Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1350
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: 99924
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:10657 original size:16 final size:17
Alignment explanation
Indices: 10636--10668 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
10626 TATTTGTCAA
10636 ACCCGCCAGTG-TTGGT
1 ACCCGCCAGTGCTTGGT
*
10652 ACCCGCCGGTGCTTGGT
1 ACCCGCCAGTGCTTGGT
10669 CGTCCTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.09, C:0.33, G:0.33, T:0.24
Consensus pattern (17 bp):
ACCCGCCAGTGCTTGGT
Found at i:12915 original size:11 final size:11
Alignment explanation
Indices: 12899--12950 Score: 68
Period size: 11 Copynumber: 4.5 Consensus size: 11
12889 CTTTACACCC
12899 AAAAAAAAACA
1 AAAAAAAAACA
12910 AAAAAAAAACCAA
1 AAAAAAAAA-C-A
12923 AACAAAAAAACA
1 AA-AAAAAAACA
*
12935 AAAAAAAAAGA
1 AAAAAAAAACA
12946 AAAAA
1 AAAAA
12951 TAGCAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
11 22 0.59
12 4 0.11
13 4 0.11
14 7 0.19
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:12916 original size:12 final size:12
Alignment explanation
Indices: 12899--12943 Score: 72
Period size: 12 Copynumber: 3.7 Consensus size: 12
12889 CTTTACACCC
12899 AAAAAAAAACAA
1 AAAAAAAAACAA
*
12911 AAAAAAAACCAA
1 AAAAAAAAACAA
12923 AACAAAAAAACAA
1 AA-AAAAAAACAA
12936 AAAAAAAA
1 AAAAAAAA
12944 GAAAAAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 19 0.63
13 11 0.37
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:12949 original size:25 final size:25
Alignment explanation
Indices: 12901--12949 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
12891 TTACACCCAA
*
12901 AAAAAAACAAAAAAAAAACCAAAAC
1 AAAAAAACAAAAAAAAAACAAAAAC
*
12926 AAAAAAACAAAAAAAAAAGAAAAA
1 AAAAAAACAAAAAAAAAACAAAAA
12950 ATAGCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (25 bp):
AAAAAAACAAAAAAAAAACAAAAAC
Found at i:12960 original size:1 final size:1
Alignment explanation
Indices: 12899--12950 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
12889 CTTTACACCC
* ** * * *
12899 AAAAAAAAACAAAAAAAAAACCAAAACAAAAAAACAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12951 TAGCAAAAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:14525 original size:28 final size:28
Alignment explanation
Indices: 14195--15145 Score: 734
Period size: 28 Copynumber: 32.8 Consensus size: 28
14185 TCCCTTTTTG
14195 CAAAGCCCACAAGCTCAGTGGCACTCCTTT
1 CAAAGCCCACAAG-TCAGTGGCACT-CTTT
**
14225 CAAAGCACACAACCCAGAGAGAGTGGCACTCTTTT
1 CAAAGC-C-C-A--CA-AGTCAGTGGCACTC-TTT
* *
14260 CAAAAAGCCCACAAGTCCGTGGCTCT-TTT
1 C--AAAGCCCACAAGTCAGTGGCACTCTTT
* *
14289 CAAAGCCCACACGTCAGTGGCAACCCTTT
1 CAAAGCCCACAAGTCAGTGGC-ACTCTTT
*
14318 CAAAAG-CCACAAGTCATTGCGCCACTACTTT
1 C-AAAGCCCACAAGTCAGTG-G-CACT-CTTT
* * * *
14349 TAAAACCCACCAA-TCAG-GGAACTATTTT
1 CAAAGCCCA-CAAGTCAGTGGCACT-CTTT
* * ** *
14377 CCAAGCCCACCAAGTCTGTGGCAAACCTT
1 CAAAGCCCA-CAAGTCAGTGGCACTCTTT
* * * *
14406 CAAAGCCCAAAAATCTCG-GGCACCCTTT
1 CAAAGCCCACAAGTC-AGTGGCACTCTTT
*
14434 CAATAGCCCACAAGTCCGTGGCATCTCCTTT
1 CAA-AGCCCACAAGTCAGTGGCA-CT-CTTT
*
14465 CAAAGCCCACAAGTCCGTGCGCACTCTTT
1 CAAAGCCCACAAGTCAGTG-GCACTCTTT
*
14494 CAAAGCCAACAAGTCAGTGGCACTCTTT
1 CAAAGCCCACAAGTCAGTGGCACTCTTT
* * *
14522 CAAAAATGCCAAAAAATC-GTGGCACTCTTTT
1 C--AAA-GCCCACAAGTCAGTGGCACTC-TTT
*
14553 CAAAG--CACAAGTTAGTGGCCAC-C-TT
1 CAAAGCCCACAAGTCAGTGG-CACTCTTT
* *
14578 CAAAGCCCACACGTCATGGTGGCACCCTTT
1 CAAAGCCCACAAGTCA--GTGGCACTCTTT
* * * *
14608 CAAAAGACCACAACTCCGTGGCCACCCTTT
1 C-AAAGCCCACAAGTCAGTGG-CACTCTTT
*
14638 C-AAGCCCACAAGTTAGTGGCACTTCTTT
1 CAAAGCCCACAAGTCAGTGGCAC-TCTTT
14666 CAAAAGCCCAC-AGTCAGCGTGGCACTCTTT
1 C-AAAGCCCACAAGTCA--GTGGCACTCTTT
* * *
14696 TAATCGCCCACAA-ACAGTGGCACTCTTTT
1 CAA-AGCCCACAAGTCAGTGGCACTC-TTT
* * * *
14725 CAAAG-CCACCAAGTTAGTGGCCCCCTTCA
1 CAAAGCCCA-CAAGTCAGTGGCACTCTT-T
14754 CAAAGCCCACAAAGTCAG-GGCACTCCTTTT
1 CAAAGCCCAC-AAGTCAGTGGCACT-C-TTT
*
14784 CAACGCCCACAAGTCAGTGGCACTCTTTT
1 CAAAGCCCACAAGTCAGTGGCACTC-TTT
* * *
14813 CAAAGCCCATAAATCAGTGGCAATCTTT
1 CAAAGCCCACAAGTCAGTGGCACTCTTT
*
14841 CAAAGCCCA-AAGTCTAGTGGCACCCTTT
1 CAAAGCCCACAAGTC-AGTGGCACTCTTT
* *
14869 CAAAGCCCA-AAGTTAGTGGCACCCTTT
1 CAAAGCCCACAAGTCAGTGGCACTCTTT
* *
14896 CAGAGCCCACAAGTCAGTGGCACCCTTT
1 CAAAGCCCACAAGTCAGTGGCACTCTTT
* * *
14924 CGAGGCCCACAAGTCAGTGGCAC-CATTG
1 CAAAGCCCACAAGTCAGTGGCACTC-TTT
* *
14952 CGAAGCCCACAATTCAGTGGCACTCTTT
1 CAAAGCCCACAAGTCAGTGGCACTCTTT
*
14980 CAAAGCCCACAAGTCAGTGGCACCCTTT
1 CAAAGCCCACAAGTCAGTGGCACTCTTT
*
15008 TAAAGCCCACAAGTCAGTGGCACTCTTT
1 CAAAGCCCACAAGTCAGTGGCACTCTTT
15036 CAAAGCCCACAAGTCAGTGGCA-TCCTTT
1 CAAAGCCCACAAGTCAGTGGCACT-CTTT
* * *
15064 CAAAGCCCACGAGTTAGTGGCATTCTTT
1 CAAAGCCCACAAGTCAGTGGCACTCTTT
*
15092 CAAAGCCCACGCAAGTCAGTGGCACCCTTT
1 CAAAGCCCA--CAAGTCAGTGGCACTCTTT
* *
15122 TAAAGCCCATGCAAGTCAATGGCA
1 CAAAGCCCA--CAAGTCAGTGGCA
15146 ACCCTTTTCA
Statistics
Matches: 754, Mismatches: 104, Indels: 126
0.77 0.11 0.13
Matches are distributed among these distances:
25 7 0.01
26 4 0.01
27 63 0.08
28 292 0.39
29 145 0.19
30 145 0.19
31 65 0.09
32 6 0.01
33 1 0.00
34 2 0.00
35 16 0.02
36 3 0.00
37 5 0.01
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (28 bp):
CAAAGCCCACAAGTCAGTGGCACTCTTT
Found at i:14994 original size:84 final size:83
Alignment explanation
Indices: 14195--15145 Score: 689
Period size: 88 Copynumber: 10.9 Consensus size: 83
14185 TCCCTTTTTG
**
14195 CAAAGCCCACAAGCTCAGTGGCACTCCTTTCAAAGCACACAACCCAGAGAGAGTGGCACTCTTTT
1 CAAAGCCCACAAG-TCAGTGGCAC-CCTTTCAAAGC-C-C-A--CA-AGTCAGTGGCAC-C-TTT
* *
14260 CAAAAAGCCCACAAGTCCGTGGCTCT-TTT
56 C--AAAGCCCACAAGTCAGTGGCACTCTTT
* * *
14289 CAAAGCCCACACGTCAGTGGCAACCCTTTCAAAAG-CCACAAGTCATTGCGCCACTACTTTTAAA
1 CAAAGCCCACAAGTCAGTGGC-ACCCTTTC-AAAGCCCACAAGTCAGTG-G-CAC--CTTTCAAA
* * *
14353 ACCCACCAA-TCAG-GGAACTATTTT
60 GCCCA-CAAGTCAGTGGCACT-CTTT
* * * * * *
14377 CCAAGCCCACCAAGTCTGTGGCAAACC-TTCAAAGCCCAAAAATCTCG-GGCACCCTTTCAATAG
1 CAAAGCCCA-CAAGTCAGTGGC-ACCCTTTCAAAGCCCACAAGTC-AGTGGCA-CCTTTCAA-AG
*
14440 CCCACAAGTCCGTGGCATCTCCTTT
61 CCCACAAGTCAGTGGCA-CT-CTTT
* * *
14465 CAAAGCCCACAAGTCCGTGCGCACTCTTTCAAAGCCAACAAGTCAGTGGCACTCTTTCAAAAATG
1 CAAAGCCCACAAGTCAGTG-GCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTC--AAA-G
* * *
14530 CCAAAAAATC-GTGGCACTCTTTT
61 CCCACAAGTCAGTGGCACTC-TTT
* *
14553 CAAAG--CACAAGTTAGTGGC-CACC-TTCAAAGCCCACACGTCATGGTGGCACCCTTTCAAAAG
1 CAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCA--GTGGCA-CCTTTC-AAAG
* * * *
14614 ACCACAACTCCGTGGCCACCCTTT
61 CCCACAAGTCAGTGG-CACTCTTT
* * * *
14638 C-AAGCCCACAAGTTAGTGGCACTTCTTTCAAAAGCCCAC-AGTCAGCGTGGCACTCTTTTAATC
1 CAAAGCCCACAAGTCAGTGGCAC-CCTTTC-AAAGCCCACAAGTCA--GTGGCAC-CTTTCAA-A
*
14701 GCCCACAA-ACAGTGGCACTCTTTT
60 GCCCACAAGTCAGTGGCACTC-TTT
* * * *
14725 CAAAG-CCACCAAGTTAGTGGCCCCCTTCACAAAGCCCACAAAGTCAG-GGCACTCCTTTTCAAC
1 CAAAGCCCA-CAAGTCAGTGGCACCCTT-TCAAAGCCCAC-AAGTCAGTGGCA--CC-TTTCAAA
14788 GCCCACAAGTCAGTGGCACTCTTTT
60 GCCCACAAGTCAGTGGCACTC-TTT
* * **
14813 CAAAGCCCATAAATCAGTGGCAATCTTTCAAAGCCCA-AAGTCTAGTGGCACCCTTTCAAAGCCC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTC-AGTGGCA-CCTTTCAAAGCCC
* *
14877 A-AAGTTAGTGGCACCCTTT
64 ACAAGTCAGTGGCACTCTTT
* * * * *
14896 CAGAGCCCACAAGTCAGTGGCACCCTTTCGAGGCCCACAAGTCAGTGGCACCATTGCGAAGCCCA
1 CAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC-TTTCAAAGCCCA
*
14961 CAATTCAGTGGCACTCTTT
65 CAAGTCAGTGGCACTCTTT
*
14980 CAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCA
1 CAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTCAAAGCCCA
15045 CAAGTCAGTGGCA-TCCTTT
65 CAAGTCAGTGGCACT-CTTT
* * ** *
15064 CAAAGCCCACGAGTTAGTGGCATTCTTTCAAAGCCCACGCAAGTCAGTGGCACCCTTTTAAAGCC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGCA-CCTTTCAAAGCC
*
15129 CATGCAAGTCAATGGCA
63 CA--CAAGTCAGTGGCA
15146 ACCCTTTTCA
Statistics
Matches: 699, Mismatches: 98, Indels: 126
0.76 0.11 0.14
Matches are distributed among these distances:
82 2 0.00
83 51 0.07
84 165 0.24
85 41 0.06
86 90 0.13
87 93 0.13
88 167 0.24
89 44 0.06
90 12 0.02
91 1 0.00
92 1 0.00
93 14 0.02
94 18 0.03
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (83 bp):
CAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCAC
AAGTCAGTGGCACTCTTT
Found at i:15699 original size:20 final size:20
Alignment explanation
Indices: 15671--15745 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
15661 TCATACCCTG
15671 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
15691 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
15711 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
15731 ATGTATCGATACATT
1 ATGTATCGATACATT
15746 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:15738 original size:40 final size:39
Alignment explanation
Indices: 15671--15748 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
15661 TCATACCCTG
* *
15671 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
15711 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
15749 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:16684 original size:23 final size:23
Alignment explanation
Indices: 16657--16708 Score: 97
Period size: 22 Copynumber: 2.3 Consensus size: 23
16647 AGCCTTTGAC
16657 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
16680 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
16702 CATGCAT
1 CATGCAT
16709 ATTTAACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.60
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:25507 original size:13 final size:12
Alignment explanation
Indices: 25486--25553 Score: 52
Period size: 13 Copynumber: 5.7 Consensus size: 12
25476 ATAATTTTAA
*
25486 ATATGATATAATT
1 ATATAATATAA-T
25499 ATATAATATAAAT
1 ATATAATAT-AAT
* *
25512 ATAAAAAATAA-
1 ATATAATATAAT
*
25523 ATATAAT-TAAA
1 ATATAATATAAT
25534 ATATAATATTAA-
1 ATATAATA-TAAT
25546 ATATAATA
1 ATATAATA
25554 ACATATTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
10 3 0.07
11 12 0.26
12 10 0.22
13 19 0.41
14 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (12 bp):
ATATAATATAAT
Found at i:25509 original size:30 final size:29
Alignment explanation
Indices: 25462--25551 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 29
25452 ATAACGAGCT
* *
25462 AATA-AATTAAATTTATAATTTTAAATAT-
1 AATATAATTAAA-ATATAATATTAAATATA
* * *
25490 GATATAATTATATAATATAAATATAAAAAATA
1 AATATAATTA-A-AATAT-AATATTAAATATA
25522 AATATAATTAAAATATAATATTAAATATA
1 AATATAATTAAAATATAATATTAAATATA
25551 A
1 A
25552 TAACATATTA
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
28 3 0.06
29 17 0.35
30 9 0.18
31 11 0.22
32 9 0.18
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (29 bp):
AATATAATTAAAATATAATATTAAATATA
Found at i:25512 original size:6 final size:6
Alignment explanation
Indices: 25491--25551 Score: 54
Period size: 6 Copynumber: 10.0 Consensus size: 6
25481 TTTAAATATG
* * *
25491 ATATAA TTATATA ATATAA ATATAAA AAATAA ATATAA TTA-AA ATAT-A
1 ATATAA ATATA-A ATATAA ATAT-AA ATATAA ATATAA ATATAA ATATAA
25539 ATATTAA ATATAA
1 ATA-TAA ATATAA
25552 TAACATATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
5 8 0.18
6 22 0.50
7 14 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAA
Found at i:25553 original size:17 final size:17
Alignment explanation
Indices: 25475--25553 Score: 50
Period size: 17 Copynumber: 5.1 Consensus size: 17
25465 AAATTAAATT
* *
25475 TATAATTTTAAATATGA
1 TATAATATTAAATATAA
25492 TAT-A-ATT--ATATAA
1 TATAATATTAAATATAA
25505 TATAA-ATATAAA-A-AA
1 TATAATAT-TAAATATAA
* *
25520 TA-AATA-TAATTAAAA
1 TATAATATTAAATATAA
25535 TATAATATTAAATATAA
1 TATAATATTAAATATAA
25552 TA
1 TA
25554 ACATATTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
13 11 0.23
14 6 0.12
15 12 0.25
16 6 0.12
17 13 0.27
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (17 bp):
TATAATATTAAATATAA
Found at i:25716 original size:11 final size:11
Alignment explanation
Indices: 25700--25734 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
25690 AGCATACCAA
25700 AATTAAAATAT
1 AATTAAAATAT
*
25711 AATTAAGATAT
1 AATTAAAATAT
25722 AA-TAAAATAT
1 AATTAAAATAT
25732 AAT
1 AAT
25735 ATAATCATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (11 bp):
AATTAAAATAT
Found at i:26047 original size:14 final size:14
Alignment explanation
Indices: 26030--26069 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
26020 ATTAGATTTT
26030 TAAATATAATTATA
1 TAAATATAATTATA
26044 TAAATATAATATATA
1 TAAATATAAT-TATA
26059 TAAA-ATAATTA
1 TAAATATAATTA
26070 AAATATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 2 0.08
14 15 0.60
15 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATATAATTATA
Found at i:26065 original size:11 final size:11
Alignment explanation
Indices: 26041--26090 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
26031 AAATATAATT
* *
26041 ATATAAATATA
1 ATATATATAAA
26052 ATATATATAAA
1 ATATATATAAA
26063 ATA-AT-TAAA
1 ATATATATAAA
26072 ATAT-TATATAA
1 ATATATATA-AA
26083 ATATATAT
1 ATATATAT
26091 TTTTTAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 8 0.24
10 4 0.12
11 18 0.55
12 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATATATATAAA
Found at i:26112 original size:31 final size:30
Alignment explanation
Indices: 26076--26148 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
26066 ATTAAAATAT
* * *
26076 TATATAAA-TATATATTTTTTAAAATTTATA
1 TATATAAATTAT-TAGTTATTAAAATTGATA
*
26106 TAATATAACTTATTAGTTATTAAAATTGATA
1 T-ATATAAATTATTAGTTATTAAAATTGATA
26137 TATAT-AATTATT
1 TATATAAATTATT
26149 TTTGATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 6 0.17
30 5 0.14
31 22 0.61
32 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (30 bp):
TATATAAATTATTAGTTATTAAAATTGATA
Found at i:26157 original size:28 final size:27
Alignment explanation
Indices: 26088--26167 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 27
26078 TATAAATATA
26088 TATTTTT-TAAAATTTATATAATATAACT
1 TATTTTTATAAAA-TTATAT-ATATAACT
*
26116 TATTAGTTATTAAAATTGATATATATAA-T
1 TATT-TTTA-TAAAATT-ATATATATAACT
26145 TATTTTTGATAAAATTAT-TATAT
1 TATTTTT-ATAAAATTATATATAT
26168 GATAAAATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
26 5 0.11
27 2 0.04
28 13 0.29
29 8 0.18
30 8 0.18
31 9 0.20
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (27 bp):
TATTTTTATAAAATTATATATATAACT
Found at i:26162 original size:15 final size:16
Alignment explanation
Indices: 26142--26175 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
26132 TGATATATAT
*
26142 AATTATT-TTTGATAA
1 AATTATTATATGATAA
26157 AATTATTATATGATAA
1 AATTATTATATGATAA
26173 AAT
1 AAT
26176 ACATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
AATTATTATATGATAA
Found at i:29171 original size:1 final size:1
Alignment explanation
Indices: 29121--29160 Score: 80
Period size: 1 Copynumber: 40.0 Consensus size: 1
29111 CTTTGTTTTG
29121 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29161 GATGGGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29173 original size:63 final size:63
Alignment explanation
Indices: 29079--29205 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
29069 AACATATCCC
*
29079 AAAAAAAAAAAAAAAAAGAGATGGGAAAAATGCTTTGTTTTGAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAGATGGGAAAAATGCTTTGTTTTGAAAAAAAAAAAAAAAAAAAAA
29142 AAAAAAAAAAAAAAAAAAAGATGGGAAAAATGCTTTGTTTTGAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAGATGGGAAAAATGCTTTGTTTTGAAAAAAAAAAAAAAAAAAAAA
29205 A
1 A
29206 GAGGCAGTGA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.14
Consensus pattern (63 bp):
AAAAAAAAAAAAAAAAAAAGATGGGAAAAATGCTTTGTTTTGAAAAAAAAAAAAAAAAAAAAA
Found at i:36450 original size:24 final size:24
Alignment explanation
Indices: 36416--36461 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
36406 GATTATATTA
*
36416 TCTTGCTGATTAAAACAGAGATGT
1 TCTTGCCGATTAAAACAGAGATGT
*
36440 TCTTGCCGATTAAACCAGAGAT
1 TCTTGCCGATTAAAACAGAGAT
36462 AATCTGTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (24 bp):
TCTTGCCGATTAAAACAGAGATGT
Found at i:37579 original size:17 final size:18
Alignment explanation
Indices: 37559--37593 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
37549 AAAAAGTCAC
37559 ATTAAT-CAAAATTTAAT
1 ATTAATGCAAAATTTAAT
*
37576 ATTAATGCAAATTTTAAT
1 ATTAATGCAAAATTTAAT
37594 TATTTGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
ATTAATGCAAAATTTAAT
Found at i:38122 original size:14 final size:15
Alignment explanation
Indices: 38095--38128 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
38085 AAAATTTTAA
*
38095 TTTATATTAGTATTT
1 TTTATATTAATATTT
38110 TTTA-ATTAATATTT
1 TTTATATTAATATTT
38124 TTTAT
1 TTTAT
38129 TTTTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTATATTAATATTT
Found at i:38177 original size:30 final size:31
Alignment explanation
Indices: 38120--38177 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
38110 TTTAATTAAT
* *
38120 ATTTTTTATTTTTATATAAATAGATATAACG
1 ATTTTTTATTTTAATATAAATAAATATAACG
**
38151 ATTTTTTA-TTTAATATATTTAAATATA
1 ATTTTTTATTTTAATATAAATAAATATA
38178 TCGCGCTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 15 0.65
31 8 0.35
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (31 bp):
ATTTTTTATTTTAATATAAATAAATATAACG
Found at i:38917 original size:19 final size:17
Alignment explanation
Indices: 38893--38931 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
38883 TCACTAGCTC
38893 ATATATTTATATTATACTT
1 ATATATTTATA-TATA-TT
*
38912 ATATATTTTTATATATT
1 ATATATTTATATATATT
38929 ATA
1 ATA
38932 ATTAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATATTTATATATATT
Found at i:42988 original size:26 final size:27
Alignment explanation
Indices: 42936--42991 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
42926 TGAAATTTTT
*
42936 TAAAAATATATATTATATATATAATTA
1 TAAAAATAAATATTATATATATAATTA
* *
42963 TAAAATATAAATATTTTATAATATTATTA
1 TAAAA-ATAAATATTATAT-ATATAATTA
42992 ATTTTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.21
28 11 0.46
29 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TAAAAATAAATATTATATATATAATTA
Found at i:43658 original size:32 final size:33
Alignment explanation
Indices: 43594--43664 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 33
43584 TAATGTGTTA
*
43594 TTTAT-TTTTATAAATTTTGATACTGATAATAT
1 TTTATATTATATAAATTTTGATACTGATAATAT
* *
43626 TTTATATTATATAAATTTTGATAC-GTTTATAT
1 TTTATATTATATAAATTTTGATACTGATAATAT
43658 TTTATAT
1 TTTATAT
43665 CGTGTTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 18 0.51
33 17 0.49
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.58
Consensus pattern (33 bp):
TTTATATTATATAAATTTTGATACTGATAATAT
Found at i:44054 original size:62 final size:64
Alignment explanation
Indices: 43979--44102 Score: 180
Period size: 64 Copynumber: 2.0 Consensus size: 64
43969 AAAATGGATG
* * * * *
43979 GTAAATAGCATTAATTAAACATAT-ATATATATGTG-ATGAAGAAATGGATGGTAAATAGCACT
1 GTAAATAGCATTAATAAAAAATATAACATATATGAGAAAGAAGAAATGGATGGTAAATAGCACT
*
44041 GTAAATAGCATTAATAAAAAATATAACATATATGAGAAAGAAGCAATGGATGGTAAATAGCA
1 GTAAATAGCATTAATAAAAAATATAACATATATGAGAAAGAAGAAATGGATGGTAAATAGCA
44103 TTAATTAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 22 0.41
63 9 0.17
64 23 0.43
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (64 bp):
GTAAATAGCATTAATAAAAAATATAACATATATGAGAAAGAAGAAATGGATGGTAAATAGCACT
Found at i:45297 original size:250 final size:251
Alignment explanation
Indices: 44854--45353 Score: 914
Period size: 250 Copynumber: 2.0 Consensus size: 251
44844 TTTTTAGGTA
44854 ATCCTCATTGAATTGACTACAGATAAAAACATAGTTTGAAACATTATCAATAATTGAGATAAAAG
1 ATCCTCATTGAATTGACTACAGATAAAAACATAGTTTGAAACATTATCAATAATTGAGATAAAAG
44919 TTGCATCTTTTACCAAAATAAAAAAAAAAAGTGAGATGATTTTTTTAAAAAAGATATGTAAAGAA
66 TTGCATCTTTTACCAAAAT-AAAAAAAAAAGTGAGATGATTTTTTTAAAAAAGATATGTAAAGAA
44984 GACATTTCAAATTGAATAAATTTAAAAATAATTTATTTTTAAAATTTTATATATTTGATATATAT
130 GACATTTCAAATTGAATAAATTTAAAAATAATTTATTTTTAAAATTTTATATATTTGATATATAT
* *
45049 GTATTTAATGTCAAGAATTAATCGTGAATTTCAAAGTTGAATCTTACTTTTGTCTCT
195 GTATTTAATGTCAAGAATTAATAGTGAATTTCAAAGTTGAATCTTAATTTTGTCTCT
45106 ATCCTCATTGAATTGACTACAGATAAAAACATAGTTTGAAACATTATCAATAATTGAGAT-AAAG
1 ATCCTCATTGAATTGACTACAGATAAAAACATAGTTTGAAACATTATCAATAATTGAGATAAAAG
* *
45170 TTTGCATCTTTTACCAAAAT-TAAAAAAAAGTGGGATGATTTTTTTAAAAAAGATATGTAAAGAA
66 -TTGCATCTTTTACCAAAATAAAAAAAAAAGTGAGATGATTTTTTTAAAAAAGATATGTAAAGAA
*
45234 GGCATTTCAAATTGAATAAATTTAAAAATAATTTATTTTTAAAATTTTATATATTTGATATATAT
130 GACATTTCAAATTGAATAAATTTAAAAATAATTTATTTTTAAAATTTTATATATTTGATATATAT
*
45299 GTATTTAATGTCAAGAATTGATAGTGAATTTCAAAGTTGAATCTTAATTTTGTCT
195 GTATTTAATGTCAAGAATTAATAGTGAATTTCAAAGTTGAATCTTAATTTTGTCT
45354 TTATATGATA
Statistics
Matches: 241, Mismatches: 6, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
250 158 0.66
251 4 0.02
252 79 0.33
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (251 bp):
ATCCTCATTGAATTGACTACAGATAAAAACATAGTTTGAAACATTATCAATAATTGAGATAAAAG
TTGCATCTTTTACCAAAATAAAAAAAAAAGTGAGATGATTTTTTTAAAAAAGATATGTAAAGAAG
ACATTTCAAATTGAATAAATTTAAAAATAATTTATTTTTAAAATTTTATATATTTGATATATATG
TATTTAATGTCAAGAATTAATAGTGAATTTCAAAGTTGAATCTTAATTTTGTCTCT
Found at i:49521 original size:43 final size:43
Alignment explanation
Indices: 49473--49554 Score: 155
Period size: 43 Copynumber: 1.9 Consensus size: 43
49463 ATAAAAAAAA
*
49473 TTAAAATTTTCATATCAAGTAATTGACTATTAAACGTTTAAAC
1 TTAAAAATTTCATATCAAGTAATTGACTATTAAACGTTTAAAC
49516 TTAAAAATTTCATATCAAGTAATTGACTATTAAACGTTT
1 TTAAAAATTTCATATCAAGTAATTGACTATTAAACGTTT
49555 TGAAATGATC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.40
Consensus pattern (43 bp):
TTAAAAATTTCATATCAAGTAATTGACTATTAAACGTTTAAAC
Found at i:50000 original size:25 final size:24
Alignment explanation
Indices: 49947--50009 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 24
49937 TTGTGTATTT
*
49947 TTTTATAAATAAATGTATTAATTATA
1 TTTTA-AAA-AAATGTATTAATTAGA
49973 TTTTAAAAAAATAGTATTTAATT-GA
1 TTTTAAAAAAAT-GTA-TTAATTAGA
49998 TTTTAAAAAAAT
1 TTTTAAAAAAAT
50010 TTACATTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
24 4 0.12
25 19 0.56
26 11 0.32
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (24 bp):
TTTTAAAAAAATGTATTAATTAGA
Found at i:50104 original size:21 final size:20
Alignment explanation
Indices: 50080--50135 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
50070 TATTATTGTT
50080 TTAATAAAATTAAAAATAATA
1 TTAAT-AAATTAAAAATAATA
* *
50101 TTAATTAACTTAAAAAATGATA
1 TTAA-TAAATT-AAAAATAATA
50123 -TAATAAATTAAAA
1 TTAATAAATTAAAA
50136 TATTAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 4 0.13
20 5 0.17
21 11 0.37
22 10 0.33
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
TTAATAAATTAAAAATAATA
Found at i:50295 original size:33 final size:32
Alignment explanation
Indices: 50243--50316 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 32
50233 TTACATTAAC
*
50243 AAATTAAAATATTAATTATTAAGTTTTT-ATAA
1 AAATAAAAATATTAATTATTAAGTTTTTAAT-A
* **
50275 AAATAAAAAGTATTTATTATTATTTTTTTAATA
1 AAATAAAAA-TATTAATTATTAAGTTTTTAATA
50308 AAATAAAAA
1 AAATAAAAA
50317 ATAATATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 8 0.22
33 26 0.72
34 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (32 bp):
AAATAAAAATATTAATTATTAAGTTTTTAATA
Found at i:50325 original size:36 final size:33
Alignment explanation
Indices: 50248--50326 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
50238 TTAACAAATT
* *
50248 AAAATATTAATTATTAAGTTTTTATAAAAATAA
1 AAAATATTTATTATTAAGTTTTTATAAAAAAAA
* **
50281 AAAGTATTTATTATTATTTTTTTAATAAAATAAAA
1 AAAATATTTATTATTAAGTTTTT-ATAAAA-AAAA
50316 AATAATATTTA
1 AA-AATATTTA
50327 ATTAAATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
33 19 0.51
34 6 0.16
35 5 0.14
36 7 0.19
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.46
Consensus pattern (33 bp):
AAAATATTTATTATTAAGTTTTTATAAAAAAAA
Found at i:50341 original size:111 final size:109
Alignment explanation
Indices: 49979--50361 Score: 370
Period size: 111 Copynumber: 3.4 Consensus size: 109
49969 TATATTTTAA
* ** *
49979 AAAAATAGTATTTAATTGATTTTAAAAAAATTTACATTAATAAATTAAAA-ATTAATT-TTTTTA
1 AAAAATAATATTTAATT-AAATTAAAAAAA-TTACATTAACAAATTAAAATATTAATTATTTTT-
* * ** *
50042 AATAAAAATTAATTAAAAAACCATTTATTATTATTGTTTTAATAAAATT
63 TATAAAAATAAATT-AAAAAGGATTTATTATTATTTTTTTAATAAAA-T
* * * *
50091 AAAAATAATA-TTAATTAACTT-AAAAAATGATA-TAATAAATTAAAATATTAATTATTTTTTAA
1 AAAAATAATATTTAATTAAATTAAAAAAATTACATTAACAAATTAAAATATTAATTATTTTTT--
* *
50153 ATAAAAAATTAAATTAAAAAGGGTTTATTATTATTATTTTTAATCAAAT
64 AT-AAAAA-TAAATTAAAAAGGATTTATTATTATT-TTTTTAATAAAAT
* *
50202 TAAAATAATATTTAAGTTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTAAGT
1 AAAAATAATATTTAA-TTAA-ATTAAAAAAATTACATTAACAAATTAAAATATTAATTATT---T
* *
50267 TTT-T-ATAA-AAA-TAAAAAGTATTTATTATTATTTTTTTAATAAAAT
61 TTTATAAAAATAAATTAAAAAGGATTTATTATTATTTTTTTAATAAAAT
*
50312 AAAAAATAATATTTAATTAAATTAAAAAAATTTACGTTAACAAATTAAAA
1 -AAAAATAATATTTAATTAAATTAAAAAAA-TTACATTAACAAATTAAAA
50362 AAATAACATT
Statistics
Matches: 230, Mismatches: 24, Indels: 36
0.79 0.08 0.12
Matches are distributed among these distances:
107 13 0.06
108 10 0.04
109 20 0.09
110 39 0.17
111 71 0.31
112 31 0.13
113 4 0.02
114 5 0.02
115 9 0.04
116 24 0.10
119 4 0.02
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (109 bp):
AAAAATAATATTTAATTAAATTAAAAAAATTACATTAACAAATTAAAATATTAATTATTTTTTAT
AAAAATAAATTAAAAAGGATTTATTATTATTTTTTTAATAAAAT
Found at i:50374 original size:23 final size:23
Alignment explanation
Indices: 50301--50388 Score: 90
Period size: 23 Copynumber: 3.8 Consensus size: 23
50291 TTATTATTTT
* *
50301 TTTAATAAAAT-AAAAAATAATA
1 TTTAATAAATTAAAAAAATAACA
*
50323 TTTAATTAAATTAAAAAAATTTAC-
1 TTTAA-TAAATTAAAAAAA-TAACA
* *
50347 GTTAACAAATTAAAAAAATAACA
1 TTTAATAAATTAAAAAAATAACA
*
50370 TTTAATGAATTAAAAAAAT
1 TTTAATAAATTAAAAAAAT
50389 TATCATTATT
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
22 8 0.15
23 33 0.62
24 10 0.19
25 2 0.04
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.33
Consensus pattern (23 bp):
TTTAATAAATTAAAAAAATAACA
Found at i:50407 original size:46 final size:46
Alignment explanation
Indices: 50308--50408 Score: 118
Period size: 46 Copynumber: 2.2 Consensus size: 46
50298 TTTTTTAATA
* *
50308 AAAT-AAAAAATAATATTTAATTAAATTAAAAAAATTTACGTTAAC
1 AAATAAAAAAATAACATTTAATTAAATTAAAAAAATTTACATTAAC
* *
50353 AAATTAAAAAAATAACATTTAA-TGAATTAAAAAAA-TTATCATTATTC
1 AAA-TAAAAAAATAACATTTAATTAAATTAAAAAAATTTA-CATTA-AC
50400 AAATAAAAA
1 AAATAAAAA
50409 CCCTATATTC
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
45 6 0.12
46 23 0.48
47 19 0.40
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (46 bp):
AAATAAAAAAATAACATTTAATTAAATTAAAAAAATTTACATTAAC
Found at i:51378 original size:13 final size:13
Alignment explanation
Indices: 51360--51385 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51350 CAATTTTTGG
51360 TGTATCGATACAT
1 TGTATCGATACAT
51373 TGTATCGATACAT
1 TGTATCGATACAT
51386 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:51397 original size:32 final size:33
Alignment explanation
Indices: 51340--51403 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
51330 TACAAGCCAA
**
51340 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
51373 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
51404 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:51410 original size:19 final size:18
Alignment explanation
Indices: 51340--51410 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
51330 TACAAGCCAA
51340 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
51360 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
51373 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
51392 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
51411 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:53496 original size:21 final size:20
Alignment explanation
Indices: 53467--53509 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
53457 GGCTAGTGTG
*
53467 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
53488 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
53508 GG
1 GG
53510 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:53968 original size:13 final size:13
Alignment explanation
Indices: 53950--53988 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
53940 ATAATCCCCC
*
53950 TGTATCGATACAG
1 TGTATCGATACAA
53963 TGTATCGATACAA
1 TGTATCGATACAA
53976 TGTATCGATACAA
1 TGTATCGATACAA
53989 AAAAAAATGT
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:59463 original size:13 final size:13
Alignment explanation
Indices: 59445--59483 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
59435 ACATTTTTCT
59445 TTGTATCGATACA
1 TTGTATCGATACA
59458 TTGTATCGATACA
1 TTGTATCGATACA
*
59471 CTGTATCGATACA
1 TTGTATCGATACA
59484 GGGGGATTAT
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:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:59647 original size:20 final size:19
Alignment explanation
Indices: 59606--59648 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
59596 ATCTTTTACA
59606 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
59626 AAATCACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
59646 AAA
1 AAA
59649 ACCAGAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:63342 original size:92 final size:91
Alignment explanation
Indices: 63238--63698 Score: 614
Period size: 92 Copynumber: 5.1 Consensus size: 91
63228 AAGGAAAAAA
* *
63238 AGAAAAAAAGAAAAATTGATTGATTGTAAATGTTAGACTGCAAGAATTAGACTAATGCATAAATT
1 AGAAAAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTGCAAGGATTAGACTAATGCATAAATT
63303 ATATTTGAGAATCAATTCTTTTTTAT
66 ATATTTGAGAATCAATTCTTTTTTAT
** *
63329 AGAACAAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTATAAAGATTAGACTAATGCATAAAT
1 AGAA-AAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTGCAAGGATTAGACTAATGCATAAAT
*
63394 TATATTTGAGATTCGAATTCTTTTTTAT
65 TATATTTGAGAATC-AATTCTTTTTTAT
* * * * *
63422 GGAAAAAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTGTAAGGATCAGACTAATGTATGAAT
1 AG-AAAAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTGCAAGGATTAGACTAATGCATAAAT
* *
63487 TATATCTAAGAATCAATTCTTTTTTAT
65 TATATTTGAGAATCAATTCTTTTTTAT
*
63514 AG-AAAAAAGAAAAGTTGATTGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATAAATT
1 AGAAAAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTGCAAGGATTAGACTAATGCATAAATT
* **
63578 ATATCTGAGAATCGGTAT-TTTTTTAT
66 ATATTTGAGAATCAAT-TCTTTTTTAT
* * * * *
63604 AG-----AA-AAAATTTGACTGATTATAAATGTCAGACTGCAAGGATTAGACTAATGCATTAATT
1 AGAAAAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTGCAAGGATTAGACTAATGCATAAATT
*
63663 ATATTTGAGAATCGATTTCTTTTTTAT
66 ATATTTGAGAATC-AATTCTTTTTTAT
63690 AGAAAAAAA
1 AGAAAAAAA
63699 TTTGACTGAT
Statistics
Matches: 328, Mismatches: 31, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
85 64 0.20
86 13 0.04
90 80 0.24
91 7 0.02
92 82 0.25
93 80 0.24
94 2 0.01
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (91 bp):
AGAAAAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTGCAAGGATTAGACTAATGCATAAATT
ATATTTGAGAATCAATTCTTTTTTAT
Found at i:63558 original size:90 final size:90
Alignment explanation
Indices: 63241--63697 Score: 602
Period size: 90 Copynumber: 5.1 Consensus size: 90
63231 GAAAAAAAGA
* *
63241 AAAAAAGAAAAATTGATTGATTGTAAATGTTAGACTGCAAGAATTAGACTAATGCATAAATTATA
1 AAAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTGCAAGGATTAGACTAATGCATAAATTATA
63306 TTTGAGAATCAATTCTTTTTTATAG
66 TTTGAGAATCAATTCTTTTTTATAG
** *
63331 AACAAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTATAAAGATTAGACTAATGCATAAATTA
1 -A-AAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTGCAAGGATTAGACTAATGCATAAATTA
* *
63396 TATTTGAGATTCGAATTCTTTTTTATGGAA
64 TATTTGAGAATC-AATTCTTTTTTAT--AG
* * * *
63426 AAAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTGTAAGGATCAGACTAATGTATGAATTATA
1 AAAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTGCAAGGATTAGACTAATGCATAAATTATA
* *
63491 TCTAAGAATCAATTCTTTTTTATAG
66 TTTGAGAATCAATTCTTTTTTATAG
*
63516 AAAAAAGAAAAGTTGATTGATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATAAATTATA
1 AAAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTGCAAGGATTAGACTAATGCATAAATTATA
* **
63581 TCTGAGAATCGGTAT-TTTTTTATAG
66 TTTGAGAATCAAT-TCTTTTTTATAG
* * * * *
63606 ----AA-AAAATTTGACTGATTATAAATGTCAGACTGCAAGGATTAGACTAATGCATTAATTATA
1 AAAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTGCAAGGATTAGACTAATGCATAAATTATA
*
63666 TTTGAGAATCGATTTCTTTTTTATAG
66 TTTGAGAATC-AATTCTTTTTTATAG
63692 AAAAAA
1 AAAAAA
63698 ATTTGACTGA
Statistics
Matches: 324, Mismatches: 31, Indels: 23
0.86 0.08 0.06
Matches are distributed among these distances:
85 64 0.20
86 13 0.04
90 83 0.26
91 2 0.01
92 81 0.25
93 79 0.24
94 1 0.00
95 1 0.00
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (90 bp):
AAAAAAGAAAAGTTGATTGATTGTAAATGTTAGACTGCAAGGATTAGACTAATGCATAAATTATA
TTTGAGAATCAATTCTTTTTTATAG
Found at i:66933 original size:20 final size:20
Alignment explanation
Indices: 66908--66981 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
66898 GTAAAAAGAC
66908 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
66928 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* * *
66948 TA-CATGTATTGATATATTGA
1 -AGAATGTATCGATACATTGA
*
66968 AAAATGTATCGATA
1 AGAATGTATCGATA
66982 ATTTGGGTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 43 0.96
21 1 0.02
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:67403 original size:88 final size:87
Alignment explanation
Indices: 67182--67440 Score: 333
Period size: 88 Copynumber: 3.0 Consensus size: 87
67172 GGTGTCTACA
* *
67182 ACTGATTGTAAATGTCAGACTGTAAGGATTAGACTAATGCATGAATTATATATGATAATCAGATT
1 ACTGATTGTAAATGTCAGACTGCAA-GATTAGACTAATGCATGAATTATATATGAAAATCAGATT
67247 CTTTTTTAT-AAAAAAAAG-TTG
65 CTTTTTTATAAAAAAAAAGATTG
* * * * * *
67268 ACTGATTGTAAATTTTAGACTGCAATGATTAGACTAATGCATAAATTATATCTGAGAATCGGATT
1 ACTGATTGTAAATGTCAGACTGCAA-GATTAGACTAATGCATGAATTATATATGAAAATCAGATT
67333 CTTTTTTATAAAAAAAAAGATTG
65 CTTTTTTATAAAAAAAAAGATTG
* * * * * *
67356 ATTGATTGTAAATGTCAAACTGCAAGAATTAGACTAATGTATGAATTATATTTAAAAATTAGATT
1 ACTGATTGTAAATGTCAGACTGCAAG-ATTAGACTAATGCATGAATTATATATGAAAATCAGATT
* *
67421 CTTTTCTATAAGAAAAAAGA
65 CTTTTTTATAAAAAAAAAGA
67441 AATACTACAA
Statistics
Matches: 149, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
86 66 0.44
87 10 0.07
88 73 0.49
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (87 bp):
ACTGATTGTAAATGTCAGACTGCAAGATTAGACTAATGCATGAATTATATATGAAAATCAGATTC
TTTTTTATAAAAAAAAAGATTG
Found at i:67579 original size:155 final size:158
Alignment explanation
Indices: 67294--67580 Score: 375
Period size: 155 Copynumber: 1.8 Consensus size: 158
67284 AGACTGCAAT
* * * *
67294 GATTAGACTAATGCATAAATTATATCTGAGAATCGGATTCTTTTTTATAAAAAAAAAGATTGATT
1 GATTAGACTAATGCATAAATTATATATAAAAATCGAATTCTTTTTTATAAAAAAAAAGATTGATT
* * * * * *
67359 GATTGTAAATGTCAAACTGCAAGAATTAGACTAATGTATGAATTATATTTAAAAATTAGATTCTT
66 GATTATAAATATCAAACTGCAAGAATTAGACTAATGCATAAATTATATTTAAAAATCAAATTCTT
67424 TTCTATAAGAAAAAAGAAATACTACAAG
131 TTCTATAAGAAAAAAGAAATACTACAAG
* * *
67452 GATTAGACTAATGCATGAATTGTATATAAAAATCGAATT-TTTTTTGT-AAAAAAAAG-TTGATT
1 GATTAGACTAATGCATAAATTATATATAAAAATCGAATTCTTTTTTATAAAAAAAAAGATTGATT
* * * * *
67514 GATTATAAGTATGACACTGCAA-AGATTAGACTAATGCATAAATTATATTTGAGAATCAAATTCT
66 GATTATAAATATCAAACTGCAAGA-ATTAGACTAATGCATAAATTATATTTAAAAATCAAATTCT
67578 TTT
130 TTT
67581 TAATAGAAAA
Statistics
Matches: 110, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
154 1 0.01
155 60 0.55
156 9 0.08
157 7 0.06
158 33 0.30
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.36
Consensus pattern (158 bp):
GATTAGACTAATGCATAAATTATATATAAAAATCGAATTCTTTTTTATAAAAAAAAAGATTGATT
GATTATAAATATCAAACTGCAAGAATTAGACTAATGCATAAATTATATTTAAAAATCAAATTCTT
TTCTATAAGAAAAAAGAAATACTACAAG
Found at i:71376 original size:298 final size:295
Alignment explanation
Indices: 70946--71604 Score: 958
Period size: 298 Copynumber: 2.2 Consensus size: 295
70936 AAAGTTAAGG
* * * *
70946 AAATTTTTTTTAGTCATTTTACAGATAAAGAAAAGCTCGTGTTTAAGTCATTATCAAAAAATAAA
1 AAATTTTTCTTAGTCATTTTACAGATAAAGAAAA-CTCGTATTTAAGTCGTTATCGAAAAATAAA
* * * * ** * **
71011 ATGTGTGCATTTGTAAATCCGAAATAAGTTATTATTGAAAAAAGTAATTTATTGTTGGCTAACAT
65 ATGTATACATCTGTAAATCCGAAATAAGTCATTATCAAAAAAAATAAAATATTGTTGGCTAACAT
* * **
71076 AAATTTAAGTTTTATCAATTATAAAAATAATACAAATACAATATTAATTAATTTTTTGAAAAATA
130 AAATTTAAGTTCTATCAACTATAAAAATAATACAAATACAATATTAATTAA-TTTTAAAAAAATA
* *
71141 AATTTGTATAGTTTATAAATAAATTAAAAAATAATTTATAAATAAAAAGTAATAATTCATGCACA
194 AATTTGTATAATTTATAAATAAATT-AAAAATAATTTATAAATAAAAAGTAATAATACATGCACA
* *
71206 ATGTTAATTAATTTTAATAAAAATAATGCATGTACAAT
258 ATATTAATTAATTTTAATAAAAATAATACATGTACAAT
* * *
71244 AAATTTTTCTTAATCATTTTACAGATAAATGAAAATTTGTATTTAAGTCGTTATCGAAAAATAAA
1 AAATTTTTCTTAGTCATTTTACAGATAAA-GAAAACTCGTATTTAAGTCGTTATCGAAAAATAAA
* *
71309 ATGTATACGTCTGTAAATCCGAAATAAGTCGTTATCAAAAAAAATAAAATATTGTTGGCTAACAT
65 ATGTATACATCTGTAAATCCGAAATAAGTCATTATCAAAAAAAATAAAATATTGTTGGCTAACAT
* **
71374 AAATTTAAGTTCTATCAACTATAAAAATAATATATGTACAATATTAATTAATTTTAAAAAAATAA
130 AAATTTAAGTTCTATCAACTATAAAAATAATACAAATACAATATTAATTAATTTTAAAAAAATAA
*
71439 ATTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGTACAAT
195 ATTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGCACAAT
71504 ATTAATTAATTTTAATAAAAATAATACATGTACAAT
260 ATTAATTAATTTTAATAAAAATAATACATGTACAAT
* * * *
71540 AAATTTTTTCTTGGTCATTTTACAGATAACGGAAAACTCATATTTAAGTTGTTATCGAAAAATAA
1 AAA-TTTTTCTTAGTCATTTTACAGATAA-AGAAAACTCGTATTTAAGTCGTTATCGAAAAATAA
71605 TACATGTAAA
Statistics
Matches: 321, Mismatches: 37, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
296 76 0.24
297 88 0.27
298 152 0.47
299 5 0.02
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.37
Consensus pattern (295 bp):
AAATTTTTCTTAGTCATTTTACAGATAAAGAAAACTCGTATTTAAGTCGTTATCGAAAAATAAAA
TGTATACATCTGTAAATCCGAAATAAGTCATTATCAAAAAAAATAAAATATTGTTGGCTAACATA
AATTTAAGTTCTATCAACTATAAAAATAATACAAATACAATATTAATTAATTTTAAAAAAATAAA
TTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGCACAATA
TTAATTAATTTTAATAAAAATAATACATGTACAAT
Found at i:72015 original size:32 final size:32
Alignment explanation
Indices: 71947--72015 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
71937 TTTTTTAAAG
*
71947 TTAATTAAATATTATTTTTTATTATAAAATAA
1 TTAATTAAATATTATTATTTATTATAAAATAA
**
71979 -TAATTAATATATTATTATTTATTA-AATTTAA
1 TTAATTAA-ATATTATTATTTATTATAAAATAA
72010 TTAATT
1 TTAATT
72016 TATAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 12 0.38
32 20 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TTAATTAAATATTATTATTTATTATAAAATAA
Found at i:74344 original size:30 final size:31
Alignment explanation
Indices: 74310--74378 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
74300 GGGTTTTAAA
*
74310 TTTAATTATTTT-AA-TTACTTATAAAATATT
1 TTTAATT-TTTTAAATTTAATTATAAAATATT
74340 TTTAATTTTTTAAATTTAATTATAAAATATT
1 TTTAATTTTTTAAATTTAATTATAAAATATT
*
74371 TTAAATTT
1 TTTAATTT
74379 AATTATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 4 0.11
30 9 0.26
31 22 0.63
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (31 bp):
TTTAATTTTTTAAATTTAATTATAAAATATT
Found at i:74372 original size:22 final size:22
Alignment explanation
Indices: 74347--74397 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
74337 ATTTTTAATT
74347 TTTTAAATTTAATTATAAAATA
1 TTTTAAATTTAATTATAAAATA
74369 TTTTAAATTTAATTATAAAATA
1 TTTTAAATTTAATTATAAAATA
*
74391 TGTTAAA
1 TTTTAAA
74398 CAAGACAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTAAATTTAATTATAAAATA
Found at i:75906 original size:15 final size:16
Alignment explanation
Indices: 75877--75909 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
75867 ATATCAAAAT
75877 TATATAAATTATAATA
1 TATATAAATTATAATA
75893 TATATAAA-TATAATA
1 TATATAAATTATAATA
75908 TA
1 TA
75910 AATACTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATATAAATTATAATA
Found at i:75908 original size:27 final size:26
Alignment explanation
Indices: 75850--75912 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 26
75840 AAAATTTATT
*
75850 TAATATAAATTATTTATATATCAAAA
1 TAATATAAATTATATATATATCAAAA
*
75876 TTATATAAATTATAATATATAT-AAATA
1 TAATATAAATTAT-ATATATATCAAA-A
75903 TAATATAAAT
1 TAATATAAAT
75913 ACTTGAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.47
27 17 0.53
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TAATATAAATTATATATATATCAAAA
Found at i:77068 original size:14 final size:15
Alignment explanation
Indices: 77049--77084 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
77039 AAACTTGTAG
77049 TTTTTATTTTTAT-T
1 TTTTTATTTTTATCT
*
77063 TTTTTATTTTTCTCT
1 TTTTTATTTTTATCT
77078 TTTTTAT
1 TTTTTAT
77085 ATAAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTATTTTTATCT
Found at i:77136 original size:25 final size:25
Alignment explanation
Indices: 77097--77172 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
77087 AAAAATTTTA
*
77097 ATTAATTAAA-ATTTTATATTATTT
1 ATTAATTAAATTTTTTATATTATTT
* * *
77121 ATTAATTAAATTTTTTATATAAATA
1 ATTAATTAAATTTTTTATATTATTT
*
77146 AATAATTAAATATTTTTA-ATTTATTT
1 ATTAATTAAAT-TTTTTATA-TTATTT
77172 A
1 A
77173 AAATGTAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
24 10 0.24
25 21 0.51
26 10 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTAATTAAATTTTTTATATTATTT
Found at i:77689 original size:18 final size:18
Alignment explanation
Indices: 77662--77697 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
77652 TGATATTGTT
77662 GTTGCCGATCTGCTTCTG
1 GTTGCCGATCTGCTTCTG
*
77680 GTTGCTGATCTGCTTCTG
1 GTTGCCGATCTGCTTCTG
77698 TCGATTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.06, C:0.25, G:0.28, T:0.42
Consensus pattern (18 bp):
GTTGCCGATCTGCTTCTG
Found at i:77786 original size:57 final size:57
Alignment explanation
Indices: 77713--77820 Score: 180
Period size: 57 Copynumber: 1.9 Consensus size: 57
77703 TTGTTTATTG
*
77713 TTGCTGTTACCAATTATTACAGTTGCTGTTAGGTTTAGTAGTTTAATTGCTTTCTAA
1 TTGCTGTTACCAATTATTACAGTTACTGTTAGGTTTAGTAGTTTAATTGCTTTCTAA
* * *
77770 TTGCTGTTGCCGATTATTACAGTTACTGTTAGGTTTAGTAGTTTAGTTGCT
1 TTGCTGTTACCAATTATTACAGTTACTGTTAGGTTTAGTAGTTTAATTGCT
77821 GCTAGTGTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.47
Consensus pattern (57 bp):
TTGCTGTTACCAATTATTACAGTTACTGTTAGGTTTAGTAGTTTAATTGCTTTCTAA
Found at i:77872 original size:19 final size:19
Alignment explanation
Indices: 77835--77883 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
77825 GTGTATTGTA
*
77835 ATTTTTTTTATTTTACTTT
1 ATTTTTTTTATTTAACTTT
*
77854 GTTTTTTTTA-TTAAGCTTT
1 ATTTTTTTTATTTAA-CTTT
77873 ATTATTTTTTA
1 ATT-TTTTTTA
77884 AAATAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 15 0.60
20 7 0.28
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (19 bp):
ATTTTTTTTATTTAACTTT
Found at i:78786 original size:16 final size:15
Alignment explanation
Indices: 78767--78813 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
78757 AAACGTGATC
78767 TAAAATAATTAAAGTT
1 TAAAATAATTAAA-TT
78783 TAAAATAATTTAAATT
1 TAAAATAA-TTAAATT
*
78799 TAAAGTAATTTAAAT
1 TAAAATAA-TTAAAT
78814 GCATTAGGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 24 0.83
17 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (15 bp):
TAAAATAATTAAATT
Found at i:79048 original size:16 final size:16
Alignment explanation
Indices: 79007--79051 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
78997 TTTTAATGTG
*
79007 AATTTAAAAAAATTTA
1 AATTTAAAATAATTTA
*
79023 AATTTAAAATTATTTA
1 AATTTAAAATAATTTA
79039 AATTTAAAATAAT
1 AATTTAAAATAAT
79052 AAATTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTTAAAATAATTTA
Found at i:80600 original size:22 final size:20
Alignment explanation
Indices: 80555--80606 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
80545 AAGTTTGTAT
*
80555 ATTTATTTTA-TATTTATATT
1 ATTT-TTTTATTATTTATATA
80575 ATTTTTCTTATTATTTCATATA
1 ATTTTT-TTATTATTT-ATATA
80597 ATTTTTTTAT
1 ATTTTTTTAT
80607 ATAATATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 7 0.25
21 9 0.32
22 10 0.36
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTTTTTATTATTTATATA
Found at i:80616 original size:24 final size:23
Alignment explanation
Indices: 80562--80619 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
80552 TATATTTATT
* *
80562 TTATATTTATATTATTTTTCTTA
1 TTATATTCATATAATTTTTCTTA
80585 TTAT-TTCATATAATTTTT-TTA
1 TTATATTCATATAATTTTTCTTA
80606 TATAATATTCATAT
1 T-T-ATATTCATAT
80620 TATGTAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.13
22 13 0.43
23 6 0.20
24 7 0.23
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (23 bp):
TTATATTCATATAATTTTTCTTA
Found at i:81987 original size:18 final size:17
Alignment explanation
Indices: 81938--81988 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
81928 AATGTATATA
*
81938 TTTAAAATAATTATCTT
1 TTTAAAATAATTATTTT
*
81955 TTTAAAATTATTATTTT
1 TTTAAAATAATTATTTT
*
81972 TTTAAAAATAAATATTT
1 TTT-AAAATAATTATTT
81989 ATATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 18 0.62
18 11 0.38
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAAAATAATTATTTT
Found at i:82368 original size:17 final size:20
Alignment explanation
Indices: 82339--82387 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 20
82329 TTGAAAAATT
*
82339 ATATTATAATATA-TT-TAA
1 ATATTAAAATATATTTATAA
82357 AT-TTAAAATATATTTATAA
1 ATATTAAAATATATTTATAA
82376 ATATTAAAATAT
1 ATATTAAAATAT
82388 TAATTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 9 0.33
18 4 0.15
19 5 0.19
20 9 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTAAAATATATTTATAA
Found at i:82379 original size:27 final size:29
Alignment explanation
Indices: 82333--82390 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
82323 GTTATATTGA
*
82333 AAAATTATATTATAATATATTTAAAT-TT
1 AAAATTATATTATAATATATTAAAATATT
82361 AAAA-TATATTTATAA-ATATTAAAATATT
1 AAAATTATA-TTATAATATATTAAAATATT
82389 AA
1 AA
82391 TTTTTAATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AAAATTATATTATAATATATTAAAATATT
Found at i:83822 original size:19 final size:19
Alignment explanation
Indices: 83777--83831 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 19
83767 TGATATGAGC
* *
83777 TTTAGGTTTTAAAAAATTA
1 TTTAGATTTTAAAAATTTA
** *
83796 AATGGATTTTAAAAATTTA
1 TTTAGATTTTAAAAATTTA
*
83815 TTTAGATTATAAAAATT
1 TTTAGATTTTAAAAATT
83832 AAAAGCCCAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTAGATTTTAAAAATTTA
Found at i:84756 original size:17 final size:17
Alignment explanation
Indices: 84734--84824 Score: 73
Period size: 17 Copynumber: 5.4 Consensus size: 17
84724 AATAATAAAA
*
84734 ATATATATTAAATTAAT
1 ATATATATTAAATTTAT
*
84751 ATATATTTTAAAATTTAT
1 ATATATATT-AAATTTAT
84769 ATA-ATATT-AA-TTAT
1 ATATATATTAAATTTAT
*
84783 -TAATTTATTAAAATTTAT
1 AT-ATATATT-AAATTTAT
* *
84801 ATAAATATAAAATTTAT
1 ATATATATTAAATTTAT
*
84818 AAATATA
1 ATATATA
84825 ATTATAATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
13 1 0.02
14 5 0.09
15 6 0.10
17 27 0.47
18 18 0.31
19 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATTAAATTTAT
Found at i:84789 original size:29 final size:30
Alignment explanation
Indices: 84731--84806 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 30
84721 TAAAATAATA
*
84731 AAAATATATATTAAATTAATATAT-ATT-TT
1 AAAATTTATA-TAAATTAATATATAATTATT
84760 AAAATTTATATAATATTAAT-TATTAATTTATT
1 AAAATTTATATAA-ATTAATATA-TAA-TTATT
84792 AAAATTTATATAAAT
1 AAAATTTATATAAAT
84807 ATAAAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
28 5 0.12
29 16 0.39
30 1 0.02
31 4 0.10
32 15 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
AAAATTTATATAAATTAATATATAATTATT
Found at i:85579 original size:29 final size:29
Alignment explanation
Indices: 85546--85603 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
85536 TTTGCCTTGA
85546 TTAGAATTGGATGGTTTAGAAACAAACAT
1 TTAGAATTGGATGGTTTAGAAACAAACAT
85575 TTAGAATTGGATGGTTTAGAAACAAACAT
1 TTAGAATTGGATGGTTTAGAAACAAACAT
85604 AAAGATACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (29 bp):
TTAGAATTGGATGGTTTAGAAACAAACAT
Found at i:93435 original size:58 final size:57
Alignment explanation
Indices: 93335--93457 Score: 142
Period size: 58 Copynumber: 2.1 Consensus size: 57
93325 TTAAATATTT
* * *
93335 TAAAATTCATGAAAGTTCCTAGATCATAGAAAATGACTTAAATG-ATATTAAAATTAA
1 TAAAATTCATGAAAGTCCCTAGATCATAGAAAATAACCTAAATGCAT-TTAAAATTAA
* * * *
93392 TAAAATTACATTAAAGTCCCTA-AGTCATTGAAAATAACCTAAATGCCTTTAAAATTTA
1 TAAAATT-CATGAAAGTCCCTAGA-TCATAGAAAATAACCTAAATGCATTTAAAATTAA
93450 TAAAATTC
1 TAAAATTC
93458 TATCCAAATC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
57 9 0.16
58 46 0.82
59 1 0.02
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (57 bp):
TAAAATTCATGAAAGTCCCTAGATCATAGAAAATAACCTAAATGCATTTAAAATTAA
Found at i:93531 original size:58 final size:58
Alignment explanation
Indices: 93364--93847 Score: 293
Period size: 58 Copynumber: 8.3 Consensus size: 58
93354 TAGATCATAG
* * * * *
93364 AAAATGACTTAAATGATATTAAAATTAATAAAATTACATTAAAGTCCCTAAGTCATTG-
1 AAAATGACTTAAATGACATTAAAATTCATAAAATTGCATCAAAGTCCTTAAGTCA-TGA
* * * * * * *
93422 AAAATAACCTAAATGCCTTTAAAATTTATAAAATT-CTATCCAAA-TCTTTAAGCCATGA
1 AAAATGACTTAAATGACATTAAAATTCATAAAATTGC-AT-CAAAGTCCTTAAGTCATGA
* * * *
93480 AAAATGACTTACATGCCATTAAAATTCATAAAATTGCATCTAAGTCCTTAAGTAATGA
1 AAAATGACTTAAATGACATTAAAATTCATAAAATTGCATCAAAGTCCTTAAGTCATGA
* * ** ** * * *
93538 AAAATGATTTAAAT-ATTATTAAAATT-ATTAAAATTATAAAAAAATCCTTAAATCATAA
1 AAAATGACTTAAATGA-CATTAAAATTCA-TAAAATTGCATCAAAGTCCTTAAGTCATGA
* * * * *
93596 AAAATGACTTAAATAATATCAAAATTCATTAAATTGCAT-ACAAGTTCC-TAAGTCATGG
1 AAAATGACTTAAATGACATTAAAATTCATAAAATTGCATCA-AAG-TCCTTAAGTCATGA
* * * * * * * * *
93654 AAAATGTCCTACATGACATCAAACTTCATAAAATTGCACCAAAGTTCTTACG-CTATAA
1 AAAATGACTTAAATGACATTAAAATTCATAAAATTGCATCAAAGTCCTTAAGTC-ATGA
* * * * * * * * ** *
93712 AAAATGACCTAAATGATATCAAATTTCATAAAATTACACCGAATTCCTTTGGTCATTGG
1 AAAATGACTTAAATGACATTAAAATTCATAAAATTGCATCAAAGTCCTTAAGTCA-TGA
* * * * * *
93771 AAAATAACTTAAATGACATTAAATTTTATAAAATTGCATAAAAAATTCTT-AGATCATGA
1 AAAATGACTTAAATGACATTAAAATTCATAAAATTGCAT-CAAAGTCCTTAAG-TCATGA
*
93830 AAAATCACTTAAATGACA
1 AAAATGACTTAAATGACA
93848 AAAAGTATGT
Statistics
Matches: 328, Mismatches: 80, Indels: 35
0.74 0.18 0.08
Matches are distributed among these distances:
57 11 0.03
58 244 0.74
59 64 0.20
60 9 0.03
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (58 bp):
AAAATGACTTAAATGACATTAAAATTCATAAAATTGCATCAAAGTCCTTAAGTCATGA
Found at i:93564 original size:9 final size:9
Alignment explanation
Indices: 93546--93578 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
93536 GAAAAATGAT
93546 TTAAATATTA
1 TTAAA-ATTA
93556 TTAAAATTA
1 TTAAAATTA
93565 TTAAAATTA
1 TTAAAATTA
93574 -TAAAA
1 TTAAAA
93579 AAATCCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 5 0.22
9 13 0.57
10 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TTAAAATTA
Found at i:93834 original size:59 final size:59
Alignment explanation
Indices: 93771--93910 Score: 153
Period size: 59 Copynumber: 2.4 Consensus size: 59
93761 TGGTCATTGG
* * * *
93771 AAAATAACTTAAATGACATTAAA-T-TTTATAAAAT-TGCATAAAAAATTCTTAGATCATGA
1 AAAATAACTTAAATGACA-AAAAGTATGTATAAAATAT-CAT-AAAAATTCCTAAATCATGA
* *
93830 AAAATCACTTAAATGACAAAAAGTATGTATAAAATATCATAAAAATTCCTAAATCATGG
1 AAAATAACTTAAATGACAAAAAGTATGTATAAAATATCATAAAAATTCCTAAATCATGA
*
93889 AAAATGAC-TAAGATGACAAAAA
1 AAAATAACTTAA-ATGACAAAAA
93911 TGCATGAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
58 6 0.09
59 51 0.73
60 12 0.17
61 1 0.01
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.28
Consensus pattern (59 bp):
AAAATAACTTAAATGACAAAAAGTATGTATAAAATATCATAAAAATTCCTAAATCATGA
Found at i:96114 original size:56 final size:55
Alignment explanation
Indices: 96036--96154 Score: 130
Period size: 56 Copynumber: 2.1 Consensus size: 55
96026 TTTTAAAAAC
* * * *
96036 ATGTCTACTTTAGACATTGTCTTAATAAGATAAGCTTATCCATACTGTCTTAACAT
1 ATGTCTACTTTAAACATTGTCTTAATAAAATAA-CCTATCCATAATGTCTTAACAT
* * ** * *
96092 ATGTTTACTTTAAATATTGTCTTGTTAAAATAACCTATCCATAATGTTTTAACAC
1 ATGTCTACTTTAAACATTGTCTTAATAAAATAACCTATCCATAATGTCTTAACAT
*
96147 ATATCTAC
1 ATGTCTAC
96155 CATAGACATT
Statistics
Matches: 51, Mismatches: 12, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
55 24 0.47
56 27 0.53
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (55 bp):
ATGTCTACTTTAAACATTGTCTTAATAAAATAACCTATCCATAATGTCTTAACAT
Found at i:96494 original size:22 final size:23
Alignment explanation
Indices: 96451--96492 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
96441 AATGTTTTTG
96451 AAACATGATTATGATTTATTTAT
1 AAACATGATTATGATTTATTTAT
*
96474 AAACATTA-TATG-TTTATTT
1 AAACATGATTATGATTTATTT
96493 TAGCATTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (23 bp):
AAACATGATTATGATTTATTTAT
Found at i:96770 original size:18 final size:18
Alignment explanation
Indices: 96747--96784 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
96737 ATTTGACTCA
*
96747 GTGATAAATAGCCATGAT
1 GTGATAAATAACCATGAT
96765 GTGATAAATAACCATGAT
1 GTGATAAATAACCATGAT
96783 GT
1 GT
96785 TAAAGATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (18 bp):
GTGATAAATAACCATGAT
Done.