Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold35
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: 4812169
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 17994 characters in sequence are not A, C, G, or T
File 1 of 30
Found at i:766 original size:9 final size:9
Alignment explanation
Indices: 747--789 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
737 TGAAGGGGGT
*
747 GGGGGTAGG
1 GGGGGAAGG
*
756 GGGGGAGGG
1 GGGGGAAGG
765 GGGGGAAAGG
1 GGGGG-AAGG
775 GGGGGAAGG
1 GGGGGAAGG
*
784 GTGGGA
1 GGGGGA
790 GGAGAAGGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.19, C:0.00, G:0.77, T:0.05
Consensus pattern (9 bp):
GGGGGAAGG
Found at i:3513 original size:13 final size:13
Alignment explanation
Indices: 3495--3519 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3485 ACACAAAGTA
3495 TGTATCGATACAT
1 TGTATCGATACAT
3508 TGTATCGATACA
1 TGTATCGATACA
3520 CGTTTAAAAG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3552 original size:20 final size:20
Alignment explanation
Indices: 3505--3557 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3495 TGTATCGATA
*
3505 CATTGTATCGATACACGTTT
1 CATTGTATCGATACACGTTG
* ** *
3525 AAAAGTATCGATACATGTTG
1 CATTGTATCGATACACGTTG
3545 CATTGTATCGATA
1 CATTGTATCGATA
3558 TACTGAAAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (20 bp):
CATTGTATCGATACACGTTG
Found at i:3619 original size:138 final size:136
Alignment explanation
Indices: 3372--3678 Score: 524
Period size: 138 Copynumber: 2.2 Consensus size: 136
3362 ACCCTGAAAA
3372 GTATCGATACACATTTAAAAGTATCGATACATGTTGCACTGTATCGATACATGAAAAAGATGTAT
1 GTATCGATACAC-TTTAAAAGTATCGATACATGTTGCACTGTATCGATACATGAAAAAGATGTAT
3437 CGATACATGTCATTGGGATTTCTTGGCAGTAGCCAAACTTGTATCGATACACAAAGTATGTATCG
65 CGATACATGTCATTGGGATTTCTTGGCAGTAGCCAAACTTGTATCGATACACAAAGTATGTATCG
3502 ATACATT
130 ATACATT
* *
3509 GTATCGATACACGTTTAAAAGTATCGATACATGTTGCATTGTATCGATATACTGAAAAAGATGTA
1 GTATCGATACAC-TTTAAAAGTATCGATACATGTTGCACTGTATCGATACA-TGAAAAAGATGTA
* *
3574 TCGATATATGTTATTGGGATTTCTTGGCAGTAGCCAAACTTGTATCGATACACAAAGTATGTATC
64 TCGATACATGTCATTGGGATTTCTTGGCAGTAGCCAAACTTGTATCGATACACAAAGTATGTATC
3639 GATACATT
129 GATACATT
**
3647 GTATCGATACACCATAAAATGTATCGATACAT
1 GTATCGATACACTTTAAAA-GTATCGATACAT
3679 TGGCTTGCAA
Statistics
Matches: 161, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
137 53 0.33
138 108 0.67
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (136 bp):
GTATCGATACACTTTAAAAGTATCGATACATGTTGCACTGTATCGATACATGAAAAAGATGTATC
GATACATGTCATTGGGATTTCTTGGCAGTAGCCAAACTTGTATCGATACACAAAGTATGTATCGA
TACATT
Found at i:3651 original size:13 final size:13
Alignment explanation
Indices: 3633--3657 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3623 ACACAAAGTA
3633 TGTATCGATACAT
1 TGTATCGATACAT
3646 TGTATCGATACA
1 TGTATCGATACA
3658 CCATAAAATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3654 original size:32 final size:33
Alignment explanation
Indices: 3613--3680 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
3603 GTAGCCAAAC
*
3613 TTGTATCGATACA-CA-AAGTATGTATCGATACA
1 TTGTATCGATACACCATAA-AATGTATCGATACA
3645 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
3678 TTG
1 TTG
3681 GCTTGCAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 18 0.55
34 2 0.06
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:7649 original size:20 final size:20
Alignment explanation
Indices: 7624--7690 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
7614 CTACCACTGT
7624 TTGTATCGATACATGGCACA
1 TTGTATCGATACATGGCACA
7644 TTGTATCGAT--AT---A-A
1 TTGTATCGATACATGGCACA
7658 -TGTATCGATACATGGCACA
1 TTGTATCGATACATGGCACA
7677 TTGTATCGATACAT
1 TTGTATCGATACAT
7691 TGTATCGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 9 0.22
14 1 0.03
15 3 0.08
18 3 0.08
19 1 0.03
20 23 0.57
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
TTGTATCGATACATGGCACA
Found at i:7667 original size:33 final size:32
Alignment explanation
Indices: 7624--7754 Score: 176
Period size: 33 Copynumber: 4.0 Consensus size: 32
7614 CTACCACTGT
*
7624 TTGTATCGATACATG-GCACATTGTATCGATATA
1 TTGTATCGATACATGTG-A-ATTGTATCGATACA
*
7657 ATGTATCGATACATG-GCACATTGTATCGATACA
1 TTGTATCGATACATGTG-A-ATTGTATCGATACA
7690 TTGTATCGATACATGTTGAATTGTATCGATACA
1 TTGTATCGATACATG-TGAATTGTATCGATACA
7723 TTGTATCGATACATGTTGAATTGTATCGATAC
1 TTGTATCGATACATG-TGAATTGTATCGATAC
7755 GTTGCTTCTA
Statistics
Matches: 93, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
33 91 0.98
34 1 0.01
35 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.37
Consensus pattern (32 bp):
TTGTATCGATACATGTGAATTGTATCGATACA
Found at i:7692 original size:13 final size:13
Alignment explanation
Indices: 7674--7736 Score: 84
Period size: 13 Copynumber: 5.3 Consensus size: 13
7664 GATACATGGC
7674 ACATTGTATCGAT
1 ACATTGTATCGAT
7687 ACATTGTATCGAT
1 ACATTGTATCGAT
7700 ACA-TGT-T-G--
1 ACATTGTATCGAT
7708 A-ATTGTATCGAT
1 ACATTGTATCGAT
7720 ACATTGTATCGAT
1 ACATTGTATCGAT
7733 ACAT
1 ACAT
7737 GTTGAATTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
7 1 0.02
8 4 0.09
9 1 0.02
10 2 0.05
11 1 0.02
12 4 0.09
13 31 0.70
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:7714 original size:20 final size:20
Alignment explanation
Indices: 7689--7754 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
7679 GTATCGATAC
7689 ATTGTATCGATACATGTTGA
1 ATTGTATCGATACATGTTGA
7709 ATTGTATCGATAC-------
1 ATTGTATCGATACATGTTGA
7722 ATTGTATCGATACATGTTGA
1 ATTGTATCGATACATGTTGA
7742 ATTGTATCGATAC
1 ATTGTATCGATAC
7755 GTTGCTTCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 13 0.33
20 26 0.67
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTGTATCGATACATGTTGA
Found at i:11540 original size:32 final size:30
Alignment explanation
Indices: 11504--11562 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
11494 GAAATCAAAT
11504 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
11536 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
11563 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:11878 original size:32 final size:33
Alignment explanation
Indices: 11822--11885 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
11812 TACAAGCCAA
*
11822 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATATTTTGTGTATCGATACAT
*
11855 TGTATCGATA-TATATTTTGTGTATCGATACA
1 TGTATCGATACAATATTTTGTGTATCGATACA
11886 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (33 bp):
TGTATCGATACAATATTTTGTGTATCGATACAT
Found at i:14110 original size:13 final size:13
Alignment explanation
Indices: 14092--14129 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
14082 ATAATCCCCC
14092 TGTATCGATACAG
1 TGTATCGATACAG
*
14105 TGTATCGATACAT
1 TGTATCGATACAG
14118 TGTATCGATACA
1 TGTATCGATACA
14130 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:18071 original size:21 final size:21
Alignment explanation
Indices: 18042--18086 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
18032 AAATTTTTAT
*
18042 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
18062 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
18084 TTT
1 TTT
18087 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:20005 original size:32 final size:30
Alignment explanation
Indices: 19969--20027 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
19959 GAAATCAAAT
19969 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
20001 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
20028 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:20239 original size:19 final size:19
Alignment explanation
Indices: 20215--20253 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
20205 TCCTGTGTGA
20215 ATGTATCGATACATATTTG
1 ATGTATCGATACATATTTG
20234 ATGTATCGATACATATTTG
1 ATGTATCGATACATATTTG
20253 A
1 A
20254 AAATATAGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (19 bp):
ATGTATCGATACATATTTG
Found at i:20323 original size:13 final size:13
Alignment explanation
Indices: 20305--20362 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
20295 CAATTTTTTG
20305 TGTATCGATACAT
1 TGTATCGATACAT
20318 TGTATCGATACATATTTT
1 TGTATCGATAC--A---T
20336 GTGTATCGATACAT
1 -TGTATCGATACAT
20350 TGTATCGATACAT
1 TGTATCGATACAT
20363 ATTTGTATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 24 0.62
14 1 0.03
15 1 0.03
17 1 0.03
18 1 0.03
19 11 0.28
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:20341 original size:32 final size:32
Alignment explanation
Indices: 20285--20366 Score: 146
Period size: 32 Copynumber: 2.5 Consensus size: 32
20275 TACAAGCCAA
*
20285 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATAC-ATATTTTGTGTATCGATACAT
20318 TGTATCGATACATATTTTGTGTATCGATACAT
1 TGTATCGATACATATTTTGTGTATCGATACAT
20350 TGTATCGATACATATTT
1 TGTATCGATACATATTT
20367 GTATCAATAC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 37 0.77
33 11 0.23
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (32 bp):
TGTATCGATACATATTTTGTGTATCGATACAT
Found at i:20342 original size:19 final size:19
Alignment explanation
Indices: 20285--20349 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
20275 TACAAGCCAA
*
20285 TGTATCGATACAATTTTTTG
1 TGTATCGATAC-ATATTTTG
20305 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
20318 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
20337 TGTATCGATACAT
1 TGTATCGATACAT
20350 TGTATCGATA
Statistics
Matches: 38, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
20 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:20454 original size:20 final size:20
Alignment explanation
Indices: 20408--20481 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
20398 ATCCCAATGA
***
20408 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGAAT
20429 CATGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
*
20449 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
*
20469 TATGTATCGATAC
1 CATGTATCGATAC
20482 TTTTAAGGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.63
21 15 0.33
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:23312 original size:21 final size:22
Alignment explanation
Indices: 23286--23328 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
23276 ATCAAATCTT
* *
23286 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAGTACTTCATTTTTCA
23307 CTTCAAAGTACTTCATTTTTCA
1 CTTCAAAGTACTTCATTTTTCA
23329 TCAAAATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.26, C:0.21, G:0.02, T:0.51
Consensus pattern (22 bp):
CTTCAAAGTACTTCATTTTTCA
Found at i:24692 original size:33 final size:33
Alignment explanation
Indices: 24655--24720 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
24645 AAAGTTGATC
24655 ACTTCACTTTCACAACGCAT-GAGTGAGCACTTT
1 ACTTCACTTTCACAACGCATGGA-TGAGCACTTT
* * * *
24688 ACTTCATTTTCGCAGCGTATGGATGAGCACTTT
1 ACTTCACTTTCACAACGCATGGATGAGCACTTT
24721 GGTGCACTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (33 bp):
ACTTCACTTTCACAACGCATGGATGAGCACTTT
Found at i:25810 original size:20 final size:20
Alignment explanation
Indices: 25764--25817 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
25754 CTACCACTAT
* *
25764 TTGTATCGATATATGGCACA
1 TTGTATCGATACATGGCAAA
* **
25784 TTATATCGATACATGTTAAA
1 TTGTATCGATACATGGCAAA
25804 TTGTATCGATACAT
1 TTGTATCGATACAT
25818 TGCTTCTAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGGCAAA
Found at i:30798 original size:20 final size:20
Alignment explanation
Indices: 30773--30827 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
30763 GTTGGGCTCA
* *
30773 ATGTATCGATATATTTTA-C
1 ATGTATCGATATAATTCATC
*
30792 TATGTATCGATACAATTCATC
1 -ATGTATCGATATAATTCATC
30813 ATGTATCGATATAAT
1 ATGTATCGATATAAT
30828 GTATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGTATCGATATAATTCATC
Found at i:31325 original size:16 final size:16
Alignment explanation
Indices: 31304--31334 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31294 ACAATATAAC
31304 TTAATAATAATTAAAT
1 TTAATAATAATTAAAT
*
31320 TTAATAGTAATTAAA
1 TTAATAATAATTAAA
31335 AATAATTTTA
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:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TTAATAATAATTAAAT
Found at i:35772 original size:28 final size:27
Alignment explanation
Indices: 35714--35774 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
35704 TCTTACACAG
** *
35714 AATTTTCAATTAAATTTTTATGCATAG
1 AATTTTCAATTAAATTTTTACACATAA
*
35741 AATTTTCAATTAAAATTTTTACATATAA
1 AATTTTCAATT-AAATTTTTACACATAA
35769 AATTTT
1 AATTTT
35775 ATTTTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (27 bp):
AATTTTCAATTAAATTTTTACACATAA
Found at i:35904 original size:26 final size:29
Alignment explanation
Indices: 35873--35935 Score: 87
Period size: 26 Copynumber: 2.3 Consensus size: 29
35863 AGTTTAAACC
* *
35873 TTTTAATTAAACT-TTCG-TATATAAAA-
1 TTTTAATTAAACTCTTAGACATATAAAAT
35899 TTTTAATTAAACTCTTAGACATATAAAAT
1 TTTTAATTAAACTCTTAGACATATAAAAT
35928 TTTTAATT
1 TTTTAATT
35936 TAGCTTTCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 13 0.41
27 3 0.09
28 8 0.25
29 8 0.25
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTTAATTAAACTCTTAGACATATAAAAT
Found at i:50309 original size:13 final size:13
Alignment explanation
Indices: 50291--50317 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
50281 ACATTATGCT
50291 TTGTATCGATACA
1 TTGTATCGATACA
50304 TTGTATCGATACA
1 TTGTATCGATACA
50317 T
1 T
50318 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:50314 original size:33 final size:32
Alignment explanation
Indices: 50272--50335 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
50262 CACACCCAGA
*
50272 TGTATCGATACAT-TATGCTTTGTATCGATACAT
1 TGTATCGATACATGT-T-CATTGTATCGATACAT
50305 TGTATCGATACATGTTCATTGTATCGATACA
1 TGTATCGATACATGTTCATTGTATCGATACA
50336 AGCACAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.48
33 14 0.48
34 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATGTTCATTGTATCGATACAT
Found at i:50347 original size:20 final size:19
Alignment explanation
Indices: 50301--50353 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
50291 TTGTATCGAT
* *
50301 ACATTGTATCGATACATGT
1 ACATTGTATCGATACAAGC
*
50320 TCATTGTATCGATACAAGC
1 ACATTGTATCGATACAAGC
50339 ACAATTGTATCGATA
1 AC-ATTGTATCGATA
50354 TATGAAACTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (19 bp):
ACATTGTATCGATACAAGC
Found at i:50445 original size:13 final size:13
Alignment explanation
Indices: 50403--50447 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
50393 GATACATGGC
50403 ACATTGTATCGAT
1 ACATTGTATCGAT
*
50416 ACAATGTATCGAT
1 ACATTGTATCGAT
50429 ACATTGTATCGAT
1 ACATTGTATCGAT
50442 ACATTG
1 ACATTG
50448 CTTCAAACGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:62831 original size:13 final size:13
Alignment explanation
Indices: 62815--62845 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
62805 CTTTGTATTA
*
62815 ATACATTGTATCG
1 ATACACTGTATCG
62828 ATACACTGTATCG
1 ATACACTGTATCG
62841 ATACA
1 ATACA
62846 GGGGAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (13 bp):
ATACACTGTATCG
Found at i:62990 original size:21 final size:20
Alignment explanation
Indices: 62966--63012 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
62956 AAATCTTTTG
62966 CAAAATACTT-ACTTTTCACTT
1 CAAAATACTTCACTTTTCA--T
* *
62987 CAAATTACTTCATTTTTCAT
1 CAAAATACTTCACTTTTCAT
63007 CAAAAT
1 CAAAAT
63013 CAATTTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 9 0.41
22 7 0.32
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (20 bp):
CAAAATACTTCACTTTTCAT
Found at i:64192 original size:20 final size:19
Alignment explanation
Indices: 64137--64192 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
64127 AAAACCCTTA
*
64137 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
64157 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
64177 AATGTATCGATACATG
1 AAAGTATCGATACATG
64193 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:64288 original size:20 final size:20
Alignment explanation
Indices: 64243--64294 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
64233 GTAGCCAAAC
* **
64243 TTGTATTGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
64263 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
64282 TTGTATCGATACA
1 TTGTATCGATACA
64295 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:66541 original size:21 final size:21
Alignment explanation
Indices: 66508--66557 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
66498 TTGCAAGTTG
*
66508 AAATAAATAAGTTGGCTAATGA
1 AAATAAATAAGTTAGCTAA-GA
*
66530 AAAT-AATGAGTTAGCTAAGAA
1 AAATAAATAAGTTAGCTAAG-A
66551 AAATAAA
1 AAATAAA
66558 AACTTGCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.04
21 17 0.71
22 6 0.25
ACGTcount: A:0.56, C:0.04, G:0.16, T:0.24
Consensus pattern (21 bp):
AAATAAATAAGTTAGCTAAGA
Found at i:68375 original size:15 final size:15
Alignment explanation
Indices: 68355--68385 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
68345 TAAAAATGTC
*
68355 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
68370 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
68385 C
1 C
68386 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:69032 original size:13 final size:13
Alignment explanation
Indices: 69014--69047 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
69004 AACAAGCTCC
*
69014 TCGATACATTGTA
1 TCGATACACTGTA
69027 TCGATACACTGTA
1 TCGATACACTGTA
69040 TCGATACA
1 TCGATACA
69048 GGGGGATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (13 bp):
TCGATACACTGTA
Found at i:69211 original size:20 final size:20
Alignment explanation
Indices: 69173--69212 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
69163 TTTTGTAAAA
69173 TACTTGTTTTTCACTTCAAAT
1 TACTTGTTTTTCAC-TCAAAT
69194 TACTTCGTTTTTCA-TCAAA
1 TACTT-GTTTTTCACTCAAA
69213 ACCAGCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (20 bp):
TACTTGTTTTTCACTCAAAT
Found at i:70709 original size:23 final size:21
Alignment explanation
Indices: 70667--70710 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
70657 GTTTAAAGTT
**
70667 TTTGCTTGACTTTGTGTTTTA
1 TTTGCTTGACTTTGAATTTTA
70688 TTTGCATTGTACTTTGAATTTTA
1 TTTGC-TTG-ACTTTGAATTTTA
70711 ATCTATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.59
Consensus pattern (21 bp):
TTTGCTTGACTTTGAATTTTA
Found at i:71538 original size:20 final size:19
Alignment explanation
Indices: 71487--71538 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
71477 CCCTTAAAAC
*
71487 TATCGATACATAATTCAAAG
1 TATCGATACAT-GTTCAAAG
*
71507 TATCGATACATGTTGCAATG
1 TATCGATACATGTT-CAAAG
71527 TATCGATACATG
1 TATCGATACATG
71539 AAAAAGATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (19 bp):
TATCGATACATGTTCAAAG
Found at i:71634 original size:20 final size:20
Alignment explanation
Indices: 71589--71640 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
71579 GTAGCTAAAC
* **
71589 TTGTATTGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
71609 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
71628 TTGTATCGATACA
1 TTGTATCGATACA
71641 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:75258 original size:20 final size:20
Alignment explanation
Indices: 75220--75259 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
75210 TTTCAAATTT
75220 CTTCATTTTCACTTCAAAATA
1 CTTCATTTTCAC-TCAAAATA
75241 CTTCATTTTTCA-TCAAAAT
1 CTTCA-TTTTCACTCAAAAT
75260 TATCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.45
Consensus pattern (20 bp):
CTTCATTTTCACTCAAAATA
Found at i:76871 original size:16 final size:16
Alignment explanation
Indices: 76818--76872 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
76808 ATTCGACTTT
*
76818 ATGTTTATTATATGTG
1 ATGTTTGTTATATGTG
**
76834 ATGTTTGCTTGCAT-T-
1 ATGTTTG-TTATATGTG
76849 ATAGTTTGTTATATGTG
1 AT-GTTTGTTATATGTG
76866 ATGTTTG
1 ATGTTTG
76873 CATGAAGAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
15 6 0.20
16 18 0.60
17 6 0.20
ACGTcount: A:0.20, C:0.04, G:0.22, T:0.55
Consensus pattern (16 bp):
ATGTTTGTTATATGTG
Found at i:77609 original size:33 final size:32
Alignment explanation
Indices: 77572--77636 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
77562 TACCACCGTT
*
77572 TGTATTGATACATG-GCACATTGTATCGATACAA
1 TGTATCGATACATGAG-A-ATTGTATCGATACAA
77605 TGTATCGATACATGAAGAATTGTATCGATACA
1 TGTATCGATACATG-AGAATTGTATCGATACA
77637 TTGCTTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATGAGAATTGTATCGATACAA
Found at i:77610 original size:13 final size:13
Alignment explanation
Indices: 77592--77616 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
77582 CATGGCACAT
77592 TGTATCGATACAA
1 TGTATCGATACAA
77605 TGTATCGATACA
1 TGTATCGATACA
77617 TGAAGAATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:79277 original size:201 final size:201
Alignment explanation
Indices: 78932--79318 Score: 641
Period size: 201 Copynumber: 1.9 Consensus size: 201
78922 ACATTTGGTC
*
78932 ATTTTGGGTTCGAGTTATTTCGAGTTTAGGTCATTCTAGATTCGAGTCATTTTTGGGTTTAGGTT
1 ATTTTGGGTTCAAGTTATTTCGAGTTTAGGTCATTCTAGATTCGAGTCATTTTTGGGTTTAGGTT
* * * *
78997 AATTAGTTTTGTATTATTGCCTTTAATGGGTCAAATTGGGTTAGGTTTGTAGACACATAATTTTG
66 AATTAGTTTTGTATTATTCCCTTTAATAGGTCAAATTGGGATAGGTTTGTAGACACATAATTTCG
* *
79062 CCCGGGCTACTTTTTTCCATAAACCATAAGTATCTGAGAATGAAAATCCAGTGGCCACTCAGATT
131 CCCAGGCTACTTTTTTCCAAAAACCATAAGTATCTGAGAATGAAAATCCAGTGGCCACTCAGATT
79127 CAAGTT
196 CAAGTT
79133 ATTTTGGGTTCAAGTTATTTCGAGTTT-GGATCATTCTAGATTCGAGTCATTTTTGGGTTTAGGT
1 ATTTTGGGTTCAAGTTATTTCGAGTTTAGG-TCATTCTAGATTCGAGTCATTTTTGGGTTTAGGT
* *
79197 TAATTGGTTTTGTATTATTCCCTTTAATAGTTCAAATTGGGATAGGTTTGTAGACACATAATTTC
65 TAATTAGTTTTGTATTATTCCCTTTAATAGGTCAAATTGGGATAGGTTTGTAGACACATAATTTC
* * * *
79262 GTCTAGGCTACTTTTTTTCAAAAACCATAAGTATTTGAGAATGAAAATCCAGTGGCC
130 GCCCAGGCTACTTTTTTCCAAAAACCATAAGTATCTGAGAATGAAAATCCAGTGGCC
79319 GCTTAAATGG
Statistics
Matches: 172, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
200 2 0.01
201 170 0.99
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.41
Consensus pattern (201 bp):
ATTTTGGGTTCAAGTTATTTCGAGTTTAGGTCATTCTAGATTCGAGTCATTTTTGGGTTTAGGTT
AATTAGTTTTGTATTATTCCCTTTAATAGGTCAAATTGGGATAGGTTTGTAGACACATAATTTCG
CCCAGGCTACTTTTTTCCAAAAACCATAAGTATCTGAGAATGAAAATCCAGTGGCCACTCAGATT
CAAGTT
Found at i:80244 original size:164 final size:165
Alignment explanation
Indices: 80050--80392 Score: 476
Period size: 165 Copynumber: 2.1 Consensus size: 165
80040 CCTATTTTCA
* * *
80050 AAATACGGAGTTTTCTACTTCGTAAATTTTTTTGGAGAGAATTTTC-TTGGGTTTTAATTTTTAA
1 AAATACAGAGTTTTCTACTCCATAAATTTTTTTGGAGAGAATTTTCATTGGGTTTTAATTTTTAA
* * *
80114 AATTCATAAAATATTATTATTTAATTCATAGTAAGTTAGTTTTCAAAAATTCATTCATTTTCATG
66 AATTCATAAAATATTATTATTTAATTAATAGTAAGTCAGTTTTCAAAAATTCATTCATTTTCATA
*
80179 GA-GTTTGATTTTTTCCTTAAAACTCTCATTTTTCTG
131 GATGTTTGAATTTTTCCTTAAAACTCT--TTTTTCTG
* * * * *
80215 AAATACTGAGTTTTCTTCTCCAT-AATTTTTTTGGGGAGGATTTTCATTGGTTTTTAATTTTTAA
1 AAATACAGAGTTTTCTACTCCATAAATTTTTTTGGAGAGAATTTTCATTGGGTTTTAATTTTTAA
* * *
80279 AATTTATCAAATATTATTATTTAATTAATATTAAGTCAGTTTTCAAAAATTCATTCATTTTCATA
66 AATTCATAAAATATTATTATTTAATTAATAGTAAGTCAGTTTTCAAAAATTCATTCATTTTCATA
* * * *
80344 GATTTTTGAATTTTTCCTTGAAACTCTTTTTTTTT
131 GATGTTTGAATTTTTCCTTAAAACTCTTTTTTCTG
80379 AAATACAGAGTTTT
1 AAATACAGAGTTTT
80393 TCTTTTTTTT
Statistics
Matches: 157, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
164 39 0.25
165 97 0.62
166 21 0.13
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (165 bp):
AAATACAGAGTTTTCTACTCCATAAATTTTTTTGGAGAGAATTTTCATTGGGTTTTAATTTTTAA
AATTCATAAAATATTATTATTTAATTAATAGTAAGTCAGTTTTCAAAAATTCATTCATTTTCATA
GATGTTTGAATTTTTCCTTAAAACTCTTTTTTCTG
Found at i:80396 original size:25 final size:26
Alignment explanation
Indices: 80368--80418 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
80358 TCCTTGAAAC
*
80368 TCTTTTTTTT-TAAATACAGAGTTTT
1 TCTTTTTTTTCGAAATACAGAGTTTT
80393 TCTTTTTTTTCGAAATACAGAGTTTT
1 TCTTTTTTTTCGAAATACAGAGTTTT
80419 CTTCTTCCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (26 bp):
TCTTTTTTTTCGAAATACAGAGTTTT
Found at i:80446 original size:190 final size:192
Alignment explanation
Indices: 80207--80557 Score: 541
Period size: 190 Copynumber: 1.8 Consensus size: 192
80197 AAAACTCTCA
* * *
80207 TTTTTCTGAAATACTGAGTTTTCTTCTCCATAATTTTTTTGGGGAGGATTTTCATTGGTTTTTAA
1 TTTTTCTGAAATACAGAGTTTTCTTCTCCATAATTTTTTTGGAGAGGATTTTCATTGGGTTTTAA
* **
80272 TTTTTAAAATTTATCAAATATTATTATTTAATTAATATTAAGTCAGTTTTCAAAAATTCATTCAT
66 TTTTTAAAATTTATCAAATATCATTATTTAATTAATATTAAAACAGTTTTCAAAAATTCATTCAT
*
80337 TTTCAT-AGATTTTTGAA-TTTTTCCTTGAAACTCTTTTTTTTTAAATACAGAGTTTTTCTTT
131 TTTCATGAG-TTTTTAAATTTTTTCCTTGAAACTCTTTTTTTTTAAATACAGAGTTTTTCTTT
80398 TTTTTC-GAAATACAGAGTTTTCTTCTTCC-TAAATTTTTTT-GAGAGGATTTTCATTGGGTTTT
1 TTTTTCTGAAATACAGAGTTTTCTTC-TCCAT-AATTTTTTTGGAGAGGATTTTCATTGGGTTTT
* *
80460 AATTTTTAAAATTTATCAAATATCATTATTTAATTCATATTAAAACGGTTTTCAAAAATTCATTC
64 AATTTTTAAAATTTATCAAATATCATTATTTAATTAATATTAAAACAGTTTTCAAAAATTCATTC
* *
80525 ATTTTTATGAGTTTTTAAATTTTTTTCTTGAAA
129 ATTTTCATGAGTTTTTAAATTTTTTCCTTGAAA
80558 TTTTTCTTTT
Statistics
Matches: 145, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
190 113 0.78
191 32 0.22
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (192 bp):
TTTTTCTGAAATACAGAGTTTTCTTCTCCATAATTTTTTTGGAGAGGATTTTCATTGGGTTTTAA
TTTTTAAAATTTATCAAATATCATTATTTAATTAATATTAAAACAGTTTTCAAAAATTCATTCAT
TTTCATGAGTTTTTAAATTTTTTCCTTGAAACTCTTTTTTTTTAAATACAGAGTTTTTCTTT
Found at i:80793 original size:2 final size:2
Alignment explanation
Indices: 80786--80825 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
80776 CAAATCAGAT
*
80786 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
80826 ACACACACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:82351 original size:163 final size:162
Alignment explanation
Indices: 82047--82662 Score: 676
Period size: 163 Copynumber: 3.9 Consensus size: 162
82037 AGATATTTCC
* * *
82047 ATATTAATCATTTTTT-ATTTTTATATATTCCTTTGGGA-TCCGTAGGGATATAAAAGATTTCAA
1 ATATTAATCATTTTTTAATCTTT-TATATTCCTATGGGAGTCCGTAGGGGTATAAAAGATTTCAA
*
82110 AAA-------A--TTTTCGGGTTTCCATTAAGGTATGAAATGATATTTTTCAAAAAATAAATAAA
65 AAACTTTTTTATCTTTTCGGGTTTCCATTAAGGTAGGAAAT-ATATTTTTCAAAAAATAAATAAA
*
82166 TAAAATTATATTAACACTTTCATAATTGAAATAA
129 TAAAATTAAATTAACACTTTCATAATTGAAATAA
82200 ATATTAATCATTTTTTAATCTTTTATATTCCTATGGGAGTCCGTAGGGGTATAAAAGATTTCAAA
1 ATATTAATCATTTTTTAATCTTTTATATTCCTATGGGAGTCCGTAGGGGTATAAAAGATTTCAAA
* *
82265 AACTTTTTGTATTTTTTCGGGTTTCCATTAAGGTAGGAAATGGTATTTTTC-AAAAATAAATAAA
66 AACTTTTT-TATCTTTTCGGGTTTCCATTAAGGTAGGAAAT-ATATTTTTCAAAAAATAAATAAA
82329 TAAAATTAAATTAACACTTTCATAATTGAAATAA
129 TAAAATTAAATTAACACTTTCATAATTGAAATAA
* * * * *
82363 ATATCAATCATTTTCTAATCTTTTATATTCCTATGGGGGCCCGTAGGGATATAAAAGATTTCAAA
1 ATATTAATCATTTTTTAATCTTTTATATTCCTATGGGAGTCCGTAGGGGTATAAAAGATTTCAAA
* ** ** * *
82428 AAGTTTTCTTATCTTTTCAAGTTTCCATTACTGTACGAAAATATATTTTTC-AAAAACAAATAAA
66 AACTTTT-TTATCTTTTCGGGTTTCCATTAAGGTA-GGAAATATATTTTTCAAAAAATAAATAAA
** * * * **
82492 TAAAATTAAGCTAATACTTTTATAACTGAGAGGAA
129 TAAAATTAAATTAACACTTTCATAATTGA-AATAA
* * * * *
82527 CT-TTAAT--TTTTTT-ATCTTTTGTATTCCTATAGGGA-TTCGTAAGGGTATAAAAGATTTTAA
1 ATATTAATCATTTTTTAATCTTTTATATTCCTAT-GGGAGTCCGTAGGGGTATAAAAGATTTCAA
* * * * * *
82587 AAACTTTTCCTATCTTTTCGGGCTTCCATTAAGGTACGAAATAAAATTTTCAAAAAAAAAATAAA
65 AAACTTTT-TTATCTTTTCGGGTTTCCATTAAGGTAGGAAATATATTTTTCAAAAAATAAATAAA
82652 -AAATATTAAAT
129 TAAA-ATTAAAT
82663 AAATATTAAA
Statistics
Matches: 394, Mismatches: 51, Indels: 29
0.83 0.11 0.06
Matches are distributed among these distances:
153 30 0.08
154 32 0.08
159 14 0.04
160 82 0.21
161 8 0.02
162 1 0.00
163 181 0.46
164 46 0.12
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (162 bp):
ATATTAATCATTTTTTAATCTTTTATATTCCTATGGGAGTCCGTAGGGGTATAAAAGATTTCAAA
AACTTTTTTATCTTTTCGGGTTTCCATTAAGGTAGGAAATATATTTTTCAAAAAATAAATAAATA
AAATTAAATTAACACTTTCATAATTGAAATAA
Found at i:82666 original size:11 final size:11
Alignment explanation
Indices: 82648--82677 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
82638 AAAAAAAAAA
82648 TAAA-AAATAT
1 TAAATAAATAT
82658 TAAATAAATAT
1 TAAATAAATAT
82669 TAAATAAAT
1 TAAATAAAT
82678 TCTTTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATAAATAT
Found at i:87515 original size:81 final size:79
Alignment explanation
Indices: 87430--87706 Score: 238
Period size: 81 Copynumber: 3.4 Consensus size: 79
87420 TTGGGGTCAA
*
87430 AGTATCCCCTCAAAAATGGTGGGGTTGGAGTATC-CCAAAGATGTTAAAATTTGGTGTTTTGGAA
1 AGTATCCCCTCAAAAATGGTGGGGTTGGAGTATCTCCAGAGATG--AAAATTTGGTGTTTTGGAA
*
87494 GTAAAAAAAAGGGCTAG
64 -TAAAAAAAAGGGATAG
* * * * * * * *
87511 AGTATCTCCTTAGAAATGGCAGGGG-TGGAGTATCTCCTGGGATGAAAGAAATTTGATGTTTAGG
1 AGTATCCCCTCAAAAATGG-TGGGGTTGGAGTATCTCCAGAGATG--A-AAATTTGGTGTTTTGG
* * *
87575 AA-ATAAAAACGGGATTGG
62 AATAAAAAAAAGGGA-TAG
* * *
87593 AGTATCCTCTTAGAAATGGTGGGGTTGGAGTATCTCCAGAGATGAAAATTTTGGTGTTTTGAGAA
1 AGTATCCCCTCAAAAATGGTGGGGTTGGAGTATCTCCAGAGATGAAAA-TTTGGTGTTTTG-GAA
* *
87658 -ATAAAAACGAGGATAG
64 TAAAAAAAAG-GGATAG
* * *
87674 AGTATCCCCTCGAAAATGATAGGGTTGGAGTAT
1 AGTATCCCCTCAAAAATGGTGGGGTTGGAGTAT
87707 ACCATGAGAA
Statistics
Matches: 159, Mismatches: 29, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
79 3 0.02
80 11 0.07
81 79 0.50
82 50 0.31
83 16 0.10
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (79 bp):
AGTATCCCCTCAAAAATGGTGGGGTTGGAGTATCTCCAGAGATGAAAATTTGGTGTTTTGGAATA
AAAAAAAGGGATAG
Found at i:87784 original size:109 final size:109
Alignment explanation
Indices: 87604--87815 Score: 300
Period size: 109 Copynumber: 1.9 Consensus size: 109
87594 GTATCCTCTT
* * * *
87604 AGAAATGGTGGGGTTGGAGTATCTCCAGAGATGAAAATTTTGGTGTTTTGAGAAATAAAAACGAG
1 AGAAATGGTGGGATTGGAGTATCTCCAGAGATGAAAAATTTGGTGTTTTCAGAAATAAAAAAGAG
* *
87669 GATAGAGTATCCCCTCGAAAATGATAGGGTTGGAGTATACCATG
66 GATAGAGTATCCCCTCAAAAATGATAGGGTTAGAGTATACCATG
* * *
87713 AGAAATGGTGGGATTGGAGTATTTCCTGAGATGAAAAATTTGGTG-TTTCAGAAATAAAAAATAG
1 AGAAATGGTGGGATTGGAGTATCTCCAGAGATGAAAAATTTGGTGTTTTCAGAAATAAAAAAGA-
* * *
87777 GGTTAGAGTATCCTCTCAAAAATTATAGGGTTAGAGTAT
65 GGATAGAGTATCCCCTCAAAAATGATAGGGTTAGAGTAT
87816 CCCCGAGATG
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
108 15 0.17
109 75 0.83
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.29
Consensus pattern (109 bp):
AGAAATGGTGGGATTGGAGTATCTCCAGAGATGAAAAATTTGGTGTTTTCAGAAATAAAAAAGAG
GATAGAGTATCCCCTCAAAAATGATAGGGTTAGAGTATACCATG
Found at i:87874 original size:77 final size:79
Alignment explanation
Indices: 87740--87909 Score: 218
Period size: 77 Copynumber: 2.2 Consensus size: 79
87730 AGTATTTCCT
* * *
87740 GAGATGAAAAATTTGGTGTTTCAGAAATAAAAAATAGGGTTAGAGTATCCTCTCAAAAATTATAG
1 GAGATGAAAAATTTGGTATTTAAGAAAT-AAAAATAGGGTTAGAGTATCCTCTCAAAAATGATAG
87805 GGTTAGAGTATCCCC
65 GGTTAGAGTATCCCC
* * * *
87820 GAGATG-AAAATTTGGTATTTAAGAAAT-AAGATGGGGTTAGAGTATTCTTTCAAAAATGATAGG
1 GAGATGAAAAATTTGGTATTTAAGAAATAAAAATAGGGTTAGAGTATCCTCTCAAAAATGATAGG
* * *
87883 GTTGGAGTATCTCT
66 GTTAGAGTATCCCC
*
87897 GAGATGCAAAATT
1 GAGATGAAAAATT
87910 CGATGTTTTA
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
77 48 0.61
78 6 0.08
79 19 0.24
80 6 0.08
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.31
Consensus pattern (79 bp):
GAGATGAAAAATTTGGTATTTAAGAAATAAAAATAGGGTTAGAGTATCCTCTCAAAAATGATAGG
GTTAGAGTATCCCC
Found at i:90536 original size:21 final size:20
Alignment explanation
Indices: 90465--90538 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
90455 AACATGGTCC
* **
90465 TGTATCGATACATTTTAGACA
1 TGTATCGATACA-TTCACTCA
90486 TGTATCGATACATTCACTCA
1 TGTATCGATACATTCACTCA
*
90506 TGTATCGATACATTCACTTA
1 TGTATCGATACATTCACTCA
*
90526 TTGTGTCGATACA
1 -TGTATCGATACA
90539 AATTATAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 24 0.51
21 23 0.49
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTCACTCA
Found at i:91863 original size:160 final size:160
Alignment explanation
Indices: 91584--91897 Score: 421
Period size: 160 Copynumber: 2.0 Consensus size: 160
91574 CTTTTTGGAC
* *
91584 TTAGCTTTTTCAATGTTAACCAATATAGCAAACTTATCGACAGTCAGGATAACATAATAACTTAA
1 TTAGCCTTTTCAATGTTAACCAATATAGCAAACTCATCGACAGTCAGGATAACATAATAACTTAA
* * * *
91649 TTAGGTCATGTTTATTCCAGTAACATTTATCCATAATGAGACAATAACGTTTCTCTTAGAACAAA
66 TCACGTCATGTTTATTCCAATAACATTTATCCATAATGAGACAACAACGTTTCTCTTAGAACAAA
* *
91714 ACTAACAACCTAGGCGGTGGTGTTTATAAT
131 ACTAACAACCCAGGCGATGGTGTTTATAAT
* * ** * * *
91744 TTAGCCTTTTCAATGTTAAGCAATGTAGTGAACTCATTGATAGTCAGGATAACATAATTACTTAA
1 TTAGCCTTTTCAATGTTAACCAATATAGCAAACTCATCGACAGTCAGGATAACATAATAACTTAA
* * * * * * *
91809 TCACGTCATGTTTTTTCTAATAACATTTATCCTTAATGAGATAACAAGGTTTCTCTTAGGATAAA
66 TCACGTCATGTTTATTCCAATAACATTTATCCATAATGAGACAACAACGTTTCTCTTAGAACAAA
*
91874 ACTAACAACCCAGGTGATGGTGTT
131 ACTAACAACCCAGGCGATGGTGTT
91898 CATTCGTGGT
Statistics
Matches: 131, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
160 131 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (160 bp):
TTAGCCTTTTCAATGTTAACCAATATAGCAAACTCATCGACAGTCAGGATAACATAATAACTTAA
TCACGTCATGTTTATTCCAATAACATTTATCCATAATGAGACAACAACGTTTCTCTTAGAACAAA
ACTAACAACCCAGGCGATGGTGTTTATAAT
Found at i:103841 original size:21 final size:20
Alignment explanation
Indices: 103809--103849 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
103799 TTTTTGTATT
*
103809 ATTTATTCAATATATATTTA
1 ATTTATTAAATATATATTTA
*
103829 ATTTGATTAAATATTTATTTA
1 ATTT-ATTAAATATATATTTA
103850 GAAAAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTATTAAATATATATTTA
Found at i:105682 original size:26 final size:27
Alignment explanation
Indices: 105645--105720 Score: 100
Period size: 26 Copynumber: 2.9 Consensus size: 27
105635 TAATGAGTTT
* *
105645 AAAAATAAGGTTGGAGTTTCCCCTT-A
1 AAAAATAGGGTTGGAGTATCCCCTTGA
* *
105671 AAAAATGGGGTTGGAGTATCCCTTTGA
1 AAAAATAGGGTTGGAGTATCCCCTTGA
*
105698 AAGAATAGGGTTGGAGTATCCCC
1 AAAAATAGGGTTGGAGTATCCCC
105721 GATGAATAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
26 21 0.50
27 21 0.50
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (27 bp):
AAAAATAGGGTTGGAGTATCCCCTTGA
Found at i:108221 original size:20 final size:21
Alignment explanation
Indices: 108192--108243 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
108182 ATAGAGTCTA
*
108192 GTATCGATACATTCACTT-AT
1 GTATCGATACATTAACTTGAT
* *
108212 GTATCAATACATTAACTTGTT
1 GTATCGATACATTAACTTGAT
108233 GTATCGATACA
1 GTATCGATACA
108244 AATTGTAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
GTATCGATACATTAACTTGAT
Found at i:114813 original size:20 final size:20
Alignment explanation
Indices: 114768--114819 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
114758 GTAGCCAAAC
* **
114768 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACAAAAAA
114788 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
114807 TTGTATCGATACA
1 TTGTATCGATACA
114820 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:117064 original size:21 final size:22
Alignment explanation
Indices: 117018--117062 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
117008 TTGCAAGATG
117018 AAATAAAGAAGTTAGCTAATGA
1 AAATAAAGAAGTTAGCTAATGA
*
117040 AAATAATG-AGTTAGCTAA-GA
1 AAATAAAGAAGTTAGCTAATGA
117060 AAA
1 AAA
117063 ATGAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (22 bp):
AAATAAAGAAGTTAGCTAATGA
Found at i:118886 original size:15 final size:15
Alignment explanation
Indices: 118866--118896 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
118856 TAAAAATCTC
*
118866 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
118881 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
118896 C
1 C
118897 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:120993 original size:13 final size:13
Alignment explanation
Indices: 120975--121000 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
120965 ACAGTTTTCC
120975 TTGTATCGATACA
1 TTGTATCGATACA
120988 TTGTATCGATACA
1 TTGTATCGATACA
121001 GGGTGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:121152 original size:20 final size:17
Alignment explanation
Indices: 121106--121153 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 17
121096 AACTTCAAAA
121106 TTCTTCAAATCTTGTTT
1 TTCTTCAAATCTTGTTT
121123 TTCACTTCAAATTACTTCGTTT
1 TT--CTTCAAA-T-CTT-GTTT
121145 TTCTTCAAA
1 TTCTTCAAA
121154 ACCAGCATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 2 0.08
19 7 0.27
20 8 0.31
21 3 0.12
22 6 0.23
ACGTcount: A:0.23, C:0.21, G:0.04, T:0.52
Consensus pattern (17 bp):
TTCTTCAAATCTTGTTT
Found at i:122878 original size:38 final size:40
Alignment explanation
Indices: 122818--122902 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 40
122808 AACGGGGGAG
* ** *
122818 TTAAAGGGGAGAATGCGTAAA-TTGCTACAATTATCTT-A
1 TTAAGGGGGAGAATGCACAAATTTGCTAAAATTATCTTGA
* * *
122856 TTAAGGGGGAGAATGTACAAATTTGTTAAAATTATTTTGA
1 TTAAGGGGGAGAATGCACAAATTTGCTAAAATTATCTTGA
122896 TTAAGGG
1 TTAAGGG
122903 AGAAATAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
38 17 0.45
39 13 0.34
40 8 0.21
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (40 bp):
TTAAGGGGGAGAATGCACAAATTTGCTAAAATTATCTTGA
Found at i:126704 original size:13 final size:13
Alignment explanation
Indices: 126686--126711 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
126676 CAATTTTTTG
126686 TGTATCGATACAT
1 TGTATCGATACAT
126699 TGTATCGATACAT
1 TGTATCGATACAT
126712 ACTTGTTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:127431 original size:21 final size:21
Alignment explanation
Indices: 127405--127466 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
127395 CTCTCCTTTG
* *
127405 TCTCCCCCGTTTATTAA-TAAA
1 TCTCCCCC-TTAATCAAGTAAA
127426 TCTCCCCCTTAATCAAGTAAA
1 TCTCCCCCTTAATCAAGTAAA
127447 TCTCCCCCTTAATCAAGTAA
1 TCTCCCCCTTAATCAAGTAA
127467 TTCTGTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.16
21 32 0.84
ACGTcount: A:0.31, C:0.32, G:0.05, T:0.32
Consensus pattern (21 bp):
TCTCCCCCTTAATCAAGTAAA
Found at i:127477 original size:29 final size:29
Alignment explanation
Indices: 127442--127498 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
127432 CCTTAATCAA
127442 GTAAATCTCCCCCTTAATCAAGTAATTCT
1 GTAAATCTCCCCCTTAATCAAGTAATTCT
127471 GTAAATCTCCCCCTTAATCAAGTAATTC
1 GTAAATCTCCCCCTTAATCAAGTAATTC
127499 ATATCAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.33
Consensus pattern (29 bp):
GTAAATCTCCCCCTTAATCAAGTAATTCT
Found at i:129310 original size:13 final size:13
Alignment explanation
Indices: 129292--129330 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
129282 ATAATCACCC
*
129292 TGTATCGATACAG
1 TGTATCGATACAA
129305 TGTATCGATACAA
1 TGTATCGATACAA
129318 TGTATCGATACAA
1 TGTATCGATACAA
129331 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:129341 original size:20 final size:20
Alignment explanation
Indices: 129316--129394 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
129306 GTATCGATAC
129316 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
129336 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
129361 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
129381 CATGTATCGATACA
1 AATGTATCGATACA
129395 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:131429 original size:15 final size:15
Alignment explanation
Indices: 131409--131439 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
131399 ATTTCGTTTG
*
131409 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
131424 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
131439 G
1 G
131440 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:133272 original size:21 final size:21
Alignment explanation
Indices: 133243--133287 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
133233 AAGTTTTCAT
*
133243 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
133263 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
133285 TTT
1 TTT
133288 CAATTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:135525 original size:13 final size:13
Alignment explanation
Indices: 135507--135532 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
135497 CAATTTTTTG
135507 TGTATCGATACAT
1 TGTATCGATACAT
135520 TGTATCGATACAT
1 TGTATCGATACAT
135533 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:136652 original size:33 final size:33
Alignment explanation
Indices: 136615--136684 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
136605 AGCCATTAGG
** * *
136615 ACAATATATCAATACTTTTTACTATGTATCGAT
1 ACAATATATCAATACAATATACCATGTATCGAT
* *
136648 ACAATGTATCGATACAATATACCATGTATCGAT
1 ACAATATATCAATACAATATACCATGTATCGAT
136681 ACAA
1 ACAA
136685 ACAGTGGCAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (33 bp):
ACAATATATCAATACAATATACCATGTATCGAT
Found at i:136674 original size:20 final size:20
Alignment explanation
Indices: 136646--136684 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
136636 CTATGTATCG
136646 ATACAATGTATCGATACAAT
1 ATACAATGTATCGATACAAT
*
136666 ATACCATGTATCGATACAA
1 ATACAATGTATCGATACAA
136685 ACAGTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (20 bp):
ATACAATGTATCGATACAAT
Found at i:136682 original size:13 final size:13
Alignment explanation
Indices: 136638--136665 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
136628 ACTTTTTACT
136638 ATGTATCGATACA
1 ATGTATCGATACA
136651 ATGTATCGATACA
1 ATGTATCGATACA
136664 AT
1 AT
136666 ATACCATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:136758 original size:19 final size:19
Alignment explanation
Indices: 136713--136768 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
136703 TTGCCAGTTT
*
136713 CATGTATCGATACAATAGAG
1 CATGTATCGATACAAT-GAA
*
136733 TATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
136752 CATGTATCCATACAATG
1 CATGTATCGATACAATG
136769 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:139382 original size:13 final size:13
Alignment explanation
Indices: 139364--139400 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
139354 ATAGTAACTT
139364 TGTATCAATACAA
1 TGTATCAATACAA
*
139377 TGTATCAATATAA
1 TGTATCAATACAA
*
139390 TGTATCGATAC
1 TGTATCAATAC
139401 TTAGAACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.35
Consensus pattern (13 bp):
TGTATCAATACAA
Found at i:145635 original size:13 final size:13
Alignment explanation
Indices: 145617--145643 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
145607 ACAATTGAGT
145617 ATGTATCGATACA
1 ATGTATCGATACA
145630 ATGTATCGATACA
1 ATGTATCGATACA
145643 A
1 A
145644 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:148651 original size:13 final size:13
Alignment explanation
Indices: 148633--148658 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
148623 CAATTTTTGG
148633 TGTATCGATACAT
1 TGTATCGATACAT
148646 TGTATCGATACAT
1 TGTATCGATACAT
148659 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:148670 original size:32 final size:33
Alignment explanation
Indices: 148613--148676 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
148603 TACAAGCCAA
**
148613 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
148646 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
148677 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:148683 original size:19 final size:18
Alignment explanation
Indices: 148613--148683 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
148603 TACAAGCCAA
148613 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
148633 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
148646 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
148665 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
148684 CTACTACCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:151069 original size:13 final size:13
Alignment explanation
Indices: 151051--151076 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
151041 ATAATCCTCC
151051 TGTATCGATACAA
1 TGTATCGATACAA
151064 TGTATCGATACAA
1 TGTATCGATACAA
151077 AGAAAAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:158229 original size:13 final size:13
Alignment explanation
Indices: 158211--158236 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
158201 CAATTTTTTG
158211 TGTATCGATACAT
1 TGTATCGATACAT
158224 TGTATCGATACAT
1 TGTATCGATACAT
158237 ATTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:158247 original size:32 final size:33
Alignment explanation
Indices: 158191--158254 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
158181 TACAACCCAA
*
158191 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATATTTTGTGTATCGATACAT
158224 TGTATCGATAC-ATATTTTGTGTATCGATACA
1 TGTATCGATACAATATTTTGTGTATCGATACA
158255 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATATTTTGTGTATCGATACAT
Found at i:158248 original size:19 final size:19
Alignment explanation
Indices: 158191--158254 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
158181 TACAACCCAA
*
158191 TGTATCGATACAATTTTTTG
1 TGTATCGATAC-ATATTTTG
158211 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
158224 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
158243 TGTATCGATACA
1 TGTATCGATACA
158255 AGTTTGGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
18 1 0.03
19 12 0.32
20 11 0.30
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:160330 original size:21 final size:20
Alignment explanation
Indices: 160301--160343 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
160291 GACTAGTGTG
* *
160301 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
160322 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
160342 GG
1 GG
160344 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:160801 original size:13 final size:13
Alignment explanation
Indices: 160783--160821 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
160773 ATAATCCCCC
*
160783 TGTATCGATACAG
1 TGTATCGATACAA
160796 TGTATCGATACAA
1 TGTATCGATACAA
160809 TGTATCGATACAA
1 TGTATCGATACAA
160822 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:162909 original size:15 final size:15
Alignment explanation
Indices: 162889--162919 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
162879 ATTTCGTTTG
*
162889 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
162904 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
162919 G
1 G
162920 GATATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:164751 original size:21 final size:21
Alignment explanation
Indices: 164722--164766 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
164712 AAGTTTTTAT
*
164722 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
164742 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
164764 TTT
1 TTT
164767 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:166997 original size:13 final size:13
Alignment explanation
Indices: 166979--167004 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
166969 TAATTTTTTG
166979 TGTATCGATACAT
1 TGTATCGATACAT
166992 TGTATCGATACAT
1 TGTATCGATACAT
167005 ATTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:167015 original size:32 final size:33
Alignment explanation
Indices: 166959--167022 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
166949 TACAAGCCAA
*
166959 TGTATCGATATAATTTTTTGTGTATCGATACAT
1 TGTATCGATATAATATTTTGTGTATCGATACAT
*
166992 TGTATCGATA-CATATTTTGTGTATCGATACA
1 TGTATCGATATAATATTTTGTGTATCGATACA
167023 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (33 bp):
TGTATCGATATAATATTTTGTGTATCGATACAT
Found at i:168846 original size:13 final size:13
Alignment explanation
Indices: 168828--168853 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
168818 CAATTTTTGG
168828 TGTATCGATACAT
1 TGTATCGATACAT
168841 TGTATCGATACAT
1 TGTATCGATACAT
168854 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:168865 original size:32 final size:33
Alignment explanation
Indices: 168808--168871 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
168798 TACAAGCCAA
**
168808 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
168841 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
168872 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:168878 original size:19 final size:18
Alignment explanation
Indices: 168808--168878 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
168798 TACAAGCCAA
168808 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
168828 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
168841 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
168860 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
168879 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:170960 original size:21 final size:20
Alignment explanation
Indices: 170931--170973 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
170921 GGCTAGTGTG
*
170931 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
170952 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
170972 GG
1 GG
170974 TGGTGCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:177621 original size:13 final size:13
Alignment explanation
Indices: 177603--177628 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
177593 CAATTTTTGG
177603 TGTATCGATACAT
1 TGTATCGATACAT
177616 TGTATCGATACAT
1 TGTATCGATACAT
177629 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:177640 original size:32 final size:33
Alignment explanation
Indices: 177583--177646 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
177573 TACAAGCCAA
**
177583 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
177616 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
177647 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:177653 original size:19 final size:18
Alignment explanation
Indices: 177583--177653 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
177573 TACAAGCCAA
177583 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
177603 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
177616 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
177635 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
177654 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:179246 original size:19 final size:20
Alignment explanation
Indices: 179209--179246 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
179199 AATTTTATTT
179209 ATTTTATTTATTGATAAATA
1 ATTTTATTTATTGATAAATA
*
179229 ATTTTATTT-TTTATAAAT
1 ATTTTATTTATTGATAAAT
179247 TTAAACAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
ATTTTATTTATTGATAAATA
Found at i:179355 original size:32 final size:31
Alignment explanation
Indices: 179308--179374 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
179298 ACTTAAATAA
* * *
179308 TAATTTTTTTTTATATATTAACAAATTATTT
1 TAATTTTATTTTATATATGAACAAATAATTT
*
179339 TAATTTTAATTTTATATATGAATAAATAATTT
1 TAATTTT-ATTTTATATATGAACAAATAATTT
179371 TAAT
1 TAAT
179375 ATCCGATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 7 0.23
32 24 0.77
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (31 bp):
TAATTTTATTTTATATATGAACAAATAATTT
Found at i:185587 original size:47 final size:47
Alignment explanation
Indices: 185518--185615 Score: 196
Period size: 47 Copynumber: 2.1 Consensus size: 47
185508 ATCTGCATTA
185518 GCCTATCACATGTGTTATGTATGTTTGGCAGATAGATGAAAGGGCAT
1 GCCTATCACATGTGTTATGTATGTTTGGCAGATAGATGAAAGGGCAT
185565 GCCTATCACATGTGTTATGTATGTTTGGCAGATAGATGAAAGGGCAT
1 GCCTATCACATGTGTTATGTATGTTTGGCAGATAGATGAAAGGGCAT
185612 GCCT
1 GCCT
185616 CTGTATGTGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.32
Consensus pattern (47 bp):
GCCTATCACATGTGTTATGTATGTTTGGCAGATAGATGAAAGGGCAT
Found at i:188590 original size:45 final size:45
Alignment explanation
Indices: 188569--188747 Score: 272
Period size: 45 Copynumber: 4.0 Consensus size: 45
188559 CCATTTAATA
* *
188569 CAAACTAAAAATCTATATAAACTTAAACCCAAACCCAATTAAAAT
1 CAAATTAAAAATCTATATAAACTTAAACTCAAACCCAATTAAAAT
* *
188614 CCAATTAAAAATTTATATAAACTTAAACTCAAACCCAATTAAAAT
1 CAAATTAAAAATCTATATAAACTTAAACTCAAACCCAATTAAAAT
*
188659 CTAATTAAAAATCTATATAAACTTAAACTCAAACCCAATTAAAAT
1 CAAATTAAAAATCTATATAAACTTAAACTCAAACCCAATTAAAAT
*
188704 CTAAA-TAAAAATTTATATAAACTTAAA-TCCAAACCCAATTAAAA
1 C-AAATTAAAAATCTATATAAACTTAAACT-CAAACCCAATTAAAA
188748 AAATAAAGTT
Statistics
Matches: 124, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
44 1 0.01
45 121 0.98
46 2 0.02
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (45 bp):
CAAATTAAAAATCTATATAAACTTAAACTCAAACCCAATTAAAAT
Found at i:188639 original size:90 final size:91
Alignment explanation
Indices: 188541--188747 Score: 294
Period size: 90 Copynumber: 2.3 Consensus size: 91
188531 AAATATAAAT
* * * * *
188541 TAAACTTAAAAGTTAAGCCCATTTAATA-CAAACTAAAAATCTATATAAACTTAAACCCAAACCC
1 TAAACTTAAAACTCAAACCCAATTAAAATCAAACTAAAAATCTATATAAACTTAAACCCAAACCC
*
188605 AATTAAAATCCAATTAAAAATTTATA
66 AATTAAAATCCAAATAAAAATTTATA
* * *
188631 TAAACTT-AAACTCAAACCCAATTAAAATCTAATTAAAAATCTATATAAACTTAAACTCAAACCC
1 TAAACTTAAAACTCAAACCCAATTAAAATCAAACTAAAAATCTATATAAACTTAAACCCAAACCC
*
188695 AATTAAAATCTAAATAAAAATTTATA
66 AATTAAAATCCAAATAAAAATTTATA
*
188721 TAAACTTAAATC-CAAACCCAATTAAAA
1 TAAACTTAAAACTCAAACCCAATTAAAA
188748 AAATAAAGTT
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
89 15 0.14
90 86 0.83
91 3 0.03
ACGTcount: A:0.54, C:0.18, G:0.01, T:0.28
Consensus pattern (91 bp):
TAAACTTAAAACTCAAACCCAATTAAAATCAAACTAAAAATCTATATAAACTTAAACCCAAACCC
AATTAAAATCCAAATAAAAATTTATA
Found at i:189323 original size:16 final size:19
Alignment explanation
Indices: 189280--189323 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
189270 TATTCTATCT
189280 TAATAATATTAGTATAACA
1 TAATAATATTAGTATAACA
*
189299 TAATTATATTA-TATAA-A
1 TAATAATATTAGTATAACA
189316 T-ATAATAT
1 TAATAATAT
189324 AAATATACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.26
17 2 0.09
18 5 0.22
19 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TAATAATATTAGTATAACA
Found at i:189402 original size:47 final size:45
Alignment explanation
Indices: 189298--189415 Score: 123
Period size: 47 Copynumber: 2.6 Consensus size: 45
189288 TTAGTATAAC
* * * *
189298 ATAATTATATTATAT-AAATATAATATAAATATACAATTTTTTAAA
1 ATAATTATAATATATAAAAT-TTATATAAAAATAAAATTTTTTAAA
* *
189343 ATTAA-TATAATATATTAAAATTTATATAAAAATAAAATATTTTTTAT
1 A-TAATTATAATATA-TAAAATTTATATAAAAATAAAAT-TTTTTAAA
189390 ATAATTATAATATAATAAAATTTATA
1 ATAATTATAATAT-ATAAAATTTATA
189416 AATATAAAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
45 9 0.15
46 21 0.34
47 30 0.49
48 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (45 bp):
ATAATTATAATATATAAAATTTATATAAAAATAAAATTTTTTAAA
Found at i:189413 original size:25 final size:24
Alignment explanation
Indices: 189345--189427 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 24
189335 TTTTTAAAAT
*
189345 TAATATAATATATTAAAATTTATA
1 TAATATAATATAATAAAATTTATA
* ***
189369 TAA-A-AATAAAATATTTTTTATA
1 TAATATAATATAATAAAATTTATA
189391 TAATTATAATATAATAAAATTTATA
1 TAA-TATAATATAATAAAATTTATA
*
189416 -AATATAAAATAA
1 TAATATAATATAA
189428 ATATACGAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
22 16 0.35
23 10 0.22
24 6 0.13
25 14 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAATATAATATAATAAAATTTATA
Found at i:189424 original size:15 final size:17
Alignment explanation
Indices: 189394--189425 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
189384 TTTTATATAA
189394 TTATAATATAATAAAAT
1 TTATAATATAATAAAAT
189411 TTATAA-AT-ATAAAAT
1 TTATAATATAATAAAAT
189426 AAATATACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTATAATATAATAAAAT
Found at i:189670 original size:15 final size:15
Alignment explanation
Indices: 189652--189681 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
189642 TATTTTATCT
189652 TTATAAATTTAAATA
1 TTATAAATTTAAATA
*
189667 TTATGAATTTAAATA
1 TTATAAATTTAAATA
189682 ATTTATATAT
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TTATAAATTTAAATA
Found at i:189847 original size:12 final size:12
Alignment explanation
Indices: 189805--189847 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
189795 ATTCAAAGTC
189805 TATTTATATTTT
1 TATTTATATTTT
* *
189817 TAGTTATAATTT
1 TATTTATATTTT
*
189829 AATTTTATATTTT
1 TA-TTTATATTTT
189842 TATTTA
1 TATTTA
189848 AAAAAATAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TATTTATATTTT
Found at i:189860 original size:25 final size:24
Alignment explanation
Indices: 189806--189860 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
189796 TTCAAAGTCT
* **
189806 ATTTATATTTTTAGTTATAATTTA
1 ATTTATATTTTTAGTTAAAAAATA
*
189830 ATTTTATATTTTTATTTAAAAAAATA
1 A-TTTATATTTTTAGTT-AAAAAATA
189856 ATTTA
1 ATTTA
189861 ATAAATCGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 18 0.72
26 6 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
ATTTATATTTTTAGTTAAAAAATA
Found at i:189923 original size:17 final size:17
Alignment explanation
Indices: 189895--189937 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
189885 GAATTCTATT
189895 AATAATATTCGAATAATA
1 AATAA-ATTCGAATAATA
**
189913 AATAAATTCGAATTTTA
1 AATAAATTCGAATAATA
189930 AATAAATT
1 AATAAATT
189938 AAGCAAATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (17 bp):
AATAAATTCGAATAATA
Found at i:190005 original size:26 final size:26
Alignment explanation
Indices: 189976--190029 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
189966 CAAATCTCAA
189976 AAATTCTCCAAAAAATCATGAAATTT
1 AAATTCTCCAAAAAATCATGAAATTT
** *
190002 AAATTCTCCAAAAGTTCCTGAAATTT
1 AAATTCTCCAAAAAATCATGAAATTT
190028 AA
1 AA
190030 CACAATGATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (26 bp):
AAATTCTCCAAAAAATCATGAAATTT
Found at i:194127 original size:21 final size:21
Alignment explanation
Indices: 194075--194127 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
194065 CAGTTGCAGC
*
194075 AATA-TTTTATGTAAATCTAT
1 AATATTTTTATGTAAATCGAT
* * *
194095 AGTATTTGTATGTAACTCGAT
1 AATATTTTTATGTAAATCGAT
*
194116 AATGTTTTTATG
1 AATATTTTTATG
194128 CAATTTGTTA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (21 bp):
AATATTTTTATGTAAATCGAT
Found at i:194654 original size:17 final size:17
Alignment explanation
Indices: 194607--194655 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
194597 CATGATTCTT
*
194607 TACACAAACATTACCTA
1 TACACAAACATTATCTA
194624 TA-AC--ACA-TAT-TA
1 TACACAAACATTATCTA
194636 TACACAAACATTATCTA
1 TACACAAACATTATCTA
194653 TAC
1 TAC
194656 TCTAATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 10
0.70 0.03 0.27
Matches are distributed among these distances:
12 4 0.15
13 4 0.15
14 3 0.12
15 3 0.12
16 5 0.19
17 7 0.27
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (17 bp):
TACACAAACATTATCTA
Found at i:194820 original size:21 final size:21
Alignment explanation
Indices: 194788--194858 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
194778 AAGAACTCAT
*
194788 TCTT-TTTT-AGAGAAATTAA
1 TCTTCTTTTAAGAGAGATTAA
* *
194807 TCATCTTTTAAGAGGGATTAA
1 TCTTCTTTTAAGAGAGATTAA
*
194828 TCTTCTTTTAAGAGAGATCAA
1 TCTTCTTTTAAGAGAGATTAA
194849 TCTTCTTTTA
1 TCTTCTTTTA
194859 TTAAGGAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
19 3 0.07
20 4 0.09
21 37 0.84
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (21 bp):
TCTTCTTTTAAGAGAGATTAA
Found at i:196268 original size:13 final size:13
Alignment explanation
Indices: 196250--196274 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
196240 CATAAAATGT
196250 TGTATCGATACAA
1 TGTATCGATACAA
196263 TGTATCGATACA
1 TGTATCGATACA
196275 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:196272 original size:33 final size:33
Alignment explanation
Indices: 196230--196299 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
196220 TTCAACGATT
196230 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
196263 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
196296 TGTA
1 TGTA
196300 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Done.