Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020765.1 Corchorus olitorius cultivar O-4 contig20798, whole genome shotgun sequence
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: 141912
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1935 original size:54 final size:54
Alignment explanation
Indices: 1862--1966 Score: 185
Period size: 54 Copynumber: 1.9 Consensus size: 54
1852 CAATGCATTC
1862 ATTGTTGTAACTCGGATATCCCAAACTATATCTATCAAATCAATCATGCAACCA
1 ATTGTTGTAACTCGGATATCCCAAACTATATCTATCAAATCAATCATGCAACCA
*
1916 ATTGTTGTAAC-CTGGATATCCCAAACTATATCTATCAAATTAATCATGCAA
1 ATTGTTGTAACTC-GGATATCCCAAACTATATCTATCAAATCAATCATGCAA
1967 GCGGAAACAA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
53 1 0.02
54 48 0.98
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (54 bp):
ATTGTTGTAACTCGGATATCCCAAACTATATCTATCAAATCAATCATGCAACCA
Found at i:2215 original size:21 final size:21
Alignment explanation
Indices: 2185--2226 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2175 TCGCTCGGTC
2185 TCTACAAACCAAAC-ATCACA
1 TCTACAAACCAAACAATCACA
2205 TCTACGAAACCAAACAATCACA
1 TCTAC-AAACCAAACAATCACA
2227 CACACACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
21 9 0.45
22 6 0.30
ACGTcount: A:0.50, C:0.33, G:0.02, T:0.14
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:2925 original size:30 final size:30
Alignment explanation
Indices: 2856--2926 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
2846 ATGGTAAATT
*
2856 AAACGTCCAAAATTGAGAGTTTAAAGGGTA
1 AAACGTCCAAAATTGAGAGTTTAAAGGGCA
** **
2886 AAATATCCAAAATTGA-AGTTTAGTGAGGCA
1 AAACGTCCAAAATTGAGAGTTTAAAG-GGCA
2916 AAACGTCCAAA
1 AAACGTCCAAA
2927 CACTATAAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
29 7 0.21
30 26 0.79
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.23
Consensus pattern (30 bp):
AAACGTCCAAAATTGAGAGTTTAAAGGGCA
Found at i:4530 original size:31 final size:31
Alignment explanation
Indices: 4495--4626 Score: 183
Period size: 31 Copynumber: 4.3 Consensus size: 31
4485 ACGGTGTCCG
** * *
4495 ACGTGGCATACCACGTGTACCAAAAAGCGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
4526 ACGTGGCACGCCACATGTACCAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
*
4557 ACGTGGTACGCCACATGTACCAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
* **
4588 ACGTGTCACGCCATGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
*
4619 ATGTGGCA
1 ACGTGGCA
4627 TGCCTCGTGG
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 90 1.00
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (31 bp):
ACGTGGCACGCCACATGTACCAAAAAGTGAC
Found at i:5184 original size:14 final size:14
Alignment explanation
Indices: 5161--5190 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5151 ATTGGTAAAT
5161 AAAAGATGAAGTGG
1 AAAAGATGAAGTGG
*
5175 AAAAGTTGAAGTGG
1 AAAAGATGAAGTGG
5189 AA
1 AA
5191 GGTGGAATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (14 bp):
AAAAGATGAAGTGG
Found at i:6062 original size:3 final size:3
Alignment explanation
Indices: 6026--6076 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
6016 AATATTCTCA
* *
6026 AAT AAT AA- AAA AAT AA- AAT AAA AAT AATT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
6070 AAT AAT A
1 AAT AAT A
6077 TACTTAGAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.83
4 3 0.07
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:7980 original size:31 final size:31
Alignment explanation
Indices: 7945--8017 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
7935 AGCTAGCCAA
7945 TAGCCATCATTCTTTTTTTGGGTATACTAGC
1 TAGCCATCATTCTTTTTTTGGGTATACTAGC
7976 TAGCCATCATTCTTTTTTTGGGTATACTAGC
1 TAGCCATCATTCTTTTTTTGGGTATACTAGC
8007 TAGCCATCATT
1 TAGCCATCATT
8018 AATTAAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (31 bp):
TAGCCATCATTCTTTTTTTGGGTATACTAGC
Found at i:8271 original size:13 final size:13
Alignment explanation
Indices: 8253--8278 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8243 TTTTTTAAAA
8253 AAAAAAAAAAATT
1 AAAAAAAAAAATT
8266 AAAAAAAAAAATT
1 AAAAAAAAAAATT
8279 TGGAGCTAGT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAAAAAAATT
Found at i:9313 original size:109 final size:109
Alignment explanation
Indices: 9122--9339 Score: 400
Period size: 109 Copynumber: 2.0 Consensus size: 109
9112 CTATTATATA
*
9122 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAGTA
1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
9187 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
*
9231 TATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
* *
9296 TAAACTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
9340 AAAATGTCTA
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 105 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (109 bp):
TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
Found at i:9916 original size:22 final size:22
Alignment explanation
Indices: 9874--9917 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
9864 TATTCATATG
*
9874 AAATTATGATAATCTCCCTATT
1 AAATTATGATAATCTCACTATT
9896 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCT-CACTATT
9918 TTTGATGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (22 bp):
AAATTATGATAATCTCACTATT
Found at i:10047 original size:22 final size:22
Alignment explanation
Indices: 10022--10078 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
10012 ACCTACTTAT
10022 GAAATTTT-ATTAACTTCCCTAA
1 GAAATTTTGA-TAACTTCCCTAA
*
10044 GAAATTTTGATAACTTCCCTAT
1 GAAATTTTGATAACTTCCCTAA
10066 GAAATTTTGATAA
1 GAAATTTTGATAA
10079 TCAACACTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
22 32 0.97
23 1 0.03
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (22 bp):
GAAATTTTGATAACTTCCCTAA
Found at i:10120 original size:22 final size:22
Alignment explanation
Indices: 10044--10125 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 22
10034 ACTTCCCTAA
* * *
10044 GAAATTTTGATAACTTCCCTAT
1 GAAATATTGATAACCTCCATAT
* * **
10066 GAAATTTTGATAATCAACACTAT
1 GAAATATTGATAACCTCCA-TAT
* *
10089 GAGATGTTGATAACCTCCATAT
1 GAAATATTGATAACCTCCATAT
*
10111 GATATATTGATAACC
1 GAAATATTGATAACC
10126 ATGTTATGAA
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
22 30 0.64
23 17 0.36
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (22 bp):
GAAATATTGATAACCTCCATAT
Found at i:10190 original size:22 final size:22
Alignment explanation
Indices: 10165--10233 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
10155 GAATTGTTAG
* *
10165 TAATCACACTCTGAATTTTTGA
1 TAATCACACTATGAAATTTTGA
*
10187 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* *
10209 TAACCTCACTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
10231 TAA
1 TAA
10234 ACCTTCCAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:10230 original size:44 final size:44
Alignment explanation
Indices: 10171--10801 Score: 224
Period size: 44 Copynumber: 14.4 Consensus size: 44
10161 TTAGTAATCA
* * *
10171 CACTCTGAATTTTTGATAATCACACTATGAAATTGTGATAACCT
1 CACTATGAAATTTTGATAATCACACTATGAAATTTTGATAACCT
* * * * *
10215 CACTATGAAATTTTGATAAAC-CTTCCAATAAAATTTTGATAAACCC
1 CACTATGAAATTTTGATAATCAC--ACTATGAAATTTTGAT-AACCT
* * * *
10261 CCCTATAAAATTTTGATAATCTC-CTTATGAAATCTTGATAA-CT
1 CACTATGAAATTTTGATAATCACAC-TATGAAATTTTGATAACCT
* *
10304 -AC----AAATTTTGATAA-CATCCCTATG-ATTTTATGATAACCT
1 CACTATGAAATTTTGATAATCA-CACTATGAAATTT-TGATAACCT
* * ** * * * * *
10343 CATTATGAACTTTTTTTAATCTC-CAAATAAAATTTTGATCTACAT
1 CACTATGAAATTTTGATAATCACAC-TATGAAATTTTGAT-AACCT
* *
10388 -ACTATGAAATTTTGATAA-CCCTCTTATGAAATTTTGATAACCTT
1 CACTATGAAATTTTGATAATCACAC-TATGAAATTTTGATAACC-T
* * * * *
10432 CA-TATGAAATTTTAAT-ATC-CTGC-CTGAAATTTTTATTA-CT
1 CACTATGAAATTTTGATAATCAC-ACTATGAAATTTTGATAACCT
* * ** *
10472 C-CATAAT-AAATGTT--TAATAAC-CT-TCCTAA-TTTGGTAACCAT
1 CAC-T-ATGAAATTTTGATAATCACACTAT-GAAATTTTGATAACC-T
* *
10513 -ACTATGAAATTTTGATAACCTCCCCCTCTTTATGAAATTTTGATAACCT
1 CACTATGAAATTTTGATAA--T--CACAC--TATGAAATTTTGATAACCT
* * * * * *
10562 CTCTATAAAATTTTGGTAATCACATTTTGAAAATTTGATAACCT
1 CACTATGAAATTTTGATAATCACACTATGAAATTTTGATAACCT
** * * * * * * *
10606 CTTTATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCC
1 CACTATGAAATTTTGATAATCACACTATGAAATTTTGATAACCT
* * *
10650 CTCTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCT
1 CACTATGAAATTTTGATAATCACACTATGAAATTTTGATAACCT
* * * * * *
10694 CACTTTGAAATTTTGATAATAACATTATAAAATTGTGATAATCTT
1 CACTATGAAATTTTGATAATCACACTATGAAATTTTGATAA-CCT
* * *
10739 C-TTAT-AAATTTTGATAATCTGATCTCTATGAAATTTCT-ATAACCA
1 CACTATGAAATTTTGATAATC--A-CACTATGAAATTT-TGATAACCT
* *
10784 CTCTATGAGA-TTTGATAA
1 CACTATGAAATTTTGATAA
10802 CCTTCTATCG
Statistics
Matches: 428, Mismatches: 106, Indels: 104
0.67 0.17 0.16
Matches are distributed among these distances:
37 4 0.01
38 23 0.05
39 13 0.03
40 15 0.04
41 11 0.03
42 18 0.04
43 22 0.05
44 200 0.47
45 38 0.09
46 49 0.11
47 5 0.01
48 1 0.00
49 4 0.01
50 25 0.06
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.40
Consensus pattern (44 bp):
CACTATGAAATTTTGATAATCACACTATGAAATTTTGATAACCT
Found at i:10248 original size:23 final size:23
Alignment explanation
Indices: 10222--10279 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
10212 CCTCACTATG
**
10222 AAATTTTGATAAACCTTCCAATA
1 AAATTTTGATAAACCCCCCAATA
*
10245 AAATTTTGATAAACCCCCCTATA
1 AAATTTTGATAAACCCCCCAATA
10268 AAATTTTGATAA
1 AAATTTTGATAA
10280 TCTCCTTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.34
Consensus pattern (23 bp):
AAATTTTGATAAACCCCCCAATA
Found at i:10415 original size:22 final size:22
Alignment explanation
Indices: 10390--10803 Score: 129
Period size: 22 Copynumber: 18.8 Consensus size: 22
10380 ATCTACATAC
10390 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCCTCT
* *
10412 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCCTCT
* *
10434 TATGAAATTTTAAT-ATCCTGC-
1 TATGAAATTTTGATAACCCT-CT
* * * *
10455 -CTGAAATTTTTATTACTCC-AT
1 TATGAAATTTTGATAAC-CCTCT
* *
10476 AAT-AAATGTTTAATAA-CCT-T
1 TATGAAAT-TTTGATAACCCTCT
** * *
10496 CCT--AA-TTTGGTAACCATAC-
1 TATGAAATTTTGATAACCCT-CT
10515 TATGAAATTTTGATAACCTCCCCCTCTT
1 TATGAAATTTTGATAA-----CCCTC-T
10543 TATGAAATTTTGATAA-CCTCT
1 TATGAAATTTTGATAACCCTCT
* * *
10564 CTATAAAATTTTGGTAATCACAT-T
1 -TATGAAATTTTGATAA-C-CCTCT
*
10588 T-TGAAAATTTGATAA-CCTCTT
1 TATGAAATTTTGATAACCCTC-T
10609 TATGAAATTTTGATAA-CCTCT
1 TATGAAATTTTGATAACCCTCT
* * *
10630 CTATAAAATTTTGTTGACCC-CT
1 -TATGAAATTTTGATAACCCTCT
* *
10652 CTATGAAATTTTGATAATCAC-AT
1 -TATGAAATTTTGATAA-CCCTCT
* *
10675 TATGTAATTTTGATAACCTCACT
1 TATGAAATTTTGATAACC-CTCT
** *
10698 T-TGAAATTTTGATAATAAC-AT
1 TATGAAATTTTGATAA-CCCTCT
* * * *
10719 TATAAAATTGTGATAATCTTCT
1 TATGAAATTTTGATAACCCTCT
**
10741 TAT-AAATTTTGATAATCTGATCT
1 TATGAAATTTTGATAA-C-CCTCT
10764 CTATGAAATTTCT-ATAACCACTC-
1 -TATGAAATTT-TGATAACC-CTCT
*
10787 TATGAGA-TTTGATAACC
1 TATGAAATTTTGATAACC
10804 TTCTATCGAA
Statistics
Matches: 293, Mismatches: 57, Indels: 85
0.67 0.13 0.20
Matches are distributed among these distances:
17 6 0.02
18 2 0.01
19 5 0.02
20 16 0.05
21 36 0.12
22 177 0.60
23 11 0.04
24 7 0.02
25 12 0.04
26 2 0.01
27 3 0.01
28 16 0.05
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCCTCT
Found at i:10442 original size:66 final size:62
Alignment explanation
Indices: 10195--10755 Score: 213
Period size: 66 Copynumber: 8.6 Consensus size: 62
10185 GATAATCACA
* * * *
10195 CTATGAAATTGTGATAACCTCACTATGAAATTTTGATAAACCTTCCAATAAAATTTTGATAAACC
1 CTATGAAATTTTGATAACCTC-TTATGAAATTTTGAT-AACCTT-CTATAAAATTTTGAT-TA--
**
10260 CCC
60 CAT
* * * * *
10263 CTATAAAATTTTGATAATCTCCTTATGAAATCTTGATAA----CTA-CAAATTTTGATAACAT
1 CTATGAAATTTTGATAACCT-CTTATGAAATTTTGATAACCTTCTATAAAATTTTGATTACAT
* * ** * * *
10321 CCCTATG-ATTTTATGATAACCTCATTATGAACTTTTTTTAATCTCCAAATAAAATTTTGATCTA
1 --CTATGAAATTT-TGATAACCTC-TTATGAAATTTTGATAACCTTC-TATAAAATTTTGAT-TA
10385 CAT
60 CAT
* * *
10388 ACTATGAAATTTTGATAACCCTCTTATGAAATTTTGATAACCTTCATATGAAATTTT-AATATCC
1 -CTATGAAATTTTGATAA-CCTCTTATGAAATTTTGATAACCTTC-TATAAAATTTTGATTA-CA
10452 T
62 T
* * * * * * * *
10453 GC-CTGAAATTTTTATTA-CTCCATAAT-AAATGTTTAATAACCTTC-CT--AA-TTTGGTAACC
1 -CTATGAAATTTTGATAACCT-C-TTATGAAAT-TTTGATAACCTTCTATAAAATTTTGATTA-C
10511 AT
61 AT
10513 ACTATGAAATTTTGATAACCTCCCCCTCTTTATGAAATTTTGATAACCTCTCTATAAAATTTTGG
1 -CTATGAAATTTTGATAA------CCTC-TTATGAAATTTTGATAACCT-TCTATAAAATTTT-G
*
10578 TAATCACAT
56 --ATTACAT
* *
10587 -TTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTCTATAAAATTTTG-TTGACCC
1 CTATGAAATTTTGATAACCTC-TTATGAAATTTTGATAACCT-TCTATAAAATTTTGATT-A--C
*
10650 CT
61 AT
* * * * * *
10652 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCACTTTGAAATTTTGATAATAAC
1 CTATGAAATTTTGATAACCTC-TTATGAAATTTTGATAACCT-TCTATAAAATTTTGAT--T-AC
10717 AT
61 AT
* * *
10719 -TATAAAATTGTGATAATCTTCTTAT-AAATTTTGATAA
1 CTATGAAATTTTGATAA-CCTCTTATGAAATTTTGATAA
10756 TCTGATCTCT
Statistics
Matches: 376, Mismatches: 73, Indels: 91
0.70 0.14 0.17
Matches are distributed among these distances:
58 1 0.00
59 8 0.02
60 33 0.09
61 22 0.06
62 6 0.02
63 6 0.02
64 30 0.08
65 19 0.05
66 152 0.40
67 32 0.09
68 38 0.10
69 4 0.01
71 2 0.01
72 17 0.05
73 1 0.00
74 3 0.01
75 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.40
Consensus pattern (62 bp):
CTATGAAATTTTGATAACCTCTTATGAAATTTTGATAACCTTCTATAAAATTTTGATTACAT
Found at i:10747 original size:21 final size:22
Alignment explanation
Indices: 10718--10758 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
10708 GATAATAACA
10718 TTATAAAATTGTGATAATCTTC
1 TTATAAAATTGTGATAATCTTC
*
10740 TTAT-AAATTTTGATAATCT
1 TTATAAAATTGTGATAATCT
10759 GATCTCTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (22 bp):
TTATAAAATTGTGATAATCTTC
Found at i:11877 original size:100 final size:100
Alignment explanation
Indices: 11631--11893 Score: 449
Period size: 99 Copynumber: 2.6 Consensus size: 100
11621 AATTTCCATT
* * *
11631 ATTAAAATATTGTTTAATAATGGCAATTTAGAAATATATTTGAAAAAAAGGGTACAATCGGAAGG
1 ATTAAAATATTATTTAATAATGACAATTTAGAAATATATTTGAAAAAAAGGATACAATCGGAAGG
11696 ATAATCTAAATTTCCATTATTTTAATATTGGAATA
66 ATAATCTAAATTTCCATTATTTTAATATTGGAATA
*
11731 ATTAAAATATTATTTAATAGTGACAATTTAGAAATATATTTGAAAAAAAGGATACAAT-GGAAGG
1 ATTAAAATATTATTTAATAATGACAATTTAGAAATATATTTGAAAAAAAGGATACAATCGGAAGG
11795 ATAATCTAAATTTCCATTATTTTAATATTGGAATA
66 ATAATCTAAATTTCCATTATTTTAATATTGGAATA
*
11830 ATTAAAATATTATTTAATAATGACGATTTAGAAATATATTTGAAAAAAAAGGAT-CAAATCGGAA
1 ATTAAAATATTATTTAATAATGACAATTTAGAAATATATTTG-AAAAAAAGGATAC-AATCGGAA
11894 AACATAAAGT
Statistics
Matches: 154, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
99 82 0.53
100 68 0.44
101 4 0.03
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.35
Consensus pattern (100 bp):
ATTAAAATATTATTTAATAATGACAATTTAGAAATATATTTGAAAAAAAGGATACAATCGGAAGG
ATAATCTAAATTTCCATTATTTTAATATTGGAATA
Found at i:16758 original size:18 final size:16
Alignment explanation
Indices: 16735--16768 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
16725 TACTAGTACA
16735 TTCTTTTCTTTTCTTTTT
1 TTCTTTT-TTTT-TTTTT
16753 TTCTTTTTTTTTTTTT
1 TTCTTTTTTTTTTTTT
16769 GATAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 4 0.25
18 7 0.44
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTCTTTTTTTTTTTTT
Found at i:16767 original size:13 final size:13
Alignment explanation
Indices: 16738--16766 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
16728 TAGTACATTC
16738 TTTTCTTTTCTTT
1 TTTTCTTTTCTTT
16751 TTTTCTTTT-TTT
1 TTTTCTTTTCTTT
16763 TTTT
1 TTTT
16767 TTGATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTCTTTTCTTT
Found at i:23390 original size:20 final size:18
Alignment explanation
Indices: 23362--23411 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 18
23352 GAAATTATCT
*
23362 TAAATAAACTAATTATAAAC
1 TAAACAAAC-AATTAT-AAC
23382 TAAACAAACAA--ATAAC
1 TAAACAAACAATTATAAC
23398 TAAACAAACAATTA
1 TAAACAAACAATTA
23412 AACCCACATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 14 0.52
17 2 0.07
18 1 0.04
19 2 0.07
20 8 0.30
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAACAAACAATTATAAC
Found at i:33173 original size:332 final size:332
Alignment explanation
Indices: 32086--34653 Score: 3186
Period size: 331 Copynumber: 7.8 Consensus size: 332
32076 GGGTGTGAAC
*
32086 GATAGTACACGATTTAAGCTAAAATTTTGCAAAAACTGAGCCGAAAAATTTTTCCTCAATTTTTT
1 GATAGTACACGATTTCAGCTAAAATTTTGCAAAAACTGAGCCGAAAAATTTTTCCTCAATTTTTT
* *
32151 GACACAATAGTCGTAAAAAGTATATAATTCAATGCCAAAAAGATTAAAACGGCTTTTCACCCTTC
66 GACACAATAGTCGTAAAAAATATATAATTCAATGCCAAAAAGATTAAAA-GGCTTTTCACGCTTC
* * * * *
32216 TAATATTGTTTTCCCTATTTTTTTGAATTAACTTCTAGTAAAAAACGAAACAAGATTCTGATGCT
130 TAATATCGTTTTTCCTATTTTTTTGAATTAATTTCTAATAAAAATCGAAACAAGATTCTGATGCT
* * *
32281 CGTAAAAACAAATCCTTAAATCCAA-TGTGACTGAGATTTGGTTATATGAATAT--ATATTTCAA
195 CGTAAAAACAAGTCTTTAAAT-CAATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAA
* ** * * * ** * *
32343 TGAGTCTTAACGCCAAAAATTATGCAAACCTGTGCTTGGG-CCCGGAACGTGTTTTTAGCCAAAA
259 GGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACATCTTTTTAGCC-AAA
* *
32407 AACTGTGATG
323 AACCGTGATA
* * * * *
32417 GTTAGCACACGATTTCAACTAAAATTTTGCAAAAACTGAGTCGAAAAATTTTTCCTTAATTTTTT
1 GATAGTACACGATTTCAGCTAAAATTTTGCAAAAACTGAGCCGAAAAATTTTTCCTCAATTTTTT
* * * * *
32482 GACACAATAATTGTAAAAATTATATAATTCAATTCCAAAAAGAGTTAAAAGGCTTTTCACGCTTT
66 GACACAATAGTCGTAAAAAATATATAATTCAATGCCAAAAAGA-TTAAAAGGCTTTTCACGCTTC
* *
32547 TAATATCGTTTTTCCTATTTTTTTGTATTAATTTCTAATAGAAATCGAAACAAGATTCTGATGCT
130 TAATATCGTTTTTCCTATTTTTTTGAATTAATTTCTAATAAAAATCGAAACAAGATTCTGATGCT
* * *
32612 AGTAAAAACAAGTCTTTAAATCAATTGTGGCTGAGATTTGGTTTGATGAATATAGATATTTCAAG
195 CGTAAAAACAAGTCTTTAAATCAATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAG
** ** *
32677 GAGTCTTGGCGCTGAAAATCAT-CTAAAACTGAGTTGGGTCCCCGGAACA-CATTTTTAGCCAAA
260 GAGTCTTGGCGCCAAAAATCATGC-AAAACTGAGCCGGGGCCCCGGAACATC-TTTTTAGCCAAA
*
32740 AACCGTGATG
323 AACCGTGATA
* * * *
32750 GATAGCACACGATTTAAGCTAAAATTTTGCAAAAACTAAGCCGAAAAAATTTTCCTCAATTTTTT
1 GATAGTACACGATTTCAGCTAAAATTTTGCAAAAACTGAGCCGAAAAATTTTTCCTCAATTTTTT
* * *
32815 AACACAATAGTCGTAAAAAGTATATAATTCAATGCCAAAAAGATTAAAACGG-TTTTCACCCTTC
66 GACACAATAGTCGTAAAAAATATATAATTCAATGCCAAAAAGATTAAAA-GGCTTTTCACGCTTC
* * * * * *
32879 TAATATTGTTTTCCCTATTTTTTTGAATTAACTTCTAGTAAAAAACGAAACAAGATTCCGATGCT
130 TAATATCGTTTTTCCTATTTTTTTGAATTAATTTCTAATAAAAATCGAAACAAGATTCTGATGCT
* * * *
32944 CGTAAAAACAAATCCTTAAATCCAA-TGTGACTAAGATTTGGTTAGATGAATATTTATATATTTC
195 CGTAAAAACAAGTCTTTAAAT-CAATTGTGACTGAGATTTGGTTAGATGAATA--TAGATATTTC
* * * * * * ** ** * *
33008 AACGAGTCTTGGCGTCAAAAATTATGCAAAATTGTGTCAAGG-CCCGGAATGTGTTTTTAGTCAA
257 AAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACATCTTTTTAGCCAA
** *
33072 AAATTGTGATG
322 AAACCGTGATA
* * * * *
33083 GTTAGAACACGATTTC-GACTAAAATTTTGCAGAAACTGAGTCGAAAAATTTTTCCTCAA-GTTT
1 GATAGTACACGATTTCAG-CTAAAATTTTGCAAAAACTGAGCCGAAAAATTTTTCCTCAATTTTT
* * * * * * *
33146 TCACACAACAGTCTTAAAAATTATATAATTCAATGCCAAAATGATTAAAATGCTTTTTACGCTTC
65 TGACACAATAGTCGTAAAAAATATATAATTCAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTC
* **
33211 TAATATCGTTTTTCCTATTTTTTTTGAATTAATTTCTAATAGAAATCGAAACAAGATAATGATGC
130 TAATATCGTTTTTCCTA-TTTTTTTGAATTAATTTCTAATAAAAATCGAAACAAGATTCTGATGC
* *
33276 TCGTAAAAACAAGTCTTTAAATCAATTGTGGCTGAGATTTGG-TATGATCAATATAGATATTTCA
194 TCGTAAAAACAAGTCTTTAAATCAATTGTGACTGAGATTTGGTTA-GATGAATATAGATATTTCA
* *
33340 AGGAGTCTTGGCGTCAAAAATCATGCAAAACTGAACCGGGGCCCCGGAACA-CTTTTTTAGCCAA
258 AGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACATC-TTTTTAGCCAA
33404 AAACC------
322 AAACCGTGATA
* * *
33409 G-T-G---ACGATTTCGGCTAAACTTTTGCAAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTT
1 GATAGTACACGATTTCAGCTAAAATTTTGCAAAAACTGAGCCGAAAAATTTTTCCTCAATTTTTT
* * * * * * * * *
33469 CAAAAAATAGTCGGAAAAAATATATGATTCAATGCGAAAAAAATTATAAGGCTTTTCACGTTTCT
66 GACACAATAGTCGTAAAAAATATATAATTCAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCT
* * * *
33534 AATTTCAG-TTTTCCTATTTTTTT-AATTAATTTTTAATAGAAATCGAAACAAGATTCTGATCCT
131 AATATC-GTTTTTCCTATTTTTTTGAATTAATTTCTAATAAAAATCGAAACAAGATTCTGATGCT
*
33597 CGTAAAAACAAGTCTTTAAATCAATTGTAGA-TGAGATTTGGTTTGATGAATATAGATATTTCAA
195 CGTAAAAACAAGTCTTTAAATCAATTGT-GACTGAGATTTGGTTAGATGAATATAGATATTTCAA
* * * *
33661 GGAGTCTTGGCGCCAAAAATCAGGCAAAACTGAGCCGGGGCCTCGGAACATCTTTTTAACTAAAA
259 GGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACATCTTTTTAGCCAAAA
*
33726 CCCGTGATA
324 ACCGTGATA
* * * *
33735 AATAGTACACGATTTTAGCTAAATTTTTGCAAAAACTGAGCAGAAAAATTTTTCCTCAATTTTTT
1 GATAGTACACGATTTCAGCTAAAATTTTGCAAAAACTGAGCCGAAAAATTTTTCCTCAATTTTTT
* * *
33800 GACACAATAGTCGTAAAAAACATATAATTCAATGCCAAAAAGATTGAAAGGGCTTTTCACGCTTT
66 GACACAATAGTCGTAAAAAATATATAATTCAATGCCAAAAAGATT-AAAAGGCTTTTCACGCTTC
* * *
33865 TAATATCGTTTTTCCTTTTTTTTTTTTGAATTAATTTCTAATAGAAATCGAAACAATATTCTGAT
130 TAATATCGTTTTTCC---TATTTTTTTGAATTAATTTCTAATAAAAATCGAAACAAGATTCTGAT
*
33930 GCTCGTAAAAACAAGTCTTTAAATCAATTGTGGCTGAGATTTGG-TATGATGAATATAGATATTT
192 GCTCGTAAAAACAAGTCTTTAAATCAATTGTGACTGAGATTTGGTTA-GATGAATATAGATATTT
* * * * *
33994 CAAAGAGTCTTGACGCCAAAAATCATGCAAAATTAAGCCGGGGCCCCGGAACACCTTTTTAGCCA
256 CAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACATCTTTTTAGCCA
* *
34059 AAAACCATCATA
321 AAAACCGTGATA
* *
34071 GATAGTACACGATTTCAGC-AAAAGTTTTGCAAAAATTGAGCCGAAAAATCTTTCCTCAATTTTT
1 GATAGTACACGATTTCAGCTAAAA-TTTTGCAAAAACTGAGCCGAAAAATTTTTCCTCAATTTTT
* * * *
34135 TCACACAATAGTCGGAAAAAATATATAGTTCAATTCCAAAAAGATTAAAAGGCTTTTCACGCTTC
65 TGACACAATAGTCGTAAAAAATATATAATTCAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTC
* * *
34200 TAATATCGTTTTTCCTATTTTTTTTAATTAATTTCTAATAAAAATCGAAACATGATTCTGGTGCT
130 TAATATCGTTTTTCCTATTTTTTTGAATTAATTTCTAATAAAAATCGAAACAAGATTCTGATGCT
* * * *
34265 CGT-AAAA-ATGTCTTTAAATCAATTGTGGCTGAGATTTGGTTTGATGAATATAGATATTTTAAG
195 CGTAAAAACAAGTCTTTAAATCAATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAG
* * * ** * * *
34328 GAGTCTTGACGCCAAAATTCATGCAAAACTGAGTCGGGGTTCCGGAAGACCTTTTTAGCGAAAAA
260 GAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACATCTTTTTAGCCAAAAA
34393 CCGTGATA
325 CCGTGATA
* *
34401 GATAGTACACGATTTCAGCTAAAATTTTGTAAAAACTGAGCCGAAAAGTTTTTCCTCAATTTTTT
1 GATAGTACACGATTTCAGCTAAAATTTTGCAAAAACTGAGCCGAAAAATTTTTCCTCAATTTTTT
* * *
34466 GACACAATAGACGTAAAAAGTATATAATTCAATGCCAAAAAGATTAAAAGGCTTTTTACGCTTCT
66 GACACAATAGTCGTAAAAAATATATAATTCAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCT
*
34531 AATAT-TTTTTTCCTATTTTTTTGAATTAATTTCTAATAAAAATCGAAACAAGATTCTGATGCTC
131 AATATCGTTTTTCCTATTTTTTTGAATTAATTTCTAATAAAAATCGAAACAAGATTCTGATGCTC
* * * * *
34595 GTAAAAACAAATCCTTAAATCCAA-TGTGACTGAAATTTGGTTATATGATATATATATAT
196 GTAAAAACAAGTCTTTAAAT-CAATTGTGACTGAGATTTGGTTAGATGA-ATATAGATAT
34654 ATATATATAT
Statistics
Matches: 1928, Mismatches: 257, Indels: 103
0.84 0.11 0.05
Matches are distributed among these distances:
320 152 0.08
321 55 0.03
322 69 0.04
323 1 0.00
324 1 0.00
325 1 0.00
326 1 0.00
327 1 0.00
328 1 0.00
329 57 0.03
330 239 0.12
331 384 0.20
332 307 0.16
333 306 0.16
334 55 0.03
335 46 0.02
336 252 0.13
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (332 bp):
GATAGTACACGATTTCAGCTAAAATTTTGCAAAAACTGAGCCGAAAAATTTTTCCTCAATTTTTT
GACACAATAGTCGTAAAAAATATATAATTCAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCT
AATATCGTTTTTCCTATTTTTTTGAATTAATTTCTAATAAAAATCGAAACAAGATTCTGATGCTC
GTAAAAACAAGTCTTTAAATCAATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGG
AGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACATCTTTTTAGCCAAAAAC
CGTGATA
Found at i:34649 original size:2 final size:2
Alignment explanation
Indices: 34636--34667 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
34626 GAAATTTGGT
34636 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
34668 TTGTTGGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35352 original size:331 final size:331
Alignment explanation
Indices: 34744--35564 Score: 888
Period size: 331 Copynumber: 2.5 Consensus size: 331
34734 GAGTCTGGCA
* * * *** ** *
34744 CCAAAAATTATGCAAAACTGTGCCTAGGCCCGGAACGTGTTTTTAGCCAAAAACTGTGATGGTTA
1 CCAAAAATCATGCAAAACTGAGCCGAGGCCCGGAACACCTTTTTAGCCAAAAACCATGATGGATA
* * *
34809 GTACACGATTTCGACTAAAATTTTGTAAAAACTGAGTGAAAAAAATTTTTCCTTAATTTTTTGAC
66 GTACACGATTTCGACTAAAATTTTGCAAAAACTGAGCG-AAAAAATTTTTCCTTAATTTTTTCAC
* * * * * *
34874 ACAACAGTTGTAAAAATTATAAAATTCAATTCCAAAAAGATTAAAAGGCTTTTCACGCTTTTAAT
130 ACAACAGTCGTAAAAAATATAAAATTCAATGCCAAAAAAATTAAAAGGCTTTTCACACTTCTAAT
*
34939 ATCGTTTTTCCTATTTTTTTGAATTAATTTCTAATAGAAATCGAAACAAGATTCTGATGCTCGTA
195 ATCGTTTTTCCTATTTTTTTGAATTAATTTCTAATAAAAATCGAAACAAGATTCTGATGCTCGTA
*
35004 AAAGCAAGTCGTTAAATCAATTGTGTCTAAGATTTCGTTTGATAAATATAGATATTTCAAGGAGT
260 AAAGAAAGTCGTTAAATCAATTGTGTCTAAGATTTCGTTTGATAAATATAGATATTTCAAGGAGT
35069 CTTAACG
325 CTTAACG
* *
35076 CCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACACCTTTTTGGCCAAAAACCATGATGGAT
1 CCAAAAATCATGCAAAACTGAGCCGAGG-CCCGGAACACCTTTTTAGCCAAAAACCATGATGGAT
* * * *
35141 AGTATACGATTTCGGCTAAAATTTTGCAAAAATTGAGCCG-AAAATTTTTTCCTTAA-TTTTTCA
65 AGTACACGATTTCGACTAAAATTTTGCAAAAACTGAG-CGAAAAAATTTTTCCTTAATTTTTTCA
* * *
35204 CACAATAGTCGTAAAAAATATATAATAT-AATGCCAAAAAAATTAAAAGGCTTTTTACACTTCTA
129 CACAACAGTCGTAAAAAATATAAAAT-TCAATGCCAAAAAAATTAAAAGGCTTTTCACACTTCTA
*
35268 ATATTGTTTTTCCTATTTTTTTGAATTAATTTCTAATAAAAATCGAAACAAGATTCTGATGCTCG
193 ATATCGTTTTTCCTATTTTTTTGAATTAATTTCTAATAAAAATCGAAACAAGATTCTGATGCTCG
* * * * *
35333 TAAAAATAAATTC-TTAAATCTAA-TGTGAC-AGAGATTT-GGTT-ATACGAATAT--ATATAT-
258 T-AAAAGAAAGTCGTTAAATC-AATTGTGTCTA-AGATTTCGTTTGATA--AATATAGATATTTC
* *
35390 -A-TA--C-TAACA
318 AAGGAGTCTTAACG
* * * *** * ** *
35399 CCAAAAATTATGCAAAATTGTGCCTG-GGCCCGGAACGTGTTTTTAACCAAAAACTGTAAT-GAT
1 CCAAAAATCATGCAAAACTGAGCC-GAGGCCCGGAACACCTTTTTAGCCAAAAACCATGATGGA-
* * * * * *
35462 TATTACACGATTTCAACTAAAATTTTGTAAAAACTGAGCCG-AAAAATTTTTACTTTATTTTTTG
64 TAGTACACGATTTCGACTAAAATTTTGCAAAAACTGAG-CGAAAAAATTTTTCCTTAATTTTTTC
* * * *
35526 ACACAATAGTTGTAAAAATTATAAAATTCAATTCCAAAA
128 ACACAACAGTCGTAAAAAATATAAAATTCAATGCCAAAA
35565 TTTTGAATTA
Statistics
Matches: 415, Mismatches: 62, Indels: 33
0.81 0.12 0.06
Matches are distributed among these distances:
321 2 0.00
322 73 0.18
323 65 0.16
324 2 0.00
326 1 0.00
327 1 0.00
329 8 0.02
330 4 0.01
331 146 0.35
332 50 0.12
333 62 0.15
334 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (331 bp):
CCAAAAATCATGCAAAACTGAGCCGAGGCCCGGAACACCTTTTTAGCCAAAAACCATGATGGATA
GTACACGATTTCGACTAAAATTTTGCAAAAACTGAGCGAAAAAATTTTTCCTTAATTTTTTCACA
CAACAGTCGTAAAAAATATAAAATTCAATGCCAAAAAAATTAAAAGGCTTTTCACACTTCTAATA
TCGTTTTTCCTATTTTTTTGAATTAATTTCTAATAAAAATCGAAACAAGATTCTGATGCTCGTAA
AAGAAAGTCGTTAAATCAATTGTGTCTAAGATTTCGTTTGATAAATATAGATATTTCAAGGAGTC
TTAACG
Found at i:37271 original size:11 final size:11
Alignment explanation
Indices: 37247--37281 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
37237 TTGACAGCGC
37247 AACAAAAACAA
1 AACAAAAACAA
* *
37258 AACGAAAACGA
1 AACAAAAACAA
37269 AACAAAAACAA
1 AACAAAAACAA
37280 AA
1 AA
37282 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:43286 original size:31 final size:31
Alignment explanation
Indices: 43249--43312 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
43239 CTGGGTTCAT
43249 TATGTCGTTAATTGGTAGATGTATGGGCATA
1 TATGTCGTTAATTGGTAGATGTATGGGCATA
43280 TATGTCGTTAATTGGTAGATGTATGGGCATA
1 TATGTCGTTAATTGGTAGATGTATGGGCATA
43311 TA
1 TA
43313 AGTTCAAGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.27, C:0.06, G:0.28, T:0.39
Consensus pattern (31 bp):
TATGTCGTTAATTGGTAGATGTATGGGCATA
Found at i:43405 original size:53 final size:51
Alignment explanation
Indices: 43280--43424 Score: 199
Period size: 50 Copynumber: 2.8 Consensus size: 51
43270 TATGGGCATA
43280 TATGTCGTTAATTGGTAGATGTATGGGCATATAAGTTCAAGGTACTGGGTTCAT
1 TATGTC-TTAATTGGTAGATGTATGGGCATATAAGTTCAA-GTA-TGGGTTCAT
*
43334 TATG---TAATTGGTAGATGTATGGACATATAAGAGTTCAAGT-TGGGTTCAT
1 TATGTCTTAATTGGTAGATGTATGGGCATAT-A-AGTTCAAGTATGGGTTCAT
43383 TATGTCATTAATTGGTAGATGTATGGGCATATAAGTTCAAGT
1 TATGTC-TTAATTGGTAGATGTATGGGCATATAAGTTCAAGT
43425 CTGACGGAAT
Statistics
Matches: 83, Mismatches: 2, Indels: 15
0.83 0.02 0.15
Matches are distributed among these distances:
49 13 0.16
50 23 0.28
51 12 0.14
52 8 0.10
53 23 0.28
54 4 0.05
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.37
Consensus pattern (51 bp):
TATGTCTTAATTGGTAGATGTATGGGCATATAAGTTCAAGTATGGGTTCAT
Found at i:45996 original size:31 final size:29
Alignment explanation
Indices: 45894--46061 Score: 101
Period size: 31 Copynumber: 5.6 Consensus size: 29
45884 TTGGGCTAAT
*
45894 TGCTCAAATAAGAGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAAC-TTTG-CAAAA
* * * * * **
45925 TACTCAAATAAGAGTCTGATCTTT-TAATT
1 TGCTCAAATAAGGGCCT-AACTTTGCAAAA
45954 TGGC-CAAATAAGGGCCTAACATTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAAC-TTTG-CAAAA
* * * **
45985 TGCTCAAATAAGGGCCCGATCTTT-TAATT
1 TGCTCAAATAAGGG-CCTAACTTTGCAAAA
46014 TGGC-CAAATAAGGGCCTAACGTTTGTCAAAA
1 T-GCTCAAATAAGGGCCTAAC-TTTG-CAAAA
46045 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
46062 GACATCGAAA
Statistics
Matches: 102, Mismatches: 23, Indels: 24
0.68 0.15 0.16
Matches are distributed among these distances:
28 6 0.06
29 33 0.32
30 7 0.07
31 50 0.49
32 6 0.06
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (29 bp):
TGCTCAAATAAGGGCCTAACTTTGCAAAA
Found at i:46057 original size:60 final size:60
Alignment explanation
Indices: 45898--46060 Score: 263
Period size: 60 Copynumber: 2.7 Consensus size: 60
45888 GCTAATTGCT
* * * * *
45898 CAAATAAGAGCCTAACGTTTGCCAAAATACTCAAATAAGAGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
45958 CAAATAAGGGCCTAACATTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
46018 CAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
46061 TGACATCGAA
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 95 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:46172 original size:29 final size:29
Alignment explanation
Indices: 46132--46352 Score: 110
Period size: 29 Copynumber: 7.4 Consensus size: 29
46122 GCAAACGTTA
*
46132 GGCCTTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGGCCAAATTAAAAGATCG
* ** * * **
46161 GGTCCTTATTTGAG-CATTTTGGCAAACATTA
1 GGCCCTTATTTG-GCCAAATT--AAAAGATCG
*
46192 GGCCCTTATTTAGCCAAATTAAAAGATCG
1 GGCCCTTATTTGGCCAAATTAAAAGATCG
** * **
46221 GGCCCTTATTTGAG-CATTTTGGCAAACG-TTA
1 GGCCCTTATTTG-GCCAAATT---AAAAGATCG
* *
46252 GGCCCTTATTTAGCCAAATTAAAAGATCA
1 GGCCCTTATTTGGCCAAATTAAAAGATCG
** * **
46281 GGCCCTTATTTGAG-CATTTTGGCAAACG-TTA
1 GGCCCTTATTTG-GCCAAATT---AAAAGATCG
*
46312 GGCCCTTATTTAGCCAAATTAAAAGATCG
1 GGCCCTTATTTGGCCAAATTAAAAGATCG
46341 GGCCCTTATTTG
1 GGCCCTTATTTG
46353 AGCATTTTGT
Statistics
Matches: 137, Mismatches: 39, Indels: 32
0.66 0.19 0.15
Matches are distributed among these distances:
28 8 0.06
29 63 0.46
30 6 0.04
31 52 0.38
32 8 0.06
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (29 bp):
GGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:46201 original size:60 final size:60
Alignment explanation
Indices: 46101--46382 Score: 483
Period size: 60 Copynumber: 4.7 Consensus size: 60
46091 ACTGATGTCA
* *
46101 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCTTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATCG
* *
46161 GGTCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTAGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATCG
*
46221 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATCA
1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATCG
46281 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATCG
* ** *
46341 GGCCCTTATTTGAGCATTTTGTCAAATATTAGGCTCTTATTT
1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTT
46383 GAGCAATTAG
Statistics
Matches: 210, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 210 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAGCCAAATTAAAAGATCG
Found at i:77901 original size:30 final size:29
Alignment explanation
Indices: 77832--77909 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
77822 ATTTATAGTG
* *
77832 TTTGGACGTTTTGCCCCATGAACTTCAAT
1 TTTGGACATTTTGCCCCCTGAACTTCAAT
*
77861 TTTGGACATTTTGTCCCCTGAACTTCAAT
1 TTTGGACATTTTGCCCCCTGAACTTCAAT
77890 TTTGAGACATTTTGCCCCCT
1 TTTG-GACATTTTGCCCCCT
77910 CAACCTAACG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 30 0.68
30 14 0.32
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (29 bp):
TTTGGACATTTTGCCCCCTGAACTTCAAT
Found at i:81452 original size:2 final size:2
Alignment explanation
Indices: 81445--81479 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
81435 TGTAGTAGTG
81445 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
81480 TGAATTTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:84026 original size:3 final size:3
Alignment explanation
Indices: 84018--84060 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
84008 GATGGTGTAA
* *
84018 AAG AAG AAG AGG ACG AAG AAG AAG AAG AAAG AAGG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AA-G AAG AAG AA
84061 CCAGTGTGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.63, C:0.02, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:90836 original size:12 final size:12
Alignment explanation
Indices: 90819--90848 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
90809 GAAATGTAAA
90819 ATCTGCATATTC
1 ATCTGCATATTC
90831 ATCTGCATATTC
1 ATCTGCATATTC
90843 ACTCTG
1 A-TCTG
90849 GGTGAATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.23, C:0.27, G:0.10, T:0.40
Consensus pattern (12 bp):
ATCTGCATATTC
Found at i:94390 original size:29 final size:32
Alignment explanation
Indices: 94358--94434 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 32
94348 ATATTTTCAA
94358 AGAGCACGTGTAAGTGTTTTT-TTTTTTGGAG
1 AGAGCACGTGTAAGTGTTTTTCTTTTTTGGAG
94389 AGAGCACGTGTAAGTGTTTTTCTTTTTT-GAG
1 AGAGCACGTGTAAGTGTTTTTCTTTTTTGGAG
* *
94420 AGAGTACTTGTAAGT
1 AGAGCACGTGTAAGT
94435 TTGATATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 37 0.86
32 6 0.14
ACGTcount: A:0.22, C:0.08, G:0.27, T:0.43
Consensus pattern (32 bp):
AGAGCACGTGTAAGTGTTTTTCTTTTTTGGAG
Found at i:98392 original size:29 final size:29
Alignment explanation
Indices: 98323--98394 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
98313 GTTGAGAGAG
* **
98323 CAAAATGTCTCAAAATTGAAGTTCAAAGGA
1 CAAAATGTC-CAAAATTGAAATTCAAAAAA
*
98353 CAAAATATCCAAAATTGAAATTCAAAAAA
1 CAAAATGTCCAAAATTGAAATTCAAAAAA
*
98382 CAAAACGTCCAAA
1 CAAAATGTCCAAA
98395 CACTACAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 28 0.78
30 8 0.22
ACGTcount: A:0.54, C:0.17, G:0.10, T:0.19
Consensus pattern (29 bp):
CAAAATGTCCAAAATTGAAATTCAAAAAA
Found at i:102172 original size:14 final size:13
Alignment explanation
Indices: 102140--102175 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
102130 TCAAACCCAA
*
102140 TTTTAAAAAGCAC
1 TTTTCAAAAGCAC
102153 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
102166 TTCTTCAAAA
1 TT-TTCAAAA
102176 CCAAGCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:110790 original size:23 final size:23
Alignment explanation
Indices: 110760--110804 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
110750 AATGCCTATG
110760 GGCCGACCCATCAATTAATCGCA
1 GGCCGACCCATCAATTAATCGCA
*
110783 GGCCGACCCATTAATTAATCGC
1 GGCCGACCCATCAATTAATCGC
110805 GGAATTCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (23 bp):
GGCCGACCCATCAATTAATCGCA
Found at i:124045 original size:2 final size:2
Alignment explanation
Indices: 124038--124063 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
124028 CAGCAAAACC
124038 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
124064 TTAATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:140929 original size:32 final size:32
Alignment explanation
Indices: 140874--140934 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
140864 TATACTATTT
* *
140874 AACATTTAGATTTGGTCTCTTCAAAAAAAAAA
1 AACATTTAGATTTGATATCTTCAAAAAAAAAA
* *
140906 AACATTTAGATTTGATATGTTCAATAAAA
1 AACATTTAGATTTGATATCTTCAAAAAAA
140935 GTCCTGATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (32 bp):
AACATTTAGATTTGATATCTTCAAAAAAAAAA
Done.