Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002047.1 Hibiscus syriacus cultivar Beakdansim tig00004169_pilon, 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: 149947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:8855 original size:17 final size:16
Alignment explanation
Indices: 8827--8875 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
8817 TCAAGCAAAA
*
8827 TTTTTATTTTTATTTG
1 TTTTTTTTTTTATTTG
8843 TTTATTTTTTTTAATTTG
1 TTT-TTTTTTTT-ATTTG
*
8861 TTTTTTATTTTATTT
1 TTTTTTTTTTTATTT
8876 TTATTCTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 7 0.24
17 14 0.48
18 8 0.28
ACGTcount: A:0.14, C:0.00, G:0.04, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTTTATTTG
Found at i:13777 original size:25 final size:25
Alignment explanation
Indices: 13742--13801 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
13732 AAACCAAAAA
*
13742 GGGTGGTCCAATAACACATTATAGT
1 GGGTGGACCAATAACACATTATAGT
13767 GGGTGGACCAATAACACATTATAGT
1 GGGTGGACCAATAACACATTATAGT
13792 GGGTGGACCA
1 GGGTGGACCA
13802 TTAAGGTCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (25 bp):
GGGTGGACCAATAACACATTATAGT
Found at i:15043 original size:31 final size:31
Alignment explanation
Indices: 14999--15065 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
14989 TACAATATAA
* *
14999 TCCCCCAATATTTAGTCCATTTGCAATATGG
1 TCCCTCAACATTTAGTCCATTTGCAATATGG
15030 TCCCTCAACATTTAGTCCATTTGCAATATGG
1 TCCCTCAACATTTAGTCCATTTGCAATATGG
15061 TCCCT
1 TCCCT
15066 GGTGTAACTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (31 bp):
TCCCTCAACATTTAGTCCATTTGCAATATGG
Found at i:16309 original size:31 final size:31
Alignment explanation
Indices: 16271--16344 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
16261 CTTTTAAAAA
*
16271 TTGCAATATAATCTCCT-AATATTTAGTCTAT
1 TTGCAATATAATC-CCTCAACATTTAGTCTAT
**
16302 TTGCAATATGGTCCCTCAACATTTAGTCTAT
1 TTGCAATATAATCCCTCAACATTTAGTCTAT
16333 TTGCAATATAAT
1 TTGCAATATAAT
16345 TCTTGACATA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 3 0.08
31 34 0.92
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (31 bp):
TTGCAATATAATCCCTCAACATTTAGTCTAT
Found at i:18352 original size:13 final size:13
Alignment explanation
Indices: 18334--18358 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18324 AGATCATTTA
18334 ATCATTTTATATT
1 ATCATTTTATATT
18347 ATCATTTTATAT
1 ATCATTTTATAT
18359 GAACATTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
ATCATTTTATATT
Found at i:18611 original size:30 final size:29
Alignment explanation
Indices: 18571--18630 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
18561 CTAATGAAAA
*
18571 ATGATGATTTTGGAACATATAAATAGTCAG
1 ATGATCATTTTGGAA-ATATAAATAGTCAG
* * *
18601 ATGATCATTTTGTAATTTTAAATAGTCAG
1 ATGATCATTTTGGAAATATAAATAGTCAG
18630 A
1 A
18631 GGGCTTAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (29 bp):
ATGATCATTTTGGAAATATAAATAGTCAG
Found at i:25415 original size:2 final size:2
Alignment explanation
Indices: 25408--25448 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
25398 GTATACATAG
* *
25408 AC AC AC AC AC AC AC AC AT AC AC AC AC AC AC AC AA AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
25449 TACATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.44, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:29352 original size:22 final size:21
Alignment explanation
Indices: 29326--29368 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
29316 TTCTTAAAAG
* *
29326 TTATAAGATAATTATTAGAATA
1 TTATAAAATAATCATTA-AATA
29348 TTATAAAATAATCATTAAATA
1 TTATAAAATAATCATTAAATA
29369 CATTAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (21 bp):
TTATAAAATAATCATTAAATA
Found at i:29465 original size:31 final size:31
Alignment explanation
Indices: 29337--29475 Score: 115
Period size: 31 Copynumber: 4.5 Consensus size: 31
29327 TATAAGATAA
29337 TTATTAGAA-TATTATAAAATAATCATTAAAT
1 TTATTA-AATTATTATAAAATAATCATTAAAT
** * **
29368 ACATTAAATTATTATAAAATAATAACTT-TCT
1 TTATTAAATTATTATAAAATAATCA-TTAAAT
* * * * *
29399 TTATCAAATTGTTAT-AAATAACCATGATAT
1 TTATTAAATTATTATAAAATAATCATTAAAT
* * *
29429 GTATTAATTTATTATAAAATAATTATTAAAT
1 TTATTAAATTATTATAAAATAATCATTAAAT
29460 TTATTAAA-TATTATAA
1 TTATTAAATTATTATAA
29476 TCACTTTATT
Statistics
Matches: 81, Mismatches: 23, Indels: 9
0.72 0.20 0.08
Matches are distributed among these distances:
29 1 0.01
30 30 0.37
31 48 0.59
32 2 0.02
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (31 bp):
TTATTAAATTATTATAAAATAATCATTAAAT
Found at i:36366 original size:19 final size:19
Alignment explanation
Indices: 36342--36378 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
36332 CCTCCAAACA
36342 TGTGCAAGGTACCCTTAAC
1 TGTGCAAGGTACCCTTAAC
36361 TGTGCAAGGTACCCTTAA
1 TGTGCAAGGTACCCTTAA
36379 ATGTCCTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (19 bp):
TGTGCAAGGTACCCTTAAC
Found at i:37406 original size:20 final size:20
Alignment explanation
Indices: 37312--37680 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
37302 GATTTTCCAT
* ** *
37312 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
37332 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
37352 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37372 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
37392 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
37412 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37432 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
37452 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
37472 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
37492 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37512 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
37532 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37552 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
37572 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
37592 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
37612 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
37632 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
37652 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
37672 AATCACAAC
1 AATCGCAAC
37681 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:38401 original size:24 final size:24
Alignment explanation
Indices: 38362--38408 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
38352 AAATTTGGTC
38362 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
38386 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
38409 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:38600 original size:12 final size:12
Alignment explanation
Indices: 38583--38607 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38573 ATATAATCCT
38583 GAAGAAGAAAAA
1 GAAGAAGAAAAA
38595 GAAGAAGAAAAA
1 GAAGAAGAAAAA
38607 G
1 G
38608 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:38731 original size:19 final size:19
Alignment explanation
Indices: 38707--38889 Score: 243
Period size: 19 Copynumber: 10.4 Consensus size: 19
38697 GCAACGAGAG
38707 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38726 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
38745 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
38759 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
38778 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38797 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
38811 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38830 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
38844 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38863 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38882 AATCGCAA
1 AATCGCAA
38890 CGAGATAATC
Statistics
Matches: 145, Mismatches: 4, Indels: 30
0.81 0.02 0.17
Matches are distributed among these distances:
14 24 0.17
16 17 0.12
17 16 0.11
19 88 0.61
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:38732 original size:33 final size:33
Alignment explanation
Indices: 38690--38870 Score: 210
Period size: 33 Copynumber: 5.3 Consensus size: 33
38680 AGTTGATAAA
*
38690 GAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 GAAAATCGCAACGAAAGAATCGCAATGCGAAAT
*
38723 GAAAATCGCAATGCGAAATGAAAATCGCAA--CGACA-
1 GAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAAT
*
38758 G--AATCGCAATGCGAAATTAAAATCGCAATGCGAAAT
1 GAAAATCGCAA--CG-AA--AGAATCGCAATGCGAAAT
38794 GAAAATCGCAACGAAAGAATCGCAATGCGAAAT
1 GAAAATCGCAACGAAAGAATCGCAATGCGAAAT
38827 GAAAATCGCAACGAAAGAATCGCAATGCGAAAT
1 GAAAATCGCAACGAAAGAATCGCAATGCGAAAT
38860 GAAAATCGCAA
1 GAAAATCGCAA
38871 TGCGAAATGA
Statistics
Matches: 130, Mismatches: 5, Indels: 26
0.81 0.03 0.16
Matches are distributed among these distances:
33 92 0.71
34 2 0.02
35 11 0.08
36 9 0.07
38 16 0.12
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.13
Consensus pattern (33 bp):
GAAAATCGCAACGAAAGAATCGCAATGCGAAAT
Found at i:38752 original size:52 final size:52
Alignment explanation
Indices: 38690--38889 Score: 284
Period size: 52 Copynumber: 3.8 Consensus size: 52
38680 AGTTGATAAA
38690 GAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
* *
38742 GAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
*
38794 GAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-
1 GAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
*
38843 G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 GAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
38890 CGAGATAATC
Statistics
Matches: 137, Mismatches: 6, Indels: 10
0.90 0.04 0.07
Matches are distributed among these distances:
47 8 0.06
49 3 0.02
50 5 0.04
51 1 0.01
52 120 0.88
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (52 bp):
GAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
Found at i:38834 original size:85 final size:85
Alignment explanation
Indices: 38726--38911 Score: 336
Period size: 85 Copynumber: 2.2 Consensus size: 85
38716 GCGAAATGAA
* *
38726 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
38791 AATGAAAATCGCAACGAAAG
66 AATGAAAATCGCAACGAAAG
38811 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
* *
38876 AATGAAAATCGCAACGAGAT
66 AATGAAAATCGCAACGAAAG
38896 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
38912 TATAAACGCA
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 97 1.00
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (85 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
AATGAAAATCGCAACGAAAG
Found at i:38927 original size:52 final size:52
Alignment explanation
Indices: 38707--38911 Score: 214
Period size: 52 Copynumber: 3.9 Consensus size: 52
38697 GCAACGAGAG
*
38707 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
*
38759 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
38811 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
* *
38863 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAAT
38912 TATAAACGCA
Statistics
Matches: 143, Mismatches: 5, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
47 8 0.06
49 6 0.04
50 6 0.04
52 123 0.86
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
Found at i:39026 original size:19 final size:19
Alignment explanation
Indices: 38918--39018 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
38908 AAATTATAAA
38918 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
38937 CCGCATTGCGA-TTTCATTT
1 -CGCATTGCGATTTTCATTT
*
38956 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
38972 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
38989 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
39008 CGCATTGCGAT
1 CGCATTGCGAT
39019 AGTCATTTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
18 10 0.14
19 34 0.46
20 10 0.14
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:39026 original size:38 final size:37
Alignment explanation
Indices: 38918--39018 Score: 140
Period size: 33 Copynumber: 2.8 Consensus size: 37
38908 AAATTATAAA
38918 CGCATTGCGATTTTCATTTCCGCATTGCGATTTCATTT
1 CGCATTGCGATTTTCATTT-CGCATTGCGATTTCATTT
*
38956 CGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATTT
38989 CGCATTGCGATTTTCATTTCGCATTGCGAT
1 CGCATTGCGATTTTCATTTCGCATTGCGAT
39019 AGTCATTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
32 6 0.11
33 18 0.33
34 2 0.04
35 5 0.09
36 7 0.13
37 1 0.02
38 16 0.29
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (37 bp):
CGCATTGCGATTTTCATTTCGCATTGCGATTTCATTT
Found at i:39144 original size:14 final size:14
Alignment explanation
Indices: 39125--39161 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
39115 CATCAATTAC
39125 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
39139 ACAAATCATCTTTT
1 ACAAATCAACTTTT
39153 ACAAATCAA
1 ACAAATCAA
39162 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:41157 original size:14 final size:14
Alignment explanation
Indices: 41138--41194 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
41128 GCGAAATGAA
*
41138 AATCGCAACGACAG
1 AATCGCAACGAAAG
41152 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
41169 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
41185 AATCGCAACG
1 AATCGCAACG
41195 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:41165 original size:33 final size:33
Alignment explanation
Indices: 41119--41211 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
41109 GCGAAACCAA
*
41119 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
41152 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
41185 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
41212 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:41176 original size:19 final size:19
Alignment explanation
Indices: 41082--41216 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
41072 TAGTTTACTT
* *
41082 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
41102 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
41121 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
41140 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
41154 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
41173 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
41187 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
41206 TCGCAATGCGA
1 TCGCAACGCGA
41217 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:41234 original size:19 final size:19
Alignment explanation
Indices: 41212--41340 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
41202 AAAATCGCAA
41212 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
41231 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
41245 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
41264 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
41278 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
41297 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
41316 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
41336 TGCGA
1 TGCGA
41341 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:41254 original size:33 final size:33
Alignment explanation
Indices: 41212--41303 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
41202 AAAATCGCAA
41212 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
41245 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
41278 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
41304 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:42290 original size:14 final size:14
Alignment explanation
Indices: 42271--42360 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
42261 TTGAAATGAA
42271 AATCGCAACGAGAG
1 AATCGCAACGAGAG
42285 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
42302 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
42318 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
42337 AATCGCAACGAGAG
1 AATCGCAACGAGAG
42351 AATCGCAACG
1 AATCGCAACG
42361 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:42308 original size:33 final size:33
Alignment explanation
Indices: 42263--42377 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
42253 GTCTTTGGTT
42263 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
42296 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
42329 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
42362 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
42378 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:42309 original size:19 final size:18
Alignment explanation
Indices: 42270--42382 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
42260 GTTGAAATGA
42270 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
42285 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
42302 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
42318 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
42335 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
42351 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
42368 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
42383 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:42413 original size:14 final size:14
Alignment explanation
Indices: 42394--42448 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
42384 TTTGGTTTCG
42394 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
42408 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
42427 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
42441 CGTTGCGA
1 CGTTGCGA
42449 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:42426 original size:33 final size:33
Alignment explanation
Indices: 42378--42448 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
42368 AAAATCGCAA
**
42378 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
42411 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
42444 TGCGA
1 TGCGA
42449 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:42456 original size:33 final size:33
Alignment explanation
Indices: 42389--42470 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
42379 GCGATTTTGG
***
42389 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
42422 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
42455 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
42471 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:42475 original size:20 final size:20
Alignment explanation
Indices: 42401--42489 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
42391 TCGCGTTGCG
42401 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
42421 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
42434 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
42454 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
42474 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
42490 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:42611 original size:33 final size:33
Alignment explanation
Indices: 42569--42639 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
42559 AATACTAACT
*
42569 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
42602 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
42635 TGAAA
1 TGAAA
42640 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:42872 original size:22 final size:22
Alignment explanation
Indices: 42820--42874 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
42810 TGGTTGTGAG
**
42820 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
42842 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
42864 GGATTTCTTCG
1 GGATTTCTTCG
42875 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:43045 original size:20 final size:20
Alignment explanation
Indices: 43020--43212 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
43010 CTTTAAATAT
43020 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
43040 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
43062 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
43081 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
43101 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
43121 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
43141 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
43161 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
43181 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
43201 CGCGTTGCGATT
1 CGCGTTGCGATT
43213 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:43207 original size:60 final size:60
Alignment explanation
Indices: 43020--43212 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
43010 CTTTAAATAT
**
43020 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
43081 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
43141 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
43201 CGCGTTGCGATT
1 CGCGTTGCGATT
43213 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:43293 original size:20 final size:20
Alignment explanation
Indices: 43268--43319 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
43258 AAGAATCGCG
*
43268 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
43288 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
43308 TTGCGATTCTGG
1 TTGCGATTCTGG
43320 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:43698 original size:41 final size:41
Alignment explanation
Indices: 43641--43900 Score: 345
Period size: 41 Copynumber: 6.4 Consensus size: 41
43631 CTATCGCAAA
43641 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
* *
43682 TTCGCGTTGCGATAGTTGAAAATCGCAATTCGCG---TTGCAT
1 TTCGCGTTGCGATAGTTGAAAATCGC-GTT-GCGATTTTCCAT
** *
43722 TTCGCGTTGCGATAGTTGAAAATCGTAATTCGCG---TTGCAT
1 TTCGCGTTGCGATAGTTGAAAATCG-CGTT-GCGATTTTCCAT
*
43762 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
* *
43803 TTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCCAT
*
43844 TTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
43885 TTCGCGTTGCGATAGT
1 TTCGCGTTGCGATAGT
43901 CTACAGTTGT
Statistics
Matches: 199, Mismatches: 12, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 69 0.35
41 120 0.60
42 3 0.02
43 3 0.02
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
Found at i:43734 original size:40 final size:40
Alignment explanation
Indices: 43641--43787 Score: 226
Period size: 40 Copynumber: 3.6 Consensus size: 40
43631 CTATCGCAAA
* *
43641 TTCGCGTTGCGATAGTTGAAAATCGC-GTT-GCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCAATTCGCG---TTGCAT
43682 TTCGCGTTGCGATAGTTGAAAATCGCAATTCGCGTTGCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCAATTCGCGTTGCAT
*
43722 TTCGCGTTGCGATAGTTGAAAATCGTAATTCGCGTTGCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCAATTCGCGTTGCAT
43762 TTCGCGTTGCGATAGTTGAAAATCGC
1 TTCGCGTTGCGATAGTTGAAAATCGC
43788 GTTGCAATTT
Statistics
Matches: 100, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
40 69 0.69
41 26 0.26
42 2 0.02
43 3 0.03
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (40 bp):
TTCGCGTTGCGATAGTTGAAAATCGCAATTCGCGTTGCAT
Found at i:43809 original size:20 final size:20
Alignment explanation
Indices: 43784--43897 Score: 122
Period size: 20 Copynumber: 5.6 Consensus size: 20
43774 TAGTTGAAAA
*
43784 TCGCGTTGCAATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
43804 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
43825 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** *
43845 TCGCGTTGCGATAGTTGAAAT
1 TCGCGTTGCGAT-TTTCCATT
43866 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
43886 TCGCGTTGCGAT
1 TCGCGTTGCGAT
43898 AGTCTACAGT
Statistics
Matches: 75, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.05
20 39 0.52
21 28 0.37
22 4 0.05
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:43934 original size:82 final size:81
Alignment explanation
Indices: 43641--43947 Score: 290
Period size: 82 Copynumber: 3.8 Consensus size: 81
43631 CTATCGCAAA
* * *
43641 TTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAAT
1 TTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCCAATTC-CGTTGCGATAGTTGAAAAT
* * *
43705 CGCAATTCGC---GTTGCAT
64 CGC-GTT-GCAATTTTCCAT
* * ** * *
43722 TTCGCGTTGCGATAGT-TGAAAATCGTAATTCGCG---TTGCATTTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTCT-ACAGTCG-CGTT-GCGATTTTCCAATTC-CGTTGCGATAGTTGAAA
43783 ATCGCGTTGCAATTTTCCAT
62 ATCGCGTTGCAATTTTCCAT
* *
43803 TTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATTC
1 TTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCAATTC-CGTTGCGATAGTTGAAAATC
*
43868 GCGTTGCGATTTTCCAT
65 GCGTTGCAATTTTCCAT
* * *
43885 TTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT-CGTTGTGATAGTTAAAAA
1 TTCGCGTTGCGATAGTCTACAGTCG-CGTTGCGATTTTCC-AATTCCGTTGCGATAGTTGAAAA
43948 AAAAGATTTT
Statistics
Matches: 197, Mismatches: 18, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
78 2 0.01
79 5 0.03
80 33 0.17
81 51 0.26
82 86 0.44
83 17 0.09
84 3 0.02
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (81 bp):
TTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCAATTCCGTTGCGATAGTTGAAAATCG
CGTTGCAATTTTCCAT
Found at i:43940 original size:41 final size:40
Alignment explanation
Indices: 43759--43925 Score: 187
Period size: 41 Copynumber: 4.0 Consensus size: 40
43749 ATTCGCGTTG
* * * *
43759 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCAATTTTC
1 CATTTC-CGTTGCGATAGTCT-ACAGTTGCGTTGCGATTTTC
*
43800 CATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCTACAGTTGCGTTGCGATTTTC
*
43841 CATTTCGCGTTGCGATAGT-TGA-AATTCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCT-ACAGTT-GCGTTGCGATTTTC
43882 CATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCTACAGTTG-CGTTGCGATTTTC
43924 CA
1 CA
43926 AATTCGTTGT
Statistics
Matches: 114, Mismatches: 6, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
40 3 0.03
41 91 0.80
42 20 0.18
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (40 bp):
CATTTCCGTTGCGATAGTCTACAGTTGCGTTGCGATTTTC
Found at i:44531 original size:6 final size:5
Alignment explanation
Indices: 44502--44541 Score: 62
Period size: 5 Copynumber: 7.6 Consensus size: 5
44492 GCCGTCCGTC
44502 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCGGG TCG
44542 TGGTAATACG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 23 0.68
6 11 0.32
ACGTcount: A:0.00, C:0.20, G:0.55, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:44537 original size:17 final size:16
Alignment explanation
Indices: 44502--44545 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 16
44492 GCCGTCCGTC
44502 TCGGGTCG-GGTCGGG
1 TCGGGTCGTGGTCGGG
44517 TCGGGTCGTGGTCGTGG
1 TCGGGTCGTGGTCG-GG
44534 TCGGGTCGTGGT
1 TCGGGTCGTGGT
44546 AATACGTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.30
16 5 0.19
17 14 0.52
ACGTcount: A:0.00, C:0.18, G:0.55, T:0.27
Consensus pattern (16 bp):
TCGGGTCGTGGTCGGG
Found at i:44654 original size:20 final size:20
Alignment explanation
Indices: 44629--44783 Score: 141
Period size: 20 Copynumber: 7.6 Consensus size: 20
44619 ACTGTAGACT
44629 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** *
44649 ATCGCAACGCGAATTTCAACT
1 ATCGCAACGCGAAATGGAA-A
44670 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * **
44690 TTCGCAACGCG-ACTGTAGACT
1 ATCGCAACGCGAAATG--GAAA
44711 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
44731 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
44752 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
44772 ATCGCAATGCGA
1 ATCGCAACGCGA
44784 TTTTCAACTA
Statistics
Matches: 103, Mismatches: 27, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
19 3 0.03
20 54 0.52
21 43 0.42
22 3 0.03
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:44671 original size:41 final size:41
Alignment explanation
Indices: 44601--44808 Score: 287
Period size: 41 Copynumber: 5.0 Consensus size: 41
44591 ACAACGAATT
*
44601 TGGAAAATCGCAACGAC-AACTGT-AGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGAA-TTTCA-ACTATCGCAACGCGAAA
44643 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
* * *
44684 TGGAAATTCGCAACGCGACTGT-AGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAATTTCA-ACTATCGCAACGCGAAA
*
44725 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
* * *
44766 TGGAAAATCGCAATGCGATTTTCAACTATCGTAACGCGAAA
1 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
44807 TG
1 TG
44809 CAACGCGAAT
Statistics
Matches: 153, Mismatches: 9, Indels: 9
0.89 0.05 0.05
Matches are distributed among these distances:
40 1 0.01
41 133 0.87
42 19 0.12
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
Found at i:44705 original size:82 final size:82
Alignment explanation
Indices: 44601--44808 Score: 328
Period size: 82 Copynumber: 2.5 Consensus size: 82
44591 ACAACGAATT
*
44601 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTC
1 TGGAAAATCGCAACG-CGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTC
44666 AACTATCGCAACGCGAAA
65 AACTATCGCAACGCGAAA
* *
44684 TGGAAATTCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTCA
44749 ACTATCGCAACGCGAAA
66 ACTATCGCAACGCGAAA
* * * *
44766 TGGAAAATCGCAATGCGATTTTCA-ACTATCGTAACGCGAAATG
1 TGGAAAATCGCAACGCGACTGT-AGACTATCGCAACGCGAAATG
44809 CAACGCGAAT
Statistics
Matches: 116, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
82 101 0.87
83 15 0.13
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (82 bp):
TGGAAAATCGCAACGCGACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTCA
ACTATCGCAACGCGAAA
Found at i:44864 original size:20 final size:20
Alignment explanation
Indices: 44841--44946 Score: 63
Period size: 20 Copynumber: 5.2 Consensus size: 20
44831 AGATCGCGTT
*
44841 GCGATTTCAACTATCGCAAC
1 GCGATTGCAACTATCGCAAC
* * *
44861 GCGAAATGGAA-AATCGCAAC
1 GCG-ATTGCAACTATCGCAAC
*
44881 GCGATCTCCAACTATCGCAAC
1 GCGAT-TGCAACTATCGCAAC
* * * *
44902 GCGAAATGGAA-AAACGCAAC
1 GCG-ATTGCAACTATCGCAAC
* *
44922 GCGATTTTCAACTATCGCAAT
1 GCGA-TTGCAACTATCGCAAC
44943 GCGA
1 GCGA
44947 AATGCAACGT
Statistics
Matches: 61, Mismatches: 19, Indels: 11
0.67 0.21 0.12
Matches are distributed among these distances:
19 2 0.03
20 30 0.49
21 28 0.46
22 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (20 bp):
GCGATTGCAACTATCGCAAC
Found at i:44875 original size:142 final size:142
Alignment explanation
Indices: 44708--44979 Score: 456
Period size: 142 Copynumber: 1.9 Consensus size: 142
44698 GCGACTGTAG
* *
44708 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACGCGAAATGGAAAA
* * * *
44773 TCGCAATGCGATTTTCAACTATCGTAACGCGAAATGCAACGCGAATTTGTGAT-GATGGAGATCG
66 ACGCAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGATAG-TGGAGATCG
44837 CGTTGCGATTTCA
130 CGTTGCGATTTCA
44850 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACGCGAAATGGAAAA
* *
44915 ACGCAACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTGAATTTGCGATAGTGGAGATCGC
66 ACGCAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGATAGTGGAGATCGC
44980 AATGCGAATT
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
142 120 0.99
143 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (142 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACGCGAAATGGAAAA
ACGCAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGATAGTGGAGATCGC
GTTGCGATTTCA
Found at i:44898 original size:41 final size:41
Alignment explanation
Indices: 44848--44950 Score: 170
Period size: 41 Copynumber: 2.5 Consensus size: 41
44838 GTTGCGATTT
*
44848 CAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
* *
44889 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
*
44930 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
44951 CAACGTGAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (41 bp):
CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
Found at i:44954 original size:21 final size:21
Alignment explanation
Indices: 44848--44954 Score: 92
Period size: 21 Copynumber: 5.2 Consensus size: 21
44838 GTTGCGATTT
44848 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
44869 GAA-AATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATG
44889 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
44910 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
44930 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
44951 CAAC
1 CAAC
44955 GTGAATTTGC
Statistics
Matches: 61, Mismatches: 23, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
20 29 0.48
21 32 0.52
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:55732 original size:57 final size:57
Alignment explanation
Indices: 55332--55725 Score: 574
Period size: 57 Copynumber: 6.9 Consensus size: 57
55322 AAACTCTAAT
* ** ** *
55332 TTCGCAACGCTGATTACCGATGTAGGTAAACAAAACTATCGCAACACGATTTTCAAA
1 TTCGCAACGCTAATTACCGACATAGGTAAACAGTACTATCGCAACGCGATTTTCAAA
* * *
55389 TTCGCAACGCTAATTATCGATATAGGTAAACAGTACTATCGCAACGAGATTTTCAAA
1 TTCGCAACGCTAATTACCGACATAGGTAAACAGTACTATCGCAACGCGATTTTCAAA
* * *
55446 TTTGCAACGCTAATTACCGACATATGTAAACAGTACTATCGCAACGCGATTTACAAA
1 TTCGCAACGCTAATTACCGACATAGGTAAACAGTACTATCGCAACGCGATTTTCAAA
* * * *
55503 TTCGCAACGTTAAGTACCGACATAGGTAAGCAGTACTATCTCAACGCGATTTTCAAA
1 TTCGCAACGCTAATTACCGACATAGGTAAACAGTACTATCGCAACGCGATTTTCAAA
* *
55560 TTCGCAACGCTAATTACCGACATGGGTAAACAGTACTATCGCAACGCGATTTACAAA
1 TTCGCAACGCTAATTACCGACATAGGTAAACAGTACTATCGCAACGCGATTTTCAAA
* *
55617 TTCGCAACGCTAATTACCGACATAGGTAAACAGTACTATCGCAATGCGATTTACAAA
1 TTCGCAACGCTAATTACCGACATAGGTAAACAGTACTATCGCAACGCGATTTTCAAA
* * *
55674 TTCGCAACGCTAATTACCGACATATGT-AACAGTACTATCACAACACGATTTT
1 TTCGCAACGCTAATTACCGACATAGGTAAACAGTACTATCGCAACGCGATTTT
55726 GGAAATTGTG
Statistics
Matches: 304, Mismatches: 33, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
56 21 0.07
57 283 0.93
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (57 bp):
TTCGCAACGCTAATTACCGACATAGGTAAACAGTACTATCGCAACGCGATTTTCAAA
Found at i:55744 original size:20 final size:20
Alignment explanation
Indices: 55719--55821 Score: 86
Period size: 20 Copynumber: 5.2 Consensus size: 20
55709 TATCACAACA
*
55719 CGATTTTGGAAATTGTGTTG
1 CGATTTTAGAAATTGTGTTG
* *
55739 CGA-TTTACAAATTCGCGTTG
1 CGATTTTAGAAATT-GTGTTG
* *
55759 CGATTTTTGAAACTGTGTTG
1 CGATTTTAGAAATTGTGTTG
* *
55779 CGA-TTTACAAATTTGCGTTG
1 CGATTTTAGAAA-TTGTGTTG
*
55799 TGATTTTAG-AATATGTGTTG
1 CGATTTTAGAAAT-TGTGTTG
55819 CGA
1 CGA
55822 AATTAGAGTT
Statistics
Matches: 63, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
19 15 0.24
20 37 0.59
21 11 0.17
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.42
Consensus pattern (20 bp):
CGATTTTAGAAATTGTGTTG
Found at i:55776 original size:40 final size:39
Alignment explanation
Indices: 55719--55821 Score: 143
Period size: 40 Copynumber: 2.6 Consensus size: 39
55709 TATCACAACA
*
55719 CGATTTTGGAAATTGTGTTGCGATTTACAAATTCGCGTTG
1 CGATTTTAGAAA-TGTGTTGCGATTTACAAATTCGCGTTG
* *
55759 CGATTTTTGAAACTGTGTTGCGATTTACAAATTTGCGTTG
1 CGATTTTAGAAA-TGTGTTGCGATTTACAAATTCGCGTTG
*
55799 TGATTTTAGAATATGTGTTGCGA
1 CGATTTTAGAA-ATGTGTTGCGA
55822 AATTAGAGTT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 56 0.98
41 1 0.02
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.42
Consensus pattern (39 bp):
CGATTTTAGAAATGTGTTGCGATTTACAAATTCGCGTTG
Found at i:55827 original size:20 final size:20
Alignment explanation
Indices: 55804--55842 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
55794 CGTTGTGATT
55804 TTAGAATAT-GTGTTGCGAAA
1 TTAGAAT-TCGTGTTGCGAAA
*
55824 TTAGAGTTCGTGTTGCGAA
1 TTAGAATTCGTGTTGCGAA
55843 TTTGTTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (20 bp):
TTAGAATTCGTGTTGCGAAA
Found at i:56923 original size:20 final size:20
Alignment explanation
Indices: 56898--56943 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
56888 TTAAAAAAGC
56898 TAAAATCCCTTTTTCATATT
1 TAAAATCCCTTTTTCATATT
56918 TAAAATCCCTTTTTCATATT
1 TAAAATCCCTTTTTCATATT
56938 TAAAAT
1 TAAAAT
56944 ACATAACCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAAATCCCTTTTTCATATT
Found at i:57260 original size:20 final size:19
Alignment explanation
Indices: 57235--57290 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
57225 ATTATATTGT
*
57235 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-AGGAATAA
57255 AAGATTACCAGAGGAATAA
1 AAGATTACCAGAGGAATAA
57274 AAGATTACCAG-GGAATA
1 AAGATTACCAGAGGAATA
57291 GGATTACTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
18 6 0.17
19 18 0.51
20 11 0.31
ACGTcount: A:0.48, C:0.11, G:0.23, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Found at i:64903 original size:22 final size:22
Alignment explanation
Indices: 64862--64933 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
64852 CACACATTTT
* *
64862 TAATAATTTTGATACTTTTTGTAA
1 TAATAATTTTTATA-ATTTT-TAA
*
64886 T-ATATTTTTTATAATTTTTAA
1 TAATAATTTTTATAATTTTTAA
*
64907 TAATAATTTTTATAATTTATTTA
1 TAATAATTTTTATAATTT-TTAA
64930 TAAT
1 TAAT
64934 TTCCAAAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 4 0.10
22 19 0.46
23 17 0.41
24 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (22 bp):
TAATAATTTTTATAATTTTTAA
Found at i:64903 original size:23 final size:23
Alignment explanation
Indices: 64862--64933 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
64852 CACACATTTT
* *
64862 TAATAATTTTGATACTTTTTGTAA
1 TAATAATTTTTATAATTTTT-TAA
*
64886 T-ATATTTTTTATAA-TTTTTAA
1 TAATAATTTTTATAATTTTTTAA
64907 TAATAATTTTTATAATTTATTT-A
1 TAATAATTTTTATAATTT-TTTAA
64930 TAAT
1 TAAT
64934 TTCCAAAGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
21 4 0.10
22 16 0.39
23 17 0.41
24 4 0.10
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (23 bp):
TAATAATTTTTATAATTTTTTAA
Found at i:64921 original size:12 final size:12
Alignment explanation
Indices: 64877--64922 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
64867 ATTTTGATAC
*
64877 TTTTTGTAATATA
1 TTTTTATAATA-A
64890 TTTTT-T-ATAA
1 TTTTTATAATAA
64900 TTTTTAATAATAA
1 TTTTT-ATAATAA
64913 TTTTTATAAT
1 TTTTTATAAT
64923 TTATTTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 6 0.20
11 3 0.10
12 7 0.23
13 14 0.47
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (12 bp):
TTTTTATAATAA
Found at i:64932 original size:20 final size:20
Alignment explanation
Indices: 64857--64962 Score: 67
Period size: 22 Copynumber: 5.2 Consensus size: 20
64847 ATTATCACAC
*
64857 ATTTTTA-ATAATTTTGATA
1 ATTTTTATATAATTTTTATA
* *
64876 CTTTTTGTAATATATTTTTTATA
1 -ATTTT-T-ATATAATTTTTATA
64899 ATTTTTAATAATAATTTTTATA
1 ATTTTT-AT-ATAATTTTTATA
**
64921 ATTTATT-TATAATTTCCA-A
1 ATTT-TTATATAATTTTTATA
* *
64940 AGTTTTA-ATGATTTTTATA
1 ATTTTTATATAATTTTTATA
64959 ATTT
1 ATTT
64963 CATGCTAAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
18 9 0.13
19 8 0.12
20 12 0.18
21 6 0.09
22 20 0.30
23 12 0.18
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (20 bp):
ATTTTTATATAATTTTTATA
Found at i:65544 original size:27 final size:27
Alignment explanation
Indices: 65509--65568 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
65499 CAAATGAAAA
*
65509 TTTTCATCAATCCACTATTACAAATAT
1 TTTTGATCAATCCACTATTACAAATAT
65536 TTTTGATCAATCCACTATTACAAATAT
1 TTTTGATCAATCCACTATTACAAATAT
65563 TTTTGA
1 TTTTGA
65569 GTGCATGTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.43
Consensus pattern (27 bp):
TTTTGATCAATCCACTATTACAAATAT
Found at i:66065 original size:25 final size:24
Alignment explanation
Indices: 66016--66081 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 24
66006 TTTTACCGTA
** *
66016 TATCGTATTA-TAATTTTATAAGT
1 TATCGTATTATTAAAATTAGAAGT
*
66039 TA-CTTATTAATTAATAATTAGAAGT
1 TATCGTATT-ATTAA-AATTAGAAGT
66064 TATCGTATTATTAAAATT
1 TATCGTATTATTAAAATT
66082 TCTTCAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
22 5 0.15
23 3 0.09
24 7 0.21
25 14 0.41
26 5 0.15
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (24 bp):
TATCGTATTATTAAAATTAGAAGT
Found at i:86171 original size:17 final size:17
Alignment explanation
Indices: 86149--86192 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
86139 ATCATTTAAA
86149 ATAAAAAAATCAAAAAT
1 ATAAAAAAATCAAAAAT
86166 ATAAAAAAATCAAAAAT
1 ATAAAAAAATCAAAAAT
86183 ATAAAAAAAT
1 ATAAAAAAAT
86193 ATGAATTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (17 bp):
ATAAAAAAATCAAAAAT
Found at i:86172 original size:9 final size:8
Alignment explanation
Indices: 86146--86193 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
86136 ATCATCATTT
86146 AAAATAAA
1 AAAATAAA
86154 AAAATCAAA
1 AAAAT-AAA
*
86163 AATATAAA
1 AAAATAAA
86171 AAAATCAAA
1 AAAAT-AAA
*
86180 AATATAAA
1 AAAATAAA
86188 AAAATA
1 AAAATA
86194 TGAATTCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 20 0.59
9 14 0.41
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAATAAA
Found at i:91856 original size:21 final size:21
Alignment explanation
Indices: 91832--91897 Score: 60
Period size: 27 Copynumber: 2.9 Consensus size: 21
91822 AGACCATAAG
91832 AATACTTTCTCCATCCAAATT
1 AATACTTTCTCCATCCAAATT
* *
91853 AATACTTCTACAATCAACGTCAAAATT
1 AATACTT-T-C--TC--CATCCAAATT
91880 AATACTTTCTCCATCCAA
1 AATACTTTCTCCATCCAA
91898 GATACCTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
21 12 0.34
22 1 0.03
23 3 0.09
25 3 0.09
26 1 0.03
27 15 0.43
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.33
Consensus pattern (21 bp):
AATACTTTCTCCATCCAAATT
Found at i:98821 original size:29 final size:29
Alignment explanation
Indices: 98779--98837 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
98769 TACACAAATG
*
98779 GTCAGCCGACTACA-ATGTGTTGTTTTGTT
1 GTCAGCCGACTACATA-GTATTGTTTTGTT
98808 GTCAGCCGACTACATAGTATTGTTTTGTT
1 GTCAGCCGACTACATAGTATTGTTTTGTT
98837 G
1 G
98838 GATCTCTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.41
Consensus pattern (29 bp):
GTCAGCCGACTACATAGTATTGTTTTGTT
Found at i:109964 original size:18 final size:20
Alignment explanation
Indices: 109926--109964 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
109916 TATATTATAA
109926 TATTTATTTTTATAAGTAAAT
1 TATTTATTTTTATAAG-AAAT
109947 TATTT-TTTTTATAA-AAAT
1 TATTTATTTTTATAAGAAAT
109965 CGTTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
20 9 0.50
21 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TATTTATTTTTATAAGAAAT
Found at i:115565 original size:6 final size:6
Alignment explanation
Indices: 115554--115743 Score: 317
Period size: 6 Copynumber: 31.7 Consensus size: 6
115544 TGGTAGCATA
*
115554 TACACG TACACG TACACG TACACG TACACG TACACA TACACG TACACG
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
115602 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
* *
115650 TACACC TACACG TACACG TACACG TACACA TACACG TACACG TACACG
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
* * * *
115698 TACACG TACACA TACACG TACACA TACACG TACACA TACACA TACA
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACA
115744 GTTGTCGTGT
Statistics
Matches: 173, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 173 1.00
ACGTcount: A:0.37, C:0.34, G:0.13, T:0.17
Consensus pattern (6 bp):
TACACG
Found at i:117888 original size:2 final size:2
Alignment explanation
Indices: 117881--117906 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
117871 ATCGATATTG
117881 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
117907 CAGTTCTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118362 original size:14 final size:14
Alignment explanation
Indices: 118343--118369 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
118333 CACAGACGCC
118343 TATTTACATCATCA
1 TATTTACATCATCA
118357 TATTTACATCATC
1 TATTTACATCATC
118370 GACACTATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (14 bp):
TATTTACATCATCA
Found at i:124219 original size:4 final size:4
Alignment explanation
Indices: 124210--124236 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
124200 AGCAATGACT
124210 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
124237 CAGGGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:131456 original size:15 final size:15
Alignment explanation
Indices: 131436--131465 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
131426 ATTGTTTTAT
131436 TATTAATCATTTAAA
1 TATTAATCATTTAAA
*
131451 TATTAATTATTTAAA
1 TATTAATCATTTAAA
131466 CACAAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAATCATTTAAA
Found at i:149446 original size:35 final size:34
Alignment explanation
Indices: 149407--149516 Score: 123
Period size: 35 Copynumber: 3.2 Consensus size: 34
149397 AAAACAGTCC
149407 TCAATTTCATTCTAAACCCCAATTTCCAAATTAAT
1 TCAATTTCATTCTAAACCCCAATTTCCAAA-TAAT
* *
149442 TCAATTTCATTCTAAACCCTAAATTCCCAAATAAT
1 TCAATTTCATTCTAAACCC-CAATTTCCAAATAAT
** * * *
149477 TC-ATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAATTTC-CAAATAAT
149511 TCAATT
1 TCAATT
149517 AAGGTTTAGA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
33 4 0.06
34 22 0.35
35 28 0.44
36 9 0.14
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCCAATTTCCAAATAAT
Done.