Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017265.1 Corchorus olitorius cultivar O-4 contig17298, 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: 91721
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2037 original size:21 final size:20
Alignment explanation
Indices: 2001--2049 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1991 CTTATCTAGT
* *
2001 TTTATCAAGTAATTTAGTTA
1 TTTATTAAGTAATTTAGTAA
*
2021 TTGTATTAAGTATTTTAGTAA
1 TT-TATTAAGTAATTTAGTAA
2042 TTTATTAA
1 TTTATTAA
2050 ACTTTCATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.53
Consensus pattern (20 bp):
TTTATTAAGTAATTTAGTAA
Found at i:4142 original size:18 final size:18
Alignment explanation
Indices: 4119--4155 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4109 GTATGTATAT
4119 TGAGAACATAATTGTAAC
1 TGAGAACATAATTGTAAC
4137 TGAGAACATAATTGTAAC
1 TGAGAACATAATTGTAAC
4155 T
1 T
4156 AATGCCCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (18 bp):
TGAGAACATAATTGTAAC
Found at i:4811 original size:2 final size:2
Alignment explanation
Indices: 4804--4853 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
4794 AAGTTTTCTC
* *
4804 TA TA TA TA TA TA TA TA TA TA TA TA GA TA GA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4846 TA TA TA TA
1 TA TA TA TA
4854 GATTATTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:5964 original size:8 final size:8
Alignment explanation
Indices: 5951--5987 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
5941 ATAATTTATT
5951 CAATTAGA
1 CAATTAGA
5959 CAATTAGA
1 CAATTAGA
5967 CAATTAGA
1 CAATTAGA
5975 CAATTAGA
1 CAATTAGA
5983 CAATT
1 CAATT
5988 GTTGAAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (8 bp):
CAATTAGA
Found at i:6496 original size:2 final size:2
Alignment explanation
Indices: 6489--6517 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6479 TTGTTATCAT
6489 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 T
6518 GATTGGGGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8269 original size:75 final size:75
Alignment explanation
Indices: 8146--8292 Score: 269
Period size: 75 Copynumber: 2.0 Consensus size: 75
8136 GAGGAAATAT
*
8146 TTCTGAAAAATTAGTTAGGTCGCAATTTGCCATTAGGCACCACAAAATTGACTGTTTATTTTAGC
1 TTCTGAAAAATCAGTTAGGTCGCAATTTGCCATTAGGCACCACAAAATTGACTGTTTATTTTAGC
8211 AATTTTTCTA
66 AATTTTTCTA
8221 TTCTGAAAAATCAGTTAGG-CTGCAATTTGCCATTAGGCACCACAAAATTGACTGTTTATTTTAG
1 TTCTGAAAAATCAGTTAGGTC-GCAATTTGCCATTAGGCACCACAAAATTGACTGTTTATTTTAG
8285 CAATTTTT
65 CAATTTTT
8293 ATATGTTGTT
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
74 1 0.01
75 69 0.99
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (75 bp):
TTCTGAAAAATCAGTTAGGTCGCAATTTGCCATTAGGCACCACAAAATTGACTGTTTATTTTAGC
AATTTTTCTA
Found at i:9837 original size:43 final size:43
Alignment explanation
Indices: 9788--9875 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
9778 AGTGACGTGT
*
9788 TCCTACCCTACTCACCCAACAAAATACTCACTTGGTATCATAC
1 TCCTACCCTACTCACCCAACAAAATACTCACTTGGTACCATAC
9831 TCCTACCCTACTCACCCAACAAAATACTCACTTGGTACCATAC
1 TCCTACCCTACTCACCCAACAAAATACTCACTTGGTACCATAC
9874 TC
1 TC
9876 ACTTGGTGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.32, C:0.39, G:0.05, T:0.25
Consensus pattern (43 bp):
TCCTACCCTACTCACCCAACAAAATACTCACTTGGTACCATAC
Found at i:9889 original size:16 final size:15
Alignment explanation
Indices: 9853--9911 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 15
9843 CACCCAACAA
9853 AATACTCACTTGGT-
1 AATACTCACTTGGTG
9867 ACCATACTCACTTGGTG
1 A--ATACTCACTTGGTG
*
9884 TAATACTCACTTAGTG
1 -AATACTCACTTGGTG
9900 AGATACTCACTT
1 A-ATACTCACTT
9912 ACAAAGCCAC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 1 0.03
15 1 0.03
16 36 0.92
18 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (15 bp):
AATACTCACTTGGTG
Found at i:11101 original size:84 final size:84
Alignment explanation
Indices: 10956--11120 Score: 258
Period size: 84 Copynumber: 2.0 Consensus size: 84
10946 TTTAGAGACA
* * *
10956 AACTGCTAAATTTATTACAAGTAAAGAGAGAGACTGTCAGATTTATTATGTTTAAACCAGCCTTT
1 AACTGCTAAATTTATTACAAGTAAAGAGAAAGACTGTCAAATGTATTATGTTTAAACCAGCCTTT
*
11021 TAATAAGTTTTCCTTCTGT
66 AAATAAGTTTTCCTTCTGT
* * *
11040 AACTGCTAAATTTATTACAATTAAAGAGAAAGGCTGTCAAATGTATTATGTTTAAAGCAGCCTTT
1 AACTGCTAAATTTATTACAAGTAAAGAGAAAGACTGTCAAATGTATTATGTTTAAACCAGCCTTT
*
11105 AAATCAGTTTTCCTTC
66 AAATAAGTTTTCCTTC
11121 AGTTTGAGCC
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 73 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.37
Consensus pattern (84 bp):
AACTGCTAAATTTATTACAAGTAAAGAGAAAGACTGTCAAATGTATTATGTTTAAACCAGCCTTT
AAATAAGTTTTCCTTCTGT
Found at i:12865 original size:42 final size:43
Alignment explanation
Indices: 12789--12871 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 43
12779 AATCCCCTGA
*
12789 TGCCACGTCATCCTGTTGACCAAGTCCACATGCCACGTCATTC
1 TGCCACGTCATCCTGTTGACCAAGTCAACATGCCACGTCATTC
* ** *
12832 TGCCATGTCAT-CTGTTGACTGAGTCAACCTGCCACGTCAT
1 TGCCACGTCATCCTGTTGACCAAGTCAACATGCCACGTCAT
12872 CTGTTGACCG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 25 0.71
43 10 0.29
ACGTcount: A:0.20, C:0.34, G:0.18, T:0.28
Consensus pattern (43 bp):
TGCCACGTCATCCTGTTGACCAAGTCAACATGCCACGTCATTC
Found at i:12870 original size:29 final size:29
Alignment explanation
Indices: 12831--12910 Score: 115
Period size: 29 Copynumber: 2.7 Consensus size: 29
12821 CCACGTCATT
*
12831 CTGCCATGTCATCTGTTGACTGAGTCAAC
1 CTGCCACGTCATCTGTTGACTGAGTCAAC
*
12860 CTGCCACGTCATCTGTTGACCGAGTCAAC
1 CTGCCACGTCATCTGTTGACTGAGTCAAC
* *
12889 CTGCCACATCATCCAGTTGACT
1 CTGCCACGTCAT-CTGTTGACT
12911 CATCCCGTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 38 0.84
30 7 0.16
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.28
Consensus pattern (29 bp):
CTGCCACGTCATCTGTTGACTGAGTCAAC
Found at i:13094 original size:29 final size:29
Alignment explanation
Indices: 13052--13227 Score: 153
Period size: 29 Copynumber: 5.8 Consensus size: 29
13042 TATTCCGCTT
13052 TGTTTGACCTTTCGGTCCTGTTTTCTGCC
1 TGTTTGACCTTTCGGTCCTGTTTTCTGCC
13081 TGTTTGACCTTTCGGTCCTGTTTTCTGCC
1 TGTTTGACCTTTCGGTCCTGTTTTCTGCC
*
13110 TGTTTGACCTTTTGGTCCTG--TT-TGACC
1 TGTTTGACCTTTCGGTCCTGTTTTCTG-CC
* ***
13137 -ATTTGATCCTGTTTTCTACCTGTTTGACCTCTTGGTCC
1 TGTTTGA-CCT-TTCGGT-CCTGTTT----TC-T-G-CC
*
13175 TGTTTGACCTTTTGGTCCTGTTTTCTGCC
1 TGTTTGACCTTTCGGTCCTGTTTTCTGCC
* *
13204 TGATTGACCTTTCGGTCCTATTTT
1 TGTTTGACCTTTCGGTCCTGTTTT
13228 TAGCGCTTGA
Statistics
Matches: 122, Mismatches: 11, Indels: 28
0.76 0.07 0.17
Matches are distributed among these distances:
26 7 0.06
27 7 0.06
28 4 0.03
29 75 0.61
30 1 0.01
31 2 0.02
32 2 0.02
35 1 0.01
36 7 0.06
37 5 0.04
38 6 0.05
39 5 0.04
ACGTcount: A:0.07, C:0.25, G:0.19, T:0.49
Consensus pattern (29 bp):
TGTTTGACCTTTCGGTCCTGTTTTCTGCC
Found at i:13122 original size:18 final size:18
Alignment explanation
Indices: 13108--13197 Score: 86
Period size: 18 Copynumber: 5.4 Consensus size: 18
13098 CTGTTTTCTG
13108 CCTGTTTGACCTTTTGGT
1 CCTGTTTGACCTTTTGGT
* *
13126 CCTGTTTGACCATTTGAT
1 CCTGTTTGACCTTTTGGT
* *
13144 CCTG-TT----TTCT--A
1 CCTGTTTGACCTTTTGGT
*
13155 CCTGTTTGACCTCTTGGT
1 CCTGTTTGACCTTTTGGT
13173 CCTGTTTGACCTTTTGGT
1 CCTGTTTGACCTTTTGGT
13191 CCTGTTT
1 CCTGTTT
13198 TCTGCCTGAT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
11 4 0.07
12 2 0.04
13 2 0.04
16 2 0.04
17 2 0.04
18 44 0.79
ACGTcount: A:0.08, C:0.24, G:0.19, T:0.49
Consensus pattern (18 bp):
CCTGTTTGACCTTTTGGT
Found at i:13133 original size:47 final size:46
Alignment explanation
Indices: 13079--13222 Score: 216
Period size: 47 Copynumber: 3.1 Consensus size: 46
13069 CTGTTTTCTG
13079 CCTGTTTGACCTTTCGGTCCTGTTTTCTGCCTGTTTGACCTTTTGGT
1 CCTGTTTGACCTTT-GGTCCTGTTTTCTGCCTGTTTGACCTTTTGGT
* * *
13126 CCTGTTTGACCATTTGATCCTGTTTTCTACCTGTTTGACCTCTTGGT
1 CCTGTTTGACC-TTTGGTCCTGTTTTCTGCCTGTTTGACCTTTTGGT
* *
13173 CCTGTTTGACCTTTTGGTCCTGTTTTCTGCCTGATTGACCTTTCGGT
1 CCTGTTTGACC-TTTGGTCCTGTTTTCTGCCTGTTTGACCTTTTGGT
13220 CCT
1 CCT
13223 ATTTTTAGCG
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
47 84 0.97
48 3 0.03
ACGTcount: A:0.07, C:0.26, G:0.19, T:0.47
Consensus pattern (46 bp):
CCTGTTTGACCTTTGGTCCTGTTTTCTGCCTGTTTGACCTTTTGGT
Found at i:18040 original size:12 final size:12
Alignment explanation
Indices: 18023--18047 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18013 TTCAGGCTGC
18023 ACCACAATCACA
1 ACCACAATCACA
18035 ACCACAATCACA
1 ACCACAATCACA
18047 A
1 A
18048 TCATCCGTTA
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:0.52, C:0.40, G:0.00, T:0.08
Consensus pattern (12 bp):
ACCACAATCACA
Found at i:18144 original size:38 final size:38
Alignment explanation
Indices: 18080--18189 Score: 134
Period size: 39 Copynumber: 2.9 Consensus size: 38
18070 TCGAGTCTAG
*
18080 CCAACAG-TTAACCCCCTGAGGCATGGGTCCACTC-TTA
1 CCAACAGTTTAA-CCCCTGAGGTATGGGTCCACTCTTTA
* *
18117 CCAACAGTTTAACCCTCTGTGGTATGGGTCTACTCTTTA
1 CCAACAGTTTAACCC-CTGAGGTATGGGTCCACTCTTTA
* *
18156 CCATCAGTTTAATCCCCTGAGGTACGGGTCCACT
1 CCAACAGTTTAA-CCCCTGAGGTATGGGTCCACT
18190 ATGCACAGCC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
37 10 0.16
38 20 0.32
39 29 0.47
40 3 0.05
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (38 bp):
CCAACAGTTTAACCCCTGAGGTATGGGTCCACTCTTTA
Found at i:30320 original size:8 final size:8
Alignment explanation
Indices: 30307--30850 Score: 348
Period size: 8 Copynumber: 71.2 Consensus size: 8
30297 AATGATCTCT
30307 TTCTTCAA
1 TTCTTCAA
30315 TTCTTCAA
1 TTCTTCAA
* *
30323 TTATTCAG
1 TTCTTCAA
*
30331 TGCTTCAA
1 TTCTTCAA
*
30339 TTATTCAA
1 TTCTTCAA
*
30347 TTCCTCAA
1 TTCTTCAA
30355 TTCTTCAAA
1 TTCTTC-AA
30364 TTCTTCAA
1 TTCTTCAA
*
30372 TTATTCAA
1 TTCTTCAA
30380 TGT-TTCCAA
1 T-TCTT-CAA
30389 TTCTTCAA
1 TTCTTCAA
*
30397 TTATTCAA
1 TTCTTCAA
*
30405 TGT-TCCAA
1 T-TCTTCAA
*
30413 TCCTTCAA
1 TTCTTCAA
*
30421 TGCTTCAA
1 TTCTTCAA
30429 -T-TTCAA
1 TTCTTCAA
30435 TTCTTCAA
1 TTCTTCAA
*
30443 TACTTCAA
1 TTCTTCAA
30451 -T-TTCAA
1 TTCTTCAA
**
30457 CACTTCAA
1 TTCTTCAA
*
30465 TGCTTCAA
1 TTCTTCAA
*
30473 TTATTCAA
1 TTCTTCAA
30481 -T-TTCAA
1 TTCTTCAA
*
30487 TGCTTCAA
1 TTCTTCAA
*
30495 TACTTCAA
1 TTCTTCAA
30503 -T-TTCAA
1 TTCTTCAA
*
30509 TTCTTCAG
1 TTCTTCAA
*
30517 TTATTCAA
1 TTCTTCAA
30525 -T-TTCAA
1 TTCTTCAA
30531 TTCTTCAA
1 TTCTTCAA
*
30539 TGCTTCAA
1 TTCTTCAA
*
30547 -T-TTCAT
1 TTCTTCAA
30553 TTCTTCAA
1 TTCTTCAA
*
30561 TGCTTCAA
1 TTCTTCAA
*
30569 -T-TTCAT
1 TTCTTCAA
30575 TTCTTCAA
1 TTCTTCAA
*
30583 TGCTTCAA
1 TTCTTCAA
30591 -T-TTCAA
1 TTCTTCAA
*
30597 TACTTCAA
1 TTCTTCAA
*
30605 TCCTTCAA
1 TTCTTCAA
30613 TTC--CAA
1 TTCTTCAA
30619 TTCTTCAA
1 TTCTTCAA
*
30627 TGCTTCAA
1 TTCTTCAA
30635 -T-TTCAA
1 TTCTTCAA
*
30641 TACTTCAA
1 TTCTTCAA
*
30649 TCCTTCAA
1 TTCTTCAA
30657 -T-TTCAA
1 TTCTTCAA
*
30663 TTCATCAA
1 TTCTTCAA
30671 -TCATTCAA
1 TTC-TTCAA
30679 TTC--CAA
1 TTCTTCAA
30685 TTCTTCAA
1 TTCTTCAA
**
30693 AGCTTCAA
1 TTCTTCAA
30701 -T-TTCAA
1 TTCTTCAA
30707 TAT-TTCAA
1 T-TCTTCAA
*
30715 TGCTTCAA
1 TTCTTCAA
30723 -T-TTCAA
1 TTCTTCAA
*
30729 TTATTCAA
1 TTCTTCAA
*
30737 TGCTTCAA
1 TTCTTCAA
*
30745 TTCCTCAA
1 TTCTTCAA
*
30753 -TCATTCAG
1 TTC-TTCAA
*
30761 TTCCTCAA
1 TTCTTCAA
*
30769 TTATTCAA
1 TTCTTCAA
*
30777 CGT-TTCAA
1 -TTCTTCAA
*
30785 TGCTTCAA
1 TTCTTCAA
*
30793 TTCTCCAA
1 TTCTTCAA
* *
30801 ATATTCAA
1 TTCTTCAA
30809 TTCTTCAA
1 TTCTTCAA
30817 TGT-TTCAA
1 T-TCTTCAA
*
30825 TTATTCAA
1 TTCTTCAA
*
30833 TTATTCAA
1 TTCTTCAA
30841 TTCTTCAA
1 TTCTTCAA
30849 TT
1 TT
30851 TTTATTTCAA
Statistics
Matches: 417, Mismatches: 76, Indels: 86
0.72 0.13 0.15
Matches are distributed among these distances:
6 70 0.17
7 14 0.03
8 311 0.75
9 22 0.05
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.44
Consensus pattern (8 bp):
TTCTTCAA
Found at i:30371 original size:25 final size:24
Alignment explanation
Indices: 30307--30850 Score: 307
Period size: 22 Copynumber: 22.8 Consensus size: 24
30297 AATGATCTCT
*
30307 TTCTTCAATTCTTCAATTATTCAG
1 TTCTTCAATTCTTCAATTATTCAA
* * **
30331 TGCTTCAATTATTCAATTCCTCAA
1 TTCTTCAATTCTTCAATTATTCAA
30355 TTCTTCAAATTCTTCAATTATTCAA
1 TTCTTC-AATTCTTCAATTATTCAA
30380 TGT-TTCCAATTCTTCAATTATTCAA
1 T-TCTT-CAATTCTTCAATTATTCAA
* *
30405 TGT-TCCAATCCTTCAATGCTTCAATTTCAA
1 T-TCTTCAATTCTTCAA---TT--A-TTCAA
*
30435 TTCTTCAATACTTCAA-T-TTCAA
1 TTCTTCAATTCTTCAATTATTCAA
** *
30457 CACTTCAATGCTTCAATTATTCAA
1 TTCTTCAATTCTTCAATTATTCAA
*
30481 -T-TTCAATGCTTCAA-TACTTCAA
1 TTCTTCAATTCTTCAATTA-TTCAA
*
30503 -T-TTCAATTCTTCAGTTATTCAA
1 TTCTTCAATTCTTCAATTATTCAA
*
30525 -T-TTCAATTCTTCAATGCTTCAATTTCAT
1 TTCTTCAATTCTTCAA---TT--A-TTCAA
* *
30553 TTCTTCAATGCTTCAA-T-TTCAT
1 TTCTTCAATTCTTCAATTATTCAA
*
30575 TTCTTCAATGCTTCAA-T-TTCAA
1 TTCTTCAATTCTTCAATTATTCAA
* * *
30597 TACTTCAATCCTTCAA-T-TCCAA
1 TTCTTCAATTCTTCAATTATTCAA
*
30619 TTCTTCAATGCTTCAA-T-TTCAA
1 TTCTTCAATTCTTCAATTATTCAA
* *
30641 TACTTCAATCCTTCAA-T-TTCAA
1 TTCTTCAATTCTTCAATTATTCAA
* *
30663 TTCATCAA-TCATTCAA-T-TCCAA
1 TTCTTCAATTC-TTCAATTATTCAA
30685 TTCTTCAAAGCTTCAATTTCAA-TATTTCAA
1 TTCTTC-AA--TTC---TTCAATTA-TTCAA
*
30715 TGCTTCAA-T-TTCAATTATTCAA
1 TTCTTCAATTCTTCAATTATTCAA
* * * *
30737 TGCTTCAATTCCTCAATCATTCAG
1 TTCTTCAATTCTTCAATTATTCAA
* * ***
30761 TTCCTCAATTATTCAACGTTTCAA
1 TTCTTCAATTCTTCAATTATTCAA
* * *
30785 TGCTTCAATTCTCCAAATATTCAA
1 TTCTTCAATTCTTCAATTATTCAA
30809 TTCTTCAATGT-TTCAATTATTCAA
1 TTCTTCAAT-TCTTCAATTATTCAA
*
30833 TTATTCAATTCTTCAATT
1 TTCTTCAATTCTTCAATT
30851 TTTATTTCAA
Statistics
Matches: 423, Mismatches: 61, Indels: 72
0.76 0.11 0.13
Matches are distributed among these distances:
21 3 0.01
22 189 0.45
23 9 0.02
24 116 0.27
25 43 0.10
26 7 0.02
27 3 0.01
28 10 0.02
29 5 0.01
30 38 0.09
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.44
Consensus pattern (24 bp):
TTCTTCAATTCTTCAATTATTCAA
Found at i:30421 original size:66 final size:62
Alignment explanation
Indices: 30310--30850 Score: 276
Period size: 58 Copynumber: 8.9 Consensus size: 62
30300 GATCTCTTTC
* * ** * *
30310 TTCAATTCTTCAATTATTCAGTGCTTCAATTATTCAATTCC-TCAATTCTTCAAATTCTTCAATT
1 TTCAA-TCTTCAATTCTTCAATTATTCAA-TGTTCAA-TCCTTCAATGCTTC-AATTCTTCAATT
30374 A
62 A
* *
30375 TTCAATGTTTCCAATTCTTCAATTATTCAATGTTCCAATCCTTCAATGCTTCAA-T-TTCAATTC
1 TTCAAT-CTT-CAATTCTTCAATTATTCAATGTT-CAATCCTTCAATGCTTCAATTCTTCAATTA
* ** *
30438 TTCAATACTTCAA-T-TTCAA-CACTTCAATGCTTCAATTATTCAAT--TTCAATGCTTCAA-TA
1 TTCAAT-CTTCAATTCTTCAATTA-TTCAATG-TTCAATCCTTCAATGCTTCAATTCTTCAATTA
* * * *
30497 CTTCAAT-TTCAATTCTTCAGTTATTCAAT-TTCAATTCTTCAATGCTTCAA-T-TTCATTTC
1 -TTCAATCTTCAATTCTTCAATTATTCAATGTTCAATCCTTCAATGCTTCAATTCTTCAATTA
* * * *
30556 TTCAATGCTTCAA-T-TTCATTTCTTCAATGCTTCAAT--TTCAATACTTCAATCCTTCAA-T-
1 TTCAAT-CTTCAATTCTTCAATTATTCAATG-TTCAATCCTTCAATGCTTCAATTCTTCAATTA
* * * * *
30614 TCCAATTCTTCAATGCTTCAA-T-TTCAATACTTCAATCCTTCAAT--TTCAATTCATCAATCA
1 TTCAA-TCTTCAATTCTTCAATTATTCAAT-GTTCAATCCTTCAATGCTTCAATTCTTCAATTA
* *** **
30674 TTCAAT-TCCAATTCTTCAAAGCTTCAAT-TTCAATATTTCAATGCTTCAA-T-TTCAATTA
1 TTCAATCTTCAATTCTTCAATTATTCAATGTTCAATCCTTCAATGCTTCAATTCTTCAATTA
* * * ** * * * *
30732 TTCAATGCTTCAATTCCTCAATCATTCAGT-TCCTCAATTATTCAACGTTTCAATGCTTCAATTC
1 TTCAAT-CTTCAATTCTTCAATTATTCAATGT--TCAATCCTTCAATGCTTCAATTCTTCAATTA
* * * ** *
30796 TCCAAATATTCAATTCTTCAATGT-TTCAATTATTCAATTATTCAATTCTTCAATT
1 TTC-AATCTTCAATTCTTCAAT-TATTCAA-TGTTCAATCCTTCAATGCTTCAATT
30851 TTTATTTCAA
Statistics
Matches: 371, Mismatches: 62, Indels: 87
0.71 0.12 0.17
Matches are distributed among these distances:
58 125 0.34
59 10 0.03
60 105 0.28
61 4 0.01
62 19 0.05
63 15 0.04
64 46 0.12
65 19 0.05
66 28 0.08
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.44
Consensus pattern (62 bp):
TTCAATCTTCAATTCTTCAATTATTCAATGTTCAATCCTTCAATGCTTCAATTCTTCAATTA
Found at i:36041 original size:41 final size:42
Alignment explanation
Indices: 35950--36179 Score: 302
Period size: 43 Copynumber: 5.5 Consensus size: 42
35940 AGAGCTCCAA
* *
35950 ATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTAT
1 ATATGTGTTTGAGGACTTTG-AATATAGATGCCCCTGTGTTAT
* * *
35993 ATATGTGTTTGGGGACTTTG-ATATAGATGTCTCTGTGTTAT
1 ATATGTGTTTGAGGACTTTGAATATAGATGCCCCTGTGTTAT
* *
36034 ATATGTGTTTGAGGACTTTGTAATAAAGGTGCCCCTGTGTTAT
1 ATATGTGTTTGAGGACTTTG-AATATAGATGCCCCTGTGTTAT
* * *
36077 ATATGTGTTTGGGGAC-TTGAATATAGGTGCCTCTGTGTTAT
1 ATATGTGTTTGAGGACTTTGAATATAGATGCCCCTGTGTTAT
* *
36118 ATATGTGTTTGAGGACTTTGGAATAAAGATGTCCCTGTGTTAT
1 ATATGTGTTTGAGGACTTT-GAATATAGATGCCCCTGTGTTAT
*
36161 ATATGTGTTTGGGGACTTT
1 ATATGTGTTTGAGGACTTT
36180 TGGTTATTGG
Statistics
Matches: 164, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
41 71 0.43
42 5 0.03
43 88 0.54
ACGTcount: A:0.21, C:0.10, G:0.27, T:0.42
Consensus pattern (42 bp):
ATATGTGTTTGAGGACTTTGAATATAGATGCCCCTGTGTTAT
Found at i:36091 original size:84 final size:85
Alignment explanation
Indices: 35950--36179 Score: 383
Period size: 84 Copynumber: 2.7 Consensus size: 85
35940 AGAGCTCCAA
* *
35950 ATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-A
1 ATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGAA
*
36014 TATAGATGTCTCTGTGTTAT
66 TATAGATGCCTCTGTGTTAT
*
36034 ATATGTGTTTGAGGACTTTGTAATAAAGGTGCCCCTGTGTTATATATGTGTTTGGGGAC-TTGAA
1 ATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGAA
*
36098 TATAGGTGCCTCTGTGTTAT
66 TATAGATGCCTCTGTGTTAT
* *
36118 ATATGTGTTTGAGGACTTTGGAATAAAGATGTCCCTGTGTTATATATGTGTTTGGGGACTTT
1 ATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
36180 TGGTTATTGG
Statistics
Matches: 137, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
83 3 0.02
84 132 0.96
85 2 0.01
ACGTcount: A:0.21, C:0.10, G:0.27, T:0.42
Consensus pattern (85 bp):
ATATGTGTTTGAGGACTTTGTAATAAAGATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGAA
TATAGATGCCTCTGTGTTAT
Found at i:37212 original size:17 final size:18
Alignment explanation
Indices: 37187--37221 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
37177 TCAAAGGCCA
37187 ATTTAGGGTTT-GATTTG
1 ATTTAGGGTTTCGATTTG
*
37204 ATTTTGGGTTTCGATTTG
1 ATTTAGGGTTTCGATTTG
37222 GAAGGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.14, C:0.03, G:0.29, T:0.54
Consensus pattern (18 bp):
ATTTAGGGTTTCGATTTG
Found at i:40518 original size:17 final size:17
Alignment explanation
Indices: 40497--40538 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
40487 TTGATCACCG
40497 GTGATCTTACATCACT-
1 GTGATCTTACATCACTA
* *
40513 GTTGATTTTAGATCACTA
1 G-TGATCTTACATCACTA
40531 GTGATCTT
1 GTGATCTT
40539 GGGGGTGATC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 19 0.90
18 1 0.05
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.43
Consensus pattern (17 bp):
GTGATCTTACATCACTA
Found at i:41059 original size:101 final size:99
Alignment explanation
Indices: 40854--41075 Score: 227
Period size: 102 Copynumber: 2.2 Consensus size: 99
40844 GGAATTGAGA
* *
40854 AAAAAAAAGTTTAAG-CCAAAATTAATTAGATTTTAGCCAAAAAAAAATGACTATAAGGGTATGT
1 AAAAAAAAGTTT-AGCCCAAAATTAATTAGAGTTTAGCCAAAAAAAAATGACTATAAGGATATGT
* * **
40918 TCTAAACTTAAAATAATTATTTCCTAGGAT-TTTT
65 TCTAAACATAAAATAATTATATCCTAGGATCTTAG
** * * *
40952 TTAAAAAAGTTTAGCCCCAAATTAATTA-AGTTTAGCCATAAATAAAAATTTTGATTTTAAGGAT
1 AAAAAAAAGTTTAGCCCAAAATTAATTAGAGTTTAGCCA-AAA-AAAAA---TGACTATAAGGAT
* * *
41016 ATG-TCTTAACATAAAATATTTATATCCTAGGGTCTTAG
61 ATGTTCTAAACATAAAATAATTATATCCTAGGATCTTAG
*
41054 AAAAAAAAGTTTAGCCCTAAAT
1 AAAAAAAAGTTTAGCCCAAAAT
41076 AAAAAAATGA
Statistics
Matches: 100, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
97 11 0.11
98 25 0.25
99 5 0.05
101 25 0.25
102 34 0.34
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (99 bp):
AAAAAAAAGTTTAGCCCAAAATTAATTAGAGTTTAGCCAAAAAAAAATGACTATAAGGATATGTT
CTAAACATAAAATAATTATATCCTAGGATCTTAG
Found at i:41483 original size:16 final size:16
Alignment explanation
Indices: 41464--41522 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
41454 TCCGAACTCA
41464 AACCCAAAAAAACCCG
1 AACCCAAAAAAACCCG
* * * *
41480 AACCCGAAAAAGCTCA
1 AACCCAAAAAAACCCG
* *
41496 AACCCGAAAAAACCAG
1 AACCCAAAAAAACCCG
41512 AACCCGAAAAA
1 AACCC-AAAAA
41523 TCTAAAACCC
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
16 29 0.88
17 4 0.12
ACGTcount: A:0.56, C:0.32, G:0.10, T:0.02
Consensus pattern (16 bp):
AACCCAAAAAAACCCG
Found at i:41496 original size:32 final size:32
Alignment explanation
Indices: 41460--41551 Score: 130
Period size: 32 Copynumber: 2.9 Consensus size: 32
41450 CCCGTCCGAA
*
41460 CTCAAACCCAAAAAAACCCGAACCCGAAAAAG
1 CTCAAACCCGAAAAAACCCGAACCCGAAAAAG
* *
41492 CTCAAACCCGAAAAAACCAGAACCCGAAAAAT
1 CTCAAACCCGAAAAAACCCGAACCCGAAAAAG
* * *
41524 CTAAAACCCGATAAAATCCGAACCCGAA
1 CTCAAACCCGAAAAAACCCGAACCCGAA
41552 CTTGAAATAA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.51, C:0.33, G:0.10, T:0.07
Consensus pattern (32 bp):
CTCAAACCCGAAAAAACCCGAACCCGAAAAAG
Found at i:41547 original size:16 final size:15
Alignment explanation
Indices: 41471--41551 Score: 72
Period size: 16 Copynumber: 5.1 Consensus size: 15
41461 TCAAACCCAA
*
41471 AAAAACCCGAACCCG
1 AAAAATCCGAACCCG
* *
41486 AAAAAGCTCAAACCCG
1 AAAAATC-CGAACCCG
*
41502 AAAAAACCAGAACCCG
1 AAAAATCC-GAACCCG
**
41518 AAAAATCTAAAACCCG
1 AAAAATC-CGAACCCG
41534 ATAAAATCCGAACCCG
1 A-AAAATCCGAACCCG
41550 AA
1 AA
41552 CTTGAAATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
15 8 0.15
16 39 0.74
17 6 0.11
ACGTcount: A:0.52, C:0.31, G:0.11, T:0.06
Consensus pattern (15 bp):
AAAAATCCGAACCCG
Found at i:42122 original size:39 final size:40
Alignment explanation
Indices: 42068--42150 Score: 150
Period size: 39 Copynumber: 2.1 Consensus size: 40
42058 CCATGTTTTG
*
42068 ATGGGATCAATTTGTTGGACTAATCGTGTAACAACATG-C
1 ATGGGATCAATTTGTTGGACCAATCGTGTAACAACATGTC
42107 ATGGGATCAATTTGTTGGACCAATCGTGTAACAACATGTC
1 ATGGGATCAATTTGTTGGACCAATCGTGTAACAACATGTC
42147 ATGG
1 ATGG
42151 AGTACCAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 37 0.88
40 5 0.12
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (40 bp):
ATGGGATCAATTTGTTGGACCAATCGTGTAACAACATGTC
Found at i:42203 original size:30 final size:30
Alignment explanation
Indices: 42167--42223 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
42157 AAATTTCGGA
42167 TCAATTTTTCTGATCATATAACAAAACGGG
1 TCAATTTTTCTGATCATATAACAAAACGGG
* *
42197 TCAATTTTTCTGGTCATATAGCAAAAC
1 TCAATTTTTCTGATCATATAACAAAAC
42224 TCCAAGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (30 bp):
TCAATTTTTCTGATCATATAACAAAACGGG
Found at i:42353 original size:46 final size:46
Alignment explanation
Indices: 42286--42379 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
42276 CTCGTCGCGA
42286 ATCGCGAAAAATGACCAACCATTATTGGCACAAATGATAATAACAC
1 ATCGCGAAAAATGACCAACCATTATTGGCACAAATGATAATAACAC
42332 ATCGCGAAAAATGACCAACCATTATTGGCACAAATGATAATAACAC
1 ATCGCGAAAAATGACCAACCATTATTGGCACAAATGATAATAACAC
42378 AT
1 AT
42380 GGCATAAGGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.20
Consensus pattern (46 bp):
ATCGCGAAAAATGACCAACCATTATTGGCACAAATGATAATAACAC
Found at i:42366 original size:23 final size:23
Alignment explanation
Indices: 42294--42368 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
42284 GAATCGCGAA
42294 AAATGACCAACCATTATTGGCAC
1 AAATGACCAACCATTATTGGCAC
** * * * *
42317 AAATGATAATAACA-CA-TCGCGAA
1 AAATGACCA-ACCATTATTGGC-AC
42340 AAATGACCAACCATTATTGGCAC
1 AAATGACCAACCATTATTGGCAC
42363 AAATGA
1 AAATGA
42369 TAATAACACA
Statistics
Matches: 36, Mismatches: 12, Indels: 8
0.64 0.21 0.14
Matches are distributed among these distances:
22 6 0.17
23 24 0.67
24 6 0.17
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.20
Consensus pattern (23 bp):
AAATGACCAACCATTATTGGCAC
Found at i:43717 original size:35 final size:35
Alignment explanation
Indices: 43647--43717 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 35
43637 GTTGTCACTT
*
43647 GCCATTGTATACTGAAGCACTCAGGCAAGTTGCAG
1 GCCATTGTATACTGAAGCACTCAGGCAAGTAGCAG
43682 GCCATTGTATACTGAAGCACTCAGGCAA-TCAGCAG
1 GCCATTGTATACTGAAGCACTCAGGCAAGT-AGCAG
43717 G
1 G
43718 GTAAATCACT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 1 0.03
35 33 0.97
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21
Consensus pattern (35 bp):
GCCATTGTATACTGAAGCACTCAGGCAAGTAGCAG
Found at i:49301 original size:65 final size:65
Alignment explanation
Indices: 49197--49326 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
49187 TATTTGGAAT
49197 GGATTTATGAAATGTGTCCATCTTATTAAGGGCAATATTAGATGGAATCTTGGAAATGGAGAGAA
1 GGATTTATGAAATGTGTCCATCTTATTAAGGGCAATATTAGATGGAATCTTGGAAATGGAGAGAA
49262 GGATTTATGAAATGTGTCCATCTTATTAAGGGCAATATTAGATGGAATCTTGGAAATGGAGAGAA
1 GGATTTATGAAATGTGTCCATCTTATTAAGGGCAATATTAGATGGAATCTTGGAAATGGAGAGAA
49327 TATTAACTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.31
Consensus pattern (65 bp):
GGATTTATGAAATGTGTCCATCTTATTAAGGGCAATATTAGATGGAATCTTGGAAATGGAGAGAA
Found at i:51390 original size:12 final size:12
Alignment explanation
Indices: 51375--51401 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
51365 ACATAATGAA
51375 GATCATGGAGAT
1 GATCATGGAGAT
51387 GATCATGGAGAT
1 GATCATGGAGAT
51399 GAT
1 GAT
51402 GTGCACATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.26
Consensus pattern (12 bp):
GATCATGGAGAT
Found at i:55507 original size:2 final size:2
Alignment explanation
Indices: 55502--55527 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55492 AAAAAAAAAC
55502 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
55528 TTCATACTAA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:60300 original size:22 final size:22
Alignment explanation
Indices: 60272--60319 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
60262 TGAACCTGGC
60272 ATCAAGTAGTAAGAGGATTCAA
1 ATCAAGTAGTAAGAGGATTCAA
60294 ATCAAGTAGTAAGAGGATTCAA
1 ATCAAGTAGTAAGAGGATTCAA
60316 ATCA
1 ATCA
60320 GTCCCTTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (22 bp):
ATCAAGTAGTAAGAGGATTCAA
Found at i:60691 original size:30 final size:30
Alignment explanation
Indices: 60628--60689 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 30
60618 TATTCTGCCA
60628 TTATTTTTTATTTAGGTTAGTATTAGGCTT
1 TTATTTTTTATTTAGGTTAGTATTAGGCTT
*
60658 TTATTTTCTTATTTTA-GTTAGTATTGGGCTT
1 TTATTTT-TTA-TTTAGGTTAGTATTAGGCTT
60689 T
1 T
60690 ATGGGCTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.24
31 18 0.62
32 4 0.14
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.61
Consensus pattern (30 bp):
TTATTTTTTATTTAGGTTAGTATTAGGCTT
Found at i:64258 original size:3 final size:3
Alignment explanation
Indices: 64250--64307 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
64240 ATATATGTGT
64250 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
64298 ATA ATA ATA A
1 ATA ATA ATA A
64308 AAAATTGTTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:65993 original size:19 final size:19
Alignment explanation
Indices: 65969--66011 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
65959 GGGCTGATGG
*
65969 TTTCGTCAATTGATTTTGA
1 TTTCGTCAATTGATTCTGA
65988 TTTCGTCAATTGATTCTGA
1 TTTCGTCAATTGATTCTGA
66007 TTTCG
1 TTTCG
66012 GTAATAAGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (19 bp):
TTTCGTCAATTGATTCTGA
Found at i:78012 original size:18 final size:17
Alignment explanation
Indices: 77966--78014 Score: 80
Period size: 17 Copynumber: 2.8 Consensus size: 17
77956 ACCTCCTGGC
77966 TTAGGATTTTATTTCCT
1 TTAGGATTTTATTTCCT
77983 TTAGGATTTTATTTCCT
1 TTAGGATTTTATTTCCT
*
78000 TTAGTACTTTTATTT
1 TTAGGA-TTTTATTT
78015 TCTCAAATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 22 0.73
18 8 0.27
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.61
Consensus pattern (17 bp):
TTAGGATTTTATTTCCT
Found at i:87771 original size:10 final size:9
Alignment explanation
Indices: 87747--87804 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
87737 ATTTCTTACC
*
87747 CTTATCTTT
1 CTTATTTTT
87756 -TTATTTTT
1 CTTATTTTT
87764 CGTTATTTTT
1 C-TTATTTTT
87774 CTT-TTTCTT
1 CTTATTT-TT
87783 -TTATTTTT
1 CTTATTTTT
*
87791 GTTTATTTTT
1 -CTTATTTTT
87801 CTTA
1 CTTA
87805 GTTACTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 14 0.34
9 10 0.24
10 17 0.41
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.76
Consensus pattern (9 bp):
CTTATTTTT
Found at i:87778 original size:16 final size:17
Alignment explanation
Indices: 87753--87790 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
87743 TACCCTTATC
87753 TTTTTATTTTTC-GTTA
1 TTTTTATTTTTCTGTTA
* *
87769 TTTTTCTTTTTCTTTTA
1 TTTTTATTTTTCTGTTA
87786 TTTTT
1 TTTTT
87791 GTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTATTTTTCTGTTA
Found at i:88970 original size:21 final size:21
Alignment explanation
Indices: 88931--88979 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
88921 TCAAAGCTTT
**
88931 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
88953 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
88974 A-GAAGC
1 AGGAAGC
88980 TACAATTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Done.