGTGGATT-A-AATGAA-TGAAGTGACCATCTTCCTGATAAGATACAGAGAAGTAGACCAAATCA
65 AGTGGATTAATAATGAAGGGAAGTG-TCATCTTCTTGATAAGATACAGAGAAGTAGACCAAATCA
* * * *
52277 ATGAAGCAAAGCTTAATACGAATGAGACTTCAAACCCCATCTTTCTAATGAGATACAGTGAAGTG
129 ATGAAGCAAAACTCAATACGAATGAGACTTCAAACCCCATCTTCCTAATGAGATACAGAGAAGTG
* * *
52342 GGTC-AATGCAATAAAGTGATCATATTCTTGATGAGATACAGAGAAGTAGACCAAATCCGCCTTC
194 GGTCAAAT-CAATAAAGTGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAATCCACCTTC
* * * * * *
52406 GTGATGAGATATAGAGAAGTGGATTAAATCAATGAAGTGGTCATCTTCCTGATGAGATACAAAGA
258 CTGATGAGATACAAAGAAGTGAATTAAATCAATGAAGCGATCATCTTCCTGATGAGATACAAAGA
* * * * * * * *
52471 AGTAGACCAAATCCATGAAACGAAGCTCAATACGAAA-GAGACTTCAAATCCCATGTTCTTAACG
323 AGTAAACCAAAGCAATGAAACGAAGCTCAATA-AAAATAAGACTTCAAACCCCATCTTCCTAACG
*
52535 AGATACGA-AGAAGTGGGTCAAAGCAATAAAGC
387 AGATA-GAGAGAAGTGGGTCAAAGCAAAAAAGC
* * * *
52567 GGTTATCTTTCTGATGAGATACAGAGAAGTAGACCAAATTTGCCTTCCTGATGAGATACAGAGAA
1 GATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATTCGCCTTCCTGATGAGATACAGAGAA
* * *
52632 GCGGATTAAATAATTGAAGCGGTAAGTGGTCATCTTCTTGATGAGATAAAGAGAAGTAGACCAAA
66 GTGGATT-AATAA-TGAAG-GG-AAGT-GTCATCTTCTTGATAAGATACAGAGAAGTAGACCAAA
* *
52697 TCAATGAAGCAAAACTCAAAACGAATGAGACTTCAAGCACCCATCTTCCTAATGAGATACAGAGA
126 TCAATGAAGCAAAACTCAATACGAATGAGACTTCAAAC-CCCATCTTCCTAATGAGATACAGAGA
52762 AGTGGGTCAAATCAATAAAGTGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAATCCACC
190 AGTGGGTCAAATCAATAAAGTGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAATCCACC
* *
52827 TTCCTGATGATATACAAAGAAGTGAATTAAATCAATGAAGCGATCATCTTCCTGATGAGATACAG
255 TTCCTGATGAGATACAAAGAAGTGAATTAAATCAATGAAGCGATCATCTTCCTGATGAGATACAA
*
52892 AGAAGTAAACCAAAGCAATGAAGCGAAGCTCAATAAAAATAAGACTTCAAACCCCATCTTCCTAA
320 AGAAGTAAACCAAAGCAATGAAACGAAGCTCAATAAAAATAAGACTTCAAACCCCATCTTCCTAA
* * **
52957 TGAGATATAGAGAAGTGGGTCAAAGCAAAAAATT
385 CGAGATAGAGAGAAGTGGGTCAAAGCAAAAAAGC
* *
52991 GATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCCGCCTTCCTGATGAGATACAAAGAA
1 GATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATTCGCCTTCCTGATGAGATACAGAGAA
* *
53056 GTGAATTCAATCAAT-AAGGCG-A---TCATCTT-TCTAATAAGATACAGAGAAGTAGACCAAAT
66 GTGGATT-AAT-AATGAAGG-GAAGTGTCATCTTCT-TGATAAGATACAGAGAAGTAGACCAAAT
* * * *
53115 TAATGAAGCGAAACTCAATATGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAG
127 CAATGAAGCAAAACTCAATACGAATGAGACTTCAAACCCCATCTTCCTAATGAGATACAGAGAAG
* * * * *
53180 TGGGTCAAACCAATAAAATAGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAA
192 TGGGTCAAATCAATAAAGTGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAA
53236 GAGATGAAGC
Statistics
Matches: 586, Mismatches: 67, Indels: 32
0.86 0.10 0.05
Matches are distributed among these distances:
416 141 0.24
417 65 0.11
418 1 0.00
419 2 0.00
420 4 0.01
421 1 0.00
422 2 0.00
423 78 0.13
424 287 0.49
425 5 0.01
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (418 bp):
GATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATTCGCCTTCCTGATGAGATACAGAGAA
GTGGATTAATAATGAAGGGAAGTGTCATCTTCTTGATAAGATACAGAGAAGTAGACCAAATCAAT
GAAGCAAAACTCAATACGAATGAGACTTCAAACCCCATCTTCCTAATGAGATACAGAGAAGTGGG
TCAAATCAATAAAGTGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAATCCACCTTCCTG
ATGAGATACAAAGAAGTGAATTAAATCAATGAAGCGATCATCTTCCTGATGAGATACAAAGAAGT
AAACCAAAGCAATGAAACGAAGCTCAATAAAAATAAGACTTCAAACCCCATCTTCCTAACGAGAT
AGAGAGAAGTGGGTCAAAGCAAAAAAGC
Found at i:54059 original size:2 final size:2
Alignment explanation
Indices: 54040--54095 Score: 69
Period size: 2 Copynumber: 28.0 Consensus size: 2
54030 TAACACCTAC
* *
54040 AT AT AA AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
54082 CCT -T AT AT AT AT AT
1 -AT AT AT AT AT AT AT
54096 GCCTATTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
1 1 0.02
2 45 0.96
3 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:54910 original size:30 final size:30
Alignment explanation
Indices: 54878--54990 Score: 115
Period size: 30 Copynumber: 3.8 Consensus size: 30
54868 TTTGACCCCT
*
54878 AAACTTCTTAAAAATTTGAATTTAACCTCT
1 AAACTTCTTAAAAATTTGAATTTAACCTCC
* *
54908 AAACTT-TTCAAAAA-TTCAGATTTAACTTCC
1 AAACTTCTT-AAAAATTTGA-ATTTAACCTCC
* *
54938 AAACTTCTCAAAAATTTGGATTTAATCC-CC
1 AAACTTCTTAAAAATTTGAATTTAA-CCTCC
**
54968 AAACTTCCAAAAAATTTGAATTT
1 AAACTTCTTAAAAATTTGAATTT
54991 GGCCCCCCGA
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
29 5 0.07
30 59 0.87
31 4 0.06
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (30 bp):
AAACTTCTTAAAAATTTGAATTTAACCTCC
Found at i:54921 original size:60 final size:60
Alignment explanation
Indices: 54846--54962 Score: 141
Period size: 60 Copynumber: 1.9 Consensus size: 60
54836 CAGGAGGTCC
* * *
54846 CTAAACTTTCTAAAAATTACA-TTTTGAC-CCCTAAACTTCTTAAAAATTTGAATTTAACCT
1 CTAAACTTTCTAAAAATT-CAGATTTAACTCCC-AAACTTCTCAAAAATTTGAATTTAACCT
* *
54906 CTAAACTTT-TCAAAAATTCAGATTTAACTTCCAAACTTCTCAAAAATTTGGATTTAA
1 CTAAACTTTCT-AAAAATTCAGATTTAACTCCCAAACTTCTCAAAAATTTGAATTTAA
54963 TCCCCAAACT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
59 3 0.06
60 44 0.90
61 2 0.04
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.38
Consensus pattern (60 bp):
CTAAACTTTCTAAAAATTCAGATTTAACTCCCAAACTTCTCAAAAATTTGAATTTAACCT
Found at i:58130 original size:26 final size:26
Alignment explanation
Indices: 58101--58151 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
58091 CATTGCTTTT
58101 GAAAAGTGCTTTTAAAAAGTATGGTG
1 GAAAAGTGCTTTTAAAAAGTATGGTG
* * *
58127 GAAAAGTGTTTTTGAAAAGTTTGGT
1 GAAAAGTGCTTTTAAAAAGTATGGT
58152 TTAAGATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.35
Consensus pattern (26 bp):
GAAAAGTGCTTTTAAAAAGTATGGTG
Found at i:58686 original size:39 final size:40
Alignment explanation
Indices: 58632--58711 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
58622 TATGCACTCA
*
58632 ATGGACACCTTTTGAAGAGTCACAATCC-TTTCAAATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
*
58671 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
58711 A
1 A
58712 CATACCTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 27 0.71
40 11 0.29
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGG
Found at i:58727 original size:39 final size:38
Alignment explanation
Indices: 58636--58728 Score: 98
Period size: 39 Copynumber: 2.4 Consensus size: 38
58626 CACTCAATGG
* * *
58636 ACACCTTTTGAAGAGTCACAATCCTTTCAAATTGGATGG
1 ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGA-GC
* *
58675 ACACCTTTTGAAGAGTCACAACCCTTTTCATATTGGA-C
1 ACACCTTTGGAAGAGTCACAACCC-TTTCAAATTGGAGC
*
58713 ATACCTCTTGGAAGAG
1 ACACCT-TTGGAAGAG
58729 ACTTGTCCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 5 0.11
39 31 0.66
40 11 0.23
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (38 bp):
ACACCTTTGGAAGAGTCACAACCCTTTCAAATTGGAGC
Found at i:66765 original size:3 final size:3
Alignment explanation
Indices: 66757--66790 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
66747 TAACAACCTA
66757 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
66791 CAAATACTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:72755 original size:31 final size:30
Alignment explanation
Indices: 72717--72796 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
72707 CCAAATTAAC
* *
72717 GATATGTGAAAGCCTTTGCGGCTATTCCTCT
1 GATATGTGAAAGCTTTTGCGGATATTCC-CT
* * *
72748 GATATGTGAAATCTTTTGTGGATTTTCCCT
1 GATATGTGAAAGCTTTTGCGGATATTCCCT
*
72778 AATATGTGAAAGCTTTTGC
1 GATATGTGAAAGCTTTTGC
72797 AACTGTTCTC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 18 0.44
31 23 0.56
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (30 bp):
GATATGTGAAAGCTTTTGCGGATATTCCCT
Found at i:78530 original size:17 final size:17
Alignment explanation
Indices: 78508--78546 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
78498 CTCCACCTTG
*
78508 ACAAGAATTCTCT-ACGA
1 ACAAGAACTCT-TAACGA
78525 ACAAGAACTCTTAACGA
1 ACAAGAACTCTTAACGA
78542 ACAAG
1 ACAAG
78547 TTTTCCACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (17 bp):
ACAAGAACTCTTAACGA
Done.