Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010933.1 Kokia drynarioides strain JFW-HI SEQ_125901, 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: 169437
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 214 characters in sequence are not A, C, G, or T
Found at i:801 original size:23 final size:23
Alignment explanation
Indices: 775--921 Score: 181
Period size: 23 Copynumber: 6.3 Consensus size: 23
765 ACACTAGCGC
775 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
798 GCTCTCTGTTTAGCA-TGTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
821 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
846 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
869 GCTCTCTGACTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
892 ACTCTCT-ATTTAGCACTGTGTGT
1 GCTCTCTGA-TTAGCACTGTGTGT
915 GCTCTCT
1 GCTCTCT
922 ATTGCCCAGC
Statistics
Matches: 107, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
22 5 0.05
23 82 0.77
25 16 0.15
26 4 0.04
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:15270 original size:15 final size:16
Alignment explanation
Indices: 15245--15274 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15235 TTTTGGTTAA
15245 AAAAGTATTTTTTTTC
1 AAAAGTATTTTTTTTC
15261 AAAA-TATTTTTTTT
1 AAAAGTATTTTTTTT
15275 GTACCAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (16 bp):
AAAAGTATTTTTTTTC
Found at i:15353 original size:18 final size:18
Alignment explanation
Indices: 15319--15362 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
15309 ATTGTTTAGT
*
15319 AATA-TTTTTATCTCAAA
1 AATACTTTTTATCCCAAA
*
15336 AATACTTTTTGTCCCAAA
1 AATACTTTTTATCCCAAA
*
15354 AGTACTTTT
1 AATACTTTT
15363 GAAAATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (18 bp):
AATACTTTTTATCCCAAA
Found at i:15470 original size:19 final size:19
Alignment explanation
Indices: 15446--15482 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
15436 GTTTTCATAA
15446 ATATTTTTAAAAATAAATT
1 ATATTTTTAAAAATAAATT
**
15465 ATATTTTTTCAAATAAAT
1 ATATTTTTAAAAATAAAT
15483 AAAAAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTTTAAAAATAAATT
Found at i:15594 original size:15 final size:16
Alignment explanation
Indices: 15549--15585 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
15539 TTATTTTCAC
*
15549 TATTTTAAATATAAAA
1 TATTTTAAATGTAAAA
15565 TATTTTAAATGTAAAA
1 TATTTTAAATGTAAAA
15581 TATTT
1 TATTT
15586 ATATTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
TATTTTAAATGTAAAA
Found at i:16966 original size:23 final size:22
Alignment explanation
Indices: 16940--16993 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
16930 GACATAATAA
16940 GGGAAAGATAA-GGGAAGAAGATG
1 GGGAAAGATAATGGG--GAAGATG
*
16963 GGGAAGAAATAATGGGGAAGATG
1 GGGAA-AGATAATGGGGAAGATG
*
16986 GGGGAAGA
1 GGGAAAGA
16994 AGATCTGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 2 0.08
23 16 0.62
24 5 0.19
25 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.46, T:0.09
Consensus pattern (22 bp):
GGGAAAGATAATGGGGAAGATG
Found at i:17062 original size:30 final size:30
Alignment explanation
Indices: 17014--17094 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
17004 ATTAAAAATC
* *
17014 AAAATTATTTAATAATTTTATTATT-TCAAA
1 AAAATAATTTAATAATTTTAATATTCT-AAA
*
17044 AAAATAATTTTAAT-ATTTTAATATTCTTAA
1 AAAATAA-TTTAATAATTTTAATATTCTAAA
17074 AAAATAATTTAATAATTTTAA
1 AAAATAATTTAATAATTTTAA
17095 AATCATTTGC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
29 6 0.13
30 32 0.71
31 7 0.16
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
AAAATAATTTAATAATTTTAATATTCTAAA
Found at i:17084 original size:21 final size:21
Alignment explanation
Indices: 17055--17096 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17045 AAATAATTTT
*
17055 AATATTTTAAT-ATTCTTAAAA
1 AATAATTTAATAATT-TTAAAA
17076 AATAATTTAATAATTTTAAAA
1 AATAATTTAATAATTTTAAAA
17097 TCATTTGCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAATTTAATAATTTTAAAA
Found at i:19441 original size:12 final size:12
Alignment explanation
Indices: 19412--19454 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
19402 CATGAACAAG
*
19412 CTCGTTTATGAT
1 CTCGTTTATAAT
*
19424 -TCGTTTATTAT
1 CTCGTTTATAAT
*
19435 CTCGTTTATAAG
1 CTCGTTTATAAT
19447 CTCGTTTA
1 CTCGTTTA
19455 AAGCCCGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (12 bp):
CTCGTTTATAAT
Found at i:19477 original size:12 final size:11
Alignment explanation
Indices: 19435--19477 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
19425 CGTTTATTAT
19435 CTCGTTTATAAG
1 CTCGTTTA-AAG
19447 CTCGTTTAAAG
1 CTCGTTTAAAG
*
19458 CCCGTTTACAAG
1 CTCGTTTA-AAG
*
19470 CTCATTTA
1 CTCGTTTA
19478 TTAGACCCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (11 bp):
CTCGTTTAAAG
Found at i:23450 original size:24 final size:24
Alignment explanation
Indices: 23419--23584 Score: 198
Period size: 23 Copynumber: 7.1 Consensus size: 24
23409 AACATTAACA
23419 AACATGTTCGCGAACGCATAAACG
1 AACATGTTCGCGAACGCATAAACG
*
23443 AACGTGTTCGCGAACGCATAAACG
1 AACATGTTCGCGAACGCATAAACG
* *
23467 AACGTGTTCGCGAACGCATAAATG
1 AACATGTTCGCGAACGCATAAACG
* *
23491 AACATGTTAGCGAA--CATTAGACG
1 AACATGTTCGCGAACGCA-TAAACG
* *
23514 AACATGTTCGCGAACG-TTAGACG
1 AACATGTTCGCGAACGCATAAACG
* *
23537 AACATGTTCGCGAACG-TTAGACG
1 AACATGTTCGCGAACGCATAAACG
*
23560 AACATGTTCGCGAACG-TTAAACG
1 AACATGTTCGCGAACGCATAAACG
23583 AA
1 AA
23585 TATATAAACG
Statistics
Matches: 130, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
22 2 0.02
23 70 0.54
24 58 0.45
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (24 bp):
AACATGTTCGCGAACGCATAAACG
Found at i:23505 original size:12 final size:12
Alignment explanation
Indices: 23490--23574 Score: 74
Period size: 12 Copynumber: 7.3 Consensus size: 12
23480 ACGCATAAAT
23490 GAACATGTTAGC
1 GAACATGTTAGC
23502 GAACA--TTAGAC
1 GAACATGTTAG-C
*
23513 GAACATGTTCGC
1 GAACATGTTAGC
23525 GAAC--GTTAGAC
1 GAACATGTTAG-C
*
23536 GAACATGTTCGC
1 GAACATGTTAGC
23548 GAAC--GTTAGAC
1 GAACATGTTAG-C
*
23559 GAACATGTTCGC
1 GAACATGTTAGC
23571 GAAC
1 GAAC
23575 GTTAAACGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
10 12 0.20
11 16 0.27
12 20 0.34
13 11 0.19
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (12 bp):
GAACATGTTAGC
Found at i:23557 original size:46 final size:47
Alignment explanation
Indices: 23419--23584 Score: 219
Period size: 46 Copynumber: 3.6 Consensus size: 47
23409 AACATTAACA
* * *
23419 AACATGTTCGCGAACGCATAAACGAACGTGTTCGCGAACGCATAAACG
1 AACATGTTCGCGAACGCATAAACGAACATGTTCGCGAACG-TTAGACG
* * * *
23467 AACGTGTTCGCGAACGCATAAATGAACATGTTAGCGAACATTAGACG
1 AACATGTTCGCGAACGCATAAACGAACATGTTCGCGAACGTTAGACG
* *
23514 AACATGTTCGCGAACG-TTAGACGAACATGTTCGCGAACGTTAGACG
1 AACATGTTCGCGAACGCATAAACGAACATGTTCGCGAACGTTAGACG
*
23560 AACATGTTCGCGAACG-TTAAACGAA
1 AACATGTTCGCGAACGCATAAACGAA
23585 TATATAAACG
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
46 49 0.47
47 20 0.19
48 35 0.34
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (47 bp):
AACATGTTCGCGAACGCATAAACGAACATGTTCGCGAACGTTAGACG
Found at i:23603 original size:11 final size:11
Alignment explanation
Indices: 23570--23644 Score: 60
Period size: 11 Copynumber: 6.6 Consensus size: 11
23560 AACATGTTCG
*
23570 CGAACGTTAAA
1 CGAACATTAAA
*
23581 CGAATATATAAA
1 CGAACAT-TAAA
23593 CGAACATTAAA
1 CGAACATTAAA
*
23604 TGAACATTAAA
1 CGAACATTAAA
* * **
23615 TGAATATGTTCA
1 CGAACAT-TAAA
*
23627 CGAACGTTAAA
1 CGAACATTAAA
23638 CGAACAT
1 CGAACAT
23645 GTTCGCGAAT
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
11 33 0.67
12 16 0.33
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (11 bp):
CGAACATTAAA
Found at i:23609 original size:46 final size:46
Alignment explanation
Indices: 23464--23610 Score: 150
Period size: 46 Copynumber: 3.2 Consensus size: 46
23454 GAACGCATAA
* * * * * *
23464 ACGAACGTGTTCGCGAACGCATAAATGAACATGTTAGCGAACATTAG
1 ACGAACATGTTCGCGAACG-TTAAACGAACATATAAACGAACATTAG
* * *** *
23511 ACGAACATGTTCGCGAACGTTAGACGAACATGTTCGCGAACGTTAG
1 ACGAACATGTTCGCGAACGTTAAACGAACATATAAACGAACATTAG
* *
23557 ACGAACATGTTCGCGAACGTTAAACGAATATATAAACGAACATTAA
1 ACGAACATGTTCGCGAACGTTAAACGAACATATAAACGAACATTAG
*
23603 ATGAACAT
1 ACGAACAT
23611 TAAATGAATA
Statistics
Matches: 85, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
46 67 0.79
47 18 0.21
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (46 bp):
ACGAACATGTTCGCGAACGTTAAACGAACATATAAACGAACATTAG
Found at i:23620 original size:34 final size:34
Alignment explanation
Indices: 23570--23644 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
23560 AACATGTTCG
*
23570 CGAACGTTAAACGAATATATAAACGAACATTAAA
1 CGAACATTAAACGAATATATAAACGAACATTAAA
* * * ** *
23604 TGAACATTAAATGAATATGTTCACGAACGTTAAA
1 CGAACATTAAACGAATATATAAACGAACATTAAA
23638 CGAACAT
1 CGAACAT
23645 GTTCGCGAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (34 bp):
CGAACATTAAACGAATATATAAACGAACATTAAA
Found at i:23631 original size:23 final size:23
Alignment explanation
Indices: 23605--23653 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
23595 AACATTAAAT
* *
23605 GAACATTAAATGAATATGTTCAC
1 GAACATTAAACGAACATGTTCAC
* *
23628 GAACGTTAAACGAACATGTTCGC
1 GAACATTAAACGAACATGTTCAC
23651 GAA
1 GAA
23654 TGATAAACGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.24
Consensus pattern (23 bp):
GAACATTAAACGAACATGTTCAC
Found at i:23660 original size:23 final size:23
Alignment explanation
Indices: 23611--23665 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
23601 AAATGAACAT
* * *
23611 TAAATGAATATGTTCACGAACGT
1 TAAACGAACATGTTCACGAACGA
* *
23634 TAAACGAACATGTTCGCGAATGA
1 TAAACGAACATGTTCACGAACGA
23657 TAAACGAAC
1 TAAACGAAC
23666 GAGCACGAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (23 bp):
TAAACGAACATGTTCACGAACGA
Found at i:24027 original size:15 final size:15
Alignment explanation
Indices: 23994--24031 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
23984 ATCCGTTAAC
23994 CCGTTGA-TCATTGA
1 CCGTTGACTCATTGA
* *
24008 CCGTTGACTCGTTTA
1 CCGTTGACTCATTGA
24023 CCGTTGACT
1 CCGTTGACT
24032 TTTGAGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.37
Consensus pattern (15 bp):
CCGTTGACTCATTGA
Found at i:31547 original size:5 final size:5
Alignment explanation
Indices: 31537--31566 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
31527 TAAAAGGGGG
31537 TCCTC TCCTC TCCTC TCCTC TCCTC TCCTC
1 TCCTC TCCTC TCCTC TCCTC TCCTC TCCTC
31567 CTCTTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
TCCTC
Found at i:33573 original size:2 final size:2
Alignment explanation
Indices: 33566--33595 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33556 TTCATACAGA
33566 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
33596 TTAGAGAATA
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:39138 original size:107 final size:107
Alignment explanation
Indices: 38952--39158 Score: 326
Period size: 107 Copynumber: 1.9 Consensus size: 107
38942 ATCCATATGG
* * *
38952 AATAAATATATTTTACGAAATAAATAATAATGGTTATAACAATCAATTGGAGGGTGTAAGGTCTT
1 AATAAATATATTTCACGAAATAAATAATAATGATTATAACAATCAATTGGAGAGTGTAAGGTCTT
*
39017 GGGTTGGACAATATTAGTAGTTCAGATCATAGATACATGTGC
66 GGATTGGACAATATTAGTAGTTCAGATCATAGATACATGTGC
* *
39059 AATAAATATATTTCACGAAATAATTAATAATGATTGTAACAATCAATTGGAGAGTGTAAGGTCTT
1 AATAAATATATTTCACGAAATAAATAATAATGATTATAACAATCAATTGGAGAGTGTAAGGTCTT
* *
39124 GGATTGGATC-ATATTGGTAGTTCATATCATAGATA
66 GGATTGGA-CAATATTAGTAGTTCAGATCATAGATA
39159 ATGCAAAAAG
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
107 90 0.99
108 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (107 bp):
AATAAATATATTTCACGAAATAAATAATAATGATTATAACAATCAATTGGAGAGTGTAAGGTCTT
GGATTGGACAATATTAGTAGTTCAGATCATAGATACATGTGC
Found at i:51000 original size:41 final size:41
Alignment explanation
Indices: 50943--51044 Score: 186
Period size: 41 Copynumber: 2.5 Consensus size: 41
50933 AGAAGGGTAC
*
50943 GCTTAGCTATAATTTCTCACTCTTTATTTCCACTATACTTG
1 GCTTAGCTATAATTTCTCACTCTTTATTTCCACTATACTCG
50984 GCTTAGCTATAATTTCTCACTCTTTATTTCCACTATACTCG
1 GCTTAGCTATAATTTCTCACTCTTTATTTCCACTATACTCG
*
51025 GCTTCGCTATAATTTCTCAC
1 GCTTAGCTATAATTTCTCAC
51045 CATATGACTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.22, C:0.26, G:0.08, T:0.44
Consensus pattern (41 bp):
GCTTAGCTATAATTTCTCACTCTTTATTTCCACTATACTCG
Found at i:55825 original size:13 final size:14
Alignment explanation
Indices: 55809--55841 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
55799 AATGAACATG
55809 TTTTATG-AAAATA
1 TTTTATGAAAAATA
*
55822 TTTTACGAAAAATA
1 TTTTATGAAAAATA
55836 TTTTAT
1 TTTTAT
55842 ATCCAAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (14 bp):
TTTTATGAAAAATA
Found at i:62731 original size:13 final size:13
Alignment explanation
Indices: 62713--62788 Score: 73
Period size: 13 Copynumber: 5.8 Consensus size: 13
62703 TTAATATAAT
62713 ATTTGATATTTAA
1 ATTTGATATTTAA
* *
62726 ATTTGATTTTTTA
1 ATTTGATATTTAA
* *
62739 ATTTGATACTTAT
1 ATTTGATATTTAA
* *
62752 ATTTTATAGTCT-A
1 ATTTGATA-TTTAA
*
62765 ATTTGATACTTAA
1 ATTTGATATTTAA
62778 ATTTGATATTT
1 ATTTGATATTT
62789 TTTTTAATTT
Statistics
Matches: 47, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
12 1 0.02
13 45 0.96
14 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.57
Consensus pattern (13 bp):
ATTTGATATTTAA
Found at i:62755 original size:26 final size:26
Alignment explanation
Indices: 62713--62790 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 26
62703 TTAATATAAT
*
62713 ATTTGATATTTAAATTTGATTTTTTA
1 ATTTGATACTTAAATTTGATTTTTTA
* * ** *
62739 ATTTGATACTTATATTTTATAGTCTA
1 ATTTGATACTTAAATTTGATTTTTTA
62765 ATTTGATACTTAAATTTGATATTTTT
1 ATTTGATACTTAAATTTGAT-TTTTT
62791 TTTAATTTAG
Statistics
Matches: 40, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
26 38 0.95
27 2 0.05
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.58
Consensus pattern (26 bp):
ATTTGATACTTAAATTTGATTTTTTA
Found at i:62805 original size:30 final size:28
Alignment explanation
Indices: 62763--62838 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 28
62753 TTTTATAGTC
*
62763 TAATTTGATACTTAAATTTGATATTTTTTT
1 TAATTTG-TACTTAAATTTGACA-TTTTTT
*
62793 TAATTTAGTACTTAAGTTTGACATTTTTT
1 TAATTT-GTACTTAAATTTGACATTTTTT
*
62822 TAAGTTGGTACTTAAAT
1 TAA-TTTGTACTTAAAT
62839 ATTTTGGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 18 0.45
30 21 0.52
31 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (28 bp):
TAATTTGTACTTAAATTTGACATTTTTT
Found at i:62832 original size:29 final size:30
Alignment explanation
Indices: 62771--62838 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
62761 TCTAATTTGA
* *
62771 TACTTAAATTTGATATTTTTTTTAATTTAG
1 TACTTAAATTTGACATTTTTTTTAAGTTAG
* *
62801 TACTTAAGTTTGACA-TTTTTTTAAGTTGG
1 TACTTAAATTTGACATTTTTTTTAAGTTAG
62830 TACTTAAAT
1 TACTTAAAT
62839 ATTTTGGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 20 0.61
30 13 0.39
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.54
Consensus pattern (30 bp):
TACTTAAATTTGACATTTTTTTTAAGTTAG
Found at i:85043 original size:10 final size:11
Alignment explanation
Indices: 85018--85042 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
85008 ATCATTCCAC
85018 TTTTCTTTTTT
1 TTTTCTTTTTT
85029 TTTTCTTTTTT
1 TTTTCTTTTTT
85040 TTT
1 TTT
85043 CAACAAATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:87433 original size:27 final size:27
Alignment explanation
Indices: 87371--87434 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
87361 GAATTTTATG
*
87371 TTTTTTAATTTTCGAAATTATTTGATA
1 TTTTTTATTTTTCGAAATTATTTGATA
** * **
87398 TAATATATTTTTCGAAATTATTTTTTA
1 TTTTTTATTTTTCGAAATTATTTGATA
87425 TTTTTTATTT
1 TTTTTTATTT
87435 GGTTGATCTT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (27 bp):
TTTTTTATTTTTCGAAATTATTTGATA
Found at i:90550 original size:39 final size:38
Alignment explanation
Indices: 90458--90553 Score: 97
Period size: 39 Copynumber: 2.5 Consensus size: 38
90448 CCGAGAGAGG
**
90458 GTGT-TGAGCAGCAAGAAAAAGAGAAGAAATTGAAGGAA
1 GTGTGTGAGCAG-AAGAAAAAGAGAAGAAAGAGAAGGAA
* * *
90496 GCT-TGTGAACGAGAAGAAAAGGAGAAGAAAGAGAAGGAC
1 G-TGTGTGAGC-AGAAGAAAAAGAGAAGAAAGAGAAGGAA
90535 GTGTGTGAGCTAGAAGAAA
1 GTGTGTGAGC-AGAAGAAA
90554 GTGAGATATG
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
38 3 0.06
39 42 0.89
40 2 0.04
ACGTcount: A:0.47, C:0.06, G:0.34, T:0.12
Consensus pattern (38 bp):
GTGTGTGAGCAGAAGAAAAAGAGAAGAAAGAGAAGGAA
Found at i:95967 original size:21 final size:21
Alignment explanation
Indices: 95943--95990 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
95933 TAGATTCAAA
**
95943 TATTTTGAACTTAAATAATTT
1 TATTTTGAAAGTAAATAATTT
* *
95964 TATTTTTAAAGTAAGTAATTT
1 TATTTTGAAAGTAAATAATTT
95985 TATTTT
1 TATTTT
95991 TAAATGATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (21 bp):
TATTTTGAAAGTAAATAATTT
Found at i:96004 original size:22 final size:20
Alignment explanation
Indices: 95956--95994 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
95946 TTTGAACTTA
95956 AATAATTTTATTTTTAAAGT
1 AATAATTTTATTTTTAAAGT
95976 AAGTAATTTTATTTTTAAA
1 AA-TAATTTTATTTTTAAA
95995 TGATGATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
AATAATTTTATTTTTAAAGT
Found at i:96075 original size:23 final size:23
Alignment explanation
Indices: 96049--96104 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
96039 ATATTATAGC
*
96049 ATATTATATGATT-ATAAAAAATT
1 ATATTATATAATTCA-AAAAAATT
*
96072 ATATTATACAATTCAAAAAAATT
1 ATATTATATAATTCAAAAAAATT
96095 ATATTATATA
1 ATATTATATA
96105 TATTATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTATATAATTCAAAAAAATT
Found at i:97131 original size:14 final size:15
Alignment explanation
Indices: 97108--97152 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
97098 AAAAAATAAA
*
97108 ATTAATTTATTATAT
1 ATTAAATTATTATAT
97123 -TTAAATTATTATAT
1 ATTAAATTATTATAT
*
97137 CATTAAATTAATATAT
1 -ATTAAATTATTATAT
97153 CCTATCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 13 0.50
16 13 0.50
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTAAATTATTATAT
Found at i:97144 original size:16 final size:16
Alignment explanation
Indices: 97108--97153 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
97098 AAAAAATAAA
*
97108 ATTAATTTATTATAT-
1 ATTAAATTATTATATC
97123 -TTAAATTATTATATC
1 ATTAAATTATTATATC
*
97138 ATTAAATTAATATATC
1 ATTAAATTATTATATC
97154 CTATCATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 13 0.48
16 14 0.52
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTAAATTATTATATC
Found at i:98775 original size:89 final size:89
Alignment explanation
Indices: 98522--98790 Score: 502
Period size: 89 Copynumber: 3.0 Consensus size: 89
98512 CACCCTTTCA
98522 ACCATTTCTACTATACAAAAATCCCCTTCTCCACTGAGAAAACAGAAACCGAGAGATACACATAA
1 ACCATTTCTACTATACAAAAATCCCCTTCTCCACTGAGAAAACAGAAACCGAGAGATACACATAA
*
98587 AATGAAACTACATTTGGCTTTGGA
66 AATGAAACTACATTTGGCTTTGGG
98611 ACCATTTCTACTATACAAAAATATCCCCTTCTCCACTGAGAAAACAGAAACCGAGAGATACACAT
1 ACCATTTCTACTATAC-AAAA-ATCCCCTTCTCCACTGAGAAAACAGAAACCGAGAGATACACAT
*
98676 AAAATCAAACTACATTTGGCTTTGGG
64 AAAATGAAACTACATTTGGCTTTGGG
98702 ACCATTTCTACTATACAAAAATCCCCTTCTCCACTGAGAAAACAGAAACCGAGAGATACACATAA
1 ACCATTTCTACTATACAAAAATCCCCTTCTCCACTGAGAAAACAGAAACCGAGAGATACACATAA
98767 AATGAAACTACATTTGGCTTTGGG
66 AATGAAACTACATTTGGCTTTGGG
98791 TTTTCTTCTT
Statistics
Matches: 175, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
89 84 0.48
90 8 0.05
91 83 0.47
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.24
Consensus pattern (89 bp):
ACCATTTCTACTATACAAAAATCCCCTTCTCCACTGAGAAAACAGAAACCGAGAGATACACATAA
AATGAAACTACATTTGGCTTTGGG
Found at i:104062 original size:2 final size:2
Alignment explanation
Indices: 104055--104100 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
104045 AACATTTTAA
104055 AT AT AT AT 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 AT AT AT AT
104097 AT AT
1 AT AT
104101 TATTTTTTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:111937 original size:19 final size:21
Alignment explanation
Indices: 111901--111945 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
111891 TAGACATTTT
* *
111901 AAAAGTATATTAATAGTAT-A
1 AAAACTATATTAAAAGTATGA
111921 AAAACTATA-TAAAAGTATGA
1 AAAACTATATTAAAAGTATGA
111941 AAAAC
1 AAAAC
111946 AAAAATGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAACTATATTAAAAGTATGA
Found at i:118185 original size:31 final size:30
Alignment explanation
Indices: 118118--118186 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
118108 ATGATAATGT
* *
118118 AAGTAACTAAAACGTAACATTTCAAACATA
1 AAGTGACTAAAACGTAACATGTCAAACATA
*
118148 AA-TGACTAAAATGTAACATGAGTCAAACA-A
1 AAGTGACTAAAACGTAACAT--GTCAAACATA
118178 AAGTGACTA
1 AAGTGACTA
118187 TTTTAATAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 15 0.45
30 5 0.15
31 13 0.39
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.22
Consensus pattern (30 bp):
AAGTGACTAAAACGTAACATGTCAAACATA
Found at i:120536 original size:23 final size:25
Alignment explanation
Indices: 120508--120554 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
120498 ACCAGTCCAT
120508 ATTATTT-TTTAATTTT-TTTTAAA
1 ATTATTTATTTAATTTTATTTTAAA
*
120531 ATTATTTATTTTATTTTATTTTAA
1 ATTATTTATTTAATTTTATTTTAA
120555 TATTTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 8 0.38
25 6 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (25 bp):
ATTATTTATTTAATTTTATTTTAAA
Found at i:133901 original size:16 final size:16
Alignment explanation
Indices: 133880--133910 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
133870 CATGTTAGAA
133880 CATATAAATTTGAAAT
1 CATATAAATTTGAAAT
*
133896 CATATATATTTGAAA
1 CATATAAATTTGAAA
133911 GTTTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
CATATAAATTTGAAAT
Found at i:134031 original size:22 final size:23
Alignment explanation
Indices: 134001--134043 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
133991 TTATTATTTT
*
134001 TATAAATTTTTA-ATTTTTTATA
1 TATAAATTTTAATATTTTTTATA
*
134023 TATATATTTTAATATTTTTTA
1 TATAAATTTTAATATTTTTTA
134044 AGTTTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TATAAATTTTAATATTTTTTATA
Found at i:134104 original size:19 final size:20
Alignment explanation
Indices: 134063--134105 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
134053 AAAAATACAA
*
134063 ATTTTAAAATTTTTATAAAT
1 ATTTTAAAATTTTTAAAAAT
134083 ATTTT-AAA-TTTTAAAAATT
1 ATTTTAAAATTTTTAAAAA-T
134102 ATTT
1 ATTT
134106 GACAGAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTAAAATTTTTAAAAAT
Found at i:148112 original size:12 final size:12
Alignment explanation
Indices: 148095--148119 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
148085 TTCCTATTTC
148095 TAAATTTTACAT
1 TAAATTTTACAT
148107 TAAATTTTACAT
1 TAAATTTTACAT
148119 T
1 T
148120 TTATTCAGTT
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAATTTTACAT
Found at i:152657 original size:23 final size:24
Alignment explanation
Indices: 152614--152663 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
152604 AACGTTCAAA
*
152614 ATATTTATAAAAACATCAAAATTT
1 ATATTTATAAAAACATCAAAAATT
*
152638 ATATTT-TAAAAA-ATTTAAAAATT
1 ATATTTATAAAAACA-TCAAAAATT
152661 ATA
1 ATA
152664 AAAAAAGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 1 0.04
23 16 0.70
24 6 0.26
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (24 bp):
ATATTTATAAAAACATCAAAAATT
Found at i:154846 original size:23 final size:23
Alignment explanation
Indices: 154797--154876 Score: 133
Period size: 23 Copynumber: 3.4 Consensus size: 23
154787 CCCGGCTCGA
*
154797 ATTTATAATACTAATTTTATTTTT
1 ATTTGTAATACTAATTTT-TTTTT
*
154821 ATTTTTAATACTAATTTTTTTTT
1 ATTTGTAATACTAATTTTTTTTT
154844 ATTTGTAATACTAATTTTTTTTT
1 ATTTGTAATACTAATTTTTTTTT
154867 ATTTGTAATA
1 ATTTGTAATA
154877 ATGATTGAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
23 37 0.69
24 17 0.31
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.64
Consensus pattern (23 bp):
ATTTGTAATACTAATTTTTTTTT
Found at i:158943 original size:17 final size:17
Alignment explanation
Indices: 158910--158994 Score: 80
Period size: 17 Copynumber: 4.8 Consensus size: 17
158900 CAAACTCCCT
158910 TTAAATTTATGTTAAAAA
1 TTAAATTTAT-TTAAAAA
*
158928 TTAAATTTGTTTAAAAA
1 TTAAATTTATTTAAAAA
* *
158945 TTTAAATTTATTTTAAAT
1 -TTAAATTTATTTAAAAA
* ** *
158963 TTAAATTTGTTTTGAAT
1 TTAAATTTATTTAAAAA
158980 TTAAATTTAATTTAA
1 TTAAATTT-ATTTAA
158995 GTTTAAATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
17 30 0.54
18 26 0.46
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTAAAAA
Found at i:158981 original size:34 final size:34
Alignment explanation
Indices: 158909--159069 Score: 205
Period size: 34 Copynumber: 4.6 Consensus size: 34
158899 CCAAACTCCC
* * **
158909 TTTAAATTTATGTTAAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTAT-TTTAAATTTAAATTTGTTT-TGAA
158945 TTTAAATTTATTTTAAATTTAAATTTGTTTTGAA
1 TTTAAATTTATTTTAAATTTAAATTTGTTTTGAA
* *
158979 TTTAAATTTAATTTAAGTTTAAATTTGTTTTGAA
1 TTTAAATTTATTTTAAATTTAAATTTGTTTTGAA
* *
159013 TTTAAATTTAATTTAAGTTTAAATTTGTTTTGAAA
1 TTTAAATTTATTTTAAATTTAAATTTGTTTTG-AA
* *
159048 TTTAAAATTATTATAAATTTAA
1 TTTAAATTTATTTTAAATTTAA
159070 GTAAAGCTCA
Statistics
Matches: 114, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
34 66 0.58
35 37 0.32
36 11 0.10
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTGTTTTGAA
Found at i:158991 original size:11 final size:12
Alignment explanation
Indices: 158942--159038 Score: 78
Period size: 11 Copynumber: 8.5 Consensus size: 12
158932 ATTTGTTTAA
158942 AAATTTAAATTT
1 AAATTTAAATTT
*
158954 -ATTTTAAATTT
1 AAATTTAAATTT
**
158965 AAATTT-GTTTT
1 AAATTTAAATTT
*
158976 GAATTTAAATTT
1 AAATTTAAATTT
*
158988 -AATTTAAGTTT
1 AAATTTAAATTT
**
158999 AAATTT-GTTTT
1 AAATTTAAATTT
*
159010 GAATTTAAATTT
1 AAATTTAAATTT
*
159022 -AATTTAAGTTT
1 AAATTTAAATTT
159033 AAATTT
1 AAATTT
159039 GTTTTGAAAT
Statistics
Matches: 66, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
11 46 0.70
12 20 0.30
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (12 bp):
AAATTTAAATTT
Found at i:158999 original size:17 final size:16
Alignment explanation
Indices: 158943--159069 Score: 119
Period size: 17 Copynumber: 7.4 Consensus size: 16
158933 TTTGTTTAAA
158943 AATTTAAATTTATTTT
1 AATTTAAATTTATTTT
*
158959 AAATTTAAATTTGTTTT
1 -AATTTAAATTTATTTT
*
158976 GAATTTAAATTTAATTT
1 -AATTTAAATTTATTTT
*
158993 AAGTTTAAATTTGTTTT
1 AA-TTTAAATTTATTTT
*
159010 GAATTTAAATTTAATTT
1 -AATTTAAATTTATTTT
*
159027 AAGTTTAAATTTGTTTT
1 AA-TTTAAATTTATTTT
* *
159044 GAAATTTAAAATTATTATA
1 --AATTTAAATTTATT-TT
159063 AATTTAA
1 AATTTAA
159070 GTAAAGCTCA
Statistics
Matches: 91, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
16 4 0.04
17 72 0.79
18 12 0.13
19 3 0.03
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.54
Consensus pattern (16 bp):
AATTTAAATTTATTTT
Found at i:159884 original size:20 final size:21
Alignment explanation
Indices: 159843--159880 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
159833 TAATATCATT
159843 ATTATTAATATATTAATAATA
1 ATTATTAATATATTAATAATA
159864 ATTA-TAATAT-TTAATAA
1 ATTATTAATATATTAATAA
159881 ATAACTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 6 0.35
21 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTATTAATATATTAATAATA
Found at i:159891 original size:19 final size:20
Alignment explanation
Indices: 159848--159891 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
159838 TCATTATTAT
*
159848 TAATATATTAATAATAATTA
1 TAATATATTAATAATAACTA
159868 TAATAT-TTAATAAATAACTA
1 TAATATATTAAT-AATAACTA
159888 -AATA
1 TAATA
159892 AAAAATGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TAATATATTAATAATAACTA
Found at i:160853 original size:30 final size:29
Alignment explanation
Indices: 160812--161088 Score: 322
Period size: 29 Copynumber: 9.4 Consensus size: 29
160802 GGAGGTCCCT
160812 AACTTCCAAAAATCCCATTTTTGACCCCAA
1 AACTTCCAAAAATCCCATTTTT-ACCCCAA
* * *
160842 AACTTCTAAAAATTCCATTTTTACCCCCA
1 AACTTCCAAAAATCCCATTTTTACCCCAA
160871 AACTTCCAAAAATCCCATTTTTGACCCCAA
1 AACTTCCAAAAATCCCATTTTT-ACCCCAA
** * **
160901 AACTTCC-AAAATTTCAATTTTACCCCTG
1 AACTTCCAAAAATCCCATTTTTACCCCAA
*
160929 AACTTCCAAAATTCCCATTTTTGACCCCAA
1 AACTTCCAAAAATCCCATTTTT-ACCCCAA
* * *
160959 AACTTCTAAAAATTCCATTTTTAACCTCAA
1 AACTTCCAAAAATCCCATTTTT-ACCCCAA
* *
160989 AACTTCCAAAAATCCCATTTTAACCTCAA
1 AACTTCCAAAAATCCCATTTTTACCCCAA
**
161018 AACTTCCAAAAATCCCATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTACCCCAA
* *
161047 AACTTTCAAAAATCTCATTTTTAACCCCAA
1 AACTTCCAAAAATCCCATTTTT-ACCCCAA
*
161077 AATTTTCCAAAA
1 AA-CTTCCAAAA
161089 TTACCCTTTT
Statistics
Matches: 207, Mismatches: 35, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
28 12 0.06
29 99 0.48
30 89 0.43
31 7 0.03
ACGTcount: A:0.37, C:0.30, G:0.02, T:0.31
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTACCCCAA
Found at i:160904 original size:59 final size:59
Alignment explanation
Indices: 160812--161078 Score: 367
Period size: 59 Copynumber: 4.5 Consensus size: 59
160802 GGAGGTCCCT
160812 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCA
1 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCA
* * * **
160871 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTC-CAAAATTTCAATTTTACCCCTG
1 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCA
* * *
160929 AACTTCCAAAATTCCCATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTTAACCTCAA
1 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTT-ACCCCCA
* * * * *
160989 AACTTCCAAAAATCCCA-TTTTAACCTCAAAACTTCCAAAAATCCCATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCA
* * *
161047 AACTTTCAAAAATCTCATTTTTAACCCCAAAA
1 AACTTCCAAAAATCCCATTTTTGACCCCAAAA
161079 TTTTCCAAAA
Statistics
Matches: 182, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
58 71 0.39
59 91 0.50
60 20 0.11
ACGTcount: A:0.37, C:0.31, G:0.02, T:0.31
Consensus pattern (59 bp):
AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCA
Found at i:161089 original size:30 final size:28
Alignment explanation
Indices: 160812--161089 Score: 268
Period size: 30 Copynumber: 9.4 Consensus size: 28
160802 GGAGGTCCCT
160812 AACTTCCAAAAATCCCATTTTTGACCCCAA
1 AACTTCC-AAAATCCCATTTTT-ACCCCAA
* * *
160842 AACTTCTAAAAATTCCATTTTTACCCCCA
1 AACTTC-CAAAATCCCATTTTTACCCCAA
160871 AACTTCCAAAAATCCCATTTTTGACCCCAA
1 AACTTCC-AAAATCCCATTTTT-ACCCCAA
** * **
160901 AACTTCCAAAATTTCAATTTTACCCCTG
1 AACTTCCAAAATCCCATTTTTACCCCAA
160929 AACTTCCAAAATTCCCATTTTTGACCCCAA
1 AACTTCCAAAA-TCCCATTTTT-ACCCCAA
* * *
160959 AACTTCTAAAAATTCCATTTTTAACCTCAA
1 AACTTC-CAAAATCCCATTTTT-ACCCCAA
* *
160989 AACTTCCAAAAATCCCATTTTAACCTCAA
1 AACTTCC-AAAATCCCATTTTTACCCCAA
**
161018 AACTTCCAAAAATCCCATTTTTACCCCCG
1 AACTTCC-AAAATCCCATTTTTACCCCAA
* *
161047 AACTTTCAAAAATCTCATTTTTAACCCCAA
1 AAC-TTCCAAAATCCCATTTTT-ACCCCAA
*
161077 AATTTTCCAAAAT
1 AA-CTTCCAAAAT
161090 TACCCTTTTA
Statistics
Matches: 205, Mismatches: 33, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
28 16 0.08
29 91 0.44
30 94 0.46
31 4 0.02
ACGTcount: A:0.37, C:0.30, G:0.02, T:0.31
Consensus pattern (28 bp):
AACTTCCAAAATCCCATTTTTACCCCAA
Found at i:164731 original size:70 final size:67
Alignment explanation
Indices: 164605--164737 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 67
164595 ATAAACAATA
* * *
164605 TAATAGTTTTGCCTTTTAACTTAATGGGTAAATATTTATCAAAATGACATAATTTTACCTTTTAA
1 TAATAGTTTTGACTTTTAACTTAAAGGGTAAATATTTATCAAAACGACATAATTTTACCTTTTAA
164670 CT
66 CT
* * *
164672 TAATGGTTTTGACTTTTAACTTTAGAAAGGGTAAATATTTATCAAAACGACGTAGTTTTACCTTT
1 TAATAGTTTTGACTTTTAAC-TT--AAAGGGTAAATATTTATCAAAACGACATAATTTTACCTTT
164737 T
63 T
164738 CTTATTCGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 18 0.32
68 2 0.04
70 37 0.65
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (67 bp):
TAATAGTTTTGACTTTTAACTTAAAGGGTAAATATTTATCAAAACGACATAATTTTACCTTTTAA
CT
Found at i:166602 original size:17 final size:17
Alignment explanation
Indices: 166580--166613 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
166570 CATATTTTTA
166580 ATAAAAATATTA-AAATT
1 ATAAAAA-ATTACAAATT
166597 ATAAAAAATTACAAATT
1 ATAAAAAATTACAAATT
166614 TTTAAGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAATTACAAATT
Found at i:167334 original size:3 final size:3
Alignment explanation
Indices: 167326--167393 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
167316 TCTGGAAGAA
167326 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
167374 ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
167394 GGAATAAAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Done.