Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012937.1 Kokia drynarioides strain JFW-HI SEQ_127955, 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: 165420
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:8479 original size:12 final size:12
Alignment explanation
Indices: 8462--8487 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8452 TTAAGGTTTA
8462 GGGGAAAAAATG
1 GGGGAAAAAATG
8474 GGGGAAAAAATG
1 GGGGAAAAAATG
8486 GG
1 GG
8488 TTTTAGCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.46, T:0.08
Consensus pattern (12 bp):
GGGGAAAAAATG
Found at i:20732 original size:16 final size:16
Alignment explanation
Indices: 20711--20742 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20701 GTTGTGGATC
20711 ACATTTTACCTTTATT
1 ACATTTTACCTTTATT
*
20727 ACATTTTATCTTTATT
1 ACATTTTACCTTTATT
20743 TTCACATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
ACATTTTACCTTTATT
Found at i:24134 original size:37 final size:37
Alignment explanation
Indices: 24084--24161 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
24074 TTACTATTAA
*
24084 TGTCGCCACATGAGTACTTCTAGATTG-AGCCCAAAAT
1 TGTCGCCACATGAGCACTTCTAGATTGCA-CCCAAAAT
*
24121 TGTCGCCGCATGAGCACTTCTAGATTGCACCCAAAAT
1 TGTCGCCACATGAGCACTTCTAGATTGCACCCAAAAT
24158 TGTC
1 TGTC
24162 ACTACAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (37 bp):
TGTCGCCACATGAGCACTTCTAGATTGCACCCAAAAT
Found at i:25145 original size:16 final size:16
Alignment explanation
Indices: 25124--25154 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25114 TTGTGGATCC
25124 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
25140 CATTTTATCTTTATT
1 CATTTTACCTTTATT
25155 TTTACATTAT
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:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:33283 original size:47 final size:47
Alignment explanation
Indices: 33216--33320 Score: 156
Period size: 47 Copynumber: 2.2 Consensus size: 47
33206 TAAACTAATA
* * * *
33216 AGAGTTTGACTCAAACAAATAAATAGAGTTTAATTGAAACAAATAAAT
1 AGAGTTT-AATCAAAAAAATAAACAGAGTTTAATTAAAACAAATAAAT
*
33264 AGAGTTTAATCAAAAAAATAAACAGAGTTTAATTAAAACAATTAAAT
1 AGAGTTTAATCAAAAAAATAAACAGAGTTTAATTAAAACAAATAAAT
33311 AGAGTTTAAT
1 AGAGTTTAAT
33321 TGAAAGATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
47 45 0.87
48 7 0.13
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.29
Consensus pattern (47 bp):
AGAGTTTAATCAAAAAAATAAACAGAGTTTAATTAAAACAAATAAAT
Found at i:33330 original size:23 final size:24
Alignment explanation
Indices: 33228--33321 Score: 145
Period size: 24 Copynumber: 4.0 Consensus size: 24
33218 AGTTTGACTC
*
33228 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAATAGAGTTTAATTA
*
33252 AAACAAATAAATAGAGTTTAATCA
1 AAACAAATAAATAGAGTTTAATTA
*
33276 AAA-AAATAAACAGAGTTTAATTA
1 AAACAAATAAATAGAGTTTAATTA
*
33299 AAACAATTAAATAGAGTTTAATT
1 AAACAAATAAATAGAGTTTAATT
33322 GAAAGATTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
23 21 0.33
24 42 0.67
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29
Consensus pattern (24 bp):
AAACAAATAAATAGAGTTTAATTA
Found at i:35279 original size:24 final size:24
Alignment explanation
Indices: 35251--35333 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 24
35241 TAGACTAATA
* *
35251 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAC
*
35275 AGAGTTTAATTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* * * *
35299 AGAGTTTAATTGAAGCAATTAAAC
1 AGAGTTTAACTCAAACAAATAAAC
35323 AGAGTTTAACT
1 AGAGTTTAACT
35334 TAAAGATTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:36466 original size:18 final size:17
Alignment explanation
Indices: 36429--36467 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
36419 ATTTTTAATA
*
36429 TATATTTTAAATGATTT
1 TATATTTTAAATGATGT
*
36446 TATATTATTAAATTATGT
1 TATATT-TTAAATGATGT
36464 TATA
1 TATA
36468 GTCTTTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
TATATTTTAAATGATGT
Found at i:41065 original size:17 final size:17
Alignment explanation
Indices: 41041--41117 Score: 111
Period size: 17 Copynumber: 4.6 Consensus size: 17
41031 GCCCAACAAG
41041 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
*
41058 AATTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* *
41075 GTTTAAATTTA-CTTAA
1 ATTTAAATTTATTTTAA
*
41091 ATTTAAATTTATTATAA
1 ATTTAAATTTATTTTAA
41108 ATTTAAATTT
1 ATTTAAATTT
41118 TAAATCTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
16 14 0.27
17 38 0.73
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:41079 original size:6 final size:6
Alignment explanation
Indices: 41041--41122 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
41031 GCCCAACAAG
* * * *
41041 ATTTAA ATTT-A TTTTAA AATTAA ATTT-A TTTTAA GTTTAA ATTT--
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
41085 ACTTAA ATTTAA ATTT-- ATTATAA ATTTAA ATTTTAA AT
1 ATTTAA ATTTAA ATTTAA ATT-TAA ATTTAA A-TTTAA AT
41123 CTTTTTAAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
4 6 0.10
5 9 0.15
6 35 0.59
7 9 0.15
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:41132 original size:23 final size:23
Alignment explanation
Indices: 41087--41132 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
41077 TTAAATTTAC
*
41087 TTAAATTTAAATTTATTATAAAT
1 TTAAATTTAAATCTATTATAAAT
*
41110 TTAAATTTTAAATCT-TTTTAAAT
1 TTAAA-TTTAAATCTATTATAAAT
41133 CAAGTTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAAATTTAAATCTATTATAAAT
Found at i:43034 original size:29 final size:29
Alignment explanation
Indices: 42954--43184 Score: 144
Period size: 29 Copynumber: 7.9 Consensus size: 29
42944 GAGGTCCCTT
* * * **
42954 AACTGTCCAAAATTTCAATTTTTACCCCCG
1 AACT-TCCAAAAATTCCATTTTAACCCCAA
** **
42984 AACTTCCAAAAATTATATTTTTAACCTTAA
1 AACTTCCAAAAATTCCA-TTTTAACCCCAA
* * *
43014 AACTTCTAAAAAATCCATTTTTACCCCAA
1 AACTTCCAAAAATTCCATTTTAACCCCAA
* * *
43043 AACTTCCATAAATTCCATCTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTAACCCCAA
* * * *
43072 AATTTCAAAAAATCCCAATTTT-ACCCTC-G
1 AACTTCCAAAAATTCC-ATTTTAACCC-CAA
* * *
43101 AACTTCTAAAAATTCCATGTTAACCTCAA
1 AACTTCCAAAAATTCCATTTTAACCCCAA
* * *
43130 AATTTCCAAAAATTCCATTTTTAGCCCC-G
1 AACTTCCAAAAATTCCA-TTTTAACCCCAA
* *
43159 AACCTCCGAAAATTCCATTTTTAACC
1 AACTTCCAAAAATTCCA-TTTTAACC
43185 TCGAAACTCT
Statistics
Matches: 153, Mismatches: 42, Indels: 13
0.74 0.20 0.06
Matches are distributed among these distances:
28 5 0.03
29 112 0.73
30 36 0.24
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTAACCCCAA
Found at i:43105 original size:58 final size:55
Alignment explanation
Indices: 42971--43176 Score: 178
Period size: 58 Copynumber: 3.5 Consensus size: 55
42961 CAAAATTTCA
** * ** *
42971 ATTTTTACCCCCGAACTTCCAAAAATTATATTTTTAACCTTAAAACTTCTAAAAAATCC
1 ATTTTTA-CCCCGAACTTCC-AAAATTCCA-TCTTAACCCCAAAATTTC-AAAAAATCC
* *
43030 ATTTTTACCCCAAAACTTCCATAAATTCCATCTTGACCCCAAAATTTCAAAAAATCCC
1 ATTTTTACCCC-GAACTTCCA-AAATTCCATCTTAACCCCAAAATTTCAAAAAAT-CC
* * * * *
43088 AATTTTACCCTCGAACTTCTAAAAATTCCATGTTAACCTCAAAATTTCCAAAAATTCC
1 ATTTTTACCC-CGAACTTC-CAAAATTCCATCTTAACCCCAAAATTT-CAAAAAATCC
*
43146 ATTTTTAGCCCCGAACCTCCGAAAATTCCAT
1 ATTTTTA-CCCCGAACTTCC-AAAATTCCAT
43177 TTTTAACCTC
Statistics
Matches: 121, Mismatches: 18, Indels: 17
0.78 0.12 0.11
Matches are distributed among these distances:
57 7 0.06
58 82 0.68
59 32 0.26
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (55 bp):
ATTTTTACCCCGAACTTCCAAAATTCCATCTTAACCCCAAAATTTCAAAAAATCC
Found at i:43189 original size:29 final size:29
Alignment explanation
Indices: 42954--43257 Score: 138
Period size: 29 Copynumber: 10.4 Consensus size: 29
42944 GAGGTCCCTT
* * * *
42954 AACTGTCCAAAATTTCAATTTTTACCCCCG
1 AACT-TCCAAAAATTCCATTTTTAACCTCG
** **
42984 AACTTCCAAAAATTATATTTTTAACCTTAA
1 AACTTCCAAAAATTCCATTTTTAACC-TCG
* * * *
43014 AACTTCTAAAAAATCCATTTTT-ACCCCAA
1 AACTTCCAAAAATTCCATTTTTAACCTC-G
* * * * *
43043 AACTTCCATAAATTCCA-TCTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTTAACCTC-G
* * * * *
43072 AATTTCAAAAAATCCCAATTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTAACCTCG
* * *
43101 AACTTCTAAAAATTCCA-TGTTAACCTCAA
1 AACTTCCAAAAATTCCATTTTTAACCTC-G
* * *
43130 AATTTCCAAAAATTCCATTTTTAGCCCCG
1 AACTTCCAAAAATTCCATTTTTAACCTCG
* *
43159 AACCTCCGAAAATTCCATTTTTAACCTCG
1 AACTTCCAAAAATTCCATTTTTAACCTCG
* *
43188 AAAC-TCTC-AAAATTACC-CTTTT-ACCCCG
1 -AACTTC-CAAAAATT-CCATTTTTAACCTCG
* * *
43216 AA-TGTCTAAGAATTCCATTTTTAACCTCT
1 AACT-TCCAAAAATTCCATTTTTAACCTCG
43245 AATCTTTCCAAAA
1 AA-C-TTCCAAAA
43258 TTACAATTTT
Statistics
Matches: 205, Mismatches: 52, Indels: 33
0.71 0.18 0.11
Matches are distributed among these distances:
27 4 0.02
28 27 0.13
29 127 0.62
30 41 0.20
31 5 0.02
32 1 0.00
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTAACCTCG
Found at i:43200 original size:87 final size:87
Alignment explanation
Indices: 42954--43201 Score: 239
Period size: 87 Copynumber: 2.8 Consensus size: 87
42944 GAGGTCCCTT
* * ** **
42954 AACTGTCCAAAATTTCAATTTTTACCCCCGAACTTCCAAAAATTATATTTTTAACCTTAAAACTT
1 AACT-TCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATTCCATTTTTAACCTCGAAACTT
* * *
43019 CTAAAAAATCCATTTTTACCCCAA
64 CTAAAAATTCCATGTTAACCCCAA
* * * * * * * * *
43043 AACTTCCATAAATTCCATCTTGACCCCAAAATTTCAAAAAATCCCAATTTTACCCTCG-AACTTC
1 AACTTCCAAAAATTCCATTTTTACCCC-GAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTC
*
43107 TAAAAATTCCATGTTAACCTCAA
65 TAAAAATTCCATGTTAACCCCAA
* * *
43130 AATTTCCAAAAATTCCATTTTTAGCCCCGAACCTCCGAAAATTCCATTTTTAACCTCGAAAC-TC
1 AACTTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTC
*
43194 TCAAAATT
65 TAAAAATT
43202 ACCCTTTTAC
Statistics
Matches: 124, Mismatches: 32, Indels: 8
0.76 0.20 0.05
Matches are distributed among these distances:
87 79 0.64
88 41 0.33
89 4 0.03
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (87 bp):
AACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTCT
AAAAATTCCATGTTAACCCCAA
Found at i:53558 original size:205 final size:201
Alignment explanation
Indices: 53201--53575 Score: 543
Period size: 205 Copynumber: 1.8 Consensus size: 201
53191 GGTTATTTCC
*
53201 TGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGATTTGAACAAATCTTCGAACCCCAGCT
1 TGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGATGTGAACAAATCTTCGAACCCCAGCT
* * * * * *
53266 TCCTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAAATGTTAGCTTTCTGATGAGATACTGAG
66 TCCTGACGAGACACTAAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATAAAATACAGAG
* **** * *
53331 AAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGAGTTGAAACAAATGGCGCAGTCA
131 AAGTGAACCAAAACCATCTTCCTGATGAAACACAGAGAAGCGAGTTGAAACAAATGGCGCAGTCA
53396 TCTTCT
196 TCTTCT
* *
53402 TGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTTGAACCCC
1 TGATGAGATACTGAGAAGAAGACCAAATCAAACCCA----CGATGTGAACAAATCTTCGAACCCC
* *
53467 AGCTTCTTGACGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATAAAATAC
62 AGCTTCCTGACGAGACACTAAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATAAAATAC
*
53532 AGGGAAGTGAACCAAAACCATCTTCCTGATGAAACACAGAGAAG
127 AGAGAAGTGAACCAAAACCATCTTCCTGATGAAACACAGAGAAG
53576 TGGCTCAAAA
Statistics
Matches: 151, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
201 36 0.24
205 115 0.76
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (201 bp):
TGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGATGTGAACAAATCTTCGAACCCCAGCT
TCCTGACGAGACACTAAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATAAAATACAGAG
AAGTGAACCAAAACCATCTTCCTGATGAAACACAGAGAAGCGAGTTGAAACAAATGGCGCAGTCA
TCTTCT
Found at i:53613 original size:205 final size:201
Alignment explanation
Indices: 53197--53637 Score: 542
Period size: 205 Copynumber: 2.2 Consensus size: 201
53187 ACGCGGTTAT
*
53197 TTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGATTTGAACAAATCTTCGAACCCC
1 TTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGATGTGAACAAATCTTCGAACCCC
* * * * *
53262 AGCTTCCTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAAATGTTAGCTTTCTGATGAGATAC
66 AGCTTCCTGACGAGACACTAAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATAAAATAC
* * **** * * ** * *
53327 TGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGAGTTGAAACAAATGGCGCA
131 AGAGAAGTGAACCAAAACCATCTTCCTGATGAAACACAGAGAAGCGAGTCAAAACAAATGACACA
53392 GTCATC
196 GTCATC
* * *
53398 TTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTTGAA
1 TTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCA----CGATGTGAACAAATCTTCGAA
* *
53463 CCCCAGCTTCTTGACGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATAAA
62 CCCCAGCTTCCTGACGAGACACTAAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATAAA
* * *
53528 ATACAGGGAAGTGAACCAAAACCATCTTCCTGATGAAACACAGAGAAGTG-GCTCAAAACAAGTG
127 ATACAGAGAAGTGAACCAAAACCATCTTCCTGATGAAACACAGAGAAGCGAG-TCAAAACAAATG
* ** *
53592 ATATGGTCGTC
191 ACACAGTCATC
* *
53603 TTCCTGATGAGATACTGAGAAGAAGGCCAAGTCAA
1 TTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
53638 TGAAATCAGA
Statistics
Matches: 202, Mismatches: 33, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
201 39 0.19
204 1 0.00
205 162 0.80
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.21
Consensus pattern (201 bp):
TTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGATGTGAACAAATCTTCGAACCCC
AGCTTCCTGACGAGACACTAAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATAAAATAC
AGAGAAGTGAACCAAAACCATCTTCCTGATGAAACACAGAGAAGCGAGTCAAAACAAATGACACA
GTCATC
Found at i:53974 original size:6 final size:6
Alignment explanation
Indices: 53953--54017 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
53943 ACCCAACAAG
* * *
53953 ATTTAA ATTT-A TTTTAA GTTTAA ATTT-- ACTTAA ATTTAA ATTT--
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
53996 ATTATAA ATTTAAA ATTTAA AT
1 ATT-TAA ATTT-AA ATTTAA AT
54018 CTTTTTAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
4 6 0.13
5 5 0.11
6 27 0.57
7 9 0.19
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:53976 original size:17 final size:17
Alignment explanation
Indices: 53953--54014 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
53943 ACCCAACAAG
53953 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* *
53970 GTTTAAATTTA-CTTAA
1 ATTTAAATTTATTTTAA
*
53986 ATTTAAATTTATTATAA
1 ATTTAAATTTATTTTAA
54003 ATTTAAAATTTA
1 ATTT-AAATTTA
54015 AATCTTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
16 14 0.37
17 17 0.45
18 7 0.18
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:55892 original size:30 final size:29
Alignment explanation
Indices: 55835--56089 Score: 250
Period size: 30 Copynumber: 8.7 Consensus size: 29
55825 AAGGTCCCTT
* *
55835 AACTGTCCAAAATTTCCATTTTTACCCTCG
1 AACT-TCCAAAAATTCCATTTTTACCCTCA
** *
55865 AACTTCCAAAAATTATATTTTTGACCCTAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTCA
* *
55895 AACTTCCAAAAATTACATTTTTACCCCCA
1 AACTTCCAAAAATTCCATTTTTACCCTCA
* *
55924 AACTTCCAAAAATTCCATTTTTAACCATAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTCA
*
55954 AACTTCCAAAAATTCTATTTTTGA-CCTCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTC-A
* * * *
55984 AACTTCTAAAAATTCCATTTCTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCTCA
*
56013 AACTTCCAAAAATTCCATTTTGA--CTACAA
1 AACTTCCAAAAATTCCATTTTTACCCT-C-A
* *
56042 AATTTCC-AAAATTCCA-TTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCA
*
56069 AACCTCCAAAAATTCCATTTT
1 AACTTCCAAAAATTCCATTTT
56090 CAACGTCGAA
Statistics
Matches: 184, Mismatches: 31, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
27 10 0.05
28 20 0.11
29 75 0.41
30 79 0.43
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCA
Found at i:55932 original size:59 final size:58
Alignment explanation
Indices: 55835--56089 Score: 253
Period size: 59 Copynumber: 4.4 Consensus size: 58
55825 AAGGTCCCTT
* * * **
55835 AACTGTCCAAAATTTCCATTTTTACCCTCGAACTTCCAAAAATTATATTTTTGACCCTAA
1 AACT-TCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTT-ACCCTAA
* *
55895 AACTTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCATAA
1 AACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTT-ACCCTAA
* * * * * ***
55954 AACTTCCAAAAATTCTATTTTTGACCTCAAAACTTCTAAAAATTCCATTTCTACCCCCG
1 AACTTCCAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATTCCATTTTTACCCTAA
* ** * * **
56013 AACTTCCAAAAATTCCATTTTGACTACAAAATTTCC-AAAATTCCA-TTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTACCCTAA
*
56069 AACCTCCAAAAATTCCATTTT
1 AACTTCCAAAAATTCCATTTT
56090 CAACGTCGAA
Statistics
Matches: 167, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
56 29 0.17
57 9 0.05
58 10 0.06
59 90 0.54
60 29 0.17
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (58 bp):
AACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTACCCTAA
Found at i:55995 original size:89 final size:88
Alignment explanation
Indices: 55835--56052 Score: 285
Period size: 89 Copynumber: 2.5 Consensus size: 88
55825 AAGGTCCCTT
* * **
55835 AACTGTCCAAAATTTCCATTTTTACCCTCGAACTTCCAAAAATTATATTTTTGACCCTAAAACTT
1 AACT-TCCAAAAATTCCATTTTTACCATAAAACTTCCAAAAATTATATTTTTGACCCTAAAACTT
*
55900 CCAAAAATTACATTTTTACCCCCA
65 CCAAAAATTACATTTCTACCCCCA
*
55924 AACTTCCAAAAATTCCATTTTTAACCATAAAACTTCCAAAAATTCTATTTTTGA-CCTCAAAACT
1 AACTTCCAAAAATTCCATTTTT-ACCATAAAACTTCCAAAAATTATATTTTTGACCCT-AAAACT
* * *
55988 TCTAAAAATTCCATTTCTACCCCCG
64 TCCAAAAATTACATTTCTACCCCCA
* * * *
56013 AACTTCCAAAAATTCCATTTTGACTACAAAATTTCCAAAA
1 AACTTCCAAAAATTCCATTTTTACCATAAAACTTCCAAAA
56053 TTCCATTTTA
Statistics
Matches: 114, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
88 35 0.31
89 79 0.69
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (88 bp):
AACTTCCAAAAATTCCATTTTTACCATAAAACTTCCAAAAATTATATTTTTGACCCTAAAACTTC
CAAAAATTACATTTCTACCCCCA
Found at i:56110 original size:57 final size:54
Alignment explanation
Indices: 55958--56122 Score: 168
Period size: 57 Copynumber: 2.9 Consensus size: 54
55948 CCATAAAACT
* * *
55958 TCCAAAAATTCTATTTTTGACCTCAAAACTTCTAAAAATTCCATTTCTACCCCCGAACT
1 TCCAAAAATTCCA-TTTTGA-CTC-AAACTT-TCAAAATTCCATTT-TACCCCCGAACC
* *
56017 TCCAAAAATTCCATTTTGACTACAAAATTTCCAAAATTCCATTTTACCCTCGAACC
1 TCCAAAAATTCCATTTTGACT-CAAACTTT-CAAAATTCCATTTTACCCCCGAACC
* *
56073 TCCAAAAATTCCATTTTCAACGTCGAAACTTTCAAAATTACCCTTTTACC
1 TCCAAAAATTCCATTTT-GAC-TC-AAACTTTCAAAATT-CCATTTTACC
56123 TTGAATGTCT
Statistics
Matches: 92, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
56 28 0.30
57 29 0.32
58 23 0.25
59 12 0.13
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (54 bp):
TCCAAAAATTCCATTTTGACTCAAACTTTCAAAATTCCATTTTACCCCCGAACC
Found at i:56513 original size:96 final size:96
Alignment explanation
Indices: 56412--56593 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 96
56402 AAAACTTTTA
*
56412 AATCGAGGCAATATTAT-TTTAT-TTCAAGTT-TAAAAAATTTACGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAATATT-TCCTTATCTTCAA-TTCT-AAAAATTTACGCCTTAACTTACTAGGTGCA
** *
56474 ATTTTTCTTCAAATCAAAATAATCGAATACCCTT
63 ACCTTTCCTCAAATCAAAATAATCGAATACCCTT
* * * *
56508 AATCGAGGCAATGTTTCCTTATCTTCGATTCTGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
1 AATCGAGGCAATATTTCCTTATCTTCAATTCTAAAAATTTACGCCTTAACTTACTAGGTGCAACC
*
56573 TTTCCTCAAATCAAGATAATC
66 TTTCCTCAAATCAAAATAATC
56594 AACATTCTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
95 1 0.01
96 68 0.92
97 5 0.07
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (96 bp):
AATCGAGGCAATATTTCCTTATCTTCAATTCTAAAAATTTACGCCTTAACTTACTAGGTGCAACC
TTTCCTCAAATCAAAATAATCGAATACCCTT
Found at i:63402 original size:2 final size:2
Alignment explanation
Indices: 63397--63422 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63387 CTAAAAGATT
63397 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
63423 CACACACAAT
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):
TA
Found at i:65113 original size:68 final size:68
Alignment explanation
Indices: 65004--65135 Score: 230
Period size: 68 Copynumber: 1.9 Consensus size: 68
64994 ATACAATCCA
65004 CCATCTAATTCAACTTACCATTCTGTCTATTTTCTATACATTACATATCAAAGTAACATTTCAAG
1 CCATCTAATTCAACTTACCATTCTGTCTATTTTCTATACATTACATATCAAAGTAACATTTCAAG
65069 CTT
66 CTT
* *
65072 CCATCTAATTTAACTTACCATT-TCGTCTATTTTCTATACATTACATATCGAAGTAACATTTCAA
1 CCATCTAATTCAACTTACCATTCT-GTCTATTTTCTATACATTACATATCAAAGTAACATTTCAA
65136 CCTTAGGATC
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
67 1 0.02
68 60 0.98
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.40
Consensus pattern (68 bp):
CCATCTAATTCAACTTACCATTCTGTCTATTTTCTATACATTACATATCAAAGTAACATTTCAAG
CTT
Found at i:69966 original size:9 final size:9
Alignment explanation
Indices: 69952--69978 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
69942 GCAACCAGAT
69952 TTTTTTTTA
1 TTTTTTTTA
69961 TTTTTTTTA
1 TTTTTTTTA
69970 TTTTTTTTA
1 TTTTTTTTA
69979 CTTTCATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:70048 original size:5 final size:5
Alignment explanation
Indices: 70017--70071 Score: 56
Period size: 5 Copynumber: 9.8 Consensus size: 5
70007 ATTTTGTATA
70017 TTTAT TTTCAT TTTCAT TTCTATT TTTAT TTTAT TTTAT ATTTAAT TTTAT
1 TTTAT TTT-AT TTT-AT TT-TA-T TTTAT TTTAT TTTAT -TTT-AT TTTAT
70068 TTTA
1 TTTA
70072 ATTATGCACT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
5 20 0.44
6 19 0.42
7 6 0.13
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:71038 original size:12 final size:13
Alignment explanation
Indices: 71023--71052 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
71013 AAAAGAACAG
71023 AAAAATTGA-AAA
1 AAAAATTGAGAAA
71035 AAAAATTGAGAAA
1 AAAAATTGAGAAA
71048 AAAAA
1 AAAAA
71053 GAAGACAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (13 bp):
AAAAATTGAGAAA
Found at i:71640 original size:13 final size:13
Alignment explanation
Indices: 71622--71652 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
71612 TTGAATGTGG
71622 GTTGAAAATTTTT
1 GTTGAAAATTTTT
71635 GTTGAAAATTTTT
1 GTTGAAAATTTTT
*
71648 CTTGA
1 GTTGA
71653 GGACAAGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (13 bp):
GTTGAAAATTTTT
Found at i:83386 original size:17 final size:17
Alignment explanation
Indices: 83364--83401 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
83354 TGGTACAAAT
83364 TTTTTAGTT-TCAATGCA
1 TTTTTA-TTATCAATGCA
*
83381 TTTTTATTATCATTGCA
1 TTTTTATTATCAATGCA
83398 TTTT
1 TTTT
83402 ATTTTGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.61
Consensus pattern (17 bp):
TTTTTATTATCAATGCA
Found at i:84010 original size:2 final size:2
Alignment explanation
Indices: 84005--84031 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
83995 TAAAAAAAAA
84005 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
84032 ATAAATGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:86512 original size:18 final size:19
Alignment explanation
Indices: 86489--86547 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 19
86479 TTATCAAGCC
86489 TTTTAT-TTTTAATATATA
1 TTTTATATTTTAATATATA
86507 TTTTATATTATTAA-AT-TA
1 TTTTATATT-TTAATATATA
* *
86525 TGTTATCGTCTTTAATATATA
1 TTTTAT-AT-TTTAATATATA
86546 TT
1 TT
86548 CTTAGCCTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
18 13 0.41
19 9 0.28
20 7 0.22
21 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTATATTTTAATATATA
Found at i:103539 original size:12 final size:12
Alignment explanation
Indices: 103524--103553 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
103514 GTGTACCAAG
*
103524 CCGTGTGGTAGA
1 CCGTGTGGCAGA
103536 CCGTGTGGCAGA
1 CCGTGTGGCAGA
103548 CCGTGT
1 CCGTGT
103554 AACTCACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGGCAGA
Found at i:112953 original size:83 final size:83
Alignment explanation
Indices: 112855--113009 Score: 292
Period size: 83 Copynumber: 1.9 Consensus size: 83
112845 ATAATATGTT
*
112855 ATTTTTTCTTTTAATATATTATGTAATTTATATTAAGTGAGAAAGAAATAAAATGCATAAATATT
1 ATTTTTACTTTTAATATATTATGTAATTTATATTAAGTGAGAAAGAAATAAAATGCATAAATATT
112920 AAAATATTGAATTTACTC
66 AAAATATTGAATTTACTC
*
112938 ATTTTTACTTTTAATATATTATGTAATTTATGTTAAGTGAGAAAGAAATAAAATGCATAAATATT
1 ATTTTTACTTTTAATATATTATGTAATTTATATTAAGTGAGAAAGAAATAAAATGCATAAATATT
113003 AAAATAT
66 AAAATAT
113010 AAAGAAATAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 70 1.00
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (83 bp):
ATTTTTACTTTTAATATATTATGTAATTTATATTAAGTGAGAAAGAAATAAAATGCATAAATATT
AAAATATTGAATTTACTC
Found at i:113007 original size:16 final size:16
Alignment explanation
Indices: 112986--113038 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
112976 GAGAAAGAAA
112986 TAAAATGCATAAATAT
1 TAAAATGCATAAATAT
* *
113002 TAAAAT--ATAAAGAAA
1 TAAAATGCATAAA-TAT
113017 TAAAATGCATAAATAT
1 TAAAATGCATAAATAT
113033 TAAAAT
1 TAAAAT
113039 ATTGAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 13 0.43
17 5 0.17
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (16 bp):
TAAAATGCATAAATAT
Found at i:113017 original size:31 final size:31
Alignment explanation
Indices: 112979--113040 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
112969 GTTAAGTGAG
112979 AAAGAAATAAAATGCATAAATATTAAAATAT
1 AAAGAAATAAAATGCATAAATATTAAAATAT
113010 AAAGAAATAAAATGCATAAATATTAAAATAT
1 AAAGAAATAAAATGCATAAATATTAAAATAT
113041 TGAATTTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (31 bp):
AAAGAAATAAAATGCATAAATATTAAAATAT
Found at i:116931 original size:14 final size:14
Alignment explanation
Indices: 116912--116940 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
116902 ATTTTTGTCA
116912 ATTGATTCCTTAGG
1 ATTGATTCCTTAGG
116926 ATTGATTCCTTAGG
1 ATTGATTCCTTAGG
116940 A
1 A
116941 GTTTATCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (14 bp):
ATTGATTCCTTAGG
Found at i:132760 original size:20 final size:21
Alignment explanation
Indices: 132735--132785 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
132725 TGGAAAATAA
*
132735 TTAATTAACGTCTTA-AA-ATT
1 TTAATTAAAG-CTTATAATATT
132755 TTAATTATAAGCTTATAATATT
1 TTAATTA-AAGCTTATAATATT
132777 TTAATTAAA
1 TTAATTAAA
132786 TAAGTTAGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.41
21 6 0.22
22 10 0.37
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (21 bp):
TTAATTAAAGCTTATAATATT
Found at i:133509 original size:58 final size:56
Alignment explanation
Indices: 133406--133514 Score: 139
Period size: 58 Copynumber: 1.9 Consensus size: 56
133396 GTAGTTTGAA
* * **
133406 GGTAATGGGTTGAATTATAAGTAAAATAAAAATATTGTTAATGTTGAGAAATTAAAT
1 GGTAATGGGTTAAATTAGAAGTAAAATAAAAATAGGGTTAATGTTGA-AAATTAAAT
*
133463 GGTAATAGGGTTAAATTAGAAGT-AAATAAAAATAAGGGTTAGTGTTGAAAAT
1 GGTAAT-GGGTTAAATTAGAAGTAAAATAAAAAT-AGGGTTAATGTTGAAAAT
133515 GTAATTAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
57 20 0.44
58 25 0.56
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (56 bp):
GGTAATGGGTTAAATTAGAAGTAAAATAAAAATAGGGTTAATGTTGAAAATTAAAT
Found at i:134485 original size:80 final size:80
Alignment explanation
Indices: 134346--134494 Score: 181
Period size: 80 Copynumber: 1.9 Consensus size: 80
134336 CAAACTGTTG
* * * * * ** * *
134346 GTTAATCCAACTAGAGCTGGGCTCATTTATTGCGGTTTATCCGCTAGGCATTGGTTGCCATGAAT
1 GTTAATCCAACTAGAGCGGGGCCCATTTATCGCGATTTATCCGCTAGGAACCGGGTGCCAAGAAT
134411 TGACGGATTTCATTT
66 TGACGGATTTCATTT
* ** *
134426 GTTAATCCAACTAGGGCGGGGCCCATTTATCGTTATTTATTCGCTAGGAACCGGGTGCCAAGAAT
1 GTTAATCCAACTAGAGCGGGGCCCATTTATCGCGATTTATCCGCTAGGAACCGGGTGCCAAGAAT
134491 TGAC
66 TGAC
134495 AGAAATGGTT
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
80 56 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (80 bp):
GTTAATCCAACTAGAGCGGGGCCCATTTATCGCGATTTATCCGCTAGGAACCGGGTGCCAAGAAT
TGACGGATTTCATTT
Found at i:136738 original size:21 final size:21
Alignment explanation
Indices: 136698--136785 Score: 104
Period size: 21 Copynumber: 4.2 Consensus size: 21
136688 ACATTATCGA
* **
136698 GGCACTGTAGTGCTTTTCAGG
1 GGCACCGTAGTGCAATTCAGG
* * *
136719 GGCATCTTAGTGCAAGTCAGG
1 GGCACCGTAGTGCAATTCAGG
*
136740 GGCACCGTAGTGCAATTCAAG
1 GGCACCGTAGTGCAATTCAGG
*
136761 GGCACCGTAGTGTAATTCAGG
1 GGCACCGTAGTGCAATTCAGG
136782 GGCA
1 GGCA
136786 TAACGTAATT
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (21 bp):
GGCACCGTAGTGCAATTCAGG
Found at i:137812 original size:23 final size:23
Alignment explanation
Indices: 137757--137812 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
137747 TGAGAGTGGC
*
137757 ATCCAGTCAGCAGCTTCTAGAAG
1 ATCCAGTCAGCAGCTTCCAGAAG
*
137780 ATCCAATCAGCAGCTTCCAGAAG
1 ATCCAGTCAGCAGCTTCCAGAAG
* *
137803 GTCTAGTCAG
1 ATCCAGTCAG
137813 TAAGGATGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.21
Consensus pattern (23 bp):
ATCCAGTCAGCAGCTTCCAGAAG
Found at i:142828 original size:72 final size:72
Alignment explanation
Indices: 142711--142850 Score: 235
Period size: 72 Copynumber: 1.9 Consensus size: 72
142701 ACATAGAAGG
* * * **
142711 CATTCTCTACATGTTGTGGATAGTCTTCATAACTATGGTTGTCACCACAAATCTTGCAACAAAAT
1 CATTCTCTACATATTGTGGACAATCTTCATAACTATGGTTGTCACCACAAATCTCACAACAAAAT
142776 GTAAGAC
66 GTAAGAC
142783 CATTCTCTACATATTGTGGACAATCTTCATAACTATGGTTGTCACCACAAATCTCACAACAAAAT
1 CATTCTCTACATATTGTGGACAATCTTCATAACTATGGTTGTCACCACAAATCTCACAACAAAAT
142848 GTA
66 GTA
142851 GGCACATCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (72 bp):
CATTCTCTACATATTGTGGACAATCTTCATAACTATGGTTGTCACCACAAATCTCACAACAAAAT
GTAAGAC
Found at i:157572 original size:159 final size:159
Alignment explanation
Indices: 157277--157595 Score: 586
Period size: 159 Copynumber: 2.0 Consensus size: 159
157267 TTGATATTTG
157277 AATGAATACAAGAGTATCTTTCAGTATTAGATTACTTTGATTCTTATTTAATACTTTTCATCTGT
1 AATGAATACAAGAGTATCTTTCAGTATTAGATTACTTTGATTCTTATTTAATACTTTTCATCTGT
* *
157342 TTATTCTTGGATCTAACTACATCAAGCACGAGAGTGCATTTATAGTCTACCGACATTGAGAGATG
66 TTATTCTTGGATCTAACTACAGCAAGCACGAGAGTGCATTTACAGTCTACCGACATTGAGAGATG
157407 TGGTGACAAGTTAGGTTAACAAGCAAGAC
131 TGGTGACAAGTTAGGTTAACAAGCAAGAC
157436 AATGAATACAAGAGTATCTTTCAGTATTAGATTACTTTGATTCTTATTTAATACTTTTCATCTGT
1 AATGAATACAAGAGTATCTTTCAGTATTAGATTACTTTGATTCTTATTTAATACTTTTCATCTGT
* *
157501 TTATTCTTGGATCTAACTACAGCAAGCATGAGAGTGCATTTGCAGTCTACCGACATTGAGAGATG
66 TTATTCTTGGATCTAACTACAGCAAGCACGAGAGTGCATTTACAGTCTACCGACATTGAGAGATG
157566 CT-GTGACAAGTTAGGTTAACAAGCAAGAC
131 -TGGTGACAAGTTAGGTTAACAAGCAAGAC
157595 A
1 A
157596 GTGAGAGTTG
Statistics
Matches: 155, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
159 154 0.99
160 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (159 bp):
AATGAATACAAGAGTATCTTTCAGTATTAGATTACTTTGATTCTTATTTAATACTTTTCATCTGT
TTATTCTTGGATCTAACTACAGCAAGCACGAGAGTGCATTTACAGTCTACCGACATTGAGAGATG
TGGTGACAAGTTAGGTTAACAAGCAAGAC
Found at i:163922 original size:51 final size:51
Alignment explanation
Indices: 163858--163957 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 51
163848 TGTTAGTAAT
* * *
163858 CATTGTCACTACA-TCCCTTTTGTCATTGCATTTTAATTGTCACTGCATTTG
1 CATTGTCACTACATTCCCATTTGGCATTGCAATTTAA-TGTCACTGCATTTG
* * * *
163909 CATTGTCATTACATTTCCATTTGGCATTGTAATTTAATGTCAGTGCATT
1 CATTGTCACTACATTCCCATTTGGCATTGCAATTTAATGTCACTGCATT
163958 AGGGACAATG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 23 0.56
52 18 0.44
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.45
Consensus pattern (51 bp):
CATTGTCACTACATTCCCATTTGGCATTGCAATTTAATGTCACTGCATTTG
Found at i:163929 original size:17 final size:17
Alignment explanation
Indices: 163877--163929 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
163867 TACATCCCTT
**
163877 TTGTCATTGCATTTTAA
1 TTGTCATTGCATTTCCA
* *
163894 TTGTCACTGCATTTGCA
1 TTGTCATTGCATTTCCA
*
163911 TTGTCATTACATTTCCA
1 TTGTCATTGCATTTCCA
163928 TT
1 TT
163930 TGGCATTGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.21, C:0.19, G:0.11, T:0.49
Consensus pattern (17 bp):
TTGTCATTGCATTTCCA
Done.