Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015352.1 Kokia drynarioides strain JFW-HI SEQ_130399, 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: 235382
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 419 characters in sequence are not A, C, G, or T
Found at i:21896 original size:1 final size:1
Alignment explanation
Indices: 21890--21973 Score: 168
Period size: 1 Copynumber: 84.0 Consensus size: 1
21880 NNNNNNNNNN
21890 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
21955 GGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGG
21974 CAAAAGGAGT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 83 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:25752 original size:21 final size:21
Alignment explanation
Indices: 25728--25769 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
25718 GTGAAGAAAA
25728 GATTCTGACCTGAAAATAAGG
1 GATTCTGACCTGAAAATAAGG
25749 GATTCTGACCTGAAAATAAGG
1 GATTCTGACCTGAAAATAAGG
25770 ACAGCAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (21 bp):
GATTCTGACCTGAAAATAAGG
Found at i:26361 original size:17 final size:16
Alignment explanation
Indices: 26312--26378 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 16
26302 TTAATGTAAT
26312 TTTTTTTAAAATTTTAA
1 TTTTTTT-AAATTTTAA
* *
26329 TTTATTTATATATTTAA
1 TTTTTTTAAAT-TTTAA
26346 TTTTTTTGAAATTTTATA
1 TTTTTTT-AAATTTTA-A
*
26364 TATTTTT-AATTTTAA
1 TTTTTTTAAATTTTAA
26379 AATGATAGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 1 0.02
16 10 0.24
17 21 0.50
18 10 0.24
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (16 bp):
TTTTTTTAAATTTTAA
Found at i:26626 original size:2 final size:2
Alignment explanation
Indices: 26619--26652 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
26609 ATTAGCAATA
26619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26653 GCAAATATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28358 original size:13 final size:13
Alignment explanation
Indices: 28340--28365 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28330 CCTATAGAAA
28340 GAAAAATTATATT
1 GAAAAATTATATT
28353 GAAAAATTATATT
1 GAAAAATTATATT
28366 TTCTACCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
GAAAAATTATATT
Found at i:28385 original size:16 final size:17
Alignment explanation
Indices: 28364--28399 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
28354 AAAAATTATA
*
28364 TTTTCTA-CCCTTCTAT
1 TTTTCTACCCCTTCAAT
28380 TTTTCTACCCCTTCAAT
1 TTTTCTACCCCTTCAAT
28397 TTT
1 TTT
28400 CCATCTTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTCTACCCCTTCAAT
Found at i:28400 original size:16 final size:16
Alignment explanation
Indices: 28363--28400 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28353 GAAAAATTAT
28363 ATTTTCTACCCTTCTA
1 ATTTTCTACCCTTCTA
*
28379 TTTTTCTACCCCTTC-A
1 ATTTTCTA-CCCTTCTA
28395 ATTTTC
1 ATTTTC
28401 CATCTTTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTCTACCCTTCTA
Found at i:31221 original size:13 final size:13
Alignment explanation
Indices: 31203--31241 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
31193 ATTGATAGCA
31203 TTTTTAATTAATT
1 TTTTTAATTAATT
* **
31216 TTTTTACTTAACA
1 TTTTTAATTAATT
31229 TTTTTAATTAATT
1 TTTTTAATTAATT
31242 AAATTTGAAT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATT
Found at i:31567 original size:31 final size:32
Alignment explanation
Indices: 31510--31570 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
31500 GATATTGTTT
*
31510 GTATGGTTTTATTTTGAACTAATTGTATTTTC
1 GTATGGTTTTATCTTGAACTAATTGTATTTTC
* *
31542 GTATGGTTTT-TCTTGTATTAATTGTATTT
1 GTATGGTTTTATCTTGAACTAATTGTATTT
31571 GTGTACAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.20, C:0.05, G:0.16, T:0.59
Consensus pattern (32 bp):
GTATGGTTTTATCTTGAACTAATTGTATTTTC
Found at i:46772 original size:13 final size:13
Alignment explanation
Indices: 46751--46792 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
46741 ACAGTTCAAA
*
46751 AAAAAAAAAAACC
1 AAAACAAAAAACC
*
46764 AAAACAAAAACCC
1 AAAACAAAAAACC
*
46777 AAATC-AAAAACC
1 AAAACAAAAAACC
46789 AAAA
1 AAAA
46793 ACCAAAACTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.76, C:0.21, G:0.00, T:0.02
Consensus pattern (13 bp):
AAAACAAAAAACC
Found at i:46800 original size:13 final size:12
Alignment explanation
Indices: 46752--46792 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
46742 CAGTTCAAAA
*
46752 AAAAAAAAAACC
1 AAAACAAAAACC
46764 AAAACAAAAACCC
1 AAAACAAAAA-CC
*
46777 AAATCAAAAACC
1 AAAACAAAAACC
46789 AAAA
1 AAAA
46793 ACCAAAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.76, C:0.22, G:0.00, T:0.02
Consensus pattern (12 bp):
AAAACAAAAACC
Found at i:47516 original size:7 final size:7
Alignment explanation
Indices: 47506--47533 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
47496 GATCCCTCTT
47506 CCCCTTC
1 CCCCTTC
47513 CCCCTTC
1 CCCCTTC
47520 CCCCTTC
1 CCCCTTC
47527 CCCCTTC
1 CCCCTTC
47534 ATTGTCACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.71, G:0.00, T:0.29
Consensus pattern (7 bp):
CCCCTTC
Found at i:47519 original size:13 final size:13
Alignment explanation
Indices: 47498--47533 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
47488 TTCGAGAAGA
*
47498 TCCCTCTTCCCCT
1 TCCCCCTTCCCCT
47511 TCCCCCTTCCCCCT
1 TCCCCCTT-CCCCT
47525 TCCCCCTTC
1 TCCCCCTTC
47534 ATTGTCACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (13 bp):
TCCCCCTTCCCCT
Found at i:51325 original size:23 final size:23
Alignment explanation
Indices: 51277--51340 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
51267 GATTTTTTAA
* *
51277 TATTAAAAATTAGATTATATTTTT
1 TATTAAAAA-TAGATTAAATTATT
51301 TATTAAAAATA-ATTAAATTAATT
1 TATTAAAAATAGATTAAATT-ATT
* *
51324 TA-TATAAATATATTAAA
1 TATTAAAAATAGATTAAA
51341 GAATAAATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 14 0.40
23 12 0.34
24 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TATTAAAAATAGATTAAATTATT
Found at i:51712 original size:12 final size:12
Alignment explanation
Indices: 51678--51714 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
51668 TCCATGGAGT
*
51678 CCCAACCCCAAC
1 CCCAACCCCAGC
51690 CCCAACCCCAGC
1 CCCAACCCCAGC
*
51702 CCCAGCCCCAGC
1 CCCAACCCCAGC
51714 C
1 C
51715 TCAGCCTCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.24, C:0.68, G:0.08, T:0.00
Consensus pattern (12 bp):
CCCAACCCCAGC
Found at i:51722 original size:6 final size:6
Alignment explanation
Indices: 51678--51720 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
51668 TCCATGGAGT
* * * *
51678 CCCAAC CCCAAC CCCAAC CCCAGC CCCAGC CCCAGC CTCAGC C
1 CCCAGC CCCAGC CCCAGC CCCAGC CCCAGC CCCAGC CCCAGC C
51721 TCGGCGACCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.23, C:0.65, G:0.09, T:0.02
Consensus pattern (6 bp):
CCCAGC
Found at i:65540 original size:37 final size:37
Alignment explanation
Indices: 65499--65571 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
65489 GTTCTCTCCT
* *
65499 GTGTCTTTTCGTTCTAAGGTTCGATTCCCTCTTTCCA
1 GTGTCTTTTCGTTCTAAGGCTCCATTCCCTCTTTCCA
65536 GTGTCTTTTCGTTCTAAGGCTCCATTCCCTCTTTCC
1 GTGTCTTTTCGTTCTAAGGCTCCATTCCCTCTTTCC
65572 CTATAAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.10, C:0.30, G:0.15, T:0.45
Consensus pattern (37 bp):
GTGTCTTTTCGTTCTAAGGCTCCATTCCCTCTTTCCA
Found at i:73576 original size:111 final size:111
Alignment explanation
Indices: 73265--73584 Score: 289
Period size: 112 Copynumber: 2.8 Consensus size: 111
73255 AATCATTTAT
* *
73265 TTTCTTGTTTACTGAAAAAATTAAAAATTAATTCTAAAAAAAAG-AGAATGAAGAAAATTAAAAA
1 TTTCTTTTTTACTGAAAAAATT-AAAATTAATTCT-AAAAAAAGTA-AAGGAA-AAAA-T--AAA
* *
73329 GATAAAATGATTTTTCTTGATAAAAATCCAAGTAATTTTCTGTAGAATCTCAAG
59 GATAAAATGATTTTTCTTG-TAAAAATCTAAGTAATTTTCTGTAAAATCTCAAG
* * * *
73383 TTTTTTCTTTTATTGGGAAAAAATTAAAATTAATTCT--AAAAA-TAAAGTAAATTAA-AAAGAT
1 TTTCTT-TTTTACT--GAAAAAATTAAAATTAATTCTAAAAAAAGTAAAGGAAA-AAATAAAGAT
* * * * *
73444 AAATTGGTTTTTACCTATAAAAATCT-AGATAATTTT-TTTAAAATCTCATA-
62 AAAATGATTTTT-CTTGTAAAAATCTAAG-TAATTTTCTGTAAAATCTCA-AG
*
73494 TCTTCTTTTTTACTAGAAAAAACTAAAATTAATTCTAAAAAAAGTAAAGGAAAAAATAAAGATAA
1 T-TTCTTTTTTACT-GAAAAAATTAAAATTAATTCTAAAAAAAGTAAAGGAAAAAATAAAGATAA
*
73559 AAT-ATTTTTCTTGTAAAATTCTAAGT
64 AATGATTTTTCTTGTAAAAATCTAAGT
73585 TTTTTCAGAT
Statistics
Matches: 164, Mismatches: 24, Indels: 35
0.74 0.11 0.16
Matches are distributed among these distances:
110 20 0.12
111 30 0.18
112 50 0.30
113 20 0.12
115 1 0.01
116 6 0.04
117 6 0.04
118 5 0.03
119 5 0.03
120 12 0.07
121 9 0.05
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (111 bp):
TTTCTTTTTTACTGAAAAAATTAAAATTAATTCTAAAAAAAGTAAAGGAAAAAATAAAGATAAAA
TGATTTTTCTTGTAAAAATCTAAGTAATTTTCTGTAAAATCTCAAG
Found at i:81580 original size:26 final size:26
Alignment explanation
Indices: 81544--81596 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
81534 TAAAGAGTAC
81544 GACGGGCGAGGGTTTTGCTTTAGCCT
1 GACGGGCGAGGGTTTTGCTTTAGCCT
81570 GACGGGCGAGGGTTTTGCTTTAGCCT
1 GACGGGCGAGGGTTTTGCTTTAGCCT
81596 G
1 G
81597 CTTTACCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.11, C:0.19, G:0.40, T:0.30
Consensus pattern (26 bp):
GACGGGCGAGGGTTTTGCTTTAGCCT
Found at i:82402 original size:28 final size:31
Alignment explanation
Indices: 82383--82449 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
82373 TTTATAATTT
*
82383 ATATATTATTATATTAAATTATTTAAATATA
1 ATATATTATTATATTAAATTATATAAATATA
* *
82414 ATTTATTATTATATTAAATTATTTAAATATA
1 ATATATTATTATATTAAATTATATAAATATA
*
82445 TTATA
1 ATATA
82450 ACTTAACTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
ATATATTATTATATTAAATTATATAAATATA
Found at i:82403 original size:10 final size:10
Alignment explanation
Indices: 82390--82447 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 10
82380 TTTATATATT
82390 ATTATATTAA
1 ATTATATTAA
82400 ATTAT-TTAA
1 ATTATATTAA
*
82409 A-TATAATTTATT
1 ATTAT-A-TTA-A
82421 ATTATATTAA
1 ATTATATTAA
82431 ATTAT-TTAA
1 ATTATATTAA
82440 A-TATATTA
1 ATTATATTA
82448 TAACTTAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
8 6 0.15
9 13 0.32
10 10 0.25
11 6 0.15
12 2 0.05
13 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTATATTAA
Found at i:82412 original size:16 final size:16
Alignment explanation
Indices: 82393--82443 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
82383 ATATATTATT
82393 ATATTAAATTATTTAA
1 ATATTAAATTATTTAA
* *
82409 ATA-TAATTTA-TTATT
1 ATATTAAATTATTTA-A
82424 ATATTAAATTATTTAA
1 ATATTAAATTATTTAA
82440 ATAT
1 ATAT
82444 ATTATAACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 3 0.11
15 9 0.32
16 13 0.46
17 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTAAATTATTTAA
Found at i:82421 original size:31 final size:31
Alignment explanation
Indices: 82386--82444 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
82376 ATAATTTATA
82386 TATTATTATATTAAATTATTTAAATATAATT
1 TATTATTATATTAAATTATTTAAATATAATT
82417 TATTATTATATTAAATTATTTAAATATA
1 TATTATTATATTAAATTATTTAAATATA
82445 TTATAACTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
TATTATTATATTAAATTATTTAAATATAATT
Found at i:82446 original size:18 final size:17
Alignment explanation
Indices: 82392--82447 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 17
82382 TATATATTAT
82392 TATATTAAATTATTTAA
1 TATATTAAATTATTTAA
* *
82409 -ATA-TAATTTA-TTAT
1 TATATTAAATTATTTAA
82423 TATATTAAATTATTTAAA
1 TATATTAAATTATTT-AA
82441 TATATTA
1 TATATTA
82448 TAACTTAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
14 3 0.10
15 9 0.29
16 9 0.29
17 2 0.06
18 8 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATTAAATTATTTAA
Found at i:86028 original size:6 final size:6
Alignment explanation
Indices: 86017--86057 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
86007 GAGTTTCACT
* *
86017 GTTGCC GTTGCC CTTGCC GTTGCT GTTGCC GTTGCC TGTTG
1 GTTGCC GTTGCC GTTGCC GTTGCC GTTGCC GTTGCC -GTTG
86058 GTGGTTTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 26 0.87
7 4 0.13
ACGTcount: A:0.00, C:0.29, G:0.32, T:0.39
Consensus pattern (6 bp):
GTTGCC
Found at i:86044 original size:18 final size:19
Alignment explanation
Indices: 86015--86057 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
86005 TTGAGTTTCA
86015 CTGTTGCCGTTGCCCTTGC
1 CTGTTGCCGTTGCCCTTGC
* *
86034 C-GTTGCTGTTGCCGTTGC
1 CTGTTGCCGTTGCCCTTGC
86052 CTGTTG
1 CTGTTG
86058 GTGGTTTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.00, C:0.30, G:0.30, T:0.40
Consensus pattern (19 bp):
CTGTTGCCGTTGCCCTTGC
Found at i:87220 original size:13 final size:14
Alignment explanation
Indices: 87179--87223 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
87169 CCTTAATTAG
*
87179 TTATTATTTTATTT
1 TTATTATTTAATTT
87193 TTATTATCTTCAATTT
1 TTATTAT-TT-AATTT
87209 TTA-TATTTAATTT
1 TTATTATTTAATTT
87222 TT
1 TT
87224 TAAATTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 7 0.25
14 9 0.32
15 5 0.18
16 7 0.25
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTATTTAATTT
Found at i:87937 original size:31 final size:31
Alignment explanation
Indices: 87902--87977 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
87892 AAAATTCATG
*
87902 AAGTACATAG-ACTAAAATTGACCAACTTAAA
1 AAGTACA-AGTACTAAAATTGACCAAATTAAA
* * *
87933 AAGTATAAGTACTAAATTTGATCAAATT--A
1 AAGTACAAGTACTAAAATTGACCAAATTAAA
87962 AAGTACAAGTACTAAA
1 AAGTACAAGTACTAAA
87978 TCCAAAACTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 16 0.41
30 2 0.05
31 21 0.54
ACGTcount: A:0.51, C:0.12, G:0.11, T:0.26
Consensus pattern (31 bp):
AAGTACAAGTACTAAAATTGACCAAATTAAA
Found at i:89063 original size:2 final size:2
Alignment explanation
Indices: 89056--89085 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
89046 AATTTTCATC
89056 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
89086 TAACATAATA
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:94020 original size:21 final size:21
Alignment explanation
Indices: 93978--94022 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
93968 ATTTAGAAAA
**
93978 AAAAAATAGAATATAATTTTT
1 AAAAAATAGAATATAAAATTT
*
93999 AAAAAATAGAATTTAAAATTT
1 AAAAAATAGAATATAAAATTT
94020 AAA
1 AAA
94023 TATTTAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (21 bp):
AAAAAATAGAATATAAAATTT
Found at i:117968 original size:5 final size:5
Alignment explanation
Indices: 117960--117999 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
117950 TTGTGAAGAG
* *
117960 ATCAT ATCAT ATCAT ATCAT ATCAT ATTAT ATCAC ATCAT
1 ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT
118000 CCGATTAGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATCAT
Found at i:119492 original size:18 final size:18
Alignment explanation
Indices: 119465--119505 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
119455 TAGGGGGTAA
119465 CCTCCAGGAGGAGG-ATAT
1 CCTCCAGGA-GAGGCATAT
*
119483 CCTCCTGGAGAGGCATAT
1 CCTCCAGGAGAGGCATAT
119501 CCTCC
1 CCTCC
119506 GGGTGGCGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.22, C:0.32, G:0.27, T:0.20
Consensus pattern (18 bp):
CCTCCAGGAGAGGCATAT
Found at i:124458 original size:6 final size:6
Alignment explanation
Indices: 124447--124472 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
124437 CCTATACCTC
124447 AAACAT AAACAT AAACAT AAACAT AA
1 AAACAT AAACAT AAACAT AAACAT AA
124473 TTAATTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAACAT
Found at i:129992 original size:18 final size:18
Alignment explanation
Indices: 129964--130006 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
129954 CGAAAAAAAA
* *
129964 TCGAGTTGACTCATATAAC
1 TCGA-TTGACTCAAACAAC
129983 TCGATTGACTCAAACAAC
1 TCGATTGACTCAAACAAC
130001 TCGATT
1 TCGATT
130007 TGTTTAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (18 bp):
TCGATTGACTCAAACAAC
Found at i:133296 original size:20 final size:20
Alignment explanation
Indices: 133265--133337 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
133255 TATAGTATTA
*
133265 AATTTGACATTTTTTTTTCT
1 AATTTGATATTTTTTTTTCT
* * *
133285 AATTTTATATTTTTTTACTCA
1 AATTTGATATTTTTTT-TTCT
* *
133306 AATTTGAAATTTTTTTTTTT
1 AATTTGATATTTTTTTTTCT
133326 AATTTGATATTT
1 AATTTGATATTT
133338 GAATTTAATA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 26 0.62
21 16 0.38
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.64
Consensus pattern (20 bp):
AATTTGATATTTTTTTTTCT
Found at i:135174 original size:10 final size:10
Alignment explanation
Indices: 135159--135192 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
135149 GATAAAGAAA
135159 GAGAGAGAGT
1 GAGAGAGAGT
135169 --GAGAGAGT
1 GAGAGAGAGT
135177 GAGAGAGAGT
1 GAGAGAGAGT
135187 GAGAGA
1 GAGAGA
135193 AGGGNNNNNN
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.36
10 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.50, T:0.09
Consensus pattern (10 bp):
GAGAGAGAGT
Found at i:135628 original size:18 final size:18
Alignment explanation
Indices: 135597--135631 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
135587 TGTCGAAAAA
*
135597 TATAAGTAAATTATATTT
1 TATAAATAAATTATATTT
*
135615 TATAAATAATTTATATT
1 TATAAATAAATTATATT
135632 AATTGTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TATAAATAAATTATATTT
Found at i:136924 original size:26 final size:26
Alignment explanation
Indices: 136882--136968 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
136872 TTTTAATATG
136882 CTTTAATTTGAGA-TTTAATTCTTATA
1 CTTTAATTT-AGATTTTAATTCTTATA
* * * *
136908 CTTTAATTTAAATTTTAGTCCTCATATG
1 CTTTAATTTAGATTTTAAT--TCTTATA
* *
136936 CTTTAATTT-GATATTGAATCCTTATA
1 CTTTAATTTAGAT-TTTAATTCTTATA
136962 CTTTAAT
1 CTTTAAT
136969 CTCTAACACC
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
25 2 0.04
26 25 0.53
27 2 0.04
28 18 0.38
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (26 bp):
CTTTAATTTAGATTTTAATTCTTATA
Found at i:136957 original size:28 final size:28
Alignment explanation
Indices: 136877--136957 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 28
136867 AGTCCTTTTA
*
136877 ATATGCTTTAATTTGAGATTTAAT--TC
1 ATATGCTTTAATTTGAAATTTAATCCTC
* * *
136903 TTATACTTTAATTT-AAATTTTAGTCCTC
1 ATATGCTTTAATTTGAAA-TTTAATCCTC
* *
136931 ATATGCTTTAATTTGATATTGAATCCT
1 ATATGCTTTAATTTGAAATTTAATCCT
136958 TATACTTTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
25 2 0.05
26 17 0.40
28 21 0.50
29 2 0.05
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (28 bp):
ATATGCTTTAATTTGAAATTTAATCCTC
Found at i:142628 original size:21 final size:20
Alignment explanation
Indices: 142580--142630 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
142570 TATAATTGTT
142580 TATTAA-ATATTTATTAAAA
1 TATTAATATATTTATTAAAA
142599 T-TGTAATATATTTATTAAAA
1 TAT-TAATATATTTATTAAAA
142619 TAATTAATATAT
1 T-ATTAATATAT
142631 ACTAAATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 4 0.14
20 14 0.50
21 8 0.29
22 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TATTAATATATTTATTAAAA
Found at i:144584 original size:12 final size:12
Alignment explanation
Indices: 144567--144597 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
144557 GTTTTTATGA
144567 AAAACAATTTTG
1 AAAACAATTTTG
144579 AAAACAATTTTG
1 AAAACAATTTTG
144591 AAAACAA
1 AAAACAA
144598 ATGTGAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.26
Consensus pattern (12 bp):
AAAACAATTTTG
Found at i:144913 original size:59 final size:59
Alignment explanation
Indices: 144791--144902 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
144781 TTTTGGGTAC
* * *
144791 TCGAGGGTAAAATGGTAATTTTAGGAAAGTCGAGGGTCAAAAACAGAATTTTTAAACAT
1 TCGAGGGTAAAATGGTACTTTTTGGAAAATCGAGGGTCAAAAACAGAATTTTTAAACAT
* **
144850 TCGAGGGTAAAATGGTACTTTTTGGAATAATCG-GGGTCGAAAATGGAATTTTT
1 TCGAGGGTAAAATGGTACTTTTTGGAA-AATCGAGGGTCAAAAACAGAATTTTT
144903 GGAAGTTCGA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 42 0.91
60 4 0.09
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (59 bp):
TCGAGGGTAAAATGGTACTTTTTGGAAAATCGAGGGTCAAAAACAGAATTTTTAAACAT
Found at i:145026 original size:29 final size:28
Alignment explanation
Indices: 144993--145236 Score: 130
Period size: 29 Copynumber: 8.5 Consensus size: 28
144983 TTCGAGCGTA
144993 AAAATGTAATGTTTGGAAAAATCGGGGTT
1 AAAATGTAAT-TTTGGAAAAATCGGGGTT
* ** * *
145022 AAAATGGAATTTTGGAAAGTTTAGGGGTA
1 AAAATGTAATTTTGGAAA-AATCGGGGTT
* * * *** *
145051 AAAATATTATTTTTGAAAAATTAAGTTT
1 AAAATGTAATTTTGGAAAAATCGGGGTT
* ** *
145079 AAAAATGGAATTTTGGAAAGTTCGAGGGTA
1 -AAAATGTAATTTTGGAAAAATCG-GGGTT
* **
145109 AAAATGTAATTTTCGTAAAAATTAGGGTT
1 AAAATGTAATTTT-GGAAAAATCGGGGTT
* * ** *
145138 AAAATGGAATTTTGTAAAGTTCGGGGGTA
1 AAAATGTAATTTTGGAAAAATC-GGGGTT
* *
145167 AAAATGTAATTTTTGG-AAAATTGAGGTT
1 AAAATGTAA-TTTTGGAAAAATCGGGGTT
* ** *
145195 AAAAATGGAATTTTGGAAAGTTCGGGGGT
1 -AAAATGTAATTTTGGAAAAATCGGGGTT
*
145224 AAAATATAATTTT
1 AAAATGTAATTTT
145237 AAAAAGTTTG
Statistics
Matches: 152, Mismatches: 55, Indels: 17
0.68 0.25 0.08
Matches are distributed among these distances:
28 38 0.25
29 102 0.67
30 12 0.08
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (28 bp):
AAAATGTAATTTTGGAAAAATCGGGGTT
Found at i:145041 original size:58 final size:58
Alignment explanation
Indices: 144979--145300 Score: 318
Period size: 58 Copynumber: 5.6 Consensus size: 58
144969 TTGGGGGTAA
* ***
144979 AAAGTTCGAGCGTAAAAATGTAATGTTTGGAAAAATCGGGGTT-AAAATGGAATTTTGG
1 AAAGTTCGAGGGTAAAAATGTAAT-TTTGGAAAAATTAAGGTTAAAAATGGAATTTTGG
* * * * *
145037 AAAGTT-TAGGGGTAAAAATATTATTTTTGAAAAATTAAGTTTAAAAATGGAATTTTGG
1 AAAGTTCGA-GGGTAAAAATGTAATTTTGGAAAAATTAAGGTTAAAAATGGAATTTTGG
* * *
145095 AAAGTTCGAGGGTAAAAATGTAATTTTCGTAAAAATTAGGGTT-AAAATGGAATTTTGT
1 AAAGTTCGAGGGTAAAAATGTAATTTT-GGAAAAATTAAGGTTAAAAATGGAATTTTGG
* *
145153 AAAGTTCGGGGGTAAAAATGTAATTTTTGG-AAAATTGAGGTTAAAAATGGAATTTTGG
1 AAAGTTCGAGGGTAAAAATGTAA-TTTTGGAAAAATTAAGGTTAAAAATGGAATTTTGG
* * * * *
145211 AAAGTTCGGGGGT-AAAATATAATTTT--AAAAAGTTTGAGG-TAAAAATGTAATTTTAG
1 AAAGTTCGAGGGTAAAAATGTAATTTTGGAAAAA--TTAAGGTTAAAAATGGAATTTTGG
* * * *
145267 ATAAGTTTGGGGGTCAAAATATAATTTTGGAAAA
1 A-AAGTTCGAGGGTAAAAATGTAATTTTGGAAAA
145301 GTTTAAGGGT
Statistics
Matches: 225, Mismatches: 26, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
55 4 0.02
56 20 0.09
57 49 0.22
58 132 0.59
59 16 0.07
60 4 0.02
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (58 bp):
AAAGTTCGAGGGTAAAAATGTAATTTTGGAAAAATTAAGGTTAAAAATGGAATTTTGG
Found at i:145138 original size:116 final size:115
Alignment explanation
Indices: 144979--145300 Score: 398
Period size: 116 Copynumber: 2.8 Consensus size: 115
144969 TTGGGGGTAA
* * **
144979 AAAGTTCGAGCGTAAAAATGTAATGTTTGGAAAAATCGGGGTTAAAATGGAATTTTGGAAAGTTT
1 AAAGTTCGAGGGTAAAAATGTAAT-TTTGTAAAAATTAGGGTTAAAATGGAATTTTGGAAAGTTT
* * *
145044 AGGGGTAAAAATATTATTTTTGAAAAATTAAGTTTAAAAATGGAATTTTGG
65 GGGGGTAAAAATATAATTTTTGAAAAATTAAGGTTAAAAATGGAATTTTGG
* *
145095 AAAGTTCGAGGGTAAAAATGTAATTTTCGTAAAAATTAGGGTTAAAATGGAATTTTGTAAAGTTC
1 AAAGTTCGAGGGTAAAAATGTAATTTT-GTAAAAATTAGGGTTAAAATGGAATTTTGGAAAGTTT
* * *
145160 GGGGGTAAAAATGTAATTTTTGGAAAATTGAGGTTAAAAATGGAATTTTGG
65 GGGGGTAAAAATATAATTTTTGAAAAATTAAGGTTAAAAATGGAATTTTGG
* * * * * *
145211 AAAGTTCGGGGGT-AAAATATAA-TTT-TAAAAAGTTTGAGGTAAAAATGTAATTTTAGATAAGT
1 AAAGTTCGAGGGTAAAAATGTAATTTTGTAAAAA-TTAG-GGTTAAAATGGAATTTTGGA-AAGT
* *
145273 TTGGGGGTCAAAATATAATTTTGGAAAA
63 TTGGGGGTAAAAATATAATTTTTGAAAA
145301 GTTTAAGGGT
Statistics
Matches: 178, Mismatches: 24, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
112 6 0.03
113 3 0.02
114 19 0.11
115 38 0.21
116 112 0.63
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (115 bp):
AAAGTTCGAGGGTAAAAATGTAATTTTGTAAAAATTAGGGTTAAAATGGAATTTTGGAAAGTTTG
GGGGTAAAAATATAATTTTTGAAAAATTAAGGTTAAAAATGGAATTTTGG
Found at i:145292 original size:30 final size:30
Alignment explanation
Indices: 145203--145328 Score: 125
Period size: 30 Copynumber: 4.3 Consensus size: 30
145193 TTAAAAATGG
* *
145203 AATTTT-GGAAAGTTCGGGGGT-AAAATAT
1 AATTTTAGAAAAGTTTGGGGGTCAAAATAT
* * *
145231 AATTTTA-AAAAGTTT-GAGGTAAAAATGT
1 AATTTTAGAAAAGTTTGGGGGTCAAAATAT
*
145259 AATTTTAGATAAGTTTGGGGGTCAAAATAT
1 AATTTTAGAAAAGTTTGGGGGTCAAAATAT
* **
145289 AATTTTGGAAAAGTTTAAGGGTCAAAATAT
1 AATTTTAGAAAAGTTTGGGGGTCAAAATAT
*
145319 GATTTCTAGA
1 AATTT-TAGA
145329 TAGTTTAGGG
Statistics
Matches: 79, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
27 4 0.05
28 25 0.32
29 7 0.09
30 40 0.51
31 3 0.04
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (30 bp):
AATTTTAGAAAAGTTTGGGGGTCAAAATAT
Found at i:146472 original size:3 final size:3
Alignment explanation
Indices: 146464--146540 Score: 73
Period size: 3 Copynumber: 24.7 Consensus size: 3
146454 GTTTTCTTTT
* * * *
146464 TTA TTA TTA TTA ATA TTA TTTA TTA CTA TTA TTA TTA TTA TTA ATG
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
146510 TTA TTTA GTA TTA TTA TTTA TTA TTA ATA TT
1 TTA -TTA TTA TTA TTA -TTA TTA TTA TTA TT
146541 GCAATAAATA
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
3 50 0.85
4 9 0.15
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:146487 original size:19 final size:18
Alignment explanation
Indices: 146464--146540 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 18
146454 GTTTTCTTTT
146464 TTATTATTATTAATATTA
1 TTATTATTATTAATATTA
* *
146482 TTTATTACTATTATTATTA
1 -TTATTATTATTAATATTA
*
146501 TTATTAATGTTATTTAGTATTA
1 TTATT-A--TTA-TTAATATTA
146523 TTATTTATTATTAATATT
1 TTA-TTATTATTAATATT
146541 GCAATAAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
18 5 0.10
19 24 0.50
20 3 0.06
21 2 0.04
22 12 0.25
23 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (18 bp):
TTATTATTATTAATATTA
Found at i:146502 original size:31 final size:31
Alignment explanation
Indices: 146464--146540 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
146454 GTTTTCTTTT
*
146464 TTATTATTATTAATATTATTTATTACTATTA
1 TTATTATTATTAATATTATTTAGTACTATTA
* *
146495 TTATTATTATTAATGTTATTTAGTATTATTA
1 TTATTATTATTAATATTATTTAGTACTATTA
146526 -T-TTATTATTAATATT
1 TTATTATTATTAATATT
146541 GCAATAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 13 0.31
30 1 0.02
31 28 0.67
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (31 bp):
TTATTATTATTAATATTATTTAGTACTATTA
Found at i:147140 original size:11 final size:11
Alignment explanation
Indices: 147120--147158 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
147110 TCACTGTAAT
*
147120 TTGGGCTTGTA
1 TTGGGTTTGTA
147131 TTGGGTTTGTA
1 TTGGGTTTGTA
* *
147142 TTGGATTGGTA
1 TTGGGTTTGTA
147153 TTGGGT
1 TTGGGT
147159 CAATTAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.10, C:0.03, G:0.38, T:0.49
Consensus pattern (11 bp):
TTGGGTTTGTA
Found at i:147293 original size:24 final size:23
Alignment explanation
Indices: 147256--147345 Score: 69
Period size: 23 Copynumber: 3.8 Consensus size: 23
147246 ATTGGACATT
*
147256 ATTTAAATATATTTTAAA-TTCAA
1 ATTTAAATA-AATTTAAATTTCAA
*
147279 ATTTATAATAAATTTAAATTTCCA
1 ATTTA-AATAAATTTAAATTTCAA
* *
147303 ATTTAAATTTAAA-ATAAACTT-AA
1 ATTTAAA--TAAATTTAAATTTCAA
*
147326 TTTTAAAATAAATTTAAATT
1 ATTT-AAATAAATTTAAATT
147346 CCGTTGGGCC
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
22 4 0.08
23 23 0.43
24 22 0.42
25 4 0.08
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAAATAAATTTAAATTTCAA
Found at i:147317 original size:7 final size:6
Alignment explanation
Indices: 147268--147345 Score: 56
Period size: 6 Copynumber: 13.3 Consensus size: 6
147258 TTAAATATAT
* *
147268 TTTAAA TTCAAA TTTATAA --TAAA TTTAAA TTTCCAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* * * *
147316 -ATAAA CTTAAT TTTAAA -ATAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
147346 CCGTTGGGCC
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
4 2 0.04
5 10 0.18
6 36 0.65
7 7 0.13
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:147330 original size:17 final size:17
Alignment explanation
Indices: 147305--147345 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
147295 AATTTCCAAT
147305 TTAAATTTAAAATAAAC
1 TTAAATTTAAAATAAAC
* *
147322 TTAATTTTAAAATAAAT
1 TTAAATTTAAAATAAAC
147339 TTAAATT
1 TTAAATT
147346 CCGTTGGGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATTTAAAATAAAC
Found at i:148108 original size:49 final size:48
Alignment explanation
Indices: 148055--148522 Score: 275
Period size: 49 Copynumber: 9.6 Consensus size: 48
148045 TGGATCCACT
*
148055 GTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCC
1 GTTGCGGCTTAGATCTTTCCCTTCATGTCT-TGAGGTACTAGGTTCGCC
* * * * * *
148104 GTTGCGACTTAAATCCTTCCCTTCGTGTCTTCGTGGTACTAGATTCGCC
1 GTTGCGGCTTAGATCTTTCCCTTCATGTCTT-GAGGTACTAGGTTCGCC
* * * * * * *
148153 GTTGCGGCTTAAATATTTCCCTTTATGTCTTTACAGTACT-GAATCCGCC
1 GTTGCGGCTTAGATCTTTCCCTTCATGTCTTGA-GGTACTAG-GTTCGCC
* * * * *
148202 GTTGCGGCTTAGATCCTTCTCTTCATGTCTCTAAGGTACTATGTTCGCT
1 GTTGCGGCTTAGATCTTTCCCTTCATGTCT-TGAGGTACTAGGTTCGCC
* * * * * * * * *
148251 GTCGTGACTTAGA-CATTTCCCTTTATATCTTTGCGGTCCT-GGATCCACC
1 GTTGCGGCTTAGATC-TTTCCCTTCATGTC-TTGAGGTACTAGG-TTCGCC
* * * *
148300 ATTGCGGCTTAGATATTTCCCTTTATGTCTCGGAGGTACTAGGTTCGCC
1 GTTGCGGCTTAGATCTTTCCCTTCATGTCT-TGAGGTACTAGGTTCGCC
* * * * * * * * *
148349 ATTGCGACTTAAACCTTTCCCTT-GTGCCTTCGTGGTACT-GGATCCGTC
1 GTTGCGGCTTAGATCTTTCCCTTCATGTCTT-GAGGTACTAGG-TTCGCC
* * *
148397 GTTACGGCTTAGATCTTTCCCTTCATTTCGTTGTGGTACT-GGATTCGCC
1 GTTGCGGCTTAGATCTTTCCCTTCATGTC-TTGAGGTACTAGG-TTCGCC
* * * * * * *
148446 GTTACGGCTTAAATCTTTCCC-TCTTGTATTTTTGTGGTACTAGATCCGCC
1 GTTGCGGCTTAGATCTTTCCCTTCATG---TCTTGAGGTACTAGGTTCGCC
*
148496 GTTACGGCTTAGATCTTTCCCTTCATG
1 GTTGCGGCTTAGATCTTTCCCTTCATG
148523 CTTCGTGGTA
Statistics
Matches: 319, Mismatches: 80, Indels: 38
0.73 0.18 0.09
Matches are distributed among these distances:
47 2 0.01
48 41 0.13
49 228 0.71
50 42 0.13
51 6 0.02
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (48 bp):
GTTGCGGCTTAGATCTTTCCCTTCATGTCTTGAGGTACTAGGTTCGCC
Found at i:148122 original size:98 final size:98
Alignment explanation
Indices: 147992--148182 Score: 247
Period size: 98 Copynumber: 1.9 Consensus size: 98
147982 TGTTTCTAAA
* * * *
147992 GTACAAGGTTCGCCATTGTGACTTAAACCCTTCCCTTTGCATCTTCGCAGTACTGGATCCACTGT
1 GTACAAGGTTCGCCATTGCGACTTAAACCCTTCCCTTCGCATCTTCGCAGTACTAGATCCACCGT
* *
148057 TGCGGCTTAGATCTTTCCCTTCATGTCTCTGAG
66 TGCGGCTTAAATATTTCCCTTCATGTCTCTGAG
* * ** ** * *
148090 GTACAAGGTTCGCCGTTGCGACTTAAATCCTTCCCTTCGTGTCTTCGTGGTACTAGATTCGCCGT
1 GTACAAGGTTCGCCATTGCGACTTAAACCCTTCCCTTCGCATCTTCGCAGTACTAGATCCACCGT
*
148155 TGCGGCTTAAATATTTCCCTTTATGTCT
66 TGCGGCTTAAATATTTCCCTTCATGTCT
148183 TTACAGTACT
Statistics
Matches: 78, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
98 78 1.00
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (98 bp):
GTACAAGGTTCGCCATTGCGACTTAAACCCTTCCCTTCGCATCTTCGCAGTACTAGATCCACCGT
TGCGGCTTAAATATTTCCCTTCATGTCTCTGAG
Found at i:148202 original size:98 final size:98
Alignment explanation
Indices: 148100--148534 Score: 366
Period size: 98 Copynumber: 4.4 Consensus size: 98
148090 GTACAAGGTT
* * * * *
148100 CGCCGTTGCGACTTAAATCCTTCCCTTCGTGTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAA
1 CGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTTCGTGGTACTAGATTCGCCGTTGCGACTTAA
* * * *
148165 ATATTTCCCTTTATGTCTTTACAGTACTGAATC
66 ACATTTCCCTTTATATCTTTGCGGTACTGAATC
* * * * *
148198 CGCCGTTGCGGCTTAGATCCTTCTCTTCATGTC-TC-TAAGGTACTATG-TTCGCTGTCGTGACT
1 CGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTTCGT--GGTACTA-GATTCGCCGTTGCGACT
* * *
148260 TAGACATTTCCCTTTATATCTTTGCGGTCCTGGATC
63 TAAACATTTCCCTTTATATCTTTGCGGTACTGAATC
* * * * * * *
148296 CACCATTGCGGCTTAGATATTTCCCTTTATGTC-TCGGAGGTACTAGGTTCGCCATTGCGACTTA
1 CGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTTC-GTGGTACTAGATTCGCCGTTGCGACTTA
* * ** * * *
148360 AACCTTTCCC-TTGTGCCTTCGTGGTACTGGATC
65 AACATTTCCCTTTATATCTTTGCGGTACTGAATC
* * * * * *
148393 CGTCGTTACGGCTTAGATCTTTCCCTTCATTTCGTT-GTGGTACTGGATTCGCCGTTACGGCTTA
1 CGCCGTTGCGGCTTAGATCTTTCCCTTCATGTC-TTCGTGGTACTAGATTCGCCGTTGCGACTTA
* * *
148457 AATC-TTTCCCTCTTGTATTTTTGTGGTACT-AGATC
65 AA-CATTTCCCT-TTATATCTTTGCGGTACTGA-ATC
*
148492 CGCCGTTACGGCTTAGATCTTTCCCTTCATG-CTTCGTGGTACT
1 CGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTTCGTGGTACT
148535 GAGACTTGTA
Statistics
Matches: 270, Mismatches: 54, Indels: 26
0.77 0.15 0.07
Matches are distributed among these distances:
96 1 0.00
97 78 0.29
98 143 0.53
99 48 0.18
ACGTcount: A:0.15, C:0.26, G:0.20, T:0.38
Consensus pattern (98 bp):
CGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTTCGTGGTACTAGATTCGCCGTTGCGACTTAA
ACATTTCCCTTTATATCTTTGCGGTACTGAATC
Found at i:148271 original size:147 final size:146
Alignment explanation
Indices: 148039--148329 Score: 350
Period size: 147 Copynumber: 2.0 Consensus size: 146
148029 TGCATCTTCG
* * * *
148039 CAGTACTGGATCCACTGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCC
1 CAGTACTGAATCCACCGTTGCGGCTTAGATCCTTCCCTTCATGTCTCTAAGGTACAAGGTTCGCC
* * * * * * *
148104 GTTGCGACTTAAATCCTTCCCTTCGTGTCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATAT
66 GTCGCGACTTAAAT-CTTCCCTTCATATCTTCGCGGTACTAGATCCACCATTGCGGCTTAAATAT
148169 TTCCCTTTATGTCTTTA
130 TTCCCTTTATGTCTTTA
* * * * *
148186 CAGTACTGAATCCGCCGTTGCGGCTTAGATCCTTCTCTTCATGTCTCTAAGGTACTATGTTCGCT
1 CAGTACTGAATCCACCGTTGCGGCTTAGATCCTTCCCTTCATGTCTCTAAGGTACAAGGTTCGCC
* * * * * *
148251 GTCGTGACTTAGACAT-TTCCCTTTATATCTTTGCGGTCCTGGATCCACCATTGCGGCTTAGATA
66 GTCGCGACTTA-A-ATCTTCCCTTCATATCTTCGCGGTACTAGATCCACCATTGCGGCTTAAATA
148315 TTTCCCTTTATGTCT
129 TTTCCCTTTATGTCT
148330 CGGAGGTACT
Statistics
Matches: 120, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
147 117 0.98
148 1 0.01
149 2 0.02
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (146 bp):
CAGTACTGAATCCACCGTTGCGGCTTAGATCCTTCCCTTCATGTCTCTAAGGTACAAGGTTCGCC
GTCGCGACTTAAATCTTCCCTTCATATCTTCGCGGTACTAGATCCACCATTGCGGCTTAAATATT
TCCCTTTATGTCTTTA
Found at i:148435 original size:97 final size:99
Alignment explanation
Indices: 148304--148522 Score: 259
Period size: 99 Copynumber: 2.2 Consensus size: 99
148294 TCCACCATTG
* * *
148304 CGGCTTAGATATTTCCCTTTATGTCTCGGAGGTACTAGG-TTCGCCATTGCGACTTAAACCTTT-
1 CGGCTTAGATCTTTCCCTTCATGTCTCGGAGGTACT-GGATTCGCCATTACGACTTAAACCTTTC
* * *
148367 CC-CTTGTGCCTTCGTGGTACTGGATCCGTCGTTA
65 CCTCTTGTACCTTCGTGGTACTAGATCCGCCGTTA
* * * *
148401 CGGCTTAGATCTTTCCCTTCAT-T-TCGTTGTGGTACTGGATTCGCCGTTACGGCTTAAATCTTT
1 CGGCTTAGATCTTTCCCTTCATGTCTCG--GAGGTACTGGATTCGCCATTACGACTTAAACCTTT
** *
148464 CCCTCTTGTATTTTTGTGGTACTAGATCCGCCGTTA
64 CCCTCTTGTACCTTCGTGGTACTAGATCCGCCGTTA
148500 CGGCTTAGATCTTTCCCTTCATG
1 CGGCTTAGATCTTTCCCTTCATG
148523 CTTCGTGGTA
Statistics
Matches: 103, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
95 3 0.03
96 3 0.03
97 47 0.46
98 2 0.02
99 48 0.47
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.39
Consensus pattern (99 bp):
CGGCTTAGATCTTTCCCTTCATGTCTCGGAGGTACTGGATTCGCCATTACGACTTAAACCTTTCC
CTCTTGTACCTTCGTGGTACTAGATCCGCCGTTA
Found at i:148502 original size:50 final size:50
Alignment explanation
Indices: 148380--148517 Score: 192
Period size: 50 Copynumber: 2.8 Consensus size: 50
148370 TTGTGCCTTC
*
148380 GTGGTACTGGATCCGTCGTTACGGCTTAGATCTTT-CC-CTTCATTTCGTT
1 GTGGTACTGGATCCGCCGTTACGGCTTAGATCTTTCCCTCTTCATTTC-TT
* * *
148429 GTGGTACTGGATTCGCCGTTACGGCTTAAATCTTTCCCTCTTGTATTT-TT
1 GTGGTACTGGATCCGCCGTTACGGCTTAGATCTTTCCCTCTT-CATTTCTT
*
148479 GTGGTACTAGATCCGCCGTTACGGCTTAGATCTTTCCCT
1 GTGGTACTGGATCCGCCGTTACGGCTTAGATCTTTCCCT
148518 TCATGCTTCG
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
49 32 0.41
50 40 0.51
51 3 0.04
52 4 0.05
ACGTcount: A:0.14, C:0.25, G:0.22, T:0.40
Consensus pattern (50 bp):
GTGGTACTGGATCCGCCGTTACGGCTTAGATCTTTCCCTCTTCATTTCTT
Found at i:160025 original size:29 final size:28
Alignment explanation
Indices: 159993--160206 Score: 125
Period size: 29 Copynumber: 7.4 Consensus size: 28
159983 GTAAAATTCT
159993 AATTTTGGAAAATCGAGGGTCAAAAATGG
1 AATTTTGGAAAATCGAGGGTC-AAAATGG
* * *
160022 AATTTTTAGATATTCGAGGGT-AAAATGG
1 AA-TTTTGGAAAATCGAGGGTCAAAATGG
*
160050 TACTTTTTGGAAGAATCG-GGGTCGAAAATGG
1 -A-ATTTTGGAA-AATCGAGGGTC-AAAATGG
* *
160081 AATTTT-TAAAAGTTAGAGGGT-AAAATGG
1 AATTTTGGAAAA--TCGAGGGTCAAAATGG
**
160109 CCTTTTTTGGAAAATC-AGGGTCAAAATGG
1 --AATTTTGGAAAATCGAGGGTCAAAATGG
* ** * *
160138 AATTTTGGAAAGTTTATGGGTAAAAATGT
1 AATTTTGGAAAATCGA-GGGTCAAAATGG
* *
160167 AATTTTTGAAAAAAT-TAGGGTCAAAAATGG
1 AA-TTTTG-GAAAATCGAGGGTC-AAAATGG
160197 AATTTTGGAA
1 AATTTTGGAA
160207 TGTTTGAGGG
Statistics
Matches: 142, Mismatches: 25, Indels: 37
0.70 0.12 0.18
Matches are distributed among these distances:
27 12 0.08
28 24 0.17
29 48 0.34
30 43 0.30
31 15 0.11
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (28 bp):
AATTTTGGAAAATCGAGGGTCAAAATGG
Found at i:160039 original size:30 final size:30
Alignment explanation
Indices: 159995--160143 Score: 107
Period size: 30 Copynumber: 5.1 Consensus size: 30
159985 AAAATTCTAA
*
159995 TTTTGGAA-AATCGAGGGTCAAAAATGGAAT
1 TTTTAGAAGAATCGAGGGTC-AAAATGGAAT
* * *
160025 TTTTAG-ATATTCGAGGGT-AAAATGGTACT
1 TTTTAGAAGAATCGAGGGTCAAAATGG-AAT
*
160054 TTTTGGAAGAATCG-GGGTCGAAAATGGAAT
1 TTTTAGAAGAATCGAGGGTC-AAAATGGAAT
* * * **
160084 TTTTAAAAG-TTAGAGGGT-AAAATGGCCTT
1 TTTTAGAAGAATCGAGGGTCAAAATGG-AAT
*
160113 TTTTGGAA-AATC-AGGGTCAAAATGGAAT
1 TTTTAGAAGAATCGAGGGTCAAAATGGAAT
160141 TTT
1 TTT
160144 GGAAAGTTTA
Statistics
Matches: 91, Mismatches: 19, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
28 23 0.25
29 29 0.32
30 32 0.35
31 7 0.08
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (30 bp):
TTTTAGAAGAATCGAGGGTCAAAATGGAAT
Found at i:160188 original size:116 final size:118
Alignment explanation
Indices: 159995--160221 Score: 275
Period size: 116 Copynumber: 1.9 Consensus size: 118
159985 AAAATTCTAA
* * *
159995 TTTTGGAAAATCGAGGGTCAAAAATGGAATTTTTAGATATTCGAGGGTAAAATGGTACTTTTTGG
1 TTTTGGAAAATCGAGGGTCAAAAATGGAATTTTTAGAAATTCGAGGGTAAAATGGTAATTTTTGA
* * * *
160060 AAGAATCGGGGTCGAAAATGGAATTTTTAAAAGTTAGAGGGTAAAATGGCCTT
66 AAAAATCAGGGTCAAAAATGGAATTTTGAAAAGTTAGAGGGTAAAATGGCCTT
* *
160113 TTTTGGAAAATC-AGGGTC-AAAATGGAA-TTTTGGAAAGTT-TATGGGTAAAAAT-GTAATTTT
1 TTTTGGAAAATCGAGGGTCAAAAATGGAATTTTTAGAAA-TTCGA-GGGT-AAAATGGTAATTTT
* * * *
160173 TGAAAAAATTAGGGTCAAAAATGGAATTTTGGAATGTTTGAGGGTAAAA
63 TGAAAAAATCAGGGTCAAAAATGGAATTTTGAAAAGTTAGAGGGTAAAA
160222 ATGTAATTTT
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
115 8 0.09
116 62 0.67
117 11 0.12
118 12 0.13
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (118 bp):
TTTTGGAAAATCGAGGGTCAAAAATGGAATTTTTAGAAATTCGAGGGTAAAATGGTAATTTTTGA
AAAAATCAGGGTCAAAAATGGAATTTTGAAAAGTTAGAGGGTAAAATGGCCTT
Found at i:160193 original size:30 final size:29
Alignment explanation
Indices: 160119--160295 Score: 137
Period size: 30 Copynumber: 6.0 Consensus size: 29
160109 CCTTTTTTGG
* * *
160119 AAAATCAGGGTC-AAAATGGAATTTTGGA
1 AAAATTAGGGTCAAAAATGTAATTTTGAA
**
160147 AAGTTTATGGGT-AAAAATGTAATTTTTGAA
1 AAAATTA-GGGTCAAAAATGTAA-TTTTGAA
* *
160177 AAAATTAGGGTCAAAAATGGAATTTTGGA
1 AAAATTAGGGTCAAAAATGTAATTTTGAA
*** *
160206 ATGTTTGAGGGT-AAAAATGTAATTTTCAA
1 AAAATT-AGGGTCAAAAATGTAATTTTGAA
*
160235 AAAATTCAAGGTCAAAAATGTAATTTTGAA
1 AAAATT-AGGGTCAAAAATGTAATTTTGAA
** *
160265 GAAGTTTAGGGGTC-AAAATATAATTTTGAA
1 -AAAATTA-GGGTCAAAAATGTAATTTTGAA
160295 A
1 A
160296 GAGTTTAAGG
Statistics
Matches: 116, Mismatches: 25, Indels: 15
0.74 0.16 0.10
Matches are distributed among these distances:
28 4 0.03
29 47 0.41
30 57 0.49
31 8 0.07
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (29 bp):
AAAATTAGGGTCAAAAATGTAATTTTGAA
Found at i:160221 original size:29 final size:28
Alignment explanation
Indices: 160125--160335 Score: 129
Period size: 30 Copynumber: 7.1 Consensus size: 28
160115 TTGGAAAATC
*
160125 AGGGTCAAAATGGAATTTTGGAAAGTTT
1 AGGGTAAAAATGGAATTTTGGAAAGTTT
* * **
160153 ATGGGTAAAAATGTAATTTTTGAAAAAATT
1 A-GGGTAAAAATGGAA-TTTTGGAAAGTTT
*
160183 AGGGTCAAAAATGGAATTTTGGAATGTTT
1 AGGGT-AAAAATGGAATTTTGGAAAGTTT
* ** * *
160212 GAGGGTAAAAATGTAATTTTCAAAAAATTC
1 -AGGGTAAAAATGGAATTTT-GGAAAGTTT
* * *
160242 AAGGTCAAAAATGTAATTTTGAAGAAGTTT
1 AGGGT-AAAAATGGAATTTTGGA-AAGTTT
* ** *
160272 AGGGGTCAAAATATAATTTTGAAAGAGTTT
1 A-GGGTAAAAATGGAATTTTGGAA-AGTTT
160302 AAGGGTTAAAATAT-GAATTTTGGACAA-TTT
1 -AGGG-TAAAA-ATGGAATTTTGGA-AAGTTT
160332 AGGG
1 AGGG
160336 ACCTTTAGGG
Statistics
Matches: 144, Mismatches: 26, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
28 1 0.01
29 49 0.34
30 74 0.51
31 17 0.12
32 3 0.02
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (28 bp):
AGGGTAAAAATGGAATTTTGGAAAGTTT
Found at i:160222 original size:59 final size:58
Alignment explanation
Indices: 160001--160295 Score: 244
Period size: 59 Copynumber: 5.0 Consensus size: 58
159991 CTAATTTTGG
* * * * *
160001 AAAATCGAGGGTCAAAAATGGAATTTTTAGATA-TTCGAGGGTAAAATGGTACTTTTTGGA
1 AAAATC-AGGGTCAAAAATGGAA-TTTTGGAAAGTTTGAGGGTAAAAT-GTAATTTTTGAA
* * * ** * *** *
160061 AGAATCGGGGTCGAAAATGGAATTTTTAAAAGTTAGAGGGTAAAATGGCCTTTTTTG-G
1 AAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAT-GTAATTTTTGAA
160119 AAAATCAGGGTC-AAAATGGAATTTTGGAAAGTTT-ATGGGTAAAAATGTAATTTTTGAA
1 AAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTGA-GGGT-AAAATGTAATTTTTGAA
* * *
160177 AAAATTAGGGTCAAAAATGGAATTTTGGAATGTTTGAGGGTAAAAATGTAA-TTTTCAA
1 AAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGT-AAAATGTAATTTTTGAA
* * * *
160235 AAAATTCAAGGTCAAAAATGTAATTTTGAAGAAGTTT-AGGGGTCAAAATATAA-TTTTGAA
1 AAAA-TCAGGGTCAAAAATGGAATTTTGGA-AAGTTTGA-GGGT-AAAATGTAATTTTTGAA
160295 A
1 A
160296 GAGTTTAAGG
Statistics
Matches: 195, Mismatches: 31, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
56 1 0.01
57 30 0.15
58 42 0.22
59 92 0.47
60 30 0.15
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (58 bp):
AAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAATGTAATTTTTGAA
Found at i:161440 original size:3 final size:3
Alignment explanation
Indices: 161406--161487 Score: 67
Period size: 3 Copynumber: 26.7 Consensus size: 3
161396 CCGTTTTTTT
* * *
161406 TTA TT- TTA TTT TTA ATA TTA TTTA TTA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
161451 TTA ATG TTA TTTA GTA TTA TTA TTTA TTA TTA ATA TT
1 TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA TT
161488 GCAATTAATA
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
2 2 0.03
3 50 0.82
4 9 0.15
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:162289 original size:17 final size:17
Alignment explanation
Indices: 162249--162292 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
162239 TTAAATTTCC
*
162249 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAACA
* *
162266 AACTTAATTTTAAAACA
1 AATTTAAATTTAAAACA
162283 AATTTAAATT
1 AATTTAAATT
162293 ATGTTGGGCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTTAAATTTAAAACA
Found at i:162464 original size:43 final size:43
Alignment explanation
Indices: 162375--162474 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
162365 GAACAATATG
* * * **
162375 CACACGCCCATATGCCTTCAAACAGTATACACACACACCCTGA
1 CACACGCCCGTGTGGCTTCAAACAGTATACACACACACCCAAA
* * *
162418 CACATGCCCGTGTGGCTTCAAATAGTATGCACACACACCCAAA
1 CACACGCCCGTGTGGCTTCAAACAGTATACACACACACCCAAA
*
162461 CACACGTCCGTGTG
1 CACACGCCCGTGTG
162475 CCTCCTTCAA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.31, C:0.36, G:0.15, T:0.18
Consensus pattern (43 bp):
CACACGCCCGTGTGGCTTCAAACAGTATACACACACACCCAAA
Found at i:165768 original size:30 final size:29
Alignment explanation
Indices: 165682--165790 Score: 116
Period size: 31 Copynumber: 3.7 Consensus size: 29
165672 TTTGGAAAAA
*
165682 GGGGTCAAAATGGAATTTTTGG-AAG-TCAT
1 GGGGTCAAAATGGAA-TTTTGGAAAGTTC-G
*
165711 TGGGTCAACAATGGAATTTTCGGAAAGTTCG
1 GGGGTCAA-AATGGAATTTT-GGAAAGTTCG
*
165742 GGGGTCAAAATTGGAATTTTGGAAAGTTTAG
1 GGGGTCAAAA-TGGAATTTTGGAAAG-TTCG
165773 GGGGT-AAAATGGAATTTT
1 GGGGTCAAAATGGAATTTT
165791 TGGAGAAATT
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
29 20 0.29
30 21 0.30
31 27 0.39
32 2 0.03
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.31
Consensus pattern (29 bp):
GGGGTCAAAATGGAATTTTGGAAAGTTCG
Found at i:165792 original size:30 final size:30
Alignment explanation
Indices: 165654--165820 Score: 143
Period size: 30 Copynumber: 5.7 Consensus size: 30
165644 TTTAGCATTC
165654 GGGGGT-AAAATGGAAATTTTTGGAAA---A
1 GGGGGTCAAAATGG-AATTTTTGGAAAGTTA
* *
165681 AGGGGTCAAAATGGAATTTTTGG-AAGTCA
1 GGGGGTCAAAATGGAATTTTTGGAAAGTTA
** * *
165710 TTGGGTCAACAATGGAATTTTCGGAAAGTTC
1 GGGGGTCAA-AATGGAATTTTTGGAAAGTTA
165741 GGGGGTCAAAATTGGAA-TTTTGGAAAGTTTA
1 GGGGGTCAAAA-TGGAATTTTTGGAAAG-TTA
*
165772 GGGGGT-AAAATGGAATTTTTGGAGAAATT-
1 GGGGGTCAAAATGGAATTTTTGGA-AAGTTA
* * *
165801 GGGGTTAAAAATGAAATTTT
1 GGGGGTCAAAATGGAATTTT
165821 AGGCATTCGA
Statistics
Matches: 116, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
26 2 0.02
27 14 0.12
28 7 0.06
29 18 0.16
30 49 0.42
31 26 0.22
ACGTcount: A:0.35, C:0.04, G:0.31, T:0.31
Consensus pattern (30 bp):
GGGGGTCAAAATGGAATTTTTGGAAAGTTA
Found at i:165812 original size:60 final size:55
Alignment explanation
Indices: 165654--165875 Score: 164
Period size: 60 Copynumber: 3.9 Consensus size: 55
165644 TTTAGCATTC
*
165654 GGGGGTAAAATGGAAATTTTTGGAAAA-AGGGGTCAAAATGGAATTTTTGGAAGTCA
1 GGGGGTAAAATGG-AATTTTTGGAAAATTGGGGTCAAAATGGAA-TTTTGGAAGTCA
** * * *
165710 TTGGGTCAACAATGGAATTTTCGGAAAGTTCGGGGGTCAAAATTGGAATTTTGGAAAGTTTA
1 GGGGGT-AA-AATGGAATTTTTGGAAAATT--GGGGTCAAAA-TGGAATTTTGG-AAG-TCA
* * * *
165772 GGGGGTAAAATGGAATTTTTGGAGAAATTGGGGTTAAAAATGAAATTTTAGGCATTC-
1 GGGGGTAAAATGGAATTTTTGGA-AAATTGGGG-TCAAAATGGAATTTT-GGAAGTCA
** * *
165829 GAAGGTAAAATGGTAATTTTTGGAACAA-TCGAGTC-AAATGGAATTTT
1 GGGGGTAAAATGG-AATTTTTGGAA-AATTGGGGTCAAAATGGAATTTT
165876 TGGTAATTTT
Statistics
Matches: 132, Mismatches: 21, Indels: 27
0.73 0.12 0.15
Matches are distributed among these distances:
55 11 0.08
56 5 0.04
57 28 0.21
58 18 0.14
59 13 0.10
60 37 0.28
61 14 0.11
62 6 0.05
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (55 bp):
GGGGGTAAAATGGAATTTTTGGAAAATTGGGGTCAAAATGGAATTTTGGAAGTCA
Found at i:165895 original size:36 final size:38
Alignment explanation
Indices: 165839--165922 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 38
165829 GAAGGTAAAA
* *
165839 TGGTAATTTTTGGAACAATCGA-GT-CAAATGGAATTTT
1 TGGTAA-TTTTGGAAAAATCGAGGTGAAAATGGAATTTT
165876 TGGTAATTTTGGAAAAATCGAGGTGAAAATGGAATTTT
1 TGGTAATTTTGGAAAAATCGAGGTGAAAATGGAATTTT
* *
165914 AGGAAATTT
1 TGGTAATTT
165923 AGGGGTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
36 14 0.34
37 8 0.20
38 19 0.46
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.36
Consensus pattern (38 bp):
TGGTAATTTTGGAAAAATCGAGGTGAAAATGGAATTTT
Found at i:165912 original size:28 final size:28
Alignment explanation
Indices: 165880--166058 Score: 112
Period size: 29 Copynumber: 6.2 Consensus size: 28
165870 AATTTTTGGT
*
165880 AATTTTGGAAAAATCGAGGTGAAAATGG
1 AATTTTGGAAAAATCGAGGTAAAAATGG
** * *
165908 AATTTTAGGAAATTTAGGGGT-AAAATGG
1 AATTTT-GGAAAAATCGAGGTAAAAATGG
**
165936 TAATTTTTGG-AAAATAAAGGTAAAAAATGG
1 -AA-TTTTGGAAAAATCGAGGT-AAAAATGG
* ** *
165966 AATCTTGGAAAGTTCGGGGGT-AAAATGG
1 AATTTTGGAAAAATC-GAGGTAAAAATGG
* *
165994 TAATTTTTGAAAAATTGAGGTTAAAAATGG
1 -AATTTTGGAAAAATCGAGG-TAAAAATGG
* ** *
166024 AATTTTCGAAAGTTCAAGGGTAAAAATGG
1 AATTTTGGAAAAATCGA-GGTAAAAATGG
166053 AATTTT
1 AATTTT
166059 TAAAAAGTTC
Statistics
Matches: 115, Mismatches: 25, Indels: 21
0.71 0.16 0.13
Matches are distributed among these distances:
28 35 0.30
29 57 0.50
30 23 0.20
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.31
Consensus pattern (28 bp):
AATTTTGGAAAAATCGAGGTAAAAATGG
Found at i:165940 original size:29 final size:27
Alignment explanation
Indices: 165901--166058 Score: 86
Period size: 28 Copynumber: 5.5 Consensus size: 27
165891 AATCGAGGTG
165901 AAAATGGAATTTTAGGAAATTTAGGGGT
1 AAAATGGAATTTT-GGAAATTTAGGGGT
* **
165929 AAAATGGTAATTTTTGGAAA-ATAAAGGT
1 AAAATGG-AA-TTTTGGAAATTTAGGGGT
* **
165957 AAAAAATGGAATCTTGGAAAGTTCGGGGGT
1 --AAAATGGAATTTTGGAAA-TTTAGGGGT
* * *
165987 AAAATGGTAATTTTTGAAAAATT-GAGGTT
1 AAAATGG-AA-TTTTGGAAATTTAG-GGGT
* * *
166016 AAAAATGGAATTTTCGAAAGTTCAAGGGT
1 -AAAATGGAATTTTGGAAA-TTTAGGGGT
166045 AAAAATGGAATTTT
1 -AAAATGGAATTTT
166059 TAAAAAGTTC
Statistics
Matches: 98, Mismatches: 20, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
28 35 0.36
29 35 0.36
30 28 0.29
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.31
Consensus pattern (27 bp):
AAAATGGAATTTTGGAAATTTAGGGGT
Found at i:165949 original size:58 final size:58
Alignment explanation
Indices: 165876--166064 Score: 217
Period size: 58 Copynumber: 3.3 Consensus size: 58
165866 ATGGAATTTT
* * *
165876 TGGTAATTTTGGAAAAATCGAGGTGAAAATGGAATTTTAGGAAA-TTTAGGGGT-AAAA
1 TGGTAATTTTTGAAAAATCGAGGTAAAAATGGAATTTT-GGAAAGTTCAGGGGTAAAAA
* ** * *
165933 TGGTAATTTTTGGAAAATAAAGGTAAAAAATGGAATCTTGGAAAGTTCGGGGGT-AAAA
1 TGGTAATTTTTGAAAAATCGAGGT-AAAAATGGAATTTTGGAAAGTTCAGGGGTAAAAA
* * *
165991 TGGTAATTTTTGAAAAATTGAGGTTAAAAATGGAATTTTCGAAAGTTCAAGGGTAAAAA
1 TGGTAATTTTTGAAAAATCGAGG-TAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAAA
166050 TGG-AATTTTT-AAAAA
1 TGGTAATTTTTGAAAAA
166065 GTTCGAGGGC
Statistics
Matches: 113, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
57 30 0.27
58 75 0.66
59 8 0.07
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.31
Consensus pattern (58 bp):
TGGTAATTTTTGAAAAATCGAGGTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAAA
Found at i:166080 original size:30 final size:30
Alignment explanation
Indices: 165974--166073 Score: 109
Period size: 30 Copynumber: 3.4 Consensus size: 30
165964 GGAATCTTGG
*
165974 AAAGTTCGGGGGT-AAAATGGTAATTTTTGAA
1 AAAGTTCGAGGGTAAAAATGG-AATTTTT-AA
* **
166005 AAA-TT-GAGGTTAAAAATGGAA-TTTTCG
1 AAAGTTCGAGGGTAAAAATGGAATTTTTAA
*
166032 AAAGTTCAAGGGTAAAAATGGAATTTTTAA
1 AAAGTTCGAGGGTAAAAATGGAATTTTTAA
166062 AAAGTTCGAGGG
1 AAAGTTCGAGGG
166074 CCAAAATATA
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
27 3 0.05
28 6 0.11
29 20 0.36
30 24 0.43
31 3 0.05
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.30
Consensus pattern (30 bp):
AAAGTTCGAGGGTAAAAATGGAATTTTTAA
Found at i:166102 original size:29 final size:28
Alignment explanation
Indices: 166056--166131 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 28
166046 AAAATGGAAT
* *
166056 TTTTAAAAAGTTCGAGGGCCAAAATATAA
1 TTTTAGAAAGTT-TAGGGCCAAAATATAA
*
166085 TTTTAGAGAAGTTTAGGGGTCAAAATATAA
1 TTTTAGA-AAGTTTA-GGGCCAAAATATAA
*
166115 TTTTAGACAGTTTAGGG
1 TTTTAGAAAGTTTAGGG
166132 ACCTCTAAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 3 0.07
29 13 0.32
30 25 0.61
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (28 bp):
TTTTAGAAAGTTTAGGGCCAAAATATAA
Found at i:166119 original size:30 final size:29
Alignment explanation
Indices: 166075--166131 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
166065 GTTCGAGGGC
166075 CAAAATATAATTTTAGAGAAGTTTAGGGGT
1 CAAAATATAATTTTAGA-AAGTTTAGGGGT
*
166105 CAAAATATAATTTTAGACAGTTTAGGG
1 CAAAATATAATTTTAGAAAGTTTAGGG
166132 ACCTCTAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.33
Consensus pattern (29 bp):
CAAAATATAATTTTAGAAAGTTTAGGGGT
Found at i:167171 original size:12 final size:12
Alignment explanation
Indices: 167151--167206 Score: 76
Period size: 12 Copynumber: 4.4 Consensus size: 12
167141 CTTTTTATTT
*
167151 TATTGTTATTAA
1 TATTATTATTAA
167163 TATTATTATTAA
1 TATTATTATTAA
167175 TATTATTATTAA
1 TATTATTATTAA
167187 TACATTTATTATTAA
1 T--A-TTATTATTAA
167202 TATTA
1 TATTA
167207 ACAAACATTC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
12 27 0.68
13 1 0.03
14 1 0.03
15 11 0.28
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:167181 original size:15 final size:15
Alignment explanation
Indices: 167163--167203 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
167153 TTGTTATTAA
*
167163 TATTATTATTA-ATAT
1 TATTATTAATACAT-T
167178 TATTATTAATACATT
1 TATTATTAATACATT
167193 TATTATTAATA
1 TATTATTAATA
167204 TTAACAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 22 0.92
16 2 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTATTAATACATT
Found at i:167877 original size:18 final size:17
Alignment explanation
Indices: 167851--167887 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
167841 AACCTTCAAT
*
167851 TTGAGCTTTTTTTTGTAA
1 TTGAACTTTTTTTT-TAA
167869 TTGAACTTTTTTTTTAA
1 TTGAACTTTTTTTTTAA
167886 TT
1 TT
167888 CAATTTAAAT
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:0.19, C:0.05, G:0.11, T:0.65
Consensus pattern (17 bp):
TTGAACTTTTTTTTTAA
Found at i:167911 original size:17 final size:18
Alignment explanation
Indices: 167884--167919 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
167874 CTTTTTTTTT
167884 AATTCAATTTAAATTTAA
1 AATTCAATTTAAATTTAA
167902 AATT-AATTTAAATTTAA
1 AATTCAATTTAAATTTAA
167919 A
1 A
167920 CTTTAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTCAATTTAAATTTAA
Found at i:167924 original size:7 final size:6
Alignment explanation
Indices: 167889--167956 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
167879 TTTTTAATTC
* **
167889 AATTTA AATTTA AAATT- AATTTA AATTTA AACTTTA AA-AGA AATGTTCA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AA-TTTA AATTTA AAT-TT-A
*
167938 AACTTA AA-TTA AATTTA AA
1 AATTTA AATTTA AATTTA AA
167957 CTCAAAATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
5 12 0.24
6 26 0.53
7 8 0.16
8 3 0.06
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:167967 original size:17 final size:17
Alignment explanation
Indices: 167893--167969 Score: 73
Period size: 17 Copynumber: 4.4 Consensus size: 17
167883 TAATTCAATT
* **
167893 TAAATTTAAAATTAATT
1 TAAATTTAAACTTAAAA
167910 TAAATTTAAACTTTAAAA
1 TAAATTTAAAC-TTAAAA
* *
167928 GAAATGTTCAAACTTAAAT
1 TAAAT-TT-AAACTTAAAA
*
167947 TAAATTTAAACTCAAAA
1 TAAATTTAAACTTAAAA
167964 TAAATT
1 TAAATT
167970 AAAAGAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
17 24 0.49
18 10 0.20
19 11 0.22
20 4 0.08
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:168382 original size:8 final size:10
Alignment explanation
Indices: 168353--168378 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
168343 TATTAACAAA
168353 TTTTAACATT
1 TTTTAACATT
168363 TTTTAACATT
1 TTTTAACATT
168373 TTTTAA
1 TTTTAA
168379 TTTTGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTTAACATT
Found at i:169703 original size:30 final size:31
Alignment explanation
Indices: 169655--169750 Score: 106
Period size: 36 Copynumber: 3.0 Consensus size: 31
169645 AATTTAATTT
169655 TTAATATTTTTA-TAATTTTAAAATATTAAA
1 TTAATATTTTTATTAATTTTAAAATATTAAA
**
169685 TTAA-ATTTTTATTAATTTTAAAGGATTAATA
1 TTAATATTTTTATTAATTTTAAAATATTAA-A
*
169716 TGTAATTTTATTTTTATTAATTTTAAAATTTTAAA
1 T-TAA---TATTTTTATTAATTTTAAAATATTAAA
169751 AGGTTAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
29 7 0.13
30 19 0.35
31 2 0.04
32 3 0.06
35 1 0.02
36 22 0.41
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (31 bp):
TTAATATTTTTATTAATTTTAAAATATTAAA
Found at i:172584 original size:28 final size:28
Alignment explanation
Indices: 172544--172599 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
172534 ATGTAGGCAT
172544 GCTAAGAGGTTGAAGTATATAAGCTGTC
1 GCTAAGAGGTTGAAGTATATAAGCTGTC
172572 GCTAAGAGGTTGAAGTATATAAGCTGTC
1 GCTAAGAGGTTGAAGTATATAAGCTGTC
172600 CCTGTCCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.29
Consensus pattern (28 bp):
GCTAAGAGGTTGAAGTATATAAGCTGTC
Found at i:177061 original size:29 final size:29
Alignment explanation
Indices: 177020--177079 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
177010 AATTAAAATA
* *
177020 TTAATTAAACTAAAATAACTTAATGGAAT
1 TTAACTAAACTAAAATAACCTAATGGAAT
* * *
177049 TTAACTAACCTAATATATCCTAATGGAAT
1 TTAACTAAACTAAAATAACCTAATGGAAT
177078 TT
1 TT
177080 CCTACTCCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.37
Consensus pattern (29 bp):
TTAACTAAACTAAAATAACCTAATGGAAT
Found at i:181131 original size:24 final size:24
Alignment explanation
Indices: 181084--181132 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
181074 CCATTTTCAC
*
181084 AATTAACCTTAATTCTACTAAATT
1 AATTAACCTTAATTATACTAAATT
*
181108 AATTAACCTTTATTATA-TATAATT
1 AATTAACCTTAATTATACTA-AATT
181132 A
1 A
181133 CTCACTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (24 bp):
AATTAACCTTAATTATACTAAATT
Found at i:194812 original size:17 final size:18
Alignment explanation
Indices: 194790--194823 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
194780 TTGTTTTATA
194790 TTTTTTT-ATTTATAATT
1 TTTTTTTAATTTATAATT
194807 TTTTTTTAATTTATAAT
1 TTTTTTTAATTTATAAT
194824 ATAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTTAATTTATAATT
Found at i:201587 original size:15 final size:15
Alignment explanation
Indices: 201567--201600 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
201557 TAAACCCAAC
201567 TAAAGTGAA-CTCAAT
1 TAAAGTGAACCT-AAT
201582 TAAAGTGAACCTAAT
1 TAAAGTGAACCTAAT
201597 TAAA
1 TAAA
201601 CTGGATTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (15 bp):
TAAAGTGAACCTAAT
Found at i:205231 original size:8 final size:8
Alignment explanation
Indices: 205218--205262 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
205208 CGAAATCTCA
205218 TTTTATTT
1 TTTTATTT
205226 TTTTATTAT
1 TTTTATT-T
205235 TTTTATTT
1 TTTTATTT
*
205243 ATTTATTT
1 TTTTATTT
205251 ATTATTATTT
1 -TT-TTATTT
205261 TT
1 TT
205263 ATAAATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 15 0.47
9 11 0.34
10 6 0.19
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTATTT
Found at i:205243 original size:21 final size:20
Alignment explanation
Indices: 205218--205264 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
205208 CGAAATCTCA
* *
205218 TTTTATTTTTTTATTATTTT
1 TTTTATTTATTTATTATTAT
205238 TATTTATTTATTTATTATTAT
1 T-TTTATTTATTTATTATTAT
205259 TTTTAT
1 TTTTAT
205265 AAATATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTATTTATTTATTATTAT
Found at i:205380 original size:63 final size:62
Alignment explanation
Indices: 205232--205412 Score: 232
Period size: 63 Copynumber: 3.0 Consensus size: 62
205222 ATTTTTTTAT
*
205232 TATTTTTATTTATTTATTTA-TTATTATT-T-T-TATA-AATATAAATAAATATAAAATAATA
1 TATTTTTATTTATTTATTTATTTATTATTGTATGAATATAA-ATAAATAAATATAAAATAATA
* *
205290 TATTTTTATTTATTTATTTATTTATTATTGTATGAATATGAATAAATAAATGTAAAATAATA
1 TATTTTTATTTATTTATTTATTTATTATTGTATGAATATAAATAAATAAATATAAAATAATA
* *
205352 TTTATTTTATTT-TATTATTTATTTATTATTTTATGAATATAAATAAATAAATA-AATAATAA
1 TAT-TTTTATTTAT-TTATTTATTTATTATTGTATGAATATAAATAAATAAATATAA-AATAA
205413 ATCCAAAGTC
Statistics
Matches: 108, Mismatches: 7, Indels: 11
0.86 0.06 0.09
Matches are distributed among these distances:
58 20 0.19
59 8 0.07
60 1 0.01
61 1 0.01
62 28 0.26
63 50 0.46
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (62 bp):
TATTTTTATTTATTTATTTATTTATTATTGTATGAATATAAATAAATAAATATAAAATAATA
Found at i:207620 original size:23 final size:23
Alignment explanation
Indices: 207546--207734 Score: 103
Period size: 23 Copynumber: 8.5 Consensus size: 23
207536 TAAACGGAAC
* * *
207546 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
207568 AAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
207590 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
207616 AAACAGAGGGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
207636 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
** * **
207655 AATTAGAGAGCACGA-GACTTGCT
1 AAACAGAGAGCAC-ACAAAGTGCT
207678 AAACAGAGAGCACA-AACAGTGCT
1 AAACAGAGAGCACACAA-AGTGCT
* * *
207701 AATCAGAGAGCACACATAGTGAT
1 AAACAGAGAGCACACAAAGTGCT
*
207724 AATCAGAGAGC
1 AAACAGAGAGC
207735 GTGCTAGTGT
Statistics
Matches: 127, Mismatches: 25, Indels: 29
0.70 0.14 0.16
Matches are distributed among these distances:
16 9 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 1 0.01
22 20 0.16
23 70 0.55
24 2 0.02
25 13 0.10
26 7 0.06
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:213446 original size:21 final size:20
Alignment explanation
Indices: 213420--213467 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
213410 NNNNNNAAAG
213420 AGAAAAAG-AGAGAAAGAAAA
1 AGAAAAAGAAGA-AAAGAAAA
*
213440 GGAAAAAGAAGAAAAGAAAA
1 AGAAAAAGAAGAAAAGAAAA
213460 AGAAAAAG
1 AGAAAAAG
213468 GGGAGGTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (20 bp):
AGAAAAAGAAGAAAAGAAAA
Found at i:213453 original size:15 final size:14
Alignment explanation
Indices: 213433--213463 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
213423 AAAAGAGAGA
213433 AAGAAAAGGAAAAAG
1 AAGAAAA-GAAAAAG
213448 AAGAAAAGAAAAAG
1 AAGAAAAGAAAAAG
213462 AA
1 AA
213464 AAAGGGGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAAAAG
Found at i:213460 original size:6 final size:6
Alignment explanation
Indices: 213420--213467 Score: 51
Period size: 6 Copynumber: 7.3 Consensus size: 6
213410 NNNNNNAAAG
*
213420 AGAAAA AGAGAGAA AGAAAA GGAAAA AGAAGAAA AGAAAA AGAAAA AG
1 AGAAAA AGA-A-AA AGAAAA AGAAAA AG-A-AAA AGAAAA AGAAAA AG
213468 GGGAGGTCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
6 22 0.61
7 4 0.11
8 10 0.28
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:214452 original size:50 final size:50
Alignment explanation
Indices: 214386--214562 Score: 212
Period size: 50 Copynumber: 3.5 Consensus size: 50
214376 ATCTTTTACT
214386 CCTAAAGCTGTAGAGGTGCAGATTGAAACTGCAATGGCAAATCTCATACA
1 CCTAAAGCTGTAGAGGTGCAGATTGAAACTGCAATGGCAAATCTCATACA
* * * ** * *
214436 CCTAAAGCTGTGGAGGTGCAAATTGAAACCGCAGCGACAAATCTTATACA
1 CCTAAAGCTGTAGAGGTGCAGATTGAAACTGCAATGGCAAATCTCATACA
* * * *
214486 CCTAAAGTTGTAGAGG-GACAGAATGAAACTGTAATGGCAAATCTCATTCA
1 CCTAAAGCTGTAGAGGTG-CAGATTGAAACTGCAATGGCAAATCTCATACA
* * *
214536 CTTAAAGCTGTAGAGGAGAAGATTGAA
1 CCTAAAGCTGTAGAGGTGCAGATTGAA
214563 GTCACAAGGA
Statistics
Matches: 103, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
49 1 0.01
50 101 0.98
51 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGTGCAGATTGAAACTGCAATGGCAAATCTCATACA
Found at i:214579 original size:100 final size:100
Alignment explanation
Indices: 214372--214595 Score: 274
Period size: 100 Copynumber: 2.2 Consensus size: 100
214362 GCGATAAAAA
* *
214372 ACAAATCTTTTACTCCTAAAGCTGTAGAGGTGCAGATTGAAACTGCAATGGCAAATCTCATACAC
1 ACAAATCTTATACTCCTAAAGCTGTAGAGGTGCAGAATGAAACTGCAATGGCAAATCTCATACAC
* * *
214437 CTAAAGCTGTGGAGGTGCAAATTGAAACCGCAGCG
66 CTAAAGCTGTAGAGGAGCAAATTGAAACCACAGCG
* * * *
214472 ACAAATCTTATACACCTAAAGTTGTAGAGG-GACAGAATGAAACTGTAATGGCAAATCTCATTCA
1 ACAAATCTTATACTCCTAAAGCTGTAGAGGTG-CAGAATGAAACTGCAATGGCAAATCTCATACA
* **
214536 CTTAAAGCTGTAGAGGAG-AAGATTGAAGTCACAAG-G
65 CCTAAAGCTGTAGAGGAGCAA-ATTGAAACCAC-AGCG
**
214572 ATGAATCTTATACTCCTAAAGCTG
1 ACAAATCTTATACTCCTAAAGCTG
214596 AAATGAAGCG
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
99 3 0.03
100 100 0.95
101 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (100 bp):
ACAAATCTTATACTCCTAAAGCTGTAGAGGTGCAGAATGAAACTGCAATGGCAAATCTCATACAC
CTAAAGCTGTAGAGGAGCAAATTGAAACCACAGCG
Found at i:214667 original size:41 final size:41
Alignment explanation
Indices: 214617--214832 Score: 157
Period size: 41 Copynumber: 5.4 Consensus size: 41
214607 AGTTACAACC
*
214617 TCCAATCTTTTACCCTAACTAGAGGGCAAGATCAAAAATCA
1 TCCAATCTTTTACCCTAACTAGAGGGCAAGATGAAAAATCA
* * * *
214658 TCCGATCTTTTTCCCCAA-TCATG-TGGC-AGATTGAAGAAAT-A
1 TCCAATCTTTTACCCTAACT-A-GAGGGCAAGA-TGAA-AAATCA
* * * *
214699 T--AATCTTTTACCCTAACCAGAGGGAAAGATTAAAGATCA
1 TCCAATCTTTTACCCTAACTAGAGGGCAAGATGAAAAATCA
** *
214738 TCCAATCTTTTACCCCGA-TCATG-GGGC-AGATTGAAGAA--A
1 TCCAATCTTTTACCCTAACT-A-GAGGGCAAGA-TGAAAAATCA
* *
214777 TCCAATCTTTTATCCTAACTAGAGGGCAAGATTAAAAATCA
1 TCCAATCTTTTACCCTAACTAGAGGGCAAGATGAAAAATCA
*
214818 TCCGATCTTTTACCC
1 TCCAATCTTTTACCC
214833 CGATCATGGG
Statistics
Matches: 130, Mismatches: 27, Indels: 36
0.67 0.14 0.19
Matches are distributed among these distances:
38 5 0.04
39 46 0.35
40 14 0.11
41 59 0.45
42 6 0.05
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (41 bp):
TCCAATCTTTTACCCTAACTAGAGGGCAAGATGAAAAATCA
Found at i:214707 original size:39 final size:39
Alignment explanation
Indices: 214657--215100 Score: 290
Period size: 39 Copynumber: 11.4 Consensus size: 39
214647 ATCAAAAATC
* * *
214657 ATCCGATCTTTTTCCCCAATCATGTGGCAGATTGAAGAA
1 ATCCAATCTTTTACCCCAATCATGGGGCAGATTGAAGAA
** * * * * *
214696 ATATAATCTTTTACCCTAACCA-GAGGGAAAGATTAAAGATC
1 ATCCAATCTTTTACCCCAATCATG-GGG-CAGATTGAAGA-A
*
214737 ATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGAA
1 ATCCAATCTTTTACCCCAATCATGGGGCAGATTGAAGAA
* * *
214776 ATCCAATCTTTTATCCTAA-C-TAGAGGGCAAGATT-AAAAA
1 ATCCAATCTTTTACCCCAATCAT-G-GGGC-AGATTGAAGAA
* * *
214815 TCATCCGATCTTTTACCCCGATCATGGGGCAGATTAAAGAA
1 --ATCCAATCTTTTACCCCAATCATGGGGCAGATTGAAGAA
* * * **
214856 ATTCAATCTTTTACCCTAACCAAAGGGCAAGATTGAAG--
1 ATCCAATCTTTTACCCCAATCATGGGGC-AGATTGAAGAA
* *
214894 A-CC-A-----T-CCCCGATCATGGGGCTGATTGAAGAA
1 ATCCAATCTTTTACCCCAATCATGGGGCAGATTGAAGAA
* * *
214925 ATCCAATCTTTTACCCTAACCA-GAGGGCAAGATTGAAGACC
1 ATCCAATCTTTTACCCCAATCATG-GGGC-AGATTGAAGA-A
* *
214966 ATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAA
1 ATCCAATCTTTTACCCCAATCATGGGGCAGATTGAAGAA
** * * ** *
215005 ATTGAATCTTTTACCCTAACCA-GAGAGAAAGATTGAAGACC
1 ATCCAATCTTTTACCCCAATCATG-G-GGCAGATTGAAGA-A
* *
215046 ATTCAATCTTTTACCCCGATCATGGGGCAGATTGAAGAA
1 ATCCAATCTTTTACCCCAATCATGGGGCAGATTGAAGAA
*
215085 ATCGAATCTTTTACCC
1 ATCCAATCTTTTACCC
215101 TAACTAGAGG
Statistics
Matches: 304, Mismatches: 70, Indels: 62
0.70 0.16 0.14
Matches are distributed among these distances:
29 8 0.03
30 10 0.03
31 2 0.01
32 2 0.01
33 1 0.00
36 1 0.00
37 2 0.01
38 7 0.02
39 104 0.34
40 77 0.25
41 84 0.28
42 5 0.02
43 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (39 bp):
ATCCAATCTTTTACCCCAATCATGGGGCAGATTGAAGAA
Found at i:214759 original size:80 final size:80
Alignment explanation
Indices: 214620--214900 Score: 393
Period size: 80 Copynumber: 3.5 Consensus size: 80
214610 TACAACCTCC
* * * * * *
214620 AATCTTTTACCCTAACTAGAGGGCAAGATCAAAAATCATCCGATCTTTTTCCCCAATCATGTGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTAAAGATCATCCGATCTTTTACCCCGATCATGGGGC
*
214685 AGATTGAAGAAATAT
66 AGATTGAAGAAATCT
* *
214700 AATCTTTTACCCTAACCAGAGGGAAAGATTAAAGATCATCCAATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTAAAGATCATCCGATCTTTTACCCCGATCATGGGGC
*
214765 AGATTGAAGAAATCC
66 AGATTGAAGAAATCT
* * *
214780 AATCTTTTATCCTAACTAGAGGGCAAGATTAAAAATCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTAAAGATCATCCGATCTTTTACCCCGATCATGGGGC
*
214845 AGATTAAAGAAAT-T
66 AGATTGAAGAAATCT
* * *
214859 CAATCTTTTACCCTAACCAAAGGGCAAGATTGAAGACCATCC
1 -AATCTTTTACCCTAACCAGAGGGCAAGATTAAAGATCATCC
214901 CCGATCATGG
Statistics
Matches: 177, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
80 177 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (80 bp):
AATCTTTTACCCTAACCAGAGGGCAAGATTAAAGATCATCCGATCTTTTACCCCGATCATGGGGC
AGATTGAAGAAATCT
Found at i:214941 original size:69 final size:73
Alignment explanation
Indices: 214827--215119 Score: 333
Period size: 80 Copynumber: 3.9 Consensus size: 73
214817 ATCCGATCTT
* * *
214827 TTACCCCGATCATGGGGCAGATTAAAGAAATTCAATCTTTTACCCTAACCAAAGGGCAAGATTGA
1 TTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGA
214892 AGA-CC-A
66 AGACCCAA
*
214898 -T-CCCCGATCATGGGGCTGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGA
1 TTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGA
*
214961 AGACCATCCGATCTT
66 AGA-C--CC-A---A
** * *
214976 TTACCCCGATCATGGGGCAGATTGAAGAAATTGAATCTTTTACCCTAACCAGAGAGAAAGATTGA
1 TTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGA
215041 AGACCATTCAA
66 AGACC---CAA
* *
215052 TCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCGAATCTTTTACCCTAACTAGAGGGCAAGA
1 ----TTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGA
215117 TTG
62 TTG
215120 TATCTACAAC
Statistics
Matches: 189, Mismatches: 15, Indels: 27
0.82 0.06 0.12
Matches are distributed among these distances:
69 61 0.32
70 1 0.01
73 2 0.01
77 1 0.01
79 3 0.02
80 121 0.64
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (73 bp):
TTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGA
AGACCCAA
Found at i:215037 original size:80 final size:80
Alignment explanation
Indices: 214899--215119 Score: 370
Period size: 80 Copynumber: 2.8 Consensus size: 80
214889 TGAAGACCAT
* *
214899 CCCCGATCATGGGGCTGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGA
1 CCCCGATCATGGGGCAGATTGAAGAAATCGAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGA
*
214964 CCATCCGATCTTTTA
66 CCATCCAATCTTTTA
* * *
214979 CCCCGATCATGGGGCAGATTGAAGAAATTGAATCTTTTACCCTAACCAGAGAGAAAGATTGAAGA
1 CCCCGATCATGGGGCAGATTGAAGAAATCGAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGA
*
215044 CCATTCAATCTTTTA
66 CCATCCAATCTTTTA
*
215059 CCCCGATCATGGGGCAGATTGAAGAAATCGAATCTTTTACCCTAACTAGAGGGCAAGATTG
1 CCCCGATCATGGGGCAGATTGAAGAAATCGAATCTTTTACCCTAACCAGAGGGCAAGATTG
215120 TATCTACAAC
Statistics
Matches: 130, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 130 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (80 bp):
CCCCGATCATGGGGCAGATTGAAGAAATCGAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGA
CCATCCAATCTTTTA
Found at i:215057 original size:229 final size:229
Alignment explanation
Indices: 214669--215119 Score: 679
Period size: 229 Copynumber: 2.0 Consensus size: 229
214659 CCGATCTTTT
* *
214669 TCCCCAATCATGTGGCAGATTGAAGAAATATAATCTTTTACCCTAACCAGAGGGAAAGATTAAAG
1 TCCCCAATCATGGGGCAGATTGAAGAAATACAATCTTTTACCCTAACCAGAGGGAAAGATTAAAG
* * *
214734 ATCATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTATCCTAACTAG
66 ACCATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAG
* * * *
214799 AGGGCAAGATTAAAAATCATCCGATCTTTTACCCCGATCATGGGGCAGATTAAAGAAATTC-AAT
131 AGAGAAAGATTAAAAACCATCCAATCTTTTACCCCGATCATGGGGCAGATTAAAGAAA-TCGAAT
214863 CTTTTACCCTAACCAAAGGGCAAGATTGAAGACCA
195 CTTTTACCCTAACCAAAGGGCAAGATTGAAGACCA
* * * * *
214898 TCCCCGATCATGGGGCTGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAG
1 TCCCCAATCATGGGGCAGATTGAAGAAATACAATCTTTTACCCTAACCAGAGGGAAAGATTAAAG
* **
214963 ACCATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATTGAATCTTTTACCCTAACCAG
66 ACCATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAG
* * * *
215028 AGAGAAAGATTGAAGACCATTCAATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCGAATC
131 AGAGAAAGATTAAAAACCATCCAATCTTTTACCCCGATCATGGGGCAGATTAAAGAAATCGAATC
* *
215093 TTTTACCCTAACTAGAGGGCAAGATTG
196 TTTTACCCTAACCAAAGGGCAAGATTG
215120 TATCTACAAC
Statistics
Matches: 198, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
228 2 0.01
229 196 0.99
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (229 bp):
TCCCCAATCATGGGGCAGATTGAAGAAATACAATCTTTTACCCTAACCAGAGGGAAAGATTAAAG
ACCATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAG
AGAGAAAGATTAAAAACCATCCAATCTTTTACCCCGATCATGGGGCAGATTAAAGAAATCGAATC
TTTTACCCTAACCAAAGGGCAAGATTGAAGACCA
Found at i:215119 original size:40 final size:40
Alignment explanation
Indices: 214915--215119 Score: 174
Period size: 40 Copynumber: 5.1 Consensus size: 40
214905 TCATGGGGCT
* *
214915 GATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAA
1 GATTGAAGAAATCGAATCTTTTACCCTAACTAGAGGGCAA
* **
214955 GATTGAAGACCATCCG-ATCTTTTACCCCGA-TCATG-GGGC-A
1 GATTGAAGA-AAT-CGAATCTTTTACCCTAACT-A-GAGGGCAA
* * * *
214995 GATTGAAGAAATTGAATCTTTTACCCTAACCAGAGAGAAA
1 GATTGAAGAAATCGAATCTTTTACCCTAACTAGAGGGCAA
* **
215035 GATTGAAGACCATTC-AATCTTTTACCCCGA-TCATG-GGGC-A
1 GATTGAAGA--AATCGAATCTTTTACCCTAACT-A-GAGGGCAA
215075 GATTGAAGAAATCGAATCTTTTACCCTAACTAGAGGGCAA
1 GATTGAAGAAATCGAATCTTTTACCCTAACTAGAGGGCAA
215115 GATTG
1 GATTG
215120 TATCTACAAC
Statistics
Matches: 127, Mismatches: 22, Indels: 32
0.70 0.12 0.18
Matches are distributed among these distances:
38 6 0.05
39 35 0.28
40 46 0.36
41 35 0.28
42 5 0.04
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (40 bp):
GATTGAAGAAATCGAATCTTTTACCCTAACTAGAGGGCAA
Found at i:219567 original size:17 final size:17
Alignment explanation
Indices: 219485--219568 Score: 55
Period size: 18 Copynumber: 4.7 Consensus size: 17
219475 CTTTTTATTT
219485 TTTTTACAAATTTAAAATA
1 TTTTTAC-AATTT-AAATA
* *
219504 TTTTTAACAATATT-TATT
1 TTTTT-ACAAT-TTAAATA
*
219522 TTTTTACAATTATTAAA-C
1 TTTTTACAA-T-TTAAATA
* *
219540 TTTTGATAATTTAAATA
1 TTTTTACAATTTAAATA
219557 TTTTTACAATTT
1 TTTTTACAATTT
219569 TTTAATTTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
16 5 0.10
17 15 0.29
18 18 0.35
19 9 0.18
20 4 0.08
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (17 bp):
TTTTTACAATTTAAATA
Found at i:220093 original size:23 final size:24
Alignment explanation
Indices: 220046--220093 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
220036 ACACCAATAT
*
220046 ATTCAAAAAAAATTTATAAATTCA
1 ATTCAAAAAAAATTTATAAAATCA
*
220070 ATTCAAAAAAATTTTA-AAAATCA
1 ATTCAAAAAAAATTTATAAAATCA
220093 A
1 A
220094 ATACAACTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.31
Consensus pattern (24 bp):
ATTCAAAAAAAATTTATAAAATCA
Found at i:220741 original size:13 final size:12
Alignment explanation
Indices: 220723--220747 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
220713 CTGTGTGTAT
220723 TTAAAAATATTA
1 TTAAAAATATTA
220735 TTAAAAATATTA
1 TTAAAAATATTA
220747 T
1 T
220748 GCGTAATAGA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAAAAATATTA
Found at i:223986 original size:20 final size:17
Alignment explanation
Indices: 223950--223988 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 17
223940 ATAAAAGTAC
223950 AATAAAAAAGAAAAATT
1 AATAAAAAAGAAAAATT
223967 AATAAATAAAGCAGAAAATT
1 AATAAA-AAAG-A-AAAATT
223987 AA
1 AA
223989 ATCAGGTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 1 0.05
20 8 0.42
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.18
Consensus pattern (17 bp):
AATAAAAAAGAAAAATT
Found at i:234424 original size:31 final size:31
Alignment explanation
Indices: 234386--234449 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
234376 AAATTACACA
234386 TTTTTTAATACATGTGATATAATATGATTGG
1 TTTTTTAATACATGTGATATAATATGATTGG
* *
234417 TTTTTTAATACATGTGGTATAATTTGATTGG
1 TTTTTTAATACATGTGATATAATATGATTGG
234448 TT
1 TT
234450 GTGATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.52
Consensus pattern (31 bp):
TTTTTTAATACATGTGATATAATATGATTGG
Done.