Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold943
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: 39020
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4242 original size:21 final size:21
Alignment explanation
Indices: 4193--4259 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
4183 CCTCTTTGAA
* * *
4193 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
4216 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
4237 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
4258 CC
1 CC
4260 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:7763 original size:16 final size:16
Alignment explanation
Indices: 7738--7769 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
7728 TAATGTGTTT
7738 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
*
7754 TGCTGTTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
7770 ATGCAGAATG
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:0.12, C:0.09, G:0.25, T:0.53
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:12192 original size:20 final size:20
Alignment explanation
Indices: 12169--12215 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
12159 GGGTTAAAAT
*
12169 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
12189 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
12209 TGAGCTG
1 TGAGCTG
12216 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:16635 original size:20 final size:20
Alignment explanation
Indices: 16612--16658 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
16602 GGGTTAAAAT
*
16612 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
16632 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
16652 TGAGCTG
1 TGAGCTG
16659 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:26146 original size:16 final size:16
Alignment explanation
Indices: 26125--26156 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
26115 TAATGTGTTT
26125 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
26141 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
26157 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:26469 original size:72 final size:73
Alignment explanation
Indices: 26344--26491 Score: 192
Period size: 72 Copynumber: 2.0 Consensus size: 73
26334 CAGGTAACAT
* * *
26344 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAAGCTGCCGAATTTATTGAGTGCAT
1 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGTGCAT
26409 GGGACTTG
66 GGGACTTG
* * * * * *
26417 GGACGGCATTTAAAGCGAAA-GTTGCTGTTGTA-TTTTCCCAACCAGCCGAATTTAGTGTGTGCA
1 GGACGGCATTTAAAG-AAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGTGCA
26480 TGGGACTTG
65 TGGGACTTG
26489 GGA
1 GGA
26492 TAGCATTAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
72 38 0.58
73 24 0.37
74 3 0.05
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (73 bp):
GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGTGCAT
GGGACTTG
Found at i:28436 original size:20 final size:20
Alignment explanation
Indices: 28413--28466 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
28403 AGTTTTTCCC
*
28413 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
28433 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
28453 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
28467 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:28448 original size:30 final size:30
Alignment explanation
Indices: 28413--28486 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
28403 AGTTTTTCCC
28413 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
28443 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
28473 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
28487 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:28476 original size:20 final size:20
Alignment explanation
Indices: 28413--28477 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
28403 AGTTTTTCCC
* * * *
28413 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
28433 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
28452 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
28473 AGCTC
1 AGCTC
28478 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:31193 original size:11 final size:11
Alignment explanation
Indices: 31168--31201 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
31158 AAAGAAATTG
31168 AAAGAAAAC-A
1 AAAGAAAACGA
31178 AAAGAAAACGA
1 AAAGAAAACGA
*
31189 AAAGAAAAAGA
1 AAAGAAAACGA
31200 AA
1 AA
31202 TTGCAAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAGAAAACGA
Found at i:31197 original size:6 final size:6
Alignment explanation
Indices: 31177--31273 Score: 61
Period size: 6 Copynumber: 15.8 Consensus size: 6
31167 GAAAGAAAAC
* ** * **
31177 AAAAGA AAACG- AAAAGA AAAAGA AATTGC AAAAGA AAAAGA AATCGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
* * * * *
31224 AAAAGT GAGAGA AAAAGA AAATGAA GAAAAGA AAATTGA AAAAGA AAAAG
1 AAAAGA AAAAGA AAAAGA AAAAG-A -AAAAGA AAA-AGA AAAAGA AAAAG
31274 CGAAAAAAGA
Statistics
Matches: 65, Mismatches: 22, Indels: 8
0.68 0.23 0.08
Matches are distributed among these distances:
5 4 0.06
6 50 0.77
7 7 0.11
8 4 0.06
ACGTcount: A:0.70, C:0.03, G:0.20, T:0.07
Consensus pattern (6 bp):
AAAAGA
Found at i:31227 original size:18 final size:18
Alignment explanation
Indices: 31155--31228 Score: 78
Period size: 18 Copynumber: 4.1 Consensus size: 18
31145 GAAAGAGATT
*
31155 GAAAAAGAAATTGAAAGAA
1 GAAAAAGAAATCGAAA-AA
* *
31174 AACAAAAGAAAACG-AAAA
1 GA-AAAAGAAATCGAAAAA
* *
31192 GAAAAAGAAATTGCAAAA
1 GAAAAAGAAATCGAAAAA
31210 GAAAAAGAAATCGAAAAA
1 GAAAAAGAAATCGAAAAA
31228 G
1 G
31229 TGAGAGAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
17 9 0.20
18 24 0.53
19 3 0.07
20 9 0.20
ACGTcount: A:0.70, C:0.05, G:0.18, T:0.07
Consensus pattern (18 bp):
GAAAAAGAAATCGAAAAA
Found at i:31255 original size:14 final size:13
Alignment explanation
Indices: 31234--31271 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
31224 AAAAGTGAGA
31234 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
31246 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
31261 GAAAAAGAAAA
1 GAAAAAGAAAA
31272 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:31285 original size:21 final size:21
Alignment explanation
Indices: 31235--31285 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
31225 AAAGTGAGAG
*
31235 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
31256 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
31277 AAAAAGAAA
1 AAAAAGAAA
31286 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:31325 original size:33 final size:33
Alignment explanation
Indices: 31288--31350 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
31278 AAAAGAAATT
31288 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
31321 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
31351 GTGAGTAATC
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:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:33150 original size:20 final size:20
Alignment explanation
Indices: 33127--33180 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
33117 AGTTTTTCCC
*
33127 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
33147 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
33167 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
33181 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:33162 original size:30 final size:30
Alignment explanation
Indices: 33127--33200 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
33117 AGTTTTTCCC
33127 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
33157 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
33187 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
33201 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:33190 original size:20 final size:20
Alignment explanation
Indices: 33127--33191 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
33117 AGTTTTTCCC
* * * *
33127 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
33147 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
33166 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
33187 AGCTC
1 AGCTC
33192 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:34827 original size:11 final size:11
Alignment explanation
Indices: 34813--34845 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
34803 AAAAAATATT
34813 AAAAAAATCGA
1 AAAAAAATCGA
34824 AAAAAAAGT-GA
1 AAAAAAA-TCGA
34835 AAAAAAATCGA
1 AAAAAAATCGA
34846 GTTAAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.05
11 18 0.90
12 1 0.05
ACGTcount: A:0.73, C:0.06, G:0.12, T:0.09
Consensus pattern (11 bp):
AAAAAAATCGA
Found at i:34863 original size:33 final size:30
Alignment explanation
Indices: 34779--34863 Score: 71
Period size: 33 Copynumber: 2.6 Consensus size: 30
34769 TGTATTGGAT
*
34779 TTAAAAAAGAGAGAAGAAATTCAAAAAAAATA
1 TTAAAAAAGA-AGAA-AAAGTCAAAAAAAATA
* *
34811 TTAAAAAAATCGAAAAAAAAGTGAAAAAAAATCGA
1 TT-AAAAAA--GAAGAAAAAGTCAAAAAAAAT--A
34846 GTTAAAAAAGAAGAAAAA
1 -TTAAAAAAGAAGAAAAA
34864 AAAAAGTGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
32 2 0.05
33 27 0.63
34 3 0.07
35 9 0.21
36 2 0.05
ACGTcount: A:0.69, C:0.04, G:0.13, T:0.14
Consensus pattern (30 bp):
TTAAAAAAGAAGAAAAAGTCAAAAAAAATA
Found at i:35896 original size:6 final size:6
Alignment explanation
Indices: 35873--35976 Score: 52
Period size: 6 Copynumber: 17.3 Consensus size: 6
35863 AAAGAAATTG
* * ** *
35873 AAAG-A AAACAA AAAGAA AACG-A AAAGAA AAAGAA ATTGCA AAAG-A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
35918 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
35969 AAAGAA AA
1 AAAGAA AA
35977 GCGAAAAAAG
Statistics
Matches: 70, Mismatches: 23, Indels: 11
0.67 0.22 0.11
Matches are distributed among these distances:
5 12 0.17
6 47 0.67
7 7 0.10
8 4 0.06
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:35907 original size:11 final size:11
Alignment explanation
Indices: 35873--35924 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
35863 AAAGAAATTG
35873 AAAGAAAACA-A
1 AAAGAAAA-AGA
*
35884 AAAGAAAACGA
1 AAAGAAAAAGA
35895 AAAGAAAAAGA
1 AAAGAAAAAGA
* *
35906 AATTGCAAAAGA
1 AA-AGAAAAAGA
35918 AAAGAAA
1 AAAGAAA
35925 TCGAAAAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 24 0.73
12 9 0.27
ACGTcount: A:0.75, C:0.06, G:0.15, T:0.04
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:35933 original size:17 final size:17
Alignment explanation
Indices: 35876--35931 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
35866 GAAATTGAAA
* *
35876 GAAAACAAAAAGAAAAC
1 GAAAAGAAAAAGAAATC
*
35893 GAAAAGAAAAAGAAATT
1 GAAAAGAAAAAGAAATC
35910 GCAAAAG-AAAAGAAATC
1 G-AAAAGAAAAAGAAATC
35927 GAAAA
1 GAAAA
35932 AGTGAGAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
16 4 0.12
17 25 0.74
18 5 0.15
ACGTcount: A:0.71, C:0.07, G:0.16, T:0.05
Consensus pattern (17 bp):
GAAAAGAAAAAGAAATC
Found at i:35960 original size:14 final size:14
Alignment explanation
Indices: 35940--35989 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
35930 AAAGTGAGAG
35940 AAAAAGAAAA-TGA
1 AAAAAGAAAAGTGA
*
35953 AGAAAAGAAAATTG-
1 A-AAAAGAAAAGTGA
*
35967 AAAAAGAAAAGCGA
1 AAAAAGAAAAGTGA
35981 AAAAAGAAA
1 AAAAAGAAA
35990 TTGAAAGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 11 0.34
14 19 0.59
15 2 0.06
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06
Consensus pattern (14 bp):
AAAAAGAAAAGTGA
Found at i:35969 original size:27 final size:26
Alignment explanation
Indices: 35939--35995 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
35929 AAAAGTGAGA
*
35939 GAAAAAGAAAA-TGAAGAAAAGAAAATT
1 GAAAAAGAAAAGCGAA-AAAAG-AAATT
35966 GAAAAAGAAAAGCGAAAAAAGAAATT
1 GAAAAAGAAAAGCGAAAAAAGAAATT
35992 GAAA
1 GAAA
35996 GAGAGCTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 9 0.32
27 16 0.57
28 3 0.11
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (26 bp):
GAAAAAGAAAAGCGAAAAAAGAAATT
Found at i:35973 original size:13 final size:13
Alignment explanation
Indices: 35939--35995 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
35929 AAAAGTGAGA
35939 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
35951 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
**
35966 GAAAAAGAAAAGC
1 GAAAAAGAAAATT
35979 GAAAAA-AGAAATT
1 GAAAAAGA-AAATT
35992 GAAA
1 GAAA
35996 GAGAGCTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
12 2 0.05
13 23 0.62
14 10 0.27
15 2 0.05
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:36042 original size:33 final size:32
Alignment explanation
Indices: 35992--36053 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
35982 AAAAGAAATT
35992 GAAAGAGAGCTTGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGCTTGAAAAGAAA-CAAGTGAAAAA
*
36025 GAAAGAGAGTCTT-AAAAGAAACGAGTGAA
1 GAAAGAGAG-CTTGAAAAGAAACAAGTGAA
36054 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 7 0.26
33 17 0.63
34 3 0.11
ACGTcount: A:0.55, C:0.06, G:0.26, T:0.13
Consensus pattern (32 bp):
GAAAGAGAGCTTGAAAAGAAACAAGTGAAAAA
Found at i:37850 original size:20 final size:20
Alignment explanation
Indices: 37827--37880 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
37817 AGTTTTTCCC
*
37827 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
37847 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
37867 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
37881 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:37862 original size:30 final size:30
Alignment explanation
Indices: 37827--37900 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
37817 AGTTTTTCCC
37827 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
37857 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
37887 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
37901 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:37890 original size:20 final size:20
Alignment explanation
Indices: 37827--37891 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
37817 AGTTTTTCCC
* * * *
37827 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
37847 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
37866 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
37887 AGCTC
1 AGCTC
37892 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:38089 original size:29 final size:30
Alignment explanation
Indices: 38057--38114 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
38047 TTAAGACTTT
* * *
38057 ATTAATTTGTCTAATTTA-ATTTATGTTTA
1 ATTAATGTGTCTAAATTATATTAATGTTTA
*
38086 ATTAGTGTGTCTAAATTATATTAATGTTT
1 ATTAATGTGTCTAAATTATATTAATGTTT
38115 GTTCAGCTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.55
Consensus pattern (30 bp):
ATTAATGTGTCTAAATTATATTAATGTTTA
Done.