Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000169.1 Kokia drynarioides strain JFW-HI SEQ_110839, 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: 41176
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:1722 original size:93 final size:94
Alignment explanation
Indices: 1563--1760 Score: 371
Period size: 93 Copynumber: 2.1 Consensus size: 94
1553 AGCCTAATAA
1563 GTAAGAAGTAAAAGAATTAAATCACTAACCGACGTTGACCGGCCGAAGACCCTTAAAGAAAATCA
1 GTAAGAAGTAAAAGAATTAAATCACTAACCGACGTTGACCGGCCGAAGACCCTTAAAGAAAATCA
1628 CT-AAAAAAAAAGAAGAGGGAAAAGAAGG
66 CTAAAAAAAAAAGAAGAGGGAAAAGAAGG
1656 GTAAGAAGTAAAAGAATTAAATCACTAACCGACGTTGACCGGCCGAAGACCCTTAAAGAAAATCA
1 GTAAGAAGTAAAAGAATTAAATCACTAACCGACGTTGACCGGCCGAAGACCCTTAAAGAAAATCA
1721 CTAAAAAAAAAAGAAGAGGGAAAAGAAGG
66 CTAAAAAAAAAAGAAGAGGGAAAAGAAGG
*
1750 GCAAGTAAGTA
1 GTAAG-AAGTA
1761 GAGCTGGTTC
Statistics
Matches: 102, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
93 67 0.66
94 30 0.29
95 5 0.05
ACGTcount: A:0.51, C:0.15, G:0.22, T:0.13
Consensus pattern (94 bp):
GTAAGAAGTAAAAGAATTAAATCACTAACCGACGTTGACCGGCCGAAGACCCTTAAAGAAAATCA
CTAAAAAAAAAAGAAGAGGGAAAAGAAGG
Found at i:1901 original size:19 final size:20
Alignment explanation
Indices: 1864--1907 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1854 ATGAAAATGT
* *
1864 ATTTT-TAAATATTATAT-A
1 ATTTTATAAATATAAAATAA
1882 ATTTTATAAATATAAAATAA
1 ATTTTATAAATATAAAATAA
1902 ATTTTA
1 ATTTTA
1908 AGCAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.23
19 10 0.45
20 7 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTATAAATATAAAATAA
Found at i:2964 original size:16 final size:17
Alignment explanation
Indices: 2943--2981 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
2933 AAAATTTAAT
2943 TTTAAA-TTATTTTGAG
1 TTTAAATTTATTTTGAG
*
2959 TTTAAATTTATTTTGGG
1 TTTAAATTTATTTTGAG
2976 TTTAAA
1 TTTAAA
2982 ATTAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTGAG
Found at i:3671 original size:3 final size:3
Alignment explanation
Indices: 3657--3692 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
3647 TTATTAAATA
*
3657 AAT AAT ATT AAT AAT AAT CAAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AA
3693 AATTCGAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3679 original size:16 final size:16
Alignment explanation
Indices: 3660--3690 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3650 TTAAATAAAT
*
3660 AATATTAATAATAATC
1 AATAATAATAATAATC
3676 AATAATAATAATAAT
1 AATAATAATAATAAT
3691 AAAATTCGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAATAATAATAATC
Found at i:4743 original size:29 final size:28
Alignment explanation
Indices: 4699--5082 Score: 202
Period size: 29 Copynumber: 13.2 Consensus size: 28
4689 CCTAGAAAGT
*
4699 CCCT-AAACTTTCCAAAAATTATATTTTGA
1 CCCTCAAACTTT-CAAAAATTACATTTT-A
* *
4728 CCCTCAAACTTTCAAAAAATTCCATTTCAA
1 CCCTCAAACTTTC-AAAAATTACATTT-TA
4758 CCC-CAAACTTTCTAAAAATTACCATTTTA
1 CCCTCAAACTTTC-AAAAATTA-CATTTTA
* *
4787 CCC-CTGAA-TTTCCAAAAATTCCATTTTTGA
1 CCCTC-AAACTTT-CAAAAATTACA-TTTT-A
*
4817 CCCT-AAACTTTCCAAAATTACTATTTTA
1 CCCTCAAACTTTCAAAAATTAC-ATTTTA
* *
4845 CCCTCAAAC-ATCAAAAAATTATATTTTTA
1 CCCTCAAACTTTC-AAAAATTACA-TTTTA
*
4874 -ACTCTAAACTTTCCAAAAATTACCATTTTA
1 CCCTC-AAACTTT-CAAAAATTA-CATTTTA
* *
4904 CTCC-CGAA-TTTCCAAAAATTCCATTTTTGA
1 C-CCTCAAACTTT-CAAAAATTACA-TTTT-A
*
4934 CCCT-TAACTTTCCAAAAATTATCATTTTA
1 CCCTCAAACTTT-CAAAAATTA-CATTTTA
* *
4963 CCCTCAGA-TGTCCAAAAATTACATTTTGA
1 CCCTCAAACT-TTCAAAAATTACATTTT-A
** *
4992 -CCTTGAACTTTCCAAAATTACCATTTTA
1 CCCTCAAACTTTCAAAAATTA-CATTTTA
*** *
5020 CCCTTGGA-TGTCCAAAAATTACATTTTTGA
1 CCCTCAAACT-TTCAAAAATTACA-TTTT-A
*
5050 CCC-CAAACTTCCAAAAATTACCATTTTA
1 CCCTCAAACTTTCAAAAATTA-CATTTTA
*
5078 TCCTC
1 CCCTC
5083 GAGCATCCAA
Statistics
Matches: 281, Mismatches: 37, Indels: 74
0.72 0.09 0.19
Matches are distributed among these distances:
28 41 0.15
29 153 0.54
30 81 0.29
31 5 0.02
32 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (28 bp):
CCCTCAAACTTTCAAAAATTACATTTTA
Found at i:4834 original size:58 final size:58
Alignment explanation
Indices: 4699--5077 Score: 392
Period size: 59 Copynumber: 6.5 Consensus size: 58
4689 CCTAGAAAGT
* * * * **
4699 CCCTAAACTTTCCAAAAATTA-TATTTTGACCCTCAAACTTTCAAAAAATTCCA-TTTCAA
1 CCCTAAACTTTCCAAAAATTACCATTTT-ACCCT-GAA-TTTCCAAAAATTACATTTTTGA
* * *
4758 CCCCAAACTTTCTAAAAATTACCATTTTACCCCTGAATTTCCAAAAATTCCATTTTTGA
1 CCCTAAACTTTCCAAAAATTACCATTTTA-CCCTGAATTTCCAAAAATTACATTTTTGA
* * ** * * *
4817 CCCTAAACTTTCC-AAAATTACTATTTTACCCTCAAACATCAAAAAATTATATTTTTAA
1 CCCTAAACTTTCCAAAAATTACCATTTTACCCT-GAATTTCCAAAAATTACATTTTTGA
* * *
4875 CTCTAAACTTTCCAAAAATTACCATTTTACTCCCGAATTTCCAAAAATTCCATTTTTGA
1 CCCTAAACTTTCCAAAAATTACCATTTTAC-CCTGAATTTCCAAAAATTACATTTTTGA
* * * *
4934 CCCTTAACTTTCCAAAAATTATCATTTTACCCTCAGATGTCCAAAAATTACA-TTTTGA
1 CCCTAAACTTTCCAAAAATTACCATTTTACCCTGA-ATTTCCAAAAATTACATTTTTGA
* * * *
4992 CCTTGAACTTTCC-AAAATTACCATTTTACCCTTGGATGTCCAAAAATTACATTTTTGA
1 CCCTAAACTTTCCAAAAATTACCATTTTACCC-TGAATTTCCAAAAATTACATTTTTGA
*
5050 CCCCAAAC-TTCCAAAAATTACCATTTTA
1 CCCTAAACTTTCCAAAAATTACCATTTTA
5078 TCCTCGAGCA
Statistics
Matches: 268, Mismatches: 42, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
57 41 0.15
58 105 0.39
59 111 0.41
60 11 0.04
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (58 bp):
CCCTAAACTTTCCAAAAATTACCATTTTACCCTGAATTTCCAAAAATTACATTTTTGA
Found at i:5091 original size:29 final size:29
Alignment explanation
Indices: 4885--5181 Score: 159
Period size: 29 Copynumber: 10.2 Consensus size: 29
4875 CTCTAAACTT
***
4885 TCCAAAAATTACCATTTTACTCC-CGAATT
1 TCCAAAAATTACCATTTTAC-CCTCGAGCA
* * *
4914 TCCAAAAATT-CCATTTTTGACCCT-TAACTT
1 TCCAAAAATTACCA-TTTT-ACCCTCGAGC-A
*
4944 TCCAAAAATTATCATTTTACCCTC-AG-A
1 TCCAAAAATTACCATTTTACCCTCGAGCA
* * *
4971 TGTCCAAAAATTA-CATTTTGA-CCTTGAACTT
1 --TCCAAAAATTACCATTTT-ACCCTCGAGC-A
*
5002 TCC-AAAATTACCATTTTACCCTTG-G-A
1 TCCAAAAATTACCATTTTACCCTCGAGCA
* * *
5028 TGTCCAAAAATTA-CATTTTTGACCC-CAAACT
1 --TCCAAAAATTACCA-TTTT-ACCCTCGAGCA
*
5059 TCCAAAAATTACCATTTTATCCTCGAGCA
1 TCCAAAAATTACCATTTTACCCTCGAGCA
* * * * * **
5088 TCCAAAATTTACCATTTTGCTCACGTGTG
1 TCCAAAAATTACCATTTTACCCTCGAGCA
* * * * *
5117 TCCAAAAATTACCATTATACCCGCAAACC
1 TCCAAAAATTACCATTTTACCCTCGAGCA
5146 TCCAAAAATTACCATTTTACCCTCGAGCA
1 TCCAAAAATTACCATTTTACCCTCGAGCA
5175 TCCAAAA
1 TCCAAAA
5182 TCACATTTTT
Statistics
Matches: 204, Mismatches: 41, Indels: 46
0.70 0.14 0.16
Matches are distributed among these distances:
28 28 0.14
29 151 0.74
30 23 0.11
31 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCTCGAGCA
Found at i:5150 original size:116 final size:114
Alignment explanation
Indices: 4763--5163 Score: 384
Period size: 117 Copynumber: 3.4 Consensus size: 114
4753 TTCAACCCCA
* * * *
4763 AACTTTCTAAAAATTACCATTTTACCCCTGAATTTCCAAAAATTCCATTTTTGACCCTAAACTTT
1 AACTTTCCAAAAATTACCATTTTACCCC-GAATCTCCAAAAATTACATTTTTGACCCCAAACTTT
* * * * * * *
4828 CC-AAAATTACTATTTTACCCTCAAACATCAAAAAATTATATTTTTAACTCTA
65 CCAAAAATTACCATTTTACCCTCAGA-GTCCAAAAATTACA-TTTTGACT-TG
* * **
4880 AACTTTCCAAAAATTACCATTTTACTCCCGAATTTCCAAAAATTCCATTTTTGACCCTTAACTTT
1 AACTTTCCAAAAATTACCATTTTAC-CCCGAATCTCCAAAAATTACATTTTTGACCCCAAACTTT
*
4945 CCAAAAATTATCATTTTACCCTCAGATGTCCAAAAATTACATTTTGACCTTG
65 CCAAAAATTACCATTTTACCCTCAGA-GTCCAAAAATTACATTTTGA-CTTG
* * *
4997 AACTTTCC-AAAATTACCATTTTACCCTTGGATGTCCAAAAATTACATTTTTGACCCCAAAC-TT
1 AACTTTCCAAAAATTACCATTTTACCC-CGAATCTCCAAAAATTACATTTTTGACCCCAAACTTT
* *
5060 CCAAAAATTACCATTTTATCCTC-GAGCATCCAAAATTTACCATTTTG-C-T-
65 CCAAAAATTACCATTTTACCCTCAGAG--TCCAAAAATTA-CATTTTGACTTG
* * * *
5109 CACGTGTGTCCAAAAATTACCATTATACCCGCAAACCTCCAAAAATTACCATTTT
1 AAC-T-T-TCCAAAAATTACCATTTTACCC-CGAATCTCCAAAAATTA-CATTTT
5164 ACCCTCGAGC
Statistics
Matches: 244, Mismatches: 28, Indels: 24
0.82 0.09 0.08
Matches are distributed among these distances:
112 2 0.01
113 3 0.01
114 4 0.02
115 38 0.16
116 80 0.33
117 81 0.33
118 36 0.15
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (114 bp):
AACTTTCCAAAAATTACCATTTTACCCCGAATCTCCAAAAATTACATTTTTGACCCCAAACTTTC
CAAAAATTACCATTTTACCCTCAGAGTCCAAAAATTACATTTTGACTTG
Found at i:9835 original size:20 final size:20
Alignment explanation
Indices: 9810--9850 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
9800 ATTGGACTTT
*
9810 AATTTTTAAATTGAAACTAA
1 AATTTTGAAATTGAAACTAA
*
9830 AATTTTGAAATTGAAATTAA
1 AATTTTGAAATTGAAACTAA
9850 A
1 A
9851 GGGATTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (20 bp):
AATTTTGAAATTGAAACTAA
Found at i:16174 original size:17 final size:17
Alignment explanation
Indices: 16152--16237 Score: 84
Period size: 17 Copynumber: 5.1 Consensus size: 17
16142 TCAAGCCCAA
* *
16152 ATTTTAATTTTTAATTT
1 ATTTTAAATTTAAATTT
16169 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
16186 ATTATAAATTTAAA-TT
1 ATTTTAAATTTAAATTT
* * *
16202 AATTTATAGTTTAAATAT
1 ATTTTA-AATTTAAATTT
* *
16220 ATTTTAAAATTGAATTT
1 ATTTTAAATTTAAATTT
16237 A
1 A
16238 ATTAAAAAGT
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
16 6 0.11
17 43 0.78
18 6 0.11
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:18143 original size:29 final size:30
Alignment explanation
Indices: 18059--18194 Score: 136
Period size: 29 Copynumber: 4.5 Consensus size: 30
18049 CTGAACTGTT
* *
18059 CAAAAATCACATTTTGACCTCTAAACTTTTT
1 CAAAAATTACATTTTGACCTCTAAAC-TTTC
* * *
18090 TAAAAATTATATTTTGACCCCTAAAC-TTC
1 CAAAAATTACATTTTGACCTCTAAACTTTC
18119 ACAAAAATTACATTTT-ACCTCTAAACTTTC
1 -CAAAAATTACATTTTGACCTCTAAACTTTC
* * *
18149 TAGAAATTACATTTTTACCCTCT-AAC-TTC
1 CAAAAATTACATTTTGA-CCTCTAAACTTTC
18178 CAAAAATTACCATTTTG
1 CAAAAATTA-CATTTTG
18195 CATTTTTACT
Statistics
Matches: 87, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
29 34 0.39
30 26 0.30
31 27 0.31
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (30 bp):
CAAAAATTACATTTTGACCTCTAAACTTTC
Found at i:18216 original size:37 final size:37
Alignment explanation
Indices: 18158--18230 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
18148 CTAGAAATTA
* *
18158 CATTTTTACCCTCTAACTTCCAAAAATTACCATTTTG
1 CATTTTTACCCTCGAACTTCCAAAAATTACAATTTTG
*
18195 CATTTTTACTCC-CGAATTTCCAAAAATTACAATTTT
1 CATTTTTAC-CCTCGAACTTCCAAAAATTACAATTTT
18231 CTCCCGAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 30 0.94
38 2 0.06
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.41
Consensus pattern (37 bp):
CATTTTTACCCTCGAACTTCCAAAAATTACAATTTTG
Found at i:18277 original size:29 final size:29
Alignment explanation
Indices: 18212--18470 Score: 134
Period size: 29 Copynumber: 8.8 Consensus size: 29
18202 ACTCCCGAAT
*
18212 TTCCAAAAATTACAATTTT-CTCC-CGAAC
1 TTCCAAAAATTACAATTTTAC-CCTCAAAC
** *
18240 TTTTAAAAAATCACAATTTTACCCTCAAAC
1 -TTCCAAAAATTACAATTTTACCCTCAAAC
* *
18270 TTCCAAAAATTACTATTTTACCCTCGAAC
1 TTCCAAAAATTACAATTTTACCCTCAAAC
* * * *
18299 TTCCAAAAAAAAAATCACATTTTTGCCCTTAAAC
1 TTCC-----AAAAATTACAATTTTACCCTCAAAC
* *
18333 TTCCAAAAAATTACCATTTTACCCTCGAAC
1 TTCC-AAAAATTACAATTTTACCCTCAAAC
* * *
18363 TT-CTAAAA-TATCATTTTTAACCCT-AAATT
1 TTCCAAAAATTA-CAATTTT-ACCCTCAAA-C
*** ** *
18392 TTTTGAAAATTATTATTTTACTCTCAAAC
1 TTCCAAAAATTACAATTTTACCCTCAAAC
* * * *
18421 TTCAAAAAATTACCATTTTACCCCCAAGC
1 TTCCAAAAATTACAATTTTACCCTCAAAC
* *
18450 TTCCAAAAGTCAC-ATTTTACC
1 TTCCAAAAATTACAATTTTACC
18471 TCCTAGTGTT
Statistics
Matches: 173, Mismatches: 44, Indels: 27
0.71 0.18 0.11
Matches are distributed among these distances:
27 2 0.01
28 19 0.11
29 89 0.51
30 38 0.22
31 2 0.01
34 23 0.13
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
TTCCAAAAATTACAATTTTACCCTCAAAC
Found at i:18340 original size:63 final size:64
Alignment explanation
Indices: 18244--18370 Score: 202
Period size: 64 Copynumber: 2.0 Consensus size: 64
18234 CCGAACTTTT
*
18244 AAAAAATCACAATTTTACCCTCAAACTTCC-AAAAATTACTATTTTACCCTCGAACTTCCAAAA
1 AAAAAATCACAATTTTACCCTCAAACTTCCAAAAAATTACCATTTTACCCTCGAACTTCCAAAA
* * * *
18307 AAAAAATCACATTTTTGCCCTTAAACTTCCAAAAAATTACCATTTTACCCTCGAACTTCTAAAA
1 AAAAAATCACAATTTTACCCTCAAACTTCCAAAAAATTACCATTTTACCCTCGAACTTCCAAAA
18371 TATCATTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
63 27 0.47
64 31 0.53
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (64 bp):
AAAAAATCACAATTTTACCCTCAAACTTCCAAAAAATTACCATTTTACCCTCGAACTTCCAAAA
Found at i:18364 original size:30 final size:30
Alignment explanation
Indices: 18198--18370 Score: 140
Period size: 29 Copynumber: 5.7 Consensus size: 30
18188 CATTTTGCAT
*
18198 TTTTACTCC-CGAATTTCC-AAAAATTACAA
1 TTTTAC-CCTCGAACTTCCAAAAAATTACAA
** *
18227 TTTT-CTCC-CGAACTTTTAAAAAATCACAA
1 TTTTAC-CCTCGAACTTCCAAAAAATTACAA
* *
18256 TTTTACCCTCAAACTTCC-AAAAATTACTA
1 TTTTACCCTCGAACTTCCAAAAAATTACAA
* *
18285 TTTTACCCTCGAACTTCCAAAAAAAAAATCACAT
1 TTTTACCCTCGAACTTCC----AAAAAATTACAA
* ** *
18319 TTTTGCCCTTAAACTTCCAAAAAATTACCA
1 TTTTACCCTCGAACTTCCAAAAAATTACAA
*
18349 TTTTACCCTCGAACTTCTAAAA
1 TTTTACCCTCGAACTTCCAAAA
18371 TATCATTTTT
Statistics
Matches: 113, Mismatches: 23, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
28 10 0.09
29 46 0.41
30 34 0.30
34 23 0.20
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (30 bp):
TTTTACCCTCGAACTTCCAAAAAATTACAA
Found at i:18574 original size:29 final size:29
Alignment explanation
Indices: 18509--18577 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
18499 CCCTTGAGTG
* * *
18509 TCCAAAAATTACCGTTTTACCTCCGAACA
1 TCCAAAAATCACCCTTTTACCCCCGAACA
* *
18538 TCCAAAAATCACCCTTTTACCCCCGAGCT
1 TCCAAAAATCACCCTTTTACCCCCGAACA
*
18567 TCCGAAAATCA
1 TCCAAAAATCA
18578 TATTTTTGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.33, C:0.35, G:0.07, T:0.25
Consensus pattern (29 bp):
TCCAAAAATCACCCTTTTACCCCCGAACA
Found at i:21765 original size:27 final size:27
Alignment explanation
Indices: 21727--21780 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
21717 TATAAGAAAC
21727 AGCTAACATTTTGCAGACTTCAGCCAT
1 AGCTAACATTTTGCAGACTTCAGCCAT
21754 AGCTAACATTTTGCAGACTTCAGCCAT
1 AGCTAACATTTTGCAGACTTCAGCCAT
21781 TTAGGACCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (27 bp):
AGCTAACATTTTGCAGACTTCAGCCAT
Found at i:23745 original size:13 final size:12
Alignment explanation
Indices: 23657--23777 Score: 73
Period size: 13 Copynumber: 9.3 Consensus size: 12
23647 TTCAATGAAG
*
23657 AAAGAAAAAAGA
1 AAAGAAAAAAAA
*
23669 AAAGAAAGAAGAA
1 AAAGAAA-AAAAA
23682 AAAGCAAAATAAAAA
1 AAAG--AAA-AAAAA
23697 AAAGAAATAAAAA
1 AAAGAAA-AAAAA
*
23710 AGAAGAAAAAACAT
1 A-AAGAAAAAA-AA
* *
23724 GAAGAAAAACAA
1 AAAGAAAAAAAA
*
23736 AAA-AAGAAAAA
1 AAAGAAAAAAAA
*
23747 GAAGAAAAAAAA
1 AAAGAAAAAAAA
*
23759 TAGAGAGAAAAAACA
1 -A-A-AGAAAAAAAA
23774 AAAG
1 AAAG
23778 GAGAGGTCGA
Statistics
Matches: 85, Mismatches: 15, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
11 8 0.09
12 19 0.22
13 29 0.34
14 9 0.11
15 20 0.24
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:23745 original size:14 final size:13
Alignment explanation
Indices: 23657--23746 Score: 74
Period size: 14 Copynumber: 6.7 Consensus size: 13
23647 TTCAATGAAG
*
23657 AAAG-AAAAAAGA
1 AAAGAAAAAAAAA
* *
23669 AAAGAAAGAAGAA
1 AAAGAAAAAAAAA
23682 AAAGCAAAATAAAAA
1 AAAG-AAAA-AAAAA
23697 AAAGAAATAAAAAA
1 AAAGAAA-AAAAAA
* * *
23711 GAAGAAAAAACAT
1 AAAGAAAAAAAAA
*
23724 GAAGAAAAACAAAA
1 AAAGAAAAA-AAAA
23738 AAAGAAAAA
1 AAAGAAAAA
23747 GAAGAAAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
12 4 0.06
13 22 0.35
14 27 0.44
15 9 0.15
ACGTcount: A:0.80, C:0.03, G:0.13, T:0.03
Consensus pattern (13 bp):
AAAGAAAAAAAAA
Found at i:23769 original size:23 final size:23
Alignment explanation
Indices: 23673--23755 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 23
23663 AAAAGAAAAG
23673 AAAGAAGAAAAAGCAAAATAAA-AA
1 AAAGAAGAAAAA-CAAAA-AAAGAA
23697 AAAGAA-ATAAAA-AAGAAGAAA-AA
1 AAAGAAGA-AAAACAA-AA-AAAGAA
*
23720 ACATGAAGAAAAACAAAAAAAGAA
1 A-AAGAAGAAAAACAAAAAAAGAA
23744 AAAGAAGAAAAA
1 AAAGAAGAAAAA
23756 AAATAGAGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
22 2 0.04
23 22 0.44
24 23 0.46
25 3 0.06
ACGTcount: A:0.80, C:0.04, G:0.13, T:0.04
Consensus pattern (23 bp):
AAAGAAGAAAAACAAAAAAAGAA
Found at i:23777 original size:36 final size:36
Alignment explanation
Indices: 23650--23776 Score: 111
Period size: 36 Copynumber: 3.5 Consensus size: 36
23640 AGTCGGATTC
* *
23650 AATGAAGAAAGAAAAAAGAAAAGAAAGAAGAA-AAAGCAA
1 AATGAAGAAA-AACAAA-AAAAGAAA-AAGAAGAAA-AAA
* *
23689 AAT-AA-AAAAA-AGAAATA-AAAAAGAAGAAAAAA
1 AATGAAGAAAAACAAAAAAAGAAAAAGAAGAAAAAA
*
23721 CATGAAGAAAAACAAAAAAAGAAAAAGAAGAAAAAA
1 AATGAAGAAAAACAAAAAAAGAAAAAGAAGAAAAAA
23757 AATAGAGAGAAAAAACAAAA
1 AAT-GA-AG-AAAAACAAAA
23777 GGAGAGGTCG
Statistics
Matches: 73, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
32 9 0.12
33 8 0.11
34 8 0.11
35 7 0.10
36 19 0.26
37 5 0.07
38 4 0.05
39 13 0.18
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.04
Consensus pattern (36 bp):
AATGAAGAAAAACAAAAAAAGAAAAAGAAGAAAAAA
Found at i:24999 original size:99 final size:99
Alignment explanation
Indices: 24770--25123 Score: 315
Period size: 99 Copynumber: 3.6 Consensus size: 99
24760 ACGAACCCGA
* * * * * * * * *
24770 TACCTCAGAAGATGTGATGGGAAAGATTGAGGCTGCAACGGCGAATCCGGTACCA-AGAA-ATGT
1 TACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGAGAACCCGGTACCATAGAAGATAT
* * * *
24833 GATAGGAAAGGTTGAGGCCGCAATGGCGAACCCGA
66 GA-AGGAAAGGTTGAGGCCGCAACGGCAAACCTGG
* * * * * *
24868 TACCAT-GAAGATTTTAAGGGAAAGGCTGAGGCCGTAATGGAGAACCCGGTACCAT-GAAGATTT
1 TACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGAGAACCCGGTACCATAGAAGATAT
* *
24931 TAAGGGAAAGGTTGAGGCCGCAACGGTAAACCTGG
66 GAA-GGAAAGGTTGAGGCCGCAACGGCAAACCTGG
* * * * * *
24966 TACTTTAGAAGATATGAAGGGAAAGGTTAAGGCCGCAA-CGACAAACCTGGTACCTTAGAAGATA
1 TACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGA-GAACCCGGTACCATAGAAGATA
* * ***
25030 TGAAGGAAAGGTTGAGGCCGTAACGACAAGTTTGG
65 TGAAGGAAAGGTTGAGGCCGCAACGGCAAACCTGG
* * * *
25065 TACCTTAGAAGATATGAA-GGAAAAGTTGAGGCCGCAATGGCGAACCCGATACCTTAGAA
1 TACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGAGAACCCGGTACCATAGAA
25124 AACAAGATGA
Statistics
Matches: 203, Mismatches: 46, Indels: 14
0.77 0.17 0.05
Matches are distributed among these distances:
97 42 0.21
98 72 0.35
99 80 0.39
100 9 0.04
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (99 bp):
TACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAATGGAGAACCCGGTACCATAGAAGATAT
GAAGGAAAGGTTGAGGCCGCAACGGCAAACCTGG
Found at i:25057 original size:49 final size:49
Alignment explanation
Indices: 24677--25123 Score: 274
Period size: 49 Copynumber: 9.1 Consensus size: 49
24667 AGAAAAAAAT
* * * * * * * *
24677 GAAGATTTTAAGGGAAGGATTGAGGCCGCGACGGCTAATCAGGTACCTTA
1 GAAGATATGAAGGAAAGG-TTGAGGCCGCAACGACAAACCCGGTACCTTA
* * * * * ** * * *
24727 GAAGTTGTGACGGGAAAGGTTGAGCCCGTAATAACGAACCCGATACCTCA
1 GAAGATATGA-AGGAAAGGTTGAGGCCGCAACGACAAACCCGGTACCTTA
* * * * * * * *
24777 GAAGATGTGATGGGAAAGATTGAGGCTGCAACGGCGAATCCGGTACC-AA
1 GAAGATATGA-AGGAAAGGTTGAGGCCGCAACGACAAACCCGGTACCTTA
* * * * * *
24826 GAA-ATGTGATAGGAAAGGTTGAGGCCGCAATGGCGAACCCGATACCAT-
1 GAAGATATGA-AGGAAAGGTTGAGGCCGCAACGACAAACCCGGTACCTTA
* * * * * * *
24874 GAAGATTTTAAGGGAAAGGCTGAGGCCGTAATGGA-GAACCCGGTACCAT-
1 GAAGATATGAA-GGAAAGGTTGAGGCCGCAA-CGACAAACCCGGTACCTTA
* * ** * *
24923 GAAGATTTTAAGGGAAAGGTTGAGGCCGCAACGGTAAACCTGGTACTTTA
1 GAAGATATGAA-GGAAAGGTTGAGGCCGCAACGACAAACCCGGTACCTTA
* *
24973 GAAGATATGAAGGGAAAGGTTAAGGCCGCAACGACAAACCTGGTACCTTA
1 GAAGATATGAA-GGAAAGGTTGAGGCCGCAACGACAAACCCGGTACCTTA
* ****
25023 GAAGATATGAAGGAAAGGTTGAGGCCGTAACGACAAGTTTGGTACCTTA
1 GAAGATATGAAGGAAAGGTTGAGGCCGCAACGACAAACCCGGTACCTTA
* * * * *
25072 GAAGATATGAAGGAAAAGTTGAGGCCGCAATGGCGAACCCGATACCTTA
1 GAAGATATGAAGGAAAGGTTGAGGCCGCAACGACAAACCCGGTACCTTA
25121 GAA
1 GAA
25124 AACAAGATGA
Statistics
Matches: 319, Mismatches: 71, Indels: 15
0.79 0.18 0.04
Matches are distributed among these distances:
48 42 0.13
49 152 0.48
50 119 0.37
51 6 0.02
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.19
Consensus pattern (49 bp):
GAAGATATGAAGGAAAGGTTGAGGCCGCAACGACAAACCCGGTACCTTA
Found at i:25109 original size:246 final size:246
Alignment explanation
Indices: 24675--25117 Score: 563
Period size: 246 Copynumber: 1.8 Consensus size: 246
24665 TGAGAAAAAA
* * * * *
24675 ATGAAGATTTTAAGGGAAGGATTGAGGCCGCGACGGCTAATCAGGTACCTTAGAAGTTGTGACGG
1 ATGAAGATTTTAAGGGAAGGATTGAGGCCGCAACGGCTAACCAGGTACCTTAGAAGATATGAAGG
* * * * * * *
24740 GAAAGGTTGAGCCCGTAATAACGAACCCGATACCTCAGAAGATGTGATGGGAAAGATTGAGGCTG
66 GAAAGGTTAAGCCCGCAACAACAAACCCGATACCTCAGAAGATATGATAGGAAAGATTGAGGCCG
* * *
24805 CAACGGCGAATCCGGTACCAAGAAATGTGATAGGAAAGGTTGAGGCCGCAATGGCGAACCCGATA
131 CAACGACGAATCCGGTACCAAGAAATATGATAGGAAAAGTTGAGGCCGCAATGGCGAACCCGATA
24870 CCATGAAGATTTTAAGGGAAAGGCTGAGGCCGTAATGGAGAACCCGGTACC
196 CCATGAAGATTTTAAGGGAAAGGCTGAGGCCGTAATGGAGAACCCGGTACC
* *
24921 ATGAAGATTTTAAGGGAAAGG-TTGAGGCCGCAACGG-TAAACCTGGTACTTTAGAAGATATGAA
1 ATGAAGATTTTAAGGG-AAGGATTGAGGCCGCAACGGCT-AACCAGGTACCTTAGAAGATATGAA
* * * * * *
24984 GGGAAAGGTTAAGGCCGCAACGACAAACCTGGTACCTTAGAAGATATGA-AGGAAAGGTTGAGGC
64 GGGAAAGGTTAAGCCCGCAACAACAAACCCGATACCTCAGAAGATATGATAGGAAAGATTGAGGC
* ** *
25048 CGTAACGAC-AAGTTTGGTACCTTAGAAGATATGA-AGGAAAAGTTGAGGCCGCAATGGCGAACC
129 CGCAACGACGAA-TCCGGTACC-AAGAA-ATATGATAGGAAAAGTTGAGGCCGCAATGGCGAACC
25111 CGATACC
191 CGATACC
25118 TTAGAAAACA
Statistics
Matches: 165, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
244 2 0.01
245 27 0.16
246 127 0.77
247 9 0.05
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.19
Consensus pattern (246 bp):
ATGAAGATTTTAAGGGAAGGATTGAGGCCGCAACGGCTAACCAGGTACCTTAGAAGATATGAAGG
GAAAGGTTAAGCCCGCAACAACAAACCCGATACCTCAGAAGATATGATAGGAAAGATTGAGGCCG
CAACGACGAATCCGGTACCAAGAAATATGATAGGAAAAGTTGAGGCCGCAATGGCGAACCCGATA
CCATGAAGATTTTAAGGGAAAGGCTGAGGCCGTAATGGAGAACCCGGTACC
Found at i:25378 original size:39 final size:39
Alignment explanation
Indices: 25328--25450 Score: 119
Period size: 39 Copynumber: 3.2 Consensus size: 39
25318 TTCCGATGTA
25328 TTACCCCGAGCTTGGGGCAGATCATCATCAGCCAATCTC
1 TTACCCCGAGCTTGGGGCAGATCATCATCAGCCAATCTC
* *
25367 TTACCCTGAGCTTGGGGCAGAT--T--GCAGCCAATTGATCTC
1 TTACCCCGAGCTTGGGGCAGATCATCATCAGCC-A---ATCTC
* * * * *
25406 TTACCCCAAGCTTGGAGCAGATCACCATTAACCAATCTC
1 TTACCCCGAGCTTGGGGCAGATCATCATCAGCCAATCTC
25445 TTACCC
1 TTACCC
25451 TGAGATAAGG
Statistics
Matches: 67, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
35 5 0.07
36 1 0.01
37 1 0.01
39 56 0.84
42 1 0.01
43 3 0.04
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (39 bp):
TTACCCCGAGCTTGGGGCAGATCATCATCAGCCAATCTC
Found at i:25482 original size:78 final size:79
Alignment explanation
Indices: 25319--25491 Score: 179
Period size: 78 Copynumber: 2.2 Consensus size: 79
25309 GAATGAATAT
* * * * * * **
25319 TCCGATGTATTACCCCGAGCTTGGGGCAGATCATCATCAGCCAATCTCTTACCCTGAGCTTGGGG
1 TCCGATCTATTACCCCAAGCTTGGAGCAGATCACCATCAACCAATCTCTTACCCTGAGATAAGGG
* *
25384 CAGATTGCAGCCAA
66 CAGATTACAACCAA
* * *
25398 T-TGATCTCTTACCCCAAGCTTGGAGCAGATCACCATTAACCAATCTCTTACCCTGAGATAAGGG
1 TCCGATCTATTACCCCAAGCTTGGAGCAGATCACCATCAACCAATCTCTTACCCTGAGATAAGGG
* * *
25462 TATATTATAACC-A
66 CAGATTACAACCAA
*
25475 TCCGATCTTTTACCCCA
1 TCCGATCTATTACCCCA
25492 GCCAAGGGGT
Statistics
Matches: 75, Mismatches: 18, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
77 2 0.03
78 72 0.96
79 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (79 bp):
TCCGATCTATTACCCCAAGCTTGGAGCAGATCACCATCAACCAATCTCTTACCCTGAGATAAGGG
CAGATTACAACCAA
Found at i:26111 original size:86 final size:87
Alignment explanation
Indices: 25902--26104 Score: 266
Period size: 86 Copynumber: 2.3 Consensus size: 87
25892 GTTATAAAAT
*
25902 GGTCGTCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCATCTTCACTAGTGAGATACAGAGA
1 GGTCGTCTTCCTGATGAGATACTGAGAAGTGAACCAAATCCATCTTCACTAGTGAGATACAGAGA
* * *
25967 AGTGGATCAAAATAAGTGTTGC
66 AGCGGATCAAAACAAGTGATGC
* * * *
25989 GGTCGTTTTCCTGATGAGATAATGAGAAGTGAACCAAATTCGTCTTC-CT-GATGAGATACAGAG
1 GGTCGTCTTCCTGATGAGATACTGAGAAGTGAACCAAATCCATCTTCACTAG-TGAGATACAGAG
* *
26052 AAGCGGATTAAAACATGTGATGC
65 AAGCGGATCAAAACAAGTGATGC
* * *
26075 GGTCATCTTCGTGAAGAGATACTGAGAAGT
1 GGTCGTCTTCCTGATGAGATACTGAGAAGT
26105 AGACCAACTC
Statistics
Matches: 100, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
85 1 0.01
86 57 0.57
87 42 0.42
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (87 bp):
GGTCGTCTTCCTGATGAGATACTGAGAAGTGAACCAAATCCATCTTCACTAGTGAGATACAGAGA
AGCGGATCAAAACAAGTGATGC
Found at i:26234 original size:296 final size:296
Alignment explanation
Indices: 25700--26236 Score: 815
Period size: 296 Copynumber: 1.8 Consensus size: 296
25690 AATGGTCAGC
* * * *
25700 TTCCTGATAAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATAATATACAGAGAAGCAGATT
1 TTCCTGATAAGATAATGAGAAGTGAACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCAGATT
* ** * * *
25765 GAAGTAAGTGAGGTGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGAAACAAA
66 AAAACAAGTGAGGCGGTCATCTTCCTGAAGAGATACAGAGAAGTAGACCAACTCAATGAAACAAA
* **
25830 GCTCAATGTGAGCGAAACTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTT
131 GCTCAATGTGAGCGAAACTTCGAACCCCAACTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCA
*
25895 ATAAAATGGTCGTCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCATCTTCACTAGTGAGAT
196 ATAAAATGGTCGTCTTCCTAATGAGATACAGAGAAGTGAACCAAATCCATCTTCACTAGTGAGAT
25960 ACAGAGAAGTGGATCAAAATAAGTGTTGCGGTCGTT
261 ACAGAGAAGTGGATCAAAATAAGTGTTGCGGTCGTT
* * *
25996 TTCCTGATGAGATAATGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATT
1 TTCCTGATAAGATAATGAGAAGTGAACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCAGATT
* * * *
26061 AAAACATGTGATGCGGTCATCTTCGTGAAGAGATACTGAGAAGTAGACCAACTCAATGAAACAAA
66 AAAACAAGTGAGGCGGTCATCTTCCTGAAGAGATACAGAGAAGTAGACCAACTCAATGAAACAAA
* * * *
26126 GCTCAATGTGAGCGAAACTTCGAACCCTAGCTTTCTAATGAGATACTGAGAAGTAGGTCGAAGCA
131 GCTCAATGTGAGCGAAACTTCGAACCCCAACTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCA
**
26191 ATAAAATGGTCAG-CTTCCTAATGAGATATTGAGAAGTGAACCAAAT
196 ATAAAATGGTC-GTCTTCCTAATGAGATACAGAGAAGTGAACCAAAT
26237 TTGTCATCTT
Statistics
Matches: 213, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
296 212 1.00
297 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (296 bp):
TTCCTGATAAGATAATGAGAAGTGAACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCAGATT
AAAACAAGTGAGGCGGTCATCTTCCTGAAGAGATACAGAGAAGTAGACCAACTCAATGAAACAAA
GCTCAATGTGAGCGAAACTTCGAACCCCAACTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCA
ATAAAATGGTCGTCTTCCTAATGAGATACAGAGAAGTGAACCAAATCCATCTTCACTAGTGAGAT
ACAGAGAAGTGGATCAAAATAAGTGTTGCGGTCGTT
Found at i:26378 original size:209 final size:209
Alignment explanation
Indices: 25996--26411 Score: 627
Period size: 209 Copynumber: 2.0 Consensus size: 209
25986 TGCGGTCGTT
* * * *
25996 TTCCTGATGAGATAATGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATT
1 TTCCTAATGAGATAATGAGAAGTGAACCAAATTCGTCATCCTGATGAGATACAAAGAAGCGAATT
* * *
26061 AAAACATGTGATGCGGTCATCTTCGTGAAGAGATACTGAGAAGTAGACCAACTCAATGAAACAAA
66 AAAACATGTGATGCGGTCATCTTCCTGAAAAGATACTGAGAAGTAGACCAAATCAATGAAACAAA
* * * * * * *
26126 GCTCAATGTGAGCGAAACTTCGAACCCTAGCTTTCTAATGAGATACTGAGAAGTAGGTCGAAGCA
131 GCTCAATATGAGCGAAACTTCGAACCCCAGCTTCCCAATGAGATACAGAGAAGCAAGTCGAAGCA
26191 ATAAAATGGTCAGC
196 ATAAAATGGTCAGC
* * *
26205 TTCCTAATGAGATATTGAGAAGTGAACCAAATTTGTCATCTTGATGAGATACAAAGAAGCGAATT
1 TTCCTAATGAGATAATGAGAAGTGAACCAAATTCGTCATCCTGATGAGATACAAAGAAGCGAATT
* *
26270 AAAACATGTGATGTGGTCATGTTCCT-AATAAGATACTGAGAAGTAGACCAAATCAATGAAACAA
66 AAAACATGTGATGCGGTCATCTTCCTGAA-AAGATACTGAGAAGTAGACCAAATCAATGAAACAA
* *
26334 AGCTCGATATGAGCGAAACTTCGAACCCCAGCTTCCCGATGAGATACAGAGAAGCAAGTCGAAGC
130 AGCTCAATATGAGCGAAACTTCGAACCCCAGCTTCCCAATGAGATACAGAGAAGCAAGTCGAAGC
26399 AATAAAATGGTCA
195 AATAAAATGGTCA
26412 CCTTTTTGAC
Statistics
Matches: 185, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
208 2 0.01
209 183 0.99
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (209 bp):
TTCCTAATGAGATAATGAGAAGTGAACCAAATTCGTCATCCTGATGAGATACAAAGAAGCGAATT
AAAACATGTGATGCGGTCATCTTCCTGAAAAGATACTGAGAAGTAGACCAAATCAATGAAACAAA
GCTCAATATGAGCGAAACTTCGAACCCCAGCTTCCCAATGAGATACAGAGAAGCAAGTCGAAGCA
ATAAAATGGTCAGC
Found at i:26868 original size:17 final size:16
Alignment explanation
Indices: 26839--26912 Score: 67
Period size: 17 Copynumber: 4.4 Consensus size: 16
26829 AAGCCCAAAT
26839 TTTAAATTTTAAATTTA
1 TTTAAA-TTTAAATTTA
*
26856 TTATAAATTTAAATTAA
1 TT-TAAATTTAAATTTA
* *
26873 TTTCTAGTTTAAATTTA
1 TTT-AAATTTAAATTTA
*
26890 TTTTAAATTTGAATTTA
1 -TTTAAATTTAAATTTA
*
26907 ATTAAA
1 TTTAAA
26913 AAAATGTCTC
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
16 6 0.13
17 33 0.72
18 7 0.15
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (16 bp):
TTTAAATTTAAATTTA
Found at i:26896 original size:11 final size:11
Alignment explanation
Indices: 26844--26899 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
26834 CAAATTTTAA
26844 ATTTTAAATTT
1 ATTTTAAATTT
*
26855 ATTATAAATTT
1 ATTTTAAATTT
** *
26866 AAATTAATTTCT
1 ATTTTAAATT-T
*
26878 AGTTTAAATTT
1 ATTTTAAATTT
26889 ATTTTAAATTT
1 ATTTTAAATTT
26900 GAATTTAATT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
11 27 0.77
12 8 0.23
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:28082 original size:17 final size:18
Alignment explanation
Indices: 28060--28098 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
28050 TATAGGTTTT
*
28060 AAAATGAAATAAAAA-GA
1 AAAATGAAAAAAAAATGA
28077 AAAATGAAAAAAAAATGA
1 AAAATGAAAAAAAAATGA
28095 AAAA
1 AAAA
28099 AGAGGTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (18 bp):
AAAATGAAAAAAAAATGA
Found at i:28090 original size:11 final size:11
Alignment explanation
Indices: 28066--28099 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
28056 TTTTAAAATG
*
28066 AAATAAAAAGAA
1 AAATGAAAA-AA
28078 AAATGAAAAAA
1 AAATGAAAAAA
28089 AAATGAAAAAA
1 AAATGAAAAAA
28100 GAGGTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (11 bp):
AAATGAAAAAA
Found at i:28800 original size:30 final size:28
Alignment explanation
Indices: 28744--29051 Score: 117
Period size: 30 Copynumber: 10.5 Consensus size: 28
28734 TAGAAGGTCT
* *
28744 CTGAACTGTTCAAAAAATCATGTTTTGACC
1 CTGAACT-TTC-AAAAATTATATTTTGACC
28774 TCTGAACTTTCTAAAAATTATATTTTGACCC
1 -CTGAACTTTC-AAAAATTATATTTTGA-CC
** *
28805 CCAAACTTTACAAAAATTATATTTTTACC
1 CTGAACTTT-CAAAAATTATATTTTGACC
* * *
28834 C--CACTTACAAAAATTACCATTTTG-CC
1 CTGAACTTTCAAAAATTA-TATTTTGACC
* * *
28860 CTCATACTTTCCAAAAATCATATTTTTACCC
1 CTGA-ACTTT-CAAAAATTATATTTTGA-CC
* * * *
28891 CTGAACTTCCAAAAATTACCATTTT-TCA
1 CTGAACTTTCAAAAATTA-TATTTTGACC
* * *
28919 CTCGAACTTTCCAGAAATCATATTTTTACCC
1 CT-GAACTTT-CAAAAATTATATTTTGA-CC
* * *
28950 CCGAAC-ATCTAAAAATTACCATTTT-ACC
1 CTGAACTTTC-AAAAATTA-TATTTTGACC
* * * **
28978 CTCGAACTTCCAAAAATCACATTTTTTCC
1 CT-GAACTTTCAAAAATTATATTTTGACC
* *
29007 CTTGAACTTCCAAAAATTTACCATTTT-ACC
1 C-TGAACTTTCAAAAA-TTA-TATTTTGACC
*
29037 CTCGAACTTCCAAAA
1 CT-GAACTTTCAAAA
29052 TTGCATTTTC
Statistics
Matches: 215, Mismatches: 39, Indels: 47
0.71 0.13 0.16
Matches are distributed among these distances:
26 12 0.06
27 9 0.04
28 13 0.06
29 67 0.31
30 91 0.42
31 23 0.11
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (28 bp):
CTGAACTTTCAAAAATTATATTTTGACC
Found at i:28836 original size:29 final size:29
Alignment explanation
Indices: 28778--28950 Score: 124
Period size: 30 Copynumber: 6.0 Consensus size: 29
28768 TTGACCTCTG
* *
28778 AACTTTCTAAAAATTATATTTTGACCCCCA
1 AACTTTCCAAAAATTATATTTTTA-CCCCA
*
28808 AACTTTACAAAAATTATATTTTTACCCC-
1 AACTTTCCAAAAATTATATTTTTACCCCA
* * *
28836 -AC-TTACAAAAATTACCA-TTTTGCCCTCA
1 AACTTTCCAAAAATTA-TATTTTTACCC-CA
* * *
28864 TACTTTCCAAAAATCATATTTTTACCCCTG
1 AACTTTCCAAAAATTATATTTTTACCCC-A
* * *
28894 AAC-TTCCAAAAATTACCATTTTT-CACTCG
1 AACTTTCCAAAAATTA-TATTTTTAC-CCCA
* *
28923 AACTTTCCAGAAATCATATTTTTACCCC
1 AACTTTCCAAAAATTATATTTTTACCCC
28951 CGAACATCTA
Statistics
Matches: 114, Mismatches: 18, Indels: 23
0.74 0.12 0.15
Matches are distributed among these distances:
26 19 0.17
27 4 0.04
29 32 0.28
30 59 0.52
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
AACTTTCCAAAAATTATATTTTTACCCCA
Found at i:28928 original size:59 final size:59
Alignment explanation
Indices: 28746--29126 Score: 329
Period size: 59 Copynumber: 6.5 Consensus size: 59
28736 GAAGGTCTCT
* * * * * * *
28746 GAACTGTTCAAAAAATCATGTTTTGACCTCTGAACTTTCTAAAAATTA-TATTTTGACCCCC
1 GAACT-TTCCAAAAATCATATTTTTACCCCTGAAC-TTCCAAAAATTACCATTTT-ACCCTC
* * * * *
28807 AAACTTTACAAAAATTATATTTTTACCCC---ACTTACAAAAATTACCATTTTGCCCTC
1 GAACTTTCCAAAAATCATATTTTTACCCCTGAACTTCCAAAAATTACCATTTTACCCTC
* *
28863 -ATACTTTCCAAAAATCATATTTTTACCCCTGAACTTCCAAAAATTACCATTTTTCACTC
1 GA-ACTTTCCAAAAATCATATTTTTACCCCTGAACTTCCAAAAATTACCATTTTACCCTC
* * * *
28922 GAACTTTCCAGAAATCATATTTTTACCCCCGAACATCTAAAAATTACCATTTTACCCTC
1 GAACTTTCCAAAAATCATATTTTTACCCCTGAACTTCCAAAAATTACCATTTTACCCTC
* * *
28981 GAAC-TTCCAAAAATCACATTTTTTCCCTTGAACTTCCAAAAATTTACCATTTTACCCTC
1 GAACTTTCCAAAAATCATATTTTTACCCCTGAACTTCCAAAAA-TTACCATTTTACCCTC
* * * *
29040 GAAC-TTCCAAAATTGC--ATTTTCACCCTCT-AACTTTCTAAAAAATTACCGTTTTACCC-C
1 GAACTTTCCAAAAAT-CATATTTTTACCC-CTGAAC-TTC-CAAAAATTACCATTTTACCCTC
*
29098 TAA-TATTCCAAAAAT-ATCATTTTTTACCC
1 GAACT-TTCCAAAAATCAT-A-TTTTTACCC
29127 TAAATTTTAT
Statistics
Matches: 264, Mismatches: 39, Indels: 34
0.78 0.12 0.10
Matches are distributed among these distances:
55 1 0.00
56 39 0.15
57 7 0.03
58 45 0.17
59 134 0.51
60 26 0.10
61 12 0.05
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (59 bp):
GAACTTTCCAAAAATCATATTTTTACCCCTGAACTTCCAAAAATTACCATTTTACCCTC
Found at i:29052 original size:29 final size:29
Alignment explanation
Indices: 28836--29199 Score: 221
Period size: 29 Copynumber: 12.3 Consensus size: 29
28826 TTTTTACCCC
* *
28836 ACTTACAAAAATTACCATTTTGCCCTC-A
1 ACTTCCAAAAATTACCATTTTACCCTCGA
* *
28864 TACTTTCCAAAAATCA-TATTTTTACCC-CTGA
1 -AC-TTCCAAAAATTACCA-TTTTACCCTC-GA
* *
28895 ACTTCCAAAAATTACCATTTTTCACTCGA
1 ACTTCCAAAAATTACCATTTTACCCTCGA
* * * *
28924 ACTTTCCAGAAATCA-TATTTTTACCCCCGA
1 AC-TTCCAAAAATTACCA-TTTTACCCTCGA
* *
28954 ACATCTAAAAATTACCATTTTACCCTCGA
1 ACTTCCAAAAATTACCATTTTACCCTCGA
* * *
28983 ACTTCCAAAAATCA-CATTTTTTCCCTTGA
1 ACTTCCAAAAATTACCA-TTTTACCCTCGA
29012 ACTTCCAAAAATTTACCATTTTACCCTCGA
1 ACTTCCAAAAA-TTACCATTTTACCCTCGA
* *
29042 ACTTCC-AAAATT-GCATTTTCACCCTCTA
1 ACTTCCAAAAATTACCATTTT-ACCCTCGA
* * *
29070 ACTTTCTAAAAAATTACCGTTTTACCC-CTA
1 AC-TTC-CAAAAATTACCATTTTACCCTCGA
* * *
29100 ATATTCCAAAAA-TATCATTTTTTACCCT-AA
1 A-CTTCCAAAAATTACCA--TTTTACCCTCGA
* ** * *
29130 ATTTTATAAAAATTACCCTTTTTCTCCT--A
1 A-CTTCCAAAAATTACCATTTTAC-CCTCGA
*
29159 AGCTTCCAAAAATTACCATTTTACCCCTCAA
1 A-CTTCCAAAAATTACCATTTTA-CCCTCGA
29190 ACTTCCAAAA
1 ACTTCCAAAA
29200 GTCGCATTTT
Statistics
Matches: 259, Mismatches: 50, Indels: 51
0.72 0.14 0.14
Matches are distributed among these distances:
27 6 0.02
28 16 0.06
29 115 0.44
30 99 0.38
31 18 0.07
32 5 0.02
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.35
Consensus pattern (29 bp):
ACTTCCAAAAATTACCATTTTACCCTCGA
Found at i:32506 original size:41 final size:42
Alignment explanation
Indices: 32456--32551 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 42
32446 TTATTTTAAT
* * *
32456 ATAAATATTTTTAATGT-ATTTTCAATTTGATTT-TTGTTTTA
1 ATAATTATTTTTAATATCATTTTCAATTTG-TTTGATGTTTTA
*
32497 ATAATTA-TTTTAATATCATTTTTAATTTGTTTGATGTTTTA
1 ATAATTATTTTTAATATCATTTTCAATTTGTTTGATGTTTTA
*
32538 AT-ATTTTTTTTAAT
1 ATAATTATTTTTAAT
32552 TTTTTTAAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
40 14 0.30
41 33 0.70
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.62
Consensus pattern (42 bp):
ATAATTATTTTTAATATCATTTTCAATTTGTTTGATGTTTTA
Found at i:41145 original size:6 final size:6
Alignment explanation
Indices: 41136--41168 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
41126 CAAATTTATT
*
41136 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
41169 TCTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:41150 original size:18 final size:18
Alignment explanation
Indices: 41127--41176 Score: 84
Period size: 17 Copynumber: 2.8 Consensus size: 18
41117 AAATTGATTC
41127 AAATTTATTTTTAAATTT
1 AAATTTATTTTTAAATTT
41145 AAATTTA-TTTTAAATTT
1 AAATTTATTTTTAAATTT
41162 AAATTTATCTTTTAA
1 AAATTTAT-TTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 17 0.57
18 7 0.23
19 6 0.20
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
AAATTTATTTTTAAATTT
Done.