Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4420.1
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: 60951
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.30
Warning! 2472 characters in sequence are not A, C, G, or T
Found at i:917 original size:6 final size:6
Alignment explanation
Indices: 885--998 Score: 70
Period size: 6 Copynumber: 18.5 Consensus size: 6
875 AAAGAAATTG
* * ** *
885 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
932 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
983 AAAGAA AAAGCAA AAA
1 AAAGAA AAAG-AA AAA
999 AAGAAATTGA
Statistics
Matches: 80, Mismatches: 22, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
5 4 0.05
6 59 0.74
7 13 0.16
8 4 0.05
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:972 original size:14 final size:13
Alignment explanation
Indices: 954--1010 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
944 AAAGTGAGAG
954 AAAAAGAAAATGA
1 AAAAAGAAAATGA
967 AGAAAAGAAAATTG-
1 A-AAAAGAAAA-TGA
*
981 AAAAAGAAAAAGCAA
1 AAAAAGAAAATG--A
*
996 AAAAAGAAATTGA
1 AAAAAGAAAATGA
1009 AA
1 AA
1011 GAGAGCTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
12 1 0.03
13 13 0.36
14 10 0.28
15 12 0.33
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.09
Consensus pattern (13 bp):
AAAAAGAAAATGA
Found at i:972 original size:15 final size:15
Alignment explanation
Indices: 952--1009 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 15
942 AAAAAGTGAG
952 AGAAAAAGAAAATGA
1 AGAAAAAGAAAATGA
967 AG-AAAAGAAAAT--
1 AGAAAAAGAAAATGA
* *
979 TGAAAAAGAAAAAGCA
1 AGAAAAAGAAAATG-A
*
995 A-AAAAAGAAATTGA
1 AGAAAAAGAAAATGA
1009 A
1 A
1010 AGAGAGCTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
12 1 0.03
13 9 0.26
14 12 0.35
15 12 0.35
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.09
Consensus pattern (15 bp):
AGAAAAAGAAAATGA
Found at i:983 original size:27 final size:27
Alignment explanation
Indices: 953--1010 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
943 AAAAGTGAGA
* *
953 GAAAAAGAAAATG-AAGAAAAGAAAATT
1 GAAAAAGAAAAAGCAAAAAAAG-AAATT
980 GAAAAAGAAAAAGCAAAAAAAGAAATT
1 GAAAAAGAAAAAGCAAAAAAAGAAATT
1007 GAAA
1 GAAA
1011 GAGAGCTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.09
Consensus pattern (27 bp):
GAAAAAGAAAAAGCAAAAAAAGAAATT
Found at i:987 original size:13 final size:12
Alignment explanation
Indices: 871--990 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
861 AGAAAGAGAT
*
871 TGAAAAAGAAAT
1 TGAAAAAGAAAA
883 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
893 -CAAAAAGAAAA
1 TGAAAAAGAAAA
*
904 CGAAAAAGAAAA
1 TGAAAAAGAAAA
* **
916 AGAAATTGCAAAA
1 TGAAAAAG-AAAA
929 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* * *
939 TCAAAAAAGTGAGA
1 T-GAAAAAG-AAAA
953 -GAAAAAGAAAA
1 TGAAAAAGAAAA
964 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
978 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
991 AGCAAAAAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
10 10 0.12
11 10 0.12
12 35 0.42
13 14 0.17
14 12 0.14
15 2 0.02
ACGTcount: A:0.71, C:0.03, G:0.17, T:0.08
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:2897 original size:20 final size:20
Alignment explanation
Indices: 2874--2919 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2864 CCAGCTCGAA
*
2874 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
2894 TTAGCTCGTGTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
2914 TTAGCT
1 TTAGCT
2920 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:2910 original size:30 final size:30
Alignment explanation
Indices: 2876--2939 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
2866 AGCTCGAATT
*
2876 AGCTCACA-TGAGCTTAATTTAGCTCGTGTG
1 AGCTCA-ATTGAGCTTAATTTAGCTCATGTG
* * *
2906 AGCTCAATTTAGCTTACTTTAGCTCATTTG
1 AGCTCAATTGAGCTTAATTTAGCTCATGTG
2936 AGCT
1 AGCT
2940 TGGCTTAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCAATTGAGCTTAATTTAGCTCATGTG
Found at i:3617 original size:133 final size:133
Alignment explanation
Indices: 3379--3643 Score: 503
Period size: 133 Copynumber: 2.0 Consensus size: 133
3369 CCGACATCAC
3379 ATTGAATGTATAATGTGCATGTAAAAAGGGGAGAACGAATTTACAAGGTACATGCTTCCATTCAT
1 ATTGAATGTATAATGTGCATGTAAAAAGGGGAGAACGAATTTACAAGGTACATGCTTCCATTCAT
*
3444 GAACCAGCCCATCATTAAAGTTTTAATTAAGAGAGATGCATGACCCATGCACCTAGCATTCGTCC
66 GAACCAGCCCATCATTAAAGCTTTAATTAAGAGAGATGCATGACCCATGCACCTAGCATTCGTCC
3509 AAT
131 AAT
*
3512 ATTGAATGTATAATGTGCATGTACAAAGGGGAGAACGAATTTACAAGGTACATGCTTCCATTCAT
1 ATTGAATGTATAATGTGCATGTAAAAAGGGGAGAACGAATTTACAAGGTACATGCTTCCATTCAT
*
3577 GAACCAGCCCATCATTAAAGCTTTAATTAAGAGAGATGCATTACCCATGCACCTAGCATTCGTCC
66 GAACCAGCCCATCATTAAAGCTTTAATTAAGAGAGATGCATGACCCATGCACCTAGCATTCGTCC
3642 AA
131 AA
3644 GAGGGGTTGG
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
133 129 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (133 bp):
ATTGAATGTATAATGTGCATGTAAAAAGGGGAGAACGAATTTACAAGGTACATGCTTCCATTCAT
GAACCAGCCCATCATTAAAGCTTTAATTAAGAGAGATGCATGACCCATGCACCTAGCATTCGTCC
AAT
Found at i:8300 original size:30 final size:31
Alignment explanation
Indices: 8266--8362 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
8256 AGCTCACTCC
*
8266 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
8296 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
8326 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
8356 TAGCTCA
1 TAGCTCA
8363 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:10055 original size:13 final size:13
Alignment explanation
Indices: 10037--10080 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
10027 TTATACAAGT
10037 AAAAAAAATTCG-
1 AAAAAAAATTCGA
*
10049 AAAAAAAATTCAA
1 AAAAAAAATTCGA
10062 AAAAAAAATAT-GA
1 AAAAAAAAT-TCGA
10075 AAAAAA
1 AAAAAA
10081 TGTGTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 11 0.39
13 16 0.57
14 1 0.04
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.14
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:10068 original size:12 final size:12
Alignment explanation
Indices: 10037--10068 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
10027 TTATACAAGT
*
10037 AAAAAAAATTCG
1 AAAAAAAATTCA
10049 AAAAAAAATTCA
1 AAAAAAAATTCA
10061 AAAAAAAA
1 AAAAAAAA
10069 ATATGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:11030 original size:15 final size:14
Alignment explanation
Indices: 10999--11057 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 14
10989 AAGAGAAAAC
10999 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
11015 AAAGTAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
11030 AAAGAAAATGTAATAA
1 AAAGAAAA-G-AAGAA
11046 AAAGAAAA-AAGA
1 AAAGAAAAGAAGA
11058 GGCAAGAGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 3 0.08
14 4 0.11
15 10 0.26
16 16 0.42
17 5 0.13
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:11158 original size:30 final size:31
Alignment explanation
Indices: 11124--11205 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
11114 TTTGAAAAGC
*
11124 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
* * *
11154 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
* *
11184 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAAAGAAAAAGAAAT
11206 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.66, C:0.01, G:0.22, T:0.11
Consensus pattern (31 bp):
AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
Found at i:11178 original size:24 final size:24
Alignment explanation
Indices: 11129--11198 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
11119 AAAGCAAAAA
*
11129 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAATGAAATT
* *
11153 GAAAAAGAGAACGAAAA-GAAATTT
1 GAAAAAGAAAAAGAAAATGAAA-TT
* ** *
11177 GAGAGTGAAAAAGAAGATGAAA
1 GAAAAAGAAAAAGAAAATGAAA
11199 AAGAAATTGA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
23 3 0.09
24 28 0.80
25 4 0.11
ACGTcount: A:0.63, C:0.01, G:0.24, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAATGAAATT
Found at i:13354 original size:30 final size:30
Alignment explanation
Indices: 13320--13416 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
13310 AGCTCACTCC
13320 TAGCTC-ACATTTAGCTCACGAGCTAAACCT
1 TAGCTCAAC-TTTAGCTCACGAGCTAAACCT
* * * * * *
13350 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
13380 CAGCTCAACTTTAGCTCACGTGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
13410 TAGCTCA
1 TAGCTCA
13417 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 48 0.96
31 2 0.04
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:15540 original size:10 final size:10
Alignment explanation
Indices: 15525--15586 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
15515 TTTGAACCAT
*
15525 TACCAATTCG
1 TACCAATTCA
*
15535 TACCAAATACCA
1 TACC-AAT-TCA
*
15547 TACCATTTCA
1 TACCAATTCA
15557 TACCAATTCCA
1 TACCAATT-CA
* *
15568 TACCATTTCG
1 TACCAATTCA
15578 TACCAATTC
1 TACCAATTC
15587 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:15570 original size:21 final size:21
Alignment explanation
Indices: 15525--15587 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
15515 TTTGAACCAT
* *
15525 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
15547 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
15568 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
15588 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:16048 original size:30 final size:31
Alignment explanation
Indices: 16014--16110 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
16004 AGCTCACTCC
*
16014 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
16044 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
16074 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
16104 TAGCTCA
1 TAGCTCA
16111 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:19487 original size:19 final size:18
Alignment explanation
Indices: 19463--19504 Score: 75
Period size: 19 Copynumber: 2.3 Consensus size: 18
19453 TAAAAAAAAG
19463 AAAAAAATTTCGAAGTAA
1 AAAAAAATTTCGAAGTAA
19481 TAAAAAAATTTCGAAGTAA
1 -AAAAAAATTTCGAAGTAA
19500 AAAAA
1 AAAAA
19505 TTCGAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (18 bp):
AAAAAAATTTCGAAGTAA
Found at i:19503 original size:15 final size:15
Alignment explanation
Indices: 19464--19518 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
19454 AAAAAAAAGA
19464 AAAAAATTTCGAAGTAAT
1 AAAAAATTTCGAAG---T
19482 AAAAAAATTTCGAAGT
1 -AAAAAATTTCGAAGT
* *
19498 AAAAAAATTCGAAAT
1 AAAAAATTTCGAAGT
19513 AAAAAA
1 AAAAAA
19519 GAATTGAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 19 0.56
16 1 0.03
19 14 0.41
ACGTcount: A:0.64, C:0.05, G:0.09, T:0.22
Consensus pattern (15 bp):
AAAAAATTTCGAAGT
Found at i:19534 original size:17 final size:16
Alignment explanation
Indices: 19459--19518 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 16
19449 TAAGTAAAAA
19459 AAAG-AAAAAAATTTCG
1 AAAGTAAAAAAA-TTCG
*
19475 AAGTAATAAAAAAATTTCG
1 AA--AGTAAAAAAA-TTCG
19494 -AAGTAAAAAAATTCG
1 AAAGTAAAAAAATTCG
19509 AAA-TAAAAAA
1 AAAGTAAAAAA
19519 GAATTGAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 11 0.29
16 13 0.34
18 2 0.05
19 12 0.32
ACGTcount: A:0.65, C:0.05, G:0.10, T:0.20
Consensus pattern (16 bp):
AAAGTAAAAAAATTCG
Found at i:19716 original size:15 final size:15
Alignment explanation
Indices: 19696--19743 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
19686 TCAAAGATGG
19696 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
19711 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
19725 GTTTATGGATATAAA
1 GTTTATGGATATGAA
19740 GTTT
1 GTTT
19744 TTGTAGGTTT
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:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:19730 original size:14 final size:14
Alignment explanation
Indices: 19690--19733 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
19680 AAGGATTCAA
19690 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
19704 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
19719 AGATGGGTTTATGG
1 AGATGGGTTTATGG
19733 A
1 A
19734 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:19759 original size:29 final size:29
Alignment explanation
Indices: 19690--19749 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
19680 AAGGATTCAA
*
19690 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
19719 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
19748 AG
1 AG
19750 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:23246 original size:21 final size:19
Alignment explanation
Indices: 23221--23282 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 19
23211 CAAATGAGAG
*
23221 AAAAAGCAAAAGAAAAGTACA
1 AAAAAGAAAAAGAAAAG-A-A
*
23242 AAAAA-ATAAAAGAAGAGAA
1 AAAAAGA-AAAAGAAAAGAA
*
23261 AAATAAGAAAAAGAAAACAA
1 AAA-AAGAAAAAGAAAAGAA
23281 AA
1 AA
23283 GAGAGTGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
19 4 0.12
20 15 0.44
21 15 0.44
ACGTcount: A:0.77, C:0.05, G:0.13, T:0.05
Consensus pattern (19 bp):
AAAAAGAAAAAGAAAAGAA
Found at i:23317 original size:22 final size:21
Alignment explanation
Indices: 23268--23328 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
23258 GAAAAATAAG
*
23268 AAAAAGAAAACAAAAGAGAGT
1 AAAAAGAAAACAAAAGAGAGA
*
23289 GAAAAGAAAATCAAAAGAG-GA
1 AAAAAGAAAA-CAAAAGAGAGA
*
23310 AAAGAAGAAAA-AGAAGAGA
1 AAA-AAGAAAACAAAAGAGA
23329 AAATTGAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 6 0.18
21 12 0.36
22 15 0.45
ACGTcount: A:0.70, C:0.03, G:0.23, T:0.03
Consensus pattern (21 bp):
AAAAAGAAAACAAAAGAGAGA
Found at i:25376 original size:16 final size:16
Alignment explanation
Indices: 25351--25382 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25341 ATAAGATTGA
*
25351 TGCATTAAATAAATTT
1 TGCATCAAATAAATTT
25367 TGCATCAAATAAATTT
1 TGCATCAAATAAATTT
25383 GAACATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (16 bp):
TGCATCAAATAAATTT
Found at i:32144 original size:248 final size:248
Alignment explanation
Indices: 31704--32200 Score: 789
Period size: 248 Copynumber: 2.0 Consensus size: 248
31694 AAAAAAGTTC
* * * *
31704 TTGTAACACCTCTTACCAATACCCGAGGCCGGGATAAGGTACGAGGTGTTACTGGACAAACATAC
1 TTGTAACACCCCTTACCAATACCCGACGCCGGGATAAGGTACGAGGTGCTACCGGACAAACATAC
* *
31769 AAACATTAAACTAAAATACGGGCCATAAAATTTCATTCATATTTCAAAACGTTCATTCACTTACA
66 AAACATTAAACTAAAATACGAGCCATAAAATTTCATTCATATTTCAAAACATTCATTCACTTACA
* * *
31834 CATAGTCCCTTATTTGAGTCTATGAAGCCCAAAACATACTTTAGAAAGTGTTCGGGACTAAACCG
131 CATAGTCCCTTATTTGAGTCTACGAAGCCCAAAACATACTTTAGAAAGGGTTCGGAACTAAACCG
* * *
31899 AGAACTTACAAAAATCTTGGAAATTTCATGCTTTAAGGCTCCACACGCCCGTG
196 AGAACTTACAAAAATCTTAGAAATTTCATACTTTAAGGCCCCACACGCCCGTG
** *
31952 TTGTAACACCCCTTACCCGTACCCGACGCTGGGATAAGGTACGAGGCT-CTACCGGACAAACATA
1 TTGTAACACCCCTTACCAATACCCGACGCCGGGATAAGGTACGAGG-TGCTACCGGACAAACATA
* *
32016 CAAATATTAAACTAAAATACGAGCCATAAAATTTCATTCATATTTCAAAGCATTCATTCACTTAC
65 CAAACATTAAACTAAAATACGAGCCATAAAATTTCATTCATATTTCAAAACATTCATTCACTTAC
* * *
32081 ACATAGTCCTTTATTTGAGTTTACGGAGCCCAAAACATACTTTAGAAAGGGTTCGGAACTAAACC
130 ACATAGTCCCTTATTTGAGTCTACGAAGCCCAAAACATACTTTAGAAAGGGTTCGGAACTAAACC
*
32146 GAGAACTTACAAAAATCTTAGAAATTTCATACTTTAAGGCCCCATACGCCCGTG
195 GAGAACTTACAAAAATCTTAGAAATTTCATACTTTAAGGCCCCACACGCCCGTG
32200 T
1 T
32201 CCCAAAGTCG
Statistics
Matches: 227, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
248 226 1.00
249 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (248 bp):
TTGTAACACCCCTTACCAATACCCGACGCCGGGATAAGGTACGAGGTGCTACCGGACAAACATAC
AAACATTAAACTAAAATACGAGCCATAAAATTTCATTCATATTTCAAAACATTCATTCACTTACA
CATAGTCCCTTATTTGAGTCTACGAAGCCCAAAACATACTTTAGAAAGGGTTCGGAACTAAACCG
AGAACTTACAAAAATCTTAGAAATTTCATACTTTAAGGCCCCACACGCCCGTG
Found at i:35305 original size:23 final size:22
Alignment explanation
Indices: 35253--35305 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
35243 TCCACGTCTT
*
35253 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
35275 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
35298 TTTCTTTT
1 TTTCTTTT
35306 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:37262 original size:59 final size:59
Alignment explanation
Indices: 37190--37306 Score: 207
Period size: 59 Copynumber: 2.0 Consensus size: 59
37180 CTTAAGATAG
*
37190 AAAAAGGCTGAAAACACAATAAGAACAGAAAATAAATTAGATAAAGATTCGGCACAAGC
1 AAAAAGGCTGAAAACACAATAAGAACAGAAAATAAATTAGATAAAGATTCAGCACAAGC
* *
37249 AAAAAGGCTGAAAACACAATAAGAACAGAAAATAGATTAGATAATGATTCAGCACAAG
1 AAAAAGGCTGAAAACACAATAAGAACAGAAAATAAATTAGATAAAGATTCAGCACAAG
37307 TAGAAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.56, C:0.13, G:0.17, T:0.15
Consensus pattern (59 bp):
AAAAAGGCTGAAAACACAATAAGAACAGAAAATAAATTAGATAAAGATTCAGCACAAGC
Found at i:37651 original size:6 final size:6
Alignment explanation
Indices: 37640--37664 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
37630 TAATTAGAAC
37640 ACTAAA ACTAAA ACTAAA ACTAAA A
1 ACTAAA ACTAAA ACTAAA ACTAAA A
37665 AAAAACTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
ACTAAA
Found at i:39728 original size:30 final size:30
Alignment explanation
Indices: 39694--39781 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
39684 CTAGCTTATA
* *
39694 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTTAAGAGCTAAACCTTAGCTCAAC
* * *
39724 TTCAGCTTAGGAG-TATAATCTCAGCTCAAC
1 TTCAGCTTAAGAGCTA-AACCTTAGCTCAAC
* * *
39754 TTTAGCTTAAGGGCTAAAGCTTAGCTCA
1 TTCAGCTTAAGAGCTAAACCTTAGCTCA
39782 TTTTAGCTCA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 2 0.04
30 43 0.91
31 2 0.04
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (30 bp):
TTCAGCTTAAGAGCTAAACCTTAGCTCAAC
Found at i:46449 original size:30 final size:30
Alignment explanation
Indices: 46415--46511 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
46405 TAAACTAAAA
*
46415 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
46445 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
46475 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
46504 ATGAGCTA
1 -TGAGCTA
46512 CTTAAACACA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:48294 original size:30 final size:30
Alignment explanation
Indices: 48223--48305 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
48213 CTTTTGTTTC
* *
48223 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
48254 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
48283 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
48306 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:48305 original size:18 final size:18
Alignment explanation
Indices: 48256--48311 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
48246 CACTCTCAAA
* *
48256 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
48273 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
48291 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
48310 TT
1 TT
48312 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:48312 original size:12 final size:12
Alignment explanation
Indices: 48281--48305 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48271 TTTTTCAATC
48281 TCATTTTCTTTT
1 TCATTTTCTTTT
48293 TCATTTTCTTTT
1 TCATTTTCTTTT
48305 T
1 T
48306 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:48323 original size:12 final size:12
Alignment explanation
Indices: 48308--48338 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
48298 TTCTTTTTGC
48308 TTTTCAAAGGCT
1 TTTTCAAAGGCT
48320 TTTTCAAAGGCT
1 TTTTCAAAGGCT
48332 TTTTCAA
1 TTTTCAA
48339 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:48426 original size:6 final size:5
Alignment explanation
Indices: 48386--48448 Score: 51
Period size: 5 Copynumber: 12.0 Consensus size: 5
48376 CTCTTGCCTC
48386 TCTTT TCTTT T-TATT TCATTT TCATTT TC--T TCTTT TGCTTT TGCTTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TCTTT TCTTT T-CTTT T-C-TTT
48434 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
48449 GTTTTCTCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
3 3 0.06
4 1 0.02
5 24 0.47
6 18 0.35
7 5 0.10
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (5 bp):
TCTTT
Found at i:50430 original size:30 final size:30
Alignment explanation
Indices: 50396--50492 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
50386 TAAACTAAAA
50396 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
50426 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
50456 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
50486 TGAGCTA
1 TGAGCTA
50493 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:50901 original size:18 final size:18
Alignment explanation
Indices: 50876--50917 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
50866 AGAGTGAAAG
50876 AAAAGAAAA-AAAACTTGA
1 AAAAGAAAACAAAA-TTGA
*
50894 ACAAGAAAACAAAATTGA
1 AAAAGAAAACAAAATTGA
50912 AAAAGA
1 AAAAGA
50918 GATTGAGCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.71, C:0.07, G:0.12, T:0.10
Consensus pattern (18 bp):
AAAAGAAAACAAAATTGA
Found at i:52235 original size:36 final size:36
Alignment explanation
Indices: 52188--52260 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
52178 GTGAATGAGA
52188 TTGAGAAAAGTTCTTTAGAGATTTTTATTCCTAGTG
1 TTGAGAAAAGTTCTTTAGAGATTTTTATTCCTAGTG
52224 TTGAGAAAAGTTCTTTAGAGATTTTTATTCCTAGTG
1 TTGAGAAAAGTTCTTTAGAGATTTTTATTCCTAGTG
52260 T
1 T
52261 CACTAATTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.45
Consensus pattern (36 bp):
TTGAGAAAAGTTCTTTAGAGATTTTTATTCCTAGTG
Found at i:54657 original size:30 final size:30
Alignment explanation
Indices: 54623--54719 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
54613 AGCTCACTCC
*
54623 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTTACGAGCTAAACCT
* * * * *
54653 TAGCTCAACTTCACCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTTACGAGCTAAACCT
* * *
54683 CAGCTCAACTTTAGCTTACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTTACGAGCTAAACCT
54713 TAGCTCA
1 TAGCTCA
54720 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTTACGAGCTAAACCT
Found at i:58813 original size:61 final size:61
Alignment explanation
Indices: 58704--58837 Score: 205
Period size: 61 Copynumber: 2.1 Consensus size: 61
58694 ATTTGAATTT
* * * *
58704 TTGTGAAACAAGGCCAGAGTGATTTCTGGATCCCCTGTTCTGACTTTAAAAATTCATCATAAA
1 TTGT-AAA-AAGGCCAGAGTGATTTCTAGATCCCCTGTTCTAAATTTAAAAATTCATAATAAA
58767 TTGTAAAAAGGCCAGAGTGATTTCTAGATCCCCTGTTCTAAATTTAAAAATTCATAATAAA
1 TTGTAAAAAGGCCAGAGTGATTTCTAGATCCCCTGTTCTAAATTTAAAAATTCATAATAAA
58828 TTGTACAAAA
1 TTGTA-AAAA
58838 ATAATTAGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
61 55 0.83
62 7 0.11
63 4 0.06
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (61 bp):
TTGTAAAAAGGCCAGAGTGATTTCTAGATCCCCTGTTCTAAATTTAAAAATTCATAATAAA
Found at i:59111 original size:56 final size:56
Alignment explanation
Indices: 59019--59125 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
59009 AATTGGCTTG
* *
59019 ACCAAAAATTCTAGAAAAAAATAGTAAATTATATATATGAGTCTAGTTTCAGCCCT
1 ACCAAAAATTCTAGAAAAAAATAGTAAAGTAGATATATGAGTCTAGTTTCAGCCCT
* * *
59075 ACCAAAAATTCTAGGAAAAATTTGCT-AAGTAGATATATGAGTCTAGTTTCA
1 ACCAAAAATTCTAGAAAAAAATAG-TAAAGTAGATATATGAGTCTAGTTTCA
59126 AGGAAAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
56 44 0.98
57 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (56 bp):
ACCAAAAATTCTAGAAAAAAATAGTAAAGTAGATATATGAGTCTAGTTTCAGCCCT
Found at i:60097 original size:15 final size:15
Alignment explanation
Indices: 60077--60124 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
60067 TCAAAGATGG
60077 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
60092 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
60106 GTTTATGGATATAAA
1 GTTTATGGATATGAA
60121 GTTT
1 GTTT
60125 TTATAGGTTT
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:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:60111 original size:14 final size:14
Alignment explanation
Indices: 60071--60114 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
60061 AAGGATTCAA
60071 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
60085 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
60100 AGATGGGTTTATGG
1 AGATGGGTTTATGG
60114 A
1 A
60115 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:60354 original size:57 final size:55
Alignment explanation
Indices: 60266--60377 Score: 188
Period size: 57 Copynumber: 2.0 Consensus size: 55
60256 AGAATATGAG
60266 AACCTCGACCCACTACTTAGCAAAGTAGGAACCTTGGCATGTTTGAACGCCACACTA
1 AACCTCGACCCACTACTTAGCAAAGTAGGAACCTTGGCATG--TGAACGCCACACTA
* *
60323 AACCTCGACCCGCTACTTAGCAAAGTAGGAACCTTGGTATGTGAACGCCACACTA
1 AACCTCGACCCACTACTTAGCAAAGTAGGAACCTTGGCATGTGAACGCCACACTA
60378 CGAGTAGTGA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
55 14 0.26
57 39 0.74
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (55 bp):
AACCTCGACCCACTACTTAGCAAAGTAGGAACCTTGGCATGTGAACGCCACACTA
Done.