Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1061
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: 63327
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:4531 original size:21 final size:21
Alignment explanation
Indices: 4482--4522 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
4472 AAGTGAAAGT
4482 GAAAAGATTAGAAAATATACC
1 GAAAAGATTAGAAAATATACC
4503 GAAAAGATTAGAAAATATAC
1 GAAAAGATTAGAAAATATAC
4523 TAACAAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.59, C:0.07, G:0.15, T:0.20
Consensus pattern (21 bp):
GAAAAGATTAGAAAATATACC
Found at i:5277 original size:20 final size:20
Alignment explanation
Indices: 5233--5307 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
5223 AAAAAGACAG
** *
5233 AATGTATCGATACATCGAAG
1 AATGTATCGATACATTAAAA
* *
5253 AATGTATCGATACATTCACA
1 AATGTATCGATACATTAAAA
* * *
5273 CATGTACCGATACACTAAAA
1 AATGTATCGATACATTAAAA
5293 AATGTATCGATACAT
1 AATGTATCGATACAT
5308 CTGGGTAAAA
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:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACATTAAAA
Found at i:5795 original size:16 final size:17
Alignment explanation
Indices: 5774--5806 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
5764 TTTTATTTAT
5774 AAATTAAA-AAATATAA
1 AAATTAAATAAATATAA
5790 AAATTAAATAAATATAA
1 AAATTAAATAAATATAA
5807 TATATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATTAAATAAATATAA
Found at i:5901 original size:12 final size:12
Alignment explanation
Indices: 5886--5928 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
5876 TATAAATTAT
*
5886 TTATTTAAAATA
1 TTATTTTAAATA
*
5898 TTATTTTCAATA
1 TTATTTTAAATA
*
5910 TAATTTTAAATA
1 TTATTTTAAATA
5922 TTATTTT
1 TTATTTT
5929 GAAGTATACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (12 bp):
TTATTTTAAATA
Found at i:5917 original size:25 final size:27
Alignment explanation
Indices: 5889--5951 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 27
5879 AAATTATTTA
5889 TTTAAAATATTATTTTCAA-TATA-AT
1 TTTAAAATATTATTTTCAAGTATACAT
*
5914 TTT-AAATATTATTTTGAAGTATACAT
1 TTTAAAATATTATTTTCAAGTATACAT
5940 TATTAAAATATT
1 T-TTAAAATATT
5952 TTTAAATGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 14 0.42
25 7 0.21
26 3 0.09
27 2 0.06
28 7 0.21
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (27 bp):
TTTAAAATATTATTTTCAAGTATACAT
Found at i:10708 original size:97 final size:97
Alignment explanation
Indices: 10574--10806 Score: 274
Period size: 97 Copynumber: 2.4 Consensus size: 97
10564 TTTTTATTCA
*
10574 CGGGGATACTC-AACCCCATTCTTTTGAGGGAATACTCCAACCT-CGTTTTCAAACTTGTCAAGA
1 CGGGGATACTCTAACCCCATTCTTTCGAGGGAATACTCCAA-CTACGTTTTCAAACTTGTCAAGA
* * * *
10637 TTTAAATTTTATTTTTGCTTAAATTGTCATCAT
65 TTCAAATCTTATTTTTGCCTAAATTATCATCAT
* ** * *
10670 CGGGGATACCCTAACCCCATTCTTTCGATGGG-ATACTCCAACTATTTTTTTAAACTTGTCACGA
1 CGGGGATACTCTAACCCCATTCTTTCGA-GGGAATACTCCAACTACGTTTTCAAACTTGTCAAGA
* *
10734 TTCAAATCTTATTTTTGCCTATATTATCATCGT
65 TTCAAATCTTATTTTTGCCTAAATTATCATCAT
* * * * *
10767 GGGGGATACTCTAACCCCATTCCTCCGAGGGTATAGTCCA
1 CGGGGATACTCTAACCCCATTCTTTCGAGGGAATACTCCA
10807 GCCCTATTTT
Statistics
Matches: 116, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
96 15 0.13
97 98 0.84
98 3 0.03
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (97 bp):
CGGGGATACTCTAACCCCATTCTTTCGAGGGAATACTCCAACTACGTTTTCAAACTTGTCAAGAT
TCAAATCTTATTTTTGCCTAAATTATCATCAT
Found at i:11709 original size:19 final size:19
Alignment explanation
Indices: 11665--11720 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
11655 CTACCAGTTT
**
11665 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
*
11685 CATGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
*
11704 CATGTATCGATATAATG
1 CATGTATCGATACAATG
11721 TATCGATACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:15298 original size:52 final size:52
Alignment explanation
Indices: 15220--15348 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
15210 CGAAATATGA
15220 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
**
15272 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
15324 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
15349 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
Found at i:15359 original size:52 final size:51
Alignment explanation
Indices: 15220--15368 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
15210 CGAAATATGA
15220 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
*
15272 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
** *
15324 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATTGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
15369 ATGTATCGAT
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 86 0.96
53 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:15459 original size:33 final size:33
Alignment explanation
Indices: 15422--15488 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
15412 AGTAGCTTAA
15422 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
15455 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
15488 A
1 A
15489 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:15462 original size:13 final size:13
Alignment explanation
Indices: 15444--15468 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15434 CAAAAAAATA
15444 TGTATCGATACAT
1 TGTATCGATACAT
15457 TGTATCGATACA
1 TGTATCGATACA
15469 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:16993 original size:20 final size:20
Alignment explanation
Indices: 16966--17020 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
16956 TAAAATTTCC
*
16966 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
16986 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
17006 AAATGTATCGATACA
1 AAATGTATCGATACA
17021 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:17064 original size:19 final size:18
Alignment explanation
Indices: 17040--17107 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
17030 CAGTAGCTAA
17040 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
17059 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
17074 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
17091 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
17108 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:17080 original size:13 final size:13
Alignment explanation
Indices: 17062--17086 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17052 ACAATACTTA
17062 TGTATCGATACAT
1 TGTATCGATACAT
17075 TGTATCGATACA
1 TGTATCGATACA
17087 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:17084 original size:32 final size:32
Alignment explanation
Indices: 17043--17105 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
17033 TAGCTAATTA
*
17043 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
17075 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
17106 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:19329 original size:13 final size:13
Alignment explanation
Indices: 19292--19331 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
19282 ATAGTAACAT
19292 ATGTATCGATACA
1 ATGTATCGATACA
* **
19305 TTGTATAAATACA
1 ATGTATCGATACA
19318 ATGTATCGATACA
1 ATGTATCGATACA
19331 A
1 A
19332 AGAACATTGT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:23894 original size:15 final size:15
Alignment explanation
Indices: 23864--23898 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
23854 TGAGTCAACT
*
23864 TCATCATTGTCATCA
1 TCATCATTATCATCA
*
23879 TCATCATTATCTTCA
1 TCATCATTATCATCA
23894 TCATC
1 TCATC
23899 TTTGTTGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.43
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:25532 original size:33 final size:33
Alignment explanation
Indices: 25495--25559 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
25485 TTTGGGACCA
* * *
25495 TGTATCGATACCATTTGTCATGTATCGATACAT
1 TGTATCGATACAATGTGCCATGTATCGATACAT
*
25528 TGTATCGATATAATGTGCCATGTATCGATACA
1 TGTATCGATACAATGTGCCATGTATCGATACA
25560 AACAGTGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCGATACAT
Found at i:27056 original size:158 final size:156
Alignment explanation
Indices: 26763--27215 Score: 457
Period size: 158 Copynumber: 2.9 Consensus size: 156
26753 GGTATTTTTG
* *
26763 TAATTTTTCTAGAATCGAGTCCTAAGTTT-TCATCGAGATGCTTTTAAGCCAAAGGTGGGCATTT
1 TAATTTTTCTAGAATCGAGTCCTAA-TTTGTCATCGAGATGCTTTTATGCCAAAGGT-GGAATTT
* * ** * * *
26827 AGGATAGGTTTATTCCATTTATGATCTTTTTTAAGT-TCTTTAGGGTTATTAGGATACTTTTATA
64 AGGATAGGTTCATCCCATTTATGATCCATTTTAAGTCT-TTTAGGGTTACTAAGATACTTTTATG
** * * ***
26891 TCAAAGGTATACTCATAGGGGTTTTTTTCA
128 TTGAAGGTATACCCATA-GAGACATTTTCA
* * * *
26921 TAATTTTTCTAGAATCAAATCCTAATTTGTC-CCTGAGATGCTTTTATGTCAAAGGTGGATATTT
1 TAATTTTTCTAGAATCGAGTCCTAATTTGTCATC-GAGATGCTTTTATGCCAAAGGTGGA-ATTT
* * *
26985 TGGATAGGTTCATCCCATTTATGATCCCTTTTAAGTCTTTTAAGGTTACTAAGATACTTTTATGT
64 AGGATAGGTTCATCCCATTTATGATCCATTTTAAGTCTTTTAGGGTTACTAAGATACTTTTATGT
27050 TGAAGGTATACCCATAGAGACATTTTCA
129 TGAAGGTATACCCATAGAGACATTTTCA
* * * *** * *
27078 TAATTGTTCTA-AAACTGAGTCATGGGTTGTCATCGGGATGCTTTTATGCCAAAGATGTGAATTT
1 TAATTTTTCTAGAATC-GAGTCCTAATTTGTCATCGAGATGCTTTTATGCCAAAGGTG-GAATTT
* ** * * *
27142 AGGATAGGTTCACCCCATTTATGAT-CATTTTAAAGTCCATTAGGGTAACCAAGATACTTTCATG
64 AGGATAGGTTCATCCCATTTATGATCCATTTT-AAGTCTTTTAGGGTTACTAAGATACTTTTATG
27206 TTGAAGGTAT
128 TTGAAGGTAT
27216 GCCCTAAGGA
Statistics
Matches: 244, Mismatches: 43, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
156 8 0.03
157 116 0.48
158 119 0.49
159 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (156 bp):
TAATTTTTCTAGAATCGAGTCCTAATTTGTCATCGAGATGCTTTTATGCCAAAGGTGGAATTTAG
GATAGGTTCATCCCATTTATGATCCATTTTAAGTCTTTTAGGGTTACTAAGATACTTTTATGTTG
AAGGTATACCCATAGAGACATTTTCA
Found at i:27152 original size:157 final size:157
Alignment explanation
Indices: 26785--27215 Score: 422
Period size: 157 Copynumber: 2.7 Consensus size: 157
26775 AATCGAGTCC
* * * * *
26785 TAAGTTTTCATCGAGATGCTTTTAAGCCAAAGGTGGGCATTTAGGATAGGTTTATTCCATTTATG
1 TAAGTTGTCATCGAGATGCTTTTATGCCAAAGGT-GGAATTTAGGATAGGTTCATCCCATTTATG
** * * * ** * * **
26850 ATCTTTTTTAAGT-TCTTTAGGGTTATTAGGATACTTTTATATCAAAGGTATACTCATAGGGGTT
65 ATCCATTTTAAGTCT-TTTAGGGTTACTAAGATACTTTTATGTTGAAGGTATACCCATAGGAGAC
* * * *
26914 TTTTTCATAATTTTTCTAGAATCAAATCC
129 ATTTTCATAATTGTTCTAAAATCAAATCA
* * * *
26943 TAATTTGTC-CCTGAGATGCTTTTATGTCAAAGGTGGATATTTTGGATAGGTTCATCCCATTTAT
1 TAAGTTGTCATC-GAGATGCTTTTATGCCAAAGGTGGA-ATTTAGGATAGGTTCATCCCATTTAT
* *
27007 GATCCCTTTTAAGTCTTTTAAGGTTACTAAGATACTTTTATGTTGAAGGTATACCCATA-GAGAC
64 GATCCATTTTAAGTCTTTTAGGGTTACTAAGATACTTTTATGTTGAAGGTATACCCATAGGAGAC
* *
27071 ATTTTCATAATTGTTCTAAAA-CTGAGTCA
129 ATTTTCATAATTGTTCTAAAATC-AAATCA
** * * *
27100 TGGGTTGTCATCGGGATGCTTTTATGCCAAAGATGTGAATTTAGGATAGGTTCACCCCATTTATG
1 TAAGTTGTCATCGAGATGCTTTTATGCCAAAGGTG-GAATTTAGGATAGGTTCATCCCATTTATG
** * * *
27165 AT-CATTTTAAAGTCCATTAGGGTAACCAAGATACTTTCATGTTGAAGGTAT
65 ATCCATTTT-AAGTCTTTTAGGGTTACTAAGATACTTTTATGTTGAAGGTAT
27216 GCCCTAAGGA
Statistics
Matches: 223, Mismatches: 43, Indels: 15
0.79 0.15 0.05
Matches are distributed among these distances:
156 6 0.03
157 115 0.52
158 101 0.45
159 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (157 bp):
TAAGTTGTCATCGAGATGCTTTTATGCCAAAGGTGGAATTTAGGATAGGTTCATCCCATTTATGA
TCCATTTTAAGTCTTTTAGGGTTACTAAGATACTTTTATGTTGAAGGTATACCCATAGGAGACAT
TTTCATAATTGTTCTAAAATCAAATCA
Found at i:31030 original size:22 final size:23
Alignment explanation
Indices: 31005--31057 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
30995 TCATTATTTT
*
31005 ATAATTAAAAAATTAAATAA-AA
1 ATAATTAAAAAAGTAAATAATAA
** * *
31027 ATAAACAAAAAAGTAATTAATTA
1 ATAATTAAAAAAGTAAATAATAA
31050 ATAATTAA
1 ATAATTAA
31058 TAAGAATATA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
ATAATTAAAAAAGTAAATAATAA
Found at i:32179 original size:24 final size:24
Alignment explanation
Indices: 32147--32194 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
32137 AGTAATTGTC
32147 AAACTTCAAAATTAAAATAAAGCT
1 AAACTTCAAAATTAAAATAAAGCT
32171 AAACTTCAAAATTAAAATAAAGCT
1 AAACTTCAAAATTAAAATAAAGCT
32195 TTCATGAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.58, C:0.12, G:0.04, T:0.25
Consensus pattern (24 bp):
AAACTTCAAAATTAAAATAAAGCT
Found at i:33096 original size:26 final size:24
Alignment explanation
Indices: 33058--33105 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
33048 TTTGCTGGCG
33058 TTTTTGATTCTTCCTGAGGAATACA
1 TTTTTGATTCTT-CTGAGGAATACA
* *
33083 TTTTTGTTTCCTTCTTAGGAATA
1 TTTTTGATT-CTTCTGAGGAATA
33106 GAATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.50
Consensus pattern (24 bp):
TTTTTGATTCTTCTGAGGAATACA
Found at i:37034 original size:20 final size:21
Alignment explanation
Indices: 37009--37062 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
36999 GTTACAAGCA
*
37009 ATGTATCGATACAATT-CATC
1 ATGTATCGATACAATTGCACC
*
37029 ATGTATCGATAC-ATTGTACC
1 ATGTATCGATACAATTGCACC
37049 ATGTATCGATACAA
1 ATGTATCGATACAA
37063 ACAGTGGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 3 0.10
20 26 0.87
21 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACAATTGCACC
Found at i:59344 original size:20 final size:20
Alignment explanation
Indices: 59316--59390 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
59306 TCATACCCTG
59316 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
59336 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
59356 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
59376 ATGTATCGATACATT
1 ATGTATCGATACATT
59391 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:59383 original size:40 final size:39
Alignment explanation
Indices: 59316--59393 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
59306 TCATACCCTG
* *
59316 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
59356 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
59394 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
Done.