Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold995
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: 32125
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:868 original size:33 final size:33
Alignment explanation
Indices: 830--892 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
820 GATTACTCAC
830 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
863 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
893 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:905 original size:13 final size:13
Alignment explanation
Indices: 889--944 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
879 TCAAGCTCTC
889 TTTCAATTTCTTT
1 TTTCAATTTCTTT
**
902 TTTCGCTTT-TCTT
1 TTTCAATTTCT-TT
915 TTTCAATTTTCTTT
1 TTTCAA-TTTCTTT
*
929 TCTTCATTTTCTTT
1 T-TTCAATTTCTTT
943 TT
1 TT
945 CTCTCACTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
12 1 0.03
13 14 0.41
14 14 0.41
15 5 0.15
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTCAATTTCTTT
Found at i:914 original size:14 final size:13
Alignment explanation
Indices: 889--944 Score: 60
Period size: 14 Copynumber: 4.2 Consensus size: 13
879 TCAAGCTCTC
*
889 TTTCAATTTCTTT
1 TTTCATTTTCTTT
*
902 TTTCGCTTTTC-TT
1 TTTC-ATTTTCTTT
915 TTTCAATTTTCTTT
1 TTTC-ATTTTCTTT
929 TCTTCATTTTCTTT
1 T-TTCATTTTCTTT
943 TT
1 TT
945 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 16 0.44
14 17 0.47
15 3 0.08
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTCATTTTCTTT
Found at i:938 original size:27 final size:26
Alignment explanation
Indices: 889--945 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
879 TCAAGCTCTC
*
889 TTTCAATTTCTTTTTTCGCTTTTCTT
1 TTTCAATTTCTTTTTTCGATTTTCTT
915 TTTCAATTTTCTTTTCTTC-ATTTTCTT
1 TTTCAA-TTTCTTTT-TTCGATTTTCTT
942 TTTC
1 TTTC
946 TCTCACTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 6 0.21
27 19 0.68
28 3 0.11
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTCAATTTCTTTTTTCGATTTTCTT
Found at i:992 original size:12 final size:12
Alignment explanation
Indices: 889--1026 Score: 81
Period size: 12 Copynumber: 11.4 Consensus size: 12
879 TCAAGCTCTC
*
889 TTTCAATTTCTTT
1 TTTCATTTTC-TT
*
902 TTTCGCTTTTCTT
1 TTTC-ATTTTCTT
915 TTTCAATTTTCTTT
1 TTTC-ATTTTC-TT
929 TCTTCATTTTCTT
1 T-TTCATTTTCTT
**
942 TTTC-TCTCACTT
1 TTTCAT-TTTCTT
*
954 TTTGA-TTTCTT
1 TTTCATTTTCTT
**
965 TTTC-TTTTGCAA
1 TTTCATTTT-CTT
*
977 TTTCTTTTTCTT
1 TTTCATTTTCTT
989 TTTCATTTTCTT
1 TTTCATTTTCTT
*
1001 TTT-GTTTTC--
1 TTTCATTTTCTT
*
1010 TTTCAATTTCTT
1 TTTCATTTTCTT
1022 TTTCA
1 TTTCA
1027 ATCTCTTTCT
Statistics
Matches: 96, Mismatches: 18, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
9 3 0.03
10 4 0.04
11 16 0.17
12 35 0.36
13 22 0.23
14 13 0.14
15 3 0.03
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (12 bp):
TTTCATTTTCTT
Found at i:1003 original size:18 final size:18
Alignment explanation
Indices: 908--1008 Score: 87
Period size: 18 Copynumber: 5.5 Consensus size: 18
898 CTTTTTTCGC
908 TTTTCTTTTTCAATTTTCTT
1 TTTTCTTTTTC-ATTTTC-T
* *
928 TTCTTCATTTTCTTTTTCT
1 TT-TTCTTTTTCATTTTCT
* ** *
947 CTCACTTTTTGA-TTTCT
1 TTTTCTTTTTCATTTTCT
* *
964 TTTTCTTTTGCAATTTCT
1 TTTTCTTTTTCATTTTCT
982 TTTTCTTTTTCATTTTCT
1 TTTTCTTTTTCATTTTCT
*
1000 TTTTGTTTT
1 TTTTCTTTT
1009 CTTTCAATTT
Statistics
Matches: 63, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
17 12 0.19
18 34 0.54
19 2 0.03
20 7 0.11
21 8 0.13
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTCTTTTTCATTTTCT
Found at i:1025 original size:6 final size:6
Alignment explanation
Indices: 908--1012 Score: 61
Period size: 6 Copynumber: 17.3 Consensus size: 6
898 CTTTTTTCGC
* * * ** *
908 TTTTCT TTTTCAA TTTTCTT TTCTTCA TTTTCT TTTTCT CTCACT TTTT-G
1 TTTTCT TTTTC-T TTTTC-T TT-TTCT TTTTCT TTTTCT TTTTCT TTTTCT
* * * * * *
958 ATTTCT TTTTCT TTTGCA ATTTCT TTTTCT TTTTCA TTTTCT TTTT-G
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
1005 TTTTCT TT
1 TTTTCT TT
1013 CAATTTCTTT
Statistics
Matches: 70, Mismatches: 25, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
5 7 0.10
6 51 0.73
7 9 0.13
8 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.72
Consensus pattern (6 bp):
TTTTCT
Found at i:1027 original size:12 final size:12
Alignment explanation
Indices: 871--1034 Score: 52
Period size: 12 Copynumber: 13.7 Consensus size: 12
861 TTTTCACTTG
871 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
882 AGCTCTCTTTCA
1 ATTTCTTTTTCA
*
894 ATTTCTTTTTTCGC
1 ATTTC-TTTTTC-A
*
908 TTTTCTTTTTCA
1 ATTTCTTTTTCA
920 ATTTTCTTTTCTTCA
1 A-TTTC-TTT-TTCA
* *
935 TTTTCTTTTTCT
1 ATTTCTTTTTCA
* ** *
947 CTCACTTTTT-G
1 ATTTCTTTTTCA
958 ATTTCTTTTTC-
1 ATTTCTTTTTCA
* ** *
969 TTTTGCAATTTCT
1 ATTT-CTTTTTCA
*
982 TTTTCTTTTTCA
1 ATTTCTTTTTCA
*
994 TTTTCTTTTT--
1 ATTTCTTTTTCA
* *
1004 GTTT-TCTTTCA
1 ATTTCTTTTTCA
1015 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
1027 ATCTCTTT
1 ATTTCTTT
1035 CTCCTTTTCT
Statistics
Matches: 111, Mismatches: 30, Indels: 23
0.68 0.18 0.14
Matches are distributed among these distances:
9 4 0.04
10 3 0.03
11 16 0.14
12 51 0.46
13 22 0.20
14 11 0.10
15 4 0.04
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.67
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:3894 original size:12 final size:11
Alignment explanation
Indices: 3879--3918 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
3869 ACTTTTCACT
*
3879 TTTTTTTTGTTC
1 TTTTTTTT-TAC
3891 TTTTTTTTTAC
1 TTTTTTTTTAC
*
3902 TTTTTTTTTAG
1 TTTTTTTTTAC
3913 TTTTTT
1 TTTTTT
3919 GCTCACTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.05, C:0.05, G:0.05, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTAC
Found at i:3903 original size:24 final size:24
Alignment explanation
Indices: 3871--3918 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3861 CTCGCAAGAC
3871 TTTTCACTTTTTTTTT-GTTCTTTT
1 TTTTCACTTTTTTTTTAGTT-TTTT
*
3895 TTTTTACTTTTTTTTTAGTTTTTT
1 TTTTCACTTTTTTTTTAGTTTTTT
3919 GCTCACTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.06, C:0.08, G:0.04, T:0.81
Consensus pattern (24 bp):
TTTTCACTTTTTTTTTAGTTTTTT
Found at i:3973 original size:18 final size:17
Alignment explanation
Indices: 3929--3962 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3919 GCTCACTTCT
3929 TTTTTTTTTGAATTTCGA
1 TTTTTTTTTGAATTTC-A
3947 TTTTTTTTTGAATTTC
1 TTTTTTTTTGAATTTC
3963 TTCTCTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.71
Consensus pattern (17 bp):
TTTTTTTTTGAATTTCA
Found at i:6188 original size:8 final size:8
Alignment explanation
Indices: 6175--6200 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
6165 TGGCGTTCAC
6175 CTATCCAT
1 CTATCCAT
6183 CTATCCAT
1 CTATCCAT
6191 CTATCCAT
1 CTATCCAT
6199 CT
1 CT
6201 TTTCACCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (8 bp):
CTATCCAT
Found at i:7008 original size:14 final size:14
Alignment explanation
Indices: 6989--7033 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
6979 AACTCATCTT
*
6989 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
7003 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
7016 AATTTAATTTAATG
1 AGTTTAATTTAATG
7030 AGTT
1 AGTT
7034 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:8041 original size:28 final size:29
Alignment explanation
Indices: 8009--8067 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
7999 ATAACCAAAC
* *
8009 CTACAAAAACTTTATAT-CATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
8037 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
8066 CT
1 CT
8068 TTGAATCCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:8309 original size:19 final size:19
Alignment explanation
Indices: 8285--8326 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
8275 TAAGTTTCAA
8285 AAAAAAAGAAAAAAAAT-TG
1 AAAAAAA-AAAAAAAATCTG
*
8304 AAAAAAAAAACAAAATCTG
1 AAAAAAAAAAAAAAATCTG
8323 AAAA
1 AAAA
8327 TTTGAACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.79, C:0.05, G:0.07, T:0.10
Consensus pattern (19 bp):
AAAAAAAAAAAAAAATCTG
Found at i:9250 original size:18 final size:18
Alignment explanation
Indices: 9227--9275 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
9217 AAAGAAAAAT
*
9227 AAAAAGAGATTGAGAGTG
1 AAAAAGAGAATGAGAGTG
* *
9245 AAAAAGAAAATGAGATTG
1 AAAAAGAGAATGAGAGTG
9263 AAAAAGAGAATGA
1 AAAAAGAGAATGA
9276 AAAAGAGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.27, T:0.14
Consensus pattern (18 bp):
AAAAAGAGAATGAGAGTG
Found at i:9277 original size:24 final size:24
Alignment explanation
Indices: 9227--9296 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 24
9217 AAAGAAAAAT
* ** * *
9227 AAAAAGAGATTGAGAGTGAAAAAG
1 AAAAAGAGATTGAAAAAGAGAATG
*
9251 AAAATGAGATTGAAAAAGAGAATG
1 AAAAAGAGATTGAAAAAGAGAATG
* * *
9275 AAAAAGAGTTTGAGAGAGAGAA
1 AAAAAGAGATTGAAAAAGAGAA
9297 AGAATGTGAA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (24 bp):
AAAAAGAGATTGAAAAAGAGAATG
Found at i:11768 original size:14 final size:14
Alignment explanation
Indices: 11749--11793 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
11739 AACTCATCTT
*
11749 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
11763 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
11776 AATTTAATTTAATG
1 AGTTTAATTTAATG
11790 AGTT
1 AGTT
11794 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:12803 original size:29 final size:29
Alignment explanation
Indices: 12770--12829 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
12760 ATAACCAAAC
* *
12770 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
12799 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
12828 CT
1 CT
12830 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:12822 original size:15 final size:15
Alignment explanation
Indices: 12776--12823 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
12766 AAACCTACAA
*
12776 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
12791 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
12805 AAACTTCATATCCAT
1 AAACTTCATATCCAT
12820 AAAC
1 AAAC
12824 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:15486 original size:35 final size:33
Alignment explanation
Indices: 15441--15515 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 33
15431 AATCTTACAA
* * *
15441 TCTTTCTCTTTTTCGT-TTTCTTTTTCTTTCATGT
1 TCTTTTTCTTTTTC-TATTTCATTTTCTATCAT-T
15475 GTCTTTTTCTTTTTCTATTTCATTTTCTATCATT
1 -TCTTTTTCTTTTTCTATTTCATTTTCTATCATT
15509 TCTTTTT
1 TCTTTTT
15516 TCTTCTCTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 7 0.19
34 2 0.06
35 27 0.75
ACGTcount: A:0.07, C:0.19, G:0.04, T:0.71
Consensus pattern (33 bp):
TCTTTTTCTTTTTCTATTTCATTTTCTATCATT
Found at i:19119 original size:56 final size:56
Alignment explanation
Indices: 19014--19120 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
19004 ATTAATGTCG
* * * * *
19014 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGCCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
19070 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
19121 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
Found at i:22606 original size:15 final size:16
Alignment explanation
Indices: 22567--22607 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
22557 AACAACACTC
22567 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
22583 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
22597 CTTTCTTTTTC
1 CTTTCTTTTTC
22608 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:22802 original size:17 final size:15
Alignment explanation
Indices: 22765--22803 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
22755 TATCTCCCAC
22765 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
22781 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
22798 TCATTT
1 TCATTT
22804 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:25337 original size:18 final size:18
Alignment explanation
Indices: 25316--25350 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25306 CACCTGAAAT
25316 TAAACACAT-TTAAACACA
1 TAAA-ACATATTAAACACA
25334 TAAAACATATTAAACAC
1 TAAAACATATTAAACAC
25351 TTAACTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAAACATATTAAACACA
Found at i:25438 original size:19 final size:19
Alignment explanation
Indices: 25411--25503 Score: 86
Period size: 19 Copynumber: 5.1 Consensus size: 19
25401 TTATTCCAAC
*
25411 AACTAAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
*
25430 AACTTAATTAACTAACATG
1 AACTTAATTAACTAAGATG
* * * *
25449 AA--TAATTTATTCCA-A-C
1 AACTTAATTAACT-AAGATG
25465 AACTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
*
25484 AACTCAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
25503 A
1 A
25504 GTAATTTATT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
16 2 0.03
17 9 0.16
18 9 0.16
19 38 0.66
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (19 bp):
AACTTAATTAACTAAGATG
Found at i:25461 original size:54 final size:54
Alignment explanation
Indices: 25401--25514 Score: 192
Period size: 54 Copynumber: 2.1 Consensus size: 54
25391 CATCATTAAA
*
25401 TTATTCCAACAACTAAATTAACTAAGATGAACTTAATTAACTAACATGAATAAT
1 TTATTCCAACAACTAAATTAACTAAGATGAACTCAATTAACTAACATGAATAAT
* * *
25455 TTATTCCAACAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAAT
1 TTATTCCAACAACTAAATTAACTAAGATGAACTCAATTAACTAACATGAATAAT
25509 TTATTC
1 TTATTC
25515 TAGTAACTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (54 bp):
TTATTCCAACAACTAAATTAACTAAGATGAACTCAATTAACTAACATGAATAAT
Found at i:25521 original size:26 final size:26
Alignment explanation
Indices: 25492--25548 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
25482 TGAACTCAAT
25492 TAACTAAGATGAGTAATTTATTCTAG
1 TAACTAAGATGAGTAATTTATTCTAG
25518 TAACTAAGATGAGTAATTTATTCTAG
1 TAACTAAGATGAGTAATTTATTCTAG
*
25544 CAACT
1 TAACT
25549 TAATTAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.37
Consensus pattern (26 bp):
TAACTAAGATGAGTAATTTATTCTAG
Found at i:28033 original size:28 final size:28
Alignment explanation
Indices: 27993--28146 Score: 256
Period size: 28 Copynumber: 5.5 Consensus size: 28
27983 TAAATTGTAC
*
27993 AGCAGTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
28021 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
28049 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
28077 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
28105 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
28132 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28147 GACTTAATAT
Statistics
Matches: 121, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 24 0.20
28 97 0.80
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:28160 original size:56 final size:56
Alignment explanation
Indices: 27968--28146 Score: 261
Period size: 56 Copynumber: 3.2 Consensus size: 56
27958 GAGATTGGCG
* * * * * *
27968 CTAAGTGTGCGGGTTTAAATTGTACAGCAGTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGCTTGATTATGTAGCA
*
28025 CTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGCTTGATTATGTAGCA
*
28081 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGCTTGATTATGTAGCA
*
28136 CTGAGTGTGCG
1 CTAAGTGTGCG
28147 GACTTAATAT
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
55 23 0.21
56 74 0.66
57 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.34
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGCTTGATTATGTAGCA
Done.